chado-1.23/000755 000765 000024 00000000000 12061672376 012604 5ustar00cainstaff000000 000000 chado-1.23/bin/000755 000765 000024 00000000000 12061672376 013354 5ustar00cainstaff000000 000000 chado-1.23/chado-module-metadata.xml000644 000765 000024 00000052523 12017446444 017450 0ustar00cainstaff000000 000000 Chado: A generic model organism database schema Chado is a modular schema for biological data This is a metadata file describing chado and its components, specified in XML. The path to each module SQL file is described, as well as other files which that module may require or use General purpose tables, including dbxrefs Standard Chado SQL Reports for the general module A DBMS API for the general module's loading functions Postgres code for helping with loading the general module Controlled vocabularies and ontologies Standard Chado SQL Views for the cv module Standard Chado SQL Reports for the cv module A DBMS API for the cv module Postgres code for finding parent and child cvterms Postgres code for populating the cvtermpath table Postgres code for working with cvterm cycles Bibliographic data on publications Species data - does not include phylogeny A DBMS API for the organism module Postgres code retrieving organism data Postgres code for helping with loading organism data Sequence and sequence features, their localization and properties Standard Chado SQL Reports for the sequence module Genetic code - maps codons to amino acids according to species specific translation table A SQL/DBMS API for the sequence module. Currently only plpgsql implementations exist Functions for operating on interval ranges Utility functions for biological sequences Projections on graph defined by featureloc feature types A DBMS API for general feature queries Postgres code for general feature queries Optional optimizations to be applied to the sequence module Views that let Chado masquerade as a GO Database. Note that this is a component of the sequence module, as the views are over both cv and sequence modules Requires testing with AmiGO Chaos is a simplified layer over chado Provides a view for every type in the SO ontology. This means you can do queries such as "SELECT * FROM gene" etc This enhances the SOFA layer with additional queries for complex feature types, such as those can be inferred from other features. A DBMS API for loading feature tables Postgres code for loading feature tables A DBMS API for doing subsequence queries Postgres code for doing subsequence queries Postgres code for doing something with feature subalignments, but I don't remember what. Allen? Postgres code for fast feature 'contains' query, requried for the DAS2 server (right?) Postgres code to flatten feature relationships; it is in some ways similar to frange. Postgres code to simplify feature relationship queries Augments sequence module with descriptions of computational analyses and features resulting from those analyses A DBMS API for the companalysis module's loading functions Postgres code for helping with loading the companalysis module In use right now in FlyBase Entity-attribute-value phenotypic character descriptions In use right now in FlyBase Genotypes and mutant alleles Not yet in production use anywhere? Non-sequence maps: genetic, radiation hybrid, cytogenetic, etc In use at IRRI For representing phylogenetic trees; the trees represent the phylogeny of some some kind of sequence feature (mainly proteins) or actual organism taxonomy trees A DBMS API for the phylogeny module Postgres code retrieving phylogeny data In use at UCLA/Allen Day model persons, institutes, groups, organizations, etc In use at FlyBase transcript or protein expression data The project table has been moved from general to its own module and has been expanded to provide properties, publications and contacts. In use at UCLA/Allen Day Alternative expression module, based on MAGE model In use at ParameciumDB For tracking stock collections For describing molecular libraries For describing cell lines A collection of bridge codes that have multiple dependencies so they don't happily go where is most obvious. A GFF-view over chado. Required by Gbrowse Standard Chado SQL Views for the sequence module Views for operating on featureloc ranges. Overlap, intersection, union, difference etc Natural diversity module for dealing with populations, samples, genotypes, phenotypes and results of other assays. chado-1.23/chado-xml/000755 000765 000024 00000000000 12061672375 014457 5ustar00cainstaff000000 000000 chado-1.23/Changes000644 000765 000024 00000031603 12061666153 014076 0ustar00cainstaff000000 000000 Version 1.23 Thu Dec 1 14:45:22 EST 2011 * Added $VERSION to Bio::GMOD::DB::Config so that when installing Bio::DB::Das::Chado it would be happy. * Changed all perl script #! lines to use /usr/bin/env perl instead of the mishmash that was being used in various scripts. * Fixed the GFF3 preprocessor so that if an insert into the sorting table fails, the script will die to avoid losing GFF lines in the resulting file. * Modified Makefile.PL so that if using PREFIX it won't stomp on the GMOD_ROOT envirnment variable (that is, everything goes in PREFIX, except what goes in GMOD_ROOT). Version 1.22 Thu Nov 17 12:48:10 EST 2011 * Created a script to automatically create the schemas dirs for a release and add them to the manifest. Version 1.21 Thu Oct 20 10:52:55 EDT 2011 * Added rudimentary support for non-public schemas in Postgres, though it's only good for Tripal at the moment. * Fixed database initialization step "make prepdb" so that the version of the schema gets set in the chadoprop table. * Fixed bug in gmod_chado_properties.pl that caused it to crash when updating the schema version. Version 1.2 Tue Aug 10 13:59:05 EDT 2010 * Added some error checking to gmod_fasta2gff3.pl (Rob) * Updated Bio::Chado::Builder to detect recent versions of go-perl. They no longer have .pl at the end of the go2fmt script name (Rob) * The GFF3 bulk loader will now ignore ##sequence-region directives; previously, their presence caused the loader to fail (Scott) * added a check for the nodes file downloaded from NCBI. There have been cases of missing nodes/parents. Code dies if parent is missing. User must check the nodes file. This needs further investigation with NCBI taxonomy. (Naama) * Fix the code in the gff-bridge in the sequence module so that GFF dumping from GBrowse will work correctly (Scott) * Added a cvprop table to capture things like obo file version from a loaded cv. (Scott) * Removed the "DB:" prefix from all of the names of databases that go into the db table. (Scott) * Removed the dependency on Log::Log4perl (it was overkill for what it was being used for) (Scott) * Bumped the version to 1.2 because of the new schema module. (Scott) * Added gmod_chado_properties.pl to examine the chadoprop table and return values on the command line (like the schema version) (Scott) * Added gmod_update_chado.pl to update the schema automatically, and added a make target (make update) to make updating easier. (Scott) * Removed cell_type ontology from 'make ontologies' list as it wasn't loading via stag_storenode.pl at release time (Scott) Version 1.11 Tue May 25 11:10:47 EDT 2010 * fixed an issue with accessing the primary_id of Bio::Annotation::DBLink objects (Naama) * Fixes issue with dependencies on CXGN-specific code. Now all db connection parameters for cxgn - contributed scripts should be passed in a gmod_config file, or in command line options as listed in the POD. * Made gmod_materialized_view_tool.pl able to accept all configuration parameters on the command line (this is to make it work with automatic MV creation for full text searching) (Scott). * fixed messed up gmod_load_cvterms.pl -p and -u options (Naama) Version 1.1 * Fixes to gmod_gff3_preprocessor.pl so that file splitting will work as expected. * Minor fix to Bio::GMOD::DB::Adaptor (used by gmod_bulk_load_gff3.pl) to silence a uninint warning. * Created a plpgsql function to share exons (called share_exons) that takes exon features that have the same boundaries as another exon and reduces them to one feature and fixes up feature_relationship entries so that the remaining exon belongs to the right transcript/genes. This may be needed for Apollo. Thanks to Robin Houston at GeneDB/Sanger Centre for contributing much of the code. * Created a function to order exons (called order_exons) that will create entries in the feature_relationship.rank column to number exons (0 based) from beginning to end in a given transcript. This was originally needed for Apollo, but by the time this function was done, Ed Lee had fixed up Apollo to not need it. * Fixed the audit module so that the triggers in it work with versions of PostgreSQL greater that 8.0. * Added so-bridge views. These are a set of views on the feature table the use SO terms for the names of the views, making it easy to query for genes by doing something like this: SELECT * FROM so.gene WHERE name='foo'. See http://gmod.org/Chado_SO_Views for more information. * Added a protein_code_gene view (depends on so-bridge); thanks to Chris Mungall. * Updated all_feature_names view to search featureprop.value and dbxref.accession and added organism_id so GBrowse can limit by organism. * Fixed gmod_bulk_load_gff3.pl to deal correctly with the case that mulitple organisms have the same common name. If the user tries to use a common name that corresponds to more than one organism, it will die gracefully. * Fixed gmod_bulk_load_gff3.pl so that featureloc.srcfeature_id will not be sometimes set incorrectly when there are multiple organisms with chromosomes (or other srcfeatures) with the same name. * Added a __DIE__ signal handler to gmod_bulk_load_gff3.pl so that the databsae will be cleaned up in most cases before the loader croaks. * Fixed gmod_bulk_load_gff3.pl so that when loading dna sequence from the fasta section it won't accidentally add sequence to a feature that has the same uniquename but different organism_id to the actual target. * Adding a update_sequences method for use by gmod_bulk_load_gff3.pl that will check the next value available to the database sequences that generate primary keys and update them when necessary. This can happen when another database load adds data to chado but does not update the sequence. * Adding the ability to specify that gmod_bulk_load_gff3.pl use the system tmp directory rather than using the current working directory for writing the temporary load files. * Added a --fastafile option to gmod_bulk_load_gff3.pl to use when loading fasta files. * Removed the cause of the error messages at the end of ontology loading: it was a patch to correct for bad behavior that DBIx::DBStag which was fixed some time ago. * Added gmod_bulk_pub_loader.pl contributed by SGN. * Added gmod_make_cvtermpath.pl contributed by SGN. Below this line are changes up until a few years ago and are included for historical purposes. --------------------------------------------------------------------------- VERSION 0.01 ============ No change log VERSION 0.02 ============ No change log VERSION 0.03 ============ all modules ditched timeentered and timelastmod columns in every table We've decided that auditing is implementation specific. We're presently working on the FB implementation, and will make that available soon changed all dbxrefstr foreign keys to dbxref_id added indexes for every foreign key column in every table all linking tables: Added primary keys to all linking tables, for consistency's sake, since we already had primary keys in some linking tables. I hope nobody objects...? general module: dbxref removed dbxref.dbxrefstr removed unique key (dbxrefstr) cv module: New table: added table cv to hold cv names cvterm changed accordingly cvpath changed accordingly cvterm_synonym changed the name of table cvterm_synonym to cvtermsynonym, since this isn't a linking table. organism module: organism_dbxref added unique key (organism_id,dbxref_id) organism made genus, species, taxgroup fields not null pub module pub added miniref added unique key (miniref) pub_author added unique key (author_id,pub_id) author added unique key (surname,givenname,suffix) sequence module Deleted table feature_organism feature added foreign key organism_id (not null) added uniquename column (not null) added unique key (organism_id,uniquename) made type_id not null featureloc added unique key (feature_id,locgroup,rank) feature_dbxref changed unique key to (feature_id,dbxref_id) - was (feature_dbxref_id, dbxref_id) OK??? feature_relationship changed type_id int attribute to not null synonym added 'type_id' to the unique key (synonym,type_id) genetic module NOTE: We don't have unique keys on genotype, phenotype, and interaction. Since we're going to be having a schema review on this module soon, I decided not to worry about these for the time being. feature_genotype added unique key (feature_id,genotype_id) feature_phenotype added unique key (feature_id,phenotype_id) phenotype_cvterm added unique key (phenotype_id,cvterm_id,prank) interaction_subj added unique key (feature_id,interaction_id) interaction_obj added unique key (feature_id,interaction_id) companalysis module analysis added unique key (program,programversion) analysisfeature changed unique key to (feature_id,analysis_id) was (feature_id) expression module expression doesn't have a unique key! But what would it be? feature_expression added unique key (expression_id,feature_id) expression_cvterm added unique key (expression_id,cvterm_id) expression_pub added unique key (expression_id,pub_id) eimage doesn't have a unique key! What would it be? expression_image added unique key (expression_id,eimage_id) map module I've skipped this one except for ditching the auditing attributes and dbxrefstr stuff... still needs lots of work! Maybe we could do a mini-review on this module sometime soon? I've got some examples of how I use a rejigged featurepos table to manage the fragmented a.gambiae genome, but I'd bet what I did can be improved upon. VERSION 0.04 ============ GENERAL CHANGES --------------- added Makefile *prop tables have been made uniform: pkey_id has been changed to type_id. all fk references to the cvterm table should now either be type_id or cvterm_id. pval field has been changed to value, and prank has been changed to rank. no pranks here! all subject/predicate/object using tables previously used subjterm_id/reltype_id/objterm_id. this has been changed to subject_id/type_id/object_id to be more generally applicable and consistent with other uses of cvterm references. MODULE CHANGES -------------- audit module no changes bin added of scripts to autogenerate graphviz and "diagram" ER diagrams from schema. added script to autogenerate Class::DBI middleware layer. this introduces an SQL::Translator dependency companalysis no changes cv cv.cvname is now cv.name. cv.cvdefinition is now cv.definition. cvterm.termdefinition is now cvterm.definition. tables cvrelationship and cvpath have been renamed as cvtermrelationship and cvtermpath, and the appropariate field and index names have changed. expression no changes general contact table has been added. data should start moving over from pub.author soon, and the contact table should be fleshed out by one of the pub projects (ie pubsearch) db table pk is now a serial int, rather than a varchar. dbxref now references db.db_id as dbxref.db_id instead of dbxref.dbname dbxrefprop and dbxrefrelationship are commented out pending review genetic no changes map no changes organism organism.abbrev changed to organism.abbreviation pub introduced a fk from author table to contact table in general module sequence no changes www added for gmod-web. this is likely to have many of the link tables removed in favor of using the general-purpose "contact" table in general module, and using a new tag-value based approach to storing user bookmarks/lists/preferences/etc VERSION 0.04 ============ MODULE CHANGES -------------- audit module no changes bin no changes companalysis table analysisinvocation removed as redundant with current usage of analysis. table analysisinvocationprop changed back to analysisprop. cv renamed table cvtermrelationship to cvterm_relationship expression no changes general tables tableinfo and project moved to metadata.sql. tables dbxrefprop and dbxrefrelationship removed for now since they caused problems with the build. genetic interaction.backgroundgenotype_id changed to interaction.background_genotype_id. map no changes organism no changes pub deleted the fk from author table to contact table in the general module, as this relation is effectively unimplementable for the vast majority of author records. sequence feature_relationship keys subjfeature_id, objfeature_id, and relrank changed to subject_id, object_id, and rank, respectively, for consistency with the rest of the schema. www no change 2005-02-08 - [cjm] db.contact_id nullable - cvterm.dbxref_id NOT NULL - added comments to cv table 2005-03-10 - [cjm] feature_cvterm_dbxref added 2005-04-20 - [cjm] changed comment style and added new comments cv and sequence modules only 2005-06-07 - [cjm] added: feature_cvterm.is_not and feature_cvterm_dbxref 2006-04-11 - [cjm] split genetic module into genetic+phenotype modules chado-1.23/Changes.GMOD000644 000765 000024 00000001557 11256710157 014627 0ustar00cainstaff000000 000000 0.003 * added a gff3 bulk loader * brought schema up to date; the most noticable change (and not backward compatible) is the removal of contact_id from the db table. * Lots more stuff, since it has been quite some time since the 0.002 release 0.002 * Added more expressive error messages to load_gff3.pl * Expanded the search space for organisms in load_gff3.pl * Added more organisms to initialize.sql * Fixed modules/expression/rad.sql to work with PG 7.4 * Added yeast GFF3 file to use as sample data * created AutoDBI.PL, which makes Makefile.PL independent of sqlfairy * parameterized LOCAL_TMP, the place where downloaded ontologies are stored. * Added a make target to remove ontology lock files 0.001 Initial release chado-1.23/Changes.sql000644 000765 000024 00000011075 11256710157 014674 0ustar00cainstaff000000 000000 --when schema elements are added, including new tables or changes to table --columns, or when initialize.sql is changed, the sql to make those changes --happen should go here. --gmod version 1.01 --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_id IN SELECT feature_id FROM feature WHERE type_id = parent_type LOOP SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; --added foreign key for pub_id to phenotype_comparison_cvterm ALTER TABLE phenotype_comparison_cvterm ADD FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade; --Changed the Audit table triggers to work with newer versions of Postgres. --This didn't change the the default schema at all (since audit.sql isn't --part of the default schema. --all_feature_name view also searches featureprop and dbxref.accesion --see the comments in modules/sequence/sequence_views.sql for more --information on how this works CREATE OR REPLACE VIEW all_feature_names ( feature_id, name ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name FROM feature UNION SELECT feature_id, name FROM feature where name is not null UNION SELECT fs.feature_id,s.name FROM feature_synonym fs, synonym s WHERE fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name FROM featureprop fp UNION SELECT fd.feature_id, d.accession FROM feature_dbxref fd, dbxref d WHERE fd.dbxref_id = d.dbxref_id; DROP VIEW all_feature_names; CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; chado-1.23/conf/000755 000765 000024 00000000000 12061672375 013530 5ustar00cainstaff000000 000000 chado-1.23/doc/000755 000765 000024 00000000000 12061672376 013351 5ustar00cainstaff000000 000000 chado-1.23/INSTALL.Chado000644 000765 000024 00000036154 11723202377 014655 0ustar00cainstaff000000 000000 $Id: INSTALL.Chado,v 1.10 2008-11-04 20:36:20 scottcain Exp $ * COMMAND-LINE INSTALL If you experience problems, please email them to the gmod-schema mailing list at gmod-schema@lists.sourceforge.net. This release will work with the most recent release of the Generic Genome Browser (GBrowse) version 1.68 or better. If you experience difficulties with GBrowse and Chado, you might want to look at getting a svn checkout of the gbrowse-stable branch. The installation instructions for GBrowse are included in that package. Additionally, for working with GBrowse, you will need the Bio::DB::Das::Chado modules that you can get from CPAN. PREREQUISITES - PostgreSQL Currently GMOD developers are using 8.1 or better (PostgreSQL 9 has not been tested). Items to do with Postgres to make it ready to go: * Make it accept TCP/IP connections by adding this line to postgresql.conf (must be done either as user root or postgres; database must be restarted in order for this change to take affect): tcpip_socket = true (This option is not available and not needed in PostgreSQL 8.1 or better.) * Create a database user with permission to drop and add databases; the database user name should be the same as your Unix user name to allow the software build to progress smoothly (must be done as user postgres; createuser is a commandline program that comes with the PostgreSQL package): $ sudo su - postgres $ createuser --createdb $ exit # to exit out of the postgres user's shell * Tell postgres that it can use the plpgsql language (as user postgres; createlang is a commandline program that comes with the PostgreSQL package): $ sudo su - postgres $ createlang plpgsql template1 $ exit # to exit out of the postgres user's shell * Edit the pg_hba.conf (either as the user 'root' or 'postgres') to give the user created above permission to access the database. Read the comments in pg_hba.conf regarding permissions. An example pg_hba.conf looks like this (which is very loose permissions): # TYPE DATABASE USER CIDR-ADDRESS METHOD local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust NOTE: If you are setting up a production Chado instance, now is a good time to decide how you want to define users and do client authenication for your database. Postgresql supports several methods for defining users, including using operating system users, LDAP, Kerberos and many others. See the Postgesql manual for more: http://www.postgresql.org/docs/8.4/interactive/client-authentication.html http://www.postgresql.org/docs/8.4/interactive/user-manag.html * For Pg 8.1+, if you want to allow remote connections, the listen_addresses option may need to be modified; it does allow a wildcard '*', which corresponds to all available IP interfaces (it does *not* specify the IP addresses that are allowed to connect). Set this in postresql.conf file, which is in the same directory as pg_hba.conf. For information on tuning postgres for performance, see http://gmod.org/wiki/PostgreSQL_Performance_Tips and http://www.varlena.com/varlena/GeneralBits/Tidbits/perf.html The two most critical parameters to tune are shared_buffers and effective_cache size. Adjusting these parameters may require modification of memory settings in /etc/sysctl.conf, see the sysctl manpage for details. Also critical for continued performance of postgres is the regular execution of the VACUUM FULL ANALYZE command. This command clears out old, deleted data and analyzes the structure of the database so that the execution planner can predict the fastest way to execute a given query. While the above link describes tuning in general, the examples given for tuning kernel parameters are Linux specific. For setting shmmax on Mac OS X boxes, edit /System/Library/StartupItems/SystemTuning/SystemTuning (for OS X 10.2) or /etc/rc (for OS X 10.3) or /etc/sysctl.conf (for OS X 10.5) to increase the values of shmmax and shmall, like this: sysctl -w kern.sysv.shmmax=52428800 # bytes: 50 megs sysctl -w kern.sysv.shmmin=1 sysctl -w kern.sysv.shmmni=32 sysctl -w kern.sysv.shmseg=8 sysctl -w kern.sysv.shmall=25600 # 4k pages: 100 megs (these are the values used on a Mac that has 1.2 G RAM) and reboot. For a Linux box with 512M RAM, use these values in /etc/sysctl.conf: kernel.shmall = 134217728 kernel.shmmax = 134217728 and make these changes to the postgresql.conf file: tcpip_socket = true # Replaced with listen_addresses in Postgres 8.0+ work_mem=2048 # This is "sort_mem" if using Postgres 7.x max_connections = 32 - BioPerl bioperl-live or a version 1.6.1 or better. See http://bioperl.org. - go-perl Can be obtained from CPAN using the cpan shell with the command cpan> install GO::Parser - ant When installing from svn, ant is needed to move GMODTools files from schema/GMODTools into schema/chado. When installing from a distribution, this is not necessary, as the files will have already been moved as part of the build process. - Perl modules The perl modules can be installed via the CPAN shell and by issuing the command 'install Bundle::GMOD' which will install all of the modules below except for SQL::Translator, which is optional. * CGI (GBrowse) * GD (GBrowse) * DBI (GBrowse, Chado) * DBD::Pg (GBrowse, Chado) * SQL::Translator (chado) (only for a custom Chado schema) * Digest::MD5 (GBrowse) * Text::Shellwords (GBrowse) * Graph (Bio-Chaos) * Data::Stag (Chado) * XML::Parser::PerlSAX (Chado) * Module::Build (Chado) * Class::DBI (GMODWeb, or with a custom Chado schema) * Class::DBI::Pg (GMODWeb, or with a custom Chado schema) * Class::DBI::Pager (GMODWeb, or with a custom Chado schema) * DBIx::DBStag (Chado) * XML::Simple (Chado) * LWP (Chado) * Template (Chado) * Bio::Chado::Schema (Chado) INSTALL THE CHADO SCHEMA - Set environmental variables First, you must set some variables in your environment. If you are using bash or a bash-like shell, this is done via a command like this: $ export VARNAME=value If you are using tcsh or another csh-like shell, it is done like this: $ setenv VARNAME value To make life easier on yourself, you will probably also want to put those commands in your .tcshrc or .bashrc file so that the envirnment variables are always available when you log in. * GMOD_ROOT: The location of your Chado installation (e.g., "/usr/local/gmod"). Will contain the source files that define the schema, as well as configuration settings and temp space. * CHADO_DB_NAME: The name of your Chado database * CHADO_DB_USERNAME: The username to connect to Chado * CHADO_DB_PASSWORD: The password for the database user [opt] * CHADO_DB_HOST: The host on which the database runs (e.g. "localhost") [opt] * CHADO_DB_PORT: The port on which the database is listening [opt] As indicated, the host, port, and password are optional. * Note: a mechanism exists to pass these variables directly to the installer during the "perl Makefile.PL" step. By giving key=value pairs, it is possible to avoid setting environmental variables. The syntax is as: $ perl Makefile.PL GMOD_ROOT=/usr/local/gmod CHADO_DB_NAME=dev_chado_01 Backward compatibility may not be maintained for this method of configuring the install process will work. - Create the Makefile and other configuration files From the chado directory (the same directory INSTALL.Chado is in) run the following command: $ perl Makefile.PL You will be prompted for several configuration values used by Chado and its associated tools: * Use the simple install (uses default database schema) [Y] Answering yes eliminates the need to have SQL::Translator installed. This is recomended, and that is all that is necessary in order to use the full schema and run GBrowse and GMODWeb on top of it. * Use values in '/home/scott/gmod/build.conf'? [Y] If `perl Makefile.PL` has been run before, answering yes to this will cause Makefile.PL to use the configuration options from the previous build. * What database server will you be using? [PostgreSQL] Specify what database vendor to use. Currently only PostgreSQL works. * What is the Chado database name? [dev_chado_allenday_05] This will be the name of the created chado database. * What is the database username? [allenday] Default user that the installed libraries should try to connect to the database as. * What is the password for 'allenday'? Password for the default user. * What is the database host? [localhost] Host of the database daemon. * What is your database port? [5432] Port of the database daemon. * Where shall downloaded ontologies go? [./tmp] The directory where ontology files and there lock files will be stored * What is the default organism (common name, or "none")? The organism name should be one what will be in the organism table. When the database is created, several organisms will be there by default; these include: human, fruitfly, mouse, mosquito, rat, Arabidopsis thaliana, worm, zebrafish, rice, and yeast. (The insert statements that create these default organisms are contained in load/etc/initialize.sql). * Do you want to make this the default chado instance? [y] You can have more than one Chado instance on a server, each with a different name. You can supply one of those names when loading GFF, for example "--dbprofile fly_staging". If you don't supply the --dbprofile option, it will just use the default database parameters. If you answered 'No' to the simple install question, AutoDBI.pm will now be created by SQL::Translator, see the CUSTOM DATABASE SCHEMAS section below for more information. - Make the schema $ make - Install the scripts and modules $ make install or $ sudo make install Probably needs to be run as root. Installs data loading scripts in perl's path (typically /usr/local/bin or /usr/bin), perl modules, as well as placing various files in $GMOD_ROOT, and creating the infastructure for logging of errors by creating $GMOD_ROOT/logs and creating the file /etc/log4perl.conf if it does not already exist. - Install the schema $ make load_schema Creates database, installs schema. This wipes out any database with the same name in the process! - Insert baseline data $ make prepdb Inserts a few useful items into fundamental Chado tables. It uses load/etc/initialize.sql. It contains information for several common organisms and source databases (e.g. Genbank). This file can be edited to add any organism or source database, using the INSERT statements for the examples as a template. Note also that the prepdb target needs to be executed before the ontologies target, but it can be executed again later, if more insert statements are added (for instance to add a new organism or database). - Load ontologies $ make ontologies Gets and installs various ontologies. Requires a network connection. Absolutely required are the Relationship Ontology and the Sequence Ontology (SO). All others are optional, though the Feature Property controlled vocabulary will typically be useful for loading GFF Files, and the Gene Ontology is generally useful for a wide variety of gene feature annotations. Note retrieved ontology files are stored in the directory specified when 'perl Makefile.PL' was run (the default is ./tmp). In order to do a repeat installation, the directory containing the downloaded ontology must be removed. In addition to 'rm -rf ./tmp', you can also issue the `make clean` command, which will clear out all of the files and directories created up until this point in the installation. Also note that loading a large ontology like the Gene Ontology will take several minutes (perhaps as long as an hour). Note that since `make ontologies` downloads ontology files from their online repositories, this step is prone to failure due to network problems. If you already have the desired ontology files locally, you can execute a command for each file to load it. Note again that the Relationship Ontology is required before all others, and the the Sequence Ontology (SO) is absolutely required for proper functioning of the database. The commands to load an ontology are: $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ go-apply-xslt oboxml_to_chadoxml - > obo_text.xml This creates a chadoxml file of the obo file - then execute: $ stag-storenode.pl \ -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \ --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml If you have other ontology format files, the commands are similar; consult the documentation for go2fmt.pl and go-apply-xslt for your file format. It is a good idea at this point to make a back up of the database, particularly if you loaded a large ontology like GO. To make a complete dump of the database, issue this command: $ pg_dump db_name > db_dump.sql and to restore the database, issue this command: $ psql db_name < db_dump.sql LOADING DATA With that, the installation of the schema is complete. Please see the HOWTOs at http://gmod.org/ for information on loading the Chado schema with data. CUSTOM DATABASE SCHEMAS If you answered 'No' to the question about doing a simple install during `perl Makefile.PL`, you must provide the files default_schema.sql and default_nofuncs.sql. The best way to create these files is using bin/chado-build-schema.pl, a perl script with a graphical user interface for interactively building a Chado schema. If you are providing table definitions of your own, you will also have to edit the file chado-module-metadata.xml to define how your tables relate to other tables in the Chado schema. While there is no documentation of the DTD of this file, it is relatively straight forward. See INSTALL.Custom for more information on how chado-build-schema.pl relates to the build process. Once your default_schema.sql and default_nofuncs.sql files are in place in the modules directory you can run `perl Makefile.PL`. chado-1.23/INSTALL.Custom000644 000765 000024 00000010616 11316305452 015100 0ustar00cainstaff000000 000000 $Id: INSTALL.Custom,v 1.7 2008-10-16 21:48:57 scottcain Exp $ The Chado schema is organized as a set of modules where each module has its own directory in chado/modules/. This structure is designed to allow the addition of custom modules to the Chado schema or to customize the installation of Chado by module. You can interactively build a schema using chado-build-schema.pl and then install from source. To do this, Makefile.PL will change and no longer ask 'do you want to use the default schema', instead, it will assume that whatever schema is currently in the modules directory is the one that will be used. (It should no doubt issue a warning indicating that is what it is doing.) In this scenario, the schema building step takes place before `perl Makefile.PL` though we will probably want a command line flag to let Makefile.PL know that the default schema is not being used so that the Class::DBI objects get rebuilt. CUSTOMIZATION USING AutoDBI.pl The following steps will create a complete schema, including schema and functions, and diagrams. 1. Run chado-build-schema.pl This script launches an application with a graphical interface. The Tk language and Perl's Tk module are required. >bin/chado-build-schema.pl Click Select all and Create Pg Schema. In order to add custom SQL statements (i.e. table create statements) you need to edit chado-module-metadata.xml to define meta data for the file, including location and any dependencies and then run chado-build-schema.pl. 2. Replace default_schema.sql with your SQL script >mv chado_schema.sql modules/default_schema.sql 3. Run bin/chado-build-schema.pl again Check SQL Only, Select All and Create Pg Schema. 4. Replace default_nofuncs.sql >mv chado_schema.sql modules/default_nofuncs.sql 5. Run Makefile.PL >perl Makefile.PL Answer 'No' to the 'Use the simple install' question. 6. Make diagrams (this step is optional and only needed for building a release). >make diagram >find . -name "*.diagram.png" -path "*modules*" -exec cp '{}' doc/diagrams/ ';' >make graphviz >find . -name "*.graphviz.png" -path "*modules*" -exec cp '{}' doc/diagrams/ ';' >make graphviz_svg >find . -name "*.graphviz.svg" -path "*modules*" -exec cp '{}' doc/diagrams/ ';' 7. Make schema html-based documentation (another optional step) >make html 8. Create audit tables (optional) This is optional. The file audit >sqlt -f PostgreSQL -t TTSchema --template modules/audit/add-audits.tmpl modules/nofuncs.sql > modules/audit/audit_tables.sql 9. edit bin/AutoDBI.PL Delete everything in the non-substituting HEREDOC, insert the corresponding section from the corresponding blib/lib/Bio/Chado/AutoDBI.pm 10. Regenerate modules/sequence/bridges/so-bridge.sql. This doesn't need to be done all the time, but should be done before a release. Note that the create-so-layer.pl script has addtional options for making materialized views for doing fast feature type-related queries (which haven't been tested; they probably don't work). Note that it requires an instance of Chado that has SO loaded. perl bin/create-so-bridge.pl -d 'dbi:Pg:database=chado' > modules/sequence/bridges/so-bridge.sql CUSTOMIZATION USING makedep.pl The following approach creates a DDL, or SQL script, that will install the tables for the selected modules. 1. Run makedep.pl >chado/modules/bin/makedep.pl --modules , > my.sql Do "modules/bin/makedep.pl --help" for more documentation. 2. Replace default_schema.sql with your SQL script >mv my.sql modules/default_schema.sql 3. Run Makefile.PL >perl Makefile.PL Answer 'Yes' to the 'Use the simple install' question. ABOUT THE Chado DDL FILES Different DDL files, or SQL scripts, are created dynamically during the typical installation. * modules/default_schema.sql default_schema.sql is used to actually instantiate the database. * modules/default_nofuncs.sql default_nofuncs.sql is a SQL or DDL file that does not contain Postgresql functions. The reason for this is at least two fold: the minor one is to create SQL that is relatively RDBMS-independent. In addition SQL::Translator frequently chokes on Postgresql functions, so there needs to be a file that represents the schema for SQLFairy to operate on for creating the audit tables and AutoDBI. This file is only used when SQLFairy is needed (that is, when creating a new build or custom schema). It is also useful to those who want to use Mysql or Oracle. chado-1.23/install_util/000755 000765 000024 00000000000 12061672376 015307 5ustar00cainstaff000000 000000 chado-1.23/lib/000755 000765 000024 00000000000 12061672375 013351 5ustar00cainstaff000000 000000 chado-1.23/LICENSE000644 000765 000024 00000021046 11636004564 013607 0ustar00cainstaff000000 000000 Artistic License 2.0 Copyright (c) 2000-2011, The Perl Foundation. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software. 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UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. chado-1.23/load/000755 000765 000024 00000000000 12061672375 013522 5ustar00cainstaff000000 000000 chado-1.23/Makefile.PL000644 000765 000024 00000062436 12061666022 014560 0ustar00cainstaff000000 000000 use ExtUtils::MakeMaker; # vim: set ft=perl ts=2 expandtab: # $Id: Makefile.PL,v 1.133 2009-09-01 15:01:14 scottcain Exp $ $| = 1; use constant INSTRUCTIONS => < { default => 'PostgreSQL' }, DBNAME => { default => $ENV{'CHADO_DB_NAME'} }, DBUSER => { default => $ENV{'CHADO_DB_USERNAME'} || $ENV{'USER'} }, DBPASS => { default => $ENV{'CHADO_DB_PASSWORD'} }, DBHOST => { default => $ENV{'CHADO_DB_HOST'} || $ENV{'HOST'} || scalar gethostent || 'localhost' }, DBPORT => { default => $ENV{'CHADO_DB_PORT'} || 5432 }, LOCAL_TMP => { default => './tmp' }, DBORGANISM => { default => '' }, APOLLO => { default => 'n' }, DEFAULT => { default => 'y' }, SCHEMA => { default => 'public' }, ); my %env2arg = ( CHADO_DB_NAME => 'DBNAME', CHADO_DB_USERNAME => 'DBUSER', CHADO_DB_PASSWORD => 'DBPASS', CHADO_DB_HOST => 'DBHOST', CHADO_DB_PORT => 'DBPORT', PREFIX => 'PREFIX', INSTALLSITEMAN1DIR => 'INSTALLSITEMAN1DIR', INSTALLSITEMAN3DIR => 'INSTALLSITEMAN3DIR', ); my $usage = <<"END"; -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- CHADO INSTALLATION HELP -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- The arguments to this script should be set in your environment per the instructions in the Chado INSTALL document. To customize installation options, provide one or more of the options (default values in parentheses): DBDRIVER The RDBMS vendor ($args{'DBDRIVER'}{'default'}) DBNAME The name of the Chado database ($args{'DBNAME'}{'default'}) DBUSER The username to use when connecting to the database ($args{'DBUSER'}{'default'}) DBPASS The password for connecting ($args{'DBPASS'}{'default'}) DBHOST The machine name where the database is running ($args{'DBHOST'}{'default'}) DBPORT The port on which the database is listening ($args{'DBPORT'}{'default'}) e.g., perl Makefile.PL DBDRIVER=PostgreSQL DBNAME=chado [...] In addition to the "global" variables above, you can also specify LOCAL_TMP, which indicates where ontology files will be stored. The default is './tmp'. Optionally, if the file "build.conf" can be found from a previous run of the Makefile.PL, you will be prompted to confirm the values saved in this file. If you wish to use the previous values without being prompted, then provide the argument "RECONFIGURE=1." If you wish to disregard any values in "load.conf" and be prompted for new arguments, provide the argument "RECONFIGURE=0." If you wish to use the defaults without being prompted, provide the argument "DEFAULTS=1." You can also use PREFIX and LIB to install perl modules in nonstandard locations as you would with a typical package install. ALTHOUGH THERE IS CURRENTLY A PROBLEM THAT DYNAMICALLY GENERATED SCRIPTS MAY NOT GET REGENERATED ON SUBSEQUENT RUNNINGS OF perl Makefile.PL WITH DIFFERENT VALUES OF LIB AND PREFIX. END # # Establish some globals. # my $PERL = $Config{'startperl'}; $PERL =~ s/^\s*#!\s*//; my $working_dir = cwd; my $lib_dir = catdir $working_dir, 'lib'; my $chado_dir = catdir $lib_dir, 'Bio/Chado'; my $build_config = catfile $working_dir, 'build.conf'; my $load_config = catfile $working_dir, 'load', 'etc', 'load.conf'; my $all_args = join( '|', qw[LIB RECONFIGURE DEFAULTS PREFIX INSTALLSITEMAN1DIR INSTALLSITEMAN3DIR INSTALL_BASE], keys %args ); my %env_required = map {$_=>1} qw(GMOD_ROOT CHADO_DB_NAME CHADO_DB_USERNAME); #CHADO_DB_PASSWORD is valid if undefined my $all_envs = join( '|', keys %env_required ); my %O; $O{GMOD_ROOT} = $ENV{GMOD_ROOT} || catdir ( '', 'usr', 'local', 'gmod', ); $O{PACKAGE_HOME} = catfile $O{GMOD_ROOT}, 'lib', 'schema'; $O{COREDEF} = catfile $working_dir, 'modules', 'idb-full.modules'; $O{EXTDEF} = catfile $working_dir, 'modules', 'extension.modules'; $O{FUNCDEF} = catfile $working_dir, 'modules', 'function.modules'; mkdir $lib_dir unless -d $lib_dir; mkdir $chado_dir unless -d $chado_dir; # # If the config file is there, parse it. # my %conf = (); if ( -e $build_config && -r _ ) { open CONF, "<$build_config" or die "Can't read file '$build_config': $!\n"; while ( ) { chomp; next if /^\#/; if ( /^($all_args)=(.+)$/o ) { $conf{ $1 } = $2; } } close CONF; } # # Parse arguments. # my %opts; my @argv = @ARGV; foreach ( @argv ) { if ( /^--?h(elp)?$/i ) { die $usage; } elsif ( /^($all_args)=(.+)$/ ) { $opts{ $1 } = $2; } elsif ( /^($all_envs)=(.+)$/ ) { $args{ $env2arg{$1} }{ default } = $2; } } @ARGV = (); push @ARGV, "PREFIX=$opts{PREFIX}" if $opts{PREFIX}; push @ARGV, "INSTALL_BASE=$opts{INSTALL_BASE}" if $opts{INSTALL_BASE}; $O{'GMOD_ROOT'} = $opts{PREFIX} if ($opts{PREFIX} and !$ENV{GMOD_ROOT}); push @ARGV, "INSTALLSITEMAN1DIR=$opts{INSTALLSITEMAN1DIR}" if $opts{INSTALLSITEMAN1DIR}; push @ARGV, "INSTALLSITEMAN3DIR=$opts{INSTALLSITEMAN3DIR}" if $opts{INSTALLSITEMAN3DIR}; push @ARGV, "LIB=$opts{LIB}" if $opts{LIB}; # # Check to see if the enviroment is there, mostly to make sure # other apps can get what they need. # my @env_missing = (); for my $key (keys %env_required) { push @env_missing, $key unless defined $ENV{ $key } or defined $args{$env2arg{$key}}{default} or defined $conf{$env2arg{$key}}; } if ( @env_missing ) { die join("\n", '*' x 72, 'The following enviroment variables not detected:', ( map { " $_"} @env_missing ), 'Please read the INSTALL document and set required environment variables.', '*' x 72, '' ); } my %VALID_DBS = ( Pg => 'PostgreSQL', #Oracle => 'Oracle', ); my %db_lookup = reverse %VALID_DBS; # # Now figure out where the values are coming from -- build.conf, # command-line, or prompt(). # my ( $DBDRIVER, $DBNAME, $DBUSER, $DBPASS, $DBHOST, $DBPORT,$SCHEMA, $SQLFILES, $EXTERNAL_DDL, $LOCAL_TMP, $DBORGANISM, $APOLLO, $DEFAULT); $O{'SIMPLE'} = prompt( "Use the simple install (uses default database schema, which contains\nall of the modules and extensions to the schema and all of the non-trigger functions.\nThis is probably what you want)", 'Y' ); if ( ! @argv && %conf ) { my $answer = prompt( "Previous configuration detected.\nUse values in '$build_config'?", 'Y' ); $opts{'RECONFIGURE'} = $answer =~ /^[Yy]/ ? 1 : 0; } if ( $opts{'RECONFIGURE'} && %conf ) { $DBDRIVER = $VALID_DBS{ $conf{'DBDRIVER'} } || ''; $DBNAME = $conf{'DBNAME'} || ''; $DBUSER = $conf{'DBUSER'} || ''; $DBPASS = $conf{'DBPASS'} || ''; $DBHOST = $conf{'DBHOST'} || ''; $DBPORT = $conf{'DBPORT'} || ''; $LOCAL_TMP= $conf{'LOCAL_TMP'}|| ''; $DBORGANISM=$conf{'DBORGANISM'}|| ''; $APOLLO = $conf{'APOLLP'} || ''; $DEFAULT = $conf{'DEFAULT'} || ''; $SCHEMA = $conf{'SCHEMA'} || ''; } elsif ( $opts{'DEFAULTS'} ) { $DBDRIVER = $args{'DBDRIVER'}{'default'}; $DBNAME = $args{'DBNAME'}{'default'}; $DBUSER = $args{'DBUSER'}{'default'}; $DBPASS = $args{'DBPASS'}{'default'}; $DBHOST = $args{'DBHOST'}{'default'}; $DBPORT = $args{'DBPORT'}{'default'}; $LOCAL_TMP= $args{'LOCAL_TMP'}{'default'}; $DBORGANISM=$args{'DBORGANISM'}{'default'}; $APOLLO = $args{'APOLLO'}{'default'}; $DEFAULT = $args{'DEFAULT'}{'default'}; $SCHEMA = $args{'SCHEMA'}{'default'}; } elsif ( %opts ) { $DBDRIVER = $opts{'DBDRIVER'} || ''; $DBNAME = $opts{'DBNAME'} || ''; $DBUSER = $opts{'DBUSER'} || ''; $DBPASS = $opts{'DBPASS'} || ''; $DBHOST = $opts{'DBHOST'} || ''; $DBPORT = $opts{'DBPORT'} || ''; $LOCAL_TMP= $opts{'LOCAL_TMP'}|| ''; $DBORGANISM=$opts{'DBORGANISM'}|| ''; $APOLLO = $opts{'APOLLO'} || ''; $DEFAULT = $opts{'DEFAULT'} || ''; $SCHEMA = $opts{'SCHEMA'} || ''; } if ( !$opts{'DEFAULTS'} && !$opts{'RECONFIGURE'} ) { # # Make sure everything has a value and looks kosher. # $DBDRIVER ||= prompt( 'What database server will you be using?', $VALID_DBS{ $conf{'DBDRIVER'} } ? $VALID_DBS{ $conf{'DBDRIVER'} } : $args{'DBDRIVER'}{'default'} ); unless ( exists $db_lookup{ $DBDRIVER } ) { print join("\n", "Sorry, '$DBDRIVER' isn't valid. Please choose from the following:", ( map { " $_" } sort values %VALID_DBS ), '' ); exit; } $DBNAME ||= prompt( 'What is the Chado database name?', $conf{'DBNAME'} || $args{'DBNAME'}{'default'} ); $DBUSER ||= prompt( 'What is the database username?', $conf{'DBUSER'} || $args{'DBUSER'}{'default'} ); $DBPASS ||= prompt( "What is the password for '$DBUSER'?", $conf{'DBPASS'} || $args{'DBPASS'}{'default'} ); $DBHOST ||= prompt( 'What is the database host?', $conf{'DBHOST'} || $args{'DBHOST'}{'default'} ); $DBPORT ||= prompt( 'What is your database port?', $conf{'DBPORT'} || $args{'DBPORT'}{'default'} ); $SCHEMA ||= prompt( 'What schema will Chado reside in?', $conf{'SCHEMA'} || $args{'SCHEMA'}{'default'} ); $LOCAL_TMP ||= prompt( 'Where shall downloaded ontologies go?', $conf{'LOCAL_TMP'} || $args{'LOCAL_TMP'}{'default'} ); $DBORGANISM||=prompt('What is the default organism (common name, or "none")?', $conf{'DBORGANISM'} || $args{'DBORGANISM'}{'default'} ); $DEFAULT ||=prompt('Do you want to make this the default chado instance?', $conf{'DEFAULT'} || $args{'DEFAULT'}{'default'} ); # $APOLLO||=prompt('Create files to use Apollo with chado?'), # $conf{'APOLLO'} || $args{'APOLLO'}{'default'} } $DBORGANISM = '' if $DBORGANISM =~ /none/i; # # Now figure out which schema modules to include. # or just go with the default # my @sqlfiles; my $external; my @funcfiles; my $rebuild_complete = 0; copy( "$working_dir/modules/default_schema.sql", "$working_dir/modules/complete.sql"); copy( "$working_dir/modules/default_nofuncs.sql", "$working_dir/modules/nofuncs.sql"); my $ant = 1; if (-e "$working_dir/../GMODTools") { print "\nCopying GMODTools from its directory using its ant build.xml ...\n"; chdir "$working_dir/../GMODTools"; system("ant", "gmodrel", "-Dgmod.dir=$working_dir") == 0 or (warn "\n\n****************\nMoving tools from GMODTools directory faild; do you have ant installed?\n****************\n\n" && $ant = 0); print "Done with GMODTools\n"; chdir $working_dir; } # # Show the user the options (esp. if using RECONFIGURE or DEFAULTS). # print join("\n", '', 'Building with the following database options:', " GMOD_ROOT=$O{'GMOD_ROOT'}", " DBDRIVER=$DBDRIVER", " DBNAME=$DBNAME", " DBUSER=$DBUSER", " DBPASS=$DBPASS", " DBHOST=$DBHOST", " DBPORT=$DBPORT", " SCHEMA=$SCHEMA", " LOCAL_TMP=$LOCAL_TMP", " DBORGANISM=$DBORGANISM", " DEFAULT=$DEFAULT", " VERSION=$VERSION", ),"\n\n"; # # Save build options. # if ( open CONF, ">$build_config" ) { $conf{'DBDRIVER'} = $db_lookup{ $DBDRIVER }; $conf{'DBNAME'} = $DBNAME; $conf{'DBUSER'} = $DBUSER; $conf{'DBPASS'} = $DBPASS; $conf{'DBHOST'} = $DBHOST; $conf{'DBPORT'} = $DBPORT; $conf{'LOCAL_TMP'}= $LOCAL_TMP; $conf{'DBORGANISM'}=$DBORGANISM; $conf{'PREFIX'} = $opts{'PREFIX'}; $conf{'LIB'} = $opts{'LIB'}; $conf{'DEFAULT'} = $DEFAULT; $conf{'VERSION'} = $VERSION; $conf{'SCHEMA'} = $SCHEMA; print CONF map { "$_=$conf{ $_ }\n" } keys %conf; close CONF or die "Can't write file '$build_config': $!\n"; } # # Write out new "load.conf" (backup if exists). # copy( $load_config, $load_config . '.old' ) if -e $load_config; my $config_template = catfile( $working_dir, 'load', 'tt2', 'load.conf.tt2' ); if ( -e $config_template ) { my $t = Template->new( ABSOLUTE => 1 ); $t->process( $config_template, { db_driver => $db_lookup{ $DBDRIVER }, db_name => $DBNAME, db_username => $DBUSER, db_password => $DBPASS, db_host => $DBHOST, db_port => $DBPORT, db_organism => $DBORGANISM, local_tmp => $LOCAL_TMP, working_dir => $working_dir, external_ddl => $external, sql_files => \@sqlfiles, }, $load_config ) or die $t->error; } else { warn "Template '$config_template' doesn't exist\n"; } #create load/log/ if it doesn't exist already if (! (-e 'load/logs') ) { mkdir ('load/logs', 0777) or die "unable to mkdir load/logs: $!\n"; } my $complete_sql; if ($O{'SIMPLE'} =~ /^[Yy]/) { system( $PERL, 'bin/AutoDBI.PL') == 0 or die "unable to run bin/AutoDBI.PL: $!\n"; } else { print STDERR < $working_dir/lib/Bio/Chado/AutoDBI.pm" ) == 0 or die "bin/pg2cdbi_viaTT.pl failed, is SQL::Translator installed?\n"; } system( "$PERL load/Build.PL load_conf=$load_config; ./Build" ) == 0 or die "unable to create Build from load/Build.PL: $!\n"; my @exe_files = ( #'load/bin/gmod_load_affymetrix.pl', #'load/bin/gmod_load_affyxls.pl', #'load/bin/gmod_load_gff3.pl', 'load/bin/gmod_bulk_load_gff3.pl', #'bin/gmod_dump_gff3.pl', 'bin/gmod_apollo_triggers.pl', 'bin/gmod_fasta2gff3.pl', 'bin/gmod_sort_gff3.pl', 'bin/gmod_materialized_view_tool.pl', 'bin/gmod_extract_dbxref_from_gff.pl', 'bin/gmod_gff3_preprocessor.pl', 'bin/gmod_make_gff_from_dbxref.pl', 'bin/gmod_load_cvterms.pl', 'bin/gmod_bulk_load_pubmed.pl', 'bin/gmod_make_cvtermpath.pl', 'bin/gmod_add_organism.pl', 'bin/gmod_chado_properties.pl', # 'bin/gmod_bulkfiles.pl', # 'bin/gmod_gff2biomart5.pl', ); if ($ant and -e "$working_dir/../GMODTools") { push @exe_files, 'bin/gmod_bulkfiles.pl', 'bin/gmod_gff2biomart5.pl'; } WriteMakefile( # 'INSTALLSITELIB' => '$(INSTALLSITEARCH)', 'NAME' => 'chado', # 'NAME' => 'gmod', 'VERSION' => $VERSION, 'PREREQ_PM' => { #'SQL::Translator' => 0.05, #'Class::DBI' => 0.94, #'Class::DBI::Pager' => 0, #'Class::DBI::Pg' => 0.02, 'Module::Build' => 0.20, 'Template' => 2.10, #'Term::ProgressBar' => 2.06, #fluff, but make sure you check load/bin/* #if this prereq is removed 'DBI' => 0, 'DBD::Pg' => 1.49, 'XML::Simple' => 2.09, 'XML::Twig' => 0, 'Bio::Chado::Schema'=> 0, 'DBIx::DBStag' => 0.11, 'GO::Parser' => 0, 'Module::Load' => 0.16, 'Bio::Root::Version'=> 1.006001, 'LWP::Simple' => 0, 'IPC::Cmd' => 0, }, 'PL_FILES' => { # 'load/bin/load_affymetrix.PLS' => 'load/bin/gmod_load_affymetrix.pl', # 'load/bin/load_affyxls.PLS' => 'load/bin/gmod_load_affyxls.pl', # 'load/bin/load_gff3.PLS' => 'load/bin/gmod_load_gff3.pl', 'load/bin/bulk_load_gff3.PLS' => 'load/bin/gmod_bulk_load_gff3.pl', 'install_util/conf_install.PLS' => 'install_util/conf_install.pl', 'install_util/src_install.PLS' => 'install_util/src_install.pl', }, EXE_FILES => \@exe_files, ($] >= 5.005 ? ## Add these new keywords supported since 5.005 ( # retrieve abstract from module AUTHOR => 'Scott Cain ') : () ), clean => { FILES => '$(DISTVNAME).tar$(SUFFIX) load/etc/load.conf build.conf ' . '_build Build lib/Bio/Chado/AutoDBI.pm '.$LOCAL_TMP }, ); print INSTRUCTIONS; #sub MY::clean { # package MY; # my $inherited = shift->SUPER::clean(@_); # $inherited =~ s/clean_subdirs/clean_subdirs rm_locks/; # $inherited; #} sub MY::install { package MY; my $inherited = shift->SUPER::install(@_); $inherited =~ s/doc_install/doc_install conf_install src_install/; $inherited; } #sub MY::install { # package MY; # my $inherited = shift->SUPER::install(@_); # $inherited =~ s/doc_install/doc_install song go cvtermpath/; # $inherited; #} sub MY::c_o { return ".SUFFIXES : .gz "; } # TODO: this should be rewritten to use the metadata xml sub MY::postamble { my $root = "GMOD_ROOT=$O{GMOD_ROOT}"; my $version = "VERSION=$VERSION"; qq{ conf_install :: \$(PERL) \"$working_dir/install_util/conf_install.pl\" '$root' '$version' src_install :: \$(PERL) \"$working_dir/install_util/src_install.pl\" '$root' #cvtermpath :: # $working_dir/bin/make_cvtermpath.sh images :: graphviz graphviz_svg diagram instructions :: \@cat Makefile.PL | head -33 | tail -24 graphviz :: \ make $working_dir/modules/companalysis/companalysis.graphviz.png \ make $working_dir/modules/contact/contact.graphviz.png \ make $working_dir/modules/cv/cv.graphviz.png \ make $working_dir/modules/expression/expression.graphviz.png \ make $working_dir/modules/general/general.graphviz.png \ make $working_dir/modules/genetic/genetic.graphviz.png \ make $working_dir/modules/phenotype/phenotype.graphviz.png \ make $working_dir/modules/library/library.graphviz.png \ make $working_dir/modules/cell_line/cell_line.graphviz.png \ make $working_dir/modules/mage/mage.graphviz.png \ make $working_dir/modules/map/map.graphviz.png \ make $working_dir/modules/organism/organism.graphviz.png \ make $working_dir/modules/phenotype/phenotype.graphviz.png \ make $working_dir/modules/phylogeny/phylogeny.graphviz.png \ make $working_dir/modules/pub/pub.graphviz.png \ make $working_dir/modules/sequence/sequence.graphviz.png \ make $working_dir/modules/www/www.graphviz.png \ make $working_dir/modules/stock/stock.graphviz.png \ make $working_dir/modules/project/project.graphviz.png \ make $working_dir/modules/natural_diversity/natural_diversity.graphviz.png \ make $working_dir/modules/nofuncs.graphviz.png graphviz_svg :: \ make $working_dir/modules/companalysis/companalysis.graphviz.svg \ make $working_dir/modules/contact/contact.graphviz.svg \ make $working_dir/modules/cv/cv.graphviz.svg \ make $working_dir/modules/expression/expression.graphviz.svg \ make $working_dir/modules/general/general.graphviz.svg \ make $working_dir/modules/genetic/genetic.graphviz.svg \ make $working_dir/modules/library/library.graphviz.svg \ make $working_dir/modules/cell_line/cell_line.graphviz.svg \ make $working_dir/modules/mage/mage.graphviz.svg \ make $working_dir/modules/map/map.graphviz.svg \ make $working_dir/modules/organism/organism.graphviz.svg \ make $working_dir/modules/phenotype/phenotype.graphviz.svg \ make $working_dir/modules/phylogeny/phylogeny.graphviz.svg \ make $working_dir/modules/pub/pub.graphviz.svg \ make $working_dir/modules/sequence/sequence.graphviz.svg \ make $working_dir/modules/www/www.graphviz.svg \ make $working_dir/modules/stock/stock.graphviz.svg \ make $working_dir/modules/project/project.graphviz.svg \ make $working_dir/modules/natural_diversity/natural_diversity.graphviz.svg \ make $working_dir/modules/nofuncs.graphviz.svg diagram :: \ make $working_dir/modules/companalysis/companalysis.diagram.png \ make $working_dir/modules/contact/contact.diagram.png \ make $working_dir/modules/cv/cv.diagram.png \ make $working_dir/modules/expression/expression.diagram.png \ make $working_dir/modules/general/general.diagram.png \ make $working_dir/modules/genetic/genetic.diagram.png \ make $working_dir/modules/library/library.diagram.png \ make $working_dir/modules/cell_line/cell_line.diagram.png \ make $working_dir/modules/mage/mage.diagram.png \ make $working_dir/modules/map/map.diagram.png \ make $working_dir/modules/organism/organism.diagram.png \ make $working_dir/modules/phenotype/phenotype.diagram.png \ make $working_dir/modules/phylogeny/phylogeny.diagram.png \ make $working_dir/modules/pub/pub.diagram.png \ make $working_dir/modules/sequence/sequence.diagram.png \ make $working_dir/modules/www/www.diagram.png \ make $working_dir/modules/stock/stock.diagram.png \ make $working_dir/modules/project/project.diagram.png \ make $working_dir/modules/natural_diversity/natural_diversity.diagram.png \ make $working_dir/modules/nofuncs.diagram.png html :: \ make $working_dir/modules/companalysis/companalysis.html \ make $working_dir/modules/contact/contact.html \ make $working_dir/modules/cv/cv.html \ make $working_dir/modules/expression/expression.html \ make $working_dir/modules/general/general.html \ make $working_dir/modules/genetic/genetic.html \ make $working_dir/modules/phenotype/phenotype.html \ make $working_dir/modules/library/library.html \ make $working_dir/modules/cell_line/cell_line.html \ make $working_dir/modules/mage/mage.html \ make $working_dir/modules/map/map.html \ make $working_dir/modules/organism/organism.html \ make $working_dir/modules/phenotype/phenotype.html \ make $working_dir/modules/phylogeny/phylogeny.html \ make $working_dir/modules/pub/pub.html \ make $working_dir/modules/sequence/sequence.html \ make $working_dir/modules/www/www.html \ make $working_dir/modules/stock/stock.html \ make $working_dir/modules/project/project.html \ make $working_dir/modules/natural_diversity/natural_diversity.html \ make $working_dir/modules/nofuncs.html tex :: \ make $working_dir/modules/companalysis/companalysis.tex \ make $working_dir/modules/contact/contact.tex \ make $working_dir/modules/cv/cv.tex \ make $working_dir/modules/expression/expression.tex \ make $working_dir/modules/general/general.tex \ make $working_dir/modules/genetic/genetic.tex \ make $working_dir/modules/phenotype/phenotype.tex \ make $working_dir/modules/library/library.tex \ make $working_dir/modules/cell_line/cell_line.tex \ make $working_dir/modules/mage/mage.tex \ make $working_dir/modules/map/map.tex \ make $working_dir/modules/organism/organism.tex \ make $working_dir/modules/phenotype/phenotype.tex \ make $working_dir/modules/phylogeny/phylogeny.tex \ make $working_dir/modules/pub/pub.tex \ make $working_dir/modules/sequence/sequence.tex \ make $working_dir/modules/www/www.tex \ make $working_dir/modules/stock/stock.tex \ make $working_dir/modules/project/project.tex \ make $working_dir/modules/natural_diversity/natural_diversity.tex \ make $working_dir/modules/nofuncs.tex %.html: %.sql $working_dir/bin/pg2html.pl \$< > \$@ %.tex: %.sql sqlt --from PostgreSQL \$< --to Latex > \$@ %.graphviz.png: %.sql sqlt-graph -o \$@ --color --db PostgreSQL -l neato --skip-tables-like "^gencode" \$< %.graphviz.svg: %.sql sqlt-graph -o \$@ --color --db PostgreSQL -l neato --skip-tables-like "^gencode" -t svg \$< %.diagram.png: %.sql $working_dir/bin/pg2diagram.pl \$< > \$@ metadata: $working_dir/bin/ddltrans cat \`find . -name \\*.sql -print\` > $working_dir/dat/chado.ddl $working_dir/bin/ddltrans -s chado -f dtd $working_dir/dat/chado.ddl > $working_dir/dat/chado.dtd $working_dir/bin/ddltrans -f html $working_dir/dat/chado.ddl > $working_dir/dat/chado.html $working_dir/bin/ddltrans -f perl $working_dir/dat/chado.ddl > $working_dir/dat/chado.pl $working_dir/bin/ddltrans -f xml $working_dir/dat/chado.ddl > $working_dir/dat/chado.xml load_schema :: \$(SHELL) $working_dir/bin/test_load.sh $DBHOST $DBPORT $DBUSER $DBNAME prepdb :: ./Build prepdb ontologies :: ./Build ontologies update :: ./Build update rm_locks :: `find $LOCAL_TMP -name "*$DBNAME" -exec rm -f '{}' ';'` }; } chado-1.23/MANIFEST000644 000765 000024 00000026576 12061672376 013755 0ustar00cainstaff000000 000000 bin/addcascades bin/AutoDBI.PL bin/chado-build-schema.pl bin/chado-fix-flybase-instance.pl bin/config.PLS bin/create-bridge-sql.pl bin/create-so-bridge.pl bin/gencode2sql.pl bin/gmod_add_organism.pl bin/gmod_apollo_triggers.pl bin/gmod_bulk_load_pubmed.pl bin/gmod_bulkfiles.pl bin/gmod_chado_properties.pl bin/gmod_dump_gff3.pl bin/gmod_extract_dbxref_from_gff.pl bin/gmod_fasta2gff3.pl bin/gmod_gff2biomart5.pl bin/gmod_gff3_preprocessor.pl bin/gmod_load_cvterms.pl bin/gmod_make_cvtermpath.pl bin/gmod_make_gff_from_dbxref.pl bin/gmod_materialized_view_tool.pl bin/gmod_sort_gff3.pl bin/gmod_update_chado.pl bin/interactions2SIF.pl bin/load_ncbi_taxonomy.pl bin/load_taxonomy_cvterms.pl bin/make_cvtermpath.pl bin/make_cvtermpath.sh bin/make_partial_indexes.pl bin/pg2cdbi.pl bin/pg2cdbi_viaTT.pl bin/pg2diagram.pl bin/pg2graphviz.pl bin/pg2graphviz_svg.pl bin/pg2html.pl bin/privileges.tmpl bin/Skip_tables.pm bin/test_load.pl bin/test_load.sh bin/ucsc_genes2gff.pl bin/ucsc_snp2gff.pl chado-module-metadata.xml chado-xml/examples/CG10833.expanded.chado-xml chado-xml/examples/CG10833.with-macros.chado-xml chado-xml/examples/CG10833.with-macros.defaults-stripped.chado-xml chado-xml/README chado-xml/xsl/chado-create-feature-nesting.xsl chado-xml/xsl/chado-expand-macros.xsl chado-xml/xsl/chado-insert-macros.xsl chado-xml/xsl/chado-remove-analysis-features.xsl chado-xml/xsl/chado-remove-default-elements.xsl chado-xml/xsl/chado-remove-feature-nesting.xsl chado-xml/xsl/README Changes Changes.GMOD Changes.sql conf/bulkfiles/anogam.xml conf/bulkfiles/blastfiles.xml conf/bulkfiles/bulkfiles_template.xml conf/bulkfiles/chadofeatconv.xml conf/bulkfiles/chadofeatsql.xml conf/bulkfiles/chadogenepagesql.xml conf/bulkfiles/dmelhetfeatconv.xml conf/bulkfiles/dmelr420.xml conf/bulkfiles/dmelr430.xml conf/bulkfiles/dpsebulk-p4.xml conf/bulkfiles/dpsebulk-p5.xml conf/bulkfiles/dpsebulk-r2.xml conf/bulkfiles/drosmelgb.xml conf/bulkfiles/fastawriter.xml conf/bulkfiles/fbbulk-hetr3.xml conf/bulkfiles/fbbulk-r3.xml conf/bulkfiles/fbbulk-r3h.xml conf/bulkfiles/fbbulk-r4.xml conf/bulkfiles/fbbulk-r41.xml conf/bulkfiles/fbbulk-r411.xml conf/bulkfiles/fbreleases.xml conf/bulkfiles/featuresets.xml conf/bulkfiles/filesets.xml conf/bulkfiles/gbrowseconf.xml conf/bulkfiles/gbrowseconf_fb.xml conf/bulkfiles/genbanksubmit.xml conf/bulkfiles/genomeweb.xml conf/bulkfiles/organisms.xml conf/bulkfiles/sgdbulk.xml conf/bulkfiles/sgdbulk1.xml conf/bulkfiles/sgdfeatconf.xml conf/bulkfiles/site_defaults.xml conf/bulkfiles/site_eugenes_defaults.xml conf/bulkfiles/spbase.xml conf/bulkfiles/spbasefeatconf.xml conf/bulkfiles/tablewriter.xml conf/bulkfiles/toacode.xml conf/bulkfiles/tognomap.xml conf/chado2apollo-apache.conf doc/about-gff2biomart.pod doc/COPYRIGHT doc/css/chado.css doc/examples/dicistronic-gene-example.chado doc/examples/dicistronic-gene-example.chaos doc/examples/dicistronic-gene-example.game doc/examples/dicistronic-gene-example.png doc/examples/dmel_NPFR1.chado doc/examples/dmel_NPFR1.chaos doc/examples/dmel_NPFR1.game doc/examples/dmel_NPFR1.png doc/gff2biomart-update.note doc/gmod-tools-readme.pod doc/index.html doc/wiki/generateChadoWikiTables.py doc/wiki/wiki.tmpl doc/xsl/scenario-to-html-inline.xsl doc/xsl/scenario-to-html.xsl INSTALL.Chado INSTALL.Custom install_util/conf_install.PLS install_util/install.pm install_util/src_install.PLS lib/Bio/Chado/Builder.pm lib/Bio/Chado/Config.pm lib/Bio/FeatureIO/chado.pm lib/Bio/FeatureIO/chadobulk.pm lib/Bio/GMOD/Bulkfiles.pm lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm lib/Bio/GMOD/Bulkfiles/BlastWriter.pm lib/Bio/GMOD/Bulkfiles/BulkWriter.pm lib/Bio/GMOD/Bulkfiles/FastaWriter.pm lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm lib/Bio/GMOD/Bulkfiles/TableWriter.pm lib/Bio/GMOD/Config.pm lib/Bio/GMOD/Config2.pm lib/Bio/GMOD/DB/Adapter.pm lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm lib/Bio/GMOD/DB/Adapter/Wormbase.pm lib/Bio/GMOD/DB/Config.pm lib/Bio/GMOD/DB/Tools/ETA.pm lib/Bio/GMOD/Load.pm lib/Bio/GMOD/Load/GFF.pm lib/Bio/GMOD/SeqUtils.pm LICENSE load/bin/bulk_load_gff3.PLS load/bin/load_gff3.PLS load/Build.PL load/etc/chap.obo load/etc/extra.sql load/etc/feature_property.obo load/etc/genbank_feature_property.obo load/etc/initialize.sql load/etc/README load/tt2/load.conf.tt2 Makefile.PL MANIFEST This list of files MANIFEST.SKIP modules/audit/add-audits.tmpl modules/audit/audit_tables.sql modules/audit/make_audit_ddl modules/bin/makedep.pl modules/bin/mk.pl modules/cell_line/cell_line.html modules/cell_line/cell_line.sql modules/companalysis/companalysis.html modules/companalysis/companalysis.sql modules/companalysis/functions/companalysis-loading.plpgsql modules/companalysis/functions/companalysis-loading.sqlapi modules/contact/contact.html modules/contact/contact.sql modules/contact/contactprop.sql modules/cv/bridges/bin/create-bridge-sql.pl modules/cv/bridges/godb-bridge.plpgsql modules/cv/bridges/godb-bridge.sql.xml modules/cv/cv-dbapi.sqli modules/cv/cv.html modules/cv/cv.sql modules/cv/functions/cv-helper.plpgsql modules/cv/functions/cv-helper.sqlapi modules/cv/functions/deductive_closure.plpgsql modules/cv/functions/deductive_closure.sqlapi modules/cv/functions/detect_cycle.plpgsql modules/cv/functions/fill_cvtermpath.plpgsql modules/cv/functions/get_subj_obj_ids.plpgsql modules/cv/views/cv-convenience-views.sql modules/cv/views/cv-logical-definitions-views.sql modules/cv/views/cv-report.sql modules/cv/views/cv-stats.sql modules/cv/views/cv-views.sql modules/default_nofuncs.sql modules/default_schema.sql modules/expression/expression.html modules/expression/expression.sql modules/extension.modules modules/function.modules modules/general/functions/general-loading.plpgsql modules/general/functions/general-loading.sqlapi modules/general/general.html modules/general/general.sql modules/general/views/general-report.sql modules/genetic/genetic.html modules/genetic/genetic.sql modules/idb-full.modules modules/library/library.html modules/library/library.sql modules/mage/mage.html modules/mage/mage.sql modules/mage/mage.views modules/map/map.html modules/map/map.sql modules/module-tables.json modules/natural_diversity/natural_diversity.html modules/natural_diversity/natural_diversity.sql modules/nofuncs.html modules/nofuncs.sql modules/organism/examples/examples-orgs.chado-xml modules/organism/functions/organism-loading.plpgsql modules/organism/functions/organism.plpgsql modules/organism/functions/organism.sqlapi modules/organism/organism.html modules/organism/organism.sql modules/phenotype/phenotype.html modules/phenotype/phenotype.sql modules/phylogeny/Changes modules/phylogeny/examples/org.chado-xml modules/phylogeny/examples/README modules/phylogeny/examples/sample-phylo.chado-xml modules/phylogeny/examples/sample-phylo.nhx modules/phylogeny/functions/phylo.plpgsql modules/phylogeny/functions/phylo.sqlapi modules/phylogeny/phylogeny.html modules/phylogeny/phylogeny.sql modules/project/project.html modules/project/project.sql modules/pub/pub.html modules/pub/pub.sql modules/sequence/apollo-bridge/ad_hoc_cv modules/sequence/apollo-bridge/apollo-triggers.plpgsql modules/sequence/apollo-bridge/apollo.inserts modules/sequence/apollo-bridge/cv_inserts.sql modules/sequence/apollo-bridge/insert_ad_doc_cv.pl modules/sequence/apollo-bridge/naming_rules.txt modules/sequence/apollo-bridge/sample_db/README modules/sequence/bdgp/bdgp-indexes.sql modules/sequence/bdgp/bdgp-views.sql modules/sequence/bdgp/bin/create-so-layer.pl modules/sequence/bdgp/doc/chado-sequence-ontology-layer.sxi modules/sequence/bdgp/populate-match-floc.sql modules/sequence/bdgp/README modules/sequence/bdgp/so-views.sql modules/sequence/bridges/bin/create-sofa-bridge.pl modules/sequence/bridges/chaos-bridge.sql.xml modules/sequence/bridges/gadfly-bridge.sql.xml modules/sequence/bridges/so-bridge.sql modules/sequence/bridges/sofa-bridge.sql modules/sequence/functions/create_soi.plpgsql modules/sequence/functions/delete-trigger.plpgsql modules/sequence/functions/feature.plpgsql modules/sequence/functions/feature.sqlapi modules/sequence/functions/feature_ids_fx.plpgsql modules/sequence/functions/feature_subalignments.plpgsql modules/sequence/functions/frange.plpgsql modules/sequence/functions/locgraph.plpgsql modules/sequence/functions/locgraph.sqlapi modules/sequence/functions/range.plpgsql modules/sequence/functions/range.sqlapi modules/sequence/functions/sequence-cv-helper.plpgsql modules/sequence/functions/sequence-cv-helper.sqlapi modules/sequence/functions/sequence-loading.plpgsql modules/sequence/functions/sequence-loading.sqlapi modules/sequence/functions/sequtil.plpgsql modules/sequence/functions/sequtil.sqlapi modules/sequence/functions/subsequence.plpgsql modules/sequence/functions/subsequence.sqlapi modules/sequence/gencode/gencode.sql modules/sequence/gencode/gencode_data.sql modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql modules/sequence/gff-bridge/sequence-gff-views.sql modules/sequence/sequence-dbapi.sqli modules/sequence/sequence.html modules/sequence/sequence.pgfunc modules/sequence/sequence.sql modules/sequence/sequence_opt.xml modules/sequence/sequence_views.sql modules/sequence/views/exon-views.sql modules/sequence/views/implicit-feature-views.sql modules/sequence/views/range-views.sql modules/sequence/views/sequence-cv-views.sql modules/sequence/views/sequence-report.sql modules/stock/stock.html modules/stock/stock.sql README README.Apollo schemas/1-1.1/diff.sql schemas/1-1.11/diff.sql schemas/1-1.2/diff.sql schemas/1.1-1.2/diff.sql schemas/1.1/default_schema.sql schemas/1.11-1.2/diff.sql schemas/1.11/default_schema.sql schemas/1.2/default_schema.sql schemas/1/default_schema.sql soi/cgi/get_xml.pl soi/README soi/scripts/dump_fasta.pl soi/scripts/dump_segment.pl soi/scripts/generegion.pl soi/SOI/Adapter.pm soi/SOI/Feature.pm soi/SOI/FeatureDecor.pm soi/SOI/GAMEHandler.pm soi/SOI/GFF3Parser.pm soi/SOI/IntersectGraph.pm soi/SOI/Outputter.pm soi/SOI/SOIHandler.pm soi/SOI/Visitor.pm soi/t/data/AE003790.cDNA.game.xml soi/t/data/AE003790.soi.xml soi/t/t_soi_parse_intersect soi/templates/features_by_name.soi soi/templates/genes_by_child_count.soi soi/templates/genes_by_GO_term.soi soi/templates/top_typed_feature.soi soi/templates/top_typed_feature_no_soi.soi soi/templates/typed_genes.soi stag-templates/chado-basicfeature.stg stag-templates/chado-cvterm.stg stag-templates/chado-cvtermgraph.stg stag-templates/chado-feature-by-direct-cvterm.stg stag-templates/chado-feature_children.stg stag-templates/chado-feature_relationship.stg stag-templates/chado-feature_synonym.stg stag-templates/chado-genemodel-with-featureloc.stg stag-templates/chado-genemodel.stg stag-templates/chado-mrna.stg stag-templates/chado-pcgenemodel.stg stag-templates/chado-protein.stg stag-templates/chado-roi.stg stag-templates/chado-upstream-of-alignment.stg stag-templates/make-publish stag-templates/README TODO UPGRADE.txt schemas/1-1.21/diff.sql schemas/1.1-1.21/diff.sql schemas/1.11-1.21/diff.sql schemas/1.2-1.21/diff.sql #the following added by generate_diff_dirs.pl schemas/1-1.22/diff.sql schemas/1.1-1.22/diff.sql schemas/1.11-1.22/diff.sql schemas/1.2-1.22/diff.sql schemas/1.21-1.22/diff.sql #the following added by generate_diff_dirs.pl schemas/1-1.23/diff.sql schemas/1.1-1.23/diff.sql schemas/1.11-1.23/diff.sql schemas/1.2-1.23/diff.sql schemas/1.21-1.23/diff.sql schemas/1.22-1.23/diff.sql META.yml Module meta-data (added by MakeMaker) chado-1.23/MANIFEST.SKIP000644 000765 000024 00000001065 11636003637 014477 0ustar00cainstaff000000 000000 ^chado.*\.tar.gz$ CVS (^|/)\. ^# \.bak$ \.swp$ \.old$ \.tmp$ \.svn ^tmp .*modules/.*\.png$ .*modules/.*\.svg$ Makefile$ ^blib/ _blib$ ^_build/ ^Build$ build.conf ^load/etc/load.conf$ ^lib/Bio/Chado/AutoDBI.pm$ ^lib/Bio/Chado/LoadDBI.pm$ ^doc/diagrams ^modules/complete.sql ^modules/www ^cas-utils ^dat/ genbank2gff3.PLS load/bin/load_affymetrix.pl load/bin/load_affyxls.pl load/bin/load_taxonomy.pl load/bin/new_gff_loader.pl load/bin/load_ontology.PLS ^src/ bin/gmod_materialize_gbrowse_views.pl Class-DBI-Pg-0.06-multiple-schemata.patch ^chaos-xml log4perl.conf chado-1.23/META.yml000644 000765 000024 00000001542 12061672376 014057 0ustar00cainstaff000000 000000 --- #YAML:1.0 name: chado version: 1.23 abstract: ~ license: ~ author: - Scott Cain generated_by: ExtUtils::MakeMaker version 6.42 distribution_type: module requires: Bio::Chado::Schema: 0 Bio::Root::Version: 1.006001 DBD::Pg: 1.49 DBI: 0 DBIx::DBStag: 0.11 GO::Parser: 0 IPC::Cmd: 0 LWP::Simple: 0 Module::Build: 0.2 Module::Load: 0.16 Template: 2.1 XML::Simple: 2.09 XML::Twig: 0 meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.3.html version: 1.3 chado-1.23/modules/000755 000765 000024 00000000000 12061672376 014254 5ustar00cainstaff000000 000000 chado-1.23/README000644 000765 000024 00000006767 11256710157 013477 0ustar00cainstaff000000 000000 $Id: README,v 1.14 2007-04-12 19:01:50 briano Exp $ INTRODUCTION ------------ Chado is a modular schema for handling all kinds of biological data. It is intended to be used as both a primary datastore schema as well as a warehouse-style schema. Chado was originally conceived as the next generation Flybase database, combining the sequence annotation database gadfly with the Harvard and Cambridge databases. We have avoided organism or project specificity in the schema, and we hope it will be of use to other projects. The modules currently in chado are: Audit - database audits Companalysis - data from computational analysis Contact - people and groups Controlled Vocabulary (cv) - controlled vocabularies and ontologies Expression - summarized RNA and protein expresssion General - identifiers Genetic - genetic data and genotypes Library - descriptions of molecular libraries Mage - microarray data Map - maps without sequence Organism - species Phenotype - phenotypic data Phylogeny - phylogenetic trees Publication (pub) - publications and references Sequence - sequences and sequence features Stock - specimens and biological collections WWW - For documentation on the various modules, see http://www.gmod.org. Other modules are possible; the existing modules cover a very large variety of use cases. Chado has a fairly abstract schema, and ontologies and controlled vocabularies (CVs) are utilised where their use is favourable to relational modeling. In particular, the sequence ontology (SO) is vital to the sequence module. Some (but not all) of the use cases we have discussed are: * Central dogma genome annotations * Genes that break the central dogma (of which there are many Annotated in fly, including polycistronic transcripts, transplicing, selenocysteine readthroughs, rna editing, ....) * Sequence variation data, including SNPs, transposable element insertions, indels, ... how this relates to phenotypes, how these effect the central dogma.... * Non-wildtype data, including representing a wildtype transcriptome and proteome on a non wildtype genome; implicit and explicit central dogma examples for mutant strains * Complex phenotypic data * Ontologies structured as graphs; querying over graph ontologies non-recursively by pre-computing the closure * Sequence ontology * Comparative data * Genetic interactions * Transgene constructs, complex genetic experiments and their results The core schema is DBMS independent. The SQL table create files can be found in the chado/modules directory. The main Chado developers are currently using PostgreSQL. INSTALLATION ------------ Please read the included INSTALL.Chado document for instructions on how to install the Chado schema. CHADO SUPPORT ------------- Please see our website for more information on Chado and the GMOD project: http://www.gmod.org/ You can send questions to the Chado mailing list: gmod-schema@lists.sourceforge.net You can browse the schema CVS repository here: http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/schema/ AUTHORS ------- Chris Mungall, David Emmert and the GMOD team October 2, 2003 chado-1.23/README.Apollo000644 000765 000024 00000007661 11636151402 014710 0ustar00cainstaff000000 000000 Note that this document is quite old, and while it may still work this way, it can't be guaranteed. Most people who use Apollo with Chado do not do it this way anymore and instead use the adapter that comes with Apollo (sometimes known as the "Crabtree adapter" after the original author Jonathan Crabtree). For more information on it, see the Apollo tutorial at the GMOD website: http://gmod.org/wiki/Apollo_Tutorial Scott 9/20/2011 This needs to be better documented, but here is a start: In order to use Apollo read/write with chado, here are things that need to be done: - grant privileges to users to several tables (list here) --in the meantime, you can grant all using sqlt and the template, bin/privileges.tmpl sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql You can edit the template to grant privileges to just specific users instead of PUBLIC, which of course would be a lot more secure. - insert several ad hoc cv terms found in modules/sequence/apollo-bridge/cv_inserts.sql. This file contains sql commands to insert several controlled vocabulary terms that Apollo expects to be in the database. This file can be recreated with additional terms as needed by editing the file modules/sequence/apollo-bridge/ad_hoc_cv and running the perl script modules/sequence/apollo-bridge/insert_ad_doc_cv.pl. The resulting sql file can be inserted into the database with this command: $ psql $DBNAME < modules/sequence/apollo-bridge/cv_inserts.sql - insert a few misc items like those found in modules/sequence/apollo-bridge/apollo.inserts Essentially, Apollo and chado have to agree about what the names of the programs in the analysis table are, and there needs to be a few terms in the cv table. About naming analysis results: there are no restrictions on what you name them, however the GFF3 bulk loader will insert them typically one of two ways: 1. If you specify the -a (--analysis) flag with an argument, the loader will look for an entry in the analysis table where analysis.name is equal to the argument supplied with -a. 2. If you don't give an argument with -a, the loader will look for analysis.name that is equal to the GFF source and type concatentated with and underscore between them, ie 'source_type', eg, 'Rice_cDNA_match'. The inserts in the db table are there so that dbxref entries in GFF files I typically process. They can be ignored unless you are loading GFF files with Dbxref entries. Then there is the uniquename_id_generator sequence, for which integers for building uniquenames are used. Then there are two interts in to cvtermprop for the suffix and prefix for uniquename generation. Generated uniquenames with be of the form: $prefix . (int from uniquename_id sequence) . $suffix For exmple, if you insert 'RICE' for the prefix and 'X' for the suffix, the resulting name of the first feature will be 'RICE000001X'; - add the functions and triggers to chado. Use the perl script: % /usr/local/bin/gmod_apollo_triggers.pl create Note that this script can also be used to drop and add the triggers in case you want to do some bulk loading and want to disactivate the triggers for that. - modify the Apollo configuration file, chado-adapter.xml. IS THERE DOCUMENTATION FOR DOING THAT IN APOLLO'S DOCS? Yes, there is a section for connecteding directly to flybase chado in the apollo doc directory: doc/html/userguide.html but it is somewhat out of date. I need to work with Mark to update it (it will probably need me to write it and have Mark proof it). I understand that these directions are somewhat vague. Getting Apollo to work with chado requires a little hands on tinkering. If you find yourself having difficulties, please contact me. Scott Cain cain@cshl.edu 4/29/05 chado-1.23/schemas/000755 000765 000024 00000000000 12061672376 014227 5ustar00cainstaff000000 000000 chado-1.23/soi/000755 000765 000024 00000000000 12061672376 013376 5ustar00cainstaff000000 000000 chado-1.23/stag-templates/000755 000765 000024 00000000000 12061672376 015536 5ustar00cainstaff000000 000000 chado-1.23/TODO000644 000765 000024 00000013771 11256710157 013300 0ustar00cainstaff000000 000000 In preparation for the 0.1 release and a talk/poster at the Biology of Genomes meeting, here is a new TODO list: BioMart bridge layer (functions and views) Complete most or all items in chado TODO list (needs prioritized, see below) -put todo items in sf system to allow comments Build demo system (based on current, 0.1 schema) on new gmod server, with (organism? yeast, rice, fly, other?) -chado -gbrowse -apollo functions? (ie, do we want to allow live, guest editting?) -turnkey -biomart -drupal (separate from gmod.org, for community stuff)? -cmap -BLAST/blastGraphic? -AmiGO? -DAS2 server? For the 0.1 release: - make the gff3 loaders validate that the uniquename is really unique before trying to insert. (HI-Done, should change to get a complete list and cache it to increase speed (although that would be LOW)) - add a function to the apollo triggers to simplify the merge and split operations (LOW-Apollo development currently unfunded) - add the ability to pass a dbprofile name to scripts (HI - should be easy) - add bioperl patching functionality similar to GBrowse (though make sure they don't stomp on each other (HI) - address flybase's use of of analysisfeature combined with feature to give source-type information (in GFF terms). This will need to be addressed in the GBrowse adaptor. (MED - not sure what is involved) - modify the bulk loader to allow 'mixed' GFF3 files (that is, containing both analysis results and annotations). See perldoc gmod_bulk_load_gff3.pl for more info (HI - this is a major pain for non-me users) - modify the bulk loader to optionally spit INSERT statements in the the files rather than the COPY FROM STDIN format as a fall back for really big files (HI) - modify the bulk loader to (optionally) make gene (foster) parents for orphan transcript types. (MED) - deprecate the use of gmod_load_gff3.pl in favor of the bulk loader - migrate ontology loading to use go-perl (instead of Class::DBI--which may completely eliminate the need for having Class::DBI installed (except for turnkey)) (Done) - Flesh out Apollo stuff to be more transparent to the person doing the installation (MED) - Make a decision on sequence shredding and implement appropriate views and functions (LOW - what we have works) - fix perl modules to conform with Todd's Bio::GMOD namespace (MED - shouldn't be too hard) - fix Bio::FeatureIO to return at least a simple value for Gap attributes (HI - should be easy) - update docs for changes in installation procedures (HI) The things below here are mostly done and just left here for historical interest -------------------------------------------------------------------- MORE TODO - make cdbi optional for the make process TODO for the next alpha release (SOON!) * Have things install in GMOD_ROOT: DONE - in src/ chado/modules - in doc/ chado/READMEs, INSTALL, doc/ DONE - in conf/ create gmod.conf, chado.conf - in examples/ chado/data sample data - in bin/ gmod_*.pl (including what is in load/bin) in docs, suggest that distribution directory be moved to /usr/local/gmod/src. Add docs for how to load genbank, blast and pfam results Tue Jan 6 01:34:51 PST 2004 - allenday Add documentation to README and/or INSTALL regarding Postgres VACUUM and ANALYZE functions. We might want to give users an example of how to set up a cron job to do this nightly. I had a 3 order of magnitude speed increase today from a 10 second ANALYZE command. See http://www.varlena.com/varlena/GeneralBits/Tidbits/perf.html which has useful information for tuning postgresql.conf as well as a suggestion for setting up the auto vacuum daemon. We might also want to build an analyze() method into the loaders, or possibly the middleware layer itself. This will dramatically speed up large loads, but requires changing the cache/flush strategy to the more complex begin-transaction/cache/flush/end-transaction/analyze strategy. -- where to start? For the next release: - fix Makefile.PL to install scripts in $GMOD_ROOT/bin (i'm not convinced I want this; I think /usr/local/bin is fine sc-3/26/04) - add documentation for creating Class::DBI classes for an existing schema-- this will no doubt be necessary for future upgrade paths (I'm thinking the way to suggest doing this is dumping the schema from the existing database, via `pg_dump -s DBNAME > sqlfile`; `pg2cdbi.pl DBNAME USERNAME PASSWORD sqlfile` - add documentation for loading ontologies when the files are already present locally. - remove hard coded passwords and other conf stuff from Class::DBI classes. - integrate Apollo - integrate a web front end (probably turnkey) - provide a custom tag processing module for load_gff3.pl - create a method for updating ontologies - Makefile.PL should also track optional modules included and allow skipping the prompting for them - create a method for populating cvtermpath (make_cvtermpath.pl is a starting point). - add support for relative coordinates in gff3 and the gbrowse adaptor - ontology name in cv table needs to be the same as the name of the root node in the dag-edit ontology file, (requested by mungall). - gene ontology (GO) needs to have its three aspects split into separate ontologies, so the bullet above would use one term below the root (eg, "biological process") as the cv.name and root node in cvterm/cvtermpath/cvtermrelationship. (requested by mungall). For following releases: - incorporate Pub* - incorporate cmap - write a bulk load utility that will quickly load GFF3 data to chado - write a utility that will delete data from the database with a GFF file as a template -- Load order needs to change. I have started adding "bridge" relationships between ontologies to the prepdb step, and this has to happen after the ontologies have already been entered so the INSERT statement can find the terms. Documentation needs to reflect this, of course. We should start using the bug tracker on SF --start using 'Bugs' in http://sourceforge.net/tracker/?group_id=27707 chado-1.23/UPGRADE.txt000644 000765 000024 00000002406 11635712056 014432 0ustar00cainstaff000000 000000 For the most up to date version of this document, please also see http://gmod.org/wiki/Updating_Chado As of Chado version 1.2, the Chado software distribution comes with a tool to upgrade the Chado schema from an old version (1.0 or newer) to a new one. This tool, gmod_update_chado.pl, will get installed with other scripts when you execute "make install" and depends on another tool, gmod_chado_properties.pl, which determines the version of the current Chado database and is also installed when you install Chado. Since this is a new tool, I strongly suggest you back up your database before trying to upgrade via this method! You have been warned! :-) To use the updater, you can start the installation like you normally would: perl Makefile.PL make make install and then, rather than doing the next step (make load_schema) which would wipe out the current database, do make update which will (hopefully) do the updating for you. Note that if you modified the schema after you installed Chado the last time, this update may fail. Please watch the output from the PostgreSQL server to look for "ERROR" statements. If you experience problems with this updating protocol, please send comments, questions and issue reports to gmod-schema@lists.sourceforge.net. chado-1.23/stag-templates/chado-basicfeature.stg000644 000765 000024 00000002402 11256707627 021767 0ustar00cainstaff000000 000000 :SELECT tfeature.*, featurepropd.*, dbxrefd.*, featureloc.*, srcfeature.name, srcfeature.uniquename, srcfeature.seqlen, srcfeature.md5checksum, feature_cvterm.*, cvterm.*, feature_relationship.* :FROM tfeature LEFT OUTER JOIN featureloc ON (tfeature.feature_id = featureloc.feature_id) LEFT OUTER JOIN feature AS srcfeature ON (featureloc.srcfeature_id = srcfeature.feature_id) LEFT OUTER JOIN feature_relationship ON (tfeature.feature_id = object_id) LEFT OUTER JOIN dbxrefd ON (tfeature.dbxref_id = dbxrefd.dbxref_id) LEFT OUTER JOIN featurepropd ON (tfeature.feature_id = featurepropd.feature_id) LEFT OUTER JOIN feature_cvterm ON (tfeature.feature_id = feature_cvterm.feature_id) LEFT OUTER JOIN cvterm USING (cvterm_id) :WHERE [tfeature.name => &name&] [tfeature.feature_id => &feature_id&] [tfeature.type => &type&] :USE NESTING (set (tfeature(dbxrefd)(featurepropd)(featureloc(srcfeature))(feature_relationship(subject))(feature_cvterm(cvterm)))) // ------------------------------------------- schema: chado desc: fetches a single feature by name does not get related features - this basic query must be used iteratively to build the full feature graph see_also: example_input: name => SELECT name FROM feature chado-1.23/stag-templates/chado-cvterm.stg000644 000765 000024 00000001671 11256707627 020641 0ustar00cainstaff000000 000000 :SELECT * :FROM cvterm INNER JOIN dbxref USING (dbxref_id) INNER JOIN db USING (db_id) INNER JOIN cv USING (cv_id) LEFT OUTER JOIN cvtermsynonym USING (cvterm_id) LEFT OUTER JOIN cvtermprop USING (cvterm_id) :WHERE [dbxref.accession => &accession&] [db.name => &dbname&] [cvterm.name => &name&] [cv.cvname => &cvname&] [cvterm.definition => &definition&] :ORDER BY cvterm.name :USE NESTING (set(cvterm(dbxref(db))(cvterm_synonym)(cvterm_prop))) // schema: chado desc: Fetches a metadata about a cvterm - synonyms, comments, definition, dbxref links to analogous cvterms in other ontologies. Does not fetch graph/relationship data REQUIRES: modules/sequence/bdgp/bdgp-views.sql example_input: cvterm_name => SELECT DISTINCT cvterm.name FROM cvterm WHERE cvterm_id IN (SELECT object_id FROM cvterm_relationship) chado-1.23/stag-templates/chado-cvtermgraph.stg000644 000765 000024 00000003312 11256707627 021655 0ustar00cainstaff000000 000000 :SELECT * :FROM cvterm INNER JOIN cvtermpath ON (cvterm.cvterm_id=cvtermpath.object_id) INNER JOIN cvterm_relationship ON (cvtermpath.subject_id=cvterm_relationship.subject_id) INNER JOIN cvterm AS subj_cvterm ON (subj_cvterm.cvterm_id=cvterm_relationship.subject_id) :WHERE [cvterm.accession => &cvterm_accession&] [cvterm.db => &cvterm_db&] [cvterm.name => &cvterm_name&] [cvterm.cvname => &cvterm_cvname&] [cvterm.definition => &cvterm_definition&] [subj_cvterm.accession => &subj_cvterm_accession&] [subj_cvterm.db => &subj_cvterm_db&] [subj_cvterm.name => &subj_cvterm_name&] [subj_cvterm.cvname => &subj_cvterm_cvname&] [subj_cvterm.definition => &subj_cvterm_definition&] :ORDER BY cvterm.name :USE NESTING (set(cvterm(cvtermpath(subj_cvterm(cvterm_relationship))))) // schema: chado desc: Fetches a graph based around a cvterm The graph is either built from object to subjects (downwards), based around cvterm OR it is build from subject to objects (upwards), based around subj_cvterm Of course, the data structure returned is not a graph As XML/Stag, the resulting data will have the object cvterm as root element, and will nest all descendents directly underneath. each descendent (subj_cvterm) will have it's parent relationships nested underneath it (with trailing cvterm_ids) - from this you can reconstruct the whole graph example_input: cvterm_accession => SELECT DISTINCT cvterm.accession FROM cvterm WHERE cvterm_id IN (SELECT object_id FROM cvterm_relationship) example_input: cvterm_name => SELECT DISTINCT cvterm.name FROM cvterm WHERE cvterm_id IN (SELECT object_id FROM cvterm_relationship) chado-1.23/stag-templates/chado-feature-by-direct-cvterm.stg000644 000765 000024 00000002131 11256707627 024142 0ustar00cainstaff000000 000000 :SELECT tfeature.*, featurepropd.*, dbxrefd.*, featureloc.*, feature_cvterm.*, xcvterm.* :FROM tfeature LEFT OUTER JOIN featureloc ON (tfeature.feature_id = featureloc.feature_id) LEFT OUTER JOIN dbxrefd ON (tfeature.dbxref_id = dbxrefd.dbxref_id) LEFT OUTER JOIN featurepropd ON (tfeature.feature_id = featurepropd.feature_id) LEFT OUTER JOIN feature_cvterm ON (tfeature.feature_id = feature_cvterm.feature_id) LEFT OUTER JOIN xcvterm USING (cvterm_id) :WHERE [xcvterm.accession => &cvterm_accession&] [xcvterm.dbname => &cvterm_dbname&] [xcvterm.name => &cvterm_name&] [tfeature.name => &name&] [tfeature.feature_id => &feature_id&] [tfeature.type => &type&] :USE NESTING (set(cxvterm(feature_cvterm(tfeature(dbxrefd)(featurepropd)(featureloc(srcfeature))(feature_relationship(subject)))))) // ------------------------------------------- schema: chado desc: fetches a single feature by name does not get related features - this basic query must be used iteratively to build the full feature graph see_also: example_input: name => SELECT name FROM feature chado-1.23/stag-templates/chado-feature_children.stg000644 000765 000024 00000000730 11256707627 022637 0ustar00cainstaff000000 000000 :SELECT tfeature.* :FROM tfeature AS mainfeature INNER JOIN feature_relationship ON (mainfeature.feature_id = feature_relationship.object_id) INNER JOIN tfeature ON (tfeature.feature_id = feature_relationship.subject_id) :WHERE [mainfeature.name = &name&] :USE NESTING (set (tfeature)) // ------------------------------------------- schema: chado desc: for any feature, this will fetch the child features example_input: name => SELECT name FROM feature chado-1.23/stag-templates/chado-feature_relationship.stg000644 000765 000024 00000001342 11256707627 023550 0ustar00cainstaff000000 000000 :SELECT tfeature.*, object.*, subject.* :FROM tfeature LEFT OUTER JOIN feature_relationship AS subjfr ON (tfeature.feature_id = subjfr.object_id) LEFT OUTER JOIN feature_relationship AS objfr ON (tfeature.feature_id = objfr.subject_id) LEFT OUTER JOIN tfeature AS object ON (object.feature_id = objfr.object_id) LEFT OUTER JOIN tfeature AS subject ON (subject.feature_id = subjfr.subject_id) :WHERE [tfeature.name = &name&] :USE NESTING (set (tfeature(object)(subject))) // ------------------------------------------- schema: chado desc: for any feature, this will fetch the contextual features in the feature graph; gets both subject and object features example_input: name => SELECT name FROM feature chado-1.23/stag-templates/chado-feature_synonym.stg000644 000765 000024 00000001042 11256707627 022560 0ustar00cainstaff000000 000000 :SELECT feature.uniquename, feature.name, synonym.name :FROM feature INNER JOIN cvterm AS ftype ON (feature.type_id = cvterm.name) INNER JOIN feature_synonym USING (feature_id) INNER JOIN synonym USING (synonym_id) :WHERE [feature.name = &name&] [feature.uniquename = &uniquename&] [synonyn.name = &synonym&] [ftype.name = &type&] :USE NESTING (set(feature(synonym))) // ------------------------------------------- schema: chado desc: feature name to synonym mapping example_input: name => SELECT name FROM feature chado-1.23/stag-templates/chado-genemodel-with-featureloc.stg000644 000765 000024 00000002447 11256707627 024402 0ustar00cainstaff000000 000000 :SELECT gene.*, transcript.*, leaf.*, leafloc.*, leaftype.name AS leaf__type, geneprop.*, gptype.name AS geneprop__type :FROM feature AS gene INNER JOIN feature_relationship AS gene2transcript ON (gene.feature_id = gene2transcript.object_id) INNER JOIN feature AS transcript ON (transcript.feature_id = gene2transcript.subject_id) INNER JOIN feature_relationship AS transcript2leaf ON (transcript.feature_id = transcript2leaf.object_id) INNER JOIN feature AS leaf ON (leaf.feature_id = transcript2leaf.subject_id) INNER JOIN featureloc AS leafloc ON (leafloc.feature_id = leaf.feature_id) INNER JOIN cvterm AS leaftype ON (leaf.type_id = leaftype.cvterm_id) LEFT OUTER JOIN featureprop AS geneprop ON (gene.feature_id = geneprop.feature_id) LEFT OUTER JOIN cvterm AS gptype ON (geneprop.type_id = gptype.cvterm_id) :WHERE [gene.name => &gene_name&] [mrna.name => &mrna_name&] [protein.name => &protein_name&] :USE NESTING (set(gene(geneprop)(transcript(leaf(leafloc))))) // schema: chado desc: fetches a gene model; may or may not be protein-coding transcripts are nested under genes exons and any proteins are nested under transcripts (check the element leaf/type for exon vs protein) example_input: name => SELECT name FROM gene chado-1.23/stag-templates/chado-genemodel.stg000644 000765 000024 00000002300 11256707627 021266 0ustar00cainstaff000000 000000 :SELECT gene.*, transcript.*, leaf.*, leaftype.name AS leaf__type, geneprop.*, gptype.name AS geneprop__type :FROM feature AS gene INNER JOIN feature_relationship AS gene2transcript ON (gene.feature_id = gene2transcript.object_id) INNER JOIN feature AS transcript ON (transcript.feature_id = gene2transcript.subject_id) INNER JOIN feature_relationship AS transcript2leaf ON (transcript.feature_id = transcript2leaf.object_id) INNER JOIN feature AS leaf ON (leaf.feature_id = transcript2leaf.subject_id) INNER JOIN cvterm AS leaftype ON (leaf.type_id = leaftype.cvterm_id) LEFT OUTER JOIN featureprop AS geneprop ON (gene.feature_id = geneprop.feature_id) LEFT OUTER JOIN cvterm AS gptype ON (geneprop.type_id = gptype.cvterm_id) :WHERE [gene.name => &gene_name&] [mrna.name => &mrna_name&] [protein.name => &protein_name&] :USE NESTING (set(gene(geneprop)(transcript(leaf)))) // schema: chado desc: fetches a gene model; may or may not be protein-coding transcripts are nested under genes exons and any proteins are nested under transcripts (check the element leaf/type for exon vs protein) example_input: name => SELECT name FROM gene chado-1.23/stag-templates/chado-mrna.stg000644 000765 000024 00000002525 11256707627 020275 0ustar00cainstaff000000 000000 :SELECT gene.*, mrna.*, exon.*, protein.*, mrnaprop.*, mptype.name AS mrnaprop__type :FROM feature AS gene INNER JOIN feature_relationship AS gene2mrna ON (gene.feature_id = gene2mrna.object_id) INNER JOIN feature AS mrna ON (mrna.feature_id = gene2mrna.subject_id) INNER JOIN feature_relationship AS mrna2exon ON (mrna.feature_id = mrna2exon.object_id) INNER JOIN feature AS exon ON (exon.feature_id = mrna2exon.subject_id) INNER JOIN feature_relationship AS mrna2protein ON (mrna.feature_id = mrna2protein.object_id) INNER JOIN feature AS protein ON (protein.feature_id = mrna2protein.subject_id) LEFT OUTER JOIN featureprop AS mrnaprop ON (mrna.feature_id = mrnaprop.feature_id) LEFT OUTER JOIN cvterm AS mptype ON (mrnaprop.type_id = mptype.cvterm_id) INNER JOIN cvterm AS proteintype ON (protein.type_id = proteintype.cvterm_id) INNER JOIN cvterm AS exontype ON (exon.type_id = exontype.cvterm_id) :WHERE [proteintype.name = 'protein'] [exontype.name = 'exon'] [mrna.name => &mrna_name&] [protein.name => &protein_name&] [gene.name => &gene_name&] :USE NESTING (set(mrna(mrnaprop)(gene)(protein)(exon))) // schema: chado desc: protein details: proteins and propertioes, plus the containing mRNA and gene example_input: protein_name => SELECT name FROM protein chado-1.23/stag-templates/chado-pcgenemodel.stg000644 000765 000024 00000002463 11256707627 021623 0ustar00cainstaff000000 000000 :SELECT gene.*, mrna.*, exon.*, protein.*, geneprop.*, gptype.name AS geneprop__type :FROM feature AS gene INNER JOIN feature_relationship AS gene2mrna ON (gene.feature_id = gene2mrna.object_id) INNER JOIN feature AS mrna ON (mrna.feature_id = gene2mrna.subject_id) INNER JOIN feature_relationship AS mrna2exon ON (mrna.feature_id = mrna2exon.object_id) INNER JOIN feature AS exon ON (exon.feature_id = mrna2exon.subject_id) INNER JOIN feature_relationship AS mrna2protein ON (mrna.feature_id = mrna2protein.object_id) INNER JOIN feature AS protein ON (protein.feature_id = mrna2protein.subject_id) INNER JOIN cvterm AS proteintype ON (protein.type_id = proteintype.cvterm_id) INNER JOIN cvterm AS exontype ON (exon.type_id = exontype.cvterm_id) LEFT OUTER JOIN featureprop AS geneprop ON (gene.feature_id = geneprop.feature_id) LEFT OUTER JOIN cvterm AS gptype ON (geneprop.type_id = gptype.cvterm_id) :WHERE [exontype.name = 'exon'] [proteintype.name = 'protein'] [gene.name => &gene_name&] [mrna.name => &mrna_name&] [protein.name => &protein_name&] :USE NESTING (set(gene(geneprop)(mrna(protein)(exon)))) // schema: chado desc: protein coding gene model; bare bones (no featureprops etc) example_input: name => SELECT name FROM gene chado-1.23/stag-templates/chado-protein.stg000644 000765 000024 00000002116 11256707627 021014 0ustar00cainstaff000000 000000 :SELECT gene.*, mrna.*, protein.*, proteinprop.*, pptype.name AS proteinprop__type :FROM feature AS gene INNER JOIN feature_relationship AS gene2mrna ON (gene.feature_id = gene2mrna.object_id) INNER JOIN feature AS mrna ON (mrna.feature_id = gene2mrna.subject_id) INNER JOIN feature_relationship AS mrna2protein ON (mrna.feature_id = mrna2protein.object_id) INNER JOIN feature AS protein ON (protein.feature_id = mrna2protein.subject_id) LEFT OUTER JOIN featureprop AS proteinprop ON (protein.feature_id = proteinprop.feature_id) LEFT OUTER JOIN cvterm AS pptype ON (proteinprop.type_id = pptype.cvterm_id) INNER JOIN cvterm AS proteintype ON (protein.type_id = proteintype.cvterm_id) :WHERE [proteintype.name = 'protein'] [protein.name => &protein_name&] [mrna.name => &mrna_name&] [gene.name => &gene_name&] :USE NESTING (set(protein(proteinprop)(mrna(gene)(exon)))) // schema: chado desc: protein details: proteins and propertioes, plus the containing mRNA and gene example_input: protein_name => SELECT name FROM protein chado-1.23/stag-templates/chado-roi.stg000644 000765 000024 00000001737 11256707627 020135 0ustar00cainstaff000000 000000 :SELECT srcfeature.*, feature.*, ftype.*, featureloc.* :FROM feature INNER JOIN cvterm AS ftype ON (feature.type_id = ftype.cvterm_id) INNER JOIN featureloc USING (feature_id) LEFT OUTER JOIN featureprop USING (feature_id) LEFT OUTER JOIN cvterm AS proptype ON (featureprop.type_id = proptype.cvterm_id) INNER JOIN feature AS srcfeature ON (featureloc.srcfeature_id = srcfeature.feature_id) :WHERE [ srcfeature.name => &src& ] [ srcfeature.feature_id => &srcfeature_id& ] [ featureloc.fmin >= &fmin& ] [ featureloc.fmax <= &fmax& ] :USE NESTING (set(srcfeature(feature(featureloc)))) // ------------------------------------------- schema: chado desc: ROI (region of interest) query for chado see_also: esncore-contigdna.stg example_input: fmin => 20000 example_input: fmax => 80000 example_input: src => SELECT DISTINCT srcfeature.name FROM feature AS srcfeature INNER JOIN featureloc ON (srcfeature_id=srcfeature.feature_id) LIMIT 10 chado-1.23/stag-templates/chado-upstream-of-alignment.stg000644 000765 000024 00000001135 11256707627 023552 0ustar00cainstaff000000 000000 :SELECT * :FROM match INNER JOIN featureloc AS hitloc ON (hitloc.feature_id = match.feature_id) INNER JOIN feature AS hitfeature ON (hitfeature.feature_id = hitloc.srcfeature_id) INNER JOIN featureloc AS qloc ON (qloc.feature_id = match.feature_id) INNER JOIN feature AS qfeature ON (qfeature.feature_id = qloc.srcfeature_id) :WHERE hitfeature.name = &name& AND qloc.rank = 0 AND hitloc.rank = 1 :USE NESTING (set (match(hitloc(hitfeature))(qloc(qfeature)))) // ------------------------------------------- schema: chado desc: gets the downstream area of an alignment see_also: chado-1.23/stag-templates/make-publish000644 000765 000024 00000000401 11256707627 020040 0ustar00cainstaff000000 000000 PUBTMPLDIR = /usr/local/share/bioconf/templates TEMPLATEBINDIR = /usr/local/bin/stagbin all: publish-templates executables publish-templates: cp *.stg $(PUBTMPLDIR) executables: find . -name "*stg" -exec stag-template2bin.pl -b $(TEMPLATEBINDIR) {} \; chado-1.23/stag-templates/README000644 000765 000024 00000006007 11256707627 016424 0ustar00cainstaff000000 000000 CHADO STAG TEMPLATES ==================== [note: this part of chado is NOT YET FULLY SUPPORTED] This directory contains SQL Templates for querying chado in stag format. The templates can either be browsed as a resource in their own right, or they can be used in conjunction with the DBStag library. These templates let you query chado via WWW Command Line API And retrieve XML or auto-objects representing nested relations from a set of templated queries. For example chado-pcgenemodel -d chado gene_name=CG1234 chado-genemodel -d chado gene_name=CR15821 chado-protein -d chado CG1234-PA chado-mrna -d chado CG1234-RA chado-feature-by-direct-cvterm -d chado cvterm_name='chaperone activity' PREREQUISITES ============= You need a local chado database, AND you need to define the BDGP views over them; see chado/modules/sequence/bdgp/bdgp-views.sql You also need Data::Stag DBIx::DBStag (version 0.02 or higher) UNERSTANDING STAG SQL TEMPLATES =============================== A stag SQL template is fairly simple - the first part is basically an SQL query with placeholder variables, and the second part is optional metadata. A placeholder variable (typically in the WHERE part of the query) looks like this [ feature.name => &name& ] This means the template user can optionally fill in a value for &name& - this can be a string match (in which case LIKE will be used) or an exact match. DBStag utilises one extension to SQL - the "USE NESTING" clause. This is for constructing hierarchical XML from the query results - DBStag will decompose the results of any SQL query back into the original relations For full documentation on templates, install DBIx::DBStag and read the pod docs for DBIx::DBStag::SQLTemplate USING STAG TEMPLATES ==================== Stag templates can either be used on the command line or via a WWW interface. Both give the option of returning either row data or hierarchical data (eg XML). The WWW interface to chado via stag templates may or may not be running here: http://www.godatabase.org/cgi-bin/ubiq/ubiq.cgi Select one of the chado databases and you will be presented with a list of possible templates; select one and then fill in the placeholder variables, or your own SQL. Alternatively, you can install DBIx::DBStag (use at least version 0.02) from CPAN or from cvs (http://stag.sf.net), then do this: setenv DBSTAG_TEMPLATE_DIRS "$HOME/gmod/schema/chado/stag-templates" (or wherever this directory resides) You can use a template by specifying its name after the slash with the following script: selectall_xml.pl -d chado /basic-feature CG1234 or you can bind specific placeholder variables like this: selectall_xml.pl -d chado /basic-feature name=CG1234 You can also generate an individual script for every templates; just type make -f make-publish PUBTMPLDIR=/my/template/dir TEMPLATEBINDIR=/my/bin (substituting appropriately) then you can just run the templates; try basic-feature -h Have fun! More documentation coming soon Chris Mungall BDGP cjm@fruitfly.org chado-1.23/soi/cgi/000755 000765 000024 00000000000 12061672376 014140 5ustar00cainstaff000000 000000 chado-1.23/soi/README000644 000765 000024 00000012244 11256707647 014266 0ustar00cainstaff000000 000000 INTRODUCTION Chado is a relational database schema for managing genomic and genetic organism data. To maintain genomic data in chado, all sequence features and their relationship are stored in 2 tables: feature and feature_relationship. The intrinsic type of a feature is stored in the feature table where the feature type is defined in the sequence ontology (SO). Parent to child relationships are stored in the feature_relationship table, with a relationship type defined in SO. By examining all feature types and relationships of every feature in a chado database one can determine how SO is instantiated (SOI) for this particular database instance. SOI can be created using a server-side function, but it could also be created using a database trigger. Once the SOI has been created, an SQL query can be written in a uniform way. Of particular interest is that the query can be made much more efficient in a RDBMS that supports server-side programming and sub-query. Traditionally, to retrieve relationship between features, a table joining is used. This kind of SQL query may result in many duplicate values coming in from database server. For example, a parent can appear as many times as the number of its children multiplied by the number of their children and so on. Using SOI, an SQL query can written in such a way that each distinct feature appears only once with feature's values plus its parent ID if any and the feature depth in a SOI sub-tree of interest. With the depth value, the parent feature is guaranteed to come in before its children so that placing children into their parent is a linear search. Two SOI modules have been implemented in perl: SOI::Adapter.pm and SOI::Feature.pm. SOI modules are lightweight, e.g. Feature.pm has about 300 lines of code. Using these 2 modules, any data model can be constructed from a chado database. An external SQL template can be used to construct a feature tree as long as the SQL conforms to the following: 1) each feature has parent ID (excluding the top node feature), 2) each feature has the tree depth value. Since constructing the feature relationship is no longer hard-coded into the SQL query, data model growth will have no exponential effect on code base and retrieval performance. Performance data from various queries show SOI modules have excellent performance compared to architectures that rely upon table joining for feature retrieval. THE soi PROJECT Currently the soi project has modules supporting only postgres chado database, soi modules should work in other dbms as long as soi (ontology) can be created. Some templates depend on server side functions (see templates and fx directories) contact: sshu@fruitfly.org CONTENTS readme: doc for soi project Directories: SOI: perl SOI modules (Adapter, Feature, Outputter) scripts: perl scripts using SOI module to query chado db and use results for some purpose, say dump xml cgi: script for web server, currently we have only get_xml.pl that serves out GAME xml for apollo fx: plpgsql functions on which some templates depend [deprecated, mv to cv or sequence module function dir] templates: soi templates SOI::Adapter can take and construct feature tree FEATURES Pros: fast lightweight seamlessly extendable flexible Cons: depends on soi created in a chado database depends on server side programming (hence plpgsql functions above) SQL is a bit harder to write? see templates for example (see ABSTRACT for more) INSTALLATION To create soi in a chado database: 1) load plpgsql functions in fx directory to the database (not just for creating soi) 2) select * from create_soi() in psql shell (need to change unique constraint on cvtermpath in current FlyBase chado dump, see gmod/schema/chado/modules/sequence/bdgp/bdgp-index.pl) General instruction to write SQL for SOI::Adapter (see templates for example): 1) use union to join top feature select with child feature select 2) top feature parent_id has to be null and soi tree depth has to be 1 3) child feature depth has to be maximum from its parent in the soi tree so a child feature is guaranteed to come in after its parent feature from server 4) each feature appears only once in the result set here is whole soi tree SQL for a type: (select c.name, c.cvterm_id, 1 as depth FROM cvterm c, cv WHERE c.cv_id = cv.cv_id and c.name IN ($top_feature_type) and cv.name = 'so') UNION (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name in ($top_feature_type) group by c.name, c.cvterm_id) here is child soi tree SQL for a type select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name in ($top_feature_type) group by c.name, c.cvterm_id performance issue: postgres v7.4 is better than v7.3 removing chromosome_arm residues form db speeds up query of golden_path_region (Dros specific?) create cluster index on featureloc for speed (see chado/modules/sequence/bdgp/bdgp-index.pl) chado-1.23/soi/scripts/000755 000765 000024 00000000000 12061672376 015065 5ustar00cainstaff000000 000000 chado-1.23/soi/SOI/000755 000765 000024 00000000000 12061672376 014030 5ustar00cainstaff000000 000000 chado-1.23/soi/t/000755 000765 000024 00000000000 12061672375 013640 5ustar00cainstaff000000 000000 chado-1.23/soi/templates/000755 000765 000024 00000000000 12061672376 015374 5ustar00cainstaff000000 000000 chado-1.23/soi/templates/features_by_name.soi000644 000765 000024 00000006401 11256707647 021426 0ustar00cainstaff000000 000000 --- get gene model, need 1 arguement, type (tRNA, etc) --- syntax: --- SQL: --- select ... --- optionally supply sql for auxillarie values of feature --- PROPERTY-SQL: --- select ... --- DBXREF-SQL: --- select ... --- ONTOLOGY-SQL: --- select ... --- parameter value format: &¶m&&, which later adapter replaces this with a value --- when pass in {param=>value} arg to get_feature_by_template function --- option parameter format: [AND sometable.colname = &&colname&&], which will be delete from sql --- if no such parameter is supplied SQL: select * FROM ((select f.*, src.uniquename as src_seq, fl.*, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) INNER join (select * from get_feature_ids_by_type_name(&&type&&, &&name&&, 'f')) as parent ON (f.feature_id = parent.feature_id) WHERE f.is_analysis = 'f' AND q.name = &&type&& and cv.name = 'so' ) UNION (select f.*, src.uniquename as src_seq, fl.*, q.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join (select * from get_feature_ids_by_type_name(&&type&&, &&name&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name = &&type&& group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) WHERE f.is_analysis = 'f')) as uf order by depth, parent_id, orderrank, rank; PROPERTY-SQL: select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join (select * from get_feature_ids_by_type_name(&&type&&, &&name&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) WHERE f.is_analysis = 'f'; ONTOLOLGY-SQL: select f.feature_id, gf.name, gfx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join (select * from get_feature_ids_by_type_name(&&type&&, &&name&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm gf ON (gf.cvterm_id = fcvt.cvterm_id) INNER join dbxref gfx ON (gf.dbxref_id = gfx.dbxref_id) INNER join db ON (gfx.db_id = db.db_id) INNER join cv ON (gf.cv_id = cv.cv_id) WHERE db.name = 'GO' and f.is_analysis = 'f'; DBXREF-SQL: select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join (select * from get_feature_ids_by_type_name(&&type&&, &&name&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) WHERE f.is_analysis = 'f'; chado-1.23/soi/templates/genes_by_child_count.soi000644 000765 000024 00000006757 11256707647 022302 0ustar00cainstaff000000 000000 --- get gene model, ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator) ---ctype must be immediate child of ptype SQL: select * FROM ((select f.*, src.uniquename as src_seq, fl.*, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) INNER join (select * from get_feature_ids_by_child_count(&&ptype&&, &&ctype&&, &&count&&, &&operator&&, 'f')) as parent ON (f.feature_id = parent.feature_id) WHERE f.is_analysis = 'f' AND q.name = 'gene' and cv.name = 'so' [and src.name IN (&&src&&)] ) UNION (select f.*, src.uniquename as src_seq, fl.*, q.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join (select * from get_feature_ids_by_child_count(&&ptype&&, &&ctype&&, &&count&&, &&operator&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name = 'gene' group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)])) as uf order by depth, parent_id, orderrank, rank; PROPERTY-SQL: select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join (select * from get_feature_ids_by_child_count(&&ptype&&, &&ctype&&, &&count&&, &&operator&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)]; ONTOLOLGY-SQL: select f.feature_id, gf.name, gfx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join (select * from get_feature_ids_by_child_count(&&ptype&&, &&ctype&&, &&count&&, &&operator&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm gf ON (gf.cvterm_id = fcvt.cvterm_id) INNER join dbxref gfx ON (gf.dbxref_id = gfx.dbxref_id) INNER join db ON (gfx.db_id = db.db_id) INNER join cv ON (gf.cv_id = cv.cv_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE db.name = 'GO' and f.is_analysis = 'f' [and src.name IN (&&src&&)]; DBXREF-SQL: select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join (select * from get_feature_ids_by_child_count(&&ptype&&, &&ctype&&, &&count&&, &&operator&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)]; chado-1.23/soi/templates/genes_by_GO_term.soi000644 000765 000024 00000003333 11256707647 021326 0ustar00cainstaff000000 000000 --- get gene model, need 2 arguements --- (aspect: a GO substree root, e.g. biological_process, and term: a GO term) --- maybe with OPTIONS section to tell SOI adapter to get auxillaries, get by default? --- this sql relies on get_feature_ids_by_ont plpgsql function installed!! SQL: select * FROM ((select f.*, src.uniquename as src_seq, fl.*, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join (select * from get_feature_ids_by_ont_root(&&aspect&&, &&term&&)) as fc ON (f.feature_id = fc.feature_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) WHERE f.is_analysis = 'f' and q.name = 'gene' and cv.name = 'so' ) UNION (select f.*, src.uniquename as src_seq, fl.*, q.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join (select * from get_feature_ids_by_ont_root(&&aspect&&, &&term&&)) as fc ON (f.feature_id = fc.feature_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name = 'gene' group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) WHERE f.is_analysis = 'f')) as uf order by depth, parent_id, orderrank, rank; chado-1.23/soi/templates/top_typed_feature.soi000644 000765 000024 00000010263 11256707647 021641 0ustar00cainstaff000000 000000 --- get non-analysis feature of the type specified along with its children, optionally constraining by src [location] --- WARNING: rely on soi is created in database --- WARNING: can not use it for chromosome_arm type feature as they don't have featureloc entry SQL: select * FROM (select src.uniquename as src_seq, f.*, fl.fmin, fl.fmax, fl.strand, fl.rank, fl.locgroup, fl.srcfeature_id, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) WHERE f.is_analysis = 'f' and q.name IN (&&type&&) and cv.name = 'so' [and src.uniquename = &&src&&] [and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&&] UNION select src.uniquename as src_seq, f.*, fl.fmin, fl.fmax, fl.strand, fl.rank, fl.locgroup, fl.srcfeature_id, t.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name IN (&&type&&) group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) WHERE f.is_analysis = 'f' [and src.uniquename = &&src&&] [and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&&] ) as uf order by depth, parent_id, orderrank, rank; PROPERTY-SQL: select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name IN (&&type&&) group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) WHERE f.is_analysis = 'f' [and src.name = &&src&&] [and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&&]; ONTOLOLGY-SQL: select f.feature_id, gf.name, gfx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name IN (&&type&&) group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm gf ON (gf.cvterm_id = fcvt.cvterm_id) INNER join dbxref gfx ON (gf.dbxref_id = gfx.dbxref_id) INNER join db ON (gfx.db_id = db.db_id) INNER join cv ON (gf.cv_id = cv.cv_id) WHERE db.name = 'GO' and f.is_analysis = 'f' [and src.name = &&src&&] [and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&&] ; DBXREF-SQL: select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name IN (&&type&&) group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) WHERE f.is_analysis = 'f' [and src.name = &&src&&] [and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&&]; chado-1.23/soi/templates/top_typed_feature_no_soi.soi000644 000765 000024 00000002467 11256707647 023216 0ustar00cainstaff000000 000000 --- get gene model, --- very slow without using soi SQL: select * FROM ((select f.*, src.uniquename as src_seq, fl.*, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) WHERE f.is_analysis = 'f' and q.name = &&type&& and cv.name = 'so' and src.uniquename = &&src&& and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&& ) UNION (select f.*, src.uniquename as src_seq, fl.*, t.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join (select feature_id, depth FROM get_sub_feature_ids_by_type_src(&&type&&, &&src&&, 'f')) as q ON (f.feature_id = q.feature_id) WHERE f.is_analysis = 'f' and src.uniquename = &&src&& and fl.fmin <= &&fmax&& and fl.fmax >= &&fmin&& )) as uf order by depth, parent_id, orderrank, rank; chado-1.23/soi/templates/typed_genes.soi000644 000765 000024 00000006452 11256707647 020432 0ustar00cainstaff000000 000000 --- get gene model, need 1 arguement, type (tRNA, etc) --- syntax: --- SQL: --- select ... --- optionally supply sql for auxillarie values of feature --- PROPERTY-SQL: --- select ... --- DBXREF-SQL: --- select ... --- ONTOLOGY-SQL: --- select ... --- parameter value format: &¶m&&, which later adapter replaces this with a value --- when pass in {param=>value} arg to get_feature_by_template function --- option parameter format: [AND sometable.colname = &&colname&&], which will be delete from sql --- if no such parameter is supplied SQL: select * FROM ((select f.*, src.uniquename as src_seq, fl.*, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) INNER join (select * from feature_ids_by_type(&&type&&, 'f')) as parent ON (f.feature_id = parent.feature_id) WHERE f.is_analysis = 'f' AND q.name = 'gene' and cv.name = 'so' [and src.name IN (&&src&&)] ) UNION (select f.*, src.uniquename as src_seq, fl.*, q.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join (select * from feature_ids_by_type(&&type&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name = 'gene' group by c.name, c.cvterm_id) as q ON (f.type_id = q.cvterm_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)])) as uf order by depth, parent_id, orderrank, rank; PROPERTY-SQL: select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join (select * from feature_ids_by_type(&&type&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)]; ONTOLOLGY-SQL: select f.feature_id, gf.name, gfx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join (select * from feature_ids_by_type(&&type&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm gf ON (gf.cvterm_id = fcvt.cvterm_id) INNER join dbxref gfx ON (gf.dbxref_id = gfx.dbxref_id) INNER join db ON (gfx.db_id = db.db_id) INNER join cv ON (gf.cv_id = cv.cv_id) WHERE db.name = 'GO' and f.is_analysis = 'f' [and src.name IN (&&src&&)]; DBXREF-SQL: select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join (select * from feature_ids_by_type(&&type&&, 'f')) as fa ON (f.feature_id = fa.feature_id) INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) WHERE f.is_analysis = 'f' [and src.name IN (&&src&&)]; chado-1.23/soi/t/data/000755 000765 000024 00000000000 12061672376 014552 5ustar00cainstaff000000 000000 chado-1.23/soi/t/t_soi_parse_intersect000644 000765 000024 00000007371 11723235041 020147 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use lib "../"; BEGIN { # to handle systems with no installed Test module # we include the t dir (where a copy of Test.pm is located) # as a fallback eval { require Test; }; use Test; plan tests => 11; } use strict; use warnings; use XML::Parser::PerlSAX; use SOI::SOIHandler; use IO; use SOI::IntersectGraph; use SOI::Visitor; #note: data/AE003790.cDNA.game.xml can be loaded into Apollo to do visual validation this test result my $handler = SOI::SOIHandler->new([qw(chromosome_arm contig transposable_element gene mRNA tRNA exon protein companalysis match match_part)]); my $parser = XML::Parser::PerlSAX->new(Handler=>$handler); $parser->parse(Source => { SystemId =>"data/AE003790.soi.xml"}); my $feature = $handler->feature; my $ig = SOI::IntersectGraph->new; my (@genes, @trs, @te, @trna, @cdnas); map{ my $f = $_; if ($f->type eq 'gene') { push @genes, $f; map{ if ($_->type eq 'mRNA') { push @trs, $_; } elsif ($_->type eq 'tRNA') { push @trna, $_; } }@{$f->nodes || []}; } elsif ($f->type eq 'transposable_element') { push @te, $f; } elsif ($f->type eq 'companalysis' && $f->sourcename && $f->sourcename eq 'na_cDNA.dros') { push @cdnas, @{$f->nodes || []}; } else { ; } }@{$feature->nodes || []}; map{$_->set_depth(0)}(@trs, @cdnas); map{SOI::Visitor->set_loc($_)}@cdnas; $ig->find_intersects(\@trs,\@cdnas,{query_type=>'exon',subject_type=>'match_part',same_strand=>1,depth=>1,threshold=>0.95}); my %tr_w_cdna; my %cdna_w_tr; my %gene_w_cdna; foreach my $tr (@trs) { my $cdnas = $ig->get_ilist($tr); next unless (@{$cdnas || []}); map{$cdna_w_tr{$_->secondary_node->src_seq}++}@{$cdnas || []}; $tr_w_cdna{$tr->uniquename}++; } foreach my $g (@genes) { if (grep{exists $tr_w_cdna{$_->uniquename}}@{$g->nodes || []}) { $gene_w_cdna{$g->uniquename}++; } } ok(scalar(@te), 3); ok(scalar(@trna), 4); ok(grep{$_ ne 'LD21171' && $_ ne 'GH14660' && $_ ne 'RE35072'}keys %cdna_w_tr, 1); ok(scalar(keys %cdna_w_tr), 37); ok(scalar(@{$ig->query_overlaps || {}}), 43); $ig->find_intersects(\@trs,\@cdnas,{query_type=>'exon',subject_type=>'match_part',same_strand=>1,depth=>1,threshold=>0.90}); %tr_w_cdna = (); %cdna_w_tr = (); %gene_w_cdna = (); foreach my $tr (@trs) { my $cdnas = $ig->get_ilist($tr); next unless (@{$cdnas || []}); map{$cdna_w_tr{$_->secondary_node->src_seq}++}@{$cdnas || []}; $tr_w_cdna{$tr->uniquename}++; } foreach my $g (@genes) { if (grep{exists $tr_w_cdna{$_->uniquename}}@{$g->nodes || []}) { $gene_w_cdna{$g->uniquename}++; } } ok(grep{$_ ne 'LD21171' && $_ ne 'GH14660' && $_ ne 'RE35072'}keys %cdna_w_tr, 0); #RE35072 now ov ok(scalar(keys %cdna_w_tr), 38); ok(scalar(@{$ig->query_overlaps || []}), 50); #printf "number of cDNA intersect w tr: %d\n", scalar(keys %cdna_w_tr); #printf "number of genes whose tr intersect w cDNA: %d\n",scalar(keys %gene_w_cdna); #printf "number of tr intersect w cDNA: %d\n", scalar(keys %tr_w_cdna); #printf "number of genes: %d\n",scalar(@genes); #printf "number of TE: %d\n", scalar(@te); #printf "number of tRNA: %d\n", scalar(@trna); #map{ # printf "%s: %s\n",$_->secondary_nodes->[0]->src_seq,join(",",map{$_->name}@{$ig->get_ilist($_) || []}); #}@cdnas; $ig->find_intersects(\@cdnas,\@trs,{query_type=>'match_part',subject_type=>'exon',same_strand=>1,depth=>1,threshold=>0.98}); ok(scalar(@{$ig->subject_overlaps || []}), 38); ok((grep{$_->name eq 'BcDNA:LD08743-RA' || $_->name eq 'BcDNA:LD08743-RD'}@{$ig->subject_overlaps || []}), 0); ok((grep{$_->name eq 'BcDNA:LD08743-RB'}@{$ig->subject_overlaps || []}),1); #printf "%s\n",join("\n",map{$_->name}@{$ig->subject_overlaps}); chado-1.23/soi/t/data/AE003790.cDNA.game.xml000644 000765 000024 00004560564 11256707644 017746 0ustar00cainstaff000000 000000 2R:1731127-2080000 CAGTCTCGTTTTGGGATTAGTAGTGGGACACACATAAATGATACGAAGAT TAACTTCGAAAGGGTACATTTCTCTGCTTAATTGACGGCCTCTCGGCGAT GTTGAAAACCTAGGAGTTAAAATAAAATTATGTTTGGAATGGCATCGTTT AAGTGGCGAGAAGTACATGATATTCTCGAGTGGCATACACTACAATACAT TACATTACAGGCTTATCATATATAAGTCGTTATTATCGTGCATCGTTATT TGGGCAGTTAGTATTGAGTGGGAGCGCTACTATTGCCTCTACACGGGAGG CTAAATACAAGAGTCTACGTTTGTATCTACCAGATACTAACTACGTTCTA CATCTAGTATGCTAAGCTCTATGTTACTTTATACAGGGATGTGTAATTAT AATCTCTACTTAGTTTGCACAGTAAAAAATCTAACTAAAACGGTTAAATA TTCATTTAAAGTATTGTCCAGAAGGCGCGCGTGCATCTAGGGCAAACAAT TGATCTATCATTAGGGGAATTAACAAATTTTCGTAGACGAGGCCAACATC TGATAATGCAATCAAAGGTAAAGGTACAACAGCTTAACACTAGGCGCCCA GATAGACAAGCTTAATAAGGATTTCAGCACACATACGTGGGCGGAAATAA CAGAATAGAAACACGAAACTATTTCCAGATCAGGAGTGTGAGGTTGTGGA AAGGACACGGCGTTTGGTGCAACCATTTTGAATGGTTAAGCACAATACGT AGGCCCTAAAAAATATCACTTTTTCGACGGCGATAGACGGCCAGTTTCCG TAGTTCTCAGTTGTGCTTGGCCCGACGACCAAACATATAGCCCTTCCAGC GCTCCGCAGTTTGTGCAATTAATGGATCGCTGTCGATGGTGGCTAACAGA AGTAACTGGTTCACGTGCGTTGCATGGTAGTCCCAGCGCGCCAGATTAGG AGCTACGCCCAGGCTCAGATGGCGCAGGTCGTAGCTGGTGCCGGAGCCAG TGTCAAATAGCAACAGCATCTTTTTAAGGGAGTGCATGCCCTGCGCGAAA AGCTTTCCAGCCTCGCGGGCGATTTTTCCCGGGGCAGTGCTGTTGAGATC GTAGAGACCCAGCAGTGAATAGATAAAGCCGTTTAGCACATAAGAGGGTG GCGTGGTGGGGTACTCCTCGTACCTGTAAAAGCCGAAAAAAGAATTTCGA TTATTGAATAAATTTGGTTCTCAAAAACAATTTTCCTATTGTTGCTGTTC CTGTTTGGTATACAGGGCGATCTTATACTCACCAGTAGAACTTGTCCATG AACTGCGCCAGAACGCCGCCATCGCGCGAGTATACCCTATAAGGCTGCAG TCCGGCTGCGGCCGCTCGAAGGTAGCGTTCATCCCCGCCGGAGTGCCAGT AGGCTCGTGCCAGCACTGAAATAGCGTGTCCCTGGCCCATGGCTGATATC CACCCCGGACGCAATTCGGCAAAGCCGTTGAGGCTGCGACGCACAGGATT GGTCCAGCCACCCGTCTTGGGGTCCTGGTTGTGGACGAACCACTCAGCCG CGTCGTAGAAGTGAGCCAGATGGTCACTGGTGGACAAGGTGATATTGTCG AAGAAGCCAAGGCCCAGAAAGCCAATAGATATTACCTCCAGATCGGAGCG CCGTATCTTTAGCGGCGAGCGTTTGTCACCCATGATGCCCTTTTGAAGGT CAATGTGCAGGTCTCGAGTGATGTGGCGCCACTTGTTCAGTGCCGAGCCT CCCAGACCGTAGTAGATGTTTGTATCCTGCACGCTCAGCAGCAGATCTGC GGGTATGTAGTGCAGGCTGTAGTTGTGACGGGTGTCCCGATTCTGAACGG TAATCATGAGACTACTGCTATTGGTTACCAGGAGCAGATCAACGCTGAGC AGAAGATCCAATGTCTGGTTTAGAGCAATGCTGATGACGCCTTCGTAACC AGGTGCCGTCTCGAACTGGACAACACTGGTGTTAAACTTGTGGTGCCAGA TGCGGGTCATGTTGCTGGTCTTGGGCGTACTCCATTCCATCTGGTTCCCG TCGCCGTCCTCCAACACGCGAACCCTGGGTGCCGGCTCTGTGAGGTTCTT GCTGTAGTGCGACAACGCGAACTGGGCAATTTGTGTGGGGTAAAAGTACC CACGCTTCTCCCATTGCGTGCTCACTGGAACGCCCTCCGCGGCACTGATG CACTTTACCCGGTCGCGCACTTCCACGTTGTAGTTCTCAAAGTACATATA GACGCCGCGCGCATCGTACTTTCCCCTGGGAAGGTTAACTTTGGCTGTGC TGTGCACCCAGTTGAACTTGGCCACCTCATTGCTGTTGGTGGAAACTGCT CCACTGACGTCGAAGTAGTTACGCAGGAAGGAAAACGGAACGTAAACCTC GTTGGCGTTCTCGTCTCGCTTGCAGTGCACGGTGTACTCCTGGTTAATGG AGCACTCAATGTCGTGCAGCGCTGTAGCTTCTCCTCCGCTGGAGGACTGC CTTGCGGACCGGTCCAGAGGACGCACAAAGTCCGGCGAAAAGGAGAAGGC GGCGCAGCGCATATACACGCCCAGAGTGATTACCACCACAGCCACTGTGA GGACAAGCAGCACGGCTTTTAGGTTCAGTCGCATGATGAAAAAGACCAGT GGCTCGCGTTGCTAAAGAAAATTCTAAGATTAGCCAACTGATAACACGAC GAAATAGACATTGTTACCTTTACCCCTTGGAATTTAGGTGGCTCCCGGTT TTCCCTGCTTACTGGAAGCGCGGGTGCGGAAAGGGCATCTCTCTGACTGC TTAGATATTTGGACATTCGGTTGGGGGCGAACTCTCTAACTGGCTTCTAG GTGAGTCATGCTCTAAATTTAAAACTGCATTCATCTGGCAGATGCATTGC TGACGATGATAATGGTGCACCAGTACGCGTACGTCTCTTTCACTGTCTCT GTCTAAAATTCCACCTGCCGAGCCTGTAGCCCTCTGAGTTCAGTCCAGGG CCATCCAAAGTTGATATTTCAAGTGCATCCAGTTCTCACTAAGCATATTT TGCTTAGATTTGCGCTGCTCTTCTCGCTTTAATGGGCGAACACTGCGAAA ACACAGAAACTGCGATACAGATGAGCAAATGTTTTGACATATGACAAATG GTCGCTCTTGGGCGGCCTATGCACGTAAGCTATCGATAACAAGCATTAAC CGTGTGCATCGTTACTTCTGTAGCTAAGTAATTTAAATAGTTTAATTTTC GAGTTTAAATAGTTTATATTCCTCCTTTGGTTGAAAATGAACTTTTATTT ATAAATTCATTGGTATTTTCAAATGTTCCCATACGCATGCTGACAACTAT CGACGAACCGATAGCATCAACACGACGGCGATTAATCAATAGTGCAATGT TTACAAAATATTTCGGGTGGATGTCGGTGAGAAGGCGCGTTTAACTAGTT TTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGC GTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTC ACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAGGTGAGAAG TGCTATCCACTTTAATTGCAAGTCTTAAGAGCAAGCTTCCATTGGCAGAT GGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTT TGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCA TGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAG TTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGC CTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTAC GCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACC CACATATTCGCAGTGGTATGCCTTTATTTACACGATCAGCCAATAAAGTC GTTATACTAAGTTCCCTCGATCCTTACTCTTCCAGACGAGTCTCAACGGC TGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCT GCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCA TGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATC ACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGT GGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAG TTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGC AGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGC TATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATG CTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTAT GAGTGCGTAGAAATATTACTTTATTCTAATATTGCTACATGTGTTTGCAT TTTAGCTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGC GGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGC CCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTA ATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCG AAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGT TTAAAAAGACATAATAGAGACTTTATTACAACATTTAGAACTCCGTGCTA CATTTGCCCGCACTGCGAAATGGTCACTGGGAGCTTCGGCTTGTTATTGG GGCCCGTGGGCACGTTCTCGATCTTGCGCATGATGAGCAGTCCATCCAGA ACCCGACCGAACACCACGTGCTTTCCGTCTAAAAAGTTGCACTTGGCGCA GGTGATAAAGAATTGGCAGCCGTTCGTCTCCTTGCCACTGTTTGCCATGG AAAGGAGGCCGGGCGAGTCGTGCTTCAGGGTAAAGTTCTCGTCGCCGAAG GTGTTGCCGTATATGCTGGTCACGCCGGTGCCGTCGCCCTGCACAAAGTC GCCGCCCTGGATCATGAAGTCCTTGATCACCCGATGGAAACTGGCGCCTT TGTAGCCAATGGGAACGCCATCCGGTCGGTACTCGCCCGTGCAGAACTGC CGGAAGTTTTCCGCCGTGCGGGGCACTGTGTCCGCAAAGAGTTCGAATAT CATTCGTCCGATTTCCTGCACACAAAAGGCGTTAGAAGGCGGAGTTATGT ACAGATTATGACTAGATTGTTTTCAGCTCACCGTTGTGCCTACGGCAATG TCGAAGAAAACGACGGGATTGTTGGAGCTTCTCAGTTGGGACTGTATTTG ATTCCAGTTAGGCATTTTAAAATTATTTTATTTGTTTATAAACTTTCTAA CAAGTCAAGATTAAGATTTTACTAAGCCGGCAGATTTTTGTTTATGTTTA TTACGATGGTTCGATGACGATGCACGACAAGTCGATAGCATCACAAGCCG GTTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTG CACATATTGGTGAAACTATTTAATAATATTTATTAAGGTGAGTTTATTTA TGATTGGATTGATTGATGAGTAGAGTGCATAAAATAGTGCATAAATATTA TTATTGTTGGATATTGTTTCGGCATTATTTTTAGTTGTTTATTTTTATTG GCAAGTTTCTCAAGGCCTGCAAAATATGTATGCATACTAACATATTTCGT GGTCCGATGGGCAGGATTTTTTCCTGATAGGATATGCGTGTGTAAATTCT TCAACATACATACGTTCCCACGCTAAAAGCTTTTATCACAAAGAATGACA GAATGACCCAAAACACTTGTATCTGTATGTACATGCATTTGTACCAAAGT GGGAAATGGAGATATGCAAGAGACAAAGCAAGTGCAGTAGCAAGCAACAA TTGTATGCCTTAGCATGCGTAAGGAGACCGATATATGTATATTTATATTT AGTTTACTTATAATTAGTTTATACTTTTAAGATGTAGTGGTAACGTTTTA AAGCAAACTTATTGAGACATATATCATATACAAAAATTAAAAAAAATACT ATTTGCGTCCCCCAAAGATCTCCCAGTTGGATTTTGGATAGACTCTTTGC CAAGGATTCCCGTAATTAGCCATTTTAGGAGTTCTGTTGGAAACGAATGG CCCCAATTAGCCCTCTCTGTTGATGAATGAAGACCTTTTATCGACATAGT ACAAAAACGTATGATAATTAATAAATATTCGTGAGCATTGTACTCAAGAA AAATGTAAATTTTCCGAAAAATATGCACGACAATGACCCCCATTTGACGT TAAGATCTGCTTAGTGAAAAATAGATTTCATGTTTTGGTAGTGACAACAC ATTCCCGGGGATCTTAATCCCATTGAGGTCTCCTTGATGAAAACCATATC CTTGGCATTGTGTTCGTTTGTGGGTGGAATATCATTTTCTAAACAGATGC ACAGCTTTATTGGATATTGGATATAGTTTTCTGTACGTTCTGGTTTGTTT AAATGTATCCTCTTGGACGACTCTGTAAATTTTATAATAATATACATTTA TAATGTACATATCAAGTTGCTTTAAACATTAAGATTGTCCTTCAAACTCC CATTACAAGACACGAGATACATTTTCCGTTGGATTGTGTTTGTATTTTTT AAAAACTTGCATAAAAAATGCCGAGATAATGTTTATAAATAAGTGCTTTT GTTCATGACAGTAACTTAAGGTAGCTAAACGGTATAAGCAGATGCAAATG AGTCTATCTTTAAATTACATGATATTCAGCAACAACTAAGGTCCTACTAG TACATAAATGGATGTTCTTAAATTCAAACTGAGCAATGTTAGTCGGTAGT CGATTGATTCATGCCTCATTTCAGCTCGACAACTAATACTAGGTAGAGGT AAATCCGCAAATCCCTTTTCGGGTCGACGCTCAGTTACTCGCCTCGTCCG TATCCACGTCTGATATATCTTTGAGTTTTACGTTGCCATTGCTGTTGTTC CTGTCATTGTCATCCGCCGCCTTTTGGAAGTTCTCCTGAAGAGTTTTGGG ATCGACGACCAGGATGGGTGTGCACCCGTCCATTAGGTGCTCGCTCTGGC TCTGGTACTGCTCCCGCGAGATGCTGCGAGTGAAGGAGAATCGCAGCGAC TTTGTCCTGGTCAGCCTCTTTTTGATGGGTGGCTTGCCCGCCACTGGAGC CAATGGCTCTGAGCTGGTCCGCTCTGAGCCTTCCGGCGTGGTTGGCACGG AGCTGGACTCCAGCTGGTGGTCCCGCAGTATTTCCTCAGCAAAGCACTTT ATCTGGGTCCAAGCTTCCAGGATGTCCTTCTCAGTGGCGTGCTCGTAGGT GACGCAGAAGCGGATCACGTAGCGGCCGTTGAACTTGGCCGGCGTCATAT GCATCTTGCCCGAGTGGTTGATCTGGGCGAGCAGCATGTGGTTGGGCTCG TCGCCAGTTCTGTAGAGAAGATTGAGTAGATCATTAAAGACCAGCATTCA GATTTAGCTGCTTTCTTCAGTTAGGTAAATACTAGCTAACGGTTAATGGT TTATAAATGGTTTAATGGTTAATAGACTTACCGCATTCGGAAGCAAACTA GGCCAAGGTGAACATCGTTGCGAACCTCAAATCGTTCATCCTTGCGCACC AGCATCTCAAACTTCTTAGCCAACGCCATATGATTTCGAATGTATTCCTG TAGGCCCCGAATGCCGTATGTCCGGAAGACGAACCACAGCTTGAGTGCCC GGAATCGGCGACTCAGGGGAATGCCGTAGTGGCGGTAGTCAACTCCGGTC AAGTGCTCGTGTCGTAGGTAGAGGGGATTCACGTTGAGCGCGCTCTTAAG GTTCATCACATCCCGCACCCACAGGGCAGAGGCATCGAAGTTCGTCAGCA GAAGCTTGTTGGGATTTGTGTTGAAGGAGTCGGCGTATTCGAGTCCTGCC GAAAAGACCCGCATCTCGGGCAGAATGAAGGAGTTTCCCGCATAGGCGCC GTCTACGTGCAGCCAAATGCTCGACACCTGGCGGCACACCTTTCCGATCT CCGTGATGTCGTCGAAAGCGCAGCCGCCGGTGGTACCCACAGTGGCCACT ACAAAGAAGGGTGTCAAGCCGGCGTTCACATCGTTTTGAATTGCTTGGCG GAGTAGGTCAACGCGCATGCGTCCATGCTCGTCGGCATCGATTATCCGGA GCTTCACCAGGGCCATCTTGGTGGCCTTTTCCACGGAGGAGTGTGCCTCA CGGCTGGCGTATGCGATCAGGCTGGGCAGGAAGACGCTGTCGTGAACGCT GGTCTGACCCTTTAGCTCGCTGATGGCCCGGGCGCGGGCTGTGATTAGAG AGACGAGAACGCACTCTGAGGCGGATCCCTGAAGGGCGCCGCCGCCTGTA CTGCCTGGGGCATCCGAAACAAAGGCCTTGGGCAGGCCAAGGGCCTTGGC GTACCAGTTCATCACGATCGTCTCCAGCTCGGCAGCCGCCGGACAGCTGG CCCAGCTGAAGCCAATTGAACCAATGGCACTGCTGAGCATGTCGCCTAGG ACCGATGGAAAAGAGTTGCCCGAGGGGAAGTAGGCGAAGAACTTGGGGTG GTTCCAGTGCACCACGCCCGGCATGATCTTCTGCTCGAAGTCCTCGAGCA CGTCCTTGAACGGCTCCGGCGACTGGGGAGCGTCGGCTGGAGATAGAGAT AAACAGGCAGTCGGGGATTAGTGGGATGGGCCTTAAATATTTCGTTTATC ACCCATAAATTTGGGGGGGCCAGCAAAGGCAGTATTTATGGCGGGTCTGT TGTTTTTGGCAGTGAGTAGAAAGATCAACAAGTAAGTCTATACGCAAGGT GTGTGTTTGCGTATGCATAATTAATTGATTTGTTTAGTTGAACTCGGGAT TGCGGCGTCCATTCCGGCGTAAATATTTAACTTAGCCAACTGCGCGGAAT TCGCCTGAAATTCGCCAGCGAAACCTACTCTCCAACCTGCCAACCTCTGA GGTGGACGGAGATCGAAGATCGGAGAGATGGCTGTCGAGTGTGCCCCAAT TATGCCGGACCCACCCACGCATCTCGTTGCGGGGCACTTGAGTCCGTGGG CTGGGGATTTTCGAATAGTTTACACTCGCACATTATTCACATGACTCTTC GGCAGCGGGCAAAACAATTAGTCAACATGATTTAACAAGTTTTTGAGAGG CATTCAGTTGCTTGTTGCTCTGGTCTGTCTTTCTTTGATTATTTTGCGCA AACGAAATATTTTCGGATTCATTGCTAATTTGTTTGGGCATAGTTAACAA ATTAGTGTATACAATTTATCACTAGTGCTATAATTAAACTTTTTCTTTCT GGTTTCAAATGGAATTCTGCGAAAACAATCAGACAAATTAGATTCGACTA ACTTCGAAGAGTATTCAAAATTTCCCAGGAAACTTAAAAACTCTATGACA TGCCATGGTGTAAATTGTCAGTAGAGTCCCGTATTTTCTATTTGCTATTA GACTATGATCAATCAGTATTGGGACATAATTATAGATGTAACCAAAATAA GGACCTGTACAGTAAGCACCTCTCAACTCAAACTTGACACAAAATAACTA AATAATTTCGATGTTCATCTTTAGCTTTTGCCGGGTCTTTGATTTTTTCA CACCTCTTCTCATTGCATGCTCACCTGGTAGCAGTTTTTTGAGGTAACCC GGATCCAAGGTGGGCGCCACGTCACGCTCCTCTATATTAGTGCCGTATTG GCATATATAATCAATCACTTCCTTGCCGTATTTGCGAAACTCTTCCACAT CCATTTTCTCTAATTTACACTTTTCGTTTATCTTCTTGTTCAAATAAATT GCAGTCTATTAAGAAGTATCTGTTGGTGCTTGGTGCTTGTATCTCTAGTG CTCGGATACTAGGCTCTCACACGGTACACAGTAGCTTATCTCGATCACTT TCGAATCCCGGTTATCTCGCACCGCACACTCGTTGCAGGTCAGCTTCCTT GACGCGAATGTCTTGCCCACTGCGCCGGAATCGTTTTTATATGGCACCGA TCGGTCTGTTGCTCCATCGCAAGATCGGCTACTCTCGGCTTCTCTCTGTG CTCGGATGTATTCCCTTCTGACACCGACACCTGTGAGGTGTGTTGTGCTC GGTGCTCGTACTGACGTTGATTGTCTCGTGATCGCACTCAAATTACTGGC CCGGAGACTCGGATCGGACTCCGTTTGGCTGGGAAACCCGCTTTGGTCAT TATGGACACATCTCTCGTTCGGCTCTCGCGTCGGGCGGAGCATTATCTTG CTTGGCGAAAAGTCCCTGGTGGGCAAGGGTTTCCAGTTGTTGGCTTAATT ATATGGTGAGTTCAATTTGAAGTGTGATTGAGCAACAGACGGTGGTTTCC TACGTACGTGTAGTCAAATTATTAATTATAATTGACCAAAATAGTTTATT ATTTAAGCTTCTGAACATTATTGAGGAATTCACAAAGAGTAATATTCGCG AGCTTGAAATGCTAAGCTATAGCGAATTTATCGCATTTTCGAGGCATAAA CTCGAATTTAATCGCGTGCTTTCTTACAGATATTTTAATTGTGCTCAATA CCTACCTCAATAAATTCTTCGACAGCATTCGCAGACTTTTTTATGACATT TAAATTAGCTTCGAATGTGAATATTCTGACACGCATGGCTCTTCGGGGAT CTTTTGGGGGTTTTAGAAAATTTCCCAAATTTGCCGTAAGTCCGGGACGT CCAAACAGTGTGCAAAGAGCCAATGAAAGAGAACAAACTTGTTTGCTCTA ATCTCTTGAAGAAGTACCGAAACTTTCCGCGGCTTATGGCAACCAGTGGG GAATCACTTCCAGTCCCAAGTGGCGAACAAGTGTCCAAACATTGACCAAA TGCGTTAGCAGAAAGTCGGATGTACGAATGGCCAACCCTGCCAAGAGGCC GAACTGATGACGTAGCTGTGAAGAGCGCCCATTGTTTCATGGAATCTCCT GCTAGGTGAAATACAAAAACACTAATATCAAAATAAACAATCGTTGCCAA ATGAAAATCACCGATTTGTTCAGTTTGCGAGGCGCGGGAACTTGGCAGAT AATGGGTGTGGGTGGGCAGACCGAACGAATGAATGGGTTTGTTGTCAGAG TCAGCATGAGGCCCCCGCAATTTGGTTGGGTGCTAATTGCCGACAAGTAC TTATCTAACTTTGCCCTGTAATGATCTATACTTACCTTCCAGTCTGTATG TTTAATGGTACGCGGTCCATCAACGTTTTCAAGAGGATTAGATAAATAGA ATGCAACCGCTTATTCGCAGGTAGTTAGGGAACACAGTTTGAATCTCACA TTGTTATAACCCGAAGGAGTGCCTTCTCATTCGTACTAAATAAGTTACTG ACTATCTTAGATCTCTCTCTAAGATAAGACAAAGCAAGCCAAACCAAATA ACAATATACAATACATTAACTGGGCGTAATCAATAGATAACCTCCTGCAG GTATTATCTTGCAAGTTCTGTTCGGAAACAACCGCAATCCGACCACTGTA ACTTTGGATGCCATGGCTTGGCTGACTCACCCGGCGCACGCGTCGCGCCT TGAAGCACCGCTCGGTGGTGGGGGCAGAGTCCGCGGCTAGAGATTCGGAG ACCGCGGGACAGAGATCGCCCCAACACCGTGACTTGACGTATTTCGCTGC TCCTCTTTCTGGGCCTGAGCTTCGCCGGAACTTTCATTCACAGTGCCAGA CACCGCGGATGACGTCGTGCTTCTAAATATAAGTTCGTATTCAGTTTACG CGGTCACACATCGAAATGCTCGATGGCCATTGCCATCATCCATCGAATCC ATCCGCCTTCTGATGCTGCTTCTGCTCCAACCCGGCTGCGTGTTTGGATG TGTGTTGGGAGCGCGGCTAACGCTTTTGTTGTCTAACCATTAATTATGGC AGTTGGCACTGCCAAACACCGATCAAAATTCCCATGAGGACGCGATACAG TCGAGCATCGCTAACTTCGATTGTGTGATATTTGGTAAAGACTTTAGATT TTGGATGTTATTTCAATGCTATTTATATTTCAAATATTTTATTTCATATT TCAATATTTACTGACAGTGTGAACAAGTTTTAAAGAGCGCCCAATCTTGG GAATCACCAATGTTTTCTAAATGAGTTCAGCTACATTTGCTCAAAGGAAT CCAGCATCTACAAAAGGGGATTTCTGTTGGTTGAGGTGAAAAAGTGTGAT TAGGCTTGAGATATGGAAGATTGATGTTCAGACTCCTCTGTCTGTCTGTT CGAGAGCTGCCTGTAGATTTTTCCAAAAATTTGCATTATATATGTGTTTT TTATTTGATGGTGCGCGTGCTTGACAATAGCTGACGGATACTGCATATGA AGATTTCGTGCTCCGAGGCTCTTCTATTTTCGTTTATTTTTGGCAATTTC GCTTGTTTTGGATTTTGCCAGATCATACCTTAGGCATTTCATTCATTCTG GTGGGGCATACTAATTTATGGGTACGGTATTTATTTATTGGTTTATTCGA TTTGGGGGTGTCAAAGATTTTGACAGACGATACTTTGAATTTCAATATAT TGGCGCCAGTAGATTATGGCTCAGGTTATTTGGCGATTTAATTAAATGAA TCCGAACTTGTTTCCAAGTTAATATTTCGTGATTTTGCGTAATAGATTCG AGCTATTAAGGTTACGATTTTATTGACAAAAGGCTGGAGAATCTTTGAAA GATGACCTTTTGCCCACCAGTTCTCTTACATCTCTATAGCCTAACCCTAT TTTTCAAAACGTAACCATAAACGATATATTTTATTAACAATTATTCATTT ACTCGCAGTTGCCATGCGATTTGTTCTATGGTGAATTTTTACACATTTCT ACTATTCCTTAAACATCCCTTAACCAATCAATCTGCACAGGTATGTCTTC GTGCTCAGCTCCATGAATGTATTTCAAAAGTCCAACGCCAAGTCAAGACT CACAGCTAATTTGACAGACGACCCATTGCATGCCTATAATGAGGTCGTGC AGAATTTGATTAAGAACTGGGAGTCGCCAGTTGTCTATCTGAAAAAACGA GGTTTCCTGCCCAGAAACTACGAGGATGCGTCAAGAATCAAGCACAGCCT GGATGCCCTGATGCAACGAATAAAAAGGGCTAAACGGGATCACACAAAGG AGGTCACTTTCAATGTAAGACCCAAAGAAATGGCAAAAGCTTACCCAAGG AATCAACGTGGCTTTCAGCTATCAACGGGCACAATGCTCTCTAGTTTGGA GCAGTTGAAAGTCATCGAAGGCCAGGCAACGAAGGCCAAGACCACGGCCA AGTCAAGTGAGCAGGAGCAAGAGCTGCTGGCAATGAAGCGGCGATTGGAA GAGTTGCAGCAGGTAGCAGGTACCGGTCAGGATCAGCCAGGATACCGTAG GCAGATTAAAGTAAATCCAATAGACAAGGATCCAGGGAAGTCAGCACAAA GTTATGATGAAATATTGCAGCGAATGATTGAAAAGACGAGCCCACACTAC TCACAGCAATCCAATTCGCATTTAGAAACCCATCCAAATCAACTAGCGCC AGCTCCTCCAGGAGCAACCCAAAAACTTGATAATGTGCAGATGGCTCCCA AAGAAGACAAGCCGCTGACTTTAGAACATATCGAGTTGCATGCGTATACA GCGCAAAGTGCTCCCCGAAATTTATTGCATAAATCCGTAGTTGATCTGCC CATACTTAGAGCAGCGGAGACCCAGAGGAGCAAGACCGCAACGGAGGCAT CTAACGTGGAATCGAAGTTGCGCGCGCCCACCTATCTGAATTGGGACATG AAAAACGGTCGACTGGATCATTACTCAAGCGTGGACAAGGAGGCCTATTT GAACCAGTTGGTGAGAGTGTTCGGGCGCAATTTGGATTTCAAGGAACCCA CTCAAAAAGGAAAAGAGCCGACAGTTTCTTAGAACCGCGGTTCTCCTTCC CAAAAACATGCACTCATCTTCATAAAACGTTTTAAAATATATGAGTTCTG TTCAATGAGTCATAATCCATTTGGAATCCATGCCCGTGCACAGTAAATAC ATCTATACGTTTCCATTTCCGATTTCATGCCGATCGACAATGATGGTACG TCATATCAATGGCATCACCATGATTATTTGGATTTCTTCTGTTTACCTTG CGCAAGAAAGCAAAGAAAAGCAGGATATTTCTGTTTACCATTTGTTAGTA CTTAAGCATATTTTTGCTTTCAATGTTGATTAAACAGAGATCAATACAAA TTTTGCTAATGGGTTGACGACATGCAGTGTTCAACCGATCACTTCAGCCT TGTATGACTATATTATATTATTATGAAATAATATTTATTGCAATTCATAA ACAAGAAAGATGTTCGTTTGATATTTTCGCCACGGCACTCATAGTATTCT ATAAAGTTTCAATATTGGAATTCAGAAAAAGCCTTTTACTGTGGCATGCC ACCGCATTGTAGATTGGTCTAGAATTCAACTAGGCGCCTGACCTAAGGAA GCGCTAATACTGTATTATAGTTGTTCCATAAACGGAGTGAATATTATTAG TTGAGGTTGTCCCGCGTGGACGATGCCTTGCGCACCGCCATGGGCGATCG TCGTGGCGATCGCTGTTCCATCTGCTGCTGCTGGACGTTCACGTAGTCCA ACTCGTTTTCCGGAGAGGGTGACGAGCCGGCTCCGGAGTTTCGTCGCGAC GACGATGGTCGTACGTTGGTGTCCAGGTGTCGGAAACTGAAAGAAAAGGA TGTGGCGGACACAAATTATTCGTTAAGCTCGGTGGTTTGTCTCTTCACTG TTTGTCTTTTAAAATACTTTCCAAGTACTTTCGAACAAGACTCACCGCAA CGAGACGTTACTGCCCTTTTCCTCGTTGTTGCTGTTGAAGAGGAATGCCA GCGGCCAGGATATCCACGAGTTGTGGTCCACCGAACTCTGGGTCCGGATA ATGGGGGCACTGCCGCGGCTCACAACGGGCGAGGGCAGCTCCATTGAGAG CTTGGGAGTGCCGGCCTTGTTGATCGCCGGGTTGTAGATCTTCGGATCGC TGACCATGCGCACGAAGAATGAGCGCTTCTGGGCCAGCGTGTCCTGCTTC TTGCGGTTCATGATCTCGGACAGCTCATCGTGCTGCTCCTTCTCCAGCAA CTCGTTGGCAAAGTCCACGATGATGTCCCAGGCGTAGTCAATGTCCTCAG CGGTCGCGTTTTGGGCCACGGCGCAGAACCTGATGATGTAGCGATCGCCC ACGCTGGCCGGAACCATGTGCAGCTTGCCGGACTCGTTGATTATGCTCAG CAGCTTCTCATTCAGCTTGTCGGAACCCTTCAGCCGAAAGCAGACCAGGC CCAGCTAATGGAATCAAATACTATTTATTTTGGTTCCACAAATCTGCGGC GAATGACTAAAACCAAACTAAAAATTAAAAATCAAAACATGAAGGTATTT GAAACTTCTAAAGTAATAGCGTGATCCGAAGTCTCTATCGTGTATGCTTA TAAGCGATTGTCTCCATCGTTTATGCTTATAAGCGATTTAAATCATAAGT ATATATTTAATATTTTCAGTTATCTGGCGAAAGTTTAGCAAGATACAAAG AAATCCTAACAATGTGCTAGCTTGATTTATTTTTACTCCCGAAATATGTA ATTAGTTGGAAAACTACAACGTGACTATCTGCAGATCCGCTACCGAATCG AATCGTATCGGCCAATTGACTTGGCCACGCTTACGCTCAACGAGTTTGAA CGTTCATGTGTCAGTCGCTGACTCGATGAATCACTTGTGGCTGTCTCTAA ATGATTTTCAATAGCAATTATGCCAAAACACTTCCATTGTCGGGTCGAAA AAGAAATCCATTTTTGCGCCCGTTTCTTTGCGGAATTTGGCGTGTAGTTG CGCACGTTTGCTTAGTTTGCTTCGTTTGCAAGGCGGTGTGAACAAGTTCA CGTCTTCGTGGTCAGAGCTTGGGCTCCGGACACTTGCGTTACCCACGAAT CAATCCATTTCCCAACTATTTTTGGACCTTACATGGGCGCTCGGCCCTTG GTCCGCATAATGGACCCGCACTCCCACCCGGTTGCCCGTGGCAAATGAAA ACCCCACACATTTCGTGGGGTGTACAAAAGAGCTTTGAACTCTGAGCATG ATTAATTACCGAAATAAACCGAATCGATTGAAAATAAAACTTAAAACACA TATAGAAAACGAAACGAAAGCAAATATGTCTCACCTTGACTTGGTTACAG ATCTCGAAGCGCTTATCTTTGAGCACGAGCTCTTCGAACCGCTTGGCCAG CTTGATATGGTGACGTATATAATGCTGCAGCCCGGAAATCCCATAGGATC GCAGCACGAACCTGAAATCATACAAGTCTTTCTACAGGCAAACTCAGAGT GGAATTGGGCAAATAATATTCTTTTGGGTGGTCACAATTAGCAATAAACG TATGTTTGGCGTTGTCATATTTCGATGTGGACTCATCTCATCTGCGGGAT AGATTCGGCACACACGGAGCACCGAAACCCTTGCTTTAACAACTAATCGC AAGCAAATACACGAGGGCATAATTTGAGTAAACAAGCCAGCATACTTAAC GCCACTCCACTCCAATCCAAAAACAATTCAATTGTCGACAACAGTCAACA GACCCATTCGCACTTGGTTGGCTATCGAGGGCTTTCGGACCCCATATGGC ACATGCTACATACCACAGCTTCAGCGAACGAAAACGCCGACTGAGTGGAA CTCCCCAATGACGATAGTCGATGGCCGCATCCGAGTAGCCGTGCTTCAGG TACAGCGGATCCACCACCAGGGCTGAAGTCAGCCGGATGCGGTCCCGCAC CCACAGCGTCGAGCAATCGAAGTTCGTCAGCAGCCATTTGTTGGGATTGG TGTTGAACGAGTCGGCGTACTCGATGCCCTGTGAATGAAATCCAGTCAGA TTGGCCATGCGTGCCGTGGGAATACCACTCACCTTCAGGAGCGGCTTCAG CTCGGGGCAGATGAAGCTGTTGCCCGCGTAGGCGGCATCCACGTGCAGCC AAACGCCCGGGAATCGCTGCAACTGCTTGCCGATCTCTGGCAGATTGTCG AACGCACACGAGCCCGTGGTACCCAGAGTGGTGGAGACGAAGAAGGGCAC CAGACCCTGCAGTTCGTCCTCCTCCATTGCCTCGTAGATCGTCTGGCCGC GCAGACTGGCGTCGTCGTCGGGCTCCAGAATGCGCAGCTTCACGAAACAG ATCATCGCCGCTTTCTCCACGCAGCTGTGCGCCTCCTTGGAGCAGTAGGC CATAAGCTTGGACAGCAGGTGACCCTCCTCCACAAACGGGTGCTGGGCCT TGAGCCTCTTGAGCGCCTGTGCCCTGGCAGCAAGCATCGTGACCAGTACG CACTCCGATGCGGAAGTCTGGTGGCCAAAATGAGCCATTGTTAGACACGG ACGAGTTAATCATGTTATATTATATGTAGATATTTAAAAACTACAAACTA AGTCGGCCTTCTTCACTCTTATAATCTATGTACCGGACCAAAGAAAGTTC CGTCGTCCTATAAAAGATTTATGTTACCTGGATGACTCCCCCTCCGGTGC TGCCCTCCTTGAGGGCCAGAAAGTGGTCCGGCAGACCGATGGCCTTGCCA AGCCAGTCGAGCACTATGGTCTCCAGCTCGGTGCACGCGGGACTGGCGGC CCAGGAGAAGCCGATGCACCCGATCCCGTCGCCCAACATGTCGCCCAGGA TAGAGGGGAACGAGTTGCCCGCCGGAAAATAGGCGTGGAAGCGAGGATGC TGCCAATGCGTCACGCCGGGCATGATCTTGTCCTCCACGTCCCTCATGAT CTGGTCCCAGTCCTCCGGCTCCTGCGGTGCCTCAGCTGTTCGAGAGGGGT GGTGAGGGAGAAACTGACCAGGTTCTGCGGTCATTTTTGTGGCTTACGTG GCAACAGGTGTCTCAAATATCCCGGCTCCACGCTGGGCGTGACCCGTCGC TCGTTCAGCGTTTCCAGATAGTTGCAGATGTACTCCACCATTTCCATGCC ACGTTTTCGAAATTCGGTGCTGTCCATTTTCGGTAGGTTTTCCAAATCGC CTTTCTGAGTGTTTTCCTATTTTTCCGTTTTCTTTTACTCCCACGGTGAG CTTTATTATGAAAAGTTTAAAAATTGTACAATGAATCAGCGTAGTGGGGC AGTACGTGCAATTATATTCAATTTTTATTGAATGAACAAATTTTCCAAAA TTTGGGGAGTCGGTTATTTCCAGATTTCCGGATATTATTCGTATTATTTT GTGTATTTATATAAAAATGTTTTTTTTTATTCTTGGACAAAGTTTTAAAA GAAAATTAGAGCAAAACAGGAAACTAGCTAAATAAATAGTTTTGAAAAAA CTGTTTTTTACCAAGCTAGAACATTTTATAATTAGGAACAACGAAACTAT TATTTTCAATTAACTTGCCGACTGTTCCTACTATATAAATAATAATAATT GTCGTCTGATTTTAGGCAAATTAAAATTGAAATAATATATTACCCCACAA AAGTGGCGTGTACCGATAAGGGATCAAAAGCATCGAAGGTACATTTTTCT TTAATTTTTATCTCTAATTATTCCTATGGTAGTTACGAGTATATAATATA TACGTTCTGACTTTTTTGTATAAAAAAAAAGTTTTACATTTTGCAAGCAT TTTGGTTAGAAAAAAACATGTTTGTCCGCTCATTGATAAAGTTTAAATTA ATATCCTTAAGTTCTGTCAAAAAAAAAAGTATTAAGCGACTACGCGAATA CGAATTTTATAACTGAAGCTGTTTTTGCTTGTATCATATTTGTATTATTG TTAAATTAACCATCTGAATAAAAAAGGTGATGTCCACACAGTTAATATAA CATCTTAAGATAACACATTTGTTATTAAATTTGTTATTAAAGTTGTGTTT CCTTGATCCTTGAATTGGTTTTCCTTTTCTCGAGTAGACCGAGTAATTTT TTAAAACAGAAACTGGAGTAACAAGAATGATTTTAAAAATTTTGAGAACA AAGAAAATCTTTTCCCAGGCAGGTTTTCGTATAGAGTCCACTTTCTTCAA AAATTCATTACAATTTGTTGGCAAACAAGAATTTATTCCGTTTTCATTGC TATGTTATTTATAGGATCTGATTTATTTCGGCTGGAGCTTTATTTGTGGC TTTTTTGAAACCGCTGATTCAATTCTGATTTGTAAACTTTACTATAAATT GGCGCTATTTTAGATTTATTTTTCTCGATATAGTGCGTTGTTCCCTAATT TTGCTTGCTTTAATCACATGTATTTAGCATAAACATCAATTTTGTTTGTA ATTAAACTGCGGTTCCTCAGGCACGTTTTACGGCTTTGTAAAGTATACAA TTCCCGCATGGTTTGACCATTATCCATTATCGAATCGACTTCCGGATCCG GGGCACTTACTTGTGCTGAGCAAATTCCGATGGGCGAATGGGAATTTTGT TTCGAACTCGAGACCACGAACCGTTGGCCCCGACTGGCAAAACCAAACTG ATCCTTGCTCTGCGGTCTGGCCAAAAGCTAAGCTCGGTCGTAGCTGCCGT GGCTGCTGCTTCTCCTTCGGCTGCCCTGGCATGTCTAATGAATGCATACT TCAGTGGGCCGGACCAGGGATGAGGGCTGAGGGTGCTGGTGGTGCTGGTT GGTGCGATTGAAATGGCAAATAAATGGAATTCTTGCGACGCTTCATTCAT AGCTGTGAGCTGTGGGAGTGGGGCTCGAAATTCGCCTGCGTTGTGCGTGA AGATATGCAGGGAATAGAATGGGCGAGCTAGAAATTAAATAACCACCGTT GCCCATGTGAGTGGTTGCACGGTGCGTATGCTTGATGCTGCGTTTAGCTG TGGAAAATTGAGTTTCGAATTGTTAAATGATTAGCAAACCTAATTTGCTC TTAAAGTGCAACTCAATTTCGCCATGGATGAGTTAATTAAAAGAACGTGT TGTCATAAACACACAACAAATTACACTGACAGGACAGCTTCCCACGTCCC GACTTCCCACTTGTTCTTGGCCGGGGTGCGAATCGTTTTATTAATAACTT CCGCGCCAAATTGAATTATTGTTCGGAACGTACTTGATGGGGATGGTGGC GATGCCAAATGATTATGACGATGGAAATGACGACAACGATGGCCCAGGCG GAGCAGAGAGGCGCAGGCAGGAGCGGAGTCGAAGGAATTTCAACGCATTC CTCTCGGAAAATTCCAGCCCGTTTTCCTTTCCCAACCCGGGCTCCTTGGA TCCGGCTGCACTGGGCCATAGAATTGTCTGGGACACGTGGCCCCATGTAC TTGCCATCATCATCCCGCACAGCCATACGAATCCTGTTCGTTTTTTTGTC GTTGTTGGATGAAAGTTCATTAATAAACTTTCATTGCTGCTGTCGAATTC AGCTGCAGCAACCATCTCCGGGCACTGAAATGTTGTTCGGCCTTAGCTTC AACAAGTGGCATCATGCTCCTGTGGTTATCATCCCCCGGTGACCTCCTTT CCCTTTGGCCACATCGCCATCCCCATCCCCATCCCAGAAGGGCTTTATTT AATGGGAAAACGCTGCGAAAACGCTCATGCATCCGCGCTCATTTAATTGC TGCAGAAATGGTTTTTTATTGACTTTTACTTGAACTCCTCCTCAAAATGA ATTATATCAATGTGCAGAGCATCATGGTTTTGTCCCTGGGTTTGCCTTAC TTCTGGGGAAAACTGATGTTTTTCGTTTCAATTATTCTCCTGATTACTAA TTTCGGAAAATAAGTTTTCTTCAATCAAGTTTTTCAACCATATACGAACC ATCTGCATTTGAAACAAATATGCGATATTGTTTTGTAAATTTAAAATTTT TCATGTTAGAACAGTCCTAAAATAAAGTGTTTAAGCTTAAATTCCTAATT GAACCCTTATCGTTTTCAAAGATTTTCAAAACTTTTTTCGAGCAACATGA CGTACGTGTAGGGTGTAGGTGAATTGCAGAATGGTTCTTCCGTTCTGTCC CTGCTCTCTCGGCTCATAAACCAAGCAATTATTCAATTTCCACGGACTGC GATGGTCGCAATAGCTGCTTCGGACAGTTTACGACGAGTGGTTGGTTGTT AAGTTGGTTCTCGAGATTCTGGACCTCCGGGCTCTTTTTTCCGCCATTAT AGGTTCAAGGTTGTTGCTGAAGCGCTTCGTCGAGATTATATTTCTGAAAG AGTGAAACAATCTTGTTTGCAGATTTTACGGAAGGCCTCAAAATGATGCA CTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGC CATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCAT GTGAGTAGCACTAACAATGTTTCAAATCCTTGCCTGAAAGCATCCATTTT GCGAAGGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCA GGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCG GCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGC CACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAA TAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGA GGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACAC GCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGAT ACTATAGATGGGTAAGCTAGAACGGAATATCAAATGCATCAGTAGCGTTA AAGTATATTCCGATTAGCTTACAAAAGCCAAATACGTCCACTGATTTTTG GGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCC ATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAAC AAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACC TGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGC GGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAA AGCCCAATTTATCACAAAAGACCAGCGGTATTAACGCAATTGCGGGCAAT AAAAGATTAGCTCTCCGAAGATAAGCGCGGTCTTTGTATAATTCTTCTTT ATAGAACTCTTATAGAACTCTTCTCAAACTTACAGTAGATGCTCTTTAAT TCGAATGTGAAGTAATCTAAATTAGAAAGTTTAATAAGCAATTATAAAGT ACAAGTAGAAGAAGAGAAATGTAAATATATATCGGTAATTTCGTTAATTT ATTTTTGCAAAGATTTCGTTATAGCTTAGTATGTCAATGGCCCCAAGTTG TTTAAAAAGGAATGAAGCGAATATGCTGCCTTATGCTAAGATAATATTAT ACAGTTTCTATACCTAGGACAATAAACAATACTTTGTGGGTTCCCTTATC AGTTGAAATTCGAAATCGGTGAGTTGGTGTTAGTTGTTTGTCAAATACAA ATTCAATACCCAGAAATTAAAATATAGCTGATAATGTGTGCTAAAGCATC TATTAAATGTGGACAGTAAGTACCAATGCAGAACAAACCGTTTATTTGAT ATTTTAGGTCAGAAAAATTAGATTGTTCTTATTCACAGCGATTGAACCAA ATTTTAATTATTTATCAAGAACTACAAAATAAAAATTGTGTCGAATGTGA TGTTTAAATCCTTTACTCATGGGATATGATTGAAAAAGGATGTTTCCAGC CCAAATTAGCAGATCAGTCCGCCGAAGGAACTTTTACTGTAATTCCGCAT TCATTGCTGTGCACACAAAGCACTTAGGAAAAGCTGCACAAATCTAATCT GGCGGATTTCAATGGCGTTATCATCCCACGAATGTGCAGGTGCCGGTGCT GGTTAGTGTGAAAAATGCTGGGCCTGCGACGAGTTCTGCGATTGGGTGCA CTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCC CGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCT CCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAAT GTGCTGGTGGTGGAGCGCGATGCTGGTGTAAGTACAAGGTGGCCTAAAAT ACGACACAGAGTTATTCAAAAAGTATCAACAATATCTTACAATTTTTGTA GGAACACCTTCAATTTTAAGGTATAGGGATCCAAAATTTACCCCAATAAT GTTTGAACCTTTGGTTTCAAAACGGTTAAAAATAATTATGTAGTTGCTTT GCTCTGATCATATATCCAATATCCAATATCTACCAATTTAATACTTTTCC TATTGTATTAAAAATTATTATTTATTCGGTATCTAACTGAAACTTATTCG CTATTGAATAACAACAATTTTTATACAATTTTCCAGTACACCAGCGCATC TACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGA ACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAG CATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCT TGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGA ACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAG CGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGAT TGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGA AGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGT TTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGG AGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGG GAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAA GCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCG ATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGTCCTGGGCTAGCCA CACCTCTGACCGTTGATCCCGATGGCACCTACTTCAGGCGGGACGGTCTT TGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAGACGAGGAGCCGGA GTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAAACGGATGTCTGGC CCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGTGAAGATACAGAGC AGCTGGGCGGGCTTCTATGACCACAACACATTTGACGCAAACGGCGTCAT CGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCCGCAGGCTTCAGTG GGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGCCATTTCCGAACTA ATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGCGCCTCGGCTTCGA ACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAATATCGTTTGACAAA TTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTTTATGTATGTACTT CTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTT CACGTTTTAGTCACGTACAGCTGTGTTGGTGTTTTGGCTGCCAGTAGTCA AGGGAATTTAGTTTAGTTTACGGGGATTTGACGTGGAATCAGCCACGAGA AGGTCGTGTGCCTACATATAATTTATTAAAATAAGGAGTTAAACATAATC GTAATATAACTTGCGAAATAATTGCTGACTTAGGATCAGATGGGGCGAGC GGGTTTGAGGGGGTCTGCCCTTGTTACTTAGTTATCGTTATGTAGCTCTA TGTGTATCTGACATCTAAACTACATACAAGATCTGCATTAGAGTCGGGTC CGCGTGGAATCGTTTCCCTGTCAGGGTGAGCCAACCCAACTTGCAAGCTA TTGGTAAATATAAATAGATGTATGTTGAATGAGTGTTTCATGCGAGTCTG ACTAATCTGGGCGGGCTCCTAAGCCTCGCTTTCGCCAGGGGCCGCGTTTT CACCCACGTTGATGGGCACGATCAGATTCTCCTTCGACATCAGATTATAT TTTGTGACGAAATGCGTGAAACGGTGGCACAGATACGTCTCGGCCTCGAA TTCGTCGAAAATGCGACGATGGTGAAAGTAGGCGTGCGAGAAGATGCGAT ACACCCGCCGACATACGGAGCCCAGCTTGGTTACCGACGACTCCTTGATG GACACCCTGGGAGAGACACTTTGCTTATTATGTGGCTAGTTCAACCATGT CGCTAAGCCTGCATACCTGCTAGGGAAGTACTTGTTGCTGTTTAGCAGAC AGGCGGCACCGTCCAGCGTGTGGCGTGTGTAGTCAATGGCCGGACATTCC TTGGGCGTCTTGTGCGCGGCGCACAGGAATATCCACTGGTCAGTGGCTGT CATCTGGGTGCACGTCGACGGCGAGCACTCCTTCTGCAGCCGCACTGCCA GGCCGTTCAGCTCCATGCAGAACTGGCGCAGGTGCTCGTACTTCCACACG CCCTCATCCTGGGCTTCGGGCATGGTCAGTATGAGTTCCACGTTGCTCGG GTCGCGCTTAATCAGCTGCTGTATGTACTGCTGCACCGCCAGCGTGCTGT CCATCTCCTCCAGGGGCTCGTCGGGCCAGCGACAGAAGTCCTGAAAGGCG AAACGGAAAACGGGTCAGACGGGCCGGGCCGGGATCGTTGTTCGGACGCC ATGTCATCGCTCACCTTGGATTTTGTGCCTGGCCGGTTCCTACGCAATAT GGTCGAGCCGTCAGCCATCTTCATGTTTCACCCGCTCGAAGACGCGATGA TCCACAACGTCTGTGCCTACGCCTTGATGAGAAAATCACTGGCAGAAACT GAATGCTAGCCTGGTCCCTGCCCCGCGGGAGTCTCCGGATGTGGGATCCC TGCACCGTAGTATGCTGAGTGTATTCTACAGGAGCTGGCACATCGCTTGA CAATTAATTGGCGTTTATCCTCCAAAACACTTTGCTTTGTGCGAGAAAAT TTCTGACAAATTCTACATACATACATATACCTATCGATTGGCCAGCGGCA GTGCGCATCGTTATCGATAGGGCGATTGCAGCCTTGCGGTATTTCGGTAT TTCCGCCAGCCCTGGCCACAAAGTGGCCACACTGTCGCTAGCCAGTCATC ATAAATACGAACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGG CATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAG CTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGAC ACAGGTGAGTGCAAGCTGCGACTTCCTTTGAAACGGAATGGCCAGTGAAA AGTTGGCCATTGTCAGGGAAACAATCTGTAATTGCAAACAACACAACAAA ACAAAGGGCATCGCAGGCGTAGGGGTCGTACCCGAAAATCAAAAAATGGG GGTTTCAGGTGGTCTCAAGTGAAAAATTGATACCGTGAGATCAAAATTGC GTCGGCAGGAAAATATTCCTGGAGTCGGTGGGCCGAAGGAAAAATCAATA ATACCATAACAACGCATACAGGCGTTTGCTGCTCTCAGAGTTAGTGGTGC GCGGGGAGCAGCCCACACATAAACCCTGCTGCTGACTCACCCAACCACCC CCAGTAATTGAGGGATTCCGCCCCAAAGAGCCACGGGCTTATCAGCACTC TGCTTTTCGGGATGTCCAACAGCTGTTGGCATTTTCCAGCCTGTCCCACC TTTTCCCCGCTCGCCCACTAACCCTTTTCCGTTTCCGCAGGCGTGGGCAA GTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACG ACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGC AAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAG GTACCCACTTCTGTTCATTTAGTGTTAATACTTAAGAAGGGATAAGTGAA AGCTCAGATTACTTCCAAAATTGAACTGAATAAATTTTTGCAAATTTCGT ATCCAAAACCCCAAGTCCAAGGCGGATAATAATTCGGCTCGTTTTTTATA TTAAATAAAATAATTTGAATAAAATTCTTACTTAATGATCCAAAATAATA ATAATATATATATATAGAGCCTTTAGTAAAAAGGCTTAATAATTTGTATT CAAAAAATTTTATTTGCTTCATTTCGGCACATTGTTGATAGATGTTTATT TAAAAAAGTTTTAATTCTATCATTTTTAATTTTTTGTGATATAAATTTTT TATACTTTACTTAAAATTAAATAGAAGTCGTCAGACAGAAATTTAATGGG TTACTAATAATTAAATAATATAAGCACTGTCATTTATATAACTGTATTGT GACGCAAAATATTTCTTGAATAGATCTATCACACGCTCTTATTACCGCGG AGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCA ACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAAC ATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGA GGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCT TCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATA AATACGGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACAT CAACAATGAGGTAAGAAGGATACATTTAACTTAGAAACTTCTTGCCACTA CATTATTATCTCGTTACTAGGCAAACGGCATTAAGATCGGCCAACAGCAC TCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGC AAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCT GGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATA GAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTA ACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAA TGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTC AGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAA ATAAACCAAAACAAACCACATTTGTGTACGTGAATGTCGTGCGTGATTTC TAAATTTTATAAAGTTTATTGAAACATTTTTAAATGTTTTATGCATGTAT TTTGTGTATATTGAAGTTAGTTTGCTAGTTACTTCGTGTAAAATCGATAG TTATACATTGGGATTTTGACAAAATGATGTGTAATATATGAACAAAAATC AAACTGTGTGAATTTTCATTGTGATTCGATTTCAGTGAGGTCCAGCTTCG CAACGCTGCGCCACGCCCCCTTTTGCAATGGGTATCTGCTCCGCTTCTCT ATACACACATACATAATTAAATATATTAATATGTTTACGTTTCCTTCTCA ACGCATTTGCTTTGTCTATTTTGTTGTGCAATCCGCTTAGTCTTTATACA TACACTAGAAAAAAAGTACTTTAACAAAATATACAAAACGTGAGGGCCGA AATGGGGTTATATAATTTACACAATCAACATGCATTAACCAGTGGTAACA CGAAATGCTGCGATTCAATGATCAATTTAGTATTTTACGAAGTTTATATA TTTAATTAACGGCGATTGCTAAGACAAAACGAAAGATACAACTGTAAACG TAAATCAAATTATTTATAATATTTGTATTTGCCCAACACAATGCGGAATA ATAAATATACATACTTACTATTAATATAATTATATAAATTAAATCGGTAC TTACCTTGGGTTCATTAGCGTTTAATCAAGTGATAGTTAACGACTAATTA GTTTTTTGGTGTCTAGATGAGAAGTAAAACACTAAGGCAAATTTAATGAG GCATTTAAAGTTGTAAACAACTCAACTTTTAAATGAAAAGAGGTCAGACA AATAATTACGCATTAGTGTAGTTTTAACCCTTTTTATTTAGTAAGAGGCT TTCGGTAGATAATTGTTGAATTAATGTCTTGTAAATATTATTAAATGGTG AATCCTTTTTTGTTTATGTACATATTTCCTAAAGTGTTCGGAATTAACAA TTTCCACTTTCTATGTCGGCTATAGGGATATAGTGTCGCATTTACTTAAT TTTTTTAAATGTGCTTACATGTTAAAACATTTTTTTACTACTGAAATATA CTATTTAGAAATATTTTTGTATTTTTTTTTAATAATACTTGAACTTTTAA GATATTACATAGGTTTGTTTCTTATTTTCTGAATCTTATCTGTGTTTTGT CTAAGAAAAAGTTTGCCAAACTGCAAAAACAAGTTTTTCGCTTCAACATT AACTATTTTTTATACCCTAATTTGCTCAGTTGGTTTTTTTTAATTGGAAA CTATTCGGATCCGTGACGTTTGATGTACAAACAAATGCTCCAAAGATTTT ATTGTGAGTTTTAGATTGATTGAAAATGGTCACTTGTTATTGCATACGTT ACATAGATTGTTGTTTATTGTATTCCCTTTAATTAATATTCGTACGAAAT GTAAGGCAATTAAAACTATTTTTCTAAATTTTGTAAAGAAGACAATTGAG GGACCCGTTTGCACCTGGCAGTGATGCACTGCATTGATATTGATTGAAAT TGAACAGTTTGTCTAGACAAAGATGCGGTTAGTAATTGCCCTAGTGCGGT AAGTATATGTTAGGTGTATATTGATACTTAGCTACGATTAGTCAAGTCAA GTATAGTCTTACAGGCTAGAGCTTAGGAATAGGCTTAGTTTCAGTTACAA TTCTGCTCTGATTTTATGGCTGCAACACCATTTGACATAAGAAACTCGTT AACATTTAATGCTAGTCCATTATTATGCTACAGTTCGGATTTGTAGTACC TCCAGTTGCCTTCTACTTGCGGCGTTCAACAGTGCAATGTAAGTAACCTA GTGTAAAAGTTGAGCTTTTTTAGTCTCTAAGACATCACTATCACTCTCCT TAGGTGCTTTCTTTTCACAGAACTCGATCAGATACGAACAGACACCAGAG AGTGCGATAAATATTCCAGCATAATAGAAGGTGTCATCCCATCTGAAAGA GGACAACGGGTGGTCAGATAACCTGTGCACAGACTGTAGAATGCCGCCCA ACTCACCTGCCCGTATACTCGTATATGACGCCTGCAATAGGGGGTCCTGC GATCATTCCAACTCCCTGAACCAGCAGCACCAGACCGTAGGCACACGTGA AATCGTCCAGATCCACAATACTGACCAGAATGCTGGGCGTAAACGAGAAG GAGCTGGCGAACGTAAATCCGAAAATAACGCACATGACCATCAGGCCCAT GTAGTTGGTAATCAGCAGGGGCATGAAGAACACAGACGCTCCGCACACTG AAAAATATAATAAATAATAAATTCAATTGATAAATTGAAAATGTGACATA GTCCAAGCACTCACCCAGCATGCACAGCGAGTAGCATATATTGATGTTCA TCCAGGACAGATCCCCCAGATAGCCAAGTCCTATCATGCCCACCGTTTGG GCAATGCCGACATCCGAAATCAACTCGGCACTCTGGCTCACGTCGTACTT GTATTGCTTCATGTAATCGGGAAGGTACAGATAGGGGATAATGAACCTGT GGAGCGTGCCAAAAAGTAGATTAGCCGCTGATTGAGCAGAGGAGCCTTAT CTGGTCAATGTTGAGGAGTTAGCATTGATTTCAACTAGTTTTCTTATCGA TCTATTAGGGCACTCGGACTCCGCAGTCGTGGGGTAAGATAAACCATGAT CTTGAACAGCTAAGGGGGCCTACTAACTGAGCTGATCGATAACGTTGTGC TTGGAATTTCACCGCTGTTGGCCAACAATATTGTTGTGCAACGCTTTTCG TTTTCGAACAGCTGCCAAAATTGTTTGCGACGTCTTCTGGCAAAATAAAC AAATTCACGCGACGGCTTGGCACATTTGTCTATTAATTTTAGCATTTATT GCGCCTTGAGTTCATGCACAGCTTGGGGCCTTTGCCAATGAAATTGTTTT TTTTTTTTTTTTATTAATATCACCAAAGAGTACTCACCAAATGAACAAAA ACAATGTAGAGAGATTGAAGAGGGCGAACTTCATGTCCAGAAAGAGTGAA AAGTCAAAGATGGACTTCATGGTGTCCACAAAGTTGTCATACCAGGTCTA TCGAAAGAGAAAGGATATTTAATTATTATTGTTCCATTAAATCTAAGCAA CACTGAGGATACGATTATTTTTGATTTTGATTGTTTACCACTGCTTTTAT CTCTACTTGAAAATTAATTAATACAAAATGTACTTTTAAAACGATTTAAA GGACTATCGCAAAAATCGAGTAAGTGTGTTTAGTCAAGACATTCATTACA AAATAATAATAGTTGTGAGTTGTTAACTAAACTATCAAGAGATTATCATC TTTCAAGGTACCAATAACTGGCTCGGTTTCTTGCGTAGGCAGAACGGAAA TCGGAGCGGTCACCTTATCAGCCCTAAAAAGTATGTATATGTGGTCCAAC TAGGCGACCAAACAGAGAGGCAGCTGATAAACAGCTTTGAGCATTAACCA GCTGGGGCTGTCGCCAAGCGACCGGCTGATAAGGGCGGACCAAGGGTCAC GGTCTACTCACATCTTCCTCCTCTTTGGCGATGGTGGTCATCGAGTTGCG GTAGATGTTGGGACAGGAGGAGGCGCGCAGCCGGTAGCGGTGCGTGTTCA GCATGGCCCCGCGGTAGTGGATCGAGTTGCGGTGAATGCGCATATCCTTA AGGAAGTTGGAGTTCCGGATCGAGATGTTGCGGCGGAGGTTCGATCGGTG GTGGCTGGGCTTCTTGGAGCGCGACAGCCGGCGGATTCCCGTGATGCTGT CCAGGCGTGCGCGACGGGTGGCCAGCTCGCTGTTCACCGACTGCTCCTGT TCCGGAATGGCGATGACGGTGGGCCTGATGCGCCTGCTCGGCTCCAGCAA TGCGAAGGTCTCGTCCTTCGAGTAGTAGCAGTGCATGTCCTCGCTCAAGA TGTCCACCGAATTGTGTCGCAGGCCATTCACCTTTAGGTTGGAGATTGAT GGTGTTGTATGCTTGGCCATGAAGATGTTTTCGTTAAGCGAGTACCGGGA GCTGGCGTGCTTCTGCGTAAGGTAGCCTTCGTCCGAGGAGCGGAGCGAGC CATTGGGAGTCCTACCAGTGGAGCGCTTTTCCGATGGAGACAGCGTCTCG ATGGAGGCCAGATAGGCCTTCTTTGCTTCCTCTGCCGCCTCGTGAGCTAT TCCGCCCATTAGGGTATCATCTGGCGAGCCTATAACGGCCGTCGATGGGG GATAGGCACCTGCTCCTGAGGACATGGACAGCAGGTTCTCTCGTGACGGC GCCTCCTCACCCTCCTTGTGGCGTAGGGAGCGTCGGCTCAGGCTCTTAAC CTCGCAGATGCTGTCAAGCTCCTGAGTGCTCAGGAAGGTGGGCAGGAAGA TCTCGCTGCGGTAGCGCTTGAGAGCGGAGTCCAACGGATCGTCAATCTGC TGGTTGGCCTCCGTGTTGTTCTTGGTCACCAACGAGTCTAGCACAGCCTC CTTTGTGATGCCGGTGTCCAGCAGCTTTTTTATTTCCTCCAGGCAGACAC TGGAGTTCGAGAAGGTGGTGACGCTTTGGGATCGACTCTCTAGACGGTTT TCCTCGATCAGCCAGTCGGGATCGCGCATGAGGGCGCCGCAAACGCATGC GTTGAGCATGGTGCCGCCAAGGATTAGAGTGGCTCCGCGCCAGCCGTACG ATTCGATTAGATAGGAAGTAAGGCGGGCGTAGACAAAGGTCCCGATGCCG GTGCCCGATGCTCCGATGCCGGTCGCAAAGGTGCGCTTCTTGTCAAACCA GAATGCAATGGACACCACCGCGGTCACATACCCGATGCCTAGGCCCAGTC CCGAAATGATACCAAAGGTCACCATGAGCATCTCGATCGAGTTGCAAAAC GAAGACAGAGCAAACCCAAAGGCAGAGACCACTCCGCCGAGGATGGTCAT CTTTCGGCAGCCGTACTTGTCCACCAGATTGGACCAGATGGGTCCCATCA ACAGGGGCACGGAGAAGAATAGCGAGGATATCCAGGCGGTCTTCGAAGTG GACTCTCCGAAGTATTCCAGCAGTTCCACGTTTATTAGGCCAAATGAGAA GCTCAGTCCGTCGGCTATAAGGGACACGACCAGAGAGGCGAACACCACCA CCCACCCATATCCACCGTCGGGCATCTTGGGCGTTTTCTTCTCCGTGGAA CTGGAGTCGATCGAGTCGCCGGACTCGTTCGAGATCAGGCGTTTGCGACG CTTCACCTGCCCATTTCCGTTCATCAGGCACGTCATGGTGCCGTCCTCCA GTTCGATGACACTGCTCCTTACCACACGGCTGTGTCCAGCCCCATCTGCG AGCTCCTCTACGGAGAGGTTGCAGAAGGTGACCTCCGGGAAGAGGTCGTG CTTGATGGCCTTGTGGAGTGGCGTGTTGGCCGGAGCAGGCGTAAGAGGCA GGGCCTGGTAATTGGAGGCGCCTCCGTTTTGGCTCTGGTTCTGGCCATTG TGGTTGTTGTTAACCGCCTCGCAGCTGTTGTTGTTGGAGGCGTTTGGATC CGTCGCTAGCTTGGCCATGTCGGAGTCCCAGTGATCGTGTTGTTGTGTAA AGGGTTCAGCTACGTCTATAAAAAGGTTTGTAAAATTTGCACTTTCTTGT CCAAGCGATTATTGGAAGTGAACACAATTTGCATTAGATTTCAGCATAAA TTTTCTTAAGTAGGCGGTAGGTAAATATTCCCTCTCTCTGTTGGTCAACT GCAGTGCGTAGCTGAAATATAGAGACAGATGGAAGGAACTTAGCGCTTGA TCGACTTTGTAACTTCCCATTTCCCCTTCTAAACTGCAGTCTGCCGCTGA TGAAACGATCAAAATGAAATGATCAAACCCTTTTCCAGTTAATAATCTTA CTAACATGGCGCTTTAAGTTCGCTTCTTAATACCTCGAATATTTACGTAT CTATATGACCAATTGCGCGACTACAACAACATCTGCCTGAAACCATTTCG TTGAAAAATCCGCGCAGAAACTGTTTGCTCATTTGGCAATTCGTTTATTT GGCTTTCGAGGCGCCTTCAACTTGACCTCAGGAAAACAGAAAGCGGACAA TTTTCAGATTTTCAGCGAGCATTTTGAGAGAACCGAAACGAGAGAGAATG ATTTTCTTCTTACATCAGTACCAAAACAAAGTGCGTCACATGAACGCGAC GTCAGCTGATGTCCCCCAATAATTATGGTATTCGAAAATGAATATTTTCA GACCAATTCTGTTTTCGTTCCCCTGAAACGGACGTCTGCGGTTAATTATA GATGGCTACACAGGCGGAATAGGGAAAAAACATCAACGATCGGACACTAG TCACTAGTTCAAATCTAAGTAGGTTTTATCCTTCTGAGGTTTCCAGTTGC CCCACTTACCCGATCGTAGTCCAGGCAATGCTCTCTCCGCACGCCAACAG CCAACTTTTGTTAACGAATAAATTGATTCGGTGATCTGCGGATTTTGCGG ATATATTCTTAAGATTTCACTGGCACTAGTTTCACTGTTTCGGCACCACC GCCAATCAATTCACCATAATTGCACAGATCTTCAGTTATGTTTAGCTCGC TCAGGGTGCGATTCGAGTGTTTATTCAGGGTGGCGGTTTTGTTGAAAATT CTTAGGCGCGGATCGCGGGGTATGTAATGCAGGAACACCTTGTTCGACTT GCCGCTGTTGTTGTAAGTACGGGGATTGTTGTTCTGGCCCTTGTCGAACG ACTTGGCGTTGGTGGTCGCGCCCGACGCGGATGCTGCAGATGTTGGTTTG CCTGCACGATAGAATGACTTGGACCGAAGGTCGTTCATTAAGAACGTTAG GGGGTTTATCACAGGCCAACGGAGAATATATTGAGCGATAATTGACGGCA ACTGGCGGCAGTTGCTGGTGATGTTGCTGTTGTTGCTGTTGCAGTTGCAG ATGCAGTTGTTGCAGTTTGTGCTGCCGGCTAGCAGATTTTGCCCTGGCAG CCACATGCGGTACTTTGTTTTCGCGGAAATCAAACACTTTTCGATTCGAT GCCAACGATGCCAACTAGCGTGCCCGGCTAGCTCGAACAAGAAATAACAA ACACAAATCGAACACAAGACTGGGCCTCACTGGCTTCTCCGGCTACTCTG CCGCTCCCCGTGTCAAGTGCGCGGCGCGTGGTGCGGAGGCGGATTCGCAG GCATTGTATATATGTATATCTTAGTATCGACGGAGGGACGACCAACGCGG CGTATGATTAATTCGTCTCTGGTGGTGCAACTCAATCGCTGCTGTCGCTG TGCTCGCCTCCTCGCTGGCGCCAGATAATGATTTATGATCCTCGTCCTCA ATTAGCAGCCTTCAGTGCAAACGCTGCAAGAGGGACAGAGGTTAGTTTTG ATTCATCTGATAAATGACTTAAATGCGAGCTTAAACCTATAAATATGTAT GTTCAATGCGCCCGGATTTCTCTGCTCTGCTAAAGTCCCACAAAAGGCGA GAGATTCACGGTGCTCTCATCTTATGTTTAAGTGCTCGATTGACTAACAA TACGAGCCTGGTATGGAATCGAGATAGTGTGTTTTCAAGGGGAATTACGT TACCGGGAACAGAATTCCTCAAAGATGTGAGGGGAGTTGAAAGGCATGTG CGACATCACATCGTATTGCCGCAATCAATTATTGTAGGTCAAATTTTAAT AGAAATTTATATATGTTTTATTTATAATCATAGGGAATTTAAACAAACCG TATGAATGAGTTATTATCAACAATAAAGCCTACAAACATACGATTTTATG TATGTTGCTATGGTAAAAGGCCAACAAAAGTCAATTTATAGTTCGATTTG AGAAATATAAAGTCTGCATAATTTGATTTACTTCATACGGATATATTTTT GTCTTTGGCAAATTTTAAATGGAAATTAGGCAGTATTATTCAATGTCAGT CGTTCGTATTTGAAAATAAGAAAACACGTTTAGCTCCGTAATGTTTTATT TCTGCACAAGCGAGTGTTATTGTTTATTTTATCTAGTGAATAAAGCTAAT TATTATTAGATTGCAGATAGTTGAGTGCTAGATTGCGGTGTTTTTGTACC AGCAAATTAGTCGAACATAAATGCTATCGGAATTTATAAAAAAATTAAAA TATTAACAAATTTTTTTTGTATACAATCTTCAAATTGTCTATCTGACTCA GTTATTAGAACTCAACTGAGATGAAAGACCAATATCGAAAGCCAAAATTT CCATGAAAGTGTAGGATGTTGATAAGATTTAAGCTGCACTCCCATAACAA TTAGAATTTGAAATTCTTGAATGAATCTTCTTGTGTACAGAGATATCTGT ATGTTAAACAACTGATCGTGGCTTTTTAAGTTCAACGTTCGATAGGCGAA ATGAACAGAAAACCCAAGTAAACAGGGAGCAACGTGCTTTATTTGCCCAG ATTTCCAGTTCTAAAACGCGATTGTCTGGCCAGCGACTGCGACTTTGGGT AGACAACGAAATTGTCCCTTATCGGAAATCAAATTCGGATCACGATTACT GTGAGTACATAGATCATCATAGTTGGATTGTGAGCGTGAGGGGCGGGCGA TAGCGATTCCCAGGCGAAAAGTGCCTGCCTATCTTTACAATATAATTGGC AGAAAATGGTTTTATTCGTTGCGATGCGATAAGCTAATGTCTAGCCCTCG AATAGGCAGATTGCAAAAATTTGAAGTTACAAAGTCGCAAACGAAAATTC AAAATGATAAATTAGGCTAACTACTTTACATGAACCTATTTTGGCCTGAT AAAGCCCACTTGGCATTACGTTTTCGTTTATCTCGTTCCAAACTAGTTCA GCAACATCTACTGCGCCCCGTGGCATGCAACACTCTTCGAATGCACTCGC GGTTGGAGCAGCACTTTCACTTTGTAGAGCACATCGTGCTCGAAACCTAA AGTCCACATCTCGCTTAGTCCGTATTTACACAACAATGGCCGAAAACAAA GAAACGCACTAGGAACGCGCTAGACAGCCGCCAACGTCGCCCTCAAGTCC ACTCGTCCCGTGCCCCGTGTCCCGTTCCGTCGCGTCGCGTCCAGCACAAT TCGGGCTGGGATGGAAGAACAACAGACCCGCAGCTCGTCGGAAGAGCGAC TAAACCTAAACCCACTCACGCCGCTGCCGGCGTAGCTATCGCATGCCTTA ATCTAATAAATTCCTTATCAAAAAGAGCGTCGGAGTATAGTATTTGCTCT ATCTGGCGTTTGTGCAGCCGCAAGTACGCGGTCGAATACTCGTGGAGTCG GTTTGTAATGACACACGCGTCGGCGTCTGTCAACATGCCAACCTTTTGTG ACGCCCGCTCCTGAGATCTTTTGGCAGTGGTCAGGTTTGGACTCGCAGCC TGCCATTCACTGCGGCATCATTATAGTACATCGGATAGTAAACAAATCAT GTGATTGTGGGTAATTGCCGTTCTAGTTACAACAGCAATGCCGGAGACTA CAGAATCAGACCAACAAAACCAGCCGAATACATTTATCTGTTGAGCTAAA CACGAACTAGTATTTAACAAATACAAATATTACCTGATTCCTAAAATTGG TATCTCACTGTCCGGCAGATTAATTCATTACAAGTTCTACAGATAGAGTG TACTTGTTTCATTGTAAGAAATTGATTTTGTTTGACTATTCCTGCTTATA TTATGTCTTCTCACATTTGACAGCTCGAAATATTTTGGATCTGGAACAAT CTGCCTTTCACTTTATCACTTGCTTCACATAACTGAGGGAACGGAGGGAT AAGCAAGTAGTACGTTTTGGGCACATAGTTGGCTCAAATTGCCTATTATA ATTAAGGCGATAAGACAAAATAACTTTCTGCGTTGTTCTTCAGGTTGGTT GATTATGAGGCAATTCCATTGTACGTTCTACACGTTGGCGATAAGTTTTA TGGCACCCAAATTTAACGCAGAGGTTCCTTTTGATGCTGACCTAGGCCAT CGAAGTTGCGTTATTGGTCTGTTACTGCGTATATGGAGGGCTTTATAAGT GGAGCTGGAAAAACCGAAACGTACATATAGGCGATTTCGGCCTACAAATA AAATGTTGGCTTATCAAAATGGCTCTAAATGAATTACATTTCTTTGATTG TTTGTTTTGATTATACAGAGAGAAGATGCCTTGAAGTGAACTGAAGGAAT TAACCCAATGTACAATACATAATTCGACTGCCCGCCTTTACTTTTCAATT GAAAGAGTTAAGCGAATTGAGGCAAGGACAAGCTGGTCACCTTGAATCGA ATTGAGTTTGCTTTTCTCAATCGCTTTCTGTATTGCCCATTAGAGTGTCA ATCCACGGAGGGAATACAGACCCTACCAGCAACCCTTGTCCTTCGAACCC TGCACTTTATGATGCCCACATCGTAGGAAAGTTCAAAACTAAAATATATT CTAAGGTCAAATGAGCAAAAAACTAAATGGCTAAAATGGCTTTTATGTGT GCTCAGCTTGCCAACATCTGATGTCGGTTTTTCTAGTCCGCTTAATTGAG GTAGATAATTGATAGTGGGTTCAGTTTTGCCAGAATAATACTGGTGGCGA TTGTTAATTGATTTGCGGTTTTGACATTTTGCTTGGGGATGGGGGATGTT GGGGTCTCACGGCAGATTCATACAGCGAATTGAATTCGCTTGTCTCACAA AACTACATATCATTGTAAATATCGGTTTAGTAAATATTTTATATAAGTAA GTTTAATGGACATTTCAAAAACAGTGACTTCATATTTGCATAAAGGATAT CTGATAATCTATATATCTATAAGGTTTCTTTCTGTTTTATAAAAAGGAAA TTGAAAATATAATTACCCCCTTTACTCGTAGAATAAAAGGGTATATAGTA TGCGTTTAAAAGTATATAAAAGTTGGAAAGAAGAGTTTCGACCCTATAAA GTATATATTCTTGATCAGAATCACTGGCCATTTTCGTCTGTCTGTCCGTT TGTCCGTCAAAATCTTGGTAACTATAAAAGCTAGAAAGTTAAGATTAGGC ACGCTGATTATATTATTCTAGTGTTTTTCTTGGCAAGTTCCATCGAAATC CCAACAAAATGTTGAAAATTCTCTTTAGCAATCCCAGTAACTGAGCAGCG CGTATCTGATAGTCTAAGAAATCGAAAATTGCGTTCTCCCTTGTCTTTTT ATATAATATATATACATACACATGGAAAAGAACCCCTTCTCTTGATGAAG CATTACTTAAATGTTTTGACTTTGGCCTTCAGTTTTCTTACGGAGGCTTA GTTACTGCTACCATAACGATATAAATTACACTGTCGTAACAGAGAAATGC CACCTTACCCCTTGGTCGAGACCACTTTTGATTTGGCTGATGCCACAACC TGAAAGCTCGACACGAAAGCCACCGCAAAAAGTCACAAAGGAGGTCGCTG GTTGCATTTAACCAACAAAGAGTGCACACACGGTTCACACAGACAGGTGT CGTTGTGCACAGGCACACACTTTCGGCGTCCTTTCATGTTTTATATTTAC CATTGGGGGCACAACAAATAACAACAATAAACTGCATCAGCAGCAATGTC ATCTCACGAAAAGTTCTGGGCTCCAAAAGGAAAGGTAAATATGCCCACAA ACATATGTAGTGGTGTTCGCATTTAAAGGATAATTATGATTTTCGCCTTC AACTTGACTAACTTTCCGGTTACACAAACACTAGGACAAAATGTCCTGTA TTGATTTTACCCCAGCTATAAGATTTATTAGTTTTTTGCCCAGGGTTGTG TGAGTTCCCCTAAATGTGTGTGTTTGTAGAGGCAGAGGATGTGCAACACG AGACTCTTGCCAATATTTGCCATCTCATATTCTCTGTGCAAAAAAAAAAA AATATTCTAGTGCTAAGTGCTCTGAATTTCTTAACATTGTGGCTCAACAC ATCATTTTTTAATTTGATATTGATTCAATAAGTTTAATTGAATTTGTTGT GCTTAATATATGTATGCAAGAACAAGCTAGCACGACGCTCAAAGTAAACT GCAGCAATATTTAAATAAACTCTCCCTTTAGAGATTTTTAAAAATGGTGC AGATTAATTAATTAAACATAATAAATAAACACATTCTCAAGGAAGATGCC TATCTTACATTCATCCAAGCCGTAAGAAGATACACAACTACAATAATTGT ATCCGGTTTTCCGGCACAATTCTGAAACTCAATTTCCCTGTGTGATTAGG GGTATTTTGAAAAATTTCTCAAAATGGGAACCAAAACAAATGGCTTTGTT TTGCCACTCTTTTTTTACTGCCTTTTGTTGCTTGCAGCCTTTTAAAAAGG GCAACTTGGCAAAAAGCGGACATTTGGCTATGCGTGTAAACAACTTCAAG GCTGGGGTGACTTTTATTTTCCTAATTCTGCTCTTGACACGGGCTCTCAG AACGGAGCTGAAAAGGTTGAATGTGAAATGCAATATGCAAACAAAAATGC AAATTGGAAATAAACAATAACGACTATGATTTAGCGCTAGAAGCAATGAT TTCGCATTTAAATGGGTAGAGTGATCGAAATGAATCCGATGAATTATTTA TACTGAAACCGCAATCAATAAATCTTACTAATAATTAAGAAATCATTAAT CATTTAAGTGGTTTGGAATTTTTTCGGCTTGCCATTCTTTTTTTTAGATC CAGATAAGATTGGATACACCAAGGGAACTTTTGCTACACAGTGCGGGAAA ATGGGTGGCAAGGTCGTTTGACGAGGGCATATGTATGATGTAATTGCGAA AAGTTCTCTTTGCGTCAAATTTGCGAACACAAATTTATCAGCGCGTCACG CAGTCTGCGACTTGTCCGGCGGATATTTACTGTGCCCAGCATACACTGAA AACAAAAACGATGATGTACTTCAATTTAGTACATATCACAACCTGCTTAC ATTACCTGTTTGCAATTAAGTATTTAATAAACAGTATGCGGTTATTAAAG GTTTAAAGTTAAAAATATCTGACTCTCAAAAGAATTGAATCGCTTACTTG CGTCACTTTCACTTCATCCTACAGATTCACACAACCCAGAGATATTACTT GCTTTGTGTTGAAAGTGCACTCCGTACTTCATTGTATATTGTTTATTTTT TGTTTTGTTTTTCTGAGTGACATTTGGGATTTTGGGTCATTTGAGTGTCG CTGATCATGCGACAGCTAGGAGTAGTAGACTCTGACTGCTCGAATTGCTG CACTTACGCGCAAATGTATGTGGTGGCGATAAACTCGTTCCTTTGTCAAC TCCGTTTACTCGATATCTTGGACCCGAGTCCAATAAACAAATCGGCAATC GGCAATGAGCAGCCAAAACAATCAATGCAACTTTGTAAGGAAATCACTTG TTGGCTTGGAAGTTCCTGCACTCGACAGTTGTTGCTCTTCTCGAGTTTAA AATTGGACTGACTGAACAGCGGCTTCCCTGTCCTTTCCACCCGCCGCCGT CTCCCTCACTCGCCTTCCCCGTCTCGCTCTGGCCACTGGCTGTGCATCGG GAGTTTTCAATTTCGAAGTGCCCGACGTGCTTGCCACCACTAAATACTTC TTCGCTTCTGCCTGTTTGTGTTCTCTTGACGCAATGGAAATTTACCAGCG ACATTATTAGATGCCATCGCATGTCTTCAGTTTTGCTGTTTCATCCGGCG CATTTCATACTTCAGGATTTAAGGGAGAGAGACCTCAACAAGAAGGGAAG CCGAAGCTAGTACACCCTTTCTGCTTGAAACCTATGAGTACGATTGCGAC TGAAATGTCGCAAATATGTACATACGTACATATGTAAGTATATATATGAT AAGGTGGAGATTCATAAGAGACCAACTTGATGATATTGTAAAGATTTTGA AATTGATGTAATGCATATTCTCAATTATATTATACAATTTAAGCTTCTTC TACAGTGTTAGAATATCCCAACTACATTAAAATTGTGCAATTACGTTGGT GGATTGTTCGCGTGCCCGAAGTGAAGTCTCCTCTACAGGATTAGCCAGAT GAAGATGAATACCATACTTGCATGCTGACCTCATTCGAAGGCTTCGTGTT GAGCGATGGGGAAGGTGATAAGTATGCAGTGGCTATTCATCAAATGCGAT TAATATAAATATATTCATCAAATCAGAGCTACGAATCAAATGCATATTCT GCATATTCCCATCTTATACGCTTAAATTTTAAACAATTAGAAATACACTT TTGAGCGGCTTGTGAAATGTTTGCATTCGTCCCACGTAGTGCGATCTCGA AGTAGATAAGATAAACTTAGATAGGGAGAGACGAATAAATTAATTAGCAA CTATTTTATTCGTTTATTCGAGACTGTGCACTAGAAGTCTATCTTTTCAA GGGTCAACAACTTGGTCTCGTGACACTTTAAATATGCCCTGCTAAATTTA AGAGATCAAAGAAAATCTGAGAGTATGCATGGGAAAACGTGGATACTTTG CTTAGGCCAATTTGGATGATAATTGCTACATGTGAATTCATGTACATATG TAAGTACAGATGAACTAATGAAGTGTCTTTAGAGCAATTAGCATAATTAA CACACTTGCGATACAATGCGACACATTCGAATTGTAGAACCGGTTCTGGG CTCCAGATCCGATTTGCCTCACACGCAATCAGCTGTTGGACTGCTCTGCG TTCACTGCTGACACACATTAATGCGGCAAAACAGATAAATAGGCAGCGAG GCAAAATAATAATAATAATAAATGCAAAGGTCTTACCGGTTTTGTCAGCT GCTACATACAGATGTTTTCGGGCTTCCCCGCTGCCCTGCCTGCACTACCA ACTTCTAGCCGCCTCAGCCGATTGAGGGTCAATGGCTTCTAAGCCAAGCC ATCTAGATACATTTCGCTTCGGATTGCGTACAAATCAAGAAGTCGCGAGC TCAAGGACGGCAGCCAAGAGAATGGTTTTCGGTTACAGCAAATCACAGTT GCAGAACGCCAAAAGAACCGAAAATCGAAGCCAAAAAAGCGTTTGCATAT ATTCAAGTATAAACATATGTATATATATATATATATATACTTCATCTTAT ATCAACAGCCACACAGAGGAAAACGCTATATTGCTCTTCTATGATAAATA ATGTACTCATTCGCTTATTCACTCATGTAGTCATTCTATTTTCCAAATTC ACTACTTTTGATTTTGCAATTACCTATTAGTCTCACTCAAAAGCTGCACA GTAAGTAATACCTTTTTGAAGCCTCTGGAAGTTTCCATTGCAGGCACAGA AAGTCAGTGTCACGTAAATGATTTCAGTTTCTCGAAGCACATGTGTAACT GTATGTATGTGCAGCTCAATCCAATGGATTTGCAACTAGGTGGGGTTGGA TGGTGCCGAAGACAAAGGCAGTAAAAGCCAAATGACTGGAGCAGCAAAAT TGCGAAATGGCCGAAACTGTGCTACAGTCACTGCGGTCTACCAGCATCCT CTCGCCTTCGTCCTTCGGAGCCACCCACCTCAGTCCACCCTTCGGCTTAT GTAAATGGAGCAAGTGCGGAGGGCGGGGCGGCGAGCTAAGTCCGTGCCCC AAGTTTTGGATTTATTTTTTAGAGTGCTTGGGATTGAATTGTGTGGCAAC CGCCACGATCCCATTGCGGTAATAACTATTGGTTTCTTTAGCTAGTAATA CAAATTGGGCTTATGCGAGCTTCCTTACTTACAATGAATATGTAAAATGA TCAGGGCTGTTGAATACCCTACTGACAAATAGAGTTTGAAAGTGGCATGC CCGAAAAACAGCATTCTACACGCGCTTTGTTGGTCTTATCTGTTGACTCA CTACACTCGGTACTCGAACCACTTTCGCTTTAAACAAAACAGTAAATACG TATGTTATAAATCGCCTCTGTTTTTGCATATTTTTTCAACGTTCACGGAA AACGTAAATCCACCAATCGTGCCAAAAACGAGTCCGAAACTACCGACCTA TAAATAGCCTCCACTCGATCATAGAATCAAAAGGTTGTGGACACGAAGCA CGAAAATAAGTCAAAAATTGTTAACTCATCGCTAGATAAAACCCAAAACA AACAAAATGTTATCATAAATTTAGACTTTTTATTGGGAATTACGCATTAC ATACACATGACATATGTGCAAACATTCATTCATACATACAAAAATGTATA TAAATACCGTTCACAAAATGCAAACGGGTCAACGTAACCCCCGAAATCTT AAGCAAACTTTGTTTAATTGCTTCTCACCTGATCACTCTGCTGAGTTGGT GAATTCGTGGCTTCTGGGCTAAATTGCAACCATTACTGGGAGTTGGTCCT GTGTCATTGCATTATCTTACATTATAGGCTGCACATTACAGTAAATGTAG TTGTTGGGCAGACGAGTATTACAAAAATACAATAAGCTCGCTCTCTCTTT CGTTTCTTTTGCGTATGCCTCTTCGTCGAATTTGTTAGCTGTTGTTTTAT GAATTTCTGCCGCCCGTCTTGCACAGTGGGATGAAATCGCTGTAGCACAC GTCCAAATCAGCTGGCTTATATATGTATGTACGATTAGAATTGGTTGCGG GTGACACTCCAGAACGCCAAGTTGCCAAACACTCTTTATAGGCGATATTA CGCACACTCAAGTTCCCGTGGAAAGTTATTATCTATCGGCTTCGCCCTGG GTCACGCCCACTGTACGGGAGTTTCGATTTTCTGCGGGGGAGGTGGGACA GTGACAACACCGCTCGGCGGCACAAGTTCAACAGAAAATGTGGGGCGACC GGAGGTCGTATAAACAAAAGCACAGTGCACCCGAGTGCGGAAATCGCGGC TGTAAGTGCTTCAAATGCACGCAGGAGTCGGGAATCGGGGAGGAACTTTC GATTCACCCAATCGCTGGATTTCAATTGATTACTTAACACGCTCTGTCGC GAGAAAAATAGGCTATCTCTACTGCCGCGGCCCTTAAAAATATAGAAAAG TCGTATAGTCCACCACACTAGCACCACACGTCCGTTCGCACTCCAATTGG AACATCATCTGACCGTTGCCGTAACAGCGGCTGTTAATGCAGCCCGTCGA GGGTGGAAATTTCGATAGCATGTATCGAAATATGGAAAAGTTGTAGTTTC AGAAAACAGAGTTACAGCGACTTACAACATGATTCCCATTAAATATTAAC AGTTGCTGCTTACCTAAGAAAGTTAAACAATTGTAATTTTAATGCGATAT GAAGTTATCGATAGTGCCCGCGCGCGAATAATGTTGTTTGGGTACTGTTA GCGTGAAACACTGTTACGTTACCCCACAGATGTTCGATTAAGCCCTCTGT TAATGAGAATGAACCGCCAACTTTATCGATAATGTTGGTTATGAAGCGTA CGCGCAGTAAGATCAAACTAATTTATGAAGAGGTGATTAAAATATTTGGA TAGACGCTCTTATACGTAATATATTAAAATTTATAAAAAGCTTAAAGAGC CTCACTAGCTGAATATAAAGTAAAATATTGTCTCTTTTAATCCATATGGT TATTACATTTTTAATTATTTGCGTTGGATAAGATTTCTGAGAAACCTCTT TTGAAATTCTATTCGTATTTTATATAATAACTTTTACAGATCCCCAGGGA ATCGTTTTGTATACTATTTTGTTGCTTCCTCTATAACTTGATAATACTGA AGTGGCGTCACACTGGCTAGGAACAGGTTAGGCTGTCATCACCCTCCGCT TCGTCAGCTGTAAAAGAGACAAAAAGTAGAAATGGAAGCTAAAAAGCCGG TCCTACCGTTAATGTCAAACAGTTGTAACTCACAAAGAATTTGAAGGCCA AACATTAGAGCGAATCCCGCAACGGCGGCCACAAGGGCCCTCCATCCGGC ATGGCTCTCAATGAGGATCTCAAAGAAGACTACGTACAGCAAGGTTCCAC AGGCGATGCCCTGGAGGACTCCGGATGGCAGACTGGGCTGACCCGCTGCC ACCTGCTGGCTGATGCCGAGGCCAACACCGATACCGATGGGTGTAACAAT GGAGAATGTCACCAGGTACAAGATGGCCAGCGAACTGCGTGTGCGGGCGA CCAGAAGCTCCATACCCACGCAGAAGGCCAACACCAACTTGTGGGCGGAG ACCGCTCCAAACATGAACCACACAGTGCTCACAGTGCCCTCCAGACCAAT GGCCATGCCCTCGAACAGTTCGTGGAGCGAAAGGGCGAGGATAATGCCCA GCCCCCTGGCAGAGGATCCATCGTCCGCTGGCACGGGCATGTGCGAGTGG CCGTGGTGATCCTTGTGTGGCTGCGGTTCCGTATCCTTAACTTCCACTTC TTCCTTCGCCTGTGGATTGAGGAGAACACTGTGACGAATGCTGCGTCCTC TTTCGAAAGCCAGACTGGCCACCGACTCTTTCCGACTAAGCTTTCCCTGG TGGTGCCGCACGAGGCTGGTCATCAGCTCGTCCAACGCGTACATCAGGAA AAAGCCCGTGCACAGCAGCATCTCCGCCAGAGCGAAGGGCGTCTTGACAA GCGAGCCGCATTCCTGGAGCGCTTCCACCACCTCGATCACCTCGGGCAGC ATGTGCAGGAAGGTGGTGCAGATGAGCACACCGCCGCCGAAAAAGAGTAG GCACCGCACCACCAATGACGAGCGGGTTTCCTCCGGACTCGCCTTCGTCC AATGGAAGCACCTGTTCAGGACGTAGGGAAGGCTGCCGCAAAGCACGGTG ATCACCACGAGCACCACCATGGAAACTATTTTGGCCACCAGCAGCGCATG GTGATCCACGTCTTGCGTTTGCTCTTGTGACATAGTTGCGGTAGCGCTCA TCTTCACCTCCCGAGTTGATAGCTTCGACTGTGCTGGCTGGAACTCACAA CCAGGCTAATGGTTTATATTTCCAGTCATATATCAGCGGGAGCCGATTGA AATCTGATCGCTGATTGATACGCGGATTCACTGGCAGACAGCGGGCAAGC CTCGCAGCCTAGTATTGTTATCAATTCGCCGTCCCCTGGACAGGTGTCTC TCGTCGGCCCACCGATAACCGAACCATAGCCGTCTGTTCTTTGCGAATTT TATGATTGAGGGAAGTTTCGTAATGTGCAGGAACTTCGGAAGTATTTCCC GAATATTATTATTATTGATACACTGAGATAATTTATTTGTCCATCCAAGG CGGTCTCATCTTAGGTTTATATGGTAAGGATTGCAGGCATGGAATTAAAA TCGCAGCACATTTTTTAAAAAGTTAAAAAGATTCTAGCCATATATGTAAA TATTCTTGACCAGGATCAGATGATTTCGCCACGCTTGTTTTTTAATTTTA CTAAATTTGTTTATAAAATAAATTTACATTTATCAAAATAAAGGTGTGAT AAATGCAGAAACTTCCATGCCAAAAGTTGTTCGAATCGGATCATTTATTT AAAAGTTATGGGCAATTTGGTAATTAGTATGTAGCAACCGGTAGGTGGAG CTAATGTGCGCACTCGGAGAATGTCCTTTTGTTGATGCCACTTATAAATT TCCCTCGCAGAAGGGCGTTTAAAGGGTATCTCATGGTCGATGACCTGACC TTGCCGTCCTCTTTCCCCATATTTATAAAGCCAAAAAGCCCACGCTTTAT TTTTCGGTAGTTTCTTTGAATTTCTCTATAGGCTTAATTGTTTTCATATA AAATTCGAGTATACCCTAGGGGCATGTGAAATGGCTCTTCCCTTTGGCCT CTCCAACTGAAATAATAAGAGTGGTAATTTGGTTTTTCAGTCATTTGGGC TTTTTAGTATGCTTACTTGCTATCTGGAGGCCAAACATCAGGACGAATCC CACCATCGACGAGAGTAAAATGCGTATGCCGGCATGGTTTTTGGCCACAA TTTCAAAGAAGACCACGTAGATGAGGGTGCCACAGGCCAGCCCCTGGAGG ATTCCTGATACCGTGCTGGGCTGATTAGCCGCGGCAGATTCGCTAACTGC AATTCCGATGCCCACGCCAATCGGAGTTACGATCGAGAAGACGAGGAGGT AAACCACGGCCAGCAGCCAGCGGGTATGGGCCATCATGATCTCCATGCCG ATGCAGAAGGCCAGAACAAGCTTGTGGACGGAAATGGCTCCGGTCATGAA CCACACCGTGCTCACACTCATCTCCAGGCCAATGGCCATGCCGCCGAAGA GTTCGTGCAGGGAGAGGGCCACGATTATTCCGAGGCCACGCAGCCAGTTG GGCTCCTTGGGGCTTTCTTCTGGCTGGACCACAATCTCTGTCCGCAGCTC CTCGCCCGCATCCTTGATCGTGACCACCTCCCGTAGCTTCCTTTGCTGCC GCCGACGAACCACAAAGTGCATGGTTTCCTCAATGCAGTACATCAGATAG AAGCCAGTGCAGAGCAGAACCTCCGGCAGGCCGAAGGGAGTGGGGGCCAG CATGCGGCAGTCCTGGAGAGCGTTCACCACCTCGACCACCTCCGGCAGCA TGTGGATGAAGGTGGTGGCTATGAGAACCCCTCCACCGAAATTAAGCAGA CACAGCACCACTTTGAATTCGCGAGCATTGTTCTCGGGCCTCTGGGTCCA CTTGTAGAAGCGATCCAGAAGATAGGGAATAAAGCAGAAGATCAGGGTAA CGAGGAAGAGCACCACTATGGCCACGATCTTGGCCACGATTAAGTGTTGG TCTACCATTGCAAACGGAGTAACTGGCCCGATATCAAGCCATTCACTTTT TATAGTGGAATTGATATCTATTCAGTTAGTGGAAGGTATCGGCGAATTGT CGAATATTTACACATATTAAGGGCTTAGTGGTTTCGACTTAAGTTGGCCG AGCAATGTGCTTTAGCGAAAGGTATACGGCAAAATTTCGGCATGATATCT TTCGGTCATTATCTACCTTTCGATTTAACACATTTTGCCACATTAGCCAT TATTTCCCTGGCTCCCAGCATGAGCTCATCGGTCTGTTTTGCCGCATTAG AATGTCAGTGGGAGTTTTCAGACTGAAATTTCAGCTGGCGAAAACAAATA ATTTGTTGTCAACGGCAGGCAAAGCCTTGTGCACCCAGGAATCTATGTGC TATCACTAGGTTGTGGAGACAGTTTCGCCTGATAACTTCGAAATTGAGAT ATCACCGCCAAATGCCCCATACTAACATAGTTCGTGAGTCAGATTAAACA TGTACCTGTACCTGTAAATATTGTGAAGCAAAGGAAATTATAAAATAAAT CACTCGTTGGGTAATCTTTGAATAGTTTTTGAATATATAATGGCGTTATT GCAACGGATAAACGGATAAACTTATTATTTAACCACGAGTTTGGGAGATT ACATTTGTCATCGTCCTTTAATTCTAGGCAAGGTTTTGAATTCTTAATAT GAGGTATTTCGATTTTTCCATTGACAATCACGTTCTTCTTCTCAAGTACA CAACTAAAGTAGCAATTGATTTTACTTTTCTTTGCTCAAACCAACCTGCT GTATGCATTGTTTTTTAATTTAGTTTATTTCTAGTTGTGAATAAAAAGCA TAAATAAGATCTCAGAGTAATTACTTACTTCAAGAGAAAAAACCGATAGT AGAGACCAATGGGGTCAGCAAGAGGGTCACGACAAACGACCTGTTTATTT TGAAGACTGAATTTAAAGATAGCAGTCAACCACATAGCAGTCATCTTTTG CATCAATTATTGATTTTCACAAAAAATAGGGTATACAACTTAAACCTTTG AAGGAGAAATGCGATTTTATATGGGTAATTGTTATTTAAGATTTTGCATT CTTAATTAATTAAATTGACCGTTCCATTGATGCCTCTCAAATAAACAACT AAACAAGAGAGAATGCGAAAGTCAATTTTCCCCGATTATAAGATACCTGT TAGTCAGCTAGTGGAAATGCGAAATTTCATCATTTTTCTCGGATATCAAT AGATATTGGGGAATGCAAATGTAAAAATTATTTAAAAGTGTGGGAGTGAC CGTTTTGGGTGTTTTGTAGGTGAAAAGAGGGCCACCGTGTTTTTGGTATA CAGATAAAAATCTAAACATTTTTCAAAAGTGTGGGCGTGGCAGTTTTGTC AAGTACAACCTCTTATTCTACGAGTAACGGGTATAAATATGAAATATATT ATTTAATACCATTAGAACAGAACGTCTACGTATTGCCGCGATTGAATTCA AATGATATTGACCATGGACTTTACCTATGCATTATCATGATCAAAATAAG ACAAACCCAACGAACAATTTTACATACATCATCCAATAGTTTATTAAGTA TCATAGGCCGTAAATAAGTTACTGTAAAAATTATTATTGACATTTATTAC ACAATATTATGGCGTTTAAATTTAAATTTAACGTAATTACTATGACTTGA TAGTGTTCTTCTGTAATTGATTTCCATGATGTACACGGGTGAGAAGACAA ATAAATGTGTAAATGTGACATACATGAGTTTTGATATTAATGGAAGCATC AGAGTTTATCAAAGTTATCAAGTTGTCTCAAAAGATATTTCAAAAGCAAT GGATTGTCTCCAGACAAGTGGTTTTCATGCGTCTAATTTAGACGATTGGA TGACAGTTTAATGTGCATAGATATGCGTGTATTATTGTGACTTTGGATAA TCATTTCAAGTTTGGTTCGCTCGCTTTTGTGTGTCTTGTCGAAAACCCTC CATCGTAGTTGACAGCCGTTCAACGTGATTCAGTACATTCTTCCCGATTC CCCAACCCATACCATTCAAGACTGCTTGGGGTGCTGGACAGGAGGCGGTG GCGCCGGCTTGAAGCACTGCAGCAGGAAGGCGGTGTAGACCACAAAGGCC ACCGCCAGAGCAATCAGAGCGTACATAAAGATGTTCAGCTCGGGCTGGCG GAAGCGGTTCTTGCGTAGCCACTCCAGCACTTCGTCCTCGGATAACAGAT CACCTTGAATGAGAACGAGAATGAGAATGAGATTTCTCCTTTGCTCCCTT CACGTTCCCACGGACATACCCCTATATATGCTGGGAAACCGACGGCGGAA GTAGACCATTGCCGGCAGCTTGGTGACGCCCCATTTCTTGGCATAACGAG AGTCGGCCATCTTGACGAAGGTGATGTCCAGGTTATCCGTCTCGCTGTCG ATGTTTTCGAGTTTTTCCAGCGCTGCAGTACTGTCCGGCTGATTGTGTTC GTCTAAGTAAAAGACATGTTTGTACTAATCGAAAAGTGTTTTAGAAAGGA TAGTAAACTCACAGAAAAAAACGGCTAAGAACTCATTTTCCTCGAGTAGT TTGTCGAGCATTTTTCGGTTTACTTCTTCTATTTCGTTTTTGATTTCGAA TACGTCCTGTGATGTTAGCCAGGTAATCACCTTGTCGTGTTGGTGTAGAT CGCCGTCGTAGAGGACGGGCACTTGTTTTCTAAAGTGTTAAAGGGTTAAA AAACTTCACCTATAGTTTTGACTATCACCTACCGGAAATAAACGAGGGAA GGTATATTCACTATCTCGTATTTCTTGGCTGCCTGGATACTAGCAATCTT TACGAAATCAATGCCGAACATGTCTGCCTCACCATCGATCTCCTCCAGCT CTTCCAAAATCTCCTCGCACTCAGCACAATCATCGTCGTCTACATAAGTG TGTGATGAGTTTTTAAGACCATTTTGTAATTCATTCAAGCTGTGATACTC ACAAAAGAAAACAACCAATAGAGTGGACTCCGCCATTAGGCGATCCAGCA TACGCTCGTTGACCTCCTCGATTTCATCAGCCAGCTCGCGGTTGTCATCA TCGATGAGCCATTCCAATACTGATTGCTCGTTCTGAAGATCCCCCTCAAA CAGTAATGGGTTTCCATTTCTGCACACAAGTTCAGATGCCTTAGAAGTTT AGTTGATAGGCAATCTTGACACTTACCTGAAATAAACCAACGCCGGGAAA GTCTTGATCGAGTAACGTTTTGCCAGCTGCGGATCCTGGATCTTGACCAT ATGAATTCCGAACACGTCGCATTCGTCATCGATCAGTTCCAAGCCCTCTA GTATCTGGTCGCATATGTTGCAGTTGATTTTGTCTGCCGAAAATACATGG TAGGTCAGTAGTTACCCAGTAGTAATTAGTGTTTATAATTAGAGCCAAGC TTGAGAATCGGTTAGCTATAGTGTAAGAGGCAAAGAAAACGCCGTAACAA AAAGGTATTCCCGTCCAAACTAAATTCCAGTGAATTCTAGAAATTTGGAA CGCAAATTGTTTATCAACAGCAAAGGAAGGGCATGCAGAAATCTCATCAT TTAGTTTGGTCGTAATACGATGAAAGCCTGGTTTAGTGCTGTCAGGATTC GATTCTGGGCACAGAACAGAGCTCCTACGGAGGGTTAGACTTGGTTAGGG CTCCATTGAGCATGCGAAGTCGGAGCTTGGGAGTTTATATTGTTTGCACG TGGAATACGGAAGGAATACCTTGTTTTTCGATACGTTTTCTTTTACGTGA GATGTAGTTTTGTACGAATTGGCTGGATGAGTGTTTTGTGGATTTGGTGG TGGTCAGGTTGCTTTCTTTAAGACTAGAGGGGGAGCAGAAACTGCGGCAG AAAGCGGGTTGCTTCCCATTGCGCTCTGGTGGCACTGAGGTCGGTACGGT TGCGATTGCGGTTTCGTTTTCGGGTTCGGTTTGAGACAGGGATAAGTTTT TGTGGTTTATGGTCGATGCAGTGTGGGCGGGGAGGATACAATAATTCAGA ATGTGATAGATCATGATAAAGTGACGGAGTGAGAACAGTTGGCCAATCGA ACCAGAGTCTGATCGATAGGAGCTACTCACAGAAATACACGGCTAGGTAC TGCGTCTCCTCCACCATTGTCTCCAGCATCTGGCGAGTGATCAGCTCAAT ACGATCTTCGGTCTTCTGGGTGATAAGCCACTGAAGAACCTCTTCCTCCT CGCTCAATTCGCCTGTAAGATAATGACTTAGTAAGGGATGCCTATCGATT GATGACTGCTTCACCCTCGAATACGTTGGGGATTCCTCCCTCGAAGTAAA CTAGAGCCGGATACTCGTGCACGCCATAGCCGTCGGCCACAGAGAAGTCC CTGGTCTTAACGAATGTTATGCCATGCTTGTCGCAATCATCATCGATGTT TTCCAACTCCTCCAAAACCTTGGTGCACTGCTCGCAGCCATCCGCATCTG ATTGTCAAAGTGGGGTTGAGAAGTATATGATTACAATTAATCAATTATTT GATTACTGTAGACAAGGACTTGACATACGGGGTACTACACAAGCACTACA TAAAAAGCAGAGCAGAAGTTGAAGGGAAGTATGATAGAGCAAACGACTAT AGTTAGTACGTTTTATAAGTCCTGATTCCACTAGCACATTTTCGGGTAAT GTGATAAGTGATAAGTGTACGTTGGAATCAGCAATTATAATTCAAATAAT ATCGTACTGAATATAAGAAATAAATCTTATCGGGGATGAGGAAGATAACA GCTAACGTTGATAATAGAAAGGAGGAGTCGAATATAACATAGAGACAGAG TTGGAGCAACAAATAGATACAGTGGGTTTCGCATGGAGATTCTAAATTCG TTGGGGTTTTTACATTCGCTGTACAAGGAGGTAGTGTGTCTAGTGTGCGT TGGCTATTGGTGTCTGGTTGTGCTGGGTTAAGTGGTTAAACATTCTTGGA CTCATTCCAGTTGCACGAGTTCTATACAGAAAGGGTGGCTACCATCCTCT TGCTTGCCAGTTGAAGCATCCGCTGGAGCAGCTGCAGAGGCTGGCGGGGA ATCCCCCTCAGAACCTGCCGCTGGCGCATCCTCCGCCCCACCAGCGGCCG CCTCGGAAGGATCCGCCTCACTGCCGAAGGCGGCAGCGGCGCTGGCTGCT CCGCCCTCCTGCTGGTGCTGATCGCGCTCCTTTTTCAGCCGCGCCTTGCG AGCCGCTTTCGAATTACAAATGTCGCACTTGGTCTTGTTCCCTACGTTTG GGGTATCGATTTGTGTGGTTCGGTTTGAGATTTCAGAGAGCACAGTCGTA AATAGAAATATAAATAAAGTCTTGTTCGGTTAGATACACAGAGCGCTGAT AAGAGGCTTAGACTAGATTTATCTAAGTGGTTATCTACAATCATAAACAC ATAGTTCGCTGCAAACTGTTTGCGCAAAAGCGTGGTAACAAACCCATAAA GTACGTTATACGCGATGCAACATATGGTTAATTTTTGAATCAATGGAATA ATTCTACATTTAAGAAGCCTGTTGGCTGATGGACGTAACGTGAAGTGAAC ATCAAATTGAACATTGTACTTTGTGCGAATTGATACCACCAAACCGATTG CAGCGCTTAAAACCTTGGTCCTCAGAGATATTGAAAATTCATCGGTTGAA TCACTGTGTGCTTTCGGTTGCAAACTTACAAAAGTAGACTGCGATGGAGC CAGACTCTTCAATCAGATGAACAAGTCTTTCGCCTTCGAGATCTTCGATA ACATCTCCACTTGGATCCTTTTGCGTGATCAGCCAAGTTAGGATCTGTTC TTCTTCGTAAAGATCACCTGCAAGGAAACGAGTTTACTCACTGAACTAAA ACCTCTCTGAACTCTGGACACCTACCGGCGTATATAACTGGCTCCTTGGA TGTGGGCTTGAAGAAGACAATGGCAGGCAGGGCGAACACTCCGTACTCCT TGGCCATCTGCTTATCGTCGATTTTGACGAAGTCGATACCAGCCTTGTCC GCTTCGTCGTCTATGTGTTCCACCTCGGCCAGGACGCGAGGACACTGCTT GCACTCATCGCTATCTGAGAGTGGCAAGTTGTGGGTTCATAAAGGTAGTC CAATCAACTGCGGACCCCTAAGACTTACAGAATATCACCGCTACGTAGTC GGAGTTCTTGCGGATCTTCTCGAACATCTTGCGGTTAACCTGCTCGATGT GATCGGTCATCTCCATGTTGGCCGGGCTCGTTAGCCAGTCCAGTACCTCC TCCTCGTCATCGATATCGCCGTCGTAGTTGATATACTTGCCCTTTCGGAA ATACGTCAGTCCTGGGGGATTCCGGAAGCCGTACTTCTTGGCCATCAGTT TGTCGTGCATCTTCACTATGTAAATGCCATATTCCGCAGCCTCGTCGTCG ATTAGTTCGATGTGCCGCAGCACTCGTGGCGAGTCGGGATCATCTTCTTT GTCTGCAATTGCAAGCGATATTCCATTGGCATTAACATGAATATTTCAAG TATTTGGATAAAGATGTTTTGATTCTGATAGACTTATTCCGTAGAAATTA TATTTTGCTCGTGTGTTTTTGGGCAGTTACAGTTTTTAGTGGGCGCGATT TACTAAAAGTATGTGAAAACCTCTTGGATTCCTTAGCATTTACAATATAT TACCTAAATACCGTTCCCGAGGTATACTTACAAAAAACAACCGCTAAAAA GTCTTTGGTGCCTATATACTCGAAAAGTTGGTCACGATTAATGAGTTGAA TGCTTTGGTCGGCCTTCTGTTCGAGAATCCAGTTGAAGACGTCCTGATTG CTTGCAATGTTACCTGTTTGCAAAATCAAACAAAATGGTTAGAACTCATC ATATTTCCATGTATTAGGTTGAAGTGTCTGGCTCGTCCATTTGGTGGCAC ATACCTGGCGGCTGCAGTTTGTCAATCAATCATCAGCTTTAATCTTGAAT ATGTATACAACATTAATGATCGCTTTGTTTATTCTCACCCCCGCCCAAAT GAAATTCGAAATCGGCACTTTGCCAAATCCCCACCCGCCCATAAACAATG TTACATTTGGCAGCCTATGATTCAAAATATATGGTTTTTGAGGGGGACAT ATGCCTCTGACGAACATACATACATATGTACATCGTCAAGGATATATTCA AGAATATATTTAAAGATTTTTTTTGGCCTATATGTTTGAAATTATTTAAG ACAAAGAATTGCGTATTTTAACAGTGCTTTAAAGTGTATATAAATAAGAG AACCTAAGTTTATTGAGTTGGATGGCTTTTATTAAATATTCTTACAATTT CATTCGGGAGCTATGTTTACAAAAGTGCTTTATGTCGATTTGCGTTTGAT TTTTACGATCTGACAATTTCCATTTCGAAAATCTTGACTTATCAGCTGCT GTTCAACAAAATTTGTTTACATATATGTTGGATTTAGTTACAATTGCGTT TAGATTGGTAGGCTTTAGCTTAAGAAAACATAATGATAAAGATTTCTAAT TCGATATTTTTCAAATACCGATAACAAAAACAACAGCGAGCGGTACAGAA ATCGCTCTCAGAAGAAAACAAATGAAACAAAATGGCGAGCTACAATATGC GAGGCCATGTTCAGCGAGAAATATTGGATTTTCGATTCCATAACAAAATT AAGTATACGGCCTGTATGCTGCTGCAACATTTCTAAAAAGTTGTGGTTAC AAATTATGGTTCCTCATGTTGTTATTATGAAAACTTATGAAAGTTGAAGG CTCTCATAGTTACACGTTTCAGTTAAATTAGCTAACAGTTGTGCACTGTC AGGTGTAAATTGTTTCAAAAAATATTTTATGCGTTTGTTCGTTCGTTTAC TATGCTTTGGCCCTTGTTTAAATTAGACTAACTACATAAATGTAAATTGT ATATTGCGACAAAAAGAAGTAGTATCAAAAAAGTTTAGGCGTTCGTTATT GACAAAAGACAATGTCCCATTAATTTGTTAATAACAAAGCTTGCTGACTA AATATACGAGCGAAAGTTCTCAGAAGTTTTATAGTTGTTTGTCGAAGTAA TTGCTTTTAGTTTGAACAAAGTTTTTTGAAATCCGTTGGCAAAATGCAAC AAATGTGTGGTTTAGTTAGTTATAGACCTGGGGACGACCTACACAGGTCG GCCCCTCTTGAAGAAAGTTAAAGCGAAAATATCAACAAAGTTTTAGTTAG TAGGTTTTCTTGATCATTATTCATTATTTCGGGTATCGTGTGATTCTGCT ACTCGTGGATCTTCTTAACGTGGAACAACGCCCAAGGCTCGCTGCTTAAA AGTGTGGAGTAAGTTCTGATCTGACACAGAAGATGTATTGGTATTTAAGT CAATGTTTTTGTGCCAGACTGTTTAGGATTAGTGCGAGGAAACCTCAATT TTATGGACACACAGCCTGCGAATTCAGTTTTCAGTTGGTTCTTGTCATAG TTGTTGTCTTTTGCAGTCACACATATGTAGATGATGTACATTAATTATAG AAACCTGTCATTGAAGGTTCTTTTGCTGGCTATACAGGTTTGAGTTGGTT TTGTATTTTGTTTTGGTTTTGGTTTTGGGTTTGGTATTGGTTTTGGTTTG ATAATTGTTCTATCAGTTGGCAACAGTGCGTATACGTGCTACTTTAGTAT GGTATATCATTCAATCATACAATCAATCACTATCTAACTGTCTGTGGTTA TCCACATTCAGTTAAACTGTTGCCTTACTCCCACAGAGAGATATCCTGAA AAATGATATCATACAAATTTTTTAGTCGATTTTGGAAAAAATTAATGCCT GCAAGACACAAGAGAAAGAAAAGAGAAGAGAAATAAACAAATAAGGTAAC GACCAAATTGTGCGTGTGTCTGTATGTGTCTGAGTATGGGCACAACAAGA GCAAAGTGATCAGGGTACAGGACAATGAGCTTGACGTCAAATGAAACTCT ATCTCGAATTGTTTATAGTGCTAAATGACAACGGTGTCTGGTCCGAGGGT CCAACGACTACGTACCGGATTTGACATTCAGTTTGCCGGACTTCTTCGCC GACTTCTGTTTGGATACCTTCTCCACCTCCTGGGACTGGTCGTCGTTGTC CTGGCCCTTGCCTACCGGCTTCTTGCCAGCCTGCGGCTTGTTGCTTCCTC CCGAGCGCTTGTTGGCATAGGAAACCTTGACCAGGGGCTTGTCCTCGTCG TCCTCATCGTCGTCATCGGTGTCCTTGGAGGGCTTGGCCTGCTTCTTGAT GGCAGCTGGCTTGGTGGACGATTTGCTGGACGCCTGGTTGGCAAACTGGA AGTTGCCGCCGCTGGGACGCTTGCCCTGATCGCCTTCGCTATGCCCGATC CGCTGGGCGGTCATCTTAGGAACTTTCGTTGACTTCTCCAATTTGGTTGG ACAGCATTGGAATGGTTTGTAATCGTTGGGCACGAAATTGTTGCCGCGCT TAGCTGAATGGCCGTCATGACCCAATCCAACATAGAAACATTCGTCATCT GTGTAAGCAAACAAACAAAAACATTTTGTCAGATTGTTTAATTTAAAAGA TTTTGGTTTTTTTTGGTTCACTATCAACAGAAGGTTCGTTACGATAAGTT AAAAAGGTTTCAACAAAAGTGCATCATTGTAGGCTAGAACTAAGAATAGA AGTCGCAAACTGGCTTTTTACACTTTTCTTAACACCTCCGATATTACCAC AGAGAAAGAAAAAGAGCAGTTAGTACGATTTTCGATTTAATTTTCATTAT ATTCAGACTTGAAAGATTCTTTGTTCTAGAGTAGAAGCGTGCTTTATGAG TGGAAGAGATTCGAAATTGTTATAAGATATAATTTAAATTATATTGCAAA ACTACAAAACTAACTGACAAAATGCTTTTGATGCTGACTGTACAAGTTTC GGATTTTGATTCTAATTTACAAACATATCAAATGTCGAGTTAAGCCCACG TTGTTGTACATTTCGTTTTCGACTAAGTGTCAGTGAGTTCACTGCGTCTC ACTTTATCGAACTTATGGTTGTTTTTGTTTATATGCTTAAATATTTTCCA TGGAACAACAGGATCGTTATAAATTAATATATATGTAAACAAACATAACG ATTACTTAAAGTATTATGAGAAAGTAAATTATAAATCGAACAAATTAGGT ATTAACACAATTGTTGTATCATTATCAAAATAGTTACGTTTTTAAATAAA AAACCTTAAGTTGCCTGGCTTAAATAATTTCAAACATTGTGTCAGCTATG TATGATTTAATATTCTTTAAACGTGTCCTTGTAGTAACAAGGACAATGGA CTTTGAAAGTGGATAAAGCTGCGGATGTAGGTGTAGGATTACTAGTTCAA GAGGATTAAAAGTATACGAATGTGGGTAGCTATTTTGACTGGACTGTGTA TTCCCAATTAAGATTGTGCCTCACATGATAGTTGATTTAGCACAGAAGCA ATGCGCAGAGCACAGACACAGAAATCACGTGATTGTAGAGTGGTTACCTT GGTTAAATGCATTTCTATTTGAATTCCTCTTCCCCAAGTCTGTAGATAGA CAATGAAATTAACTTTAGTCAAAGTTACAGAGTGTTTTTTTTTTTGGCAT AGTACAGTGTACAAGGATGTGTTCTCGGGTGGGATGAAATTGGGAAGGGA ATTTAAGTCGGGTTGGACAAAACATTGAACAACTTGAAGTTAGTGCGTCA ATGGCAACTCACATTCAGGTATTACCTATTTCATCTATAAGCCGACCTGA GCAAAGGTCAGCAAGACGGTGTATCGTTCGACCTTTGGCCGTGTGCCTAT ATTTTGGTTTACTTTTAATATCCTCTTCTTCTTCTTCGTCGTCCTCATTA TCGTCCTCCCCTGTTGCGTCCTCGTCATCCTTATCCTTGTCGTCCCCGTC GTCGTTATCATCCTCGTCCTCATGGTCTTTTTTGTTATCGTCGTCCCCGT CATCATCGTCATCGTCCTCCTCGTCCCCGTCCTCATCATCCTCGTCATCT CCCTTATTATCTTCGTTGTCATTTTCGTCCTCATCTTCGTCGTTTTCATC CTCATCGTCCTTGTCGTCTTCATTATTATCTTCTTCGTTATCTTCGTCGT CCTTATTATTATCTTCTTCGTCATCCTCGTCGTTATCATTATTGTCTTCT TCGTCATCCTCGTCGTCTTCATCGTCATCTTCGTCGTCATTATTATTATC TTCTTCGTTATCCTCGTCCTTGTCGTCCTCATTGTCATCTCCGTCATCGT CGTCCCCATCATTATCTTCATCTTCGTTTTCATTATTGTCCTCTTCGTCA TCCTCGTCGTCTCCATTATTATCATCTTCATCATCCTCGTCATCGTCATC ATTATTGTCATCTTCTTCTTCGTCCTCGTCGTCCTCGTCGTTCCCGTTAT TATCATCTTCTTCGTCATCCTCGTCGTCCTCATCATTATCATCTTCGTCA TCCCCATTTTCATTATCTTTATCATCATCCTCATCATCGTCATCCCTAGC AGTATCTTTCTCCCCTGTTTCATCTTCGTTATCCCCATTTTCATCATCAT CAGTTTCTAGTCTTTTTTTATGTAATCTCTCATTGCGAATCGAATTCTGC AGACGCTTTAATCTTTCTCTTTTATCCTCATCGCTTTCTTTGGGATAGCG CAATTTAACAATTTTTTCATTACTGTCGCCGTCATCATTGCCTATATAAG AAATTATCATTACGTATTGTACTTTTAATTTAGGCAAGAAACGGGTAAAT GATATTGGATTTATAATTTTTAAGATTTATGAAATCTTCTTTGACTTTGT ATCGAAAGTTTGGCTTATGATCGTGAGTTATAAAGCATAAACACGTTTAA GAAAGGACGCTTACTCTTTTGATTGACTAACCACTGCAGCACACGGTTTT CATTTTTGAGATTACCTATAGGAGAAAATACTGTTAGTTCAGGCTGTAAT AATATACCAAAGATCCCCAACTTACCATCATACATAATCGGGACGCCGGT CTCGTAGTAGACCAAAGCTGGAAATGCGAAAATGCCAATTTCATGAGCCA GCTTAACATCATTTGATTTGACAAATTGTATTCCGTGCTTGTCGGTGTCA TCGTCGATGTTCTCCAACTCCTCCAAGATGTCGGAACACGATTCGCATTC ATCGTCGTCTGTGGTACAAACAATCAATGTCAACCAAAGATCTTATTGAA CTTAATGAGAAATACACTTACAGAAGAACACAGCCAGGTGCTCAACATCG TTGATCAAAACTTGCAGGGTCTTACGATCGACAGATTCAATGACATCAGC TGTGGACTCGTGCAAATCAATAACCCACTCGAGAATTTCCTCTTCCTTCA TCAGGTCACCTTTTAAAGAAAATTACAAACATGTACCTTGGCTAATAAAG TATTCATTAAATGTATCAGCACTCACCGGTGTAAATTGTTCTAAACTTAT GTCTATAAAATGCAAGTGCCGGCAGACCGGGCAGGTCGTACTCCTTATCA ATATCGTCGTCGGATGTCTTTACAAAGTCAATGTCTTTTTCCTCGCATTC GTCATCGATGTTCTCCAGCTCGTTAAGGATCTTTTGGGCCTTCTTATCGC CCTCAGCGTCTGCAGAAAACGGTTTTAAGGATAATACAATATAAGGTTTT AAGTTGGCTTACAGAAGAATACGACAACGTGATCGTTTTCAGCCAAGATC TTGTCCAACATCTTCACATTGACCTCCTCAATTTTTCCGGGAATTTCAAG GGTCTCGTCGTCAGTAATCCAGGCCAACACCTCGTCCTCGTCGTCCAGAT CACCGGTAAAGTGAAGTGGATCACGATTCCTGAAGAACACCAGACGTGGA TAGGTCTTGACGTTGTATTTCTTGGCAATTCCGGTATCCTCAGTGGTAAC AAAAATTATGCCAGCCTCATCCAATTCATCGTCGATGCTTTCCAGGGCGT TCAGAGTGTGCTCACAGGTCTCTCCGGGCTCGCAGGGACCCGTAAAGAAG ACGACGACATATTCGTGTTCGTTGATCAGAGTGACCAGGATCTCATCGGT AACCTCCTCGATAGTAGCTGTCTTTTTCTGGACAAGAAGCCACTCGAGCA CCTCATCCTCGTTCATCAGATCGCCTTCATAGAGGGCCGGGATCTTGTTT TCGAAGTAGATGAGGGCGGGCAAATGATCGAGACCATATTCCTTGGCCTC AGCGGCGTTATCAATGCGGACGATGACAATTCCCTCCTTCTCCAGCTCGT CATCAATGTTCTCCAGTTCGTTCAGGATGCGCATATCCTGCTTATCGTCC TTGTCGTCTGTGAGCGAATGGTAATGATTGCAAAGGCGTAGGTACATTAG CAGTGTGGTCTACTCACAGAATATAACCGCCAAGTGCTCGGTGTTCTCGA CCAACTTGTCCTTCATCTCATCGGTGACCTCGGGAATTTCGGAATAGCGC TTCTGGTGCACCAACCAGCCAAGCAGCTCATCCTCTTTCATCAGATCACC CTCGTAGATGTGTGGAATTCCACGTTCAAAGAGTACAATCGATGGTATCT CATCGATACCCCATTCTTTGGCCTCCTTGTCATCATCGATCTTGACAAAG GCAATATCGTTCTGATCGCACTCATCGTCGATGTTTTCCAGTTCTGCGAG GATTTTCTGTGATTTCTTTTGGTCTTTGTCGTCTGCGAAGATGATTTCAT AGGATAATTTAACAATTGTCTGCAACGCGTTGGAGGCTATGTAATTAACT GATCAACAAACTGCTGTTTTGCTCAACTTGTAACGTGAAACCTACAATCT ACACTGTTCTAACGGTCTTTGCAGAGATATACCTTCACGAAAAGGGGTCT ACTAGTTATTATTGTTTAGTTTTAAGTTAATACTTTTTCCAAGCGCCATT GAAAATTACTACTAGAAAGCGGGGTTAATGTTACGATTGCAGTCACCCCA GAAGTACAACACCAATTCAACTGTACAATATCAACAGAGATAGGGAGTCG AGTGCGCAAGCGTCCTGGCACAAAGTCGCAATGGGGCCCTGAAATAACTT ACAGAAAAGAACAGCAACATGGGGCATTTTCTCAATGATTAAGTCCAACA TTTCGTCGGTGATGTCCTCGATTTGATCGGAACTCGTTTGGTCTGTTAGC CATTTCAGAAGCTTCTCCTCGTCCTCCAGATTGCCCTCGTAAATAGTTGG AATGCCTTTTTCAAAGTATATCAGTTTAGGAACTTTATTGATGCCATATT CAACGGCCTCCTCGGGATTGTCGATCTTCACGAAAGTAATGCCCAATGCG TCGCACTCGTCGTCAATGTTCTCCAGCTCCTCGAGCACTTTCTGGGACTT CTTGTCGTTGTTGTCGTCTGGAAAACAGCTTATGAGCAAAACGTGTTCGC CGCCTTAGGCGCAATGGGTACGGGGTTTCAATATTTACAGAACAGCACGG CAATGACGCGTCCTTCTTTGATCATTGTATCGAGCATTTCGTCGGTGACG TCCTCGATCTCATCCCGTTCCAACTGTCCCAACAACCATTTCAGAATCTG CTCCTCGTCCATGAGATCGCCGTCGTACACATTTGGAATTTCTTTTTCAA AGTAAACAATGGCCGGAATCTGCAGGTCGAATTATGTTATTTGTGTCAAA GACGTTTCAATTGCCAGCTCGCTGGAATCCTACCGAATCGATTCCGTAAT CGGCTGCCGCCTTGGCATCGTCGATTTTCACAAACTGAATGCCATGCTTG TCGCAGTCGTCGTCGATTTGCTCTAGCTCCTCTAACACGGTCATCGAGTC GTCGTTTCCATGATCATCTGCAGATTAATGTCAGTCGGTTATCGCGTGTC GCGCCTCGCGGAAATTCTCATCTACATACAAAACAGCACAACCAGATTGT CGATATTGCTGATCAGCGTCGACAGAGTCTTCGAAGTGACGTCTTCAATC ACATCATCTTCATCGCCCGTCGACTTATTCTGCACCAACCATTCCAAGAC GTCCTCCTCCCGCTGAAGTTCACCTGGAGACACAGTTCGATATTAGCGAA ATGAATACCGAGCTCAGCATGGGATTGATGTGTGTTGGTCTGAATTCGAT TTGAGTGGTGGGTGGTGCAGGTTTCAAGAGAATGTGGTTTGGGATGGAGG TACCTTCGTATATGATCGGAGTCTGGTGGCGGTAATAGACCAAGGCTGGC AGATTGCCTAGATTGTATTCGTCGGCCAAGGCCTCGTCGTGTATCTTCAC AAACCCGATGCCCAGCTGGTCAGCTTCGTCGTCGATATTCTCCAGCTCCT GCAAGGCCTTGGCGCACTTGCGGCATTGCTGTTTGTCTGGCAGTCGCGAT CGCGGATTTGGTGGATTGTTTCATAGAATCAGGCAAACAATAGATAATTA GGGCCGTCTGGCAGAGGGGTAACGTCTTGGTAAGCAAGGAGTAGAGCACA GAACATCAGGGTGGGCTCTGGTGTTGGGTATTATAATACACGGATAGGAA GAACATTCAGGTATTATATTTCGTGCGGCCGTAAGTTATTCTGCGGGGTG TTATTGTGGAGCCATCTCAGACATATGTGAGTGCATGCAAGGGCCATGGA GTTCCACTTAACGCTACGGTTACCCAATCTTTCCCAGGCGATTCGTTTAT TTACACAATTTGTTTACAACATCCCTATCAGTCTGCGTGCAACCTGTTGC AATGTGCTTGTCTTGGTAAAGGAAATACATATGTACATATCAGAGTGGTT TAATAAAAGAGGAATGGTTTTTTCTGAAAGCTCTCTCCTTGCATTTACCT TTTCCTCTATTTCTTTGTGTTGGGCTTACCACATTCGTAAATGTGTTTTC GGCAAGCTTTCGCTTCTCTGGCCGACGCTGCGTATACGTAATATTTATTT CTGTTGCTTCGTCGGTGAACTTGTCAGTGTGATAGCTGCCTGGCCACATG TTTATGGCAACCTATCACCGCATCTTTCCGAATGCAGTTAGCCGGCGGTA GTGCCCAGAATGACACGCCTTCAAAAGCCATTACCCCGACCAAAATACAT ACGTATGTCTCTAATTTCCCCGATCGACGCGACTCATTCCCAGCAGCTGT TTGAGTGGGTGTCGCCAAGGTGACAAGGCCAACGCACACACTCGCTCGCG AAAATGTCTCATAATTTACTGCACAATGCACAATGATGGCAAAACATACA TATGTACCCACATATGTGCTAAATCGAGAAAATCAGACGTGTTTGCGAGC CTTCAACTTTCTCCCTGACGGACTGACCAATTTTTGGCCCTGCCGCAGAC ATGGGCAAATGTTGCACTTAACTAAAAATAGTGCAAGTCAGTCGGGAAAG AGCCACGCACACACAGTTATAGATCTGCAGTGGGACGGACGGATACGAAT ATATCGGTATAGGTATTCGTATATTATGTAAACCAGCATTTGGCTGCGAC AACTGAAGATCTGCCCATAACCATGCACTGCCGGCTCGTGTGCGCCATGT TGATGTATTGCTGAATGCAAGAGCAATTAAAAGCGCTGTCTGTCTGCAGC CCCTGATGGATTCAAACTCAATTGCGGGGGGATGGCCGGGGGCGCAGTGA AGGGGGCGGGCGGGACAATGGGCCACGATTTCTTGTCTTGGGTCACCTAC ATGCTGTTCGCATCTATGCATACATACATGCATCTATGCATCTATGCATC TTGCATTAGGATAAGCGTTTTGTTTTTTGTATGCTGTCTGCGTTTGATAA AAATACCTATGGATAGTGTAGCGGATGCTACAGAAATGTTCTTGTGAATT CACACACTTGCCATGTGAGTGTGGCTATAGTTAGTTGTTTCAGAATTAAG CAAAAATAACAGCAGCAGCAAGAACAGCGAAAAATCATTTTGTTGGCCCA CCAACTGCTTGAGTTTTCTATTTTTAACACTAAAATTGTAGGTGGCTGTG TCGGAAAGAGACGGATGGCCACGAATACTTTGTTGTTGGCCAACACATCA CCGTGTGTGTATGTATGTACGTTGTACATATATATGTACATATGTATGCC ACATCTGCAAGTATTGAATTTATGCTTTTTTATAGGTAAATTCCTTCCTT TCTCCAAAATTCACACAAATTCGAATATCGTCTCCGGGGAAAATCTCCCA CGCTCGACAATTTCTATATTGTGATCCAACTTCAATAGATCAGTGCGAAT CCCCAATTTTCATCCTGCTATCCACCGGCTTGTCCAAATCACAGGGTTAG GGATTGGGTTGTGATTCGTGGTGTGGCGGATGAGAAGTTTTGTGGGGGGG GGGTTATAGAGAAGAAGACGTCGTGCCGACAAAAACATAATCTGGCGCCG AGCCCAGACATTCATCTGCATTGCTTCTGTTGTTGTAATGTTTATTATTA TACGTATACGTAATATGTGTGTCTGCCTTGGTCGATAGCGAACGCGAAAA TGAGAGATCTTGTTTTTTTAAAAAATTACTAAGAATTACTACTCGTACAG TGGTGATTGTATATATTTAAGGTTGTGTCCTTTACCTAGGCCATCGACGT TAACTGGTCAGCAGGAGAGCTTAAGTAAAGATTGAATAAAATTGGTTTGG CCCACGCTAATTGGTGCATTGTAAACTGGAATCTGAATCCCTAGCGTTCG ATTTTAGCAAGCACCAACACACACTGGATTTTTCGGTTATTTGGGTTATG CAGTCAATAAGGAAATACATATTTACATATCGAATTGCGGGCATTGCGGA ATAATCTTTTCATTTCAACTTTGGTATTACTGGAATCAGGAAAATTATGG TGGAATAAGGGTAAAACATTGTCAATGAATTAATTTGGGGGAAACAAAGT TTCAAAGTAGGTAATTATAAGGAGAGTGCAAGATAGAAGGTTCCCAGTAC TGTTCACGGAAAACTTACCCATAACCCTGGGCGGGCATGTTTCATGATCT GGACCTGCAGTCGTTTGATAGAATAGATATTGGATTGATAAATTGTCCTT TTGCATTTTGGCTCAAAGAGGGTTCGAAACACCGCCGGAAGAGAAATTAT TATTATATATAGATAGCTATATTAAATGTTAAGTATGCCGCCACTTAGCT TCGGTTAGTTACAAGTAGTATACGTATTTATAGATAGAGTACAGACATAC GCAAAAGATATTGATTTATGGAATAGAATGTACAGAATAGGTAGTTTTGA AAGTAGTTCTAGTACCTAGCTGTATGATTTTTAGTCACAAGAGAGCTAAA CTGTTTGTGTTCGCTAAAAACTGCAACTGCTTTGAAAAAGAATATCATCA TTTCAAGTGTCCGACACTAGAGTGTTCGGAGTGCTAAACGTTTGAAGAAC TATGTATGTGCTACGGTTAAGTCATTCACACTTACAGAACAGAACGGCTA CGAAGTCGGTGTCCTCGATGATCTTCTGCAATATCTTGGCATTGACCTCC TCGATGCGATCGGGCAAGTCCATGGCCTCCAAGGAGGTGAGGAAATCGAG CACTCCTTCCTCGTCCATGAGATCCCCATCATATATGATGGGCTCCTTTT CCCTGCGGTTTTCGAGATATGGATTCGATTCGATTAGGTCTTGTGTCTTG TTTGTGGTGGGGGAATTACCTACCTGAAGTAGGTGAGGGCGGGGAAGTTC TTGATGCCATACTGTTTGGCTAGTCGTTTGTCGTTGATTTTCACGAAGTC CACACCGAAGGAGTCGGTGTCATCGTCGATTTTCTCGAGTTCCGCTAAAA CCTTATCACAGGTCACGCAGCTTCGCGCATCTGAAATCGTAGAAGCCGAG CGTGTGAGTACTAAAGATCGATTATATGTAGATACCGGCAGCGATTGACA GTCGGCAACTGCTGCATGTGACGCCACAAGAGACCATAACTAAATTCCCA TTCGAATTGAAAGCCCAAAGCCCAAAGCCCTGGCAGAAGTGGAGCCAAAT GCCGCAAAGATTATTCATTCCTATATAGTAGATGCAGGATGCATCATCGG ACCGCGCAATCGAAAATAAGCCTGAATGAATGAATGAAATGACAGCAGCG CCAGGCCAATTCTGTGCTATTAATGCGGCAGCAACTGCCAACAAATATGC TGAAATTCTAAATTAATTCATAAAATTCATGCGGCCACTATTAGGGAAAT GAATTGCAGCCCACAAAAGACCACCGTTGGCCCACGTCTCTACAAACGTT CTGGTTGGTTAAACGGCAGACCAGACTGCAAAATCGGAATCATTAATACA TCGCCGAGTAAACAGCCATTTCGATTGTTTGGCAATCCGTTCAAAACAAT CTTTCACTGCTTGGAAAGTAATCGCGAGTTGGCCGAATACCCCCCCCCCC TGCCTACTCCATACTCCTAATGCTGTTATTTACGGGCTCCAACACTAAGG TGTTTCCTGTGTACACCAGGTGCTTTGGAAAATCCACTGCAGGATGTTTG ATTTAAAATCATCAGAGTGCTATCGCATGCAGTGCAATAACATAAATAGC GTTCACTTGAAATAATAAACACATTTAGCTTATCGATAGAATTCGTTTAC ATATTGAACTATCTGCGATTTAATTGCCAAAACTATTCAATGCTCTGCCA TTTGCGTAGATATTCCATGATTATTTCGATTGTCGGCCAGCGTCATTGGG CCTGAGGCTTTTGGACTTAAAATATTTTCATTGTCAACAATTATTTTTGG AATTGCCGCCAATGCTAATGAAACACATCGTGAGGTATATGTACATATAC ATATAAAGGAGAATATTACAATCCGAAGATCACTTTCGTGTTTATTAACT TTGACATTGGGGAACAGCGCGCAAATGCCCAATCTATATTTAAACTGATT AAAGAGATTTAATAAATAAGCCATTCTTTCACGCGAACGGTAACCATTTT TTTTTTTTTTTTTTTTTTGGTTACCCAAAAACAGGTCACCAATGGGACCC ACTGGACAAGGGGATTGAAAATAAATTTAAAAGGGCAGGAAATCTGTTGG CAACTGCTGGAAGGAAATTAAATTCTGCTTCATAGGTATGTAGGTATATT TTGTGCCAAAAGTTTGCGCCAAAATAGACTAAAAAACCGAAAATATAAAA AGCTGCAAAGACGATTTCTCACAGCCAAGAGAGATTTCTCTACTCATAAA CAGATCGCAAAGATAGCGCAGAAATGAAAAAAATATAGAAAAGGGAAGGC AGCACAGACTACTGGCAACTCGGGGAGGAAATGAAGAAATAGAAAAAAAA TAAAAAATTAACCGAATGAAAATCGCGGACATTTCGAGCAACGAATTTTT CACATATTTTCATTTGTATGTGAATTTTTAGAATTTTCACTAGCGAAAAT TTATATAATATGGCTTCTGTTACTATTTCGAGTCCGGTACGGTCCGGTCT GACGATAAATGAGCGGTGCCCGGACGACCCCGAGAGCACTGGCATAACCA CCCTCCCACTTACACCAGAAAACGGCCACGTAATCCTTGTCGGCCAGGAG CTTCTCCAGCTGCTTGGCATTGACCTCCTCGATGACGGCCTCCGGCTCCG GAGGCGCCACTGGCTGCGAGCCCTTCTTGTTGTTGTTGTTGCCTGCACCA CTCACATGTCCGGGAAAACTCAGGGCCAGCAGAGCACACACGAGCAGCGA GAGAGTCTTGAGGCGGGTGAAAGTCATCCTGCGATCGGTTACGGTTCTGA TGTGCTTTAGGCCCTTAACGCGAACATGCGTGCGCGTGTCTGCTCGTTTT GGTGTGTTCTACAGTTTATAGTGTTATAATTGTATAATTGATTCGTTCTC GTCGTTTGGGGTCTTTCGTTATTAAAATTTGTATTCCTTTGAGAATCGGT CACTATTTTTAGTTGATAATGGTGTTTCTTCTTTCGCAATTTATTTTATG TATAACAACTTTTTGTTCACTGATACATATATACGGGGTTCGTATATGCA CAGGCGAGATATATGTGGGGTATATACGAGAATAATTAGATTATATATGT GGTTTCTTGCTTCTATTAATTGAACGTTTTCCGCGGACTGTACTCTTTGC TCTTCAGATTTTGTTCCACTCCGTGCAGAGGTCCGCTCGCAACTGAAATT ATTTTGGTGGAATCTCGGTGCCATTCAAGAGGCCTTGCCCGAGCTTTAGG GATCGGGATCGTGGACTTCGTGCTTTGGCGCAGCTTTTCCGCTCCCCCGA AAAGCTTTCGCGTCGAGCACAGGAGCGCCAATCGAGTGAGCAGTGTGGTG AAATCAGGCAAAGAGCAAGAGTTTCCCTTTTGAATTGCAGTTCTCTGTTT ATGCATTCGGTGCAAACAAGAAAGTGACTACGAATAGTCCTATAAAAACA AACTCGGAGAATCGCTTTCATTATGCGCTACAACAATTCACAGTACTTTG TATTCCCCATTTTCCCTTTGGTAAACACTTTTAACAATGTGTTTCGAGCT AACATTTTGTCAACGTTATGCTTAGTCTAAAATAGAAAGGATTAAACTTC CCTTTGCTAAGAGACATAACGTGACATTGTTGAATCTTTAAGTTTTATAG TTCCAAAAATCTATGCGTTTATAGAGATAGGAGGACATGAACAGATCGAA TCGGTTAATGATCCTCAATAAGAATAAATGTAAATTCTAGGGACGGAAAC GTTTCCTTCCAGCAGTCAACTATTATGTAAAAATCAACAAATATACCAAA TTTTGAATAGGATCTAGAGAATGATTTAAAGTTACTGTTAAATAAGCCTT CTCGAAAACTGTTGGTCATCGAAAACATGGAAGATGAGACCGGATTTACA AGTGGTTTTCTGTCCTTAATAGCTTTATTTGTATTGATTAATGTAAGAAT TCTCAAATTCTAAAGATTGGCATCAAAACCTGATCCAACTAATAATGAAT CCTTTTCAACTGGTTATCAACTATGACCTTTGTTAACGTCAAACCACCCT CGCGAATTATTTGGAGTTCGTTTCTGCAACACACACAAAAATGAAAGTCT CGGTATCTTGGTACCTGTATTAATGTTATGGAGGTTTATTCAATATTTTA CAATAAAGCTAGGCAAGTGATAAATCAGAAATGTTTTAATCAATTCGGAT ATGTTCAAAAAATCTAGTGATGCAGTTGCACTTTTTCTCGGAGACTCCCT TGTTTATAATTTGCAGGACAAATAAACAAAAATAATACAGCCTATTTTGG GCTTTCAAACAAACAACATGGCCGCCATTTGGATTTGAATAGCTATCGAT AGGTGCCGTCGGCCAGCTGACAATCCATCCACTGCCTATCGATAATATCT AGCTGAGCAAGATGTACGGATTTGTGAGCACACACTTTAGTTTTTCGTTA GGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGC AAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATA CCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGAC CAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCG ATCTGTGACGCGGTTTAAACCAAGGTAACTCCGCTATCCATGAATAAAAT CAGCTCTTCCCACGGGTGCTTCCGCCATGGGGCCACAGTGCGGGTCCTGT GGCCAATTCACCTTGAACCCAGTATTGCAGAAGGGGCCGCATACCAAGTC CAATTCCCTGCGCTTGTGTGTATACCTGCGCCTCTTCCGCATGTGTGTGC ATAAACATTGACGCCCACCCGCCCGATAAACAGCTGTTAGACCGATTGCC GTCCGCTTCCCCAGATTTCCAAGGCGGTCGAGGCGGAAAAGGGGAAGGCC CCTTATGAGCGTAGGCTTGACGGGGGCGGGCCCGTGTTTGTGGCAAGGCG AAGGTGAAAGTCATCAGCTGATATGGGCCAGCCTGCTAAACCCGTTATGC AGAGCAGCTGTTCGACGCCAACTTCATATGTGGGACAAAATCCCAGCCGC GAACTCACATACTGGGTTCCCCAGTTATATCCGGATAGCGGGCACCTCGC TATCGCAGGCCGATATAAATTAGAGGCTTTCGCGCTGCAGATGTGAGGCC TAATTGAAGATTTCTTTGTTCGTTCGCAGGCTGCACGACACTTCGAGGAC TTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGTAAGC GAACAATGCTTCATTACTCTCTCCCTCTCCGGACTATCAAATTATCCGCT GTTGAATTTTTGTAGGTACCAGAAGAGAATCGGCACCTATGACAAGCAAG AATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTC AATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGT GCGAGGTGTGTTTAACCTGACTGACCCCAAATAGTGCCCATAATTGAAAC ACATTTTTTAGGTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTAC TCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTAT GCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCT TGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACA GCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTG CTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGA GTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCC TAAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACC GCCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATC TGCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGAC GTCGCAAGAAGATTGTGCGGTAAGAACGAAGCTCTTTTCGGAACCAAATA TTGAATTCTTTTTTTAGAGTTCGACAAGTGGAGGCTGACTTGTCCCAGGC CAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATCG AAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTGT GCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTAT CAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGCC CACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAGA AAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACTG GCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCGT GCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGAA AGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGGA GGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGACA ACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGCT CCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTGT GACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAATG AATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACATT ATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCAC CGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCTG ATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGAA GATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATAG CAGCCTCGACCGTAGTATGTATTACCAACCAAATTTGCATCTTCGTTCAC GCTATAACATTGAACTTATAAAGTTAGCTGCACCATTTGGGATCAGCGAG ATGCCAAAAAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATC GAACGCGTGGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGT GGTCTTCTCTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCG AGGTATGTTGCCGGGAAGGTTTTGGTGGAGGAGACTACTTATTACTGGTC AAATGCACTCAGGTCACACTCGGGAGCGATGCAGAGAAGGCCAGTGAGAT TAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCATCGGCATCGC TCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTGGGAGCGCATG GTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCCTCATACTGTT CATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGCTTCCTTTACG CCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCGAAAGTCAAAT CTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGACCTGGCTGAG CGTGAGGTCGTATTTGAAGGTAAATATAAACATCCGCGTATTTCTTGATC AAAGGCACTGAGTTGCATTCCCCATAGAAACGCGGACCCCAGCGATCGGT GGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCT TCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTT ACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCG CTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGG TGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCA AAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGC CGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTG CCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTA TCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAAT CAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTA CAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTA GTTAAGTGAATAAATTTAAGCGAGCCAATGTTTATGCTTGTCACGTGATT GTTTAGCTACGTTAACAAGCCCACTAACGACTACGTAAACCAACAGAAAT TAGTATTTACCTACTTACCTTCTAGAGCGACCTGCACAATCACAAATCAT GTTTAGGCAAATTGTGCAATGCAATGAATCGCATGAAAGTTCATAGAACT TTAAGCCTAAAATCAGTGCACCTATTGTAGTTGGCTGTTCATTCTGTTAC AGTCCCAAGTTAAATTCCTAAGGCGGTCTCAGCTAGTGTTGCAATTAATA AATGTTAGTAAACTATAATAAAAATCTCGTTTAAAATAATATGCTTTGTC TATCTTACTAGTATATACCAATTGGATGTTTATAGCTGTGAAAGCAACAA ATTGGTTCTACCTTTTTCTTCATTGGATAGAAAGATCTGATCTAGATGTT AATCTTTAATCTTTGTTGAAAACTATATCCTTTTTTCTTTCTGTGCAACA CCCGTCTGCTCTTCGTTAATCGATAGTTGGCTCAATAGCGATCGACCAGC TGTTGCTGTTATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTC GCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACC CCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCT GCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGC ATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAGGTGCATATAAACAGG CTGTATTTATGTTTACATACCAGCTAAAGTCCAAGCTTTTTTAGGAAAAT GCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCA GGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGG GTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCG CCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGA GGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGGGT AGGTCTGAAAAATCCAAGTTGATCGAAGTTCCACATCAGAACTTTTAGCG CTTGCATAGCACATTCAGTCTGCAGAAGACAAGGTTACGCGTCATTAGGG TTAATTAGGTCGTAGATTATATTTAGATTATAATTATAGATCGGCATAAA TAGCCGATCCGATCTAGCCGTGCCCCCAGTCTGTCTGTTCGTATAAACGT AACGATCTCCGGAACTATTCAAGATATTTTGTGAGTCTCATAGTGAAGGT GGAAAATAAATAAATTGTGTACGAAATTTTTTAAATTATCAAAAATAATA TGCAATTTTCATTACAGAACTGAGTGTTTGGTGGTGGCCAACGATGCCAC TGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCG CTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATTTACCTTGTGGAC TCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTTTCCAGACAAACT GCACTTCGGACGCATCTTCTACAACCAGGCAAACATGTCGGCCCAGGGAA TTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCCGGAGGAGCTTAC GTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAAGCAGGGAACTAT ATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTGGAGAGGAAGTGT CTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAGACTTCTGGGGTC ACCGACCACTATGCCTTAGACGACGAACACGCCTTGTATCTGGCCCGCCA GATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGTACAACGATCAGC TGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACTCCGCCGTCTGCC GTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGGCATCGTAGGTCC CAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTGCGCGCATCGTCG ACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGTGAGACTTTGGTG TGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAATAGTCGGAAACAA TGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCCACTTCATTCAGT TGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAAAATATTACTGGT AAGTTGATATGTGGAGTGGCTGGGCGATTAAATAATGATATCGATCTATG TAGGCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGCCAAAAAC GGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCAAGTTCAC GGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATGTGCGGTC GGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCGCATCTCA GTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGA TCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGC TGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTAC AGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCG TCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGG AGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGA AATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACT GTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTG ATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAA CTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTT ATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACAC ACATTTAAATGTATAATGTATAACAAAACAATTTATTTTATTAGTATTAA GGGTTGTAAGAGTAAAACCAGTAAGATTGACACAGCTGGGATCAAACAAA GCCGCCTATCTAGTGCATACCACTGTTACACTTTTAGTGGTGTTCAATAT AAATATTTTCTTCTGAAAATAAATACGTTTTATTGCTAAATTTCATGCTG TCGTACATTTATAATTGTATTTTTTAAAAATAACAGTCGATATCGCTATA TAGTGGACCACGGACTATCGTTCATCTCTAGCGCCTATCGATAGACCTCC ATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCC TAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTC CTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAAC GACCAACTGATTAGGTGAGTTTATCACAGGATCCCACGATTGACCGGTTG AATGTCCACTGCATCCACAGTGTGAGTGAGTCAGTGAGTGAGTCTCTCTC CGTTTACATATATGTGTGTGTGTGTGTGCGGCTCCTCAACTTATTCGCAA AAAAGAAAAGAAGAAATCGCAAACCTAGAAGTAGCGTCAGCAGAAAAGAA AGTTCATCGGTATGTGGCGATTTAAAATAACTCTGCCGAAAACTTCAAGT GCACACTTGGCCGAATAAATAGCTGTACATCGCGGAGCCTGCGTGCGCCT GTGTGCGTGCCTGTGCGTGTGCATTGTATATTTAAATGTCGCCTGCTGCT GCTTCGCTTCCTCCTCCAAAAATAAAATTCCCTATCCTGGTTCCTTGCAA GTGTGAGTGACTATCATCTCGGCGAGTGTGTGTGTGTGTGCGTGCGTTTG TTTGTTCTTGCCACAGCCGCAGAAAGAGGCCGCAAAAATTCCGGTGCAGT GTACATATATATGGTGGAAGGTGCCCAACCCCTACTACCTCGTTTCCGAT GCTCGCGACGTCTGGAAAAGCGTGGAAAACATATTGCCTGAGTTTAAGCC ATCGTTTCGATGACGTCATTCTTCTGCGGCTTATCTGTCAAGCCCCCGCA TTTCTTCAGATGGCATGTCTGTGTGTGTGAGCTGTCCAGTTACCAATGAT TCTCGGACTTGTTTTGTTTTCCTTTAGCTCAAGTTACTATTTTTATTGGC TTAATTAAAATGGGCTCCGCCGACGCAGCTTTTTGGCCTTCCCGATGCTG CTCTACTAGAATGCCGGTTTCTTTTCGATTTCCACTCAAAAACACTGGGA GCACTCACTCACAGTTTCGAGCGGATTTGGCTCAATAGCATCGGAATGTT TATTTGTTGCTCAAACAGCTTATTGTTGTTGCCGCACTTCCACTCTCAGC AGATTGTATCACACCTGGGGATGTGGACTAACACATGTCCAAATATGATT CAAATATGGAAGTCTCTCCAAGTGGGCTAGAAATGAAAACCCCTGCTAGT GGCCCTGCTTCGCTCCTCTTTTCTGTTTCCCTGGTTCTGCTTAATTAGTT CGCTTTCAACTTCCGCTGCACGCGCCCACATCCACACTGACTTATCGACA GCCACAACAAACTACACTGGCCAAAAAAAAAAAAAACCATCGCCTGGGTC ATCAATTCCGCAGTTTCTCGTCTCCAAATGTCACACATCAGCGACTTACC AACTAGGAATTTTGTGGATATAATGATCTCCGATGAGTTATCAAGCATAT GACTCAATAGCACTCAAAATACGAATCTAAACTGCAACTCATTTGTTTTC CCCATCTTATGGATGCAAATAAGCATTCGTATCAGTTGACTTTAATGCAA GGAACTTTTTGAAACAGTCACTGATTTAAGAGGGATTTGACTGGAAAAAT ATAGCGCATTTGTTTGAAATTTCTTTAGTAGTTAGTTTTAAACTACAAGG TTTATTTGAAATGATAAGTTTTTACTATAAAAATTGTATTTCAAATAGAA TCTTGATTTTATAAATAGCTTTACTTTCCAGAAACTTAAATGTATTATGA TTATTGACTAATGTTATTTATTTAGAGTTTTTTGAGTCATCGAATTTCAG TCTTATCCACTTATTGGAAAATAACAAACCGGACAGTCTAAAAGACGACT GATAAAAATGCGACTAATATAGTAATATAGTAATAATAAATAGTGCAAAC TAATATAGTGTAATATATTACATGCAGGGGAAATATGCAATTGGAATGCG TAGTTTTTTGAGATAGAACAGAAAGCATATGATTTCTTCATAGAAAACAT TATTCCTCTGTGTAGTAATCCCAACTTGTATTTGGGACACTGCTATTGTT GTGCCTTCTCTGGCGGGGGCACTTAAATCAATAAACGAGCAGCAAATCGC TCCGCATTTGAATTGAAGTTTCGCCCTTTCGGGTCAATGCACCGTACACT CGCGCAGCGAAAAGGTGGAGAGTCGGAGTTTTACGGAAACACCGAAAGGC CCACGGCCGACGTGAGTCAGTGTATTTATAGGCCGGCTCCCAAATGCCGG CTAATTCTTTATCTCATCTGGCCCACGTCAGATGGCCCATGCCCATGCTC TATGTTCCTGCTGGCCAGGCTGACATTGATAATGCCAATGACGCGCTCCA TGAGTAATCTCCATCTTCGCGTCGCAACGAAGCGGATCGATATCGCCGCA TTGTAGCGGCGAACAGTCCAAGTTCATTGTTCGCCCGTTCCAGTATCCGC GGAGCATTTTCTTTCGTTCGATCGCCTTTTATGCTCTCGTAAGTGTAGAG ATGGGTCTGAAGAGGATTTATCTTCTGAAGTTCAGAAAAAGTGCTCTTGC GACATATCCAAATCCATATCTTGAACATTGACTAAAGCAAAGATACTGGT TACTTGTAAGGATAAAATTGTTTGGGGTCATGAAACGCAGTAAATCAGTG CATATGTACATATGGCACTCTGCCACTCTGTGTCTTTACGAATAGTTATG AGTGATTTTAAATATGGAATTTGTCCAGTGTGCGATTTTGGTTTCCGCAT TACGTATATTTTGAAAAATAACAGGATGGCGACTAAGTGGTCAAAAAACA GGCCTTGAGAATGTTGCTTTTCAGTAGAGATTTCAGAGGTAGATTAGTTT GTATAAGTCCTGCCAGTTGGTCACAGAGCGTAAAACGAAGTAAAAGAAAA ACGAAAGTAATTTGTACAGTTCGATTTCGTTTTGCAAATTGAGTTTTATC AAGAAAGGTTAGTTTATCGGAAATCCAGCCAGAAGTACGTCGGATATACA GAGGTGGTAAGTGCATCGGGCAGATTGGTATGCTGAATCCGGGAAGTAAG ACAATTAGCTTTTGGTGTGGAAATGCCTATTTGTGGTTCGGTCTGTTCGG TCCAGAGCTAACTAGCCAAACTACTTTCGAGGAACAAATTCTGCAGATTG TGGAATGAGTGAGCAACGGTAACATGTCCAATAACAATCATTTGGCGTTC CCTGTTGCCGTTTGCTTTGCTGATGACTATCGTGATCTTGATATTGAGCA CGCACATGGGACACGCTTCAATGCACCCCGAGCTAAAACAATTATTAGCC GCCGCAATTAAGAGCCGTTCATGGCGCTAGCACTCCCACACGGACTGCAT GTGGAGCCGCCACTGTGCAGTTACCAACTAACCAGCCTTTTGCATCTTCG TTTCAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAAC GTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCT AGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGC TCTGCACAGGTAAGTGGGCTTGACTCGTCTACAAAGTGCTGGGATCAACC TACGCTTCCACTTCTAGGTGCAGCTTACTGTCAGTTCATGGACATGCTGT TTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAG CACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGAT GTCTGTGGATAAGGTACATATGCCCGCTTGCTTACATTACTTTTCTATTT TTCGAACCTTTATTTAATTTTGACACACAAATCCACCCGATCCGAAGAAT GTAGAGTGGACATGGGCACGGTACAGTGGAAGCGCTTAAAGCGTCGCTAA AAGCATATGTCCACTGTACCAATATACTCTTGTATGTTGTGACTAACTAC GATTTCCGTTACAAATCAACTTCACGACTACGCAACCACCGACAACCACA GATCATTCCAGTTGATAAACTGATTAAGGGACGCTTTCAAGACAACTTTG AGTTCCTTCAATGGTTTAAAAAATTCTTCGACGCCAATTACGACGGTCGC GAGTACGACCCCGTGGCTCAGCGGGGCGGAGTCAAGCTGGGCAATGGCAA CGGACACGGCAGCAACGGAGGCAGTGGCGTGGGCAGCAGCAACAACGATC TCCATCTGATGCACCGGCGACCATTGCAGGCTCCAGCTTCTGGCGGACGA ATGCCAGCACGGGTCATCGCTTCAACTGGTACGGTTCTGTCGAAGCTACG AACTCCGGTGTGGAAGAGCCATTTGCTTGCCATTTCATTTGAGTTGCGAA GCGAACGAACGTGAAGCACGCAGCGGAACTAGGCAAAACTGGGATGCCAC ACAACACCACACAAAACTTCACCAACCCCACTGGCCTTGAGCTGCTGGCG CACCAAGTAATACACAAAATGCACACACATTCAGTCGCATCAAAGCACAC AGCACACATGTTGGAGGATCTGTTGTTGTCCCACATCCAACCCACTAACT CCTCTTCATCCCCGTACAGTGATGGGAAATACCCAAATATTTGTATTTAT ATAGATCCGCGACATGGACAATACTTTTGAAGCCATAATTACTTAGGCAT ATGTGGGCGGATTTCCAACTGCAAAGTGTACAAGATTTCTTTATTACAAG GTTAAACGCAAATAATAGTTTAGATCTTATCTTTGGAAGTGGCTAAGTCT GCGATCAATTTAACTGAAAATCCATCCCCATCATTGCAAAGTTATTATTT ATACACATCTTTTTTATCTGGTGCTTTGGCTGGCCAAAGAGTTCTGTTTT CCAAATTCATACTGTATGTTTGTTTAATCTTTGTTCCCATTGCATTTGGA TTCACCACACGCTCTCTCACCTGTTTGCATATCTCTCGCCCATTTTACTT TTAGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATT TCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGC AGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGG ATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCA GCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCT GCAGTGAAGCCCAGTATGTTTTGGTTTGGTTCCCAATTGAATCCTTCTAT CGCTATCTCTTCTTTCATTATCGTACGCACTATCCACATGATCAGACAAT TGTACATATCGCATGCCCAGGTCCATGTAGATGTTGCACATCCTCCAAGT AAACACAAAAGCACGAATAGAAGACAAATGCTGTCTGTGCTTCACGTTTG TTGATTCCTTATGCTTTTATACATACCTCCGACCTGGATGTTCGCATACT AAACTCAATCGCCTTGCCCATTCCAGCAGTATCCAAGGTGCTGCCGCGCA CGAACAACGCAGCCCCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACG GGCACGGTCAAGAAGAACGACGTGAGCAATTCGGTCAACAATCAACAAAT AGAAGAGATGTCAAATCAGGTGGGTCAAGATCAAGAAAATGAGAAAAAAA CCGGTACTAATATTATGGATCAGGTGATGGATATGCGCATAAACCTGGAG GGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGA AATTCTGTAAGTAATGAAATCAACAGGTTGAATTAAGAACGCCATGCCTA CCTGCTATTATATTTCTAGTTGCCAAGAAGCCGATGACGCCGAGGCGCAT CCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTAGGACA AGTCTGTACTCTTTTTACCCGGCCCTGCAATCGCTTAGACTTATATTTTC TATTTGCAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGA GGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGC ATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTT ATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAA CAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCC ACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCG TCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCAC GATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATA TTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCT AATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACA GACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGA TTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCT ATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGAC TTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAAC GGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAA AATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTAT ATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGA ACGTCTAAACACAACTTTTTGATTTCCGGCTTTCACATTACATCACTACG CACGGACAAGTTACTCCAAGCGGAAACTTTCACCCCTCCATTTCTCTTCT CTGATCATTGTAAATAATTTGTTAACACACCACACCACTCACATGATAGT CAACCTGTCCTTTCGACAGACACAAGTAAATGTATGATTATGCTCACACA CCACAGCATCGAGTGTGCCACCCACGCCATGATCTATAACCTAATTCTAG AATAAAAACATGTGTTGCTTGATTCAAAATTAATGCATTTCTCTTTTCGC ACACGGGCAGGGCCCTACAACCAATCCTAAATCTATTTGACGGCGCTCTG GATGTGTGGCTGCTTGTGGGTGCCGTCACAGAAGGGTCTGTGGGTGGTCT GTTTGCAGTTGCAGAGCCAGTAGTCTCCCGACTTCTCCACCTTGAACCGA ATGGGCCTGGAAAGCACAGGGGTATTACTTCGTCGCATAGCTCTGGCTCG AGCACCTATGTACATACCTCTGCTTGATCTTCAGGAACTCGTTCTTGTGC ATTCCATCGCAGAGGGGCTGAGACTTGGACTTGCCGCACAGGCACCAGCT GTATGTTTTATCTGTTGGAATCGCGAGTTGTGGTTATGTAAATACTTGTT CTCTGCGCACCGATACGATGCGATTTCTCAATAATACCTTTGTCCAGGTG GATCTTGAAGGGGCGCTTGTCGAAGATCGTACCGTTCTCCTTTTGCAGAA CGGCCGTTTGCTTATCCTCGAGCAGGTTACTGGGAATTGTTTTGGCCGAG TCCACCGGTTTTGCGCTGGAACTGTAGCATGCCTGCATGGGAGTAATGCC TTGAAATCAGGGGGTGATCTATCTTGGCTATGGGGGATGCCTACCTTGAG CAACCAGGATGCCCCCAGGTTCCGTCTTAGTATCATTGACATTCTAACGC TAATTTATTTTTGTTCTCTTTATTTAAGCTGATGATTGCAGTGTCGAAAG TATCGATATGTTGTCATCGGTGGTGATGGTGTTGCAAGGTCGTACCACTA CTTTTACCAAGCTCAAATGGGCTCATTGAGAGTATGGATAGATACTGCTT TAATTTACATCTAAAAGTTCACAAATATATGTCTCTTCTGGTAGCGAGAA AGAAAAAATGTTGCAGATTTTCAAACTGGGCAGTGCTGCCAGACCGCCCC AGCTGAATGCACAGTGGTGCAAAACGTTCGGGCTGAATGTTAATGTTATC GGCAGTCACTCCTATCGATGCTCTATCTGCCGTTATCGCTGCCCAAGGTC GCCAATTTAAAATTTGATTTCAGAATTCCGGAATCTGTTCAGCTGATAAG CAGAGATATGATTCCGATGCGCCTGGAAATGTCTCTCCTCGTTTGGAGGT ATTTTAGCGTCTATCGCAGACATTCATCTTAATGAAAGCTCGTTATGTGC CCCATACTTGACTAGGGAATTCTGAGTTCCGACCGACGGGTGCACACGCC GAATTCTCGCAGATAACACGATTTATCAAGCGGCCCCGTTAGACAAACTG ATTAGCCCGACAGCCCAGAGATCTTCTACGTAATATACTTTATTTTACAA TACAAATACTACATATGCGGGGTGTCTTACGAACCTCTTCCAGTAAAATA TTAAGGGGAATTAATGCACGGGTTTACTCGAAACCTTTTTAACTTTGAGT TAACAACTAAAACAAAACACCCCTCTTGGAATGCCACAGTCGTTTTGTTT GCATTCCTAGCCAATCCAATAACGGCGAAACCGATATTTCTGGGACACCC CTGAGCCCGTCTAGAACTCGTCGTTGAACGGGTAGTACTTATGGCCCGAC ATTCCCGAAAAGGGTACCGTGCGCTGCCCGGTGTGATACTGCTCCATGCC GGCGACGTCGTCTGGACTCAGCTCGAAGTCGAAGACGCGGAAGTTCTCCT CGATGCGGGCCTTGTTCGACGACTTGGGCAGTGGCACCACGCCTAGCTGG ACCAGATAACGCAGGCAGATCTGTGCCGTGGTGCGGCCGTACTTCTTGGC CAGATTCTGGGCATGCTCGTCGTAGAGGAAGGGCGGCCACTGCCGAGCGG GCTGGGGACGTGCCAGGGGGCAGTAGGCGCAGATGACCAGTCCGTGGCGC TTGGCATGCTCCCGGAGCTGGCGCTGCTGAAAGCCTGGGTGGCACTCCAC CTGGTTCACTACCGGCCGGATGCGGCAGTTGGCTAGCACTCGCTCCGTCT GCGCGGCGTTGAAGTTGGACAGGCCGATGCTGCGCGTCAGGCCCAGATCC ACCAGCTTCTCCATCTCGCGCCAGGTGTCCAGATAGTCCACGTCCGTCAG CTCCAGGGTTCCGTGCACGTTGCTGTCATTGTGGAACTTCTGGCCCACCG GCATGTGCATCAGGTAGAGGTCTACGTATTCCAAACCCAGGTTGCTAAGG CTCAGGCGGCAGGCGCGCTCCACCAATGCAGGGTCGTGGTGGATTCCGCC TAGCTTGGTGGTCACGAAAACCTCCTCGCGTGTGACCACTCCCTCGGCGA TCTTCTCGGAGATCGCCTGGCCCACCTCAGCCTCGTTCTCGTAGACGAAG GCGGTGTCCAGGTGCCGGTAGCCCACGTCGAGGGCGTGGCGCGTTGAGTG GTAGGCGTCCGACTCGAACGACTTCCAGGTGCCAAGGCCCAGAGTTGGCA TCTCGCGCCCGTTGTTCAGCCGGATGGTGGGAGCCAGATTGGTCATCTTG TCGCTGGCGCTGATAATTAACGCTGTGCAAATTGGACGCTTCTAAGTCTA AACCAGTGCTACTACGCCTTTCTCGCGATCAAATCTCTATCTGTTCCAGC TCGTCGAAAGCTTCGCGGACAACTGTTGGCTCGCACAGCCGGTTTCGATG ATTTTGTCACGGCGGCCGAGCAGCTGCTGTGTCATCCGGTGACGTCACGG ACAACGCGCGGTTATTCCCACCAGCGTTGCCAAGCTGGCCTTTTCCCACT ACATCTAGCGTTTTTCAAAAGCTCAGCGGGGGAGGAATTGCGATCTAAAA TCTGGCGCGATGTATAAAAATATTTCAAGGTACGCACACAAGTAAGCTTA ATTTTAACGTTTAAAAACATAAGAACGACATTAATTGAATTGTATAGCAT ACCAGCTATGCGAGGTTTTCTCCAATTGCTGAATCGATCGCGAGTGTATG GCAGTGTTGTGTCCAGCAGCGACTAGCGGGAATTATTCAAAGCAGATTTT TAAGACAAATTTGAATTAAAATCAAATGCCGTAAAGAGCAGATAAGGTGA GAGTAAATCAAACGTCTAATATCATGGACCAACTCCATCCGAAAAAAGCC CAAGTAGGGGGCGGTTTACATAGATGGAATTTAGAAAAGATCAAGACAGA AGAGTTGGCGGGAAAACGAGCAGGTAATTGTTTGGCTAACACAAGTCCAG GAGTGGTCATCTCTAAATGCTTAGACCTGATGGGATAGGAACTTAAATTA GTTTGAATAAAATTTTGTTTTAAAGCCCTTACGTGTATAAATTAAACCAA AAACTCAAAGCATTTTTAAAATATCACAGATTGAACTCCGATTCCATATT GCCCAAAACTATAAAGAACAGTTAAGCTTTCAAAAATAATATAGCGCCCT CTGAATACAAATAAAAAAAACCAGTAGCAGCTTGCTAACACATAAATCTT TATTCGAATATTAGTTGAGTTCAAAATGTTAGACATTCAAAGATATATTT TGTTACGCTTAGGTTCAACATTTAGGGTATTGAAATATCTGCTCTGCATT GCACAAATCTCACTTCGGGGTATGGGTTTTCTGGTTATTAGAATATGTAA TTGGTAGTACGGCTAAAAGATCGCTGCTTCTGCTGTACATACCATAATCG ATGGATTAATTACTTCTAAGTGGTTGTTGGTGTTGTCTTCTTACTGTGAG CTCTGTGAGCCGTCTCGTCATCCCCATTACGAACTATTTAATCTACTTTG CTATTTGGTAGGTAAGTAAACTTCGAGATTGTTTTGCGTTAGACATGTAA ACACTGATTTGAACATTTATTGGTTAGAACAAGTTACGGCTCAAACATTT ACTGACTGATTACGACTGATTGGCTTTAGCTATATCCTGTTAACGGAGGT ATATACGTATAGCATGAATATATCTTTTTTGTGCATCAGTGAGTTACCCA ATGATGTTGAATTTATGCAAGTGCCTAGGCTATATTGGAGAAAATAAAAG TTCGTAGAGTTATGTTTTGAGATTGTCAAATCGAATCACAAGTGAAATTG GAAATTTTCCCTTTTGGAGTACTTGCATATTTGATATATGTACTATATAG TATGCAAAGTGTATTATTGAAAGTGCACAACAATAACAATAGTGGTGGTG TATTGTTGGTATTACGTCTACATATGTAGCAGTACTAAAAATGTAGAAAC ATTTTTGGTTTTGACACGTAAGGAGTTTCCGTTGTGGGAAACGATTTCTT AACACTAAAATAGTTTCTACGGTCCATATGCTAGATTAATGCATCTGCTA GATAAATATTCCTAGGTATGTGTACTTTTCTTGTGCCATTAGCACCAAAG AGTTGGCTTATTTCGAATATTTCCTCAGAGGATTGTAAGATTGCGTTGGG TTTAAAACGCCTACACAATTCTATGTGAGTGATTCTGATAGATTCTACCC GTTTCCGTAGCACGTGGTGTAGATAAAGTAATTAATGGCTTTCCAACTCT ACTTACAAACTGTACCATACTAAAATTGGTGTTGCGTTGCTTGTAAATCA ATTCGAAATTGTTACATCTCATTAACTATGAACTAAAGAATATTGTTTCG TTTGAATCGGTTCGTTATATCTATAAAAGTATTATTGAATATTCGTTTGC ATTTGCTTTGTTTTATTTTTGAAGGAGAAACCACTGGATTATAGTTGAAT ATATTGTTTGATTTTGATTGGTTTTCGTAAAGAAAAGTATTAATTATTAC GACATTTACATTCTACGCATCATGGTCAAAGTTTTGGTTACATCTAGGAA TGGTGTTTACGTGATAAATCGTTGTTCGAGAGACCTTTACTTGGGAGAGG AGTTGGGTTAGATTGGTAACTACAAGTACAATTACTGACTGAGGTTGGCT AATGAAGGCGAAAAATGATATAGTCGAATCCCCGACCTAAGGATAGTCGG TAGTATGTATTAACATACCCCGCCATTTATATAGAGTTTTTCGGAATTGG TTTTAGCAAATAATAAATAGTTTAGTTTATAATTAAGAAAAGTATTGGCT TAACCAAATATTAAAACTACTGATGATCACGATGCTTGGGCATTTTGTTG ACGCAGACGGACGTTCTTTGTTCTTTCTCCGGTCGGATCATATATAGTTA GTTCATAGGATCAAGAATATGCCCCTCGTTTTCTACTGCTACCGACTATA GTAATTAATACCTTGGATATAAATACATACATACATATGTTGTACAGTTG TGTTCAAAAAATAGGTAGTGTCAAAGCCACGATTTCCATAATTACATTTT ACACTTGGTGAAGAACCACAGAGTTCCACACCCACAATTTATTGGACCTA AGGGAAATCCTTTAATAGTTAGAACAATTGTTTGATTGCATTTTCATTGA GAGATCTAACAACGACTATTTGGATAAATACTCCCCATATTTAAAACACA GTTGCACGTGTAATAAATACATGTAAATATTTTTCGTATTTCTATATATG TATGTATGTACATAACTACAACTAATAAGGTCCCTCTCCAGTGTTTAGTT ATTTGAATGCACTTGCATTTGCACTTTCTTATCTAATGTAGCATAAAAAA GGCATCCACTTTCTACAAAATAAAACGAATTTGGGCTGTGTGTAAATAAA TATTAATAAATGGTTTCGTATTTTATTTCCAAGTTGCCGTAAAAGGAGAT GGGGTGACGGAATACCAAATGAAAATAAGATTGAAAACTATAAATAAAGT AACTTATCCGCTACGTAGCTTACTTGTTAATAACTAGCTGTAACTAGACT GTTTAATAGTTGGTTTTAGTTTAGGGTTTATAAAAATATAGATTCCATGC TCTCGAAAACGTTGTACAACTTTACAAATTATTCTACCAGCTCGCGCGGG ATTTATAGAGTAATGGTTTGTGGGAAATTATGCTGTATAGTTGTGTTTGT TTTGATGTTGCCTCCTATAAATGTTTAGTATCACACACGTCCAAGTTTAG TTTTTATTCGTTTCGGTTTCCGCGGGGAATTGCCGAATTTCAAATTGTTT TCCATCTTTTCCATCGTTTTGTACTAAAGCAAAAAGTTTCTCGTTTGCAT TAAAATGCGTTTGGGTTTCAGTTCATTAGAAGATTGAGATAGTTCCTAGT CGGGTCGTAGATATAGTACACTGTAGCTTAGGCTAATGCGGATGCGGATG CGGACGAAAGTTGGTCCGGGCTGTGGTGGCCGTGGCCCAATTGGCTTTCG GAAAGCAACAACAACCCGGCTAAGCTCATAACTGTGCAGCTAATTGCGGT TGATTAACACACACTAGGGTTAGACACTTAATACGCGCTACAGGCTAATT GGATGACAGCTCCACAAGGGCTTAGAGCTTCCTGGTGGGCTCCACCTTCT GGGACATGGCGGTGAGTACCCGCTGGTTGTCGATGACGCGGAAGCTGCTG ATGTACGACCTCACCTCGCCCTCGCTCTTCGGGGACGGCGGCTCTAGTCC TGTTCCAAATCGAAATCGATGAGCAAATTAATTTTCAAAGGGGGTTTATT GGTCTTACCCAGACTCCTGGAGCGACAAAAGCGGATGGTGCGCATCGTCT GGGCCATCATGTGCATCTTCTCGAAGTTCACCAGGCCGTCCAGGCTGGTC TTGTTGCCCTCATGGGCGAAGGTCATGTCCTTGAGCAGGAGCGGCATGAA GGGAATCAACGGCGGCTGCAGCTTGCCCACGAACACTCGGTACGCCCTGT GGTTGCGACTGGGGTCGATCAGGGCCTCGAACTCCTGGAAGATCTTCCTG AACTTCGACGGAATCTTTTCCCAGGTCTGTTGCAGCCTGGACACCGCCAT GTTGGACAGACCCATTACCACAGCGAAGAAGGCGTTTAGGTTCTGGTACT CCTTGCAGCTGTAACGAGATAAAGAAGCTAGCTTACTACTCTGTCTTTGG CTGGAATGGGTGTTTCTCTAAGCCTAAAAGTGGTGATAGTGTAATAAGAA TATGTATTCAGCATTTAATTAATACTATGGTACTAATTTATTCTAATAGG AGCCTATAGTGGGTCTAGATCTATAGTAGTTAAGATCATGATTTTTTGTC TTCAATATACAAATATGCTTCCAAAGAAATATACTCCAATTTTATGTTCA TGGTAGCTCACTACGCAGTTTAATTAATATCTACAACTTACTACGCGGCC AGCTTGATGAACTTCCGGACCAGACCGACGCGTTTGCTCAGACTGGGAGT GGACACCAGTTCGGTGACAATCCAGTACTGCACCTCGTTGAATCGGCGCA GGAACACATCCAAGTTGGCAGTGATCTGCGGGTGGAAGTGTGAAATTCAG TCAGCATGAAAGTTGTGTATTCTAAACGTATGTCCCCTTAGCTTTGGGCC ATCTTTAATAAGTTCGACTGGTAAAACTCTGGGCTAACTCAATTTGCAAG CAGATGACAAATGGCTGCATTTTGCGGTCAGAGCCTGGCAGGATAATTAC CCAAACGAGACTTCTGAGACTTTTCGGCAAAGTTTGCCTTCCTACCTTGC CAAAGTGATGCCGCCCGAAGGTGTGGTAGAGCAATTCGTATTCATGGACG GCCCAGAAGAGGTCCCACTCGAACAGGGTGATGTGGTAGGCCAGCTCCTT GGTGCTCAGTATCTCCAGGTCGATGTCCACACCCTCGGTGGGGCACTCCT GCTCCTGCAGTTGGGTCTGCGGAATGAGCAAGTATAAAAAATGGTCATCC AACATCCAAGTTGGTCAGCGCTTACCAAGGCATCCAGGTGGTCCTTGACG GAGACGAAAAGGCGGCCGTTGAGCGACAGACCCGTGGGTATGCTGACATC GTTGTCCTTGAACACGGACCGCTCCCCGTTTGACTTGACCTCGACGAGGA CGAGATCTTCGGGACCCCGATTTAGCTGCAGCTTGTCGGCGGCACACGCT TTGATGAGCTCCGCCGTGGTGTGCATGGGGAATCGCAGGGTACAGTAGGT GTGGTCGGCGCAGTAAACGCGGAAGATGACTTAAAAAGCAGAGTTGAGTT TACGATAAGTGATACTAGTGTATTAAATCACTATTGAATGAACACCTACT ATCATCATCTGGTCGGATGACCGTCTTTGAAGGCGTCGCATTGCCACTGA AAAGGCAGATGGGCTGGCCGTTGGGCGGGAGCTTCCACTTCTGGCCGGCG TTCTGGTTGCGGTCCTCCTGGTAGCGCGCCATCTGGGTGAGCACGTTGTG CACTATGCTGGTCTCCTCGTTCAGGTCGGGATCGGCCTCCACCTCGGCGG CGAGGTCCTCGATAAAGTCGCACACGCTGGGCTCCTCGAAGGCCGCGTGG CGGACGGCCATGACCCACTTTTGCATGAACTGGATCACGCGCTTCTTAAA GTTGATTATATACTCCCGATCCTCGGGCGTTTGGGCGTCCTCATGGGCAT CGCAGTGGAAGGTGCACGGCGGTTAAGGCGGAAACCAATTTCTTTTGTGA TTGTGAATCGTATTTAGAATGGGATTTGCTGGGTTATGAAAATCTGTCCG GCGCAACTTCTTACTCGCTACCTTACAGGGTCAGTCAGTCCCAAATTGGG CTTCCCATCTTGGGAATCTGGTTATTGATTTCTTCCAACCTTATTGCTCC GCCCTGCCTGCTTATTAAACTCATCACGTATTTCGATGCAGATTGTGAGA TTAGTTTCAGGCATCATTGACCAGAGCTCTCCACCCCCCCCCCCCCCCCA CCGTGCCCGCGGACCTCTGGCAACCATCCAACATCCACCTTCACCCCCAT TGAAGCACCCCGAAAATGCTGACCCAAGTCATCTTTGCGGCTTTGTTTCA ACTGAAGTTGGAAGCGGAAGTGTTGCTTGTTAGCATTTTCTGCTACACTC GAGCCCAAAAGCCACCCGAAAGTCCAGGCCACCCGCACCCACTCCCGCTG GTCGGGATCGGGGTCATGTGTGGAGGCTTGCGTGCTGGCGGCACTTAAAC TGTCGCTGTGGAAATGTTTTGAATTCCCACCCAGGAGAACGTGACTCGGG CGCGAGATGGACGACATGAAGAGTGCGTTTTTGCAGTTTAAGTGCAGCCT GACTGTCGAGGACCTAGCTAAACGGACCTTGGAAACGCTAGGCTTCCTAC ATGGGGATTTAAAGAGCTTCAAGGCGGGGATTAAGCTGGAATTGAAAGGG GGAAAACCTAAAAGGCTTACGGAATTTTTTTGGTGATTTTTGTTGTTTTA AAAAGGATATTAATTGGCCAATTCATCAACCAGCTGAACGACGGGCATGA AAACGATGTGTGTGAGCAGGAAGTCGTCCAAGAACGGATCCATTCCACCC ACGGACTGGCCCAGTCGCGTCTCCAGCAGGTGCTCCAGCATCTTGGCCGG AGTTCCCGACATCACCGTATATCTGTGGGATAAGATATTCAAATGTATCT AGATTTTAAGGCAAAAAGGCCAGGTATCTGGGTTTAGAAGTTAAATGCTG CTTTAACTAAGGGTGCTAAATGGGATGTATTTTCTTCAACCGAAGATGCC AGAAGGGAGAAACAAAGCCTACATTCTGTCACACAACCGTAACCCATCAA ATCAAATTCCTACTTCCATTTAAATTTGAAGGCACATTAAAAATTGATTA GACACTCACTTAAATGCCGAATGCTGTCCACGTTGCTTAGCCACGCGCTC GAGCACTAAAACATCCTTGCCGTGCTCCTGCAATCTCAGAGTATTGGCCT CCACATCGCGCAGTATCCGGTTGAAGTGTTCCTTGTCCACGCGCAGCAAG TGGCAATTGTTCTCCTTCAGTACGATGGTAGCAGCTCTGCGGGAAGAAGG TCGGGGAATTAGATGTCTCAAGGATCTACCTATGGGATGGATGTGTTTCG AGGAATGTTTGAACAGCAGTCTTGTGACTTCGTCCTGGTTAGCCACACAT TCATATGGTGAAAACGCGTAAATAGCCATAAATGTGAGGCAGCCCTCGTG CACTTGATGGTTTGCCAACCCCCCGCAGAGTCGGAAATATTTTAAATTGG ATTTCAGCGGCAGATGCACATGCAGTTGGCAAATAAACTCAATTGATATA TGCAGAATTATTGCCGGTATGCTGATACGAGCGACGTGGATGGAAGCGCG ATTTATTATATTTGTTGAAGGCAAACAAGCTCTTTGACTATTTTAATTAA CACAAAAGCCGAGTGGGAGCTTAAACTAGTTATCCTTTCATTGGAGCATT AAAAACGGAAGTGCACGCATACGGACTAATAAGCCTGCAGACAAACGGAT CCTGACAGTTGGATTTCCTCTGCTCAGCTGGGGAGCTCCCCACCCATGAA CACAATGGAAACGAATTCCATTCTTTGGCAACTCTTTGATAGTTTCTGCC TTTGCCATCCGCTCAAGCGTCGGCTGGCGAAATGGCTTACAAATTGGACG GGGGCCTTGGCCGATACTTTGTTTCTATTTGAATTGTTTGCCTTAAAATC GCACACAATGCCGCTTGTTGTCTGTCGCTGTTGCGGAGGAGCTTGTGGCC AGTTATCTCGACCGTTGCACCAAGTGGGCTGTGGTATAACTTGTTTGGCC CATTGTGGCTATGCGGCCATTGTCCGTTGAGCTGTCAGCCAGGAGGAGGA GGTGGGAACCACAGAAGGGTTCAGCATGAAGGGTTTTGGTTTCTCACAAC TTTTGGCCGGAGAGACGGACCAGCCAGTTAACAATTGCTCAATGGAATCG TCGCAATTGGTGCGCCATCACTCACCTGGGTGCGTCGTTTATCAAGGCCA GTTTCCCGAAATCATCCCCAGTCTTCAGAGTGGCAACAGTTCCCTTGCCG TGTATCACAACGTCTACCGATCCCTTGAGTAAGATGTACCAGGAGCGTCC TTCGTCGCCTTGATTGAATACTGTTAATGGGTTAAGAGTGTTAAGGGATA AGACTCGTTGTTAGTACTTATAGCTGCGTCGGTGTGGGTTGGCTGACCCA TTATTGAGCCATAATTAGCCGGGGCTTAATTAAAAAGTTTTCCAACTTCT CCCTTCCCTCCCTTTTCCACCCTTTCTCCGCTTTGGAGAATCTCAACTGC GCCGCCTGGGAGCTATTAATCCTGCGGCCGGATACTCACATATTGTTCCC GCCTGGGCATGAGCCTCGAACACGAAAATCGACGACAGTTCCCGCTTTAT GCTGGTCGACAAGTGGGAGAGTGCGGCAATGTGGACCAGTTCCTCGAAGA CCAGCTCCAGCTCCTCCGATGTCCGTTCGTGAGAACTGCGAATTAAGGAA TATAAGAAATGAAGGGATCTTAATCGAATTTACAGGTGAGAATTCATTAT GCGGACGCAGTGCAATGTCCTTTTTATATATATTTATATTTGAGTATCGG ACCCAACTAATGGCAGTAAAAGACTCATACCTATGCTAATATTAAAATAT TTTAGATTTATTATCTAAAGTATCTATCTTTCATTACTCTGCCAATGCAA TATCATTGAAGTATCTTTGTAGTAAGTTCAAAGAATTAAAATTGTAACAA CTGTCTTGAATACGAGAATGTGTGAGTATGGGAATGTATCGTTGGTAAGG ACTTAATTTGTGTTAATTGGTTCACCGCGTTGTTTCAATAGTTCTGACGT CTGTGTGCGGAAGTAATTATGCGTCACAAGTAAATTATCCATATTGCAAA CGTCCGTGGGAAACGGACGTAAATTACTCATTGAATTATAGTATATTGCA CGGTTTTTTATTACTTTTATAGGAATGTTAGTATATACATTAAATGCTTT ATTTTTTAACCCTAAAACCTATTCCCATTAAAGCCGCCGTACTTACGGTT TGCGCAATATCATACGCAGTGTGGCGTCCGGTCCGCGCTGGAAGAGTGCG CTGAGCGCCTCGCGGATGTGCTCGTTGGCCGCTCCGAGGTCCTCCGCCTG GGGCACGCCCGCTGCCGCCGTGCCGCCCTCCTCGTCGATGCGAAAGCGGT AGAGGAAGCACTTGTCCTTGAAGGGCTGCTCTTTGTTGACTGCGGAACGG CACCGATTAGGGAATTGAGCGCGTGGAGTCTGATGGAACTTACCGTGTGC GAGTACTCCTTCCTCGAGGAGCGCTTGCCACATGCCAGCCGCCTGGGCTC GGGTGTGGACGATGGGCGAGAGGTTGACCAGCCAGTCGACGAGCTCGGTG CCGGGGGCGCACTTACGGATTAGCTTGCCGGAGACCTATTCAGGTGGCAT GATTAGCATCCCAATGATGACACCTCCCACTCCGGCACTCCGGGCACACT CACCTTGCGATCCTTCAGACAGCTCGAGTTGTCGGCGACGAGTAGTGTGC GTAGGGCCCAGCCCATGCGGTTCATAGCAGGACTCGGTGTCTGGAAATGT CAAACTCTTTCAACTTCCGTTCTCGAAAGTCCGGAGCGAGTGTCAAAGGC AGAGGAAGTGTCCCGAAAGGAGACCCTTCCCCGCGCGCCCACTCATGGAA ACCACATAAATATTTTGTAATTCCCCTGACGGCCTCTGGAGCAGCAAATT AACTCATTTGTCGTCGTCAATGTCAGGACATTACATTTGTGTTATTTATG CGAGTTCCACGGTGGGACTCCGTTGGTTTCTTTGTGCCCTTGGCTCTTAC CTCGGTGATGGGCAGCGCTGGGTTTGGGTGGTCGGGGCTGAGGGGTCGTT TCGTGGGCGATGTGGCTGCGGCTGTCGCTTGTACGCTCGGTCCAAAACCT GGAGAGGCAGCCATAGTTCAAGTTAGTCAGTTAAGTTACTTTAGTGTTAC GTTCGATAGCTGAGCACAGGCAGTTTCAAAATGATGTGAATGCCGCATTA ATGAAAGTTCTCAAAGCCAATTATCGGATTAATGGAGTGTTGAGCATGAC GCCAGTATAAAATATGTTTTTCAAATAATAACAAAAGCAGATACTCTCCA ACCATTAATCACCGAGTGCATTTGGAGTGTTAGTCATGCGAAAACTTTGT GATAGACTTAATTGGATCTTTTGTCTACATACCGTTCTTCAACTTGCAGT TGGTGAATATGTCATTCATTAACTCCTTGTTTTTCTGCAATGGAAAGCGT AAATGGCCATTAGTATTGGGTGTTTCAGCCTGGTTCAGCTCTGCGATTCC CATTACGTTGCTCATTTCAAATGCCGTCGACTGCGGACGCGTCATCTGCC CACGCTCCAGCTGCCTACGCCACTTGACGGCGGCGGAAGTGGCGCCAGTT GCGGCCTTGGTGGCCTTGGAGGCCCCTAATGTGGCCCCCACCTGGTCATC CCCGCCGCTGTGGCGTCGGTAGCGAAGCAGAAGGACGCCGGGACTCCGCT CACTGCCGGCCACGATCTGCGTGGACCAGCGCTGCCTGCCGGCTGCCATG TGGGGAAACCTTTGGCTTCACTTTCACTTGGGAGCGGAGTTCAAGCTCGC AGGTAATTGCTGGCAAACGCTTCTCCAGGTACTGATAGCGTCAGGAGGCA ACAATCACACGAACGCCGCGGCTCGCTGTTTGCAATTACTTATCAGGCAC AAGGGTTGTCAAAGCCCCAACATTGTTCATGATTCAAACAACATCTTTAA CCCAAGAAGTGACAACATTCTAGGAACCTTAAAGGTCTTATAAAAACTTT TTAATTAAGAAACTTTAAAAACTTTAAAAGTTTCCCCTAGCTCGCATAAT TTTAAATTGATACATATTTAAGAAAGTAAGGATAGCAAAATTAGTTAAAT ATATACTGATAAAGGGTCCATATATAGTATGAGCAATTCAGCTGGTCTAA AAGCGCAATTACTTAAAATCTAATTATAAATTGTAAAATTATATGGATGT AACTGTAAAAAGGATGTACATTTCACAAAAGTATATGGTATGTACTAAAC TTTTACTGGTTTCAACGGTATCTGACAGTCGAGGCGATCCCTTCTGTCTA TTAATTAAACATGAAAGTCAAATGTTGTACTCTCGCTTTTTTCGATTTCC CGCACTTAACGAGACTCATTAGCTTGAAATGGGTTAAAATCGAAGCCAAG ACGCAACCTGGCAACACTTCGTGTTCCGCCCGTCGATAAGCGACTTACGC TGCGTTGGCGTCGCCGTCGAAGCTAATTAAACTCGCTTGCTTATCAAACG CACGCCGAAATGAATGCCACCCACTGGGTGGCGTAGGGCTTTCGAGGAGC GGTGTAGCAAGAGTTCCAGATTTCCTTCGCCTTGAAAGTCGGACGTGGTA ATAGAACCGTGATGTTTCCTGGTAAAGGAAACTTTACATTGGCATTGACT GATTAACGGTCCGAGGTTTCATTAATATGTATCATATTGAGCAAACTGAG CAAACTGTAGGAAAGGAAGACCTTTATTCTAAATAGGAGAAGAATTCTCA TCATGCCAATGTTCTTATTGGTGAAATTCAGCAAAGAATTTTGTTTAACT AAATTTTAGTCGGTACCACTATCTGAGACTAAAGCTATTTGAGCTGGAGT GAATATTTCTTATCAGCCTAAATGCAAACAAGTTTTTATGAGGCGTGGTA CATTGTCATTTTTAAGTGTTTTTCGGTGATAAAATTGATATTCTCGTAAC TTGTAGTGCAAGAGGATGAAATATATTGGTTGGAAAGCATGCAAAAGAAA AGAAACAAATGTGAATTTACAAATACTTATCTAACTGCAACTGGTTTAAA ACCAGTGAATACACTTTCCTGCTTATTGTTTTTGCTTAGCATTGAATTAA GCTCGGCTTAAAGAGTTTCAGTTTTTCAAGGGAAAGAGAGCGAAAAATAC TTTGTTGTTATTAAATTATTAAGACGATGGCCCATTTATTTCTTTTCACT TCCGCAACGCAGTAGAGAAAATCACAAGGAGCTTTTGAGCAAGCAAGCGA ATGCTTTCCTGGTAGACATTTAGGTTTATACTTTCCGTTCAATGGAACAA GGAATCCGAACCATCTGCACTAATAGAAGGAATTTCTTGTTTCTTTCCGG CAACTTAACCAAAGGGAAATAACACTGCAGAGTGCTGCAGGACTTTCGAG AAAATCCCAAGGATTTACCGAGAGTGTGTTCATTGAGCAGTGCTCGAAAC ATTGATGAAATTAAAATTGATCGACGCAGCATGCACGTTGATGACTCCAG TGAGTTTGTGTCCCTCCTCGCTGAAGGCTTTGAAATCCTTTGGAGATCCA GCCCTCTCCTCCTCACGCAACTGGCTCCCTTGCGGGTTCACATGTGCAAC TTGTGTTTGTGCATAAATAAATAACCTCGTGACCATGGACATGCAACTGT GCATGCCAAGGGGCTCTCAATGGAGCCGGCTGCAATATTTATGGCCTGGT TATTACGCAGACCACATGTTTGGCAATGCCGTGGTTGCGACGGCGGGCAG AACATATAACACGCCCGGAATTAAATGCAAATATTTCGCAAGCAAGTGGC ATTGAATCGCATCAATCGCATTGAGTGTGAAAGTAGCACATTCGGCGGCA ATCTGGGAATTTACTGCAAGTGGCAAGTGTAATTTCCACCATTGATGCAA CTTCTGCATCCGACCTGAGCACAAATCGGAACCGGCTACTCGCATTTTTC CAATCCCAATCCCTATCGCAATAGCAATCCCTATCCCGATGCCAATTCCA ATCCGAGTGAATTGCTTGTCCGGAATAATTGGCAGCCATTGAATGGTAAG TGGCTGTAGTAGCTACTTGGACTGGTATTCGGATTTGTGCCCCGGGCTTC GGTGAAATGAGACTGGTAATTAACCCGAAATTCCCTTTCACCCGCCACAT GCGACTACAATGGCTTTCAAAGACATTTTTAATTTGGTCCTCACAAGCAA ATATTTGCGCACAAATCAAATGCTCGACTATGCTGCAAAGTGGGCGGGAC GAGCCAAGGATGACAAGTTCCATGAACTCGATGGCGTATATCCCTTGCGC TCTTGCGAATATTTCTCTTATTCCCCTTCAATTTGCCCCCTGATTTTATC GCATTTACGCAGTGCCATTCGCAGTGGCAAAACGCCCCCAGTTCGAATTT TTATGGTCTTGCATCCATAGCATCCACAGCATCCGCCATCGACTTTCACT TCATTGTTGCACACTGCGTATACGTGACATGTGGTGGCCCTGCTGTCGCA GCTACTTTGTTATCGTTCAGTTCAGTTCAGTTCAGTTCAGTTCAGCTCAG CTCAACTGGGCTGCCTCTGGGGTAAGCCAATGCTGGCATAATGTTGCAAA ATGCTATTCGCCCCGAATTGGGGCTTGCTCCCGCTCCTGCTCCTGCTCAT CCTTCTAACAAATAAGGTAAACAGACGAACCTCACTAATTCTGGTTGCTC GCCTGTGTGCCGGGCTCATATCTTTTGTGGCTGCCGCAGGAGATGACTTG GGGTCCTGGCTGAATGGCATTGTTAGTGGGGTTTCTGAGTACAACACACA CTTTTCACATTGAGATTTGCATTCGGACACTGGCAGAAAGAAGGTGTCGA GTTGTTGGGGATACTCGGGATATCAGGTCCTCAAAGCGATGTATTTTGTG TTTGGCTGGCATCCTATGGCTTACTATTTATTTCTAGAGTATTTCCAGCT TCCGTTTCGCTCAGTGCACATTTTGCCGATTGTGTGTGTGGTCCTCTCAA ATATTTACATTTTGGCATATGTAAGCCATGTTGTGTGGTTGACTGTAGTC AAAAAGATGCTTAACCACATTCCAGCCTTGTGGCATGCCAAATGCAAATA TAATTCATTTTCCGTTCAAAGGCATTTCCATGGAAATTAGGCCAATCGAA CCAATCCGAATAACCAGCTCGGCTCACCAGCAAGCCTTTCCAATTAATTA TCCAGCCCCCAGAGTCCTGTCAATCCAGCCAAGTGCGCGGGAACATGCGA CGCGGATACAATGATGCATTGCAATGCTAAGCTAAGCCCGCCATTACCTT CTAATGCCATTATCCATATACTCGTAAGTAAAGGCGAAACAAAGAATTAC TTAGCCCACGGGGGAACTTGGCTTAATGCCCCACTCTGTGGCAAAGCCAG AGCACTTAACAAGGCCAAGGGCCCAAATTACTAGCCATGTGTTTTAGGAC TTAGGCCGGGGTTCGTTGGGTAATATGTCCTCGGGCCCAGGCATCATTAA ATGTTAATTGAAATTTTAATTAAATATTTTCCACAATGACGAAGGAATAC CGCAAATAGTCGAGGCCCGCTTCTCGAATTTCTGCATATCATTTTGGCAA CTCATTAAAAGAACAGAAGTGCGCGAAACAGACGGATTGATTCCTTTGAC AGAAGTGGAATGTGCAAGAACAGGGGCGAAAATCGATTTGCGTAACTTAC TACCCCAAACTTACCTCCCAGATGAGTCGAAAGTCCTGCTGCTCCACCCG CAGCAGCTCGCAGGTGGTCTTCGTCACTACGGTGCTGTCCCGCGGCAAGT CATGCAGTACGGACTCCCCGAATGTGGCACCCACGCCCAGGTTGCACAGA GTAACTGCGCTCTGAAAATAAATAAGGGCAGAATATAAAGTTAGACAGCG CCCAGGTTGGACTTAAAGTATGCTAGTTTCTGTTCCAGGTACTCCCCGAA TGGAAAGAGCTTAAATAATAGTTTACCCAAGGGGAAGAGAAGCAACCGAC ATTTGCAGCTCAGTTTTGATATTTCAGCGATGTAGCCACGTTTCTCCATA AGCATTTCTAGCTCAAATTAAGAACTTTTATTAGCAAATACCTCATAATT TATTTTGTAGAACCATTTAGTTGAACCATTTTAGTAGAACCTACCCTTTT TGTATACCTAATACTTTATCAACTGAATGATTCCACAACCCAGCTAAGAA ACATATTATGTTAAAATCTATAAATGGTATTTTGCACCACCACTGCGAAC TCAGCCATGGGAGAGTGAGGGTATCCGCAAGTTGGAGTTCGAAAATGCCC ACCTAGATACATCTCTGCAGATTAAGCACTCTGTGGCGGCATGGCTGCTC CAGTCTTGGGCTTGTCTTTCGCTGGCATCTTACCCAATTAACGCAAATGG CCGCAATTTGCTCGTGGTGGCAGGGACAAACATTTGCTTAAAACTCTGTA ATCGCTTCATTGTCGCATTTCCCGCAAAACCACGGGCACTGAAGCACCAC AGCGCCCAAATGCAAGCCGGGAAATGGGGCCGAGGAGGAAGTGCAGCCCA CTTCACTGCTTCGGATGTAACGAACGCGGATTGGAGCTGTCTAACCGCAA CATTGCAATGACATTTTCAATTACCCAGCTGCGTTTGCATCGGACTGTTT GTTTTCCCACCAGACTTCTCGGAGTTCTGGGCCACACTTCTTGATGCTTG GCACTTGAAGGCCCGAGGGCTTCGCAGACCCATTTCTGTGGTGAATCCGA GAACCCGAGAATTGGAGAAGCGAAGAATCCGAGAACACGGGAATCTTGGC CCTTCCGTGTAATTGGCTTAAGAAGACTTGCGAGCGACCGCAGAAATTGT TAAACTCACATTAGCCGACACATGTGTGCACAGTTATTACGGCGCACGGA GACCATAAAATACACTTTAATTAATTCCCGGTCTGTGTAATTACAAAGCT GCTGCTGTGGCACCTTTCTTTTGGCCAACATCGCAGCCGCAAGTCTCACT CACTCGCTTTTCTGCTGATTTATTGCGGCTTTTGTTTTTTGACAAGTGTC AAAAAGAGTCTGCCACGCCCCTTCCCGCTTACAAGCTGAATTTGATTGCT TTCTAATTTATTGCAGCATTAAAAGTTGACCTACAGACGCAAAGGGAGAG GGAGACGGTGGATGGCGGCAGAAAGAGACGGCTACAGACGAGCCGAAAGA GACGGAGCGCTAGTGAAAAGCTGCCAACAGACCGAGTTTTGTCAACCAGC ATTTCCCTTTTCGCAATTTCCTCGAGCCGGCGAGAACTGAATTGAATTTA CGCCCAAACAATAATATTTGGAAAGCTGCCCAGCTTTGTGTGTTTGCCAG TTGGGAAAAGGCTCTGTGGGCGTTTGCCTTAGCTTAATTTTATTTAACGT GCGGAAGATTGAGTTTAATATAACAAGCTTAAAACAACGCTATATTCATT GTGGTGTATATATTTTTGCAGTTATCAAGGAGAGACTGGCCAATAGAACG ATATGTAATATGAACTTTTGTGAAATCCACACTGACCATTTGAAATTGTT ATATTGAGAGGAGTTGTAAATCGTATCCAATTTTATTTTCAATTCATAGT TGGGTACATATTTAAAGCAAATCTCTGCACTTTCTGCGTTGCAGTAGCCA GAAAAACGATTACCCTGCTGCAGCCAATTTCTCATGTGTGTCAATGCCAC GATAACTTTGGTCACGGGGCTTAAATGCTGTTATCGAACTATTTGGCTTC CCAACCTAACTTGATTGCTTTTTTAAACTAAAAGCTTTAAAAAAGAGGTT ATGTTCTGGTTAAAGTTGAAGGTCGAAATAACAAAACTGCCATCAGAATG TTTTCATATCCTCTTTTTTTTTGGATTTTTCTATTGATATTTCAATTGAA CCGTAAGATTGTTATACTACGTGATAATCAATTCTATAAAATGAATACAA CCCAAAAAATATTCTCCAAACTGAAAAAATTGTAAAACCATTTTTAATTA AGCTTTCCAGAACCTAGAATATTGAGGAAACAACCCAAACTTATTTCTAA ATCTGTATGTTCTATGTAGCTTGCTATTGCTATAATGATGGCTGAATTAC ATTGATGATTCGTTCATCATCTCTTCTGGGTCCGGATTACACTCTCCCAA GGATTCTCCACTGACACCCTGGGTGATGTCAAGGGCTGTGATAATAAAAC GTTTCGGAAACACTGCTATTGCTGTGGGGAAAATACGGTTATTGCCGCCA GCTTATATCTACGGATGATATGGAGTCAGAAACACGGCTATTGCCCGCTG TTATCAACGGATGGGATGGCTTCGGTATCTATGTTATAGCCGTGTGAGAG CACGTACATTTTTCTCGTTTCGTGTTCGCCACTGGATCTTTACATAAATG CGGGGTTGCAATGCAATGTTTTACCTTTGCATAATGTCGCGTTGATTGCT CCACGTTATACGTACAACTGCGACGAAATAGCATTTTCCCTCCTTGTCTC TCGTGACGCCCTCTCGCTCACTCACTCACTCACGGTGCCACTGGAATTCA GTTTGTGGATTTCGGACACTCGGCCAGTTGTGCATATTCAAATTGCGCTG AGCGACATTTGAAAATATGAGCAGCCCACAAAAACAACGAAAAATGCAAC ACGTTACCCGGATTAAATGGAATTGTTGATGGGTTTGCTTGGTCTGTTGC CCGCTGCTATTTCTGATTGCAGGTTGTGGACGTGCGCTCACAATAGTGAC CTCCCACTAACTAGGCTAAAAGCAAGCACGCGCTGCCGAAAATATTGCCA GCATTCCGGACCCACATGCTCCGGACCCACAGCTGCCATTGATAAACGAC GCGGACGCGTGTCACTTCGGGCCTCAATTAGGAACTCTTTTAGCCGGCTT CCCAGCCAGTTTCAGTTTCAGATTCAGCACTCGAGACCCGACTCCAGTTT TCCCAACCGCGCGGCGACGACTCGCAAAGCGAACTGAAATCGAAGTAGCC GCCAACTGAGCAGCGGCTGGATGTCAGCGGAACCGGCAGAGACTCTGTTG CATGTGGCCGGCTCTTTGTGCAACGTGATGTTGCAAGTTGCTCGAGTGTG GCCAACAGCAACAGCAACACCTGCAACATCAGCAGCAGCAGCAAGCTAGG TTGGACGGTTAAATTGGAACGCTCTGTGCGATGACAGCTCAATTGACCAC ATGTGTCAAATAAGTGACTGCCAAATATTAGCTATCTAGAATGGAATCCG AAAATGGGAGTGATTTATGTAACAGGGAGTGACGGAACTACTCTTTTCTT ACACTCATAGGTCGGAACTTGGAATGAACGTTCAAGGGAGTTCAAAAATA AATAAACTTTCGTTAAACTTTAGCAAACTAAACATAAGTGATACAAAGGC CATTTTAAATTCGGTGTGCAGCAGTGAGGCAGCGCCTCACATCCCGATAC GGTGGCATGGCAGACTTTGGTGACGCTTGGTGCATGCAATTAATCCGCGC AAAAGTTCCGGGCGCAGACCGTGGCCATGTCCATGGGCATATCCATGTCG GCGGACATGCCCGTATCCATGCCCACAGCTAAGGCAATAGCGATAGCGAT AGTGGCGGTGAAACCTAAGCCCTGTCCCTGGCCATGCCACATGCACCCAC GGCATTGTTTTTGGCCAAATGTCCAGTATCCCACGTCCAAGTCGACTTTT TGTTCACTGGCGCGCTTGACAAACTATTTACGCACATATGAGCACGCTTC CGTCCGTCGCAGTTGCAATTGCTGCTGCTTCTGCTGTTGCTGCAACATTT GATGCCGCTGCAGTTGGTCTCGCATTGCAGCACTCGTTCCAATTCAGTTG GGCAAACAAGGATGTGGACTTAACTTTGGGCGATGGCGATGCGTGCTTCT TGCTTTGATGGTGCTGGGGCTAATGGAATTTCAGATGAGATGCTGCTGGT TGGGAATTGAAAGTTTTCGGGCCAAACAACCTTAAAGTTGCGGCTTTAAA CAGTCGAAATGCTTTGTGGCTTGGGTTGAACAACCTTGACACTTTTATTT CAGTTATGCTTTATCTTCATGTCGGTGGTTTTGCACTTGTTTTTTGTTTA GCCGCACTTGTTTCTTGCGGGCTAGTAATTAAATTTAGTTCGCCCTCCCA CGGCGAAGGTAGGGCCAAGTGCCAGGCCAAGTCAAAGATTTCTCGAAATG CTTAGAAAAAACCGAGCGTTGTATGCTCAGGCAGCGTGTATCCGCCAGAT ACAAGTATCACATATTTCATTCAGAAAAACTATTTGCTTACGGCATTCGC GCGGTTTGAATAAATCACTGACTACGTTATTTGTTTAATTAATTATGATA ATTAGGCCATCAGTTATTAATTGGAAAATATTCACTTGTTTGTGGTTTTT AATCCGGCTATAGGTTCATAAAACGTGTCTATTACCGGATGATGAGCTAG TGCCAATAAGAGAGTATATAATTAGTTTTATCAAACTACATTTTGTGTTC CCATAACCGTTAGATTCACGCCCATTACAGAGCACAATTTACACGCCCCC GATTTTCCCACCTTTAGACACTTGCCTCAATTTCCACGCGTTGCATGCGC CGCTGACGTTAGATAAACATTTCCCTACCAGCATAATTAAAATAAGATGG GATACTATTAATCCGGAGGGGCATAAAATACATTTTAAATGACTGTTCCA ATTTCCGCGTTACAAGCCAGCCCAAAAAGTAGAATATACATACATAAAAA TGTATTTAAAGTTTGAAATTTATACAAGAAATTTTCAATTCTCGAATTAA TTAGTTGTTTGCTTTCAACTTCAATAAGTTCGATTGTACTCACATTGCTA AATATAAATTATTCTTTAGAATGAACTAGACAGACTGCTTAGCGTCATTG ACCGGAAACTTAAATCACTCAATCGTACACTAAACGAATAAAGTTCTGGA AATGAAAACAGTTTCCAGCTAAAATAAGAAATATACTACTACGTTTGCCA TTGAGAATAAATAAAACAAAAGTCAAGTGCTGACAACTATAGTTCTTGTT CGTGCTAACTAGCCCAGACGATCTAGCCATGCCCGTCTCGATGTCTGTCT GTCCGTTATGTCCGTATGTCCGTCTGTCCGTTTGTCCGTTTGTCCGTTTG TCCGTTCGTTCGTGTGAAAGTCGAGATATCCGGGAACCATAAAAGCTAGA AAGTTGAGACTTGACAACAGGTATTTAATAGAATCTAATAGCTGCCCTCA AGTATATTACTATCTTGTTTTTGAATACACGAACAAAAGCAGTGTTATTT AATAATTCAGCTACATTATACGATATCACCAAAAAAATCTATGATAAGCG GGCGAACCAATCAGTGACTAATCCGTAAAAGTTATCTCATAGTCTGGCCG AGGCATTGACATTTGCGAACAGTTCGACGTGGTAAAGTCATTATTTCTTT TCAGGTAGGGCTTACCTCAATTAGCCGACTCGTGTTGCATGCTTCAGCAC CATATTTTAATTTGGGGTTTTCGCTGCTACGGTTGAGCAACCTAACGAGT GTGGCATGAGGTATGCAAAACATTAGAGCGTCTGGGAATAGTAATTATTT TCGCTCAGCTATACAGAGGAAAGTCATTGACTCTAACAACATTATGACTA GTCAGGTGGCGATTCGCGTGGCATGTTGCAACTTAAGCCGAATGCAATTT ATGAACCTGCAAATCTGATGGGAACAACATTTGCCTGAATGCATCTAACT GGTAGACAATTAGATCTTCTAAACTGTGAACATAAGTGATTTATCACAGG CCAATAAGTTAATATGGCTGTTTAGGTTAAGGTTATTTAATAATTGAACA GTCTAAAATGTACATCACTTTAGCTTTGGATCCTAAGCTATATACATGGG AGCAACGAATATGGAGGTTAGATGCGTTCCACTCGCAAGTAGATGCCCCC AACGGTGCCCAAAACTATGGACATGGGACTATACTTCAGTGGGATCTCTG TCGTATCGCAGACGGATACCCTGAACCGGCTGATGATCTGAGCCAAACCG ATGCGAGCCTGCATTTGTCCAAACCGCATCCCGATGCAGTTCCGCGGCCC GTCGCCGAAGGGCAGCCACTCCACGGACTCCCGGGCGGCCACTTTCTCCG GCGAGAAGCGCTCCGGATCAAAGGTCTCCGGATTCGGATAAAGATCCTCG TCGCGGTGGTAGGCGCAAGCGGGGATTATGACCTGTGTGCCCTTCTCAAT CACAAGCTTTTCATGGCCCGGCACCACGTAGTCGTTGAGGGCCTTCCGTT CGAGGTGGGGCACCAGTGTGTAGAGCCTCAGGGTTTCTGAAGAGCAATGT TGGGTAAAACCAGTTACAATCCCTCTTGGGGCTGTGCTTCAGACAGAACA CCTACCTGAGATGACCTGGTTCAAGTAGGTCATGGCTTTGATGGATTCGT ACGTTAGCTGCCCCTCCTGTTCCTCCAGCACCGTTTGGATCTCGTTGCGC AGCCTGTCCTGAATGTCCTGATTCTGAGCCAACTCATACAGGCAGTAACT CATTGTCGAGGAGGAGGTCTCAAATCCGGCCACATAAAAGACGAACACCT GGGCGGCCAGTTCGCCGATGTCCATGCCCTCGATCACCTCTCCGTTGTCC AGGGTGACGCGCCCCTTCTGCTTCAGTTCAATCAGCAGGTTCATGAAGTC GTTCCTCTTGAAGTTCTCCCGCTCCCTGAGGGCAATCGTGTCGTTGACCA GGCGCATGAAGAACTGGTGGACGTCCTCGGGCATCATGCGCATTCTCAAC CTGCTGGCCAGCTTGGGAAAGCTGAACACGAACATGGTCAGCAGTTTCCC GTGGCGCATATCGGTGAACACCTTCTGTCCCATGGTGCGGAAATCACTGA CAGGGGTGCGCAGCGTGTTACACTCAATGCCGAAGGCACAGGTGCCAATC ACATCGGTGGTGAACCTGGCCATCAGCTCCTTGATCTCGAGCACAGCGCC GTTCTGGGCGGCGGGCACCTGCTCCGTGATCACCTTGACGAACTCCTCAG ACACCTTGATCACCGTCGGGAACATGAACTTCATCTTGCCCGAGGTGAAA GTCGGCGTCAGCCTCTGGCGCATGTCCTTCCACTTCTTTCCGTCCAGGTT GAACAGGTGCTGCGTGAGCGGGTCGTCGCGCCCGTTGTGAAACTGGCCAC GATCGGCAAAGTTCGAGAAATCCTTGATCAGGATGTTCTTGGCCAGCTGG GTGTCCACGATGAAGGCGGCCGGCTTGTGCAGAAAGTAAAAGCCCACGAA GGGAAAGCCGCTCTTCCGGTACTTGTTGTAGTAGTCGTAGAAGAAGTCGT GCATCACCCGGTTCTTCCGGAACCCGACCATGTTGCCATACAGTGGGTGA GGAGCATCGTGTGGCACGCCGCGGCGATTCCAGTAGTTGAAGTTGCGGTG GTACAAGTAGGCCAAAAGCGAGGAGATCGCGATCAACAGGTATATTAGAA CAAACATTTTGCGTAGCTGCTCCCTTTTCGCAATCGTCGTGCTCGACCTA CGACGAATTACTGATCACCACAATATGTTCGCACACTTTTTATAAGATTC CCCTGCGACGCACAGGCATGACAGCATGTGAGCTAGCTAGCTAAATATTT CTATCACCATGACTACTACTTTTAAGTTGTTGTCATGATTACAGACTCGG CGATAATATGCAGGCACTTTTCAAACCGATTTAAGAGCACTTTCAAAGAG ATACTCATACGCTTGACTGCAAAAATGCTCGCGAATCAAAATATAAACAA ATGATAACGAGATTGTTGTTAAACAAACCGGTTGGTGCTTGGGTAAAAAG TGTCCCATCAGGTTTTATCACTCATTTATAAGCTCGGCATGTGCGAAAAG TAGAGGTAGCATTAAATGGTAAATACACATCGATATGCGGAAAATGTATC AAATCATTGTATTACTATAAAAACGCAATGACACGGTCATTCAAAGTAGC TTCAAATGTACAGGACGATCCCACTTGTAACTAAAGGTAAAGGTGTTTAA GTAATGGGTATTTGATAGCCGAGCGTTCCATCTAGCTTTCATTATCAGCG ACAACACCAAGCTCTTTTGCTTTTTATGAGAGATTCAAGATTTGACATAA GAGATATTCTCTTGATGTTCTACTGTTCTATTGCAGTGGATCTACATGCA AACAAACGATTACAAGATTGTTATTAAACAAGCTGGTTAAGGATCATAAA GGTTTTTCTCCTATGCGATTCAATATTTATTAGAAAACAGAGCAAATATA ATTAAATGAGTTTTTAAGCCTTGGGAATCGGAGCGAACATTATCGCATGA AATTGTTAATGACATAATTTCCCGTAGATAAATACATACACGGACATACA CATTTAAAATGTCACCCATTTATTTCAGTAATTAGCACCCCACTACAACG TTAATGTTTGGTGTTCCACGGCGATAAAACGAATGAATTCGCTGGGAGAA CCAATAACTCTTTCTAAGAGCTATTTAAACGCTTCACTGTTTGAATGACG ATCAAAATATAAACAGTAGATAACTTGATTGTCGTTAAACTGGTCGCGGT TGGTTTTAAACATTATAATCGCATCGGGTTTTATTGCTCATTTGGAAACA ACACATCAACTGTGCTGTGTTAAATTATATTTAGCATATATGTGATTAAA ATGTATTCATTCGAAAGCAATGTCGCGTAGTTAAATCTACATGTCACACC AACATTTAAAATGACTAATAAATTTAGTTTGTTGCCTTATCTCGTTTTAT TTTCAGAAATCAGTGCTAATGTACAACACAAGATCTAATTAAAGGAGCAT TTTTTCTGCAGTGTTCGGATTTTTAAATATGTTTTGAGATGAGAGAAGTT TAACTGTGGTTAACACAAGGAAGTATTCCACATTAATCTGGGTGCTTAGA GTATCGCTTATGAAGCCCAATAGTTAATAAGGGCACATTATTGTAATGAT ATCTCATCTGAATTACCAGCCACACAATTGTGTGTGCTTAACGCCCCGAT TAAGCTTACGGTTAGCCGCTCCCTAAGTCGCGTTCTAAAAGGGTATAAGC CGATTAGGATGTGCATTTGTGCCGGGAAATCTCCTTATTTTGTCGGTTGG GAAAGCGGGAACACTAACGCGATTATGGCGGATTTATTTTCTCCGATTCG AGGGAGCCAAGGCAATATTGACCTTGTGCATTTCTTATCACAAGCTGCTC GAATTATTGGCACAGCCCCAGGGCAGATCAGAGTAGACCAGAGACTTATC TGGGAGTGTTCTTGGCTGTCATTGTCTTGAACTGGTCGTGTTGCTTAGTG CTTAGTGCTGCAACTGACACTTCCATGTCCCACTCTGACCTGGGAGTTTA GACAGCAAGTGGCGCGAAAAGGTGAGCAACGATTCGATTTGAATCTAATC GCCGATACAAATCAAGTCCTCCTGCCCGACCTTGAAGTGCTCAGTCTCGG CCCACATGGGTCAGGGTGTTCCATACAAGCCCGCATTAAGATGGGAAACA AATATAACGCAAAGCGCGTCGTTCTTGGCATAATGAAGCGCCCGACGAGA AGAAAGAAAGGCATTGAGGAAGCGGCGAGGAAAAACTAGATTGCCTCTCT GGCTGCACTTATGCGCTAAATAAAAATGCAAATCTAAATGCAGCTAAGAG CCGAGAAGGGCCCAAGAAGCCAGGCGAGCTCACAAAGGAAACCCCACGCC GACGGCGCACAATGCAGATTCTTAAAGAATGAAGAACGCGCTCGAGGGCC CTCTAAGTCGACATCTGACTGCCGCAGTCTCTGGCGGATTGTTGTCTCCG GGTAGACGGCCTAGCTAATTGCAGATGCATCTCGGCTGCATGTCGCGGAC TTCTTGTAAACAGTCGCCTAATTGTTTGCTCCGCAGAGGTGTTGCGCCCC AAAGACGCAGCTCTTTCGAATGCAAATGCTGACTGAGAAGGGGTGCCCCG AGTGCCTGTCCAAGTCCCAACCCCAATCCCCTCAAGGCTGGGTACAGCAT GAGCGAGCGCCTTGAATAAATTAGTTTTATTTGTGTCTGGATGTGGGGCA ATCTAAACAAATCGTGAGCGGAGAGCATGGGATTCTGCATTTCCTGTGGG GTGACAACAGTGACGATGTCGCGTCTGCGTGTTATGTAAATCACAAGGAA AGCCGAAATGGAGGGGCGCAGTTGGGGGAATCCCCTACGTCAATACAGAA ACACACGCCTCTGCAGAACCCAACCTTTGCAGCATAATCATAATCATCAC AAGAAGCATCTTGATGAATTGTAATAGGCTTTAAGCCTTCTGAGTGCGCA TTCGAGTGAAACAGCACCCACTCCAGTTAAATACGCGAACTCCCCAGGCA GCGGCAATAATTAGCCAGATTCCACTTTGTCGCAGGATGACAATGGCACA TTCCTCCTGCGGGATTTTTCAATCACCGCCAGACTCTTGGAGCAGCGGGA TGATGGCTGATTGAATTTCTGGGCTGACATATTCGAGCCGCGATTGTGAT TGCGATTGCTATTGCTGTTGTGATTGTGATTGTGATTGTGTGGCATGTGT GGCAGCTGCTGCTCCGTATTGATTCGGTGCTGATTGTCTGCCGAGGGCTT TGTTTCATCGCAGCTCTACTGTCTTCGGCGGAAGCCATAAAAAGATGACC GGGTGTGATGTACTGACAAGTGCTGGGTCAATGTGTCAAAAGAGAGAGCC CGATGCGGCTGTTCATCAGGCGAGATGACACAGATTGTCCCTCGCACACC GGCCAAGTTGCAAATTGTTGACTTATGCTGTTGCAACTGGAGCGGACTGG CAGTAGTTGCCACCCAGAGATCCGCGTTTACGTGGCGCAATAAAACGCTC GCTGGTGAGCACCGTGAATATGTTTTATGTGCCCAGATGGCACCACGTGG CGTATACGCACTTTAAACCAAAATTGCCTTTTGTGCCGTGAATTTAGAAG AGGTACACGCCAGAGCTTTGGGCAAATAAATGACAAAGCCATTTGTAATG AAATATTAAGGCCGGCAGTAAAAGGAAGATCTGGAGGAGTGGTTGGGGCG TTGGACGCAGCGGGAAATGGGCCGGAAAACATCAGCATTATACTTATTCA TTATGCTGCTGGTCTAGGCGTGGGCGTTTACGCATTCGCATTCCAGATCG TGGGCGGAGCGGTGCTAGCATGAGTTTTATTGGACGCACATCACATAAAC ATGATGCGGTACGGGCATTTGGAGCGTGGAGCACATGGCCCGAAGGCAGG AGGAAAATCGATACCCACATGGCCACATGAGCAACCCAAAGATCTGGCCA AAAGCGAGGCGTTGCAGTTTCCATGGCGCAGGTAGCAGAATTTAAATGGA TTAGGGTAACTGTGTCAGAAATCAATTATTCAAATGGAGTCGCATGCACG CATCAAATTAAATTTCCACTCAAACGAAAACAAAGTGTATTTTCAAAAGC AAATTAATTGCTCTGTGCTTCCCGTTTTGGCAAATCTAGTTTTGTCCCCA GGCAGCAGCAAAAATAAATCCAACTAGATTTCCACGATGACAACAGCAAA TCACGATTGCCCTTTATGGGCATGCCACCAAATAAGAAACGGGTATGATT GTGAATAAAAACCCTTTCAAGTTGTCACTACTGAAGTGGTTGGTTGGTTG CTTTGCTCGACTTTTGCTGGCAACTGTGGCTTTAAGCCACAGCCACAGCC AGAGTCCCACGCTTTTAGCCACCGAAATGTAAATTGGGCAAAACGCATGC CGAGCAAACTTCTTTTCCCATGGCTGGCAGAACGGGGGAAAAGGTCGATA AGAATATTGTTTAACTCAATTCAGCACGCGAATCTGAACTCAGCCCGATT TGTTGATAAAAAGTGAAAGTGGAAAGTGGAAAGCGAAAAGGCAACAGAAC AGCGCGGGGTGGGGAGGGAAGGGGAGTCGATTCGCAGCCCCGGGCAATCA AATTGAAAATTCTCCATTGTGCAAATATTGATTTTGTTCGCTGCATAAAG TTTATGCGTCCAAATCGAGAAACTCAAGTAGACCAGGGAAAATTCGGCTT GTAATTTCCTCTGCGATAAGCAAGAAGTTGGGAGCCATTCTCAATCCGTC TGCGATCTCAAGTGTCTGGGGCAAGGTCGCTTTTTGTGGCAGTCTCGTTC CGTCTTTTTTTTTTTGCCCGGCTAATTCGACGCCCTTGCCAGTGGAGTCG TGTGTTGCGAGTTTTATATTTTTCCCAACATATTATTTATGGTAATCGAC ATCAAATGCCGCCATTAAGCTTATTGCCATGGCAAGCGGCAACAGCAAAG GCGTTTTCTTGCTGCTTTTTGCTGCTTTTTTTGGGCTCTGTGCTTCTGCT GTTTATAGGCTTCCAAAGCTAAAAATATTGTACATCTGCATGGGTAAATT CTAAAAAGATGTGGAAGTACATGAACAGATTTAGTCGAACTTTTCTATAC ACTATCTGTTCATATCTATTCCCTGATAATATGAATAGAACATAAATTTC AGTTTTGAATTGTGTACCCAATAACTTTTTTTTTACTATTAATGCACTTG AATATTGTTTTGATATTAATAATTGTTGATATTAATAATTATCTATTGTC CATTTTAAATTCATTCTAATGAATATTATATATATATTATACACAGCATC GAATTGAGTTGCTCGATTGAAATCTGAAGATTCTACGAAACATTACATCT TTTCGCCGAAAAGTTTTAATTTTTTTTTTTGTCAGGGTATTTTAACAGCA TTTGCATACCGTGTAGGCGATTTCTCATATTCGAAGCGTTGAATTTTTGA ATGAATTTATGACAAGCACGTCCCTCCGCTGAAAATCTCCCTCTCGTTTG GCAATAATTTGTTTGTATCTCATATTTGATTTGCGTTATGTACGCACTGT GTGAGTTGGCGAGGGGGTGTGTATCTTTTGGCACCTTATCAGCAGATTAT TTGCATAATTTGAGAATATTTTTCGAATCGAACATTGGCTTTCCACGAAT CGCTGCTCGAGCTTACCTAATGAAGCAGTGGCCAGAGATACCGATTAGAA ATCGTCCTATTCCGATGGCGCGTGTTCAGCCAGCACTGAATGTGTGTGTG TGCTTATTAAATTATTGCAGAGTTGCTAATGGAAAAAGTCGTGCGATAAA AATGAATTTATTGCATTTTTCGGTTAATTTGCCATTGTAAACTTATTTAA TTACGAACTTTTTCCATGCTAATGCAAACTTTTCAGCGAGCAAGGAGTAA ACTACCTAAATGGGGATGGGAGATGCCCGCTGATGGATAATTGCCCCGAG CTGAAAGTGCCCCATTTCATCCGCTGTTGTTATAAATAAATAAACATTAT GAAACCACTTTTATCCTGATTAATATCATCATGCGCTCACCTCCGCACAT GCATGTGCATACATACACACGTACGAGAGTATAAACATTTTTGTTTAAGG CCCCGGAAAACTGCTTTTTAACCGCCCACTCGAACTCCGTCCTCCGCCCA AGCTATTAAAGATTATTAAAAGCACCTTGATCTCGGGAGAAGGAGTTCCC TCCCATGTGGCGCTGATGCTCTTGCTCTGTGGCACGCAGACCAAACGTAT TGATCCATAAAGCGTATAAAACACGAGCAGTATTTGTATCTTACGTTGGG ATGCGATGAGGTGGGCGGATTGCGGACCGAAGGGGTTGTTGGTGGATGGA GATGTGCATGCGGATGATCTTTGACCTTCGGCAAGGTTGTACCCCCACTT TCTATTTTAGGCCCAATTAGGTTGCAGCTATTCTCTTTAGGCATAACCCC GGTGAACATAAATCTCCGTATGTACACAATGCTCATCGAGAGTGAGCCAT GTCTTCATCTGCAGAGGTGGTTCCCTCCCCGGGCATTATCAATCTTTCAT CTTCGTCTGCATTTGTTATAGTCGAGCTCCCCTAGTTGAGCACTCATTTA TGCATTTTATTGGCTCTTGGCTAGCTTGGAGCACCATCAATCATCTCGAT GGCTATTCAGTTGCGATCTACTCTGCCTTTTGTGCTTATATTTATTATTT GGACGGGCCGTCATAAGTGGTCCACCTGTTGGCCGAATAGCCTGCCCAGC AGTTTGCCAATAATTTTAATCAATTATGCAAATCGCATTTATTGGCCCAT GATTTATGCGATATATATGCATATCGTGCATATATGTATAAGATGGACGA AATGGAGCGAGAAGAGCTGTGTTGACAGTCGGAACTGATTTGGAGCCCAA GGAGCCATTACTCATCTTTCCGGAAGTTCTGTGTGTGCCCACTCACATCA CTCAGCCCAGGTGAAGTGTTCTGTTCGTGGTGCTAATAATATACATATAC CCATATAAGAAGAAGAACCCATTCTGGTTCACGTTTACCCAACTGGCTTT GCAAGCAGTTCTTTCCAGATAAGAAGGCGATAAGAACCCTATACGAGTAC GAGTATATGAGGCCAATGCAAATAGCAGATACGCACCAGAGGAGAATTCG CTGCTCTTTCCGCTGCAACCTTCCAGCAGATTTAATGAATGAAATCAACT TGAATTAAATTCCTCCATATTGCGGCTTTGTTTCTGGCTTTATTTGTTTA CACACACTGCAGCTGTTGAATCACCAGAGAGGCGAGAAATGTGTTTTCGG CTGCCTTGCTTTGTTTCGCTTGGAAGGTAATAAATTTTTAACACAATTGC ATTGCATAAACAATTTCAAAACTGCACTCGAAATGGGCCTGTTTACACTC CGTTGTCGTGTCGATTACATTTTTGGCCAATAGCCAAGCACTCAGATTTA ACTGGTTTATTTCGACTTGGCGAACGCCCGCGCGCGAATCTTTCAGCACA GCCCACGCACTTTCTGCAGCATGGTTAACTTGAAGATACTCGAATCGCAC AGGGAAACAGATACGGATGGGCTCCAATGGAGGTGATATAGAGGCGTAAA CAGAGGCAGAGATTCAAACCGAACCGAACCAAACCGAACTGAACCTCTGG GCCAGCGATCGAGTTGTGCGCCGCTGGAGAGCTCGGCACGTATTAATTTC TGCGGCAGCACTAAAGTATCCGAAAGATACGTTCCGCTGGTCGCGCACCA GCGCACATAGCCGCCACATATGTGGGCAACTTCGCTGCCGGCGTCGCCAA CTTGTTTGACAGCGAGGTAAACACAACCGGAGCACAGATCTGCCTCGTCT TCGGCCCTTCTGGATGTTTATATTTACACGTCGGGTCGGATCGGATCGGG CGGGGGTGATCTCGATGGGTCAGATGCGCGACGGGTGTCGTTGATTTCAA TGAAGAGCCACAATTTGTCGTCTCAAGTGGCTCGTTTATCTGCATCCGAC GCGGTTTATTCTAAGTCTGAGATTCAGACATCCGACAGCTCCCGACAGTT TCCCCCAGCCCCTATCTGTTTGTTGGGCAAAATGATTGGATTCAACAGTA ACATTAACATTAGCCCTAAGTTAGCTGGTTCTTGATGCCATCGTATGCAA ATGGCTCCCATCGGAATTGGACAGAATTCGGAGTTTTTGGCTAATTAAAA GTTTCGTCGAACGGGGCCACAAATGAGGTCGAATGAGGCCAGTATCTGCG ATTTGTATTTGCCCAAAGAGCGAATGCTTCCGCTTTGAGGTGTCTTGACG GAAATGGCTCTTACAAATCAAATCAAATGTTTTGTGGCTTGAGGCTTTTG TATCCCACAAAACGAGTAGAGTGTGTGTGCTCTATTTAAGCCGAGAGATT TCACTGCTCATCCAATTATTTGTGGAGATGCTTTCTCCGAGCGCGGGTCG CACAGATCAAACACCTACGAATTGAGTGAACTTGAATATCGATGCTGCTG GGTCACCAGGGTGGCCGTGGCCCGAAACTGGTCTGGAGGAAGCCCCGATC ACCTGCACCTAATGATACATAATTACATGTGGGCAAAGTTTCAGTTTCCA AAGCATTTTCATTAGTTTGATGGCCTTTCTGCCAGGGAAGGCCTGCTCGG GCGTTCCGGCTGTAATTATATAATCATTTTAATTGGATCCGGCAATGTTT GCCGGCGCGGCGGCACCGTCGACACATAACAAAGATTAATCGTGCTTATG TCGGCGGGTCAGGAGACAAGAAGTCGAGCTAGACGAGCACAAGTACGAGT CATGTCTCAGTATCTTGCAGATACTTCGCTACATGCAAGGTCGCTTGAGT GGGTGGGGTTGGTATCCCGAATGCAGATTCCATTGCAATACAACATTAAT TCAATTATAACGGCGCTCTGCAGGTGCGACGCCCCCGCATGACTTTGCCT TGGGCAGCTTCGGGGTTACTCTGCCAAGACATTTATGAATTAGTTGCAAT TTGTATCTGCCTCAGCTGTTTTTGCTACCTAAGGCCGCCCGCTCGCATTT CATTAGTCCCAAATTGGCGTCATCACGTGATCGGAGGTGGTCAAGGGGAA ATCCGTAGAACTCCAAGCGGAACTCGCACCAACTGACAGTGGCAGTCGGC GAAGTAACACATTCACACATAAATTTCCAGCACTCCGGTGTATCTTTCAG AAGCGGCACTTCTACTTTTGATGAGCACCTCTCGCAGCGCGCATCATTTC AAATTAATTGTGGGTCTATTGATAGGGCCCTTCTTTGTTTTGGGGAACTG ACGCTGAGATATCTATGTGTTTATCCGGCTCTGGAAATTGGGCTGTGCGT GTCGCACGCCACATTCATTCACCGAAATTCATAACACTCGCCGGCGAACG AAGTGTCAAAAACAGTTTCATAGGCCCAAAACACCGTGCATTCGCTTGAA TAATGTATTATGGTATAATTGCGGGGGTTGCCCACAGGCAAATCCATTCC GGCTTTTCCCAAAGCCAATCAGCCGGAAAAATTATACAAACGCAAATAAA AGGCAGCGGGAAATTCGGGTCAGCAAAGATGTTAACAGGAACGAATCGCT TTGATAAACCGGAGCGAAAGAAAATTTATTTTGTATACGGAATCGATTAA AGCCGGTTGCTGATAAATTTTCTTTTAGTTTTCACATTCATGTTTTCAAT GGACGGGGCCCACTGAATATAAGCAAATCAATCGAAAGCTATAAAACCTT AATATTTACAAATATAGAAGATAGTACTTTTCCGAATGAATGTATGCCAA GGCAAAAAACGCATGAATATTTTGAATTGGGCGTAGACGAATTAACACAA TGGACCATAATAATAATAAATTTCTTATAATCAGAATGAAAGTTAACTTT AGCACTTAAAAGTCGAAATACCTTTATAAATTTTACGCTTTAGAACTTGC CCGATATAAAATATAAGTTACGACTTGCAAGCATATAATCCTGATTTTAT CAGAAATGTCGAAAGCGGATTTTAAGCTTCGATTGAGTTACGTATGAATA ACAGAGGCATGATGAACGATGACGATTCAAGGGTCTTATCCTCATTATTA GATCACCTCCATTAGCCCTTTGCCGGCGATACTGAAAAGGATTGCAGGGC ACTCTGCCCACACTTGGACCACTTGCCACCAGGACCGGCACTGCAATTCC CAGTGCCACATGCTCGACAGGCCACAGCCACCATATTAGTAAGCTGAGGT CAGGCATGCTGCCACTGTCATGCCCCACTTAACCATAAATACTCGAATTT CCATTGCAGCCACTCGTGCACGGAGCGCACCCGAGGAGGAGCTCCACATC GAGACCCAGACCCCACACACACACTGCTCGGCCCCAGTTCCCAATTCGGA CCATTTCAATTAGCAGACACCTCTCTGGACAGAACCCACCAAATGAACTC GGCCGTGGCGAGGCACAGATGGATGTGGCGCCACCATATGTACGTACGTA CTACGTAGTACAGTGTACACATGTACTCGTGCATTCAGAACACTGGGCTG GAAAAAAATGCTGGCCAATATCCTGGCGGAAATTAATGTTGCTGTGGCAA GCACAAAGCCAGAAGGAGGGCAACGGCGGAACGGAAAAAAATTGAATGCC ACAAACCGATATGATTCGCTGCGGGAATGGGAAGGGGGCGGATACCCGGC CTTTCTCCGTTGTCAGCAGTTCCTTTTTCCTGCTGCTCACATCGACGGAT GAGGAGGGGCTCAGACCGCAGCCAGGCACGCCCCCACTTGAGTCAAACCC AACCCCCAACCCAGGCCCAAATCCCCGGAATATTGAGCATGCACGGCGGA TCGGATATGCAACACGGCGGGTACGCCGAGTAATCACTATCAATTATATT GCTCAGCACGCGCATTGTCTCGCACTCTGCGCACGGCGGAATAGTGTTCC AGGATGTCTCATCTCCTGACTGGTGTAAGTAAGGACTTACCTTGCCATCG GCATCGGCGTGGGCATGGTATCGCACCTCCAGCGATCCGCCGAGCACTGC ATACCAGAAGCGTCCCTGCTCGCCGGCGCGAAAAACTGCGGGGAGGAGAA GTTTGAGTTAGCCACCTCTGTCGCATAGTTAATCCCCGCAATCCAGCACT CACGAGTCACCCCCTTCTCCAGGTCCTCATAGAATCCGCACATGGCCAAC TGCTGGAGCGCAGATCCCGGGAGGCGACACAGCGGCTCCACGCGACGCAA CCGGCACGAAATTAGCTCCACATCACGCAGGTTCCGGTCGCAAGGACTGA AAATCGTTTAAAAGTGGTTAGACGTTAATGTACTTTAAAATCACTTGCCG TGCTAGTATGGGTTTCAGATTAATATAAACATGCAGCTTATTAAATATTT CTATGTGCAATTTGAATTTTATAGAAGATAACACACTTGAGCCGCGCTAC CGCAAAAAAAAAAAAAAACAATATCGCACTCATATATGATGACTTGTTTA CATAAGTGGTGTATAATATTTGTTAAAGGTGGAAAGTTTGAACGAAGTTT TTTCCGTATAAACATCGAAATCACGGAAACTTTAAAGATCACGCTTCTCC CTAATCACTTCAATAACAAATGCAATCTGGAAAACAGTATATGGTTGCAG TATCAGCACTTCTCTCGCACTCCCTTTACAGGGTAAGAGGTATGGAATAG TCGAGACACTGAAATATTGTTTCTATAAAGTTCTTATTATATCTGACATT TGACCTTGTATCTGATAGTGGATTATCTCGTTCATAGCATTCTCTCTATA TGTTATAAAAAATAAATAAGTACGCTTGTCATGCAGCTTTCATTTCGGCT ACTGATTAAGTTTATTGTTAAATACTAACATTCTGCATTAAGGTTACCAG GAAGATTTACCTAGCTTATCACAACGAATAACAAATTATCAAAGAGGACA ATTATAAAACAAAGCAAAATGCTCCTTTGAAATAACAAAAGTAAAAAATT AATACGTGTAAAGGACTCTGAGAAATGAGTCGTTTCTGAACTCAAAACAA CCGAACAATAGACTGCAATAAGGAAAGAAGAAACCAAAAAAAAAAGAACA CGAAGAATAACGAGTATTTTGCATTTATAATTTACTGACTCTATGAAAAG CACTTCACGTGGATTATTCTATTTTTGGATCTACTTTTGGAAGGCCATAA ACTGAATAAAAATGAGGAGAAATGGCAAAGCAAAGTATTAGTTCAACAAT GAACTCAAATTAAAAATTCCAGTGTCATTTGTGCTCGGTTTGTGCGCGCA TTAAGTATGCAAATTATATTTTTTGCCTGTCTGTGTGCAAGTCAATTGAA AAATGAATAAATAAGTATAAGAGTTTCCGGGCAAGAATCTGCAGGAAACG GAAGTCCGCCCAGAATAATGAGAAGAAGGGCAGGGAAATGGCGAAGCAAT GAGAGTGAAGCGTCAACTAATTGCATTTGAGAAAAAGTTAGCTGTCAGAT CTAATAAGGAGTTCTCAAATTCAGGAAGTGCAAGTAAGTTAATTTTAAAT AATAAAAATTAAATCACCTTGCTTTAAAAAAAAAATAAAGTTTTTCCCCC TAGGAAAACAATACAAATCGCGCTATAAATAATGTTTTTACATGTCTAAC AGACAACAAATTGCGCCTTGCTGCCATGCGGCATGTTACCAAAAGTTTTA AACAATTTTCAGGCGAGCTCCCGCCCACCATAAATCCCCCAATGCCGCCC ACACTGGAGACCCCACCCAACTTTCGCCTAATTAAAAATTCCATAAAACT CAGACGGAGCGGGTGCGTCCGCAGGAAGGGCTGACCTGGGCAGACAAAGG CAGCTTGCAGTCAGGAATAGATCCCAAGCTTGCCCCTGGCCGGGCATCAT CTGCATCGAGGGCTACTTTTGCAGCGAGGCGTCTACTTTTTTGGCGCAGC CTGCGAACAACTTTCATCCGGCTCCTGAAGGTGAACTGTCTTGCCGGGCT CATGCATAATTCATTCGCCAGTAGAAGCGGCAATTTCGGGAACCGAGTGC CGAGAAGGGGGGCCACTAACCGTTTCTGGGTTTGTCGTTAACCAAACAGC CAGGTGGCTGTTGGTGGGCGAAAGGCGAAGGACGAAGGGAGTGATCCAAA GAGCCGGAAGCGCGTTGGGACACATCCTAGGCAGCCAGCTCGTTGTTTAT TATAATGGTTTTTGCGGTTTTTAGGCACACGCCCGAAAGTTTAGTTTCGG AATTTTGTAATTGGCGTGCCGGCGATTCGTCAGCCTTAAAGCTGCGGGGA AGGGTGGCCTCCTCGCACACATTAAAGCTGCTTTGGCACACGTGGCGTAT GATAAATGTGCGGCGGCACTTGTAAGTAAGACGATTGTTCCTCCGCCGGG AAGGGGAAGCCATCAATATCAATTGCTGTCTGCTGGCTTTGCCACTTCAC GCCTTACGTTCTGCGATTACCTTGCCTCCTTCCAAGGATTCTCCGATGGC ATGCACCGAGTGCTCCCTCGTCCTTTATCTCCAGGTGCGCTTAAGCCCAG ATCGCTCTTGATAAGCCGAATTACCAGTCAGCATGACGTGCCCTTCTTGG CTGTGCCATTAATTCTGTCCAAATTAAATCGTTTATTTTGTCTTCGCTCC CTACTTTAGTACGAGGCCATTTGTATTAGGTCCATAAGAAGGAGCAGCCG AAGAGCTGTGAAAGAAATCTGGATCTGCATACTGCACCCTGGCATCCTGG CACCCTTGCGCTACTAGGCCCTTTCTCTTTGGGCGGGGCAAACAAAAGGC AGCGGTCTGCAAATGTTTGCCCAGGCACAAGGCAAACAGTTTGCTTTAAG CCCTTGCCACTTGACCTTTCTTTTTTCCCGCTGCCGCGCACAGTCACATG AGTGCCCGCTGACCCCTGACCCCTCATGCTTTAGTGCGAGTGCGGCAGAA GCGTTTAAGCGTTGACAGAGCGTGAAATTTGAAGAGATTGTCCTCTGATT GATGGTGTGTGTGCGCGGCGGTTAGGGGCGGGCCGGTATGAGGCGGAGGC ACGCCCCATTCGGATAACACCAATGAAATATAAGGCCACTCTGCAATAAT AGAGTGTGCCGCACAACTGAGCAGTCGGTGGGGACAGGCGGGGCTAATAA TGGTAATGGTAATGGTGGCACTCGTCCAGCGATGCCCCAGCTGAAATCCA ACAAATTGCATCAAGTGGTTGCTGGGAAGAATGTGTGCTCGATTCCCGGC CATTTACGGTTGGGCAAATCGATTTAGACACTTTGAAAAACAATTTTGAT CTCTGGTCAATGTTTGATTAGCTCGAATCAAGTTCAACTTAAGCTTAAGT ACTGCGCACACACTAAAATAAATTTGGTTATTCCGTAATTGTATATAAAT ATTTTACACGCTAAATGCTGACTATTCTGTTGATTGATGCAATAGTAAAT GCTTTAGAATGCTGACTATTCTGTTGACTGTTGCAATAGTAAATGCTTTA GAAATAGCATGTCATCAGGAGAGATACTCCATCTCACATATGAGCTTTTT CATTAATTTAGATAAGGGTAATGTTATTATGTTGGCTGTGAAAAGATAAA TACTGTGGTGTCCAGATAAAATGAAACCGCTCTCTTAAATGGAAAGTATA AAGTCTGACATCAACTAAAAAAAAAAAACAATAGTCCCGTGCCTCTGTTT TATTCCACTAAAATAATGTTTGCACAAGACTAAACTCCATCCAATTGCAA AGCACATATTTACGTAAAAAATGTATGTGCATTAAAACCTCTGAAATGCG GAGCTTTCAGCAGAAATATATATATTTTCAATTAAATTATAGTATTTTTA TACTTTTACAGCGGTTTAATTATTATTTTTGCACGACAGAAAACACTTTT CAGGCATAGCTCATGAAATGAATGGTAAATTACTTTAATGCTTTATCATA ATATAAATTGTATTTTAAGAGTAGTATCATTAAATGGGTTGGTTTATTTA TAGCGAACTACAATTACATTTATTTTGCATTTCAATTCACAAGAAAGATA TGAATGTCATGATTAAAGTCCTGTTTTTATTTTCCTTTGTTCGGTGTCCA AATCAGGAATGATGAAATAATTGCTGTGCAGAAGGCGGCTCATTGAGTTA CGGAGAATTGATATCGAGATTTAATAAAGCGGATAATTCGTGGCAGGCCG TGTCCACAAAGTGGATGGATTGGCCATTTGCCAGCCATCAAGGATGGAGG AGGATGGGGCACCCCGATGTTGGTTCTTGACAAATGAATGTCGAGCATGA CGGCAACATTTTAAAATGTTTCGCTTCTCGTTCTCGTTTTGTTTGTACTC CACGTCGAGCTTTTCATTCAACTTACACGTACGTCGATGTGTGAGTACGT GTCTGCTCCGGGAAAACAGAGGAAAGAAACTTGTGCACTCAGCTGGGAAA TGCCTTAAATTTAAGAGAAAGCATTCCGTTTCAGCTAAGGAAACTTTTGG AGCTAAAAACTTAGAATTTAAAGAAAAGTTCCCCAAAATCGCTGCTCATT AATTGTGCAGCTCATTAAAAAATCACTTACCGTTTGTCCATTGCAGTTAT CCATTCCATCGCCATGTTGAATTTTTATTTAAATCTCCCTCGCTCGATTA GTTTCGCCGTTTGACACAAGTTATGATACAAGTTATGAACAGCACATTCC ACAAACACCAAACCAAATAGTTGCCCCAACTTTGAGCAGAGCACATAAAT CGAGGCGGAGCGGCTCCAAAGTGGTGCAAATTAATTGCCCGTTGCGGCCC AGGAAAGCGAAATCAAAATACCGAGTAATGGCGGCGCTCGCACCCAGTTT GCAGTCACCTCAATCCGCGATGTGGCCGTCAATCTGCGATTCCCTTTGAA TACGACATGCCAGGTGGCTCGGCCCAGCGAGGCACTCGAAATCCGCTTTT GGGAGCGTTGGAGCGAGCTCCTTTCGAGTTGGAGCCAGGGGTAAGTGGAC GTAGCTCGTTGATTAGGCGAAAGTTTGGAAATGGATTTCAGTTTGAGCTC CCGTTTGGCTGGCGACGAGGATTTCGATACCGAGCAGCTGCAAAGTTAAA TTGGGCGAATGTGAGTCTAAATTCACTATACAGCAGTCGTAAGTGTAAGC TAGCCTTGGGATGTCGGACTCTAATATAATTTATATAAAATGCCAGCAGC AGATGTAAAAGTTTCCCTCTTTCCGATTTTTTCAGCCACATAACTAATGT GAATTGCTATTGTTGGACTTGCCAAAAAGGGTTTTCCCAACTGCTGATAG CTGCCCAGAAGGCCCCACTGCGTCAGTGTGTGTGTGCTTGTGTGTGCTTG TGGGTATCTGTGTCGCCAACAAAAGCAAATGTTATGAATAAGCTTTGATG CCTGCTCGGCCGGCGAGGGGGTGTTGTGGTGCAGGAGAGCGGTGAGGGCG GAGCACCAACAAACTGTTGGCGCACAAATCTAACAATAGATTTCCAGATA ACAATAGATTACTCCACACACACGGCGTATACTTAATGCGCTGTCAATGG GCATTCTAATTTCCCAGTATGCCCAAATCCAGATCGTATGGCATGCGAAG GCACGATCTAACCGCGAATTCGTTACCGAACTCCATGTTTACCCATGCGC TGCACTATCTGTATCTGTACCGCAAACGAATGCGTATTTTGTTCTGCGTC AATGGGAAAAAACATAATTTATACCACCCCATCAGAAGTGCAGTGGCTTT CGTCAGCGAAATGGAACTGCAGGCGGAACAAGTGTTCGAGTGACGGCTCA AAAGGAAAGACATCGCGAAGGACCATCAGCTCGCATATGAATAATTAAGT ATTCGCCATCGTGGCCAGCCCGCGAAGGCGCCCGAATGTATGCCACGTTT TCTGACGTGTCGTTCGCTCGCTGGCTGGCTCCACGTACATAAATGGCGAC AAAAGTCCCGGGGGCGATAAGACTGATATTGGCGATATTCCGAGTGGACG ACTCGATAAGCGGCCACTTTCGAACGAGTTGTCCATCCTGCCAGCAAATG CAATTAGTGTCCGGAGTGGCGGTTAGGGAATTGAATTGAACAAGCTTTGA AATCGCCCTGGAAACAGATGTTCCATGTAATTTCCACTTTAGGGTTTCAA ACTTTGTTTTAATTAAGCAACCGAGTGAAAGCAAAACTTTGAACCACAAT AGATGTGATTTAACTGCCCACTGCAGCCGTTGCCAAACGGAAAACTTAGC CATTTAGCTTGGTCATGTGGCGAAGAAACATCATGAATCGAATACTCACG CATCCTCTGAACGGAGAAAAGGATCAGAAGATGCAAGAGTAACAGAGATC CCGCAGCAGAATTCGATATTTTAAAGTCCTTCTTGTTGGCAAACACTTTT TGGCACGGAAAATGAACTTTTAGTTTCGAACCCACGCGACATACCGAAAT CCAGCGAATACCTGAAATCGAACCGACTTCAAACGAATATTTAAATGAAC CACTTGCTAACGGCTTTCAAGCACTTGGTATATACAGTTCTTGGGCAAAC ATTTCAGTTCTCGACCTCCGCTGAAGCGCTATCGCGTCCGATTCATTTGG TAGTCGCGTCGCAACTGCTCGGCCGCCTTCCATTTTCCGACTTCCGAGCG GCGCTCTTCACCACGCTCCTGTCCTGCGCCTCGCAGGTGGGTTTCCCGGC GGAGATTGGGGGTCGTGGTGGGTTGTTGGAAGTTACTCATTGCCGATGAC TGCAGTGTTGACGGCTGCGGTGCGGTACTTTTGGCCTTGTTCCGCCTTCC CGCCGTCCCTTTCCGTCACTCACATATTTTGGCGCGTTTTTTAGCAACAA GTTTGACAAATCTTCGGCACAGTGGGCTTACATCCAAATCGGTGTGGTCA AAATCCAAATAAAATTTGGCACACGAAAAAACGTAATTTCAAAGTAGTTC TAATTAAATACAGTTTCTTTGCTTATAGTGTTTGAAATTATACTACTTTT GTTATAATATTTATTATAATTTGAATCCCATTATTTTGTGATATGAATGG ATTTCTACTATTCTTTTACGATTTTAAACTTAATATTAATTTAATTTAAA TATTATTCTTATTCATTTACTGCCTACACTTATATACGATAATCAGCAAA GAGATACAATTTGTATAAAGATGGCTATAATGATATAGCATTTAACATAT AAATTTATGTTCTTGTTTGATTTATTTGTTTTACTTACTTGCTTATTGCT TATTAGTATAGATTGTCTTAAGTCCTCACATGATTAGTGAGAGGTTTGGT TTTATCTTTTATATGTTAATTGCGCTGTTATGTTACTGTTACTGCATTGT ATGGATTCATCGCTTCTAAATAAATAAATATAAAAAAAAAAAAAATATAG ATTGTGTATTGGGCTTTAAAGATGAAAAGTTAATCGAATCTGATATGTTG TATTACGAATAATATTGCTTGCCTAGTCTACTTGAAATAACAATTTGTTT TGACTCTATTCACTCGAATGTTTAGCAACATTTGCTGCTCGCTCTCCTAT TCTACGTGCTCCACAACAAACTGTTGAGCGTTATTTTGGTGAGTCGTCGC AGTTGACCAGCTCTTCAACAGGCACTTGTCCGTCCGCTCGGCCGTCGGGC GAACAGCGGACAACCCCGCACCGCGCCCCGGGCGGAACTGCCTCACACCC TCGCCTGAAAGTGCACATAAAATGGAATCGCAATGCGAAACAATCAACAT GTCAATTAAATAATGCACACCAGCAGCGGACACGAAACAACGGACAGAAT TTACGGAGCGAGTGCGTGAACACCCGGACTTTTGGTCACTTGGACACTTG GACATTCACTGACGGCTTGTCACATTCAGCTAATGAATCAACGGCGATTC AGTCGTGTTCGCTCCTGAAAAGGTGCGAAAATGCAAAGCTTTCCTTTTGT TTTCCACCTTTCCCAGAGCCGCTGTTGTTGTGGTCGCCACCACAATATTT ACGGCACTCTCGAGTGCCTTTATTTCCGCATGAATCATTCCCAGTTTCGG TTCCAGCTCCACAGGCTGCCCCAGCGCATATAAATTCTTGGCTTTTTCCC CCAGCTGTTAATGCACAGAAAGAAAAATAGTTAAGGTGGATCGTAGTCTG GTATTCCTAGATAGGTATTTCATTATACACAAACGGGTGTAGCATAGGAT AAGTGCAAAGATGAATTACTTCTACTAATATAATTAGACATAATTAACAA TAACGGTATAGCACTAAATAGAACTGACGTAATAAAAGTGGAAGACTACT TTCCCTGTGTTGCAGGGTTTTTTTTTTTTTTTGGTTTTTCATGGGGTCTG CCTGTCGCATTTTTTATGAGCCTCCCCCATGTTGACAGGACCACCATAGA CATTTTTTCGGGCTTGCCAATGCGGAATGAAATTCCAAGAATTTAACGGC CGCTTTGCCTGCTGAATATGTCATCACATGGCGTTGAATCCTGCTCCACC AGACACAACACAACGACCCGGCGGTAATTATGATAAATGCGATCTTAATA AACTCGGCTGGTGGGCACGGCTGGCTTTGAAGGCCTTCATGGCCAAGTGC GGGCTCATCATGGCCGGTCCTAATGCATTTTCTTTTCATCATCAACGCAT GTGGCACCTGGTCTAATGGCGCTTCCTGCCACCCTGCCTGTGGCCCATTA GCAGAAAATGCTGTTGTACATTGATCGACTCGTCGTCAGCTAGTCGTTGT TGTCGAAGTCCTTGTCCAGGACTTTGGCTCACCATCCTCAGCCAGTCGCT TCAAAAGTCAGTCACTGGTGCCGTCGGAACGTGTTTACGACCTGATTGCA CTTACCCACCCACCTGCTGATGTCATTATTATCGCATGTGTGGCACACTG GCTCTTTAGTTGCATTAATGGTTATTCAATCAGCGTTTAACGCAAATTGC CTATTAAAGCTGCCCTGTGTTCCTGGGCTCCCTTCATGCAAATGTTTGCG TATTATGGCCATGTAATTTGATTAGCTGATAAATGAGGTAACGCCAGCGC ACGTGCAATCAGGAACGCCAGCGCCACTGCCTTCATGTTTTGACTGGCTA ATAAGGCACTCGCATATTCCGCAGGTTCCTGATAGATTCACCCCACATTC CCTAACCACCATGGCGGTGCACCAGTCGACCAACGTGTAGCACACATTTG GGCGCAACTCAAGCTGTTCAGTGCGAATATTGATGTTTGCCTGTCGGGGA TTTTCATGTAAACGCATTGATTAATGTTCTTGAGAATCAGATGATTGGAC ATCCACTGCACTTATTTGATATATATATATACATATTTATATATATATAT ATATATTGTGTTCTTAGCTAATTAATTCGGTGCTGATAGGCAGGGTATCG ATCTGTACTTTTATATTGTTAAGCCCTTAAAGACGCTCAAGCAATAACCA ATCACTGATTCCAGCTTGTCAGCAGAATTTAGCTGAATAACTTAGTTTCC ACAGAAAACCCCATACAAATACTGAATTAGTGGCGAGGAGATTTCCTGTC AATACCCTCCGCCATCCGGCAAATACGCGCAAATCAAAAGTTAATAGACG CGATGGAGTCTCTGTCATTTGCATTCAACCAAAAACTTGATTATCCGCGC GATTTACGGAGCGCAATTTTGGGCGGAAGGGCGGACTGGGGTATGGAGCG GGCAGACTGTGTGCTTAATGAGCTCAGTGAAATGTGTGCTTAAAATTAAC TTTCAGCCAACAAACCCGTCCCTGCCAATTGTCCCCGTCGCCATCGTTCT CCTAGTCAGTCGCTTTGGCAGCTGTTGCTCAGCCAGAAGTGGTTCATGGC TCATAATTACGCATTCAATTCGACAGGCAGCTAGCTCCAAAGGATCCAGC TGGAGCTGCCCAAATCGGAGAAGGGTGGCCGGTCGCCCGAAACTGCTTTA ATAATTAAGTCTCTTGAACATCAAGACATCGTGTCGGACAACAAAAGTGC CGGGGCAAACACAAGGGGAAGCAGGAGGTCCTTGGAGTGGAGCAAGCACT TCGCCGTGTGTCCGTCCACTTGGCCATGTCATCTGCCAACCAACATCCTG GGACTGCGACTGCAGCCCGCTTGGTGCGAGTAAAAACTAATTTCTCGCCT TGCTGAGCATAATTTTATGCAATTGTTTTCTGATTAAATTCCACACTGAA AGTGCCCCGGTCTGCACCCGCATGTTGCATGATGCGTGCCACTTGGCCGA CTGGCATTTTCATGTGGGACAGCTTTTCGGCCGAGTTTCCGGGTGGCGGA AGCACTGGAGTTCGATTTGGACATAACTTTGCTAGCGCCTCCATCTTGCT GCACTTAAGGTTTTTATTATTTGCTGTCAGACGGCACCACGTGGCGGATA CTTGATGTGCAAGTGGAACGTTAATCGCCCCATAATTGGATTAATCAACG GCCGGCAGCGGAACGCCATTAATAGGCCAAAGCCCCAGCAAACCTCACAC CCGTGTGCTGGAGCCACCTTGGAGTGGCAGGTTCAATGGCGTTCGGCTTT GAGCCCTAATGGGTTCTTCGACTGGGGAAAGCGTCCCGTATCGGGTGCAT TGAACGGCGCACCATCTGCCACTTCCATCGGCATTGGCCAGCACATAGCA CAGAAAAAACGGAATTGGAAAACCGAAACCAATTTACATTTTGTTTACCT TTTGGCCAGCACACCTCGACGTCCATCGTATTTGCCTTCGAAAGAGATGC GCCAGTAACTGGGCAGTTCCACCTAGTATATAGGATCTATAGATCTGTTT TTTAAGCATTTCCGATTTCATTAAATTTCCATTAAAGCAAGCTAAACATA TAGTTTTACCTCGGAATGGATATATAGAACCGTTCTCAACTTATTTCCGA TTTTACTAAACTTTACTAAAGCAAGCTGAACCTTATGTCACAAGATTTTC ATACTCCTCCCTTATAATTTTTGATGGAGCTGCGCTCGAATGGGGTGCAT TGGCTCCATTCTATTCTTATCATTAGATCAAATAAATGTAATTTAAGATT TCCCATAAAGATATCCCTTCAGCGCCAACAGATCCCACCTCCTTTAAAGC TACCTGTGCAAATATTTTCCCTTACCAGACTCACCACCTCTGGTTTTTTG TGCCTTCTCCGACTTTGAATGGCTGGAATTTATCGCTTAACTCCGCACAG CAGCTGAATGGTGTGGCATGGGGCTTGGGGATGCCATGGGGATGGGATAG AAAAGGCGTTGAAACTGAGTGTGTAAGTTTTAATTTTATTTTCTCACTTC ATTTGGAGGGTTTGCCTTGGCTCCGCTTTGCTGGCGACTACAACACTTTA CATACATTTGCATAAGCACTCCGGCAGTTTAAGCAAGCTGTCCGGGAAGT TAATAAACAGGATTCGCCTTTTGCTCAGTTGCTTGTGGATGGCCAATCCG GGAGGAGCTGCCGCATTAACGCCATCTAGCAGGGAGTTAAGTTTTCTGGC TTCTTCTGGGCTCCTTTGCGACTGGAATCTGATTGCGGATCGCGTCCAGG TGTGACGCCGGTGCTGTCAGACGCCTGATTATTTGTGGCTTATTGCGCTA ATGCGAAGCTTATCGCATGAAAATCGCATTAACATCATTTGCAAGACGCC ACAACGTCCTTGGCCCTCCCAGCTACCGCCCACCTCCTAGGCTGTTTGAT TAGCCAGTTCCCGGGCCCATAAACAAATACCGTGCAAATATCGCATTCGG CGTGGGCTGGCCGTTTTGTTTGCCTAGTTAATCAAGGCAGCCCGGCGGCC ATTAGGCGCACAAATATTGCCCAGAATTCCGAGTTGTTTGTCCATCGCAA ATACGCAGCATCGAGGCGTCCAAGGCTATTATCTTTGACCCAGTTTCGAC TCACTTGCTCACAAACGCAGGTAAATAAGTTTGAATTATTAACGATCACT CGGAGATGCTCATCAAGGACGAAAACAACGCAACATATCACAAAATAATT AGTTGTGCCAACCCAGATATAAGGTTTATCGTCGATAATCCCGGCTTAGA AAGTTGATGGCTCCTTTCCAATGGATAATGAATACCTAACAGTAGCTGGC AGCACGGAATACAAACACTTTTGATAGGAAACACTTGTTAATGGAAAGAG ACTTCATGTTTTAATACGCATACAACTTAACACACTTCGCCCTACGCCAT CATCGCTATCTGTAATATGACCTCTTAAGTTGATTCATTTTATTCGCACA CATCCTTGTGTCGATTCCCAGAACATTTGGCTGGCCCCACCTTCGGTATT GGACCGCCCCAACTTGATTTTGTGAATCTTCTTCTGCGGACGACGGCTCA GTTTATGTCGTAGCCCTGGAACAACAGTGTCGGCGGCAGCAGGAGGAGCT ACGTGCCGCCATCGGAGATATCGTCCTGTGCGTGCCTGAAGGACCAGAAA AAGGAGCTGCGACAATGGGGCTACCCTCTCGAACTGGCGCGTTTGATGCG CTTTTGATAATTTGGCCGAGACGCCTGAGCCGCGTGACATCTTTGTTGCC GTCGACGGCAGTGTCGCCATCAGGTTGATAAATAGTTTTACCGGCAACTC GACTTTCCCGGCTGTTTTGCTGCACCTTTCTCGCATTACAACAGCCCCGG AGTTGGTTTAAATTAAAAAGCGTCCATCAAGCATTTCCCCAGCGAAAATG CAGCCGGACTGCGTTGGACTGCCGAAGGCGACAGGACTTTGTATATCCTC GTTTTTATTTCGCAGGCAGGTGCTTCAATTCTCAGGCTCTGCCTGCCTCA CCGACGCTGAAGCTTTAAAATATTCCGCATTCAGGAAAAGAAGAGCGGTA ACACAAGCTCAAATTATATCAAACGAAAAGATTTTACACTCACTGGAGGT CCATAAAGTTGAAAAACCTCTCTTTACTGTCTTTCAATTTTAATTGAATC AAATTAATTATATAATTCGGGAACTATTGAGCAAATTAAATTGATGTATC GTTTTCTAATCAGGTTATCCATAGCCATAGACATTTAATATCGCTTGTTA TCGTATTTTTGCCCAATTGTGGCCAATACGAGGTAATTTTCATTGATTTC CGGCTATTTTAAGGGCGTTTTGGGTGTCAAGTGTCGTTACGAGCGCCCTC CGATGTTTTTTTTGGCGGGGATTTGTCCATAAATAATTCATTGGAACATG TAACAGAAGTGCGTCAAGTGGTTCCCCCTCCCCGCTCCAACGCACACGCA TTGGATTACATGGGACGTGGACGCGTCTGCCGCACTTCGCCGGAGTGGAT GTCTATTTTTTATGGCACCCCGGGGAAATGACGTACTATGAATGCCGGTT TAATACACAAAACTTTGACAATATTGTCGCACAGTTAGCGCGGATACACA CACCAACCATGATACTCATACCACCCCATACCACACCATGCCATATCACA TCCACGGCAGGCAATACAGACTTGTAGCCAGACAAATGTGCGAATAAATG GGCTATTTTTGTGCGGCCTGCGTCTATTGTTAGCGAAGTTATTCAATCGC TGTTGCACACACGAACTCGGACAACGCCACGAATGGCAAACAAATGGTTG GTGTATCAACAAATCGATCATTTTTCCGCACTTGAGCTGAAATCATTGAG TGACTGCAAGTTCGGCCAGGGCCCCAAAATAAAGATTTAAAGCAAACAAA TGCGGTGTGTATCTGCCGGGTTTGCGTCACTCCGAAAATGGCACACGCAA ATAAAGTTAACGTTAAAGTTAAAGAGCGGAAAACGAGCTGAGGATGTGGA ACTTTATCAAGTATACGCCCATTTGGCCCATAAGCCATTCGCTTGTGGGC TGAGCCATTGCTGGCCCCATTGATTCCGGCCATCTTTCTCGTCTCGTCTC GTCTCGTCTCGCAAAAGTAGGCAACAGTTGGGAAGCAAGCTTGATTAATT ATCCAACTTTCCCCAGACATTTGCATTTGCATTAGTAGATCTTAAATGGA AATCAAAACAGGCCATTGAATGCACAGAGAGGAATTATCTTATGGCTGTT TGCTATCAATAATTCGAACACGCTAGGTGTTACTTTGAAACATACTTGTG CCATTTCGAACTTCAGTGTGTTTTCTCTCAGTGTTCCAGAGAGATGTATC CAAGGACTCTTTTATGACCTCACTTTCGCCGCTTTGTGCTCGGTCGAGTA CACAAATGAAATCCTTCTTTTCACTTCCCTCGAACGGTTTTATTTAAGTT TCGCGCTCATTGTTTTTATTTGCTTTTAATAGGCGGACAAGAAGTTGTGG CCGGAATCCAGCCTTCGGTGGCAACTTTAGTGGCTGCCAGTGTTTGCTCT AACATTGAAAAAGTTTTTTCCACCGCTTTCTTCGCAGGCATCGGCTCATA AAACGAACTGCAGACCCACTTGCCTTTCACTTCACCTGGGCTTTCCATTT CTAGGTGCGAATGACAAAGGGGCGAGGCTGGGCGGTGCGGAAGAGCCCGC AAACTTTTCCCAACAACAAAAGGTCACTGAACAATTGACAAAGGCGGCGT GCTGCTGTCTCAGGACTTGCCAAACGCCATTTAAAAAGTTTTGCATAATA GTTGGCCCACGATCTCGCGAAGTACCCGCCAGGGCAGAATTTCTCCAATG CCAGAACAATATAGCCATTAAAATCATAAAAAAAAAACAAAGACAATGTT ATAGTCGAGTTCACCGGCTATCAGATACCCGTTACTCAGTGATATTTTTC GGCATATGTATAGAAATCGCAAAGATAATTAGTGAAGTAGGTAAAATCTA CCTGTTTAACTTTTAAGCATTAGCAATAACTCAACGTTCGTGCGGAGCAC GGCTAGATATCCTTCCTAAGGAGACGATTCCTTCTACCTGTATACTTTTT AGAGAATCTAGTACCCTATGAAAACCCTCTTACCGTTATAGTATGTTCTA ACATCAACTTTACTGACTGGCCATTATTTCACTGAAATCATTCGATTATT TTTAAGTCTTAGTACCTTATGTTGGGAATATAATCATATTGTGGTTAAGT TGATTTTTATACAAAGTGATTAGGCACGATTAAGCCAACTCCAACAATGT TTATTGTTTTAACTTACTTTCGGAAGAAGCTGTAGCATAATAATAATAAT TAATTGTTATAATAATTTGTTAGTTTTATCAAACAAGTGTTTTCCTAGTT TAAATAGAAATTAAATTCAAAGGTGCAAATACGTTACAGGCTGTGTGACC AGTGCGCGCATGGTATATTTTAGTGCGTTCCCCAACACTCGAAGCCGCCA CGGCCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGA AAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCG TTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGA CAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGGTGAGTGG AGTGCGCGGTGGCCCAGGGCTCTTCTGGCCAAGATTTCAGGGGCGTGGTG GGGCGGGGGCGCAGGCGGCTTTTGTGTAGTGCAATTATATAAGGTGGAAG TGGGGAAGTAGGGGGTCCGGGATAGAAACGCCACAGATAAGCACGCGAAA TGCACTCCGTAATTGGGGGAACTGCCAACTGGCAGAGGCTGTTATGTAAA CCTTTTTTTCAGCGGCACCTGAATTGGATAAAATGGGTAATGGCGTGATT CTCCGAACTTGCAGATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAG CAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGA GATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGA CCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTG ATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTG TCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACA CGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAG GTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACAT GAACAACTTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCA AGTGAGTGGGAGCAATCCCTACGAGCTGGAACGTTACTAATACCACGCCC TTTGCAGGAACGAAGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAG TCCGTCGAGGATCGCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTG CGCCTGCTGCTCCACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGT ACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCG CGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAG CGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGG GGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGC CTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTA GGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTG AGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTT ACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACA GTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACCAGC CGGGCGACATTGTGATGGGCAATCAGGGCACTCCCATTCATTTAGGGGGC TGTGGGTGAGGTCTCGTCGTTCATCTGAATGTCGTCGGCGGAGTAAAAGT CCTGGGTTACCGGGATGACGCGGTCGTTGGTCTCGTCATCCTCCTCATCG TGACTGTCCGTGTCCTCGCTGTCGTCGTTGGCTGCACAAGGGCAATTGGA CGTAAAAACGATAATGGTAATCCGAATGCAGTGTCCTGCCGTACTCACCA TCCTCGTCGTCGGTCTCAATTCCGGGTATGGTGAGCATTTTGCCCAGCGG CTGCAGATCTGTGCCGGCCGTCTTAAGGGACTCTCGCTGTACGGTTTAAG TTTATAACAATTTATACAGAAAGCGGTGTCTGGAGAGAACTCACCCAGTT GCTCCTTTCATCCTCATAACGCCGCGTCTGCGATTCTTCGTTTACGGAGG CAGGAGCCATGTCCAACCAGTAGCGATTGGCCACGGAGACTTTGAGCGTG GGAAAGAATGGAATCATTGACATTTTCGACGGAATCTTGAATGCGCTGTT TTCAATATTTGTTGTTCTTTCTCTGGAAGCCTTTGATGCGATCTGGCAAC GCCGCAACATACGCTGTAAATAATACCAATTTTACAGGGGCGTAGTCGTA GGGGCGCATTAAACGCAAATTACAATATTAATTGTAATTGTAATTCATCA ATCTAACTATGTATTTTGTTATTGTCAAGGGAAGTCCGATAACCAAGGGC TTAATACAGCTTACTCAAAAATATATATCTTCACTATTACAAATTGACCT TAAGAATCAGAACATAACCAAAACGAATAATATATATTATTCAAAATCTT TTTATTTATTAAAGAAGCTATAAAAATTGGACAAACTAGACACAGGAACG GTATTCCCTTGCAGTTTTATTGGTAGTAAAGTTCCAGATTCATGCCATCG TGAATTTCATCTAAGAAAGCGAAAAAGAAATGCGGGTAAAGCAAGGCGTT ACAAGGACACTAAACAAGGGCTTACAGTCAGATAGGCGAATCGGGTCCTT GAAGATTGTGTACCACTTCTTCAGGACAATCTTCTCGTGCTTTGTGCCCG TTTGTGCCGCGATTAGTTTCTTGAGGTCCCCAATCGTGTCGTCCGGGTTG CACTTGACGCGCACCTGTGGGTTAATCGTTGGTTAACGATGCTTGCAGTT GCCTTGGGTACTTAGCTGCTTACCTTCTTGCCAAGACGATCGTTACACGT TATTTCTATCATATTTTATGGCTTTGCTAGACAAATCACAACAATAAATT CTTGATTTGTTGTGGTATTATTGCTTAGGGTTGTCAAATACCCTTTACCG AATACCGAGTGGTTTGAGGGATCGCTAATTGTCCGCAATGCTATCGATAT TTTATTTAATTTTAAATATGTTTAAATAACAATCATATAGAAAGTCGAAG TTAAAGATATCAGAAGTCTGAAAGTATACTTAGAAAGCTCAATTGCTTGT CATGACGCAAATCTATCACATCCTTGTAAAACGATAATATTTGTTAACAA ATTTATATTTAAATTTCAGTCTTCTTCTTAGTTATCAAGCCAGAAGTCGA ATGTTTCGGCGTTAATAGAAAAATAATGTATGTTTGCATATTTGCACACC TCATTCAAATTATTTTTCTTTGTTGAACAAAAGATAAAAGTGTAAAAATT AAATTTTTTATTCTTGACCCATTATTTCTCTTGGTTAATGAAAACAAATT CCGTTTCTCAACGTTCCCTTTAATAATCCATGTGAACAATCGATAGGCGG CGAAACATCGATGATTGCTAGAATAATCGATGTGTCTTCCCCGTTCATTC GAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGG AGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAG CTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAA GTATGTCACATATTTGCGGGCAAACTGCCGAAAGCACTGTGCGGAGTTTT TGTTTGTGTGCGTGCGTGCCTCATTTTTACATTCACGTACATACATATGT ACATATATGTACGCTATGACGCAGCTGTGGAAAACTTGTTTGGGTTTCCA TTTCACCGAATCACGGAATCAACGAATATTTGCGCCTGTGCTGCGAACTC ATTTTGGGCAGTAAGCCATTGTATTGATTATCGCGCGTTGTTTGTGGATG GCGTGGTCCGCCGGAGCACCCTGTAGCGTCTACATCCCTACCCCGCTCCC TGGAGTCCGATATCTGTGCGCGAAAGGCCGGGCGGGCGTCGTTTTCGGCT ATGTGGCCCAACACCAATGGATCCCCACGGTCACTGGCAGCAATTCGCGA TCCGAAATGCTCCGCCCTATTTTTAGACGCGGTCTTTGCGGCCTGCCTAC TTACCTACCTCCCCAATGCATTCTAATTAAAAACCGGGCACTGCGCTCAT TTCCACACGCATTGCATTGCATAATGCGGCATTAATGTGGCGGGGAAAGC TCGCTTCGGAAAGCACTCGAGCATTGAAGTGAAGAGACCGAATGTTTTCC AGCTGCCCAATTGTAAACAACCCACGCCTAGCACGCACACACACGCACAC GCACACACACACAGACTGGTTTTAATGTTTACTCCAAATAAATCGTTGCC CATGTTAATTATTTGTGTCTTCGCAGGGCCCGAGCACTGGAGGGAATCTA ATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTC CAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACG CCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCC AATGTGCAGTAAGTATCTGGGATACTCCCGAAATAGGCCTACGGACGAAG CCCTTTATCGCGAACCCATAACATTATTTTTAGCCCTTATAAGTAGTAAA ATTGTAAGCATACAATATGTTTACGGAGTTCGAGTCAATTTCATTTTGAG AATTAGGAGAATTCAGTTTAAACTCTATAATTATTTCCTATTTGGTCCTG AGTCACCTTTTTCTATACTGACCATTGGTTTCAGTAAGCAAGTTGGACTG TAGTAAGACACATCCATAGCGACTGTATGTTTGTATGCCGTGTGCTGCCG CCATGACGTCACCTTTTTGTTATTCACGCTCGCCGCGAATTTGAATTTCG AAGCGGGTAGAAAACGAAGGCAAAGCCGCATACAGGGTGCAGCATCTGGT CGAGCTTCGTTAGTTTTTGGCGCCTATTTCGAGAGCGCCTGGTCGGTCTG ATGATCAGTCTTCAAGACTCGATGACGACATTCGGAGTCCAACGTCGGCC GTCAGAAATCGTTTTCACGTTTTAGCCTCTAAATCGAGCATGCTGGGGTG GGCTAACAGTCGTTTGCGCTGAAGGCCAGCGGCGGTTATAAGCATATTTT TGTGTTTTTGTTTTGATACGTTGTACTCGTCGTTTCAAACGATTCCGAGC ACGTTATCACGGACTTACTGAAATATTTTTCCCAAATCTTACCTCTTCTC TGCAGAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAA AACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACG ACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTC ACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAA CAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAA AGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTAT CTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAAGTGAGTGAA TCATTTCTACACATTTTAAACAGTATACTAATGATGCTATTTTGCAGCAA AACTCCCAAGACGGACTATACCTACTCAGAACTGTCCCCTCACCGACGCC AGTTGGCGCCAGGAATTGTGGCCATGCCCAATATGTCCAGAAAGAGCCTA GAGAACCATAACGATCGAGTCAACTACATGGTCCAGCAGAACCCTGCGCA AGAGGAGTTCATCCGCCGCCGCTACCAGTCCAAGTATACCCAGCAGGTTA ACTATGACTCCGCAGATGAACTGGACGCCACATTTGGGCAGCAAAAGCAG AGCTGGTGGCTTATCCGCCTCATCCAACTGGTTGTTAGCAGCATTACCAC CGTGTGGAGTCGGGTGACCAATCTCTCGGCCACGGAGACGACTGCCTATC AAAACTACCACGCTAAGCGCCAGCAGAGTCAACAAGTTGGACTTTGGTGG AAAATAGTACAGACCATCGGAGGAGGACTTGCAAGTTTGCTGCGCTACCT GTATGTTTTCATCGGATCGGTGCTGAGTTTGGACACGTGGTTGCTGCGAT CCTCGGATGCGGAAAACAAGTCGAAAAAGCGCTTCCTCATATTTCTGCTG ATTTTGTTGCCCTTGCTGCTGCTGTCGGGTGAGTAGGATTTAAAGCACCG TCCGATTTTTGATGTAAAGTAAAATATGTTAGAGCGTGTGCCGTGACCTT GTACCGGTTCGAGAATTCATACTACATGCATATAGATCACCTCCAGTCGT TGTATTTATAAACTCGTCTGGTCGTTGGCAGTCGCGTGACGCCATCGATA ATTTGTTAGTAAAATCCCGCGGATCAGATTTAAGTGGCCATGTGATGACA TATTTTATTTTCCATTCACCGTCTGCCAAGGTTAAACGCCTAATTTGCTT TGCCTTTGCAGGTCTGTTCTATTACATACACCCCAATGAAACTTTCCCAC CCAAATCCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATC GATGTGAAAGACTACCTGAACCAGGAGCAGTTCGAATCGCTACGCTCTCA GGCCGCCGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTT TGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTA TTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGC AATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGC CCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGT ACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGT TTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATA GGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAAC AAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTT CAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTA GGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTT AAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTAT ACAAAAATAAATCGCAAACAATTTCATATGAAACATCAAGTACAAAGAAG AGTTGTTTGTTTTATTTGCCATTTGTTGGAAGTTCGCTAAATGGTAAGTA AGATGTAAACAAAGCAATATTAGTTGGCCAGAATCGAACTCTATCCTTCT GCATTTGTGTTGGAATAACCCCAAAAACGAGTTCCCTGTTACCTCAGTCC GGTTGATAATTGAAGTTGGTAGGGACTGTAAATGTAGAAGGATTGCCAAC TAATAGTGCTATGTTTAATTTTCTCCTTCCCCAGGATGGTTGCTCTTGCA GGAGGATCAACGTAGTGCTTACGTTCAGCGTGCGGAAGCACTGTTGCCGC TGCCACTATCTATTTTCGGCTCCCTACGTAGTCGATTTTCAAATGCTGGA GCCACCTTGAAAAGTTGGATGGAAGTGCCCACCGTCAGGAGTCCCCAGCG GGAAGCCGAGGCCATTAAGGTAAACATGGCCAGCATTGAACAGAACATCC AGAAAGCCTTGACTGCCGAGGAATACGAAAATATCTTAAACCATGTAAAC AGCTACGTGCAGCAGTTGGTCGAGCTGAAAATGCAGCAGCATTCCAAGGA GCTCGCACCGCAACAGATTGAACTCTTTGTTAAGCTGATGAAGGAAAACC TCAAGCAGATTATGTACAAAACGGAGCTAAGCGAAAAGGATTTGTCTGAT CTGGCCATAAAACTGAAACTGGAGCTGCAAAGCTCAGGCGGTTGGCAAGA TGGAGCGAAACTATCACAAGCTAACTTAGAGGAGATAACCAAGCTAATTA AAGCAGAGGTTCACCTCCACGAATCGCACTACACCATTCAATTGGACAGG ATAGACTTTGCATCCCTGCTGGAGCGTATTCTTGCTGCGCCAGCATTGGC AGACTTTGTAGATGCTCGAATAAGTCTTCGGGTGGGAGAGCTCGAGCCAA AGGAGAGTTCCGGTTCCTCAGATGCAGAAGTCCAAATTGAGCGTCTGAAC AGGGAAATCGCCTTCATTAAGTTGGCTCTCTCTGACAAGCAAGCGGAGAA CGCCGATCTGCACCAATCAATCAGCAATCTGAAGCTCGGCCAAGAGGATT TGCTGGAACGCATACAGCAGCACGAACTTTCCCAGGATAGGCGCTTCCAC GGGTTGCTGGCTGAAATAGAAAACAAACTGTCTGCGCTTAACGACTCGCA GTTTGCTCTTCTCAACAAGCAGATCAAGCTATCCCTTGTCGAAATTCTGG GCTTTAAGCAATCCACCGCTGGCGGTTCCGCTGGCCAATTGGATGACTTC GATCTGCAGACCTGGGTACGCAGCATGTTTGTGGCCAAGGACTACCTGGA GCAGCAGCTGCTAGAGCTGAACAAGCGCACCAATAACAACATTCGCGACG AGATTGAGCGTTCGAGCATCCTGCTGATGAGCGACATTAGCCAACGACTC AAACGGGAGATTCTTCTGGTTGTGGAGGCCAAGCATAACGAGAGCACCAA AGCGTTGAAGGGCCATATCCGCGAAGAGGAGGTGCGCCAGATAGTCAAGA CGGTGCTAGCTATTTACGATGCCGACAAGACGGGCCTGGTGGACTTCGCC CTGGAGTCGGCGGGCGGCCAAATCCTTTCCACGCGTTGCACTGAGAGCTA CCAGACAAAGTCAGCCCAGATATCGGTGTTTGGAATTCCACTCTGGTATC CCACCAACACGCCGCGGGTCGCCATTTCACCCAATGTGCAGCCAGGGGAA TGCTGGGCATTCCAAGGGTTTCCCGGATTTCTAGGCAAGTCGCGGGTAAA TAGTAATTGCTAAAACAGTCCTTATAGTTTTCTTCCCACAGTGCTAAAGC TCAACTCGTTGGTGTACGTCACTGGATTCACCCTAGAGCACATACCGAAG AGTCTATCCCCCACAGGAAGAATAGAATCAGCTCCTCGCAACTTCACTGT CTGGGTAAGTTTGACTAAGGGTGAAAGGAAGTGGTGCATTTCTAATACGA CTTATCCATCAACTCAGGGCTTGGAGCAGGAGAAGGACCAGGAACCCGTA TTGTTCGGCGATTACCAGTTTGAGGACAATGGTGCTTCCCTCCAGTACTT TGCCGTTCAAAACCTGGACATCAAACGGCCGTACGAGATCGTCGAACTGC GGATCGAGACGAACCATGGCCATCCCACCTATACATGCCTCTACCGGTTT CGCGTGCACGGCAAGCCGCCGGCCACATAAATCTGTTCAAATCTCTTCTA GTGACCTAAGTACTGCCAGGTGTACATAATGTCTGTGCCTTAAAAAGGAA ACTAAACAATATATCACTGCGAGATGTGGATCAACGGAGCCCAGCCGCTT TCAACAATGCGAACTATGTAAAAAGTAAGGCTATATAGATTGTAAGTGTT TTGTATCATATCGTAGATTTGAAGTGTTTAAATCACATTAAGGTTAACTT GTACATAGCATATTATTTAAGTCAGGACTAGAGTCCCTATAAGTACTATA ATATTTATTAGTATTTAGTTATTTCCCTGAAATCAATCATCGTTCCTTTA AGTCTACTCTACTTACGTATGCAAGTTTCCAACCCGTAAACGTAGCACTA TACCCCAGTTTATAAACAAATTTCAAATTCCAATCTCGGCGTCAAAAAAA TGATCTTGTCCTGAATCAGACTGATCTTCTAACTTTATCCTAATCCAATC TTCCTCGGCCAGAAGCTTTTCTTTAGAAACTTCTTTAACGTTCAATTATG TTTAGAATCAAAGCTTTATGCTGATTGAGACGAGAAGTTGATCATGGCCT GGTCTCCAAGCGGAAGCTGTGTTTACTTTAAGTTTTGTTATCTATCTTAT CGGGTACCTAAGTGCTGGCAAAGGCAATGACAAAAACAAAGACAAAGGAA ATGCCGCCGAGATTGAAATGTGAAATTTGTTTATAAACTGGGGTAGGGTG CTATGTTTTCGGGTTGGATAACTTGCATATCTTTTACCATGTTTGCCATG TTTAAAAGCGTTTTGAAGGTAATAGTCATAGTTTGTCTAAGCCACACACT TGCTGGAAATGTATAGTTTAAGCTATATCTAAGCTAAAATGTTTTACCAT GAAAACTTGCAAATTCCTTATAAATGCGATAGCGATTTGAATTCACACCT CTAAAATAGTGACAAATAAAATTGAAACTCACTGAATAACTCGATCGAAT AAAAGCTGCCTGCATCCCTCCCAATGAAACAATCTATTTCAAGTTTTCCT TACTTGTCGTATACGTAATATGTCTAAAGAGTGAACCCAAAAATAGTTGA TAATTAAAAATATAGTTTTCTCTTGTTTCTATAAGTTTACTTAATTGGCT AAGTTTGTATCTACTTCCTGCGTTCATTAAGGTTTTTCACCATTTTTAAC AATAAACACATTGCTGTGAAAAAACGTTTTCTTAATCAAAAGGCAGGCGA AAAAATGGCTGTCAAAGCCATGGGAAGTAATTAACCTTTGCTATCCGGCT TCTGTAATTAGTTATTTCTGGACGCCAGCGAAGGATTGGGAAAAAAGGAT GCTCAGTTCAAAATCATTTGCTTGTATCCTTTGCTATCTACAATACATTT AGATAGTGTGTAGAAAATGTCCATTTAAATCGGATTTAATTGCATAATGA CGCATTTTACTCTTGACTGCAGTTGCTTATAATTTGCTAACGATTTCCAT GTTATTGTTAAGCCGATTTGGTATAAATGATGATGCAGGACTTGTGCTCC AACCTGATGAATATATTAAGTGCATTTCTGTTTCAGGCAGACTCGTCTTC GGTAATTTAATATGAAAATACCTTTGCAACTGTTGACTCCGCACGGATGT GTCATTTCGTCTGGGGTTAATGCAAATTGTCTTTTAATTTGTTGTGCCAG CAAATTCCTGGCGCTGGCAAGTCAAAGGATTTCATCTTCAAGCGTCAGCG AAGGTATGCACTTAATTAAAGCCAGCTGACTGTCTCAAACAGAGCTGATG TGATGGAGCATCTTGGATGGCAGGATGGCAGGACCCCGTCAAAGGGACCA CCTGCGGATGTATGAAATTTCTGCGAATAGAACGACCAGGCCGCTGGGTC GCCATTAGGCAGATTCCCGCCTCGGAAGGCGGAATGTCCTCGTTTGAGCC TGAATTACAGGCATCGCTCGGGCGTGTGTGTAATTGCGGAGTTGCCCCGC CTACACACACGCATTAAGTTTAATTGCCACCGGGGCCCGAAAACTTTTAA TTTCGCGGGGCGTAAGTTCAGCATATTCATTTCGCACCTGCTCGATGGCG GGAAAGAAGTGGCGCATGCAGCACGCTTAATTTGTTTACACAAATCTTGC TCAAATGCCAGCCACCTCCGCCGGCGAATTCCCATCGGGGAATAAAAAAT GAAACGACTCTGGGAACCGGCGGCACTCAGTTCGGGCAGCAAAACTTTCG TCCTGCGAGAGTGTAACAATTAAACTGCAGCTAAAAATAGTGACTAATGA GAAAAGTTTGCAGCAGTAGCAGCGGCTGTAAAAAAATGTAGGCAACGCAA CAACTTTCCTCTGAATCGAGAATCGAGTCGAGCTGAGTGTTTAAGTTGGC GGCAACTTTTCTCTATTTTGTATTGAATTTGCTAGCGTGTTGGACCGCCA TTTGCTGGCCTTAATGGATCAGCTAGCTGAAGTGTGCCAGCCATAAAGGG AGTTGCAATCTAGCCGAGACAATAAAACCCAAGCCATCATATCACACTCT TATCCCCCAGACGCAGGAAAACTTTGGAAAAGTTTACGGCCTGGTTTGAT AAGGAAATTCTTCAAGTTTCTGCAAAAAGATGCTTGGCCGGTGCTCAATT TGTATAGGAGTGGGGTCTTGTCTCCTTGTAACGCAACTAGGCCCAAATGA TTGCTTCCGATCCGAGGATCCATTCGTCGTTCACCAAGTCAACCTGCAAA GCAGCGTTTATGGCCGCTTCTGGCAAAAATAGCTGGCACATTTAAATGAC GTGACACTGGACATGACACCGGAAACCGATTGGCCGTACAGTGAAGTGGC GCCCGCAGTTGCATCCGCATTAGGTATGCGCATACTCTTTCATGGGCGGC TGAGAAAGTTTTGTTTGCCATGCAAATCTGTTTGCGATGTGCAAGGAAGT GCGGCAGCGCTTAGTTAGAGACACTTGTGTGACTTGTTGGCGTAATTGAA TTCATTTGGGGGTCGGTCGACTGCCGGAGGAGAAAGTGCCAGCACAATAA CTATTTAACAAACCGTTATGCACACATTTTGATAACTTTCAATTTGATTC CACTCTGCGGCGACATGGCAGCTCAACTCAGCTCGGCTCAGCGGGAGCAG GAAGAGGAGCAGCAGCACGAGGAAGTGTTGTGCTCTGCGGCCATAATGAA ATAAACTTGTCACACAGTCGGCAGAAGTCATTTGCCCCATGTCCTGTTTT CCGAAACTACGTCCGCCGGATGAACTAAGGCCCAGGGGTCAAAGTTCGGC AGGCTGGCAGCTGGCAGCTGGTGTGCCGCCCTCATTGGAAATTTAATTAC GCATGGCACTTGTTTACCGATCCAAAGTTAAGCCTTGCTCCCGAGCGAAC GTGCGCATTAACCTTAATTAAGTGACAAACAATCCAAGTTCGTCACGACA TCATTTTATTTACAGGCAATTGAATTTTAATAGGATTTCGCCTTGGCGAG AATCTCCTTGTCTTAGCTATCACCCAGGCGAGAGCCTCCTCCCCTTGGAG CTGGAGTCCTGAAATCCTCGCACCGACGGCCGACTGGCCATTTGCATGGC TCTTGGCAACGCAACTCTTTGGACTGTCGGCCATTATTTCGCACTTCTGT GTAATTTAATTCATTTGCAATGCCTTTGCGAATTATGTGGATGGGAGGTT TACTCTGCCATTTGCCGTTTGCCATTTACCATTTGCCTTTGGCCTGCCAT CGCCTGCCATGTCCTGCCCTCCAGTGCCTCGGGATTCGTGTCCTTTTGGC GGCCCAGTGTTTGGCCTTAAAGTCCTTTTGCGGCCACGGTGCCACAGAAA CCCCGAAAACCGCAAGCCACTTTCGTGATCCTTCATGGGAGTCATCTTAA CGCATCATTTAAGCCGGCAGGGCAGTTGACTGCCCCAAAGAGGGTCAGAT AACGTTCGTCCTTGCTGCTCTTAATTAAAGATTAAATGTGCTAAGTTGTC GGGACTTTTGGCAGAAGGACGTTGCTTTAATATCGCCCATTCGCTCGATG TCCTGTTGGCTGTGTTTGGTGGAGGGCGGGCGTGGATGTGTGCTGGTTCC TGGTCCATCCATGCATCCATCCATCAATCAATCAATTACGCTTGGAAGTG CGCCAGGATAATAAAACGTGCCTGAAACGGAGTTTTGTCAGCAAAATTTA CGATCAACTTGGCAGAAGCCGTATTACGAACTTATGCATTGAAGAAATGT CCTTTAAGCCCGTTATTAACAAGAAATCGAAGGTATTGCATTTCTTTTTA GGAAATTCGTGGCGTTGCTGCATATATAAAAATGTTGTATCTATAAAATG GAACTTAAAGAATTCTCAGTCAATTGCAAATTTAAGGATCTGCCTTCTAA AAGTTTAATTTTATATCAGCTTTTTTAGTATTTCCAATATTTTTAAAAAT AGATAAGCAAATAGGCAACTTTAAAAAGAAGAAAACATATTTCTTATCAT ATAGGTCGTCGTAAAGTGAATATCTTTTTATACTTCGATTTGTGTGTCGT TTTAAAAATTGCATGACTCATAAAAGAAACGTGGATTTCACTGTAAGTTT GCATATAGAATAAAAGGCAACGCAACATATTGTTGTTGAAGAGTAAGTTG CAAAAATTGTGTGTAAGTCCTTTTCACAAATAATGGATGTGCCATTGAAG TATACTCGTACACTTCAGTCACTTGCCGAAGTTAAGTTGCCTTCTTACTT GAAGATTGTCGGGAACTTTAAACGTTTTTATTTCCAACAGACTTTATGTT GTTCTTTACGCCTCGTCAGATTTAAAACATTTATGCTTGAGCACAGCTAT ACATACAGCATACATATATAATGTGATTTTCCTGCAACCTACAATACATA CATATTAATTCAGTTCGGAAGCTGCGAAATTGCTGGCCATTGTTTGATTG CTGTAAATGCCGGACTAAGCTGGCAAAGCAATTATTTACCTAAATGGTTT GCCCACGTCAATGGCAATTGTCTGCGATTTCCATTTGGCTGAAATGTGTT GCATACAGGCTGTCAGAAGGCCGTCAGAGGCATACGAACAATGAAATCCG GCAAAAGGGACGTACTGCTGCCGAGGAGGCCAGTTGGGCGCTGCAACAAA AGCAGGATAAGGCAAACTTTTTAATTGAAAACCAACAAAAATATAACGTC AAAAGTTGCAAGTGGTTGACACTTCGAAAAAGCCCCTCCACCGAACCACC CCGCCGCCCATCCAGACCTTGCAGTCCGTCAATCCGTCCCACCCGTCGTA TGCGTAATATTGGGGCTGGCAGGCAGCAAGAGTAAACGAAACGAAACGAT ATGAATCCTTTGCGACAGCCGTTACCAGTACATCCAGTGCTTTAAGCGTA TATGCACACACGTGTGGATGTCCAAGTCCACTGGTCTTTAATCAGGAGGA GAGCTATTGCCACATCGTTATGAGGAGACTCGAGGAGGCGCCGCACTTGT ATATATATTTAAATTTAAGATTATGGCCGTACGTGGAGTGCGCCGAGTGC ACTCGTGACTGGCGGATTGGGATGGCGATTGCTGTTGACACAATTCCGCA TTGGGCTCTTTCTCTCATTGCGTTTTATTTACGTCTCTGCAACTTATCGA AGTTGGCATATGATGCTCGCAGTTCGCGCGTTTTTTAAGCCGCCTGCACG CGTCCGAGCTGCCGACTCCGCAGAGCTTAACTGCATCATCAACAGCTGCA GTTGGTAAACAACCAGCCAACCGCTGCCACCCACTGGCACCTTCTGCCAC CCAATTCATCCACCACCACGCCGCCGGCGATGTAATGTGATTATTCAGTT GTTTTGCTCGCAATTAAAACAAATTGTGCCCGCTGTGGGCGAAAGCATAA ACAAACTGCTGGATGCCAGCGAATCGTATTTGTGCGAACAATGATGGTCG CAATTCGATTATTCAACCAGTTGCACGGCTTCAGCTCGAATTAATCTCTA ACCCGGACATCCTTGGGTTCGTGATTAAATCGCTCATAAGGCCAGCAACG GGCCATAAAAAATCAATTGCGACTGTGGCAATGTCACAAAGATTTACGTT TCAATTTCAGATTCTGCCACAATAAAAACCAACGCGAAGGGGACGGTGTG TATCCCTGGAACACGCACACATGTGTGCAAAGCAGGATTCCTGCAGGACT CAGACGAGTGTGTTTGTGTGTGTGTGCCTGCGACTTTGTGTGTGGCTATA AGCTGGCTTAGCAGATTTGTTGCCGAAATTAGCAGGCTGTGGGGATCAAA AAAAGGGAGCGGTCGTCGTGCAGGATATCTATTTTGGGTAAAGGAATTCG GCGTCGTTCGAACAGATTTATGCGCCATAAAAGAGCGGCTAGACGTGAAC GAACATGTCAGCAAGGACTCGCTTCATGGCGACCAATAAAAAAGGAACCC GACTGGCAATAAAAAGTGAAATGCCCGATCAGCACAGCCCACCCTCTGAG CACCTTTCAACATAACCGGTTACTGTTTTAATATTTAGTCCTTGGCCACA ATACTCTTATTTATCCGAATGCAAATACCTTATGTTTGCACTACGCTTTT GTCCATTCCGTCCATTCATGCTGGTTGTTTCTGTTAATTCAAAGTCAACA GCCCCGAAATAAAACCCGAGCCCATTGTGTTTGCCTAAGGTAATTACAAA GGCAATGTTTACTTATGGCCCTTCATTAATATGTGAAAAGGTCCTTGCTC TTTCCCCGCCGTGCGGATTTTAATTGCGGCACATACGTGTTTTATTGCGT GCAACTTGTTGGGGCCTATCCTGCGGCCAACTTGGGCCTAAGCCAGTCGA AACAGCTAAAAGGATCAGGGGGATACAGCCGCGTAGCTGGCTGACAAGTT GTCGCAGCCGCAGGTGCGGAGCAGCTCTCACCGTGCACTTTGATAAAGTT CCAGGATAATGCAGAGTCCTCTGCTAAGTATGCCACTGAGATAGCAGCCC CATCTCCACCCACGCTTGCCACCCACTTCAGCCCACACTTGCAAAAAGTC ATTAGCTGTTACCCATTTTGTGGGGTGTTTTAATATTGTAGCATTAGCAT TAGAAGCTAATAATTCCTTTCAATGTTCAATTAGGCCTTATTAATCAGAT TTAATATCTAATATATTGCATTTTAACTGAAAATACTCGAAAAGTGAAGA ATAGTGTCTTGCCAGCGCTAAGCAAAGGGTATCTGATAGGCGATGAACCC GACTATAGCTTCCCCCCTTGACTGATTCTGTTCTTTGACTTTTTAAACGC ATTTAAAGTGTACCTAAAACTTTTCTTTAAGCAATGACAATTTCTGAGTG TATCCTTAAGTCTTAGGGCTGTGGTGGTACCCCACTCATCCATTCGATGC GCTGCAACCTCTTGCAGCCCCATAATTGCCATAGCAACGCCAACTTTTGC GATTCTTGAGCACGGCGAGCCGGGAGATGGGTGATGGGCGATGGGATCGG GGAGCTGGGAGCTGGGAGCTGGAAGCGCTTTCACTCTGTTGTTTTCAAAT TGCTTTTAGCAATCCCTCATACTTTTGTGTTACACTTCAATGGCAAACGA CGAGGCCCGCGCCTTCCACATTTTCCATTCGCTGCGCCATAATTACAGGT GCAGCACGAAATGGCTCGCAATTGCATTTCGTCTTCAGCGTTCGTAATCA GACAATTTTGAAGTGTTTTGCATTTAAGTTTCGCTTTAATCAGGCCGCTG GCCGGCGGAGGACAAACTTTTCGGTCACGAGACAAAAGGCGCAGATAACA GCTATGAAAACAGGAAGTTGCCCCAGGCCACCGACCAGTGCTGCCAAGGG AAACACCGAATATAACGGAACTCGTTTCAAATATTCATTGTAAATATTGT ATTCTACCCATCTGTTTTCAAAATTTAGGCAACTCTTAAAGTGAGACCCC CCCCCCCCTTTTAACAATATATAACATCAAATTAGCGTAACCGAAGATGT CATTCTAGTTTTTGATATTACCTGATAAGGTTTTAATACATTTAGTTCTA ATTAATAAAATAAATAAATAAAGTAACTGGACAGCACTGGCACAAGTACT ATATCTGAAACACGGAACCCAGAACAGGGAGCCAAAAGAGCTGTTAAGTA AGAGCCACAGTTGGAGAAGTCTCTAGTTCATTCGTTACGTTATTTTTGTG TTAACTGATTTCCATACTGTTGTTAGTTTCGCCAACTATGCACCTAGGTA CACACACTGATGGGTGTGGGTTCACTTTCCAACTTCTGTTTGGTACACGG AAAAACTTTTAAGCATTTTCACACCCACTGAGTGCGTTTGAAGCGAATTT AATTCCGATATATCGGTTCGCCTTAAAGCTTTTTCAGCTTAATCAATGGA AAATGTGCACATGTGAAATGGAAGGTGATTTCAATTGCAGTATCAATTTA ATTTAATAGTCATCAAGCTCCATCGAAGGCTGGAAGCAGGAATTTACACA GGTAAATCTGGCTTTGCCACAAAATAAAACGCACGAAAAGCACGAATCAA ACGTTCAGTTATCGATAATCCACATATTTGTTATAAAATGAAATTCGCAT TTCCATGACAGGGCATTAAGATATTTCCAGAATCAAGAACGTATTAAATA TCCAATTCGCAGGGTATTATCCCGCCAACGAAGTGAACCAGAGCTTTTAG TTCTCGTTTTCAGAGGATCCGCAACAAAAACACTCGTTTATTCCACAGAT TATTCCACAATGCCACAGAGGAGCGTCTGTCAAAGAGCTGCAGACTCAAG TGTCGAATGAGTTTTAGCATATTAAATATTTACATTTGGCATATAGCATA TATATGGTATATGGCTTTGCAAGCGTAATGTCAGCCCAAGGCCGTCCCGG ACCGCCCAGCCCCGCAACGCTACGAGATTAGGCCAAGATGATGGCTCTGG CTAGATAGCCACTTGGTTCTGGTCAGGGCCAACTCAGGCGGCGGATGGAG GCTTGGAATTTATAATTGTGATTTAATTTGCATAAACTTAAGACATCTGC CTTGGGGCAGCAGCTCATGTCCTGCCATCATCATTTTTATGGCCCGGACA AGGCATCCAAGCCTAAATTTTAAAACAATATGTCTAATATTTATGGCCGA AGTTTTGCAATAGGCTTTGTTGCGGCTTATGAAAGGATTAGTCTAAGATG CTCGAAAGCAACCTTGGTCGAAACAAAGAATGCTCACTGAGAAATCTGTA AAGGGCTGATGACAGTTTTATTAAATTTCCACGTGATTTGCAAAGATTTA TGTCGGTTCACAAACTAAAAAAAAAAGAGTAATGAAGGCACTAAAAGAAA TTCCTCAATTTCTATAAAAACAACGCGACGTTCCCAGGTATAAAAATAGT ATATTGCCATTTAAATTTTTACTCTTTTAATGTTAATACATTTTAAAACA ATTTTCTTTAACATTTGTGGCAAATATTATGAACGCTAACATCGGAAGTA AAATAAAGCGATTTAACTATTTCCATAGATTATTTTCACAATATTTGAAT GTGAGTAGGTAAAAAGTAAGATTTTTCATAATAATTAATTATTAATATGC AACCCTTTTAGCACGGATGACCGGTTGAAGTGACAATATATGTAGGCCAC AACTCTTAATTAAATGGTTATTCATATAATGCATAGTTAAATATTTAAAT ACATTTGCTCATACGCTCTTTTTGCTGGTTATGATTTCGATTAATGCGCG CATTTGTGGGGAGCAATATAATTGCTTTGGCAAACATTAAATTCATATCG GATCGGCATCATCTGCCAACTGGCAATATTTAGCCATAACGATATAAATA TTTTCTGCATAAATTGCTTGCATACGGATAACGATTTGCATTCACATAAA TATTCAGCACTTAGATTGGGTCAATTGCCATCCCTCATATGACCGGAAGT GAATGGATTGTTACATCTGGAGCAACTTCTTGACCGTGATTTATCTGGCG CATTCATCGCCAACTGTTGCTCAAAATCCAAGGATACTCAAAGAGTGGAG GAGTAGCTCTCCATTTTGGCCGGGTATTGTTATATTGTGTTAATGCATGA CGTTGTTAGGCAGCTCAAAGTGTACAAAAGAAATTAGCAAACTTGAAAAA TAAGAAAAGCTGCGAATTCAGCGGCAACTGTTGACAGTTATCCTGGCACA AACACGCATTGTAATGTCTAACAAGCTTCACAGCAAACATCGCCCGTCAC TCAACGGCCTCACAGTCCTGACAGGTCCTGCGTCCTTAAGTGTGTGTGGC TGTGTGTCGGTGGGTGTGTACGGGTGTGTGGGCGTCTGTCATTTACATAT TTACACTTTGTTCCCGGTGCCTTGGACTGAACTTTAGCCCGTGGTGGTGC TGTGCGCCACATGTCCTGCCCCAAGCATGTCCCGCTCGGAAAAATATCCA AATATTTTACTTTAACGCAGTGCTAATGTAACTATGCTCCTCCACATGCA CGTCCCCACGGTTCCTCTGCTCAAAATCCTTGTTTGTTTAAAGTATCACT TTTAAAAATTTAAGCGTTCAGCCATTTTCCGCTGACATTATAATGTGCAA AAACAATTGAATAGAGATTGAAACGTTCAACTTACGCGCTTATTAAAGTA ATTGAGTTTTAAAGAATTTGAAACCTGCACAAGTTTCCCCATCCCATCAT TTCTCAATAAAAAGTATCAAGTTGTAAGATTAAGAATTTTAAGAAGTATT TCACTATCAAAGCTTTTTTTTTTTTAAGTGGGGAGGTGATAATTGCGGGT TGAAGGACCACTCGACGAATATTGCATATACTGTATAGGCTGTATAGACT GTATAGACTGTATACTTATCAGTTCATCAGTTACCCCTTTGGCAAAACCC AAGATTGAGCACCCACATGCATACATTGCTGCTTCGCGCAGGTCATTCTT GGTAGTGATTACAAGATACTGACTGAGAAGATACTTTCATCTGCAGTGAT ATATTTTCCCCCGTGCAATGCGATTAAGACAACTGCCGGCGGTGGCGACA ATGCATTTTAAGGTGGCAAGTGCGAGCCCAAATGGCCCAAAGGCGCCAAA GGGAAAATGCAATTTCCACCGAAAATAACGGATAGCGGCCTGTAGCTGAT TCACTTTGGTGCAATTTGCATGAATCCGGTGGCTAACATACGGCTAACAG GCGCTGTTATCGTTGCTGCCGCAGCTGTGTTTATTGCGCACAACTCATTC ATAAAAGCGGGGAGAGCGCTCTCTCGGAGGAGATAGAGAGAGAGACAGAG AGAGAGAGAGAGAGCGGAGATTGAGTTGTCGGCGGCTGCTGTGCTTGTGT GCAATAAATACAAAGGACTCAGCATCCGCGGCAACAGTGCCGTCGCAGTG CTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCC GTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGA TGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTC CGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAA ACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGT CGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAACGTAAATTA AATACCACCCGGCCACGCGGCATTCGGACCGCCTTTATTAGAAGTTATGG CTGCCAACCTTTGCCAGCTTTGTTTCATCCATCAATGTGTGCGACAGTCA CGTGGGTGTGCGGATTGGGATCCGGACTTGGTTGCGATTGGGATCGAGAT GGGGTGGGGATTGGGATTGGGATTGCCGCTGGCATGGCGCTAATTTCTCA CACTTCAAACGTGGCAATGAATTTCCGCTCCAGCCTCCTGCGGATGCTTT CGTTCCGTTTGGCTTTGCTTTGCTTTCCCAGCCACCATGTTCCCAGCTCC CCGATTTCCCGGTGGCGCCCCTCACTCCCTGACCACCTAACACCCTTACC CGCTCCAGTGCTCGTGCCATTTGGATAGCTAAGCCTCTCCAGTGCCACAG ATTAAATGGATTGACGGTGCAGTTACCACGGCCGTTGGATAAACACGAGC ACGAGCACTTGGACCGGGAGTGTGCGTCCATCGGGGAAGACCTCCTCCGT ATTCACTTCTTTATGATTAGTTAATGGGATTCAATTTCATTCGAAATCAG CCGCCACAGAACGTGGCAATCGCAGCTGCCGCAGCTTCCTTCGCAAATTT CGTAAGGCAACTTTCTGAAGGAAACACTTGTTGGGTCTTTCTCAACTAAC CAGGCACGTAGCTCCGGCGAAAGGAGTACCAAGTGGGGGAGTTGGGAGGC GGAGGACGAAAGCCGAACGGCTGAAGGCCGGGGAAAGTGAATCACAGTTG CGCCATTAGGAGGCCGTGAAATAAATTCAATATAAGCGGGTCCTAATGGC GGTAGTTGAGTTCCATTTACATTCAGCCTCCATAAATTGGCATGGCTGCG AAAATCGTTGCCTACTTAAGAGGGCCCACATTTAGCAGGCGCAGCACCGG CATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACA AACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGC TAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCT AAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTC GCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGC TCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCA GAGCAAAAATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCG TGAAATCCGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGC ATGACGAGCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCT GGGATTACTCTGCCGGACGAAGGGTGAGTGGAGCGTCTGGGAGTCTGGGA GTCCCTCAATCTTCGGACTGAGCAGCTCTCTGTCGCCGATTGCTTTGCTT GAATTATGGAGAGCAGTCGGAATAAAAGGAGAATCCGTTTTACAGCCTTA TTAAATCTGTATTACATAAATTACGGCAAGCGTTTCACTCTGCATTTTTA TGAGTGCTTTGCGCTTTCACATTTCACATTTTCCATTTGCCTTTCCCTGC TTTTATGTCATAATGAGTGCAGCCTTTTGATTTAATGACAACTGTTTGCC ATAAAACAACATACATATGCACACACAGCGCTGACTTTTATGTGGCCCGT GATTTATTTCACTTCTTATTTTTATGATAATTTATCAAATATGCATAATA AAATGCCAGCAAACGTTTATGGCCTCTGTGAATTTTGCCAAAATTTCATT TGTAAGGTGGCAACAGCTTGCCGATCGGATTTTGTGTGCTGAATTCCTAC TGCAGGGTGGACCTTGTTCTGTCCTAAGTAACGAATTATAAACCACGATT GTTGTATATACCACTAAGGGACTGTAAGCGATGCCTGTTTCCCTGCTCTA TAAGTCTTTCATTTTGTAGACAGGCTTCAATAATCGAGGAGGCAGTTCAC GTAGTGACGAATGTAGAGTCAATATTTAATTGTGTTCGGACCATGCGATG CATTAAAATATTCGCAAATTTAGTAGAAAACATTTTATAGTATTATGCGA TTTCACGTAGAAACCTTTCCTTAACACTTTGGCTTAAAAATGTTTCTATC TTTGGGTGTTTCATAGACTTTGTAGCTTGAAGTCTAATCACTTTAAGTTT AAGACTAGGCCATCGATTTTCATTTTCTGTAATGGATCATATGTATATAT TTTTAATCAGTAAAGGCTTTTCCTTTTTACTTGCTTTTGCTTGTTTTATA CATTAGTTTGGTATATTTCAAAGAATCCATAAAAACTTTGAGATGTTGAT AAGATATTTGTGACTATTCAAAGGGAAACTGCCTTGAACTTTTGAACCGC TCTTCTTTGTTTTCTCTTGAGATATGAAATGACCAAAAAGGTTCACTGTC GCCTTTTGTTTTTGTTAACAACTCCACTATAGCTTAATTATTTTTTATGA TTCTTTATCTACGTTCAACATTTTTATGCGAAATGTGCTGTTCAACGGAG ATAAATACCGATTTTAGATATTTTTAACTTAAGCTATTAAGACAAATTCG AGCACAAGATATTATTAAATGGTGTTCTTAATATTCACACTTAGTGATTT TATTAATTCGTTTCGCTTTGTAATGTTTTTATTGATTTGAGCTCAATTTT GTTTTCTTCAAAACGGAATTACTGGTTGATAATCTCACGATTACAGCAAT CAGGGTAATCTGCGTTTGGGTTTGTGTACTTTCCAAACTTTTTGCCGGGG GGAAGTCCATAGGCACCACATCTAAAGTAAGTTCGTATATAGTATAGTAT ATAGAGTTGTAAAAAGCAAACATACGATTGGATTTCTGCCGCACTATTTT CTCCGCATATGATTCGCTCACACCTCTGTGGGTGGCGTGCACTTTGACCT TTTTCAAGAACCAAACCCTCGAGAACACACTTTCCAGGATGGGTTGGATC CTCGAAGACGCCTCGGACAACGGCAGCTTCGTAGCCCGAAACTAAGAGAA CGGCGATTGCCGCAAGTAGCACGGTAGATGAACGCATCTTGGAGCCTTCA AATCCCAACCTACACTGAACAGCCCAGTCAATTCTGAGAATATAAACGCT TTATCTATCGGTGGCCGGTCAGGCAAGTCGTCGGAATAAATATTTGTATA AGTAGCCAGAGCTTCGGAATAAAATTAGTGCTTTGCTCACACAAACGCAT TTATTACTACAATAATCATTCGAGACGGGCAGCACTTTGTTGTCGAGCCG ATAATGGACAAATAAAAATGCCAAGCACTTTAAGTATGGATTTTACTAAT CTGTTTGTTTTTATAACTATACTTATGGCCCATATACATATTCTGTGCGT TTTAATTAATAGATAGTTATCATTCTTGTTCTTCATGCATTTTGAATACA CTAATGAAAAGCCTCAGGTGAACTGAGATATGTGGAGATATTTTACCACT GCATCAGGATTAACATTTTATCATAGTTTATTAAGAAATATTTTGCAAGT GATTTATAAACGCATATAATTCATAATGTAATCGTTTACACTTGTTGTGC TCAGCTAACTTAAATCCTATTCAAAAAGTTTTGTTCTGCCAAATAATAAT AAAGTTCAGGGGTTTTATTTCGATTTAATAAAGTCCAAAATGTTAATTAG TTTAATGTTCACGTTATCACACTTTTGTTATTCAACTTGCTCATATTTAA GCCGTAATCAGCAGCGGCAAAACCAAATCAATATATGCCCAAATATTTCC TAATAAACAAAACAGCATATGCTGCTAAACGTGGGAATATGTTATGCGGG TCCACCCTATAGTAAATATAATTTCTATTTTTTCTGACTCTGTTCGCATG AGAAAAGCCAAACCAGCACGGGATTATTTTGCATTTGTTCTCGCCCTTTC GCAGCTTTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGA CCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGC AGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGC CAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGC AGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGC ACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGA CAGAAGGTAGGATGACGCCAGAGGCAATATTTCAAATCGGTCTTTCACTG GTTGAACGCTGCTATTTAGTCAGAAAAGAACAGTTCACTGGCTTAAAAAC GAGTTAAATGAATTATAACAGTGCTTAGCCGTACATTTGTGGTTTCTGTG CAACTCGGAAGCAGCTAGAGAAGTTCCTGCAGCACCTTTGTAGCTAAATC AGTAGCGAAAATGTTAGCTAGACCTGTATAATTTAACAAGTACTATGATT TTTCTACTTCGTCATCTTCTTTTGACTCAACCCTCGTTTTATTCAGTGAA TCCTTCAGACATCCGTTTTTGTGGGTGTAAGGCTGCAATGGAACTCTGCG TCTGTGGTCATTTGAATAACCATAATCGGACGAGCGTTCCTGGTAATTGA ACAAAGAGAGTGCATAATTTGAATTTGTGGCTCGTTACCGCACATGTGAT GATATGAATGCCAGACCCAGAGCAGTCTCCCTGCTCCTTCAGCCGAGATG TGTGCTTTGCTCGCCCATTCATTGTATCTCAGGCCATCAAATCGGCTGGC GTTGTGATTGATTGTCTGGTTGTGGGTGCACATGTTCCCACATGTTCAGT GTACATATATTGTATAAGCCGCAGGAGCACCTGCTGGCCGAACTTGTCGG AGGAGAAACATCTAAGTTATTTGCTATATCCCTTTCCAGGTTCCGCGCCT GGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGATCTTCTGCTGGT GGGAGAAGTGCGGTTGGTTCTGCGTCGGCTTTTCCCGGCATGCATAATAT AACGAGAAACTTTTGCCTTTTTCTCGCAGATAAGGCCAATGTAAACAAGG CGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGAC GGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATA TCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGA GGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAAT GACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTC GGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAAC ACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACAC AAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCA GCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAA AGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCA CCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCA CTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCT ACTACGACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCAC CAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCA GCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGAC AAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACA GCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTC TGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGC AGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCG GCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGAC AACGACAACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGG GAAGGACGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACA AGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGA TGTGAGTTGGGAGGTTGAGTAGGGTCCTCACTTTGGTCGGGCATTGTGTT GGAAAAGTAGCGCAAAAACATATCCATCTCCAAACGTAAGCATTGGAAAT AAATGCCAGAACTTCCTGTTAGATTAAAAGTTGAGGGACAATGTTTGTCC TTTCTGAGTGATACTGTTATTGTGCGAATGATAGTCCTAAGGAATCTTCA AGAGACTTCCTCCTTTGTTGGGTGATTTTTCTAATTTTAAGATGAACTAG GGAAGCGAACTGAAGCCAAGCCTCCTTACAGACTAAAACTATTATCCTCC ATTTGTCAGAAGCTCAGGGTATTTATAAGACTCGGTCCCCGAAAGTAGCT TTTACGGAAAACCCCAAGGGAAGGCCTTACCCAATTAGTCTGGGGGAAAC TGCCACTTCATTGGCTGCCCGGACGAGAAGCTTGAACTCTGCGCCTTCGG TGGTGTGCCCAGTGAGCCCGAAATGCTTCTGGTAATGGGGTTTTTCATGC TCGAGCTGGTTTATTATTTACCATGCAGTCAAGTCGAATTAACAGTCTGT GCTTTATTCCCGACCAGCTTGGACAGATGCAACCCGATCGCCGTGGACCA GACGCGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCT GAATGCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGC CGGCATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGG AGCATCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGT CTTCTTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCG TTGTCAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGC CAAACGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAA TGGCAACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACC CAGTGGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGAT CAGCCTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTAT AACAACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGTAAGC AAGCAAGTCGAAGGAGGTGGCCGTCCAAGGGGATTATCGTAGCACAGAGA AATAAATATCCTCGGGCATTTGCGGTCAAGCTGCTATTTGGTCAGTTTGC TTCCATCTGTTTGAGTTTATATTACTATACTTTTTCATTGCGACAAAGAT TTTGCCAGACTAAAATCGTATTGTCAAGTCCTTTGCGTTTTGATAAGAAC TGCATCAGCTGAGTAAGCCTATTTAAAATATTATTTAAGCCTTTTCAATC ATTTTGCTAAATTCAGTAAGAGAGGACAAAGCCAAATAAAAATCTCTGAT AAAATAAGCGGTATAATCATTCGATTGCCGGCTAAACATTCCGACGTGAG TCTGGGTAATGAAAACAACATTCCCGTATTTCACTACTGCGCATAACAAT TGCTCACTTCTAATCCCATTTAAACTGCAAATCAAACGCTACTCGTTCTA GGCAAACTGTATAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTG CCTGCAGTGCATTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCG TCACCTGCAGTCCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTC GATGCGACTGGTTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAAC GGCAGGTGGCAAGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGC TGTGGGAGTTTTTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAA AGCCACAACTGCAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAA CGAACGAATCGAATCTAATCGAATCGATTCGAATCACACTCACAACAACT GCACTACAGAACTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCA ACTCAATATGAATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAG TGCCCCAAGCACTCTCTAAAACGAAACCTATCAGCAGACATATATTATAT TCGTACCAAACTATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGG GGAATGAATAAAGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGAC TTTAAGCTGAATGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTC CGCAACAAAAATCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTT ATAGATGTACCAAACAGAAGTATATAGTATATACAAACATATACGAGTAT CTACTCTATATCTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAG TTCGGTGGGATCAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAA CCGTGTAGAGTTTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACG AGTAACTTATACAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAAC AATGACAAATAATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATA TTAAAAGCAAACAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCG CTTCTTTGGAAATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTT AGGAGCAATGTATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAA GACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTAT TTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTAT TTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTA GGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAA TACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACAT TCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGG CATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATAC CGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGT ATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTA AAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACT ACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCA TCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATC GACATGAATAAACCGAAACCCAACTAAGGCATTTCGAAACATGGCTCTAT TTCATTTCAGTGTTTGTAATCCTATTTGCAAAAGGTAAGACTGCGAGTTA ATTAATGCCGTGCATCATTGTCCATAATGCGGGCGAATTGGTCCACCGGC ATACATAAATCATGTAGCCCAAGGTTGGTGCAACATTAGATACATATATT CCTCTTATGATGGCTCATACATGGGTGCTATTTACTAAAGTATCACTTTA CTCTTTCCATCCTGCTAGTCGTCTTCGCTGCCGGACTCGAAGCCTGAATC CTCTTCGAGTTCGGCTAGAATGAAGGCTTCTATGGCCATCTGCAGGGCAA GGACGTCTCCTTCGCCAGGATCGGGTCCTTGCAGCATGGCCGTCGGTGGA CCCGCGTAGTGGGAGAAGGCTTCGCGCTGCCTGCCCAAGGACCGCACCGC GAGCTGGTTGTCCCCTCCTCCGTCCATCTTAGTGGGTCCGGTGCAGGGCT ATTGGTACCCGATCGGAGCTGGAAGTCGGCTGGAAACAAATGATGGCGCT TGGGCGCTGGGCTTGTGTTTTTTGGAATTTTGAGTATATGCTTTTCGATC GGCATTCAAAACGTGTTTGAATATCCCTGGCCGATGTGACAGGCCTCGCA AAAGCAGTGCGAATGCGGAAATTGCCTGCGGCAGATTGGCTGTTTAATAT TGTTAAATAAAGCGCTTCGGGACGAGTTATTAGTTTTCCAAAGCCGTTTG TGTTTGTGTGCGCAGCGCAATCATCGCAGTGACAGCCGACCGCAGGGCAC TTTCAAGCTGTGTGTGCGTGTGTGTGTGTGTAACCGGAAGCGGAAGTCGC GTCCCGTTCCGTTCGGCGCCGCTCCCTTTCGCATGCCGCCTACGCACGCA TTACGTACCCGCCCCGTTGCCTGACCGCATAAAGCCATTTGGCCATTTTG GCAACAAGCCCTAGCCCACAGCACCCGCTGACACAAAGTAGTCAGCCGCA CAATACTTTGCTGTCAATTTGTGATAACGGCAGCTTTATTTGAAAATATG TGCGACTTTATTTCCCGGCTGTGCCGAGCCGATTTTGCGGCCACACTGGC TGACAGCTGCTAGATGGTTTGTCGGTTGGCCAGCAGTGGATAGTGGGGTG GTGGGCAGTGGGCTGCTGATAGAACGTGTGAAATTGAATATTTACAAGAG CCCTTTCAGGTGGAAGTGCCCCATGTTGTCGGCCATGAATAGTGGGGCTT AGAGCGATTTGCGATGTTCGACTCGCAAAAGGAAGCCAACAAAGGGTGGC GGATCCGTTTCAACCACTTCTACCGAGCCGAACCGAGTTCGCATTCCGCA TTATTATTTTTATGGCCAGCAGCAGTGAGGAGCCGAAGGTCTCAACTAAT TAAATTTCCCAGATGTGTGTGTGTGTGTGTTTGCATGCACATATTTAAAT TGGCTCTGCCAGGCCACATAGCTGGCTATGTATGACTATATGACTATATT CCGGACTGCATTCTGGGTCGGAGAGTTGGTTGAGCAATGCACATTTTTAA TTACGCTGCACATTTGCATTTGAATTGCGCATTTTACAGGCTGATAAGCC GAAATAAAGGCAACAGTTGTGCAGTGGCTGCCAAAGATATGTTGGCTCTG GCCACGCCCCCATGCAGCTGCACACTCGCTCGTGTTTTTTACAGATCCCC AGAATGTGTAATTTTCGAGTTGACAACTTTTGTCCCAAAGCAGTGACCTC GTTACGCCCACACAGCCGGCTATATAGTATACTATACTATATTGCATTAG AGCCGTGCTCCTCCTTCAAAACAGAATCTGCCCGCAGCCATAACCCCAGT GAGCCGGGCGGGCACAAAGGATACGGTGGAGGAGGAGAAGAAGGAGGGAC TGGAATGGAATGGATTGGATTGGGTTGGATCGGATGGTGAAAGCGAGTGC AGAATGCCTTTCAATGAAATGCAAAGCAGAGAAAGTTGGAGAACAAAAGG CATACGGAGCTTTTAAATTTTACTGCCTTCGCTTCGATTCCGGGCGCTAA TGGAAACCCTGCATTTCCATTTTACCTTCTAGTCCGGGGAGAATTTTCCC GATCGACCATTCTGCTAATGGAAAAACATTCAGCGCTGCGCCTTTGAAAT TCTTGAAGTTCAAGGACCCTCTGTTTCAGTCCGTAGGTGCACTACTTCTG TCACTATGTCACTATTAAACGGGAAAATTAAGCTCCCTCCGCAAATCAAT GACACTGGTGTCCCATTTCTCGCCATCCCCAAAAACACGTGTCTAGGATG GGGACTTTTCAACCGCCTACTGGGCTGATGTTTAAGCCATTTTTAATGAC AGCCTGACGCCTGACAACGGCTAATGATGGCGGCTAGCCAAAGTTTTGCG GCTTTTGCGGATTAAAATTGAAAACGCTTGCATTCATTAATCCTGCCAAC GGAAAAACCCAACTAGAACGTGACATGAGGCAGGTGTCGCATTAATTAGT GTAAGCATTCACACGGCTCCCACTCCACAGCTTGCGAAATGAAAGTTTCC TCGGGCGGGCGGTTTCATTTCGCCGAGATGTGTCACTCCGCAATTTGGGT CAAGATGGCTTGAGTTAAATTATTGCAAACGGCATTCCGCACCGTCTTCC TGCCCCTCGAAGTCCTCGAATCGAGGACACGTGCCTATTTGCATAGATAA CCTCAGGCCAGTGAATCAACTCCTTTGATAGCCTCCAATAGCAAAAGCTT TCAAATGCGATTATTGAATTATTGGGCAATAAGACTAGAAGGCACAATTA AAACCAGTCTTTGCGCCTAAAACATTACAGTGTCCATCTGAAAAATGTCT AAATAAAGCGGCTTTAATTTTTTAATATCTTTAAAATTTATTTAGGCAGA TAAAAAGTGACATTAACATTAGTATGCGTGATATAATAGCCATTTTTTCA CACCACTAAATTTCATGTTTTGTGGCAATAACATTTTAATTTACTGTTTT TGACCTGGAGGTAAGTTATGCTAATGTTTAACATAAACATACATTATCGT ATTTAATTAAATTTTAAGGCAATGGAATCTAAAAGGCGTCATTGTACCAA AAAAGTACAGTCTCAAAAGTAGACAACTACATATAATGAAGTTTAGTGTT AAAAGGTGAATATGTGAATTTGAATATACTCAATGTCTTAGTTTGCGAAA CTGAGAAATGGCTTTAGTCCCAGGACGTGCAAACAGTTGAGCAAGCCTTT TATGAATTTTCATAGAACATTTAACACAATCCAGGAGAACTAGCTCTTTG CCAGCATCCAGCATTGATCATTCAGTTGGCACCGTGTCTGGCCCCAAACA AGAATTCCACAAAAGCGCCCAACTTCCCATCTTATCCAGCCCCCATTTCT GGCTGCCTGATGCCGATGTGTCTGTTACCTGGGGCAAGCCAGAAGGCAGT TTCCAGAGATGAGATGCTCCGAGAGATGAACAGCTGATGACCGTGACTGT GCCTTTGTGCTGGCGAGACCCAGACCCCCAGGCACCCAGTCTTCCAAGTC TTTCGAGTCTTGTGGTGGCATCTGAGGGGTGAACATACAAATTAATCTTC ATCTGGCACTCGCACCCACAACACCACCCAACTAAGCTTCTGACCGCTCA AGCTCGCTATTTGAAAGCGATGCGAAAAAGACAATAACAAATCAACGTAC TGATACTAAGGGAAAGCTGCCATGGTTTATTGCAATCAACTTAAATCTTA ACACTATTATCTGGCAATTATCGGGCATTTTATATAAGCAGTAACTTTTT TGATTGGTCCCGGTCGAGGACAATGAAGTGAAATCGTTTCGAAGCTTACT ATGATATATATTAATGATATGATATATATATAGATAAAATAAAGGGAAAC AATTTGAACAGCGGCTTACTTGAAACGGACGGATGGACAGAAGGGCATAT GGATACGGATCAGGAACATATGTCTATGAATACCATTAGCGCGTACTTTA TATGCAAATTTTTGCCACGACGTATTGATTTAAGTGTTATTTAGTACAAT TTTCGACCATTTCAGTTTCAAACGTTTAAATAAGAAAAGGTATCATATAT TTAAGAACTTGGTGAAACTTTGCAGAAATTGCTTCTAATGGAAACAACTT AGGGAAGTATGTTATTTTTGATACTTCAAGAGTAAGTCGTTGAAATTGAT ATCAGATTATACTGTTGTCGAGAACTGAAAACTAAACTGTCTATCTAATT CAGATGCTTATTTCTATTAATAACTGGCAGGCAGTTCCACCTCTAATCCC ATTGTGCGGAGTGTAAGCCAACGACTGACTTGGTATTTAAAGCTCCTCCG TGACTCGGTCAGAGCAAACAGTTCCTGGACCACTGGCTTCATGGCCCTTT GTGTAATACCTCTGTTGGGAAATGCCTTTCAGCTCGCTCCTCCTTCAATC TGCTCTCGGTCAGAAGCCACTGGGGCAAACAAGTCCGCCCCAATGGGTAT TTACCAAGTGTCAGTCACTTTTTCTGCACTTTCCTTAATTACTGTCATTG GCCGCCGCTGCCATTTTGTTCCAGAGCTCTTGTGAATTTGCAGTCATCAA AATATTGTGGCCGAATTATGTAGCGATAGTTGTGTGACGAATTTTGGAAT ATTATATGCATTTTTCGCTAGTCCTTCCAGAGTGCTCTGTTTTTGAAAGC TGTGGCTTTGAGTTATCCTAGTTGGTCAACAAATGGTTTTCGGCATTTTG GAGCACTTTAACTGGCTAATTCTCGGGCAAAATGCACAAATTGTGTAATT TTCAAGTTAACAGCTCTTGACCTGGTTCAGAGTGGCAGTCCTCCGCAAAT CCTTCTGTTGATTTGGTCCGCGGAATTTAGTTTGTTTTGTAACAGCGCTC AAATATGCAAAAGCGCAATTGTGTGTTAAGTTGGCTTTGTTGCCGCGTGT GTGCATGCTTTTAGGCTCAGGGGTAGTCGAGGCATTTTATGCGACTGCCA CAAGTTTGTTGGCAAAAGTTTGAGCCCGTAAAACTTTTAATTCAGTGCCT ACCAACCAGTTGTTCCCGGCCATCCTATCCATCCAGCCCATCCAGCCCAT CCAGCCCATCCAGCCCATCCAACCCATCCAATCCATGGAGCTCATGGTTG CCATGAACAGCAGTAGTAACAGTAACAGGCTTTTAGCGAATACACACATT AAGCCCTTTGCTGCTCGGTCTGTCCTTTATGAAAGGGTTCAGGAGCAAAA GTTTCGCATACACCTTAGGATCCTGCCTGGTGGCTGGCTGTTGGTGCTCA ACTAACAACAATTCGGGGGTTAAAAGCGGGCGAGTGAGTGCAGGTCGAGA ACAAATGAGGAAAATATGCTTCAATAACAAAACACTCAACACTTAGGAGC ACGGGAACAAGTGAGCACAGGACGAGTGCTAAAAGGAACAACGACCGATT TACATAAGGACCCCAAACAGACGCACCAACCATCCATCCATCCATATCCA ACCATCCGGAGAAATGCAAACACGACCAGGACACCCAGAACACCCAGAAC AGCCAGACACTCGGAAAAACAAGCGTCTATTGTGGCGGAAAACTTTTTGC GCCGTTGAAAGGCATTTTTCGATGCAGAAAAAGATTTATTAATATTTAAC AGCCCAGCTAGAGGAAAACACACGAAATTTTCCGGGATATGCAAACATAA TAACTGTTGCAGCAGCCAGGGTGAAAGTTCAACATGGACGTAAGTGGACT TTGCTGTGTACCAGTTTTCTGACTGCGACTTGTCCCGCTCCTGACTTCAA TATCCTGCAGACTAGCCGGACTGCAGGAAGCACTTTGTGGACGGGCAGAA TACCCCACGGAGCGCCAAATGGCGGCCAGTCACGGATTTGGTCCTCCCAG CCCAGATCCTTCCTGCCGGACGCCCACGACCATTGCATCAGGGTGGGTCA CATTGTTTGACAAGAAAATGCTGTTGGAGCAATGCATTCCTAGGAAGAAC GCTTTAAGCCTCTGCAATCGGATTTAAATGTTAAGGAAAGTTATCATTGT ATCACCATTAAATTATGAAGTAATTTAACCGATAGTTTCTAGAGTTTTGC CTTTAATATATATCAAATCCCCTAGTATCAACTTCGAATGGTTAAGTTGT AAGAGGAATTTAAGAATTGTCGTTATAAGTACGTCTTCTTATTATTATGG CTTCAATTTGCTGGTGCTGTCCTGTAAGCTTGATACACCCTGTCGTGCGT TTCTTGCACAACCGCCCGCCACAACGGCAAACAAAAGGGCAGGATGAAGC GGATGGGGATGGGTATTGGGGTTGGTCCGAAATCTGGGGACTGGGACTGC GGCATGCATTATTGAGTATGAAGGACCCACTGATTTTTTCGGTTAGCGAC TTCCCTTGCCGAGCGATGACAATGCGAAGAGGGCCGTGCAATTGCCATCA AACGTAGCGCCAAAAGCCGAGCCGAACTCATTAGGCTTGCAACGCCGAGT GGTGGCCGTGCTCTAATTATGCCGTCTCTATCTAATTCCCCTTCCCAGCC AGCTCGGCTTTCTGCTTCGCTTGTGTTCTCCCAGTGTCCTGGCTCTTTGG TGCTTTGCTATTCTGGTGTCCTGGTGTCGTGGACTTCTTTTTGGCCCGCC CAGGCAAACTGTGATTGTGGGCGGAGCGAAATCGGAGGAGGCAGTTCCGC TGGATGGACAATGGGAATGCGATCGGCTCCTCGGGCTTTTGACTTTACTG TTGTCCCACATAATGACCATAAAAGGGGTTCATGGCGAAGGAACTGCTGG TTTGACCTTCAGCGGGCATTAAAAAGAAATAAATAATAAATCAACTCGGG CATGAAATATTCAATAACCTAAACCGACAAAGATTTACTGCTCAGCCGTT TATTTCGTGCGACCCAAGAATAAAAAGCCGGCATGAGAAAAAAAAACACT TTGTAAGCAATTTGGGCAGGAAAAAGCTGGCTGGATCTGTTTTGAAAACT GCCAACTAAACAAGAAGTCACTCAAGGCCCGAAAGCACACATAGGGCCAC CCACACGCCTGCCACACAAATTGAAAGAGTTGCCAAAGTTGATTGCTGGC TAAACGAAAGGTGGCCCAAAGCCTGCCCGGCAGTCGGTAGACGGACTATT CTTACTAACCTGGCCTTAACCTGGCTTAGAGGACCGCCTTTGACGCCCTT CATAATTTGCCAGGACGACCACGACAGCCGCACACTTGAGAGCTGCTCTG TAGCCACAAAGGAAAATATAAATTGTTTTTATTTCTGTGCGAACGAGGAA ATGGAATAATCAAAAGATAATGACACAAAGGGAAATGGAGGAAAAGTCAT CATCGTCGGCCACGTGAAATAGCGAAAGTTTACCTCACAACTACCACATA TTTTACAGATGTCAGATAGCGCGTATGCGGGCTACGAACTTCCTAATCCT GGCCAACAACAGCCCGTGTTGCCATCAGTCCGTAGTGCCTGCCACAATTC CGGCAATCTGTCCGGCGGGCGGGGATATCACTGCCAAAAAGACATTTAAT ACACGCAAATAAATATCGCCGGCGAGTCTCGTGTGCAGTGTACACAGACC GGAAACAGAAAGGCTACAATTCAGGATACGGAAAAGGGTGGCAGGGGTTG GGGAGTGGAAGCAGTCAGTCGCAGGATATGGCCATGAGAAATTAGTGGAG TTTTGCCGCATAAATTGCCGCCCATACTAGCTTATATACCACAGAAGCAA TCTGGTTCAGCATTTTAGGGAAATTCTAAGGACTCTATTCTGTTGTGACT ACGATGGAATGCAAAAAACTAATGAAACAGAATTTTCGGATTTAATATTC AGAATTTTTATCGGTAGCTTTTATAACTGAAGTTATACACACTATAAATC AGCCAACTATGTTTAAACAATGCTTTCCAGAAATTTATGTGAATTGTATG CCAATCAAGTTGGGCTTCATAATTCATTGCTGATTAAATTTTATGCCAGA TGTAGGTAATCAAAAACTGATATACATATATACTAATAATAATAATAATA ATAATAATACTCGAAATTGTGAATTGTGCTGAAACTTGAGCAACACAAGC GGCTTTGTGTATCTTGCAGAAATATTTGTAGTTAATTGTTAATTGAATTC AGCTTTTCAAAGTTGTGTAGTTTGAAATAATTGTAACTTGCATCAGTTAC ATAAACTTCTACCGAAAAATAATAATGATAATCCATAAGATACCTGAAGA CGGGAAACATTGTTGTAGGATCTACAGCGAACATGGCGACCAGTGCTAGT GAGTAACTAAAATCACAATGATTGCCGTTGAGGTTTGTTTGCACTTGTTG GCAAATGCCCTAAATACTCGTACGCCACTGTGGTGGTGAGCATTCAGATG GGATGGAAGTGGGCAGTGGGCAGTGGGAGTGGAAATAAAGCTTCGGAGGA GTCACGCTCGTAATTTTCCATAGGCAACATTTGCCATGATAATACGTAAT ATACATAACAACCACAGTTATGCGAGGCCGGGGGCGATTCCGACCCTCAT GCATATTGATGGTATGCCGAAAATAGTTCCTCAAAGATAATAAATAGATG CCAAACGCAGTGGCCAGCGCTAGCAGCTCTGCTTTCGGCCAACATAGCGC ACTAAACACAGCCAGCTGCTGCTGCTGTTAACATTTCGTACTCAGCTCGC TGCTGTGGGGTCAGTTGAGTTGATTTTGGGGCTCTGGGGATTACACTGGA TAATTGCAGTCTATTGCAGGGCCAGAACCAGATCCAGAGCTACAGCTACA GGCTTCTCAGCACTGCCCCTTCCGACTGCCAAGGTTGCCGGGATCATAAA TCACAATCAAATTACTGGCTGATTATTCCGAGTCGGGATGCATGAAATGG ATTAATGCCGCACGGCGGAACCTAATAAATCAATGGCCAACAGGAACGGC GCATAACTCGGCTGGAGCACTTTGACTTGGGTAATTAAATTACGTGGCCC GCGGCAGCGCGCCTTTGACATCCCAGAGAGGTCCTTTGTTCGGCTTTTTA TTTGCGAATCGACGGCGCAATCTGTTAACGCGTTTGCAAATAAAAATTAT CAAATTATTTTGGCCCGATTTCGGGCGGCTCCCGGCCATGTGTGCTCGCT CAATCAATTATTCTGCCGATTTCGGGTATTTGCATGTGCAAATCTGATTT ACACGCACAAATGAATATTAAATTGCTTGAATCAATTGAGTTCAAGTACA CTCCGCACTCACCCTGCACTCGCTGTAGATTTTTGAGTTCGCAGTGCTCA ATCACAATGGCATAAATCGCGCCACGAGTGCAAAGTGAAATTTGGAAAGG TGCCTTCCCGCACTTCCGCCGCTTTCCCCCATATGGATCTCTACTATCCG TCTGCCCGACTTACGCACTCGATATGTCCGAAACAAGAAGTGGAGGAATT CTTCGAAAACTCAAGAAAGACTCCGAACCAATTTAACGAACAATCAGCAG GTGTAATGTCACGTTTGGCCACTTCAAATATACATTTTTTTTGGTATAAC AACGGCCTGAGGATCATGTAAACAGTGGAAGTATTTGGAATTGACCCACT TTGGAATGCATTTTTGGTCGAATTTAAATTAAATTCAACTTTTTTGCCTG CAGATTCCCGCTTAAACTCGGACATTCCTGTATTATGATGCTCCTTTCTC AGCGCGTTGAATCCCGTGCGCTGGTGACATGCACGCGTATGAAATTCCAG AACACAAACTTTATTGAATTTCGCCCTAATTTTTTCGACTTCAAAGTCAA GACTTTGTTGCTGATTGTCGTAAGGGTTTTAATATGGCCAAATCGTCGGT CTGGCGTTTATTAAATTTTATTTGTGAGCAGCGCACAACAAACTTTTGTG TTGTGCTGTATGGCTCACTGCATGTGCAGTTGACATCTTTATGGGAACAT AGTTGGTACGAGTATACGGCTGTGGCTCTGCCCTCGTCCGTTGACATTTT CGGTAACTGGGAGGGGGGATGGCAGGACTTAGCCATATTTATTTGCCAAG CTACATACACAGAAATATACGGCAGTGGCAGAACGTATATTATGTACTGA GCAAACTTCGTTAAATGTTTAAAGTCTCAATCAATTATGCAGTTTTCCTT GTCGTCATGCTTTTTGTGCACGGCAATGAATAAGAAATGATTTTAAAATT TCTGACGGGCAATCTTAAAATGTTTCATTGCCTTAAAACCATTTCGTTCC ACCATGTTAGTAAATTGCCCGGATTTCAGATAGCTCTGCCAAACATCCTT AATTTACTCACTTTCGATTCTCTGGCTAACAAATGGGCCACAATTAATTA CACATGTGGGAGGTGGCTAGTGGGTGTAGCTCCTGTCCGCTCGTCTGGGC TCATATATCAGCTGATAACTGGATGTGGCATGAAAGCCGTTTTCGGGGCA GCGGCAGCAGTCAGCACGGCCATGAATACATTAAGTTGCTGCCACGTCTA ATTGCCTCGTTGTTTGTTTGTTTGTTGCTGTGGCTCCTCGGCGGTGTAAC AGGTGCGTTCGCTCCTTTGGGCAGCTCCACGGTTTCGGTGTCGAAATGTA TTTTTACCATAAATTAAACAACGGACCATAAAAACTTCCACAAACGGCCC GGCAAAGTGTTTCCAACCCGTTCCGCAGTTTGAACCTTTTTTGGCGTGTT TGCCACCGCCAACCGTAAATTCCGGGGAGCCAAAACTCATTTAAAATGTC CAACCCGTGCATGAGTTTCGAGAGCATATTTCATAAGCACACTCCCCGAC CAACTTGTGTGTTTTCATAAAGCATTTAAACAGCATTATAAATTTGCTTA GCTGCAAACGGGGCTTGCTCATTTCTGCATTCTCGATCACGACCGAAAGG ATTCGCCTGCTCACGTAATGGGACTTATGCCCGATAATGTGCTCCTCCTT GGCATTTGGCCCCCGGGGCGTTAACAGCCCGCCGGTTGCACCTGCAGCCA TGCGAAGGGGTGTCCTGGCCAGCAGGAAGGGGGCAGCCAGACAAAGGACC TCCCCCTTCTTGGCCAGCCGAGTCGAGCTCCGCAACTCCTGAACCGAACC TCTGAGCCACTCGAAGTGTGCGCGTGACATTCGGCGGCCGTGACAGGCGG CCCTTTTTGAATAATGCCCGTCAAGTGGCGGCCACCATATTGAGTGAGTA CGGTACAGGGAGTGGGGCAATGGCAGTCCTGTGATTTATGAGACAACTTT TTTATTTCAATATTGTGTTTTCTCCATCGGACTCCTCCTGCGTGTGTCTG TTTAATAAAATGCTCTGATTAAGTACAAAGTGTATATCGAATATTTATGA ATGTCTTCTCTAACTTCCTTCTTTCACGATGCAGAACGCTCCTCATAATT ATGACAAATTGATTTTATGTAAGCGAACAATGGCACTGAGTGAATTCGCC GTCTGCGACGAATCCGAAGAATGAAATTTGAAACGAAGCTCAATTTGGGT TTCTTGAAAGAGCTTATTGACTGCTGGGCTCGAAAATGACGCAGATATTG GCTGTCAGCTAAATAGGTTGTTATTTCTCGTTTAAAATTTAAAAACCCTC AAAGTAATTGCCGTAATTATGCAAATTTTTTTTCGAATAAAATATCTATA ATTGAATAGCGGTAGCTTCCGTCCGTCAGCTGCAATAAGTACATAACTGG GCAAAAATGGCGTTTTTATTTGATTCCTCATATGAGTATGCACCTGTCAA TCAGACCTATAAGCCAGCATGTTTCCGAACAATTCCTTTAACACAATACC AGCTTTAAATACCCAACGCATCTTCTATTTCATTTGAGTCACAACAAAAT CAGCCCCATTAAGTATGCTATCGATTTAGACTGCTGGCTGTGTTAAGCAC TTTATGCTCAGTCAGTTGTGCGAGCAGAGTTCAACGCACAATTACACAGC CGAGAACTGGTTGGCAGTCATTAATTTTAATGTTTATATTTTCATTTGCT GGCAGCCGGGCGATTGTCCGTCGAGTGTTGTGACTGCGGCGTTTTTATCT CAGGCACGCAGCACAATTAAGCAGCATTTAAATGCTCGACTGGTCGCAAC CGGTCCAAAATCAACCAGGCCGAACCAAAAGCAACCCGACTCTTTGAGTG GACATGCAATAATTGATATTTCAATGGAGCCGCACCGTCCATTGAATCTG CAATCTCGACTGCTGCAAAACTCCTGTGGTCGTCCGTTAATGGTGATGTA TTTTTACTTTGATTGCGTCCATAGTTGCAGTGGCAAACGTTAAGCGGATT TCATAGAGTGCAACAAATGCCAATAAGCGTGGGATGTAGAGTGCTGCACG TGCCCGGCATAAATCGATGTCGCTCTCCCTGCCCCTGCCCCTGCCCCTGC CCCTGCCCCTGCCCCTGCTCTTCCACTGCAGCAGTTTCAGTGTCCTGTTC CACTCCCCAGAGTGCCGGGAATAGGGAATTATATGTACGCATAGTGCGGC ATGAATATGAAGTGCGTGCTCCGGGCAGAAGGGTCAAAGCGGGTCCCTGG CATCCTTACTCCCAGCTCACGGCTCCCAGTTCCATGATCATGATCACTTT TCCGCAAATCAGCTGAGCACATCATTCATTCAAATTTGACCCTTTTTGCG TCGGAAGAGGACGCAACACTTTCGTCCTGCGGCACAGCAAACTGTGGGAA AATTATGCAAATGCTGCGGCGGCTTTACTAATATGCTCATTTGCATTTGC CTCCGCATTGTTTACCGAATTGGCCAGCCATCGATGGAGCAGGGGACTTG ATTATGCAGGGCACACGGCTGCCGGTTCTCAATTCCAGGATCTCGGCCAA GTTATGCGCTGAAGCATGTAATTCTTCCAGTATTTTTCACACCCTCCGGT CGAAGGAGCTTGACTTGACTTATTAATGTCCTGGATGCGAAAGGGTAGTG TTTCCGTGCCCAGACTGTTTGCCATGCGCCCAGCCCGGCTCTGCCTGCTA ATCGCTCGGGAATCTCTTTAAAGTCCGGCCAACTTTTCTGATGGATAGCT GGCTGACTGGCGTGGGTGCTGTGTTTACTTAGGGCATCAATACATCACTT AGTGGCAAATTTATGCGTTCGCTTGGCAAGTAGTTTCAAATATCAGCAAC TATCTGCTTTAAGCTTAAATCGCTGCGAGTGTTCATGGCGAGCACTGACC GCATACTCCAATATCCCGTGGCCGGGTTCAATTTATGGCCACACGAAACG CGCTATGAAAAATGTGGTCAACATCCAGCGAGGCACGTTCCCTGGGCAAC GCCAACCAGGACCCCCGAAAACCAAGCAATCGGAAGGGCCGAGGGGTGTG TGGCGCACCAACTGGAAAAATAATTACACAAATTATGATCGAGTGCGAGT GCATGCACAAATTAACAAATGAATTTTCGCCTGCTCTGTAGGCACGGCGG ATGCGTAATGCAGCACATTGCTCATACGCAGTGGGTGCCGTTCGAAGCAG TTGGCATTTAACTCCGGAGCAATAACGGGGCATTAGAGCTGCTTAGCAGC CACTGTGTGACCTCGGAGTCTGGCATGTCCCCTCCATGGCTGCTAAGTCC GCTTGAGCATTCGACTAAGCCCATTTAATTGTCTTCATTAGCGCGCTTAA AGTTACATTTAATCCGCAACCGACTGTTTCCTTTTCCGTTTCCGTTCCGC GCAGACGGGAAGGTGTATTTGGCGATGGAAAGCGAATTGAGCGAAGGCTT TTGCTAATTAGACGCGGACCCATCGCGACTCGGGTGCAATGAGCTGTGGC AGTCGTGGAGTGAGTGCTTCGAGTGCATTACTTTCCAGTCCAATATATCA AATTTAAATGCGGCCCACACACACTCTAAATTTAATGTGTAGCGGAGCGA TGGGGGAAGGCAGGCAAGGAGCAAAGCAATTTGTTTCACCACGAGTAATT TGTCTTCAAAAAGCAAATGTTTTGCAATTTGTTAACAAGAACATTTTTCG CTTTATGCTCCCACCGAACCTCTTGTCCCTTGTTTTACTTTTTGCTTTTC CCTGCATGTATTTGTTGGCAGGCGCTTGGCGGCTTGTTTGCCATCGTTTG GTTTTTGCCTCTTTGTTTACATTGTTCGCGCGGAGCCAGACTCCGACCCG GGCTCCTGAATTTCCAGGACTTTCGGGTATGGAGAGCACCAAAGCCGAGG CCACTGCAAACGCAAATTGCGGGGAAGCTGGCCCCCGAGCAGATAAGATG GAAAATACCGCTCTGCGCTTGTAATAAATGAGTGTACTGCCTAAAATTGA AAGTAAATACATATCGGCAGACATGCCGGACCAGCAGGATATCTTTAGTC CAAGCCCAAGAGAAGGACATGCAGAGCGGTAGCGGGTTGTCGGGCGGTTG GTGGTCAGGAGGCGAGAGCTTCCACTGAACCAGTGGACCCAGAACCCACT TGTTGGCCACGGTTCACCCGGCAGCGAACTCTTAATTGATTTCGCGCTAA TTGGTCCGACCCAACAACGACGCTGGTTGATGTTTAACAATTTGCAAATA TAAATATTACCAACGGTGTCCAATTATGGATTTCCCAATGCACTCATGTG CATTCATATTCAATTATCTTCCTGGGCGGGCTTGTTAATTGCTCTTAAAT CTGTGCGAGCCGGAAAATTCTCTCTTCGCAGGCGAATTTCCAGCAGCCGG CAGCGAAGCGGTTTGAACGGTTTGTGCGACTTTTCAGTTCTGGCATGGGA AATTCATTTTATTTCATTTACATTCATCACCTTTTTTCTTTCTCTCAGGG TTTTAGCCCCTTCGAATCGGTATGGAATCAGTCAAAACCGTAGAAAACCA CTGCTCTGGTGGTCATGTGCATGACCGGAAATCCACTCCGTCGGCGTGCC GTAATGTCATAGATATTCAGATTCACGGTTGGGGTTAGTTTATTGAATCT GTATATATAATATACAAATTATCCATAATCGAATAAGCTATCCTTATCTT TGTGGTAGGTCTTTGTACAAGTATGTATGTACTTGTTTATTAAGATTGCT AATCACGATTAACTTAGTAAAGATAATTTGGGTTTGTTTGAAATATTTGG CTATACTATGAAGAACTTTTTTTTTAAGATTAAGGTTAGAAGATAGTTTA GTTATCTGCTACAGTTTCCCGACCTTCATTGTTCGACCATAGCTGCACAA ATTTAATCTGGAGAGAATAACATTTGCTGGGGAAACTGGGTAAGGTCAAA AAGTAAGGCCCGTAGTCCCTGCTGCTGTTCTCTTGATGGTTTTATGCTTT GTAATCATGGCCAGCGCACACACACACACTCACATTCGGGCTACCACAAA GCGACACAATTTGAACTTTAACACCTTCGGTGACAGCCAGCTGTATGACC TCAGGCGCAATTTCGTGTAAATAACACGAAAATAACAAAAACATCCTCGA GCGGTTGAGAATAAGGCTCCGACCTCTCGACCACGCCCCCAGGCGCACTG CCAATCTCAATCCCATCTCCCACCATCCACCTCCGCCCATCATTCGGTCT GTGGGCTAGTTGGTGTGAGTGCTGCCGTAGTTGGCCATTATGCGCATAAA ATATAAGAGGGTTGTTCATATCCCCAGCACAATGGATGCATAAATCTACG CTACTTTGCAGGAAAGGACGAAAGGCGGGGGACAGGACGAAAGACACAGT CGGTGAAAGTCTCTGCCCTCGGATCGCACGCAAGATTTATTTTAACATTT TTATTATTAGTTTCCCGTCTCGTTTGGCCTTTCAGAAGTTCCTTGCGGTC ATGCTGCATTAGCTTTGGCTTCCATCACAAATTGCTTGAAAATGGCATTG TAAATTATGGTTTACTTTTAAAGAACTTCATTGAAACTTGATTGGAGCCT CATTCACAGCCTTCGCCTCAACCACTTCCCGTCGCCCACCTCAGAACATT CCCACCTACTCCCACTTTGGCAACCCTTGTGTGCCACTTACAGTTGTACA AGGGATCGAGTTTTCCATTCGAATGCCTTCGAGCCCGTTCCGATTCGATG CTATTGTGTTTGGCTTAAATGTCAGCTGTCATTGGCCATAATTTCAGTTT ATTGTTTTGCCAAAAACAAAACCCCGGCCCAGCCGCCTTTAGCGGAAGGA GCCCTTTTCCGGGCCTGACAATTCCATTTACTCATTTTGGGCTCGCTGTC GCTGATAATTGGACATAAAAGGCTATCGGCAGGGAATAGCACGGCGTTTC AGATGGCCCAAACTTCCTCGATTTGGGGAAGTAAGTAAGAAATTTGTAAA AAAAAAAAACTGACGATTTAGGACTTAGAGATTTAGTTCCTTAAGCTTAC TGTTATTCTCCTCCTTCTTTATTTTAAACATTTCTATCTGCCTGTAATGA TTGGGAAAAGTTTAGTTACGTGGCTTTATTTGGTTCTTCCATGATATGAA CTTCCTACCACCTATGAATGTTACTATTATTGCAATGGTTTCATGTTTGA AAGCCGAAATAAAAAAAAAAAACAGCGGTCTTCTATTTTGCATTGACTGG TTAACAAAGGATATTAAAAGCTCAAATCTAAAACTTTAACTAGGAAATTA ATAATTAAATGGCAAAATCGTGTGCCTCTGGCCTTTCTGAAACCGTTCGG GATGGGTGGAGTTCGGGGCTTACTTGTTGCAGACCCTTTCTGAAATTAAA AACTTTTCCCTAATGTGCATTAAAATCCTTTCATTTCTCAATTTTTTCAA TTTCCATAAGCGCTGACCCCATGCATTTCGCAAGCCTTGTAATTTTCCAA TTTGCTTTTCTTGCTTAGTGTCTGTTCTGCCTTTTCACTTTCCACTCCGT GCTTTTTCTGCTGACTCGTGCGCCTAATTGTAAGTAACAAGCGGGCAACA GCATTTACAGCTCGGAAAATGCCAATGGAAATCGCTTATAGCTCGGGGAA AAGCGAAAAAAATAAAATGTGCCGGCGGGTGGAGGCGGGAAGGGGCCCAG AAGGAGCCAAGGAAAAATTATAAATGGCGGCGAAAAATTCTTTGCAAACA CTTTTTCACGCTTGATTAATTTTGGTTCGGCAGTCGCTAGCTCCCATCCC TTCCCCATTTTGGTTTTATTTTATTACCATCCATTTTTTAAATGCAAAGT GTTAAGTTTGACAGTTTTGGGTCTACTGTGGGGCATTATGCACACCTCAC TAGATATGCGCGAAAGTCGCCATCGCAAGGAGCAAGCAGCTCCGTCATGC GAATCCCTCAAGCTGACAGGCTGCTTTTAATTAATGCAATCGCAGGTCCT TCCACCTTGGGCTCATTGCGGAACAGCTCTCGAAATCAATTCGAGATTTT TCTTCAGCCTCCGCCGGTCAATGAGCACATCATTAAGGCCCTCAAAGGGA ACCCCGCCCACTCCAGGACCTCGATTTCTGGCAGTATGCTAGGGTTCAAA AGCCACTTCATCGGATTGAATGGATGAACCGGTCTGGCCATGGATTGCCT CTGTGTTAGCGTTCTGCGCTTATTTATGTTAGTGTCTTGCACTCAAGCTG CTTCTCACACACAAAGCCATGTACTCGGCTCCGCATTCAATTTACTAATG CACATCGCTTCTCCGGGCAGGAATCCATGTGCTGACATCCCTGCGATTCC AGTGAAGACGTTGTCCCTTCCCCCACCGACTTAGGGTAAGAGAAAGTTAT TGCCGACGCATATCGAGCATATCGTCGAGCGAAATCGCGCCGCATTGTAA TCAAGCCAGATGCTGTATCCCAGCCCAAATAGAAATTTAAACTGCAACCA ACTGATATGGGTTGTTATTCGATGTTCTATTGGCCGCAACCCCAGCAGTG GAGGCAAAGAGAGTCGTGTTTCCACGGTGAATTCATTTCATTTTTGGTTA ACCATGCTCCGGTCTTGTTTCGCATGTTATCTCGATAATTAATTCGATTG CTGCAGCCCCCAAATCCGAAAGTTACCTTCAACCGCCTTGGCCAACATGC GGTATGCGTGATGTGAAATTTAAGCTCACTTACTTGGCTGTTTACCCTCA AACACTCCAGCTGAACGGCTGGAGAGCTGTTGTTGACTCTATCTGGAGTC TGGCAGGTGGATTCAGCAAGCTGGAATCTGGCACAACTACCCAAAGGAGC TCGAATAGGTGTTTGAGCGTTGATTTAACGCCATTCGTTAGTGTTTGCCC AGCTCGCTTGATCTAACGCAGCCAACTCTTTGGAGGCCAATCCAATCGGC CACTTTCAGCTCGCTTAAATTCCGTGGAGCTAAATTTACCCGGCGTCCGA ACAAATTCACTTAAAATGCTGCTCGGCGCTGGGCGGGGCGGGGCAATGAA AATAAACGACTTCGCATCAGAATAAAACGCTAAAAAATTAAGAAAAATGC GATGACGACCAGGACAGGAGTAAGGTCAGGCCCCAAGTAAACGGAAGAGG ACCCAGGGAACCCAAGGGCAGAAGCAGCAGCTGGAGCAGGAACAGGAACT GGAGGAGGAAAGAATACGCAAATAAAGCTCCCAGCTGGCGGCAGGTGGTT GAGGCAATACAAATTGTTTTGAATTTAAATTGGACAACAGTTGCAGATAC TTTTCGAGCCCCTCCTAAGCTTTAATCTGTGGCCAGACACTTGATCGCAG CGCTTTCGCATCGAAATATGTAACGACAGCTCCAAGGTTGCGGCAAGGAT GCCAGCGTCGGCGTTTTGTGTTTGTGCAACGTGGCGTGAATGAGCAACGG CAAAGGTGCCCTGCCCCAGATACCTCCCCCCACCCAAAACCTTCGCCAAG CCATCAGTGTCAACGTGTCTCGGCTACATCTGCACCTGCAGTTGAAGTGC AAATGTGCAGTGTAATTAAAAGAGTGTGCACGTGCAGACCCTGGCAGAGC AATTCACATAGAAAAAGGCAAGCGAAAGGTCCTTCAAGAGCCGACCTAGT GGTAATTTCGGGAAATTCGAGTCCTCCGTCCAGATGGCTTACTGATTGCT GCCCGCTGGCCTATATGCCTGCCAATCCATAACCATAATCCAGCTGGAGG ACCAATATAATAGAGCCACATCCCTGCAGCCCGTCCCATTTCAATTAACG TTTGACCGGTCTTAATTCGAAACCAATGCAGTCCTTTTATCCTTCACGGG AAAAAACCAGATAAATAAATCAATTCGTCTCGTGAAATAACGATGAATCC GAGAGGTGTCAACTTTTCCTTTTAGGTAATTTATGGAAATCGATAATCTT TTATCTTTTGGGCAAAGCGAAATCTATGGGAACTACATCATAAAATGATA AGTAGCACGAATATTGACCCACATCGATAAGTTTCGTGCTTATGGAAAAA TTATCGTTTTATTTTCCCAGGTGTAGCCTTAAGACCATGTAAATTAGTTT TCAGGTGAAATGCAAACCGAAGTCGGAATCACAAGCAGGGCGAAGCTGGT TTGGTCATCAGATGGGACGATGCGATGGACGAGCACTTGACTTGAATATG TGATAATTGGGTTTTTTGCCCATGCAACCGACGGACATCCCAGACGCCCC TAGATTCTGCCCTTCGTTTCACATTTTGCCTTTGCTAATTGCTATTTCTG GAAAATTGCAGCAGCAGATAAAAAGTGCTGGGCAAAAGGGAAATATATGT GCTGAAATTGTTTGATATCCCCACTCATGTTAAATTAAAATATTTAGCTA GTCAGCAGGAGTCAGCTGGTATGCAATGTTAAATATTAAATGCTGACCAA AAATCCGATGAAAATTCCATTATTTAGCTGTCGGCCGGCCATCGATCCCT TTTTGCAATGAATAAAATTTTCATCCACTTAAACGCATTGCACATTCAGA ACTTCAAGCCCGAAATATTTCCTCTGCCACTTCACGGCGAAACTCCCCGA CGAGGCTTTAATCTAGGCACAGAAATGGGAAAAGAAAGTGCGAACATGGA ATAAATCTTGGCCAGCATTGTCCTGGCAGCGCAGCCGGAACCAATCCTGA TCCTGAGAGGGAGCCAAAACCACAGCCAAACATCGAAGCACTTAGCAACT GCCTAATTTATGGCCCTGTCTGACAATGTGCACGGCAATGTGAATGTGAA TGCGAATACGAATCTGAATGGGAATCCCAATCCCAATCCGAATGCGAATG CGAATGTTTGAGCGCCGGGAGGCCAGACGGTCCACACAGACATGAGGCAA ATATCAGGCGATTAGCCACAGACGATTGCATTGAAACAAAGCTGGAAATG GGGATTGGGTTGGGCAGGCAACTCCTCATCGCCGGCAAATCGATCCACAT TTAAATATCTTTGTGGGCTTGCGTCGGCCAGCATCTGTAGCCGAAATCGA TGTTTGAATAATTGTAATTGAATTAGATGGGATTGTTTTGACTCTGGCTG GCACGCGTCCTTACACCATTGGCGCACACATCTCAGCTCGACATTTATTG GTAGAGCAAGTGCTGCACGGTAGTCACGTAGTTGGCAACTGGAGGCGGGA GGGAAGCAGCTCCGGAGTTCAAAGTTTTGTTTTGGGACACATGACATGCA AAGGCGAAATCACAAAATACTGAAACGTGCTTTTTGACATTTTTGCAATG TATTTAGGCACGTGCAATATCCATCTCGGGGAGTGTGTGTGTGCGATTCC TTTGCCAAATTGAATTTAGCTGCCAAAAGTGATATCGATTTAAAGGCGAA AGCCGAGCGGAATCGGCAGCAACAGCATTAGGGTCAATTACCGCTGCAAA GTGAATTGTCAACAAAATCGAAACCCAAAAGAGGCGGCAAACTGAATTCA ACACATTGTCCAACTGCCAACTATCACACACACACACGCTCTCAGTCGAT CCAGGATGTTCCAGGATGGGGCGCACTTTCATTATCTGTGCAAATATTTG CCAAAAATGGCAGTTGGCAGTTGTCTCCTGTCCTGCGAGAGTTGCTGGCC CGACACTTTTGGGCATCCTAGTGCAAGTTTTAAGCCGCTTAGTCCCAGCT CTTTCCCATTACCCCCACCCCGCTACCCACTCGACAAAGTGAAAGTTATT CTACACACAGACACTCGTTCAAACTAACCCTGCGGTGCACATTTCATAAA TGTGGCTGAAGAAAAACTATTTTCATGTTCCTGGGTTGCGTGGGCCTTTG CGAAACTTTCGTCCTCCTATGTCGGCTGTCCCTCAACACAACTTTTTGTC TGCGCCGGAAACTATGGCCCATCCTCCCAGCAAGCATGCCGTAAATATTT GCCTGTGCGGCACAGATGCAAACACGTCGCCAGTTTGACTTTAAGACTCA CCTGAAGGGACGACCAGCCACGAAGTTAACACATCAACTGTCCCGCAGCA GCAAAGGGATCAGCAGCTGCACTGACACAAAAATTTGGCGACAACGGACC TGAAGTTATGTGAATATTATGGTAATCTGAGAATAGAGCATTATAGAACC TATACCGTCATTTGCCTCGTGCAAATCATCCATGGGCATGTATTGTACAT TTTGAATGAACCGTGGACTGTAGTTAACTTAGTAACGAAATGCGCCGCAA AGTCGCCAAAGTCTACTATAATTGTTGAGGAACGATACTTTACTTTGCTT TACCAATAACCAAACACGTAGCTTCAATATTTTTCCCACTGCACTCGTGC AGCAATAGTAGTCAAGGGTGAAGAAAGTTGGCCAACTTTCTGTGGGCATA TATTTGGATGTGTTATTGGAAAATTTTCAATTTGCTATTGAGAACGTACG GCGGCGGTATGATGGGATGTGGTTGGTTGATCAAGGGCAGAGTGCGTAAC AAATTTTATACTCCAGAAAGCTAATTAACTTCTCTTTACGAGGCATAAAC TTCCGCCATTATACGCATTTATTTTCATGCGAAAATAAACAAATACCCAA ACACGAGCCGCCGACACGAGAAAGTAATGTTTTGACGGCTCCTTTTGTGC GCGCGTATACTTCTTTATGCATTAACAGGACGAGGAGCACGCAAGCAAAC ACAAACAAAGCCACGGGCCGCGTGAATTTACGACAGAGCCGCCGTCAAGG GGGTTCGGTGGGGGTCCTTTTGAGGTCCTGGAGAGGCGATACCTCTGCTG GTACTTAGCAACTTTAGCAAGGAGTATTTATTTAGCACGTGTTCCCACGT CCTTCTGCTCCTGGCACATTTGCTGCTTGCTTTTAATTAACAAATGCCTT CCATCGGTTTCGACAATCGTAGAGCGTTAATGTTAATAGAAGGCCGTAAA CTTACCTGGATGCGGAAGTAGACATAAATTAGGCTTGGCCTTTACTGCCG CCGGGCATCATAATCTACTGGCCCATCAAAAGTCATGATTATAACTTGAT TTGATAGCGGCTTTGGTCCAATCTGTCTGGATTACTGAAGAATGCACAAT CAATGTAATTTTTGCATAAATGTACTACCCAAGTTACTACCAAGGATAAT CACAGTACTGACAACTAATGCTGCAGTAAGTGCATATAGTGTAATGAATT GTCCTTGGAAATTCATAAAGTTAGGTGATGTCCAGCTGGTTTTTTGAAGG TTACTTTTAAATTGGTAGGAAAGCCAAATGTTAAACAAGTTACCAAGCAA TTTCAAGAATGGATACATCACTTGACAAATGACTTCTTAAATGGCCATTT TAATTCATCCATTTGACGGCCAGATCACATTTCTAATCACATCGTGCAAA AGCCACGTAGAATAGAACATTTATTTAGGGAAGAACCCTTCACCTTTGCA TATAATTTTTTTATGAACAGTTGGAGAAGGGTTGGAGGAAACTGTGCATT GGGTCTTTAAACAAGTAAAGCGCTAAAAATAAAACAACCTACACATTTAG CTATCATTGCTTTACAAATTCCATTACCCTAATCCGAAACCGACTGTTAA CTTTTTTCAAGACCTCATTACCAAATGGAATACTTTAAGCCAGTACTGAA AGTTTGTTACGATTAATTACTAACTGAAATACTCGTACATCTCGACGCCG GCTGAAATTTATTGACAGTCTGAAAAACGAAATCTTAGTTCAAAGTTAAC AAATGCATCTATGACTCAGTTAATAATTTGATCGAACTTACTTAATATAA TTGATAGTATTTAATGTTGAACTCCGAATATCAAGTCCACGTCTGGTTGC TCTAGAGCAGCTAGATGGCCTTTACTGTTGGCTAACCAAGATGGCCCACA GCTACCGACTGCAACCGATAATCGCTGAAACTTGCAGTGAGTCAAATTGC ATAACAAACATAATTTTAATTAAATCAACAACTTGGTCGGCAACACACTA TATCATAATTGCCACGCGCCACCCACAAAAGCGCACTTGGCCAAGTTTAA TTAAAATGTCAGAATCGTTGTACACGTAAATTGTAATTGCATTTTTTTGG TTTGCTCGCTGAGGTAATAATTACACACAACACATCGGCAGTATGCTCAA AAGCTGTTTAGGCAAAATTAAACGAATTTGCATATTCAATTGAACCGAAC ACATAGGCTCGGCAATGAATAACGCATGGATGAGCTTATTTCTGCAATTA AAAGTTGTCAATTAGTTTAAAGTGCAGCTGGTAAAAATTCCATTGTCGAC TAACATCTACATATTTGAAAATGCTGCTAAAAGAACACACATTACGAAAA GAATTAGATACGAAACACCTCCATTATTAGCACCCAACTTCTTCTGGCAT TGTATTTTGTTTTATTCCGTATCAAATTGTAAATTATTTGTATATAGAGT ATTTATGTATGTATATGTATATAGTCTTCATTTTACAATGGTTGTGAATT ACAAAATCGGTAGGTGTTTAATGACGCTGCTCTCGCCCTCGGTTCTCTAA CAAAACTAATGAAAGTAAAATCAAATGAAAGAAAAGAAAAGTAAACAAAT TTTTATAAAAATAGTTTCGATGGTTTCTTACTTTCTTTCTGATTTTGTTG CATTTATTGTTACTCTTATTATTTCAAAATACAGCTTATCATTAGTTTGA ACAATAAAATTTTGATTACGAAAACGAATTAAGTCCGATGACCCCCATCA CTTTCTTACTAAATTCGCTATGTTTGACACGACAATTTGCAGGGAAATGT GACTGATTAAGGGGGCCTCAGCTAGGATGAACAGTATCGATTCTATCAGC TATTGTCATGAAAACTTCCGGGACGTACAAATATACAGACGTTACAGAAA GGAGCTCGTACAAATTTGGTAGGTAGGTGTTAACTCTTAAGTGATTGAGG TTTAGTCTATGATTTGCCTTTGTTAAATTTACAACAATTTCATACTTGCG TAACAACAAGCCGATCAAAGGGCCGAGTACCTGCCCTTCGCTCTGCTTGA TTTTGGGCGCAAAATGTAGGTAGTTCGTTAGGTTTTTTATATATTTTTGG CAGGATGTAGTTTTATGTTATGTTTTATACGTTAAGCGTCCAGGTCTGCT CGGTTATGCTCGCTTAAGTTCGATTAGATGATTTAGCTCGGCATTCTCTA ACCCTATCTGTGCCACACCCGCACTCAACTGATTTCGCTAATATTAAATT ATAAAAAATAAATAATCGAAACCATAATGGTAATAGACAATAAGTTCTTT TTCAATTCGTCCTCAGCGCGCTTTGTTGCAATAGAGAAATTAAGCGTAGC TACGAGCTTCTACAAGCAGTTCTCTGTCTCTCCTCCAATCCATTCCGCCC ATTTTTATCAGTTCAGTCCTCGTTTCATTGCTAGACCTAGTCCTCGTCCT TTGACGTTCCGGCTGATGTGGACGCGTGGTCGTTGGCACTTTCACTGGCT TTGCCGTCAGACGTGGCTGCTCCCGCTGAAGCCGGCGCAGCATCGCTTCC ATTCTTGTTGCGGGCGTCCTCCTTGGCCTCCAGAGCGCGGATGCGGTTCT CTTGCTTGACGATGATCGCCTTAAGTTTGCGGATCTCGTCTTGTATGGTG CGCAGGTCCTTTTCCTTTTGAAGTGAACCAATAAGTTAATCATACAACCG CTGAAGGAGTGCAAGTACTCACCGATAAAACCGCTGCAGGCGGTCCACCT TCGCTAGCCTCATTGTTATTTCCGGACGCAAAGTTGCCGCCGCCCGCGCT GCTGCTCGTTGCACCGGAGCTAGCGCTGTCGCCTCTAGGCTTGTTCAGGA TGTTGCCCGCCTTCTTCGCTGGTAGCGATTTGTTTACCGACGAGGACACG TAGCCACCCTGTACAATGGAAACGCGATCCTGATTAGGCGGGTAAGAAAA TCTGTTCGTTTCAGAACACAACAAACAACAATGAACACAACGACAAGCGC CACGCGCATTCGCGTGCGTGTTAGGGCCAAGTGTGCATTTATGCGGCGTG TTACTGTATCCAATAGGAGACTTTAATAAGTTAGCTAACATTTAGAATAC TAAACCATTTTAGATCATTGTGAATACTCTTTATTCCGGTCGTCACTAAA ACATTCTTAAGATGCCTCGTCTCAAGTGACATTGTACAACGGAGAACGAG GACTGTAGTCTGTGTATTGGAGTGGAATGTGGCTGGGCGGACAAGGCACA AACGTAGATAACGCAGAAAAAACGTAAGTAAAGCAAGCGCAGGCATCACA CGCTGGTAGGTAGCCACCGGCAAATGCTGGGAGTAAGCTTTAAACGGAAC TCACAAGTAGCTCACTTGGAGTCCTTGTGCTAGCAGACAAAAGCAACTGC AAAAGCCGTTGGAATACATTGTAGAAGGGGCGTCCACAGTGGCAGCGACT GCCTCATCGACTTCGAGCCGCATTGCCATCTGTGGACAAGCCCCGCTGGC GCACATGCTGATATATATCCTATATCTTGTACGCTCTTATCGCCGGCGGA ATGGTTGGCAGTGTGGCCGAACCGTTGCCGCATTCGGCGGCGAGCGCTGT ATTCGCAACACGGAATAAAAGTCTGAGCTGCTTCTGCACCTTAGCCACTT ACTTTGAGCGAAAATGTGATCGGATCCGCATCCTTGCCATCGATCCACTC CTCCGCGGTGATGGCAGCGTCTTCCGCTAGCGTATCGGGGTAGAGATCCT CCTGGAAAAGATCCGATTTGCGCGGCACAGTCATCGAGATGACCTGACAC AGACCGTTGTTGTTCATGCGATAGAACTTGGCGACCTCGCAGGTGGTCAC ATCACAGCCTCGCTTGGGCATCAGACCAATACCACGCTGCGGCTCTGTAG TCTGAAACGTGTTTATGTAGTGCACAAAAGGAGGTTCGGGCGTTACCTGT TCGATGAGATTTTGGTTAGATAATATTCATATGTAATATTGTAGATTTAC TTGTACTAACCTCGAAATACCGAATGACCGAGTCACCTTTTCCACACAAG TAGATCATGTTCGTGTCTGCGTCGTAAAGAGGGAACATTACGCCGTTGGA CGTGTCCAGCTCCACCATGACAATGGGTTCGTTAAGGGCATCCGGTGCGC GCAGGGAGTACTGACGCTCCGAGCTACGGTTGAAGCCTGTGGTGAAGATC AGACCGTGACGTAGGAAAATGGCCCTCGTGGCCTTGGAGCCCTCATGACA CATGGCTTCGCTCTCCAGCTCGGCAGTGCGCGGATCGTAGATGCGGATCT TTTTATCCTTGCAGGTGGTAACCAACTTAGAGCCATCCCAGTTGAAGCAG GCGCTGTAAACGATGTCCGGATGGGAGTCGATGTGCACGAGGATTTCACC AGTGCCCACGTTCCAAATCACGACCTTCGCAATACAGAGAGTATAAGCAT GGGCTTCTGAAGAAGTGTTAGCATTCGCTCACCTGGTTATCGGAGCCGGC GGTAAGCAGCACGTTGAGCGCAGAGGGATGCCACAACACCAGACCCACGC GACGCTGGTGGAAAACCAGGTCGACCACGGGTTCGGTGAGTGTTCGCGAC AGCCCGCCATCGGGGATCTGCCACACTTTGACCACACAGTCCTCTGAGCC GGAGGCGATCACGTTGTCGTTGTGGGGGCACCAGGCGATGTCCAGCACAG GACCCTTGTGACCGCCCACCAAAGGGTGGTCAGCCGCAATGCGACCAACC TGAAAGAGTCCATTAAATTTCAATTAGCTCGATACGCCACAGTAAATTTT TATAATTGATGGCGACTAAGTCATGAGCAGCAACCATTGCAAAACTGCAA CCTCGCGACCCATTAGCCCAATTCCTGAATTATTATTTATAGCCGACTCC GACTGCACTCGGTTCTGCTATGTTCGCTAATCTGCCAAGCAGGCAATTTA TAATTGTAAACTTCATGCCAATTGCTTCCGAATATGGCCCTAGAATTATA GAAAATTGGAATGCCGAATAGCTCCCATCGAAATCTATATATTTCGAAGC ATATTATAACAAATAGTAATGGTAAACTATTTCAAATTTAACATTGTTAT ATATTATTAGATAATATTCTTTGTTCATCGCTTTCAATAAATGTATTAAA ATGTATCATTCCAAAAAGTTTCTCGAATGAGTTCCATGAGTGTAAATCTA TTTTGGTTTTTTCAAGAACTTGTGCTTGTTCTTGCCTACACTTGCCACAT GCGGCCAACCTTGGCGACTAGATGGATCTCACTCATCATCCAGTGCCCAT AAAATAAGTAAAATAGGGCGTGTGAAAGCCGCTCCACATAGAAATCATCA CTTAAAAAAGCGGCAACTGCTTAGAGTGAAAAAAACGATCGCTTGCCGCG CGTTTTGCATACAAATTTTTGTTTCAAATGGAACGACCATCGGTGTACTT CCATATATGTTTTCATCAAAAGAGGAGCATCGGAAGATTAGGGGAATGGG TGCTTCTGCTGCCCACACTATTTGCTGGAGCTGCGCGCAAAACTACAACT AAACAGAAGCCCGAATAGCTGAATCTGGGGCAGGACGGCCAAAAGATTTT GAGATTGAAAATGCAATTTAGTGGAATACAAACAATTAGTTTTTAGCGGA ATAAGTCGCCGAGCTGAGTGTGCATTTCGATGCAATGATTCGCCCGAATA TCATTTTTGTATTCATTTAACTGGCTGCTCCTCTGCCTCTCTCTAAAATT AGACGATTTGTTTGTCATGTTGGCTAGTGGCCAAATTACAAAAGTGCGCC AGCTAGCAGTATCGCTGCCGCGGTAGTAGCAGAATCTATAACTATTTATA AACACATGTGAGATTGGGTGGAGTCATGCGAAATCCGTCGACGTCACTCG CGACGTGGCAACAAGCCCGCAAATGGCCGCAAACTTTATGCCAAAAGGGC GCTATAAATAGTTGCCCATTGTCTTGTTTAAAAATACCCCACCAAGCTGG CCGCGTCGGGGCAGACGCACGTAGACGAGTGCAACTATAATAGGTCCGGT GGCGCACTCACTTTGTTGTGTGGCAGGACGATGAAGGCTCCGCCGCCCGC CGACTCTACGATAATGGCCAGGAACTTGGGATTCACCGCGCAGAATGTGG AGTCCCAGCTGGACTTGGATACCCGTATGTTGTCGTAGCACTGCTCCCGC TTGAGAGCCTGTCCGTAGACGTGGCGGAACTTGGAGCTGCGCACTACGCG AAATGACATCTTGATGCTGCAGTGGCTTGGGTCAGCGATCAGTCCTGAGC TTCTCTACGTCTAGCTCTGAAAAGAAATGAGACGTACGAAGGATAGTTAG CAATGTAGGGGAATTTCTTACGCGTTTGGTATTTTCCACCCTTTGCCCTT AATAACAAGTCTTCAAGCGAAATCGTTTAGCCGTATTCTTTCCGCACCTG AATGAGATATGAAACCCCTACTTTTTGGCAGAGATTTGAACACTCATTTG ATAGGTTTTGTTTTCTACACAGTTCTGTGAAACCTGAAAATCGTGATCTT AGCCTTATCCGAGTTCTGAGCGACGCATAAACCGACCGAATAGCAATGTT ATTCGCTTTCAGCTTCGCTCACTTATGTGTTAGCTTAACGCGTTTTTCTT TCACCGCGCTTCGCAGCCTCGATTAGTTCAATAAATTTGCATATGCTAAT TTCGCTTGTTGCGAAAATCAATGAGCTTTCCATTCGCAGCTTGCTATTGA CGCGCTGACTTTGTCCGCGAGAGGTTGCATCAAATTGCTTATGGCATCAC TAATGTTGGCGACTGAAAGCGCCGGAAACGGCGGGAGGCGCCTAGAACGC TTTCACCTGCCACTTGGCAACTGCCACATTCGGGTCCACTTTCGTTAATG AAGCGCCAGCCGGAACGTGTCGAACTATCAGTTTTCCATACCCCTTTCTT TCAGGATGACATCATAACGCCAAAATAGCCACTCCAGCAATGAGTAGCCT TCCAACACGTAAGTTATGGCTGAGCAAACCGATCCCGCAGGCCAACCTAA GCCCAAACATATACCTAACACTCCGGGAGACTTCTAGATAGCTACGTGTT TGAAGCAGAATTCATTTCTGGGTTGGGCCGAGCCCGGCAGGCTTCCACTC CGAACAGCTTTCGTTTTTAATCAGAGAAGTGCCATAAAATTATTTGCCTC TTTTGCCTCGTTGCTTCGTTTTGTTTTGCTCAAAGATATTCATATTTATT GCAAGCACTAAACTTTGTCATTGACCCCTTTAAACTGGCCCCAAAGCAGA CCCCAGAATTGATTACTTTCTACGCTGTCTGTTTTTGGCCACAAGGTGAG CCCCGGAGGGCTTTGTTCTTGGGTGGGTGTGGGTATCGACATGGCCTCTC CACTGATAAGGAAATATCAGCTCGGAGTTGGCTAAACACCACAGAGATAA TGTTAAGTGCTACGCCTATGTAGTCCAAAACGACGCCGAAATGTTTGCCA CCAACTGGAAAATACTCCTAAGCACTGTACCCGGAATATATCTATCTATA TATATATATATATATCTGCGGCGTGTGTATGCGTTGTTATTTATGTGTTT ATATGCCAAACACCTTCGTTTGCAGGCGGGAAAATTTTTGTTTCGCGGCT GAAGGTCAAACTTATTAATAGAAAATTAAATCATCTTAGGCGAAATGAAA TTTTCATATACAAACACAGTGCACGATGCTCAAAGCAGCGTTGTAAATCG CATTTGATGTGTTTATTTATTTCGTTGGCATCGCTGGCACCTGCCATGCC TGAGTTATCATAGTCGAGCCACCCCCATCCACTCCCACTTCCCCGATCGA TCATAATTGCATTCGCAATTCCGCTCGCAATGGCCAAAAAAGTGGCCTCT TCTGCGCTTAATCAACTTGACCGTCGGTGGTTTTATCAGCGGACCACTCA GCGATTAACGGAAGTGTGGGTTCAAGAAAATCGCTGAAGAAATGAAAATC TTTGAAGAACTCATTCCCGACGCCCATTACCCGGGTGGTGTGATTGAATA CCCAGCATCACATTGCATTCCATTCTTTACAGTGGGCCCCAAATGTAAGG CTGTTTCTGAAGATATTCGAAAGGAAATTAAGTCAAAGGTTCAAATTAGT ACCGGATCTTCAAAACTCACATTAGATGGAAGTCCACAATCTACCTAGTT ATTGTGTTTAAGTCTAGTATTATATTTATTCACAATAGATGTCAAAGGTG CGAGCGTCACTAGTTTCTCAAATTGTTCAACAGTGTTTTTCTTTTCTTCT AAAAACTCGCTTGAGTACATTCGGAAATTACCTATAACCTGCGATTCTGA TCAGGAATATATTCTTCATAGGGTCGGAATCGTTGCAACGTTTTCGACGA ATCAGAATAAACTTCTCTATAAATGAAAGGTATGTATACCTTAATAACAA TGAAATGGGGTTAAATAACATAATGATTTTGATAGTATAATTAGAATTAA TAGAATTCCGTTTGAAAAAGGTCTTGAAAAAGGTCCTGAGTCAGATTTTG GTTCTAGGAGGCGTCTCTGCCAGAATTAGAAACAGGCTGTTGCTGAATCA TTATTGAAAAGTAACCAACTAATCCGCACGCCACTTAACCAGCGGGTGTC AACCAACTTTCAGCAGCGACTGTCTTGTAATCGCGTTAACCATTTGACAA TGGGGCTGTTGTGGGGCCCTCCAGCAATTTGTGTTGAAATCGCGAGAGAT GCAACCGTCGCTGAATTGATGCGAATGCGATGGTCCAGCGATCGGGGACT GGCCGAGAATTGACTTAATGCTTGATTGCAAATCTTGCCGCTTTGTCGAC ACGTTGTGTTCACCGGCCACTTCCGTTATAATGACATCTCTATTCCCCAA GTACACTCGAAAAAGAATCTATTAAATGTGTAGGACCACATGCCATCATG GTTTCCGGATTAAAGTAGCTACAACTGATAGTTCAAACTTTTCCTAAAGC ATAGGGCACAAAACCATTCTTGTATAGACAAAACTGTTATTAATAAATAT GTATTAAACATACTCCGCTTAACTCATGTGTAGAGTTATTGGATATGGAG TTTTGTAAACTCAAGTGCTTCCCTTTAACGTGTCACCACAATTACATAGA GGCAGGTGGTTTAAAACAAAATTAATACTATATAATTATGGATTAAAACT TTGTCTTGATACGTGAAGATATCAGACCAGTTGTAGCTCAGTCAGGTGTT ATCAATACGGCATCATACATTGTATACATATATGTTTGCGTTGCGCGGCT TGGTTTTGATTAACTCGTGGTATCTTTTCTTCCTGTGCACAGCTGCAGCG ACACCTAATCAGCTGGCCAATGATCAATGCCACATGCATGAGTCACCCCT GATAAGGGGCCCGCTGTTTATCGGCTGTCGGCTGCACTGGAAACTTTCGC CGTTCGCCTCATCTCGACTGGATGGTGAGGTTGATGGCGATGATGATGAT GATGATGTCATTGATGCAGGCGCAACGTCATTGGTTGTGCAGCTCATATA CATGCACATACACACACAGGCGTGTGTGTGTTGAAGGTTCATCAAACTGA TTGCAGAGTGTGCGTGCCTGACGGCGATTAGCCAAAGTTTTTGACAAAAA GCGCGCAAGTGTCGCGGCAGACTCACTGGCTTGCAGCACAGTGGGTGTCG TCGCTGTACGAGTGAAAGTGGAACTCTGCTGCTAAAATTAACCCCATGCA TATGCAGTGCCCCACCCGACACCCATCACGTCCCCTCGCCATCACAAGTG GCGCTGGCTTTTGTTGCTGTCTTAATTGCCGCTCGTTCTTTTTCTCCCCA GCTCCCCCCACTGTGACCGCCATCCGTTTGTTTCTATTTTTCCATTTGCG CTTAGTCAGACCGGGCGGCAATTGTGAATGCCTGTGCACCCTAGAAATTC AAAGTACATGGATTTTTTTGAGACCGAATGGGCGAATAAAAGTACCTTTC CCTTTTAAGAATTACACATTCGATGCCTAACTATAGCCCTGAACGCGTAT TCCAGGTAAAACGATGTCTACCTGATTAATGTGAAACGTGAAGCACTGAG AAAAAATTATCCCGGGATTTTAGAAAATCACCTTTTATTCTCAAACGCTA TAAAGACGAGCAATTGAACAAAGAAGACTTTTCTTACGTCTAGAGATATC CATGTAATATTCATTTTAGAAAAGTTAAATCAATGGTTTTAGAAAAGCTT TCAAGAAAATTTTTTTTCTTTATATGTATGTTGCCATTACAAGAAAAAGA AAAATCCGTAACTAATGTACACTGATGCTTAAATGGGTGGAGATATTTTG AATCAATGACGGTTTCCTAAAATCAAGGTTAATTTTATTCTAGGTGTAGT CAAGTAAAAGTTAATTTATCCAGATATGGCTTAGAAATAATAGATAAATC ACCCTATGTAGGTTTTGTAGATTAAATTCTAAATTAAGGTTTTGGGCTTT CTTAAGCATTATTAGCGATCTATATTTTTCGGTTCCAAGTCTATGATGAT GATAATTTCTTAATTTAATATTAGTGGGTGGACTGTAAAACTCCAACTTC AGATGTTCCTTCTATCCAAAAGGGTATTCAAGCAGTGGCTTCCCAAAATT ACGTGCTTCCTAGTTCTTTTCGGAGGTATTGCCGCCAATTGGCGTGTCCA TTGCCAGTCTAACTGGCGTTCATACGTGCGCCTGTTTTGCGATCGTCGAA CAGCTGTTGTTCGCCGAGTAATCGCGACATTGGCTGACGCATAAACGCGA TCGGCGTTTGGACTCGAATGTGTATGTGTGTGTGCTTCATTCCAGTGCAT TTCTCATATTTTTGTCACTAATTGGTGTTGGCTAAGTTTCGCTTCTTAAC CCATTTGGGGAGCAACCGAAATAGCTGTGCGTGTGGGCGTATGCTGTGCG CTCTCTCGCTTGCTCGCGCGCACTTTGGAAGACACCTCTGGAGGTCGCTT GTTTTTCACACTTGCTCTCGCTCGCACGCACGAAATGAACCGTAATTGTG GACTCGGGCCCATTGGAAGCCACGTTTATGGCTAGCCAATATTCCGAAAT TTTAAATGCCAGCTCATTTTGGCGCCCTTTGAGAGCACACCCCCTTCGAC CATCAGTAACTTGTTGCTTCCACCAGCAACAATTGGCACAGTCTCTCCCC CTTTTCCTTTCTCCCGCACTCGGCCACTCTTCCCCGCTCTCTCGCTCACG CGCAGCGTAAACAAGTGAGAGCCGGAAAGGAAAAGCCAGACAAATTACAG CGAAACGCAAGGAAGAAAAAACAAATACCATAAAAAAACAATTAATACAA TCAAGTGCGAAACAACAATTTCGACTGCGAGTTGTTTGATTTCATTCGCT CGTTTTTGCAACGTTTTTCGGCACTGGCGCTGCCAAAGACGCTGCTGCTT GGCTCTCTTTATTCCCTTTTTTGGGTGTTGGACTCATATAACACGGTGAG CGAGCGGGAGAGCTGATGGCGAAACTTTTATAGCGGTACTCTTCACATGC ACTGCGTTCGCCGCTCCGCTCGCACAAGAAAGCACGCACACCAGCGCACG CACGCCACACTCGGCGCACACATGCTCACACGCACACACACGTATGGTCG CAAGGCGGCTGTCGCACTTATTTTTTTACCGTGATTTTTAATGATTTTGT AATACGCGCGTTCATTACTTAAGCGCCGCATTTGCATCGAGCACTCGCAA CGTCACCTGGAAAATGCGCAGCTTCAGCTGACACCGAGCTTAAATACTCA TATTCCGCAAAAATACCGCTGTGATTCATTGCAACCGCTTTGCTTTTGCT TGACATTTAATGTGGCGGCACAGAAGCGGCCGCAAGAAACCAAAATACCA CCACTCACTTTATCTATCACTCCACTCACTGGGGCCAGCGCATTCAGCGG GATTCAACTAGAGATTTTGCACACGACTCCGGCTGGAAACTTAAGGCACT TCTTTTCAGACTTTTCAGTCAGCAGAAAGACGGGACGAGTACAAAATGCC GACGAGAGCGCGCTGAGCATCTAAGAGCAAGTTCGACACTGTTGTTCGAG GCAAGTTGTTGATATCAGCGCAGTTCGCGTTCACGTTCACCGGGCGCTGC GTTCATCCGCGTGGCGTTGCCACCTGGGCCGAAACTGCCATGGAATTAGC TAGATCCAGCTATTGTTTGTGTTGGGCTGAAGGCTCCCAATTGGACAATT TTTATTGACCACTTAAATAAATATAATTGCTTATTCAATATCTATTATCA TTTAATTTCTTATCTAAATCCAAGTCCAAGACAGTAAAATATTTTTTAAT TATGTACCAGCAGAGCTGTCGGAACTAAGAAAATCGCGAAAACATAGCAA CATTGTCTGTCGGTGGCCGCATGCATCCCTGACGGGGAATATGGTAGCCC TAAACAGCTGACTGCGCGGGTCTCATTTGAATTTCGGGACCGACTTCTTC CGGACCTGAAATATTTTTAATTTAGCTGGAGTTTTGTCAAGTGCGGAAGG TGTATACCTTTCTCGGGCTTTATCAGGCATCGTAGCACCTCTACAAAAGG ATATTCTAGCAGCACCGCCACCAGCGCTGCCACGAATTGAGTGAGTATGA ACACGCTAAATACGTTGCACAGCTAAAATGGTGATAAAGTCAATTGGACC AAAAGTTTACATATACATTTGTACATATGTAAAACCCAAAGATAGTAATA CTACCAGAAAGAAGCTGGAGACGTAGACCGGTTGTCTAAAATTGCCCGCC ACTGTTCTTAGGACGACAATGTGCCAGAGAAACGACTGAAATGAGATTCT TGCCAAAGGGCGAAACGCCGGCAATGTGCAGAAATCGTAGGCAATGCCTA TCGTAGATTCGTGAGTGACTTAGTGACTATCATTTAAACCTGTTACCCAC CTCCAACCTTGCGGCACATGAGGATCACGAATCCTGCGCATATTAGCACC CACAGGATCTTGTGGATGCCCGCATACAAGGCTAGCCATAGCGATGGCTT CGCAAAGTCCTGTCGAATAAAGATGTAGCCGGAGAAAAGGACTCCCAACG TGGCCAGCACAAGCAGCCACATGGCCAGATCGTACTTAAGATGACCCAGA AGTTCTACATTTCCAGAACGCTGCCTAAGGTAAAAATGACCGCACAGAAA ACCAAACAGATAGCCACCCAAATTTGTGTAAAAGGGCGGATACATTTGGT AAAATGTGTCGGAATGTCGGAAGTACAAGTAGCGATATGTTCTAGGGATA TTCACTTATCATAGACTGAAAAATAGATCGATATTTATAAAAACCTACTC CGGACGAATATGGTAGATACCATCCAGCTCGAGAACGTAGGTCAGTACAG CAGGCACTGCAAAGGCAAGTGCTAAAAGAGTTGTGTAGATTGTCCTTGTC AGCTTGGGATGCCTAAAATCACAGAGGTATTTTTGTAATACTACAAAAAG GGCAAGGGACTCACTTTTTGGTTATAATAATTACTATAAGGAAGAGCTCG AATAGCTGCATGTCTGCTCCTAAGTACCACGTCTGATGGGAGCACTATAA TGCAATTAGGATGGGTAAGGTGGCTTAAACTCAAGTTATCCTTTCTGAAA TACCGAAGAATTGTTTTAATAACGTACACTGTCTTCCAGCATGTGGTTGG TCACGAAAAACACGTTCTTCCACCAGTTGGCGCGACAGAAGACCCGTTCG GCCTCCGTAAGATGTCGCCAAAAGGGTCCGTTTTGAAGGCGCACCAGCAG TGTTCCATTGAACAGGATGAGAGCGAGAAGCGATGGCAGAAGTCTAAAGT ATCTGTAGGAAAACACTCGAAAGTACACAGCAATGCACTCAAGCGTGCCA GTCTTGGGTTGAATCTGTTGGCGTTTGGTGAATTTCACGTAGAGAAGGAA GCCGCTCATAACAAAAAATATCTGGATGACCAGGCTGCCGTTTTGAAATA TTGAAGTCTCGAACCGGAACAGGAACTGTTCGAAGAACTCCGGATTTTCT ATTGGAACAGTCATAAAGACCATAAGCGTGTGGCCCAAGATCACTACAAA TACGCCGATCACCCGAAACCCGTCGAAAAAGCTCACATCCCGCGAGAAAT CTGAGTTATACGGCTCAACCAATCGATGATAATTTCGAACCACTGAGAAG GATGTAAGGAGTCGCTGTCCTGGAGGCATACCGAAATCAACTTGAGAGTT GTCTAATTCTGTAGTTCATATCCACTTACGTCGATCCATTAGTGGCTCTC GATAAAAACTTTCTGATTTTTGCGAGTTCATCTTGCTCAGGCGATAGTCA AGGAAAGACGAACACAAAGTTATAAAGAGTATAACTACCAGAATACCATA AAACGCCAAATCAAGCAAATCTAAGGAAATAAACTTTACGCAGTGCTCCA CATACCAAAAGCAGAAAATAACAGTACAATAGCTGTACAGTGCAAAGTTT TTAGAAAGTGCAACTATAGCTTGTCAGCAATAAACTTAGCCCTACTTACC CATCTTCAAGTCCTTATCCGAGGCCGAGACACAGTACTCGATAAGGCTCC GAGTTCTAAGTGAAAACTTCTCACTGAACTTTTGGTTTAGACAGCCTTTC ACAACCTCTTTATTAAAGAGATCCCTATCTGAATTCATTGCATCCCGACG GTGTACCTTATCGTAGTAAGATATAAGTTCCTTATCCAGAATTTCTTCTT TCTCGTACTCCCTGAACTCGGATAAGTGATTGATTCTTTGCTTACAGCTC TCCAGACACACGCCCCTAAAAACGCGATCATGGCGAAAACGGTGTTTTGA GTCCTGTGAAACTTGGTCGATTTGGTGCCATAGAGCAGAGCTAGCATTGG GTAAAATCTCGACGTACACCAAACAGTAAGTACCAGCTTGATTATCCAGA CAGAGATCGTAGTCATCAAGTTGGTACAGGGCAGGCATGTGTCTGTAGAG AGTTACTGCGCTCCCAATTTCACCTGATATAGTTCGATATAGGATTAAGT TCACGGTACTTACAGTTGAACGATCCAGATAAAAAGTGTCCTTGTCCCAG AGACAATATGGCCGAAAGAACACCTATTTCCAACCAGCGGAGCATGTTGC GTGTGTTTGGTCTAACACTTGAAGATCAACTATTGCGAATCTTTGCTCGA TTTGTCTTACCAATTTAGCGATAGCGTGCTACACCGTCAAGCTTGGCTGC GTTTTCCAAAGATATTTCTATAAATTACTTCGACTTGACGAAATCACAGC TATTAAGTGGCTGCCGTTTATTTTATTTTATTGAACTTCAATTTTTTTTT TCATAGGAAGCTTCCTATTGCTTAACCCAAGTAGCGCCCAGTGAATATCG GCAGATCGTAATGGGTCTTCACGTAGAAAGCAAAAGGATGGTTGGCAATG AAGTGTTTGCGACTGAAGGCAGCTACGGCCATCACCCGCCATACTGAGGA GGAACCATGAAAACGAAGCAGACTTTTAGACATTTGCTTTTAGACTTTAT TGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATA TAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACA ATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGC TTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTA GTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGT TGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAAC GTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATA CCTGTGAATTGGGATTACATTGCATTTCAGTTCAATGGTTGTGATTGGTG GATTTTGATGGAGTGCTAACTTCAAAACTTATTGATTCTTCCCGCAAACA AAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACA TGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACAT GACCATTCCTGCAAATGAACATCAAAGTCGTAGCTCAAGGGTTATATAAC TCGAATTAGTAAGTGGCCAAACTGGTAATGGAGCAGATGCAATTTATTTC TCGTAATGTATGCCACCCAGGTATGCCGATAAATGGATTATCCCAAAGCT TCAGACAAATGCTTAATTTCCATTGTAAATAAATAGCTGTCTTTATTGTT TTGCCAAAGAATCAGGTACCATCACAGCTCATCATGCTCGCTGGAGGCGA AGGTATTTTCCTCGAGCCGCACAACTGAGCCCCAAAACAATGGCAGATCC TTCTGATGCACAAGGACATAGGTGAAAGGATGGTCGGCAAAGAACTCAAT TGGTTCCTCAGGCGACATAATAGCGCGCTTCCTACGCACCGCCATGCCTG CAGGATGGGAAGAAGACAAGACAGACACGGATGAACAAATGGGACATGCA CAGGATGATGGATGCCAAAAAATACCAATGACTTTGACCACTTACCCGTG GCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTG TATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAA ATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAGCTGGAGGAGGTTT ATATTAACATGAAGTCCATATCATTGCTTATGTGTTTAAAGTAAAGCTCA CCTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTG GGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGA GAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGG TGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGT TCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTC CTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAA AGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCC TTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATAC ATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCC AATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTC TGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCG CAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCT GACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGC TCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGT CTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAA AGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCG TACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGC GGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGA GGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTGTAAGTATCCAAATC GACCGTGGATGAGGTGTGCTCGTTTTCATAAATTTATGTAATTGCAGTGT ACTGATGAGTCACCTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGC CGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTG CCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAA ATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGG CCTTTGAGCAACAACTGAATTCTCTCAGCGAGCGTACATTGTTTTTATAC TCGCATATGCATATGTATTCCCCCACAAAACAATGATTTCTCTTCAGTTC GTGCTCCCAAACGGGTTTTTCTCTCGCCTGCCTTCGGTGTTCTCATTGAT TTCACTCTTTACATCCATAATGCGTTTTCTTTCACTGGCTTTTTAAAGTC AAACTGCCGGATAACTCACCACATGGCACCAAACGATAATCCATACTCAG TAATTTTGCTTACAGTAAACCTAGTCTGCAAAGCGTACGTAATAGACTGG CCTGACTTCAGGTCCACACGATTTACTGCGACCTTATCAGCCAAAGCTCA GCTTGAGCTTGTTATTGTCTTCGACAATAATGGGATTTTTTCCGTTCCCT GATAACAGAGGAAAGCTGAAACTGAAATCATTCCCTACCTAAATTTGTTT ATTATATTTTGCCAAAAATTCTAGGGAGAAGTCAATAGAATGAGTCAATA GAATCGAATAACACCCTTTATATACCTTCAAAGGCAGATTTATGTTATAA TAATAAATAATAATAATAATAATAAATAATAGATAATTCCTACACGTTTA ATGTGTCAAATGTTTAATAAGTAACTTAAGTGGAAGTACAATTTATTTCT CAACTATTTCCCACGCCAAAGATATACATATTTATTTTTCCTTTAGGTAC ATGTGTTACATTTTTCAGACTGCTCAACCTTGGTTGTGATAAAATGACCG GCAAATAGAAGGCCATGGGTGTTGTCCTTTATAGCATAGAAGAAAGGTCT ATTAGCGTGGAATACCTTTGGAGGTCCTTGGCGCGCAGGCATGCTTCTAA ATGTGGCAACCGCAGCTGAACAAGAAGTTTAAATTAGTTAATGCGAATAT ATACATATTTGAGTGAAATTTTTAATATTGGACTTGCTTAGCACCTCGTA TGACATTCGTAAGAATATCCGGAGTACTAGATATAAGAGGCTTTCAAATT GCCAAAAGTTTTGGAACCTTTTTTTTTTGCAGGCTCACCCGTTGCGGCTG CAGCTTCAGTGCCCACTTCGTTAATCTCGATAAATGCTTTGTGGACGATC TGGGAGACAAAAAGGCTTTCCTCGGATTGTAGCATTCCCCCAAGCTCTGC CTGACCACTGAATATTCGGTTCATGCCCATCTGTGAGTAGCCAGGTTGCG TATAATCAAATTTCAATAACAAATCCATTTCAGCTAACCAGCATTAAAAC CTGGGATAGTTCTTGCTGGAACTCGGCTGTAAAGCTAGGAATCTTCACAT CCACTTTTTCCAGATTCATTGCTGATGACACTACCTCTAGGGAAATATCA CTAAGTTTCTTTTCGAGGCTCGTGAGATTCGACTTCTCATCAGGAAGTAA AATGATCATGGCCAAATTACAGGCACTATAATTCATTCTAAGGGCAGTGG CTTCGAACATGGGAAGTACGGCAAAAAAGAAGTTCTCGCACACATGCATC ATTCTCACTCTGGTAGGTCTATCCGATCCGAAGAAATCCTCTTCGCGGGT TTCTTTTTCATTGAAACTGATTGACCACTCACCCTTGAAGTGAATACCGT TTACTAGGCACAGCCGCGAGTCCTTGGTAAGAACTCTTGGACCGATTATG TCCTTGATCAGGTTGTTGGTCTGTGACTCCACCCATTTGTTGATTATGCT GGCAGCCTGCTCGCTGCCAAAGTCAATCTCCATTGGCTTGGAGCGAAACT TCTGCTCTAGTATGTGACCAAACTGCTCGTCAACTTGGAGACCCTTCATA ACATATAGGCCGTTTGCCATTTTAAGAACCTGGCACTGTTCATAGGACTT GAGGACGACACCAAAGCTTTCAGCTACTTGCTGAGCTTCTAGCCCACCGA AACGGAGCCCCTCGTCCATCTCCTTAGCTGTAGCCGATCCCTCGGATGTT CCCATCCGCAGCATGGCCGCAGAGATGTGGATGGATAATGGGGAGTAGAT GATGTTTAGGCCAGCACTTGCCCGGCACAAATGGTCGTGCAGACAAAGAG CGAATTGTTCCAAGCCCTGTGCGAACTCCTCATCTTTCATGATGAAGAAA GCAGACGATCTCAGGTTAAATATGTTAAATATGCGTCTACGATAGAAGAA TCAGTGAGTACTCATTTTTCGAAAGAGATTCAGATTGACTTATCAGCAGT TTGAGCAAATATTTTAATAAGAAGCTAGATGAGCTATCAACACCATTCCA ATTTCGGGTACGCCAGGAACTTCTCTCCGTCGAGAGCGCTTGCCACTTCA GACTCTCTTGGAATTTATCTAATCGAGTTGCAGTTCGTTCAGTTCTGACT TACTGCGATTCGCGGCGTTAGTCAATTCCGCGCAGTTTGACGGAAACCAC GCTCATTCTCCGGCTGCCTTCCGATTGTATCCGTGAGATTGTTTTTTCCG GTGTAAGTTATCAGCGCACCCATAGGGTCAGCGACGCCCTCACCTGTTTC GCCGATCCAAAATAGCTTATCAGTGCACGTAGAGAAATTTATTGTTTCAT GTCCACATTGATCGATGATTTGTAAATTAAAGAAATTCCGAAACTTACTT AGTAGGCTAAGTTACGGTAATCTAAATATGCAGTAATCCCCTCTATGCAG TAGAGGGTATTGTTAAATTTTAAATATCTGAAAACATCAACAACCTTATC AGGTGACGTGTGTTATTTTATCTTTGAATTACTATCGCGTCGTTTGCTAT AAGGCAATTTGTTATGACGAAAGCAAGTTCTAGTTGACTTCACTTTACTT TCTACATCGGTTCTATTAAAAATATAATAGGGAATTATTATTATTATTTT AAAATAAATAGTAGCACCTAGTAGCAGTTGTAAGCTAATACGTCATTCTG GGATTTCGGATTTATTTTTAATTAGCATAGGCAATTTTGAAAATGTTTTA TTTTATTAAAGATTGAATCCGAATTCGAAATTGTTCTGGATTGATCAAGT TGGCGCTTAACAGCTGGCGATAATGCCAAATGAGATAATGAGATTTGGCC CGAAAATGTCTTATTTTTGTATACTTATGTTACATTTAAGTATTTAAAAA TATAAATTAAAACATATATTTTTTTGCCCAGATCGAGATGAGCGAACCCC AAGAAGGCAGAAATCAGTTTGCGCGAAATCTGATAGATGTCATTACCAAA GATGCCCTGCAACAGAGCAAAGACCCCCACATAAATACGGTTTTCTCTCC AGCATCCGTCCAAAGTGCATTGACCTTGGCATTTATGGGGGCTTCCGGAT CTACAGCAGAGGAGCTAAGGAATGGGCTTCAGCTAGGACCAGGAGATCGC CATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTA CGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACG ATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTC CAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCA GCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACC TGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAAT GTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCAC ATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATA TGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAG GCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAAT TCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCA ACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTC GAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCA GGTACTTAATCAGGTAAGATACATTTAACCGATAATAGTGGCTTTGTTTT AATAACAATGTAATATCTGATATTTATTCTCAGCTGGGTATTACGGAAGT CTTCAGCGATAAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCC AAAAAATCTCGGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCA GGATCGGAGGCAGCAGCAGTCAGTTGTAAGTGAAATCAGCTGCTTGCAAC TCAAACTTGCTCGTACTAATCTCAACTCTGATTCCCACACTCAGTCATGA AGATAGTACCCATGATGCTCAACATGAACAAGAAGCTCTTCAAGGCGGAT CACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGG CCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGT CACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGA GACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCA ATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCC AGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGG CGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGG TCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAA AATACAAAGCAATAAATTACCTATAATAACTTATGATTTAAATTAAATTC ATAGAAAATAATAAAACAATATGGTGAAGACGTTTGCTATGGCATTAACT TTTAACTTACAAAGACTATCCGCTTTCGTTGAATTCGATTTGCTTTAGTC TGTAAAAGTAAAAAATATCAAGTTTAATATGCATGAACAGAATTTCCGAA CGCTGAAAACGAATTGATAATTAACATCCCCAAACTAGGCATTTTCCTGT GGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTT TCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGA GACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGG AGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCA GCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACC CATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGA ATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAG TCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTG GGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCA GCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAG GGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTT CCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGG GAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAG CTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGA AGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGC CGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAA TTTCGTGATGAACTCAAAGAGACCTTAGAGAAGGTAAGACTCCGTCAAGA AAAACACGGTTGTGCCACTTTGACGCTCGATTCTATTTAAGCTGGGCATC CGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAA GTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGA ACGAGGAGGGAGCGGAGGCCGCAGGTGCCACATGTAAGTACCGATTTGGT TATCAGCGTCGAATGTTGACTCCTATATACTCACTGTTCCCAATGATTCC CAGCTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCC GATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCA GGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTTAA ATTAAAATTCCAAGCGGAGTGATTACATTTTAAGTTAAGGATCAATGTGG ACAGCAGTCCACGTTGTGACGGAAGGGTAACGCAGCGAAGGTAGGTTGTC CAGTAGGTTGGTAATAGGGAGTAGAAGTGGTATTTTGCCAAAAATAAAAA GTGTAATGATTTCTGATTCTTCGTTCGGAAAAGTTTCAAATATGTTAATT TTAACTCATTTAAATACGCCATGTATTTTAAGTGTCCTGGTGAACCGAGC GATTTTATTATTATTATATATTAAAAAAAAACGACTAGTTTAGCGGAGAA AAAACACTAAAAAGTTAAACATCCACCACCAATGAACCTAGAAGCATTCG ATAAAAGTCGTTAAAAAGGCAATTTAAAACACTATTCTCGGTTCCTAAAC GTATTATGTCTAAATACCACAGATAAAAAACAAGTGAAAAGCCTTTCTCG AGTCCCTCGCGTACCTGCAAATTGGAAGTGGTATGTATGTGATATTCGAG CTACTCGACTACGGCGGTCTCTCCAGTTTTTAATAAACAAAATTGATATT TTTAAGCCGATACTAACGTAAAAAAAAAGTAAAAAGACATTCACATGCTA GCGATGGACTTAAAATCTCTTGGGAAACAGAAATTAATTTCCCCACAGTG TGCCGTTGTAGGGCCAGAAAGAAAATCAGTCTTCAGTTCGAGGCAGAACT TTTAATACGTGGACGGTTTTTGTAGCCATTGAAATCAGCGCTCCACGAAC TTAACTACAATCAAATCCTCTACAGATAATTAAGGTAACTGTACATACAC ACATATATGTATGTACTTGCTGATCTAGTATACATACTTAGAAATTAATT TTTTCACTTTCGATGTGATTTCCGGAGAGAGGAGTATTTCTATTTGTAAA CAAAATGACATAATTGCTTGTCAACATCTGCAAAATTAAGAGAGCCTTTT CGGAAGAGAATGATTGCCAAGTAAAGAGAACCAGAAACACAGTGCTCTCT CTTAACATAATTCCCAATTTTGATTATTTGAGTCACCACCAACTAATAAA ACGGATCTACAAATGAGCCACTAATAAATGAAGACTTATTAGTGGCTTTT AACTATGCAAACATTCTTATTATATAGACATATAATAACATATATCTATT TTAGTTTAGTGACCTTAATGAGTGTAAAAATTAAAAGGGTTGGAAATTTA TATCTTATATTATAATGTATATTCATTACTTTCCTGAACTTTCAAACATT ATTATAAATAATGTAATTTTCCAAAAGGATTATTTGTTTCTGTACCAACT GACAATTTATTTGTTTGCACACACTTTAAGCTTTTCCCTTTCTTTGATTC AAAAGCTTGTACTCTCTCTTGATTCTTCGTTAGTATCGTAAATAGTAAAC TGGTGTGAAGATTCATCTTATCCAAAAACCAGTTGTGTTATGGTGGTATT ACAGGAGAACGAAAAAACATATGGAGAGAACCAGTCTAAACACAGTTTGA TTTCAAAGTAAAAACTTCGAATTCCGTTCAGTTTTCCCAATCATGTCAGG TAGGGAAGATACTTGCACAAGCTGTCTGTTAACGAATTATTGACCTACTT TACTGCTCTTCCGGTATTTTCATGTCCTTGTCCTGCAGTCAAGGCCACGT GTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTT AACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTT TGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCAT CTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGC ACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGAC CGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGA AGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATT TTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAG CAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGG ACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAA ATCAAGGACCTCATTGCTCCGGAATCTCTGGACGCAGATACTTCGGCCAT CCTGGTCAATGCCATCTACTTCAAGGCCGACTGGCAGAGCAGCTTTCCTG ATTACGCCACTTACGCCAGCGACTTCGTCAACCACGGAGGTCGGAAGGTC AGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGAC CGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCG TTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAG GAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAG GCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCC CTCTACAGGCAGCCCTCGAGGAGGTGAGTCCTTAAGCCTAAGATATCTAA ATACTAGATTGGTGACCCGAATACTAGTGGCCAATAACCTAAATGCTCTG CAGCTTTAAAATTCGATGTGTGCGATATGTTGTGTTGAACTATTTTTGAA TGTTTGATATACCATAAATAGATTCGCCATGGCTGTCCGTTTGTCTGTTC TTATGAACCCCTTCAGAAGTAAAAGCTCGCGAAAAAGTTTTGATGGAGCA TACAGACTCAATTTCAAAACATAACCACGTCCGGTAGACTTTTTGATAAT ATGTGTATATATAATATTTCTGAATATGTTTATTTAGAATAGAAAATAAC TACTGATATACCAAAAACATTTTTGCTACTCCCATGAAGTACTTACATTC TTGAACAGCATTAATTTGGACTCTTTCAGTTGGGCATTAAGAAACTGTTC TCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACG CATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCA CTACGGCCAGTGGAGCAACCTGTAAGTCTGTCCGTAAACATAAATATACG AACATTTTTGACAGTCTTTATTCCTTTCATTTCAGTTATCAAGGTCTCGG TGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCAT CCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCA CGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGT CCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCACAAGTACCGACA GGTATATCAACCTGGCTACTTGATTAGTTTTGGGTTGCATAATACTTTTG GCCTTCCTGTTTGCTGCTTCTGTAATTAGAGCCATCCGAGCTGACGTTGA TAGTTTATTAAGAGGACTTGGCTCGGTTCAGCCTCCGATCCTGGCCGAGT GCCAGGCTCTTTGGCAGTCCTGTATCGGCCTCCTGTGTGTGTGCGCAGGG GTAATAAATCAAAGTTGGTATAGCTATCAATCCCTGACACAGCCGCTCAG ACAAAAAGAGTCAAGAACGATGGCGAACTGCGCTGCGAAGAACTGGCAAT TTGAATGCCAGTGGTAAAAGTGGCCGAAGTCCAAACACACAAGGACCTGT GGACTGTCGGACTCACGGACACGCACATGGCCAAAAGTCAACAACTGTGT TGGCAATTTGCTGCAATCATCCAGCAACACATCCCCTCCTTCCGGTCCTT CCGCAACCTGTCTCGTCCTTCCTGCCATCGCACTACCATTTCCCAGGAGC CGATGTTTATGAGTGCAGCTAAATTGTTGTTCTCCGTGTTTCGCTCGCTT TTCCTGCAGCTTTTTCTGCTCTGCCGCGAGGATTTTCGAAATCCTTGACC GCTGACGGCACTCACATAAGTGCTTCACACATAGCCCACCATAGGGCCAC CTCTTGTGGCGGATATTTGCATATTTCTAAACAGGTGTAAATTAAATTTG ACAAATTTAGCGCGTCCTTGTCATTTCCTGCCGCCCCGGGCAGCACTTTT AATAACGTTTTGTGACATTTACATACCTTTCGAGGCCTGGTCATGATGCC GGTCCATTATTCACGTTTATTGTGGGCGAAATGATGCAGTTGGCTGGGAT GTGAGACAATTAGAGCGGGACCTACGGGCGTGTAAAACATTTTAATTAAA TCCGTGCTGACGTGCCGCTTGGTTTTCCACTTGATTTCTGGGAATTCTGT TACACTTTCGAAGGTTTTGTTGTGCGTTTCGTTTTTCTCGGGCACTAATT GGTGGCCAGGGCGGTGCCGAAACTTCGACTCGGTTGTCACGGGCGACGCT CAAGTTTCCGTCAGCAAATTGAAATTGAAATGACAACACAACAGGAGCTG TAGCACCAGGAGACAGACATCAACCGCATTGGGAGGAGCAAAGGATTGCA TCTGGCGCACCTGAAAATGGGAATTTAGCGACAAGTGCCGAGCATAAAGT TCAGTTGTGGGCGGTGTTTGGGCGGTGTTTAGGCGGTGGGTGGAGACGAG TGGGTGGCTGGGGGCCACGAATCGCTGGGCACTCGCTTGCCATAACCAGG AGTCCTCCGCCTTTGGTTAGGCCTTTTGCTAGTCCTGCGGCTGACAGCCC TGCATCATTTGCCAAATTGACAGGAAGCGTTAGATCTGCTCGCCACCTAC GAGAGTGGGCCAATTTAGTCACTATTATAGCCCCAATCAGCCAGTTCTTA GTAGTTTTTAGTTATTCCGCTGGCATGCAATCCATGAACTTGCATTGTTC AGTATAAGCTGCTTTTAAATCCTTCAGTTACAATACCGACCATTTAAGTA TACACACAAAAAGCAAATACTTGTTTATCTCCGAATACAAGGTACTCAAT TCAGTTAACGCTCCCTTTAAGCATTTAGGAATTGTGATTTACAGGGCCAC AAGTTAAATTGGTAGTATTCACAATGTTTATAAGCAAATATTAATTAAAT TAGCAACTTTGCAAAAATTTGTTTTCTCCGAGTCATATTAAGATAGTTAA AAAATACATACACATTTGAATGGGTGTAAACGGAGTTCTAGTTTAACATG CTAACCATTATGTTTCAGAGACCCTAACTTTTGCGAACTATTGTGACTCT CGAAAGTTGTGCTGCACTGTGTGTGTTTAAAGCTTCCCTTTGAGGATGTG TGTGCCAACTACACCGTGTGGGGGGAGGGGGGGGGGGCAACTCCGCAGGT GGCAGGGTCGAAACGATTACTCCTTCTGCAACGTGGAACAGACAATTGTG GAGGCAAATTGTAATTGTAACTCACTTTTAAGTGCGTCTGACAAGTTTGG TAATTAAGGAATTATGTCATGCGCACGTTTGCCATTCAGAAGGACCCTTG CCGTAACTGGCTGTGGGAGGTGGAGCGTTTTTGATTGCATTGGCTACATT GGTTACCTGGGGTTTCCTGTGTCGCATTCTGTGTCCCGAATGTTGCATTT TTGCAATTGGCATTTAATTTCGAAAGCTGCTAAGTTGAGCATTGTGTTTA TGCACGCTGCACTCCCATTGAAAGTTATCCCCATTGTTGGAACCCAGAGC AGGCTAGTCGAGACTCTAGGTGACCCTGCGCACCCAAGGTGTTCAAAACT TTTCACTTTCCCACGGACCACGTGAAAGGGGGACTGGCTACCGCAAAATG ATAATAGAATCCCAGTTCGCTCCAATGGAGACTGGGCACAATTTACCGCT CGTCCTGGCATCGCACGCTCGCCCACAAAGAGCAGGTCAGAAAGGACTGT GCGGAAGGACGATTTGATGCTCTGAAGAGCGTCACACTGACAGCAGCTGC CAATGTGCGTATCTGTGCGAGTCAGGTTAATGAAATACTTGGAACATGCC TCCTGCCAGCCGGTCAAGCGGCCTGTCTCGTCCTGCGTGGCCAAAGGACA TGTCGAGACGGATGTCCCTTTTTTTTCGAGCCTGCGAGTGTGTGGATCTC CGCTCAGGGCGATGGAAAGTGCAAAACTTTGTTAGCACTTTGAATTTAAT ACATGCTATTGAATATTAACGAGCTGTTTCGGCGTAGAATGAGGAGTAAG TAAACAAGGTTTGGCCGACAATTATCGAGTATACGCCCCGTGTGCCGCCT TGGCTGCCTGTTTGCCTTTTGGCAGCTTGTGGGCTCTGTGGGTAATTAAC ATTTGTACGTCAATATTTGCAGTGGCAGCCGCTGGCATCTAAATGAAAAT CTCCACGTGACATGAGATACTCTTTGCATCTCATTAGATTTAATTACCAT TTCAGGTATTTTGTATTATGTTTTGCGAGATATGTAAACATTTGTATAGA TTCTGATGGGTACTTCTTATGTTTCTGTATCGAAAATCTGAACCAATGTT TAGTGAACGAAATGTTTTAGTTGGGACATAGATGCCAATCCCCCAATAAC AAACTTAGGGTCGTCTGCCCAAAATTGAACTGTCACAGGAATTATTACCA ACTGACCGCAGCTGACAATGCCGTAGGGGTAAGCCTTTCATCCTTTCGAG CAGGTTCGAGGGGCAGACCCATAATCCGACTGAAGCTTAAAGCACGGGTT CAGACCTCAGCTAGTGCTGAGCAAGGAACTTAGCTTTGTCCTGCCGACGC CTGCGTCCTGATTCGCTGTAGCGTTTGCTTGTTCGCAACCACAACCTGCA ACACGTTGTGTTTTGAATGCTTTGGCGGCAAACACTCGTGGCCTGTTGGA TGAATATAAAAGCAAAGTCCCATGCTGGCTGCCAAACAGTTCCCTGCTAG ACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGG ATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCC TAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGGGT GAATAACCAGAACATAAATCAGAAATTTAATCAATCTCACGTGCCGAATT GCAGTTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCA GGTAAGCCCACCTCGCAGCACTGCGTCGCAATCCCTATGACCTATTAAGG CTTGGTGGAGCAGTCCGGCGCGGAGTGGAGTGCGGTCACCCGGAATGCTT CCATCCGGGTCGTCCAAGTAACTCCTCCACTTTATGGCCACATTAAGGCA TAAACAGGGGCAGAAAAACAAAGCACGTTCTGAGTGCAAGTGCAAAAGAA ACGACTTTAAAGTGCCTGCCAACGGGACAAGTTGCGGTTATGGCGAAAAA TTCAAATTTCTCGCATCCTGACCTGCCGAATTCCCACTCTTCATCCAGCC CTAGGTGCGTCTTTGATATCCAATTTTAACGGCAGCATTCGCTGGCATAA TAAAAATTTATCGTAAGCGCATTAAATTTGTAGCCGCCGCAAGTTTCGCT CCGTTCCCTTCGCTTTCCTATTCGACATGTAGAGACAAAGAGTCTTCGCA GCAGTTAACATGTCTAAGTAAGCTCTAAGTTGCCACCAGATCTGCCTTTT GTGTGTCCCGGACGGAGGAGGCTGGGCGGATGGGAGCCGTGCCATGTTGT GCATTTTTATTACGATTACACAGCTCACACATGGCAGAAAGCACTGAAGC GGGATGGGTGACAATCATCCCCTAGGAGCCCCTAGAAAATCCACCGTGAG GGTCCGTCATAAATTCTAAATTTGACAAATAAATAAAAGGTGGATGGGGG ACTCGATGGCCATGCTCAATCCATTTGTGCACTGGTTTTGTGGATCTATA ATCGGATTTAACATGTATTTTTATCCCGTACGAAAATTGCTCTATGGGGA CTCCATATTCCATACGATTTCGATACTTTCGTTATTGATAGACTAGGACT CCAATGTCGCTTTAAGCAACAAATGCAAGTTGTCTAAAATGTTGAAGCAT TTTTAATTTGCTTCGATAAATTAAACATTCTGAGCCAAGGAGTGCTTAAA ATCCGACACTTTTCTAAGTTTATTTTCTGTTTAGTTATATCGAAATTTGG GGCAAAAACAAACAGTTCCCATGAGACCAGGCATATCATTTGATTATTTA TTCCCTGTTAAAATATAATACCATGGTTCCCAGACTGATGATGAATTGAA TTTGATTTAAATGAGACTTTCTAGGTTTTTAGAAGAATTTAATTTAATTC TCTTCTTCTGTGCAGCCACGGCTTTATTGGGTTTCATTGGTTTTGATACT TTTTAAGTCGAGACCAATTGCACTAGATTTATCACTTCCTTCAGAGGTAT CACCATTTCCAAAGAAACGCTTCGTCTTCCATTTCCATGTCAGTACTTCT AAGAACCCACGTCGCAAAAAGCAGCACTTTAATTTGGGCTCATATTGCCT ACGCTTACAGCTTACTTTCATGAAATTCATTCGCTTAATTGTATTTTTCG ATTGTTTTTCCAAGTATTTCTTTCTTGAGATGAAAAGTCAACAGACAGTC GGCAAAAAATGGGTTTGTGTTTTTCGTTTTTTCCAACAACATGAGGGTCC TCGGTAATCGGAAACCGCAACTGTTTGCTTAACTCCCTCCGAGATTGTAT AATTAATTTCACATAAAGCCTAGTCGCGAGTTTGACTTTTTAAAGGCATT CTCAGGGGGAGCAGCTCCTAGGTGACGTGGCCCCACCCCTCACTCTCACC TGTCGCCTTCATCCCCCAATGTGTGTACACAGTCGCTTGTAAATGATTGT GCTCCATATGTTTATGCTAGATTAAACGGTTTTCCTGCCAAACTGCGAAT GGGAATAAAACACACACGCGCGCGCACACACACACACACACACGGCAGCT ATGCAGATGCCCCCGTAGGTATGCCAGCTTTTTTATTGTATCTTAAGCTG TGCCAGCTGCGCAGCTCCTCGGGGAGCGCCCGACTCGGACGCACACTTTA TCATAATGGAGTCTAGACCGGATGCCTGAAGTGCGATGGCATTTACCATA GTTTGCATTTCTACGCTCCCTGTGCTGCTGGCCTTCGCATCTGCTCATCT TTTGGTCCAATCGAGTTGGTATTAAAGTCATGCCTTCTGAGTGAGGTTCA TTAATCCCACCGCACTCACAGTCGCTTGTCAAGTCGCAAGGCAGCCCGAG AGGCCGCTTGTCTGTAAAGGCTATTAATTATATGTGACTTATTTAATTGA TAAACTGGGCATTTCGCCCTTCATACCTTCGGCATAGTACAGTGCTCTGG ATGTTGCAGCTGACACCTTCAAGAACGAGCCATTTGCTGTGGCTGAGTGT GTACTTCGCATCACTCATACGCACTGTGGTACGCAATGGCTTATCCCTGA GAATTCCGGCAGCTGGCATGAATTGCAATCCGTATGCAAAGCGCAAATTG AAAATGCACACGAAAGCTGAAGAGTAGGGGGGGGGTGATGAGAGGGGGAT GTGGCACCCAAAGTGGCAACTAAATGCTGGCAAAATGGCAAAACTGCACG CCTTTAAAATTGTTTTTGTTCCTCCCGCCTTGTTGTATTAAAATTAAAAG CACATAAAAGGTTCAAAGCTTCCACTTGGCCTGACAACGGTCCTCTTCTC TCGCAACAGAACATAACAGGACGGAAAAGAACAGGTCCTGGCCCTATGTG CGAGTTCGTGTTTCCGCCCTAATGCCTCCATTTCCACTTATTTTAATAGT TTTTGCTCTTTCCGGGCGGCACTTGTGAGCCTCTTGGCCGCCAATGGCTT CATTGAAATTTGGGCACACACACGGCCGGCATATTTGTGGGTGAGCAGGC TCTTGATGTTGCGGCCGCATTTGATTAAAGTGCTGGACCATGCTTGTTGT CTTCCACTCTTTGGCCATGATTATCATCTCGATGGGGATGTGTGTTTGGG TTTGTGCTGATTTTATGGTCCGACGGATTTCTCTTTTTTGGCTTCCACCA TCCACCGCCAGTGCCCCTTTTTTCCGGCTTTATTGAAATTGTATTGTACA AAATTGTATCAACGAGCGGGCGATGGAGCACGTTTGAAGCCACTTAATGA CCATTAAATGCTTGCCAACAGAACTACGAAGATTCCAGGAATGCGAGCTC AGCCAAAGCAAATACGAATCGCATTATATTAAAAGCAATTTTAACTTTTG AGACAAATGCCCATTTGGACGACTGCTACTAGAGGCGGGAGACGGGTGGA GCTCGCTGTGGCACGTTCCTCGACTGGATTTTATAATGGATGAACTGAAA GTATGCCAAATGCGCCTTAGCTCGGCGTACTTATACATTCATGCAGCACA ATTTGCAGTAATTGCACAGCGATTCAAGACACCGCTCGTGGAAAATGTTT CCCTTCAAACAGGAAATTAATCTAGGACAGCGCCGCCCACGTTCCCACGG ACCCACGGATCCGCCACGGAGGACCAAAGCGGCCAGTGGGGAGCTGTTAT GGCTCTTTGCGCTGCAACCTAATTAACGTGAACAATTCAGTCACATTAAC AATGCATACTCACGTTGAAATTGTTTATAATTTGATAACACGCCTGAGCG AGCAGGGCGGTGCCTGCCCGAAGTTTGCACTCGATCAAGTGGAAAATCAA AACTAAAGACAAGGCCAGAGCCACTGGAAGGGTGGGAAGTGCATTCCCAG AGGGGGAGGAGCGTTGGCCAACCGAAGGCAACTCACCGCAGACAGACTCC TTGCCAAAACTTTGTTCGGTTCAATTTCAAAGTGTCAAATGCAGTCAGGC CAAACGAAACACTGAATGAAGACGGAATATCCTGCAAGTCCATAGATCGC TGTCATCGCTTAGTAGAGATGAGGAAAAAGTGCCTCGGTTATTGTCAGAA GCCCGTGCTCATGAGCAGCCTGTCAGAGCAGTCGAAAGGGTACACAAGCC CGCTGGATCCATGGATTTATGCCAGAAAAAATGGAAAGCCATCAGCATAT GCCTCACTGAATCACTCGCAATATACATGGGCGTCCTCCAATCCACGCGC CGGAGCTATTGACAATCTCGGCTAAACTTCCGCTACCCCTTTTGTTGCCA CTTTGCCTGGCTATCCAGCACCGTTTCGCATTTTCCATTCCAAATACCAG CCCTCTGCGGCAGAGCAATCAATAAGTTCGTATATCCGTCAACCAACCCT CAGAACCGGCAGCATACGCCTCCACTGCTCCACTGCTCGAGTGGATTCTC TAAAAGTTTAGCTGCCGTTTTTTGCCATTTTTGTTTTCCAACGGCGGCCA GCACGATGATAATATCAAATTGAGTTCGTTTTTCAGCGCCCTGCCTTTAA ACATTTACGGCGCGAAAGTGGCTAAGTGGTATTCAAAAATCGATTCCAGG CCGCGGTCTGCCAATCTCCCACCTCAAACACGACAAATCTGACCAGCTTT TATGGGCTGATAAAGCAATTAATTTCAAATCGCCACGGGCAGGCGCAAGT AAGGGGAGATGGAAAAAGAAATCAGATCTGAACCTGATAGGCAATTTGGG GGTCGAAAGATAAAATTAGCCAGCAGAGAGGGCCACAATCAGGGGCCTCA TCAGGGCCGATAAAGATTACGTATATTATTATGTTAATCGAGATTATGAT GACAGTCATCAGCGCCTCATTAGAATGGGCAGGCAAAATCTGCTTTCTCC GTCGTTTTTGTCCTTTCGACTCTGGTTCCTTATAGACACCGAACTCCGCG ACCACCACCCAGACACACAAATCTCTTTATAATCGTCCCAGCCCTGTCGT CTTTGACAAGGGAAATGTTGGCCTAGGAGCGGGCGTGTCCAGGAAGTCGG GTCGTTTTAAGGGTGGTTGGGATGGTTGGGATGCTTGGGATGGGGTGTGG AGAAGAATGGATGGCCGGAGGGCTTTGTGCCTACACTTATAAATTTTTAT TTGTTGGCATTCCGCAATTTATTTTATATCTTTTCCAGCGGCCGTGGCAA CTCCTGCCAGTTGGCCATTCTGTCTGTTTGTCCGTAAGTCTGTCCGTCCG TCAATTTGCTGGCTTTCGCAACGCTCTGTCAATGCCTGGCGGCCTTTTTT GGAGGCGCCGCGGCTGCTCGTTCTCAGGTCGTTACCATTTGAGAAAGTTT GAAGCCGTAAGGCGGCATCGCAGGAATCTAGTCAAAGGAAGCCGTATACA CCGCCGTACGGTGAAGTATGACAAGAGGCCTAATCAAATTATGCCCACTT TCTTGGCCGCTGACGTTGGACTGCCGGATGATACAAAACAAAGTAGGTTA TGCTGAAAGCAGGAGATGTGCTCATTAGGCCAGATGCGAGTGGAGTGTGC TGATCTGATTGTCGGCTTTTCGGTCTGCCCATTAGTAGGATGTCGAAATG ACGGGACAACGGGACGTATGCGTAATATATGTGTCTGAAACATCACAGTT CGACAGTTCGTAGCTTATTGGCCAAAGTCTGGACGTCCCTGGACGTTCTG GGATTCCCGGCGTGCTGCTGAGCGTTTGGTCTTCGGGGGACCCAGTCCTC GGAATGCCAGGAATGCTGTTTGTGATTTTTCTTTCCGCTTTCCTTTTAAC ATTTTTCACCGTGTCGCAGCGGCGCTTTCCCCGTTTTCCACTGCTGCTTT TTTGTTTGCTCGTGTTTCCGCCATTTCCCCGCCATCTCCTGCTGTTTCCC GAAGTCACTCACGCGGAAAGCGCGTTGCGTGCTTTATGAATCTGTCCTGG CACAGCTTCTCTATTACGTTCTAGACAACTTGAACTTGTTCCCTGTCTCA TTCTACGTATCCGTCTTCGCCGTCGTCTTCGTCTTGTCCGGGAACTCCAG CTCGTTTCCGTTGGATTCTCAGCTGCGTCCTTTGTGGATGGGATCCTTCG TGGCATTGCCATGTCTCCAACGTCCCGCGGCATTCGTGTTTATTAAGTCT AATTCAATTTTGCGTGAATTTTATTTGTTGCATACATTAGGGCCGATGAC GTTGAAACATCCCCCACGAATACGGATCCTGAGAACTGAGGTGCTGCGCC GTCGTCACAGTTGTAATTACACACTTAGCAATTTAGAGAGTTCTTCTATG AAGTTTTTAATTAAAACTTTGATAAATTAGCTCAATTTATATCCACCCAG ATATTTACCATTTAACAAAAGCGCCCCATTCCCTTCTATCTGTCGTCTCA ATCCCTCCCCTTCATGTTGGTGTGCATTTCTTTGTGAGTGCAGATTTCCC ATTTTAATTGAAATTTACCAAGGAGGTCTTGGTCTTTGAAAGTGCGGAGA CGTGCATGGCTAGGCACATAGCGAGCAGGATGCGGAGTAAATTAAATTGA CAAAGTAAATAAGTACTGGGAAAAATGTAAATAAATATGCCTTTCATGGT CTCATGAAATTGGTTCAAGTCGGCACAACTGCTCTTTGCTCTCCAGCGCC ACACACACCACTTCCCCCCCCCCCCCCCCTCACTACAACCGCTTAGGGCA ATCCGATTTTGGCCAAGTTGTAAAAGCGAAGCTTTTCATATTCGCCAGCA ATTGCATTCTATCCTATTTGTATCGGGCATAAGTATATGGAAATTTATGG CTGTGACGGCAATCCCACATTTGTTTCAATTATTCACAGTTTGAGTGAAA CGGAAAGCAGCTACATGCATATAAATTCAGCTCAACTGTCAAGTGCGAAT TTGCTTGGCATTGGAGAACAATTGCGTGGAGGCTGGGGGAGGAGCTTGAG TGCTGTTCGGCAAGCTTATACATTTTTATCCCTCTTGGCAGAGACGCGTG CACTAAGTAAACCCGCTCGAGCTGCCTAAATTGTCGAGGACATGTGTGTG TGTGCTCGCAATTTCCCGTGCTGAAAACTGGGAAAGTGGCCCCAAGTGGG TCACAATCGGGCCAAGTCAAATCAATTGACGCCAAGACGCGTCTGCACAC ACACAGCCATTGTCCTCGTGTTTGCTGCCAACACGATTAACCCACAAACG GCTCAGGCAGACGTGCCCCTTTGGATCCTCCTTCTCGTGGAGATTGTGGC AAGTCCGACTGCCACTGACATTGCAAACGCAACTGCAGCTGCAGATGCAG CCTCAGCTTTTGCTGTTGCAGTTGCTGTTGCCGTTTCTGTTGCGAGAAAC GTGGCCACTCAAGGGGAGCCCACTTTGTGCTCGCTCCTTACCAATTCCAC TTTGCCATTACTTCGATTCCCCGGCCAACGGGGCGAATGGGTAACGAGCC GTGATGGGAAATGGCTAGGTACTTCCGCCCCAGTACTTTTTCACTCAGTT TTCAGTTACCGGCACTTTTGGGACCATTTTTCGATGCTTAATTGAAAATG GGTATTCAGATATTTTTATTTTCTAAATAAAACCTTAAATGGAACTGGAA GTATTAAGGTACACAAAATATCGGAAGCAAGTGAACAAGCTGTAAGTAAT AAAATTTGTAGGTTAATAACCCAATATGTTAATATTTAATCTTGAAAAGA AAACTCATAAGTCGACATCTATTTTCTGATAAAAGTCTGAGCCGAAATCG TTTTTTCCATAGATAAGTTTACTTAGCTAAGCGGAATATTCGCATCACTA CTGCCGACCAATACAAATGAAAATCACGACGGAGCCTGCACTCTTTTGGC CAAAAGGCAAGCACAAAGGCAAAGGAGGGTGAGTCTCACTGCTTCCCCGG CGTCTGTGGTTTGTTTGTGTATAATTTGTGGCACTGCCAGCTGTTGACAA TCGATGACAACCCTCCAGGAGTGGCTGCACCAACGCCAGCCTTCGGCACC TGCTGCCCCAGGAAGCCCCTGCCGGCTTCTCCTTTCGCGCGCCTGATTAA GTTTTTGCATTAATTTCGCTACACCCTCGATGGCGCTATCCTGGTGCTTG TCCTTGGTGCTTGTTTGCTTAGCCATTAGCCGGGGATTCTGTGACCTGCG GGTCGTTTGAGCGGATCGTTGGGGTTGCAGGCTGCCAGCGAGTGCCTGAC CTTTTTGCCAGCCATGCAGTAGCTCCCACCGCCTTCAGCTTTCAGCTTTC AGCTTTCGCCTTGCTGGCTTTTCATGCTTCGGTTGCAATCGAATTTATTG GATCCCCTTTTTAGCCAACTCGCAGTCGCAGTTCTCATCAGCCCAAAGTC GATTACTGAATTTGCGTGCGGAACCTTTTCTTGATTGCAAAATAGCAGAG AACTCGATTAGAGTGCGATAGAGTGTATCTTCGGATAGGGGCTATAGATA ACGAGTCTATCCAGTCGATAAAATGCCAGCGCTAAGCACCTTTGAAATAG CTCTGCTGCTCACAAAGTCAATTAGGGAAGTATCCGCATCAGCTCCAGCT ACTGATTCTGATCCTGTTTCTATTTCTGCTCCCATTGTCCAATTAGCCTA GTCACCAGCCACATGGCTTTGGCTCAGGCTCTCCCATTTGCATCAGACTC GTGTTGCTGCAGTTAATTTGTTGTTTCTGCAGCTAAGTTTTCGCTCCACA CAGTTGGCTCATTACGGACCCGAAGGGTCATAGTGAGCTCAGTTCAAGTG CAAACTGTTCGCCCGATGCCGGGCGGACAAAAGGACCTCAACCTCGTCCT CATCCTCGCCCTGGTCATTGCCATCTATATTTGGATACCTCCACAAAGTT TTTCACAACACTTAAGTCGAACGGATAAAAGGCGTCCTTCTCCTCAGCCT TTTGAGGGGATGTGAGGAGTACACAACCTCCACCTCGGGACTCTGGCAGC CCAACTGCCCCTTCCGGCTCCCAGCCATTTGCCGTGATTAGTATAAATAA GTAACAGTTAGTGACCCATTTTCTGCACACCATTGAGCCAGAAAGAAAAA AGGCTTTAATGGCTCGCCTCCACCATGAAATTGGTGAGGACAGATATGAG TTTGTTAGGGTGGACTTCTGGTTGCGTAATGTTTCATCCCTTTGCCACAA TACGAGTATGAATGTATTTTATATCAAGTATGTAAATATACATATTCTAC CCTAGGAGGAATAAAAACTAATCTTATTATCTGCATTCCCAAGCAACCGA GCTGCTATGTCAAAGAAAAAGTGAAAGTTTAAGTCAAACTAAGATTTCAA TTTAGTTATATTTTCCTGTGACATTCAAATGTCAAAGGTGAAAATAGTAC CAATATTCGAATAAACTTTCGCTGGGAAATGATAATTAATATATTTTTGT ATTTTTGTGTTTCATATGCGCATTTTTAGTATTTAAAAAGTCGCCCTGCA CTGAATCTCTTTTTATGAAAGTAGTCAGTTTTATCAAAAATCGAACATTA CAGTGGTCCACCTTAGTTTTACCTGCTCAATCCAACGATGATGGTGCGCG GCTCCCATCCGAAATTGAATTTATGGCACCGCTTCGTGCCTCTGAGATTA ATATAGGCCACACCGCCCGAGACGTGTGGAAAGGTGTTAGGCGTCCTACT GCGGGTCAGAGGTCAGATGGACGATCCGGAGCTGTCATCATCGCAGTAAT CAACAGTTTAACGGCATCGCCTGGTGGCCTAGATACTGCGACGCCACTTT GTAATCGTTAAGCTGGTCCTACAGCCAACTACAACTGCCACGGCTTGTAG AAGGGGTATGGACTGGTAGGCGAGGGATGGGGTGAAGTGATAATGTGGCT GGGACCCGGTCCTGACCAGAATCATACCCATAAAATCATTTGTTTATCGC TGCGGCCGCTTTCGGGCCCATTAGTAGTTCAAATTCAACGCCATAAATCC CCGAATCGGTGAAAACAGGGCTAATTCCTTAGCATGCATGGGTGCTTGGG TGTTTAGTGTTTGCTGTTTGCTGTTTGGCGTCAGATGGCAAATGACGCGA CGCTCGGCATGCAACATAAAAGCTTATTTTATGATTTAAGCACCACAAGG CCACAACTCACAGCTCACAGCACGAGCAGCCATATTGCGAATGTTAATCG CACATAAAGCGTAATGTTTAATGCTTAATGGTGTTCAAAAGCCCAGTCTC CTCAACCCCAAAAATGTTGCCAAATTTGTGTACATGTATTTTGTGTTGCG GAATTTACATTAACAAACGGCAAACTAATCAAGTTGAACGAAAAGCCACT GCAATTAGTTGTGGTCGAGAAGTGGCTAACCGGAGAATTAGAAGTCATTT AAGAAGTTTAGGTTCGGAGAAGTTTCAAGGGAATTCAAAGCGTTCGCTTT TTGTAATTACAAAGTTGTGCGTCGGGTTTAGTGTAATAAATACATTTTAA TTACTTAATTTGTTATATTTATAAGCACCAGTAAAAATCCCATCAGGCAG TTAACACAACTTTCGAAAACAATAAGTGTTGTGAAAGAATCGGTACAATG TATTTTATGGCTACTTTTGTTTAAGATGGTTCTTTTGAAGCTATAATAAT TTTTTAGTGAAATCTTATTATTGTAAGATACACATTTTTCTACAAGTTTT AAAATATGAGTGGGTTTACATAAATATACGTGTGCATATAGATTTAATTA ATTTTAAAGATTTAATTAATTTAAAAAAAAAAATCACGTTGTAATAACTT TTAATATACCCCGTGAATAAATGAGTTATTTCTATCATTAAAAACGTGTG CGAAAGCTTAAGCCTTTTGGGATTTAACATATGTTTGTATATTGTTCACA AATTGTTTTTCAACTTTTGAAATGCTAAAGTCTCTTTCTGTGACTAGTTT GTTGGCTTATCATAAATAAAGTTATCAAGGAACATAGAAAAAATGGATTT TAAACAAAGGACAACAAAAAATTAAAATTTATTCGGTGTTATTTTTATCA GAAGTACAAAAGAAAAAAAATCAAGGTTTATCAATAAGTTCTCTTGATCA ATGGGCTTAAACTACATACATACATATGTACATGGCAAGCATTTCTCTCA GTGTGACAGCTGATGGCTGGAGCTTAACGCACATGTCCATCATCTGCAAC AAAGGCGGTTAACACGGATGGCTGGTGCGTCCAAGCGGAAGTAGTTCACC ACCGAACCAGGCCAAAATCCCCAGAGCCGCACCAGAGTTTGCAACTTTTC GCGGCCTTTTCGTGATATGTCGGATCAACTTGTGATATCCCTGCGGTATT TGAGGCATTTTAATCAACTGGCAACGCAGCAGGACGCATTGGAATGCGGC TAATAAATATTTATAAATGTTGCCCCGCACAAATTGTTTGACGTGGTCCG CTTGTTTCCGCAAATATGAAAGTTTAGAATTCTATGTCTGACCAGAAACG AGTGACAGCACATCCCCAGCCCTGACCCTTTGGCCACTGTCCTCCGCTCC CTGCCCCCTGCCACACATGGTCCACATGGCCCCAGTCCCTCCGGACCAGT TGAGTCCTTAAGCCCCGGTGCTCGCTTGCTATCGTGTTATATGCCATGCC ATCCTTGCCATTGCCAACAAGTGCAGAGAGTGCCAGAGCCGCGGCAACAG GCAAATGTGCTTTTAATGACATTTTAAACGGCCTCGGGCGCAGGAATGCA TCCGATCTGTCTTATCCTCTAAGAAACTAATCAATAAGATGCTCGGCACA CATATGGCCCCCAATCCTGGCTCCCCCCGGCCCCGGACTCCATGTTACCT TCGCCGGAGGGGCAAGCTGAACAGATTCGCAATAATCGGGGGATGGGGCA GGAACACAAATTGATTTCCAGGAAAGCGAAAAAGGGAACGTCAGAACGGC CAATTCGAGTATTTTCATTCTTTTATTTTGTGCGTCTGTTGTGATGGCAG CCTTGCATTTCCTAACTGCTCGAGCAAACACGTTCCCAAAAGTTTTGAGG TCCTCTGCCCTTTGAGTTGTTGATGACATGTTTCCGTAGTCCGTAGTCCG TAGTCCGAGGTCCGTCGTCCGCAGTCGGGATGATAAAAACAAAAAATGTC AACAACAGGAACGCTTTTATTTGCGGAAAACAGAAAAATTAATTCAAGTT TGGCTCTTTCGGCTTGCTTTAAAATGTAAAGCGGAAACTTTTGGCCAGGA CTTGCCTTTCTTTTATGTTTTCCACAGCTGTTGGCAGTTGTCTTCGGCGT GGGCCTAGTAGATTTAATTAAATTTTTGTACAGAAAAACATTCTGAAGGC TGCTGCGTGTGCGAAAGTTTGCGAGCGTTGCCCGGGATTCGGGAATATGT TGAAAATAGAGTTCTCATGGGGGAAAATCGGCGACAGCACTGGGTTTTAA TATTGATATTTAAATTTTCTAATTTACTCTACCCGTGGGAAATTCCCACC CCTCCCTCTCAGTTATATCATTATCCGCTTGCTTTCGGCTTATCTGAGGC ACATCCACACGCTACTTCACATGGCATAATGCAGTGCAAACAGTATGTCC CACAGGGCGTATGAAATTCTCCCGTTGTGTGCAGCCTCTTTGCGTAAAAT AGATGCAAATTAATATGCATTTCTATGCTGCTGCTACTGCTGGGCTGGGC TGGAAACAACAAACAAAATCTTCCGTGCTGGTGATTTTTCATTAAAAATT ACCCCGAGCACAATGTAAATAGTTGTGAATTTACAAGGATGCCTGCCTTC GCAAGTGCAGTGCAGCTCAAGTTCAGGTGGTTTTTGCATTTCGAAATTCG GAATTCGGCCAGACGAGCCGAGAAATTAAAAACACTTTGCTTCGCTTTAG GCCAGGTCCACATCCTCACATGGCCACATGCATTTCATATTCCCTAAGTT TGCTTGCAAGGTTAACGTAAACATGGGCGGAATAACAAACCCCACTTGAG TGCTGAACGAATGATTATGAAAGTGCCTCGGCGCTTTGACTTTCAGATCT AAAAGTCATAAATCCGTGCGGATATTTGCCATCTGCTGCAAACGAACCGG GCCATTACTGCACTCCACCAGGTGATTGGGTCGTAAACCACCTGTGTCTG GGAGGCAAGTGCACTTCACCTTTCTGCAGGTGAGGCGACCAGTTTGCTAG TTTTCACTCTGATTCATTAGCCCCGGAATAATTAACAGCCGATGCAGCCT GCACACTTAAATTGATCCTTATTATCTGCACGCGGGACGGAACTCAGTCA GTTCAGTGGGCGTCTAACCAAATTTGCCCACTCATGGGCGGCAGCAACCT GTTCAGTTGATGGCAATAAATTGCATTTGCTGGAAAACCTAATTACATTA AGTTGCAATTACGGGAACAGAGAGCGCCGTAGGATTGCCCAGGTGCACAT GGCACAGGTGCAAATGGTCCTCCGTTGGCGCGCTTTAAGAAAAACTGCAA AATTGCTGCAAATTGAATTGGCTGCACTTAGCCTGCACATTACATCACAT CACATGTAAACTGCAAGGCCAAGCGGCTGAAAGTCCGAAAGGAAGTGCAT TTACCACTCCAGCGCTCCACTCGCTGTGTTTGTTTGATGAGGCCAACATA TGTACGTTTTTGGTTCTTGTTTGGATTGCATCCGGGGAATTCGGCCCCAG AGCGGCCTCCTCAATTGGAGTGTCTTAGTTGTATCAATGTTTGTATCCGG ATGCCATACGTTCATCTGATTTGCAGAGCGAGCACGTGAGCAGATTATGA TTACATGCAGCGAGCTGCATGCCACTGCAGTTTGAGATACTTTGAGCCCG GGCAGCGCATCCTTTGGCAAAGCCAATCAGGGGCAGCAAACAGAAATGGA TGGCATCCAGAGTTTTGGAACTACATTTTCAGATTCAAATGGCTTCGGGT GGGTTACCGTTCGGTAAAATTGTGAAAACTGTAGCTTTGATGCCTGATTT GAATGCGATTGCATTGTTGCTTTGAAGTTTTCTTTCAAATAATAATTCAT TTTACTCACACACTTGCGGAGGATTGGTATTTGTTTTGCCTAGTTTAAAT ATGCAAAAGTACTAACTTATTAAAAGATTGAATAGATTGAAAGTGAGAAA CCGAGCTAAATTTCACCGCATTTCTTTGCATCCACAGCTTCGCACAACTT CGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCC GTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACT GAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACT CCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAA CAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCG CAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACG TCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTC CTTCTGGGCGGCGCCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCT GTTCAAAACCTACACGGACAAATATCGCGCCACCGTCGAGGATCTCTACA ATCGCGAGTACGACCTGGGGGGCGTCACACTAAAGGTGAGTACTCGCCCG ATTCCCCTGTTCCGGTTACAATGGAACAAGTATGGGCCAGCTTTTTGTCC CTTTTTGGTGACATTTTGAGTGGAATTTTACTGTAATTGGTTTCTAAGAG CTGAAATGTCAGAAATGCATTCCCAACTATATGTCTCAGTGCTCGTCTTA AAAGCCACTCATTCTCATCCTGCAAAATCCTACTTTTGGGAAAAACTAAC GGCTAGGAGAAGATTTTTATTTAAGAATGCAGCTGAATTACTTGACTTCT AAGCGCACATCATCATCAAATTAAGCCAAATTAAGTAAATATAATTTTTG ATAGGCCTATGTAGTTTAATTATAAGATATCAGGAGTCTGATCGCTGGTT GGCGTAAAAGGTAAACTAAGAAATTAATCCCAGATTTGTTATTCCAAACA ATTTAAACCGACTGCAGTGGGACGACTTTATTTACCCAATCAACGTTGTG GTCATCAACTCGCCGGCAATGCCATAGGTAATGCCGCAAATTAGGCAGAA ATCTACTAATTGGATGTCTGGAGAACATCCAAAGCACAGGGCTCCGCAGC CTTACGCTCCATATGCAAAGTATTAGGCAGGACACGTGTGCTTCTGGTCT CCTGGCAATTGAGTAGCTCCCTGAAAGCCTATTTGGAGCGGAGTGGAGCA GGCAGGAGTGGTTGGCGGTCTTTGGGGTCGGCATCTTGAGCCATCTCTGC CAGAGGCACAACTCAGGAAGATTACATTTGTATATTAAAGATGAAAACGC AAATTGAACGAATGAATCTCAACTGGCTTAAATGTACTTACGGCAGTCTT GGTGAATAGTTTCCAGCCCCATCCCTTCACCCCAAACCGACAGACCGACT GACAAACTGACTGACAGCTTGTGGGCGGAGACTCATTAATCAAATTTGCA CACGCTCAAAACAGCGGAAGCAACTTGGAAAATGTGGCCCACTTCCCAGC CCGCTAAGCCACCAGTGCTGCCGGCGGAAGAGTTCCGGACTTGCGTGCCC TATTACGCTACTTAGGAGCTCGATTAATGGGTAATAACTTGTGTCATGCC CGGGAAGGAAGAACGAAGGAGTATACCGGAAACTGATAACTGCTGCTTAT TATTTTAATCGGGCCTTTATCTGCTACGGATAACGGATAACCATATGGAT GTTAATAGCACACGAGTGGGAGGAGCCTGCGTGGTCGCAGGCATCACAGC TGCCTCCGACGCATCCTTACGACCATGTCATGAAATGGAAAACTTCTGAT GGAACATCATTCACTGCTCCGCTGGAGCTGATTATACGCTGTTCAAACTT GTCTTACACCACAAGCACATGTTCGGCGAACAAAAGTTGCTGGGAAAGTT GATTAATAGGTGGGCTGCCTGGCTGGCTGAAGCTGCTGAGCTTCATTATC GGGATTCTAGCTGGCAAAATTGATTCCTGGATGTGCTTTGGTGACACTGG CTCTCTAGGAGGCGGCGTCGTTGCCGGGCTCTTGTCTTCGATTTAATTAA TTTCATTTTAGCGACCGACGGGTGCGCATCCATTACTTAAGCCCGCCCAG ATTGAATTCCACACGGGAACTGTCACCCGACCCCAAAGTGATTTATTCCC GGCCACCTTGGGTGCAGTGTCCAGACGGTCAGGCGGCCAGGCGACCAGGT GGCCAAATGGCTAGGTGCATCCAAATCAGGTTGGCCTGGACCATTGGCCG CCGGGGCTTGCTATCCAAGCTCGAGTAGCGCCCACAGCCCGCTGAGACTG ATTGCCGGAGCAGCATGTGGCCATCAAACGGGAACATTCTATTGCACTAA ACGATTTTTGGTCTTTAAAAGCAATTTCGTGTATGTATGTACGTGAATGT GCAAGTGCGCACAGCAGGACGCATTTGATGCCTTAAACATGGATGGTCGA ACAAAGGCGGGCCGGCGAACAAAAGCCGAGCGACCGGGAATGGTGTCAAA AATATAAATTGTGTCATTCTGCAAAGTGTTTTAATAAAGTTTACTCATTT CGGCCAAACAATGCGTTACAAATTTGCGTCACAATGGCCCAGGCTGTCAA TTGGTGGGCTAAGGACCAAGAGGAGATCACGTCGACAGGGCTAAATGGTT AGATTCGCTGGCTCTGGCTCTTTGGCTTTCTGGCCTCTGCGTGCCATTGA CATTCCGGATCGCGTTCTATGCGTATCGCGTACTCGACGCGGCATTATAC TCGTAACCAACATAACAGATGCTGACACGGGGATTAGTTGGCTTCAACCA GGAGTCACGACCCCCGGGTCACCGTCCAGATGGCCAGACAACCGGACACC GCCGATTGGGCGGGGCATTCGTCCTTGTGCTTTCCACGGACATATCGTTT AAAAAGCACTCCATTAAATGTCCTGCGTACAAAGGGCAGTGCCAACAGCA GTGAAAACGACGCCCAAAATAATGGATAAAAAGGGATCCGGACCATGTTT TCCTATATTTAAAGTACCAGAATTTAATGTCGGATTCACTTAAAATGTAT ATTCCTCGCTCTGGCCTCACTGAAAACAATAGCTATGTTTATTTCCATCT GAATTTGTATCTCCAAAGATATACCAAACTTTAGCTTTTAAGCCCTATTT CCATGCCATTAAAACAGTTGAAAAAACTATACCATTTGAGCACTTTGTCG CCACTAACAAAGTTAATAAACGTTGCGCGGCAATATATTTATACACCTAA AAGAAACTAGGACGGAATACTTTAGGGCAAGTCGAAGTTTATACACCCTT ACCGCTTCAACTTTTTCCTATCACCATTATAATATAGGAGTACTCCTTTT TTTTTCAAAAGGTTTTCTATCAGTATTCCATTAATATTTAAATCTTTACT AAGGCAGCTATATGATGTAGTAAGCAGAAATCCAGCAGATAGCTTTTATA CTGAGCGACTACTTTAAAATGAATAAAACTACAATATAATTCCCTCTTCA AGAGTATATAACCATACTTGGCAAATTTCCGATAATAACTTTTCGTCGGT CTTTTTTAGCTGCAGCAACCTTTTGTAACTGACACCTTTGGACCAAAAGA CTTTCACATTGTTAAAATCAAGCGTTGGAAAATGGGAACTTTTAGTCTCT TAAATTTGATTTAGGTTTGGTCATCATAGTAAAGAAGTGACAAGAATTTT AGCATCAATAAAAATAATTCTAAATTATTAAAAAAAAACAAAATTTGTAC TGCCTACTTTCTATAAGATACATGGTCTAAAGGAGAGCACAGCAAGTAAT CAAATAGATTCGTTTAAATATTAATTTTGTTCAGCTCCAACATCTCCCAA CATCACAGTGCTGCCTTTAATCAAAGGACCTGCAAAATAAAATTGGGACG GTGGTTTATCGTGAATGAATGTAGTTTCATGGAAACCTTTTTTTGTTTAA ATTGAACGTCAATGATCTGAAACGCGGCGGGTTAAATTAAAAACCACGAA CGCTCCATGCGGACGCGGGATCTCATTGATGGCAGTTTACTGCCATCCAC GGCTGGCGGCCATCCAAATTAAATTATGCGTAATTTTTCCGCCCTCATCC CTTTCAGGTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCA TGCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCG GCCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGAT CCGCGAGCAGCGTGGCGACTTTCAGGTGAGTTACAGGTGCAGCTGCAGTC CGCACTTCGCACTCAGCACTCCTGCATTTTGCATGTAATCAGCGGCGCCT GAAATGCGGAAGCCTGAAAGGACCCTCGTCCTGCGCCACAATCCGAAAAG CAATTATAAATGTTCCCCTTTGTGGCGGAGGAGTCAAGCCGAGCGGCAGA GGTTTAGGCTTTTTGCTCGGACTCGGCTCTAAAGTTGCACAGTGGGTCAG GATCACGGTATCAACCGCATGGTAGCGGTATCAACCAAAGGCGTGAGCAA AATGTGGACAACAAGACAAATGGTTTAAGAAGCTTCCAATTTCGAATAAG ACATCTGTTAAGACTATTAAAGAGTGATCAGTTAATATTCGTTATGATCG AGGTAATGTCATTATCTCCTCTTTAATGTCAGATACTTCGAGTGGGTTTT CTTTTCAGGTAGGTATTACTGTGCAACATAGGGTTACCAATTTCGTGCCC ATGTGCGATAGTTAGCGCTATTGTTTCCGAGGGCTTTCACGGTTTCCGCT TTCCGCCGCCATTGTTCGAACGAGTATCAATTACGGCGCAATACGCTTTG TCCGCATCCCGATTTTGGGCGGACAAGGATGCTTGTGCCGCTACGAGTGC CACTGCTAATCCTTTTCGCTTCGCAGGACATCCCCATTGTGATCGCCGGG AACAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGT GACCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGTAAGTTGGCACTT GCCCACATGAATCGCACAGGATACGGTCGCCGTAAAATGCGCAACAGCTG CTGCACGCGACAGCAATTAGGGGACAACTGCCAAAAGTTGTGCAACAAGG CCCGAGCCACAAAGCCGCAAAACCGCCAAACAGCTGCAATTTTCATAAGT AACGAAACACAGTGGAATTAAAATGGAGCCATAAATTCGTGCCGCCCCAG AAGAGCTGCAATTGCAAGAGGCTGCCGGCAGCAAATGGCAACAGCGCAAT TAAATTGCTAGAAATGAAATTAAGCGACTGAGAGCGTGACGGCGGCCATG GAAGGGAGTTGGGCCATCGAAATCAGTTGCATTGTCCACGGAACGGCTGC TGCGCTCATTAAATGCCATTTGTTAGCTGGGAAAGTGTTGGAGCAAGAGT CGAGCACTGAAAAAAATTACTAGGAATGGGGGGAATCACGATAATCACAG CGGCCACAGGTATAAAGTAAAGTAGTGTGAATACGTTAATACGTAAGCAT TTCAGGCAGTAAATATAAAATTGATAAGTGAAAAGAAAAGTTCAAGTTGA ACTTTCTATCTTTTCATTAATACTTGAACACCCTGAAACTTCAAACAGTA TTTTTGTGAGTGCAGCTAGGTGGAAATCGCATCAGGAGGAGGAATATAGC ATTTCGCTATTTGCACAAAGGATGTTTCCCCATAATAGCTCCTAATTGGC CATCTTGTGCCGCAAACGGTGATGCTGTCATGTTGGCCATCTACATGCAA CCGTCGACGGGGACAACTCGTCGTATGAGTGATACATTGGAGTGGTCTTT GAATACTAAGCAGTGGGGCATTCCATATGCGCATATGCATGGGATGCATG GGGTCCTTCAACTTGGCTGCTCTAGAACTGTTCGATTGTTGCTCTGGGGA ACCGGTGTGGGGCTGTGAGGAGTATGATTAGTAGTGGTGATTTGTGTTTC CTCTGAAACACAATGGGTGAAAACTTTAGAGCTCGTCAGAGCCGAGCAGC AAACCGACATTGTGTTAAATGAATAAACCACAGAAAGTTTCAAATACATT TGACGAATGAACGCATATAAAATGCAGAAAGGTGATAGGTGAAGTGTACA AATATTTATATTTATTTCATATCGGACTCGTGTAGAGTTTCCTAGCTGTT TCATTTGTTCAATTTCAGGACTTTAAAGTTTAAGTTACCGAATTCAGAAT AAGCCCAGTTGTACAGTACTACAGCTTTTGTCAGTAAAAGTAGACCGCAG ACCGAATCGGTGAGTGGTAAACGAGTACAACTGGCCTGATTAAAGTCTTT GTTTGCCACATTAACAATTTTAATGCATTTCTCGCGTGACAACCAGCCGT GAAAGCACGGCCGCATCCTGGCGATCCGCCGGTGAAAAGGACTCGCTGAC CAGCACATATTTCAGAGGCGCTTTTCGCGAGGTAATTGCTTCCTTAATAA ACTGTGGGGCAGGACTCGTAAAAATCACTTGCAATCACATACGTGCCTGC CGCTGGGATTGGGACTGCTGGCATAATTCCATACGAGTGTCCTGCGAAAG TCGCCGGGATGGGCGGCGGCAAAGTGGGGAGTGGCACGCTCGCGTTGCTG TTTAAGCAAGCGTGCGTAAACTTATTTAAAAGCGACCAAAGAGCGTCACG CAGGAGGCGCGCTCAACCGCAAAATGGAGATGACAGAGGCCGCAGGACGA AGGATTGGGCATGTGGGATGGAGTATGAAGGACGCGGGAAAAGGGACACG AGACGCAGTACAGTTGGCGTGAGCATTACGTACAAATCTCTGTTGGATTA AACATTCACGCAGATTGATGGTGCGGTTTTGTTCCCGGGAGCGGGAAACA CCTTGAACCCATCGCCACAATCTCACACCTAGAGGATTCCCCACGTTCCT CACTCCCGTGAAGGTGTGTGTGTGTGTGGGTGTGGTGTTTCCTGGCATCG AGCTGCAATGCAATTTGTTGCTGCCTGTCTGTCTGCGGTTAAACGCTTTA AGAGCATGCCACTCAAGTGCATTTATCTGCCTGAATGGGCACTATCCCCC CCCCCCCCCACATTGTGCTCAGTGTATGCCACACACCGTAGGGATACATT GGGGCAGGTCCTACCTGGGTAAGTGGTTTACTGTGCCGAAGGTGGGACAA TGTATTTATTCAACATTTAATTGCAAAGTCATGCGCATTTTCCTGCCGTT TGGGCACCCAGCGTTAATGCGCAAAATAAACGTGCGATATCAATTTTACT TTGATTTACTGTTATTGCAGCTTACGGCATTAACAATTCGGCCATCTATT TGTTTATTTTGCTAAGTCAGCCGTTGTAACTTTAATTAAATGAAGCTGCC TGAAATGCTAAAATATTCTGTGTCACTCTGTCAGCTGTTTCTGTAGCATA AAAAAGGAAATAAATATAGCTTTTTATTACAAAGAAATCCATTTTATGAA TATTAATTCAGAACAAGTGTAAATGCAAGCTGCAGTTGAATAAAACCCCT TTCAAATAACATTGGGAACAGCGTTTAAATAAATATACATTTCCAAATTT TTTGGGGTCATCTTGCAATCATTCACTTTGTTCAAAAAAATTTTAATATT TAACAGTTTAATTTGTAGAACTCCGAAGTAGCGTAATACCACTGCAATAA AATATTAATAACTATACATAAAATAAAACCATAAGAAGAAGCTCAACTTA TAGCTTAACAAATTCTGAACTAAAAATTAGTAGAAATAGGAAACTTTAAT CTACAGTTATGCCACTTATTACCAAAATTGTAAATGCAAGGAAAATATTT TTCCAGAATGGGTCTTTCAAGATTATATAGTGTGATATAGGTACTACACT CACTCACTCACTTAGTGAAAACTAAAAATTTTAAGCACAATTTGTAAATT TTTATTTCTTTAATATCTAATTTCATTAAATTTTGCTTGTCCGATTGTAA AATATAAATTAATTTTAACGACATTCATAAATTTTCTGCGTGCACATCTG TTTCATTTCAATTAAACAACTAATTAGGGAGGAAAGAAGTAACTAAAATA AATTAATGTAGTAAGCAAACTTTCCACTGAAAATGTGTGAATGCGAAGTA CAATCGAAAATTTTTCGGAAAAAAGCCCATAAAGGGCAATTCTGATGTAA GCCAAACTGGAATATTTTGACTAGAAATAAGCCTTTCGTCGGATGGCCAC ATACATTTAAGCTGGAAATCCTCCTGACAGTCGGGTACTGTGTAATCCTG CCATCGCCTGTGTGTTGAACATCACCTGTCCTCGCCAACATCATCGTCCT CGTCATAATCATAGTCCTTGCTTCATGCCCATCTCATTCCTATCCTCATC CTAGTCTTAACCCTGGTCTCAGTATTGTGGGGCCAGCGCGGATCGTGGCC GCATCCTGCAGTGAATCCTTAGTGCCGCACCATTTTAAAGCGAACATGAC ATGCTTAATTTGGCCATTAGCAACATTTGTTTCGTTCGGCCCCCCGGACG GTGGTCCGGATGGATGGCCCACTTGGTCGTGGCGGGCACAAAAACTCTGT TTCGCATTGAACATGCCACATTGTTGGGCTGGTTTTGTTTGGCTTTTTTG GCTCGGTTTTCGGTTTGGATCGGCTTGGGTTTTTTGTGCCACAATCGCTT TGTTTCGGGCCACCAAAATTCGCTGATGTATGCATTGCGTATGCGCTATA TAGACGGTCGCCCCTGAAATTATGCAACCTTTTTAAACCGCCCTTCCTCC CCCGCAGGGCGAAAGTGCTGGAGTGCTCCGCGAAGGAGGACAGCAACGTG ACGGACCTCTTCAAGTCCCTGCTCTCCCTGTCCCGCTTCCTGCCCGCCAG CAGTAGTGGGAGCGGGGGCAGCGGGGGCGGCGGCGAGGCGGCGCCCAGCG GTTTCAAGCGGCGTTCTTCGGCCTACGTCAGCGCATCGTCCAGTCGCAGT AAGTATTCGCAAATGCTCTCATGTATGCTGACAGACCCAAAAATTGTGAA ACTGGTAGTATATGTATATACAGATGGTAGTGGGGGTATAGGGAAACCAG CTTACTATTTAAATGTGTCAGCAATTCAACATATTTTAAACATATACCTC GATAAAACCAAGTGGAAGAAAGGTTGTAGCTTTCAGGGCCAGATCGTAAA TATAGGGAAATGTGATCATCTTTTTTTTTTATTTATGCTCAAAGTGTAAA ATTAAGAACTAAATTAAATATTATAGATATTAGATAAATATACATACACA GCAACTTCTTTTACAAGAGTGATATTTTCCTAATATCAATATTTTCTTAA AATATTGTTAATCTCCTCGACTATCAGATACTCGTTACTCAGTTAATGGG AATGCAAGGAAAAAAGTTTTGAAGCAATTGTGAGAGTTAGAGTGGGTGTG GCAATCTTATGAAACCAAGCGTCTCTAGAATCTGCATGCTTAATCTTAAT CTTTTATAGTTCCCGAGCTCTATACGTTCATACGGTCAAACAAAAGAACG GACTAGTTTTGTATTTTTGATCAAGAATATGTTTACTTTAAAGTGTCGGA AGCGGCTCCATCTACCTGGTACATACTTTTCAACGAATATAGTGTAGCCT TTAACCCTTCGAGTAAGGTGTATAAATATATAAATATCAAAGCGTACTTG CTCACATTTATGATAAAGGATGCCCCGAATATCTAAATGAAATCTAAACA GCTAGCTAAAAGTTTATGCCTTATGGCACAATTTTCACGGTAGTGAGCGA CAGAAATAGTTTCGGTTGCATTTAACACGATTAAATCCCTTGAGTCGCTC AACAATGCATCCTGGAATGGCAAATTGCCTTGGTATCCATCATGCCAGCA AAACCAGCATAACACCCAGAGCTTAGAGCACAATCTCTCCATGGATGCAA CACTTGATTTGTTGCCATGGCTAGGTAAAATGGAAATGAAAACCAGATGA TGCAAGCCCTTTGTTGATTGTTTTTGGCCTCGTCGGTTGGCCGTAACAGT TTCAAATGTCAATTAAACATTCATATGCGCCGGCTGTGATTGAAAGTCAG ACCTGTAACCTGAACAGCTTTATTCGGGGATTTAAGTGCCGCCGTAAGGA GCTTAATTAGTGCGAAATTAAAATGCGAGTGCGCTGCACATTAATGCAAT AATTAAGCCGGTTGCGGGTCGCAGATGTCACTAAGCCGTGCTGAAGCCCA ATCAATAATTGATGCACATTTATGAATGTATTCAGTATTTTAAACAGGAG GGAAGCCCCACGCACATGGTGCCAATTAATTGGAATTCTTTAAATGCGGC CAGGATAGCTAGGATAACTTTTGGCAATTTGGCTAATTGAATGCAATTAG CATTCCTGCTTCAATTGCCGCCTCCGTCCACTGCCACCGCCTTTGGGCTA ATTAATTGTGGGAACTCGGGATCAGAAGTGGAGTAAAACGGGCCGTCGAG ACCCTTTCTTCCGACCCAATTGACAAAGACAAACTCTTTTTCATTATTCA TCAGACGACAAAGTGAAGGAAGCACCGAAAAGCAAAGCAAAGCCAGGCAA AAAGCCGTCGCGACGGGGTTAAAGGCTTCATAAGGACGAATTCGCTTTCG GCGAGTCCTTCGCCGCGCGATGTTCAAACGAATTCAATTTTATCAAAATG TTTCCGAGCGAGCACGTGTATTAATTAAACAGCTTGACCTCCTAATTACC CTGTAATGGAATGCTTTATTATCTCATTAAAAACTTAGTTCACAGCACAT GAAAATAGAACACAAAGGCCAAGACAACAGCCAACGGCTCGAGAAGTTCC GAATTTTGCCGAGCTCGTCAAAGTATAAATATCTAGTTAATTAATGTTGC CTCGACTGGCGCGGTGCCCAAATAATTAATTTCATTTTTTTTTGGGAAGG CAAAAGGTTGCGGAATCATTACGGATCCCGCCCAGTCAGCGATGCCAATA TTGTAAGTGTTCGCCCTAAAGTCCTTTCGTGAAATTCCGCTGCTGTCCCC GTGAGCCATTCAAATTAAGTGCAAAGTTGGTCAACGGCGTATATGCAAGT ACTTAACTTCCAACAACTTTAAATTCAAATGGCCGAGGAGCACATTAATG TCCTGCCACCGAGCATATCAAATGCCTGCCGAAAAATGCTGTCAAATTCT CGGTCTGGCTCCAACTGTCGATGACAGGCGGACAGGACACGCCGACAATG GCGGTGGTCTCAAGGACGAGGGACGGGGGTCGAAGGACGAAGGTCGAGTA GCAGACTGTCTCCGGTAGTTCAGAGGTTGCGGCACTCTGAGGTGGGAGGG GTGACAGCGGTGACACCGACGCCCTGAATGTGCCACCGAAAATAGGTCTA AGCACTTAATCACCGGCAGCTCGAGGGGACCCAAGTCAAGTAATTGCCTT AAAAAGCACAGCGCGACGTATGCAAAGCAAATCGCAGAAATTTCATTTAC GACCCTGCCATTTTGTGGCTGAGATTGTGCCACACGTGTTTACGGCTTGC AAGTGGAGAGGTTGGAGGATGGGTGATGGGTGATGTGAGATGGGCGGCAC GAAAAATGGACGGGCCATGGTAAGATGAGACAAAGCCAATGCTACAGGCC ACATACATGTGCTGCGGCCGGAAAACCCACTTTTCCTCCGCTTCCCACAT TGTTGCCGGCTTTTCCACGGCACTCGCGTGGTTTTGGCCCAGCGGTGCTT GCGCCGCAAGCCGTTTTGTTTCAGAGCCACAAACCAGAGCCTAACTCAAT TGTGGGTATTCCCTAACACACACATTACATGCTAAACATATTTGAGCCAC GTTCGTGGGAGTGTTGCCCCTATTCGCAGCGAAACAACGAACAATCACTG TAAGTTGTGCGCCAGTAAGTTGTGGCCATCTTCACTTTTTTCAATAAATT TAAAATTGCTTTAAACTTCCAAGTTCATCATTGATTTCATTCATTTATTC ATGTTTGGCAACTTGAAGAACCGCTTTGTACAAATAAGCTTATCGATCAA ATGAATTACACACTCTTGAGTAATTATACGCTTAATAACATGCAGTTAGC ACTAAAAAGATATCATTGACATCTAAAACTACCCCACTTATTGAGCATTA AAACTTCAACAATTATAAATAACAATTATGTTAGTGCACTTTCGGGTGAT TTTGCAATTGATTTCAATCAAAAACAATTGCGTTTGACTGCAATTGCGCC TGCATTGACAGCAGTTTCTCATTTTACATGGCACCAAATTGTCAGAAAAA ATACACGTTTATGTAAAGCTCTTTTTTGCCGAAAGTTTCAACTTCGTGGT ATCAGATGCGGCGAAATTGATGTGGCAAATCCTTGTTATGCCCTTGCTGG CAGGATAATAAACGCCCTTTGCGGCACTCGACTGTTTTGCGTTTTTCTTT CCTGGTATTAGCGCTTTTCCACGGCACGTCCTCTGTCTTTGTGATGGAAC CAAACCATACCAGACCAGAGCGGAGCAGTGTAGAAAATAAAACAAATTTA ATTTAAATTTCCGTAACACGACGCACGCATCAATTCCTGCCGCATATGCA CAATGTATATGCCCAAAACCGAAGCCCACTCCTATTTGTTTTTGTGCCTC GATGGCGGCACTGCTGCTGTGTGCGAGTCCTCGTTTCCGATTCATCCGCA GATCAGAGGGACCTTGCTCCCCAAAATGGGAACGGGAATGGGAATGTGAA TGCCGCCCCAGCGAAGCCGTATTTGTAGTCCTGGCATTTTCGCGCGCTTT CTGTCAGCGGCAGCAATTGTGCCTCTTATGCCACCCATCCCCAACACCCA CTGCCCCTCCCGCAACCAACTTGACGCGCTTGACGCCTTTTTTTGACAAC AATGGCGTCGGCGGCCATTTTGTTTGCACTCGACACCGCCGACACCCGAA AAGTATGCAACACTCTGCCGCAGAGTGCCACTGGTGGCTCAATAATGCTG TTTGCACGGATCATTTGGGCTTCGGCGGACGTAGTTCGCTGCTAAGCTGC AGAGTTTAATAACTAAATTGACTTGGTTCTGGCCTGGCATTCTGTGGCAT TCCCTTTGTATTTGTCTTGCGGCTCCACAGCCCCACTGCCGCACAGCCCC TTGCTCCGTCAGCTGCCAATTGTTTTCCCATTGTAAGCCCTTCTTTGTTG GCGGCTTTATTTCTCGCCCGGCGGAACAAAAAGGTTTGTTTACCGCCAAG GCAAACATCTGAGCGAACACCTTTGTGCGACTTTATCACTCTGCTTGGCA GTCGAAGCCGCCTGATTGAGGATTACCGGAAAGTTAATGACTCCATTGAC ACTGATTTTCCCTACTTAATAGGTTCAACTTTGGAGACAGCTTTTGAGCC ACTTAATTGAAAGTGATGTGCAGTCTCTTAAAGTTTATTGCACAAAAAAA TGCTAAAAAAATACATTTAGCGAAGTTCAGCCAACAAAAAACAATTTCTT GCATTTAACTTAATAAGCCCTAAGTATCCTAACTAGTGTCATTAGTTTAT GTTTAGTATATCAGTAACACCACTTTCTTTCTTTATGCTTTACCTATTTT CTCTCTAGCCCTGATATATGATATTCTTGAAAGAATATCCTGAATCTTTG AAGCGCAAACAAACTTCCGCATACCATTTACTACTACATCCATGATTTTA ATTGAACTTCGACTTGTTTCGTATGTTTTGACGACCTTCCTCTGCCAACT GAGAATGAGTATCCTTGCCACTTCTGGCTGCTCCTTTGAGTCCGCATTTC ATATGAGCGGCACATGCATGTCGCACAGATCCGAAAGGAGTGGGATTACC TCGATTCTTGAGATGAACTTTGACTGTGCAAACGACTGTAAAAAATCCCA TTTCGAGCGGTAACTCTGCAATGTGCAACTCGCTTCCCGGCTCTTTGTGT GCGTCGTTCATAAGTTAATTACGTCAGCGGCTGCAGCGGATGGCAGGCTG TTGGGATACCGGGATGTTGGGATGTCCGGATGTTCCAGTTGCTCCGGCAA CTGGCAACTGGCAACTGGGAAGGACATCAGTGGGGCAAATTGGATTTGCG CTGCACTCGCAGCTCCGAAATCGCACAGTCCCTTTGAGTCGGCATACGGC CACCATTAAATGCACTCGTGGATACTAATTAGCCGCGCGTTCCCATCTAT TTGTTGCAGATAAAAATCGGATGAACAGCCCGGCCCTGGGAGGCGCCGGC GGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCGTGGACGCCGTGGATGT GGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCTCGTTCCAGGTGAGTGC AACACGTGCCTGCTCATTCAGATAGAGTCCCTGGCCAGATCCGGTTCCCG CCTGGCCGCCCTGCTGACCACTTCCACCCGCTTCCATTCCAGATCGCTCA TACGCCGTGCATCACGCAAGACCAAGCAGCAAATCAACAACGCATCCGAC GACTGCAACGTGCAGTAAACCATTATTTTGGCCGCCAGCGTCGAGCTTAA TTATGTTATTTAGTTATTACGAGTATGTTGCCACAATGTGAATTAATAAT GGACGCCAGTTAATTAGCGTGCATAAACAAGTGGCGCCGTATTTATGTTC GGTGCACTGAGCTGATTATTCTGATAAAGCTACCCAGTTCACAAAAACCT CTTGCTCAAGGGCACAAAAATTTCGATGAATTTGCTACGCGGCAAAACAT TTTATAGTTTGTAACCACCAGAGCTTCGAAACGATGCCGTCATGACACTG GCCTCAGATTATATGATATTTCGTAAGCAACTCTGATTAGGTAAATTTAT ATTTCATTATGAATAGATATCCTAGCTTATAAGCCGTGAATCAAATCAAA TTTCTTTAACAACACTATAAGTAAGTACGCTATAAGTACAGCAAAAGCAA ACACAAATACTTATTCTGCGACATTTTAATCCAGTGTCATAGCGGCATAA AAGATAAGGTATTATTCCGACACTGAGCTGACTTGCGAGGCATTGTGCAC ACAAATCGATTTGAGTTGCGGTCATTAAGGTTGGAAGGGACCAGGTTTAT TTAAATTTAAAATTAACTTTTATACGACAAACAATTTCGATTTTCGCAAA CTTCAGTACAGCTCTGGGTGCCCGATTTGAATTTAATTTAGATGTCTCCC ACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCGTTCTCCTCGAAAGGAG TTCCTTTTGATGGCAAAATAATGGCTCAACGCGACTGAGTACGAGGTTTT TCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACTGGCGGATTGTCATAAT ATTGTGACAGGTGGCATAGCCCTAAGGTACATTCTAGGATACTACTTTAT GAATCTCTATCTGCACCCTTAGCCGACACCATGGTTAATATTTGAACGTT CCGTGTACACATCTATATATTAATACAGCTCCGATAAGAATGTTTATATT GGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCGAATACGAAAGGAATCG CAAGTTTTGCAAAAATAAGGCAATTTCGCGGCATTCTCCGCGGCTCCAGC CACGTAAAATAACAAGAACTTTGCCAGAGAGCACAGAGCAATTTACTATG CAAAAAACGTAATTGTAAAATAAATTTGGTGAGGGAAGGGAGGAGAGGAG GGTGCCGAATGCTTATCAAGGATAATACAGGGTGAACTTCTTATGCCAAA ACGCCAAAATGCCAAATCAAATAGCCCACAATGCACATCCTGTTCGCAGG AGGCTTGCGGCAGCGAATAATCGATAAATCTGTTTTTAATACGCAACTTG TATCCATTCGCACAAGTTACACTTGCATCTGGGTGGGTGGTGCGTGGGTG TGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTGTTTGTTCACCGGAATG TGCTTAGCAATAAGATTTATTTAAAAGACTACATTTAGGCGGTACCGAGT ACGGCGGAGATATCTAAATGATCTGTAAATGGATGAAATACGGCATATGC AAAGTGAATTGTGATTAAACCAAATACATCTAGACACACGTGTGTGTGGC ACTGTGTGCAAGCTGAAAAATGCAGCAAACAATGCACCCAGTGATTGCAG TAATGGATTCCAGCTACTGTAAACACCTGGGAAATGTCAGAGGCGTCTGA ATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAG TTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTT ACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGT GTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTT ACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCG CGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTA TCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCT ACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCG CACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACT ACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGT GTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACA ATTGTATTAGCCAGTTAAAATAAACCACAATGCGTCCCAGGCATCGGTGT TTGAAAATGTTTGATTCCCCTGCATAATGGATTCTGTTTCGTTTCGCATT CCGTTTCCATCGGCGCACCGAGGCATCGCACTACGGGTCCATGGGACCAC GGGATCCGCACTCGGATCCGAATCGCCCTGCCCACCGGCGGCTGCCAGCC TGGAAAATGGCACAGTGAGCAGTTTGCACTAAATCAATTAAAACTAGTGC AGCACCGACCGCAGCATCCATTAAAAGTAACTAATGGAATTTCATTCGAA TTATATATTGCGATTCCCATAAATTCTGCAATTGCGTAAATGCCGATTGC CGGCTTAAAGCAGCCGTGCTGCTGCTGATTTGAAATTTGCATATTTATAT GGGGGGTGTGGTGTTGGATTTCGGAATGGGGCATCTGGGGGCTTGCGAGG AGCCAGCCGCTTTGGCGTTCGCGGCAAACAATAAACAGCTTTGCTAATGA GATTGCATTATGCGCAATTCAGAATGCAATTTACTGTGGCATTGATTTTG CATTAAATTGGCTTAGGCCGAGCGCTCCGCTTGGATCGGAAAAGTGCGGG AAACCCCAATTTGCTGCTGGCACGTCTGAGCTTAGAATTATGTTCTTAGA ACGACTTAATGCAAATTTCAAATTCAAATTGCAACGGAAGTGCGGCGCCA CCTGGCGGTTACCACGAGCGCGTTCAGGCGGCGCCCTCTTGCGGAAATCT CGCAAGTGAAACAGCTGTTTCCAGCTGCTGGTTTTTTTTAGCACATTTAT CCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGGTAACTTG AGAGAAATTAACTCCTGCAGGCTTGACTAGCTAACACCTGGCAATGCTCC ACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGG CGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGT GGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGAT GTGGATGAGGCACTGGAACTGGCCTCCAAGGATGGTAAGCTGACCTTTAG GATGTTCCCTTTGCAAATTGTGCTTTAAATTGGGAGTCCCCATTGCACGT CCCTTTTAAATTACTTTCTGATTGAGCTACTCACTTTCTGAAGAGCATCT GATGTTTATTCCATCAATTTTCATAGTAATACGAATATGTTGCTTACTCC CCATACCGCGATTTTATTGTACACTCTCAATTCACAAGTGGTTTTCCTCG ACAGAGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGA ATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCA AGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTAC GATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAA GCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGA GAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAG ATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGA GGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATG GGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCC AACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTGGTATTCGACC CTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCCACCGTCAAGA AGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACGCTGTGAGCCT TGCCAAATCAGGTACTCATTGTTAATACCTTACCCCCAAATGTGCAGACG ATACTAACAGTTTGTCTTCCGTTTTAGCCAAGTTTTGGAGTCTATTGCCG GAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAAC ACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACAT GCATTTACATTCAATGCGTTTACATTTATTTTATTATTGTTTCTCGCGTC TAAATGCAAATGAATTCAAAAATACGCATTACAACTTTGATTTGTTAGGT TACATCTGGTTTGGTTTCTTCGATCTGCAGTTAACACAGATCCACTAGGA TTTAGGATTAACATTTAGATGTGTAAATAATTGTTGCATATGGCTCAGTT TATTAACGTTCGTGATTACGCACTGCTATGTGGTGAATATAAAATGGATC GCCCAAAAAAATATATGTATTTCTTTCGACTCGAACTTGTATAATCTCTC TGGAGTCTATTCTAAACTCTAATAGAGTGTCATAGCTTAATTATTGCCAC GTTTTTGGTTACGAGTTTGCCAATATTCATCAATTATTGGTGAAGCCTTG AAAAGCCTATATACAAAATATTTTGTAAATATTTAAAAAGTCTATCAACT ATAATTAGTACGCTTGTAGGTATTAAAAGGTTCGAATTCGGGGGATAGGA AATATGTTTACCTTATGTTTACCGTTGAAGTTAAAGTGTAAAACAACCAA AATCTGGAGCTAAAAATTGAATTTTGTTCTAAGTTTGATGAACTGATATG AATACAAATGATATTGTTAGTATTTAACATTGTCAGACGGGCAATGTCTA TTCACTCGGGGATGCATTTAAAATGGCAATAAAAGATTCAGTCCAATGGA AATGATATGATATGAACATGTTCATATAGCACTTTAAGTCGGTGCGAAAT ATTCTGGGGAAGACTGATCTCCCACGTTCCCCTTTCCGCTTGGCAGTAGA TAGTTATAGTTCTTAAAAGCATTTCAAATTGCGTTACTTCTTTCTAGATT TTTTTTAAAGTTACAGTGGGATACCGAGTATTTTGTTAACGTGTTAACTC TATTTATTCAATACAATGTTTTATGGGTTATATTTGAAAATACGCTCAGA CATAGCCCAATTGACATGAAGTTGACAGTTTGCAAAAAAAATTAAATTTC AAAAGTAAAAAATACTCAAAACATGTACGATAAATTCCATTTATTAGGCG TCAGATTAGTTTCGAGTGTTTGTTAAACTCATATTCATATGTATGTACAT AAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATAT CTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAA ACATAAACATAACTGTCTTCCATATTGTATTCACTTAACAGAGAAAGCCT TTCGACACATTTTTGGGATACAGGAAATCAAGAAAGGTATTGATTAGTTC GATTTATGCTTAATGCTCCTGTTAAATATCGTATATCGAATATATATTAT ATATCGTAATCATATGTATTTAAGTTGTATGCTGTGTTTCGAGTTTTCAG TTTCAAACCAAACTCTGCAGAGCCCTGCAGTCGAGCAGGCGTCGGGCCTC ATGATTATTCATAGATTAATTATTATGGTAATAAATATGCTGCTTCGCTT AGCCTATAGGTTAATTCAATGTATCTTGGGAGCGCTGCGATCGTTGATCT TCTGGTTACGCTTTAAGGTGGCTCCGCGCTTGATTTGATCCATCAGCGAT TCGTGACAGATGCGAGGGTCCGGCTGAAAGAGTCCACAAAGATCGGATTA GATGGGCACTTTGCTGGCAAAACCTTAGGTTATCTATCGTTAGATCGGAG AGCAGTTAGTTGGCAGAACGTAGCACTGAGTGTATTAGCTGCCAGCTGGC TTAGTGGGCTTCAAACGAACGAGAACGACTAGGAACGAACAAAATACCTT AGCACTTAGCACTGATCTTCGCAAGTGGCATTGGTGGTTGTGCTGGTGTT GGGATAGGTGGGTGGTCTACGGTATTGCGCACTGGGTCGCGATAGTTTTT GCGGATTTTGATACATCTAATAGCCATGGTGACATGGACAGAGCATAGAG AGTGTTGGCAATCGGATGAGTTGCTGTCGAAGTGCACTACTTACCAGGGC CTTGCTGTTGATGAGATTTCGCACGGCAAATGCTCGTCCAGACATTCCCT GCTTCGCCAGCTTCGCGTTGAGATTCTCGAGGAATTCGGCCTTGGTCTTG GCACGAATACTGCCAGTCTTTTCGATATTTGTGCTTGTGGCATAGTCTAT TGATATGCGTTGTCGATACGGGTACCGATTCGGGTGCATAAAAGAAAATG GTAAGCAAACATGATCGATCAATGGTGGTGTGGATGTTGGCTTGCGCAGA AGTGGTTAATATGGTGGTAAATCCAAATGGATATGCAAAATAAAACTCAA CAATTGTTGGTAAGAGTTAGACTCGGAGATGACTGATGATTGGAAAGATT GGAATGAAAGTTGACTGCGGATCGAGCTGCGGCGGAAACTGCAATCCCTT CTTGTTGACCCGATAGTTTCCAGACGCACTTGACACAATCTCAATCATGT TAATTGGCAACACTTTCCAAACGAAAACTCAAACGCAAACGAAACAAAAG CAAAAGAACATATGCAGCATGCGCCAAAGGAAAACTTAGAGCTAACGTCA AATCAAAATTGAATGCTCGCAATCGAGCGAAATAGAAAGTCAGCAAAACA ATAATATACAACAAGCAGCGCGCTCATTCCTTGCAATAAAATCATACGTA ATGAAATCAAACCAACTCAAATCGAATCGAATGGAATCAATTCAAATCCA GCTCGCGCTCTTACTTGGATGATGTGCCTGGGAATGGGCATGGGCATTGT GGTTATAGTAGGCAGCGCCGCCGTTGCTGTTGCCCCCGGCAGCATCGCGA TAGTAGTGCTGCTGCTGCTGAGCCTGCTGCTGCTGGTGATGGTGGCCGCC ACGCGAGGTTGTGGCATAAATGCTAGCCAAGGACCCAGTAACGGGCGAGC CGCACGTGGGCGAGGCCGAGGGCGAGTGAAACTTGACGGCCGTTGTCTGT ATGAATGGATTCGTTGATACGAATATCTTTTGCTGCACACTTGAGTGGCG TGAAGGAATGGGCGGCTGGCGTTGCTGGTGTTGTTGGTGCTGCTGGTGGT GCTGCTGCTGTTCTTGCTGTTGCTGATGCTGCTGCTCCGCCAAGTGCTGC TGCTGTGCAGCTCTAAGCTTCTGCTGGGGCAGCGGCAACTGCGGACGCTG ACCTAGGTGCCCATTGCCGTTGCCAATGCCCATGCCTGCCGGCTGTTGAT ACTGCTGCTGGTGCTGCAACCGCTGCTGCTGCTGCATCATATTCTTGGGC AGCGTGGCCGTAGACGAGGCTGCTGCATAGGCGCTCGAGTGAGTCGCGTT CTGGCCAGTGGGCGGACGGGCCATCTTCTTGGGCATCGTGGCCGATGCAC CGGCGGCGTAAATGGGCGGCGGTGGGGGATCCTCCAGAGGAGGCGGACAG GTGTAGTGCTGCTGCTGCGGCGGCTGGTGGTGCTGATGGGAATGAGCCTG TCTCATGTTCGGCGATTGCGCAGCTGCTGGATTTTTGGTAAACGAACTTG AGTAGATGGCCATGTCTTTGCTGTTAGCAACTGCTGCATTCGGCGGCTGA GGTGGCTGATAATGCGAACTGGCCGAGCCAGAGGTCGCTGCCGTTGTCGG TGGGGATGCGGATGAAGAGTTCGAGAATGAGCTGACTTTGGAGAGCAACG ATGATGTGGATGAAGACAGGGGGAAGTGAGGCAATGCATTGAAAGAGGTG GTCGGTGTTAGAATGGACGGTTTAGTGCTGCTGTTGGCCGCATGAGCGGA TGACATTGCTGATGATGAGGTGCCGAAACTAGCGTAAATTCTATGCTGTT GCTGGTGCTGCAGCTGGATTTGTTCAGATTTACCGTCAAAGTGTTGCTGC TGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCC TCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTT GGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCATTGAGCTGTGCAATTAGG TTCGGATTCGCCTTTGGCTGTGTCGGTGGCAGTGGGTGAGCATGTCCGTT GGGACTGGGGCTGCTGGTGCGGAAGCTGGACATGCTGTTGACCAGTTTGG GCTGGGCGTATATGCCGCCGCCACCCCCTCCGCCCGCGGCTGGTGATGAG GTGCGGAACGTCTGGTCGTGAATGTGTGTCAGTGATGGTGTGTTTGTGGC ATGAGAGAAACGAGAAGAAGACGGGCACAAATTAAAAGTTAGCCAAAGCA CGACCAAAGCTAAGCACTAGAGTAATCTATGACTATGGCATTACAACTAA GCTGGAAGGAGGGCAGTCGTGTTAGGCCAGAGAGGCGCTCCCAAAGACGC CTGTTAGTCTTGGTTAGTAGCCCGCGAGATACCCGCTGGTCACTTACGGC ATCGACTTGGTAGACAGGCGGTTGCTGTGGCTGATGCAGATGCTGATGTT GCTGCTGGAGGGTAAAGCGTTGCTGGTTGGCCATCTGCTGACCGCCGGGC TGTTGGCCGCTGGCCAAGGCCTGGGCATAGGCGTGCAGATCCAAGTAGGA GTCGTAGTACACGGTCAGGTCCTCTTTGAGGGGGGAGTTGTGCGCAGACT ACGTGGGGGATTGGGGTTTCGGTTTGTGTGTGGTAGTGGTGAAGCAAACG TAAGTTGAAATAAAATGAAATCATAAGTTGTAGAAGAAGATGGCTAAATT TCAAGGTGGCTCTAGACTCGTGCACTAGTTAGACCCAATGAATATTACCT AACTCTCACGCCGAACTATACTGGCTTTTGTTGGGGAATAAATGTCGAGT CTTCCAAGTCGTATTTCTATGCTCAATGAGCTCAAAGTATACCTACATTT GTAGGTAGAAAATGTATGGAACAAAGCTTATGCTTGTTTACCGGGGCTAG GCAACTAGAATCCCTACAGTTTACGATTAGTGATTAGCTTATTGTAGCTT TAAACTTTTTAGCCAGATATATGAATTTTCTAACTAAAGCCAAATACATC TTCATCTGGTTGCATAAATTTTTGGTCAGAAGCATAAACTACACATTAAT AGTACCCAATTTGGGTTGTAAACTCAAATAGTCAGGTGAGAGTAGGAAAT CAAACATTTTGGTACAAATGGAAACCGGATGCGAACCGAGCACACACCTG CAATAGGGGTTGCTGCTGCTGCACCTGTTGCTGCTGTTGCTGCTGAAGCT GCTGCTGCTGTTGCTGCTGCATGCGTCTGAGGGACACAGGTGATGCTGGC TGGTGCCGCATGGCTGCCAGGGCTCTTACCGTCTCCGATACCTTCAGCGC TGAGCTGGGAATCTGGGGCATGGCGTCCAGCATGAATGGCGGTGGCGGCG GTAAGTGCTCGCTGGAGCTGCTTAGTTGGTGATTCTGCTGCGACAGAGTC GCGTGCTGTGGTTGCTGCTGCAGCTGCGTTGCGTAATTAAATCATAAGTT AAAGAATAAAAGCATAGAGGAAACCAAAGAGTGTGTGACCCAGAGTGTGA ACCCAGGCTTAGCGACTAGCTTAGATTAAGTGGCTAACTTAATTGGGTGT AGGTAATTGAAGGCTTAACTCACCCCGACCGAGGCATTGGGACTGGGGGT CACCGACGAACTGCGTCTGACTGGCGGCGGTGGCTTGGACTGATTAATGG ACGATCGACGCCCGATGCGCGTGGAGCCACCGCCGGCTGCTCCTCCTGGG AAAAGTAAAAATCCTTGTTAGTGAGGCGGGCATTTTGATGATTTAGTCAT TAATTTCTGCTGTTATTCACAGTAATGTACAGTTATCAGTTTATACACTT GGCACACAAAACACAGGACACCATCTAATACCAGTAGTTAGCGATAGACG CAGAGTTAGGATCTGCTGATCGAGAAAGTTATGAACGTTCTTGGTCTGCT GTGAATCATAATGATGACCCTGAAGCGAGTGGAAAAGCGTTAATGGCTGT GATGGCACTTTCGATACCACTTCATGTCGAAAAGACATTTCCCCTAATTT AAGCGATTTTGCAAAATGCAATTTTGTAAAAAAAATTTTGTAGTTACAAA CGATCGAATCTGATTAGTGATTAAGCATTTAGCAGTTAGTGGCAGTATCA TGCGGGTTTTGAGTTGTCTATTGATGATCTGAACTTAATGATTGTGACTT GATGGTATGAGCGTAGTGCTTAGCGAGAGAAACCAACTCCAATTTCAAAA AGGTTACCACATCGAACTTATAGCAAAAATGAGAAACCCAAAACCGCGTA AAGTTACTTCGGCAAGCACAAAATGATAAGGATACTTGCAAAGGTACAAC AAAGTAGGAAAGTTTTCAAAATAAGGAATCAAAAACCAAAACCAAATAAA CCCAAACAAATCAAAATCAAATTGAAACGAAACGAACCCGACAAAGAAGC CGGCCGGGGCGTAATGCACGGCTTGAGATGGGCATTGGCATTGGAAATGC TATTGGCGTGGTGGGGATTGGCTGGGGCATTGGAGCACACATATGGATGG GCGGGTGGTCGGTCACTGGCGGGCAACATCGATGGCCGGGCATTTGATGG TGATGAAGTGGTGGCTGGTAATGGTAATGACGATAGCGATGACGATGATA ATGGCAAATGGCCGCGAGGTGATGACGGTGACAATGCCATTGTGGGCGTC TTGCACTGCGTGTGATTGGATGTGGCTGTCTGATTTTGGTTTGGCATTCT ATGATTTGGATTCGGGTACGGGTCTGTGGATGCTGTTGCGGTTGCAAATG CAGATGCTGATGCAGTAATATTGGCGGCTTGTTGATTAGTGACATTACAG TTTCTGGTTTGGGGCGACTGTGGTGAGTGTTGCTGTTCTTGTGGTGCTTG CTGCTGCTGCTGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCT GCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCT AGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGC AGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCA GCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGC TGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTACCGCCTG CTCACTGGGTGTTTTACCTCTTTGCGGGCTACCGCGTCCGAGGAGCTGCA ACTGCTGCTCACTGGTGGCGCGAAACGAGGAGAGTCGCTGCTTGGCGGGC GCCACAGTTGCTGTTGGCGGTGCCTGGCCACCGGCAGAGTCCGGCGAGGA GTCCGGCGAACCGGCCAAATTGGCGGGCAACTGCTGCAGCTCGCGCATCT CGTGCAGCTGCAGCGCGTGGGGCTGCGGATCCTTAGTCCGCAGCACTACA ATCTCAGAGTTCTGCTTCACGAACTCAATGTCGGGTGTGTTGGGAATCTG GTGGTCGTAGATCACCACCACGGCACTGCCGCTGTCGCTGCAGGTATCCA CATAGGCGTGGCGTGGCTGGCCGAGACAAACGCTGTCGGAGGCCAGCGAA ACAGCGTCCTCCCGATTGGCATTGGCCGCAAAGTGCGCGAAAGTGGGATT CTCGTAGCCGCCGGCCGTTAGGCCACCGGTCAGCGAACTCGTCTCGCTCA CATAGCAGCGACTCAGCTCCGAATCGCTGGCGCCCAGCAGATCCCGGTCC CGATCCCGATCCCGCCGCCTGACGTCCATATCGTCGCCGGCCAGTTCGTC GGACGTGGTGTCGGATATGTCCGTGCCGCAGCCGCTCGAGTTCGTCTGAT TGCTGATGGCGCATGGCTCGATGTTGCTGGTGGCGGGCAGGTTGTTGTTG TCGCTGCTGCTGATGCTGCTGGTCGTCGTATTGTTGTTGTTGCTACTGGT GGTGCTGCCGCTTATGATGTTGCTCGGCGGTTTGACCTTGCCCTCATCGA TCTCGCGTTGGAACGAGTCTAGTTCGCCAATTAAATTATTTAGTGCTTGT ATTGAATCTTCGAAAGACTTGTCTGTTAAGTTCATATTTTCAAATTTGTT GGTATTGATTTTGGAGATGGTGTTGTTGTTGTTGTTGTGGTGCAGTTGGT TCATTGTGAATAATAGTTTACAGATGACAGAGATTTTGGGTAGGGTGAAC ATAAAGTCGAAACCGAAAAATATTCAATGGTTTCAAGTTGATTTTTGTGC AGTTGTTGCCGTTGCGTTTACACAACAAACCAAAAAACAGGGGAGGGAAA AACAAAAAAGAAATTTGGGGGTTAAAAAATATTCACGATATGTTTATCAA TTATAAATAAAAATGGGCGCTGGACATGAAAGTTGGAGACTGGGGAATCT CATGTTTAAAGTGCTCTTTTGTGCTGGGTGGGCAGGGTACTATGATCAAT TGACACACTTCGCCTTCAACGATCCAGCTGATTGCTGATGCAACTTACCC ATTTCCTGCTGCTCCGCCTCGGATCGTCGAGTTCCGCCTCCCGAAGCTGG GGAACCGGATGCAATCTGCATGGGAGCTGGGGGCGATACCGCTGCCGCTG CTGCCGCCTTTTCGAACATTGAAGCCTTCTGCAGGACTGAGGCCCTTGAT CGCTCATCCGTCTCGTCCGCTACGCTGTTGGCTGGACCCTGATCCTGTCC TGCAGCGGCTTGCTCGGTGATTTTCAGCACCTCGCTGGAGGGAGGCGTCG GGGAGCTGACCTGGTAGACAAATCCCAAACCGGACCCAGGACCTAAGCTG CTGCCACTGGGAGTACCTGCGGCAGTGGACGTGGGGGAGTTGGTTAGCAG GGGCGAGTAATGGTTCTGTGGCGTGGAGCTGCCACTGGACGGCGAGGTGG TGTTCGTGTTGGTGCTGGTGCTGTGGTTGTGCTGGCCCACCAGCGAGCCG CAAGCGACGGTGGAGTCGATCGACGGATGCGAGTGAAGTGACGAGGCCGT CGAGGATATGGAATGGGAGCGTGTGGCAGTGGCTGAGTGGTGATTCTGCT GCGATTGATGATGCTGCTGCTGCTGCTGGAGGAGCTGATGAGAGCCGGTG GAGTCGTTGGAATGCTGGGAGCTGGTCGAGTCAATGGAGCTCTGCTGCTG CAGAGGCGGCGTAGAGGGCTTCTGCTGCTGATTGGTCTGCTTCAAAGCGG CCATGGTGGCCAGCTCCGACATGTTCACATAGGTGGGCGGCGTCTGGGGC TGCTGATTTTGCTGCTGCTGCTGCTGCTGTGCATGATGCGCTGCGGACAG CTCTGTGTGCGGATGATGTTAGCAAGGACATGCGGGTGGACACGGTTATT AGTAAGACTGATGGGATTAGCCAAAGGCAAGCGTGCACACAAATACACGG AGACAAGCTGGGCAATTGCTGGTCATGGCGCACCACCTACCTTTCGTGAT ATGAGCCGGAATCGGCGAGGGGCACTGGCGCTGCAGCAGGTTATTCCCGC TACCCTGGCGGTGGTTACTCTGGGCCGAAAGGGGTCGCTCCAACGACGAG CAGCGCTGAAAAGTGGGTAAGTCCATTGGTTAGTCACGGTGCAAATCGAA ATGTTTTGGGTTTAATGATGAGGCGACTTAAAGGTCCTAGTTGTCAGTGG TCTAGCGGGGCGCATGCAGATGAGCGCGCTGTCGGATCTACGATTGGTGG GGCTCTGACTCTGGAATACTCACCACATGGGCTGGCTTCTATGGCGAGTG TCATGGCCAACAGAACGAGAGAGACAACTTAATAGAATGTACAAAATCAA TAGACGGTTTACCGCCTATTCGAATAGCCTCCATCTATAACATCGCCTAC AGTTAATATCTAAAGACTAACTCAAATATATTTGCCAAACGCAAAAAACC ATAAATAATGTTTTTGAAATCTTGGATTTGTTGGATCTGTTGGATTTTTT TTAATGCAACTCTATCTTTAATTTAATTTAAGTTATTAATTTTAGTTGGT CTTTGATTGTCCAAGTGCGTTTTCTCTGCTTTATGACCAGAGAAAAGCTT AAACAGACAAGAATTTGTCTCATTTTGTAATGTACTATACATATTGTCGT AATAACCAATTAAAAGTAGTTTAAATATTTTATTTTATTTTTATAACTAA TTAGTTATTTTATAACTAATCCATACTTACAACTGGCAAAGGAGGCCGGC TAAGTGAGGCAGCCGGTGATTTCTGGGTGGCCGGAGTGGCTTGTCCGGAT AACGGCTGTCCATTCGGGGCTGCTGTTCCGTTGTTCAGGCAGCTGCCCGA CTCGTGAATGGTCTCCGGGTTTTGGAACGTGTAGACGGTCAGCGGCGGAC GCTGGTGACCCTTTTCGTATGCCGTCGAAATCGTGTGCGGACGGTCAGCG GTCGGTGGCAGGGTGTCGACGCCATCCTGGGAATGTGGGGGCCAGGTGGA GACATTTGCCGTCTGGTTCGTTGCATTCGAAGTCTGCGAGGAATCAGCAG AGTAGTTAGTAAAATCAGGGCAGTCAAAGATTTCGCGGAGAAGTATTTGT AATTTGGTCAAATTTAACAGAAGAAAATTAAATGAAAACCTGTGTTGTTA AAGCTGGCGATGAGCAAAAGCCACTATCACTGGATTCACCAGGTTTCAAG CGAATTGCGGGCGTTACAAACTAAAAAAAAAACAAAAACGAAACACAAAA GAACATTGATGAAAACCAAGAAATGAGCGGACGCCACAATGCCGAATGCG GGTTTGATGGTGACCAGGCAACTAGGAAACCCTCTGGCATGACGCACCTG CGAAAGGGAGCGCGGATAGTGATGGTGACCGGGCGAGTTGCTCGAGCCGC TGCTGTTCATACTGCTGATGGAGCAGACGGAGCTCTTTCGGGAACCCAGC GAGTTGGAGCAGCCGCCGCCCTGCGAGCCGGAACCGCCACCCGGGGACTC CGGGTACAGATTAATGCTGGCCTTAGCGTCATGGATAAGCTCCTCGGAGG CCTGGGGCAGAACACTAGGCTCCTTGGTTACTAGGGCAATTGACTGCATG GCTTCCTGTAAAATTTATACTATTAATAGTAACTGAGCTGACAATGCATA CACCGCTCTACGCACCTGTAGGTGACCCAACTCTGACATGACCTCGCACT CCTCGTGCACCACTGGCTGAAGCATGTGGACGAAGCTGCAGTAGCGCAGA CGCTCCTCCACCATGGCCGCCCTCAAGGATTTCTTCTCGACTTCCTCCAA TTCTGCCCGGCGCAGGGTAACATCCTGCATGTGCGAGTCCATCAGGGACT GCAATCCGTCCGTCTGACCCTTGCGCGCCTTCTTCTGCAGGCGCAGTGTG TCGCTGGAACGCTTCTTCAGTTCACTGCGACAGCGCTTATACTCTTTGGC ATGGTCTTTGTCGATGGTGGCCACCGTGCGCTTCCAGTCCTCGATCCTCT CCTGCAGCGGCTGCACCAGGCAATCCATAATGGTGCTGGTGAAGGTCTTC AGACGCGTCTCCACCGCCTTGTGGCGGAGGCAAACGCGGGTTAGGGCGGT GCCGATCTCCTTCGAGGCGCCTGCAATCGAAGGAATACGAATTATCATTT TAGATCAAAGATTCCATTGGAAACTATATTCTTTGACTGTGGATGATTTC CCACAGCCAAACTTCGCGAAATGTTAAAATCCAATGTTTTATTCAAAAAG TTGTCATGTGTGTATTAGACGTAGCTTATGTGAGGCACTAGGTTCCACTT TCCAATTGTTTCGCCATCGAATGCCTAGAACTTGTATGTTTCGTAACCCA AATTTAGTTGCGACTAAAAAACAGTACGATCAGGCAAGTAAGCATGCAAT ATTAAACAGTTGCCAAATTAAATTACTGGAGGGGAACCATCCACGGGCCA CGAGGAATTAAACTGGCAGCGGAAATGTTTAGAGCATGCAGCAACCATCG CACGCCATGGGCTGTCGTTTCAATTTGGTGGCGCAGCAGACAGCATTGCA TGCGACACGAATCGGGACTCCATTCCTCCAGTCTGTGGTCCCGACTCCCA AGTCCCAAGTCCCAAGTCCCGTGTGTTAATGCCATGCCACAGATAGAATC AAAGGCGGATCCGGGACAACTGGTCAGGCCAACAGCTACTGCTCTTGCCT CTGCTTCTGCGTCTGCATATCACGAGCAAATGACAGGCGGTCCGATTATC TCGGACTGCCTCCGACTCAAAGACTGACTTTTGCCATTCTCGTTTAATGT GTAATTATCTACCAAATAGGCAGCAGCTTATGCATTCTCCTTTGACATGC CGGTTCTCTGAGGCACTTGCTCCAAATCCCAAATAATTGAATGGATATGA GCTGAGTGCCCAGAAACACCACCACCTTGACGACCCATCAAAATGACCGT GTGCCAAGTGCGAATCGAGAATCTACAACCGAGGCTCGAGTTGCGTTCCA CCCTCGTTTGGGGCGTCACTATAGGCGAACTGACACTTGTGCCGATGCTT GACCGAACTAAGTCAAGTAACCACTAAAACTAATGAAACCATTTAGCAAG TGCAAACGACCAGGCCAGCAGGCTTCTGGTGTCCAAAAGGGGTGGCTAGC CCTCAATGGCAGGAATTACGAGGATGTGCACTTAACACCAGCCACACACC AAAGCCATGGAGTAGCGTTAAGAGTATCAAGTACCCATGGCGGGAGTGGA TCAATATATGCTAATGCCAAGCTACGTGTGCGGATGATTGAAGAGTTAAG TCTGCCAATCCAGCAGCAGTGCTAAATCGGAATTCAGAAGCTTAACTGAA TAAAGCCGGTTTGCCGTACAAATCTCATCTACAGTTTTATCAATCAACAG CAAATACGTATAAAGCACTTAATTTATTGTTATTTCCAACTGGAATACGA AGGAAATTAGCCGTGGATAATTACTTTATGCCCCGAATTGAATTATTAAA CGGGCATTTACTACATAAATACTTTTTTTTAACTAGCTTTTACAATAACA CATCAGCACGAAAGCCTAAAAATTCACAAAAAATGCTTTTAAATGCGATA GTAAATATATTATTAAATGTATCATCTCCTCAATAGAAATGTTTTAATCG CACGACTAACTAGTATTTTTAGATTGCATGCTTATGAATATAACTATTTC ATTGGTTAACGAATAACGAATACGGAATAGTAATTAGGTGTTACTTTGTT ACCACCACATCCTACAAGCCTATTCCCTAGTTTCAGTCCGTATATCCGCG TTAAGACCTCGTTGGAATTGAGTAAGGATTTGGAACATCAATAAATTCAT GATAATTGAATAATGTCAATGTAACAGCCACATCTTTAAGCTTGAGCGAC TTCCCCAAAGCGGCGATTGGTAACGATCACAGCTCTCCCATCTGGTAATT TTCGCATTTCCCGTGCGGACTGAGGTGGGCTGTGAGAAACGGACGTCGGA CGTTGCATAATCGGGCACTCGATAAATAAATATAAATAGCAGAACCAGCG AAATGCGTGAGCTCAGACAGAACAGCAACATCGCCAGTCGGACGCAGAGA AGGGGAAAATCAACAACGTAAACACCGAAAGCATGAATGTGTATAAAAAT CAGATCGATGACCGCCGCCGACTGCGCGTAGACCCATGAATAATGAGCAG CGGAAAGCTATGATGCAGTACCTGGGCGGGGGAATGGAGGGGAATCCCCT GTACTTTCAGTAGCGGCTGATAGGCGAGCAGACCAGACGAGTCCGCGGTT TGAACTTACCTCTTGAGTTGGTCGCCGCATCGGCTATCTTTTGGAAGGCA TCCAAATAGGCGGCGATTGCCTGGATGGCGGCCCTGTGAAGAGATGAGAG CAAATACAACATCATTATTATTGTGGGACCCAGCCAGATAGATTTAATAA ACATTCTCTCCAATTGCCCGTGGGCGACATTTCAATTAGGCGAAAGCTAA AAAAAAAACACATGGAATATCCACAGTCTCTGCAGTAACTAAATATTTGA ATACCCTTTCCGATGAAATATGCTAAGAAGTAGTAGGTTCTCATACGATT GGAACCATAGTAAGTGATAAGCTAGTTTAACAAGCGCTGATTGAACTAAT TGCACCTGCTCCGCTTTTGGCGTAATATACCCACATCTAGGGTATACAAA AGTGGTGCCCATCTGGGCGTCTTGATCCGGGCGTCCTCACCTAGCGGGGA ATCGGTCAAGATGTGTGTCAAGCGCAGTGGGCAAGCACTCGGAGCGAGTT TTGGCAAGCCCCGTGATTTGAACTCGGACAACAGGATTTGGGGTAGTGAT TAATGCAGCCGCTATTTGGCGGCGGCTATATACTTATGCCCAGACATTGC CGCGAGAAAATTTGGGCCAAGTCTGAGCATAAAAAGCACAGAGAAAATAA AACAAACAAATGCCACCCCACGAGCAGAAATTTAGCAACAGCAGAAAGAG CACAAAAATAATCATAGACACATTATATGTTTTACGACTGAGTGTGAGGA AGTGGAAAGCATAAGGGCAAGCATTTAGGCAAACAAATTTGTTTATTTAC ACGCAGTTCTCGTTCTAAAGTTTTGCAACTGCGCTCGTTAGTGGGCTGCT GTTGAAATATCATTTTCCAGAATGGAGCAACCAATTCACACCCAAAGTAA ACTCACCTCAAACAAGTGTGCAGTTTTCCGGCCTTAGCCACAAAATCCTC CCACAGGGGCGAAGTGTTCTGCAACAAAAAAAGAGAGTAAATTAGTTTAA CAATTGTATAAAATATTTTTGTTCCATTATATTGGGACTTGGGAACGAGT CGTAGGTTTTACAGCCATAATTAATTAATCAAAATTTAAACGAAACTAAA AAAATGCAACTTACTATAGATGTAGATGACAAAAGTGAAAAATTTTCCAT TTAAGATAAAATATATAAAATACATTTAAAGGCGTGATTGCCCAAAAGTT CAAAGTTCATATCGTCATCGTTTTTTCGCTGGATTAAATCTAATTGAGTT TGACTTTTGTTGTCTGCGCATTTCATTAAATGCGAATAAAGCAGAAAATT ATGGTGCAAACTCAACGAGCAAACAACCCAAACATGACATCAACGAATAA GCAAAGTGAGAGACACATTTAATGTAATCAAAGTGGGTGAGCTCCGATCC ATATGGCTCCGATTGAATACGGAATCGAGCAATCCCCTAGGGGAGATGCT TTTAATTAAGTTGCTGAGGTAATCTGGATTAATCAAATTTGCATATTAAT AAGACTTCTAGTAAAAGAGCGAGAGTACAAGTCCAAAAGAAAGTCGTCAT CATCATTATAATACAAGATGGATTGATTGGACTTTTATGAACATGGGGAA GTTTCGTCAATAATCCACAAGTTCTCCCCTCAATAATCACTGGAAGCTCA TATTTGGCCAAAAAGCGAACTGAAATGGCTCCCACATGGGTTTTTCTCAC ACAATCCTGTTCAGCCAACTTACTTATTTGGTCAAGACCACAAAGAGCTG CCGCTGGCTTCTGGCCAAGTATCAGTGTCACGATGGCCGAACGGCAGCAG ATTGTTAAGAGGCAGCCGTAAAAGGCCGCCAAAGACTTTATGTGTGCTTC TTTCTTTAAGAGAAATAATAGCGAGTGAGGACGCGCAAATGGTCAATAAA AGCGAAAACGAGTTTTCGTTTTGTTTTGTTTTGGCTCGCTTCAATTACAC AACATATGACATTGAAAATAAGAGCCAGACGAGCGAAGCAGCCAAAGATC GAAAGCAGCAGGAGGCGTCTGAATGAAGACATAAAATGTTCCCATTTGGT GACCACTGTGATAACAGGAGCAGATTCATCAAGCCCAAATAGCAACTGCC AATTGCAGTTGCATTTAACTTTCGGTTTTTGCGCAATCGGGCAGTAATAA ATACCATTAAAATGTCAATTGCTAAATCAAAATCGATTTCAATGCAAAAT GCCCAAAAGAAGCCTGAGCTCTGGGCCATGGCAATTGCATAAACAGCACT GCTCAAAGGTAAACGAACGAACGAGACAATGGCAGCGGAAAAGCCGGGAA ATGCGCAAATAAATGCAACAGCTCAAGCAAAAACTTAACGGAAATCGATT TTTGGCTATTTTTGCCAGCTTTTATTTATTTATTTTTTTTTTTTGTTCAT ATACTCGTTTTGCCATGCAACCACTGGGTGCAACAAAAACCCTAAACAAT TGCCAGCTCCACAAAAACGAATTGAACGCGGTATTCAAGCGATGATAACG ACTTCTTTCCCCCTTTCACAAAACACCACATGCGACATGAAATAAATAAT AAATTGGGTTTGAAAAAGTATGTTCGAAACTATTGTATTGGGAATTCGTT CGTTTCAAGTTAAGGCAAAAATACAAATACTATTGATAATAACACTTTAA GTACTTTTCTCGTGATATCACCATCGTATAGATTTAAATAAATTCAAAGA ATGTGATGTGTGGGATGATAGAGAAATCGAGGAAAATCAATAAATATCCA AGAAAAATCGCGACAGAATAAATTCCAAAAAGACCAAAAGCGACCAAAAT TTTTCAAAGCCTATAAGCTGATTTTTTCAATGATTGAACCACGTTTCCAA GACGCGGCCCACATGCAAATTATTATTGTTTATTTGTTGCAAAACCATTT TTTGTGTGCGACAGCCGACCGCCAGCGACAGCTTGATAAGCGGTTCTTGC CTCGCATGCGTGGGCAGCGTCTTGTCGGCGTTTTGTGAATGAGCATTTTG TAGTCGTGGAGCGATATAGCCACCACCAATAAGCCAGCCATCCACTCGCG GGCCAAAACACGCGAAGCTGTCATTACGTTGACCAGGCCCAAACCATTCG CGTCCGCGTTGGCGTGGATGTTGTGTTTCGTGCTAGCGTTGGGAGAGAGC TCAGCTGGTCCTGATCCCAGTGTTCGGGCATCGCCTTATGAATGGGCGAG TGGAGCTGGATTGCCTAGCAGCCAGACGCATAGTAAAAGTGCCGCAGCTA ACAAAACCCCTTTTCAACTTAATTTCAAGATCCATTTAGTTAGCTACTGA AATTGTTAAATGTTTGTCTTAGCGGTGGTTTGAATGCATTTACTTTTTAT TCATTGTCCTCATATTTCTAGAGTATTTACTGTTTACTGTTTAGTAACCA GTCATCGAGCTGAAAGATCTCGTTCCCGCCAGTTCGTGGTTGTATTCAAA ACACTTTCCAGTTTCCGTCAGACATCGAAATCGAGTCTAAGCGCAGGGGA AGACAGCGAGTGCAATGGACGTGGTGCATCCATGCACATATAGTACACCA CAACCGCTCCATGTGTATCCATTTATCTTGGCAAGCCAACTCGGCCGGGA AGTGAGCTAGACACCTAAAAACCCACAATTTATGCCAGTCAGAGCAAACT GGAAAAGTTCACACAACCACCACGAGGAGACCCACACCCATGCACACAAC ACACAGCTAACAACAAACGTGTGGCTGGCATTATAAACTCTTGATCTTTC CAATAGCCTACAAAGGCTGCCCACACGGACCGGCTCTCCAGCTGGTTCAC AGCCCCATTCATGCTGCAATTTTGTTGCTATTTCGGTGCTGCTCCTCGAT AAGGCCCCAAAGATTCCCAGCAGCGGCTAGGTGGATAGAGGCGGAGATGG CCAAAAAAAACGGGTTCAGAGCCATGCCGTCGCCACGTCCTACATTGCCA GCTTTTTGGGTTGGCGAACAAAGCCACTGCCTCCAGAAAGAGCCGTTTCT TATGCTAAATCCAAGAGCCTGCCTGCGAAGCAGAAGTCCGCACTGATTGA TTTTCTATGAGGTCCGACGTACCATATACTATATAGTATAGTGAGTGCCC GCGGCCATAATTTCGGCTTTGGCCAGATGTTGACTTTACCGGATTGCCCG GAGCGGCCTGCACAATCGTGCGCTGCTAATTTGCACCTAAAGACGGTCTT TGTTTCTGGCTCTTCGGTTTAGAAAGTAGAAAATTATTCGCCGGGAATAT GAAATGAAAGTGTTCCGAGGCTTACCTCCCTGCCGTTTAAAAGTTTTCGC AAATCTGTAAGAAACATTTTCCGTGAATTGGCAAGAGCTTTGCAAATTGA CAAATCGATTGCTGCGATTTGAATCGATCGGAACTTATGCCAATCATCAT CGGGTAATCCAATAACCGACAATTGTATTTGCATATTCCCCATCCAGCAA CGGCAGTCATGACCCCAAAAAAATGCAGTCAGTATACGGTTCTCCTTTGT CTGCACGTCGTTACCCGAGAAGGTACTTGCCACACGCAGCTAGCCGATAT GGAAACCGCAACTTGAACTCAAGTTGCCGTCAACGCGTGCCACCAACCAC AAAACAAAACGAATCAAGAAGTTAACTGATTGGGGATATGGAAGGTAAAA CAAGCCCCTAAAGTTATGAGATCTGTTAAAACACGATGCAATGTTTAAAT TGTTATTGAATGTAGGAATTAAGAACACTATGTTTAATATTATACAATAT TGAAAAAAAAAATACACATTCAACAAAATAGTCTATTGTTCCAACTACTG CAACTTTAGTGGTTCTCCTATGATCTCCAAACAAATTGGGTTTGGGCGCG GTATATTCCTCTCATCTAGTGCGTTAAACAATATGACAAGTTTATGACGT CCTCTAAGAAGAGGTCCACGAAAATTCTCAAATTTTAGTATGAGATCGAA GGGCTCGTGTACCAGAACGGTCTGTAAGAAATCAGAATATTTTCAAAATA TTGTGCAATAAAAAATGGTAGTGTCCTTTGCACACAACCATATGAATAAT CTGCATCCCATATGAGAACTATTCCCATATGCTATTATATTCCACCGTAT TTGGTTGTCAAATTGCTTGAACTCCACTTACATCAGGCCCTCTGAAGCAC TTCTTTTCCACCTCATGGCGATTGGTTATAAACCTTGTCCAATACTTATA CCAATACTGGTTCTTGTCGTACATGATGGAGCAAAAGTTCTGGGTGGCCA TGCTAAAGACAGTGGGCTCCCAAGTGCCGCGGTTGAAGTGAAAAACATCA AGTCTCGCCTACACGGATGCAAGAGTTTTGATATTAGAATCGATGATTAT TCCGAAGCTTGCAGTTTGTGTTACAGTAATCCGATCGGTGGGCTGCACAT CCCACACGACGGTGGCGTTCCCGGATACATGAAGTATATCCCCTTTCTGG TCGATTACAATGTCGTCTAAGTTGAGTGCCTGGCGGATGTTGATGGATCC GGGAGGACCATCAGTGCACGTCGAAAATATGTCCGGATCCTCGAGCAATA ATTCATAGTCTGTGGCCCAGGAACTGGTCACTCCTAATAAGAGTAGCAGC ACAAATATCATGATGACCATAGAACCGAAAACTGTGAGATCCGACCCCTT TATAGCCACTGCCACAATAGAGTTTTTGATATGTTTTATTTATACACCTT TTAAAATGATGACATCTAATCATGGTATGCCATCGTACATTGATTCAACA CGCAACAATGTAACAACCATCTCCTGTTAATCAGACGTTGTCAAACTCTA ACAATATAATTGGCAAATCACGTTATGTGACCCTTGAAAATATTCGTGCT TAAACATTGTAAAACAAGATGTTTTAATAATAATAACTTTTGGGCTAGAA AAAAAAACAAGTTTGAAACAAAAAACAAATTCCCCAAAGATTTTCTTGGC GATCACATATCCGTGTGGGCGTGACAGTTTTGGGCGGTTTTTGGTCGTTA GAGGGTGTGGTAGAGTAGGCGTGGCAATCTTCTGAAAGTACTTCTCTATA ATCTGCATCCCTTATCTTATCAATATAGCTTTTATAGCTCCCGAGATCAC ATACGGGCATAAGGTTGATCAAACGAAAAAAAAGGTTCGCGTCACCTGTT ACACACTTTGTACCAAATCAAGTACATATATCAAGTTCAGAATAGTTGAT ATATTTTATTTATATTTATATTTTTAAGATTGCTTTTTATTTTCAAAATA TGTAGATATTGGGTTTATATTGTTTTTTAGGTTACTGATATCGCGCCTTG AACAGATTAAGCCCTTAATTAATTTATCTTCTCGGCCTCTCCCCTGATTT CGAAGCAAATGGAATTACGGCGTGGCACATCCTTCTCATCGACCGCCTCA AAGGTGACCACAGCTTTGTAACGACCCCTGAGAGTTGCACCACGAATGTC CGTTAGACGCAGCTGCAGATCGAATGGATTGTGCATTATAACGGTCTGTA ATGGAATCCCAAGGTTAAAGTCACCGCGCCAGAGATGGACTGTTTTGTTT GCAGGGAAAACTCACACCACGCGTTTTAAAACACTTCTCCATCACCTCAT CGCGGTTCGAAATGTGTTTGGTCCAGTACTTAAACCACGACTGATTCTCA TCAAACATTGAGGCGCAGAAGTCCGGCGTGGCCATGCTAAATACAGTCGG TTCCCAGCTGCCGCGGTTGTAATGCATTATTGCAAACCTGGCCTTAAAAG CAATTGTTTATTAATAATCTTATTTCGTATAAGGAATGCGGGCATTACGG ATATGCGATCTGTGGGCTCCACATCCCAGATTGAGGTGACACTCTCGGAC AGGTGAATGATGTCCATGTCCTGGTCGACTACCAGATCGCCAATATCGAA GGCATCGTGGAATCCAATCGATCCCGGCGGCGGTTCAGTGCAGGGTGAAA AGATATCAGGGTCCTCCAGCAACAGCTCGTAGTCTGCGGCCCAGGAACTA GCAAAGCCAAATACGAACAGCATGAGAGTTCTCATGATGACAATAGTATC ACCTGGTGGGATGAGACCCTTTTATAGTACTTGCCATCATGATCTCTTCT ATCATTGCTATCATGTCATCATGTATCCACTCGACATGCAACAAAGTTAC AACCATTTTGTTTGCCAGACATTATTTTAAATCGACATTTAAAGCAAGAA GCTCACTTCAACCATAACAAGTTTCGAGGAAATCAGTGCCAATGAAAATA GTCCTTATTAAACGATCAAAACAATCATTCCTGTTAATCTTATATTTATT AAGATATATAAGCTAAATACTAAAGGTTTTAGCCATTAGCATAACAACTT GTATGCCAAATAGGCATTTAGATTGTTATACTTGTAAAAGTATAACCTTT TGTTCTTCTTGAATTCAATGCTAAAATCTTTGTAGGCTCCTTGATTAAAT TAAATTTTTACTTTTTTCATCGAAAATTAAACGATTTCATAAATTCCGTA ACTATTTTGCATAATTGGGTGCGACAACTACACACCTACAACAAGTCAAA TGGACACTTTCCGCAATTTAATCACAGCTTGTGAATCACAAGTGCAATTT CATATTCATTTTAATTAACTAGCCTTGGATTGCTGTTGAAGCTGACATCA TACATGCAGAGCACTCGGCACAGTTCAAAACACCAAGTAAGCTATGCACA TCAGTCGTTCCACATTAACAGAGGGAACAGCATCTAGAATTGTTCCCGCA AAGTTATTTATGGAATAATGCAAAGTAATTAATACAACTAAGATGATTCT CATGCTCTCCAATTGTTTGTGGAGTCTGAAGGGGAAATGCATTCCGCATT CTTGTCTGATCTCAGATTTCACTGTCTCCATGTGGGAGGAAGCAGGCATA TGGAACGGGTTGCAATGGTGACCTGCGTCAAGATCTAAACAAAAAATGAT TTGTATATTTTATCCATTTTTTCCGAACATAGCAGCTAGACATAACAATT GTACACATTAACACAATTGTTTTCAAAGCTTAAGGACCTTGCTCCACATA TGAACTGAATGATGGCATCCTGTCCACATCCTGTTCGGTGCCACAGTGAA CTGCCACTTCCAGTTGAGATTCAGCCTTGAAATGGCTTTCAGACTTTTCA AACGCGCCAACGCTAGAGGGACAGGGGGAAGCTCACGGGGCATTGTTATA GAAATGGAAACAGCTGCGAGTGCTGCCATAAATAAAAACTTATTAGGTCT TGTCGATGGTATTTCACTATATAGTAACTCGTCTATAAATAAACAAAACA TAGAAATTGACTTTCGTCTTATAGCCCACGCAACCCCAGGCGTAAGCCAA ACGCACAGAATCGAAAAGTTCAATGAAAGCAATTAGTGAACATTTTTAAT AAAACTATTTTCTAAATATAAAAAAGAAAATTCGCCCAACGTGGGGCTCG AACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGC CGGGCACTTGTGAAGATCGCCGATAAAAGCTCACATTTGCTGATTAAGCT TAAGAATCATACAAATTGATATAAAGAGAATTTAAAGGATCAAAATATTA CCAAGAGAGAATCAATAGCCTTTTAAAAGTAGCCAAAGAATTGTCGCCAA TTAGCTTGCAACAAATAAGTTTAGGCCCAAATTTACTTTACATAAATTAC ATTGACAATATAGAATATTTATCGTAAATATTCAACTCATAACAAAACAA GAGAAAATGTTTTAGTCTAGTTTCCCGACTATCAGATACCCGTTACTCAG CTAGTGGCAATGTCAACTAGAAATTTCCTTATTTTTTCTGGCTTATCGAT TGATATTGGGGAATAATATGAGAAAAACATAAGAAAATGGTCGCAAACGC TTCCTTCTGCCTGGTACATACTTTTTAACGAATATAGTATAAGCAAAGAC CCTAGAATTCTAGTGTTATTATAGTAAATTCTAGTTATTCTAGTGTCTTT GGTATACGGGTATAAAAATTATAAATTACTTCTATAAACACATTGCTAAA TATGAGAAAGCATATTTATACATGCGCATATAAGCCGGATTAAAGGCAAC GGGCGCTTTGCTGTCAAACCTAGAAACATTGTTGTAATACCTTTAGCCTT TTGTTTTATTCGAAATGGTTATGCAGATTCACAAGATGCATTTGTATCAT ATATACACAAACTATTTTTAGCTTCCAAATTAATTGGGACTCATTTTAGG CAAATTAAATATGCTTAATAATTTTCCAATTAGTAAAAAATCAATTGCCG AAAGTGGAGCTCAAAAAATGTTTATTAATTGTATATTAATTTTGAATTAA AATAAAAAACATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTA AGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCATGTGTTCTTGACAT CTGACTGTCAAAATCATCGAAATCGTAATAGTTTTAAATTTAAACTTATA CTATAAGCTTAAAGAATAATGGTGGTATAAAAACCCTGTGGTGCTAAAAA CAAGACGAAAGCGTATTGACTAGTCCCTCGCCCATCTAGTCAAGTTTAAA GCCCATTTGCATTTAGATAAAGATCAAGCCAGCTTATCCTTACATGCATT TTTATCTACCTATTTAAAAATAATTCTATTCAGCAGGTTTTGACAAGATA AATAAATTGTAATTTATAGATAAATTGATTTATAAAAAATCATAAACCAT AATAAATCATTTATATAATTATATGTACATGAGCACATCGGCTTTAAGCC TAATTAGTTAAGTAAAGGATATGTGATAGTCGAGAGTCTCGACATAATGG GTTTCCTCTGGTAATCAATTAACTATTAAAATTTGTATATTTACTACAAA ATATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAG TCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACAAAATTGCCGT CTGTCAAAACTCGGGAAAATATATCAAATGGGGTTAGGAACTATAGACAT GCGTCTAGTATTTTGTTTAGAAATGAAAAACAAGATAGAATTCTAAAGTC GTGTTCCCTGACTATCAGATACCCGTTTCTCAGCTAGTGTGAATGCGAAC GCGAAATTTCATAATTTTTCTGGGATATTGATAGATATAGAAAAATTGGA AAGGTTTAGAACGTTAGAGTGGACGTGGCAAAAAGTTTTTTTTTAGCAAA TCTATAGAAATTTAAGCAACTAATAACATTATGAAAAAATGTCCAACAAT TTTTCAAATATATGTGGGCGCAGCCGATTTTGGCGGTTTTAGGGCGTTAC AGTGAGCGTGGCAGCATGGGTCAACAAAATTGCCCTGCGTCTTTGTCTCA AGTCTCTAGAATCTGTATGCTGAATCTCAACCTTCTAGCTTTTATAGATC TCGACGCTCATACGGACAGACGGGCATGGCTAGATCGACTAGGCTATTGA TCCTGATTAAGAATATGTCTACTTTATATAGTCGCAAACGCTTCCTCATG CCTGTTACATACTCCTCAACCAATTTAATTTACGAGTAACGGGTATAAAA ATCATTTTTATATATAATTACATCCATCCATGTTCGCATATGCTTTAAGC CTAATTAGTTAATTAAAAGATATCCGATAGTCGAGAGTCTCGACAATTGA TTTTCTCTGGTAATCAATTAACTATTAAAATTTGAATATTTACTACAAAA TATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGT CTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAATGAATTTGCTGTC TGCCAAAACTCCGGAAAATATATGGGGTAAATGGGGTTATGAACTTGACA TTCGTCTAATATTTAGTTTAGAAAAACAGTCACGCGAATTTTTAATCGAA CATACTTATTTTCGTGCCAAAAGAGATACGCCCTTTTTAAATTATTAAAG ACAATGATTTTATCATATCATAATCATATTATACTGTGTGCAATTAGAAT CATAGACGACCCCTAAGCTGTATATAACGTGCAGTTTTTAGCACTATGTA CCCATCCTCATACTGGAAAGCTTGTTAATATGAAGGCTACTTTTACAATC CTGGTGCTCCAAGTGGTCATCTGTTTGGCTGGAGCGACTGAGTACCAGTT AACATTGGACAAAGATGGCTTGTTAGCACCATGCGAGAATCAGCCCGGAA ATCCTTCTGGTTTTGAAGCGATGGTGGATACTTCCTCCCTTAAAGTACAT AACCTTGGTTCGAAAGTTCGAATTGAAGGAGAGCAGAAAGTGGTCTGGAA AGATGTCCAGCCTGGAGACACATTAAAGGCAAGTCCCTAAGGAAACTTTT CCTAATAAACTATTTGAATATCGCGCAGGTATTTGGTCAAGTCTATCGCC TGGATAAGGGCACTTGGCAGAAGACTATGTTTACGGCCAGCTCCAATAAC TTTTGCAAAAACATGTTTGATAAGAACCAATACTGGTATAATTTCTGGAC AAAGTATATTAGCAACTCCGACGAGATTAAGGAAAAGTGCTTGACCACAC CAGGGGTAAGAAAATGTACCTCCTAGTTTGGTCACTGGTCATTTCTCATA AACACAATATTGTAGGCCGTTTTAAAGTACAAAGACTACGAACTGGACTT GAAGACCAGCTTGAATGTTCCGAATCTGGATGGGCGCTACAAGCTGGTGG TCCAAATAGAGGCCTTCGATAAGCGCAATGTAAGGCGCCCAGTTCCCATT TGCATAGAGTTCCGTGGAACTGCAGGACAGGTCTAATCACGACAATTGTA TATGCATGCTGAACATACAGCGAAACACCATTAAAGTCTATAATTGGAGC ACATCAAACAAGGTGAATAATGGTGGTGAGGGGGGGGAGGGTGTGGTGTT GTTGTGTGTCATTACACGGGTCGCTAAAGTTGAATGCGAACTTCTGAACT TCTGTTCAGTTCATCATGGAATCCAAAATGAGTCGGCCGAAGCAACCGGA CTGGCTCGCCGAGCTGTGCCAGGAGTCCTCCATCCACGGCATGCCCTACA TCGCCCGCAGGGATCTACACTGGGCCGAGCGCCTCTTTTGGACATTCATA ATCCTGGGCTCGGCCTACTACGCCATCAGCAGCTGCCTTAACCAATGGTA CCGGTTCCGGGACAATCCTATTGTCTACGAGTACGAATATCTCTTTGGGC TGCGCATCTTCCCCTTCGTGGGGATAACACTGTGCCCTAGGTACCACGAC GAAACGGAGATCCCAAGGCTTATAAATCAGTGAGTGTTTCGATTTACATT GGTAAATTGAAAGCACTAATATATTATAAAATATCAAGAACTTGGGGAGT GGATCCCAGCGAAGACAAAGAAAAAGCTGTGTACTACAGAAAGTTTCTGC TTGCAATCAACGGCCTTCGTTACTCCACTCTGGAGACGCTGGAACCCTTC GAGAATGATACCACTTTGGACAACGTGAATTACTTGAACATTTTGCTCAC GCTGCAAAAAAAGGTAATAGCGGTTAAAATCCCGCCAGAACTGGCGCCAA TCATTACTGAGGTGGGTCTGTGCCAAACATCCAGCCAGTTAAACCGATAC GGAAATCCCTACGGCAAACTGTAAGTCTGCGCCTAAATAACATTAAATAT AAAACAAAAAAAATAAATTATTAAATAATAAAATAAATAAGCTATTCTTT CTTTAATTTCGCTTTTTGCTTTACATATTTTTTGTGCCCATCAAGAGAAT TTACATTTACATTTTTACTTAACGCTTTTATCTAAGAGAAACACAGGATA TGGAACCCATGAAACAGTGCGGCTATTTGAGTAATTGCATCACATCTCTG AAGCCTATAAATAGCATTGTTGCCCCCATATTTATGGTAGGCAGCATTTA TCATTCTTTTTTGAAATACACTGTTAAGCGAATCCAACTTTACAGTACCT TCACGATGTCGAAGAAATGATGCTACCCGACGACATGCGAACTCCCTCTT TTGATGCTAAAGACATCGAATCCAAGGATCTCGATATTATGCTACATACC ACATCGGCGGAAAGCGAGGTGCGAAATCTACCGGTAGCATATCGCAAGTG TCGCTTCAGTGACGAAAACAATCTGCAGTATTACAGTGTGAGTTTTAGAC CTTTACCCGTACCAATTGCGTCCAATCAAAACAGCAACATGTCCTTTTAG CCCTACCACCCAAGTCTTTGCCGACTTGAGTGCCGAATCAAATGGGCCCT GAGCCTGTGCAACTGCAAGCCCTATTTCTACGTAGCAGCTCCCGAAGTTC CAATCTGCACAGTATCCGGAATGCTCTGCCTAGCCCGGTCCAAGTGGCTT GAAAGACCATGCGATTGCTATCCGTCTTGTCGCGAGGAAACCTTTACCAT CTTCAAAGTGTCTGACCAGACTGGGGTGGGTGAAAGAATGTTGTATCCTT AAGCCCCCAATTATTGCAATTTAGAATTTACTTTCTTCAGGGCGATGACA ACTACTCTGGCGAGAGGTTCGAGCGGACGCTGATCATCAACCTGCAAATT TCGAGGATGGGCATAAATCGGCGGGTTGTATTCAGCACGGATCAGTTGAT AATGTCGTTTGGTGGAGCCATTGGCCTCTTTCTTGGAGCCAGCTTCATGA CCATATACGGCGTGGTATACTTTTTTCTAACTTTCATAGCTTATACATGC AAGAACCGATTTTGCAAGCGTTTTTTTTTTTAAGTAATTAAAATTGCTTC TTAATATATACATATATATGTAGGTAATGCAAATATATACATATAAGTTA AGAACCCTCTTCTTGCGCTCTTCGTCAGGACTCACCAGCGCTCGGCTCTC GTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCTGTCTAGTAACATG TTCGTGTAAGTTACGAACCCTCTTCTTGCGATCTTCGTCAGGACTCACCA GCGCTCGGCTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCT GTCTAGGAACATGTTTGTGTATGTGTGCATTCGGAACAAGTGCCGTTGGT CGCACTCAGGGTGAGGGGTCAACGGGGGAAGCGGATATAAAAGCAGCGGG GCGGGAGAAGAGGTCCCAGTCTCGAACGGACACATAACGGAACCGCTAGC AGATCGCGAACTGAATCTTAAAATAAAGCTAATCGTAAACTCGAACCCTC TTAACTATCTTGACTATTATTTGGAGAACCACAGCATGTTGGTTGTCATA TCAAGGTGAGGTATGCGGCAGCGAGTGCCGAGAACCCTGATGCAAGTGGA ACTTGCGTTAACTGGCGCCCGAACAGGGACCGGCAATGTCCGGCCGATAA AAGTGATACGAAAAAATTGTGGAAATTTGTGCGTAAAAATAGTGGTGGTG TGCATAAGTCAGATTAAGATCTGAAATCCATAAATGAAAAAGAAGTGCTG CGTGAGCTGTGTATAAAATGATAAAATAGCAATTACCCGCTGCCGGGGGG AACTACGCCCATCCCGGGGCGCAACAAATATTGCATAATTCAATAAAAGG TGTAAAATTTCTAAAATAAAAATGTAAACCTATGTTGCGCCAAGACCTAA TTTAAATTAATAAAACAACGACCCGCTACCGGAGGACGCCACGTCGCCCA TGCCGAGCGCAAAAGTTGTACGATACCTATAACATAATTAAAACACGATC AACCCACTGCGGCGGTACGGCTTGTGGGAAAATTTTTTTTTTTTTCTCTC CTTGCCAATTCGCGAGTGCAAAAGATTGTGTATAATAAACCAATAATTAA CCATTGCAGCAGTTTACCTGCGGCAGTACGAGTAATATGAGCGCCCAGAG TGATAAGGTGGTGTGTGGCAGCTTGTTGGATACGTTAAGTGGTGTGGAAT GCACCCAAAAAAAACCGCCCAACAAGTTGTGTGGCGGCCGTACCTTAGTA GGCAACCAGCCAAAAGGGATACTACGGAACCACCGTGCCCAGTGCCGAAA TAAATTAGAGGTCATCAATAAAAAACTGTAACAGCACGCACGCAAGGAAA AAATATTGCAAAATGGAATAGCGCACAAAAATTGTATAAACACATGCACA ACACCACAATTCAAAGGAAAACAAAATATTCATGCTGTAGGGGTACAACC TAAACGACGAAAACTAATAAAGAGCATACAAGGGTGAGTGAAATATTTCA TTAAACTTTATTGCCATATTTGCTAAATTTAGAGAAATAAAGAAAAAGCA AAGAAGAACAGATATTCTTTTTTATCGGGTTAAAACCGTTGTCTCACATT TCCGTAAAGTAATAACGAATTCTGTTGCCTTGAAAGCTTCCTGCATCTTT CCAACGCAAACTAAAAATCAAAATGGAAGAGACCCTGCGTGCTCTTAGCG AGTCCCTCAATGCCCTGACCAACGTGGTGACAGGCATTAAGGAAGATATT AAGAAAAATAATGATAGGTTGGCTATTTTAGAACAGGAGCGCGGGAACGC TGACCCTACGGTCGACCAACCGCAACCCCTGGTGCGCGCACGCACCGAGT ATGAGCTGAGAGAGATATCGGTCCTCCCTGACTGCGTCAAAGAACTGCAG GCGTTCGAAGGACGGCAGGAGGCTTACCTGTCTTGGATAAACAGGGCACA GTCAATACTGACCGAATATGACTTGATTAAAACCAGACCCCTGTATAGGG CAATTGTCTTGCATATTAGACAGAAAATAAGGGGACACGCCGACATGGCC TTGGCGGCCTATGGCGTCCAAGACGACGATTGGGACGACATAAAACGAGT CTTGGCGCTGCATTACGCAGACAAACGAGACTTACGTACGCTTGAGCATG AGCTTGGCGCTATGTGCCAAGGTTCTAGACCACTAGATAGGTTCTATATG GACGTTAATGGCCATCTCTCGTTGATCTTAAATAACTTGAAGGCCAGAAA CCACCCTCGTGAAGTAGTCAACGCTTTGATAGAAACCTATAGAGACAAGG CTTTGGATGTTTTTATCCGAGGAGTGGGGAGAGATTGTTCCAAACACTTA CTTGTCCGCAGCCCGAAGAATCTACCAGAGGCTTACTCTTTTTGTATGGG ATTGCAGAATGTAATGTCAAGAAATTTCACAGCTCAGAACTATCAACCGT CAGGTGCCCCAAGATTCGCAGGCCCATATCAACATCAGGCCAGGCCACCG TTCCGAACCCCTTTTTCTCCTGGTTCAGGCAGATTTTCGCAAAACTCCTA CAGAACTCAGGGTCCTAGACAGGCCATAAAAATGGAATCCAATCGGTCGG GTCAATCTTACCAATCAGGATACAGTGGTCGCCAGGAAGAAGGCTCCGGT ATTAAGAGAATGTCCGAAGGAAACAACCCATTCCAAAAGGCACAAAGATT GTACCACATGGAATTGGCACCACCCCCGCTAGCCCCGGCGGCTAGTGGAG ATAACCAAGGACGTTCACACGAGGGTTACTATGATGACGAGTCTCAAGCT GTCGAGAGAAGCAACAATTATCCTCCGCAGAAAAACGTGGAAGGAGTTAC AGATGCTCCACATAACCTTGAGACTGAGGGAGGGGCAAATTTTATGACCA ACGCCTCTCCAGTGTACCGTACTTAGAGTATGCTACGGAGAGGGGAGAAA GGCTGAAGTTTTTGATCGACACGGGGGCGAACAAAAACTTTATTAGCCGA AGACTTGCAGCCGGGTGTACCACAGTCCGTAAACCCTTCTCCGTACTGTC CGCTGCGGGTAACATCATGATAACGCACCGCCTAGTTGGTAAATTCTTCA AACCACTAGGGAACGACTCGGATATTACCTTTTTCGTACTACCGAATTTA CATTCCTTTGATGGTATCATTGGCGACGATACTCTCAAAGACTTAAAAGC CATAGTGGATAGGAAAAACAATTGTTTGATAATAACCCCAGGAATTAAAA TCCCTCTTTTGGCGAGAGCTTCAATAAACGTTAACCCGCTACTCGCCGCC GAACACCCAGATGGTACACAAGAAATTTTGAATTCCCTTCTCGGGGAATT TCCCCGCATCTTCGAGCCCCCCTTATCTGGAATGTCCGTGGAGACGGCCG TCAAGGCTGAAATCCGGACAAACACACAAGACCCGATCTATGCTAAAAGT TATCCTTACCCAGTCAACATGCGCGGAGAAGTCGAACGTCAAATCGATGA ACTGCTGCAGGACGGTATAATTCGACCCTCTAATAGCCCTTACAATTCCC CTATCTGGATAGTCCCGAAGAAACCTAAACCAAACGGAGAAAAACAATAT CGCATGGTAGTCGATTTCAAGCGGTTAAATACCGTCACCATACCCGACAC TTACCCCATCCCAGATATAAACGCTACGCTAGCCAGCCTTGGCAATGCCA AATACTTTACCACCCTAGATTTGACTTCTGGATTCCATCAAATCCACATG AAGGAAAGCGACATTCCAAAGACAGCTTTCTCTACTCTAAATGGAAAGTA CGAGTTCCTCCGTCTACCATTCGGTTTGAAGAATGCACCTGCAATCTTCC AAAGAATGATCGATGATATTTTGCGCGAGCATATTGGCAAGGTCTGCTAC GTTTATATTGACGATATCATCGTCTTCAGTGAAGATTATGACACACACTG GAAAAATCTCCGATTGGTATTAGCGAGTTTATCAAAAGCTAACCTCCAAG TGAACCTTGAGAAGTCGCATTTTTTAGACACGCAGGTAGAATTTTTAGGA TATATCGTCACGGCCGATGGCATTAAGGCAGATCCGAAAAAGGTCAGAGC GATTAGCGAAATGCCTCCTCCGACCTCTGTTAAGGAGTTAAAAAGATTTC TAGGCATGACCTCGTACTACAGGAAGTTCATTCAGGACTATGCGAAGGTA GCAAAGCCCCTTACAAACTTGACGCGTGGATTGTACGCTAATATAAAGTC TTCACAATCAAGCAAAGTGCCAATTACATTAGACGAGACGGCCCTACAGT CTTTTAATGATTTAAAATCAATTCTCTGTTCTTCTGAAATACTGGCGTTC CCATGTTTCACTAAACCTTTCCATCTAACCACGGACGCTTCTAACTGGGC CATCGGAGCTGTCCTCTCACAGGACGACCAGGGTAGAGATAGGCCGATAG CGTACATTTCCCGTTCATTAAATAAGACGGAGGAAAACTACGCTACTATC GAAAAGGAAATGCTCGCGATAATTTGGTCATTGGACAATCTTCGGGCTTA CTTATATGGCGCTGGTACTATTAAAGTATATACTGACCATCAACCTCTAA CGTTTGCCCTAGGCAACAGAAATTTCAATGCGAAGCTAAAACGCTGGAAG GCTCGTATAGAGGAATACAACTGCGAACTCATCTACAAGCCTGGGAAATC TAATGTGGTGGCTGACGCGCTTTCACGCATTCCGCCTCAGCTTAACCAGT TGAGCACCGATTTAGATGCTAATCCCGAGGATGACATGCAGTCTTTGGCT ACTGCCCATAGCGCTTTACATGACAGTTCACGATTGATTCCCCACGTTGA ATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGT CAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATT CCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTG TCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGC AACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGG ATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGA AATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTC GTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATC CGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAG ACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCAT GTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTA AGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTC AAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTACATTACT TCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTGTTATGC CCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTATTATGC TCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCCACTCTA CGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACCTTCAAA CCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCA CTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAA GGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGAC ATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAA TAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTG TTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAA AAGGTACAGGAAGACAACAAGATAACAGTTAAAACCAGATCAGGAAAAAT TTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAA AAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGC TAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAATAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAGTTAAGAAATA CAAAAAGAAATACAAAAAAAACTATAAAAAAAATAATATAAAAAAATACA GATTATAAGAAATAAGAAATAAGAAATATAAAAAAATAAAAATATAAGTA CACAAAATGTACCGTACCCCCACACACTACGTAGTCTTAGAACAACTTAG ACGACCAGATATTTACGAATTGTCTTTTTGTAAGCGCGATTTCTGCATGC GGCGCAAATCCCGCTCACTGGACTGGCTGGGGTCGGCTTGGAAATGGGTA GCTGGATCTCCAGATGCTGCTGATTGGAACGCCGTCTTGGCCGCGCAAGC GACGGCTTCGAGGAACTGCAAAAACTGGAGGAGGCTAGCTGTATCCCTCG GCTACTGAAGTAACCAACGAGTGGTTAAGCAAGTCGACGATGGAATGCTC CTCCTGACCAACTTCAACGGAACTCTAAGAACGGCTGCAGAGAACTACGA CCTGATCGGCTCCTTTATCATCCAATTCGACAATGAGACGATAATGGTCA ACGGTCAAAACTATTCCAGTTACTCGGTCAGTCATCTAATGGCGATGCCG GCCGTGTTGAGCCACATAACGGCCAGCAACTTTCAACTTTCTCTGGAATA CGTCCACGACGTGAGCATGAAGAATTTGGAAAAGATGTCCAACATGGCGA GTGAGCTACTAGCCTCTCTTCTCACCGAGGCGGCACTCGCAATCTGCATA TTCCTAGGCTTTTATTTCCTATGGAAGAAGCTGATGTCCACCAAAGGCAT GCCCGATGTCCGCGAGATTGCCGCAAACTTAGAAGCATTGGGCCAAACCG AGCTGAACAAGGCTCACTAATCTGCGGGACGCAGATCTTGAGGGGGGAGG AGTTAAGAACCCTCTTCTTGCGCTCTTCGTCAGGACTCACCAGCGCTCGG CTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCTGTCTAGTA ACATGTTCGTGTAAGTTACGAACCCTCTTCTTGCGATCTTCGTCAGGACT CACCAGCGCTCGGCTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGG GGCCTGTCTAGGAACATGTTTGTGTATGTGTGCATTCGGAACAAGTGCCG TTGGTCGCACTCAGGGTGAGGGGTCAACGGGGGAAGCGGATATAAAAGCA GCGGGGCGGGAGAAGAGGTCCCAGTCTCGAACGGACACATAACGGAACCG CTAGCAGATCGCGAACTGAATCTTAAAATAAAGCTAATCGTAAACTCGAA CCCTCTTAACTATCTTGACTATTATTTGGAGAACCACAGCATGTTGGTTG TCATATCAAGGTGAGGTATGCGGCAGCGAGTGCCGAGAACCCTGATGCAA GTGGAACTTGCGTTAACTTATATACTGAACAGTTTTGAAAAGTTATTAAG TAACAAATAATCAATATCAAATTATCCCTTTTGATGTAAATTAAAATATA CAAATGCTGAATGGGGGCTTTTATGATTTTAGTAACATACAGAGAAACGA CGGATAAAGGCTTTGTTAATCGTAGGGAAAAATTATGTTAATTGTACTTT TGGGGTTATATTGTTATATTTTAAATTGTGAAACTCTCAAGGGTATTAAA CTGCGGCTTGCGAAAGCAAAACCCATCCTCACTACATTTATTTCAATGTT AATATATCGTTGTTAAGGAAATCATAATATTTTTAAGTGATCAATAAAAA GCACCACACATAAAACATATATAATAAACAATACAATAAACATATAAACT AAACTGGAACATGAAGTAAGACCAGTATATCCACTGAGCGCACATTATTA TGCAAATAAAATGAAATTGTTTTAAACTTAACGACACCAGAATGGTTTGA TGTTCCGGCCGGGCATCGTAAGCAAATTAAAGTCTCGGCAATTGTTGCAG GGCCACTGGGAGGAAGCCTCAAAAGTGAAGAAAGCGACACGTTCAGTTCG GTTCAGCTGGGTTCAGAGAGCAGAAAAATTTCACTTTTGCGGAAAACTCA TAACGAACAGTGTAGTGCGTTTTTCCAACGTCTTCGGTTACCATCCGATG ATAGCGCAGCTGAGATTTCCTTTGTGAAATGTGACAATTTGTCTGCTTAT CCGGCGATTACTCGCCGTGCGATGAGGTTGTTCAGCTTGGCATCTCCATC TCCATCCCACACACTCGCCACACTTGCTCCAAAATGCAGCCAACGGAGCG AAGCGGTTGGGTAAAGTTAACAACCTTTAGGTTTGCTCAATTGTTCGTTT TTCGATTCGCCTTCCACATGCGTGAATAAACTTTGGAGCGTCTAAGCCAA GCGCGAATTAGCCGCATTTAGTTGCCGGCTATCTGCGGGTTTCCCGTTAG GAAAAACAATTTCAGAAATGAAATTAGCAAATAATGTAAGACTTTACGCT TATTGAAGTTGCGGCAGCCTCAAAGAAGTTTCTGTTTCTGCCTTGGCATG GGCATACATTTGTTCTGGTCTGTTGCCAAAAAATAAGAATGGTAATGGTA GAAAAACCAAACCAAAGTCAGACGGAGAGGCAGCCAAGCAATTAAAACGA AACTAATTTTAGTGCCTGTGTGTGCAGTAGCACAGCCTTCTGCCTTTCGG CTTACTACTATAACCTTTTAGCAAACACAGGGGCTAAATGCTGTCCGCTC TCTCCGGTCCGGCGGCTCATTTGCATCTGCTACAACTTTGTGACATTTGC AATGGCATTTGCTGGCTTAGCAAAAATTAGCCAGCGGATCTGCCCACAAA GCTACAGCGCCTGCTACGGCAGTCTCTTGCCATGAATCAGGCCAAAATCA GAGCACGGCGGCAAGGCAGCAAGAATTACATGGTAAGGTGATCCGAGCAC AGACGAATGTATGTGGCCATGTAGCCAGCCATTCATATTGCACATGCTGC GGCGTTACGAGTATGTACATATGTGTGTGTTTCTGCTCTAGTTCACACTC AGGTTGGAAAACACACAGAAAAAGAGCAGCAACTTCTTCTGCACAATTGC GTGCCGAACAATTTCCAAATTTCATAAATACAAAATGCACTCGCCCGCAT CTGACAGCAGTCTGCAGAAGCCTCCAAAGTTCGGCTCACACTCCCCGAGG GAAGTCGCCCTGCATTCTCCTATTGTCCTATTAATAGCGAGCCGCGGGCG GGACGGCGGTGCGATTCATCTCTCCCCTGCCCCTTCTTCAATAGTTTAAT TTATTTCGGTACTATGCCCGCCGACAGACCCAAGACACAGCGAATGAATT CCAACACCTGTCCGTCCGTCCATGCGACTGAGGCGACTGCGAGCAGCTGG CGGGAGAACTACAATCACAATGTGCTGAAAATGTAATTTTCCCCGGCATA GCAAATGAGGCATAAGCGACGAGGGTTTTAAAATCACAAACTAAGAATGC GCTGGCAGTCAAGGGAAATAAGTAATAGCTAAAGTCAAAAATTCTTTTAA AGTCTTTAAGATATGACTCAATAGTCAAGTGATAGAACACTGATAGTTTC AACTCATTTGTGATTAAAATGTTTAAATAGGCCCGAACAGTACTCAAGTT CGTAATCGAAGTGAGATGGAAGTGCCTTAAATTCGTCACTTTATTTTAAT TCCTGCCTTTAAGTAACTTGTCATAGATAGCTCTCTTTAGTCATATAACA TCCTATGACATCATTTTGCATTTGGATATCCCTTTCCATTGATTCTCTGC CAAGAGGCTTAGCCGGCGATAAAGATTTGCCCACTTCGAGACACCGAACG CTCAGCGTTAATTTACGCTTGTTAAATGAAATTGCCTGGCTCGCCGTTAT ATAAGCGCAATAAACATTTTGTTTGAAAGTAAGTTGCCACAAATGGCGTC ATGGGTGCCATAAATTATTGATACCACACACTGGCCAGATAGCAATGAAA TCAATTAATGATAAATAAAATCAACAAAAAGTTCGCGGAGTAAATTTTCG TGTTTCGCCACGGGCTGTTGATAAATGCGAAAAATGCGAAGTGTTTTTGT GTGACTTTCATGGATTCTATTTTGCAGTTTCAATGCTTGCCATTTAATCA ATTAGAAGAGATACGAGAACGAAGCAGTTTTTGTTTCAAATTAGAGGAAG TACGCATTGTGCAGAAAACATTTATTTTGCATTAATCTATAGCTTTGGAA TCATATTGCTCTGTGCTTTGCTGTTCACATTTCTTCATCTCTATCTGCTT GAGACTTTTATTTACACACGAGAGAATTTCATACCAATACTGTGAGTTCT TGACACACTGACAAGCAATTGAGACAATCGTATGGTCGAAACAATTTCAG CATTATGTGGCTTTTCTGTTAAATAAACACTGACCCTGTGTTCACGTATA TACATACGTACATATACTTATGTATATGCTTCCCCAAAATGCTTCAAAGT TCCAGGAAGCCGAATACGAAAACGGAACATTCAGTTTCGGGGTTCGTGTT TAAAATTACACTGCATTTCCGCAGAAACTGTAGAATAACACGTGAAAAAC TCACCTTCATGTCATTGATAATCTGCTGAAATAGACTACCCAGCGCGGAG CTATCGCGTTCCAGACTTAGATCCATGTTTCTTAGTGTTAGCTGGTTTGG TAGGGATGGATATCGATTGGTTTCGTTCGTCGTTCAATTGCTCGGTATCA GTTTACTTGGATGACTTTTACTTTTGATTATTTATTTTCCTCATTATATT CTTGTGTTGCTTGTTGTGATCTGAAAAGAGGGGAACGTAATTATTTATAA ATAACCATGCTTTACGAACCGACTTGGACACACTTCCGATCGAAATCTGT CTTATCCCGCGTAAATCTCTGAGATTCGTCGCACCAAACGACTCTCGTAA ATAATCAGAGATGTAAACTAGCGTCTTTCCAAACAAGAAATTATGCTTAA TTAGGCTTATTAATATACGACTTGGCGATGGAGAGTGGGAGTTCCCTTGA TGGCGTAGGCGCAGTATAAAACTTTATTTGGGGATCGTTGACCCAAATTG AGAGCGCGTTAAGTGCGTGAGTGTGGGGCTCCTGCTGATATGACTCTTTG ATTTATTGTTTATGCAGCGGGGCTAATAGCTAATTATTAATTGATAATTG ATATGTCTTCCAGCGAAGTACAGGAAGTGGCATACGCAATTTACACAATT TACGGGCCTTGCAATCGAAACTCCGGACCTGAGACCCATGTAAACGACTC TCGAAGGGGGGAAGTGCAATAGTGCAATAGTTTTGACCCATTTGTGGGTT CGCCATACGTGACTAATTCTATGGCGCTTTCGAAAGTGCAGATAAGTCGA GAAATCTAACGCCAGCCAGCCTTGGAAGCAATTAGAGGCGTTTAATGTAC AGCTACTTCCATTCGAGCAATAACCTTCGACCGGGCGGCACTGGCCAAAG CGCGGCTCGGATCTTAAGTCGGCTTTTAAGGCCGTATCTCTTCAAGTCAG TTCTTTTTGGGCTGATTGCGAGGGAAGTTATTCGGATACAAGTGCTTGTT CGTCTCATTGTGCGTCTGTCTGTGCAACTCTGTTGCACTCAGAAAGCGTT CACAATAGACACTCAAGCGTGGAGGAAGCACAGTGATAAACAGACGCAAC AACGAGAGCTGATTGCCCAGACTGCGTATCTTTCGTCTATGTCTGCGTGA AGACGCAGAAGAAAGCATCAAAGTGCTAGTTCGCCGGAAAAGAAGGAAAG CGAAAAAGTTTGCCGACTAAGAGATTACTAGTAGTGGAATAACTGCATTC GGAAAATGAGGAGAACAAACTTCTCTCTATATATGTATGTATGCAAACCT TCAACCACAAAGCGAAAACATAAGAAAAATCGTTGCAATCATAGATACGT CTATATTTGCATTTGCTAATTTAACTGAATACGTACTTAAAATCGAGCAA TGATCGTAGTACAAAGTTTATTGAATGTAATAATCATTGATATGGAAATT AAAGTATCAAAATATACATGTTTAAGACAATCCAAAGGTCGATTGATCTG AATAGCGAATCTACATGGTTTAAATAGACAAATAAAATCGATTTATCTAG TCATCCTCCTAAAATTGTTACTTTGGTGTTCATTTAAGATAGATGCCCTA TAAGAAAAGGGTATCAAGATGGTTCATACGAAACTTGCAGCAAAACAAAC TGACGCACATTCTTACAAACATCGTGGAAGTACAAGTAGACTTTCTGCTG CCTCTCTTTTTGTTCGCTAGCTTCTTTTTAGCTGAATAGTGTAAATGACC TCTCGAGATAAAATTGTGGTTACAACGCAAACGATGACAGGCCGGCTTTG TTGTCGCTGTTGTTGGTGTTGTTGATGTTGTTGGTGTTGCTGGTGTTGTT GGGGCTGTTGGTATTGTTGGTGTTGCAGTTTCCTTTGCAGTGCGGAAATA ACTTGTTGTTGTTTTCGGCAATTGAGTGCGTTAAATCTGGTTTAAGATGC ATATATGTATATACACGAAACATTGACCCAGTTAACTGGCTGCATTTAAA TCATAAGCCCAAACTGGTTGGACAAGTAGTGCATGCTTATATTGGGTCTA CGAGACTTCTGCGGCGGAAATAGGAGCTTTTCTCAGCACAGCGATGAACT CGCGATTGTGGGCTTGGGAAATTCGCAGAGAGCATGGGCCATACAACCAG CCTAAGGTCAGGCCTGCAGATCGTGATGCGATCGGGAAATCTGTTTCGGC GGCAGTAGCCAAAGTCCAAATTGCCAAATCGTGAAGAAAAAAACAAAAAC AAAAACAAAAGCAGGAAAACGACAATTTCGCAAAGTAGCCCCAGAAGAAG AGCAAAACCTTTTTCCAAGCCTCAAAACGGTGGAAAATGGGCCATATTGT GTAAGGGGCACGTTGTGGAAGGCAACCCGCATAAAAACTCGCTCAAATGT CAAGATGAGAATGATGACGCAGTGGCGTTGTTCCTGCGACTGATGATTAT GCTGGATGCGTTTTAGTTTCAAATACGCATATTTTCCGCCCTATTTACTG CCGTTCTCTTTGCGGCTCTGTATCTGCGGTTTCTCCGAGATTTGTGTATT GAAACAAACGGAAGCTGCTTTGGTTGAAATGGGCAGGAAGTTGGAGGGCA CCAGCCAGGGAATACTCATTTTCGTTTGCTTCACAGCAGAAGGTCAGACC ATAATATTAATGTGTTTAATATCAAATCATAAAGAAACGAAAGATGGATG TATCTGTGGACATTTTGCCCAAAAATGACATAGCCACTATTTAGATAGGC TAAAAACAATAGCACTAAATAAATTAAATAAAAGTTACCAATTTTTTAAA TTCATTAAGATTTATCATTGGCTTCCTTCATAAATATCTGGATGTAAGTA TGGTAAACTTATAAAAAATTACATTTTATCGCTGTTTTATTGTCTTGGCC GCATCTGTACCCTGTCTGTATACCATTTATGTTGCATGTTGTCTGGATTT CTATTGCAAGAAGTGACTTGACTGACGGAAAGCAGAGAGGGGCAACTGTG GCACACACTTTTGTCAAGGGCGACAGACAGACAGAGTTGCTGCCGTTAAT TGCTTACCAAAGATGTGAGCACACGCACCGCCATTTCTGTCCCATTTGAA TTTCCCCCTTGCATACTGCGTTCTTAGGCGTAAATGCAGATGAGCAGCAT TAGGGTGGACCAACAACGTGTTGCAGCAATAACATTGGAGACTAAACCAG AACTTGGGAGTCCCCTGACGCTGTTCCGCTGTTCAGCGCATAATGACACA TTAATTCACTTTGAAACCACTTCCTCGGCTATTCTAAAAATAATTACTGA TAGCTTATGCGTAAAGATTGCATAAACAATGAACCATACGAACGATTGTA CTTTCTCGAGTTTTTCCAAGCTGAGCTGAAAGTTTCTCTAACACTCTAAG GAAATATCTCTCAGAATGGTCCATGTTGAATATGATAAATAATCAAGCAA AGAATCAAGGCCTGAAAATAGATCCAAAACTTACAATTCCCAGCCCACCA CTTTAATGCACTGCCGGATACTTTCCTATCCACTCTGCCTATAAAGTTCT GTTTTTCTTGTGCCCCATAAGTTCTGGTTGGGATTTGGTAAAACAAATAA TTTTACAGCTGCCTTTGGAGATTTGTATACTAGGAAAAGTGAAGTGCGGG TGTCGGCGAAAATCTCCAATGTCAGGCTGGCTTTTAGCGGATTTATGTGT TGTTTTATAAGTTGTAAGGTAAGCGATACATTGTGGCCGGCAAATTGTGC TGCAGCATCACCAGCGGACGGCCCGTCATGACTTTACACTTTCACCAACA ACTACTACGGGTGGTATCAACAACTTGACACCAACAACTGCGGCCATCTG TGGTCAGCCAAGTGTCGAGATGCCTCGGCCTGATCTTAGTCTGGGGGCTT GGAGTTTGGGGTCTCTCGTCTTGAGTAGGGGGTCTGGTTCCTCTATTCCG GGGTTAGGAAAGCGCCGATCATCGAATGAAATGTGTCGAGTGGTCGCGCG ATGAAAAGAAAAGCGAAAAGAACGCATAAAACGATGATAATCAAAAGATC AAGTTTTATATGAACAGAATCGACAACGTCACCAGCAGAAACTCAGAAAC ACACATCTGCTCAAACATTGATGTTTATCTATGGGTTTCTATCTTTAGCG TCATCTGTGCTTTGCACTGCATTTTCTATTTGATGTTTCTGGGATTTGTG TTTGTGAGGGCATCTGCTTTAGCTCTCTCTCCCCCCGAATGCCAACCCCC CCCCCCCCCTTCGACAACACCCACTGACGCGTATGGCACGTCATTAACCC AAATTTTCTATGAATAAAATATAGCGAAAAGGAAAACACTCAGTGTTTAT GTTTGCAAGCATGCCTTGAGAAATCTCTGTCTATTTCACTCCAAAGGCTA CTTTGATTCGAATCTAATTGAATAATTCGCGGGCTGCGCATTTAACACGC TGTAAAATAGGCCAATTCATCGATAATTGAAGCTGATAGGCATCCCACCT TCTTGATAGGCTCACCATCTAATCAGTAGCACTGTAAACACGCGTTTGTT TTGGCCACGAATGTGGAAATCGATGAGTATCGATCGGAAGTTATCAAGCG GCTGAAGCTGACCGAAGAAAATTAAATTCAGGAGAATGTGGAGCACAAAA CTCATTTCGCAATGCAAACGCCCACAAATGTGTAAACACAACGGCCCGCC CGAAATAAACTTTCGGCATTTAGCGGCGTTTAATCGATTTGTGCATAAAA TTATATGTTTACACATGGCAAGGCAGCCGAAACGAAAATAAAGTCGAGAT ACACAACATGACCCATTGGCGAAACATGGCGGTGGGTTGTTTCTTTTCCA GCGCATTTCCACTCGAAATTCAGCGGATTAGTCATTTTAATAAAAAACAC AACCACGTCTTAGGTGTAGCCTACTTTATAGATTTTCTACATAATTTAAT TCAATCGAGAAGATATTCAAGCAATTAAACACACTTCTCTATTTGATTTT CTTGTTATAAGTTTCATTTAAAGTGTGCAGGCACCTAATGTGTCAGCTAT TTTATTATTTTAAATAAAAATTAAAATAGGAAGAGCTTATTAGTATATTT CTTCACACTGAGGTAAACCGATTCACTGTTCTCGACTTCATCTCAACTCA TTAGAGAGCGGAAATTCTCGACAACTCAATGTTAAGGTGGGTAAATTTGC TTTTACTAATTTTAACAAAGGCCCGAGAACATTGTCTATTATTAACACCA CAACCACTCCCGCTCTCCTGCCGGTTTTCTGGGCGTTTTGGCCATGGCCA ATGGTTATTAATGATTAACCGGAGTGCCGTTAGCCGGCACATGTTACTCC GTACTTTGTCATGTTTGTTATGTTCTTGTTTGCTGGTTCCATCAGCACGT TTTGTTTCTGCCTTCCTCATGACAGCTTTGTGGCCATCAGCAATGGGGAT TTCTCTGCCTTTCTCCGGCCTTTCCAGTCTCGTTAGCGTGAAAAGCTTTG CCCAGCTTTTGTTTTTCTTGCATAAGAAAATGCCAGTTGCTCAGGCATCT TGGTTTTGCTAATTTCCCAGCCCCGCCATAACTCGCGGAAAAGAAACGAG AATTGAAGGAAATACGTTTTAGTGTCGCTTCTCACTTCTCGCAGAACCCT GAACCCTTGACATTTTCACCCAGGGCGGCGATAAAGTTTTATACTTTTTA ATGAGCTCCACGTTCTCTGCCAGCGCAATTCAGCCGCACGCAGCCCACCC CAAGTGAAAACCGCTTGAGGCGAAGGCGAATCTCGGGTTGGATTAGACAC GATTTTCATTAGGACGAACCCCGAAAATCGAAAGTGGTTACGAAAGATTC CACTCGAGTGGGCGATCCAGCAGTCTAGAGTCGCGGACTCATTCGAACTC AGATTCATTCAAACAACAAGGAACGCCCATGCAGTTCACCAATCAAACGA AAACGAAAATCTTTTTGTGAGTGGGCAGCGAGAAACTCGAATTGCAGCAG CGCAGCGACATGCTAAACAAATGCAGACATTCAGGCTAAGTGACTTAAAA GTTTTACAAGTTTTCAGCCGTTTTTTCTTGTTTACCAATTGAAAACAGTT GCCGCATTATAATGTAAAGAGGACGTAACAGCGGTTCCGAAAGGCGAGTA TTAAAGATATATGAATAATGTACCAATTATTTTACATTTAGTGGGAAAAA CTATTAGCGCCTTTAGAACTGAAGTGATCCAGCTAAAATACTGAATGGGG GTTTTGTGTTTACAGTAGGCTAAAGAACATTCAAAATATTACGAGTATTA ATTTTTCGAAAACCATCAATGAGAAAACATATTTGCACAACAAACAGTTA ACGTTTTTCCTTTGTTTTGGCCTTGCTCTCGTGCTTGTGAAAGAATGTTG TTGTTTCTATGCAACGGAGGTGGAGGTGGGGGTTGGTCAGTTGGAGCGGC CTTTCTCCATAGGACACAATATTTTTTTATATTCACTGGTATTTGTTTTT CTGCTTTTGTGAATTTCTGTTTGCATTTTGTTAAGGCGCAAGTGCCTGGT TTCTGTTTATATAAGCGTAGTAAGATCACCGAAAAAAGTTGCTCGTTTTC AAATTATAATATTTCACTTATTTTTATATTTTTATCATTTTAGTAAGAAG GAACATTAATTTCCTTCTCTTAGTATATCAAAATGTATGATTTTCCAATT TAGGTAAAACATTTAGGTTTCCTCCAAACGATCACGTTCGAAATACAGGT TTTTTCTCTCGGTGCAGGAGCAAGTTTCTTGCCAATGGCCGACAGCTGTT TGTGGCTAATTTTATCTTTCTTTCTGAGACCCTCTGTTGTTTTGGATTCT CTCGTTTTTGGCAATTGCACAGGTGCGGCAGTTGGATGGTTTGCGGATTG GGTTACTCCACGCGAATCAGATAGCCCAAGGCATCCTTTCGAATTTGAGT ACTACTTTGTGTCTAAGCAGCGTATAGTATATACGATATAGCGACTTGGC GAATGCACCGGCCGACATTTCAGGCCAAACGGTCTCCGTTGCTGGAAAGT TCTGCATCATTTGTTTAGACAAATGCGCGAGAAAACATTCCCGGGACGTA AACAAACCCCGGCAATAATATTTTAATAATTACGCTTATCTGCTCCATTT GACGGCGCGCACAAAAGTCGTTTGAAAGGTATGCAAAGAGAACGAGACGT GCGATAAGGGAGCCGGGAATGGGAACTCAACTTTCGAGCATTTAGTCCGC ACCATGGGTGTCAACGTGCCGCTCCGGTTCCTGTTGCGATTACGGGTTGA AAGGAACACAAAGCCGCCACCTCGCGAAAAAACGACCCATTCGGAGTCGG ACAAAAAATTAGCTTGTTCAGATAAACCGAGTTCAGGTAACACAGTCCAA AGAGAAGTCCCTGCACTTGCGCAATTACCGCGCAACTTCAAAAGGGGAGT TGTGCACAGAGAAAACTTTATGGCAGTCGAAAAATCGGAAAATCTGACTT CGCACAAATTTTGTGGACCGAAAACACTTCACAGCACTTCATTGGCACAA TTTGTCAAAAATCACTAAATGTATATTGTTTGACTTCAAGAGGTTTAATA ATTCACTAATTTATCTTACAAAAAGAATTAGTTACATGAAATTGGTTGTT GATTTTGTTATAGAAATTATTATTATTATTATGTTGCTGGCCATCAAAGA TATGTTTTCTTCAAAACAAAATTACAAATATATAAAACCTAAACATTTTT TATGAAACTCCTTTTTTTTAACGTGTATAACAAATCCTGTTTGGATTGGC CGTGAACGGAGTTTTCGGTTCTCACGACCGCCTGGAATGGTCACTGGAAG TCCTTGGACCTGGAATCGGTCCAAACTTGTTGTTGGTGAACTGCAGCTTC CATTCCCTCCCCTTACTCCATCCCCCTAGCCAACGCTCTTCGCCCCTCTC CCAACCCCAGTAATTGGCATTATTAGCCCACACTCGATTCTTTTTGTTGT TCTTGAAGGATACTTACGGTGCACTTCCGACTGTAAAATATCGCAGGGCG ACTTTATGCAGCTTGCTTGATTTTTCGGCCGACGATGTTGCAGACAATTA GGCGATGATGTTGATGCTTGCACTTCTGCGGTCACGGTGTTGTTGTTGTT CTAGCATTGCATTTCCAGGCGGCAAAAGCGCACACAAAGGATAGAAGCGG TTGTGAGTGCGAGCGGGGTGTATTCTCCCGTTATTCCCCTCTATTTCCTC TCTCTCCTTCTTACGCCCAGTTTCGTGTGCTTTGCTTTTGCATTTGCTTT TCTTTGCTTTGTTCAAACTCAAACAAACTACCCCAGAACCGTTGATCCTG ACTGCCTTGTTGTTGCTGCTGCTGCTGTTGTTGTTGTTGTTTTGTTTTCT GTTATGTTATACACTCACAGACACACGTACACACACGCACACAGTGGGCT GGCAGACAGACGCTTAATTTTCCGTTTTCCTCGGGAAATCGCAAACAATT ATTCGCTTATTTTTGCACCGAATCTGACACTTATATGCTCGCACTTCGAA CTGCACTTCCAATTGGTTCGCGCATTCCTTTTCCGGTTAGAAAACAGTTA GAAGTTTGCCGCTGCAACCGCTATTTTCGCCAAGTCTACGACTGACTTTC CGAGCGCATTTTCGTTTTCCTCCGGTGCGAAAGGGCTTTCCTATAGACAA ACAAAAAACCGTAAAACAACCGCGACCGATTCGTTCGAGAGTCGAGTGTC TGGGTCAGTGTGACCATCGCTCGAAGCTGGGAAAATACACCTCTGTAGTG TGACCACGTCTAGGAAAAATCACTTGGCAGCGAGGTCACATTCGCTGTTA ACCGTTCTGCGAATCGGGAATGTTACCTATCATGCAAACTTTTAAAATTG AAAATATGGTTATTTTTGGCGCGTTCGATGTTCCAGTTGACATAAAAGTC AATTGAATAAAAAACCAAAAATTTTGTTATAAAAATTTGAAGAGAATAAC TCATGTTTTAGAGTAGAGTTCCTAGGAAACGGAAGTGCCGAAGACATTAA CTAAGCACTCGGGCTAAATGAGTGTTAATTTGGAAAACCATGAATTCTAT AGATTGAAAACAAATTATATAAATTTAACGTCGTTTACTTTAAATAATGG CCTCTGCATTTGCTGCAAATTCACCTTTTATGCATAGAATTCTTTTTAAG AGTCCTATTTTCCGATGGTATGAAAGTGTTCGATATAACAACTAAATTAT TTATTTGTTCACGTTGTTGAGCTTGGTGCAAAAGATTATAAAAGTCATCG TCAGCATTATCACACAAGTCCACAGCTTAGGAAAATCAACGAAAAAGGTG CATATACAAATATAAAAACAACTTAAACGCTTTGTAAAGCAAACAATACA AAATATGCGATGCTCCAGCAGAGCCTCCTTTAAAGCTTGTCCACCCGTTC CACACTGAGTTTGATGTCCGACTTGGGCATCAAGAGCAGTCTCCGGTTGT CGTACTCCACGGGAATCGAGGTCTCCGCAGAGGGAGCGTATCTGTGCTGC CTCAGCAGAGCCACCAGGCCCACCAGAAGCTGCTGCTCTGCAAAGCGAGC GGCAATGCATCCTCGCAGGCCATCGCCGAAAGGCAGGAACGCAGCTGCCG GGCGGGATCGCCTTGCCTGTTCCTCAAAGCGCTCCGGGTAGAACCGCTGG GGGTTTTCATAAATGCCAGGATCCATGTGTATCGCCGCCGTTGGTATCAG CACATTGTTGCCTTTGGCAATTACAAACACCGATCCGGGCACTTCGAATT CTTTGGTAGCCCGGCGTAGCAGGAAGGGATGTGGAGTGTGCAGGCGAAGC GTTTCTAAAAAAAAGGTGAAGTCATTGGAGCTATAAAGAGCTTTTCAATA TTTGGTACTCACCATTGAGGACTTGCTTCGTATACCTGAGCTCCCTTAGG CACTCCGGTGTCACTTGGCCACCATGCTCCTCCAGTGCCTTGTTAATCTC GAGCCTGGTTCGATCTTGCACCTCAGGCTGGCGGGCCAACTCGTAGAGGC AGAATGCTAGGGTGGCATTCAGGGGGCCCAAGCCAGCCAGAACGAAGCCG AAGGCTTGGCCCGCAATCTCGATGTCGGTGAGCGGCTTTTCTGCGTTGGA ATATAGCTGCAGAAAGGTCTGGAGTGGCTGGCGATCCCTTCTTCGATGCA ACTGCAACTGCGACAGGGCCACTTTTTGGAAGTAAGCTGTAGCAGGTTCT GCGTAGCTTTTGTACTGAAGAAGGCGAGCGATGAGCGGAAACTCAAGCGC CAGATAAGCCTGCCACATCCTAAAGTCCGCCCAGTAGTTGCGCGTCCACT TAGCGAACTCCACGTTATCCTGCCCTACTAGTCCAAAGGCCATTGACGCC ATAACGTCCGTATTGTATGCACCCACGAGTTCGCTTATATTGATAGTTTG AAGGCTCTTTTCGCCCAGGTCCCTTTGAATTCTGGAGGAGATTTGCGACA GTCTGACCAGCAGCTTCTGCATGTTGGCCGGAGTGAAAACCTCTGCAGAT TTGGCGTGCAGTGACCGCCACTTGTGACCGTCCAGCTGAAGGAGATTATG CGACAGCGGCTCTCCACTGGGATTACTATAAAGGCCTCGGGACGTAAAGT GTCCCGCGTCGGTGAAGATTATTTGGTGGACTAGCTTCAGGTCCAGCGCC AAGATGAACGGCTTGAGGCAGGCGTAGAATCCCACAAACGGCGCCCTGCC CTTGTATGCGGTGTAGATATCCTGCAAGGCGTCCTGGGCATGCCTCTTCC CGCTCACCACGCCCTTAATGTTGCCCCACAGGAACTTGGGCTTTTCGTGC AGGATCCCCCGCCGTTTCCAGTAGCCCAGACTGAACTTGACCAGGGCGTA GACCACTGACAGCGCACCCAGGGCGGTGAGCAGGGTGCGGTGCATTAGAT CCATGCTCACTCAGCTGTCTTTTCCGGCTTTTACAATATGTTCGCGCTGT TTGATATGCTTAACAGCTGGCAGTAGCTGCTTGTCGAGGTTCTGGGGCTC AATGCCGCCGGTTTATCAGCGCCATTATCGTGCGGTCCGATTTAATAATT GATAAGGTCCATTGAGTATCGGCCGCTAAAATGGAAGAGAAACGTGGCTA TAAGGCAACTTTCAGTAAGTAATAGTAATCAAGAGCTGAGCGGGATTTAT TGCTAAAATAGGTACGGAGAGTTGCGACTACGGCTGCAAGATGAGGCAGA GGTTGTACGTGCTGCCGGCGAACTCGTCAACGGGCACCCAACGAACGTAG CCCAGATCGATTAAGTGCTGCCGGGAGCTGGGCACGCCTACGAAATGCGG ATCCTAAAAAGGGAAGCGAGCGATTAGTTCACCAGTTCATAAAATGAGCT AATTCGCTGACTCACCACCACCTGCAGGAAGATGCGACCGCGTGCACTGC AATGGTAGCCGGTAATAGCCTTGGAGGCGGTGTCACTCAGACCGCCCATG GCGACGAAGCCTTGGTACTTCTCAAAATAGCTCCGAAGCTCGCCGAGGAT CTCGTCCGAGCTAAGCTCCTTGGCGTGAAGAATCTTGCACGGCACCTGGT GCAGCACATCGATCACGTAGAACTCCTCGAGCGTTCCGATCCAGTCGCGC GAGCCCACGAACTCTGGACCCTTGTCGCCGATGGCCACCAGGATCTGCTG AATCTCCCGGATGGAAGGAACATGACCGCTCGACCCCTGTCGACGTTGGA TCCAGGAAATGGCCGATTGCAGGGTGCGGTAGCCACAACCCCAGCCAGCA TCCTGGTGGCCATCGCATCCGTAGTGGAAGTAGTTAAAGCCACCGCGGGT AACTAGCGTCCGCCCGCCTTCAGTGGGCGTGGTCAGCGCGCCTTGCGGAT CCTCTAGAAGTGGATATGCATAGTCCTTTGGTACAATTTTCAAGGACGCC GCGGAGGAGTCCCCAAACTCTTCTGCACACTTTTCCGCCGCCATAGGAAT TGTTTTCGAAACTGAGTAATTTGATAGCCTAGGCCTGATTCACCTGCTCC TTTTCTTTTTTGTTTATTTACCTTGGGCAGCCGTAATTTGTTTTGTGAAA GTGAAATCGCAGCAAAGAAATTGGAATGTTTTTTTTTTTGCTCTGGCTAG AGATGGTACAAGCTGAATCGTCATGCACCAATGACAAAGTCAGCCAAAAT AAAATAACAATAATGCGGAAAATAAAATTAACGAATATAAGAATGAGTCA TGATGAAAGGCTATTCCGCCCAAAATTTTGATAAAATTTATATTTTTATA TTAAGCAATGTTGTCATAATTGTTTTACTACAATTATCCATCACCAACTC TCTCATCGAATTATCGATAACAGCCCGTTTGTAGCGCCTAAATTTAAACG CATCTATTTGGTTTTCTCTTATTTCTCATGCATTTCAAATTTTATTTGAA TTATTAAATGTACATTATTGTGTTTAGAGTTCATAAATATGTTTTCGCAT TTATGTGTGTGGGTGTCTCAACGCTTTATATATTAACACCATTCCCCTTG AATTGTGTTCGTTTAATTTTTAGTTTTTGGTGACCAAACATTAGTACATC GTTTTTAATAATTGGTAAAATTTGTAGCACTCCATAAACTACGATTTGTA AAATTGAAATATTTGCATTATTGGTTTTCAACTATTTTCGGATTGCTGAT TGTTACTGAGTTGCAGTTTTGTTAATGTTTTAAAGTTAGCTTAAAAATGC ATTTTGGATAACTTCGCCGAGTTTTACAATAAATATATGGGATGCCGTTT GCAATATGTGTCTGTGCACCAATTAAAATACCTTAATTACGTCGTGCGTC TAAATGTTTTGTTATCTTCTCGTTTTTGGTTTGTGCCAGCAACGGTTTAA AAGAGGTCGATTGAAAATTATAAGTACAATCATAAAATACATTTATTAAA TATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATC ATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTAT ACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTC CTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTC TAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAA CTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTAC AGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTC TCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAA AACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTG CAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAAT TGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAAT CTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACAC AGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTT CAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGG ATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGA GAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGC GCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTT CTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGG CCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGG GCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCA CAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCA TGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAG CTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTC GGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGT AGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACG CCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGT CTTGTTCTTCAGCAACTCCAGTGCGAGTTTCTCTGGAAAAGCAGATGTTG TTAGAGATGCGGATCGCGTGCGGTTGTTGCCACTACTCACCCTGTCCGTC GACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGT GTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACC GCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAG AGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCA CCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGG CTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAG ATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCG TGGTGTACAAATAGTGCATTGAGTCATCTAGAACAATAGTACAATAATTA GTTTTGAAATGGAACAAGTTGAAGAATTTGTCGACAACATTCTAATTCAT ATGATCCGAAACTTACCACCAGTAAGGATTAATACGATGAGTTCGCAGGC GAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACT TTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATA AGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACAT CTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGA TATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATA CTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATT GGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACT CCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGC AAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGAT GGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGA GTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCC CGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTG TCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCT TGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCC TTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGC CAGCTCGTGCTTATCGAAAAGTTTGGGGTCCTTCGTCGCCGAGATCTCGC AGAGCAAGTTGGTCGTGTTCGCCGGACTGACACTGGTCGTCTTCAGCTTT TCAATCAAATCGTCGATTTCAGCTGCTTAAGGCGGTAAGAAAAGAACATT GGTTAGTTAGGGCACTTGAACAACATAAAGGGTCATCTTATTGTTTTGGC AACTAAATGTTTCCCTGGTCATTGGAATAAAGTTTGGTGATGATGAGTAA CGTGAGTGAGTAAGTAAGAAAAGAAACCATCAATTATAAGTCAAGTTATG AGTGGTTGTATTACATATCCAGCTCCCATTTAAAGTGTTCTTAGTTTTTA ACTATTTAAATACTATTGTATTTATTTAGGGTATTTTATGTATACTTTTT CGTTCCATTTGACGGAGCACGCAATCCACCTTTCCCTTCCTGCACCGACC AAGTTGAGAACCGCAAAATTGATTGCCAATTTCGATTATCGTCGCTGACT GGACGAAGTCAAGACAAATGCTTTCAAAGCAAGAAGTTATGGCTTTACGG CCTGGCACAAAAGAACTTTCTTTCTCCTTCAGGAATAGAAAGCTTTTTTG TGTTTTTGCATCTCCAGTTCGAACCGTTTTTGATCCATTGGAAACGTTCG AGAAAACTCGTGAAGCGTGTGCCACATTAAAGCTTCATTTGGCCCCAAAA AAACAGATGGCTCGGATTATAAAAGGACCCAGGATGGGCGACGATTTACA TAAGTCCTGGTCATGGACAAATGAAAAGGAAAACGGAAAAACAATCGGGA TTTAATGTATTGTAATGATGAAGGTTTAGGTTCACTTATTCAGCATAAAT GCTTCGGAATTCAGCTTTTCAGGGGAGTTATCTTAAATGTTAGTGGGTAT GAGTTGGTTCTAAAATGATAAAACTTGTTATTATTAAGCAACGTTATACA ATTTTAATGATAGTACCCAAGCCAGAGATAATACAACTTTTGTGTTGAAT TTAAATTGTATATATTCGATATTAAGCCAGTACGAATAGAGCCCTTTTGT GACCAACATTATCACAATATTATTATTTCAGTCAGACCTTTTCTGCCGAC AAGCACACACGCTGGAAAATACATTCCGATGTGGCACTCCAGCAGGACGA GGGCCAAAGGACGAAGGGCAAGGACCAGACTCCGGCGCTCGACAACTGGC GACAGTTGGTGGCAACAGCAACAGCAAGGTTGTGGACTGGGGTCGCAATT CAACAAACTTTGTGGAGCATAAATAATGAATAAGTAAAACAAAAAGCAAA GTGAACCCTTCAGCCGGGCGGGCAACCATCGTCATCATCATCAACATCAT CCAACGTAGGCAACATCCACGATTTGGCATAGAAACAGCAACAAAGGACG CAACAGCAGCAGCAGAAGCAGCCTGCACAACAGCTCACTAACTCGCAGAC AAGTTGCACTTAGAAATGTAACCCCAACTAAAGAGAACATAAGTGTATAG GCTGAATTCGAGGGTACCGACTATAAGATACCCTAGTGCTGAAGCAACAA AACATCACAAATTGTACGTCAGATTGTACAACAACATAATAGAATACGGG TTCAACTTCTGCATCCGTTTGTAACGACTTTAAGATACACCATCTGATAT CGAACTCTCTTTATTATAACTAGCTGTTTAGTGTTACTCTTGAGTAGTGT GTTTTCCAATGGTTAAAGGATTTAAATACAAAAGAATCATGCCTCCGAGT TCTTTTCTGTTTGGGTAAATAATAATTAAGAATAATAATAAGATATAGGT AAATTATGAACTCAAGTCTGTTTCAAACTATCTTATTCCGAATGAAAACT TTACTAGGTATTTCAGCTATTTCCGTGCAGACAGACATACAATTAGGAGT CCAATATACCCTTTAAATCGAAACGCAGCCAGTGGAAATGTGCATATGTA TTGCGGGATGCATCTGCATATTCAGGTAAAAAGGGGAATTGTTGTATTTG TTTGTCCGACGCAGCTGACTGAATGCAATTGGACAGGTGGCAGAGACGCG TCGCATCGCCCGCCCGGCGGAGTGGCAGGTTGACAGGGATGAGGAATGCA GGAGGACGACAGGTGCTGTGGCAGTGGCAGTGGCAATAGTAGCGTCACTT CCGTCTGACAGAAGGTGGCCCAGACCAGCTCCGTAATGCGTCTCGGTTGC TGCTTCGCCGCCTTTTGCGTGCCTCCGAATGTTTGCTTTGGTAACTGGTA CTCGTTGGTATTCAGAGTATGCCACTCGTCCATCCAGCCATCAACCCATC CATCCAGCCATCAATCCATCCATCCATACATTCCGTTCGAGTTCCGTGGC AAGTTCGTTAGCTCTTCGTTGCGGAAGCGGGATTCGTTCGAGGCATTTAT TCGCCTGAATTTCTGGGGCAATGGCTTCATTTTATTTTCGTGTTTCCTTT TTTCTGGGCATGATTGGGGCCTATGGCCTGCGTTTTATTTCCACTCCGTT GTGGTATTTTATTTTCTCCATTACGCGATTCACCAACTTTGGCCACGTAC AAAAATAGCAAATAGCAAACGGCACAGAAATCACAAAAAAACTAGTGCAA ACTTATTGTTGTTGCATGCTTAATTCATGTGCAACTGGCGACGCTAATGT CGGTTTTAGTTGTATTTTAGCTTTTTGGGCCCTGTTGCCAAGTGAAAAAT TCGGGAAAAGTGGGTTAAGTTGGAGGCAGAGGCATGGCACAGAAAATGGC AGCCATGGGAACGAACCTTATAATTCAAACGAAATGATTCCTTTTGCATG GATAACTAGGTGATGTAAGTGAAAAGGTATAATTCATGATCCACTCGAGT TATGATAAATTGAAAAAAATGGAAGCTTGCAAAGTAAAAGTGAGCCCACT TTTGCGGGGCTCTTAAATATACCAAACCACAATGTACAATACAATAAACC ATATAATATAAGGATTGCGTATTTTTAAAACTACTCTTTATTTACACCGT GCACTAATCCCTACATCTATCAATAGAAAAGTACAGAGTATCAGACTGGC ACGTCCTGATTCAAAGACTCGTTCTCGAGCAACAGTCGACTGTGACCAGA CTTTCCCAGCTGGAGCAACGCCTGGCAAGCGGGAGTGGACATCTGGCTGA CATGCTGGAGCAACTTCTGGTCGTTGTTTCCCTGCCTCGCCCTGAGAAAC AGATTATCCCCTGGAATCAGAAGTAATTTGAAGTGCCTGGTACTGGACAA AGTTTAATAGTTCTCACTCCAACTCCGCTCTTGCCTGCACTTATGTTTGA GGTCCGAGATGTAAACCTCCTCGATTTCTACTTCCAGTTCGGCCAACTGC TGTTCTGTGTACTTGGACAGAGTCGTCGGATTCATGTAGTAGGCAATGTG GTTCGTCCGACTGAGCCGTCGAGCGCTGTGGGTTCTGGAGAAGATTGGGC CTGTATACGCCAGTCTCAGCATCCGAGTGAGTCTAGAACTCACCTGGTTA GCGTAAAACTGTAAGCAGGAGCGCCTGCGATGAAGTGCATGGTGACGAAG AGAAAAACCAGAGCAGCCACCACTCCGATGACGAGTTGCTGTGTTTGGTA GAGTGACTGCCTCTGGGGCATCCGCTGATTGGCCCCCCGATAAGGCCTTC TGAAAGCGGCTCCCAGATCGTTCCCATTTGCCTCATTGAATTCACTTTCC CCGCGATAATCCTTGTACTGCGAGGGATCCTGGTCGTGGCAGTCGCCCAC TGCCGTTGCTATGTTGTACTCAATCCTTTTCTGGCAGTCCGTGAGGCAGT CAGCCGCCTCGCTGATCCGCCGGAAGGCCTGCTCAGCCCCAGGAGATTTG TTCTTGTCCGGATGGAGGCGCAGGGCCAGCTTGTGGTAGGCCCGCTTCAC CTCGGAGTAGGTGGCATGATGAGAGATGCGCAGCACCTCGTAGTGATTGC GGCACCGCAGGACCTTCTGCACCACGTCCAGCATCTCGAGTGTGAACTTG TGGGGCAGGGCGTCAGATTTGCGAGTTGGGCCTATGGTCCGCTGGGCCTC GCCCTTCAGCCTCAGTCTCAAAATGATATTCTTTAGCTCCAGCAGCGCCA TGATCTCATCGTGGTTCTGTAAGCCTTCCAGATCCTCGTTGATCTGCCTC AGAGCGTGCTCGTAGTGTCCCAGGCACAGGTCACTCACCACCTTGTCGAC GCAGTGATGCCTCCTCGCCTGCAGGATTCCCATTGTGAAGTCGTCGTCCT CCAGTTCTTGGTTACTTTCTTCTCCTTCCCAGCAGCGTGAGAAGACAAAA AAGGATTCGTTTTTCTCTGTTCGTTTGCAAATTTTAAATTTTGGTTTGTT GTTCTGGGACAATCCACCGAGTTGGTGAATTTAACAAAGTGCTTTTGTAT GTATATTAGAGGTAGCCGAAATAGTTTCGAACTAAGTTGACTGTATATGT ATATGTAGCTGCAAACTTAAATACAAATTGACTTTCGCCAGTCAACATTT TGTATGTCAACACAATGAACACTTGAGAAAAGACAACTTGAATCCGTTTT TTACATACCAGCCAGCTTATTGAACATTTAAATCATGCAGTACTCGTGTA AATACCAACGAATTTACCAACTTAAAAGTTGACACAAGTTGTACAAGTTG CTTAGTTTAGAGCGGAAAAAACTAAAAGTTTGCACACAAGTTGCACACTT GAAGCACACAAGTTAGAACGTTCTGTCGATGGGGGATTCCCCAAAATGCC AACCCTCTTTTGGCCCCGTAAAGTATGCTCCACAACTTGTCAAGGGGACA CACATAGCCTCCTCGAAAAGACTCGAAAGTTAATTGAAATTAATTTCTAT GCCAATTTGAATAGGGCACGAACTCAATTAAAACAGAGCTAGCCACCAAC CACCCCACAATTTCATCTTTTCAAGGCGGCCTGCTCGCCCCATTCATTCT CAAGGCCATTAGAAGGGCCAAAATCTTATTAGCAGTTAAAAGAATAAAGC GAGTGGAAGGCGCTAGGCACGGGGAAATCACAAGTCACCCAGCTAGATTT GAAGCAAATGAAGCAACGACGCCGGAATACGCAAGAAGGAGGTGGAAAAG GACAATAAATTCGAAGCCGGGCAAACTACAATAACAGCCAGCTAATCTGG GTAAGCTGCGTGGAACGAATGGAAAAGCCCAAAATAATAACAATAACAAT AAAGAGGCAGCAGCTCCGGAATCTAGAATCTGGAATCTGGCGAGGGGAGC GGCCTGCTTTGGCAGCTGATATCCTCTTCCTTATCAGACTCCCAGCCTCG GGGTTGATGGTAGCCACAGCCTCAAGGACAGCAGTCAAATTGCGTCGAAG ACGCCGAGCGAAAGCGTCGACAAATGCAGTCACAAAGGACCAATTAAAGT CCAAAGTGACTGAGCCGCAGGGAGGACGTGGCAAGCATCTCGCAGCTGGG ATCTGCACAGCGAGTAAATCATGCCGCAACGGTCCAATGGCCTGCATCCT TGAATTTTATAGATGTCCTTTCATTAGATTTCAAAACAATCTATAGTAAT GTCGAATAGTATTTCAATGTACTATACTTCAGGTATAAAACTTATGTAAC ACTTAATGAATGCTCCGAATGACAGGTCTTGAAAATCATATATTCAGCGC AAGTTTCCCAGTGCTTGCATATGAATTAAAATGAACAAGAACCACGAATT GTTTTCAGTGTGGAAATGGGTCTCGCTACGCTGGGCGCAGCTGGTGGGTT CTGTAGACAAGTGAGGTGTACAGTGGTGTGGGGATTGGGATGCAGCACCC CTCCTGAAAAAGGGGAAGTTTCGAGGCCGGGATTGCCGGCGCGTTCAAGT GCTGTTTGTTGTCGTTCTGCACAGGTTCCCCTCGGGAAAGGGTATACAAA CAGTACAGTCTGTGGCCAGTGTTTATGTATGTGTTGATTCGGTGCAGTCA CGTTTGAAAACTAAGAAGTTTAGAGACTTGTTTACGTTTAACAATTCTCA TCGGTGACTGACCCAAATATAACACATCCAGTGCGTACGTTACACATCCA ACTACACTGAGAAACACAAGAAAAAAAGGGGTTTCTTTTAGTTAGTCACA GCTTTATCTTGACAATGACTGCGCTTTGACTGCAAAGTAGTATCGAATTT TAAGCCCTTTTAAGCTTAATCTGTGAAGATTGTCCTAATTGTAATGTTTA TCAACAATTCAACAAAGTTGCCATAGATTTCTCACTGTGCATGACTTCAT CGTTTTGTTTGCTATATCACCCCCCGTGGGGATAAAACGAATTGTGAGGA CTGCGGGGAGTGTTGCGACACGCCGGTAAACCTGGCACCTCGCAGGAGGC ATATTCTCATTTATTAATGCGTCGTCACTGCTGTTCCCAGTTCCCATTCC TATTCCTCCTGTGCTGCGGTGGAGTGGGCGGCTCGGGTGGCGGGTTCGTG CAAAACGGTGGTGGCCGCTGTCTCAGCCGCACTTAATTCCCGCCAGAACT GCCGGGGCCATTAAAGGATAAAAGAGCGGGATTTCTGATTGGGAAGCGCT GACCCTGTTGGCCGCGATAAGTGGGTGCGCACAGCAGCAGGAGCACGGCA TCTGCCTAATCCGACCGGCCCACTGTGCAGTGGGATGGGGAGTGGGGAGC ATAAGTATTGATTTTTCTCACATGTCCCCGGCAAACACACACATCTTGTC TAGGGAGCCGCATCGCCCGCCCCCACCCCACTGCCCCTGCTCGGAGCAAC TTCCTCCGACACCTGGCAGCGATTTGGAAGTTTTCGCAGCTCGTAAATGC TGCACTGCAGCCATAAAACGGCCGCTGCAATGACTCGCATGAATTGCGTT TGTTTATGCTATGGAAAAGGAATCCGGGGTCTGCTGTATGTCGTTTGGGA TGCTCCATAGGCAGAGAAATGCTCGATGTTACTCACTCGCCATGTTTGCC GCCTTTGTTGATTATTCCGCTGCTGCTTCTTCCGTTTTTATGCTTTTCTG CTTTTCTTGCTCTGCGTTGGTTGCGATTCCAGGCACGTTGTATCACTGTT AGCTTGTAACAAACACTGCTGATAGGCTAATGACTGCTGCGCGCAACTGA ACACATTTCACGGCTTTCTTTCAGTCGCGTCTCCGTTCAACTTCCGCAAT ATCCGTATAATTCGTATTATCCGTGTAATCCGTATTTTCCGAATCGCGTT CAGACGTTCACACCAACAACTGCAATTCTAGTGTGACCGCAGAGCTCGAG CTGCACGATACCTCCAATGAGAGATGCCATATCGATGCTTACGCATTTTA TTAACATCGATAGACATTTCTAGAATGTCTAGACTTTAATGCTTGGATTT TCCAAAAACTATAATCTGTTTCCAAAAAGTTATCGATAAGTATCGATCAG TGTTGAAACTATTTGTATTTTATATTAAATTCTGGGGTGTGACTAGTAAT ATTAGGAATATAAGCTTTAAAGAAAAAATCGAATTCTTTATAAGTGATTT AGTTCGAACGTTAACTTAAGATTTGCCACCACAATCGGAAAGTAGCTATT TTCTAGCTAGCTTTGCCCATTAATCGATTGGTGGCAACACTGGTCGGCAC ATCCCACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTG AACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGA CGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACC GCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAA ACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGAT AACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCA ACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGG GCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTT CGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGG AGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGA CTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGT CCAACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCA AGGAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTC TTCCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAA GGTCTCGACTGCGCAATTGTGGGATTCAGGTTCTAATGGTCCTCTTTTTT CCTCGCAGCTCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCA TCGCCGCCGAGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGC CCAGCAGAGTAAGCCAGGAAGAGGTCGACAATGTGGTCCCTGGGCCTCCG ATACAGTGAACGCTGCCTCAGGCAGGCAGTCCAAAGTCTCATGCACGCAA TTTCGGTTGGATTTTGTTAACTCGAATGCGGGATCTGCTCATAATTTGAT TAGTCATTGAATTGGTTAGCACATATGTATGGTTCTTGATTTGGACGAGA GATATACGTGATTTTTGTGATGTCATCATCTCTACATTCTGATTGCCAAG CCCTTTTTTAAGCTCTATGAAATATTAGCACTAATATCAATTGAACTTCT AATTAGGAATGATTGCAAAAACATGGTTAAGTGTTAAGTAAATAATCAAT TCGATATAAAGAAAGTTTCGTGCTGTTTAGGCTTTGTATTGGATGGTTTA GTTTAATGTGTTTTAATGTGCACAAAAATTACCCTATTATTTTGAAGGAT ATATAGTGTAGAAACGATATATATAGGGTTTCTAGCAGATAGCTCGAGTT TTAAAATTCAACTGCAAATTGGCATTGGCTAAAGGTGCGATACAATCACC GATTGATCTGTTCTGCGGAGCTTTCGCTGTTCTTCTTGATTAACTGCTCG CTAACACTCCGTCCCGTTCATGAGAAATCCATTTCACTGCGCACACTAAC CTCTAACAACACAGGCACACAACTTATGTTCATTTCGTTATTTGTTTACG ATCGATTCGCAGAACACGATGACTACCGTCGTGCCGCTGACTATGCTAGA TTATCATGGAACAGTAAGCACCTCACTTGCAATACCAAGCCCGAGATCCT CCGTCGGAACGATCGCCAGATTCGTCAATTAAACCTCACTTTTCCTCTCT TCCAGAAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGA CGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAG TCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCT GCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCAC CGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCG ACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGT AAAGGCCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACC ACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCG CCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACT CTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGGTGGGTCTCA TTCTCAACATTTGTGGTTAATTAGCCGTGGCAGTGTCTTAGAATTTACAA CTTAGAACAAACAAGTTAGATTTACATCTTCGAAATCGAAGTTCAACGAT TAGGCTCTGCGAAAATGGTTTTTAAAGCCTGAGCATCTTGAATAAGAGCT GTTTTCTATAAAACAAATTCATTGTTGCAGGTTTTCATGTTTTCATAGGA AAACGCATTAGAACCAACTTCCCAACTACTGATTAACATGTTTGATATCA TTTACAAGGAAGAACTAAATATTCACTTGACTAACGCCTGGCCAGTTTCC TCCACAGAATCCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTG GACGAGGTGGATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCG ATGCTGCCTGGCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCC GCCTCCTGGTCAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAA CCCCTAACCCCTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGA TTTTAAATAGACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGAT AAACGAAATAAAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAAT ACCATACTGATATTTGATATTGATTTGATATTTGGTATCAATGGGCTTCT GTGGTTCTGTGGTTATACCATAATAACTTTGAGGTATCGTAGTTCTAATC ACCAACAGGCAAATTGATCTAACTCGAAAGAGTTTTTGAAATTCTGGGCA ATAGAAATTGGATCATGTATACATATAAAAAATGACTATTATATAAAATG GTATGTACAGCTGTGTTCAGAAAAATAGCAGTGCGAGGAATACTAATTAA TACAAAGGTATTTTTCCATGTCCCTTTTCGGAATTGACTTTTTATTCCAC TTATTTTTGTTAAATGGAATGTGTATATAGGGAAAAAAAGAAAATCCGGT TAGTTTTTCATGTTATCCTTTTTTTATTTACTTTCTTAAGCGAAATCACA ACTTTTAGGCTGTTCATAAGAATAGCAGTGTCTGGTTTTGACCAACGTAA AGTCAGGAAATGATCAATATTTTTAAAAAGTGAGTTTGATTAATTCGTAC ATTTAAAAGGGGAGTAAATGAAAAAAATTATATATTAGTGGGTAAAGGAC AGCACTGCTCCCAGGAGAAAAGAATGTTAATTATTAAGCTTAGAAAGGAA GTAAAAACATATATGAACATTCAAAAAACCCTTGAATGTTCTGCCAAAAT GGTATCCAATGTCATTAAATATGAATGGAAGCCCGAAAACCGTGGTTCCA TAGATATAACCACAGATATATAGCATCGACGCATTGTTTCTTACAGCAAA GTCTATCCTTTTGCATCCTTTAGGGACATAAAGTCTGAGCTCAACTTGGG AATCAGGGACGATACTATTCGAAGACGACTACTAAATCAAAATTTCAGTG CGAGGAGTTCACGAAAGGTTCCCCTACTTAGCCCAAGGCATATTTAGGCA AGGTTAAGCTTCGCTAAAACCTACCTAAACTGGCCAGTCTTCAAATGGCG TAATATCCTTTGGACTGATGGGTCAAAAATCGTGCAATTTGGTGGAACGG GTTCACTACAGTATATCTGACGACCTCCAAACACGGAATACCACCCAAAA CACCCACTGAAGACTTTCAACCACGGTGAACCTAAAATTGTGGTATATGC TTGTTTTTTTTTTTACAATGGTATGAGTCCATAACATATGATTTATGGTA TTATAGACCAAATAGCATATGTAAATATACTCATTGATGTCTTACTGTAA TATTCTGAATATAATATGCCCTTAAAATGGACATTCCACCAGGATAATGA TCCGAAATGCAGAAGCAAATCGGCAAAGAATAGGTTCACCCAAAAATGGA ATAGATGCAATGCCGTGGCCAGCACCACCTTACGATTTAAACCCGATTGA AAACCTGTGGGGGGAAATTAAACAAAATGTGTCGAAGAACTCCCCGACGT CTAAGGCTTAGATTTGGAAAGTTGTGCAGGATGTATGGGCAAAAATTCCC CCAAATGATGCCAGGACCTGGTGGACTCCATGCTGCGTGGGTGTAAGGCT GTGCTGGCTAACAAAGGCTATCCAGCCAAGTATTAGGCCCGAATTAACGT ATTAAAAAGAAAAACTAAGTTAGTTCTAGGTCAAGTTGAATTTTGTTACT GTTTTTTTCAATATTTACATTGAAAACCAGAGTTTCTACCTATTTTGTTG TTTTAATCTATATTTTCGAAACTATTGAAGAAATAAAAGTGAAACATTTG TTAAATTGTTTAAAATTAAATACCTAATGATATTATAAAAAAAAAAAATC CCATTAAAACTGTAAATCCTAGGAATTTTTGATCTTAAACTCTCAGGTCC AAAGCACTGCTATTTTTATGAACACAGCTGTATATATAGAAAATATTTGC TAAAGTAACTACTACTCTTGCGATTTATGAAAACGGATTCATTCAACCAC TTTTATGACGAATTTCATTGTATTAATATCTCAATACTGTAGGTCTGAGA AAAATGATACATTCTGTTTGGTCAGCTGCAAGTTGAGTATACTGACAGAA AAAAATATTTCAATAATGTGCGAAAGGAATTTTGACTGAAAACGCTGAGA ATGATCTTTTGTTTGAGTGAGATTGATTTCACAGTAGTTTTACTTTCTGT GTACATGCTAATTTGATACCCCGCACCCATGGGAAGCAGCTTGAGGTTTT TCCGCGGCATTAGTGCATTTTCGAAATTGCTCGAGTGTGACGCATGCAGA TCTCAATCTCGACCACGGGCTTTTCGTCGCCAGCGAGTGTCCCTCCCCTT GGAAGGCAATCTCACTTATGTCATTCATTTGACGCTAATTCGACATTTAC AGAAAGTATTTGCTCGAGGAAGATAACCAGAAGTGCAAGCAAATGATTCA TAATTGATTCTATTTTGACAATAATTGGGAAGACAGCACTGTAGGAAAAA GGGGGCAATATGATCATATTCCAAATAATATGAATATTGATCATTTTAAT TTCAAATTGTGTATATTCTTAGTAATCATATTGTATGTATGGCTTTTCCA TTTGGGAAAATCCGTATGAGTTATATTTTATTCCTAAGAATTCGTGTTGC ATTCAAAATTGCTGAAACAGAAATAGCTGCAAAAAATCTTGATTTGTTCG TGCCAATTGTTACATTGCTTTAATATTTTAATCTTTAGTAAATGTGGGCA ATCCATCGAGATGATCTTCAGCGCTTGTATCTATTAGATACACTTAATTT TCCATCTTTAGGGGCAATGACTCATCCCAGTACGAGTTTCATTTAGATAG TGCGATTTCGATCAATGGAGATACGAAATTCTATTTCTCTTTGTGTGCCG AGCGTTGTGGAAATACATTTAAATACGGAACAACGTGAGGTTAATTGTGC GGAGCACACTTGTTAATTAGGGAATGTCAGCGGGCGCGACAGTTGGCGCT CCCCTCACCCCTTCCCAACCCACCGAAATCCGAAAATAATGCTTCCAAGC CACGTTTTCATTGGATTACGTAAGCTGTAAACCAGTTTATGATGTTGTTG TTGTTACTGTTGTTGCCAGTGTGTGTCAAGGAAAAGCTAAACACAATTAC AACGCCCTTCTGTCTGGTAATTAAAAACGGAAGCCATGCCCGAAGCCATA GTAGGCTGGCTAACGAGACCTGCACATCGGCCCAAACTGGTTGGCTTTGG CTTTAGGCCACTTTCGAGGAAAATCCGCCCACGACGAGCCGAAAACCGCA AAACACGTCCGCCAGTGGAAATCGCATCGAAAGTTTTGCGGTTTCGAGCC ATTTTTCCATTAACTCGAAATTCTAGAAGATCAATTCAAATCAATGTTCA TGTGAGATTTTCCTTATGAATACCTGTATTTTTATATACCGAGATACGTA TGTACAAACAATCTTATCCTACAATTTCCTGTTTTTGAGGCAGCTTTATC TTATAAAAACTGTTCGAAACAAAATTATAATTTCCATATACATATCTTCA ACGTGAGGTTTTTGCTCCCTTTTTTCTGTTCTTAATTTTCCTATTGGCCA GGCAATAGTGCATTTGCATAAATAAAACATTTATTGGTAGTAAAAGTTAA ACAAATATGTACGTAATTCCCGAAACATTTCAAATTTGCATAAATAAACA AACGCGATTGGTAACAGAGAGCGGAAAAACAAGTTACAGTAATTACCGTT GGGAGGGGGTGACGAAACAAACCAAAACAAAACGAATTATGCTCGTGTGA GTGTGCGCGACGCAACAGGTTGAGGCTGCTTGGCGCAGCTTTTGACCGAT CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGA GAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGA AACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAG GCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAA GCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTA GGCCAGCGAAACGACATAACGCTCCAAGTGGTAAAGTGAGACCTGCCAGT GGCGGCACCCAACCCGAAAAAGCCTAACCAGCGACCACTTTCCAGTTATC CAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGT AACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCAC CTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACC TGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAAC GAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCA GGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTA GCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGCGTCAATGCC AACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGAGGCCACCTT TCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCTGCCAGCTGT GCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTCTCGGAGACC CTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGCCGCCGCGGT TAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGGAGCAGACCA CAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTATCCCTACATC TGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCT GCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATG CTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCA GCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTG TCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATA CGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGT CAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAA CGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACAC CCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAA TGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTG CGTGTTTCCCAAATAAAATGCCGAAATACCTAACTTTTCACGCTTGTATC TGAATTTCTTAATTCCATTCCATTTTTTTCGTCTCCCGAACGATCAGTTG CAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAA TGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTG CTCTGTTCGGTGAGTAGCATAGATACATTTAAGATTACATAATTTCGAGC GGCCAAGCTTAGATCGACTTCTCAGCCTTTTAGGCTGGCAGTGAGATCAT AACTTTCGTGCGGAATAAACTGGTTTTCCCAAAATTGGTGTTTTCAGTAT TGAAAGGCTGAGAAAGTCGAGGCCCACAAAAGTGGTGAGCATGAGTACAT TTTAAAGCCACAGAAGGCACTCTCGTTAAATGCATTTTTGTATTTTTGTG TTCTTTAGGTCGGCTTTCATATTTACATATCATGAAATTAAACATATCTC AATTAATGTTTATTAAGGACCCTTAAAGTAGGATCTATTATAGCATTTAT GGTGTCTCTTTTCCGGTCAGCACTATCACTTTCCGGTTACGAAACGCACT GTACGTGCAAAGTGGGGGCAGAGCTTGAGATCATCATCAGTATTCCAAAA CCAGTTATTAAAATTGGGCTACGTTTGTGACGTAGCGGTATCCGAAAAAT TCTGTATAATTTTGTGTACACTACGTACACTTTTGTTTACTTTGGAGTCC CAAAACCAGTTTGTGTTGTTTCGGTCCCCACAACCGAGCCCCACATCCAC AAACATGCATCCCATTAGTCGGAGTCAGTCCGAGGTTAACTGGTTCCAAA TGGCAACCAAACAATCATTGAAACGCCAGCAACGGTGGCATTTCGATATG GTTTTGCAACTTCTAACTCACTGCCCCAAAGTCACTGCACCGCCAGGTGG AACTGTACTTCGTCCAACCAGTTTGGGGCTGGGACCCTGACTTGCTGCTG GTGGGAAATCTGACTGCGTCGGAGTACCAGCGCATTATTCGCGTCACGCA AACATGGATGTCATTCACTACGGGCGGAAAAACATCAGCACACGGCGCTA ATTCTTCAATCGTATGCAGTATACGGATATAGAAAATTTACAAAACAAAA CCATTTTTTGTTGATGGGAAATCGGTAAACGAGATGGATGACCTATCTAC TTGAAATAGGTCATTTGATTTGTTCAAGAGTTCCAATCCGCAGTTCTCCA ACCTTTTTGATAATTTAAAGTAGCTGCAATTAACTTAAGAACCAACATGG AAACATACAAATATTTTGTCTGTGTGTAAAGTCTGCCGCCACTTCAGTGG AAAGTTGTGTAATGGTTCAAGAGGGGGGGGGGGGGGGGGAAGGGGGTCTC ACCCAAAAATAGTTGACTTAATTTAATGTGAACTTGCTCCCATTGTGAGA CGACGAGCCAAAACTCGGAAACAACGAAATATCATCTACACACGCACATC ATGGAATGGAAACACGGGGGTCGTTGGCGGTACACTTGAACTCAATTTTC CGAGGGAGGGCGATCTAGAAATGCCAGACGAATGCGAGTGGGTGGACTGG TTATTATTATAATTGTGGACCAGTGTCGAAATGTCGCTCTCTTCTGATCG GATGCGATGCTAACTATTCTGATCCCACGAACCGCTGAGCTCGGCGGCTG AGTCATGCTGCAGTTTGGCGCAATCCTACGAATTTATGAACTATAGTTTG GCTGGGGGTGGATCTAATCTAATGACTACGTCAACTGATACAATCAAAGC CAAAGTAAATATGTTTTTAATAGTTATCGTCGATGGCCAGGCGCTTTTAT GCATAATCTTAATTAACGAAGCGAATCGGATTGATAAGAGATAAGCTTGT GATAGCCATGCAAATAGCCAATCTGAAACTCTATAAACGAAAATCGCCGA AGAACTGGGCAATAATAGAAAGTAGTTTTAATAATAAAGCAGGTGATTTC GCCATATCGCAAATATTGAAATGCATGTCCCTGGAAGTAGTTCCAGTTTC TCGCAGTGCATATTATTTGTCGAACAACAGGCATGAGCTTTTAACGCCTA CAAGCTTTTTAATGAAACAAAAAAGCTAATGATATCCCAGCCAGCATTTA TATGGATGAATATTCTTCAGGCGATTTGGTATCGCAAATCTTGTCAAATC ATTTGATCAAATTAAATCATAAATAACTTAGAACTGTATTAATTTATTAC ATGATTAGTAAGTCCAATATAAAACGGATATGAAGTGATTGTTTTTGACC AATTTCTGTCAAAATCTGAGGGCTTGAGAATTCAAGTTTAGTTAGATTAG ACAACCCTGGTTGGCTCAGGATTGATAAACTCAACATTTCCCTTCCTCAG ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGT CCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCG TAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGC TGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGGTAGAGTA CTGATCCTGCATCGTGCCATTCATCTTGCAATTCAAAATGTATTCTTTGT GGCAGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTG GTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGA CGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGG ACGCGATTCAGATCAGCGTAAGTATTTAGGGACTTCCAAGGACATGTGAC CCGCCTTCAACTGACTTTCTGCCGCTCCCGCAGATGAAATGCTGCGGACG CAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCT GCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGC AAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTA TGCCGGTCTGGTCATCGCCGCCATCGAAGTAAGTTATTGTCCAGAGTAAC GCAATCGAACGAAATCGATCATCGAATCTAGGTGCTTCCCCATGTGAATT TCGAAAATATGATGGATGGGTTCATGTTACCTACCTTCCATTGTGATTTC TTGGGGATAACCAAAAAGTACTAAGTAATGTAAATCATAATTCGTAGCAA TGCAGTTTAGTTTGTTATTTTACCATAAGCGTTATGAGATTTACACCTAC ATGTATATTCTTCCAATATACCATACTCTGTTTGCTTTCAGTTTGTGGGA TTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCG TGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTG AAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGAT ACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCA GCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTT CAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTAT ACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA GAGTTCAGTCTTTGTCTTAATGGGAAAGCTTACATTGTTTGCAATTCGAC TTAATCCCTAAAGCACCTATTTTTCTAAATTGCCACGGGAGGATTTCGGC CATTCGCGATAACGTTTTAATCTGCAAAGTAATAAGTATAAATAGAGTTG GCCGAAACCAACAAGTACACTTTGATTACAGATCATTATCAATCATTGGC TCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGT TAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTT TATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATT CCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGG GAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTA GGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATA TGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGT GGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGG AATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACC ATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGAC CACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACA AGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGG CCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAAT AGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATC GAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAG CACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCA ACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATC ATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACAC CCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAG TGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACC ACCATCGTAAGCACTCGGAAATCACCCACTGACCGAAATTGGATTCTAAA TGACTTGGCATTCCTTTCAGTACGCCATCTGCATGCTGATTCTGTTCGGC CTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCT GTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCG CCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCGTAAGTTTATCGAAA TTCACCATCAGATGTCATTAGTTTTTTCCGGATATTTACGTATCTATTCC ATTGCAGTTCTCTTGCTGTGGCAACACGGGATACCAACAGTATGAAACCG TGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCG GAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTG GGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCT TCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGG AAGCGCTAGAGCCGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCAT AGCATAAATCCAACACACGAATTCCTCACTCACTCACTCACCGTAAATAA ACCAGAATAGGTTAAGCCCAATGAAATATTATTGCTTATTCGCTGTCTAC CTCTGGCTGCCGTCTATCTAATCAAGACAGGTTGATGTTTTTCCAAAAAG TATGTCCTTATCGGCCTGTTAGCCGAGTGCCGCGTTTCCGAGATCGAATG CCCTCAGTAGTGGTGAATCACCTCCATATGGCAATGGCTATCGATCTCCG CCCGCCGCCCAGTGCCCATTATCTATTTTTCGTTTCGGCCATGATTATGA TAACAGGCACTTGCGTATCTTTCCTCCGATAGCGCCCGTGTCTGTTGGCC AATTTAAAAACAGTAGCCCATCTGGAGGAGCAGTCCAATCGAACGACAGT AAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGA TAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATAT ACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATAT TGTCAATATCGTGTTTTTGGTAAGTGCTTGTCGGTTGAGTATCTAAGTAA AAGGAATTAATAATGTAATGAGACGTGTAACAATAGACCAAACACTACTG GGTGCAGATCCCAAATAGGTTCCAATTATGGATAACTTCATACTCTCCAA TTACTTGTGTTATAATGAACTTCCAAAAAATGTCCATTAATTATGTTAAT TTATTTATCAAACTGTAGATGTTTATTTATTTGCATATAAGACCTTCTAG CTGACTTCTGTCATTCATTAATCAAGTCATATGCAATAAATATTTGTGCA ACAAATATCGAACATGTATTATTTAAAACAAGTGAAATGAAATTTGAAAA TCCATAAATTACGCATCGGTCGCTTCCTTTCGATTGTCTTTGAGTCACAA GGTTTAACACTATTATTCATATAAATGTGCTGGCATAGATAATAATATCT ATCTGTAATGCAAGTGTGGACGGACATACAGAATTTTATCAGTTGATTGA CATTATCAGTGTTTTGTAATATAAGTAATGAGCCCAAAATGAGCTTCAAA GGGGGCACACATGCACACAAGTTCACATTTTAGCAAGGCTAAGTTGGAGT GAATAAAAGATCATTTAGAGAATAAACTAAGGAAATACAACAAACTATTA TTTACAAATGATTTATTATTTATCCAAATAAATGTGTAGTTACTCGCAGT ATTAACGCAGCTAAAAGATACATTTTTCACCTTAAGAATTATGCCAAAAA CAAGATAAAGGTGATTAACGTTTGTTTTTTTTATCAGCTACGTTTTTAAA CTAGCCATATCCGTCTGATTGTGAATTTCATTAATTTGTATGCAAGTATA AGACTTGATTATTCACTTTGTTAATCACTTTGTCAACTTAAAGAATCAAA TGAAGAAATTTAAGTAAATCTTGGTCACCGACATCCTGAAGGCTATTTTA AAAGCTCATATCTTAGTCCAGTTTGCGGACAAGTTTTCAGTACATAGATA TTCCCGGATAATTAGAAGTCCATAAAACATTCATTATAATGTGGTATGCT TATGACCATAAAACTGTTAGGCAACCAGAGATGCCTTCTAGTAATACTCC GAATACTTCCAGATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCAT GCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGAACTGTACTTC GTCCAACCAGTTTGGGGCTGGGACCCTGACTTGCTGCTGGTGGGAAATCT GACTGCGTCGGAGTACCAGCGCATTATTCGCGTCACGCAAACATGGATGT CATTCACTACGGGCGGAAAAACATCAGCACACGGCGCTAATTCTTCAATC GTATGCAGTATACGGATATAGAAAATTTACAAAACAAAACCATTTTTTGT TGATGGGAAATCGGTAAACGAGATGGATGACCTATCTACTTGAAATAGGT CATTTGATTTGTTCAAGAGTTCCAATCCGCAGTTCTCCAACCTTTTTGAT AATTTAAAGTAGCTGCAATTAACTTAAGAACCAACATGGAAACATACAAA TATTTTGTCTGTGTGTAAAGTCTGCCGCCACTTCAGTGGAAAGTTGTGTA ATGGTTCAAGAGGGGGGGGGGGGGGGGGAAGGGGGTCTCACCCAAAAATA GTTGACTTAATTTAATGTGAACTTGCTCCCATTGTGAGACGACGAGCCAA AACTCGGAAACAACGAAATATCATCTACACACGCACATCATGGAATGGAA ACACGGGGGTCGTTGGCGGTACACTTGAACTCAATTTTCCGAGGGAGGGC GATCTAGAAATGCCAGACGAATGCGAGTGGGTGGACTGGTTATTATTATA ATTGTGGACCAGTGTCGAAATGTCGCTCTCTTCTGATCGGATGCGATGCT AACTATTCTGATCCCACGAACCGCTGAGCTCGGCGGCTGAGTCATGCTGC AGTTTGGCGCAATCCTACGAATTTATGAACTATAGTTTGGCTGGGGGTGG ATCTAATCTAATGACTACGTCAACTGATACAATCAAAGCCAAAGTAAATA TGTTTTTAATAGTTATCGTCGATGGCCAGGCGCTTTTATGCATAATCTTA ATTAACGAAGCGAATCGGATTGATAAGAGATAAGCTTGTGATAGCCATGC AAATAGCCAATCTGAAACTCTATAAACGAAAATCGCCGAAGAACTGGGCA ATAATAGAAAGTAGTTTTAATAATAAAGCAGGTGATTTCGCCATATCGCA AATATTGAAATGCATGTCCCTGGAAGTAGTTCCAGTTTCTCGCAGTGCAT ATTATTTGTCGAACAACAGGCATGAGCTTTTAACGCCTACAAGCTTTTTA ATGAAACAAAAAAGCTAATGATATCCCAGCCAGCATTTATATGGATGAAT ATTCTTCAGGCGATTTGGTATCGCAAATCTTGTCAAATCATTTGATCAAA TTAAATCATAAATAACTTAGAACTGTATTAATTTATTACATGATTAGTAA GTCCAATATAAAACGGATATGAAGTGATTGTTTTTGACCAATTTCTGTCA AAATCTGAGGGCTTGAGAATTCAAGTTTAGTTAGATTAGACAACCCTGGT TGGCTCAGGATTGATAAACTCAACATTTCCCTTCCTCAGATATGCGGCAT ATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGG ATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATC ATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGC CATTCGGGAATCCTACTGCATGTCCATGACGGTAGAGTACTGATCCTGCA TCGTGCCATTCATCTTGCAATTCAAAATGTATTCTTTGTGGCAGTACTCG ATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACAT GTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGA AGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAG ATCAGCGTAAGTATTTAGGGACTTCCAAGGACATGTGACCCGCCTTCAAC TGACTTTCTGCCGCTCCCGCAGATGAAATGCTGCGGACGCAGTGGCTACA CCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACC AACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTT CGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGG TCATCGCCGCCATCGAAGTAAGTTATTGTCCAGAGTAACGCAATCGAACG AAATCGATCATCGAATCTAGGTGCTTCCCCATGTGAATTTCGAAAATATG ATGGATGGGTTCATGTTACCTACCTTCCATTGTGATTTCTTGGGGATAAC CAAAAAGTACTAAGTAATGTAAATCATAATTCGTAGCAATGCAGTTTAGT TTGTTATTTTACCATAAGCGTTATGAGATTTACACCTACATGTATATCTT CCAATATACCATACTCTGTTTGCTTTCAGTTTGTGGGATTCGTTTTCGCC TGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTA ATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTA CGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCAT TCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATG ACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACT GAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGAT TGCAATAAACGGAGAAATTTATTTACAATTTACGAAAAGAGTTCAGTCTT TGTCTTAATGGGAAAGCTTACATTGTTTGCAATTCGACTTAATCCCTAAA GCACCTATTTTTCTAAATTGCCACGGGAGGATTTCGGCCATTCGCGATAA CGTTTTAATCTGCAAAGTAATAAGTATAAATAGAGTTGGCCGAAACCAAC AAGTACACTTTGATTACAGATCATTATCAATCATTGGCTCTATTGACATA TTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTT TAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGG GCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAA CCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGC TAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATC GGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCG TGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAA TGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGG GCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATG AATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGAT CTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCA TCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAG CGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTG TCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGAT TATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTG TCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCG TGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACG ATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCC GATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCG GATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTAAGC ACTCGGAAATCACCCACTGACCGAAATTGGATTCTAAATGACTTGGCATT CCTTTCAGTACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCC CTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGG CAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACC CCATGGATGCCCTCCAGTTGGCCGTAAGTTTATCGAAATTCACCATCAGA TGTCATTAGTTTTTTCCGGATATTTACGTATCTATTCCATTGCAGTTCTC TTGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCT GCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGC CAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATAC GGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCA TCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGC CGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCA ACACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGT TAAGCCCAATGAAATATTATTGCTTATTCGCTGTCTACCTCTGGCTGCCG TCTATCTAATCAAGACAGGTTGATGTTTTTCCAAAAAGTATGTCCTTATC GGCCTGTTAGCCGAGTGCCGCGTTTCCGAGATCGAATGCCCTCAGTAGTG GTGAATCACCTCCATATGGCAATGGCTATCGATCTCCGCCCGCCGCCCAG TGCCCATTATCTATTTTTCGTTTCGGCCATGATTATGATAACAGGCACTT GCGTATCTTTCCTCCGATAGCGCCCGTGTCTGTTGGCCAATTTAAAAACA GTAGCCCATCTGGAGGAGCAGTCCAATCGAACGACAGTAAACGACGCGAG TGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGT GTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATG GGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGT GTTTTTGGTAAGTGCTTGTCGGTTGAGTATCTAAGTAAAAGGAATTAATA ATGTAATGAGACGTGTAACAATAGACCAAACACTACTGGGTGCAGATCCC AAATAGGTTCCAATTATGGATAACTTCATACTCTCCAATTACTTGTGTTA TAATGAACTTCCAAAAAATGTCCATTAATTATGTTAATTTATTTATCAAA CTGTAGATGTTTATTTATTTGCATATAAGACCTTCTAGCTGACTTCTGTC ATTCATTAATCAAGTCATATGCAATAAATATTTGTGCAACAAATATCGAA CATGTATTATTTAAAACAAGTGAAATGAAATTTGAAAATCCATAAATTAC GCATCGGTCGCTTCCTTTCGATTGTCTTTGAGTCACAAGGTTTAACACTA TTATTCATATAAATGTGCTGGCATAGATAATAATATCTATCTGTAATGCA AGTGTGGACGGACATACAGAATTTTATCAGTTGATTGACATTATCAGTGT TTTGTAATATAAGTAATGAGCCCAAAATGAGCTTCAAAGGGGGCACACAT GCACACAAGTTCACATTTTAGCAAGGCTAAGTTGGAGTGAATAAAAGATC ATTTAGAGAATAAACTAAGGAAATACAACAAACTATTATTTACAAATGAT TTATTATTTATCCAAATAAATGTGTAGTTACTCGCAGTATTAACGCAGCT AAAAGATACATTTTTCACCTTAAGAATTATGCCAAAAACAAGATAAAGGT GATTAACGTTTGTTTTTTTTATCAGCTACGTTTTTAAACTAGCCATATCC GTCTGATTGTGAATTTCATTAATTTGTATGCAAGTATAAGACTTGATTAT TCACTTTGTTAATCACTTTGTCAACTTAAAGAATCAAATGAAGAAATTTA AGTAAATCTTGGTCACCGACATCCTGAAGGCTATTTTAAAAGCTCATATC TTAGTCCAGTTTGCGGACAAGTTTTCAGTACATAGATATTCCCGGATAAT TAGAAGTCCATAAAACATTCATTATAATGTGGTATGCTTATGACCATAAA ACTGTTAGGCAACCAGAGATGCCTTCTAGTAATACTCCGAATACTTCCAG ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCT GAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCA TCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGG TGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCGGTAAGTTT GCGTGAAGAGCATATCCCAAGGAATTCGAGCTAATTGAAGTTGAATGCTT TGCAGTACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTT ACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAA TCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTC TTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAAC AACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCA GGCCACATGCAACACCCCCTCGGTCTACCAGTCGAGGCCCGGCTGCAGCG CCAAGTTCGAGGAGTTCTGGAACGACAACATGGACATCATCCGCTGGTCC GGCCTCGGCCTCTGCATCTTCGACCTGGTCGTCTTCCTCATCGCCGGCGC CCTGACCAACTGCATGCGCAGCCAGAACGCAGGTCGCCAGGTGTACGCCT AAACTTGTGAGGAACAAGCCAAAGGCCAAAGGATCTACATATGTCTACTT ATGTTACCATATAACAAACTGTTTTTCGAGCCGTGCCAATATTAATATAT ACGTCTACATTTCGCCTATTTATCAGTTACTACTTATGTTATTCTTTATA CTCTTTTTGGAGCAATGCCAATATTAATATATACCGCTACAACATTTACC ATTACTCGTCTTTCTTATAAGGATAAATGGGTTATTTTACCAATTATGAT TTTTCTAACTGGCTTAAAACTTCTAAAGAGTATATTTGTTCATCTATGTT TTCCTACAGAATGTGCAGTATTTGAGGCATACACTTAGGCTGTTTTTTTT TTTTTTTTTTGATTGCCCTAATGTTTTCCATAAGTTGGAAAATTTTGGAG AATTGCTGTTATGTTACGCATATGTTAAGACAATAACATTGACCTGAATG TGATAACATTAAATTTCCCTTATTAACATTTGGAACATATCCAAAAAATT CCAATCGCTCCAACTAAGTAACATTTAACAATTTCTCCAATTTATTATGT GACATTCTCAACTTTCAAATAGAAATTTCAATTGTGACTAGATAATGCTA CTAATACTAATTTCAAAGAGAATTAGCCAATCCAAGACGAAATCAAATAA TATTATTATATTATTATATTATTATTATTAATAATAGCTTTGTAACCCTG ACTAAATCATTGACAAATGATTAACGAATCCAAGGTGCAAGAGTTCAACT TGTGATTGATTTATCCAACTGATATTCACACAGCTTTAATATGCATATTA CTGGATTTACGCCGGCTTTAAAATAGGTTTGAAAAAGTCAGGAATAGCGA TCTAAAAAGAAGAAATACATTCACCAAATATTTTTGACTTTCGACTAGAA GGCACGATTTTTTTAACATTGCGTTGATCAATGTTTTGAAAACCAAACTG ACATTGGCATGTAGATGTTTTGCTTATCAACACAATTTGTTATATTCGAA AGAGAAGACAAATATGATAATTATTGCTTTGCGTTAATGTAGAATATATA TATATATATTTTCAAAATATTTGTGTTGATTATATTAAAGAATACATACT TTACCATTTATTAATTAGTCCACATAGTGAAAAGAATTTGTTTCTTAGAG TTATCGAGTTTTCCCCAAAAATCACATGAAACTACAAAACCAAGATATGA TGTGGACTTTTTCTTGCTAGTAAATATAGTATTATTAAGTCAACACCTAT CGTTCCCATACTCCATCATTCTAGATACTAATGTTAGGATGCAGTTGTTT TGCTGTTTTCATATCTCGATCTCCCTTGCACTCTCATTGGCTTAGTAAGA AGTATCTATTAGTCGAGATATATTTATTTTAACCTTATCGTGAAATGTCT TTGTTTGGACCATAAACTATCAAATGTCGCAATTATATACAGTAAGCATG CGAAGCACTTTGTTTTATTTATTCATATTGACTTTATGACGTTAAAGAGG GTCGGGAGATAATCCTAATACTATGCTACTAATTCATCGTTTCATCGTTT AGTAGTTCTGGCGTCTCTGCGAGTTGCGGGTCTGATTGGCCAGGCAGCAG GCGAAAATGAAGGCCACAAGCTGAAAAAAGTACCATTCAGTTTGGCGAAT TCAAAGAACATTATACGCAATCCTCACCTCAACAGCAGTCACACCCAGGC CAGCGTACTTGATGATGCTCACGTTGGTGTCCCAGAAGGAATCAACGGCC TTCAGGCAACTGGATCGCGTCATGACTTGGGTTAGTGCGCAGGTTCCATT GGAGGGCGAGTCGCAGCAGGAGGCGGGATACGTAATGCCGTAATCAGCGA AGCCGTTCAAGCCGCAGCACTTGAACTGGAATCAGAGTATATTCTCGGTT AAGCTATCTTTATGAATGTGGAACAACAGTAGACAATCTTCATTGAATAT GAAGTAAATAACAAAAAGAATTCACAATGTAATGCTTGAGGGTCAGCAGA ACTCACCGATCGCTGCAGTGTGTCCATGAGGAGGGCATCGGTCTTGCGTT GATCCCATATGGTCTGGACGATCTTCTCCAAAGATTGCTGTATCTGCACA TGGTCCACCCACACGTAGATAATGAGAGCTAGCTGACTAACCAACAGCAC CAGCATGACCACAGAGTACTGAAAGCAGGAAGGAGCAAGTTGGATTCAAA TGTTGCACCCAGCAGGGCATGTATCATGGGCACCTACCGAGGTCAGAGCA CAGGAATTCTCGCGTATGGCGCCGCAGCATCCCATGAAGGCTACCAGGAA GACTACGCAGCCAAGGACCAGGATGATGATGGCCACGCTGTTTGCCGTGA AGGTCTCGCCAACGCCCGAGAAGTCCTTTATGGTGGACACCATGATGGAG CCGAAGGTGATAAGCAAAATGCCGCATATCTACGTTTGGAAAAACGAAGA GTGTGTGCTAGTTAGTCAGTGGTTTTGGCACCACTCATGGTGGGTGGTGA ATCAGGCCTATTGGATAACAGTCACCCCGCCCAAGTTCCAACTAACTGTC TTCGACCGCAAAACTTACTCCGTTTGTGGAGGGAAATGAGAGTCACAAAA AATATGAATATGTGTACATATGAAGACCACATCATTTTTATTGTGTTCAC ATTAGACCGGATTGATTGTCCATTATGTAAAAATCCAAACCTAACTAGCA TTTGATATATATATAACTACGCCTGTGTTTTTGCATTGTGATTTGCGATC GACGCATTGCTTGCGTCGCTGGGAGGCTGTAAACAATTTCATCACGAATA CTATGTGGTCCCAAGATCTTTGAGGGGGATGGTTCTGAAAATTGTCTACG AACGTATGGTATTACTCATGCCCTTATCTTTCCGAGTACAATGTGTTTTC CGACAACTGTTTCGGCTCATTAGCCGTAATTACGTTCGGCATTGGCATGC AATGATTTATTTAAAGAATGTCAGGTTTCTAACCACTTCCAACCACTTTT CCCAGTATTTTTCGATAAGATAACTTTTGAAAGGAGTATCCATGGCTCTT TGGACGAAATCTTGAGCTTCGAGAGTTCATTTTTCATTGTTTGCCAGATA AGATACCACCCGTTTTTTCACTATTGCTGATCTATGTACATATCTCTTGA GAACCTAGAGTCTTACCACAAACAGTATGTTGAATATGAACAGCACATAT TTCACAAAAACGCCGCCGCAATCCATTGCTGAGATGTACTTGTGTATCAC TTGTGTTCGATTTAAGAGTAAGACGTTCGATGCGATTTCGTTCGTGGTCC GCTTGATACTGAAAAAGTCTGATATATAACAATATTTTTATGAGCGCATT TCCTATCGCGAAAAGCTCTGTTAGATTTTAGCTCTGAATTTAGCGGCGAT AAGAAAAGCGTTGCTGCAGTGGTAGAGATTTCCCAAAAAGTACCTAGGTA TCAAATTGAATAGTAGGTTTTGAGGTCTATTGATAAAAAATTATTAATTT CATATTAAACAAGTTAAAGACGAACCATACATAATATGAGAAACTAGTTG AATAACATCGATATACTAAATCACTTAGCAATAATGTGTAGTAAAACTTA ATAATATAACGATTTTAAAGGAATTTAGAGATTATCTGCAAGATGTGCTT AATGTGGCTCAGTTGGAACAAGGTGTTAGCTCAATGGAATCTAGTGGAAA TGTGCAATTGAAAGGCGGTTACCGAAGTTCCGCTCCTTATCAAAGTTCTC TTGCTGTGCTGACTTTTGCTGGCATATTTAGGGCTTGTTTTGGCGAATCG GAGGTTATAAGAGCGCTCCGCCACGGTCACACTGACTAACAGAAAGCTGT TCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTT AAAGTCGAAGGTAATGATGCTCTCTAAACTAGACCAATTAAAGCTAGTGA GATTCTCGGAATTAGCCAGCGAACTGCAAACGGAAACGAGTGGTGTTCGT TTGGCGCTCCCAGCTCGCCAGAGCACAAAAGCAAATGATGCTGCACGCCG CAAAAAGTGGTTGGGAAGAAGAAGCAGTGCAAAAAAGGACGAGGAGAAGG AGAAGGCAGGAAAACAAAAGACTGCGTAGTACGTGTGGAAAAGTGTTGTG CAAGGGAGTCGGGCGGCGCGTATGCTGCGCTTCCTCTTCTCCTTGACAAA GTGCAGTGAACTTTTCCCATTTTCCCCACTTGAATCTTCGAGTCCCATTG ACGCGGCCTTCGTTGTCTGTTGTCCGCATTTTTGTTGTTGTTGTTGCCGC AGCGGGCACGCTGCATTTGTTATTGCCTTTGTTGTTGCCCGGGCAACGCA TTCGGAAGGGCGCCAAAGAGAACGGGGTGATAATGGGATGCTTCTGAAAG CCTTATCGCCACTGGCCTCAAGCAGCAGCCCTCTCTATTAGTCTTGTCAT TACCAACCCCCCCCCCCCTCCCCCTGACAACCCATGTGTATTTCGTTTAT TTACGTGATTTCGCTTGAAAATGTACATTTAGCCGGCCAATTGATTCATT TGCACACCCGTTTTAATACGACGCATTCGATTGCGCTCTTTTCGCTTCCC CTTCCAGACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTA TGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCGGTGAGTATA CATATGTGTGTGTCTTGATTATGTTTACGTTTCTGGTTTATAACCGACGA AATCGAAACCGATACAAAACCGGTAAAAAAGAGTTGCGTGAAAGCCACAA TGGGACACTATGTTACGAAAGTGCTGTCGAAATAAGAGTCGATAAATTCA TTCGCATACACCGTGTGCATTGTGCATACTCAACAGTGTGTTATCCAGTG ATAAATCCGCGTATATGTATATCCACGATATATTGAAACTTTAGTTATAT GCCCCTGGAGAGACGCGGCGCATTGAGAAGTCGAGAACTCGTGCTTTTCT GTTGTTTGCCCGCTGATTCAGTCTGAGACTCGTTATTGAACTCTGGTGAT GTCATCGCCGACGCCTTCCGTTCAGCTTCCATTCCAGCAACTGGACGGTT TGCTTTGGGGCCGAAACAACCCGGTTCTGAAAAGTCGAAATCACAAATGG CTGGGATTTGCAAGAAAAATGAATAAATCCCTAACAGTCAAAAATTTGTA TCTAAGTCTCTGAAAGGATTTCCGGTAATTAAAAAAAGACTCGCAATTCC TTAGTTAGATATGGATTTTCAGCTATGCCAAAAAAAAGTTAGTTATCAGT TTAAATATAGTTTAATAAAACAGGAATATGTATACAAATATTTATATATG CACATAAAACATAAAAAAACACATATGTACATATGTATATACATACTCTT AAATACATAAAATAACTTATGTGCTCATTATGGATCAATTTCCAACTTAT TGAAGAGTTATAATTATGGTATTTTAAAATAATTCCACATCCCCTTGCTT CACAAATGAGTACGTAAACACTTTCTGGTTAGAAAAAAGATACGATTTCA TTTAACATTTCTGTGTAATATTAAACTCTTATAAACACGATTGCATGTTC GCCCTCAGCGCATTTTTAAAGTAGAGTTTTGGGTTTCAAATGGGCTTTGA GCACTCCCACGAACACACACGTGATAGCCTTGCCGGGCCAAAAGCCTGCA AACTGCGTTTAAAATAATAATTAAGCAAATGATATTGTACTCATCGTAAA TTTTTGAATACTTTGCATTCGCTAAGGCGCCTGCAAAAACACGGCCAATG TATGTGAGTCACTAACTTGAAACAACAAAGCGAAAAGCGAAACGAATTAT AAATATAAAACGATACAGCTGCGGTCAAAATGTTATCAACTATGCTGAAA AATCCCACAACATAAAAATTTATAAACGAAGTATTATCATCTCGCAATGG TATTCTATTACTCTTCTTCCTCTTTACTCTGTACATACATAAGTAGATAA ATGAGCAGAAAGAACCAAAGCGGGGACGAAAATAAAAACTTGTTGCTCTA TAGAAAGAAGAGTGATAAAACAAAGGTAACAGCAATCAACTGGTTGGCAG AGCCGAAGTTTGTAGTATACAACAGTCTACACTTACAGCGAGCCGTGTTT ATATTTATCTGGCCCGATCGAGTATATAGCCGAGTACATAGCACACTTGA CAGACAAGCCAAATAAATTAACAAGCCGCTTTTAGAGCTCGCCGAGCACC ACCACAGCTAAAAGTGAAAAAGCTGCCGCCACGCTTGAAAAACAGCAGCG ACAAGCAAAATGGCAGAACAACAGTTCGCAGTTTTTCAGAAAAATGTTTA AAAAAAACCACTCGATTACTGTCAGAATGATAAACACATTGGTTTCCACT ATCCCATAAAAATTGCATTATTTTCATTGAAAGTCTCGTAAAGTATAGGA TTTTCGGTCAAATTAGGTGTTTGTTATATGTTAATGTTAGTTACTCCTCA GTCTGTGTGAGCGGGGTTTTCCCAGTCCCTTGGCAAAAAGTGTGCTAGAA CATATGACGAAACTGTATTGCCATAATTAGCGCAACAAGTCAGTCACAGC TGCTGTCGGGTAAAAGGGCGTGCAGTGCCGGCCATGAGTGTAAGGCCGAC TGGTATTGAATGACCTGCATTCAGCTTATCGATAGCCGTTTCCTGTGCCA CAAGTTGTAGTGCAAACAACTTCTGGAGTAAATATTTATATGTATATCCG TTTAGCCAAAGCCAAACAGAATATCGAAAATCGCCTCGAATTTTGTCCGA TGACGTGTCAATAGTTGAGTTTCGGCTTTTCTAAGGAATTTTCTGTATTG GAATGGTATGGGGAAAGTGATTCACATTCTAGGGTACGTGTCTTGTATAC TCTATAGTATACTCTACTATACTATACTATGATAGTTCTTTGCTTGAATT TGCTCATAGGTGCACAAGGTTTTATATCCAGATTTCTTTAAAACAATTCA AAAAGTCGTCCCCTTATATGTAAAAAGCTTTGAGATAGTGTATATATCTT TTCATCTGTGTTCGATGCAGCGTGACATATATTCATTGCATGACTACGCC AATTAAAATGTACACTTTAATCTTGCATTTGAGCATTCCCATCACGCATT TGTCCTGTTGCTCATCGGGTAGCTCAAAACTGATGTCCCCCCACCACCTA CCTAAGCACACTCAAGTTTACTTGTTCGATTCGGGGATGCAGGCAGTTTG GCGCCAATCGAGCCATTCACATCGTTGGGTGTGGTTCCCCACATTAATAA ATATATATCTATCTTTTTATTGCGGTACGCAAAACTCTCAACTATTTTCG TTTCCCTTGAGGGTTGTTTTTCTGTTTAATTTTGTGCTTTTTTTTTGTCG GCAATATGATCTCAGACCCTTGCTAAGGGCTTTCTGGTATTTGCAAAAGC AATTTGCATTGTATTCTCATTCCAGTGTGACGTCATTGAAGCTGTCGCCA ACAGTTTTGGGCGAAATGTGGCCAACAGCATTGTCTCGGCCATATTTATG TGGATTGTGTAATGTCCGCGTTAGCCGAAATCGGGCTGAAATGAGTAAAA GCTGGGGAGGAAAAGTTGGCGGCTGCAAACAGGTTTCCAAACGAAAACTC TTGTTTTCATGTCGCATTTTGTTTATTGGTGCTGGAAAAGTGGAACAATT AGCAGAGTGCCGGGGTTTTGCTTTCCTTTGTTCGCATTTGAAAATACTTT TGGTTCGATTTTGACACGGAATTAAATCCAGCTGCCACCGCCGCCAACGT TTCATTCTAGTTTTCAATCTGTGGAGCTATAGCCAGGCAGCCCACACGCC ACTTAGATATGAATACAGAAATACAGATACAGTGGCCGCGAGCATCATGT ACACATAATGAAATCAAGCAGATTCAATTGATGACCGACCGCGTAATTGG GGCTGCAAGTCGGCCATTCGTTCCTGCCGAAAGATCAAAGTTGATTTGCA TTGTCTGACCAGCTGAACTGAGCCCAGCCGTAAAATCAAAAACTACGGTG TACCGCAGACTTGGTCGAGATTTCCGTGGCATTGTCATGTGTGAATGTCA CGGGATGCGCGTCCCTCGGCTGGCTTTCAGTTCTCATCTTGAGCTGCCTT ATCTTATCCGAGCGAATCGGACGGCCTTAGCCTTGTTTGGGCAGCAAATA CTCTTGGACCAATATTATGGTGGTAGCAAACTATTTTAGTGGGGAATTAC GTAACGCGCTTACTTATTTTAATTATCATGAACCATGCGCCGCTTATGGC GTGCCTGAGCCTGACCAGGAATCCCTGAGGTCAGCTACTGGGTTCTGTGG TAATTAAGTCTTTTTAGCATGGTAATTGCGAAAGTTCTTCCACTCCGGCA CTTTCAATTAAACTAAACGAGACCGAGCTGATTAATTTGAACTATATTTA GAGCTGTTTGTTAGAAGTGAAAATGCAGTGCGTATCTTATGATGTATCTG TTATGTCTTGTCTTTAGCTTATTGAGTTCATTTTATCGCCAAGTTAAAAC TATGTCTAACCCTTTGTTTCTCTTTCTTCGCCTACAGGTTATCGGCATCT TGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAA GTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCT TATCAGCTTGGGCTCGATTGTGGTCTTCATTTCATTCCTGGGATGCTGCG GTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTG CTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCA CAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGA ATTCTGAACATACTTATAAGGGAGGTGTCTTCGACACCATTCAGAAATCG GTAAGTGCTTTAATAACCAAGCACTTTCCATATATATGACTTCACAACGC AATCTTTAGTTGCACTGCTGCGGATCAAGCTCTGCTCTGGACTACATCGG CAAGGGAGACTTGGTGCCCCCAAGTTGTTGCAGCGGTTCGTGCCTGATCC CGACTAACTACTACCCGGGATGCCGTGGAAAGTTCGTCGAATTAATGACC ACTGGATCTGATAACGCTAAATATGTGGGCATCGGCCTCATCGGAATAGA GGTGAAAATTATACGCTAAATATAAGTTTCTCAAGCCGCTTTATTAACGA AATATCCATTTTAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGGCCAAC AACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATC CATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCA CATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATAC ACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAA ACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATA TCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGC AAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACC GAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTT CAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAG AAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTA AGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGA TTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGAA ATTTATGAATAAAGCATTTACTATGTATTTATATACCAATACCGTTGCGT TTATACAATTGTTCAGGGGCTGAAAACGAAAACTGATGCCAGTAATAATT TGCTCGCCTTCAGGCGGTTTGTTATGTCCTCAAGTTGTCATGGCAGCGAC TTTAGCTTATTAAGCAATATACTCGTATGTGAACTAGATATTACTAGAAA TAGAATTACTAGATACCCTTTGGGCTTCCACGGCCACTTCAAATTTGTGT GCGCTCGCCAAGGATATTATTGCGATAATGGCGGGTAATATAATTGCTTA CGCAACTACGCTGATTCCTTAATGAAATTCGATAATTAGAGCCATTACTC ATTTTTTTTTTTTTTTTAATGTTCTATAGCTTTAGCCTGTTTTCTGAGTG CCAGCATAGATCAGTTCAGCTCAGAATCGCAGTCATGTGCTGTTTGCTCG AGCACATTTTCAAAATTCTGATTTTTATCTTTGCCATTTTTATAAACTTT CTTGTGACCGTCAACTTAGTAATACATTTCTACTATATTAAGGTTCATGG ACCACAAGGTGATGCAGAATATTATAAGCTTAACACTATGGAAATACATT TTTTTACTATTTGGCACAGATTTCACTTCGGGAATAGAAAATTACTACAT ATTATGGACAATGCAAAGCTGGTGCGGAGCCCTAATGGTCGTAATCAAGT TGAAGGTTTGCGAAGGCTCCATTTCTTTTTATAAGAAGACTCTTACCCCC GCCGAACTTTTGCGTATAGGATC 2R 1731128 2080000 RE04135 ACGTTCGCGTCAAGGAAGCTGACCTGCAACGAGTGTGCGGTGCGAGATAA CCGGGATTCGAAAGTGATCGAGATAAGCTACTGTGTACCGTGTGAGAGCC TAGTATCCGAGCACTAGAGATACAAGCACCAAGCACCAACAGATACTTCT TAATAGACTGCAATTTATTTGAACAAGAAGATAAACGAAAAGTGTAAATT AGAGAAAATGGATGTGGAAGAGTTTCGCAAATACGGCAAGGAAGTGATTG ATTATATATGCCAATACAGCACTAATATAGAGGAGCGTGACGTGGCGCCC ACCTTGGATCCGGGTTACCTCAAAAAACTGCTACCAGCCGACGCTCCCCA GTCGCCGGAGCCGTTCAAGGACGTGCTCGAGGACTTCGAGCAGAAGATCA TGCCGGGCGTGGTGCACTGGAACCACCCCAAGTTCTTCGCCTACTTCCCC TCGGGCAACTCTTTTCCATCGGTCCTAGGCGACATGCTCAGCAGTGCCAT TGGTTCAATTGGCTTCAGCTGGGCCAGCTGTCCGGCGGCTGCCGAGCTGG AGACGATCGTGATGAACTGGTACGCCAAGGCCCTTGGCCTGCCCAAGGCC TTTGTTTCGGATGCCCCAGGCAGTACAGGCGGCGGCGCCCTTCAGGGATC CGCCTCAGAGTGCGTTCTCGTCTCTCTAATCACAGCCCGCGCCCGGGCCA TCAGCGAGCTAAAGGGTCAGACCAGCGTTCACGACAGCGTCTTCCTGCCC AGCCTGATCGCATACGCCAGCCGTGAGGCACACTCCTCCGTGGAAAAGGC CACCAAGATGGCCCTGGTGAAGCTCCGGATAATCGATGCCGACGAGCATG GACGCATGCGCGTTGACCTACTCCGCCAAGCAATTCAAAACGATGTGAAC GCCGGCTTGACACCCTTCTTTGTAGTGGCCACTGTGGGTACCACCGGCGG CTGCGCTTTCGACGACATCACGGAGATCGGAAAGGTGTGCCGCCAGGTGT CGAGCATTTGGCTGCACGTAGACGGCGCCTATGCGGGAAACTCCTTCATT CTGCCCGAGATGCGGGTCTTTTCGGCAGGACTCGAATACGCCGACTCCTT CAACACAAATCCCAACAAGCTTCTGCTGACGAACTTCGATGCCTCTGCCC TGTGGGTGCGGGATGTGATGAACCTTAAGAGCGCGCTCAACGTGAATCCC CTCTACCTACGACACGAGCACTTGACCGGAGTTGACTACCGCCACTACGG CATTCCCCTGAGTCGCCGATTCCGGGCACTCAAGCTGTGGTTCGTCTTCC GGACATACGGCATTCGGGGCCTACAGGAATACATTCGAAATCATATGGCG TTGGCTAAGAAGTTTGAGATGCTGGTGCGCAAGGATGAACGATTTGAGGT TCGCAACGATGTTCACCTTGGCCTAGTTTGCTTCCGAATGCGAACTGGCG ACGAGCCCAACCACATGCTGCTCGCCCAGATCAACCACTCGGGCAAGATG CATATGACGCCGGCCAAGTTCAACGGCCGCTACGTGATCCGCTTCTGCGT CACCTACGAGCACGCCACTGAGAAGGACATCCTGGAAGCTTGGACCCAGA TAAAGTGCTTTGCTGAGGAAATACTGCGGGACCACCAGCTGGAGTCCAGC TCCGTGCCAACCACGCCGGAAGGCTCAGAGCGGACCAGCTCAGAGCCATT GGCTCCAGTGGCGGGCAAGCCACCCATCAAAAAGAGGCTGACCAGGACAA AGTCGCTGCGATTCTCCTTCACTCGCAGCATCTCGCGGGAGCAGTACCAG AGCCAGAGCGAGCACCTAATGGACGGGTGCACACCCATCCTGGTCGTCGA TCCCAAAACTCTTCAGGAGAACTTCCAAAAGGCGGCGGATGACAATGACA GGAACAACAGCAATGGCAACGTAAAACTCAAAGATATATCAGACGTGGAT ACGGACGAGGCGAGTAACTGAGCGTCGACCCGAAAAGGGATTTGCGGATT TACCTCTACCTAGTATTAGTTGTCGAGCTGAAATGAGGCATGAATCAATC GACTACCGACTAACATTGCTCAGTTTGAATTTAAGAACATCCATTTATGT ACTAGTAGGACCTTAGTTGTTGCTGAATATCATGTAATTTAAAGATAGAC TCATTTGCATCTGCTTATACCGTTTAGCTACCTTAAGTTACTGTCATGAA CAAAAGCACTTATTTATAAACATTATCTCGGCATTTTTTATGCAAGTTTT TAAAAAATACAAACACAATCAACGGAAAAAAAAAAAAAAAA RE31022 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCC ATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATT TAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAA TCAATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCG AAGCCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACAT CCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCT AAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTA TTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCA TATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGC GCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCA TGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAAAAAAAAA AAAAA RE35072 ATGTATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGC ACATATTGGTGAAACTATTTAATAATATTTATTAAGATTTTACGGAAGGC CTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAG CAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATT TTTTGTGGATGCATGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAG TTTGCTCAGTAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAG CGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCA AGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGA GTCGGCAATAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAA AGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTAT AGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGC TGCCGGATACTATAGATGGCTTACAAAAGCCAAATACGTCCACTGATTTT TGGGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCG CCATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGA ACAAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAA CCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAA GCGGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAAT AAAGCCCAATTTATCGCAAAAAAAAAAAAAAA AT24862 GGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAG CTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGT ACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTG GACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGG AGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGA TCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTG CTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCC AGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGC AGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCA CAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCA CATGCTAATCCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGC AGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTG CAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGA CCTCAAGCAGGTACTTAATCAGCTGGGTATTACGGAAGTCTTCAGCGATA AGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTCG GCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGGC AGCAGCAGTCAGTTTCATGAAGATAGTACCCATGATGCTCAACATGAACA AGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCCG CAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTGG ATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTACA ATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCCA CTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCAG TAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATAT GAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGGG GAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGATC GCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAAC TTAAAAAAAAAAAAAAAAAAAAAAAA GH08636 ATTTGTGAGCACACACTTTAGTTTTTCGTTAGGAACGGGACGTTCGTTCT GTTGCGCACCAAATTTTTTCGGACCCAATGCAAATGCAAACGCTTTTGCG GCGTGTGTAGTGCATTCAAAATTACCAGATACCCAACGGGATCCAAAGTT CCCAGAGCAGTGGCACCGGAATCGATGCGACCAGCAGTCAGCGGAAGCGT AAGAAATTCGCGCCTAGGTGGACAAAAATCGATCTGTGACGCGGTTTAAA CCAAGGCTGCACGACACTTCGAGGACTTTTATGTGATTATTACTATGAAA TTGGATGAAATAGTTGCATGGTACCAGAAGAGAATCGGCACCTATGACAA GCAAGAATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATA GTGTCAATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGAC TTGGTGCGAGGTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTACT CACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTATG CCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCTT GTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACAG CAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTGC TTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGAG TCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCCT AAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACCG CCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATCT GCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGACG TCGCAAGAAGATTGTGCGAGTTCGACAAGTGGAGGCTGACTTGTCCCAGG CCAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATC GAAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTG TGCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTA TCAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGC CCACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAG AAAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACT GGCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCG TGCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGA AAGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGG AGGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGAC AACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGC TCCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTG TGACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAAT GAATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACAT TATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCA CCGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCT GATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGA AGATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATA GCAGCCTCGACCGTATTAGCTGCACCATTTGGGATCAGCGAGATGCCAAA AAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATCGAACGCGT GGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGTGGTCTTCT CTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCGAGGTCACA CTCGGGAGCGATGCAGAGAAGGCCAGTGAGATTAGCTACTTTAACATGCC GCAGCTGCTGTGGGAGAAGTCATCGGCATCGCTCTTCACCCTGCTGGGCC TTGCCTTCGGCGACAGCCAGTGGGAGCGCATGGTATTGGCTCTGGGCTTT GTCCAACGCCTTTGCCTGACCCTCATACTGTTCATAATATTCGCCGTTGC AGAGCGCACCTTCAAGCAACGCTTCCTTTACGCCAAACTCTTCTCCCACC TAACTTCATCACGTAGGGCTCGAAAGTCAAATCTTCCCCACTTCCGTTTG AACAAGGTGCGTAACATCAAGACCTGGCTGAGCGTGAGGTCGTATTTGAA GAAACGCGGACCCCAGCGATCGGTGGATATCATCGTTTCCGCCGCCTTCA TAGTAACCCTCCTGTTGCTGGCCTTCCTCAGCGTCGAGTGGCTGAAGGAT TCGGCTCATCTGCACACACACCTTACCTTGGAGGCCCTAATCTGGTCCAT AACAATCGGTATCTTTCTGCTGCGCTTCATGACCCTAGGTCAGAAGATAC AGCACAAGTACCGCAGTGTGTCGGTGCTGATTACGGAGCAAATTAACTTG TATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTC GAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGC CATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATC AAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGG CTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCG CAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGA AATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCC AAAAAAAAAAAAAAAAAAA SD07915 TGCGATTTCACTTTCACAAAAAAAATTACGGCTGCCGAAGCGGCCGATAC TCAATGGACCTTATCAATTATTAAATCGGACCGCACGATAATGGCGCTGA TAAACCGGCGGCATTGAGCCCCAGAACCTCGACAAGCAGCTACTGCCAGC TGTTAAGCATATCAAACAGCGCGAACATATTGTAAAAGCCGGAAAAGACA GCTGAGTGAGCATGGATCTAATGCACCGCACCCTGCTCACCGCCCTGGGT GCGCTGTCAGTGGTCTACGCCCTGGTCAAGTTCAGTCTGGGCTACTGGAA ACGGCGGGGGATCCTGCACGAAAAGCCCAAGTTCCTGTGGGGCAACATTA AGGGCGTGGTGAGCGGGAAGAGGCATGCCCAGGACGCCTTGCAGGATATC TACACCGCATACAAGGGCAGGGCGCCGTTTGTGGGATTCTACGCCTGCCT CAAGCCGTTCATCTTGGCGCTGGACCTGAAGCTAGTCCACCAAATAATCT TCACCGACGCGGGACACTTTACGTCCCGAGGCCTTTATAGTAATCCCAGT GGAGAGCCGCTGTCGCATAATCTCCTTCAGCTGGACGGTCACAAGTGGCG GTCACTGCACGCCAAATCTGCAGAGGTTTTCACTCCGGCCAACATGCAGA AGCTGCTGGTCAGACTGTCGCAAATCTCCTCCAGAATTCAAAGGGACCTG GGCGAAAAGAGCCTTCAAACTATCAATATAAGCGAACTCGTGGGTGCATA CAATACGGACGTTATGGCGTCAATGGCCTTTGGACTAGTAGGGCAGGATA ACGTGGAGTTCGCTAAGTGGACGCGCAACTACTGGGCGGACTTTAGGATG TGGCAGGCTTATCTGGCGCTTGAGTTTCCGCTCATCGCTCGCCTTCTTCA GTACAAAAGCTACGCAGAACCTGCTACAGCTTACTTCCAAAAAGTGGCCC TGTCGCAGTTGCAGGAGCATCGAAGAAGGGATCGCCAGCCACTCCAGACC TTTCTGCAGCTATATTCCAACGCAGAAAAGCCGCTCACCGACATCGAGAT TGCGGGCCAAGCCTTCGGCTTCGTTCTGGCTGGCTTGGGCCCCCTGAATG CCACCCTGGCATTCTGCCTCTACGAGTTGGCCCGCCAGCCTGAGGTGCAA GATCGAACCAGGCTCGAGATTAACAAGACACTGGAAGAGCATTGTGGCCA AGTGACACCGGAGTGCCTAAGGGAGCTCAGGTATACGAAGCAAGTCCTCA ATGAAACGCTTCGCCTGCACACTCCACATCCCTTCCTGCTACGCCGGGCT ACCAAAGAATTCGAAGTGCCCGGATCGGTGTTTGTAATTGCCAAAGGCAA CAATGTGCTGATACCAACGGCGGCGATACACATGGATCCTGGCATTTATG AAAACCCCCAGCGGTTCTATCCGGAGCGCTTTGAGGAACAGGCAAGGCGA TCCCGCCCGGCAGCTGCGTTCCTGCCTTTCGGCGATGGCCTGCGAGGATG CATTGCCGCTCGCTTTGCAGAGCAGCAGCTTCTGGTGGGCCTGGTGGCTC TGCTGAGGCAGCACAGATACGCTCCCTCTTCGGAGACCTCGATTCCCGTG GAGTACGACAACCGGAGACTGCTCTTGATGCCCAAGTCGGACATCAAACT CAGTGTGGAACGGGTGGACAAGCTTTAAAGGAGGCTCTGCTGGAGCATCG CATATTTTGTATTGTTTGCTTTATAAAGCGTTTAAGTTGTTTTTATATTT GTATATGCACCTTTTTCGTTGATTTTCCTAAGCTGTGGACTTGTGTGATA ATGCTGACGATGACTTTTATAATCTTTTGCACCAAGCTCAACAACGTGAA CAAATAAATAATTTAGTTGTTAAAAAAAAAAAAAAAAAAAAA RE28276 AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGA CTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGAT GCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGC TTTGTGTGCGGTTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTA TACGCCAGCTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCG GAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGG TGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTT GGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAAT GCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAG GCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTA GCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGAC CTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCACCGGCGTGGGCAAGAG CTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCG CCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACA CTAAAGGTGGACATCCTGGGCACGTCGGGTGACATGCAGTTCCCGGCCAT GCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGG CCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATC CGCGAGCAGCGTGGCGACTTTCAGGACATCCCCATTGTGATCGCCGGGAA CAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGA CCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGGCGAAAGTGCTGGAG TGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCT CTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCG GGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCC TACGTCAGCGCATCGTCCAGTCGCAATAAAAATCGGATGAACAGCCCGGC CCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCG TGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCT CGTTCCAGATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAAT CAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCG CCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCAC AATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGG CGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACC CAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTG CTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGA TGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCT TATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGC CGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATA AGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAG TGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTT GCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGG AAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAA TTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTT AATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCG TTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGA CTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACT GGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTC TAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGG TTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGA TAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCG AATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCAT TCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCAC AGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGG GAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTG AACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGC ACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTT TTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGT GGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTG TTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACAT TTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGAT GAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGA CACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATG CACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAA TGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGT CCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAAC CGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTAC CTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACG TTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGAC TAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGC GGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCG ATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAG TTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGA TCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCT AAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCA AATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCG TCCCAAAAAAAAAAAAAAAA LD41464 CACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAACG AAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACGCC CAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGCCA CCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAACAG TCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAACT AAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAACGC GGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGCAC TGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCGAG GCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAGCG CCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACTGG ACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCCAA CTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAGGA GAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTTCC TGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAGCTC CCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCGAG TCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGAAAC ACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACAAA ACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTCGC TCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCATCT ACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCAGC GCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCGCA GTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCATTT CGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGGCC TCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATCGA GGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACACC TGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCATTG CACAGCAACGTGCTGCAGATAAGCAGCAGCCAGTTTCCTCCACAGAATCC GAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGGAT CCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTGGC CAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGTCA GCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCCCT TTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAGAC ATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATAAA GCACACAACTATGGCGTCCCTATTTTCCAATCGCCAAAAAAAAAAAAAAA AAAAAAAAAAA LD21194 TGTTTTGGAGGATAAACGCCAATTAATTGTCAAGCGATGTGCCAGCTCCT GTAGAATACACTCAGCATACTACGGTGCAGGGATCCCACATCCGGAGACT CCCGCGGGGCAGGGACCAGGCTAGCATTCAGTTTCTGCCAGTGATTTTCT CATCAAGGCGTAGGCACAGACGTTGTGGATCATCGCGTCTTCGAGCGGGT GAAACATGAAGATGGCTGACGGCTCGACCATATTGCGTAGGAACCGGCCA GGCACAAAATCCAAGGACTTCTGTCGCTGGCCCGACGAGCCCCTGGAGGA GATGGACAGCACGCTGGCGGTGCAGCAGTACATACAGCAGCTGATTAAGC GCGACCCGAGCAACGTGGAACTCATACTGACCATGCCCGAAGCCCAGGAT GAGGGCGTGTGGAAGTACGAGCACCTGCGCCAGTTCTGCATGGAGCTGAA CGGCCTGGCAGTGCGGCTGCAGAAGGAGTGCTCGCCGTCGACGTGCACCC AGATGACAGCCACTGACCAGTGGATATTCCTGTGCGCCGCGCACAAGACG CCCAAGGAATGTCCGGCCATTGACTACACACGCCACACGCTGGACGGTGC CGCCTGTCTGCTAAACAGCAACAAGTACTTCCCTAGCAGGGTGTCCATCA AGGAGTCGTCGGTAACCAAGCTGGGCTCCGTATGTCGGCGGGTGTATCGC ATCTTCTCGCACGCCTACTTTCACCATCGTCGCATTTTCGACGAATTCGA GGCCGAGACGTATCTGTGCCACCGTTTCACGCATTTCGTCACAAAATATA ATCTGATGTCGAAGGAGAATCTGATCGTGCCCATCAACGTGGGTGAAAAC GCGGCCCCTGGCGAAAGCGAGGCTTAGGAGCCCGCCCAGATTAGTCAGAC TCGCATGAAACACTCATTCAACATACATCTATTTATATTTACCAATAGCT TGCAAGTTGGGTTGGCTCACCCTGACAGGGAAACGATTCCACGCGGACCC GACTCTAATGCAGATCTTGTATGTAGTTTAGATGTCAGATACACATAGAG CTACATAACGATAACTAAGTAACAAGGGCAGACCCCCTCAAACCCGCTCG CCCCATCTGATCCTAAGTCAGCAATTATTTCGCAAGTTATATTACGATTA TGTTTAACTCCTTATTTTAATAAATTATATGTAGGCACACGACCTTCTCG TGGCTGATTCCACGTCAAATCCCCGTAAACTAAACTAAATTCCCTTGACT ACTGGCAGCCAAAACACCAACACAGCTGTACGTGACTAAAACGTGAACTT TACTATACAAAATTACTATATACACAACAGAAATTGCAATAAAAGAAGTA CATACATAAAAAAAAAAAAAAAAAAAAAAA GH04835 CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGA CTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCA TTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAAT GGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGA AGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGT ACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAA GCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATA AGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGC CCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGT TTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCC CAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATT CACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACG GAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAG TAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAAC ATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGA ACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCT GTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGG TGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGA GGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGT CACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACG CCTGCTGCACCACCATCTACGCCATCTGCATGCTGATTCTGTTCGGCCTG CAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTC CAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCC AGGGATACCCCATGGATGCCCTCCAGTTGGCCTTCTCTTGCTGTGGCAAC ACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAA GGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCT GCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACGGACCTGATTCGA TGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTC GTGCTGCCTCGCCAGCGCGATGAGGAAGCGCTAGAGCCGAAGTCAGATAC AATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAACACACGAATTCC TCACTCACTCACTCACCGTAAATAAACCAGAATAGGTTAAGCCCAAAAAA AAAAAAAAAAAA RE34119 AGTTGCGAGCGGACCTCTGCACGGAGTGGAACAAAATCTGAAGAGCAAAG AGTACAGTCCGCGGAAAACGTTCAATTAATAGAAGCAAGAAACCACATAT ATAATCTAATTATTCTCGTATATACCCCACATATATCTCGCCTGTGCATA TACGAACCCCGTATATATGTATCAGTGAACAAAAAGTTGTTATACATAAA ATAAATTGCGAAAGAAGAAACACCATTATCAACTAAAAATAGTGACCGAT TCTCAAAGGAATACAAATTTTAATAACGAAAGACCCCAAACGACGAGAAC GAATCAATTATACAATTATAACACTATAAACTGTAGAACACACCAAAACG AGCAGACACGCGCACGCATGTTCGCGTTAAGGGCCTAAAGCACATCAGAA CCGTAACCGATCGCAGGATGACTTTCACCCGCCTCAAGACTCTCTCGCTG CTCGTGTGTGCTCTGCTGGCCCTGAGTTTTCCCGGACATGTGAGTGGTGC AGGCAACAACAACAACAAGAAGGGCTCGCAGCCAGTGGCGCCTCCGGAGC CGGAGGCCGTCATCGAGGAGGTCAATGCCAAGCAGCTGGAGAAGCTCCTG GCCGACAAGGATTACGTGGCCGTTTTCTGGTATGCGCGAAGCTGCGTGAC CTGTGATAAGGTTTTAGCGGAACTCGAGAAAATCGACGATGACACCGACT CCTTCGGTGTGGACTTCGTGAAAATCAACGACAAACGACTAGCCAAACAG TATGGCATCAAGAACTTCCCCGCCCTCACCTACTTCAGGGAAAAGGAGCC CATCATATATGATGGGGATCTCATGGACGAGGAAGGAGTGCTCGATTTCC TCACCTCCTTGGAGGCCATGGACTTGCCCGATCGCATCGAGGAGGTCAAT GCCAAGATATTGCAGAAGATCATCGAGGACACCGACTTCGTAGCCGTTCT GTTCTACGACAAAGACCAAAAGAAATCACAGAAAATCCTCGCAGAACTGG AAAACATCGACGATGAGTGCGATCAGAACGATATTGCCTTTGTCAAGATC GATGATGACAAGGAGGCCAAAGAATGGGGTATCGATGAGATACCATCGAT TGTACTCTTTGAACGTGGAATTCCACACATCTACGAGGGTGATCTGATGA AAGAGGATGAGCTGCTTGGCTGGTTGGTGCACCAGAAGCGCTATTCCGAA ATTCCCGAGGTCACCGATGAGATGAAGGACAAGTTGGTCGAGAACACCGA GCACTTGGCGGTTATATTCTACGACAAGGACGATAAGCAGGATATGCGCA TCCTGAACGAACTGGAGAACATTGATGACGAGCTGGAGAAGGAGGGAATT GTCATCGTCCGCATTGATAACGCCGCTGAGGCCAAGGAATATGGTCTCGA TCATTTGCCCGCCCTCATCTACTTCGAAAACAAGATCCCGGCCCTCTATG AAGGCGATCTGATGAACGAGGATGAGGTGCTCGAGTGGCTTCTTGTCCAG AAAAAGACAGCTAATATCGAGGAGGTTACCGATGAGATCCTGGTCACTCT GATCAACGAACACGAATATGTCGTCGTCTTCTTTACGGGTGCCTGCGAGC CCGGAGAGACCTGTGAGCACACTCTGAACGCCCTGGAAAGCATCGACGAT GAATTGGATGAGGCTGGCATAATTTTTGTTACCACTGAGGTTACCGGAAT TGCCAAGAAATACAACGTCAAGACCTATCCACGTCTGGTGCTCTTCAGGA ATCGTGATCCACTTCACTTTACCGGTGATCTGGACGACGAGGACGAGGTG TTGGCCTGGATTACTGACGACGAGACCCTTGAAATTCCCGGAAAAATTGA GGAGGTCAATGTGAAGATGTTGGACAAGATCTTGGCTGAAAACGATCACG TTGTCGTATTCTTCTACGCTGAGGGCGATAAGAAGGCCCAAAAGATCCTT AACGAGCTGGAGAACATCGATGACGAATGCGAGGAAAAAGACATTGACTT TGTAAAGACATCCGACGACGATATTGATAAGGAGTACGACCTGCCCGGTC TGCCGGCACTTGCATTTTATAGACATAAGTTTAGAACAATTTACACCGGT GACCTGATGAAGGAAGAGGAAATTCTCGAGTGGGTTATTGATTTGCACGA GTCCACAGCTGATGTCATTGAATCTGTCGATCGTAAGACCCTGCAAGTTT TGATCAACGATGTTGAGCACCTGGCTGTGTTCTTCTACGACGATGAATGC GAATCGTGTTCCGACATCTTGGAGGAGTTGGAGAACATCGACGATGACAC CGACAAGCACGGAATACAATTTGTCAAATCAACTGATGTTAAGCTGGCTC ATGAAATTGGCATTTTCGCATTTCCAGCTTTGGTCTACTACGAGACCGGC GTCCCGATTATGTATGATGGTAATCTCAAAAATGAAAACCGTGTGCTGCA GTGGTTAGTCAATCAAAAGAATGACGAATGTTTCTATGTTGGATTGGGTC ATGACGGCCATTCAGCTAGCGCGGCAACAATTTCGTGCCCAACGATTACA AACCATTCCAATGCTGTCCAACCAAATTGGAGAAGTCAACGAAAGTTCCT AAGATGACCGCCCAGCGGATCGGGCATAGCGAAGGCGATCAGGGCAAGCG TCCCAGCGGCGGCAACTTCCAGTTTGCCAACCAGGCGTCCAGCAAATCGT CCACCAAGCCAGCTGCCATCAAGAAGCAGGCCAAGCCCTCCAAGGACACC GATGACGACGATGAGGACGACGAGGACAAGCCCCTGGTCAAGGTTTCCTA TGCCAACAAGCGCTCGGGAGGAAGCAACAAGCCGCAGGCTGGCAAGAAGC CGGTAGGCAAGGGCCAGGACAACGACGACCAGTCCCAGGAGGTGGAGAAG GTATCCAAACAGAAGTCGGCGAAGAAGTCCGGCAAACTGAATGTCAAATC CGGATATCTCTCTGTGGGAGTAAGGCAACAGTTTAACTGAATGTGGATAA CCACAGACAGTTAGATAGTGATTGATTGTATGATTGAATGATATACCATA CTAAAGTAGCACGTATACGCACTGTTGCCAACTGATAGAACAATTATCAA ACCAAAACCAATACCAAACCCAAAACCAAAACCAAAACAAAATACAAAAC CAACTCAAACCTGTATAGCCAGCAAAAGAACCTTCAATGACAGGTTTCTA TAATTAATGTACATCATCTACATATGTGTGACTGCAAAAGACAACAACTA TGACAAGAACCAACTGAAAACTGAATTCGCAGGCTGTGTGTCCATAAAAT TGAGGTTTCCTCGCACTAATCCTAAACAGTCTGGCACAAAAACATTGACT TAAATACCAATACATCTTCTGTGTCAGATCAGAACTTACTCCACACTTTT AAGCAGCGAGCCTTGGGCGTTGTTCCACGTTAAGAAGATCCACGAGTAGC AGAATCACACGATACCCGAAATAATGAATAATGATCAAGAAAACCTACTA ACTAAAACTTTGTTGATATTTTCGCTTTAACTTTCTTCAAGAGGGGCCGA CCTGTGTAGGTCGTCCCCAGGTCTATAACTAACTAAACCACACATTTGTT GCATTTTGCCAACGGATTTCAAAAAACTTTGTTCAAACTAAAAGCAATTA CTTCGACAAACAACTATAAAACTTCTGAGAACTTTCGCTCGTATATTTAG TCAGCAAGCTTTGTTATTAACAAATTAATGGGACATTGTCTTTTGTCAAT AACGAACGCCTAAACTTTTTTGATACTACTTCTTTTTGTCGCAATATACA ATTTACATTTATGTAGTTAGTCTAATTTAAACAAGGGCCAAAGCATAGTA AACGAACGAACAAACGCATAAAATATTTTTTGAAACAATTTACACCTGAC AGTGCACAACTGTTAGCTAATTTAACTGAAACGTGTAACTATGAGAGCCT TCAACTTTCATAAGTTTTCATAATAACAACATGAGGAACCATAATTTGTA ACCACAACTTTTTAGAAATGTTGCAGCAGCATACAGGCCGTATACTTAAT TTTGTTATGGAATCGAAAATCCAATATTTCTCGCTGAACATGGCCTCGCA TATTGTAGCTCGCCATTTTGTTTCATTTGTTTTCTTCTGAGAGCGATTTC TGTACCGCTCGCTGTTGTTTTTGTTATCGGTATTTGAAAAATATCGAATT AGAAATCTTTATCATTATGTTTTCTTAAGCTAAAGCCTACCAATCTAAAC GCAATTGTAACTAAATCCAACATATATGTAAACAAATTTTGTTGAACAGC AGCTGATAAGTCAAGATTTTCGAAATGGAAATTGTCAGATCGTAAAAATC AAACGCAAATCGACATAAAGCACTTTTGTAAACATAGCTCCCGAATGAAA TTGTAAGAATATTTAATAAAAGCCATCCAACTCAAAAAAAAAAAAAAAA SD10607 AGCTGGCAGAGTGCTTTCTGGGCCTCACCAAGTGCGACGACACAAACGTG CGCAAGGAGGCGGCCAAGTGCATTGCGGAGATCACCAAGTCCGAGGTGCA GCGCAAGAAGTTCACCAAGAGGAATATAATAGCCGCATTTCTGGAGTGCT TGCGACAAGTGCCCACGTCCGACGGCAGTATGGAGCTGCCCATACAGATT TGTCGGGCACTGGGCAATATCTGCTACCTAAACGACGAAGCCAGGGACTT AATACTCGAGCTGGAGGGCGATGCTGTTCTACTGCGACTGCTGGACATCA CAACCATCGAGGACGTGGCCAATGCGGCGCAATTCATCAAAGTGCGCGGC GGCTTGCTGTCCAACTATTTGCTCGGAGGCGAGGGCTTGGCCAAGCGGGC CATGGAGTTGGGCGTGATGAAGAAGCTGCAAGGCATCATCGACATTGGCG CCTCCAATGTGGAACAGCATGAGGATCTGCTGCTGAACACGCTTCCACTG CTCAGTATACTCACCGAGAACGTGGCGGATCTGAACTTCGACTCTTCCCT GAATATCCAGCTGTCTCGCATTCTGGCCGCTTCCACGAATCCCGATCTTG CCGAGATGTGCCTGGAGCTGCTCCATTACCAGGCGGAGAGCGACGAAGTC AAGCTTATTTTGGCCAAGGACGGTCTGTGCGAAACCATCTACAACCTGCT GGAAAAGTACAAGACTCTGGCCAGCACAAGTGAGGCCAGGGCGCTGATGA AACTCGCCTGCGAACTCATCGTATTAATCCTTACTGGTGATGACTCAATG CACTATTTGTACACCACGCCGCTGCTGAAGAACATGGTCGATTGGCTGGA CTCGACGGACATCGATCTGCTAACCACCGGCGTGCTGGCCCTGGGTAACT TTGCGCGCACCGATAGCCACTGCATCTACTTTGTGGAGCAGCAGACCATG AACAAGCTGCTCGAGGTGCTGGCCAAGAACAACGGCGTCAAGGACGATGT GCGCCTGCAGCACGCTCTTCTCTCCGCGCTGCGCAACCTGGTCATCCCGA AGCCAAACAAGAACGCGGTAATCCAGGCGGGCCTGGTGCAGACCATTCTT CCCATGCTCGAAATACACCAGCCACCAGTCGTCTTCAAGCTGCTGGGCAC ACTTCGCATGACCGTCGACGGACAGGAGAAACTCGCACTGGAGTTGCTGA AGAACAAGACTCTGATCGAGCAGCTGGTGCACTGGAGCAAATCGTCGGAC TATGCGGGCGTCACCGGCGAGTCTCTGCGCCTCATGGCCTGGCTGATCAA GCACGCCTACCTCAGCAAAATCGCATACGCACTGCCGCGCAAGGGCGATG CACCCGCCGAACAGATTGCCGACAAGATTCCGCTAACGCAAGACTACGAT CGCAGTAGCTTGAGCGAGTTCCTTGCCAACGAGGGCACCGTGGAGGCCAT GGTCAGCATGCTCACAGCTCAGCACCTGGTCATGCAGAACGAGGCGCTGA TTGCCCTGTGCATCCTGTCCGTGGTGTACCTGTCGCAGCCCAGCGAGGCG GCGCAGGCCCAGCTGCTGCAGGACGAGCTGGTCAAGTGCGAGGTCGGCAA GAAGTTGGCCGAGCTCATCAGCAAGTCGTCGGACACGATGACCAAGGAGA TTGTCGAGAACCTGCAGAACTGCGTGAACTTGCTCAAATCTTCCGAGCAG CTGGTGGCGCATCTGGAACAGCATAACATCAACGAGCTGCTGAAGTCTAT ACCCATTCTCACCGAATACTGCACCTTGTAAGAAAACGGGGACTGTCATT GCATTTATCCCAGCACCGCAGGATGCCTCACAGTGGGATGGGTCGATTTG CACGATTGAACATAACATAAATACTTTAGGGGTAAGCAGTTATCTTTGGA AGTTATCTGTGTGGTCTTACCAAGAGAAACGCCAATACTTATTCGTAACG ATACAAAGATTAATACGTTGCGCTAATGTGCTAAACTCCACTTTACTACT TAATAACAATTTTGTTAAATTGTAATTAAATCCACTCTCTTGAGATTCAC TGACGTTCCACGATTCCAAATAGCCAAAGATAAATGTTTGCCACTATTAG AGCATGTTTTAAAAAAAATCAGCCCACCCTTAGCCACACAGACACACTCA GAACCGGAGAAAATAGTAGTTTTCACCCCAAAGCAACGATTCAGATGTAG ACTTGACTGTAGTTTGGTAAGAAGAAAGTGCAGATTCACAAGTTAAGCAG TTAATCAGTTAAGCACACTGGAACACGCGAACACGAGAGGAGCAGAAAGT ATTTTTTAGACGCAAGCGTATGTTGACTGCATTTATGAGGAGAATCCGAT GTAGTGAGGAGTCACAAATCGTATGAATATTTATAGCATACATACATAAC ATATACGTATAAATATAATAATATTAATAATTTAGCATATTAATCTTTTC TGTTACATGATTTTTAAGAGCACAATAACAACAAATCGTGGTGATATCGC TAAATATATTTAATAAATGTATTTTATGATTGTACTTATAAAAAAAAAAA AAAAAAA GM15292 CGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAATTTGTGG GATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGC CGTGCGGAATATTAATCGGCAAAGGACTAAGGCCTTGCACTAATTTTAAT TGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTG ATACAGATGGCCATTAAAATTTGCATAATCTCAAGCGTAAGCAGCGTAAT GCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTT GTTCAAAGTTACACTGATTGTGCTAATATGTTTAACTGTACAAAATAACT TATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTCACGA AAAAAAAAAAAAAAAAAAAAAA LD08743 CTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTC GCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTA AAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACT GATTAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAAC GTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCT AGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGC TCTGCACAGGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAAT TCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTA CATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGG ATAAGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAAT TTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGG CAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCG GATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCC AGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTC TGCAGTGAAGCCCATATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCC CAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAG AACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAA TCAGGTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAG ACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCC GATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATA TGCGACTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACG AGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTG CATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTT TATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTA ACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGC CACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTC GTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCA CGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCAT ATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATC TAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCAC AGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTG ATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCC TATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGA CTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAA CGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACA AAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTA TATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCG AACGTCTAAACACAAAAAAAAAAAAAAAAAA LD21171 TGGGGAATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAA CCAGGTCAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCAT CTGATTCCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACA ATCGTGTCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCAC ATTTGCAACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAA ATTCGGATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAAT TTGTGAAATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGG AGATTCGTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGT ACGATCCGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTA CGAGAGACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACT ACCCATGTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTA TACCTAAGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCT GCAGTCAAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTAC ATTACTTCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTG TTATGCCCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTA TTATGCTCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCC ACTCTACGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACC TTCAAACCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTC CGTTCACTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCT CGTCAAGGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTA GAGGACATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGC TCGGAATAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAG TTTTTGTTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGA TGCGAAAAGGTACAGGAAGACAACAAGGTAACAGTTAAAACCAGATCAGG AAAAATTTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACAT TTAAAAAAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGT GGCAGCTAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACAT TAATAAAAAAAAAAAAAAAAAAAAAAAA RE12054 CATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGAC GGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATA TCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATT ACTAAGGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATAC CAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGATC GAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTGC ACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCAAACGATAATAGAG GAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGTT CGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCCA AACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAAG CGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGAC CACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAACG GTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTAC AGGGATGCTGGTGAATACTGGAACAAAACTCCCAAGACGGACTATACCTA CTCAGAACTGTCCCCTCACCGACGCCAGTTGGCGCCAGGAATTGTGGCCA TGCCCAATATGTCCAGAAAGAGCCTAGAGAACCATAACGATCGAGTCAAC TACATGGTCCAGCAGAACCCTGCGCAAGAGGAGTTCATCCGCCGCCGCTA CCAGTCCAAGTATACCCAGCAGGTTAACTATGACTCCGCAGATGAACTGG ACGCCACATTTGGGCAGCAAAAGCAGAGCTGGTGGCTTATCCGCCTCATC CAACTGGTTGTTAGCAGCATTACCACCGTGTGGAGTCGGGTGACCAATCT CTCGGCCACGGAGACGACTGCCTATCAAAACTACCACGCTAAGCGCCAGC AGAGTCAACAAGTTGGACTTTGGTGGAAAATAGTACAGACCATCGGAGGA GGACTTGCAAGTTTGCTGCGCTACCTGTATGTTTTCATCGGATCGGTGCT GAGTTTGGACACGTGGTTGCTGCGATCCTCGGATGCGGAAAACAAGTCGA AAAAGCGCTTCCTCATATTTCTGCTGATTTTGTTGCCCTTGCTGCTGCTG TCGGGTCTGTTCTATTACATACACCCCAATGAAACTTTCCCACCCAAATC CCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTGA AAGACTACCTGAACCAGGGAGCAGTTCGAATCGCTACGCTCTCAGGCCGC CGGGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACT TGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAG GGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGG CAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTG CACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAA TAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCG CACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAA CCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATG CAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATT GTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCG TTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAA CGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAA ATAAATCGCAAACAATTTCATATGAAACATCAAAAAAAAAAAAAAAA LD24696 AAGCTTTCGACGAGCTGGAACAGATAGAGATTTGATCGCGAGAAAGGCGT AGTAGCACTGGTTTAGACTTAGAAGCGTCCAATTTGCACAGCGTTAATTA TCAGCGCCAGCGACAAGATGACCAATCTGGCTCCCACCATCCGGCTGAAC AACGGGCGCGAGATGCCAACTCTGGGCCTTGGCACCTGGAAGTCGTTCGA GTCGGACGCCTACCACTCAACGCGCCACGCCCTCGACGTGGGCTACCGGC ACCTGGACACCGCCTTCGTCTACGAGAACGAGGCTGAGGTGGGCCAGGCG ATCTCCGAGAAGATCGCCGAGGGAGTGGTCACACGCGAGGAGGTTTTCGT GACCACCAAGCTAGGCGGAATCCACCACGACCCTGCATTGGTGGAGCGCG CCTGCCGCCTGAGCCTTAGCAACCTGGGTTTGGAATACGTAGACCTCTAC CTGATGCACATGCCGGTGGGCCAGAAGTTCCACAATGACAGCAACGTGCA CGGAACCCTGGAGCTGACGGACGTGGACTATCTGGACACCTGGCGCGAGA TGGAGAAGCTGGTGGATCTGGGCCTGACGCGCAGCATCGGCCTGTCCAAC TTCAACGCCGCGCAGACGGAGCGAGTGCTAGCCAACTGCCGCATCCGGCC GGTAGTGAACCAGGTGGAGTGCCACCCAGGCTTTCAGCAGCGCCAGCTCC GGGAGCATGCCAAGCGCCACGGACTGGTCATCTGCGCCTACTGCCCCCTG GCACGTCCCCAGCCCGCTCGGCAGTGGCCGCCCTTCCTCTACGACGAGCA TGCCCAGAATCTGGCCAAGAAGTACGGCCGCACCACGGCACAGATCTGCC TGCGTTATCTGGTCCAGCTAGGCGTGGTGCCACTGCCCAAGTCGTCGAAC AAGGCCCGCATCGAGGAGAACTTCCGCGTCTTCGACTTCGAGCTGAGTCC AGACGACGTCGCCGGCATGGAGCAGTATCACACCGGGCAGCGCACGGTAC CCTTTTCGGGAATGTCGGGCCATAAGTACTACCCGTTCAACGACGAGTTC TAGACGGGCTCAGGGGTGTCCCAGAAATATCGGTTTCGCCGTTATTGGAT TGGCTAGGAATGCAAACAAAACGACTGTGGCATTCCAAGAGGGGTGTTTT GTTTTAGTTGTTAACTCAAAGTTAAAAAGGTTTCGAGTAAACCCGTGCAT TAATTCCCCTTAATATTTTACTGGAAGAGGTTCGTAAGACACCCCGCATA TGTAGTATTTGTATTGTAAAATAAAGTATATTACGTAGAAAAAAAAAAAA AAAAAA GH01501 CTCTCCAGCGGCGCACAACTCGATCGCTGGCCCAGAGGTTCAGTTCGGTT TGGTTCGGTTCGGTTTGAATCTCTGCCTCTGTTTACGCCTCTATATCACC TCCATTGGAGCCCATCCGTATCTGTTTCCCTGTGCGATTCGAGTATCTTC AAGTTAACCATGCTGCAGAAAGTGCGTGGGCTGTGCTGAAAGATTCGCGC GCGGGCGTTCGCCAAGTCGAAATAAACCAGTTAAATCTGAGTGCTTGGCT ATTGGCCAAAAATGTAATCGACACGACAACGGAGTGTAAACAGGCCCATT TCGAGTGCAGTTTTGAAATTGTTTATGCAATGCAATTGTGTTAAAAATTT ATTACCTTCCAAGCGAAACAAAGCAAGGCAGCCGAAAACACATTTCTCGC CTCTCTGGTGATTCAACAGCTGCAGTGTGTGTAAACAAATAAAGCCAGAA ACAAAGCCGCAATATGGAGGAATTTAATTCAAGTTGATTTCATTCATTAA ATCTGCTGGAAGGTTGCAGCGGAAAGAGCAGCGAATTCTCCTCTGAGCGC AGTTACTCTGTGCAACCTGGGCGTGGGTGCCACATTCGGGGAGTCCGTAC TGCATGACTTGCCGCGGGACAGCACCGTAGTGACGAAGACCACCTGCGAG CTGCTGCGGGTGGAGCAGCAGGACTTTCGACTCATCTGGGAGAAAAACAA GGAGTTAATGAATGACATATTCACCAACTGCAAGTTGAAGAACGGTTTTG GACCGAGCGTACAAGCGACAGCCGCAGCCACATCGCCCACGAAACGACCC CTCAGCCCCGACCACCCAAACCCAGCGCTGCCCATCACCGAGACACCGAG TCCTGCTATGAACCGCATGGGCTGGGCCCTACGCACACTACTCGTCGCCG ACAACTCGAGCTGTCTGAAGGATCGCAAGGTCTCCGGCAAGCTAATCCGT AAGTGCGCCCCCGGCACCGAGCTCGTCGACTGGCTGGTCAACCTCTCGCC CATCGTCCACACCCGAGCCCAGGCGGCTGGCATGTGGCAAGCGCTCCTCG AGGAAGGAGTACTCGCACACGTCAACAAAGAGCAGCCCTTCAAGGACAAG TGCTTCCTCTACCGCTTTCGCATCGACGAGGAGGGCGGCACGGCGGCAGC GGGCGTGCCCCAGGCGGAGGACCTCGGAGCGGCCAACGAGCACATCCGCG AGGCGCTCAGCGCACTCTTCCAGCGCGGACCGGACGCCACACTGCGTATG ATATTGCGCAAACCTTCTCACGAACGGACATCGGAGGAGCTGGAGCTGGT CTTCGAGGAACTGGTCCACATTGCCGCACTCTCCCACTTGTCGACCAGCA TAAAGCGGGAACTGTCGTCGATTTTCGTGTTCGAGGCTCATGCCCAGGCG GGAACAATATTATTCAATCAAGGCGACGAAGGACGCTCCTGGTACATCTT ACTCAAGGGATCGGTAGACGTTGTGATACACGGCAAGGGAACTGTTGCCA CTCTGAAGACTGGGGATGATTTCGGGAAACTGGCCTTGATAAACGACGCA CCCAGAGCTGCTACCATCGTACTGAAGGAGAACAATTGCCACTTGCTGCG CGTGGACAAGGAACACTTCAACCGGATACTGCGCGATGTGGAGGCCAATA CTCTGAGATTGCAGGAGCACGGCAAGGATGTTTTAGTGCTCGAGCGCGTG GCTAAGCAACGTGGACAGCATTCGGCATTTAAATATACGGTGATGTCGGG AACTCCGGCCAAGATGCTGGAGCACCTGCTGGAGACGCGACTGGGCCAGT CCGTGGGTGGAATGGATCCGTTCTTGGACGACTTCCTGCTCACACACATC GTTTTCATGCCCGTCGTTCAGCTGGTTGATGAATTGGCCAATTACTTCCA CTGCGATGCCCATGAGGACGCCCAAACGCCCGAGGATCGGGAGTATATAA TCAACTTTAAGAAGCGCGTGATCCAGTTCATGCAAAAGTGGGTCATGGCC GTCCGCCACGCGGCCTTCGAGGAGCCCAGCGTGTGCGACTTTATCGAGGA CCTCGCCGCCGAGGTGGAGGCCGATCCCGACCTGAACGAGGAGACCAGCA TAGTGCACAACGTGCTCACCCAGATGGCGCGCTACCAGGAGGACCGCAAC CAGAACGCCGGCCAGAAGTGGAAGCTCCCGCCCAACGGCCAGCCCATCTG CCTTTTCAGTGGCAATGCGACGCCTTCAAAGACGGTCATCCGACCAGATG ATGATATCATCTTCCGCGTTTACTGCGCCGACCACACCTACTGTACCCTG CGATTCCCCATGCACACCACGGCGGAGCTCATCAAAGCGTGTGCCGCCGA CAAGCTGCAGCTAAATCGGGGTCCCGAAGATCTCGTCCTCGTCGAGGTCA AGTCAAACGGGGAGCGGTCCGTGTTCAAGGACAACGATGTCAGCATACCC ACGGGTCTGTCGCTCAACGGCCGCCTTTTCGTCTCCGTCAAGGACCACCT GGATGCCTTGACCCAACTGCAGGAGCAGGAGTGCCCCACCGAGGGTGTGG ACATCGACCTGGAGATACTGAGCACCAAGGAGCTGGCCTACCACATCACC CTGTTCGAGTGGGACCTCTTCTGGGCCGTCCATGAATACGAATTGCTCTA CCACACCTTCGGGCGGCATCACTTTGGCAAGATCACTGCCAACTTGGATG TGTTCCTGCGCCGATTCAACGAGGTGCAGTACTGGATTGTCACCGAACTG GTGTCCACTCCCAGTCTGAGCAAACGCGTCGGTCTGGTCCGGAAGTTCAT CAAGCTGGCCGCGTACTGCAAGGAGTACCAGAACCTAAACGCCTTCTTCG CTGTGGTAATGGGTCTGTCCAACATGGCGGTGTCCAGGCTGCAACAGACC TGGGAAAAGATTCCGTCGAAGTTCAGGAAGATCTTCCAGGAGTTCGAGGC CCTGATCGACCCCAGTCGCAACCACAGGGCGTACCGAGTGTTCGTGGGCA AGCTGCAGCCGCCGTTGATTCCCTTCATGCCGCTCCTGCTCAAGGACATG ACCTTCGCCCATGAGGGCAACAAGACCAGCCTGGACGGCCTGGTGAACTT CGAGAAGATGCACATGATGGCCCAGACGATGCGCACCATCCGCTTTTGTC GCTCCAGGAGTCTGGGACTAGAGCCGCCGTCCCCGAAGAGCGAGGGCGAG GTGAGGTCGTACATCAGCAGCTTCCGCGTCATCGACAACCAGCGGGTACT CACCGCCATGTCCCAGAAGGTGGAGCCCACCAGGAAGCTCTAAGCCCTTG TGGAGCTGTCATCCAATTAGCCTGTAGCGCGTATTAAGTGTCTAACCCTA GTGTGTGTTAATCAACCGCAATTAGCTGCACAGTTATGAGCTTAGCCGGG TTGTTGTTGCTTTCCGAAAGCCAATTGGGCCACGGCCACCACAGCCCGGA CCAACTTTCGTCCGCATCCGCATCCGCATTAGCCTAAGCTACAGTGTACT ATATCTACGACCCGACTAGGAACTATCTCAATCTTCTAATGAACTGAAAC CCAAACGCATTTTAATGCAAACGAGAAACCTTTTGCTTTAGTACAAAACG ATGGAAAAGATGGAAAACAATTTGAAATTCGGCAATTCCCCGCGGAAACC GAAACGAATAAAAACTAAACTTGGACGTGTGTGATACTAAACATTTATAG GAGGCAACATCAAAACAAACACAACTATACAGCATAATTTCCCACAAACC ATTACTCTATAAATCCCGCGCGAGCTGGTAGAATAATTTGTAAAGTTGTA CAACGTTTTCGAGAGCATGGAATCTATATTTTTATAAACCCTAAACTAAA ACCAACTATTAAACAGTCTAGTTACAGCTAGTTATTAACAAGTAAGCTAC GTAGCGGATAAGTTACTTTATTTATAGTTTTCAATCTTATTTTCATTTGG TATTCCGTCACCCCATCTCCTTTTACGGCAACTTGGAAATAAAATACGAA ACCATTTATTAATATTTATTTACACACAAAAAAAAAAAAAAAAAA GH04125 AGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGCATTTTCCTGTGGG TCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTTTCC AAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGAGAC CATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGGAGC TGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCAGCC AGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACCCAT ACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGAATC AGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAGTCC ATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTGGGT GCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCAGCA TGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAGGGC CAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTTCCA AGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGGGAA CATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAGCTG CCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGAAGT GGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGCCGC TGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAATTT CGTGATGAACTCAAAGAGACCTTAGAGAAGCTGGGCATCCGAGAGCTATT CACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGGCGGCA AAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGGAGGGA GCGGAGGCCGCAGGTGCCACATCTGTGGCCGTCACAAATCGAGCGGGATT TTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCGCGATG CGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAAATAAA AACAATATTTAAATTTTAAAAAAAAAAAAAAAAAAA GH21896 CTTTGCAGACTAGGTTTACTGTAAGCAAAATTACTGAGTATGGATTATCG TTTGGTGCCATGTGGTGAGTTATCCGGCAGTTTGACTTTAAAAAGCCAGT GAAAGAAAACGCATTATGGATGTAAAGAGTGAAATCAATGAGAACACCGA AGGCAGGCGAGAGAAAAACCCGTTTGGGAGCACGAACTGAAGAGAAATCA TTGTTTTGTGGGGGAATACATATGCATATGCGAGTATAAAAACAATGTAC GCTCGCTGAGAGAATTCAGTTGTTGCTCAAAGGCCACATTATAAAAGTCG AGGGCGATAGCCGGTTTATAAAAAGAAATTAATTTACACACTCGAAGCCG CTGGTGAAAAACAGTACCAGCAGTCGGAGCAGGCAGTTAATTACCCTTTC CGATAATCAAGCTAGTGAATCCCCGGCGAAACGGCCAACCGGAGAGATAT AGTGAACACCGTTTGTGGAGGTGACTCATCAGTACACTGCAATTACATAA ATTTATGAAAACGAGCACACCTCATCCACGGTCGATTTGGATACTTACAG GTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCACCG GTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTTCGC CCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGGGGC AGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACTTGT GCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCTGGA CCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACAGTT TTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATCGCC AACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGATCA GCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTTCCA AAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGCACC AACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGAATC GCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGCACC AGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGGGAG CGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTACGC CGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGGACT CAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTGCCC GCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCAGTC GTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAGAGT TCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGGATG TTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCCATT GAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGGAGG GAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCCATG CTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATTTAA CTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAATCA ATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCGAAG CCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACATCCT TAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCTAAA TAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTATTC ATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCATAT TCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGCGCA ATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCATGT AGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAAAAAAAAAAAA AAAA LD37992 CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAA CAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATT TTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCC TTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTG AATGCGCTGGCCCCAGTGAGTGGAGTGATAGATAAAAGCTAGACGTAGAG AAGCTCAGGACTGATCGCTGACCCAAGCCACTGCAGCATCAAGATGTCAT TTCGCGTAGTGCGCAGCTCCAAGTTCCGCCACGTCTACGGACAGGCTCTC AAGCGGGAGCAGTGCTACGACAACATACGGGTATCCAAGTCCAGCTGGGA CTCCACATTCTGCGCGGTGAATCCCAAGTTCCTGGCCATTATCGTAGAGT CGGCGGGCGGCGGAGCCTTCATCGTCCTGCCACACAACAAAGTTGGTCGC ATTGCGGCTGACCACCCTTTGGTGGGCGGTCACAAGGGTCCTGTGCTGGA CATCGCCTGGTGCCCCCACAACGACAACGTGATCGCCTCCGGCTCAGAGG ACTGTGTGGTCAAAGTGTGGCAGATCCCCGATGGCGGGCTGTCGCGAACA CTCACCGAACCCGTGGTCGACCTGGTTTTCCACCAGCGTCGCGTGGGTCT GGTGTTGTGGCATCCCTCTGCGCTCAACGTGCTGCTTACCGCCGGCTCCG ATAACCAGGTCGTGATTTGGAACGTGGGCACTGGTGAAATCCTCGTGCAC ATCGACTCCCATCCGGACATCGTTTACAGCGCCTGCTTCAACTGGGATGG CTCTAAGTTGGTTACCACCTGCAAGGATAAAAAGATCCGCATCTACGATC CGCGCACTGCCGAGCTGGAGAGCGAAGCCATGTGTCATGAGGGCTCCAAG GCCACGAGGGCCATTTTCCTACGTCACGGTCTGATCTTCACCACAGGCTT CAACCGTAGCTCGGAGCGTCAGTACTCCCTGCGCGCACCGGATGCCCTTA ACGAACCCATTGTCATGGTGGAGCTGGACACGTCCAACGGCGTAATGTTC CCTCTTTACGACGCAGACACGAACATGATCTACTTGTGTGGAAAAGGTGA CTCGGTCATTCGGTATTTCGAGGTAACGCCCGAACCTCCTTTTGTGCACT ACATAAACACGTTTCAGACTACAGAGCCGCAGCGTGGTATTGGTCTGATG CCCAAGCGAGGCTGTGATGTGACCACCTGCGAGGTCGCCAAGTTCTATCG CATGAACAACAACGGTCTGTGTCAGGTCATCTCGATGACTGTGCCGCGCA AATCGGATCTTTTCCAGGAGGATCTCTACCCCGATACGCTAGCGGAAGAC GCTGCCATCACCGCGGAGGAGTGGATCGATGGCAAGGATGCGGATCCGAT CACATTTTCGCTCAAAGGTGGCTACGTGTCCTCGTCGGTAAACAAATCGC TACCAGCGAAGAAGGCGGGCAACATCCTGAACAAGCCTAGAGGCGACAGC GCTAGCTCCGGTGCAACGAGCAGCAGCGCGGGCGGCGGCAACTTTGCGTC CGGAAATAACAATGAGGCTAGCGAAGGTGGACCGCCTGCAGCGGTTTTAT CGGAAAAGGACCTGCGCACCATACAAGACGAGATCCGCAAACTTAAGGCG ATCATCGTCAAGCAAGAGAACCGCATCCGCGCTCTGGAGGCCAAGGAGGA CGCCCGCAACAAGAATGGAAGCGATGCTGCGCCGGCTTCAGCGGGAGCAG CCACGTCTGACGGCAAAGCCAGTGAAAGTGCCAACGACCACGCGTCCACA TCAGCCGGAACGTCAAAGGACGAGGACTAGGTCTAGCAATGAAACGAGGA CTGAACTGATAAAAATGGGCGGAATGGATTGGAGGAGAGACAGAGAACTG CTTGTAGAAGCTCGTAGCTACGCTTAATTTCTCTATTGCAACAAAGCGCG CTGAGGACGAATTGAAAAAGAACTTATTGTCTATTACCATTATGGTTTCG ATTATTTATTTTTTATAATTTAATATTAGCGAAATCAGTTGAGTGCGGGT GTGGCACAGATAGGGTTAGAGAATGCCGAGCTAAATCATCTAATCGAACT TAAGCGAGCATAACCGAGCAGACCTGGACGCTTAACGTATAAAACATAAC ATAAAACTACATCCTGCCAAAAATATATAAAAAACCTAACGAACTACCTA CATTTTGCGCCCAAAATCAAGCAGAGCGAAGGGCAGGTACTCGGCCCTTT GATCGGCTTGTTGTTACGCAAGTATGAAATTGTTGTAAATTTAACAAAGG CAAATCATAGACTAAACCTCAATCACTTAAGAGTTAACACCTACCTACCA AATTTGTACGAGCTCCTTTCTGTAACGTCTGTATATTTGTACGTCCCGGA AGTTTTCATGACAATAGCTGATAGAATCGATACTGTTCATCCTAGCTGAG GCCCCCTTAATCAGTCACATTTCCCTGCAAATTGTCGTGTCAAACATAGC GAATTTAGTAAGAAAGTGATGGGGGTCATCGGACTTAATTCGTTTTCGTA ATCAAAATTTTATTGTTCAAACTAATGATAAGCTGTATTTTGAAATAATA AGAGTAACAATAAATGCAACAAAATCAGAAAGAAAGTAAGAAACCATCGA AACTATTTTTATAAAAATTTGTTTACTTTTCTTTTCTTTCATTTGATTTT ACTTTCATTAGTTTTGTTAGAGAACCGAGGGCGAGAGCAGCGTCATTAAA CACCTACCGATTTTGTAATTCACAACCATTGTAAAATGAAGACTATATAC ATATACATACATAAATACTCTATATACAAATAATTTACAATTTGATACGG AATAAAACAAAATACAATGCCAGAAGAAGTTGGGTGCTAATAAAAAAAAA AAAAAAAAAAAAAAAAAA GH02863 ACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCGCTCGTTAAGTGGCA AGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAGTCCTGATAATAGGT GGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTGAAGTCCCGGGCCCT GCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGAGCGCGATGCTGGTT ACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTC TCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGT TAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACG GCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAAC TCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGA GGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGG GATGCCACGGGATTGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTC ATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGG TTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTG TGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGC GTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGAT TGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGG AGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGT CCTGGGCTAGCCACACCTCTGACCGTTGATCCCGATGGCACCTACTTCAG GCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAG ACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAA ACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGT GAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCACAACACATTTGACG CAAACGGCGTCATCGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCC GCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGC CATTTCCGAACTAATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGC GCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAAT ATCGTTTGACAAATTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTT TATGTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTT GTATAGTAAAGTTCACGTTTTAGTCAAAAAAAAAAAAAAAAAAAAA GH05668 TTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCGTAA AATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGTTGCAGTTCTT CATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAATGAGCTGC GGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGCTCTGTTC GATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAG TCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCC GTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGG CTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGTACTCGA TCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACATG TGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGAA GGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAGA TCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAG GGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCCGCTGGGA GACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTCTGGGACA GGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTA TAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAA TTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATAT TTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCA GCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGA TCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAA ATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAAT TTAAAAAAAAAAAAAAAAAA LD30953 TGCGAACGGACGTGTGGTGCTAGTGTGGTGGACTATACGACTTTTCTATA TTTTTAAGGGCCGCGGCAGTAGAGATAGCCTATTTTTCTCGCGACAGAGC GTGTTAAGTAATCAATTGAAATCCAGCGATTGGGTGAATCGAAAGTTCCT CCCCGATTCCCGACTCCTGCGTGCATTTGAAGCACTTACAGCCGCGATTT CCGCACTCGGGTGCACTGTGCTTTTGTTTATACGACCTCCGGTCGCCCCA CATTTTCTGTTGAACTTGTGCCGCCGAGCGGTGTTGTCACTGTCCCACCT CCCCCGCAGAAAATCGAAACTCCCGTACAGTGGGCGTGACCCAGGGCGAA GCCGATAGATAATAACTTTCCACGGGAACTTGAGTGTGCGTAATATCGCC TATAAAGAGTGTTTGGCAACTTGGCGTTCTGGAGTGTCACCCGCAACCAA TTCTAATCGTACATACATATATAAGCCAGCTGATTTGGACGTGTGCTACA GCGATTTCATCCCACTGTGCAAGACGGGCGGCAGAAATTCATAAAACAAC AGCTAACAAATTCGACGAAGAGGCATACGCAAAAGAAACGAAAGAGAGAG CGAGCTTATTGTATTTTTGTAATACTCGTCTGCCCAACAACTACATTTAC TGTAATGTGCAGCCTATAATGTAAGATAATGCAATGACACAGGACCAACT CCCAGTAATGGTTGCAATTTAGCCCAGAAGCCACGAATTCACCAACTCAG CAGAGTGATCAGCGTTTGCACTGAAGGCTGCTAATTGAGGACGAGGATCA TAAATCATTATCTGGCGCCAGCGAGGAGGCGAGCACAGCGACAGCAGCGA TTGAGTTGCACCACCAGAGACGAATTAATCATACGCCGCGTTGGTCGTCC CTCCGTCGATACTAAGATATACATATATACAATGCCTGCGAATCCGCCTC CGCACCACGCGCCGCGCACTTGACACGGGGAGCGGCAGAGTAGCCGGAGA AGCCAGTGAGGCCCAGTCTTGTGTTCGATTTGTGTTTGTTATTTCTTGTT CGAGCTAGCCGGGCACGCTAGTTGGCATCGTTGGCATCGAATCGAAAAGT GTTTGATTTCCGCGAAAACAAAGTACCGCATGTGGCTGCCAGGGCAAAAT CTGCTAGCCGGCAGCACAAACTGCAACAACTGCATCTGCAACTGCAACAG CAACAACAGCAACATCACCAGCAACTGCCGCCAGTTGCCGTCAATTATCG CTCAATATATTCTCCGTTGGCCTGTGATAAACCCCCTAACGTTCTTAATG AACGACCTTCGGTCCAAGTCATTCTATCGTGCAGGCAAACCAACATCTGC AGCATCCGCGTCGGGCGCGACCACCAACGCCAAGTCGTTCGACAAGGGCC AGAACAACAATCCCCGTACTTACAACAACAGCGGCAAGTCGAACAAGGTG TTCCTGCATTACATACCCCGCGATCCGCGCCTAAGAATTTTCAACAAAAC CGCCACCCTGAATAAACACTCGAATCGCACCCTGAGCGAGCTAAACATAA CTGAAGATCTGTGCAATTATGGTGAATTGATTGGCGGTGGTGCCGAAACA GTGAAACTAGTGCCAGTGAAATCTTAAGAATATATCCGCAAAATCCGCAG ATCACCGAATCAATTTATTCGTTAACAAAAGTTGGCTGTTGGCGTGCGGA GAGAGCATTGCCTGGACTACGATCGGCTACGCACTGCAGTTGACCAACAG AGAGAGGGAATATTTACCTACCGCCTACTTAAGAAAATTTATGCTGAAAT CTAATGCAAATTGTGTTCACTTCCAATAATCGCTTGGACAAGAAAGTGCA AATTTTACAAACCTTTTTATAGACGTAGCTGAACCCTTTACACAACAACA CGATCACTGGGACTCCGACATGGCCAAGCTAGCGACGGATCCAAACGCCT CCAACAACAACAGCTGCGAGGCGGTTAACAACAACCACAATGGCCAGAAC CAGAGCCAAAACGGAGGCGCCTCCAATTACCAGGCCCTGCCTCTTACGCC TGCTCCGGCCAACACGCCACTCCACAAGGCCATCAAGCACGACCTCTTCC CGGAGGTCACCTTCTGCAACCTCTCCGTAGAGGAGCTCGCAGATGGGGCT GGACACAGCCGTGTGGTAAGGAGCAGTGTCATCGAACTGGAGGACGGCAC CATGACGTGCCTGATGAACGGAAATGGGCAGGTGAAGCGTCGCAAACGCC TGATCTCGAACGAGTCCGGCGACTCGATCGACTCCAGTTCCACGGAGAAG AAAACGCCCAAGATGCCCGACGGTGGATATGGGTGGGTGGTGGTGTTCGC CTCTCTGGTCGTGTCCCTTATAGCCGACGGACTGAGCTTCTCATTTGGCC TAATAAACGTGGAACTGCTGGAATACTTCGGAGAGTCCACTTCGAAGACC GCCTGGATATCCTCGCTATTCTTCTCCGTGCCCCTGTTGATGGGACCCAT CTGGTCCAATCTGGTGGACAAGTACGGCTGCCGAAAGATGACCATCCTCG GCGGAGTGGTCTCTGCCTTTGGGTTTGCTCTGTCTTCGTTTTGCAACTCG ATCGAGATGCTCATGGTGACCTTTGGTATCATTTCGGGACTGGGCCTAGG CATCGGGTATGTGACCGCGGTGGTGTCCATTGCATTCTGGTTTGACAAGA AGCGCACCTTTGCGACCGGCATCGGAGCATCGGGCACCGGCATCGGGACC TTTGTCTACGCCCGCCTTACTTCCTATCTAATCGAATCGTACGGCTGGCG CGGAGCCACTCTAATCCTTGGCGGCACCATGCTCAACGCATGCGTTTGCG GCGCCCTCATGCGCGATCCCGACTGGCTGATCGAGGAAAACCGTCTAGAG AGTCGATCCCAAAGCGTCACCACCTTCTCGAACTCCAGTGTCTGCCTGGA GGAAATAAAAAAGCTGCTGGACACCGGCATCACAAAGGAGGCTGTGCTAG ACTCGTTGGTGACCAAGAACAACACGGAGGCCAACCAGCAGATTGACGAT CCGTTGGACTCCGCTCTCAAGCGCTACCGCAGCGAGATCTTCCTGCCCAC CTTCCTGAGCACTCAGGAGCTTGACAGCATCTGCGAGGTTAAGAGCCTGA GCCGACGCTCCCTACGCCACAAGGAGGGTGAGGAGGCGCCGTCACGAGAG AACCTGCTGTCCATGTCCTCAGGAGCAGGTGCCTATCCCCCATCGACGGC CGTTATAGGCTCGCCAGATGATACCCTAATGGGCGGAATAGCTCACGAGG CGGCAGAGGAAGCAAAGAAGGCCTATCTGGCCTCCATCGAGACGCTGTCT CCATCGGAAAAGCGCTCCACTGGTAGGACTCCCAATGGCTCGCTCCGCTC CTCGGACGAAGGCTACCTTACGCAGAAGCACGCCAGCTCCCGGTACTCGC TTAACGAAAACATCTTCATGGCCAAGCATACAACACCATCAATCTCCAAC CTAAAGGTGAATGGCCTGCGACACAATTCGGTGGACATCTTGAGCGAGGA CATGCACTGCTACTACTCGAAGGACGAGACCTTCGCATTGCTGGAGCCGA GCAGGCGCATCAGGCCCACCGTCATCGCCATTCCGGAACAGGAGCAGTCG GTGAACAGCGAGCTGGCCACCCGTCGCGCACGCCTGGACAGCATCACGGG AATCCGCCGGCTGTCGCGCTCCAAGAAGCCCAGCCACCACCGATCGAACC TCCGCCGCAACATCTCGATCCGGAACTCCAACTTCCTTAAGGATATGCGC ATTCACCGCAACTCGATCCACTACCGCGGGGCCATGCTGAACACGCACCG CTACCGGCTGCGCGCCTCCTCCTGTCCCAACATCTACCGCAACTCGATGA CCACCATCGCCAAAGAGGAGGAAGATACCTGGTATGACAACTTTGTGGAC ACCATGAAGTCCATCTTTGACTTTTCACTCTTTCTGGACATGAAGTTCGC CCTCTTCAATCTCTCTACATTGTTTTTGTTCATTTGGTTCATTATCCCCT ATCTGTACCTTCCCGATTACATGAAGCAATACAAGTACGACGTGAGCCAG AGTGCCGAGTTGATTTCGGATGTCGGCATTGCCCAAACGGTGGGCATGAT AGGACTTGGCTATCTGGGGGATCTGTCCTGGATGAACATCAATATATGCT ACTCGCTGTGCATGCTGGTGTGCGGAGCGTCTGTGTTCTTCATGCCCCTG CTGATTACCAACTACATGGGCCTGATGGTCATGTGCGTTATTTTCGGATT TACGTTCGCCAGCTCCTTCTCGTTTACGCCCAGCATTCTGGTCAGTATTG TGGATCTGGACGATTTCACGTGTGCCTACGGTCTGGTGCTGCTGGTTCAG GGAGTTGGAATGATCGCAGGACCCCCTATTGCAGGCGTCATATACGAGTA TACGGGCAGATGGGATGACACCTTCTATTATGCTGGAATATTTATCGCAC TCTCTGGTGTCTGTTCGTATCTGATCGAGTTCTGTGAAAAGAAAGCACCT AAGGAGAGTGATAGTGATGTCTTAGAGACTAAAAAAGCTCAACTTTTACA CTAGGTTACTTACATTGCACTGTTGAACGCCGCAAGTAGAAGGCAACTGG AGGTACTACAAATCCGAACTGTAGCATAATAATGGACTAGCATTAAATGT TAACGAGTTTCTTATGTCAAATGGTGTTGCAGCCATAAAATCAGAGCAGA ATTGTAACTGAAACTAAGCCTATTCCTAAGCTCTAGCCTGTAAGACTATA CTTGACTTGACTAATCGTAGCTAAGTATCAATATACACCTAACATATACT TACCGCACTAGGGCAATTACTAACCGCATCTTTGTCTAGACAAACTGTTC AATTTCAATCAATATCAATGCAGTGCATCACTGCCAGGTGCAAACGGGTC CCTCAATTGTCTTCTTTACAAAATTTAGAAAAATAGTTTTAATTGCCTTA CATTTCGTACGAATATTAATTAAAGGGAATACAATAAACAACAATCTATG TAACGTAAAAAAAAAAAAAAAAAA GH01619 AACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGGCATTACGAG ATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAGCTTAAAACA TGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGACACAGGCGTG GGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGT GCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCG ACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCT TTCAGATCTATCACACGCTCTTATTACCGCGGAGCTGCTGGCGCCTTGCT GGTGTACGACATCACGCGACGGGAGACCTTCAACCACCTGACCACCTGGC TGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGTCATTATGCTGATA GGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGAAGAAAGAGGAGGG CGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATGGAGACTTCTGCGC GCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATACGGCCAAAGAGATT TACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACAATGAGGCAAACGG CATTAAGATCGGCCAACAGCACTCCCCCACAAACCCGTCGCTCCCAGGAG CCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTGCTAGGAGTAAACC GCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCCGCTTCTGTAAAAG CTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGGAACAGATTTCTTG TTTTCTATCTCAACCGTAACTAACCACGTAAACATAGCTACCACTAATCT AGCAATTGGACACTAAGCTAAATGTTAAAACCATTAAGATCAGACAGTTA CAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTTTACCAAAAAAAAC CAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAACCACAAAAAAAAA AAAAAAAAAA RE27841 ATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACTC GCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAAA TGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAGC CAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGGT AGACAAGCAGTCCGCCGAGTACAAGGAAAATGCCAGAGAGATGGCCAGTT TGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGGA CAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGGA GCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGTG CTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGGA ATCGTCACCGGAGTGGGACGCGTTTGCGGAACTGAGTGTTTGGTGGTGGC CAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGA AGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATT TACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTT TCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATGT CGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCC GGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAA GCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTG GAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAG ACTTCTGGGGTCACCGACAACTATGCCTTAGACGACGAACACGCCTTGTA TCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGT ACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACT CCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGG CATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTG CGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGT GAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAAT AGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCC ACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAA AATATTACTGGCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGC CAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCA AGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATG TGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCG CATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCA CCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCC CAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCC CTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCA ACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCC GGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATG CTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTT CGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGT ACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTAC GAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACA AATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAA AACACACACATTTAAATGTATAATGTATAACAAAACAAAAAAAAAAAAAA A RE57156 AGACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAA TACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAAC GGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCA GTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGT GCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAA CGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGACA GCTGAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCC GGCGAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCA AACTTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAG TGCGACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGAT CACCAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAG CCGCATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATG GAGCTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAA CGACGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTAC TGCGACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAA TTCATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGA GGGCTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAG GCATCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTG CTGAACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCT GAACTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTT CCACGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAG GCGGAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGA AACCATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTG AGGCCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTT ACTGGTGATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAA CATGGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCG TGCTGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTT GTGGAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAA CGGCGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGC GCAACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGC CTGGTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGT CTTCAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGGAGAAAC TCGCACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCAC TGGAGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCT CATGGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCAC TGCCGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCG CTAACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGA GGGCACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCA TGCAGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTG TCGCAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGT CAAGTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGG ACACGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTG CTCAAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAA CGGGCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAG AAAACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACA GTGGGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGG TAAGCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGC CAATACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCT AAACTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATC CACTCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATA AATGTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTA GCCACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAA GCAACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCA GATTCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAAC ACGAGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCAT TTATGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTT ATAGCATACATACATAACATATACGTATAAATATAATAATATTAATAATT TAGCATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAAC AAATCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTG TACTTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCA AAAACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATT TTAATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTG TAAAACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAAC ATTAACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAA AACCAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGC TACAAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAA AAACTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATA AAGCGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTC TAAACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATG AGAAATAAGAGAAAACCAAAAAAAAAAAAAAA LD08659 GCTTGACTAGCTAACACCTGGCAATGCTCCACAGACATTGGGGCCAACCT GACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACCCAGAAGCACGAGC CCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACAGGGACTGCAGAAA GTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATGAGGCACTGGAACT GGCCTCCAAGGATGAGCGCATCTACACGACAGTGGGAACACATCCCACCC GGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGA TCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGG TCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGT ACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTT CTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAA TCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAG GAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATA GGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCG CAAGCTACCCAACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTG GTATTCGACCCTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCC ACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACG CTGTGAGCCTTGCCAAATCAGCCAAGTTTTGGAGTCTATTGCCGGAATCA AACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAACACATTG GACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACATGCATTT AAAAAAAAAAAAAAAAAAA GH14660 TACAAAGCAGGCCACAGGACCAGCATTTTCCACAGACACAACAGCAGGAT ATTGATGGCAGTAGTCCACCAGTAGAACTTGCAAGGCGCCAGCTGCCCCC CAAGCCCACCAGTTTGAGTATTTTTAACGGCCCCGTGCCCACTGCGGGCG ATAGGCCTGTCGTGCCGCGAAAGTCGGACTTTAAGGCTGATCTAGATGCT AAAATACGCAGGCAAAAGCAGAAGGTTAAACAGCAGTTGCAGCAGCAGCA GCAGCAACAGCAGCAAGAGCAGCAAGAAACGCAGCAGCAGCAGCAAGCAC CACAAGAACAGCAACACTCACCACAGTCGCCCCAAACCAGAAACTGTAAT GTCACTAATCAACAAGCCGCCAATATTACTGCATCAGCATCTGCATTTGC AACCGCAACAGCATCCACAGACCCGTACCCGAATCCAAATCATAGAATGC CAAACCAAAATCAGACAGCCACATCCAATCACACGCAGTGCAAGACGCCC ACAATGGCATTGTCACCGTCATCACCTCGCGGCCATTTGCCATTATCATC GTCATCGCTATCGTCATTACCATTACCAGCCACCACTTCATCACCATCAA ATGCCCGGCCATCGATGTTGCCCGCCAGTGACCGACCACCCGCCCATCCA TATGTGTGCTCCAATGCCCCAGCCAATCCCCACCACGCCAATAGCATTTC CAATGCCAATGCCCATCTCAAGCCGTGCATTACGCCCCGGCCGGCTTCTT TGTCGGGTTCGTTTCGTTTCAATTTGATTTTGATTTGTTTGGGTTTATTT GGTTTTGGTTTTTGATTCCTTATTTTGAAAACTTTCCTACTTTGTTGTAC CTTTGCAAGTATCCTTATCATTTTGTGCTTGCCGAAGTAACTTTACGCGG TTTTGGGTTTCTCATTTTTGCTATAAGTTCGATGTGGTAACCTTTTTGAA ATTGGAGTTGGTTTCTCTCGCTAAGCACTACGCTCATACCATCAAGTCAC AATCATTAAGTTCAGATCATCAATAGACAACTCAAAACCCGCATGATACT GCCACTAACTGCTAAATGCTTAATCACTAATCAGATTCGATCGTTTGTAA CTACAAAATTTTTTTTACAAAATTGCATTTTGCAAAATCGCTTAAATTAG GGGAAATGTCTTTTCGACATGAAGTGGTATCGAAAGTGCCATCACAGCCA TTAACGCTTTTCCACTCGCTTCAGGGTCATCATTATGATTCACAGCAGAC CAAGAACGTTCATAACTTTCTCGATCAGCAGATCCTAACTCTGCGTCTAT CGCTAACTACTGGTATTAGATGGTGTCCTGTGTTTTGTGTGCCAAGTGTA TAAACTGATAACTGTACATTACTGTGAATAACAGCAGAAATTAATGACTA AATCATCAAAATGCCCGCCTCACTAACAAGGATTTTTACTTTTCCCAGGA GGAGCAGCCGGCGGTGGCTCCACGCGCATCGGGCGTCGATCGTCCATTAA TCAGTCCAAGCCACCGCCGCCAGTCAGACGCAGTTCGTCGGTGACCCCCA GTCCCAATGCCTCGGTCGGGGTGAGTTAAGCCTTCAATTACCTACACCCA ATTAAGTTAGCCACTTAATCTAAGCTAGTCGCTAAGCCTGGGTTCACACT CTGGGTCACACACTCTTTGGTTTCCTCTATGCTTTTATTCTTTAACTTAT GATTTAATTACGCAACGCAGCTGCAGCAGCAACCACAGCACGCGACTCTG TCGCAGCAGAATCACCAACTAAGCAGCTCCAGCGAGCACTTACCGCCGCC ACCGCCATTCATGCTGGACGCCATGCCCCAGATTCCCAGCTCAGCGCTGA AGGTATCGGAGACGGTAAGAGCCCTGGCAGCCATGCGGCACCAGCCAGCA TCACCTGTGTCCCTCAGACGCATGCAGCAGCAACAGCAGCAGCAGCTTCA GCAGCAACAGCAGCAACAGGTGCAGCAGCAGCAACCCCTATTGCAGGTGT GTGCTCGGTTCGCATCCGGTTTCCATTTGTACCAAAATGTTTGATTTCCT ACTCTCACCTGACTATTTGAGTTTACAACCCAAATTGGGTACTATTAATG TGTAGTTTATGCTTCTGACCAAAAATTTATGCAACCAGATGAAGATGTAT TTGGCTTTAGTTAGAAAATTCATATATCTGGCTAAAAAGTTTAAAGCTAC AATAAGCTAATCACTAATCGTAAACTGTAGGGATTCTAGTTGCCTAGCCC CGGTAAACAAGCATAAGCTTTGTTCCATACATTTTCTACCTACAAATGTA GGTATACTTTGAGCTCATTGAGCATAGAAATACGACTTGGAAGACTCGAC ATTTATTCCCCAACAAAAGCCAGTATAGTTCGGCGTGAGAGTTAGGTAAT ATTCATTGGGTCTAACTAGTGCACGAGTCTAGAGCCACCTTGAAATTTAG CCATCTTCTTCTACAACTTATGATTTCATTTTATTTCAACTTACGTTTGC TTCACCACTACCACACACAAACCGAAACCCCAATCCCCCACGTAGTCTGC GCACAACTCCCCCCTCAAAGAGGACCTGACCGTGTACTACGACTCCTACT TGGATCTGCACGCCTATGCCCAGGCCTTGGCCAGCGGCCAACAGCCCGGC GGTCAGCAGATGGCCAACCAGCAACGCTTTACCCTCCAGCAGCAACATCA GCATCTGCATCAGCCACAGCAACCGCCTGTCTACCAAGTCGATGCCGTAA GTGACCAGCGGGTATCTCGCGGGCTACTAACCAAGACTAACAGGCGTCTT TGGGAGCGCCTCTCTGGCCTAACACGACTGCCCTCCTTCCAGCTTAGTTG TAATGCCATAGTCATAGATTACTCTAGTGCTTAGCTTTGGTCGTGCTTTG GCTAACTTTTAATTTGTGCCCGTCTTCTTCTCGTTTCTCTCATGCCACAA ACACACCATCACTGACACACATTCACGACCAGACGTTCCGCACCTCATCA CCAGCCGCGGGCGGAGGGGGTGGCGGCGGCATATACGCCCAGCCCAAACT GGTCAACAGCATGTCCAGCTTCCGCACCAGCAGCCCCAGTCCCAACGGAC ATGCTCACCCACTGCCACCGACACAGCCAAAGGCGAATCCGAACCTAATT GCACAGCTCAATGCACGACTCAGCGGCAAACAGCAGCAGCACCAACAGCA GCAGCATATCGAGGGGATCTACGGCAACCAGCAGGCGCCCGGAGGAGAGT CGATCTACATGCGGAGTGGCCTGTCCATGTCGCAGCCGCAACAGCAGCAA CACTTTGACGACTATGCCACAAGCACAAATATCGAAAAGACTGGCAGTAT TCGTGCCAAGACCAAGGCCGAATTCCTCGAGAATCTCAACGCGAAGCTGG CGAAGCAGGGAATGTCTGGACGAGCATTTGCCGTGCGAAATCTCATCAAC AGCAAGGCCCTGCCGGACCCTCGCATCTGTCACGAATCGCTGATGGATCA AATCAAGCGCGGAGCCACCTTAAAGCGTAACCAGAAGATCAACGATCGCA GCGCTCCCAAGATACATTGAATTAACCTATAGGCTAAGCGAAGCAGCATA TTTATTACCATAATAATTAATCTATGAATAATCATGAGGCCCGACGCCTG CTCGACTGCAGGGCTCTGCAGAGTTTGGTTTGAAACTGAAAACTCGAAAC ACAGCATACAACTTAAATACATATGATTACGATATATAATATATATTCGA TATACGATATTTAACAGGAGCATTAAGCATAAATCGAACTAATCAATACC TTTCTTGATTTCCTGTATCCCAAAAATGTGTCGAAAGGCTTTCTCTGTTA AGTGAATACAATATGGAAGACAGTTATGTTTATGTTTATTTATATCTGCA ACTCGAATTTATCTTTAGAGAACCTTTGTTTGAAGATATTTTATGTTTAT GTATTTCCTGTATTTATAATTTCCCTTGCTTATTTATGTACATACATATG AATATGAGTTTAACAAACACTCGAAACTAATCTGACGCCTAATAAATGGA ATTTATCGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAA LP02831 TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACA CCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAAT ACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTC AACTTTATTTTATATATTGTCAATATCGTGTTTTTGATCGTTGGCATCCT ACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATG TCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTC CTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTT TCGGCAGAGTGTCTGCATGACCGGCGCGTACACCAGCATGGTTTTTGTGC TCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCT GCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCA TGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTG ATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACC TGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTA CCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACA ACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTG GTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAA CGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCC AAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTC GAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGT TACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAA TATATACCGCTACAACATTTAAAAAAAAAAAAAAAAAA RE41364 ATCTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTGG GCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTA GCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGA ATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTGC CGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCC ACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGT TAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAG GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCA GTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAA CTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATTA TACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTT TTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTA CGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAG CGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTAT CGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAA GCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGA GCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGAC GTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGGT GATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTT ACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGAC GCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGAC TGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGT ATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACA TATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTAT TTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAAT GAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTG ATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCT TAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAA TTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAA ATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGG AAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTC GTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAG ATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAA GCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTG TCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTAT TTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGA TTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTA TGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTC TAAACACAAAAAAAAAAAAAAAA SD10395 ATCTCTACCACTGCAGCAACGCTTTTCTTATCGCCGCTAAATTCAGAGCT AAAATCTAACAGAGCTTTTCGCGATAGGAAATGCGATCATAAAAATATTG TTATATATCAGACTTTTTCAGTATCAAGCGGACCACGAACGAAATCGCAT CGAACGTCTTACTCTTAAATCGAACACAAGTGATATAAAGTACATCTCAG CAATGGATTGCGGCGGCGTTTTTGTGAAATATGTGCTGTTCATATTCAAC ATACTGTTTGTGATATGCGGCATTTTGCTTATCACCTTCGGCTCTATCAT GGTGTCCACCATAAAGGACTTCTCGGGCGTCGGCGAGACCTTCACGGCCA ACAGCGTGGCCATCATCATCCTGGTCCTTGGCTGCGTAGTCTTCCTGGTA GCCTTCATGGGATGCTGCGGCGCCATACGCGAGAATTCCTGTGCTCTGAC CTCGTACTCTGTGGTCATGCTGGTGCTGCTGGTTAGTCAGCTAGCTCTCA TTATCTACGTGTGGGTGGACCATGTGCAGATACAGCAATCTTTGGAGAAG ATCGTCCAGACCATATGGGATCAACGCAAGACCGATGCCCTCCTCATGGA CACACTGCAGCGATCGTTCAAGTGCTGCGGCTTGAACGGCTTCGCTGATT ACGGCATTACGTATCCCGCCTCCTGCTGCGACTCGCCCTCCAATGGAACC TGCGCACTAACCCAAGTCATGACGCGATCCAGTTGCCTGAAGGCCGTTGA TTCCTTCTGGGACACCAACGTGAGCATCATCAAGTACGCTGGCCTGGGTG TGACTGCTGTTGAGCTTGTGGCCTTCATTTTCGCCTGCTGCCTGGCCAAT CAGACCCGCAACTCGCAGAGACGCCAGAACTACTAAACGATGAAACGCCA TTAGTAACATAGTATTAGGATTATCTCCCGACCCTCTTTAACGTCATAAA GTCAATATGAATAAATAAAACAAAGTGCTTCGCATGCTTACTGTATATAA AAAAAAAAAAAAAAAA GH17623 CACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCAT TCAAAAGGCGGAAAACTCAAGGTGTGTGTGTGGGTTTTGTTTTCAAATTC CGTGTGCTTGTGTGTGTGAGAGAGGGCGAGAGCGACAGTGTCGTAGCAGG CAGTGTTGTAAGGTGCCGAAACAGCGATCCCAACCGGCACACTAGTTGTC CTGCTCGCACTCCAGTGAGGCAAATGTCAAAGTCTGGTCAGTAGCAAAAC AGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCATTAGTT GGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCCAAGTGG TAAATTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAG GACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCAT CTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGC CGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGC CTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCA GCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGA TCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGC GTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGA GGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCT GCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTC TCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGC CGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGG AGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTAT CCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAA GGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCT GCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTT CCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGT GCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAA TATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAG TACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGA CTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAA TTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAA TAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGT GTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAAAAAAAAAA AAAAAAAAAAAA RE15841 AGTGAATCCGCGTATCAATCAGCGATCAGATTTCAATCGGCTCCCGCTGA TATATGACTGGAAATATAAACCATTAGCCTGGTTGTGAGTTCCAGCCAGC ACAGTCGAAGCTATCAACTCGGGAGGTGAAGATGAGCGCTACCGCAACTA TGTCACAAGAGCAAACGCAAGACGTGGATCACCATGCGCTGCTGGTGGCC AAAATAGTTTCCATGGTGGTGCTCGTGGTGATCACCGTGCTTTGCGGCAG CCTTCCCTACGTCCTGAACAGGTGCTTCCATTGGACGAAGGCGAGTCCGG AGGAAACCCGCTCGTCATTGGTGGTGCGGTGCCTACTCTTTTTCGGCGGC GGTGTGCTCATCTGCACCACCTTCCTGCACATGCTGCCCGAGGTGATCGA GGTGGTGGAAGCGCTCCAGGAATGCGGCTCGCTTGTCAAGACGCCCTTCG CTCTGGCGGAGATGCTGCTGTGCACGGGCTTTTTCCTGATGTACGCGTTG GACGAGCTGATGACCAGCCTCGTGCGGCACCACCAGGGAAAGCTTAGTCG GAAAGAGTCGGTGGCCAGTCTGGCTTTCGAAAGAGGACGCAGCATTCGTC ACAGTGTTCTCCTCAATCCACAGGCGAAGGAAGAAGTGGAAGTTAAGGAT ACGGAACCGCAGCCACACAAGGATCACCACGGCCACTCGCACATGCCCGT GCCAGCGGACGATGGATCCTCTGCCAGGGGGCTGGGCATTATCCTCGCCC TTTCGCTCCACGAACTGTTCGAGGGCATGGCCATTGGTCTGGAGGGCACT GTGAGCACTGTGTGGTTCATGTTTGGAGCGGTCTCCGCCCACAAGTTGGT GTTGGCCTTCTGCGTGGGTATGGAGCTTCTGGTCGCCCGCACACGCAGTT CGCTGGCCATCTTGTACCTGGTGACATTCTCCATTGTTACACCCATCGGT ATCGGTGTTGGCCTCGGCATCAGCCAGCAGGTGGCAGCGGGTCAGCCCAG TCTGCCATCCGGAGTCCTCCAGGGCATCGCCTGTGGAACCTTGCTGTACG TAGTCTTCTTTGAGATCCTCATTGAGAGCCATGCCGGATGGAGGGCCCTT GTGGCCGCCGTTGCGGGATTCGCTCTAATGTTTGGCCTTCAAATTCTTTC TGACGAAGCGGAGGGTGATGACAGCCTAACCTGTTCCTAGCCAGTGTGAC GCCACTTCAGTATTATCAAGTTATAGAGGAAGCAACAAAATAGTATACAA AACGATTCCCTGGGGATCTGTAAAAGTTATTATATAAAATACGAATAGAA TTTCAAAAGAGGTTTCTCAGAAATCTTATCCAACGCAAATAATTAAAAAT GTAATAACCATATGGATTAAAAGAGACAATATTTTACTCTAAAAAAAAAA AAAAAA RE40412 GACACTGCAATCATCAGCTTAAATAAAGAGAACAAAAATAAATTAGCGTT AGAATGTCAATGATACTAAGACGGAACCTGGGGGCATCCTGGTTGCTCAA GGCATGCTACAGTTCCAGCGCAAAACCGGTGGACTCGGCCAAAACAATTC CCAGTAACCTGCTCGAGGATAAGCAAACGGCCGTTCTGCAAAAGGAGAAC GGTACGATCTTCGACAAGCGCCCCTTCAAGATCCACCTGGACAAAGATAA AACATACAGCTGGTGCCTGTGCGGCAAGTCCAAGTCTCAGCCCCTCTGCG ATGGAATGCACAAGAACGAGTTCCTGAAGATCAAGCAGAGGCCCATTCGG TTCAAGGTGGAGAAGTCGGGAGACTACTGGCTCTGCAACTGCAAACAGAC CACCCACAGACCCTTCTGTGACGGCACCCACAAGCAGCCACACATCCAGA GCGCCGTCAAATAGATTTAGGATTGGTTGTAGGGCCCTGCCCGTGTGCGA AAAGAGAAATGCATTAATTTTGAATCAAAAAAAAAAAAAA RE12209 ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGA ATATAAATTGGTGATAATTTAAAGTCGAAGACGGTACAGTAAAGCAACAT CAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCA ACACCATTGTGTCGGTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTG ATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCC GATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGG ACTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGC ATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCT GACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAA TGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGA GGTGTCTTCGACACCATTCAGAAATCGTTGCACTGCTGCGGATCAAGCTC TGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCA GCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAG TTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCAT CGGCCTCATCGGAATAGAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGG CCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGT GTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACA CCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGG GATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACG GAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTT TGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAA CGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTT AAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATAT TTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCG AAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGT TTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGG AAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCAT AAGGAATTTATGAATAAAGCATTTACTATGTATTTATATACCAAAAAAAA AAAAAAAA RE34115 AGCGGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTC AGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCG ATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGT AATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAA CTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATC ACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCG AAAATTAAACCAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGC CATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAG CCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGA GCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAA GGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCG GTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGG GCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGC AGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCT TCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGT CCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGGCT TTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGA CACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGA TGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGAC AACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTC CCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCA GGGCAGCGGCGTGCTTCACCAACGAGCACAAGTACACGCACGGACAGAAG GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGAT CTTCTGCTGGTGGGAGAAGTGCGATAAGGCCAATGTAAACAAGGCGAGGA CGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGAC GGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCA CGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAG TTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTAC GAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTA TAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAA GCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACAC GAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACA GCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAA CGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCG TCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTC CAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACG ACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAG CACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACA GCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGG CATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAG GGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGA GGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCA GGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGG GCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGAC AACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGA CGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACG CTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGATCTTGG ACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCT TCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCC ATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGA TGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCA TCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAAC GATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACT AACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATG GCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAG GTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAG CAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTG TCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCA GGGCGTATGTGCAATGTTTTGGGCAAACTGTATAAAATTGGTGACATTCT GCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGA CTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCG CTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTT TGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTG GAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGT GATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATA GAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATT CGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCAT GTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTG TAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCT ATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAA GCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGGAGAAGAAGGAAATCG CAGTTGGCTCACAGTTTAGACTTTAAGCTGGATGTTTATGCATTTTATAA GAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGC AGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTA TATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAA CCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGAT TATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAA CGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAA TCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAAC GTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTG CATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATC TATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACA AACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTT AAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTG CGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGC ATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAG GGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATT TTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGA ACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAA TATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTAT TGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAAT TCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGT ATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCAC ACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTG AAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGG CATTTCAAAAAAAAAAAAAAAA LD44494 CGGTGAGAAGGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTA AGTGCAATAGTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTC CAACGGCGACCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGC GAACGAACTGCTCGGCAGATGGACTGGAGATCCAGGAGCAGGCAGTCAAG TTTTACCAGCAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGA CGAGTGTCAGTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAAC GCGGTTGGCCGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTG CTGGGCATGCAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGT CGTTCACCTGCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACA GTCCCTGCTATATGCTGACCCACATATTCGCAGTGACGAGTCTCAACGGC TGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCT GCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCA TGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATC ACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGT GGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAG TTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGC AGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGC TATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATG CTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTAT GACTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGC GGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCT TAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATT TGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAA ACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTA AAAAGACATAATAGAGACTTTATTACAACATTTAAAAAAAAAAAAAAAAA A LD23740 CCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGAAAA ACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCGTTT CAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGACAG ATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGATGCGCGCCAT CAGCAATGGCACCGCCCAGCTGGAGCAGCAGGCGCAGCCCAAGGAGGCCC AGGAGCCGCAGATCAAGAAGTTCGAGATCTACCGCTGGAACCCGGACAAC GCCGGCGAGAAGCCGTACATGCAGACCTACGAGGTGGACCTGCGCGAGTG CGGCCCCATGGTGCTGGACGCGCTGATCAAGATCAAGAACGAGATGGACC CCACGCTCACCTTTAGGCGCTCCTGTCGCGAGGGCATCTGCGGCTCCTGC GCCATGAACATCGGCGGCACCAACACGCTGGCCTGCATCAGCAAGATCGA CATCAACACCTCCAAGTCGCTGAAGGTGTACCCGCTGCCCCATATGTACG TGGTGCGCGACCTGGTCCCGGACATGAACAACTTCTACGAGCAGTACCGC AACATCCAGCCCTGGCTGCAGCGCAAGAACGAAGCGGGCGAGAAGAAGGG CAAGGCCCAGTACCTGCAGTCCGTCGAGGATCGCTCCAAGTTGGACGGCC TGTACGAGTGCATCCTGTGCGCCTGCTGCTCCACCTCGTGCCCCTCGTAC TGGTGGAACGCCGAGAAGTACCTGGGCCCCGCCGTGCTGATGCAGGCCTA CCGCTGGATCATCGACTCGCGTGACGAGAACTCCGCCGAGCGTCTGAACA AGTTGAAGGACCCCTTCAGCGTCTACCGGTGCCACACGATCATGAACTGC ACGCGCACCTGCCCCAAGGGGCTCAATCCCGGCCGTGCCATCGCCGAGAT CAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGCCGGCTCCGAAGCTGGAGA CGGCGGCGCTGCACAAGTAGGGCCCAAGTCCTCTACTCCCAGTTCGTCCC CTGCTGTCCTTAACCAGTGAGCTAAGCCTCCGAAAATGTGTATTGGAGAC TCCTCCAGCCAACATGCTTACTATGTTATAATTTATTTAAGCCTAAAGTA TCCGACACTTGTTATTACAGTTTGTAAAGGGAACAAGACGCGAAAATAAA TAATTGTGTATCCACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RE02548 AGTTTTCCCAATCATGTCAGTCAAGGCCACGTGTTCACTTCTGCTGCTCC AGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCC GCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTC CCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCT TGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAA CTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATT GGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGG ACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTC AAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGC TGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTA ATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCT CCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTA CTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCA GCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCC CAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGT CGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGC CTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATA GACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCA GCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCG AGGAGTTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGC CTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGC GATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTTTA TCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTC ATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTT ATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAAT ATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCA AAAAAAAAAAAAAA CG33352 CG33352 gene CG33352 cyto_range 42E1-42E1 comment DGC clone GH14660 appears problematic: unspliced intron::DATE:2003-03-14 18:03:48::TS:1047683028000 comment Flag Cambridge (NEW): corresponds to old CG9469; should be reinstated as CG9469, after new CG9469 is renamed.::DATE:2003-02-21 17:57:41::TS:1045868261000 gbunit AE003790 Gadfly CG33352 FlyBase FBgn0053352 CG33352-RA transcript comment Corresponds to cDNA described in FBrf0137468.::DATE:2003-07-22 14:04:11::TS:1058897051000 status not done owner crosby Gadfly CG33352-RA FlyBase FBtr0086193 translate offset 265998 265996 CG33352:1 exon 265998 265516 Gadfly CG33352:1 FlyBase FBex0070433 CG33352:2 exon 265455 265198 Gadfly CG33352:2 FlyBase FBex0070432 CG33352:3 exon 264883 264581 Gadfly CG33352:3 FlyBase FBex0070431 CG33352:4 exon 263955 263841 Gadfly CG33352:4 FlyBase FBex0070430 CG33352:5 exon 263702 262899 Gadfly CG33352:5 FlyBase FBex0070429 CG33352:6 exon 262472 260838 Gadfly CG33352:6 FlyBase FBex0070428 CG33352:7 exon 260145 260024 Gadfly CG33352:7 FlyBase FBex0070427 CG33352:8 exon 259873 259598 Gadfly CG33352:8 FlyBase FBex0070426 CG33352:9 exon 259048 258848 Gadfly CG33352:9 FlyBase FBex0070425 CG33352:10 exon 258611 257165 Gadfly CG33352:10 FlyBase FBex0070424 CG33352:11 exon 256567 256445 Gadfly CG33352:11 FlyBase FBex0070423 CG33352:12 exon 256366 256256 Gadfly CG33352:12 FlyBase FBex0070422 ATGATAATTCGTATTCCTTCGATTGCAGGCGCCTCGAAGGAGATCGGCAC CGCCCTAACCCGCGTTTGCCTCCGCCACAAGGCGGTGGAGACGCGTCTGA AGACCTTCACCAGCACCATTATGGATTGCCTGGTGCAGCCGCTGCAGGAG AGGATCGAGGACTGGAAGCGCACGGTGGCCACCATCGACAAAGACCATGC CAAAGAGTATAAGCGCTGTCGCAGTGAACTGAAGAAGCGTTCCAGCGACA CACTGCGCCTGCAGAAGAAGGCGCGCAAGGGTCAGACGGACGGATTGCAG TCCCTGATGGACTCGCACATGCAGGATGTTACCCTGCGCCGGGCAGAATT GGAGGAAGTCGAGAAGAAATCCTTGAGGGCGGCCATGGTGGAGGAGCGTC TGCGCTACTGCAGCTTCGTCCACATGCTTCAGCCAGTGGTGCACGAGGAG TGCGAGGTCATGTCAGAGTTGGGTCACCTACAGGAAGCCATGCAGTCAAT TGCCCTAGTAACCAAGGAGCCTAGTGTTCTGCCCCAGGCCTCCGAGGAGC TTATCCATGACGCTAAGGCCAGCATTAATCTGTACCCGGAGTCCCCGGGT GGCGGTTCCGGCTCGCAGGGCGGCGGCTGCTCCAACTCGCTGGGTTCCCG AAAGAGCTCCGTCTGCTCCATCAGCAGTATGAACAGCAGCGGCTCGAGCA ACTCGCCCGGTCACCATCACTATCCGCGCTCCCTTTCGCAGACTTCGAAT GCAACGAACCAGACGGCAAATGTCTCCACCTGGCCCCCACATTCCCAGGA TGGCGTCGACACCCTGCCACCGACCGCTGACCGTCCGCACACGATTTCGA CGGCATACGAAAAGGGTCACCAGCGTCCGCCGCTGACCGTCTACACGTTC CAAAACCCGGAGACCATTCACGAGTCGGGCAGCTGCCTGAACAACGGAAC AGCAGCCCCGAATGGACAGCCGTTATCCGGACAAGCCACTCCGGCCACCC AGAAATCACCGGCTGCCTCACTTAGCCGGCCTCCTTTGCCAGTTCGCTGC TCGTCGTTGGAGCGACCCCTTTCGGCCCAGAGTAACCACCGCCAGGGTAG CGGGAATAACCTGCTGCAGCGCCAGTGCCCCTCGCCGATTCCGGCTCATA TCACGAAAGAGCTGTCCGCAGCGCATCATGCACAGCAGCAGCAGCAGCAG CAAAATCAGCAGCCCCAGACGCCGCCCACCTATGTGAACATGTCGGAGCT GGCCACCATGGCCGCTTTGAAGCAGACCAATCAGCAGCAGAAGCCCTCTA CGCCGCCTCTGCAGCAGCAGAGCTCCATTGACTCGACCAGCTCCCAGCAT TCCAACGACTCCACCGGCTCTCATCAGCTCCTCCAGCAGCAGCAGCAGCA TCATCAATCGCAGCAGAATCACCACTCAGCCACTGCCACACGCTCCCATT CCATATCCTCGACGGCCTCGTCACTTCACTCGCATCCGTCGATCGACTCC ACCGTCGCTTGCGGCTCGCTGGTGGGCCAGCACAACCACAGCACCAGCAC CAACACGAACACCACCTCGCCGTCCAGTGGCAGCTCCACGCCACAGAACC ATTACTCGCCCCTGCTAACCAACTCCCCCACGTCCACTGCCGCAGGTACT CCCAGTGGCAGCAGCTTAGGTCCTGGGTCCGGTTTGGGATTTGTCTACCA GGTCAGCTCCCCGACGCCTCCCTCCAGCGAGGTGCTGAAAATCACCGAGC AAGCCGCTGCAGGACAGGATCAGGGTCCAGCCAACAGCGTAGCGGACGAG ACGGATGAGCGATCAAGGGCCTCAGTCCTGCAGAAGGCTTCAATGTTCGA AAAGGCGGCAGCAGCGGCAGCGGTATCGCCCCCAGCTCCCATGCAGATTG CATCCGGTTCCCCAGCTTCGGGAGGCGGAACTCGACGATCCGAGGCGGAG CAGCAGGAAATGGACAAGTCTTTCGAAGATTCAATACAAGCACTAAATAA TTTAATTGGCGAACTAGACTCGTTCCAACGCGAGATCGATGAGGGCAAGG TCAAACCGCCGAGCAACATCATAAGCGGCAGCACCACCAGTAGCAACAAC AACAATACGACGACCAGCAGCATCAGCAGCAGCGACAACAACAACCTGCC CGCCACCAGCAACATCGAGCCATGCGCCATCAGCAATCAGACGAACTCGA GCGGCTGCGGCACGGACATATCCGACACCACGTCCGACGAACTGGCCGGC GACGATATGGACGTCAGGCGGCGGGATCGGGATCGGGACCGGGATCTGCT GGGCGCCAGCGATTCGGAGCTGAGTCGCTGCTATGTGAGCGAGACGAGTT CGCTGACCGGTGGCCTAACGGCCGGCGGCTACGAGAATCCCACTTTCGCG CACTTTGCGGCCAATGCCAATCGGGAGGACGCTGTTTCGCTGGCCTCCGA CAGCGTTTGTCTCGGCCAGCCACGCCACGCCTATGTGGATACCTGCAGCG ACAGCGGCAGTGCCGTGGTGGTGATCTACGACCACCAGATTCCCAACACA CCCGACATTGAGTTCGTGAAGCAGAACTCTGAGATTGTAGTGCTGCGGAC TAAGGATCCGCAGCCCCACGCGCTGCAGCTGCACGAGATGCGCGAGCTGC AGCAGTTGCCCGCCAATTTGGCCGGTTCGCCGGACTCCTCGCCGGACTCT GCCGGTGGCCAGGCACCGCCAACAGCAACTGTGGCGCCCGCCAAGCAGCG ACTCTCCTCGTTTCGCGCCACCAGTGAGCAGCAGTTGCAGCTCCTCGGAC GCGGTAGCCCGCAAAGAGGTAAAACACCCAGTGAGCAGGCGGTACAAAGC AGGCCACAGGACCAGCATTTTCCACAGACACAACAGCAGGATATTGATGG CAGTAGTCCACCAGTAGAACTTGCAAGGCGCCAGCTGCCCCCCAAGCCCA CCAGTTTGAGTATTTTTAACGGCCCCGTGCCCACTGCGGGCGATAGGCCT GTCGTGCCGCGAAAGTCGGACTTTAAGGCTGATCTAGATGCTAAAATACG CAGGCAAAAGCAGAAGGTTAAACAGCAGTTGCAGCAGCAGCAGCAGCAAC AGCAGCAAGAGCAGCAAGAAACGCAGCAGCAGCAGCAAGCACCACAAGAA CAGCAACACTCACCACAGTCGCCCCAAACCAGAAACTGTAATGTCACTAA TCAACAAGCCGCCAATATTACTGCATCAGCATCTGCATTTGCAACCGCAA CAGCATCCACAGACCCGTACCCGAATCCAAATCATAGAATGCCAAACCAA AATCAGACAGCCACATCCAATCACACGCAGTGCAAGACGCCCACAATGGC ATTGTCACCGTCATCACCTCGCGGCCATTTGCCATTATCATCGTCATCGC TATCGTCATTACCATTACCAGCCACCACTTCATCACCATCAAATGCCCGG CCATCGATGTTGCCCGCCAGTGACCGACCACCCGCCCATCCATATGTGTG CTCCAATGCCCCAGCCAATCCCCACCACGCCAATAGCATTTCCAATGCCA ATGCCCATCTCAAGCCGTGCATTACGCCCCGGCCGGCTTCTTTGTCGGGA GGAGCAGCCGGCGGTGGCTCCACGCGCATCGGGCGTCGATCGTCCATTAA TCAGTCCAAGCCACCGCCGCCAGTCAGACGCAGTTCGTCGGTGACCCCCA GTCCCAATGCCTCGGTCGGGCTGCAGCAGCAACCACAGCACGCGACTCTG TCGCAGCAGAATCACCAACTAAGCAGCTCCAGCGAGCACTTACCGCCGCC ACCGCCATTCATGCTGGACGCCATGCCCCAGATTCCCAGCTCAGCGCTGA AGGTATCGGAGACGGTAAGAGCCCTGGCAGCCATGCGGCACCAGCCAGCA TCACCTGTGTCCCTCAGACGCATGCAGCAGCAACAGCAGCAGCAGCTTCA GCAGCAACAGCAGCAACAGGTGCAGCAGCAGCAACCCCTATTGCAGTCTG CGCACAACTCCCCCCTCAAAGAGGACCTGACCGTGTACTACGACTCCTAC TTGGATCTGCACGCCTATGCCCAGGCCTTGGCCAGCGGCCAACAGCCCGG CGGTCAGCAGATGGCCAACCAGCAACGCTTTACCCTCCAGCAGCAACATC AGCATCTGCATCAGCCACAGCAACCGCCTGTCTACCAAGTCGATGCCACG TTCCGCACCTCATCACCAGCCGCGGGCGGAGGGGGTGGCGGCGGCATATA CGCCCAGCCCAAACTGGTCAACAGCATGTCCAGCTTCCGCACCAGCAGCC CCAGTCCCAACGGACATGCTCACCCACTGCCACCGACACAGCCAAAGGCG AATCCGAACCTAATTGCACAGCTCAATGCACGACTCAGCGGCAAACAGCA GCAGCACCAACAGCAGCAGCATATCGAGGGGATCTACGGCAACCAGCAGG CGCCCGGAGGAGAGTCGATCTACATGCGGAGTGGCCTGTCCATGTCGCAG CCGCAACAGCAGCAACACTTTGACGGTAAATCTGAACAAATCCAGCTGCA GCACCAGCAACAGCATAGAATTTACGCTAGTTTCGGCACCTCATCATCAG CAATGTCATCCGCTCATGCGGCCAACAGCAGCACTAAACCGTCCATTCTA ACACCGACCACCTCTTTCAATGCATTGCCTCACTTCCCCCTGTCTTCATC CACATCATCGTTGCTCTCCAAAGTCAGCTCATTCTCGAACTCTTCATCCG CATCCCCACCGACAACGGCAGCGACCTCTGGCTCGGCCAGTTCGCATTAT CAGCCACCTCAGCCGCCGAATGCAGCAGTTGCTAACAGCAAAGACATGGC CATCTACTCAAGTTCGTTTACCAAAAATCCAGCAGCTGCGCAATCGCCGA ACATGAGACAGGCTCATTCCCATCAGCACCACCAGCCGCCGCAGCAGCAG CACTACACCTGTCCGCCTCCTCTGGAGGATCCCCCACCGCCGCCCATTTA CGCCGCCGGTGCATCGGCCACGATGCCCAAGAAGATGGCCCGTCCGCCCA CTGGCCAGAACGCGACTCACTCGAGCGCCTATGCAGCAGCCTCGTCTACG GCCACGCTGCCCAAGAATATGATGCAGCAGCAGCAGCGGTTGCAGCACCA GCAGCAGTATCAACAGCCGGCAGGCATGGGCATTGGCAACGGCAATGGGC ACCTAGGTCAGCGTCCGCAGTTGCCGCTGCCCCAGCAGAAGCTTAGAGCT GCACAGCAGCAGCACTTGGCGGAGCAGCAGCATCAGCAACAGCAAGAACA GCAGCAGCACCACCAGCAGCACCAACAACACCAGCAACGCCAGCCGCCCA TTCCTTCACGCCACTCAAGTGTGCAGCAAAAGATATTCGTATCAACGAAT CCATTCATACAGACAACGGCCGTCAAGTTTCACTCGCCCTCGGCCTCGCC CACGTGCGGCTCGCCCGTTACTGGGTCCTTGGCTAGCATTTATGCCACAA CCTCGCGTGGCGGCCACCATCACCAGCAGCAGCAGGCTCAGCAGCAGCAG CACTACTATCGCGATGCTGCCGGGGGCAACAGCAACGGCGGCGCTGCCTA CTATAACCACAATGCCCATGCCCATTCCCAGGCACATCATCCAAACTGGC AGTATTCGTGCCAAGACCAAGGCCGAATTCCTCGAGAATCTCAACGCGAA GCTGGCGAAGCAGGGAATGTCTGGACGAGCATTTGCCGTGCGAAATCTCA TCAACAGCAAGGCCCTGATGTATCAAAATCCGCAAAAACTATCGCGACCC AGTGCGCAATACCGTAGACCACCCACCTATCCCAACACCAGCACAACCAC CAATGCCACTTGCGAAGATCAGTGCTAA MIIRIPSIAGASKEIGTALTRVCLRHKAVETRLKTFTSTIMDCLVQPLQE RIEDWKRTVATIDKDHAKEYKRCRSELKKRSSDTLRLQKKARKGQTDGLQ SLMDSHMQDVTLRRAELEEVEKKSLRAAMVEERLRYCSFVHMLQPVVHEE CEVMSELGHLQEAMQSIALVTKEPSVLPQASEELIHDAKASINLYPESPG GGSGSQGGGCSNSLGSRKSSVCSISSMNSSGSSNSPGHHHYPRSLSQTSN ATNQTANVSTWPPHSQDGVDTLPPTADRPHTISTAYEKGHQRPPLTVYTF QNPETIHESGSCLNNGTAAPNGQPLSGQATPATQKSPAASLSRPPLPVRC SSLERPLSAQSNHRQGSGNNLLQRQCPSPIPAHITKELSAAHHAQQQQQQ QNQQPQTPPTYVNMSELATMAALKQTNQQQKPSTPPLQQQSSIDSTSSQH SNDSTGSHQLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDS TVACGSLVGQHNHSTSTNTNTTSPSSGSSTPQNHYSPLLTNSPTSTAAGT PSGSSLGPGSGLGFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADE TDERSRASVLQKASMFEKAAAAAAVSPPAPMQIASGSPASGGGTRRSEAE QQEMDKSFEDSIQALNNLIGELDSFQREIDEGKVKPPSNIISGSTTSSNN NNTTTSSISSSDNNNLPATSNIEPCAISNQTNSSGCGTDISDTTSDELAG DDMDVRRRDRDRDRDLLGASDSELSRCYVSETSSLTGGLTAGGYENPTFA HFAANANREDAVSLASDSVCLGQPRHAYVDTCSDSGSAVVVIYDHQIPNT PDIEFVKQNSEIVVLRTKDPQPHALQLHEMRELQQLPANLAGSPDSSPDS AGGQAPPTATVAPAKQRLSSFRATSEQQLQLLGRGSPQRGKTPSEQAVQS RPQDQHFPQTQQQDIDGSSPPVELARRQLPPKPTSLSIFNGPVPTAGDRP VVPRKSDFKADLDAKIRRQKQKVKQQLQQQQQQQQQEQQETQQQQQAPQE QQHSPQSPQTRNCNVTNQQAANITASASAFATATASTDPYPNPNHRMPNQ NQTATSNHTQCKTPTMALSPSSPRGHLPLSSSSLSSLPLPATTSSPSNAR PSMLPASDRPPAHPYVCSNAPANPHHANSISNANAHLKPCITPRPASLSG GAAGGGSTRIGRRSSINQSKPPPPVRRSSSVTPSPNASVGLQQQPQHATL SQQNHQLSSSSEHLPPPPPFMLDAMPQIPSSALKVSETVRALAAMRHQPA SPVSLRRMQQQQQQQLQQQQQQQVQQQQPLLQSAHNSPLKEDLTVYYDSY LDLHAYAQALASGQQPGGQQMANQQRFTLQQQHQHLHQPQQPPVYQVDAT FRTSSPAAGGGGGGGIYAQPKLVNSMSSFRTSSPSPNGHAHPLPPTQPKA NPNLIAQLNARLSGKQQQHQQQQHIEGIYGNQQAPGGESIYMRSGLSMSQ PQQQQHFDGKSEQIQLQHQQQHRIYASFGTSSSAMSSAHAANSSTKPSIL TPTTSFNALPHFPLSSSTSSLLSKVSSFSNSSSASPPTTAATSGSASSHY QPPQPPNAAVANSKDMAIYSSSFTKNPAAAQSPNMRQAHSHQHHQPPQQQ HYTCPPPLEDPPPPPIYAAGASATMPKKMARPPTGQNATHSSAYAAASST ATLPKNMMQQQQRLQHQQQYQQPAGMGIGNGNGHLGQRPQLPLPQQKLRA AQQQHLAEQQHQQQQEQQQHHQQHQQHQQRQPPIPSRHSSVQQKIFVSTN PFIQTTAVKFHSPSASPTCGSPVTGSLASIYATTSRGGHHHQQQQAQQQQ HYYRDAAGGNSNGGAAYYNHNAHAHSQAHHPNWQYSCQDQGRIPRESQRE AGEAGNVWTSICRAKSHQQQGPDVSKSAKTIATQCAIP Tsp42Ee CG10106 gene Tsp42Ee cyto_range 42E5-42E5 gbunit AE003790 symbol Tsp42Ee sp_status Perfect match to SwissProt real (computational) GO GO:16021 FlyBase FBgn0029506 FlyBase FBan0010106 FlyBase FBgn0033126 GO GO:0016021 integral to membrane Tsp42Ee-RA transcript owner crosby sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAF59311 Gadfly CG10106-RA FlyBase FBtr0086180 translate offset 342832 342834 Tsp42Ee:1 exon 342031 342110 Tsp42Ee:2 exon 342808 342891 Tsp42Ee:3 exon 346788 347150 Tsp42Ee:4 exon 347210 347401 Tsp42Ee:5 exon 347465 348139 ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGA ATATAAATTGGTGATAATTTAAAGTCGAAGACGGTACAGTAAAGCAACAT CAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCA ACACCATTGTGTCGGTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTG ATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCC GATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGG TCTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGC ATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCT GACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAA TGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGA GGTGTCTTCGACACCATTCAGAAATCGTTGCACTGCTGCGGATCAAGCTC TGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCA GCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAG TTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCAT CGGCCTCATCGGAATAGAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGG CCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGT GTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACA CCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGG GATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACG GAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTT TGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAA CGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTT AAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATAT TTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCG AAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGT TTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGG AAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCAT AAGAAATTTATGAATAAAGCATTTACTATGTATTTATATACCAA MDCGTSMVKYILFIFNTIVSVIGILGIVYGVLILKSIGVVEVNGQVGFPI QALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLT FVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSLHCCGSSSA LDYIGKGDLVPPSCCSGSCLIPTNYYPGCRGKFVELMTTGSDNAKYVGIG LIGIELIGFIFACCLANNVRNYKRRNAY CheB42a CG33348 gene CheB42a cyto_range 42E1-42E1 gbunit AE003790 comment Flag Cambridge: gene split (internal view only). CheB42a corresponds to the 5' end of CG15242.::DATE:2003-03-14 16:14:41::TS:1047676481000 comment Gene split based on EST/cDNA and BLAST data.::DATE:2003-03-14 16:16:50::TS:1047676610000 symbol CheB42a sp_status Not in SwissProt real (computational) Gadfly CG33348 FlyBase FBgn0053348 FlyBase FBgn0033120 FlyBase FBan0015242 CheB42a-RA transcript comment unusual splice provisional (internal view only)::DATE:2004-01-12 11:13:36::TS:1073924016000 validation_flag unusual splice comment GC splice donor site postulated::DATE:2003-03-14 16:11:36::TS:1047676296000 sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70837 owner crosby Gadfly CG33348-RA FlyBase FBtr0086168 translate offset 279280 279282 CheB42a:1 exon 279257 279528 CheB42a:2 exon 279579 279755 CheB42a:3 exon 279816 280062 CTCATACTGGAAAGCTTGTTAATATGAAGGCTACTTTTACAATCCTGGTG CTCCAAGTGGTCATCTGTTTGGCTGGAGCGACTGAGTACCAGTTAACATT GGACAAAGATGGCTTGTTAGCACCATGCGAGAATCAGCCCGGAAATCCTT CTGGTTTTGAAGCGATGGTGGATACTTCCTCCCTTAAAGTACATAACCTT GGTTCGAAAGTTCGAATTGAAGGAGAGCAGAAAGTGGTCTGGAAAGATGT CCAGCCTGGAGACACATTAAAGGTATTTGGTCAAGTCTATCGCCTGGATA AGGGCACTTGGCAGAAGACTATGTTTACGGCCAGCTCCAATAACTTTTGC AAAAACATGTTTGATAAGAACCAATACTGGTATAATTTCTGGACAAAGTA TATTAGCAACTCCGACGAGATTAAGGAAAAGTGCTTGACCACACCAGGGG CCGTTTTAAAGTACAAAGACTACGAACTGGACTTGAAGACCAGCTTGAAT GTTCCGAATCTGGATGGGCGCTACAAGCTGGTGGTCCAAATAGAGGCCTT CGATAAGCGCAATGTAAGGCGCCCAGTTCCCATTTGCATAGAGTTCCGTG GAACTGCAGGACAGGTCTAATCACGACAATTGTATATGCATGCTGAACAT ACAGCGAAACACCATTAAAGTCTATAATTGGAGCACATCAAACAAG MKATFTILVLQVVICLAGATEYQLTLDKDGLLAPCENQPGNPSGFEAMVD TSSLKVHNLGSKVRIEGEQKVVWKDVQPGDTLKVFGQVYRLDKGTWQKTM FTASSNNFCKNMFDKNQYWYNFWTKYISNSDEIKEKCLTTPGAVLKYKDY ELDLKTSLNVPNLDGRYKLVVQIEAFDKRNVRRPVPICIEFRGTAGQV CG33349 CG33349 gene CG33349 cyto_range 42E1-42E1 comment Transposon inserted immediately 3' of gene.::DATE:2002-03-07 10:07:50::TS:1015513670000 comment Gene split based on EST/cDNA and BLAST data::DATE:2003-03-14 16:16:50::TS:1047676610000 comment Flag Cambridge: gene split (internal view only).::DATE:2003-03-14 16:14:41::TS:1047676481000 gbunit AE003790 Gadfly CG33349 FlyBase FBan0015242 FlyBase FBgn0053349 FlyBase FBgn0033120 CG33349-RA transcript owner crosby status not done Gadfly CG33349-RA FlyBase FBtr0086169 translate offset 280166 280168 CG33349:4 exon 280160 280479 CG33349:5 exon 280539 280820 CG33349:6 exon 280987 281086 CG33349:7 exon 281146 281337 CG33349:8 exon 281401 281625 CG33349:9 exon 281691 281933 TTCATCATGGAATCCAAAATGAGTCGGCCGAAGCAACCGGACTGGCTCGC CGAGCTGTGCCAGGAGTCCTCCATCCACGGCATGCCCTACATCGCCCGCA GGGATCTACACTGGGCCGAGCGCCTCTTTTGGACATTCATAATCCTGGGC TCGGCCTACTACGCCATCAGCAGCTGCCTTAACCAATGGTACCGGTTCCG GGACAATCCTATTGTCTACGAGTACGAATATCTCTTTGGGCTGCGCATCT TCCCCTTCGTGGGGATAACACTGTGCCCTAGGTACCACGACGAAACGGAG ATCCCAAGGCTTATAAATCAAACTTGGGGAGTGGATCCCAGCGAAGACAA AGAAAAAGCTGTGTACTACAGAAAGTTTCTGCTTGCAATCAACGGCCTTC GTTACTCCACTCTGGAGACGCTGGAACCCTTCGAGAATGATACCACTTTG GACAACGTGAATTACTTGAACATTTTGCTCACGCTGCAAAAAAAGGTAAT AGCGGTTAAAATCCCGCCAGAACTGGCGCCAATCATTACTGAGGTGGGTC TGTGCCAAACATCCAGCCAGTTAAACCGATACGGAAATCCCTACGGCAAA CTAGAAACACAGGATATGGAACCCATGAAACAGTGCGGCTATTTGAGTAA TTGCATCACATCTCTGAAGCCTATAAATAGCATTGTTGCCCCCATATTTA TGTACCTTCACGATGTCGAAGAAATGATGCTACCCGACGACATGCGAACT CCCTCTTTTGATGCTAAAGACATCGAATCCAAGGATCTCGATATTATGCT ACATACCACATCGGCGGAAAGCGAGGTGCGAAATCTACCGGTAGCATATC GCAAGTGTCGCTTCAGTGACGAAAACAATCTGCAGTATTACAGTCCCTAC CACCCAAGTCTTTGCCGACTTGAGTGCCGAATCAAATGGGCCCTGAGCCT GTGCAACTGCAAGCCCTATTTCTACGTAGCAGCTCCCGAAGTTCCAATCT GCACAGTATCCGGAATGCTCTGCCTAGCCCGGTCCAAGTGGCTTGAAAGA CCATGCGATTGCTATCCGTCTTGTCGCGAGGAAACCTTTACCATCTTCAA AGTGTCTGACCAGACTGGGGGCGATGACAACTACTCTGGCGAGAGGTTCG AGCGGACGCTGATCATCAACCTGCAAATTTCGAGGATGGGCATAAATCGG CGGGTTGTATTCAGCACGGATCAGTTGATAATGTCGTTTGGTGGAGCCAT TGGCCTCTTTCTTGGAGCCAGCTTCATGACCATATACGGCGTGGTATACT TTTTTCTAACTTTCATAGCTTATACATGCAAGAACCGATTTTGCAAGCGT TTTTTTTTTTAA MESKMSRPKQPDWLAELCQESSIHGMPYIARRDLHWAERLFWTFIILGSA YYAISSCLNQWYRFRDNPIVYEYEYLFGLRIFPFVGITLCPRYHDETEIP RLINQTWGVDPSEDKEKAVYYRKFLLAINGLRYSTLETLEPFENDTTLDN VNYLNILLTLQKKVIAVKIPPELAPIITEVGLCQTSSQLNRYGNPYGKLE TQDMEPMKQCGYLSNCITSLKPINSIVAPIFMYLHDVEEMMLPDDMRTPS FDAKDIESKDLDIMLHTTSAESEVRNLPVAYRKCRFSDENNLQYYSPYHP SLCRLECRIKWALSLCNCKPYFYVAAPEVPICTVSGMLCLARSKWLERPC DCYPSCREETFTIFKVSDQTGGDDNYSGERFERTLIINLQISRMGINRRV VFSTDQLIMSFGGAIGLFLGASFMTIYGVVYFFLTFIAYTCKNRFCKRFF F CG9445 CG9445 gene CG9445 cyto_range 42D3-42D3 problem true symbol CG9445 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0040674 FlyBase FBan0009445 GO GO:0007498 mesoderm development CG9445-RA transcript owner crosby protein_id AAF57402 sp_comment Perfect match to HYPO SP record with corresponding FBgn Gadfly CG9445-RA FlyBase FBtr0086210 translate offset 168577 168575 CG9445:1 exon 168702 167849 CCGATCGAAAAGCATATACTCAAAATTCCAAAAAACACAAGCCCAGCGCC CAAGCGCCATCATTTGTTTCCAGCCGACTTCCAGCTCCGATCGGGTACCA ATAGCCCTGCACCGGACCCACTAAGATGGACGGAGGAGGGGACAACCAGC TCGCGGTGCGGTCCTTGGGCAGGCAGCGCGAAGCCTTCTCCCACTACGCG GGTCCACCGACGGCCATGCTGCAAGGACCCGATCCTGGCGAAGGAGACGT CCTTGCCCTGCAGATGGCCATAGAAGCCTTCATTCTAGCCGAACTCGAAG AGGATTCAGGCTTCGAGTCCGGCAGCGAAGACGACTAGCAGGATGGAAAG AGTAAAGTGATACTTTAGTAAATAGCACCCATGTATGAGCCATCATAAGA GGAATATATGTATCTAATGTTGCACCAACCTTGGGCTACATGATTTATGT ATGCCGGTGGACCAATTCGCCCGCATTATGGACAATGATGCACGGCATTA ATTAACTCGCAGTCTTACCTTTTGCAAATAGGATTACAAACACTGAAATG AAATAGAGCCATGTTTCGAAATGCCTTAGTTGGGTTTCGGTTTATTCATG TCGATTTGATTTCAATTTGATTTCAAACACAAATTCCATTTAAACACAGG GATGCCGGTGCATCTGTATCTGTGTGCGAGTTGCAGATTAGTAGAGAGTT GTAGTTACATTTATTTTACACATACATAAATACGCATATTTGTATACATT TTTAATATGCTCGTTCAAGATGAATTTTTCTATTTTTCTTCGAATTTACC ATACGCTCTCTTGTGCAACATCAATAATAAATATTTACGTTTGTCTGCAT CGGT MDGGGDNQLAVRSLGRQREAFSHYAGPPTAMLQGPDPGEGDVLALQMAIE AFILAELEEDSGFESGSEDD CG3450 CG3450 gene CG3450 cyto_range 42D1-42D1 symbol CG3450 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0033105 FlyBase FBan0003450 CG3450-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAF57398 owner crosby Gadfly CG3450-RA FlyBase FBtr0086211 translate offset 140212 140210 CG3450:1 exon 140212 140174 CG3450:2 exon 140114 139976 CG3450:3 exon 139910 139850 ATGATAGAAATAACGTGTAACGATCGTCTTGGCAAGAAGGTGCGCGTCAA GTGCAACCCGGACGACACGATTGGGGACCTCAAGAAACTAATCGCGGCAC AAACGGGCACAAAGCACGAGAAGATTGTCCTGAAGAAGTGGTACACAATC TTCAAGGACCCGATTCGCCTATCTGACTATGAAATTCACGATGGCATGAA TCTGGAACTTTACTACCAATAAAACTGCAAGGGAATACC MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTI FKDPIRLSDYEIHDGMNLELYYQ Tsp42Ed CG12846 gene Tsp42Ed cyto_range 42E5-42E5 sp_status Perfect match to SwissProt real (computational) gbunit AE003790 symbol Tsp42Ed GO GO:16021 FlyBase FBgn0029507 FlyBase FBgn0033125 FlyBase FBan0012846 GO GO:0016021 integral to membrane Tsp42Ed-RA transcript sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAF59312 owner crosby Gadfly CG12846-RA FlyBase FBtr0086181 translate offset 341426 341424 Tsp42Ed:1 exon 341629 341367 Tsp42Ed:2 exon 340629 340438 Tsp42Ed:3 exon 340368 340207 Tsp42Ed:4 exon 340075 339878 Tsp42Ed:5 exon 339820 339635 ATCTCTACCACTGCAGCAACGCTTTTCTTATCGCCGCTAAATTCAGAGCT AAAATCTAACAGAGCTTTTCGCGATAGGAAATGCGCTCATAAAAATATTG TTATATATCAGACTTTTTCAGTATCAAGCGGACCACGAACGAAATCGCAT CGAACGTCTTACTCTTAAATCGAACACAAGTGATACACAAGTACATCTCA GCAATGGATTGCGGCGGCGTTTTTGTGAAATATGTGCTGTTCATATTCAA CATACTGTTTGTGATATGCGGCATTTTGCTTATCACCTTCGGCTCCATCA TGGTGTCCACCATAAAGGACTTCTCGGGCGTTGGCGAGACCTTCACGGCA AACAGCGTGGCCATCATCATCCTGGTCCTTGGCTGCGTAGTCTTCCTGGT AGCCTTCATGGGATGCTGCGGCGCCATACGCGAGAATTCCTGTGCTCTGA CCTCGTACTCTGTGGTCATGCTGGTGCTGTTGGTTAGTCAGCTAGCTCTC ATTATCTACGTGTGGGTGGACCATGTGCAGATACAGCAATCTTTGGAGAA GATCGTCCAGACCATATGGGATCAACGCAAGACCGATGCCCTCCTCATGG ACACACTGCAGCGATCGTTCAAGTGCTGCGGCTTGAACGGCTTCGCTGAT TACGGCATTACGTATCCCGCCTCCTGCTGCGACTCGCCCTCCAATGGAAC CTGCGCACTAACCCAAGTCATGACGCGATCCAGTTGCCTGAAGGCCGTTG ATTCCTTCTGGGACACCAACGTGAGCATCATCAAGTACGCTGGCCTGGGT GTGACTGCTGTTGAGCTTGTGGCCTTCATTTTCGCCTGCTGCCTGGCCAA TCAGACCCGCAACTCGCAGAGACGCCAGAACTACTAAACGATGAAACGAT GAATTAGTAGCATAGTATTAGGATTATCTCCCGACCCTCTTTAACGTCAT AAAGTCAATATGAATAAATAAAACAAAGTGCTTCGCATGCTTACTGTATA T MDCGGVFVKYVLFIFNILFVICGILLITFGSIMVSTIKDFSGVGETFTAN SVAIIILVLGCVVFLVAFMGCCGAIRENSCALTSYSVVMLVLLVSQLALI IYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRSFKCCGLNGFADY GITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGV TAVELVAFIFACCLANQTRNSQRRQNY CG9454 CG9454 gene CG9454 cyto_range 42D4-42D4 gbunit AE003790 sp_status Not in SwissProt real (computational) symbol CG9454 FlyBase FBan0009454 FlyBase FBgn0033112 GO GO:0004867 serine protease inhibitor activity CG9454-RA transcript protein_id AAF57406 sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) owner crosby Gadfly CG9454-RA FlyBase FBtr0086194 translate offset 210490 210488 CG9454:1 exon 210490 209639 CG9454:2 exon 209580 209377 ATGAAAGATGAGGAGTTCGCACAGGGCTTGGAACAATTCGCTCTTTGTCT GCACGACCATTTGTGCCGGGCAAGTGCTGGCCTAAACATCATCTACTCCC CATTATCCATCCACATCTCTGCGGCCATGCTGCGGATGGGAACATCCGAG GGATCGGCTACAGCTAAGGAGATGGACGAGGGGCTCCGTTTCGGTGGGCT AGAAGCTCAGCAAGTAGCTGAAAGCTTTGGTGTCGTCCTCAAGTCCTATG AACAGTGCCAGGTTCTTAAAATGGCAAACGGCCTATATGTTATGAAGGGT CTCCAAGTTGACGAGCAGTTTGGTCACATACTAGAGCAGAAGTTTCGCTC CAAGCCAATGGAGATTGACTTTGGCAGCGAGCAGGCTGCCAGCATAATCA ACAAATGGGTGGAGTCACAGACCAACAACCTGATCAAGGACATAATCGGT CCAAGAGTTCTTACCAAGGACTCGCGGCTGTGCCTAGTAAACGGTATTCA CTTCAAGGGTGAGTGGTCAATCAGTTTCAATGAAAAAGAAACCCGCGAAG AGGATTTCTTCGGATCGGATAGACCTACCAGAGTGAGAATGATGCATGTG TGCGAGAACTTCTTTTTTGCCGTACTTCCCATGTTCGAAGCCACTGCCCT TAGAATGAATTATAGTGCCTGTAATTTGGCCATGATCATTTTACTTCCTG ATGAGAAGTCGAATCTCACGAGCCTCGAAAAGAAACTTAGTGATATTTCC CTAGAGGTAGTGTCATCAGCAATGAATCTGGAAAAAGTGGATGTGAAGAT TCCTAGCTTTACAGCCGAGTTCCAGCAAGAACTATCCCAGGTTTTAATGC TGATGGGCATGAACCGAATATTCAGTGGTCAGGCAGAGCTTGGGGGAATG CTACAATCCGAGGAAAGCCTTTTTGTCTCCCAGATCGTCCACAAAGCATT TATCGAGATTAACGAAGTGGGCACTGAAGCTGCAGCCGCAACGGGTGAGC CTGCAAAAAAAAAAGGTTCCAAAACTTTTGGCAATTTGAAAGCCTCTTAT ATCTAG MKDEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSE GSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKG LQVDEQFGHILEQKFRSKPMEIDFGSEQAASIINKWVESQTNNLIKDIIG PRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVRMMHV CENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDIS LEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLMGMNRIFSGQAELGGM LQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKKGSKTFGNLKASY I CG30159 CG30159 gene CG30159 gbunit AE003790 sp_status Not in SwissProt real (computational) comment Flag Cambridge: gene split (internal view only).::DATE:2002-02-13 10:34:00::TS:1013614440000 symbol CG30159 cyto_range 42E4-42E4 encoded_symbol CG3364 Gadfly CG30159 FlyBase FBgn0050159 FlyBase FBgn0033123 FlyBase FBan0030159 CG30159-RB transcript owner andy Gadfly CG30159-RB FlyBase FBtr0089760 translate offset 322903 322905 CG30159:3 exon 322726 322830 CG30159:4 exon 322896 324083 CAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCA TTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCC AAGTGTTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCA GGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCA TCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAG CCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCG CCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGC AGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCG ATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCG CGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCG AGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTC TGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGT CTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCG CCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTG GAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTA TCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCA AGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCC TGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGT TCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTG TGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAA ATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAA GTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCG ACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTA ATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAA ATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTG TGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAA MEAAKDFAVAKYQDLCNFLERDTRGSELAIYGTSAIMLAVAYAKRKPAYL VRQFKQPSHIPERLINERVMHTGKIAGVKQQEQDTLLMIQHRPLFPIFTS SKRLLPVKLPGVRVNANGYSWLQQCLIGREATFLPLKSAKGQDFVVCQLC LVHPPRGNRLLDVSETLLKLRFARFVQDAAAAVKKNGKYYQHLKKVEQTT AEKEAWLSWAAGYPYIWRRYNELRQRWLPKEKLLPELVR CG30159-RA transcript protein_id AAM70842 owner crosby comment EST evidence indicates that 5' UTR overlaps that of neighboring gene on the same strand.::DATE:2003-03-14 17:39:04::TS:1047681544000 sp_comment Perfect match to HYPO SP record with corresponding FBgn status not done Gadfly CG30159-RA FlyBase FBtr0089761 translate offset 322903 322905 CG30159:2 exon 322461 322830 CG30159:4 exon 322896 324083 CAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCG TAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGT GTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGA GAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATC CCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCA AAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAG CGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAA ACGACATAACGCTCCAAGTGTTATCCAATGGAGGCGGCCAAGGATTTTGC GGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCG GCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCC TATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTC GCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGA TCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCAC CGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAA ACTGCCGGGCGTGCGCGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGT GTCTCATTGGGCGCGAGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGA CAGGACTTTGTTGTCTGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAA CCGCCTGCTGGACGTCTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGAT TCGTGCAGGATGCCGCCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAG CATCTGAAGAAGGTGGAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTC CTGGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGC AGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTG CGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGC CACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGC CTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTG TTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACA AACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGG GGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTA CGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCAT TTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGT GCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAA ATACCTAA MEAAKDFAVAKYQDLCNFLERDTRGSELAIYGTSAIMLAVAYAKRKPAYL VRQFKQPSHIPERLINERVMHTGKIAGVKQQEQDTLLMIQHRPLFPIFTS SKRLLPVKLPGVRVNANGYSWLQQCLIGREATFLPLKSAKGQDFVVCQLC LVHPPRGNRLLDVSETLLKLRFARFVQDAAAAVKKNGKYYQHLKKVEQTT AEKEAWLSWAAGYPYIWRRYNELRQRWLPKEKLLPELVR CG15237 CG15237 gene CG15237 cyto_range 42D1-42D1 symbol CG15237 comment Gene prediction data only.::DATE:2002-02-14 10:09:31::TS:1013699371000 gbunit AE003790 sp_status Not in SwissProt real (computational) FlyBase FBgn0033104 FlyBase FBan0015237 CG15237-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn owner crosby protein_id AAF57397 Gadfly CG15237-RA FlyBase FBtr0086212 translate offset 139467 139465 CG15237:1 exon 139467 139345 CG15237:2 exon 139286 139199 CG15237:3 exon 139131 138992 ATGATTCCATTCTTTCCCACGCTCAAAGTCTCCGTGGCCAATCGCTACTG GTTGGACATGGCTCCTGCCTCCGTAAACGAAGAATCGCAGACGCGGCGTT ATGAGGATGAAAGGAGCAACTGGCGAGAGTCCCTTAAGACGGCCGGCACA GATCTGCAGCCGCTGGGCAAAATGCTCACCATACCCGGAATTGAGACCGA CGACGAGGATGCCAACGACGACAGCGAGGACACGGACAGTCACGATGAGG AGGATGACGAGACCAACGACCGCGTCATCCCGGTAACCCAGGACTTTTAC TCCGCCGACGACATTCAGATGAACGACGAGACCTCACCCACAGCCCCCTA A MIPFFPTLKVSVANRYWLDMAPASVNEESQTRRYEDERSNWRESLKTAGT DLQPLGKMLTIPGIETDDEDANDDSEDTDSHDEEDDETNDRVIPVTQDFY SADDIQMNDETSPTAP Spn4 CG9453 gene Spn4 cyto_range 42D4-42D4 comment DGC clone may be problematic (GH21896): represents unique EST.::DATE:2002-03-07 00:18:50::TS:1015478330000 sp_status Curator examined, accepted symbol Spn4 gbunit AE003790 FlyBase FBan0009453 FlyBase FBgn0028985 FlyBase FBgn0033111 GO GO:0004867 serine protease inhibitor activity Spn4-RC transcript comment Only one EST supports this alternative transcript (DGC:GH21896).::DATE:2002-03-07 00:18:25::TS:1015478305000 owner crosby protein_id AAF57405 sp_comment Imperfect match to REAL SP with corresponding FBgn Gadfly CG9453-RC FlyBase FBtr0086195 translate offset 208179 208177 Spn4:1 exon 208698 207202 Spn4:2 exon 207137 206996 Spn4:3 exon 206508 206371 Spn4:4 exon 206301 205924 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTGAGTTATCCGGCAGTTTGA CTTTAAAAAGCCAGTGAAAGAAAACGCATTATGGATGTAAAGAGTGAAAT CAATGAGAACACCGAAGGCAGGCGAGAGAAAAACCCGTTTGGGAGCACGA ACTGAAGAGAAATCATTGTTTTGTGGGGGAATACATATGCATATGCGAGT ATAAAAACAATGTACGCTCGCTGAGAGAATTCAGTTGTTGCTCAAAGGCC ACATTATAAAAGTCGAGGGCGATAGCCGGTTTATAAAAAGAAATTAATTT ACACACTCGAAGCCGCTGGTGAAAAACAGTACCAGCAGTCGGAGCAGGCA GTTAATTACCCTTTCCGATAATCAAGCTAGTGAATCCCCGGCGAAACGGC CAACCGGAGAGATATAGTGAACACCGTTTGTGGAGGTGACTCATCAGTAC ACTGCAATTACATAAATTTATGAAAACGAGCACACCTCATCCACGGTCGA TTTGGATACTTACAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTC TTCCCGTTTCCACCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGC CCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACG GCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTT TCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGAC GGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGC AAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAG ATCTTGCGCATCGCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCG CCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGA GCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGG GTTGAGCAGCGCACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGT ATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGG GCACCTGGCAGCACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTT CACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGA GCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAAC TGCCCTACAAGGACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACC AAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTC GCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCA GGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTG GGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACA AAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTG AAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATG TGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGT CCAGCATCCATTTAACTATTACATTATCAATAAGGATTCTACTATTTTGT TTGCGGGAAGAATCAATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCG CTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATT TACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCA TAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTC GAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTG GCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAAT TATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTAT ACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTC TAAAA MKTSTPHPRSIWILTGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFAR RLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQ GLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQL LSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESR LVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYAD LPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSL YETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLK VSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNY YIINKDSTILFAGRINKF Spn4-RB transcript protein_id AAG22208 sp_comment Imperfect match to REAL SP with corresponding FBgn comment Encodes protein variant A (FBrf0151323).::DATE:2002-03-07 00:15:14::TS:1015478114000 owner crosby Gadfly CG9453-RB FlyBase FBtr0086196 translate offset 208644 208642 Spn4:5 exon 208698 208620 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:7 exon 206897 206663 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGCATGGCGGTGCGTAGGAAGCGCGCTATTATGTCGCCTGAGGAACCA ATTGAGTTCTTTGCCGACCATCCTTTCACCTATGTCCTTGTGCATCAGAA GGATCTGCCATTGTTTTGGGGCTCAGTTGTGCGGCTCGAGGAAAATACCT TCGCCTCCAGCGAGCATGATGAGCTGTGATGGTACCTGATTCTTTGGCAA AACAATAAAGACAGCTATTTATTTACAATGGAAATTAA MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKD LPLFWGSVVRLEENTFASSEHDEL Spn4-RA transcript comment Encodes protein variant E (FBrf0151323).::DATE:2003-02-21 17:15:26::TS:1045865726000 owner crosby protein_id AAG22209 sp_comment Imperfect match to REAL SP with corresponding FBgn Gadfly CG9453-RA FlyBase FBtr0086197 translate offset 208062 208060 Spn4:8 exon 208416 208214 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:7 exon 206897 206663 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGCATGGCGGTGCGTAGGAAGCGC GCTATTATGTCGCCTGAGGAACCAATTGAGTTCTTTGCCGACCATCCTTT CACCTATGTCCTTGTGCATCAGAAGGATCTGCCATTGTTTTGGGGCTCAG TTGTGCGGCTCGAGGAAAATACCTTCGCCTCCAGCGAGCATGATGAGCTG TGATGGTACCTGATTCTTTGGCAAAACAATAAAGACAGCTATTTATTTAC AATGGAAATTAA MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMAVRRKRAIMSPEEP IEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL Spn4-RD transcript comment Encodes protein variant C (FBrf0151323).::DATE:2003-02-21 17:13:54::TS:1045865634000 status not done owner crosby Gadfly CG9453-RD FlyBase FBtr0086198 translate offset 208644 208642 Spn4:5 exon 208698 208620 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:4 exon 206301 205924 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCG ATACGTTTCAATGTCGACCATCCATTTACATTTTACATCCTTAACAAGGA CTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAAC ATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGT GCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTT ACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGCGCAATTGATGAT CTTATATATACACTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGC CTCAATAAAGTCTAAAAGCAAATGTCTAAAA MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMFMSLTSLPMPKPDPIRFNVDHPFTFYILNKDS TALFAGSIKKL Spn4-RE transcript status not done comment Encodes protein variant B (FBrf0151323).::DATE:2003-02-21 17:12:35::TS:1045865555000 owner crosby Gadfly CG9453-RE FlyBase FBtr0086199 translate offset 208644 208642 Spn4:5 exon 208698 208620 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:9 exon 206508 206302 Spn4:10 exon 206206 205924 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCC GTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGA TTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAAGTTAGCACT CCATCAAAATCCACCAATCACAACCATTGAACTGAAATGCAATGTAATCC CAATTCACAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCT AAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTA TTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCA TATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGC GCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCA TGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAA MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNYYIINKDS TILFAGRINKF Spn4-RF transcript comment Encodes protein variant B (FBrf0151323).::DATE:2003-02-21 17:12:07::TS:1045865527000 status not done owner crosby Gadfly CG9453-RF FlyBase FBtr0086200 translate offset 208644 208642 Spn4:5 exon 208698 208620 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:3 exon 206508 206371 Spn4:4 exon 206301 205924 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCC GTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGA TTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAAGTATGTTTA TGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCGATACGTTTCAAT GTCGACCATCCATTTACATTTTACATCCTTAACAAGGACTCAACCGCTCT CTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAAT CCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCA GTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATA AGGATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACA CTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTC TAAAAGCAAATGTCTAAAA MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNYYIINKDS TILFAGRINKF Spn4-RG transcript status not done comment Encodes protein variant G (FBrf0151323).::DATE:2003-02-21 17:17:48::TS:1045865868000 owner crosby Gadfly CG9453-RG FlyBase FBtr0086201 translate offset 208062 208060 Spn4:8 exon 208416 208214 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:4 exon 206301 205924 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGTATGTTTATGAGCCTTACTTCG CTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATT TACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCA TAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTC GAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTG GCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAAT TATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTAT ACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTC TAAAA MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMFMSLTSLPMPKPDP IRFNVDHPFTFYILNKDSTALFAGSIKKL Spn4-RH transcript comment Encodes protein variant F (FBrf0151323).::DATE:2003-02-21 17:16:52::TS:1045865812000 status not done owner crosby Gadfly CG9453-RH FlyBase FBtr0086202 translate offset 208062 208060 Spn4:8 exon 208416 208214 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:9 exon 206508 206302 Spn4:10 exon 206206 205924 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCC ATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATT TAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAA TCAATAAGTTTTGAAGTTAGCACTCCATCAAAATCCACCAATCACAACCA TTGAACTGAAATGCAATGTAATCCCAATTCACAGGACTCAACCGCTCTCT TCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAATCC ACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGT CCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAG GATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACACT TAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTA AAAGCAAATGTCTAAAA MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQP VQFHVQHPFNYYIINKDSTILFAGRINKF Spn4-RI transcript comment Encodes protein variant D (FBrf0151323).::DATE:2003-02-21 17:14:53::TS:1045865693000 owner crosby status not done Gadfly CG9453-RI FlyBase FBtr0086203 translate offset 208644 208642 Spn4:5 exon 208698 208620 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:11 exon 205893 205679 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGTATGGCGGGTGATGGCCGTAGCTGCCTTCAGTCGCAAACACTTCATT GCCAACCATCCTTTTGCTTTCTACGTGAAGACCCATTACGATCTGCCGAT ATTCACTGGGCGCTACTTGGGTTAAGCAATAGGAAGCTTCCTATGAAAAA AAAAATTGAAGTTCAATAAAATAAAATAAACGGCAGCCACTTAATAGCTG TGATTTCGTCAAGTCGAA MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATVWRVMAVAAFSRKHFIANHPFAFYVKTHYDLPIF TGRYLG Spn4-RJ transcript status not done comment Encodes protein variant H (FBrf0151323).::DATE:2003-02-21 17:18:10::TS:1045865890000 owner crosby Gadfly CG9453-RJ FlyBase FBtr0086204 translate offset 208062 208060 Spn4:8 exon 208416 208214 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:11 exon 205893 205679 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGTATGGCGGGTGATGGCCGTAGCT GCCTTCAGTCGCAAACACTTCATTGCCAACCATCCTTTTGCTTTCTACGT GAAGACCCATTACGATCTGCCGATATTCACTGGGCGCTACTTGGGTTAAG CAATAGGAAGCTTCCTATGAAAAAAAAAATTGAAGTTCAATAAAATAAAA TAAACGGCAGCCACTTAATAGCTGTGATTTCGTCAAGTCGAA MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATVWRVMAVAAFSRKHFI ANHPFAFYVKTHYDLPIFTGRYLG Spn4-RK transcript status not done owner crosby comment Encodes protein variant F (FBrf0151323).::DATE:2003-02-21 17:17:13::TS:1045865833000 Gadfly CG9453-RK FlyBase FBtr0086205 translate offset 208062 208060 Spn4:8 exon 208416 208214 Spn4:6 exon 208133 207202 Spn4:2 exon 207137 206996 Spn4:3 exon 206508 206371 Spn4:4 exon 206301 205924 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCC ATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATT TAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAA TCAATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCG AAGCCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACAT CCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCT AAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTA TTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCA TATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGC GCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCA TGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAA MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQP VQFHVQHPFNYYIINKDSTILFAGRINKF CG15235 CG15235 gene CG15235 cyto_range 42C10-42D1 comment Gene prediction data only.::DATE:2002-02-14 10:05:26::TS:1013699126000 gbunit AE003790 symbol CG15235 sp_status Not in SwissProt real (computational) GO GO:17034 FlyBase FBgn0033103 FlyBase FBan0015235 GO GO:0017034 Rap guanyl-nucleotide exchange factor activity CG15235-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAF57395 owner crosby Gadfly CG15235-RA FlyBase FBtr0086213 translate offset 122885 122883 CG15235:1 exon 122885 122848 CG15235:2 exon 122396 122254 CG15235:3 exon 122185 121893 ATGAACGAGATAATCCACTATCAGATACAAGGTCAAATTCCTTGCGACCG GAACCTGCGTGATGTGGAGCTAATTTCGTGCCGGTTGCGTCGCGTGGAGC CGCTGTGTCGCCTCCCGGGATCTGCGCTCCAGCAGTTGGCCATGTGCGGA TTCTATGAGGACCTGGAGAAGGGGGTGACTCTTTTTCGCGCCGGCGAGCA GGGACGCTTCTGGTATGCAGTGCTCGGCGGATCGCTGGAGGTGCGATACC ATGCCCACGCCGATGCCGATGGCAAGGTAAGTCCTTACTTACACCAGTCA GGAGATGAGACATCCTGGAACACTATTCCGCCGTGCGCAGAGTGCGAGAC AATGCGCGTGCTGAGCAATATAATTGATAGTGATTACTCGGCGTACCCGC CGTGTTGCATATCCGATCCGCCGTGCATGCTCAATATTCCGGGGATTTGG GCCTGGGTTGGGGGTTGGGTTTGA MNEIIHYQIQGQIPCDRNLRDVELISCRLRRVEPLCRLPGSALQQLAMCG FYEDLEKGVTLFRAGEQGRFWYAVLGGSLEVRYHAHADADGKVSPYLHQS GDETSWNTIPPCAECETMRVLSNIIDSDYSAYPPCCISDPPCMLNIPGIW AWVGGWV vimar CG3572 gene vimar description D.melanogaster FlyBase-curated sequence: vimar.v004 sp_status Curator examined, accepted comment Comment: Reference sequence of vimar == FBgn0022960 gbunit AE003790 cyto_range 42E1-42E4 comment DGC clone appears problematic (SD10607): incomplete CDS (approximately 40aa short at amino terminus).::DATE:2002-03-07 00:39:32::TS:1015479572000 comment Comment: Reference sequence based on BDGP genomic sequence. symbol vimar comment Comment: This record is derived from the following: AC009342 AC009342.5 21-MAR-2001 AF034421 AF034421.1 25-FEB-2000 AQ034041 AQ034041.1 08-JUL-1998 AI543723 AI543723.2 23-APR-2001 AA264054 AA264054.1 19-APR-2001 AW944649 AW944649.1 19-APR-2001 AF171836 AF171836.1 23-AUG-1999 FlyBase FBgn0021806 FlyBase FBan0003572 FlyBase FBgn0027729 FlyBase CG3572 FlyBase FBgn0022960 GO GO:0017160 Ral interactor activity vimar-RC transcript owner crosby protein_id AAF57418 sp_comment Imperfect match to REAL SP with corresponding FBgn Gadfly CG3572-RA FlyBase FBtr0086182 translate offset 315193 315191 vimar:1 exon 315484 315187 evidence experimental vimar:2 exon 308375 307467 vimar:3 exon 307377 306991 evidence experimental vimar:4 exon 306932 305057 evidence experimental citation FBrf0102180 ACACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAA TACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAAC GGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCA GTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGT GCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAA CGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGACA GCTGAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCC GGCGAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCA AACTTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAG TGCGACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGAT CACCAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAG CCGCATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATG GAGCTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAA CGACGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTAC TGCGACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAA TTCATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGA GGGCTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAG GCATCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTG CTGAACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCT GAACTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTT CCACGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAG GCGGAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGA AACCATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTG AGGCCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTT ACTGGTGATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAA CATGGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCG TGCTGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTT GTGGAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAA CGGCGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGC GCAACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGC CTGGTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGT CTTCAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGGAGAAAC TCGCACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCAC TGGAGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCT CATGGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCAC TGCCGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCG CTAACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGA GGGCACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCA TGCAGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTG TCGCAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGT CAAGTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGG ACACGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTG CTCAAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAA CGAGCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAG AAAACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACA GTGGGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGG TAAGCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGC CAATACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCT AAACTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATC CACTCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATA AATGTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTA GCCACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAA GCAACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCA GATTCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAAC ACGAGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCAT TTATGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTT ATAGCATACATACATAACATATACGTATAAATATAATAATATTAATAATT TAGCATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAAC AAATCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTG TACTTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCA AAAACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATT TTAATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTG TAAAACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAAC ATTAACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAA AACCAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGC TACAAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAA AAACTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATA AAGCGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTC TAAACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATG AGAAATAAGAGAAAACCAAA MATAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLG LTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSD GSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVAN AAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHE DLLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELL HYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIV LILTGDDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHC IYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVI QAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQEKLALELLKNKTLIEQ LVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIAD KIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSV VYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNC VNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL vimar-RB transcript owner crosby evidence experimental status not done citation FBrf0102180 Gadfly CG3572-RB FlyBase FBtr0086183 translate offset 315193 315191 vimar:1 exon 315484 315187 evidence experimental vimar:5 exon 308372 307467 evidence experimental vimar:3 exon 307377 306991 evidence experimental vimar:4 exon 306932 305057 evidence experimental citation FBrf0102180 polyA_site citation FBrf0102180 evidence experimental ACACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAA TACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAAC GGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCA GTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGT GCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAA CGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGACT GAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCCGGC GAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCAAAC TTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAGTGC GACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGATCAC CAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAGCCG CATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATGGAG CTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAACGA CGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTACTGC GACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAATTC ATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGAGGG CTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAGGCA TCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTGCTG AACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCTGAA CTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTTCCA CGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAGGCG GAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGAAAC CATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTGAGG CCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTTACT GGTGATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAACAT GGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCGTGC TGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTTGTG GAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAACGG CGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGCGCA ACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGCCTG GTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGTCTT CAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGGAGAAACTCG CACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCACTGG AGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCTCAT GGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCACTGC CGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCGCTA ACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGAGGG CACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCATGC AGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTGTCG CAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGTCAA GTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGGACA CGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTGCTC AAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAACGA GCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAGAAA ACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACAGTG GGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGGTAA GCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGCCAA TACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCTAAA CTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATCCAC TCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATAAAT GTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTAGCC ACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAAGCA ACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCAGAT TCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAACACG AGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCATTTA TGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTTATA GCATACATACATAACATATACGTATAAATATAATAATATTAATAATTTAG CATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAACAAA TCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTGTAC TTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCAAAA ACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATTTTA ATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTGTAA AACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAACATT AACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAAAAC CAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGCTAC AAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAAAAA CTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATAAAG CGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTCTAA ACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATGAGA AATAAGAGAAAACCAAA MATEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGL TKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDG SMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANA AQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHED LLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLH YQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVL ILTGDDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCI YFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQ AGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQEKLALELLKNKTLIEQL VHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADK IPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVV YLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCV NLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL insertion_site evidence experimental comment 8 bp insertion associated host repeat citation FBrf0102180 insertion_site evidence experimental citation FBrf0102180 comment P{lacW} insertion 16bp downstream of the start site of the 3.5kb cDNA, GB:AF034421 CG30156 CG30156 gene CG30156 symbol CG30156 cyto_range 42E1-42E3 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBan0030156 FlyBase FBgn0050156 GO GO:0006952 defense response GO GO:0006457 protein folding GO GO:0006950 response to stress GO GO:0019538 protein metabolism CG30156-RA transcript protein_id AAM70840 sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn owner crosby Gadfly CG30156-RA FlyBase FBtr0086184 translate offset 312483 312481 CG30156:1 exon 312761 311744 CG30156:2 exon 311684 311518 CG30156:3 exon 311460 311221 GTTGACATACAAAATGTTGACTGGCGAAAGTCAATTTGTATTTAAGTTTG CAGCTACATATACATATACAGTCAACTTAGTTCGAAACTATTTCGGCTAC CTCTAATATACATACAAAAGCACTTTGTTAAATTCACCAACTCGGTGGAT TGTCCCAGAACAACAAACCAAAATTTAAAATTTGCAAACGAACAGAGAAA AACGAATCCTTTTTTGTCTTCTCACGCTGCTGGGAAGGAGAAGAAAGTAA CCAAGAACTGGAGGACGACGACTTCACAATGGGAATCCTGCAGGCGAGGA GGCATCACTGCGTCGACAAGGTGGTGAGTGACCTGTGCCTGGGACACTAC GAGCACGCTCTGAGGCAGATCAACGAGGATCTGGAAGGCTTACAGAACCA CGATGAGATCATGGCGCTGCTGGAGCTAAAGAATATCATTTTGAGACTGA GGCTGAAGGGCGAGGCCCAGCGGACCATAGGCCCAACTCGCAAATCTGAC GCCCTGCCCCACAAGTTCACACTCGAGATGCTGGACGTGGTGCAGAAGGT CCTGCGGTGCCGCAATCACTACGAGGTGCTGCGCATCTCTCATCATGCCA CCTACTCCGAGGTGAAGCGGGCCTACCACAAGCTGGCCCTGCGCCTCCAT CCGGACAAGAACAAATCTCCTGGGGCTGAGCAGGCCTTCCGGCGGATCAG CGAGGCGGCTGACTGCCTCACGGACTGCCAGAAAAGGATTGAGTACAACA TAGCAACGGCAGTGGGCGACTGCCACGACCAGGATCCCTCGCAGTACAAG GATTATCGCGGGGAAAGTGAATTCAATGAGGCAAATGGGAACGATCTGGG AGCCGCTTTCAGAAGGCCTTATCGGGGGGCCAATCAGCGGATGCCCCAGA GGCAGTCACTCTACCAAACACAGCAACTCGTCATCGGAGTGGTGGCTGCT CTGGTTTTTCTCTTCGTCACCATGCACTTCATCGCAGGCGCTCCTGCTTA CAGTTTTACGCTAACCAGAACCCACAGCGCTCGACGGCTCAGTCGGACGA ACCACATTGCCTACTACATGAATCCGACGACTCTGTCCAAGTACACAGAA CAGCAGTTGGCCGAACTGGAAGTAGAAATCGAGGAGGTTTACATCTCGGA CCTCAAACATAAGTGCAGGCAAGAGCGGAGTTGGAGGGATAATCTGTTTC TCAGGGCGAGGCAGGGAAACAACGACCAGAAGTTGCTCCAGCATGTCAGC CAGATGTCCACTCCCGCTTGCCAGGCGTTGCTCCAGCTGGGAAAGTCTGG TCACAGTCGACTGTTGCTCGAGAACGAGTCTTTGAATCAGGACGTGCCAG TCTGATACTCTGTACTTTTCTATTGATAGATGTAGGGATTAGTGCACGGT GTAAATAAAGAGTAGTTTTAAAAAT MGILQARRHHCVDKVVSDLCLGHYEHALRQINEDLEGLQNHDEIMALLEL KNIILRLRLKGEAQRTIGPTRKSDALPHKFTLEMLDVVQKVLRCRNHYEV LRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDC QKRIEYNIATAVGDCHDQDPSQYKDYRGESEFNEANGNDLGAAFRRPYRG ANQRMPQRQSLYQTQQLVIGVVAALVFLFVTMHFIAGAPAYSFTLTRTHS ARRLSRTNHIAYYMNPTTLSKYTEQQLAELEVEIEEVYISDLKHKCRQER SWRDNLFLRARQGNNDQKLLQHVSQMSTPACQALLQLGKSGHSRLLLENE SLNQDVPV Cyp6u1 CG3567 gene Cyp6u1 cyto_range 42E1-42E1 symbol Cyp6u1 gbunit AE003790 sp_status Curator examined, accepted GO GO:5792 GO GO:15034 FlyBase FBgn0033121 FlyBase FBan0003567 GO GO:0005489 electron transporter activity GO GO:0005792 microsome GO GO:0016020 membrane Cyp6u1-RA transcript owner crosby sp_comment Imperfect match to REAL SP with corresponding FBgn protein_id AAF57417 Gadfly CG3567-RA FlyBase FBtr0086185 translate offset 303604 303602 Cyp6u1:1 exon 304761 304722 Cyp6u1:2 exon 303775 302563 Cyp6u1:3 exon 302504 301887 TGCGATTTCACTTTCACAAAACAAATTACGGCTGCCCAAGCGGCCGATAC TCAATGGACCTTATCAATTATTAAATCGGACCGCACGATAATGGCGCTGA TAAACCGGCGGCATTGAGCCCCAGAACCTCGACAAGCAGCTACTGCCAGC TGTTAAGCATATCAAACAGCGCGAACATATTGTAAAAGCCGGAAAAGACA GCTGAGTGAGCATGGATCTAATGCACCGCACCCTGCTCACCGCCCTGGGT GCGCTGTCAGTGGTCTACGCCCTGGTCAAGTTCAGTCTGGGCTACTGGAA ACGGCGGGGGATCCTGCACGAAAAGCCCAAGTTCCTGTGGGGCAACATTA AGGGCGTGGTGAGCGGGAAGAGGCATGCCCAGGACGCCTTGCAGGATATC TACACCGCATACAAGGGCAGGGCGCCGTTTGTGGGATTCTACGCCTGCCT CAAGCCGTTCATCTTGGCGCTGGACCTGAAGCTAGTCCACCAAATAATCT TCACCGACGCGGGACACTTTACGTCCCGAGGCCTTTATAGTAATCCCAGT GGAGAGCCGCTGTCGCATAATCTCCTTCAGCTGGACGGTCACAAGTGGCG GTCACTGCACGCCAAATCTGCAGAGGTTTTCACTCCGGCCAACATGCAGA AGCTGCTGGTCAGACTGTCGCAAATCTCCTCCAGAATTCAAAGGGACCTG GGCGAAAAGAGCCTTCAAACTATCAATATAAGCGAACTCGTGGGTGCATA CAATACGGACGTTATGGCGTCAATGGCCTTTGGACTAGTAGGGCAGGATA ACGTGGAGTTCGCTAAGTGGACGCGCAACTACTGGGCGGACTTTAGGATG TGGCAGGCTTATCTGGCGCTTGAGTTTCCGCTCATCGCTCGCCTTCTTCA GTACAAAAGCTACGCAGAACCTGCTACAGCTTACTTCCAAAAAGTGGCCC TGTCGCAGTTGCAGTTGCATCGAAGAAGGGATCGCCAGCCACTCCAGACC TTTCTGCAGCTATATTCCAACGCAGAAAAGCCGCTCACCGACATCGAGAT TGCGGGCCAAGCCTTCGGCTTCGTTCTGGCTGGCTTGGGCCCCCTGAATG CCACCCTAGCATTCTGCCTCTACGAGTTGGCCCGCCAGCCTGAGGTGCAA GATCGAACCAGGCTCGAGATTAACAAGGCACTGGAGGAGCATGGTGGCCA AGTGACACCGGAGTGCCTAAGGGAGCTCAGGTATACGAAGCAAGTCCTCA ATGAAACGCTTCGCCTGCACACTCCACATCCCTTCCTGCTACGCCGGGCT ACCAAAGAATTCGAAGTGCCCGGATCGGTGTTTGTAATTGCCAAAGGCAA CAATGTGCTGATACCAACGGCGGCGATACACATGGATCCTGGCATTTATG AAAACCCCCAGCGGTTCTACCCGGAGCGCTTTGAGGAACAGGCAAGGCGA TCCCGCCCGGCAGCTGCGTTCCTGCCTTTCGGCGATGGCCTGCGAGGATG CATTGCCGCTCGCTTTGCAGAGCAGCAGCTTCTGGTGGGCCTGGTGGCTC TGCTGAGGCAGCACAGATACGCTCCCTCTGCGGAGACCTCGATTCCCGTG GAGTACGACAACCGGAGACTGCTCTTGATGCCCAAGTCGGACATCAAACT CAGTGTGGAACGGGTGGACAAGCTTTAAAGGAGGCTCTGCTGGAGCATCG CATATTTTGTATTGTTTGCTTTACAAAGCGTTTAAGTTGTTTTTATATTT GTATATGCACCTTTTTCGTTGATTTTCCTAAGCTGTGGACTTGTGTGATA ATGCTGACGATGACTTTTATAATCTTTTGCACCAAGCTCAACAACGTGAA CAAATAAATAATTTAGTTGTT MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVV SGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDA GHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLV RLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEF AKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL QLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLA FCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNETL RLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQ RFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQ HRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL CG9447 CG9447 gene CG9447 cyto_range 42D4-42D4 symbol CG9447 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBan0009447 FlyBase FBgn0033110 CG9447-RA transcript owner crosby status not done Gadfly CG9447-RA FlyBase FBtr0086206 translate offset 205388 205386 CG9447:1 exon 205388 204950 CG9447:2 exon 204820 204680 CG9447:3 exon 204619 204078 CG9447:4 exon 203994 203915 CG9447:5 exon 203862 203749 CG9447:6 exon 203691 203343 ATGCCTGCCCTGTACCAACTTGATGACTACGATCTCTGTCTGGATAATCA AGCTGGTACTTACTGTTTGGTGTACGTCGAGATTTTACCCAATGCTAGCT CTGCTCTATGGCACCAAATCGACCAAGTTTCACAGGACTCAAAACACCGT TTTCGCCATGATCGCGTTTTTAGGGGCGTGTGTCTGGAGAGCTGTAAGCA AAGAATCAATCACTTATCCGAGTTCAGGGAGTACGAGAAAGAAGAAATTC TGGATAAGGAACTTATATCTTACTACGATAAGGTACACCGTCGGGATGCA ATGAATTCAGATAGGGATCTCTTTAATAAAGAGGTTGTGAAAGGCTGTCT AAACCAAAAGTTCAGTGAGAAGTTTTCACTTAGAACTCGGAGCCTTATCG AGTACTGTGTCTCGGCCTCGGATAAGGACTTGAAGATGGATTTGCTTGAT TTGGCGTTTTATGGTATTCTGGTAGTTATACTCTTTATAACTTTGTGTTC GTCTTTCCTTGACTATCGCCTGAGCAAGATGAACTCGCAAAAATCAGAAA GTTTTTATCGAGAGCCACTAATGGATCGACGACAGCGACTCCTTACATCC TTCTCAGTGGTTCGAAATTATCATCGATTGGTTGAGCCGTATAACTCAGA TTTCTCGCGGGATGTGAGCTTTTTCGACGGGTTTCGGGTGATCGGCGTAT TTGTAGTGATCTTGGGCCACACGCTTATGGTCTTTATGACTGTTCCAATA GAAAATCCGGAGTTCTTCGAACAGTTCCTGTTCCGGTTCGAGACTTCAAT ATTTCAAAACGGCAGCCTGGTCATCCAGATATTTTTTGTTATGAGCGGCT TCCTTCTCTACGTGAAATTCACCAAACGCCAACAGATTCAACCCAAGACT GGCACGCTTGAGTGCATTGCTGTGTACTTTCGAGTGTTTTCCTACAGATA CTTTAGACTTCTGCCATCGCTTCTCGCTCTCATCCTGTTCAATGGAACAC TGCTGGTGCGCCTTCAAAACGGACCCTTTTGGCGACATCTTACGGAGGCC GAACGGGTCTTCTGTCGCGCCAACTGGTGGAAGAACGTGTTTTTCGTGAC CAACCACATGCTGGAAGACAGTTGCTCCCATCAGACGTGGTACTTAGGAG CAGACATGCAGCTATTCGAGCTCTTCCTTATAGTAATTATTATAACCAAA AAGCATCCCAAGCTGACAAGGACAATCTACACAACTCTTTTAGCACTTGC CTTTGCAGTGCCTGCTGTACTGACCTACGTTCTCGAGCTGGATGGTATCT ACCATATTCGTCCGGAAACATATCGCTACTTGTACTTCCGACATTCCGAC ACATTTTACCAAATGTATCCGCCCTTTTACACAAATTTGGGTGGCTATCT GTTTGGTTTTCTGTGCGGTCATTTTTACCTTAGGCAGCGTTCTGGAAATG TAGAACTTCTGGGTCATCTTAAGTACGATCTGGCCATGTGGCTGCTTGTG CTGGCCACGTTGGGAGTCCTTTTCTCCGGCTACATCTTTATTCGACAGGA CTTTGCGAAGCCATCGCTATGGCTAGCCTTGTATGCGGGCATCCACAAGA TCCTGTGGGTGCTAATATGCGCAGGATTCGTGATCCTCATGTGCCGCAAG GTTGGAGGTGGGTAA MPALYQLDDYDLCLDNQAGTYCLVYVEILPNASSALWHQIDQVSQDSKHR FRHDRVFRGVCLESCKQRINHLSEFREYEKEEILDKELISYYDKVHRRDA MNSDRDLFNKEVVKGCLNQKFSEKFSLRTRSLIEYCVSASDKDLKMDLLD LAFYGILVVILFITLCSSFLDYRLSKMNSQKSESFYREPLMDRRQRLLTS FSVVRNYHRLVEPYNSDFSRDVSFFDGFRVIGVFVVILGHTLMVFMTVPI ENPEFFEQFLFRFETSIFQNGSLVIQIFFVMSGFLLYVKFTKRQQIQPKT GTLECIAVYFRVFSYRYFRLLPSLLALILFNGTLLVRLQNGPFWRHLTEA ERVFCRANWWKNVFFVTNHMLEDSCSHQTWYLGADMQLFELFLIVIIITK KHPKLTRTIYTTLLALAFAVPAVLTYVLELDGIYHIRPETYRYLYFRHSD TFYQMYPPFYTNLGGYLFGFLCGHFYLRQRSGNVELLGHLKYDLAMWLLV LATLGVLFSGYIFIRQDFAKPSLWLALYAGIHKILWVLICAGFVILMCRK VGGG coro CG9446 gene coro cyto_range 42D4-42D4 sp_status Not in SwissProt real (computational) symbol coro gbunit AE003790 GO GO:3779 FlyBase FBan0009446 FlyBase FBgn0033109 GO GO:0003779 actin binding GO GO:0015629 actin cytoskeleton coro-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn owner crosby protein_id AAF57403 Gadfly CG9446-RA FlyBase FBtr0086207 translate offset 196659 196657 coro:1 exon 202544 202309 coro:2 exon 196716 196462 coro:3 exon 195149 194883 coro:4 exon 194824 194411 coro:5 exon 194346 194053 coro:6 exon 193308 193123 coro:7 exon 193064 191776 CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAA CAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATT TTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCC TTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTG AATGCGCTGGCCCCAGTGAGTGGAGTGATAGATAAAAGCTAGACGTAGAG AAGCTCAGGACTGATCGCTGACCCAAGCCACTGCAGCATCAAGATGTCAT TTCGCGTAGTGCGCAGCTCCAAGTTCCGCCACGTCTACGGACAGGCTCTC AAGCGGGAGCAGTGCTACGACAACATACGGGTATCCAAGTCCAGCTGGGA CTCCACATTCTGCGCGGTGAATCCCAAGTTCCTGGCCATTATCGTAGAGT CGGCGGGCGGCGGAGCCTTCATCGTCCTGCCACACAACAAAGTTGGTCGC ATTGCGGCTGACCACCCTTTGGTGGGCGGTCACAAGGGTCCTGTGCTGGA CATCGCCTGGTGCCCCCACAACGACAACGTGATCGCCTCCGGCTCAGAGG ACTGTGTGGTCAAAGTGTGGCAGATCCCCGATGGCGGGCTGTCGCGAACA CTCACCGAACCCGTGGTCGACCTGGTTTTCCACCAGCGTCGCGTGGGTCT GGTGTTGTGGCATCCCTCTGCGCTCAACGTGCTGCTTACCGCCGGCTCCG ATAACCAGGTCGTGATTTGGAACGTGGGCACTGGTGAAATCCTCGTGCAC ATCGACTCCCATCCGGACATCGTTTACAGCGCCTGCTTCAACTGGGATGG CTCTAAGTTGGTTACCACCTGCAAGGATAAAAAGATCCGCATCTACGATC CGCGCACTGCCGAGCTGGAGAGCGAAGCCATGTGTCATGAGGGCTCCAAG GCCACGAGGGCCATTTTCCTACGTCACGGTCTGATCTTCACCACAGGCTT CAACCGTAGCTCGGAGCGTCAGTACTCCCTGCGCGCACCGGATGCCCTTA ACGAACCCATTGTCATGGTGGAGCTGGACACGTCCAACGGCGTAATGTTC CCTCTTTACGACGCAGACACGAACATGATCTACTTGTGTGGAAAAGGTGA CTCGGTCATTCGGTATTTCGAGGTAACGCCCGAACCTCCTTTTGTGCACT ACATAAACACGTTTCAGACTACAGAGCCGCAGCGTGGTATTGGTCTGATG CCCAAGCGAGGCTGTGATGTGACCACCTGCGAGGTCGCCAAGTTCTATCG CATGAACAACAACGGTCTGTGTCAGGTCATCTCGATGACTGTGCCGCGCA AATCGGATCTTTTCCAGGAGGATCTCTACCCCGATACGCTAGCGGAAGAC GCTGCCATCACCGCGGAGGAGTGGATCGATGGCAAGGATGCGGATCCGAT CACATTTTCGCTCAAAGGTGGCTACGTGTCCTCGTCGGTAAACAAATCGC TACCAGCGAAGAAGGCGGGCAACATCCTGAACAAGCCTAGAGGCGACAGC GCTAGCTCCGGTGCAACGAGCAGCAGCGCGGGCGGCGGCAACTTTGCGTC CGGAAATAACAATGAGGCTAGCGAAGGTGGACCGCCTGCAGCGGTTTTAT CGGAAAAGGACCTGCGCACCATACAAGACGAGATCCGCAAACTTAAGGCG ATCATCGTCAAGCAAGAGAACCGCATCCGCGCTCTGGAGGCCAAGGAGGA CGCCCGCAACAAGAATGGAAGCGATGCTGCGCCGGCTTCAGCGGGAGCAG CCACGTCTGACGGCAAAGCCAGTGAAAGTGCCAACGACCACGCGTCCACA TCAGCCGGAACGTCAAAGGACGAGGACTAGGTCTAGCAATGAAACGAGGA CTGAACTGATAAAAATGGGCGGAATGGATTGGAGGAGAGACAGAGAACTG CTTGTAGAAGCTCGTAGCTACGCTTAATTTCTCTATTGCAACAAAGCGCG CTGAGGACGAATTGAAAAAGAACTTATTGTCTATTACCATTATGGTTTCG ATTATTTATTTTTTATAATTTAATATTAGCGAAATCAGTTGAGTGCGGGT GTGGCACAGATAGGGTTAGAGAATGCCGAGCTAAATCATCTAATCGAACT TAAGCGAGCATAACCGAGCAGACCTGGACGCTTAACGTATAAAACATAAC ATAAAACTACATCCTGCCAAAAATATATAAAAAACCTAACGAACTACCTA CATTTTGCGCCCAAAATCAAGCAGAGCGAAGGGCAGGTACTCGGCCCTTT GATCGGCTTGTTGTTACGCAAGTATGAAATTGTTGTAAATTTAACAAAGG CAAATCATAGACTAAACCTCAATCACTTAAGAGTTAACACCTACCTACCA AATTTGTACGAGCTCCTTTCTGTAACGTCTGTATATTTGTACGTCCCGGA AGTTTTCATGACAATAGCTGATAGAATCGATACTGTTCATCCTAGCTGAG GCCCCCTTAATCAGTCACATTTCCCTGCAAATTGTCGTGTCAAACATAGC GAATTTAGTAAGAAAGTGATGGGGGTCATCGGACTTAATTCGTTTTCGTA ATCAAAATTTTATTGTTCAAACTAATGATAAGCTGTATTTTGAAATAATA AGAGTAACAATAAATGCAACAAAATCAGAAAGAAAGTAAGAAACCATCGA AACTATTTTTATAAAAATTTGTTTACTTTTCTTTTCTTTCATTTGATTTT ACTTTCATTAGTTTTGTTAGAGAACCGAGGGCGAGAGCAGCGTCATTAAA CACCTACCGATTTTGTAATTCACAACCATTGTAAAATGAAGACTATATAC ATATACATACATAAATACTCTATATACAAATAATTTACAATTTGATACGG AATAAAACAAAATACAATGCCAGAAGAAGTTGGGTGCTAAT MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED coro-RB transcript owner crosby protein_id AAM70835 status not done sp_comment Perfect match to HYPO SP record with corresponding FBgn comment Only one EST supports this alternative transcript::DATE:2002-02-13 03:08:30::TS:1013587710000 Gadfly CG9446-RB FlyBase FBtr0086208 translate offset 196659 196657 coro:8 exon 196832 196772 coro:2 exon 196716 196462 coro:3 exon 195149 194883 coro:4 exon 194824 194411 coro:5 exon 194346 194053 coro:6 exon 193308 193123 coro:7 exon 193064 191776 GGCTAAACGATTTCGCTTGAAGACTTGTTATTAAGGGCAAAGGGTGGAAA ATACCAAACGCAGCTAGACGTAGAGAAGCTCAGGACTGATCGCTGACCCA AGCCACTGCAGCATCAAGATGTCATTTCGCGTAGTGCGCAGCTCCAAGTT CCGCCACGTCTACGGACAGGCTCTCAAGCGGGAGCAGTGCTACGACAACA TACGGGTATCCAAGTCCAGCTGGGACTCCACATTCTGCGCGGTGAATCCC AAGTTCCTGGCCATTATCGTAGAGTCGGCGGGCGGCGGAGCCTTCATCGT CCTGCCACACAACAAAGTTGGTCGCATTGCGGCTGACCACCCTTTGGTGG GCGGTCACAAGGGTCCTGTGCTGGACATCGCCTGGTGCCCCCACAACGAC AACGTGATCGCCTCCGGCTCAGAGGACTGTGTGGTCAAAGTGTGGCAGAT CCCCGATGGCGGGCTGTCGCGAACACTCACCGAACCCGTGGTCGACCTGG TTTTCCACCAGCGTCGCGTGGGTCTGGTGTTGTGGCATCCCTCTGCGCTC AACGTGCTGCTTACCGCCGGCTCCGATAACCAGGTCGTGATTTGGAACGT GGGCACTGGTGAAATCCTCGTGCACATCGACTCCCATCCGGACATCGTTT ACAGCGCCTGCTTCAACTGGGATGGCTCTAAGTTGGTTACCACCTGCAAG GATAAAAAGATCCGCATCTACGATCCGCGCACTGCCGAGCTGGAGAGCGA AGCCATGTGTCATGAGGGCTCCAAGGCCACGAGGGCCATTTTCCTACGTC ACGGTCTGATCTTCACCACAGGCTTCAACCGTAGCTCGGAGCGTCAGTAC TCCCTGCGCGCACCGGATGCCCTTAACGAACCCATTGTCATGGTGGAGCT GGACACGTCCAACGGCGTAATGTTCCCTCTTTACGACGCAGACACGAACA TGATCTACTTGTGTGGAAAAGGTGACTCGGTCATTCGGTATTTCGAGGTA ACGCCCGAACCTCCTTTTGTGCACTACATAAACACGTTTCAGACTACAGA GCCGCAGCGTGGTATTGGTCTGATGCCCAAGCGAGGCTGTGATGTGACCA CCTGCGAGGTCGCCAAGTTCTATCGCATGAACAACAACGGTCTGTGTCAG GTCATCTCGATGACTGTGCCGCGCAAATCGGATCTTTTCCAGGAGGATCT CTACCCCGATACGCTAGCGGAAGACGCTGCCATCACCGCGGAGGAGTGGA TCGATGGCAAGGATGCGGATCCGATCACATTTTCGCTCAAAGGTGGCTAC GTGTCCTCGTCGGTAAACAAATCGCTACCAGCGAAGAAGGCGGGCAACAT CCTGAACAAGCCTAGAGGCGACAGCGCTAGCTCCGGTGCAACGAGCAGCA GCGCGGGCGGCGGCAACTTTGCGTCCGGAAATAACAATGAGGCTAGCGAA GGTGGACCGCCTGCAGCGGTTTTATCGGAAAAGGACCTGCGCACCATACA AGACGAGATCCGCAAACTTAAGGCGATCATCGTCAAGCAAGAGAACCGCA TCCGCGCTCTGGAGGCCAAGGAGGACGCCCGCAACAAGAATGGAAGCGAT GCTGCGCCGGCTTCAGCGGGAGCAGCCACGTCTGACGGCAAAGCCAGTGA AAGTGCCAACGACCACGCGTCCACATCAGCCGGAACGTCAAAGGACGAGG ACTAGGTCTAGCAATGAAACGAGGACTGAACTGATAAAAATGGGCGGAAT GGATTGGAGGAGAGACAGAGAACTGCTTGTAGAAGCTCGTAGCTACGCTT AATTTCTCTATTGCAACAAAGCGCGCTGAGGACGAATTGAAAAAGAACTT ATTGTCTATTACCATTATGGTTTCGATTATTTATTTTTTATAATTTAATA TTAGCGAAATCAGTTGAGTGCGGGTGTGGCACAGATAGGGTTAGAGAATG CCGAGCTAAATCATCTAATCGAACTTAAGCGAGCATAACCGAGCAGACCT GGACGCTTAACGTATAAAACATAACATAAAACTACATCCTGCCAAAAATA TATAAAAAACCTAACGAACTACCTACATTTTGCGCCCAAAATCAAGCAGA GCGAAGGGCAGGTACTCGGCCCTTTGATCGGCTTGTTGTTACGCAAGTAT GAAATTGTTGTAAATTTAACAAAGGCAAATCATAGACTAAACCTCAATCA CTTAAGAGTTAACACCTACCTACCAAATTTGTACGAGCTCCTTTCTGTAA CGTCTGTATATTTGTACGTCCCGGAAGTTTTCATGACAATAGCTGATAGA ATCGATACTGTTCATCCTAGCTGAGGCCCCCTTAATCAGTCACATTTCCC TGCAAATTGTCGTGTCAAACATAGCGAATTTAGTAAGAAAGTGATGGGGG TCATCGGACTTAATTCGTTTTCGTAATCAAAATTTTATTGTTCAAACTAA TGATAAGCTGTATTTTGAAATAATAAGAGTAACAATAAATGCAACAAAAT CAGAAAGAAAGTAAGAAACCATCGAAACTATTTTTATAAAAATTTGTTTA CTTTTCTTTTCTTTCATTTGATTTTACTTTCATTAGTTTTGTTAGAGAAC CGAGGGCGAGAGCAGCGTCATTAAACACCTACCGATTTTGTAATTCACAA CCATTGTAAAATGAAGACTATATACATATACATACATAAATACTCTATAT ACAAATAATTTACAATTTGATACGGAATAAAACAAAATACAATGCCAGAA GAAGTTGGGTGCTAAT MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED coro-RC transcript status not done owner crosby Gadfly CG9446-RC FlyBase FBtr0086209 translate offset 196659 196657 coro:9 exon 202544 202330 coro:2 exon 196716 196462 coro:3 exon 195149 194883 coro:4 exon 194824 194411 coro:5 exon 194346 194053 coro:6 exon 193308 193123 coro:7 exon 193064 191776 CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAA CAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATT TTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCC TTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTG AATGCGCTGGCCCCAAGCTAGACGTAGAGAAGCTCAGGACTGATCGCTGA CCCAAGCCACTGCAGCATCAAGATGTCATTTCGCGTAGTGCGCAGCTCCA AGTTCCGCCACGTCTACGGACAGGCTCTCAAGCGGGAGCAGTGCTACGAC AACATACGGGTATCCAAGTCCAGCTGGGACTCCACATTCTGCGCGGTGAA TCCCAAGTTCCTGGCCATTATCGTAGAGTCGGCGGGCGGCGGAGCCTTCA TCGTCCTGCCACACAACAAAGTTGGTCGCATTGCGGCTGACCACCCTTTG GTGGGCGGTCACAAGGGTCCTGTGCTGGACATCGCCTGGTGCCCCCACAA CGACAACGTGATCGCCTCCGGCTCAGAGGACTGTGTGGTCAAAGTGTGGC AGATCCCCGATGGCGGGCTGTCGCGAACACTCACCGAACCCGTGGTCGAC CTGGTTTTCCACCAGCGTCGCGTGGGTCTGGTGTTGTGGCATCCCTCTGC GCTCAACGTGCTGCTTACCGCCGGCTCCGATAACCAGGTCGTGATTTGGA ACGTGGGCACTGGTGAAATCCTCGTGCACATCGACTCCCATCCGGACATC GTTTACAGCGCCTGCTTCAACTGGGATGGCTCTAAGTTGGTTACCACCTG CAAGGATAAAAAGATCCGCATCTACGATCCGCGCACTGCCGAGCTGGAGA GCGAAGCCATGTGTCATGAGGGCTCCAAGGCCACGAGGGCCATTTTCCTA CGTCACGGTCTGATCTTCACCACAGGCTTCAACCGTAGCTCGGAGCGTCA GTACTCCCTGCGCGCACCGGATGCCCTTAACGAACCCATTGTCATGGTGG AGCTGGACACGTCCAACGGCGTAATGTTCCCTCTTTACGACGCAGACACG AACATGATCTACTTGTGTGGAAAAGGTGACTCGGTCATTCGGTATTTCGA GGTAACGCCCGAACCTCCTTTTGTGCACTACATAAACACGTTTCAGACTA CAGAGCCGCAGCGTGGTATTGGTCTGATGCCCAAGCGAGGCTGTGATGTG ACCACCTGCGAGGTCGCCAAGTTCTATCGCATGAACAACAACGGTCTGTG TCAGGTCATCTCGATGACTGTGCCGCGCAAATCGGATCTTTTCCAGGAGG ATCTCTACCCCGATACGCTAGCGGAAGACGCTGCCATCACCGCGGAGGAG TGGATCGATGGCAAGGATGCGGATCCGATCACATTTTCGCTCAAAGGTGG CTACGTGTCCTCGTCGGTAAACAAATCGCTACCAGCGAAGAAGGCGGGCA ACATCCTGAACAAGCCTAGAGGCGACAGCGCTAGCTCCGGTGCAACGAGC AGCAGCGCGGGCGGCGGCAACTTTGCGTCCGGAAATAACAATGAGGCTAG CGAAGGTGGACCGCCTGCAGCGGTTTTATCGGAAAAGGACCTGCGCACCA TACAAGACGAGATCCGCAAACTTAAGGCGATCATCGTCAAGCAAGAGAAC CGCATCCGCGCTCTGGAGGCCAAGGAGGACGCCCGCAACAAGAATGGAAG CGATGCTGCGCCGGCTTCAGCGGGAGCAGCCACGTCTGACGGCAAAGCCA GTGAAAGTGCCAACGACCACGCGTCCACATCAGCCGGAACGTCAAAGGAC GAGGACTAGGTCTAGCAATGAAACGAGGACTGAACTGATAAAAATGGGCG GAATGGATTGGAGGAGAGACAGAGAACTGCTTGTAGAAGCTCGTAGCTAC GCTTAATTTCTCTATTGCAACAAAGCGCGCTGAGGACGAATTGAAAAAGA ACTTATTGTCTATTACCATTATGGTTTCGATTATTTATTTTTTATAATTT AATATTAGCGAAATCAGTTGAGTGCGGGTGTGGCACAGATAGGGTTAGAG AATGCCGAGCTAAATCATCTAATCGAACTTAAGCGAGCATAACCGAGCAG ACCTGGACGCTTAACGTATAAAACATAACATAAAACTACATCCTGCCAAA AATATATAAAAAACCTAACGAACTACCTACATTTTGCGCCCAAAATCAAG CAGAGCGAAGGGCAGGTACTCGGCCCTTTGATCGGCTTGTTGTTACGCAA GTATGAAATTGTTGTAAATTTAACAAAGGCAAATCATAGACTAAACCTCA ATCACTTAAGAGTTAACACCTACCTACCAAATTTGTACGAGCTCCTTTCT GTAACGTCTGTATATTTGTACGTCCCGGAAGTTTTCATGACAATAGCTGA TAGAATCGATACTGTTCATCCTAGCTGAGGCCCCCTTAATCAGTCACATT TCCCTGCAAATTGTCGTGTCAAACATAGCGAATTTAGTAAGAAAGTGATG GGGGTCATCGGACTTAATTCGTTTTCGTAATCAAAATTTTATTGTTCAAA CTAATGATAAGCTGTATTTTGAAATAATAAGAGTAACAATAAATGCAACA AAATCAGAAAGAAAGTAAGAAACCATCGAAACTATTTTTATAAAAATTTG TTTACTTTTCTTTTCTTTCATTTGATTTTACTTTCATTAGTTTTGTTAGA GAACCGAGGGCGAGAGCAGCGTCATTAAACACCTACCGATTTTGTAATTC ACAACCATTGTAAAATGAAGACTATATACATATACATACATAAATACTCT ATATACAAATAATTTACAATTTGATACGGAATAAAACAAAATACAATGCC AGAAGAAGTTGGGTGCTAAT MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED BS{}759 TE18876 transposable_element BS{}759 element BS cyto_range 42D1-42D1 gbunit AE003790 Gadfly TE18876 FlyBase FBti0018876 BS{}759 transcript BS{}759 exon 129369 129495 opus{}760 TE19040 transposable_element opus{}760 gbunit AE003790 cyto_range 42E1-42E1 element opus Gadfly TE19040 FlyBase FBti0019040 opus{}760 transcript opus{}760 exon 281994 289518 HB{}761 TE19973 transposable_element HB{}761 element HB gbunit AE003790 cyto_range 42E4-42E4 Gadfly TE19973 FlyBase FBti0019973 HB{}761 transcript HB{}761 exon 318903 320532 CG3267 CG3267 gene CG3267 cyto_range 42C7-42C7 sp_status Not in SwissProt real (computational) comment See Minigene report for CG3267: confusion about the 2 adjacent genes CG3267 and CG3265(Eb1), largely due to the way that the strain identifier "l(2)04524" has been used to describe both of them in the literature.::DATE:1969-12-31 19:00:00::TS:0 symbol CG3267 gbunit AE003790 GO GO:4492 FlyBase FBgn0042083 FlyBase FBan0003267 GO GO:0004658 propionyl-CoA carboxylase activity GO GO:0016421 CoA carboxylase activity GO GO:0004485 methylcrotonoyl-CoA carboxylase activity GO GO:0005759 mitochondrial matrix GO GO:0009087 methionine catabolism GO GO:0006567 threonine catabolism GO GO:0006574 valine catabolism GO GO:0007563 regulation of eclosion GO GO:0006551 leucine metabolism GO GO:0009062 fatty acid catabolism GO GO:0006550 isoleucine catabolism CG3267-RA transcript owner pavel protein_id AAM70824 sp_comment Perfect match to HYPO SP record with corresponding FBgn Gadfly CG3267-RA FlyBase FBtr0086126 translate offset 76260 76262 CG3267:1 exon 76160 76385 CG3267:2 exon 76445 76698 CG3267:3 exon 77018 77898 CG3267:4 exon 77954 78729 TATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACT CGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAA ATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAG CCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGG TAGACAAGCAGTCCGCCGAGTACAAGGAAAATGCCAGAGAGATGGCCAGT TTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGG ACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGG AGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGT GCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGG AATCGTCACCGGAGTGGGACGCGTTTGCGGAACTGAGTGTTTGGTGGTGG CCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAG AAGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCAT TTACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCT TTCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATG TCGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGC CGGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGA AGCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACT GGAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAA GACTTCTGGGGTCACCGACCACTATGCCTTAGACGACGAACACGCCTTGT ATCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCG TACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTAC TCCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACG GCATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATT GCGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGG TGAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAA TAGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCC CACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCA AAATATTACTGGCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTG CCAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCC AAGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCAT GTGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGC GCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATC ACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGC CCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGC CCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCC AACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGC CGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTAT GCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATT TCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATG TACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTA CGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAAC AAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACA AAACACACACATTTAAATGTATAATGTATAACAAAAC MIRLNWLFRSSSVLLRSQVRLLHVGDANVLHSEVDKQSAEYKENAREMAS LVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELS ALAGHELYGEEVVNSGGIVTGVGRVCGTECLVVANDATVKGGSYYPITVK KHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANM SAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAAT GEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNS YNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVI ARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGA HFIQLCAQRKIPLVFLQNITGFMVGRDAEANGIAKNGAKMVTAVACANVP KFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQI TEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPA NTRQILGLSLKAALNNAGQETKFGVFRM BcDNA:LD08743 CG3265 gene BcDNA:LD08743 cyto_range 42C7-42C7 comment See Minigene report for CG3267: confusion about the 2 adjacent genes CG3267 and CG3265(Eb1), largely due to the way that the strain identifier "l(2)04524" has been used to describe both of them in the literature.::DATE:1969-12-31 19:00:00::TS:0 gbunit AE003790 comment EST data support existence of multiple transcripts::DATE:2002-02-13 14:10:37::TS:1013627437000 sp_status Curator examined, accepted symbol Eb1 GO GO:7017 GO GO:8017 GO GO:5875 FlyBase FBgn0027066 FlyBase FBgn0010578 FlyBase FBan0003265 GO GO:0008017 microtubule binding GO GO:0005875 microtubule associated complex GO GO:0007017 microtubule-based process GO GO:0040001 mitotic spindle positioning and orientation BcDNA:LD08743-RB transcript owner campbell sp_comment Imperfect match to REAL SP with corresponding FBgn protein_id AAM70827 Gadfly CG3265-RB FlyBase FBtr0086127 translate offset 82439 82441 BcDNA:LD08743:1 exon 78967 79164 BcDNA:LD08743:2 exon 82407 82559 BcDNA:LD08743:3 exon 82618 82763 BcDNA:LD08743:4 exon 83955 84213 BcDNA:LD08743:5 exon 84477 84619 BcDNA:LD08743:6 exon 84674 84756 BcDNA:LD08743:7 exon 84820 84892 BcDNA:LD08743:8 exon 84960 85814 ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCG AGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGA CGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGG TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTT TACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGA CGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGA CTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAG TATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATAC ATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTA TTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAA TGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGT GATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGC TTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATA ATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTA AATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATG GAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACT CGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTA GATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTA AGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTT GTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTA TTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATG ATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTT ATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGT CTAAACACAA MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY BcDNA:LD08743-RC transcript protein_id AAM70825 owner campbell comment Although this alternative transcript is supported by multiple EST evidence, gene prediction information (Genscan) had to be used to deduce the 3' end of its exon 4.::DATE:2002-02-13 14:10:47::TS:1013627447000 sp_comment Blast failed problem true Gadfly CG3265-RC FlyBase FBtr0086128 translate offset 82439 82441 BcDNA:LD08743:1 exon 78967 79164 BcDNA:LD08743:2 exon 82407 82559 BcDNA:LD08743:3 exon 82618 82763 BcDNA:LD08743:10 exon 83002 83307 BcDNA:LD08743:4 exon 83955 84213 BcDNA:LD08743:5 exon 84477 84619 BcDNA:LD08743:6 exon 84674 84756 BcDNA:LD08743:7 exon 84820 84892 BcDNA:LD08743:8 exon 84960 85814 ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATC ATTCCAGTTGATAAACTGATTAAGGGACGCTTTCAAGACAACTTTGAGTT CCTTCAATGGTTTAAAAAATTCTTCGACGCCAATTACGACGGTCGCGAGT ACGACCCCGTGGCTCAGCGGGGCGGAGTCAAGCTGGGCAATGGCAACGGA CACGGCAGCAACGGAGGCAGTGGCGTGGGCAGCAGCAACAACGATCTCCA TCTGATGCACCGGCGACCATTGCAGGCTCCAGCTTCTGGCGGACGAATGC CAGCACGGGTCATCGCTTCAACTGGTACGGTTCTGTCGAAGCTACGAACT CCGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTT CGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCA GGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGA TCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAG CAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTG CAGTGAAGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCC CCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAA GAACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAA ATCAGGTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGA GACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGC CGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTAT ATGCGACTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGAC GAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCT GCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGT TTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACT AACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCG CCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGT CGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCC ACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCA TATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATAT CTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCA CAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTT GATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATC CTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTG ACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCA ACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAAC AAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCT ATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGC GAACGTCTAAACACAA MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPVDKLIKGR FQDNFEFLQWFKKFFDANYDGREYDPVAQRGGVKLGNGNGHGSNGGSGVG SSNNDLHLMHRRPLQAPASGGRMPARVIASTGTVLSKLRTPIIPIDKLVK GRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGT AASGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACAN STGTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDI EILCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY BcDNA:LD08743-RD transcript sp_comment Imperfect match to REAL SP with corresponding FBgn owner pavel protein_id AAM70828 Gadfly CG3265-RD FlyBase FBtr0086129 translate offset 82439 82441 BcDNA:LD08743:11 exon 79307 79359 BcDNA:LD08743:2 exon 82407 82559 BcDNA:LD08743:3 exon 82618 82763 BcDNA:LD08743:4 exon 83955 84213 BcDNA:LD08743:5 exon 84477 84619 BcDNA:LD08743:6 exon 84674 84756 BcDNA:LD08743:7 exon 84820 84892 BcDNA:LD08743:8 exon 84960 85814 AAAGAAGAAATCGCAAACCTAGAAGTAGCGTCAGCAGAAAAGAAAGTTCA TCGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTC TACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGC TTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCT GCACAGGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCA GTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACAT ACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATA AGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTC GAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAG GGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGAT CGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGC AGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGC AGTGAAGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCC CAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAG AACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAA TCAGGTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAG ACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCC GATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATA TGCGACTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACG AGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTG CATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTT TATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTA ACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGC CACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTC GTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCA CGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCAT ATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATC TAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCAC AGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTG ATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCC TATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGA CTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAA CGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACA AAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTA TATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCG AACGTCTAAACACAA MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY BcDNA:LD08743-RA transcript sp_comment Imperfect match to REAL SP with corresponding FBgn protein_id AAM70826 owner pavel Gadfly CG3265-RA FlyBase FBtr0086130 translate offset 82439 82441 BcDNA:LD08743:12 exon 81859 82006 BcDNA:LD08743:2 exon 82407 82559 BcDNA:LD08743:3 exon 82618 82763 BcDNA:LD08743:4 exon 83955 84213 BcDNA:LD08743:5 exon 84477 84619 BcDNA:LD08743:6 exon 84674 84756 BcDNA:LD08743:7 exon 84820 84892 BcDNA:LD08743:8 exon 84960 85814 CCTGCCAGTTGGTCACAGAGCGTAAAACGAAGTAAAAGAAAAACGAAAGT AATTTGTACAGTTCGATTTCGTTTTGCAAATTGAGTTTTATCAAGAAAGG TTAGTTTATCGGAAATCCAGCCAGAAGTACGTCGGATATACAGAGGTGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCG AGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGA CGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGG TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTT TACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGA CGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGA CTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAG TATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATAC ATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTA TTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAA TGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGT GATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGC TTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATA ATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTA AATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATG GAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACT CGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTA GATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTA AGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTT GTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTA TTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATG ATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTT ATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGT CTAAACACAA MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY BcDNA:LD08743-RE transcript owner campbell Gadfly CG3265-RE FlyBase FBtr0086131 translate offset 82439 82441 BcDNA:LD08743:1 exon 78967 79164 BcDNA:LD08743:2 exon 82407 82559 BcDNA:LD08743:3 exon 82618 82763 BcDNA:LD08743:4 exon 83955 84213 BcDNA:LD08743:9 exon 84480 84619 BcDNA:LD08743:6 exon 84674 84756 BcDNA:LD08743:7 exon 84820 84892 BcDNA:LD08743:8 exon 84960 85814 ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCATATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGAGC AGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGACGT GAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGGTGA TGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTAC TTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGACGC CGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTG AGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTAT TAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATA TTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTT AGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGA AGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGAT TAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTA ACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATT TTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAAT TGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAA AGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGT AACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGAT TAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGC ACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTC GTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTT TGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATT GTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATG TGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTA AACACAA MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPISKVLPRTNNAAPASRINACANSTG TVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEIL CQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY CG3271 CG3271 gene CG3271 cyto_range 42C3-42C3 symbol CG3271 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0033088 FlyBase FBan0003271 CG3271-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAM70808 owner campbell Gadfly CG3271-RA FlyBase FBtr0086118 translate offset 3457 3459 CG3271:1 exon 3384 3592 CG3271:2 exon 3649 3965 CG3271:3 exon 4036 4840 AATCAATAGTGCAATGTTTACAAAATATTTCGGGTGGATGTCGGTGAGAA GGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATA GTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGA CCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACT GCTCGGCAGATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAG CAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCA GTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGC CGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATG CAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCT GCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCT ATATGCTGACCCACATATTCGCAGTGACGAGTCTCAACGGCTGGATCTGG TCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTA CGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGC GGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCA TTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTT CAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGG CAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTAC TTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCT TGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTC TGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGAGTGCGTA GAAATATTACTTTATTCTAATATTGCTACATGTGTTTGCATTTTAGCTTC ATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGG CTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGC ACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAAC AGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCC TTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGA CATAATAGAGACTTTATTACAACATTTAGAA MSSRSLSAIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSADGLEI QEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGK WPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFA VTSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSL FLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWC HFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIP LASLYYECVEILLYSNIATCVCILAS CG3271-RB transcript owner pavel comment Only one EST supports this alternative transcript::DATE:2002-03-11 11:41:08::TS:1015864868000 sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70807 Gadfly CG3271-RB FlyBase FBtr0086119 translate offset 3457 3459 CG3271:1 exon 3384 3592 CG3271:2 exon 3649 3965 CG3271:4 exon 4036 4502 CG3271:5 exon 4556 4840 AATCAATAGTGCAATGTTTACAAAATATTTCGGGTGGATGTCGGTGAGAA GGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATA GTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGA CCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACT GCTCGGCAGATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAG CAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCA GTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGC CGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATG CAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCT GCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCT ATATGCTGACCCACATATTCGCAGTGACGAGTCTCAACGGCTGGATCTGG TCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTA CGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGC GGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCA TTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTT CAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGG CAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTAC TTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCT TGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTC TGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGACTTCATG ATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTA TTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACG CAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGA GCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTT GACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACAT AATAGAGACTTTATTACAACATTTAGAA MSSRSLSAIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSADGLEI QEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGK WPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFA VTSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSL FLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWC HFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIP LASLYYDFMIEDCRTLRKEKAAAGGYSFYN CG9430 CG9430 gene CG9430 cyto_range 42C6-42C6 gbunit AE003790 comment Gene prediction data only::DATE:2002-02-13 11:51:41::TS:1013619101000 sp_status Not in SwissProt real (computational) symbol CG9430 FlyBase FBgn0033097 FlyBase FBan0009430 GO GO:0006812 cation transport GO GO:0006811 ion transport GO GO:0006810 transport CG9430-RA transcript owner pavel sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAM70820 Gadfly CG9430-RA FlyBase FBtr0086138 translate offset 49308 49306 CG9430:1 exon 49308 48391 ATGGTAGACCAACACTTAATCGTGGCCAAGATCGTGGCCATAGTGGTGCT CTTCCTCGTTACCCTGATCTTCTGCTTTATTCCCTATCTTCTGGATCGCT TCTACAAGTGGACCCAGAGGCCCGAGAACAATGCTCGCGAATTCAAAGTG GTGCTGTGTCTGCTTAATTTCGGTGGAGGGGTTCTCATAGCCACCACCTT CATCCACATGCTGCCGGAGGTGGTCGAGGTGGTGAACGCTCTCCAGGACT GCCGCATGCTGGCCCCCACTCCCTTCGGCCTGCCGGAGGTTCTGCTCTGC ACTGGCTTCTATCTGATGTACTGCATTGAGGAAACCATGCACTTTGTGGT TCGTCGGCGGCAGCAAAGGAAGCTACGGGAGGTGGTCACGATCAAGGATG CGGGCGAGGAGCTGCGGACAGAGATTGTGGTCCAGCCAGAAGAAAGCCCC AAGGAGCCCAACTGGCTGCGTGGCCTCGGAATAATCGTGGCCCTCTCCCT GCACGAACTCTTCGGCGGCATGGCCATTGGCCTGGAGATGAGTGTGAGCA CGGTGTGGTTCATGACCGGAGCCATTTCCGTCCACAAGCTTGTTCTGGCC TTCTGCATCGGCATGGAGATCATGATGGCCCATACCCGCTGGCTGCTGGC CGTGGTTTACCTCCTCGTCTTCTCGATCGTAACTCCGATTGGCGTGGGCA TCGGAATTGCAGTTAGCGAATCTGCCGCGGCTAATCAGCCCAGCACGGTA TCAGGAATCCTCCAGGGGCTGGCCTGTGGCACCCTCATCTACGTGGTCTT CTTTGAAATTGTGGCCAAAAACCATGCCGGCATACGCATTTTACTCTCGT CGATGGTGGGATTCGTCCTGATGTTTGGCCTCCAGATAGCAAGTAAGCAT ACTAAAAAGCCCAAATGA MVDQHLIVAKIVAIVVLFLVTLIFCFIPYLLDRFYKWTQRPENNAREFKV VLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLC TGFYLMYCIEETMHFVVRRRQQRKLREVVTIKDAGEELRTEIVVQPEESP KEPNWLRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLA FCIGMEIMMAHTRWLLAVVYLLVFSIVTPIGVGIGIAVSESAAANQPSTV SGILQGLACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIASKH TKKPK Epac CG3427 gene Epac cyto_range 42C8-42C10 gbunit AE003790 symbol CG3427 sp_status Not in SwissProt real (computational) FlyBase FBgn0033102 FlyBase FBan0003427 GO GO:0017132 cyclic nucleotide dependent guanyl-nucleotide exchange factor activity Epac-RA transcript comment unusual splice provisional (internal view only)::DATE:2004-01-12 11:13:35::TS:1073924015000 protein_id AAM70831 owner mhuang validation_flag unusual splice sp_comment Perfect match to HYPO SP record with corresponding FBgn comment Unconventional splice site postulated::DATE:2002-07-31 12:07:33::TS:1028131653000 comment DGC evidence (GH01501) strongly suggests that the 11th intron of this transcript uses AT-AC splice donor and acceptor.::DATE:2002-07-31 12:07:40::TS:1028131660000 Gadfly CG3427-RA FlyBase FBtr0086132 translate offset 99119 99117 Epac:1 exon 118781 118237 Epac:2 exon 103561 103415 Epac:3 exon 99134 99083 Epac:4 exon 98798 98701 Epac:5 exon 98440 98354 Epac:6 exon 98285 98144 Epac:7 exon 98089 97897 Epac:8 exon 97335 97190 Epac:9 exon 96970 96826 Epac:10 exon 95886 95710 Epac:11 exon 95472 95311 Epac:12 exon 94511 94150 Epac:13 exon 94079 93826 Epac:14 exon 93766 93596 Epac:15 exon 93375 93242 Epac:16 exon 92958 92609 Epac:17 exon 92549 91687 CTCTCCAGCGGCGCACAACTCGATCGCTGGCCCAGAGGTTCAGTTCGGTT TGGTTCGGTTCGGTTTGAATCTCTGCCTCTGTTTACGCCTCTATATCACC TCCATTGGAGCCCATCCGTATCTGTTTCCCTGTGCGATTCGAGTATCTTC AAGTTAACCATGCTGCAGAAAGTGCGTGGGCTGTGCTGAAAGATTCGCGC GCGGGCGTTCGCCAAGTCGAAATAAACCAGTTAAATCTGAGTGCTTGGCT ATTGGCCAAAAATGTAATCGACACGACAACGGAGTGTAAACAGGCCCATT TCGAGTGCAGTTTTGAAATTGTTTATGCAATGCAATTGTGTTAAAAATTT ATTACCTTCCAAGCGAAACAAAGCAAGGCAGCCGAAAACACATTTCTCGC CTCTCTGGTGATTCAACAGCTGCAGTGTGTGTAAACAAATAAAGCCAGAA ACAAAGCCGCAATATGGAGGAATTTAATTCAAGTTGATTTCATTCATTAA ATCTGCTGGAAGGTTGCAGCGGAAAGAGCAGCGAATTCTCCTCTGAGCGC AGTTACTCTGTGCAACCTGGGCGTGGGTGCCACATTCGGGGAGTCCGTAC TGCATGACTTGCCGCGGGACAGCACCGTAGTGACGAAGACCACCTGCGAG CTGCTGCGGGTGGAGCAGCAGGACTTTCGACTCATCTGGGAGAAAAACAA GGAGTTAATGAATGACATATTCACCAACTGCAAGTTGAAGAACGGTTTTG GACCGAGCGTACAAGCGACAGCCGCAGCCACATCGCCCACGAAACGACCC CTCAGCCCCGACCACCCAAACCCAGCGCTGCCCATCACCGAGACACCGAG TCCTGCTATGAACCGCATGGGCTGGGCCCTACGCACACTACTCGTCGCCG ACAACTCGAGCTGTCTGAAGGATCGCAAGGTCTCCGGCAAGCTAATCCGT AAGTGCGCCCCCGGCACCGAGCTCGTCGACTGGCTGGTCAACCTCTCGCC CATCGTCCACACCCGAGCCCAGGCGGCTGGCATGTGGCAAGCGCTCCTCG AGGAAGGAGTACTCGCACACGTCAACAAAGAGCAGCCCTTCAAGGACAAG TGCTTCCTCTACCGCTTTCGCATCGACGAGGAGGGCGGCACGGCGGCAGC GGGCGTGCCCCAGGCGGAGGACCTCGGAGCGGCCAACGAGCACATCCGCG AGGCGCTCAGCGCACTCTTCCAGCGCGGACCGGACGCCACACTGCGTATG ATATTGCGCAAACCTTCTCACGAACGGACATCGGAGGAGCTGGAGCTGGT CTTCGAGGAACTGGTCCACATTGCCGCACTCTCCCACTTGTCGACCAGCA TAAAGCGGGAACTGTCGTCGATTTTCGTGTTCGAGGCTCATGCCCAGGCG GGAACAATATTATTCAATCAAGGCGACGAAGGACGCTCCTGGTACATCTT ACTCAAGGGATCGGTAGACGTTGTGATACACGGCAAGGGAACTGTTGCCA CTCTGAAGACTGGGGATGATTTCGGGAAACTGGCCTTGATAAACGACGCA CCCAGAGCTGCTACCATCGTACTGAAGGAGAACAATTGCCACTTGCTGCG CGTGGACAAGGAACACTTCAACCGGATACTGCGCGATGTGGAGGCCAATA CTCTGAGATTGCAGGAGCACGGCAAGGATGTTTTAGTGCTCGAGCGCGTG GCTAAGCAACGTGGACAGCATTCGGCATTTAAATATACGGTGATGTCGGG AACTCCGGCCAAGATGCTGGAGCACCTGCTGGAGACGCGACTGGGCCAGT CCGTGGGTGGAATGGATCCGTTCTTGGACGACTTCCTGCTCACACACATC GTTTTCATGCCCGTCGTTCAGCTGGTTGATGAATTGGCCAATTACTTCCA CTGCGATGCCCATGAGGACGCCCAAACGCCCGAGGATCGGGAGTATATAA TCAACTTTAAGAAGCGCGTGATCCAGTTCATGCAAAAGTGGGTCATGGCC GTCCGCCACGCGGCCTTCGAGGAGCCCAGCGTGTGCGACTTTATCGAGGA CCTCGCCGCCGAGGTGGAGGCCGATCCCGACCTGAACGAGGAGACCAGCA TAGTGCACAACGTGCTCACCCAGATGGCGCGCTACCAGGAGGACCGCAAC CAGAACGCCGGCCAGAAGTGGAAGCTCCCGCCCAACGGCCAGCCCATCTG CCTTTTCAGTGGCAATGCGACGCCTTCAAAGACGGTCATCCGACCAGATG ATGATATCATCTTCCGCGTTTACTGCGCCGACCACACCTACTGTACCCTG CGATTCCCCATGCACACCACGGCGGAGCTCATCAAAGCGTGTGCCGCCGA CAAGCTGCAGCTAAATCGGGGTCCCGAAGATCTCGTCCTCGTCGAGGTCA AGTCAAACGGGGAGCGGTCCGTGTTCAAGGACAACGATGTCAGCATACCC ACGGGTCTGTCGCTCAACGGCCGCCTTTTCGTCTCCGTCAAGGACCACCT GGATGCCTTGACCCAACTGCAGGAGCAGGAGTGCCCCACCGAGGGTGTGG ACATCGACCTGGAGATACTGAGCACCAAGGAGCTGGCCTACCACATCACC CTGTTCGAGTGGGACCTCTTCTGGGCCGTCCATGAATACGAATTGCTCTA CCACACCTTCGGGCGGCATCACTTTGGCAAGATCACTGCCAACTTGGATG TGTTCCTGCGCCGATTCAACGAGGTGCAGTACTGGATTGTCACCGAACTG GTGTCCACTCCCAGTCTGAGCAAACGCGTCGGTCTGGTCCGGAAGTTCAT CAAGCTGGCCGCGTACTGCAAGGAGTACCAGAACCTAAACGCCTTCTTCG CTGTGGTAATGGGTCTGTCCAACATGGCGGTGTCCAGGCTGCAACAGACC TGGGAAAAGATTCCGTCGAAGTTCAGGAAGATCTTCCAGGAGTTCGAGGC CCTGATCGACCCCAGTCGCAACCACAGGGCGTACCGAGTGTTCGTGGGCA AGCTGCAGCCGCCGTTGATTCCCTTCATGCCGCTCCTGCTCAAGGACATG ACCTTCGCCCATGAGGGCAACAAGACCAGCCTGGACGGCCTGGTGAACTT CGAGAAGATGCACATGATGGCCCAGACGATGCGCACCATCCGCTTTTGTC GCTCCAGGAGTCTGGGACTAGAGCCGCCGTCCCCGAAGAGCGAGGGCGAG GTGAGGTCGTACATCAGCAGCTTCCGCGTCATCGACAACCAGCGGGTACT CACCGCCATGTCCCAGAAGGTGGAGCCCACCAGGAAGCTCTAAGCCCTTG TGGAGCTGTCATCCAATTAGCCTGTAGCGCGTATTAAGTGTCTAACCCTA GTGTGTGTTAATCAACCGCAATTAGCTGCACAGTTATGAGCTTAGCCGGG TTGTTGTTGCTTTCCGAAAGCCAATTGGGCCACGGCCACCACAGCCCGGA CCAACTTTCGTCCGCATCCGCATCCGCATTAGCCTAAGCTACAGTGTACT ATATCTACGACCCGACTAGGAACTATCTCAATCTTCTAATGAACTGAAAC CCAAACGCATTTTAATGCAAACGAGAAACTTTTTGCTTTAGTACAAAACG ATGGAAAAGATGGAAAACAATTTGAAATTCGGCAATTCCCCGCGGAAACC GAAACGAATAAAAACTAAACTTGGACGTGTGTGATACTAAACATTTATAG GAGGCAACATCAAAACAAACACAACTATACAGCATAATTTCCCACAAACC ATTACTCTATAAATCCCGCGCGAGCTGGTAGAATAATTTGTAAAGTTGTA CAACGTTTTCGAGAGCATGGAATCTATATTTTTATAAACCCTAAACTAAA ACCAACTATTAAACAGTCTAGTTACAGCTAGTTATTAACAAGTAAGCTAC GTAGCGGATAAGTTACTTTATTTATAGTTTTCAATCTTATTTTCATTTGG TATTCCGTCACCCCATCTCCTTTTACGGCAACTTGGAAATAAAATACGAA ACCATTTATTAATATTTATTTACACACA MNDIFTNCKLKNGFGPSVQATAAATSPTKRPLSPDHPNPALPITETPSPA MNRMGWALRTLLVADNSSCLKDRKVSGKLIRKCAPGTELVDWLVNLSPIV HTRAQAAGMWQALLEEGVLAHVNKEQPFKDKCFLYRFRIDEEGGTAAAGV PQAEDLGAANEHIREALSALFQRGPDATLRMILRKPSHERTSEELELVFE ELVHIAALSHLSTSIKRELSSIFVFEAHAQAGTILFNQGDEGRSWYILLK GSVDVVIHGKGTVATLKTGDDFGKLALINDAPRAATIVLKENNCHLLRVD KEHFNRILRDVEANTLRLQEHGKDVLVLERVAKQRGQHSAFKYTVMSGTP AKMLEHLLETRLGQSVGGMDPFLDDFLLTHIVFMPVVQLVDELANYFHCD AHEDAQTPEDREYIINFKKRVIQFMQKWVMAVRHAAFEEPSVCDFIEDLA AEVEADPDLNEETSIVHNVLTQMARYQEDRNQNAGQKWKLPPNGQPICLF SGNATPSKTVIRPDDDIIFRVYCADHTYCTLRFPMHTTAELIKACAADKL QLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDA LTQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHT FGRHHFGKITANLDVFLRRFNEVQYWIVTELVSTPSLSKRVGLVRKFIKL AAYCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALI DPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEK MHMMAQTMRTIRFCRSRSLGLEPPSPKSEGEVRSYISSFRVIDNQRVLTA MSQKVEPTRKL CG9422 CG9422 gene CG9422 cyto_range 42C3-42C4 comment DGC clone RE35072 appears problematic: incomplete CDS::DATE:2003-05-28 17:02:14::TS:1054155734000 symbol CG9422 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0063682 FlyBase FBgn0033092 FlyBase FBan0009422 CG9422-RA transcript status not done sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) owner pavel protein_id AAM70813 Gadfly CG9422-RA FlyBase FBtr0086120 translate offset 21493 21495 CG9422:1 exon 5602 5687 CG9422:2 exon 21473 21600 CG9422:3 exon 21657 21838 CG9422:4 exon 21895 22011 CG9422:5 exon 22068 22369 TTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGC ACATATTGGTGAAACTATTTAATAATATTTATTAAGATTTTACGGAAGGC CTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAG CAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATT TTTTGTGGATGCATGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAG TTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAG CGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCA AGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGTGTG GAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCAC ACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGG ATACTATAGATGGCTTACAAAAGCCAAATACGTCCACTGATTTTTGGGAT GGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCA GCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAAC GGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACCTGCC GCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGCGGAC CATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAAAGCC CAATTTATCACAAAA MMHYRKAENVEKELSKSDLPFEDCMPKSQKDFLWMHVKGGTKVSNVIEFA QEALNKGEHRCVVWSGSGGGVVKTISCAEVLKRSHPLYQVTRMAYTSVEE HWKPQMEGLEEIIVTRQIPTLHILMSLDELPDTIDGLQKPNTSTDFWDGG GAQQQPHPRSQPRHQQQPHKPGAGRGGRPNKRTRPGRNKPGQQPEKPAAE ENLPAS CG9422-RC transcript owner pavel protein_id AAM70814 sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) Gadfly CG9422-RC FlyBase FBtr0086121 translate offset 21493 21495 CG9422:6 exon 5630 5687 CG9422:2 exon 21473 21600 CG9422:3 exon 21657 21838 CG9422:4 exon 21895 22011 CG9422:5 exon 22068 22369 GCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATAT TTATTAAGATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCG AGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGC ATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCATGTAAAAGGCGGTAC CAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCG AGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACC ATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGAC GCGCATGGCCTACACCAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAG GCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTC ATGAGTCTGGACGAGCTGCCGGATACTATAGATGGCTTACAAAAGCCAAA TACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATC CACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGG CGTGGGGGTCGGCCGAACAAACGGACCAGACCCGGACGCAATAAACCAGG CCAACAACCCGAAAAACCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGA GTCAAGGTTGAGATAAGCGGACCATGCGAAGATTTTCTTATTTGCCCTTT GTAAGGATGTACAAATAAAGCCCAATTTATCACAAAA MMHYRKAENVEKELSKSDLPFEDCMPKSQKDFLWMHVKGGTKVSNVIEFA QEALNKGEHRCVVWSGSGGGVVKTISCAEVLKRSHPLYQVTRMAYTSVEE HWKPQMEGLEEIIVTRQIPTLHILMSLDELPDTIDGLQKPNTSTDFWDGG GAQQQPHPRSQPRHQQQPHKPGAGRGGRPNKRTRPGRNKPGQQPEKPAAE ENLPAS ZIP1 CG9428 gene ZIP1 cyto_range 42C6-42C6 gbunit AE003790 symbol ZIP1 sp_status Curator examined, accepted FlyBase FBgn0033096 FlyBase FBan0009428 GO GO:0046873 metal ion transporter activity ZIP1-RA transcript owner pavel protein_id AAM70819 sp_comment Imperfect match to REAL SP with corresponding FBgn Gadfly CG9428-RA FlyBase FBtr0086139 translate offset 47451 47449 ZIP1:1 exon 47582 46434 ZIP1:2 exon 46357 46120 AGTGAATCCGCGTATCAATCAGCGATCAGATTTCAATCGGCTCCCGCTGA TATATGACTGGAAATATAAACCATTAGCCTGGTTGTGAGTTCCAGCCAGC ACAGTCGAAGCTATCAACTCGGGAGGTGAAGATGAGCGCTACCGCAACTA TGTCACAAGAGCAAACGCAAGACGTGGATCACCATGCGCTGCTGGTGGCC AAAATAGTTTCCATGGTGGTGCTCGTGGTGATCACCGTGCTTTGCGGCAG CCTTCCCTACGTCCTGAACAGGTGCTTCCATTGGACGAAGGCGAGTCCGG AGGAAACCCGCTCGTCATTGGTGGTGCGGTGCCTACTCTTTTTCGGCGGC GGTGTGCTCATCTGCACCACCTTCCTGCACATGCTGCCCGAGGTGATCGA GGTGGTGGAAGCGCTCCAGGAATGCGGCTCGCTTGTCAAGACGCCCTTCG CTCTGGCGGAGATGCTGCTGTGCACGGGCTTTTTCCTGATGTACGCGTTG GACGAGCTGATGACCAGCCTCGTGCGGCACCACCAGGGAAAGCTTAGTCG GAAAGAGTCGGTGGCCAGTCTGGCTTTCGAAAGAGGACGCAGCATTCGTC ACAGTGTTCTCCTCAATCCACAGGCGAAGGAAGAAGTGGAAGTTAAGGAT ACGGAACCGCAGCCACACAAGGATCACCACGGCCACTCGCACATGCCCGT GCCAGCGGACGATGGATCCTCTGCCAGGGGGCTGGGCATTATCCTCGCCC TTTCGCTCCACGAACTGTTCGAGGGCATGGCCATTGGTCTGGAGGGCACT GTGAGCACTGTGTGGTTCATGTTTGGAGCGGTCTCCGCCCACAAGTTGGT GTTGGCCTTCTGCGTGGGTATGGAGCTTCTGGTCGCCCGCACACGCAGTT CGCTGGCCATCTTGTACCTGGTGACATTCTCCATTGTTACACCCATCGGT ATCGGTGTTGGCCTCGGCATCAGCCAGCAGGTGGCAGCGGGTCAGCCCAG TCTGCCATCCGGAGTCCTCCAGGGCATCGCCTGTGGAACCTTGCTGTACG TAGTCTTCTTTGAGATCCTCATTGAGAGCCATGCCGGATGGAGGGCCCTT GTGGCCGCCGTTGCGGGATTCGCTCTAATGTTTGGCCTTCAAATTCTTTC TGACGAAGCGGAGGGTGATGACAGCCTAACCTGTTCCTAGCCAGTGTGAC GCCACTTCAGTATTATCAAGTTATAGAGGAAGCAACAAAATAGTATACAA AACGATTCCCTGGGGATCTGTAAAAGTTATTATATAAAATACGAATAGAA TTTCAAAAGAGGTTTCTCAGAAATCTTATCCAACGCAAATAATTAAAAAT GTAATAACCATATGGATTAAAAGAGACAATATTTTAC MSATATMSQEQTQDVDHHALLVAKIVSMVVLVVITVLCGSLPYVLNRCFH WTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPEVIEVVEALQECGS LVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFE RGRSIRHSVLLNPQAKEEVEVKDTEPQPHKDHHGHSHMPVPADDGSSARG LGIILALSLHELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELL VARTRSSLAILYLVTFSIVTPIGIGVGLGISQQVAAGQPSLPSGVLQGIA CGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILSDEAEGDDSLT CS CG3409 CG3409 gene CG3409 cyto_range 42C5-42C6 gbunit AE003790 symbol CG3409 sp_status Not in SwissProt real (computational) FlyBase FBgn0033095 FlyBase FBan0003409 GO GO:0008028 monocarboxylic acid transporter activity CG3409-RA transcript sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70818 owner simonp Gadfly CG3409-RA FlyBase FBtr0086140 translate offset 34168 34166 CG3409:1 exon 45640 44879 CG3409:2 exon 35973 35010 CG3409:3 exon 34361 32162 CG3409:4 exon 31697 31588 CG3409:5 exon 31146 30965 CG3409:6 exon 30897 30657 CG3409:7 exon 30592 29895 TGCGAACGGACGTGTGGTGCTAGTGTGGTGGACTATACGACTTTTCTATA TTTTTAAGGGCCGCGGCAGTAGAGATAGCCTATTTTTCTCGCGACAGAGC GTGTTAAGTAATCAATTGAAATCCAGCGATTGGGTGAATCGAAAGTTCCT CCCCGATTCCCGACTCCTGCGTGCATTTGAAGCACTTACAGCCGCGATTT CCGCACTCGGGTGCACTGTGCTTTTGTTTATACGACCTCCGGTCGCCCCA CATTTTCTGTTGAACTTGTGCCGCCGAGCGGTGTTGTCACTGTCCCACCT CCCCCGCAGAAAATCGAAACTCCCGTACAGTGGGCGTGACCCAGGGCGAA GCCGATAGATAATAACTTTCCACGGGAACTTGAGTGTGCGTAATATCGCC TATAAAGAGTGTTTGGCAACTTGGCGTTCTGGAGTGTCACCCGCAACCAA TTCTAATCGTACATACATATATAAGCCAGCTGATTTGGACGTGTGCTACA GCGATTTCATCCCACTGTGCAAGACGGGCGGCAGAAATTCATAAAACAAC AGCTAACAAATTCGACGAAGAGGCATACGCAAAAGAAACGAAAGAGAGAG CGAGCTTATTGTATTTTTGTAATACTCGTCTGCCCAACAACTACATTTAC TGTAATGTGCAGCCTATAATGTAAGATAATGCAATGACACAGGACCAACT CCCAGTAATGGTTGCAATTTAGCCCAGAAGCCACGAATTCACCAACTCAG CAGAGTGATCAGCGTTTGCACTGAAGGCTGCTAATTGAGGACGAGGATCA TAAATCATTATCTGGCGCCAGCGAGGAGGCGAGCACAGCGACAGCAGCGA TTGAGTTGCACCACCAGAGACGAATTAATCATACGCCGCGTTGGTCGTCC CTCCGTCGATACTAAGATATACATATATACAATGCCTGCGAATCCGCCTC CGCACCACGCGCCGCGCACTTGACACGGGGAGCGGCAGAGTAGCCGGAGA AGCCAGTGAGGCCCAGTCTTGTGTTCGATTTGTGTTTGTTATTTCTTGTT CGAGCTAGCCGGGCACGCTAGTTGGCATCGTTGGCATCGAATCGAAAAGT GTTTGATTTCCGCGAAAACAAAGTACCGCATGTGGCTGCCAGGGCAAAAT CTGCTAGCCGGCAGCACAAACTGCAACAACTGCATCTGCAACTGCAACAG CAACAACAGCAACATCACCAGCAACTGCCGCCAGTTGCCGTCAATTATCG CTCAATATATTCTCCGTTGGCCTGTGATAAACCCCCTAACGTTCTTAATG AACGACCTTCGGTCCAAGTCATTCTATCGTGCAGGCAAACCAACATCTGC AGCATCCGCGTCGGGCGCGACCACCAACGCCAAGTCGTTCGACAAGGGCC AGAACAACAATCCCCGTACTTACAACAACAGCGGCAAGTCGAACAAGGTG TTCCTGCATTACATACCCCGCGATCCGCGCCTAAGAATTTTCAACAAAAC CGCCACCCTGAATAAACACTCGAATCGCACCCTGAGCGAGCTAAACATAA CTGAAGATCTGTGCAATTATGGTGAATTGATTGGCGGTGGTGCCGAAACA GTGAAACTAGTGCCAGTGAAATCTTAAGAATATATCCGCAAAATCCGCAG ATCACCGAATCAATTTATTCGTTAACAAAAGTTGGCTGTTGGCGTGCGGA GAGAGCATTGCCTGGACTACGATCGGCTACGCACTGCAGTTGACCAACAG AGAGAGGGAATATTTACCTACCGCCTACTTAAGAAAATTTATGCTGAAAT CTAATGCAAATTGTGTTCACTTCCAATAATCGCTTGGACAAGAAAGTGCA AATTTTACAAACCTTTTTATAGACGTAGCTGAACCCTTTACACAACAACA CGATCACTGGGACTCCGACATGGCCAAGCTAGCGACGGATCCAAACGCCT CCAACAACAACAGCTGCGAGGCGGTTAACAACAACCACAATGGCCAGAAC CAGAGCCAAAACGGAGGCGCCTCCAATTACCAGGCCCTGCCTCTTACGCC TGCTCCGGCCAACACGCCACTCCACAAGGCCATCAAGCACGACCTCTTCC CGGAGGTCACCTTCTGCAACCTCTCCGTAGAGGAGCTCGCAGATGGGGCT GGACACAGCCGTGTGGTAAGGAGCAGTGTCATCGAACTGGAGGACGGCAC CATGACGTGCCTGATGAACGGAAATGGGCAGGTGAAGCGTCGCAAACGCC TGATCTCGAACGAGTCCGGCGACTCGATCGACTCCAGTTCCACGGAGAAG AAAACGCCCAAGATGCCCGACGGTGGATATGGGTGGGTGGTGGTGTTCGC CTCTCTGGTCGTGTCCCTTATAGCCGACGGACTGAGCTTCTCATTTGGCC TAATAAACGTGGAACTGCTGGAATACTTCGGAGAGTCCACTTCGAAGACC GCCTGGATATCCTCGCTATTCTTCTCCGTGCCCCTGTTGATGGGACCCAT CTGGTCCAATCTGGTGGACAAGTACGGCTGCCGAAAGATGACCATCCTCG GCGGAGTGGTCTCTGCCTTTGGGTTTGCTCTGTCTTCGTTTTGCAACTCG ATCGAGATGCTCATGGTGACCTTTGGTATCATTTCGGGACTGGGCCTAGG CATCGGGTATGTGACCGCGGTGGTGTCCATTGCATTCTGGTTTGACAAGA AGCGCACCTTTGCGACCGGCATCGGAGCATCGGGCACCGGCATCGGGACC TTTGTCTACGCCCGCCTTACTTCCTATCTAATCGAATCGTACGGCTGGCG CGGAGCCACTCTAATCCTTGGCGGCACCATGCTCAACGCATGCGTTTGCG GCGCCCTCATGCGCGATCCCGACTGGCTGATCGAGGAAAACCGTCTAGAG AGTCGATCCCAAAGCGTCACCACCTTCTCGAACTCCAGTGTCTGCCTGGA GGAAATAAAAAAGCTGCTGGACACCGGCATCACAAAGGAGGCTGTGCTAG ACTCGTTGGTGACCAAGAACAACACGGAGGCCAACCAGCAGATTGACGAT CCGTTGGACTCCGCTCTCAAGCGCTACCGCAGCGAGATCTTCCTGCCCAC CTTCCTGAGCACTCAGGAGCTTGACAGCATCTGCGAGGTTAAGAGCCTGA GCCGACGCTCCCTACGCCACAAGGAGGGTGAGGAGGCGCCGTCACGAGAG AACCTGCTGTCCATGTCCTCAGGAGCAGGTGCCTATCCCCCATCGACGGC CGTTATAGGCTCGCCAGATGATACCCTAATGGGCGGAATAGCTCACGAGG CGGCAGAGGAAGCAAAGAAGGCCTATCTGGCCTCCATCGAGACGCTGTCT CCATCGGAAAAGCGCTCCACTGGTAGGACTCCCAATGGCTCGCTCCGCTC CTCGGACGAAGGCTACCTTACGCAGAAGCACGCCAGCTCCCGGTACTCGC TTAACGAAAACATCTTCATGGCCAAGCATACAACACCATCAATCTCCAAC CTAAAGGTGAATGGCCTGCGACACAATTCGGTGGACATCTTGAGCGAGGA CATGCACTGCTACTACTCGAAGGACGAGACCTTCGCATTGCTGGAGCCGA GCAGGCGCATCAGGCCCACCGTCATCGCCATTCCGGAACAGGAGCAGTCG GTGAACAGCGAGCTGGCCACCCGTCGCGCACGCCTGGACAGCATCACGGG AATCCGCCGGCTGTCGCGCTCCAAGAAGCCCAGCCACCACCGATCGAACC TCCGCCGCAACATCTCGATCCGGAACTCCAACTTCCTTAAGGATATGCGC ATTCACCGCAACTCGATCCACTACCGCGGGGCCATGCTGAACACGCACCG CTACCGGCTGCGCGCCTCCTCCTGTCCCAACATCTACCGCAACTCGATGA CCACCATCGCCAAAGAGGAGGAAGATACCTGGTATGACAACTTTGTGGAC ACCATGAAGTCCATCTTTGACTTTTCACTCTTTCTGGACATGAAGTTCGC CCTCTTCAATCTCTCTACATTGTTTTTGTTCATTTGGTTCATTATCCCCT ATCTGTACCTTCCCGATTACATGAAGCAATACAAGTACGACGTGAGCCAG AGTGCCGAGTTGATTTCGGATGTCGGCATTGCCCAAACGGTGGGCATGAT AGGACTTGGCTATCTGGGGGATCTGTCCTGGATGAACATCAATATATGCT ACTCGCTGTGCATGCTGGTGTGCGGAGCGTCTGTGTTCTTCATGCCCCTG CTGATTACCAACTACATGGGCCTGATGGTCATGTGCGTTATTTTCGGATT TACGTTCGCCAGCTCCTTCTCGTTTACGCCCAGCATTCTGGTCAGTATTG TGGATCTGGACGATTTCACGTGTGCCTACGGTCTGGTGCTGCTGGTTCAG GGAGTTGGAATGATCGCAGGACCCCCTATTGCAGGCGTCATATACGAGTA TACGGGCAGATGGGATGACACCTTCTATTATGCTGGAATATTTATCGCAC TCTCTGGTGTCTGTTCGTATCTGATCGAGTTCTGTGAAAAGAAAGCACCT AAGGAGAGTGATAGTGATGTCTTAGAGACTAAAAAAGCTCAACTTTTACA CTAGGTTACTTACATTGCACTGTTGAACGCCGCAAGTAGAAGGCAACTGG AGGTACTACAAATCCGAACTGTAGCATAATAATGGACTAGCATTAAATGT TAACGAGTTTCTTATGTCAAATGGTGTTGCAGCCATAAAATCAGAGCAGA ATTGTAACTGAAACTAAGCCTATTCCTAAGCTCTAGCCTGTAAGACTATA CTTGACTTGACTAATCGTAGCTAAGTATCAATATACACCTAACATATACT TACCGCACTAGGGCAATTACTAACCGCATCTTTGTCTAGACAAACTGTTC AATTTCAATCAATATCAATGCAGTGCATCACTGCCAGGTGCAAACGGGTC CCTCAATTGTCTTCTTTACAAAATTTAGAAAAATAGTTTTAATTGCCTTA CATTTCGTACGAATATTAATTAAAGGGAATACAATAAACAACAATCTATG TAACGTATGCAATAACAAGTGACCATTTTCAATCAATCTAAAACTCACAA TAAAATCTTTGGAGCATTTGTTTGTACATCAAACGTCACGGATCCGAATA GTTTCCA MAKLATDPNASNNNSCEAVNNNHNGQNQSQNGGASNYQALPLTPAPANTP LHKAIKHDLFPEVTFCNLSVEELADGAGHSRVVRSSVIELEDGTMTCLMN GNGQVKRRKRLISNESGDSIDSSSTEKKTPKMPDGGYGWVVVFASLVVSL IADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVD KYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFGIISGLGLGIGYVTA VVSIAFWFDKKRTFATGIGASGTGIGTFVYARLTSYLIESYGWRGATLIL GGTMLNACVCGALMRDPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLL DTGITKEAVLDSLVTKNNTEANQQIDDPLDSALKRYRSEIFLPTFLSTQE LDSICEVKSLSRRSLRHKEGEEAPSRENLLSMSSGAGAYPPSTAVIGSPD DTLMGGIAHEAAEEAKKAYLASIETLSPSEKRSTGRTPNGSLRSSDEGYL TQKHASSRYSLNENIFMAKHTTPSISNLKVNGLRHNSVDILSEDMHCYYS KDETFALLEPSRRIRPTVIAIPEQEQSVNSELATRRARLDSITGIRRLSR SKKPSHHRSNLRRNISIRNSNFLKDMRIHRNSIHYRGAMLNTHRYRLRAS SCPNIYRNSMTTIAKEEEDTWYDNFVDTMKSIFDFSLFLDMKFALFNLST LFLFIWFIIPYLYLPDYMKQYKYDVSQSAELISDVGIAQTVGMIGLGYLG DLSWMNINICYSLCMLVCGASVFFMPLLITNYMGLMVMCVIFGFTFASSF SFTPSILVSIVDLDDFTCAYGLVLLVQGVGMIAGPPIAGVIYEYTGRWDD TFYYAGIFIALSGVCSYLIEFCEKKAPKESDSDVLETKKAQLLH CG15909 CG15909 gene CG15909 cyto_range 42C3-42C3 sp_status Not in SwissProt real (computational) gbunit AE003790 symbol CG15909 FlyBase FBan0015909 FlyBase FBgn0033090 CG15909-RA transcript protein_id AAM70811 sp_comment Perfect match to HYPO SP record with corresponding FBgn owner pavel Gadfly CG15909-RA FlyBase FBtr0086122 translate offset 13014 13016 CG15909:1 exon 13014 13030 CG15909:2 exon 13091 14132 ATGCGATTTGTTCTATGGTATGTCTTCGTGCTCAGCTCCATGAATGTATT TCAAAAGTCCAACGCCAAGTCAAGACTCACAGCTAATTTGACAGACGACC CATTGCATGCCTATAATGAGGTCGTGCAGAATTTGATTAAGAACTGGGAG TCGCCAGTTGTCTATCTGAAAAAACGAGGTTTCCTGCCCAGAAACTACGA GGATGCGTCAAGAATCAAGCACAGCCTGGATGCCCTGATGCAACGAATAA AAAGGGCTAAACGGGATCACACAAAGGAGGTCACTTTCAATGTAAGACCC AAAGAAATGGCAAAAGCTTACCCAAGGAATCAACGTGGCTTTCAGCTATC AACGGGCACAATGCTCTCTAGTTTGGAGCAGTTGAAAGTCATCGAAGGCC AGGCAACGAAGGCCAAGACCACGGCCAAGTCAAGTGAGCAGGAGCAAGAG CTGCTGGCAATGAAGCGGCGATTGGAAGAGTTGCAGCAGGTAGCAGGTAC CGGTCAGGATCAGCCAGGATACCGTAGGCAGATTAAAGTAAATCCAATAG ACAAGGATCCAGGGAAGTCAGCACAAAGTTATGATGAAATATTGCAGCGA ATGATTGAAAAGACGAGCCCACACTACTCACAGCAATCCAATTCGCATTT AGAAACCCATCCAAATCAACTAGCGCCAGCTCCTCCAGGAGCAACCCAAA AACTTGATAATGTGCAGATGGCTCCCAAAGAAGACAAGCCGCTGACTTTA GAACATATCGAGTTGCATGCGTATACAGCGCAAAGTGCTCCCCGAAATTT ATTGCATAAATCCGTAGTTGATCTGCCCATACTTAGAGCAGCGGAGACCC AGAGGAGCAAGACCGCAACGGAGGCATCTAACGTGGAATCGAAGTTGCGC GCGCCCACCTATCTGAATTGGGACATGAAAAACGGTCGACTGGATCATTA CTCAAGCGTGGACAAGGAGGCCTATTTGAACCAGTTGGTGAGAGTGTTCG GGCGCAATTTGGATTTCAAGGAACCCACTCAAAAAGGAAAAGAGCCGACA GTTTCTTAG MRFVLWYVFVLSSMNVFQKSNAKSRLTANLTDDPLHAYNEVVQNLIKNWE SPVVYLKKRGFLPRNYEDASRIKHSLDALMQRIKRAKRDHTKEVTFNVRP KEMAKAYPRNQRGFQLSTGTMLSSLEQLKVIEGQATKAKTTAKSSEQEQE LLAMKRRLEELQQVAGTGQDQPGYRRQIKVNPIDKDPGKSAQSYDEILQR MIEKTSPHYSQQSNSHLETHPNQLAPAPPGATQKLDNVQMAPKEDKPLTL EHIELHAYTAQSAPRNLLHKSVVDLPILRAAETQRSKTATEASNVESKLR APTYLNWDMKNGRLDHYSSVDKEAYLNQLVRVFGRNLDFKEPTQKGKEPT VS CG3403 CG3403 gene CG3403 cyto_range 42C5-42C5 gbunit AE003790 sp_status Not in SwissProt real (computational) symbol CG3403 FlyBase FBgn0033094 FlyBase FBan0003403 GO GO:0007049 cell cycle GO GO:0007067 mitosis GO GO:0000910 cytokinesis CG3403-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn owner pavel protein_id AAM70816 Gadfly CG3403-RA FlyBase FBtr0086141 translate offset 26174 26172 CG3403:1 exon 26400 26115 CG3403:2 exon 26040 25667 CG3403:3 exon 25606 24889 ATTTTCTCGCACAAAGCAAAGTGTTTTGGAGGATAAACGCCAATTAATTG TCAAGCGATGTGCCAGCTCCTGTAGAATACACTCAGCATACTACGGTGCA GGGATCCCACATCCGGAGACTCCCGCGGGGCAGGGACCAGGCTAGCATTC AGTTTCTGCCAGTGATTTTCTCATCAAGGCGTAGGCACAGACGTTGTGGA TCATCGCGTCTTCGAGCGGGTGAAACATGAAGATGGCTGACGGCTCGACC ATATTGCGTAGGAACCGGCCAGGCACAAAATCCAAGGACTTCTGTCGCTG GCCCGACGAGCCCCTGGAGGAGATGGACAGCACGCTGGCGGTGCAGCAGT ACATACAGCAGCTGATTAAGCGCGACCCGAGCAACGTGGAACTCATACTG ACCATGCCCGAAGCCCAGGATGAGGGCGTGTGGAAGTACGAGCACCTGCG CCAGTTCTGCATGGAGCTGAACGGCCTGGCAGTGCGGCTGCAGAAGGAGT GCTCGCCGTCGACGTGCACCCAGATGACAGCCACTGACCAGTGGATATTC CTGTGCGCCGCGCACAAGACGCCCAAGGAATGTCCGGCCATTGACTACAC ACGCCACACGCTGGACGGTGCCGCCTGTCTGCTAAACAGCAACAAGTACT TCCCTAGCAGGGTGTCCATCAAGGAGTCGTCGGTAACCAAGCTGGGCTCC GTATGTCGGCGGGTGTATCGCATCTTCTCGCACGCCTACTTTCACCATCG TCGCATTTTCGACGAATTCGAGGCCGAGACGTATCTGTGCCACCGTTTCA CGCATTTCGTCACAAAATATAATCTGATGTCGAAGGAGAATCTGATCGTG CCCATCAACGTGGGTGAAAACGCGGCCCCTGGCGAAAGCGAGGCTTAGGA GCCCGCCCAGATTAGTCAGACTCGCATGAAACACTCATTCAACATACATC TATTTATATTTACCAATAGCTTGCAAGTTGGGTTGGCTCACCCTGACAGG GAAACGATTCCACGCGGACCCGACTCTAATGCAGATCTTGTATGTAGTTT AGATGTCAGATACACATAGAGCTACATAACGATAACTAAGTAACAAGGGC AGACCCCCTCAAACCCGCTCGCCCCATCTGATCCTAAGTCAGCAATTATT TCGCAAGTTATATTACGATTATGTTTAACTCCTTATTTTAATAAATTATA TGTAGGCACACGACCTTCTCGTGGCTGATTCCACGTCAAATCCCCGTAAA CTAAACTAAATTCCCTTGACTACTGGCAGCCAAAACACCAACACAGCTGT ACGTGACTAAAACGTGAACTTTACTATACAAAATTACTATATACACAACA GAAATTGCAATAAAAGAAGTACATACAT MKMADGSTILRRNRPGTKSKDFCRWPDEPLEEMDSTLAVQQYIQQLIKRD PSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQM TATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKE SSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNL MSKENLIVPINVGENAAPGESEA Cyp6a2 CG9438 gene Cyp6a2 cyto_range 42C8-42C9 symbol Cyp6a2 gbunit AE003790 sp_status Perfect match to SwissProt real (computational) GO GO:15034 GO GO:5792 GO GO:16352 FlyBase FBgn0010312 FlyBase FBgn0000473 FlyBase FBan0009438 GO GO:0005489 electron transporter activity GO GO:0005792 microsome GO GO:0016020 membrane GO GO:0017085 response to insecticide Cyp6a2-RA transcript protein_id AAM70832 owner cdsmith sp_comment Perfect match to REAL SP with corresponding FBgn Gadfly CG9438-RA FlyBase FBtr0086133 translate offset 111207 111205 Cyp6a2:1 exon 111230 110106 Cyp6a2:2 exon 110036 109490 CGAAAAGGGAGCAGCTACGCAAAATGTTTGTTCTAATATACCTGTTGATC GCGATCTCCTCGCTTTTGGCCTACTTGTACCACCGCAACTTCAACTACTG GAATCGCCGCGGCGTGCCACACGATGCTCCTCACCCACTGTATGGCAACA TGGTCGGGTTCCGGAAGAACCGGGTGATGCACGACTTCTTCTACGACTAC TACAACAAGTACCGGAAGAGCGGCTTTCCCTTCGTGGGCTTTTACTTTCT GCACAAGCCGGCCGCCTTCATCGTGGACACCCAGCTGGCCAAGAACATCC TGATCAAGGATTTCTCGAACTTTGCCGATCGTGGCCAGTTTCACAACGGG CGCGACGACCCGCTCACGCAGCACCTGTTCAACCTGGACGGAAAGAAGTG GAAGGACATGCGCCAGAGGCTGACGCCGACTTTCACCTCGGGCAAGATGA AGTTCATGTTCCCGACGGTGATCAAGGTGTCTGAGGAGTTCGTCAAGGTG ATCACGGAGCAGGTGCCCGCCGCCCAGAACGGCGCTGTGCTCGAGATCAA GGAGCTGATGGCCAGGTTCACCACCGATGTGATTGGCACCTGTGCCTTCG GCATTGAGTGTAACACGCTGCGCACCCCTGTCAGTGATTTCCGCACCATG GGACAGAAGGTGTTCACCGATATGCGCCACGGGAAACTGCTGACCATGTT CGTGTTCAGCTTTCCCAAGCTGGCCAGCAGGTTGAGAATGCGCATGATGC CCGAGGACGTCCACCAGTTCTTCATGCGCCTGGTCAACGACACGATTGCC CTCAGGGAGCGGGAGAACTTCAAGAGGAACGACTTCATGAACCTGCTGAT TGAACTGAAGCAGAAGGGGCGCGTCACCCTGGACAACGGAGAGGTGATCG AGGGCATGGACATCGGCGAACTGGCCGCCCAGGTGTTCGTCTTTTATGTG GCCGGATTTGAGACCTCCTCCTCGACAATGAGTTACTGCCTGTATGAGTT GGCTCAGAATCAGGACATTCAGGACAGGCTGCGCAACGAGATCCAAACGG TGCTGGAGGAACAGGAGGGGCAGCTAACGTACGAATCCATCAAAGCCATG ACCTACTTGAACCAGGTCATCTCAGAAACCCTGAGGCTCTACACACTGGT GCCCCACCTCGAACGGAAGGCCCTCAACGACTACGTGGTGCCGGGCCATG AAAAGCTTGTGATTGAGAAGGGCACACAGGTCATAATCCCCGCTTGCGCC TACCACCGCGACGAGGATCTTTATCCGAATCCGGAGACCTTTGATCCGGA GCGCTTCTCGCCGGAGAAAGTGGCCGCCCGGGAGTCCGTGGAGTGGCTGC CCTTCGGCGACGGGCCGCGGAACTGCATCGGGATGCGGTTTGGACAAATG CAGGCTCGCATCGGTTTGGCTCAGATCATCAGCCGGTTCAGGGTATCCGT CTGCGATACGACAGAGATCCCACTGAAGTATAGTCCCATGTCCATAGTTT TGGGCACCGTTGGGGGCATCTACTTGCGAGTGGAACGCATCTAACCTCCA TATTCGTTGCTCCCATGTATATAGCTTAGGATCCAAAGCTAAAGTGATGT ACATTTTAGACTGTTCAATTATTAAATAACCTTAACCTAAACAGCCATAT TAACTTATTGGCCTGTGATAAA MFVLIYLLIAISSLLAYLYHRNFNYWNRRGVPHDAPHPLYGNMVGFRKNR VMHDFFYDYYNKYRKSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNF ADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVI KVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLR TPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASRLRMRMMPEDVHQFF MRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGEL AAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ LTYESIKAMTYLNQVISETLRLYTLVPHLERKALNDYVVPGHEKLVIEKG TQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRN CIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIY LRVERI CG3270 CG3270 gene CG3270 cyto_range 42C4-42C5 sp_status Not in SwissProt real (computational) gbunit AE003790 comment This gene model is supported by only one EST/DGC evidence (GH02863) which indicates that the resulting translation product is possibly shorter than the predicted one.::DATE:2002-02-13 11:31:01::TS:1013617861000 symbol CG3270 FlyBase FBgn0033093 FlyBase FBan0003270 CG3270-RA transcript owner pavel sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAM70815 Gadfly CG3270-RA FlyBase FBtr0086123 translate offset 23215 23217 CG3270:1 exon 23215 23427 CG3270:2 exon 23737 24962 ATGCTGGGCCTGCGACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCG CTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAG TCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTG AAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGA GCGCGATGCTGGTTACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAG TGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGA TACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTG CTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACA TCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAG CTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGA GGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATC CGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCG AATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGG CCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGA AGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCG CGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGT AGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTC AGGGTAAGAATTGTCCTGGGCTAGCCACACCTCTGACCGTTGATCCCGAT GGCACCTACTTCAGGCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCG CAGTCCAAACGAAGACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACC ACGGGTACTTTGAAACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCT GCTTTTGAGTCTGTGAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCA CAACACATTTGACGCAAACGGCGTCATCGGCAGGCATCCTCACTACAGCA ATCTCTTCATTGCCGCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCC GCCGTGGGTCGAGCCATTTCCGAACTAATCTTGGACGGCAAGTTTACCAC ACTGGATCTGTCGCGCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTA TGCACGAAGTGAATATCGTTTGACAAATTTATCACAGGAGGATCGTACTT GCCCTTGGTGTGTTTATGTATGTACTTCTTTTATTGCAATTTCTGTTGTG TATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTC MLGLRRVLRLGALRQLRSLSGKPQGDVLPGSCGVLIIGGGGMGASSAFWL KSRALQLGRKLNVLVVERDAGYTSASTVLSVGGVRQQFSLAENIEMSLFG YNFVVNGREHLGDVDLCYQPNGYLILASEKGAHILAKNSKLQNELGARNE LLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGA NFANGSVVGFEWNDSGGLSGAVVDAGDVLQRTVKFDTCVLAAGAYSGQVA RLAGIGDKEAKEASLSVALPVEPRKRYVYVVSTQGKNCPGLATPLTVDPD GTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVP AFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTP AVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV Rab2 CG3269 gene Rab2 comment Comment: Reference sequence based on BDGP genomic sequence. sp_status Perfect match to SwissProt real (computational) cyto_range 42C5-42C5 gbunit AE003790 description D.melanogaster FlyBase-curated sequence: Rab2.v004 symbol Rab2 comment Comment: This record is derived from the following: AC007593 AC007593.5 10-MAR-2001 D84313 D84313.1 06-AUG-1997 AB035352 AB035352.1 04-DEC-1999 AI062422 AI062422.1 19-APR-2001 AW940056 AW940056.1 19-APR-2001 comment Comment: Reference sequence of Rab2 == FBgn0014009 GO GO:3931 GO GO:5525 GO GO:3928 FlyBase FBgn0014009 FlyBase CG3269 FlyBase FBan0003269 GO GO:0003931 Rho small monomeric GTPase activity Rab2-RA transcript sp_comment Perfect match to REAL SP with corresponding FBgn evidence experimental protein_id AAM70817 owner pavel Gadfly CG3269-RA FlyBase FBtr0086124 translate offset 26659 26661 Rab2:1 exon 26497 26704 evidence experimental Rab2:2 exon 27191 27350 evidence experimental Rab2:3 exon 27824 28160 evidence experimental Rab2:4 exon 28221 29711 evidence experimental comment A region of 35bp in cDNA GB:D84313 does not align with the reference sequence. This region of discontinuity is 260 bases upstream of the 3' end of the transcript. GTATTTCCGCCAGCCCTGGCCACAAAGTGGCCACACTGTCGCTAGCCAGT CATCATAAATACGAACAGATTGGAAAACGTACAAGAATTGCGTATTATCT GTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCG TCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGG AGACACAGGCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGC GATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGC ATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGC TGGGCAGGAGGCTTTCAGATCTATCACACGCTCTTATTACCGCGGAGCTG CTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCAC CTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGT CATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGA AGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATG GAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATAC GGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACA ATGAGGCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCG TCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTG CTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCC GCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGG AACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAG CTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAA GATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTT TACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAA CCACATTTGTGTACGTGAATGTCGTGCGTGATTTCTAAATTTTATAAAGT TTATTGAAACATTTTTAAATGTTTTATGCATGTATTTTGTGTATATTGAA GTTAGTTTGCTAGTTACTTCGTGTAAAATCGATAGTTATACATTGGGATT TTGACAAAATGATGTGTAATATATGAACAAAAATCAAACTGTGTGAATTT TCATTGTGATTCGATTTCAGTGAGGTCCAGCTTCGCAACGCTGCGCCACG CCCCCTTTTGCAATGGGTATCTGCTCCGCTTCTCTATACACACATACATA ATTAAATATATTAATATGTTTACGTTTCCTTCTCAACGCATTTGCTTTGT CTATTTTGTTGTGCAATCCGCTTAGTCTTTATACATACACTAGAAAAAAA GTACTTTAACAAAATATACAAAACGTGAGGGCCGAAATGGGGTTATATAA TTTACACAATCAACATGCATTAACCAGTGGTAACACGAAATGCTGCGATT CAATGATCAATTTAGTATTTTACGAAGTTTATATATTTAATTAACGGCGA TTGCTAAGACAAAACGAAAGATACAACTGTAAACGTAAATCAAATTATTT ATAATATTTGTATTTGCCCAACACAATGCGGAATAATAAATATACATACT TACTATTAATATAATTATATAAATTAAATCGGTACTTACCTTGGGTTCAT TAGCGTTTAATCAAGTGATAGTTAACGACTAATTAGTTTTTTGGTGTCTA GATGAGAAGTAAAACACTAAGGCAAATTTAATGAGGCATTTAAAGTTGTA AACAACTCAACTTTTAAATGAAAAGAGGTCAGACAAATAATTACGCATTA GTGTAGTTTTAACCCTTTTTATTTAGTAAGAGGCTTTCGGTAGATAATTG TTGAATTAATGTCTTGTAAATATTATTAAATGGTGAATCCTTTTTTGTTT ATGTACATATTTCCTAAAGTGTTCGGAATTAACAATTTCCACTTTCTATG TCGGCTATAGGGATATAGTGTCGCATTTACTTAATTTTTTTAAATGTGCT TACATGTTAAAACATTTTTTTACTACTGAAATATACTATTTAGAAA MSYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI DGKQIKLQIWDTAGQEAFRSITRSYYRGAAGALLVYDITRRETFNHLTTW LEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSA RTAANVEEAFINTAKEIYEKIQEGVFDINNEANGIKIGQQHSPTNPSLPG AGGAAGAANSGCC CG30446 CG30446 gene CG30446 cyto_range 42C3-42C4 gbunit AE003790 sp_status Not in SwissProt real (computational) comment Flag Cambridge: gene split (internal view only)::DATE:2002-02-12 17:32:52::TS:1013553172000 encoded_symbol CG3686 symbol CG30446 FlyBase FBgn0033091 FlyBase FBan0030446 FlyBase FBgn0050446 GO GO:0004058 aromatic-L-amino-acid decarboxylase activity CG30446-RA transcript owner pavel sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70812 Gadfly CG30446-RA FlyBase FBtr0086142 translate offset 18277 18275 CG30446:1 exon 19737 19661 CG30446:2 exon 18350 18148 CG30446:3 exon 18085 17778 CG30446:4 exon 17617 17183 CG30446:5 exon 17128 16914 CG30446:6 exon 16561 16435 CG30446:7 exon 15554 15046 CG30446:8 exon 14936 14747 CCAGTCGGGGCCAACGGTTCGTGGTCTCGAGTTCGAAACAAAATTCCCAT TCGCCCATCGGAATTTGCTCAGCACAACTCACCGTGGGAGTAAAAGAAAA CGGAAAAATAGGAAAACACTCAGAAAGGCGATTTGGAAAACCTACCGAAA ATGGACAGCACCGAATTTCGAAAACGTGGCATGGAAATGGTGGAGTACAT CTGCAACTATCTGGAAACGCTGAACGAGCGACGGGTCACGCCCAGCGTGG AGCCGGGATATTTGAGACACCTGTTGCCACCTGAGGCACCGCAGGAGCCG GAGGACTGGGACCAGATCATGAGGGACGTGGAGGACAAGATCATGCCCGG CGTGACGCATTGGCAGCATCCTCGCTTCCACGCCTATTTTCCGGCGGGCA ACTCGTTCCCCTCTATCCTGGGCGACATGTTGGGCGACGGGATCGGGTGC ATCGGCTTCTCCTGGGCCGCCAGTCCCGCGTGCACCGAGCTGGAGACCAT AGTGCTCGACTGGCTTGGCAAGGCCATCGGTCTGCCGGACCACTTTCTGG CCCTCAAGGAGGGCAGCACCGGAGGGGGAGTCATCCAGACTTCCGCATCG GAGTGCGTACTGGTCACGATGCTTGCTGCCAGGGCACAGGCGCTCAAGAG GCTCAAGGCCCAGCACCCGTTTGTGGAGGAGGGTCACCTGCTGTCCAAGC TTATGGCCTACTGCTCCAAGGAGGCGCACAGCTGCGTGGAGAAAGCGGCG ATGATCTGTTTCGTGAAGCTGCGCATTCTGGAGCCCGACGACGACGCCAG TCTGCGCGGCCAGACGATCTACGAGGCAATGGAGGAGGACGAACTGCAGG GTCTGGTGCCCTTCTTCGTCTCCACCACTCTGGGTACCACGGGCTCGTGT GCGTTCGACAATCTGCCAGAGATCGGCAAGCAGTTGCAGCGATTCCCGGG CGTTTGGCTGCACGTGGATGCCGCCTACGCGGGCAACAGCTTCATCTGCC CCGAGCTGAAGCCGCTCCTGAAGGGCATCGAGTACGCCGACTCGTTCAAC ACCAATCCCAACAAATGGCTGCTGACGAACTTCGATTGCTCGACGCTGTG GGTGCGGGACCGCATCCGGCTGACTTCAGCCCTGGTGGTGGATCCGCTGT ACCTGAAGCACGGCTACTCGGATGCGGCCATCGACTATCGTCATTGGGGA GTTCCACTCAGTCGGCGTTTTCGTTCGCTGAAGCTGTGGTTCGTGCTGCG ATCCTATGGGATTTCCGGGCTGCAGCATTATATACGTCACCATATCAAGC TGGCCAAGCGGTTCGAAGAGCTCGTGCTCAAAGATAAGCGCTTCGAGATC TGTAACCAAGTCAAGCTGGGCCTGGTCTGCTTTCGGCTGAAGGGTTCCGA CAAGCTGAATGAGAAGCTGCTGAGCATAATCAACGAGTCCGGCAAGCTGC ACATGGTTCCGGCCAGCGTGGGCGATCGCTACATCATCAGGTTCTGCGCC GTGGCCCAAAACGCGACCGCTGAGGACATTGACTACGCCTGGGACATCAT CGTGGACTTTGCCAACGAGTTGCTGGAGAAGGAGCAGCACGATGAGCTGT CCGAGATCATGAACCGCAAGAAGCAGGACACGCTGGCCCAGAAGCGCTCA TTCTTCGTGCGCATGGTCAGCGATCCGAAGATCTACAACCCGGCGATCAA CAAGGCCGGCACTCCCAAGCTCTCAATGGAGCTGCCCTCGCCCGTTGTGA GCCGCGGCAGTGCCCCCATTATCCGGACCCAGAGTTCGGTGGACCACAAC TCGTGGATATCCTGGCCGCTGGCATTCCTCTTCAACAGCAACAACGAGGA AAAGGGCAGTAACGTCTCGTTGCGTTTCCGACACCTGGACACCAACGTAC GACCATCGTCGTCGCGACGAAACTCCGGAGCCGGCTCGTCACCCTCTCCG GAAAACGAGTTGGACTACGTGAACGTCCAGCAGCAGCAGATGGAACAGCG ATCGCCACGACGATCGCCCATGGCGGTGCGCAAGGCATCGTCCACGCGGG ACAACCTCAACTAA MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLPPEAPQEP EDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGC IGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQTSAS ECVLVTMLAARAQALKRLKAQHPFVEEGHLLSKLMAYCSKEAHSCVEKAA MICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSC AFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKGIEYADSFN TNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWG VPLSRRFRSLKLWFVLRSYGISGLQHYIRHHIKLAKRFEELVLKDKRFEI CNQVKLGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCA VAQNATAEDIDYAWDIIVDFANELLEKEQHDELSEIMNRKKQDTLAQKRS FFVRMVSDPKIYNPAINKAGTPKLSMELPSPVVSRGSAPIIRTQSSVDHN SWISWPLAFLFNSNNEEKGSNVSLRFRHLDTNVRPSSSRRNSGAGSSPSP ENELDYVNVQQQQMEQRSPRRSPMAVRKASSTRDNLN CG9436 CG9436 gene CG9436 cyto_range 42C7-42C8 symbol CG9436 gbunit AE003790 sp_status Not in SwissProt real (computational) GO GO:4032 FlyBase FBan0009436 FlyBase FBgn0033101 GO GO:0004032 aldehyde reductase activity CG9436-RA transcript status not done sp_comment Perfect match to HYPO SP record with corresponding FBgn owner pavel protein_id AAM70830 Gadfly CG9436-RA FlyBase FBtr0086134 translate offset 88546 88544 CG9436:1 exon 88661 87376 GCTTTCGACGAGCTGGAACAGATAGAGATTTGATCGCGAGAAAGGCGTAG TAGCACTGGTTTAGACTTAGAAGCGTCCAATTTGCACAGCGTTAATTATC AGCGCCAGCGACAAGATGACCAATCTGGCTCCCACCATCCGGCTGAACAA CGGGCGCGAGATGCCAACTCTGGGCCTTGGCACCTGGAAGTCGTTCGAGT CGGACGCCTACCACTCAACGCGCCACGCCCTCGACGTGGGCTACCGGCAC CTGGACACCGCCTTCGTCTACGAGAACGAGGCTGAGGTGGGCCAGGCGAT CTCCGAGAAGATCGCCGAGGGAGTGGTCACACGCGAGGAGGTTTTCGTGA CCACCAAGCTAGGCGGAATCCACCACGACCCTGCATTGGTGGAGCGCGCC TGCCGCCTGAGCCTTAGCAACCTGGGTTTGGAATACGTAGACCTCTACCT GATGCACATGCCGGTGGGCCAGAAGTTCCACAATGACAGCAACGTGCACG GAACCCTGGAGCTGACGGACGTGGACTATCTGGACACCTGGCGCGAGATG GAGAAGCTGGTGGATCTGGGCCTGACGCGCAGCATCGGCCTGTCCAACTT CAACGCCGCGCAGACGGAGCGAGTGCTAGCCAACTGCCGCATCCGGCCGG TAGTGAACCAGGTGGAGTGCCACCCAGGCTTTCAGCAGCGCCAGCTCCGG GAGCATGCCAAGCGCCACGGACTGGTCATCTGCGCCTACTGCCCCCTGGC ACGTCCCCAGCCCGCTCGGCAGTGGCCGCCCTTCCTCTACGACGAGCATG CCCAGAATCTGGCCAAGAAGTACGGCCGCACCACGGCACAGATCTGCCTG CGTTATCTGGTCCAGCTAGGCGTGGTGCCACTGCCCAAGTCGTCGAACAA GGCCCGCATCGAGGAGAACTTCCGCGTCTTCGACTTCGAGCTGAGTCCAG ACGACGTCGCCGGCATGGAGCAGTATCACACCGGGCAGCGCACGGTACCC TTTTCGGGAATGTCGGGCCATAAGTACTACCCGTTCAACGACGAGTTCTA GACGGGCTCAGGGGTGTCCCAGAAATATCGGTTTCGCCGTTATTGGATTG GCTAGGAATGCAAACAAAACGACTGTGGCATTCCAAGAGGGGTGTTTTGT TTTAGTTGTTAACTCAAAGTTAAAAAGGTTTCGAGTAAACCCGTGCATTA ATTCCCCTTAATATTTTACTGGAAGAGGTTCGTAAGACACCCCGCATATG TAGTATTTGTATTGTAAAATAAAGTATATTACGTAG MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAF VYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSL SNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVD LGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKR HGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQ LGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMS GHKYYPFNDEF CG3420 CG3420 gene CG3420 cyto_range 42C7-42C7 sp_status Not in SwissProt real (computational) gbunit AE003790 symbol CG3420 FlyBase FBgn0033100 FlyBase FBan0003420 FlyBase FBgn0047109 CG3420-RA transcript sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70829 owner simonp Gadfly CG3420-RA FlyBase FBtr0086135 translate offset 86742 86740 CG3420:1 exon 86795 86695 CG3420:2 exon 86632 86488 CG3420:3 exon 86411 86318 CG3420:4 exon 86256 86065 GACACTGCAATCATCAGCTTAAATAAAGAGAACAAAAATAAATTAGCGTT AGAATGTCAATGATACTAAGACGGAACCTGGGGGCATCCTGGTTGCTCAA GGCATGCTACAGTTCCAGCGCAAAACCGGTGGACTCGGCCAAAACAATTC CCAGTAACCTGCTCGAGGATAAGCAAACGGCCGTTCTGCAAAAGGAGAAC GGTACGATCTTCGACAAGCGCCCCTTCAAGATCCACCTGGACAAAGATAA AACATACAGCTGGTGCCTGTGCGGCAAGTCCAAGTCTCAGCCCCTCTGCG ATGGAATGCACAAGAACGAGTTCCTGAAGATCAAGCAGAGGCCCATTCGG TTCAAGGTGGAGAAGTCGGGAGACTACTGGCTCTGCAACTGCAAACAGAC CACCCACAGACCCTTCTGTGACGGCACCCACAAGCAGCCACACATCCAGA GCGCCGTCAAATAGATTTAGGATTGGTTGTAGGGCCCTGCCCGTGTGCGA AAAGAGAAATGCATTAATTTTGAATCAAGCAA MSMILRRNLGASWLLKACYSSSAKPVDSAKTIPSNLLEDKQTAVLQKENG TIFDKRPFKIHLDKDKTYSWCLCGKSKSQPLCDGMHKNEFLKIKQRPIRF KVEKSGDYWLCNCKQTTHRPFCDGTHKQPHIQSAVK phtf CG3268 gene phtf symbol phtf cyto_range 42C7-42C7 gbunit AE003790 sp_status Curator examined, accepted FlyBase FBgn0028579 FlyBase FBan0003268 FlyBase FBgn0028488 phtf-RA transcript protein_id AAM70823 owner pavel sp_comment Imperfect match to REAL SP with corresponding FBgn Gadfly CG3268-RA FlyBase FBtr0086125 translate offset 72519 72521 phtf:1 exon 71642 71924 phtf:2 exon 72480 72544 phtf:3 exon 72616 72755 phtf:4 exon 72812 73319 phtf:5 exon 73368 74314 phtf:6 exon 74374 74552 phtf:7 exon 74613 74969 phtf:8 exon 75028 75919 ATAATATCTAGCTGAGCAAGATGTACGGATTTGTGAGCACACACTTTAGT TTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGG ACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAAT TACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAAT CGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGA CAAAAATCGATCTGTGACGCGGTTTAAACCAAGGCTGCACGACACTTCGA GGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGT ACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTC GAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAA GCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAGGTTCCACGTTCC CTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATT CTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGAC CACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAA CCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGAC TATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGA TGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCC TCAGTGCCCTGCTTATTCCGTGCGCCCTAAGCTTGCTGATCAGTCTCATC CACTCACAAATTGTAGCCACTAACACCGCCTCGGGTGTCTCTGGCGGGAG TAGCAAGAACAAGCTGCGTCGCATATCTGCAAGCTACTTAAGCGACAAAG CAGCAACCAGGGAGAACCGGGTGCGACGTCGCAAGAAGATTGTGCGAGTT CGACAAGTGGAGGCTGACTTGTCCCAGGCCAGCAGTAACATATCACTTCC AAACAGAAGAACCGCAACCAGCACAATCGAAGTTCTTCCCAGACCGGTCA CGCCTTTGCCTTCACCAACAGTTACCTGTGCCACGGTGCCAGACCCCACC ACGCCGACTACGCCTTCGCCATCTGTTATCAGGCGGAGCACCAACGAGGA GACCTATTTGACAACGACTGCAATCAGCCCACTAACGCAACCGCTGGCAG CCATAGACGCATGCTACGATCTCAGCAGAAAGGCAGGGGGAGCTGCTCCC GAAAGCCCCAAAAAGCGCAACGTCAACTGGCACACGCCTATTCAGATATA CGCTACCTACGAGCTGGGCGAAGAGCCGTGCTCCAGCAGAAAAGTCGCAG AAGAAAGTGCGCCTGAGTCGGTTGGAGAAAGATTGTGTTCCGTCAAGCCA GACTACCAGACGCGTCGAAACATCGGGGAGGACGATGGCTTCGAGAGTCT GAATGGAAAGAGCTCAAGTGGAGAGGACAACAACCATTCGCCTTTGCCAA ACGCGGTGGCTGTTGCGGCTCCACCAGCTCCTGTTCAGACCAATCAGTTG CGTCTGCGATTAAACACAACAAACGGTGTGACCGCCAGTGCTTCTCCAAC CGAGAAGAAACCCCAGTCGCGCGGCAATGAATCCTCAACGAGTTGCGCCG AATCGGATGAGTGCGATGATGCCGACATTATGTCCAGTCCCGCCTCGGGC TGTAACCAAGAGTGCACCACTTCTGCCACCGACTGGCTGGGGGTGACGAC AAATAGCGAAGACTGCAGTTACACCTCTGATCTGGATCACTCTGACGGGG GCTTGAAGCACACGGCCTTTAGCGACGAAGATCCTGGAGAGCTGGACATC ACCCCTACCACTATACTAAATCCACATAGCAGCCTCGACCGTATTAGCTG CACCATTTGGGATCAGCGAGATGCCAAAAAGGCGCAGCTTTCCGTGCTGG AGATCGCGTCTTGCATAATCGAACGCGTGGACTCAATGGGCGAGGCCAAC GACTACATCTACATAGGCGTGGTCTTCTCTTTCCTGCTCACATTGATTCC CATCTTCTGCCGTCTCTGCGAGGTCACACTCGGGAGCGATGCAGAGAAGG CCAGTGAGATTAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCA TCGGCATCGCTCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTG GGAGCGCATGGTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCC TCATACTGTTCATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGC TTCCTTTACGCCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCG AAAGTCAAATCTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGA CCTGGCTGAGCGTGAGGTCGTATTTGAAGAAACGCGGACCCCAGCGATCG GTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGC CTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACC TTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTG CGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTC GGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGC CAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCC GCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAG TGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCC TATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAA ATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAG TACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAAT TAGTTAAGTGAATAAATTTAAGCGAGCCAATGTTTATGCTTGTCACGTGA TTGTTTAGCTACGTTAACAAGCCCACTAACGACTACGTAAACCAACAGAA ATTAGTATTTACCTACTTACCTTCTAGAGCGACCTGCACAATCACAAATC ATGTTTAGGCAAATTGTGCAATGCAATGAATCGCATGAAAGTTCATAGAA CTTTAAGCCTAAAATCAGTGCACCTATTGTAGTTGGCTGTTCATTCTGTT ACAGTCCCAAGTTAAATTCCTAAGGCGGTCTCAGCTAGTGTTGCAATTAA TAAATGTTAGTAAACTATAAT MKLDEIVAWYQKRIGTYDKQEWEKTVEQRILDGFNSVNLKNTKLKTELID VDLVRGSTFPKAKPKQSLLTVIRLAILRYVLLPLYAQWWVKQTTPNAFGF ILVLYLTQLTNWAIYVLHSSRIVPLDYEKPPNGTLLQAEADGDASDKDAD KESEEHAALLSALLIPCALSLLISLIHSQIVATNTASGVSGGSSKNKLRR ISASYLSDKAATRENRVRRRKKIVRVRQVEADLSQASSNISLPNRRTATS TIEVLPRPVTPLPSPTVTCATVPDPTTPTTPSPSVIRRSTNEETYLTTTA ISPLTQPLAAIDACYDLSRKAGGAAPESPKKRNVNWHTPIQIYATYELGE EPCSSRKVAEESAPESVGERLCSVKPDYQTRRNIGEDDGFESLNGKSSSG EDNNHSPLPNAVAVAAPPAPVQTNQLRLRLNTTNGVTASASPTEKKPQSR GNESSTSCAESDECDDADIMSSPASGCNQECTTSATDWLGVTTNSEDCSY TSDLDHSDGGLKHTAFSDEDPGELDITPTTILNPHSSLDRISCTIWDQRD AKKAQLSVLEIASCIIERVDSMGEANDYIYIGVVFSFLLTLIPIFCRLCE VTLGSDAEKASEISYFNMPQLLWEKSSASLFTLLGLAFGDSQWERMVLAL GFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHF RLNKVRNIKTWLSVRSYLKKRGPQRSVDIIVSAAFIVTLLLLAFLSVEWL KDSAHLHTHLTLEALIWSITIGIFLLRFMTLGQKIQHKYRSVSVLITEQI NLYLQIEQKPKKKDELMVSNSVLKLAADLLKELETPFKLSGLSANPYLFT TIKVVILSALSGVLSEVLGFKLKLHKIKIK SdhB CG3283 gene SdhB comment Comment: This record is derived from the following: L27705 L27705.1 02-FEB-1995 AA820233 AA820233.1 25-FEB-1999 gbunit AE003790 description D.melanogaster FlyBase-curated sequence: SdhB.v006 symbol SdhB cyto_range 42D1-42D1 sp_status Perfect match to SwissProt real (computational) comment Comment: Reference sequence of SdhB == FBgn0014028 GO GO:8177 GO GO:6099 GO GO:8136 FlyBase FBgn0014028 FlyBase CG3283 FlyBase FBan0003283 GO GO:0008177 succinate dehydrogenase (ubiquinone) activity GO GO:0005749 respiratory chain complex II (sensu Eukarya) GO GO:0006099 tricarboxylic acid cycle SdhB-RA transcript protein_id AAF57396 evidence experimental sp_comment Perfect match to REAL SP with corresponding FBgn owner crosby Gadfly CG3283-RA FlyBase FBtr0086156 translate offset 137530 137532 SdhB:1 exon 137386 137592 evidence experimental SdhB:2 exon 137865 138301 evidence experimental SdhB:3 exon 138358 138948 evidence experimental polyA_site evidence experimental CACTCGAAGCCGCCACGGCCACACTGCACCCTCAGTTTCGTGCAACTTTT TGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATT GCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTG GCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAG GAACCAGATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGG CGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTAC CGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGA GGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGA TCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAG GGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGC CTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACC CGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACATGAACAAC TTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCAAGAACGA AGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAGTCCGTCGAGGATC GCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTGCGCCTGCTGCTCC ACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGC CGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACT CCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGC CACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGG CCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGC CGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCT CTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCG AAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAAT TTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGA ACAAGACGCGAAAATAAATAATTGTGTATCCACCA MLATEARQILSRVGSLVARNQMRAISNGTAQLEQQAQPKEAQEPQIKKFE IYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSC REGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDM NNFYEQYRNIQPWLQRKNEAGEKKGKAQYLQSVEDRSKLDGLYECILCAC CSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVY RCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAALHK region evidence predicted comment protein feature standard_name iron-sulfur cluster I region evidence predicted comment protein feature standard_name iron-sulfur cluster II region standard_name iron-sulfur cluster III evidence predicted comment protein feature CG30445 CG30445 gene CG30445 cyto_range 42C3-42C3 gbunit AE003790 encoded_symbol CG3686 symbol CG30445 comment Flag Cambridge: gene split (internal view only)::DATE:2002-02-12 17:31:32::TS:1013553092000 sp_status Not in SwissProt real (computational) FlyBase FBgn0033091 FlyBase FBan0030445 FlyBase FBgn0050445 GO GO:0004058 aromatic-L-amino-acid decarboxylase activity CG30445-RA transcript owner simonp protein_id AAM70810 sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CG30445-RA FlyBase FBtr0086143 translate offset 9954 9952 CG30445:1 exon 10161 9825 CG30445:2 exon 8836 7732 CG30445:3 exon 7609 6771 ACATTCGCGTCAAGGAAGCTGACCTGCAACGAGTGTGCGGTGCGAGATAA CCGGGATTCGAAAGTGATCGAGATAAGCTACTGTGTACCGTGTGAGAGCC TAGTATCCGAGCACTAGAGATACAAGCACCAAGCACCAACAGATACTTCT TAATAGACTGCAATTTATTTGAACAAGAAGATAAACGAAAAGTGTAAATT AGAGAAAATGGATGTGGAAGAGTTTCGCAAATACGGCAAGGAAGTGATTG ATTATATATGCCAATACGGCACTAATATAGAGGAGCGTGACGTGGCGCCC ACCTTGGATCCGGGTTACCTCAAAAAACTGCTACCAGCCGACGCTCCCCA GTCGCCGGAGCCGTTCAAGGACGTGCTCGAGGACTTCGAGCAGAAGATCA TGCCGGGCGTGGTGCACTGGAACCACCCCAAGTTCTTCGCCTACTTCCCC TCGGGCAACTCTTTTCCATCGGTCCTAGGCGACATGCTCAGCAGTGCCAT TGGTTCAATTGGCTTCAGCTGGGCCAGCTGTCCGGCGGCTGCCGAGCTGG AGACGATCGTGATGAACTGGTACGCCAAGGCCCTTGGCCTGCCCAAGGCC TTTGTTTCGGATGCCCCAGGCAGTACAGGCGGCGGCGCCCTTCAGGGATC CGCCTCAGAGTGCGTTCTCGTCTCTCTAATCACAGCCCGCGCCCGGGCCA TCAGCGAGCTAAAGGGTCAGACCAGCGTTCACGACAGCGTCTTCCTGCCC AGCCTGATCGCATACGCCAGCCGTGAGGCACACTCCTCCGTGGAAAAGGC CACCAAGATGGCCCTGGTGAAGCTCCGGATAATCGATGCCGACGAGCATG GACGCATGCGCGTTGACCTACTCCGCCAAGCAATTCAAAACGATGTGAAC GCCGGCTTGACACCCTTCTTTGTAGTGGCCACTGTGGGTACCACCGGCGG CTGCGCTTTCGACGACATCACGGAGATCGGAAAGGTGTGCCGCCAGGTGT CGAGCATTTGGCTGCACGTAGACGGCGCCTATGCGGGAAACTCCTTCATT CTGCCCGAGATGCGGGTCTTTTCGGCAGGACTCGAATACGCCGACTCCTT CAACACAAATCCCAACAAGCTTCTGCTGACGAACTTCGATGCCTCTGCCC TGTGGGTGCGGGATGTGATGAACCTTAAGAGCGCGCTCAACGTGAATCCC CTCTACCTACGACACGAGCACTTGACCGGAGTTGACTACCGCCACTACGG CATTCCCCTGAGTCGCCGATTCCGGGCACTCAAGCTGTGGTTCGTCTTCC GGACATACGGCATTCGGGGCCTACAGGAATACATTCGAAATCATATGGCG TTGGCTAAGAAGTTTGAGATGCTGGTGCGCAAGGATGAACGATTTGAGGT TCGCAACGATGTTCACCTTGGCCTAGTTTGCTTCCGAATGCGAACTGGCG ACGAGCCCAACCACATGCTGCTCGCCCAGATCAACCACTCGGGCAAGATG CATATGACGCCGGCCAAGTTCAACGGCCGCTACGTGATCCGCTTCTGCGT CACCTACGAGCACGCCACTGAGAAGGACATCCTGGAAGCTTGGACCCAGA TAAAGTGCTTTGCTGAGGAAATACTGCGGGACCACCAGCTGGAGTCCAGC TCCGTGCCAACCACGCCGGAAGGCTCAGAGCGGACCAGCTCAGAGCCATT GGCTCCAGTGGCGGGCAAGCCACCCATCAAAAAGAGGCTGACCAGGACAA AGTCGCTGCGATTCTCCTTCACTCGCAGCATCTCGCGGGAGCAGTACCAG AGCCAGAGCGAGCACCTAATGGACGGGTGCACACCCATCCTGGTCGTCGA TCCCAAAACTCTTCAGGAGAACTTCCAAAAGGCGGCGGATGACAATGACA GGAACAACAGCAATGGCAACGTAAAACTCAAAGATATATCAGACGTGGAT ACGGACGAGGCGAGTAACTGAGCGTCGACCCGAAAAGGGATTTGCGGATT TACCTCTACCTAGTATTAGTTGTCGAGCTGAAATGAGGCATGAATCAATC GACTACCGACTAACATTGCTCAGTTTGAATTTAAGAACATCCATTTATGT ACTAGTAGGACCTTAGTTGTTGCTGAATATCATGTAATTTAAAGATAGAC TCATTTGCATCTGCTTATACCGTTTAGCTACCTTAAGTTACTGTCATGAA CAAAAGCACTTATTTATAAACATTATCTCGGCATTTTTTATGCAAGTTTT TAAAAAATACAAACACAATCCAACGGAAAAT MDVEEFRKYGKEVIDYICQYGTNIEERDVAPTLDPGYLKKLLPADAPQSP EPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGS IGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSAS ECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEKATK MALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCA FDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNT NPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGVDYRHYGIP LSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRN DVHLGLVCFRMRTGDEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTY EHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPLAP VAGKPPIKKRLTRTKSLRFSFTRSISREQYQSQSEHLMDGCTPILVVDPK TLQENFQKAADDNDRNNSNGNVKLKDISDVDTDEASN l(2)01289 CG9432 gene l(2)01289 cyto_range 42C6-42C7 encoded_symbol CG30444 gbunit AE003790 comment Flag Cambridge: gene merge (internal view only)::DATE:2002-07-19 16:33:46::TS:1027110826000 symbol l(2)01289 sp_status Perfect match to SwissProt real (computational) FlyBase FBgn0033099 FlyBase FBan0009432 FlyBase FBgn0013956 FlyBase FBgn0010482 FlyBase FBgn0033098 FlyBase FBgn0050444 GO GO:0003756 protein disulfide isomerase activity GO GO:0005886 plasma membrane l(2)01289-RA transcript owner campbell sp_comment Imperfect match to REAL SP with corresponding FBgn protein_id AAM70821 Gadfly CG9432-RA FlyBase FBtr0086136 translate offset 70027 70025 l(2)01289:1 exon 70419 69814 l(2)01289:2 exon 68130 67974 l(2)01289:3 exon 67902 67736 l(2)01289:4 exon 63032 62718 l(2)01289:5 exon 62657 62013 l(2)01289:6 exon 61959 61777 l(2)01289:7 exon 61709 61572 l(2)01289:8 exon 61508 61326 l(2)01289:9 exon 61265 61215 l(2)01289:10 exon 58848 58366 l(2)01289:11 exon 58095 56604 GTGGAACAAAATCTGAAGAGCAAAGAGTACAGTCCGCGGAAAACGTTCAA TTAATAGAAGCAAGAAACCACATATATAATCTAATTATTCTCGTATATAC CCCACATATATCTCGCCTGTGCATATACGAACCCCGTATATATGTATCAG TGAACAAAAAGTTGTTATACATAAAATAAATTGCGAAAGAAGAAACACCA TTATCAACTAAAAATAGTGACCGATTCTCAAAGGAATACAAATTTTAATA ACGAAAGACCCCAAACGACGAGAACGAATCAATTATACAATTATAACACT ATAAACTGTAGAACACACCAAAACGAGCAGACACGCGCACGCATGTTCGC GTTAAGGGCCTAAAGCACATCAGAACCGTAACCGATCGCAGGATGACTTT CACCCGCCTCAAGACTCTCTCGCTGCTCGTGTGTGCTCTGCTGGCCCTGA GTTTTCCCGGACATGTGAGTGGTGCAGGCAACAACAACAACAAGAAGGGC TCGCAGCCAGTGGCGCCTCCGGAGCCGGAGGCCGTCATCGAGGAGGTCAA TGCCAAGCAGCTGGAGAAGCTCCTGGCCGACAAGGATTACGTGGCCGTTT TCTGGTATGCGCGAAGCTGCGTGACCTGTGATAAGGTTTTAGCGGAACTC GAGAAAATCGACGATGACACCGACTCCTTCGGTGTGGACTTCGTGAAAAT CAACGACAAACGACTAGCCAAACAGTATGGCATCAAGAACTTCCCCGCCC TCACCTACTTCAGGGAAAAGGAGCCCATCATATATGATGGGGATCTCATG GACGAGGAAGGAGTGCTCGATTTCCTCACCTCCTTGGAGGCCATGGACTT GCCCGATCGCATCGAGGAGGTCAATGCCAAGATATTGCAGAAGATCATCG AGGACACCGACTTCGTAGCCGTTCTGTTCTACGACAAAGACCAAAAGAAA TCACAGAAAATCCTCGCAGAACTGGAAAACATCGACGATGAGTGCGATCA GAACGATATTGCCTTTGTCAAGATCGATGATGACAAGGAGGCCAAAGAAT GGGGTATCGATGAGATACCATCGATTGTACTCTTTGAACGTGGAATTCCA CACATCTACGAGGGTGATCTGATGAAAGAGGATGAGCTGCTTGGCTGGTT GGTGCACCAGAAGCGCTATTCCGAAATTCCCGAGGTCACCGATGAGATGA AGGACAAGTTGGTCGAGAACACCGAGCACTTGGCGGTTATATTCTACGAC AAGGACGATAAGCAGGATATGCGCATCCTGAACGAACTGGAGAACATTGA TGACGAGCTGGAGAAGGAGGGAATTGTCATCGTCCGCATTGATAACGCCG CTGAGGCCAAGGAATATGGTCTCGATCATTTGCCCGCCCTCATCTACTTC GAAAACAAGATCCCGGCCCTCTATGAAGGCGATCTGATGAACGAGGATGA GGTGCTCGAGTGGCTTCTTGTCCAGAAAAAGACAGCTACTATCGAGGAGG TTACCGATGAGATCCTGGTCACTCTGATCAACGAACACGAATATGTCGTC GTCTTCTTTACGGGTCCCTGCGAGCCCGGAGAGACCTGTGAGCACACTCT GAACGCCCTGGAAAGCATCGACGATGAATTGGATGAGGCTGGCATAATTT TTGTTACCACTGAGGATACCGGAATTGCCAAGAAATACAACGTCAAGACC TATCCACGTCTGGTGTTCTTCAGGAATCGTGATCCACTTCACTTTACCGG TGATCTGGACGACGAGGACGAGGTGTTGGCCTGGATTACTGACGACGAGA CCCTTGAAATTCCCGGAAAAATTGAGGAGGTCAATGTGAAGATGTTGGAC AAGATCTTGGCTGAAAACGATCACGTTGTCGTATTCTTCTACGCTGAGGG CGATAAGAAGGCCCAAAAGATCCTTAACGAGCTGGAGAACATCGATGACG AATGCGAGGAAAAAGACATTGACTTTGTAAAGACATCCGACGACGATATT GATAAGGAGTACGACCTGCCCGGTCTGCCGGCACTTGCATTTTATAGACA TAAGTTTAGAACAATTTACACCGGTGACCTGATGAAGGAAGAGGAAATTC TCGAGTGGGTTATTGATTTGCACGAGTCCACAGCTGATGTCATTGAATCT GTCGATCGTAAGACCCTGCAAGTTTTGATCAACGATGTTGAGCACCTGGC TGTGTTCTTCTACGACGATGAATGCGAATCGTGTTCCGACATCTTGGAGG AGTTGGAGAACATCGACGATGACACCGACAAGCACGGAATACAATTTGTC AAATCAAATGATGTTAAGCTGGCTCATGAAATTGGCATTTTCGCATTTCC AGCTTTGGTCTACTACGAGACCGGCGTCCCGATTATGTATGATGGTAATC TCAAAAATGAAAACCGTGTGCTGCAGTGGTTAGTCAATCAAAAGAATGAC GAATGTTTCTATGTTGGATTGGGTCATGACGGCCATTCAGCTAAGCGCGG CAACAATTTCGTGCCCAACGATTACAAACCATTCCAATGCTGTCCAACCA AATTGGAGAAGTCAACGAAAGTTCCTAAGATGACCGCCCAGCGGATCGGG CATAGCGAAGGCGATCAGGGCAAGCGTCCCAGCGGCGGCAACTTCCAGTT TGCCAACCAGGCGTCCAGCAAATCGTCCACCAAGCCAGCTGCCATCAAGA AGCAGGCCAAGCCCTCCAAGGACACCGATGACGACGATGAGGACGACGAG GACAAGCCCCTGGTCAAGGTTTCCTATGCCAACAAGCGCTCGGGAGGAAG CAACAAGCCGCAGGCTGGCAAGAAGCCGGTAGGCAAGGGCCAGGACAACG ACGACCAGTCCCAGGAGGTGGAGAAGGTATCCAAACAGAAGTCGGCGAAG AAGTCCGGCAAACTGAATGTCAAATCCGGATATCTCTCTGTGGGAGTAAG GCAACAGTTTAACTGAATGTGGATAACCACAGACAGTTAGATAGTGATTG ATTGTATGATTGAATGATATACCATACTAAAGTAGCACGTATACGCACTG TTGCCAACTGATAGAACAATTATCAAACCAAAACCAATACCAAACCCAAA ACCAAAACCAAAACAAAATACAAAACCAACTCAAACCTGTATAGCCAGCA AAAGAACCTTCAATGACAGGTTTCTATAATTAATGTACATCATCTACATA TGTGTGACTGCAAAAGACAACAACTATGACAAGAACCAACTGAAAACTGA ATTCGCAGGCTGTGTGTCCATAAAATTGAGGTTTCCTCGCACTAATCCTA AACAGTCTGGCACAAAAACATTGACTTAAATACCAATACATCTTCTGTGT CAGATCAGAACTTACTCCACACTTTTAAGCAGCGAGCCTTGGGCGTTGTT CCACGTTAAGAAGATCCACGAGTAGCAGAATCACACGATACCCGAAATAA TGAATAATGATCAAGAAAACCTACTAACTAAAACTTTGTTGATATTTTCG CTTTAACTTTCTTCAAGAGGGGCCGACCTGTGTAGGTCGTCCCCAGGTCT ATAACTAACTAAACCACACATTTGTTGCATTTTGCCAACGGATTTCAAAA AACTTTGTTCAAACTAAAAGCAATTACTTCGACAAACAACTATAAAACTT CTGAGAACTTTCGCTCGTATATTTAGTCAGCAAGCTTTGTTATTAACAAA TTAATGGGACATTGTCTTTTGTCAATAACGAACGCCTAAACTTTTTTGAT ACTACTTCTTTTTGTCGCAATATACAATTTACATTTATGTAGTTAGTCTA ATTTAAACAAGGGCCAAAGCATAGTAAACGAACGAACAAACGCATAAAAT ATTTTTTGAAACAATTTACACCTGACAGTGCACAACTGTTAGCTAATTTA ACTGAAACGTGTAACTATGAGAGCCTTCAACTTTCATAAGTTTTCATAAT AACAACATGAGGAACCATAATTTGTAACCACAACTTTTTAGAAATGTTGC AGCAGCATACAGGCCGTATACTTAATTTTGTTATGGAATCGAAAATCCAA TATTTCTCGCTGAACATGGCCTCGCATATTGTAGCTCGCCATTTTGTTTC ATTTGTTTTCTTCTGAGAGCGATTTCTGTACCGCTCGCTGTTGTTTTTGT TATCGGTATTTGAAAAATATCGAATTAGAAATCTTTATCATTATGTTTTC TTAAGCTAAAGCCTACCAATCTAAACGCAATTGTAACTAAATCCAACATA TATGTAAACAAATTTTGTTGAACAGCAGCTGATAAGTCAAGATTTTCGAA ATGGAAATTGTCAGATCGTAAAAATCAAACGCAAATCGACATAAAGCACT TTTGTAAACATAGCTCCCGAATGAAATTGTAAGAATATTTAATAAAAGCC ATCCAACTCAATAAACTTAG MTFTRLKTLSLLVCALLALSFPGHVSGAGNNNNKKGSQPVAPPEPEAVIE EVNAKQLEKLLADKDYVAVFWYARSCVTCDKVLAELEKIDDDTDSFGVDF VKINDKRLAKQYGIKNFPALTYFREKEPIIYDGDLMDEEGVLDFLTSLEA MDLPDRIEEVNAKILQKIIEDTDFVAVLFYDKDQKKSQKILAELENIDDE CDQNDIAFVKIDDDKEAKEWGIDEIPSIVLFERGIPHIYEGDLMKEDELL GWLVHQKRYSEIPEVTDEMKDKLVENTEHLAVIFYDKDDKQDMRILNELE NIDDELEKEGIVIVRIDNAAEAKEYGLDHLPALIYFENKIPALYEGDLMN EDEVLEWLLVQKKTATIEEVTDEILVTLINEHEYVVVFFTGPCEPGETCE HTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLH FTGDLDDEDEVLAWITDDETLEIPGKIEEVNVKMLDKILAENDHVVVFFY AEGDKKAQKILNELENIDDECEEKDIDFVKTSDDDIDKEYDLPGLPALAF YRHKFRTIYTGDLMKEEEILEWVIDLHESTADVIESVDRKTLQVLINDVE HLAVFFYDDECESCSDILEELENIDDDTDKHGIQFVKSNDVKLAHEIGIF AFPALVYYETGVPIMYDGNLKNENRVLQWLVNQKNDECFYVGLGHDGHSA KRGNNFVPNDYKPFQCCPTKLEKSTKVPKMTAQRIGHSEGDQGKRPSGGN FQFANQASSKSSTKPAAIKKQAKPSKDTDDDDEDDEDKPLVKVSYANKRS GGSNKPQAGKKPVGKGQDNDDQSQEVEKVSKQKSAKKSGKLNVKSGYLSV GVRQQFN l(2)01289-RB transcript owner mhuang sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAN16126 Gadfly CG9432-RB FlyBase FBtr0086137 translate offset 70027 70025 l(2)01289:1 exon 70419 69814 l(2)01289:2 exon 68130 67974 l(2)01289:3 exon 67902 67736 l(2)01289:13 exon 67304 67269 l(2)01289:14 exon 64686 64504 l(2)01289:15 exon 64373 64230 l(2)01289:16 exon 64167 64034 l(2)01289:17 exon 63969 63789 l(2)01289:18 exon 63717 63403 l(2)01289:4 exon 63032 62718 l(2)01289:5 exon 62657 62013 l(2)01289:6 exon 61959 61777 l(2)01289:7 exon 61709 61572 l(2)01289:8 exon 61508 61326 l(2)01289:19 exon 56163 56032 l(2)01289:20 exon 55802 55479 l(2)01289:21 exon 55414 55226 l(2)01289:22 exon 55167 55030 l(2)01289:23 exon 53797 53615 l(2)01289:24 exon 53562 53431 l(2)01289:25 exon 52683 52527 l(2)01289:26 exon 52469 52303 l(2)01289:27 exon 52239 52083 l(2)01289:28 exon 52029 51863 l(2)01289:29 exon 51802 51620 l(2)01289:30 exon 51553 50874 GTGGAACAAAATCTGAAGAGCAAAGAGTACAGTCCGCGGAAAACGTTCAA TTAATAGAAGCAAGAAACCACATATATAATCTAATTATTCTCGTATATAC CCCACATATATCTCGCCTGTGCATATACGAACCCCGTATATATGTATCAG TGAACAAAAAGTTGTTATACATAAAATAAATTGCGAAAGAAGAAACACCA TTATCAACTAAAAATAGTGACCGATTCTCAAAGGAATACAAATTTTAATA ACGAAAGACCCCAAACGACGAGAACGAATCAATTATACAATTATAACACT ATAAACTGTAGAACACACCAAAACGAGCAGACACGCGCACGCATGTTCGC GTTAAGGGCCTAAAGCACATCAGAACCGTAACCGATCGCAGGATGACTTT CACCCGCCTCAAGACTCTCTCGCTGCTCGTGTGTGCTCTGCTGGCCCTGA GTTTTCCCGGACATGTGAGTGGTGCAGGCAACAACAACAACAAGAAGGGC TCGCAGCCAGTGGCGCCTCCGGAGCCGGAGGCCGTCATCGAGGAGGTCAA TGCCAAGCAGCTGGAGAAGCTCCTGGCCGACAAGGATTACGTGGCCGTTT TCTGGTATGCGCGAAGCTGCGTGACCTGTGATAAGGTTTTAGCGGAACTC GAGAAAATCGACGATGACACCGACTCCTTCGGTGTGGACTTCGTGAAAAT CAACGACAAACGACTAGCCAAACAGTATGGCATCAAGAACTTCCCCGCCC TCACCTACTTCAGGGAAAAGGAGCCCATCATATATGATGGGGATCTCATG GACGAGGAAGGAGTGCTCGATTTCCTCACCTCCTTGGAGGCCATGGACTT GCCCGATCGCATCGAGGAGGTCAATGCCAAGATATTGCAGAAGATCATCG AGGACACCGACTTCGTAGCCGTTCTGTTCTGTCCAGATCATGAAACATGC CCGCCCAGGGTTATGGACAAACAGCAATGCCGCAAGTGCGCCAAGGCCTT GCAGGAGCTGGAGAATATCGACGACGAAGCTGACCAGCTGGGCATCGGGT TTGTGAAGATACACGACGAGGCCTTGGCCGACGAATACAATCTAGGCAAT CTGCCAGCCTTGGTCTATTACCGCCACCAGACTCCGATCATATACGAAGG TGAACTTCAGCGGGAGGAGGACGTCTTGGAATGGTTGGTGCAGAATAAGT CGACGGGCGATGAAGATGATGTGATTGAAGACGTCACTTCGAAGACTCTG TCGACGCTGATCAGCAATATCGACAATCTGGTTGTGCTGTTTTATGATCA TGGAAACGACGACTCGATGACCGTGTTAGAGGAGCTAGAGCAAATCGACG ACGACTGCGACAAGCATGGCATTCAGTTTGTGAAAATCGACGATGCCAAG GCGGCAGCCGATTACGGAATCGATTCGATTCCGGCCATTGTTTACTTTGA AAAAGAAATTCCAAATGTGTACGACGGCGATCTCATGGACGAGGAGCAGA TTCTGAAATGGTTGTTGGGACAGTTGGAACGGGATGAGATCGAGGACGTC ACCGACGAAATGCTCGATACAATGATCAAAGAAGGACGCGTCATTGCCGT GCTGTTCTACGACAACAACGACAAGAAGTCCCAGAAAGTGCTCGAGGAGC TGGAGAACATTGACGACGAGTGCGACGCATTGGGCATTACTTTCGTGAAG ATCGACAATCCCGAGGAGGCCGTTGAATATGGCATCAATAAAGTTCCTAA ACTGATATACTTTGAAAAAGGCATTCCAACTATTTACGAGGGCAATCTGG AGGACGAGGAGAAGCTTCTGAAATGGCTAACAGACCAAACGAGTTCCGAT CAAATCGAGGACATCACCGACGAAATGTTGGACTTAATCATTGAGAAAAT GCCCCATGTTGCTGTTCTTTTCTACGACAAAGACCAAAAGAAATCACAGA AAATCCTCGCAGAACTGGAAAACATCGACGATGAGTGCGATCAGAACGAT ATTGCCTTTGTCAAGATCGATGATGACAAGGAGGCCAAAGAATGGGGTAT CGATGAGATACCATCGATTGTACTCTTTGAACGTGGAATTCCACACATCT ACGAGGGTGATCTGATGAAAGAGGATGAGCTGCTTGGCTGGTTGGTGCAC CAGAAGCGCTATTCCGAAATTCCCGAGGTCACCGATGAGATGAAGGACAA GTTGGTCGAGAACACCGAGCACTTGGCGGTTATATTCTACGACAAGGACG ATAAGCAGGATATGCGCATCCTGAACGAACTGGAGAACATTGATGACGAG CTGGAGAAGGAGGGAATTGTCATCGTCCGCATTGATAACGCCGCTGAGGC CAAGGAATATGGTCTCGATCATTTGCCCGCCCTCATCTACTTCGAAAACA AGATCCCGGCCCTCTATGAAGGCGATCTGATGAACGAGGATGAGGTGCTC GAGTGGCTTCTTGTCCAGAAAAAGACAGCTACTATCGAGGAGGTTACCGA TGAGATCCTGGTCACTCTGATCAACGAACACGAATATGTCGTCGTCTTCT TTACGGGTCCCTGCGAGCCCGGAGAGACCTGTGAGCACACTCTGAACGCC CTGGAAAGCATCGACGATGAATTGGATGAGGCTGGCATAATTTTTGTTAC CACTGAGGATACCGGAATTGCCAAGAAATACAACGTCAAGACCTATCCAC GTCTGGTGTTCTTCAGGAATCGTGATCCACTTCACTTTACCGGTGATCTG GACGACGAGGACGAGGTGTTGGCCTGGATTACTGACGACGAGACCCTTGA AATTCCCGGAAAAATTGAGGAGGTCAATGTGAAGATGTTGGACAAGATCT TGGCTGAAAACGATCACGTTGTCGTATTCTTCTACGCTGAGGGCGATAAG AAGGCCCAAAAGATCCTTAACGAGCTGGAGAACATCGATGACGAATGCGA GGAAAAAGACATTGACTTTGTAAAGACATCCGACGACGATATTGATAAGG AGTACGACCTGCCCGGTCTGCCGGCACTTGCATTTTATAGACATAAGTTT AGAACAATTTACACCGGTGACCTGATGAAGGAAGAGGAAATTCTCGAGTG GGTTATTGATTTGCACGAGTCCACAGCTGATGTCATTGAATCTGTCGATC GTAAGACCCTGCAAGTTTTGATCAACGATGTTGAGCACCTGGCTGTGTTC TTCTACGACGATGAATGCGAATCGTGTTCCGACATCTTGGAGGAGTTGGA GAACATCGACGATGACACCGACAAGCACGGAATACAATTTGTCAAATCAA ATGATGTTAAGCTGGCTCATGAAATTGGCATTTTCGCATTTCCAGCTTTG GTCTACTACGAGACCGGCGTCCCGATTATGTATGATGGTAACATTGCAAG CAATCAGGACGTCTTCAACTGGATTCTCGAACAGAAGGCCGACCAAAGCA TTCAACTCATTAATCGTGACCAACTTTTCGAGTATATAGGCACCAAAGAC TTTTTAGCGGTTGTTTTTTACAAAGAAGATGATCCCGACTCGCCACGAGT GCTGCGGCACATCGAACTAATCGACGACGAGGCTGCGGAATATGGCATTT ACATAGTGAAGATGCACGACAAACTGATGGCCAAGAAGTACGGCTTCCGG AATCCCCCAGGACTGACGTATTTCCGAAAGGGCAAGTATATCAACTACGA CGGCGATATCGATGACGAGGAGGAGGTACTGGACTGGCTAACGAGCCCGG CCAACATGGAGATGACCGATCACATCGAGCAGGTTAACCGCAAGATGTTC GAGAAGATCCGCAAGAACTCCGACTACGTAGCGGTGATATTCTATAGCGA TGAGTGCAAGCAGTGTCCTCGCGTCCTGGCCGAGGTGGAACACATAGACG ACGAAGCGGACAAGGCTGGTATCGACTTCGTCAAAATCGACGATAAGCAG ATGGCCAAGGAGTACGGAGTGTTCGCCCTGCCTGCCATTGTCTTCTTCAA GCCCACATCCAAGGAGCCAGTTATATACGCCGGTGATCTTTACGAAGAAG AACAGATCCTAACTTGGCTGATCACGCAAAAGGATCCAAGTGGAGATGTT ATCGAAGATCTCGAAGGCGAAAGACTTGTTCATCTGATTGAAGAGTCTGG CTCCATCGCAGTCTACTTTTATGCGGATGGCTGCGAGCAGTGCACCAAGG TTTTGGAGGAGTTGGAAAACATCGATGATGATTGCGACAAGCATGGCATA ACATTCGTTAAGACCAGGGACTTCTCTGTGGCCGACGGCTATGGCGTGCA CGAGTATCCGGCTCTAGTTTACTTCGAGGGAGGAATCCCCAACGTATTCG AGGGCGAATTGAGCGAGGAGGAAGAGGTTCTTCAGTGGCTTATCACCCAG AAGACCGAAGATCGTATTGAGCTGATCACTCGCCAGATGCTGGAGACAAT GGTGGAGGAGACGCAGTACCTAGCCGTGTATTTCTACAAAATCAACTGCA ACATATGCGACCAGATACTAGAGGGCTTGGAACTGATCGATGACGAATGC GACGTGTTCGGAATTCATATGGTCAAGATCCAGGATCCGCAGCTGGCAAA ACGTTACTCGATCAAGACTTTCCCGGCGTTGGTTTATTTCAGAAATGGAA ACCCATTACTGTTTGAGGGGGATCTTCAGAACGAGCAATCAGTATTGGAA TGGCTCATCGATGATGACAACCGCGAGCTGGCTGATGAAATCGAGGAGGT CAACGAGCGTATGCTGGATCGCCTAATGGCGGAGTCCACTCTATTGGTTG TTTTCTTTTACGACGATGATTGTGCTGAGTGCGAGGAGATTTTGGAAGAG CTGGAGGAGATCGATGGTGAGGCAGACATGTTCGGCATTGATTTCGTAAA GATTGCTAGTATCCAGGCAGCCAAGAAATACGAGATAGTGAATATACCTT CCCTCGTTTATTTCCGAAAACAAGTGCCCGTCCTCTACGACGGCGATCTA CACCAACACGACAAGGTGATTACCTGGCTAACATCACAGGACGTATTCGA AATCAAAAACGAAATAGAAGAAGTAAACCGAAAAATGCTCGACAAACTAC TCGAGGAAAATGAGTTCTTAGCCGTTTTTTTCTACGAACACAATCAGCCG GACAGTACTGCAGCGCTGGAAAAACTCGAAAACATCGACAGCGAGACGGA TAACCTGGACATCACCTTCGTCAAGATGGCCGACTCTCGTTATGCCAAGA AATGGGGCGTCACCAAGCTGCCGGCAATGGTCTACTTCCGCCGTCGGTTT CCCAGCATATATAGGGGTGATCTGTTATCCGAGGACGAAGTGCTGGAGTG GCTACGCAAGAACCGCTTCCGCCAGCCCGAGCTGAACATCTTTATGTACG CTCTGATTGCTCTGGCGGTGGCCTTTGTGGTCTACACCGCCTTCCTGCTG CAGTGCTTCAAGCCGGCGCCACCGCCTCCTGTCCAGCACCCCAAGCAGTC TTGAATGGTATGGGTTGGGGAATCGGGAAGAATGTACTGAATCACGTTGA ACGGCTGTCAACTACGATGGAGGGTTTTCGACAAGACACACAAAAGCGAG CGAACCAAACTTGAAATGATTATCCAAAGTCACAATAATACACGCATATC TATGCACATTAAACTGTCATCCAATCGTCTAAATTAGACGCATGAAAACC ACTTGTCTGGAGACAATCCATTGCTTTTGAAATATCTTTTGAGACAACTT GATAACTTTGATAAACTCTGATGCTTCCATTAATATCAAAACTCATGTAT GTCACATTTACACATTTATTTGTCTTCTCACCCGTGTACATCATGGAAAT CAATTACAGAAGAACACTATCAAGTCATAGTAATTACGTTAAATTTAAAT TTAAACGCCATAATATTGTGTAATAAATGTCAATAATAATTTTTACAGTA ACTTATTTACGGCCTATGATACTTAATAAACTATTGGATGATGTAT MTFTRLKTLSLLVCALLALSFPGHVSGAGNNNNKKGSQPVAPPEPEAVIE EVNAKQLEKLLADKDYVAVFWYARSCVTCDKVLAELEKIDDDTDSFGVDF VKINDKRLAKQYGIKNFPALTYFREKEPIIYDGDLMDEEGVLDFLTSLEA MDLPDRIEEVNAKILQKIIEDTDFVAVLFCPDHETCPPRVMDKQQCRKCA KALQELENIDDEADQLGIGFVKIHDEALADEYNLGNLPALVYYRHQTPII YEGELQREEDVLEWLVQNKSTGDEDDVIEDVTSKTLSTLISNIDNLVVLF YDHGNDDSMTVLEELEQIDDDCDKHGIQFVKIDDAKAAADYGIDSIPAIV YFEKEIPNVYDGDLMDEEQILKWLLGQLERDEIEDVTDEMLDTMIKEGRV IAVLFYDNNDKKSQKVLEELENIDDECDALGITFVKIDNPEEAVEYGINK VPKLIYFEKGIPTIYEGNLEDEEKLLKWLTDQTSSDQIEDITDEMLDLII EKMPHVAVLFYDKDQKKSQKILAELENIDDECDQNDIAFVKIDDDKEAKE WGIDEIPSIVLFERGIPHIYEGDLMKEDELLGWLVHQKRYSEIPEVTDEM KDKLVENTEHLAVIFYDKDDKQDMRILNELENIDDELEKEGIVIVRIDNA AEAKEYGLDHLPALIYFENKIPALYEGDLMNEDEVLEWLLVQKKTATIEE VTDEILVTLINEHEYVVVFFTGPCEPGETCEHTLNALESIDDELDEAGII FVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWITDDE TLEIPGKIEEVNVKMLDKILAENDHVVVFFYAEGDKKAQKILNELENIDD ECEEKDIDFVKTSDDDIDKEYDLPGLPALAFYRHKFRTIYTGDLMKEEEI LEWVIDLHESTADVIESVDRKTLQVLINDVEHLAVFFYDDECESCSDILE ELENIDDDTDKHGIQFVKSNDVKLAHEIGIFAFPALVYYETGVPIMYDGN IASNQDVFNWILEQKADQSIQLINRDQLFEYIGTKDFLAVVFYKEDDPDS PRVLRHIELIDDEAAEYGIYIVKMHDKLMAKKYGFRNPPGLTYFRKGKYI NYDGDIDDEEEVLDWLTSPANMEMTDHIEQVNRKMFEKIRKNSDYVAVIF YSDECKQCPRVLAEVEHIDDEADKAGIDFVKIDDKQMAKEYGVFALPAIV FFKPTSKEPVIYAGDLYEEEQILTWLITQKDPSGDVIEDLEGERLVHLIE ESGSIAVYFYADGCEQCTKVLEELENIDDDCDKHGITFVKTRDFSVADGY GVHEYPALVYFEGGIPNVFEGELSEEEEVLQWLITQKTEDRIELITRQML ETMVEETQYLAVYFYKINCNICDQILEGLELIDDECDVFGIHMVKIQDPQ LAKRYSIKTFPALVYFRNGNPLLFEGDLQNEQSVLEWLIDDDNRELADEI EEVNERMLDRLMAESTLLVVFFYDDDCAECEEILEELEEIDGEADMFGID FVKIASIQAAKKYEIVNIPSLVYFRKQVPVLYDGDLHQHDKVITWLTSQD VFEIKNEIEEVNRKMLDKLLEENEFLAVFFYEHNQPDSTAALEKLENIDS ETDNLDITFVKMADSRYAKKWGVTKLPAMVYFRRRFPSIYRGDLLSEDEV LEWLRKNRFRQPELNIFMYALIALAVAFVVYTAFLLQCFKPAPPPPVQHP KQS CG17266 CG17266 gene CG17266 cyto_range 42C3-42C3 sp_status Not in SwissProt real (computational) gbunit AE003790 symbol CG17266 GO GO:3734 GO GO:6371 GO GO:5681 GO GO:3755 FlyBase FBgn0033089 FlyBase FBan0017266 GO GO:0003755 peptidyl-prolyl cis-trans isomerase activity GO GO:0030532 small nuclear ribonucleoprotein complex GO GO:0005681 spliceosome complex GO GO:0000398 nuclear mRNA splicing, via spliceosome CG17266-RA transcript owner pavel protein_id AAM70809 sp_comment Perfect match to HYPO SP record with corresponding FBgn Gadfly CG17266-RA FlyBase FBtr0086144 translate offset 5465 5463 CG17266:1 exon 5527 5382 CG17266:2 exon 5315 4848 GCTTAGTAAAATCTTAATCTTGACTTGTTAGAAAGTTTATAAACAAATAA AATAATTTTAAAATGCCTAACTGGAATCAAATACAGTCCCAACTGAGAAG CTCCAACAATCCCGTCGTTTTCTTCGACATTGCCGTAGGCACAACGGAAA TCGGACGAATGATATTCGAACTCTTTGCGGACACAGTGCCCCGCACGGCG GAAAACTTCCGGCAGTTCTGCACGGGCGAGTACCGACCGGATGGCGTTCC CATTGGCTACAAAGGCGCCAGTTTCCATCGGGTGATCAAGGACTTCATGA TCCAGGGCGGCGACTTTGTGCAGGGCGACGGCACCGGCGTGACCAGCATA TACGGCAACACCTTCGGCGACGAGAACTTTACCCTGAAGCACGACTCGCC CGGCCTCCTTTCCATGGCAAACAGTGGCAAGGAGACGAACGGCTGCCAAT TCTTTATCACCTGCGCCAAGTGCAACTTTTTAGACGGAAAGCACGTGGTG TTCGGTCGGGTTCTGGATGGACTGCTCATCATGCGCAAGATCGAGAACGT GCCCACGGGCCCCAATAACAAGCCGAAGCTCCCAGTGACCATTTCGCAGT GCGGGCAAATGTAG MPNWNQIQSQLRSSNNPVVFFDIAVGTTEIGRMIFELFADTVPRTAENFR QFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNT FGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRV LDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM CG3287 CG3287 gene CG3287 sp_status Not in SwissProt real (computational) cyto_range 42D1-42D1 gbunit AE003790 symbol BEST:LD11166 FlyBase FBgn0033106 FlyBase FBan0003287 FlyBase FBgn0028954 GO GO:0006410 transcription, RNA-dependent GO GO:0006357 regulation of transcription from Pol II promoter GO GO:0006366 transcription from Pol II promoter GO GO:0007049 cell cycle GO GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism CG3287-RB transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAG22207 owner campbell Gadfly CG3287-RB FlyBase FBtr0086157 translate offset 141704 141706 CG3287:1 exon 140795 140950 CG3287:2 exon 141677 141858 CG3287:3 exon 142556 142891 CG3287:4 exon 142948 143528 CG3287:5 exon 143812 144580 TCATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGA CGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCAT ATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATAT TACTAAGGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATA CCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGAT CGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTG CACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCAAACGATAATAGA GGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGT TCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCC AAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAA GCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGA CCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAAC GGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTA CAGGGATGCTGGTGAATACTGGAACAAAACTCCCAAGACGGACTATACCT ACTCAGAACTGTCCCCTCACCGACGCCAGTTGGCGCCAGGAATTGTGGCC ATGCCCAATATGTCCAGAAAGAGCCTAGAGAACCATAACGATCGAGTCAA CTACATGGTCCAGCAGAACCCTGCGCAAGAGGAGTTCATCCGCCGCCGCT ACCAGTCCAAGTATACCCAGCAGGTTAACTATGACTCCGCAGATGAACTG GACGCCACATTTGGGCAGCAAAAGCAGAGCTGGTGGCTTATCCGCCTCAT CCAACTGGTTGTTAGCAGCATTACCACCGTGTGGAGTCGGGTGACCAATC TCTCGGCCACGGAGACGACTGCCTATCAAAACTACCACGCTAAGCGCCAG CAGAGTCAACAAGTTGGACTTTGGTGGAAAATAGTACAGACCATCGGAGG AGGACTTGCAAGTTTGCTGCGCTACCTGTATGTTTTCATCGGATCGGTGC TGAGTTTGGACACGTGGTTGCTGCGATCCTCGGATGCGGAAAACAAGTCG AAAAAGCGCTTCCTCATATTTCTGCTGATTTTGTTGCCCTTGCTGCTGCT GTCGGGTCTGTTCTATTACATACACCCCAATGAAACTTTCCCACCCAAAT CCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTG AAAGACTACCTGAACCAGGAGCAGTTCGAATCGCTACGCTCTCAGGCCGC CGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACT TGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAG GGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGG CAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTG CACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAA TAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCG CACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAA CCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATG CAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATT GTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCG TTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAA CGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAA ATAAATCGCAAACAATTTCATATG MSENTYQIETRRRSRSKTPFLRSSCDHENCEHAGEEGHVHHLKRKSAAPN VQTIIEEHIVESSISKKTRAKAFAQLTSDYSSDDMTPDAKRKQNSITATV TSILTKRSGGATSTPRNRSQLETTQNTLNSAQEKLNQSNGNLSSGNVSDY LAYIEYRDAGEYWNKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLEN HNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSW WLIRLIQLVVSSITTVWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKI VQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKRFLIFLLIL LPLLLLSGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFES LRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV CG3287-RC transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAM70833 owner campbell Gadfly CG3287-RC FlyBase FBtr0086158 translate offset 141704 141706 CG3287:6 exon 140797 141858 CG3287:3 exon 142556 142891 CG3287:4 exon 142948 143528 CG3287:7 exon 143812 144597 ATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACG GTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATAT CCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTA CTAAGTATGTCACATATTTGCGGGCAAACTGCCGAAAGCACTGTGCGGAG TTTTTGTTTGTGTGCGTGCGTGCCTCATTTTTACATTCACGTACATACAT ATGTACATATATGTACGCTATGACGCAGCTGTGGAAAACTTGTTTGGGTT TCCATTTCACCGAATCACGGAATCAACGAATATTTGCGCCTGTGCTGCGA ACTCATTTTGGGCAGTAAGCCATTGTATTGATTATCGCGCGTTGTTTGTG GATGGCGTGGTCCGCCGGAGCACCCTGTAGCGTCTACATCCCTACCCCGC TCCCTGGAGTCCGATATCTGTGCGCGAAAGGCCGGGCGGGCGTCGTTTTC GGCTATGTGGCCCAACACCAATGGATCCCCACGGTCACTGGCAGCAATTC GCGATCCGAAATGCTCCGCCCTATTTTTAGACGCGGTCTTTGCGGCCTGC CTACTTACCTACCTCCCCAATGCATTCTAATTAAAAACCGGGCACTGCGC TCATTTCCACACGCATTGCATTGCATAATGCGGCATTAATGTGGCGGGGA AAGCTCGCTTCGGAAAGCACTCGAGCATTGAAGTGAAGAGACCGAATGTT TTCCAGCTGCCCAATTGTAAACAACCCACGCCTAGCACGCACACACACGC ACACGCACACACACACAGACTGGTTTTAATGTTTACTCCAAATAAATCGT TGCCCATGTTAATTATTTGTGTCTTCGCAGGGCCCGAGCACTGGAGGGAA TCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGC GTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAG CACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGC CCCCAATGTGCAAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCA GTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCG AGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGC CACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACAC CGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCC CAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAG CGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAACA AAACTCCCAAGACGGACTATACCTACTCAGAACTGTCCCCTCACCGACGC CAGTTGGCGCCAGGAATTGTGGCCATGCCCAATATGTCCAGAAAGAGCCT AGAGAACCATAACGATCGAGTCAACTACATGGTCCAGCAGAACCCTGCGC AAGAGGAGTTCATCCGCCGCCGCTACCAGTCCAAGTATACCCAGCAGGTT AACTATGACTCCGCAGATGAACTGGACGCCACATTTGGGCAGCAAAAGCA GAGCTGGTGGCTTATCCGCCTCATCCAACTGGTTGTTAGCAGCATTACCA CCGTGTGGAGTCGGGTGACCAATCTCTCGGCCACGGAGACGACTGCCTAT CAAAACTACCACGCTAAGCGCCAGCAGAGTCAACAAGTTGGACTTTGGTG GAAAATAGTACAGACCATCGGAGGAGGACTTGCAAGTTTGCTGCGCTACC TGTATGTTTTCATCGGATCGGTGCTGAGTTTGGACACGTGGTTGCTGCGA TCCTCGGATGCGGAAAACAAGTCGAAAAAGCGCTTCCTCATATTTCTGCT GATTTTGTTGCCCTTGCTGCTGCTGTCGGGTCTGTTCTATTACATACACC CCAATGAAACTTTCCCACCCAAATCCCTGTCCGAATACACATTCACCCTA CCTGAGTTGCCCAAAATCGATGTGAAAGACTACCTGAACCAGGAGCAGTT CGAATCGCTACGCTCTCAGGCCGCCGAGCATGCGGTCCGCGTTCGCGATT GGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTC AACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCG TGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGA TCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTC TTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCC GTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCG TCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTA ACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGG ATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTC ATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAAC TAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTT TGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAA ACATCAAGTACAAAG MSENTYQIETRRRSRSKTPFLRSSCDHENCEHAGEEGHVHHLKRKSAAPN VQTIIEEHIVESSISKKTRAKAFAQLTSDYSSDDMTPDAKRKQNSITATV TSILTKRSGGATSTPRNRSQLETTQNTLNSAQEKLNQSNGNLSSGNVSDY LAYIEYRDAGEYWNKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLEN HNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSW WLIRLIQLVVSSITTVWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKI VQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKRFLIFLLIL LPLLLLSGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFES LRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV CG3194 CG3194 gene CG3194 cyto_range 42C3-42C3 comment DGC clone SD14112 appears problematic: incomplete CDS::DATE:2002-03-11 14:08:41::TS:1015873721000 symbol CG3194 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0033087 FlyBase FBan0003194 CG3194-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn owner pavel protein_id AAM70806 Gadfly CG3194-RA FlyBase FBtr0086145 translate offset 2816 2814 CG3194:1 exon 3120 2718 CG3194:2 exon 2661 1283 CG3194:3 exon 1173 807 CTGTATCGCAGTTTCTGTGTTTTCGCAGTGTTCGCCCATTAAAGCGAGAA GAGCAGCGCAAATCTAAGCAAAATATGCTTAGTGAGAACTGGATGCACTT GAAATATCAACTTTGGATGGCCCTGGACTGAACTCAGAGGGCTACAGGCT CGGCAGGTGGAATTTTAGACAGAGACAGTGAAAGAGACGTACGCGTACTG GTGCACCATTATCATCGTCAGCAATGCATCTGCCAGATGAATGCAGTTTT AAATTTAGAGCATGACTCACCTAGAAGCCAGTTAGAGAGTTCGCCCCCAA CCGAATGTCCAAATATCTAAGCAGTCAGAGAGATGCCCTTTCCGCACCCG CGCTTCCAGTAAGCAGGGAAAACCGGGAGCCACCTAAATTCCAAGGGGTA AAGCAACGCGAGCCACTGGTCTTTTTCATCATGCGACTGAACCTAAAAGC CGTGCTGCTTGTCCTCACAGTGGCTGTGGTGGTAATCACTCTGGGCGTGT ATATGCGCTGCGCCGCCTTCTCCTTTTCGCCGGACTTTGTGCGTCCTCTG GACCGGTCCGCAAGGCAGTCCTCCAGCGGAGGAGAAGCTACAGCGCTGCA CGACATTGAGTGCTCCATTAACCAGGAGTACACCGTGCACTGCAAGCGAG ACGAGAACGCCAACGAGGTTTACGTTCCGTTTTCCTTCCTGCGTAACTAC TTCGACGTCAGTGGAGCAGTTTCCACCAACAGCAATGAGGTGGCCAAGTT CAACTGGGTGCACAGCACAGCCAAAGTTAACCTTCCCAGGGGAAAGTACG ATGCGCGCGGCGTCTATATGTACTTTGAGAACTACAACGTGGAAGTGCGC GACCGGGTAAAGTGCATCAGTGCCGCGGAGGGCGTTCCAGTGAGCACGCA ATGGGAGAAGCGTGGGTACTTTTACCCCACACAAATTGCCCAGTTCGCGT TGTCGCACTACAGCAAGAACCTCACAGAGCCGGCACCCAGGGTTCGCGTG TTGGAGGACGGCGACGGGAACCAGATGGAATGGAGTACGCCCAAGACCAG CAACATGACCCGCATCTGGCACCACAAGTTTAACACCAGTGTTGTCCAGT TCGAGACGGCACCTGGTTACGAAGGCGTCATCAGCATTGCTCTAAACCAG ACATTGGATCTTCTGCTCAGCGTTGATCTGCTCCTGGTAACCAATAGCAG TAGTCTCATGATTACCGTTCAGAATCGGGACACCCGTCACAACTACAGCC TGCACTACATACCCGCAGATCTGCTGCTGAGCGTGCAGGATACAAACATC TACTACGGTCTGGGAGGCTCGGCACTGAACAAGTGGCGCCACATCACTCG AGACCTGCACATTGACCTTCAAAAGGGCATCATGGGTGACAAACGCTCGC CGCTAAAGATACGGCGCTCCGATCTGGAGGTAATATCTATTGGCTTTCTG GGCCTTGGCTTCTTCGACAATATCACCTTGTCCACCAGTGACCATCTGGC TCACTTCTACGACGCGGCTGAGTGGTTCGTCCACAACCAGGACCCCAAGA CGGGTGGCTGGACCAATCCTGTGCGTCGCAGCCTCAACGGCTTTGCCGAA TTGCGTCCGGGGTGGATATCAGCCATGGGCCAGGGACACGCTATTTCAGT GCTGGCACGAGCCTACTGGCACTCCGGCGGGGATGAACGCTACCTTCGAG CGGCCGCAGCCGGACTGCAGCCTTATAGGGTATACTCGCGCGATGGCGGC GTTCTGGCGCAGTTCATGGACAAGTTCTACTGGTACGAGGAGTACCCCAC CACGCCACCCTCTTATGTGCTAAACGGCTTTATCTATTCACTGCTGGGTC TCTACGATCTCAACAGCACTGCCCCGGGAAAAATCGCCCGCGAGGCTGGA AAGCTTTTCGCGCAGGGCATGCACTCCCTTAAAAAGATGCTGTTGCTATT TGACACTGGCTCCGGCACCAGCTACGACCTGCGCCATCTGAGCCTGGGCG TAGCTCCTAATCTGGCGCGCTGGGACTACCATGCAACGCACGTGAACCAG TTACTTCTGTTAGCCACCATCGACAGCGATCCATTAATTGCACAAACTGC GGAGCGCTGGAAGGGCTATATGTTTGGTCGTCGGGCCAAGCACAACTGA MSKYLSSQRDALSAPALPVSRENREPPKFQGVKQREPLVFFIMRLNLKAV LLVLTVAVVVITLGVYMRCAAFSFSPDFVRPLDRSARQSSSGGEATALHD IECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFN WVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQW EKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLEDGDGNQMEWSTPKTSN MTRIWHHKFNTSVVQFETAPGYEGVISIALNQTLDLLLSVDLLLVTNSSS LMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRD LHIDLQKGIMGDKRSPLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAH FYDAAEWFVHNQDPKTGGWTNPVRRSLNGFAELRPGWISAMGQGHAISVL ARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYWYEEYPTT PPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFD TGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAE RWKGYMFGRRAKHN CG18584 CG18584 gene CG18584 cyto_range 42D1-42D1 gbunit AE003790 sp_status Not in SwissProt real (computational) symbol CG18584 FlyBase FBgn0033107 FlyBase FBan0018584 CG18584-RA transcript protein_id AAF57400 owner campbell sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) Gadfly CG18584-RA FlyBase FBtr0086159 translate offset 144969 144971 CG18584:1 exon 144835 146345 CG18584:2 exon 146400 146504 CG18584:3 exon 146568 146780 GATGGTTGCTCTTGCAGGAGGATCAACGTAGTGCTTACGTTCAGCGTGCG GAAGCACTGTTGCCGCTGCCACTATCTATTTTCGGCTCCCTACGTAGTCG ATTTTCAAATGCTGGAGCCACCTTGAAAAGTTGGATGGAAGTGCCCACCG TCAGGAGTCCCCAGCGGGAAGCCGAGGCCATTAAGGTAAACATGGCCAGC ATTGAACAGAACATCCAGAAAGCCTTGACTGCCGAGGAATACGAAAATAT CTTAAACCATGTAAACAGCTACGTGCAGCAGTTGGTCGAGCTGAAAATGC AGCAGCATTCCAAGGAGCTCGCACCGCAACAGATTGAACTCTTTGTTAAG CTGATGAAGGAAAACCTCAAGCAGATTATGTACAAAACGGAGCTAAGCGA AAAGGATTTGTCTGATCTGGCCATAAAACTGAAACTGGAGCTGCAAAGCT CAGGCGGTTGGCAAGATGGAGCGAAACTATCACAAGCTAACTTAGAGGAG ATAACCAAGCTAATTAAAGCAGAGGTTCACCTCCACGAATCGCACTACAC CATTCAATTGGACAGGATAGACTTTGCATCCCTGCTGGAGCGTATTCTTG CTGCGCCAGCATTGGCAGACTTTGTAGATGCTCGAATAAGTCTTCGGGTG GGAGAGCTCGAGCCAAAGGAGAGTTCCGGTTCCTCAGATGCAGAAGTCCA AATTGAGCGTCTGAACAGGGAAATCGCCTTCATTAAGTTGGCTCTCTCTG ACAAGCAAGCGGAGAACGCCGATCTGCACCAATCAATCAGCAATCTGAAG CTCGGCCAAGAGGATTTGCTGGAACGCATACAGCAGCACGAACTTTCCCA GGATAGGCGCTTCCACGGGTTGCTGGCTGAAATAGAAAACAAACTGTCTG CGCTTAACGACTCGCAGTTTGCTCTTCTCAACAAGCAGATCAAGCTATCC CTTGTCGAAATTCTGGGCTTTAAGCAATCCACCGCTGGCGGTTCCGCTGG CCAATTGGATGACTTCGATCTGCAGACCTGGGTACGCAGCATGTTTGTGG CCAAGGACTACCTGGAGCAGCAGCTGCTAGAGCTGAACAAGCGCACCAAT AACAACATTCGCGACGAGATTGAGCGTTCGAGCATCCTGCTGATGAGCGA CATTAGCCAACGACTCAAACGGGAGATTCTTCTGGTTGTGGAGGCCAAGC ATAACGAGAGCACCAAAGCGTTGAAGGGCCATATCCGCGAAGAGGAGGTG CGCCAGATAGTCAAGACGGTGCTAGCTATTTACGATGCCGACAAGACGGG CCTGGTGGACTTCGCCCTGGAGTCGGCGGGCGGCCAAATCCTTTCCACGC GTTGCACTGAGAGCTACCAGACAAAGTCAGCCCAGATATCGGTGTTTGGA ATTCCACTCTGGTATCCCACCAACACGCCGCGGGTCGCCATTTCACCCAA TGTGCAGCCAGGGGAATGCTGGGCATTCCAAGGGTTTCCCGGATTTCTAG GCAAGTCGCGGCTCAACTCGTTGGTGTACGTCACTGGATTCACCCTAGAG CACATACCGAAGAGTCTATCCCCCACAGGAAGAATAGAATCAGCTCCTCG CAACTTCACTGTCTGGGGCTTGGAGCAGGAGAAGGACCAGGAACCCGTAT TGTTCGGCGATTACCAGTTTGAGGACAATGGTGCTTCCCTCCAGTACTTT GCCGTTCAAAACCTGGACATCAAACGGCCGTACGAGATCGTCGAACTGCG GATCGAGACGAACCATGGCCATCCCACCTATACATGCCTCTACCGGTTTC GCGTGCACGGCAAGCCGCCGGCCACATAA MEVPTVRSPQREAEAIKVNMASIEQNIQKALTAEEYENILNHVNSYVQQL VELKMQQHSKELAPQQIELFVKLMKENLKQIMYKTELSEKDLSDLAIKLK LELQSSGGWQDGAKLSQANLEEITKLIKAEVHLHESHYTIQLDRIDFASL LERILAAPALADFVDARISLRVGELEPKESSGSSDAEVQIERLNREIAFI KLALSDKQAENADLHQSISNLKLGQEDLLERIQQHELSQDRRFHGLLAEI ENKLSALNDSQFALLNKQIKLSLVEILGFKQSTAGGSAGQLDDFDLQTWV RSMFVAKDYLEQQLLELNKRTNNNIRDEIERSSILLMSDISQRLKREILL VVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGG QILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECWAFQG FPGFLGKSRLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVWGLEQEK DQEPVLFGDYQFEDNGASLQYFAVQNLDIKRPYEIVELRIETNHGHPTYT CLYRFRVHGKPPAT CG17002 CG17002 gene CG17002 cyto_range 42E4-42E4 symbol CG17002 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBan0017002 FlyBase FBgn0033122 GO GO:0006605 protein targeting CG17002-RB transcript protein_id AAF57419 status not done sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) owner crosby Gadfly CG17002-RB FlyBase FBtr0086170 translate offset 316120 316122 CG17002:1 exon 315503 316551 CG17002:2 exon 316609 316708 CG17002:3 exon 317413 317463 CG17002:4 exon 317556 318040 CG17002:5 exon 318346 318699 GCACGATACCTCCAATGAGAGATGCCATATCGATGCTTACGCATTTTATT AACATCGATAGACATTTCTAGAATGTCTAGACTTTAATGCTTGGATTTTC CAAAAACTATAATCTGTTTCCAAAAAGTTATCGATAAGTATCGATCAGTG TTGAAACTATTTGTATTTTATATTAAATTCTGGGGTGTGACTAGTAATAT TAGGAATATAAGCTTTAAAGAAAAAATCGAATTCTTTATAAGTGATTTAG TTCGAACGTTAACTTAAGATTTGCCACCACAATCGGAAAGTAGCTATTTT CTAGCTAGCTTTGCCCATTAATCGATTGGTGGCAACACTGGTCGGCACAT CCCACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAA CGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACG CCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGC CACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAAC AGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAA CTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAAC GCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGC ACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCG AGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAG CGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACT GGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCC AACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAG GAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTT CCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAGC TCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCG AGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGAA ACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACA AAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTC GCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCAT CTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCA GCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCG CAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCAT TTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGG CCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATC GAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACA CCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCAT TGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGTTTCCTCCACAGAAT CCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGG ATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTG GCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGT CAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCC CTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAG ACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATA AAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAA MPPASAVNNSNAAAQAAKAERAEKLRGALKGFIVADRQRRQEEFEAQCEE QRLRREREEVERQNQVALDDTRGQITRLDEQLADLHSQKHQLTVQLKKVL NEDETRKKLAKENELFAIQQAAASSPVFLPPLRLQHQHHTLMQKLPSGGQ PGKRGRSPSPPSQQQAYYKSAASYAQQKHDDYRRAADYARLSWNKTAAQY PGTGTVFYQTVAPPPTTQHQADARLQSIYNYNLPLRQAYHVDLPSATVSK PPDSQSPKAPSQSQPMQVLHINLDQPTISQADLVAQAGGSLSVKASQPHV TMEKLPDRYHIEVKHDGQPPSHVPPPPHLLPEGVIFKPLLNELSLHSNVL QISSSQFPPQNPKTAGSITQGYAPGRGGSAHEQQLARQQLAMLPGQPGAP SGSGSAQPPPGQQMHYTRRLY CG15236 CG15236 gene CG15236 cyto_range 42D3-42D3 symbol CG15236 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0033108 FlyBase FBan0015236 CG15236-RB transcript owner crosby sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) protein_id AAM70834 Gadfly CG15236-RB FlyBase FBtr0086160 translate offset 159691 159693 CG15236:1 exon 158133 158442 CG15236:2 exon 159336 159823 CG15236:3 exon 162405 162706 CG15236:4 exon 163390 163462 CG15236:5 exon 163530 164701 CG15236:6 exon 165268 165844 CG15236:7 exon 166302 168135 AACAGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTC AGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCG ATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGT AATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAA CTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATC ACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCG AAAATTAAACCAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGC CATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAG CCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGA GCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAA GGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCG GTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGG GCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGC AGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCT TCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGT CCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGGCT TTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGA CACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGA TGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGAC AACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTC CCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCA GGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGACAGAAG GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGAT CTTCTGCTGGTGGGAGAAGTGCGATAAGGCCAATGTAAACAAGGCGAGGA CGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGAC GGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCA CGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAG TTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTAC GAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTA TAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAA GCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACAC GAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACA GCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAA CGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCG TCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTC CAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACG ACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAG CACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACA GCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGG CATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAG GGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGA GGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCA GGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGG GCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGAC AACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGA CGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACG CTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGATCTTGG ACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCT TCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCC ATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGA TGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCA TCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAAC GATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACT AACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATG GCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAG GTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAG CAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTG TCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCA GGGCGTATGTGCAATGTTTTGGGCAAACTGTATAAAATTGGTGACATTCT GCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGA CTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCG CTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTT TGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTG GAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGT GATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATA GAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATT CGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCAT GTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTG TAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCT ATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAA GCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGAAGAAGAAGGAAATCG CAGTTGGCTCACAGTTTAGACTTTAAGCTGAATGTTTATGCATTTTATAA GAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGC AGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTA TATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAA CCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGAT TATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAA CGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAA TCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAAC GTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTG CATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATC TATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACA AACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTT AAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTG CGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGC ATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAG GGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATT TTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGA ACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAA TATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTAT TGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAAT TCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGT ATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCAC ACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTG AAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGG CATTTC MPSVKSAESEILLGIIRSDSMTSGNSLRSCLLLATILGLLCRTKALPFEY LDEHEDFNYDLDTAQSQAKYDARLLSQQMLSDAELQRQGLSDGQDNALDG DSAAAQGTGAGSHLDAVSSVHDDLEPHSRAAACFTNGHKYTHGQKVPRLD ACEVCLCMDGEIFCWWEKCDKANVNKARTAGDNAGLGLGVEDDGDGNGNG DGDGDYSDPYRHESTTGKSTKVHKAARKVGKRHKHRKNQKNFNDYEVYHS QREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNYNIIKQHKHEQQQQ QLKIPQQLHQQQQQQNVAALGVNHAAKATHYQQAASTPLPTPPPPSEHPQ HSHHPHQQAHSSSKILNFPENLPALLYYDYKTEEHEHHQHQHHQQHLLHE KQRLLQQQQQQQQQQQQMVQQEALARQKASESASEPESRAGGTAEGGVEP SGDLAADKNSDEAETDSDILPEPPTKQPRAAATQWPTPSSNSSARALMTS NVASTSTAATTTTTKTSKTKTTTATTGRTTTTTTATGTNEMVTSTLSGME KSGATVAATDLGQMQPDRRGPDAERDDAFHRWLTSTELNADNTNSMDDSL ERETPASTIIDDVGTANKSDRSIGGIGGIGKDNGNDAVFFRSSYNDYSSE FNGSVVNIDITLTAVDVHPRRQTDLIANGNRTSGANDNGNSCSSQVGAAG TTMNPVAVSTSSSTRSSNNQDQPQQSPVVPPYTLTTIITTAPMAPGRMCN VLGKLYKIGDILPQDTGNCLQCICTDAVTPDEMPSVTCSPHNCPPLVLPD LFDATGY CG15236-RA transcript protein_id AAF57401 owner crosby sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) Gadfly CG15236-RA FlyBase FBtr0086161 translate offset 159691 159693 CG15236:8 exon 158183 158280 CG15236:9 exon 159256 159823 CG15236:3 exon 162405 162706 CG15236:4 exon 163390 163462 CG15236:5 exon 163530 164701 CG15236:6 exon 165268 165844 CG15236:7 exon 166302 168135 AGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCG ATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATTT GAGTTCCATTTACATTCAGCCTCCATAAATTGGCATGGCTGCGAAAATCG TTGCCTACTTAAGAGGGCCCACATTTAGCAGGCGCAGCACCGGCATTGTG AATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACT CGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTA AACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGG CGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGT CGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGT GTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAA AATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCGTGAAATC CGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGCATGACGA GCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCTGGGATTA CTCTGCCGGACGAAGGCTTTGCCCTTTGAGTATTTAGACGAGCACGAGGA CTTCAACTACGACCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCC GTCTGCTCTCGCAGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGG CTGAGCGACGGCCAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCA GGGGACTGGAGCAGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACG ACCTGGAGCCGCACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAG TACACGCACGGACAGAAGGTTCCGCGCCTGGATGCCTGCGAGGTGTGTCT CTGCATGGACGGCGAGATCTTCTGCTGGTGGGAGAAGTGCGATAAGGCCA ATGTAAACAAGGCGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGT GTCGAGGACGACGGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTA TTCAGATCCATATCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGC ATAAAGCGGCGAGGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAA AAGAATTTTAATGACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCA GCAGCAGCAGTCGGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGA TGCAGCAAAAACACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATA ATCAAGCAACACAAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCA GCAGCTACATCAGCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTA ATCACGCAGCAAAGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTG CCAACTCCCCCACCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACA CCAACAGGCGCACTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGC CAGCCCTGCTCTACTACGACTACAAGACGGAGGAGCACGAGCACCACCAG CACCAGCACCACCAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCA GCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGG CGTTGGCGCGACAAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGG GCCGGAGGCACAGCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGC TGATAAAAACTCTGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGC CGCCTACAAAGCAGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCT AGTAACAGCTCGGCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATC CACGGCTGCGACAACGACAACGACAAAGACATCGAAAACGAAAACGACAA CGGCGACAACGGGAAGGACGACGACGACGACAACGGCGACAGGCACAAAT GAAATGGTGACAAGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGT TGCAGCCACAGATCTTGGACAGATGCAACCCGATCGCCGTGGACCAGACG CGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCTGAAT GCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGCCGGC ATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGGAGCA TCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGTCTTC TTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCGTTGT CAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGCCAAA CGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAATGGC AACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACCCAGT GGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGATCAGC CTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTATAACA ACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGCAAACTGTA TAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTGCCTGCAGTGCA TTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCGTCACCTGCAGT CCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTCGATGCGACTGG TTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAACGGCAGGTGGCA AGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGCTGTGGGAGTTT TTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAAAGCCACAACTG CAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAACGAACGAATCG AATCTAATCGAATCGATTCGAATCACACTCACAACAACTGCACTACAGAA CTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCAACTCAATATGA ATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAGTGCCCCAAGCA CTCTCTAAAACGAAACCTATCAGCAGACATATATTATATTCGTACCAAAC TATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGGGGAATGAATAA AGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGACTTTAAGCTGAA TGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTCCGCAACAAAAA TCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTTATAGATGTACC AAACAGAAGTATATAGTATATACAAACATATACGAGTATCTACTCTATAT CTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAGTTCGGTGGGAT CAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAACCGTGTAGAGT TTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACGAGTAACTTATA CAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAACAATGACAAATA ATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATATTAAAAGCAAA CAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCGCTTCTTTGGAA ATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTTAGGAGCAATGT ATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAAGACACCATATC GAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAAC TTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTT TCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAA CATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAG TAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTT TTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCA TGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACA AACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTC GAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATAC AAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTA CTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTT AAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAA ACCGAAACCCAACTAAGGCATTTC MPSVKSAESEILLGIIRSDSMTSGNSLRSCLLLATILGLLCRTKALPFEY LDEHEDFNYDLDTAQSQAKYDARLLSQQMLSDAELQRQGLSDGQDNALDG DSAAAQGTGAGSHLDAVSSVHDDLEPHSRAAACFTNGHKYTHGQKVPRLD ACEVCLCMDGEIFCWWEKCDKANVNKARTAGDNAGLGLGVEDDGDGNGNG DGDGDYSDPYRHESTTGKSTKVHKAARKVGKRHKHRKNQKNFNDYEVYHS QREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNYNIIKQHKHEQQQQ QLKIPQQLHQQQQQQNVAALGVNHAAKATHYQQAASTPLPTPPPPSEHPQ HSHHPHQQAHSSSKILNFPENLPALLYYDYKTEEHEHHQHQHHQQHLLHE KQRLLQQQQQQQQQQQQMVQQEALARQKASESASEPESRAGGTAEGGVEP SGDLAADKNSDEAETDSDILPEPPTKQPRAAATQWPTPSSNSSARALMTS NVASTSTAATTTTTKTSKTKTTTATTGRTTTTTTATGTNEMVTSTLSGME KSGATVAATDLGQMQPDRRGPDAERDDAFHRWLTSTELNADNTNSMDDSL ERETPASTIIDDVGTANKSDRSIGGIGGIGKDNGNDAVFFRSSYNDYSSE FNGSVVNIDITLTAVDVHPRRQTDLIANGNRTSGANDNGNSCSSQVGAAG TTMNPVAVSTSSSTRSSNNQDQPQQSPVVPPYTLTTIITTAPMAPGRMCN VLGKLYKIGDILPQDTGNCLQCICTDAVTPDEMPSVTCSPHNCPPLVLPD LFDATGY Tsp42Ea CG18817 gene Tsp42Ea cyto_range 42E4-42E5 comment Flag Cambridge: gene split/merge (internal view only).::DATE:2002-02-13 10:59:57::TS:1013615997000 encoded_symbol CG18742 comment EST evidence indicates that 5' UTR overlaps that of neighboring gene on the same strand.::DATE:2003-03-14 17:40:41::TS:1047681641000 symbol Tsp42Ea sp_status Perfect match to SwissProt real (computational) gbunit AE003790 GO GO:16021 FlyBase FBgn0029508 FlyBase FBan0018817 FlyBase FBgn0042099 FlyBase FBgn0042140 FlyBase FBgn0033123 FlyBase FBgn0064940 GO GO:0016021 integral to membrane Tsp42Ea-RA transcript sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAG22311 owner sima Gadfly CG18817-RA FlyBase FBtr0086171 translate offset 324200 324202 Tsp42Ea:1 exon 322451 322552 Tsp42Ea:2 exon 324148 324259 Tsp42Ea:3 exon 332740 332931 Tsp42Ea:4 exon 332995 333156 Tsp42Ea:5 exon 333223 333417 Tsp42Ea:6 exon 333680 334036 CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGG CAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTA ATTTGCTCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTG CTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAAC CCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGA TTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCC ATGACGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTT GGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCG ACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATG GACGCGATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGA CTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACA ACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTT GAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCAT CGCCGCCATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACA GCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAA GGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCA ATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATC TCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGAT CACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGT TTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAA ATTTATTTACAATTTACGAA MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY Tsp42Ea-RB transcript owner crosby sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAG22210 Gadfly CG18817-RB FlyBase FBtr0086172 translate offset 324200 324202 Tsp42Ea:1 exon 322451 322552 Tsp42Ea:2 exon 324148 324259 Tsp42Ea:7 exon 326451 326642 Tsp42Ea:8 exon 326706 326867 Tsp42Ea:9 exon 326934 327128 Tsp42Ea:10 exon 327392 327750 CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGG CAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTA ATTTGCTCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTG CTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAAC CCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGA TTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCC ATGACGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTT GGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCG ACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATG GACGCGATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGA CTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACA ACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTT GAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCAT CGCCGCCATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACA GCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAA GGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCA ATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATC TCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGAT CACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGT TTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAA ATTTATTTACAATTTACGAAAA MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY Tsp42Ea-RC transcript owner crosby protein_id AAF57420 sp_comment Perfect match to REAL SP with corresponding FBgn Gadfly CG18817-RC FlyBase FBtr0086173 translate offset 324200 324202 Tsp42Ea:1 exon 322451 322552 Tsp42Ea:11 exon 324154 324259 Tsp42Ea:7 exon 326451 326642 Tsp42Ea:8 exon 326706 326867 Tsp42Ea:9 exon 326934 327128 Tsp42Ea:10 exon 327392 327750 CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAAT GAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGC TCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTC AGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCA GGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCT GGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACG TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGAT CTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGG TCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCG ATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGC CTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCC GCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTC TGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGC CATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTC GGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTT GCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTA CGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGC GTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTT TGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACT GTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTAT TTACAATTTACGAAAA MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY CG9455 CG9455 gene CG9455 cyto_range 42D4-42D4 symbol CG9455 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBan0009455 FlyBase FBgn0033113 GO GO:0004867 serine protease inhibitor activity CG9455-RA transcript protein_id AAF57407 comment Shares UTR: 3' UTR sequences shared with downstream gene::DATE:2002-12-10 13:44:47::TS:1039545887000 owner sima comment Shares CDS: 3' CDS shared with downstream gene::DATE:2002-12-10 13:45:25::TS:1039545925000 sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) comment Evidence indicates that 3' UTR overlaps 5' UTR, translation start, and first intron of downstream gene; extends to coordinate AE003790: 943750 (based upon 3' extent of AT24862 ).::DATE:2002-02-12 03:18:06::TS:1013501886000 Gadfly CG9455-RA FlyBase FBtr0086162 translate offset 211538 211540 CG9455:1 exon 211491 212413 CG9455:2 exon 212484 212625 CG9455:3 exon 212695 213186 TATTTAAAAATATAAATTAAAACATATATTTTTTTGCCCAGATCGAGATG AGCGAACCCCAAGAAGGCAGAAATCAGTTTGCGCGAAATCTGATAGATGT CATTACCAAAGATGCCCTGCAACAGAGCAAAGACCCCCACATAAATACGG TTTTCTCTCCAGCATCCGTCCAAAGTGCATTGACCTTGGCATTTATGGGG GCTTCCGGATCTACAGCAGAGGAGCTAAGGAATGGGCTTCAGCTAGGACC AGGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGA GCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTG TACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGT GGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGG GAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAG ATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCT GCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGC CAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTG CAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCC ACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTC ACATGCTAATTCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAG CAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTT GCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGG ACCTCAAGCAGGTACTTAATCAGCTGGGTATTACGGAAGTCTTCAGCGAT AAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTC GGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGG CAGCAGCAGTCAGTTTCATGAAGATAGTACCCATGATGCTCAACATGAAC AAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCC GCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTG GATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTAC AATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCC ACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCA GTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATA TGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGG GGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGAT CGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAA CTTATGA MSEPQEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFM GASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNR LYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEH KITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTH VQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQEL EQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQLGITEVFS DKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVSFMKIVPMMLNM NKKLFKADHPFVFYIRNPQAVFFAGRFSNPKSGSGSGEEGLSREGFDANM YNV Spn1 CG9456 gene Spn1 cyto_range 42D4-42D4 symbol Spn1 sp_status Curator examined, accepted gbunit AE003790 FlyBase FBan0009456 FlyBase FBgn0028988 FlyBase FBgn0033114 GO GO:0004867 serine protease inhibitor activity Spn1-RA transcript comment Shares UTR: 5' UTR sequences shared with upstream gene::DATE:2002-12-10 13:47:38::TS:1039546058000 protein_id AAF57408 owner sima sp_comment Imperfect match to REAL SP with corresponding FBgn comment Evidence indicates that 5' UTR overlaps 3' UTR of upstream gene (based upon extent of AJ251744).::DATE:2002-03-08 03:17:51::TS:1015575471000 Gadfly CG9456-RA FlyBase FBtr0086163 translate offset 213105 213107 Spn1:1 exon 212778 213117 Spn1:2 exon 213389 214233 Spn1:3 exon 214292 214433 Spn1:4 exon 214504 214648 CCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATC TGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGT ACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATC CCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCT CAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATA TATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTC GGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGCATTTTCCT GTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTAC TTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATA GAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAA GGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGG CAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGA CCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCT GAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGG AGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAG TGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGG CAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTA AGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACC TTCCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAAT GGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCG AGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGA GAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAG GCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCG AATTTCGTGATGAACTCAAAGAGACCTTAGAGAAGCTGGGCATCCGAGAG CTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGG CGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGG AGGGAGCGGAGGCCGCAGGTGCCACATCTGTGGCCGTCACAAATCGAGCG GGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCG CGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAA ATAAAAACAATATTTAAATTTT MYYLCIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFM GAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRI YVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGK IKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSV PVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALE EKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKLGIRELFTDKSDLS GLFADKSGGKVSQVSHKAFLEVNEEGAEAAGATSVAVTNRAGFSTFLMAD HPFAFVIRDANTIYFQGRVVSP CG30157 CG30157 gene CG30157 cyto_range 42E1-42E1 gbunit AE003790 sp_status Not in SwissProt real (computational) symbol CG30157 FlyBase FBgn0050157 FlyBase FBan0030157 GO GO:0005554 molecular_function unknown GO GO:0008372 cellular_component unknown GO GO:0000004 biological_process unknown CG30157-RA transcript owner crosby protein_id AAM70838 sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CG30157-RA FlyBase FBtr0086186 translate offset 304644 304642 CG30157:1 exon 304644 304066 CG30157:2 exon 304003 303878 ATGGCGGCGGAAAAGTGTGCAGAAGAGTTTGGGGACTCCTCCGCGGCGTC CTTGAAAATTGTACCAAAGGACTATGCATATCCACTTCTAGAGGATCCGC AAGGCGCGCTGACCACGCCCACTGAAGGCGGGCGGACGCTAGTTACCCGC GGTGGCTTTAACTACTTCCACTACGGATGCGATGGCCACCAGGATGCTGG CTGGGGTTGTGGCTACCGCACCCTGCAATCGGCCATTTCCTGGATCCAAC GTCGACAGGGGTCGAGCGGTCATGTTCCTTCCATCCGGGAGATTCAGCAG ATCCTGGTGGCCATCGGCGACAAGGGTCCAGAGTTCGTGGGCTCGCGCGA CTGGATCGGAACGCTCGAGGAGTTCTACGTGATCGATGTGCTGCACCAGG TGCCGTGCAAGATTCTTCACGCCAAGGAGCTTAGCTCGGACGAGATCCTC GGCGAGCTTCGGAGCTATTTTGAGAAGTACCAAGGCTTCGTCGCCATGGG CGGTCTGAGTGACACCGCCTCCAAGGCTATTACCGGCTACCATTGCAGTG CACGCGGTCGCATCTTCCTGCAGGTGGTGGATCCGCATTTCGTAGGCGTG CCCAGCTCCCGGCAGCACTTAATCGATCTGGGCTACGTTCGTTGGGTGCC CGTTGACGAGTTCGCCGGCAGCACGTACAACCTCTGCCTCATCTTGCAGC CGTAG MAAEKCAEEFGDSSAASLKIVPKDYAYPLLEDPQGALTTPTEGGRTLVTR GGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQ ILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSDEIL GELRSYFEKYQGFVAMGGLSDTASKAITGYHCSARGRIFLQVVDPHFVGV PSSRQHLIDLGYVRWVPVDEFAGSTYNLCLILQP CR30303 CR30303 tRNA CR30303 cyto_range 42E1-42E1 gbunit AE003790 comment tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:37:00::TS:1019007420000 anticodon CTT sp_status Not in SwissProt real (computational) aminoacid Lys symbol CR30303 FlyBase FBgn0050303 FlyBase FBan0030303 CR30303-RA tRNA sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CR30303-RA FlyBase FBtr0086187 CR30303:1 exon 278980 278908 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG CG9460 CG9460 gene CG9460 cyto_range 42D4-42D4 symbol CG9460 sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBan0009460 FlyBase FBgn0033115 GO GO:0004867 serine protease inhibitor activity CG9460-RA transcript protein_id AAF57409 sp_comment Perfect match to HYPO SP record with corresponding FBgn owner crosby Gadfly CG9460-RA FlyBase FBtr0086164 translate offset 216193 216195 CG9460:1 exon 216180 216199 CG9460:2 exon 216289 217223 CG9460:3 exon 217630 217771 CG9460:4 exon 217836 218041 AGTTTTCCCAATCATGTCAGTCAAGGCCACGTGTTCACTTCTGCTGCTCC AGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCC GCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTC CCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCT TGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAA CTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATT GGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGG ACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTC AAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGC TGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTA ATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCT CCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTA CTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCA GCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCC CAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGT CGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGC CTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATA GACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCA GCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCG AGGAGTTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGC CTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGC GATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTTTA TCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTC ATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTT ATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAAT ATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCA CAA MSVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGR NIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLL AKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENV NFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKAD WQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELP YTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKF KFEFDVPLQAALEELGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEV NEKGTTASGATFIKVSVESLTIGEEVFEFIADHPFFFAIKDAQNTLFLGH VSQL CR30302 CR30302 tRNA CR30302 cyto_range 42E1-42E1 sp_status Not in SwissProt real (computational) symbol CR30302 gbunit AE003790 comment tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:39:00::TS:1019007540000 anticodon CTT aminoacid Lys FlyBase FBgn0050302 FlyBase FBan0030302 CR30302-RA tRNA sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CR30302-RA FlyBase FBtr0086188 CR30302:1 exon 278131 278059 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG CR30301 CR30301 tRNA CR30301 cyto_range 42E1-42E1 aminoacid Lys symbol CR30301 gbunit AE003790 comment tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:40:00::TS:1019007600000 sp_status Not in SwissProt real (computational) anticodon CTT FlyBase FBgn0050301 FlyBase FBan0030301 CR30301-RA tRNA sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CR30301-RA FlyBase FBtr0086189 CR30301:1 exon 277585 277513 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG Tsp42Eb CG18816 gene Tsp42Eb cyto_range 42E4-42E4 sp_status Perfect match to SwissProt real (computational) symbol Tsp42Eb gbunit AE003790 GO GO:16021 FlyBase FBgn0042139 FlyBase FBan0018816 FlyBase FBgn0042086 GO GO:0016021 integral to membrane Tsp42Eb-RA transcript protein_id AAM70843 owner crosby sp_comment Perfect match to REAL SP with corresponding FBgn Gadfly CG18816-RA FlyBase FBtr0086176 translate offset 328705 328707 Tsp42Eb:4 exon 327940 328956 Tsp42Eb:2 exon 329021 329185 Tsp42Eb:3 exon 329258 329626 CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGA CTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCA TTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAAT GGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGA AGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGT ACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAA GCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATA AGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGC CCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGT TTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCC CAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATT CACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACG GAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAG TAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAAC ATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGA ACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCT GTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGG TGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGA GGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGT CACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACG CCTGCTGCACCACCATCTACGCCATCTGCATGCTGATTCTGTTCGGCCTG CAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTC CAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCC AGGGATACCCCATGGATGCCCTCCAGTTGGCCTTCTCTTGCTGTGGCAAC ACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAA GGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCT GCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACGGACCTGATTCGA TGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTC GTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCCGAAGTCAGATAC AATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAACACACGAATTCC TCACTCACTCACTCACCGTAAATAAACCAGAATAGGTTAAGCCCAATGAA A MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR Tsp42Eb-RB transcript owner crosby comment Only one EST supports this alternative transcript::DATE:2003-03-14 17:28:14::TS:1047680894000 sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAG22312 Gadfly CG18816-RB FlyBase FBtr0086177 translate offset 328705 328707 Tsp42Eb:1 exon 328628 328956 Tsp42Eb:2 exon 329021 329185 Tsp42Eb:3 exon 329258 329626 AGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAA CGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTT CAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCC TGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACG GCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGT CATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCA TTCGCGAGAACGCCTGCTGCACCACCATCTACGCCATCTGCATGCTGATT CTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGA CAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGA ACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCTTCTCT TGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTG CTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCC AGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACG GACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCAT CTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCC GAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAA CACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGTT AAGCCCAATGAAA MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR CR30300 CR30300 tRNA CR30300 cyto_range 42E1-42E1 anticodon CTT symbol CR30300 comment tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:40:00::TS:1019007600000 aminoacid Lys sp_status Not in SwissProt real (computational) gbunit AE003790 FlyBase FBgn0050300 FlyBase FBan0030300 CR30300-RA tRNA sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn Gadfly CR30300-RA FlyBase FBtr0086190 CR30300:1 exon 276655 276583 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG CG30158 CG30158 gene CG30158 cyto_range 42D4-42D6 comment Gene merge based on BLASTX and partial EST data; no experimental evidence for some internal splice sites.::DATE:2002-03-07 13:59:40::TS:1015527580000 encoded_symbol CG15243 comment Flag Cambridge: gene merge; based primarily upon protein homology to various Ras-related proteins; example: U97592 (AAB52874). DGC:RE28276 spans (not yet fully sequenced).::DATE:2002-02-12 16:57:56::TS:1013551076000 gbunit AE003790 sp_status Not in SwissProt real (computational) symbol CG30158 FlyBase FBgn0040676 FlyBase FBan0030158 FlyBase FBgn0040675 FlyBase FBgn0063683 FlyBase FBgn0050158 FlyBase FBgn0033116 GO GO:0005525 GTP binding CG30158-RA transcript protein_id AAF57410 owner crosby sp_comment Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) Gadfly CG30158-RA FlyBase FBtr0086165 translate offset 235971 235973 CG30158:1 exon 221538 221698 CG30158:2 exon 221755 221801 CG30158:3 exon 235638 236135 CG30158:4 exon 239708 239875 CG30158:5 exon 240527 240636 CG30158:6 exon 244408 244598 CG30158:7 exon 249810 249942 CG30158:8 exon 250043 252388 AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGA CTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGAT GCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGC TTTGTGTGCGGTTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTA TACGCCAGCTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCG GAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGG TGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTT GGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAAT GCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAG GCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTA GCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGAC CTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCGCCGGCGTGGGCAAGAG CTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCG CCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACA CTAAAGGTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCAT GCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGG CCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATC CGCGAGCAGCGTGGCGACTTTCAGGACATCCCCATTGTGATCGCCGGGAA CAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGA CCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGGCGAAAGTGCTGGAG TGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCT CTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCG GGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCC TACGTCAGCGCATCGTCCAGTCGCAATAAAAATCGGATGAACAGCCCGGC CCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCG TGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCT CGTTCCAGATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAAT CAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCG CCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCAC AATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGG CGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACC CAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTG CTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGA TGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCT GATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGC CGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATA AGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAG TGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTT GCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGG AAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAA TTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTT AATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCG TTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGA CTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACT GGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTC TAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGG TTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGA TAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCG AATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCAT TCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCAC AGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGG GAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTG AACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGC ACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTT TTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGT GGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTG TTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACAT TTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGAT GAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGA CACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATG CACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAA TGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGT CCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAAC CGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTAC CTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACG TTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGAC TAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGC GGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCG ATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAG TTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGA TCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCT AAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCA AATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCG TCCC MADLERIRLVLLGGAGVGKSSIVKRFLFKTYTDKYRATVEDLYNREYDLG GVTLKVDILDTSGDMQFPAMRRLSIATAHAFMLVYAATSAPSFQCVKQCF EEIREQRGDFQDIPIVIAGNKADLATTHREVKLEEVTDWVFCELPRLRAK VLECSAKEDSNVTDLFKSLLSLSRFLPASSSGSGGSGGGGEAAPSGFKRR SSAYVSASSSRNKNRMNSPALGGAGGSGGDKKGSSLVDAVDVATTSAEAK LKPRSRSLIRRASRKTKQQINNASDDCNVQ CG33350 CG33350 gene CG33350 cyto_range 42E1-42E1 sp_status Not in SwissProt real (computational) comment Flag Cambridge: gene split (internal view only)::DATE:2003-03-14 16:24:23::TS:1047677063000 gbunit AE003790 symbol CG15241 comment Gene split based on BLASTX data::DATE:2003-03-14 16:24:38::TS:1047677078000 Gadfly CG33350 FlyBase FBgn0053350 FlyBase FBgn0033119 FlyBase FBan0015241 CG33350-RA transcript owner crosby sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAF57415 Gadfly CG33350-RA FlyBase FBtr0086191 translate offset 275173 275171 CG33350:1 exon 275173 274949 CG33350:2 exon 274892 274716 CG33350:3 exon 274645 274469 ATGCTGTTCGTATTTGGCTTTGCTAGTTCCTGGGCCGCAGACTACGAGCT GTTGCTGGAGGACCCTGATATCTTTTCACCCTGCACTGAACCGCCGCCGG GATCGATTGGATTCCACGATGCCTTCGATATTGGCGATCTGGTAGTCGAC CAGGACATGGACATCATTCACCTGTCCGAGAGTGTCACCTCAATCTGGGA TGTGGAGCCCACAGATCGCATATCCGCCAGGTTTGCAATAATGCATTACA ACCGCGGCAGCTGGGAACCGACTGTATTTAGCATGGCCACGCCGGACTTC TGCGCCTCAATGTTTGATGAGAATCAGTCGTGGTTTAAGTACTGGACCAA ACACATTTCGAACCGCGATGAGGTGATGGAGAAGTGTTTTAAAACGCGTG GTACCGTTATAATGCACAATCCATTCGATCTGCAGCTGCGTCTAACGGAC ATTCGTGGTGCAACTCTCAGGGGTCGTTACAAAGCTGTGGTCACCTTTGA GGCGGTCGATGAGAAGGATGTGCCACGCCGTAATTCCATTTGCTTCGAAA TCAGGGGAGAGGCCGAGAAGATAAATTAA MLFVFGFASSWAADYELLLEDPDIFSPCTEPPPGSIGFHDAFDIGDLVVD QDMDIIHLSESVTSIWDVEPTDRISARFAIMHYNRGSWEPTVFSMATPDF CASMFDENQSWFKYWTKHISNRDEVMEKCFKTRGTVIMHNPFDLQLRLTD IRGATLRGRYKAVVTFEAVDEKDVPRRNSICFEIRGEAEKIN CG30160 CG30160 gene CG30160 cyto_range 42E5-42E5 sp_status Possible incorrect identifier (computational) comment Flag Cambridge: another Tsp42E::DATE:2002-02-13 10:58:42::TS:1013615922000 symbol CG30160 gbunit AE003790 FlyBase FBgn0050160 FlyBase FBan0030160 GO GO:0016021 integral to membrane CG30160-RA transcript owner crosby protein_id AAM70844 sp_comment Perfect match to SP record corresponding to different FBgn Gadfly CG30160-RA FlyBase FBtr0086178 translate offset 334993 334995 CG30160:1 exon 334993 335244 CG30160:2 exon 335309 335473 CG30160:3 exon 335546 335797 ATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCT GGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGC TCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAG ACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGC CTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCA TCTACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCC ATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGC AGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGG ATGCCCTCCAGTTGGCCTTCTCTTGCTGTGGCAACACGGGATACCAACAG TATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGT GTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCG TCGATTTCTGGGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATC ATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAG CGCGATGAGGAAGCGCTAG MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR CG33351 CG33351 gene CG33351 cyto_range 42E1-42E1 gbunit AE003790 comment Flag Cambridge: gene split (internal view only)::DATE:2003-03-14 16:25:40::TS:1047677140000 comment Gene split based on BLASTX data::DATE:2003-03-14 16:25:57::TS:1047677157000 Gadfly CG33351 FlyBase FBgn0053351 FlyBase FBan0015241 FlyBase FBgn0033119 CG33351-RA transcript status not done owner crosby Gadfly CG33351-RA FlyBase FBtr0086192 translate offset 273761 273759 CG33351:4 exon 273761 273525 CG33351:5 exon 273458 273282 CG33351:6 exon 273121 272945 ATGATATTTGTGCTGCTACTCTTATTAGGAGTGACCAGTTCCTGGGCCAC AGACTATGAATTATTGCTCGAGGATCCGGACATATTTTCGACGTGCACTG ATGGTCCTCCCGGATCCATCAACATCCGCCAGGCACTCAACTTAGACGAC ATTGTAATCGACCAGAAAGGGGATATACTTCATGTATCCGGGAACGCCAC CGTCGTGTGGGATGTGCAGCCCACCGATCGGATTACTGCGAGACTTGATG TTTTTCACTTCAACCGCGGCACTTGGGAGCCCACTGTCTTTAGCATGGCC ACCCAGAACTTTTGCTCCATCATGTACGACAAGAACCAGTATTGGTATAA GTATTGGACAAGGTTTATAACCAATCGCCATGAGGTGGAAAAGAAGTGCT TCAGAGGGCCTGATACCGTTCTGGTACACGAGCCCTTCGATCTCATACTA AAATTTGAGAATTTTCGTGGACCTCTTCTTAGAGGACGTCATAAACTTGT CATATTGTTTAACGCACTAGATGAGAGGAATATACCGCGCCCAAACCCAA TTTGTTTGGAGATCATAGGAGAACCACTAAAGTTGCAGTAG MIFVLLLLLGVTSSWATDYELLLEDPDIFSTCTDGPPGSINIRQALNLDD IVIDQKGDILHVSGNATVVWDVQPTDRITARLDVFHFNRGTWEPTVFSMA TQNFCSIMYDKNQYWYKYWTRFITNRHEVEKKCFRGPDTVLVHEPFDLIL KFENFRGPLLRGRHKLVILFNALDERNIPRPNPICLEIIGEPLKLQ CG3358 CG3358 gene CG3358 cyto_range 42D6-42E1 symbol CG3358 gbunit AE003790 sp_status Not in SwissProt real (computational) FlyBase FBgn0033117 FlyBase FBan0003358 CG3358-RA transcript sp_comment Perfect match to HYPO SP record with corresponding FBgn protein_id AAF57413 owner crosby Gadfly CG3358-RA FlyBase FBtr0086166 translate offset 253281 253283 CG3358:5 exon 253146 253434 CG3358:3 exon 253655 254261 CG3358:4 exon 254328 254456 TTTATCCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGGTA ACTTGAGAGAAATTAACTCCTGCAGGCTTGACTAGCTAACACCTGGCAAT GCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGC TACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCG CGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGA AGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATGAGCGCATCTAC ACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCC AGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCA AGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTC TGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGC GGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGG ACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGC GGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCAT CCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGA CGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATG CTAGAAACCGACTGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACA CAAGCACGTGACCACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGA CAGCTGAATCCCTAATAGACGGACGCTGTGAGCCTTGCCAAATCAGCCAA GTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGC TGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGA GTAAAGAATAAAACAACATGCATTT MFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASK DERIYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDY DRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNK IEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLP NDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEP CQISQVLESIAGIKQEPKEQLAALYYQNTLDLFFGTGESKE CG3358-RB transcript protein_id AAM70836 owner crosby sp_comment Perfect match to HYPO SP record with corresponding FBgn Gadfly CG3358-RB FlyBase FBtr0086167 translate offset 253153 253155 CG3358:1 exon 253146 253192 CG3358:2 exon 253255 253434 CG3358:3 exon 253655 254261 CG3358:4 exon 254328 254456 TTTATCCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGACA TTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACC CAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACA GGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATG AGGCACTGGAACTGGCCTCCAAGGATGAGCGCATCTACACGACAGTGGGA ACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTA TGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCG TAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAA ACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAA ACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCA TCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTG CACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGG CGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACG CAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATGCTAGAAACCGAC TGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACACAAGCACGTGAC CACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCC TAATAGACGGACGCTGTGAGCCTTGCCAAATCAGCCAAGTTTTGGAGTCT ATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTA CCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAA ACAACATGCATTT MQRRCFGMAMKYIDIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGL QKVIVTAGCLKDVDEALELASKDERIYTTVGTHPTRCEEFVPDPEGYYDQ LRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLP LFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGL YIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTK FPTVKKKEKWTAESLIDGRCEPCQISQVLESIAGIKQEPKEQLAALYYQN TLDLFFGTGESKE Tsp42Ec CG12847 gene Tsp42Ec cyto_range 42E5-42E5 sp_status Perfect match to SwissProt real (computational) symbol Tsp42Ec gbunit AE003790 GO GO:16021 FlyBase FBgn0033124 FlyBase FBan0012847 GO GO:0016021 integral to membrane Tsp42Ec-RA transcript owner crosby sp_comment Perfect match to REAL SP with corresponding FBgn protein_id AAF59313 Gadfly CG12847-RA FlyBase FBtr0086179 translate offset 336348 336350 Tsp42Ec:1 exon 336222 336407 Tsp42Ec:2 exon 337501 337692 Tsp42Ec:3 exon 337756 338397 TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACA CCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAAT ACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTC AACTTTATTTTATATATTGTCAATATCGTGTTTTTGATCGTTGGCATCCT ACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATG TCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTC CTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTT TCGGCAGAGTGTCTGCATGACCGGCGCGTACACCAGCATGGTTTTTGTGC TCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCT GCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCA TGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTG ATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACC TGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTA CCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACA ACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTG GTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAA CGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCC AAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTC GAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGT TACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAA TATATACCGCTACAACATTT MGCLSGIVNFILYIVNIVFLIVGILLIVLGSIMLSDLSRFDVAGSGTDPN TIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGAYTSMVFVLFILQLVLT CWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNN IGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSG LGLCIFDLVVFLIAGALTNCMRSQNAGRQVYA blastx_masked aa_SPTR.primate type BLASTX Similarity to Other Species qseq_type genomic trnascan-se type tRNAscan-SE type Gene Prediction Program qseq_type genomic blastx_masked aa_SPTR.dros type BLASTX Similarity to Fly qseq_type genomic blastx_masked aa_SPTR.worm type BLASTX Similarity to Other Species qseq_type genomic blastx_masked aa_SPTR.rodent type BLASTX Similarity to Other Species qseq_type genomic blastx_masked aa_SPTR.othvert type BLASTX Similarity to Other Species qseq_type genomic blastx_masked aa_SPTR.othinv type BLASTX Similarity to Other Species qseq_type genomic tblastx na_dbEST.insect type BLASTX Similarity to Other Species qseq_type genomic blastx_masked aa_SPTR.yeast type BLASTX Similarity to Other Species qseq_type genomic blastx_masked aa_users_i.dros type BLASTX Similarity to Fly qseq_type genomic promoter dummy qseq_type genomic genscan dummy type Genscan type Gene Prediction qseq_type genomic piecegenie dummy blastx_masked aa_SPTR.plant type BLASTX Similarity to Other Species qseq_type genomic JOSHTRANSPOSON Sept type Transposon qseq_type genomic sim4 na_EST.all_nr.dros type Fly ESTs qseq_type genomic locator cytology qseq_type genomic sim4 na_DGC.dros type Fly cDNA Sequences type DGC qseq_type genomic blastx_masked aa_SP.real.dros type BLASTX Similarity to Fly qseq_type genomic clonelocator scaffoldBACs type BAC Scaffold qseq_type genomic blastx_masked aa_SPTR.insect type BLASTX Similarity to Other Species qseq_type genomic tblastx na_unigene.rodent type BLASTX Similarity to Other Species qseq_type genomic repeatmasker qseq_type genomic pinsertion blastx_masked aa_TR.real.dros type BLASTX Similarity to Fly qseq_type genomic sim4 na_pe.dros type P Element qseq_type genomic sim4 na_gadfly.dros.RELEASE2 sim4 na_users_i.dros type BLASTX Similarity to Fly qseq_type genomic blastx_masked aa_SP.hyp.dros type BLASTX Similarity to Fly qseq_type genomic sim4 na_adh.cDNAs.dros type Fly ESTs qseq_type genomic sim4 na_affy_oligo.dros qseq_type genomic sim4 na_gb.dros type Community type Fly cDNA Sequences qseq_type genomic sim4 na_cDNA.dros type Fly cDNA Sequences type DGC qseq_type genomic 2604432 100 NULL:1988089 208416 208214 CTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACT 1 203 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTTATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTACCAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTGAATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTGGAG 100 NULL:1988090 208133 207202 CTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTGGGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGAGAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGGTGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGTTCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTCCTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAAAGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCCTTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATACATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCCAATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTG 204 1135 ---GTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAG 100 NULL:1988091 207137 206996 CCGTGGCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTGTATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAAATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAGCTG 1136 1277 ---CTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCACGG 100 NULL:1988092 206508 206371 TTCAAAACTTATTGATTCTTCCCGCAAACAAAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACATGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACATGACCATTCCTG 1278 1415 ---GAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAA 100 NULL:1988093 206301 205924 TTTTAGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTAGTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGTTGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAACGTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATACCTG 1416 1793 ---GTATGTTTATGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAA 2598660 99 NULL:1983279 286745 288122 CGTTGAATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGTCAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATTCCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTGTCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGCAACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGGATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGAAATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTCGTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATCCGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAGACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCATGTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTAAGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTCAAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTACATTACTTCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTGTTATGCCCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTATTATGCTCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCCACTCTACGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACCTTCAAACCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCACTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAAGGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGACATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAATAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTGTTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAAAAGGTACAGGAAGACAACAAGATAACAGTTAAAACCAGATCAGGAAAAATTTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAAAAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGCTAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAATAAAAAAAAAAAAAAAAAAAAAAAA 1 1378 TGGGGAATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGTCAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATTCCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTGTCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGCAACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGGATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGAAATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTCGTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATCCGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAGACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCATGTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTAAGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTCAAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTACATTACTTCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTGTTATGCCCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTATTATGCTCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCCACTCTACGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACCTTCAAACCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCACTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAAGGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGACATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAATAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTGTTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAAAAGGTACAGGAAGACAACAAGGTAACAGTTAAAACCAGATCAGGAAAAATTTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAAAAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGCTAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAATAAAAAAAAAAAAAAAAAAAAAAAA 2598571 100 NULL:1983202 71670 71924 ATTTGTGAGCACACACTTTAGTTTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCGATCTGTGACGCGGTTTAAACCAAGGTA 1 255 ATTTGTGAGCACACACTTTAGTTTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCGATCTGTGACGCGGTTTAAACCAAG--- 100 NULL:1983203 72480 72544 GCTGCACGACACTTCGAGGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGTA 256 320 GCTGCACGACACTTCGAGGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATG--- 100 NULL:1983204 72616 72755 GTACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAGGTG 321 460 GTACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAG--- 100 NULL:1983205 72812 73319 GTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCCTAAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACCGCCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATCTGCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGACGTCGCAAGAAGATTGTGCG 461 968 GTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCCTAAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACCGCCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATCTGCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGACGTCGCAAGAAGATTGTGCG 100 NULL:1983206 73368 74314 TAGAGTTCGACAAGTGGAGGCTGACTTGTCCCAGGCCAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATCGAAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTGTGCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTATCAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGCCCACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAGAAAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACTGGCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCGTGCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGAAAGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGGAGGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGACAACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGCTCCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTGTGACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAATGAATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACATTATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCACCGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCTGATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGAAGATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATAGCAGCCTCGACCGTAGTA 969 1915 ---AGTTCGACAAGTGGAGGCTGACTTGTCCCAGGCCAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATCGAAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTGTGCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTATCAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGCCCACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAGAAAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACTGGCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCGTGCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGAAAGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGGAGGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGACAACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGCTCCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTGTGACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAATGAATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACATTATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCACCGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCTGATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGAAGATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATAGCAGCCTCGACCGTA--- 100 NULL:1983207 74374 74552 TTAGCTGCACCATTTGGGATCAGCGAGATGCCAAAAAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATCGAACGCGTGGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGTGGTCTTCTCTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCGAGGTA 1916 2094 TTAGCTGCACCATTTGGGATCAGCGAGATGCCAAAAAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATCGAACGCGTGGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGTGGTCTTCTCTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCGAG--- 100 NULL:1983208 74613 74969 GTCACACTCGGGAGCGATGCAGAGAAGGCCAGTGAGATTAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCATCGGCATCGCTCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTGGGAGCGCATGGTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCCTCATACTGTTCATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGCTTCCTTTACGCCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCGAAAGTCAAATCTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGACCTGGCTGAGCGTGAGGTCGTATTTGAAGGTA 2095 2451 GTCACACTCGGGAGCGATGCAGAGAAGGCCAGTGAGATTAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCATCGGCATCGCTCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTGGGAGCGCATGGTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCCTCATACTGTTCATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGCTTCCTTTACGCCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCGAAAGTCAAATCTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGACCTGGCTGAGCGTGAGGTCGTATTTGAAG--- 99 NULL:1983209 75028 75629 AAACGCGGACCCCAGCGATCGGTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCCAAT-GTT 2452 3054 AAACGCGGACCCCAGCGATCGGTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCCAAAA--- 2598628 99 NULL:1983252 211742 212413 GGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAATTCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCAGGTACTTAATCAGGTA 1 672 GGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAATCCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCAGGTACTTAATCAG--- 100 NULL:1983253 212484 212625 CTGGGTATTACGGAAGTCTTCAGCGATAAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTCGGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGGCAGCAGCAGTCAGTTGTA 673 814 CTGGGTATTACGGAAGTCTTCAGCGATAAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTCGGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGGCAGCAGCAGTCAGTT--- 99 NULL:1983254 212695 213186 TCATGAAGATAGTACCCATGATGCTCAACATGAACAAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAACTTATGATTT 815 1305 TCATGAAGATAGTACCCATGATGCTCAACATGAACAAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAACTTA-AA--- 2598555 97 NULL:1983189 5602 5687 TTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATATTTATTAAGGTG 1 86 ATGTATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATATTTATTAAG--- 100 NULL:1983190 21473 21600 ATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCATGTG 87 214 ATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCAT--- 99 NULL:1983191 21657 22011 GTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAATAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGATACTATAGATGGGTA 215 569 GTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCAGTAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAATAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGATACTATAGATGG--- 99 NULL:1983192 22068 22369 CTTACAAAAGCCAAATACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGCGGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAAAGCCCAATTTATCACAAAA 570 871 CTTACAAAAGCCAAATACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGCGGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAAAGCCCAATTTATCGCAAAA 2598645 100 NULL:1983266 221538 221698 AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGGGTG 1 161 AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGG--- 100 NULL:1983267 221755 221801 TTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCAGGTA 162 208 TTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCAG--- 99 NULL:1983268 235638 236135 CTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCGCCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCGCCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACACTAAAGGTG 209 706 CTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCACCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCGCCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACACTAAAG--- 99 NULL:1983269 239708 239875 GTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCATGCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGGCCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATCCGCGAGCAGCGTGGCGACTTTCAGGTG 707 874 GTGGACATCCTGGGCACGTCGGGTGACATGCAGTTCCCGGCCATGCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGGCCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATCCGCGAGCAGCGTGGCGACTTTCAG--- 100 NULL:1983270 240527 240636 GACATCCCCATTGTGATCGCCGGGAACAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGACCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGTA 875 984 GACATCCCCATTGTGATCGCCGGGAACAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGACCGACTGGGTCTTCTGCGAACTGCCGCGCTTACG--- 100 NULL:1983271 244408 244598 GGCGAAAGTGCTGGAGTGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCTCTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCGGGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCCTACGTCAGCGCATCGTCCAGTCGCAGTA 985 1175 GGCGAAAGTGCTGGAGTGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCTCTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCGGGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCCTACGTCAGCGCATCGTCCAGTCGCA--- 100 NULL:1983272 249810 249942 ATAAAAATCGGATGAACAGCCCGGCCCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCGTGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCTCGTTCCAGGTG 1176 1308 ATAAAAATCGGATGAACAGCCCGGCCCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCGTGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCTCGTTCCAG--- 99 NULL:1983273 250043 252383 ATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAATCAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCGCCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCACAATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGGCGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACCCAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTGCTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGATGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCTGATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGCCGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATAAGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAGTGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTTGCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGGAAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAATTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTTAATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCGTTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGACTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACTGGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTCTAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGGTTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGATAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCGAATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCATTCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCACAGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGGGAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTGAACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGCACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTTTTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGTGGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTGTTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACATTTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGATGAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGACACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATGCACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAATGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCGTC 1309 3649 ATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAATCAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCGCCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCACAATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGGCGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACCCAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTGCTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGATGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCTTATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGCCGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATAAGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAGTGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTTGCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGGAAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAATTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTTAATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCGTTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGACTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACTGGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTCTAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGGTTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGATAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCGAATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCATTCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCACAGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGGGAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTGAACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGCACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTTTTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGTGGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTGTTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACATTTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGATGAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGACACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATGCACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAATGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGC--- 2604450 95 NULL:1988104 304761 304722 CTTGGGCAGCCGTAATTTGTTTTGTGAAAGTGAAATCGCA 1 40 TGCGATTTCACTTTCACAAAAAAAATTACGGCTGCCGAAG 99 NULL:1988105 303775 302563 TA...CACCATTGAGGACTTGCTTCGTATACCTGAGCTCCCTTAGGCACTCCGGTGTCACTTGGCCACCATGCTCCTCCAGTGCCTTGTTAATCTCGAGCCTGGTTCGATCTTGCACCTCAGGCTGGCGGGCCAACTCGTAGAGGCAGAATGCTAGGGTGGCATTCAGGGGGCCCAAGCCAGCCAGAACGAAGCCGAAGGCTTGGCCCGCAATCTCGATGTCGGTGAGCGGCTTTTCTGCGTTGGAATATAGCTGCAGAAAGGTCTGGAGTGGCTGGCGATCCCTTCTTCGATGCAACTGCAACTGCGACAGGGCCACTTTTTGGAAGTAAGCTGTAGCAGGTTCTGCGTAGCTTTTGTACTGAAGAAGGCGAGCGATGAGCGGAAACTCAAGCGCCAGATAAGCCTGCCACATCCTAAAGTCCGCCCAGTAGTTGCGCGTCCACTTAGCGAACTCCACGTTATCCTGCCCTACTAGTCCAAAGGCCATTGACGCCATAACGTCCGTATTGTATGCACCCACGAGTTCGCTTATATTGATAGTTTGAAGGCTCTTTTCGCCCAGGTCCCTTTGAATTCTGGAGGAGATTTGCGACAGTCTGACCAGCAGCTTCTGCATGTTGGCCGGAGTGAAAACCTCTGCAGATTTGGCGTGCAGTGACCGCCACTTGTGACCGTCCAGCTGAAGGAGATTATGCGACAGCGGCTCTCCACTGGGATTACTATAAAGGCCTCGGGACGTAAAGTGTCCCGCGTCGGTGAAGATTATTTGGTGGACTAGCTTCAGGTCCAGCGCCAAGATGAACGGCTTGAGGCAGGCGTAGAATCCCACAAACGGCGCCCTGCCCTTGTATGCGGTGTAGATATCCTGCAAGGCGTCCTGGGCATGCCTCTTCCCGCTCACCACGCCCTTAATGTTGCCCCACAGGAACTTGGGCTTTTCGTGCAGGATCCCCCGCCGTTTCCAGTAGCCCAGACTGAACTTGACCAGGGCGTAGACCACTGACAGCGCACCCAGGGCGGTGAGCAGGGTGCGGTGCATTAGATCCATGCTCACTCAGCTGTCTTTTCCGGCTTTTACAATATGTTCGCGCTGTTTGATATGCTTAACAGCTGGCAGTAGCTGCTTGTCGAGGTTCTGGGGCTCAATGCCGCCGGTTTATCAGCGCCATTATCGTGCGGTCCGATTTAATAATTGATAAGGTCCATTGAGTATCGGCCGCTA 41 1253 ---CGGCCGATACTCAATGGACCTTATCAATTATTAAATCGGACCGCACGATAATGGCGCTGATAAACCGGCGGCATTGAGCCCCAGAACCTCGACAAGCAGCTACTGCCAGCTGTTAAGCATATCAAACAGCGCGAACATATTGTAAAAGCCGGAAAAGACAGCTGAGTGAGCATGGATCTAATGCACCGCACCCTGCTCACCGCCCTGGGTGCGCTGTCAGTGGTCTACGCCCTGGTCAAGTTCAGTCTGGGCTACTGGAAACGGCGGGGGATCCTGCACGAAAAGCCCAAGTTCCTGTGGGGCAACATTAAGGGCGTGGTGAGCGGGAAGAGGCATGCCCAGGACGCCTTGCAGGATATCTACACCGCATACAAGGGCAGGGCGCCGTTTGTGGGATTCTACGCCTGCCTCAAGCCGTTCATCTTGGCGCTGGACCTGAAGCTAGTCCACCAAATAATCTTCACCGACGCGGGACACTTTACGTCCCGAGGCCTTTATAGTAATCCCAGTGGAGAGCCGCTGTCGCATAATCTCCTTCAGCTGGACGGTCACAAGTGGCGGTCACTGCACGCCAAATCTGCAGAGGTTTTCACTCCGGCCAACATGCAGAAGCTGCTGGTCAGACTGTCGCAAATCTCCTCCAGAATTCAAAGGGACCTGGGCGAAAAGAGCCTTCAAACTATCAATATAAGCGAACTCGTGGGTGCATACAATACGGACGTTATGGCGTCAATGGCCTTTGGACTAGTAGGGCAGGATAACGTGGAGTTCGCTAAGTGGACGCGCAACTACTGGGCGGACTTTAGGATGTGGCAGGCTTATCTGGCGCTTGAGTTTCCGCTCATCGCTCGCCTTCTTCAGTACAAAAGCTACGCAGAACCTGCTACAGCTTACTTCCAAAAAGTGGCCCTGTCGCAGTTGCAGGAGCATCGAAGAAGGGATCGCCAGCCACTCCAGACCTTTCTGCAGCTATATTCCAACGCAGAAAAGCCGCTCACCGACATCGAGATTGCGGGCCAAGCCTTCGGCTTCGTTCTGGCTGGCTTGGGCCCCCTGAATGCCACCCTGGCATTCTGCCTCTACGAGTTGGCCCGCCAGCCTGAGGTGCAAGATCGAACCAGGCTCGAGATTAACAAGACACTGGAAGAGCATTGTGGCCAAGTGACACCGGAGTGCCTAAGGGAGCTCAGGTATACGAAGCAAGTCCTCAATG-------- 99 NULL:1988106 302504 301890 AACTAAATTATTTATTTGTTCACGTTGTTGAGCTTGGTGCAAAAGATTATAAAAGTCATCGTCAGCATTATCACACAAGTCCACAGCTTAGGAAAATCAACGAAAAAGGTGCATATACAAATATAAAAACAACTTAAACGCTTTGTAAAGCAAACAATACAAAATATGCGATGCTCCAGCAGAGCCTCCTTTAAAGCTTGTCCACCCGTTCCACACTGAGTTTGATGTCCGACTTGGGCATCAAGAGCAGTCTCCGGTTGTCGTACTCCACGGGAATCGAGGTCTCCGCAGAGGGAGCGTATCTGTGCTGCCTCAGCAGAGCCACCAGGCCCACCAGAAGCTGCTGCTCTGCAAAGCGAGCGGCAATGCATCCTCGCAGGCCATCGCCGAAAGGCAGGAACGCAGCTGCCGGGCGGGATCGCCTTGCCTGTTCCTCAAAGCGCTCCGGGTAGAACCGCTGGGGGTTTTCATAAATGCCAGGATCCATGTGTATCGCCGCCGTTGGTATCAGCACATTGTTGCCTTTGGCAATTACAAACACCGATCCGGGCACTTCGAATTCTTTGGTAGCCCGGCGTAGCAGGAAGGGATGTGGAGTGTGCAGGCGAAGCGTTT 1254 1868 AAACGCTTCGCCTGCACACTCCACATCCCTTCCTGCTACGCCGGGCTACCAAAGAATTCGAAGTGCCCGGATCGGTGTTTGTAATTGCCAAAGGCAACAATGTGCTGATACCAACGGCGGCGATACACATGGATCCTGGCATTTATGAAAACCCCCAGCGGTTCTATCCGGAGCGCTTTGAGGAACAGGCAAGGCGATCCCGCCCGGCAGCTGCGTTCCTGCCTTTCGGCGATGGCCTGCGAGGATGCATTGCCGCTCGCTTTGCAGAGCAGCAGCTTCTGGTGGGCCTGGTGGCTCTGCTGAGGCAGCACAGATACGCTCCCTCTTCGGAGACCTCGATTCCCGTGGAGTACGACAACCGGAGACTGCTCTTGATGCCCAAGTCGGACATCAAACTCAGTGTGGAACGGGTGGACAAGCTTTAAAGGAGGCTCTGCTGGAGCATCGCATATTTTGTATTGTTTGCTTTATAAAGCGTTTAAGTTGTTTTTATATTTGTATATGCACCTTTTTCGTTGATTTTCCTAAGCTGTGGACTTGTGTGATAATGCTGACGATGACTTTTATAATCTTTTGCACCAAGCTCAACAACGTGAACAAATAAATAATTTAGTT 2598662 100 NULL:1983281 315855 316551 CACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCCAACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAGGAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTTCCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAG 1 697 CACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCCAACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAGGAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTTCCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAG 100 NULL:1983282 316609 316708 CAGCTCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCGAGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGAGTA 698 797 ---CTCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCGAGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGA--- 100 NULL:1983283 317413 317463 AACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACAGTA 798 848 AACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACA--- 100 NULL:1983284 317556 318040 AAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGGCCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGGTG 849 1333 AAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGGCCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAG--- 99 NULL:1983285 318346 318699 TTTCCTCCACAGAATCCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGGATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTGGCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGTCAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCCCTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAGACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATAAAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAA 1334 1687 TTTCCTCCACAGAATCCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGGATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTGGCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGTCAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCCCTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAGACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATAAAGCACACAACTATGGCGTCCCTATTTTCCAATCGCCAA 2604364 100 NULL:1988029 26379 26115 CTTGGATTTTGTGCCTGGCCGGTTCCTACGCAATATGGTCGAGCCGTCAGCCATCTTCATGTTTCACCCGCTCGAAGACGCGATGATCCACAACGTCTGTGCCTACGCCTTGATGAGAAAATCACTGGCAGAAACTGAATGCTAGCCTGGTCCCTGCCCCGCGGGAGTCTCCGGATGTGGGATCCCTGCACCGTAGTATGCTGAGTGTATTCTACAGGAGCTGGCACATCGCTTGACAATTAATTGGCGTTTATCCTCCAAAACA 1 265 TGTTTTGGAGGATAAACGCCAATTAATTGTCAAGCGATGTGCCAGCTCCTGTAGAATACACTCAGCATACTACGGTGCAGGGATCCCACATCCGGAGACTCCCGCGGGGCAGGGACCAGGCTAGCATTCAGTTTCTGCCAGTGATTTTCTCATCAAGGCGTAGGCACAGACGTTGTGGATCATCGCGTCTTCGAGCGGGTGAAACATGAAGATGGCTGACGGCTCGACCATATTGCGTAGGAACCGGCCAGGCACAAAATCCAAG 100 NULL:1988030 26040 25667 CTGCTAGGGAAGTACTTGTTGCTGTTTAGCAGACAGGCGGCACCGTCCAGCGTGTGGCGTGTGTAGTCAATGGCCGGACATTCCTTGGGCGTCTTGTGCGCGGCGCACAGGAATATCCACTGGTCAGTGGCTGTCATCTGGGTGCACGTCGACGGCGAGCACTCCTTCTGCAGCCGCACTGCCAGGCCGTTCAGCTCCATGCAGAACTGGCGCAGGTGCTCGTACTTCCACACGCCCTCATCCTGGGCTTCGGGCATGGTCAGTATGAGTTCCACGTTGCTCGGGTCGCGCTTAATCAGCTGCTGTATGTACTGCTGCACCGCCAGCGTGCTGTCCATCTCCTCCAGGGGCTCGTCGGGCCAGCGACAGAAGTCCTG 266 639 ---GACTTCTGTCGCTGGCCCGACGAGCCCCTGGAGGAGATGGACAGCACGCTGGCGGTGCAGCAGTACATACAGCAGCTGATTAAGCGCGACCCGAGCAACGTGGAACTCATACTGACCATGCCCGAAGCCCAGGATGAGGGCGTGTGGAAGTACGAGCACCTGCGCCAGTTCTGCATGGAGCTGAACGGCCTGGCAGTGCGGCTGCAGAAGGAGTGCTCGCCGTCGACGTGCACCCAGATGACAGCCACTGACCAGTGGATATTCCTGTGCGCCGCGCACAAGACGCCCAAGGAATGTCCGGCCATTGACTACACACGCCACACGCTGGACGGTGCCGCCTGTCTGCTAAACAGCAACAAGTACTTCCCTAGCAG 100 NULL:1988031 25606 24891 GTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTCACGTACAGCTGTGTTGGTGTTTTGGCTGCCAGTAGTCAAGGGAATTTAGTTTAGTTTACGGGGATTTGACGTGGAATCAGCCACGAGAAGGTCGTGTGCCTACATATAATTTATTAAAATAAGGAGTTAAACATAATCGTAATATAACTTGCGAAATAATTGCTGACTTAGGATCAGATGGGGCGAGCGGGTTTGAGGGGGTCTGCCCTTGTTACTTAGTTATCGTTATGTAGCTCTATGTGTATCTGACATCTAAACTACATACAAGATCTGCATTAGAGTCGGGTCCGCGTGGAATCGTTTCCCTGTCAGGGTGAGCCAACCCAACTTGCAAGCTATTGGTAAATATAAATAGATGTATGTTGAATGAGTGTTTCATGCGAGTCTGACTAATCTGGGCGGGCTCCTAAGCCTCGCTTTCGCCAGGGGCCGCGTTTTCACCCACGTTGATGGGCACGATCAGATTCTCCTTCGACATCAGATTATATTTTGTGACGAAATGCGTGAAACGGTGGCACAGATACGTCTCGGCCTCGAATTCGTCGAAAATGCGACGATGGTGAAAGTAGGCGTGCGAGAAGATGCGATACACCCGCCGACATACGGAGCCCAGCTTGGTTACCGACGACTCCTTGATGGACACC 640 1355 GGTGTCCATCAAGGAGTCGTCGGTAACCAAGCTGGGCTCCGTATGTCGGCGGGTGTATCGCATCTTCTCGCACGCCTACTTTCACCATCGTCGCATTTTCGACGAATTCGAGGCCGAGACGTATCTGTGCCACCGTTTCACGCATTTCGTCACAAAATATAATCTGATGTCGAAGGAGAATCTGATCGTGCCCATCAACGTGGGTGAAAACGCGGCCCCTGGCGAAAGCGAGGCTTAGGAGCCCGCCCAGATTAGTCAGACTCGCATGAAACACTCATTCAACATACATCTATTTATATTTACCAATAGCTTGCAAGTTGGGTTGGCTCACCCTGACAGGGAAACGATTCCACGCGGACCCGACTCTAATGCAGATCTTGTATGTAGTTTAGATGTCAGATACACATAGAGCTACATAACGATAACTAAGTAACAAGGGCAGACCCCCTCAAACCCGCTCGCCCCATCTGATCCTAAGTCAGCAATTATTTCGCAAGTTATATTACGATTATGTTTAACTCCTTATTTTAATAAATTATATGTAGGCACACGACCTTCTCGTGGCTGATTCCACGTCAAATCCCCGTAAACTAAACTAAATTCCCTTGACTACTGGCAGCCAAAACACCAACACAGCTGTACGTGACTAAAACGTGAACTTTACTATACAAAATTACTATATACACAACAGAAATTGCAATAAAAGAAGTACATAC 2598681 100 NULL:1983297 327940 328956 CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTA 1 1017 CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATC--- 100 NULL:1983298 329021 329185 TACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCC 1018 1182 TACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCC 99 NULL:1983299 329258 329626 1183 1551 2604455 99 NULL:1988108 308255 307467 CACCAGTAAGGATTAATACGATGAGTTCGCAGGCGAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACTTTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATAAGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACATCTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGATATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATACTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATTGGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACTCCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGCAAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGATGGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGAGTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCCCGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTGTCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCT 1 789 AGCTGGCAGAGTGCTTTCTGGGCCTCACCAAGTGCGACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGATCACCAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAGCCGCATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATGGAGCTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAACGACGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTACTGCGACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAATTCATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGAGGGCTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAGGCATCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTGCTGAACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGGCGGATCTGAACTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTTCCACGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAGGCGGAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGAAACCATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTGAGGCCAGGGCGCTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTTACTGGTG 99 NULL:1988109 307377 306991 CCTGTCCGTCGACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGTGTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACCGCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAGAGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCACCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGGCTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAGATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCGTGGTGTACAAATAGTGCATTGAGTCATCTA 790 1176 ---ATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAACATGGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCGTGCTGGCCCTGGGTAACTTTGCGCGCACCGATAGCCACTGCATCTACTTTGTGGAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAACGGCGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGCGCAACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGCCTGGTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGTCTTCAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGG 99 NULL:1988110 306932 305569 TATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTCCTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTCTAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAACTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTACAGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTCTCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAAAACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTGCAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAATTGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAATCTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACACAGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTTCAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGGATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGAGAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGCGCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTTCTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGGCCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGGGCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCACAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCATGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAGCTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTCGGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGTAGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACGCCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGTCTTGTTCTTCAGCAACTCCAGTGCGAGTTTCT 1177 2540 AGAAACTCGCACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCACTGGAGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCTCATGGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCACTGCCGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCGCTAACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGAGGGCACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCATGCAGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTGTCGCAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGTCAAGTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGGACACGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTGCTCAAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAACGAGCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAGAAAACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACAGTGGGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGGTAAGCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGCCAATACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCTAAACTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATCCACTCTCTTGAGATTCACTGACGTTCCACGATTCCAAATAGCCAAAGATAAATGTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTAGCCACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAAGCAACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCAGATTCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAACACGAGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATGTTGACTGCATTTATGAGGAGAATCCGATGTAGTGAGGAGTCACAAATCGTATGAATATTTATAGCATACATACATAACATATACGTATAAATATAATAATATTAATAATTTAGCATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAACAAATCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTGTACTTATA 2604382 100 NULL:1988044 70444 69814 ACCAGAAAACGGCCACGTAATCCTTGTCGGCCAGGAGCTTCTCCAGCTGCTTGGCATTGACCTCCTCGATGACGGCCTCCGGCTCCGGAGGCGCCACTGGCTGCGAGCCCTTCTTGTTGTTGTTGTTGCCTGCACCACTCACATGTCCGGGAAAACTCAGGGCCAGCAGAGCACACACGAGCAGCGAGAGAGTCTTGAGGCGGGTGAAAGTCATCCTGCGATCGGTTACGGTTCTGATGTGCTTTAGGCCCTTAACGCGAACATGCGTGCGCGTGTCTGCTCGTTTTGGTGTGTTCTACAGTTTATAGTGTTATAATTGTATAATTGATTCGTTCTCGTCGTTTGGGGTCTTTCGTTATTAAAATTTGTATTCCTTTGAGAATCGGTCACTATTTTTAGTTGATAATGGTGTTTCTTCTTTCGCAATTTATTTTATGTATAACAACTTTTTGTTCACTGATACATATATACGGGGTTCGTATATGCACAGGCGAGATATATGTGGGGTATATACGAGAATAATTAGATTATATATGTGGTTTCTTGCTTCTATTAATTGAACGTTTTCCGCGGACTGTACTCTTTGCTCTTCAGATTTTGTTCCACTCCGTGCAGAGGTCCGCTCGCAACT 1 631 AGTTGCGAGCGGACCTCTGCACGGAGTGGAACAAAATCTGAAGAGCAAAGAGTACAGTCCGCGGAAAACGTTCAATTAATAGAAGCAAGAAACCACATATATAATCTAATTATTCTCGTATATACCCCACATATATCTCGCCTGTGCATATACGAACCCCGTATATATGTATCAGTGAACAAAAAGTTGTTATACATAAAATAAATTGCGAAAGAAGAAACACCATTATCAACTAAAAATAGTGACCGATTCTCAAAGGAATACAAATTTTAATAACGAAAGACCCCAAACGACGAGAACGAATCAATTATACAATTATAACACTATAAACTGTAGAACACACCAAAACGAGCAGACACGCGCACGCATGTTCGCGTTAAGGGCCTAAAGCACATCAGAACCGTAACCGATCGCAGGATGACTTTCACCCGCCTCAAGACTCTCTCGCTGCTCGTGTGTGCTCTGCTGGCCCTGAGTTTTCCCGGACATGTGAGTGGTGCAGGCAACAACAACAACAAGAAGGGCTCGCAGCCAGTGGCGCCTCCGGAGCCGGAGGCCGTCATCGAGGAGGTCAATGCCAAGCAGCTGGAGAAGCTCCTGGCCGACAAGGATTACGTGGCCGTTTTCTGGT 100 NULL:1988045 68130 67974 CTGAAGTAGGTGAGGGCGGGGAAGTTCTTGATGCCATACTGTTTGGCTAGTCGTTTGTCGTTGATTTTCACGAAGTCCACACCGAAGGAGTCGGTGTCATCGTCGATTTTCTCGAGTTCCGCTAAAACCTTATCACAGGTCACGCAGCTTCGCGCATCTG 632 788 ---ATGCGCGAAGCTGCGTGACCTGTGATAAGGTTTTAGCGGAACTCGAGAAAATCGACGATGACACCGACTCCTTCGGTGTGGACTTCGTGAAAATCAACGACAAACGACTAGCCAAACAGTATGGCATCAAGAACTTCCCCGCCCTCACCTACTTCAG 100 NULL:1988046 67902 67736 G...TACAGAACAGAACGGCTACGAAGTCGGTGTCCTCGATGATCTTCTGCAATATCTTGGCATTGACCTCCTCGATGCGATCGGGCAAGTCCATGGCCTCCAAGGAGGTGAGGAAATCGAGCACTCCTTCCTCGTCCATGAGATCCCCATCATATATGATGGGCTCCTTTTCCCTG 789 955 ---GGAAAAGGAGCCCATCATATATGATGGGGATCTCATGGACGAGGAAGGAGTGCTCGATTTCCTCACCTCCTTGGAGGCCATGGACTTGCCCGATCGCATCGAGGAGGTCAATGCCAAGATATTGCAGAAGATCATCGAGGACACCGACTTCGTAGCCGTTCTGTTCT------- 100 NULL:1988047 63032 62718 AGAATATAACCGCCAAGTGCTCGGTGTTCTCGACCAACTTGTCCTTCATCTCATCGGTGACCTCGGGAATTTCGGAATAGCGCTTCTGGTGCACCAACCAGCCAAGCAGCTCATCCTCTTTCATCAGATCACCCTCGTAGATGTGTGGAATTCCACGTTCAAAGAGTACAATCGATGGTATCTCATCGATACCCCATTCTTTGGCCTCCTTGTCATCATCGATCTTGACAAAGGCAATATCGTTCTGATCGCACTCATCGTCGATGTTTTCCAGTTCTGCGAGGATTTTCTGTGATTTCTTTTGGTCTTTGTCGT 956 1270 ACGACAAAGACCAAAAGAAATCACAGAAAATCCTCGCAGAACTGGAAAACATCGACGATGAGTGCGATCAGAACGATATTGCCTTTGTCAAGATCGATGATGACAAGGAGGCCAAAGAATGGGGTATCGATGAGATACCATCGATTGTACTCTTTGAACGTGGAATTCCACACATCTACGAGGGTGATCTGATGAAAGAGGATGAGCTGCTTGGCTGGTTGGTGCACCAGAAGCGCTATTCCGAAATTCCCGAGGTCACCGATGAGATGAAGGACAAGTTGGTCGAGAACACCGAGCACTTGGCGGTTATATTCT 99 NULL:1988048 62657 62013 AGAAGAATACGACAACGTGATCGTTTTCAGCCAAGATCTTGTCCAACATCTTCACATTGACCTCCTCAATTTTTCCGGGAATTTCAAGGGTCTCGTCGTCAGTAATCCAGGCCAACACCTCGTCCTCGTCGTCCAGATCACCGGTAAAGTGAAGTGGATCACGATTCCTGAAGAACACCAGACGTGGATAGGTCTTGACGTTGTATTTCTTGGCAATTCCGGTATCCTCAGTGGTAACAAAAATTATGCCAGCCTCATCCAATTCATCGTCGATGCTTTCCAGGGCGTTCAGAGTGTGCTCACAGGTCTCTCCGGGCTCGCAGGGACCCGTAAAGAAGACGACGACATATTCGTGTTCGTTGATCAGAGTGACCAGGATCTCATCGGTAACCTCCTCGATAGTAGCTGTCTTTTTCTGGACAAGAAGCCACTCGAGCACCTCATCCTCGTTCATCAGATCGCCTTCATAGAGGGCCGGGATCTTGTTTTCGAAGTAGATGAGGGCGGGCAAATGATCGAGACCATATTCCTTGGCCTCAGCGGCGTTATCAATGCGGACGATGACAATTCCCTCCTTCTCCAGCTCGTCATCAATGTTCTCCAGTTCGTTCAGGATGCGCATATCCTGCTTATCGTCCTTGTCGTCTG 1271 1915 ---ACGACAAGGACGATAAGCAGGATATGCGCATCCTGAACGAACTGGAGAACATTGATGACGAGCTGGAGAAGGAGGGAATTGTCATCGTCCGCATTGATAACGCCGCTGAGGCCAAGGAATATGGTCTCGATCATTTGCCCGCCCTCATCTACTTCGAAAACAAGATCCCGGCCCTCTATGAAGGCGATCTGATGAACGAGGATGAGGTGCTCGAGTGGCTTCTTGTCCAGAAAAAGACAGCTAATATCGAGGAGGTTACCGATGAGATCCTGGTCACTCTGATCAACGAACACGAATATGTCGTCGTCTTCTTTACGGGTGCCTGCGAGCCCGGAGAGACCTGTGAGCACACTCTGAACGCCCTGGAAAGCATCGACGATGAATTGGATGAGGCTGGCATAATTTTTGTTACCACTGAGGTTACCGGAATTGCCAAGAAATACAACGTCAAGACCTATCCACGTCTGGTGCTCTTCAGGAATCGTGATCCACTTCACTTTACCGGTGATCTGGACGACGAGGACGAGGTGTTGGCCTGGATTACTGACGACGAGACCCTTGAAATTCCCGGAAAAATTGAGGAGGTCAATGTGAAGATGTTGGACAAGATCTTGGCTGAAAACGATCACGTTGTCGTATTCTTCT 100 NULL:1988049 61959 61777 CGGTGTAAATTGTTCTAAACTTATGTCTATAAAATGCAAGTGCCGGCAGACCGGGCAGGTCGTACTCCTTATCAATATCGTCGTCGGATGTCTTTACAAAGTCAATGTCTTTTTCCTCGCATTCGTCATCGATGTTCTCCAGCTCGTTAAGGATCTTTTGGGCCTTCTTATCGCCCTCAGCGTCTG 1916 2098 ---ACGCTGAGGGCGATAAGAAGGCCCAAAAGATCCTTAACGAGCTGGAGAACATCGATGACGAATGCGAGGAAAAAGACATTGACTTTGTAAAGACATCCGACGACGATATTGATAAGGAGTACGACCTGCCCGGTCTGCCGGCACTTGCATTTTATAGACATAAGTTTAGAACAATTTACACCG 100 NULL:1988050 61709 61572 AGAAGAACACAGCCAGGTGCTCAACATCGTTGATCAAAACTTGCAGGGTCTTACGATCGACAGATTCAATGACATCAGCTGTGGACTCGTGCAAATCAATAACCCACTCGAGAATTTCCTCTTCCTTCATCAGGTCACCTT 2099 2236 ---GTGACCTGATGAAGGAAGAGGAAATTCTCGAGTGGGTTATTGATTTGCACGAGTCCACAGCTGATGTCATTGAATCTGTCGATCGTAAGACCCTGCAAGTTTTGATCAACGATGTTGAGCACCTGGCTGTGTTCTTCT 99 NULL:1988051 61508 61326 CATCATACATAATCGGGACGCCGGTCTCGTAGTAGACCAAAGCTGGAAATGCGAAAATGCCAATTTCATGAGCCAGCTTAACATCATTTGATTTGACAAATTGTATTCCGTGCTTGTCGGTGTCATCGTCGATGTTCTCCAACTCCTCCAAGATGTCGGAACACGATTCGCATTCATCGTCGTCTG 2237 2419 ---ACGACGATGAATGCGAATCGTGTTCCGACATCTTGGAGGAGTTGGAGAACATCGACGATGACACCGACAAGCACGGAATACAATTTGTCAAATCAACTGATGTTAAGCTGGCTCATGAAATTGGCATTTTCGCATTTCCAGCTTTGGTCTACTACGAGACCGGCGTCCCGATTATGTATGATG 100 NULL:1988052 61265 61215 TCTTTTGATTGACTAACCACTGCAGCACACGGTTTTCATTTTTGAGATTACCTA 2420 2470 ---GTAATCTCAAAAATGAAAACCGTGTGCTGCAGTGGTTAGTCAATCAAAAGA 99 NULL:1988053 58848 58366 CGGATTTGACATTCAGTTTGCCGGACTTCTTCGCCGACTTCTGTTTGGATACCTTCTCCACCTCCTGGGACTGGTCGTCGTTGTCCTGGCCCTTGCCTACCGGCTTCTTGCCAGCCTGCGGCTTGTTGCTTCCTCCCGAGCGCTTGTTGGCATAGGAAACCTTGACCAGGGGCTTGTCCTCGTCGTCCTCATCGTCGTCATCGGTGTCCTTGGAGGGCTTGGCCTGCTTCTTGATGGCAGCTGGCTTGGTGGACGATTTGCTGGACGCCTGGTTGGCAAACTGGAAGTTGCCGCCGCTGGGACGCTTGCCCTGATCGCCTTCGCTATGCCCGATCCGCTGGGCGGTCATCTTAGGAACTTTCGTTGACTTCTCCAATTTGGTTGGACAGCATTGGAATGGTTTGTAATCGTTGGGCACGAAATTGTTGCCGCGCTTAGCTGAATGGCCGTCATGACCCAATCCAACATAGAAACATTCGTCATCTG 2471 2952 ---ATGACGAATGTTTCTATGTTGGATTGGGTCATGACGGCCATTCAGCT-AGCGCGGCAACAATTTCGTGCCCAACGATTACAAACCATTCCAATGCTGTCCAACCAAATTGGAGAAGTCAACGAAAGTTCCTAAGATGACCGCCCAGCGGATCGGGCATAGCGAAGGCGATCAGGGCAAGCGTCCCAGCGGCGGCAACTTCCAGTTTGCCAACCAGGCGTCCAGCAAATCGTCCACCAAGCCAGCTGCCATCAAGAAGCAGGCCAAGCCCTCCAAGGACACCGATGACGACGATGAGGACGACGAGGACAAGCCCCTGGTCAAGGTTTCCTATGCCAACAAGCGCTCGGGAGGAAGCAACAAGCCGCAGGCTGGCAAGAAGCCGGTAGGCAAGGGCCAGGACAACGACGACCAGTCCCAGGAGGTGGAGAAGGTATCCAAACAGAAGTCGGCGAAGAAGTCCGGCAAACTGAATGTCAAATCCG 99 NULL:1988054 58095 56609 TTTATTGAGTTGGATGGCTTTTATTAAATATTCTTACAATTTCATTCGGGAGCTATGTTTACAAAAGTGCTTTATGTCGATTTGCGTTTGATTTTTACGATCTGACAATTTCCATTTCGAAAATCTTGACTTATCAGCTGCTGTTCAACAAAATTTGTTTACATATATGTTGGATTTAGTTACAATTGCGTTTAGATTGGTAGGCTTTAGCTTAAGAAAACATAATGATAAAGATTTCTAATTCGATATTTTTCAAATACCGATAACAAAAACAACAGCGAGCGGTACAGAAATCGCTCTCAGAAGAAAACAAATGAAACAAAATGGCGAGCTACAATATGCGAGGCCATGTTCAGCGAGAAATATTGGATTTTCGATTCCATAACAAAATTAAGTATACGGCCTGTATGCTGCTGCAACATTTCTAAAAAGTTGTGGTTACAAATTATGGTTCCTCATGTTGTTATTATGAAAACTTATGAAAGTTGAAGGCTCTCATAGTTACACGTTTCAGTTAAATTAGCTAACAGTTGTGCACTGTCAGGTGTAAATTGTTTCAAAAAATATTTTATGCGTTTGTTCGTTCGTTTACTATGCTTTGGCCCTTGTTTAAATTAGACTAACTACATAAATGTAAATTGTATATTGCGACAAAAAGAAGTAGTATCAAAAAAGTTTAGGCGTTCGTTATTGACAAAAGACAATGTCCCATTAATTTGTTAATAACAAAGCTTGCTGACTAAATATACGAGCGAAAGTTCTCAGAAGTTTTATAGTTGTTTGTCGAAGTAATTGCTTTTAGTTTGAACAAAGTTTTTTGAAATCCGTTGGCAAAATGCAACAAATGTGTGGTTTAGTTAGTTATAGACCTGGGGACGACCTACACAGGTCGGCCCCTCTTGAAGAAAGTTAAAGCGAAAATATCAACAAAGTTTTAGTTAGTAGGTTTTCTTGATCATTATTCATTATTTCGGGTATCGTGTGATTCTGCTACTCGTGGATCTTCTTAACGTGGAACAACGCCCAAGGCTCGCTGCTTAAAAGTGTGGAGTAAGTTCTGATCTGACACAGAAGATGTATTGGTATTTAAGTCAATGTTTTTGTGCCAGACTGTTTAGGATTAGTGCGAGGAAACCTCAATTTTATGGACACACAGCCTGCGAATTCAGTTTTCAGTTGGTTCTTGTCATAGTTGTTGTCTTTTGCAGTCACACATATGTAGATGATGTACATTAATTATAGAAACCTGTCATTGAAGGTTCTTTTGCTGGCTATACAGGTTTGAGTTGGTTTTGTATTTTGTTTTGGTTTTGGTTTTGGGTTTGGTATTGGTTTTGGTTTGATAATTGTTCTATCAGTTGGCAACAGTGCGTATACGTGCTACTTTAGTATGGTATATCATTCAATCATACAATCAATCACTATCTAACTGTCTGTGGTTATCCACATTCAGTTAAACTGTTGCCTTACTCCCACAGAGAGATATCCTG 2953 4439 ---GATATCTCTCTGTGGGAGTAAGGCAACAGTTTAACTGAATGTGGATAACCACAGACAGTTAGATAGTGATTGATTGTATGATTGAATGATATACCATACTAAAGTAGCACGTATACGCACTGTTGCCAACTGATAGAACAATTATCAAACCAAAACCAATACCAAACCCAAAACCAAAACCAAAACAAAATACAAAACCAACTCAAACCTGTATAGCCAGCAAAAGAACCTTCAATGACAGGTTTCTATAATTAATGTACATCATCTACATATGTGTGACTGCAAAAGACAACAACTATGACAAGAACCAACTGAAAACTGAATTCGCAGGCTGTGTGTCCATAAAATTGAGGTTTCCTCGCACTAATCCTAAACAGTCTGGCACAAAAACATTGACTTAAATACCAATACATCTTCTGTGTCAGATCAGAACTTACTCCACACTTTTAAGCAGCGAGCCTTGGGCGTTGTTCCACGTTAAGAAGATCCACGAGTAGCAGAATCACACGATACCCGAAATAATGAATAATGATCAAGAAAACCTACTAACTAAAACTTTGTTGATATTTTCGCTTTAACTTTCTTCAAGAGGGGCCGACCTGTGTAGGTCGTCCCCAGGTCTATAACTAACTAAACCACACATTTGTTGCATTTTGCCAACGGATTTCAAAAAACTTTGTTCAAACTAAAAGCAATTACTTCGACAAACAACTATAAAACTTCTGAGAACTTTCGCTCGTATATTTAGTCAGCAAGCTTTGTTATTAACAAATTAATGGGACATTGTCTTTTGTCAATAACGAACGCCTAAACTTTTTTGATACTACTTCTTTTTGTCGCAATATACAATTTACATTTATGTAGTTAGTCTAATTTAAACAAGGGCCAAAGCATAGTAAACGAACGAACAAACGCATAAAATATTTTTTGAAACAATTTACACCTGACAGTGCACAACTGTTAGCTAATTTAACTGAAACGTGTAACTATGAGAGCCTTCAACTTTCATAAGTTTTCATAATAACAACATGAGGAACCATAATTTGTAACCACAACTTTTTAGAAATGTTGCAGCAGCATACAGGCCGTATACTTAATTTTGTTATGGAATCGAAAATCCAATATTTCTCGCTGAACATGGCCTCGCATATTGTAGCTCGCCATTTTGTTTCATTTGTTTTCTTCTGAGAGCGATTTCTGTACCGCTCGCTGTTGTTTTTGTTATCGGTATTTGAAAAATATCGAATTAGAAATCTTTATCATTATGTTTTCTTAAGCTAAAGCCTACCAATCTAAACGCAATTGTAACTAAATCCAACATATATGTAAACAAATTTTGTTGAACAGCAGCTGATAAGTCAAGATTTTCGAAATGGAAATTGTCAGATCGTAAAAATCAAACGCAAATCGACATAAAGCACTTTTGTAAACATAGCTCCCGAATGAAATTGTAAGAATATTTAATAAAAGCCATCCAACTCAAAAAA 2604439 100 NULL:1988095 208683 207202 TG...CACCTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTGGGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGAGAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGGTGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGTTCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTCCTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAAAGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCCTTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATACATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCCAATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTGTAAGTATCCAAATCGACCGTGGATGAGGTGTGCTCGTTTTCATAAATTTATGTAATTGCAGTGTACTGATGAGTCACCTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACTGAATTCTCTCAGCGAGCGTACATTGTTTTTATACTCGCATATGCATATGTATTCCCCCACAAAACAATGATTTCTCTTCAGTTCGTGCTCCCAAACGGGTTTTTCTCTCGCCTGCCTTCGGTGTTCTCATTGATTTCACTCTTTACATCCATAATGCGTTTTCTTTCACTGGCTTTTTAAAGTCAAACTGCCGGATAACTCACCACATGGCACCAAACGATAATCCATACTCAGTAATTTTGCTTACAGTAAACCTAGTCTGCAAAG 1 1482 CTTTGCAGACTAGGTTTACTGTAAGCAAAATTACTGAGTATGGATTATCGTTTGGTGCCATGTGGTGAGTTATCCGGCAGTTTGACTTTAAAAAGCCAGTGAAAGAAAACGCATTATGGATGTAAAGAGTGAAATCAATGAGAACACCGAAGGCAGGCGAGAGAAAAACCCGTTTGGGAGCACGAACTGAAGAGAAATCATTGTTTTGTGGGGGAATACATATGCATATGCGAGTATAAAAACAATGTACGCTCGCTGAGAGAATTCAGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTTATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTACCAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTGAATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTGGAGGTGACTCATCAGTACACTGCAATTACATAAATTTATGAAAACGAGCACACCTCATCCACGGTCGATTTGGATACTTACAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAG-------- 100 NULL:1988096 207137 206996 G...TACCCGTGGCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTGTATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAAATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAG 1483 1624 CTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCACGG------- 100 NULL:1988097 206508 206371 TTCAAAACTTATTGATTCTTCCCGCAAACAAAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACATGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACATGACCATTC 1625 1762 GAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAA 99 NULL:1988098 206301 205924 TTTT-AGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTAGTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGTTGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAACGTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATACCTG 1763 2141 ---GTATGTTTATGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAAA 2598669 100 NULL:1983287 322464 322552 TTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTG 1 89 TTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAG--- 100 NULL:1983288 324148 324259 TTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGCTCTGTTCGGTG 90 201 TTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGCTCTGTTCG--- 100 NULL:1983289 326451 326642 ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGGTA 202 393 ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACG--- 100 NULL:1983290 326706 326867 TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAGATCAGCGTA 394 555 TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAGATCAGC--- 100 NULL:1983291 326934 327128 ATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAAGTA 556 750 ATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA--- 99 NULL:1983292 327392 327750 TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA 751 1109 TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTAAAAAAA 2604369 100 NULL:1988033 45640 44879 CTGATCACTCTGCTGAGTTGGTGAATTCGTGGCTTCTGGGCTAAATTGCAACCATTACTGGGAGTTGGTCCTGTGTCATTGCATTATCTTACATTATAGGCTGCACATTACAGTAAATGTAGTTGTTGGGCAGACGAGTATTACAAAAATACAATAAGCTCGCTCTCTCTTTCGTTTCTTTTGCGTATGCCTCTTCGTCGAATTTGTTAGCTGTTGTTTTATGAATTTCTGCCGCCCGTCTTGCACAGTGGGATGAAATCGCTGTAGCACACGTCCAAATCAGCTGGCTTATATATGTATGTACGATTAGAATTGGTTGCGGGTGACACTCCAGAACGCCAAGTTGCCAAACACTCTTTATAGGCGATATTACGCACACTCAAGTTCCCGTGGAAAGTTATTATCTATCGGCTTCGCCCTGGGTCACGCCCACTGTACGGGAGTTTCGATTTTCTGCGGGGGAGGTGGGACAGTGACAACACCGCTCGGCGGCACAAGTTCAACAGAAAATGTGGGGCGACCGGAGGTCGTATAAACAAAAGCACAGTGCACCCGAGTGCGGAAATCGCGGCTGTAAGTGCTTCAAATGCACGCAGGAGTCGGGAATCGGGGAGGAACTTTCGATTCACCCAATCGCTGGATTTCAATTGATTACTTAACACGCTCTGTCGCGAGAAAAATAGGCTATCTCTACTGCCGCGGCCCTTAAAAATATAGAAAAGTCGTATAGTCCACCACACTAGCACCACACGTCCGTTCGCA 1 762 TGCGAACGGACGTGTGGTGCTAGTGTGGTGGACTATACGACTTTTCTATATTTTTAAGGGCCGCGGCAGTAGAGATAGCCTATTTTTCTCGCGACAGAGCGTGTTAAGTAATCAATTGAAATCCAGCGATTGGGTGAATCGAAAGTTCCTCCCCGATTCCCGACTCCTGCGTGCATTTGAAGCACTTACAGCCGCGATTTCCGCACTCGGGTGCACTGTGCTTTTGTTTATACGACCTCCGGTCGCCCCACATTTTCTGTTGAACTTGTGCCGCCGAGCGGTGTTGTCACTGTCCCACCTCCCCCGCAGAAAATCGAAACTCCCGTACAGTGGGCGTGACCCAGGGCGAAGCCGATAGATAATAACTTTCCACGGGAACTTGAGTGTGCGTAATATCGCCTATAAAGAGTGTTTGGCAACTTGGCGTTCTGGAGTGTCACCCGCAACCAATTCTAATCGTACATACATATATAAGCCAGCTGATTTGGACGTGTGCTACAGCGATTTCATCCCACTGTGCAAGACGGGCGGCAGAAATTCATAAAACAACAGCTAACAAATTCGACGAAGAGGCATACGCAAAAGAAACGAAAGAGAGAGCGAGCTTATTGTATTTTTGTAATACTCGTCTGCCCAACAACTACATTTACTGTAATGTGCAGCCTATAATGTAAGATAATGCAATGACACAGGACCAACTCCCAGTAATGGTTGCAATTTAGCCCAGAAGCCACGAATTCACCAACTCAGCAGAGTGATCAG 100 NULL:1988034 35973 35010 CCGATCGTAGTCCAGGCAATGCTCTCTCCGCACGCCAACAGCCAACTTTTGTTAACGAATAAATTGATTCGGTGATCTGCGGATTTTGCGGATATATTCTTAAGATTTCACTGGCACTAGTTTCACTGTTTCGGCACCACCGCCAATCAATTCACCATAATTGCACAGATCTTCAGTTATGTTTAGCTCGCTCAGGGTGCGATTCGAGTGTTTATTCAGGGTGGCGGTTTTGTTGAAAATTCTTAGGCGCGGATCGCGGGGTATGTAATGCAGGAACACCTTGTTCGACTTGCCGCTGTTGTTGTAAGTACGGGGATTGTTGTTCTGGCCCTTGTCGAACGACTTGGCGTTGGTGGTCGCGCCCGACGCGGATGCTGCAGATGTTGGTTTGCCTGCACGATAGAATGACTTGGACCGAAGGTCGTTCATTAAGAACGTTAGGGGGTTTATCACAGGCCAACGGAGAATATATTGAGCGATAATTGACGGCAACTGGCGGCAGTTGCTGGTGATGTTGCTGTTGTTGCTGTTGCAGTTGCAGATGCAGTTGTTGCAGTTTGTGCTGCCGGCTAGCAGATTTTGCCCTGGCAGCCACATGCGGTACTTTGTTTTCGCGGAAATCAAACACTTTTCGATTCGATGCCAACGATGCCAACTAGCGTGCCCGGCTAGCTCGAACAAGAAATAACAAACACAAATCGAACACAAGACTGGGCCTCACTGGCTTCTCCGGCTACTCTGCCGCTCCCCGTGTCAAGTGCGCGGCGCGTGGTGCGGAGGCGGATTCGCAGGCATTGTATATATGTATATCTTAGTATCGACGGAGGGACGACCAACGCGGCGTATGATTAATTCGTCTCTGGTGGTGCAACTCAATCGCTGCTGTCGCTGTGCTCGCCTCCTCGCTGGCGCCAGATAATGATTTATGATCCTCGTCCTCAATTAGCAGCCTTCAGTGCAAACGCTG 763 1726 ---CGTTTGCACTGAAGGCTGCTAATTGAGGACGAGGATCATAAATCATTATCTGGCGCCAGCGAGGAGGCGAGCACAGCGACAGCAGCGATTGAGTTGCACCACCAGAGACGAATTAATCATACGCCGCGTTGGTCGTCCCTCCGTCGATACTAAGATATACATATATACAATGCCTGCGAATCCGCCTCCGCACCACGCGCCGCGCACTTGACACGGGGAGCGGCAGAGTAGCCGGAGAAGCCAGTGAGGCCCAGTCTTGTGTTCGATTTGTGTTTGTTATTTCTTGTTCGAGCTAGCCGGGCACGCTAGTTGGCATCGTTGGCATCGAATCGAAAAGTGTTTGATTTCCGCGAAAACAAAGTACCGCATGTGGCTGCCAGGGCAAAATCTGCTAGCCGGCAGCACAAACTGCAACAACTGCATCTGCAACTGCAACAGCAACAACAGCAACATCACCAGCAACTGCCGCCAGTTGCCGTCAATTATCGCTCAATATATTCTCCGTTGGCCTGTGATAAACCCCCTAACGTTCTTAATGAACGACCTTCGGTCCAAGTCATTCTATCGTGCAGGCAAACCAACATCTGCAGCATCCGCGTCGGGCGCGACCACCAACGCCAAGTCGTTCGACAAGGGCCAGAACAACAATCCCCGTACTTACAACAACAGCGGCAAGTCGAACAAGGTGTTCCTGCATTACATACCCCGCGATCCGCGCCTAAGAATTTTCAACAAAACCGCCACCCTGAATAAACACTCGAATCGCACCCTGAGCGAGCTAAACATAACTGAAGATCTGTGCAATTATGGTGAATTGATTGGCGGTGGTGCCGAAACAGTGAAACTAGTGCCAGTGAAATCTTAAGAATATATCCGCAAAATCCGCAGATCACCGAATCAATTTATTCGTTAACAAAAGTTGGCTGTTGGCGTGCGGAGAGAGCATTGCCTGGACTACGATCGG 100 NULL:1988035 34361 32162 ATCTTCCTCCTCTTTGGCGATGGTGGTCATCGAGTTGCGGTAGATGTTGGGACAGGAGGAGGCGCGCAGCCGGTAGCGGTGCGTGTTCAGCATGGCCCCGCGGTAGTGGATCGAGTTGCGGTGAATGCGCATATCCTTAAGGAAGTTGGAGTTCCGGATCGAGATGTTGCGGCGGAGGTTCGATCGGTGGTGGCTGGGCTTCTTGGAGCGCGACAGCCGGCGGATTCCCGTGATGCTGTCCAGGCGTGCGCGACGGGTGGCCAGCTCGCTGTTCACCGACTGCTCCTGTTCCGGAATGGCGATGACGGTGGGCCTGATGCGCCTGCTCGGCTCCAGCAATGCGAAGGTCTCGTCCTTCGAGTAGTAGCAGTGCATGTCCTCGCTCAAGATGTCCACCGAATTGTGTCGCAGGCCATTCACCTTTAGGTTGGAGATTGATGGTGTTGTATGCTTGGCCATGAAGATGTTTTCGTTAAGCGAGTACCGGGAGCTGGCGTGCTTCTGCGTAAGGTAGCCTTCGTCCGAGGAGCGGAGCGAGCCATTGGGAGTCCTACCAGTGGAGCGCTTTTCCGATGGAGACAGCGTCTCGATGGAGGCCAGATAGGCCTTCTTTGCTTCCTCTGCCGCCTCGTGAGCTATTCCGCCCATTAGGGTATCATCTGGCGAGCCTATAACGGCCGTCGATGGGGGATAGGCACCTGCTCCTGAGGACATGGACAGCAGGTTCTCTCGTGACGGCGCCTCCTCACCCTCCTTGTGGCGTAGGGAGCGTCGGCTCAGGCTCTTAACCTCGCAGATGCTGTCAAGCTCCTGAGTGCTCAGGAAGGTGGGCAGGAAGATCTCGCTGCGGTAGCGCTTGAGAGCGGAGTCCAACGGATCGTCAATCTGCTGGTTGGCCTCCGTGTTGTTCTTGGTCACCAACGAGTCTAGCACAGCCTCCTTTGTGATGCCGGTGTCCAGCAGCTTTTTTATTTCCTCCAGGCAGACACTGGAGTTCGAGAAGGTGGTGACGCTTTGGGATCGACTCTCTAGACGGTTTTCCTCGATCAGCCAGTCGGGATCGCGCATGAGGGCGCCGCAAACGCATGCGTTGAGCATGGTGCCGCCAAGGATTAGAGTGGCTCCGCGCCAGCCGTACGATTCGATTAGATAGGAAGTAAGGCGGGCGTAGACAAAGGTCCCGATGCCGGTGCCCGATGCTCCGATGCCGGTCGCAAAGGTGCGCTTCTTGTCAAACCAGAATGCAATGGACACCACCGCGGTCACATACCCGATGCCTAGGCCCAGTCCCGAAATGATACCAAAGGTCACCATGAGCATCTCGATCGAGTTGCAAAACGAAGACAGAGCAAACCCAAAGGCAGAGACCACTCCGCCGAGGATGGTCATCTTTCGGCAGCCGTACTTGTCCACCAGATTGGACCAGATGGGTCCCATCAACAGGGGCACGGAGAAGAATAGCGAGGATATCCAGGCGGTCTTCGAAGTGGACTCTCCGAAGTATTCCAGCAGTTCCACGTTTATTAGGCCAAATGAGAAGCTCAGTCCGTCGGCTATAAGGGACACGACCAGAGAGGCGAACACCACCACCCACCCATATCCACCGTCGGGCATCTTGGGCGTTTTCTTCTCCGTGGAACTGGAGTCGATCGAGTCGCCGGACTCGTTCGAGATCAGGCGTTTGCGACGCTTCACCTGCCCATTTCCGTTCATCAGGCACGTCATGGTGCCGTCCTCCAGTTCGATGACACTGCTCCTTACCACACGGCTGTGTCCAGCCCCATCTGCGAGCTCCTCTACGGAGAGGTTGCAGAAGGTGACCTCCGGGAAGAGGTCGTGCTTGATGGCCTTGTGGAGTGGCGTGTTGGCCGGAGCAGGCGTAAGAGGCAGGGCCTGGTAATTGGAGGCGCCTCCGTTTTGGCTCTGGTTCTGGCCATTGTGGTTGTTGTTAACCGCCTCGCAGCTGTTGTTGTTGGAGGCGTTTGGATCCGTCGCTAGCTTGGCCATGTCGGAGTCCCAGTGATCGTGTTGTTGTGTAAAGGGTTCAGCTACGTCTATAAAAAGGTTTGTAAAATTTGCACTTTCTTGTCCAAGCGATTATTGGAAGTGAACACAATTTGCATTAGATTTCAGCATAAATTTTCTTAAGTAGGCGGTAGGTAAATATTCCCTCTCTCTGTTGGTCAACTGCAGTGCGTAG 1727 3926 CTACGCACTGCAGTTGACCAACAGAGAGAGGGAATATTTACCTACCGCCTACTTAAGAAAATTTATGCTGAAATCTAATGCAAATTGTGTTCACTTCCAATAATCGCTTGGACAAGAAAGTGCAAATTTTACAAACCTTTTTATAGACGTAGCTGAACCCTTTACACAACAACACGATCACTGGGACTCCGACATGGCCAAGCTAGCGACGGATCCAAACGCCTCCAACAACAACAGCTGCGAGGCGGTTAACAACAACCACAATGGCCAGAACCAGAGCCAAAACGGAGGCGCCTCCAATTACCAGGCCCTGCCTCTTACGCCTGCTCCGGCCAACACGCCACTCCACAAGGCCATCAAGCACGACCTCTTCCCGGAGGTCACCTTCTGCAACCTCTCCGTAGAGGAGCTCGCAGATGGGGCTGGACACAGCCGTGTGGTAAGGAGCAGTGTCATCGAACTGGAGGACGGCACCATGACGTGCCTGATGAACGGAAATGGGCAGGTGAAGCGTCGCAAACGCCTGATCTCGAACGAGTCCGGCGACTCGATCGACTCCAGTTCCACGGAGAAGAAAACGCCCAAGATGCCCGACGGTGGATATGGGTGGGTGGTGGTGTTCGCCTCTCTGGTCGTGTCCCTTATAGCCGACGGACTGAGCTTCTCATTTGGCCTAATAAACGTGGAACTGCTGGAATACTTCGGAGAGTCCACTTCGAAGACCGCCTGGATATCCTCGCTATTCTTCTCCGTGCCCCTGTTGATGGGACCCATCTGGTCCAATCTGGTGGACAAGTACGGCTGCCGAAAGATGACCATCCTCGGCGGAGTGGTCTCTGCCTTTGGGTTTGCTCTGTCTTCGTTTTGCAACTCGATCGAGATGCTCATGGTGACCTTTGGTATCATTTCGGGACTGGGCCTAGGCATCGGGTATGTGACCGCGGTGGTGTCCATTGCATTCTGGTTTGACAAGAAGCGCACCTTTGCGACCGGCATCGGAGCATCGGGCACCGGCATCGGGACCTTTGTCTACGCCCGCCTTACTTCCTATCTAATCGAATCGTACGGCTGGCGCGGAGCCACTCTAATCCTTGGCGGCACCATGCTCAACGCATGCGTTTGCGGCGCCCTCATGCGCGATCCCGACTGGCTGATCGAGGAAAACCGTCTAGAGAGTCGATCCCAAAGCGTCACCACCTTCTCGAACTCCAGTGTCTGCCTGGAGGAAATAAAAAAGCTGCTGGACACCGGCATCACAAAGGAGGCTGTGCTAGACTCGTTGGTGACCAAGAACAACACGGAGGCCAACCAGCAGATTGACGATCCGTTGGACTCCGCTCTCAAGCGCTACCGCAGCGAGATCTTCCTGCCCACCTTCCTGAGCACTCAGGAGCTTGACAGCATCTGCGAGGTTAAGAGCCTGAGCCGACGCTCCCTACGCCACAAGGAGGGTGAGGAGGCGCCGTCACGAGAGAACCTGCTGTCCATGTCCTCAGGAGCAGGTGCCTATCCCCCATCGACGGCCGTTATAGGCTCGCCAGATGATACCCTAATGGGCGGAATAGCTCACGAGGCGGCAGAGGAAGCAAAGAAGGCCTATCTGGCCTCCATCGAGACGCTGTCTCCATCGGAAAAGCGCTCCACTGGTAGGACTCCCAATGGCTCGCTCCGCTCCTCGGACGAAGGCTACCTTACGCAGAAGCACGCCAGCTCCCGGTACTCGCTTAACGAAAACATCTTCATGGCCAAGCATACAACACCATCAATCTCCAACCTAAAGGTGAATGGCCTGCGACACAATTCGGTGGACATCTTGAGCGAGGACATGCACTGCTACTACTCGAAGGACGAGACCTTCGCATTGCTGGAGCCGAGCAGGCGCATCAGGCCCACCGTCATCGCCATTCCGGAACAGGAGCAGTCGGTGAACAGCGAGCTGGCCACCCGTCGCGCACGCCTGGACAGCATCACGGGAATCCGCCGGCTGTCGCGCTCCAAGAAGCCCAGCCACCACCGATCGAACCTCCGCCGCAACATCTCGATCCGGAACTCCAACTTCCTTAAGGATATGCGCATTCACCGCAACTCGATCCACTACCGCGGGGCCATGCTGAACACGCACCGCTACCGGCTGCGCGCCTCCTCCTGTCCCAACATCTACCGCAACTCGATGACCACCATCGCCAAAGAGGAGGAAGAT 100 NULL:1988036 31697 31588 CAAATGAACAAAAACAATGTAGAGAGATTGAAGAGGGCGAACTTCATGTCCAGAAAGAGTGAAAAGTCAAAGATGGACTTCATGGTGTCCACAAAGTTGTCATACCAGGTCTA 3927 4036 ---ACCTGGTATGACAACTTTGTGGACACCATGAAGTCCATCTTTGACTTTTCACTCTTTCTGGACATGAAGTTCGCCCTCTTCAATCTCTCTACATTGTTTTTGTTCATTTG 100 NULL:1988037 31146 30965 CCAGCATGCACAGCGAGTAGCATATATTGATGTTCATCCAGGACAGATCCCCCAGATAGCCAAGTCCTATCATGCCCACCGTTTGGGCAATGCCGACATCCGAAATCAACTCGGCACTCTGGCTCACGTCGTACTTGTATTGCTTCATGTAATCGGGAAGGTACAGATAGGGGATAATGAACCTG 4037 4218 ---GTTCATTATCCCCTATCTGTACCTTCCCGATTACATGAAGCAATACAAGTACGACGTGAGCCAGAGTGCCGAGTTGATTTCGGATGTCGGCATTGCCCAAACGGTGGGCATGATAGGACTTGGCTATCTGGGGGATCTGTCCTGGATGAACATCAATATATGCTACTCGCTGTGCATGCTGG 100 NULL:1988038 30897 30657 CTGCCCGTATACTCGTATATGACGCCTGCAATAGGGGGTCCTGCGATCATTCCAACTCCCTGAACCAGCAGCACCAGACCGTAGGCACACGTGAAATCGTCCAGATCCACAATACTGACCAGAATGCTGGGCGTAAACGAGAAGGAGCTGGCGAACGTAAATCCGAAAATAACGCACATGACCATCAGGCCCATGTAGTTGGTAATCAGCAGGGGCATGAAGAACACAGACGCTCCGCACACTG 4219 4459 ---TGTGCGGAGCGTCTGTGTTCTTCATGCCCCTGCTGATTACCAACTACATGGGCCTGATGGTCATGTGCGTTATTTTCGGATTTACGTTCGCCAGCTCCTTCTCGTTTACGCCCAGCATTCTGGTCAGTATTGTGGATCTGGACGATTTCACGTGTGCCTACGGTCTGGTGCTGCTGGTTCAGGGAGTTGGAATGATCGCAGGACCCCCTATTGCAGGCGTCATATACGAGTATACGGGCAG 100 NULL:1988039 30592 29998 GTTACATAGATTGTTGTTTATTGTATTCCCTTTAATTAATATTCGTACGAAATGTAAGGCAATTAAAACTATTTTTCTAAATTTTGTAAAGAAGACAATTGAGGGACCCGTTTGCACCTGGCAGTGATGCACTGCATTGATATTGATTGAAATTGAACAGTTTGTCTAGACAAAGATGCGGTTAGTAATTGCCCTAGTGCGGTAAGTATATGTTAGGTGTATATTGATACTTAGCTACGATTAGTCAAGTCAAGTATAGTCTTACAGGCTAGAGCTTAGGAATAGGCTTAGTTTCAGTTACAATTCTGCTCTGATTTTATGGCTGCAACACCATTTGACATAAGAAACTCGTTAACATTTAATGCTAGTCCATTATTATGCTACAGTTCGGATTTGTAGTACCTCCAGTTGCCTTCTACTTGCGGCGTTCAACAGTGCAATGTAAGTAACCTAGTGTAAAAGTTGAGCTTTTTTAGTCTCTAAGACATCACTATCACTCTCCTTAGGTGCTTTCTTTTCACAGAACTCGATCAGATACGAACAGACACCAGAGAGTGCGATAAATATTCCAGCATAATAGAAGGTGTCATCCCATCTG 4460 5054 ---ATGGGATGACACCTTCTATTATGCTGGAATATTTATCGCACTCTCTGGTGTCTGTTCGTATCTGATCGAGTTCTGTGAAAAGAAAGCACCTAAGGAGAGTGATAGTGATGTCTTAGAGACTAAAAAAGCTCAACTTTTACACTAGGTTACTTACATTGCACTGTTGAACGCCGCAAGTAGAAGGCAACTGGAGGTACTACAAATCCGAACTGTAGCATAATAATGGACTAGCATTAAATGTTAACGAGTTTCTTATGTCAAATGGTGTTGCAGCCATAAAATCAGAGCAGAATTGTAACTGAAACTAAGCCTATTCCTAAGCTCTAGCCTGTAAGACTATACTTGACTTGACTAATCGTAGCTAAGTATCAATATACACCTAACATATACTTACCGCACTAGGGCAATTACTAACCGCATCTTTGTCTAGACAAACTGTTCAATTTCAATCAATATCAATGCAGTGCATCACTGCCAGGTGCAAACGGGTCCCTCAATTGTCTTCTTTACAAAATTTAGAAAAATAGTTTTAATTGCCTTACATTTCGTACGAATATTAATTAAAGGGAATACAATAAACAACAATCTATGTAAC 2598597 100 NULL:1983225 79009 79164 CTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGGTG 1 156 CTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAG--- 100 NULL:1983226 82407 82559 TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 157 309 TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAG--- 100 NULL:1983227 82618 82763 GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 310 455 GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAG--- 100 NULL:1983228 83955 84213 ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCA 456 714 ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCA 100 NULL:1983229 84480 84619 CAGG 715 854 ---G 100 NULL:1983230 84674 84756 TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTGTA 855 937 TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCT--- 100 NULL:1983231 84820 84892 TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTA 938 1010 TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAG--- 100 NULL:1983232 84960 85814 GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 1011 1865 GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 2598686 100 NULL:1983301 333375 333417 CGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA 1 43 CGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA 98 NULL:1983302 333680 334038 TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCA-AATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA 44 403 TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGGCAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTAAAATTTGCATAATCTCAAGCGTAAGCAGCGTAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGATTGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTCACGAAAA 2604401 99 NULL:1988061 88663 87371 ATCTTCTACGTAATATACTTTATTTTACAATACAAATACTACATATGCGGGGTGTCTTACGAACCTCTTCCAGTAAAATATTAAGGGGAATTAATGCACGGGTTTACTCGAAACCTTTTTAACTTTGAGTTAACAACTAAAACAAAACACCCCTCTTGGAATGCCACAGTCGTTTTGTTTGCATTCCTAGCCAATCCAATAACGGCGAAACCGATATTTCTGGGACACCCCTGAGCCCGTCTAGAACTCGTCGTTGAACGGGTAGTACTTATGGCCCGACATTCCCGAAAAGGGTACCGTGCGCTGCCCGGTGTGATACTGCTCCATGCCGGCGACGTCGTCTGGACTCAGCTCGAAGTCGAAGACGCGGAAGTTCTCCTCGATGCGGGCCTTGTTCGACGACTTGGGCAGTGGCACCACGCCTAGCTGGACCAGATAACGCAGGCAGATCTGTGCCGTGGTGCGGCCGTACTTCTTGGCCAGATTCTGGGCATGCTCGTCGTAGAGGAAGGGCGGCCACTGCCGAGCGGGCTGGGGACGTGCCAGGGGGCAGTAGGCGCAGATGACCAGTCCGTGGCGCTTGGCATGCTCCCGGAGCTGGCGCTGCTGAAAGCCTGGGTGGCACTCCACCTGGTTCACTACCGGCCGGATGCGGCAGTTGGCTAGCACTCGCTCCGTCTGCGCGGCGTTGAAGTTGGACAGGCCGATGCTGCGCGTCAGGCCCAGATCCACCAGCTTCTCCATCTCGCGCCAGGTGTCCAGATAGTCCACGTCCGTCAGCTCCAGGGTTCCGTGCACGTTGCTGTCATTGTGGAACTTCTGGCCCACCGGCATGTGCATCAGGTAGAGGTCTACGTATTCCAAACCCAGGTTGCTAAGGCTCAGGCGGCAGGCGCGCTCCACCAATGCAGGGTCGTGGTGGATTCCGCCTAGCTTGGTGGTCACGAAAACCTCCTCGCGTGTGACCACTCCCTCGGCGATCTTCTCGGAGATCGCCTGGCCCACCTCAGCCTCGTTCTCGTAGACGAAGGCGGTGTCCAGGTGCCGGTAGCCCACGTCGAGGGCGTGGCGCGTTGAGTGGTAGGCGTCCGACTCGAACGACTTCCAGGTGCCAAGGCCCAGAGTTGGCATCTCGCGCCCGTTGTTCAGCCGGATGGTGGGAGCCAGATTGGTCATCTTGTCGCTGGCGCTGATAATTAACGCTGTGCAAATTGGACGCTTCTAAGTCTAAACCAGTGCTACTACGCCTTTCTCGCGATCAAATCTCTATCTGTTCCAGCTCGTCGAAAGCTT 1 1292 AAGCTTTCGACGAGCTGGAACAGATAGAGATTTGATCGCGAGAAAGGCGTAGTAGCACTGGTTTAGACTTAGAAGCGTCCAATTTGCACAGCGTTAATTATCAGCGCCAGCGACAAGATGACCAATCTGGCTCCCACCATCCGGCTGAACAACGGGCGCGAGATGCCAACTCTGGGCCTTGGCACCTGGAAGTCGTTCGAGTCGGACGCCTACCACTCAACGCGCCACGCCCTCGACGTGGGCTACCGGCACCTGGACACCGCCTTCGTCTACGAGAACGAGGCTGAGGTGGGCCAGGCGATCTCCGAGAAGATCGCCGAGGGAGTGGTCACACGCGAGGAGGTTTTCGTGACCACCAAGCTAGGCGGAATCCACCACGACCCTGCATTGGTGGAGCGCGCCTGCCGCCTGAGCCTTAGCAACCTGGGTTTGGAATACGTAGACCTCTACCTGATGCACATGCCGGTGGGCCAGAAGTTCCACAATGACAGCAACGTGCACGGAACCCTGGAGCTGACGGACGTGGACTATCTGGACACCTGGCGCGAGATGGAGAAGCTGGTGGATCTGGGCCTGACGCGCAGCATCGGCCTGTCCAACTTCAACGCCGCGCAGACGGAGCGAGTGCTAGCCAACTGCCGCATCCGGCCGGTAGTGAACCAGGTGGAGTGCCACCCAGGCTTTCAGCAGCGCCAGCTCCGGGAGCATGCCAAGCGCCACGGACTGGTCATCTGCGCCTACTGCCCCCTGGCACGTCCCCAGCCCGCTCGGCAGTGGCCGCCCTTCCTCTACGACGAGCATGCCCAGAATCTGGCCAAGAAGTACGGCCGCACCACGGCACAGATCTGCCTGCGTTATCTGGTCCAGCTAGGCGTGGTGCCACTGCCCAAGTCGTCGAACAAGGCCCGCATCGAGGAGAACTTCCGCGTCTTCGACTTCGAGCTGAGTCCAGACGACGTCGCCGGCATGGAGCAGTATCACACCGGGCAGCGCACGGTACCCTTTTCGGGAATGTCGGGCCATAAGTACTACCCGTTCAACGACGAGTTCTAGACGGGCTCAGGGGTGTCCCAGAAATATCGGTTTCGCCGTTATTGGATTGGCTAGGAATGCAAACAAAACGACTGTGGCATTCCAAGAGGGGTGTTTTGTTTTAGTTGTTAACTCAAAGTTAAAAAGGTTTCGAGTAAACCCGTGCATTAATTCCCCTTAATATTTTACTGGAAGAGGTTCGTAAGACACCCCGCATATGTAGTATTTGTATTGTAAAATAAAGTATATTACGTAGAAAA- 2598612 100 NULL:1983238 140796 140950 CATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAAGTA 1 155 CATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAA--- 100 NULL:1983239 141677 141858 GGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCA 156 337 GGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCA 100 NULL:1983240 142556 142891 CAGAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAA 338 673 ---AACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAA 100 NULL:1983241 142948 143528 CAGGTCTGTTCTA 674 1254 ---GTCTGTTCTA 99 NULL:1983242 143812 144599 TTACATACACCCCAATGAAACTTTCCCACCCAAATCCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTGAAAGACTACCTGAACCA-GGAGCAGTTCGAATCGCTACGCTCTCAGGCCGCCGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAAACATCAAGTACAAAGAA 1255 2043 TTACATACACCCCAATGAAACTTTCCCACCCAAATCCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTGAAAGACTACCTGAACCAGGGAGCAGTTCGAATCGCTACGCTCTCAGGCCGCCGGGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAAACATCAAAAAAAAAAAA 2604404 100 NULL:1988063 118781 118237 CAGAGGAGAATTCGCTGCTCTTTCCGCTGCAACCTTCCAGCAGATTTAATGAATGAAATCAACTTGAATTAAATTCCTCCATATTGCGGCTTTGTTTCTGGCTTTATTTGTTTACACACACTGCAGCTGTTGAATCACCAGAGAGGCGAGAAATGTGTTTTCGGCTGCCTTGCTTTGTTTCGCTTGGAAGGTAATAAATTTTTAACACAATTGCATTGCATAAACAATTTCAAAACTGCACTCGAAATGGGCCTGTTTACACTCCGTTGTCGTGTCGATTACATTTTTGGCCAATAGCCAAGCACTCAGATTTAACTGGTTTATTTCGACTTGGCGAACGCCCGCGCGCGAATCTTTCAGCACAGCCCACGCACTTTCTGCAGCATGGTTAACTTGAAGATACTCGAATCGCACAGGGAAACAGATACGGATGGGCTCCAATGGAGGTGATATAGAGGCGTAAACAGAGGCAGAGATTCAAACCGAACCGAACCAAACCGAACTGAACCTCTGGGCCAGCGATCGAGTTGTGCGCCGCTGGAGAG 1 545 CTCTCCAGCGGCGCACAACTCGATCGCTGGCCCAGAGGTTCAGTTCGGTTTGGTTCGGTTCGGTTTGAATCTCTGCCTCTGTTTACGCCTCTATATCACCTCCATTGGAGCCCATCCGTATCTGTTTCCCTGTGCGATTCGAGTATCTTCAAGTTAACCATGCTGCAGAAAGTGCGTGGGCTGTGCTGAAAGATTCGCGCGCGGGCGTTCGCCAAGTCGAAATAAACCAGTTAAATCTGAGTGCTTGGCTATTGGCCAAAAATGTAATCGACACGACAACGGAGTGTAAACAGGCCCATTTCGAGTGCAGTTTTGAAATTGTTTATGCAATGCAATTGTGTTAAAAATTTATTACCTTCCAAGCGAAACAAAGCAAGGCAGCCGAAAACACATTTCTCGCCTCTCTGGTGATTCAACAGCTGCAGTGTGTGTAAACAAATAAAGCCAGAAACAAAGCCGCAATATGGAGGAATTTAATTCAAGTTGATTTCATTCATTAAATCTGCTGGAAGGTTGCAGCGGAAAGAGCAGCGAATTCTCCTCTG 100 NULL:1988064 103561 103415 CTCCCAGATGAGTCGAAAGTCCTGCTGCTCCACCCGCAGCAGCTCGCAGGTGGTCTTCGTCACTACGGTGCTGTCCCGCGGCAAGTCATGCAGTACGGACTCCCCGAATGTGGCACCCACGCCCAGGTTGCACAGAGTAACTGCGCT 546 692 AGCGCAGTTACTCTGTGCAACCTGGGCGTGGGTGCCACATTCGGGGAGTCCGTACTGCATGACTTGCCGCGGGACAGCACCGTAGTGACGAAGACCACCTGCGAGCTGCTGCGGGTGGAGCAGCAGGACTTTCGACTCATCTGGGAG 100 NULL:1988065 99134 99083 CGTTCTTCAACTTGCAGTTGGTGAATATGTCATTCATTAACTCCTTGTTTTTCTG 693 744 ---AAAAACAAGGAGTTAATGAATGACATATTCACCAACTGCAAGTTGAAGAACG 100 NULL:1988066 98798 98701 CTCGGTGATGGGCAGCGCTGGGTTTGGGTGGTCGGGGCTGAGGGGTCGTTTCGTGGGCGATGTGGCTGCGGCTGTCGCTTGTACGCTCGGTCCAAAACCTG 745 842 ---GTTTTGGACCGAGCGTACAAGCGACAGCCGCAGCCACATCGCCCACGAAACGACCCCTCAGCCCCGACCACCCAAACCCAGCGCTGCCCATCACCGAG 100 NULL:1988067 98440 98354 CTTGCGATCCTTCAGACAGCTCGAGTTGTCGGCGACGAGTAGTGTGCGTAGGGCCCAGCCCATGCGGTTCATAGCAGGACTCGGTGTCTG 843 929 ---ACACCGAGTCCTGCTATGAACCGCATGGGCTGGGCCCTACGCACACTACTCGTCGCCGACAACTCGAGCTGTCTGAAGGATCGCAAG 100 NULL:1988068 98285 98144 CGTGTGCGAGTACTCCTTCCTCGAGGAGCGCTTGCCACATGCCAGCCGCCTGGGCTCGGGTGTGGACGATGGGCGAGAGGTTGACCAGCCAGTCGACGAGCTCGGTGCCGGGGGCGCACTTACGGATTAGCTTGCCGGAGACCTA 930 1071 ---GTCTCCGGCAAGCTAATCCGTAAGTGCGCCCCCGGCACCGAGCTCGTCGACTGGCTGGTCAACCTCTCGCCCATCGTCCACACCCGAGCCCAGGCGGCTGGCATGTGGCAAGCGCTCCTCGAGGAAGGAGTACTCGCACACG 100 NULL:1988069 98089 97897 GGTTTGCGCAATATCATACGCAGTGTGGCGTCCGGTCCGCGCTGGAAGAGTGCGCTGAGCGCCTCGCGGATGTGCTCGTTGGCCGCTCCGAGGTCCTCCGCCTGGGGCACGCCCGCTGCCGCCGTGCCGCCCTCCTCGTCGATGCGAAAGCGGTAGAGGAAGCACTTGTCCTTGAAGGGCTGCTCTTTGTTGACTG 1072 1264 ---TCAACAAAGAGCAGCCCTTCAAGGACAAGTGCTTCCTCTACCGCTTTCGCATCGACGAGGAGGGCGGCACGGCGGCAGCGGGCGTGCCCCAGGCGGAGGACCTCGGAGCGGCCAACGAGCACATCCGCGAGGCGCTCAGCGCACTCTTCCAGCGCGGACCGGACGCCACACTGCGTATGATATTGCGCAAACC 100 NULL:1988070 97335 97190 ATATTGTTCCCGCCTGGGCATGAGCCTCGAACACGAAAATCGACGACAGTTCCCGCTTTATGCTGGTCGACAAGTGGGAGAGTGCGGCAATGTGGACCAGTTCCTCGAAGACCAGCTCCAGCTCCTCCGATGTCCGTTCGTGAGAACTG 1265 1410 ---TTCTCACGAACGGACATCGGAGGAGCTGGAGCTGGTCTTCGAGGAACTGGTCCACATTGCCGCACTCTCCCACTTGTCGACCAGCATAAAGCGGGAACTGTCGTCGATTTTCGTGTTCGAGGCTCATGCCCAGGCGGGAACAATAT 100 NULL:1988071 96970 96826 CTGGGTGCGTCGTTTATCAAGGCCAGTTTCCCGAAATCATCCCCAGTCTTCAGAGTGGCAACAGTTCCCTTGCCGTGTATCACAACGTCTACCGATCCCTTGAGTAAGATGTACCAGGAGCGTCCTTCGTCGCCTTGATTGAATACTG 1411 1555 ---TATTCAATCAAGGCGACGAAGGACGCTCCTGGTACATCTTACTCAAGGGATCGGTAGACGTTGTGATACACGGCAAGGGAACTGTTGCCACTCTGAAGACTGGGGATGATTTCGGGAAACTGGCCTTGATAAACGACGCACCCAG 100 NULL:1988072 95886 95710 TTAAATGCCGAATGCTGTCCACGTTGCTTAGCCACGCGCTCGAGCACTAAAACATCCTTGCCGTGCTCCTGCAATCTCAGAGTATTGGCCTCCACATCGCGCAGTATCCGGTTGAAGTGTTCCTTGTCCACGCGCAGCAAGTGGCAATTGTTCTCCTTCAGTACGATGGTAGCAGCTCTG 1556 1732 ---AGCTGCTACCATCGTACTGAAGGAGAACAATTGCCACTTGCTGCGCGTGGACAAGGAACACTTCAACCGGATACTGCGCGATGTGGAGGCCAATACTCTGAGATTGCAGGAGCACGGCAAGGATGTTTTAGTGCTCGAGCGCGTGGCTAAGCAACGTGGACAGCATTCGGCATTTAA 100 NULL:1988073 95472 95311 TAATTGGCCAATTCATCAACCAGCTGAACGACGGGCATGAAAACGATGTGTGTGAGCAGGAAGTCGTCCAAGAACGGATCCATTCCACCCACGGACTGGCCCAGTCGCGTCTCCAGCAGGTGCTCCAGCATCTTGGCCGGAGTTCCCGACATCACCGTATATCTG 1733 1894 ---ATATACGGTGATGTCGGGAACTCCGGCCAAGATGCTGGAGCACCTGCTGGAGACGCGACTGGGCCAGTCCGTGGGTGGAATGGATCCGTTCTTGGACGACTTCCTGCTCACACACATCGTTTTCATGCCCGTCGTTCAGCTGGTTGATGAATTGGCCAATTA 100 NULL:1988074 94511 94150 TATCATCATCTGGTCGGATGACCGTCTTTGAAGGCGTCGCATTGCCACTGAAAAGGCAGATGGGCTGGCCGTTGGGCGGGAGCTTCCACTTCTGGCCGGCGTTCTGGTTGCGGTCCTCCTGGTAGCGCGCCATCTGGGTGAGCACGTTGTGCACTATGCTGGTCTCCTCGTTCAGGTCGGGATCGGCCTCCACCTCGGCGGCGAGGTCCTCGATAAAGTCGCACACGCTGGGCTCCTCGAAGGCCGCGTGGCGGACGGCCATGACCCACTTTTGCATGAACTGGATCACGCGCTTCTTAAAGTTGATTATATACTCCCGATCCTCGGGCGTTTGGGCGTCCTCATGGGCATCGCAGTGGAAGGTG 1895 2256 ---CTTCCACTGCGATGCCCATGAGGACGCCCAAACGCCCGAGGATCGGGAGTATATAATCAACTTTAAGAAGCGCGTGATCCAGTTCATGCAAAAGTGGGTCATGGCCGTCCGCCACGCGGCCTTCGAGGAGCCCAGCGTGTGCGACTTTATCGAGGACCTCGCCGCCGAGGTGGAGGCCGATCCCGACCTGAACGAGGAGACCAGCATAGTGCACAACGTGCTCACCCAGATGGCGCGCTACCAGGAGGACCGCAACCAGAACGCCGGCCAGAAGTGGAAGCTCCCGCCCAACGGCCAGCCCATCTGCCTTTTCAGTGGCAATGCGACGCCTTCAAAGACGGTCATCCGACCAGATGATGATA 100 NULL:1988075 94079 93826 TGACGGAGACGAAAAGGCGGCCGTTGAGCGACAGACCCGTGGGTATGCTGACATCGTTGTCCTTGAACACGGACCGCTCCCCGTTTGACTTGACCTCGACGAGGACGAGATCTTCGGGACCCCGATTTAGCTGCAGCTTGTCGGCGGCACACGCTTTGATGAGCTCCGCCGTGGTGTGCATGGGGAATCGCAGGGTACAGTAGGTGTGGTCGGCGCAGTAAACGCGGAAGATGACTT 2257 2510 ---TCATCTTCCGCGTTTACTGCGCCGACCACACCTACTGTACCCTGCGATTCCCCATGCACACCACGGCGGAGCTCATCAAAGCGTGTGCCGCCGACAAGCTGCAGCTAAATCGGGGTCCCGAAGATCTCGTCCTCGTCGAGGTCAAGTCAAACGGGGAGCGGTCCGTGTTCAAGGACAACGATGTCAGCATACCCACGGGTCTGTCGCTCAACGGCCGCCTTTTCGTCTCCGTCA 100 NULL:1988076 93766 93596 TACCAAGGCATCCAGGTGGTCCT 2511 2681 AGGACCACCTGGATGCCTTG--- 100 NULL:1988077 93375 93242 G...TACTACGCGGCCAGCTTGATGAACTTCCGGACCAGACCGACGCGTTTGCTCAGACTGGGAGTGGACACCAGTTCGGTGACAATCCAGTACTGCACCTCGTTGAATCGGCGCAGGAACACATCCAAGTTGGCAGTGAT 2682 2815 ATCACTGCCAACTTGGATGTGTTCCTGCGCCGATTCAACGAGGTGCAGTACTGGATTGTCACCGAACTGGTGTCCACTCCCAGTCTGAGCAAACGCGTCGGTCTGGTCCGGAAGTTCATCAAGCTGGCCGCGTA------- 100 NULL:1988078 92958 92609 CCAGACTCCTGGAGCGACAAAAGCGGATGGTGCGCATCGTCTGGGCCATCATGTGCATCTTCTCGAAGTTCACCAGGCCGTCCAGGCTGGTCTTGTTGCCCTCATGGGCGAAGGTCATGTCCTTGAGCAGGAGCGGCATGAAGGGAATCAACGGCGGCTGCAGCTTGCCCACGAACACTCGGTACGCCCTGTGGTTGCGACTGGGGTCGATCAGGGCCTCGAACTCCTGGAAGATCTTCCTGAACTTCGACGGAATCTTTTCCCAGGTCTGTTGCAGCCTGGACACCGCCATGTTGGACAGACCCATTACCACAGCGAAGAAGGCGTTTAGGTTCTGGTACTCCTTGCAG 2816 3165 CTGCAAGGAGTACCAGAACCTAAACGCCTTCTTCGCTGTGGTAATGGGTCTGTCCAACATGGCGGTGTCCAGGCTGCAACAGACCTGGGAAAAGATTCCGTCGAAGTTCAGGAAGATCTTCCAGGAGTTCGAGGCCCTGATCGACCCCAGTCGCAACCACAGGGCGTACCGAGTGTTCGTGGGCAAGCTGCAGCCGCCGTTGATTCCCTTCATGCCGCTCCTGCTCAAGGACATGACCTTCGCCCATGAGGGCAACAAGACCAGCCTGGACGGCCTGGTGAACTTCGAGAAGATGCACATGATGGCCCAGACGATGCGCACCATCCGCTTTTGTCGCTCCAGGAGTCTGG 99 NULL:1988079 92549 91687 TGTGTGTAAATAAATATTAATAAATGGTTTCGTATTTTATTTCCAAGTTGCCGTAAAAGGAGATGGGGTGACGGAATACCAAATGAAAATAAGATTGAAAACTATAAATAAAGTAACTTATCCGCTACGTAGCTTACTTGTTAATAACTAGCTGTAACTAGACTGTTTAATAGTTGGTTTTAGTTTAGGGTTTATAAAAATATAGATTCCATGCTCTCGAAAACGTTGTACAACTTTACAAATTATTCTACCAGCTCGCGCGGGATTTATAGAGTAATGGTTTGTGGGAAATTATGCTGTATAGTTGTGTTTGTTTTGATGTTGCCTCCTATAAATGTTTAGTATCACACACGTCCAAGTTTAGTTTTTATTCGTTTCGGTTTCCGCGGGGAATTGCCGAATTTCAAATTGTTTTCCATCTTTTCCATCGTTTTGTACTAAAGCAAAAAGTTTCTCGTTTGCATTAAAATGCGTTTGGGTTTCAGTTCATTAGAAGATTGAGATAGTTCCTAGTCGGGTCGTAGATATAGTACACTGTAGCTTAGGCTAATGCGGATGCGGATGCGGACGAAAGTTGGTCCGGGCTGTGGTGGCCGTGGCCCAATTGGCTTTCGGAAAGCAACAACAACCCGGCTAAGCTCATAACTGTGCAGCTAATTGCGGTTGATTAACACACACTAGGGTTAGACACTTAATACGCGCTACAGGCTAATTGGATGACAGCTCCACAAGGGCTTAGAGCTTCCTGGTGGGCTCCACCTTCTGGGACATGGCGGTGAGTACCCGCTGGTTGTCGATGACGCGGAAGCTGCTGATGTACGACCTCACCTCGCCCTCGCTCTTCGGGGACGGCGGCTCTAGTCCTG 3166 4028 ---GACTAGAGCCGCCGTCCCCGAAGAGCGAGGGCGAGGTGAGGTCGTACATCAGCAGCTTCCGCGTCATCGACAACCAGCGGGTACTCACCGCCATGTCCCAGAAGGTGGAGCCCACCAGGAAGCTCTAAGCCCTTGTGGAGCTGTCATCCAATTAGCCTGTAGCGCGTATTAAGTGTCTAACCCTAGTGTGTGTTAATCAACCGCAATTAGCTGCACAGTTATGAGCTTAGCCGGGTTGTTGTTGCTTTCCGAAAGCCAATTGGGCCACGGCCACCACAGCCCGGACCAACTTTCGTCCGCATCCGCATCCGCATTAGCCTAAGCTACAGTGTACTATATCTACGACCCGACTAGGAACTATCTCAATCTTCTAATGAACTGAAACCCAAACGCATTTTAATGCAAACGAGAAACCTTTTGCTTTAGTACAAAACGATGGAAAAGATGGAAAACAATTTGAAATTCGGCAATTCCCCGCGGAAACCGAAACGAATAAAAACTAAACTTGGACGTGTGTGATACTAAACATTTATAGGAGGCAACATCAAAACAAACACAACTATACAGCATAATTTCCCACAAACCATTACTCTATAAATCCCGCGCGAGCTGGTAGAATAATTTGTAAAGTTGTACAACGTTTTCGAGAGCATGGAATCTATATTTTTATAAACCCTAAACTAAAACCAACTATTAAACAGTCTAGTTACAGCTAGTTATTAACAAGTAAGCTACGTAGCGGATAAGTTACTTTATTTATAGTTTTCAATCTTATTTTCATTTGGTATTCCGTCACCCCATCTCCTTTTACGGCAACTTGGAAATAAAATACGAAACCATTTATTAATATTTATTTACACACA 2598633 100 NULL:1983256 213083 213117 AGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTA 1 35 AGAGTTCGTTGTAGACGGTCAAATGTATTACTTGT--- 100 NULL:1983257 213389 214233 GCATTTTCCTGTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTTCCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAATTTCGTGATGAACTCAAAGAGACCTTAGAGAAGGTA 36 880 GCATTTTCCTGTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTTCCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAATTTCGTGATGAACTCAAAGAGACCTTAGAGAAG--- 100 NULL:1983258 214292 214433 CTGGGCATCCGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGGAGGGAGCGGAGGCCGCAGGTGCCACATGTA 881 1022 CTGGGCATCCGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGGAGGGAGCGGAGGCCGCAGGTGCCACAT--- 100 NULL:1983259 214504 214651 CTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTTAAA 1023 1170 CTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTTAAA 2604423 99 NULL:1988087 193064 191769 CTCCATTATTAGCACCCAACTTCTTCTGGCATTGTATTTTGTTTTATTCCGTATCAAATTGTAAATTATTTGTATATAGAGTATTTATGTATGTATATGTATATAGTCTTCATTTTACAATGGTTGTGAATTACAAAATCGGTAGGTGTTTAATGACGCTGCTCTCGCCCTCGGTTCTCTAACAAAACTAATGAAAGTAAAATCAAATGAAAGAAAAGAAAAGTAAACAAATTTTTATAAAAATAGTTTCGATGGTTTCTTACTTTCTTTCTGATTTTGTTGCATTTATTGTTACTCTTATTATTTCAAAATACAGCTTATCATTAGTTTGAACAATAAAATTTTGATTACGAAAACGAATTAAGTCCGATGACCCCCATCACTTTCTTACTAAATTCGCTATGTTTGACACGACAATTTGCAGGGAAATGTGACTGATTAAGGGGGCCTCAGCTAGGATGAACAGTATCGATTCTATCAGCTATTGTCATGAAAACTTCCGGGACGTACAAATATACAGACGTTACAGAAAGGAGCTCGTACAAATTTGGTAGGTAGGTGTTAACTCTTAAGTGATTGAGGTTTAGTCTATGATTTGCCTTTGTTAAATTTACAACAATTTCATACTTGCGTAACAACAAGCCGATCAAAGGGCCGAGTACCTGCCCTTCGCTCTGCTTGATTTTGGGCGCAAAATGTAGGTAGTTCGTTAGGTTTTTTATATATTTTTGGCAGGATGTAGTTTTATGTTATGTTTTATACGTTAAGCGTCCAGGTCTGCTCGGTTATGCTCGCTTAAGTTCGATTAGATGATTTAGCTCGGCATTCTCTAACCCTATCTGTGCCACACCCGCACTCAACTGATTTCGCTAATATTAAATTATAAAAAATAAATAATCGAAACCATAATGGTAATAGACAATAAGTTCTTTTTCAATTCGTCCTCAGCGCGCTTTGTTGCAATAGAGAAATTAAGCGTAGCTACGAGCTTCTACAAGCAGTTCTCTGTCTCTCCTCCAATCCATTCCGCCCATTTTTATCAGTTCAGTCCTCGTTTCATTGCTAGACCTAGTCCTCGTCCTTTGACGTTCCGGCTGATGTGGACGCGTGGTCGTTGGCACTTTCACTGGCTTTGCCGTCAGACGTGGCTGCTCCCGCTGAAGCCGGCGCAGCATCGCTTCCATTCTTGTTGCGGGCGTCCTCCTTGGCCTCCAGAGCGCGGATGCGGTTCTCTTGCTTGACGATGATCGCCTTAAGTTTGCGGATCTCGTCTTGTATGGTGCGCAGGTCCTTTTCCTT 1653 2945 ---GAAAAGGACCTGCGCACCATACAAGACGAGATCCGCAAACTTAAGGCGATCATCGTCAAGCAAGAGAACCGCATCCGCGCTCTGGAGGCCAAGGAGGACGCCCGCAACAAGAATGGAAGCGATGCTGCGCCGGCTTCAGCGGGAGCAGCCACGTCTGACGGCAAAGCCAGTGAAAGTGCCAACGACCACGCGTCCACATCAGCCGGAACGTCAAAGGACGAGGACTAGGTCTAGCAATGAAACGAGGACTGAACTGATAAAAATGGGCGGAATGGATTGGAGGAGAGACAGAGAACTGCTTGTAGAAGCTCGTAGCTACGCTTAATTTCTCTATTGCAACAAAGCGCGCTGAGGACGAATTGAAAAAGAACTTATTGTCTATTACCATTATGGTTTCGATTATTTATTTTTTATAATTTAATATTAGCGAAATCAGTTGAGTGCGGGTGTGGCACAGATAGGGTTAGAGAATGCCGAGCTAAATCATCTAATCGAACTTAAGCGAGCATAACCGAGCAGACCTGGACGCTTAACGTATAAAACATAACATAAAACTACATCCTGCCAAAAATATATAAAAAACCTAACGAACTACCTACATTTTGCGCCCAAAATCAAGCAGAGCGAAGGGCAGGTACTCGGCCCTTTGATCGGCTTGTTGTTACGCAAGTATGAAATTGTTGTAAATTTAACAAAGGCAAATCATAGACTAAACCTCAATCACTTAAGAGTTAACACCTACCTACCAAATTTGTACGAGCTCCTTTCTGTAACGTCTGTATATTTGTACGTCCCGGAAGTTTTCATGACAATAGCTGATAGAATCGATACTGTTCATCCTAGCTGAGGCCCCCTTAATCAGTCACATTTCCCTGCAAATTGTCGTGTCAAACATAGCGAATTTAGTAAGAAAGTGATGGGGGTCATCGGACTTAATTCGTTTTCGTAATCAAAATTTTATTGTTCAAACTAATGATAAGCTGTATTTTGAAATAATAAGAGTAACAATAAATGCAACAAAATCAGAAAGAAAGTAAGAAACCATCGAAACTATTTTTATAAAAATTTGTTTACTTTTCTTTTCTTTCATTTGATTTTACTTTCATTAGTTTTGTTAGAGAACCGAGGGCGAGAGCAGCGTCATTAAACACCTACCGATTTTGTAATTCACAACCATTGTAAAATGAAGACTATATACATATACATACATAAATACTCTATATACAAATAATTTACAATTTGATACGGAATAAAACAAAATACAATGCCAGAAGAAGTTGGGTGCTAATAAA--A- 100 NULL:1988081 202544 202309 TTTATCTATCACTCCACTCACTGGGGCCAGCGCATTCAGCGGGATTCAACTAGAGATTTTGCACACGACTCCGGCTGGAAACTTAAGGCACTTCTTTTCAGACTTTTCAGTCAGCAGAAAGACGGGACGAGTACAAAATGCCGACGAGAGCGCGCTGAGCATCTAAGAGCAAGTTCGACACTGTTGTTCGAGGCAAGTTGTTGATATCAGCGCAGTTCGCGTTCACGTTCACCGGG 1 236 CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAACAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATTTTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCCTTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTGAATGCGCTGGCCCCAGTGAGTGGAGTGATAGATAAA 100 NULL:1988082 196716 196462 TTTGTTGTGTGGCAGGACGATGAAGGCTCCGCCGCCCGCCGACTCTACGATAATGGCCAGGAACTTGGGATTCACCGCGCAGAATGTGGAGTCCCAGCTGGACTTGGATACCCGTATGTTGTCGTAGCACTGCTCCCGCTTGAGAGCCTGTCCGTAGACGTGGCGGAACTTGGAGCTGCGCACTACGCGAAATGACATCTTGATGCTGCAGTGGCTTGGGTCAGCGATCAGTCCTGAGCTTCTCTACGTCTAGCTCTG 237 491 ---AGCTAGACGTAGAGAAGCTCAGGACTGATCGCTGACCCAAGCCACTGCAGCATCAAGATGTCATTTCGCGTAGTGCGCAGCTCCAAGTTCCGCCACGTCTACGGACAGGCTCTCAAGCGGGAGCAGTGCTACGACAACATACGGGTATCCAAGTCCAGCTGGGACTCCACATTCTGCGCGGTGAATCCCAAGTTCCTGGCCATTATCGTAGAGTCGGCGGGCGGCGGAGCCTTCATCGTCCTGCCACACAACAAA 100 NULL:1988083 195149 194883 TT...CACCTGGTTATCGGAGCCGGCGGTAAGCAGCACGTTGAGCGCAGAGGGATGCCACAACACCAGACCCACGCGACGCTGGTGGAAAACCAGGTCGACCACGGGTTCGGTGAGTGTTCGCGACAGCCCGCCATCGGGGATCTGCCACACTTTGACCACACAGTCCTCTGAGCCGGAGGCGATCACGTTGTCGTTGTGGGGGCACCAGGCGATGTCCAGCACAGGACCCTTGTGACCGCCCACCAAAGGGTGGTCAGCCGCAATGCGACCAACCTG 492 758 ---GTTGGTCGCATTGCGGCTGACCACCCTTTGGTGGGCGGTCACAAGGGTCCTGTGCTGGACATCGCCTGGTGCCCCCACAACGACAACGTGATCGCCTCCGGCTCAGAGGACTGTGTGGTCAAAGTGTGGCAGATCCCCGATGGCGGGCTGTCGCGAACACTCACCGAACCCGTGGTCGACCTGGTTTTCCACCAGCGTCGCGTGGGTCTGGTGTTGTGGCATCCCTCTGCGCTCAACGTGCTGCTTACCGCCGGCTCCGATAACCAG-------- 100 NULL:1988084 194824 194411 CTCGAAATACCGAATGACCGAGTCACCTTTTCCACACAAGTAGATCATGTTCGTGTCTGCGTCGTAAAGAGGGAACATTACGCCGTTGGACGTGTCCAGCTCCACCATGACAATGGGTTCGTTAAGGGCATCCGGTGCGCGCAGGGAGTACTGACGCTCCGAGCTACGGTTGAAGCCTGTGGTGAAGATCAGACCGTGACGTAGGAAAATGGCCCTCGTGGCCTTGGAGCCCTCATGACACATGGCTTCGCTCTCCAGCTCGGCAGTGCGCGGATCGTAGATGCGGATCTTTTTATCCTTGCAGGTGGTAACCAACTTAGAGCCATCCCAGTTGAAGCAGGCGCTGTAAACGATGTCCGGATGGGAGTCGATGTGCACGAGGATTTCACCAGTGCCCACGTTCCAAATCACGAC 759 1172 GTCGTGATTTGGAACGTGGGCACTGGTGAAATCCTCGTGCACATCGACTCCCATCCGGACATCGTTTACAGCGCCTGCTTCAACTGGGATGGCTCTAAGTTGGTTACCACCTGCAAGGATAAAAAGATCCGCATCTACGATCCGCGCACTGCCGAGCTGGAGAGCGAAGCCATGTGTCATGAGGGCTCCAAGGCCACGAGGGCCATTTTCCTACGTCACGGTCTGATCTTCACCACAGGCTTCAACCGTAGCTCGGAGCGTCAGTACTCCCTGCGCGCACCGGATGCCCTTAACGAACCCATTGTCATGGTGGAGCTGGACACGTCCAACGGCGTAATGTTCCCTCTTTACGACGCAGACACGAACATGATCTACTTGTGTGGAAAAGGTGACTCGGTCATTCGGTATTTCGAG 100 NULL:1988085 194346 194053 TTTGAGCGAAAATGTGATCGGATCCGCATCCTTGCCATCGATCCACTCCTCCGCGGTGATGGCAGCGTCTTCCGCTAGCGTATCGGGGTAGAGATCCTCCTGGAAAAGATCCGATTTGCGCGGCACAGTCATCGAGATGACCTGACACAGACCGTTGTTGTTCATGCGATAGAACTTGGCGACCTCGCAGGTGGTCACATCACAGCCTCGCTTGGGCATCAGACCAATACCACGCTGCGGCTCTGTAGTCTGAAACGTGTTTATGTAGTGCACAAAAGGAGGTTCGGGCGTTACCTG 1173 1466 ---GTAACGCCCGAACCTCCTTTTGTGCACTACATAAACACGTTTCAGACTACAGAGCCGCAGCGTGGTATTGGTCTGATGCCCAAGCGAGGCTGTGATGTGACCACCTGCGAGGTCGCCAAGTTCTATCGCATGAACAACAACGGTCTGTGTCAGGTCATCTCGATGACTGTGCCGCGCAAATCGGATCTTTTCCAGGAGGATCTCTACCCCGATACGCTAGCGGAAGACGCTGCCATCACCGCGGAGGAGTGGATCGATGGCAAGGATGCGGATCCGATCACATTTTCGCTCAAA 100 NULL:1988086 193308 193123 CGATAAAACCGCTGCAGGCGGTCCACCTTCGCTAGCCTCATTGTTATTTCCGGACGCAAAGTTGCCGCCGCCCGCGCTGCTGCTCGTTGCACCGGAGCTAGCGCTGTCGCCTCTAGGCTTGTTCAGGATGTTGCCCGCCTTCTTCGCTGGTAGCGATTTGTTTACCGACGAGGACACGTAGCCACCCTG 1467 1652 ---GGTGGCTACGTGTCCTCGTCGGTAAACAAATCGCTACCAGCGAAGAAGGCGGGCAACATCCTGAACAAGCCTAGAGGCGACAGCGCTAGCTCCGGTGCAACGAGCAGCAGCGCGGGCGGCGGCAACTTTGCGTCCGGAAATAACAATGAGGCTAGCGAAGGTGGACCGCCTGCAGCGGTTTTATCG 2598561 100 NULL:1983194 23229 23427 ACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGAGCGCGATGCTGGT 1 199 ACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGAGCGCGATGCTGGT 100 NULL:1983195 23737 24959 TA...CAGTACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGTCCTGGGCTAGCCACACCTCTGACCGTTGATCCCGATGGCACCTACTTCAGGCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAGACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAAACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGTGAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCACAACACATTTGACGCAAACGGCGTCATCGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCCGCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGCCATTTCCGAACTAATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGCGCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAATATCGTTTGACAAATTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTTTATGTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTC 200 1422 --------TACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGTCCTGGGCTAGCCACACCTCTGACCGTTGATCCCGATGGCACCTACTTCAGGCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAGACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAAACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGTGAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCACAACACATTTGACGCAAACGGCGTCATCGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCCGCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGCCATTTCCGAACTAATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGCGCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAATATCGTTTGACAAATTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTTTATGTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTTCACGTTTTA--- 2598619 99 NULL:1983244 158133 158442 AACAGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAACGTA 1 310 AGCGGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAAC--- 100 NULL:1983245 159336 159823 CAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGGGTG 311 798 CAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGG--- 99 NULL:1983246 162405 162706 CTTTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGACAGAAGGTA 799 1100 CTTTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCAGGGCAGCGGCGTGCTTCACCAACGAGCACAAGTACACGCACGGACAGAAG--- 100 NULL:1983247 163390 163462 GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGATCTTCTGCTGGTGGGAGAAGTGCG 1101 1173 GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGATCTTCTGCTGGTGGGAGAAGTGCG 100 NULL:1983248 163530 164701 ATAAGGCCAATGTAAACAAGGCGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACGACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGACAACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGACGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGATGTG 1174 2345 ATAAGGCCAATGTAAACAAGGCGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACGACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGACAACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGACGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGAT--- 100 NULL:1983249 165268 165844 CTTGGACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGTA 2346 2922 CTTGGACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGG--- 99 NULL:1983250 166302 168135 GCAAACTGTATAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATTCGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCTATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGACTTTAAGCTGAATGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTATATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGGCATTTCGAA 2923 4756 GCAAACTGTATAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATTCGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCTATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGGAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGACTTTAAGCTGGATGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTATATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGGCATTTC--- 2598549 100 NULL:1983184 3425 3592 CGGTGAGAAGGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAGGTG 1 168 CGGTGAGAAGGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAG--- 100 NULL:1983185 3649 3965 ATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACCCACATATTCGCAGTG 169 485 ATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACCCACATATTCGCAGTG 100 NULL:1983186 4036 4502 ACGAGTCTCAACGGCTGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGAGTG 486 952 ACGAGTCTCAACGGCTGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGA--- 99 NULL:1983187 4556 4840 CTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACATAATAGAGACTTTATTACAACATTTAGAACTC 953 1236 CTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACATAATAGAGACTTTATTACAACATTTA-AA--- 2598565 100 NULL:1983197 26560 26704 AACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGACACAG 1 145 AACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGACACAG 100 NULL:1983198 27191 27350 CAGGCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAGGTA 146 305 ---GCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAG--- 100 NULL:1983199 27824 28160 ATCTATCACACGCTCTTATTACCGCGGAGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATACGGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACAATGAGGTA 306 642 ATCTATCACACGCTCTTATTACCGCGGAGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATACGGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACAATGAG--- 99 NULL:1983200 28221 28623 GCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAACCACATTTGTG 643 1044 GCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAACCACA-AA--- 2598581 100 NULL:1983211 76161 76385 ATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAGGTG 1 225 ATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAG--- 100 NULL:1983212 76445 76698 GAAAATGCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGGGTA 226 479 GAAAATGCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGG--- 99 NULL:1983213 77018 77898 AACTGAGTGTTTGGTGGTGGCCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATTTACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTTTCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATGTCGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCCGGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAAGCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTGGAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAGACTTCTGGGGTCACCGACCACTATGCCTTAGACGACGAACACGCCTTGTATCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGTACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACTCCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGGCATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTGCGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGTGAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAATAGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCCACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAAAATATTACTGGTA 480 1360 AACTGAGTGTTTGGTGGTGGCCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATTTACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTTTCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATGTCGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCCGGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAAGCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTGGAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAGACTTCTGGGGTCACCGACAACTATGCCTTAGACGACGAACACGCCTTGTATCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGTACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACTCCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGGCATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTGCGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGTGAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAATAGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCCACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAAAATATTACTG--- 100 NULL:1983214 77954 78730 GCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGCCAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCAAGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATGTGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCGCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACACACATTTAAATGTATAATGTATAACAAAACAATT 1361 2137 GCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGCCAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCAAGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATGTGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCGCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACACACATTTAAATGTATAATGTATAACAAAACA--- 2604460 99 NULL:1988112 315484 315187 TCGCCATGTTTGCCGCCTTTGTTGATTATTCCGCTGCTGCTTCTTCCGTTTTTATGCTTTTCTGCTTTTCTTGCTCTGCGTTGGTTGCGATTCCAGGCACGTTGTATCACTGTTAGCTTGTAACAAACACTGCTGATAGGCTAATGACTGCTGCGCGCAACTGAACACATTTCACGGCTTTCTTTCAGTCGCGTCTCCGTTCAACTTCCGCAATATCCGTATAATTCGTATTATCCGTGTAATCCGTATTTTCCGAATCGCGTTCAGACGTTCACACCAACAACTGCAATTCTAGTGT 1 298 AGACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAATACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAACGGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCAGTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGTGCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAACGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGA 100 NULL:1988113 308375 307467 CACCAGTAAGGATTAATACGATGAGTTCGCAGGCGAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACTTTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATAAGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACATCTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGATATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATACTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATTGGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACTCCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGCAAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGATGGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGAGTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCCCGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTGTCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCTCGTGCTTATCGAAAAGTTTGGGGTCCTTCGTCGCCGAGATCTCGCAGAGCAAGTTGGTCGTGTTCGCCGGACTGACACTGGTCGTCTTCAGCTTTTCAATCAAATCGTCGATTTCAGCTGCTT 299 1207 ---CAGCTGAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCCGGCGAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCAAACTTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAGTGCGACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGATCACCAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAGCCGCATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATGGAGCTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAACGACGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTACTGCGACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAATTCATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGAGGGCTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAGGCATCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTGCTGAACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCTGAACTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTTCCACGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAGGCGGAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGAAACCATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTGAGGCCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTTACTGGTG 100 NULL:1988114 307377 306991 CCTGTCCGTCGACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGTGTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACCGCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAGAGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCACCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGGCTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAGATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCGTGGTGTACAAATAGTGCATTGAGTCATCTA 1208 1594 ---ATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAACATGGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCGTGCTGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTTGTGGAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAACGGCGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGCGCAACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGCCTGGTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGTCTTCAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGG 99 NULL:1988115 306932 305057 TTTGGTTTTCTCTTATTTCTCATGCATTTCAAATTTTATTTGAATTATTAAATGTACATTATTGTGTTTAGAGTTCATAAATATGTTTTCGCATTTATGTGTGTGGGTGTCTCAACGCTTTATATATTAACACCATTCCCCTTGAATTGTGTTCGTTTAATTTTTAGTTTTTGGTGACCAAACATTAGTACATCGTTTTTAATAATTGGTAAAATTTGTAGCACTCCATAAACTACGATTTGTAAAATTGAAATATTTGCATTATTGGTTTTCAACTATTTTCGGATTGCTGATTGTTACTGAGTTGCAGTTTTGTTAATGTTTTAAAGTTAGCTTAAAAATGCATTTTGGATAACTTCGCCGAGTTTTACAATAAATATATGGGATGCCGTTTGCAATATGTGTCTGTGCACCAATTAAAATACCTTAATTACGTCGTGCGTCTAAATGTTTTGTTATCTTCTCGTTTTTGGTTTGTGCCAGCAACGGTTTAAAAGAGGTCGATTGAAAATTATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTCCTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTCTAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAACTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTACAGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTCTCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAAAACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTGCAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAATTGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAATCTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACACAGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTTCAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGGATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGAGAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGCGCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTTCTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGGCCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGGGCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCACAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCATGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAGCTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTCGGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGTAGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACGCCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGTCTTGTTCTTCAGCAACTCCAGTGCGAGTTTCTCTG 1595 3470 ---AGAAACTCGCACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCACTGGAGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCTCATGGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCACTGCCGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCGCTAACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGAGGGCACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCATGCAGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTGTCGCAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGTCAAGTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGGACACGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTGCTCAAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAACGGGCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAGAAAACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACAGTGGGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGGTAAGCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGCCAATACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCTAAACTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATCCACTCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATAAATGTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTAGCCACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAAGCAACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCAGATTCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAACACGAGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCATTTATGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTTATAGCATACATACATAACATATACGTATAAATATAATAATATTAATAATTTAGCATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAACAAATCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTGTACTTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCAAAAACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATTTTAATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTGTAAAACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAACATTAACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAAAACCAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGCTACAAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAAAAACTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATAAAGCGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTCTAAACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATGAGAAATAAGAGAAAACCAAA 2598639 100 NULL:1983261 216180 216199 AGTTTTCCCAATCATGTCAGGTA 1 20 AGTTTTCCCAATCATGTCAG--- 100 NULL:1983262 216289 217223 TCAAGGCCACGTGTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCTCCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTACTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCAGCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCGAGGAGGTG 21 955 TCAAGGCCACGTGTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCTCCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTACTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCAGCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCGAGGAG--- 100 NULL:1983263 217630 217771 TTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTGTA 956 1097 TTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCT--- 99 NULL:1983264 217836 218041 TTATCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCACAA 1098 1303 TTATCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCAAAA 2598655 100 NULL:1983275 253221 253434 GCTTGACTAGCTAACACCTGGCAATGCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATGGTA 1 214 GCTTGACTAGCTAACACCTGGCAATGCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATG--- 100 NULL:1983276 253655 254261 AGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACGCTGTGAGCCTTGCCAAATCAGGTA 215 821 AGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACGCTGTGAGCCTTGCCAAATCAG--- 99 NULL:1983277 254328 254459 CCAAGTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACATGCATTTACATTC 822 953 CCAAGTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACATGCATTTAAA--- 2604445 100 NULL:1988100 261593 258284 CGTCAAAGTGTTGCTGCTGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCCTCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTTGGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCATTGAGCTGTGCAATTAGGTTCGGATTCGCCTTTGGCTGTGTCGGTGGCAGTGGGTGAGCATGTCCGTTGGGACTGGGGCTGCTGGTGCGGAAGCTGGACATGCTGTTGACCAGTTTGGGCTGGGCGTATATGCCGCCGCCACCCCCTCCGCCCGCGGCTGGTGATGAGGTGCGGAACGTCTGGTCGTGAATGTGTGTCAGTGATGGTGTGTTTGTGGCATGAGAGAAACGAGAAGAAGACGGGCACAAATTAAAAGTTAGCCAAAGCACGACCAAAGCTAAGCACTAGAGTAATCTATGACTATGGCATTACAACTAAGCTGGAAGGAGGGCAGTCGTGTTAGGCCAGAGAGGCGCTCCCAAAGACGCCTGTTAGTCTTGGTTAGTAGCCCGCGAGATACCCGCTGGTCACTTACGGCATCGACTTGGTAGACAGGCGGTTGCTGTGGCTGATGCAGATGCTGATGTTGCTGCTGGAGGGTAAAGCGTTGCTGGTTGGCCATCTGCTGACCGCCGGGCTGTTGGCCGCTGGCCAAGGCCTGGGCATAGGCGTGCAGATCCAAGTAGGAGTCGTAGTACACGGTCAGGTCCTCTTTGAGGGGGGAGTTGTGCGCAGACTACGTGGGGGATTGGGGTTTCGGTTTGTGTGTGGTAGTGGTGAAGCAAACGTAAGTTGAAATAAAATGAAATCATAAGTTGTAGAAGAAGATGGCTAAATTTCAAGGTGGCTCTAGACTCGTGCACTAGTTAGACCCAATGAATATTACCTAACTCTCACGCCGAACTATACTGGCTTTTGTTGGGGAATAAATGTCGAGTCTTCCAAGTCGTATTTCTATGCTCAATGAGCTCAAAGTATACCTACATTTGTAGGTAGAAAATGTATGGAACAAAGCTTATGCTTGTTTACCGGGGCTAGGCAACTAGAATCCCTACAGTTTACGATTAGTGATTAGCTTATTGTAGCTTTAAACTTTTTAGCCAGATATATGAATTTTCTAACTAAAGCCAAATACATCTTCATCTGGTTGCATAAATTTTTGGTCAGAAGCATAAACTACACATTAATAGTACCCAATTTGGGTTGTAAACTCAAATAGTCAGGTGAGAGTAGGAAATCAAACATTTTGGTACAAATGGAAACCGGATGCGAACCGAGCACACACCTGCAATAGGGGTTGCTGCTGCTGCACCTGTTGCTGCTGTTGCTGCTGAAGCTGCTGCTGCTGTTGCTGCTGCATGCGTCTGAGGGACACAGGTGATGCTGGCTGGTGCCGCATGGCTGCCAGGGCTCTTACCGTCTCCGATACCTTCAGCGCTGAGCTGGGAATCTGGGGCATGGCGTCCAGCATGAATGGCGGTGGCGGCGGTAAGTGCTCGCTGGAGCTGCTTAGTTGGTGATTCTGCTGCGACAGAGTCGCGTGCTGTGGTTGCTGCTGCAGCTGCGTTGCGTAATTAAATCATAAGTTAAAGAATAAAAGCATAGAGGAAACCAAAGAGTGTGTGACCCAGAGTGTGAACCCAGGCTTAGCGACTAGCTTAGATTAAGTGGCTAACTTAATTGGGTGTAGGTAATTGAAGGCTTAACTCACCCCGACCGAGGCATTGGGACTGGGGGTCACCGACGAACTGCGTCTGACTGGCGGCGGTGGCTTGGACTGATTAATGGACGATCGACGCCCGATGCGCGTGGAGCCACCGCCGGCTGCTCCTCCTGGGAAAAGTAAAAATCCTTGTTAGTGAGGCGGGCATTTTGATGATTTAGTCATTAATTTCTGCTGTTATTCACAGTAATGTACAGTTATCAGTTTATACACTTGGCACACAAAACACAGGACACCATCTAATACCAGTAGTTAGCGATAGACGCAGAGTTAGGATCTGCTGATCGAGAAAGTTATGAACGTTCTTGGTCTGCTGTGAATCATAATGATGACCCTGAAGCGAGTGGAAAAGCGTTAATGGCTGTGATGGCACTTTCGATACCACTTCATGTCGAAAAGACATTTCCCCTAATTTAAGCGATTTTGCAAAATGCAATTTTGTAAAAAAAATTTTGTAGTTACAAACGATCGAATCTGATTAGTGATTAAGCATTTAGCAGTTAGTGGCAGTATCATGCGGGTTTTGAGTTGTCTATTGATGATCTGAACTTAATGATTGTGACTTGATGGTATGAGCGTAGTGCTTAGCGAGAGAAACCAACTCCAATTTCAAAAAGGTTACCACATCGAACTTATAGCAAAAATGAGAAACCCAAAACCGCGTAAAGTTACTTCGGCAAGCACAAAATGATAAGGATACTTGCAAAGGTACAACAAAGTAGGAAAGTTTTCAAAATAAGGAATCAAAAACCAAAACCAAATAAACCCAAACAAATCAAAATCAAATTGAAACGAAACGAACCCGACAAAGAAGCCGGCCGGGGCGTAATGCACGGCTTGAGATGGGCATTGGCATTGGAAATGCTATTGGCGTGGTGGGGATTGGCTGGGGCATTGGAGCACACATATGGATGGGCGGGTGGTCGGTCACTGGCGGGCAACATCGATGGCCGGGCATTTGATGGTGATGAAGTGGTGGCTGGTAATGGTAATGACGATAGCGATGACGATGATAATGGCAAATGGCCGCGAGGTGATGACGGTGACAATGCCATTGTGGGCGTCTTGCACTGCGTGTGATTGGATGTGGCTGTCTGATTTTGGTTTGGCATTCTATGATTTGGATTCGGGTACGGGTCTGTGGATGCTGTTGCGGTTGCAAATGCAGATGCTGATGCAGTAATATTGGCGGCTTGTTGATTAGTGACATTACAGTTTCTGGTTTGGGGCGACTGTGGTGAGTGTTGCTGTTCTTGTGGTGCTTGCTGCTGCTGCTGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCTGCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCTAGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGCAGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCAGCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGCTGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTA 1 3310 TACAAAGCAGGCCACAGGACCAGCATTTTCCACAGACACAACAGCAGGATATTGATGGCAGTAGTCCACCAGTAGAACTTGCAAGGCGCCAGCTGCCCCCCAAGCCCACCAGTTTGAGTATTTTTAACGGCCCCGTGCCCACTGCGGGCGATAGGCCTGTCGTGCCGCGAAAGTCGGACTTTAAGGCTGATCTAGATGCTAAAATACGCAGGCAAAAGCAGAAGGTTAAACAGCAGTTGCAGCAGCAGCAGCAGCAACAGCAGCAAGAGCAGCAAGAAACGCAGCAGCAGCAGCAAGCACCACAAGAACAGCAACACTCACCACAGTCGCCCCAAACCAGAAACTGTAATGTCACTAATCAACAAGCCGCCAATATTACTGCATCAGCATCTGCATTTGCAACCGCAACAGCATCCACAGACCCGTACCCGAATCCAAATCATAGAATGCCAAACCAAAATCAGACAGCCACATCCAATCACACGCAGTGCAAGACGCCCACAATGGCATTGTCACCGTCATCACCTCGCGGCCATTTGCCATTATCATCGTCATCGCTATCGTCATTACCATTACCAGCCACCACTTCATCACCATCAAATGCCCGGCCATCGATGTTGCCCGCCAGTGACCGACCACCCGCCCATCCATATGTGTGCTCCAATGCCCCAGCCAATCCCCACCACGCCAATAGCATTTCCAATGCCAATGCCCATCTCAAGCCGTGCATTACGCCCCGGCCGGCTTCTTTGTCGGGTTCGTTTCGTTTCAATTTGATTTTGATTTGTTTGGGTTTATTTGGTTTTGGTTTTTGATTCCTTATTTTGAAAACTTTCCTACTTTGTTGTACCTTTGCAAGTATCCTTATCATTTTGTGCTTGCCGAAGTAACTTTACGCGGTTTTGGGTTTCTCATTTTTGCTATAAGTTCGATGTGGTAACCTTTTTGAAATTGGAGTTGGTTTCTCTCGCTAAGCACTACGCTCATACCATCAAGTCACAATCATTAAGTTCAGATCATCAATAGACAACTCAAAACCCGCATGATACTGCCACTAACTGCTAAATGCTTAATCACTAATCAGATTCGATCGTTTGTAACTACAAAATTTTTTTTACAAAATTGCATTTTGCAAAATCGCTTAAATTAGGGGAAATGTCTTTTCGACATGAAGTGGTATCGAAAGTGCCATCACAGCCATTAACGCTTTTCCACTCGCTTCAGGGTCATCATTATGATTCACAGCAGACCAAGAACGTTCATAACTTTCTCGATCAGCAGATCCTAACTCTGCGTCTATCGCTAACTACTGGTATTAGATGGTGTCCTGTGTTTTGTGTGCCAAGTGTATAAACTGATAACTGTACATTACTGTGAATAACAGCAGAAATTAATGACTAAATCATCAAAATGCCCGCCTCACTAACAAGGATTTTTACTTTTCCCAGGAGGAGCAGCCGGCGGTGGCTCCACGCGCATCGGGCGTCGATCGTCCATTAATCAGTCCAAGCCACCGCCGCCAGTCAGACGCAGTTCGTCGGTGACCCCCAGTCCCAATGCCTCGGTCGGGGTGAGTTAAGCCTTCAATTACCTACACCCAATTAAGTTAGCCACTTAATCTAAGCTAGTCGCTAAGCCTGGGTTCACACTCTGGGTCACACACTCTTTGGTTTCCTCTATGCTTTTATTCTTTAACTTATGATTTAATTACGCAACGCAGCTGCAGCAGCAACCACAGCACGCGACTCTGTCGCAGCAGAATCACCAACTAAGCAGCTCCAGCGAGCACTTACCGCCGCCACCGCCATTCATGCTGGACGCCATGCCCCAGATTCCCAGCTCAGCGCTGAAGGTATCGGAGACGGTAAGAGCCCTGGCAGCCATGCGGCACCAGCCAGCATCACCTGTGTCCCTCAGACGCATGCAGCAGCAACAGCAGCAGCAGCTTCAGCAGCAACAGCAGCAACAGGTGCAGCAGCAGCAACCCCTATTGCAGGTGTGTGCTCGGTTCGCATCCGGTTTCCATTTGTACCAAAATGTTTGATTTCCTACTCTCACCTGACTATTTGAGTTTACAACCCAAATTGGGTACTATTAATGTGTAGTTTATGCTTCTGACCAAAAATTTATGCAACCAGATGAAGATGTATTTGGCTTTAGTTAGAAAATTCATATATCTGGCTAAAAAGTTTAAAGCTACAATAAGCTAATCACTAATCGTAAACTGTAGGGATTCTAGTTGCCTAGCCCCGGTAAACAAGCATAAGCTTTGTTCCATACATTTTCTACCTACAAATGTAGGTATACTTTGAGCTCATTGAGCATAGAAATACGACTTGGAAGACTCGACATTTATTCCCCAACAAAAGCCAGTATAGTTCGGCGTGAGAGTTAGGTAATATTCATTGGGTCTAACTAGTGCACGAGTCTAGAGCCACCTTGAAATTTAGCCATCTTCTTCTACAACTTATGATTTCATTTTATTTCAACTTACGTTTGCTTCACCACTACCACACACAAACCGAAACCCCAATCCCCCACGTAGTCTGCGCACAACTCCCCCCTCAAAGAGGACCTGACCGTGTACTACGACTCCTACTTGGATCTGCACGCCTATGCCCAGGCCTTGGCCAGCGGCCAACAGCCCGGCGGTCAGCAGATGGCCAACCAGCAACGCTTTACCCTCCAGCAGCAACATCAGCATCTGCATCAGCCACAGCAACCGCCTGTCTACCAAGTCGATGCCGTAAGTGACCAGCGGGTATCTCGCGGGCTACTAACCAAGACTAACAGGCGTCTTTGGGAGCGCCTCTCTGGCCTAACACGACTGCCCTCCTTCCAGCTTAGTTGTAATGCCATAGTCATAGATTACTCTAGTGCTTAGCTTTGGTCGTGCTTTGGCTAACTTTTAATTTGTGCCCGTCTTCTTCTCGTTTCTCTCATGCCACAAACACACCATCACTGACACACATTCACGACCAGACGTTCCGCACCTCATCACCAGCCGCGGGCGGAGGGGGTGGCGGCGGCATATACGCCCAGCCCAAACTGGTCAACAGCATGTCCAGCTTCCGCACCAGCAGCCCCAGTCCCAACGGACATGCTCACCCACTGCCACCGACACAGCCAAAGGCGAATCCGAACCTAATTGCACAGCTCAATGCACGACTCAGCGGCAAACAGCAGCAGCACCAACAGCAGCAGCATATCGAGGGGATCTACGGCAACCAGCAGGCGCCCGGAGGAGAGTCGATCTACATGCGGAGTGGCCTGTCCATGTCGCAGCCGCAACAGCAGCAACACTTTGACG 100 NULL:1988101 256596 256445 CAGGGCCTTGCTGTTGATGAGATTTCGCACGGCAAATGCTCGTCCAGACATTCCCTGCTTCGCCAGCTTCGCGTTGAGATTCTCGAGGAATTCGGCCTTGGTCTTGGCACGAATACTGCCAGTCTTTTCGATATTTGTGCTTGTGGCATAGTCTA 3311 3462 ---ACTATGCCACAAGCACAAATATCGAAAAGACTGGCAGTATTCGTGCCAAGACCAAGGCCGAATTCCTCGAGAATCTCAACGCGAAGCTGGCGAAGCAGGGAATGTCTGGACGAGCATTTGCCGTGCGAAATCTCATCAACAGCAAGGCCCTG 99 NULL:1988102 256073 255473 ATGTACGATAAATTCCATTTATTAGGCGTCAGATTAGTTTCGAGTGTTTGTTAAACTCATATTCATATGTATGTACATAAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATATCTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAAACATAAACATAACTGTCTTCCATATTGTATTCACTTAACAGAGAAAGCCTTTCGACACATTTTTGGGATACAGGAAATCAAGAAAGGTATTGATTAGTTCGATTTATGCTTAATGCTCCTGTTAAATATCGTATATCGAATATATATTATATATCGTAATCATATGTATTTAAGTTGTATGCTGTGTTTCGAGTTTTCAGTTTCAAACCAAACTCTGCAGAGCCCTGCAGTCGAGCAGGCGTCGGGCCTCATGATTATTCATAGATTAATTATTATGGTAATAAATATGCTGCTTCGCTTAGCCTATAGGTTAATTCAATGTATCTTGGGAGCGCTGCGATCGTTGATCTTCTGGTTACGCTTTAAGGTGGCTCCGCGCTTGATTTGATCCATCAGCGATTCGTGACAGATGCGAGGGTCCGGCTG 3463 4063 ---CCGGACCCTCGCATCTGTCACGAATCGCTGATGGATCAAATCAAGCGCGGAGCCACCTTAAAGCGTAACCAGAAGATCAACGATCGCAGCGCTCCCAAGATACATTGAATTAACCTATAGGCTAAGCGAAGCAGCATATTTATTACCATAATAATTAATCTATGAATAATCATGAGGCCCGACGCCTGCTCGACTGCAGGGCTCTGCAGAGTTTGGTTTGAAACTGAAAACTCGAAACACAGCATACAACTTAAATACATATGATTACGATATATAATATATATTCGATATACGATATTTAACAGGAGCATTAAGCATAAATCGAACTAATCAATACCTTTCTTGATTTCCTGTATCCCAAAAATGTGTCGAAAGGCTTTCTCTGTTAAGTGAATACAATATGGAAGACAGTTATGTTTATGTTTATTTATATCTGCAACTCGAATTTATCTTTAGAGAACCTTTGTTTGAAGATATTTTATGTTTATGTATTTCCTGTATTTATAATTTCCCTTGCTTATTTATGTACATACATATGAATATGAGTTTAACAAACACTCGAAACTAATCTGACGCCTAATAAATGGAATTTATCGTAAAA 2598690 100 NULL:1983304 336222 336407 TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGTGTTTTTGGTA 1 186 TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGTGTTTTTG--- 100 NULL:1983305 337501 337692 ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCGGTA 187 378 ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCG--- 100 NULL:1983306 337756 338398 TACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTACCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACAACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTGGTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAACGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCCAAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTCGAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGTTACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAATATATACCGCTACAACATTTA 379 1021 TACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTACCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACAACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTGGTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAACGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCCAAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTCGAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGTTACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAATATATACCGCTACAACATTTA 2604359 99 NULL:1988025 10161 9825 CTGGTAGCAGTTTTTTGAGGTAACCCGGATCCAAGGTGGGCGCCACGTCACGCTCCTCTATATTAGTGCCGTATTGGCATATATAATCAATCACTTCCTTGCCGTATTTGCGAAACTCTTCCACATCCATTTTCTCTAATTTACACTTTTCGTTTATCTTCTTGTTCAAATAAATTGCAGTCTATTAAGAAGTATCTGTTGGTGCTTGGTGCTTGTATCTCTAGTGCTCGGATACTAGGCTCTCACACGGTACACAGTAGCTTATCTCGATCACTTTCGAATCCCGGTTATCTCGCACCGCACACTCGTTGCAGGTCAGCTTCCTTGACGCGAATGT 1 337 ACGTTCGCGTCAAGGAAGCTGACCTGCAACGAGTGTGCGGTGCGAGATAACCGGGATTCGAAAGTGATCGAGATAAGCTACTGTGTACCGTGTGAGAGCCTAGTATCCGAGCACTAGAGATACAAGCACCAAGCACCAACAGATACTTCTTAATAGACTGCAATTTATTTGAACAAGAAGATAAACGAAAAGTGTAAATTAGAGAAAATGGATGTGGAAGAGTTTCGCAAATACGGCAAGGAAGTGATTGATTATATATGCCAATACAGCACTAATATAGAGGAGCGTGACGTGGCGCCCACCTTGGATCCGGGTTACCTCAAAAAACTGCTACCAG 100 NULL:1988026 8836 7732 CGCATTCGGAAGCAAACTAGGCCAAGGTGAACATCGTTGCGAACCTCAAATCGTTCATCCTTGCGCACCAGCATCTCAAACTTCTTAGCCAACGCCATATGATTTCGAATGTATTCCTGTAGGCCCCGAATGCCGTATGTCCGGAAGACGAACCACAGCTTGAGTGCCCGGAATCGGCGACTCAGGGGAATGCCGTAGTGGCGGTAGTCAACTCCGGTCAAGTGCTCGTGTCGTAGGTAGAGGGGATTCACGTTGAGCGCGCTCTTAAGGTTCATCACATCCCGCACCCACAGGGCAGAGGCATCGAAGTTCGTCAGCAGAAGCTTGTTGGGATTTGTGTTGAAGGAGTCGGCGTATTCGAGTCCTGCCGAAAAGACCCGCATCTCGGGCAGAATGAAGGAGTTTCCCGCATAGGCGCCGTCTACGTGCAGCCAAATGCTCGACACCTGGCGGCACACCTTTCCGATCTCCGTGATGTCGTCGAAAGCGCAGCCGCCGGTGGTACCCACAGTGGCCACTACAAAGAAGGGTGTCAAGCCGGCGTTCACATCGTTTTGAATTGCTTGGCGGAGTAGGTCAACGCGCATGCGTCCATGCTCGTCGGCATCGATTATCCGGAGCTTCACCAGGGCCATCTTGGTGGCCTTTTCCACGGAGGAGTGTGCCTCACGGCTGGCGTATGCGATCAGGCTGGGCAGGAAGACGCTGTCGTGAACGCTGGTCTGACCCTTTAGCTCGCTGATGGCCCGGGCGCGGGCTGTGATTAGAGAGACGAGAACGCACTCTGAGGCGGATCCCTGAAGGGCGCCGCCGCCTGTACTGCCTGGGGCATCCGAAACAAAGGCCTTGGGCAGGCCAAGGGCCTTGGCGTACCAGTTCATCACGATCGTCTCCAGCTCGGCAGCCGCCGGACAGCTGGCCCAGCTGAAGCCAATTGAACCAATGGCACTGCTGAGCATGTCGCCTAGGACCGATGGAAAAGAGTTGCCCGAGGGGAAGTAGGCGAAGAACTTGGGGTGGTTCCAGTGCACCACGCCCGGCATGATCTTCTGCTCGAAGTCCTCGAGCACGTCCTTGAACGGCTCCGGCGACTGGGGAGCGTCGGCTG 338 1442 ---CCGACGCTCCCCAGTCGCCGGAGCCGTTCAAGGACGTGCTCGAGGACTTCGAGCAGAAGATCATGCCGGGCGTGGTGCACTGGAACCACCCCAAGTTCTTCGCCTACTTCCCCTCGGGCAACTCTTTTCCATCGGTCCTAGGCGACATGCTCAGCAGTGCCATTGGTTCAATTGGCTTCAGCTGGGCCAGCTGTCCGGCGGCTGCCGAGCTGGAGACGATCGTGATGAACTGGTACGCCAAGGCCCTTGGCCTGCCCAAGGCCTTTGTTTCGGATGCCCCAGGCAGTACAGGCGGCGGCGCCCTTCAGGGATCCGCCTCAGAGTGCGTTCTCGTCTCTCTAATCACAGCCCGCGCCCGGGCCATCAGCGAGCTAAAGGGTCAGACCAGCGTTCACGACAGCGTCTTCCTGCCCAGCCTGATCGCATACGCCAGCCGTGAGGCACACTCCTCCGTGGAAAAGGCCACCAAGATGGCCCTGGTGAAGCTCCGGATAATCGATGCCGACGAGCATGGACGCATGCGCGTTGACCTACTCCGCCAAGCAATTCAAAACGATGTGAACGCCGGCTTGACACCCTTCTTTGTAGTGGCCACTGTGGGTACCACCGGCGGCTGCGCTTTCGACGACATCACGGAGATCGGAAAGGTGTGCCGCCAGGTGTCGAGCATTTGGCTGCACGTAGACGGCGCCTATGCGGGAAACTCCTTCATTCTGCCCGAGATGCGGGTCTTTTCGGCAGGACTCGAATACGCCGACTCCTTCAACACAAATCCCAACAAGCTTCTGCTGACGAACTTCGATGCCTCTGCCCTGTGGGTGCGGGATGTGATGAACCTTAAGAGCGCGCTCAACGTGAATCCCCTCTACCTACGACACGAGCACTTGACCGGAGTTGACTACCGCCACTACGGCATTCCCCTGAGTCGCCGATTCCGGGCACTCAAGCTGTGGTTCGTCTTCCGGACATACGGCATTCGGGGCCTACAGGAATACATTCGAAATCATATGGCGTTGGCTAAGAAGTTTGAGATGCTGGTGCGCAAGGATGAACGATTTGAGGTTCGCAACGATGTTCACCTTGGCCTAGTTTGCTTCCGAATGCG 99 NULL:1988027 7609 6771 ATTTTCCGTTGGATTGTGTTTGTATTTTTTAAAAACTTGCATAAAAAATGCCGAGATAATGTTTATAAATAAGTGCTTTTGTTCATGACAGTAACTTAAGGTAGCTAAACGGTATAAGCAGATGCAAATGAGTCTATCTTTAAATTACATGATATTCAGCAACAACTAAGGTCCTACTAGTACATAAATGGATGTTCTTAAATTCAAACTGAGCAATGTTAGTCGGTAGTCGATTGATTCATGCCTCATTTCAGCTCGACAACTAATACTAGGTAGAGGTAAATCCGCAAATCCCTTTTCGGGTCGACGCTCAGTTACTCGCCTCGTCCGTATCCACGTCTGATATATCTTTGAGTTTTACGTTGCCATTGCTGTTGTTCCTGTCATTGTCATCCGCCGCCTTTTGGAAGTTCTCCTGAAGAGTTTTGGGATCGACGACCAGGATGGGTGTGCACCCGTCCATTAGGTGCTCGCTCTGGCTCTGGTACTGCTCCCGCGAGATGCTGCGAGTGAAGGAGAATCGCAGCGACTTTGTCCTGGTCAGCCTCTTTTTGATGGGTGGCTTGCCCGCCACTGGAGCCAATGGCTCTGAGCTGGTCCGCTCTGAGCCTTCCGGCGTGGTTGGCACGGAGCTGGACTCCAGCTGGTGGTCCCGCAGTATTTCCTCAGCAAAGCACTTTATCTGGGTCCAAGCTTCCAGGATGTCCTTCTCAGTGGCGTGCTCGTAGGTGACGCAGAAGCGGATCACGTAGCGGCCGTTGAACTTGGCCGGCGTCATATGCATCTTGCCCGAGTGGTTGATCTGGGCGAGCAGCATGTGGTTGGGCTCGTCGCCAGTTCTG 1443 2280 ---AACTGGCGACGAGCCCAACCACATGCTGCTCGCCCAGATCAACCACTCGGGCAAGATGCATATGACGCCGGCCAAGTTCAACGGCCGCTACGTGATCCGCTTCTGCGTCACCTACGAGCACGCCACTGAGAAGGACATCCTGGAAGCTTGGACCCAGATAAAGTGCTTTGCTGAGGAAATACTGCGGGACCACCAGCTGGAGTCCAGCTCCGTGCCAACCACGCCGGAAGGCTCAGAGCGGACCAGCTCAGAGCCATTGGCTCCAGTGGCGGGCAAGCCACCCATCAAAAAGAGGCTGACCAGGACAAAGTCGCTGCGATTCTCCTTCACTCGCAGCATCTCGCGGGAGCAGTACCAGAGCCAGAGCGAGCACCTAATGGACGGGTGCACACCCATCCTGGTCGTCGATCCCAAAACTCTTCAGGAGAACTTCCAAAAGGCGGCGGATGACAATGACAGGAACAACAGCAATGGCAACGTAAAACTCAAAGATATATCAGACGTGGATACGGACGAGGCGAGTAACTGAGCGTCGACCCGAAAAGGGATTTGCGGATTTACCTCTACCTAGTATTAGTTGTCGAGCTGAAATGAGGCATGAATCAATCGACTACCGACTAACATTGCTCAGTTTGAATTTAAGAACATCCATTTATGTACTAGTAGGACCTTAGTTGTTGCTGAATATCATGTAATTTAAAGATAGACTCATTTGCATCTGCTTATACCGTTTAGCTACCTTAAGTTACTGTCATGAACAAAAGCACTTATTTATAAACATTATCTCGGCATTTTTTATGCAAGTTTTTAAAAAATACAAACACAAT-CAACGGAAAAA 2598587 99 NULL:1983216 78967 79164 ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAG 1 197 ATC-TTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAG 100 NULL:1983217 82407 82559 G...CAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 198 350 -------TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAG--- 100 NULL:1983218 82618 82763 GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 351 496 GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAG--- 100 NULL:1983219 83955 84213 ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCAGTA 497 755 ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCA--- 100 NULL:1983220 84477 84619 CAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGGTG 756 898 CAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAG--- 100 NULL:1983221 84674 84756 GTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTGTA 899 981 GTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCT--- 100 NULL:1983222 84820 84892 TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTA 982 1054 TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAG--- 100 NULL:1983223 84960 85814 GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 1055 1909 GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 2598677 100 NULL:1983295 322896 324083 TTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGCGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGAGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCTGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTCTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGCCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGGAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAA 355 1542 TTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGCGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGAGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCTGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTCTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGCCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGGAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAA 100 NULL:1983294 322482 322835 CACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCCAAGTGGTAAAGTG 1 354 CACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCCAAGTGGTAAA--- 2604466 98 NULL:1988117 341629 341367 CCACAAACAGTATGTTGAATATGAACAGCACATATTTCACAAAAACGCCGCCGCAATCCATTGCTGAGATGTACTTGTGTATCACTTGTGTTCGATTTAAGAGTAAGACGTTCGATGCGATTTCGTTCGTGGTCCGCTTGATACTGAAAAAGTCTGATATATAACAATATTTTTATGAGCGCATTTCCTATCGCGAAAAGCTCTGTTAGATTTTAGCTCTGAATTTAGCGGCGATAAGAAAAGCGTTGCTGCAGTGGTAGAGAT 1 262 ATCTCTACCACTGCAGCAACGCTTTTCTTATCGCCGCTAAATTCAGAGCTAAAATCTAACAGAGCTTTTCGCGATAGGAAATGCGATCATAAAAATATTGTTATATATCAGACTTTTTCAGTATCAAGCGGACCACGAACGAAATCGCATCGAACGTCTTACTCTTAAATCGAACACAAGTGATATA-AAGTACATCTCAGCAATGGATTGCGGCGGCGTTTTTGTGAAATATGTGCTGTTCATATTCAACATACTGTTTGTG- 98 NULL:1988118 340629 340438 263 454 99 NULL:1988119 340368 340207 CGATCGCTGCAGTGTGTCCATGAGGAGGGCATCGGTCTTGCGTTGATCCCATATGGTCTGGACGATCTTCTCCAAAGATTGCTGTATCTGCACATGGTCCACCCACACGTAGATAATGAGAGCTAGCTGACTAACCAACAGCACCAGCATGACCACAGAGTA 455 616 TACTCTGTGGTCATGCTGGTGCTGCTGGTTAGTCAGCTAGCTCTCATTATCTACGTGTGGGTGGACCATGTGCAGATACAGCAATCTTTGGAGAAGATCGTCCAGACCATATGGGATCAACGCAAGACCGATGCCCTCCTCATGGACACACTGCAGCGATCG 100 NULL:1988120 340075 339878 CTCAACAGCAGTCACACCCAGGCCAGCGTACTTGATGATGCTCACGTTGGTGTCCCAGAAGGAATCAACGGCCTTCAGGCAACTGGATCGCGTCATGACTTGGGTTAGTGCGCAGGTTCCATTGGAGGGCGAGTCGCAGCAGGAGGCGGGATACGTAATGCCGTAATCAGCGAAGCCGTTCAAGCCGCAGCACTTGAACTG 617 814 ---TTCAAGTGCTGCGGCTTGAACGGCTTCGCTGATTACGGCATTACGTATCCCGCCTCCTGCTGCGACTCGCCCTCCAATGGAACCTGCGCACTAACCCAAGTCATGACGCGATCCAGTTGCCTGAAGGCCGTTGATTCCTTCTGGGACACCAACGTGAGCATCATCAAGTACGCTGGCCTGGGTGTGACTGCTGTTGAG 97 NULL:1988121 339820 339633 TTATATACAGTAAGCATGCGAAGCACTTTGTTTTATTTATTCATATTGACTTTATGACGTTAAAGAGGGTCGGGAGATAATCCTAATACTATGCTACTAATTCATCGTTTCATCGTTTAGTAGTTCTGGCGTCTCTGCGAGTTGCGGGTCTGATTGGCCAGGCAGCAGGCGAAAATGAAGGCCACAAGCTG 815 1000 ---CTTGTGGCCTTCATTTTCGCCTGCTGCCTGGCCAATCAGACCCGCAACTCGCAGAGACGCCAGAACTACTAAACGATGAAACGCC--ATTAGTAACATAGTATTAGGATTATCTCCCGACCCTCTTTAACGTCATAAAGTCAATATGAATAAATAAAACAAAGTGCTTCGCATGCTTACTGTATATAA 2604378 100 NULL:1988041 47582 46434 AAAGAATTTGAAGGCCAAACATTAGAGCGAATCCCGCAACGGCGGCCACAAGGGCCCTCCATCCGGCATGGCTCTCAATGAGGATCTCAAAGAAGACTACGTACAGCAAGGTTCCACAGGCGATGCCCTGGAGGACTCCGGATGGCAGACTGGGCTGACCCGCTGCCACCTGCTGGCTGATGCCGAGGCCAACACCGATACCGATGGGTGTAACAATGGAGAATGTCACCAGGTACAAGATGGCCAGCGAACTGCGTGTGCGGGCGACCAGAAGCTCCATACCCACGCAGAAGGCCAACACCAACTTGTGGGCGGAGACCGCTCCAAACATGAACCACACAGTGCTCACAGTGCCCTCCAGACCAATGGCCATGCCCTCGAACAGTTCGTGGAGCGAAAGGGCGAGGATAATGCCCAGCCCCCTGGCAGAGGATCCATCGTCCGCTGGCACGGGCATGTGCGAGTGGCCGTGGTGATCCTTGTGTGGCTGCGGTTCCGTATCCTTAACTTCCACTTCTTCCTTCGCCTGTGGATTGAGGAGAACACTGTGACGAATGCTGCGTCCTCTTTCGAAAGCCAGACTGGCCACCGACTCTTTCCGACTAAGCTTTCCCTGGTGGTGCCGCACGAGGCTGGTCATCAGCTCGTCCAACGCGTACATCAGGAAAAAGCCCGTGCACAGCAGCATCTCCGCCAGAGCGAAGGGCGTCTTGACAAGCGAGCCGCATTCCTGGAGCGCTTCCACCACCTCGATCACCTCGGGCAGCATGTGCAGGAAGGTGGTGCAGATGAGCACACCGCCGCCGAAAAAGAGTAGGCACCGCACCACCAATGACGAGCGGGTTTCCTCCGGACTCGCCTTCGTCCAATGGAAGCACCTGTTCAGGACGTAGGGAAGGCTGCCGCAAAGCACGGTGATCACCACGAGCACCACCATGGAAACTATTTTGGCCACCAGCAGCGCATGGTGATCCACGTCTTGCGTTTGCTCTTGTGACATAGTTGCGGTAGCGCTCATCTTCACCTCCCGAGTTGATAGCTTCGACTGTGCTGGCTGGAACTCACAACCAGGCTAATGGTTTATATTTCCAGTCATATATCAGCGGGAGCCGATTGAAATCTGATCGCTGATTGATACGCGGATTCACT 1 1149 AGTGAATCCGCGTATCAATCAGCGATCAGATTTCAATCGGCTCCCGCTGATATATGACTGGAAATATAAACCATTAGCCTGGTTGTGAGTTCCAGCCAGCACAGTCGAAGCTATCAACTCGGGAGGTGAAGATGAGCGCTACCGCAACTATGTCACAAGAGCAAACGCAAGACGTGGATCACCATGCGCTGCTGGTGGCCAAAATAGTTTCCATGGTGGTGCTCGTGGTGATCACCGTGCTTTGCGGCAGCCTTCCCTACGTCCTGAACAGGTGCTTCCATTGGACGAAGGCGAGTCCGGAGGAAACCCGCTCGTCATTGGTGGTGCGGTGCCTACTCTTTTTCGGCGGCGGTGTGCTCATCTGCACCACCTTCCTGCACATGCTGCCCGAGGTGATCGAGGTGGTGGAAGCGCTCCAGGAATGCGGCTCGCTTGTCAAGACGCCCTTCGCTCTGGCGGAGATGCTGCTGTGCACGGGCTTTTTCCTGATGTACGCGTTGGACGAGCTGATGACCAGCCTCGTGCGGCACCACCAGGGAAAGCTTAGTCGGAAAGAGTCGGTGGCCAGTCTGGCTTTCGAAAGAGGACGCAGCATTCGTCACAGTGTTCTCCTCAATCCACAGGCGAAGGAAGAAGTGGAAGTTAAGGATACGGAACCGCAGCCACACAAGGATCACCACGGCCACTCGCACATGCCCGTGCCAGCGGACGATGGATCCTCTGCCAGGGGGCTGGGCATTATCCTCGCCCTTTCGCTCCACGAACTGTTCGAGGGCATGGCCATTGGTCTGGAGGGCACTGTGAGCACTGTGTGGTTCATGTTTGGAGCGGTCTCCGCCCACAAGTTGGTGTTGGCCTTCTGCGTGGGTATGGAGCTTCTGGTCGCCCGCACACGCAGTTCGCTGGCCATCTTGTACCTGGTGACATTCTCCATTGTTACACCCATCGGTATCGGTGTTGGCCTCGGCATCAGCCAGCAGGTGGCAGCGGGTCAGCCCAGTCTGCCATCCGGAGTCCTCCAGGGCATCGCCTGTGGAACCTTGCTGTACGTAGTCTTCTTTGAGATCCTCATTGAGAGCCATGCCGGATGGAGGGCCCTTGTGGCCGCCGTTGCGGGATTCGCTCTAATGTTTGGCCTTCAAATTCTTT 100 NULL:1988042 46357 46120 GTAAAATATTGTCTCTTTTAATCCATATGGTTATTACATTTTTAATTATTTGCGTTGGATAAGATTTCTGAGAAACCTCTTTTGAAATTCTATTCGTATTTTATATAATAACTTTTACAGATCCCCAGGGAATCGTTTTGTATACTATTTTGTTGCTTCCTCTATAACTTGATAATACTGAAGTGGCGTCACACTGGCTAGGAACAGGTTAGGCTGTCATCACCCTCCGCTTCGTCAGCTG 1150 1387 ---CTGACGAAGCGGAGGGTGATGACAGCCTAACCTGTTCCTAGCCAGTGTGACGCCACTTCAGTATTATCAAGTTATAGAGGAAGCAACAAAATAGTATACAAAACGATTCCCTGGGGATCTGTAAAAGTTATTATATAAAATACGAATAGAATTTCAAAAGAGGTTTCTCAGAAATCTTATCCAACGCAAATAATTAAAAATGTAATAACCATATGGATTAAAAGAGACAATATTTTAC 2598695 100 NULL:1983308 342031 342110 ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTTAAAGTCGAAGGTA 1 80 ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTTAAAGTCGAAG--- 100 NULL:1983309 342808 342891 ACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCGGTG 81 164 ACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCG--- 99 NULL:1983310 346788 347150 GTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGGTCTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGAGGTGTCTTCGACACCATTCAGAAATCG 165 527 GTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGGACTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGAGGTGTCTTCGACACCATTCAGAAATCG 100 NULL:1983311 347210 347401 TAGTTGCACTGCTGCGGATCAAGCTCTGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCAGCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAGTTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCATCGGCCTCATCGGAATAGAG 528 719 ---TTGCACTGCTGCGGATCAAGCTCTGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCAGCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAGTTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCATCGGCCTCATCGGAATAGAG 99 NULL:1983312 347465 348139 TAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGGCCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGAAATTTATGAATAAAGCATTTACTATGTATTTATATACCAA 720 1394 ---CTGATCGGCTTTATCTTTGCCTGCTGCCTGGCCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGGAATTTATGAATAAAGCATTTACTATGTATTTATATACCAA 2604395 100 NULL:1988056 86795 86695 TG...TACCTTGAGCAACCAGGATGCCCCCAGGTTCCGTCTTAGTATCATTGACATTCTAACGCTAATTTATTTTTGTTCTCTTTATTTAAGCTGATGATTGCAGTGTC 1 101 GACACTGCAATCATCAGCTTAAATAAAGAGAACAAAAATAAATTAGCGTTAGAATGTCAATGATACTAAGACGGAACCTGGGGGCATCCTGGTTGCTCAAG-------- 100 NULL:1988057 86632 86488 TACCTTTGTCCAGGTGGATCTTGAAGGGGCGCTTGTCGAAGATCGTACCGTTCTCCTTTTGCAGAACGGCCGTTTGCTTATCCTCGAGCAGGTTACTGGGAATTGTTTTGGCCGAGTCCACCGGTTTTGCGCTGGAACTGTAGCATGC 102 246 GCATGCTACAGTTCCAGCGCAAAACCGGTGGACTCGGCCAAAACAATTCCCAGTAACCTGCTCGAGGATAAGCAAACGGCCGTTCTGCAAAAGGAGAACGGTACGATCTTCGACAAGCGCCCCTTCAAGATCCACCTGGACAAAG--- 100 NULL:1988058 86411 86318 CTCTGCTTGATCTTCAGGAACTCGTTCTTGTGCATTCCATCGCAGAGGGGCTGAGACTTGGACTTGCCGCACAGGCACCAGCTGTATGTTTTAT 247 340 ATAAAACATACAGCTGGTGCCTGTGCGGCAAGTCCAAGTCTCAGCCCCTCTGCGATGGAATGCACAAGAACGAGTTCCTGAAGATCAAGCAGAG 98 NULL:1988059 86256 86065 TTGCTTGATTCAAAATTAATGCATTTCTCTTTTCGCACACGGGCAGGGCCCTACAACCAATCCTAAATCTATTTGACGGCGCTCTGGATGTGTGGCTGCTTGTGGGTGCCGTCACAGAAGGGTCTGTGGGTGGTCTGTTTGCAGTTGCAGAGCCAGTAGTCTCCCGACTTCTCCACCTTGAACCGAATGGGC 341 532 GCCCATTCGGTTCAAGGTGGAGAAGTCGGGAGACTACTGGCTCTGCAACTGCAAACAGACCACCCACAGACCCTTCTGTGACGGCACCCACAAGCAGCCACACATCCAGAGCGCCGTCAAATAGATTTAGGATTGGTTGTAGGGCCCTGCCCGTGTGCGAAAAGAGAAATGCATTAATTTTGAATCAAAAAA 2598607 100 NULL:1983235 137865 138301 ATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACATGAACAACTTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCAAGTG 190 626 ATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACATGAACAACTTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCAA--- 100 NULL:1983236 138358 138948 GAACGAAGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAGTCCGTCGAGGATCGCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTGCGCCTGCTGCTCCACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACCAGCC 627 1217 GAACGAAGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAGTCCGTCGAGGATCGCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTGCGCCTGCTGCTCCACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACCA--- 100 NULL:1983234 137404 137592 CCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGGTG 1 189 CCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAG--- chado-1.23/soi/t/data/AE003790.soi.xml000644 000765 000024 00025437453 11256707644 017066 0ustar00cainstaff000000 000000 Drosophila 0 2R 0 20302755 melanogaster 2R 2080000 1731127 0 2R:1731127-2080000 CAGTCTCGTTTTGGGATTAGTAGTGGGACACACATAAATGATACGAAGAT TAACTTCGAAAGGGTACATTTCTCTGCTTAATTGACGGCCTCTCGGCGAT GTTGAAAACCTAGGAGTTAAAATAAAATTATGTTTGGAATGGCATCGTTT AAGTGGCGAGAAGTACATGATATTCTCGAGTGGCATACACTACAATACAT TACATTACAGGCTTATCATATATAAGTCGTTATTATCGTGCATCGTTATT TGGGCAGTTAGTATTGAGTGGGAGCGCTACTATTGCCTCTACACGGGAGG CTAAATACAAGAGTCTACGTTTGTATCTACCAGATACTAACTACGTTCTA CATCTAGTATGCTAAGCTCTATGTTACTTTATACAGGGATGTGTAATTAT AATCTCTACTTAGTTTGCACAGTAAAAAATCTAACTAAAACGGTTAAATA TTCATTTAAAGTATTGTCCAGAAGGCGCGCGTGCATCTAGGGCAAACAAT TGATCTATCATTAGGGGAATTAACAAATTTTCGTAGACGAGGCCAACATC TGATAATGCAATCAAAGGTAAAGGTACAACAGCTTAACACTAGGCGCCCA GATAGACAAGCTTAATAAGGATTTCAGCACACATACGTGGGCGGAAATAA CAGAATAGAAACACGAAACTATTTCCAGATCAGGAGTGTGAGGTTGTGGA AAGGACACGGCGTTTGGTGCAACCATTTTGAATGGTTAAGCACAATACGT AGGCCCTAAAAAATATCACTTTTTCGACGGCGATAGACGGCCAGTTTCCG TAGTTCTCAGTTGTGCTTGGCCCGACGACCAAACATATAGCCCTTCCAGC GCTCCGCAGTTTGTGCAATTAATGGATCGCTGTCGATGGTGGCTAACAGA AGTAACTGGTTCACGTGCGTTGCATGGTAGTCCCAGCGCGCCAGATTAGG AGCTACGCCCAGGCTCAGATGGCGCAGGTCGTAGCTGGTGCCGGAGCCAG TGTCAAATAGCAACAGCATCTTTTTAAGGGAGTGCATGCCCTGCGCGAAA AGCTTTCCAGCCTCGCGGGCGATTTTTCCCGGGGCAGTGCTGTTGAGATC GTAGAGACCCAGCAGTGAATAGATAAAGCCGTTTAGCACATAAGAGGGTG GCGTGGTGGGGTACTCCTCGTACCTGTAAAAGCCGAAAAAAGAATTTCGA TTATTGAATAAATTTGGTTCTCAAAAACAATTTTCCTATTGTTGCTGTTC CTGTTTGGTATACAGGGCGATCTTATACTCACCAGTAGAACTTGTCCATG AACTGCGCCAGAACGCCGCCATCGCGCGAGTATACCCTATAAGGCTGCAG TCCGGCTGCGGCCGCTCGAAGGTAGCGTTCATCCCCGCCGGAGTGCCAGT AGGCTCGTGCCAGCACTGAAATAGCGTGTCCCTGGCCCATGGCTGATATC CACCCCGGACGCAATTCGGCAAAGCCGTTGAGGCTGCGACGCACAGGATT GGTCCAGCCACCCGTCTTGGGGTCCTGGTTGTGGACGAACCACTCAGCCG CGTCGTAGAAGTGAGCCAGATGGTCACTGGTGGACAAGGTGATATTGTCG AAGAAGCCAAGGCCCAGAAAGCCAATAGATATTACCTCCAGATCGGAGCG CCGTATCTTTAGCGGCGAGCGTTTGTCACCCATGATGCCCTTTTGAAGGT CAATGTGCAGGTCTCGAGTGATGTGGCGCCACTTGTTCAGTGCCGAGCCT CCCAGACCGTAGTAGATGTTTGTATCCTGCACGCTCAGCAGCAGATCTGC GGGTATGTAGTGCAGGCTGTAGTTGTGACGGGTGTCCCGATTCTGAACGG TAATCATGAGACTACTGCTATTGGTTACCAGGAGCAGATCAACGCTGAGC AGAAGATCCAATGTCTGGTTTAGAGCAATGCTGATGACGCCTTCGTAACC AGGTGCCGTCTCGAACTGGACAACACTGGTGTTAAACTTGTGGTGCCAGA TGCGGGTCATGTTGCTGGTCTTGGGCGTACTCCATTCCATCTGGTTCCCG TCGCCGTCCTCCAACACGCGAACCCTGGGTGCCGGCTCTGTGAGGTTCTT GCTGTAGTGCGACAACGCGAACTGGGCAATTTGTGTGGGGTAAAAGTACC CACGCTTCTCCCATTGCGTGCTCACTGGAACGCCCTCCGCGGCACTGATG CACTTTACCCGGTCGCGCACTTCCACGTTGTAGTTCTCAAAGTACATATA GACGCCGCGCGCATCGTACTTTCCCCTGGGAAGGTTAACTTTGGCTGTGC TGTGCACCCAGTTGAACTTGGCCACCTCATTGCTGTTGGTGGAAACTGCT CCACTGACGTCGAAGTAGTTACGCAGGAAGGAAAACGGAACGTAAACCTC GTTGGCGTTCTCGTCTCGCTTGCAGTGCACGGTGTACTCCTGGTTAATGG AGCACTCAATGTCGTGCAGCGCTGTAGCTTCTCCTCCGCTGGAGGACTGC CTTGCGGACCGGTCCAGAGGACGCACAAAGTCCGGCGAAAAGGAGAAGGC GGCGCAGCGCATATACACGCCCAGAGTGATTACCACCACAGCCACTGTGA GGACAAGCAGCACGGCTTTTAGGTTCAGTCGCATGATGAAAAAGACCAGT GGCTCGCGTTGCTAAAGAAAATTCTAAGATTAGCCAACTGATAACACGAC GAAATAGACATTGTTACCTTTACCCCTTGGAATTTAGGTGGCTCCCGGTT TTCCCTGCTTACTGGAAGCGCGGGTGCGGAAAGGGCATCTCTCTGACTGC TTAGATATTTGGACATTCGGTTGGGGGCGAACTCTCTAACTGGCTTCTAG GTGAGTCATGCTCTAAATTTAAAACTGCATTCATCTGGCAGATGCATTGC TGACGATGATAATGGTGCACCAGTACGCGTACGTCTCTTTCACTGTCTCT GTCTAAAATTCCACCTGCCGAGCCTGTAGCCCTCTGAGTTCAGTCCAGGG CCATCCAAAGTTGATATTTCAAGTGCATCCAGTTCTCACTAAGCATATTT TGCTTAGATTTGCGCTGCTCTTCTCGCTTTAATGGGCGAACACTGCGAAA ACACAGAAACTGCGATACAGATGAGCAAATGTTTTGACATATGACAAATG GTCGCTCTTGGGCGGCCTATGCACGTAAGCTATCGATAACAAGCATTAAC CGTGTGCATCGTTACTTCTGTAGCTAAGTAATTTAAATAGTTTAATTTTC GAGTTTAAATAGTTTATATTCCTCCTTTGGTTGAAAATGAACTTTTATTT ATAAATTCATTGGTATTTTCAAATGTTCCCATACGCATGCTGACAACTAT CGACGAACCGATAGCATCAACACGACGGCGATTAATCAATAGTGCAATGT TTACAAAATATTTCGGGTGGATGTCGGTGAGAAGGCGCGTTTAACTAGTT TTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGC GTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTC ACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAGGTGAGAAG TGCTATCCACTTTAATTGCAAGTCTTAAGAGCAAGCTTCCATTGGCAGAT GGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTT TGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCA TGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAG TTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGC CTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTAC GCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACC CACATATTCGCAGTGGTATGCCTTTATTTACACGATCAGCCAATAAAGTC GTTATACTAAGTTCCCTCGATCCTTACTCTTCCAGACGAGTCTCAACGGC TGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCT GCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCA TGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATC ACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGT GGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAG TTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGC AGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGC TATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATG CTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTAT GAGTGCGTAGAAATATTACTTTATTCTAATATTGCTACATGTGTTTGCAT TTTAGCTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGC GGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGC CCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTA ATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCG AAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGT TTAAAAAGACATAATAGAGACTTTATTACAACATTTAGAACTCCGTGCTA CATTTGCCCGCACTGCGAAATGGTCACTGGGAGCTTCGGCTTGTTATTGG GGCCCGTGGGCACGTTCTCGATCTTGCGCATGATGAGCAGTCCATCCAGA ACCCGACCGAACACCACGTGCTTTCCGTCTAAAAAGTTGCACTTGGCGCA GGTGATAAAGAATTGGCAGCCGTTCGTCTCCTTGCCACTGTTTGCCATGG AAAGGAGGCCGGGCGAGTCGTGCTTCAGGGTAAAGTTCTCGTCGCCGAAG GTGTTGCCGTATATGCTGGTCACGCCGGTGCCGTCGCCCTGCACAAAGTC GCCGCCCTGGATCATGAAGTCCTTGATCACCCGATGGAAACTGGCGCCTT TGTAGCCAATGGGAACGCCATCCGGTCGGTACTCGCCCGTGCAGAACTGC CGGAAGTTTTCCGCCGTGCGGGGCACTGTGTCCGCAAAGAGTTCGAATAT CATTCGTCCGATTTCCTGCACACAAAAGGCGTTAGAAGGCGGAGTTATGT ACAGATTATGACTAGATTGTTTTCAGCTCACCGTTGTGCCTACGGCAATG TCGAAGAAAACGACGGGATTGTTGGAGCTTCTCAGTTGGGACTGTATTTG ATTCCAGTTAGGCATTTTAAAATTATTTTATTTGTTTATAAACTTTCTAA CAAGTCAAGATTAAGATTTTACTAAGCCGGCAGATTTTTGTTTATGTTTA TTACGATGGTTCGATGACGATGCACGACAAGTCGATAGCATCACAAGCCG GTTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTG CACATATTGGTGAAACTATTTAATAATATTTATTAAGGTGAGTTTATTTA TGATTGGATTGATTGATGAGTAGAGTGCATAAAATAGTGCATAAATATTA TTATTGTTGGATATTGTTTCGGCATTATTTTTAGTTGTTTATTTTTATTG GCAAGTTTCTCAAGGCCTGCAAAATATGTATGCATACTAACATATTTCGT GGTCCGATGGGCAGGATTTTTTCCTGATAGGATATGCGTGTGTAAATTCT TCAACATACATACGTTCCCACGCTAAAAGCTTTTATCACAAAGAATGACA GAATGACCCAAAACACTTGTATCTGTATGTACATGCATTTGTACCAAAGT GGGAAATGGAGATATGCAAGAGACAAAGCAAGTGCAGTAGCAAGCAACAA TTGTATGCCTTAGCATGCGTAAGGAGACCGATATATGTATATTTATATTT AGTTTACTTATAATTAGTTTATACTTTTAAGATGTAGTGGTAACGTTTTA AAGCAAACTTATTGAGACATATATCATATACAAAAATTAAAAAAAATACT ATTTGCGTCCCCCAAAGATCTCCCAGTTGGATTTTGGATAGACTCTTTGC CAAGGATTCCCGTAATTAGCCATTTTAGGAGTTCTGTTGGAAACGAATGG CCCCAATTAGCCCTCTCTGTTGATGAATGAAGACCTTTTATCGACATAGT ACAAAAACGTATGATAATTAATAAATATTCGTGAGCATTGTACTCAAGAA AAATGTAAATTTTCCGAAAAATATGCACGACAATGACCCCCATTTGACGT TAAGATCTGCTTAGTGAAAAATAGATTTCATGTTTTGGTAGTGACAACAC ATTCCCGGGGATCTTAATCCCATTGAGGTCTCCTTGATGAAAACCATATC CTTGGCATTGTGTTCGTTTGTGGGTGGAATATCATTTTCTAAACAGATGC ACAGCTTTATTGGATATTGGATATAGTTTTCTGTACGTTCTGGTTTGTTT AAATGTATCCTCTTGGACGACTCTGTAAATTTTATAATAATATACATTTA TAATGTACATATCAAGTTGCTTTAAACATTAAGATTGTCCTTCAAACTCC CATTACAAGACACGAGATACATTTTCCGTTGGATTGTGTTTGTATTTTTT AAAAACTTGCATAAAAAATGCCGAGATAATGTTTATAAATAAGTGCTTTT GTTCATGACAGTAACTTAAGGTAGCTAAACGGTATAAGCAGATGCAAATG AGTCTATCTTTAAATTACATGATATTCAGCAACAACTAAGGTCCTACTAG TACATAAATGGATGTTCTTAAATTCAAACTGAGCAATGTTAGTCGGTAGT CGATTGATTCATGCCTCATTTCAGCTCGACAACTAATACTAGGTAGAGGT AAATCCGCAAATCCCTTTTCGGGTCGACGCTCAGTTACTCGCCTCGTCCG TATCCACGTCTGATATATCTTTGAGTTTTACGTTGCCATTGCTGTTGTTC CTGTCATTGTCATCCGCCGCCTTTTGGAAGTTCTCCTGAAGAGTTTTGGG ATCGACGACCAGGATGGGTGTGCACCCGTCCATTAGGTGCTCGCTCTGGC TCTGGTACTGCTCCCGCGAGATGCTGCGAGTGAAGGAGAATCGCAGCGAC TTTGTCCTGGTCAGCCTCTTTTTGATGGGTGGCTTGCCCGCCACTGGAGC CAATGGCTCTGAGCTGGTCCGCTCTGAGCCTTCCGGCGTGGTTGGCACGG AGCTGGACTCCAGCTGGTGGTCCCGCAGTATTTCCTCAGCAAAGCACTTT ATCTGGGTCCAAGCTTCCAGGATGTCCTTCTCAGTGGCGTGCTCGTAGGT GACGCAGAAGCGGATCACGTAGCGGCCGTTGAACTTGGCCGGCGTCATAT GCATCTTGCCCGAGTGGTTGATCTGGGCGAGCAGCATGTGGTTGGGCTCG TCGCCAGTTCTGTAGAGAAGATTGAGTAGATCATTAAAGACCAGCATTCA GATTTAGCTGCTTTCTTCAGTTAGGTAAATACTAGCTAACGGTTAATGGT TTATAAATGGTTTAATGGTTAATAGACTTACCGCATTCGGAAGCAAACTA GGCCAAGGTGAACATCGTTGCGAACCTCAAATCGTTCATCCTTGCGCACC AGCATCTCAAACTTCTTAGCCAACGCCATATGATTTCGAATGTATTCCTG TAGGCCCCGAATGCCGTATGTCCGGAAGACGAACCACAGCTTGAGTGCCC GGAATCGGCGACTCAGGGGAATGCCGTAGTGGCGGTAGTCAACTCCGGTC AAGTGCTCGTGTCGTAGGTAGAGGGGATTCACGTTGAGCGCGCTCTTAAG GTTCATCACATCCCGCACCCACAGGGCAGAGGCATCGAAGTTCGTCAGCA GAAGCTTGTTGGGATTTGTGTTGAAGGAGTCGGCGTATTCGAGTCCTGCC GAAAAGACCCGCATCTCGGGCAGAATGAAGGAGTTTCCCGCATAGGCGCC GTCTACGTGCAGCCAAATGCTCGACACCTGGCGGCACACCTTTCCGATCT CCGTGATGTCGTCGAAAGCGCAGCCGCCGGTGGTACCCACAGTGGCCACT ACAAAGAAGGGTGTCAAGCCGGCGTTCACATCGTTTTGAATTGCTTGGCG GAGTAGGTCAACGCGCATGCGTCCATGCTCGTCGGCATCGATTATCCGGA GCTTCACCAGGGCCATCTTGGTGGCCTTTTCCACGGAGGAGTGTGCCTCA CGGCTGGCGTATGCGATCAGGCTGGGCAGGAAGACGCTGTCGTGAACGCT GGTCTGACCCTTTAGCTCGCTGATGGCCCGGGCGCGGGCTGTGATTAGAG AGACGAGAACGCACTCTGAGGCGGATCCCTGAAGGGCGCCGCCGCCTGTA CTGCCTGGGGCATCCGAAACAAAGGCCTTGGGCAGGCCAAGGGCCTTGGC GTACCAGTTCATCACGATCGTCTCCAGCTCGGCAGCCGCCGGACAGCTGG CCCAGCTGAAGCCAATTGAACCAATGGCACTGCTGAGCATGTCGCCTAGG ACCGATGGAAAAGAGTTGCCCGAGGGGAAGTAGGCGAAGAACTTGGGGTG GTTCCAGTGCACCACGCCCGGCATGATCTTCTGCTCGAAGTCCTCGAGCA CGTCCTTGAACGGCTCCGGCGACTGGGGAGCGTCGGCTGGAGATAGAGAT AAACAGGCAGTCGGGGATTAGTGGGATGGGCCTTAAATATTTCGTTTATC ACCCATAAATTTGGGGGGGCCAGCAAAGGCAGTATTTATGGCGGGTCTGT TGTTTTTGGCAGTGAGTAGAAAGATCAACAAGTAAGTCTATACGCAAGGT GTGTGTTTGCGTATGCATAATTAATTGATTTGTTTAGTTGAACTCGGGAT TGCGGCGTCCATTCCGGCGTAAATATTTAACTTAGCCAACTGCGCGGAAT TCGCCTGAAATTCGCCAGCGAAACCTACTCTCCAACCTGCCAACCTCTGA GGTGGACGGAGATCGAAGATCGGAGAGATGGCTGTCGAGTGTGCCCCAAT TATGCCGGACCCACCCACGCATCTCGTTGCGGGGCACTTGAGTCCGTGGG CTGGGGATTTTCGAATAGTTTACACTCGCACATTATTCACATGACTCTTC GGCAGCGGGCAAAACAATTAGTCAACATGATTTAACAAGTTTTTGAGAGG CATTCAGTTGCTTGTTGCTCTGGTCTGTCTTTCTTTGATTATTTTGCGCA AACGAAATATTTTCGGATTCATTGCTAATTTGTTTGGGCATAGTTAACAA ATTAGTGTATACAATTTATCACTAGTGCTATAATTAAACTTTTTCTTTCT GGTTTCAAATGGAATTCTGCGAAAACAATCAGACAAATTAGATTCGACTA ACTTCGAAGAGTATTCAAAATTTCCCAGGAAACTTAAAAACTCTATGACA TGCCATGGTGTAAATTGTCAGTAGAGTCCCGTATTTTCTATTTGCTATTA GACTATGATCAATCAGTATTGGGACATAATTATAGATGTAACCAAAATAA GGACCTGTACAGTAAGCACCTCTCAACTCAAACTTGACACAAAATAACTA AATAATTTCGATGTTCATCTTTAGCTTTTGCCGGGTCTTTGATTTTTTCA CACCTCTTCTCATTGCATGCTCACCTGGTAGCAGTTTTTTGAGGTAACCC GGATCCAAGGTGGGCGCCACGTCACGCTCCTCTATATTAGTGCCGTATTG GCATATATAATCAATCACTTCCTTGCCGTATTTGCGAAACTCTTCCACAT CCATTTTCTCTAATTTACACTTTTCGTTTATCTTCTTGTTCAAATAAATT GCAGTCTATTAAGAAGTATCTGTTGGTGCTTGGTGCTTGTATCTCTAGTG CTCGGATACTAGGCTCTCACACGGTACACAGTAGCTTATCTCGATCACTT TCGAATCCCGGTTATCTCGCACCGCACACTCGTTGCAGGTCAGCTTCCTT GACGCGAATGTCTTGCCCACTGCGCCGGAATCGTTTTTATATGGCACCGA TCGGTCTGTTGCTCCATCGCAAGATCGGCTACTCTCGGCTTCTCTCTGTG CTCGGATGTATTCCCTTCTGACACCGACACCTGTGAGGTGTGTTGTGCTC GGTGCTCGTACTGACGTTGATTGTCTCGTGATCGCACTCAAATTACTGGC CCGGAGACTCGGATCGGACTCCGTTTGGCTGGGAAACCCGCTTTGGTCAT TATGGACACATCTCTCGTTCGGCTCTCGCGTCGGGCGGAGCATTATCTTG CTTGGCGAAAAGTCCCTGGTGGGCAAGGGTTTCCAGTTGTTGGCTTAATT ATATGGTGAGTTCAATTTGAAGTGTGATTGAGCAACAGACGGTGGTTTCC TACGTACGTGTAGTCAAATTATTAATTATAATTGACCAAAATAGTTTATT ATTTAAGCTTCTGAACATTATTGAGGAATTCACAAAGAGTAATATTCGCG AGCTTGAAATGCTAAGCTATAGCGAATTTATCGCATTTTCGAGGCATAAA CTCGAATTTAATCGCGTGCTTTCTTACAGATATTTTAATTGTGCTCAATA CCTACCTCAATAAATTCTTCGACAGCATTCGCAGACTTTTTTATGACATT TAAATTAGCTTCGAATGTGAATATTCTGACACGCATGGCTCTTCGGGGAT CTTTTGGGGGTTTTAGAAAATTTCCCAAATTTGCCGTAAGTCCGGGACGT CCAAACAGTGTGCAAAGAGCCAATGAAAGAGAACAAACTTGTTTGCTCTA ATCTCTTGAAGAAGTACCGAAACTTTCCGCGGCTTATGGCAACCAGTGGG GAATCACTTCCAGTCCCAAGTGGCGAACAAGTGTCCAAACATTGACCAAA TGCGTTAGCAGAAAGTCGGATGTACGAATGGCCAACCCTGCCAAGAGGCC GAACTGATGACGTAGCTGTGAAGAGCGCCCATTGTTTCATGGAATCTCCT GCTAGGTGAAATACAAAAACACTAATATCAAAATAAACAATCGTTGCCAA ATGAAAATCACCGATTTGTTCAGTTTGCGAGGCGCGGGAACTTGGCAGAT AATGGGTGTGGGTGGGCAGACCGAACGAATGAATGGGTTTGTTGTCAGAG TCAGCATGAGGCCCCCGCAATTTGGTTGGGTGCTAATTGCCGACAAGTAC TTATCTAACTTTGCCCTGTAATGATCTATACTTACCTTCCAGTCTGTATG TTTAATGGTACGCGGTCCATCAACGTTTTCAAGAGGATTAGATAAATAGA ATGCAACCGCTTATTCGCAGGTAGTTAGGGAACACAGTTTGAATCTCACA TTGTTATAACCCGAAGGAGTGCCTTCTCATTCGTACTAAATAAGTTACTG ACTATCTTAGATCTCTCTCTAAGATAAGACAAAGCAAGCCAAACCAAATA ACAATATACAATACATTAACTGGGCGTAATCAATAGATAACCTCCTGCAG GTATTATCTTGCAAGTTCTGTTCGGAAACAACCGCAATCCGACCACTGTA ACTTTGGATGCCATGGCTTGGCTGACTCACCCGGCGCACGCGTCGCGCCT TGAAGCACCGCTCGGTGGTGGGGGCAGAGTCCGCGGCTAGAGATTCGGAG ACCGCGGGACAGAGATCGCCCCAACACCGTGACTTGACGTATTTCGCTGC TCCTCTTTCTGGGCCTGAGCTTCGCCGGAACTTTCATTCACAGTGCCAGA CACCGCGGATGACGTCGTGCTTCTAAATATAAGTTCGTATTCAGTTTACG CGGTCACACATCGAAATGCTCGATGGCCATTGCCATCATCCATCGAATCC ATCCGCCTTCTGATGCTGCTTCTGCTCCAACCCGGCTGCGTGTTTGGATG TGTGTTGGGAGCGCGGCTAACGCTTTTGTTGTCTAACCATTAATTATGGC AGTTGGCACTGCCAAACACCGATCAAAATTCCCATGAGGACGCGATACAG TCGAGCATCGCTAACTTCGATTGTGTGATATTTGGTAAAGACTTTAGATT TTGGATGTTATTTCAATGCTATTTATATTTCAAATATTTTATTTCATATT TCAATATTTACTGACAGTGTGAACAAGTTTTAAAGAGCGCCCAATCTTGG GAATCACCAATGTTTTCTAAATGAGTTCAGCTACATTTGCTCAAAGGAAT CCAGCATCTACAAAAGGGGATTTCTGTTGGTTGAGGTGAAAAAGTGTGAT TAGGCTTGAGATATGGAAGATTGATGTTCAGACTCCTCTGTCTGTCTGTT CGAGAGCTGCCTGTAGATTTTTCCAAAAATTTGCATTATATATGTGTTTT TTATTTGATGGTGCGCGTGCTTGACAATAGCTGACGGATACTGCATATGA AGATTTCGTGCTCCGAGGCTCTTCTATTTTCGTTTATTTTTGGCAATTTC GCTTGTTTTGGATTTTGCCAGATCATACCTTAGGCATTTCATTCATTCTG GTGGGGCATACTAATTTATGGGTACGGTATTTATTTATTGGTTTATTCGA TTTGGGGGTGTCAAAGATTTTGACAGACGATACTTTGAATTTCAATATAT TGGCGCCAGTAGATTATGGCTCAGGTTATTTGGCGATTTAATTAAATGAA TCCGAACTTGTTTCCAAGTTAATATTTCGTGATTTTGCGTAATAGATTCG AGCTATTAAGGTTACGATTTTATTGACAAAAGGCTGGAGAATCTTTGAAA GATGACCTTTTGCCCACCAGTTCTCTTACATCTCTATAGCCTAACCCTAT TTTTCAAAACGTAACCATAAACGATATATTTTATTAACAATTATTCATTT ACTCGCAGTTGCCATGCGATTTGTTCTATGGTGAATTTTTACACATTTCT ACTATTCCTTAAACATCCCTTAACCAATCAATCTGCACAGGTATGTCTTC GTGCTCAGCTCCATGAATGTATTTCAAAAGTCCAACGCCAAGTCAAGACT CACAGCTAATTTGACAGACGACCCATTGCATGCCTATAATGAGGTCGTGC AGAATTTGATTAAGAACTGGGAGTCGCCAGTTGTCTATCTGAAAAAACGA GGTTTCCTGCCCAGAAACTACGAGGATGCGTCAAGAATCAAGCACAGCCT GGATGCCCTGATGCAACGAATAAAAAGGGCTAAACGGGATCACACAAAGG AGGTCACTTTCAATGTAAGACCCAAAGAAATGGCAAAAGCTTACCCAAGG AATCAACGTGGCTTTCAGCTATCAACGGGCACAATGCTCTCTAGTTTGGA GCAGTTGAAAGTCATCGAAGGCCAGGCAACGAAGGCCAAGACCACGGCCA AGTCAAGTGAGCAGGAGCAAGAGCTGCTGGCAATGAAGCGGCGATTGGAA GAGTTGCAGCAGGTAGCAGGTACCGGTCAGGATCAGCCAGGATACCGTAG GCAGATTAAAGTAAATCCAATAGACAAGGATCCAGGGAAGTCAGCACAAA GTTATGATGAAATATTGCAGCGAATGATTGAAAAGACGAGCCCACACTAC TCACAGCAATCCAATTCGCATTTAGAAACCCATCCAAATCAACTAGCGCC AGCTCCTCCAGGAGCAACCCAAAAACTTGATAATGTGCAGATGGCTCCCA AAGAAGACAAGCCGCTGACTTTAGAACATATCGAGTTGCATGCGTATACA GCGCAAAGTGCTCCCCGAAATTTATTGCATAAATCCGTAGTTGATCTGCC CATACTTAGAGCAGCGGAGACCCAGAGGAGCAAGACCGCAACGGAGGCAT CTAACGTGGAATCGAAGTTGCGCGCGCCCACCTATCTGAATTGGGACATG AAAAACGGTCGACTGGATCATTACTCAAGCGTGGACAAGGAGGCCTATTT GAACCAGTTGGTGAGAGTGTTCGGGCGCAATTTGGATTTCAAGGAACCCA CTCAAAAAGGAAAAGAGCCGACAGTTTCTTAGAACCGCGGTTCTCCTTCC CAAAAACATGCACTCATCTTCATAAAACGTTTTAAAATATATGAGTTCTG TTCAATGAGTCATAATCCATTTGGAATCCATGCCCGTGCACAGTAAATAC ATCTATACGTTTCCATTTCCGATTTCATGCCGATCGACAATGATGGTACG TCATATCAATGGCATCACCATGATTATTTGGATTTCTTCTGTTTACCTTG CGCAAGAAAGCAAAGAAAAGCAGGATATTTCTGTTTACCATTTGTTAGTA CTTAAGCATATTTTTGCTTTCAATGTTGATTAAACAGAGATCAATACAAA TTTTGCTAATGGGTTGACGACATGCAGTGTTCAACCGATCACTTCAGCCT TGTATGACTATATTATATTATTATGAAATAATATTTATTGCAATTCATAA ACAAGAAAGATGTTCGTTTGATATTTTCGCCACGGCACTCATAGTATTCT ATAAAGTTTCAATATTGGAATTCAGAAAAAGCCTTTTACTGTGGCATGCC ACCGCATTGTAGATTGGTCTAGAATTCAACTAGGCGCCTGACCTAAGGAA GCGCTAATACTGTATTATAGTTGTTCCATAAACGGAGTGAATATTATTAG TTGAGGTTGTCCCGCGTGGACGATGCCTTGCGCACCGCCATGGGCGATCG TCGTGGCGATCGCTGTTCCATCTGCTGCTGCTGGACGTTCACGTAGTCCA ACTCGTTTTCCGGAGAGGGTGACGAGCCGGCTCCGGAGTTTCGTCGCGAC GACGATGGTCGTACGTTGGTGTCCAGGTGTCGGAAACTGAAAGAAAAGGA TGTGGCGGACACAAATTATTCGTTAAGCTCGGTGGTTTGTCTCTTCACTG TTTGTCTTTTAAAATACTTTCCAAGTACTTTCGAACAAGACTCACCGCAA CGAGACGTTACTGCCCTTTTCCTCGTTGTTGCTGTTGAAGAGGAATGCCA GCGGCCAGGATATCCACGAGTTGTGGTCCACCGAACTCTGGGTCCGGATA ATGGGGGCACTGCCGCGGCTCACAACGGGCGAGGGCAGCTCCATTGAGAG CTTGGGAGTGCCGGCCTTGTTGATCGCCGGGTTGTAGATCTTCGGATCGC TGACCATGCGCACGAAGAATGAGCGCTTCTGGGCCAGCGTGTCCTGCTTC TTGCGGTTCATGATCTCGGACAGCTCATCGTGCTGCTCCTTCTCCAGCAA CTCGTTGGCAAAGTCCACGATGATGTCCCAGGCGTAGTCAATGTCCTCAG CGGTCGCGTTTTGGGCCACGGCGCAGAACCTGATGATGTAGCGATCGCCC ACGCTGGCCGGAACCATGTGCAGCTTGCCGGACTCGTTGATTATGCTCAG CAGCTTCTCATTCAGCTTGTCGGAACCCTTCAGCCGAAAGCAGACCAGGC CCAGCTAATGGAATCAAATACTATTTATTTTGGTTCCACAAATCTGCGGC GAATGACTAAAACCAAACTAAAAATTAAAAATCAAAACATGAAGGTATTT GAAACTTCTAAAGTAATAGCGTGATCCGAAGTCTCTATCGTGTATGCTTA TAAGCGATTGTCTCCATCGTTTATGCTTATAAGCGATTTAAATCATAAGT ATATATTTAATATTTTCAGTTATCTGGCGAAAGTTTAGCAAGATACAAAG AAATCCTAACAATGTGCTAGCTTGATTTATTTTTACTCCCGAAATATGTA ATTAGTTGGAAAACTACAACGTGACTATCTGCAGATCCGCTACCGAATCG AATCGTATCGGCCAATTGACTTGGCCACGCTTACGCTCAACGAGTTTGAA CGTTCATGTGTCAGTCGCTGACTCGATGAATCACTTGTGGCTGTCTCTAA ATGATTTTCAATAGCAATTATGCCAAAACACTTCCATTGTCGGGTCGAAA AAGAAATCCATTTTTGCGCCCGTTTCTTTGCGGAATTTGGCGTGTAGTTG CGCACGTTTGCTTAGTTTGCTTCGTTTGCAAGGCGGTGTGAACAAGTTCA CGTCTTCGTGGTCAGAGCTTGGGCTCCGGACACTTGCGTTACCCACGAAT CAATCCATTTCCCAACTATTTTTGGACCTTACATGGGCGCTCGGCCCTTG GTCCGCATAATGGACCCGCACTCCCACCCGGTTGCCCGTGGCAAATGAAA ACCCCACACATTTCGTGGGGTGTACAAAAGAGCTTTGAACTCTGAGCATG ATTAATTACCGAAATAAACCGAATCGATTGAAAATAAAACTTAAAACACA TATAGAAAACGAAACGAAAGCAAATATGTCTCACCTTGACTTGGTTACAG ATCTCGAAGCGCTTATCTTTGAGCACGAGCTCTTCGAACCGCTTGGCCAG CTTGATATGGTGACGTATATAATGCTGCAGCCCGGAAATCCCATAGGATC GCAGCACGAACCTGAAATCATACAAGTCTTTCTACAGGCAAACTCAGAGT GGAATTGGGCAAATAATATTCTTTTGGGTGGTCACAATTAGCAATAAACG TATGTTTGGCGTTGTCATATTTCGATGTGGACTCATCTCATCTGCGGGAT AGATTCGGCACACACGGAGCACCGAAACCCTTGCTTTAACAACTAATCGC AAGCAAATACACGAGGGCATAATTTGAGTAAACAAGCCAGCATACTTAAC GCCACTCCACTCCAATCCAAAAACAATTCAATTGTCGACAACAGTCAACA GACCCATTCGCACTTGGTTGGCTATCGAGGGCTTTCGGACCCCATATGGC ACATGCTACATACCACAGCTTCAGCGAACGAAAACGCCGACTGAGTGGAA CTCCCCAATGACGATAGTCGATGGCCGCATCCGAGTAGCCGTGCTTCAGG TACAGCGGATCCACCACCAGGGCTGAAGTCAGCCGGATGCGGTCCCGCAC CCACAGCGTCGAGCAATCGAAGTTCGTCAGCAGCCATTTGTTGGGATTGG TGTTGAACGAGTCGGCGTACTCGATGCCCTGTGAATGAAATCCAGTCAGA TTGGCCATGCGTGCCGTGGGAATACCACTCACCTTCAGGAGCGGCTTCAG CTCGGGGCAGATGAAGCTGTTGCCCGCGTAGGCGGCATCCACGTGCAGCC AAACGCCCGGGAATCGCTGCAACTGCTTGCCGATCTCTGGCAGATTGTCG AACGCACACGAGCCCGTGGTACCCAGAGTGGTGGAGACGAAGAAGGGCAC CAGACCCTGCAGTTCGTCCTCCTCCATTGCCTCGTAGATCGTCTGGCCGC GCAGACTGGCGTCGTCGTCGGGCTCCAGAATGCGCAGCTTCACGAAACAG ATCATCGCCGCTTTCTCCACGCAGCTGTGCGCCTCCTTGGAGCAGTAGGC CATAAGCTTGGACAGCAGGTGACCCTCCTCCACAAACGGGTGCTGGGCCT TGAGCCTCTTGAGCGCCTGTGCCCTGGCAGCAAGCATCGTGACCAGTACG CACTCCGATGCGGAAGTCTGGTGGCCAAAATGAGCCATTGTTAGACACGG ACGAGTTAATCATGTTATATTATATGTAGATATTTAAAAACTACAAACTA AGTCGGCCTTCTTCACTCTTATAATCTATGTACCGGACCAAAGAAAGTTC CGTCGTCCTATAAAAGATTTATGTTACCTGGATGACTCCCCCTCCGGTGC TGCCCTCCTTGAGGGCCAGAAAGTGGTCCGGCAGACCGATGGCCTTGCCA AGCCAGTCGAGCACTATGGTCTCCAGCTCGGTGCACGCGGGACTGGCGGC CCAGGAGAAGCCGATGCACCCGATCCCGTCGCCCAACATGTCGCCCAGGA TAGAGGGGAACGAGTTGCCCGCCGGAAAATAGGCGTGGAAGCGAGGATGC TGCCAATGCGTCACGCCGGGCATGATCTTGTCCTCCACGTCCCTCATGAT CTGGTCCCAGTCCTCCGGCTCCTGCGGTGCCTCAGCTGTTCGAGAGGGGT GGTGAGGGAGAAACTGACCAGGTTCTGCGGTCATTTTTGTGGCTTACGTG GCAACAGGTGTCTCAAATATCCCGGCTCCACGCTGGGCGTGACCCGTCGC TCGTTCAGCGTTTCCAGATAGTTGCAGATGTACTCCACCATTTCCATGCC ACGTTTTCGAAATTCGGTGCTGTCCATTTTCGGTAGGTTTTCCAAATCGC CTTTCTGAGTGTTTTCCTATTTTTCCGTTTTCTTTTACTCCCACGGTGAG CTTTATTATGAAAAGTTTAAAAATTGTACAATGAATCAGCGTAGTGGGGC AGTACGTGCAATTATATTCAATTTTTATTGAATGAACAAATTTTCCAAAA TTTGGGGAGTCGGTTATTTCCAGATTTCCGGATATTATTCGTATTATTTT GTGTATTTATATAAAAATGTTTTTTTTTATTCTTGGACAAAGTTTTAAAA GAAAATTAGAGCAAAACAGGAAACTAGCTAAATAAATAGTTTTGAAAAAA CTGTTTTTTACCAAGCTAGAACATTTTATAATTAGGAACAACGAAACTAT TATTTTCAATTAACTTGCCGACTGTTCCTACTATATAAATAATAATAATT GTCGTCTGATTTTAGGCAAATTAAAATTGAAATAATATATTACCCCACAA AAGTGGCGTGTACCGATAAGGGATCAAAAGCATCGAAGGTACATTTTTCT TTAATTTTTATCTCTAATTATTCCTATGGTAGTTACGAGTATATAATATA TACGTTCTGACTTTTTTGTATAAAAAAAAAGTTTTACATTTTGCAAGCAT TTTGGTTAGAAAAAAACATGTTTGTCCGCTCATTGATAAAGTTTAAATTA ATATCCTTAAGTTCTGTCAAAAAAAAAAGTATTAAGCGACTACGCGAATA CGAATTTTATAACTGAAGCTGTTTTTGCTTGTATCATATTTGTATTATTG TTAAATTAACCATCTGAATAAAAAAGGTGATGTCCACACAGTTAATATAA CATCTTAAGATAACACATTTGTTATTAAATTTGTTATTAAAGTTGTGTTT CCTTGATCCTTGAATTGGTTTTCCTTTTCTCGAGTAGACCGAGTAATTTT TTAAAACAGAAACTGGAGTAACAAGAATGATTTTAAAAATTTTGAGAACA AAGAAAATCTTTTCCCAGGCAGGTTTTCGTATAGAGTCCACTTTCTTCAA AAATTCATTACAATTTGTTGGCAAACAAGAATTTATTCCGTTTTCATTGC TATGTTATTTATAGGATCTGATTTATTTCGGCTGGAGCTTTATTTGTGGC TTTTTTGAAACCGCTGATTCAATTCTGATTTGTAAACTTTACTATAAATT GGCGCTATTTTAGATTTATTTTTCTCGATATAGTGCGTTGTTCCCTAATT TTGCTTGCTTTAATCACATGTATTTAGCATAAACATCAATTTTGTTTGTA ATTAAACTGCGGTTCCTCAGGCACGTTTTACGGCTTTGTAAAGTATACAA TTCCCGCATGGTTTGACCATTATCCATTATCGAATCGACTTCCGGATCCG GGGCACTTACTTGTGCTGAGCAAATTCCGATGGGCGAATGGGAATTTTGT TTCGAACTCGAGACCACGAACCGTTGGCCCCGACTGGCAAAACCAAACTG ATCCTTGCTCTGCGGTCTGGCCAAAAGCTAAGCTCGGTCGTAGCTGCCGT GGCTGCTGCTTCTCCTTCGGCTGCCCTGGCATGTCTAATGAATGCATACT TCAGTGGGCCGGACCAGGGATGAGGGCTGAGGGTGCTGGTGGTGCTGGTT GGTGCGATTGAAATGGCAAATAAATGGAATTCTTGCGACGCTTCATTCAT AGCTGTGAGCTGTGGGAGTGGGGCTCGAAATTCGCCTGCGTTGTGCGTGA AGATATGCAGGGAATAGAATGGGCGAGCTAGAAATTAAATAACCACCGTT GCCCATGTGAGTGGTTGCACGGTGCGTATGCTTGATGCTGCGTTTAGCTG TGGAAAATTGAGTTTCGAATTGTTAAATGATTAGCAAACCTAATTTGCTC TTAAAGTGCAACTCAATTTCGCCATGGATGAGTTAATTAAAAGAACGTGT TGTCATAAACACACAACAAATTACACTGACAGGACAGCTTCCCACGTCCC GACTTCCCACTTGTTCTTGGCCGGGGTGCGAATCGTTTTATTAATAACTT CCGCGCCAAATTGAATTATTGTTCGGAACGTACTTGATGGGGATGGTGGC GATGCCAAATGATTATGACGATGGAAATGACGACAACGATGGCCCAGGCG GAGCAGAGAGGCGCAGGCAGGAGCGGAGTCGAAGGAATTTCAACGCATTC CTCTCGGAAAATTCCAGCCCGTTTTCCTTTCCCAACCCGGGCTCCTTGGA TCCGGCTGCACTGGGCCATAGAATTGTCTGGGACACGTGGCCCCATGTAC TTGCCATCATCATCCCGCACAGCCATACGAATCCTGTTCGTTTTTTTGTC GTTGTTGGATGAAAGTTCATTAATAAACTTTCATTGCTGCTGTCGAATTC AGCTGCAGCAACCATCTCCGGGCACTGAAATGTTGTTCGGCCTTAGCTTC AACAAGTGGCATCATGCTCCTGTGGTTATCATCCCCCGGTGACCTCCTTT CCCTTTGGCCACATCGCCATCCCCATCCCCATCCCAGAAGGGCTTTATTT AATGGGAAAACGCTGCGAAAACGCTCATGCATCCGCGCTCATTTAATTGC TGCAGAAATGGTTTTTTATTGACTTTTACTTGAACTCCTCCTCAAAATGA ATTATATCAATGTGCAGAGCATCATGGTTTTGTCCCTGGGTTTGCCTTAC TTCTGGGGAAAACTGATGTTTTTCGTTTCAATTATTCTCCTGATTACTAA TTTCGGAAAATAAGTTTTCTTCAATCAAGTTTTTCAACCATATACGAACC ATCTGCATTTGAAACAAATATGCGATATTGTTTTGTAAATTTAAAATTTT TCATGTTAGAACAGTCCTAAAATAAAGTGTTTAAGCTTAAATTCCTAATT GAACCCTTATCGTTTTCAAAGATTTTCAAAACTTTTTTCGAGCAACATGA CGTACGTGTAGGGTGTAGGTGAATTGCAGAATGGTTCTTCCGTTCTGTCC CTGCTCTCTCGGCTCATAAACCAAGCAATTATTCAATTTCCACGGACTGC GATGGTCGCAATAGCTGCTTCGGACAGTTTACGACGAGTGGTTGGTTGTT AAGTTGGTTCTCGAGATTCTGGACCTCCGGGCTCTTTTTTCCGCCATTAT AGGTTCAAGGTTGTTGCTGAAGCGCTTCGTCGAGATTATATTTCTGAAAG AGTGAAACAATCTTGTTTGCAGATTTTACGGAAGGCCTCAAAATGATGCA CTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGC CATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCAT GTGAGTAGCACTAACAATGTTTCAAATCCTTGCCTGAAAGCATCCATTTT GCGAAGGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCA GGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCG GCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGC CACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAA TAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGA GGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACAC GCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGAT ACTATAGATGGGTAAGCTAGAACGGAATATCAAATGCATCAGTAGCGTTA AAGTATATTCCGATTAGCTTACAAAAGCCAAATACGTCCACTGATTTTTG GGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCC ATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAAC AAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACC TGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGC GGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAA AGCCCAATTTATCACAAAAGACCAGCGGTATTAACGCAATTGCGGGCAAT AAAAGATTAGCTCTCCGAAGATAAGCGCGGTCTTTGTATAATTCTTCTTT ATAGAACTCTTATAGAACTCTTCTCAAACTTACAGTAGATGCTCTTTAAT TCGAATGTGAAGTAATCTAAATTAGAAAGTTTAATAAGCAATTATAAAGT ACAAGTAGAAGAAGAGAAATGTAAATATATATCGGTAATTTCGTTAATTT ATTTTTGCAAAGATTTCGTTATAGCTTAGTATGTCAATGGCCCCAAGTTG TTTAAAAAGGAATGAAGCGAATATGCTGCCTTATGCTAAGATAATATTAT ACAGTTTCTATACCTAGGACAATAAACAATACTTTGTGGGTTCCCTTATC AGTTGAAATTCGAAATCGGTGAGTTGGTGTTAGTTGTTTGTCAAATACAA ATTCAATACCCAGAAATTAAAATATAGCTGATAATGTGTGCTAAAGCATC TATTAAATGTGGACAGTAAGTACCAATGCAGAACAAACCGTTTATTTGAT ATTTTAGGTCAGAAAAATTAGATTGTTCTTATTCACAGCGATTGAACCAA ATTTTAATTATTTATCAAGAACTACAAAATAAAAATTGTGTCGAATGTGA TGTTTAAATCCTTTACTCATGGGATATGATTGAAAAAGGATGTTTCCAGC CCAAATTAGCAGATCAGTCCGCCGAAGGAACTTTTACTGTAATTCCGCAT TCATTGCTGTGCACACAAAGCACTTAGGAAAAGCTGCACAAATCTAATCT GGCGGATTTCAATGGCGTTATCATCCCACGAATGTGCAGGTGCCGGTGCT GGTTAGTGTGAAAAATGCTGGGCCTGCGACGAGTTCTGCGATTGGGTGCA CTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCC CGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCT CCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAAT GTGCTGGTGGTGGAGCGCGATGCTGGTGTAAGTACAAGGTGGCCTAAAAT ACGACACAGAGTTATTCAAAAAGTATCAACAATATCTTACAATTTTTGTA GGAACACCTTCAATTTTAAGGTATAGGGATCCAAAATTTACCCCAATAAT GTTTGAACCTTTGGTTTCAAAACGGTTAAAAATAATTATGTAGTTGCTTT GCTCTGATCATATATCCAATATCCAATATCTACCAATTTAATACTTTTCC TATTGTATTAAAAATTATTATTTATTCGGTATCTAACTGAAACTTATTCG CTATTGAATAACAACAATTTTTATACAATTTTCCAGTACACCAGCGCATC TACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGA ACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAG CATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCT TGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGA ACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAG CGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGAT TGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGA AGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGT TTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGG AGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGG GAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAA GCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCG ATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGTCCTGGGCTAGCCA CACCTCTGACCGTTGATCCCGATGGCACCTACTTCAGGCGGGACGGTCTT TGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAGACGAGGAGCCGGA GTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAAACGGATGTCTGGC CCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGTGAAGATACAGAGC AGCTGGGCGGGCTTCTATGACCACAACACATTTGACGCAAACGGCGTCAT CGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCCGCAGGCTTCAGTG GGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGCCATTTCCGAACTA ATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGCGCCTCGGCTTCGA ACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAATATCGTTTGACAAA TTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTTTATGTATGTACTT CTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTT CACGTTTTAGTCACGTACAGCTGTGTTGGTGTTTTGGCTGCCAGTAGTCA AGGGAATTTAGTTTAGTTTACGGGGATTTGACGTGGAATCAGCCACGAGA AGGTCGTGTGCCTACATATAATTTATTAAAATAAGGAGTTAAACATAATC GTAATATAACTTGCGAAATAATTGCTGACTTAGGATCAGATGGGGCGAGC GGGTTTGAGGGGGTCTGCCCTTGTTACTTAGTTATCGTTATGTAGCTCTA TGTGTATCTGACATCTAAACTACATACAAGATCTGCATTAGAGTCGGGTC CGCGTGGAATCGTTTCCCTGTCAGGGTGAGCCAACCCAACTTGCAAGCTA TTGGTAAATATAAATAGATGTATGTTGAATGAGTGTTTCATGCGAGTCTG ACTAATCTGGGCGGGCTCCTAAGCCTCGCTTTCGCCAGGGGCCGCGTTTT CACCCACGTTGATGGGCACGATCAGATTCTCCTTCGACATCAGATTATAT TTTGTGACGAAATGCGTGAAACGGTGGCACAGATACGTCTCGGCCTCGAA TTCGTCGAAAATGCGACGATGGTGAAAGTAGGCGTGCGAGAAGATGCGAT ACACCCGCCGACATACGGAGCCCAGCTTGGTTACCGACGACTCCTTGATG GACACCCTGGGAGAGACACTTTGCTTATTATGTGGCTAGTTCAACCATGT CGCTAAGCCTGCATACCTGCTAGGGAAGTACTTGTTGCTGTTTAGCAGAC AGGCGGCACCGTCCAGCGTGTGGCGTGTGTAGTCAATGGCCGGACATTCC TTGGGCGTCTTGTGCGCGGCGCACAGGAATATCCACTGGTCAGTGGCTGT CATCTGGGTGCACGTCGACGGCGAGCACTCCTTCTGCAGCCGCACTGCCA GGCCGTTCAGCTCCATGCAGAACTGGCGCAGGTGCTCGTACTTCCACACG CCCTCATCCTGGGCTTCGGGCATGGTCAGTATGAGTTCCACGTTGCTCGG GTCGCGCTTAATCAGCTGCTGTATGTACTGCTGCACCGCCAGCGTGCTGT CCATCTCCTCCAGGGGCTCGTCGGGCCAGCGACAGAAGTCCTGAAAGGCG AAACGGAAAACGGGTCAGACGGGCCGGGCCGGGATCGTTGTTCGGACGCC ATGTCATCGCTCACCTTGGATTTTGTGCCTGGCCGGTTCCTACGCAATAT GGTCGAGCCGTCAGCCATCTTCATGTTTCACCCGCTCGAAGACGCGATGA TCCACAACGTCTGTGCCTACGCCTTGATGAGAAAATCACTGGCAGAAACT GAATGCTAGCCTGGTCCCTGCCCCGCGGGAGTCTCCGGATGTGGGATCCC TGCACCGTAGTATGCTGAGTGTATTCTACAGGAGCTGGCACATCGCTTGA CAATTAATTGGCGTTTATCCTCCAAAACACTTTGCTTTGTGCGAGAAAAT TTCTGACAAATTCTACATACATACATATACCTATCGATTGGCCAGCGGCA GTGCGCATCGTTATCGATAGGGCGATTGCAGCCTTGCGGTATTTCGGTAT TTCCGCCAGCCCTGGCCACAAAGTGGCCACACTGTCGCTAGCCAGTCATC ATAAATACGAACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGG CATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAG CTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGAC ACAGGTGAGTGCAAGCTGCGACTTCCTTTGAAACGGAATGGCCAGTGAAA AGTTGGCCATTGTCAGGGAAACAATCTGTAATTGCAAACAACACAACAAA ACAAAGGGCATCGCAGGCGTAGGGGTCGTACCCGAAAATCAAAAAATGGG GGTTTCAGGTGGTCTCAAGTGAAAAATTGATACCGTGAGATCAAAATTGC GTCGGCAGGAAAATATTCCTGGAGTCGGTGGGCCGAAGGAAAAATCAATA ATACCATAACAACGCATACAGGCGTTTGCTGCTCTCAGAGTTAGTGGTGC GCGGGGAGCAGCCCACACATAAACCCTGCTGCTGACTCACCCAACCACCC CCAGTAATTGAGGGATTCCGCCCCAAAGAGCCACGGGCTTATCAGCACTC TGCTTTTCGGGATGTCCAACAGCTGTTGGCATTTTCCAGCCTGTCCCACC TTTTCCCCGCTCGCCCACTAACCCTTTTCCGTTTCCGCAGGCGTGGGCAA GTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACG ACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGC AAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAG GTACCCACTTCTGTTCATTTAGTGTTAATACTTAAGAAGGGATAAGTGAA AGCTCAGATTACTTCCAAAATTGAACTGAATAAATTTTTGCAAATTTCGT ATCCAAAACCCCAAGTCCAAGGCGGATAATAATTCGGCTCGTTTTTTATA TTAAATAAAATAATTTGAATAAAATTCTTACTTAATGATCCAAAATAATA ATAATATATATATATAGAGCCTTTAGTAAAAAGGCTTAATAATTTGTATT CAAAAAATTTTATTTGCTTCATTTCGGCACATTGTTGATAGATGTTTATT TAAAAAAGTTTTAATTCTATCATTTTTAATTTTTTGTGATATAAATTTTT TATACTTTACTTAAAATTAAATAGAAGTCGTCAGACAGAAATTTAATGGG TTACTAATAATTAAATAATATAAGCACTGTCATTTATATAACTGTATTGT GACGCAAAATATTTCTTGAATAGATCTATCACACGCTCTTATTACCGCGG AGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCA ACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAAC ATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGA GGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCT TCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATA AATACGGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACAT CAACAATGAGGTAAGAAGGATACATTTAACTTAGAAACTTCTTGCCACTA CATTATTATCTCGTTACTAGGCAAACGGCATTAAGATCGGCCAACAGCAC TCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGC AAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCT GGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATA GAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTA ACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAA TGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTC AGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAA ATAAACCAAAACAAACCACATTTGTGTACGTGAATGTCGTGCGTGATTTC TAAATTTTATAAAGTTTATTGAAACATTTTTAAATGTTTTATGCATGTAT TTTGTGTATATTGAAGTTAGTTTGCTAGTTACTTCGTGTAAAATCGATAG TTATACATTGGGATTTTGACAAAATGATGTGTAATATATGAACAAAAATC AAACTGTGTGAATTTTCATTGTGATTCGATTTCAGTGAGGTCCAGCTTCG CAACGCTGCGCCACGCCCCCTTTTGCAATGGGTATCTGCTCCGCTTCTCT ATACACACATACATAATTAAATATATTAATATGTTTACGTTTCCTTCTCA ACGCATTTGCTTTGTCTATTTTGTTGTGCAATCCGCTTAGTCTTTATACA TACACTAGAAAAAAAGTACTTTAACAAAATATACAAAACGTGAGGGCCGA AATGGGGTTATATAATTTACACAATCAACATGCATTAACCAGTGGTAACA CGAAATGCTGCGATTCAATGATCAATTTAGTATTTTACGAAGTTTATATA TTTAATTAACGGCGATTGCTAAGACAAAACGAAAGATACAACTGTAAACG TAAATCAAATTATTTATAATATTTGTATTTGCCCAACACAATGCGGAATA ATAAATATACATACTTACTATTAATATAATTATATAAATTAAATCGGTAC TTACCTTGGGTTCATTAGCGTTTAATCAAGTGATAGTTAACGACTAATTA GTTTTTTGGTGTCTAGATGAGAAGTAAAACACTAAGGCAAATTTAATGAG GCATTTAAAGTTGTAAACAACTCAACTTTTAAATGAAAAGAGGTCAGACA AATAATTACGCATTAGTGTAGTTTTAACCCTTTTTATTTAGTAAGAGGCT TTCGGTAGATAATTGTTGAATTAATGTCTTGTAAATATTATTAAATGGTG AATCCTTTTTTGTTTATGTACATATTTCCTAAAGTGTTCGGAATTAACAA TTTCCACTTTCTATGTCGGCTATAGGGATATAGTGTCGCATTTACTTAAT TTTTTTAAATGTGCTTACATGTTAAAACATTTTTTTACTACTGAAATATA CTATTTAGAAATATTTTTGTATTTTTTTTTAATAATACTTGAACTTTTAA GATATTACATAGGTTTGTTTCTTATTTTCTGAATCTTATCTGTGTTTTGT CTAAGAAAAAGTTTGCCAAACTGCAAAAACAAGTTTTTCGCTTCAACATT AACTATTTTTTATACCCTAATTTGCTCAGTTGGTTTTTTTTAATTGGAAA CTATTCGGATCCGTGACGTTTGATGTACAAACAAATGCTCCAAAGATTTT ATTGTGAGTTTTAGATTGATTGAAAATGGTCACTTGTTATTGCATACGTT ACATAGATTGTTGTTTATTGTATTCCCTTTAATTAATATTCGTACGAAAT GTAAGGCAATTAAAACTATTTTTCTAAATTTTGTAAAGAAGACAATTGAG GGACCCGTTTGCACCTGGCAGTGATGCACTGCATTGATATTGATTGAAAT TGAACAGTTTGTCTAGACAAAGATGCGGTTAGTAATTGCCCTAGTGCGGT AAGTATATGTTAGGTGTATATTGATACTTAGCTACGATTAGTCAAGTCAA GTATAGTCTTACAGGCTAGAGCTTAGGAATAGGCTTAGTTTCAGTTACAA TTCTGCTCTGATTTTATGGCTGCAACACCATTTGACATAAGAAACTCGTT AACATTTAATGCTAGTCCATTATTATGCTACAGTTCGGATTTGTAGTACC TCCAGTTGCCTTCTACTTGCGGCGTTCAACAGTGCAATGTAAGTAACCTA GTGTAAAAGTTGAGCTTTTTTAGTCTCTAAGACATCACTATCACTCTCCT TAGGTGCTTTCTTTTCACAGAACTCGATCAGATACGAACAGACACCAGAG AGTGCGATAAATATTCCAGCATAATAGAAGGTGTCATCCCATCTGAAAGA GGACAACGGGTGGTCAGATAACCTGTGCACAGACTGTAGAATGCCGCCCA ACTCACCTGCCCGTATACTCGTATATGACGCCTGCAATAGGGGGTCCTGC GATCATTCCAACTCCCTGAACCAGCAGCACCAGACCGTAGGCACACGTGA AATCGTCCAGATCCACAATACTGACCAGAATGCTGGGCGTAAACGAGAAG GAGCTGGCGAACGTAAATCCGAAAATAACGCACATGACCATCAGGCCCAT GTAGTTGGTAATCAGCAGGGGCATGAAGAACACAGACGCTCCGCACACTG AAAAATATAATAAATAATAAATTCAATTGATAAATTGAAAATGTGACATA GTCCAAGCACTCACCCAGCATGCACAGCGAGTAGCATATATTGATGTTCA TCCAGGACAGATCCCCCAGATAGCCAAGTCCTATCATGCCCACCGTTTGG GCAATGCCGACATCCGAAATCAACTCGGCACTCTGGCTCACGTCGTACTT GTATTGCTTCATGTAATCGGGAAGGTACAGATAGGGGATAATGAACCTGT GGAGCGTGCCAAAAAGTAGATTAGCCGCTGATTGAGCAGAGGAGCCTTAT CTGGTCAATGTTGAGGAGTTAGCATTGATTTCAACTAGTTTTCTTATCGA TCTATTAGGGCACTCGGACTCCGCAGTCGTGGGGTAAGATAAACCATGAT CTTGAACAGCTAAGGGGGCCTACTAACTGAGCTGATCGATAACGTTGTGC TTGGAATTTCACCGCTGTTGGCCAACAATATTGTTGTGCAACGCTTTTCG TTTTCGAACAGCTGCCAAAATTGTTTGCGACGTCTTCTGGCAAAATAAAC AAATTCACGCGACGGCTTGGCACATTTGTCTATTAATTTTAGCATTTATT GCGCCTTGAGTTCATGCACAGCTTGGGGCCTTTGCCAATGAAATTGTTTT TTTTTTTTTTTTATTAATATCACCAAAGAGTACTCACCAAATGAACAAAA ACAATGTAGAGAGATTGAAGAGGGCGAACTTCATGTCCAGAAAGAGTGAA AAGTCAAAGATGGACTTCATGGTGTCCACAAAGTTGTCATACCAGGTCTA TCGAAAGAGAAAGGATATTTAATTATTATTGTTCCATTAAATCTAAGCAA CACTGAGGATACGATTATTTTTGATTTTGATTGTTTACCACTGCTTTTAT CTCTACTTGAAAATTAATTAATACAAAATGTACTTTTAAAACGATTTAAA GGACTATCGCAAAAATCGAGTAAGTGTGTTTAGTCAAGACATTCATTACA AAATAATAATAGTTGTGAGTTGTTAACTAAACTATCAAGAGATTATCATC TTTCAAGGTACCAATAACTGGCTCGGTTTCTTGCGTAGGCAGAACGGAAA TCGGAGCGGTCACCTTATCAGCCCTAAAAAGTATGTATATGTGGTCCAAC TAGGCGACCAAACAGAGAGGCAGCTGATAAACAGCTTTGAGCATTAACCA GCTGGGGCTGTCGCCAAGCGACCGGCTGATAAGGGCGGACCAAGGGTCAC GGTCTACTCACATCTTCCTCCTCTTTGGCGATGGTGGTCATCGAGTTGCG GTAGATGTTGGGACAGGAGGAGGCGCGCAGCCGGTAGCGGTGCGTGTTCA GCATGGCCCCGCGGTAGTGGATCGAGTTGCGGTGAATGCGCATATCCTTA AGGAAGTTGGAGTTCCGGATCGAGATGTTGCGGCGGAGGTTCGATCGGTG GTGGCTGGGCTTCTTGGAGCGCGACAGCCGGCGGATTCCCGTGATGCTGT CCAGGCGTGCGCGACGGGTGGCCAGCTCGCTGTTCACCGACTGCTCCTGT TCCGGAATGGCGATGACGGTGGGCCTGATGCGCCTGCTCGGCTCCAGCAA TGCGAAGGTCTCGTCCTTCGAGTAGTAGCAGTGCATGTCCTCGCTCAAGA TGTCCACCGAATTGTGTCGCAGGCCATTCACCTTTAGGTTGGAGATTGAT GGTGTTGTATGCTTGGCCATGAAGATGTTTTCGTTAAGCGAGTACCGGGA GCTGGCGTGCTTCTGCGTAAGGTAGCCTTCGTCCGAGGAGCGGAGCGAGC CATTGGGAGTCCTACCAGTGGAGCGCTTTTCCGATGGAGACAGCGTCTCG ATGGAGGCCAGATAGGCCTTCTTTGCTTCCTCTGCCGCCTCGTGAGCTAT TCCGCCCATTAGGGTATCATCTGGCGAGCCTATAACGGCCGTCGATGGGG GATAGGCACCTGCTCCTGAGGACATGGACAGCAGGTTCTCTCGTGACGGC GCCTCCTCACCCTCCTTGTGGCGTAGGGAGCGTCGGCTCAGGCTCTTAAC CTCGCAGATGCTGTCAAGCTCCTGAGTGCTCAGGAAGGTGGGCAGGAAGA TCTCGCTGCGGTAGCGCTTGAGAGCGGAGTCCAACGGATCGTCAATCTGC TGGTTGGCCTCCGTGTTGTTCTTGGTCACCAACGAGTCTAGCACAGCCTC CTTTGTGATGCCGGTGTCCAGCAGCTTTTTTATTTCCTCCAGGCAGACAC TGGAGTTCGAGAAGGTGGTGACGCTTTGGGATCGACTCTCTAGACGGTTT TCCTCGATCAGCCAGTCGGGATCGCGCATGAGGGCGCCGCAAACGCATGC GTTGAGCATGGTGCCGCCAAGGATTAGAGTGGCTCCGCGCCAGCCGTACG ATTCGATTAGATAGGAAGTAAGGCGGGCGTAGACAAAGGTCCCGATGCCG GTGCCCGATGCTCCGATGCCGGTCGCAAAGGTGCGCTTCTTGTCAAACCA GAATGCAATGGACACCACCGCGGTCACATACCCGATGCCTAGGCCCAGTC CCGAAATGATACCAAAGGTCACCATGAGCATCTCGATCGAGTTGCAAAAC GAAGACAGAGCAAACCCAAAGGCAGAGACCACTCCGCCGAGGATGGTCAT CTTTCGGCAGCCGTACTTGTCCACCAGATTGGACCAGATGGGTCCCATCA ACAGGGGCACGGAGAAGAATAGCGAGGATATCCAGGCGGTCTTCGAAGTG GACTCTCCGAAGTATTCCAGCAGTTCCACGTTTATTAGGCCAAATGAGAA GCTCAGTCCGTCGGCTATAAGGGACACGACCAGAGAGGCGAACACCACCA CCCACCCATATCCACCGTCGGGCATCTTGGGCGTTTTCTTCTCCGTGGAA CTGGAGTCGATCGAGTCGCCGGACTCGTTCGAGATCAGGCGTTTGCGACG CTTCACCTGCCCATTTCCGTTCATCAGGCACGTCATGGTGCCGTCCTCCA GTTCGATGACACTGCTCCTTACCACACGGCTGTGTCCAGCCCCATCTGCG AGCTCCTCTACGGAGAGGTTGCAGAAGGTGACCTCCGGGAAGAGGTCGTG CTTGATGGCCTTGTGGAGTGGCGTGTTGGCCGGAGCAGGCGTAAGAGGCA GGGCCTGGTAATTGGAGGCGCCTCCGTTTTGGCTCTGGTTCTGGCCATTG TGGTTGTTGTTAACCGCCTCGCAGCTGTTGTTGTTGGAGGCGTTTGGATC CGTCGCTAGCTTGGCCATGTCGGAGTCCCAGTGATCGTGTTGTTGTGTAA AGGGTTCAGCTACGTCTATAAAAAGGTTTGTAAAATTTGCACTTTCTTGT CCAAGCGATTATTGGAAGTGAACACAATTTGCATTAGATTTCAGCATAAA TTTTCTTAAGTAGGCGGTAGGTAAATATTCCCTCTCTCTGTTGGTCAACT GCAGTGCGTAGCTGAAATATAGAGACAGATGGAAGGAACTTAGCGCTTGA TCGACTTTGTAACTTCCCATTTCCCCTTCTAAACTGCAGTCTGCCGCTGA TGAAACGATCAAAATGAAATGATCAAACCCTTTTCCAGTTAATAATCTTA CTAACATGGCGCTTTAAGTTCGCTTCTTAATACCTCGAATATTTACGTAT CTATATGACCAATTGCGCGACTACAACAACATCTGCCTGAAACCATTTCG TTGAAAAATCCGCGCAGAAACTGTTTGCTCATTTGGCAATTCGTTTATTT GGCTTTCGAGGCGCCTTCAACTTGACCTCAGGAAAACAGAAAGCGGACAA TTTTCAGATTTTCAGCGAGCATTTTGAGAGAACCGAAACGAGAGAGAATG ATTTTCTTCTTACATCAGTACCAAAACAAAGTGCGTCACATGAACGCGAC GTCAGCTGATGTCCCCCAATAATTATGGTATTCGAAAATGAATATTTTCA GACCAATTCTGTTTTCGTTCCCCTGAAACGGACGTCTGCGGTTAATTATA GATGGCTACACAGGCGGAATAGGGAAAAAACATCAACGATCGGACACTAG TCACTAGTTCAAATCTAAGTAGGTTTTATCCTTCTGAGGTTTCCAGTTGC CCCACTTACCCGATCGTAGTCCAGGCAATGCTCTCTCCGCACGCCAACAG CCAACTTTTGTTAACGAATAAATTGATTCGGTGATCTGCGGATTTTGCGG ATATATTCTTAAGATTTCACTGGCACTAGTTTCACTGTTTCGGCACCACC GCCAATCAATTCACCATAATTGCACAGATCTTCAGTTATGTTTAGCTCGC TCAGGGTGCGATTCGAGTGTTTATTCAGGGTGGCGGTTTTGTTGAAAATT CTTAGGCGCGGATCGCGGGGTATGTAATGCAGGAACACCTTGTTCGACTT GCCGCTGTTGTTGTAAGTACGGGGATTGTTGTTCTGGCCCTTGTCGAACG ACTTGGCGTTGGTGGTCGCGCCCGACGCGGATGCTGCAGATGTTGGTTTG CCTGCACGATAGAATGACTTGGACCGAAGGTCGTTCATTAAGAACGTTAG GGGGTTTATCACAGGCCAACGGAGAATATATTGAGCGATAATTGACGGCA ACTGGCGGCAGTTGCTGGTGATGTTGCTGTTGTTGCTGTTGCAGTTGCAG ATGCAGTTGTTGCAGTTTGTGCTGCCGGCTAGCAGATTTTGCCCTGGCAG CCACATGCGGTACTTTGTTTTCGCGGAAATCAAACACTTTTCGATTCGAT GCCAACGATGCCAACTAGCGTGCCCGGCTAGCTCGAACAAGAAATAACAA ACACAAATCGAACACAAGACTGGGCCTCACTGGCTTCTCCGGCTACTCTG CCGCTCCCCGTGTCAAGTGCGCGGCGCGTGGTGCGGAGGCGGATTCGCAG GCATTGTATATATGTATATCTTAGTATCGACGGAGGGACGACCAACGCGG CGTATGATTAATTCGTCTCTGGTGGTGCAACTCAATCGCTGCTGTCGCTG TGCTCGCCTCCTCGCTGGCGCCAGATAATGATTTATGATCCTCGTCCTCA ATTAGCAGCCTTCAGTGCAAACGCTGCAAGAGGGACAGAGGTTAGTTTTG ATTCATCTGATAAATGACTTAAATGCGAGCTTAAACCTATAAATATGTAT GTTCAATGCGCCCGGATTTCTCTGCTCTGCTAAAGTCCCACAAAAGGCGA GAGATTCACGGTGCTCTCATCTTATGTTTAAGTGCTCGATTGACTAACAA TACGAGCCTGGTATGGAATCGAGATAGTGTGTTTTCAAGGGGAATTACGT TACCGGGAACAGAATTCCTCAAAGATGTGAGGGGAGTTGAAAGGCATGTG CGACATCACATCGTATTGCCGCAATCAATTATTGTAGGTCAAATTTTAAT AGAAATTTATATATGTTTTATTTATAATCATAGGGAATTTAAACAAACCG TATGAATGAGTTATTATCAACAATAAAGCCTACAAACATACGATTTTATG TATGTTGCTATGGTAAAAGGCCAACAAAAGTCAATTTATAGTTCGATTTG AGAAATATAAAGTCTGCATAATTTGATTTACTTCATACGGATATATTTTT GTCTTTGGCAAATTTTAAATGGAAATTAGGCAGTATTATTCAATGTCAGT CGTTCGTATTTGAAAATAAGAAAACACGTTTAGCTCCGTAATGTTTTATT TCTGCACAAGCGAGTGTTATTGTTTATTTTATCTAGTGAATAAAGCTAAT TATTATTAGATTGCAGATAGTTGAGTGCTAGATTGCGGTGTTTTTGTACC AGCAAATTAGTCGAACATAAATGCTATCGGAATTTATAAAAAAATTAAAA TATTAACAAATTTTTTTTGTATACAATCTTCAAATTGTCTATCTGACTCA GTTATTAGAACTCAACTGAGATGAAAGACCAATATCGAAAGCCAAAATTT CCATGAAAGTGTAGGATGTTGATAAGATTTAAGCTGCACTCCCATAACAA TTAGAATTTGAAATTCTTGAATGAATCTTCTTGTGTACAGAGATATCTGT ATGTTAAACAACTGATCGTGGCTTTTTAAGTTCAACGTTCGATAGGCGAA ATGAACAGAAAACCCAAGTAAACAGGGAGCAACGTGCTTTATTTGCCCAG ATTTCCAGTTCTAAAACGCGATTGTCTGGCCAGCGACTGCGACTTTGGGT AGACAACGAAATTGTCCCTTATCGGAAATCAAATTCGGATCACGATTACT GTGAGTACATAGATCATCATAGTTGGATTGTGAGCGTGAGGGGCGGGCGA TAGCGATTCCCAGGCGAAAAGTGCCTGCCTATCTTTACAATATAATTGGC AGAAAATGGTTTTATTCGTTGCGATGCGATAAGCTAATGTCTAGCCCTCG AATAGGCAGATTGCAAAAATTTGAAGTTACAAAGTCGCAAACGAAAATTC AAAATGATAAATTAGGCTAACTACTTTACATGAACCTATTTTGGCCTGAT AAAGCCCACTTGGCATTACGTTTTCGTTTATCTCGTTCCAAACTAGTTCA GCAACATCTACTGCGCCCCGTGGCATGCAACACTCTTCGAATGCACTCGC GGTTGGAGCAGCACTTTCACTTTGTAGAGCACATCGTGCTCGAAACCTAA AGTCCACATCTCGCTTAGTCCGTATTTACACAACAATGGCCGAAAACAAA GAAACGCACTAGGAACGCGCTAGACAGCCGCCAACGTCGCCCTCAAGTCC ACTCGTCCCGTGCCCCGTGTCCCGTTCCGTCGCGTCGCGTCCAGCACAAT TCGGGCTGGGATGGAAGAACAACAGACCCGCAGCTCGTCGGAAGAGCGAC TAAACCTAAACCCACTCACGCCGCTGCCGGCGTAGCTATCGCATGCCTTA ATCTAATAAATTCCTTATCAAAAAGAGCGTCGGAGTATAGTATTTGCTCT ATCTGGCGTTTGTGCAGCCGCAAGTACGCGGTCGAATACTCGTGGAGTCG GTTTGTAATGACACACGCGTCGGCGTCTGTCAACATGCCAACCTTTTGTG ACGCCCGCTCCTGAGATCTTTTGGCAGTGGTCAGGTTTGGACTCGCAGCC TGCCATTCACTGCGGCATCATTATAGTACATCGGATAGTAAACAAATCAT GTGATTGTGGGTAATTGCCGTTCTAGTTACAACAGCAATGCCGGAGACTA CAGAATCAGACCAACAAAACCAGCCGAATACATTTATCTGTTGAGCTAAA CACGAACTAGTATTTAACAAATACAAATATTACCTGATTCCTAAAATTGG TATCTCACTGTCCGGCAGATTAATTCATTACAAGTTCTACAGATAGAGTG TACTTGTTTCATTGTAAGAAATTGATTTTGTTTGACTATTCCTGCTTATA TTATGTCTTCTCACATTTGACAGCTCGAAATATTTTGGATCTGGAACAAT CTGCCTTTCACTTTATCACTTGCTTCACATAACTGAGGGAACGGAGGGAT AAGCAAGTAGTACGTTTTGGGCACATAGTTGGCTCAAATTGCCTATTATA ATTAAGGCGATAAGACAAAATAACTTTCTGCGTTGTTCTTCAGGTTGGTT GATTATGAGGCAATTCCATTGTACGTTCTACACGTTGGCGATAAGTTTTA TGGCACCCAAATTTAACGCAGAGGTTCCTTTTGATGCTGACCTAGGCCAT CGAAGTTGCGTTATTGGTCTGTTACTGCGTATATGGAGGGCTTTATAAGT GGAGCTGGAAAAACCGAAACGTACATATAGGCGATTTCGGCCTACAAATA AAATGTTGGCTTATCAAAATGGCTCTAAATGAATTACATTTCTTTGATTG TTTGTTTTGATTATACAGAGAGAAGATGCCTTGAAGTGAACTGAAGGAAT TAACCCAATGTACAATACATAATTCGACTGCCCGCCTTTACTTTTCAATT GAAAGAGTTAAGCGAATTGAGGCAAGGACAAGCTGGTCACCTTGAATCGA ATTGAGTTTGCTTTTCTCAATCGCTTTCTGTATTGCCCATTAGAGTGTCA ATCCACGGAGGGAATACAGACCCTACCAGCAACCCTTGTCCTTCGAACCC TGCACTTTATGATGCCCACATCGTAGGAAAGTTCAAAACTAAAATATATT CTAAGGTCAAATGAGCAAAAAACTAAATGGCTAAAATGGCTTTTATGTGT GCTCAGCTTGCCAACATCTGATGTCGGTTTTTCTAGTCCGCTTAATTGAG GTAGATAATTGATAGTGGGTTCAGTTTTGCCAGAATAATACTGGTGGCGA TTGTTAATTGATTTGCGGTTTTGACATTTTGCTTGGGGATGGGGGATGTT GGGGTCTCACGGCAGATTCATACAGCGAATTGAATTCGCTTGTCTCACAA AACTACATATCATTGTAAATATCGGTTTAGTAAATATTTTATATAAGTAA GTTTAATGGACATTTCAAAAACAGTGACTTCATATTTGCATAAAGGATAT CTGATAATCTATATATCTATAAGGTTTCTTTCTGTTTTATAAAAAGGAAA TTGAAAATATAATTACCCCCTTTACTCGTAGAATAAAAGGGTATATAGTA TGCGTTTAAAAGTATATAAAAGTTGGAAAGAAGAGTTTCGACCCTATAAA GTATATATTCTTGATCAGAATCACTGGCCATTTTCGTCTGTCTGTCCGTT TGTCCGTCAAAATCTTGGTAACTATAAAAGCTAGAAAGTTAAGATTAGGC ACGCTGATTATATTATTCTAGTGTTTTTCTTGGCAAGTTCCATCGAAATC CCAACAAAATGTTGAAAATTCTCTTTAGCAATCCCAGTAACTGAGCAGCG CGTATCTGATAGTCTAAGAAATCGAAAATTGCGTTCTCCCTTGTCTTTTT ATATAATATATATACATACACATGGAAAAGAACCCCTTCTCTTGATGAAG CATTACTTAAATGTTTTGACTTTGGCCTTCAGTTTTCTTACGGAGGCTTA GTTACTGCTACCATAACGATATAAATTACACTGTCGTAACAGAGAAATGC CACCTTACCCCTTGGTCGAGACCACTTTTGATTTGGCTGATGCCACAACC TGAAAGCTCGACACGAAAGCCACCGCAAAAAGTCACAAAGGAGGTCGCTG GTTGCATTTAACCAACAAAGAGTGCACACACGGTTCACACAGACAGGTGT CGTTGTGCACAGGCACACACTTTCGGCGTCCTTTCATGTTTTATATTTAC CATTGGGGGCACAACAAATAACAACAATAAACTGCATCAGCAGCAATGTC ATCTCACGAAAAGTTCTGGGCTCCAAAAGGAAAGGTAAATATGCCCACAA ACATATGTAGTGGTGTTCGCATTTAAAGGATAATTATGATTTTCGCCTTC AACTTGACTAACTTTCCGGTTACACAAACACTAGGACAAAATGTCCTGTA TTGATTTTACCCCAGCTATAAGATTTATTAGTTTTTTGCCCAGGGTTGTG TGAGTTCCCCTAAATGTGTGTGTTTGTAGAGGCAGAGGATGTGCAACACG AGACTCTTGCCAATATTTGCCATCTCATATTCTCTGTGCAAAAAAAAAAA AATATTCTAGTGCTAAGTGCTCTGAATTTCTTAACATTGTGGCTCAACAC ATCATTTTTTAATTTGATATTGATTCAATAAGTTTAATTGAATTTGTTGT GCTTAATATATGTATGCAAGAACAAGCTAGCACGACGCTCAAAGTAAACT GCAGCAATATTTAAATAAACTCTCCCTTTAGAGATTTTTAAAAATGGTGC AGATTAATTAATTAAACATAATAAATAAACACATTCTCAAGGAAGATGCC TATCTTACATTCATCCAAGCCGTAAGAAGATACACAACTACAATAATTGT ATCCGGTTTTCCGGCACAATTCTGAAACTCAATTTCCCTGTGTGATTAGG GGTATTTTGAAAAATTTCTCAAAATGGGAACCAAAACAAATGGCTTTGTT TTGCCACTCTTTTTTTACTGCCTTTTGTTGCTTGCAGCCTTTTAAAAAGG GCAACTTGGCAAAAAGCGGACATTTGGCTATGCGTGTAAACAACTTCAAG GCTGGGGTGACTTTTATTTTCCTAATTCTGCTCTTGACACGGGCTCTCAG AACGGAGCTGAAAAGGTTGAATGTGAAATGCAATATGCAAACAAAAATGC AAATTGGAAATAAACAATAACGACTATGATTTAGCGCTAGAAGCAATGAT TTCGCATTTAAATGGGTAGAGTGATCGAAATGAATCCGATGAATTATTTA TACTGAAACCGCAATCAATAAATCTTACTAATAATTAAGAAATCATTAAT CATTTAAGTGGTTTGGAATTTTTTCGGCTTGCCATTCTTTTTTTTAGATC CAGATAAGATTGGATACACCAAGGGAACTTTTGCTACACAGTGCGGGAAA ATGGGTGGCAAGGTCGTTTGACGAGGGCATATGTATGATGTAATTGCGAA AAGTTCTCTTTGCGTCAAATTTGCGAACACAAATTTATCAGCGCGTCACG CAGTCTGCGACTTGTCCGGCGGATATTTACTGTGCCCAGCATACACTGAA AACAAAAACGATGATGTACTTCAATTTAGTACATATCACAACCTGCTTAC ATTACCTGTTTGCAATTAAGTATTTAATAAACAGTATGCGGTTATTAAAG GTTTAAAGTTAAAAATATCTGACTCTCAAAAGAATTGAATCGCTTACTTG CGTCACTTTCACTTCATCCTACAGATTCACACAACCCAGAGATATTACTT GCTTTGTGTTGAAAGTGCACTCCGTACTTCATTGTATATTGTTTATTTTT TGTTTTGTTTTTCTGAGTGACATTTGGGATTTTGGGTCATTTGAGTGTCG CTGATCATGCGACAGCTAGGAGTAGTAGACTCTGACTGCTCGAATTGCTG CACTTACGCGCAAATGTATGTGGTGGCGATAAACTCGTTCCTTTGTCAAC TCCGTTTACTCGATATCTTGGACCCGAGTCCAATAAACAAATCGGCAATC GGCAATGAGCAGCCAAAACAATCAATGCAACTTTGTAAGGAAATCACTTG TTGGCTTGGAAGTTCCTGCACTCGACAGTTGTTGCTCTTCTCGAGTTTAA AATTGGACTGACTGAACAGCGGCTTCCCTGTCCTTTCCACCCGCCGCCGT CTCCCTCACTCGCCTTCCCCGTCTCGCTCTGGCCACTGGCTGTGCATCGG GAGTTTTCAATTTCGAAGTGCCCGACGTGCTTGCCACCACTAAATACTTC TTCGCTTCTGCCTGTTTGTGTTCTCTTGACGCAATGGAAATTTACCAGCG ACATTATTAGATGCCATCGCATGTCTTCAGTTTTGCTGTTTCATCCGGCG CATTTCATACTTCAGGATTTAAGGGAGAGAGACCTCAACAAGAAGGGAAG CCGAAGCTAGTACACCCTTTCTGCTTGAAACCTATGAGTACGATTGCGAC TGAAATGTCGCAAATATGTACATACGTACATATGTAAGTATATATATGAT AAGGTGGAGATTCATAAGAGACCAACTTGATGATATTGTAAAGATTTTGA AATTGATGTAATGCATATTCTCAATTATATTATACAATTTAAGCTTCTTC TACAGTGTTAGAATATCCCAACTACATTAAAATTGTGCAATTACGTTGGT GGATTGTTCGCGTGCCCGAAGTGAAGTCTCCTCTACAGGATTAGCCAGAT GAAGATGAATACCATACTTGCATGCTGACCTCATTCGAAGGCTTCGTGTT GAGCGATGGGGAAGGTGATAAGTATGCAGTGGCTATTCATCAAATGCGAT TAATATAAATATATTCATCAAATCAGAGCTACGAATCAAATGCATATTCT GCATATTCCCATCTTATACGCTTAAATTTTAAACAATTAGAAATACACTT TTGAGCGGCTTGTGAAATGTTTGCATTCGTCCCACGTAGTGCGATCTCGA AGTAGATAAGATAAACTTAGATAGGGAGAGACGAATAAATTAATTAGCAA CTATTTTATTCGTTTATTCGAGACTGTGCACTAGAAGTCTATCTTTTCAA GGGTCAACAACTTGGTCTCGTGACACTTTAAATATGCCCTGCTAAATTTA AGAGATCAAAGAAAATCTGAGAGTATGCATGGGAAAACGTGGATACTTTG CTTAGGCCAATTTGGATGATAATTGCTACATGTGAATTCATGTACATATG TAAGTACAGATGAACTAATGAAGTGTCTTTAGAGCAATTAGCATAATTAA CACACTTGCGATACAATGCGACACATTCGAATTGTAGAACCGGTTCTGGG CTCCAGATCCGATTTGCCTCACACGCAATCAGCTGTTGGACTGCTCTGCG TTCACTGCTGACACACATTAATGCGGCAAAACAGATAAATAGGCAGCGAG GCAAAATAATAATAATAATAAATGCAAAGGTCTTACCGGTTTTGTCAGCT GCTACATACAGATGTTTTCGGGCTTCCCCGCTGCCCTGCCTGCACTACCA ACTTCTAGCCGCCTCAGCCGATTGAGGGTCAATGGCTTCTAAGCCAAGCC ATCTAGATACATTTCGCTTCGGATTGCGTACAAATCAAGAAGTCGCGAGC TCAAGGACGGCAGCCAAGAGAATGGTTTTCGGTTACAGCAAATCACAGTT GCAGAACGCCAAAAGAACCGAAAATCGAAGCCAAAAAAGCGTTTGCATAT ATTCAAGTATAAACATATGTATATATATATATATATATACTTCATCTTAT ATCAACAGCCACACAGAGGAAAACGCTATATTGCTCTTCTATGATAAATA ATGTACTCATTCGCTTATTCACTCATGTAGTCATTCTATTTTCCAAATTC ACTACTTTTGATTTTGCAATTACCTATTAGTCTCACTCAAAAGCTGCACA GTAAGTAATACCTTTTTGAAGCCTCTGGAAGTTTCCATTGCAGGCACAGA AAGTCAGTGTCACGTAAATGATTTCAGTTTCTCGAAGCACATGTGTAACT GTATGTATGTGCAGCTCAATCCAATGGATTTGCAACTAGGTGGGGTTGGA TGGTGCCGAAGACAAAGGCAGTAAAAGCCAAATGACTGGAGCAGCAAAAT TGCGAAATGGCCGAAACTGTGCTACAGTCACTGCGGTCTACCAGCATCCT CTCGCCTTCGTCCTTCGGAGCCACCCACCTCAGTCCACCCTTCGGCTTAT GTAAATGGAGCAAGTGCGGAGGGCGGGGCGGCGAGCTAAGTCCGTGCCCC AAGTTTTGGATTTATTTTTTAGAGTGCTTGGGATTGAATTGTGTGGCAAC CGCCACGATCCCATTGCGGTAATAACTATTGGTTTCTTTAGCTAGTAATA CAAATTGGGCTTATGCGAGCTTCCTTACTTACAATGAATATGTAAAATGA TCAGGGCTGTTGAATACCCTACTGACAAATAGAGTTTGAAAGTGGCATGC CCGAAAAACAGCATTCTACACGCGCTTTGTTGGTCTTATCTGTTGACTCA CTACACTCGGTACTCGAACCACTTTCGCTTTAAACAAAACAGTAAATACG TATGTTATAAATCGCCTCTGTTTTTGCATATTTTTTCAACGTTCACGGAA AACGTAAATCCACCAATCGTGCCAAAAACGAGTCCGAAACTACCGACCTA TAAATAGCCTCCACTCGATCATAGAATCAAAAGGTTGTGGACACGAAGCA CGAAAATAAGTCAAAAATTGTTAACTCATCGCTAGATAAAACCCAAAACA AACAAAATGTTATCATAAATTTAGACTTTTTATTGGGAATTACGCATTAC ATACACATGACATATGTGCAAACATTCATTCATACATACAAAAATGTATA TAAATACCGTTCACAAAATGCAAACGGGTCAACGTAACCCCCGAAATCTT AAGCAAACTTTGTTTAATTGCTTCTCACCTGATCACTCTGCTGAGTTGGT GAATTCGTGGCTTCTGGGCTAAATTGCAACCATTACTGGGAGTTGGTCCT GTGTCATTGCATTATCTTACATTATAGGCTGCACATTACAGTAAATGTAG TTGTTGGGCAGACGAGTATTACAAAAATACAATAAGCTCGCTCTCTCTTT CGTTTCTTTTGCGTATGCCTCTTCGTCGAATTTGTTAGCTGTTGTTTTAT GAATTTCTGCCGCCCGTCTTGCACAGTGGGATGAAATCGCTGTAGCACAC GTCCAAATCAGCTGGCTTATATATGTATGTACGATTAGAATTGGTTGCGG GTGACACTCCAGAACGCCAAGTTGCCAAACACTCTTTATAGGCGATATTA CGCACACTCAAGTTCCCGTGGAAAGTTATTATCTATCGGCTTCGCCCTGG GTCACGCCCACTGTACGGGAGTTTCGATTTTCTGCGGGGGAGGTGGGACA GTGACAACACCGCTCGGCGGCACAAGTTCAACAGAAAATGTGGGGCGACC GGAGGTCGTATAAACAAAAGCACAGTGCACCCGAGTGCGGAAATCGCGGC TGTAAGTGCTTCAAATGCACGCAGGAGTCGGGAATCGGGGAGGAACTTTC GATTCACCCAATCGCTGGATTTCAATTGATTACTTAACACGCTCTGTCGC GAGAAAAATAGGCTATCTCTACTGCCGCGGCCCTTAAAAATATAGAAAAG TCGTATAGTCCACCACACTAGCACCACACGTCCGTTCGCACTCCAATTGG AACATCATCTGACCGTTGCCGTAACAGCGGCTGTTAATGCAGCCCGTCGA GGGTGGAAATTTCGATAGCATGTATCGAAATATGGAAAAGTTGTAGTTTC AGAAAACAGAGTTACAGCGACTTACAACATGATTCCCATTAAATATTAAC AGTTGCTGCTTACCTAAGAAAGTTAAACAATTGTAATTTTAATGCGATAT GAAGTTATCGATAGTGCCCGCGCGCGAATAATGTTGTTTGGGTACTGTTA GCGTGAAACACTGTTACGTTACCCCACAGATGTTCGATTAAGCCCTCTGT TAATGAGAATGAACCGCCAACTTTATCGATAATGTTGGTTATGAAGCGTA CGCGCAGTAAGATCAAACTAATTTATGAAGAGGTGATTAAAATATTTGGA TAGACGCTCTTATACGTAATATATTAAAATTTATAAAAAGCTTAAAGAGC CTCACTAGCTGAATATAAAGTAAAATATTGTCTCTTTTAATCCATATGGT TATTACATTTTTAATTATTTGCGTTGGATAAGATTTCTGAGAAACCTCTT TTGAAATTCTATTCGTATTTTATATAATAACTTTTACAGATCCCCAGGGA ATCGTTTTGTATACTATTTTGTTGCTTCCTCTATAACTTGATAATACTGA AGTGGCGTCACACTGGCTAGGAACAGGTTAGGCTGTCATCACCCTCCGCT TCGTCAGCTGTAAAAGAGACAAAAAGTAGAAATGGAAGCTAAAAAGCCGG TCCTACCGTTAATGTCAAACAGTTGTAACTCACAAAGAATTTGAAGGCCA AACATTAGAGCGAATCCCGCAACGGCGGCCACAAGGGCCCTCCATCCGGC ATGGCTCTCAATGAGGATCTCAAAGAAGACTACGTACAGCAAGGTTCCAC AGGCGATGCCCTGGAGGACTCCGGATGGCAGACTGGGCTGACCCGCTGCC ACCTGCTGGCTGATGCCGAGGCCAACACCGATACCGATGGGTGTAACAAT GGAGAATGTCACCAGGTACAAGATGGCCAGCGAACTGCGTGTGCGGGCGA CCAGAAGCTCCATACCCACGCAGAAGGCCAACACCAACTTGTGGGCGGAG ACCGCTCCAAACATGAACCACACAGTGCTCACAGTGCCCTCCAGACCAAT GGCCATGCCCTCGAACAGTTCGTGGAGCGAAAGGGCGAGGATAATGCCCA GCCCCCTGGCAGAGGATCCATCGTCCGCTGGCACGGGCATGTGCGAGTGG CCGTGGTGATCCTTGTGTGGCTGCGGTTCCGTATCCTTAACTTCCACTTC TTCCTTCGCCTGTGGATTGAGGAGAACACTGTGACGAATGCTGCGTCCTC TTTCGAAAGCCAGACTGGCCACCGACTCTTTCCGACTAAGCTTTCCCTGG TGGTGCCGCACGAGGCTGGTCATCAGCTCGTCCAACGCGTACATCAGGAA AAAGCCCGTGCACAGCAGCATCTCCGCCAGAGCGAAGGGCGTCTTGACAA GCGAGCCGCATTCCTGGAGCGCTTCCACCACCTCGATCACCTCGGGCAGC ATGTGCAGGAAGGTGGTGCAGATGAGCACACCGCCGCCGAAAAAGAGTAG GCACCGCACCACCAATGACGAGCGGGTTTCCTCCGGACTCGCCTTCGTCC AATGGAAGCACCTGTTCAGGACGTAGGGAAGGCTGCCGCAAAGCACGGTG ATCACCACGAGCACCACCATGGAAACTATTTTGGCCACCAGCAGCGCATG GTGATCCACGTCTTGCGTTTGCTCTTGTGACATAGTTGCGGTAGCGCTCA TCTTCACCTCCCGAGTTGATAGCTTCGACTGTGCTGGCTGGAACTCACAA CCAGGCTAATGGTTTATATTTCCAGTCATATATCAGCGGGAGCCGATTGA AATCTGATCGCTGATTGATACGCGGATTCACTGGCAGACAGCGGGCAAGC CTCGCAGCCTAGTATTGTTATCAATTCGCCGTCCCCTGGACAGGTGTCTC TCGTCGGCCCACCGATAACCGAACCATAGCCGTCTGTTCTTTGCGAATTT TATGATTGAGGGAAGTTTCGTAATGTGCAGGAACTTCGGAAGTATTTCCC GAATATTATTATTATTGATACACTGAGATAATTTATTTGTCCATCCAAGG CGGTCTCATCTTAGGTTTATATGGTAAGGATTGCAGGCATGGAATTAAAA TCGCAGCACATTTTTTAAAAAGTTAAAAAGATTCTAGCCATATATGTAAA TATTCTTGACCAGGATCAGATGATTTCGCCACGCTTGTTTTTTAATTTTA CTAAATTTGTTTATAAAATAAATTTACATTTATCAAAATAAAGGTGTGAT AAATGCAGAAACTTCCATGCCAAAAGTTGTTCGAATCGGATCATTTATTT AAAAGTTATGGGCAATTTGGTAATTAGTATGTAGCAACCGGTAGGTGGAG CTAATGTGCGCACTCGGAGAATGTCCTTTTGTTGATGCCACTTATAAATT TCCCTCGCAGAAGGGCGTTTAAAGGGTATCTCATGGTCGATGACCTGACC TTGCCGTCCTCTTTCCCCATATTTATAAAGCCAAAAAGCCCACGCTTTAT TTTTCGGTAGTTTCTTTGAATTTCTCTATAGGCTTAATTGTTTTCATATA AAATTCGAGTATACCCTAGGGGCATGTGAAATGGCTCTTCCCTTTGGCCT CTCCAACTGAAATAATAAGAGTGGTAATTTGGTTTTTCAGTCATTTGGGC TTTTTAGTATGCTTACTTGCTATCTGGAGGCCAAACATCAGGACGAATCC CACCATCGACGAGAGTAAAATGCGTATGCCGGCATGGTTTTTGGCCACAA TTTCAAAGAAGACCACGTAGATGAGGGTGCCACAGGCCAGCCCCTGGAGG ATTCCTGATACCGTGCTGGGCTGATTAGCCGCGGCAGATTCGCTAACTGC AATTCCGATGCCCACGCCAATCGGAGTTACGATCGAGAAGACGAGGAGGT AAACCACGGCCAGCAGCCAGCGGGTATGGGCCATCATGATCTCCATGCCG ATGCAGAAGGCCAGAACAAGCTTGTGGACGGAAATGGCTCCGGTCATGAA CCACACCGTGCTCACACTCATCTCCAGGCCAATGGCCATGCCGCCGAAGA GTTCGTGCAGGGAGAGGGCCACGATTATTCCGAGGCCACGCAGCCAGTTG GGCTCCTTGGGGCTTTCTTCTGGCTGGACCACAATCTCTGTCCGCAGCTC CTCGCCCGCATCCTTGATCGTGACCACCTCCCGTAGCTTCCTTTGCTGCC GCCGACGAACCACAAAGTGCATGGTTTCCTCAATGCAGTACATCAGATAG AAGCCAGTGCAGAGCAGAACCTCCGGCAGGCCGAAGGGAGTGGGGGCCAG CATGCGGCAGTCCTGGAGAGCGTTCACCACCTCGACCACCTCCGGCAGCA TGTGGATGAAGGTGGTGGCTATGAGAACCCCTCCACCGAAATTAAGCAGA CACAGCACCACTTTGAATTCGCGAGCATTGTTCTCGGGCCTCTGGGTCCA CTTGTAGAAGCGATCCAGAAGATAGGGAATAAAGCAGAAGATCAGGGTAA CGAGGAAGAGCACCACTATGGCCACGATCTTGGCCACGATTAAGTGTTGG TCTACCATTGCAAACGGAGTAACTGGCCCGATATCAAGCCATTCACTTTT TATAGTGGAATTGATATCTATTCAGTTAGTGGAAGGTATCGGCGAATTGT CGAATATTTACACATATTAAGGGCTTAGTGGTTTCGACTTAAGTTGGCCG AGCAATGTGCTTTAGCGAAAGGTATACGGCAAAATTTCGGCATGATATCT TTCGGTCATTATCTACCTTTCGATTTAACACATTTTGCCACATTAGCCAT TATTTCCCTGGCTCCCAGCATGAGCTCATCGGTCTGTTTTGCCGCATTAG AATGTCAGTGGGAGTTTTCAGACTGAAATTTCAGCTGGCGAAAACAAATA ATTTGTTGTCAACGGCAGGCAAAGCCTTGTGCACCCAGGAATCTATGTGC TATCACTAGGTTGTGGAGACAGTTTCGCCTGATAACTTCGAAATTGAGAT ATCACCGCCAAATGCCCCATACTAACATAGTTCGTGAGTCAGATTAAACA TGTACCTGTACCTGTAAATATTGTGAAGCAAAGGAAATTATAAAATAAAT CACTCGTTGGGTAATCTTTGAATAGTTTTTGAATATATAATGGCGTTATT GCAACGGATAAACGGATAAACTTATTATTTAACCACGAGTTTGGGAGATT ACATTTGTCATCGTCCTTTAATTCTAGGCAAGGTTTTGAATTCTTAATAT GAGGTATTTCGATTTTTCCATTGACAATCACGTTCTTCTTCTCAAGTACA CAACTAAAGTAGCAATTGATTTTACTTTTCTTTGCTCAAACCAACCTGCT GTATGCATTGTTTTTTAATTTAGTTTATTTCTAGTTGTGAATAAAAAGCA TAAATAAGATCTCAGAGTAATTACTTACTTCAAGAGAAAAAACCGATAGT AGAGACCAATGGGGTCAGCAAGAGGGTCACGACAAACGACCTGTTTATTT TGAAGACTGAATTTAAAGATAGCAGTCAACCACATAGCAGTCATCTTTTG CATCAATTATTGATTTTCACAAAAAATAGGGTATACAACTTAAACCTTTG AAGGAGAAATGCGATTTTATATGGGTAATTGTTATTTAAGATTTTGCATT CTTAATTAATTAAATTGACCGTTCCATTGATGCCTCTCAAATAAACAACT AAACAAGAGAGAATGCGAAAGTCAATTTTCCCCGATTATAAGATACCTGT TAGTCAGCTAGTGGAAATGCGAAATTTCATCATTTTTCTCGGATATCAAT AGATATTGGGGAATGCAAATGTAAAAATTATTTAAAAGTGTGGGAGTGAC CGTTTTGGGTGTTTTGTAGGTGAAAAGAGGGCCACCGTGTTTTTGGTATA CAGATAAAAATCTAAACATTTTTCAAAAGTGTGGGCGTGGCAGTTTTGTC AAGTACAACCTCTTATTCTACGAGTAACGGGTATAAATATGAAATATATT ATTTAATACCATTAGAACAGAACGTCTACGTATTGCCGCGATTGAATTCA AATGATATTGACCATGGACTTTACCTATGCATTATCATGATCAAAATAAG ACAAACCCAACGAACAATTTTACATACATCATCCAATAGTTTATTAAGTA TCATAGGCCGTAAATAAGTTACTGTAAAAATTATTATTGACATTTATTAC ACAATATTATGGCGTTTAAATTTAAATTTAACGTAATTACTATGACTTGA TAGTGTTCTTCTGTAATTGATTTCCATGATGTACACGGGTGAGAAGACAA ATAAATGTGTAAATGTGACATACATGAGTTTTGATATTAATGGAAGCATC AGAGTTTATCAAAGTTATCAAGTTGTCTCAAAAGATATTTCAAAAGCAAT GGATTGTCTCCAGACAAGTGGTTTTCATGCGTCTAATTTAGACGATTGGA TGACAGTTTAATGTGCATAGATATGCGTGTATTATTGTGACTTTGGATAA TCATTTCAAGTTTGGTTCGCTCGCTTTTGTGTGTCTTGTCGAAAACCCTC CATCGTAGTTGACAGCCGTTCAACGTGATTCAGTACATTCTTCCCGATTC CCCAACCCATACCATTCAAGACTGCTTGGGGTGCTGGACAGGAGGCGGTG GCGCCGGCTTGAAGCACTGCAGCAGGAAGGCGGTGTAGACCACAAAGGCC ACCGCCAGAGCAATCAGAGCGTACATAAAGATGTTCAGCTCGGGCTGGCG GAAGCGGTTCTTGCGTAGCCACTCCAGCACTTCGTCCTCGGATAACAGAT CACCTTGAATGAGAACGAGAATGAGAATGAGATTTCTCCTTTGCTCCCTT CACGTTCCCACGGACATACCCCTATATATGCTGGGAAACCGACGGCGGAA GTAGACCATTGCCGGCAGCTTGGTGACGCCCCATTTCTTGGCATAACGAG AGTCGGCCATCTTGACGAAGGTGATGTCCAGGTTATCCGTCTCGCTGTCG ATGTTTTCGAGTTTTTCCAGCGCTGCAGTACTGTCCGGCTGATTGTGTTC GTCTAAGTAAAAGACATGTTTGTACTAATCGAAAAGTGTTTTAGAAAGGA TAGTAAACTCACAGAAAAAAACGGCTAAGAACTCATTTTCCTCGAGTAGT TTGTCGAGCATTTTTCGGTTTACTTCTTCTATTTCGTTTTTGATTTCGAA TACGTCCTGTGATGTTAGCCAGGTAATCACCTTGTCGTGTTGGTGTAGAT CGCCGTCGTAGAGGACGGGCACTTGTTTTCTAAAGTGTTAAAGGGTTAAA AAACTTCACCTATAGTTTTGACTATCACCTACCGGAAATAAACGAGGGAA GGTATATTCACTATCTCGTATTTCTTGGCTGCCTGGATACTAGCAATCTT TACGAAATCAATGCCGAACATGTCTGCCTCACCATCGATCTCCTCCAGCT CTTCCAAAATCTCCTCGCACTCAGCACAATCATCGTCGTCTACATAAGTG TGTGATGAGTTTTTAAGACCATTTTGTAATTCATTCAAGCTGTGATACTC ACAAAAGAAAACAACCAATAGAGTGGACTCCGCCATTAGGCGATCCAGCA TACGCTCGTTGACCTCCTCGATTTCATCAGCCAGCTCGCGGTTGTCATCA TCGATGAGCCATTCCAATACTGATTGCTCGTTCTGAAGATCCCCCTCAAA CAGTAATGGGTTTCCATTTCTGCACACAAGTTCAGATGCCTTAGAAGTTT AGTTGATAGGCAATCTTGACACTTACCTGAAATAAACCAACGCCGGGAAA GTCTTGATCGAGTAACGTTTTGCCAGCTGCGGATCCTGGATCTTGACCAT ATGAATTCCGAACACGTCGCATTCGTCATCGATCAGTTCCAAGCCCTCTA GTATCTGGTCGCATATGTTGCAGTTGATTTTGTCTGCCGAAAATACATGG TAGGTCAGTAGTTACCCAGTAGTAATTAGTGTTTATAATTAGAGCCAAGC TTGAGAATCGGTTAGCTATAGTGTAAGAGGCAAAGAAAACGCCGTAACAA AAAGGTATTCCCGTCCAAACTAAATTCCAGTGAATTCTAGAAATTTGGAA CGCAAATTGTTTATCAACAGCAAAGGAAGGGCATGCAGAAATCTCATCAT TTAGTTTGGTCGTAATACGATGAAAGCCTGGTTTAGTGCTGTCAGGATTC GATTCTGGGCACAGAACAGAGCTCCTACGGAGGGTTAGACTTGGTTAGGG CTCCATTGAGCATGCGAAGTCGGAGCTTGGGAGTTTATATTGTTTGCACG TGGAATACGGAAGGAATACCTTGTTTTTCGATACGTTTTCTTTTACGTGA GATGTAGTTTTGTACGAATTGGCTGGATGAGTGTTTTGTGGATTTGGTGG TGGTCAGGTTGCTTTCTTTAAGACTAGAGGGGGAGCAGAAACTGCGGCAG AAAGCGGGTTGCTTCCCATTGCGCTCTGGTGGCACTGAGGTCGGTACGGT TGCGATTGCGGTTTCGTTTTCGGGTTCGGTTTGAGACAGGGATAAGTTTT TGTGGTTTATGGTCGATGCAGTGTGGGCGGGGAGGATACAATAATTCAGA ATGTGATAGATCATGATAAAGTGACGGAGTGAGAACAGTTGGCCAATCGA ACCAGAGTCTGATCGATAGGAGCTACTCACAGAAATACACGGCTAGGTAC TGCGTCTCCTCCACCATTGTCTCCAGCATCTGGCGAGTGATCAGCTCAAT ACGATCTTCGGTCTTCTGGGTGATAAGCCACTGAAGAACCTCTTCCTCCT CGCTCAATTCGCCTGTAAGATAATGACTTAGTAAGGGATGCCTATCGATT GATGACTGCTTCACCCTCGAATACGTTGGGGATTCCTCCCTCGAAGTAAA CTAGAGCCGGATACTCGTGCACGCCATAGCCGTCGGCCACAGAGAAGTCC CTGGTCTTAACGAATGTTATGCCATGCTTGTCGCAATCATCATCGATGTT TTCCAACTCCTCCAAAACCTTGGTGCACTGCTCGCAGCCATCCGCATCTG ATTGTCAAAGTGGGGTTGAGAAGTATATGATTACAATTAATCAATTATTT GATTACTGTAGACAAGGACTTGACATACGGGGTACTACACAAGCACTACA TAAAAAGCAGAGCAGAAGTTGAAGGGAAGTATGATAGAGCAAACGACTAT AGTTAGTACGTTTTATAAGTCCTGATTCCACTAGCACATTTTCGGGTAAT GTGATAAGTGATAAGTGTACGTTGGAATCAGCAATTATAATTCAAATAAT ATCGTACTGAATATAAGAAATAAATCTTATCGGGGATGAGGAAGATAACA GCTAACGTTGATAATAGAAAGGAGGAGTCGAATATAACATAGAGACAGAG TTGGAGCAACAAATAGATACAGTGGGTTTCGCATGGAGATTCTAAATTCG TTGGGGTTTTTACATTCGCTGTACAAGGAGGTAGTGTGTCTAGTGTGCGT TGGCTATTGGTGTCTGGTTGTGCTGGGTTAAGTGGTTAAACATTCTTGGA CTCATTCCAGTTGCACGAGTTCTATACAGAAAGGGTGGCTACCATCCTCT TGCTTGCCAGTTGAAGCATCCGCTGGAGCAGCTGCAGAGGCTGGCGGGGA ATCCCCCTCAGAACCTGCCGCTGGCGCATCCTCCGCCCCACCAGCGGCCG CCTCGGAAGGATCCGCCTCACTGCCGAAGGCGGCAGCGGCGCTGGCTGCT CCGCCCTCCTGCTGGTGCTGATCGCGCTCCTTTTTCAGCCGCGCCTTGCG AGCCGCTTTCGAATTACAAATGTCGCACTTGGTCTTGTTCCCTACGTTTG GGGTATCGATTTGTGTGGTTCGGTTTGAGATTTCAGAGAGCACAGTCGTA AATAGAAATATAAATAAAGTCTTGTTCGGTTAGATACACAGAGCGCTGAT AAGAGGCTTAGACTAGATTTATCTAAGTGGTTATCTACAATCATAAACAC ATAGTTCGCTGCAAACTGTTTGCGCAAAAGCGTGGTAACAAACCCATAAA GTACGTTATACGCGATGCAACATATGGTTAATTTTTGAATCAATGGAATA ATTCTACATTTAAGAAGCCTGTTGGCTGATGGACGTAACGTGAAGTGAAC ATCAAATTGAACATTGTACTTTGTGCGAATTGATACCACCAAACCGATTG CAGCGCTTAAAACCTTGGTCCTCAGAGATATTGAAAATTCATCGGTTGAA TCACTGTGTGCTTTCGGTTGCAAACTTACAAAAGTAGACTGCGATGGAGC CAGACTCTTCAATCAGATGAACAAGTCTTTCGCCTTCGAGATCTTCGATA ACATCTCCACTTGGATCCTTTTGCGTGATCAGCCAAGTTAGGATCTGTTC TTCTTCGTAAAGATCACCTGCAAGGAAACGAGTTTACTCACTGAACTAAA ACCTCTCTGAACTCTGGACACCTACCGGCGTATATAACTGGCTCCTTGGA TGTGGGCTTGAAGAAGACAATGGCAGGCAGGGCGAACACTCCGTACTCCT TGGCCATCTGCTTATCGTCGATTTTGACGAAGTCGATACCAGCCTTGTCC GCTTCGTCGTCTATGTGTTCCACCTCGGCCAGGACGCGAGGACACTGCTT GCACTCATCGCTATCTGAGAGTGGCAAGTTGTGGGTTCATAAAGGTAGTC CAATCAACTGCGGACCCCTAAGACTTACAGAATATCACCGCTACGTAGTC GGAGTTCTTGCGGATCTTCTCGAACATCTTGCGGTTAACCTGCTCGATGT GATCGGTCATCTCCATGTTGGCCGGGCTCGTTAGCCAGTCCAGTACCTCC TCCTCGTCATCGATATCGCCGTCGTAGTTGATATACTTGCCCTTTCGGAA ATACGTCAGTCCTGGGGGATTCCGGAAGCCGTACTTCTTGGCCATCAGTT TGTCGTGCATCTTCACTATGTAAATGCCATATTCCGCAGCCTCGTCGTCG ATTAGTTCGATGTGCCGCAGCACTCGTGGCGAGTCGGGATCATCTTCTTT GTCTGCAATTGCAAGCGATATTCCATTGGCATTAACATGAATATTTCAAG TATTTGGATAAAGATGTTTTGATTCTGATAGACTTATTCCGTAGAAATTA TATTTTGCTCGTGTGTTTTTGGGCAGTTACAGTTTTTAGTGGGCGCGATT TACTAAAAGTATGTGAAAACCTCTTGGATTCCTTAGCATTTACAATATAT TACCTAAATACCGTTCCCGAGGTATACTTACAAAAAACAACCGCTAAAAA GTCTTTGGTGCCTATATACTCGAAAAGTTGGTCACGATTAATGAGTTGAA TGCTTTGGTCGGCCTTCTGTTCGAGAATCCAGTTGAAGACGTCCTGATTG CTTGCAATGTTACCTGTTTGCAAAATCAAACAAAATGGTTAGAACTCATC ATATTTCCATGTATTAGGTTGAAGTGTCTGGCTCGTCCATTTGGTGGCAC ATACCTGGCGGCTGCAGTTTGTCAATCAATCATCAGCTTTAATCTTGAAT ATGTATACAACATTAATGATCGCTTTGTTTATTCTCACCCCCGCCCAAAT GAAATTCGAAATCGGCACTTTGCCAAATCCCCACCCGCCCATAAACAATG TTACATTTGGCAGCCTATGATTCAAAATATATGGTTTTTGAGGGGGACAT ATGCCTCTGACGAACATACATACATATGTACATCGTCAAGGATATATTCA AGAATATATTTAAAGATTTTTTTTGGCCTATATGTTTGAAATTATTTAAG ACAAAGAATTGCGTATTTTAACAGTGCTTTAAAGTGTATATAAATAAGAG AACCTAAGTTTATTGAGTTGGATGGCTTTTATTAAATATTCTTACAATTT CATTCGGGAGCTATGTTTACAAAAGTGCTTTATGTCGATTTGCGTTTGAT TTTTACGATCTGACAATTTCCATTTCGAAAATCTTGACTTATCAGCTGCT GTTCAACAAAATTTGTTTACATATATGTTGGATTTAGTTACAATTGCGTT TAGATTGGTAGGCTTTAGCTTAAGAAAACATAATGATAAAGATTTCTAAT TCGATATTTTTCAAATACCGATAACAAAAACAACAGCGAGCGGTACAGAA ATCGCTCTCAGAAGAAAACAAATGAAACAAAATGGCGAGCTACAATATGC GAGGCCATGTTCAGCGAGAAATATTGGATTTTCGATTCCATAACAAAATT AAGTATACGGCCTGTATGCTGCTGCAACATTTCTAAAAAGTTGTGGTTAC AAATTATGGTTCCTCATGTTGTTATTATGAAAACTTATGAAAGTTGAAGG CTCTCATAGTTACACGTTTCAGTTAAATTAGCTAACAGTTGTGCACTGTC AGGTGTAAATTGTTTCAAAAAATATTTTATGCGTTTGTTCGTTCGTTTAC TATGCTTTGGCCCTTGTTTAAATTAGACTAACTACATAAATGTAAATTGT ATATTGCGACAAAAAGAAGTAGTATCAAAAAAGTTTAGGCGTTCGTTATT GACAAAAGACAATGTCCCATTAATTTGTTAATAACAAAGCTTGCTGACTA AATATACGAGCGAAAGTTCTCAGAAGTTTTATAGTTGTTTGTCGAAGTAA TTGCTTTTAGTTTGAACAAAGTTTTTTGAAATCCGTTGGCAAAATGCAAC AAATGTGTGGTTTAGTTAGTTATAGACCTGGGGACGACCTACACAGGTCG GCCCCTCTTGAAGAAAGTTAAAGCGAAAATATCAACAAAGTTTTAGTTAG TAGGTTTTCTTGATCATTATTCATTATTTCGGGTATCGTGTGATTCTGCT ACTCGTGGATCTTCTTAACGTGGAACAACGCCCAAGGCTCGCTGCTTAAA AGTGTGGAGTAAGTTCTGATCTGACACAGAAGATGTATTGGTATTTAAGT CAATGTTTTTGTGCCAGACTGTTTAGGATTAGTGCGAGGAAACCTCAATT TTATGGACACACAGCCTGCGAATTCAGTTTTCAGTTGGTTCTTGTCATAG TTGTTGTCTTTTGCAGTCACACATATGTAGATGATGTACATTAATTATAG AAACCTGTCATTGAAGGTTCTTTTGCTGGCTATACAGGTTTGAGTTGGTT TTGTATTTTGTTTTGGTTTTGGTTTTGGGTTTGGTATTGGTTTTGGTTTG ATAATTGTTCTATCAGTTGGCAACAGTGCGTATACGTGCTACTTTAGTAT GGTATATCATTCAATCATACAATCAATCACTATCTAACTGTCTGTGGTTA TCCACATTCAGTTAAACTGTTGCCTTACTCCCACAGAGAGATATCCTGAA AAATGATATCATACAAATTTTTTAGTCGATTTTGGAAAAAATTAATGCCT GCAAGACACAAGAGAAAGAAAAGAGAAGAGAAATAAACAAATAAGGTAAC GACCAAATTGTGCGTGTGTCTGTATGTGTCTGAGTATGGGCACAACAAGA GCAAAGTGATCAGGGTACAGGACAATGAGCTTGACGTCAAATGAAACTCT ATCTCGAATTGTTTATAGTGCTAAATGACAACGGTGTCTGGTCCGAGGGT CCAACGACTACGTACCGGATTTGACATTCAGTTTGCCGGACTTCTTCGCC GACTTCTGTTTGGATACCTTCTCCACCTCCTGGGACTGGTCGTCGTTGTC CTGGCCCTTGCCTACCGGCTTCTTGCCAGCCTGCGGCTTGTTGCTTCCTC CCGAGCGCTTGTTGGCATAGGAAACCTTGACCAGGGGCTTGTCCTCGTCG TCCTCATCGTCGTCATCGGTGTCCTTGGAGGGCTTGGCCTGCTTCTTGAT GGCAGCTGGCTTGGTGGACGATTTGCTGGACGCCTGGTTGGCAAACTGGA AGTTGCCGCCGCTGGGACGCTTGCCCTGATCGCCTTCGCTATGCCCGATC CGCTGGGCGGTCATCTTAGGAACTTTCGTTGACTTCTCCAATTTGGTTGG ACAGCATTGGAATGGTTTGTAATCGTTGGGCACGAAATTGTTGCCGCGCT TAGCTGAATGGCCGTCATGACCCAATCCAACATAGAAACATTCGTCATCT GTGTAAGCAAACAAACAAAAACATTTTGTCAGATTGTTTAATTTAAAAGA TTTTGGTTTTTTTTGGTTCACTATCAACAGAAGGTTCGTTACGATAAGTT AAAAAGGTTTCAACAAAAGTGCATCATTGTAGGCTAGAACTAAGAATAGA AGTCGCAAACTGGCTTTTTACACTTTTCTTAACACCTCCGATATTACCAC AGAGAAAGAAAAAGAGCAGTTAGTACGATTTTCGATTTAATTTTCATTAT ATTCAGACTTGAAAGATTCTTTGTTCTAGAGTAGAAGCGTGCTTTATGAG TGGAAGAGATTCGAAATTGTTATAAGATATAATTTAAATTATATTGCAAA ACTACAAAACTAACTGACAAAATGCTTTTGATGCTGACTGTACAAGTTTC GGATTTTGATTCTAATTTACAAACATATCAAATGTCGAGTTAAGCCCACG TTGTTGTACATTTCGTTTTCGACTAAGTGTCAGTGAGTTCACTGCGTCTC ACTTTATCGAACTTATGGTTGTTTTTGTTTATATGCTTAAATATTTTCCA TGGAACAACAGGATCGTTATAAATTAATATATATGTAAACAAACATAACG ATTACTTAAAGTATTATGAGAAAGTAAATTATAAATCGAACAAATTAGGT ATTAACACAATTGTTGTATCATTATCAAAATAGTTACGTTTTTAAATAAA AAACCTTAAGTTGCCTGGCTTAAATAATTTCAAACATTGTGTCAGCTATG TATGATTTAATATTCTTTAAACGTGTCCTTGTAGTAACAAGGACAATGGA CTTTGAAAGTGGATAAAGCTGCGGATGTAGGTGTAGGATTACTAGTTCAA GAGGATTAAAAGTATACGAATGTGGGTAGCTATTTTGACTGGACTGTGTA TTCCCAATTAAGATTGTGCCTCACATGATAGTTGATTTAGCACAGAAGCA ATGCGCAGAGCACAGACACAGAAATCACGTGATTGTAGAGTGGTTACCTT GGTTAAATGCATTTCTATTTGAATTCCTCTTCCCCAAGTCTGTAGATAGA CAATGAAATTAACTTTAGTCAAAGTTACAGAGTGTTTTTTTTTTTGGCAT AGTACAGTGTACAAGGATGTGTTCTCGGGTGGGATGAAATTGGGAAGGGA ATTTAAGTCGGGTTGGACAAAACATTGAACAACTTGAAGTTAGTGCGTCA ATGGCAACTCACATTCAGGTATTACCTATTTCATCTATAAGCCGACCTGA GCAAAGGTCAGCAAGACGGTGTATCGTTCGACCTTTGGCCGTGTGCCTAT ATTTTGGTTTACTTTTAATATCCTCTTCTTCTTCTTCGTCGTCCTCATTA TCGTCCTCCCCTGTTGCGTCCTCGTCATCCTTATCCTTGTCGTCCCCGTC GTCGTTATCATCCTCGTCCTCATGGTCTTTTTTGTTATCGTCGTCCCCGT CATCATCGTCATCGTCCTCCTCGTCCCCGTCCTCATCATCCTCGTCATCT CCCTTATTATCTTCGTTGTCATTTTCGTCCTCATCTTCGTCGTTTTCATC CTCATCGTCCTTGTCGTCTTCATTATTATCTTCTTCGTTATCTTCGTCGT CCTTATTATTATCTTCTTCGTCATCCTCGTCGTTATCATTATTGTCTTCT TCGTCATCCTCGTCGTCTTCATCGTCATCTTCGTCGTCATTATTATTATC TTCTTCGTTATCCTCGTCCTTGTCGTCCTCATTGTCATCTCCGTCATCGT CGTCCCCATCATTATCTTCATCTTCGTTTTCATTATTGTCCTCTTCGTCA TCCTCGTCGTCTCCATTATTATCATCTTCATCATCCTCGTCATCGTCATC ATTATTGTCATCTTCTTCTTCGTCCTCGTCGTCCTCGTCGTTCCCGTTAT TATCATCTTCTTCGTCATCCTCGTCGTCCTCATCATTATCATCTTCGTCA TCCCCATTTTCATTATCTTTATCATCATCCTCATCATCGTCATCCCTAGC AGTATCTTTCTCCCCTGTTTCATCTTCGTTATCCCCATTTTCATCATCAT CAGTTTCTAGTCTTTTTTTATGTAATCTCTCATTGCGAATCGAATTCTGC AGACGCTTTAATCTTTCTCTTTTATCCTCATCGCTTTCTTTGGGATAGCG CAATTTAACAATTTTTTCATTACTGTCGCCGTCATCATTGCCTATATAAG AAATTATCATTACGTATTGTACTTTTAATTTAGGCAAGAAACGGGTAAAT GATATTGGATTTATAATTTTTAAGATTTATGAAATCTTCTTTGACTTTGT ATCGAAAGTTTGGCTTATGATCGTGAGTTATAAAGCATAAACACGTTTAA GAAAGGACGCTTACTCTTTTGATTGACTAACCACTGCAGCACACGGTTTT CATTTTTGAGATTACCTATAGGAGAAAATACTGTTAGTTCAGGCTGTAAT AATATACCAAAGATCCCCAACTTACCATCATACATAATCGGGACGCCGGT CTCGTAGTAGACCAAAGCTGGAAATGCGAAAATGCCAATTTCATGAGCCA GCTTAACATCATTTGATTTGACAAATTGTATTCCGTGCTTGTCGGTGTCA TCGTCGATGTTCTCCAACTCCTCCAAGATGTCGGAACACGATTCGCATTC ATCGTCGTCTGTGGTACAAACAATCAATGTCAACCAAAGATCTTATTGAA CTTAATGAGAAATACACTTACAGAAGAACACAGCCAGGTGCTCAACATCG TTGATCAAAACTTGCAGGGTCTTACGATCGACAGATTCAATGACATCAGC TGTGGACTCGTGCAAATCAATAACCCACTCGAGAATTTCCTCTTCCTTCA TCAGGTCACCTTTTAAAGAAAATTACAAACATGTACCTTGGCTAATAAAG TATTCATTAAATGTATCAGCACTCACCGGTGTAAATTGTTCTAAACTTAT GTCTATAAAATGCAAGTGCCGGCAGACCGGGCAGGTCGTACTCCTTATCA ATATCGTCGTCGGATGTCTTTACAAAGTCAATGTCTTTTTCCTCGCATTC GTCATCGATGTTCTCCAGCTCGTTAAGGATCTTTTGGGCCTTCTTATCGC CCTCAGCGTCTGCAGAAAACGGTTTTAAGGATAATACAATATAAGGTTTT AAGTTGGCTTACAGAAGAATACGACAACGTGATCGTTTTCAGCCAAGATC TTGTCCAACATCTTCACATTGACCTCCTCAATTTTTCCGGGAATTTCAAG GGTCTCGTCGTCAGTAATCCAGGCCAACACCTCGTCCTCGTCGTCCAGAT CACCGGTAAAGTGAAGTGGATCACGATTCCTGAAGAACACCAGACGTGGA TAGGTCTTGACGTTGTATTTCTTGGCAATTCCGGTATCCTCAGTGGTAAC AAAAATTATGCCAGCCTCATCCAATTCATCGTCGATGCTTTCCAGGGCGT TCAGAGTGTGCTCACAGGTCTCTCCGGGCTCGCAGGGACCCGTAAAGAAG ACGACGACATATTCGTGTTCGTTGATCAGAGTGACCAGGATCTCATCGGT AACCTCCTCGATAGTAGCTGTCTTTTTCTGGACAAGAAGCCACTCGAGCA CCTCATCCTCGTTCATCAGATCGCCTTCATAGAGGGCCGGGATCTTGTTT TCGAAGTAGATGAGGGCGGGCAAATGATCGAGACCATATTCCTTGGCCTC AGCGGCGTTATCAATGCGGACGATGACAATTCCCTCCTTCTCCAGCTCGT CATCAATGTTCTCCAGTTCGTTCAGGATGCGCATATCCTGCTTATCGTCC TTGTCGTCTGTGAGCGAATGGTAATGATTGCAAAGGCGTAGGTACATTAG CAGTGTGGTCTACTCACAGAATATAACCGCCAAGTGCTCGGTGTTCTCGA CCAACTTGTCCTTCATCTCATCGGTGACCTCGGGAATTTCGGAATAGCGC TTCTGGTGCACCAACCAGCCAAGCAGCTCATCCTCTTTCATCAGATCACC CTCGTAGATGTGTGGAATTCCACGTTCAAAGAGTACAATCGATGGTATCT CATCGATACCCCATTCTTTGGCCTCCTTGTCATCATCGATCTTGACAAAG GCAATATCGTTCTGATCGCACTCATCGTCGATGTTTTCCAGTTCTGCGAG GATTTTCTGTGATTTCTTTTGGTCTTTGTCGTCTGCGAAGATGATTTCAT AGGATAATTTAACAATTGTCTGCAACGCGTTGGAGGCTATGTAATTAACT GATCAACAAACTGCTGTTTTGCTCAACTTGTAACGTGAAACCTACAATCT ACACTGTTCTAACGGTCTTTGCAGAGATATACCTTCACGAAAAGGGGTCT ACTAGTTATTATTGTTTAGTTTTAAGTTAATACTTTTTCCAAGCGCCATT GAAAATTACTACTAGAAAGCGGGGTTAATGTTACGATTGCAGTCACCCCA GAAGTACAACACCAATTCAACTGTACAATATCAACAGAGATAGGGAGTCG AGTGCGCAAGCGTCCTGGCACAAAGTCGCAATGGGGCCCTGAAATAACTT ACAGAAAAGAACAGCAACATGGGGCATTTTCTCAATGATTAAGTCCAACA TTTCGTCGGTGATGTCCTCGATTTGATCGGAACTCGTTTGGTCTGTTAGC CATTTCAGAAGCTTCTCCTCGTCCTCCAGATTGCCCTCGTAAATAGTTGG AATGCCTTTTTCAAAGTATATCAGTTTAGGAACTTTATTGATGCCATATT CAACGGCCTCCTCGGGATTGTCGATCTTCACGAAAGTAATGCCCAATGCG TCGCACTCGTCGTCAATGTTCTCCAGCTCCTCGAGCACTTTCTGGGACTT CTTGTCGTTGTTGTCGTCTGGAAAACAGCTTATGAGCAAAACGTGTTCGC CGCCTTAGGCGCAATGGGTACGGGGTTTCAATATTTACAGAACAGCACGG CAATGACGCGTCCTTCTTTGATCATTGTATCGAGCATTTCGTCGGTGACG TCCTCGATCTCATCCCGTTCCAACTGTCCCAACAACCATTTCAGAATCTG CTCCTCGTCCATGAGATCGCCGTCGTACACATTTGGAATTTCTTTTTCAA AGTAAACAATGGCCGGAATCTGCAGGTCGAATTATGTTATTTGTGTCAAA GACGTTTCAATTGCCAGCTCGCTGGAATCCTACCGAATCGATTCCGTAAT CGGCTGCCGCCTTGGCATCGTCGATTTTCACAAACTGAATGCCATGCTTG TCGCAGTCGTCGTCGATTTGCTCTAGCTCCTCTAACACGGTCATCGAGTC GTCGTTTCCATGATCATCTGCAGATTAATGTCAGTCGGTTATCGCGTGTC GCGCCTCGCGGAAATTCTCATCTACATACAAAACAGCACAACCAGATTGT CGATATTGCTGATCAGCGTCGACAGAGTCTTCGAAGTGACGTCTTCAATC ACATCATCTTCATCGCCCGTCGACTTATTCTGCACCAACCATTCCAAGAC GTCCTCCTCCCGCTGAAGTTCACCTGGAGACACAGTTCGATATTAGCGAA ATGAATACCGAGCTCAGCATGGGATTGATGTGTGTTGGTCTGAATTCGAT TTGAGTGGTGGGTGGTGCAGGTTTCAAGAGAATGTGGTTTGGGATGGAGG TACCTTCGTATATGATCGGAGTCTGGTGGCGGTAATAGACCAAGGCTGGC AGATTGCCTAGATTGTATTCGTCGGCCAAGGCCTCGTCGTGTATCTTCAC AAACCCGATGCCCAGCTGGTCAGCTTCGTCGTCGATATTCTCCAGCTCCT GCAAGGCCTTGGCGCACTTGCGGCATTGCTGTTTGTCTGGCAGTCGCGAT CGCGGATTTGGTGGATTGTTTCATAGAATCAGGCAAACAATAGATAATTA GGGCCGTCTGGCAGAGGGGTAACGTCTTGGTAAGCAAGGAGTAGAGCACA GAACATCAGGGTGGGCTCTGGTGTTGGGTATTATAATACACGGATAGGAA GAACATTCAGGTATTATATTTCGTGCGGCCGTAAGTTATTCTGCGGGGTG TTATTGTGGAGCCATCTCAGACATATGTGAGTGCATGCAAGGGCCATGGA GTTCCACTTAACGCTACGGTTACCCAATCTTTCCCAGGCGATTCGTTTAT TTACACAATTTGTTTACAACATCCCTATCAGTCTGCGTGCAACCTGTTGC AATGTGCTTGTCTTGGTAAAGGAAATACATATGTACATATCAGAGTGGTT TAATAAAAGAGGAATGGTTTTTTCTGAAAGCTCTCTCCTTGCATTTACCT TTTCCTCTATTTCTTTGTGTTGGGCTTACCACATTCGTAAATGTGTTTTC GGCAAGCTTTCGCTTCTCTGGCCGACGCTGCGTATACGTAATATTTATTT CTGTTGCTTCGTCGGTGAACTTGTCAGTGTGATAGCTGCCTGGCCACATG TTTATGGCAACCTATCACCGCATCTTTCCGAATGCAGTTAGCCGGCGGTA GTGCCCAGAATGACACGCCTTCAAAAGCCATTACCCCGACCAAAATACAT ACGTATGTCTCTAATTTCCCCGATCGACGCGACTCATTCCCAGCAGCTGT TTGAGTGGGTGTCGCCAAGGTGACAAGGCCAACGCACACACTCGCTCGCG AAAATGTCTCATAATTTACTGCACAATGCACAATGATGGCAAAACATACA TATGTACCCACATATGTGCTAAATCGAGAAAATCAGACGTGTTTGCGAGC CTTCAACTTTCTCCCTGACGGACTGACCAATTTTTGGCCCTGCCGCAGAC ATGGGCAAATGTTGCACTTAACTAAAAATAGTGCAAGTCAGTCGGGAAAG AGCCACGCACACACAGTTATAGATCTGCAGTGGGACGGACGGATACGAAT ATATCGGTATAGGTATTCGTATATTATGTAAACCAGCATTTGGCTGCGAC AACTGAAGATCTGCCCATAACCATGCACTGCCGGCTCGTGTGCGCCATGT TGATGTATTGCTGAATGCAAGAGCAATTAAAAGCGCTGTCTGTCTGCAGC CCCTGATGGATTCAAACTCAATTGCGGGGGGATGGCCGGGGGCGCAGTGA AGGGGGCGGGCGGGACAATGGGCCACGATTTCTTGTCTTGGGTCACCTAC ATGCTGTTCGCATCTATGCATACATACATGCATCTATGCATCTATGCATC TTGCATTAGGATAAGCGTTTTGTTTTTTGTATGCTGTCTGCGTTTGATAA AAATACCTATGGATAGTGTAGCGGATGCTACAGAAATGTTCTTGTGAATT CACACACTTGCCATGTGAGTGTGGCTATAGTTAGTTGTTTCAGAATTAAG CAAAAATAACAGCAGCAGCAAGAACAGCGAAAAATCATTTTGTTGGCCCA CCAACTGCTTGAGTTTTCTATTTTTAACACTAAAATTGTAGGTGGCTGTG TCGGAAAGAGACGGATGGCCACGAATACTTTGTTGTTGGCCAACACATCA CCGTGTGTGTATGTATGTACGTTGTACATATATATGTACATATGTATGCC ACATCTGCAAGTATTGAATTTATGCTTTTTTATAGGTAAATTCCTTCCTT TCTCCAAAATTCACACAAATTCGAATATCGTCTCCGGGGAAAATCTCCCA CGCTCGACAATTTCTATATTGTGATCCAACTTCAATAGATCAGTGCGAAT CCCCAATTTTCATCCTGCTATCCACCGGCTTGTCCAAATCACAGGGTTAG GGATTGGGTTGTGATTCGTGGTGTGGCGGATGAGAAGTTTTGTGGGGGGG GGGTTATAGAGAAGAAGACGTCGTGCCGACAAAAACATAATCTGGCGCCG AGCCCAGACATTCATCTGCATTGCTTCTGTTGTTGTAATGTTTATTATTA TACGTATACGTAATATGTGTGTCTGCCTTGGTCGATAGCGAACGCGAAAA TGAGAGATCTTGTTTTTTTAAAAAATTACTAAGAATTACTACTCGTACAG TGGTGATTGTATATATTTAAGGTTGTGTCCTTTACCTAGGCCATCGACGT TAACTGGTCAGCAGGAGAGCTTAAGTAAAGATTGAATAAAATTGGTTTGG CCCACGCTAATTGGTGCATTGTAAACTGGAATCTGAATCCCTAGCGTTCG ATTTTAGCAAGCACCAACACACACTGGATTTTTCGGTTATTTGGGTTATG CAGTCAATAAGGAAATACATATTTACATATCGAATTGCGGGCATTGCGGA ATAATCTTTTCATTTCAACTTTGGTATTACTGGAATCAGGAAAATTATGG TGGAATAAGGGTAAAACATTGTCAATGAATTAATTTGGGGGAAACAAAGT TTCAAAGTAGGTAATTATAAGGAGAGTGCAAGATAGAAGGTTCCCAGTAC TGTTCACGGAAAACTTACCCATAACCCTGGGCGGGCATGTTTCATGATCT GGACCTGCAGTCGTTTGATAGAATAGATATTGGATTGATAAATTGTCCTT TTGCATTTTGGCTCAAAGAGGGTTCGAAACACCGCCGGAAGAGAAATTAT TATTATATATAGATAGCTATATTAAATGTTAAGTATGCCGCCACTTAGCT TCGGTTAGTTACAAGTAGTATACGTATTTATAGATAGAGTACAGACATAC GCAAAAGATATTGATTTATGGAATAGAATGTACAGAATAGGTAGTTTTGA AAGTAGTTCTAGTACCTAGCTGTATGATTTTTAGTCACAAGAGAGCTAAA CTGTTTGTGTTCGCTAAAAACTGCAACTGCTTTGAAAAAGAATATCATCA TTTCAAGTGTCCGACACTAGAGTGTTCGGAGTGCTAAACGTTTGAAGAAC TATGTATGTGCTACGGTTAAGTCATTCACACTTACAGAACAGAACGGCTA CGAAGTCGGTGTCCTCGATGATCTTCTGCAATATCTTGGCATTGACCTCC TCGATGCGATCGGGCAAGTCCATGGCCTCCAAGGAGGTGAGGAAATCGAG CACTCCTTCCTCGTCCATGAGATCCCCATCATATATGATGGGCTCCTTTT CCCTGCGGTTTTCGAGATATGGATTCGATTCGATTAGGTCTTGTGTCTTG TTTGTGGTGGGGGAATTACCTACCTGAAGTAGGTGAGGGCGGGGAAGTTC TTGATGCCATACTGTTTGGCTAGTCGTTTGTCGTTGATTTTCACGAAGTC CACACCGAAGGAGTCGGTGTCATCGTCGATTTTCTCGAGTTCCGCTAAAA CCTTATCACAGGTCACGCAGCTTCGCGCATCTGAAATCGTAGAAGCCGAG CGTGTGAGTACTAAAGATCGATTATATGTAGATACCGGCAGCGATTGACA GTCGGCAACTGCTGCATGTGACGCCACAAGAGACCATAACTAAATTCCCA TTCGAATTGAAAGCCCAAAGCCCAAAGCCCTGGCAGAAGTGGAGCCAAAT GCCGCAAAGATTATTCATTCCTATATAGTAGATGCAGGATGCATCATCGG ACCGCGCAATCGAAAATAAGCCTGAATGAATGAATGAAATGACAGCAGCG CCAGGCCAATTCTGTGCTATTAATGCGGCAGCAACTGCCAACAAATATGC TGAAATTCTAAATTAATTCATAAAATTCATGCGGCCACTATTAGGGAAAT GAATTGCAGCCCACAAAAGACCACCGTTGGCCCACGTCTCTACAAACGTT CTGGTTGGTTAAACGGCAGACCAGACTGCAAAATCGGAATCATTAATACA TCGCCGAGTAAACAGCCATTTCGATTGTTTGGCAATCCGTTCAAAACAAT CTTTCACTGCTTGGAAAGTAATCGCGAGTTGGCCGAATACCCCCCCCCCC TGCCTACTCCATACTCCTAATGCTGTTATTTACGGGCTCCAACACTAAGG TGTTTCCTGTGTACACCAGGTGCTTTGGAAAATCCACTGCAGGATGTTTG ATTTAAAATCATCAGAGTGCTATCGCATGCAGTGCAATAACATAAATAGC GTTCACTTGAAATAATAAACACATTTAGCTTATCGATAGAATTCGTTTAC ATATTGAACTATCTGCGATTTAATTGCCAAAACTATTCAATGCTCTGCCA TTTGCGTAGATATTCCATGATTATTTCGATTGTCGGCCAGCGTCATTGGG CCTGAGGCTTTTGGACTTAAAATATTTTCATTGTCAACAATTATTTTTGG AATTGCCGCCAATGCTAATGAAACACATCGTGAGGTATATGTACATATAC ATATAAAGGAGAATATTACAATCCGAAGATCACTTTCGTGTTTATTAACT TTGACATTGGGGAACAGCGCGCAAATGCCCAATCTATATTTAAACTGATT AAAGAGATTTAATAAATAAGCCATTCTTTCACGCGAACGGTAACCATTTT TTTTTTTTTTTTTTTTTTGGTTACCCAAAAACAGGTCACCAATGGGACCC ACTGGACAAGGGGATTGAAAATAAATTTAAAAGGGCAGGAAATCTGTTGG CAACTGCTGGAAGGAAATTAAATTCTGCTTCATAGGTATGTAGGTATATT TTGTGCCAAAAGTTTGCGCCAAAATAGACTAAAAAACCGAAAATATAAAA AGCTGCAAAGACGATTTCTCACAGCCAAGAGAGATTTCTCTACTCATAAA CAGATCGCAAAGATAGCGCAGAAATGAAAAAAATATAGAAAAGGGAAGGC AGCACAGACTACTGGCAACTCGGGGAGGAAATGAAGAAATAGAAAAAAAA TAAAAAATTAACCGAATGAAAATCGCGGACATTTCGAGCAACGAATTTTT CACATATTTTCATTTGTATGTGAATTTTTAGAATTTTCACTAGCGAAAAT TTATATAATATGGCTTCTGTTACTATTTCGAGTCCGGTACGGTCCGGTCT GACGATAAATGAGCGGTGCCCGGACGACCCCGAGAGCACTGGCATAACCA CCCTCCCACTTACACCAGAAAACGGCCACGTAATCCTTGTCGGCCAGGAG CTTCTCCAGCTGCTTGGCATTGACCTCCTCGATGACGGCCTCCGGCTCCG GAGGCGCCACTGGCTGCGAGCCCTTCTTGTTGTTGTTGTTGCCTGCACCA CTCACATGTCCGGGAAAACTCAGGGCCAGCAGAGCACACACGAGCAGCGA GAGAGTCTTGAGGCGGGTGAAAGTCATCCTGCGATCGGTTACGGTTCTGA TGTGCTTTAGGCCCTTAACGCGAACATGCGTGCGCGTGTCTGCTCGTTTT GGTGTGTTCTACAGTTTATAGTGTTATAATTGTATAATTGATTCGTTCTC GTCGTTTGGGGTCTTTCGTTATTAAAATTTGTATTCCTTTGAGAATCGGT CACTATTTTTAGTTGATAATGGTGTTTCTTCTTTCGCAATTTATTTTATG TATAACAACTTTTTGTTCACTGATACATATATACGGGGTTCGTATATGCA CAGGCGAGATATATGTGGGGTATATACGAGAATAATTAGATTATATATGT GGTTTCTTGCTTCTATTAATTGAACGTTTTCCGCGGACTGTACTCTTTGC TCTTCAGATTTTGTTCCACTCCGTGCAGAGGTCCGCTCGCAACTGAAATT ATTTTGGTGGAATCTCGGTGCCATTCAAGAGGCCTTGCCCGAGCTTTAGG GATCGGGATCGTGGACTTCGTGCTTTGGCGCAGCTTTTCCGCTCCCCCGA AAAGCTTTCGCGTCGAGCACAGGAGCGCCAATCGAGTGAGCAGTGTGGTG AAATCAGGCAAAGAGCAAGAGTTTCCCTTTTGAATTGCAGTTCTCTGTTT ATGCATTCGGTGCAAACAAGAAAGTGACTACGAATAGTCCTATAAAAACA AACTCGGAGAATCGCTTTCATTATGCGCTACAACAATTCACAGTACTTTG TATTCCCCATTTTCCCTTTGGTAAACACTTTTAACAATGTGTTTCGAGCT AACATTTTGTCAACGTTATGCTTAGTCTAAAATAGAAAGGATTAAACTTC CCTTTGCTAAGAGACATAACGTGACATTGTTGAATCTTTAAGTTTTATAG TTCCAAAAATCTATGCGTTTATAGAGATAGGAGGACATGAACAGATCGAA TCGGTTAATGATCCTCAATAAGAATAAATGTAAATTCTAGGGACGGAAAC GTTTCCTTCCAGCAGTCAACTATTATGTAAAAATCAACAAATATACCAAA TTTTGAATAGGATCTAGAGAATGATTTAAAGTTACTGTTAAATAAGCCTT CTCGAAAACTGTTGGTCATCGAAAACATGGAAGATGAGACCGGATTTACA AGTGGTTTTCTGTCCTTAATAGCTTTATTTGTATTGATTAATGTAAGAAT TCTCAAATTCTAAAGATTGGCATCAAAACCTGATCCAACTAATAATGAAT CCTTTTCAACTGGTTATCAACTATGACCTTTGTTAACGTCAAACCACCCT CGCGAATTATTTGGAGTTCGTTTCTGCAACACACACAAAAATGAAAGTCT CGGTATCTTGGTACCTGTATTAATGTTATGGAGGTTTATTCAATATTTTA CAATAAAGCTAGGCAAGTGATAAATCAGAAATGTTTTAATCAATTCGGAT ATGTTCAAAAAATCTAGTGATGCAGTTGCACTTTTTCTCGGAGACTCCCT TGTTTATAATTTGCAGGACAAATAAACAAAAATAATACAGCCTATTTTGG GCTTTCAAACAAACAACATGGCCGCCATTTGGATTTGAATAGCTATCGAT AGGTGCCGTCGGCCAGCTGACAATCCATCCACTGCCTATCGATAATATCT AGCTGAGCAAGATGTACGGATTTGTGAGCACACACTTTAGTTTTTCGTTA GGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGC AAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATA CCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGAC CAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCG ATCTGTGACGCGGTTTAAACCAAGGTAACTCCGCTATCCATGAATAAAAT CAGCTCTTCCCACGGGTGCTTCCGCCATGGGGCCACAGTGCGGGTCCTGT GGCCAATTCACCTTGAACCCAGTATTGCAGAAGGGGCCGCATACCAAGTC CAATTCCCTGCGCTTGTGTGTATACCTGCGCCTCTTCCGCATGTGTGTGC ATAAACATTGACGCCCACCCGCCCGATAAACAGCTGTTAGACCGATTGCC GTCCGCTTCCCCAGATTTCCAAGGCGGTCGAGGCGGAAAAGGGGAAGGCC CCTTATGAGCGTAGGCTTGACGGGGGCGGGCCCGTGTTTGTGGCAAGGCG AAGGTGAAAGTCATCAGCTGATATGGGCCAGCCTGCTAAACCCGTTATGC AGAGCAGCTGTTCGACGCCAACTTCATATGTGGGACAAAATCCCAGCCGC GAACTCACATACTGGGTTCCCCAGTTATATCCGGATAGCGGGCACCTCGC TATCGCAGGCCGATATAAATTAGAGGCTTTCGCGCTGCAGATGTGAGGCC TAATTGAAGATTTCTTTGTTCGTTCGCAGGCTGCACGACACTTCGAGGAC TTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGTAAGC GAACAATGCTTCATTACTCTCTCCCTCTCCGGACTATCAAATTATCCGCT GTTGAATTTTTGTAGGTACCAGAAGAGAATCGGCACCTATGACAAGCAAG AATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTC AATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGT GCGAGGTGTGTTTAACCTGACTGACCCCAAATAGTGCCCATAATTGAAAC ACATTTTTTAGGTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTAC TCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTAT GCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCT TGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACA GCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTG CTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGA GTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCC TAAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACC GCCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATC TGCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGAC GTCGCAAGAAGATTGTGCGGTAAGAACGAAGCTCTTTTCGGAACCAAATA TTGAATTCTTTTTTTAGAGTTCGACAAGTGGAGGCTGACTTGTCCCAGGC CAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATCG AAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTGT GCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTAT CAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGCC CACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAGA AAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACTG GCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCGT GCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGAA AGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGGA GGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGACA ACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGCT CCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTGT GACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAATG AATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACATT ATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCAC CGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCTG ATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGAA GATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATAG CAGCCTCGACCGTAGTATGTATTACCAACCAAATTTGCATCTTCGTTCAC GCTATAACATTGAACTTATAAAGTTAGCTGCACCATTTGGGATCAGCGAG ATGCCAAAAAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATC GAACGCGTGGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGT GGTCTTCTCTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCG AGGTATGTTGCCGGGAAGGTTTTGGTGGAGGAGACTACTTATTACTGGTC AAATGCACTCAGGTCACACTCGGGAGCGATGCAGAGAAGGCCAGTGAGAT TAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCATCGGCATCGC TCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTGGGAGCGCATG GTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCCTCATACTGTT CATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGCTTCCTTTACG CCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCGAAAGTCAAAT CTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGACCTGGCTGAG CGTGAGGTCGTATTTGAAGGTAAATATAAACATCCGCGTATTTCTTGATC AAAGGCACTGAGTTGCATTCCCCATAGAAACGCGGACCCCAGCGATCGGT GGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCT TCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTT ACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCG CTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGG TGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCA AAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGC CGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTG CCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTA TCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAAT CAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTA CAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTA GTTAAGTGAATAAATTTAAGCGAGCCAATGTTTATGCTTGTCACGTGATT GTTTAGCTACGTTAACAAGCCCACTAACGACTACGTAAACCAACAGAAAT TAGTATTTACCTACTTACCTTCTAGAGCGACCTGCACAATCACAAATCAT GTTTAGGCAAATTGTGCAATGCAATGAATCGCATGAAAGTTCATAGAACT TTAAGCCTAAAATCAGTGCACCTATTGTAGTTGGCTGTTCATTCTGTTAC AGTCCCAAGTTAAATTCCTAAGGCGGTCTCAGCTAGTGTTGCAATTAATA AATGTTAGTAAACTATAATAAAAATCTCGTTTAAAATAATATGCTTTGTC TATCTTACTAGTATATACCAATTGGATGTTTATAGCTGTGAAAGCAACAA ATTGGTTCTACCTTTTTCTTCATTGGATAGAAAGATCTGATCTAGATGTT AATCTTTAATCTTTGTTGAAAACTATATCCTTTTTTCTTTCTGTGCAACA CCCGTCTGCTCTTCGTTAATCGATAGTTGGCTCAATAGCGATCGACCAGC TGTTGCTGTTATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTC GCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACC CCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCT GCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGC ATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAGGTGCATATAAACAGG CTGTATTTATGTTTACATACCAGCTAAAGTCCAAGCTTTTTTAGGAAAAT GCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCA GGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGG GTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCG CCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGA GGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGGGT AGGTCTGAAAAATCCAAGTTGATCGAAGTTCCACATCAGAACTTTTAGCG CTTGCATAGCACATTCAGTCTGCAGAAGACAAGGTTACGCGTCATTAGGG TTAATTAGGTCGTAGATTATATTTAGATTATAATTATAGATCGGCATAAA TAGCCGATCCGATCTAGCCGTGCCCCCAGTCTGTCTGTTCGTATAAACGT AACGATCTCCGGAACTATTCAAGATATTTTGTGAGTCTCATAGTGAAGGT GGAAAATAAATAAATTGTGTACGAAATTTTTTAAATTATCAAAAATAATA TGCAATTTTCATTACAGAACTGAGTGTTTGGTGGTGGCCAACGATGCCAC TGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCG CTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATTTACCTTGTGGAC TCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTTTCCAGACAAACT GCACTTCGGACGCATCTTCTACAACCAGGCAAACATGTCGGCCCAGGGAA TTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCCGGAGGAGCTTAC GTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAAGCAGGGAACTAT ATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTGGAGAGGAAGTGT CTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAGACTTCTGGGGTC ACCGACCACTATGCCTTAGACGACGAACACGCCTTGTATCTGGCCCGCCA GATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGTACAACGATCAGC TGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACTCCGCCGTCTGCC GTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGGCATCGTAGGTCC CAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTGCGCGCATCGTCG ACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGTGAGACTTTGGTG TGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAATAGTCGGAAACAA TGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCCACTTCATTCAGT TGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAAAATATTACTGGT AAGTTGATATGTGGAGTGGCTGGGCGATTAAATAATGATATCGATCTATG TAGGCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGCCAAAAAC GGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCAAGTTCAC GGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATGTGCGGTC GGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCGCATCTCA GTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGA TCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGC TGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTAC AGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCG TCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGG AGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGA AATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACT GTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTG ATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAA CTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTT ATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACAC ACATTTAAATGTATAATGTATAACAAAACAATTTATTTTATTAGTATTAA GGGTTGTAAGAGTAAAACCAGTAAGATTGACACAGCTGGGATCAAACAAA GCCGCCTATCTAGTGCATACCACTGTTACACTTTTAGTGGTGTTCAATAT AAATATTTTCTTCTGAAAATAAATACGTTTTATTGCTAAATTTCATGCTG TCGTACATTTATAATTGTATTTTTTAAAAATAACAGTCGATATCGCTATA TAGTGGACCACGGACTATCGTTCATCTCTAGCGCCTATCGATAGACCTCC ATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCC TAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTC CTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAAC GACCAACTGATTAGGTGAGTTTATCACAGGATCCCACGATTGACCGGTTG AATGTCCACTGCATCCACAGTGTGAGTGAGTCAGTGAGTGAGTCTCTCTC CGTTTACATATATGTGTGTGTGTGTGTGCGGCTCCTCAACTTATTCGCAA AAAAGAAAAGAAGAAATCGCAAACCTAGAAGTAGCGTCAGCAGAAAAGAA AGTTCATCGGTATGTGGCGATTTAAAATAACTCTGCCGAAAACTTCAAGT GCACACTTGGCCGAATAAATAGCTGTACATCGCGGAGCCTGCGTGCGCCT GTGTGCGTGCCTGTGCGTGTGCATTGTATATTTAAATGTCGCCTGCTGCT GCTTCGCTTCCTCCTCCAAAAATAAAATTCCCTATCCTGGTTCCTTGCAA GTGTGAGTGACTATCATCTCGGCGAGTGTGTGTGTGTGTGCGTGCGTTTG TTTGTTCTTGCCACAGCCGCAGAAAGAGGCCGCAAAAATTCCGGTGCAGT GTACATATATATGGTGGAAGGTGCCCAACCCCTACTACCTCGTTTCCGAT GCTCGCGACGTCTGGAAAAGCGTGGAAAACATATTGCCTGAGTTTAAGCC ATCGTTTCGATGACGTCATTCTTCTGCGGCTTATCTGTCAAGCCCCCGCA TTTCTTCAGATGGCATGTCTGTGTGTGTGAGCTGTCCAGTTACCAATGAT TCTCGGACTTGTTTTGTTTTCCTTTAGCTCAAGTTACTATTTTTATTGGC TTAATTAAAATGGGCTCCGCCGACGCAGCTTTTTGGCCTTCCCGATGCTG CTCTACTAGAATGCCGGTTTCTTTTCGATTTCCACTCAAAAACACTGGGA GCACTCACTCACAGTTTCGAGCGGATTTGGCTCAATAGCATCGGAATGTT TATTTGTTGCTCAAACAGCTTATTGTTGTTGCCGCACTTCCACTCTCAGC AGATTGTATCACACCTGGGGATGTGGACTAACACATGTCCAAATATGATT CAAATATGGAAGTCTCTCCAAGTGGGCTAGAAATGAAAACCCCTGCTAGT GGCCCTGCTTCGCTCCTCTTTTCTGTTTCCCTGGTTCTGCTTAATTAGTT CGCTTTCAACTTCCGCTGCACGCGCCCACATCCACACTGACTTATCGACA GCCACAACAAACTACACTGGCCAAAAAAAAAAAAAACCATCGCCTGGGTC ATCAATTCCGCAGTTTCTCGTCTCCAAATGTCACACATCAGCGACTTACC AACTAGGAATTTTGTGGATATAATGATCTCCGATGAGTTATCAAGCATAT GACTCAATAGCACTCAAAATACGAATCTAAACTGCAACTCATTTGTTTTC CCCATCTTATGGATGCAAATAAGCATTCGTATCAGTTGACTTTAATGCAA GGAACTTTTTGAAACAGTCACTGATTTAAGAGGGATTTGACTGGAAAAAT ATAGCGCATTTGTTTGAAATTTCTTTAGTAGTTAGTTTTAAACTACAAGG TTTATTTGAAATGATAAGTTTTTACTATAAAAATTGTATTTCAAATAGAA TCTTGATTTTATAAATAGCTTTACTTTCCAGAAACTTAAATGTATTATGA TTATTGACTAATGTTATTTATTTAGAGTTTTTTGAGTCATCGAATTTCAG TCTTATCCACTTATTGGAAAATAACAAACCGGACAGTCTAAAAGACGACT GATAAAAATGCGACTAATATAGTAATATAGTAATAATAAATAGTGCAAAC TAATATAGTGTAATATATTACATGCAGGGGAAATATGCAATTGGAATGCG TAGTTTTTTGAGATAGAACAGAAAGCATATGATTTCTTCATAGAAAACAT TATTCCTCTGTGTAGTAATCCCAACTTGTATTTGGGACACTGCTATTGTT GTGCCTTCTCTGGCGGGGGCACTTAAATCAATAAACGAGCAGCAAATCGC TCCGCATTTGAATTGAAGTTTCGCCCTTTCGGGTCAATGCACCGTACACT CGCGCAGCGAAAAGGTGGAGAGTCGGAGTTTTACGGAAACACCGAAAGGC CCACGGCCGACGTGAGTCAGTGTATTTATAGGCCGGCTCCCAAATGCCGG CTAATTCTTTATCTCATCTGGCCCACGTCAGATGGCCCATGCCCATGCTC TATGTTCCTGCTGGCCAGGCTGACATTGATAATGCCAATGACGCGCTCCA TGAGTAATCTCCATCTTCGCGTCGCAACGAAGCGGATCGATATCGCCGCA TTGTAGCGGCGAACAGTCCAAGTTCATTGTTCGCCCGTTCCAGTATCCGC GGAGCATTTTCTTTCGTTCGATCGCCTTTTATGCTCTCGTAAGTGTAGAG ATGGGTCTGAAGAGGATTTATCTTCTGAAGTTCAGAAAAAGTGCTCTTGC GACATATCCAAATCCATATCTTGAACATTGACTAAAGCAAAGATACTGGT TACTTGTAAGGATAAAATTGTTTGGGGTCATGAAACGCAGTAAATCAGTG CATATGTACATATGGCACTCTGCCACTCTGTGTCTTTACGAATAGTTATG AGTGATTTTAAATATGGAATTTGTCCAGTGTGCGATTTTGGTTTCCGCAT TACGTATATTTTGAAAAATAACAGGATGGCGACTAAGTGGTCAAAAAACA GGCCTTGAGAATGTTGCTTTTCAGTAGAGATTTCAGAGGTAGATTAGTTT GTATAAGTCCTGCCAGTTGGTCACAGAGCGTAAAACGAAGTAAAAGAAAA ACGAAAGTAATTTGTACAGTTCGATTTCGTTTTGCAAATTGAGTTTTATC AAGAAAGGTTAGTTTATCGGAAATCCAGCCAGAAGTACGTCGGATATACA GAGGTGGTAAGTGCATCGGGCAGATTGGTATGCTGAATCCGGGAAGTAAG ACAATTAGCTTTTGGTGTGGAAATGCCTATTTGTGGTTCGGTCTGTTCGG TCCAGAGCTAACTAGCCAAACTACTTTCGAGGAACAAATTCTGCAGATTG TGGAATGAGTGAGCAACGGTAACATGTCCAATAACAATCATTTGGCGTTC CCTGTTGCCGTTTGCTTTGCTGATGACTATCGTGATCTTGATATTGAGCA CGCACATGGGACACGCTTCAATGCACCCCGAGCTAAAACAATTATTAGCC GCCGCAATTAAGAGCCGTTCATGGCGCTAGCACTCCCACACGGACTGCAT GTGGAGCCGCCACTGTGCAGTTACCAACTAACCAGCCTTTTGCATCTTCG TTTCAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAAC GTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCT AGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGC TCTGCACAGGTAAGTGGGCTTGACTCGTCTACAAAGTGCTGGGATCAACC TACGCTTCCACTTCTAGGTGCAGCTTACTGTCAGTTCATGGACATGCTGT TTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAG CACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGAT GTCTGTGGATAAGGTACATATGCCCGCTTGCTTACATTACTTTTCTATTT TTCGAACCTTTATTTAATTTTGACACACAAATCCACCCGATCCGAAGAAT GTAGAGTGGACATGGGCACGGTACAGTGGAAGCGCTTAAAGCGTCGCTAA AAGCATATGTCCACTGTACCAATATACTCTTGTATGTTGTGACTAACTAC GATTTCCGTTACAAATCAACTTCACGACTACGCAACCACCGACAACCACA GATCATTCCAGTTGATAAACTGATTAAGGGACGCTTTCAAGACAACTTTG AGTTCCTTCAATGGTTTAAAAAATTCTTCGACGCCAATTACGACGGTCGC GAGTACGACCCCGTGGCTCAGCGGGGCGGAGTCAAGCTGGGCAATGGCAA CGGACACGGCAGCAACGGAGGCAGTGGCGTGGGCAGCAGCAACAACGATC TCCATCTGATGCACCGGCGACCATTGCAGGCTCCAGCTTCTGGCGGACGA ATGCCAGCACGGGTCATCGCTTCAACTGGTACGGTTCTGTCGAAGCTACG AACTCCGGTGTGGAAGAGCCATTTGCTTGCCATTTCATTTGAGTTGCGAA GCGAACGAACGTGAAGCACGCAGCGGAACTAGGCAAAACTGGGATGCCAC ACAACACCACACAAAACTTCACCAACCCCACTGGCCTTGAGCTGCTGGCG CACCAAGTAATACACAAAATGCACACACATTCAGTCGCATCAAAGCACAC AGCACACATGTTGGAGGATCTGTTGTTGTCCCACATCCAACCCACTAACT CCTCTTCATCCCCGTACAGTGATGGGAAATACCCAAATATTTGTATTTAT ATAGATCCGCGACATGGACAATACTTTTGAAGCCATAATTACTTAGGCAT ATGTGGGCGGATTTCCAACTGCAAAGTGTACAAGATTTCTTTATTACAAG GTTAAACGCAAATAATAGTTTAGATCTTATCTTTGGAAGTGGCTAAGTCT GCGATCAATTTAACTGAAAATCCATCCCCATCATTGCAAAGTTATTATTT ATACACATCTTTTTTATCTGGTGCTTTGGCTGGCCAAAGAGTTCTGTTTT CCAAATTCATACTGTATGTTTGTTTAATCTTTGTTCCCATTGCATTTGGA TTCACCACACGCTCTCTCACCTGTTTGCATATCTCTCGCCCATTTTACTT TTAGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATT TCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGC AGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGG ATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCA GCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCT GCAGTGAAGCCCAGTATGTTTTGGTTTGGTTCCCAATTGAATCCTTCTAT CGCTATCTCTTCTTTCATTATCGTACGCACTATCCACATGATCAGACAAT TGTACATATCGCATGCCCAGGTCCATGTAGATGTTGCACATCCTCCAAGT AAACACAAAAGCACGAATAGAAGACAAATGCTGTCTGTGCTTCACGTTTG TTGATTCCTTATGCTTTTATACATACCTCCGACCTGGATGTTCGCATACT AAACTCAATCGCCTTGCCCATTCCAGCAGTATCCAAGGTGCTGCCGCGCA CGAACAACGCAGCCCCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACG GGCACGGTCAAGAAGAACGACGTGAGCAATTCGGTCAACAATCAACAAAT AGAAGAGATGTCAAATCAGGTGGGTCAAGATCAAGAAAATGAGAAAAAAA CCGGTACTAATATTATGGATCAGGTGATGGATATGCGCATAAACCTGGAG GGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGA AATTCTGTAAGTAATGAAATCAACAGGTTGAATTAAGAACGCCATGCCTA CCTGCTATTATATTTCTAGTTGCCAAGAAGCCGATGACGCCGAGGCGCAT CCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTAGGACA AGTCTGTACTCTTTTTACCCGGCCCTGCAATCGCTTAGACTTATATTTTC TATTTGCAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGA GGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGC ATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTT ATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAA CAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCC ACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCG TCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCAC GATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATA TTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCT AATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACA GACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGA TTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCT ATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGAC TTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAAC GGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAA AATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTAT ATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGA ACGTCTAAACACAACTTTTTGATTTCCGGCTTTCACATTACATCACTACG CACGGACAAGTTACTCCAAGCGGAAACTTTCACCCCTCCATTTCTCTTCT CTGATCATTGTAAATAATTTGTTAACACACCACACCACTCACATGATAGT CAACCTGTCCTTTCGACAGACACAAGTAAATGTATGATTATGCTCACACA CCACAGCATCGAGTGTGCCACCCACGCCATGATCTATAACCTAATTCTAG AATAAAAACATGTGTTGCTTGATTCAAAATTAATGCATTTCTCTTTTCGC ACACGGGCAGGGCCCTACAACCAATCCTAAATCTATTTGACGGCGCTCTG GATGTGTGGCTGCTTGTGGGTGCCGTCACAGAAGGGTCTGTGGGTGGTCT GTTTGCAGTTGCAGAGCCAGTAGTCTCCCGACTTCTCCACCTTGAACCGA ATGGGCCTGGAAAGCACAGGGGTATTACTTCGTCGCATAGCTCTGGCTCG AGCACCTATGTACATACCTCTGCTTGATCTTCAGGAACTCGTTCTTGTGC ATTCCATCGCAGAGGGGCTGAGACTTGGACTTGCCGCACAGGCACCAGCT GTATGTTTTATCTGTTGGAATCGCGAGTTGTGGTTATGTAAATACTTGTT CTCTGCGCACCGATACGATGCGATTTCTCAATAATACCTTTGTCCAGGTG GATCTTGAAGGGGCGCTTGTCGAAGATCGTACCGTTCTCCTTTTGCAGAA CGGCCGTTTGCTTATCCTCGAGCAGGTTACTGGGAATTGTTTTGGCCGAG TCCACCGGTTTTGCGCTGGAACTGTAGCATGCCTGCATGGGAGTAATGCC TTGAAATCAGGGGGTGATCTATCTTGGCTATGGGGGATGCCTACCTTGAG CAACCAGGATGCCCCCAGGTTCCGTCTTAGTATCATTGACATTCTAACGC TAATTTATTTTTGTTCTCTTTATTTAAGCTGATGATTGCAGTGTCGAAAG TATCGATATGTTGTCATCGGTGGTGATGGTGTTGCAAGGTCGTACCACTA CTTTTACCAAGCTCAAATGGGCTCATTGAGAGTATGGATAGATACTGCTT TAATTTACATCTAAAAGTTCACAAATATATGTCTCTTCTGGTAGCGAGAA AGAAAAAATGTTGCAGATTTTCAAACTGGGCAGTGCTGCCAGACCGCCCC AGCTGAATGCACAGTGGTGCAAAACGTTCGGGCTGAATGTTAATGTTATC GGCAGTCACTCCTATCGATGCTCTATCTGCCGTTATCGCTGCCCAAGGTC GCCAATTTAAAATTTGATTTCAGAATTCCGGAATCTGTTCAGCTGATAAG CAGAGATATGATTCCGATGCGCCTGGAAATGTCTCTCCTCGTTTGGAGGT ATTTTAGCGTCTATCGCAGACATTCATCTTAATGAAAGCTCGTTATGTGC CCCATACTTGACTAGGGAATTCTGAGTTCCGACCGACGGGTGCACACGCC GAATTCTCGCAGATAACACGATTTATCAAGCGGCCCCGTTAGACAAACTG ATTAGCCCGACAGCCCAGAGATCTTCTACGTAATATACTTTATTTTACAA TACAAATACTACATATGCGGGGTGTCTTACGAACCTCTTCCAGTAAAATA TTAAGGGGAATTAATGCACGGGTTTACTCGAAACCTTTTTAACTTTGAGT TAACAACTAAAACAAAACACCCCTCTTGGAATGCCACAGTCGTTTTGTTT GCATTCCTAGCCAATCCAATAACGGCGAAACCGATATTTCTGGGACACCC CTGAGCCCGTCTAGAACTCGTCGTTGAACGGGTAGTACTTATGGCCCGAC ATTCCCGAAAAGGGTACCGTGCGCTGCCCGGTGTGATACTGCTCCATGCC GGCGACGTCGTCTGGACTCAGCTCGAAGTCGAAGACGCGGAAGTTCTCCT CGATGCGGGCCTTGTTCGACGACTTGGGCAGTGGCACCACGCCTAGCTGG ACCAGATAACGCAGGCAGATCTGTGCCGTGGTGCGGCCGTACTTCTTGGC CAGATTCTGGGCATGCTCGTCGTAGAGGAAGGGCGGCCACTGCCGAGCGG GCTGGGGACGTGCCAGGGGGCAGTAGGCGCAGATGACCAGTCCGTGGCGC TTGGCATGCTCCCGGAGCTGGCGCTGCTGAAAGCCTGGGTGGCACTCCAC CTGGTTCACTACCGGCCGGATGCGGCAGTTGGCTAGCACTCGCTCCGTCT GCGCGGCGTTGAAGTTGGACAGGCCGATGCTGCGCGTCAGGCCCAGATCC ACCAGCTTCTCCATCTCGCGCCAGGTGTCCAGATAGTCCACGTCCGTCAG CTCCAGGGTTCCGTGCACGTTGCTGTCATTGTGGAACTTCTGGCCCACCG GCATGTGCATCAGGTAGAGGTCTACGTATTCCAAACCCAGGTTGCTAAGG CTCAGGCGGCAGGCGCGCTCCACCAATGCAGGGTCGTGGTGGATTCCGCC TAGCTTGGTGGTCACGAAAACCTCCTCGCGTGTGACCACTCCCTCGGCGA TCTTCTCGGAGATCGCCTGGCCCACCTCAGCCTCGTTCTCGTAGACGAAG GCGGTGTCCAGGTGCCGGTAGCCCACGTCGAGGGCGTGGCGCGTTGAGTG GTAGGCGTCCGACTCGAACGACTTCCAGGTGCCAAGGCCCAGAGTTGGCA TCTCGCGCCCGTTGTTCAGCCGGATGGTGGGAGCCAGATTGGTCATCTTG TCGCTGGCGCTGATAATTAACGCTGTGCAAATTGGACGCTTCTAAGTCTA AACCAGTGCTACTACGCCTTTCTCGCGATCAAATCTCTATCTGTTCCAGC TCGTCGAAAGCTTCGCGGACAACTGTTGGCTCGCACAGCCGGTTTCGATG ATTTTGTCACGGCGGCCGAGCAGCTGCTGTGTCATCCGGTGACGTCACGG ACAACGCGCGGTTATTCCCACCAGCGTTGCCAAGCTGGCCTTTTCCCACT ACATCTAGCGTTTTTCAAAAGCTCAGCGGGGGAGGAATTGCGATCTAAAA TCTGGCGCGATGTATAAAAATATTTCAAGGTACGCACACAAGTAAGCTTA ATTTTAACGTTTAAAAACATAAGAACGACATTAATTGAATTGTATAGCAT ACCAGCTATGCGAGGTTTTCTCCAATTGCTGAATCGATCGCGAGTGTATG GCAGTGTTGTGTCCAGCAGCGACTAGCGGGAATTATTCAAAGCAGATTTT TAAGACAAATTTGAATTAAAATCAAATGCCGTAAAGAGCAGATAAGGTGA GAGTAAATCAAACGTCTAATATCATGGACCAACTCCATCCGAAAAAAGCC CAAGTAGGGGGCGGTTTACATAGATGGAATTTAGAAAAGATCAAGACAGA AGAGTTGGCGGGAAAACGAGCAGGTAATTGTTTGGCTAACACAAGTCCAG GAGTGGTCATCTCTAAATGCTTAGACCTGATGGGATAGGAACTTAAATTA GTTTGAATAAAATTTTGTTTTAAAGCCCTTACGTGTATAAATTAAACCAA AAACTCAAAGCATTTTTAAAATATCACAGATTGAACTCCGATTCCATATT GCCCAAAACTATAAAGAACAGTTAAGCTTTCAAAAATAATATAGCGCCCT CTGAATACAAATAAAAAAAACCAGTAGCAGCTTGCTAACACATAAATCTT TATTCGAATATTAGTTGAGTTCAAAATGTTAGACATTCAAAGATATATTT TGTTACGCTTAGGTTCAACATTTAGGGTATTGAAATATCTGCTCTGCATT GCACAAATCTCACTTCGGGGTATGGGTTTTCTGGTTATTAGAATATGTAA TTGGTAGTACGGCTAAAAGATCGCTGCTTCTGCTGTACATACCATAATCG ATGGATTAATTACTTCTAAGTGGTTGTTGGTGTTGTCTTCTTACTGTGAG CTCTGTGAGCCGTCTCGTCATCCCCATTACGAACTATTTAATCTACTTTG CTATTTGGTAGGTAAGTAAACTTCGAGATTGTTTTGCGTTAGACATGTAA ACACTGATTTGAACATTTATTGGTTAGAACAAGTTACGGCTCAAACATTT ACTGACTGATTACGACTGATTGGCTTTAGCTATATCCTGTTAACGGAGGT ATATACGTATAGCATGAATATATCTTTTTTGTGCATCAGTGAGTTACCCA ATGATGTTGAATTTATGCAAGTGCCTAGGCTATATTGGAGAAAATAAAAG TTCGTAGAGTTATGTTTTGAGATTGTCAAATCGAATCACAAGTGAAATTG GAAATTTTCCCTTTTGGAGTACTTGCATATTTGATATATGTACTATATAG TATGCAAAGTGTATTATTGAAAGTGCACAACAATAACAATAGTGGTGGTG TATTGTTGGTATTACGTCTACATATGTAGCAGTACTAAAAATGTAGAAAC ATTTTTGGTTTTGACACGTAAGGAGTTTCCGTTGTGGGAAACGATTTCTT AACACTAAAATAGTTTCTACGGTCCATATGCTAGATTAATGCATCTGCTA GATAAATATTCCTAGGTATGTGTACTTTTCTTGTGCCATTAGCACCAAAG AGTTGGCTTATTTCGAATATTTCCTCAGAGGATTGTAAGATTGCGTTGGG TTTAAAACGCCTACACAATTCTATGTGAGTGATTCTGATAGATTCTACCC GTTTCCGTAGCACGTGGTGTAGATAAAGTAATTAATGGCTTTCCAACTCT ACTTACAAACTGTACCATACTAAAATTGGTGTTGCGTTGCTTGTAAATCA ATTCGAAATTGTTACATCTCATTAACTATGAACTAAAGAATATTGTTTCG TTTGAATCGGTTCGTTATATCTATAAAAGTATTATTGAATATTCGTTTGC ATTTGCTTTGTTTTATTTTTGAAGGAGAAACCACTGGATTATAGTTGAAT ATATTGTTTGATTTTGATTGGTTTTCGTAAAGAAAAGTATTAATTATTAC GACATTTACATTCTACGCATCATGGTCAAAGTTTTGGTTACATCTAGGAA TGGTGTTTACGTGATAAATCGTTGTTCGAGAGACCTTTACTTGGGAGAGG AGTTGGGTTAGATTGGTAACTACAAGTACAATTACTGACTGAGGTTGGCT AATGAAGGCGAAAAATGATATAGTCGAATCCCCGACCTAAGGATAGTCGG TAGTATGTATTAACATACCCCGCCATTTATATAGAGTTTTTCGGAATTGG TTTTAGCAAATAATAAATAGTTTAGTTTATAATTAAGAAAAGTATTGGCT TAACCAAATATTAAAACTACTGATGATCACGATGCTTGGGCATTTTGTTG ACGCAGACGGACGTTCTTTGTTCTTTCTCCGGTCGGATCATATATAGTTA GTTCATAGGATCAAGAATATGCCCCTCGTTTTCTACTGCTACCGACTATA GTAATTAATACCTTGGATATAAATACATACATACATATGTTGTACAGTTG TGTTCAAAAAATAGGTAGTGTCAAAGCCACGATTTCCATAATTACATTTT ACACTTGGTGAAGAACCACAGAGTTCCACACCCACAATTTATTGGACCTA AGGGAAATCCTTTAATAGTTAGAACAATTGTTTGATTGCATTTTCATTGA GAGATCTAACAACGACTATTTGGATAAATACTCCCCATATTTAAAACACA GTTGCACGTGTAATAAATACATGTAAATATTTTTCGTATTTCTATATATG TATGTATGTACATAACTACAACTAATAAGGTCCCTCTCCAGTGTTTAGTT ATTTGAATGCACTTGCATTTGCACTTTCTTATCTAATGTAGCATAAAAAA GGCATCCACTTTCTACAAAATAAAACGAATTTGGGCTGTGTGTAAATAAA TATTAATAAATGGTTTCGTATTTTATTTCCAAGTTGCCGTAAAAGGAGAT GGGGTGACGGAATACCAAATGAAAATAAGATTGAAAACTATAAATAAAGT AACTTATCCGCTACGTAGCTTACTTGTTAATAACTAGCTGTAACTAGACT GTTTAATAGTTGGTTTTAGTTTAGGGTTTATAAAAATATAGATTCCATGC TCTCGAAAACGTTGTACAACTTTACAAATTATTCTACCAGCTCGCGCGGG ATTTATAGAGTAATGGTTTGTGGGAAATTATGCTGTATAGTTGTGTTTGT TTTGATGTTGCCTCCTATAAATGTTTAGTATCACACACGTCCAAGTTTAG TTTTTATTCGTTTCGGTTTCCGCGGGGAATTGCCGAATTTCAAATTGTTT TCCATCTTTTCCATCGTTTTGTACTAAAGCAAAAAGTTTCTCGTTTGCAT TAAAATGCGTTTGGGTTTCAGTTCATTAGAAGATTGAGATAGTTCCTAGT CGGGTCGTAGATATAGTACACTGTAGCTTAGGCTAATGCGGATGCGGATG CGGACGAAAGTTGGTCCGGGCTGTGGTGGCCGTGGCCCAATTGGCTTTCG GAAAGCAACAACAACCCGGCTAAGCTCATAACTGTGCAGCTAATTGCGGT TGATTAACACACACTAGGGTTAGACACTTAATACGCGCTACAGGCTAATT GGATGACAGCTCCACAAGGGCTTAGAGCTTCCTGGTGGGCTCCACCTTCT GGGACATGGCGGTGAGTACCCGCTGGTTGTCGATGACGCGGAAGCTGCTG ATGTACGACCTCACCTCGCCCTCGCTCTTCGGGGACGGCGGCTCTAGTCC TGTTCCAAATCGAAATCGATGAGCAAATTAATTTTCAAAGGGGGTTTATT GGTCTTACCCAGACTCCTGGAGCGACAAAAGCGGATGGTGCGCATCGTCT GGGCCATCATGTGCATCTTCTCGAAGTTCACCAGGCCGTCCAGGCTGGTC TTGTTGCCCTCATGGGCGAAGGTCATGTCCTTGAGCAGGAGCGGCATGAA GGGAATCAACGGCGGCTGCAGCTTGCCCACGAACACTCGGTACGCCCTGT GGTTGCGACTGGGGTCGATCAGGGCCTCGAACTCCTGGAAGATCTTCCTG AACTTCGACGGAATCTTTTCCCAGGTCTGTTGCAGCCTGGACACCGCCAT GTTGGACAGACCCATTACCACAGCGAAGAAGGCGTTTAGGTTCTGGTACT CCTTGCAGCTGTAACGAGATAAAGAAGCTAGCTTACTACTCTGTCTTTGG CTGGAATGGGTGTTTCTCTAAGCCTAAAAGTGGTGATAGTGTAATAAGAA TATGTATTCAGCATTTAATTAATACTATGGTACTAATTTATTCTAATAGG AGCCTATAGTGGGTCTAGATCTATAGTAGTTAAGATCATGATTTTTTGTC TTCAATATACAAATATGCTTCCAAAGAAATATACTCCAATTTTATGTTCA TGGTAGCTCACTACGCAGTTTAATTAATATCTACAACTTACTACGCGGCC AGCTTGATGAACTTCCGGACCAGACCGACGCGTTTGCTCAGACTGGGAGT GGACACCAGTTCGGTGACAATCCAGTACTGCACCTCGTTGAATCGGCGCA GGAACACATCCAAGTTGGCAGTGATCTGCGGGTGGAAGTGTGAAATTCAG TCAGCATGAAAGTTGTGTATTCTAAACGTATGTCCCCTTAGCTTTGGGCC ATCTTTAATAAGTTCGACTGGTAAAACTCTGGGCTAACTCAATTTGCAAG CAGATGACAAATGGCTGCATTTTGCGGTCAGAGCCTGGCAGGATAATTAC CCAAACGAGACTTCTGAGACTTTTCGGCAAAGTTTGCCTTCCTACCTTGC CAAAGTGATGCCGCCCGAAGGTGTGGTAGAGCAATTCGTATTCATGGACG GCCCAGAAGAGGTCCCACTCGAACAGGGTGATGTGGTAGGCCAGCTCCTT GGTGCTCAGTATCTCCAGGTCGATGTCCACACCCTCGGTGGGGCACTCCT GCTCCTGCAGTTGGGTCTGCGGAATGAGCAAGTATAAAAAATGGTCATCC AACATCCAAGTTGGTCAGCGCTTACCAAGGCATCCAGGTGGTCCTTGACG GAGACGAAAAGGCGGCCGTTGAGCGACAGACCCGTGGGTATGCTGACATC GTTGTCCTTGAACACGGACCGCTCCCCGTTTGACTTGACCTCGACGAGGA CGAGATCTTCGGGACCCCGATTTAGCTGCAGCTTGTCGGCGGCACACGCT TTGATGAGCTCCGCCGTGGTGTGCATGGGGAATCGCAGGGTACAGTAGGT GTGGTCGGCGCAGTAAACGCGGAAGATGACTTAAAAAGCAGAGTTGAGTT TACGATAAGTGATACTAGTGTATTAAATCACTATTGAATGAACACCTACT ATCATCATCTGGTCGGATGACCGTCTTTGAAGGCGTCGCATTGCCACTGA AAAGGCAGATGGGCTGGCCGTTGGGCGGGAGCTTCCACTTCTGGCCGGCG TTCTGGTTGCGGTCCTCCTGGTAGCGCGCCATCTGGGTGAGCACGTTGTG CACTATGCTGGTCTCCTCGTTCAGGTCGGGATCGGCCTCCACCTCGGCGG CGAGGTCCTCGATAAAGTCGCACACGCTGGGCTCCTCGAAGGCCGCGTGG CGGACGGCCATGACCCACTTTTGCATGAACTGGATCACGCGCTTCTTAAA GTTGATTATATACTCCCGATCCTCGGGCGTTTGGGCGTCCTCATGGGCAT CGCAGTGGAAGGTGCACGGCGGTTAAGGCGGAAACCAATTTCTTTTGTGA TTGTGAATCGTATTTAGAATGGGATTTGCTGGGTTATGAAAATCTGTCCG GCGCAACTTCTTACTCGCTACCTTACAGGGTCAGTCAGTCCCAAATTGGG CTTCCCATCTTGGGAATCTGGTTATTGATTTCTTCCAACCTTATTGCTCC GCCCTGCCTGCTTATTAAACTCATCACGTATTTCGATGCAGATTGTGAGA TTAGTTTCAGGCATCATTGACCAGAGCTCTCCACCCCCCCCCCCCCCCCA CCGTGCCCGCGGACCTCTGGCAACCATCCAACATCCACCTTCACCCCCAT TGAAGCACCCCGAAAATGCTGACCCAAGTCATCTTTGCGGCTTTGTTTCA ACTGAAGTTGGAAGCGGAAGTGTTGCTTGTTAGCATTTTCTGCTACACTC GAGCCCAAAAGCCACCCGAAAGTCCAGGCCACCCGCACCCACTCCCGCTG GTCGGGATCGGGGTCATGTGTGGAGGCTTGCGTGCTGGCGGCACTTAAAC TGTCGCTGTGGAAATGTTTTGAATTCCCACCCAGGAGAACGTGACTCGGG CGCGAGATGGACGACATGAAGAGTGCGTTTTTGCAGTTTAAGTGCAGCCT GACTGTCGAGGACCTAGCTAAACGGACCTTGGAAACGCTAGGCTTCCTAC ATGGGGATTTAAAGAGCTTCAAGGCGGGGATTAAGCTGGAATTGAAAGGG GGAAAACCTAAAAGGCTTACGGAATTTTTTTGGTGATTTTTGTTGTTTTA AAAAGGATATTAATTGGCCAATTCATCAACCAGCTGAACGACGGGCATGA AAACGATGTGTGTGAGCAGGAAGTCGTCCAAGAACGGATCCATTCCACCC ACGGACTGGCCCAGTCGCGTCTCCAGCAGGTGCTCCAGCATCTTGGCCGG AGTTCCCGACATCACCGTATATCTGTGGGATAAGATATTCAAATGTATCT AGATTTTAAGGCAAAAAGGCCAGGTATCTGGGTTTAGAAGTTAAATGCTG CTTTAACTAAGGGTGCTAAATGGGATGTATTTTCTTCAACCGAAGATGCC AGAAGGGAGAAACAAAGCCTACATTCTGTCACACAACCGTAACCCATCAA ATCAAATTCCTACTTCCATTTAAATTTGAAGGCACATTAAAAATTGATTA GACACTCACTTAAATGCCGAATGCTGTCCACGTTGCTTAGCCACGCGCTC GAGCACTAAAACATCCTTGCCGTGCTCCTGCAATCTCAGAGTATTGGCCT CCACATCGCGCAGTATCCGGTTGAAGTGTTCCTTGTCCACGCGCAGCAAG TGGCAATTGTTCTCCTTCAGTACGATGGTAGCAGCTCTGCGGGAAGAAGG TCGGGGAATTAGATGTCTCAAGGATCTACCTATGGGATGGATGTGTTTCG AGGAATGTTTGAACAGCAGTCTTGTGACTTCGTCCTGGTTAGCCACACAT TCATATGGTGAAAACGCGTAAATAGCCATAAATGTGAGGCAGCCCTCGTG CACTTGATGGTTTGCCAACCCCCCGCAGAGTCGGAAATATTTTAAATTGG ATTTCAGCGGCAGATGCACATGCAGTTGGCAAATAAACTCAATTGATATA TGCAGAATTATTGCCGGTATGCTGATACGAGCGACGTGGATGGAAGCGCG ATTTATTATATTTGTTGAAGGCAAACAAGCTCTTTGACTATTTTAATTAA CACAAAAGCCGAGTGGGAGCTTAAACTAGTTATCCTTTCATTGGAGCATT AAAAACGGAAGTGCACGCATACGGACTAATAAGCCTGCAGACAAACGGAT CCTGACAGTTGGATTTCCTCTGCTCAGCTGGGGAGCTCCCCACCCATGAA CACAATGGAAACGAATTCCATTCTTTGGCAACTCTTTGATAGTTTCTGCC TTTGCCATCCGCTCAAGCGTCGGCTGGCGAAATGGCTTACAAATTGGACG GGGGCCTTGGCCGATACTTTGTTTCTATTTGAATTGTTTGCCTTAAAATC GCACACAATGCCGCTTGTTGTCTGTCGCTGTTGCGGAGGAGCTTGTGGCC AGTTATCTCGACCGTTGCACCAAGTGGGCTGTGGTATAACTTGTTTGGCC CATTGTGGCTATGCGGCCATTGTCCGTTGAGCTGTCAGCCAGGAGGAGGA GGTGGGAACCACAGAAGGGTTCAGCATGAAGGGTTTTGGTTTCTCACAAC TTTTGGCCGGAGAGACGGACCAGCCAGTTAACAATTGCTCAATGGAATCG TCGCAATTGGTGCGCCATCACTCACCTGGGTGCGTCGTTTATCAAGGCCA GTTTCCCGAAATCATCCCCAGTCTTCAGAGTGGCAACAGTTCCCTTGCCG TGTATCACAACGTCTACCGATCCCTTGAGTAAGATGTACCAGGAGCGTCC TTCGTCGCCTTGATTGAATACTGTTAATGGGTTAAGAGTGTTAAGGGATA AGACTCGTTGTTAGTACTTATAGCTGCGTCGGTGTGGGTTGGCTGACCCA TTATTGAGCCATAATTAGCCGGGGCTTAATTAAAAAGTTTTCCAACTTCT CCCTTCCCTCCCTTTTCCACCCTTTCTCCGCTTTGGAGAATCTCAACTGC GCCGCCTGGGAGCTATTAATCCTGCGGCCGGATACTCACATATTGTTCCC GCCTGGGCATGAGCCTCGAACACGAAAATCGACGACAGTTCCCGCTTTAT GCTGGTCGACAAGTGGGAGAGTGCGGCAATGTGGACCAGTTCCTCGAAGA CCAGCTCCAGCTCCTCCGATGTCCGTTCGTGAGAACTGCGAATTAAGGAA TATAAGAAATGAAGGGATCTTAATCGAATTTACAGGTGAGAATTCATTAT GCGGACGCAGTGCAATGTCCTTTTTATATATATTTATATTTGAGTATCGG ACCCAACTAATGGCAGTAAAAGACTCATACCTATGCTAATATTAAAATAT TTTAGATTTATTATCTAAAGTATCTATCTTTCATTACTCTGCCAATGCAA TATCATTGAAGTATCTTTGTAGTAAGTTCAAAGAATTAAAATTGTAACAA CTGTCTTGAATACGAGAATGTGTGAGTATGGGAATGTATCGTTGGTAAGG ACTTAATTTGTGTTAATTGGTTCACCGCGTTGTTTCAATAGTTCTGACGT CTGTGTGCGGAAGTAATTATGCGTCACAAGTAAATTATCCATATTGCAAA CGTCCGTGGGAAACGGACGTAAATTACTCATTGAATTATAGTATATTGCA CGGTTTTTTATTACTTTTATAGGAATGTTAGTATATACATTAAATGCTTT ATTTTTTAACCCTAAAACCTATTCCCATTAAAGCCGCCGTACTTACGGTT TGCGCAATATCATACGCAGTGTGGCGTCCGGTCCGCGCTGGAAGAGTGCG CTGAGCGCCTCGCGGATGTGCTCGTTGGCCGCTCCGAGGTCCTCCGCCTG GGGCACGCCCGCTGCCGCCGTGCCGCCCTCCTCGTCGATGCGAAAGCGGT AGAGGAAGCACTTGTCCTTGAAGGGCTGCTCTTTGTTGACTGCGGAACGG CACCGATTAGGGAATTGAGCGCGTGGAGTCTGATGGAACTTACCGTGTGC GAGTACTCCTTCCTCGAGGAGCGCTTGCCACATGCCAGCCGCCTGGGCTC GGGTGTGGACGATGGGCGAGAGGTTGACCAGCCAGTCGACGAGCTCGGTG CCGGGGGCGCACTTACGGATTAGCTTGCCGGAGACCTATTCAGGTGGCAT GATTAGCATCCCAATGATGACACCTCCCACTCCGGCACTCCGGGCACACT CACCTTGCGATCCTTCAGACAGCTCGAGTTGTCGGCGACGAGTAGTGTGC GTAGGGCCCAGCCCATGCGGTTCATAGCAGGACTCGGTGTCTGGAAATGT CAAACTCTTTCAACTTCCGTTCTCGAAAGTCCGGAGCGAGTGTCAAAGGC AGAGGAAGTGTCCCGAAAGGAGACCCTTCCCCGCGCGCCCACTCATGGAA ACCACATAAATATTTTGTAATTCCCCTGACGGCCTCTGGAGCAGCAAATT AACTCATTTGTCGTCGTCAATGTCAGGACATTACATTTGTGTTATTTATG CGAGTTCCACGGTGGGACTCCGTTGGTTTCTTTGTGCCCTTGGCTCTTAC CTCGGTGATGGGCAGCGCTGGGTTTGGGTGGTCGGGGCTGAGGGGTCGTT TCGTGGGCGATGTGGCTGCGGCTGTCGCTTGTACGCTCGGTCCAAAACCT GGAGAGGCAGCCATAGTTCAAGTTAGTCAGTTAAGTTACTTTAGTGTTAC GTTCGATAGCTGAGCACAGGCAGTTTCAAAATGATGTGAATGCCGCATTA ATGAAAGTTCTCAAAGCCAATTATCGGATTAATGGAGTGTTGAGCATGAC GCCAGTATAAAATATGTTTTTCAAATAATAACAAAAGCAGATACTCTCCA ACCATTAATCACCGAGTGCATTTGGAGTGTTAGTCATGCGAAAACTTTGT GATAGACTTAATTGGATCTTTTGTCTACATACCGTTCTTCAACTTGCAGT TGGTGAATATGTCATTCATTAACTCCTTGTTTTTCTGCAATGGAAAGCGT AAATGGCCATTAGTATTGGGTGTTTCAGCCTGGTTCAGCTCTGCGATTCC CATTACGTTGCTCATTTCAAATGCCGTCGACTGCGGACGCGTCATCTGCC CACGCTCCAGCTGCCTACGCCACTTGACGGCGGCGGAAGTGGCGCCAGTT GCGGCCTTGGTGGCCTTGGAGGCCCCTAATGTGGCCCCCACCTGGTCATC CCCGCCGCTGTGGCGTCGGTAGCGAAGCAGAAGGACGCCGGGACTCCGCT CACTGCCGGCCACGATCTGCGTGGACCAGCGCTGCCTGCCGGCTGCCATG TGGGGAAACCTTTGGCTTCACTTTCACTTGGGAGCGGAGTTCAAGCTCGC AGGTAATTGCTGGCAAACGCTTCTCCAGGTACTGATAGCGTCAGGAGGCA ACAATCACACGAACGCCGCGGCTCGCTGTTTGCAATTACTTATCAGGCAC AAGGGTTGTCAAAGCCCCAACATTGTTCATGATTCAAACAACATCTTTAA CCCAAGAAGTGACAACATTCTAGGAACCTTAAAGGTCTTATAAAAACTTT TTAATTAAGAAACTTTAAAAACTTTAAAAGTTTCCCCTAGCTCGCATAAT TTTAAATTGATACATATTTAAGAAAGTAAGGATAGCAAAATTAGTTAAAT ATATACTGATAAAGGGTCCATATATAGTATGAGCAATTCAGCTGGTCTAA AAGCGCAATTACTTAAAATCTAATTATAAATTGTAAAATTATATGGATGT AACTGTAAAAAGGATGTACATTTCACAAAAGTATATGGTATGTACTAAAC TTTTACTGGTTTCAACGGTATCTGACAGTCGAGGCGATCCCTTCTGTCTA TTAATTAAACATGAAAGTCAAATGTTGTACTCTCGCTTTTTTCGATTTCC CGCACTTAACGAGACTCATTAGCTTGAAATGGGTTAAAATCGAAGCCAAG ACGCAACCTGGCAACACTTCGTGTTCCGCCCGTCGATAAGCGACTTACGC TGCGTTGGCGTCGCCGTCGAAGCTAATTAAACTCGCTTGCTTATCAAACG CACGCCGAAATGAATGCCACCCACTGGGTGGCGTAGGGCTTTCGAGGAGC GGTGTAGCAAGAGTTCCAGATTTCCTTCGCCTTGAAAGTCGGACGTGGTA ATAGAACCGTGATGTTTCCTGGTAAAGGAAACTTTACATTGGCATTGACT GATTAACGGTCCGAGGTTTCATTAATATGTATCATATTGAGCAAACTGAG CAAACTGTAGGAAAGGAAGACCTTTATTCTAAATAGGAGAAGAATTCTCA TCATGCCAATGTTCTTATTGGTGAAATTCAGCAAAGAATTTTGTTTAACT AAATTTTAGTCGGTACCACTATCTGAGACTAAAGCTATTTGAGCTGGAGT GAATATTTCTTATCAGCCTAAATGCAAACAAGTTTTTATGAGGCGTGGTA CATTGTCATTTTTAAGTGTTTTTCGGTGATAAAATTGATATTCTCGTAAC TTGTAGTGCAAGAGGATGAAATATATTGGTTGGAAAGCATGCAAAAGAAA AGAAACAAATGTGAATTTACAAATACTTATCTAACTGCAACTGGTTTAAA ACCAGTGAATACACTTTCCTGCTTATTGTTTTTGCTTAGCATTGAATTAA GCTCGGCTTAAAGAGTTTCAGTTTTTCAAGGGAAAGAGAGCGAAAAATAC TTTGTTGTTATTAAATTATTAAGACGATGGCCCATTTATTTCTTTTCACT TCCGCAACGCAGTAGAGAAAATCACAAGGAGCTTTTGAGCAAGCAAGCGA ATGCTTTCCTGGTAGACATTTAGGTTTATACTTTCCGTTCAATGGAACAA GGAATCCGAACCATCTGCACTAATAGAAGGAATTTCTTGTTTCTTTCCGG CAACTTAACCAAAGGGAAATAACACTGCAGAGTGCTGCAGGACTTTCGAG AAAATCCCAAGGATTTACCGAGAGTGTGTTCATTGAGCAGTGCTCGAAAC ATTGATGAAATTAAAATTGATCGACGCAGCATGCACGTTGATGACTCCAG TGAGTTTGTGTCCCTCCTCGCTGAAGGCTTTGAAATCCTTTGGAGATCCA GCCCTCTCCTCCTCACGCAACTGGCTCCCTTGCGGGTTCACATGTGCAAC TTGTGTTTGTGCATAAATAAATAACCTCGTGACCATGGACATGCAACTGT GCATGCCAAGGGGCTCTCAATGGAGCCGGCTGCAATATTTATGGCCTGGT TATTACGCAGACCACATGTTTGGCAATGCCGTGGTTGCGACGGCGGGCAG AACATATAACACGCCCGGAATTAAATGCAAATATTTCGCAAGCAAGTGGC ATTGAATCGCATCAATCGCATTGAGTGTGAAAGTAGCACATTCGGCGGCA ATCTGGGAATTTACTGCAAGTGGCAAGTGTAATTTCCACCATTGATGCAA CTTCTGCATCCGACCTGAGCACAAATCGGAACCGGCTACTCGCATTTTTC CAATCCCAATCCCTATCGCAATAGCAATCCCTATCCCGATGCCAATTCCA ATCCGAGTGAATTGCTTGTCCGGAATAATTGGCAGCCATTGAATGGTAAG TGGCTGTAGTAGCTACTTGGACTGGTATTCGGATTTGTGCCCCGGGCTTC GGTGAAATGAGACTGGTAATTAACCCGAAATTCCCTTTCACCCGCCACAT GCGACTACAATGGCTTTCAAAGACATTTTTAATTTGGTCCTCACAAGCAA ATATTTGCGCACAAATCAAATGCTCGACTATGCTGCAAAGTGGGCGGGAC GAGCCAAGGATGACAAGTTCCATGAACTCGATGGCGTATATCCCTTGCGC TCTTGCGAATATTTCTCTTATTCCCCTTCAATTTGCCCCCTGATTTTATC GCATTTACGCAGTGCCATTCGCAGTGGCAAAACGCCCCCAGTTCGAATTT TTATGGTCTTGCATCCATAGCATCCACAGCATCCGCCATCGACTTTCACT TCATTGTTGCACACTGCGTATACGTGACATGTGGTGGCCCTGCTGTCGCA GCTACTTTGTTATCGTTCAGTTCAGTTCAGTTCAGTTCAGTTCAGCTCAG CTCAACTGGGCTGCCTCTGGGGTAAGCCAATGCTGGCATAATGTTGCAAA ATGCTATTCGCCCCGAATTGGGGCTTGCTCCCGCTCCTGCTCCTGCTCAT CCTTCTAACAAATAAGGTAAACAGACGAACCTCACTAATTCTGGTTGCTC GCCTGTGTGCCGGGCTCATATCTTTTGTGGCTGCCGCAGGAGATGACTTG GGGTCCTGGCTGAATGGCATTGTTAGTGGGGTTTCTGAGTACAACACACA CTTTTCACATTGAGATTTGCATTCGGACACTGGCAGAAAGAAGGTGTCGA GTTGTTGGGGATACTCGGGATATCAGGTCCTCAAAGCGATGTATTTTGTG TTTGGCTGGCATCCTATGGCTTACTATTTATTTCTAGAGTATTTCCAGCT TCCGTTTCGCTCAGTGCACATTTTGCCGATTGTGTGTGTGGTCCTCTCAA ATATTTACATTTTGGCATATGTAAGCCATGTTGTGTGGTTGACTGTAGTC AAAAAGATGCTTAACCACATTCCAGCCTTGTGGCATGCCAAATGCAAATA TAATTCATTTTCCGTTCAAAGGCATTTCCATGGAAATTAGGCCAATCGAA CCAATCCGAATAACCAGCTCGGCTCACCAGCAAGCCTTTCCAATTAATTA TCCAGCCCCCAGAGTCCTGTCAATCCAGCCAAGTGCGCGGGAACATGCGA CGCGGATACAATGATGCATTGCAATGCTAAGCTAAGCCCGCCATTACCTT CTAATGCCATTATCCATATACTCGTAAGTAAAGGCGAAACAAAGAATTAC TTAGCCCACGGGGGAACTTGGCTTAATGCCCCACTCTGTGGCAAAGCCAG AGCACTTAACAAGGCCAAGGGCCCAAATTACTAGCCATGTGTTTTAGGAC TTAGGCCGGGGTTCGTTGGGTAATATGTCCTCGGGCCCAGGCATCATTAA ATGTTAATTGAAATTTTAATTAAATATTTTCCACAATGACGAAGGAATAC CGCAAATAGTCGAGGCCCGCTTCTCGAATTTCTGCATATCATTTTGGCAA CTCATTAAAAGAACAGAAGTGCGCGAAACAGACGGATTGATTCCTTTGAC AGAAGTGGAATGTGCAAGAACAGGGGCGAAAATCGATTTGCGTAACTTAC TACCCCAAACTTACCTCCCAGATGAGTCGAAAGTCCTGCTGCTCCACCCG CAGCAGCTCGCAGGTGGTCTTCGTCACTACGGTGCTGTCCCGCGGCAAGT CATGCAGTACGGACTCCCCGAATGTGGCACCCACGCCCAGGTTGCACAGA GTAACTGCGCTCTGAAAATAAATAAGGGCAGAATATAAAGTTAGACAGCG CCCAGGTTGGACTTAAAGTATGCTAGTTTCTGTTCCAGGTACTCCCCGAA TGGAAAGAGCTTAAATAATAGTTTACCCAAGGGGAAGAGAAGCAACCGAC ATTTGCAGCTCAGTTTTGATATTTCAGCGATGTAGCCACGTTTCTCCATA AGCATTTCTAGCTCAAATTAAGAACTTTTATTAGCAAATACCTCATAATT TATTTTGTAGAACCATTTAGTTGAACCATTTTAGTAGAACCTACCCTTTT TGTATACCTAATACTTTATCAACTGAATGATTCCACAACCCAGCTAAGAA ACATATTATGTTAAAATCTATAAATGGTATTTTGCACCACCACTGCGAAC TCAGCCATGGGAGAGTGAGGGTATCCGCAAGTTGGAGTTCGAAAATGCCC ACCTAGATACATCTCTGCAGATTAAGCACTCTGTGGCGGCATGGCTGCTC CAGTCTTGGGCTTGTCTTTCGCTGGCATCTTACCCAATTAACGCAAATGG CCGCAATTTGCTCGTGGTGGCAGGGACAAACATTTGCTTAAAACTCTGTA ATCGCTTCATTGTCGCATTTCCCGCAAAACCACGGGCACTGAAGCACCAC AGCGCCCAAATGCAAGCCGGGAAATGGGGCCGAGGAGGAAGTGCAGCCCA CTTCACTGCTTCGGATGTAACGAACGCGGATTGGAGCTGTCTAACCGCAA CATTGCAATGACATTTTCAATTACCCAGCTGCGTTTGCATCGGACTGTTT GTTTTCCCACCAGACTTCTCGGAGTTCTGGGCCACACTTCTTGATGCTTG GCACTTGAAGGCCCGAGGGCTTCGCAGACCCATTTCTGTGGTGAATCCGA GAACCCGAGAATTGGAGAAGCGAAGAATCCGAGAACACGGGAATCTTGGC CCTTCCGTGTAATTGGCTTAAGAAGACTTGCGAGCGACCGCAGAAATTGT TAAACTCACATTAGCCGACACATGTGTGCACAGTTATTACGGCGCACGGA GACCATAAAATACACTTTAATTAATTCCCGGTCTGTGTAATTACAAAGCT GCTGCTGTGGCACCTTTCTTTTGGCCAACATCGCAGCCGCAAGTCTCACT CACTCGCTTTTCTGCTGATTTATTGCGGCTTTTGTTTTTTGACAAGTGTC AAAAAGAGTCTGCCACGCCCCTTCCCGCTTACAAGCTGAATTTGATTGCT TTCTAATTTATTGCAGCATTAAAAGTTGACCTACAGACGCAAAGGGAGAG GGAGACGGTGGATGGCGGCAGAAAGAGACGGCTACAGACGAGCCGAAAGA GACGGAGCGCTAGTGAAAAGCTGCCAACAGACCGAGTTTTGTCAACCAGC ATTTCCCTTTTCGCAATTTCCTCGAGCCGGCGAGAACTGAATTGAATTTA CGCCCAAACAATAATATTTGGAAAGCTGCCCAGCTTTGTGTGTTTGCCAG TTGGGAAAAGGCTCTGTGGGCGTTTGCCTTAGCTTAATTTTATTTAACGT GCGGAAGATTGAGTTTAATATAACAAGCTTAAAACAACGCTATATTCATT GTGGTGTATATATTTTTGCAGTTATCAAGGAGAGACTGGCCAATAGAACG ATATGTAATATGAACTTTTGTGAAATCCACACTGACCATTTGAAATTGTT ATATTGAGAGGAGTTGTAAATCGTATCCAATTTTATTTTCAATTCATAGT TGGGTACATATTTAAAGCAAATCTCTGCACTTTCTGCGTTGCAGTAGCCA GAAAAACGATTACCCTGCTGCAGCCAATTTCTCATGTGTGTCAATGCCAC GATAACTTTGGTCACGGGGCTTAAATGCTGTTATCGAACTATTTGGCTTC CCAACCTAACTTGATTGCTTTTTTAAACTAAAAGCTTTAAAAAAGAGGTT ATGTTCTGGTTAAAGTTGAAGGTCGAAATAACAAAACTGCCATCAGAATG TTTTCATATCCTCTTTTTTTTTGGATTTTTCTATTGATATTTCAATTGAA CCGTAAGATTGTTATACTACGTGATAATCAATTCTATAAAATGAATACAA CCCAAAAAATATTCTCCAAACTGAAAAAATTGTAAAACCATTTTTAATTA AGCTTTCCAGAACCTAGAATATTGAGGAAACAACCCAAACTTATTTCTAA ATCTGTATGTTCTATGTAGCTTGCTATTGCTATAATGATGGCTGAATTAC ATTGATGATTCGTTCATCATCTCTTCTGGGTCCGGATTACACTCTCCCAA GGATTCTCCACTGACACCCTGGGTGATGTCAAGGGCTGTGATAATAAAAC GTTTCGGAAACACTGCTATTGCTGTGGGGAAAATACGGTTATTGCCGCCA GCTTATATCTACGGATGATATGGAGTCAGAAACACGGCTATTGCCCGCTG TTATCAACGGATGGGATGGCTTCGGTATCTATGTTATAGCCGTGTGAGAG CACGTACATTTTTCTCGTTTCGTGTTCGCCACTGGATCTTTACATAAATG CGGGGTTGCAATGCAATGTTTTACCTTTGCATAATGTCGCGTTGATTGCT CCACGTTATACGTACAACTGCGACGAAATAGCATTTTCCCTCCTTGTCTC TCGTGACGCCCTCTCGCTCACTCACTCACTCACGGTGCCACTGGAATTCA GTTTGTGGATTTCGGACACTCGGCCAGTTGTGCATATTCAAATTGCGCTG AGCGACATTTGAAAATATGAGCAGCCCACAAAAACAACGAAAAATGCAAC ACGTTACCCGGATTAAATGGAATTGTTGATGGGTTTGCTTGGTCTGTTGC CCGCTGCTATTTCTGATTGCAGGTTGTGGACGTGCGCTCACAATAGTGAC CTCCCACTAACTAGGCTAAAAGCAAGCACGCGCTGCCGAAAATATTGCCA GCATTCCGGACCCACATGCTCCGGACCCACAGCTGCCATTGATAAACGAC GCGGACGCGTGTCACTTCGGGCCTCAATTAGGAACTCTTTTAGCCGGCTT CCCAGCCAGTTTCAGTTTCAGATTCAGCACTCGAGACCCGACTCCAGTTT TCCCAACCGCGCGGCGACGACTCGCAAAGCGAACTGAAATCGAAGTAGCC GCCAACTGAGCAGCGGCTGGATGTCAGCGGAACCGGCAGAGACTCTGTTG CATGTGGCCGGCTCTTTGTGCAACGTGATGTTGCAAGTTGCTCGAGTGTG GCCAACAGCAACAGCAACACCTGCAACATCAGCAGCAGCAGCAAGCTAGG TTGGACGGTTAAATTGGAACGCTCTGTGCGATGACAGCTCAATTGACCAC ATGTGTCAAATAAGTGACTGCCAAATATTAGCTATCTAGAATGGAATCCG AAAATGGGAGTGATTTATGTAACAGGGAGTGACGGAACTACTCTTTTCTT ACACTCATAGGTCGGAACTTGGAATGAACGTTCAAGGGAGTTCAAAAATA AATAAACTTTCGTTAAACTTTAGCAAACTAAACATAAGTGATACAAAGGC CATTTTAAATTCGGTGTGCAGCAGTGAGGCAGCGCCTCACATCCCGATAC GGTGGCATGGCAGACTTTGGTGACGCTTGGTGCATGCAATTAATCCGCGC AAAAGTTCCGGGCGCAGACCGTGGCCATGTCCATGGGCATATCCATGTCG GCGGACATGCCCGTATCCATGCCCACAGCTAAGGCAATAGCGATAGCGAT AGTGGCGGTGAAACCTAAGCCCTGTCCCTGGCCATGCCACATGCACCCAC GGCATTGTTTTTGGCCAAATGTCCAGTATCCCACGTCCAAGTCGACTTTT TGTTCACTGGCGCGCTTGACAAACTATTTACGCACATATGAGCACGCTTC CGTCCGTCGCAGTTGCAATTGCTGCTGCTTCTGCTGTTGCTGCAACATTT GATGCCGCTGCAGTTGGTCTCGCATTGCAGCACTCGTTCCAATTCAGTTG GGCAAACAAGGATGTGGACTTAACTTTGGGCGATGGCGATGCGTGCTTCT TGCTTTGATGGTGCTGGGGCTAATGGAATTTCAGATGAGATGCTGCTGGT TGGGAATTGAAAGTTTTCGGGCCAAACAACCTTAAAGTTGCGGCTTTAAA CAGTCGAAATGCTTTGTGGCTTGGGTTGAACAACCTTGACACTTTTATTT CAGTTATGCTTTATCTTCATGTCGGTGGTTTTGCACTTGTTTTTTGTTTA GCCGCACTTGTTTCTTGCGGGCTAGTAATTAAATTTAGTTCGCCCTCCCA CGGCGAAGGTAGGGCCAAGTGCCAGGCCAAGTCAAAGATTTCTCGAAATG CTTAGAAAAAACCGAGCGTTGTATGCTCAGGCAGCGTGTATCCGCCAGAT ACAAGTATCACATATTTCATTCAGAAAAACTATTTGCTTACGGCATTCGC GCGGTTTGAATAAATCACTGACTACGTTATTTGTTTAATTAATTATGATA ATTAGGCCATCAGTTATTAATTGGAAAATATTCACTTGTTTGTGGTTTTT AATCCGGCTATAGGTTCATAAAACGTGTCTATTACCGGATGATGAGCTAG TGCCAATAAGAGAGTATATAATTAGTTTTATCAAACTACATTTTGTGTTC CCATAACCGTTAGATTCACGCCCATTACAGAGCACAATTTACACGCCCCC GATTTTCCCACCTTTAGACACTTGCCTCAATTTCCACGCGTTGCATGCGC CGCTGACGTTAGATAAACATTTCCCTACCAGCATAATTAAAATAAGATGG GATACTATTAATCCGGAGGGGCATAAAATACATTTTAAATGACTGTTCCA ATTTCCGCGTTACAAGCCAGCCCAAAAAGTAGAATATACATACATAAAAA TGTATTTAAAGTTTGAAATTTATACAAGAAATTTTCAATTCTCGAATTAA TTAGTTGTTTGCTTTCAACTTCAATAAGTTCGATTGTACTCACATTGCTA AATATAAATTATTCTTTAGAATGAACTAGACAGACTGCTTAGCGTCATTG ACCGGAAACTTAAATCACTCAATCGTACACTAAACGAATAAAGTTCTGGA AATGAAAACAGTTTCCAGCTAAAATAAGAAATATACTACTACGTTTGCCA TTGAGAATAAATAAAACAAAAGTCAAGTGCTGACAACTATAGTTCTTGTT CGTGCTAACTAGCCCAGACGATCTAGCCATGCCCGTCTCGATGTCTGTCT GTCCGTTATGTCCGTATGTCCGTCTGTCCGTTTGTCCGTTTGTCCGTTTG TCCGTTCGTTCGTGTGAAAGTCGAGATATCCGGGAACCATAAAAGCTAGA AAGTTGAGACTTGACAACAGGTATTTAATAGAATCTAATAGCTGCCCTCA AGTATATTACTATCTTGTTTTTGAATACACGAACAAAAGCAGTGTTATTT AATAATTCAGCTACATTATACGATATCACCAAAAAAATCTATGATAAGCG GGCGAACCAATCAGTGACTAATCCGTAAAAGTTATCTCATAGTCTGGCCG AGGCATTGACATTTGCGAACAGTTCGACGTGGTAAAGTCATTATTTCTTT TCAGGTAGGGCTTACCTCAATTAGCCGACTCGTGTTGCATGCTTCAGCAC CATATTTTAATTTGGGGTTTTCGCTGCTACGGTTGAGCAACCTAACGAGT GTGGCATGAGGTATGCAAAACATTAGAGCGTCTGGGAATAGTAATTATTT TCGCTCAGCTATACAGAGGAAAGTCATTGACTCTAACAACATTATGACTA GTCAGGTGGCGATTCGCGTGGCATGTTGCAACTTAAGCCGAATGCAATTT ATGAACCTGCAAATCTGATGGGAACAACATTTGCCTGAATGCATCTAACT GGTAGACAATTAGATCTTCTAAACTGTGAACATAAGTGATTTATCACAGG CCAATAAGTTAATATGGCTGTTTAGGTTAAGGTTATTTAATAATTGAACA GTCTAAAATGTACATCACTTTAGCTTTGGATCCTAAGCTATATACATGGG AGCAACGAATATGGAGGTTAGATGCGTTCCACTCGCAAGTAGATGCCCCC AACGGTGCCCAAAACTATGGACATGGGACTATACTTCAGTGGGATCTCTG TCGTATCGCAGACGGATACCCTGAACCGGCTGATGATCTGAGCCAAACCG ATGCGAGCCTGCATTTGTCCAAACCGCATCCCGATGCAGTTCCGCGGCCC GTCGCCGAAGGGCAGCCACTCCACGGACTCCCGGGCGGCCACTTTCTCCG GCGAGAAGCGCTCCGGATCAAAGGTCTCCGGATTCGGATAAAGATCCTCG TCGCGGTGGTAGGCGCAAGCGGGGATTATGACCTGTGTGCCCTTCTCAAT CACAAGCTTTTCATGGCCCGGCACCACGTAGTCGTTGAGGGCCTTCCGTT CGAGGTGGGGCACCAGTGTGTAGAGCCTCAGGGTTTCTGAAGAGCAATGT TGGGTAAAACCAGTTACAATCCCTCTTGGGGCTGTGCTTCAGACAGAACA CCTACCTGAGATGACCTGGTTCAAGTAGGTCATGGCTTTGATGGATTCGT ACGTTAGCTGCCCCTCCTGTTCCTCCAGCACCGTTTGGATCTCGTTGCGC AGCCTGTCCTGAATGTCCTGATTCTGAGCCAACTCATACAGGCAGTAACT CATTGTCGAGGAGGAGGTCTCAAATCCGGCCACATAAAAGACGAACACCT GGGCGGCCAGTTCGCCGATGTCCATGCCCTCGATCACCTCTCCGTTGTCC AGGGTGACGCGCCCCTTCTGCTTCAGTTCAATCAGCAGGTTCATGAAGTC GTTCCTCTTGAAGTTCTCCCGCTCCCTGAGGGCAATCGTGTCGTTGACCA GGCGCATGAAGAACTGGTGGACGTCCTCGGGCATCATGCGCATTCTCAAC CTGCTGGCCAGCTTGGGAAAGCTGAACACGAACATGGTCAGCAGTTTCCC GTGGCGCATATCGGTGAACACCTTCTGTCCCATGGTGCGGAAATCACTGA CAGGGGTGCGCAGCGTGTTACACTCAATGCCGAAGGCACAGGTGCCAATC ACATCGGTGGTGAACCTGGCCATCAGCTCCTTGATCTCGAGCACAGCGCC GTTCTGGGCGGCGGGCACCTGCTCCGTGATCACCTTGACGAACTCCTCAG ACACCTTGATCACCGTCGGGAACATGAACTTCATCTTGCCCGAGGTGAAA GTCGGCGTCAGCCTCTGGCGCATGTCCTTCCACTTCTTTCCGTCCAGGTT GAACAGGTGCTGCGTGAGCGGGTCGTCGCGCCCGTTGTGAAACTGGCCAC GATCGGCAAAGTTCGAGAAATCCTTGATCAGGATGTTCTTGGCCAGCTGG GTGTCCACGATGAAGGCGGCCGGCTTGTGCAGAAAGTAAAAGCCCACGAA GGGAAAGCCGCTCTTCCGGTACTTGTTGTAGTAGTCGTAGAAGAAGTCGT GCATCACCCGGTTCTTCCGGAACCCGACCATGTTGCCATACAGTGGGTGA GGAGCATCGTGTGGCACGCCGCGGCGATTCCAGTAGTTGAAGTTGCGGTG GTACAAGTAGGCCAAAAGCGAGGAGATCGCGATCAACAGGTATATTAGAA CAAACATTTTGCGTAGCTGCTCCCTTTTCGCAATCGTCGTGCTCGACCTA CGACGAATTACTGATCACCACAATATGTTCGCACACTTTTTATAAGATTC CCCTGCGACGCACAGGCATGACAGCATGTGAGCTAGCTAGCTAAATATTT CTATCACCATGACTACTACTTTTAAGTTGTTGTCATGATTACAGACTCGG CGATAATATGCAGGCACTTTTCAAACCGATTTAAGAGCACTTTCAAAGAG ATACTCATACGCTTGACTGCAAAAATGCTCGCGAATCAAAATATAAACAA ATGATAACGAGATTGTTGTTAAACAAACCGGTTGGTGCTTGGGTAAAAAG TGTCCCATCAGGTTTTATCACTCATTTATAAGCTCGGCATGTGCGAAAAG TAGAGGTAGCATTAAATGGTAAATACACATCGATATGCGGAAAATGTATC AAATCATTGTATTACTATAAAAACGCAATGACACGGTCATTCAAAGTAGC TTCAAATGTACAGGACGATCCCACTTGTAACTAAAGGTAAAGGTGTTTAA GTAATGGGTATTTGATAGCCGAGCGTTCCATCTAGCTTTCATTATCAGCG ACAACACCAAGCTCTTTTGCTTTTTATGAGAGATTCAAGATTTGACATAA GAGATATTCTCTTGATGTTCTACTGTTCTATTGCAGTGGATCTACATGCA AACAAACGATTACAAGATTGTTATTAAACAAGCTGGTTAAGGATCATAAA GGTTTTTCTCCTATGCGATTCAATATTTATTAGAAAACAGAGCAAATATA ATTAAATGAGTTTTTAAGCCTTGGGAATCGGAGCGAACATTATCGCATGA AATTGTTAATGACATAATTTCCCGTAGATAAATACATACACGGACATACA CATTTAAAATGTCACCCATTTATTTCAGTAATTAGCACCCCACTACAACG TTAATGTTTGGTGTTCCACGGCGATAAAACGAATGAATTCGCTGGGAGAA CCAATAACTCTTTCTAAGAGCTATTTAAACGCTTCACTGTTTGAATGACG ATCAAAATATAAACAGTAGATAACTTGATTGTCGTTAAACTGGTCGCGGT TGGTTTTAAACATTATAATCGCATCGGGTTTTATTGCTCATTTGGAAACA ACACATCAACTGTGCTGTGTTAAATTATATTTAGCATATATGTGATTAAA ATGTATTCATTCGAAAGCAATGTCGCGTAGTTAAATCTACATGTCACACC AACATTTAAAATGACTAATAAATTTAGTTTGTTGCCTTATCTCGTTTTAT TTTCAGAAATCAGTGCTAATGTACAACACAAGATCTAATTAAAGGAGCAT TTTTTCTGCAGTGTTCGGATTTTTAAATATGTTTTGAGATGAGAGAAGTT TAACTGTGGTTAACACAAGGAAGTATTCCACATTAATCTGGGTGCTTAGA GTATCGCTTATGAAGCCCAATAGTTAATAAGGGCACATTATTGTAATGAT ATCTCATCTGAATTACCAGCCACACAATTGTGTGTGCTTAACGCCCCGAT TAAGCTTACGGTTAGCCGCTCCCTAAGTCGCGTTCTAAAAGGGTATAAGC CGATTAGGATGTGCATTTGTGCCGGGAAATCTCCTTATTTTGTCGGTTGG GAAAGCGGGAACACTAACGCGATTATGGCGGATTTATTTTCTCCGATTCG AGGGAGCCAAGGCAATATTGACCTTGTGCATTTCTTATCACAAGCTGCTC GAATTATTGGCACAGCCCCAGGGCAGATCAGAGTAGACCAGAGACTTATC TGGGAGTGTTCTTGGCTGTCATTGTCTTGAACTGGTCGTGTTGCTTAGTG CTTAGTGCTGCAACTGACACTTCCATGTCCCACTCTGACCTGGGAGTTTA GACAGCAAGTGGCGCGAAAAGGTGAGCAACGATTCGATTTGAATCTAATC GCCGATACAAATCAAGTCCTCCTGCCCGACCTTGAAGTGCTCAGTCTCGG CCCACATGGGTCAGGGTGTTCCATACAAGCCCGCATTAAGATGGGAAACA AATATAACGCAAAGCGCGTCGTTCTTGGCATAATGAAGCGCCCGACGAGA AGAAAGAAAGGCATTGAGGAAGCGGCGAGGAAAAACTAGATTGCCTCTCT GGCTGCACTTATGCGCTAAATAAAAATGCAAATCTAAATGCAGCTAAGAG CCGAGAAGGGCCCAAGAAGCCAGGCGAGCTCACAAAGGAAACCCCACGCC GACGGCGCACAATGCAGATTCTTAAAGAATGAAGAACGCGCTCGAGGGCC CTCTAAGTCGACATCTGACTGCCGCAGTCTCTGGCGGATTGTTGTCTCCG GGTAGACGGCCTAGCTAATTGCAGATGCATCTCGGCTGCATGTCGCGGAC TTCTTGTAAACAGTCGCCTAATTGTTTGCTCCGCAGAGGTGTTGCGCCCC AAAGACGCAGCTCTTTCGAATGCAAATGCTGACTGAGAAGGGGTGCCCCG AGTGCCTGTCCAAGTCCCAACCCCAATCCCCTCAAGGCTGGGTACAGCAT GAGCGAGCGCCTTGAATAAATTAGTTTTATTTGTGTCTGGATGTGGGGCA ATCTAAACAAATCGTGAGCGGAGAGCATGGGATTCTGCATTTCCTGTGGG GTGACAACAGTGACGATGTCGCGTCTGCGTGTTATGTAAATCACAAGGAA AGCCGAAATGGAGGGGCGCAGTTGGGGGAATCCCCTACGTCAATACAGAA ACACACGCCTCTGCAGAACCCAACCTTTGCAGCATAATCATAATCATCAC AAGAAGCATCTTGATGAATTGTAATAGGCTTTAAGCCTTCTGAGTGCGCA TTCGAGTGAAACAGCACCCACTCCAGTTAAATACGCGAACTCCCCAGGCA GCGGCAATAATTAGCCAGATTCCACTTTGTCGCAGGATGACAATGGCACA TTCCTCCTGCGGGATTTTTCAATCACCGCCAGACTCTTGGAGCAGCGGGA TGATGGCTGATTGAATTTCTGGGCTGACATATTCGAGCCGCGATTGTGAT TGCGATTGCTATTGCTGTTGTGATTGTGATTGTGATTGTGTGGCATGTGT GGCAGCTGCTGCTCCGTATTGATTCGGTGCTGATTGTCTGCCGAGGGCTT TGTTTCATCGCAGCTCTACTGTCTTCGGCGGAAGCCATAAAAAGATGACC GGGTGTGATGTACTGACAAGTGCTGGGTCAATGTGTCAAAAGAGAGAGCC CGATGCGGCTGTTCATCAGGCGAGATGACACAGATTGTCCCTCGCACACC GGCCAAGTTGCAAATTGTTGACTTATGCTGTTGCAACTGGAGCGGACTGG CAGTAGTTGCCACCCAGAGATCCGCGTTTACGTGGCGCAATAAAACGCTC GCTGGTGAGCACCGTGAATATGTTTTATGTGCCCAGATGGCACCACGTGG CGTATACGCACTTTAAACCAAAATTGCCTTTTGTGCCGTGAATTTAGAAG AGGTACACGCCAGAGCTTTGGGCAAATAAATGACAAAGCCATTTGTAATG AAATATTAAGGCCGGCAGTAAAAGGAAGATCTGGAGGAGTGGTTGGGGCG TTGGACGCAGCGGGAAATGGGCCGGAAAACATCAGCATTATACTTATTCA TTATGCTGCTGGTCTAGGCGTGGGCGTTTACGCATTCGCATTCCAGATCG TGGGCGGAGCGGTGCTAGCATGAGTTTTATTGGACGCACATCACATAAAC ATGATGCGGTACGGGCATTTGGAGCGTGGAGCACATGGCCCGAAGGCAGG AGGAAAATCGATACCCACATGGCCACATGAGCAACCCAAAGATCTGGCCA AAAGCGAGGCGTTGCAGTTTCCATGGCGCAGGTAGCAGAATTTAAATGGA TTAGGGTAACTGTGTCAGAAATCAATTATTCAAATGGAGTCGCATGCACG CATCAAATTAAATTTCCACTCAAACGAAAACAAAGTGTATTTTCAAAAGC AAATTAATTGCTCTGTGCTTCCCGTTTTGGCAAATCTAGTTTTGTCCCCA GGCAGCAGCAAAAATAAATCCAACTAGATTTCCACGATGACAACAGCAAA TCACGATTGCCCTTTATGGGCATGCCACCAAATAAGAAACGGGTATGATT GTGAATAAAAACCCTTTCAAGTTGTCACTACTGAAGTGGTTGGTTGGTTG CTTTGCTCGACTTTTGCTGGCAACTGTGGCTTTAAGCCACAGCCACAGCC AGAGTCCCACGCTTTTAGCCACCGAAATGTAAATTGGGCAAAACGCATGC CGAGCAAACTTCTTTTCCCATGGCTGGCAGAACGGGGGAAAAGGTCGATA AGAATATTGTTTAACTCAATTCAGCACGCGAATCTGAACTCAGCCCGATT TGTTGATAAAAAGTGAAAGTGGAAAGTGGAAAGCGAAAAGGCAACAGAAC AGCGCGGGGTGGGGAGGGAAGGGGAGTCGATTCGCAGCCCCGGGCAATCA AATTGAAAATTCTCCATTGTGCAAATATTGATTTTGTTCGCTGCATAAAG TTTATGCGTCCAAATCGAGAAACTCAAGTAGACCAGGGAAAATTCGGCTT GTAATTTCCTCTGCGATAAGCAAGAAGTTGGGAGCCATTCTCAATCCGTC TGCGATCTCAAGTGTCTGGGGCAAGGTCGCTTTTTGTGGCAGTCTCGTTC CGTCTTTTTTTTTTTGCCCGGCTAATTCGACGCCCTTGCCAGTGGAGTCG TGTGTTGCGAGTTTTATATTTTTCCCAACATATTATTTATGGTAATCGAC ATCAAATGCCGCCATTAAGCTTATTGCCATGGCAAGCGGCAACAGCAAAG GCGTTTTCTTGCTGCTTTTTGCTGCTTTTTTTGGGCTCTGTGCTTCTGCT GTTTATAGGCTTCCAAAGCTAAAAATATTGTACATCTGCATGGGTAAATT CTAAAAAGATGTGGAAGTACATGAACAGATTTAGTCGAACTTTTCTATAC ACTATCTGTTCATATCTATTCCCTGATAATATGAATAGAACATAAATTTC AGTTTTGAATTGTGTACCCAATAACTTTTTTTTTACTATTAATGCACTTG AATATTGTTTTGATATTAATAATTGTTGATATTAATAATTATCTATTGTC CATTTTAAATTCATTCTAATGAATATTATATATATATTATACACAGCATC GAATTGAGTTGCTCGATTGAAATCTGAAGATTCTACGAAACATTACATCT TTTCGCCGAAAAGTTTTAATTTTTTTTTTTGTCAGGGTATTTTAACAGCA TTTGCATACCGTGTAGGCGATTTCTCATATTCGAAGCGTTGAATTTTTGA ATGAATTTATGACAAGCACGTCCCTCCGCTGAAAATCTCCCTCTCGTTTG GCAATAATTTGTTTGTATCTCATATTTGATTTGCGTTATGTACGCACTGT GTGAGTTGGCGAGGGGGTGTGTATCTTTTGGCACCTTATCAGCAGATTAT TTGCATAATTTGAGAATATTTTTCGAATCGAACATTGGCTTTCCACGAAT CGCTGCTCGAGCTTACCTAATGAAGCAGTGGCCAGAGATACCGATTAGAA ATCGTCCTATTCCGATGGCGCGTGTTCAGCCAGCACTGAATGTGTGTGTG TGCTTATTAAATTATTGCAGAGTTGCTAATGGAAAAAGTCGTGCGATAAA AATGAATTTATTGCATTTTTCGGTTAATTTGCCATTGTAAACTTATTTAA TTACGAACTTTTTCCATGCTAATGCAAACTTTTCAGCGAGCAAGGAGTAA ACTACCTAAATGGGGATGGGAGATGCCCGCTGATGGATAATTGCCCCGAG CTGAAAGTGCCCCATTTCATCCGCTGTTGTTATAAATAAATAAACATTAT GAAACCACTTTTATCCTGATTAATATCATCATGCGCTCACCTCCGCACAT GCATGTGCATACATACACACGTACGAGAGTATAAACATTTTTGTTTAAGG CCCCGGAAAACTGCTTTTTAACCGCCCACTCGAACTCCGTCCTCCGCCCA AGCTATTAAAGATTATTAAAAGCACCTTGATCTCGGGAGAAGGAGTTCCC TCCCATGTGGCGCTGATGCTCTTGCTCTGTGGCACGCAGACCAAACGTAT TGATCCATAAAGCGTATAAAACACGAGCAGTATTTGTATCTTACGTTGGG ATGCGATGAGGTGGGCGGATTGCGGACCGAAGGGGTTGTTGGTGGATGGA GATGTGCATGCGGATGATCTTTGACCTTCGGCAAGGTTGTACCCCCACTT TCTATTTTAGGCCCAATTAGGTTGCAGCTATTCTCTTTAGGCATAACCCC GGTGAACATAAATCTCCGTATGTACACAATGCTCATCGAGAGTGAGCCAT GTCTTCATCTGCAGAGGTGGTTCCCTCCCCGGGCATTATCAATCTTTCAT CTTCGTCTGCATTTGTTATAGTCGAGCTCCCCTAGTTGAGCACTCATTTA TGCATTTTATTGGCTCTTGGCTAGCTTGGAGCACCATCAATCATCTCGAT GGCTATTCAGTTGCGATCTACTCTGCCTTTTGTGCTTATATTTATTATTT GGACGGGCCGTCATAAGTGGTCCACCTGTTGGCCGAATAGCCTGCCCAGC AGTTTGCCAATAATTTTAATCAATTATGCAAATCGCATTTATTGGCCCAT GATTTATGCGATATATATGCATATCGTGCATATATGTATAAGATGGACGA AATGGAGCGAGAAGAGCTGTGTTGACAGTCGGAACTGATTTGGAGCCCAA GGAGCCATTACTCATCTTTCCGGAAGTTCTGTGTGTGCCCACTCACATCA CTCAGCCCAGGTGAAGTGTTCTGTTCGTGGTGCTAATAATATACATATAC CCATATAAGAAGAAGAACCCATTCTGGTTCACGTTTACCCAACTGGCTTT GCAAGCAGTTCTTTCCAGATAAGAAGGCGATAAGAACCCTATACGAGTAC GAGTATATGAGGCCAATGCAAATAGCAGATACGCACCAGAGGAGAATTCG CTGCTCTTTCCGCTGCAACCTTCCAGCAGATTTAATGAATGAAATCAACT TGAATTAAATTCCTCCATATTGCGGCTTTGTTTCTGGCTTTATTTGTTTA CACACACTGCAGCTGTTGAATCACCAGAGAGGCGAGAAATGTGTTTTCGG CTGCCTTGCTTTGTTTCGCTTGGAAGGTAATAAATTTTTAACACAATTGC ATTGCATAAACAATTTCAAAACTGCACTCGAAATGGGCCTGTTTACACTC CGTTGTCGTGTCGATTACATTTTTGGCCAATAGCCAAGCACTCAGATTTA ACTGGTTTATTTCGACTTGGCGAACGCCCGCGCGCGAATCTTTCAGCACA GCCCACGCACTTTCTGCAGCATGGTTAACTTGAAGATACTCGAATCGCAC AGGGAAACAGATACGGATGGGCTCCAATGGAGGTGATATAGAGGCGTAAA CAGAGGCAGAGATTCAAACCGAACCGAACCAAACCGAACTGAACCTCTGG GCCAGCGATCGAGTTGTGCGCCGCTGGAGAGCTCGGCACGTATTAATTTC TGCGGCAGCACTAAAGTATCCGAAAGATACGTTCCGCTGGTCGCGCACCA GCGCACATAGCCGCCACATATGTGGGCAACTTCGCTGCCGGCGTCGCCAA CTTGTTTGACAGCGAGGTAAACACAACCGGAGCACAGATCTGCCTCGTCT TCGGCCCTTCTGGATGTTTATATTTACACGTCGGGTCGGATCGGATCGGG CGGGGGTGATCTCGATGGGTCAGATGCGCGACGGGTGTCGTTGATTTCAA TGAAGAGCCACAATTTGTCGTCTCAAGTGGCTCGTTTATCTGCATCCGAC GCGGTTTATTCTAAGTCTGAGATTCAGACATCCGACAGCTCCCGACAGTT TCCCCCAGCCCCTATCTGTTTGTTGGGCAAAATGATTGGATTCAACAGTA ACATTAACATTAGCCCTAAGTTAGCTGGTTCTTGATGCCATCGTATGCAA ATGGCTCCCATCGGAATTGGACAGAATTCGGAGTTTTTGGCTAATTAAAA GTTTCGTCGAACGGGGCCACAAATGAGGTCGAATGAGGCCAGTATCTGCG ATTTGTATTTGCCCAAAGAGCGAATGCTTCCGCTTTGAGGTGTCTTGACG GAAATGGCTCTTACAAATCAAATCAAATGTTTTGTGGCTTGAGGCTTTTG TATCCCACAAAACGAGTAGAGTGTGTGTGCTCTATTTAAGCCGAGAGATT TCACTGCTCATCCAATTATTTGTGGAGATGCTTTCTCCGAGCGCGGGTCG CACAGATCAAACACCTACGAATTGAGTGAACTTGAATATCGATGCTGCTG GGTCACCAGGGTGGCCGTGGCCCGAAACTGGTCTGGAGGAAGCCCCGATC ACCTGCACCTAATGATACATAATTACATGTGGGCAAAGTTTCAGTTTCCA AAGCATTTTCATTAGTTTGATGGCCTTTCTGCCAGGGAAGGCCTGCTCGG GCGTTCCGGCTGTAATTATATAATCATTTTAATTGGATCCGGCAATGTTT GCCGGCGCGGCGGCACCGTCGACACATAACAAAGATTAATCGTGCTTATG TCGGCGGGTCAGGAGACAAGAAGTCGAGCTAGACGAGCACAAGTACGAGT CATGTCTCAGTATCTTGCAGATACTTCGCTACATGCAAGGTCGCTTGAGT GGGTGGGGTTGGTATCCCGAATGCAGATTCCATTGCAATACAACATTAAT TCAATTATAACGGCGCTCTGCAGGTGCGACGCCCCCGCATGACTTTGCCT TGGGCAGCTTCGGGGTTACTCTGCCAAGACATTTATGAATTAGTTGCAAT TTGTATCTGCCTCAGCTGTTTTTGCTACCTAAGGCCGCCCGCTCGCATTT CATTAGTCCCAAATTGGCGTCATCACGTGATCGGAGGTGGTCAAGGGGAA ATCCGTAGAACTCCAAGCGGAACTCGCACCAACTGACAGTGGCAGTCGGC GAAGTAACACATTCACACATAAATTTCCAGCACTCCGGTGTATCTTTCAG AAGCGGCACTTCTACTTTTGATGAGCACCTCTCGCAGCGCGCATCATTTC AAATTAATTGTGGGTCTATTGATAGGGCCCTTCTTTGTTTTGGGGAACTG ACGCTGAGATATCTATGTGTTTATCCGGCTCTGGAAATTGGGCTGTGCGT GTCGCACGCCACATTCATTCACCGAAATTCATAACACTCGCCGGCGAACG AAGTGTCAAAAACAGTTTCATAGGCCCAAAACACCGTGCATTCGCTTGAA TAATGTATTATGGTATAATTGCGGGGGTTGCCCACAGGCAAATCCATTCC GGCTTTTCCCAAAGCCAATCAGCCGGAAAAATTATACAAACGCAAATAAA AGGCAGCGGGAAATTCGGGTCAGCAAAGATGTTAACAGGAACGAATCGCT TTGATAAACCGGAGCGAAAGAAAATTTATTTTGTATACGGAATCGATTAA AGCCGGTTGCTGATAAATTTTCTTTTAGTTTTCACATTCATGTTTTCAAT GGACGGGGCCCACTGAATATAAGCAAATCAATCGAAAGCTATAAAACCTT AATATTTACAAATATAGAAGATAGTACTTTTCCGAATGAATGTATGCCAA GGCAAAAAACGCATGAATATTTTGAATTGGGCGTAGACGAATTAACACAA TGGACCATAATAATAATAAATTTCTTATAATCAGAATGAAAGTTAACTTT AGCACTTAAAAGTCGAAATACCTTTATAAATTTTACGCTTTAGAACTTGC CCGATATAAAATATAAGTTACGACTTGCAAGCATATAATCCTGATTTTAT CAGAAATGTCGAAAGCGGATTTTAAGCTTCGATTGAGTTACGTATGAATA ACAGAGGCATGATGAACGATGACGATTCAAGGGTCTTATCCTCATTATTA GATCACCTCCATTAGCCCTTTGCCGGCGATACTGAAAAGGATTGCAGGGC ACTCTGCCCACACTTGGACCACTTGCCACCAGGACCGGCACTGCAATTCC CAGTGCCACATGCTCGACAGGCCACAGCCACCATATTAGTAAGCTGAGGT CAGGCATGCTGCCACTGTCATGCCCCACTTAACCATAAATACTCGAATTT CCATTGCAGCCACTCGTGCACGGAGCGCACCCGAGGAGGAGCTCCACATC GAGACCCAGACCCCACACACACACTGCTCGGCCCCAGTTCCCAATTCGGA CCATTTCAATTAGCAGACACCTCTCTGGACAGAACCCACCAAATGAACTC GGCCGTGGCGAGGCACAGATGGATGTGGCGCCACCATATGTACGTACGTA CTACGTAGTACAGTGTACACATGTACTCGTGCATTCAGAACACTGGGCTG GAAAAAAATGCTGGCCAATATCCTGGCGGAAATTAATGTTGCTGTGGCAA GCACAAAGCCAGAAGGAGGGCAACGGCGGAACGGAAAAAAATTGAATGCC ACAAACCGATATGATTCGCTGCGGGAATGGGAAGGGGGCGGATACCCGGC CTTTCTCCGTTGTCAGCAGTTCCTTTTTCCTGCTGCTCACATCGACGGAT GAGGAGGGGCTCAGACCGCAGCCAGGCACGCCCCCACTTGAGTCAAACCC AACCCCCAACCCAGGCCCAAATCCCCGGAATATTGAGCATGCACGGCGGA TCGGATATGCAACACGGCGGGTACGCCGAGTAATCACTATCAATTATATT GCTCAGCACGCGCATTGTCTCGCACTCTGCGCACGGCGGAATAGTGTTCC AGGATGTCTCATCTCCTGACTGGTGTAAGTAAGGACTTACCTTGCCATCG GCATCGGCGTGGGCATGGTATCGCACCTCCAGCGATCCGCCGAGCACTGC ATACCAGAAGCGTCCCTGCTCGCCGGCGCGAAAAACTGCGGGGAGGAGAA GTTTGAGTTAGCCACCTCTGTCGCATAGTTAATCCCCGCAATCCAGCACT CACGAGTCACCCCCTTCTCCAGGTCCTCATAGAATCCGCACATGGCCAAC TGCTGGAGCGCAGATCCCGGGAGGCGACACAGCGGCTCCACGCGACGCAA CCGGCACGAAATTAGCTCCACATCACGCAGGTTCCGGTCGCAAGGACTGA AAATCGTTTAAAAGTGGTTAGACGTTAATGTACTTTAAAATCACTTGCCG TGCTAGTATGGGTTTCAGATTAATATAAACATGCAGCTTATTAAATATTT CTATGTGCAATTTGAATTTTATAGAAGATAACACACTTGAGCCGCGCTAC CGCAAAAAAAAAAAAAAACAATATCGCACTCATATATGATGACTTGTTTA CATAAGTGGTGTATAATATTTGTTAAAGGTGGAAAGTTTGAACGAAGTTT TTTCCGTATAAACATCGAAATCACGGAAACTTTAAAGATCACGCTTCTCC CTAATCACTTCAATAACAAATGCAATCTGGAAAACAGTATATGGTTGCAG TATCAGCACTTCTCTCGCACTCCCTTTACAGGGTAAGAGGTATGGAATAG TCGAGACACTGAAATATTGTTTCTATAAAGTTCTTATTATATCTGACATT TGACCTTGTATCTGATAGTGGATTATCTCGTTCATAGCATTCTCTCTATA TGTTATAAAAAATAAATAAGTACGCTTGTCATGCAGCTTTCATTTCGGCT ACTGATTAAGTTTATTGTTAAATACTAACATTCTGCATTAAGGTTACCAG GAAGATTTACCTAGCTTATCACAACGAATAACAAATTATCAAAGAGGACA ATTATAAAACAAAGCAAAATGCTCCTTTGAAATAACAAAAGTAAAAAATT AATACGTGTAAAGGACTCTGAGAAATGAGTCGTTTCTGAACTCAAAACAA CCGAACAATAGACTGCAATAAGGAAAGAAGAAACCAAAAAAAAAAGAACA CGAAGAATAACGAGTATTTTGCATTTATAATTTACTGACTCTATGAAAAG CACTTCACGTGGATTATTCTATTTTTGGATCTACTTTTGGAAGGCCATAA ACTGAATAAAAATGAGGAGAAATGGCAAAGCAAAGTATTAGTTCAACAAT GAACTCAAATTAAAAATTCCAGTGTCATTTGTGCTCGGTTTGTGCGCGCA TTAAGTATGCAAATTATATTTTTTGCCTGTCTGTGTGCAAGTCAATTGAA AAATGAATAAATAAGTATAAGAGTTTCCGGGCAAGAATCTGCAGGAAACG GAAGTCCGCCCAGAATAATGAGAAGAAGGGCAGGGAAATGGCGAAGCAAT GAGAGTGAAGCGTCAACTAATTGCATTTGAGAAAAAGTTAGCTGTCAGAT CTAATAAGGAGTTCTCAAATTCAGGAAGTGCAAGTAAGTTAATTTTAAAT AATAAAAATTAAATCACCTTGCTTTAAAAAAAAAATAAAGTTTTTCCCCC TAGGAAAACAATACAAATCGCGCTATAAATAATGTTTTTACATGTCTAAC AGACAACAAATTGCGCCTTGCTGCCATGCGGCATGTTACCAAAAGTTTTA AACAATTTTCAGGCGAGCTCCCGCCCACCATAAATCCCCCAATGCCGCCC ACACTGGAGACCCCACCCAACTTTCGCCTAATTAAAAATTCCATAAAACT CAGACGGAGCGGGTGCGTCCGCAGGAAGGGCTGACCTGGGCAGACAAAGG CAGCTTGCAGTCAGGAATAGATCCCAAGCTTGCCCCTGGCCGGGCATCAT CTGCATCGAGGGCTACTTTTGCAGCGAGGCGTCTACTTTTTTGGCGCAGC CTGCGAACAACTTTCATCCGGCTCCTGAAGGTGAACTGTCTTGCCGGGCT CATGCATAATTCATTCGCCAGTAGAAGCGGCAATTTCGGGAACCGAGTGC CGAGAAGGGGGGCCACTAACCGTTTCTGGGTTTGTCGTTAACCAAACAGC CAGGTGGCTGTTGGTGGGCGAAAGGCGAAGGACGAAGGGAGTGATCCAAA GAGCCGGAAGCGCGTTGGGACACATCCTAGGCAGCCAGCTCGTTGTTTAT TATAATGGTTTTTGCGGTTTTTAGGCACACGCCCGAAAGTTTAGTTTCGG AATTTTGTAATTGGCGTGCCGGCGATTCGTCAGCCTTAAAGCTGCGGGGA AGGGTGGCCTCCTCGCACACATTAAAGCTGCTTTGGCACACGTGGCGTAT GATAAATGTGCGGCGGCACTTGTAAGTAAGACGATTGTTCCTCCGCCGGG AAGGGGAAGCCATCAATATCAATTGCTGTCTGCTGGCTTTGCCACTTCAC GCCTTACGTTCTGCGATTACCTTGCCTCCTTCCAAGGATTCTCCGATGGC ATGCACCGAGTGCTCCCTCGTCCTTTATCTCCAGGTGCGCTTAAGCCCAG ATCGCTCTTGATAAGCCGAATTACCAGTCAGCATGACGTGCCCTTCTTGG CTGTGCCATTAATTCTGTCCAAATTAAATCGTTTATTTTGTCTTCGCTCC CTACTTTAGTACGAGGCCATTTGTATTAGGTCCATAAGAAGGAGCAGCCG AAGAGCTGTGAAAGAAATCTGGATCTGCATACTGCACCCTGGCATCCTGG CACCCTTGCGCTACTAGGCCCTTTCTCTTTGGGCGGGGCAAACAAAAGGC AGCGGTCTGCAAATGTTTGCCCAGGCACAAGGCAAACAGTTTGCTTTAAG CCCTTGCCACTTGACCTTTCTTTTTTCCCGCTGCCGCGCACAGTCACATG AGTGCCCGCTGACCCCTGACCCCTCATGCTTTAGTGCGAGTGCGGCAGAA GCGTTTAAGCGTTGACAGAGCGTGAAATTTGAAGAGATTGTCCTCTGATT GATGGTGTGTGTGCGCGGCGGTTAGGGGCGGGCCGGTATGAGGCGGAGGC ACGCCCCATTCGGATAACACCAATGAAATATAAGGCCACTCTGCAATAAT AGAGTGTGCCGCACAACTGAGCAGTCGGTGGGGACAGGCGGGGCTAATAA TGGTAATGGTAATGGTGGCACTCGTCCAGCGATGCCCCAGCTGAAATCCA ACAAATTGCATCAAGTGGTTGCTGGGAAGAATGTGTGCTCGATTCCCGGC CATTTACGGTTGGGCAAATCGATTTAGACACTTTGAAAAACAATTTTGAT CTCTGGTCAATGTTTGATTAGCTCGAATCAAGTTCAACTTAAGCTTAAGT ACTGCGCACACACTAAAATAAATTTGGTTATTCCGTAATTGTATATAAAT ATTTTACACGCTAAATGCTGACTATTCTGTTGATTGATGCAATAGTAAAT GCTTTAGAATGCTGACTATTCTGTTGACTGTTGCAATAGTAAATGCTTTA GAAATAGCATGTCATCAGGAGAGATACTCCATCTCACATATGAGCTTTTT CATTAATTTAGATAAGGGTAATGTTATTATGTTGGCTGTGAAAAGATAAA TACTGTGGTGTCCAGATAAAATGAAACCGCTCTCTTAAATGGAAAGTATA AAGTCTGACATCAACTAAAAAAAAAAAACAATAGTCCCGTGCCTCTGTTT TATTCCACTAAAATAATGTTTGCACAAGACTAAACTCCATCCAATTGCAA AGCACATATTTACGTAAAAAATGTATGTGCATTAAAACCTCTGAAATGCG GAGCTTTCAGCAGAAATATATATATTTTCAATTAAATTATAGTATTTTTA TACTTTTACAGCGGTTTAATTATTATTTTTGCACGACAGAAAACACTTTT CAGGCATAGCTCATGAAATGAATGGTAAATTACTTTAATGCTTTATCATA ATATAAATTGTATTTTAAGAGTAGTATCATTAAATGGGTTGGTTTATTTA TAGCGAACTACAATTACATTTATTTTGCATTTCAATTCACAAGAAAGATA TGAATGTCATGATTAAAGTCCTGTTTTTATTTTCCTTTGTTCGGTGTCCA AATCAGGAATGATGAAATAATTGCTGTGCAGAAGGCGGCTCATTGAGTTA CGGAGAATTGATATCGAGATTTAATAAAGCGGATAATTCGTGGCAGGCCG TGTCCACAAAGTGGATGGATTGGCCATTTGCCAGCCATCAAGGATGGAGG AGGATGGGGCACCCCGATGTTGGTTCTTGACAAATGAATGTCGAGCATGA CGGCAACATTTTAAAATGTTTCGCTTCTCGTTCTCGTTTTGTTTGTACTC CACGTCGAGCTTTTCATTCAACTTACACGTACGTCGATGTGTGAGTACGT GTCTGCTCCGGGAAAACAGAGGAAAGAAACTTGTGCACTCAGCTGGGAAA TGCCTTAAATTTAAGAGAAAGCATTCCGTTTCAGCTAAGGAAACTTTTGG AGCTAAAAACTTAGAATTTAAAGAAAAGTTCCCCAAAATCGCTGCTCATT AATTGTGCAGCTCATTAAAAAATCACTTACCGTTTGTCCATTGCAGTTAT CCATTCCATCGCCATGTTGAATTTTTATTTAAATCTCCCTCGCTCGATTA GTTTCGCCGTTTGACACAAGTTATGATACAAGTTATGAACAGCACATTCC ACAAACACCAAACCAAATAGTTGCCCCAACTTTGAGCAGAGCACATAAAT CGAGGCGGAGCGGCTCCAAAGTGGTGCAAATTAATTGCCCGTTGCGGCCC AGGAAAGCGAAATCAAAATACCGAGTAATGGCGGCGCTCGCACCCAGTTT GCAGTCACCTCAATCCGCGATGTGGCCGTCAATCTGCGATTCCCTTTGAA TACGACATGCCAGGTGGCTCGGCCCAGCGAGGCACTCGAAATCCGCTTTT GGGAGCGTTGGAGCGAGCTCCTTTCGAGTTGGAGCCAGGGGTAAGTGGAC GTAGCTCGTTGATTAGGCGAAAGTTTGGAAATGGATTTCAGTTTGAGCTC CCGTTTGGCTGGCGACGAGGATTTCGATACCGAGCAGCTGCAAAGTTAAA TTGGGCGAATGTGAGTCTAAATTCACTATACAGCAGTCGTAAGTGTAAGC TAGCCTTGGGATGTCGGACTCTAATATAATTTATATAAAATGCCAGCAGC AGATGTAAAAGTTTCCCTCTTTCCGATTTTTTCAGCCACATAACTAATGT GAATTGCTATTGTTGGACTTGCCAAAAAGGGTTTTCCCAACTGCTGATAG CTGCCCAGAAGGCCCCACTGCGTCAGTGTGTGTGTGCTTGTGTGTGCTTG TGGGTATCTGTGTCGCCAACAAAAGCAAATGTTATGAATAAGCTTTGATG CCTGCTCGGCCGGCGAGGGGGTGTTGTGGTGCAGGAGAGCGGTGAGGGCG GAGCACCAACAAACTGTTGGCGCACAAATCTAACAATAGATTTCCAGATA ACAATAGATTACTCCACACACACGGCGTATACTTAATGCGCTGTCAATGG GCATTCTAATTTCCCAGTATGCCCAAATCCAGATCGTATGGCATGCGAAG GCACGATCTAACCGCGAATTCGTTACCGAACTCCATGTTTACCCATGCGC TGCACTATCTGTATCTGTACCGCAAACGAATGCGTATTTTGTTCTGCGTC AATGGGAAAAAACATAATTTATACCACCCCATCAGAAGTGCAGTGGCTTT CGTCAGCGAAATGGAACTGCAGGCGGAACAAGTGTTCGAGTGACGGCTCA AAAGGAAAGACATCGCGAAGGACCATCAGCTCGCATATGAATAATTAAGT ATTCGCCATCGTGGCCAGCCCGCGAAGGCGCCCGAATGTATGCCACGTTT TCTGACGTGTCGTTCGCTCGCTGGCTGGCTCCACGTACATAAATGGCGAC AAAAGTCCCGGGGGCGATAAGACTGATATTGGCGATATTCCGAGTGGACG ACTCGATAAGCGGCCACTTTCGAACGAGTTGTCCATCCTGCCAGCAAATG CAATTAGTGTCCGGAGTGGCGGTTAGGGAATTGAATTGAACAAGCTTTGA AATCGCCCTGGAAACAGATGTTCCATGTAATTTCCACTTTAGGGTTTCAA ACTTTGTTTTAATTAAGCAACCGAGTGAAAGCAAAACTTTGAACCACAAT AGATGTGATTTAACTGCCCACTGCAGCCGTTGCCAAACGGAAAACTTAGC CATTTAGCTTGGTCATGTGGCGAAGAAACATCATGAATCGAATACTCACG CATCCTCTGAACGGAGAAAAGGATCAGAAGATGCAAGAGTAACAGAGATC CCGCAGCAGAATTCGATATTTTAAAGTCCTTCTTGTTGGCAAACACTTTT TGGCACGGAAAATGAACTTTTAGTTTCGAACCCACGCGACATACCGAAAT CCAGCGAATACCTGAAATCGAACCGACTTCAAACGAATATTTAAATGAAC CACTTGCTAACGGCTTTCAAGCACTTGGTATATACAGTTCTTGGGCAAAC ATTTCAGTTCTCGACCTCCGCTGAAGCGCTATCGCGTCCGATTCATTTGG TAGTCGCGTCGCAACTGCTCGGCCGCCTTCCATTTTCCGACTTCCGAGCG GCGCTCTTCACCACGCTCCTGTCCTGCGCCTCGCAGGTGGGTTTCCCGGC GGAGATTGGGGGTCGTGGTGGGTTGTTGGAAGTTACTCATTGCCGATGAC TGCAGTGTTGACGGCTGCGGTGCGGTACTTTTGGCCTTGTTCCGCCTTCC CGCCGTCCCTTTCCGTCACTCACATATTTTGGCGCGTTTTTTAGCAACAA GTTTGACAAATCTTCGGCACAGTGGGCTTACATCCAAATCGGTGTGGTCA AAATCCAAATAAAATTTGGCACACGAAAAAACGTAATTTCAAAGTAGTTC TAATTAAATACAGTTTCTTTGCTTATAGTGTTTGAAATTATACTACTTTT GTTATAATATTTATTATAATTTGAATCCCATTATTTTGTGATATGAATGG ATTTCTACTATTCTTTTACGATTTTAAACTTAATATTAATTTAATTTAAA TATTATTCTTATTCATTTACTGCCTACACTTATATACGATAATCAGCAAA GAGATACAATTTGTATAAAGATGGCTATAATGATATAGCATTTAACATAT AAATTTATGTTCTTGTTTGATTTATTTGTTTTACTTACTTGCTTATTGCT TATTAGTATAGATTGTCTTAAGTCCTCACATGATTAGTGAGAGGTTTGGT TTTATCTTTTATATGTTAATTGCGCTGTTATGTTACTGTTACTGCATTGT ATGGATTCATCGCTTCTAAATAAATAAATATAAAAAAAAAAAAAATATAG ATTGTGTATTGGGCTTTAAAGATGAAAAGTTAATCGAATCTGATATGTTG TATTACGAATAATATTGCTTGCCTAGTCTACTTGAAATAACAATTTGTTT TGACTCTATTCACTCGAATGTTTAGCAACATTTGCTGCTCGCTCTCCTAT TCTACGTGCTCCACAACAAACTGTTGAGCGTTATTTTGGTGAGTCGTCGC AGTTGACCAGCTCTTCAACAGGCACTTGTCCGTCCGCTCGGCCGTCGGGC GAACAGCGGACAACCCCGCACCGCGCCCCGGGCGGAACTGCCTCACACCC TCGCCTGAAAGTGCACATAAAATGGAATCGCAATGCGAAACAATCAACAT GTCAATTAAATAATGCACACCAGCAGCGGACACGAAACAACGGACAGAAT TTACGGAGCGAGTGCGTGAACACCCGGACTTTTGGTCACTTGGACACTTG GACATTCACTGACGGCTTGTCACATTCAGCTAATGAATCAACGGCGATTC AGTCGTGTTCGCTCCTGAAAAGGTGCGAAAATGCAAAGCTTTCCTTTTGT TTTCCACCTTTCCCAGAGCCGCTGTTGTTGTGGTCGCCACCACAATATTT ACGGCACTCTCGAGTGCCTTTATTTCCGCATGAATCATTCCCAGTTTCGG TTCCAGCTCCACAGGCTGCCCCAGCGCATATAAATTCTTGGCTTTTTCCC CCAGCTGTTAATGCACAGAAAGAAAAATAGTTAAGGTGGATCGTAGTCTG GTATTCCTAGATAGGTATTTCATTATACACAAACGGGTGTAGCATAGGAT AAGTGCAAAGATGAATTACTTCTACTAATATAATTAGACATAATTAACAA TAACGGTATAGCACTAAATAGAACTGACGTAATAAAAGTGGAAGACTACT TTCCCTGTGTTGCAGGGTTTTTTTTTTTTTTTGGTTTTTCATGGGGTCTG CCTGTCGCATTTTTTATGAGCCTCCCCCATGTTGACAGGACCACCATAGA CATTTTTTCGGGCTTGCCAATGCGGAATGAAATTCCAAGAATTTAACGGC CGCTTTGCCTGCTGAATATGTCATCACATGGCGTTGAATCCTGCTCCACC AGACACAACACAACGACCCGGCGGTAATTATGATAAATGCGATCTTAATA AACTCGGCTGGTGGGCACGGCTGGCTTTGAAGGCCTTCATGGCCAAGTGC GGGCTCATCATGGCCGGTCCTAATGCATTTTCTTTTCATCATCAACGCAT GTGGCACCTGGTCTAATGGCGCTTCCTGCCACCCTGCCTGTGGCCCATTA GCAGAAAATGCTGTTGTACATTGATCGACTCGTCGTCAGCTAGTCGTTGT TGTCGAAGTCCTTGTCCAGGACTTTGGCTCACCATCCTCAGCCAGTCGCT TCAAAAGTCAGTCACTGGTGCCGTCGGAACGTGTTTACGACCTGATTGCA CTTACCCACCCACCTGCTGATGTCATTATTATCGCATGTGTGGCACACTG GCTCTTTAGTTGCATTAATGGTTATTCAATCAGCGTTTAACGCAAATTGC CTATTAAAGCTGCCCTGTGTTCCTGGGCTCCCTTCATGCAAATGTTTGCG TATTATGGCCATGTAATTTGATTAGCTGATAAATGAGGTAACGCCAGCGC ACGTGCAATCAGGAACGCCAGCGCCACTGCCTTCATGTTTTGACTGGCTA ATAAGGCACTCGCATATTCCGCAGGTTCCTGATAGATTCACCCCACATTC CCTAACCACCATGGCGGTGCACCAGTCGACCAACGTGTAGCACACATTTG GGCGCAACTCAAGCTGTTCAGTGCGAATATTGATGTTTGCCTGTCGGGGA TTTTCATGTAAACGCATTGATTAATGTTCTTGAGAATCAGATGATTGGAC ATCCACTGCACTTATTTGATATATATATATACATATTTATATATATATAT ATATATTGTGTTCTTAGCTAATTAATTCGGTGCTGATAGGCAGGGTATCG ATCTGTACTTTTATATTGTTAAGCCCTTAAAGACGCTCAAGCAATAACCA ATCACTGATTCCAGCTTGTCAGCAGAATTTAGCTGAATAACTTAGTTTCC ACAGAAAACCCCATACAAATACTGAATTAGTGGCGAGGAGATTTCCTGTC AATACCCTCCGCCATCCGGCAAATACGCGCAAATCAAAAGTTAATAGACG CGATGGAGTCTCTGTCATTTGCATTCAACCAAAAACTTGATTATCCGCGC GATTTACGGAGCGCAATTTTGGGCGGAAGGGCGGACTGGGGTATGGAGCG GGCAGACTGTGTGCTTAATGAGCTCAGTGAAATGTGTGCTTAAAATTAAC TTTCAGCCAACAAACCCGTCCCTGCCAATTGTCCCCGTCGCCATCGTTCT CCTAGTCAGTCGCTTTGGCAGCTGTTGCTCAGCCAGAAGTGGTTCATGGC TCATAATTACGCATTCAATTCGACAGGCAGCTAGCTCCAAAGGATCCAGC TGGAGCTGCCCAAATCGGAGAAGGGTGGCCGGTCGCCCGAAACTGCTTTA ATAATTAAGTCTCTTGAACATCAAGACATCGTGTCGGACAACAAAAGTGC CGGGGCAAACACAAGGGGAAGCAGGAGGTCCTTGGAGTGGAGCAAGCACT TCGCCGTGTGTCCGTCCACTTGGCCATGTCATCTGCCAACCAACATCCTG GGACTGCGACTGCAGCCCGCTTGGTGCGAGTAAAAACTAATTTCTCGCCT TGCTGAGCATAATTTTATGCAATTGTTTTCTGATTAAATTCCACACTGAA AGTGCCCCGGTCTGCACCCGCATGTTGCATGATGCGTGCCACTTGGCCGA CTGGCATTTTCATGTGGGACAGCTTTTCGGCCGAGTTTCCGGGTGGCGGA AGCACTGGAGTTCGATTTGGACATAACTTTGCTAGCGCCTCCATCTTGCT GCACTTAAGGTTTTTATTATTTGCTGTCAGACGGCACCACGTGGCGGATA CTTGATGTGCAAGTGGAACGTTAATCGCCCCATAATTGGATTAATCAACG GCCGGCAGCGGAACGCCATTAATAGGCCAAAGCCCCAGCAAACCTCACAC CCGTGTGCTGGAGCCACCTTGGAGTGGCAGGTTCAATGGCGTTCGGCTTT GAGCCCTAATGGGTTCTTCGACTGGGGAAAGCGTCCCGTATCGGGTGCAT TGAACGGCGCACCATCTGCCACTTCCATCGGCATTGGCCAGCACATAGCA CAGAAAAAACGGAATTGGAAAACCGAAACCAATTTACATTTTGTTTACCT TTTGGCCAGCACACCTCGACGTCCATCGTATTTGCCTTCGAAAGAGATGC GCCAGTAACTGGGCAGTTCCACCTAGTATATAGGATCTATAGATCTGTTT TTTAAGCATTTCCGATTTCATTAAATTTCCATTAAAGCAAGCTAAACATA TAGTTTTACCTCGGAATGGATATATAGAACCGTTCTCAACTTATTTCCGA TTTTACTAAACTTTACTAAAGCAAGCTGAACCTTATGTCACAAGATTTTC ATACTCCTCCCTTATAATTTTTGATGGAGCTGCGCTCGAATGGGGTGCAT TGGCTCCATTCTATTCTTATCATTAGATCAAATAAATGTAATTTAAGATT TCCCATAAAGATATCCCTTCAGCGCCAACAGATCCCACCTCCTTTAAAGC TACCTGTGCAAATATTTTCCCTTACCAGACTCACCACCTCTGGTTTTTTG TGCCTTCTCCGACTTTGAATGGCTGGAATTTATCGCTTAACTCCGCACAG CAGCTGAATGGTGTGGCATGGGGCTTGGGGATGCCATGGGGATGGGATAG AAAAGGCGTTGAAACTGAGTGTGTAAGTTTTAATTTTATTTTCTCACTTC ATTTGGAGGGTTTGCCTTGGCTCCGCTTTGCTGGCGACTACAACACTTTA CATACATTTGCATAAGCACTCCGGCAGTTTAAGCAAGCTGTCCGGGAAGT TAATAAACAGGATTCGCCTTTTGCTCAGTTGCTTGTGGATGGCCAATCCG GGAGGAGCTGCCGCATTAACGCCATCTAGCAGGGAGTTAAGTTTTCTGGC TTCTTCTGGGCTCCTTTGCGACTGGAATCTGATTGCGGATCGCGTCCAGG TGTGACGCCGGTGCTGTCAGACGCCTGATTATTTGTGGCTTATTGCGCTA ATGCGAAGCTTATCGCATGAAAATCGCATTAACATCATTTGCAAGACGCC ACAACGTCCTTGGCCCTCCCAGCTACCGCCCACCTCCTAGGCTGTTTGAT TAGCCAGTTCCCGGGCCCATAAACAAATACCGTGCAAATATCGCATTCGG CGTGGGCTGGCCGTTTTGTTTGCCTAGTTAATCAAGGCAGCCCGGCGGCC ATTAGGCGCACAAATATTGCCCAGAATTCCGAGTTGTTTGTCCATCGCAA ATACGCAGCATCGAGGCGTCCAAGGCTATTATCTTTGACCCAGTTTCGAC TCACTTGCTCACAAACGCAGGTAAATAAGTTTGAATTATTAACGATCACT CGGAGATGCTCATCAAGGACGAAAACAACGCAACATATCACAAAATAATT AGTTGTGCCAACCCAGATATAAGGTTTATCGTCGATAATCCCGGCTTAGA AAGTTGATGGCTCCTTTCCAATGGATAATGAATACCTAACAGTAGCTGGC AGCACGGAATACAAACACTTTTGATAGGAAACACTTGTTAATGGAAAGAG ACTTCATGTTTTAATACGCATACAACTTAACACACTTCGCCCTACGCCAT CATCGCTATCTGTAATATGACCTCTTAAGTTGATTCATTTTATTCGCACA CATCCTTGTGTCGATTCCCAGAACATTTGGCTGGCCCCACCTTCGGTATT GGACCGCCCCAACTTGATTTTGTGAATCTTCTTCTGCGGACGACGGCTCA GTTTATGTCGTAGCCCTGGAACAACAGTGTCGGCGGCAGCAGGAGGAGCT ACGTGCCGCCATCGGAGATATCGTCCTGTGCGTGCCTGAAGGACCAGAAA AAGGAGCTGCGACAATGGGGCTACCCTCTCGAACTGGCGCGTTTGATGCG CTTTTGATAATTTGGCCGAGACGCCTGAGCCGCGTGACATCTTTGTTGCC GTCGACGGCAGTGTCGCCATCAGGTTGATAAATAGTTTTACCGGCAACTC GACTTTCCCGGCTGTTTTGCTGCACCTTTCTCGCATTACAACAGCCCCGG AGTTGGTTTAAATTAAAAAGCGTCCATCAAGCATTTCCCCAGCGAAAATG CAGCCGGACTGCGTTGGACTGCCGAAGGCGACAGGACTTTGTATATCCTC GTTTTTATTTCGCAGGCAGGTGCTTCAATTCTCAGGCTCTGCCTGCCTCA CCGACGCTGAAGCTTTAAAATATTCCGCATTCAGGAAAAGAAGAGCGGTA ACACAAGCTCAAATTATATCAAACGAAAAGATTTTACACTCACTGGAGGT CCATAAAGTTGAAAAACCTCTCTTTACTGTCTTTCAATTTTAATTGAATC AAATTAATTATATAATTCGGGAACTATTGAGCAAATTAAATTGATGTATC GTTTTCTAATCAGGTTATCCATAGCCATAGACATTTAATATCGCTTGTTA TCGTATTTTTGCCCAATTGTGGCCAATACGAGGTAATTTTCATTGATTTC CGGCTATTTTAAGGGCGTTTTGGGTGTCAAGTGTCGTTACGAGCGCCCTC CGATGTTTTTTTTGGCGGGGATTTGTCCATAAATAATTCATTGGAACATG TAACAGAAGTGCGTCAAGTGGTTCCCCCTCCCCGCTCCAACGCACACGCA TTGGATTACATGGGACGTGGACGCGTCTGCCGCACTTCGCCGGAGTGGAT GTCTATTTTTTATGGCACCCCGGGGAAATGACGTACTATGAATGCCGGTT TAATACACAAAACTTTGACAATATTGTCGCACAGTTAGCGCGGATACACA CACCAACCATGATACTCATACCACCCCATACCACACCATGCCATATCACA TCCACGGCAGGCAATACAGACTTGTAGCCAGACAAATGTGCGAATAAATG GGCTATTTTTGTGCGGCCTGCGTCTATTGTTAGCGAAGTTATTCAATCGC TGTTGCACACACGAACTCGGACAACGCCACGAATGGCAAACAAATGGTTG GTGTATCAACAAATCGATCATTTTTCCGCACTTGAGCTGAAATCATTGAG TGACTGCAAGTTCGGCCAGGGCCCCAAAATAAAGATTTAAAGCAAACAAA TGCGGTGTGTATCTGCCGGGTTTGCGTCACTCCGAAAATGGCACACGCAA ATAAAGTTAACGTTAAAGTTAAAGAGCGGAAAACGAGCTGAGGATGTGGA ACTTTATCAAGTATACGCCCATTTGGCCCATAAGCCATTCGCTTGTGGGC TGAGCCATTGCTGGCCCCATTGATTCCGGCCATCTTTCTCGTCTCGTCTC GTCTCGTCTCGCAAAAGTAGGCAACAGTTGGGAAGCAAGCTTGATTAATT ATCCAACTTTCCCCAGACATTTGCATTTGCATTAGTAGATCTTAAATGGA AATCAAAACAGGCCATTGAATGCACAGAGAGGAATTATCTTATGGCTGTT TGCTATCAATAATTCGAACACGCTAGGTGTTACTTTGAAACATACTTGTG CCATTTCGAACTTCAGTGTGTTTTCTCTCAGTGTTCCAGAGAGATGTATC CAAGGACTCTTTTATGACCTCACTTTCGCCGCTTTGTGCTCGGTCGAGTA CACAAATGAAATCCTTCTTTTCACTTCCCTCGAACGGTTTTATTTAAGTT TCGCGCTCATTGTTTTTATTTGCTTTTAATAGGCGGACAAGAAGTTGTGG CCGGAATCCAGCCTTCGGTGGCAACTTTAGTGGCTGCCAGTGTTTGCTCT AACATTGAAAAAGTTTTTTCCACCGCTTTCTTCGCAGGCATCGGCTCATA AAACGAACTGCAGACCCACTTGCCTTTCACTTCACCTGGGCTTTCCATTT CTAGGTGCGAATGACAAAGGGGCGAGGCTGGGCGGTGCGGAAGAGCCCGC AAACTTTTCCCAACAACAAAAGGTCACTGAACAATTGACAAAGGCGGCGT GCTGCTGTCTCAGGACTTGCCAAACGCCATTTAAAAAGTTTTGCATAATA GTTGGCCCACGATCTCGCGAAGTACCCGCCAGGGCAGAATTTCTCCAATG CCAGAACAATATAGCCATTAAAATCATAAAAAAAAAACAAAGACAATGTT ATAGTCGAGTTCACCGGCTATCAGATACCCGTTACTCAGTGATATTTTTC GGCATATGTATAGAAATCGCAAAGATAATTAGTGAAGTAGGTAAAATCTA CCTGTTTAACTTTTAAGCATTAGCAATAACTCAACGTTCGTGCGGAGCAC GGCTAGATATCCTTCCTAAGGAGACGATTCCTTCTACCTGTATACTTTTT AGAGAATCTAGTACCCTATGAAAACCCTCTTACCGTTATAGTATGTTCTA ACATCAACTTTACTGACTGGCCATTATTTCACTGAAATCATTCGATTATT TTTAAGTCTTAGTACCTTATGTTGGGAATATAATCATATTGTGGTTAAGT TGATTTTTATACAAAGTGATTAGGCACGATTAAGCCAACTCCAACAATGT TTATTGTTTTAACTTACTTTCGGAAGAAGCTGTAGCATAATAATAATAAT TAATTGTTATAATAATTTGTTAGTTTTATCAAACAAGTGTTTTCCTAGTT TAAATAGAAATTAAATTCAAAGGTGCAAATACGTTACAGGCTGTGTGACC AGTGCGCGCATGGTATATTTTAGTGCGTTCCCCAACACTCGAAGCCGCCA CGGCCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGA AAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCG TTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGA CAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGGTGAGTGG AGTGCGCGGTGGCCCAGGGCTCTTCTGGCCAAGATTTCAGGGGCGTGGTG GGGCGGGGGCGCAGGCGGCTTTTGTGTAGTGCAATTATATAAGGTGGAAG TGGGGAAGTAGGGGGTCCGGGATAGAAACGCCACAGATAAGCACGCGAAA TGCACTCCGTAATTGGGGGAACTGCCAACTGGCAGAGGCTGTTATGTAAA CCTTTTTTTCAGCGGCACCTGAATTGGATAAAATGGGTAATGGCGTGATT CTCCGAACTTGCAGATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAG CAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGA GATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGA CCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTG ATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTG TCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACA CGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAG GTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACAT GAACAACTTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCA AGTGAGTGGGAGCAATCCCTACGAGCTGGAACGTTACTAATACCACGCCC TTTGCAGGAACGAAGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAG TCCGTCGAGGATCGCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTG CGCCTGCTGCTCCACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGT ACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCG CGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAG CGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGG GGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGC CTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTA GGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTG AGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTT ACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACA GTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACCAGC CGGGCGACATTGTGATGGGCAATCAGGGCACTCCCATTCATTTAGGGGGC TGTGGGTGAGGTCTCGTCGTTCATCTGAATGTCGTCGGCGGAGTAAAAGT CCTGGGTTACCGGGATGACGCGGTCGTTGGTCTCGTCATCCTCCTCATCG TGACTGTCCGTGTCCTCGCTGTCGTCGTTGGCTGCACAAGGGCAATTGGA CGTAAAAACGATAATGGTAATCCGAATGCAGTGTCCTGCCGTACTCACCA TCCTCGTCGTCGGTCTCAATTCCGGGTATGGTGAGCATTTTGCCCAGCGG CTGCAGATCTGTGCCGGCCGTCTTAAGGGACTCTCGCTGTACGGTTTAAG TTTATAACAATTTATACAGAAAGCGGTGTCTGGAGAGAACTCACCCAGTT GCTCCTTTCATCCTCATAACGCCGCGTCTGCGATTCTTCGTTTACGGAGG CAGGAGCCATGTCCAACCAGTAGCGATTGGCCACGGAGACTTTGAGCGTG GGAAAGAATGGAATCATTGACATTTTCGACGGAATCTTGAATGCGCTGTT TTCAATATTTGTTGTTCTTTCTCTGGAAGCCTTTGATGCGATCTGGCAAC GCCGCAACATACGCTGTAAATAATACCAATTTTACAGGGGCGTAGTCGTA GGGGCGCATTAAACGCAAATTACAATATTAATTGTAATTGTAATTCATCA ATCTAACTATGTATTTTGTTATTGTCAAGGGAAGTCCGATAACCAAGGGC TTAATACAGCTTACTCAAAAATATATATCTTCACTATTACAAATTGACCT TAAGAATCAGAACATAACCAAAACGAATAATATATATTATTCAAAATCTT TTTATTTATTAAAGAAGCTATAAAAATTGGACAAACTAGACACAGGAACG GTATTCCCTTGCAGTTTTATTGGTAGTAAAGTTCCAGATTCATGCCATCG TGAATTTCATCTAAGAAAGCGAAAAAGAAATGCGGGTAAAGCAAGGCGTT ACAAGGACACTAAACAAGGGCTTACAGTCAGATAGGCGAATCGGGTCCTT GAAGATTGTGTACCACTTCTTCAGGACAATCTTCTCGTGCTTTGTGCCCG TTTGTGCCGCGATTAGTTTCTTGAGGTCCCCAATCGTGTCGTCCGGGTTG CACTTGACGCGCACCTGTGGGTTAATCGTTGGTTAACGATGCTTGCAGTT GCCTTGGGTACTTAGCTGCTTACCTTCTTGCCAAGACGATCGTTACACGT TATTTCTATCATATTTTATGGCTTTGCTAGACAAATCACAACAATAAATT CTTGATTTGTTGTGGTATTATTGCTTAGGGTTGTCAAATACCCTTTACCG AATACCGAGTGGTTTGAGGGATCGCTAATTGTCCGCAATGCTATCGATAT TTTATTTAATTTTAAATATGTTTAAATAACAATCATATAGAAAGTCGAAG TTAAAGATATCAGAAGTCTGAAAGTATACTTAGAAAGCTCAATTGCTTGT CATGACGCAAATCTATCACATCCTTGTAAAACGATAATATTTGTTAACAA ATTTATATTTAAATTTCAGTCTTCTTCTTAGTTATCAAGCCAGAAGTCGA ATGTTTCGGCGTTAATAGAAAAATAATGTATGTTTGCATATTTGCACACC TCATTCAAATTATTTTTCTTTGTTGAACAAAAGATAAAAGTGTAAAAATT AAATTTTTTATTCTTGACCCATTATTTCTCTTGGTTAATGAAAACAAATT CCGTTTCTCAACGTTCCCTTTAATAATCCATGTGAACAATCGATAGGCGG CGAAACATCGATGATTGCTAGAATAATCGATGTGTCTTCCCCGTTCATTC GAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGG AGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAG CTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAA GTATGTCACATATTTGCGGGCAAACTGCCGAAAGCACTGTGCGGAGTTTT TGTTTGTGTGCGTGCGTGCCTCATTTTTACATTCACGTACATACATATGT ACATATATGTACGCTATGACGCAGCTGTGGAAAACTTGTTTGGGTTTCCA TTTCACCGAATCACGGAATCAACGAATATTTGCGCCTGTGCTGCGAACTC ATTTTGGGCAGTAAGCCATTGTATTGATTATCGCGCGTTGTTTGTGGATG GCGTGGTCCGCCGGAGCACCCTGTAGCGTCTACATCCCTACCCCGCTCCC TGGAGTCCGATATCTGTGCGCGAAAGGCCGGGCGGGCGTCGTTTTCGGCT ATGTGGCCCAACACCAATGGATCCCCACGGTCACTGGCAGCAATTCGCGA TCCGAAATGCTCCGCCCTATTTTTAGACGCGGTCTTTGCGGCCTGCCTAC TTACCTACCTCCCCAATGCATTCTAATTAAAAACCGGGCACTGCGCTCAT TTCCACACGCATTGCATTGCATAATGCGGCATTAATGTGGCGGGGAAAGC TCGCTTCGGAAAGCACTCGAGCATTGAAGTGAAGAGACCGAATGTTTTCC AGCTGCCCAATTGTAAACAACCCACGCCTAGCACGCACACACACGCACAC GCACACACACACAGACTGGTTTTAATGTTTACTCCAAATAAATCGTTGCC CATGTTAATTATTTGTGTCTTCGCAGGGCCCGAGCACTGGAGGGAATCTA ATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTC CAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACG CCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCC AATGTGCAGTAAGTATCTGGGATACTCCCGAAATAGGCCTACGGACGAAG CCCTTTATCGCGAACCCATAACATTATTTTTAGCCCTTATAAGTAGTAAA ATTGTAAGCATACAATATGTTTACGGAGTTCGAGTCAATTTCATTTTGAG AATTAGGAGAATTCAGTTTAAACTCTATAATTATTTCCTATTTGGTCCTG AGTCACCTTTTTCTATACTGACCATTGGTTTCAGTAAGCAAGTTGGACTG TAGTAAGACACATCCATAGCGACTGTATGTTTGTATGCCGTGTGCTGCCG CCATGACGTCACCTTTTTGTTATTCACGCTCGCCGCGAATTTGAATTTCG AAGCGGGTAGAAAACGAAGGCAAAGCCGCATACAGGGTGCAGCATCTGGT CGAGCTTCGTTAGTTTTTGGCGCCTATTTCGAGAGCGCCTGGTCGGTCTG ATGATCAGTCTTCAAGACTCGATGACGACATTCGGAGTCCAACGTCGGCC GTCAGAAATCGTTTTCACGTTTTAGCCTCTAAATCGAGCATGCTGGGGTG GGCTAACAGTCGTTTGCGCTGAAGGCCAGCGGCGGTTATAAGCATATTTT TGTGTTTTTGTTTTGATACGTTGTACTCGTCGTTTCAAACGATTCCGAGC ACGTTATCACGGACTTACTGAAATATTTTTCCCAAATCTTACCTCTTCTC TGCAGAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAA AACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACG ACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTC ACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAA CAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAA AGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTAT CTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAAGTGAGTGAA TCATTTCTACACATTTTAAACAGTATACTAATGATGCTATTTTGCAGCAA AACTCCCAAGACGGACTATACCTACTCAGAACTGTCCCCTCACCGACGCC AGTTGGCGCCAGGAATTGTGGCCATGCCCAATATGTCCAGAAAGAGCCTA GAGAACCATAACGATCGAGTCAACTACATGGTCCAGCAGAACCCTGCGCA AGAGGAGTTCATCCGCCGCCGCTACCAGTCCAAGTATACCCAGCAGGTTA ACTATGACTCCGCAGATGAACTGGACGCCACATTTGGGCAGCAAAAGCAG AGCTGGTGGCTTATCCGCCTCATCCAACTGGTTGTTAGCAGCATTACCAC CGTGTGGAGTCGGGTGACCAATCTCTCGGCCACGGAGACGACTGCCTATC AAAACTACCACGCTAAGCGCCAGCAGAGTCAACAAGTTGGACTTTGGTGG AAAATAGTACAGACCATCGGAGGAGGACTTGCAAGTTTGCTGCGCTACCT GTATGTTTTCATCGGATCGGTGCTGAGTTTGGACACGTGGTTGCTGCGAT CCTCGGATGCGGAAAACAAGTCGAAAAAGCGCTTCCTCATATTTCTGCTG ATTTTGTTGCCCTTGCTGCTGCTGTCGGGTGAGTAGGATTTAAAGCACCG TCCGATTTTTGATGTAAAGTAAAATATGTTAGAGCGTGTGCCGTGACCTT GTACCGGTTCGAGAATTCATACTACATGCATATAGATCACCTCCAGTCGT TGTATTTATAAACTCGTCTGGTCGTTGGCAGTCGCGTGACGCCATCGATA ATTTGTTAGTAAAATCCCGCGGATCAGATTTAAGTGGCCATGTGATGACA TATTTTATTTTCCATTCACCGTCTGCCAAGGTTAAACGCCTAATTTGCTT TGCCTTTGCAGGTCTGTTCTATTACATACACCCCAATGAAACTTTCCCAC CCAAATCCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATC GATGTGAAAGACTACCTGAACCAGGAGCAGTTCGAATCGCTACGCTCTCA GGCCGCCGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTT TGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTA TTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGC AATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGC CCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGT ACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGT TTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATA GGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAAC AAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTT CAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTA GGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTT AAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTAT ACAAAAATAAATCGCAAACAATTTCATATGAAACATCAAGTACAAAGAAG AGTTGTTTGTTTTATTTGCCATTTGTTGGAAGTTCGCTAAATGGTAAGTA AGATGTAAACAAAGCAATATTAGTTGGCCAGAATCGAACTCTATCCTTCT GCATTTGTGTTGGAATAACCCCAAAAACGAGTTCCCTGTTACCTCAGTCC GGTTGATAATTGAAGTTGGTAGGGACTGTAAATGTAGAAGGATTGCCAAC TAATAGTGCTATGTTTAATTTTCTCCTTCCCCAGGATGGTTGCTCTTGCA GGAGGATCAACGTAGTGCTTACGTTCAGCGTGCGGAAGCACTGTTGCCGC TGCCACTATCTATTTTCGGCTCCCTACGTAGTCGATTTTCAAATGCTGGA GCCACCTTGAAAAGTTGGATGGAAGTGCCCACCGTCAGGAGTCCCCAGCG GGAAGCCGAGGCCATTAAGGTAAACATGGCCAGCATTGAACAGAACATCC AGAAAGCCTTGACTGCCGAGGAATACGAAAATATCTTAAACCATGTAAAC AGCTACGTGCAGCAGTTGGTCGAGCTGAAAATGCAGCAGCATTCCAAGGA GCTCGCACCGCAACAGATTGAACTCTTTGTTAAGCTGATGAAGGAAAACC TCAAGCAGATTATGTACAAAACGGAGCTAAGCGAAAAGGATTTGTCTGAT CTGGCCATAAAACTGAAACTGGAGCTGCAAAGCTCAGGCGGTTGGCAAGA TGGAGCGAAACTATCACAAGCTAACTTAGAGGAGATAACCAAGCTAATTA AAGCAGAGGTTCACCTCCACGAATCGCACTACACCATTCAATTGGACAGG ATAGACTTTGCATCCCTGCTGGAGCGTATTCTTGCTGCGCCAGCATTGGC AGACTTTGTAGATGCTCGAATAAGTCTTCGGGTGGGAGAGCTCGAGCCAA AGGAGAGTTCCGGTTCCTCAGATGCAGAAGTCCAAATTGAGCGTCTGAAC AGGGAAATCGCCTTCATTAAGTTGGCTCTCTCTGACAAGCAAGCGGAGAA CGCCGATCTGCACCAATCAATCAGCAATCTGAAGCTCGGCCAAGAGGATT TGCTGGAACGCATACAGCAGCACGAACTTTCCCAGGATAGGCGCTTCCAC GGGTTGCTGGCTGAAATAGAAAACAAACTGTCTGCGCTTAACGACTCGCA GTTTGCTCTTCTCAACAAGCAGATCAAGCTATCCCTTGTCGAAATTCTGG GCTTTAAGCAATCCACCGCTGGCGGTTCCGCTGGCCAATTGGATGACTTC GATCTGCAGACCTGGGTACGCAGCATGTTTGTGGCCAAGGACTACCTGGA GCAGCAGCTGCTAGAGCTGAACAAGCGCACCAATAACAACATTCGCGACG AGATTGAGCGTTCGAGCATCCTGCTGATGAGCGACATTAGCCAACGACTC AAACGGGAGATTCTTCTGGTTGTGGAGGCCAAGCATAACGAGAGCACCAA AGCGTTGAAGGGCCATATCCGCGAAGAGGAGGTGCGCCAGATAGTCAAGA CGGTGCTAGCTATTTACGATGCCGACAAGACGGGCCTGGTGGACTTCGCC CTGGAGTCGGCGGGCGGCCAAATCCTTTCCACGCGTTGCACTGAGAGCTA CCAGACAAAGTCAGCCCAGATATCGGTGTTTGGAATTCCACTCTGGTATC CCACCAACACGCCGCGGGTCGCCATTTCACCCAATGTGCAGCCAGGGGAA TGCTGGGCATTCCAAGGGTTTCCCGGATTTCTAGGCAAGTCGCGGGTAAA TAGTAATTGCTAAAACAGTCCTTATAGTTTTCTTCCCACAGTGCTAAAGC TCAACTCGTTGGTGTACGTCACTGGATTCACCCTAGAGCACATACCGAAG AGTCTATCCCCCACAGGAAGAATAGAATCAGCTCCTCGCAACTTCACTGT CTGGGTAAGTTTGACTAAGGGTGAAAGGAAGTGGTGCATTTCTAATACGA CTTATCCATCAACTCAGGGCTTGGAGCAGGAGAAGGACCAGGAACCCGTA TTGTTCGGCGATTACCAGTTTGAGGACAATGGTGCTTCCCTCCAGTACTT TGCCGTTCAAAACCTGGACATCAAACGGCCGTACGAGATCGTCGAACTGC GGATCGAGACGAACCATGGCCATCCCACCTATACATGCCTCTACCGGTTT CGCGTGCACGGCAAGCCGCCGGCCACATAAATCTGTTCAAATCTCTTCTA GTGACCTAAGTACTGCCAGGTGTACATAATGTCTGTGCCTTAAAAAGGAA ACTAAACAATATATCACTGCGAGATGTGGATCAACGGAGCCCAGCCGCTT TCAACAATGCGAACTATGTAAAAAGTAAGGCTATATAGATTGTAAGTGTT TTGTATCATATCGTAGATTTGAAGTGTTTAAATCACATTAAGGTTAACTT GTACATAGCATATTATTTAAGTCAGGACTAGAGTCCCTATAAGTACTATA ATATTTATTAGTATTTAGTTATTTCCCTGAAATCAATCATCGTTCCTTTA AGTCTACTCTACTTACGTATGCAAGTTTCCAACCCGTAAACGTAGCACTA TACCCCAGTTTATAAACAAATTTCAAATTCCAATCTCGGCGTCAAAAAAA TGATCTTGTCCTGAATCAGACTGATCTTCTAACTTTATCCTAATCCAATC TTCCTCGGCCAGAAGCTTTTCTTTAGAAACTTCTTTAACGTTCAATTATG TTTAGAATCAAAGCTTTATGCTGATTGAGACGAGAAGTTGATCATGGCCT GGTCTCCAAGCGGAAGCTGTGTTTACTTTAAGTTTTGTTATCTATCTTAT CGGGTACCTAAGTGCTGGCAAAGGCAATGACAAAAACAAAGACAAAGGAA ATGCCGCCGAGATTGAAATGTGAAATTTGTTTATAAACTGGGGTAGGGTG CTATGTTTTCGGGTTGGATAACTTGCATATCTTTTACCATGTTTGCCATG TTTAAAAGCGTTTTGAAGGTAATAGTCATAGTTTGTCTAAGCCACACACT TGCTGGAAATGTATAGTTTAAGCTATATCTAAGCTAAAATGTTTTACCAT GAAAACTTGCAAATTCCTTATAAATGCGATAGCGATTTGAATTCACACCT CTAAAATAGTGACAAATAAAATTGAAACTCACTGAATAACTCGATCGAAT AAAAGCTGCCTGCATCCCTCCCAATGAAACAATCTATTTCAAGTTTTCCT TACTTGTCGTATACGTAATATGTCTAAAGAGTGAACCCAAAAATAGTTGA TAATTAAAAATATAGTTTTCTCTTGTTTCTATAAGTTTACTTAATTGGCT AAGTTTGTATCTACTTCCTGCGTTCATTAAGGTTTTTCACCATTTTTAAC AATAAACACATTGCTGTGAAAAAACGTTTTCTTAATCAAAAGGCAGGCGA AAAAATGGCTGTCAAAGCCATGGGAAGTAATTAACCTTTGCTATCCGGCT TCTGTAATTAGTTATTTCTGGACGCCAGCGAAGGATTGGGAAAAAAGGAT GCTCAGTTCAAAATCATTTGCTTGTATCCTTTGCTATCTACAATACATTT AGATAGTGTGTAGAAAATGTCCATTTAAATCGGATTTAATTGCATAATGA CGCATTTTACTCTTGACTGCAGTTGCTTATAATTTGCTAACGATTTCCAT GTTATTGTTAAGCCGATTTGGTATAAATGATGATGCAGGACTTGTGCTCC AACCTGATGAATATATTAAGTGCATTTCTGTTTCAGGCAGACTCGTCTTC GGTAATTTAATATGAAAATACCTTTGCAACTGTTGACTCCGCACGGATGT GTCATTTCGTCTGGGGTTAATGCAAATTGTCTTTTAATTTGTTGTGCCAG CAAATTCCTGGCGCTGGCAAGTCAAAGGATTTCATCTTCAAGCGTCAGCG AAGGTATGCACTTAATTAAAGCCAGCTGACTGTCTCAAACAGAGCTGATG TGATGGAGCATCTTGGATGGCAGGATGGCAGGACCCCGTCAAAGGGACCA CCTGCGGATGTATGAAATTTCTGCGAATAGAACGACCAGGCCGCTGGGTC GCCATTAGGCAGATTCCCGCCTCGGAAGGCGGAATGTCCTCGTTTGAGCC TGAATTACAGGCATCGCTCGGGCGTGTGTGTAATTGCGGAGTTGCCCCGC CTACACACACGCATTAAGTTTAATTGCCACCGGGGCCCGAAAACTTTTAA TTTCGCGGGGCGTAAGTTCAGCATATTCATTTCGCACCTGCTCGATGGCG GGAAAGAAGTGGCGCATGCAGCACGCTTAATTTGTTTACACAAATCTTGC TCAAATGCCAGCCACCTCCGCCGGCGAATTCCCATCGGGGAATAAAAAAT GAAACGACTCTGGGAACCGGCGGCACTCAGTTCGGGCAGCAAAACTTTCG TCCTGCGAGAGTGTAACAATTAAACTGCAGCTAAAAATAGTGACTAATGA GAAAAGTTTGCAGCAGTAGCAGCGGCTGTAAAAAAATGTAGGCAACGCAA CAACTTTCCTCTGAATCGAGAATCGAGTCGAGCTGAGTGTTTAAGTTGGC GGCAACTTTTCTCTATTTTGTATTGAATTTGCTAGCGTGTTGGACCGCCA TTTGCTGGCCTTAATGGATCAGCTAGCTGAAGTGTGCCAGCCATAAAGGG AGTTGCAATCTAGCCGAGACAATAAAACCCAAGCCATCATATCACACTCT TATCCCCCAGACGCAGGAAAACTTTGGAAAAGTTTACGGCCTGGTTTGAT AAGGAAATTCTTCAAGTTTCTGCAAAAAGATGCTTGGCCGGTGCTCAATT TGTATAGGAGTGGGGTCTTGTCTCCTTGTAACGCAACTAGGCCCAAATGA TTGCTTCCGATCCGAGGATCCATTCGTCGTTCACCAAGTCAACCTGCAAA GCAGCGTTTATGGCCGCTTCTGGCAAAAATAGCTGGCACATTTAAATGAC GTGACACTGGACATGACACCGGAAACCGATTGGCCGTACAGTGAAGTGGC GCCCGCAGTTGCATCCGCATTAGGTATGCGCATACTCTTTCATGGGCGGC TGAGAAAGTTTTGTTTGCCATGCAAATCTGTTTGCGATGTGCAAGGAAGT GCGGCAGCGCTTAGTTAGAGACACTTGTGTGACTTGTTGGCGTAATTGAA TTCATTTGGGGGTCGGTCGACTGCCGGAGGAGAAAGTGCCAGCACAATAA CTATTTAACAAACCGTTATGCACACATTTTGATAACTTTCAATTTGATTC CACTCTGCGGCGACATGGCAGCTCAACTCAGCTCGGCTCAGCGGGAGCAG GAAGAGGAGCAGCAGCACGAGGAAGTGTTGTGCTCTGCGGCCATAATGAA ATAAACTTGTCACACAGTCGGCAGAAGTCATTTGCCCCATGTCCTGTTTT CCGAAACTACGTCCGCCGGATGAACTAAGGCCCAGGGGTCAAAGTTCGGC AGGCTGGCAGCTGGCAGCTGGTGTGCCGCCCTCATTGGAAATTTAATTAC GCATGGCACTTGTTTACCGATCCAAAGTTAAGCCTTGCTCCCGAGCGAAC GTGCGCATTAACCTTAATTAAGTGACAAACAATCCAAGTTCGTCACGACA TCATTTTATTTACAGGCAATTGAATTTTAATAGGATTTCGCCTTGGCGAG AATCTCCTTGTCTTAGCTATCACCCAGGCGAGAGCCTCCTCCCCTTGGAG CTGGAGTCCTGAAATCCTCGCACCGACGGCCGACTGGCCATTTGCATGGC TCTTGGCAACGCAACTCTTTGGACTGTCGGCCATTATTTCGCACTTCTGT GTAATTTAATTCATTTGCAATGCCTTTGCGAATTATGTGGATGGGAGGTT TACTCTGCCATTTGCCGTTTGCCATTTACCATTTGCCTTTGGCCTGCCAT CGCCTGCCATGTCCTGCCCTCCAGTGCCTCGGGATTCGTGTCCTTTTGGC GGCCCAGTGTTTGGCCTTAAAGTCCTTTTGCGGCCACGGTGCCACAGAAA CCCCGAAAACCGCAAGCCACTTTCGTGATCCTTCATGGGAGTCATCTTAA CGCATCATTTAAGCCGGCAGGGCAGTTGACTGCCCCAAAGAGGGTCAGAT AACGTTCGTCCTTGCTGCTCTTAATTAAAGATTAAATGTGCTAAGTTGTC GGGACTTTTGGCAGAAGGACGTTGCTTTAATATCGCCCATTCGCTCGATG TCCTGTTGGCTGTGTTTGGTGGAGGGCGGGCGTGGATGTGTGCTGGTTCC TGGTCCATCCATGCATCCATCCATCAATCAATCAATTACGCTTGGAAGTG CGCCAGGATAATAAAACGTGCCTGAAACGGAGTTTTGTCAGCAAAATTTA CGATCAACTTGGCAGAAGCCGTATTACGAACTTATGCATTGAAGAAATGT CCTTTAAGCCCGTTATTAACAAGAAATCGAAGGTATTGCATTTCTTTTTA GGAAATTCGTGGCGTTGCTGCATATATAAAAATGTTGTATCTATAAAATG GAACTTAAAGAATTCTCAGTCAATTGCAAATTTAAGGATCTGCCTTCTAA AAGTTTAATTTTATATCAGCTTTTTTAGTATTTCCAATATTTTTAAAAAT AGATAAGCAAATAGGCAACTTTAAAAAGAAGAAAACATATTTCTTATCAT ATAGGTCGTCGTAAAGTGAATATCTTTTTATACTTCGATTTGTGTGTCGT TTTAAAAATTGCATGACTCATAAAAGAAACGTGGATTTCACTGTAAGTTT GCATATAGAATAAAAGGCAACGCAACATATTGTTGTTGAAGAGTAAGTTG CAAAAATTGTGTGTAAGTCCTTTTCACAAATAATGGATGTGCCATTGAAG TATACTCGTACACTTCAGTCACTTGCCGAAGTTAAGTTGCCTTCTTACTT GAAGATTGTCGGGAACTTTAAACGTTTTTATTTCCAACAGACTTTATGTT GTTCTTTACGCCTCGTCAGATTTAAAACATTTATGCTTGAGCACAGCTAT ACATACAGCATACATATATAATGTGATTTTCCTGCAACCTACAATACATA CATATTAATTCAGTTCGGAAGCTGCGAAATTGCTGGCCATTGTTTGATTG CTGTAAATGCCGGACTAAGCTGGCAAAGCAATTATTTACCTAAATGGTTT GCCCACGTCAATGGCAATTGTCTGCGATTTCCATTTGGCTGAAATGTGTT GCATACAGGCTGTCAGAAGGCCGTCAGAGGCATACGAACAATGAAATCCG GCAAAAGGGACGTACTGCTGCCGAGGAGGCCAGTTGGGCGCTGCAACAAA AGCAGGATAAGGCAAACTTTTTAATTGAAAACCAACAAAAATATAACGTC AAAAGTTGCAAGTGGTTGACACTTCGAAAAAGCCCCTCCACCGAACCACC CCGCCGCCCATCCAGACCTTGCAGTCCGTCAATCCGTCCCACCCGTCGTA TGCGTAATATTGGGGCTGGCAGGCAGCAAGAGTAAACGAAACGAAACGAT ATGAATCCTTTGCGACAGCCGTTACCAGTACATCCAGTGCTTTAAGCGTA TATGCACACACGTGTGGATGTCCAAGTCCACTGGTCTTTAATCAGGAGGA GAGCTATTGCCACATCGTTATGAGGAGACTCGAGGAGGCGCCGCACTTGT ATATATATTTAAATTTAAGATTATGGCCGTACGTGGAGTGCGCCGAGTGC ACTCGTGACTGGCGGATTGGGATGGCGATTGCTGTTGACACAATTCCGCA TTGGGCTCTTTCTCTCATTGCGTTTTATTTACGTCTCTGCAACTTATCGA AGTTGGCATATGATGCTCGCAGTTCGCGCGTTTTTTAAGCCGCCTGCACG CGTCCGAGCTGCCGACTCCGCAGAGCTTAACTGCATCATCAACAGCTGCA GTTGGTAAACAACCAGCCAACCGCTGCCACCCACTGGCACCTTCTGCCAC CCAATTCATCCACCACCACGCCGCCGGCGATGTAATGTGATTATTCAGTT GTTTTGCTCGCAATTAAAACAAATTGTGCCCGCTGTGGGCGAAAGCATAA ACAAACTGCTGGATGCCAGCGAATCGTATTTGTGCGAACAATGATGGTCG CAATTCGATTATTCAACCAGTTGCACGGCTTCAGCTCGAATTAATCTCTA ACCCGGACATCCTTGGGTTCGTGATTAAATCGCTCATAAGGCCAGCAACG GGCCATAAAAAATCAATTGCGACTGTGGCAATGTCACAAAGATTTACGTT TCAATTTCAGATTCTGCCACAATAAAAACCAACGCGAAGGGGACGGTGTG TATCCCTGGAACACGCACACATGTGTGCAAAGCAGGATTCCTGCAGGACT CAGACGAGTGTGTTTGTGTGTGTGTGCCTGCGACTTTGTGTGTGGCTATA AGCTGGCTTAGCAGATTTGTTGCCGAAATTAGCAGGCTGTGGGGATCAAA AAAAGGGAGCGGTCGTCGTGCAGGATATCTATTTTGGGTAAAGGAATTCG GCGTCGTTCGAACAGATTTATGCGCCATAAAAGAGCGGCTAGACGTGAAC GAACATGTCAGCAAGGACTCGCTTCATGGCGACCAATAAAAAAGGAACCC GACTGGCAATAAAAAGTGAAATGCCCGATCAGCACAGCCCACCCTCTGAG CACCTTTCAACATAACCGGTTACTGTTTTAATATTTAGTCCTTGGCCACA ATACTCTTATTTATCCGAATGCAAATACCTTATGTTTGCACTACGCTTTT GTCCATTCCGTCCATTCATGCTGGTTGTTTCTGTTAATTCAAAGTCAACA GCCCCGAAATAAAACCCGAGCCCATTGTGTTTGCCTAAGGTAATTACAAA GGCAATGTTTACTTATGGCCCTTCATTAATATGTGAAAAGGTCCTTGCTC TTTCCCCGCCGTGCGGATTTTAATTGCGGCACATACGTGTTTTATTGCGT GCAACTTGTTGGGGCCTATCCTGCGGCCAACTTGGGCCTAAGCCAGTCGA AACAGCTAAAAGGATCAGGGGGATACAGCCGCGTAGCTGGCTGACAAGTT GTCGCAGCCGCAGGTGCGGAGCAGCTCTCACCGTGCACTTTGATAAAGTT CCAGGATAATGCAGAGTCCTCTGCTAAGTATGCCACTGAGATAGCAGCCC CATCTCCACCCACGCTTGCCACCCACTTCAGCCCACACTTGCAAAAAGTC ATTAGCTGTTACCCATTTTGTGGGGTGTTTTAATATTGTAGCATTAGCAT TAGAAGCTAATAATTCCTTTCAATGTTCAATTAGGCCTTATTAATCAGAT TTAATATCTAATATATTGCATTTTAACTGAAAATACTCGAAAAGTGAAGA ATAGTGTCTTGCCAGCGCTAAGCAAAGGGTATCTGATAGGCGATGAACCC GACTATAGCTTCCCCCCTTGACTGATTCTGTTCTTTGACTTTTTAAACGC ATTTAAAGTGTACCTAAAACTTTTCTTTAAGCAATGACAATTTCTGAGTG TATCCTTAAGTCTTAGGGCTGTGGTGGTACCCCACTCATCCATTCGATGC GCTGCAACCTCTTGCAGCCCCATAATTGCCATAGCAACGCCAACTTTTGC GATTCTTGAGCACGGCGAGCCGGGAGATGGGTGATGGGCGATGGGATCGG GGAGCTGGGAGCTGGGAGCTGGAAGCGCTTTCACTCTGTTGTTTTCAAAT TGCTTTTAGCAATCCCTCATACTTTTGTGTTACACTTCAATGGCAAACGA CGAGGCCCGCGCCTTCCACATTTTCCATTCGCTGCGCCATAATTACAGGT GCAGCACGAAATGGCTCGCAATTGCATTTCGTCTTCAGCGTTCGTAATCA GACAATTTTGAAGTGTTTTGCATTTAAGTTTCGCTTTAATCAGGCCGCTG GCCGGCGGAGGACAAACTTTTCGGTCACGAGACAAAAGGCGCAGATAACA GCTATGAAAACAGGAAGTTGCCCCAGGCCACCGACCAGTGCTGCCAAGGG AAACACCGAATATAACGGAACTCGTTTCAAATATTCATTGTAAATATTGT ATTCTACCCATCTGTTTTCAAAATTTAGGCAACTCTTAAAGTGAGACCCC CCCCCCCCTTTTAACAATATATAACATCAAATTAGCGTAACCGAAGATGT CATTCTAGTTTTTGATATTACCTGATAAGGTTTTAATACATTTAGTTCTA ATTAATAAAATAAATAAATAAAGTAACTGGACAGCACTGGCACAAGTACT ATATCTGAAACACGGAACCCAGAACAGGGAGCCAAAAGAGCTGTTAAGTA AGAGCCACAGTTGGAGAAGTCTCTAGTTCATTCGTTACGTTATTTTTGTG TTAACTGATTTCCATACTGTTGTTAGTTTCGCCAACTATGCACCTAGGTA CACACACTGATGGGTGTGGGTTCACTTTCCAACTTCTGTTTGGTACACGG AAAAACTTTTAAGCATTTTCACACCCACTGAGTGCGTTTGAAGCGAATTT AATTCCGATATATCGGTTCGCCTTAAAGCTTTTTCAGCTTAATCAATGGA AAATGTGCACATGTGAAATGGAAGGTGATTTCAATTGCAGTATCAATTTA ATTTAATAGTCATCAAGCTCCATCGAAGGCTGGAAGCAGGAATTTACACA GGTAAATCTGGCTTTGCCACAAAATAAAACGCACGAAAAGCACGAATCAA ACGTTCAGTTATCGATAATCCACATATTTGTTATAAAATGAAATTCGCAT TTCCATGACAGGGCATTAAGATATTTCCAGAATCAAGAACGTATTAAATA TCCAATTCGCAGGGTATTATCCCGCCAACGAAGTGAACCAGAGCTTTTAG TTCTCGTTTTCAGAGGATCCGCAACAAAAACACTCGTTTATTCCACAGAT TATTCCACAATGCCACAGAGGAGCGTCTGTCAAAGAGCTGCAGACTCAAG TGTCGAATGAGTTTTAGCATATTAAATATTTACATTTGGCATATAGCATA TATATGGTATATGGCTTTGCAAGCGTAATGTCAGCCCAAGGCCGTCCCGG ACCGCCCAGCCCCGCAACGCTACGAGATTAGGCCAAGATGATGGCTCTGG CTAGATAGCCACTTGGTTCTGGTCAGGGCCAACTCAGGCGGCGGATGGAG GCTTGGAATTTATAATTGTGATTTAATTTGCATAAACTTAAGACATCTGC CTTGGGGCAGCAGCTCATGTCCTGCCATCATCATTTTTATGGCCCGGACA AGGCATCCAAGCCTAAATTTTAAAACAATATGTCTAATATTTATGGCCGA AGTTTTGCAATAGGCTTTGTTGCGGCTTATGAAAGGATTAGTCTAAGATG CTCGAAAGCAACCTTGGTCGAAACAAAGAATGCTCACTGAGAAATCTGTA AAGGGCTGATGACAGTTTTATTAAATTTCCACGTGATTTGCAAAGATTTA TGTCGGTTCACAAACTAAAAAAAAAAGAGTAATGAAGGCACTAAAAGAAA TTCCTCAATTTCTATAAAAACAACGCGACGTTCCCAGGTATAAAAATAGT ATATTGCCATTTAAATTTTTACTCTTTTAATGTTAATACATTTTAAAACA ATTTTCTTTAACATTTGTGGCAAATATTATGAACGCTAACATCGGAAGTA AAATAAAGCGATTTAACTATTTCCATAGATTATTTTCACAATATTTGAAT GTGAGTAGGTAAAAAGTAAGATTTTTCATAATAATTAATTATTAATATGC AACCCTTTTAGCACGGATGACCGGTTGAAGTGACAATATATGTAGGCCAC AACTCTTAATTAAATGGTTATTCATATAATGCATAGTTAAATATTTAAAT ACATTTGCTCATACGCTCTTTTTGCTGGTTATGATTTCGATTAATGCGCG CATTTGTGGGGAGCAATATAATTGCTTTGGCAAACATTAAATTCATATCG GATCGGCATCATCTGCCAACTGGCAATATTTAGCCATAACGATATAAATA TTTTCTGCATAAATTGCTTGCATACGGATAACGATTTGCATTCACATAAA TATTCAGCACTTAGATTGGGTCAATTGCCATCCCTCATATGACCGGAAGT GAATGGATTGTTACATCTGGAGCAACTTCTTGACCGTGATTTATCTGGCG CATTCATCGCCAACTGTTGCTCAAAATCCAAGGATACTCAAAGAGTGGAG GAGTAGCTCTCCATTTTGGCCGGGTATTGTTATATTGTGTTAATGCATGA CGTTGTTAGGCAGCTCAAAGTGTACAAAAGAAATTAGCAAACTTGAAAAA TAAGAAAAGCTGCGAATTCAGCGGCAACTGTTGACAGTTATCCTGGCACA AACACGCATTGTAATGTCTAACAAGCTTCACAGCAAACATCGCCCGTCAC TCAACGGCCTCACAGTCCTGACAGGTCCTGCGTCCTTAAGTGTGTGTGGC TGTGTGTCGGTGGGTGTGTACGGGTGTGTGGGCGTCTGTCATTTACATAT TTACACTTTGTTCCCGGTGCCTTGGACTGAACTTTAGCCCGTGGTGGTGC TGTGCGCCACATGTCCTGCCCCAAGCATGTCCCGCTCGGAAAAATATCCA AATATTTTACTTTAACGCAGTGCTAATGTAACTATGCTCCTCCACATGCA CGTCCCCACGGTTCCTCTGCTCAAAATCCTTGTTTGTTTAAAGTATCACT TTTAAAAATTTAAGCGTTCAGCCATTTTCCGCTGACATTATAATGTGCAA AAACAATTGAATAGAGATTGAAACGTTCAACTTACGCGCTTATTAAAGTA ATTGAGTTTTAAAGAATTTGAAACCTGCACAAGTTTCCCCATCCCATCAT TTCTCAATAAAAAGTATCAAGTTGTAAGATTAAGAATTTTAAGAAGTATT TCACTATCAAAGCTTTTTTTTTTTTAAGTGGGGAGGTGATAATTGCGGGT TGAAGGACCACTCGACGAATATTGCATATACTGTATAGGCTGTATAGACT GTATAGACTGTATACTTATCAGTTCATCAGTTACCCCTTTGGCAAAACCC AAGATTGAGCACCCACATGCATACATTGCTGCTTCGCGCAGGTCATTCTT GGTAGTGATTACAAGATACTGACTGAGAAGATACTTTCATCTGCAGTGAT ATATTTTCCCCCGTGCAATGCGATTAAGACAACTGCCGGCGGTGGCGACA ATGCATTTTAAGGTGGCAAGTGCGAGCCCAAATGGCCCAAAGGCGCCAAA GGGAAAATGCAATTTCCACCGAAAATAACGGATAGCGGCCTGTAGCTGAT TCACTTTGGTGCAATTTGCATGAATCCGGTGGCTAACATACGGCTAACAG GCGCTGTTATCGTTGCTGCCGCAGCTGTGTTTATTGCGCACAACTCATTC ATAAAAGCGGGGAGAGCGCTCTCTCGGAGGAGATAGAGAGAGAGACAGAG AGAGAGAGAGAGAGCGGAGATTGAGTTGTCGGCGGCTGCTGTGCTTGTGT GCAATAAATACAAAGGACTCAGCATCCGCGGCAACAGTGCCGTCGCAGTG CTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCC GTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGA TGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTC CGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAA ACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGT CGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAACGTAAATTA AATACCACCCGGCCACGCGGCATTCGGACCGCCTTTATTAGAAGTTATGG CTGCCAACCTTTGCCAGCTTTGTTTCATCCATCAATGTGTGCGACAGTCA CGTGGGTGTGCGGATTGGGATCCGGACTTGGTTGCGATTGGGATCGAGAT GGGGTGGGGATTGGGATTGGGATTGCCGCTGGCATGGCGCTAATTTCTCA CACTTCAAACGTGGCAATGAATTTCCGCTCCAGCCTCCTGCGGATGCTTT CGTTCCGTTTGGCTTTGCTTTGCTTTCCCAGCCACCATGTTCCCAGCTCC CCGATTTCCCGGTGGCGCCCCTCACTCCCTGACCACCTAACACCCTTACC CGCTCCAGTGCTCGTGCCATTTGGATAGCTAAGCCTCTCCAGTGCCACAG ATTAAATGGATTGACGGTGCAGTTACCACGGCCGTTGGATAAACACGAGC ACGAGCACTTGGACCGGGAGTGTGCGTCCATCGGGGAAGACCTCCTCCGT ATTCACTTCTTTATGATTAGTTAATGGGATTCAATTTCATTCGAAATCAG CCGCCACAGAACGTGGCAATCGCAGCTGCCGCAGCTTCCTTCGCAAATTT CGTAAGGCAACTTTCTGAAGGAAACACTTGTTGGGTCTTTCTCAACTAAC CAGGCACGTAGCTCCGGCGAAAGGAGTACCAAGTGGGGGAGTTGGGAGGC GGAGGACGAAAGCCGAACGGCTGAAGGCCGGGGAAAGTGAATCACAGTTG CGCCATTAGGAGGCCGTGAAATAAATTCAATATAAGCGGGTCCTAATGGC GGTAGTTGAGTTCCATTTACATTCAGCCTCCATAAATTGGCATGGCTGCG AAAATCGTTGCCTACTTAAGAGGGCCCACATTTAGCAGGCGCAGCACCGG CATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACA AACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGC TAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCT AAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTC GCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGC TCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCA GAGCAAAAATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCG TGAAATCCGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGC ATGACGAGCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCT GGGATTACTCTGCCGGACGAAGGGTGAGTGGAGCGTCTGGGAGTCTGGGA GTCCCTCAATCTTCGGACTGAGCAGCTCTCTGTCGCCGATTGCTTTGCTT GAATTATGGAGAGCAGTCGGAATAAAAGGAGAATCCGTTTTACAGCCTTA TTAAATCTGTATTACATAAATTACGGCAAGCGTTTCACTCTGCATTTTTA TGAGTGCTTTGCGCTTTCACATTTCACATTTTCCATTTGCCTTTCCCTGC TTTTATGTCATAATGAGTGCAGCCTTTTGATTTAATGACAACTGTTTGCC ATAAAACAACATACATATGCACACACAGCGCTGACTTTTATGTGGCCCGT GATTTATTTCACTTCTTATTTTTATGATAATTTATCAAATATGCATAATA AAATGCCAGCAAACGTTTATGGCCTCTGTGAATTTTGCCAAAATTTCATT TGTAAGGTGGCAACAGCTTGCCGATCGGATTTTGTGTGCTGAATTCCTAC TGCAGGGTGGACCTTGTTCTGTCCTAAGTAACGAATTATAAACCACGATT GTTGTATATACCACTAAGGGACTGTAAGCGATGCCTGTTTCCCTGCTCTA TAAGTCTTTCATTTTGTAGACAGGCTTCAATAATCGAGGAGGCAGTTCAC GTAGTGACGAATGTAGAGTCAATATTTAATTGTGTTCGGACCATGCGATG CATTAAAATATTCGCAAATTTAGTAGAAAACATTTTATAGTATTATGCGA TTTCACGTAGAAACCTTTCCTTAACACTTTGGCTTAAAAATGTTTCTATC TTTGGGTGTTTCATAGACTTTGTAGCTTGAAGTCTAATCACTTTAAGTTT AAGACTAGGCCATCGATTTTCATTTTCTGTAATGGATCATATGTATATAT TTTTAATCAGTAAAGGCTTTTCCTTTTTACTTGCTTTTGCTTGTTTTATA CATTAGTTTGGTATATTTCAAAGAATCCATAAAAACTTTGAGATGTTGAT AAGATATTTGTGACTATTCAAAGGGAAACTGCCTTGAACTTTTGAACCGC TCTTCTTTGTTTTCTCTTGAGATATGAAATGACCAAAAAGGTTCACTGTC GCCTTTTGTTTTTGTTAACAACTCCACTATAGCTTAATTATTTTTTATGA TTCTTTATCTACGTTCAACATTTTTATGCGAAATGTGCTGTTCAACGGAG ATAAATACCGATTTTAGATATTTTTAACTTAAGCTATTAAGACAAATTCG AGCACAAGATATTATTAAATGGTGTTCTTAATATTCACACTTAGTGATTT TATTAATTCGTTTCGCTTTGTAATGTTTTTATTGATTTGAGCTCAATTTT GTTTTCTTCAAAACGGAATTACTGGTTGATAATCTCACGATTACAGCAAT CAGGGTAATCTGCGTTTGGGTTTGTGTACTTTCCAAACTTTTTGCCGGGG GGAAGTCCATAGGCACCACATCTAAAGTAAGTTCGTATATAGTATAGTAT ATAGAGTTGTAAAAAGCAAACATACGATTGGATTTCTGCCGCACTATTTT CTCCGCATATGATTCGCTCACACCTCTGTGGGTGGCGTGCACTTTGACCT TTTTCAAGAACCAAACCCTCGAGAACACACTTTCCAGGATGGGTTGGATC CTCGAAGACGCCTCGGACAACGGCAGCTTCGTAGCCCGAAACTAAGAGAA CGGCGATTGCCGCAAGTAGCACGGTAGATGAACGCATCTTGGAGCCTTCA AATCCCAACCTACACTGAACAGCCCAGTCAATTCTGAGAATATAAACGCT TTATCTATCGGTGGCCGGTCAGGCAAGTCGTCGGAATAAATATTTGTATA AGTAGCCAGAGCTTCGGAATAAAATTAGTGCTTTGCTCACACAAACGCAT TTATTACTACAATAATCATTCGAGACGGGCAGCACTTTGTTGTCGAGCCG ATAATGGACAAATAAAAATGCCAAGCACTTTAAGTATGGATTTTACTAAT CTGTTTGTTTTTATAACTATACTTATGGCCCATATACATATTCTGTGCGT TTTAATTAATAGATAGTTATCATTCTTGTTCTTCATGCATTTTGAATACA CTAATGAAAAGCCTCAGGTGAACTGAGATATGTGGAGATATTTTACCACT GCATCAGGATTAACATTTTATCATAGTTTATTAAGAAATATTTTGCAAGT GATTTATAAACGCATATAATTCATAATGTAATCGTTTACACTTGTTGTGC TCAGCTAACTTAAATCCTATTCAAAAAGTTTTGTTCTGCCAAATAATAAT AAAGTTCAGGGGTTTTATTTCGATTTAATAAAGTCCAAAATGTTAATTAG TTTAATGTTCACGTTATCACACTTTTGTTATTCAACTTGCTCATATTTAA GCCGTAATCAGCAGCGGCAAAACCAAATCAATATATGCCCAAATATTTCC TAATAAACAAAACAGCATATGCTGCTAAACGTGGGAATATGTTATGCGGG TCCACCCTATAGTAAATATAATTTCTATTTTTTCTGACTCTGTTCGCATG AGAAAAGCCAAACCAGCACGGGATTATTTTGCATTTGTTCTCGCCCTTTC GCAGCTTTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGA CCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGC AGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGC CAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGC AGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGC ACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGA CAGAAGGTAGGATGACGCCAGAGGCAATATTTCAAATCGGTCTTTCACTG GTTGAACGCTGCTATTTAGTCAGAAAAGAACAGTTCACTGGCTTAAAAAC GAGTTAAATGAATTATAACAGTGCTTAGCCGTACATTTGTGGTTTCTGTG CAACTCGGAAGCAGCTAGAGAAGTTCCTGCAGCACCTTTGTAGCTAAATC AGTAGCGAAAATGTTAGCTAGACCTGTATAATTTAACAAGTACTATGATT TTTCTACTTCGTCATCTTCTTTTGACTCAACCCTCGTTTTATTCAGTGAA TCCTTCAGACATCCGTTTTTGTGGGTGTAAGGCTGCAATGGAACTCTGCG TCTGTGGTCATTTGAATAACCATAATCGGACGAGCGTTCCTGGTAATTGA ACAAAGAGAGTGCATAATTTGAATTTGTGGCTCGTTACCGCACATGTGAT GATATGAATGCCAGACCCAGAGCAGTCTCCCTGCTCCTTCAGCCGAGATG TGTGCTTTGCTCGCCCATTCATTGTATCTCAGGCCATCAAATCGGCTGGC GTTGTGATTGATTGTCTGGTTGTGGGTGCACATGTTCCCACATGTTCAGT GTACATATATTGTATAAGCCGCAGGAGCACCTGCTGGCCGAACTTGTCGG AGGAGAAACATCTAAGTTATTTGCTATATCCCTTTCCAGGTTCCGCGCCT GGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGATCTTCTGCTGGT GGGAGAAGTGCGGTTGGTTCTGCGTCGGCTTTTCCCGGCATGCATAATAT AACGAGAAACTTTTGCCTTTTTCTCGCAGATAAGGCCAATGTAAACAAGG CGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGAC GGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATA TCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGA GGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAAT GACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTC GGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAAC ACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACAC AAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCA GCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAA AGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCA CCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCA CTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCT ACTACGACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCAC CAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCA GCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGAC AAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACA GCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTC TGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGC AGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCG GCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGAC AACGACAACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGG GAAGGACGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACA AGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGA TGTGAGTTGGGAGGTTGAGTAGGGTCCTCACTTTGGTCGGGCATTGTGTT GGAAAAGTAGCGCAAAAACATATCCATCTCCAAACGTAAGCATTGGAAAT AAATGCCAGAACTTCCTGTTAGATTAAAAGTTGAGGGACAATGTTTGTCC TTTCTGAGTGATACTGTTATTGTGCGAATGATAGTCCTAAGGAATCTTCA AGAGACTTCCTCCTTTGTTGGGTGATTTTTCTAATTTTAAGATGAACTAG GGAAGCGAACTGAAGCCAAGCCTCCTTACAGACTAAAACTATTATCCTCC ATTTGTCAGAAGCTCAGGGTATTTATAAGACTCGGTCCCCGAAAGTAGCT TTTACGGAAAACCCCAAGGGAAGGCCTTACCCAATTAGTCTGGGGGAAAC TGCCACTTCATTGGCTGCCCGGACGAGAAGCTTGAACTCTGCGCCTTCGG TGGTGTGCCCAGTGAGCCCGAAATGCTTCTGGTAATGGGGTTTTTCATGC TCGAGCTGGTTTATTATTTACCATGCAGTCAAGTCGAATTAACAGTCTGT GCTTTATTCCCGACCAGCTTGGACAGATGCAACCCGATCGCCGTGGACCA GACGCGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCT GAATGCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGC CGGCATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGG AGCATCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGT CTTCTTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCG TTGTCAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGC CAAACGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAA TGGCAACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACC CAGTGGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGAT CAGCCTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTAT AACAACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGTAAGC AAGCAAGTCGAAGGAGGTGGCCGTCCAAGGGGATTATCGTAGCACAGAGA AATAAATATCCTCGGGCATTTGCGGTCAAGCTGCTATTTGGTCAGTTTGC TTCCATCTGTTTGAGTTTATATTACTATACTTTTTCATTGCGACAAAGAT TTTGCCAGACTAAAATCGTATTGTCAAGTCCTTTGCGTTTTGATAAGAAC TGCATCAGCTGAGTAAGCCTATTTAAAATATTATTTAAGCCTTTTCAATC ATTTTGCTAAATTCAGTAAGAGAGGACAAAGCCAAATAAAAATCTCTGAT AAAATAAGCGGTATAATCATTCGATTGCCGGCTAAACATTCCGACGTGAG TCTGGGTAATGAAAACAACATTCCCGTATTTCACTACTGCGCATAACAAT TGCTCACTTCTAATCCCATTTAAACTGCAAATCAAACGCTACTCGTTCTA GGCAAACTGTATAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTG CCTGCAGTGCATTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCG TCACCTGCAGTCCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTC GATGCGACTGGTTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAAC GGCAGGTGGCAAGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGC TGTGGGAGTTTTTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAA AGCCACAACTGCAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAA CGAACGAATCGAATCTAATCGAATCGATTCGAATCACACTCACAACAACT GCACTACAGAACTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCA ACTCAATATGAATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAG TGCCCCAAGCACTCTCTAAAACGAAACCTATCAGCAGACATATATTATAT TCGTACCAAACTATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGG GGAATGAATAAAGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGAC TTTAAGCTGAATGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTC CGCAACAAAAATCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTT ATAGATGTACCAAACAGAAGTATATAGTATATACAAACATATACGAGTAT CTACTCTATATCTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAG TTCGGTGGGATCAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAA CCGTGTAGAGTTTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACG AGTAACTTATACAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAAC AATGACAAATAATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATA TTAAAAGCAAACAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCG CTTCTTTGGAAATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTT AGGAGCAATGTATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAA GACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTAT TTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTAT TTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTA GGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAA TACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACAT TCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGG CATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATAC CGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGT ATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTA AAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACT ACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCA TCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATC GACATGAATAAACCGAAACCCAACTAAGGCATTTCGAAACATGGCTCTAT TTCATTTCAGTGTTTGTAATCCTATTTGCAAAAGGTAAGACTGCGAGTTA ATTAATGCCGTGCATCATTGTCCATAATGCGGGCGAATTGGTCCACCGGC ATACATAAATCATGTAGCCCAAGGTTGGTGCAACATTAGATACATATATT CCTCTTATGATGGCTCATACATGGGTGCTATTTACTAAAGTATCACTTTA CTCTTTCCATCCTGCTAGTCGTCTTCGCTGCCGGACTCGAAGCCTGAATC CTCTTCGAGTTCGGCTAGAATGAAGGCTTCTATGGCCATCTGCAGGGCAA GGACGTCTCCTTCGCCAGGATCGGGTCCTTGCAGCATGGCCGTCGGTGGA CCCGCGTAGTGGGAGAAGGCTTCGCGCTGCCTGCCCAAGGACCGCACCGC GAGCTGGTTGTCCCCTCCTCCGTCCATCTTAGTGGGTCCGGTGCAGGGCT ATTGGTACCCGATCGGAGCTGGAAGTCGGCTGGAAACAAATGATGGCGCT TGGGCGCTGGGCTTGTGTTTTTTGGAATTTTGAGTATATGCTTTTCGATC GGCATTCAAAACGTGTTTGAATATCCCTGGCCGATGTGACAGGCCTCGCA AAAGCAGTGCGAATGCGGAAATTGCCTGCGGCAGATTGGCTGTTTAATAT TGTTAAATAAAGCGCTTCGGGACGAGTTATTAGTTTTCCAAAGCCGTTTG TGTTTGTGTGCGCAGCGCAATCATCGCAGTGACAGCCGACCGCAGGGCAC TTTCAAGCTGTGTGTGCGTGTGTGTGTGTGTAACCGGAAGCGGAAGTCGC GTCCCGTTCCGTTCGGCGCCGCTCCCTTTCGCATGCCGCCTACGCACGCA TTACGTACCCGCCCCGTTGCCTGACCGCATAAAGCCATTTGGCCATTTTG GCAACAAGCCCTAGCCCACAGCACCCGCTGACACAAAGTAGTCAGCCGCA CAATACTTTGCTGTCAATTTGTGATAACGGCAGCTTTATTTGAAAATATG TGCGACTTTATTTCCCGGCTGTGCCGAGCCGATTTTGCGGCCACACTGGC TGACAGCTGCTAGATGGTTTGTCGGTTGGCCAGCAGTGGATAGTGGGGTG GTGGGCAGTGGGCTGCTGATAGAACGTGTGAAATTGAATATTTACAAGAG CCCTTTCAGGTGGAAGTGCCCCATGTTGTCGGCCATGAATAGTGGGGCTT AGAGCGATTTGCGATGTTCGACTCGCAAAAGGAAGCCAACAAAGGGTGGC GGATCCGTTTCAACCACTTCTACCGAGCCGAACCGAGTTCGCATTCCGCA TTATTATTTTTATGGCCAGCAGCAGTGAGGAGCCGAAGGTCTCAACTAAT TAAATTTCCCAGATGTGTGTGTGTGTGTGTTTGCATGCACATATTTAAAT TGGCTCTGCCAGGCCACATAGCTGGCTATGTATGACTATATGACTATATT CCGGACTGCATTCTGGGTCGGAGAGTTGGTTGAGCAATGCACATTTTTAA TTACGCTGCACATTTGCATTTGAATTGCGCATTTTACAGGCTGATAAGCC GAAATAAAGGCAACAGTTGTGCAGTGGCTGCCAAAGATATGTTGGCTCTG GCCACGCCCCCATGCAGCTGCACACTCGCTCGTGTTTTTTACAGATCCCC AGAATGTGTAATTTTCGAGTTGACAACTTTTGTCCCAAAGCAGTGACCTC GTTACGCCCACACAGCCGGCTATATAGTATACTATACTATATTGCATTAG AGCCGTGCTCCTCCTTCAAAACAGAATCTGCCCGCAGCCATAACCCCAGT GAGCCGGGCGGGCACAAAGGATACGGTGGAGGAGGAGAAGAAGGAGGGAC TGGAATGGAATGGATTGGATTGGGTTGGATCGGATGGTGAAAGCGAGTGC AGAATGCCTTTCAATGAAATGCAAAGCAGAGAAAGTTGGAGAACAAAAGG CATACGGAGCTTTTAAATTTTACTGCCTTCGCTTCGATTCCGGGCGCTAA TGGAAACCCTGCATTTCCATTTTACCTTCTAGTCCGGGGAGAATTTTCCC GATCGACCATTCTGCTAATGGAAAAACATTCAGCGCTGCGCCTTTGAAAT TCTTGAAGTTCAAGGACCCTCTGTTTCAGTCCGTAGGTGCACTACTTCTG TCACTATGTCACTATTAAACGGGAAAATTAAGCTCCCTCCGCAAATCAAT GACACTGGTGTCCCATTTCTCGCCATCCCCAAAAACACGTGTCTAGGATG GGGACTTTTCAACCGCCTACTGGGCTGATGTTTAAGCCATTTTTAATGAC AGCCTGACGCCTGACAACGGCTAATGATGGCGGCTAGCCAAAGTTTTGCG GCTTTTGCGGATTAAAATTGAAAACGCTTGCATTCATTAATCCTGCCAAC GGAAAAACCCAACTAGAACGTGACATGAGGCAGGTGTCGCATTAATTAGT GTAAGCATTCACACGGCTCCCACTCCACAGCTTGCGAAATGAAAGTTTCC TCGGGCGGGCGGTTTCATTTCGCCGAGATGTGTCACTCCGCAATTTGGGT CAAGATGGCTTGAGTTAAATTATTGCAAACGGCATTCCGCACCGTCTTCC TGCCCCTCGAAGTCCTCGAATCGAGGACACGTGCCTATTTGCATAGATAA CCTCAGGCCAGTGAATCAACTCCTTTGATAGCCTCCAATAGCAAAAGCTT TCAAATGCGATTATTGAATTATTGGGCAATAAGACTAGAAGGCACAATTA AAACCAGTCTTTGCGCCTAAAACATTACAGTGTCCATCTGAAAAATGTCT AAATAAAGCGGCTTTAATTTTTTAATATCTTTAAAATTTATTTAGGCAGA TAAAAAGTGACATTAACATTAGTATGCGTGATATAATAGCCATTTTTTCA CACCACTAAATTTCATGTTTTGTGGCAATAACATTTTAATTTACTGTTTT TGACCTGGAGGTAAGTTATGCTAATGTTTAACATAAACATACATTATCGT ATTTAATTAAATTTTAAGGCAATGGAATCTAAAAGGCGTCATTGTACCAA AAAAGTACAGTCTCAAAAGTAGACAACTACATATAATGAAGTTTAGTGTT AAAAGGTGAATATGTGAATTTGAATATACTCAATGTCTTAGTTTGCGAAA CTGAGAAATGGCTTTAGTCCCAGGACGTGCAAACAGTTGAGCAAGCCTTT TATGAATTTTCATAGAACATTTAACACAATCCAGGAGAACTAGCTCTTTG CCAGCATCCAGCATTGATCATTCAGTTGGCACCGTGTCTGGCCCCAAACA AGAATTCCACAAAAGCGCCCAACTTCCCATCTTATCCAGCCCCCATTTCT GGCTGCCTGATGCCGATGTGTCTGTTACCTGGGGCAAGCCAGAAGGCAGT TTCCAGAGATGAGATGCTCCGAGAGATGAACAGCTGATGACCGTGACTGT GCCTTTGTGCTGGCGAGACCCAGACCCCCAGGCACCCAGTCTTCCAAGTC TTTCGAGTCTTGTGGTGGCATCTGAGGGGTGAACATACAAATTAATCTTC ATCTGGCACTCGCACCCACAACACCACCCAACTAAGCTTCTGACCGCTCA AGCTCGCTATTTGAAAGCGATGCGAAAAAGACAATAACAAATCAACGTAC TGATACTAAGGGAAAGCTGCCATGGTTTATTGCAATCAACTTAAATCTTA ACACTATTATCTGGCAATTATCGGGCATTTTATATAAGCAGTAACTTTTT TGATTGGTCCCGGTCGAGGACAATGAAGTGAAATCGTTTCGAAGCTTACT ATGATATATATTAATGATATGATATATATATAGATAAAATAAAGGGAAAC AATTTGAACAGCGGCTTACTTGAAACGGACGGATGGACAGAAGGGCATAT GGATACGGATCAGGAACATATGTCTATGAATACCATTAGCGCGTACTTTA TATGCAAATTTTTGCCACGACGTATTGATTTAAGTGTTATTTAGTACAAT TTTCGACCATTTCAGTTTCAAACGTTTAAATAAGAAAAGGTATCATATAT TTAAGAACTTGGTGAAACTTTGCAGAAATTGCTTCTAATGGAAACAACTT AGGGAAGTATGTTATTTTTGATACTTCAAGAGTAAGTCGTTGAAATTGAT ATCAGATTATACTGTTGTCGAGAACTGAAAACTAAACTGTCTATCTAATT CAGATGCTTATTTCTATTAATAACTGGCAGGCAGTTCCACCTCTAATCCC ATTGTGCGGAGTGTAAGCCAACGACTGACTTGGTATTTAAAGCTCCTCCG TGACTCGGTCAGAGCAAACAGTTCCTGGACCACTGGCTTCATGGCCCTTT GTGTAATACCTCTGTTGGGAAATGCCTTTCAGCTCGCTCCTCCTTCAATC TGCTCTCGGTCAGAAGCCACTGGGGCAAACAAGTCCGCCCCAATGGGTAT TTACCAAGTGTCAGTCACTTTTTCTGCACTTTCCTTAATTACTGTCATTG GCCGCCGCTGCCATTTTGTTCCAGAGCTCTTGTGAATTTGCAGTCATCAA AATATTGTGGCCGAATTATGTAGCGATAGTTGTGTGACGAATTTTGGAAT ATTATATGCATTTTTCGCTAGTCCTTCCAGAGTGCTCTGTTTTTGAAAGC TGTGGCTTTGAGTTATCCTAGTTGGTCAACAAATGGTTTTCGGCATTTTG GAGCACTTTAACTGGCTAATTCTCGGGCAAAATGCACAAATTGTGTAATT TTCAAGTTAACAGCTCTTGACCTGGTTCAGAGTGGCAGTCCTCCGCAAAT CCTTCTGTTGATTTGGTCCGCGGAATTTAGTTTGTTTTGTAACAGCGCTC AAATATGCAAAAGCGCAATTGTGTGTTAAGTTGGCTTTGTTGCCGCGTGT GTGCATGCTTTTAGGCTCAGGGGTAGTCGAGGCATTTTATGCGACTGCCA CAAGTTTGTTGGCAAAAGTTTGAGCCCGTAAAACTTTTAATTCAGTGCCT ACCAACCAGTTGTTCCCGGCCATCCTATCCATCCAGCCCATCCAGCCCAT CCAGCCCATCCAGCCCATCCAACCCATCCAATCCATGGAGCTCATGGTTG CCATGAACAGCAGTAGTAACAGTAACAGGCTTTTAGCGAATACACACATT AAGCCCTTTGCTGCTCGGTCTGTCCTTTATGAAAGGGTTCAGGAGCAAAA GTTTCGCATACACCTTAGGATCCTGCCTGGTGGCTGGCTGTTGGTGCTCA ACTAACAACAATTCGGGGGTTAAAAGCGGGCGAGTGAGTGCAGGTCGAGA ACAAATGAGGAAAATATGCTTCAATAACAAAACACTCAACACTTAGGAGC ACGGGAACAAGTGAGCACAGGACGAGTGCTAAAAGGAACAACGACCGATT TACATAAGGACCCCAAACAGACGCACCAACCATCCATCCATCCATATCCA ACCATCCGGAGAAATGCAAACACGACCAGGACACCCAGAACACCCAGAAC AGCCAGACACTCGGAAAAACAAGCGTCTATTGTGGCGGAAAACTTTTTGC GCCGTTGAAAGGCATTTTTCGATGCAGAAAAAGATTTATTAATATTTAAC AGCCCAGCTAGAGGAAAACACACGAAATTTTCCGGGATATGCAAACATAA TAACTGTTGCAGCAGCCAGGGTGAAAGTTCAACATGGACGTAAGTGGACT TTGCTGTGTACCAGTTTTCTGACTGCGACTTGTCCCGCTCCTGACTTCAA TATCCTGCAGACTAGCCGGACTGCAGGAAGCACTTTGTGGACGGGCAGAA TACCCCACGGAGCGCCAAATGGCGGCCAGTCACGGATTTGGTCCTCCCAG CCCAGATCCTTCCTGCCGGACGCCCACGACCATTGCATCAGGGTGGGTCA CATTGTTTGACAAGAAAATGCTGTTGGAGCAATGCATTCCTAGGAAGAAC GCTTTAAGCCTCTGCAATCGGATTTAAATGTTAAGGAAAGTTATCATTGT ATCACCATTAAATTATGAAGTAATTTAACCGATAGTTTCTAGAGTTTTGC CTTTAATATATATCAAATCCCCTAGTATCAACTTCGAATGGTTAAGTTGT AAGAGGAATTTAAGAATTGTCGTTATAAGTACGTCTTCTTATTATTATGG CTTCAATTTGCTGGTGCTGTCCTGTAAGCTTGATACACCCTGTCGTGCGT TTCTTGCACAACCGCCCGCCACAACGGCAAACAAAAGGGCAGGATGAAGC GGATGGGGATGGGTATTGGGGTTGGTCCGAAATCTGGGGACTGGGACTGC GGCATGCATTATTGAGTATGAAGGACCCACTGATTTTTTCGGTTAGCGAC TTCCCTTGCCGAGCGATGACAATGCGAAGAGGGCCGTGCAATTGCCATCA AACGTAGCGCCAAAAGCCGAGCCGAACTCATTAGGCTTGCAACGCCGAGT GGTGGCCGTGCTCTAATTATGCCGTCTCTATCTAATTCCCCTTCCCAGCC AGCTCGGCTTTCTGCTTCGCTTGTGTTCTCCCAGTGTCCTGGCTCTTTGG TGCTTTGCTATTCTGGTGTCCTGGTGTCGTGGACTTCTTTTTGGCCCGCC CAGGCAAACTGTGATTGTGGGCGGAGCGAAATCGGAGGAGGCAGTTCCGC TGGATGGACAATGGGAATGCGATCGGCTCCTCGGGCTTTTGACTTTACTG TTGTCCCACATAATGACCATAAAAGGGGTTCATGGCGAAGGAACTGCTGG TTTGACCTTCAGCGGGCATTAAAAAGAAATAAATAATAAATCAACTCGGG CATGAAATATTCAATAACCTAAACCGACAAAGATTTACTGCTCAGCCGTT TATTTCGTGCGACCCAAGAATAAAAAGCCGGCATGAGAAAAAAAAACACT TTGTAAGCAATTTGGGCAGGAAAAAGCTGGCTGGATCTGTTTTGAAAACT GCCAACTAAACAAGAAGTCACTCAAGGCCCGAAAGCACACATAGGGCCAC CCACACGCCTGCCACACAAATTGAAAGAGTTGCCAAAGTTGATTGCTGGC TAAACGAAAGGTGGCCCAAAGCCTGCCCGGCAGTCGGTAGACGGACTATT CTTACTAACCTGGCCTTAACCTGGCTTAGAGGACCGCCTTTGACGCCCTT CATAATTTGCCAGGACGACCACGACAGCCGCACACTTGAGAGCTGCTCTG TAGCCACAAAGGAAAATATAAATTGTTTTTATTTCTGTGCGAACGAGGAA ATGGAATAATCAAAAGATAATGACACAAAGGGAAATGGAGGAAAAGTCAT CATCGTCGGCCACGTGAAATAGCGAAAGTTTACCTCACAACTACCACATA TTTTACAGATGTCAGATAGCGCGTATGCGGGCTACGAACTTCCTAATCCT GGCCAACAACAGCCCGTGTTGCCATCAGTCCGTAGTGCCTGCCACAATTC CGGCAATCTGTCCGGCGGGCGGGGATATCACTGCCAAAAAGACATTTAAT ACACGCAAATAAATATCGCCGGCGAGTCTCGTGTGCAGTGTACACAGACC GGAAACAGAAAGGCTACAATTCAGGATACGGAAAAGGGTGGCAGGGGTTG GGGAGTGGAAGCAGTCAGTCGCAGGATATGGCCATGAGAAATTAGTGGAG TTTTGCCGCATAAATTGCCGCCCATACTAGCTTATATACCACAGAAGCAA TCTGGTTCAGCATTTTAGGGAAATTCTAAGGACTCTATTCTGTTGTGACT ACGATGGAATGCAAAAAACTAATGAAACAGAATTTTCGGATTTAATATTC AGAATTTTTATCGGTAGCTTTTATAACTGAAGTTATACACACTATAAATC AGCCAACTATGTTTAAACAATGCTTTCCAGAAATTTATGTGAATTGTATG CCAATCAAGTTGGGCTTCATAATTCATTGCTGATTAAATTTTATGCCAGA TGTAGGTAATCAAAAACTGATATACATATATACTAATAATAATAATAATA ATAATAATACTCGAAATTGTGAATTGTGCTGAAACTTGAGCAACACAAGC GGCTTTGTGTATCTTGCAGAAATATTTGTAGTTAATTGTTAATTGAATTC AGCTTTTCAAAGTTGTGTAGTTTGAAATAATTGTAACTTGCATCAGTTAC ATAAACTTCTACCGAAAAATAATAATGATAATCCATAAGATACCTGAAGA CGGGAAACATTGTTGTAGGATCTACAGCGAACATGGCGACCAGTGCTAGT GAGTAACTAAAATCACAATGATTGCCGTTGAGGTTTGTTTGCACTTGTTG GCAAATGCCCTAAATACTCGTACGCCACTGTGGTGGTGAGCATTCAGATG GGATGGAAGTGGGCAGTGGGCAGTGGGAGTGGAAATAAAGCTTCGGAGGA GTCACGCTCGTAATTTTCCATAGGCAACATTTGCCATGATAATACGTAAT ATACATAACAACCACAGTTATGCGAGGCCGGGGGCGATTCCGACCCTCAT GCATATTGATGGTATGCCGAAAATAGTTCCTCAAAGATAATAAATAGATG CCAAACGCAGTGGCCAGCGCTAGCAGCTCTGCTTTCGGCCAACATAGCGC ACTAAACACAGCCAGCTGCTGCTGCTGTTAACATTTCGTACTCAGCTCGC TGCTGTGGGGTCAGTTGAGTTGATTTTGGGGCTCTGGGGATTACACTGGA TAATTGCAGTCTATTGCAGGGCCAGAACCAGATCCAGAGCTACAGCTACA GGCTTCTCAGCACTGCCCCTTCCGACTGCCAAGGTTGCCGGGATCATAAA TCACAATCAAATTACTGGCTGATTATTCCGAGTCGGGATGCATGAAATGG ATTAATGCCGCACGGCGGAACCTAATAAATCAATGGCCAACAGGAACGGC GCATAACTCGGCTGGAGCACTTTGACTTGGGTAATTAAATTACGTGGCCC GCGGCAGCGCGCCTTTGACATCCCAGAGAGGTCCTTTGTTCGGCTTTTTA TTTGCGAATCGACGGCGCAATCTGTTAACGCGTTTGCAAATAAAAATTAT CAAATTATTTTGGCCCGATTTCGGGCGGCTCCCGGCCATGTGTGCTCGCT CAATCAATTATTCTGCCGATTTCGGGTATTTGCATGTGCAAATCTGATTT ACACGCACAAATGAATATTAAATTGCTTGAATCAATTGAGTTCAAGTACA CTCCGCACTCACCCTGCACTCGCTGTAGATTTTTGAGTTCGCAGTGCTCA ATCACAATGGCATAAATCGCGCCACGAGTGCAAAGTGAAATTTGGAAAGG TGCCTTCCCGCACTTCCGCCGCTTTCCCCCATATGGATCTCTACTATCCG TCTGCCCGACTTACGCACTCGATATGTCCGAAACAAGAAGTGGAGGAATT CTTCGAAAACTCAAGAAAGACTCCGAACCAATTTAACGAACAATCAGCAG GTGTAATGTCACGTTTGGCCACTTCAAATATACATTTTTTTTGGTATAAC AACGGCCTGAGGATCATGTAAACAGTGGAAGTATTTGGAATTGACCCACT TTGGAATGCATTTTTGGTCGAATTTAAATTAAATTCAACTTTTTTGCCTG CAGATTCCCGCTTAAACTCGGACATTCCTGTATTATGATGCTCCTTTCTC AGCGCGTTGAATCCCGTGCGCTGGTGACATGCACGCGTATGAAATTCCAG AACACAAACTTTATTGAATTTCGCCCTAATTTTTTCGACTTCAAAGTCAA GACTTTGTTGCTGATTGTCGTAAGGGTTTTAATATGGCCAAATCGTCGGT CTGGCGTTTATTAAATTTTATTTGTGAGCAGCGCACAACAAACTTTTGTG TTGTGCTGTATGGCTCACTGCATGTGCAGTTGACATCTTTATGGGAACAT AGTTGGTACGAGTATACGGCTGTGGCTCTGCCCTCGTCCGTTGACATTTT CGGTAACTGGGAGGGGGGATGGCAGGACTTAGCCATATTTATTTGCCAAG CTACATACACAGAAATATACGGCAGTGGCAGAACGTATATTATGTACTGA GCAAACTTCGTTAAATGTTTAAAGTCTCAATCAATTATGCAGTTTTCCTT GTCGTCATGCTTTTTGTGCACGGCAATGAATAAGAAATGATTTTAAAATT TCTGACGGGCAATCTTAAAATGTTTCATTGCCTTAAAACCATTTCGTTCC ACCATGTTAGTAAATTGCCCGGATTTCAGATAGCTCTGCCAAACATCCTT AATTTACTCACTTTCGATTCTCTGGCTAACAAATGGGCCACAATTAATTA CACATGTGGGAGGTGGCTAGTGGGTGTAGCTCCTGTCCGCTCGTCTGGGC TCATATATCAGCTGATAACTGGATGTGGCATGAAAGCCGTTTTCGGGGCA GCGGCAGCAGTCAGCACGGCCATGAATACATTAAGTTGCTGCCACGTCTA ATTGCCTCGTTGTTTGTTTGTTTGTTGCTGTGGCTCCTCGGCGGTGTAAC AGGTGCGTTCGCTCCTTTGGGCAGCTCCACGGTTTCGGTGTCGAAATGTA TTTTTACCATAAATTAAACAACGGACCATAAAAACTTCCACAAACGGCCC GGCAAAGTGTTTCCAACCCGTTCCGCAGTTTGAACCTTTTTTGGCGTGTT TGCCACCGCCAACCGTAAATTCCGGGGAGCCAAAACTCATTTAAAATGTC CAACCCGTGCATGAGTTTCGAGAGCATATTTCATAAGCACACTCCCCGAC CAACTTGTGTGTTTTCATAAAGCATTTAAACAGCATTATAAATTTGCTTA GCTGCAAACGGGGCTTGCTCATTTCTGCATTCTCGATCACGACCGAAAGG ATTCGCCTGCTCACGTAATGGGACTTATGCCCGATAATGTGCTCCTCCTT GGCATTTGGCCCCCGGGGCGTTAACAGCCCGCCGGTTGCACCTGCAGCCA TGCGAAGGGGTGTCCTGGCCAGCAGGAAGGGGGCAGCCAGACAAAGGACC TCCCCCTTCTTGGCCAGCCGAGTCGAGCTCCGCAACTCCTGAACCGAACC TCTGAGCCACTCGAAGTGTGCGCGTGACATTCGGCGGCCGTGACAGGCGG CCCTTTTTGAATAATGCCCGTCAAGTGGCGGCCACCATATTGAGTGAGTA CGGTACAGGGAGTGGGGCAATGGCAGTCCTGTGATTTATGAGACAACTTT TTTATTTCAATATTGTGTTTTCTCCATCGGACTCCTCCTGCGTGTGTCTG TTTAATAAAATGCTCTGATTAAGTACAAAGTGTATATCGAATATTTATGA ATGTCTTCTCTAACTTCCTTCTTTCACGATGCAGAACGCTCCTCATAATT ATGACAAATTGATTTTATGTAAGCGAACAATGGCACTGAGTGAATTCGCC GTCTGCGACGAATCCGAAGAATGAAATTTGAAACGAAGCTCAATTTGGGT TTCTTGAAAGAGCTTATTGACTGCTGGGCTCGAAAATGACGCAGATATTG GCTGTCAGCTAAATAGGTTGTTATTTCTCGTTTAAAATTTAAAAACCCTC AAAGTAATTGCCGTAATTATGCAAATTTTTTTTCGAATAAAATATCTATA ATTGAATAGCGGTAGCTTCCGTCCGTCAGCTGCAATAAGTACATAACTGG GCAAAAATGGCGTTTTTATTTGATTCCTCATATGAGTATGCACCTGTCAA TCAGACCTATAAGCCAGCATGTTTCCGAACAATTCCTTTAACACAATACC AGCTTTAAATACCCAACGCATCTTCTATTTCATTTGAGTCACAACAAAAT CAGCCCCATTAAGTATGCTATCGATTTAGACTGCTGGCTGTGTTAAGCAC TTTATGCTCAGTCAGTTGTGCGAGCAGAGTTCAACGCACAATTACACAGC CGAGAACTGGTTGGCAGTCATTAATTTTAATGTTTATATTTTCATTTGCT GGCAGCCGGGCGATTGTCCGTCGAGTGTTGTGACTGCGGCGTTTTTATCT CAGGCACGCAGCACAATTAAGCAGCATTTAAATGCTCGACTGGTCGCAAC CGGTCCAAAATCAACCAGGCCGAACCAAAAGCAACCCGACTCTTTGAGTG GACATGCAATAATTGATATTTCAATGGAGCCGCACCGTCCATTGAATCTG CAATCTCGACTGCTGCAAAACTCCTGTGGTCGTCCGTTAATGGTGATGTA TTTTTACTTTGATTGCGTCCATAGTTGCAGTGGCAAACGTTAAGCGGATT TCATAGAGTGCAACAAATGCCAATAAGCGTGGGATGTAGAGTGCTGCACG TGCCCGGCATAAATCGATGTCGCTCTCCCTGCCCCTGCCCCTGCCCCTGC CCCTGCCCCTGCCCCTGCTCTTCCACTGCAGCAGTTTCAGTGTCCTGTTC CACTCCCCAGAGTGCCGGGAATAGGGAATTATATGTACGCATAGTGCGGC ATGAATATGAAGTGCGTGCTCCGGGCAGAAGGGTCAAAGCGGGTCCCTGG CATCCTTACTCCCAGCTCACGGCTCCCAGTTCCATGATCATGATCACTTT TCCGCAAATCAGCTGAGCACATCATTCATTCAAATTTGACCCTTTTTGCG TCGGAAGAGGACGCAACACTTTCGTCCTGCGGCACAGCAAACTGTGGGAA AATTATGCAAATGCTGCGGCGGCTTTACTAATATGCTCATTTGCATTTGC CTCCGCATTGTTTACCGAATTGGCCAGCCATCGATGGAGCAGGGGACTTG ATTATGCAGGGCACACGGCTGCCGGTTCTCAATTCCAGGATCTCGGCCAA GTTATGCGCTGAAGCATGTAATTCTTCCAGTATTTTTCACACCCTCCGGT CGAAGGAGCTTGACTTGACTTATTAATGTCCTGGATGCGAAAGGGTAGTG TTTCCGTGCCCAGACTGTTTGCCATGCGCCCAGCCCGGCTCTGCCTGCTA ATCGCTCGGGAATCTCTTTAAAGTCCGGCCAACTTTTCTGATGGATAGCT GGCTGACTGGCGTGGGTGCTGTGTTTACTTAGGGCATCAATACATCACTT AGTGGCAAATTTATGCGTTCGCTTGGCAAGTAGTTTCAAATATCAGCAAC TATCTGCTTTAAGCTTAAATCGCTGCGAGTGTTCATGGCGAGCACTGACC GCATACTCCAATATCCCGTGGCCGGGTTCAATTTATGGCCACACGAAACG CGCTATGAAAAATGTGGTCAACATCCAGCGAGGCACGTTCCCTGGGCAAC GCCAACCAGGACCCCCGAAAACCAAGCAATCGGAAGGGCCGAGGGGTGTG TGGCGCACCAACTGGAAAAATAATTACACAAATTATGATCGAGTGCGAGT GCATGCACAAATTAACAAATGAATTTTCGCCTGCTCTGTAGGCACGGCGG ATGCGTAATGCAGCACATTGCTCATACGCAGTGGGTGCCGTTCGAAGCAG TTGGCATTTAACTCCGGAGCAATAACGGGGCATTAGAGCTGCTTAGCAGC CACTGTGTGACCTCGGAGTCTGGCATGTCCCCTCCATGGCTGCTAAGTCC GCTTGAGCATTCGACTAAGCCCATTTAATTGTCTTCATTAGCGCGCTTAA AGTTACATTTAATCCGCAACCGACTGTTTCCTTTTCCGTTTCCGTTCCGC GCAGACGGGAAGGTGTATTTGGCGATGGAAAGCGAATTGAGCGAAGGCTT TTGCTAATTAGACGCGGACCCATCGCGACTCGGGTGCAATGAGCTGTGGC AGTCGTGGAGTGAGTGCTTCGAGTGCATTACTTTCCAGTCCAATATATCA AATTTAAATGCGGCCCACACACACTCTAAATTTAATGTGTAGCGGAGCGA TGGGGGAAGGCAGGCAAGGAGCAAAGCAATTTGTTTCACCACGAGTAATT TGTCTTCAAAAAGCAAATGTTTTGCAATTTGTTAACAAGAACATTTTTCG CTTTATGCTCCCACCGAACCTCTTGTCCCTTGTTTTACTTTTTGCTTTTC CCTGCATGTATTTGTTGGCAGGCGCTTGGCGGCTTGTTTGCCATCGTTTG GTTTTTGCCTCTTTGTTTACATTGTTCGCGCGGAGCCAGACTCCGACCCG GGCTCCTGAATTTCCAGGACTTTCGGGTATGGAGAGCACCAAAGCCGAGG CCACTGCAAACGCAAATTGCGGGGAAGCTGGCCCCCGAGCAGATAAGATG GAAAATACCGCTCTGCGCTTGTAATAAATGAGTGTACTGCCTAAAATTGA AAGTAAATACATATCGGCAGACATGCCGGACCAGCAGGATATCTTTAGTC CAAGCCCAAGAGAAGGACATGCAGAGCGGTAGCGGGTTGTCGGGCGGTTG GTGGTCAGGAGGCGAGAGCTTCCACTGAACCAGTGGACCCAGAACCCACT TGTTGGCCACGGTTCACCCGGCAGCGAACTCTTAATTGATTTCGCGCTAA TTGGTCCGACCCAACAACGACGCTGGTTGATGTTTAACAATTTGCAAATA TAAATATTACCAACGGTGTCCAATTATGGATTTCCCAATGCACTCATGTG CATTCATATTCAATTATCTTCCTGGGCGGGCTTGTTAATTGCTCTTAAAT CTGTGCGAGCCGGAAAATTCTCTCTTCGCAGGCGAATTTCCAGCAGCCGG CAGCGAAGCGGTTTGAACGGTTTGTGCGACTTTTCAGTTCTGGCATGGGA AATTCATTTTATTTCATTTACATTCATCACCTTTTTTCTTTCTCTCAGGG TTTTAGCCCCTTCGAATCGGTATGGAATCAGTCAAAACCGTAGAAAACCA CTGCTCTGGTGGTCATGTGCATGACCGGAAATCCACTCCGTCGGCGTGCC GTAATGTCATAGATATTCAGATTCACGGTTGGGGTTAGTTTATTGAATCT GTATATATAATATACAAATTATCCATAATCGAATAAGCTATCCTTATCTT TGTGGTAGGTCTTTGTACAAGTATGTATGTACTTGTTTATTAAGATTGCT AATCACGATTAACTTAGTAAAGATAATTTGGGTTTGTTTGAAATATTTGG CTATACTATGAAGAACTTTTTTTTTAAGATTAAGGTTAGAAGATAGTTTA GTTATCTGCTACAGTTTCCCGACCTTCATTGTTCGACCATAGCTGCACAA ATTTAATCTGGAGAGAATAACATTTGCTGGGGAAACTGGGTAAGGTCAAA AAGTAAGGCCCGTAGTCCCTGCTGCTGTTCTCTTGATGGTTTTATGCTTT GTAATCATGGCCAGCGCACACACACACACTCACATTCGGGCTACCACAAA GCGACACAATTTGAACTTTAACACCTTCGGTGACAGCCAGCTGTATGACC TCAGGCGCAATTTCGTGTAAATAACACGAAAATAACAAAAACATCCTCGA GCGGTTGAGAATAAGGCTCCGACCTCTCGACCACGCCCCCAGGCGCACTG CCAATCTCAATCCCATCTCCCACCATCCACCTCCGCCCATCATTCGGTCT GTGGGCTAGTTGGTGTGAGTGCTGCCGTAGTTGGCCATTATGCGCATAAA ATATAAGAGGGTTGTTCATATCCCCAGCACAATGGATGCATAAATCTACG CTACTTTGCAGGAAAGGACGAAAGGCGGGGGACAGGACGAAAGACACAGT CGGTGAAAGTCTCTGCCCTCGGATCGCACGCAAGATTTATTTTAACATTT TTATTATTAGTTTCCCGTCTCGTTTGGCCTTTCAGAAGTTCCTTGCGGTC ATGCTGCATTAGCTTTGGCTTCCATCACAAATTGCTTGAAAATGGCATTG TAAATTATGGTTTACTTTTAAAGAACTTCATTGAAACTTGATTGGAGCCT CATTCACAGCCTTCGCCTCAACCACTTCCCGTCGCCCACCTCAGAACATT CCCACCTACTCCCACTTTGGCAACCCTTGTGTGCCACTTACAGTTGTACA AGGGATCGAGTTTTCCATTCGAATGCCTTCGAGCCCGTTCCGATTCGATG CTATTGTGTTTGGCTTAAATGTCAGCTGTCATTGGCCATAATTTCAGTTT ATTGTTTTGCCAAAAACAAAACCCCGGCCCAGCCGCCTTTAGCGGAAGGA GCCCTTTTCCGGGCCTGACAATTCCATTTACTCATTTTGGGCTCGCTGTC GCTGATAATTGGACATAAAAGGCTATCGGCAGGGAATAGCACGGCGTTTC AGATGGCCCAAACTTCCTCGATTTGGGGAAGTAAGTAAGAAATTTGTAAA AAAAAAAAACTGACGATTTAGGACTTAGAGATTTAGTTCCTTAAGCTTAC TGTTATTCTCCTCCTTCTTTATTTTAAACATTTCTATCTGCCTGTAATGA TTGGGAAAAGTTTAGTTACGTGGCTTTATTTGGTTCTTCCATGATATGAA CTTCCTACCACCTATGAATGTTACTATTATTGCAATGGTTTCATGTTTGA AAGCCGAAATAAAAAAAAAAAACAGCGGTCTTCTATTTTGCATTGACTGG TTAACAAAGGATATTAAAAGCTCAAATCTAAAACTTTAACTAGGAAATTA ATAATTAAATGGCAAAATCGTGTGCCTCTGGCCTTTCTGAAACCGTTCGG GATGGGTGGAGTTCGGGGCTTACTTGTTGCAGACCCTTTCTGAAATTAAA AACTTTTCCCTAATGTGCATTAAAATCCTTTCATTTCTCAATTTTTTCAA TTTCCATAAGCGCTGACCCCATGCATTTCGCAAGCCTTGTAATTTTCCAA TTTGCTTTTCTTGCTTAGTGTCTGTTCTGCCTTTTCACTTTCCACTCCGT GCTTTTTCTGCTGACTCGTGCGCCTAATTGTAAGTAACAAGCGGGCAACA GCATTTACAGCTCGGAAAATGCCAATGGAAATCGCTTATAGCTCGGGGAA AAGCGAAAAAAATAAAATGTGCCGGCGGGTGGAGGCGGGAAGGGGCCCAG AAGGAGCCAAGGAAAAATTATAAATGGCGGCGAAAAATTCTTTGCAAACA CTTTTTCACGCTTGATTAATTTTGGTTCGGCAGTCGCTAGCTCCCATCCC TTCCCCATTTTGGTTTTATTTTATTACCATCCATTTTTTAAATGCAAAGT GTTAAGTTTGACAGTTTTGGGTCTACTGTGGGGCATTATGCACACCTCAC TAGATATGCGCGAAAGTCGCCATCGCAAGGAGCAAGCAGCTCCGTCATGC GAATCCCTCAAGCTGACAGGCTGCTTTTAATTAATGCAATCGCAGGTCCT TCCACCTTGGGCTCATTGCGGAACAGCTCTCGAAATCAATTCGAGATTTT TCTTCAGCCTCCGCCGGTCAATGAGCACATCATTAAGGCCCTCAAAGGGA ACCCCGCCCACTCCAGGACCTCGATTTCTGGCAGTATGCTAGGGTTCAAA AGCCACTTCATCGGATTGAATGGATGAACCGGTCTGGCCATGGATTGCCT CTGTGTTAGCGTTCTGCGCTTATTTATGTTAGTGTCTTGCACTCAAGCTG CTTCTCACACACAAAGCCATGTACTCGGCTCCGCATTCAATTTACTAATG CACATCGCTTCTCCGGGCAGGAATCCATGTGCTGACATCCCTGCGATTCC AGTGAAGACGTTGTCCCTTCCCCCACCGACTTAGGGTAAGAGAAAGTTAT TGCCGACGCATATCGAGCATATCGTCGAGCGAAATCGCGCCGCATTGTAA TCAAGCCAGATGCTGTATCCCAGCCCAAATAGAAATTTAAACTGCAACCA ACTGATATGGGTTGTTATTCGATGTTCTATTGGCCGCAACCCCAGCAGTG GAGGCAAAGAGAGTCGTGTTTCCACGGTGAATTCATTTCATTTTTGGTTA ACCATGCTCCGGTCTTGTTTCGCATGTTATCTCGATAATTAATTCGATTG CTGCAGCCCCCAAATCCGAAAGTTACCTTCAACCGCCTTGGCCAACATGC GGTATGCGTGATGTGAAATTTAAGCTCACTTACTTGGCTGTTTACCCTCA AACACTCCAGCTGAACGGCTGGAGAGCTGTTGTTGACTCTATCTGGAGTC TGGCAGGTGGATTCAGCAAGCTGGAATCTGGCACAACTACCCAAAGGAGC TCGAATAGGTGTTTGAGCGTTGATTTAACGCCATTCGTTAGTGTTTGCCC AGCTCGCTTGATCTAACGCAGCCAACTCTTTGGAGGCCAATCCAATCGGC CACTTTCAGCTCGCTTAAATTCCGTGGAGCTAAATTTACCCGGCGTCCGA ACAAATTCACTTAAAATGCTGCTCGGCGCTGGGCGGGGCGGGGCAATGAA AATAAACGACTTCGCATCAGAATAAAACGCTAAAAAATTAAGAAAAATGC GATGACGACCAGGACAGGAGTAAGGTCAGGCCCCAAGTAAACGGAAGAGG ACCCAGGGAACCCAAGGGCAGAAGCAGCAGCTGGAGCAGGAACAGGAACT GGAGGAGGAAAGAATACGCAAATAAAGCTCCCAGCTGGCGGCAGGTGGTT GAGGCAATACAAATTGTTTTGAATTTAAATTGGACAACAGTTGCAGATAC TTTTCGAGCCCCTCCTAAGCTTTAATCTGTGGCCAGACACTTGATCGCAG CGCTTTCGCATCGAAATATGTAACGACAGCTCCAAGGTTGCGGCAAGGAT GCCAGCGTCGGCGTTTTGTGTTTGTGCAACGTGGCGTGAATGAGCAACGG CAAAGGTGCCCTGCCCCAGATACCTCCCCCCACCCAAAACCTTCGCCAAG CCATCAGTGTCAACGTGTCTCGGCTACATCTGCACCTGCAGTTGAAGTGC AAATGTGCAGTGTAATTAAAAGAGTGTGCACGTGCAGACCCTGGCAGAGC AATTCACATAGAAAAAGGCAAGCGAAAGGTCCTTCAAGAGCCGACCTAGT GGTAATTTCGGGAAATTCGAGTCCTCCGTCCAGATGGCTTACTGATTGCT GCCCGCTGGCCTATATGCCTGCCAATCCATAACCATAATCCAGCTGGAGG ACCAATATAATAGAGCCACATCCCTGCAGCCCGTCCCATTTCAATTAACG TTTGACCGGTCTTAATTCGAAACCAATGCAGTCCTTTTATCCTTCACGGG AAAAAACCAGATAAATAAATCAATTCGTCTCGTGAAATAACGATGAATCC GAGAGGTGTCAACTTTTCCTTTTAGGTAATTTATGGAAATCGATAATCTT TTATCTTTTGGGCAAAGCGAAATCTATGGGAACTACATCATAAAATGATA AGTAGCACGAATATTGACCCACATCGATAAGTTTCGTGCTTATGGAAAAA TTATCGTTTTATTTTCCCAGGTGTAGCCTTAAGACCATGTAAATTAGTTT TCAGGTGAAATGCAAACCGAAGTCGGAATCACAAGCAGGGCGAAGCTGGT TTGGTCATCAGATGGGACGATGCGATGGACGAGCACTTGACTTGAATATG TGATAATTGGGTTTTTTGCCCATGCAACCGACGGACATCCCAGACGCCCC TAGATTCTGCCCTTCGTTTCACATTTTGCCTTTGCTAATTGCTATTTCTG GAAAATTGCAGCAGCAGATAAAAAGTGCTGGGCAAAAGGGAAATATATGT GCTGAAATTGTTTGATATCCCCACTCATGTTAAATTAAAATATTTAGCTA GTCAGCAGGAGTCAGCTGGTATGCAATGTTAAATATTAAATGCTGACCAA AAATCCGATGAAAATTCCATTATTTAGCTGTCGGCCGGCCATCGATCCCT TTTTGCAATGAATAAAATTTTCATCCACTTAAACGCATTGCACATTCAGA ACTTCAAGCCCGAAATATTTCCTCTGCCACTTCACGGCGAAACTCCCCGA CGAGGCTTTAATCTAGGCACAGAAATGGGAAAAGAAAGTGCGAACATGGA ATAAATCTTGGCCAGCATTGTCCTGGCAGCGCAGCCGGAACCAATCCTGA TCCTGAGAGGGAGCCAAAACCACAGCCAAACATCGAAGCACTTAGCAACT GCCTAATTTATGGCCCTGTCTGACAATGTGCACGGCAATGTGAATGTGAA TGCGAATACGAATCTGAATGGGAATCCCAATCCCAATCCGAATGCGAATG CGAATGTTTGAGCGCCGGGAGGCCAGACGGTCCACACAGACATGAGGCAA ATATCAGGCGATTAGCCACAGACGATTGCATTGAAACAAAGCTGGAAATG GGGATTGGGTTGGGCAGGCAACTCCTCATCGCCGGCAAATCGATCCACAT TTAAATATCTTTGTGGGCTTGCGTCGGCCAGCATCTGTAGCCGAAATCGA TGTTTGAATAATTGTAATTGAATTAGATGGGATTGTTTTGACTCTGGCTG GCACGCGTCCTTACACCATTGGCGCACACATCTCAGCTCGACATTTATTG GTAGAGCAAGTGCTGCACGGTAGTCACGTAGTTGGCAACTGGAGGCGGGA GGGAAGCAGCTCCGGAGTTCAAAGTTTTGTTTTGGGACACATGACATGCA AAGGCGAAATCACAAAATACTGAAACGTGCTTTTTGACATTTTTGCAATG TATTTAGGCACGTGCAATATCCATCTCGGGGAGTGTGTGTGTGCGATTCC TTTGCCAAATTGAATTTAGCTGCCAAAAGTGATATCGATTTAAAGGCGAA AGCCGAGCGGAATCGGCAGCAACAGCATTAGGGTCAATTACCGCTGCAAA GTGAATTGTCAACAAAATCGAAACCCAAAAGAGGCGGCAAACTGAATTCA ACACATTGTCCAACTGCCAACTATCACACACACACACGCTCTCAGTCGAT CCAGGATGTTCCAGGATGGGGCGCACTTTCATTATCTGTGCAAATATTTG CCAAAAATGGCAGTTGGCAGTTGTCTCCTGTCCTGCGAGAGTTGCTGGCC CGACACTTTTGGGCATCCTAGTGCAAGTTTTAAGCCGCTTAGTCCCAGCT CTTTCCCATTACCCCCACCCCGCTACCCACTCGACAAAGTGAAAGTTATT CTACACACAGACACTCGTTCAAACTAACCCTGCGGTGCACATTTCATAAA TGTGGCTGAAGAAAAACTATTTTCATGTTCCTGGGTTGCGTGGGCCTTTG CGAAACTTTCGTCCTCCTATGTCGGCTGTCCCTCAACACAACTTTTTGTC TGCGCCGGAAACTATGGCCCATCCTCCCAGCAAGCATGCCGTAAATATTT GCCTGTGCGGCACAGATGCAAACACGTCGCCAGTTTGACTTTAAGACTCA CCTGAAGGGACGACCAGCCACGAAGTTAACACATCAACTGTCCCGCAGCA GCAAAGGGATCAGCAGCTGCACTGACACAAAAATTTGGCGACAACGGACC TGAAGTTATGTGAATATTATGGTAATCTGAGAATAGAGCATTATAGAACC TATACCGTCATTTGCCTCGTGCAAATCATCCATGGGCATGTATTGTACAT TTTGAATGAACCGTGGACTGTAGTTAACTTAGTAACGAAATGCGCCGCAA AGTCGCCAAAGTCTACTATAATTGTTGAGGAACGATACTTTACTTTGCTT TACCAATAACCAAACACGTAGCTTCAATATTTTTCCCACTGCACTCGTGC AGCAATAGTAGTCAAGGGTGAAGAAAGTTGGCCAACTTTCTGTGGGCATA TATTTGGATGTGTTATTGGAAAATTTTCAATTTGCTATTGAGAACGTACG GCGGCGGTATGATGGGATGTGGTTGGTTGATCAAGGGCAGAGTGCGTAAC AAATTTTATACTCCAGAAAGCTAATTAACTTCTCTTTACGAGGCATAAAC TTCCGCCATTATACGCATTTATTTTCATGCGAAAATAAACAAATACCCAA ACACGAGCCGCCGACACGAGAAAGTAATGTTTTGACGGCTCCTTTTGTGC GCGCGTATACTTCTTTATGCATTAACAGGACGAGGAGCACGCAAGCAAAC ACAAACAAAGCCACGGGCCGCGTGAATTTACGACAGAGCCGCCGTCAAGG GGGTTCGGTGGGGGTCCTTTTGAGGTCCTGGAGAGGCGATACCTCTGCTG GTACTTAGCAACTTTAGCAAGGAGTATTTATTTAGCACGTGTTCCCACGT CCTTCTGCTCCTGGCACATTTGCTGCTTGCTTTTAATTAACAAATGCCTT CCATCGGTTTCGACAATCGTAGAGCGTTAATGTTAATAGAAGGCCGTAAA CTTACCTGGATGCGGAAGTAGACATAAATTAGGCTTGGCCTTTACTGCCG CCGGGCATCATAATCTACTGGCCCATCAAAAGTCATGATTATAACTTGAT TTGATAGCGGCTTTGGTCCAATCTGTCTGGATTACTGAAGAATGCACAAT CAATGTAATTTTTGCATAAATGTACTACCCAAGTTACTACCAAGGATAAT CACAGTACTGACAACTAATGCTGCAGTAAGTGCATATAGTGTAATGAATT GTCCTTGGAAATTCATAAAGTTAGGTGATGTCCAGCTGGTTTTTTGAAGG TTACTTTTAAATTGGTAGGAAAGCCAAATGTTAAACAAGTTACCAAGCAA TTTCAAGAATGGATACATCACTTGACAAATGACTTCTTAAATGGCCATTT TAATTCATCCATTTGACGGCCAGATCACATTTCTAATCACATCGTGCAAA AGCCACGTAGAATAGAACATTTATTTAGGGAAGAACCCTTCACCTTTGCA TATAATTTTTTTATGAACAGTTGGAGAAGGGTTGGAGGAAACTGTGCATT GGGTCTTTAAACAAGTAAAGCGCTAAAAATAAAACAACCTACACATTTAG CTATCATTGCTTTACAAATTCCATTACCCTAATCCGAAACCGACTGTTAA CTTTTTTCAAGACCTCATTACCAAATGGAATACTTTAAGCCAGTACTGAA AGTTTGTTACGATTAATTACTAACTGAAATACTCGTACATCTCGACGCCG GCTGAAATTTATTGACAGTCTGAAAAACGAAATCTTAGTTCAAAGTTAAC AAATGCATCTATGACTCAGTTAATAATTTGATCGAACTTACTTAATATAA TTGATAGTATTTAATGTTGAACTCCGAATATCAAGTCCACGTCTGGTTGC TCTAGAGCAGCTAGATGGCCTTTACTGTTGGCTAACCAAGATGGCCCACA GCTACCGACTGCAACCGATAATCGCTGAAACTTGCAGTGAGTCAAATTGC ATAACAAACATAATTTTAATTAAATCAACAACTTGGTCGGCAACACACTA TATCATAATTGCCACGCGCCACCCACAAAAGCGCACTTGGCCAAGTTTAA TTAAAATGTCAGAATCGTTGTACACGTAAATTGTAATTGCATTTTTTTGG TTTGCTCGCTGAGGTAATAATTACACACAACACATCGGCAGTATGCTCAA AAGCTGTTTAGGCAAAATTAAACGAATTTGCATATTCAATTGAACCGAAC ACATAGGCTCGGCAATGAATAACGCATGGATGAGCTTATTTCTGCAATTA AAAGTTGTCAATTAGTTTAAAGTGCAGCTGGTAAAAATTCCATTGTCGAC TAACATCTACATATTTGAAAATGCTGCTAAAAGAACACACATTACGAAAA GAATTAGATACGAAACACCTCCATTATTAGCACCCAACTTCTTCTGGCAT TGTATTTTGTTTTATTCCGTATCAAATTGTAAATTATTTGTATATAGAGT ATTTATGTATGTATATGTATATAGTCTTCATTTTACAATGGTTGTGAATT ACAAAATCGGTAGGTGTTTAATGACGCTGCTCTCGCCCTCGGTTCTCTAA CAAAACTAATGAAAGTAAAATCAAATGAAAGAAAAGAAAAGTAAACAAAT TTTTATAAAAATAGTTTCGATGGTTTCTTACTTTCTTTCTGATTTTGTTG CATTTATTGTTACTCTTATTATTTCAAAATACAGCTTATCATTAGTTTGA ACAATAAAATTTTGATTACGAAAACGAATTAAGTCCGATGACCCCCATCA CTTTCTTACTAAATTCGCTATGTTTGACACGACAATTTGCAGGGAAATGT GACTGATTAAGGGGGCCTCAGCTAGGATGAACAGTATCGATTCTATCAGC TATTGTCATGAAAACTTCCGGGACGTACAAATATACAGACGTTACAGAAA GGAGCTCGTACAAATTTGGTAGGTAGGTGTTAACTCTTAAGTGATTGAGG TTTAGTCTATGATTTGCCTTTGTTAAATTTACAACAATTTCATACTTGCG TAACAACAAGCCGATCAAAGGGCCGAGTACCTGCCCTTCGCTCTGCTTGA TTTTGGGCGCAAAATGTAGGTAGTTCGTTAGGTTTTTTATATATTTTTGG CAGGATGTAGTTTTATGTTATGTTTTATACGTTAAGCGTCCAGGTCTGCT CGGTTATGCTCGCTTAAGTTCGATTAGATGATTTAGCTCGGCATTCTCTA ACCCTATCTGTGCCACACCCGCACTCAACTGATTTCGCTAATATTAAATT ATAAAAAATAAATAATCGAAACCATAATGGTAATAGACAATAAGTTCTTT TTCAATTCGTCCTCAGCGCGCTTTGTTGCAATAGAGAAATTAAGCGTAGC TACGAGCTTCTACAAGCAGTTCTCTGTCTCTCCTCCAATCCATTCCGCCC ATTTTTATCAGTTCAGTCCTCGTTTCATTGCTAGACCTAGTCCTCGTCCT TTGACGTTCCGGCTGATGTGGACGCGTGGTCGTTGGCACTTTCACTGGCT TTGCCGTCAGACGTGGCTGCTCCCGCTGAAGCCGGCGCAGCATCGCTTCC ATTCTTGTTGCGGGCGTCCTCCTTGGCCTCCAGAGCGCGGATGCGGTTCT CTTGCTTGACGATGATCGCCTTAAGTTTGCGGATCTCGTCTTGTATGGTG CGCAGGTCCTTTTCCTTTTGAAGTGAACCAATAAGTTAATCATACAACCG CTGAAGGAGTGCAAGTACTCACCGATAAAACCGCTGCAGGCGGTCCACCT TCGCTAGCCTCATTGTTATTTCCGGACGCAAAGTTGCCGCCGCCCGCGCT GCTGCTCGTTGCACCGGAGCTAGCGCTGTCGCCTCTAGGCTTGTTCAGGA TGTTGCCCGCCTTCTTCGCTGGTAGCGATTTGTTTACCGACGAGGACACG TAGCCACCCTGTACAATGGAAACGCGATCCTGATTAGGCGGGTAAGAAAA TCTGTTCGTTTCAGAACACAACAAACAACAATGAACACAACGACAAGCGC CACGCGCATTCGCGTGCGTGTTAGGGCCAAGTGTGCATTTATGCGGCGTG TTACTGTATCCAATAGGAGACTTTAATAAGTTAGCTAACATTTAGAATAC TAAACCATTTTAGATCATTGTGAATACTCTTTATTCCGGTCGTCACTAAA ACATTCTTAAGATGCCTCGTCTCAAGTGACATTGTACAACGGAGAACGAG GACTGTAGTCTGTGTATTGGAGTGGAATGTGGCTGGGCGGACAAGGCACA AACGTAGATAACGCAGAAAAAACGTAAGTAAAGCAAGCGCAGGCATCACA CGCTGGTAGGTAGCCACCGGCAAATGCTGGGAGTAAGCTTTAAACGGAAC TCACAAGTAGCTCACTTGGAGTCCTTGTGCTAGCAGACAAAAGCAACTGC AAAAGCCGTTGGAATACATTGTAGAAGGGGCGTCCACAGTGGCAGCGACT GCCTCATCGACTTCGAGCCGCATTGCCATCTGTGGACAAGCCCCGCTGGC GCACATGCTGATATATATCCTATATCTTGTACGCTCTTATCGCCGGCGGA ATGGTTGGCAGTGTGGCCGAACCGTTGCCGCATTCGGCGGCGAGCGCTGT ATTCGCAACACGGAATAAAAGTCTGAGCTGCTTCTGCACCTTAGCCACTT ACTTTGAGCGAAAATGTGATCGGATCCGCATCCTTGCCATCGATCCACTC CTCCGCGGTGATGGCAGCGTCTTCCGCTAGCGTATCGGGGTAGAGATCCT CCTGGAAAAGATCCGATTTGCGCGGCACAGTCATCGAGATGACCTGACAC AGACCGTTGTTGTTCATGCGATAGAACTTGGCGACCTCGCAGGTGGTCAC ATCACAGCCTCGCTTGGGCATCAGACCAATACCACGCTGCGGCTCTGTAG TCTGAAACGTGTTTATGTAGTGCACAAAAGGAGGTTCGGGCGTTACCTGT TCGATGAGATTTTGGTTAGATAATATTCATATGTAATATTGTAGATTTAC TTGTACTAACCTCGAAATACCGAATGACCGAGTCACCTTTTCCACACAAG TAGATCATGTTCGTGTCTGCGTCGTAAAGAGGGAACATTACGCCGTTGGA CGTGTCCAGCTCCACCATGACAATGGGTTCGTTAAGGGCATCCGGTGCGC GCAGGGAGTACTGACGCTCCGAGCTACGGTTGAAGCCTGTGGTGAAGATC AGACCGTGACGTAGGAAAATGGCCCTCGTGGCCTTGGAGCCCTCATGACA CATGGCTTCGCTCTCCAGCTCGGCAGTGCGCGGATCGTAGATGCGGATCT TTTTATCCTTGCAGGTGGTAACCAACTTAGAGCCATCCCAGTTGAAGCAG GCGCTGTAAACGATGTCCGGATGGGAGTCGATGTGCACGAGGATTTCACC AGTGCCCACGTTCCAAATCACGACCTTCGCAATACAGAGAGTATAAGCAT GGGCTTCTGAAGAAGTGTTAGCATTCGCTCACCTGGTTATCGGAGCCGGC GGTAAGCAGCACGTTGAGCGCAGAGGGATGCCACAACACCAGACCCACGC GACGCTGGTGGAAAACCAGGTCGACCACGGGTTCGGTGAGTGTTCGCGAC AGCCCGCCATCGGGGATCTGCCACACTTTGACCACACAGTCCTCTGAGCC GGAGGCGATCACGTTGTCGTTGTGGGGGCACCAGGCGATGTCCAGCACAG GACCCTTGTGACCGCCCACCAAAGGGTGGTCAGCCGCAATGCGACCAACC TGAAAGAGTCCATTAAATTTCAATTAGCTCGATACGCCACAGTAAATTTT TATAATTGATGGCGACTAAGTCATGAGCAGCAACCATTGCAAAACTGCAA CCTCGCGACCCATTAGCCCAATTCCTGAATTATTATTTATAGCCGACTCC GACTGCACTCGGTTCTGCTATGTTCGCTAATCTGCCAAGCAGGCAATTTA TAATTGTAAACTTCATGCCAATTGCTTCCGAATATGGCCCTAGAATTATA GAAAATTGGAATGCCGAATAGCTCCCATCGAAATCTATATATTTCGAAGC ATATTATAACAAATAGTAATGGTAAACTATTTCAAATTTAACATTGTTAT ATATTATTAGATAATATTCTTTGTTCATCGCTTTCAATAAATGTATTAAA ATGTATCATTCCAAAAAGTTTCTCGAATGAGTTCCATGAGTGTAAATCTA TTTTGGTTTTTTCAAGAACTTGTGCTTGTTCTTGCCTACACTTGCCACAT GCGGCCAACCTTGGCGACTAGATGGATCTCACTCATCATCCAGTGCCCAT AAAATAAGTAAAATAGGGCGTGTGAAAGCCGCTCCACATAGAAATCATCA CTTAAAAAAGCGGCAACTGCTTAGAGTGAAAAAAACGATCGCTTGCCGCG CGTTTTGCATACAAATTTTTGTTTCAAATGGAACGACCATCGGTGTACTT CCATATATGTTTTCATCAAAAGAGGAGCATCGGAAGATTAGGGGAATGGG TGCTTCTGCTGCCCACACTATTTGCTGGAGCTGCGCGCAAAACTACAACT AAACAGAAGCCCGAATAGCTGAATCTGGGGCAGGACGGCCAAAAGATTTT GAGATTGAAAATGCAATTTAGTGGAATACAAACAATTAGTTTTTAGCGGA ATAAGTCGCCGAGCTGAGTGTGCATTTCGATGCAATGATTCGCCCGAATA TCATTTTTGTATTCATTTAACTGGCTGCTCCTCTGCCTCTCTCTAAAATT AGACGATTTGTTTGTCATGTTGGCTAGTGGCCAAATTACAAAAGTGCGCC AGCTAGCAGTATCGCTGCCGCGGTAGTAGCAGAATCTATAACTATTTATA AACACATGTGAGATTGGGTGGAGTCATGCGAAATCCGTCGACGTCACTCG CGACGTGGCAACAAGCCCGCAAATGGCCGCAAACTTTATGCCAAAAGGGC GCTATAAATAGTTGCCCATTGTCTTGTTTAAAAATACCCCACCAAGCTGG CCGCGTCGGGGCAGACGCACGTAGACGAGTGCAACTATAATAGGTCCGGT GGCGCACTCACTTTGTTGTGTGGCAGGACGATGAAGGCTCCGCCGCCCGC CGACTCTACGATAATGGCCAGGAACTTGGGATTCACCGCGCAGAATGTGG AGTCCCAGCTGGACTTGGATACCCGTATGTTGTCGTAGCACTGCTCCCGC TTGAGAGCCTGTCCGTAGACGTGGCGGAACTTGGAGCTGCGCACTACGCG AAATGACATCTTGATGCTGCAGTGGCTTGGGTCAGCGATCAGTCCTGAGC TTCTCTACGTCTAGCTCTGAAAAGAAATGAGACGTACGAAGGATAGTTAG CAATGTAGGGGAATTTCTTACGCGTTTGGTATTTTCCACCCTTTGCCCTT AATAACAAGTCTTCAAGCGAAATCGTTTAGCCGTATTCTTTCCGCACCTG AATGAGATATGAAACCCCTACTTTTTGGCAGAGATTTGAACACTCATTTG ATAGGTTTTGTTTTCTACACAGTTCTGTGAAACCTGAAAATCGTGATCTT AGCCTTATCCGAGTTCTGAGCGACGCATAAACCGACCGAATAGCAATGTT ATTCGCTTTCAGCTTCGCTCACTTATGTGTTAGCTTAACGCGTTTTTCTT TCACCGCGCTTCGCAGCCTCGATTAGTTCAATAAATTTGCATATGCTAAT TTCGCTTGTTGCGAAAATCAATGAGCTTTCCATTCGCAGCTTGCTATTGA CGCGCTGACTTTGTCCGCGAGAGGTTGCATCAAATTGCTTATGGCATCAC TAATGTTGGCGACTGAAAGCGCCGGAAACGGCGGGAGGCGCCTAGAACGC TTTCACCTGCCACTTGGCAACTGCCACATTCGGGTCCACTTTCGTTAATG AAGCGCCAGCCGGAACGTGTCGAACTATCAGTTTTCCATACCCCTTTCTT TCAGGATGACATCATAACGCCAAAATAGCCACTCCAGCAATGAGTAGCCT TCCAACACGTAAGTTATGGCTGAGCAAACCGATCCCGCAGGCCAACCTAA GCCCAAACATATACCTAACACTCCGGGAGACTTCTAGATAGCTACGTGTT TGAAGCAGAATTCATTTCTGGGTTGGGCCGAGCCCGGCAGGCTTCCACTC CGAACAGCTTTCGTTTTTAATCAGAGAAGTGCCATAAAATTATTTGCCTC TTTTGCCTCGTTGCTTCGTTTTGTTTTGCTCAAAGATATTCATATTTATT GCAAGCACTAAACTTTGTCATTGACCCCTTTAAACTGGCCCCAAAGCAGA CCCCAGAATTGATTACTTTCTACGCTGTCTGTTTTTGGCCACAAGGTGAG CCCCGGAGGGCTTTGTTCTTGGGTGGGTGTGGGTATCGACATGGCCTCTC CACTGATAAGGAAATATCAGCTCGGAGTTGGCTAAACACCACAGAGATAA TGTTAAGTGCTACGCCTATGTAGTCCAAAACGACGCCGAAATGTTTGCCA CCAACTGGAAAATACTCCTAAGCACTGTACCCGGAATATATCTATCTATA TATATATATATATATCTGCGGCGTGTGTATGCGTTGTTATTTATGTGTTT ATATGCCAAACACCTTCGTTTGCAGGCGGGAAAATTTTTGTTTCGCGGCT GAAGGTCAAACTTATTAATAGAAAATTAAATCATCTTAGGCGAAATGAAA TTTTCATATACAAACACAGTGCACGATGCTCAAAGCAGCGTTGTAAATCG CATTTGATGTGTTTATTTATTTCGTTGGCATCGCTGGCACCTGCCATGCC TGAGTTATCATAGTCGAGCCACCCCCATCCACTCCCACTTCCCCGATCGA TCATAATTGCATTCGCAATTCCGCTCGCAATGGCCAAAAAAGTGGCCTCT TCTGCGCTTAATCAACTTGACCGTCGGTGGTTTTATCAGCGGACCACTCA GCGATTAACGGAAGTGTGGGTTCAAGAAAATCGCTGAAGAAATGAAAATC TTTGAAGAACTCATTCCCGACGCCCATTACCCGGGTGGTGTGATTGAATA CCCAGCATCACATTGCATTCCATTCTTTACAGTGGGCCCCAAATGTAAGG CTGTTTCTGAAGATATTCGAAAGGAAATTAAGTCAAAGGTTCAAATTAGT ACCGGATCTTCAAAACTCACATTAGATGGAAGTCCACAATCTACCTAGTT ATTGTGTTTAAGTCTAGTATTATATTTATTCACAATAGATGTCAAAGGTG CGAGCGTCACTAGTTTCTCAAATTGTTCAACAGTGTTTTTCTTTTCTTCT AAAAACTCGCTTGAGTACATTCGGAAATTACCTATAACCTGCGATTCTGA TCAGGAATATATTCTTCATAGGGTCGGAATCGTTGCAACGTTTTCGACGA ATCAGAATAAACTTCTCTATAAATGAAAGGTATGTATACCTTAATAACAA TGAAATGGGGTTAAATAACATAATGATTTTGATAGTATAATTAGAATTAA TAGAATTCCGTTTGAAAAAGGTCTTGAAAAAGGTCCTGAGTCAGATTTTG GTTCTAGGAGGCGTCTCTGCCAGAATTAGAAACAGGCTGTTGCTGAATCA TTATTGAAAAGTAACCAACTAATCCGCACGCCACTTAACCAGCGGGTGTC AACCAACTTTCAGCAGCGACTGTCTTGTAATCGCGTTAACCATTTGACAA TGGGGCTGTTGTGGGGCCCTCCAGCAATTTGTGTTGAAATCGCGAGAGAT GCAACCGTCGCTGAATTGATGCGAATGCGATGGTCCAGCGATCGGGGACT GGCCGAGAATTGACTTAATGCTTGATTGCAAATCTTGCCGCTTTGTCGAC ACGTTGTGTTCACCGGCCACTTCCGTTATAATGACATCTCTATTCCCCAA GTACACTCGAAAAAGAATCTATTAAATGTGTAGGACCACATGCCATCATG GTTTCCGGATTAAAGTAGCTACAACTGATAGTTCAAACTTTTCCTAAAGC ATAGGGCACAAAACCATTCTTGTATAGACAAAACTGTTATTAATAAATAT GTATTAAACATACTCCGCTTAACTCATGTGTAGAGTTATTGGATATGGAG TTTTGTAAACTCAAGTGCTTCCCTTTAACGTGTCACCACAATTACATAGA GGCAGGTGGTTTAAAACAAAATTAATACTATATAATTATGGATTAAAACT TTGTCTTGATACGTGAAGATATCAGACCAGTTGTAGCTCAGTCAGGTGTT ATCAATACGGCATCATACATTGTATACATATATGTTTGCGTTGCGCGGCT TGGTTTTGATTAACTCGTGGTATCTTTTCTTCCTGTGCACAGCTGCAGCG ACACCTAATCAGCTGGCCAATGATCAATGCCACATGCATGAGTCACCCCT GATAAGGGGCCCGCTGTTTATCGGCTGTCGGCTGCACTGGAAACTTTCGC CGTTCGCCTCATCTCGACTGGATGGTGAGGTTGATGGCGATGATGATGAT GATGATGTCATTGATGCAGGCGCAACGTCATTGGTTGTGCAGCTCATATA CATGCACATACACACACAGGCGTGTGTGTGTTGAAGGTTCATCAAACTGA TTGCAGAGTGTGCGTGCCTGACGGCGATTAGCCAAAGTTTTTGACAAAAA GCGCGCAAGTGTCGCGGCAGACTCACTGGCTTGCAGCACAGTGGGTGTCG TCGCTGTACGAGTGAAAGTGGAACTCTGCTGCTAAAATTAACCCCATGCA TATGCAGTGCCCCACCCGACACCCATCACGTCCCCTCGCCATCACAAGTG GCGCTGGCTTTTGTTGCTGTCTTAATTGCCGCTCGTTCTTTTTCTCCCCA GCTCCCCCCACTGTGACCGCCATCCGTTTGTTTCTATTTTTCCATTTGCG CTTAGTCAGACCGGGCGGCAATTGTGAATGCCTGTGCACCCTAGAAATTC AAAGTACATGGATTTTTTTGAGACCGAATGGGCGAATAAAAGTACCTTTC CCTTTTAAGAATTACACATTCGATGCCTAACTATAGCCCTGAACGCGTAT TCCAGGTAAAACGATGTCTACCTGATTAATGTGAAACGTGAAGCACTGAG AAAAAATTATCCCGGGATTTTAGAAAATCACCTTTTATTCTCAAACGCTA TAAAGACGAGCAATTGAACAAAGAAGACTTTTCTTACGTCTAGAGATATC CATGTAATATTCATTTTAGAAAAGTTAAATCAATGGTTTTAGAAAAGCTT TCAAGAAAATTTTTTTTCTTTATATGTATGTTGCCATTACAAGAAAAAGA AAAATCCGTAACTAATGTACACTGATGCTTAAATGGGTGGAGATATTTTG AATCAATGACGGTTTCCTAAAATCAAGGTTAATTTTATTCTAGGTGTAGT CAAGTAAAAGTTAATTTATCCAGATATGGCTTAGAAATAATAGATAAATC ACCCTATGTAGGTTTTGTAGATTAAATTCTAAATTAAGGTTTTGGGCTTT CTTAAGCATTATTAGCGATCTATATTTTTCGGTTCCAAGTCTATGATGAT GATAATTTCTTAATTTAATATTAGTGGGTGGACTGTAAAACTCCAACTTC AGATGTTCCTTCTATCCAAAAGGGTATTCAAGCAGTGGCTTCCCAAAATT ACGTGCTTCCTAGTTCTTTTCGGAGGTATTGCCGCCAATTGGCGTGTCCA TTGCCAGTCTAACTGGCGTTCATACGTGCGCCTGTTTTGCGATCGTCGAA CAGCTGTTGTTCGCCGAGTAATCGCGACATTGGCTGACGCATAAACGCGA TCGGCGTTTGGACTCGAATGTGTATGTGTGTGTGCTTCATTCCAGTGCAT TTCTCATATTTTTGTCACTAATTGGTGTTGGCTAAGTTTCGCTTCTTAAC CCATTTGGGGAGCAACCGAAATAGCTGTGCGTGTGGGCGTATGCTGTGCG CTCTCTCGCTTGCTCGCGCGCACTTTGGAAGACACCTCTGGAGGTCGCTT GTTTTTCACACTTGCTCTCGCTCGCACGCACGAAATGAACCGTAATTGTG GACTCGGGCCCATTGGAAGCCACGTTTATGGCTAGCCAATATTCCGAAAT TTTAAATGCCAGCTCATTTTGGCGCCCTTTGAGAGCACACCCCCTTCGAC CATCAGTAACTTGTTGCTTCCACCAGCAACAATTGGCACAGTCTCTCCCC CTTTTCCTTTCTCCCGCACTCGGCCACTCTTCCCCGCTCTCTCGCTCACG CGCAGCGTAAACAAGTGAGAGCCGGAAAGGAAAAGCCAGACAAATTACAG CGAAACGCAAGGAAGAAAAAACAAATACCATAAAAAAACAATTAATACAA TCAAGTGCGAAACAACAATTTCGACTGCGAGTTGTTTGATTTCATTCGCT CGTTTTTGCAACGTTTTTCGGCACTGGCGCTGCCAAAGACGCTGCTGCTT GGCTCTCTTTATTCCCTTTTTTGGGTGTTGGACTCATATAACACGGTGAG CGAGCGGGAGAGCTGATGGCGAAACTTTTATAGCGGTACTCTTCACATGC ACTGCGTTCGCCGCTCCGCTCGCACAAGAAAGCACGCACACCAGCGCACG CACGCCACACTCGGCGCACACATGCTCACACGCACACACACGTATGGTCG CAAGGCGGCTGTCGCACTTATTTTTTTACCGTGATTTTTAATGATTTTGT AATACGCGCGTTCATTACTTAAGCGCCGCATTTGCATCGAGCACTCGCAA CGTCACCTGGAAAATGCGCAGCTTCAGCTGACACCGAGCTTAAATACTCA TATTCCGCAAAAATACCGCTGTGATTCATTGCAACCGCTTTGCTTTTGCT TGACATTTAATGTGGCGGCACAGAAGCGGCCGCAAGAAACCAAAATACCA CCACTCACTTTATCTATCACTCCACTCACTGGGGCCAGCGCATTCAGCGG GATTCAACTAGAGATTTTGCACACGACTCCGGCTGGAAACTTAAGGCACT TCTTTTCAGACTTTTCAGTCAGCAGAAAGACGGGACGAGTACAAAATGCC GACGAGAGCGCGCTGAGCATCTAAGAGCAAGTTCGACACTGTTGTTCGAG GCAAGTTGTTGATATCAGCGCAGTTCGCGTTCACGTTCACCGGGCGCTGC GTTCATCCGCGTGGCGTTGCCACCTGGGCCGAAACTGCCATGGAATTAGC TAGATCCAGCTATTGTTTGTGTTGGGCTGAAGGCTCCCAATTGGACAATT TTTATTGACCACTTAAATAAATATAATTGCTTATTCAATATCTATTATCA TTTAATTTCTTATCTAAATCCAAGTCCAAGACAGTAAAATATTTTTTAAT TATGTACCAGCAGAGCTGTCGGAACTAAGAAAATCGCGAAAACATAGCAA CATTGTCTGTCGGTGGCCGCATGCATCCCTGACGGGGAATATGGTAGCCC TAAACAGCTGACTGCGCGGGTCTCATTTGAATTTCGGGACCGACTTCTTC CGGACCTGAAATATTTTTAATTTAGCTGGAGTTTTGTCAAGTGCGGAAGG TGTATACCTTTCTCGGGCTTTATCAGGCATCGTAGCACCTCTACAAAAGG ATATTCTAGCAGCACCGCCACCAGCGCTGCCACGAATTGAGTGAGTATGA ACACGCTAAATACGTTGCACAGCTAAAATGGTGATAAAGTCAATTGGACC AAAAGTTTACATATACATTTGTACATATGTAAAACCCAAAGATAGTAATA CTACCAGAAAGAAGCTGGAGACGTAGACCGGTTGTCTAAAATTGCCCGCC ACTGTTCTTAGGACGACAATGTGCCAGAGAAACGACTGAAATGAGATTCT TGCCAAAGGGCGAAACGCCGGCAATGTGCAGAAATCGTAGGCAATGCCTA TCGTAGATTCGTGAGTGACTTAGTGACTATCATTTAAACCTGTTACCCAC CTCCAACCTTGCGGCACATGAGGATCACGAATCCTGCGCATATTAGCACC CACAGGATCTTGTGGATGCCCGCATACAAGGCTAGCCATAGCGATGGCTT CGCAAAGTCCTGTCGAATAAAGATGTAGCCGGAGAAAAGGACTCCCAACG TGGCCAGCACAAGCAGCCACATGGCCAGATCGTACTTAAGATGACCCAGA AGTTCTACATTTCCAGAACGCTGCCTAAGGTAAAAATGACCGCACAGAAA ACCAAACAGATAGCCACCCAAATTTGTGTAAAAGGGCGGATACATTTGGT AAAATGTGTCGGAATGTCGGAAGTACAAGTAGCGATATGTTCTAGGGATA TTCACTTATCATAGACTGAAAAATAGATCGATATTTATAAAAACCTACTC CGGACGAATATGGTAGATACCATCCAGCTCGAGAACGTAGGTCAGTACAG CAGGCACTGCAAAGGCAAGTGCTAAAAGAGTTGTGTAGATTGTCCTTGTC AGCTTGGGATGCCTAAAATCACAGAGGTATTTTTGTAATACTACAAAAAG GGCAAGGGACTCACTTTTTGGTTATAATAATTACTATAAGGAAGAGCTCG AATAGCTGCATGTCTGCTCCTAAGTACCACGTCTGATGGGAGCACTATAA TGCAATTAGGATGGGTAAGGTGGCTTAAACTCAAGTTATCCTTTCTGAAA TACCGAAGAATTGTTTTAATAACGTACACTGTCTTCCAGCATGTGGTTGG TCACGAAAAACACGTTCTTCCACCAGTTGGCGCGACAGAAGACCCGTTCG GCCTCCGTAAGATGTCGCCAAAAGGGTCCGTTTTGAAGGCGCACCAGCAG TGTTCCATTGAACAGGATGAGAGCGAGAAGCGATGGCAGAAGTCTAAAGT ATCTGTAGGAAAACACTCGAAAGTACACAGCAATGCACTCAAGCGTGCCA GTCTTGGGTTGAATCTGTTGGCGTTTGGTGAATTTCACGTAGAGAAGGAA GCCGCTCATAACAAAAAATATCTGGATGACCAGGCTGCCGTTTTGAAATA TTGAAGTCTCGAACCGGAACAGGAACTGTTCGAAGAACTCCGGATTTTCT ATTGGAACAGTCATAAAGACCATAAGCGTGTGGCCCAAGATCACTACAAA TACGCCGATCACCCGAAACCCGTCGAAAAAGCTCACATCCCGCGAGAAAT CTGAGTTATACGGCTCAACCAATCGATGATAATTTCGAACCACTGAGAAG GATGTAAGGAGTCGCTGTCCTGGAGGCATACCGAAATCAACTTGAGAGTT GTCTAATTCTGTAGTTCATATCCACTTACGTCGATCCATTAGTGGCTCTC GATAAAAACTTTCTGATTTTTGCGAGTTCATCTTGCTCAGGCGATAGTCA AGGAAAGACGAACACAAAGTTATAAAGAGTATAACTACCAGAATACCATA AAACGCCAAATCAAGCAAATCTAAGGAAATAAACTTTACGCAGTGCTCCA CATACCAAAAGCAGAAAATAACAGTACAATAGCTGTACAGTGCAAAGTTT TTAGAAAGTGCAACTATAGCTTGTCAGCAATAAACTTAGCCCTACTTACC CATCTTCAAGTCCTTATCCGAGGCCGAGACACAGTACTCGATAAGGCTCC GAGTTCTAAGTGAAAACTTCTCACTGAACTTTTGGTTTAGACAGCCTTTC ACAACCTCTTTATTAAAGAGATCCCTATCTGAATTCATTGCATCCCGACG GTGTACCTTATCGTAGTAAGATATAAGTTCCTTATCCAGAATTTCTTCTT TCTCGTACTCCCTGAACTCGGATAAGTGATTGATTCTTTGCTTACAGCTC TCCAGACACACGCCCCTAAAAACGCGATCATGGCGAAAACGGTGTTTTGA GTCCTGTGAAACTTGGTCGATTTGGTGCCATAGAGCAGAGCTAGCATTGG GTAAAATCTCGACGTACACCAAACAGTAAGTACCAGCTTGATTATCCAGA CAGAGATCGTAGTCATCAAGTTGGTACAGGGCAGGCATGTGTCTGTAGAG AGTTACTGCGCTCCCAATTTCACCTGATATAGTTCGATATAGGATTAAGT TCACGGTACTTACAGTTGAACGATCCAGATAAAAAGTGTCCTTGTCCCAG AGACAATATGGCCGAAAGAACACCTATTTCCAACCAGCGGAGCATGTTGC GTGTGTTTGGTCTAACACTTGAAGATCAACTATTGCGAATCTTTGCTCGA TTTGTCTTACCAATTTAGCGATAGCGTGCTACACCGTCAAGCTTGGCTGC GTTTTCCAAAGATATTTCTATAAATTACTTCGACTTGACGAAATCACAGC TATTAAGTGGCTGCCGTTTATTTTATTTTATTGAACTTCAATTTTTTTTT TCATAGGAAGCTTCCTATTGCTTAACCCAAGTAGCGCCCAGTGAATATCG GCAGATCGTAATGGGTCTTCACGTAGAAAGCAAAAGGATGGTTGGCAATG AAGTGTTTGCGACTGAAGGCAGCTACGGCCATCACCCGCCATACTGAGGA GGAACCATGAAAACGAAGCAGACTTTTAGACATTTGCTTTTAGACTTTAT TGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATA TAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACA ATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGC TTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTA GTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGT TGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAAC GTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATA CCTGTGAATTGGGATTACATTGCATTTCAGTTCAATGGTTGTGATTGGTG GATTTTGATGGAGTGCTAACTTCAAAACTTATTGATTCTTCCCGCAAACA AAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACA TGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACAT GACCATTCCTGCAAATGAACATCAAAGTCGTAGCTCAAGGGTTATATAAC TCGAATTAGTAAGTGGCCAAACTGGTAATGGAGCAGATGCAATTTATTTC TCGTAATGTATGCCACCCAGGTATGCCGATAAATGGATTATCCCAAAGCT TCAGACAAATGCTTAATTTCCATTGTAAATAAATAGCTGTCTTTATTGTT TTGCCAAAGAATCAGGTACCATCACAGCTCATCATGCTCGCTGGAGGCGA AGGTATTTTCCTCGAGCCGCACAACTGAGCCCCAAAACAATGGCAGATCC TTCTGATGCACAAGGACATAGGTGAAAGGATGGTCGGCAAAGAACTCAAT TGGTTCCTCAGGCGACATAATAGCGCGCTTCCTACGCACCGCCATGCCTG CAGGATGGGAAGAAGACAAGACAGACACGGATGAACAAATGGGACATGCA CAGGATGATGGATGCCAAAAAATACCAATGACTTTGACCACTTACCCGTG GCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTG TATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAA ATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAGCTGGAGGAGGTTT ATATTAACATGAAGTCCATATCATTGCTTATGTGTTTAAAGTAAAGCTCA CCTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTG GGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGA GAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGG TGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGT TCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTC CTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAA AGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCC TTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATAC ATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCC AATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTC TGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCG CAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCT GACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGC TCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGT CTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAA AGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCG TACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGC GGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGA GGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTGTAAGTATCCAAATC GACCGTGGATGAGGTGTGCTCGTTTTCATAAATTTATGTAATTGCAGTGT ACTGATGAGTCACCTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGC CGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTG CCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAA ATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGG CCTTTGAGCAACAACTGAATTCTCTCAGCGAGCGTACATTGTTTTTATAC TCGCATATGCATATGTATTCCCCCACAAAACAATGATTTCTCTTCAGTTC GTGCTCCCAAACGGGTTTTTCTCTCGCCTGCCTTCGGTGTTCTCATTGAT TTCACTCTTTACATCCATAATGCGTTTTCTTTCACTGGCTTTTTAAAGTC AAACTGCCGGATAACTCACCACATGGCACCAAACGATAATCCATACTCAG TAATTTTGCTTACAGTAAACCTAGTCTGCAAAGCGTACGTAATAGACTGG CCTGACTTCAGGTCCACACGATTTACTGCGACCTTATCAGCCAAAGCTCA GCTTGAGCTTGTTATTGTCTTCGACAATAATGGGATTTTTTCCGTTCCCT GATAACAGAGGAAAGCTGAAACTGAAATCATTCCCTACCTAAATTTGTTT ATTATATTTTGCCAAAAATTCTAGGGAGAAGTCAATAGAATGAGTCAATA GAATCGAATAACACCCTTTATATACCTTCAAAGGCAGATTTATGTTATAA TAATAAATAATAATAATAATAATAAATAATAGATAATTCCTACACGTTTA ATGTGTCAAATGTTTAATAAGTAACTTAAGTGGAAGTACAATTTATTTCT CAACTATTTCCCACGCCAAAGATATACATATTTATTTTTCCTTTAGGTAC ATGTGTTACATTTTTCAGACTGCTCAACCTTGGTTGTGATAAAATGACCG GCAAATAGAAGGCCATGGGTGTTGTCCTTTATAGCATAGAAGAAAGGTCT ATTAGCGTGGAATACCTTTGGAGGTCCTTGGCGCGCAGGCATGCTTCTAA ATGTGGCAACCGCAGCTGAACAAGAAGTTTAAATTAGTTAATGCGAATAT ATACATATTTGAGTGAAATTTTTAATATTGGACTTGCTTAGCACCTCGTA TGACATTCGTAAGAATATCCGGAGTACTAGATATAAGAGGCTTTCAAATT GCCAAAAGTTTTGGAACCTTTTTTTTTTGCAGGCTCACCCGTTGCGGCTG CAGCTTCAGTGCCCACTTCGTTAATCTCGATAAATGCTTTGTGGACGATC TGGGAGACAAAAAGGCTTTCCTCGGATTGTAGCATTCCCCCAAGCTCTGC CTGACCACTGAATATTCGGTTCATGCCCATCTGTGAGTAGCCAGGTTGCG TATAATCAAATTTCAATAACAAATCCATTTCAGCTAACCAGCATTAAAAC CTGGGATAGTTCTTGCTGGAACTCGGCTGTAAAGCTAGGAATCTTCACAT CCACTTTTTCCAGATTCATTGCTGATGACACTACCTCTAGGGAAATATCA CTAAGTTTCTTTTCGAGGCTCGTGAGATTCGACTTCTCATCAGGAAGTAA AATGATCATGGCCAAATTACAGGCACTATAATTCATTCTAAGGGCAGTGG CTTCGAACATGGGAAGTACGGCAAAAAAGAAGTTCTCGCACACATGCATC ATTCTCACTCTGGTAGGTCTATCCGATCCGAAGAAATCCTCTTCGCGGGT TTCTTTTTCATTGAAACTGATTGACCACTCACCCTTGAAGTGAATACCGT TTACTAGGCACAGCCGCGAGTCCTTGGTAAGAACTCTTGGACCGATTATG TCCTTGATCAGGTTGTTGGTCTGTGACTCCACCCATTTGTTGATTATGCT GGCAGCCTGCTCGCTGCCAAAGTCAATCTCCATTGGCTTGGAGCGAAACT TCTGCTCTAGTATGTGACCAAACTGCTCGTCAACTTGGAGACCCTTCATA ACATATAGGCCGTTTGCCATTTTAAGAACCTGGCACTGTTCATAGGACTT GAGGACGACACCAAAGCTTTCAGCTACTTGCTGAGCTTCTAGCCCACCGA AACGGAGCCCCTCGTCCATCTCCTTAGCTGTAGCCGATCCCTCGGATGTT CCCATCCGCAGCATGGCCGCAGAGATGTGGATGGATAATGGGGAGTAGAT GATGTTTAGGCCAGCACTTGCCCGGCACAAATGGTCGTGCAGACAAAGAG CGAATTGTTCCAAGCCCTGTGCGAACTCCTCATCTTTCATGATGAAGAAA GCAGACGATCTCAGGTTAAATATGTTAAATATGCGTCTACGATAGAAGAA TCAGTGAGTACTCATTTTTCGAAAGAGATTCAGATTGACTTATCAGCAGT TTGAGCAAATATTTTAATAAGAAGCTAGATGAGCTATCAACACCATTCCA ATTTCGGGTACGCCAGGAACTTCTCTCCGTCGAGAGCGCTTGCCACTTCA GACTCTCTTGGAATTTATCTAATCGAGTTGCAGTTCGTTCAGTTCTGACT TACTGCGATTCGCGGCGTTAGTCAATTCCGCGCAGTTTGACGGAAACCAC GCTCATTCTCCGGCTGCCTTCCGATTGTATCCGTGAGATTGTTTTTTCCG GTGTAAGTTATCAGCGCACCCATAGGGTCAGCGACGCCCTCACCTGTTTC GCCGATCCAAAATAGCTTATCAGTGCACGTAGAGAAATTTATTGTTTCAT GTCCACATTGATCGATGATTTGTAAATTAAAGAAATTCCGAAACTTACTT AGTAGGCTAAGTTACGGTAATCTAAATATGCAGTAATCCCCTCTATGCAG TAGAGGGTATTGTTAAATTTTAAATATCTGAAAACATCAACAACCTTATC AGGTGACGTGTGTTATTTTATCTTTGAATTACTATCGCGTCGTTTGCTAT AAGGCAATTTGTTATGACGAAAGCAAGTTCTAGTTGACTTCACTTTACTT TCTACATCGGTTCTATTAAAAATATAATAGGGAATTATTATTATTATTTT AAAATAAATAGTAGCACCTAGTAGCAGTTGTAAGCTAATACGTCATTCTG GGATTTCGGATTTATTTTTAATTAGCATAGGCAATTTTGAAAATGTTTTA TTTTATTAAAGATTGAATCCGAATTCGAAATTGTTCTGGATTGATCAAGT TGGCGCTTAACAGCTGGCGATAATGCCAAATGAGATAATGAGATTTGGCC CGAAAATGTCTTATTTTTGTATACTTATGTTACATTTAAGTATTTAAAAA TATAAATTAAAACATATATTTTTTTGCCCAGATCGAGATGAGCGAACCCC AAGAAGGCAGAAATCAGTTTGCGCGAAATCTGATAGATGTCATTACCAAA GATGCCCTGCAACAGAGCAAAGACCCCCACATAAATACGGTTTTCTCTCC AGCATCCGTCCAAAGTGCATTGACCTTGGCATTTATGGGGGCTTCCGGAT CTACAGCAGAGGAGCTAAGGAATGGGCTTCAGCTAGGACCAGGAGATCGC CATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTA CGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACG ATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTC CAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCA GCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACC TGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAAT GTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCAC ATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATA TGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAG GCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAAT TCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCA ACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTC GAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCA GGTACTTAATCAGGTAAGATACATTTAACCGATAATAGTGGCTTTGTTTT AATAACAATGTAATATCTGATATTTATTCTCAGCTGGGTATTACGGAAGT CTTCAGCGATAAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCC AAAAAATCTCGGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCA GGATCGGAGGCAGCAGCAGTCAGTTGTAAGTGAAATCAGCTGCTTGCAAC TCAAACTTGCTCGTACTAATCTCAACTCTGATTCCCACACTCAGTCATGA AGATAGTACCCATGATGCTCAACATGAACAAGAAGCTCTTCAAGGCGGAT CACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGG CCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGT CACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGA GACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCA ATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCC AGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGG CGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGG TCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAA AATACAAAGCAATAAATTACCTATAATAACTTATGATTTAAATTAAATTC ATAGAAAATAATAAAACAATATGGTGAAGACGTTTGCTATGGCATTAACT TTTAACTTACAAAGACTATCCGCTTTCGTTGAATTCGATTTGCTTTAGTC TGTAAAAGTAAAAAATATCAAGTTTAATATGCATGAACAGAATTTCCGAA CGCTGAAAACGAATTGATAATTAACATCCCCAAACTAGGCATTTTCCTGT GGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTT TCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGA GACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGG AGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCA GCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACC CATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGA ATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAG TCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTG GGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCA GCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAG GGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTT CCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGG GAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAG CTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGA AGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGC CGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAA TTTCGTGATGAACTCAAAGAGACCTTAGAGAAGGTAAGACTCCGTCAAGA AAAACACGGTTGTGCCACTTTGACGCTCGATTCTATTTAAGCTGGGCATC CGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAA GTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGA ACGAGGAGGGAGCGGAGGCCGCAGGTGCCACATGTAAGTACCGATTTGGT TATCAGCGTCGAATGTTGACTCCTATATACTCACTGTTCCCAATGATTCC CAGCTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCC GATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCA GGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTTAA ATTAAAATTCCAAGCGGAGTGATTACATTTTAAGTTAAGGATCAATGTGG ACAGCAGTCCACGTTGTGACGGAAGGGTAACGCAGCGAAGGTAGGTTGTC CAGTAGGTTGGTAATAGGGAGTAGAAGTGGTATTTTGCCAAAAATAAAAA GTGTAATGATTTCTGATTCTTCGTTCGGAAAAGTTTCAAATATGTTAATT TTAACTCATTTAAATACGCCATGTATTTTAAGTGTCCTGGTGAACCGAGC GATTTTATTATTATTATATATTAAAAAAAAACGACTAGTTTAGCGGAGAA AAAACACTAAAAAGTTAAACATCCACCACCAATGAACCTAGAAGCATTCG ATAAAAGTCGTTAAAAAGGCAATTTAAAACACTATTCTCGGTTCCTAAAC GTATTATGTCTAAATACCACAGATAAAAAACAAGTGAAAAGCCTTTCTCG AGTCCCTCGCGTACCTGCAAATTGGAAGTGGTATGTATGTGATATTCGAG CTACTCGACTACGGCGGTCTCTCCAGTTTTTAATAAACAAAATTGATATT TTTAAGCCGATACTAACGTAAAAAAAAAGTAAAAAGACATTCACATGCTA GCGATGGACTTAAAATCTCTTGGGAAACAGAAATTAATTTCCCCACAGTG TGCCGTTGTAGGGCCAGAAAGAAAATCAGTCTTCAGTTCGAGGCAGAACT TTTAATACGTGGACGGTTTTTGTAGCCATTGAAATCAGCGCTCCACGAAC TTAACTACAATCAAATCCTCTACAGATAATTAAGGTAACTGTACATACAC ACATATATGTATGTACTTGCTGATCTAGTATACATACTTAGAAATTAATT TTTTCACTTTCGATGTGATTTCCGGAGAGAGGAGTATTTCTATTTGTAAA CAAAATGACATAATTGCTTGTCAACATCTGCAAAATTAAGAGAGCCTTTT CGGAAGAGAATGATTGCCAAGTAAAGAGAACCAGAAACACAGTGCTCTCT CTTAACATAATTCCCAATTTTGATTATTTGAGTCACCACCAACTAATAAA ACGGATCTACAAATGAGCCACTAATAAATGAAGACTTATTAGTGGCTTTT AACTATGCAAACATTCTTATTATATAGACATATAATAACATATATCTATT TTAGTTTAGTGACCTTAATGAGTGTAAAAATTAAAAGGGTTGGAAATTTA TATCTTATATTATAATGTATATTCATTACTTTCCTGAACTTTCAAACATT ATTATAAATAATGTAATTTTCCAAAAGGATTATTTGTTTCTGTACCAACT GACAATTTATTTGTTTGCACACACTTTAAGCTTTTCCCTTTCTTTGATTC AAAAGCTTGTACTCTCTCTTGATTCTTCGTTAGTATCGTAAATAGTAAAC TGGTGTGAAGATTCATCTTATCCAAAAACCAGTTGTGTTATGGTGGTATT ACAGGAGAACGAAAAAACATATGGAGAGAACCAGTCTAAACACAGTTTGA TTTCAAAGTAAAAACTTCGAATTCCGTTCAGTTTTCCCAATCATGTCAGG TAGGGAAGATACTTGCACAAGCTGTCTGTTAACGAATTATTGACCTACTT TACTGCTCTTCCGGTATTTTCATGTCCTTGTCCTGCAGTCAAGGCCACGT GTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTT AACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTT TGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCAT CTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGC ACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGAC CGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGA AGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATT TTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAG CAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGG ACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAA ATCAAGGACCTCATTGCTCCGGAATCTCTGGACGCAGATACTTCGGCCAT CCTGGTCAATGCCATCTACTTCAAGGCCGACTGGCAGAGCAGCTTTCCTG ATTACGCCACTTACGCCAGCGACTTCGTCAACCACGGAGGTCGGAAGGTC AGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGAC CGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCG TTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAG GAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAG GCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCC CTCTACAGGCAGCCCTCGAGGAGGTGAGTCCTTAAGCCTAAGATATCTAA ATACTAGATTGGTGACCCGAATACTAGTGGCCAATAACCTAAATGCTCTG CAGCTTTAAAATTCGATGTGTGCGATATGTTGTGTTGAACTATTTTTGAA TGTTTGATATACCATAAATAGATTCGCCATGGCTGTCCGTTTGTCTGTTC TTATGAACCCCTTCAGAAGTAAAAGCTCGCGAAAAAGTTTTGATGGAGCA TACAGACTCAATTTCAAAACATAACCACGTCCGGTAGACTTTTTGATAAT ATGTGTATATATAATATTTCTGAATATGTTTATTTAGAATAGAAAATAAC TACTGATATACCAAAAACATTTTTGCTACTCCCATGAAGTACTTACATTC TTGAACAGCATTAATTTGGACTCTTTCAGTTGGGCATTAAGAAACTGTTC TCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACG CATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCA CTACGGCCAGTGGAGCAACCTGTAAGTCTGTCCGTAAACATAAATATACG AACATTTTTGACAGTCTTTATTCCTTTCATTTCAGTTATCAAGGTCTCGG TGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCAT CCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCA CGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGT CCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCACAAGTACCGACA GGTATATCAACCTGGCTACTTGATTAGTTTTGGGTTGCATAATACTTTTG GCCTTCCTGTTTGCTGCTTCTGTAATTAGAGCCATCCGAGCTGACGTTGA TAGTTTATTAAGAGGACTTGGCTCGGTTCAGCCTCCGATCCTGGCCGAGT GCCAGGCTCTTTGGCAGTCCTGTATCGGCCTCCTGTGTGTGTGCGCAGGG GTAATAAATCAAAGTTGGTATAGCTATCAATCCCTGACACAGCCGCTCAG ACAAAAAGAGTCAAGAACGATGGCGAACTGCGCTGCGAAGAACTGGCAAT TTGAATGCCAGTGGTAAAAGTGGCCGAAGTCCAAACACACAAGGACCTGT GGACTGTCGGACTCACGGACACGCACATGGCCAAAAGTCAACAACTGTGT TGGCAATTTGCTGCAATCATCCAGCAACACATCCCCTCCTTCCGGTCCTT CCGCAACCTGTCTCGTCCTTCCTGCCATCGCACTACCATTTCCCAGGAGC CGATGTTTATGAGTGCAGCTAAATTGTTGTTCTCCGTGTTTCGCTCGCTT TTCCTGCAGCTTTTTCTGCTCTGCCGCGAGGATTTTCGAAATCCTTGACC GCTGACGGCACTCACATAAGTGCTTCACACATAGCCCACCATAGGGCCAC CTCTTGTGGCGGATATTTGCATATTTCTAAACAGGTGTAAATTAAATTTG ACAAATTTAGCGCGTCCTTGTCATTTCCTGCCGCCCCGGGCAGCACTTTT AATAACGTTTTGTGACATTTACATACCTTTCGAGGCCTGGTCATGATGCC GGTCCATTATTCACGTTTATTGTGGGCGAAATGATGCAGTTGGCTGGGAT GTGAGACAATTAGAGCGGGACCTACGGGCGTGTAAAACATTTTAATTAAA TCCGTGCTGACGTGCCGCTTGGTTTTCCACTTGATTTCTGGGAATTCTGT TACACTTTCGAAGGTTTTGTTGTGCGTTTCGTTTTTCTCGGGCACTAATT GGTGGCCAGGGCGGTGCCGAAACTTCGACTCGGTTGTCACGGGCGACGCT CAAGTTTCCGTCAGCAAATTGAAATTGAAATGACAACACAACAGGAGCTG TAGCACCAGGAGACAGACATCAACCGCATTGGGAGGAGCAAAGGATTGCA TCTGGCGCACCTGAAAATGGGAATTTAGCGACAAGTGCCGAGCATAAAGT TCAGTTGTGGGCGGTGTTTGGGCGGTGTTTAGGCGGTGGGTGGAGACGAG TGGGTGGCTGGGGGCCACGAATCGCTGGGCACTCGCTTGCCATAACCAGG AGTCCTCCGCCTTTGGTTAGGCCTTTTGCTAGTCCTGCGGCTGACAGCCC TGCATCATTTGCCAAATTGACAGGAAGCGTTAGATCTGCTCGCCACCTAC GAGAGTGGGCCAATTTAGTCACTATTATAGCCCCAATCAGCCAGTTCTTA GTAGTTTTTAGTTATTCCGCTGGCATGCAATCCATGAACTTGCATTGTTC AGTATAAGCTGCTTTTAAATCCTTCAGTTACAATACCGACCATTTAAGTA TACACACAAAAAGCAAATACTTGTTTATCTCCGAATACAAGGTACTCAAT TCAGTTAACGCTCCCTTTAAGCATTTAGGAATTGTGATTTACAGGGCCAC AAGTTAAATTGGTAGTATTCACAATGTTTATAAGCAAATATTAATTAAAT TAGCAACTTTGCAAAAATTTGTTTTCTCCGAGTCATATTAAGATAGTTAA AAAATACATACACATTTGAATGGGTGTAAACGGAGTTCTAGTTTAACATG CTAACCATTATGTTTCAGAGACCCTAACTTTTGCGAACTATTGTGACTCT CGAAAGTTGTGCTGCACTGTGTGTGTTTAAAGCTTCCCTTTGAGGATGTG TGTGCCAACTACACCGTGTGGGGGGAGGGGGGGGGGGCAACTCCGCAGGT GGCAGGGTCGAAACGATTACTCCTTCTGCAACGTGGAACAGACAATTGTG GAGGCAAATTGTAATTGTAACTCACTTTTAAGTGCGTCTGACAAGTTTGG TAATTAAGGAATTATGTCATGCGCACGTTTGCCATTCAGAAGGACCCTTG CCGTAACTGGCTGTGGGAGGTGGAGCGTTTTTGATTGCATTGGCTACATT GGTTACCTGGGGTTTCCTGTGTCGCATTCTGTGTCCCGAATGTTGCATTT TTGCAATTGGCATTTAATTTCGAAAGCTGCTAAGTTGAGCATTGTGTTTA TGCACGCTGCACTCCCATTGAAAGTTATCCCCATTGTTGGAACCCAGAGC AGGCTAGTCGAGACTCTAGGTGACCCTGCGCACCCAAGGTGTTCAAAACT TTTCACTTTCCCACGGACCACGTGAAAGGGGGACTGGCTACCGCAAAATG ATAATAGAATCCCAGTTCGCTCCAATGGAGACTGGGCACAATTTACCGCT CGTCCTGGCATCGCACGCTCGCCCACAAAGAGCAGGTCAGAAAGGACTGT GCGGAAGGACGATTTGATGCTCTGAAGAGCGTCACACTGACAGCAGCTGC CAATGTGCGTATCTGTGCGAGTCAGGTTAATGAAATACTTGGAACATGCC TCCTGCCAGCCGGTCAAGCGGCCTGTCTCGTCCTGCGTGGCCAAAGGACA TGTCGAGACGGATGTCCCTTTTTTTTCGAGCCTGCGAGTGTGTGGATCTC CGCTCAGGGCGATGGAAAGTGCAAAACTTTGTTAGCACTTTGAATTTAAT ACATGCTATTGAATATTAACGAGCTGTTTCGGCGTAGAATGAGGAGTAAG TAAACAAGGTTTGGCCGACAATTATCGAGTATACGCCCCGTGTGCCGCCT TGGCTGCCTGTTTGCCTTTTGGCAGCTTGTGGGCTCTGTGGGTAATTAAC ATTTGTACGTCAATATTTGCAGTGGCAGCCGCTGGCATCTAAATGAAAAT CTCCACGTGACATGAGATACTCTTTGCATCTCATTAGATTTAATTACCAT TTCAGGTATTTTGTATTATGTTTTGCGAGATATGTAAACATTTGTATAGA TTCTGATGGGTACTTCTTATGTTTCTGTATCGAAAATCTGAACCAATGTT TAGTGAACGAAATGTTTTAGTTGGGACATAGATGCCAATCCCCCAATAAC AAACTTAGGGTCGTCTGCCCAAAATTGAACTGTCACAGGAATTATTACCA ACTGACCGCAGCTGACAATGCCGTAGGGGTAAGCCTTTCATCCTTTCGAG CAGGTTCGAGGGGCAGACCCATAATCCGACTGAAGCTTAAAGCACGGGTT CAGACCTCAGCTAGTGCTGAGCAAGGAACTTAGCTTTGTCCTGCCGACGC CTGCGTCCTGATTCGCTGTAGCGTTTGCTTGTTCGCAACCACAACCTGCA ACACGTTGTGTTTTGAATGCTTTGGCGGCAAACACTCGTGGCCTGTTGGA TGAATATAAAAGCAAAGTCCCATGCTGGCTGCCAAACAGTTCCCTGCTAG ACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGG ATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCC TAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGGGT GAATAACCAGAACATAAATCAGAAATTTAATCAATCTCACGTGCCGAATT GCAGTTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCA GGTAAGCCCACCTCGCAGCACTGCGTCGCAATCCCTATGACCTATTAAGG CTTGGTGGAGCAGTCCGGCGCGGAGTGGAGTGCGGTCACCCGGAATGCTT CCATCCGGGTCGTCCAAGTAACTCCTCCACTTTATGGCCACATTAAGGCA TAAACAGGGGCAGAAAAACAAAGCACGTTCTGAGTGCAAGTGCAAAAGAA ACGACTTTAAAGTGCCTGCCAACGGGACAAGTTGCGGTTATGGCGAAAAA TTCAAATTTCTCGCATCCTGACCTGCCGAATTCCCACTCTTCATCCAGCC CTAGGTGCGTCTTTGATATCCAATTTTAACGGCAGCATTCGCTGGCATAA TAAAAATTTATCGTAAGCGCATTAAATTTGTAGCCGCCGCAAGTTTCGCT CCGTTCCCTTCGCTTTCCTATTCGACATGTAGAGACAAAGAGTCTTCGCA GCAGTTAACATGTCTAAGTAAGCTCTAAGTTGCCACCAGATCTGCCTTTT GTGTGTCCCGGACGGAGGAGGCTGGGCGGATGGGAGCCGTGCCATGTTGT GCATTTTTATTACGATTACACAGCTCACACATGGCAGAAAGCACTGAAGC GGGATGGGTGACAATCATCCCCTAGGAGCCCCTAGAAAATCCACCGTGAG GGTCCGTCATAAATTCTAAATTTGACAAATAAATAAAAGGTGGATGGGGG ACTCGATGGCCATGCTCAATCCATTTGTGCACTGGTTTTGTGGATCTATA ATCGGATTTAACATGTATTTTTATCCCGTACGAAAATTGCTCTATGGGGA CTCCATATTCCATACGATTTCGATACTTTCGTTATTGATAGACTAGGACT CCAATGTCGCTTTAAGCAACAAATGCAAGTTGTCTAAAATGTTGAAGCAT TTTTAATTTGCTTCGATAAATTAAACATTCTGAGCCAAGGAGTGCTTAAA ATCCGACACTTTTCTAAGTTTATTTTCTGTTTAGTTATATCGAAATTTGG GGCAAAAACAAACAGTTCCCATGAGACCAGGCATATCATTTGATTATTTA TTCCCTGTTAAAATATAATACCATGGTTCCCAGACTGATGATGAATTGAA TTTGATTTAAATGAGACTTTCTAGGTTTTTAGAAGAATTTAATTTAATTC TCTTCTTCTGTGCAGCCACGGCTTTATTGGGTTTCATTGGTTTTGATACT TTTTAAGTCGAGACCAATTGCACTAGATTTATCACTTCCTTCAGAGGTAT CACCATTTCCAAAGAAACGCTTCGTCTTCCATTTCCATGTCAGTACTTCT AAGAACCCACGTCGCAAAAAGCAGCACTTTAATTTGGGCTCATATTGCCT ACGCTTACAGCTTACTTTCATGAAATTCATTCGCTTAATTGTATTTTTCG ATTGTTTTTCCAAGTATTTCTTTCTTGAGATGAAAAGTCAACAGACAGTC GGCAAAAAATGGGTTTGTGTTTTTCGTTTTTTCCAACAACATGAGGGTCC TCGGTAATCGGAAACCGCAACTGTTTGCTTAACTCCCTCCGAGATTGTAT AATTAATTTCACATAAAGCCTAGTCGCGAGTTTGACTTTTTAAAGGCATT CTCAGGGGGAGCAGCTCCTAGGTGACGTGGCCCCACCCCTCACTCTCACC TGTCGCCTTCATCCCCCAATGTGTGTACACAGTCGCTTGTAAATGATTGT GCTCCATATGTTTATGCTAGATTAAACGGTTTTCCTGCCAAACTGCGAAT GGGAATAAAACACACACGCGCGCGCACACACACACACACACACGGCAGCT ATGCAGATGCCCCCGTAGGTATGCCAGCTTTTTTATTGTATCTTAAGCTG TGCCAGCTGCGCAGCTCCTCGGGGAGCGCCCGACTCGGACGCACACTTTA TCATAATGGAGTCTAGACCGGATGCCTGAAGTGCGATGGCATTTACCATA GTTTGCATTTCTACGCTCCCTGTGCTGCTGGCCTTCGCATCTGCTCATCT TTTGGTCCAATCGAGTTGGTATTAAAGTCATGCCTTCTGAGTGAGGTTCA TTAATCCCACCGCACTCACAGTCGCTTGTCAAGTCGCAAGGCAGCCCGAG AGGCCGCTTGTCTGTAAAGGCTATTAATTATATGTGACTTATTTAATTGA TAAACTGGGCATTTCGCCCTTCATACCTTCGGCATAGTACAGTGCTCTGG ATGTTGCAGCTGACACCTTCAAGAACGAGCCATTTGCTGTGGCTGAGTGT GTACTTCGCATCACTCATACGCACTGTGGTACGCAATGGCTTATCCCTGA GAATTCCGGCAGCTGGCATGAATTGCAATCCGTATGCAAAGCGCAAATTG AAAATGCACACGAAAGCTGAAGAGTAGGGGGGGGGTGATGAGAGGGGGAT GTGGCACCCAAAGTGGCAACTAAATGCTGGCAAAATGGCAAAACTGCACG CCTTTAAAATTGTTTTTGTTCCTCCCGCCTTGTTGTATTAAAATTAAAAG CACATAAAAGGTTCAAAGCTTCCACTTGGCCTGACAACGGTCCTCTTCTC TCGCAACAGAACATAACAGGACGGAAAAGAACAGGTCCTGGCCCTATGTG CGAGTTCGTGTTTCCGCCCTAATGCCTCCATTTCCACTTATTTTAATAGT TTTTGCTCTTTCCGGGCGGCACTTGTGAGCCTCTTGGCCGCCAATGGCTT CATTGAAATTTGGGCACACACACGGCCGGCATATTTGTGGGTGAGCAGGC TCTTGATGTTGCGGCCGCATTTGATTAAAGTGCTGGACCATGCTTGTTGT CTTCCACTCTTTGGCCATGATTATCATCTCGATGGGGATGTGTGTTTGGG TTTGTGCTGATTTTATGGTCCGACGGATTTCTCTTTTTTGGCTTCCACCA TCCACCGCCAGTGCCCCTTTTTTCCGGCTTTATTGAAATTGTATTGTACA AAATTGTATCAACGAGCGGGCGATGGAGCACGTTTGAAGCCACTTAATGA CCATTAAATGCTTGCCAACAGAACTACGAAGATTCCAGGAATGCGAGCTC AGCCAAAGCAAATACGAATCGCATTATATTAAAAGCAATTTTAACTTTTG AGACAAATGCCCATTTGGACGACTGCTACTAGAGGCGGGAGACGGGTGGA GCTCGCTGTGGCACGTTCCTCGACTGGATTTTATAATGGATGAACTGAAA GTATGCCAAATGCGCCTTAGCTCGGCGTACTTATACATTCATGCAGCACA ATTTGCAGTAATTGCACAGCGATTCAAGACACCGCTCGTGGAAAATGTTT CCCTTCAAACAGGAAATTAATCTAGGACAGCGCCGCCCACGTTCCCACGG ACCCACGGATCCGCCACGGAGGACCAAAGCGGCCAGTGGGGAGCTGTTAT GGCTCTTTGCGCTGCAACCTAATTAACGTGAACAATTCAGTCACATTAAC AATGCATACTCACGTTGAAATTGTTTATAATTTGATAACACGCCTGAGCG AGCAGGGCGGTGCCTGCCCGAAGTTTGCACTCGATCAAGTGGAAAATCAA AACTAAAGACAAGGCCAGAGCCACTGGAAGGGTGGGAAGTGCATTCCCAG AGGGGGAGGAGCGTTGGCCAACCGAAGGCAACTCACCGCAGACAGACTCC TTGCCAAAACTTTGTTCGGTTCAATTTCAAAGTGTCAAATGCAGTCAGGC CAAACGAAACACTGAATGAAGACGGAATATCCTGCAAGTCCATAGATCGC TGTCATCGCTTAGTAGAGATGAGGAAAAAGTGCCTCGGTTATTGTCAGAA GCCCGTGCTCATGAGCAGCCTGTCAGAGCAGTCGAAAGGGTACACAAGCC CGCTGGATCCATGGATTTATGCCAGAAAAAATGGAAAGCCATCAGCATAT GCCTCACTGAATCACTCGCAATATACATGGGCGTCCTCCAATCCACGCGC CGGAGCTATTGACAATCTCGGCTAAACTTCCGCTACCCCTTTTGTTGCCA CTTTGCCTGGCTATCCAGCACCGTTTCGCATTTTCCATTCCAAATACCAG CCCTCTGCGGCAGAGCAATCAATAAGTTCGTATATCCGTCAACCAACCCT CAGAACCGGCAGCATACGCCTCCACTGCTCCACTGCTCGAGTGGATTCTC TAAAAGTTTAGCTGCCGTTTTTTGCCATTTTTGTTTTCCAACGGCGGCCA GCACGATGATAATATCAAATTGAGTTCGTTTTTCAGCGCCCTGCCTTTAA ACATTTACGGCGCGAAAGTGGCTAAGTGGTATTCAAAAATCGATTCCAGG CCGCGGTCTGCCAATCTCCCACCTCAAACACGACAAATCTGACCAGCTTT TATGGGCTGATAAAGCAATTAATTTCAAATCGCCACGGGCAGGCGCAAGT AAGGGGAGATGGAAAAAGAAATCAGATCTGAACCTGATAGGCAATTTGGG GGTCGAAAGATAAAATTAGCCAGCAGAGAGGGCCACAATCAGGGGCCTCA TCAGGGCCGATAAAGATTACGTATATTATTATGTTAATCGAGATTATGAT GACAGTCATCAGCGCCTCATTAGAATGGGCAGGCAAAATCTGCTTTCTCC GTCGTTTTTGTCCTTTCGACTCTGGTTCCTTATAGACACCGAACTCCGCG ACCACCACCCAGACACACAAATCTCTTTATAATCGTCCCAGCCCTGTCGT CTTTGACAAGGGAAATGTTGGCCTAGGAGCGGGCGTGTCCAGGAAGTCGG GTCGTTTTAAGGGTGGTTGGGATGGTTGGGATGCTTGGGATGGGGTGTGG AGAAGAATGGATGGCCGGAGGGCTTTGTGCCTACACTTATAAATTTTTAT TTGTTGGCATTCCGCAATTTATTTTATATCTTTTCCAGCGGCCGTGGCAA CTCCTGCCAGTTGGCCATTCTGTCTGTTTGTCCGTAAGTCTGTCCGTCCG TCAATTTGCTGGCTTTCGCAACGCTCTGTCAATGCCTGGCGGCCTTTTTT GGAGGCGCCGCGGCTGCTCGTTCTCAGGTCGTTACCATTTGAGAAAGTTT GAAGCCGTAAGGCGGCATCGCAGGAATCTAGTCAAAGGAAGCCGTATACA CCGCCGTACGGTGAAGTATGACAAGAGGCCTAATCAAATTATGCCCACTT TCTTGGCCGCTGACGTTGGACTGCCGGATGATACAAAACAAAGTAGGTTA TGCTGAAAGCAGGAGATGTGCTCATTAGGCCAGATGCGAGTGGAGTGTGC TGATCTGATTGTCGGCTTTTCGGTCTGCCCATTAGTAGGATGTCGAAATG ACGGGACAACGGGACGTATGCGTAATATATGTGTCTGAAACATCACAGTT CGACAGTTCGTAGCTTATTGGCCAAAGTCTGGACGTCCCTGGACGTTCTG GGATTCCCGGCGTGCTGCTGAGCGTTTGGTCTTCGGGGGACCCAGTCCTC GGAATGCCAGGAATGCTGTTTGTGATTTTTCTTTCCGCTTTCCTTTTAAC ATTTTTCACCGTGTCGCAGCGGCGCTTTCCCCGTTTTCCACTGCTGCTTT TTTGTTTGCTCGTGTTTCCGCCATTTCCCCGCCATCTCCTGCTGTTTCCC GAAGTCACTCACGCGGAAAGCGCGTTGCGTGCTTTATGAATCTGTCCTGG CACAGCTTCTCTATTACGTTCTAGACAACTTGAACTTGTTCCCTGTCTCA TTCTACGTATCCGTCTTCGCCGTCGTCTTCGTCTTGTCCGGGAACTCCAG CTCGTTTCCGTTGGATTCTCAGCTGCGTCCTTTGTGGATGGGATCCTTCG TGGCATTGCCATGTCTCCAACGTCCCGCGGCATTCGTGTTTATTAAGTCT AATTCAATTTTGCGTGAATTTTATTTGTTGCATACATTAGGGCCGATGAC GTTGAAACATCCCCCACGAATACGGATCCTGAGAACTGAGGTGCTGCGCC GTCGTCACAGTTGTAATTACACACTTAGCAATTTAGAGAGTTCTTCTATG AAGTTTTTAATTAAAACTTTGATAAATTAGCTCAATTTATATCCACCCAG ATATTTACCATTTAACAAAAGCGCCCCATTCCCTTCTATCTGTCGTCTCA ATCCCTCCCCTTCATGTTGGTGTGCATTTCTTTGTGAGTGCAGATTTCCC ATTTTAATTGAAATTTACCAAGGAGGTCTTGGTCTTTGAAAGTGCGGAGA CGTGCATGGCTAGGCACATAGCGAGCAGGATGCGGAGTAAATTAAATTGA CAAAGTAAATAAGTACTGGGAAAAATGTAAATAAATATGCCTTTCATGGT CTCATGAAATTGGTTCAAGTCGGCACAACTGCTCTTTGCTCTCCAGCGCC ACACACACCACTTCCCCCCCCCCCCCCCCTCACTACAACCGCTTAGGGCA ATCCGATTTTGGCCAAGTTGTAAAAGCGAAGCTTTTCATATTCGCCAGCA ATTGCATTCTATCCTATTTGTATCGGGCATAAGTATATGGAAATTTATGG CTGTGACGGCAATCCCACATTTGTTTCAATTATTCACAGTTTGAGTGAAA CGGAAAGCAGCTACATGCATATAAATTCAGCTCAACTGTCAAGTGCGAAT TTGCTTGGCATTGGAGAACAATTGCGTGGAGGCTGGGGGAGGAGCTTGAG TGCTGTTCGGCAAGCTTATACATTTTTATCCCTCTTGGCAGAGACGCGTG CACTAAGTAAACCCGCTCGAGCTGCCTAAATTGTCGAGGACATGTGTGTG TGTGCTCGCAATTTCCCGTGCTGAAAACTGGGAAAGTGGCCCCAAGTGGG TCACAATCGGGCCAAGTCAAATCAATTGACGCCAAGACGCGTCTGCACAC ACACAGCCATTGTCCTCGTGTTTGCTGCCAACACGATTAACCCACAAACG GCTCAGGCAGACGTGCCCCTTTGGATCCTCCTTCTCGTGGAGATTGTGGC AAGTCCGACTGCCACTGACATTGCAAACGCAACTGCAGCTGCAGATGCAG CCTCAGCTTTTGCTGTTGCAGTTGCTGTTGCCGTTTCTGTTGCGAGAAAC GTGGCCACTCAAGGGGAGCCCACTTTGTGCTCGCTCCTTACCAATTCCAC TTTGCCATTACTTCGATTCCCCGGCCAACGGGGCGAATGGGTAACGAGCC GTGATGGGAAATGGCTAGGTACTTCCGCCCCAGTACTTTTTCACTCAGTT TTCAGTTACCGGCACTTTTGGGACCATTTTTCGATGCTTAATTGAAAATG GGTATTCAGATATTTTTATTTTCTAAATAAAACCTTAAATGGAACTGGAA GTATTAAGGTACACAAAATATCGGAAGCAAGTGAACAAGCTGTAAGTAAT AAAATTTGTAGGTTAATAACCCAATATGTTAATATTTAATCTTGAAAAGA AAACTCATAAGTCGACATCTATTTTCTGATAAAAGTCTGAGCCGAAATCG TTTTTTCCATAGATAAGTTTACTTAGCTAAGCGGAATATTCGCATCACTA CTGCCGACCAATACAAATGAAAATCACGACGGAGCCTGCACTCTTTTGGC CAAAAGGCAAGCACAAAGGCAAAGGAGGGTGAGTCTCACTGCTTCCCCGG CGTCTGTGGTTTGTTTGTGTATAATTTGTGGCACTGCCAGCTGTTGACAA TCGATGACAACCCTCCAGGAGTGGCTGCACCAACGCCAGCCTTCGGCACC TGCTGCCCCAGGAAGCCCCTGCCGGCTTCTCCTTTCGCGCGCCTGATTAA GTTTTTGCATTAATTTCGCTACACCCTCGATGGCGCTATCCTGGTGCTTG TCCTTGGTGCTTGTTTGCTTAGCCATTAGCCGGGGATTCTGTGACCTGCG GGTCGTTTGAGCGGATCGTTGGGGTTGCAGGCTGCCAGCGAGTGCCTGAC CTTTTTGCCAGCCATGCAGTAGCTCCCACCGCCTTCAGCTTTCAGCTTTC AGCTTTCGCCTTGCTGGCTTTTCATGCTTCGGTTGCAATCGAATTTATTG GATCCCCTTTTTAGCCAACTCGCAGTCGCAGTTCTCATCAGCCCAAAGTC GATTACTGAATTTGCGTGCGGAACCTTTTCTTGATTGCAAAATAGCAGAG AACTCGATTAGAGTGCGATAGAGTGTATCTTCGGATAGGGGCTATAGATA ACGAGTCTATCCAGTCGATAAAATGCCAGCGCTAAGCACCTTTGAAATAG CTCTGCTGCTCACAAAGTCAATTAGGGAAGTATCCGCATCAGCTCCAGCT ACTGATTCTGATCCTGTTTCTATTTCTGCTCCCATTGTCCAATTAGCCTA GTCACCAGCCACATGGCTTTGGCTCAGGCTCTCCCATTTGCATCAGACTC GTGTTGCTGCAGTTAATTTGTTGTTTCTGCAGCTAAGTTTTCGCTCCACA CAGTTGGCTCATTACGGACCCGAAGGGTCATAGTGAGCTCAGTTCAAGTG CAAACTGTTCGCCCGATGCCGGGCGGACAAAAGGACCTCAACCTCGTCCT CATCCTCGCCCTGGTCATTGCCATCTATATTTGGATACCTCCACAAAGTT TTTCACAACACTTAAGTCGAACGGATAAAAGGCGTCCTTCTCCTCAGCCT TTTGAGGGGATGTGAGGAGTACACAACCTCCACCTCGGGACTCTGGCAGC CCAACTGCCCCTTCCGGCTCCCAGCCATTTGCCGTGATTAGTATAAATAA GTAACAGTTAGTGACCCATTTTCTGCACACCATTGAGCCAGAAAGAAAAA AGGCTTTAATGGCTCGCCTCCACCATGAAATTGGTGAGGACAGATATGAG TTTGTTAGGGTGGACTTCTGGTTGCGTAATGTTTCATCCCTTTGCCACAA TACGAGTATGAATGTATTTTATATCAAGTATGTAAATATACATATTCTAC CCTAGGAGGAATAAAAACTAATCTTATTATCTGCATTCCCAAGCAACCGA GCTGCTATGTCAAAGAAAAAGTGAAAGTTTAAGTCAAACTAAGATTTCAA TTTAGTTATATTTTCCTGTGACATTCAAATGTCAAAGGTGAAAATAGTAC CAATATTCGAATAAACTTTCGCTGGGAAATGATAATTAATATATTTTTGT ATTTTTGTGTTTCATATGCGCATTTTTAGTATTTAAAAAGTCGCCCTGCA CTGAATCTCTTTTTATGAAAGTAGTCAGTTTTATCAAAAATCGAACATTA CAGTGGTCCACCTTAGTTTTACCTGCTCAATCCAACGATGATGGTGCGCG GCTCCCATCCGAAATTGAATTTATGGCACCGCTTCGTGCCTCTGAGATTA ATATAGGCCACACCGCCCGAGACGTGTGGAAAGGTGTTAGGCGTCCTACT GCGGGTCAGAGGTCAGATGGACGATCCGGAGCTGTCATCATCGCAGTAAT CAACAGTTTAACGGCATCGCCTGGTGGCCTAGATACTGCGACGCCACTTT GTAATCGTTAAGCTGGTCCTACAGCCAACTACAACTGCCACGGCTTGTAG AAGGGGTATGGACTGGTAGGCGAGGGATGGGGTGAAGTGATAATGTGGCT GGGACCCGGTCCTGACCAGAATCATACCCATAAAATCATTTGTTTATCGC TGCGGCCGCTTTCGGGCCCATTAGTAGTTCAAATTCAACGCCATAAATCC CCGAATCGGTGAAAACAGGGCTAATTCCTTAGCATGCATGGGTGCTTGGG TGTTTAGTGTTTGCTGTTTGCTGTTTGGCGTCAGATGGCAAATGACGCGA CGCTCGGCATGCAACATAAAAGCTTATTTTATGATTTAAGCACCACAAGG CCACAACTCACAGCTCACAGCACGAGCAGCCATATTGCGAATGTTAATCG CACATAAAGCGTAATGTTTAATGCTTAATGGTGTTCAAAAGCCCAGTCTC CTCAACCCCAAAAATGTTGCCAAATTTGTGTACATGTATTTTGTGTTGCG GAATTTACATTAACAAACGGCAAACTAATCAAGTTGAACGAAAAGCCACT GCAATTAGTTGTGGTCGAGAAGTGGCTAACCGGAGAATTAGAAGTCATTT AAGAAGTTTAGGTTCGGAGAAGTTTCAAGGGAATTCAAAGCGTTCGCTTT TTGTAATTACAAAGTTGTGCGTCGGGTTTAGTGTAATAAATACATTTTAA TTACTTAATTTGTTATATTTATAAGCACCAGTAAAAATCCCATCAGGCAG TTAACACAACTTTCGAAAACAATAAGTGTTGTGAAAGAATCGGTACAATG TATTTTATGGCTACTTTTGTTTAAGATGGTTCTTTTGAAGCTATAATAAT TTTTTAGTGAAATCTTATTATTGTAAGATACACATTTTTCTACAAGTTTT AAAATATGAGTGGGTTTACATAAATATACGTGTGCATATAGATTTAATTA ATTTTAAAGATTTAATTAATTTAAAAAAAAAAATCACGTTGTAATAACTT TTAATATACCCCGTGAATAAATGAGTTATTTCTATCATTAAAAACGTGTG CGAAAGCTTAAGCCTTTTGGGATTTAACATATGTTTGTATATTGTTCACA AATTGTTTTTCAACTTTTGAAATGCTAAAGTCTCTTTCTGTGACTAGTTT GTTGGCTTATCATAAATAAAGTTATCAAGGAACATAGAAAAAATGGATTT TAAACAAAGGACAACAAAAAATTAAAATTTATTCGGTGTTATTTTTATCA GAAGTACAAAAGAAAAAAAATCAAGGTTTATCAATAAGTTCTCTTGATCA ATGGGCTTAAACTACATACATACATATGTACATGGCAAGCATTTCTCTCA GTGTGACAGCTGATGGCTGGAGCTTAACGCACATGTCCATCATCTGCAAC AAAGGCGGTTAACACGGATGGCTGGTGCGTCCAAGCGGAAGTAGTTCACC ACCGAACCAGGCCAAAATCCCCAGAGCCGCACCAGAGTTTGCAACTTTTC GCGGCCTTTTCGTGATATGTCGGATCAACTTGTGATATCCCTGCGGTATT TGAGGCATTTTAATCAACTGGCAACGCAGCAGGACGCATTGGAATGCGGC TAATAAATATTTATAAATGTTGCCCCGCACAAATTGTTTGACGTGGTCCG CTTGTTTCCGCAAATATGAAAGTTTAGAATTCTATGTCTGACCAGAAACG AGTGACAGCACATCCCCAGCCCTGACCCTTTGGCCACTGTCCTCCGCTCC CTGCCCCCTGCCACACATGGTCCACATGGCCCCAGTCCCTCCGGACCAGT TGAGTCCTTAAGCCCCGGTGCTCGCTTGCTATCGTGTTATATGCCATGCC ATCCTTGCCATTGCCAACAAGTGCAGAGAGTGCCAGAGCCGCGGCAACAG GCAAATGTGCTTTTAATGACATTTTAAACGGCCTCGGGCGCAGGAATGCA TCCGATCTGTCTTATCCTCTAAGAAACTAATCAATAAGATGCTCGGCACA CATATGGCCCCCAATCCTGGCTCCCCCCGGCCCCGGACTCCATGTTACCT TCGCCGGAGGGGCAAGCTGAACAGATTCGCAATAATCGGGGGATGGGGCA GGAACACAAATTGATTTCCAGGAAAGCGAAAAAGGGAACGTCAGAACGGC CAATTCGAGTATTTTCATTCTTTTATTTTGTGCGTCTGTTGTGATGGCAG CCTTGCATTTCCTAACTGCTCGAGCAAACACGTTCCCAAAAGTTTTGAGG TCCTCTGCCCTTTGAGTTGTTGATGACATGTTTCCGTAGTCCGTAGTCCG TAGTCCGAGGTCCGTCGTCCGCAGTCGGGATGATAAAAACAAAAAATGTC AACAACAGGAACGCTTTTATTTGCGGAAAACAGAAAAATTAATTCAAGTT TGGCTCTTTCGGCTTGCTTTAAAATGTAAAGCGGAAACTTTTGGCCAGGA CTTGCCTTTCTTTTATGTTTTCCACAGCTGTTGGCAGTTGTCTTCGGCGT GGGCCTAGTAGATTTAATTAAATTTTTGTACAGAAAAACATTCTGAAGGC TGCTGCGTGTGCGAAAGTTTGCGAGCGTTGCCCGGGATTCGGGAATATGT TGAAAATAGAGTTCTCATGGGGGAAAATCGGCGACAGCACTGGGTTTTAA TATTGATATTTAAATTTTCTAATTTACTCTACCCGTGGGAAATTCCCACC CCTCCCTCTCAGTTATATCATTATCCGCTTGCTTTCGGCTTATCTGAGGC ACATCCACACGCTACTTCACATGGCATAATGCAGTGCAAACAGTATGTCC CACAGGGCGTATGAAATTCTCCCGTTGTGTGCAGCCTCTTTGCGTAAAAT AGATGCAAATTAATATGCATTTCTATGCTGCTGCTACTGCTGGGCTGGGC TGGAAACAACAAACAAAATCTTCCGTGCTGGTGATTTTTCATTAAAAATT ACCCCGAGCACAATGTAAATAGTTGTGAATTTACAAGGATGCCTGCCTTC GCAAGTGCAGTGCAGCTCAAGTTCAGGTGGTTTTTGCATTTCGAAATTCG GAATTCGGCCAGACGAGCCGAGAAATTAAAAACACTTTGCTTCGCTTTAG GCCAGGTCCACATCCTCACATGGCCACATGCATTTCATATTCCCTAAGTT TGCTTGCAAGGTTAACGTAAACATGGGCGGAATAACAAACCCCACTTGAG TGCTGAACGAATGATTATGAAAGTGCCTCGGCGCTTTGACTTTCAGATCT AAAAGTCATAAATCCGTGCGGATATTTGCCATCTGCTGCAAACGAACCGG GCCATTACTGCACTCCACCAGGTGATTGGGTCGTAAACCACCTGTGTCTG GGAGGCAAGTGCACTTCACCTTTCTGCAGGTGAGGCGACCAGTTTGCTAG TTTTCACTCTGATTCATTAGCCCCGGAATAATTAACAGCCGATGCAGCCT GCACACTTAAATTGATCCTTATTATCTGCACGCGGGACGGAACTCAGTCA GTTCAGTGGGCGTCTAACCAAATTTGCCCACTCATGGGCGGCAGCAACCT GTTCAGTTGATGGCAATAAATTGCATTTGCTGGAAAACCTAATTACATTA AGTTGCAATTACGGGAACAGAGAGCGCCGTAGGATTGCCCAGGTGCACAT GGCACAGGTGCAAATGGTCCTCCGTTGGCGCGCTTTAAGAAAAACTGCAA AATTGCTGCAAATTGAATTGGCTGCACTTAGCCTGCACATTACATCACAT CACATGTAAACTGCAAGGCCAAGCGGCTGAAAGTCCGAAAGGAAGTGCAT TTACCACTCCAGCGCTCCACTCGCTGTGTTTGTTTGATGAGGCCAACATA TGTACGTTTTTGGTTCTTGTTTGGATTGCATCCGGGGAATTCGGCCCCAG AGCGGCCTCCTCAATTGGAGTGTCTTAGTTGTATCAATGTTTGTATCCGG ATGCCATACGTTCATCTGATTTGCAGAGCGAGCACGTGAGCAGATTATGA TTACATGCAGCGAGCTGCATGCCACTGCAGTTTGAGATACTTTGAGCCCG GGCAGCGCATCCTTTGGCAAAGCCAATCAGGGGCAGCAAACAGAAATGGA TGGCATCCAGAGTTTTGGAACTACATTTTCAGATTCAAATGGCTTCGGGT GGGTTACCGTTCGGTAAAATTGTGAAAACTGTAGCTTTGATGCCTGATTT GAATGCGATTGCATTGTTGCTTTGAAGTTTTCTTTCAAATAATAATTCAT TTTACTCACACACTTGCGGAGGATTGGTATTTGTTTTGCCTAGTTTAAAT ATGCAAAAGTACTAACTTATTAAAAGATTGAATAGATTGAAAGTGAGAAA CCGAGCTAAATTTCACCGCATTTCTTTGCATCCACAGCTTCGCACAACTT CGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCC GTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACT GAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACT CCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAA CAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCG CAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACG TCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTC CTTCTGGGCGGCGCCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCT GTTCAAAACCTACACGGACAAATATCGCGCCACCGTCGAGGATCTCTACA ATCGCGAGTACGACCTGGGGGGCGTCACACTAAAGGTGAGTACTCGCCCG ATTCCCCTGTTCCGGTTACAATGGAACAAGTATGGGCCAGCTTTTTGTCC CTTTTTGGTGACATTTTGAGTGGAATTTTACTGTAATTGGTTTCTAAGAG CTGAAATGTCAGAAATGCATTCCCAACTATATGTCTCAGTGCTCGTCTTA AAAGCCACTCATTCTCATCCTGCAAAATCCTACTTTTGGGAAAAACTAAC GGCTAGGAGAAGATTTTTATTTAAGAATGCAGCTGAATTACTTGACTTCT AAGCGCACATCATCATCAAATTAAGCCAAATTAAGTAAATATAATTTTTG ATAGGCCTATGTAGTTTAATTATAAGATATCAGGAGTCTGATCGCTGGTT GGCGTAAAAGGTAAACTAAGAAATTAATCCCAGATTTGTTATTCCAAACA ATTTAAACCGACTGCAGTGGGACGACTTTATTTACCCAATCAACGTTGTG GTCATCAACTCGCCGGCAATGCCATAGGTAATGCCGCAAATTAGGCAGAA ATCTACTAATTGGATGTCTGGAGAACATCCAAAGCACAGGGCTCCGCAGC CTTACGCTCCATATGCAAAGTATTAGGCAGGACACGTGTGCTTCTGGTCT CCTGGCAATTGAGTAGCTCCCTGAAAGCCTATTTGGAGCGGAGTGGAGCA GGCAGGAGTGGTTGGCGGTCTTTGGGGTCGGCATCTTGAGCCATCTCTGC CAGAGGCACAACTCAGGAAGATTACATTTGTATATTAAAGATGAAAACGC AAATTGAACGAATGAATCTCAACTGGCTTAAATGTACTTACGGCAGTCTT GGTGAATAGTTTCCAGCCCCATCCCTTCACCCCAAACCGACAGACCGACT GACAAACTGACTGACAGCTTGTGGGCGGAGACTCATTAATCAAATTTGCA CACGCTCAAAACAGCGGAAGCAACTTGGAAAATGTGGCCCACTTCCCAGC CCGCTAAGCCACCAGTGCTGCCGGCGGAAGAGTTCCGGACTTGCGTGCCC TATTACGCTACTTAGGAGCTCGATTAATGGGTAATAACTTGTGTCATGCC CGGGAAGGAAGAACGAAGGAGTATACCGGAAACTGATAACTGCTGCTTAT TATTTTAATCGGGCCTTTATCTGCTACGGATAACGGATAACCATATGGAT GTTAATAGCACACGAGTGGGAGGAGCCTGCGTGGTCGCAGGCATCACAGC TGCCTCCGACGCATCCTTACGACCATGTCATGAAATGGAAAACTTCTGAT GGAACATCATTCACTGCTCCGCTGGAGCTGATTATACGCTGTTCAAACTT GTCTTACACCACAAGCACATGTTCGGCGAACAAAAGTTGCTGGGAAAGTT GATTAATAGGTGGGCTGCCTGGCTGGCTGAAGCTGCTGAGCTTCATTATC GGGATTCTAGCTGGCAAAATTGATTCCTGGATGTGCTTTGGTGACACTGG CTCTCTAGGAGGCGGCGTCGTTGCCGGGCTCTTGTCTTCGATTTAATTAA TTTCATTTTAGCGACCGACGGGTGCGCATCCATTACTTAAGCCCGCCCAG ATTGAATTCCACACGGGAACTGTCACCCGACCCCAAAGTGATTTATTCCC GGCCACCTTGGGTGCAGTGTCCAGACGGTCAGGCGGCCAGGCGACCAGGT GGCCAAATGGCTAGGTGCATCCAAATCAGGTTGGCCTGGACCATTGGCCG CCGGGGCTTGCTATCCAAGCTCGAGTAGCGCCCACAGCCCGCTGAGACTG ATTGCCGGAGCAGCATGTGGCCATCAAACGGGAACATTCTATTGCACTAA ACGATTTTTGGTCTTTAAAAGCAATTTCGTGTATGTATGTACGTGAATGT GCAAGTGCGCACAGCAGGACGCATTTGATGCCTTAAACATGGATGGTCGA ACAAAGGCGGGCCGGCGAACAAAAGCCGAGCGACCGGGAATGGTGTCAAA AATATAAATTGTGTCATTCTGCAAAGTGTTTTAATAAAGTTTACTCATTT CGGCCAAACAATGCGTTACAAATTTGCGTCACAATGGCCCAGGCTGTCAA TTGGTGGGCTAAGGACCAAGAGGAGATCACGTCGACAGGGCTAAATGGTT AGATTCGCTGGCTCTGGCTCTTTGGCTTTCTGGCCTCTGCGTGCCATTGA CATTCCGGATCGCGTTCTATGCGTATCGCGTACTCGACGCGGCATTATAC TCGTAACCAACATAACAGATGCTGACACGGGGATTAGTTGGCTTCAACCA GGAGTCACGACCCCCGGGTCACCGTCCAGATGGCCAGACAACCGGACACC GCCGATTGGGCGGGGCATTCGTCCTTGTGCTTTCCACGGACATATCGTTT AAAAAGCACTCCATTAAATGTCCTGCGTACAAAGGGCAGTGCCAACAGCA GTGAAAACGACGCCCAAAATAATGGATAAAAAGGGATCCGGACCATGTTT TCCTATATTTAAAGTACCAGAATTTAATGTCGGATTCACTTAAAATGTAT ATTCCTCGCTCTGGCCTCACTGAAAACAATAGCTATGTTTATTTCCATCT GAATTTGTATCTCCAAAGATATACCAAACTTTAGCTTTTAAGCCCTATTT CCATGCCATTAAAACAGTTGAAAAAACTATACCATTTGAGCACTTTGTCG CCACTAACAAAGTTAATAAACGTTGCGCGGCAATATATTTATACACCTAA AAGAAACTAGGACGGAATACTTTAGGGCAAGTCGAAGTTTATACACCCTT ACCGCTTCAACTTTTTCCTATCACCATTATAATATAGGAGTACTCCTTTT TTTTTCAAAAGGTTTTCTATCAGTATTCCATTAATATTTAAATCTTTACT AAGGCAGCTATATGATGTAGTAAGCAGAAATCCAGCAGATAGCTTTTATA CTGAGCGACTACTTTAAAATGAATAAAACTACAATATAATTCCCTCTTCA AGAGTATATAACCATACTTGGCAAATTTCCGATAATAACTTTTCGTCGGT CTTTTTTAGCTGCAGCAACCTTTTGTAACTGACACCTTTGGACCAAAAGA CTTTCACATTGTTAAAATCAAGCGTTGGAAAATGGGAACTTTTAGTCTCT TAAATTTGATTTAGGTTTGGTCATCATAGTAAAGAAGTGACAAGAATTTT AGCATCAATAAAAATAATTCTAAATTATTAAAAAAAAACAAAATTTGTAC TGCCTACTTTCTATAAGATACATGGTCTAAAGGAGAGCACAGCAAGTAAT CAAATAGATTCGTTTAAATATTAATTTTGTTCAGCTCCAACATCTCCCAA CATCACAGTGCTGCCTTTAATCAAAGGACCTGCAAAATAAAATTGGGACG GTGGTTTATCGTGAATGAATGTAGTTTCATGGAAACCTTTTTTTGTTTAA ATTGAACGTCAATGATCTGAAACGCGGCGGGTTAAATTAAAAACCACGAA CGCTCCATGCGGACGCGGGATCTCATTGATGGCAGTTTACTGCCATCCAC GGCTGGCGGCCATCCAAATTAAATTATGCGTAATTTTTCCGCCCTCATCC CTTTCAGGTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCA TGCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCG GCCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGAT CCGCGAGCAGCGTGGCGACTTTCAGGTGAGTTACAGGTGCAGCTGCAGTC CGCACTTCGCACTCAGCACTCCTGCATTTTGCATGTAATCAGCGGCGCCT GAAATGCGGAAGCCTGAAAGGACCCTCGTCCTGCGCCACAATCCGAAAAG CAATTATAAATGTTCCCCTTTGTGGCGGAGGAGTCAAGCCGAGCGGCAGA GGTTTAGGCTTTTTGCTCGGACTCGGCTCTAAAGTTGCACAGTGGGTCAG GATCACGGTATCAACCGCATGGTAGCGGTATCAACCAAAGGCGTGAGCAA AATGTGGACAACAAGACAAATGGTTTAAGAAGCTTCCAATTTCGAATAAG ACATCTGTTAAGACTATTAAAGAGTGATCAGTTAATATTCGTTATGATCG AGGTAATGTCATTATCTCCTCTTTAATGTCAGATACTTCGAGTGGGTTTT CTTTTCAGGTAGGTATTACTGTGCAACATAGGGTTACCAATTTCGTGCCC ATGTGCGATAGTTAGCGCTATTGTTTCCGAGGGCTTTCACGGTTTCCGCT TTCCGCCGCCATTGTTCGAACGAGTATCAATTACGGCGCAATACGCTTTG TCCGCATCCCGATTTTGGGCGGACAAGGATGCTTGTGCCGCTACGAGTGC CACTGCTAATCCTTTTCGCTTCGCAGGACATCCCCATTGTGATCGCCGGG AACAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGT GACCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGTAAGTTGGCACTT GCCCACATGAATCGCACAGGATACGGTCGCCGTAAAATGCGCAACAGCTG CTGCACGCGACAGCAATTAGGGGACAACTGCCAAAAGTTGTGCAACAAGG CCCGAGCCACAAAGCCGCAAAACCGCCAAACAGCTGCAATTTTCATAAGT AACGAAACACAGTGGAATTAAAATGGAGCCATAAATTCGTGCCGCCCCAG AAGAGCTGCAATTGCAAGAGGCTGCCGGCAGCAAATGGCAACAGCGCAAT TAAATTGCTAGAAATGAAATTAAGCGACTGAGAGCGTGACGGCGGCCATG GAAGGGAGTTGGGCCATCGAAATCAGTTGCATTGTCCACGGAACGGCTGC TGCGCTCATTAAATGCCATTTGTTAGCTGGGAAAGTGTTGGAGCAAGAGT CGAGCACTGAAAAAAATTACTAGGAATGGGGGGAATCACGATAATCACAG CGGCCACAGGTATAAAGTAAAGTAGTGTGAATACGTTAATACGTAAGCAT TTCAGGCAGTAAATATAAAATTGATAAGTGAAAAGAAAAGTTCAAGTTGA ACTTTCTATCTTTTCATTAATACTTGAACACCCTGAAACTTCAAACAGTA TTTTTGTGAGTGCAGCTAGGTGGAAATCGCATCAGGAGGAGGAATATAGC ATTTCGCTATTTGCACAAAGGATGTTTCCCCATAATAGCTCCTAATTGGC CATCTTGTGCCGCAAACGGTGATGCTGTCATGTTGGCCATCTACATGCAA CCGTCGACGGGGACAACTCGTCGTATGAGTGATACATTGGAGTGGTCTTT GAATACTAAGCAGTGGGGCATTCCATATGCGCATATGCATGGGATGCATG GGGTCCTTCAACTTGGCTGCTCTAGAACTGTTCGATTGTTGCTCTGGGGA ACCGGTGTGGGGCTGTGAGGAGTATGATTAGTAGTGGTGATTTGTGTTTC CTCTGAAACACAATGGGTGAAAACTTTAGAGCTCGTCAGAGCCGAGCAGC AAACCGACATTGTGTTAAATGAATAAACCACAGAAAGTTTCAAATACATT TGACGAATGAACGCATATAAAATGCAGAAAGGTGATAGGTGAAGTGTACA AATATTTATATTTATTTCATATCGGACTCGTGTAGAGTTTCCTAGCTGTT TCATTTGTTCAATTTCAGGACTTTAAAGTTTAAGTTACCGAATTCAGAAT AAGCCCAGTTGTACAGTACTACAGCTTTTGTCAGTAAAAGTAGACCGCAG ACCGAATCGGTGAGTGGTAAACGAGTACAACTGGCCTGATTAAAGTCTTT GTTTGCCACATTAACAATTTTAATGCATTTCTCGCGTGACAACCAGCCGT GAAAGCACGGCCGCATCCTGGCGATCCGCCGGTGAAAAGGACTCGCTGAC CAGCACATATTTCAGAGGCGCTTTTCGCGAGGTAATTGCTTCCTTAATAA ACTGTGGGGCAGGACTCGTAAAAATCACTTGCAATCACATACGTGCCTGC CGCTGGGATTGGGACTGCTGGCATAATTCCATACGAGTGTCCTGCGAAAG TCGCCGGGATGGGCGGCGGCAAAGTGGGGAGTGGCACGCTCGCGTTGCTG TTTAAGCAAGCGTGCGTAAACTTATTTAAAAGCGACCAAAGAGCGTCACG CAGGAGGCGCGCTCAACCGCAAAATGGAGATGACAGAGGCCGCAGGACGA AGGATTGGGCATGTGGGATGGAGTATGAAGGACGCGGGAAAAGGGACACG AGACGCAGTACAGTTGGCGTGAGCATTACGTACAAATCTCTGTTGGATTA AACATTCACGCAGATTGATGGTGCGGTTTTGTTCCCGGGAGCGGGAAACA CCTTGAACCCATCGCCACAATCTCACACCTAGAGGATTCCCCACGTTCCT CACTCCCGTGAAGGTGTGTGTGTGTGTGGGTGTGGTGTTTCCTGGCATCG AGCTGCAATGCAATTTGTTGCTGCCTGTCTGTCTGCGGTTAAACGCTTTA AGAGCATGCCACTCAAGTGCATTTATCTGCCTGAATGGGCACTATCCCCC CCCCCCCCCACATTGTGCTCAGTGTATGCCACACACCGTAGGGATACATT GGGGCAGGTCCTACCTGGGTAAGTGGTTTACTGTGCCGAAGGTGGGACAA TGTATTTATTCAACATTTAATTGCAAAGTCATGCGCATTTTCCTGCCGTT TGGGCACCCAGCGTTAATGCGCAAAATAAACGTGCGATATCAATTTTACT TTGATTTACTGTTATTGCAGCTTACGGCATTAACAATTCGGCCATCTATT TGTTTATTTTGCTAAGTCAGCCGTTGTAACTTTAATTAAATGAAGCTGCC TGAAATGCTAAAATATTCTGTGTCACTCTGTCAGCTGTTTCTGTAGCATA AAAAAGGAAATAAATATAGCTTTTTATTACAAAGAAATCCATTTTATGAA TATTAATTCAGAACAAGTGTAAATGCAAGCTGCAGTTGAATAAAACCCCT TTCAAATAACATTGGGAACAGCGTTTAAATAAATATACATTTCCAAATTT TTTGGGGTCATCTTGCAATCATTCACTTTGTTCAAAAAAATTTTAATATT TAACAGTTTAATTTGTAGAACTCCGAAGTAGCGTAATACCACTGCAATAA AATATTAATAACTATACATAAAATAAAACCATAAGAAGAAGCTCAACTTA TAGCTTAACAAATTCTGAACTAAAAATTAGTAGAAATAGGAAACTTTAAT CTACAGTTATGCCACTTATTACCAAAATTGTAAATGCAAGGAAAATATTT TTCCAGAATGGGTCTTTCAAGATTATATAGTGTGATATAGGTACTACACT CACTCACTCACTTAGTGAAAACTAAAAATTTTAAGCACAATTTGTAAATT TTTATTTCTTTAATATCTAATTTCATTAAATTTTGCTTGTCCGATTGTAA AATATAAATTAATTTTAACGACATTCATAAATTTTCTGCGTGCACATCTG TTTCATTTCAATTAAACAACTAATTAGGGAGGAAAGAAGTAACTAAAATA AATTAATGTAGTAAGCAAACTTTCCACTGAAAATGTGTGAATGCGAAGTA CAATCGAAAATTTTTCGGAAAAAAGCCCATAAAGGGCAATTCTGATGTAA GCCAAACTGGAATATTTTGACTAGAAATAAGCCTTTCGTCGGATGGCCAC ATACATTTAAGCTGGAAATCCTCCTGACAGTCGGGTACTGTGTAATCCTG CCATCGCCTGTGTGTTGAACATCACCTGTCCTCGCCAACATCATCGTCCT CGTCATAATCATAGTCCTTGCTTCATGCCCATCTCATTCCTATCCTCATC CTAGTCTTAACCCTGGTCTCAGTATTGTGGGGCCAGCGCGGATCGTGGCC GCATCCTGCAGTGAATCCTTAGTGCCGCACCATTTTAAAGCGAACATGAC ATGCTTAATTTGGCCATTAGCAACATTTGTTTCGTTCGGCCCCCCGGACG GTGGTCCGGATGGATGGCCCACTTGGTCGTGGCGGGCACAAAAACTCTGT TTCGCATTGAACATGCCACATTGTTGGGCTGGTTTTGTTTGGCTTTTTTG GCTCGGTTTTCGGTTTGGATCGGCTTGGGTTTTTTGTGCCACAATCGCTT TGTTTCGGGCCACCAAAATTCGCTGATGTATGCATTGCGTATGCGCTATA TAGACGGTCGCCCCTGAAATTATGCAACCTTTTTAAACCGCCCTTCCTCC CCCGCAGGGCGAAAGTGCTGGAGTGCTCCGCGAAGGAGGACAGCAACGTG ACGGACCTCTTCAAGTCCCTGCTCTCCCTGTCCCGCTTCCTGCCCGCCAG CAGTAGTGGGAGCGGGGGCAGCGGGGGCGGCGGCGAGGCGGCGCCCAGCG GTTTCAAGCGGCGTTCTTCGGCCTACGTCAGCGCATCGTCCAGTCGCAGT AAGTATTCGCAAATGCTCTCATGTATGCTGACAGACCCAAAAATTGTGAA ACTGGTAGTATATGTATATACAGATGGTAGTGGGGGTATAGGGAAACCAG CTTACTATTTAAATGTGTCAGCAATTCAACATATTTTAAACATATACCTC GATAAAACCAAGTGGAAGAAAGGTTGTAGCTTTCAGGGCCAGATCGTAAA TATAGGGAAATGTGATCATCTTTTTTTTTTATTTATGCTCAAAGTGTAAA ATTAAGAACTAAATTAAATATTATAGATATTAGATAAATATACATACACA GCAACTTCTTTTACAAGAGTGATATTTTCCTAATATCAATATTTTCTTAA AATATTGTTAATCTCCTCGACTATCAGATACTCGTTACTCAGTTAATGGG AATGCAAGGAAAAAAGTTTTGAAGCAATTGTGAGAGTTAGAGTGGGTGTG GCAATCTTATGAAACCAAGCGTCTCTAGAATCTGCATGCTTAATCTTAAT CTTTTATAGTTCCCGAGCTCTATACGTTCATACGGTCAAACAAAAGAACG GACTAGTTTTGTATTTTTGATCAAGAATATGTTTACTTTAAAGTGTCGGA AGCGGCTCCATCTACCTGGTACATACTTTTCAACGAATATAGTGTAGCCT TTAACCCTTCGAGTAAGGTGTATAAATATATAAATATCAAAGCGTACTTG CTCACATTTATGATAAAGGATGCCCCGAATATCTAAATGAAATCTAAACA GCTAGCTAAAAGTTTATGCCTTATGGCACAATTTTCACGGTAGTGAGCGA CAGAAATAGTTTCGGTTGCATTTAACACGATTAAATCCCTTGAGTCGCTC AACAATGCATCCTGGAATGGCAAATTGCCTTGGTATCCATCATGCCAGCA AAACCAGCATAACACCCAGAGCTTAGAGCACAATCTCTCCATGGATGCAA CACTTGATTTGTTGCCATGGCTAGGTAAAATGGAAATGAAAACCAGATGA TGCAAGCCCTTTGTTGATTGTTTTTGGCCTCGTCGGTTGGCCGTAACAGT TTCAAATGTCAATTAAACATTCATATGCGCCGGCTGTGATTGAAAGTCAG ACCTGTAACCTGAACAGCTTTATTCGGGGATTTAAGTGCCGCCGTAAGGA GCTTAATTAGTGCGAAATTAAAATGCGAGTGCGCTGCACATTAATGCAAT AATTAAGCCGGTTGCGGGTCGCAGATGTCACTAAGCCGTGCTGAAGCCCA ATCAATAATTGATGCACATTTATGAATGTATTCAGTATTTTAAACAGGAG GGAAGCCCCACGCACATGGTGCCAATTAATTGGAATTCTTTAAATGCGGC CAGGATAGCTAGGATAACTTTTGGCAATTTGGCTAATTGAATGCAATTAG CATTCCTGCTTCAATTGCCGCCTCCGTCCACTGCCACCGCCTTTGGGCTA ATTAATTGTGGGAACTCGGGATCAGAAGTGGAGTAAAACGGGCCGTCGAG ACCCTTTCTTCCGACCCAATTGACAAAGACAAACTCTTTTTCATTATTCA TCAGACGACAAAGTGAAGGAAGCACCGAAAAGCAAAGCAAAGCCAGGCAA AAAGCCGTCGCGACGGGGTTAAAGGCTTCATAAGGACGAATTCGCTTTCG GCGAGTCCTTCGCCGCGCGATGTTCAAACGAATTCAATTTTATCAAAATG TTTCCGAGCGAGCACGTGTATTAATTAAACAGCTTGACCTCCTAATTACC CTGTAATGGAATGCTTTATTATCTCATTAAAAACTTAGTTCACAGCACAT GAAAATAGAACACAAAGGCCAAGACAACAGCCAACGGCTCGAGAAGTTCC GAATTTTGCCGAGCTCGTCAAAGTATAAATATCTAGTTAATTAATGTTGC CTCGACTGGCGCGGTGCCCAAATAATTAATTTCATTTTTTTTTGGGAAGG CAAAAGGTTGCGGAATCATTACGGATCCCGCCCAGTCAGCGATGCCAATA TTGTAAGTGTTCGCCCTAAAGTCCTTTCGTGAAATTCCGCTGCTGTCCCC GTGAGCCATTCAAATTAAGTGCAAAGTTGGTCAACGGCGTATATGCAAGT ACTTAACTTCCAACAACTTTAAATTCAAATGGCCGAGGAGCACATTAATG TCCTGCCACCGAGCATATCAAATGCCTGCCGAAAAATGCTGTCAAATTCT CGGTCTGGCTCCAACTGTCGATGACAGGCGGACAGGACACGCCGACAATG GCGGTGGTCTCAAGGACGAGGGACGGGGGTCGAAGGACGAAGGTCGAGTA GCAGACTGTCTCCGGTAGTTCAGAGGTTGCGGCACTCTGAGGTGGGAGGG GTGACAGCGGTGACACCGACGCCCTGAATGTGCCACCGAAAATAGGTCTA AGCACTTAATCACCGGCAGCTCGAGGGGACCCAAGTCAAGTAATTGCCTT AAAAAGCACAGCGCGACGTATGCAAAGCAAATCGCAGAAATTTCATTTAC GACCCTGCCATTTTGTGGCTGAGATTGTGCCACACGTGTTTACGGCTTGC AAGTGGAGAGGTTGGAGGATGGGTGATGGGTGATGTGAGATGGGCGGCAC GAAAAATGGACGGGCCATGGTAAGATGAGACAAAGCCAATGCTACAGGCC ACATACATGTGCTGCGGCCGGAAAACCCACTTTTCCTCCGCTTCCCACAT TGTTGCCGGCTTTTCCACGGCACTCGCGTGGTTTTGGCCCAGCGGTGCTT GCGCCGCAAGCCGTTTTGTTTCAGAGCCACAAACCAGAGCCTAACTCAAT TGTGGGTATTCCCTAACACACACATTACATGCTAAACATATTTGAGCCAC GTTCGTGGGAGTGTTGCCCCTATTCGCAGCGAAACAACGAACAATCACTG TAAGTTGTGCGCCAGTAAGTTGTGGCCATCTTCACTTTTTTCAATAAATT TAAAATTGCTTTAAACTTCCAAGTTCATCATTGATTTCATTCATTTATTC ATGTTTGGCAACTTGAAGAACCGCTTTGTACAAATAAGCTTATCGATCAA ATGAATTACACACTCTTGAGTAATTATACGCTTAATAACATGCAGTTAGC ACTAAAAAGATATCATTGACATCTAAAACTACCCCACTTATTGAGCATTA AAACTTCAACAATTATAAATAACAATTATGTTAGTGCACTTTCGGGTGAT TTTGCAATTGATTTCAATCAAAAACAATTGCGTTTGACTGCAATTGCGCC TGCATTGACAGCAGTTTCTCATTTTACATGGCACCAAATTGTCAGAAAAA ATACACGTTTATGTAAAGCTCTTTTTTGCCGAAAGTTTCAACTTCGTGGT ATCAGATGCGGCGAAATTGATGTGGCAAATCCTTGTTATGCCCTTGCTGG CAGGATAATAAACGCCCTTTGCGGCACTCGACTGTTTTGCGTTTTTCTTT CCTGGTATTAGCGCTTTTCCACGGCACGTCCTCTGTCTTTGTGATGGAAC CAAACCATACCAGACCAGAGCGGAGCAGTGTAGAAAATAAAACAAATTTA ATTTAAATTTCCGTAACACGACGCACGCATCAATTCCTGCCGCATATGCA CAATGTATATGCCCAAAACCGAAGCCCACTCCTATTTGTTTTTGTGCCTC GATGGCGGCACTGCTGCTGTGTGCGAGTCCTCGTTTCCGATTCATCCGCA GATCAGAGGGACCTTGCTCCCCAAAATGGGAACGGGAATGGGAATGTGAA TGCCGCCCCAGCGAAGCCGTATTTGTAGTCCTGGCATTTTCGCGCGCTTT CTGTCAGCGGCAGCAATTGTGCCTCTTATGCCACCCATCCCCAACACCCA CTGCCCCTCCCGCAACCAACTTGACGCGCTTGACGCCTTTTTTTGACAAC AATGGCGTCGGCGGCCATTTTGTTTGCACTCGACACCGCCGACACCCGAA AAGTATGCAACACTCTGCCGCAGAGTGCCACTGGTGGCTCAATAATGCTG TTTGCACGGATCATTTGGGCTTCGGCGGACGTAGTTCGCTGCTAAGCTGC AGAGTTTAATAACTAAATTGACTTGGTTCTGGCCTGGCATTCTGTGGCAT TCCCTTTGTATTTGTCTTGCGGCTCCACAGCCCCACTGCCGCACAGCCCC TTGCTCCGTCAGCTGCCAATTGTTTTCCCATTGTAAGCCCTTCTTTGTTG GCGGCTTTATTTCTCGCCCGGCGGAACAAAAAGGTTTGTTTACCGCCAAG GCAAACATCTGAGCGAACACCTTTGTGCGACTTTATCACTCTGCTTGGCA GTCGAAGCCGCCTGATTGAGGATTACCGGAAAGTTAATGACTCCATTGAC ACTGATTTTCCCTACTTAATAGGTTCAACTTTGGAGACAGCTTTTGAGCC ACTTAATTGAAAGTGATGTGCAGTCTCTTAAAGTTTATTGCACAAAAAAA TGCTAAAAAAATACATTTAGCGAAGTTCAGCCAACAAAAAACAATTTCTT GCATTTAACTTAATAAGCCCTAAGTATCCTAACTAGTGTCATTAGTTTAT GTTTAGTATATCAGTAACACCACTTTCTTTCTTTATGCTTTACCTATTTT CTCTCTAGCCCTGATATATGATATTCTTGAAAGAATATCCTGAATCTTTG AAGCGCAAACAAACTTCCGCATACCATTTACTACTACATCCATGATTTTA ATTGAACTTCGACTTGTTTCGTATGTTTTGACGACCTTCCTCTGCCAACT GAGAATGAGTATCCTTGCCACTTCTGGCTGCTCCTTTGAGTCCGCATTTC ATATGAGCGGCACATGCATGTCGCACAGATCCGAAAGGAGTGGGATTACC TCGATTCTTGAGATGAACTTTGACTGTGCAAACGACTGTAAAAAATCCCA TTTCGAGCGGTAACTCTGCAATGTGCAACTCGCTTCCCGGCTCTTTGTGT GCGTCGTTCATAAGTTAATTACGTCAGCGGCTGCAGCGGATGGCAGGCTG TTGGGATACCGGGATGTTGGGATGTCCGGATGTTCCAGTTGCTCCGGCAA CTGGCAACTGGCAACTGGGAAGGACATCAGTGGGGCAAATTGGATTTGCG CTGCACTCGCAGCTCCGAAATCGCACAGTCCCTTTGAGTCGGCATACGGC CACCATTAAATGCACTCGTGGATACTAATTAGCCGCGCGTTCCCATCTAT TTGTTGCAGATAAAAATCGGATGAACAGCCCGGCCCTGGGAGGCGCCGGC GGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCGTGGACGCCGTGGATGT GGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCTCGTTCCAGGTGAGTGC AACACGTGCCTGCTCATTCAGATAGAGTCCCTGGCCAGATCCGGTTCCCG CCTGGCCGCCCTGCTGACCACTTCCACCCGCTTCCATTCCAGATCGCTCA TACGCCGTGCATCACGCAAGACCAAGCAGCAAATCAACAACGCATCCGAC GACTGCAACGTGCAGTAAACCATTATTTTGGCCGCCAGCGTCGAGCTTAA TTATGTTATTTAGTTATTACGAGTATGTTGCCACAATGTGAATTAATAAT GGACGCCAGTTAATTAGCGTGCATAAACAAGTGGCGCCGTATTTATGTTC GGTGCACTGAGCTGATTATTCTGATAAAGCTACCCAGTTCACAAAAACCT CTTGCTCAAGGGCACAAAAATTTCGATGAATTTGCTACGCGGCAAAACAT TTTATAGTTTGTAACCACCAGAGCTTCGAAACGATGCCGTCATGACACTG GCCTCAGATTATATGATATTTCGTAAGCAACTCTGATTAGGTAAATTTAT ATTTCATTATGAATAGATATCCTAGCTTATAAGCCGTGAATCAAATCAAA TTTCTTTAACAACACTATAAGTAAGTACGCTATAAGTACAGCAAAAGCAA ACACAAATACTTATTCTGCGACATTTTAATCCAGTGTCATAGCGGCATAA AAGATAAGGTATTATTCCGACACTGAGCTGACTTGCGAGGCATTGTGCAC ACAAATCGATTTGAGTTGCGGTCATTAAGGTTGGAAGGGACCAGGTTTAT TTAAATTTAAAATTAACTTTTATACGACAAACAATTTCGATTTTCGCAAA CTTCAGTACAGCTCTGGGTGCCCGATTTGAATTTAATTTAGATGTCTCCC ACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCGTTCTCCTCGAAAGGAG TTCCTTTTGATGGCAAAATAATGGCTCAACGCGACTGAGTACGAGGTTTT TCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACTGGCGGATTGTCATAAT ATTGTGACAGGTGGCATAGCCCTAAGGTACATTCTAGGATACTACTTTAT GAATCTCTATCTGCACCCTTAGCCGACACCATGGTTAATATTTGAACGTT CCGTGTACACATCTATATATTAATACAGCTCCGATAAGAATGTTTATATT GGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCGAATACGAAAGGAATCG CAAGTTTTGCAAAAATAAGGCAATTTCGCGGCATTCTCCGCGGCTCCAGC CACGTAAAATAACAAGAACTTTGCCAGAGAGCACAGAGCAATTTACTATG CAAAAAACGTAATTGTAAAATAAATTTGGTGAGGGAAGGGAGGAGAGGAG GGTGCCGAATGCTTATCAAGGATAATACAGGGTGAACTTCTTATGCCAAA ACGCCAAAATGCCAAATCAAATAGCCCACAATGCACATCCTGTTCGCAGG AGGCTTGCGGCAGCGAATAATCGATAAATCTGTTTTTAATACGCAACTTG TATCCATTCGCACAAGTTACACTTGCATCTGGGTGGGTGGTGCGTGGGTG TGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTGTTTGTTCACCGGAATG TGCTTAGCAATAAGATTTATTTAAAAGACTACATTTAGGCGGTACCGAGT ACGGCGGAGATATCTAAATGATCTGTAAATGGATGAAATACGGCATATGC AAAGTGAATTGTGATTAAACCAAATACATCTAGACACACGTGTGTGTGGC ACTGTGTGCAAGCTGAAAAATGCAGCAAACAATGCACCCAGTGATTGCAG TAATGGATTCCAGCTACTGTAAACACCTGGGAAATGTCAGAGGCGTCTGA ATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAG TTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTT ACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGT GTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTT ACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCG CGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTA TCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCT ACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCG CACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACT ACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGT GTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACA ATTGTATTAGCCAGTTAAAATAAACCACAATGCGTCCCAGGCATCGGTGT TTGAAAATGTTTGATTCCCCTGCATAATGGATTCTGTTTCGTTTCGCATT CCGTTTCCATCGGCGCACCGAGGCATCGCACTACGGGTCCATGGGACCAC GGGATCCGCACTCGGATCCGAATCGCCCTGCCCACCGGCGGCTGCCAGCC TGGAAAATGGCACAGTGAGCAGTTTGCACTAAATCAATTAAAACTAGTGC AGCACCGACCGCAGCATCCATTAAAAGTAACTAATGGAATTTCATTCGAA TTATATATTGCGATTCCCATAAATTCTGCAATTGCGTAAATGCCGATTGC CGGCTTAAAGCAGCCGTGCTGCTGCTGATTTGAAATTTGCATATTTATAT GGGGGGTGTGGTGTTGGATTTCGGAATGGGGCATCTGGGGGCTTGCGAGG AGCCAGCCGCTTTGGCGTTCGCGGCAAACAATAAACAGCTTTGCTAATGA GATTGCATTATGCGCAATTCAGAATGCAATTTACTGTGGCATTGATTTTG CATTAAATTGGCTTAGGCCGAGCGCTCCGCTTGGATCGGAAAAGTGCGGG AAACCCCAATTTGCTGCTGGCACGTCTGAGCTTAGAATTATGTTCTTAGA ACGACTTAATGCAAATTTCAAATTCAAATTGCAACGGAAGTGCGGCGCCA CCTGGCGGTTACCACGAGCGCGTTCAGGCGGCGCCCTCTTGCGGAAATCT CGCAAGTGAAACAGCTGTTTCCAGCTGCTGGTTTTTTTTAGCACATTTAT CCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGGTAACTTG AGAGAAATTAACTCCTGCAGGCTTGACTAGCTAACACCTGGCAATGCTCC ACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGG CGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGT GGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGAT GTGGATGAGGCACTGGAACTGGCCTCCAAGGATGGTAAGCTGACCTTTAG GATGTTCCCTTTGCAAATTGTGCTTTAAATTGGGAGTCCCCATTGCACGT CCCTTTTAAATTACTTTCTGATTGAGCTACTCACTTTCTGAAGAGCATCT GATGTTTATTCCATCAATTTTCATAGTAATACGAATATGTTGCTTACTCC CCATACCGCGATTTTATTGTACACTCTCAATTCACAAGTGGTTTTCCTCG ACAGAGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGA ATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCA AGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTAC GATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAA GCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGA GAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAG ATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGA GGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATG GGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCC AACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTGGTATTCGACC CTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCCACCGTCAAGA AGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACGCTGTGAGCCT TGCCAAATCAGGTACTCATTGTTAATACCTTACCCCCAAATGTGCAGACG ATACTAACAGTTTGTCTTCCGTTTTAGCCAAGTTTTGGAGTCTATTGCCG GAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAAC ACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACAT GCATTTACATTCAATGCGTTTACATTTATTTTATTATTGTTTCTCGCGTC TAAATGCAAATGAATTCAAAAATACGCATTACAACTTTGATTTGTTAGGT TACATCTGGTTTGGTTTCTTCGATCTGCAGTTAACACAGATCCACTAGGA TTTAGGATTAACATTTAGATGTGTAAATAATTGTTGCATATGGCTCAGTT TATTAACGTTCGTGATTACGCACTGCTATGTGGTGAATATAAAATGGATC GCCCAAAAAAATATATGTATTTCTTTCGACTCGAACTTGTATAATCTCTC TGGAGTCTATTCTAAACTCTAATAGAGTGTCATAGCTTAATTATTGCCAC GTTTTTGGTTACGAGTTTGCCAATATTCATCAATTATTGGTGAAGCCTTG AAAAGCCTATATACAAAATATTTTGTAAATATTTAAAAAGTCTATCAACT ATAATTAGTACGCTTGTAGGTATTAAAAGGTTCGAATTCGGGGGATAGGA AATATGTTTACCTTATGTTTACCGTTGAAGTTAAAGTGTAAAACAACCAA AATCTGGAGCTAAAAATTGAATTTTGTTCTAAGTTTGATGAACTGATATG AATACAAATGATATTGTTAGTATTTAACATTGTCAGACGGGCAATGTCTA TTCACTCGGGGATGCATTTAAAATGGCAATAAAAGATTCAGTCCAATGGA AATGATATGATATGAACATGTTCATATAGCACTTTAAGTCGGTGCGAAAT ATTCTGGGGAAGACTGATCTCCCACGTTCCCCTTTCCGCTTGGCAGTAGA TAGTTATAGTTCTTAAAAGCATTTCAAATTGCGTTACTTCTTTCTAGATT TTTTTTAAAGTTACAGTGGGATACCGAGTATTTTGTTAACGTGTTAACTC TATTTATTCAATACAATGTTTTATGGGTTATATTTGAAAATACGCTCAGA CATAGCCCAATTGACATGAAGTTGACAGTTTGCAAAAAAAATTAAATTTC AAAAGTAAAAAATACTCAAAACATGTACGATAAATTCCATTTATTAGGCG TCAGATTAGTTTCGAGTGTTTGTTAAACTCATATTCATATGTATGTACAT AAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATAT CTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAA ACATAAACATAACTGTCTTCCATATTGTATTCACTTAACAGAGAAAGCCT TTCGACACATTTTTGGGATACAGGAAATCAAGAAAGGTATTGATTAGTTC GATTTATGCTTAATGCTCCTGTTAAATATCGTATATCGAATATATATTAT ATATCGTAATCATATGTATTTAAGTTGTATGCTGTGTTTCGAGTTTTCAG TTTCAAACCAAACTCTGCAGAGCCCTGCAGTCGAGCAGGCGTCGGGCCTC ATGATTATTCATAGATTAATTATTATGGTAATAAATATGCTGCTTCGCTT AGCCTATAGGTTAATTCAATGTATCTTGGGAGCGCTGCGATCGTTGATCT TCTGGTTACGCTTTAAGGTGGCTCCGCGCTTGATTTGATCCATCAGCGAT TCGTGACAGATGCGAGGGTCCGGCTGAAAGAGTCCACAAAGATCGGATTA GATGGGCACTTTGCTGGCAAAACCTTAGGTTATCTATCGTTAGATCGGAG AGCAGTTAGTTGGCAGAACGTAGCACTGAGTGTATTAGCTGCCAGCTGGC TTAGTGGGCTTCAAACGAACGAGAACGACTAGGAACGAACAAAATACCTT AGCACTTAGCACTGATCTTCGCAAGTGGCATTGGTGGTTGTGCTGGTGTT GGGATAGGTGGGTGGTCTACGGTATTGCGCACTGGGTCGCGATAGTTTTT GCGGATTTTGATACATCTAATAGCCATGGTGACATGGACAGAGCATAGAG AGTGTTGGCAATCGGATGAGTTGCTGTCGAAGTGCACTACTTACCAGGGC CTTGCTGTTGATGAGATTTCGCACGGCAAATGCTCGTCCAGACATTCCCT GCTTCGCCAGCTTCGCGTTGAGATTCTCGAGGAATTCGGCCTTGGTCTTG GCACGAATACTGCCAGTCTTTTCGATATTTGTGCTTGTGGCATAGTCTAT TGATATGCGTTGTCGATACGGGTACCGATTCGGGTGCATAAAAGAAAATG GTAAGCAAACATGATCGATCAATGGTGGTGTGGATGTTGGCTTGCGCAGA AGTGGTTAATATGGTGGTAAATCCAAATGGATATGCAAAATAAAACTCAA CAATTGTTGGTAAGAGTTAGACTCGGAGATGACTGATGATTGGAAAGATT GGAATGAAAGTTGACTGCGGATCGAGCTGCGGCGGAAACTGCAATCCCTT CTTGTTGACCCGATAGTTTCCAGACGCACTTGACACAATCTCAATCATGT TAATTGGCAACACTTTCCAAACGAAAACTCAAACGCAAACGAAACAAAAG CAAAAGAACATATGCAGCATGCGCCAAAGGAAAACTTAGAGCTAACGTCA AATCAAAATTGAATGCTCGCAATCGAGCGAAATAGAAAGTCAGCAAAACA ATAATATACAACAAGCAGCGCGCTCATTCCTTGCAATAAAATCATACGTA ATGAAATCAAACCAACTCAAATCGAATCGAATGGAATCAATTCAAATCCA GCTCGCGCTCTTACTTGGATGATGTGCCTGGGAATGGGCATGGGCATTGT GGTTATAGTAGGCAGCGCCGCCGTTGCTGTTGCCCCCGGCAGCATCGCGA TAGTAGTGCTGCTGCTGCTGAGCCTGCTGCTGCTGGTGATGGTGGCCGCC ACGCGAGGTTGTGGCATAAATGCTAGCCAAGGACCCAGTAACGGGCGAGC CGCACGTGGGCGAGGCCGAGGGCGAGTGAAACTTGACGGCCGTTGTCTGT ATGAATGGATTCGTTGATACGAATATCTTTTGCTGCACACTTGAGTGGCG TGAAGGAATGGGCGGCTGGCGTTGCTGGTGTTGTTGGTGCTGCTGGTGGT GCTGCTGCTGTTCTTGCTGTTGCTGATGCTGCTGCTCCGCCAAGTGCTGC TGCTGTGCAGCTCTAAGCTTCTGCTGGGGCAGCGGCAACTGCGGACGCTG ACCTAGGTGCCCATTGCCGTTGCCAATGCCCATGCCTGCCGGCTGTTGAT ACTGCTGCTGGTGCTGCAACCGCTGCTGCTGCTGCATCATATTCTTGGGC AGCGTGGCCGTAGACGAGGCTGCTGCATAGGCGCTCGAGTGAGTCGCGTT CTGGCCAGTGGGCGGACGGGCCATCTTCTTGGGCATCGTGGCCGATGCAC CGGCGGCGTAAATGGGCGGCGGTGGGGGATCCTCCAGAGGAGGCGGACAG GTGTAGTGCTGCTGCTGCGGCGGCTGGTGGTGCTGATGGGAATGAGCCTG TCTCATGTTCGGCGATTGCGCAGCTGCTGGATTTTTGGTAAACGAACTTG AGTAGATGGCCATGTCTTTGCTGTTAGCAACTGCTGCATTCGGCGGCTGA GGTGGCTGATAATGCGAACTGGCCGAGCCAGAGGTCGCTGCCGTTGTCGG TGGGGATGCGGATGAAGAGTTCGAGAATGAGCTGACTTTGGAGAGCAACG ATGATGTGGATGAAGACAGGGGGAAGTGAGGCAATGCATTGAAAGAGGTG GTCGGTGTTAGAATGGACGGTTTAGTGCTGCTGTTGGCCGCATGAGCGGA TGACATTGCTGATGATGAGGTGCCGAAACTAGCGTAAATTCTATGCTGTT GCTGGTGCTGCAGCTGGATTTGTTCAGATTTACCGTCAAAGTGTTGCTGC TGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCC TCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTT GGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCATTGAGCTGTGCAATTAGG TTCGGATTCGCCTTTGGCTGTGTCGGTGGCAGTGGGTGAGCATGTCCGTT GGGACTGGGGCTGCTGGTGCGGAAGCTGGACATGCTGTTGACCAGTTTGG GCTGGGCGTATATGCCGCCGCCACCCCCTCCGCCCGCGGCTGGTGATGAG GTGCGGAACGTCTGGTCGTGAATGTGTGTCAGTGATGGTGTGTTTGTGGC ATGAGAGAAACGAGAAGAAGACGGGCACAAATTAAAAGTTAGCCAAAGCA CGACCAAAGCTAAGCACTAGAGTAATCTATGACTATGGCATTACAACTAA GCTGGAAGGAGGGCAGTCGTGTTAGGCCAGAGAGGCGCTCCCAAAGACGC CTGTTAGTCTTGGTTAGTAGCCCGCGAGATACCCGCTGGTCACTTACGGC ATCGACTTGGTAGACAGGCGGTTGCTGTGGCTGATGCAGATGCTGATGTT GCTGCTGGAGGGTAAAGCGTTGCTGGTTGGCCATCTGCTGACCGCCGGGC TGTTGGCCGCTGGCCAAGGCCTGGGCATAGGCGTGCAGATCCAAGTAGGA GTCGTAGTACACGGTCAGGTCCTCTTTGAGGGGGGAGTTGTGCGCAGACT ACGTGGGGGATTGGGGTTTCGGTTTGTGTGTGGTAGTGGTGAAGCAAACG TAAGTTGAAATAAAATGAAATCATAAGTTGTAGAAGAAGATGGCTAAATT TCAAGGTGGCTCTAGACTCGTGCACTAGTTAGACCCAATGAATATTACCT AACTCTCACGCCGAACTATACTGGCTTTTGTTGGGGAATAAATGTCGAGT CTTCCAAGTCGTATTTCTATGCTCAATGAGCTCAAAGTATACCTACATTT GTAGGTAGAAAATGTATGGAACAAAGCTTATGCTTGTTTACCGGGGCTAG GCAACTAGAATCCCTACAGTTTACGATTAGTGATTAGCTTATTGTAGCTT TAAACTTTTTAGCCAGATATATGAATTTTCTAACTAAAGCCAAATACATC TTCATCTGGTTGCATAAATTTTTGGTCAGAAGCATAAACTACACATTAAT AGTACCCAATTTGGGTTGTAAACTCAAATAGTCAGGTGAGAGTAGGAAAT CAAACATTTTGGTACAAATGGAAACCGGATGCGAACCGAGCACACACCTG CAATAGGGGTTGCTGCTGCTGCACCTGTTGCTGCTGTTGCTGCTGAAGCT GCTGCTGCTGTTGCTGCTGCATGCGTCTGAGGGACACAGGTGATGCTGGC TGGTGCCGCATGGCTGCCAGGGCTCTTACCGTCTCCGATACCTTCAGCGC TGAGCTGGGAATCTGGGGCATGGCGTCCAGCATGAATGGCGGTGGCGGCG GTAAGTGCTCGCTGGAGCTGCTTAGTTGGTGATTCTGCTGCGACAGAGTC GCGTGCTGTGGTTGCTGCTGCAGCTGCGTTGCGTAATTAAATCATAAGTT AAAGAATAAAAGCATAGAGGAAACCAAAGAGTGTGTGACCCAGAGTGTGA ACCCAGGCTTAGCGACTAGCTTAGATTAAGTGGCTAACTTAATTGGGTGT AGGTAATTGAAGGCTTAACTCACCCCGACCGAGGCATTGGGACTGGGGGT CACCGACGAACTGCGTCTGACTGGCGGCGGTGGCTTGGACTGATTAATGG ACGATCGACGCCCGATGCGCGTGGAGCCACCGCCGGCTGCTCCTCCTGGG AAAAGTAAAAATCCTTGTTAGTGAGGCGGGCATTTTGATGATTTAGTCAT TAATTTCTGCTGTTATTCACAGTAATGTACAGTTATCAGTTTATACACTT GGCACACAAAACACAGGACACCATCTAATACCAGTAGTTAGCGATAGACG CAGAGTTAGGATCTGCTGATCGAGAAAGTTATGAACGTTCTTGGTCTGCT GTGAATCATAATGATGACCCTGAAGCGAGTGGAAAAGCGTTAATGGCTGT GATGGCACTTTCGATACCACTTCATGTCGAAAAGACATTTCCCCTAATTT AAGCGATTTTGCAAAATGCAATTTTGTAAAAAAAATTTTGTAGTTACAAA CGATCGAATCTGATTAGTGATTAAGCATTTAGCAGTTAGTGGCAGTATCA TGCGGGTTTTGAGTTGTCTATTGATGATCTGAACTTAATGATTGTGACTT GATGGTATGAGCGTAGTGCTTAGCGAGAGAAACCAACTCCAATTTCAAAA AGGTTACCACATCGAACTTATAGCAAAAATGAGAAACCCAAAACCGCGTA AAGTTACTTCGGCAAGCACAAAATGATAAGGATACTTGCAAAGGTACAAC AAAGTAGGAAAGTTTTCAAAATAAGGAATCAAAAACCAAAACCAAATAAA CCCAAACAAATCAAAATCAAATTGAAACGAAACGAACCCGACAAAGAAGC CGGCCGGGGCGTAATGCACGGCTTGAGATGGGCATTGGCATTGGAAATGC TATTGGCGTGGTGGGGATTGGCTGGGGCATTGGAGCACACATATGGATGG GCGGGTGGTCGGTCACTGGCGGGCAACATCGATGGCCGGGCATTTGATGG TGATGAAGTGGTGGCTGGTAATGGTAATGACGATAGCGATGACGATGATA ATGGCAAATGGCCGCGAGGTGATGACGGTGACAATGCCATTGTGGGCGTC TTGCACTGCGTGTGATTGGATGTGGCTGTCTGATTTTGGTTTGGCATTCT ATGATTTGGATTCGGGTACGGGTCTGTGGATGCTGTTGCGGTTGCAAATG CAGATGCTGATGCAGTAATATTGGCGGCTTGTTGATTAGTGACATTACAG TTTCTGGTTTGGGGCGACTGTGGTGAGTGTTGCTGTTCTTGTGGTGCTTG CTGCTGCTGCTGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCT GCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCT AGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGC AGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCA GCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGC TGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTACCGCCTG CTCACTGGGTGTTTTACCTCTTTGCGGGCTACCGCGTCCGAGGAGCTGCA ACTGCTGCTCACTGGTGGCGCGAAACGAGGAGAGTCGCTGCTTGGCGGGC GCCACAGTTGCTGTTGGCGGTGCCTGGCCACCGGCAGAGTCCGGCGAGGA GTCCGGCGAACCGGCCAAATTGGCGGGCAACTGCTGCAGCTCGCGCATCT CGTGCAGCTGCAGCGCGTGGGGCTGCGGATCCTTAGTCCGCAGCACTACA ATCTCAGAGTTCTGCTTCACGAACTCAATGTCGGGTGTGTTGGGAATCTG GTGGTCGTAGATCACCACCACGGCACTGCCGCTGTCGCTGCAGGTATCCA CATAGGCGTGGCGTGGCTGGCCGAGACAAACGCTGTCGGAGGCCAGCGAA ACAGCGTCCTCCCGATTGGCATTGGCCGCAAAGTGCGCGAAAGTGGGATT CTCGTAGCCGCCGGCCGTTAGGCCACCGGTCAGCGAACTCGTCTCGCTCA CATAGCAGCGACTCAGCTCCGAATCGCTGGCGCCCAGCAGATCCCGGTCC CGATCCCGATCCCGCCGCCTGACGTCCATATCGTCGCCGGCCAGTTCGTC GGACGTGGTGTCGGATATGTCCGTGCCGCAGCCGCTCGAGTTCGTCTGAT TGCTGATGGCGCATGGCTCGATGTTGCTGGTGGCGGGCAGGTTGTTGTTG TCGCTGCTGCTGATGCTGCTGGTCGTCGTATTGTTGTTGTTGCTACTGGT GGTGCTGCCGCTTATGATGTTGCTCGGCGGTTTGACCTTGCCCTCATCGA TCTCGCGTTGGAACGAGTCTAGTTCGCCAATTAAATTATTTAGTGCTTGT ATTGAATCTTCGAAAGACTTGTCTGTTAAGTTCATATTTTCAAATTTGTT GGTATTGATTTTGGAGATGGTGTTGTTGTTGTTGTTGTGGTGCAGTTGGT TCATTGTGAATAATAGTTTACAGATGACAGAGATTTTGGGTAGGGTGAAC ATAAAGTCGAAACCGAAAAATATTCAATGGTTTCAAGTTGATTTTTGTGC AGTTGTTGCCGTTGCGTTTACACAACAAACCAAAAAACAGGGGAGGGAAA AACAAAAAAGAAATTTGGGGGTTAAAAAATATTCACGATATGTTTATCAA TTATAAATAAAAATGGGCGCTGGACATGAAAGTTGGAGACTGGGGAATCT CATGTTTAAAGTGCTCTTTTGTGCTGGGTGGGCAGGGTACTATGATCAAT TGACACACTTCGCCTTCAACGATCCAGCTGATTGCTGATGCAACTTACCC ATTTCCTGCTGCTCCGCCTCGGATCGTCGAGTTCCGCCTCCCGAAGCTGG GGAACCGGATGCAATCTGCATGGGAGCTGGGGGCGATACCGCTGCCGCTG CTGCCGCCTTTTCGAACATTGAAGCCTTCTGCAGGACTGAGGCCCTTGAT CGCTCATCCGTCTCGTCCGCTACGCTGTTGGCTGGACCCTGATCCTGTCC TGCAGCGGCTTGCTCGGTGATTTTCAGCACCTCGCTGGAGGGAGGCGTCG GGGAGCTGACCTGGTAGACAAATCCCAAACCGGACCCAGGACCTAAGCTG CTGCCACTGGGAGTACCTGCGGCAGTGGACGTGGGGGAGTTGGTTAGCAG GGGCGAGTAATGGTTCTGTGGCGTGGAGCTGCCACTGGACGGCGAGGTGG TGTTCGTGTTGGTGCTGGTGCTGTGGTTGTGCTGGCCCACCAGCGAGCCG CAAGCGACGGTGGAGTCGATCGACGGATGCGAGTGAAGTGACGAGGCCGT CGAGGATATGGAATGGGAGCGTGTGGCAGTGGCTGAGTGGTGATTCTGCT GCGATTGATGATGCTGCTGCTGCTGCTGGAGGAGCTGATGAGAGCCGGTG GAGTCGTTGGAATGCTGGGAGCTGGTCGAGTCAATGGAGCTCTGCTGCTG CAGAGGCGGCGTAGAGGGCTTCTGCTGCTGATTGGTCTGCTTCAAAGCGG CCATGGTGGCCAGCTCCGACATGTTCACATAGGTGGGCGGCGTCTGGGGC TGCTGATTTTGCTGCTGCTGCTGCTGCTGTGCATGATGCGCTGCGGACAG CTCTGTGTGCGGATGATGTTAGCAAGGACATGCGGGTGGACACGGTTATT AGTAAGACTGATGGGATTAGCCAAAGGCAAGCGTGCACACAAATACACGG AGACAAGCTGGGCAATTGCTGGTCATGGCGCACCACCTACCTTTCGTGAT ATGAGCCGGAATCGGCGAGGGGCACTGGCGCTGCAGCAGGTTATTCCCGC TACCCTGGCGGTGGTTACTCTGGGCCGAAAGGGGTCGCTCCAACGACGAG CAGCGCTGAAAAGTGGGTAAGTCCATTGGTTAGTCACGGTGCAAATCGAA ATGTTTTGGGTTTAATGATGAGGCGACTTAAAGGTCCTAGTTGTCAGTGG TCTAGCGGGGCGCATGCAGATGAGCGCGCTGTCGGATCTACGATTGGTGG GGCTCTGACTCTGGAATACTCACCACATGGGCTGGCTTCTATGGCGAGTG TCATGGCCAACAGAACGAGAGAGACAACTTAATAGAATGTACAAAATCAA TAGACGGTTTACCGCCTATTCGAATAGCCTCCATCTATAACATCGCCTAC AGTTAATATCTAAAGACTAACTCAAATATATTTGCCAAACGCAAAAAACC ATAAATAATGTTTTTGAAATCTTGGATTTGTTGGATCTGTTGGATTTTTT TTAATGCAACTCTATCTTTAATTTAATTTAAGTTATTAATTTTAGTTGGT CTTTGATTGTCCAAGTGCGTTTTCTCTGCTTTATGACCAGAGAAAAGCTT AAACAGACAAGAATTTGTCTCATTTTGTAATGTACTATACATATTGTCGT AATAACCAATTAAAAGTAGTTTAAATATTTTATTTTATTTTTATAACTAA TTAGTTATTTTATAACTAATCCATACTTACAACTGGCAAAGGAGGCCGGC TAAGTGAGGCAGCCGGTGATTTCTGGGTGGCCGGAGTGGCTTGTCCGGAT AACGGCTGTCCATTCGGGGCTGCTGTTCCGTTGTTCAGGCAGCTGCCCGA CTCGTGAATGGTCTCCGGGTTTTGGAACGTGTAGACGGTCAGCGGCGGAC GCTGGTGACCCTTTTCGTATGCCGTCGAAATCGTGTGCGGACGGTCAGCG GTCGGTGGCAGGGTGTCGACGCCATCCTGGGAATGTGGGGGCCAGGTGGA GACATTTGCCGTCTGGTTCGTTGCATTCGAAGTCTGCGAGGAATCAGCAG AGTAGTTAGTAAAATCAGGGCAGTCAAAGATTTCGCGGAGAAGTATTTGT AATTTGGTCAAATTTAACAGAAGAAAATTAAATGAAAACCTGTGTTGTTA AAGCTGGCGATGAGCAAAAGCCACTATCACTGGATTCACCAGGTTTCAAG CGAATTGCGGGCGTTACAAACTAAAAAAAAAACAAAAACGAAACACAAAA GAACATTGATGAAAACCAAGAAATGAGCGGACGCCACAATGCCGAATGCG GGTTTGATGGTGACCAGGCAACTAGGAAACCCTCTGGCATGACGCACCTG CGAAAGGGAGCGCGGATAGTGATGGTGACCGGGCGAGTTGCTCGAGCCGC TGCTGTTCATACTGCTGATGGAGCAGACGGAGCTCTTTCGGGAACCCAGC GAGTTGGAGCAGCCGCCGCCCTGCGAGCCGGAACCGCCACCCGGGGACTC CGGGTACAGATTAATGCTGGCCTTAGCGTCATGGATAAGCTCCTCGGAGG CCTGGGGCAGAACACTAGGCTCCTTGGTTACTAGGGCAATTGACTGCATG GCTTCCTGTAAAATTTATACTATTAATAGTAACTGAGCTGACAATGCATA CACCGCTCTACGCACCTGTAGGTGACCCAACTCTGACATGACCTCGCACT CCTCGTGCACCACTGGCTGAAGCATGTGGACGAAGCTGCAGTAGCGCAGA CGCTCCTCCACCATGGCCGCCCTCAAGGATTTCTTCTCGACTTCCTCCAA TTCTGCCCGGCGCAGGGTAACATCCTGCATGTGCGAGTCCATCAGGGACT GCAATCCGTCCGTCTGACCCTTGCGCGCCTTCTTCTGCAGGCGCAGTGTG TCGCTGGAACGCTTCTTCAGTTCACTGCGACAGCGCTTATACTCTTTGGC ATGGTCTTTGTCGATGGTGGCCACCGTGCGCTTCCAGTCCTCGATCCTCT CCTGCAGCGGCTGCACCAGGCAATCCATAATGGTGCTGGTGAAGGTCTTC AGACGCGTCTCCACCGCCTTGTGGCGGAGGCAAACGCGGGTTAGGGCGGT GCCGATCTCCTTCGAGGCGCCTGCAATCGAAGGAATACGAATTATCATTT TAGATCAAAGATTCCATTGGAAACTATATTCTTTGACTGTGGATGATTTC CCACAGCCAAACTTCGCGAAATGTTAAAATCCAATGTTTTATTCAAAAAG TTGTCATGTGTGTATTAGACGTAGCTTATGTGAGGCACTAGGTTCCACTT TCCAATTGTTTCGCCATCGAATGCCTAGAACTTGTATGTTTCGTAACCCA AATTTAGTTGCGACTAAAAAACAGTACGATCAGGCAAGTAAGCATGCAAT ATTAAACAGTTGCCAAATTAAATTACTGGAGGGGAACCATCCACGGGCCA CGAGGAATTAAACTGGCAGCGGAAATGTTTAGAGCATGCAGCAACCATCG CACGCCATGGGCTGTCGTTTCAATTTGGTGGCGCAGCAGACAGCATTGCA TGCGACACGAATCGGGACTCCATTCCTCCAGTCTGTGGTCCCGACTCCCA AGTCCCAAGTCCCAAGTCCCGTGTGTTAATGCCATGCCACAGATAGAATC AAAGGCGGATCCGGGACAACTGGTCAGGCCAACAGCTACTGCTCTTGCCT CTGCTTCTGCGTCTGCATATCACGAGCAAATGACAGGCGGTCCGATTATC TCGGACTGCCTCCGACTCAAAGACTGACTTTTGCCATTCTCGTTTAATGT GTAATTATCTACCAAATAGGCAGCAGCTTATGCATTCTCCTTTGACATGC CGGTTCTCTGAGGCACTTGCTCCAAATCCCAAATAATTGAATGGATATGA GCTGAGTGCCCAGAAACACCACCACCTTGACGACCCATCAAAATGACCGT GTGCCAAGTGCGAATCGAGAATCTACAACCGAGGCTCGAGTTGCGTTCCA CCCTCGTTTGGGGCGTCACTATAGGCGAACTGACACTTGTGCCGATGCTT GACCGAACTAAGTCAAGTAACCACTAAAACTAATGAAACCATTTAGCAAG TGCAAACGACCAGGCCAGCAGGCTTCTGGTGTCCAAAAGGGGTGGCTAGC CCTCAATGGCAGGAATTACGAGGATGTGCACTTAACACCAGCCACACACC AAAGCCATGGAGTAGCGTTAAGAGTATCAAGTACCCATGGCGGGAGTGGA TCAATATATGCTAATGCCAAGCTACGTGTGCGGATGATTGAAGAGTTAAG TCTGCCAATCCAGCAGCAGTGCTAAATCGGAATTCAGAAGCTTAACTGAA TAAAGCCGGTTTGCCGTACAAATCTCATCTACAGTTTTATCAATCAACAG CAAATACGTATAAAGCACTTAATTTATTGTTATTTCCAACTGGAATACGA AGGAAATTAGCCGTGGATAATTACTTTATGCCCCGAATTGAATTATTAAA CGGGCATTTACTACATAAATACTTTTTTTTAACTAGCTTTTACAATAACA CATCAGCACGAAAGCCTAAAAATTCACAAAAAATGCTTTTAAATGCGATA GTAAATATATTATTAAATGTATCATCTCCTCAATAGAAATGTTTTAATCG CACGACTAACTAGTATTTTTAGATTGCATGCTTATGAATATAACTATTTC ATTGGTTAACGAATAACGAATACGGAATAGTAATTAGGTGTTACTTTGTT ACCACCACATCCTACAAGCCTATTCCCTAGTTTCAGTCCGTATATCCGCG TTAAGACCTCGTTGGAATTGAGTAAGGATTTGGAACATCAATAAATTCAT GATAATTGAATAATGTCAATGTAACAGCCACATCTTTAAGCTTGAGCGAC TTCCCCAAAGCGGCGATTGGTAACGATCACAGCTCTCCCATCTGGTAATT TTCGCATTTCCCGTGCGGACTGAGGTGGGCTGTGAGAAACGGACGTCGGA CGTTGCATAATCGGGCACTCGATAAATAAATATAAATAGCAGAACCAGCG AAATGCGTGAGCTCAGACAGAACAGCAACATCGCCAGTCGGACGCAGAGA AGGGGAAAATCAACAACGTAAACACCGAAAGCATGAATGTGTATAAAAAT CAGATCGATGACCGCCGCCGACTGCGCGTAGACCCATGAATAATGAGCAG CGGAAAGCTATGATGCAGTACCTGGGCGGGGGAATGGAGGGGAATCCCCT GTACTTTCAGTAGCGGCTGATAGGCGAGCAGACCAGACGAGTCCGCGGTT TGAACTTACCTCTTGAGTTGGTCGCCGCATCGGCTATCTTTTGGAAGGCA TCCAAATAGGCGGCGATTGCCTGGATGGCGGCCCTGTGAAGAGATGAGAG CAAATACAACATCATTATTATTGTGGGACCCAGCCAGATAGATTTAATAA ACATTCTCTCCAATTGCCCGTGGGCGACATTTCAATTAGGCGAAAGCTAA AAAAAAAACACATGGAATATCCACAGTCTCTGCAGTAACTAAATATTTGA ATACCCTTTCCGATGAAATATGCTAAGAAGTAGTAGGTTCTCATACGATT GGAACCATAGTAAGTGATAAGCTAGTTTAACAAGCGCTGATTGAACTAAT TGCACCTGCTCCGCTTTTGGCGTAATATACCCACATCTAGGGTATACAAA AGTGGTGCCCATCTGGGCGTCTTGATCCGGGCGTCCTCACCTAGCGGGGA ATCGGTCAAGATGTGTGTCAAGCGCAGTGGGCAAGCACTCGGAGCGAGTT TTGGCAAGCCCCGTGATTTGAACTCGGACAACAGGATTTGGGGTAGTGAT TAATGCAGCCGCTATTTGGCGGCGGCTATATACTTATGCCCAGACATTGC CGCGAGAAAATTTGGGCCAAGTCTGAGCATAAAAAGCACAGAGAAAATAA AACAAACAAATGCCACCCCACGAGCAGAAATTTAGCAACAGCAGAAAGAG CACAAAAATAATCATAGACACATTATATGTTTTACGACTGAGTGTGAGGA AGTGGAAAGCATAAGGGCAAGCATTTAGGCAAACAAATTTGTTTATTTAC ACGCAGTTCTCGTTCTAAAGTTTTGCAACTGCGCTCGTTAGTGGGCTGCT GTTGAAATATCATTTTCCAGAATGGAGCAACCAATTCACACCCAAAGTAA ACTCACCTCAAACAAGTGTGCAGTTTTCCGGCCTTAGCCACAAAATCCTC CCACAGGGGCGAAGTGTTCTGCAACAAAAAAAGAGAGTAAATTAGTTTAA CAATTGTATAAAATATTTTTGTTCCATTATATTGGGACTTGGGAACGAGT CGTAGGTTTTACAGCCATAATTAATTAATCAAAATTTAAACGAAACTAAA AAAATGCAACTTACTATAGATGTAGATGACAAAAGTGAAAAATTTTCCAT TTAAGATAAAATATATAAAATACATTTAAAGGCGTGATTGCCCAAAAGTT CAAAGTTCATATCGTCATCGTTTTTTCGCTGGATTAAATCTAATTGAGTT TGACTTTTGTTGTCTGCGCATTTCATTAAATGCGAATAAAGCAGAAAATT ATGGTGCAAACTCAACGAGCAAACAACCCAAACATGACATCAACGAATAA GCAAAGTGAGAGACACATTTAATGTAATCAAAGTGGGTGAGCTCCGATCC ATATGGCTCCGATTGAATACGGAATCGAGCAATCCCCTAGGGGAGATGCT TTTAATTAAGTTGCTGAGGTAATCTGGATTAATCAAATTTGCATATTAAT AAGACTTCTAGTAAAAGAGCGAGAGTACAAGTCCAAAAGAAAGTCGTCAT CATCATTATAATACAAGATGGATTGATTGGACTTTTATGAACATGGGGAA GTTTCGTCAATAATCCACAAGTTCTCCCCTCAATAATCACTGGAAGCTCA TATTTGGCCAAAAAGCGAACTGAAATGGCTCCCACATGGGTTTTTCTCAC ACAATCCTGTTCAGCCAACTTACTTATTTGGTCAAGACCACAAAGAGCTG CCGCTGGCTTCTGGCCAAGTATCAGTGTCACGATGGCCGAACGGCAGCAG ATTGTTAAGAGGCAGCCGTAAAAGGCCGCCAAAGACTTTATGTGTGCTTC TTTCTTTAAGAGAAATAATAGCGAGTGAGGACGCGCAAATGGTCAATAAA AGCGAAAACGAGTTTTCGTTTTGTTTTGTTTTGGCTCGCTTCAATTACAC AACATATGACATTGAAAATAAGAGCCAGACGAGCGAAGCAGCCAAAGATC GAAAGCAGCAGGAGGCGTCTGAATGAAGACATAAAATGTTCCCATTTGGT GACCACTGTGATAACAGGAGCAGATTCATCAAGCCCAAATAGCAACTGCC AATTGCAGTTGCATTTAACTTTCGGTTTTTGCGCAATCGGGCAGTAATAA ATACCATTAAAATGTCAATTGCTAAATCAAAATCGATTTCAATGCAAAAT GCCCAAAAGAAGCCTGAGCTCTGGGCCATGGCAATTGCATAAACAGCACT GCTCAAAGGTAAACGAACGAACGAGACAATGGCAGCGGAAAAGCCGGGAA ATGCGCAAATAAATGCAACAGCTCAAGCAAAAACTTAACGGAAATCGATT TTTGGCTATTTTTGCCAGCTTTTATTTATTTATTTTTTTTTTTTGTTCAT ATACTCGTTTTGCCATGCAACCACTGGGTGCAACAAAAACCCTAAACAAT TGCCAGCTCCACAAAAACGAATTGAACGCGGTATTCAAGCGATGATAACG ACTTCTTTCCCCCTTTCACAAAACACCACATGCGACATGAAATAAATAAT AAATTGGGTTTGAAAAAGTATGTTCGAAACTATTGTATTGGGAATTCGTT CGTTTCAAGTTAAGGCAAAAATACAAATACTATTGATAATAACACTTTAA GTACTTTTCTCGTGATATCACCATCGTATAGATTTAAATAAATTCAAAGA ATGTGATGTGTGGGATGATAGAGAAATCGAGGAAAATCAATAAATATCCA AGAAAAATCGCGACAGAATAAATTCCAAAAAGACCAAAAGCGACCAAAAT TTTTCAAAGCCTATAAGCTGATTTTTTCAATGATTGAACCACGTTTCCAA GACGCGGCCCACATGCAAATTATTATTGTTTATTTGTTGCAAAACCATTT TTTGTGTGCGACAGCCGACCGCCAGCGACAGCTTGATAAGCGGTTCTTGC CTCGCATGCGTGGGCAGCGTCTTGTCGGCGTTTTGTGAATGAGCATTTTG TAGTCGTGGAGCGATATAGCCACCACCAATAAGCCAGCCATCCACTCGCG GGCCAAAACACGCGAAGCTGTCATTACGTTGACCAGGCCCAAACCATTCG CGTCCGCGTTGGCGTGGATGTTGTGTTTCGTGCTAGCGTTGGGAGAGAGC TCAGCTGGTCCTGATCCCAGTGTTCGGGCATCGCCTTATGAATGGGCGAG TGGAGCTGGATTGCCTAGCAGCCAGACGCATAGTAAAAGTGCCGCAGCTA ACAAAACCCCTTTTCAACTTAATTTCAAGATCCATTTAGTTAGCTACTGA AATTGTTAAATGTTTGTCTTAGCGGTGGTTTGAATGCATTTACTTTTTAT TCATTGTCCTCATATTTCTAGAGTATTTACTGTTTACTGTTTAGTAACCA GTCATCGAGCTGAAAGATCTCGTTCCCGCCAGTTCGTGGTTGTATTCAAA ACACTTTCCAGTTTCCGTCAGACATCGAAATCGAGTCTAAGCGCAGGGGA AGACAGCGAGTGCAATGGACGTGGTGCATCCATGCACATATAGTACACCA CAACCGCTCCATGTGTATCCATTTATCTTGGCAAGCCAACTCGGCCGGGA AGTGAGCTAGACACCTAAAAACCCACAATTTATGCCAGTCAGAGCAAACT GGAAAAGTTCACACAACCACCACGAGGAGACCCACACCCATGCACACAAC ACACAGCTAACAACAAACGTGTGGCTGGCATTATAAACTCTTGATCTTTC CAATAGCCTACAAAGGCTGCCCACACGGACCGGCTCTCCAGCTGGTTCAC AGCCCCATTCATGCTGCAATTTTGTTGCTATTTCGGTGCTGCTCCTCGAT AAGGCCCCAAAGATTCCCAGCAGCGGCTAGGTGGATAGAGGCGGAGATGG CCAAAAAAAACGGGTTCAGAGCCATGCCGTCGCCACGTCCTACATTGCCA GCTTTTTGGGTTGGCGAACAAAGCCACTGCCTCCAGAAAGAGCCGTTTCT TATGCTAAATCCAAGAGCCTGCCTGCGAAGCAGAAGTCCGCACTGATTGA TTTTCTATGAGGTCCGACGTACCATATACTATATAGTATAGTGAGTGCCC GCGGCCATAATTTCGGCTTTGGCCAGATGTTGACTTTACCGGATTGCCCG GAGCGGCCTGCACAATCGTGCGCTGCTAATTTGCACCTAAAGACGGTCTT TGTTTCTGGCTCTTCGGTTTAGAAAGTAGAAAATTATTCGCCGGGAATAT GAAATGAAAGTGTTCCGAGGCTTACCTCCCTGCCGTTTAAAAGTTTTCGC AAATCTGTAAGAAACATTTTCCGTGAATTGGCAAGAGCTTTGCAAATTGA CAAATCGATTGCTGCGATTTGAATCGATCGGAACTTATGCCAATCATCAT CGGGTAATCCAATAACCGACAATTGTATTTGCATATTCCCCATCCAGCAA CGGCAGTCATGACCCCAAAAAAATGCAGTCAGTATACGGTTCTCCTTTGT CTGCACGTCGTTACCCGAGAAGGTACTTGCCACACGCAGCTAGCCGATAT GGAAACCGCAACTTGAACTCAAGTTGCCGTCAACGCGTGCCACCAACCAC AAAACAAAACGAATCAAGAAGTTAACTGATTGGGGATATGGAAGGTAAAA CAAGCCCCTAAAGTTATGAGATCTGTTAAAACACGATGCAATGTTTAAAT TGTTATTGAATGTAGGAATTAAGAACACTATGTTTAATATTATACAATAT TGAAAAAAAAAATACACATTCAACAAAATAGTCTATTGTTCCAACTACTG CAACTTTAGTGGTTCTCCTATGATCTCCAAACAAATTGGGTTTGGGCGCG GTATATTCCTCTCATCTAGTGCGTTAAACAATATGACAAGTTTATGACGT CCTCTAAGAAGAGGTCCACGAAAATTCTCAAATTTTAGTATGAGATCGAA GGGCTCGTGTACCAGAACGGTCTGTAAGAAATCAGAATATTTTCAAAATA TTGTGCAATAAAAAATGGTAGTGTCCTTTGCACACAACCATATGAATAAT CTGCATCCCATATGAGAACTATTCCCATATGCTATTATATTCCACCGTAT TTGGTTGTCAAATTGCTTGAACTCCACTTACATCAGGCCCTCTGAAGCAC TTCTTTTCCACCTCATGGCGATTGGTTATAAACCTTGTCCAATACTTATA CCAATACTGGTTCTTGTCGTACATGATGGAGCAAAAGTTCTGGGTGGCCA TGCTAAAGACAGTGGGCTCCCAAGTGCCGCGGTTGAAGTGAAAAACATCA AGTCTCGCCTACACGGATGCAAGAGTTTTGATATTAGAATCGATGATTAT TCCGAAGCTTGCAGTTTGTGTTACAGTAATCCGATCGGTGGGCTGCACAT CCCACACGACGGTGGCGTTCCCGGATACATGAAGTATATCCCCTTTCTGG TCGATTACAATGTCGTCTAAGTTGAGTGCCTGGCGGATGTTGATGGATCC GGGAGGACCATCAGTGCACGTCGAAAATATGTCCGGATCCTCGAGCAATA ATTCATAGTCTGTGGCCCAGGAACTGGTCACTCCTAATAAGAGTAGCAGC ACAAATATCATGATGACCATAGAACCGAAAACTGTGAGATCCGACCCCTT TATAGCCACTGCCACAATAGAGTTTTTGATATGTTTTATTTATACACCTT TTAAAATGATGACATCTAATCATGGTATGCCATCGTACATTGATTCAACA CGCAACAATGTAACAACCATCTCCTGTTAATCAGACGTTGTCAAACTCTA ACAATATAATTGGCAAATCACGTTATGTGACCCTTGAAAATATTCGTGCT TAAACATTGTAAAACAAGATGTTTTAATAATAATAACTTTTGGGCTAGAA AAAAAAACAAGTTTGAAACAAAAAACAAATTCCCCAAAGATTTTCTTGGC GATCACATATCCGTGTGGGCGTGACAGTTTTGGGCGGTTTTTGGTCGTTA GAGGGTGTGGTAGAGTAGGCGTGGCAATCTTCTGAAAGTACTTCTCTATA ATCTGCATCCCTTATCTTATCAATATAGCTTTTATAGCTCCCGAGATCAC ATACGGGCATAAGGTTGATCAAACGAAAAAAAAGGTTCGCGTCACCTGTT ACACACTTTGTACCAAATCAAGTACATATATCAAGTTCAGAATAGTTGAT ATATTTTATTTATATTTATATTTTTAAGATTGCTTTTTATTTTCAAAATA TGTAGATATTGGGTTTATATTGTTTTTTAGGTTACTGATATCGCGCCTTG AACAGATTAAGCCCTTAATTAATTTATCTTCTCGGCCTCTCCCCTGATTT CGAAGCAAATGGAATTACGGCGTGGCACATCCTTCTCATCGACCGCCTCA AAGGTGACCACAGCTTTGTAACGACCCCTGAGAGTTGCACCACGAATGTC CGTTAGACGCAGCTGCAGATCGAATGGATTGTGCATTATAACGGTCTGTA ATGGAATCCCAAGGTTAAAGTCACCGCGCCAGAGATGGACTGTTTTGTTT GCAGGGAAAACTCACACCACGCGTTTTAAAACACTTCTCCATCACCTCAT CGCGGTTCGAAATGTGTTTGGTCCAGTACTTAAACCACGACTGATTCTCA TCAAACATTGAGGCGCAGAAGTCCGGCGTGGCCATGCTAAATACAGTCGG TTCCCAGCTGCCGCGGTTGTAATGCATTATTGCAAACCTGGCCTTAAAAG CAATTGTTTATTAATAATCTTATTTCGTATAAGGAATGCGGGCATTACGG ATATGCGATCTGTGGGCTCCACATCCCAGATTGAGGTGACACTCTCGGAC AGGTGAATGATGTCCATGTCCTGGTCGACTACCAGATCGCCAATATCGAA GGCATCGTGGAATCCAATCGATCCCGGCGGCGGTTCAGTGCAGGGTGAAA AGATATCAGGGTCCTCCAGCAACAGCTCGTAGTCTGCGGCCCAGGAACTA GCAAAGCCAAATACGAACAGCATGAGAGTTCTCATGATGACAATAGTATC ACCTGGTGGGATGAGACCCTTTTATAGTACTTGCCATCATGATCTCTTCT ATCATTGCTATCATGTCATCATGTATCCACTCGACATGCAACAAAGTTAC AACCATTTTGTTTGCCAGACATTATTTTAAATCGACATTTAAAGCAAGAA GCTCACTTCAACCATAACAAGTTTCGAGGAAATCAGTGCCAATGAAAATA GTCCTTATTAAACGATCAAAACAATCATTCCTGTTAATCTTATATTTATT AAGATATATAAGCTAAATACTAAAGGTTTTAGCCATTAGCATAACAACTT GTATGCCAAATAGGCATTTAGATTGTTATACTTGTAAAAGTATAACCTTT TGTTCTTCTTGAATTCAATGCTAAAATCTTTGTAGGCTCCTTGATTAAAT TAAATTTTTACTTTTTTCATCGAAAATTAAACGATTTCATAAATTCCGTA ACTATTTTGCATAATTGGGTGCGACAACTACACACCTACAACAAGTCAAA TGGACACTTTCCGCAATTTAATCACAGCTTGTGAATCACAAGTGCAATTT CATATTCATTTTAATTAACTAGCCTTGGATTGCTGTTGAAGCTGACATCA TACATGCAGAGCACTCGGCACAGTTCAAAACACCAAGTAAGCTATGCACA TCAGTCGTTCCACATTAACAGAGGGAACAGCATCTAGAATTGTTCCCGCA AAGTTATTTATGGAATAATGCAAAGTAATTAATACAACTAAGATGATTCT CATGCTCTCCAATTGTTTGTGGAGTCTGAAGGGGAAATGCATTCCGCATT CTTGTCTGATCTCAGATTTCACTGTCTCCATGTGGGAGGAAGCAGGCATA TGGAACGGGTTGCAATGGTGACCTGCGTCAAGATCTAAACAAAAAATGAT TTGTATATTTTATCCATTTTTTCCGAACATAGCAGCTAGACATAACAATT GTACACATTAACACAATTGTTTTCAAAGCTTAAGGACCTTGCTCCACATA TGAACTGAATGATGGCATCCTGTCCACATCCTGTTCGGTGCCACAGTGAA CTGCCACTTCCAGTTGAGATTCAGCCTTGAAATGGCTTTCAGACTTTTCA AACGCGCCAACGCTAGAGGGACAGGGGGAAGCTCACGGGGCATTGTTATA GAAATGGAAACAGCTGCGAGTGCTGCCATAAATAAAAACTTATTAGGTCT TGTCGATGGTATTTCACTATATAGTAACTCGTCTATAAATAAACAAAACA TAGAAATTGACTTTCGTCTTATAGCCCACGCAACCCCAGGCGTAAGCCAA ACGCACAGAATCGAAAAGTTCAATGAAAGCAATTAGTGAACATTTTTAAT AAAACTATTTTCTAAATATAAAAAAGAAAATTCGCCCAACGTGGGGCTCG AACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGC CGGGCACTTGTGAAGATCGCCGATAAAAGCTCACATTTGCTGATTAAGCT TAAGAATCATACAAATTGATATAAAGAGAATTTAAAGGATCAAAATATTA CCAAGAGAGAATCAATAGCCTTTTAAAAGTAGCCAAAGAATTGTCGCCAA TTAGCTTGCAACAAATAAGTTTAGGCCCAAATTTACTTTACATAAATTAC ATTGACAATATAGAATATTTATCGTAAATATTCAACTCATAACAAAACAA GAGAAAATGTTTTAGTCTAGTTTCCCGACTATCAGATACCCGTTACTCAG CTAGTGGCAATGTCAACTAGAAATTTCCTTATTTTTTCTGGCTTATCGAT TGATATTGGGGAATAATATGAGAAAAACATAAGAAAATGGTCGCAAACGC TTCCTTCTGCCTGGTACATACTTTTTAACGAATATAGTATAAGCAAAGAC CCTAGAATTCTAGTGTTATTATAGTAAATTCTAGTTATTCTAGTGTCTTT GGTATACGGGTATAAAAATTATAAATTACTTCTATAAACACATTGCTAAA TATGAGAAAGCATATTTATACATGCGCATATAAGCCGGATTAAAGGCAAC GGGCGCTTTGCTGTCAAACCTAGAAACATTGTTGTAATACCTTTAGCCTT TTGTTTTATTCGAAATGGTTATGCAGATTCACAAGATGCATTTGTATCAT ATATACACAAACTATTTTTAGCTTCCAAATTAATTGGGACTCATTTTAGG CAAATTAAATATGCTTAATAATTTTCCAATTAGTAAAAAATCAATTGCCG AAAGTGGAGCTCAAAAAATGTTTATTAATTGTATATTAATTTTGAATTAA AATAAAAAACATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTA AGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCATGTGTTCTTGACAT CTGACTGTCAAAATCATCGAAATCGTAATAGTTTTAAATTTAAACTTATA CTATAAGCTTAAAGAATAATGGTGGTATAAAAACCCTGTGGTGCTAAAAA CAAGACGAAAGCGTATTGACTAGTCCCTCGCCCATCTAGTCAAGTTTAAA GCCCATTTGCATTTAGATAAAGATCAAGCCAGCTTATCCTTACATGCATT TTTATCTACCTATTTAAAAATAATTCTATTCAGCAGGTTTTGACAAGATA AATAAATTGTAATTTATAGATAAATTGATTTATAAAAAATCATAAACCAT AATAAATCATTTATATAATTATATGTACATGAGCACATCGGCTTTAAGCC TAATTAGTTAAGTAAAGGATATGTGATAGTCGAGAGTCTCGACATAATGG GTTTCCTCTGGTAATCAATTAACTATTAAAATTTGTATATTTACTACAAA ATATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAG TCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACAAAATTGCCGT CTGTCAAAACTCGGGAAAATATATCAAATGGGGTTAGGAACTATAGACAT GCGTCTAGTATTTTGTTTAGAAATGAAAAACAAGATAGAATTCTAAAGTC GTGTTCCCTGACTATCAGATACCCGTTTCTCAGCTAGTGTGAATGCGAAC GCGAAATTTCATAATTTTTCTGGGATATTGATAGATATAGAAAAATTGGA AAGGTTTAGAACGTTAGAGTGGACGTGGCAAAAAGTTTTTTTTTAGCAAA TCTATAGAAATTTAAGCAACTAATAACATTATGAAAAAATGTCCAACAAT TTTTCAAATATATGTGGGCGCAGCCGATTTTGGCGGTTTTAGGGCGTTAC AGTGAGCGTGGCAGCATGGGTCAACAAAATTGCCCTGCGTCTTTGTCTCA AGTCTCTAGAATCTGTATGCTGAATCTCAACCTTCTAGCTTTTATAGATC TCGACGCTCATACGGACAGACGGGCATGGCTAGATCGACTAGGCTATTGA TCCTGATTAAGAATATGTCTACTTTATATAGTCGCAAACGCTTCCTCATG CCTGTTACATACTCCTCAACCAATTTAATTTACGAGTAACGGGTATAAAA ATCATTTTTATATATAATTACATCCATCCATGTTCGCATATGCTTTAAGC CTAATTAGTTAATTAAAAGATATCCGATAGTCGAGAGTCTCGACAATTGA TTTTCTCTGGTAATCAATTAACTATTAAAATTTGAATATTTACTACAAAA TATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGT CTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAATGAATTTGCTGTC TGCCAAAACTCCGGAAAATATATGGGGTAAATGGGGTTATGAACTTGACA TTCGTCTAATATTTAGTTTAGAAAAACAGTCACGCGAATTTTTAATCGAA CATACTTATTTTCGTGCCAAAAGAGATACGCCCTTTTTAAATTATTAAAG ACAATGATTTTATCATATCATAATCATATTATACTGTGTGCAATTAGAAT CATAGACGACCCCTAAGCTGTATATAACGTGCAGTTTTTAGCACTATGTA CCCATCCTCATACTGGAAAGCTTGTTAATATGAAGGCTACTTTTACAATC CTGGTGCTCCAAGTGGTCATCTGTTTGGCTGGAGCGACTGAGTACCAGTT AACATTGGACAAAGATGGCTTGTTAGCACCATGCGAGAATCAGCCCGGAA ATCCTTCTGGTTTTGAAGCGATGGTGGATACTTCCTCCCTTAAAGTACAT AACCTTGGTTCGAAAGTTCGAATTGAAGGAGAGCAGAAAGTGGTCTGGAA AGATGTCCAGCCTGGAGACACATTAAAGGCAAGTCCCTAAGGAAACTTTT CCTAATAAACTATTTGAATATCGCGCAGGTATTTGGTCAAGTCTATCGCC TGGATAAGGGCACTTGGCAGAAGACTATGTTTACGGCCAGCTCCAATAAC TTTTGCAAAAACATGTTTGATAAGAACCAATACTGGTATAATTTCTGGAC AAAGTATATTAGCAACTCCGACGAGATTAAGGAAAAGTGCTTGACCACAC CAGGGGTAAGAAAATGTACCTCCTAGTTTGGTCACTGGTCATTTCTCATA AACACAATATTGTAGGCCGTTTTAAAGTACAAAGACTACGAACTGGACTT GAAGACCAGCTTGAATGTTCCGAATCTGGATGGGCGCTACAAGCTGGTGG TCCAAATAGAGGCCTTCGATAAGCGCAATGTAAGGCGCCCAGTTCCCATT TGCATAGAGTTCCGTGGAACTGCAGGACAGGTCTAATCACGACAATTGTA TATGCATGCTGAACATACAGCGAAACACCATTAAAGTCTATAATTGGAGC ACATCAAACAAGGTGAATAATGGTGGTGAGGGGGGGGAGGGTGTGGTGTT GTTGTGTGTCATTACACGGGTCGCTAAAGTTGAATGCGAACTTCTGAACT TCTGTTCAGTTCATCATGGAATCCAAAATGAGTCGGCCGAAGCAACCGGA CTGGCTCGCCGAGCTGTGCCAGGAGTCCTCCATCCACGGCATGCCCTACA TCGCCCGCAGGGATCTACACTGGGCCGAGCGCCTCTTTTGGACATTCATA ATCCTGGGCTCGGCCTACTACGCCATCAGCAGCTGCCTTAACCAATGGTA CCGGTTCCGGGACAATCCTATTGTCTACGAGTACGAATATCTCTTTGGGC TGCGCATCTTCCCCTTCGTGGGGATAACACTGTGCCCTAGGTACCACGAC GAAACGGAGATCCCAAGGCTTATAAATCAGTGAGTGTTTCGATTTACATT GGTAAATTGAAAGCACTAATATATTATAAAATATCAAGAACTTGGGGAGT GGATCCCAGCGAAGACAAAGAAAAAGCTGTGTACTACAGAAAGTTTCTGC TTGCAATCAACGGCCTTCGTTACTCCACTCTGGAGACGCTGGAACCCTTC GAGAATGATACCACTTTGGACAACGTGAATTACTTGAACATTTTGCTCAC GCTGCAAAAAAAGGTAATAGCGGTTAAAATCCCGCCAGAACTGGCGCCAA TCATTACTGAGGTGGGTCTGTGCCAAACATCCAGCCAGTTAAACCGATAC GGAAATCCCTACGGCAAACTGTAAGTCTGCGCCTAAATAACATTAAATAT AAAACAAAAAAAATAAATTATTAAATAATAAAATAAATAAGCTATTCTTT CTTTAATTTCGCTTTTTGCTTTACATATTTTTTGTGCCCATCAAGAGAAT TTACATTTACATTTTTACTTAACGCTTTTATCTAAGAGAAACACAGGATA TGGAACCCATGAAACAGTGCGGCTATTTGAGTAATTGCATCACATCTCTG AAGCCTATAAATAGCATTGTTGCCCCCATATTTATGGTAGGCAGCATTTA TCATTCTTTTTTGAAATACACTGTTAAGCGAATCCAACTTTACAGTACCT TCACGATGTCGAAGAAATGATGCTACCCGACGACATGCGAACTCCCTCTT TTGATGCTAAAGACATCGAATCCAAGGATCTCGATATTATGCTACATACC ACATCGGCGGAAAGCGAGGTGCGAAATCTACCGGTAGCATATCGCAAGTG TCGCTTCAGTGACGAAAACAATCTGCAGTATTACAGTGTGAGTTTTAGAC CTTTACCCGTACCAATTGCGTCCAATCAAAACAGCAACATGTCCTTTTAG CCCTACCACCCAAGTCTTTGCCGACTTGAGTGCCGAATCAAATGGGCCCT GAGCCTGTGCAACTGCAAGCCCTATTTCTACGTAGCAGCTCCCGAAGTTC CAATCTGCACAGTATCCGGAATGCTCTGCCTAGCCCGGTCCAAGTGGCTT GAAAGACCATGCGATTGCTATCCGTCTTGTCGCGAGGAAACCTTTACCAT CTTCAAAGTGTCTGACCAGACTGGGGTGGGTGAAAGAATGTTGTATCCTT AAGCCCCCAATTATTGCAATTTAGAATTTACTTTCTTCAGGGCGATGACA ACTACTCTGGCGAGAGGTTCGAGCGGACGCTGATCATCAACCTGCAAATT TCGAGGATGGGCATAAATCGGCGGGTTGTATTCAGCACGGATCAGTTGAT AATGTCGTTTGGTGGAGCCATTGGCCTCTTTCTTGGAGCCAGCTTCATGA CCATATACGGCGTGGTATACTTTTTTCTAACTTTCATAGCTTATACATGC AAGAACCGATTTTGCAAGCGTTTTTTTTTTTAAGTAATTAAAATTGCTTC TTAATATATACATATATATGTAGGTAATGCAAATATATACATATAAGTTA AGAACCCTCTTCTTGCGCTCTTCGTCAGGACTCACCAGCGCTCGGCTCTC GTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCTGTCTAGTAACATG TTCGTGTAAGTTACGAACCCTCTTCTTGCGATCTTCGTCAGGACTCACCA GCGCTCGGCTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCT GTCTAGGAACATGTTTGTGTATGTGTGCATTCGGAACAAGTGCCGTTGGT CGCACTCAGGGTGAGGGGTCAACGGGGGAAGCGGATATAAAAGCAGCGGG GCGGGAGAAGAGGTCCCAGTCTCGAACGGACACATAACGGAACCGCTAGC AGATCGCGAACTGAATCTTAAAATAAAGCTAATCGTAAACTCGAACCCTC TTAACTATCTTGACTATTATTTGGAGAACCACAGCATGTTGGTTGTCATA TCAAGGTGAGGTATGCGGCAGCGAGTGCCGAGAACCCTGATGCAAGTGGA ACTTGCGTTAACTGGCGCCCGAACAGGGACCGGCAATGTCCGGCCGATAA AAGTGATACGAAAAAATTGTGGAAATTTGTGCGTAAAAATAGTGGTGGTG TGCATAAGTCAGATTAAGATCTGAAATCCATAAATGAAAAAGAAGTGCTG CGTGAGCTGTGTATAAAATGATAAAATAGCAATTACCCGCTGCCGGGGGG AACTACGCCCATCCCGGGGCGCAACAAATATTGCATAATTCAATAAAAGG TGTAAAATTTCTAAAATAAAAATGTAAACCTATGTTGCGCCAAGACCTAA TTTAAATTAATAAAACAACGACCCGCTACCGGAGGACGCCACGTCGCCCA TGCCGAGCGCAAAAGTTGTACGATACCTATAACATAATTAAAACACGATC AACCCACTGCGGCGGTACGGCTTGTGGGAAAATTTTTTTTTTTTTCTCTC CTTGCCAATTCGCGAGTGCAAAAGATTGTGTATAATAAACCAATAATTAA CCATTGCAGCAGTTTACCTGCGGCAGTACGAGTAATATGAGCGCCCAGAG TGATAAGGTGGTGTGTGGCAGCTTGTTGGATACGTTAAGTGGTGTGGAAT GCACCCAAAAAAAACCGCCCAACAAGTTGTGTGGCGGCCGTACCTTAGTA GGCAACCAGCCAAAAGGGATACTACGGAACCACCGTGCCCAGTGCCGAAA TAAATTAGAGGTCATCAATAAAAAACTGTAACAGCACGCACGCAAGGAAA AAATATTGCAAAATGGAATAGCGCACAAAAATTGTATAAACACATGCACA ACACCACAATTCAAAGGAAAACAAAATATTCATGCTGTAGGGGTACAACC TAAACGACGAAAACTAATAAAGAGCATACAAGGGTGAGTGAAATATTTCA TTAAACTTTATTGCCATATTTGCTAAATTTAGAGAAATAAAGAAAAAGCA AAGAAGAACAGATATTCTTTTTTATCGGGTTAAAACCGTTGTCTCACATT TCCGTAAAGTAATAACGAATTCTGTTGCCTTGAAAGCTTCCTGCATCTTT CCAACGCAAACTAAAAATCAAAATGGAAGAGACCCTGCGTGCTCTTAGCG AGTCCCTCAATGCCCTGACCAACGTGGTGACAGGCATTAAGGAAGATATT AAGAAAAATAATGATAGGTTGGCTATTTTAGAACAGGAGCGCGGGAACGC TGACCCTACGGTCGACCAACCGCAACCCCTGGTGCGCGCACGCACCGAGT ATGAGCTGAGAGAGATATCGGTCCTCCCTGACTGCGTCAAAGAACTGCAG GCGTTCGAAGGACGGCAGGAGGCTTACCTGTCTTGGATAAACAGGGCACA GTCAATACTGACCGAATATGACTTGATTAAAACCAGACCCCTGTATAGGG CAATTGTCTTGCATATTAGACAGAAAATAAGGGGACACGCCGACATGGCC TTGGCGGCCTATGGCGTCCAAGACGACGATTGGGACGACATAAAACGAGT CTTGGCGCTGCATTACGCAGACAAACGAGACTTACGTACGCTTGAGCATG AGCTTGGCGCTATGTGCCAAGGTTCTAGACCACTAGATAGGTTCTATATG GACGTTAATGGCCATCTCTCGTTGATCTTAAATAACTTGAAGGCCAGAAA CCACCCTCGTGAAGTAGTCAACGCTTTGATAGAAACCTATAGAGACAAGG CTTTGGATGTTTTTATCCGAGGAGTGGGGAGAGATTGTTCCAAACACTTA CTTGTCCGCAGCCCGAAGAATCTACCAGAGGCTTACTCTTTTTGTATGGG ATTGCAGAATGTAATGTCAAGAAATTTCACAGCTCAGAACTATCAACCGT CAGGTGCCCCAAGATTCGCAGGCCCATATCAACATCAGGCCAGGCCACCG TTCCGAACCCCTTTTTCTCCTGGTTCAGGCAGATTTTCGCAAAACTCCTA CAGAACTCAGGGTCCTAGACAGGCCATAAAAATGGAATCCAATCGGTCGG GTCAATCTTACCAATCAGGATACAGTGGTCGCCAGGAAGAAGGCTCCGGT ATTAAGAGAATGTCCGAAGGAAACAACCCATTCCAAAAGGCACAAAGATT GTACCACATGGAATTGGCACCACCCCCGCTAGCCCCGGCGGCTAGTGGAG ATAACCAAGGACGTTCACACGAGGGTTACTATGATGACGAGTCTCAAGCT GTCGAGAGAAGCAACAATTATCCTCCGCAGAAAAACGTGGAAGGAGTTAC AGATGCTCCACATAACCTTGAGACTGAGGGAGGGGCAAATTTTATGACCA ACGCCTCTCCAGTGTACCGTACTTAGAGTATGCTACGGAGAGGGGAGAAA GGCTGAAGTTTTTGATCGACACGGGGGCGAACAAAAACTTTATTAGCCGA AGACTTGCAGCCGGGTGTACCACAGTCCGTAAACCCTTCTCCGTACTGTC CGCTGCGGGTAACATCATGATAACGCACCGCCTAGTTGGTAAATTCTTCA AACCACTAGGGAACGACTCGGATATTACCTTTTTCGTACTACCGAATTTA CATTCCTTTGATGGTATCATTGGCGACGATACTCTCAAAGACTTAAAAGC CATAGTGGATAGGAAAAACAATTGTTTGATAATAACCCCAGGAATTAAAA TCCCTCTTTTGGCGAGAGCTTCAATAAACGTTAACCCGCTACTCGCCGCC GAACACCCAGATGGTACACAAGAAATTTTGAATTCCCTTCTCGGGGAATT TCCCCGCATCTTCGAGCCCCCCTTATCTGGAATGTCCGTGGAGACGGCCG TCAAGGCTGAAATCCGGACAAACACACAAGACCCGATCTATGCTAAAAGT TATCCTTACCCAGTCAACATGCGCGGAGAAGTCGAACGTCAAATCGATGA ACTGCTGCAGGACGGTATAATTCGACCCTCTAATAGCCCTTACAATTCCC CTATCTGGATAGTCCCGAAGAAACCTAAACCAAACGGAGAAAAACAATAT CGCATGGTAGTCGATTTCAAGCGGTTAAATACCGTCACCATACCCGACAC TTACCCCATCCCAGATATAAACGCTACGCTAGCCAGCCTTGGCAATGCCA AATACTTTACCACCCTAGATTTGACTTCTGGATTCCATCAAATCCACATG AAGGAAAGCGACATTCCAAAGACAGCTTTCTCTACTCTAAATGGAAAGTA CGAGTTCCTCCGTCTACCATTCGGTTTGAAGAATGCACCTGCAATCTTCC AAAGAATGATCGATGATATTTTGCGCGAGCATATTGGCAAGGTCTGCTAC GTTTATATTGACGATATCATCGTCTTCAGTGAAGATTATGACACACACTG GAAAAATCTCCGATTGGTATTAGCGAGTTTATCAAAAGCTAACCTCCAAG TGAACCTTGAGAAGTCGCATTTTTTAGACACGCAGGTAGAATTTTTAGGA TATATCGTCACGGCCGATGGCATTAAGGCAGATCCGAAAAAGGTCAGAGC GATTAGCGAAATGCCTCCTCCGACCTCTGTTAAGGAGTTAAAAAGATTTC TAGGCATGACCTCGTACTACAGGAAGTTCATTCAGGACTATGCGAAGGTA GCAAAGCCCCTTACAAACTTGACGCGTGGATTGTACGCTAATATAAAGTC TTCACAATCAAGCAAAGTGCCAATTACATTAGACGAGACGGCCCTACAGT CTTTTAATGATTTAAAATCAATTCTCTGTTCTTCTGAAATACTGGCGTTC CCATGTTTCACTAAACCTTTCCATCTAACCACGGACGCTTCTAACTGGGC CATCGGAGCTGTCCTCTCACAGGACGACCAGGGTAGAGATAGGCCGATAG CGTACATTTCCCGTTCATTAAATAAGACGGAGGAAAACTACGCTACTATC GAAAAGGAAATGCTCGCGATAATTTGGTCATTGGACAATCTTCGGGCTTA CTTATATGGCGCTGGTACTATTAAAGTATATACTGACCATCAACCTCTAA CGTTTGCCCTAGGCAACAGAAATTTCAATGCGAAGCTAAAACGCTGGAAG GCTCGTATAGAGGAATACAACTGCGAACTCATCTACAAGCCTGGGAAATC TAATGTGGTGGCTGACGCGCTTTCACGCATTCCGCCTCAGCTTAACCAGT TGAGCACCGATTTAGATGCTAATCCCGAGGATGACATGCAGTCTTTGGCT ACTGCCCATAGCGCTTTACATGACAGTTCACGATTGATTCCCCACGTTGA ATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGT CAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATT CCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTG TCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGC AACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGG ATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGA AATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTC GTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATC CGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAG ACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCAT GTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTA AGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTC AAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTACATTACT TCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTGTTATGC CCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTATTATGC TCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCCACTCTA CGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACCTTCAAA CCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCA CTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAA GGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGAC ATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAA TAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTG TTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAA AAGGTACAGGAAGACAACAAGATAACAGTTAAAACCAGATCAGGAAAAAT TTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAA AAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGC TAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAATAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAGTTAAGAAATA CAAAAAGAAATACAAAAAAAACTATAAAAAAAATAATATAAAAAAATACA GATTATAAGAAATAAGAAATAAGAAATATAAAAAAATAAAAATATAAGTA CACAAAATGTACCGTACCCCCACACACTACGTAGTCTTAGAACAACTTAG ACGACCAGATATTTACGAATTGTCTTTTTGTAAGCGCGATTTCTGCATGC GGCGCAAATCCCGCTCACTGGACTGGCTGGGGTCGGCTTGGAAATGGGTA GCTGGATCTCCAGATGCTGCTGATTGGAACGCCGTCTTGGCCGCGCAAGC GACGGCTTCGAGGAACTGCAAAAACTGGAGGAGGCTAGCTGTATCCCTCG GCTACTGAAGTAACCAACGAGTGGTTAAGCAAGTCGACGATGGAATGCTC CTCCTGACCAACTTCAACGGAACTCTAAGAACGGCTGCAGAGAACTACGA CCTGATCGGCTCCTTTATCATCCAATTCGACAATGAGACGATAATGGTCA ACGGTCAAAACTATTCCAGTTACTCGGTCAGTCATCTAATGGCGATGCCG GCCGTGTTGAGCCACATAACGGCCAGCAACTTTCAACTTTCTCTGGAATA CGTCCACGACGTGAGCATGAAGAATTTGGAAAAGATGTCCAACATGGCGA GTGAGCTACTAGCCTCTCTTCTCACCGAGGCGGCACTCGCAATCTGCATA TTCCTAGGCTTTTATTTCCTATGGAAGAAGCTGATGTCCACCAAAGGCAT GCCCGATGTCCGCGAGATTGCCGCAAACTTAGAAGCATTGGGCCAAACCG AGCTGAACAAGGCTCACTAATCTGCGGGACGCAGATCTTGAGGGGGGAGG AGTTAAGAACCCTCTTCTTGCGCTCTTCGTCAGGACTCACCAGCGCTCGG CTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGGGGCCTGTCTAGTA ACATGTTCGTGTAAGTTACGAACCCTCTTCTTGCGATCTTCGTCAGGACT CACCAGCGCTCGGCTCTCGTGTTTTCGGGCCCCGTCAGCAGGCGACTCGG GGCCTGTCTAGGAACATGTTTGTGTATGTGTGCATTCGGAACAAGTGCCG TTGGTCGCACTCAGGGTGAGGGGTCAACGGGGGAAGCGGATATAAAAGCA GCGGGGCGGGAGAAGAGGTCCCAGTCTCGAACGGACACATAACGGAACCG CTAGCAGATCGCGAACTGAATCTTAAAATAAAGCTAATCGTAAACTCGAA CCCTCTTAACTATCTTGACTATTATTTGGAGAACCACAGCATGTTGGTTG TCATATCAAGGTGAGGTATGCGGCAGCGAGTGCCGAGAACCCTGATGCAA GTGGAACTTGCGTTAACTTATATACTGAACAGTTTTGAAAAGTTATTAAG TAACAAATAATCAATATCAAATTATCCCTTTTGATGTAAATTAAAATATA CAAATGCTGAATGGGGGCTTTTATGATTTTAGTAACATACAGAGAAACGA CGGATAAAGGCTTTGTTAATCGTAGGGAAAAATTATGTTAATTGTACTTT TGGGGTTATATTGTTATATTTTAAATTGTGAAACTCTCAAGGGTATTAAA CTGCGGCTTGCGAAAGCAAAACCCATCCTCACTACATTTATTTCAATGTT AATATATCGTTGTTAAGGAAATCATAATATTTTTAAGTGATCAATAAAAA GCACCACACATAAAACATATATAATAAACAATACAATAAACATATAAACT AAACTGGAACATGAAGTAAGACCAGTATATCCACTGAGCGCACATTATTA TGCAAATAAAATGAAATTGTTTTAAACTTAACGACACCAGAATGGTTTGA TGTTCCGGCCGGGCATCGTAAGCAAATTAAAGTCTCGGCAATTGTTGCAG GGCCACTGGGAGGAAGCCTCAAAAGTGAAGAAAGCGACACGTTCAGTTCG GTTCAGCTGGGTTCAGAGAGCAGAAAAATTTCACTTTTGCGGAAAACTCA TAACGAACAGTGTAGTGCGTTTTTCCAACGTCTTCGGTTACCATCCGATG ATAGCGCAGCTGAGATTTCCTTTGTGAAATGTGACAATTTGTCTGCTTAT CCGGCGATTACTCGCCGTGCGATGAGGTTGTTCAGCTTGGCATCTCCATC TCCATCCCACACACTCGCCACACTTGCTCCAAAATGCAGCCAACGGAGCG AAGCGGTTGGGTAAAGTTAACAACCTTTAGGTTTGCTCAATTGTTCGTTT TTCGATTCGCCTTCCACATGCGTGAATAAACTTTGGAGCGTCTAAGCCAA GCGCGAATTAGCCGCATTTAGTTGCCGGCTATCTGCGGGTTTCCCGTTAG GAAAAACAATTTCAGAAATGAAATTAGCAAATAATGTAAGACTTTACGCT TATTGAAGTTGCGGCAGCCTCAAAGAAGTTTCTGTTTCTGCCTTGGCATG GGCATACATTTGTTCTGGTCTGTTGCCAAAAAATAAGAATGGTAATGGTA GAAAAACCAAACCAAAGTCAGACGGAGAGGCAGCCAAGCAATTAAAACGA AACTAATTTTAGTGCCTGTGTGTGCAGTAGCACAGCCTTCTGCCTTTCGG CTTACTACTATAACCTTTTAGCAAACACAGGGGCTAAATGCTGTCCGCTC TCTCCGGTCCGGCGGCTCATTTGCATCTGCTACAACTTTGTGACATTTGC AATGGCATTTGCTGGCTTAGCAAAAATTAGCCAGCGGATCTGCCCACAAA GCTACAGCGCCTGCTACGGCAGTCTCTTGCCATGAATCAGGCCAAAATCA GAGCACGGCGGCAAGGCAGCAAGAATTACATGGTAAGGTGATCCGAGCAC AGACGAATGTATGTGGCCATGTAGCCAGCCATTCATATTGCACATGCTGC GGCGTTACGAGTATGTACATATGTGTGTGTTTCTGCTCTAGTTCACACTC AGGTTGGAAAACACACAGAAAAAGAGCAGCAACTTCTTCTGCACAATTGC GTGCCGAACAATTTCCAAATTTCATAAATACAAAATGCACTCGCCCGCAT CTGACAGCAGTCTGCAGAAGCCTCCAAAGTTCGGCTCACACTCCCCGAGG GAAGTCGCCCTGCATTCTCCTATTGTCCTATTAATAGCGAGCCGCGGGCG GGACGGCGGTGCGATTCATCTCTCCCCTGCCCCTTCTTCAATAGTTTAAT TTATTTCGGTACTATGCCCGCCGACAGACCCAAGACACAGCGAATGAATT CCAACACCTGTCCGTCCGTCCATGCGACTGAGGCGACTGCGAGCAGCTGG CGGGAGAACTACAATCACAATGTGCTGAAAATGTAATTTTCCCCGGCATA GCAAATGAGGCATAAGCGACGAGGGTTTTAAAATCACAAACTAAGAATGC GCTGGCAGTCAAGGGAAATAAGTAATAGCTAAAGTCAAAAATTCTTTTAA AGTCTTTAAGATATGACTCAATAGTCAAGTGATAGAACACTGATAGTTTC AACTCATTTGTGATTAAAATGTTTAAATAGGCCCGAACAGTACTCAAGTT CGTAATCGAAGTGAGATGGAAGTGCCTTAAATTCGTCACTTTATTTTAAT TCCTGCCTTTAAGTAACTTGTCATAGATAGCTCTCTTTAGTCATATAACA TCCTATGACATCATTTTGCATTTGGATATCCCTTTCCATTGATTCTCTGC CAAGAGGCTTAGCCGGCGATAAAGATTTGCCCACTTCGAGACACCGAACG CTCAGCGTTAATTTACGCTTGTTAAATGAAATTGCCTGGCTCGCCGTTAT ATAAGCGCAATAAACATTTTGTTTGAAAGTAAGTTGCCACAAATGGCGTC ATGGGTGCCATAAATTATTGATACCACACACTGGCCAGATAGCAATGAAA TCAATTAATGATAAATAAAATCAACAAAAAGTTCGCGGAGTAAATTTTCG TGTTTCGCCACGGGCTGTTGATAAATGCGAAAAATGCGAAGTGTTTTTGT GTGACTTTCATGGATTCTATTTTGCAGTTTCAATGCTTGCCATTTAATCA ATTAGAAGAGATACGAGAACGAAGCAGTTTTTGTTTCAAATTAGAGGAAG TACGCATTGTGCAGAAAACATTTATTTTGCATTAATCTATAGCTTTGGAA TCATATTGCTCTGTGCTTTGCTGTTCACATTTCTTCATCTCTATCTGCTT GAGACTTTTATTTACACACGAGAGAATTTCATACCAATACTGTGAGTTCT TGACACACTGACAAGCAATTGAGACAATCGTATGGTCGAAACAATTTCAG CATTATGTGGCTTTTCTGTTAAATAAACACTGACCCTGTGTTCACGTATA TACATACGTACATATACTTATGTATATGCTTCCCCAAAATGCTTCAAAGT TCCAGGAAGCCGAATACGAAAACGGAACATTCAGTTTCGGGGTTCGTGTT TAAAATTACACTGCATTTCCGCAGAAACTGTAGAATAACACGTGAAAAAC TCACCTTCATGTCATTGATAATCTGCTGAAATAGACTACCCAGCGCGGAG CTATCGCGTTCCAGACTTAGATCCATGTTTCTTAGTGTTAGCTGGTTTGG TAGGGATGGATATCGATTGGTTTCGTTCGTCGTTCAATTGCTCGGTATCA GTTTACTTGGATGACTTTTACTTTTGATTATTTATTTTCCTCATTATATT CTTGTGTTGCTTGTTGTGATCTGAAAAGAGGGGAACGTAATTATTTATAA ATAACCATGCTTTACGAACCGACTTGGACACACTTCCGATCGAAATCTGT CTTATCCCGCGTAAATCTCTGAGATTCGTCGCACCAAACGACTCTCGTAA ATAATCAGAGATGTAAACTAGCGTCTTTCCAAACAAGAAATTATGCTTAA TTAGGCTTATTAATATACGACTTGGCGATGGAGAGTGGGAGTTCCCTTGA TGGCGTAGGCGCAGTATAAAACTTTATTTGGGGATCGTTGACCCAAATTG AGAGCGCGTTAAGTGCGTGAGTGTGGGGCTCCTGCTGATATGACTCTTTG ATTTATTGTTTATGCAGCGGGGCTAATAGCTAATTATTAATTGATAATTG ATATGTCTTCCAGCGAAGTACAGGAAGTGGCATACGCAATTTACACAATT TACGGGCCTTGCAATCGAAACTCCGGACCTGAGACCCATGTAAACGACTC TCGAAGGGGGGAAGTGCAATAGTGCAATAGTTTTGACCCATTTGTGGGTT CGCCATACGTGACTAATTCTATGGCGCTTTCGAAAGTGCAGATAAGTCGA GAAATCTAACGCCAGCCAGCCTTGGAAGCAATTAGAGGCGTTTAATGTAC AGCTACTTCCATTCGAGCAATAACCTTCGACCGGGCGGCACTGGCCAAAG CGCGGCTCGGATCTTAAGTCGGCTTTTAAGGCCGTATCTCTTCAAGTCAG TTCTTTTTGGGCTGATTGCGAGGGAAGTTATTCGGATACAAGTGCTTGTT CGTCTCATTGTGCGTCTGTCTGTGCAACTCTGTTGCACTCAGAAAGCGTT CACAATAGACACTCAAGCGTGGAGGAAGCACAGTGATAAACAGACGCAAC AACGAGAGCTGATTGCCCAGACTGCGTATCTTTCGTCTATGTCTGCGTGA AGACGCAGAAGAAAGCATCAAAGTGCTAGTTCGCCGGAAAAGAAGGAAAG CGAAAAAGTTTGCCGACTAAGAGATTACTAGTAGTGGAATAACTGCATTC GGAAAATGAGGAGAACAAACTTCTCTCTATATATGTATGTATGCAAACCT TCAACCACAAAGCGAAAACATAAGAAAAATCGTTGCAATCATAGATACGT CTATATTTGCATTTGCTAATTTAACTGAATACGTACTTAAAATCGAGCAA TGATCGTAGTACAAAGTTTATTGAATGTAATAATCATTGATATGGAAATT AAAGTATCAAAATATACATGTTTAAGACAATCCAAAGGTCGATTGATCTG AATAGCGAATCTACATGGTTTAAATAGACAAATAAAATCGATTTATCTAG TCATCCTCCTAAAATTGTTACTTTGGTGTTCATTTAAGATAGATGCCCTA TAAGAAAAGGGTATCAAGATGGTTCATACGAAACTTGCAGCAAAACAAAC TGACGCACATTCTTACAAACATCGTGGAAGTACAAGTAGACTTTCTGCTG CCTCTCTTTTTGTTCGCTAGCTTCTTTTTAGCTGAATAGTGTAAATGACC TCTCGAGATAAAATTGTGGTTACAACGCAAACGATGACAGGCCGGCTTTG TTGTCGCTGTTGTTGGTGTTGTTGATGTTGTTGGTGTTGCTGGTGTTGTT GGGGCTGTTGGTATTGTTGGTGTTGCAGTTTCCTTTGCAGTGCGGAAATA ACTTGTTGTTGTTTTCGGCAATTGAGTGCGTTAAATCTGGTTTAAGATGC ATATATGTATATACACGAAACATTGACCCAGTTAACTGGCTGCATTTAAA TCATAAGCCCAAACTGGTTGGACAAGTAGTGCATGCTTATATTGGGTCTA CGAGACTTCTGCGGCGGAAATAGGAGCTTTTCTCAGCACAGCGATGAACT CGCGATTGTGGGCTTGGGAAATTCGCAGAGAGCATGGGCCATACAACCAG CCTAAGGTCAGGCCTGCAGATCGTGATGCGATCGGGAAATCTGTTTCGGC GGCAGTAGCCAAAGTCCAAATTGCCAAATCGTGAAGAAAAAAACAAAAAC AAAAACAAAAGCAGGAAAACGACAATTTCGCAAAGTAGCCCCAGAAGAAG AGCAAAACCTTTTTCCAAGCCTCAAAACGGTGGAAAATGGGCCATATTGT GTAAGGGGCACGTTGTGGAAGGCAACCCGCATAAAAACTCGCTCAAATGT CAAGATGAGAATGATGACGCAGTGGCGTTGTTCCTGCGACTGATGATTAT GCTGGATGCGTTTTAGTTTCAAATACGCATATTTTCCGCCCTATTTACTG CCGTTCTCTTTGCGGCTCTGTATCTGCGGTTTCTCCGAGATTTGTGTATT GAAACAAACGGAAGCTGCTTTGGTTGAAATGGGCAGGAAGTTGGAGGGCA CCAGCCAGGGAATACTCATTTTCGTTTGCTTCACAGCAGAAGGTCAGACC ATAATATTAATGTGTTTAATATCAAATCATAAAGAAACGAAAGATGGATG TATCTGTGGACATTTTGCCCAAAAATGACATAGCCACTATTTAGATAGGC TAAAAACAATAGCACTAAATAAATTAAATAAAAGTTACCAATTTTTTAAA TTCATTAAGATTTATCATTGGCTTCCTTCATAAATATCTGGATGTAAGTA TGGTAAACTTATAAAAAATTACATTTTATCGCTGTTTTATTGTCTTGGCC GCATCTGTACCCTGTCTGTATACCATTTATGTTGCATGTTGTCTGGATTT CTATTGCAAGAAGTGACTTGACTGACGGAAAGCAGAGAGGGGCAACTGTG GCACACACTTTTGTCAAGGGCGACAGACAGACAGAGTTGCTGCCGTTAAT TGCTTACCAAAGATGTGAGCACACGCACCGCCATTTCTGTCCCATTTGAA TTTCCCCCTTGCATACTGCGTTCTTAGGCGTAAATGCAGATGAGCAGCAT TAGGGTGGACCAACAACGTGTTGCAGCAATAACATTGGAGACTAAACCAG AACTTGGGAGTCCCCTGACGCTGTTCCGCTGTTCAGCGCATAATGACACA TTAATTCACTTTGAAACCACTTCCTCGGCTATTCTAAAAATAATTACTGA TAGCTTATGCGTAAAGATTGCATAAACAATGAACCATACGAACGATTGTA CTTTCTCGAGTTTTTCCAAGCTGAGCTGAAAGTTTCTCTAACACTCTAAG GAAATATCTCTCAGAATGGTCCATGTTGAATATGATAAATAATCAAGCAA AGAATCAAGGCCTGAAAATAGATCCAAAACTTACAATTCCCAGCCCACCA CTTTAATGCACTGCCGGATACTTTCCTATCCACTCTGCCTATAAAGTTCT GTTTTTCTTGTGCCCCATAAGTTCTGGTTGGGATTTGGTAAAACAAATAA TTTTACAGCTGCCTTTGGAGATTTGTATACTAGGAAAAGTGAAGTGCGGG TGTCGGCGAAAATCTCCAATGTCAGGCTGGCTTTTAGCGGATTTATGTGT TGTTTTATAAGTTGTAAGGTAAGCGATACATTGTGGCCGGCAAATTGTGC TGCAGCATCACCAGCGGACGGCCCGTCATGACTTTACACTTTCACCAACA ACTACTACGGGTGGTATCAACAACTTGACACCAACAACTGCGGCCATCTG TGGTCAGCCAAGTGTCGAGATGCCTCGGCCTGATCTTAGTCTGGGGGCTT GGAGTTTGGGGTCTCTCGTCTTGAGTAGGGGGTCTGGTTCCTCTATTCCG GGGTTAGGAAAGCGCCGATCATCGAATGAAATGTGTCGAGTGGTCGCGCG ATGAAAAGAAAAGCGAAAAGAACGCATAAAACGATGATAATCAAAAGATC AAGTTTTATATGAACAGAATCGACAACGTCACCAGCAGAAACTCAGAAAC ACACATCTGCTCAAACATTGATGTTTATCTATGGGTTTCTATCTTTAGCG TCATCTGTGCTTTGCACTGCATTTTCTATTTGATGTTTCTGGGATTTGTG TTTGTGAGGGCATCTGCTTTAGCTCTCTCTCCCCCCGAATGCCAACCCCC CCCCCCCCCTTCGACAACACCCACTGACGCGTATGGCACGTCATTAACCC AAATTTTCTATGAATAAAATATAGCGAAAAGGAAAACACTCAGTGTTTAT GTTTGCAAGCATGCCTTGAGAAATCTCTGTCTATTTCACTCCAAAGGCTA CTTTGATTCGAATCTAATTGAATAATTCGCGGGCTGCGCATTTAACACGC TGTAAAATAGGCCAATTCATCGATAATTGAAGCTGATAGGCATCCCACCT TCTTGATAGGCTCACCATCTAATCAGTAGCACTGTAAACACGCGTTTGTT TTGGCCACGAATGTGGAAATCGATGAGTATCGATCGGAAGTTATCAAGCG GCTGAAGCTGACCGAAGAAAATTAAATTCAGGAGAATGTGGAGCACAAAA CTCATTTCGCAATGCAAACGCCCACAAATGTGTAAACACAACGGCCCGCC CGAAATAAACTTTCGGCATTTAGCGGCGTTTAATCGATTTGTGCATAAAA TTATATGTTTACACATGGCAAGGCAGCCGAAACGAAAATAAAGTCGAGAT ACACAACATGACCCATTGGCGAAACATGGCGGTGGGTTGTTTCTTTTCCA GCGCATTTCCACTCGAAATTCAGCGGATTAGTCATTTTAATAAAAAACAC AACCACGTCTTAGGTGTAGCCTACTTTATAGATTTTCTACATAATTTAAT TCAATCGAGAAGATATTCAAGCAATTAAACACACTTCTCTATTTGATTTT CTTGTTATAAGTTTCATTTAAAGTGTGCAGGCACCTAATGTGTCAGCTAT TTTATTATTTTAAATAAAAATTAAAATAGGAAGAGCTTATTAGTATATTT CTTCACACTGAGGTAAACCGATTCACTGTTCTCGACTTCATCTCAACTCA TTAGAGAGCGGAAATTCTCGACAACTCAATGTTAAGGTGGGTAAATTTGC TTTTACTAATTTTAACAAAGGCCCGAGAACATTGTCTATTATTAACACCA CAACCACTCCCGCTCTCCTGCCGGTTTTCTGGGCGTTTTGGCCATGGCCA ATGGTTATTAATGATTAACCGGAGTGCCGTTAGCCGGCACATGTTACTCC GTACTTTGTCATGTTTGTTATGTTCTTGTTTGCTGGTTCCATCAGCACGT TTTGTTTCTGCCTTCCTCATGACAGCTTTGTGGCCATCAGCAATGGGGAT TTCTCTGCCTTTCTCCGGCCTTTCCAGTCTCGTTAGCGTGAAAAGCTTTG CCCAGCTTTTGTTTTTCTTGCATAAGAAAATGCCAGTTGCTCAGGCATCT TGGTTTTGCTAATTTCCCAGCCCCGCCATAACTCGCGGAAAAGAAACGAG AATTGAAGGAAATACGTTTTAGTGTCGCTTCTCACTTCTCGCAGAACCCT GAACCCTTGACATTTTCACCCAGGGCGGCGATAAAGTTTTATACTTTTTA ATGAGCTCCACGTTCTCTGCCAGCGCAATTCAGCCGCACGCAGCCCACCC CAAGTGAAAACCGCTTGAGGCGAAGGCGAATCTCGGGTTGGATTAGACAC GATTTTCATTAGGACGAACCCCGAAAATCGAAAGTGGTTACGAAAGATTC CACTCGAGTGGGCGATCCAGCAGTCTAGAGTCGCGGACTCATTCGAACTC AGATTCATTCAAACAACAAGGAACGCCCATGCAGTTCACCAATCAAACGA AAACGAAAATCTTTTTGTGAGTGGGCAGCGAGAAACTCGAATTGCAGCAG CGCAGCGACATGCTAAACAAATGCAGACATTCAGGCTAAGTGACTTAAAA GTTTTACAAGTTTTCAGCCGTTTTTTCTTGTTTACCAATTGAAAACAGTT GCCGCATTATAATGTAAAGAGGACGTAACAGCGGTTCCGAAAGGCGAGTA TTAAAGATATATGAATAATGTACCAATTATTTTACATTTAGTGGGAAAAA CTATTAGCGCCTTTAGAACTGAAGTGATCCAGCTAAAATACTGAATGGGG GTTTTGTGTTTACAGTAGGCTAAAGAACATTCAAAATATTACGAGTATTA ATTTTTCGAAAACCATCAATGAGAAAACATATTTGCACAACAAACAGTTA ACGTTTTTCCTTTGTTTTGGCCTTGCTCTCGTGCTTGTGAAAGAATGTTG TTGTTTCTATGCAACGGAGGTGGAGGTGGGGGTTGGTCAGTTGGAGCGGC CTTTCTCCATAGGACACAATATTTTTTTATATTCACTGGTATTTGTTTTT CTGCTTTTGTGAATTTCTGTTTGCATTTTGTTAAGGCGCAAGTGCCTGGT TTCTGTTTATATAAGCGTAGTAAGATCACCGAAAAAAGTTGCTCGTTTTC AAATTATAATATTTCACTTATTTTTATATTTTTATCATTTTAGTAAGAAG GAACATTAATTTCCTTCTCTTAGTATATCAAAATGTATGATTTTCCAATT TAGGTAAAACATTTAGGTTTCCTCCAAACGATCACGTTCGAAATACAGGT TTTTTCTCTCGGTGCAGGAGCAAGTTTCTTGCCAATGGCCGACAGCTGTT TGTGGCTAATTTTATCTTTCTTTCTGAGACCCTCTGTTGTTTTGGATTCT CTCGTTTTTGGCAATTGCACAGGTGCGGCAGTTGGATGGTTTGCGGATTG GGTTACTCCACGCGAATCAGATAGCCCAAGGCATCCTTTCGAATTTGAGT ACTACTTTGTGTCTAAGCAGCGTATAGTATATACGATATAGCGACTTGGC GAATGCACCGGCCGACATTTCAGGCCAAACGGTCTCCGTTGCTGGAAAGT TCTGCATCATTTGTTTAGACAAATGCGCGAGAAAACATTCCCGGGACGTA AACAAACCCCGGCAATAATATTTTAATAATTACGCTTATCTGCTCCATTT GACGGCGCGCACAAAAGTCGTTTGAAAGGTATGCAAAGAGAACGAGACGT GCGATAAGGGAGCCGGGAATGGGAACTCAACTTTCGAGCATTTAGTCCGC ACCATGGGTGTCAACGTGCCGCTCCGGTTCCTGTTGCGATTACGGGTTGA AAGGAACACAAAGCCGCCACCTCGCGAAAAAACGACCCATTCGGAGTCGG ACAAAAAATTAGCTTGTTCAGATAAACCGAGTTCAGGTAACACAGTCCAA AGAGAAGTCCCTGCACTTGCGCAATTACCGCGCAACTTCAAAAGGGGAGT TGTGCACAGAGAAAACTTTATGGCAGTCGAAAAATCGGAAAATCTGACTT CGCACAAATTTTGTGGACCGAAAACACTTCACAGCACTTCATTGGCACAA TTTGTCAAAAATCACTAAATGTATATTGTTTGACTTCAAGAGGTTTAATA ATTCACTAATTTATCTTACAAAAAGAATTAGTTACATGAAATTGGTTGTT GATTTTGTTATAGAAATTATTATTATTATTATGTTGCTGGCCATCAAAGA TATGTTTTCTTCAAAACAAAATTACAAATATATAAAACCTAAACATTTTT TATGAAACTCCTTTTTTTTAACGTGTATAACAAATCCTGTTTGGATTGGC CGTGAACGGAGTTTTCGGTTCTCACGACCGCCTGGAATGGTCACTGGAAG TCCTTGGACCTGGAATCGGTCCAAACTTGTTGTTGGTGAACTGCAGCTTC CATTCCCTCCCCTTACTCCATCCCCCTAGCCAACGCTCTTCGCCCCTCTC CCAACCCCAGTAATTGGCATTATTAGCCCACACTCGATTCTTTTTGTTGT TCTTGAAGGATACTTACGGTGCACTTCCGACTGTAAAATATCGCAGGGCG ACTTTATGCAGCTTGCTTGATTTTTCGGCCGACGATGTTGCAGACAATTA GGCGATGATGTTGATGCTTGCACTTCTGCGGTCACGGTGTTGTTGTTGTT CTAGCATTGCATTTCCAGGCGGCAAAAGCGCACACAAAGGATAGAAGCGG TTGTGAGTGCGAGCGGGGTGTATTCTCCCGTTATTCCCCTCTATTTCCTC TCTCTCCTTCTTACGCCCAGTTTCGTGTGCTTTGCTTTTGCATTTGCTTT TCTTTGCTTTGTTCAAACTCAAACAAACTACCCCAGAACCGTTGATCCTG ACTGCCTTGTTGTTGCTGCTGCTGCTGTTGTTGTTGTTGTTTTGTTTTCT GTTATGTTATACACTCACAGACACACGTACACACACGCACACAGTGGGCT GGCAGACAGACGCTTAATTTTCCGTTTTCCTCGGGAAATCGCAAACAATT ATTCGCTTATTTTTGCACCGAATCTGACACTTATATGCTCGCACTTCGAA CTGCACTTCCAATTGGTTCGCGCATTCCTTTTCCGGTTAGAAAACAGTTA GAAGTTTGCCGCTGCAACCGCTATTTTCGCCAAGTCTACGACTGACTTTC CGAGCGCATTTTCGTTTTCCTCCGGTGCGAAAGGGCTTTCCTATAGACAA ACAAAAAACCGTAAAACAACCGCGACCGATTCGTTCGAGAGTCGAGTGTC TGGGTCAGTGTGACCATCGCTCGAAGCTGGGAAAATACACCTCTGTAGTG TGACCACGTCTAGGAAAAATCACTTGGCAGCGAGGTCACATTCGCTGTTA ACCGTTCTGCGAATCGGGAATGTTACCTATCATGCAAACTTTTAAAATTG AAAATATGGTTATTTTTGGCGCGTTCGATGTTCCAGTTGACATAAAAGTC AATTGAATAAAAAACCAAAAATTTTGTTATAAAAATTTGAAGAGAATAAC TCATGTTTTAGAGTAGAGTTCCTAGGAAACGGAAGTGCCGAAGACATTAA CTAAGCACTCGGGCTAAATGAGTGTTAATTTGGAAAACCATGAATTCTAT AGATTGAAAACAAATTATATAAATTTAACGTCGTTTACTTTAAATAATGG CCTCTGCATTTGCTGCAAATTCACCTTTTATGCATAGAATTCTTTTTAAG AGTCCTATTTTCCGATGGTATGAAAGTGTTCGATATAACAACTAAATTAT TTATTTGTTCACGTTGTTGAGCTTGGTGCAAAAGATTATAAAAGTCATCG TCAGCATTATCACACAAGTCCACAGCTTAGGAAAATCAACGAAAAAGGTG CATATACAAATATAAAAACAACTTAAACGCTTTGTAAAGCAAACAATACA AAATATGCGATGCTCCAGCAGAGCCTCCTTTAAAGCTTGTCCACCCGTTC CACACTGAGTTTGATGTCCGACTTGGGCATCAAGAGCAGTCTCCGGTTGT CGTACTCCACGGGAATCGAGGTCTCCGCAGAGGGAGCGTATCTGTGCTGC CTCAGCAGAGCCACCAGGCCCACCAGAAGCTGCTGCTCTGCAAAGCGAGC GGCAATGCATCCTCGCAGGCCATCGCCGAAAGGCAGGAACGCAGCTGCCG GGCGGGATCGCCTTGCCTGTTCCTCAAAGCGCTCCGGGTAGAACCGCTGG GGGTTTTCATAAATGCCAGGATCCATGTGTATCGCCGCCGTTGGTATCAG CACATTGTTGCCTTTGGCAATTACAAACACCGATCCGGGCACTTCGAATT CTTTGGTAGCCCGGCGTAGCAGGAAGGGATGTGGAGTGTGCAGGCGAAGC GTTTCTAAAAAAAAGGTGAAGTCATTGGAGCTATAAAGAGCTTTTCAATA TTTGGTACTCACCATTGAGGACTTGCTTCGTATACCTGAGCTCCCTTAGG CACTCCGGTGTCACTTGGCCACCATGCTCCTCCAGTGCCTTGTTAATCTC GAGCCTGGTTCGATCTTGCACCTCAGGCTGGCGGGCCAACTCGTAGAGGC AGAATGCTAGGGTGGCATTCAGGGGGCCCAAGCCAGCCAGAACGAAGCCG AAGGCTTGGCCCGCAATCTCGATGTCGGTGAGCGGCTTTTCTGCGTTGGA ATATAGCTGCAGAAAGGTCTGGAGTGGCTGGCGATCCCTTCTTCGATGCA ACTGCAACTGCGACAGGGCCACTTTTTGGAAGTAAGCTGTAGCAGGTTCT GCGTAGCTTTTGTACTGAAGAAGGCGAGCGATGAGCGGAAACTCAAGCGC CAGATAAGCCTGCCACATCCTAAAGTCCGCCCAGTAGTTGCGCGTCCACT TAGCGAACTCCACGTTATCCTGCCCTACTAGTCCAAAGGCCATTGACGCC ATAACGTCCGTATTGTATGCACCCACGAGTTCGCTTATATTGATAGTTTG AAGGCTCTTTTCGCCCAGGTCCCTTTGAATTCTGGAGGAGATTTGCGACA GTCTGACCAGCAGCTTCTGCATGTTGGCCGGAGTGAAAACCTCTGCAGAT TTGGCGTGCAGTGACCGCCACTTGTGACCGTCCAGCTGAAGGAGATTATG CGACAGCGGCTCTCCACTGGGATTACTATAAAGGCCTCGGGACGTAAAGT GTCCCGCGTCGGTGAAGATTATTTGGTGGACTAGCTTCAGGTCCAGCGCC AAGATGAACGGCTTGAGGCAGGCGTAGAATCCCACAAACGGCGCCCTGCC CTTGTATGCGGTGTAGATATCCTGCAAGGCGTCCTGGGCATGCCTCTTCC CGCTCACCACGCCCTTAATGTTGCCCCACAGGAACTTGGGCTTTTCGTGC AGGATCCCCCGCCGTTTCCAGTAGCCCAGACTGAACTTGACCAGGGCGTA GACCACTGACAGCGCACCCAGGGCGGTGAGCAGGGTGCGGTGCATTAGAT CCATGCTCACTCAGCTGTCTTTTCCGGCTTTTACAATATGTTCGCGCTGT TTGATATGCTTAACAGCTGGCAGTAGCTGCTTGTCGAGGTTCTGGGGCTC AATGCCGCCGGTTTATCAGCGCCATTATCGTGCGGTCCGATTTAATAATT GATAAGGTCCATTGAGTATCGGCCGCTAAAATGGAAGAGAAACGTGGCTA TAAGGCAACTTTCAGTAAGTAATAGTAATCAAGAGCTGAGCGGGATTTAT TGCTAAAATAGGTACGGAGAGTTGCGACTACGGCTGCAAGATGAGGCAGA GGTTGTACGTGCTGCCGGCGAACTCGTCAACGGGCACCCAACGAACGTAG CCCAGATCGATTAAGTGCTGCCGGGAGCTGGGCACGCCTACGAAATGCGG ATCCTAAAAAGGGAAGCGAGCGATTAGTTCACCAGTTCATAAAATGAGCT AATTCGCTGACTCACCACCACCTGCAGGAAGATGCGACCGCGTGCACTGC AATGGTAGCCGGTAATAGCCTTGGAGGCGGTGTCACTCAGACCGCCCATG GCGACGAAGCCTTGGTACTTCTCAAAATAGCTCCGAAGCTCGCCGAGGAT CTCGTCCGAGCTAAGCTCCTTGGCGTGAAGAATCTTGCACGGCACCTGGT GCAGCACATCGATCACGTAGAACTCCTCGAGCGTTCCGATCCAGTCGCGC GAGCCCACGAACTCTGGACCCTTGTCGCCGATGGCCACCAGGATCTGCTG AATCTCCCGGATGGAAGGAACATGACCGCTCGACCCCTGTCGACGTTGGA TCCAGGAAATGGCCGATTGCAGGGTGCGGTAGCCACAACCCCAGCCAGCA TCCTGGTGGCCATCGCATCCGTAGTGGAAGTAGTTAAAGCCACCGCGGGT AACTAGCGTCCGCCCGCCTTCAGTGGGCGTGGTCAGCGCGCCTTGCGGAT CCTCTAGAAGTGGATATGCATAGTCCTTTGGTACAATTTTCAAGGACGCC GCGGAGGAGTCCCCAAACTCTTCTGCACACTTTTCCGCCGCCATAGGAAT TGTTTTCGAAACTGAGTAATTTGATAGCCTAGGCCTGATTCACCTGCTCC TTTTCTTTTTTGTTTATTTACCTTGGGCAGCCGTAATTTGTTTTGTGAAA GTGAAATCGCAGCAAAGAAATTGGAATGTTTTTTTTTTTGCTCTGGCTAG AGATGGTACAAGCTGAATCGTCATGCACCAATGACAAAGTCAGCCAAAAT AAAATAACAATAATGCGGAAAATAAAATTAACGAATATAAGAATGAGTCA TGATGAAAGGCTATTCCGCCCAAAATTTTGATAAAATTTATATTTTTATA TTAAGCAATGTTGTCATAATTGTTTTACTACAATTATCCATCACCAACTC TCTCATCGAATTATCGATAACAGCCCGTTTGTAGCGCCTAAATTTAAACG CATCTATTTGGTTTTCTCTTATTTCTCATGCATTTCAAATTTTATTTGAA TTATTAAATGTACATTATTGTGTTTAGAGTTCATAAATATGTTTTCGCAT TTATGTGTGTGGGTGTCTCAACGCTTTATATATTAACACCATTCCCCTTG AATTGTGTTCGTTTAATTTTTAGTTTTTGGTGACCAAACATTAGTACATC GTTTTTAATAATTGGTAAAATTTGTAGCACTCCATAAACTACGATTTGTA AAATTGAAATATTTGCATTATTGGTTTTCAACTATTTTCGGATTGCTGAT TGTTACTGAGTTGCAGTTTTGTTAATGTTTTAAAGTTAGCTTAAAAATGC ATTTTGGATAACTTCGCCGAGTTTTACAATAAATATATGGGATGCCGTTT GCAATATGTGTCTGTGCACCAATTAAAATACCTTAATTACGTCGTGCGTC TAAATGTTTTGTTATCTTCTCGTTTTTGGTTTGTGCCAGCAACGGTTTAA AAGAGGTCGATTGAAAATTATAAGTACAATCATAAAATACATTTATTAAA TATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATC ATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTAT ACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTC CTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTC TAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAA CTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTAC AGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTC TCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAA AACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTG CAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAAT TGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAAT CTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACAC AGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTT CAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGG ATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGA GAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGC GCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTT CTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGG CCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGG GCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCA CAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCA TGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAG CTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTC GGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGT AGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACG CCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGT CTTGTTCTTCAGCAACTCCAGTGCGAGTTTCTCTGGAAAAGCAGATGTTG TTAGAGATGCGGATCGCGTGCGGTTGTTGCCACTACTCACCCTGTCCGTC GACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGT GTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACC GCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAG AGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCA CCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGG CTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAG ATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCG TGGTGTACAAATAGTGCATTGAGTCATCTAGAACAATAGTACAATAATTA GTTTTGAAATGGAACAAGTTGAAGAATTTGTCGACAACATTCTAATTCAT ATGATCCGAAACTTACCACCAGTAAGGATTAATACGATGAGTTCGCAGGC GAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACT TTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATA AGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACAT CTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGA TATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATA CTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATT GGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACT CCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGC AAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGAT GGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGA GTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCC CGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTG TCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCT TGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCC TTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGC CAGCTCGTGCTTATCGAAAAGTTTGGGGTCCTTCGTCGCCGAGATCTCGC AGAGCAAGTTGGTCGTGTTCGCCGGACTGACACTGGTCGTCTTCAGCTTT TCAATCAAATCGTCGATTTCAGCTGCTTAAGGCGGTAAGAAAAGAACATT GGTTAGTTAGGGCACTTGAACAACATAAAGGGTCATCTTATTGTTTTGGC AACTAAATGTTTCCCTGGTCATTGGAATAAAGTTTGGTGATGATGAGTAA CGTGAGTGAGTAAGTAAGAAAAGAAACCATCAATTATAAGTCAAGTTATG AGTGGTTGTATTACATATCCAGCTCCCATTTAAAGTGTTCTTAGTTTTTA ACTATTTAAATACTATTGTATTTATTTAGGGTATTTTATGTATACTTTTT CGTTCCATTTGACGGAGCACGCAATCCACCTTTCCCTTCCTGCACCGACC AAGTTGAGAACCGCAAAATTGATTGCCAATTTCGATTATCGTCGCTGACT GGACGAAGTCAAGACAAATGCTTTCAAAGCAAGAAGTTATGGCTTTACGG CCTGGCACAAAAGAACTTTCTTTCTCCTTCAGGAATAGAAAGCTTTTTTG TGTTTTTGCATCTCCAGTTCGAACCGTTTTTGATCCATTGGAAACGTTCG AGAAAACTCGTGAAGCGTGTGCCACATTAAAGCTTCATTTGGCCCCAAAA AAACAGATGGCTCGGATTATAAAAGGACCCAGGATGGGCGACGATTTACA TAAGTCCTGGTCATGGACAAATGAAAAGGAAAACGGAAAAACAATCGGGA TTTAATGTATTGTAATGATGAAGGTTTAGGTTCACTTATTCAGCATAAAT GCTTCGGAATTCAGCTTTTCAGGGGAGTTATCTTAAATGTTAGTGGGTAT GAGTTGGTTCTAAAATGATAAAACTTGTTATTATTAAGCAACGTTATACA ATTTTAATGATAGTACCCAAGCCAGAGATAATACAACTTTTGTGTTGAAT TTAAATTGTATATATTCGATATTAAGCCAGTACGAATAGAGCCCTTTTGT GACCAACATTATCACAATATTATTATTTCAGTCAGACCTTTTCTGCCGAC AAGCACACACGCTGGAAAATACATTCCGATGTGGCACTCCAGCAGGACGA GGGCCAAAGGACGAAGGGCAAGGACCAGACTCCGGCGCTCGACAACTGGC GACAGTTGGTGGCAACAGCAACAGCAAGGTTGTGGACTGGGGTCGCAATT CAACAAACTTTGTGGAGCATAAATAATGAATAAGTAAAACAAAAAGCAAA GTGAACCCTTCAGCCGGGCGGGCAACCATCGTCATCATCATCAACATCAT CCAACGTAGGCAACATCCACGATTTGGCATAGAAACAGCAACAAAGGACG CAACAGCAGCAGCAGAAGCAGCCTGCACAACAGCTCACTAACTCGCAGAC AAGTTGCACTTAGAAATGTAACCCCAACTAAAGAGAACATAAGTGTATAG GCTGAATTCGAGGGTACCGACTATAAGATACCCTAGTGCTGAAGCAACAA AACATCACAAATTGTACGTCAGATTGTACAACAACATAATAGAATACGGG TTCAACTTCTGCATCCGTTTGTAACGACTTTAAGATACACCATCTGATAT CGAACTCTCTTTATTATAACTAGCTGTTTAGTGTTACTCTTGAGTAGTGT GTTTTCCAATGGTTAAAGGATTTAAATACAAAAGAATCATGCCTCCGAGT TCTTTTCTGTTTGGGTAAATAATAATTAAGAATAATAATAAGATATAGGT AAATTATGAACTCAAGTCTGTTTCAAACTATCTTATTCCGAATGAAAACT TTACTAGGTATTTCAGCTATTTCCGTGCAGACAGACATACAATTAGGAGT CCAATATACCCTTTAAATCGAAACGCAGCCAGTGGAAATGTGCATATGTA TTGCGGGATGCATCTGCATATTCAGGTAAAAAGGGGAATTGTTGTATTTG TTTGTCCGACGCAGCTGACTGAATGCAATTGGACAGGTGGCAGAGACGCG TCGCATCGCCCGCCCGGCGGAGTGGCAGGTTGACAGGGATGAGGAATGCA GGAGGACGACAGGTGCTGTGGCAGTGGCAGTGGCAATAGTAGCGTCACTT CCGTCTGACAGAAGGTGGCCCAGACCAGCTCCGTAATGCGTCTCGGTTGC TGCTTCGCCGCCTTTTGCGTGCCTCCGAATGTTTGCTTTGGTAACTGGTA CTCGTTGGTATTCAGAGTATGCCACTCGTCCATCCAGCCATCAACCCATC CATCCAGCCATCAATCCATCCATCCATACATTCCGTTCGAGTTCCGTGGC AAGTTCGTTAGCTCTTCGTTGCGGAAGCGGGATTCGTTCGAGGCATTTAT TCGCCTGAATTTCTGGGGCAATGGCTTCATTTTATTTTCGTGTTTCCTTT TTTCTGGGCATGATTGGGGCCTATGGCCTGCGTTTTATTTCCACTCCGTT GTGGTATTTTATTTTCTCCATTACGCGATTCACCAACTTTGGCCACGTAC AAAAATAGCAAATAGCAAACGGCACAGAAATCACAAAAAAACTAGTGCAA ACTTATTGTTGTTGCATGCTTAATTCATGTGCAACTGGCGACGCTAATGT CGGTTTTAGTTGTATTTTAGCTTTTTGGGCCCTGTTGCCAAGTGAAAAAT TCGGGAAAAGTGGGTTAAGTTGGAGGCAGAGGCATGGCACAGAAAATGGC AGCCATGGGAACGAACCTTATAATTCAAACGAAATGATTCCTTTTGCATG GATAACTAGGTGATGTAAGTGAAAAGGTATAATTCATGATCCACTCGAGT TATGATAAATTGAAAAAAATGGAAGCTTGCAAAGTAAAAGTGAGCCCACT TTTGCGGGGCTCTTAAATATACCAAACCACAATGTACAATACAATAAACC ATATAATATAAGGATTGCGTATTTTTAAAACTACTCTTTATTTACACCGT GCACTAATCCCTACATCTATCAATAGAAAAGTACAGAGTATCAGACTGGC ACGTCCTGATTCAAAGACTCGTTCTCGAGCAACAGTCGACTGTGACCAGA CTTTCCCAGCTGGAGCAACGCCTGGCAAGCGGGAGTGGACATCTGGCTGA CATGCTGGAGCAACTTCTGGTCGTTGTTTCCCTGCCTCGCCCTGAGAAAC AGATTATCCCCTGGAATCAGAAGTAATTTGAAGTGCCTGGTACTGGACAA AGTTTAATAGTTCTCACTCCAACTCCGCTCTTGCCTGCACTTATGTTTGA GGTCCGAGATGTAAACCTCCTCGATTTCTACTTCCAGTTCGGCCAACTGC TGTTCTGTGTACTTGGACAGAGTCGTCGGATTCATGTAGTAGGCAATGTG GTTCGTCCGACTGAGCCGTCGAGCGCTGTGGGTTCTGGAGAAGATTGGGC CTGTATACGCCAGTCTCAGCATCCGAGTGAGTCTAGAACTCACCTGGTTA GCGTAAAACTGTAAGCAGGAGCGCCTGCGATGAAGTGCATGGTGACGAAG AGAAAAACCAGAGCAGCCACCACTCCGATGACGAGTTGCTGTGTTTGGTA GAGTGACTGCCTCTGGGGCATCCGCTGATTGGCCCCCCGATAAGGCCTTC TGAAAGCGGCTCCCAGATCGTTCCCATTTGCCTCATTGAATTCACTTTCC CCGCGATAATCCTTGTACTGCGAGGGATCCTGGTCGTGGCAGTCGCCCAC TGCCGTTGCTATGTTGTACTCAATCCTTTTCTGGCAGTCCGTGAGGCAGT CAGCCGCCTCGCTGATCCGCCGGAAGGCCTGCTCAGCCCCAGGAGATTTG TTCTTGTCCGGATGGAGGCGCAGGGCCAGCTTGTGGTAGGCCCGCTTCAC CTCGGAGTAGGTGGCATGATGAGAGATGCGCAGCACCTCGTAGTGATTGC GGCACCGCAGGACCTTCTGCACCACGTCCAGCATCTCGAGTGTGAACTTG TGGGGCAGGGCGTCAGATTTGCGAGTTGGGCCTATGGTCCGCTGGGCCTC GCCCTTCAGCCTCAGTCTCAAAATGATATTCTTTAGCTCCAGCAGCGCCA TGATCTCATCGTGGTTCTGTAAGCCTTCCAGATCCTCGTTGATCTGCCTC AGAGCGTGCTCGTAGTGTCCCAGGCACAGGTCACTCACCACCTTGTCGAC GCAGTGATGCCTCCTCGCCTGCAGGATTCCCATTGTGAAGTCGTCGTCCT CCAGTTCTTGGTTACTTTCTTCTCCTTCCCAGCAGCGTGAGAAGACAAAA AAGGATTCGTTTTTCTCTGTTCGTTTGCAAATTTTAAATTTTGGTTTGTT GTTCTGGGACAATCCACCGAGTTGGTGAATTTAACAAAGTGCTTTTGTAT GTATATTAGAGGTAGCCGAAATAGTTTCGAACTAAGTTGACTGTATATGT ATATGTAGCTGCAAACTTAAATACAAATTGACTTTCGCCAGTCAACATTT TGTATGTCAACACAATGAACACTTGAGAAAAGACAACTTGAATCCGTTTT TTACATACCAGCCAGCTTATTGAACATTTAAATCATGCAGTACTCGTGTA AATACCAACGAATTTACCAACTTAAAAGTTGACACAAGTTGTACAAGTTG CTTAGTTTAGAGCGGAAAAAACTAAAAGTTTGCACACAAGTTGCACACTT GAAGCACACAAGTTAGAACGTTCTGTCGATGGGGGATTCCCCAAAATGCC AACCCTCTTTTGGCCCCGTAAAGTATGCTCCACAACTTGTCAAGGGGACA CACATAGCCTCCTCGAAAAGACTCGAAAGTTAATTGAAATTAATTTCTAT GCCAATTTGAATAGGGCACGAACTCAATTAAAACAGAGCTAGCCACCAAC CACCCCACAATTTCATCTTTTCAAGGCGGCCTGCTCGCCCCATTCATTCT CAAGGCCATTAGAAGGGCCAAAATCTTATTAGCAGTTAAAAGAATAAAGC GAGTGGAAGGCGCTAGGCACGGGGAAATCACAAGTCACCCAGCTAGATTT GAAGCAAATGAAGCAACGACGCCGGAATACGCAAGAAGGAGGTGGAAAAG GACAATAAATTCGAAGCCGGGCAAACTACAATAACAGCCAGCTAATCTGG GTAAGCTGCGTGGAACGAATGGAAAAGCCCAAAATAATAACAATAACAAT AAAGAGGCAGCAGCTCCGGAATCTAGAATCTGGAATCTGGCGAGGGGAGC GGCCTGCTTTGGCAGCTGATATCCTCTTCCTTATCAGACTCCCAGCCTCG GGGTTGATGGTAGCCACAGCCTCAAGGACAGCAGTCAAATTGCGTCGAAG ACGCCGAGCGAAAGCGTCGACAAATGCAGTCACAAAGGACCAATTAAAGT CCAAAGTGACTGAGCCGCAGGGAGGACGTGGCAAGCATCTCGCAGCTGGG ATCTGCACAGCGAGTAAATCATGCCGCAACGGTCCAATGGCCTGCATCCT TGAATTTTATAGATGTCCTTTCATTAGATTTCAAAACAATCTATAGTAAT GTCGAATAGTATTTCAATGTACTATACTTCAGGTATAAAACTTATGTAAC ACTTAATGAATGCTCCGAATGACAGGTCTTGAAAATCATATATTCAGCGC AAGTTTCCCAGTGCTTGCATATGAATTAAAATGAACAAGAACCACGAATT GTTTTCAGTGTGGAAATGGGTCTCGCTACGCTGGGCGCAGCTGGTGGGTT CTGTAGACAAGTGAGGTGTACAGTGGTGTGGGGATTGGGATGCAGCACCC CTCCTGAAAAAGGGGAAGTTTCGAGGCCGGGATTGCCGGCGCGTTCAAGT GCTGTTTGTTGTCGTTCTGCACAGGTTCCCCTCGGGAAAGGGTATACAAA CAGTACAGTCTGTGGCCAGTGTTTATGTATGTGTTGATTCGGTGCAGTCA CGTTTGAAAACTAAGAAGTTTAGAGACTTGTTTACGTTTAACAATTCTCA TCGGTGACTGACCCAAATATAACACATCCAGTGCGTACGTTACACATCCA ACTACACTGAGAAACACAAGAAAAAAAGGGGTTTCTTTTAGTTAGTCACA GCTTTATCTTGACAATGACTGCGCTTTGACTGCAAAGTAGTATCGAATTT TAAGCCCTTTTAAGCTTAATCTGTGAAGATTGTCCTAATTGTAATGTTTA TCAACAATTCAACAAAGTTGCCATAGATTTCTCACTGTGCATGACTTCAT CGTTTTGTTTGCTATATCACCCCCCGTGGGGATAAAACGAATTGTGAGGA CTGCGGGGAGTGTTGCGACACGCCGGTAAACCTGGCACCTCGCAGGAGGC ATATTCTCATTTATTAATGCGTCGTCACTGCTGTTCCCAGTTCCCATTCC TATTCCTCCTGTGCTGCGGTGGAGTGGGCGGCTCGGGTGGCGGGTTCGTG CAAAACGGTGGTGGCCGCTGTCTCAGCCGCACTTAATTCCCGCCAGAACT GCCGGGGCCATTAAAGGATAAAAGAGCGGGATTTCTGATTGGGAAGCGCT GACCCTGTTGGCCGCGATAAGTGGGTGCGCACAGCAGCAGGAGCACGGCA TCTGCCTAATCCGACCGGCCCACTGTGCAGTGGGATGGGGAGTGGGGAGC ATAAGTATTGATTTTTCTCACATGTCCCCGGCAAACACACACATCTTGTC TAGGGAGCCGCATCGCCCGCCCCCACCCCACTGCCCCTGCTCGGAGCAAC TTCCTCCGACACCTGGCAGCGATTTGGAAGTTTTCGCAGCTCGTAAATGC TGCACTGCAGCCATAAAACGGCCGCTGCAATGACTCGCATGAATTGCGTT TGTTTATGCTATGGAAAAGGAATCCGGGGTCTGCTGTATGTCGTTTGGGA TGCTCCATAGGCAGAGAAATGCTCGATGTTACTCACTCGCCATGTTTGCC GCCTTTGTTGATTATTCCGCTGCTGCTTCTTCCGTTTTTATGCTTTTCTG CTTTTCTTGCTCTGCGTTGGTTGCGATTCCAGGCACGTTGTATCACTGTT AGCTTGTAACAAACACTGCTGATAGGCTAATGACTGCTGCGCGCAACTGA ACACATTTCACGGCTTTCTTTCAGTCGCGTCTCCGTTCAACTTCCGCAAT ATCCGTATAATTCGTATTATCCGTGTAATCCGTATTTTCCGAATCGCGTT CAGACGTTCACACCAACAACTGCAATTCTAGTGTGACCGCAGAGCTCGAG CTGCACGATACCTCCAATGAGAGATGCCATATCGATGCTTACGCATTTTA TTAACATCGATAGACATTTCTAGAATGTCTAGACTTTAATGCTTGGATTT TCCAAAAACTATAATCTGTTTCCAAAAAGTTATCGATAAGTATCGATCAG TGTTGAAACTATTTGTATTTTATATTAAATTCTGGGGTGTGACTAGTAAT ATTAGGAATATAAGCTTTAAAGAAAAAATCGAATTCTTTATAAGTGATTT AGTTCGAACGTTAACTTAAGATTTGCCACCACAATCGGAAAGTAGCTATT TTCTAGCTAGCTTTGCCCATTAATCGATTGGTGGCAACACTGGTCGGCAC ATCCCACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTG AACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGA CGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACC GCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAA ACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGAT AACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCA ACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGG GCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTT CGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGG AGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGA CTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGT CCAACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCA AGGAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTC TTCCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAA GGTCTCGACTGCGCAATTGTGGGATTCAGGTTCTAATGGTCCTCTTTTTT CCTCGCAGCTCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCA TCGCCGCCGAGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGC CCAGCAGAGTAAGCCAGGAAGAGGTCGACAATGTGGTCCCTGGGCCTCCG ATACAGTGAACGCTGCCTCAGGCAGGCAGTCCAAAGTCTCATGCACGCAA TTTCGGTTGGATTTTGTTAACTCGAATGCGGGATCTGCTCATAATTTGAT TAGTCATTGAATTGGTTAGCACATATGTATGGTTCTTGATTTGGACGAGA GATATACGTGATTTTTGTGATGTCATCATCTCTACATTCTGATTGCCAAG CCCTTTTTTAAGCTCTATGAAATATTAGCACTAATATCAATTGAACTTCT AATTAGGAATGATTGCAAAAACATGGTTAAGTGTTAAGTAAATAATCAAT TCGATATAAAGAAAGTTTCGTGCTGTTTAGGCTTTGTATTGGATGGTTTA GTTTAATGTGTTTTAATGTGCACAAAAATTACCCTATTATTTTGAAGGAT ATATAGTGTAGAAACGATATATATAGGGTTTCTAGCAGATAGCTCGAGTT TTAAAATTCAACTGCAAATTGGCATTGGCTAAAGGTGCGATACAATCACC GATTGATCTGTTCTGCGGAGCTTTCGCTGTTCTTCTTGATTAACTGCTCG CTAACACTCCGTCCCGTTCATGAGAAATCCATTTCACTGCGCACACTAAC CTCTAACAACACAGGCACACAACTTATGTTCATTTCGTTATTTGTTTACG ATCGATTCGCAGAACACGATGACTACCGTCGTGCCGCTGACTATGCTAGA TTATCATGGAACAGTAAGCACCTCACTTGCAATACCAAGCCCGAGATCCT CCGTCGGAACGATCGCCAGATTCGTCAATTAAACCTCACTTTTCCTCTCT TCCAGAAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGA CGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAG TCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCT GCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCAC CGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCG ACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGT AAAGGCCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACC ACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCG CCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACT CTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGGTGGGTCTCA TTCTCAACATTTGTGGTTAATTAGCCGTGGCAGTGTCTTAGAATTTACAA CTTAGAACAAACAAGTTAGATTTACATCTTCGAAATCGAAGTTCAACGAT TAGGCTCTGCGAAAATGGTTTTTAAAGCCTGAGCATCTTGAATAAGAGCT GTTTTCTATAAAACAAATTCATTGTTGCAGGTTTTCATGTTTTCATAGGA AAACGCATTAGAACCAACTTCCCAACTACTGATTAACATGTTTGATATCA TTTACAAGGAAGAACTAAATATTCACTTGACTAACGCCTGGCCAGTTTCC TCCACAGAATCCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTG GACGAGGTGGATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCG ATGCTGCCTGGCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCC GCCTCCTGGTCAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAA CCCCTAACCCCTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGA TTTTAAATAGACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGAT AAACGAAATAAAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAAT ACCATACTGATATTTGATATTGATTTGATATTTGGTATCAATGGGCTTCT GTGGTTCTGTGGTTATACCATAATAACTTTGAGGTATCGTAGTTCTAATC ACCAACAGGCAAATTGATCTAACTCGAAAGAGTTTTTGAAATTCTGGGCA ATAGAAATTGGATCATGTATACATATAAAAAATGACTATTATATAAAATG GTATGTACAGCTGTGTTCAGAAAAATAGCAGTGCGAGGAATACTAATTAA TACAAAGGTATTTTTCCATGTCCCTTTTCGGAATTGACTTTTTATTCCAC TTATTTTTGTTAAATGGAATGTGTATATAGGGAAAAAAAGAAAATCCGGT TAGTTTTTCATGTTATCCTTTTTTTATTTACTTTCTTAAGCGAAATCACA ACTTTTAGGCTGTTCATAAGAATAGCAGTGTCTGGTTTTGACCAACGTAA AGTCAGGAAATGATCAATATTTTTAAAAAGTGAGTTTGATTAATTCGTAC ATTTAAAAGGGGAGTAAATGAAAAAAATTATATATTAGTGGGTAAAGGAC AGCACTGCTCCCAGGAGAAAAGAATGTTAATTATTAAGCTTAGAAAGGAA GTAAAAACATATATGAACATTCAAAAAACCCTTGAATGTTCTGCCAAAAT GGTATCCAATGTCATTAAATATGAATGGAAGCCCGAAAACCGTGGTTCCA TAGATATAACCACAGATATATAGCATCGACGCATTGTTTCTTACAGCAAA GTCTATCCTTTTGCATCCTTTAGGGACATAAAGTCTGAGCTCAACTTGGG AATCAGGGACGATACTATTCGAAGACGACTACTAAATCAAAATTTCAGTG CGAGGAGTTCACGAAAGGTTCCCCTACTTAGCCCAAGGCATATTTAGGCA AGGTTAAGCTTCGCTAAAACCTACCTAAACTGGCCAGTCTTCAAATGGCG TAATATCCTTTGGACTGATGGGTCAAAAATCGTGCAATTTGGTGGAACGG GTTCACTACAGTATATCTGACGACCTCCAAACACGGAATACCACCCAAAA CACCCACTGAAGACTTTCAACCACGGTGAACCTAAAATTGTGGTATATGC TTGTTTTTTTTTTTACAATGGTATGAGTCCATAACATATGATTTATGGTA TTATAGACCAAATAGCATATGTAAATATACTCATTGATGTCTTACTGTAA TATTCTGAATATAATATGCCCTTAAAATGGACATTCCACCAGGATAATGA TCCGAAATGCAGAAGCAAATCGGCAAAGAATAGGTTCACCCAAAAATGGA ATAGATGCAATGCCGTGGCCAGCACCACCTTACGATTTAAACCCGATTGA AAACCTGTGGGGGGAAATTAAACAAAATGTGTCGAAGAACTCCCCGACGT CTAAGGCTTAGATTTGGAAAGTTGTGCAGGATGTATGGGCAAAAATTCCC CCAAATGATGCCAGGACCTGGTGGACTCCATGCTGCGTGGGTGTAAGGCT GTGCTGGCTAACAAAGGCTATCCAGCCAAGTATTAGGCCCGAATTAACGT ATTAAAAAGAAAAACTAAGTTAGTTCTAGGTCAAGTTGAATTTTGTTACT GTTTTTTTCAATATTTACATTGAAAACCAGAGTTTCTACCTATTTTGTTG TTTTAATCTATATTTTCGAAACTATTGAAGAAATAAAAGTGAAACATTTG TTAAATTGTTTAAAATTAAATACCTAATGATATTATAAAAAAAAAAAATC CCATTAAAACTGTAAATCCTAGGAATTTTTGATCTTAAACTCTCAGGTCC AAAGCACTGCTATTTTTATGAACACAGCTGTATATATAGAAAATATTTGC TAAAGTAACTACTACTCTTGCGATTTATGAAAACGGATTCATTCAACCAC TTTTATGACGAATTTCATTGTATTAATATCTCAATACTGTAGGTCTGAGA AAAATGATACATTCTGTTTGGTCAGCTGCAAGTTGAGTATACTGACAGAA AAAAATATTTCAATAATGTGCGAAAGGAATTTTGACTGAAAACGCTGAGA ATGATCTTTTGTTTGAGTGAGATTGATTTCACAGTAGTTTTACTTTCTGT GTACATGCTAATTTGATACCCCGCACCCATGGGAAGCAGCTTGAGGTTTT TCCGCGGCATTAGTGCATTTTCGAAATTGCTCGAGTGTGACGCATGCAGA TCTCAATCTCGACCACGGGCTTTTCGTCGCCAGCGAGTGTCCCTCCCCTT GGAAGGCAATCTCACTTATGTCATTCATTTGACGCTAATTCGACATTTAC AGAAAGTATTTGCTCGAGGAAGATAACCAGAAGTGCAAGCAAATGATTCA TAATTGATTCTATTTTGACAATAATTGGGAAGACAGCACTGTAGGAAAAA GGGGGCAATATGATCATATTCCAAATAATATGAATATTGATCATTTTAAT TTCAAATTGTGTATATTCTTAGTAATCATATTGTATGTATGGCTTTTCCA TTTGGGAAAATCCGTATGAGTTATATTTTATTCCTAAGAATTCGTGTTGC ATTCAAAATTGCTGAAACAGAAATAGCTGCAAAAAATCTTGATTTGTTCG TGCCAATTGTTACATTGCTTTAATATTTTAATCTTTAGTAAATGTGGGCA ATCCATCGAGATGATCTTCAGCGCTTGTATCTATTAGATACACTTAATTT TCCATCTTTAGGGGCAATGACTCATCCCAGTACGAGTTTCATTTAGATAG TGCGATTTCGATCAATGGAGATACGAAATTCTATTTCTCTTTGTGTGCCG AGCGTTGTGGAAATACATTTAAATACGGAACAACGTGAGGTTAATTGTGC GGAGCACACTTGTTAATTAGGGAATGTCAGCGGGCGCGACAGTTGGCGCT CCCCTCACCCCTTCCCAACCCACCGAAATCCGAAAATAATGCTTCCAAGC CACGTTTTCATTGGATTACGTAAGCTGTAAACCAGTTTATGATGTTGTTG TTGTTACTGTTGTTGCCAGTGTGTGTCAAGGAAAAGCTAAACACAATTAC AACGCCCTTCTGTCTGGTAATTAAAAACGGAAGCCATGCCCGAAGCCATA GTAGGCTGGCTAACGAGACCTGCACATCGGCCCAAACTGGTTGGCTTTGG CTTTAGGCCACTTTCGAGGAAAATCCGCCCACGACGAGCCGAAAACCGCA AAACACGTCCGCCAGTGGAAATCGCATCGAAAGTTTTGCGGTTTCGAGCC ATTTTTCCATTAACTCGAAATTCTAGAAGATCAATTCAAATCAATGTTCA TGTGAGATTTTCCTTATGAATACCTGTATTTTTATATACCGAGATACGTA TGTACAAACAATCTTATCCTACAATTTCCTGTTTTTGAGGCAGCTTTATC TTATAAAAACTGTTCGAAACAAAATTATAATTTCCATATACATATCTTCA ACGTGAGGTTTTTGCTCCCTTTTTTCTGTTCTTAATTTTCCTATTGGCCA GGCAATAGTGCATTTGCATAAATAAAACATTTATTGGTAGTAAAAGTTAA ACAAATATGTACGTAATTCCCGAAACATTTCAAATTTGCATAAATAAACA AACGCGATTGGTAACAGAGAGCGGAAAAACAAGTTACAGTAATTACCGTT GGGAGGGGGTGACGAAACAAACCAAAACAAAACGAATTATGCTCGTGTGA GTGTGCGCGACGCAACAGGTTGAGGCTGCTTGGCGCAGCTTTTGACCGAT CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGA GAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGA AACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAG GCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAA GCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTA GGCCAGCGAAACGACATAACGCTCCAAGTGGTAAAGTGAGACCTGCCAGT GGCGGCACCCAACCCGAAAAAGCCTAACCAGCGACCACTTTCCAGTTATC CAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGT AACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCAC CTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACC TGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAAC GAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCA GGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTA GCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGCGTCAATGCC AACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGAGGCCACCTT TCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCTGCCAGCTGT GCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTCTCGGAGACC CTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGCCGCCGCGGT TAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGGAGCAGACCA CAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTATCCCTACATC TGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCT GCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATG CTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCA GCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTG TCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATA CGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGT CAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAA CGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACAC CCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAA TGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTG CGTGTTTCCCAAATAAAATGCCGAAATACCTAACTTTTCACGCTTGTATC TGAATTTCTTAATTCCATTCCATTTTTTTCGTCTCCCGAACGATCAGTTG CAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAA TGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTG CTCTGTTCGGTGAGTAGCATAGATACATTTAAGATTACATAATTTCGAGC GGCCAAGCTTAGATCGACTTCTCAGCCTTTTAGGCTGGCAGTGAGATCAT AACTTTCGTGCGGAATAAACTGGTTTTCCCAAAATTGGTGTTTTCAGTAT TGAAAGGCTGAGAAAGTCGAGGCCCACAAAAGTGGTGAGCATGAGTACAT TTTAAAGCCACAGAAGGCACTCTCGTTAAATGCATTTTTGTATTTTTGTG TTCTTTAGGTCGGCTTTCATATTTACATATCATGAAATTAAACATATCTC AATTAATGTTTATTAAGGACCCTTAAAGTAGGATCTATTATAGCATTTAT GGTGTCTCTTTTCCGGTCAGCACTATCACTTTCCGGTTACGAAACGCACT GTACGTGCAAAGTGGGGGCAGAGCTTGAGATCATCATCAGTATTCCAAAA CCAGTTATTAAAATTGGGCTACGTTTGTGACGTAGCGGTATCCGAAAAAT TCTGTATAATTTTGTGTACACTACGTACACTTTTGTTTACTTTGGAGTCC CAAAACCAGTTTGTGTTGTTTCGGTCCCCACAACCGAGCCCCACATCCAC AAACATGCATCCCATTAGTCGGAGTCAGTCCGAGGTTAACTGGTTCCAAA TGGCAACCAAACAATCATTGAAACGCCAGCAACGGTGGCATTTCGATATG GTTTTGCAACTTCTAACTCACTGCCCCAAAGTCACTGCACCGCCAGGTGG AACTGTACTTCGTCCAACCAGTTTGGGGCTGGGACCCTGACTTGCTGCTG GTGGGAAATCTGACTGCGTCGGAGTACCAGCGCATTATTCGCGTCACGCA AACATGGATGTCATTCACTACGGGCGGAAAAACATCAGCACACGGCGCTA ATTCTTCAATCGTATGCAGTATACGGATATAGAAAATTTACAAAACAAAA CCATTTTTTGTTGATGGGAAATCGGTAAACGAGATGGATGACCTATCTAC TTGAAATAGGTCATTTGATTTGTTCAAGAGTTCCAATCCGCAGTTCTCCA ACCTTTTTGATAATTTAAAGTAGCTGCAATTAACTTAAGAACCAACATGG AAACATACAAATATTTTGTCTGTGTGTAAAGTCTGCCGCCACTTCAGTGG AAAGTTGTGTAATGGTTCAAGAGGGGGGGGGGGGGGGGGAAGGGGGTCTC ACCCAAAAATAGTTGACTTAATTTAATGTGAACTTGCTCCCATTGTGAGA CGACGAGCCAAAACTCGGAAACAACGAAATATCATCTACACACGCACATC ATGGAATGGAAACACGGGGGTCGTTGGCGGTACACTTGAACTCAATTTTC CGAGGGAGGGCGATCTAGAAATGCCAGACGAATGCGAGTGGGTGGACTGG TTATTATTATAATTGTGGACCAGTGTCGAAATGTCGCTCTCTTCTGATCG GATGCGATGCTAACTATTCTGATCCCACGAACCGCTGAGCTCGGCGGCTG AGTCATGCTGCAGTTTGGCGCAATCCTACGAATTTATGAACTATAGTTTG GCTGGGGGTGGATCTAATCTAATGACTACGTCAACTGATACAATCAAAGC CAAAGTAAATATGTTTTTAATAGTTATCGTCGATGGCCAGGCGCTTTTAT GCATAATCTTAATTAACGAAGCGAATCGGATTGATAAGAGATAAGCTTGT GATAGCCATGCAAATAGCCAATCTGAAACTCTATAAACGAAAATCGCCGA AGAACTGGGCAATAATAGAAAGTAGTTTTAATAATAAAGCAGGTGATTTC GCCATATCGCAAATATTGAAATGCATGTCCCTGGAAGTAGTTCCAGTTTC TCGCAGTGCATATTATTTGTCGAACAACAGGCATGAGCTTTTAACGCCTA CAAGCTTTTTAATGAAACAAAAAAGCTAATGATATCCCAGCCAGCATTTA TATGGATGAATATTCTTCAGGCGATTTGGTATCGCAAATCTTGTCAAATC ATTTGATCAAATTAAATCATAAATAACTTAGAACTGTATTAATTTATTAC ATGATTAGTAAGTCCAATATAAAACGGATATGAAGTGATTGTTTTTGACC AATTTCTGTCAAAATCTGAGGGCTTGAGAATTCAAGTTTAGTTAGATTAG ACAACCCTGGTTGGCTCAGGATTGATAAACTCAACATTTCCCTTCCTCAG ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGT CCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCG TAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGC TGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGGTAGAGTA CTGATCCTGCATCGTGCCATTCATCTTGCAATTCAAAATGTATTCTTTGT GGCAGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTG GTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGA CGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGG ACGCGATTCAGATCAGCGTAAGTATTTAGGGACTTCCAAGGACATGTGAC CCGCCTTCAACTGACTTTCTGCCGCTCCCGCAGATGAAATGCTGCGGACG CAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCT GCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGC AAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTA TGCCGGTCTGGTCATCGCCGCCATCGAAGTAAGTTATTGTCCAGAGTAAC GCAATCGAACGAAATCGATCATCGAATCTAGGTGCTTCCCCATGTGAATT TCGAAAATATGATGGATGGGTTCATGTTACCTACCTTCCATTGTGATTTC TTGGGGATAACCAAAAAGTACTAAGTAATGTAAATCATAATTCGTAGCAA TGCAGTTTAGTTTGTTATTTTACCATAAGCGTTATGAGATTTACACCTAC ATGTATATTCTTCCAATATACCATACTCTGTTTGCTTTCAGTTTGTGGGA TTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCG TGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTG AAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGAT ACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCA GCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTT CAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTAT ACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA GAGTTCAGTCTTTGTCTTAATGGGAAAGCTTACATTGTTTGCAATTCGAC TTAATCCCTAAAGCACCTATTTTTCTAAATTGCCACGGGAGGATTTCGGC CATTCGCGATAACGTTTTAATCTGCAAAGTAATAAGTATAAATAGAGTTG GCCGAAACCAACAAGTACACTTTGATTACAGATCATTATCAATCATTGGC TCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGT TAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTT TATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATT CCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGG GAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTA GGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATA TGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGT GGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGG AATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACC ATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGAC CACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACA AGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGG CCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAAT AGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATC GAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAG CACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCA ACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATC ATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACAC CCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAG TGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACC ACCATCGTAAGCACTCGGAAATCACCCACTGACCGAAATTGGATTCTAAA TGACTTGGCATTCCTTTCAGTACGCCATCTGCATGCTGATTCTGTTCGGC CTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCT GTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCG CCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCGTAAGTTTATCGAAA TTCACCATCAGATGTCATTAGTTTTTTCCGGATATTTACGTATCTATTCC ATTGCAGTTCTCTTGCTGTGGCAACACGGGATACCAACAGTATGAAACCG TGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCG GAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTG GGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCT TCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGG AAGCGCTAGAGCCGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCAT AGCATAAATCCAACACACGAATTCCTCACTCACTCACTCACCGTAAATAA ACCAGAATAGGTTAAGCCCAATGAAATATTATTGCTTATTCGCTGTCTAC CTCTGGCTGCCGTCTATCTAATCAAGACAGGTTGATGTTTTTCCAAAAAG TATGTCCTTATCGGCCTGTTAGCCGAGTGCCGCGTTTCCGAGATCGAATG CCCTCAGTAGTGGTGAATCACCTCCATATGGCAATGGCTATCGATCTCCG CCCGCCGCCCAGTGCCCATTATCTATTTTTCGTTTCGGCCATGATTATGA TAACAGGCACTTGCGTATCTTTCCTCCGATAGCGCCCGTGTCTGTTGGCC AATTTAAAAACAGTAGCCCATCTGGAGGAGCAGTCCAATCGAACGACAGT AAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGA TAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATAT ACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATAT TGTCAATATCGTGTTTTTGGTAAGTGCTTGTCGGTTGAGTATCTAAGTAA AAGGAATTAATAATGTAATGAGACGTGTAACAATAGACCAAACACTACTG GGTGCAGATCCCAAATAGGTTCCAATTATGGATAACTTCATACTCTCCAA TTACTTGTGTTATAATGAACTTCCAAAAAATGTCCATTAATTATGTTAAT TTATTTATCAAACTGTAGATGTTTATTTATTTGCATATAAGACCTTCTAG CTGACTTCTGTCATTCATTAATCAAGTCATATGCAATAAATATTTGTGCA ACAAATATCGAACATGTATTATTTAAAACAAGTGAAATGAAATTTGAAAA TCCATAAATTACGCATCGGTCGCTTCCTTTCGATTGTCTTTGAGTCACAA GGTTTAACACTATTATTCATATAAATGTGCTGGCATAGATAATAATATCT ATCTGTAATGCAAGTGTGGACGGACATACAGAATTTTATCAGTTGATTGA CATTATCAGTGTTTTGTAATATAAGTAATGAGCCCAAAATGAGCTTCAAA GGGGGCACACATGCACACAAGTTCACATTTTAGCAAGGCTAAGTTGGAGT GAATAAAAGATCATTTAGAGAATAAACTAAGGAAATACAACAAACTATTA TTTACAAATGATTTATTATTTATCCAAATAAATGTGTAGTTACTCGCAGT ATTAACGCAGCTAAAAGATACATTTTTCACCTTAAGAATTATGCCAAAAA CAAGATAAAGGTGATTAACGTTTGTTTTTTTTATCAGCTACGTTTTTAAA CTAGCCATATCCGTCTGATTGTGAATTTCATTAATTTGTATGCAAGTATA AGACTTGATTATTCACTTTGTTAATCACTTTGTCAACTTAAAGAATCAAA TGAAGAAATTTAAGTAAATCTTGGTCACCGACATCCTGAAGGCTATTTTA AAAGCTCATATCTTAGTCCAGTTTGCGGACAAGTTTTCAGTACATAGATA TTCCCGGATAATTAGAAGTCCATAAAACATTCATTATAATGTGGTATGCT TATGACCATAAAACTGTTAGGCAACCAGAGATGCCTTCTAGTAATACTCC GAATACTTCCAGATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCAT GCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGAACTGTACTTC GTCCAACCAGTTTGGGGCTGGGACCCTGACTTGCTGCTGGTGGGAAATCT GACTGCGTCGGAGTACCAGCGCATTATTCGCGTCACGCAAACATGGATGT CATTCACTACGGGCGGAAAAACATCAGCACACGGCGCTAATTCTTCAATC GTATGCAGTATACGGATATAGAAAATTTACAAAACAAAACCATTTTTTGT TGATGGGAAATCGGTAAACGAGATGGATGACCTATCTACTTGAAATAGGT CATTTGATTTGTTCAAGAGTTCCAATCCGCAGTTCTCCAACCTTTTTGAT AATTTAAAGTAGCTGCAATTAACTTAAGAACCAACATGGAAACATACAAA TATTTTGTCTGTGTGTAAAGTCTGCCGCCACTTCAGTGGAAAGTTGTGTA ATGGTTCAAGAGGGGGGGGGGGGGGGGGAAGGGGGTCTCACCCAAAAATA GTTGACTTAATTTAATGTGAACTTGCTCCCATTGTGAGACGACGAGCCAA AACTCGGAAACAACGAAATATCATCTACACACGCACATCATGGAATGGAA ACACGGGGGTCGTTGGCGGTACACTTGAACTCAATTTTCCGAGGGAGGGC GATCTAGAAATGCCAGACGAATGCGAGTGGGTGGACTGGTTATTATTATA ATTGTGGACCAGTGTCGAAATGTCGCTCTCTTCTGATCGGATGCGATGCT AACTATTCTGATCCCACGAACCGCTGAGCTCGGCGGCTGAGTCATGCTGC AGTTTGGCGCAATCCTACGAATTTATGAACTATAGTTTGGCTGGGGGTGG ATCTAATCTAATGACTACGTCAACTGATACAATCAAAGCCAAAGTAAATA TGTTTTTAATAGTTATCGTCGATGGCCAGGCGCTTTTATGCATAATCTTA ATTAACGAAGCGAATCGGATTGATAAGAGATAAGCTTGTGATAGCCATGC AAATAGCCAATCTGAAACTCTATAAACGAAAATCGCCGAAGAACTGGGCA ATAATAGAAAGTAGTTTTAATAATAAAGCAGGTGATTTCGCCATATCGCA AATATTGAAATGCATGTCCCTGGAAGTAGTTCCAGTTTCTCGCAGTGCAT ATTATTTGTCGAACAACAGGCATGAGCTTTTAACGCCTACAAGCTTTTTA ATGAAACAAAAAAGCTAATGATATCCCAGCCAGCATTTATATGGATGAAT ATTCTTCAGGCGATTTGGTATCGCAAATCTTGTCAAATCATTTGATCAAA TTAAATCATAAATAACTTAGAACTGTATTAATTTATTACATGATTAGTAA GTCCAATATAAAACGGATATGAAGTGATTGTTTTTGACCAATTTCTGTCA AAATCTGAGGGCTTGAGAATTCAAGTTTAGTTAGATTAGACAACCCTGGT TGGCTCAGGATTGATAAACTCAACATTTCCCTTCCTCAGATATGCGGCAT ATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGG ATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATC ATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGC CATTCGGGAATCCTACTGCATGTCCATGACGGTAGAGTACTGATCCTGCA TCGTGCCATTCATCTTGCAATTCAAAATGTATTCTTTGTGGCAGTACTCG ATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACAT GTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGA AGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAG ATCAGCGTAAGTATTTAGGGACTTCCAAGGACATGTGACCCGCCTTCAAC TGACTTTCTGCCGCTCCCGCAGATGAAATGCTGCGGACGCAGTGGCTACA CCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACC AACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTT CGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGG TCATCGCCGCCATCGAAGTAAGTTATTGTCCAGAGTAACGCAATCGAACG AAATCGATCATCGAATCTAGGTGCTTCCCCATGTGAATTTCGAAAATATG ATGGATGGGTTCATGTTACCTACCTTCCATTGTGATTTCTTGGGGATAAC CAAAAAGTACTAAGTAATGTAAATCATAATTCGTAGCAATGCAGTTTAGT TTGTTATTTTACCATAAGCGTTATGAGATTTACACCTACATGTATATCTT CCAATATACCATACTCTGTTTGCTTTCAGTTTGTGGGATTCGTTTTCGCC TGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTA ATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTA CGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCAT TCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATG ACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACT GAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGAT TGCAATAAACGGAGAAATTTATTTACAATTTACGAAAAGAGTTCAGTCTT TGTCTTAATGGGAAAGCTTACATTGTTTGCAATTCGACTTAATCCCTAAA GCACCTATTTTTCTAAATTGCCACGGGAGGATTTCGGCCATTCGCGATAA CGTTTTAATCTGCAAAGTAATAAGTATAAATAGAGTTGGCCGAAACCAAC AAGTACACTTTGATTACAGATCATTATCAATCATTGGCTCTATTGACATA TTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTT TAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGG GCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAA CCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGC TAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATC GGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCG TGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAA TGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGG GCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATG AATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGAT CTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCA TCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAG CGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTG TCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGAT TATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTG TCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCG TGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACG ATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCC GATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCG GATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTAAGC ACTCGGAAATCACCCACTGACCGAAATTGGATTCTAAATGACTTGGCATT CCTTTCAGTACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCC CTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGG CAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACC CCATGGATGCCCTCCAGTTGGCCGTAAGTTTATCGAAATTCACCATCAGA TGTCATTAGTTTTTTCCGGATATTTACGTATCTATTCCATTGCAGTTCTC TTGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCT GCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGC CAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATAC GGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCA TCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGC CGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCA ACACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGT TAAGCCCAATGAAATATTATTGCTTATTCGCTGTCTACCTCTGGCTGCCG TCTATCTAATCAAGACAGGTTGATGTTTTTCCAAAAAGTATGTCCTTATC GGCCTGTTAGCCGAGTGCCGCGTTTCCGAGATCGAATGCCCTCAGTAGTG GTGAATCACCTCCATATGGCAATGGCTATCGATCTCCGCCCGCCGCCCAG TGCCCATTATCTATTTTTCGTTTCGGCCATGATTATGATAACAGGCACTT GCGTATCTTTCCTCCGATAGCGCCCGTGTCTGTTGGCCAATTTAAAAACA GTAGCCCATCTGGAGGAGCAGTCCAATCGAACGACAGTAAACGACGCGAG TGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGT GTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATG GGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGT GTTTTTGGTAAGTGCTTGTCGGTTGAGTATCTAAGTAAAAGGAATTAATA ATGTAATGAGACGTGTAACAATAGACCAAACACTACTGGGTGCAGATCCC AAATAGGTTCCAATTATGGATAACTTCATACTCTCCAATTACTTGTGTTA TAATGAACTTCCAAAAAATGTCCATTAATTATGTTAATTTATTTATCAAA CTGTAGATGTTTATTTATTTGCATATAAGACCTTCTAGCTGACTTCTGTC ATTCATTAATCAAGTCATATGCAATAAATATTTGTGCAACAAATATCGAA CATGTATTATTTAAAACAAGTGAAATGAAATTTGAAAATCCATAAATTAC GCATCGGTCGCTTCCTTTCGATTGTCTTTGAGTCACAAGGTTTAACACTA TTATTCATATAAATGTGCTGGCATAGATAATAATATCTATCTGTAATGCA AGTGTGGACGGACATACAGAATTTTATCAGTTGATTGACATTATCAGTGT TTTGTAATATAAGTAATGAGCCCAAAATGAGCTTCAAAGGGGGCACACAT GCACACAAGTTCACATTTTAGCAAGGCTAAGTTGGAGTGAATAAAAGATC ATTTAGAGAATAAACTAAGGAAATACAACAAACTATTATTTACAAATGAT TTATTATTTATCCAAATAAATGTGTAGTTACTCGCAGTATTAACGCAGCT AAAAGATACATTTTTCACCTTAAGAATTATGCCAAAAACAAGATAAAGGT GATTAACGTTTGTTTTTTTTATCAGCTACGTTTTTAAACTAGCCATATCC GTCTGATTGTGAATTTCATTAATTTGTATGCAAGTATAAGACTTGATTAT TCACTTTGTTAATCACTTTGTCAACTTAAAGAATCAAATGAAGAAATTTA AGTAAATCTTGGTCACCGACATCCTGAAGGCTATTTTAAAAGCTCATATC TTAGTCCAGTTTGCGGACAAGTTTTCAGTACATAGATATTCCCGGATAAT TAGAAGTCCATAAAACATTCATTATAATGTGGTATGCTTATGACCATAAA ACTGTTAGGCAACCAGAGATGCCTTCTAGTAATACTCCGAATACTTCCAG ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCT GAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCA TCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGG TGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCGGTAAGTTT GCGTGAAGAGCATATCCCAAGGAATTCGAGCTAATTGAAGTTGAATGCTT TGCAGTACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTT ACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAA TCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTC TTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAAC AACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCA GGCCACATGCAACACCCCCTCGGTCTACCAGTCGAGGCCCGGCTGCAGCG CCAAGTTCGAGGAGTTCTGGAACGACAACATGGACATCATCCGCTGGTCC GGCCTCGGCCTCTGCATCTTCGACCTGGTCGTCTTCCTCATCGCCGGCGC CCTGACCAACTGCATGCGCAGCCAGAACGCAGGTCGCCAGGTGTACGCCT AAACTTGTGAGGAACAAGCCAAAGGCCAAAGGATCTACATATGTCTACTT ATGTTACCATATAACAAACTGTTTTTCGAGCCGTGCCAATATTAATATAT ACGTCTACATTTCGCCTATTTATCAGTTACTACTTATGTTATTCTTTATA CTCTTTTTGGAGCAATGCCAATATTAATATATACCGCTACAACATTTACC ATTACTCGTCTTTCTTATAAGGATAAATGGGTTATTTTACCAATTATGAT TTTTCTAACTGGCTTAAAACTTCTAAAGAGTATATTTGTTCATCTATGTT TTCCTACAGAATGTGCAGTATTTGAGGCATACACTTAGGCTGTTTTTTTT TTTTTTTTTTGATTGCCCTAATGTTTTCCATAAGTTGGAAAATTTTGGAG AATTGCTGTTATGTTACGCATATGTTAAGACAATAACATTGACCTGAATG TGATAACATTAAATTTCCCTTATTAACATTTGGAACATATCCAAAAAATT CCAATCGCTCCAACTAAGTAACATTTAACAATTTCTCCAATTTATTATGT GACATTCTCAACTTTCAAATAGAAATTTCAATTGTGACTAGATAATGCTA CTAATACTAATTTCAAAGAGAATTAGCCAATCCAAGACGAAATCAAATAA TATTATTATATTATTATATTATTATTATTAATAATAGCTTTGTAACCCTG ACTAAATCATTGACAAATGATTAACGAATCCAAGGTGCAAGAGTTCAACT TGTGATTGATTTATCCAACTGATATTCACACAGCTTTAATATGCATATTA CTGGATTTACGCCGGCTTTAAAATAGGTTTGAAAAAGTCAGGAATAGCGA TCTAAAAAGAAGAAATACATTCACCAAATATTTTTGACTTTCGACTAGAA GGCACGATTTTTTTAACATTGCGTTGATCAATGTTTTGAAAACCAAACTG ACATTGGCATGTAGATGTTTTGCTTATCAACACAATTTGTTATATTCGAA AGAGAAGACAAATATGATAATTATTGCTTTGCGTTAATGTAGAATATATA TATATATATTTTCAAAATATTTGTGTTGATTATATTAAAGAATACATACT TTACCATTTATTAATTAGTCCACATAGTGAAAAGAATTTGTTTCTTAGAG TTATCGAGTTTTCCCCAAAAATCACATGAAACTACAAAACCAAGATATGA TGTGGACTTTTTCTTGCTAGTAAATATAGTATTATTAAGTCAACACCTAT CGTTCCCATACTCCATCATTCTAGATACTAATGTTAGGATGCAGTTGTTT TGCTGTTTTCATATCTCGATCTCCCTTGCACTCTCATTGGCTTAGTAAGA AGTATCTATTAGTCGAGATATATTTATTTTAACCTTATCGTGAAATGTCT TTGTTTGGACCATAAACTATCAAATGTCGCAATTATATACAGTAAGCATG CGAAGCACTTTGTTTTATTTATTCATATTGACTTTATGACGTTAAAGAGG GTCGGGAGATAATCCTAATACTATGCTACTAATTCATCGTTTCATCGTTT AGTAGTTCTGGCGTCTCTGCGAGTTGCGGGTCTGATTGGCCAGGCAGCAG GCGAAAATGAAGGCCACAAGCTGAAAAAAGTACCATTCAGTTTGGCGAAT TCAAAGAACATTATACGCAATCCTCACCTCAACAGCAGTCACACCCAGGC CAGCGTACTTGATGATGCTCACGTTGGTGTCCCAGAAGGAATCAACGGCC TTCAGGCAACTGGATCGCGTCATGACTTGGGTTAGTGCGCAGGTTCCATT GGAGGGCGAGTCGCAGCAGGAGGCGGGATACGTAATGCCGTAATCAGCGA AGCCGTTCAAGCCGCAGCACTTGAACTGGAATCAGAGTATATTCTCGGTT AAGCTATCTTTATGAATGTGGAACAACAGTAGACAATCTTCATTGAATAT GAAGTAAATAACAAAAAGAATTCACAATGTAATGCTTGAGGGTCAGCAGA ACTCACCGATCGCTGCAGTGTGTCCATGAGGAGGGCATCGGTCTTGCGTT GATCCCATATGGTCTGGACGATCTTCTCCAAAGATTGCTGTATCTGCACA TGGTCCACCCACACGTAGATAATGAGAGCTAGCTGACTAACCAACAGCAC CAGCATGACCACAGAGTACTGAAAGCAGGAAGGAGCAAGTTGGATTCAAA TGTTGCACCCAGCAGGGCATGTATCATGGGCACCTACCGAGGTCAGAGCA CAGGAATTCTCGCGTATGGCGCCGCAGCATCCCATGAAGGCTACCAGGAA GACTACGCAGCCAAGGACCAGGATGATGATGGCCACGCTGTTTGCCGTGA AGGTCTCGCCAACGCCCGAGAAGTCCTTTATGGTGGACACCATGATGGAG CCGAAGGTGATAAGCAAAATGCCGCATATCTACGTTTGGAAAAACGAAGA GTGTGTGCTAGTTAGTCAGTGGTTTTGGCACCACTCATGGTGGGTGGTGA ATCAGGCCTATTGGATAACAGTCACCCCGCCCAAGTTCCAACTAACTGTC TTCGACCGCAAAACTTACTCCGTTTGTGGAGGGAAATGAGAGTCACAAAA AATATGAATATGTGTACATATGAAGACCACATCATTTTTATTGTGTTCAC ATTAGACCGGATTGATTGTCCATTATGTAAAAATCCAAACCTAACTAGCA TTTGATATATATATAACTACGCCTGTGTTTTTGCATTGTGATTTGCGATC GACGCATTGCTTGCGTCGCTGGGAGGCTGTAAACAATTTCATCACGAATA CTATGTGGTCCCAAGATCTTTGAGGGGGATGGTTCTGAAAATTGTCTACG AACGTATGGTATTACTCATGCCCTTATCTTTCCGAGTACAATGTGTTTTC CGACAACTGTTTCGGCTCATTAGCCGTAATTACGTTCGGCATTGGCATGC AATGATTTATTTAAAGAATGTCAGGTTTCTAACCACTTCCAACCACTTTT CCCAGTATTTTTCGATAAGATAACTTTTGAAAGGAGTATCCATGGCTCTT TGGACGAAATCTTGAGCTTCGAGAGTTCATTTTTCATTGTTTGCCAGATA AGATACCACCCGTTTTTTCACTATTGCTGATCTATGTACATATCTCTTGA GAACCTAGAGTCTTACCACAAACAGTATGTTGAATATGAACAGCACATAT TTCACAAAAACGCCGCCGCAATCCATTGCTGAGATGTACTTGTGTATCAC TTGTGTTCGATTTAAGAGTAAGACGTTCGATGCGATTTCGTTCGTGGTCC GCTTGATACTGAAAAAGTCTGATATATAACAATATTTTTATGAGCGCATT TCCTATCGCGAAAAGCTCTGTTAGATTTTAGCTCTGAATTTAGCGGCGAT AAGAAAAGCGTTGCTGCAGTGGTAGAGATTTCCCAAAAAGTACCTAGGTA TCAAATTGAATAGTAGGTTTTGAGGTCTATTGATAAAAAATTATTAATTT CATATTAAACAAGTTAAAGACGAACCATACATAATATGAGAAACTAGTTG AATAACATCGATATACTAAATCACTTAGCAATAATGTGTAGTAAAACTTA ATAATATAACGATTTTAAAGGAATTTAGAGATTATCTGCAAGATGTGCTT AATGTGGCTCAGTTGGAACAAGGTGTTAGCTCAATGGAATCTAGTGGAAA TGTGCAATTGAAAGGCGGTTACCGAAGTTCCGCTCCTTATCAAAGTTCTC TTGCTGTGCTGACTTTTGCTGGCATATTTAGGGCTTGTTTTGGCGAATCG GAGGTTATAAGAGCGCTCCGCCACGGTCACACTGACTAACAGAAAGCTGT TCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTT AAAGTCGAAGGTAATGATGCTCTCTAAACTAGACCAATTAAAGCTAGTGA GATTCTCGGAATTAGCCAGCGAACTGCAAACGGAAACGAGTGGTGTTCGT TTGGCGCTCCCAGCTCGCCAGAGCACAAAAGCAAATGATGCTGCACGCCG CAAAAAGTGGTTGGGAAGAAGAAGCAGTGCAAAAAAGGACGAGGAGAAGG AGAAGGCAGGAAAACAAAAGACTGCGTAGTACGTGTGGAAAAGTGTTGTG CAAGGGAGTCGGGCGGCGCGTATGCTGCGCTTCCTCTTCTCCTTGACAAA GTGCAGTGAACTTTTCCCATTTTCCCCACTTGAATCTTCGAGTCCCATTG ACGCGGCCTTCGTTGTCTGTTGTCCGCATTTTTGTTGTTGTTGTTGCCGC AGCGGGCACGCTGCATTTGTTATTGCCTTTGTTGTTGCCCGGGCAACGCA TTCGGAAGGGCGCCAAAGAGAACGGGGTGATAATGGGATGCTTCTGAAAG CCTTATCGCCACTGGCCTCAAGCAGCAGCCCTCTCTATTAGTCTTGTCAT TACCAACCCCCCCCCCCCTCCCCCTGACAACCCATGTGTATTTCGTTTAT TTACGTGATTTCGCTTGAAAATGTACATTTAGCCGGCCAATTGATTCATT TGCACACCCGTTTTAATACGACGCATTCGATTGCGCTCTTTTCGCTTCCC CTTCCAGACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTA TGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCGGTGAGTATA CATATGTGTGTGTCTTGATTATGTTTACGTTTCTGGTTTATAACCGACGA AATCGAAACCGATACAAAACCGGTAAAAAAGAGTTGCGTGAAAGCCACAA TGGGACACTATGTTACGAAAGTGCTGTCGAAATAAGAGTCGATAAATTCA TTCGCATACACCGTGTGCATTGTGCATACTCAACAGTGTGTTATCCAGTG ATAAATCCGCGTATATGTATATCCACGATATATTGAAACTTTAGTTATAT GCCCCTGGAGAGACGCGGCGCATTGAGAAGTCGAGAACTCGTGCTTTTCT GTTGTTTGCCCGCTGATTCAGTCTGAGACTCGTTATTGAACTCTGGTGAT GTCATCGCCGACGCCTTCCGTTCAGCTTCCATTCCAGCAACTGGACGGTT TGCTTTGGGGCCGAAACAACCCGGTTCTGAAAAGTCGAAATCACAAATGG CTGGGATTTGCAAGAAAAATGAATAAATCCCTAACAGTCAAAAATTTGTA TCTAAGTCTCTGAAAGGATTTCCGGTAATTAAAAAAAGACTCGCAATTCC TTAGTTAGATATGGATTTTCAGCTATGCCAAAAAAAAGTTAGTTATCAGT TTAAATATAGTTTAATAAAACAGGAATATGTATACAAATATTTATATATG CACATAAAACATAAAAAAACACATATGTACATATGTATATACATACTCTT AAATACATAAAATAACTTATGTGCTCATTATGGATCAATTTCCAACTTAT TGAAGAGTTATAATTATGGTATTTTAAAATAATTCCACATCCCCTTGCTT CACAAATGAGTACGTAAACACTTTCTGGTTAGAAAAAAGATACGATTTCA TTTAACATTTCTGTGTAATATTAAACTCTTATAAACACGATTGCATGTTC GCCCTCAGCGCATTTTTAAAGTAGAGTTTTGGGTTTCAAATGGGCTTTGA GCACTCCCACGAACACACACGTGATAGCCTTGCCGGGCCAAAAGCCTGCA AACTGCGTTTAAAATAATAATTAAGCAAATGATATTGTACTCATCGTAAA TTTTTGAATACTTTGCATTCGCTAAGGCGCCTGCAAAAACACGGCCAATG TATGTGAGTCACTAACTTGAAACAACAAAGCGAAAAGCGAAACGAATTAT AAATATAAAACGATACAGCTGCGGTCAAAATGTTATCAACTATGCTGAAA AATCCCACAACATAAAAATTTATAAACGAAGTATTATCATCTCGCAATGG TATTCTATTACTCTTCTTCCTCTTTACTCTGTACATACATAAGTAGATAA ATGAGCAGAAAGAACCAAAGCGGGGACGAAAATAAAAACTTGTTGCTCTA TAGAAAGAAGAGTGATAAAACAAAGGTAACAGCAATCAACTGGTTGGCAG AGCCGAAGTTTGTAGTATACAACAGTCTACACTTACAGCGAGCCGTGTTT ATATTTATCTGGCCCGATCGAGTATATAGCCGAGTACATAGCACACTTGA CAGACAAGCCAAATAAATTAACAAGCCGCTTTTAGAGCTCGCCGAGCACC ACCACAGCTAAAAGTGAAAAAGCTGCCGCCACGCTTGAAAAACAGCAGCG ACAAGCAAAATGGCAGAACAACAGTTCGCAGTTTTTCAGAAAAATGTTTA AAAAAAACCACTCGATTACTGTCAGAATGATAAACACATTGGTTTCCACT ATCCCATAAAAATTGCATTATTTTCATTGAAAGTCTCGTAAAGTATAGGA TTTTCGGTCAAATTAGGTGTTTGTTATATGTTAATGTTAGTTACTCCTCA GTCTGTGTGAGCGGGGTTTTCCCAGTCCCTTGGCAAAAAGTGTGCTAGAA CATATGACGAAACTGTATTGCCATAATTAGCGCAACAAGTCAGTCACAGC TGCTGTCGGGTAAAAGGGCGTGCAGTGCCGGCCATGAGTGTAAGGCCGAC TGGTATTGAATGACCTGCATTCAGCTTATCGATAGCCGTTTCCTGTGCCA CAAGTTGTAGTGCAAACAACTTCTGGAGTAAATATTTATATGTATATCCG TTTAGCCAAAGCCAAACAGAATATCGAAAATCGCCTCGAATTTTGTCCGA TGACGTGTCAATAGTTGAGTTTCGGCTTTTCTAAGGAATTTTCTGTATTG GAATGGTATGGGGAAAGTGATTCACATTCTAGGGTACGTGTCTTGTATAC TCTATAGTATACTCTACTATACTATACTATGATAGTTCTTTGCTTGAATT TGCTCATAGGTGCACAAGGTTTTATATCCAGATTTCTTTAAAACAATTCA AAAAGTCGTCCCCTTATATGTAAAAAGCTTTGAGATAGTGTATATATCTT TTCATCTGTGTTCGATGCAGCGTGACATATATTCATTGCATGACTACGCC AATTAAAATGTACACTTTAATCTTGCATTTGAGCATTCCCATCACGCATT TGTCCTGTTGCTCATCGGGTAGCTCAAAACTGATGTCCCCCCACCACCTA CCTAAGCACACTCAAGTTTACTTGTTCGATTCGGGGATGCAGGCAGTTTG GCGCCAATCGAGCCATTCACATCGTTGGGTGTGGTTCCCCACATTAATAA ATATATATCTATCTTTTTATTGCGGTACGCAAAACTCTCAACTATTTTCG TTTCCCTTGAGGGTTGTTTTTCTGTTTAATTTTGTGCTTTTTTTTTGTCG GCAATATGATCTCAGACCCTTGCTAAGGGCTTTCTGGTATTTGCAAAAGC AATTTGCATTGTATTCTCATTCCAGTGTGACGTCATTGAAGCTGTCGCCA ACAGTTTTGGGCGAAATGTGGCCAACAGCATTGTCTCGGCCATATTTATG TGGATTGTGTAATGTCCGCGTTAGCCGAAATCGGGCTGAAATGAGTAAAA GCTGGGGAGGAAAAGTTGGCGGCTGCAAACAGGTTTCCAAACGAAAACTC TTGTTTTCATGTCGCATTTTGTTTATTGGTGCTGGAAAAGTGGAACAATT AGCAGAGTGCCGGGGTTTTGCTTTCCTTTGTTCGCATTTGAAAATACTTT TGGTTCGATTTTGACACGGAATTAAATCCAGCTGCCACCGCCGCCAACGT TTCATTCTAGTTTTCAATCTGTGGAGCTATAGCCAGGCAGCCCACACGCC ACTTAGATATGAATACAGAAATACAGATACAGTGGCCGCGAGCATCATGT ACACATAATGAAATCAAGCAGATTCAATTGATGACCGACCGCGTAATTGG GGCTGCAAGTCGGCCATTCGTTCCTGCCGAAAGATCAAAGTTGATTTGCA TTGTCTGACCAGCTGAACTGAGCCCAGCCGTAAAATCAAAAACTACGGTG TACCGCAGACTTGGTCGAGATTTCCGTGGCATTGTCATGTGTGAATGTCA CGGGATGCGCGTCCCTCGGCTGGCTTTCAGTTCTCATCTTGAGCTGCCTT ATCTTATCCGAGCGAATCGGACGGCCTTAGCCTTGTTTGGGCAGCAAATA CTCTTGGACCAATATTATGGTGGTAGCAAACTATTTTAGTGGGGAATTAC GTAACGCGCTTACTTATTTTAATTATCATGAACCATGCGCCGCTTATGGC GTGCCTGAGCCTGACCAGGAATCCCTGAGGTCAGCTACTGGGTTCTGTGG TAATTAAGTCTTTTTAGCATGGTAATTGCGAAAGTTCTTCCACTCCGGCA CTTTCAATTAAACTAAACGAGACCGAGCTGATTAATTTGAACTATATTTA GAGCTGTTTGTTAGAAGTGAAAATGCAGTGCGTATCTTATGATGTATCTG TTATGTCTTGTCTTTAGCTTATTGAGTTCATTTTATCGCCAAGTTAAAAC TATGTCTAACCCTTTGTTTCTCTTTCTTCGCCTACAGGTTATCGGCATCT TGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAA GTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCT TATCAGCTTGGGCTCGATTGTGGTCTTCATTTCATTCCTGGGATGCTGCG GTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTG CTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCA CAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGA ATTCTGAACATACTTATAAGGGAGGTGTCTTCGACACCATTCAGAAATCG GTAAGTGCTTTAATAACCAAGCACTTTCCATATATATGACTTCACAACGC AATCTTTAGTTGCACTGCTGCGGATCAAGCTCTGCTCTGGACTACATCGG CAAGGGAGACTTGGTGCCCCCAAGTTGTTGCAGCGGTTCGTGCCTGATCC CGACTAACTACTACCCGGGATGCCGTGGAAAGTTCGTCGAATTAATGACC ACTGGATCTGATAACGCTAAATATGTGGGCATCGGCCTCATCGGAATAGA GGTGAAAATTATACGCTAAATATAAGTTTCTCAAGCCGCTTTATTAACGA AATATCCATTTTAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGGCCAAC AACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATC CATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCA CATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATAC ACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAA ACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATA TCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGC AAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACC GAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTT CAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAG AAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTA AGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGA TTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGAA ATTTATGAATAAAGCATTTACTATGTATTTATATACCAATACCGTTGCGT TTATACAATTGTTCAGGGGCTGAAAACGAAAACTGATGCCAGTAATAATT TGCTCGCCTTCAGGCGGTTTGTTATGTCCTCAAGTTGTCATGGCAGCGAC TTTAGCTTATTAAGCAATATACTCGTATGTGAACTAGATATTACTAGAAA TAGAATTACTAGATACCCTTTGGGCTTCCACGGCCACTTCAAATTTGTGT GCGCTCGCCAAGGATATTATTGCGATAATGGCGGGTAATATAATTGCTTA CGCAACTACGCTGATTCCTTAATGAAATTCGATAATTAGAGCCATTACTC ATTTTTTTTTTTTTTTTAATGTTCTATAGCTTTAGCCTGTTTTCTGAGTG CCAGCATAGATCAGTTCAGCTCAGAATCGCAGTCATGTGCTGTTTGCTCG AGCACATTTTCAAAATTCTGATTTTTATCTTTGCCATTTTTATAAACTTT CTTGTGACCGTCAACTTAGTAATACATTTCTACTATATTAAGGTTCATGG ACCACAAGGTGATGCAGAATATTATAAGCTTAACACTATGGAAATACATT TTTTTACTATTTGGCACAGATTTCACTTCGGGAATAGAAAATTACTACAT ATTATGGACAATGCAAAGCTGGTGCGGAGCCCTAATGGTCGTAATCAAGT TGAAGGTTTGCGAAGGCTCCATTTCTTTTTATAAGAAGACTCTTACCCCC GCCGAACTTTTGCGTATAGGATC 348873 2R 1 2R:1731127-2080000 265998 256255 Drosophila 0 CG33352 0 0 9743 melanogaster 2R:1731127-2080000 -1 CG33352 CG33352 FBgn0053352 42E1-42E1 DGC clone GH14660 appears problematic: unspliced intron::DATE:2003-03-14 18:03:48::TS:1047683028000 Flag Cambridge (NEW): corresponds to old CG9469; should be reinstated as CG9469, after new CG9469 is renamed.::DATE:2003-02-21 17:57:41::TS:1045868261000 AE003790 265998 256255 0 CG33352-RA 0 partof ATGATAATTCGTATTCCTTCGATTGCAGGCGCCTCGAAGGAGATCGGCAC CGCCCTAACCCGCGTTTGCCTCCGCCACAAGGCGGTGGAGACGCGTCTGA AGACCTTCACCAGCACCATTATGGATTGCCTGGTGCAGCCGCTGCAGGAG AGGATCGAGGACTGGAAGCGCACGGTGGCCACCATCGACAAAGACCATGC CAAAGAGTATAAGCGCTGTCGCAGTGAACTGAAGAAGCGTTCCAGCGACA CACTGCGCCTGCAGAAGAAGGCGCGCAAGGGTCAGACGGACGGATTGCAG TCCCTGATGGACTCGCACATGCAGGATGTTACCCTGCGCCGGGCAGAATT GGAGGAAGTCGAGAAGAAATCCTTGAGGGCGGCCATGGTGGAGGAGCGTC TGCGCTACTGCAGCTTCGTCCACATGCTTCAGCCAGTGGTGCACGAGGAG TGCGAGGTCATGTCAGAGTTGGGTCACCTACAGGAAGCCATGCAGTCAAT TGCCCTAGTAACCAAGGAGCCTAGTGTTCTGCCCCAGGCCTCCGAGGAGC TTATCCATGACGCTAAGGCCAGCATTAATCTGTACCCGGAGTCCCCGGGT GGCGGTTCCGGCTCGCAGGGCGGCGGCTGCTCCAACTCGCTGGGTTCCCG AAAGAGCTCCGTCTGCTCCATCAGCAGTATGAACAGCAGCGGCTCGAGCA ACTCGCCCGGTCACCATCACTATCCGCGCTCCCTTTCGCAGACTTCGAAT GCAACGAACCAGACGGCAAATGTCTCCACCTGGCCCCCACATTCCCAGGA TGGCGTCGACACCCTGCCACCGACCGCTGACCGTCCGCACACGATTTCGA CGGCATACGAAAAGGGTCACCAGCGTCCGCCGCTGACCGTCTACACGTTC CAAAACCCGGAGACCATTCACGAGTCGGGCAGCTGCCTGAACAACGGAAC AGCAGCCCCGAATGGACAGCCGTTATCCGGACAAGCCACTCCGGCCACCC AGAAATCACCGGCTGCCTCACTTAGCCGGCCTCCTTTGCCAGTTCGCTGC TCGTCGTTGGAGCGACCCCTTTCGGCCCAGAGTAACCACCGCCAGGGTAG CGGGAATAACCTGCTGCAGCGCCAGTGCCCCTCGCCGATTCCGGCTCATA TCACGAAAGAGCTGTCCGCAGCGCATCATGCACAGCAGCAGCAGCAGCAG CAAAATCAGCAGCCCCAGACGCCGCCCACCTATGTGAACATGTCGGAGCT GGCCACCATGGCCGCTTTGAAGCAGACCAATCAGCAGCAGAAGCCCTCTA CGCCGCCTCTGCAGCAGCAGAGCTCCATTGACTCGACCAGCTCCCAGCAT TCCAACGACTCCACCGGCTCTCATCAGCTCCTCCAGCAGCAGCAGCAGCA TCATCAATCGCAGCAGAATCACCACTCAGCCACTGCCACACGCTCCCATT CCATATCCTCGACGGCCTCGTCACTTCACTCGCATCCGTCGATCGACTCC ACCGTCGCTTGCGGCTCGCTGGTGGGCCAGCACAACCACAGCACCAGCAC CAACACGAACACCACCTCGCCGTCCAGTGGCAGCTCCACGCCACAGAACC ATTACTCGCCCCTGCTAACCAACTCCCCCACGTCCACTGCCGCAGGTACT CCCAGTGGCAGCAGCTTAGGTCCTGGGTCCGGTTTGGGATTTGTCTACCA GGTCAGCTCCCCGACGCCTCCCTCCAGCGAGGTGCTGAAAATCACCGAGC AAGCCGCTGCAGGACAGGATCAGGGTCCAGCCAACAGCGTAGCGGACGAG ACGGATGAGCGATCAAGGGCCTCAGTCCTGCAGAAGGCTTCAATGTTCGA AAAGGCGGCAGCAGCGGCAGCGGTATCGCCCCCAGCTCCCATGCAGATTG CATCCGGTTCCCCAGCTTCGGGAGGCGGAACTCGACGATCCGAGGCGGAG CAGCAGGAAATGGACAAGTCTTTCGAAGATTCAATACAAGCACTAAATAA TTTAATTGGCGAACTAGACTCGTTCCAACGCGAGATCGATGAGGGCAAGG TCAAACCGCCGAGCAACATCATAAGCGGCAGCACCACCAGTAGCAACAAC AACAATACGACGACCAGCAGCATCAGCAGCAGCGACAACAACAACCTGCC CGCCACCAGCAACATCGAGCCATGCGCCATCAGCAATCAGACGAACTCGA GCGGCTGCGGCACGGACATATCCGACACCACGTCCGACGAACTGGCCGGC GACGATATGGACGTCAGGCGGCGGGATCGGGATCGGGACCGGGATCTGCT GGGCGCCAGCGATTCGGAGCTGAGTCGCTGCTATGTGAGCGAGACGAGTT CGCTGACCGGTGGCCTAACGGCCGGCGGCTACGAGAATCCCACTTTCGCG CACTTTGCGGCCAATGCCAATCGGGAGGACGCTGTTTCGCTGGCCTCCGA CAGCGTTTGTCTCGGCCAGCCACGCCACGCCTATGTGGATACCTGCAGCG ACAGCGGCAGTGCCGTGGTGGTGATCTACGACCACCAGATTCCCAACACA CCCGACATTGAGTTCGTGAAGCAGAACTCTGAGATTGTAGTGCTGCGGAC TAAGGATCCGCAGCCCCACGCGCTGCAGCTGCACGAGATGCGCGAGCTGC AGCAGTTGCCCGCCAATTTGGCCGGTTCGCCGGACTCCTCGCCGGACTCT GCCGGTGGCCAGGCACCGCCAACAGCAACTGTGGCGCCCGCCAAGCAGCG ACTCTCCTCGTTTCGCGCCACCAGTGAGCAGCAGTTGCAGCTCCTCGGAC GCGGTAGCCCGCAAAGAGGTAAAACACCCAGTGAGCAGGCGGTACAAAGC AGGCCACAGGACCAGCATTTTCCACAGACACAACAGCAGGATATTGATGG CAGTAGTCCACCAGTAGAACTTGCAAGGCGCCAGCTGCCCCCCAAGCCCA CCAGTTTGAGTATTTTTAACGGCCCCGTGCCCACTGCGGGCGATAGGCCT GTCGTGCCGCGAAAGTCGGACTTTAAGGCTGATCTAGATGCTAAAATACG CAGGCAAAAGCAGAAGGTTAAACAGCAGTTGCAGCAGCAGCAGCAGCAAC AGCAGCAAGAGCAGCAAGAAACGCAGCAGCAGCAGCAAGCACCACAAGAA CAGCAACACTCACCACAGTCGCCCCAAACCAGAAACTGTAATGTCACTAA TCAACAAGCCGCCAATATTACTGCATCAGCATCTGCATTTGCAACCGCAA CAGCATCCACAGACCCGTACCCGAATCCAAATCATAGAATGCCAAACCAA AATCAGACAGCCACATCCAATCACACGCAGTGCAAGACGCCCACAATGGC ATTGTCACCGTCATCACCTCGCGGCCATTTGCCATTATCATCGTCATCGC TATCGTCATTACCATTACCAGCCACCACTTCATCACCATCAAATGCCCGG CCATCGATGTTGCCCGCCAGTGACCGACCACCCGCCCATCCATATGTGTG CTCCAATGCCCCAGCCAATCCCCACCACGCCAATAGCATTTCCAATGCCA ATGCCCATCTCAAGCCGTGCATTACGCCCCGGCCGGCTTCTTTGTCGGGA GGAGCAGCCGGCGGTGGCTCCACGCGCATCGGGCGTCGATCGTCCATTAA TCAGTCCAAGCCACCGCCGCCAGTCAGACGCAGTTCGTCGGTGACCCCCA GTCCCAATGCCTCGGTCGGGCTGCAGCAGCAACCACAGCACGCGACTCTG TCGCAGCAGAATCACCAACTAAGCAGCTCCAGCGAGCACTTACCGCCGCC ACCGCCATTCATGCTGGACGCCATGCCCCAGATTCCCAGCTCAGCGCTGA AGGTATCGGAGACGGTAAGAGCCCTGGCAGCCATGCGGCACCAGCCAGCA TCACCTGTGTCCCTCAGACGCATGCAGCAGCAACAGCAGCAGCAGCTTCA GCAGCAACAGCAGCAACAGGTGCAGCAGCAGCAACCCCTATTGCAGTCTG CGCACAACTCCCCCCTCAAAGAGGACCTGACCGTGTACTACGACTCCTAC TTGGATCTGCACGCCTATGCCCAGGCCTTGGCCAGCGGCCAACAGCCCGG CGGTCAGCAGATGGCCAACCAGCAACGCTTTACCCTCCAGCAGCAACATC AGCATCTGCATCAGCCACAGCAACCGCCTGTCTACCAAGTCGATGCCACG TTCCGCACCTCATCACCAGCCGCGGGCGGAGGGGGTGGCGGCGGCATATA CGCCCAGCCCAAACTGGTCAACAGCATGTCCAGCTTCCGCACCAGCAGCC CCAGTCCCAACGGACATGCTCACCCACTGCCACCGACACAGCCAAAGGCG AATCCGAACCTAATTGCACAGCTCAATGCACGACTCAGCGGCAAACAGCA GCAGCACCAACAGCAGCAGCATATCGAGGGGATCTACGGCAACCAGCAGG CGCCCGGAGGAGAGTCGATCTACATGCGGAGTGGCCTGTCCATGTCGCAG CCGCAACAGCAGCAACACTTTGACGGTAAATCTGAACAAATCCAGCTGCA GCACCAGCAACAGCATAGAATTTACGCTAGTTTCGGCACCTCATCATCAG CAATGTCATCCGCTCATGCGGCCAACAGCAGCACTAAACCGTCCATTCTA ACACCGACCACCTCTTTCAATGCATTGCCTCACTTCCCCCTGTCTTCATC CACATCATCGTTGCTCTCCAAAGTCAGCTCATTCTCGAACTCTTCATCCG CATCCCCACCGACAACGGCAGCGACCTCTGGCTCGGCCAGTTCGCATTAT CAGCCACCTCAGCCGCCGAATGCAGCAGTTGCTAACAGCAAAGACATGGC CATCTACTCAAGTTCGTTTACCAAAAATCCAGCAGCTGCGCAATCGCCGA ACATGAGACAGGCTCATTCCCATCAGCACCACCAGCCGCCGCAGCAGCAG CACTACACCTGTCCGCCTCCTCTGGAGGATCCCCCACCGCCGCCCATTTA CGCCGCCGGTGCATCGGCCACGATGCCCAAGAAGATGGCCCGTCCGCCCA CTGGCCAGAACGCGACTCACTCGAGCGCCTATGCAGCAGCCTCGTCTACG GCCACGCTGCCCAAGAATATGATGCAGCAGCAGCAGCGGTTGCAGCACCA GCAGCAGTATCAACAGCCGGCAGGCATGGGCATTGGCAACGGCAATGGGC ACCTAGGTCAGCGTCCGCAGTTGCCGCTGCCCCAGCAGAAGCTTAGAGCT GCACAGCAGCAGCACTTGGCGGAGCAGCAGCATCAGCAACAGCAAGAACA GCAGCAGCACCACCAGCAGCACCAACAACACCAGCAACGCCAGCCGCCCA TTCCTTCACGCCACTCAAGTGTGCAGCAAAAGATATTCGTATCAACGAAT CCATTCATACAGACAACGGCCGTCAAGTTTCACTCGCCCTCGGCCTCGCC CACGTGCGGCTCGCCCGTTACTGGGTCCTTGGCTAGCATTTATGCCACAA CCTCGCGTGGCGGCCACCATCACCAGCAGCAGCAGGCTCAGCAGCAGCAG CACTACTATCGCGATGCTGCCGGGGGCAACAGCAACGGCGGCGCTGCCTA CTATAACCACAATGCCCATGCCCATTCCCAGGCACATCATCCAAACTGGC AGTATTCGTGCCAAGACCAAGGCCGAATTCCTCGAGAATCTCAACGCGAA GCTGGCGAAGCAGGGAATGTCTGGACGAGCATTTGCCGTGCGAAATCTCA TCAACAGCAAGGCCCTGATGTATCAAAATCCGCAAAAACTATCGCGACCC AGTGCGCAATACCGTAGACCACCCACCTATCCCAACACCAGCACAACCAC CAATGCCACTTGCGAAGATCAGTGCTAA 5878 2R:1731127-2080000 -1 CG33352-RA CG33352-RA FBtr0086193 Corresponds to cDNA described in FBrf0137468.::DATE:2003-07-22 14:04:11::TS:1058897051000 not done crosby 265998 265515 0 CG33352:1 1 0 partof 483 2R:1731127-2080000 -1 CG33352:1 CG33352:1 FBex0070433 265455 265197 0 CG33352:2 2 0 partof 258 2R:1731127-2080000 -1 CG33352:2 CG33352:2 FBex0070432 264883 264580 0 CG33352:3 3 0 partof 303 2R:1731127-2080000 -1 CG33352:3 CG33352:3 FBex0070431 263955 263840 0 CG33352:4 4 0 partof 115 2R:1731127-2080000 -1 CG33352:4 CG33352:4 FBex0070430 263702 262898 0 CG33352:5 5 0 partof 804 2R:1731127-2080000 -1 CG33352:5 CG33352:5 FBex0070429 262472 260837 0 CG33352:6 6 0 partof 1635 2R:1731127-2080000 -1 CG33352:6 CG33352:6 FBex0070428 260145 260023 0 CG33352:7 7 0 partof 122 2R:1731127-2080000 -1 CG33352:7 CG33352:7 FBex0070427 259873 259597 0 CG33352:8 8 0 partof 276 2R:1731127-2080000 -1 CG33352:8 CG33352:8 FBex0070426 259048 258847 0 CG33352:9 9 0 partof 201 2R:1731127-2080000 -1 CG33352:9 CG33352:9 FBex0070425 258611 257164 0 CG33352:10 10 0 partof 1447 2R:1731127-2080000 -1 CG33352:10 CG33352:10 FBex0070424 256567 256444 0 CG33352:11 11 0 partof 123 2R:1731127-2080000 -1 CG33352:11 CG33352:11 FBex0070423 256366 256255 0 CG33352:12 12 0 partof 111 2R:1731127-2080000 -1 CG33352:12 CG33352:12 FBex0070422 265998 256319 0 CG33352-PA 0 producedby MIIRIPSIAGASKEIGTALTRVCLRHKAVETRLKTFTSTIMDCLVQPLQE RIEDWKRTVATIDKDHAKEYKRCRSELKKRSSDTLRLQKKARKGQTDGLQ SLMDSHMQDVTLRRAELEEVEKKSLRAAMVEERLRYCSFVHMLQPVVHEE CEVMSELGHLQEAMQSIALVTKEPSVLPQASEELIHDAKASINLYPESPG GGSGSQGGGCSNSLGSRKSSVCSISSMNSSGSSNSPGHHHYPRSLSQTSN ATNQTANVSTWPPHSQDGVDTLPPTADRPHTISTAYEKGHQRPPLTVYTF QNPETIHESGSCLNNGTAAPNGQPLSGQATPATQKSPAASLSRPPLPVRC SSLERPLSAQSNHRQGSGNNLLQRQCPSPIPAHITKELSAAHHAQQQQQQ QNQQPQTPPTYVNMSELATMAALKQTNQQQKPSTPPLQQQSSIDSTSSQH SNDSTGSHQLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDS TVACGSLVGQHNHSTSTNTNTTSPSSGSSTPQNHYSPLLTNSPTSTAAGT PSGSSLGPGSGLGFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADE TDERSRASVLQKASMFEKAAAAAAVSPPAPMQIASGSPASGGGTRRSEAE QQEMDKSFEDSIQALNNLIGELDSFQREIDEGKVKPPSNIISGSTTSSNN NNTTTSSISSSDNNNLPATSNIEPCAISNQTNSSGCGTDISDTTSDELAG DDMDVRRRDRDRDRDLLGASDSELSRCYVSETSSLTGGLTAGGYENPTFA HFAANANREDAVSLASDSVCLGQPRHAYVDTCSDSGSAVVVIYDHQIPNT PDIEFVKQNSEIVVLRTKDPQPHALQLHEMRELQQLPANLAGSPDSSPDS AGGQAPPTATVAPAKQRLSSFRATSEQQLQLLGRGSPQRGKTPSEQAVQS RPQDQHFPQTQQQDIDGSSPPVELARRQLPPKPTSLSIFNGPVPTAGDRP VVPRKSDFKADLDAKIRRQKQKVKQQLQQQQQQQQQEQQETQQQQQAPQE QQHSPQSPQTRNCNVTNQQAANITASASAFATATASTDPYPNPNHRMPNQ NQTATSNHTQCKTPTMALSPSSPRGHLPLSSSSLSSLPLPATTSSPSNAR PSMLPASDRPPAHPYVCSNAPANPHHANSISNANAHLKPCITPRPASLSG GAAGGGSTRIGRRSSINQSKPPPPVRRSSSVTPSPNASVGLQQQPQHATL SQQNHQLSSSSEHLPPPPPFMLDAMPQIPSSALKVSETVRALAAMRHQPA SPVSLRRMQQQQQQQLQQQQQQQVQQQQPLLQSAHNSPLKEDLTVYYDSY LDLHAYAQALASGQQPGGQQMANQQRFTLQQQHQHLHQPQQPPVYQVDAT FRTSSPAAGGGGGGGIYAQPKLVNSMSSFRTSSPSPNGHAHPLPPTQPKA NPNLIAQLNARLSGKQQQHQQQQHIEGIYGNQQAPGGESIYMRSGLSMSQ PQQQQHFDGKSEQIQLQHQQQHRIYASFGTSSSAMSSAHAANSSTKPSIL TPTTSFNALPHFPLSSSTSSLLSKVSSFSNSSSASPPTTAATSGSASSHY QPPQPPNAAVANSKDMAIYSSSFTKNPAAAQSPNMRQAHSHQHHQPPQQQ HYTCPPPLEDPPPPPIYAAGASATMPKKMARPPTGQNATHSSAYAAASST ATLPKNMMQQQQRLQHQQQYQQPAGMGIGNGNGHLGQRPQLPLPQQKLRA AQQQHLAEQQHQQQQEQQQHHQQHQQHQQRQPPIPSRHSSVQQKIFVSTN PFIQTTAVKFHSPSASPTCGSPVTGSLASIYATTSRGGHHHQQQQAQQQQ HYYRDAAGGNSNGGAAYYNHNAHAHSQAHHPNWQYSCQDQGRIPRESQRE AGEAGNVWTSICRAKSHQQQGPDVSKSAKTIATQCAIP 1938 2R:1731127-2080000 -1 CG33352-PA CG33352-PA FBpp0085520 348139 342030 Drosophila 0 Tsp42Ee 0 0 6109 melanogaster 2R:1731127-2080000 1 CG10106 GO:16021 FBgn0029506 FBan0010106 FBgn0033126 42E5-42E5 AE003790 Tsp42Ee Perfect match to SwissProt real (computational) integral to membrane GO:0016021 348139 342030 0 Tsp42Ee-RA 0 partof 076b8833fdac8314c4c8447214bd7872 ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGA ATATAAATTGGTGATAATTTAAAGTCGAAGACGGTACAGTAAAGCAACAT CAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCA ACACCATTGTGTCGGTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTG ATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCC GATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGG TCTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGC ATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCT GACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAA TGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGA GGTGTCTTCGACACCATTCAGAAATCGTTGCACTGCTGCGGATCAAGCTC TGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCA GCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAG TTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCAT CGGCCTCATCGGAATAGAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGG CCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGT GTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACA CCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGG GATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACG GAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTT TGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAA CGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTT AAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATAT TTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCG AAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGT TTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGG AAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCAT AAGAAATTTATGAATAAAGCATTTACTATGTATTTATATACCAA 1394 2R:1731127-2080000 1 CG10106-RA CG10106-RA FBtr0086180 crosby Perfect match to REAL SP with corresponding FBgn AAF59311 342110 342030 0 Tsp42Ee:1 1 0 partof 80 2R:1731127-2080000 1 CG10106:1 342891 342807 0 Tsp42Ee:2 2 0 partof 84 2R:1731127-2080000 1 CG10106:2 347150 346787 0 Tsp42Ee:3 3 0 partof 363 2R:1731127-2080000 1 CG10106:3 347401 347209 0 Tsp42Ee:4 4 0 partof 192 2R:1731127-2080000 1 CG10106:4 348139 347464 0 Tsp42Ee:5 5 0 partof 675 2R:1731127-2080000 1 CG10106:5 347533 342831 0 Tsp42Ee-PA 0 producedby MDCGTSMVKYILFIFNTIVSVIGILGIVYGVLILKSIGVVEVNGQVGFPI QALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLT FVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSLHCCGSSSA LDYIGKGDLVPPSCCSGSCLIPTNYYPGCRGKFVELMTTGSDNAKYVGIG LIGIELIGFIFACCLANNVRNYKRRNAY 228 2R:1731127-2080000 1 CG10106-PA CG10106-PA FBpp0085512 AAF59311.1 280062 279256 Drosophila 0 CheB42a 0 0 806 melanogaster 2R:1731127-2080000 1 CG33348 CG33348 FBgn0053348 FBgn0033120 FBan0015242 42E1-42E1 AE003790 Flag Cambridge: gene split (internal view only). CheB42a corresponds to the 5' end of CG15242.::DATE:2003-03-14 16:14:41::TS:1047676481000 Gene split based on EST/cDNA and BLAST data.::DATE:2003-03-14 16:16:50::TS:1047676610000 CheB42a Not in SwissProt real (computational) 280062 279256 0 CheB42a-RA 0 partof 801a4c50b8d81beefea74e1c5d4f358d CTCATACTGGAAAGCTTGTTAATATGAAGGCTACTTTTACAATCCTGGTG CTCCAAGTGGTCATCTGTTTGGCTGGAGCGACTGAGTACCAGTTAACATT GGACAAAGATGGCTTGTTAGCACCATGCGAGAATCAGCCCGGAAATCCTT CTGGTTTTGAAGCGATGGTGGATACTTCCTCCCTTAAAGTACATAACCTT GGTTCGAAAGTTCGAATTGAAGGAGAGCAGAAAGTGGTCTGGAAAGATGT CCAGCCTGGAGACACATTAAAGGTATTTGGTCAAGTCTATCGCCTGGATA AGGGCACTTGGCAGAAGACTATGTTTACGGCCAGCTCCAATAACTTTTGC AAAAACATGTTTGATAAGAACCAATACTGGTATAATTTCTGGACAAAGTA TATTAGCAACTCCGACGAGATTAAGGAAAAGTGCTTGACCACACCAGGGG CCGTTTTAAAGTACAAAGACTACGAACTGGACTTGAAGACCAGCTTGAAT GTTCCGAATCTGGATGGGCGCTACAAGCTGGTGGTCCAAATAGAGGCCTT CGATAAGCGCAATGTAAGGCGCCCAGTTCCCATTTGCATAGAGTTCCGTG GAACTGCAGGACAGGTCTAATCACGACAATTGTATATGCATGCTGAACAT ACAGCGAAACACCATTAAAGTCTATAATTGGAGCACATCAAACAAG 696 2R:1731127-2080000 1 CG33348-RA CG33348-RA FBtr0086168 unusual splice provisional (internal view only)::DATE:2004-01-12 11:13:36::TS:1073924016000 unusual splice GC splice donor site postulated::DATE:2003-03-14 16:11:36::TS:1047676296000 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70837 crosby 279528 279256 0 CheB42a:1 1 0 partof 272 2R:1731127-2080000 1 CG33348:1 279755 279578 0 CheB42a:2 2 0 partof 177 2R:1731127-2080000 1 CG33348:2 280062 279815 0 CheB42a:3 3 0 partof 247 2R:1731127-2080000 1 CG33348:3 279983 279279 0 CheB42a-PA 0 producedby MKATFTILVLQVVICLAGATEYQLTLDKDGLLAPCENQPGNPSGFEAMVD TSSLKVHNLGSKVRIEGEQKVVWKDVQPGDTLKVFGQVYRLDKGTWQKTM FTASSNNFCKNMFDKNQYWYNFWTKYISNSDEIKEKCLTTPGAVLKYKDY ELDLKTSLNVPNLDGRYKLVVQIEAFDKRNVRRPVPICIEFRGTAGQV 198 2R:1731127-2080000 1 CG33348-PA AAM70837.1 281933 280159 Drosophila 0 CG33349 0 0 1774 melanogaster 2R:1731127-2080000 1 CG33349 CG33349 FBan0015242 FBgn0053349 FBgn0033120 42E1-42E1 Transposon inserted immediately 3' of gene.::DATE:2002-03-07 10:07:50::TS:1015513670000 Gene split based on EST/cDNA and BLAST data::DATE:2003-03-14 16:16:50::TS:1047676610000 Flag Cambridge: gene split (internal view only).::DATE:2003-03-14 16:14:41::TS:1047676481000 AE003790 281933 280159 0 CG33349-RA 0 partof TTCATCATGGAATCCAAAATGAGTCGGCCGAAGCAACCGGACTGGCTCGC CGAGCTGTGCCAGGAGTCCTCCATCCACGGCATGCCCTACATCGCCCGCA GGGATCTACACTGGGCCGAGCGCCTCTTTTGGACATTCATAATCCTGGGC TCGGCCTACTACGCCATCAGCAGCTGCCTTAACCAATGGTACCGGTTCCG GGACAATCCTATTGTCTACGAGTACGAATATCTCTTTGGGCTGCGCATCT TCCCCTTCGTGGGGATAACACTGTGCCCTAGGTACCACGACGAAACGGAG ATCCCAAGGCTTATAAATCAAACTTGGGGAGTGGATCCCAGCGAAGACAA AGAAAAAGCTGTGTACTACAGAAAGTTTCTGCTTGCAATCAACGGCCTTC GTTACTCCACTCTGGAGACGCTGGAACCCTTCGAGAATGATACCACTTTG GACAACGTGAATTACTTGAACATTTTGCTCACGCTGCAAAAAAAGGTAAT AGCGGTTAAAATCCCGCCAGAACTGGCGCCAATCATTACTGAGGTGGGTC TGTGCCAAACATCCAGCCAGTTAAACCGATACGGAAATCCCTACGGCAAA CTAGAAACACAGGATATGGAACCCATGAAACAGTGCGGCTATTTGAGTAA TTGCATCACATCTCTGAAGCCTATAAATAGCATTGTTGCCCCCATATTTA TGTACCTTCACGATGTCGAAGAAATGATGCTACCCGACGACATGCGAACT CCCTCTTTTGATGCTAAAGACATCGAATCCAAGGATCTCGATATTATGCT ACATACCACATCGGCGGAAAGCGAGGTGCGAAATCTACCGGTAGCATATC GCAAGTGTCGCTTCAGTGACGAAAACAATCTGCAGTATTACAGTCCCTAC CACCCAAGTCTTTGCCGACTTGAGTGCCGAATCAAATGGGCCCTGAGCCT GTGCAACTGCAAGCCCTATTTCTACGTAGCAGCTCCCGAAGTTCCAATCT GCACAGTATCCGGAATGCTCTGCCTAGCCCGGTCCAAGTGGCTTGAAAGA CCATGCGATTGCTATCCGTCTTGTCGCGAGGAAACCTTTACCATCTTCAA AGTGTCTGACCAGACTGGGGGCGATGACAACTACTCTGGCGAGAGGTTCG AGCGGACGCTGATCATCAACCTGCAAATTTCGAGGATGGGCATAAATCGG CGGGTTGTATTCAGCACGGATCAGTTGATAATGTCGTTTGGTGGAGCCAT TGGCCTCTTTCTTGGAGCCAGCTTCATGACCATATACGGCGTGGTATACT TTTTTCTAACTTTCATAGCTTATACATGCAAGAACCGATTTTGCAAGCGT TTTTTTTTTTAA 1362 2R:1731127-2080000 1 CG33349-RA CG33349-RA FBtr0086169 crosby not done 280479 280159 0 CG33349:4 1 0 partof 320 2R:1731127-2080000 1 CG33349:4 280820 280538 0 CG33349:5 2 0 partof 282 2R:1731127-2080000 1 CG33349:5 281086 280986 0 CG33349:6 3 0 partof 100 2R:1731127-2080000 1 CG33349:6 281337 281145 0 CG33349:7 4 0 partof 192 2R:1731127-2080000 1 CG33349:7 281625 281400 0 CG33349:8 5 0 partof 225 2R:1731127-2080000 1 CG33349:8 281933 281690 0 CG33349:9 6 0 partof 243 2R:1731127-2080000 1 CG33349:9 281930 280165 0 CG33349-PA 0 producedby MESKMSRPKQPDWLAELCQESSIHGMPYIARRDLHWAERLFWTFIILGSA YYAISSCLNQWYRFRDNPIVYEYEYLFGLRIFPFVGITLCPRYHDETEIP RLINQTWGVDPSEDKEKAVYYRKFLLAINGLRYSTLETLEPFENDTTLDN VNYLNILLTLQKKVIAVKIPPELAPIITEVGLCQTSSQLNRYGNPYGKLE TQDMEPMKQCGYLSNCITSLKPINSIVAPIFMYLHDVEEMMLPDDMRTPS FDAKDIESKDLDIMLHTTSAESEVRNLPVAYRKCRFSDENNLQYYSPYHP SLCRLECRIKWALSLCNCKPYFYVAAPEVPICTVSGMLCLARSKWLERPC DCYPSCREETFTIFKVSDQTGGDDNYSGERFERTLIINLQISRMGINRRV VFSTDQLIMSFGGAIGLFLGASFMTIYGVVYFFLTFIAYTCKNRFCKRFF F 451 2R:1731127-2080000 1 CG33349-PA CG33349-PA FBpp0085501 168702 167848 Drosophila 0 CG9445 0 0 854 melanogaster 2R:1731127-2080000 -1 CG9445 FBgn0040674 FBan0009445 42D3-42D3 true CG9445 Not in SwissProt real (computational) AE003790 mesoderm development GO:0007498 168702 167848 0 CG9445-RA 0 partof 05b93ccd5765a570c18b99a69784afa3 CCGATCGAAAAGCATATACTCAAAATTCCAAAAAACACAAGCCCAGCGCC CAAGCGCCATCATTTGTTTCCAGCCGACTTCCAGCTCCGATCGGGTACCA ATAGCCCTGCACCGGACCCACTAAGATGGACGGAGGAGGGGACAACCAGC TCGCGGTGCGGTCCTTGGGCAGGCAGCGCGAAGCCTTCTCCCACTACGCG GGTCCACCGACGGCCATGCTGCAAGGACCCGATCCTGGCGAAGGAGACGT CCTTGCCCTGCAGATGGCCATAGAAGCCTTCATTCTAGCCGAACTCGAAG AGGATTCAGGCTTCGAGTCCGGCAGCGAAGACGACTAGCAGGATGGAAAG AGTAAAGTGATACTTTAGTAAATAGCACCCATGTATGAGCCATCATAAGA GGAATATATGTATCTAATGTTGCACCAACCTTGGGCTACATGATTTATGT ATGCCGGTGGACCAATTCGCCCGCATTATGGACAATGATGCACGGCATTA ATTAACTCGCAGTCTTACCTTTTGCAAATAGGATTACAAACACTGAAATG AAATAGAGCCATGTTTCGAAATGCCTTAGTTGGGTTTCGGTTTATTCATG TCGATTTGATTTCAATTTGATTTCAAACACAAATTCCATTTAAACACAGG GATGCCGGTGCATCTGTATCTGTGTGCGAGTTGCAGATTAGTAGAGAGTT GTAGTTACATTTATTTTACACATACATAAATACGCATATTTGTATACATT TTTAATATGCTCGTTCAAGATGAATTTTTCTATTTTTCTTCGAATTTACC ATACGCTCTCTTGTGCAACATCAATAATAAATATTTACGTTTGTCTGCAT CGGT 854 2R:1731127-2080000 -1 CG9445-RA CG9445-RA FBtr0086210 crosby AAF57402 Perfect match to HYPO SP record with corresponding FBgn 168702 167848 0 CG9445:1 1 0 partof 854 2R:1731127-2080000 -1 CG9445:1 168577 168367 0 CG9445-PA 0 producedby MDGGGDNQLAVRSLGRQREAFSHYAGPPTAMLQGPDPGEGDVLALQMAIE AFILAELEEDSGFESGSEDD 70 2R:1731127-2080000 -1 CG9445-PA CG9445-PA FBpp0085528 AAF57402.1 140212 139849 Drosophila 0 CG3450 0 0 363 melanogaster 2R:1731127-2080000 -1 CG3450 FBgn0033105 FBan0003450 42D1-42D1 CG3450 Not in SwissProt real (computational) AE003790 140212 139849 0 CG3450-RA 0 partof 298623955524284a93400ce2e1a74ff2 ATGATAGAAATAACGTGTAACGATCGTCTTGGCAAGAAGGTGCGCGTCAA GTGCAACCCGGACGACACGATTGGGGACCTCAAGAAACTAATCGCGGCAC AAACGGGCACAAAGCACGAGAAGATTGTCCTGAAGAAGTGGTACACAATC TTCAAGGACCCGATTCGCCTATCTGACTATGAAATTCACGATGGCATGAA TCTGGAACTTTACTACCAATAAAACTGCAAGGGAATACC 239 2R:1731127-2080000 -1 CG3450-RA CG3450-RA FBtr0086211 Perfect match to HYPO SP record with corresponding FBgn AAF57398 crosby 140212 140173 0 CG3450:1 1 0 partof 39 2R:1731127-2080000 -1 CG3450:1 140114 139975 0 CG3450:2 2 0 partof 139 2R:1731127-2080000 -1 CG3450:2 139910 139849 0 CG3450:3 3 0 partof 61 2R:1731127-2080000 -1 CG3450:3 140212 139869 0 CG3450-PA 0 producedby MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTI FKDPIRLSDYEIHDGMNLELYYQ 73 2R:1731127-2080000 -1 CG3450-PA CG3450-PA FBpp0085529 AAF57398.1 341629 339634 Drosophila 0 Tsp42Ed 0 0 1995 melanogaster 2R:1731127-2080000 -1 CG12846 GO:16021 FBgn0029507 FBgn0033125 FBan0012846 42E5-42E5 Perfect match to SwissProt real (computational) AE003790 Tsp42Ed integral to membrane GO:0016021 341629 339634 0 Tsp42Ed-RA 0 partof 8ab57aaf8ce3e480218880a4eabaad76 ATCTCTACCACTGCAGCAACGCTTTTCTTATCGCCGCTAAATTCAGAGCT AAAATCTAACAGAGCTTTTCGCGATAGGAAATGCGCTCATAAAAATATTG TTATATATCAGACTTTTTCAGTATCAAGCGGACCACGAACGAAATCGCAT CGAACGTCTTACTCTTAAATCGAACACAAGTGATACACAAGTACATCTCA GCAATGGATTGCGGCGGCGTTTTTGTGAAATATGTGCTGTTCATATTCAA CATACTGTTTGTGATATGCGGCATTTTGCTTATCACCTTCGGCTCCATCA TGGTGTCCACCATAAAGGACTTCTCGGGCGTTGGCGAGACCTTCACGGCA AACAGCGTGGCCATCATCATCCTGGTCCTTGGCTGCGTAGTCTTCCTGGT AGCCTTCATGGGATGCTGCGGCGCCATACGCGAGAATTCCTGTGCTCTGA CCTCGTACTCTGTGGTCATGCTGGTGCTGTTGGTTAGTCAGCTAGCTCTC ATTATCTACGTGTGGGTGGACCATGTGCAGATACAGCAATCTTTGGAGAA GATCGTCCAGACCATATGGGATCAACGCAAGACCGATGCCCTCCTCATGG ACACACTGCAGCGATCGTTCAAGTGCTGCGGCTTGAACGGCTTCGCTGAT TACGGCATTACGTATCCCGCCTCCTGCTGCGACTCGCCCTCCAATGGAAC CTGCGCACTAACCCAAGTCATGACGCGATCCAGTTGCCTGAAGGCCGTTG ATTCCTTCTGGGACACCAACGTGAGCATCATCAAGTACGCTGGCCTGGGT GTGACTGCTGTTGAGCTTGTGGCCTTCATTTTCGCCTGCTGCCTGGCCAA TCAGACCCGCAACTCGCAGAGACGCCAGAACTACTAAACGATGAAACGAT GAATTAGTAGCATAGTATTAGGATTATCTCCCGACCCTCTTTAACGTCAT AAAGTCAATATGAATAAATAAAACAAAGTGCTTCGCATGCTTACTGTATA T 1001 2R:1731127-2080000 -1 CG12846-RA CG12846-RA FBtr0086181 Perfect match to REAL SP with corresponding FBgn AAF59312 crosby 341629 341366 0 Tsp42Ed:1 1 0 partof 263 2R:1731127-2080000 -1 CG12846:1 340629 340437 0 Tsp42Ed:2 2 0 partof 192 2R:1731127-2080000 -1 CG12846:2 340368 340206 0 Tsp42Ed:3 3 0 partof 162 2R:1731127-2080000 -1 CG12846:3 340075 339877 0 Tsp42Ed:4 4 0 partof 198 2R:1731127-2080000 -1 CG12846:4 339820 339634 0 Tsp42Ed:5 5 0 partof 186 2R:1731127-2080000 -1 CG12846:5 341426 339751 0 Tsp42Ed-PA 0 producedby MDCGGVFVKYVLFIFNILFVICGILLITFGSIMVSTIKDFSGVGETFTAN SVAIIILVLGCVVFLVAFMGCCGAIRENSCALTSYSVVMLVLLVSQLALI IYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRSFKCCGLNGFADY GITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGV TAVELVAFIFACCLANQTRNSQRRQNY 227 2R:1731127-2080000 -1 CG12846-PA CG12846-PA FBpp0085513 AAF59312.3 210490 209376 Drosophila 0 CG9454 0 0 1114 melanogaster 2R:1731127-2080000 -1 CG9454 FBan0009454 FBgn0033112 42D4-42D4 AE003790 Not in SwissProt real (computational) CG9454 serine protease inhibitor activity GO:0004867 210490 209376 0 CG9454-RA 0 partof d7af7b2b7f5f23dac304f3a8d72aa9af ATGAAAGATGAGGAGTTCGCACAGGGCTTGGAACAATTCGCTCTTTGTCT GCACGACCATTTGTGCCGGGCAAGTGCTGGCCTAAACATCATCTACTCCC CATTATCCATCCACATCTCTGCGGCCATGCTGCGGATGGGAACATCCGAG GGATCGGCTACAGCTAAGGAGATGGACGAGGGGCTCCGTTTCGGTGGGCT AGAAGCTCAGCAAGTAGCTGAAAGCTTTGGTGTCGTCCTCAAGTCCTATG AACAGTGCCAGGTTCTTAAAATGGCAAACGGCCTATATGTTATGAAGGGT CTCCAAGTTGACGAGCAGTTTGGTCACATACTAGAGCAGAAGTTTCGCTC CAAGCCAATGGAGATTGACTTTGGCAGCGAGCAGGCTGCCAGCATAATCA ACAAATGGGTGGAGTCACAGACCAACAACCTGATCAAGGACATAATCGGT CCAAGAGTTCTTACCAAGGACTCGCGGCTGTGCCTAGTAAACGGTATTCA CTTCAAGGGTGAGTGGTCAATCAGTTTCAATGAAAAAGAAACCCGCGAAG AGGATTTCTTCGGATCGGATAGACCTACCAGAGTGAGAATGATGCATGTG TGCGAGAACTTCTTTTTTGCCGTACTTCCCATGTTCGAAGCCACTGCCCT TAGAATGAATTATAGTGCCTGTAATTTGGCCATGATCATTTTACTTCCTG ATGAGAAGTCGAATCTCACGAGCCTCGAAAAGAAACTTAGTGATATTTCC CTAGAGGTAGTGTCATCAGCAATGAATCTGGAAAAAGTGGATGTGAAGAT TCCTAGCTTTACAGCCGAGTTCCAGCAAGAACTATCCCAGGTTTTAATGC TGATGGGCATGAACCGAATATTCAGTGGTCAGGCAGAGCTTGGGGGAATG CTACAATCCGAGGAAAGCCTTTTTGTCTCCCAGATCGTCCACAAAGCATT TATCGAGATTAACGAAGTGGGCACTGAAGCTGCAGCCGCAACGGGTGAGC CTGCAAAAAAAAAAGGTTCCAAAACTTTTGGCAATTTGAAAGCCTCTTAT ATCTAG 1056 2R:1731127-2080000 -1 CG9454-RA CG9454-RA FBtr0086194 AAF57406 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) crosby 210490 209638 0 CG9454:1 1 0 partof 852 2R:1731127-2080000 -1 CG9454:1 209580 209376 0 CG9454:2 2 0 partof 204 2R:1731127-2080000 -1 CG9454:2 210490 209379 0 CG9454-PA 0 producedby MKDEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSE GSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKG LQVDEQFGHILEQKFRSKPMEIDFGSEQAASIINKWVESQTNNLIKDIIG PRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVRMMHV CENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDIS LEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLMGMNRIFSGQAELGGM LQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKKGSKTFGNLKASY I 351 2R:1731127-2080000 -1 CG9454-PA CG9454-PA FBpp0085521 AAF57406.2 324083 322460 Drosophila 0 CG30159 0 0 1623 melanogaster 2R:1731127-2080000 1 CG30159 CG30159 FBgn0050159 FBgn0033123 FBan0030159 AE003790 Not in SwissProt real (computational) Flag Cambridge: gene split (internal view only).::DATE:2002-02-13 10:34:00::TS:1013614440000 CG30159 42E4-42E4 CG3364 324083 322725 0 CG30159-RB 0 partof CAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCA TTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCC AAGTGTTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCA GGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCA TCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAG CCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCG CCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGC AGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCG ATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCG CGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCG AGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTC TGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGT CTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCG CCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTG GAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTA TCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCA AGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCC TGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGT TCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTG TGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAA ATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAA GTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCG ACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTA ATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAA ATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTG TGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAA 1293 2R:1731127-2080000 1 CG30159-RB CG30159-RB FBtr0089760 andy 322830 322725 0 CG30159:3 1 0 partof 105 2R:1731127-2080000 1 CG30159:3 324083 322895 0 CG30159:4 2 0 partof 1188 2R:1731127-2080000 1 CG30159:4 323619 322902 0 CG30159-PB 0 producedby 5c7e03a5a217f0beb78792636a404979 MEAAKDFAVAKYQDLCNFLERDTRGSELAIYGTSAIMLAVAYAKRKPAYL VRQFKQPSHIPERLINERVMHTGKIAGVKQQEQDTLLMIQHRPLFPIFTS SKRLLPVKLPGVRVNANGYSWLQQCLIGREATFLPLKSAKGQDFVVCQLC LVHPPRGNRLLDVSETLLKLRFARFVQDAAAAVKKNGKYYQHLKKVEQTT AEKEAWLSWAAGYPYIWRRYNELRQRWLPKEKLLPELVR 239 2R:1731127-2080000 1 CG30159-PB CG30159-PB FBpp0088701 324083 322460 0 CG30159-RA 0 partof e05c5135ad6fe798c93ba9d6b59346cd CAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCG TAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGT GTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGA GAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATC CCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCA AAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAG CGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAA ACGACATAACGCTCCAAGTGTTATCCAATGGAGGCGGCCAAGGATTTTGC GGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCG GCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCC TATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTC GCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGA TCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCAC CGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAA ACTGCCGGGCGTGCGCGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGT GTCTCATTGGGCGCGAGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGA CAGGACTTTGTTGTCTGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAA CCGCCTGCTGGACGTCTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGAT TCGTGCAGGATGCCGCCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAG CATCTGAAGAAGGTGGAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTC CTGGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGC AGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTG CGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGC CACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGC CTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTG TTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACA AACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGG GGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTA CGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCAT TTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGT GCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAA ATACCTAA 1558 2R:1731127-2080000 1 CG30159-RA CG30159-RA FBtr0089761 AAM70842 crosby EST evidence indicates that 5' UTR overlaps that of neighboring gene on the same strand.::DATE:2003-03-14 17:39:04::TS:1047681544000 Perfect match to HYPO SP record with corresponding FBgn not done 322830 322460 0 CG30159:2 1 0 partof 370 2R:1731127-2080000 1 CG30159:2 324083 322895 0 CG30159:4 2 0 partof 1188 2R:1731127-2080000 1 CG30159:4 323619 322902 0 CG30159-PA 0 producedby 5c7e03a5a217f0beb78792636a404979 MEAAKDFAVAKYQDLCNFLERDTRGSELAIYGTSAIMLAVAYAKRKPAYL VRQFKQPSHIPERLINERVMHTGKIAGVKQQEQDTLLMIQHRPLFPIFTS SKRLLPVKLPGVRVNANGYSWLQQCLIGREATFLPLKSAKGQDFVVCQLC LVHPPRGNRLLDVSETLLKLRFARFVQDAAAAVKKNGKYYQHLKKVEQTT AEKEAWLSWAAGYPYIWRRYNELRQRWLPKEKLLPELVR 239 2R:1731127-2080000 1 CG30159-PA CG30159-PA FBpp0088702 AAM70842.1 139467 138991 Drosophila 0 CG15237 0 0 476 melanogaster 2R:1731127-2080000 -1 CG15237 FBgn0033104 FBan0015237 42D1-42D1 CG15237 Gene prediction data only.::DATE:2002-02-14 10:09:31::TS:1013699371000 AE003790 Not in SwissProt real (computational) 139467 138991 0 CG15237-RA 0 partof 8a19b3f6409512a1d6decb0619d99f6f ATGATTCCATTCTTTCCCACGCTCAAAGTCTCCGTGGCCAATCGCTACTG GTTGGACATGGCTCCTGCCTCCGTAAACGAAGAATCGCAGACGCGGCGTT ATGAGGATGAAAGGAGCAACTGGCGAGAGTCCCTTAAGACGGCCGGCACA GATCTGCAGCCGCTGGGCAAAATGCTCACCATACCCGGAATTGAGACCGA CGACGAGGATGCCAACGACGACAGCGAGGACACGGACAGTCACGATGAGG AGGATGACGAGACCAACGACCGCGTCATCCCGGTAACCCAGGACTTTTAC TCCGCCGACGACATTCAGATGAACGACGAGACCTCACCCACAGCCCCCTA A 351 2R:1731127-2080000 -1 CG15237-RA CG15237-RA FBtr0086212 Perfect match to HYPO SP record with corresponding FBgn crosby AAF57397 139467 139344 0 CG15237:1 1 0 partof 123 2R:1731127-2080000 -1 CG15237:1 139286 139198 0 CG15237:2 2 0 partof 88 2R:1731127-2080000 -1 CG15237:2 139131 138991 0 CG15237:3 3 0 partof 140 2R:1731127-2080000 -1 CG15237:3 139467 138994 0 CG15237-PA 0 producedby MIPFFPTLKVSVANRYWLDMAPASVNEESQTRRYEDERSNWRESLKTAGT DLQPLGKMLTIPGIETDDEDANDDSEDTDSHDEEDDETNDRVIPVTQDFY SADDIQMNDETSPTAP 116 2R:1731127-2080000 -1 CG15237-PA CG15237-PA FBpp0085530 AAF57397.1 208698 205678 Drosophila 0 Spn4 0 0 3020 melanogaster 2R:1731127-2080000 -1 CG9453 FBan0009453 FBgn0028985 FBgn0033111 42D4-42D4 DGC clone may be problematic (GH21896): represents unique EST.::DATE:2002-03-07 00:18:50::TS:1015478330000 Curator examined, accepted Spn4 AE003790 serine protease inhibitor activity GO:0004867 208698 205923 0 Spn4-RC 0 partof 297b85c10bae16e0f274d0d0d6ad8f93 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTGAGTTATCCGGCAGTTTGA CTTTAAAAAGCCAGTGAAAGAAAACGCATTATGGATGTAAAGAGTGAAAT CAATGAGAACACCGAAGGCAGGCGAGAGAAAAACCCGTTTGGGAGCACGA ACTGAAGAGAAATCATTGTTTTGTGGGGGAATACATATGCATATGCGAGT ATAAAAACAATGTACGCTCGCTGAGAGAATTCAGTTGTTGCTCAAAGGCC ACATTATAAAAGTCGAGGGCGATAGCCGGTTTATAAAAAGAAATTAATTT ACACACTCGAAGCCGCTGGTGAAAAACAGTACCAGCAGTCGGAGCAGGCA GTTAATTACCCTTTCCGATAATCAAGCTAGTGAATCCCCGGCGAAACGGC CAACCGGAGAGATATAGTGAACACCGTTTGTGGAGGTGACTCATCAGTAC ACTGCAATTACATAAATTTATGAAAACGAGCACACCTCATCCACGGTCGA TTTGGATACTTACAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTC TTCCCGTTTCCACCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGC CCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACG GCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTT TCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGAC GGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGC AAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAG ATCTTGCGCATCGCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCG CCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGA GCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGG GTTGAGCAGCGCACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGT ATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGG GCACCTGGCAGCACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTT CACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGA GCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAAC TGCCCTACAAGGACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACC AAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTC GCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCA GGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTG GGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACA AAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTG AAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATG TGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGT CCAGCATCCATTTAACTATTACATTATCAATAAGGATTCTACTATTTTGT TTGCGGGAAGAATCAATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCG CTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATT TACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCA TAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTC GAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTG GCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAAT TATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTAT ACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTC TAAAA 2155 2R:1731127-2080000 -1 CG9453-RC CG9453-RC FBtr0086195 Only one EST supports this alternative transcript (DGC:GH21896).::DATE:2002-03-07 00:18:25::TS:1015478305000 crosby AAF57405 Imperfect match to REAL SP with corresponding FBgn 208698 207201 0 Spn4:1 1 0 partof 1497 2R:1731127-2080000 -1 CG9453:1 207137 206995 0 Spn4:2 2 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206508 206370 0 Spn4:3 3 0 partof 138 2R:1731127-2080000 -1 CG9453:3 206301 205923 0 Spn4:4 4 0 partof 378 2R:1731127-2080000 -1 CG9453:4 208179 206374 0 Spn4-PC 0 producedby MKTSTPHPRSIWILTGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFAR RLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQ GLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQL LSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESR LVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYAD LPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSL YETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLK VSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNY YIINKDSTILFAGRINKF 418 2R:1731127-2080000 -1 CG9453-PC CG9453-PC FBpp0085522 AAF57405.2 208698 206662 0 Spn4-RB 0 partof 6e03ec4a46ee783d26a8251c5b8837a2 AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGCATGGCGGTGCGTAGGAAGCGCGCTATTATGTCGCCTGAGGAACCA ATTGAGTTCTTTGCCGACCATCCTTTCACCTATGTCCTTGTGCATCAGAA GGATCTGCCATTGTTTTGGGGCTCAGTTGTGCGGCTCGAGGAAAATACCT TCGCCTCCAGCGAGCATGATGAGCTGTGATGGTACCTGATTCTTTGGCAA AACAATAAAGACAGCTATTTATTTACAATGGAAATTAA 1388 2R:1731127-2080000 -1 CG9453-RB CG9453-RB FBtr0086196 AAG22208 Imperfect match to REAL SP with corresponding FBgn Encodes protein variant A (FBrf0151323).::DATE:2002-03-07 00:15:14::TS:1015478114000 crosby 208698 208619 0 Spn4:5 1 0 partof 79 2R:1731127-2080000 -1 CG9453:5 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206897 206662 0 Spn4:7 4 0 partof 235 2R:1731127-2080000 -1 CG9453:7 208644 206724 0 Spn4-PB 0 producedby MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKD LPLFWGSVVRLEENTFASSEHDEL 424 2R:1731127-2080000 -1 CG9453-PB CG9453-PB FBpp0085523 AAG22208.1 208416 206662 0 Spn4-RA 0 partof 89f5dae9f1a68d1510d87f1adf2bb1d6 AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGCATGGCGGTGCGTAGGAAGCGC GCTATTATGTCGCCTGAGGAACCAATTGAGTTCTTTGCCGACCATCCTTT CACCTATGTCCTTGTGCATCAGAAGGATCTGCCATTGTTTTGGGGCTCAG TTGTGCGGCTCGAGGAAAATACCTTCGCCTCCAGCGAGCATGATGAGCTG TGATGGTACCTGATTCTTTGGCAAAACAATAAAGACAGCTATTTATTTAC AATGGAAATTAA 1512 2R:1731127-2080000 -1 CG9453-RA CG9453-RA FBtr0086197 Encodes protein variant E (FBrf0151323).::DATE:2003-02-21 17:15:26::TS:1045865726000 crosby AAG22209 Imperfect match to REAL SP with corresponding FBgn 208416 208213 0 Spn4:8 1 0 partof 203 2R:1731127-2080000 -1 CG9453:8 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206897 206662 0 Spn4:7 4 0 partof 235 2R:1731127-2080000 -1 CG9453:7 208062 206724 0 Spn4-PA 0 producedby MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMAVRRKRAIMSPEEP IEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 392 2R:1731127-2080000 -1 CG9453-PA CG9453-PA FBpp0085524 AAG22209.1 208698 205923 0 Spn4-RD 0 partof AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCG ATACGTTTCAATGTCGACCATCCATTTACATTTTACATCCTTAACAAGGA CTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAAC ATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGT GCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTT ACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGCGCAATTGATGAT CTTATATATACACTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGC CTCAATAAAGTCTAAAAGCAAATGTCTAAAA 1531 2R:1731127-2080000 -1 CG9453-RD CG9453-RD FBtr0086198 Encodes protein variant C (FBrf0151323).::DATE:2003-02-21 17:13:54::TS:1045865634000 not done crosby 208698 208619 0 Spn4:5 1 0 partof 79 2R:1731127-2080000 -1 CG9453:5 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206301 205923 0 Spn4:4 4 0 partof 378 2R:1731127-2080000 -1 CG9453:4 208644 206167 0 Spn4-PD 0 producedby MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMFMSLTSLPMPKPDPIRFNVDHPFTFYILNKDS TALFAGSIKKL 411 2R:1731127-2080000 -1 CG9453-PD 208698 205923 0 Spn4-RE 0 partof AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCC GTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGA TTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAAGTTAGCACT CCATCAAAATCCACCAATCACAACCATTGAACTGAAATGCAATGTAATCC CAATTCACAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCT AAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTA TTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCA TATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGC GCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCA TGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAA 1643 2R:1731127-2080000 -1 CG9453-RE CG9453-RE FBtr0086199 not done Encodes protein variant B (FBrf0151323).::DATE:2003-02-21 17:12:35::TS:1045865555000 crosby 208698 208619 0 Spn4:5 1 0 partof 79 2R:1731127-2080000 -1 CG9453:5 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206508 206301 0 Spn4:9 4 0 partof 207 2R:1731127-2080000 -1 CG9453:9 206206 205923 0 Spn4:10 5 0 partof 283 2R:1731127-2080000 -1 CG9453:10 208644 206374 0 Spn4-PE 0 producedby MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNYYIINKDS TILFAGRINKF 411 2R:1731127-2080000 -1 CG9453-PE 208698 205923 0 Spn4-RF 0 partof AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGGAATGGTCATGTGCTACGCCTCCATGCTCACGTTCGAACCGCAGCCC GTCCAATTCCATGTCCAGCATCCATTTAACTATTACATTATCAATAAGGA TTCTACTATTTTGTTTGCGGGAAGAATCAATAAGTTTTGAAGTATGTTTA TGAGCCTTACTTCGCTGCCCATGCCGAAGCCGGATCCGATACGTTTCAAT GTCGACCATCCATTTACATTTTACATCCTTAACAAGGACTCAACCGCTCT CTTCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAAT CCACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCA GTCCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATA AGGATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACA CTTAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTC TAAAAGCAAATGTCTAAAA 1669 2R:1731127-2080000 -1 CG9453-RF CG9453-RF FBtr0086200 Encodes protein variant B (FBrf0151323).::DATE:2003-02-21 17:12:07::TS:1045865527000 not done crosby 208698 208619 0 Spn4:5 1 0 partof 79 2R:1731127-2080000 -1 CG9453:5 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206508 206370 0 Spn4:3 4 0 partof 138 2R:1731127-2080000 -1 CG9453:3 206301 205923 0 Spn4:4 5 0 partof 378 2R:1731127-2080000 -1 CG9453:4 208644 206374 0 Spn4-PF 0 producedby MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATGMVMCYASMLTFEPQPVQFHVQHPFNYYIINKDS TILFAGRINKF 411 2R:1731127-2080000 -1 CG9453-PF 208416 205923 0 Spn4-RG 0 partof AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGTATGTTTATGAGCCTTACTTCG CTGCCCATGCCGAAGCCGGATCCGATACGTTTCAATGTCGACCATCCATT TACATTTTACATCCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCA TAAAGAAACTCTAAATAGGCAAACATACTAACCAATCCACAATGTTACTC GAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTG GCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAGGATTCACAAAAT TATAGTCTGTGCGCAATTGATGATCTTATATATACACTTAATATTTTTAT ACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTC TAAAA 1655 2R:1731127-2080000 -1 CG9453-RG CG9453-RG FBtr0086201 not done Encodes protein variant G (FBrf0151323).::DATE:2003-02-21 17:17:48::TS:1045865868000 crosby 208416 208213 0 Spn4:8 1 0 partof 203 2R:1731127-2080000 -1 CG9453:8 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206301 205923 0 Spn4:4 4 0 partof 378 2R:1731127-2080000 -1 CG9453:4 208062 206167 0 Spn4-PG 0 producedby MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMFMSLTSLPMPKPDP IRFNVDHPFTFYILNKDSTALFAGSIKKL 379 2R:1731127-2080000 -1 CG9453-PG 208416 205923 0 Spn4-RH 0 partof AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCC ATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATT TAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAA TCAATAAGTTTTGAAGTTAGCACTCCATCAAAATCCACCAATCACAACCA TTGAACTGAAATGCAATGTAATCCCAATTCACAGGACTCAACCGCTCTCT TCGCTGGCAGCATAAAGAAACTCTAAATAGGCAAACATACTAACCAATCC ACAATGTTACTCGAGGGTCTCGTATTCATTTAACGTGCAAGCGGGTCAGT CCTATATTGCTGGCTTGACGAGCATATTCAGCTTTTACATTGTCTATAAG GATTCACAAAATTATAGTCTGTGCGCAATTGATGATCTTATATATACACT TAATATTTTTATACTAACCAAGCATGTAGCCGTAGCCTCAATAAAGTCTA AAAGCAAATGTCTAAAA 1767 2R:1731127-2080000 -1 CG9453-RH CG9453-RH FBtr0086202 Encodes protein variant F (FBrf0151323).::DATE:2003-02-21 17:16:52::TS:1045865812000 not done crosby 208416 208213 0 Spn4:8 1 0 partof 203 2R:1731127-2080000 -1 CG9453:8 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206508 206301 0 Spn4:9 4 0 partof 207 2R:1731127-2080000 -1 CG9453:9 206206 205923 0 Spn4:10 5 0 partof 283 2R:1731127-2080000 -1 CG9453:10 208062 206374 0 Spn4-PH 0 producedby MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQP VQFHVQHPFNYYIINKDSTILFAGRINKF 379 2R:1731127-2080000 -1 CG9453-PH 208698 205678 0 Spn4-RI 0 partof AGTCTATTACGTACGCTTTGCAGACTAGGTTTACTGTAAGCAAAATTACT GAGTATGGATTATCGTTTGGTGCCATGTGGTTGCTGGTTGCTCCCCCTGC TCGGCCTAGCCCTCTTCCCGTTTCCACCGGTCCACACGGCTGACGTCACC ATGGCTGACGCCGCCCACCAGGAGTTCGCCCGCCGGCTGGCCCTTTTCTC TATCAACGTGTACGGCAAGCTGTCGGGGCAGAAGCCCGGCGAGAACATCG TCTTCTCGCCCTTTTCCATCCAGACTTGTGCGGCGATGGCCAGGCTGGGT GCAGAAAACGAGACGGCTACCCAGCTGGACCAGGGACTGGGCTTGGCCTC TAGTGACCCAGAGCAAATCGCACACAGTTTTCACCAGGTGCTGGCCGCCT ACCAGGACAGTCAGATCTTGCGCATCGCCAACAAGATTTTCGTCATGGAT GGCTACCAGCTGCGCCAGGAGTTTGATCAGCTGTTATCCAAGCAGTTCCT CTCGGCGGCTCAGAGCGTGGACTTTTCCAAAAATGTACAAGCAGCGGCCA CCATCAACAATTGGGTTGAGCAGCGCACCAACCATCTGATCAAGGACCTT GTGCCGGCTGATGTATTGAACTCCGAATCGCGACTCGTCCTTGTGAACGC CATTCACTTCAAGGGCACCTGGCAGCACCAGTTCGCCAAACACTTAACCC GCCCAGACACCTTTCACCTGGATGGGGAGCGAACAGTTCAGGTTCCGATG ATGAGTTTAAAGGAGCGGTTCCGCTACGCCGATCTGCCGGCGCTAGATGC CATGGCTCTGGAACTGCCCTACAAGGACTCAGACCTCTCTATGCTGATCG TACTGCCCAACACCAAGACGGGTCTGCCCGCTCTGGAGGAGAAGTTGCGC CTCACGACCCTCTCGCAGATCACGCAGTCGTTGTACGAAACAAAGGTAGC GCTCAAATTGCCCAGGTTCAAGGCAGAGTTCCAAGTGGAATTGTCTGAGG TTTTCCAGAAGCTGGGCATGTCAAGGATGTTCTCCGATCAGGCTGAATTT GGAAAAATGCTACAAAGTCCGGAGCCATTGAAAGTGTCAGCCATCATACA CAAGGCCTTCATTGAAGTCAACGAGGAGGGAACGGAGGCTGCGGCCGCCA CGGTATGGCGGGTGATGGCCGTAGCTGCCTTCAGTCGCAAACACTTCATT GCCAACCATCCTTTTGCTTTCTACGTGAAGACCCATTACGATCTGCCGAT ATTCACTGGGCGCTACTTGGGTTAAGCAATAGGAAGCTTCCTATGAAAAA AAAAATTGAAGTTCAATAAAATAAAATAAACGGCAGCCACTTAATAGCTG TGATTTCGTCAAGTCGAA 1368 2R:1731127-2080000 -1 CG9453-RI CG9453-RI FBtr0086203 Encodes protein variant D (FBrf0151323).::DATE:2003-02-21 17:14:53::TS:1045865693000 crosby not done 208698 208619 0 Spn4:5 1 0 partof 79 2R:1731127-2080000 -1 CG9453:5 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 205893 205678 0 Spn4:11 4 0 partof 215 2R:1731127-2080000 -1 CG9453:11 208644 205774 0 Spn4-PI 0 producedby MDYRLVPCGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSI NVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASS DPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLS AAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAI HFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM ALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL KLPRFKAEFQVELSEVFQKLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHK AFIEVNEEGTEAAAATVWRVMAVAAFSRKHFIANHPFAFYVKTHYDLPIF TGRYLG 406 2R:1731127-2080000 -1 CG9453-PI 208416 205678 0 Spn4-RJ 0 partof AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGTATGGCGGGTGATGGCCGTAGCT GCCTTCAGTCGCAAACACTTCATTGCCAACCATCCTTTTGCTTTCTACGT GAAGACCCATTACGATCTGCCGATATTCACTGGGCGCTACTTGGGTTAAG CAATAGGAAGCTTCCTATGAAAAAAAAAATTGAAGTTCAATAAAATAAAA TAAACGGCAGCCACTTAATAGCTGTGATTTCGTCAAGTCGAA 1492 2R:1731127-2080000 -1 CG9453-RJ CG9453-RJ FBtr0086204 not done Encodes protein variant H (FBrf0151323).::DATE:2003-02-21 17:18:10::TS:1045865890000 crosby 208416 208213 0 Spn4:8 1 0 partof 203 2R:1731127-2080000 -1 CG9453:8 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 205893 205678 0 Spn4:11 4 0 partof 215 2R:1731127-2080000 -1 CG9453:11 208062 205774 0 Spn4-PJ 0 producedby MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATVWRVMAVAAFSRKHFI ANHPFAFYVKTHYDLPIFTGRYLG 374 2R:1731127-2080000 -1 CG9453-PJ 208416 205923 0 Spn4-RK 0 partof AGTTGTTGCTCAAAGGCCACATTATAAAAGTCGAGGGCGATAGCCGGTTT ATAAAAAGAAATTAATTTACACACTCGAAGCCGCTGGTGAAAAACAGTAC CAGCAGTCGGAGCAGGCAGTTAATTACCCTTTCCGATAATCAAGCTAGTG AATCCCCGGCGAAACGGCCAACCGGAGAGATATAGTGAACACCGTTTGTG GAGGTTGCTGGTTGCTCCCCCTGCTCGGCCTAGCCCTCTTCCCGTTTCCA CCGGTCCACACGGCTGACGTCACCATGGCTGACGCCGCCCACCAGGAGTT CGCCCGCCGGCTGGCCCTTTTCTCTATCAACGTGTACGGCAAGCTGTCGG GGCAGAAGCCCGGCGAGAACATCGTCTTCTCGCCCTTTTCCATCCAGACT TGTGCGGCGATGGCCAGGCTGGGTGCAGAAAACGAGACGGCTACCCAGCT GGACCAGGGACTGGGCTTGGCCTCTAGTGACCCAGAGCAAATCGCACACA GTTTTCACCAGGTGCTGGCCGCCTACCAGGACAGTCAGATCTTGCGCATC GCCAACAAGATTTTCGTCATGGATGGCTACCAGCTGCGCCAGGAGTTTGA TCAGCTGTTATCCAAGCAGTTCCTCTCGGCGGCTCAGAGCGTGGACTTTT CCAAAAATGTACAAGCAGCGGCCACCATCAACAATTGGGTTGAGCAGCGC ACCAACCATCTGATCAAGGACCTTGTGCCGGCTGATGTATTGAACTCCGA ATCGCGACTCGTCCTTGTGAACGCCATTCACTTCAAGGGCACCTGGCAGC ACCAGTTCGCCAAACACTTAACCCGCCCAGACACCTTTCACCTGGATGGG GAGCGAACAGTTCAGGTTCCGATGATGAGTTTAAAGGAGCGGTTCCGCTA CGCCGATCTGCCGGCGCTAGATGCCATGGCTCTGGAACTGCCCTACAAGG ACTCAGACCTCTCTATGCTGATCGTACTGCCCAACACCAAGACGGGTCTG CCCGCTCTGGAGGAGAAGTTGCGCCTCACGACCCTCTCGCAGATCACGCA GTCGTTGTACGAAACAAAGGTAGCGCTCAAATTGCCCAGGTTCAAGGCAG AGTTCCAAGTGGAATTGTCTGAGGTTTTCCAGAAGCTGGGCATGTCAAGG ATGTTCTCCGATCAGGCTGAATTTGGAAAAATGCTACAAAGTCCGGAGCC ATTGAAAGTGTCAGCCATCATACACAAGGCCTTCATTGAAGTCAACGAGG AGGGAACGGAGGCTGCGGCCGCCACGGGAATGGTCATGTGCTACGCCTCC ATGCTCACGTTCGAACCGCAGCCCGTCCAATTCCATGTCCAGCATCCATT TAACTATTACATTATCAATAAGGATTCTACTATTTTGTTTGCGGGAAGAA TCAATAAGTTTTGAAGTATGTTTATGAGCCTTACTTCGCTGCCCATGCCG AAGCCGGATCCGATACGTTTCAATGTCGACCATCCATTTACATTTTACAT CCTTAACAAGGACTCAACCGCTCTCTTCGCTGGCAGCATAAAGAAACTCT AAATAGGCAAACATACTAACCAATCCACAATGTTACTCGAGGGTCTCGTA TTCATTTAACGTGCAAGCGGGTCAGTCCTATATTGCTGGCTTGACGAGCA TATTCAGCTTTTACATTGTCTATAAGGATTCACAAAATTATAGTCTGTGC GCAATTGATGATCTTATATATACACTTAATATTTTTATACTAACCAAGCA TGTAGCCGTAGCCTCAATAAAGTCTAAAAGCAAATGTCTAAAA 1793 2R:1731127-2080000 -1 CG9453-RK CG9453-RK FBtr0086205 not done crosby Encodes protein variant F (FBrf0151323).::DATE:2003-02-21 17:17:13::TS:1045865833000 208416 208213 0 Spn4:8 1 0 partof 203 2R:1731127-2080000 -1 CG9453:8 208133 207201 0 Spn4:6 2 0 partof 932 2R:1731127-2080000 -1 CG9453:6 207137 206995 0 Spn4:2 3 0 partof 142 2R:1731127-2080000 -1 CG9453:2 206508 206370 0 Spn4:3 4 0 partof 138 2R:1731127-2080000 -1 CG9453:3 206301 205923 0 Spn4:4 5 0 partof 378 2R:1731127-2080000 -1 CG9453:4 208062 206374 0 Spn4-PK 0 producedby MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLG AENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMD GYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDL VPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPM MSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKLGMSRMFSDQAEF GKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGMVMCYASMLTFEPQP VQFHVQHPFNYYIINKDSTILFAGRINKF 379 2R:1731127-2080000 -1 CG9453-PK 122885 121892 Drosophila 0 CG15235 0 0 993 melanogaster 2R:1731127-2080000 -1 CG15235 GO:17034 FBgn0033103 FBan0015235 42C10-42D1 Gene prediction data only.::DATE:2002-02-14 10:05:26::TS:1013699126000 AE003790 CG15235 Not in SwissProt real (computational) Rap guanyl-nucleotide exchange factor activity GO:0017034 122885 121892 0 CG15235-RA 0 partof 9dadaaeebf0e93335692738212f6f1b2 ATGAACGAGATAATCCACTATCAGATACAAGGTCAAATTCCTTGCGACCG GAACCTGCGTGATGTGGAGCTAATTTCGTGCCGGTTGCGTCGCGTGGAGC CGCTGTGTCGCCTCCCGGGATCTGCGCTCCAGCAGTTGGCCATGTGCGGA TTCTATGAGGACCTGGAGAAGGGGGTGACTCTTTTTCGCGCCGGCGAGCA GGGACGCTTCTGGTATGCAGTGCTCGGCGGATCGCTGGAGGTGCGATACC ATGCCCACGCCGATGCCGATGGCAAGGTAAGTCCTTACTTACACCAGTCA GGAGATGAGACATCCTGGAACACTATTCCGCCGTGCGCAGAGTGCGAGAC AATGCGCGTGCTGAGCAATATAATTGATAGTGATTACTCGGCGTACCCGC CGTGTTGCATATCCGATCCGCCGTGCATGCTCAATATTCCGGGGATTTGG GCCTGGGTTGGGGGTTGGGTTTGA 474 2R:1731127-2080000 -1 CG15235-RA CG15235-RA FBtr0086213 Perfect match to HYPO SP record with corresponding FBgn AAF57395 crosby 122885 122847 0 CG15235:1 1 0 partof 38 2R:1731127-2080000 -1 CG15235:1 122396 122253 0 CG15235:2 2 0 partof 143 2R:1731127-2080000 -1 CG15235:2 122185 121892 0 CG15235:3 3 0 partof 293 2R:1731127-2080000 -1 CG15235:3 122885 121895 0 CG15235-PA 0 producedby MNEIIHYQIQGQIPCDRNLRDVELISCRLRRVEPLCRLPGSALQQLAMCG FYEDLEKGVTLFRAGEQGRFWYAVLGGSLEVRYHAHADADGKVSPYLHQS GDETSWNTIPPCAECETMRVLSNIIDSDYSAYPPCCISDPPCMLNIPGIW AWVGGWV 157 2R:1731127-2080000 -1 CG15235-PA CG15235-PA FBpp0085531 AAF57395.1 315484 305056 Drosophila 0 vimar 0 0 10428 melanogaster 2R:1731127-2080000 -1 CG3572 FBgn0021806 FBan0003572 FBgn0027729 CG3572 FBgn0022960 D.melanogaster FlyBase-curated sequence: vimar.v004 Curator examined, accepted Comment: Reference sequence of vimar == FBgn0022960 AE003790 42E1-42E4 DGC clone appears problematic (SD10607): incomplete CDS (approximately 40aa short at amino terminus).::DATE:2002-03-07 00:39:32::TS:1015479572000 Comment: Reference sequence based on BDGP genomic sequence. vimar Comment: This record is derived from the following: AC009342 AC009342.5 21-MAR-2001 AF034421 AF034421.1 25-FEB-2000 AQ034041 AQ034041.1 08-JUL-1998 AI543723 AI543723.2 23-APR-2001 AA264054 AA264054.1 19-APR-2001 AW944649 AW944649.1 19-APR-2001 AF171836 AF171836.1 23-AUG-1999 Ral interactor activity GO:0017160 315484 305056 0 vimar-RC 0 partof be662f35819a0cbed5873d2ac051ebb2 ACACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAA TACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAAC GGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCA GTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGT GCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAA CGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGACA GCTGAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCC GGCGAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCA AACTTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAG TGCGACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGAT CACCAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAG CCGCATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATG GAGCTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAA CGACGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTAC TGCGACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAA TTCATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGA GGGCTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAG GCATCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTG CTGAACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCT GAACTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTT CCACGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAG GCGGAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGA AACCATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTG AGGCCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTT ACTGGTGATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAA CATGGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCG TGCTGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTT GTGGAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAA CGGCGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGC GCAACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGC CTGGTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGT CTTCAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGGAGAAAC TCGCACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCAC TGGAGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCT CATGGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCAC TGCCGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCG CTAACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGA GGGCACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCA TGCAGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTG TCGCAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGT CAAGTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGG ACACGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTG CTCAAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAA CGAGCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAG AAAACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACA GTGGGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGG TAAGCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGC CAATACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCT AAACTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATC CACTCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATA AATGTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTA GCCACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAA GCAACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCA GATTCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAAC ACGAGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCAT TTATGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTT ATAGCATACATACATAACATATACGTATAAATATAATAATATTAATAATT TAGCATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAAC AAATCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTG TACTTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCA AAAACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATT TTAATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTG TAAAACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAAC ATTAACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAA AACCAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGC TACAAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAA AAACTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATA AAGCGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTC TAAACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATG AGAAATAAGAGAAAACCAAA 3470 2R:1731127-2080000 -1 CG3572-RC CG3572-RA FBtr0086182 crosby AAF57418 Imperfect match to REAL SP with corresponding FBgn 315484 315186 0 vimar:1 1 0 partof 298 2R:1731127-2080000 -1 CG3572:1 experimental 308375 307466 0 vimar:2 2 0 partof 909 2R:1731127-2080000 -1 CG3572:2 307377 306990 0 vimar:3 3 0 partof 387 2R:1731127-2080000 -1 CG3572:3 experimental 306932 305056 0 vimar:4 4 0 partof 1876 2R:1731127-2080000 -1 CG3572:4 experimental FBrf0102180 315193 306330 0 vimar-PC 0 producedby MATAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLG LTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSD GSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVAN AAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHE DLLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELL HYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIV LILTGDDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHC IYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVI QAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQEKLALELLKNKTLIEQ LVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIAD KIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSV VYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNC VNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 635 2R:1731127-2080000 -1 CG3572-PC CG3572-PA FBpp0085514 315484 305056 0 vimar-RB 0 partof 30133761a6069d7567f5453eb0a771dd ACACTAGAATTGCAGTTGTTGGTGTGAACGTCTGAACGCGATTCGGAAAA TACGGATTACACGGATAATACGAATTATACGGATATTGCGGAAGTTGAAC GGAGACGCGACTGAAAGAAAGCCGTGAAATGTGTTCAGTTGCGCGCAGCA GTCATTAGCCTATCAGCAGTGTTTGTTACAAGCTAACAGTGATACAACGT GCCTGGAATCGCAACCAACGCAGAGCAAGAAAAGCAGAAAAGCATAAAAA CGGAAGAAGCAGCAGCGGAATAATCAACAAAGGCGGCAAACATGGCGACT GAAATCGACGATTTGATTGAAAAGCTGAAGACGACCAGTGTCAGTCCGGC GAACACGACCAACTTGCTCTGCGAGATCTCGGCGACGAAGGACCCCAAAC TTTTCGATAAGCACGAGCTGGCAGAGTGCTTTCTGGGCCTCACCAAGTGC GACGACACAAACGTGCGCAAGGAGGCGGCCAAGTGCATTGCGGAGATCAC CAAGTCCGAGGTGCAGCGCAAGAAGTTCACCAAGAGGAATATAATAGCCG CATTTCTGGAGTGCTTGCGACAAGTGCCCACGTCCGACGGCAGTATGGAG CTGCCCATACAGATTTGTCGGGCACTGGGCAATATCTGCTACCTAAACGA CGAAGCCAGGGACTTAATACTCGAGCTGGAGGGCGATGCTGTTCTACTGC GACTGCTGGACATCACAACCATCGAGGACGTGGCCAATGCGGCGCAATTC ATCAAAGTGCGCGGCGGCTTGCTGTCCAACTATTTGCTCGGAGGCGAGGG CTTGGCCAAGCGGGCCATGGAGTTGGGCGTGATGAAGAAGCTGCAAGGCA TCATCGACATTGGCGCCTCCAATGTGGAACAGCATGAGGATCTGCTGCTG AACACGCTTCCACTGCTCAGTATACTCACCGAGAACGTGTCGGATCTGAA CTTCGACTCTTCCCTGAATATCCAGCTGTCTCGCATTCTGGCCGCTTCCA CGAATCCCGATCTTGCCGAGATGTGCCTGGAGCTGCTCCATTACCAGGCG GAGAGCGACGAAGTCAAGCTTATTTTGGCCAAGGACGGTCTGTGCGAAAC CATCTACAACCTGCTGGAAAAGTACAAGACTCTGGCCAGCACAAGTGAGG CCAGGGCGTTGATGAAACTCGCCTGCGAACTCATCGTATTAATCCTTACT GGTGATGACTCAATGCACTATTTGTACACCACGCCGCTGCTGAAGAACAT GGTCGATTGGCTGGACTCGACGGACATCGATCTGCTAACCACCGGCGTGC TGGCCCTGGGCAACTTTGCGCGCACCGATAGCCACTGCATCTACTTTGTG GAGCAGCAGACCATGAACAAGCTGCTCGAGGTGCTGGCCAAGAACAACGG CGTCAAGGACGATGTGCGCCTGCAGCACGCTCTTCTCTCCGCGCTGCGCA ACCTGGTCATCCCGAAGCCAAACAAGAACGCGGTAATCCAGGCGGGCCTG GTGCAGACCATTCTTCCCATGCTCGAAATACACCAGCCACCAGTCGTCTT CAAGCTGCTGGGCACACTTCGCATGACCGTCGACGGACAGGAGAAACTCG CACTGGAGTTGCTGAAGAACAAGACTCTGATCGAGCAGCTGGTGCACTGG AGCAAATCGTCGGACTATGCGGGCGTCACCGGCGAGTCTCTGCGCCTCAT GGCCTGGCTGATCAAGCACGCCTACCTCAGCAAAATCGCATACGCACTGC CGCGCAAGGGCGATGCACCCGCCGAACAGATTGCCGACAAGATTCCGCTA ACGCAAGACTACGATCGCAGTAGCTTGAGCGAGTTCCTTGCCAACGAGGG CACCGTGGAGGCCATGGTCAGCATGCTCACAGCTCAGCACCTGGTCATGC AGAACGAGGCGCTGATTGCCCTGTGCATCCTGTCCGTGGTGTACCTGTCG CAGCCCAGCGAGGCGGCGCAGGCCCAGCTGCTGCAGGACGAGCTGGTCAA GTGCGAGGTCGGCAAGAAGTTGGCCGAGCTCATCAGCAAGTCGTCGGACA CGATGACCAAGGAGATTGTCGAGAACCTGCAGAACTGCGTGAACTTGCTC AAATCTTCCGAGCAGCTGGTGGCGCATCTGGAACAGCATAACATCAACGA GCTGCTGAAGTCTATACCCATTCTCACCGAATACTGCACCTTGTAAGAAA ACGGGGACTGTCATTGCATTTATCCCAGCACCGCAGGATGCCTCACAGTG GGATGGGTCGATTTGCACGATTGAACATAACATAAATACTTTAGGGGTAA GCAGTTATCTTTGGAAGTTATCTGTGTGGTCTTACCAAGAGAAACGCCAA TACTTATTCGTAACGATACAAAGATTAATACGTTGCGCTAATGTGCTAAA CTCCACTTTACTACTTAATAACAATTTTGTTAAATTGTAATTAAATCCAC TCTCTTGAGATTCACTGACGTTGCACGATTCCAAATAGCCAAAGATAAAT GTTTGCCACTATTAGAGCATGTTTTAAAAAAAATCAGCCCACCCTTAGCC ACACAGACACACTCAGAACCGGAGAAAATAGTAGTTTTCACCCCAAAGCA ACGATTCAGATGTAGACTTGACTGTAGTTTGGTAAGAAGAAAGTGCAGAT TCACAAGTTAAGCAGTTAATCAGTTAAGCACACTGGAACACGCGAACACG AGAGGAGCAGAAAGTATTTTTTAGACGCAAGCGTATTTTGACTGCATTTA TGAAGAGAATCCGATGTAGTAAGGAGTCACAAATCGTATGAATATTTATA GCATACATACATAACATATACGTATAAATATAATAATATTAATAATTTAG CATATTAATCTTTTCTGTTACATGATTTTTAAGAGCACAATAACAACAAA TCGTGGTGATATCGCTAAATATATTTAATAAATGTATTTTATGATTGTAC TTATAATTTTCAATCGACCTCTTTTAAACCGTTGCTGGCACAAACCAAAA ACGAGAAGATAACAAAACATTTAGACGCACGACGTAATTAAGGTATTTTA ATTGGTGCACAGACACATATTGCAAACGGCATCCCATATATTTATTGTAA AACTCGGCGAAGTTATCCAAAATGCATTTTTAAGCTAACTTTAAAACATT AACAAAACTGCAACTCAGTAACAATCAGCAATCCGAAAATAGTTGAAAAC CAATAATGCAAATATTTCAATTTTACAAATCGTAGTTTATGGAGTGCTAC AAATTTTACCAATTATTAAAAACGATGTACTAATGTTTGGTCACCAAAAA CTAAAAATTAAACGAACACAATTCAAGGGGAATGGTGTTAATATATAAAG CGTTGAGACACCCACACACATAAATGCGAAAACATATTTATGAACTCTAA ACACAATAATGTACATTTAATAATTCAAATAAAATTTGAAATGCATGAGA AATAAGAGAAAACCAAA 3467 2R:1731127-2080000 -1 CG3572-RB CG3572-RB FBtr0086183 crosby experimental not done FBrf0102180 315484 315186 0 vimar:1 1 0 partof 298 2R:1731127-2080000 -1 CG3572:1 experimental 308372 307466 0 vimar:5 2 0 partof 906 2R:1731127-2080000 -1 CG3572:5 experimental 307377 306990 0 vimar:3 3 0 partof 387 2R:1731127-2080000 -1 CG3572:3 experimental 306932 305056 0 vimar:4 4 0 partof 1876 2R:1731127-2080000 -1 CG3572:4 experimental FBrf0102180 315193 306330 0 vimar-PB 0 producedby MATEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGL TKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDG SMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANA AQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHED LLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLH YQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVL ILTGDDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCI YFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQ AGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQEKLALELLKNKTLIEQL VHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADK IPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVV YLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCV NLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 634 2R:1731127-2080000 -1 CG3572-PB AAF57418.1 predicted 305057 305056 0 0 partof 2R:1731127-2080000 1 vimar-polyA_site-2036184..2036184 FBrf0102180 experimental 315463 315455 0 0 partof 2R:1731127-2080000 -1 P{lacW}vimar[k16722] experimental 8 bp insertion associated host repeat FBrf0102180 315456 315454 0 0 partof 2R:1731127-2080000 -1 P{lacW}vimar[B6-2-30] experimental FBrf0102180 P{lacW} insertion 16bp downstream of the start site of the 3.5kb cDNA, GB:AF034421 312761 311220 Drosophila 0 CG30156 0 0 1541 melanogaster 2R:1731127-2080000 -1 CG30156 FBan0030156 FBgn0050156 CG30156 42E1-42E3 Not in SwissProt real (computational) AE003790 defense response GO:0006952 protein folding GO:0006457 response to stress GO:0006950 protein metabolism GO:0019538 312761 311220 0 CG30156-RA 0 partof 47f050df7b45661bbcc568c09fa42ed9 GTTGACATACAAAATGTTGACTGGCGAAAGTCAATTTGTATTTAAGTTTG CAGCTACATATACATATACAGTCAACTTAGTTCGAAACTATTTCGGCTAC CTCTAATATACATACAAAAGCACTTTGTTAAATTCACCAACTCGGTGGAT TGTCCCAGAACAACAAACCAAAATTTAAAATTTGCAAACGAACAGAGAAA AACGAATCCTTTTTTGTCTTCTCACGCTGCTGGGAAGGAGAAGAAAGTAA CCAAGAACTGGAGGACGACGACTTCACAATGGGAATCCTGCAGGCGAGGA GGCATCACTGCGTCGACAAGGTGGTGAGTGACCTGTGCCTGGGACACTAC GAGCACGCTCTGAGGCAGATCAACGAGGATCTGGAAGGCTTACAGAACCA CGATGAGATCATGGCGCTGCTGGAGCTAAAGAATATCATTTTGAGACTGA GGCTGAAGGGCGAGGCCCAGCGGACCATAGGCCCAACTCGCAAATCTGAC GCCCTGCCCCACAAGTTCACACTCGAGATGCTGGACGTGGTGCAGAAGGT CCTGCGGTGCCGCAATCACTACGAGGTGCTGCGCATCTCTCATCATGCCA CCTACTCCGAGGTGAAGCGGGCCTACCACAAGCTGGCCCTGCGCCTCCAT CCGGACAAGAACAAATCTCCTGGGGCTGAGCAGGCCTTCCGGCGGATCAG CGAGGCGGCTGACTGCCTCACGGACTGCCAGAAAAGGATTGAGTACAACA TAGCAACGGCAGTGGGCGACTGCCACGACCAGGATCCCTCGCAGTACAAG GATTATCGCGGGGAAAGTGAATTCAATGAGGCAAATGGGAACGATCTGGG AGCCGCTTTCAGAAGGCCTTATCGGGGGGCCAATCAGCGGATGCCCCAGA GGCAGTCACTCTACCAAACACAGCAACTCGTCATCGGAGTGGTGGCTGCT CTGGTTTTTCTCTTCGTCACCATGCACTTCATCGCAGGCGCTCCTGCTTA CAGTTTTACGCTAACCAGAACCCACAGCGCTCGACGGCTCAGTCGGACGA ACCACATTGCCTACTACATGAATCCGACGACTCTGTCCAAGTACACAGAA CAGCAGTTGGCCGAACTGGAAGTAGAAATCGAGGAGGTTTACATCTCGGA CCTCAAACATAAGTGCAGGCAAGAGCGGAGTTGGAGGGATAATCTGTTTC TCAGGGCGAGGCAGGGAAACAACGACCAGAAGTTGCTCCAGCATGTCAGC CAGATGTCCACTCCCGCTTGCCAGGCGTTGCTCCAGCTGGGAAAGTCTGG TCACAGTCGACTGTTGCTCGAGAACGAGTCTTTGAATCAGGACGTGCCAG TCTGATACTCTGTACTTTTCTATTGATAGATGTAGGGATTAGTGCACGGT GTAAATAAAGAGTAGTTTTAAAAAT 1425 2R:1731127-2080000 -1 CG30156-RA CG30156-RA FBtr0086184 AAM70840 Hits nothing in SP, and no SP entry corresponds to this FBgn crosby 312761 311743 0 CG30156:1 1 0 partof 1018 2R:1731127-2080000 -1 CG30156:1 311684 311517 0 CG30156:2 2 0 partof 167 2R:1731127-2080000 -1 CG30156:2 311460 311220 0 CG30156:3 3 0 partof 240 2R:1731127-2080000 -1 CG30156:3 312483 311293 0 CG30156-PA 0 producedby MGILQARRHHCVDKVVSDLCLGHYEHALRQINEDLEGLQNHDEIMALLEL KNIILRLRLKGEAQRTIGPTRKSDALPHKFTLEMLDVVQKVLRCRNHYEV LRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDC QKRIEYNIATAVGDCHDQDPSQYKDYRGESEFNEANGNDLGAAFRRPYRG ANQRMPQRQSLYQTQQLVIGVVAALVFLFVTMHFIAGAPAYSFTLTRTHS ARRLSRTNHIAYYMNPTTLSKYTEQQLAELEVEIEEVYISDLKHKCRQER SWRDNLFLRARQGNNDQKLLQHVSQMSTPACQALLQLGKSGHSRLLLENE SLNQDVPV 358 2R:1731127-2080000 -1 CG30156-PA CG30156-PA FBpp0085515 AAM70840.1 304761 301886 Drosophila 0 Cyp6u1 0 0 2875 melanogaster 2R:1731127-2080000 -1 CG3567 GO:5792 GO:15034 FBgn0033121 FBan0003567 42E1-42E1 Cyp6u1 AE003790 Curator examined, accepted electron transporter activity GO:0005489 microsome GO:0005792 membrane GO:0016020 304761 301886 0 Cyp6u1-RA 0 partof a3f3897ae0e9bf432c4919e6d84d3a92 TGCGATTTCACTTTCACAAAACAAATTACGGCTGCCCAAGCGGCCGATAC TCAATGGACCTTATCAATTATTAAATCGGACCGCACGATAATGGCGCTGA TAAACCGGCGGCATTGAGCCCCAGAACCTCGACAAGCAGCTACTGCCAGC TGTTAAGCATATCAAACAGCGCGAACATATTGTAAAAGCCGGAAAAGACA GCTGAGTGAGCATGGATCTAATGCACCGCACCCTGCTCACCGCCCTGGGT GCGCTGTCAGTGGTCTACGCCCTGGTCAAGTTCAGTCTGGGCTACTGGAA ACGGCGGGGGATCCTGCACGAAAAGCCCAAGTTCCTGTGGGGCAACATTA AGGGCGTGGTGAGCGGGAAGAGGCATGCCCAGGACGCCTTGCAGGATATC TACACCGCATACAAGGGCAGGGCGCCGTTTGTGGGATTCTACGCCTGCCT CAAGCCGTTCATCTTGGCGCTGGACCTGAAGCTAGTCCACCAAATAATCT TCACCGACGCGGGACACTTTACGTCCCGAGGCCTTTATAGTAATCCCAGT GGAGAGCCGCTGTCGCATAATCTCCTTCAGCTGGACGGTCACAAGTGGCG GTCACTGCACGCCAAATCTGCAGAGGTTTTCACTCCGGCCAACATGCAGA AGCTGCTGGTCAGACTGTCGCAAATCTCCTCCAGAATTCAAAGGGACCTG GGCGAAAAGAGCCTTCAAACTATCAATATAAGCGAACTCGTGGGTGCATA CAATACGGACGTTATGGCGTCAATGGCCTTTGGACTAGTAGGGCAGGATA ACGTGGAGTTCGCTAAGTGGACGCGCAACTACTGGGCGGACTTTAGGATG TGGCAGGCTTATCTGGCGCTTGAGTTTCCGCTCATCGCTCGCCTTCTTCA GTACAAAAGCTACGCAGAACCTGCTACAGCTTACTTCCAAAAAGTGGCCC TGTCGCAGTTGCAGTTGCATCGAAGAAGGGATCGCCAGCCACTCCAGACC TTTCTGCAGCTATATTCCAACGCAGAAAAGCCGCTCACCGACATCGAGAT TGCGGGCCAAGCCTTCGGCTTCGTTCTGGCTGGCTTGGGCCCCCTGAATG CCACCCTAGCATTCTGCCTCTACGAGTTGGCCCGCCAGCCTGAGGTGCAA GATCGAACCAGGCTCGAGATTAACAAGGCACTGGAGGAGCATGGTGGCCA AGTGACACCGGAGTGCCTAAGGGAGCTCAGGTATACGAAGCAAGTCCTCA ATGAAACGCTTCGCCTGCACACTCCACATCCCTTCCTGCTACGCCGGGCT ACCAAAGAATTCGAAGTGCCCGGATCGGTGTTTGTAATTGCCAAAGGCAA CAATGTGCTGATACCAACGGCGGCGATACACATGGATCCTGGCATTTATG AAAACCCCCAGCGGTTCTACCCGGAGCGCTTTGAGGAACAGGCAAGGCGA TCCCGCCCGGCAGCTGCGTTCCTGCCTTTCGGCGATGGCCTGCGAGGATG CATTGCCGCTCGCTTTGCAGAGCAGCAGCTTCTGGTGGGCCTGGTGGCTC TGCTGAGGCAGCACAGATACGCTCCCTCTGCGGAGACCTCGATTCCCGTG GAGTACGACAACCGGAGACTGCTCTTGATGCCCAAGTCGGACATCAAACT CAGTGTGGAACGGGTGGACAAGCTTTAAAGGAGGCTCTGCTGGAGCATCG CATATTTTGTATTGTTTGCTTTACAAAGCGTTTAAGTTGTTTTTATATTT GTATATGCACCTTTTTCGTTGATTTTCCTAAGCTGTGGACTTGTGTGATA ATGCTGACGATGACTTTTATAATCTTTTGCACCAAGCTCAACAACGTGAA CAAATAAATAATTTAGTTGTT 1871 2R:1731127-2080000 -1 CG3567-RA CG3567-RA FBtr0086185 crosby Imperfect match to REAL SP with corresponding FBgn AAF57417 304761 304721 0 Cyp6u1:1 1 0 partof 40 2R:1731127-2080000 -1 CG3567:1 303775 302562 0 Cyp6u1:2 2 0 partof 1213 2R:1731127-2080000 -1 CG3567:2 302504 301886 0 Cyp6u1:3 3 0 partof 618 2R:1731127-2080000 -1 CG3567:3 303604 302082 0 Cyp6u1-PA 0 producedby MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVV SGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDA GHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLV RLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEF AKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL QLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLA FCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNETL RLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQ RFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQ HRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 488 2R:1731127-2080000 -1 CG3567-PA CG3567-PA FBpp0085516 AAF57417.1 205388 203342 Drosophila 0 CG9447 0 0 2046 melanogaster 2R:1731127-2080000 -1 CG9447 FBan0009447 FBgn0033110 42D4-42D4 CG9447 Not in SwissProt real (computational) AE003790 205388 203342 0 CG9447-RA 0 partof ATGCCTGCCCTGTACCAACTTGATGACTACGATCTCTGTCTGGATAATCA AGCTGGTACTTACTGTTTGGTGTACGTCGAGATTTTACCCAATGCTAGCT CTGCTCTATGGCACCAAATCGACCAAGTTTCACAGGACTCAAAACACCGT TTTCGCCATGATCGCGTTTTTAGGGGCGTGTGTCTGGAGAGCTGTAAGCA AAGAATCAATCACTTATCCGAGTTCAGGGAGTACGAGAAAGAAGAAATTC TGGATAAGGAACTTATATCTTACTACGATAAGGTACACCGTCGGGATGCA ATGAATTCAGATAGGGATCTCTTTAATAAAGAGGTTGTGAAAGGCTGTCT AAACCAAAAGTTCAGTGAGAAGTTTTCACTTAGAACTCGGAGCCTTATCG AGTACTGTGTCTCGGCCTCGGATAAGGACTTGAAGATGGATTTGCTTGAT TTGGCGTTTTATGGTATTCTGGTAGTTATACTCTTTATAACTTTGTGTTC GTCTTTCCTTGACTATCGCCTGAGCAAGATGAACTCGCAAAAATCAGAAA GTTTTTATCGAGAGCCACTAATGGATCGACGACAGCGACTCCTTACATCC TTCTCAGTGGTTCGAAATTATCATCGATTGGTTGAGCCGTATAACTCAGA TTTCTCGCGGGATGTGAGCTTTTTCGACGGGTTTCGGGTGATCGGCGTAT TTGTAGTGATCTTGGGCCACACGCTTATGGTCTTTATGACTGTTCCAATA GAAAATCCGGAGTTCTTCGAACAGTTCCTGTTCCGGTTCGAGACTTCAAT ATTTCAAAACGGCAGCCTGGTCATCCAGATATTTTTTGTTATGAGCGGCT TCCTTCTCTACGTGAAATTCACCAAACGCCAACAGATTCAACCCAAGACT GGCACGCTTGAGTGCATTGCTGTGTACTTTCGAGTGTTTTCCTACAGATA CTTTAGACTTCTGCCATCGCTTCTCGCTCTCATCCTGTTCAATGGAACAC TGCTGGTGCGCCTTCAAAACGGACCCTTTTGGCGACATCTTACGGAGGCC GAACGGGTCTTCTGTCGCGCCAACTGGTGGAAGAACGTGTTTTTCGTGAC CAACCACATGCTGGAAGACAGTTGCTCCCATCAGACGTGGTACTTAGGAG CAGACATGCAGCTATTCGAGCTCTTCCTTATAGTAATTATTATAACCAAA AAGCATCCCAAGCTGACAAGGACAATCTACACAACTCTTTTAGCACTTGC CTTTGCAGTGCCTGCTGTACTGACCTACGTTCTCGAGCTGGATGGTATCT ACCATATTCGTCCGGAAACATATCGCTACTTGTACTTCCGACATTCCGAC ACATTTTACCAAATGTATCCGCCCTTTTACACAAATTTGGGTGGCTATCT GTTTGGTTTTCTGTGCGGTCATTTTTACCTTAGGCAGCGTTCTGGAAATG TAGAACTTCTGGGTCATCTTAAGTACGATCTGGCCATGTGGCTGCTTGTG CTGGCCACGTTGGGAGTCCTTTTCTCCGGCTACATCTTTATTCGACAGGA CTTTGCGAAGCCATCGCTATGGCTAGCCTTGTATGCGGGCATCCACAAGA TCCTGTGGGTGCTAATATGCGCAGGATTCGTGATCCTCATGTGCCGCAAG GTTGGAGGTGGGTAA 1665 2R:1731127-2080000 -1 CG9447-RA CG9447-RA FBtr0086206 crosby not done 205388 204949 0 CG9447:1 1 0 partof 439 2R:1731127-2080000 -1 CG9447:1 204820 204679 0 CG9447:2 2 0 partof 141 2R:1731127-2080000 -1 CG9447:2 204619 204077 0 CG9447:3 3 0 partof 542 2R:1731127-2080000 -1 CG9447:3 203994 203914 0 CG9447:4 4 0 partof 80 2R:1731127-2080000 -1 CG9447:4 203862 203748 0 CG9447:5 5 0 partof 114 2R:1731127-2080000 -1 CG9447:5 203691 203342 0 CG9447:6 6 0 partof 349 2R:1731127-2080000 -1 CG9447:6 205388 203345 0 CG9447-PA 0 producedby MPALYQLDDYDLCLDNQAGTYCLVYVEILPNASSALWHQIDQVSQDSKHR FRHDRVFRGVCLESCKQRINHLSEFREYEKEEILDKELISYYDKVHRRDA MNSDRDLFNKEVVKGCLNQKFSEKFSLRTRSLIEYCVSASDKDLKMDLLD LAFYGILVVILFITLCSSFLDYRLSKMNSQKSESFYREPLMDRRQRLLTS FSVVRNYHRLVEPYNSDFSRDVSFFDGFRVIGVFVVILGHTLMVFMTVPI ENPEFFEQFLFRFETSIFQNGSLVIQIFFVMSGFLLYVKFTKRQQIQPKT GTLECIAVYFRVFSYRYFRLLPSLLALILFNGTLLVRLQNGPFWRHLTEA ERVFCRANWWKNVFFVTNHMLEDSCSHQTWYLGADMQLFELFLIVIIITK KHPKLTRTIYTTLLALAFAVPAVLTYVLELDGIYHIRPETYRYLYFRHSD TFYQMYPPFYTNLGGYLFGFLCGHFYLRQRSGNVELLGHLKYDLAMWLLV LATLGVLFSGYIFIRQDFAKPSLWLALYAGIHKILWVLICAGFVILMCRK VGGG 554 2R:1731127-2080000 -1 CG9447-PA CG9447-PA FBpp0085525 AAF57404.1 202544 191775 Drosophila 0 coro 0 0 10769 melanogaster 2R:1731127-2080000 -1 CG9446 GO:3779 FBan0009446 FBgn0033109 42D4-42D4 Not in SwissProt real (computational) coro AE003790 actin binding GO:0003779 actin cytoskeleton GO:0015629 202544 191775 0 coro-RA 0 partof 1733cc786414514d15febdf4d92b5d27 CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAA CAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATT TTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCC TTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTG AATGCGCTGGCCCCAGTGAGTGGAGTGATAGATAAAAGCTAGACGTAGAG AAGCTCAGGACTGATCGCTGACCCAAGCCACTGCAGCATCAAGATGTCAT TTCGCGTAGTGCGCAGCTCCAAGTTCCGCCACGTCTACGGACAGGCTCTC AAGCGGGAGCAGTGCTACGACAACATACGGGTATCCAAGTCCAGCTGGGA CTCCACATTCTGCGCGGTGAATCCCAAGTTCCTGGCCATTATCGTAGAGT CGGCGGGCGGCGGAGCCTTCATCGTCCTGCCACACAACAAAGTTGGTCGC ATTGCGGCTGACCACCCTTTGGTGGGCGGTCACAAGGGTCCTGTGCTGGA CATCGCCTGGTGCCCCCACAACGACAACGTGATCGCCTCCGGCTCAGAGG ACTGTGTGGTCAAAGTGTGGCAGATCCCCGATGGCGGGCTGTCGCGAACA CTCACCGAACCCGTGGTCGACCTGGTTTTCCACCAGCGTCGCGTGGGTCT GGTGTTGTGGCATCCCTCTGCGCTCAACGTGCTGCTTACCGCCGGCTCCG ATAACCAGGTCGTGATTTGGAACGTGGGCACTGGTGAAATCCTCGTGCAC ATCGACTCCCATCCGGACATCGTTTACAGCGCCTGCTTCAACTGGGATGG CTCTAAGTTGGTTACCACCTGCAAGGATAAAAAGATCCGCATCTACGATC CGCGCACTGCCGAGCTGGAGAGCGAAGCCATGTGTCATGAGGGCTCCAAG GCCACGAGGGCCATTTTCCTACGTCACGGTCTGATCTTCACCACAGGCTT CAACCGTAGCTCGGAGCGTCAGTACTCCCTGCGCGCACCGGATGCCCTTA ACGAACCCATTGTCATGGTGGAGCTGGACACGTCCAACGGCGTAATGTTC CCTCTTTACGACGCAGACACGAACATGATCTACTTGTGTGGAAAAGGTGA CTCGGTCATTCGGTATTTCGAGGTAACGCCCGAACCTCCTTTTGTGCACT ACATAAACACGTTTCAGACTACAGAGCCGCAGCGTGGTATTGGTCTGATG CCCAAGCGAGGCTGTGATGTGACCACCTGCGAGGTCGCCAAGTTCTATCG CATGAACAACAACGGTCTGTGTCAGGTCATCTCGATGACTGTGCCGCGCA AATCGGATCTTTTCCAGGAGGATCTCTACCCCGATACGCTAGCGGAAGAC GCTGCCATCACCGCGGAGGAGTGGATCGATGGCAAGGATGCGGATCCGAT CACATTTTCGCTCAAAGGTGGCTACGTGTCCTCGTCGGTAAACAAATCGC TACCAGCGAAGAAGGCGGGCAACATCCTGAACAAGCCTAGAGGCGACAGC GCTAGCTCCGGTGCAACGAGCAGCAGCGCGGGCGGCGGCAACTTTGCGTC CGGAAATAACAATGAGGCTAGCGAAGGTGGACCGCCTGCAGCGGTTTTAT CGGAAAAGGACCTGCGCACCATACAAGACGAGATCCGCAAACTTAAGGCG ATCATCGTCAAGCAAGAGAACCGCATCCGCGCTCTGGAGGCCAAGGAGGA CGCCCGCAACAAGAATGGAAGCGATGCTGCGCCGGCTTCAGCGGGAGCAG CCACGTCTGACGGCAAAGCCAGTGAAAGTGCCAACGACCACGCGTCCACA TCAGCCGGAACGTCAAAGGACGAGGACTAGGTCTAGCAATGAAACGAGGA CTGAACTGATAAAAATGGGCGGAATGGATTGGAGGAGAGACAGAGAACTG CTTGTAGAAGCTCGTAGCTACGCTTAATTTCTCTATTGCAACAAAGCGCG CTGAGGACGAATTGAAAAAGAACTTATTGTCTATTACCATTATGGTTTCG ATTATTTATTTTTTATAATTTAATATTAGCGAAATCAGTTGAGTGCGGGT GTGGCACAGATAGGGTTAGAGAATGCCGAGCTAAATCATCTAATCGAACT TAAGCGAGCATAACCGAGCAGACCTGGACGCTTAACGTATAAAACATAAC ATAAAACTACATCCTGCCAAAAATATATAAAAAACCTAACGAACTACCTA CATTTTGCGCCCAAAATCAAGCAGAGCGAAGGGCAGGTACTCGGCCCTTT GATCGGCTTGTTGTTACGCAAGTATGAAATTGTTGTAAATTTAACAAAGG CAAATCATAGACTAAACCTCAATCACTTAAGAGTTAACACCTACCTACCA AATTTGTACGAGCTCCTTTCTGTAACGTCTGTATATTTGTACGTCCCGGA AGTTTTCATGACAATAGCTGATAGAATCGATACTGTTCATCCTAGCTGAG GCCCCCTTAATCAGTCACATTTCCCTGCAAATTGTCGTGTCAAACATAGC GAATTTAGTAAGAAAGTGATGGGGGTCATCGGACTTAATTCGTTTTCGTA ATCAAAATTTTATTGTTCAAACTAATGATAAGCTGTATTTTGAAATAATA AGAGTAACAATAAATGCAACAAAATCAGAAAGAAAGTAAGAAACCATCGA AACTATTTTTATAAAAATTTGTTTACTTTTCTTTTCTTTCATTTGATTTT ACTTTCATTAGTTTTGTTAGAGAACCGAGGGCGAGAGCAGCGTCATTAAA CACCTACCGATTTTGTAATTCACAACCATTGTAAAATGAAGACTATATAC ATATACATACATAAATACTCTATATACAAATAATTTACAATTTGATACGG AATAAAACAAAATACAATGCCAGAAGAAGTTGGGTGCTAAT 2941 2R:1731127-2080000 -1 CG9446-RA CG9446-RA FBtr0086207 Perfect match to HYPO SP record with corresponding FBgn crosby AAF57403 202544 202308 0 coro:1 1 0 partof 236 2R:1731127-2080000 -1 CG9446:1 196716 196461 0 coro:2 2 0 partof 255 2R:1731127-2080000 -1 CG9446:2 195149 194882 0 coro:3 3 0 partof 267 2R:1731127-2080000 -1 CG9446:3 194824 194410 0 coro:4 4 0 partof 414 2R:1731127-2080000 -1 CG9446:4 194346 194052 0 coro:5 5 0 partof 294 2R:1731127-2080000 -1 CG9446:5 193308 193122 0 coro:6 6 0 partof 186 2R:1731127-2080000 -1 CG9446:6 193064 191775 0 coro:7 7 0 partof 1289 2R:1731127-2080000 -1 CG9446:7 196659 192839 0 coro-PA 0 producedby MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED 528 2R:1731127-2080000 -1 CG9446-PA CG9446-PA FBpp0085526 AAF57403.1 196832 191775 0 coro-RB 0 partof 125c6f0c0988d225d169cf4be85b4ab8 GGCTAAACGATTTCGCTTGAAGACTTGTTATTAAGGGCAAAGGGTGGAAA ATACCAAACGCAGCTAGACGTAGAGAAGCTCAGGACTGATCGCTGACCCA AGCCACTGCAGCATCAAGATGTCATTTCGCGTAGTGCGCAGCTCCAAGTT CCGCCACGTCTACGGACAGGCTCTCAAGCGGGAGCAGTGCTACGACAACA TACGGGTATCCAAGTCCAGCTGGGACTCCACATTCTGCGCGGTGAATCCC AAGTTCCTGGCCATTATCGTAGAGTCGGCGGGCGGCGGAGCCTTCATCGT CCTGCCACACAACAAAGTTGGTCGCATTGCGGCTGACCACCCTTTGGTGG GCGGTCACAAGGGTCCTGTGCTGGACATCGCCTGGTGCCCCCACAACGAC AACGTGATCGCCTCCGGCTCAGAGGACTGTGTGGTCAAAGTGTGGCAGAT CCCCGATGGCGGGCTGTCGCGAACACTCACCGAACCCGTGGTCGACCTGG TTTTCCACCAGCGTCGCGTGGGTCTGGTGTTGTGGCATCCCTCTGCGCTC AACGTGCTGCTTACCGCCGGCTCCGATAACCAGGTCGTGATTTGGAACGT GGGCACTGGTGAAATCCTCGTGCACATCGACTCCCATCCGGACATCGTTT ACAGCGCCTGCTTCAACTGGGATGGCTCTAAGTTGGTTACCACCTGCAAG GATAAAAAGATCCGCATCTACGATCCGCGCACTGCCGAGCTGGAGAGCGA AGCCATGTGTCATGAGGGCTCCAAGGCCACGAGGGCCATTTTCCTACGTC ACGGTCTGATCTTCACCACAGGCTTCAACCGTAGCTCGGAGCGTCAGTAC TCCCTGCGCGCACCGGATGCCCTTAACGAACCCATTGTCATGGTGGAGCT GGACACGTCCAACGGCGTAATGTTCCCTCTTTACGACGCAGACACGAACA TGATCTACTTGTGTGGAAAAGGTGACTCGGTCATTCGGTATTTCGAGGTA ACGCCCGAACCTCCTTTTGTGCACTACATAAACACGTTTCAGACTACAGA GCCGCAGCGTGGTATTGGTCTGATGCCCAAGCGAGGCTGTGATGTGACCA CCTGCGAGGTCGCCAAGTTCTATCGCATGAACAACAACGGTCTGTGTCAG GTCATCTCGATGACTGTGCCGCGCAAATCGGATCTTTTCCAGGAGGATCT CTACCCCGATACGCTAGCGGAAGACGCTGCCATCACCGCGGAGGAGTGGA TCGATGGCAAGGATGCGGATCCGATCACATTTTCGCTCAAAGGTGGCTAC GTGTCCTCGTCGGTAAACAAATCGCTACCAGCGAAGAAGGCGGGCAACAT CCTGAACAAGCCTAGAGGCGACAGCGCTAGCTCCGGTGCAACGAGCAGCA GCGCGGGCGGCGGCAACTTTGCGTCCGGAAATAACAATGAGGCTAGCGAA GGTGGACCGCCTGCAGCGGTTTTATCGGAAAAGGACCTGCGCACCATACA AGACGAGATCCGCAAACTTAAGGCGATCATCGTCAAGCAAGAGAACCGCA TCCGCGCTCTGGAGGCCAAGGAGGACGCCCGCAACAAGAATGGAAGCGAT GCTGCGCCGGCTTCAGCGGGAGCAGCCACGTCTGACGGCAAAGCCAGTGA AAGTGCCAACGACCACGCGTCCACATCAGCCGGAACGTCAAAGGACGAGG ACTAGGTCTAGCAATGAAACGAGGACTGAACTGATAAAAATGGGCGGAAT GGATTGGAGGAGAGACAGAGAACTGCTTGTAGAAGCTCGTAGCTACGCTT AATTTCTCTATTGCAACAAAGCGCGCTGAGGACGAATTGAAAAAGAACTT ATTGTCTATTACCATTATGGTTTCGATTATTTATTTTTTATAATTTAATA TTAGCGAAATCAGTTGAGTGCGGGTGTGGCACAGATAGGGTTAGAGAATG CCGAGCTAAATCATCTAATCGAACTTAAGCGAGCATAACCGAGCAGACCT GGACGCTTAACGTATAAAACATAACATAAAACTACATCCTGCCAAAAATA TATAAAAAACCTAACGAACTACCTACATTTTGCGCCCAAAATCAAGCAGA GCGAAGGGCAGGTACTCGGCCCTTTGATCGGCTTGTTGTTACGCAAGTAT GAAATTGTTGTAAATTTAACAAAGGCAAATCATAGACTAAACCTCAATCA CTTAAGAGTTAACACCTACCTACCAAATTTGTACGAGCTCCTTTCTGTAA CGTCTGTATATTTGTACGTCCCGGAAGTTTTCATGACAATAGCTGATAGA ATCGATACTGTTCATCCTAGCTGAGGCCCCCTTAATCAGTCACATTTCCC TGCAAATTGTCGTGTCAAACATAGCGAATTTAGTAAGAAAGTGATGGGGG TCATCGGACTTAATTCGTTTTCGTAATCAAAATTTTATTGTTCAAACTAA TGATAAGCTGTATTTTGAAATAATAAGAGTAACAATAAATGCAACAAAAT CAGAAAGAAAGTAAGAAACCATCGAAACTATTTTTATAAAAATTTGTTTA CTTTTCTTTTCTTTCATTTGATTTTACTTTCATTAGTTTTGTTAGAGAAC CGAGGGCGAGAGCAGCGTCATTAAACACCTACCGATTTTGTAATTCACAA CCATTGTAAAATGAAGACTATATACATATACATACATAAATACTCTATAT ACAAATAATTTACAATTTGATACGGAATAAAACAAAATACAATGCCAGAA GAAGTTGGGTGCTAAT 2766 2R:1731127-2080000 -1 CG9446-RB CG9446-RB FBtr0086208 crosby AAM70835 not done Perfect match to HYPO SP record with corresponding FBgn Only one EST supports this alternative transcript::DATE:2002-02-13 03:08:30::TS:1013587710000 196832 196771 0 coro:8 1 0 partof 61 2R:1731127-2080000 -1 CG9446:8 196716 196461 0 coro:2 2 0 partof 255 2R:1731127-2080000 -1 CG9446:2 195149 194882 0 coro:3 3 0 partof 267 2R:1731127-2080000 -1 CG9446:3 194824 194410 0 coro:4 4 0 partof 414 2R:1731127-2080000 -1 CG9446:4 194346 194052 0 coro:5 5 0 partof 294 2R:1731127-2080000 -1 CG9446:5 193308 193122 0 coro:6 6 0 partof 186 2R:1731127-2080000 -1 CG9446:6 193064 191775 0 coro:7 7 0 partof 1289 2R:1731127-2080000 -1 CG9446:7 196659 192839 0 coro-PB 0 producedby MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED 528 2R:1731127-2080000 -1 CG9446-PB CG9446-PB FBpp0085527 AAM70835.1 202544 191775 0 coro-RC 0 partof CCCGGTGAACGTGAACGCGAACTGCGCTGATATCAACAACTTGCCTCGAA CAACAGTGTCGAACTTGCTCTTAGATGCTCAGCGCGCTCTCGTCGGCATT TTGTACTCGTCCCGTCTTTCTGCTGACTGAAAAGTCTGAAAAGAAGTGCC TTAAGTTTCCAGCCGGAGTCGTGTGCAAAATCTCTAGTTGAATCCCGCTG AATGCGCTGGCCCCAAGCTAGACGTAGAGAAGCTCAGGACTGATCGCTGA CCCAAGCCACTGCAGCATCAAGATGTCATTTCGCGTAGTGCGCAGCTCCA AGTTCCGCCACGTCTACGGACAGGCTCTCAAGCGGGAGCAGTGCTACGAC AACATACGGGTATCCAAGTCCAGCTGGGACTCCACATTCTGCGCGGTGAA TCCCAAGTTCCTGGCCATTATCGTAGAGTCGGCGGGCGGCGGAGCCTTCA TCGTCCTGCCACACAACAAAGTTGGTCGCATTGCGGCTGACCACCCTTTG GTGGGCGGTCACAAGGGTCCTGTGCTGGACATCGCCTGGTGCCCCCACAA CGACAACGTGATCGCCTCCGGCTCAGAGGACTGTGTGGTCAAAGTGTGGC AGATCCCCGATGGCGGGCTGTCGCGAACACTCACCGAACCCGTGGTCGAC CTGGTTTTCCACCAGCGTCGCGTGGGTCTGGTGTTGTGGCATCCCTCTGC GCTCAACGTGCTGCTTACCGCCGGCTCCGATAACCAGGTCGTGATTTGGA ACGTGGGCACTGGTGAAATCCTCGTGCACATCGACTCCCATCCGGACATC GTTTACAGCGCCTGCTTCAACTGGGATGGCTCTAAGTTGGTTACCACCTG CAAGGATAAAAAGATCCGCATCTACGATCCGCGCACTGCCGAGCTGGAGA GCGAAGCCATGTGTCATGAGGGCTCCAAGGCCACGAGGGCCATTTTCCTA CGTCACGGTCTGATCTTCACCACAGGCTTCAACCGTAGCTCGGAGCGTCA GTACTCCCTGCGCGCACCGGATGCCCTTAACGAACCCATTGTCATGGTGG AGCTGGACACGTCCAACGGCGTAATGTTCCCTCTTTACGACGCAGACACG AACATGATCTACTTGTGTGGAAAAGGTGACTCGGTCATTCGGTATTTCGA GGTAACGCCCGAACCTCCTTTTGTGCACTACATAAACACGTTTCAGACTA CAGAGCCGCAGCGTGGTATTGGTCTGATGCCCAAGCGAGGCTGTGATGTG ACCACCTGCGAGGTCGCCAAGTTCTATCGCATGAACAACAACGGTCTGTG TCAGGTCATCTCGATGACTGTGCCGCGCAAATCGGATCTTTTCCAGGAGG ATCTCTACCCCGATACGCTAGCGGAAGACGCTGCCATCACCGCGGAGGAG TGGATCGATGGCAAGGATGCGGATCCGATCACATTTTCGCTCAAAGGTGG CTACGTGTCCTCGTCGGTAAACAAATCGCTACCAGCGAAGAAGGCGGGCA ACATCCTGAACAAGCCTAGAGGCGACAGCGCTAGCTCCGGTGCAACGAGC AGCAGCGCGGGCGGCGGCAACTTTGCGTCCGGAAATAACAATGAGGCTAG CGAAGGTGGACCGCCTGCAGCGGTTTTATCGGAAAAGGACCTGCGCACCA TACAAGACGAGATCCGCAAACTTAAGGCGATCATCGTCAAGCAAGAGAAC CGCATCCGCGCTCTGGAGGCCAAGGAGGACGCCCGCAACAAGAATGGAAG CGATGCTGCGCCGGCTTCAGCGGGAGCAGCCACGTCTGACGGCAAAGCCA GTGAAAGTGCCAACGACCACGCGTCCACATCAGCCGGAACGTCAAAGGAC GAGGACTAGGTCTAGCAATGAAACGAGGACTGAACTGATAAAAATGGGCG GAATGGATTGGAGGAGAGACAGAGAACTGCTTGTAGAAGCTCGTAGCTAC GCTTAATTTCTCTATTGCAACAAAGCGCGCTGAGGACGAATTGAAAAAGA ACTTATTGTCTATTACCATTATGGTTTCGATTATTTATTTTTTATAATTT AATATTAGCGAAATCAGTTGAGTGCGGGTGTGGCACAGATAGGGTTAGAG AATGCCGAGCTAAATCATCTAATCGAACTTAAGCGAGCATAACCGAGCAG ACCTGGACGCTTAACGTATAAAACATAACATAAAACTACATCCTGCCAAA AATATATAAAAAACCTAACGAACTACCTACATTTTGCGCCCAAAATCAAG CAGAGCGAAGGGCAGGTACTCGGCCCTTTGATCGGCTTGTTGTTACGCAA GTATGAAATTGTTGTAAATTTAACAAAGGCAAATCATAGACTAAACCTCA ATCACTTAAGAGTTAACACCTACCTACCAAATTTGTACGAGCTCCTTTCT GTAACGTCTGTATATTTGTACGTCCCGGAAGTTTTCATGACAATAGCTGA TAGAATCGATACTGTTCATCCTAGCTGAGGCCCCCTTAATCAGTCACATT TCCCTGCAAATTGTCGTGTCAAACATAGCGAATTTAGTAAGAAAGTGATG GGGGTCATCGGACTTAATTCGTTTTCGTAATCAAAATTTTATTGTTCAAA CTAATGATAAGCTGTATTTTGAAATAATAAGAGTAACAATAAATGCAACA AAATCAGAAAGAAAGTAAGAAACCATCGAAACTATTTTTATAAAAATTTG TTTACTTTTCTTTTCTTTCATTTGATTTTACTTTCATTAGTTTTGTTAGA GAACCGAGGGCGAGAGCAGCGTCATTAAACACCTACCGATTTTGTAATTC ACAACCATTGTAAAATGAAGACTATATACATATACATACATAAATACTCT ATATACAAATAATTTACAATTTGATACGGAATAAAACAAAATACAATGCC AGAAGAAGTTGGGTGCTAAT 2920 2R:1731127-2080000 -1 CG9446-RC CG9446-RC FBtr0086209 not done crosby 202544 202329 0 coro:9 1 0 partof 215 2R:1731127-2080000 -1 CG9446:9 196716 196461 0 coro:2 2 0 partof 255 2R:1731127-2080000 -1 CG9446:2 195149 194882 0 coro:3 3 0 partof 267 2R:1731127-2080000 -1 CG9446:3 194824 194410 0 coro:4 4 0 partof 414 2R:1731127-2080000 -1 CG9446:4 194346 194052 0 coro:5 5 0 partof 294 2R:1731127-2080000 -1 CG9446:5 193308 193122 0 coro:6 6 0 partof 186 2R:1731127-2080000 -1 CG9446:6 193064 191775 0 coro:7 7 0 partof 1289 2R:1731127-2080000 -1 CG9446:7 196659 192839 0 coro-PC 0 producedby MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAII VESAGGGAFIVLPHNKVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASG SEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTA GSDNQVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRI YDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPD ALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVTPEPPF VHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTV PRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKGGYVSSSVN KSLPAKKAGNILNKPRGDSASSGATSSSAGGGNFASGNNNEASEGGPPAA VLSEKDLRTIQDEIRKLKAIIVKQENRIRALEAKEDARNKNGSDAAPASA GAATSDGKASESANDHASTSAGTSKDED 528 2R:1731127-2080000 -1 CG9446-PC 129495 129368 Drosophila 0 BS{}759 0 0 127 melanogaster 2R:1731127-2080000 1 TE18876 TE18876 FBti0018876 BS 42D1-42D1 AE003790 289518 281993 Drosophila 0 opus{}760 0 0 7525 melanogaster 2R:1731127-2080000 1 TE19040 TE19040 FBti0019040 AE003790 42E1-42E1 opus 320532 318902 Drosophila 0 HB{}761 0 0 1630 melanogaster 2R:1731127-2080000 1 TE19973 TE19973 FBti0019973 HB AE003790 42E4-42E4 78729 76159 Drosophila 0 CG3267 0 0 2570 melanogaster 2R:1731127-2080000 1 CG3267 GO:4492 FBgn0042083 FBan0003267 42C7-42C7 Not in SwissProt real (computational) See Minigene report for CG3267: confusion about the 2 adjacent genes CG3267 and CG3265(Eb1), largely due to the way that the strain identifier "l(2)04524" has been used to describe both of them in the literature.::DATE:1969-12-31 19:00:00::TS:0 CG3267 AE003790 propionyl-CoA carboxylase activity GO:0004658 CoA carboxylase activity GO:0016421 methylcrotonoyl-CoA carboxylase activity GO:0004485 mitochondrial matrix GO:0005759 methionine catabolism GO:0009087 threonine catabolism GO:0006567 valine catabolism GO:0006574 regulation of eclosion GO:0007563 leucine metabolism GO:0006551 fatty acid catabolism GO:0009062 isoleucine catabolism GO:0006550 78729 76159 0 CG3267-RA 0 partof c9fe2e6bed009e91ab486ecabc90cdb0 TATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACT CGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAA ATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAG CCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGG TAGACAAGCAGTCCGCCGAGTACAAGGAAAATGCCAGAGAGATGGCCAGT TTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGG ACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGG AGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGT GCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGG AATCGTCACCGGAGTGGGACGCGTTTGCGGAACTGAGTGTTTGGTGGTGG CCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAG AAGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCAT TTACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCT TTCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATG TCGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGC CGGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGA AGCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACT GGAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAA GACTTCTGGGGTCACCGACCACTATGCCTTAGACGACGAACACGCCTTGT ATCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCG TACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTAC TCCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACG GCATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATT GCGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGG TGAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAA TAGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCC CACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCA AAATATTACTGGCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTG CCAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCC AAGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCAT GTGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGC GCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATC ACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGC CCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGC CCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCC AACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGC CGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTAT GCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATT TCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATG TACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTA CGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAAC AAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACA AAACACACACATTTAAATGTATAATGTATAACAAAAC 2137 2R:1731127-2080000 1 CG3267-RA CG3267-RA FBtr0086126 pavel AAM70824 Perfect match to HYPO SP record with corresponding FBgn 76385 76159 0 CG3267:1 1 0 partof 226 2R:1731127-2080000 1 CG3267:1 76698 76444 0 CG3267:2 2 0 partof 254 2R:1731127-2080000 1 CG3267:2 77898 77017 0 CG3267:3 3 0 partof 881 2R:1731127-2080000 1 CG3267:3 78729 77953 0 CG3267:4 4 0 partof 776 2R:1731127-2080000 1 CG3267:4 78426 76259 0 CG3267-PA 0 producedby MIRLNWLFRSSSVLLRSQVRLLHVGDANVLHSEVDKQSAEYKENAREMAS LVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELS ALAGHELYGEEVVNSGGIVTGVGRVCGTECLVVANDATVKGGSYYPITVK KHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANM SAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAAT GEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNS YNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVI ARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGA HFIQLCAQRKIPLVFLQNITGFMVGRDAEANGIAKNGAKMVTAVACANVP KFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQI TEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPA NTRQILGLSLKAALNNAGQETKFGVFRM 578 2R:1731127-2080000 1 CG3267-PA CG3267-PA FBpp0085460 AAM70824.1 85814 78966 Drosophila 0 BcDNA:LD08743 0 0 6848 melanogaster 2R:1731127-2080000 1 CG3265 GO:7017 GO:8017 GO:5875 FBgn0027066 FBgn0010578 FBan0003265 42C7-42C7 See Minigene report for CG3267: confusion about the 2 adjacent genes CG3267 and CG3265(Eb1), largely due to the way that the strain identifier "l(2)04524" has been used to describe both of them in the literature.::DATE:1969-12-31 19:00:00::TS:0 AE003790 EST data support existence of multiple transcripts::DATE:2002-02-13 14:10:37::TS:1013627437000 Curator examined, accepted Eb1 microtubule binding GO:0008017 microtubule associated complex GO:0005875 microtubule-based process GO:0007017 mitotic spindle positioning and orientation GO:0040001 85814 78966 0 BcDNA:LD08743-RB 0 partof 7d873eda1da606dfdfb6162413324e8d ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCG AGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGA CGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGG TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTT TACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGA CGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGA CTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAG TATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATAC ATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTA TTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAA TGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGT GATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGC TTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATA ATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTA AATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATG GAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACT CGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTA GATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTA AGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTT GTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTA TTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATG ATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTT ATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGT CTAAACACAA 1910 2R:1731127-2080000 1 CG3265-RB CG3265-RB FBtr0086127 campbell Imperfect match to REAL SP with corresponding FBgn AAM70827 79164 78966 0 BcDNA:LD08743:1 1 0 partof 198 2R:1731127-2080000 1 CG3265:1 82559 82406 0 BcDNA:LD08743:2 2 0 partof 153 2R:1731127-2080000 1 CG3265:2 82763 82617 0 BcDNA:LD08743:3 3 0 partof 146 2R:1731127-2080000 1 CG3265:3 84213 83954 0 BcDNA:LD08743:4 4 0 partof 259 2R:1731127-2080000 1 CG3265:4 84619 84476 0 BcDNA:LD08743:5 5 0 partof 143 2R:1731127-2080000 1 CG3265:5 84756 84673 0 BcDNA:LD08743:6 6 0 partof 83 2R:1731127-2080000 1 CG3265:6 84892 84819 0 BcDNA:LD08743:7 7 0 partof 73 2R:1731127-2080000 1 CG3265:7 85814 84959 0 BcDNA:LD08743:8 8 0 partof 855 2R:1731127-2080000 1 CG3265:8 85007 82438 0 BcDNA:LD08743-PB 0 producedby MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY 291 2R:1731127-2080000 1 CG3265-PB CG3265-PB FBpp0085461 AAM70827.1 85814 78966 0 BcDNA:LD08743-RC 0 partof bbb3c9abe288db11f8b3ecffa2e7720c ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATC ATTCCAGTTGATAAACTGATTAAGGGACGCTTTCAAGACAACTTTGAGTT CCTTCAATGGTTTAAAAAATTCTTCGACGCCAATTACGACGGTCGCGAGT ACGACCCCGTGGCTCAGCGGGGCGGAGTCAAGCTGGGCAATGGCAACGGA CACGGCAGCAACGGAGGCAGTGGCGTGGGCAGCAGCAACAACGATCTCCA TCTGATGCACCGGCGACCATTGCAGGCTCCAGCTTCTGGCGGACGAATGC CAGCACGGGTCATCGCTTCAACTGGTACGGTTCTGTCGAAGCTACGAACT CCGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTT CGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCA GGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGA TCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAG CAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTG CAGTGAAGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCC CCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAA GAACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAA ATCAGGTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGA GACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGC CGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTAT ATGCGACTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGAC GAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCT GCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGT TTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACT AACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCG CCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGT CGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCC ACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCA TATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATAT CTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCA CAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTT GATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATC CTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTG ACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCA ACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAAC AAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCT ATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGC GAACGTCTAAACACAA 2216 2R:1731127-2080000 1 CG3265-RC CG3265-RC FBtr0086128 AAM70825 campbell Although this alternative transcript is supported by multiple EST evidence, gene prediction information (Genscan) had to be used to deduce the 3' end of its exon 4.::DATE:2002-02-13 14:10:47::TS:1013627447000 Blast failed true 79164 78966 0 BcDNA:LD08743:1 1 0 partof 198 2R:1731127-2080000 1 CG3265:1 82559 82406 0 BcDNA:LD08743:2 2 0 partof 153 2R:1731127-2080000 1 CG3265:2 82763 82617 0 BcDNA:LD08743:3 3 0 partof 146 2R:1731127-2080000 1 CG3265:3 83307 83001 0 BcDNA:LD08743:10 4 0 partof 306 2R:1731127-2080000 1 CG3265:10 84213 83954 0 BcDNA:LD08743:4 5 0 partof 259 2R:1731127-2080000 1 CG3265:4 84619 84476 0 BcDNA:LD08743:5 6 0 partof 143 2R:1731127-2080000 1 CG3265:5 84756 84673 0 BcDNA:LD08743:6 7 0 partof 83 2R:1731127-2080000 1 CG3265:6 84892 84819 0 BcDNA:LD08743:7 8 0 partof 73 2R:1731127-2080000 1 CG3265:7 85814 84959 0 BcDNA:LD08743:8 9 0 partof 855 2R:1731127-2080000 1 CG3265:8 85007 82438 0 BcDNA:LD08743-PC 0 producedby MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPVDKLIKGR FQDNFEFLQWFKKFFDANYDGREYDPVAQRGGVKLGNGNGHGSNGGSGVG SSNNDLHLMHRRPLQAPASGGRMPARVIASTGTVLSKLRTPIIPIDKLVK GRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGT AASGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACAN STGTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDI EILCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY 393 2R:1731127-2080000 1 CG3265-PC CG3265-PC FBpp0085462 AAM70825.1 85814 79306 0 BcDNA:LD08743-RD 0 partof eedb6c3bdb4b409593b6da800d8d0b2d AAAGAAGAAATCGCAAACCTAGAAGTAGCGTCAGCAGAAAAGAAAGTTCA TCGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTC TACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGC TTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCT GCACAGGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCA GTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACAT ACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATA AGATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTC GAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAG GGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGAT CGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGC AGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGC AGTGAAGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCC CAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAG AACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAA TCAGGTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAG ACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCC GATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATA TGCGACTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACG AGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTG CATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTT TATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTA ACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGC CACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTC GTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCA CGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCAT ATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATC TAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCAC AGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTG ATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCC TATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGA CTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAA CGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACA AAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTA TATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCG AACGTCTAAACACAA 1765 2R:1731127-2080000 1 CG3265-RD CG3265-RD FBtr0086129 Imperfect match to REAL SP with corresponding FBgn pavel AAM70828 79359 79306 0 BcDNA:LD08743:11 1 0 partof 53 2R:1731127-2080000 1 CG3265:11 82559 82406 0 BcDNA:LD08743:2 2 0 partof 153 2R:1731127-2080000 1 CG3265:2 82763 82617 0 BcDNA:LD08743:3 3 0 partof 146 2R:1731127-2080000 1 CG3265:3 84213 83954 0 BcDNA:LD08743:4 4 0 partof 259 2R:1731127-2080000 1 CG3265:4 84619 84476 0 BcDNA:LD08743:5 5 0 partof 143 2R:1731127-2080000 1 CG3265:5 84756 84673 0 BcDNA:LD08743:6 6 0 partof 83 2R:1731127-2080000 1 CG3265:6 84892 84819 0 BcDNA:LD08743:7 7 0 partof 73 2R:1731127-2080000 1 CG3265:7 85814 84959 0 BcDNA:LD08743:8 8 0 partof 855 2R:1731127-2080000 1 CG3265:8 85007 82438 0 BcDNA:LD08743-PD 0 producedby MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY 291 2R:1731127-2080000 1 CG3265-PD CG3265-PD FBpp0085463 AAM70828.1 85814 81858 0 BcDNA:LD08743-RA 0 partof ebc3c274805093201ec296eae959c25c CCTGCCAGTTGGTCACAGAGCGTAAAACGAAGTAAAAGAAAAACGAAAGT AATTTGTACAGTTCGATTTCGTTTTGCAAATTGAGTTTTATCAAGAAAGG TTAGTTTATCGGAAATCCAGCCAGAAGTACGTCGGATATACAGAGGTGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCACAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCG AGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGA CGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGG TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTT TACTTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGA CGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGA CTGAGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAG TATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATAC ATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTA TTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAA TGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGT GATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGC TTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATA ATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTA AATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATG GAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACT CGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTA GATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTA AGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTT GTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTA TTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATG ATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTT ATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGT CTAAACACAA 1860 2R:1731127-2080000 1 CG3265-RA CG3265-RA FBtr0086130 Imperfect match to REAL SP with corresponding FBgn AAM70826 pavel 82006 81858 0 BcDNA:LD08743:12 1 0 partof 148 2R:1731127-2080000 1 CG3265:12 82559 82406 0 BcDNA:LD08743:2 2 0 partof 153 2R:1731127-2080000 1 CG3265:2 82763 82617 0 BcDNA:LD08743:3 3 0 partof 146 2R:1731127-2080000 1 CG3265:3 84213 83954 0 BcDNA:LD08743:4 4 0 partof 259 2R:1731127-2080000 1 CG3265:4 84619 84476 0 BcDNA:LD08743:5 5 0 partof 143 2R:1731127-2080000 1 CG3265:5 84756 84673 0 BcDNA:LD08743:6 6 0 partof 83 2R:1731127-2080000 1 CG3265:6 84892 84819 0 BcDNA:LD08743:7 7 0 partof 73 2R:1731127-2080000 1 CG3265:7 85814 84959 0 BcDNA:LD08743:8 8 0 partof 855 2R:1731127-2080000 1 CG3265:8 85007 82438 0 BcDNA:LD08743-PA 0 producedby MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPTVSKVLPRTNNAAPASRINACANST GTVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEI LCQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY 291 2R:1731127-2080000 1 CG3265-PA CG3265-PA FBpp0085464 AAM70826.1 85814 78966 0 BcDNA:LD08743-RE 0 partof ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTG GGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTT AGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGG AATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGTG CCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTC CACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGG TTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACA GGTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCC AGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGA ACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGATT ATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTT TTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATT ACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGA GCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTA TCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGA AGCCCATATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGAGC AGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGACGT GAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGGTGA TGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTAC TTCTCTAAGTTGCGGGATATTGAAATTCTTTGCCAAGAAGCCGATGACGC CGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTG AGGATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTAT TAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATA TTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTT AGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGA AGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGAT TAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTA ACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATT TTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAAT TGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAA AGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGT AACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGAT TAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGC ACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTC GTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTT TGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATT GTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATG TGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTA AACACAA 1907 2R:1731127-2080000 1 CG3265-RE CG3265-RE FBtr0086131 campbell 79164 78966 0 BcDNA:LD08743:1 1 0 partof 198 2R:1731127-2080000 1 CG3265:1 82559 82406 0 BcDNA:LD08743:2 2 0 partof 153 2R:1731127-2080000 1 CG3265:2 82763 82617 0 BcDNA:LD08743:3 3 0 partof 146 2R:1731127-2080000 1 CG3265:3 84213 83954 0 BcDNA:LD08743:4 4 0 partof 259 2R:1731127-2080000 1 CG3265:4 84619 84479 0 BcDNA:LD08743:9 5 0 partof 140 2R:1731127-2080000 1 CG3265:9 84756 84673 0 BcDNA:LD08743:6 6 0 partof 83 2R:1731127-2080000 1 CG3265:6 84892 84819 0 BcDNA:LD08743:7 7 0 partof 73 2R:1731127-2080000 1 CG3265:7 85814 84959 0 BcDNA:LD08743:8 8 0 partof 855 2R:1731127-2080000 1 CG3265:8 85007 82438 0 BcDNA:LD08743-PE 0 producedby MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTGAAYCQFMDM LFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKIIPIDKLVKGR FQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAA SGVSSSYRRGPSATTRPAMTSAVKPISKVLPRTNNAAPASRINACANSTG TVKKNDVSNSVNNQQIEEMSNQVMDMRINLEGLEKERDFYFSKLRDIEIL CQEADDAEAHPIIQKILDILYATEDGFAPPDDAPPEDEEY 290 2R:1731127-2080000 1 CG3265-PE 4840 3383 Drosophila 0 CG3271 0 0 1457 melanogaster 2R:1731127-2080000 1 CG3271 FBgn0033088 FBan0003271 42C3-42C3 CG3271 Not in SwissProt real (computational) AE003790 4840 3383 0 CG3271-RA 0 partof eb4f20f1bdc17d87026c7ff8fee2a0d5 AATCAATAGTGCAATGTTTACAAAATATTTCGGGTGGATGTCGGTGAGAA GGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATA GTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGA CCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACT GCTCGGCAGATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAG CAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCA GTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGC CGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATG CAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCT GCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCT ATATGCTGACCCACATATTCGCAGTGACGAGTCTCAACGGCTGGATCTGG TCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTA CGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGC GGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCA TTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTT CAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGG CAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTAC TTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCT TGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTC TGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGAGTGCGTA GAAATATTACTTTATTCTAATATTGCTACATGTGTTTGCATTTTAGCTTC ATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGG CTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGC ACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAAC AGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCC TTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGA CATAATAGAGACTTTATTACAACATTTAGAA 1331 2R:1731127-2080000 1 CG3271-RA CG3271-RA FBtr0086118 Perfect match to HYPO SP record with corresponding FBgn AAM70808 campbell 3592 3383 0 CG3271:1 1 0 partof 209 2R:1731127-2080000 1 CG3271:1 3965 3648 0 CG3271:2 2 0 partof 317 2R:1731127-2080000 1 CG3271:2 4840 4035 0 CG3271:3 3 0 partof 805 2R:1731127-2080000 1 CG3271:3 4560 3456 0 CG3271-PA 0 producedby MSSRSLSAIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSADGLEI QEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGK WPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFA VTSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSL FLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWC HFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIP LASLYYECVEILLYSNIATCVCILAS 326 2R:1731127-2080000 1 CG3271-PA CG3271-PA FBpp0085452 AAM70808.1 4840 3383 0 CG3271-RB 0 partof a3c9d5d957bee17ded13e80672a97a50 AATCAATAGTGCAATGTTTACAAAATATTTCGGGTGGATGTCGGTGAGAA GGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATA GTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGA CCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACT GCTCGGCAGATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAG CAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCA GTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGC CGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATG CAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCT GCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCT ATATGCTGACCCACATATTCGCAGTGACGAGTCTCAACGGCTGGATCTGG TCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTA CGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGC GGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCA TTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTT CAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGG CAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTAC TTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCT TGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTC TGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGACTTCATG ATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTA TTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACG CAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGA GCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTT GACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACAT AATAGAGACTTTATTACAACATTTAGAA 1278 2R:1731127-2080000 1 CG3271-RB CG3271-RB FBtr0086119 pavel Only one EST supports this alternative transcript::DATE:2002-03-11 11:41:08::TS:1015864868000 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70807 3592 3383 0 CG3271:1 1 0 partof 209 2R:1731127-2080000 1 CG3271:1 3965 3648 0 CG3271:2 2 0 partof 317 2R:1731127-2080000 1 CG3271:2 4502 4035 0 CG3271:4 3 0 partof 467 2R:1731127-2080000 1 CG3271:4 4840 4555 0 CG3271:5 4 0 partof 285 2R:1731127-2080000 1 CG3271:5 4625 3456 0 CG3271-PB 0 producedby MSSRSLSAIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSADGLEI QEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGK WPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFA VTSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSL FLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWC HFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIP LASLYYDFMIEDCRTLRKEKAAAGGYSFYN 330 2R:1731127-2080000 1 CG3271-PB CG3271-PB FBpp0085453 AAM70807.1 49308 48390 Drosophila 0 CG9430 0 0 918 melanogaster 2R:1731127-2080000 -1 CG9430 FBgn0033097 FBan0009430 42C6-42C6 AE003790 Gene prediction data only::DATE:2002-02-13 11:51:41::TS:1013619101000 Not in SwissProt real (computational) CG9430 cation transport GO:0006812 ion transport GO:0006811 transport GO:0006810 49308 48390 0 CG9430-RA 0 partof 4376006f84e8f7a87f8f5b9e329b995d ATGGTAGACCAACACTTAATCGTGGCCAAGATCGTGGCCATAGTGGTGCT CTTCCTCGTTACCCTGATCTTCTGCTTTATTCCCTATCTTCTGGATCGCT TCTACAAGTGGACCCAGAGGCCCGAGAACAATGCTCGCGAATTCAAAGTG GTGCTGTGTCTGCTTAATTTCGGTGGAGGGGTTCTCATAGCCACCACCTT CATCCACATGCTGCCGGAGGTGGTCGAGGTGGTGAACGCTCTCCAGGACT GCCGCATGCTGGCCCCCACTCCCTTCGGCCTGCCGGAGGTTCTGCTCTGC ACTGGCTTCTATCTGATGTACTGCATTGAGGAAACCATGCACTTTGTGGT TCGTCGGCGGCAGCAAAGGAAGCTACGGGAGGTGGTCACGATCAAGGATG CGGGCGAGGAGCTGCGGACAGAGATTGTGGTCCAGCCAGAAGAAAGCCCC AAGGAGCCCAACTGGCTGCGTGGCCTCGGAATAATCGTGGCCCTCTCCCT GCACGAACTCTTCGGCGGCATGGCCATTGGCCTGGAGATGAGTGTGAGCA CGGTGTGGTTCATGACCGGAGCCATTTCCGTCCACAAGCTTGTTCTGGCC TTCTGCATCGGCATGGAGATCATGATGGCCCATACCCGCTGGCTGCTGGC CGTGGTTTACCTCCTCGTCTTCTCGATCGTAACTCCGATTGGCGTGGGCA TCGGAATTGCAGTTAGCGAATCTGCCGCGGCTAATCAGCCCAGCACGGTA TCAGGAATCCTCCAGGGGCTGGCCTGTGGCACCCTCATCTACGTGGTCTT CTTTGAAATTGTGGCCAAAAACCATGCCGGCATACGCATTTTACTCTCGT CGATGGTGGGATTCGTCCTGATGTTTGGCCTCCAGATAGCAAGTAAGCAT ACTAAAAAGCCCAAATGA 918 2R:1731127-2080000 -1 CG9430-RA CG9430-RA FBtr0086138 pavel Perfect match to HYPO SP record with corresponding FBgn AAM70820 49308 48390 0 CG9430:1 1 0 partof 918 2R:1731127-2080000 -1 CG9430:1 49308 48393 0 CG9430-PA 0 producedby MVDQHLIVAKIVAIVVLFLVTLIFCFIPYLLDRFYKWTQRPENNAREFKV VLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLC TGFYLMYCIEETMHFVVRRRQQRKLREVVTIKDAGEELRTEIVVQPEESP KEPNWLRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLA FCIGMEIMMAHTRWLLAVVYLLVFSIVTPIGVGIGIAVSESAAANQPSTV SGILQGLACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIASKH TKKPK 305 2R:1731127-2080000 -1 CG9430-PA CG9430-PA FBpp0085471 AAM70820.1 118781 91686 Drosophila 0 Epac 0 0 27095 melanogaster 2R:1731127-2080000 -1 CG3427 FBgn0033102 FBan0003427 42C8-42C10 AE003790 CG3427 Not in SwissProt real (computational) cyclic nucleotide dependent guanyl-nucleotide exchange factor activity GO:0017132 118781 91686 0 Epac-RA 0 partof bd1399d84a86874d7e1abcb0f81637a4 CTCTCCAGCGGCGCACAACTCGATCGCTGGCCCAGAGGTTCAGTTCGGTT TGGTTCGGTTCGGTTTGAATCTCTGCCTCTGTTTACGCCTCTATATCACC TCCATTGGAGCCCATCCGTATCTGTTTCCCTGTGCGATTCGAGTATCTTC AAGTTAACCATGCTGCAGAAAGTGCGTGGGCTGTGCTGAAAGATTCGCGC GCGGGCGTTCGCCAAGTCGAAATAAACCAGTTAAATCTGAGTGCTTGGCT ATTGGCCAAAAATGTAATCGACACGACAACGGAGTGTAAACAGGCCCATT TCGAGTGCAGTTTTGAAATTGTTTATGCAATGCAATTGTGTTAAAAATTT ATTACCTTCCAAGCGAAACAAAGCAAGGCAGCCGAAAACACATTTCTCGC CTCTCTGGTGATTCAACAGCTGCAGTGTGTGTAAACAAATAAAGCCAGAA ACAAAGCCGCAATATGGAGGAATTTAATTCAAGTTGATTTCATTCATTAA ATCTGCTGGAAGGTTGCAGCGGAAAGAGCAGCGAATTCTCCTCTGAGCGC AGTTACTCTGTGCAACCTGGGCGTGGGTGCCACATTCGGGGAGTCCGTAC TGCATGACTTGCCGCGGGACAGCACCGTAGTGACGAAGACCACCTGCGAG CTGCTGCGGGTGGAGCAGCAGGACTTTCGACTCATCTGGGAGAAAAACAA GGAGTTAATGAATGACATATTCACCAACTGCAAGTTGAAGAACGGTTTTG GACCGAGCGTACAAGCGACAGCCGCAGCCACATCGCCCACGAAACGACCC CTCAGCCCCGACCACCCAAACCCAGCGCTGCCCATCACCGAGACACCGAG TCCTGCTATGAACCGCATGGGCTGGGCCCTACGCACACTACTCGTCGCCG ACAACTCGAGCTGTCTGAAGGATCGCAAGGTCTCCGGCAAGCTAATCCGT AAGTGCGCCCCCGGCACCGAGCTCGTCGACTGGCTGGTCAACCTCTCGCC CATCGTCCACACCCGAGCCCAGGCGGCTGGCATGTGGCAAGCGCTCCTCG AGGAAGGAGTACTCGCACACGTCAACAAAGAGCAGCCCTTCAAGGACAAG TGCTTCCTCTACCGCTTTCGCATCGACGAGGAGGGCGGCACGGCGGCAGC GGGCGTGCCCCAGGCGGAGGACCTCGGAGCGGCCAACGAGCACATCCGCG AGGCGCTCAGCGCACTCTTCCAGCGCGGACCGGACGCCACACTGCGTATG ATATTGCGCAAACCTTCTCACGAACGGACATCGGAGGAGCTGGAGCTGGT CTTCGAGGAACTGGTCCACATTGCCGCACTCTCCCACTTGTCGACCAGCA TAAAGCGGGAACTGTCGTCGATTTTCGTGTTCGAGGCTCATGCCCAGGCG GGAACAATATTATTCAATCAAGGCGACGAAGGACGCTCCTGGTACATCTT ACTCAAGGGATCGGTAGACGTTGTGATACACGGCAAGGGAACTGTTGCCA CTCTGAAGACTGGGGATGATTTCGGGAAACTGGCCTTGATAAACGACGCA CCCAGAGCTGCTACCATCGTACTGAAGGAGAACAATTGCCACTTGCTGCG CGTGGACAAGGAACACTTCAACCGGATACTGCGCGATGTGGAGGCCAATA CTCTGAGATTGCAGGAGCACGGCAAGGATGTTTTAGTGCTCGAGCGCGTG GCTAAGCAACGTGGACAGCATTCGGCATTTAAATATACGGTGATGTCGGG AACTCCGGCCAAGATGCTGGAGCACCTGCTGGAGACGCGACTGGGCCAGT CCGTGGGTGGAATGGATCCGTTCTTGGACGACTTCCTGCTCACACACATC GTTTTCATGCCCGTCGTTCAGCTGGTTGATGAATTGGCCAATTACTTCCA CTGCGATGCCCATGAGGACGCCCAAACGCCCGAGGATCGGGAGTATATAA TCAACTTTAAGAAGCGCGTGATCCAGTTCATGCAAAAGTGGGTCATGGCC GTCCGCCACGCGGCCTTCGAGGAGCCCAGCGTGTGCGACTTTATCGAGGA CCTCGCCGCCGAGGTGGAGGCCGATCCCGACCTGAACGAGGAGACCAGCA TAGTGCACAACGTGCTCACCCAGATGGCGCGCTACCAGGAGGACCGCAAC CAGAACGCCGGCCAGAAGTGGAAGCTCCCGCCCAACGGCCAGCCCATCTG CCTTTTCAGTGGCAATGCGACGCCTTCAAAGACGGTCATCCGACCAGATG ATGATATCATCTTCCGCGTTTACTGCGCCGACCACACCTACTGTACCCTG CGATTCCCCATGCACACCACGGCGGAGCTCATCAAAGCGTGTGCCGCCGA CAAGCTGCAGCTAAATCGGGGTCCCGAAGATCTCGTCCTCGTCGAGGTCA AGTCAAACGGGGAGCGGTCCGTGTTCAAGGACAACGATGTCAGCATACCC ACGGGTCTGTCGCTCAACGGCCGCCTTTTCGTCTCCGTCAAGGACCACCT GGATGCCTTGACCCAACTGCAGGAGCAGGAGTGCCCCACCGAGGGTGTGG ACATCGACCTGGAGATACTGAGCACCAAGGAGCTGGCCTACCACATCACC CTGTTCGAGTGGGACCTCTTCTGGGCCGTCCATGAATACGAATTGCTCTA CCACACCTTCGGGCGGCATCACTTTGGCAAGATCACTGCCAACTTGGATG TGTTCCTGCGCCGATTCAACGAGGTGCAGTACTGGATTGTCACCGAACTG GTGTCCACTCCCAGTCTGAGCAAACGCGTCGGTCTGGTCCGGAAGTTCAT CAAGCTGGCCGCGTACTGCAAGGAGTACCAGAACCTAAACGCCTTCTTCG CTGTGGTAATGGGTCTGTCCAACATGGCGGTGTCCAGGCTGCAACAGACC TGGGAAAAGATTCCGTCGAAGTTCAGGAAGATCTTCCAGGAGTTCGAGGC CCTGATCGACCCCAGTCGCAACCACAGGGCGTACCGAGTGTTCGTGGGCA AGCTGCAGCCGCCGTTGATTCCCTTCATGCCGCTCCTGCTCAAGGACATG ACCTTCGCCCATGAGGGCAACAAGACCAGCCTGGACGGCCTGGTGAACTT CGAGAAGATGCACATGATGGCCCAGACGATGCGCACCATCCGCTTTTGTC GCTCCAGGAGTCTGGGACTAGAGCCGCCGTCCCCGAAGAGCGAGGGCGAG GTGAGGTCGTACATCAGCAGCTTCCGCGTCATCGACAACCAGCGGGTACT CACCGCCATGTCCCAGAAGGTGGAGCCCACCAGGAAGCTCTAAGCCCTTG TGGAGCTGTCATCCAATTAGCCTGTAGCGCGTATTAAGTGTCTAACCCTA GTGTGTGTTAATCAACCGCAATTAGCTGCACAGTTATGAGCTTAGCCGGG TTGTTGTTGCTTTCCGAAAGCCAATTGGGCCACGGCCACCACAGCCCGGA CCAACTTTCGTCCGCATCCGCATCCGCATTAGCCTAAGCTACAGTGTACT ATATCTACGACCCGACTAGGAACTATCTCAATCTTCTAATGAACTGAAAC CCAAACGCATTTTAATGCAAACGAGAAACTTTTTGCTTTAGTACAAAACG ATGGAAAAGATGGAAAACAATTTGAAATTCGGCAATTCCCCGCGGAAACC GAAACGAATAAAAACTAAACTTGGACGTGTGTGATACTAAACATTTATAG GAGGCAACATCAAAACAAACACAACTATACAGCATAATTTCCCACAAACC ATTACTCTATAAATCCCGCGCGAGCTGGTAGAATAATTTGTAAAGTTGTA CAACGTTTTCGAGAGCATGGAATCTATATTTTTATAAACCCTAAACTAAA ACCAACTATTAAACAGTCTAGTTACAGCTAGTTATTAACAAGTAAGCTAC GTAGCGGATAAGTTACTTTATTTATAGTTTTCAATCTTATTTTCATTTGG TATTCCGTCACCCCATCTCCTTTTACGGCAACTTGGAAATAAAATACGAA ACCATTTATTAATATTTATTTACACACA 4028 2R:1731127-2080000 -1 CG3427-RA CG3427-RA FBtr0086132 unusual splice provisional (internal view only)::DATE:2004-01-12 11:13:35::TS:1073924015000 AAM70831 mhuang unusual splice Perfect match to HYPO SP record with corresponding FBgn Unconventional splice site postulated::DATE:2002-07-31 12:07:33::TS:1028131653000 DGC evidence (GH01501) strongly suggests that the 11th intron of this transcript uses AT-AC splice donor and acceptor.::DATE:2002-07-31 12:07:40::TS:1028131660000 118781 118236 0 Epac:1 1 0 partof 545 2R:1731127-2080000 -1 CG3427:1 103561 103414 0 Epac:2 2 0 partof 147 2R:1731127-2080000 -1 CG3427:2 99134 99082 0 Epac:3 3 0 partof 52 2R:1731127-2080000 -1 CG3427:3 98798 98700 0 Epac:4 4 0 partof 98 2R:1731127-2080000 -1 CG3427:4 98440 98353 0 Epac:5 5 0 partof 87 2R:1731127-2080000 -1 CG3427:5 98285 98143 0 Epac:6 6 0 partof 142 2R:1731127-2080000 -1 CG3427:6 98089 97896 0 Epac:7 7 0 partof 193 2R:1731127-2080000 -1 CG3427:7 97335 97189 0 Epac:8 8 0 partof 146 2R:1731127-2080000 -1 CG3427:8 96970 96825 0 Epac:9 9 0 partof 145 2R:1731127-2080000 -1 CG3427:9 95886 95709 0 Epac:10 10 0 partof 177 2R:1731127-2080000 -1 CG3427:10 95472 95310 0 Epac:11 11 0 partof 162 2R:1731127-2080000 -1 CG3427:11 94511 94149 0 Epac:12 12 0 partof 362 2R:1731127-2080000 -1 CG3427:12 94079 93825 0 Epac:13 13 0 partof 254 2R:1731127-2080000 -1 CG3427:13 93766 93595 0 Epac:14 14 0 partof 171 2R:1731127-2080000 -1 CG3427:14 93375 93241 0 Epac:15 15 0 partof 134 2R:1731127-2080000 -1 CG3427:15 92958 92608 0 Epac:16 16 0 partof 350 2R:1731127-2080000 -1 CG3427:16 92549 91686 0 Epac:17 17 0 partof 863 2R:1731127-2080000 -1 CG3427:17 99119 92424 0 Epac-PA 0 producedby MNDIFTNCKLKNGFGPSVQATAAATSPTKRPLSPDHPNPALPITETPSPA MNRMGWALRTLLVADNSSCLKDRKVSGKLIRKCAPGTELVDWLVNLSPIV HTRAQAAGMWQALLEEGVLAHVNKEQPFKDKCFLYRFRIDEEGGTAAAGV PQAEDLGAANEHIREALSALFQRGPDATLRMILRKPSHERTSEELELVFE ELVHIAALSHLSTSIKRELSSIFVFEAHAQAGTILFNQGDEGRSWYILLK GSVDVVIHGKGTVATLKTGDDFGKLALINDAPRAATIVLKENNCHLLRVD KEHFNRILRDVEANTLRLQEHGKDVLVLERVAKQRGQHSAFKYTVMSGTP AKMLEHLLETRLGQSVGGMDPFLDDFLLTHIVFMPVVQLVDELANYFHCD AHEDAQTPEDREYIINFKKRVIQFMQKWVMAVRHAAFEEPSVCDFIEDLA AEVEADPDLNEETSIVHNVLTQMARYQEDRNQNAGQKWKLPPNGQPICLF SGNATPSKTVIRPDDDIIFRVYCADHTYCTLRFPMHTTAELIKACAADKL QLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDA LTQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHT FGRHHFGKITANLDVFLRRFNEVQYWIVTELVSTPSLSKRVGLVRKFIKL AAYCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALI DPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEK MHMMAQTMRTIRFCRSRSLGLEPPSPKSEGEVRSYISSFRVIDNQRVLTA MSQKVEPTRKL 861 2R:1731127-2080000 -1 CG3427-PA CG3427-PA FBpp0085465 AAM70831.2 22369 5601 Drosophila 0 CG9422 0 0 16768 melanogaster 2R:1731127-2080000 1 CG9422 FBgn0063682 FBgn0033092 FBan0009422 42C3-42C4 DGC clone RE35072 appears problematic: incomplete CDS::DATE:2003-05-28 17:02:14::TS:1054155734000 CG9422 Not in SwissProt real (computational) AE003790 22369 5601 0 CG9422-RA 0 partof 1708b46717b8aec1389c86a68f5edcb6 TTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGC ACATATTGGTGAAACTATTTAATAATATTTATTAAGATTTTACGGAAGGC CTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAG CAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATT TTTTGTGGATGCATGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAG TTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAG CGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCA AGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGTGTG GAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCAC ACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGG ATACTATAGATGGCTTACAAAAGCCAAATACGTCCACTGATTTTTGGGAT GGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCA GCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAAC GGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACCTGCC GCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGCGGAC CATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAAAGCC CAATTTATCACAAAA 815 2R:1731127-2080000 1 CG9422-RA CG9422-RA FBtr0086120 not done Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) pavel AAM70813 5687 5601 0 CG9422:1 1 0 partof 86 2R:1731127-2080000 1 CG9422:1 21600 21472 0 CG9422:2 2 0 partof 128 2R:1731127-2080000 1 CG9422:2 21838 21656 0 CG9422:3 3 0 partof 182 2R:1731127-2080000 1 CG9422:3 22011 21894 0 CG9422:4 4 0 partof 117 2R:1731127-2080000 1 CG9422:4 22369 22067 0 CG9422:5 5 0 partof 302 2R:1731127-2080000 1 CG9422:5 22278 21492 0 CG9422-PA 0 producedby MMHYRKAENVEKELSKSDLPFEDCMPKSQKDFLWMHVKGGTKVSNVIEFA QEALNKGEHRCVVWSGSGGGVVKTISCAEVLKRSHPLYQVTRMAYTSVEE HWKPQMEGLEEIIVTRQIPTLHILMSLDELPDTIDGLQKPNTSTDFWDGG GAQQQPHPRSQPRHQQQPHKPGAGRGGRPNKRTRPGRNKPGQQPEKPAAE ENLPAS 206 2R:1731127-2080000 1 CG9422-PA CG9422-PA FBpp0085454 AAM70813.1 22369 5629 0 CG9422-RC 0 partof 557f7f26ee13c4af0e5d72cf066a7040 GCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATAT TTATTAAGATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCG AGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGC ATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCATGTAAAAGGCGGTAC CAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCG AGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACC ATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGAC GCGCATGGCCTACACCAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAG GCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTC ATGAGTCTGGACGAGCTGCCGGATACTATAGATGGCTTACAAAAGCCAAA TACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATC CACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGG CGTGGGGGTCGGCCGAACAAACGGACCAGACCCGGACGCAATAAACCAGG CCAACAACCCGAAAAACCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGA GTCAAGGTTGAGATAAGCGGACCATGCGAAGATTTTCTTATTTGCCCTTT GTAAGGATGTACAAATAAAGCCCAATTTATCACAAAA 787 2R:1731127-2080000 1 CG9422-RC CG9422-RC FBtr0086121 pavel AAM70814 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) 5687 5629 0 CG9422:6 1 0 partof 58 2R:1731127-2080000 1 CG9422:6 21600 21472 0 CG9422:2 2 0 partof 128 2R:1731127-2080000 1 CG9422:2 21838 21656 0 CG9422:3 3 0 partof 182 2R:1731127-2080000 1 CG9422:3 22011 21894 0 CG9422:4 4 0 partof 117 2R:1731127-2080000 1 CG9422:4 22369 22067 0 CG9422:5 5 0 partof 302 2R:1731127-2080000 1 CG9422:5 22278 21492 0 CG9422-PC 0 producedby MMHYRKAENVEKELSKSDLPFEDCMPKSQKDFLWMHVKGGTKVSNVIEFA QEALNKGEHRCVVWSGSGGGVVKTISCAEVLKRSHPLYQVTRMAYTSVEE HWKPQMEGLEEIIVTRQIPTLHILMSLDELPDTIDGLQKPNTSTDFWDGG GAQQQPHPRSQPRHQQQPHKPGAGRGGRPNKRTRPGRNKPGQQPEKPAAE ENLPAS 206 2R:1731127-2080000 1 CG9422-PC CG9422-PC FBpp0085455 AAM70814.1 47582 46119 Drosophila 0 ZIP1 0 0 1463 melanogaster 2R:1731127-2080000 -1 CG9428 FBgn0033096 FBan0009428 42C6-42C6 AE003790 ZIP1 Curator examined, accepted metal ion transporter activity GO:0046873 47582 46119 0 ZIP1-RA 0 partof e5d909a13325b42cc787309732ba91b0 AGTGAATCCGCGTATCAATCAGCGATCAGATTTCAATCGGCTCCCGCTGA TATATGACTGGAAATATAAACCATTAGCCTGGTTGTGAGTTCCAGCCAGC ACAGTCGAAGCTATCAACTCGGGAGGTGAAGATGAGCGCTACCGCAACTA TGTCACAAGAGCAAACGCAAGACGTGGATCACCATGCGCTGCTGGTGGCC AAAATAGTTTCCATGGTGGTGCTCGTGGTGATCACCGTGCTTTGCGGCAG CCTTCCCTACGTCCTGAACAGGTGCTTCCATTGGACGAAGGCGAGTCCGG AGGAAACCCGCTCGTCATTGGTGGTGCGGTGCCTACTCTTTTTCGGCGGC GGTGTGCTCATCTGCACCACCTTCCTGCACATGCTGCCCGAGGTGATCGA GGTGGTGGAAGCGCTCCAGGAATGCGGCTCGCTTGTCAAGACGCCCTTCG CTCTGGCGGAGATGCTGCTGTGCACGGGCTTTTTCCTGATGTACGCGTTG GACGAGCTGATGACCAGCCTCGTGCGGCACCACCAGGGAAAGCTTAGTCG GAAAGAGTCGGTGGCCAGTCTGGCTTTCGAAAGAGGACGCAGCATTCGTC ACAGTGTTCTCCTCAATCCACAGGCGAAGGAAGAAGTGGAAGTTAAGGAT ACGGAACCGCAGCCACACAAGGATCACCACGGCCACTCGCACATGCCCGT GCCAGCGGACGATGGATCCTCTGCCAGGGGGCTGGGCATTATCCTCGCCC TTTCGCTCCACGAACTGTTCGAGGGCATGGCCATTGGTCTGGAGGGCACT GTGAGCACTGTGTGGTTCATGTTTGGAGCGGTCTCCGCCCACAAGTTGGT GTTGGCCTTCTGCGTGGGTATGGAGCTTCTGGTCGCCCGCACACGCAGTT CGCTGGCCATCTTGTACCTGGTGACATTCTCCATTGTTACACCCATCGGT ATCGGTGTTGGCCTCGGCATCAGCCAGCAGGTGGCAGCGGGTCAGCCCAG TCTGCCATCCGGAGTCCTCCAGGGCATCGCCTGTGGAACCTTGCTGTACG TAGTCTTCTTTGAGATCCTCATTGAGAGCCATGCCGGATGGAGGGCCCTT GTGGCCGCCGTTGCGGGATTCGCTCTAATGTTTGGCCTTCAAATTCTTTC TGACGAAGCGGAGGGTGATGACAGCCTAACCTGTTCCTAGCCAGTGTGAC GCCACTTCAGTATTATCAAGTTATAGAGGAAGCAACAAAATAGTATACAA AACGATTCCCTGGGGATCTGTAAAAGTTATTATATAAAATACGAATAGAA TTTCAAAAGAGGTTTCTCAGAAATCTTATCCAACGCAAATAATTAAAAAT GTAATAACCATATGGATTAAAAGAGACAATATTTTAC 1387 2R:1731127-2080000 -1 CG9428-RA CG9428-RA FBtr0086139 pavel AAM70819 Imperfect match to REAL SP with corresponding FBgn 47582 46433 0 ZIP1:1 1 0 partof 1149 2R:1731127-2080000 -1 CG9428:1 46357 46119 0 ZIP1:2 2 0 partof 238 2R:1731127-2080000 -1 CG9428:2 47451 46319 0 ZIP1-PA 0 producedby MSATATMSQEQTQDVDHHALLVAKIVSMVVLVVITVLCGSLPYVLNRCFH WTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPEVIEVVEALQECGS LVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFE RGRSIRHSVLLNPQAKEEVEVKDTEPQPHKDHHGHSHMPVPADDGSSARG LGIILALSLHELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELL VARTRSSLAILYLVTFSIVTPIGIGVGLGISQQVAAGQPSLPSGVLQGIA CGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILSDEAEGDDSLT CS 352 2R:1731127-2080000 -1 CG9428-PA CG9428-PA FBpp0085472 AAM70819.2 45640 29894 Drosophila 0 CG3409 0 0 15746 melanogaster 2R:1731127-2080000 -1 CG3409 FBgn0033095 FBan0003409 42C5-42C6 AE003790 CG3409 Not in SwissProt real (computational) monocarboxylic acid transporter activity GO:0008028 45640 29894 0 CG3409-RA 0 partof c7184c2996320b7e695c8d137bcc7e69 TGCGAACGGACGTGTGGTGCTAGTGTGGTGGACTATACGACTTTTCTATA TTTTTAAGGGCCGCGGCAGTAGAGATAGCCTATTTTTCTCGCGACAGAGC GTGTTAAGTAATCAATTGAAATCCAGCGATTGGGTGAATCGAAAGTTCCT CCCCGATTCCCGACTCCTGCGTGCATTTGAAGCACTTACAGCCGCGATTT CCGCACTCGGGTGCACTGTGCTTTTGTTTATACGACCTCCGGTCGCCCCA CATTTTCTGTTGAACTTGTGCCGCCGAGCGGTGTTGTCACTGTCCCACCT CCCCCGCAGAAAATCGAAACTCCCGTACAGTGGGCGTGACCCAGGGCGAA GCCGATAGATAATAACTTTCCACGGGAACTTGAGTGTGCGTAATATCGCC TATAAAGAGTGTTTGGCAACTTGGCGTTCTGGAGTGTCACCCGCAACCAA TTCTAATCGTACATACATATATAAGCCAGCTGATTTGGACGTGTGCTACA GCGATTTCATCCCACTGTGCAAGACGGGCGGCAGAAATTCATAAAACAAC AGCTAACAAATTCGACGAAGAGGCATACGCAAAAGAAACGAAAGAGAGAG CGAGCTTATTGTATTTTTGTAATACTCGTCTGCCCAACAACTACATTTAC TGTAATGTGCAGCCTATAATGTAAGATAATGCAATGACACAGGACCAACT CCCAGTAATGGTTGCAATTTAGCCCAGAAGCCACGAATTCACCAACTCAG CAGAGTGATCAGCGTTTGCACTGAAGGCTGCTAATTGAGGACGAGGATCA TAAATCATTATCTGGCGCCAGCGAGGAGGCGAGCACAGCGACAGCAGCGA TTGAGTTGCACCACCAGAGACGAATTAATCATACGCCGCGTTGGTCGTCC CTCCGTCGATACTAAGATATACATATATACAATGCCTGCGAATCCGCCTC CGCACCACGCGCCGCGCACTTGACACGGGGAGCGGCAGAGTAGCCGGAGA AGCCAGTGAGGCCCAGTCTTGTGTTCGATTTGTGTTTGTTATTTCTTGTT CGAGCTAGCCGGGCACGCTAGTTGGCATCGTTGGCATCGAATCGAAAAGT GTTTGATTTCCGCGAAAACAAAGTACCGCATGTGGCTGCCAGGGCAAAAT CTGCTAGCCGGCAGCACAAACTGCAACAACTGCATCTGCAACTGCAACAG CAACAACAGCAACATCACCAGCAACTGCCGCCAGTTGCCGTCAATTATCG CTCAATATATTCTCCGTTGGCCTGTGATAAACCCCCTAACGTTCTTAATG AACGACCTTCGGTCCAAGTCATTCTATCGTGCAGGCAAACCAACATCTGC AGCATCCGCGTCGGGCGCGACCACCAACGCCAAGTCGTTCGACAAGGGCC AGAACAACAATCCCCGTACTTACAACAACAGCGGCAAGTCGAACAAGGTG TTCCTGCATTACATACCCCGCGATCCGCGCCTAAGAATTTTCAACAAAAC CGCCACCCTGAATAAACACTCGAATCGCACCCTGAGCGAGCTAAACATAA CTGAAGATCTGTGCAATTATGGTGAATTGATTGGCGGTGGTGCCGAAACA GTGAAACTAGTGCCAGTGAAATCTTAAGAATATATCCGCAAAATCCGCAG ATCACCGAATCAATTTATTCGTTAACAAAAGTTGGCTGTTGGCGTGCGGA GAGAGCATTGCCTGGACTACGATCGGCTACGCACTGCAGTTGACCAACAG AGAGAGGGAATATTTACCTACCGCCTACTTAAGAAAATTTATGCTGAAAT CTAATGCAAATTGTGTTCACTTCCAATAATCGCTTGGACAAGAAAGTGCA AATTTTACAAACCTTTTTATAGACGTAGCTGAACCCTTTACACAACAACA CGATCACTGGGACTCCGACATGGCCAAGCTAGCGACGGATCCAAACGCCT CCAACAACAACAGCTGCGAGGCGGTTAACAACAACCACAATGGCCAGAAC CAGAGCCAAAACGGAGGCGCCTCCAATTACCAGGCCCTGCCTCTTACGCC TGCTCCGGCCAACACGCCACTCCACAAGGCCATCAAGCACGACCTCTTCC CGGAGGTCACCTTCTGCAACCTCTCCGTAGAGGAGCTCGCAGATGGGGCT GGACACAGCCGTGTGGTAAGGAGCAGTGTCATCGAACTGGAGGACGGCAC CATGACGTGCCTGATGAACGGAAATGGGCAGGTGAAGCGTCGCAAACGCC TGATCTCGAACGAGTCCGGCGACTCGATCGACTCCAGTTCCACGGAGAAG AAAACGCCCAAGATGCCCGACGGTGGATATGGGTGGGTGGTGGTGTTCGC CTCTCTGGTCGTGTCCCTTATAGCCGACGGACTGAGCTTCTCATTTGGCC TAATAAACGTGGAACTGCTGGAATACTTCGGAGAGTCCACTTCGAAGACC GCCTGGATATCCTCGCTATTCTTCTCCGTGCCCCTGTTGATGGGACCCAT CTGGTCCAATCTGGTGGACAAGTACGGCTGCCGAAAGATGACCATCCTCG GCGGAGTGGTCTCTGCCTTTGGGTTTGCTCTGTCTTCGTTTTGCAACTCG ATCGAGATGCTCATGGTGACCTTTGGTATCATTTCGGGACTGGGCCTAGG CATCGGGTATGTGACCGCGGTGGTGTCCATTGCATTCTGGTTTGACAAGA AGCGCACCTTTGCGACCGGCATCGGAGCATCGGGCACCGGCATCGGGACC TTTGTCTACGCCCGCCTTACTTCCTATCTAATCGAATCGTACGGCTGGCG CGGAGCCACTCTAATCCTTGGCGGCACCATGCTCAACGCATGCGTTTGCG GCGCCCTCATGCGCGATCCCGACTGGCTGATCGAGGAAAACCGTCTAGAG AGTCGATCCCAAAGCGTCACCACCTTCTCGAACTCCAGTGTCTGCCTGGA GGAAATAAAAAAGCTGCTGGACACCGGCATCACAAAGGAGGCTGTGCTAG ACTCGTTGGTGACCAAGAACAACACGGAGGCCAACCAGCAGATTGACGAT CCGTTGGACTCCGCTCTCAAGCGCTACCGCAGCGAGATCTTCCTGCCCAC CTTCCTGAGCACTCAGGAGCTTGACAGCATCTGCGAGGTTAAGAGCCTGA GCCGACGCTCCCTACGCCACAAGGAGGGTGAGGAGGCGCCGTCACGAGAG AACCTGCTGTCCATGTCCTCAGGAGCAGGTGCCTATCCCCCATCGACGGC CGTTATAGGCTCGCCAGATGATACCCTAATGGGCGGAATAGCTCACGAGG CGGCAGAGGAAGCAAAGAAGGCCTATCTGGCCTCCATCGAGACGCTGTCT CCATCGGAAAAGCGCTCCACTGGTAGGACTCCCAATGGCTCGCTCCGCTC CTCGGACGAAGGCTACCTTACGCAGAAGCACGCCAGCTCCCGGTACTCGC TTAACGAAAACATCTTCATGGCCAAGCATACAACACCATCAATCTCCAAC CTAAAGGTGAATGGCCTGCGACACAATTCGGTGGACATCTTGAGCGAGGA CATGCACTGCTACTACTCGAAGGACGAGACCTTCGCATTGCTGGAGCCGA GCAGGCGCATCAGGCCCACCGTCATCGCCATTCCGGAACAGGAGCAGTCG GTGAACAGCGAGCTGGCCACCCGTCGCGCACGCCTGGACAGCATCACGGG AATCCGCCGGCTGTCGCGCTCCAAGAAGCCCAGCCACCACCGATCGAACC TCCGCCGCAACATCTCGATCCGGAACTCCAACTTCCTTAAGGATATGCGC ATTCACCGCAACTCGATCCACTACCGCGGGGCCATGCTGAACACGCACCG CTACCGGCTGCGCGCCTCCTCCTGTCCCAACATCTACCGCAACTCGATGA CCACCATCGCCAAAGAGGAGGAAGATACCTGGTATGACAACTTTGTGGAC ACCATGAAGTCCATCTTTGACTTTTCACTCTTTCTGGACATGAAGTTCGC CCTCTTCAATCTCTCTACATTGTTTTTGTTCATTTGGTTCATTATCCCCT ATCTGTACCTTCCCGATTACATGAAGCAATACAAGTACGACGTGAGCCAG AGTGCCGAGTTGATTTCGGATGTCGGCATTGCCCAAACGGTGGGCATGAT AGGACTTGGCTATCTGGGGGATCTGTCCTGGATGAACATCAATATATGCT ACTCGCTGTGCATGCTGGTGTGCGGAGCGTCTGTGTTCTTCATGCCCCTG CTGATTACCAACTACATGGGCCTGATGGTCATGTGCGTTATTTTCGGATT TACGTTCGCCAGCTCCTTCTCGTTTACGCCCAGCATTCTGGTCAGTATTG TGGATCTGGACGATTTCACGTGTGCCTACGGTCTGGTGCTGCTGGTTCAG GGAGTTGGAATGATCGCAGGACCCCCTATTGCAGGCGTCATATACGAGTA TACGGGCAGATGGGATGACACCTTCTATTATGCTGGAATATTTATCGCAC TCTCTGGTGTCTGTTCGTATCTGATCGAGTTCTGTGAAAAGAAAGCACCT AAGGAGAGTGATAGTGATGTCTTAGAGACTAAAAAAGCTCAACTTTTACA CTAGGTTACTTACATTGCACTGTTGAACGCCGCAAGTAGAAGGCAACTGG AGGTACTACAAATCCGAACTGTAGCATAATAATGGACTAGCATTAAATGT TAACGAGTTTCTTATGTCAAATGGTGTTGCAGCCATAAAATCAGAGCAGA ATTGTAACTGAAACTAAGCCTATTCCTAAGCTCTAGCCTGTAAGACTATA CTTGACTTGACTAATCGTAGCTAAGTATCAATATACACCTAACATATACT TACCGCACTAGGGCAATTACTAACCGCATCTTTGTCTAGACAAACTGTTC AATTTCAATCAATATCAATGCAGTGCATCACTGCCAGGTGCAAACGGGTC CCTCAATTGTCTTCTTTACAAAATTTAGAAAAATAGTTTTAATTGCCTTA CATTTCGTACGAATATTAATTAAAGGGAATACAATAAACAACAATCTATG TAACGTATGCAATAACAAGTGACCATTTTCAATCAATCTAAAACTCACAA TAAAATCTTTGGAGCATTTGTTTGTACATCAAACGTCACGGATCCGAATA GTTTCCA 5157 2R:1731127-2080000 -1 CG3409-RA CG3409-RA FBtr0086140 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70818 simonp 45640 44878 0 CG3409:1 1 0 partof 762 2R:1731127-2080000 -1 CG3409:1 35973 35009 0 CG3409:2 2 0 partof 964 2R:1731127-2080000 -1 CG3409:2 34361 32161 0 CG3409:3 3 0 partof 2200 2R:1731127-2080000 -1 CG3409:3 31697 31587 0 CG3409:4 4 0 partof 110 2R:1731127-2080000 -1 CG3409:4 31146 30964 0 CG3409:5 5 0 partof 182 2R:1731127-2080000 -1 CG3409:5 30897 30656 0 CG3409:6 6 0 partof 241 2R:1731127-2080000 -1 CG3409:6 30592 29894 0 CG3409:7 7 0 partof 698 2R:1731127-2080000 -1 CG3409:7 34168 30450 0 CG3409-PA 0 producedby MAKLATDPNASNNNSCEAVNNNHNGQNQSQNGGASNYQALPLTPAPANTP LHKAIKHDLFPEVTFCNLSVEELADGAGHSRVVRSSVIELEDGTMTCLMN GNGQVKRRKRLISNESGDSIDSSSTEKKTPKMPDGGYGWVVVFASLVVSL IADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVD KYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFGIISGLGLGIGYVTA VVSIAFWFDKKRTFATGIGASGTGIGTFVYARLTSYLIESYGWRGATLIL GGTMLNACVCGALMRDPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLL DTGITKEAVLDSLVTKNNTEANQQIDDPLDSALKRYRSEIFLPTFLSTQE LDSICEVKSLSRRSLRHKEGEEAPSRENLLSMSSGAGAYPPSTAVIGSPD DTLMGGIAHEAAEEAKKAYLASIETLSPSEKRSTGRTPNGSLRSSDEGYL TQKHASSRYSLNENIFMAKHTTPSISNLKVNGLRHNSVDILSEDMHCYYS KDETFALLEPSRRIRPTVIAIPEQEQSVNSELATRRARLDSITGIRRLSR SKKPSHHRSNLRRNISIRNSNFLKDMRIHRNSIHYRGAMLNTHRYRLRAS SCPNIYRNSMTTIAKEEEDTWYDNFVDTMKSIFDFSLFLDMKFALFNLST LFLFIWFIIPYLYLPDYMKQYKYDVSQSAELISDVGIAQTVGMIGLGYLG DLSWMNINICYSLCMLVCGASVFFMPLLITNYMGLMVMCVIFGFTFASSF SFTPSILVSIVDLDDFTCAYGLVLLVQGVGMIAGPPIAGVIYEYTGRWDD TFYYAGIFIALSGVCSYLIEFCEKKAPKESDSDVLETKKAQLLH 894 2R:1731127-2080000 -1 CG3409-PA CG3409-PA FBpp0085473 AAM70818.2 14132 13013 Drosophila 0 CG15909 0 0 1119 melanogaster 2R:1731127-2080000 1 CG15909 FBan0015909 FBgn0033090 42C3-42C3 Not in SwissProt real (computational) AE003790 CG15909 14132 13013 0 CG15909-RA 0 partof 59e252a353786deb77b896d4295d62c8 ATGCGATTTGTTCTATGGTATGTCTTCGTGCTCAGCTCCATGAATGTATT TCAAAAGTCCAACGCCAAGTCAAGACTCACAGCTAATTTGACAGACGACC CATTGCATGCCTATAATGAGGTCGTGCAGAATTTGATTAAGAACTGGGAG TCGCCAGTTGTCTATCTGAAAAAACGAGGTTTCCTGCCCAGAAACTACGA GGATGCGTCAAGAATCAAGCACAGCCTGGATGCCCTGATGCAACGAATAA AAAGGGCTAAACGGGATCACACAAAGGAGGTCACTTTCAATGTAAGACCC AAAGAAATGGCAAAAGCTTACCCAAGGAATCAACGTGGCTTTCAGCTATC AACGGGCACAATGCTCTCTAGTTTGGAGCAGTTGAAAGTCATCGAAGGCC AGGCAACGAAGGCCAAGACCACGGCCAAGTCAAGTGAGCAGGAGCAAGAG CTGCTGGCAATGAAGCGGCGATTGGAAGAGTTGCAGCAGGTAGCAGGTAC CGGTCAGGATCAGCCAGGATACCGTAGGCAGATTAAAGTAAATCCAATAG ACAAGGATCCAGGGAAGTCAGCACAAAGTTATGATGAAATATTGCAGCGA ATGATTGAAAAGACGAGCCCACACTACTCACAGCAATCCAATTCGCATTT AGAAACCCATCCAAATCAACTAGCGCCAGCTCCTCCAGGAGCAACCCAAA AACTTGATAATGTGCAGATGGCTCCCAAAGAAGACAAGCCGCTGACTTTA GAACATATCGAGTTGCATGCGTATACAGCGCAAAGTGCTCCCCGAAATTT ATTGCATAAATCCGTAGTTGATCTGCCCATACTTAGAGCAGCGGAGACCC AGAGGAGCAAGACCGCAACGGAGGCATCTAACGTGGAATCGAAGTTGCGC GCGCCCACCTATCTGAATTGGGACATGAAAAACGGTCGACTGGATCATTA CTCAAGCGTGGACAAGGAGGCCTATTTGAACCAGTTGGTGAGAGTGTTCG GGCGCAATTTGGATTTCAAGGAACCCACTCAAAAAGGAAAAGAGCCGACA GTTTCTTAG 1059 2R:1731127-2080000 1 CG15909-RA CG15909-RA FBtr0086122 AAM70811 Perfect match to HYPO SP record with corresponding FBgn pavel 13030 13013 0 CG15909:1 1 0 partof 17 2R:1731127-2080000 1 CG15909:1 14132 13090 0 CG15909:2 2 0 partof 1042 2R:1731127-2080000 1 CG15909:2 14129 13013 0 CG15909-PA 0 producedby MRFVLWYVFVLSSMNVFQKSNAKSRLTANLTDDPLHAYNEVVQNLIKNWE SPVVYLKKRGFLPRNYEDASRIKHSLDALMQRIKRAKRDHTKEVTFNVRP KEMAKAYPRNQRGFQLSTGTMLSSLEQLKVIEGQATKAKTTAKSSEQEQE LLAMKRRLEELQQVAGTGQDQPGYRRQIKVNPIDKDPGKSAQSYDEILQR MIEKTSPHYSQQSNSHLETHPNQLAPAPPGATQKLDNVQMAPKEDKPLTL EHIELHAYTAQSAPRNLLHKSVVDLPILRAAETQRSKTATEASNVESKLR APTYLNWDMKNGRLDHYSSVDKEAYLNQLVRVFGRNLDFKEPTQKGKEPT VS 352 2R:1731127-2080000 1 CG15909-PA CG15909-PA FBpp0085456 AAM70811.1 26400 24888 Drosophila 0 CG3403 0 0 1512 melanogaster 2R:1731127-2080000 -1 CG3403 FBgn0033094 FBan0003403 42C5-42C5 AE003790 Not in SwissProt real (computational) CG3403 cell cycle GO:0007049 mitosis GO:0007067 cytokinesis GO:0000910 26400 24888 0 CG3403-RA 0 partof a6277dc04be7e5852f2365374f0ec747 ATTTTCTCGCACAAAGCAAAGTGTTTTGGAGGATAAACGCCAATTAATTG TCAAGCGATGTGCCAGCTCCTGTAGAATACACTCAGCATACTACGGTGCA GGGATCCCACATCCGGAGACTCCCGCGGGGCAGGGACCAGGCTAGCATTC AGTTTCTGCCAGTGATTTTCTCATCAAGGCGTAGGCACAGACGTTGTGGA TCATCGCGTCTTCGAGCGGGTGAAACATGAAGATGGCTGACGGCTCGACC ATATTGCGTAGGAACCGGCCAGGCACAAAATCCAAGGACTTCTGTCGCTG GCCCGACGAGCCCCTGGAGGAGATGGACAGCACGCTGGCGGTGCAGCAGT ACATACAGCAGCTGATTAAGCGCGACCCGAGCAACGTGGAACTCATACTG ACCATGCCCGAAGCCCAGGATGAGGGCGTGTGGAAGTACGAGCACCTGCG CCAGTTCTGCATGGAGCTGAACGGCCTGGCAGTGCGGCTGCAGAAGGAGT GCTCGCCGTCGACGTGCACCCAGATGACAGCCACTGACCAGTGGATATTC CTGTGCGCCGCGCACAAGACGCCCAAGGAATGTCCGGCCATTGACTACAC ACGCCACACGCTGGACGGTGCCGCCTGTCTGCTAAACAGCAACAAGTACT TCCCTAGCAGGGTGTCCATCAAGGAGTCGTCGGTAACCAAGCTGGGCTCC GTATGTCGGCGGGTGTATCGCATCTTCTCGCACGCCTACTTTCACCATCG TCGCATTTTCGACGAATTCGAGGCCGAGACGTATCTGTGCCACCGTTTCA CGCATTTCGTCACAAAATATAATCTGATGTCGAAGGAGAATCTGATCGTG CCCATCAACGTGGGTGAAAACGCGGCCCCTGGCGAAAGCGAGGCTTAGGA GCCCGCCCAGATTAGTCAGACTCGCATGAAACACTCATTCAACATACATC TATTTATATTTACCAATAGCTTGCAAGTTGGGTTGGCTCACCCTGACAGG GAAACGATTCCACGCGGACCCGACTCTAATGCAGATCTTGTATGTAGTTT AGATGTCAGATACACATAGAGCTACATAACGATAACTAAGTAACAAGGGC AGACCCCCTCAAACCCGCTCGCCCCATCTGATCCTAAGTCAGCAATTATT TCGCAAGTTATATTACGATTATGTTTAACTCCTTATTTTAATAAATTATA TGTAGGCACACGACCTTCTCGTGGCTGATTCCACGTCAAATCCCCGTAAA CTAAACTAAATTCCCTTGACTACTGGCAGCCAAAACACCAACACAGCTGT ACGTGACTAAAACGTGAACTTTACTATACAAAATTACTATATACACAACA GAAATTGCAATAAAAGAAGTACATACAT 1378 2R:1731127-2080000 -1 CG3403-RA CG3403-RA FBtr0086141 Perfect match to HYPO SP record with corresponding FBgn pavel AAM70816 26400 26114 0 CG3403:1 1 0 partof 286 2R:1731127-2080000 -1 CG3403:1 26040 25666 0 CG3403:2 2 0 partof 374 2R:1731127-2080000 -1 CG3403:2 25606 24888 0 CG3403:3 3 0 partof 718 2R:1731127-2080000 -1 CG3403:3 26174 25371 0 CG3403-PA 0 producedby MKMADGSTILRRNRPGTKSKDFCRWPDEPLEEMDSTLAVQQYIQQLIKRD PSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQM TATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKE SSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNL MSKENLIVPINVGENAAPGESEA 223 2R:1731127-2080000 -1 CG3403-PA CG3403-PA FBpp0085474 AAM70816.1 111230 109489 Drosophila 0 Cyp6a2 0 0 1741 melanogaster 2R:1731127-2080000 -1 CG9438 GO:15034 GO:5792 GO:16352 FBgn0010312 FBgn0000473 FBan0009438 42C8-42C9 Cyp6a2 AE003790 Perfect match to SwissProt real (computational) electron transporter activity GO:0005489 microsome GO:0005792 membrane GO:0016020 response to insecticide GO:0017085 111230 109489 0 Cyp6a2-RA 0 partof cb742d4794cefbb7d43d0919f6871442 CGAAAAGGGAGCAGCTACGCAAAATGTTTGTTCTAATATACCTGTTGATC GCGATCTCCTCGCTTTTGGCCTACTTGTACCACCGCAACTTCAACTACTG GAATCGCCGCGGCGTGCCACACGATGCTCCTCACCCACTGTATGGCAACA TGGTCGGGTTCCGGAAGAACCGGGTGATGCACGACTTCTTCTACGACTAC TACAACAAGTACCGGAAGAGCGGCTTTCCCTTCGTGGGCTTTTACTTTCT GCACAAGCCGGCCGCCTTCATCGTGGACACCCAGCTGGCCAAGAACATCC TGATCAAGGATTTCTCGAACTTTGCCGATCGTGGCCAGTTTCACAACGGG CGCGACGACCCGCTCACGCAGCACCTGTTCAACCTGGACGGAAAGAAGTG GAAGGACATGCGCCAGAGGCTGACGCCGACTTTCACCTCGGGCAAGATGA AGTTCATGTTCCCGACGGTGATCAAGGTGTCTGAGGAGTTCGTCAAGGTG ATCACGGAGCAGGTGCCCGCCGCCCAGAACGGCGCTGTGCTCGAGATCAA GGAGCTGATGGCCAGGTTCACCACCGATGTGATTGGCACCTGTGCCTTCG GCATTGAGTGTAACACGCTGCGCACCCCTGTCAGTGATTTCCGCACCATG GGACAGAAGGTGTTCACCGATATGCGCCACGGGAAACTGCTGACCATGTT CGTGTTCAGCTTTCCCAAGCTGGCCAGCAGGTTGAGAATGCGCATGATGC CCGAGGACGTCCACCAGTTCTTCATGCGCCTGGTCAACGACACGATTGCC CTCAGGGAGCGGGAGAACTTCAAGAGGAACGACTTCATGAACCTGCTGAT TGAACTGAAGCAGAAGGGGCGCGTCACCCTGGACAACGGAGAGGTGATCG AGGGCATGGACATCGGCGAACTGGCCGCCCAGGTGTTCGTCTTTTATGTG GCCGGATTTGAGACCTCCTCCTCGACAATGAGTTACTGCCTGTATGAGTT GGCTCAGAATCAGGACATTCAGGACAGGCTGCGCAACGAGATCCAAACGG TGCTGGAGGAACAGGAGGGGCAGCTAACGTACGAATCCATCAAAGCCATG ACCTACTTGAACCAGGTCATCTCAGAAACCCTGAGGCTCTACACACTGGT GCCCCACCTCGAACGGAAGGCCCTCAACGACTACGTGGTGCCGGGCCATG AAAAGCTTGTGATTGAGAAGGGCACACAGGTCATAATCCCCGCTTGCGCC TACCACCGCGACGAGGATCTTTATCCGAATCCGGAGACCTTTGATCCGGA GCGCTTCTCGCCGGAGAAAGTGGCCGCCCGGGAGTCCGTGGAGTGGCTGC CCTTCGGCGACGGGCCGCGGAACTGCATCGGGATGCGGTTTGGACAAATG CAGGCTCGCATCGGTTTGGCTCAGATCATCAGCCGGTTCAGGGTATCCGT CTGCGATACGACAGAGATCCCACTGAAGTATAGTCCCATGTCCATAGTTT TGGGCACCGTTGGGGGCATCTACTTGCGAGTGGAACGCATCTAACCTCCA TATTCGTTGCTCCCATGTATATAGCTTAGGATCCAAAGCTAAAGTGATGT ACATTTTAGACTGTTCAATTATTAAATAACCTTAACCTAAACAGCCATAT TAACTTATTGGCCTGTGATAAA 1672 2R:1731127-2080000 -1 CG9438-RA CG9438-RA FBtr0086133 AAM70832 cdsmith Perfect match to REAL SP with corresponding FBgn 111230 110105 0 Cyp6a2:1 1 0 partof 1125 2R:1731127-2080000 -1 CG9438:1 110036 109489 0 Cyp6a2:2 2 0 partof 547 2R:1731127-2080000 -1 CG9438:2 111207 109620 0 Cyp6a2-PA 0 producedby MFVLIYLLIAISSLLAYLYHRNFNYWNRRGVPHDAPHPLYGNMVGFRKNR VMHDFFYDYYNKYRKSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNF ADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVI KVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLR TPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASRLRMRMMPEDVHQFF MRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGEL AAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ LTYESIKAMTYLNQVISETLRLYTLVPHLERKALNDYVVPGHEKLVIEKG TQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRN CIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIY LRVERI 506 2R:1731127-2080000 -1 CG9438-PA CG9438-PA FBpp0085466 AAM70832.1 24962 23214 Drosophila 0 CG3270 0 0 1748 melanogaster 2R:1731127-2080000 1 CG3270 FBgn0033093 FBan0003270 42C4-42C5 Not in SwissProt real (computational) AE003790 This gene model is supported by only one EST/DGC evidence (GH02863) which indicates that the resulting translation product is possibly shorter than the predicted one.::DATE:2002-02-13 11:31:01::TS:1013617861000 CG3270 24962 23214 0 CG3270-RA 0 partof 4453adc02f7796aca396d556a8c4d657 ATGCTGGGCCTGCGACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCG CTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAG TCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTG AAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGA GCGCGATGCTGGTTACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAG TGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGA TACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTG CTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACA TCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAG CTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGA GGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATC CGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCG AATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGG CCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGA AGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCG CGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGT AGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTC AGGGTAAGAATTGTCCTGGGCTAGCCACACCTCTGACCGTTGATCCCGAT GGCACCTACTTCAGGCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCG CAGTCCAAACGAAGACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACC ACGGGTACTTTGAAACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCT GCTTTTGAGTCTGTGAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCA CAACACATTTGACGCAAACGGCGTCATCGGCAGGCATCCTCACTACAGCA ATCTCTTCATTGCCGCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCC GCCGTGGGTCGAGCCATTTCCGAACTAATCTTGGACGGCAAGTTTACCAC ACTGGATCTGTCGCGCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTA TGCACGAAGTGAATATCGTTTGACAAATTTATCACAGGAGGATCGTACTT GCCCTTGGTGTGTTTATGTATGTACTTCTTTTATTGCAATTTCTGTTGTG TATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTC 1439 2R:1731127-2080000 1 CG3270-RA CG3270-RA FBtr0086123 pavel Perfect match to HYPO SP record with corresponding FBgn AAM70815 23427 23214 0 CG3270:1 1 0 partof 213 2R:1731127-2080000 1 CG3270:1 24962 23736 0 CG3270:2 2 0 partof 1226 2R:1731127-2080000 1 CG3270:2 24843 23214 0 CG3270-PA 0 producedby MLGLRRVLRLGALRQLRSLSGKPQGDVLPGSCGVLIIGGGGMGASSAFWL KSRALQLGRKLNVLVVERDAGYTSASTVLSVGGVRQQFSLAENIEMSLFG YNFVVNGREHLGDVDLCYQPNGYLILASEKGAHILAKNSKLQNELGARNE LLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGA NFANGSVVGFEWNDSGGLSGAVVDAGDVLQRTVKFDTCVLAAGAYSGQVA RLAGIGDKEAKEASLSVALPVEPRKRYVYVVSTQGKNCPGLATPLTVDPD GTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVP AFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTP AVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 440 2R:1731127-2080000 1 CG3270-PA CG3270-PA FBpp0085457 AAM70815.1 29711 26496 Drosophila 0 Rab2 0 0 3215 melanogaster 2R:1731127-2080000 1 CG3269 GO:3931 GO:5525 GO:3928 FBgn0014009 CG3269 FBan0003269 Comment: Reference sequence based on BDGP genomic sequence. Perfect match to SwissProt real (computational) 42C5-42C5 AE003790 D.melanogaster FlyBase-curated sequence: Rab2.v004 Rab2 Comment: This record is derived from the following: AC007593 AC007593.5 10-MAR-2001 D84313 D84313.1 06-AUG-1997 AB035352 AB035352.1 04-DEC-1999 AI062422 AI062422.1 19-APR-2001 AW940056 AW940056.1 19-APR-2001 Comment: Reference sequence of Rab2 == FBgn0014009 Rho small monomeric GTPase activity GO:0003931 29711 26496 0 Rab2-RA 0 partof ec190943bebdb7efe2544fe2af43f471 GTATTTCCGCCAGCCCTGGCCACAAAGTGGCCACACTGTCGCTAGCCAGT CATCATAAATACGAACAGATTGGAAAACGTACAAGAATTGCGTATTATCT GTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCG TCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGG AGACACAGGCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGC GATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGC ATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGC TGGGCAGGAGGCTTTCAGATCTATCACACGCTCTTATTACCGCGGAGCTG CTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCAC CTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGT CATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGA AGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATG GAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATAC GGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACA ATGAGGCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCG TCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTG CTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCC GCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGG AACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAG CTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAA GATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTT TACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAA CCACATTTGTGTACGTGAATGTCGTGCGTGATTTCTAAATTTTATAAAGT TTATTGAAACATTTTTAAATGTTTTATGCATGTATTTTGTGTATATTGAA GTTAGTTTGCTAGTTACTTCGTGTAAAATCGATAGTTATACATTGGGATT TTGACAAAATGATGTGTAATATATGAACAAAAATCAAACTGTGTGAATTT TCATTGTGATTCGATTTCAGTGAGGTCCAGCTTCGCAACGCTGCGCCACG CCCCCTTTTGCAATGGGTATCTGCTCCGCTTCTCTATACACACATACATA ATTAAATATATTAATATGTTTACGTTTCCTTCTCAACGCATTTGCTTTGT CTATTTTGTTGTGCAATCCGCTTAGTCTTTATACATACACTAGAAAAAAA GTACTTTAACAAAATATACAAAACGTGAGGGCCGAAATGGGGTTATATAA TTTACACAATCAACATGCATTAACCAGTGGTAACACGAAATGCTGCGATT CAATGATCAATTTAGTATTTTACGAAGTTTATATATTTAATTAACGGCGA TTGCTAAGACAAAACGAAAGATACAACTGTAAACGTAAATCAAATTATTT ATAATATTTGTATTTGCCCAACACAATGCGGAATAATAAATATACATACT TACTATTAATATAATTATATAAATTAAATCGGTACTTACCTTGGGTTCAT TAGCGTTTAATCAAGTGATAGTTAACGACTAATTAGTTTTTTGGTGTCTA GATGAGAAGTAAAACACTAAGGCAAATTTAATGAGGCATTTAAAGTTGTA AACAACTCAACTTTTAAATGAAAAGAGGTCAGACAAATAATTACGCATTA GTGTAGTTTTAACCCTTTTTATTTAGTAAGAGGCTTTCGGTAGATAATTG TTGAATTAATGTCTTGTAAATATTATTAAATGGTGAATCCTTTTTTGTTT ATGTACATATTTCCTAAAGTGTTCGGAATTAACAATTTCCACTTTCTATG TCGGCTATAGGGATATAGTGTCGCATTTACTTAATTTTTTTAAATGTGCT TACATGTTAAAACATTTTTTTACTACTGAAATATACTATTTAGAAA 2196 2R:1731127-2080000 1 CG3269-RA CG3269-RA FBtr0086124 Perfect match to REAL SP with corresponding FBgn experimental AAM70817 pavel 26704 26496 0 Rab2:1 1 0 partof 208 2R:1731127-2080000 1 CG3269:1 experimental 27350 27190 0 Rab2:2 2 0 partof 160 2R:1731127-2080000 1 CG3269:2 experimental 28160 27823 0 Rab2:3 3 0 partof 337 2R:1731127-2080000 1 CG3269:3 experimental 29711 28220 0 Rab2:4 4 0 partof 1491 2R:1731127-2080000 1 CG3269:4 experimental A region of 35bp in cDNA GB:D84313 does not align with the reference sequence. This region of discontinuity is 260 bases upstream of the 3' end of the transcript. 28316 26658 0 Rab2-PA 0 producedby MSYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI DGKQIKLQIWDTAGQEAFRSITRSYYRGAAGALLVYDITRRETFNHLTTW LEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSA RTAANVEEAFINTAKEIYEKIQEGVFDINNEANGIKIGQQHSPTNPSLPG AGGAAGAANSGCC 213 2R:1731127-2080000 1 CG3269-PA CG3269-PA FBpp0085458 AAM70817.1 predicted 19737 14746 Drosophila 0 CG30446 0 0 4991 melanogaster 2R:1731127-2080000 -1 CG30446 FBgn0033091 FBan0030446 FBgn0050446 42C3-42C4 AE003790 Not in SwissProt real (computational) Flag Cambridge: gene split (internal view only)::DATE:2002-02-12 17:32:52::TS:1013553172000 CG3686 CG30446 aromatic-L-amino-acid decarboxylase activity GO:0004058 19737 14746 0 CG30446-RA 0 partof 0b46694679d62882490c0efcbb962e09 CCAGTCGGGGCCAACGGTTCGTGGTCTCGAGTTCGAAACAAAATTCCCAT TCGCCCATCGGAATTTGCTCAGCACAACTCACCGTGGGAGTAAAAGAAAA CGGAAAAATAGGAAAACACTCAGAAAGGCGATTTGGAAAACCTACCGAAA ATGGACAGCACCGAATTTCGAAAACGTGGCATGGAAATGGTGGAGTACAT CTGCAACTATCTGGAAACGCTGAACGAGCGACGGGTCACGCCCAGCGTGG AGCCGGGATATTTGAGACACCTGTTGCCACCTGAGGCACCGCAGGAGCCG GAGGACTGGGACCAGATCATGAGGGACGTGGAGGACAAGATCATGCCCGG CGTGACGCATTGGCAGCATCCTCGCTTCCACGCCTATTTTCCGGCGGGCA ACTCGTTCCCCTCTATCCTGGGCGACATGTTGGGCGACGGGATCGGGTGC ATCGGCTTCTCCTGGGCCGCCAGTCCCGCGTGCACCGAGCTGGAGACCAT AGTGCTCGACTGGCTTGGCAAGGCCATCGGTCTGCCGGACCACTTTCTGG CCCTCAAGGAGGGCAGCACCGGAGGGGGAGTCATCCAGACTTCCGCATCG GAGTGCGTACTGGTCACGATGCTTGCTGCCAGGGCACAGGCGCTCAAGAG GCTCAAGGCCCAGCACCCGTTTGTGGAGGAGGGTCACCTGCTGTCCAAGC TTATGGCCTACTGCTCCAAGGAGGCGCACAGCTGCGTGGAGAAAGCGGCG ATGATCTGTTTCGTGAAGCTGCGCATTCTGGAGCCCGACGACGACGCCAG TCTGCGCGGCCAGACGATCTACGAGGCAATGGAGGAGGACGAACTGCAGG GTCTGGTGCCCTTCTTCGTCTCCACCACTCTGGGTACCACGGGCTCGTGT GCGTTCGACAATCTGCCAGAGATCGGCAAGCAGTTGCAGCGATTCCCGGG CGTTTGGCTGCACGTGGATGCCGCCTACGCGGGCAACAGCTTCATCTGCC CCGAGCTGAAGCCGCTCCTGAAGGGCATCGAGTACGCCGACTCGTTCAAC ACCAATCCCAACAAATGGCTGCTGACGAACTTCGATTGCTCGACGCTGTG GGTGCGGGACCGCATCCGGCTGACTTCAGCCCTGGTGGTGGATCCGCTGT ACCTGAAGCACGGCTACTCGGATGCGGCCATCGACTATCGTCATTGGGGA GTTCCACTCAGTCGGCGTTTTCGTTCGCTGAAGCTGTGGTTCGTGCTGCG ATCCTATGGGATTTCCGGGCTGCAGCATTATATACGTCACCATATCAAGC TGGCCAAGCGGTTCGAAGAGCTCGTGCTCAAAGATAAGCGCTTCGAGATC TGTAACCAAGTCAAGCTGGGCCTGGTCTGCTTTCGGCTGAAGGGTTCCGA CAAGCTGAATGAGAAGCTGCTGAGCATAATCAACGAGTCCGGCAAGCTGC ACATGGTTCCGGCCAGCGTGGGCGATCGCTACATCATCAGGTTCTGCGCC GTGGCCCAAAACGCGACCGCTGAGGACATTGACTACGCCTGGGACATCAT CGTGGACTTTGCCAACGAGTTGCTGGAGAAGGAGCAGCACGATGAGCTGT CCGAGATCATGAACCGCAAGAAGCAGGACACGCTGGCCCAGAAGCGCTCA TTCTTCGTGCGCATGGTCAGCGATCCGAAGATCTACAACCCGGCGATCAA CAAGGCCGGCACTCCCAAGCTCTCAATGGAGCTGCCCTCGCCCGTTGTGA GCCGCGGCAGTGCCCCCATTATCCGGACCCAGAGTTCGGTGGACCACAAC TCGTGGATATCCTGGCCGCTGGCATTCCTCTTCAACAGCAACAACGAGGA AAAGGGCAGTAACGTCTCGTTGCGTTTCCGACACCTGGACACCAACGTAC GACCATCGTCGTCGCGACGAAACTCCGGAGCCGGCTCGTCACCCTCTCCG GAAAACGAGTTGGACTACGTGAACGTCCAGCAGCAGCAGATGGAACAGCG ATCGCCACGACGATCGCCCATGGCGGTGCGCAAGGCATCGTCCACGCGGG ACAACCTCAACTAA 2064 2R:1731127-2080000 -1 CG30446-RA CG30446-RA FBtr0086142 pavel Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70812 19737 19660 0 CG30446:1 1 0 partof 77 2R:1731127-2080000 -1 CG30446:1 18350 18147 0 CG30446:2 2 0 partof 203 2R:1731127-2080000 -1 CG30446:2 18085 17777 0 CG30446:3 3 0 partof 308 2R:1731127-2080000 -1 CG30446:3 17617 17182 0 CG30446:4 4 0 partof 435 2R:1731127-2080000 -1 CG30446:4 17128 16913 0 CG30446:5 5 0 partof 215 2R:1731127-2080000 -1 CG30446:5 16561 16434 0 CG30446:6 6 0 partof 127 2R:1731127-2080000 -1 CG30446:6 15554 15045 0 CG30446:7 7 0 partof 509 2R:1731127-2080000 -1 CG30446:7 14936 14746 0 CG30446:8 8 0 partof 190 2R:1731127-2080000 -1 CG30446:8 18277 14749 0 CG30446-PA 0 producedby MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLPPEAPQEP EDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGC IGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQTSAS ECVLVTMLAARAQALKRLKAQHPFVEEGHLLSKLMAYCSKEAHSCVEKAA MICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSC AFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKGIEYADSFN TNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWG VPLSRRFRSLKLWFVLRSYGISGLQHYIRHHIKLAKRFEELVLKDKRFEI CNQVKLGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCA VAQNATAEDIDYAWDIIVDFANELLEKEQHDELSEIMNRKKQDTLAQKRS FFVRMVSDPKIYNPAINKAGTPKLSMELPSPVVSRGSAPIIRTQSSVDHN SWISWPLAFLFNSNNEEKGSNVSLRFRHLDTNVRPSSSRRNSGAGSSPSP ENELDYVNVQQQQMEQRSPRRSPMAVRKASSTRDNLN 637 2R:1731127-2080000 -1 CG30446-PA CG30446-PA FBpp0085475 AAM70812.1 88661 87375 Drosophila 0 CG9436 0 0 1286 melanogaster 2R:1731127-2080000 -1 CG9436 GO:4032 FBan0009436 FBgn0033101 42C7-42C8 CG9436 AE003790 Not in SwissProt real (computational) aldehyde reductase activity GO:0004032 88661 87375 0 CG9436-RA 0 partof 7d51874c944a64d7a4c4d40a1d5172d7 GCTTTCGACGAGCTGGAACAGATAGAGATTTGATCGCGAGAAAGGCGTAG TAGCACTGGTTTAGACTTAGAAGCGTCCAATTTGCACAGCGTTAATTATC AGCGCCAGCGACAAGATGACCAATCTGGCTCCCACCATCCGGCTGAACAA CGGGCGCGAGATGCCAACTCTGGGCCTTGGCACCTGGAAGTCGTTCGAGT CGGACGCCTACCACTCAACGCGCCACGCCCTCGACGTGGGCTACCGGCAC CTGGACACCGCCTTCGTCTACGAGAACGAGGCTGAGGTGGGCCAGGCGAT CTCCGAGAAGATCGCCGAGGGAGTGGTCACACGCGAGGAGGTTTTCGTGA CCACCAAGCTAGGCGGAATCCACCACGACCCTGCATTGGTGGAGCGCGCC TGCCGCCTGAGCCTTAGCAACCTGGGTTTGGAATACGTAGACCTCTACCT GATGCACATGCCGGTGGGCCAGAAGTTCCACAATGACAGCAACGTGCACG GAACCCTGGAGCTGACGGACGTGGACTATCTGGACACCTGGCGCGAGATG GAGAAGCTGGTGGATCTGGGCCTGACGCGCAGCATCGGCCTGTCCAACTT CAACGCCGCGCAGACGGAGCGAGTGCTAGCCAACTGCCGCATCCGGCCGG TAGTGAACCAGGTGGAGTGCCACCCAGGCTTTCAGCAGCGCCAGCTCCGG GAGCATGCCAAGCGCCACGGACTGGTCATCTGCGCCTACTGCCCCCTGGC ACGTCCCCAGCCCGCTCGGCAGTGGCCGCCCTTCCTCTACGACGAGCATG CCCAGAATCTGGCCAAGAAGTACGGCCGCACCACGGCACAGATCTGCCTG CGTTATCTGGTCCAGCTAGGCGTGGTGCCACTGCCCAAGTCGTCGAACAA GGCCCGCATCGAGGAGAACTTCCGCGTCTTCGACTTCGAGCTGAGTCCAG ACGACGTCGCCGGCATGGAGCAGTATCACACCGGGCAGCGCACGGTACCC TTTTCGGGAATGTCGGGCCATAAGTACTACCCGTTCAACGACGAGTTCTA GACGGGCTCAGGGGTGTCCCAGAAATATCGGTTTCGCCGTTATTGGATTG GCTAGGAATGCAAACAAAACGACTGTGGCATTCCAAGAGGGGTGTTTTGT TTTAGTTGTTAACTCAAAGTTAAAAAGGTTTCGAGTAAACCCGTGCATTA ATTCCCCTTAATATTTTACTGGAAGAGGTTCGTAAGACACCCCGCATATG TAGTATTTGTATTGTAAAATAAAGTATATTACGTAG 1286 2R:1731127-2080000 -1 CG9436-RA CG9436-RA FBtr0086134 not done Perfect match to HYPO SP record with corresponding FBgn pavel AAM70830 88661 87375 0 CG9436:1 1 0 partof 1286 2R:1731127-2080000 -1 CG9436:1 88546 87613 0 CG9436-PA 0 producedby MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAF VYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSL SNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVD LGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKR HGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQ LGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMS GHKYYPFNDEF 311 2R:1731127-2080000 -1 CG9436-PA CG9436-PA FBpp0085467 AAM70830.1 86795 86064 Drosophila 0 CG3420 0 0 731 melanogaster 2R:1731127-2080000 -1 CG3420 FBgn0033100 FBan0003420 FBgn0047109 42C7-42C7 Not in SwissProt real (computational) AE003790 CG3420 86795 86064 0 CG3420-RA 0 partof a4a8eec608bfa410fcfe455b3b1d10ea GACACTGCAATCATCAGCTTAAATAAAGAGAACAAAAATAAATTAGCGTT AGAATGTCAATGATACTAAGACGGAACCTGGGGGCATCCTGGTTGCTCAA GGCATGCTACAGTTCCAGCGCAAAACCGGTGGACTCGGCCAAAACAATTC CCAGTAACCTGCTCGAGGATAAGCAAACGGCCGTTCTGCAAAAGGAGAAC GGTACGATCTTCGACAAGCGCCCCTTCAAGATCCACCTGGACAAAGATAA AACATACAGCTGGTGCCTGTGCGGCAAGTCCAAGTCTCAGCCCCTCTGCG ATGGAATGCACAAGAACGAGTTCCTGAAGATCAAGCAGAGGCCCATTCGG TTCAAGGTGGAGAAGTCGGGAGACTACTGGCTCTGCAACTGCAAACAGAC CACCCACAGACCCTTCTGTGACGGCACCCACAAGCAGCCACACATCCAGA GCGCCGTCAAATAGATTTAGGATTGGTTGTAGGGCCCTGCCCGTGTGCGA AAAGAGAAATGCATTAATTTTGAATCAAGCAA 532 2R:1731127-2080000 -1 CG3420-RA CG3420-RA FBtr0086135 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70829 simonp 86795 86694 0 CG3420:1 1 0 partof 101 2R:1731127-2080000 -1 CG3420:1 86632 86487 0 CG3420:2 2 0 partof 145 2R:1731127-2080000 -1 CG3420:2 86411 86317 0 CG3420:3 3 0 partof 94 2R:1731127-2080000 -1 CG3420:3 86256 86064 0 CG3420:4 4 0 partof 192 2R:1731127-2080000 -1 CG3420:4 86742 86135 0 CG3420-PA 0 producedby MSMILRRNLGASWLLKACYSSSAKPVDSAKTIPSNLLEDKQTAVLQKENG TIFDKRPFKIHLDKDKTYSWCLCGKSKSQPLCDGMHKNEFLKIKQRPIRF KVEKSGDYWLCNCKQTTHRPFCDGTHKQPHIQSAVK 136 2R:1731127-2080000 -1 CG3420-PA CG3420-PA FBpp0085468 AAM70829.2 75919 71641 Drosophila 0 phtf 0 0 4278 melanogaster 2R:1731127-2080000 1 CG3268 FBgn0028579 FBan0003268 FBgn0028488 phtf 42C7-42C7 AE003790 Curator examined, accepted 75919 71641 0 phtf-RA 0 partof 9a56d414329a94cb5617ec2fe7638725 ATAATATCTAGCTGAGCAAGATGTACGGATTTGTGAGCACACACTTTAGT TTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGG ACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAAT TACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAAT CGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGA CAAAAATCGATCTGTGACGCGGTTTAAACCAAGGCTGCACGACACTTCGA GGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGT ACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTC GAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAA GCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAGGTTCCACGTTCC CTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATT CTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGAC CACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAA CCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGAC TATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGA TGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCC TCAGTGCCCTGCTTATTCCGTGCGCCCTAAGCTTGCTGATCAGTCTCATC CACTCACAAATTGTAGCCACTAACACCGCCTCGGGTGTCTCTGGCGGGAG TAGCAAGAACAAGCTGCGTCGCATATCTGCAAGCTACTTAAGCGACAAAG CAGCAACCAGGGAGAACCGGGTGCGACGTCGCAAGAAGATTGTGCGAGTT CGACAAGTGGAGGCTGACTTGTCCCAGGCCAGCAGTAACATATCACTTCC AAACAGAAGAACCGCAACCAGCACAATCGAAGTTCTTCCCAGACCGGTCA CGCCTTTGCCTTCACCAACAGTTACCTGTGCCACGGTGCCAGACCCCACC ACGCCGACTACGCCTTCGCCATCTGTTATCAGGCGGAGCACCAACGAGGA GACCTATTTGACAACGACTGCAATCAGCCCACTAACGCAACCGCTGGCAG CCATAGACGCATGCTACGATCTCAGCAGAAAGGCAGGGGGAGCTGCTCCC GAAAGCCCCAAAAAGCGCAACGTCAACTGGCACACGCCTATTCAGATATA CGCTACCTACGAGCTGGGCGAAGAGCCGTGCTCCAGCAGAAAAGTCGCAG AAGAAAGTGCGCCTGAGTCGGTTGGAGAAAGATTGTGTTCCGTCAAGCCA GACTACCAGACGCGTCGAAACATCGGGGAGGACGATGGCTTCGAGAGTCT GAATGGAAAGAGCTCAAGTGGAGAGGACAACAACCATTCGCCTTTGCCAA ACGCGGTGGCTGTTGCGGCTCCACCAGCTCCTGTTCAGACCAATCAGTTG CGTCTGCGATTAAACACAACAAACGGTGTGACCGCCAGTGCTTCTCCAAC CGAGAAGAAACCCCAGTCGCGCGGCAATGAATCCTCAACGAGTTGCGCCG AATCGGATGAGTGCGATGATGCCGACATTATGTCCAGTCCCGCCTCGGGC TGTAACCAAGAGTGCACCACTTCTGCCACCGACTGGCTGGGGGTGACGAC AAATAGCGAAGACTGCAGTTACACCTCTGATCTGGATCACTCTGACGGGG GCTTGAAGCACACGGCCTTTAGCGACGAAGATCCTGGAGAGCTGGACATC ACCCCTACCACTATACTAAATCCACATAGCAGCCTCGACCGTATTAGCTG CACCATTTGGGATCAGCGAGATGCCAAAAAGGCGCAGCTTTCCGTGCTGG AGATCGCGTCTTGCATAATCGAACGCGTGGACTCAATGGGCGAGGCCAAC GACTACATCTACATAGGCGTGGTCTTCTCTTTCCTGCTCACATTGATTCC CATCTTCTGCCGTCTCTGCGAGGTCACACTCGGGAGCGATGCAGAGAAGG CCAGTGAGATTAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCA TCGGCATCGCTCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTG GGAGCGCATGGTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCC TCATACTGTTCATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGC TTCCTTTACGCCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCG AAAGTCAAATCTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGA CCTGGCTGAGCGTGAGGTCGTATTTGAAGAAACGCGGACCCCAGCGATCG GTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGC CTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACC TTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTG CGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTC GGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGC CAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCC GCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAG TGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCC TATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAA ATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAG TACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAAT TAGTTAAGTGAATAAATTTAAGCGAGCCAATGTTTATGCTTGTCACGTGA TTGTTTAGCTACGTTAACAAGCCCACTAACGACTACGTAAACCAACAGAA ATTAGTATTTACCTACTTACCTTCTAGAGCGACCTGCACAATCACAAATC ATGTTTAGGCAAATTGTGCAATGCAATGAATCGCATGAAAGTTCATAGAA CTTTAAGCCTAAAATCAGTGCACCTATTGTAGTTGGCTGTTCATTCTGTT ACAGTCCCAAGTTAAATTCCTAAGGCGGTCTCAGCTAGTGTTGCAATTAA TAAATGTTAGTAAACTATAAT 3371 2R:1731127-2080000 1 CG3268-RA CG3268-RA FBtr0086125 AAM70823 pavel Imperfect match to REAL SP with corresponding FBgn 71924 71641 0 phtf:1 1 0 partof 283 2R:1731127-2080000 1 CG3268:1 72544 72479 0 phtf:2 2 0 partof 65 2R:1731127-2080000 1 CG3268:2 72755 72615 0 phtf:3 3 0 partof 140 2R:1731127-2080000 1 CG3268:3 73319 72811 0 phtf:4 4 0 partof 508 2R:1731127-2080000 1 CG3268:4 74314 73367 0 phtf:5 5 0 partof 947 2R:1731127-2080000 1 CG3268:5 74552 74373 0 phtf:6 6 0 partof 179 2R:1731127-2080000 1 CG3268:6 74969 74612 0 phtf:7 7 0 partof 357 2R:1731127-2080000 1 CG3268:7 75919 75027 0 phtf:8 8 0 partof 892 2R:1731127-2080000 1 CG3268:8 75510 72518 0 phtf-PA 0 producedby MKLDEIVAWYQKRIGTYDKQEWEKTVEQRILDGFNSVNLKNTKLKTELID VDLVRGSTFPKAKPKQSLLTVIRLAILRYVLLPLYAQWWVKQTTPNAFGF ILVLYLTQLTNWAIYVLHSSRIVPLDYEKPPNGTLLQAEADGDASDKDAD KESEEHAALLSALLIPCALSLLISLIHSQIVATNTASGVSGGSSKNKLRR ISASYLSDKAATRENRVRRRKKIVRVRQVEADLSQASSNISLPNRRTATS TIEVLPRPVTPLPSPTVTCATVPDPTTPTTPSPSVIRRSTNEETYLTTTA ISPLTQPLAAIDACYDLSRKAGGAAPESPKKRNVNWHTPIQIYATYELGE EPCSSRKVAEESAPESVGERLCSVKPDYQTRRNIGEDDGFESLNGKSSSG EDNNHSPLPNAVAVAAPPAPVQTNQLRLRLNTTNGVTASASPTEKKPQSR GNESSTSCAESDECDDADIMSSPASGCNQECTTSATDWLGVTTNSEDCSY TSDLDHSDGGLKHTAFSDEDPGELDITPTTILNPHSSLDRISCTIWDQRD AKKAQLSVLEIASCIIERVDSMGEANDYIYIGVVFSFLLTLIPIFCRLCE VTLGSDAEKASEISYFNMPQLLWEKSSASLFTLLGLAFGDSQWERMVLAL GFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHF RLNKVRNIKTWLSVRSYLKKRGPQRSVDIIVSAAFIVTLLLLAFLSVEWL KDSAHLHTHLTLEALIWSITIGIFLLRFMTLGQKIQHKYRSVSVLITEQI NLYLQIEQKPKKKDELMVSNSVLKLAADLLKELETPFKLSGLSANPYLFT TIKVVILSALSGVLSEVLGFKLKLHKIKIK 880 2R:1731127-2080000 1 CG3268-PA CG3268-PA FBpp0085459 AAM70823.1 138948 137385 Drosophila 0 SdhB 0 0 1563 melanogaster 2R:1731127-2080000 1 CG3283 GO:8177 GO:6099 GO:8136 FBgn0014028 CG3283 FBan0003283 Comment: This record is derived from the following: L27705 L27705.1 02-FEB-1995 AA820233 AA820233.1 25-FEB-1999 AE003790 D.melanogaster FlyBase-curated sequence: SdhB.v006 SdhB 42D1-42D1 Perfect match to SwissProt real (computational) Comment: Reference sequence of SdhB == FBgn0014028 succinate dehydrogenase (ubiquinone) activity GO:0008177 respiratory chain complex II (sensu Eukarya) GO:0005749 tricarboxylic acid cycle GO:0006099 138948 137385 0 SdhB-RA 0 partof 3b2ec0729c66fd66bb164fc91fda33ea CACTCGAAGCCGCCACGGCCACACTGCACCCTCAGTTTCGTGCAACTTTT TGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATT GCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTG GCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAG GAACCAGATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGG CGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTAC CGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGA GGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGA TCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAG GGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGC CTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACC CGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACATGAACAAC TTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCAAGAACGA AGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAGTCCGTCGAGGATC GCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTGCGCCTGCTGCTCC ACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGC CGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACT CCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGC CACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGG CCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGC CGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCT CTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCG AAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAAT TTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGA ACAAGACGCGAAAATAAATAATTGTGTATCCACCA 1235 2R:1731127-2080000 1 CG3283-RA CG3283-RA FBtr0086156 AAF57396 experimental Perfect match to REAL SP with corresponding FBgn crosby 137592 137385 0 SdhB:1 1 0 partof 207 2R:1731127-2080000 1 CG3283:1 experimental 138301 137864 0 SdhB:2 2 0 partof 437 2R:1731127-2080000 1 CG3283:2 experimental 138948 138357 0 SdhB:3 3 0 partof 591 2R:1731127-2080000 1 CG3283:3 experimental 138748 137529 0 SdhB-PA 0 producedby MLATEARQILSRVGSLVARNQMRAISNGTAQLEQQAQPKEAQEPQIKKFE IYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSC REGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDM NNFYEQYRNIQPWLQRKNEAGEKKGKAQYLQSVEDRSKLDGLYECILCAC CSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVY RCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAALHK 297 2R:1731127-2080000 1 CG3283-PA CG3283-PA FBpp0085489 AAF57396.1 predicted 138948 138947 0 0 partof 2R:1731127-2080000 1 SdhB-polyA_site-1870075..1870075 experimental 136620 136611 0 0 partof 2R:1731127-2080000 1 SdhB-misc_feature-1867739..1867747 predicted protein feature iron-sulfur cluster I 136717 136706 0 0 partof 2R:1731127-2080000 1 SdhB-misc_feature-1867834..1867844 predicted protein feature iron-sulfur cluster II 136774 136763 0 0 partof 2R:1731127-2080000 1 SdhB-misc_feature-1867891..1867901 iron-sulfur cluster III predicted protein feature 10161 6770 Drosophila 0 CG30445 0 0 3391 melanogaster 2R:1731127-2080000 -1 CG30445 FBgn0033091 FBan0030445 FBgn0050445 42C3-42C3 AE003790 CG3686 CG30445 Flag Cambridge: gene split (internal view only)::DATE:2002-02-12 17:31:32::TS:1013553092000 Not in SwissProt real (computational) aromatic-L-amino-acid decarboxylase activity GO:0004058 10161 6770 0 CG30445-RA 0 partof 42174445550811f958da68638bed9339 ACATTCGCGTCAAGGAAGCTGACCTGCAACGAGTGTGCGGTGCGAGATAA CCGGGATTCGAAAGTGATCGAGATAAGCTACTGTGTACCGTGTGAGAGCC TAGTATCCGAGCACTAGAGATACAAGCACCAAGCACCAACAGATACTTCT TAATAGACTGCAATTTATTTGAACAAGAAGATAAACGAAAAGTGTAAATT AGAGAAAATGGATGTGGAAGAGTTTCGCAAATACGGCAAGGAAGTGATTG ATTATATATGCCAATACGGCACTAATATAGAGGAGCGTGACGTGGCGCCC ACCTTGGATCCGGGTTACCTCAAAAAACTGCTACCAGCCGACGCTCCCCA GTCGCCGGAGCCGTTCAAGGACGTGCTCGAGGACTTCGAGCAGAAGATCA TGCCGGGCGTGGTGCACTGGAACCACCCCAAGTTCTTCGCCTACTTCCCC TCGGGCAACTCTTTTCCATCGGTCCTAGGCGACATGCTCAGCAGTGCCAT TGGTTCAATTGGCTTCAGCTGGGCCAGCTGTCCGGCGGCTGCCGAGCTGG AGACGATCGTGATGAACTGGTACGCCAAGGCCCTTGGCCTGCCCAAGGCC TTTGTTTCGGATGCCCCAGGCAGTACAGGCGGCGGCGCCCTTCAGGGATC CGCCTCAGAGTGCGTTCTCGTCTCTCTAATCACAGCCCGCGCCCGGGCCA TCAGCGAGCTAAAGGGTCAGACCAGCGTTCACGACAGCGTCTTCCTGCCC AGCCTGATCGCATACGCCAGCCGTGAGGCACACTCCTCCGTGGAAAAGGC CACCAAGATGGCCCTGGTGAAGCTCCGGATAATCGATGCCGACGAGCATG GACGCATGCGCGTTGACCTACTCCGCCAAGCAATTCAAAACGATGTGAAC GCCGGCTTGACACCCTTCTTTGTAGTGGCCACTGTGGGTACCACCGGCGG CTGCGCTTTCGACGACATCACGGAGATCGGAAAGGTGTGCCGCCAGGTGT CGAGCATTTGGCTGCACGTAGACGGCGCCTATGCGGGAAACTCCTTCATT CTGCCCGAGATGCGGGTCTTTTCGGCAGGACTCGAATACGCCGACTCCTT CAACACAAATCCCAACAAGCTTCTGCTGACGAACTTCGATGCCTCTGCCC TGTGGGTGCGGGATGTGATGAACCTTAAGAGCGCGCTCAACGTGAATCCC CTCTACCTACGACACGAGCACTTGACCGGAGTTGACTACCGCCACTACGG CATTCCCCTGAGTCGCCGATTCCGGGCACTCAAGCTGTGGTTCGTCTTCC GGACATACGGCATTCGGGGCCTACAGGAATACATTCGAAATCATATGGCG TTGGCTAAGAAGTTTGAGATGCTGGTGCGCAAGGATGAACGATTTGAGGT TCGCAACGATGTTCACCTTGGCCTAGTTTGCTTCCGAATGCGAACTGGCG ACGAGCCCAACCACATGCTGCTCGCCCAGATCAACCACTCGGGCAAGATG CATATGACGCCGGCCAAGTTCAACGGCCGCTACGTGATCCGCTTCTGCGT CACCTACGAGCACGCCACTGAGAAGGACATCCTGGAAGCTTGGACCCAGA TAAAGTGCTTTGCTGAGGAAATACTGCGGGACCACCAGCTGGAGTCCAGC TCCGTGCCAACCACGCCGGAAGGCTCAGAGCGGACCAGCTCAGAGCCATT GGCTCCAGTGGCGGGCAAGCCACCCATCAAAAAGAGGCTGACCAGGACAA AGTCGCTGCGATTCTCCTTCACTCGCAGCATCTCGCGGGAGCAGTACCAG AGCCAGAGCGAGCACCTAATGGACGGGTGCACACCCATCCTGGTCGTCGA TCCCAAAACTCTTCAGGAGAACTTCCAAAAGGCGGCGGATGACAATGACA GGAACAACAGCAATGGCAACGTAAAACTCAAAGATATATCAGACGTGGAT ACGGACGAGGCGAGTAACTGAGCGTCGACCCGAAAAGGGATTTGCGGATT TACCTCTACCTAGTATTAGTTGTCGAGCTGAAATGAGGCATGAATCAATC GACTACCGACTAACATTGCTCAGTTTGAATTTAAGAACATCCATTTATGT ACTAGTAGGACCTTAGTTGTTGCTGAATATCATGTAATTTAAAGATAGAC TCATTTGCATCTGCTTATACCGTTTAGCTACCTTAAGTTACTGTCATGAA CAAAAGCACTTATTTATAAACATTATCTCGGCATTTTTTATGCAAGTTTT TAAAAAATACAAACACAATCCAACGGAAAAT 2281 2R:1731127-2080000 -1 CG30445-RA CG30445-RA FBtr0086143 simonp AAM70810 Hits nothing in SP, and no SP entry corresponds to this FBgn 10161 9824 0 CG30445:1 1 0 partof 337 2R:1731127-2080000 -1 CG30445:1 8836 7731 0 CG30445:2 2 0 partof 1105 2R:1731127-2080000 -1 CG30445:2 7609 6770 0 CG30445:3 3 0 partof 839 2R:1731127-2080000 -1 CG30445:3 9954 7083 0 CG30445-PA 0 producedby MDVEEFRKYGKEVIDYICQYGTNIEERDVAPTLDPGYLKKLLPADAPQSP EPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGS IGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSAS ECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEKATK MALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCA FDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNT NPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGVDYRHYGIP LSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRN DVHLGLVCFRMRTGDEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTY EHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPLAP VAGKPPIKKRLTRTKSLRFSFTRSISREQYQSQSEHLMDGCTPILVVDPK TLQENFQKAADDNDRNNSNGNVKLKDISDVDTDEASN 587 2R:1731127-2080000 -1 CG30445-PA CG30445-PA FBpp0085476 AAM70810.2 70419 50873 Drosophila 0 l(2)01289 0 0 19546 melanogaster 2R:1731127-2080000 -1 CG9432 FBgn0033099 FBan0009432 FBgn0013956 FBgn0010482 FBgn0033098 FBgn0050444 42C6-42C7 CG30444 AE003790 Flag Cambridge: gene merge (internal view only)::DATE:2002-07-19 16:33:46::TS:1027110826000 l(2)01289 Perfect match to SwissProt real (computational) protein disulfide isomerase activity GO:0003756 plasma membrane GO:0005886 70419 56603 0 l(2)01289-RA 0 partof c78fa6b217af51d81f0321a019c74ca5 GTGGAACAAAATCTGAAGAGCAAAGAGTACAGTCCGCGGAAAACGTTCAA TTAATAGAAGCAAGAAACCACATATATAATCTAATTATTCTCGTATATAC CCCACATATATCTCGCCTGTGCATATACGAACCCCGTATATATGTATCAG TGAACAAAAAGTTGTTATACATAAAATAAATTGCGAAAGAAGAAACACCA TTATCAACTAAAAATAGTGACCGATTCTCAAAGGAATACAAATTTTAATA ACGAAAGACCCCAAACGACGAGAACGAATCAATTATACAATTATAACACT ATAAACTGTAGAACACACCAAAACGAGCAGACACGCGCACGCATGTTCGC GTTAAGGGCCTAAAGCACATCAGAACCGTAACCGATCGCAGGATGACTTT CACCCGCCTCAAGACTCTCTCGCTGCTCGTGTGTGCTCTGCTGGCCCTGA GTTTTCCCGGACATGTGAGTGGTGCAGGCAACAACAACAACAAGAAGGGC TCGCAGCCAGTGGCGCCTCCGGAGCCGGAGGCCGTCATCGAGGAGGTCAA TGCCAAGCAGCTGGAGAAGCTCCTGGCCGACAAGGATTACGTGGCCGTTT TCTGGTATGCGCGAAGCTGCGTGACCTGTGATAAGGTTTTAGCGGAACTC GAGAAAATCGACGATGACACCGACTCCTTCGGTGTGGACTTCGTGAAAAT CAACGACAAACGACTAGCCAAACAGTATGGCATCAAGAACTTCCCCGCCC TCACCTACTTCAGGGAAAAGGAGCCCATCATATATGATGGGGATCTCATG GACGAGGAAGGAGTGCTCGATTTCCTCACCTCCTTGGAGGCCATGGACTT GCCCGATCGCATCGAGGAGGTCAATGCCAAGATATTGCAGAAGATCATCG AGGACACCGACTTCGTAGCCGTTCTGTTCTACGACAAAGACCAAAAGAAA TCACAGAAAATCCTCGCAGAACTGGAAAACATCGACGATGAGTGCGATCA GAACGATATTGCCTTTGTCAAGATCGATGATGACAAGGAGGCCAAAGAAT GGGGTATCGATGAGATACCATCGATTGTACTCTTTGAACGTGGAATTCCA CACATCTACGAGGGTGATCTGATGAAAGAGGATGAGCTGCTTGGCTGGTT GGTGCACCAGAAGCGCTATTCCGAAATTCCCGAGGTCACCGATGAGATGA AGGACAAGTTGGTCGAGAACACCGAGCACTTGGCGGTTATATTCTACGAC AAGGACGATAAGCAGGATATGCGCATCCTGAACGAACTGGAGAACATTGA TGACGAGCTGGAGAAGGAGGGAATTGTCATCGTCCGCATTGATAACGCCG CTGAGGCCAAGGAATATGGTCTCGATCATTTGCCCGCCCTCATCTACTTC GAAAACAAGATCCCGGCCCTCTATGAAGGCGATCTGATGAACGAGGATGA GGTGCTCGAGTGGCTTCTTGTCCAGAAAAAGACAGCTACTATCGAGGAGG TTACCGATGAGATCCTGGTCACTCTGATCAACGAACACGAATATGTCGTC GTCTTCTTTACGGGTCCCTGCGAGCCCGGAGAGACCTGTGAGCACACTCT GAACGCCCTGGAAAGCATCGACGATGAATTGGATGAGGCTGGCATAATTT TTGTTACCACTGAGGATACCGGAATTGCCAAGAAATACAACGTCAAGACC TATCCACGTCTGGTGTTCTTCAGGAATCGTGATCCACTTCACTTTACCGG TGATCTGGACGACGAGGACGAGGTGTTGGCCTGGATTACTGACGACGAGA CCCTTGAAATTCCCGGAAAAATTGAGGAGGTCAATGTGAAGATGTTGGAC AAGATCTTGGCTGAAAACGATCACGTTGTCGTATTCTTCTACGCTGAGGG CGATAAGAAGGCCCAAAAGATCCTTAACGAGCTGGAGAACATCGATGACG AATGCGAGGAAAAAGACATTGACTTTGTAAAGACATCCGACGACGATATT GATAAGGAGTACGACCTGCCCGGTCTGCCGGCACTTGCATTTTATAGACA TAAGTTTAGAACAATTTACACCGGTGACCTGATGAAGGAAGAGGAAATTC TCGAGTGGGTTATTGATTTGCACGAGTCCACAGCTGATGTCATTGAATCT GTCGATCGTAAGACCCTGCAAGTTTTGATCAACGATGTTGAGCACCTGGC TGTGTTCTTCTACGACGATGAATGCGAATCGTGTTCCGACATCTTGGAGG AGTTGGAGAACATCGACGATGACACCGACAAGCACGGAATACAATTTGTC AAATCAAATGATGTTAAGCTGGCTCATGAAATTGGCATTTTCGCATTTCC AGCTTTGGTCTACTACGAGACCGGCGTCCCGATTATGTATGATGGTAATC TCAAAAATGAAAACCGTGTGCTGCAGTGGTTAGTCAATCAAAAGAATGAC GAATGTTTCTATGTTGGATTGGGTCATGACGGCCATTCAGCTAAGCGCGG CAACAATTTCGTGCCCAACGATTACAAACCATTCCAATGCTGTCCAACCA AATTGGAGAAGTCAACGAAAGTTCCTAAGATGACCGCCCAGCGGATCGGG CATAGCGAAGGCGATCAGGGCAAGCGTCCCAGCGGCGGCAACTTCCAGTT TGCCAACCAGGCGTCCAGCAAATCGTCCACCAAGCCAGCTGCCATCAAGA AGCAGGCCAAGCCCTCCAAGGACACCGATGACGACGATGAGGACGACGAG GACAAGCCCCTGGTCAAGGTTTCCTATGCCAACAAGCGCTCGGGAGGAAG CAACAAGCCGCAGGCTGGCAAGAAGCCGGTAGGCAAGGGCCAGGACAACG ACGACCAGTCCCAGGAGGTGGAGAAGGTATCCAAACAGAAGTCGGCGAAG AAGTCCGGCAAACTGAATGTCAAATCCGGATATCTCTCTGTGGGAGTAAG GCAACAGTTTAACTGAATGTGGATAACCACAGACAGTTAGATAGTGATTG ATTGTATGATTGAATGATATACCATACTAAAGTAGCACGTATACGCACTG TTGCCAACTGATAGAACAATTATCAAACCAAAACCAATACCAAACCCAAA ACCAAAACCAAAACAAAATACAAAACCAACTCAAACCTGTATAGCCAGCA AAAGAACCTTCAATGACAGGTTTCTATAATTAATGTACATCATCTACATA TGTGTGACTGCAAAAGACAACAACTATGACAAGAACCAACTGAAAACTGA ATTCGCAGGCTGTGTGTCCATAAAATTGAGGTTTCCTCGCACTAATCCTA AACAGTCTGGCACAAAAACATTGACTTAAATACCAATACATCTTCTGTGT CAGATCAGAACTTACTCCACACTTTTAAGCAGCGAGCCTTGGGCGTTGTT CCACGTTAAGAAGATCCACGAGTAGCAGAATCACACGATACCCGAAATAA TGAATAATGATCAAGAAAACCTACTAACTAAAACTTTGTTGATATTTTCG CTTTAACTTTCTTCAAGAGGGGCCGACCTGTGTAGGTCGTCCCCAGGTCT ATAACTAACTAAACCACACATTTGTTGCATTTTGCCAACGGATTTCAAAA AACTTTGTTCAAACTAAAAGCAATTACTTCGACAAACAACTATAAAACTT CTGAGAACTTTCGCTCGTATATTTAGTCAGCAAGCTTTGTTATTAACAAA TTAATGGGACATTGTCTTTTGTCAATAACGAACGCCTAAACTTTTTTGAT ACTACTTCTTTTTGTCGCAATATACAATTTACATTTATGTAGTTAGTCTA ATTTAAACAAGGGCCAAAGCATAGTAAACGAACGAACAAACGCATAAAAT ATTTTTTGAAACAATTTACACCTGACAGTGCACAACTGTTAGCTAATTTA ACTGAAACGTGTAACTATGAGAGCCTTCAACTTTCATAAGTTTTCATAAT AACAACATGAGGAACCATAATTTGTAACCACAACTTTTTAGAAATGTTGC AGCAGCATACAGGCCGTATACTTAATTTTGTTATGGAATCGAAAATCCAA TATTTCTCGCTGAACATGGCCTCGCATATTGTAGCTCGCCATTTTGTTTC ATTTGTTTTCTTCTGAGAGCGATTTCTGTACCGCTCGCTGTTGTTTTTGT TATCGGTATTTGAAAAATATCGAATTAGAAATCTTTATCATTATGTTTTC TTAAGCTAAAGCCTACCAATCTAAACGCAATTGTAACTAAATCCAACATA TATGTAAACAAATTTTGTTGAACAGCAGCTGATAAGTCAAGATTTTCGAA ATGGAAATTGTCAGATCGTAAAAATCAAACGCAAATCGACATAAAGCACT TTTGTAAACATAGCTCCCGAATGAAATTGTAAGAATATTTAATAAAAGCC ATCCAACTCAATAAACTTAG 4420 2R:1731127-2080000 -1 CG9432-RA CG9432-RA FBtr0086136 campbell Imperfect match to REAL SP with corresponding FBgn AAM70821 70419 69813 0 l(2)01289:1 1 0 partof 606 2R:1731127-2080000 -1 CG9432:1 68130 67973 0 l(2)01289:2 2 0 partof 157 2R:1731127-2080000 -1 CG9432:2 67902 67735 0 l(2)01289:3 3 0 partof 167 2R:1731127-2080000 -1 CG9432:3 63032 62717 0 l(2)01289:4 4 0 partof 315 2R:1731127-2080000 -1 CG9432:4 62657 62012 0 l(2)01289:5 5 0 partof 645 2R:1731127-2080000 -1 CG9432:5 61959 61776 0 l(2)01289:6 6 0 partof 183 2R:1731127-2080000 -1 CG9432:6 61709 61571 0 l(2)01289:7 7 0 partof 138 2R:1731127-2080000 -1 CG9432:7 61508 61325 0 l(2)01289:8 8 0 partof 183 2R:1731127-2080000 -1 CG9432:8 61265 61214 0 l(2)01289:9 9 0 partof 51 2R:1731127-2080000 -1 CG9432:9 58848 58365 0 l(2)01289:10 10 0 partof 483 2R:1731127-2080000 -1 CG9432:10 58095 56603 0 l(2)01289:11 11 0 partof 1492 2R:1731127-2080000 -1 CG9432:11 70027 58060 0 l(2)01289-PA 0 producedby MTFTRLKTLSLLVCALLALSFPGHVSGAGNNNNKKGSQPVAPPEPEAVIE EVNAKQLEKLLADKDYVAVFWYARSCVTCDKVLAELEKIDDDTDSFGVDF VKINDKRLAKQYGIKNFPALTYFREKEPIIYDGDLMDEEGVLDFLTSLEA MDLPDRIEEVNAKILQKIIEDTDFVAVLFYDKDQKKSQKILAELENIDDE CDQNDIAFVKIDDDKEAKEWGIDEIPSIVLFERGIPHIYEGDLMKEDELL GWLVHQKRYSEIPEVTDEMKDKLVENTEHLAVIFYDKDDKQDMRILNELE NIDDELEKEGIVIVRIDNAAEAKEYGLDHLPALIYFENKIPALYEGDLMN EDEVLEWLLVQKKTATIEEVTDEILVTLINEHEYVVVFFTGPCEPGETCE HTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLH FTGDLDDEDEVLAWITDDETLEIPGKIEEVNVKMLDKILAENDHVVVFFY AEGDKKAQKILNELENIDDECEEKDIDFVKTSDDDIDKEYDLPGLPALAF YRHKFRTIYTGDLMKEEEILEWVIDLHESTADVIESVDRKTLQVLINDVE HLAVFFYDDECESCSDILEELENIDDDTDKHGIQFVKSNDVKLAHEIGIF AFPALVYYETGVPIMYDGNLKNENRVLQWLVNQKNDECFYVGLGHDGHSA KRGNNFVPNDYKPFQCCPTKLEKSTKVPKMTAQRIGHSEGDQGKRPSGGN FQFANQASSKSSTKPAAIKKQAKPSKDTDDDDEDDEDKPLVKVSYANKRS GGSNKPQAGKKPVGKGQDNDDQSQEVEKVSKQKSAKKSGKLNVKSGYLSV GVRQQFN 857 2R:1731127-2080000 -1 CG9432-PA CG9432-PA FBpp0085469 AAM70821.2 70419 50873 0 l(2)01289-RB 0 partof c99ab4b6d7225141695836473c99d2ef GTGGAACAAAATCTGAAGAGCAAAGAGTACAGTCCGCGGAAAACGTTCAA TTAATAGAAGCAAGAAACCACATATATAATCTAATTATTCTCGTATATAC CCCACATATATCTCGCCTGTGCATATACGAACCCCGTATATATGTATCAG TGAACAAAAAGTTGTTATACATAAAATAAATTGCGAAAGAAGAAACACCA TTATCAACTAAAAATAGTGACCGATTCTCAAAGGAATACAAATTTTAATA ACGAAAGACCCCAAACGACGAGAACGAATCAATTATACAATTATAACACT ATAAACTGTAGAACACACCAAAACGAGCAGACACGCGCACGCATGTTCGC GTTAAGGGCCTAAAGCACATCAGAACCGTAACCGATCGCAGGATGACTTT CACCCGCCTCAAGACTCTCTCGCTGCTCGTGTGTGCTCTGCTGGCCCTGA GTTTTCCCGGACATGTGAGTGGTGCAGGCAACAACAACAACAAGAAGGGC TCGCAGCCAGTGGCGCCTCCGGAGCCGGAGGCCGTCATCGAGGAGGTCAA TGCCAAGCAGCTGGAGAAGCTCCTGGCCGACAAGGATTACGTGGCCGTTT TCTGGTATGCGCGAAGCTGCGTGACCTGTGATAAGGTTTTAGCGGAACTC GAGAAAATCGACGATGACACCGACTCCTTCGGTGTGGACTTCGTGAAAAT CAACGACAAACGACTAGCCAAACAGTATGGCATCAAGAACTTCCCCGCCC TCACCTACTTCAGGGAAAAGGAGCCCATCATATATGATGGGGATCTCATG GACGAGGAAGGAGTGCTCGATTTCCTCACCTCCTTGGAGGCCATGGACTT GCCCGATCGCATCGAGGAGGTCAATGCCAAGATATTGCAGAAGATCATCG AGGACACCGACTTCGTAGCCGTTCTGTTCTGTCCAGATCATGAAACATGC CCGCCCAGGGTTATGGACAAACAGCAATGCCGCAAGTGCGCCAAGGCCTT GCAGGAGCTGGAGAATATCGACGACGAAGCTGACCAGCTGGGCATCGGGT TTGTGAAGATACACGACGAGGCCTTGGCCGACGAATACAATCTAGGCAAT CTGCCAGCCTTGGTCTATTACCGCCACCAGACTCCGATCATATACGAAGG TGAACTTCAGCGGGAGGAGGACGTCTTGGAATGGTTGGTGCAGAATAAGT CGACGGGCGATGAAGATGATGTGATTGAAGACGTCACTTCGAAGACTCTG TCGACGCTGATCAGCAATATCGACAATCTGGTTGTGCTGTTTTATGATCA TGGAAACGACGACTCGATGACCGTGTTAGAGGAGCTAGAGCAAATCGACG ACGACTGCGACAAGCATGGCATTCAGTTTGTGAAAATCGACGATGCCAAG GCGGCAGCCGATTACGGAATCGATTCGATTCCGGCCATTGTTTACTTTGA AAAAGAAATTCCAAATGTGTACGACGGCGATCTCATGGACGAGGAGCAGA TTCTGAAATGGTTGTTGGGACAGTTGGAACGGGATGAGATCGAGGACGTC ACCGACGAAATGCTCGATACAATGATCAAAGAAGGACGCGTCATTGCCGT GCTGTTCTACGACAACAACGACAAGAAGTCCCAGAAAGTGCTCGAGGAGC TGGAGAACATTGACGACGAGTGCGACGCATTGGGCATTACTTTCGTGAAG ATCGACAATCCCGAGGAGGCCGTTGAATATGGCATCAATAAAGTTCCTAA ACTGATATACTTTGAAAAAGGCATTCCAACTATTTACGAGGGCAATCTGG AGGACGAGGAGAAGCTTCTGAAATGGCTAACAGACCAAACGAGTTCCGAT CAAATCGAGGACATCACCGACGAAATGTTGGACTTAATCATTGAGAAAAT GCCCCATGTTGCTGTTCTTTTCTACGACAAAGACCAAAAGAAATCACAGA AAATCCTCGCAGAACTGGAAAACATCGACGATGAGTGCGATCAGAACGAT ATTGCCTTTGTCAAGATCGATGATGACAAGGAGGCCAAAGAATGGGGTAT CGATGAGATACCATCGATTGTACTCTTTGAACGTGGAATTCCACACATCT ACGAGGGTGATCTGATGAAAGAGGATGAGCTGCTTGGCTGGTTGGTGCAC CAGAAGCGCTATTCCGAAATTCCCGAGGTCACCGATGAGATGAAGGACAA GTTGGTCGAGAACACCGAGCACTTGGCGGTTATATTCTACGACAAGGACG ATAAGCAGGATATGCGCATCCTGAACGAACTGGAGAACATTGATGACGAG CTGGAGAAGGAGGGAATTGTCATCGTCCGCATTGATAACGCCGCTGAGGC CAAGGAATATGGTCTCGATCATTTGCCCGCCCTCATCTACTTCGAAAACA AGATCCCGGCCCTCTATGAAGGCGATCTGATGAACGAGGATGAGGTGCTC GAGTGGCTTCTTGTCCAGAAAAAGACAGCTACTATCGAGGAGGTTACCGA TGAGATCCTGGTCACTCTGATCAACGAACACGAATATGTCGTCGTCTTCT TTACGGGTCCCTGCGAGCCCGGAGAGACCTGTGAGCACACTCTGAACGCC CTGGAAAGCATCGACGATGAATTGGATGAGGCTGGCATAATTTTTGTTAC CACTGAGGATACCGGAATTGCCAAGAAATACAACGTCAAGACCTATCCAC GTCTGGTGTTCTTCAGGAATCGTGATCCACTTCACTTTACCGGTGATCTG GACGACGAGGACGAGGTGTTGGCCTGGATTACTGACGACGAGACCCTTGA AATTCCCGGAAAAATTGAGGAGGTCAATGTGAAGATGTTGGACAAGATCT TGGCTGAAAACGATCACGTTGTCGTATTCTTCTACGCTGAGGGCGATAAG AAGGCCCAAAAGATCCTTAACGAGCTGGAGAACATCGATGACGAATGCGA GGAAAAAGACATTGACTTTGTAAAGACATCCGACGACGATATTGATAAGG AGTACGACCTGCCCGGTCTGCCGGCACTTGCATTTTATAGACATAAGTTT AGAACAATTTACACCGGTGACCTGATGAAGGAAGAGGAAATTCTCGAGTG GGTTATTGATTTGCACGAGTCCACAGCTGATGTCATTGAATCTGTCGATC GTAAGACCCTGCAAGTTTTGATCAACGATGTTGAGCACCTGGCTGTGTTC TTCTACGACGATGAATGCGAATCGTGTTCCGACATCTTGGAGGAGTTGGA GAACATCGACGATGACACCGACAAGCACGGAATACAATTTGTCAAATCAA ATGATGTTAAGCTGGCTCATGAAATTGGCATTTTCGCATTTCCAGCTTTG GTCTACTACGAGACCGGCGTCCCGATTATGTATGATGGTAACATTGCAAG CAATCAGGACGTCTTCAACTGGATTCTCGAACAGAAGGCCGACCAAAGCA TTCAACTCATTAATCGTGACCAACTTTTCGAGTATATAGGCACCAAAGAC TTTTTAGCGGTTGTTTTTTACAAAGAAGATGATCCCGACTCGCCACGAGT GCTGCGGCACATCGAACTAATCGACGACGAGGCTGCGGAATATGGCATTT ACATAGTGAAGATGCACGACAAACTGATGGCCAAGAAGTACGGCTTCCGG AATCCCCCAGGACTGACGTATTTCCGAAAGGGCAAGTATATCAACTACGA CGGCGATATCGATGACGAGGAGGAGGTACTGGACTGGCTAACGAGCCCGG CCAACATGGAGATGACCGATCACATCGAGCAGGTTAACCGCAAGATGTTC GAGAAGATCCGCAAGAACTCCGACTACGTAGCGGTGATATTCTATAGCGA TGAGTGCAAGCAGTGTCCTCGCGTCCTGGCCGAGGTGGAACACATAGACG ACGAAGCGGACAAGGCTGGTATCGACTTCGTCAAAATCGACGATAAGCAG ATGGCCAAGGAGTACGGAGTGTTCGCCCTGCCTGCCATTGTCTTCTTCAA GCCCACATCCAAGGAGCCAGTTATATACGCCGGTGATCTTTACGAAGAAG AACAGATCCTAACTTGGCTGATCACGCAAAAGGATCCAAGTGGAGATGTT ATCGAAGATCTCGAAGGCGAAAGACTTGTTCATCTGATTGAAGAGTCTGG CTCCATCGCAGTCTACTTTTATGCGGATGGCTGCGAGCAGTGCACCAAGG TTTTGGAGGAGTTGGAAAACATCGATGATGATTGCGACAAGCATGGCATA ACATTCGTTAAGACCAGGGACTTCTCTGTGGCCGACGGCTATGGCGTGCA CGAGTATCCGGCTCTAGTTTACTTCGAGGGAGGAATCCCCAACGTATTCG AGGGCGAATTGAGCGAGGAGGAAGAGGTTCTTCAGTGGCTTATCACCCAG AAGACCGAAGATCGTATTGAGCTGATCACTCGCCAGATGCTGGAGACAAT GGTGGAGGAGACGCAGTACCTAGCCGTGTATTTCTACAAAATCAACTGCA ACATATGCGACCAGATACTAGAGGGCTTGGAACTGATCGATGACGAATGC GACGTGTTCGGAATTCATATGGTCAAGATCCAGGATCCGCAGCTGGCAAA ACGTTACTCGATCAAGACTTTCCCGGCGTTGGTTTATTTCAGAAATGGAA ACCCATTACTGTTTGAGGGGGATCTTCAGAACGAGCAATCAGTATTGGAA TGGCTCATCGATGATGACAACCGCGAGCTGGCTGATGAAATCGAGGAGGT CAACGAGCGTATGCTGGATCGCCTAATGGCGGAGTCCACTCTATTGGTTG TTTTCTTTTACGACGATGATTGTGCTGAGTGCGAGGAGATTTTGGAAGAG CTGGAGGAGATCGATGGTGAGGCAGACATGTTCGGCATTGATTTCGTAAA GATTGCTAGTATCCAGGCAGCCAAGAAATACGAGATAGTGAATATACCTT CCCTCGTTTATTTCCGAAAACAAGTGCCCGTCCTCTACGACGGCGATCTA CACCAACACGACAAGGTGATTACCTGGCTAACATCACAGGACGTATTCGA AATCAAAAACGAAATAGAAGAAGTAAACCGAAAAATGCTCGACAAACTAC TCGAGGAAAATGAGTTCTTAGCCGTTTTTTTCTACGAACACAATCAGCCG GACAGTACTGCAGCGCTGGAAAAACTCGAAAACATCGACAGCGAGACGGA TAACCTGGACATCACCTTCGTCAAGATGGCCGACTCTCGTTATGCCAAGA AATGGGGCGTCACCAAGCTGCCGGCAATGGTCTACTTCCGCCGTCGGTTT CCCAGCATATATAGGGGTGATCTGTTATCCGAGGACGAAGTGCTGGAGTG GCTACGCAAGAACCGCTTCCGCCAGCCCGAGCTGAACATCTTTATGTACG CTCTGATTGCTCTGGCGGTGGCCTTTGTGGTCTACACCGCCTTCCTGCTG CAGTGCTTCAAGCCGGCGCCACCGCCTCCTGTCCAGCACCCCAAGCAGTC TTGAATGGTATGGGTTGGGGAATCGGGAAGAATGTACTGAATCACGTTGA ACGGCTGTCAACTACGATGGAGGGTTTTCGACAAGACACACAAAAGCGAG CGAACCAAACTTGAAATGATTATCCAAAGTCACAATAATACACGCATATC TATGCACATTAAACTGTCATCCAATCGTCTAAATTAGACGCATGAAAACC ACTTGTCTGGAGACAATCCATTGCTTTTGAAATATCTTTTGAGACAACTT GATAACTTTGATAAACTCTGATGCTTCCATTAATATCAAAACTCATGTAT GTCACATTTACACATTTATTTGTCTTCTCACCCGTGTACATCATGGAAAT CAATTACAGAAGAACACTATCAAGTCATAGTAATTACGTTAAATTTAAAT TTAAACGCCATAATATTGTGTAATAAATGTCAATAATAATTTTTACAGTA ACTTATTTACGGCCTATGATACTTAATAAACTATTGGATGATGTAT 5996 2R:1731127-2080000 -1 CG9432-RB CG9432-RB FBtr0086137 mhuang Perfect match to REAL SP with corresponding FBgn AAN16126 70419 69813 0 l(2)01289:1 1 0 partof 606 2R:1731127-2080000 -1 CG9432:1 68130 67973 0 l(2)01289:2 2 0 partof 157 2R:1731127-2080000 -1 CG9432:2 67902 67735 0 l(2)01289:3 3 0 partof 167 2R:1731127-2080000 -1 CG9432:3 67304 67268 0 l(2)01289:13 4 0 partof 36 2R:1731127-2080000 -1 CG9432:13 64686 64503 0 l(2)01289:14 5 0 partof 183 2R:1731127-2080000 -1 CG9432:14 64373 64229 0 l(2)01289:15 6 0 partof 144 2R:1731127-2080000 -1 CG9432:15 64167 64033 0 l(2)01289:16 7 0 partof 134 2R:1731127-2080000 -1 CG9432:16 63969 63788 0 l(2)01289:17 8 0 partof 181 2R:1731127-2080000 -1 CG9432:17 63717 63402 0 l(2)01289:18 9 0 partof 315 2R:1731127-2080000 -1 CG9432:18 63032 62717 0 l(2)01289:4 10 0 partof 315 2R:1731127-2080000 -1 CG9432:4 62657 62012 0 l(2)01289:5 11 0 partof 645 2R:1731127-2080000 -1 CG9432:5 61959 61776 0 l(2)01289:6 12 0 partof 183 2R:1731127-2080000 -1 CG9432:6 61709 61571 0 l(2)01289:7 13 0 partof 138 2R:1731127-2080000 -1 CG9432:7 61508 61325 0 l(2)01289:8 14 0 partof 183 2R:1731127-2080000 -1 CG9432:8 56163 56031 0 l(2)01289:19 15 0 partof 132 2R:1731127-2080000 -1 CG9432:19 55802 55478 0 l(2)01289:20 16 0 partof 324 2R:1731127-2080000 -1 CG9432:20 55414 55225 0 l(2)01289:21 17 0 partof 189 2R:1731127-2080000 -1 CG9432:21 55167 55029 0 l(2)01289:22 18 0 partof 138 2R:1731127-2080000 -1 CG9432:22 53797 53614 0 l(2)01289:23 19 0 partof 183 2R:1731127-2080000 -1 CG9432:23 53562 53430 0 l(2)01289:24 20 0 partof 132 2R:1731127-2080000 -1 CG9432:24 52683 52526 0 l(2)01289:25 21 0 partof 157 2R:1731127-2080000 -1 CG9432:25 52469 52302 0 l(2)01289:26 22 0 partof 167 2R:1731127-2080000 -1 CG9432:26 52239 52082 0 l(2)01289:27 23 0 partof 157 2R:1731127-2080000 -1 CG9432:27 52029 51862 0 l(2)01289:28 24 0 partof 167 2R:1731127-2080000 -1 CG9432:28 51802 51619 0 l(2)01289:29 25 0 partof 183 2R:1731127-2080000 -1 CG9432:29 51553 50873 0 l(2)01289:30 26 0 partof 680 2R:1731127-2080000 -1 CG9432:30 70027 51368 0 l(2)01289-PB 0 producedby MTFTRLKTLSLLVCALLALSFPGHVSGAGNNNNKKGSQPVAPPEPEAVIE EVNAKQLEKLLADKDYVAVFWYARSCVTCDKVLAELEKIDDDTDSFGVDF VKINDKRLAKQYGIKNFPALTYFREKEPIIYDGDLMDEEGVLDFLTSLEA MDLPDRIEEVNAKILQKIIEDTDFVAVLFCPDHETCPPRVMDKQQCRKCA KALQELENIDDEADQLGIGFVKIHDEALADEYNLGNLPALVYYRHQTPII YEGELQREEDVLEWLVQNKSTGDEDDVIEDVTSKTLSTLISNIDNLVVLF YDHGNDDSMTVLEELEQIDDDCDKHGIQFVKIDDAKAAADYGIDSIPAIV YFEKEIPNVYDGDLMDEEQILKWLLGQLERDEIEDVTDEMLDTMIKEGRV IAVLFYDNNDKKSQKVLEELENIDDECDALGITFVKIDNPEEAVEYGINK VPKLIYFEKGIPTIYEGNLEDEEKLLKWLTDQTSSDQIEDITDEMLDLII EKMPHVAVLFYDKDQKKSQKILAELENIDDECDQNDIAFVKIDDDKEAKE WGIDEIPSIVLFERGIPHIYEGDLMKEDELLGWLVHQKRYSEIPEVTDEM KDKLVENTEHLAVIFYDKDDKQDMRILNELENIDDELEKEGIVIVRIDNA AEAKEYGLDHLPALIYFENKIPALYEGDLMNEDEVLEWLLVQKKTATIEE VTDEILVTLINEHEYVVVFFTGPCEPGETCEHTLNALESIDDELDEAGII FVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWITDDE TLEIPGKIEEVNVKMLDKILAENDHVVVFFYAEGDKKAQKILNELENIDD ECEEKDIDFVKTSDDDIDKEYDLPGLPALAFYRHKFRTIYTGDLMKEEEI LEWVIDLHESTADVIESVDRKTLQVLINDVEHLAVFFYDDECESCSDILE ELENIDDDTDKHGIQFVKSNDVKLAHEIGIFAFPALVYYETGVPIMYDGN IASNQDVFNWILEQKADQSIQLINRDQLFEYIGTKDFLAVVFYKEDDPDS PRVLRHIELIDDEAAEYGIYIVKMHDKLMAKKYGFRNPPGLTYFRKGKYI NYDGDIDDEEEVLDWLTSPANMEMTDHIEQVNRKMFEKIRKNSDYVAVIF YSDECKQCPRVLAEVEHIDDEADKAGIDFVKIDDKQMAKEYGVFALPAIV FFKPTSKEPVIYAGDLYEEEQILTWLITQKDPSGDVIEDLEGERLVHLIE ESGSIAVYFYADGCEQCTKVLEELENIDDDCDKHGITFVKTRDFSVADGY GVHEYPALVYFEGGIPNVFEGELSEEEEVLQWLITQKTEDRIELITRQML ETMVEETQYLAVYFYKINCNICDQILEGLELIDDECDVFGIHMVKIQDPQ LAKRYSIKTFPALVYFRNGNPLLFEGDLQNEQSVLEWLIDDDNRELADEI EEVNERMLDRLMAESTLLVVFFYDDDCAECEEILEELEEIDGEADMFGID FVKIASIQAAKKYEIVNIPSLVYFRKQVPVLYDGDLHQHDKVITWLTSQD VFEIKNEIEEVNRKMLDKLLEENEFLAVFFYEHNQPDSTAALEKLENIDS ETDNLDITFVKMADSRYAKKWGVTKLPAMVYFRRRFPSIYRGDLLSEDEV LEWLRKNRFRQPELNIFMYALIALAVAFVVYTAFLLQCFKPAPPPPVQHP KQS 1703 2R:1731127-2080000 -1 CG9432-PB CG9432-PB FBpp0085470 AAN16126.1 5527 4847 Drosophila 0 CG17266 0 0 680 melanogaster 2R:1731127-2080000 -1 CG17266 GO:3734 GO:6371 GO:5681 GO:3755 FBgn0033089 FBan0017266 42C3-42C3 Not in SwissProt real (computational) AE003790 CG17266 peptidyl-prolyl cis-trans isomerase activity GO:0003755 small nuclear ribonucleoprotein complex GO:0030532 spliceosome complex GO:0005681 nuclear mRNA splicing, via spliceosome GO:0000398 5527 4847 0 CG17266-RA 0 partof 19b2e6ee7eccea8c9c34eee1370a1cbb GCTTAGTAAAATCTTAATCTTGACTTGTTAGAAAGTTTATAAACAAATAA AATAATTTTAAAATGCCTAACTGGAATCAAATACAGTCCCAACTGAGAAG CTCCAACAATCCCGTCGTTTTCTTCGACATTGCCGTAGGCACAACGGAAA TCGGACGAATGATATTCGAACTCTTTGCGGACACAGTGCCCCGCACGGCG GAAAACTTCCGGCAGTTCTGCACGGGCGAGTACCGACCGGATGGCGTTCC CATTGGCTACAAAGGCGCCAGTTTCCATCGGGTGATCAAGGACTTCATGA TCCAGGGCGGCGACTTTGTGCAGGGCGACGGCACCGGCGTGACCAGCATA TACGGCAACACCTTCGGCGACGAGAACTTTACCCTGAAGCACGACTCGCC CGGCCTCCTTTCCATGGCAAACAGTGGCAAGGAGACGAACGGCTGCCAAT TCTTTATCACCTGCGCCAAGTGCAACTTTTTAGACGGAAAGCACGTGGTG TTCGGTCGGGTTCTGGATGGACTGCTCATCATGCGCAAGATCGAGAACGT GCCCACGGGCCCCAATAACAAGCCGAAGCTCCCAGTGACCATTTCGCAGT GCGGGCAAATGTAG 614 2R:1731127-2080000 -1 CG17266-RA CG17266-RA FBtr0086144 pavel AAM70809 Perfect match to HYPO SP record with corresponding FBgn 5527 5381 0 CG17266:1 1 0 partof 146 2R:1731127-2080000 -1 CG17266:1 5315 4847 0 CG17266:2 2 0 partof 468 2R:1731127-2080000 -1 CG17266:2 5465 4850 0 CG17266-PA 0 producedby MPNWNQIQSQLRSSNNPVVFFDIAVGTTEIGRMIFELFADTVPRTAENFR QFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNT FGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRV LDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 183 2R:1731127-2080000 -1 CG17266-PA CG17266-PA FBpp0085477 AAM70809.1 144597 140794 Drosophila 0 CG3287 0 0 3803 melanogaster 2R:1731127-2080000 1 CG3287 FBgn0033106 FBan0003287 FBgn0028954 Not in SwissProt real (computational) 42D1-42D1 AE003790 BEST:LD11166 transcription, RNA-dependent GO:0006410 regulation of transcription from Pol II promoter GO:0006357 transcription from Pol II promoter GO:0006366 cell cycle GO:0007049 nucleobase, nucleoside, nucleotide and nucleic acid metabolism GO:0006139 144580 140794 0 CG3287-RB 0 partof 46a5f11335218df324ce0330001ed7f6 TCATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGA CGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCAT ATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATAT TACTAAGGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATA CCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGAT CGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTG CACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCAAACGATAATAGA GGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGT TCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCC AAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAA GCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGA CCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAAC GGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTA CAGGGATGCTGGTGAATACTGGAACAAAACTCCCAAGACGGACTATACCT ACTCAGAACTGTCCCCTCACCGACGCCAGTTGGCGCCAGGAATTGTGGCC ATGCCCAATATGTCCAGAAAGAGCCTAGAGAACCATAACGATCGAGTCAA CTACATGGTCCAGCAGAACCCTGCGCAAGAGGAGTTCATCCGCCGCCGCT ACCAGTCCAAGTATACCCAGCAGGTTAACTATGACTCCGCAGATGAACTG GACGCCACATTTGGGCAGCAAAAGCAGAGCTGGTGGCTTATCCGCCTCAT CCAACTGGTTGTTAGCAGCATTACCACCGTGTGGAGTCGGGTGACCAATC TCTCGGCCACGGAGACGACTGCCTATCAAAACTACCACGCTAAGCGCCAG CAGAGTCAACAAGTTGGACTTTGGTGGAAAATAGTACAGACCATCGGAGG AGGACTTGCAAGTTTGCTGCGCTACCTGTATGTTTTCATCGGATCGGTGC TGAGTTTGGACACGTGGTTGCTGCGATCCTCGGATGCGGAAAACAAGTCG AAAAAGCGCTTCCTCATATTTCTGCTGATTTTGTTGCCCTTGCTGCTGCT GTCGGGTCTGTTCTATTACATACACCCCAATGAAACTTTCCCACCCAAAT CCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTG AAAGACTACCTGAACCAGGAGCAGTTCGAATCGCTACGCTCTCAGGCCGC CGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACT TGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAG GGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGG CAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTG CACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAA TAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCG CACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAA CCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATG CAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATT GTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCG TTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAA CGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAA ATAAATCGCAAACAATTTCATATG 2024 2R:1731127-2080000 1 CG3287-RB CG3287-RB FBtr0086157 Perfect match to HYPO SP record with corresponding FBgn AAG22207 campbell 140950 140794 0 CG3287:1 1 0 partof 156 2R:1731127-2080000 1 CG3287:1 141858 141676 0 CG3287:2 2 0 partof 182 2R:1731127-2080000 1 CG3287:2 142891 142555 0 CG3287:3 3 0 partof 336 2R:1731127-2080000 1 CG3287:3 143528 142947 0 CG3287:4 4 0 partof 581 2R:1731127-2080000 1 CG3287:4 144580 143811 0 CG3287:5 5 0 partof 769 2R:1731127-2080000 1 CG3287:5 144086 141703 0 CG3287-PB 0 producedby MSENTYQIETRRRSRSKTPFLRSSCDHENCEHAGEEGHVHHLKRKSAAPN VQTIIEEHIVESSISKKTRAKAFAQLTSDYSSDDMTPDAKRKQNSITATV TSILTKRSGGATSTPRNRSQLETTQNTLNSAQEKLNQSNGNLSSGNVSDY LAYIEYRDAGEYWNKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLEN HNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSW WLIRLIQLVVSSITTVWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKI VQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKRFLIFLLIL LPLLLLSGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFES LRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV 449 2R:1731127-2080000 1 CG3287-PB CG3287-PB FBpp0085490 AAG22207.2 144597 140796 0 CG3287-RC 0 partof a7ab23af0d47036c6daf2ee8a5bb4d9b ATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACG GTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATAT CCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTA CTAAGTATGTCACATATTTGCGGGCAAACTGCCGAAAGCACTGTGCGGAG TTTTTGTTTGTGTGCGTGCGTGCCTCATTTTTACATTCACGTACATACAT ATGTACATATATGTACGCTATGACGCAGCTGTGGAAAACTTGTTTGGGTT TCCATTTCACCGAATCACGGAATCAACGAATATTTGCGCCTGTGCTGCGA ACTCATTTTGGGCAGTAAGCCATTGTATTGATTATCGCGCGTTGTTTGTG GATGGCGTGGTCCGCCGGAGCACCCTGTAGCGTCTACATCCCTACCCCGC TCCCTGGAGTCCGATATCTGTGCGCGAAAGGCCGGGCGGGCGTCGTTTTC GGCTATGTGGCCCAACACCAATGGATCCCCACGGTCACTGGCAGCAATTC GCGATCCGAAATGCTCCGCCCTATTTTTAGACGCGGTCTTTGCGGCCTGC CTACTTACCTACCTCCCCAATGCATTCTAATTAAAAACCGGGCACTGCGC TCATTTCCACACGCATTGCATTGCATAATGCGGCATTAATGTGGCGGGGA AAGCTCGCTTCGGAAAGCACTCGAGCATTGAAGTGAAGAGACCGAATGTT TTCCAGCTGCCCAATTGTAAACAACCCACGCCTAGCACGCACACACACGC ACACGCACACACACACAGACTGGTTTTAATGTTTACTCCAAATAAATCGT TGCCCATGTTAATTATTTGTGTCTTCGCAGGGCCCGAGCACTGGAGGGAA TCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGC GTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAG CACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGC CCCCAATGTGCAAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCA GTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCG AGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGC CACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACAC CGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCC CAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAG CGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAACA AAACTCCCAAGACGGACTATACCTACTCAGAACTGTCCCCTCACCGACGC CAGTTGGCGCCAGGAATTGTGGCCATGCCCAATATGTCCAGAAAGAGCCT AGAGAACCATAACGATCGAGTCAACTACATGGTCCAGCAGAACCCTGCGC AAGAGGAGTTCATCCGCCGCCGCTACCAGTCCAAGTATACCCAGCAGGTT AACTATGACTCCGCAGATGAACTGGACGCCACATTTGGGCAGCAAAAGCA GAGCTGGTGGCTTATCCGCCTCATCCAACTGGTTGTTAGCAGCATTACCA CCGTGTGGAGTCGGGTGACCAATCTCTCGGCCACGGAGACGACTGCCTAT CAAAACTACCACGCTAAGCGCCAGCAGAGTCAACAAGTTGGACTTTGGTG GAAAATAGTACAGACCATCGGAGGAGGACTTGCAAGTTTGCTGCGCTACC TGTATGTTTTCATCGGATCGGTGCTGAGTTTGGACACGTGGTTGCTGCGA TCCTCGGATGCGGAAAACAAGTCGAAAAAGCGCTTCCTCATATTTCTGCT GATTTTGTTGCCCTTGCTGCTGCTGTCGGGTCTGTTCTATTACATACACC CCAATGAAACTTTCCCACCCAAATCCCTGTCCGAATACACATTCACCCTA CCTGAGTTGCCCAAAATCGATGTGAAAGACTACCTGAACCAGGAGCAGTT CGAATCGCTACGCTCTCAGGCCGCCGAGCATGCGGTCCGCGTTCGCGATT GGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTC AACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCG TGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGA TCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTC TTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCC GTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCG TCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTA ACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGG ATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTC ATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAAC TAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTT TGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAA ACATCAAGTACAAAG 2765 2R:1731127-2080000 1 CG3287-RC CG3287-RC FBtr0086158 Perfect match to HYPO SP record with corresponding FBgn AAM70833 campbell 141858 140796 0 CG3287:6 1 0 partof 1062 2R:1731127-2080000 1 CG3287:6 142891 142555 0 CG3287:3 2 0 partof 336 2R:1731127-2080000 1 CG3287:3 143528 142947 0 CG3287:4 3 0 partof 581 2R:1731127-2080000 1 CG3287:4 144597 143811 0 CG3287:7 4 0 partof 786 2R:1731127-2080000 1 CG3287:7 144086 141703 0 CG3287-PC 0 producedby MSENTYQIETRRRSRSKTPFLRSSCDHENCEHAGEEGHVHHLKRKSAAPN VQTIIEEHIVESSISKKTRAKAFAQLTSDYSSDDMTPDAKRKQNSITATV TSILTKRSGGATSTPRNRSQLETTQNTLNSAQEKLNQSNGNLSSGNVSDY LAYIEYRDAGEYWNKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLEN HNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSW WLIRLIQLVVSSITTVWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKI VQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKRFLIFLLIL LPLLLLSGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFES LRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV 449 2R:1731127-2080000 1 CG3287-PC CG3287-PC FBpp0085491 AAM70833.1 3120 806 Drosophila 0 CG3194 0 0 2314 melanogaster 2R:1731127-2080000 -1 CG3194 FBgn0033087 FBan0003194 42C3-42C3 DGC clone SD14112 appears problematic: incomplete CDS::DATE:2002-03-11 14:08:41::TS:1015873721000 CG3194 Not in SwissProt real (computational) AE003790 3120 806 0 CG3194-RA 0 partof 2d9574afadc0a853138d2b24a3835773 CTGTATCGCAGTTTCTGTGTTTTCGCAGTGTTCGCCCATTAAAGCGAGAA GAGCAGCGCAAATCTAAGCAAAATATGCTTAGTGAGAACTGGATGCACTT GAAATATCAACTTTGGATGGCCCTGGACTGAACTCAGAGGGCTACAGGCT CGGCAGGTGGAATTTTAGACAGAGACAGTGAAAGAGACGTACGCGTACTG GTGCACCATTATCATCGTCAGCAATGCATCTGCCAGATGAATGCAGTTTT AAATTTAGAGCATGACTCACCTAGAAGCCAGTTAGAGAGTTCGCCCCCAA CCGAATGTCCAAATATCTAAGCAGTCAGAGAGATGCCCTTTCCGCACCCG CGCTTCCAGTAAGCAGGGAAAACCGGGAGCCACCTAAATTCCAAGGGGTA AAGCAACGCGAGCCACTGGTCTTTTTCATCATGCGACTGAACCTAAAAGC CGTGCTGCTTGTCCTCACAGTGGCTGTGGTGGTAATCACTCTGGGCGTGT ATATGCGCTGCGCCGCCTTCTCCTTTTCGCCGGACTTTGTGCGTCCTCTG GACCGGTCCGCAAGGCAGTCCTCCAGCGGAGGAGAAGCTACAGCGCTGCA CGACATTGAGTGCTCCATTAACCAGGAGTACACCGTGCACTGCAAGCGAG ACGAGAACGCCAACGAGGTTTACGTTCCGTTTTCCTTCCTGCGTAACTAC TTCGACGTCAGTGGAGCAGTTTCCACCAACAGCAATGAGGTGGCCAAGTT CAACTGGGTGCACAGCACAGCCAAAGTTAACCTTCCCAGGGGAAAGTACG ATGCGCGCGGCGTCTATATGTACTTTGAGAACTACAACGTGGAAGTGCGC GACCGGGTAAAGTGCATCAGTGCCGCGGAGGGCGTTCCAGTGAGCACGCA ATGGGAGAAGCGTGGGTACTTTTACCCCACACAAATTGCCCAGTTCGCGT TGTCGCACTACAGCAAGAACCTCACAGAGCCGGCACCCAGGGTTCGCGTG TTGGAGGACGGCGACGGGAACCAGATGGAATGGAGTACGCCCAAGACCAG CAACATGACCCGCATCTGGCACCACAAGTTTAACACCAGTGTTGTCCAGT TCGAGACGGCACCTGGTTACGAAGGCGTCATCAGCATTGCTCTAAACCAG ACATTGGATCTTCTGCTCAGCGTTGATCTGCTCCTGGTAACCAATAGCAG TAGTCTCATGATTACCGTTCAGAATCGGGACACCCGTCACAACTACAGCC TGCACTACATACCCGCAGATCTGCTGCTGAGCGTGCAGGATACAAACATC TACTACGGTCTGGGAGGCTCGGCACTGAACAAGTGGCGCCACATCACTCG AGACCTGCACATTGACCTTCAAAAGGGCATCATGGGTGACAAACGCTCGC CGCTAAAGATACGGCGCTCCGATCTGGAGGTAATATCTATTGGCTTTCTG GGCCTTGGCTTCTTCGACAATATCACCTTGTCCACCAGTGACCATCTGGC TCACTTCTACGACGCGGCTGAGTGGTTCGTCCACAACCAGGACCCCAAGA CGGGTGGCTGGACCAATCCTGTGCGTCGCAGCCTCAACGGCTTTGCCGAA TTGCGTCCGGGGTGGATATCAGCCATGGGCCAGGGACACGCTATTTCAGT GCTGGCACGAGCCTACTGGCACTCCGGCGGGGATGAACGCTACCTTCGAG CGGCCGCAGCCGGACTGCAGCCTTATAGGGTATACTCGCGCGATGGCGGC GTTCTGGCGCAGTTCATGGACAAGTTCTACTGGTACGAGGAGTACCCCAC CACGCCACCCTCTTATGTGCTAAACGGCTTTATCTATTCACTGCTGGGTC TCTACGATCTCAACAGCACTGCCCCGGGAAAAATCGCCCGCGAGGCTGGA AAGCTTTTCGCGCAGGGCATGCACTCCCTTAAAAAGATGCTGTTGCTATT TGACACTGGCTCCGGCACCAGCTACGACCTGCGCCATCTGAGCCTGGGCG TAGCTCCTAATCTGGCGCGCTGGGACTACCATGCAACGCACGTGAACCAG TTACTTCTGTTAGCCACCATCGACAGCGATCCATTAATTGCACAAACTGC GGAGCGCTGGAAGGGCTATATGTTTGGTCGTCGGGCCAAGCACAACTGA 2149 2R:1731127-2080000 -1 CG3194-RA CG3194-RA FBtr0086145 Perfect match to HYPO SP record with corresponding FBgn pavel AAM70806 3120 2717 0 CG3194:1 1 0 partof 403 2R:1731127-2080000 -1 CG3194:1 2661 1282 0 CG3194:2 2 0 partof 1379 2R:1731127-2080000 -1 CG3194:2 1173 806 0 CG3194:3 3 0 partof 367 2R:1731127-2080000 -1 CG3194:3 2816 809 0 CG3194-PA 0 producedby MSKYLSSQRDALSAPALPVSRENREPPKFQGVKQREPLVFFIMRLNLKAV LLVLTVAVVVITLGVYMRCAAFSFSPDFVRPLDRSARQSSSGGEATALHD IECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFN WVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQW EKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLEDGDGNQMEWSTPKTSN MTRIWHHKFNTSVVQFETAPGYEGVISIALNQTLDLLLSVDLLLVTNSSS LMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRD LHIDLQKGIMGDKRSPLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAH FYDAAEWFVHNQDPKTGGWTNPVRRSLNGFAELRPGWISAMGQGHAISVL ARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYWYEEYPTT PPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFD TGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAE RWKGYMFGRRAKHN 614 2R:1731127-2080000 -1 CG3194-PA CG3194-PA FBpp0085478 AAM70806.1 146780 144834 Drosophila 0 CG18584 0 0 1946 melanogaster 2R:1731127-2080000 1 CG18584 FBgn0033107 FBan0018584 42D1-42D1 AE003790 Not in SwissProt real (computational) CG18584 146780 144834 0 CG18584-RA 0 partof 8791a88f68a81b94eefa125057386f4c GATGGTTGCTCTTGCAGGAGGATCAACGTAGTGCTTACGTTCAGCGTGCG GAAGCACTGTTGCCGCTGCCACTATCTATTTTCGGCTCCCTACGTAGTCG ATTTTCAAATGCTGGAGCCACCTTGAAAAGTTGGATGGAAGTGCCCACCG TCAGGAGTCCCCAGCGGGAAGCCGAGGCCATTAAGGTAAACATGGCCAGC ATTGAACAGAACATCCAGAAAGCCTTGACTGCCGAGGAATACGAAAATAT CTTAAACCATGTAAACAGCTACGTGCAGCAGTTGGTCGAGCTGAAAATGC AGCAGCATTCCAAGGAGCTCGCACCGCAACAGATTGAACTCTTTGTTAAG CTGATGAAGGAAAACCTCAAGCAGATTATGTACAAAACGGAGCTAAGCGA AAAGGATTTGTCTGATCTGGCCATAAAACTGAAACTGGAGCTGCAAAGCT CAGGCGGTTGGCAAGATGGAGCGAAACTATCACAAGCTAACTTAGAGGAG ATAACCAAGCTAATTAAAGCAGAGGTTCACCTCCACGAATCGCACTACAC CATTCAATTGGACAGGATAGACTTTGCATCCCTGCTGGAGCGTATTCTTG CTGCGCCAGCATTGGCAGACTTTGTAGATGCTCGAATAAGTCTTCGGGTG GGAGAGCTCGAGCCAAAGGAGAGTTCCGGTTCCTCAGATGCAGAAGTCCA AATTGAGCGTCTGAACAGGGAAATCGCCTTCATTAAGTTGGCTCTCTCTG ACAAGCAAGCGGAGAACGCCGATCTGCACCAATCAATCAGCAATCTGAAG CTCGGCCAAGAGGATTTGCTGGAACGCATACAGCAGCACGAACTTTCCCA GGATAGGCGCTTCCACGGGTTGCTGGCTGAAATAGAAAACAAACTGTCTG CGCTTAACGACTCGCAGTTTGCTCTTCTCAACAAGCAGATCAAGCTATCC CTTGTCGAAATTCTGGGCTTTAAGCAATCCACCGCTGGCGGTTCCGCTGG CCAATTGGATGACTTCGATCTGCAGACCTGGGTACGCAGCATGTTTGTGG CCAAGGACTACCTGGAGCAGCAGCTGCTAGAGCTGAACAAGCGCACCAAT AACAACATTCGCGACGAGATTGAGCGTTCGAGCATCCTGCTGATGAGCGA CATTAGCCAACGACTCAAACGGGAGATTCTTCTGGTTGTGGAGGCCAAGC ATAACGAGAGCACCAAAGCGTTGAAGGGCCATATCCGCGAAGAGGAGGTG CGCCAGATAGTCAAGACGGTGCTAGCTATTTACGATGCCGACAAGACGGG CCTGGTGGACTTCGCCCTGGAGTCGGCGGGCGGCCAAATCCTTTCCACGC GTTGCACTGAGAGCTACCAGACAAAGTCAGCCCAGATATCGGTGTTTGGA ATTCCACTCTGGTATCCCACCAACACGCCGCGGGTCGCCATTTCACCCAA TGTGCAGCCAGGGGAATGCTGGGCATTCCAAGGGTTTCCCGGATTTCTAG GCAAGTCGCGGCTCAACTCGTTGGTGTACGTCACTGGATTCACCCTAGAG CACATACCGAAGAGTCTATCCCCCACAGGAAGAATAGAATCAGCTCCTCG CAACTTCACTGTCTGGGGCTTGGAGCAGGAGAAGGACCAGGAACCCGTAT TGTTCGGCGATTACCAGTTTGAGGACAATGGTGCTTCCCTCCAGTACTTT GCCGTTCAAAACCTGGACATCAAACGGCCGTACGAGATCGTCGAACTGCG GATCGAGACGAACCATGGCCATCCCACCTATACATGCCTCTACCGGTTTC GCGTGCACGGCAAGCCGCCGGCCACATAA 1829 2R:1731127-2080000 1 CG18584-RA CG18584-RA FBtr0086159 AAF57400 campbell Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) 146345 144834 0 CG18584:1 1 0 partof 1511 2R:1731127-2080000 1 CG18584:1 146504 146399 0 CG18584:2 2 0 partof 105 2R:1731127-2080000 1 CG18584:2 146780 146567 0 CG18584:3 3 0 partof 213 2R:1731127-2080000 1 CG18584:3 146777 144968 0 CG18584-PA 0 producedby MEVPTVRSPQREAEAIKVNMASIEQNIQKALTAEEYENILNHVNSYVQQL VELKMQQHSKELAPQQIELFVKLMKENLKQIMYKTELSEKDLSDLAIKLK LELQSSGGWQDGAKLSQANLEEITKLIKAEVHLHESHYTIQLDRIDFASL LERILAAPALADFVDARISLRVGELEPKESSGSSDAEVQIERLNREIAFI KLALSDKQAENADLHQSISNLKLGQEDLLERIQQHELSQDRRFHGLLAEI ENKLSALNDSQFALLNKQIKLSLVEILGFKQSTAGGSAGQLDDFDLQTWV RSMFVAKDYLEQQLLELNKRTNNNIRDEIERSSILLMSDISQRLKREILL VVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGG QILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECWAFQG FPGFLGKSRLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVWGLEQEK DQEPVLFGDYQFEDNGASLQYFAVQNLDIKRPYEIVELRIETNHGHPTYT CLYRFRVHGKPPAT 564 2R:1731127-2080000 1 CG18584-PA CG18584-PA FBpp0085492 AAF57400.2 318699 315502 Drosophila 0 CG17002 0 0 3197 melanogaster 2R:1731127-2080000 1 CG17002 FBan0017002 FBgn0033122 42E4-42E4 CG17002 Not in SwissProt real (computational) AE003790 protein targeting GO:0006605 318699 315502 0 CG17002-RB 0 partof c58d4e11f126585af95b581d436b87f1 GCACGATACCTCCAATGAGAGATGCCATATCGATGCTTACGCATTTTATT AACATCGATAGACATTTCTAGAATGTCTAGACTTTAATGCTTGGATTTTC CAAAAACTATAATCTGTTTCCAAAAAGTTATCGATAAGTATCGATCAGTG TTGAAACTATTTGTATTTTATATTAAATTCTGGGGTGTGACTAGTAATAT TAGGAATATAAGCTTTAAAGAAAAAATCGAATTCTTTATAAGTGATTTAG TTCGAACGTTAACTTAAGATTTGCCACCACAATCGGAAAGTAGCTATTTT CTAGCTAGCTTTGCCCATTAATCGATTGGTGGCAACACTGGTCGGCACAT CCCACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAA CGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACG CCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGC CACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAAC AGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAA CTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAAC GCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGC ACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCG AGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAG CGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACT GGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCC AACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAG GAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTT CCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAGC TCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCG AGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGAA ACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACA AAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTC GCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCAT CTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCA GCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCG CAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCAT TTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGG CCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATC GAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACA CCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCAT TGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGTTTCCTCCACAGAAT CCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGG ATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTG GCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGT CAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCC CTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAG ACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATA AAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAA 2039 2R:1731127-2080000 1 CG17002-RB CG17002-RB FBtr0086170 AAF57419 not done Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) crosby 316551 315502 0 CG17002:1 1 0 partof 1049 2R:1731127-2080000 1 CG17002:1 316708 316608 0 CG17002:2 2 0 partof 100 2R:1731127-2080000 1 CG17002:2 317463 317412 0 CG17002:3 3 0 partof 51 2R:1731127-2080000 1 CG17002:3 318040 317555 0 CG17002:4 4 0 partof 485 2R:1731127-2080000 1 CG17002:4 318699 318345 0 CG17002:5 5 0 partof 354 2R:1731127-2080000 1 CG17002:5 318540 316119 0 CG17002-PB 0 producedby MPPASAVNNSNAAAQAAKAERAEKLRGALKGFIVADRQRRQEEFEAQCEE QRLRREREEVERQNQVALDDTRGQITRLDEQLADLHSQKHQLTVQLKKVL NEDETRKKLAKENELFAIQQAAASSPVFLPPLRLQHQHHTLMQKLPSGGQ PGKRGRSPSPPSQQQAYYKSAASYAQQKHDDYRRAADYARLSWNKTAAQY PGTGTVFYQTVAPPPTTQHQADARLQSIYNYNLPLRQAYHVDLPSATVSK PPDSQSPKAPSQSQPMQVLHINLDQPTISQADLVAQAGGSLSVKASQPHV TMEKLPDRYHIEVKHDGQPPSHVPPPPHLLPEGVIFKPLLNELSLHSNVL QISSSQFPPQNPKTAGSITQGYAPGRGGSAHEQQLARQQLAMLPGQPGAP SGSGSAQPPPGQQMHYTRRLY 421 2R:1731127-2080000 1 CG17002-PB CG17002-PB FBpp0085502 AAF57419.2 168135 158132 Drosophila 0 CG15236 0 0 10003 melanogaster 2R:1731127-2080000 1 CG15236 FBgn0033108 FBan0015236 42D3-42D3 CG15236 Not in SwissProt real (computational) AE003790 168135 158132 0 CG15236-RB 0 partof fe139f976dcc5edc5da247de0084f989 AACAGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTC AGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCG ATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGT AATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAA CTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATC ACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCG AAAATTAAACCAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGC CATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAG CCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGA GCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAA GGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCG GTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGG GCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGC AGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCT TCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGT CCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGGCT TTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGA CACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGA TGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGAC AACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTC CCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCA GGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGACAGAAG GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGAT CTTCTGCTGGTGGGAGAAGTGCGATAAGGCCAATGTAAACAAGGCGAGGA CGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGAC GGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCA CGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAG TTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTAC GAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTA TAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAA GCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACAC GAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACA GCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAA CGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCG TCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTC CAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACG ACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAG CACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACA GCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGG CATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAG GGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGA GGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCA GGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGG GCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGAC AACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGA CGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACG CTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGATCTTGG ACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCT TCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCC ATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGA TGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCA TCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAAC GATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACT AACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATG GCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAG GTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAG CAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTG TCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCA GGGCGTATGTGCAATGTTTTGGGCAAACTGTATAAAATTGGTGACATTCT GCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGA CTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCG CTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTT TGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTG GAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGT GATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATA GAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATT CGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCAT GTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTG TAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCT ATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAA GCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGAAGAAGAAGGAAATCG CAGTTGGCTCACAGTTTAGACTTTAAGCTGAATGTTTATGCATTTTATAA GAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGC AGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTA TATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAA CCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGAT TATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAA CGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAA TCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAAC GTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTG CATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATC TATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACA AACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTT AAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTG CGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGC ATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAG GGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATT TTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGA ACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAA TATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTAT TGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAAT TCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGT ATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCAC ACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTG AAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGG CATTTC 4756 2R:1731127-2080000 1 CG15236-RB CG15236-RB FBtr0086160 crosby Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) AAM70834 158442 158132 0 CG15236:1 1 0 partof 310 2R:1731127-2080000 1 CG15236:1 159823 159335 0 CG15236:2 2 0 partof 488 2R:1731127-2080000 1 CG15236:2 162706 162404 0 CG15236:3 3 0 partof 302 2R:1731127-2080000 1 CG15236:3 163462 163389 0 CG15236:4 4 0 partof 73 2R:1731127-2080000 1 CG15236:4 164701 163529 0 CG15236:5 5 0 partof 1172 2R:1731127-2080000 1 CG15236:5 165844 165267 0 CG15236:6 6 0 partof 577 2R:1731127-2080000 1 CG15236:6 168135 166301 0 CG15236:7 7 0 partof 1834 2R:1731127-2080000 1 CG15236:7 166465 159690 0 CG15236-PB 0 producedby MPSVKSAESEILLGIIRSDSMTSGNSLRSCLLLATILGLLCRTKALPFEY LDEHEDFNYDLDTAQSQAKYDARLLSQQMLSDAELQRQGLSDGQDNALDG DSAAAQGTGAGSHLDAVSSVHDDLEPHSRAAACFTNGHKYTHGQKVPRLD ACEVCLCMDGEIFCWWEKCDKANVNKARTAGDNAGLGLGVEDDGDGNGNG DGDGDYSDPYRHESTTGKSTKVHKAARKVGKRHKHRKNQKNFNDYEVYHS QREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNYNIIKQHKHEQQQQ QLKIPQQLHQQQQQQNVAALGVNHAAKATHYQQAASTPLPTPPPPSEHPQ HSHHPHQQAHSSSKILNFPENLPALLYYDYKTEEHEHHQHQHHQQHLLHE KQRLLQQQQQQQQQQQQMVQQEALARQKASESASEPESRAGGTAEGGVEP SGDLAADKNSDEAETDSDILPEPPTKQPRAAATQWPTPSSNSSARALMTS NVASTSTAATTTTTKTSKTKTTTATTGRTTTTTTATGTNEMVTSTLSGME KSGATVAATDLGQMQPDRRGPDAERDDAFHRWLTSTELNADNTNSMDDSL ERETPASTIIDDVGTANKSDRSIGGIGGIGKDNGNDAVFFRSSYNDYSSE FNGSVVNIDITLTAVDVHPRRQTDLIANGNRTSGANDNGNSCSSQVGAAG TTMNPVAVSTSSSTRSSNNQDQPQQSPVVPPYTLTTIITTAPMAPGRMCN VLGKLYKIGDILPQDTGNCLQCICTDAVTPDEMPSVTCSPHNCPPLVLPD LFDATGY 807 2R:1731127-2080000 1 CG15236-PB CG15236-PB FBpp0085493 AAM70834.1 168135 158182 0 CG15236-RA 0 partof ab14f0493eb1470b3d60afa3948abbac AGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCG ATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATTT GAGTTCCATTTACATTCAGCCTCCATAAATTGGCATGGCTGCGAAAATCG TTGCCTACTTAAGAGGGCCCACATTTAGCAGGCGCAGCACCGGCATTGTG AATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACT CGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTA AACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGG CGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGT CGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGT GTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAA AATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCGTGAAATC CGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGCATGACGA GCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCTGGGATTA CTCTGCCGGACGAAGGCTTTGCCCTTTGAGTATTTAGACGAGCACGAGGA CTTCAACTACGACCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCC GTCTGCTCTCGCAGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGG CTGAGCGACGGCCAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCA GGGGACTGGAGCAGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACG ACCTGGAGCCGCACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAG TACACGCACGGACAGAAGGTTCCGCGCCTGGATGCCTGCGAGGTGTGTCT CTGCATGGACGGCGAGATCTTCTGCTGGTGGGAGAAGTGCGATAAGGCCA ATGTAAACAAGGCGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGT GTCGAGGACGACGGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTA TTCAGATCCATATCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGC ATAAAGCGGCGAGGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAA AAGAATTTTAATGACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCA GCAGCAGCAGTCGGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGA TGCAGCAAAAACACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATA ATCAAGCAACACAAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCA GCAGCTACATCAGCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTA ATCACGCAGCAAAGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTG CCAACTCCCCCACCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACA CCAACAGGCGCACTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGC CAGCCCTGCTCTACTACGACTACAAGACGGAGGAGCACGAGCACCACCAG CACCAGCACCACCAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCA GCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGG CGTTGGCGCGACAAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGG GCCGGAGGCACAGCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGC TGATAAAAACTCTGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGC CGCCTACAAAGCAGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCT AGTAACAGCTCGGCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATC CACGGCTGCGACAACGACAACGACAAAGACATCGAAAACGAAAACGACAA CGGCGACAACGGGAAGGACGACGACGACGACAACGGCGACAGGCACAAAT GAAATGGTGACAAGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGT TGCAGCCACAGATCTTGGACAGATGCAACCCGATCGCCGTGGACCAGACG CGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCTGAAT GCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGCCGGC ATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGGAGCA TCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGTCTTC TTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCGTTGT CAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGCCAAA CGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAATGGC AACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACCCAGT GGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGATCAGC CTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTATAACA ACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGCAAACTGTA TAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTGCCTGCAGTGCA TTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCGTCACCTGCAGT CCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTCGATGCGACTGG TTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAACGGCAGGTGGCA AGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGCTGTGGGAGTTT TTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAAAGCCACAACTG CAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAACGAACGAATCG AATCTAATCGAATCGATTCGAATCACACTCACAACAACTGCACTACAGAA CTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCAACTCAATATGA ATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAGTGCCCCAAGCA CTCTCTAAAACGAAACCTATCAGCAGACATATATTATATTCGTACCAAAC TATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGGGGAATGAATAA AGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGACTTTAAGCTGAA TGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTCCGCAACAAAAA TCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTTATAGATGTACC AAACAGAAGTATATAGTATATACAAACATATACGAGTATCTACTCTATAT CTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAGTTCGGTGGGAT CAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAACCGTGTAGAGT TTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACGAGTAACTTATA CAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAACAATGACAAATA ATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATATTAAAAGCAAA CAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCGCTTCTTTGGAA ATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTTAGGAGCAATGT ATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAAGACACCATATC GAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAAC TTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTT TCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAA CATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAG TAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTT TTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCA TGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACA AACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTC GAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATAC AAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTA CTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTT AAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAA ACCGAAACCCAACTAAGGCATTTC 4624 2R:1731127-2080000 1 CG15236-RA CG15236-RA FBtr0086161 AAF57401 crosby Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) 158280 158182 0 CG15236:8 1 0 partof 98 2R:1731127-2080000 1 CG15236:8 159823 159255 0 CG15236:9 2 0 partof 568 2R:1731127-2080000 1 CG15236:9 162706 162404 0 CG15236:3 3 0 partof 302 2R:1731127-2080000 1 CG15236:3 163462 163389 0 CG15236:4 4 0 partof 73 2R:1731127-2080000 1 CG15236:4 164701 163529 0 CG15236:5 5 0 partof 1172 2R:1731127-2080000 1 CG15236:5 165844 165267 0 CG15236:6 6 0 partof 577 2R:1731127-2080000 1 CG15236:6 168135 166301 0 CG15236:7 7 0 partof 1834 2R:1731127-2080000 1 CG15236:7 166465 159690 0 CG15236-PA 0 producedby MPSVKSAESEILLGIIRSDSMTSGNSLRSCLLLATILGLLCRTKALPFEY LDEHEDFNYDLDTAQSQAKYDARLLSQQMLSDAELQRQGLSDGQDNALDG DSAAAQGTGAGSHLDAVSSVHDDLEPHSRAAACFTNGHKYTHGQKVPRLD ACEVCLCMDGEIFCWWEKCDKANVNKARTAGDNAGLGLGVEDDGDGNGNG DGDGDYSDPYRHESTTGKSTKVHKAARKVGKRHKHRKNQKNFNDYEVYHS QREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNYNIIKQHKHEQQQQ QLKIPQQLHQQQQQQNVAALGVNHAAKATHYQQAASTPLPTPPPPSEHPQ HSHHPHQQAHSSSKILNFPENLPALLYYDYKTEEHEHHQHQHHQQHLLHE KQRLLQQQQQQQQQQQQMVQQEALARQKASESASEPESRAGGTAEGGVEP SGDLAADKNSDEAETDSDILPEPPTKQPRAAATQWPTPSSNSSARALMTS NVASTSTAATTTTTKTSKTKTTTATTGRTTTTTTATGTNEMVTSTLSGME KSGATVAATDLGQMQPDRRGPDAERDDAFHRWLTSTELNADNTNSMDDSL ERETPASTIIDDVGTANKSDRSIGGIGGIGKDNGNDAVFFRSSYNDYSSE FNGSVVNIDITLTAVDVHPRRQTDLIANGNRTSGANDNGNSCSSQVGAAG TTMNPVAVSTSSSTRSSNNQDQPQQSPVVPPYTLTTIITTAPMAPGRMCN VLGKLYKIGDILPQDTGNCLQCICTDAVTPDEMPSVTCSPHNCPPLVLPD LFDATGY 807 2R:1731127-2080000 1 CG15236-PA CG15236-PA FBpp0085494 AAF57401.2 334036 322450 Drosophila 0 Tsp42Ea 0 0 11586 melanogaster 2R:1731127-2080000 1 CG18817 GO:16021 FBgn0029508 FBan0018817 FBgn0042099 FBgn0042140 FBgn0033123 FBgn0064940 42E4-42E5 Flag Cambridge: gene split/merge (internal view only).::DATE:2002-02-13 10:59:57::TS:1013615997000 CG18742 EST evidence indicates that 5' UTR overlaps that of neighboring gene on the same strand.::DATE:2003-03-14 17:40:41::TS:1047681641000 Tsp42Ea Perfect match to SwissProt real (computational) AE003790 integral to membrane GO:0016021 334036 322450 0 Tsp42Ea-RA 0 partof 89760df53e9dadb0befe991210a82024 CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGG CAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTA ATTTGCTCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTG CTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAAC CCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGA TTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCC ATGACGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTT GGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCG ACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATG GACGCGATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGA CTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACA ACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTT GAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCAT CGCCGCCATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACA GCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAA GGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCA ATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATC TCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGAT CACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGT TTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAA ATTTATTTACAATTTACGAA 1120 2R:1731127-2080000 1 CG18817-RA CG18817-RA FBtr0086171 Perfect match to REAL SP with corresponding FBgn AAG22311 sima 322552 322450 0 Tsp42Ea:1 1 0 partof 102 2R:1731127-2080000 1 CG18817:1 324259 324147 0 Tsp42Ea:2 2 0 partof 112 2R:1731127-2080000 1 CG18817:2 332931 332739 0 Tsp42Ea:3 3 0 partof 192 2R:1731127-2080000 1 CG18817:3 333156 332994 0 Tsp42Ea:4 4 0 partof 162 2R:1731127-2080000 1 CG18817:4 333417 333222 0 Tsp42Ea:5 5 0 partof 195 2R:1731127-2080000 1 CG18817:5 334036 333679 0 Tsp42Ea:6 6 0 partof 357 2R:1731127-2080000 1 CG18817:6 333748 324199 0 Tsp42Ea-PA 0 producedby MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY 226 2R:1731127-2080000 1 CG18817-PA CG18817-PA FBpp0085503 AAG22311.2 327750 322450 0 Tsp42Ea-RB 0 partof 4636b758150438767125ff423d5f5ae6 CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGG CAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTA ATTTGCTCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTG CTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAAC CCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGA TTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCC ATGACGTACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTT GGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCG ACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATG GACGCGATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGA CTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACA ACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTT GAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCAT CGCCGCCATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACA GCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAA GGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCA ATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATC TCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGAT CACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGT TTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAA ATTTATTTACAATTTACGAAAA 1122 2R:1731127-2080000 1 CG18817-RB CG18817-RB FBtr0086172 crosby Perfect match to REAL SP with corresponding FBgn AAG22210 322552 322450 0 Tsp42Ea:1 1 0 partof 102 2R:1731127-2080000 1 CG18817:1 324259 324147 0 Tsp42Ea:2 2 0 partof 112 2R:1731127-2080000 1 CG18817:2 326642 326450 0 Tsp42Ea:7 3 0 partof 192 2R:1731127-2080000 1 CG18817:7 326867 326705 0 Tsp42Ea:8 4 0 partof 162 2R:1731127-2080000 1 CG18817:8 327128 326933 0 Tsp42Ea:9 5 0 partof 195 2R:1731127-2080000 1 CG18817:9 327750 327391 0 Tsp42Ea:10 6 0 partof 359 2R:1731127-2080000 1 CG18817:10 327460 324199 0 Tsp42Ea-PB 0 producedby MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY 226 2R:1731127-2080000 1 CG18817-PB CG18817-PB FBpp0085504 AAG22210.2 327750 322450 0 Tsp42Ea-RC 0 partof 88665682ab237e0e5e77be006d2d36dc CAGTTTAGTTCAGTTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGC GGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCA AGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAAT GAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGC TCTGTTCGATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTC AGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCA GGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCT GGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACG TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGAT CTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGG TCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCG ATTCAGATCAGCATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGC CTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCC GCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTC TGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGC CATCGAATTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTC GGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTT GCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTA CGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGC GTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTT TGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACT GTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTAT TTACAATTTACGAAAA 1116 2R:1731127-2080000 1 CG18817-RC CG18817-RC FBtr0086173 crosby AAF57420 Perfect match to REAL SP with corresponding FBgn 322552 322450 0 Tsp42Ea:1 1 0 partof 102 2R:1731127-2080000 1 CG18817:1 324259 324153 0 Tsp42Ea:11 2 0 partof 106 2R:1731127-2080000 1 CG18817:11 326642 326450 0 Tsp42Ea:7 3 0 partof 192 2R:1731127-2080000 1 CG18817:7 326867 326705 0 Tsp42Ea:8 4 0 partof 162 2R:1731127-2080000 1 CG18817:8 327128 326933 0 Tsp42Ea:9 5 0 partof 195 2R:1731127-2080000 1 CG18817:9 327750 327391 0 Tsp42Ea:10 6 0 partof 359 2R:1731127-2080000 1 CG18817:10 327460 324199 0 Tsp42Ea-PC 0 producedby MSCGISMVKYILFIFNLLCSICGILLIVFGALLFSKVRNMDDFAEALRTQ QVPVTMIILGTIILLISWFGCCGAIRESYCMSMTYSILLFVLMIGQLALV IYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISMKCCGRSGYTDY AYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIA AIEFVGFVFACCLANSIRNYRRRAEY 226 2R:1731127-2080000 1 CG18817-PC CG18817-PC FBpp0085505 AAF57420.2 213186 211490 Drosophila 0 CG9455 0 0 1696 melanogaster 2R:1731127-2080000 1 CG9455 FBan0009455 FBgn0033113 42D4-42D4 CG9455 Not in SwissProt real (computational) AE003790 serine protease inhibitor activity GO:0004867 213186 211490 0 CG9455-RA 0 partof 148e50f6b9277026cdc03416c8dd5c53 TATTTAAAAATATAAATTAAAACATATATTTTTTTGCCCAGATCGAGATG AGCGAACCCCAAGAAGGCAGAAATCAGTTTGCGCGAAATCTGATAGATGT CATTACCAAAGATGCCCTGCAACAGAGCAAAGACCCCCACATAAATACGG TTTTCTCTCCAGCATCCGTCCAAAGTGCATTGACCTTGGCATTTATGGGG GCTTCCGGATCTACAGCAGAGGAGCTAAGGAATGGGCTTCAGCTAGGACC AGGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGA GCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTG TACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGT GGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGG GAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAG ATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCT GCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGC CAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTG CAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCC ACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTC ACATGCTAATTCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAG CAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTT GCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGG ACCTCAAGCAGGTACTTAATCAGCTGGGTATTACGGAAGTCTTCAGCGAT AAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTC GGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGG CAGCAGCAGTCAGTTTCATGAAGATAGTACCCATGATGCTCAACATGAAC AAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCC GCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTG GATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTAC AATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCC ACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCA GTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATA TGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGG GGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGAT CGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAA CTTATGA 1557 2R:1731127-2080000 1 CG9455-RA CG9455-RA FBtr0086162 AAF57407 Shares UTR: 3' UTR sequences shared with downstream gene::DATE:2002-12-10 13:44:47::TS:1039545887000 sima Shares CDS: 3' CDS shared with downstream gene::DATE:2002-12-10 13:45:25::TS:1039545925000 Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) Evidence indicates that 3' UTR overlaps 5' UTR, translation start, and first intron of downstream gene; extends to coordinate AE003790: 943750 (based upon 3' extent of AT24862 ).::DATE:2002-02-12 03:18:06::TS:1013501886000 212413 211490 0 CG9455:1 1 0 partof 923 2R:1731127-2080000 1 CG9455:1 212625 212483 0 CG9455:2 2 0 partof 142 2R:1731127-2080000 1 CG9455:2 213186 212694 0 CG9455:3 3 0 partof 492 2R:1731127-2080000 1 CG9455:3 212885 211537 0 CG9455-PA 0 producedby MSEPQEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFM GASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNR LYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEH KITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTH VQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQEL EQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQLGITEVFS DKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVSFMKIVPMMLNM NKKLFKADHPFVFYIRNPQAVFFAGRFSNPKSGSGSGEEGLSREGFDANM YNV 403 2R:1731127-2080000 1 CG9455-PA CG9455-PA FBpp0085495 AAF57407.2 214648 212777 Drosophila 0 Spn1 0 0 1871 melanogaster 2R:1731127-2080000 1 CG9456 FBan0009456 FBgn0028988 FBgn0033114 42D4-42D4 Spn1 Curator examined, accepted AE003790 serine protease inhibitor activity GO:0004867 214648 212777 0 Spn1-RA 0 partof 3a6ce17d99493ea4ddb07b72baf00fee CCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATC TGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGT ACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATC CCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCT CAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATA TATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTC GGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGCATTTTCCT GTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTAC TTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATA GAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAA GGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGG CAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGA CCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCT GAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGG AGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAG TGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGG CAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTA AGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACC TTCCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAAT GGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCG AGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGA GAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAG GCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCG AATTTCGTGATGAACTCAAAGAGACCTTAGAGAAGCTGGGCATCCGAGAG CTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGG CGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGG AGGGAGCGGAGGCCGCAGGTGCCACATCTGTGGCCGTCACAAATCGAGCG GGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCG CGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAA ATAAAAACAATATTTAAATTTT 1472 2R:1731127-2080000 1 CG9456-RA CG9456-RA FBtr0086163 Shares UTR: 5' UTR sequences shared with upstream gene::DATE:2002-12-10 13:47:38::TS:1039546058000 AAF57408 sima Imperfect match to REAL SP with corresponding FBgn Evidence indicates that 5' UTR overlaps 3' UTR of upstream gene (based upon extent of AJ251744).::DATE:2002-03-08 03:17:51::TS:1015575471000 213117 212777 0 Spn1:1 1 0 partof 340 2R:1731127-2080000 1 CG9456:1 214233 213388 0 Spn1:2 2 0 partof 845 2R:1731127-2080000 1 CG9456:2 214433 214291 0 Spn1:3 3 0 partof 142 2R:1731127-2080000 1 CG9456:3 214648 214503 0 Spn1:4 4 0 partof 145 2R:1731127-2080000 1 CG9456:4 214619 213104 0 Spn1-PA 0 producedby MYYLCIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFM GAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRI YVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGK IKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSV PVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALE EKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKLGIRELFTDKSDLS GLFADKSGGKVSQVSHKAFLEVNEEGAEAAGATSVAVTNRAGFSTFLMAD HPFAFVIRDANTIYFQGRVVSP 372 2R:1731127-2080000 1 CG9456-PA CG9456-PA FBpp0085496 AAF57408.2 304644 303877 Drosophila 0 CG30157 0 0 767 melanogaster 2R:1731127-2080000 -1 CG30157 FBgn0050157 FBan0030157 42E1-42E1 AE003790 Not in SwissProt real (computational) CG30157 molecular_function unknown GO:0005554 cellular_component unknown GO:0008372 biological_process unknown GO:0000004 304644 303877 0 CG30157-RA 0 partof 302cdad32ce860f41cc25d7048178a26 ATGGCGGCGGAAAAGTGTGCAGAAGAGTTTGGGGACTCCTCCGCGGCGTC CTTGAAAATTGTACCAAAGGACTATGCATATCCACTTCTAGAGGATCCGC AAGGCGCGCTGACCACGCCCACTGAAGGCGGGCGGACGCTAGTTACCCGC GGTGGCTTTAACTACTTCCACTACGGATGCGATGGCCACCAGGATGCTGG CTGGGGTTGTGGCTACCGCACCCTGCAATCGGCCATTTCCTGGATCCAAC GTCGACAGGGGTCGAGCGGTCATGTTCCTTCCATCCGGGAGATTCAGCAG ATCCTGGTGGCCATCGGCGACAAGGGTCCAGAGTTCGTGGGCTCGCGCGA CTGGATCGGAACGCTCGAGGAGTTCTACGTGATCGATGTGCTGCACCAGG TGCCGTGCAAGATTCTTCACGCCAAGGAGCTTAGCTCGGACGAGATCCTC GGCGAGCTTCGGAGCTATTTTGAGAAGTACCAAGGCTTCGTCGCCATGGG CGGTCTGAGTGACACCGCCTCCAAGGCTATTACCGGCTACCATTGCAGTG CACGCGGTCGCATCTTCCTGCAGGTGGTGGATCCGCATTTCGTAGGCGTG CCCAGCTCCCGGCAGCACTTAATCGATCTGGGCTACGTTCGTTGGGTGCC CGTTGACGAGTTCGCCGGCAGCACGTACAACCTCTGCCTCATCTTGCAGC CGTAG 705 2R:1731127-2080000 -1 CG30157-RA CG30157-RA FBtr0086186 crosby AAM70838 Hits nothing in SP, and no SP entry corresponds to this FBgn 304644 304065 0 CG30157:1 1 0 partof 579 2R:1731127-2080000 -1 CG30157:1 304003 303877 0 CG30157:2 2 0 partof 126 2R:1731127-2080000 -1 CG30157:2 304644 303880 0 CG30157-PA 0 producedby MAAEKCAEEFGDSSAASLKIVPKDYAYPLLEDPQGALTTPTEGGRTLVTR GGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQ ILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSDEIL GELRSYFEKYQGFVAMGGLSDTASKAITGYHCSARGRIFLQVVDPHFVGV PSSRQHLIDLGYVRWVPVDEFAGSTYNLCLILQP 234 2R:1731127-2080000 -1 CG30157-PA CG30157-PA FBpp0085517 AAM70838.1 278980 278907 Drosophila 0 CR30303 0 0 73 melanogaster 2R:1731127-2080000 -1 CR30303 FBgn0050303 FBan0030303 42E1-42E1 AE003790 tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:37:00::TS:1019007420000 CTT Not in SwissProt real (computational) Lys CR30303 278980 278907 0 CR30303-RA 0 partof 580155509c9a983c006e89f85c647225 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG 73 2R:1731127-2080000 -1 CR30303-RA CR30303-RA FBtr0086187 Hits nothing in SP, and no SP entry corresponds to this FBgn 278980 278907 0 CR30303:1 1 0 partof 73 2R:1731127-2080000 -1 CR30303:1 218041 216179 Drosophila 0 CG9460 0 0 1862 melanogaster 2R:1731127-2080000 1 CG9460 FBan0009460 FBgn0033115 42D4-42D4 CG9460 Not in SwissProt real (computational) AE003790 serine protease inhibitor activity GO:0004867 218041 216179 0 CG9460-RA 0 partof 07f8c81c1e5497d06a8340d46a097d5e AGTTTTCCCAATCATGTCAGTCAAGGCCACGTGTTCACTTCTGCTGCTCC AGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCC GCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTC CCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCT TGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAA CTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATT GGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGG ACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTC AAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGC TGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTA ATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCT CCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTA CTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCA GCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCC CAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGT CGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGC CTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATA GACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCA GCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCG AGGAGTTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGC CTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGC GATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTTTA TCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTC ATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTT ATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAAT ATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCA CAA 1303 2R:1731127-2080000 1 CG9460-RA CG9460-RA FBtr0086164 AAF57409 Perfect match to HYPO SP record with corresponding FBgn crosby 216199 216179 0 CG9460:1 1 0 partof 20 2R:1731127-2080000 1 CG9460:1 217223 216288 0 CG9460:2 2 0 partof 935 2R:1731127-2080000 1 CG9460:2 217771 217629 0 CG9460:3 3 0 partof 142 2R:1731127-2080000 1 CG9460:3 218041 217835 0 CG9460:4 4 0 partof 206 2R:1731127-2080000 1 CG9460:4 217963 216192 0 CG9460-PA 0 producedby MSVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGR NIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLL AKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENV NFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKAD WQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELP YTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKF KFEFDVPLQAALEELGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEV NEKGTTASGATFIKVSVESLTIGEEVFEFIADHPFFFAIKDAQNTLFLGH VSQL 404 2R:1731127-2080000 1 CG9460-PA CG9460-PA FBpp0085497 AAF57409.1 278131 278058 Drosophila 0 CR30302 0 0 73 melanogaster 2R:1731127-2080000 -1 CR30302 FBgn0050302 FBan0030302 42E1-42E1 Not in SwissProt real (computational) CR30302 AE003790 tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:39:00::TS:1019007540000 CTT Lys 278131 278058 0 CR30302-RA 0 partof 580155509c9a983c006e89f85c647225 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG 73 2R:1731127-2080000 -1 CR30302-RA CR30302-RA FBtr0086188 Hits nothing in SP, and no SP entry corresponds to this FBgn 278131 278058 0 CR30302:1 1 0 partof 73 2R:1731127-2080000 -1 CR30302:1 277585 277512 Drosophila 0 CR30301 0 0 73 melanogaster 2R:1731127-2080000 -1 CR30301 FBgn0050301 FBan0030301 42E1-42E1 Lys CR30301 AE003790 tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:40:00::TS:1019007600000 Not in SwissProt real (computational) CTT 277585 277512 0 CR30301-RA 0 partof 580155509c9a983c006e89f85c647225 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG 73 2R:1731127-2080000 -1 CR30301-RA CR30301-RA FBtr0086189 Hits nothing in SP, and no SP entry corresponds to this FBgn 277585 277512 0 CR30301:1 1 0 partof 73 2R:1731127-2080000 -1 CR30301:1 329626 327939 Drosophila 0 Tsp42Eb 0 0 1687 melanogaster 2R:1731127-2080000 1 CG18816 GO:16021 FBgn0042139 FBan0018816 FBgn0042086 42E4-42E4 Perfect match to SwissProt real (computational) Tsp42Eb AE003790 integral to membrane GO:0016021 329626 327939 0 Tsp42Eb-RA 0 partof 754db62cb2aa204f8a5b71aab37e7de6 CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGA CTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCA TTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAAT GGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGA AGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGT ACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAA GCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATA AGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGC CCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGT TTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCC CAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATT CACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACG GAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAG TAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAAC ATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGA ACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCT GTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGG TGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGA GGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGT CACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACG CCTGCTGCACCACCATCTACGCCATCTGCATGCTGATTCTGTTCGGCCTG CAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTC CAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCC AGGGATACCCCATGGATGCCCTCCAGTTGGCCTTCTCTTGCTGTGGCAAC ACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAA GGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCT GCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACGGACCTGATTCGA TGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTC GTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCCGAAGTCAGATAC AATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAACACACGAATTCC TCACTCACTCACTCACCGTAAATAAACCAGAATAGGTTAAGCCCAATGAA A 1551 2R:1731127-2080000 1 CG18816-RA CG18816-RA FBtr0086176 AAM70843 crosby Perfect match to REAL SP with corresponding FBgn 328956 327939 0 Tsp42Eb:4 1 0 partof 1017 2R:1731127-2080000 1 CG18816:4 329185 329020 0 Tsp42Eb:2 2 0 partof 165 2R:1731127-2080000 1 CG18816:2 329626 329257 0 Tsp42Eb:3 3 0 partof 369 2R:1731127-2080000 1 CG18816:3 329506 328704 0 Tsp42Eb-PA 0 producedby MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR 222 2R:1731127-2080000 1 CG18816-PA CG18816-PA FBpp0085508 AAM70843.1 329626 328627 0 Tsp42Eb-RB 0 partof a22bad6362f27ffcc5507fb2051eb7c0 AGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAA CGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTT CAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCC TGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACG GCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGT CATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCA TTCGCGAGAACGCCTGCTGCACCACCATCTACGCCATCTGCATGCTGATT CTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGA CAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGA ACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCTTCTCT TGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTG CTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCC AGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACG GACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCAT CTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCC GAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAA CACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGTT AAGCCCAATGAAA 863 2R:1731127-2080000 1 CG18816-RB CG18816-RB FBtr0086177 crosby Only one EST supports this alternative transcript::DATE:2003-03-14 17:28:14::TS:1047680894000 Perfect match to REAL SP with corresponding FBgn AAG22312 328956 328627 0 Tsp42Eb:1 1 0 partof 329 2R:1731127-2080000 1 CG18816:1 329185 329020 0 Tsp42Eb:2 2 0 partof 165 2R:1731127-2080000 1 CG18816:2 329626 329257 0 Tsp42Eb:3 3 0 partof 369 2R:1731127-2080000 1 CG18816:3 329506 328704 0 Tsp42Eb-PB 0 producedby MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR 222 2R:1731127-2080000 1 CG18816-PB CG18816-PB FBpp0085509 AAG22312.2 276655 276582 Drosophila 0 CR30300 0 0 73 melanogaster 2R:1731127-2080000 -1 CR30300 FBgn0050300 FBan0030300 42E1-42E1 CTT CR30300 tRNA type: putative tRNA-Lys implied by tRNAScan-SE analysis. (internal view only)::DATE:2002-04-16 21:40:00::TS:1019007600000 Lys Not in SwissProt real (computational) AE003790 276655 276582 0 CR30300-RA 0 partof 580155509c9a983c006e89f85c647225 GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGT GGGTTCGAGCCCCACGTTGGGCG 73 2R:1731127-2080000 -1 CR30300-RA CR30300-RA FBtr0086190 Hits nothing in SP, and no SP entry corresponds to this FBgn 276655 276582 0 CR30300:1 1 0 partof 73 2R:1731127-2080000 -1 CR30300:1 252388 221537 Drosophila 0 CG30158 0 0 30851 melanogaster 2R:1731127-2080000 1 CG30158 FBgn0040676 FBan0030158 FBgn0040675 FBgn0063683 FBgn0050158 FBgn0033116 42D4-42D6 Gene merge based on BLASTX and partial EST data; no experimental evidence for some internal splice sites.::DATE:2002-03-07 13:59:40::TS:1015527580000 CG15243 Flag Cambridge: gene merge; based primarily upon protein homology to various Ras-related proteins; example: U97592 (AAB52874). DGC:RE28276 spans (not yet fully sequenced).::DATE:2002-02-12 16:57:56::TS:1013551076000 AE003790 Not in SwissProt real (computational) CG30158 GTP binding GO:0005525 252388 221537 0 CG30158-RA 0 partof 2fa0e0c4ec67e7d1d1b734f5d98e19ee AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGA CTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGAT GCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGC TTTGTGTGCGGTTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTA TACGCCAGCTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCG GAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGG TGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTT GGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAAT GCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAG GCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTA GCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGAC CTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCGCCGGCGTGGGCAAGAG CTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCG CCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACA CTAAAGGTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCAT GCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGG CCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATC CGCGAGCAGCGTGGCGACTTTCAGGACATCCCCATTGTGATCGCCGGGAA CAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGA CCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGGCGAAAGTGCTGGAG TGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCT CTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCG GGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCC TACGTCAGCGCATCGTCCAGTCGCAATAAAAATCGGATGAACAGCCCGGC CCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCG TGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCT CGTTCCAGATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAAT CAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCG CCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCAC AATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGG CGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACC CAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTG CTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGA TGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCT GATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGC CGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATA AGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAG TGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTT GCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGG AAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAA TTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTT AATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCG TTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGA CTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACT GGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTC TAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGG TTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGA TAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCG AATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCAT TCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCAC AGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGG GAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTG AACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGC ACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTT TTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGT GGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTG TTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACAT TTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGAT GAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGA CACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATG CACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAA TGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGT CCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAAC CGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTAC CTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACG TTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGAC TAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGC GGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCG ATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAG TTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGA TCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCT AAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCA AATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCG TCCC 3654 2R:1731127-2080000 1 CG30158-RA CG30158-RA FBtr0086165 AAF57410 crosby Imperfect match to HYPO SP record with corresponding FBgn (assume that new one is better) 221698 221537 0 CG30158:1 1 0 partof 161 2R:1731127-2080000 1 CG30158:1 221801 221754 0 CG30158:2 2 0 partof 47 2R:1731127-2080000 1 CG30158:2 236135 235637 0 CG30158:3 3 0 partof 498 2R:1731127-2080000 1 CG30158:3 239875 239707 0 CG30158:4 4 0 partof 168 2R:1731127-2080000 1 CG30158:4 240636 240526 0 CG30158:5 5 0 partof 110 2R:1731127-2080000 1 CG30158:5 244598 244407 0 CG30158:6 6 0 partof 191 2R:1731127-2080000 1 CG30158:6 249942 249809 0 CG30158:7 7 0 partof 133 2R:1731127-2080000 1 CG30158:7 252388 250042 0 CG30158:8 8 0 partof 2346 2R:1731127-2080000 1 CG30158:8 250115 235970 0 CG30158-PA 0 producedby MADLERIRLVLLGGAGVGKSSIVKRFLFKTYTDKYRATVEDLYNREYDLG GVTLKVDILDTSGDMQFPAMRRLSIATAHAFMLVYAATSAPSFQCVKQCF EEIREQRGDFQDIPIVIAGNKADLATTHREVKLEEVTDWVFCELPRLRAK VLECSAKEDSNVTDLFKSLLSLSRFLPASSSGSGGSGGGGEAAPSGFKRR SSAYVSASSSRNKNRMNSPALGGAGGSGGDKKGSSLVDAVDVATTSAEAK LKPRSRSLIRRASRKTKQQINNASDDCNVQ 280 2R:1731127-2080000 1 CG30158-PA CG30158-PA FBpp0085498 AAF57410.2 275173 274468 Drosophila 0 CG33350 0 0 705 melanogaster 2R:1731127-2080000 -1 CG33350 CG33350 FBgn0053350 FBgn0033119 FBan0015241 42E1-42E1 Not in SwissProt real (computational) Flag Cambridge: gene split (internal view only)::DATE:2003-03-14 16:24:23::TS:1047677063000 AE003790 CG15241 Gene split based on BLASTX data::DATE:2003-03-14 16:24:38::TS:1047677078000 275173 274468 0 CG33350-RA 0 partof aebef6dbe41eb5824d88e635d0be0b2e ATGCTGTTCGTATTTGGCTTTGCTAGTTCCTGGGCCGCAGACTACGAGCT GTTGCTGGAGGACCCTGATATCTTTTCACCCTGCACTGAACCGCCGCCGG GATCGATTGGATTCCACGATGCCTTCGATATTGGCGATCTGGTAGTCGAC CAGGACATGGACATCATTCACCTGTCCGAGAGTGTCACCTCAATCTGGGA TGTGGAGCCCACAGATCGCATATCCGCCAGGTTTGCAATAATGCATTACA ACCGCGGCAGCTGGGAACCGACTGTATTTAGCATGGCCACGCCGGACTTC TGCGCCTCAATGTTTGATGAGAATCAGTCGTGGTTTAAGTACTGGACCAA ACACATTTCGAACCGCGATGAGGTGATGGAGAAGTGTTTTAAAACGCGTG GTACCGTTATAATGCACAATCCATTCGATCTGCAGCTGCGTCTAACGGAC ATTCGTGGTGCAACTCTCAGGGGTCGTTACAAAGCTGTGGTCACCTTTGA GGCGGTCGATGAGAAGGATGTGCCACGCCGTAATTCCATTTGCTTCGAAA TCAGGGGAGAGGCCGAGAAGATAAATTAA 579 2R:1731127-2080000 -1 CG33350-RA CG33350-RA FBtr0086191 crosby Perfect match to HYPO SP record with corresponding FBgn AAF57415 275173 274948 0 CG33350:1 1 0 partof 225 2R:1731127-2080000 -1 CG33350:1 274892 274715 0 CG33350:2 2 0 partof 177 2R:1731127-2080000 -1 CG33350:2 274645 274468 0 CG33350:3 3 0 partof 177 2R:1731127-2080000 -1 CG33350:3 275173 274471 0 CG33350-PA 0 producedby MLFVFGFASSWAADYELLLEDPDIFSPCTEPPPGSIGFHDAFDIGDLVVD QDMDIIHLSESVTSIWDVEPTDRISARFAIMHYNRGSWEPTVFSMATPDF CASMFDENQSWFKYWTKHISNRDEVMEKCFKTRGTVIMHNPFDLQLRLTD IRGATLRGRYKAVVTFEAVDEKDVPRRNSICFEIRGEAEKIN 192 2R:1731127-2080000 -1 CG33350-PA CG33350-PA FBpp0085518 335797 334992 Drosophila 0 CG30160 0 0 805 melanogaster 2R:1731127-2080000 1 CG30160 FBgn0050160 FBan0030160 42E5-42E5 Possible incorrect identifier (computational) Flag Cambridge: another Tsp42E::DATE:2002-02-13 10:58:42::TS:1013615922000 CG30160 AE003790 integral to membrane GO:0016021 335797 334992 0 CG30160-RA 0 partof 3277899d93195a24a2a5b940ec4d38f8 ATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCT GGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGC TCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAG ACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGC CTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCA TCTACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCC ATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGC AGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGG ATGCCCTCCAGTTGGCCTTCTCTTGCTGTGGCAACACGGGATACCAACAG TATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGT GTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCG TCGATTTCTGGGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATC ATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAG CGCGATGAGGAAGCGCTAG 669 2R:1731127-2080000 1 CG30160-RA CG30160-RA FBtr0086178 crosby AAM70844 Perfect match to SP record corresponding to different FBgn 335244 334992 0 CG30160:1 1 0 partof 252 2R:1731127-2080000 1 CG30160:1 335473 335308 0 CG30160:2 2 0 partof 165 2R:1731127-2080000 1 CG30160:2 335797 335545 0 CG30160:3 3 0 partof 252 2R:1731127-2080000 1 CG30160:3 335794 334992 0 CG30160-PA 0 producedby MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQ TIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIYAICMLILFGLQLALS IWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAFSCCGNTGYQQ YETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLI IALFELGIFIMSCCLASAMRKR 222 2R:1731127-2080000 1 CG30160-PA CG30160-PA FBpp0085510 AAM70844.1 273761 272944 Drosophila 0 CG33351 0 0 817 melanogaster 2R:1731127-2080000 -1 CG33351 CG33351 FBgn0053351 FBan0015241 FBgn0033119 42E1-42E1 AE003790 Flag Cambridge: gene split (internal view only)::DATE:2003-03-14 16:25:40::TS:1047677140000 Gene split based on BLASTX data::DATE:2003-03-14 16:25:57::TS:1047677157000 273761 272944 0 CG33351-RA 0 partof ATGATATTTGTGCTGCTACTCTTATTAGGAGTGACCAGTTCCTGGGCCAC AGACTATGAATTATTGCTCGAGGATCCGGACATATTTTCGACGTGCACTG ATGGTCCTCCCGGATCCATCAACATCCGCCAGGCACTCAACTTAGACGAC ATTGTAATCGACCAGAAAGGGGATATACTTCATGTATCCGGGAACGCCAC CGTCGTGTGGGATGTGCAGCCCACCGATCGGATTACTGCGAGACTTGATG TTTTTCACTTCAACCGCGGCACTTGGGAGCCCACTGTCTTTAGCATGGCC ACCCAGAACTTTTGCTCCATCATGTACGACAAGAACCAGTATTGGTATAA GTATTGGACAAGGTTTATAACCAATCGCCATGAGGTGGAAAAGAAGTGCT TCAGAGGGCCTGATACCGTTCTGGTACACGAGCCCTTCGATCTCATACTA AAATTTGAGAATTTTCGTGGACCTCTTCTTAGAGGACGTCATAAACTTGT CATATTGTTTAACGCACTAGATGAGAGGAATATACCGCGCCCAAACCCAA TTTGTTTGGAGATCATAGGAGAACCACTAAAGTTGCAGTAG 591 2R:1731127-2080000 -1 CG33351-RA CG33351-RA FBtr0086192 not done crosby 273761 273524 0 CG33351:4 1 0 partof 237 2R:1731127-2080000 -1 CG33351:4 273458 273281 0 CG33351:5 2 0 partof 177 2R:1731127-2080000 -1 CG33351:5 273121 272944 0 CG33351:6 3 0 partof 177 2R:1731127-2080000 -1 CG33351:6 273761 272947 0 CG33351-PA 0 producedby MIFVLLLLLGVTSSWATDYELLLEDPDIFSTCTDGPPGSINIRQALNLDD IVIDQKGDILHVSGNATVVWDVQPTDRITARLDVFHFNRGTWEPTVFSMA TQNFCSIMYDKNQYWYKYWTRFITNRHEVEKKCFRGPDTVLVHEPFDLIL KFENFRGPLLRGRHKLVILFNALDERNIPRPNPICLEIIGEPLKLQ 196 2R:1731127-2080000 -1 CG33351-PA CG33351-PA FBpp0085519 254456 253145 Drosophila 0 CG3358 0 0 1311 melanogaster 2R:1731127-2080000 1 CG3358 FBgn0033117 FBan0003358 42D6-42E1 CG3358 AE003790 Not in SwissProt real (computational) 254456 253145 0 CG3358-RA 0 partof 53fd4476ad28714bf0d0b190e9a876e4 TTTATCCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGGTA ACTTGAGAGAAATTAACTCCTGCAGGCTTGACTAGCTAACACCTGGCAAT GCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGC TACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCG CGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGA AGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATGAGCGCATCTAC ACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCC AGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCA AGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTC TGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGC GGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGG ACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGC GGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCAT CCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGA CGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATG CTAGAAACCGACTGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACA CAAGCACGTGACCACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGA CAGCTGAATCCCTAATAGACGGACGCTGTGAGCCTTGCCAAATCAGCCAA GTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGC TGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGA GTAAAGAATAAAACAACATGCATTT 1025 2R:1731127-2080000 1 CG3358-RA CG3358-RA FBtr0086166 Perfect match to HYPO SP record with corresponding FBgn AAF57413 crosby 253434 253145 0 CG3358:5 1 0 partof 289 2R:1731127-2080000 1 CG3358:5 254261 253654 0 CG3358:3 2 0 partof 607 2R:1731127-2080000 1 CG3358:3 254456 254327 0 CG3358:4 3 0 partof 129 2R:1731127-2080000 1 CG3358:4 254439 253280 0 CG3358-PA 0 producedby MFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASK DERIYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDY DRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNK IEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLP NDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEP CQISQVLESIAGIKQEPKEQLAALYYQNTLDLFFGTGESKE 291 2R:1731127-2080000 1 CG3358-PA CG3358-PA FBpp0085499 AAF57413.1 254456 253145 0 CG3358-RB 0 partof 75434b79036882417b9213e6cd54763e TTTATCCATGCAGCGGCGTTGTTTTGGAATGGCCATGAAATATATTGACA TTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACC CAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACA GGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATG AGGCACTGGAACTGGCCTCCAAGGATGAGCGCATCTACACGACAGTGGGA ACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTA TGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCG TAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAA ACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAA ACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCA TCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTG CACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGG CGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACG CAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATGCTAGAAACCGAC TGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACACAAGCACGTGAC CACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCC TAATAGACGGACGCTGTGAGCCTTGCCAAATCAGCCAAGTTTTGGAGTCT ATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTA CCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAA ACAACATGCATTT 963 2R:1731127-2080000 1 CG3358-RB CG3358-RB FBtr0086167 AAM70836 crosby Perfect match to HYPO SP record with corresponding FBgn 253192 253145 0 CG3358:1 1 0 partof 47 2R:1731127-2080000 1 CG3358:1 253434 253254 0 CG3358:2 2 0 partof 180 2R:1731127-2080000 1 CG3358:2 254261 253654 0 CG3358:3 3 0 partof 607 2R:1731127-2080000 1 CG3358:3 254456 254327 0 CG3358:4 4 0 partof 129 2R:1731127-2080000 1 CG3358:4 254439 253152 0 CG3358-PB 0 producedby MQRRCFGMAMKYIDIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGL QKVIVTAGCLKDVDEALELASKDERIYTTVGTHPTRCEEFVPDPEGYYDQ LRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLP LFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGL YIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTK FPTVKKKEKWTAESLIDGRCEPCQISQVLESIAGIKQEPKEQLAALYYQN TLDLFFGTGESKE 313 2R:1731127-2080000 1 CG3358-PB CG3358-PB FBpp0085500 AAM70836.1 338397 336221 Drosophila 0 Tsp42Ec 0 0 2176 melanogaster 2R:1731127-2080000 1 CG12847 GO:16021 FBgn0033124 FBan0012847 42E5-42E5 Perfect match to SwissProt real (computational) Tsp42Ec AE003790 integral to membrane GO:0016021 338397 336221 0 Tsp42Ec-RA 0 partof 9eae86df15cbfef4879ef11964900b43 TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACA CCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAAT ACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTC AACTTTATTTTATATATTGTCAATATCGTGTTTTTGATCGTTGGCATCCT ACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATG TCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTC CTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTT TCGGCAGAGTGTCTGCATGACCGGCGCGTACACCAGCATGGTTTTTGTGC TCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCT GCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCA TGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTG ATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACC TGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTA CCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACA ACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTG GTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAA CGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCC AAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTC GAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGT TACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAA TATATACCGCTACAACATTT 1020 2R:1731127-2080000 1 CG12847-RA CG12847-RA FBtr0086179 crosby Perfect match to REAL SP with corresponding FBgn AAF59313 336407 336221 0 Tsp42Ec:1 1 0 partof 186 2R:1731127-2080000 1 CG12847:1 337692 337500 0 Tsp42Ec:2 2 0 partof 192 2R:1731127-2080000 1 CG12847:2 338397 337755 0 Tsp42Ec:3 3 0 partof 642 2R:1731127-2080000 1 CG12847:3 338199 336347 0 Tsp42Ec-PA 0 producedby MGCLSGIVNFILYIVNIVFLIVGILLIVLGSIMLSDLSRFDVAGSGTDPN TIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGAYTSMVFVLFILQLVLT CWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNN IGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSG LGLCIFDLVVFLIAGALTNCMRSQNAGRQVYA 232 2R:1731127-2080000 1 CG12847-PA CG12847-PA FBpp0085511 AAF59313.2 blastx_masked 1.0 aa_users_i.dros 1.0 2003-01-14 22:45:26 BLASTX Similarity to Fly genomic 2606001 340629 340437 1 0 0 0 322 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTS 192 2R:1731127-2080000 -1 NULL:1989438 FBgn0029507-u1 20 84 1 1 0 340368 340206 1 0 0 0 265 partof YSVVMLVLLVSQLALIIYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRS 162 2R:1731127-2080000 -1 NULL:1989439 FBgn0029507-u1 84 138 1 1 0 340108 339862 1 0 0 0 368 partof DSLTENIL*FQFKCCGLNGFADYGITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGVTAVEVRIAY 246 2R:1731127-2080000 -1 NULL:1989440 FBgn0029507-u1 127 208 1 1 0 2606005 340629 340449 1 0 0 0 153 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1989442 FBgn0029508-u1 20 80 1 1 0 340368 340203 1 0 0 0 103 partof YSVVMLVLLVSQLALIIYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRSV 165 2R:1731127-2080000 -1 NULL:1989443 FBgn0029508-u1 84 139 1 1 0 2606008 340629 340299 1 0 0 0 139 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTSVGAHDTCPAGCNI*IQLAPSCFQYSVVMLVLLVSQLALIIYVWVDH 330 2R:1731127-2080000 -1 NULL:1989445 FBgn0033124-u1 20 125 1 1 0 2605863 302505 302151 1 0 0 0 161 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAP-SAETSIPVEY 354 2R:1731127-2080000 -1 NULL:1989300 FBgn0034053-u1 373 490 1 1 0 2605865 302508 302097 1 0 0 0 147 partof LETLRLHTPHPFLLRRATKE---FEVPGS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE-QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 411 2R:1731127-2080000 -1 NULL:1989302 FBgn0033775-u1 376 515 1 1 0 2605867 302514 302172 1 0 0 0 190 partof FFLETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAE 342 2R:1731127-2080000 -1 NULL:1989304 FBgn0033397-u1 376 489 1 1 0 2605869 302770 302563 1 0 0 0 126 partof EIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 207 2R:1731127-2080000 -1 NULL:1989306 FBgn0033303-u1 66 133 1 1 0 302505 302157 1 0 0 0 191 partof ETLRLHTPH--PFLLRRATKE-FEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGD-GLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPV 348 2R:1731127-2080000 -1 NULL:1989307 FBgn0033303-u1 133 251 1 1 0 2605872 302941 302563 1 0 0 0 143 partof FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIE-----------IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 378 2R:1731127-2080000 -1 NULL:1989309 FBgn0013771-u1 228 365 1 1 0 302505 302091 1 0 0 0 280 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989310 FBgn0013771-u1 365 504 1 1 0 2605875 302953 302563 1 0 0 0 163 partof LALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL-----------YS-NAEKPL---TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 390 2R:1731127-2080000 -1 NULL:1989312 FBgn0033982-u1 233 377 1 1 0 2605877 303016 302563 1 0 0 0 162 partof NVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPL-----------TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 453 2R:1731127-2080000 -1 NULL:1989314 FBgn0033981-u1 201 365 1 1 0 2605879 303019 302563 1 0 0 0 183 partof DNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPLQTFL--------QLYSNAE--KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 456 2R:1731127-2080000 -1 NULL:1989316 FBgn0039519-u1 201 367 1 1 0 302505 302091 1 0 0 0 288 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYD-NRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989317 FBgn0039519-u1 367 507 1 1 0 2605882 303088 302563 1 0 0 0 164 partof ISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA---YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD---RQPL-QTFLQLYSNA----EKPL----TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 525 2R:1731127-2080000 -1 NULL:1989319 FBgn0025454-u1 178 369 1 1 0 2605884 303133 302563 1 0 0 0 189 partof RIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQKVALSQLQLH-----RRRDRQPLQTFLQL-YSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 570 2R:1731127-2080000 -1 NULL:1989321 FBgn0033980-u1 158 362 1 1 0 2605886 303151 302566 1 0 0 0 160 partof LSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADF--RMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQT-FLQLYSNAEKPLTDIE------------IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEH-GGQVTPECLRELRYTKQVL 585 2R:1731127-2080000 -1 NULL:1989323 FBgn0031126-u1 164 375 1 1 0 2605888 303175 302566 1 0 0 0 212 partof NMQKLLVRLSQISSRI---QRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQP---LQTFLQLYS-----NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1989325 FBgn0033978-u1 143 361 1 1 0 302508 302085 1 0 0 0 284 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1989326 FBgn0033978-u1 361 502 1 1 0 2600941 326642 326441 1 0 0 0 330 partof LPQICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMT 201 2R:1731127-2080000 1 NULL:1985177 FBgn0029508-u1 17 84 1 1 0 326882 326705 1 0 0 0 266 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985178 FBgn0029508-u1 84 143 1 1 0 327128 326909 1 0 0 0 374 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIAAIE 219 2R:1731127-2080000 1 NULL:1985179 FBgn0029508-u1 128 203 1 1 0 327460 327388 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1985180 FBgn0029508-u1 202 226 1 1 0 2600946 326819 326450 1 0 0 0 157 partof ICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQYSILLFVLMIGQLALVIY-MWVQKDKYLEIMGDVVEKAW 369 2R:1731127-2080000 1 NULL:1985182 FBgn0029507-u1 20 139 1 1 0 2600948 326711 326456 1 0 0 0 162 partof GILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SC-IVPFILQFKMYSLWQYS 255 2R:1731127-2080000 1 NULL:1985184 FBgn0042086-u1 22 105 1 1 0 327131 326912 1 0 0 0 133 partof 219 2R:1731127-2080000 1 NULL:1985185 FBgn0042086-u1 133 206 1 1 0 2605891 303175 302566 1 0 0 0 210 partof NMQKLLVRLSQISSRIQRDLGEKSL-QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFLQLYSN-----AEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1989328 FBgn0015714-u1 142 360 1 1 0 2605893 303247 302563 1 0 0 0 189 partof NLLQLDGHKWRSLHAKSAEVF-TPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM-WQAYLAL-EFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFL---QLYSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 684 2R:1731127-2080000 -1 NULL:1989330 FBgn0033979-u1 128 362 1 1 0 2605895 303253 302563 1 0 0 0 179 partof SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSQLQLHRRRDRQPLQTFLQLYSN--AEKPLTDIEI-AGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 690 2R:1731127-2080000 -1 NULL:1989332 FBgn0031182-u1 136 383 1 1 0 2605897 303523 302569 1 0 0 0 220 partof YWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDG-HKWRSLHAKSAEVFTPANMQ-----KLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG---QDNVEFAKWTRNYW-ADFRMWQAYLALEF-PLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTF-LQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQV 954 2R:1731127-2080000 -1 NULL:1989334 FBgn0033697-u1 23 354 1 1 0 302508 302106 1 0 0 0 155 partof LETLRLHTPHPFLLRRATKE----FEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERF-EEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 402 2R:1731127-2080000 -1 NULL:1989335 FBgn0033697-u1 355 494 1 1 0 2600951 326882 326705 1 0 0 0 113 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDY-MDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985187 FBgn0042086-u1 84 144 1 1 0 2600953 327131 326843 1 0 0 0 152 partof 288 2R:1731127-2080000 1 NULL:1985189 FBgn0029507-u1 103 205 1 1 0 2600955 328956 328704 1 0 0 0 435 partof 252 2R:1731127-2080000 1 NULL:1985191 FBgn0042086-u1 0 84 1 1 0 329272 329020 1 0 0 0 290 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCG 252 2R:1731127-2080000 1 NULL:1985192 FBgn0042086-u1 84 160 1 1 0 2600958 328950 328704 1 0 0 0 228 partof 246 2R:1731127-2080000 1 NULL:1985194 FBgn0033124-u1 0 82 1 1 0 329308 329020 1 0 0 0 88 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPS 288 2R:1731127-2080000 1 NULL:1985195 FBgn0033124-u1 84 173 1 1 0 2600961 328962 328704 1 0 0 0 210 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1985197 FBgn0029507-u1 0 86 1 1 0 329500 329257 1 0 0 0 138 partof FSCCGNTGYQQYE-TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMR 243 2R:1731127-2080000 1 NULL:1985198 FBgn0029507-u1 138 219 1 1 0 2600964 329317 329011 1 0 0 0 120 partof 306 2R:1731127-2080000 1 NULL:1985200 FBgn0029508-u1 81 177 1 1 0 2600966 329521 329230 1 0 0 0 176 partof 291 2R:1731127-2080000 1 NULL:1985202 FBgn0029508-u1 129 225 1 1 0 2600968 329506 329242 1 0 0 0 463 partof 264 2R:1731127-2080000 1 NULL:1985204 FBgn0042086-u1 134 222 1 1 0 2600970 329524 329257 1 0 0 0 220 partof 267 2R:1731127-2080000 1 NULL:1985206 FBgn0033124-u1 136 230 1 1 0 2600972 332931 332730 1 0 0 0 330 partof 201 2R:1731127-2080000 1 NULL:1985208 FBgn0029508-u1 17 84 1 1 0 333171 332994 1 0 0 0 266 partof 177 2R:1731127-2080000 1 NULL:1985209 FBgn0029508-u1 84 143 1 1 0 333417 333198 1 0 0 0 374 partof 219 2R:1731127-2080000 1 NULL:1985210 FBgn0029508-u1 128 203 1 1 0 333748 333676 1 0 0 0 127 partof QFVGFVFACCLANSIRNYRRRAEY 72 2R:1731127-2080000 1 NULL:1985211 FBgn0029508-u1 202 226 1 1 0 2600977 333108 332739 1 0 0 0 157 partof 369 2R:1731127-2080000 1 NULL:1985213 FBgn0029507-u1 20 139 1 1 0 2600979 333000 332745 1 0 0 0 162 partof 255 2R:1731127-2080000 1 NULL:1985215 FBgn0042086-u1 22 105 1 1 0 333420 333201 1 0 0 0 133 partof DFLPLPQMKCCGRSGYTDYAYQGKFPPSCCS--D-TNNCRWETVYRR-GCKVTFVEFWDRNSDIIKYAGLVIAAIEV 219 2R:1731127-2080000 1 NULL:1985216 FBgn0042086-u1 133 206 1 1 0 2600982 333171 332994 1 0 0 0 113 partof 177 2R:1731127-2080000 1 NULL:1985218 FBgn0042086-u1 84 144 1 1 0 2600984 333420 333132 1 0 0 0 152 partof YMDAIQISVSI*GLPRTC-DPPSTDFLPLPQM----KCCGRSGYTDYAYQGKFPPSCCSDTNN--CRWETVYRRG-CKVTFVEFWDRNSDIIKYAGLVIAAIEV 288 2R:1731127-2080000 1 NULL:1985220 FBgn0029507-u1 103 205 1 1 0 2600986 335244 334992 1 0 0 0 435 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTI 252 2R:1731127-2080000 1 NULL:1985222 FBgn0042086-u1 0 84 1 1 0 335560 335308 1 0 0 0 290 partof 252 2R:1731127-2080000 1 NULL:1985223 FBgn0042086-u1 84 160 1 1 0 2600989 335238 334992 1 0 0 0 228 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCT 246 2R:1731127-2080000 1 NULL:1985225 FBgn0033124-u1 0 82 1 1 0 335596 335308 1 0 0 0 88 partof 288 2R:1731127-2080000 1 NULL:1985226 FBgn0033124-u1 84 173 1 1 0 2600992 335250 334992 1 0 0 0 210 partof 258 2R:1731127-2080000 1 NULL:1985228 FBgn0029507-u1 0 86 1 1 0 335788 335545 1 0 0 0 138 partof 243 2R:1731127-2080000 1 NULL:1985229 FBgn0029507-u1 138 219 1 1 0 2600995 335605 335299 1 0 0 0 120 partof SFQYAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPSSCC 306 2R:1731127-2080000 1 NULL:1985231 FBgn0029508-u1 81 177 1 1 0 2600997 335809 335518 1 0 0 0 176 partof DIYVSIPLQFSCCGNTGYQQYE---TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQ 291 2R:1731127-2080000 1 NULL:1985233 FBgn0029508-u1 129 225 1 1 0 2600999 335794 335530 1 0 0 0 463 partof SIPLQFSCCGNTGYQQYETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR 264 2R:1731127-2080000 1 NULL:1985235 FBgn0042086-u1 134 222 1 1 0 2605900 303523 302803 1 0 0 0 155 partof YWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK--GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSQLQLHRRRDRQPLQTFLQL 720 2R:1731127-2080000 -1 NULL:1989337 FBgn0031182-u1 44 299 1 1 0 302505 302130 1 0 0 0 167 partof ETLRLHTPHPFLLRRATKE--FEV-P---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLL 375 2R:1731127-2080000 -1 NULL:1989338 FBgn0031182-u1 383 514 1 1 0 2605903 303538 302566 1 0 0 0 259 partof KFSLGYWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACL-KPFILALDLKLVHQIIF-TDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----------VGQDNVEFAKWTRNYWADFRMW---QAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQ-VTPECLRELRYTKQVL 972 2R:1731127-2080000 -1 NULL:1989340 FBgn0030949-u1 17 344 1 1 0 302508 302094 1 0 0 0 166 partof LETLRLHTPHPFLLRRATKEFEVP------GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989341 FBgn0030949-u1 344 485 1 1 0 2605906 303544 302629 1 0 0 0 181 partof LVKFSLGYWKR---RGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL--------GEKSLQTINISELVGAYNTDVMASMAFGL-VGQ-DNVEFAKWTRNYWADFRMWQAYL----ALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD-RQP--LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALE 915 2R:1731127-2080000 -1 NULL:1989343 FBgn0015038-u1 16 339 1 1 0 302505 302166 1 0 0 0 148 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETS 339 2R:1731127-2080000 -1 NULL:1989344 FBgn0015038-u1 362 479 1 1 0 2605909 303556 302836 1 0 0 0 156 partof VVYALVKFSLGYWKRRGILHEKPKFLWGNIK-GVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS--RGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKL--LVRLSQISSR--IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG--QD-NVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPA-----TAYFQKVALSQLQLHRRR 720 2R:1731127-2080000 -1 NULL:1989346 FBgn0015040-u1 15 267 1 1 0 2605911 303562 302878 1 0 0 0 301 partof LSVVYAL-VKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPAN---MQKLLVRLS-QISSRIQRDLGEKSLQ--TINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYF 684 2R:1731127-2080000 -1 NULL:1989348 FBgn0033302-u1 11 250 1 1 0 302782 302563 1 0 0 0 141 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1989349 FBgn0033302-u1 297 371 1 1 0 302505 302091 1 0 0 0 299 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989350 FBgn0033302-u1 371 509 1 1 0 2605915 303565 302566 1 0 0 0 457 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT----INISELVGAYNTDVMASMAFGLV--GQDN--VEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQT-FLQLYSNAEK--PLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 999 2R:1731127-2080000 -1 NULL:1989352 FBgn0013773-u1 10 354 1 1 0 302505 302082 1 0 0 0 251 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989353 FBgn0013773-u1 355 497 1 1 0 2605918 303565 303028 1 0 0 0 178 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS-RGLYSNPSGEPLSHNLLQLDGH--------KWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1989355 FBgn0038037-u1 11 201 1 1 0 302466 302094 1 0 0 0 210 partof RRATKE--FEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSD--IKLSVER 372 2R:1731127-2080000 -1 NULL:1989356 FBgn0038037-u1 388 515 1 1 0 2605921 303565 302644 1 0 0 0 197 partof ALSVV-YALVKFSLGYWK---RRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQ-LDGHKWRSLHAKSAEVFTPANMQKLLVRLSQ-ISSRIQR-DLGEKSLQ-----TINISELVGAYNTDVMASMAFGLV--GQDNV--EFAKWTRN--YWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD-RQP--LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEI 921 2R:1731127-2080000 -1 NULL:1989358 FBgn0015039-u1 8 334 1 1 0 302505 302169 1 0 0 0 134 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAET 336 2R:1731127-2080000 -1 NULL:1989359 FBgn0015039-u1 362 478 1 1 0 2605924 303565 303028 1 0 0 0 168 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDA-LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHF----TSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1989361 FBgn0031432-u1 14 201 1 1 0 2605926 303571 302836 1 0 0 0 258 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK---SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM-WQAYLAL-EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRR 735 2R:1731127-2080000 -1 NULL:1989363 FBgn0033979-u1 8 263 1 1 0 302583 302091 1 0 0 0 274 partof IRSKSSMVSTKY*KAL-YSSNDFTFFLE-----TLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 492 2R:1731127-2080000 -1 NULL:1989364 FBgn0033979-u1 330 500 1 1 0 2605929 303571 302764 1 0 0 0 258 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFA----KWTRNYWADF-RMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD---RQPLQTFLQLYSNAEKPLTDIEI 807 2R:1731127-2080000 -1 NULL:1989366 FBgn0038194-u1 7 286 1 1 0 302797 302581 1 0 0 0 141 partof NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRY 216 2R:1731127-2080000 -1 NULL:1989367 FBgn0038194-u1 293 365 1 1 0 302508 302094 1 0 0 0 185 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDI--KLSVER 414 2R:1731127-2080000 -1 NULL:1989368 FBgn0038194-u1 370 508 1 1 0 2605933 303580 302803 1 0 0 0 264 partof LTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSG--KRHAQDA--LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRL----SQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRM---WQAYLA----LEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 777 2R:1731127-2080000 -1 NULL:1989370 FBgn0033982-u1 9 282 1 1 0 302505 302124 1 0 0 0 202 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMP 381 2R:1731127-2080000 -1 NULL:1989371 FBgn0033982-u1 377 505 1 1 0 2605936 303583 302788 1 0 0 0 294 partof LLTALGALSVVYALVKFSL----GYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFLQLYSNAE 795 2R:1731127-2080000 -1 NULL:1989373 FBgn0015714-u1 1 281 1 1 0 302508 302085 1 0 0 0 265 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1989374 FBgn0015714-u1 360 501 1 1 0 2605939 303583 303028 1 0 0 0 266 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL---QTINISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1989376 FBgn0033980-u1 4 193 1 1 0 302505 302091 1 0 0 0 278 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA-PSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989377 FBgn0033980-u1 362 501 1 1 0 2605942 303583 302737 1 0 0 0 328 partof LLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVL 846 2R:1731127-2080000 -1 NULL:1989379 FBgn0033981-u1 6 295 1 1 0 302505 302091 1 0 0 0 282 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989380 FBgn0033981-u1 365 504 1 1 0 2605945 303583 302803 1 0 0 0 277 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAY-KGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQT---INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQ--AYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 780 2R:1731127-2080000 -1 NULL:1989382 FBgn0000473-u1 6 274 1 1 0 302941 302563 1 0 0 0 165 partof FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPLQTFL-QLYSNAEKPLT--------DI-EIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 378 2R:1731127-2080000 -1 NULL:1989383 FBgn0000473-u1 229 367 1 1 0 302505 302091 1 0 0 0 270 partof ETLRLHTPHPFLLRRATKEFEVPG-SVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989384 FBgn0000473-u1 367 506 1 1 0 2605949 303583 302875 1 0 0 0 200 partof LLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG--RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQ 708 2R:1731127-2080000 -1 NULL:1989386 FBgn0033065-u1 2 248 1 1 0 302412 302091 1 0 0 0 178 partof GNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 321 2R:1731127-2080000 -1 NULL:1989387 FBgn0033065-u1 398 505 1 1 0 2605952 303583 302566 1 0 0 0 163 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGK-RHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL----GEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYF-QKVALSQLQLHRRRD-RQPLQTF------------LQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1017 2R:1731127-2080000 -1 NULL:1989389 FBgn0032693-u1 2 338 1 1 0 302505 302094 1 0 0 0 150 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE------QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRL-LLMPKSDIKLSVER 411 2R:1731127-2080000 -1 NULL:1989390 FBgn0032693-u1 339 483 1 1 0 2605955 303583 303028 1 0 0 0 167 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQIS-------SRIQRDL--GEKSLQTI-NISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1989392 FBgn0031126-u1 7 204 1 1 0 302505 302097 1 0 0 0 173 partof ETLRLHTPHPFLLRRAT----KEFEV--PGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 408 2R:1731127-2080000 -1 NULL:1989393 FBgn0031126-u1 376 518 1 1 0 2605958 303583 302635 1 0 0 0 189 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLW-GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS---RGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQ---DN----VEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKA 948 2R:1731127-2080000 -1 NULL:1989395 FBgn0031688-u1 7 338 1 1 0 302505 302106 1 0 0 0 172 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ---ARRS-RPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 399 2R:1731127-2080000 -1 NULL:1989396 FBgn0031688-u1 356 496 1 1 0 2605961 303583 302734 1 0 0 0 312 partof LLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ-LYSNAEKPLTDIEIAGQAFGFVLA 849 2R:1731127-2080000 -1 NULL:1989398 FBgn0033978-u1 3 297 1 1 0 2605963 303586 302566 1 0 0 0 403 partof TLLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKR-HAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWAD---FRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPL-QTFLQLYSNAEKPLTDIE-IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1020 2R:1731127-2080000 -1 NULL:1989400 FBgn0033304-u1 2 351 1 1 0 302505 302085 1 0 0 0 307 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 420 2R:1731127-2080000 -1 NULL:1989401 FBgn0033304-u1 352 492 1 1 0 2605966 303586 302533 1 0 0 0 212 partof TLLTALGA-LSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTD--AGHFTSRGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTP---ANMQKLLVRLS-QISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGLVGQ---DN-VEFAKWTRNYWAD-FR-MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDR-QPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNGEYQILKSSL 1053 2R:1731127-2080000 -1 NULL:1989403 FBgn0031689-u1 5 367 1 1 0 2605968 303586 302737 1 0 0 0 289 partof TLLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLG---EKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVL 849 2R:1731127-2080000 -1 NULL:1989405 FBgn0013771-u1 4 295 1 1 0 2605970 303595 302563 1 0 0 0 1779 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1032 2R:1731127-2080000 -1 NULL:1989407 FBgn0033121-u1 0 344 1 1 0 302505 302082 1 0 0 0 724 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989408 FBgn0033121-u1 344 485 1 1 0 2605973 303595 303028 1 0 0 0 221 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFL-WGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1989410 FBgn0039006-u1 0 192 1 1 0 302505 302082 1 0 0 0 213 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV-ERVDKL 423 2R:1731127-2080000 -1 NULL:1989411 FBgn0039006-u1 375 514 1 1 0 2605976 303595 302566 1 0 0 0 390 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGE---KSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM---WQAYLALEFPLIARL-LQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAE-KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1029 2R:1731127-2080000 -1 NULL:1989413 FBgn0031726-u1 0 348 1 1 0 302505 302088 1 0 0 0 274 partof ETLRLHTPHPFLLRRATKEFEVP----GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA--PSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1989414 FBgn0031726-u1 349 492 1 1 0 2605979 303595 303028 1 0 0 0 225 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT---INISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1989416 FBgn0034756-u1 0 188 1 1 0 302508 302094 1 0 0 0 191 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989417 FBgn0034756-u1 374 510 1 1 0 2605982 303595 302548 1 0 0 0 222 partof MHRTLLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRG---LYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTP-------ANMQKLLVRLSQISSRIQRDLGEKSLQTINIS-ELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALE--FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTP-ECLRELRYTKQVLNGEYQI 1047 2R:1731127-2080000 -1 NULL:1989419 FBgn0030339-u1 0 361 1 1 0 2605984 303598 302836 1 0 0 0 223 partof LMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYT--AYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL---GEKSLQTI--NISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA---YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRR 762 2R:1731127-2080000 -1 NULL:1989421 FBgn0025454-u1 1 267 1 1 0 302505 302082 1 0 0 0 179 partof ETLRLHTPHPFLLRR-ATKEFEVPGSV-----FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989422 FBgn0025454-u1 369 515 1 1 0 2605987 303604 303028 1 0 0 0 173 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEP---LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 576 2R:1731127-2080000 -1 NULL:1989424 FBgn0028940-u1 0 197 1 1 0 302505 302091 1 0 0 0 185 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ--ARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989425 FBgn0028940-u1 362 505 1 1 0 2605990 303604 302803 1 0 0 0 260 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 801 2R:1731127-2080000 -1 NULL:1989427 FBgn0013772-u1 0 274 1 1 0 302782 302563 1 0 0 0 171 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1989428 FBgn0013772-u1 294 367 1 1 0 302505 302091 1 0 0 0 302 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989429 FBgn0013772-u1 367 506 1 1 0 2605994 303604 302731 1 0 0 0 232 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT-------INISELVGAYNTDVMASMAFGLVGQD----NVEFAKWTRNYWADFRMWQAY---LALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAG 873 2R:1731127-2080000 -1 NULL:1989431 FBgn0033696-u1 0 303 1 1 0 302508 302094 1 0 0 0 238 partof LETLRLHTPHPFLLRRAT--KEFEV-P-GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989432 FBgn0033696-u1 372 514 1 1 0 2605997 303604 302833 1 0 0 0 304 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG-RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD 771 2R:1731127-2080000 -1 NULL:1989434 FBgn0039519-u1 0 265 1 1 0 2605999 340623 340440 1 0 0 0 162 partof GILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALT 183 2R:1731127-2080000 -1 NULL:1989436 FBgn0042086-u1 22 83 1 1 0 2601001 335812 335545 1 0 0 0 220 partof FSCCGNTGYQQYE----TVPSSCCGYKDRTKVCEA-EIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQI 267 2R:1731127-2080000 1 NULL:1985237 FBgn0033124-u1 136 230 1 1 0 2601003 336572 336347 1 0 0 0 115 partof MGCLSGIVNFILYIVNIVFLVSACRLSI*VKGINNVMRRVTIDQTLLGADPK*VPIMDN------FILSNYLCYNELPKNV 225 2R:1731127-2080000 1 NULL:1985239 FBgn0033124-u1 0 79 1 1 0 2601005 337701 337494 1 0 0 0 136 partof FQIVGILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGAVSL 207 2R:1731127-2080000 1 NULL:1985241 FBgn0029507-u1 18 87 1 1 0 338196 337755 1 0 0 0 205 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH--DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVY 441 2R:1731127-2080000 1 NULL:1985242 FBgn0029507-u1 84 227 1 1 0 2601008 337692 337494 1 0 0 0 329 partof FQIVGILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGA 198 2R:1731127-2080000 1 NULL:1985244 FBgn0033124-u1 18 84 1 1 0 338199 337755 1 0 0 0 810 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVYA 444 2R:1731127-2080000 1 NULL:1985245 FBgn0033124-u1 84 232 1 1 0 2601011 337686 337506 1 0 0 0 172 partof GILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMT 180 2R:1731127-2080000 1 NULL:1985247 FBgn0042086-u1 22 82 1 1 0 338175 337755 1 0 0 0 292 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTA---MGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQ 420 2R:1731127-2080000 1 NULL:1985248 FBgn0042086-u1 84 222 1 1 0 2601014 338172 337746 1 0 0 0 194 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRS 426 2R:1731127-2080000 1 NULL:1985250 FBgn0029508-u1 81 219 1 1 0 2601016 347156 346742 1 0 0 0 205 partof VKTMSNPLFLFLRLQVI--GILGIVYGVLILKSIG-VVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSVS 414 2R:1731127-2080000 1 NULL:1985252 FBgn0042086-u1 3 141 1 1 0 2601018 347150 346748 1 0 0 0 173 partof TMSNPLFLFLRL-QVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKS 402 2R:1731127-2080000 1 NULL:1985254 FBgn0033134-u1 6 125 1 1 0 347413 347212 1 0 0 0 104 partof HCCGSSSALDYIG-K--GDLVPPSCCSG-SCLIPTNYYP-GCRGKFVELMTTGSDNAKYVGIGLIGIEVKII 201 2R:1731127-2080000 1 NULL:1985255 FBgn0033134-u1 126 198 1 1 0 2601022 347150 346763 1 0 0 0 198 partof LFLFLRLQVI-GILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKS 387 2R:1731127-2080000 1 NULL:1985257 FBgn0029507-u1 11 138 1 1 0 2601024 347153 346763 1 0 0 0 233 partof LFLF-LRLQVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 390 2R:1731127-2080000 1 NULL:1985259 FBgn0029508-u1 11 139 1 1 0 2601026 347135 346787 1 0 0 0 189 partof VIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKG-GVFD 348 2R:1731127-2080000 1 NULL:1985261 FBgn0033124-u1 20 134 1 1 0 347389 347215 1 0 0 0 99 partof CCGSSSALDYIGKGDLVPPSCCS-----GSCLIPTNYY--PGCRGKFVELMTTGSDNAKYVGIGL 174 2R:1731127-2080000 1 NULL:1985262 FBgn0033124-u1 138 203 1 1 0 2601029 347533 347170 1 0 0 0 107 partof ALSIYMTSQRNL*LHCCGS--SSALDY-IGKGDLVPPSCCSGSCLIPTNYYP-GCRGKFVELMTTGSDNAKYVGIGLIGIEVKII----R*I*VSQAALLTKYPF*LIGFIFACCLANNVRNYKRRNAY 363 2R:1731127-2080000 1 NULL:1985264 FBgn0029508-u1 97 226 1 1 0 promoter 1.0 dummy 2003-01-13 18:42:19 genomic genscan 1.0 dummy 2003-01-13 21:17:03 Genscan Gene Prediction genomic 4563 3456 1 0 0 338422,339529-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980893 3592 3456 1 0 0 1 0 4.6 partof 136 2R:1731127-2080000 1 NULL:1980894 3917 3648 1 0 0 2 0 18.65 partof 269 2R:1731127-2080000 1 NULL:1980895 4563 4035 1 0 0 3 0 27.35 partof 528 2R:1731127-2080000 1 NULL:1980896 3592 3456 1 0 0 1 0 4.6 partof 136 2R:1731127-2080000 1 NULL:1980894 3917 3648 1 0 0 2 0 18.65 partof 269 2R:1731127-2080000 1 NULL:1980895 4563 4035 1 0 0 3 0 27.35 partof 528 2R:1731127-2080000 1 NULL:1980896 14132 13112 1 0 0 348078,349098-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980897 14132 13112 1 0 0 1 0 60.46 partof 1020 2R:1731127-2080000 1 NULL:1980898 14132 13112 1 0 0 1 0 60.46 partof 1020 2R:1731127-2080000 1 NULL:1980898 20612 20351 1 0 0 355317,355578-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980899 20612 20351 1 0 0 1 0 11.16 partof 261 2R:1731127-2080000 1 NULL:1980900 20612 20351 1 0 0 1 0 11.16 partof 261 2R:1731127-2080000 1 NULL:1980900 22336 21492 1 0 0 356458,357302-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980901 21600 21492 1 0 0 1 0 6.82 partof 108 2R:1731127-2080000 1 NULL:1980902 21838 21656 1 0 0 2 0 11.37 partof 182 2R:1731127-2080000 1 NULL:1980903 22011 21894 1 0 0 3 0 4.98 partof 117 2R:1731127-2080000 1 NULL:1980904 22336 22143 1 0 0 4 0 -3.81 partof 193 2R:1731127-2080000 1 NULL:1980905 21600 21492 1 0 0 1 0 6.82 partof 108 2R:1731127-2080000 1 NULL:1980902 21838 21656 1 0 0 2 0 11.37 partof 182 2R:1731127-2080000 1 NULL:1980903 22011 21894 1 0 0 3 0 4.98 partof 117 2R:1731127-2080000 1 NULL:1980904 22336 22143 1 0 0 4 0 -3.81 partof 193 2R:1731127-2080000 1 NULL:1980905 24846 23214 1 0 0 358180,359812-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980906 23427 23214 1 0 0 1 0 22.54 partof 213 2R:1731127-2080000 1 NULL:1980907 24846 23736 1 0 0 2 0 116.46 partof 1110 2R:1731127-2080000 1 NULL:1980908 23427 23214 1 0 0 1 0 22.54 partof 213 2R:1731127-2080000 1 NULL:1980907 24846 23736 1 0 0 2 0 116.46 partof 1110 2R:1731127-2080000 1 NULL:1980908 28319 26658 1 0 0 361624,363285-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980909 26704 26658 1 0 0 1 0 8.14 partof 46 2R:1731127-2080000 1 NULL:1980910 27350 27190 1 0 0 2 0 28.55 partof 160 2R:1731127-2080000 1 NULL:1980911 28160 27823 1 0 0 3 0 43.82 partof 337 2R:1731127-2080000 1 NULL:1980912 28319 28220 1 0 0 4 0 -2.37 partof 99 2R:1731127-2080000 1 NULL:1980913 26704 26658 1 0 0 1 0 8.14 partof 46 2R:1731127-2080000 1 NULL:1980910 27350 27190 1 0 0 2 0 28.55 partof 160 2R:1731127-2080000 1 NULL:1980911 28160 27823 1 0 0 3 0 43.82 partof 337 2R:1731127-2080000 1 NULL:1980912 28319 28220 1 0 0 4 0 -2.37 partof 99 2R:1731127-2080000 1 NULL:1980913 75513 71126 1 0 0 406092,410479-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980914 71192 71126 1 0 0 1 0 -2.03 partof 66 2R:1731127-2080000 1 NULL:1980915 72544 72479 1 0 0 2 0 10.42 partof 65 2R:1731127-2080000 1 NULL:1980916 72755 72615 1 0 0 3 0 19.91 partof 140 2R:1731127-2080000 1 NULL:1980917 73319 72811 1 0 0 4 0 43.73 partof 508 2R:1731127-2080000 1 NULL:1980918 74314 73553 1 0 0 5 0 75.11 partof 761 2R:1731127-2080000 1 NULL:1980919 74969 74373 1 0 0 6 0 26.39 partof 596 2R:1731127-2080000 1 NULL:1980920 75513 75027 1 0 0 7 0 33.1 partof 486 2R:1731127-2080000 1 NULL:1980921 71192 71126 1 0 0 1 0 -2.03 partof 66 2R:1731127-2080000 1 NULL:1980915 72544 72479 1 0 0 2 0 10.42 partof 65 2R:1731127-2080000 1 NULL:1980916 72755 72615 1 0 0 3 0 19.91 partof 140 2R:1731127-2080000 1 NULL:1980917 73319 72811 1 0 0 4 0 43.73 partof 508 2R:1731127-2080000 1 NULL:1980918 74314 73553 1 0 0 5 0 75.11 partof 761 2R:1731127-2080000 1 NULL:1980919 74969 74373 1 0 0 6 0 26.39 partof 596 2R:1731127-2080000 1 NULL:1980920 75513 75027 1 0 0 7 0 33.1 partof 486 2R:1731127-2080000 1 NULL:1980921 85010 76459 1 0 0 411425,419976-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980922 76698 76459 1 0 0 1 0 18.2 partof 239 2R:1731127-2080000 1 NULL:1980923 77898 77017 1 0 0 2 0 89.67 partof 881 2R:1731127-2080000 1 NULL:1980924 78394 77953 1 0 0 3 0 44.73 partof 441 2R:1731127-2080000 1 NULL:1980925 82559 82406 1 0 0 4 0 12.24 partof 153 2R:1731127-2080000 1 NULL:1980926 82763 82617 1 0 0 5 0 17.2 partof 146 2R:1731127-2080000 1 NULL:1980927 83307 83001 1 0 0 6 0 23.05 partof 306 2R:1731127-2080000 1 NULL:1980928 84213 83954 1 0 0 7 0 15.74 partof 259 2R:1731127-2080000 1 NULL:1980929 84756 84476 1 0 0 8 0 27.44 partof 280 2R:1731127-2080000 1 NULL:1980930 84892 84819 1 0 0 9 0 3.91 partof 73 2R:1731127-2080000 1 NULL:1980931 85010 84959 1 0 0 10 0 1.23 partof 51 2R:1731127-2080000 1 NULL:1980932 76698 76459 1 0 0 1 0 18.2 partof 239 2R:1731127-2080000 1 NULL:1980923 77898 77017 1 0 0 2 0 89.67 partof 881 2R:1731127-2080000 1 NULL:1980924 78394 77953 1 0 0 3 0 44.73 partof 441 2R:1731127-2080000 1 NULL:1980925 82559 82406 1 0 0 4 0 12.24 partof 153 2R:1731127-2080000 1 NULL:1980926 82763 82617 1 0 0 5 0 17.2 partof 146 2R:1731127-2080000 1 NULL:1980927 83307 83001 1 0 0 6 0 23.05 partof 306 2R:1731127-2080000 1 NULL:1980928 84213 83954 1 0 0 7 0 15.74 partof 259 2R:1731127-2080000 1 NULL:1980929 84756 84476 1 0 0 8 0 27.44 partof 280 2R:1731127-2080000 1 NULL:1980930 84892 84819 1 0 0 9 0 3.91 partof 73 2R:1731127-2080000 1 NULL:1980931 85010 84959 1 0 0 10 0 1.23 partof 51 2R:1731127-2080000 1 NULL:1980932 351885 342831 1 0 0 224019,233073-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980933 342891 342831 1 0 0 1 0 9.85 partof 60 2R:1731127-2080000 1 NULL:1980934 347150 346787 1 0 0 2 0 41.48 partof 363 2R:1731127-2080000 1 NULL:1980935 347401 347209 1 0 0 3 0 10.29 partof 192 2R:1731127-2080000 1 NULL:1980936 348384 348287 1 0 0 4 0 -2.52 partof 97 2R:1731127-2080000 1 NULL:1980937 342891 342831 1 0 0 1 0 9.85 partof 60 2R:1731127-2080000 1 NULL:1980934 347150 346787 1 0 0 2 0 41.48 partof 363 2R:1731127-2080000 1 NULL:1980935 347401 347209 1 0 0 3 0 10.29 partof 192 2R:1731127-2080000 1 NULL:1980936 348384 348287 1 0 0 4 0 -2.52 partof 97 2R:1731127-2080000 1 NULL:1980937 318543 316119 1 0 0 197307,199731-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980941 316551 316119 1 0 0 1 0 82.81 partof 432 2R:1731127-2080000 1 NULL:1980942 316708 316608 1 0 0 2 0 11.18 partof 100 2R:1731127-2080000 1 NULL:1980943 318040 317555 1 0 0 3 0 71.34 partof 485 2R:1731127-2080000 1 NULL:1980944 318543 318357 1 0 0 4 0 8.19 partof 186 2R:1731127-2080000 1 NULL:1980945 316551 316119 1 0 0 1 0 82.81 partof 432 2R:1731127-2080000 1 NULL:1980942 316708 316608 1 0 0 2 0 11.18 partof 100 2R:1731127-2080000 1 NULL:1980943 318040 317555 1 0 0 3 0 71.34 partof 485 2R:1731127-2080000 1 NULL:1980944 318543 318357 1 0 0 4 0 8.19 partof 186 2R:1731127-2080000 1 NULL:1980945 338202 337536 1 0 0 218724,219390-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980946 337692 337536 1 0 0 1 0 30.61 partof 156 2R:1731127-2080000 1 NULL:1980947 338202 337755 1 0 0 2 0 60.72 partof 447 2R:1731127-2080000 1 NULL:1980948 337692 337536 1 0 0 1 0 30.61 partof 156 2R:1731127-2080000 1 NULL:1980947 338202 337755 1 0 0 2 0 60.72 partof 447 2R:1731127-2080000 1 NULL:1980948 335797 331273 1 0 0 212461,216985-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980949 331450 331273 1 0 0 1 0 0.41 partof 177 2R:1731127-2080000 1 NULL:1980950 332931 332739 1 0 0 2 0 26.79 partof 192 2R:1731127-2080000 1 NULL:1980951 333156 332994 1 0 0 3 0 19.27 partof 162 2R:1731127-2080000 1 NULL:1980952 333417 333222 1 0 0 4 0 42.01 partof 195 2R:1731127-2080000 1 NULL:1980953 334818 334730 1 0 0 5 0 -2.46 partof 88 2R:1731127-2080000 1 NULL:1980954 335244 334906 1 0 0 6 0 39.74 partof 338 2R:1731127-2080000 1 NULL:1980955 335473 335308 1 0 0 7 0 25.26 partof 165 2R:1731127-2080000 1 NULL:1980956 335797 335545 1 0 0 8 0 32.84 partof 252 2R:1731127-2080000 1 NULL:1980957 331450 331273 1 0 0 1 0 0.41 partof 177 2R:1731127-2080000 1 NULL:1980950 332931 332739 1 0 0 2 0 26.79 partof 192 2R:1731127-2080000 1 NULL:1980951 333156 332994 1 0 0 3 0 19.27 partof 162 2R:1731127-2080000 1 NULL:1980952 333417 333222 1 0 0 4 0 42.01 partof 195 2R:1731127-2080000 1 NULL:1980953 334818 334730 1 0 0 5 0 -2.46 partof 88 2R:1731127-2080000 1 NULL:1980954 335244 334906 1 0 0 6 0 39.74 partof 338 2R:1731127-2080000 1 NULL:1980955 335473 335308 1 0 0 7 0 25.26 partof 165 2R:1731127-2080000 1 NULL:1980956 335797 335545 1 0 0 8 0 32.84 partof 252 2R:1731127-2080000 1 NULL:1980957 329509 322902 1 0 0 204090,210697-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980958 323613 322902 1 0 0 1 0 125.21 partof 711 2R:1731127-2080000 1 NULL:1980959 325161 324996 1 0 0 2 0 2.66 partof 165 2R:1731127-2080000 1 NULL:1980960 326642 326450 1 0 0 3 0 26.79 partof 192 2R:1731127-2080000 1 NULL:1980961 326867 326705 1 0 0 4 0 19.27 partof 162 2R:1731127-2080000 1 NULL:1980962 327128 326933 1 0 0 5 0 42.01 partof 195 2R:1731127-2080000 1 NULL:1980963 328530 328442 1 0 0 6 0 -2.46 partof 88 2R:1731127-2080000 1 NULL:1980964 328956 328618 1 0 0 7 0 39.74 partof 338 2R:1731127-2080000 1 NULL:1980965 329185 329020 1 0 0 8 0 25.26 partof 165 2R:1731127-2080000 1 NULL:1980966 329509 329257 1 0 0 9 0 32.84 partof 252 2R:1731127-2080000 1 NULL:1980967 323613 322902 1 0 0 1 0 125.21 partof 711 2R:1731127-2080000 1 NULL:1980959 325161 324996 1 0 0 2 0 2.66 partof 165 2R:1731127-2080000 1 NULL:1980960 326642 326450 1 0 0 3 0 26.79 partof 192 2R:1731127-2080000 1 NULL:1980961 326867 326705 1 0 0 4 0 19.27 partof 162 2R:1731127-2080000 1 NULL:1980962 327128 326933 1 0 0 5 0 42.01 partof 195 2R:1731127-2080000 1 NULL:1980963 328530 328442 1 0 0 6 0 -2.46 partof 88 2R:1731127-2080000 1 NULL:1980964 328956 328618 1 0 0 7 0 39.74 partof 338 2R:1731127-2080000 1 NULL:1980965 329185 329020 1 0 0 8 0 25.26 partof 165 2R:1731127-2080000 1 NULL:1980966 329509 329257 1 0 0 9 0 32.84 partof 252 2R:1731127-2080000 1 NULL:1980967 288970 279279 1 0 0 160467,170158-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1980968 279444 279279 1 0 0 1 0 2.06 partof 165 2R:1731127-2080000 1 NULL:1980969 279755 279578 1 0 0 2 0 6.42 partof 177 2R:1731127-2080000 1 NULL:1980970 279929 279815 1 0 0 3 0 11.14 partof 114 2R:1731127-2080000 1 NULL:1980971 280479 280159 1 0 0 4 0 32.26 partof 320 2R:1731127-2080000 1 NULL:1980972 280820 280538 1 0 0 5 0 17.03 partof 282 2R:1731127-2080000 1 NULL:1980973 281086 280986 1 0 0 6 0 -6.09 partof 100 2R:1731127-2080000 1 NULL:1980974 281337 281145 1 0 0 7 0 15.99 partof 192 2R:1731127-2080000 1 NULL:1980975 281864 281690 1 0 0 8 0 9.14 partof 174 2R:1731127-2080000 1 NULL:1980976 284818 283536 1 0 0 9 0 35.1 partof 1282 2R:1731127-2080000 1 NULL:1980977 287887 284826 1 0 0 10 0 165.17 partof 3061 2R:1731127-2080000 1 NULL:1980978 288970 288510 1 0 0 11 0 33.26 partof 460 2R:1731127-2080000 1 NULL:1980979 279444 279279 1 0 0 1 0 2.06 partof 165 2R:1731127-2080000 1 NULL:1980969 279755 279578 1 0 0 2 0 6.42 partof 177 2R:1731127-2080000 1 NULL:1980970 279929 279815 1 0 0 3 0 11.14 partof 114 2R:1731127-2080000 1 NULL:1980971 280479 280159 1 0 0 4 0 32.26 partof 320 2R:1731127-2080000 1 NULL:1980972 280820 280538 1 0 0 5 0 17.03 partof 282 2R:1731127-2080000 1 NULL:1980973 281086 280986 1 0 0 6 0 -6.09 partof 100 2R:1731127-2080000 1 NULL:1980974 281337 281145 1 0 0 7 0 15.99 partof 192 2R:1731127-2080000 1 NULL:1980975 281864 281690 1 0 0 8 0 9.14 partof 174 2R:1731127-2080000 1 NULL:1980976 284818 283536 1 0 0 9 0 35.1 partof 1282 2R:1731127-2080000 1 NULL:1980977 287887 284826 1 0 0 10 0 165.17 partof 3061 2R:1731127-2080000 1 NULL:1980978 288970 288510 1 0 0 11 0 33.26 partof 460 2R:1731127-2080000 1 NULL:1980979 86638 86132 1 0 0 421604,421098-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985329 86638 86460 1 0 0 1 0 15.62 partof 178 2R:1731127-2080000 -1 NULL:1985330 86411 86317 1 0 0 2 0 10.12 partof 94 2R:1731127-2080000 -1 NULL:1985331 86256 86132 1 0 0 3 0 8.06 partof 124 2R:1731127-2080000 -1 NULL:1985332 86638 86460 1 0 0 1 0 15.62 partof 178 2R:1731127-2080000 -1 NULL:1985330 86411 86317 1 0 0 2 0 10.12 partof 94 2R:1731127-2080000 -1 NULL:1985331 86256 86132 1 0 0 3 0 8.06 partof 124 2R:1731127-2080000 -1 NULL:1985332 88546 87610 1 0 0 423512,422576-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985333 88546 87610 1 0 0 1 0 172.19 partof 936 2R:1731127-2080000 -1 NULL:1985334 88546 87610 1 0 0 1 0 172.19 partof 936 2R:1731127-2080000 -1 NULL:1985334 99449 92421 1 0 0 434415,427387-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985335 99449 99082 1 0 0 1 0 37.59 partof 367 2R:1731127-2080000 -1 NULL:1985336 98798 98700 1 0 0 2 0 11.23 partof 98 2R:1731127-2080000 -1 NULL:1985337 98440 98353 1 0 0 3 0 1.17 partof 87 2R:1731127-2080000 -1 NULL:1985338 98285 98143 1 0 0 4 0 13.63 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2R:1731127-2080000 -1 NULL:1985413 194824 194410 1 0 0 7 0 51.3 partof 414 2R:1731127-2080000 -1 NULL:1985414 194346 194052 1 0 0 8 0 26.21 partof 294 2R:1731127-2080000 -1 NULL:1985415 193879 193765 1 0 0 9 0 1.34 partof 114 2R:1731127-2080000 -1 NULL:1985416 193308 193122 1 0 0 10 0 17.19 partof 186 2R:1731127-2080000 -1 NULL:1985417 193064 192836 1 0 0 11 0 37.03 partof 228 2R:1731127-2080000 -1 NULL:1985418 169046 168364 1 0 0 50234,49552-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985419 169046 169008 1 0 0 1 0 2.19 partof 38 2R:1731127-2080000 -1 NULL:1985420 168530 168364 1 0 0 2 0 18.69 partof 166 2R:1731127-2080000 -1 NULL:1985421 169046 169008 1 0 0 1 0 2.19 partof 38 2R:1731127-2080000 -1 NULL:1985420 168530 168364 1 0 0 2 0 18.69 partof 166 2R:1731127-2080000 -1 NULL:1985421 140212 138991 1 0 0 21400,20179-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985422 140212 140173 1 0 0 1 0 0.18 partof 39 2R:1731127-2080000 -1 NULL:1985423 140114 139975 1 0 0 2 0 16.34 partof 139 2R:1731127-2080000 -1 NULL:1985424 139439 139344 1 0 0 3 0 5.48 partof 95 2R:1731127-2080000 -1 NULL:1985425 139286 139198 1 0 0 4 0 7.14 partof 88 2R:1731127-2080000 -1 NULL:1985426 139131 138991 1 0 0 5 0 22.73 partof 140 2R:1731127-2080000 -1 NULL:1985427 140212 140173 1 0 0 1 0 0.18 partof 39 2R:1731127-2080000 -1 NULL:1985423 140114 139975 1 0 0 2 0 16.34 partof 139 2R:1731127-2080000 -1 NULL:1985424 139439 139344 1 0 0 3 0 5.48 partof 95 2R:1731127-2080000 -1 NULL:1985425 139286 139198 1 0 0 4 0 7.14 partof 88 2R:1731127-2080000 -1 NULL:1985426 139131 138991 1 0 0 5 0 22.73 partof 140 2R:1731127-2080000 -1 NULL:1985427 134736 119507 1 0 0 15924,695-AE003790.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985428 134736 134691 1 0 0 1 0 -5.1 partof 45 2R:1731127-2080000 -1 NULL:1985429 134535 134390 1 0 0 2 0 20.86 partof 145 2R:1731127-2080000 -1 NULL:1985430 132872 132798 1 0 0 3 0 -5.27 partof 74 2R:1731127-2080000 -1 NULL:1985431 130204 130057 1 0 0 4 0 8.63 partof 147 2R:1731127-2080000 -1 NULL:1985432 128137 128006 1 0 0 5 0 0.59 partof 131 2R:1731127-2080000 -1 NULL:1985433 127187 126943 1 0 0 6 0 11.4 partof 244 2R:1731127-2080000 -1 NULL:1985434 124876 124754 1 0 0 7 0 -6.11 partof 122 2R:1731127-2080000 -1 NULL:1985435 122396 122253 1 0 0 8 0 10.8 partof 143 2R:1731127-2080000 -1 NULL:1985436 122185 122090 1 0 0 9 0 13.78 partof 95 2R:1731127-2080000 -1 NULL:1985437 119564 119507 1 0 0 10 0 -2.21 partof 57 2R:1731127-2080000 -1 NULL:1985438 134736 134691 1 0 0 1 0 -5.1 partof 45 2R:1731127-2080000 -1 NULL:1985429 134535 134390 1 0 0 2 0 20.86 partof 145 2R:1731127-2080000 -1 NULL:1985430 132872 132798 1 0 0 3 0 -5.27 partof 74 2R:1731127-2080000 -1 NULL:1985431 130204 130057 1 0 0 4 0 8.63 partof 147 2R:1731127-2080000 -1 NULL:1985432 128137 128006 1 0 0 5 0 0.59 partof 131 2R:1731127-2080000 -1 NULL:1985433 127187 126943 1 0 0 6 0 11.4 partof 244 2R:1731127-2080000 -1 NULL:1985434 124876 124754 1 0 0 7 0 -6.11 partof 122 2R:1731127-2080000 -1 NULL:1985435 122396 122253 1 0 0 8 0 10.8 partof 143 2R:1731127-2080000 -1 NULL:1985436 122185 122090 1 0 0 9 0 13.78 partof 95 2R:1731127-2080000 -1 NULL:1985437 119564 119507 1 0 0 10 0 -2.21 partof 57 2R:1731127-2080000 -1 NULL:1985438 2634 806 1 0 0 337600,335772-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985265 2634 1282 1 0 0 1 0 167.71 partof 1352 2R:1731127-2080000 -1 NULL:1985266 1173 806 1 0 0 2 0 21.48 partof 367 2R:1731127-2080000 -1 NULL:1985267 2634 1282 1 0 0 1 0 167.71 partof 1352 2R:1731127-2080000 -1 NULL:1985266 1173 806 1 0 0 2 0 21.48 partof 367 2R:1731127-2080000 -1 NULL:1985267 5465 4847 1 0 0 340431,339813-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985268 5465 5381 1 0 0 1 0 3.32 partof 84 2R:1731127-2080000 -1 NULL:1985269 5315 4847 1 0 0 2 0 66.27 partof 468 2R:1731127-2080000 -1 NULL:1985270 5465 5381 1 0 0 1 0 3.32 partof 84 2R:1731127-2080000 -1 NULL:1985269 5315 4847 1 0 0 2 0 66.27 partof 468 2R:1731127-2080000 -1 NULL:1985270 9954 7080 1 0 0 344920,342046-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985271 9954 9824 1 0 0 1 0 18.01 partof 130 2R:1731127-2080000 -1 NULL:1985272 8836 7731 1 0 0 2 0 180.42 partof 1105 2R:1731127-2080000 -1 NULL:1985273 7609 7080 1 0 0 3 0 68.03 partof 529 2R:1731127-2080000 -1 NULL:1985274 9954 9824 1 0 0 1 0 18.01 partof 130 2R:1731127-2080000 -1 NULL:1985272 8836 7731 1 0 0 2 0 180.42 partof 1105 2R:1731127-2080000 -1 NULL:1985273 7609 7080 1 0 0 3 0 68.03 partof 529 2R:1731127-2080000 -1 NULL:1985274 18277 14746 1 0 0 353243,349712-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985275 18277 18147 1 0 0 1 0 16.71 partof 130 2R:1731127-2080000 -1 NULL:1985276 18085 17777 1 0 0 2 0 33.17 partof 308 2R:1731127-2080000 -1 NULL:1985277 17617 16913 1 0 0 3 0 115.56 partof 704 2R:1731127-2080000 -1 NULL:1985278 16561 16434 1 0 0 4 0 11.98 partof 127 2R:1731127-2080000 -1 NULL:1985279 15554 15045 1 0 0 5 0 87.37 partof 509 2R:1731127-2080000 -1 NULL:1985280 14936 14746 1 0 0 6 0 28.72 partof 190 2R:1731127-2080000 -1 NULL:1985281 18277 18147 1 0 0 1 0 16.71 partof 130 2R:1731127-2080000 -1 NULL:1985276 18085 17777 1 0 0 2 0 33.17 partof 308 2R:1731127-2080000 -1 NULL:1985277 17617 16913 1 0 0 3 0 115.56 partof 704 2R:1731127-2080000 -1 NULL:1985278 16561 16434 1 0 0 4 0 11.98 partof 127 2R:1731127-2080000 -1 NULL:1985279 15554 15045 1 0 0 5 0 87.37 partof 509 2R:1731127-2080000 -1 NULL:1985280 14936 14746 1 0 0 6 0 28.72 partof 190 2R:1731127-2080000 -1 NULL:1985281 26174 25368 1 0 0 361140,360334-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985282 26174 26114 1 0 0 1 0 6.95 partof 60 2R:1731127-2080000 -1 NULL:1985283 26040 25666 1 0 0 2 0 68.36 partof 374 2R:1731127-2080000 -1 NULL:1985284 25606 25368 1 0 0 3 0 17.74 partof 238 2R:1731127-2080000 -1 NULL:1985285 26174 26114 1 0 0 1 0 6.95 partof 60 2R:1731127-2080000 -1 NULL:1985283 26040 25666 1 0 0 2 0 68.36 partof 374 2R:1731127-2080000 -1 NULL:1985284 25606 25368 1 0 0 3 0 17.74 partof 238 2R:1731127-2080000 -1 NULL:1985285 34168 30447 1 0 0 369134,365413-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985286 34168 32161 1 0 0 1 0 274.13 partof 2007 2R:1731127-2080000 -1 NULL:1985287 31697 31587 1 0 0 2 0 11.88 partof 110 2R:1731127-2080000 -1 NULL:1985288 31146 30964 1 0 0 3 0 16.21 partof 182 2R:1731127-2080000 -1 NULL:1985289 30897 30656 1 0 0 4 0 26.71 partof 241 2R:1731127-2080000 -1 NULL:1985290 30592 30447 1 0 0 5 0 2.58 partof 145 2R:1731127-2080000 -1 NULL:1985291 34168 32161 1 0 0 1 0 274.13 partof 2007 2R:1731127-2080000 -1 NULL:1985287 31697 31587 1 0 0 2 0 11.88 partof 110 2R:1731127-2080000 -1 NULL:1985288 31146 30964 1 0 0 3 0 16.21 partof 182 2R:1731127-2080000 -1 NULL:1985289 30897 30656 1 0 0 4 0 26.71 partof 241 2R:1731127-2080000 -1 NULL:1985290 30592 30447 1 0 0 5 0 2.58 partof 145 2R:1731127-2080000 -1 NULL:1985291 37936 35108 1 0 0 372902,370074-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985292 37936 37769 1 0 0 1 0 10.61 partof 167 2R:1731127-2080000 -1 NULL:1985293 35664 35108 1 0 0 2 0 28.5 partof 556 2R:1731127-2080000 -1 NULL:1985294 37936 37769 1 0 0 1 0 10.61 partof 167 2R:1731127-2080000 -1 NULL:1985293 35664 35108 1 0 0 2 0 28.5 partof 556 2R:1731127-2080000 -1 NULL:1985294 47451 45278 1 0 0 382417,380244-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985295 47451 46406 1 0 0 1 0 97.85 partof 1045 2R:1731127-2080000 -1 NULL:1985296 45331 45278 1 0 0 2 0 -0.51 partof 53 2R:1731127-2080000 -1 NULL:1985297 47451 46406 1 0 0 1 0 97.85 partof 1045 2R:1731127-2080000 -1 NULL:1985296 45331 45278 1 0 0 2 0 -0.51 partof 53 2R:1731127-2080000 -1 NULL:1985297 49308 48390 1 0 0 384274,383356-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985298 49308 48390 1 0 0 1 0 117.55 partof 918 2R:1731127-2080000 -1 NULL:1985299 49308 48390 1 0 0 1 0 117.55 partof 918 2R:1731127-2080000 -1 NULL:1985299 70027 51365 1 0 0 404993,386331-AE003789.Feb-dummy-genscan 0 0 2R:1731127-2080000 NULL:1985300 70027 69813 1 0 0 1 0 36.51 partof 214 2R:1731127-2080000 -1 NULL:1985301 68130 67973 1 0 0 2 0 33.07 partof 157 2R:1731127-2080000 -1 NULL:1985302 67902 67735 1 0 0 3 0 24.4 partof 167 2R:1731127-2080000 -1 NULL:1985303 65289 65148 1 0 0 4 0 3.82 partof 141 2R:1731127-2080000 -1 NULL:1985304 64686 64503 1 0 0 5 0 19.56 partof 183 2R:1731127-2080000 -1 NULL:1985305 64373 64229 1 0 0 6 0 17.15 partof 144 2R:1731127-2080000 -1 NULL:1985306 64167 64033 1 0 0 7 0 26.76 partof 134 2R:1731127-2080000 -1 NULL:1985307 63969 63788 1 0 0 8 0 11.54 partof 181 2R:1731127-2080000 -1 NULL:1985308 63753 63402 1 0 0 9 0 42.99 partof 351 2R:1731127-2080000 -1 NULL:1985309 63086 62717 1 0 0 10 0 52.48 partof 369 2R:1731127-2080000 -1 NULL:1985310 62657 62012 1 0 0 11 0 102.66 partof 645 2R:1731127-2080000 -1 NULL:1985311 61959 61776 1 0 0 12 0 34.86 partof 183 2R:1731127-2080000 -1 NULL:1985312 61709 61571 1 0 0 13 0 17.64 partof 138 2R:1731127-2080000 -1 NULL:1985313 61508 61325 1 0 0 14 0 31.06 partof 183 2R:1731127-2080000 -1 NULL:1985314 61041 60075 1 0 0 15 0 233.19 partof 966 2R:1731127-2080000 -1 NULL:1985315 58848 58365 1 0 0 16 0 78.2 partof 483 2R:1731127-2080000 -1 NULL:1985316 56163 56031 1 0 0 17 0 7.72 partof 132 2R:1731127-2080000 -1 NULL:1985317 55802 55478 1 0 0 18 0 68.85 partof 324 2R:1731127-2080000 -1 NULL:1985318 55414 55225 1 0 0 19 0 31.06 partof 189 2R:1731127-2080000 -1 NULL:1985319 55167 55029 1 0 0 20 0 13.54 partof 138 2R:1731127-2080000 -1 NULL:1985320 54591 54441 1 0 0 21 0 7.73 partof 150 2R:1731127-2080000 -1 NULL:1985321 53797 53614 1 0 0 22 0 16.86 partof 183 2R:1731127-2080000 -1 NULL:1985322 53562 53430 1 0 0 23 0 12.82 partof 132 2R:1731127-2080000 -1 NULL:1985323 52683 52526 1 0 0 24 0 23.97 partof 157 2R:1731127-2080000 -1 NULL:1985324 52469 52082 1 0 0 25 0 34.2 partof 387 2R:1731127-2080000 -1 NULL:1985325 52029 51862 1 0 0 26 0 5.9 partof 167 2R:1731127-2080000 -1 NULL:1985326 51802 51619 1 0 0 27 0 23.26 partof 183 2R:1731127-2080000 -1 NULL:1985327 51553 51365 1 0 0 28 0 23.35 partof 188 2R:1731127-2080000 -1 NULL:1985328 70027 69813 1 0 0 1 0 36.51 partof 214 2R:1731127-2080000 -1 NULL:1985301 68130 67973 1 0 0 2 0 33.07 partof 157 2R:1731127-2080000 -1 NULL:1985302 67902 67735 1 0 0 3 0 24.4 partof 167 2R:1731127-2080000 -1 NULL:1985303 65289 65148 1 0 0 4 0 3.82 partof 141 2R:1731127-2080000 -1 NULL:1985304 64686 64503 1 0 0 5 0 19.56 partof 183 2R:1731127-2080000 -1 NULL:1985305 64373 64229 1 0 0 6 0 17.15 partof 144 2R:1731127-2080000 -1 NULL:1985306 64167 64033 1 0 0 7 0 26.76 partof 134 2R:1731127-2080000 -1 NULL:1985307 63969 63788 1 0 0 8 0 11.54 partof 181 2R:1731127-2080000 -1 NULL:1985308 63753 63402 1 0 0 9 0 42.99 partof 351 2R:1731127-2080000 -1 NULL:1985309 63086 62717 1 0 0 10 0 52.48 partof 369 2R:1731127-2080000 -1 NULL:1985310 62657 62012 1 0 0 11 0 102.66 partof 645 2R:1731127-2080000 -1 NULL:1985311 61959 61776 1 0 0 12 0 34.86 partof 183 2R:1731127-2080000 -1 NULL:1985312 61709 61571 1 0 0 13 0 17.64 partof 138 2R:1731127-2080000 -1 NULL:1985313 61508 61325 1 0 0 14 0 31.06 partof 183 2R:1731127-2080000 -1 NULL:1985314 61041 60075 1 0 0 15 0 233.19 partof 966 2R:1731127-2080000 -1 NULL:1985315 58848 58365 1 0 0 16 0 78.2 partof 483 2R:1731127-2080000 -1 NULL:1985316 56163 56031 1 0 0 17 0 7.72 partof 132 2R:1731127-2080000 -1 NULL:1985317 55802 55478 1 0 0 18 0 68.85 partof 324 2R:1731127-2080000 -1 NULL:1985318 55414 55225 1 0 0 19 0 31.06 partof 189 2R:1731127-2080000 -1 NULL:1985319 55167 55029 1 0 0 20 0 13.54 partof 138 2R:1731127-2080000 -1 NULL:1985320 54591 54441 1 0 0 21 0 7.73 partof 150 2R:1731127-2080000 -1 NULL:1985321 53797 53614 1 0 0 22 0 16.86 partof 183 2R:1731127-2080000 -1 NULL:1985322 53562 53430 1 0 0 23 0 12.82 partof 132 2R:1731127-2080000 -1 NULL:1985323 52683 52526 1 0 0 24 0 23.97 partof 157 2R:1731127-2080000 -1 NULL:1985324 52469 52082 1 0 0 25 0 34.2 partof 387 2R:1731127-2080000 -1 NULL:1985325 52029 51862 1 0 0 26 0 5.9 partof 167 2R:1731127-2080000 -1 NULL:1985326 51802 51619 1 0 0 27 0 23.26 partof 183 2R:1731127-2080000 -1 NULL:1985327 51553 51365 1 0 0 28 0 23.35 partof 188 2R:1731127-2080000 -1 NULL:1985328 JOSHTRANSPOSON 1.0 Sept 1.0 2003-04-16 18:01:39 Transposon genomic 320532 318902 1 0 0 JOSHTRANSPOSON-HB{}761-pred 0 0 1630 2R:1731127-2080000 1 JOSHTRANSPOSON-HB{}761-pred 129495 129368 1 0 0 JOSHTRANSPOSON-BS{}759-pred 0 0 127 2R:1731127-2080000 1 JOSHTRANSPOSON-BS{}759-pred 289518 281993 1 0 0 JOSHTRANSPOSON-opus{}760-pred 0 0 7525 2R:1731127-2080000 1 JOSHTRANSPOSON-opus{}760-pred blastx_masked 1.0 aa_SPTR.plant 1.0 2003-01-13 22:33:49 BLASTX Similarity to Other Species genomic 2604473 5309 4850 1 0 0 0 627 partof GRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVL-DGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 459 2R:1731127-2080000 -1 NULL:1988123 Q9ZRQ9 35 189 1 1 0 2604476 5309 4850 1 0 0 0 604 partof GRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVL-DGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 459 2R:1731127-2080000 -1 NULL:1988125 Q9ZVJ4 45 199 1 1 0 2604479 5318 4850 1 0 0 0 489 partof QEIGRMIFELFADTVPRTAENFRQFCTGE--YRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1988127 O64456 14 171 1 1 0 2604482 8840 7733 1 0 0 0 773 partof PADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEKATKMALV---KLRIIDADEHGR--MRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL---TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRM 1107 2R:1731127-2080000 -1 NULL:1988129 Q9M0G4 105 471 1 1 0 7602 7416 1 0 0 0 104 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR-DH 186 2R:1731127-2080000 -1 NULL:1988130 Q9M0G4 481 544 1 1 0 2604485 8846 7733 1 0 0 0 822 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEKATKMALV---KLRII--DADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTG---VDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRM 1113 2R:1731127-2080000 -1 NULL:1988132 Q9SMY2 51 418 1 1 0 2604487 8846 7733 1 0 0 0 841 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEKATKMALV---KLRII--DADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTG---VDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRM 1113 2R:1731127-2080000 -1 NULL:1988134 Q9SK68 40 408 1 1 0 2604489 15524 15344 1 0 0 0 101 partof SDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAE-DIDYAWDIIVDFANELL 180 2R:1731127-2080000 -1 NULL:1988136 O82415 450 510 1 1 0 2604492 15524 15344 1 0 0 0 101 partof SDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAE-DIDYAWDIIVDFANELL 180 2R:1731127-2080000 -1 NULL:1988138 P54768 450 510 1 1 0 2604495 15542 15344 1 0 0 0 104 partof CFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAE-DIDYAWDIIVDFANELL 198 2R:1731127-2080000 -1 NULL:1988140 P54771 449 514 1 1 0 2604498 18125 17777 1 0 0 0 308 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1988142 Q9SK68 33 143 1 1 0 17620 17146 1 0 0 0 227 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFV---KLRILEPDDDAS--LRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANL 474 2R:1731127-2080000 -1 NULL:1988143 Q9SK68 142 294 1 1 0 17128 16870 1 0 0 0 244 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDA--AIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1988144 Q9SK68 284 371 1 1 0 2598702 3606 3480 1 0 0 0 78 partof IVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSAGEKCY 126 2R:1731127-2080000 1 NULL:1983314 AAK95279 9 50 1 1 0 3974 3644 1 0 0 0 142 partof ADGLEIQEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLR------LLRKFRREVRPDSPCYM----LTHIFAVVCL 330 2R:1731127-2080000 1 NULL:1983315 AAK95279 56 174 1 1 0 4509 4041 1 0 0 0 200 partof LNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPLASLYYECV 468 2R:1731127-2080000 1 NULL:1983316 AAK95279 173 327 1 1 0 2598707 3887 3680 1 0 0 0 146 partof FYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVH 207 2R:1731127-2080000 1 NULL:1983318 Q9FX73 61 130 1 1 0 4509 4038 1 0 0 0 262 partof SLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPLASLYYECV 471 2R:1731127-2080000 1 NULL:1983319 Q9FX73 167 322 1 1 0 2598711 3974 3686 1 0 0 0 139 partof QQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLR------LLRKFRREVRPDSPCYM----LTHIFAVVCL 288 2R:1731127-2080000 1 NULL:1983321 Q9FIS5 1 107 1 1 0 4509 4041 1 0 0 0 200 partof LNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPLASLYYECV 468 2R:1731127-2080000 1 NULL:1983322 Q9FIS5 106 260 1 1 0 2598715 27351 27189 1 0 0 0 267 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983324 P92963 15 69 1 1 0 28160 27821 1 0 0 0 466 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNE 339 2R:1731127-2080000 1 NULL:1983325 P92963 68 181 1 1 0 2598719 27351 27189 1 0 0 0 274 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983327 P36863 15 69 1 1 0 28160 27821 1 0 0 0 486 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNE 339 2R:1731127-2080000 1 NULL:1983328 P36863 68 181 1 1 0 2598722 27351 27189 1 0 0 0 274 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983330 Q39570 15 69 1 1 0 28160 27821 1 0 0 0 486 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNE 339 2R:1731127-2080000 1 NULL:1983331 Q39570 68 181 1 1 0 2598725 76648 76429 1 0 0 0 192 partof SKLF*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGE 219 2R:1731127-2080000 1 NULL:1983333 O49501 57 130 1 1 0 77909 77024 1 0 0 0 963 partof CLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVK--------------AATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 885 2R:1731127-2080000 1 NULL:1983334 O49501 148 447 1 1 0 78168 77931 1 0 0 0 291 partof IMISIYVGFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQ 237 2R:1731127-2080000 1 NULL:1983335 O49501 436 515 1 1 0 2598730 76648 76429 1 0 0 0 192 partof SKLF*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGE 219 2R:1731127-2080000 1 NULL:1983337 Q9LDD8 57 130 1 1 0 77909 77024 1 0 0 0 998 partof CLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 885 2R:1731127-2080000 1 NULL:1983338 Q9LDD8 148 433 1 1 0 78426 77931 1 0 0 0 542 partof IMISIYVGFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 495 2R:1731127-2080000 1 NULL:1983339 Q9LDD8 422 587 1 1 0 2598735 76648 76429 1 0 0 0 192 partof SKLF*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGE 219 2R:1731127-2080000 1 NULL:1983341 AAK62371 57 130 1 1 0 77909 76997 1 0 0 0 999 partof ICNFHYRTECLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 912 2R:1731127-2080000 1 NULL:1983342 AAK62371 140 433 1 1 0 78426 77931 1 0 0 0 542 partof IMISIYVGFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 495 2R:1731127-2080000 1 NULL:1983343 AAK62371 422 587 1 1 0 2598740 82561 82438 1 0 0 0 81 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1983345 Q9FGQ6 0 40 1 1 0 82763 82616 1 0 0 0 124 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1983346 Q9FGQ6 39 88 1 1 0 84209 83957 1 0 0 0 124 partof IPIDKLVKGRFQDNFEFLQWFKKFFDANYDGR-DYDASAVREGAPMGFGSGAVKSLPGTAASGVSSSYRRGPSATTRPAMTSAVK 252 2R:1731127-2080000 1 NULL:1983347 Q9FGQ6 89 168 1 1 0 2598744 82763 82616 1 0 0 0 125 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1983349 Q9FJJ5 39 88 1 1 0 2598746 138320 137936 1 0 0 0 486 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK*VGAIP 384 2R:1731127-2080000 1 NULL:1983351 Q9FM32 47 173 1 1 0 138691 138349 1 0 0 0 417 partof LCRNEAGEKKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKL 342 2R:1731127-2080000 1 NULL:1983352 Q9FM32 163 276 1 1 0 2598749 138320 137936 1 0 0 0 482 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK*VGAIP 384 2R:1731127-2080000 1 NULL:1983354 Q9LTZ2 48 174 1 1 0 138691 138388 1 0 0 0 413 partof QYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKL 303 2R:1731127-2080000 1 NULL:1983355 Q9LTZ2 176 277 1 1 0 2598752 138320 137936 1 0 0 0 482 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK*VGAIP 384 2R:1731127-2080000 1 NULL:1983357 AAK59518 48 174 1 1 0 138691 138388 1 0 0 0 413 partof QYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKL 303 2R:1731127-2080000 1 NULL:1983358 AAK59518 176 277 1 1 0 2598756 212407 211633 1 0 0 0 274 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGL-QLGPGDRHHI-ALNFGEFWRTSCNYGDRG-PVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSE-GATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY----DYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEI--F-LPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1983360 Q40076 36 302 1 1 0 2598758 212416 211633 1 0 0 0 283 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDR-HHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEG-ATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY----DYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEI--F-LPRMCIEYDVDLKQVLNQV 783 2R:1731127-2080000 1 NULL:1983362 Q9ST57 36 302 1 1 0 2598760 212431 211633 1 0 0 0 278 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGD---RHHIALNFGEF-WRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEG-ATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY----DYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEI--F-LPRMCIEYDVDLKQVLNQVRYI*P 798 2R:1731127-2080000 1 NULL:1983364 P93692 36 307 1 1 0 2598762 214245 213471 1 0 0 0 305 partof NLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSE-DKEAVAARYGALLNDLQGQ---EEGPILKLANRIYVNDQYSLNQNYN-LAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDA-QVIELPYL----NSNLSMTIFLPREVEGLSALEEKIV---GFAR---PLVAKEV-YLKLPKFKIEFRDELKETLEKVRLR 774 2R:1731127-2080000 1 NULL:1983366 Q43492 35 307 1 1 0 2598764 214245 213471 1 0 0 0 294 partof NLVVSPVSIETILSMVFMGAEGSTAKELQSALGL--PSEDKE--AVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYN-LAVREPFKSEAESISLTNGPV-AAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLD-AQVIELPYLNSN----LSMTIFLPREVEGLSALEEKIVG---FARPLVAKEVY----LKLPKFKIEFRDELKETLEKVRLR 774 2R:1731127-2080000 1 NULL:1983368 Q40076 36 308 1 1 0 2598766 214245 213471 1 0 0 0 297 partof NLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPS-EDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYN-LAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDA-QVIELPYLNSN----LSMTIFLPREVEGLSALEEKIVG----FARPLVAKEVYL---KLPKFKIEFRDELKETLEKVRLR 774 2R:1731127-2080000 1 NULL:1983370 Q9ST58 36 305 1 1 0 2598768 217109 216335 1 0 0 0 261 partof MANTL--NYSKSPAGEAQFASQLFGQLAKS--QSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTE-VAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYT-GTD---IVFLIILPQEEQGLAIVEEKL 774 2R:1731127-2080000 1 NULL:1983372 Q9ST58 0 261 1 1 0 2598770 217109 216335 1 0 0 0 263 partof MANTL--NYSKSPAGEAQFASQLFGQLAKS--QSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTE-VAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYT-GTD---IVFLIILPQEEQGLAIVEEKL 774 2R:1731127-2080000 1 NULL:1983374 P93693 0 262 1 1 0 2598773 217109 216335 1 0 0 0 262 partof MANTL--NYSKSPAGEAQFASQLFGQLAKSQSG--RNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTE-VAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTM--SQEDYFRFGELTELKAKVVELPYT-GTD---IVFLIILPQEEQGLAIVEEKL 774 2R:1731127-2080000 1 NULL:1983376 P93692 0 261 1 1 0 2598775 254271 253656 1 0 0 0 568 partof RIYTTVGTHPTRCEEFVP--DPEGYYDQLRSRIKAN--RTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEPCQIRYSL 615 2R:1731127-2080000 1 NULL:1983378 Q9SVC1 54 259 1 1 0 2604502 18248 17777 1 0 0 0 310 partof HGNGGVHLQLSGNAERATGHAQRG--AGIFETPVAT*ATKMTAEPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 471 2R:1731127-2080000 -1 NULL:1988146 Q9SMY2 2 154 1 1 0 17620 17146 1 0 0 0 208 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFV---KLRILEPDDDAS--LRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANL 474 2R:1731127-2080000 -1 NULL:1988147 Q9SMY2 153 304 1 1 0 17128 16870 1 0 0 0 244 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDA--AIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1988148 Q9SMY2 294 381 1 1 0 2604506 18248 17777 1 0 0 0 310 partof HGNGGVHLQLSGNAERATGHAQRG--AGIFETPVAT*ATKMTAEPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 471 2R:1731127-2080000 -1 NULL:1988150 Q9SMY3 2 154 1 1 0 17620 17146 1 0 0 0 208 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFV---KLRILEPDDDAS--LRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANL 474 2R:1731127-2080000 -1 NULL:1988151 Q9SMY3 153 304 1 1 0 17128 16870 1 0 0 0 235 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDA--AIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1988152 Q9SMY3 294 381 1 1 0 2604510 88525 87649 1 0 0 0 569 partof IRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHN----DSNV--HGTLEL-TDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW---PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDD---VAGMEQYHTGQRTVPFSGM 876 2R:1731127-2080000 -1 NULL:1988154 Q9SJV1 2 305 1 1 0 2604513 88525 87673 1 0 0 0 552 partof IRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHN----DSNV--HGTLEL-TDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW---PPFLYDEHAQNLAKKYGR-TTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVA---GMEQ-YHTGQ 852 2R:1731127-2080000 -1 NULL:1988156 Q9FVN7 2 299 1 1 0 2604516 88525 87673 1 0 0 0 562 partof IRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHN----DSNV--HGTLEL-TDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW---PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDD---VAGMEQ-YHTGQ 852 2R:1731127-2080000 -1 NULL:1988158 Q9SJV2 2 298 1 1 0 2604519 110955 109635 1 0 0 0 243 partof DTQLAKNILIKDFSNFADRGQFHNGRD---DPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMK-FMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFP--KLA---SXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVP-GHEKLVIEKGTQVIIPACAYHRDEDLY-PNPETFDPERFSPEKVAARES-VEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYL 1320 2R:1731127-2080000 -1 NULL:1988160 O64631 84 503 1 1 0 2604522 110964 109623 1 0 0 0 246 partof FIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRT--PVSDFRTM--GQKVFTDMRH----GKLLTMF-VFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRE--RENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAP-RGIVT----G---FTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARES--VEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVER 1341 2R:1731127-2080000 -1 NULL:1988162 AAK52956 90 541 1 1 0 2604525 111006 109710 1 0 0 0 242 partof FPFVGFYFLHKPAAFIVDTQLAKNI--LIK-DFSNFADRGQFHNGR-DDPLTQHLFNLDGKKWKDMRQRLTPTFTSGK-MKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRT--PVSDFRTMGQKVFTDMRHGKLLTMFVFS---FPKLASXXXXXXMPEDVHQFFMRLVNDTIA-LRERENF--KRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNP-ETFDPERF-SPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSV 1296 2R:1731127-2080000 -1 NULL:1988164 Q9LTN1 79 505 1 1 0 2604528 140126 139976 1 0 0 0 183 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1988166 Q9FGZ9 9 59 1 1 0 2604531 140126 139976 1 0 0 0 183 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1988168 AAK48954 9 59 1 1 0 2604534 140126 139976 1 0 0 0 178 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1988170 Q9M1U1 9 59 1 1 0 2604537 208071 207186 1 0 0 0 342 partof DVTMADAAHQEFARRLA-LFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDP-EQIAHSFHQ-VLAAYQDSQILRIA--NKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHL-DGERTVQVPMMSLKERFRYADLPALDAM-ALELPYKDS----DLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL---KLPRFKAEFQVELSEVFQKVSFTL 885 2R:1731127-2080000 -1 NULL:1988172 P93692 7 306 1 1 0 2604539 208071 207186 1 0 0 0 364 partof DVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDP-EQIAHSFHQ-VLA--AYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHL-DGERTVQVPMMSLKERFRYADLPALDAM-ALELPYKDS----DLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL---KLPRFKAEFQVELSEVFQKVSFTL 885 2R:1731127-2080000 -1 NULL:1988174 Q9ST57 7 306 1 1 0 2604541 208071 207186 1 0 0 0 327 partof DVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDP-EQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAM-ALELPYKDS----DLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVAL---KLPRFKAEFQVELSEVFQKVSFTL 885 2R:1731127-2080000 -1 NULL:1988176 Q9ST58 7 306 1 1 0 2604543 210406 209644 1 0 0 0 242 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLE-----AQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA--ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATAL--RMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDV---KIPSFTAEFQQELSQVL 762 2R:1731127-2080000 -1 NULL:1988178 P93692 36 299 1 1 0 209580 209466 1 0 0 0 81 partof MGMNRIFSGQAELGGMLQSE--ESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1988179 P93692 301 341 1 1 0 2604546 210418 209644 1 0 0 0 252 partof SAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLE-----AQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA--ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATAL--RMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDV---KIPSFTAEFQQELSQVL 774 2R:1731127-2080000 -1 NULL:1988181 Q9ST57 32 299 1 1 0 209580 209466 1 0 0 0 75 partof MGMNRIFSGQAELGGMLQSE--ESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1988182 Q9ST57 301 341 1 1 0 2604549 210451 209644 1 0 0 0 240 partof ALCLHDH-LCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGL-EAQQVAESFGVVL---KSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE--QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFF-GSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACN------LAMIILLPDEKSNLTSLEKKLSD----ISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 807 2R:1731127-2080000 -1 NULL:1988184 Q9SH52 13 295 1 1 0 2604552 302505 302094 1 0 0 0 194 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE--QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL-SVER 411 2R:1731127-2080000 -1 NULL:1988186 AAL06942 246 383 1 1 0 2604554 302505 302094 1 0 0 0 194 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE--QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL-SVER 411 2R:1731127-2080000 -1 NULL:1988188 O64853 384 521 1 1 0 2604556 302505 302151 1 0 0 0 171 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFE---EQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQH--RYAPSAETSIPVEY 354 2R:1731127-2080000 -1 NULL:1988190 BAB64180 401 521 1 1 0 2604558 312453 311925 1 0 0 0 229 partof CVDKVVSDLCL-GHYEHALRQIN--EDLEGLQNHDEIMALLELKNIILRLRLKGEAQRTI-GPTRKSDALPHKFTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYNIATAVGDCHDQDPSQYKDYRGESEFNEAN 528 2R:1731127-2080000 -1 NULL:1988192 Q9FH28 10 186 1 1 0 locator 1.0 cytology 1.0 2003-04-01 18:47:46 genomic 2601403 311240 311238 1 0 0 0 0 partof 2 2R:1731127-2080000 -1 NULL:1985609 band-42E2 -1 1 -1 1 0 2596001 24287 18204 1 0 0 0 0 partof 6083 2R:1731127-2080000 1 NULL:1981174 band-42C4 0 6083 1 1 0 2596004 41143 24287 1 0 0 0 0 partof 16856 2R:1731127-2080000 1 NULL:1981176 band-42C5 0 16856 1 1 0 2596007 64387 41143 1 0 0 0 0 partof 23244 2R:1731127-2080000 1 NULL:1981178 band-42C6 0 23244 1 1 0 2596010 87630 64387 1 0 0 0 0 partof 23243 2R:1731127-2080000 1 NULL:1981180 band-42C7 0 23243 1 1 0 2596013 110215 87630 1 0 0 0 0 partof 22585 2R:1731127-2080000 1 NULL:1981182 band-42C8 0 22585 1 1 0 2596016 111861 110215 1 0 0 0 0 partof 1646 2R:1731127-2080000 1 NULL:1981184 band-42C9 0 1646 1 1 0 2596019 122397 111861 1 0 0 0 0 partof 10536 2R:1731127-2080000 1 NULL:1981186 band-42C10 0 10536 1 1 0 2596022 154529 122397 1 0 0 0 0 partof 32132 2R:1731127-2080000 1 NULL:1981188 band-42D1 0 32132 1 1 0 2596025 253679 122397 1 0 0 0 0 partof 131282 2R:1731127-2080000 1 NULL:1981190 band-42D 0 131282 1 1 0 2596028 156175 154529 1 0 0 0 0 partof 1646 2R:1731127-2080000 1 NULL:1981192 band-42D2 0 1646 1 1 0 2596031 174282 156175 1 0 0 0 0 partof 18107 2R:1731127-2080000 1 NULL:1981194 band-42D3 0 18107 1 1 0 2596034 236275 174282 1 0 0 0 0 partof 61993 2R:1731127-2080000 1 NULL:1981196 band-42D4 0 61993 1 1 0 2596037 239451 236275 1 0 0 0 0 partof 3176 2R:1731127-2080000 1 NULL:1981198 band-42D5 0 3176 1 1 0 2596040 253679 239451 1 0 0 0 0 partof 14228 2R:1731127-2080000 1 NULL:1981200 band-42D6 0 14228 1 1 0 2596043 311239 253679 1 0 0 0 0 partof 57560 2R:1731127-2080000 1 NULL:1981202 band-42E1 0 57560 1 1 0 2596046 391149 253679 1 0 0 0 0 partof 137470 2R:1731127-2080000 1 NULL:1981204 band-42E 0 137470 1 1 0 2596049 315341 311239 1 0 0 0 0 partof 4102 2R:1731127-2080000 1 NULL:1981206 band-42E3 0 4102 1 1 0 2596052 331821 315341 1 0 0 0 0 partof 16480 2R:1731127-2080000 1 NULL:1981208 band-42E4 0 16480 1 1 0 2596055 367150 331821 1 0 0 0 0 partof 35329 2R:1731127-2080000 1 NULL:1981210 band-42E5 0 35329 1 1 0 2588342 122397 -78836 1 0 0 0 0 partof 201233 2R:1731127-2080000 1 NULL:1975139 band-42C 0 201233 1 1 0 2588348 18204 -14101 1 0 0 0 0 partof 32305 2R:1731127-2080000 1 NULL:1975143 band-42C3 0 32305 1 1 0 2563225 475300 -731091 1 0 0 0 0 partof 1206391 2R:1731127-2080000 1 NULL:1954757 band-42 0 1206391 1 1 0 sim4 1.0 na_EST.all_nr.dros 1.0 2003-01-13 19:43:32 Fly ESTs genomic 2599268 140950 140795 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1983775 RH49446.5prime 0 156 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983776 RH49446.5prime 156 338 1 1 0 142816 142555 1 0 0 0 98 partof 261 2R:1731127-2080000 1 NULL:1983777 RH49446.5prime 338 597 1 1 0 2605381 304761 304721 1 0 0 0 95 partof 40 2R:1731127-2080000 -1 NULL:1988861 SD07915:contig1 0 40 1 1 0 303775 302562 1 0 0 0 100 partof 1213 2R:1731127-2080000 -1 NULL:1988862 SD07915:contig1 40 1253 1 1 0 302504 301886 1 0 0 0 100 partof 618 2R:1731127-2080000 -1 NULL:1988863 SD07915:contig1 1253 1871 1 1 0 2605385 304767 304721 1 0 0 0 100 partof 46 2R:1731127-2080000 -1 NULL:1988865 RE01444:contig1 0 46 1 1 0 303775 303259 1 0 0 0 99 partof 516 2R:1731127-2080000 -1 NULL:1988866 RE01444:contig1 46 562 1 1 0 302415 301880 1 0 0 0 99 partof 535 2R:1731127-2080000 -1 NULL:1988867 RE01444:contig2 562 1097 1 1 0 2600440 342110 342034 1 0 0 0 98 partof 76 2R:1731127-2080000 1 NULL:1984718 RE34157.5prime 0 76 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984719 RE34157.5prime 76 160 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984720 RE34157.5prime 160 523 1 1 0 347367 347209 1 0 0 0 98 partof 158 2R:1731127-2080000 1 NULL:1984721 RE34157.5prime 523 681 1 1 0 2600446 342110 342036 1 0 0 0 100 partof 74 2R:1731127-2080000 1 NULL:1984723 RE68806.5prime 0 74 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984724 RE68806.5prime 74 158 1 1 0 347117 346787 1 0 0 0 100 partof 330 2R:1731127-2080000 1 NULL:1984725 RE68806.5prime 158 488 1 1 0 2599273 140950 140795 1 0 0 0 99 partof 155 2R:1731127-2080000 1 NULL:1983779 RH23420.5prime 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983780 RH23420.5prime 155 337 1 1 0 142829 142555 1 0 0 0 99 partof 274 2R:1731127-2080000 1 NULL:1983781 RH23420.5prime 337 611 1 1 0 2599278 140950 140795 1 0 0 0 100 partof 155 2R:1731127-2080000 1 NULL:1983783 RE29506.5prime 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983784 RE29506.5prime 155 337 1 1 0 142876 142555 1 0 0 0 100 partof 321 2R:1731127-2080000 1 NULL:1983785 RE29506.5prime 337 658 1 1 0 2604733 138305 138134 1 0 0 0 97 partof 171 2R:1731127-2080000 -1 NULL:1988352 SD27316.5prime_revcomp 9 180 1 1 0 138112 137864 1 0 0 0 97 partof 248 2R:1731127-2080000 -1 NULL:1988353 SD27316.5prime_revcomp 180 428 1 1 0 137592 137442 1 0 0 0 98 partof 150 2R:1731127-2080000 -1 NULL:1988354 SD27316.5prime_revcomp 428 576 1 1 0 2605391 304767 304721 1 0 0 0 100 partof 46 2R:1731127-2080000 -1 NULL:1988869 RE54174.5prime 0 46 1 1 0 303775 303180 1 0 0 0 100 partof 595 2R:1731127-2080000 -1 NULL:1988870 RE54174.5prime 46 641 1 1 0 2604738 138947 138357 1 0 0 0 100 partof 590 2R:1731127-2080000 -1 NULL:1988356 GH16502.3prime_revcomp 212 802 1 1 0 138301 138089 1 0 0 0 99 partof 212 2R:1731127-2080000 -1 NULL:1988357 GH16502.3prime_revcomp 0 212 1 1 0 2605395 304767 304721 1 0 0 0 100 partof 46 2R:1731127-2080000 -1 NULL:1988872 RE24184.5prime 0 46 1 1 0 303775 303185 1 0 0 0 100 partof 590 2R:1731127-2080000 -1 NULL:1988873 RE24184.5prime 46 636 1 1 0 2600451 342110 342036 1 0 0 0 100 partof 74 2R:1731127-2080000 1 NULL:1984727 RE26059.5prime 0 74 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984728 RE26059.5prime 74 158 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984729 RE26059.5prime 158 521 1 1 0 347323 347209 1 0 0 0 100 partof 114 2R:1731127-2080000 1 NULL:1984730 RE26059.5prime 521 635 1 1 0 2605399 304767 304721 1 0 0 0 100 partof 46 2R:1731127-2080000 -1 NULL:1988875 RE08362.5prime 0 46 1 1 0 303775 303209 1 0 0 0 100 partof 566 2R:1731127-2080000 -1 NULL:1988876 RE08362.5prime 46 612 1 1 0 2600457 342110 342037 1 0 0 0 100 partof 73 2R:1731127-2080000 1 NULL:1984732 RE17431.5prime 0 73 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984733 RE17431.5prime 73 157 1 1 0 347121 346787 1 0 0 0 100 partof 334 2R:1731127-2080000 1 NULL:1984734 RE17431.5prime 157 491 1 1 0 2599283 140950 140795 1 0 0 0 99 partof 155 2R:1731127-2080000 1 NULL:1983787 RH22815.5prime 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983788 RH22815.5prime 155 337 1 1 0 142891 142555 1 0 0 0 99 partof 336 2R:1731127-2080000 1 NULL:1983789 RH22815.5prime 337 673 1 1 0 2599288 140950 140795 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1983791 RH23453.5prime 0 156 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983792 RH23453.5prime 156 338 1 1 0 142891 142555 1 0 0 0 100 partof 336 2R:1731127-2080000 1 NULL:1983793 RH23453.5prime 338 674 1 1 0 2604742 159405 158772 1 0 0 0 99 partof 633 2R:1731127-2080000 -1 NULL:1988359 RH46829.5prime 0 633 1 1 0 2604745 159405 158783 1 0 0 0 99 partof 622 2R:1731127-2080000 -1 NULL:1988361 RH44584.5prime 0 622 1 1 0 2604748 168702 167848 1 0 0 0 100 partof 854 2R:1731127-2080000 -1 NULL:1988363 GH08071.5prime 0 854 1 1 0 2600462 342110 342037 1 0 0 0 98 partof 73 2R:1731127-2080000 1 NULL:1984736 RE07269.5prime 0 73 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984737 RE07269.5prime 73 157 1 1 0 347121 346787 1 0 0 0 99 partof 334 2R:1731127-2080000 1 NULL:1984738 RE07269.5prime 157 491 1 1 0 2600467 342110 342037 1 0 0 0 100 partof 73 2R:1731127-2080000 1 NULL:1984740 RE17990.5prime 0 73 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984741 RE17990.5prime 73 157 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984742 RE17990.5prime 157 521 1 1 0 347298 347209 1 0 0 0 100 partof 89 2R:1731127-2080000 1 NULL:1984743 RE17990.5prime 521 610 1 1 0 2599293 140950 140795 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1983795 RH40561.5prime 0 156 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983796 RH40561.5prime 156 338 1 1 0 142891 142555 1 0 0 0 98 partof 336 2R:1731127-2080000 1 NULL:1983797 RH40561.5prime 338 676 1 1 0 2599298 140950 140795 1 0 0 0 100 partof 155 2R:1731127-2080000 1 NULL:1983799 RE12054:contig1 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983800 RE12054:contig1 155 337 1 1 0 142891 142547 1 0 0 0 98 partof 344 2R:1731127-2080000 1 NULL:1983801 RE12054:contig1 337 681 1 1 0 143528 142947 1 0 0 0 99 partof 581 2R:1731127-2080000 1 NULL:1983802 RE12054:contig1 681 1262 1 1 0 144599 143811 1 0 0 0 97 partof 788 2R:1731127-2080000 1 NULL:1983803 RE12054:contig1 1262 2050 1 1 0 2604751 168702 168032 1 0 0 0 100 partof 670 2R:1731127-2080000 -1 NULL:1988365 GH16767.5prime 0 670 1 1 0 2604753 168702 168040 1 0 0 0 99 partof 662 2R:1731127-2080000 -1 NULL:1988367 GH18518.5prime 0 664 1 1 0 2604756 192403 192029 1 0 0 0 99 partof 374 2R:1731127-2080000 -1 NULL:1988369 LD16378.3prime_revcomp 0 375 1 1 0 2604759 192506 192034 1 0 0 0 100 partof 472 2R:1731127-2080000 -1 NULL:1988371 LD45770.3prime_revcomp 0 472 1 1 0 2600473 342110 342037 1 0 0 0 100 partof 73 2R:1731127-2080000 1 NULL:1984745 RE24817.5prime 0 73 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984746 RE24817.5prime 73 157 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984747 RE24817.5prime 157 520 1 1 0 347358 347209 1 0 0 0 98 partof 149 2R:1731127-2080000 1 NULL:1984748 RE24817.5prime 520 669 1 1 0 2600479 342110 342040 1 0 0 0 98 partof 70 2R:1731127-2080000 1 NULL:1984750 RE48907.5prime 0 70 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984751 RE48907.5prime 70 154 1 1 0 347117 346787 1 0 0 0 99 partof 330 2R:1731127-2080000 1 NULL:1984752 RE48907.5prime 154 484 1 1 0 2604762 192655 192034 1 0 0 0 99 partof 621 2R:1731127-2080000 -1 NULL:1988373 LD27639.3prime_revcomp 0 620 1 1 0 2604765 192671 191999 1 0 0 0 97 partof 672 2R:1731127-2080000 -1 NULL:1988375 SD13092.5prime 0 683 1 1 0 2604768 194733 194410 1 0 0 0 98 partof 323 2R:1731127-2080000 -1 NULL:1988377 LD21092:contig1 0 323 1 1 0 194346 194082 1 0 0 0 100 partof 264 2R:1731127-2080000 -1 NULL:1988378 LD21092:contig1 323 587 1 1 0 192649 192029 1 0 0 0 99 partof 620 2R:1731127-2080000 -1 NULL:1988379 LD21092:contig2 587 1207 1 1 0 2600484 342110 342040 1 0 0 0 98 partof 70 2R:1731127-2080000 1 NULL:1984754 RE50807.5prime 0 70 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984755 RE50807.5prime 70 154 1 1 0 347117 346787 1 0 0 0 99 partof 330 2R:1731127-2080000 1 NULL:1984756 RE50807.5prime 154 483 1 1 0 2600489 342110 342040 1 0 0 0 98 partof 70 2R:1731127-2080000 1 NULL:1984758 RE48882.5prime 0 70 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984759 RE48882.5prime 70 154 1 1 0 347121 346787 1 0 0 0 99 partof 334 2R:1731127-2080000 1 NULL:1984760 RE48882.5prime 154 488 1 1 0 2604774 195044 194882 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988381 AT11609.5prime 0 162 1 1 0 194824 194481 1 0 0 0 99 partof 343 2R:1731127-2080000 -1 NULL:1988382 AT11609.5prime 162 505 1 1 0 2604778 195107 194882 1 0 0 0 99 partof 225 2R:1731127-2080000 -1 NULL:1988384 CK00234:contig1 0 225 1 1 0 194824 194435 1 0 0 0 96 partof 389 2R:1731127-2080000 -1 NULL:1988385 CK00234:contig1 225 614 1 1 0 193064 192498 1 0 0 0 96 partof 566 2R:1731127-2080000 -1 NULL:1988386 CK00234:contig2 614 1180 1 1 0 2599601 213117 213073 1 0 0 0 100 partof 44 2R:1731127-2080000 1 NULL:1984032 GH27551.5prime 0 44 1 1 0 214021 213388 1 0 0 0 99 partof 633 2R:1731127-2080000 1 NULL:1984033 GH27551.5prime 44 678 1 1 0 2600494 342110 342040 1 0 0 0 98 partof 70 2R:1731127-2080000 1 NULL:1984762 RE50782.5prime 0 70 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984763 RE50782.5prime 70 154 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984764 RE50782.5prime 154 517 1 1 0 347244 347209 1 0 0 0 97 partof 35 2R:1731127-2080000 1 NULL:1984765 RE50782.5prime 517 552 1 1 0 2599605 213117 213082 1 0 0 0 100 partof 35 2R:1731127-2080000 1 NULL:1984035 GH28573.5prime 0 35 1 1 0 214007 213388 1 0 0 0 100 partof 619 2R:1731127-2080000 1 NULL:1984036 GH28573.5prime 35 654 1 1 0 2599609 213117 213084 1 0 0 0 100 partof 33 2R:1731127-2080000 1 NULL:1984038 GH05478.5prime 0 33 1 1 0 214020 213388 1 0 0 0 99 partof 632 2R:1731127-2080000 1 NULL:1984039 GH05478.5prime 33 665 1 1 0 2604784 195107 194882 1 0 0 0 98 partof 225 2R:1731127-2080000 -1 NULL:1988388 CK00018.5prime 0 227 1 1 0 194824 194658 1 0 0 0 97 partof 166 2R:1731127-2080000 -1 NULL:1988389 CK00018.5prime 227 396 1 1 0 2604788 195141 194882 1 0 0 0 99 partof 259 2R:1731127-2080000 -1 NULL:1988391 RE45818.5prime 0 259 1 1 0 194824 194410 1 0 0 0 99 partof 414 2R:1731127-2080000 -1 NULL:1988392 RE45818.5prime 259 673 1 1 0 194346 194300 1 0 0 0 95 partof 46 2R:1731127-2080000 -1 NULL:1988393 RE45818.5prime 673 718 1 1 0 2599613 213117 213084 1 0 0 0 100 partof 33 2R:1731127-2080000 1 NULL:1984041 GH04125:contig1 0 33 1 1 0 214233 213388 1 0 0 0 99 partof 845 2R:1731127-2080000 1 NULL:1984042 GH04125:contig1 33 878 1 1 0 214434 214291 1 0 0 0 97 partof 143 2R:1731127-2080000 1 NULL:1984043 GH04125:contig1 878 1021 1 1 0 214648 214503 1 0 0 0 100 partof 145 2R:1731127-2080000 1 NULL:1984044 GH04125:contig1 1021 1166 1 1 0 2599618 216199 216178 1 0 0 0 95 partof 21 2R:1731127-2080000 1 NULL:1984046 RE02548:contig1 0 21 1 1 0 217223 216288 1 0 0 0 100 partof 935 2R:1731127-2080000 1 NULL:1984047 RE02548:contig1 21 956 1 1 0 217771 217629 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984048 RE02548:contig1 956 1098 1 1 0 218037 217835 1 0 0 0 100 partof 202 2R:1731127-2080000 1 NULL:1984049 RE02548:contig1 1098 1300 1 1 0 2604793 195141 194882 1 0 0 0 99 partof 259 2R:1731127-2080000 -1 NULL:1988395 RE46922.5prime 0 259 1 1 0 194824 194653 1 0 0 0 98 partof 171 2R:1731127-2080000 -1 NULL:1988396 RE46922.5prime 259 430 1 1 0 2604797 196702 196461 1 0 0 0 97 partof 241 2R:1731127-2080000 -1 NULL:1988398 LD04776.5prime 0 239 1 1 0 195149 194961 1 0 0 0 98 partof 188 2R:1731127-2080000 -1 NULL:1988399 LD04776.5prime 239 425 1 1 0 2599623 216199 216179 1 0 0 0 100 partof 20 2R:1731127-2080000 1 NULL:1984051 UNKNOWN_RE02231:contig1 0 20 1 1 0 217223 216288 1 0 0 0 100 partof 935 2R:1731127-2080000 1 NULL:1984052 UNKNOWN_RE02231:contig1 20 955 1 1 0 217771 217629 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984053 UNKNOWN_RE02231:contig1 955 1097 1 1 0 217988 217835 1 0 0 0 100 partof 153 2R:1731127-2080000 1 NULL:1984054 UNKNOWN_RE02231:contig1 1097 1250 1 1 0 2599629 216199 216179 1 0 0 0 100 partof 20 2R:1731127-2080000 1 NULL:1984056 UNKNOWN_RE02772:contig1 0 20 1 1 0 217223 216288 1 0 0 0 100 partof 935 2R:1731127-2080000 1 NULL:1984057 UNKNOWN_RE02772:contig1 20 955 1 1 0 217771 217629 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984058 UNKNOWN_RE02772:contig1 955 1097 1 1 0 218041 217835 1 0 0 0 98 partof 206 2R:1731127-2080000 1 NULL:1984059 UNKNOWN_RE02772:contig1 1097 1303 1 1 0 2599634 216199 216181 1 0 0 0 100 partof 18 2R:1731127-2080000 1 NULL:1984061 UNKNOWN_RE02556:contig1 0 18 1 1 0 216903 216288 1 0 0 0 100 partof 615 2R:1731127-2080000 1 NULL:1984062 UNKNOWN_RE02556:contig1 18 633 1 1 0 2599638 221752 221537 1 0 0 0 100 partof 215 2R:1731127-2080000 1 NULL:1984064 RE05206.5prime 0 215 1 1 0 2599641 221698 221537 1 0 0 0 100 partof 161 2R:1731127-2080000 1 NULL:1984066 RE28276:contig1 0 161 1 1 0 221801 221754 1 0 0 0 100 partof 47 2R:1731127-2080000 1 NULL:1984067 RE28276:contig1 161 208 1 1 0 236135 235637 1 0 0 0 99 partof 498 2R:1731127-2080000 1 NULL:1984068 RE28276:contig1 208 706 1 1 0 239768 239707 1 0 0 0 98 partof 61 2R:1731127-2080000 1 NULL:1984069 RE28276:contig1 706 767 1 1 0 249942 249841 1 0 0 0 92 partof 101 2R:1731127-2080000 1 NULL:1984070 RE28276:contig2 767 868 1 1 0 250284 250042 1 0 0 0 98 partof 242 2R:1731127-2080000 1 NULL:1984071 RE28276:contig2 868 1110 1 1 0 251391 250423 1 0 0 0 99 partof 968 2R:1731127-2080000 1 NULL:1984072 RE28276:contig3 1110 2078 1 1 0 251643 251494 1 0 0 0 95 partof 149 2R:1731127-2080000 1 NULL:1984073 RE28276:contig4 2078 2227 1 1 0 252388 251782 1 0 0 0 99 partof 606 2R:1731127-2080000 1 NULL:1984074 RE28276:contig5 2227 2833 1 1 0 2599654 226211 225656 1 0 0 0 97 partof 555 2R:1731127-2080000 1 NULL:1984076 SD27176.5prime 0 563 1 1 0 2599657 253192 253145 1 0 0 0 93 partof 47 2R:1731127-2080000 1 NULL:1984078 GM06164.5prime 0 49 1 1 0 253434 253254 1 0 0 0 94 partof 180 2R:1731127-2080000 1 NULL:1984079 GM06164.5prime 49 237 1 1 0 253779 253654 1 0 0 0 100 partof 125 2R:1731127-2080000 1 NULL:1984080 GM06164.5prime 237 362 1 1 0 2599662 253192 253163 1 0 0 0 96 partof 29 2R:1731127-2080000 1 NULL:1984082 SD25585.5prime 0 29 1 1 0 253434 253254 1 0 0 0 100 partof 180 2R:1731127-2080000 1 NULL:1984083 SD25585.5prime 29 209 1 1 0 254127 253654 1 0 0 0 99 partof 473 2R:1731127-2080000 1 NULL:1984084 SD25585.5prime 209 682 1 1 0 2599667 253192 253168 1 0 0 0 100 partof 24 2R:1731127-2080000 1 NULL:1984086 GM01841.5prime 0 24 1 1 0 253434 253254 1 0 0 0 99 partof 180 2R:1731127-2080000 1 NULL:1984087 GM01841.5prime 24 204 1 1 0 253989 253654 1 0 0 0 99 partof 335 2R:1731127-2080000 1 NULL:1984088 GM01841.5prime 204 539 1 1 0 2599672 253434 253220 1 0 0 0 100 partof 214 2R:1731127-2080000 1 NULL:1984090 LD08659:contig1 0 214 1 1 0 254261 253654 1 0 0 0 100 partof 607 2R:1731127-2080000 1 NULL:1984091 LD08659:contig1 214 821 1 1 0 254456 254327 1 0 0 0 100 partof 129 2R:1731127-2080000 1 NULL:1984092 LD08659:contig1 821 950 1 1 0 2599676 258222 257739 1 0 0 0 98 partof 483 2R:1731127-2080000 1 NULL:1984094 RH63947.5prime 0 484 1 1 0 2599679 258267 257739 1 0 0 0 100 partof 528 2R:1731127-2080000 1 NULL:1984096 RH32922.5prime 0 528 1 1 0 2599682 258432 257739 1 0 0 0 100 partof 693 2R:1731127-2080000 1 NULL:1984098 RH38629.5prime 0 693 1 1 0 2599685 270766 270071 1 0 0 0 98 partof 695 2R:1731127-2080000 1 NULL:1984100 SD24388.3prime_revcomp 0 697 1 1 0 2599688 282402 281991 1 0 0 0 99 partof 411 2R:1731127-2080000 1 NULL:1984102 UNKNOWN_GH24078:contig1 72 483 1 1 0 2605004 202475 202308 1 0 0 0 99 partof 167 2R:1731127-2080000 -1 NULL:1988563 AT08250.5prime 0 167 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988564 AT08250.5prime 167 422 1 1 0 195149 194882 1 0 0 0 99 partof 267 2R:1731127-2080000 -1 NULL:1988565 AT08250.5prime 422 688 1 1 0 194824 194795 1 0 0 0 96 partof 29 2R:1731127-2080000 -1 NULL:1988566 AT08250.5prime 688 717 1 1 0 2599690 282908 282317 1 0 0 0 99 partof 591 2R:1731127-2080000 1 NULL:1984104 RE05855.5prime 0 590 1 1 0 2599692 282942 282337 1 0 0 0 99 partof 605 2R:1731127-2080000 1 NULL:1984106 LD06340:contig1 0 605 1 1 0 289110 288873 1 0 0 0 100 partof 237 2R:1731127-2080000 1 NULL:1984107 LD06340:contig2 605 842 1 1 0 289398 289146 1 0 0 0 99 partof 252 2R:1731127-2080000 1 NULL:1984108 LD06340:contig2 842 1094 1 1 0 2605010 202475 202308 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1988568 LD15561.5prime 0 167 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988569 LD15561.5prime 167 421 1 1 0 195149 194888 1 0 0 0 97 partof 261 2R:1731127-2080000 -1 NULL:1988570 LD15561.5prime 421 678 1 1 0 2599696 288098 286742 1 0 0 0 98 partof 1356 2R:1731127-2080000 1 NULL:1984110 LD21171:contig1 0 1356 1 1 0 2599698 287259 286744 1 0 0 0 98 partof 515 2R:1731127-2080000 1 NULL:1984112 LD40475.5prime 0 515 1 1 0 2605015 202475 202329 1 0 0 0 100 partof 146 2R:1731127-2080000 -1 NULL:1988572 LD32977.5prime 0 146 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988573 LD32977.5prime 146 401 1 1 0 195149 194952 1 0 0 0 100 partof 197 2R:1731127-2080000 -1 NULL:1988574 LD32977.5prime 401 598 1 1 0 2605020 202475 202308 1 0 0 0 99 partof 167 2R:1731127-2080000 -1 NULL:1988576 SD10833.5prime 0 167 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988577 SD10833.5prime 167 422 1 1 0 195149 195047 1 0 0 0 98 partof 102 2R:1731127-2080000 -1 NULL:1988578 SD10833.5prime 422 524 1 1 0 2605025 202475 202308 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1988580 LD40585.5prime 0 167 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988581 LD40585.5prime 167 422 1 1 0 195149 195062 1 0 0 0 100 partof 87 2R:1731127-2080000 -1 NULL:1988582 LD40585.5prime 422 509 1 1 0 2605030 202477 202308 1 0 0 0 100 partof 169 2R:1731127-2080000 -1 NULL:1988584 LD37923.5prime 0 169 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988585 LD37923.5prime 169 424 1 1 0 195149 194971 1 0 0 0 100 partof 178 2R:1731127-2080000 -1 NULL:1988586 LD37923.5prime 424 602 1 1 0 2605035 202477 202308 1 0 0 0 100 partof 169 2R:1731127-2080000 -1 NULL:1988588 LD22142.5prime 0 169 1 1 0 196716 196461 1 0 0 0 97 partof 255 2R:1731127-2080000 -1 NULL:1988589 LD22142.5prime 169 423 1 1 0 195149 194998 1 0 0 0 96 partof 151 2R:1731127-2080000 -1 NULL:1988590 LD22142.5prime 423 573 1 1 0 2605040 202483 202308 1 0 0 0 99 partof 175 2R:1731127-2080000 -1 NULL:1988592 RE22854.5prime 0 175 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988593 RE22854.5prime 175 430 1 1 0 195149 194939 1 0 0 0 100 partof 210 2R:1731127-2080000 -1 NULL:1988594 RE22854.5prime 430 640 1 1 0 2605045 202484 202308 1 0 0 0 100 partof 176 2R:1731127-2080000 -1 NULL:1988596 RE19178.5prime 0 176 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988597 RE19178.5prime 176 431 1 1 0 195149 194971 1 0 0 0 98 partof 178 2R:1731127-2080000 -1 NULL:1988598 RE19178.5prime 431 609 1 1 0 2600104 322552 322482 1 0 0 0 100 partof 70 2R:1731127-2080000 1 NULL:1984445 GH20321.5prime 0 70 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984446 GH20321.5prime 70 182 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984447 GH20321.5prime 182 374 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984448 GH20321.5prime 374 536 1 1 0 327018 326933 1 0 0 0 100 partof 85 2R:1731127-2080000 1 NULL:1984449 GH20321.5prime 536 621 1 1 0 2605050 202484 202308 1 0 0 0 100 partof 176 2R:1731127-2080000 -1 NULL:1988600 RE20466.5prime 0 176 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988601 RE20466.5prime 176 431 1 1 0 195149 194980 1 0 0 0 100 partof 169 2R:1731127-2080000 -1 NULL:1988602 RE20466.5prime 431 600 1 1 0 2605055 202484 202308 1 0 0 0 100 partof 176 2R:1731127-2080000 -1 NULL:1988604 RH46244.5prime 0 176 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988605 RH46244.5prime 176 431 1 1 0 195149 194987 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988606 RH46244.5prime 431 593 1 1 0 2600111 322835 322483 1 0 0 0 100 partof 352 2R:1731127-2080000 1 NULL:1984451 UNKNOWN_GH15825:contig1 0 352 1 1 0 323787 322895 1 0 0 0 100 partof 892 2R:1731127-2080000 1 NULL:1984452 UNKNOWN_GH15825:contig1 352 1244 1 1 0 324083 323833 1 0 0 0 100 partof 250 2R:1731127-2080000 1 NULL:1984453 UNKNOWN_GH15825:contig2 1244 1494 1 1 0 2600117 322552 322483 1 0 0 0 100 partof 69 2R:1731127-2080000 1 NULL:1984455 LP03018.5prime 0 69 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984456 LP03018.5prime 69 181 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984457 LP03018.5prime 181 373 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984458 LP03018.5prime 373 535 1 1 0 327045 326933 1 0 0 0 99 partof 112 2R:1731127-2080000 1 NULL:1984459 LP03018.5prime 535 647 1 1 0 2605060 202484 202308 1 0 0 0 100 partof 176 2R:1731127-2080000 -1 NULL:1988608 RE01126.5prime 0 176 1 1 0 196716 196468 1 0 0 0 98 partof 248 2R:1731127-2080000 -1 NULL:1988609 RE01126.5prime 176 424 1 1 0 2605064 202486 202308 1 0 0 0 100 partof 178 2R:1731127-2080000 -1 NULL:1988611 GM05686.5prime 0 178 1 1 0 196716 196461 1 0 0 0 97 partof 255 2R:1731127-2080000 -1 NULL:1988612 GM05686.5prime 178 433 1 1 0 195149 194962 1 0 0 0 98 partof 187 2R:1731127-2080000 -1 NULL:1988613 GM05686.5prime 433 618 1 1 0 2605069 202486 202308 1 0 0 0 100 partof 178 2R:1731127-2080000 -1 NULL:1988615 LD21795.5prime 0 178 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988616 LD21795.5prime 178 433 1 1 0 195149 195018 1 0 0 0 97 partof 131 2R:1731127-2080000 -1 NULL:1988617 LD21795.5prime 433 564 1 1 0 2600124 322552 322490 1 0 0 0 98 partof 62 2R:1731127-2080000 1 NULL:1984461 GH16202.5prime 0 62 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984462 GH16202.5prime 62 174 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984463 GH16202.5prime 174 366 1 1 0 326808 326705 1 0 0 0 100 partof 103 2R:1731127-2080000 1 NULL:1984464 GH16202.5prime 366 469 1 1 0 2605074 202487 202308 1 0 0 0 100 partof 179 2R:1731127-2080000 -1 NULL:1988619 RE73075.5prime 0 179 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988620 RE73075.5prime 179 434 1 1 0 195149 195033 1 0 0 0 99 partof 116 2R:1731127-2080000 -1 NULL:1988621 RE73075.5prime 434 551 1 1 0 2600130 322552 322490 1 0 0 0 100 partof 62 2R:1731127-2080000 1 NULL:1984466 GH16205.5prime 0 62 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984467 GH16205.5prime 62 174 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984468 GH16205.5prime 174 366 1 1 0 326808 326705 1 0 0 0 100 partof 103 2R:1731127-2080000 1 NULL:1984469 GH16205.5prime 366 469 1 1 0 2605079 202487 202308 1 0 0 0 98 partof 179 2R:1731127-2080000 -1 NULL:1988623 RE65603.5prime 0 179 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988624 RE65603.5prime 179 434 1 1 0 195149 195086 1 0 0 0 100 partof 63 2R:1731127-2080000 -1 NULL:1988625 RE65603.5prime 434 497 1 1 0 2600136 322552 322490 1 0 0 0 100 partof 62 2R:1731127-2080000 1 NULL:1984471 GH20920.5prime 0 62 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984472 GH20920.5prime 62 174 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984473 GH20920.5prime 174 366 1 1 0 326871 326705 1 0 0 0 98 partof 166 2R:1731127-2080000 1 NULL:1984474 GH20920.5prime 366 533 1 1 0 2605084 202487 202308 1 0 0 0 100 partof 179 2R:1731127-2080000 -1 NULL:1988627 RE04692.5prime 0 179 1 1 0 196716 196464 1 0 0 0 100 partof 252 2R:1731127-2080000 -1 NULL:1988628 RE04692.5prime 179 431 1 1 0 2605088 202487 202308 1 0 0 0 100 partof 179 2R:1731127-2080000 -1 NULL:1988630 RE67058.5prime 0 179 1 1 0 196716 196624 1 0 0 0 96 partof 92 2R:1731127-2080000 -1 NULL:1988631 RE67058.5prime 179 273 1 1 0 2600142 322552 322490 1 0 0 0 100 partof 62 2R:1731127-2080000 1 NULL:1984476 GH18094.5prime 0 62 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984477 GH18094.5prime 62 174 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984478 GH18094.5prime 174 366 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984479 GH18094.5prime 366 528 1 1 0 327050 326933 1 0 0 0 100 partof 117 2R:1731127-2080000 1 NULL:1984480 GH18094.5prime 528 645 1 1 0 2600149 322552 322494 1 0 0 0 100 partof 58 2R:1731127-2080000 1 NULL:1984482 GH25246.5prime 0 58 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984483 GH25246.5prime 58 170 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984484 GH25246.5prime 170 362 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984485 GH25246.5prime 362 524 1 1 0 327050 326933 1 0 0 0 99 partof 117 2R:1731127-2080000 1 NULL:1984486 GH25246.5prime 524 641 1 1 0 2605092 202488 202308 1 0 0 0 98 partof 180 2R:1731127-2080000 -1 NULL:1988633 RE02193.5prime 0 182 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988634 RE02193.5prime 182 437 1 1 0 195149 194980 1 0 0 0 97 partof 169 2R:1731127-2080000 -1 NULL:1988635 RE02193.5prime 437 606 1 1 0 2605097 202488 202308 1 0 0 0 99 partof 180 2R:1731127-2080000 -1 NULL:1988637 RE31238.5prime 0 181 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988638 RE31238.5prime 181 436 1 1 0 195149 195086 1 0 0 0 100 partof 63 2R:1731127-2080000 -1 NULL:1988639 RE31238.5prime 436 499 1 1 0 2600156 322911 322568 1 0 0 0 99 partof 343 2R:1731127-2080000 1 NULL:1984488 BE978175 7 350 1 1 0 2600159 322835 322725 1 0 0 0 100 partof 110 2R:1731127-2080000 1 NULL:1984490 SD22112.5prime 0 110 1 1 0 323331 322895 1 0 0 0 100 partof 436 2R:1731127-2080000 1 NULL:1984491 SD22112.5prime 110 546 1 1 0 2600163 322830 322730 1 0 0 0 100 partof 100 2R:1731127-2080000 1 NULL:1984493 GH24931.5prime 0 100 1 1 0 323440 322895 1 0 0 0 100 partof 545 2R:1731127-2080000 1 NULL:1984494 GH24931.5prime 100 645 1 1 0 2600167 322830 322734 1 0 0 0 100 partof 96 2R:1731127-2080000 1 NULL:1984496 SD10973.5prime 0 96 1 1 0 323300 322895 1 0 0 0 100 partof 405 2R:1731127-2080000 1 NULL:1984497 SD10973.5prime 96 501 1 1 0 2600171 322830 322735 1 0 0 0 100 partof 95 2R:1731127-2080000 1 NULL:1984499 HL07495.5prime 0 95 1 1 0 323248 322895 1 0 0 0 99 partof 353 2R:1731127-2080000 1 NULL:1984500 HL07495.5prime 95 448 1 1 0 2600175 322835 322735 1 0 0 0 100 partof 100 2R:1731127-2080000 1 NULL:1984502 SD15078.5prime 0 100 1 1 0 323388 322895 1 0 0 0 99 partof 493 2R:1731127-2080000 1 NULL:1984503 SD15078.5prime 100 593 1 1 0 2600179 322830 322744 1 0 0 0 100 partof 86 2R:1731127-2080000 1 NULL:1984505 GM26863.5prime 0 86 1 1 0 323437 322895 1 0 0 0 100 partof 542 2R:1731127-2080000 1 NULL:1984506 GM26863.5prime 86 628 1 1 0 2605403 304767 304721 1 0 0 0 95 partof 46 2R:1731127-2080000 -1 NULL:1988878 RE14989.5prime 37 85 1 1 0 303775 303494 1 0 0 0 99 partof 281 2R:1731127-2080000 -1 NULL:1988879 RE14989.5prime 85 365 1 1 0 2605407 304772 304721 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988881 RE06529.5prime 0 51 1 1 0 303775 303196 1 0 0 0 100 partof 579 2R:1731127-2080000 -1 NULL:1988882 RE06529.5prime 51 630 1 1 0 2600183 323745 323154 1 0 0 0 99 partof 591 2R:1731127-2080000 1 NULL:1984508 GH12972.5prime 0 591 1 1 0 2600186 323784 323154 1 0 0 0 100 partof 630 2R:1731127-2080000 1 NULL:1984510 GH19487.5prime 0 630 1 1 0 2600189 324081 323527 1 0 0 0 99 partof 554 2R:1731127-2080000 1 NULL:1984512 LP01956.3prime_revcomp 0 555 1 1 0 2605411 304772 304721 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988884 RE07044.5prime 0 51 1 1 0 303775 303263 1 0 0 0 99 partof 512 2R:1731127-2080000 -1 NULL:1988885 RE07044.5prime 51 562 1 1 0 2605415 304772 304721 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988887 RE17933.5prime 0 51 1 1 0 303775 303353 1 0 0 0 99 partof 422 2R:1731127-2080000 -1 NULL:1988888 RE17933.5prime 51 473 1 1 0 2605419 308255 307464 1 0 0 0 99 partof 791 2R:1731127-2080000 -1 NULL:1988890 SD10607:contig1 0 791 1 1 0 307377 306990 1 0 0 0 95 partof 387 2R:1731127-2080000 -1 NULL:1988891 SD10607:contig1 791 1178 1 1 0 306932 305567 1 0 0 0 100 partof 1365 2R:1731127-2080000 -1 NULL:1988892 SD10607:contig1 1178 2543 1 1 0 2600191 328956 327941 1 0 0 0 100 partof 1015 2R:1731127-2080000 1 NULL:1984514 GH04835:contig1 0 1015 1 1 0 329185 329020 1 0 0 0 97 partof 165 2R:1731127-2080000 1 NULL:1984515 GH04835:contig1 1015 1180 1 1 0 329626 329257 1 0 0 0 97 partof 369 2R:1731127-2080000 1 NULL:1984516 GH04835:contig1 1180 1549 1 1 0 2599304 141216 140796 1 0 0 0 100 partof 420 2R:1731127-2080000 1 NULL:1983805 RE03591.5prime 0 420 1 1 0 2600195 328956 328624 1 0 0 0 99 partof 332 2R:1731127-2080000 1 NULL:1984518 RE74963.5prime 0 331 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984519 RE74963.5prime 331 496 1 1 0 329320 329257 1 0 0 0 98 partof 63 2R:1731127-2080000 1 NULL:1984520 RE74963.5prime 496 559 1 1 0 2599307 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983807 RE58950.5prime 0 154 1 1 0 141856 141676 1 0 0 0 95 partof 180 2R:1731127-2080000 1 NULL:1983808 RE58950.5prime 154 335 1 1 0 2605423 312570 311743 1 0 0 0 99 partof 827 2R:1731127-2080000 -1 NULL:1988894 AT02529:contig1 0 827 1 1 0 311684 311517 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1988895 AT02529:contig1 827 994 1 1 0 311460 311220 1 0 0 0 100 partof 240 2R:1731127-2080000 -1 NULL:1988896 AT02529:contig1 994 1234 1 1 0 2605427 312678 312218 1 0 0 0 98 partof 460 2R:1731127-2080000 -1 NULL:1988898 AI946324 0 463 1 1 0 2599311 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983810 RE56750.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983811 RE56750.5prime 154 336 1 1 0 142744 142555 1 0 0 0 100 partof 189 2R:1731127-2080000 1 NULL:1983812 RE56750.5prime 336 525 1 1 0 2599316 140950 140796 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1983814 RE74620.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983815 RE74620.5prime 154 336 1 1 0 142749 142555 1 0 0 0 100 partof 194 2R:1731127-2080000 1 NULL:1983816 RE74620.5prime 336 530 1 1 0 2605430 312691 312008 1 0 0 0 99 partof 683 2R:1731127-2080000 -1 NULL:1988900 AT09779.5prime 0 683 1 1 0 2605433 312693 312092 1 0 0 0 99 partof 601 2R:1731127-2080000 -1 NULL:1988902 AT11393.5prime 0 601 1 1 0 2605436 312700 312412 1 0 0 0 93 partof 288 2R:1731127-2080000 -1 NULL:1988904 BE662047 0 291 1 1 0 2605439 312708 312127 1 0 0 0 99 partof 581 2R:1731127-2080000 -1 NULL:1988906 LP10145.5prime 0 581 1 1 0 2599321 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983818 RE49604.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983819 RE49604.5prime 154 336 1 1 0 142751 142555 1 0 0 0 95 partof 196 2R:1731127-2080000 1 NULL:1983820 RE49604.5prime 336 532 1 1 0 2599326 140950 140796 1 0 0 0 98 partof 154 2R:1731127-2080000 1 NULL:1983822 RE07865.5prime 0 153 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983823 RE07865.5prime 153 335 1 1 0 142762 142555 1 0 0 0 100 partof 207 2R:1731127-2080000 1 NULL:1983824 RE07865.5prime 335 542 1 1 0 2605442 312737 312302 1 0 0 0 99 partof 435 2R:1731127-2080000 -1 NULL:1988908 AT17434.5prime 0 435 1 1 0 2605445 312745 312093 1 0 0 0 99 partof 652 2R:1731127-2080000 -1 NULL:1988910 GH05253.5prime 0 652 1 1 0 2600500 342110 342045 1 0 0 0 94 partof 65 2R:1731127-2080000 1 NULL:1984767 SD12558.5prime 11 78 1 1 0 342891 342807 1 0 0 0 98 partof 84 2R:1731127-2080000 1 NULL:1984768 SD12558.5prime 78 162 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984769 SD12558.5prime 162 527 1 1 0 347245 347209 1 0 0 0 100 partof 36 2R:1731127-2080000 1 NULL:1984770 SD12558.5prime 527 563 1 1 0 2605448 312761 312176 1 0 0 0 99 partof 585 2R:1731127-2080000 -1 NULL:1988912 AT29763.5prime 0 585 1 1 0 2600506 342110 342048 1 0 0 0 92 partof 62 2R:1731127-2080000 1 NULL:1984772 BE978253 0 63 1 1 0 342891 342807 1 0 0 0 96 partof 84 2R:1731127-2080000 1 NULL:1984773 BE978253 63 147 1 1 0 346837 346787 1 0 0 0 94 partof 50 2R:1731127-2080000 1 NULL:1984774 BE978253 147 197 1 1 0 2599331 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983826 RE01623.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983827 RE01623.5prime 154 336 1 1 0 142775 142555 1 0 0 0 100 partof 220 2R:1731127-2080000 1 NULL:1983828 RE01623.5prime 336 556 1 1 0 2599336 140950 140796 1 0 0 0 98 partof 154 2R:1731127-2080000 1 NULL:1983830 RE58077.5prime 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983831 RE58077.5prime 155 337 1 1 0 142786 142555 1 0 0 0 99 partof 231 2R:1731127-2080000 1 NULL:1983832 RE58077.5prime 337 568 1 1 0 2605451 315457 315186 1 0 0 0 99 partof 271 2R:1731127-2080000 -1 NULL:1988914 RE54322.5prime 0 272 1 1 0 308372 307951 1 0 0 0 99 partof 421 2R:1731127-2080000 -1 NULL:1988915 RE54322.5prime 272 693 1 1 0 2605455 315457 315186 1 0 0 0 99 partof 271 2R:1731127-2080000 -1 NULL:1988917 RE56580.5prime 0 272 1 1 0 308372 308015 1 0 0 0 100 partof 357 2R:1731127-2080000 -1 NULL:1988918 RE56580.5prime 272 629 1 1 0 2600511 342110 342054 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1984776 SD05521.5prime 0 56 1 1 0 342891 342807 1 0 0 0 98 partof 84 2R:1731127-2080000 1 NULL:1984777 SD05521.5prime 56 140 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984778 SD05521.5prime 140 503 1 1 0 347284 347209 1 0 0 0 98 partof 75 2R:1731127-2080000 1 NULL:1984779 SD05521.5prime 503 578 1 1 0 2605459 315457 315186 1 0 0 0 99 partof 271 2R:1731127-2080000 -1 NULL:1988920 RE52127.5prime 0 272 1 1 0 308372 308019 1 0 0 0 100 partof 353 2R:1731127-2080000 -1 NULL:1988921 RE52127.5prime 272 625 1 1 0 2600517 342110 342054 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1984781 AT09895.5prime 0 56 1 1 0 342891 342807 1 0 0 0 97 partof 84 2R:1731127-2080000 1 NULL:1984782 AT09895.5prime 56 140 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984783 AT09895.5prime 140 504 1 1 0 347362 347209 1 0 0 0 100 partof 153 2R:1731127-2080000 1 NULL:1984784 AT09895.5prime 504 657 1 1 0 2599341 140950 140796 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1983834 RE44158.5prime 0 154 1 1 0 141858 141676 1 0 0 0 99 partof 182 2R:1731127-2080000 1 NULL:1983835 RE44158.5prime 154 336 1 1 0 142788 142555 1 0 0 0 99 partof 233 2R:1731127-2080000 1 NULL:1983836 RE44158.5prime 336 569 1 1 0 2599346 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983838 RE17007.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983839 RE17007.5prime 154 336 1 1 0 142791 142555 1 0 0 0 99 partof 236 2R:1731127-2080000 1 NULL:1983840 RE17007.5prime 336 572 1 1 0 2604801 196714 196461 1 0 0 0 100 partof 253 2R:1731127-2080000 -1 NULL:1988401 LD46141.5prime 0 253 1 1 0 195149 194882 1 0 0 0 100 partof 267 2R:1731127-2080000 -1 NULL:1988402 LD46141.5prime 253 520 1 1 0 194824 194720 1 0 0 0 100 partof 104 2R:1731127-2080000 -1 NULL:1988403 LD46141.5prime 520 624 1 1 0 2604806 196832 196771 1 0 0 0 96 partof 61 2R:1731127-2080000 -1 NULL:1988405 AT25214.5prime 0 60 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988406 AT25214.5prime 60 315 1 1 0 195149 194882 1 0 0 0 100 partof 267 2R:1731127-2080000 -1 NULL:1988407 AT25214.5prime 315 582 1 1 0 194824 194674 1 0 0 0 97 partof 150 2R:1731127-2080000 -1 NULL:1988408 AT25214.5prime 582 732 1 1 0 2605463 315461 315186 1 0 0 0 100 partof 275 2R:1731127-2080000 -1 NULL:1988923 RE30587.5prime 0 275 1 1 0 308372 307993 1 0 0 0 100 partof 379 2R:1731127-2080000 -1 NULL:1988924 RE30587.5prime 275 654 1 1 0 2605467 315461 315186 1 0 0 0 100 partof 275 2R:1731127-2080000 -1 NULL:1988926 RE32079.5prime 0 275 1 1 0 308372 308143 1 0 0 0 99 partof 229 2R:1731127-2080000 -1 NULL:1988927 RE32079.5prime 275 504 1 1 0 2600523 342110 342057 1 0 0 0 100 partof 53 2R:1731127-2080000 1 NULL:1984786 AT28144.5prime 0 53 1 1 0 342891 342807 1 0 0 0 98 partof 84 2R:1731127-2080000 1 NULL:1984787 AT28144.5prime 53 137 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984788 AT28144.5prime 137 501 1 1 0 347260 347209 1 0 0 0 100 partof 51 2R:1731127-2080000 1 NULL:1984789 AT28144.5prime 501 552 1 1 0 2600529 342110 342057 1 0 0 0 100 partof 53 2R:1731127-2080000 1 NULL:1984791 AT03411.5prime 0 53 1 1 0 342891 342807 1 0 0 0 98 partof 84 2R:1731127-2080000 1 NULL:1984792 AT03411.5prime 53 137 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984793 AT03411.5prime 137 500 1 1 0 347392 347209 1 0 0 0 100 partof 183 2R:1731127-2080000 1 NULL:1984794 AT03411.5prime 500 683 1 1 0 2599351 140950 140796 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1983842 RE05556.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983843 RE05556.5prime 154 336 1 1 0 142795 142555 1 0 0 0 99 partof 240 2R:1731127-2080000 1 NULL:1983844 RE05556.5prime 336 576 1 1 0 2599356 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983846 RE60163.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983847 RE60163.5prime 154 336 1 1 0 142804 142555 1 0 0 0 100 partof 249 2R:1731127-2080000 1 NULL:1983848 RE60163.5prime 336 585 1 1 0 2604812 202330 202308 1 0 0 0 95 partof 22 2R:1731127-2080000 -1 NULL:1988410 RE48057.5prime 0 22 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988411 RE48057.5prime 22 277 1 1 0 195149 194882 1 0 0 0 100 partof 267 2R:1731127-2080000 -1 NULL:1988412 RE48057.5prime 277 544 1 1 0 194824 194765 1 0 0 0 100 partof 59 2R:1731127-2080000 -1 NULL:1988413 RE48057.5prime 544 603 1 1 0 2605471 315465 315186 1 0 0 0 97 partof 279 2R:1731127-2080000 -1 NULL:1988929 RE72183.5prime 6 285 1 1 0 308372 308054 1 0 0 0 99 partof 318 2R:1731127-2080000 -1 NULL:1988930 RE72183.5prime 285 603 1 1 0 2604818 202330 202308 1 0 0 0 95 partof 22 2R:1731127-2080000 -1 NULL:1988415 RE60533.5prime 0 22 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988416 RE60533.5prime 22 277 1 1 0 195149 195046 1 0 0 0 96 partof 103 2R:1731127-2080000 -1 NULL:1988417 RE60533.5prime 277 379 1 1 0 2605475 315470 315186 1 0 0 0 99 partof 284 2R:1731127-2080000 -1 NULL:1988932 RE56250.5prime 0 285 1 1 0 308372 308017 1 0 0 0 99 partof 355 2R:1731127-2080000 -1 NULL:1988933 RE56250.5prime 285 640 1 1 0 2605479 315471 315186 1 0 0 0 100 partof 285 2R:1731127-2080000 -1 NULL:1988935 RE63331.5prime 0 285 1 1 0 308372 307962 1 0 0 0 98 partof 410 2R:1731127-2080000 -1 NULL:1988936 RE63331.5prime 285 695 1 1 0 2600535 342110 342058 1 0 0 0 100 partof 52 2R:1731127-2080000 1 NULL:1984796 SD28293.5prime 0 52 1 1 0 343388 342807 1 0 0 0 94 partof 581 2R:1731127-2080000 1 NULL:1984797 SD28293.5prime 52 635 1 1 0 2600539 342110 342058 1 0 0 0 100 partof 52 2R:1731127-2080000 1 NULL:1984799 GM04289.5prime 0 52 1 1 0 342891 342807 1 0 0 0 96 partof 84 2R:1731127-2080000 1 NULL:1984800 GM04289.5prime 52 136 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984801 GM04289.5prime 136 499 1 1 0 347266 347209 1 0 0 0 100 partof 57 2R:1731127-2080000 1 NULL:1984802 GM04289.5prime 499 556 1 1 0 2599361 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983850 RE04281.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983851 RE04281.5prime 154 336 1 1 0 142831 142555 1 0 0 0 95 partof 276 2R:1731127-2080000 1 NULL:1983852 RE04281.5prime 336 606 1 1 0 2599366 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983854 RE67561.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983855 RE67561.5prime 154 336 1 1 0 142877 142555 1 0 0 0 98 partof 322 2R:1731127-2080000 1 NULL:1983856 RE67561.5prime 336 658 1 1 0 2604823 202330 202308 1 0 0 0 95 partof 22 2R:1731127-2080000 -1 NULL:1988419 RE48091.5prime 0 22 1 1 0 196716 196499 1 0 0 0 98 partof 217 2R:1731127-2080000 -1 NULL:1988420 RE48091.5prime 22 239 1 1 0 2605483 315471 315186 1 0 0 0 100 partof 285 2R:1731127-2080000 -1 NULL:1988938 RE60292.5prime 0 285 1 1 0 308375 307980 1 0 0 0 100 partof 395 2R:1731127-2080000 -1 NULL:1988939 RE60292.5prime 285 680 1 1 0 2604827 202330 202308 1 0 0 0 95 partof 22 2R:1731127-2080000 -1 NULL:1988422 RE47217.5prime 0 22 1 1 0 196716 196509 1 0 0 0 99 partof 207 2R:1731127-2080000 -1 NULL:1988423 RE47217.5prime 22 229 1 1 0 2605487 315479 315186 1 0 0 0 99 partof 293 2R:1731127-2080000 -1 NULL:1988941 RE65104.5prime 0 293 1 1 0 308372 307993 1 0 0 0 100 partof 379 2R:1731127-2080000 -1 NULL:1988942 RE65104.5prime 293 672 1 1 0 2600545 342110 342062 1 0 0 0 95 partof 48 2R:1731127-2080000 1 NULL:1984804 LD16071.5prime 0 48 1 1 0 342891 342807 1 0 0 0 98 partof 84 2R:1731127-2080000 1 NULL:1984805 LD16071.5prime 48 132 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984806 LD16071.5prime 132 495 1 1 0 347337 347209 1 0 0 0 97 partof 128 2R:1731127-2080000 1 NULL:1984807 LD16071.5prime 495 624 1 1 0 2599371 140950 140796 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1983858 RE39462.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983859 RE39462.5prime 154 336 1 1 0 142885 142555 1 0 0 0 100 partof 330 2R:1731127-2080000 1 NULL:1983860 RE39462.5prime 336 666 1 1 0 2599376 140950 140796 1 0 0 0 98 partof 154 2R:1731127-2080000 1 NULL:1983862 RE07508.5prime 0 155 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983863 RE07508.5prime 155 337 1 1 0 142886 142555 1 0 0 0 99 partof 331 2R:1731127-2080000 1 NULL:1983864 RE07508.5prime 337 668 1 1 0 2604831 202422 202308 1 0 0 0 100 partof 114 2R:1731127-2080000 -1 NULL:1988425 LD46932.5prime 0 114 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988426 LD46932.5prime 114 369 1 1 0 195149 194967 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988427 LD46932.5prime 369 551 1 1 0 2605491 315479 315186 1 0 0 0 100 partof 293 2R:1731127-2080000 -1 NULL:1988944 RE45682.5prime 0 293 1 1 0 308372 308058 1 0 0 0 99 partof 314 2R:1731127-2080000 -1 NULL:1988945 RE45682.5prime 293 608 1 1 0 2604836 202422 202308 1 0 0 0 100 partof 114 2R:1731127-2080000 -1 NULL:1988429 LD01847.5prime 0 114 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988430 LD01847.5prime 114 369 1 1 0 195149 195047 1 0 0 0 99 partof 102 2R:1731127-2080000 -1 NULL:1988431 LD01847.5prime 369 471 1 1 0 2605495 315479 315186 1 0 0 0 99 partof 293 2R:1731127-2080000 -1 NULL:1988947 RE36253.5prime 0 293 1 1 0 308372 308194 1 0 0 0 100 partof 178 2R:1731127-2080000 -1 NULL:1988948 RE36253.5prime 293 471 1 1 0 2600551 342110 342063 1 0 0 0 91 partof 47 2R:1731127-2080000 1 NULL:1984809 LD05541.5prime 0 47 1 1 0 342891 342807 1 0 0 0 96 partof 84 2R:1731127-2080000 1 NULL:1984810 LD05541.5prime 47 130 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984811 LD05541.5prime 130 492 1 1 0 347384 347209 1 0 0 0 99 partof 175 2R:1731127-2080000 1 NULL:1984812 LD05541.5prime 492 668 1 1 0 2605499 315484 315186 1 0 0 0 99 partof 298 2R:1731127-2080000 -1 NULL:1988950 RE57156.5prime 0 298 1 1 0 308375 308136 1 0 0 0 99 partof 239 2R:1731127-2080000 -1 NULL:1988951 RE57156.5prime 298 537 1 1 0 2600557 342110 342082 1 0 0 0 100 partof 28 2R:1731127-2080000 1 NULL:1984814 RE21546.5prime 0 28 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984815 RE21546.5prime 28 112 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984816 RE21546.5prime 112 475 1 1 0 347395 347209 1 0 0 0 99 partof 186 2R:1731127-2080000 1 NULL:1984817 RE21546.5prime 475 661 1 1 0 2599381 140950 140796 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1983866 RE34840.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983867 RE34840.5prime 154 336 1 1 0 142886 142555 1 0 0 0 100 partof 331 2R:1731127-2080000 1 NULL:1983868 RE34840.5prime 336 667 1 1 0 2599386 140950 140796 1 0 0 0 100 partof 154 2R:1731127-2080000 1 NULL:1983870 RE34959.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983871 RE34959.5prime 154 336 1 1 0 142890 142555 1 0 0 0 100 partof 335 2R:1731127-2080000 1 NULL:1983872 RE34959.5prime 336 671 1 1 0 2604841 202435 202308 1 0 0 0 100 partof 127 2R:1731127-2080000 -1 NULL:1988433 GM02487.5prime 0 127 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988434 GM02487.5prime 127 381 1 1 0 195149 194927 1 0 0 0 97 partof 222 2R:1731127-2080000 -1 NULL:1988435 GM02487.5prime 381 601 1 1 0 2604846 202435 202308 1 0 0 0 100 partof 127 2R:1731127-2080000 -1 NULL:1988437 GM25756.5prime 0 127 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988438 GM25756.5prime 127 382 1 1 0 195149 195045 1 0 0 0 100 partof 104 2R:1731127-2080000 -1 NULL:1988439 GM25756.5prime 382 486 1 1 0 2600563 347360 346850 1 0 0 0 99 partof 510 2R:1731127-2080000 1 NULL:1984819 RH60517.5prime 0 509 1 1 0 2600566 347431 346850 1 0 0 0 98 partof 581 2R:1731127-2080000 1 NULL:1984821 RH28602.5prime 0 582 1 1 0 2600569 347436 346850 1 0 0 0 98 partof 586 2R:1731127-2080000 1 NULL:1984823 RH34365.5prime 0 585 1 1 0 2599391 140950 140796 1 0 0 0 98 partof 154 2R:1731127-2080000 1 NULL:1983874 RE30406.5prime 0 154 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983875 RE30406.5prime 154 336 1 1 0 142891 142555 1 0 0 0 100 partof 336 2R:1731127-2080000 1 NULL:1983876 RE30406.5prime 336 672 1 1 0 2599396 140950 140816 1 0 0 0 100 partof 134 2R:1731127-2080000 1 NULL:1983878 LD35815:contig1 0 134 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983879 LD35815:contig1 134 316 1 1 0 142889 142555 1 0 0 0 99 partof 334 2R:1731127-2080000 1 NULL:1983880 LD35815:contig1 316 650 1 1 0 144597 144082 1 0 0 0 98 partof 515 2R:1731127-2080000 1 NULL:1983881 LD35815:contig2 650 1165 1 1 0 2604851 202445 202308 1 0 0 0 100 partof 137 2R:1731127-2080000 -1 NULL:1988441 LD18823.5prime 0 137 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988442 LD18823.5prime 137 391 1 1 0 195149 194893 1 0 0 0 98 partof 256 2R:1731127-2080000 -1 NULL:1988443 LD18823.5prime 391 645 1 1 0 2604856 202445 202308 1 0 0 0 100 partof 137 2R:1731127-2080000 -1 NULL:1988445 LD06985.5prime 0 137 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988446 LD06985.5prime 137 391 1 1 0 195149 194916 1 0 0 0 98 partof 233 2R:1731127-2080000 -1 NULL:1988447 LD06985.5prime 391 620 1 1 0 2600572 347493 346850 1 0 0 0 99 partof 643 2R:1731127-2080000 1 NULL:1984825 RH41670.5prime 0 642 1 1 0 2600575 347523 346850 1 0 0 0 98 partof 673 2R:1731127-2080000 1 NULL:1984827 RH14080.5prime 0 674 1 1 0 2600578 347150 346877 1 0 0 0 98 partof 273 2R:1731127-2080000 1 NULL:1984829 RE09713.TN_G9615 0 273 1 1 0 347401 347209 1 0 0 0 97 partof 192 2R:1731127-2080000 1 NULL:1984830 RE09713.TN_G9615 273 465 1 1 0 347525 347464 1 0 0 0 100 partof 61 2R:1731127-2080000 1 NULL:1984831 RE09713.TN_G9615 465 526 1 1 0 2604861 202449 202308 1 0 0 0 100 partof 141 2R:1731127-2080000 -1 NULL:1988449 LD33336.5prime 0 141 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988450 LD33336.5prime 141 396 1 1 0 195149 195033 1 0 0 0 100 partof 116 2R:1731127-2080000 -1 NULL:1988451 LD33336.5prime 396 512 1 1 0 2604866 202456 202308 1 0 0 0 99 partof 148 2R:1731127-2080000 -1 NULL:1988453 LD12243.5prime 0 149 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988454 LD12243.5prime 149 401 1 1 0 195149 194903 1 0 0 0 98 partof 246 2R:1731127-2080000 -1 NULL:1988455 LD12243.5prime 401 644 1 1 0 2600583 347401 347229 1 0 0 0 100 partof 172 2R:1731127-2080000 1 NULL:1984833 GM31773.5prime 0 172 1 1 0 347593 347464 1 0 0 0 99 partof 129 2R:1731127-2080000 1 NULL:1984834 GM31773.5prime 172 301 1 1 0 2600587 347401 347250 1 0 0 0 100 partof 151 2R:1731127-2080000 1 NULL:1984836 LP07972.5prime 0 151 1 1 0 347890 347464 1 0 0 0 100 partof 426 2R:1731127-2080000 1 NULL:1984837 LP07972.5prime 151 577 1 1 0 2604871 202458 202308 1 0 0 0 100 partof 150 2R:1731127-2080000 -1 NULL:1988457 LD44095.5prime 0 150 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988458 LD44095.5prime 150 405 1 1 0 195149 194927 1 0 0 0 100 partof 222 2R:1731127-2080000 -1 NULL:1988459 LD44095.5prime 405 627 1 1 0 2604876 202458 202308 1 0 0 0 100 partof 150 2R:1731127-2080000 -1 NULL:1988461 LD37905.5prime 0 150 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988462 LD37905.5prime 150 405 1 1 0 195149 195119 1 0 0 0 100 partof 30 2R:1731127-2080000 -1 NULL:1988463 LD37905.5prime 405 435 1 1 0 2599700 288144 287879 1 0 0 0 97 partof 265 2R:1731127-2080000 1 NULL:1984114 SD07874.5prime 0 268 1 1 0 2600591 347401 347378 1 0 0 0 100 partof 23 2R:1731127-2080000 1 NULL:1984839 RH03191.5prime 0 23 1 1 0 347895 347464 1 0 0 0 98 partof 431 2R:1731127-2080000 1 NULL:1984840 RH03191.5prime 23 457 1 1 0 2599702 288582 288096 1 0 0 0 99 partof 486 2R:1731127-2080000 1 NULL:1984116 RH52219.5prime 0 485 1 1 0 2599704 288583 288096 1 0 0 0 99 partof 487 2R:1731127-2080000 1 NULL:1984118 RH52990.5prime 0 486 1 1 0 2599706 288583 288098 1 0 0 0 99 partof 485 2R:1731127-2080000 1 NULL:1984120 RH39177.5prime 0 485 1 1 0 2599708 288648 288098 1 0 0 0 99 partof 550 2R:1731127-2080000 1 NULL:1984122 RH42278.5prime 0 550 1 1 0 2604881 202460 202308 1 0 0 0 100 partof 152 2R:1731127-2080000 -1 NULL:1988465 LD15977.5prime 0 152 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988466 LD15977.5prime 152 407 1 1 0 195149 194882 1 0 0 0 99 partof 267 2R:1731127-2080000 -1 NULL:1988467 LD15977.5prime 407 672 1 1 0 194824 194748 1 0 0 0 97 partof 76 2R:1731127-2080000 -1 NULL:1988468 LD15977.5prime 672 748 1 1 0 2604887 202460 202329 1 0 0 0 99 partof 131 2R:1731127-2080000 -1 NULL:1988470 SD08055.5prime 0 131 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988471 SD08055.5prime 131 386 1 1 0 195149 194939 1 0 0 0 99 partof 210 2R:1731127-2080000 -1 NULL:1988472 SD08055.5prime 386 596 1 1 0 2599710 288732 288098 1 0 0 0 99 partof 634 2R:1731127-2080000 1 NULL:1984124 RH61871.5prime 0 634 1 1 0 2599712 288582 288100 1 0 0 0 99 partof 482 2R:1731127-2080000 1 NULL:1984126 RH55857.5prime 0 482 1 1 0 2599714 288583 288100 1 0 0 0 99 partof 483 2R:1731127-2080000 1 NULL:1984128 RH54175.5prime 0 483 1 1 0 2599716 289398 288978 1 0 0 0 98 partof 420 2R:1731127-2080000 1 NULL:1984130 GH28346.3prime_revcomp 0 420 1 1 0 2599718 306169 305695 1 0 0 0 99 partof 474 2R:1731127-2080000 1 NULL:1984132 LP04395.TN_G7939 0 474 1 1 0 2604892 202460 202308 1 0 0 0 98 partof 152 2R:1731127-2080000 -1 NULL:1988474 LD16980.5prime 0 154 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988475 LD16980.5prime 154 409 1 1 0 195149 194962 1 0 0 0 97 partof 187 2R:1731127-2080000 -1 NULL:1988476 LD16980.5prime 409 594 1 1 0 2604897 202460 202308 1 0 0 0 100 partof 152 2R:1731127-2080000 -1 NULL:1988478 LD36646.5prime 0 152 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988479 LD36646.5prime 152 407 1 1 0 195149 195046 1 0 0 0 100 partof 103 2R:1731127-2080000 -1 NULL:1988480 LD36646.5prime 407 510 1 1 0 2599721 309997 309514 1 0 0 0 98 partof 483 2R:1731127-2080000 1 NULL:1984134 AT31865.3prime_revcomp 0 483 1 1 0 2599724 311460 311220 1 0 0 0 100 partof 240 2R:1731127-2080000 1 NULL:1984136 GH05437.3prime 322 562 1 1 0 311684 311517 1 0 0 0 100 partof 167 2R:1731127-2080000 1 NULL:1984137 GH05437.3prime 155 322 1 1 0 311898 311743 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1984138 GH05437.3prime 0 155 1 1 0 2599729 316169 315502 1 0 0 0 100 partof 667 2R:1731127-2080000 1 NULL:1984140 RH50121.5prime 0 667 1 1 0 2599732 316152 315837 1 0 0 0 98 partof 315 2R:1731127-2080000 1 NULL:1984142 LD04148.5prime 0 316 1 1 0 2599735 316253 315838 1 0 0 0 99 partof 415 2R:1731127-2080000 1 NULL:1984144 GM32458.5prime 0 415 1 1 0 2599738 316335 315838 1 0 0 0 99 partof 497 2R:1731127-2080000 1 NULL:1984146 RE28019.5prime 0 497 1 1 0 2599741 316551 315854 1 0 0 0 98 partof 697 2R:1731127-2080000 1 NULL:1984148 LD41464:contig1 0 697 1 1 0 316708 316608 1 0 0 0 100 partof 100 2R:1731127-2080000 1 NULL:1984149 LD41464:contig1 697 797 1 1 0 317463 317412 1 0 0 0 100 partof 51 2R:1731127-2080000 1 NULL:1984150 LD41464:contig1 797 848 1 1 0 318040 317555 1 0 0 0 99 partof 485 2R:1731127-2080000 1 NULL:1984151 LD41464:contig1 848 1333 1 1 0 318699 318345 1 0 0 0 100 partof 354 2R:1731127-2080000 1 NULL:1984152 LD41464:contig1 1333 1687 1 1 0 2599747 316168 315858 1 0 0 0 98 partof 310 2R:1731127-2080000 1 NULL:1984154 HL01939.5prime 0 310 1 1 0 2599750 316497 315866 1 0 0 0 99 partof 631 2R:1731127-2080000 1 NULL:1984156 AT19206.5prime 0 632 1 1 0 2599753 316360 315868 1 0 0 0 98 partof 492 2R:1731127-2080000 1 NULL:1984158 RE41060.5prime 0 491 1 1 0 2599756 316481 315872 1 0 0 0 100 partof 609 2R:1731127-2080000 1 NULL:1984160 GH20137.5prime 0 609 1 1 0 2599759 316419 315880 1 0 0 0 97 partof 539 2R:1731127-2080000 1 NULL:1984162 LD07418.5prime 0 538 1 1 0 2599762 316505 315920 1 0 0 0 99 partof 585 2R:1731127-2080000 1 NULL:1984164 GH13130.5prime 0 585 1 1 0 2599765 317642 317198 1 0 0 0 100 partof 444 2R:1731127-2080000 1 NULL:1984166 RH29168.5prime 0 444 1 1 0 2599768 317722 317198 1 0 0 0 100 partof 524 2R:1731127-2080000 1 NULL:1984168 RH25222.5prime 0 524 1 1 0 2599771 317742 317198 1 0 0 0 100 partof 544 2R:1731127-2080000 1 NULL:1984170 RH22964.5prime 0 544 1 1 0 2599774 317756 317198 1 0 0 0 98 partof 558 2R:1731127-2080000 1 NULL:1984172 RH15403.5prime 0 558 1 1 0 2599777 317789 317198 1 0 0 0 100 partof 591 2R:1731127-2080000 1 NULL:1984174 RH24622.5prime 0 591 1 1 0 2599780 317791 317198 1 0 0 0 99 partof 593 2R:1731127-2080000 1 NULL:1984176 RH36526.5prime 0 593 1 1 0 2599783 317801 317198 1 0 0 0 99 partof 603 2R:1731127-2080000 1 NULL:1984178 RH20960.5prime 0 603 1 1 0 2599786 317817 317198 1 0 0 0 100 partof 619 2R:1731127-2080000 1 NULL:1984180 RH36296.5prime 0 619 1 1 0 2605102 202489 202308 1 0 0 0 98 partof 181 2R:1731127-2080000 -1 NULL:1988641 RE21458.5prime 0 184 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988642 RE21458.5prime 184 439 1 1 0 195149 194926 1 0 0 0 99 partof 223 2R:1731127-2080000 -1 NULL:1988643 RE21458.5prime 439 662 1 1 0 2599789 317841 317198 1 0 0 0 99 partof 643 2R:1731127-2080000 1 NULL:1984182 RH72993.5prime 0 643 1 1 0 2605107 202489 202308 1 0 0 0 99 partof 181 2R:1731127-2080000 -1 NULL:1988645 RE18024.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988646 RE18024.5prime 182 437 1 1 0 195149 195084 1 0 0 0 100 partof 65 2R:1731127-2080000 -1 NULL:1988647 RE18024.5prime 437 502 1 1 0 2599792 317845 317198 1 0 0 0 99 partof 647 2R:1731127-2080000 1 NULL:1984184 RH37484.5prime 0 647 1 1 0 2599795 317847 317198 1 0 0 0 100 partof 649 2R:1731127-2080000 1 NULL:1984186 RH36503.5prime 0 649 1 1 0 2599798 317850 317198 1 0 0 0 100 partof 652 2R:1731127-2080000 1 NULL:1984188 RH12093.5prime 0 652 1 1 0 2605112 202489 202308 1 0 0 0 99 partof 181 2R:1731127-2080000 -1 NULL:1988649 RE02274.5prime 0 182 1 1 0 196716 196537 1 0 0 0 98 partof 179 2R:1731127-2080000 -1 NULL:1988650 RE02274.5prime 182 361 1 1 0 2605116 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988652 RE30002.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988653 RE30002.5prime 182 437 1 1 0 195149 194906 1 0 0 0 99 partof 243 2R:1731127-2080000 -1 NULL:1988654 RE30002.5prime 437 680 1 1 0 2599002 137592 137405 1 0 0 0 99 partof 187 2R:1731127-2080000 1 NULL:1983572 RE74614.5prime 0 187 1 1 0 138280 137864 1 0 0 0 99 partof 416 2R:1731127-2080000 1 NULL:1983573 RE74614.5prime 187 603 1 1 0 2599006 137592 137406 1 0 0 0 99 partof 186 2R:1731127-2080000 1 NULL:1983575 RH62663.5prime 0 186 1 1 0 138209 137864 1 0 0 0 100 partof 345 2R:1731127-2080000 1 NULL:1983576 RH62663.5prime 186 531 1 1 0 2605121 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988656 RE05468.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988657 RE05468.5prime 182 437 1 1 0 195149 194927 1 0 0 0 98 partof 222 2R:1731127-2080000 -1 NULL:1988658 RE05468.5prime 437 659 1 1 0 2605126 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988660 RE23448.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988661 RE23448.5prime 182 437 1 1 0 195149 194939 1 0 0 0 100 partof 210 2R:1731127-2080000 -1 NULL:1988662 RE23448.5prime 437 647 1 1 0 2599010 137592 137406 1 0 0 0 99 partof 186 2R:1731127-2080000 1 NULL:1983578 RH04116.5prime 0 186 1 1 0 138299 137864 1 0 0 0 100 partof 435 2R:1731127-2080000 1 NULL:1983579 RH04116.5prime 186 621 1 1 0 2599014 137592 137406 1 0 0 0 99 partof 186 2R:1731127-2080000 1 NULL:1983581 RH66149.5prime 0 186 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983582 RH66149.5prime 186 623 1 1 0 138376 138357 1 0 0 0 100 partof 19 2R:1731127-2080000 1 NULL:1983583 RH66149.5prime 623 642 1 1 0 2599019 137592 137407 1 0 0 0 99 partof 185 2R:1731127-2080000 1 NULL:1983585 RE14655.5prime 0 185 1 1 0 138137 137864 1 0 0 0 100 partof 273 2R:1731127-2080000 1 NULL:1983586 RE14655.5prime 185 458 1 1 0 2605131 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988664 RH54996.5prime 0 183 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988665 RH54996.5prime 183 438 1 1 0 195149 194964 1 0 0 0 100 partof 185 2R:1731127-2080000 -1 NULL:1988666 RH54996.5prime 438 623 1 1 0 2605136 202490 202308 1 0 0 0 98 partof 182 2R:1731127-2080000 -1 NULL:1988668 RE62233.5prime 0 184 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988669 RE62233.5prime 184 439 1 1 0 195149 194966 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1988670 RE62233.5prime 439 622 1 1 0 2599023 137592 137407 1 0 0 0 99 partof 185 2R:1731127-2080000 1 NULL:1983588 RE38942.5prime 0 185 1 1 0 138270 137864 1 0 0 0 98 partof 406 2R:1731127-2080000 1 NULL:1983589 RE38942.5prime 185 593 1 1 0 2599027 137592 137414 1 0 0 0 99 partof 178 2R:1731127-2080000 1 NULL:1983591 RH28149.5prime 0 178 1 1 0 138041 137864 1 0 0 0 98 partof 177 2R:1731127-2080000 1 NULL:1983592 RH28149.5prime 178 356 1 1 0 2605141 202490 202308 1 0 0 0 98 partof 182 2R:1731127-2080000 -1 NULL:1988672 RE16130.5prime 0 184 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988673 RE16130.5prime 184 439 1 1 0 195149 194967 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988674 RE16130.5prime 439 622 1 1 0 2605146 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988676 RE74508.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988677 RE74508.5prime 182 437 1 1 0 195149 194982 1 0 0 0 99 partof 167 2R:1731127-2080000 -1 NULL:1988678 RE74508.5prime 437 604 1 1 0 2600200 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984522 RE35547.5prime 0 329 1 1 0 329138 329020 1 0 0 0 100 partof 118 2R:1731127-2080000 1 NULL:1984523 RE35547.5prime 329 447 1 1 0 2600204 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984525 RE59422.5prime 0 329 1 1 0 329147 329020 1 0 0 0 100 partof 127 2R:1731127-2080000 1 NULL:1984526 RE59422.5prime 329 456 1 1 0 2600208 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984528 RE38778.5prime 0 329 1 1 0 329192 329020 1 0 0 0 97 partof 172 2R:1731127-2080000 1 NULL:1984529 RE38778.5prime 329 501 1 1 0 2599031 137592 137414 1 0 0 0 99 partof 178 2R:1731127-2080000 1 NULL:1983594 RH09609.5prime 0 178 1 1 0 138202 137864 1 0 0 0 100 partof 338 2R:1731127-2080000 1 NULL:1983595 RH09609.5prime 178 516 1 1 0 2599035 137592 137414 1 0 0 0 99 partof 178 2R:1731127-2080000 1 NULL:1983597 RH70017.5prime 0 178 1 1 0 138234 137864 1 0 0 0 100 partof 370 2R:1731127-2080000 1 NULL:1983598 RH70017.5prime 178 548 1 1 0 2599039 137592 137414 1 0 0 0 98 partof 178 2R:1731127-2080000 1 NULL:1983600 RH74008.5prime 0 178 1 1 0 138234 137864 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1983601 RH74008.5prime 178 548 1 1 0 2605151 202490 202308 1 0 0 0 96 partof 182 2R:1731127-2080000 -1 NULL:1988680 RE07155.5prime 0 187 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988681 RE07155.5prime 187 442 1 1 0 195149 194983 1 0 0 0 100 partof 166 2R:1731127-2080000 -1 NULL:1988682 RE07155.5prime 442 608 1 1 0 2605156 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988684 RE17667.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988685 RE17667.5prime 182 437 1 1 0 195149 194987 1 0 0 0 98 partof 162 2R:1731127-2080000 -1 NULL:1988686 RE17667.5prime 437 599 1 1 0 2600212 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984531 RE46266.5prime 0 329 1 1 0 329185 329020 1 0 0 0 98 partof 165 2R:1731127-2080000 1 NULL:1984532 RE46266.5prime 329 494 1 1 0 329276 329257 1 0 0 0 100 partof 19 2R:1731127-2080000 1 NULL:1984533 RE46266.5prime 494 513 1 1 0 2600217 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984535 RE24975.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984536 RE24975.5prime 329 494 1 1 0 329305 329257 1 0 0 0 100 partof 48 2R:1731127-2080000 1 NULL:1984537 RE24975.5prime 494 542 1 1 0 2599043 137592 137414 1 0 0 0 98 partof 178 2R:1731127-2080000 1 NULL:1983603 RH64356.5prime 0 178 1 1 0 138279 137864 1 0 0 0 99 partof 415 2R:1731127-2080000 1 NULL:1983604 RH64356.5prime 178 593 1 1 0 2599047 137592 137414 1 0 0 0 99 partof 178 2R:1731127-2080000 1 NULL:1983606 RH55219.5prime 0 178 1 1 0 138302 137864 1 0 0 0 99 partof 438 2R:1731127-2080000 1 NULL:1983607 RH55219.5prime 178 615 1 1 0 2605161 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988688 RE19814.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988689 RE19814.5prime 182 437 1 1 0 195149 194993 1 0 0 0 100 partof 156 2R:1731127-2080000 -1 NULL:1988690 RE19814.5prime 437 593 1 1 0 2605166 202490 202308 1 0 0 0 98 partof 182 2R:1731127-2080000 -1 NULL:1988692 RE30981.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988693 RE30981.5prime 182 437 1 1 0 195149 195029 1 0 0 0 100 partof 120 2R:1731127-2080000 -1 NULL:1988694 RE30981.5prime 437 557 1 1 0 2600222 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984539 RE03981.5prime 0 329 1 1 0 329185 329020 1 0 0 0 99 partof 165 2R:1731127-2080000 1 NULL:1984540 RE03981.5prime 329 494 1 1 0 329312 329257 1 0 0 0 98 partof 55 2R:1731127-2080000 1 NULL:1984541 RE03981.5prime 494 548 1 1 0 2600227 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984543 RE36721.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984544 RE36721.5prime 329 494 1 1 0 329315 329257 1 0 0 0 98 partof 58 2R:1731127-2080000 1 NULL:1984545 RE36721.5prime 494 551 1 1 0 2599051 137592 137414 1 0 0 0 98 partof 178 2R:1731127-2080000 1 NULL:1983609 LD23017.5prime 0 176 1 1 0 138301 137864 1 0 0 0 98 partof 437 2R:1731127-2080000 1 NULL:1983610 LD23017.5prime 176 610 1 1 0 138382 138357 1 0 0 0 100 partof 25 2R:1731127-2080000 1 NULL:1983611 LD23017.5prime 610 635 1 1 0 2599056 137576 137415 1 0 0 0 99 partof 161 2R:1731127-2080000 1 NULL:1983613 RE37462.5prime 0 161 1 1 0 2599059 137592 137415 1 0 0 0 100 partof 177 2R:1731127-2080000 1 NULL:1983615 SD10902.5prime 0 177 1 1 0 138234 137864 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1983616 SD10902.5prime 177 547 1 1 0 2605171 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988696 RE35131.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988697 RE35131.5prime 182 437 1 1 0 195149 195046 1 0 0 0 100 partof 103 2R:1731127-2080000 -1 NULL:1988698 RE35131.5prime 437 540 1 1 0 2605176 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988700 RE06791.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988701 RE06791.5prime 182 437 1 1 0 195149 195076 1 0 0 0 100 partof 73 2R:1731127-2080000 -1 NULL:1988702 RE06791.5prime 437 510 1 1 0 2600232 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984547 RE62452.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984548 RE62452.5prime 329 494 1 1 0 329316 329257 1 0 0 0 100 partof 59 2R:1731127-2080000 1 NULL:1984549 RE62452.5prime 494 553 1 1 0 2600237 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984551 RE11838.5prime 0 329 1 1 0 329185 329020 1 0 0 0 99 partof 165 2R:1731127-2080000 1 NULL:1984552 RE11838.5prime 329 494 1 1 0 329320 329257 1 0 0 0 96 partof 63 2R:1731127-2080000 1 NULL:1984553 RE11838.5prime 494 557 1 1 0 2599063 137592 137416 1 0 0 0 98 partof 176 2R:1731127-2080000 1 NULL:1983618 RH58934.5prime 0 177 1 1 0 138237 137864 1 0 0 0 100 partof 373 2R:1731127-2080000 1 NULL:1983619 RH58934.5prime 177 550 1 1 0 2599067 137592 137417 1 0 0 0 98 partof 175 2R:1731127-2080000 1 NULL:1983621 RE18905.5prime 0 175 1 1 0 138197 137864 1 0 0 0 100 partof 333 2R:1731127-2080000 1 NULL:1983622 RE18905.5prime 175 508 1 1 0 2605181 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988704 RE47576.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988705 RE47576.5prime 182 437 1 1 0 195149 195077 1 0 0 0 98 partof 72 2R:1731127-2080000 -1 NULL:1988706 RE47576.5prime 437 509 1 1 0 2605186 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988708 RE40469.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988709 RE40469.5prime 182 437 1 1 0 195149 195085 1 0 0 0 100 partof 64 2R:1731127-2080000 -1 NULL:1988710 RE40469.5prime 437 501 1 1 0 2600242 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984555 RE02433.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984556 RE02433.5prime 329 494 1 1 0 329322 329257 1 0 0 0 96 partof 65 2R:1731127-2080000 1 NULL:1984557 RE02433.5prime 494 559 1 1 0 2600247 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984559 RE15428.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984560 RE15428.5prime 329 494 1 1 0 329335 329257 1 0 0 0 97 partof 78 2R:1731127-2080000 1 NULL:1984561 RE15428.5prime 494 572 1 1 0 2599071 137592 137417 1 0 0 0 98 partof 175 2R:1731127-2080000 1 NULL:1983624 RE17340.5prime 0 175 1 1 0 138302 137864 1 0 0 0 99 partof 438 2R:1731127-2080000 1 NULL:1983625 RE17340.5prime 175 615 1 1 0 2599075 137592 137417 1 0 0 0 100 partof 175 2R:1731127-2080000 1 NULL:1983627 GH26050.5prime 0 175 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983628 GH26050.5prime 175 612 1 1 0 138373 138357 1 0 0 0 100 partof 16 2R:1731127-2080000 1 NULL:1983629 GH26050.5prime 612 628 1 1 0 2605191 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988712 RE23416.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988713 RE23416.5prime 182 437 1 1 0 195149 195098 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988714 RE23416.5prime 437 488 1 1 0 2605196 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988716 RE13441.5prime 0 183 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988717 RE13441.5prime 183 438 1 1 0 195149 195107 1 0 0 0 100 partof 42 2R:1731127-2080000 -1 NULL:1988718 RE13441.5prime 438 480 1 1 0 2600252 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984563 RE24729.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984564 RE24729.5prime 329 494 1 1 0 329375 329257 1 0 0 0 100 partof 118 2R:1731127-2080000 1 NULL:1984565 RE24729.5prime 494 612 1 1 0 2600257 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984567 RE45455.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984568 RE45455.5prime 329 494 1 1 0 329399 329257 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984569 RE45455.5prime 494 636 1 1 0 2599080 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983631 RE20292.5prime 0 174 1 1 0 138188 137864 1 0 0 0 100 partof 324 2R:1731127-2080000 1 NULL:1983632 RE20292.5prime 174 498 1 1 0 2599084 137592 137418 1 0 0 0 99 partof 174 2R:1731127-2080000 1 NULL:1983634 RE41255.5prime 0 174 1 1 0 138197 137864 1 0 0 0 99 partof 333 2R:1731127-2080000 1 NULL:1983635 RE41255.5prime 174 508 1 1 0 2599088 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983637 RE03511.5prime 0 174 1 1 0 138282 137864 1 0 0 0 99 partof 418 2R:1731127-2080000 1 NULL:1983638 RE03511.5prime 174 592 1 1 0 2600262 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984571 RE52518.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984572 RE52518.5prime 329 494 1 1 0 329429 329257 1 0 0 0 98 partof 172 2R:1731127-2080000 1 NULL:1984573 RE52518.5prime 494 666 1 1 0 2600267 328956 328627 1 0 0 0 99 partof 329 2R:1731127-2080000 1 NULL:1984575 RE34148.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984576 RE34148.5prime 329 494 1 1 0 329441 329257 1 0 0 0 98 partof 184 2R:1731127-2080000 1 NULL:1984577 RE34148.5prime 494 677 1 1 0 2599092 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983640 RE16231.5prime 0 174 1 1 0 138283 137864 1 0 0 0 99 partof 419 2R:1731127-2080000 1 NULL:1983641 RE16231.5prime 174 593 1 1 0 2599096 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983643 RE51964.5prime 0 174 1 1 0 138302 137864 1 0 0 0 99 partof 438 2R:1731127-2080000 1 NULL:1983644 RE51964.5prime 174 614 1 1 0 2600272 328956 328627 1 0 0 0 100 partof 329 2R:1731127-2080000 1 NULL:1984579 RE53491.5prime 0 329 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984580 RE53491.5prime 329 494 1 1 0 329441 329257 1 0 0 0 98 partof 184 2R:1731127-2080000 1 NULL:1984581 RE53491.5prime 494 677 1 1 0 2600277 328956 328643 1 0 0 0 100 partof 313 2R:1731127-2080000 1 NULL:1984583 LP07645.5prime 0 313 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984584 LP07645.5prime 313 478 1 1 0 329399 329257 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984585 LP07645.5prime 478 620 1 1 0 2605503 320299 319875 1 0 0 0 92 partof 424 2R:1731127-2080000 -1 NULL:1988953 AI945638 0 427 1 1 0 2605505 329623 329257 1 0 0 0 99 partof 366 2R:1731127-2080000 -1 NULL:1988955 LP04610.3prime_revcomp 203 569 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 -1 NULL:1988956 LP04610.3prime_revcomp 38 203 1 1 0 328956 328918 1 0 0 0 100 partof 38 2R:1731127-2080000 -1 NULL:1988957 LP04610.3prime_revcomp 0 38 1 1 0 2600282 328956 328643 1 0 0 0 100 partof 313 2R:1731127-2080000 1 NULL:1984587 LP06381.5prime 0 313 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984588 LP06381.5prime 313 478 1 1 0 329479 329257 1 0 0 0 100 partof 222 2R:1731127-2080000 1 NULL:1984589 LP06381.5prime 478 700 1 1 0 2600287 328956 328643 1 0 0 0 100 partof 313 2R:1731127-2080000 1 NULL:1984591 LP06288:contig1 0 313 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984592 LP06288:contig1 313 478 1 1 0 329623 329257 1 0 0 0 98 partof 366 2R:1731127-2080000 1 NULL:1984593 LP06288:contig1 478 844 1 1 0 2605510 341490 341366 1 0 0 0 100 partof 124 2R:1731127-2080000 -1 NULL:1988959 LP09806.5prime 0 124 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988960 LP09806.5prime 124 316 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988961 LP09806.5prime 316 478 1 1 0 340075 339953 1 0 0 0 100 partof 122 2R:1731127-2080000 -1 NULL:1988962 LP09806.5prime 478 600 1 1 0 2605516 341490 341366 1 0 0 0 98 partof 124 2R:1731127-2080000 -1 NULL:1988964 SD21850.5prime 0 123 1 1 0 340629 340437 1 0 0 0 98 partof 192 2R:1731127-2080000 -1 NULL:1988965 SD21850.5prime 123 315 1 1 0 340368 340206 1 0 0 0 99 partof 162 2R:1731127-2080000 -1 NULL:1988966 SD21850.5prime 315 477 1 1 0 340075 340005 1 0 0 0 98 partof 70 2R:1731127-2080000 -1 NULL:1988967 SD21850.5prime 477 547 1 1 0 2599403 141361 140818 1 0 0 0 99 partof 543 2R:1731127-2080000 1 NULL:1983883 SD03445.5prime 0 543 1 1 0 2600292 328956 328659 1 0 0 0 100 partof 297 2R:1731127-2080000 1 NULL:1984595 LP09834.5prime 0 297 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984596 LP09834.5prime 297 462 1 1 0 329428 329257 1 0 0 0 99 partof 171 2R:1731127-2080000 1 NULL:1984597 LP09834.5prime 462 633 1 1 0 2599406 141429 140818 1 0 0 0 99 partof 611 2R:1731127-2080000 1 NULL:1983885 SD19894.5prime 0 611 1 1 0 2600297 328956 328669 1 0 0 0 99 partof 287 2R:1731127-2080000 1 NULL:1984599 LP11118.5prime 0 287 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1984600 LP11118.5prime 287 452 1 1 0 329388 329257 1 0 0 0 98 partof 131 2R:1731127-2080000 1 NULL:1984601 LP11118.5prime 452 583 1 1 0 2599409 141470 140818 1 0 0 0 99 partof 652 2R:1731127-2080000 1 NULL:1983887 SD03457.5prime 0 652 1 1 0 2605522 341492 341366 1 0 0 0 100 partof 126 2R:1731127-2080000 -1 NULL:1988969 LP07615.5prime 0 126 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988970 LP07615.5prime 126 318 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988971 LP07615.5prime 318 480 1 1 0 340075 340024 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988972 LP07615.5prime 480 531 1 1 0 2605528 341499 341366 1 0 0 0 100 partof 133 2R:1731127-2080000 -1 NULL:1988974 GH07074.5prime 0 133 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988975 GH07074.5prime 133 325 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988976 GH07074.5prime 325 487 1 1 0 340075 340024 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1988977 GH07074.5prime 487 538 1 1 0 2599412 140950 140818 1 0 0 0 100 partof 132 2R:1731127-2080000 1 NULL:1983889 LD06205.5prime 0 132 1 1 0 141858 141676 1 0 0 0 99 partof 182 2R:1731127-2080000 1 NULL:1983890 LD06205.5prime 132 313 1 1 0 142722 142555 1 0 0 0 100 partof 167 2R:1731127-2080000 1 NULL:1983891 LD06205.5prime 313 480 1 1 0 2599417 140950 140818 1 0 0 0 100 partof 132 2R:1731127-2080000 1 NULL:1983893 LD11166.5prime 0 132 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983894 LD11166.5prime 132 314 1 1 0 142743 142555 1 0 0 0 99 partof 188 2R:1731127-2080000 1 NULL:1983895 LD11166.5prime 314 501 1 1 0 2605534 341506 341366 1 0 0 0 100 partof 140 2R:1731127-2080000 -1 NULL:1988979 RE26686.5prime 8 148 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988980 RE26686.5prime 148 340 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988981 RE26686.5prime 340 502 1 1 0 340075 339997 1 0 0 0 100 partof 78 2R:1731127-2080000 -1 NULL:1988982 RE26686.5prime 502 580 1 1 0 2599422 140950 140818 1 0 0 0 100 partof 132 2R:1731127-2080000 1 NULL:1983897 LD09144.5prime 0 132 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983898 LD09144.5prime 132 314 1 1 0 142851 142555 1 0 0 0 99 partof 296 2R:1731127-2080000 1 NULL:1983899 LD09144.5prime 314 609 1 1 0 2599427 140950 140818 1 0 0 0 100 partof 132 2R:1731127-2080000 1 NULL:1983901 LD20885.5prime 0 132 1 1 0 141858 141676 1 0 0 0 99 partof 182 2R:1731127-2080000 1 NULL:1983902 LD20885.5prime 132 313 1 1 0 142891 142555 1 0 0 0 99 partof 336 2R:1731127-2080000 1 NULL:1983903 LD20885.5prime 313 649 1 1 0 143000 142947 1 0 0 0 98 partof 53 2R:1731127-2080000 1 NULL:1983904 LD20885.5prime 649 702 1 1 0 2605540 341510 341366 1 0 0 0 99 partof 144 2R:1731127-2080000 -1 NULL:1988984 RE37638.5prime 0 145 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988985 RE37638.5prime 145 337 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988986 RE37638.5prime 337 499 1 1 0 340075 340027 1 0 0 0 95 partof 48 2R:1731127-2080000 -1 NULL:1988987 RE37638.5prime 499 547 1 1 0 2605546 341510 341366 1 0 0 0 100 partof 144 2R:1731127-2080000 -1 NULL:1988989 RE40542.5prime 0 144 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988990 RE40542.5prime 144 336 1 1 0 340368 340196 1 0 0 0 97 partof 172 2R:1731127-2080000 -1 NULL:1988991 RE40542.5prime 336 509 1 1 0 2599433 140950 140821 1 0 0 0 100 partof 129 2R:1731127-2080000 1 NULL:1983906 LD46478.5prime 0 129 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983907 LD46478.5prime 129 311 1 1 0 142611 142555 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1983908 LD46478.5prime 311 367 1 1 0 2599438 140950 140822 1 0 0 0 97 partof 128 2R:1731127-2080000 1 NULL:1983910 RE38636.5prime 0 128 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983911 RE38636.5prime 128 310 1 1 0 142725 142555 1 0 0 0 100 partof 170 2R:1731127-2080000 1 NULL:1983912 RE38636.5prime 310 480 1 1 0 2605551 341510 341366 1 0 0 0 99 partof 144 2R:1731127-2080000 -1 NULL:1988993 RE46954.5prime 0 145 1 1 0 340629 340437 1 0 0 0 99 partof 192 2R:1731127-2080000 -1 NULL:1988994 RE46954.5prime 145 337 1 1 0 340368 340216 1 0 0 0 96 partof 152 2R:1731127-2080000 -1 NULL:1988995 RE46954.5prime 337 491 1 1 0 2605556 341629 341366 1 0 0 0 98 partof 263 2R:1731127-2080000 -1 NULL:1988997 SD10395:contig1 0 263 1 1 0 340629 340437 1 0 0 0 98 partof 192 2R:1731127-2080000 -1 NULL:1988998 SD10395:contig1 263 455 1 1 0 340368 340206 1 0 0 0 99 partof 162 2R:1731127-2080000 -1 NULL:1988999 SD10395:contig1 455 617 1 1 0 340075 339877 1 0 0 0 99 partof 198 2R:1731127-2080000 -1 NULL:1989000 SD10395:contig1 617 815 1 1 0 339820 339634 1 0 0 0 96 partof 186 2R:1731127-2080000 -1 NULL:1989001 SD10395:contig1 815 1001 1 1 0 2599443 140954 140824 1 0 0 0 96 partof 130 2R:1731127-2080000 1 NULL:1983914 LD24821.5prime 0 133 1 1 0 142891 142796 1 0 0 0 100 partof 95 2R:1731127-2080000 1 NULL:1983915 LD24821.5prime 133 228 1 1 0 143272 142947 1 0 0 0 99 partof 325 2R:1731127-2080000 1 NULL:1983916 LD24821.5prime 228 553 1 1 0 2599448 140950 140825 1 0 0 0 97 partof 125 2R:1731127-2080000 1 NULL:1983918 SD15510.5prime 0 125 1 1 0 141736 141676 1 0 0 0 96 partof 60 2R:1731127-2080000 1 NULL:1983919 SD15510.5prime 125 185 1 1 0 2604902 202460 202308 1 0 0 0 99 partof 152 2R:1731127-2080000 -1 NULL:1988482 LD16972.5prime 0 152 1 1 0 196716 196596 1 0 0 0 98 partof 120 2R:1731127-2080000 -1 NULL:1988483 LD16972.5prime 152 272 1 1 0 2604906 202462 202308 1 0 0 0 100 partof 154 2R:1731127-2080000 -1 NULL:1988485 LD05710.5prime 0 154 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988486 LD05710.5prime 154 409 1 1 0 195149 194976 1 0 0 0 99 partof 173 2R:1731127-2080000 -1 NULL:1988487 LD05710.5prime 409 582 1 1 0 2599452 140950 140827 1 0 0 0 99 partof 123 2R:1731127-2080000 1 NULL:1983921 SD22754.5prime 0 123 1 1 0 142157 141676 1 0 0 0 99 partof 481 2R:1731127-2080000 1 NULL:1983922 SD22754.5prime 123 604 1 1 0 2599456 140950 140827 1 0 0 0 100 partof 123 2R:1731127-2080000 1 NULL:1983924 LD14675.5prime 0 123 1 1 0 141858 141676 1 0 0 0 99 partof 182 2R:1731127-2080000 1 NULL:1983925 LD14675.5prime 123 305 1 1 0 142773 142555 1 0 0 0 98 partof 218 2R:1731127-2080000 1 NULL:1983926 LD14675.5prime 305 523 1 1 0 2604911 202462 202308 1 0 0 0 100 partof 154 2R:1731127-2080000 -1 NULL:1988489 LD35293.5prime 0 154 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988490 LD35293.5prime 154 409 1 1 0 195149 195046 1 0 0 0 99 partof 103 2R:1731127-2080000 -1 NULL:1988491 LD35293.5prime 409 512 1 1 0 2604916 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988493 LD28262.5prime 0 159 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988494 LD28262.5prime 159 412 1 1 0 195149 194884 1 0 0 0 99 partof 265 2R:1731127-2080000 -1 NULL:1988495 LD28262.5prime 412 676 1 1 0 2599461 140950 140831 1 0 0 0 100 partof 119 2R:1731127-2080000 1 NULL:1983928 LD11636.5prime 0 119 1 1 0 141858 141676 1 0 0 0 99 partof 182 2R:1731127-2080000 1 NULL:1983929 LD11636.5prime 119 301 1 1 0 142664 142555 1 0 0 0 99 partof 109 2R:1731127-2080000 1 NULL:1983930 LD11636.5prime 301 410 1 1 0 2599466 140950 140855 1 0 0 0 100 partof 95 2R:1731127-2080000 1 NULL:1983932 LD47003.5prime 0 95 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983933 LD47003.5prime 95 277 1 1 0 142878 142555 1 0 0 0 100 partof 323 2R:1731127-2080000 1 NULL:1983934 LD47003.5prime 277 600 1 1 0 2604921 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988497 LD21990.5prime 0 159 1 1 0 196716 196461 1 0 0 0 97 partof 255 2R:1731127-2080000 -1 NULL:1988498 LD21990.5prime 159 414 1 1 0 195149 194992 1 0 0 0 99 partof 157 2R:1731127-2080000 -1 NULL:1988499 LD21990.5prime 414 571 1 1 0 2604926 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988501 LD07546.5prime 0 159 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988502 LD07546.5prime 159 414 1 1 0 195149 194998 1 0 0 0 98 partof 151 2R:1731127-2080000 -1 NULL:1988503 LD07546.5prime 414 562 1 1 0 2599471 141830 141559 1 0 0 0 96 partof 271 2R:1731127-2080000 1 NULL:1983936 RH19903.5prime 0 271 1 1 0 2599474 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983938 RH17888.5prime 0 298 1 1 0 142795 142555 1 0 0 0 100 partof 240 2R:1731127-2080000 1 NULL:1983939 RH17888.5prime 298 538 1 1 0 2599478 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983941 RH10961.5prime 0 298 1 1 0 142803 142555 1 0 0 0 99 partof 248 2R:1731127-2080000 1 NULL:1983942 RH10961.5prime 298 546 1 1 0 2604931 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988505 LD18630.5prime 0 159 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988506 LD18630.5prime 159 413 1 1 0 195149 195008 1 0 0 0 98 partof 141 2R:1731127-2080000 -1 NULL:1988507 LD18630.5prime 413 552 1 1 0 2604936 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988509 LD42232.5prime 0 159 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988510 LD42232.5prime 159 414 1 1 0 195149 195008 1 0 0 0 100 partof 141 2R:1731127-2080000 -1 NULL:1988511 LD42232.5prime 414 555 1 1 0 2599482 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983944 RH54908.5prime 0 297 1 1 0 142823 142555 1 0 0 0 100 partof 268 2R:1731127-2080000 1 NULL:1983945 RH54908.5prime 297 565 1 1 0 2599486 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983947 RH17624.5prime 0 298 1 1 0 142880 142555 1 0 0 0 100 partof 325 2R:1731127-2080000 1 NULL:1983948 RH17624.5prime 298 623 1 1 0 2604941 202467 202308 1 0 0 0 100 partof 159 2R:1731127-2080000 -1 NULL:1988513 LD40763.5prime 0 159 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988514 LD40763.5prime 159 414 1 1 0 195149 195053 1 0 0 0 100 partof 96 2R:1731127-2080000 -1 NULL:1988515 LD40763.5prime 414 510 1 1 0 2604946 202467 202308 1 0 0 0 99 partof 159 2R:1731127-2080000 -1 NULL:1988517 LD27174.5prime 0 158 1 1 0 196716 196464 1 0 0 0 98 partof 252 2R:1731127-2080000 -1 NULL:1988518 LD27174.5prime 158 409 1 1 0 2599490 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983950 RH69328.5prime 0 298 1 1 0 142886 142555 1 0 0 0 100 partof 331 2R:1731127-2080000 1 NULL:1983951 RH69328.5prime 298 629 1 1 0 2599494 141858 141559 1 0 0 0 98 partof 299 2R:1731127-2080000 1 NULL:1983953 RH44377.5prime 0 298 1 1 0 142890 142555 1 0 0 0 100 partof 335 2R:1731127-2080000 1 NULL:1983954 RH44377.5prime 298 633 1 1 0 2599498 141810 141560 1 0 0 0 93 partof 250 2R:1731127-2080000 1 NULL:1983956 RH18506.5prime 0 250 1 1 0 2604950 202470 202308 1 0 0 0 97 partof 162 2R:1731127-2080000 -1 NULL:1988520 LD31740.5prime 0 164 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988521 LD31740.5prime 164 419 1 1 0 195149 194939 1 0 0 0 99 partof 210 2R:1731127-2080000 -1 NULL:1988522 LD31740.5prime 419 628 1 1 0 2604955 202471 202308 1 0 0 0 98 partof 163 2R:1731127-2080000 -1 NULL:1988524 RE05710.5prime 0 165 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988525 RE05710.5prime 165 420 1 1 0 195149 195115 1 0 0 0 100 partof 34 2R:1731127-2080000 -1 NULL:1988526 RE05710.5prime 420 454 1 1 0 2604960 202472 202308 1 0 0 0 100 partof 164 2R:1731127-2080000 -1 NULL:1988528 RE13103.5prime 0 164 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988529 RE13103.5prime 164 419 1 1 0 195149 194914 1 0 0 0 99 partof 235 2R:1731127-2080000 -1 NULL:1988530 RE13103.5prime 419 654 1 1 0 2604965 202472 202308 1 0 0 0 98 partof 164 2R:1731127-2080000 -1 NULL:1988532 RE15554.5prime 0 164 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988533 RE15554.5prime 164 419 1 1 0 195149 194967 1 0 0 0 97 partof 182 2R:1731127-2080000 -1 NULL:1988534 RE15554.5prime 419 599 1 1 0 2604970 202472 202308 1 0 0 0 98 partof 164 2R:1731127-2080000 -1 NULL:1988536 RE18210.5prime 0 164 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988537 RE18210.5prime 164 419 1 1 0 195149 194981 1 0 0 0 99 partof 168 2R:1731127-2080000 -1 NULL:1988538 RE18210.5prime 419 587 1 1 0 2604975 202472 202308 1 0 0 0 98 partof 164 2R:1731127-2080000 -1 NULL:1988540 RE18295.5prime 0 164 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988541 RE18295.5prime 164 419 1 1 0 195149 195030 1 0 0 0 99 partof 119 2R:1731127-2080000 -1 NULL:1988542 RE18295.5prime 419 538 1 1 0 2599801 317851 317198 1 0 0 0 100 partof 653 2R:1731127-2080000 1 NULL:1984190 RH69233.5prime 0 653 1 1 0 2599804 317852 317198 1 0 0 0 99 partof 654 2R:1731127-2080000 1 NULL:1984192 RH43418.5prime 0 654 1 1 0 2599807 317856 317198 1 0 0 0 99 partof 658 2R:1731127-2080000 1 NULL:1984194 RH14346.5prime 0 657 1 1 0 2604980 202472 202308 1 0 0 0 100 partof 164 2R:1731127-2080000 -1 NULL:1988544 LD43058.5prime 0 164 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988545 LD43058.5prime 164 419 1 1 0 195149 195047 1 0 0 0 97 partof 102 2R:1731127-2080000 -1 NULL:1988546 LD43058.5prime 419 524 1 1 0 2604985 202472 202308 1 0 0 0 100 partof 164 2R:1731127-2080000 -1 NULL:1988548 RE46034.5prime 0 164 1 1 0 196716 196467 1 0 0 0 99 partof 249 2R:1731127-2080000 -1 NULL:1988549 RE46034.5prime 164 413 1 1 0 2604989 202473 202308 1 0 0 0 99 partof 165 2R:1731127-2080000 -1 NULL:1988551 RE67756.5prime 0 165 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988552 RE67756.5prime 165 420 1 1 0 195149 194880 1 0 0 0 99 partof 269 2R:1731127-2080000 -1 NULL:1988553 RE67756.5prime 420 688 1 1 0 2599810 322552 322450 1 0 0 0 99 partof 102 2R:1731127-2080000 1 NULL:1984196 RH15924.5prime 0 102 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984197 RH15924.5prime 102 214 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984198 RH15924.5prime 214 406 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984199 RH15924.5prime 406 568 1 1 0 327019 326933 1 0 0 0 100 partof 86 2R:1731127-2080000 1 NULL:1984200 RH15924.5prime 568 654 1 1 0 2599817 322830 322460 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1984202 RH05177.5prime 0 370 1 1 0 323001 322895 1 0 0 0 97 partof 106 2R:1731127-2080000 1 NULL:1984203 RH05177.5prime 370 476 1 1 0 2604994 202473 202308 1 0 0 0 100 partof 165 2R:1731127-2080000 -1 NULL:1988555 LD08223.5prime 0 165 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988556 LD08223.5prime 165 419 1 1 0 195149 194994 1 0 0 0 94 partof 155 2R:1731127-2080000 -1 NULL:1988557 LD08223.5prime 419 569 1 1 0 2604999 202473 202308 1 0 0 0 100 partof 165 2R:1731127-2080000 -1 NULL:1988559 LD28293.5prime 0 165 1 1 0 196716 196461 1 0 0 0 98 partof 255 2R:1731127-2080000 -1 NULL:1988560 LD28293.5prime 165 420 1 1 0 195149 195016 1 0 0 0 99 partof 133 2R:1731127-2080000 -1 NULL:1988561 LD28293.5prime 420 553 1 1 0 2599821 322830 322460 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1984205 RH28313.5prime 0 370 1 1 0 323114 322895 1 0 0 0 97 partof 219 2R:1731127-2080000 1 NULL:1984206 RH28313.5prime 370 588 1 1 0 2599825 322830 322460 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1984208 RH52707.5prime 0 370 1 1 0 323126 322895 1 0 0 0 100 partof 231 2R:1731127-2080000 1 NULL:1984209 RH52707.5prime 370 601 1 1 0 2599829 322830 322460 1 0 0 0 99 partof 370 2R:1731127-2080000 1 NULL:1984211 RH06188.5prime 0 370 1 1 0 323146 322895 1 0 0 0 99 partof 251 2R:1731127-2080000 1 NULL:1984212 RH06188.5prime 370 622 1 1 0 2599833 322552 322460 1 0 0 0 98 partof 92 2R:1731127-2080000 1 NULL:1984214 RH16922.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984215 RH16922.5prime 92 204 1 1 0 326642 326450 1 0 0 0 98 partof 192 2R:1731127-2080000 1 NULL:1984216 RH16922.5prime 204 396 1 1 0 326769 326705 1 0 0 0 100 partof 64 2R:1731127-2080000 1 NULL:1984217 RH16922.5prime 396 460 1 1 0 2599839 322552 322460 1 0 0 0 98 partof 92 2R:1731127-2080000 1 NULL:1984219 RH46913.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984220 RH46913.5prime 92 204 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984221 RH46913.5prime 204 396 1 1 0 326810 326705 1 0 0 0 100 partof 105 2R:1731127-2080000 1 NULL:1984222 RH46913.5prime 396 501 1 1 0 2599845 322552 322460 1 0 0 0 96 partof 92 2R:1731127-2080000 1 NULL:1984224 RH17952.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984225 RH17952.5prime 92 204 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984226 RH17952.5prime 204 396 1 1 0 326817 326705 1 0 0 0 97 partof 112 2R:1731127-2080000 1 NULL:1984227 RH17952.5prime 396 507 1 1 0 2599851 322552 322460 1 0 0 0 98 partof 92 2R:1731127-2080000 1 NULL:1984229 RH62824.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984230 RH62824.5prime 92 204 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984231 RH62824.5prime 204 396 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984232 RH62824.5prime 396 558 1 1 0 326974 326933 1 0 0 0 100 partof 41 2R:1731127-2080000 1 NULL:1984233 RH62824.5prime 558 599 1 1 0 2599858 322552 322460 1 0 0 0 98 partof 92 2R:1731127-2080000 1 NULL:1984235 RH61018.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984236 RH61018.5prime 92 204 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984237 RH61018.5prime 204 396 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984238 RH61018.5prime 396 558 1 1 0 327044 326933 1 0 0 0 99 partof 111 2R:1731127-2080000 1 NULL:1984239 RH61018.5prime 558 670 1 1 0 2599865 322830 322461 1 0 0 0 100 partof 369 2R:1731127-2080000 1 NULL:1984241 RE48757.5prime 0 369 1 1 0 322967 322895 1 0 0 0 100 partof 72 2R:1731127-2080000 1 NULL:1984242 RE48757.5prime 369 441 1 1 0 2599869 322830 322461 1 0 0 0 100 partof 369 2R:1731127-2080000 1 NULL:1984244 RE50657.5prime 0 369 1 1 0 323167 322895 1 0 0 0 99 partof 272 2R:1731127-2080000 1 NULL:1984245 RE50657.5prime 369 641 1 1 0 2599873 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984247 RE40130.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984248 RE40130.5prime 91 203 1 1 0 326489 326450 1 0 0 0 100 partof 39 2R:1731127-2080000 1 NULL:1984249 RE40130.5prime 203 242 1 1 0 2599878 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984251 RE66743.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984252 RE66743.5prime 91 203 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984253 RE66743.5prime 203 395 1 1 0 326720 326705 1 0 0 0 100 partof 15 2R:1731127-2080000 1 NULL:1984254 RE66743.5prime 395 410 1 1 0 2599884 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984256 RE29570.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984257 RE29570.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984258 RE29570.5prime 203 395 1 1 0 326750 326705 1 0 0 0 97 partof 45 2R:1731127-2080000 1 NULL:1984259 RE29570.5prime 395 440 1 1 0 2605201 202490 202308 1 0 0 0 98 partof 182 2R:1731127-2080000 -1 NULL:1988720 RE13770.5prime 0 184 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988721 RE13770.5prime 184 439 1 1 0 195149 195108 1 0 0 0 100 partof 41 2R:1731127-2080000 -1 NULL:1988722 RE13770.5prime 439 480 1 1 0 2605206 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988724 RH39557.5prime 0 183 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988725 RH39557.5prime 183 438 1 1 0 195149 195108 1 0 0 0 100 partof 41 2R:1731127-2080000 -1 NULL:1988726 RH39557.5prime 438 479 1 1 0 2599890 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984261 RE21265.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984262 RE21265.5prime 91 203 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984263 RE21265.5prime 203 395 1 1 0 326800 326705 1 0 0 0 100 partof 95 2R:1731127-2080000 1 NULL:1984264 RE21265.5prime 395 490 1 1 0 2599896 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984266 RE47894.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984267 RE47894.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984268 RE47894.5prime 203 395 1 1 0 326801 326705 1 0 0 0 96 partof 96 2R:1731127-2080000 1 NULL:1984269 RE47894.5prime 395 493 1 1 0 2605211 202490 202308 1 0 0 0 99 partof 182 2R:1731127-2080000 -1 NULL:1988728 RE37784.5prime 0 182 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988729 RE37784.5prime 182 437 1 1 0 195149 195113 1 0 0 0 100 partof 36 2R:1731127-2080000 -1 NULL:1988730 RE37784.5prime 437 473 1 1 0 2605216 202490 202308 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1988732 RE75079.5prime 0 182 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988733 RE75079.5prime 182 437 1 1 0 195149 195124 1 0 0 0 100 partof 25 2R:1731127-2080000 -1 NULL:1988734 RE75079.5prime 437 462 1 1 0 2599100 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983646 RE73096.5prime 0 174 1 1 0 138305 137864 1 0 0 0 99 partof 441 2R:1731127-2080000 1 NULL:1983647 RE73096.5prime 174 617 1 1 0 2599104 137592 137418 1 0 0 0 100 partof 174 2R:1731127-2080000 1 NULL:1983649 RE01167:contig1 0 174 1 1 0 138097 137864 1 0 0 0 99 partof 233 2R:1731127-2080000 1 NULL:1983650 RE01167:contig1 174 407 1 1 0 138947 138706 1 0 0 0 99 partof 241 2R:1731127-2080000 1 NULL:1983651 RE01167:contig2 407 648 1 1 0 2605221 202490 202308 1 0 0 0 96 partof 182 2R:1731127-2080000 -1 NULL:1988736 RE08112.5prime 0 188 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988737 RE08112.5prime 188 443 1 1 0 195149 195126 1 0 0 0 100 partof 23 2R:1731127-2080000 -1 NULL:1988738 RE08112.5prime 443 466 1 1 0 2605226 202490 202308 1 0 0 0 97 partof 182 2R:1731127-2080000 -1 NULL:1988740 RE74053.5prime 0 183 1 1 0 196716 196449 1 0 0 0 98 partof 267 2R:1731127-2080000 -1 NULL:1988741 RE74053.5prime 183 448 1 1 0 2599110 137592 137419 1 0 0 0 98 partof 173 2R:1731127-2080000 1 NULL:1983653 RH39445.5prime 0 173 1 1 0 138236 137864 1 0 0 0 99 partof 372 2R:1731127-2080000 1 NULL:1983654 RH39445.5prime 173 545 1 1 0 2599114 137592 137419 1 0 0 0 98 partof 173 2R:1731127-2080000 1 NULL:1983656 RH39191.5prime 0 173 1 1 0 138254 137864 1 0 0 0 99 partof 390 2R:1731127-2080000 1 NULL:1983657 RH39191.5prime 173 562 1 1 0 2599118 137592 137419 1 0 0 0 98 partof 173 2R:1731127-2080000 1 NULL:1983659 RH61015.5prime 0 173 1 1 0 138305 137864 1 0 0 0 99 partof 441 2R:1731127-2080000 1 NULL:1983660 RH61015.5prime 173 616 1 1 0 2605230 202490 202302 1 0 0 0 96 partof 188 2R:1731127-2080000 -1 NULL:1988743 RE41228.5prime 0 192 1 1 0 2605233 202492 202308 1 0 0 0 100 partof 184 2R:1731127-2080000 -1 NULL:1988745 LD38369.5prime 0 184 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988746 LD38369.5prime 184 439 1 1 0 195149 195045 1 0 0 0 100 partof 104 2R:1731127-2080000 -1 NULL:1988747 LD38369.5prime 439 543 1 1 0 2605238 202493 202308 1 0 0 0 100 partof 185 2R:1731127-2080000 -1 NULL:1988749 LD08391.5prime 0 185 1 1 0 196716 196491 1 0 0 0 100 partof 225 2R:1731127-2080000 -1 NULL:1988750 LD08391.5prime 185 410 1 1 0 2599122 137592 137419 1 0 0 0 98 partof 173 2R:1731127-2080000 1 NULL:1983662 RH10490.5prime 0 173 1 1 0 138305 137864 1 0 0 0 99 partof 441 2R:1731127-2080000 1 NULL:1983663 RH10490.5prime 173 616 1 1 0 2599126 137592 137420 1 0 0 0 100 partof 172 2R:1731127-2080000 1 NULL:1983665 GH06277.5prime 0 172 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983666 GH06277.5prime 172 609 1 1 0 138374 138357 1 0 0 0 100 partof 17 2R:1731127-2080000 1 NULL:1983667 GH06277.5prime 609 626 1 1 0 2605242 202496 202308 1 0 0 0 100 partof 188 2R:1731127-2080000 -1 NULL:1988752 LD42280.5prime 0 188 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988753 LD42280.5prime 188 443 1 1 0 195149 195019 1 0 0 0 100 partof 130 2R:1731127-2080000 -1 NULL:1988754 LD42280.5prime 443 573 1 1 0 2605247 202507 202308 1 0 0 0 100 partof 199 2R:1731127-2080000 -1 NULL:1988756 RE63884.5prime 0 199 1 1 0 196716 196461 1 0 0 0 99 partof 255 2R:1731127-2080000 -1 NULL:1988757 RE63884.5prime 199 454 1 1 0 195149 195026 1 0 0 0 99 partof 123 2R:1731127-2080000 -1 NULL:1988758 RE63884.5prime 454 577 1 1 0 2600302 333417 333374 1 0 0 0 100 partof 43 2R:1731127-2080000 1 NULL:1984603 GM15292.5prime 0 43 1 1 0 334038 333679 1 0 0 0 98 partof 359 2R:1731127-2080000 1 NULL:1984604 GM15292.5prime 43 403 1 1 0 2600305 336407 336221 1 0 0 0 100 partof 186 2R:1731127-2080000 1 NULL:1984606 LP02831:contig1 0 186 1 1 0 337692 337500 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984607 LP02831:contig1 186 378 1 1 0 338397 337755 1 0 0 0 100 partof 642 2R:1731127-2080000 1 NULL:1984608 LP02831:contig1 378 1020 1 1 0 2600309 342110 342030 1 0 0 0 97 partof 80 2R:1731127-2080000 1 NULL:1984610 RE12209:contig1 0 80 1 1 0 342891 342802 1 0 0 0 100 partof 89 2R:1731127-2080000 1 NULL:1984611 RE12209:contig1 80 169 1 1 0 347150 346786 1 0 0 0 100 partof 364 2R:1731127-2080000 1 NULL:1984612 RE12209:contig1 169 533 1 1 0 347405 347209 1 0 0 0 100 partof 196 2R:1731127-2080000 1 NULL:1984613 RE12209:contig1 533 729 1 1 0 348139 347464 1 0 0 0 100 partof 675 2R:1731127-2080000 1 NULL:1984614 RE12209:contig1 729 1404 1 1 0 2599131 137592 137427 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1983669 SD13406.5prime 0 165 1 1 0 138301 137864 1 0 0 0 98 partof 437 2R:1731127-2080000 1 NULL:1983670 SD13406.5prime 165 602 1 1 0 138454 138357 1 0 0 0 92 partof 97 2R:1731127-2080000 1 NULL:1983671 SD13406.5prime 602 698 1 1 0 2599136 137592 137432 1 0 0 0 100 partof 160 2R:1731127-2080000 1 NULL:1983673 GH06580.5prime 0 160 1 1 0 138271 137864 1 0 0 0 100 partof 407 2R:1731127-2080000 1 NULL:1983674 GH06580.5prime 160 567 1 1 0 2605252 202527 202308 1 0 0 0 100 partof 219 2R:1731127-2080000 -1 NULL:1988760 LD19921.5prime 0 219 1 1 0 196716 196449 1 0 0 0 98 partof 267 2R:1731127-2080000 -1 NULL:1988761 LD19921.5prime 219 483 1 1 0 2605256 202544 202308 1 0 0 0 100 partof 236 2R:1731127-2080000 -1 NULL:1988763 LD37992:contig1 0 236 1 1 0 196716 196461 1 0 0 0 100 partof 255 2R:1731127-2080000 -1 NULL:1988764 LD37992:contig1 236 491 1 1 0 195149 195032 1 0 0 0 100 partof 117 2R:1731127-2080000 -1 NULL:1988765 LD37992:contig1 491 608 1 1 0 192419 191775 1 0 0 0 100 partof 644 2R:1731127-2080000 -1 NULL:1988766 LD37992:contig2 608 1252 1 1 0 2600315 342110 342031 1 0 0 0 97 partof 79 2R:1731127-2080000 1 NULL:1984616 RE29816.5prime 0 79 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984617 RE29816.5prime 79 163 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984618 RE29816.5prime 163 528 1 1 0 347275 347209 1 0 0 0 100 partof 66 2R:1731127-2080000 1 NULL:1984619 RE29816.5prime 528 594 1 1 0 2599140 137592 137433 1 0 0 0 100 partof 159 2R:1731127-2080000 1 NULL:1983676 GH07452.5prime 0 159 1 1 0 138299 137864 1 0 0 0 100 partof 435 2R:1731127-2080000 1 NULL:1983677 GH07452.5prime 159 594 1 1 0 2599144 137592 137433 1 0 0 0 100 partof 159 2R:1731127-2080000 1 NULL:1983679 LP09437.5prime 0 159 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983680 LP09437.5prime 159 596 1 1 0 138427 138357 1 0 0 0 100 partof 70 2R:1731127-2080000 1 NULL:1983681 LP09437.5prime 596 666 1 1 0 2599149 137592 137437 1 0 0 0 100 partof 155 2R:1731127-2080000 1 NULL:1983683 GM09577.5prime 0 155 1 1 0 138301 137864 1 0 0 0 98 partof 437 2R:1731127-2080000 1 NULL:1983684 GM09577.5prime 155 589 1 1 0 138380 138357 1 0 0 0 100 partof 23 2R:1731127-2080000 1 NULL:1983685 GM09577.5prime 589 612 1 1 0 2605261 207691 207201 1 0 0 0 100 partof 490 2R:1731127-2080000 -1 NULL:1988768 LP01171.5prime 0 490 1 1 0 207137 207008 1 0 0 0 99 partof 129 2R:1731127-2080000 -1 NULL:1988769 LP01171.5prime 490 619 1 1 0 2605265 208100 207508 1 0 0 0 99 partof 592 2R:1731127-2080000 -1 NULL:1988771 SD23190.5prime 0 592 1 1 0 2600321 342110 342031 1 0 0 0 98 partof 79 2R:1731127-2080000 1 NULL:1984621 RE04317.5prime 0 79 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984622 RE04317.5prime 79 163 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984623 RE04317.5prime 163 527 1 1 0 347281 347209 1 0 0 0 97 partof 72 2R:1731127-2080000 1 NULL:1984624 RE04317.5prime 527 598 1 1 0 2605268 208367 208213 1 0 0 0 97 partof 154 2R:1731127-2080000 -1 NULL:1988773 LD29516.5prime 30 183 1 1 0 208133 207857 1 0 0 0 97 partof 276 2R:1731127-2080000 -1 NULL:1988774 LD29516.5prime 183 458 1 1 0 2600327 342110 342031 1 0 0 0 97 partof 79 2R:1731127-2080000 1 NULL:1984626 RE19806.5prime 0 80 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984627 RE19806.5prime 80 164 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984628 RE19806.5prime 164 527 1 1 0 347283 347209 1 0 0 0 98 partof 74 2R:1731127-2080000 1 NULL:1984629 RE19806.5prime 527 600 1 1 0 2599154 137592 137441 1 0 0 0 100 partof 151 2R:1731127-2080000 1 NULL:1983687 HL04834.5prime 0 151 1 1 0 138144 137864 1 0 0 0 99 partof 280 2R:1731127-2080000 1 NULL:1983688 HL04834.5prime 151 429 1 1 0 2599158 137592 137442 1 0 0 0 100 partof 150 2R:1731127-2080000 1 NULL:1983690 LD04493.5prime 0 150 1 1 0 138102 137864 1 0 0 0 99 partof 238 2R:1731127-2080000 1 NULL:1983691 LD04493.5prime 150 387 1 1 0 2605272 208400 208213 1 0 0 0 100 partof 187 2R:1731127-2080000 -1 NULL:1988776 GM32312.5prime 0 187 1 1 0 208133 207652 1 0 0 0 95 partof 481 2R:1731127-2080000 -1 NULL:1988777 GM32312.5prime 187 692 1 1 0 2605276 208401 208213 1 0 0 0 98 partof 188 2R:1731127-2080000 -1 NULL:1988779 GM27507.5prime 0 188 1 1 0 208133 207701 1 0 0 0 99 partof 432 2R:1731127-2080000 -1 NULL:1988780 GM27507.5prime 188 620 1 1 0 2600333 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984631 RH31301.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984632 RH31301.5prime 77 161 1 1 0 347032 346787 1 0 0 0 100 partof 245 2R:1731127-2080000 1 NULL:1984633 RH31301.5prime 161 406 1 1 0 2600338 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984635 RE05120.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984636 RE05120.5prime 77 161 1 1 0 347072 346787 1 0 0 0 98 partof 285 2R:1731127-2080000 1 NULL:1984637 RE05120.5prime 161 446 1 1 0 2599162 137592 137442 1 0 0 0 98 partof 150 2R:1731127-2080000 1 NULL:1983693 LD23688.5prime 0 150 1 1 0 138115 137864 1 0 0 0 99 partof 251 2R:1731127-2080000 1 NULL:1983694 LD23688.5prime 150 400 1 1 0 2599166 137592 137442 1 0 0 0 100 partof 150 2R:1731127-2080000 1 NULL:1983696 LD36628.5prime 0 150 1 1 0 138210 137864 1 0 0 0 100 partof 346 2R:1731127-2080000 1 NULL:1983697 LD36628.5prime 150 496 1 1 0 2605280 208416 208213 1 0 0 0 99 partof 203 2R:1731127-2080000 -1 NULL:1988782 RE31022.5prime 0 202 1 1 0 208133 207651 1 0 0 0 99 partof 482 2R:1731127-2080000 -1 NULL:1988783 RE31022.5prime 202 683 1 1 0 2605284 208416 208213 1 0 0 0 99 partof 203 2R:1731127-2080000 -1 NULL:1988785 RH62218.5prime 0 205 1 1 0 208133 207709 1 0 0 0 99 partof 424 2R:1731127-2080000 -1 NULL:1988786 RH62218.5prime 205 629 1 1 0 2605288 208416 208213 1 0 0 0 100 partof 203 2R:1731127-2080000 -1 NULL:1988788 RE27141.5prime 0 203 1 1 0 208133 207718 1 0 0 0 100 partof 415 2R:1731127-2080000 -1 NULL:1988789 RE27141.5prime 203 618 1 1 0 2600343 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984639 RE67533.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984640 RE67533.5prime 77 161 1 1 0 347115 346787 1 0 0 0 100 partof 328 2R:1731127-2080000 1 NULL:1984641 RE67533.5prime 161 489 1 1 0 2600348 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984643 RE13158.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984644 RE13158.5prime 77 161 1 1 0 347117 346787 1 0 0 0 100 partof 330 2R:1731127-2080000 1 NULL:1984645 RE13158.5prime 161 491 1 1 0 2599170 137592 137442 1 0 0 0 100 partof 150 2R:1731127-2080000 1 NULL:1983699 GH26166.5prime 0 150 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983700 GH26166.5prime 150 587 1 1 0 138413 138357 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1983701 GH26166.5prime 587 643 1 1 0 2599175 137592 137446 1 0 0 0 100 partof 146 2R:1731127-2080000 1 NULL:1983703 GH10713.5prime 0 146 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983704 GH10713.5prime 146 583 1 1 0 138413 138357 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1983705 GH10713.5prime 583 639 1 1 0 2605292 208416 208213 1 0 0 0 98 partof 203 2R:1731127-2080000 -1 NULL:1988791 RE53284.5prime 0 203 1 1 0 208133 207764 1 0 0 0 100 partof 369 2R:1731127-2080000 -1 NULL:1988792 RE53284.5prime 203 572 1 1 0 2605296 208416 208213 1 0 0 0 100 partof 203 2R:1731127-2080000 -1 NULL:1988794 RE53279.5prime 0 203 1 1 0 208133 207811 1 0 0 0 100 partof 322 2R:1731127-2080000 -1 NULL:1988795 RE53279.5prime 203 525 1 1 0 2600353 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984647 RH35316.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984648 RH35316.5prime 77 161 1 1 0 347117 346787 1 0 0 0 99 partof 330 2R:1731127-2080000 1 NULL:1984649 RH35316.5prime 161 491 1 1 0 2600358 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984651 RE06195.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984652 RE06195.5prime 77 161 1 1 0 347118 346787 1 0 0 0 100 partof 331 2R:1731127-2080000 1 NULL:1984653 RE06195.5prime 161 492 1 1 0 2599180 137592 137446 1 0 0 0 100 partof 146 2R:1731127-2080000 1 NULL:1983707 GH14484.5prime 0 146 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983708 GH14484.5prime 146 583 1 1 0 138420 138357 1 0 0 0 100 partof 63 2R:1731127-2080000 1 NULL:1983709 GH14484.5prime 583 646 1 1 0 2599185 137592 137448 1 0 0 0 100 partof 144 2R:1731127-2080000 1 NULL:1983711 SD12815.5prime 8 152 1 1 0 138237 137864 1 0 0 0 100 partof 373 2R:1731127-2080000 1 NULL:1983712 SD12815.5prime 152 525 1 1 0 2599189 137592 137448 1 0 0 0 99 partof 144 2R:1731127-2080000 1 NULL:1983714 LD06366.5prime 0 144 1 1 0 138301 137864 1 0 0 0 99 partof 437 2R:1731127-2080000 1 NULL:1983715 LD06366.5prime 144 580 1 1 0 138458 138357 1 0 0 0 98 partof 101 2R:1731127-2080000 1 NULL:1983716 LD06366.5prime 580 680 1 1 0 2600363 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984655 RE03617.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984656 RE03617.5prime 77 161 1 1 0 347120 346787 1 0 0 0 99 partof 333 2R:1731127-2080000 1 NULL:1984657 RE03617.5prime 161 494 1 1 0 2600368 342110 342033 1 0 0 0 98 partof 77 2R:1731127-2080000 1 NULL:1984659 RE64307.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984660 RE64307.5prime 77 161 1 1 0 347120 346787 1 0 0 0 99 partof 333 2R:1731127-2080000 1 NULL:1984661 RE64307.5prime 161 494 1 1 0 2599194 137592 137449 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983718 GH03290.5prime 0 143 1 1 0 138116 137864 1 0 0 0 100 partof 252 2R:1731127-2080000 1 NULL:1983719 GH03290.5prime 143 395 1 1 0 2599198 137592 137449 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983721 LD40491.5prime 0 143 1 1 0 138227 137864 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1983722 LD40491.5prime 143 506 1 1 0 2600373 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984663 RE05475.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984664 RE05475.5prime 77 161 1 1 0 347124 346787 1 0 0 0 99 partof 337 2R:1731127-2080000 1 NULL:1984665 RE05475.5prime 161 499 1 1 0 2600378 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984667 RH38942.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984668 RH38942.5prime 77 161 1 1 0 347156 346787 1 0 0 0 98 partof 369 2R:1731127-2080000 1 NULL:1984669 RH38942.5prime 161 531 1 1 0 2600383 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984671 RE23789.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984672 RE23789.5prime 77 161 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984673 RE23789.5prime 161 524 1 1 0 347230 347209 1 0 0 0 100 partof 21 2R:1731127-2080000 1 NULL:1984674 RE23789.5prime 524 545 1 1 0 2600389 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984676 RH66671.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984677 RH66671.5prime 77 161 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984678 RH66671.5prime 161 524 1 1 0 347260 347209 1 0 0 0 100 partof 51 2R:1731127-2080000 1 NULL:1984679 RH66671.5prime 524 575 1 1 0 2599501 142469 142306 1 0 0 0 100 partof 163 2R:1731127-2080000 1 NULL:1983958 RE70026.5prime 0 163 1 1 0 142891 142555 1 0 0 0 100 partof 336 2R:1731127-2080000 1 NULL:1983959 RE70026.5prime 163 499 1 1 0 143017 142947 1 0 0 0 97 partof 70 2R:1731127-2080000 1 NULL:1983960 RE70026.5prime 499 569 1 1 0 2599506 142891 142832 1 0 0 0 100 partof 59 2R:1731127-2080000 1 NULL:1983962 LD37667.5prime 0 59 1 1 0 143440 142947 1 0 0 0 99 partof 493 2R:1731127-2080000 1 NULL:1983963 LD37667.5prime 59 552 1 1 0 2600395 342110 342033 1 0 0 0 98 partof 77 2R:1731127-2080000 1 NULL:1984681 RE54656.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984682 RE54656.5prime 77 161 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984683 RE54656.5prime 161 524 1 1 0 347266 347209 1 0 0 0 100 partof 57 2R:1731127-2080000 1 NULL:1984684 RE54656.5prime 524 581 1 1 0 2599510 143528 142940 1 0 0 0 98 partof 588 2R:1731127-2080000 1 NULL:1983965 LD36551.5prime 0 588 1 1 0 143853 143811 1 0 0 0 100 partof 42 2R:1731127-2080000 1 NULL:1983966 LD36551.5prime 588 630 1 1 0 2599514 143528 143475 1 0 0 0 92 partof 53 2R:1731127-2080000 1 NULL:1983968 BE976985 0 54 1 1 0 144376 143811 1 0 0 0 95 partof 565 2R:1731127-2080000 1 NULL:1983969 BE976985 54 643 1 1 0 2599518 144448 143875 1 0 0 0 100 partof 573 2R:1731127-2080000 1 NULL:1983971 LD31151.5prime 0 573 1 1 0 2599521 144580 144018 1 0 0 0 99 partof 562 2R:1731127-2080000 1 NULL:1983973 GH09887.3prime_revcomp 0 564 1 1 0 2599524 144599 144136 1 0 0 0 98 partof 463 2R:1731127-2080000 1 NULL:1983975 RH58635.5prime 0 465 1 1 0 2599527 144591 144314 1 0 0 0 99 partof 277 2R:1731127-2080000 1 NULL:1983977 GH13837.3prime_revcomp 0 277 1 1 0 2599530 149188 148578 1 0 0 0 99 partof 610 2R:1731127-2080000 1 NULL:1983979 SD06785:contig1 0 610 1 1 0 152228 151823 1 0 0 0 99 partof 405 2R:1731127-2080000 1 NULL:1983980 SD06785:contig2 610 1015 1 1 0 2599535 158442 158132 1 0 0 0 97 partof 310 2R:1731127-2080000 1 NULL:1983982 RE34115:contig1 0 310 1 1 0 159823 159335 1 0 0 0 100 partof 488 2R:1731127-2080000 1 NULL:1983983 RE34115:contig1 310 798 1 1 0 162706 162404 1 0 0 0 100 partof 302 2R:1731127-2080000 1 NULL:1983984 RE34115:contig1 798 1100 1 1 0 163467 163389 1 0 0 0 96 partof 78 2R:1731127-2080000 1 NULL:1983985 RE34115:contig1 1100 1178 1 1 0 164701 163535 1 0 0 0 100 partof 1166 2R:1731127-2080000 1 NULL:1983986 RE34115:contig2 1178 2344 1 1 0 165844 165267 1 0 0 0 100 partof 577 2R:1731127-2080000 1 NULL:1983987 RE34115:contig2 2344 2921 1 1 0 168135 166301 1 0 0 0 100 partof 1834 2R:1731127-2080000 1 NULL:1983988 RE34115:contig2 2921 4755 1 1 0 2599543 158280 158182 1 0 0 0 100 partof 98 2R:1731127-2080000 1 NULL:1983990 RE02428.5prime 0 98 1 1 0 159579 159255 1 0 0 0 98 partof 324 2R:1731127-2080000 1 NULL:1983991 RE02428.5prime 98 422 1 1 0 2599547 166948 166496 1 0 0 0 99 partof 452 2R:1731127-2080000 1 NULL:1983993 HL03411.5prime 0 451 1 1 0 2599550 197929 197356 1 0 0 0 100 partof 573 2R:1731127-2080000 1 NULL:1983995 SD19073.5prime 0 573 1 1 0 2599553 206301 205927 1 0 0 0 98 partof 374 2R:1731127-2080000 1 NULL:1983997 SD01756.3prime 89 463 1 1 0 206458 206370 1 0 0 0 98 partof 88 2R:1731127-2080000 1 NULL:1983998 SD01756.3prime 0 89 1 1 0 2599557 211822 211416 1 0 0 0 99 partof 406 2R:1731127-2080000 1 NULL:1984000 AI945798 0 405 1 1 0 2599560 212128 211439 1 0 0 0 99 partof 689 2R:1731127-2080000 1 NULL:1984002 AT05873.5prime 0 689 1 1 0 2599563 212065 211449 1 0 0 0 100 partof 616 2R:1731127-2080000 1 NULL:1984004 AT23082.5prime 0 616 1 1 0 2599566 212013 211452 1 0 0 0 99 partof 561 2R:1731127-2080000 1 NULL:1984006 AT14522.5prime 0 561 1 1 0 2599569 211894 211478 1 0 0 0 99 partof 416 2R:1731127-2080000 1 NULL:1984008 AI946612 16 432 1 1 0 2599572 212173 211512 1 0 0 0 99 partof 661 2R:1731127-2080000 1 NULL:1984010 AT28033.5prime 0 663 1 1 0 2599575 212082 211708 1 0 0 0 97 partof 374 2R:1731127-2080000 1 NULL:1984012 BE978317 0 377 1 1 0 2599578 212413 211741 1 0 0 0 99 partof 672 2R:1731127-2080000 1 NULL:1984014 AT24862:contig1 0 672 1 1 0 212625 212483 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1984015 AT24862:contig1 672 814 1 1 0 213182 212688 1 0 0 0 97 partof 494 2R:1731127-2080000 1 NULL:1984016 AT24862:contig1 814 1308 1 1 0 2598921 137592 137385 1 0 0 0 99 partof 207 2R:1731127-2080000 1 NULL:1983511 RH13851.5prime 0 207 1 1 0 138280 137864 1 0 0 0 99 partof 416 2R:1731127-2080000 1 NULL:1983512 RH13851.5prime 207 623 1 1 0 2598925 137592 137385 1 0 0 0 99 partof 207 2R:1731127-2080000 1 NULL:1983514 RH63194.5prime 0 207 1 1 0 138302 137864 1 0 0 0 99 partof 438 2R:1731127-2080000 1 NULL:1983515 RH63194.5prime 207 647 1 1 0 2599582 212413 211845 1 0 0 0 100 partof 568 2R:1731127-2080000 1 NULL:1984018 AT30445.5prime 0 568 1 1 0 212548 212483 1 0 0 0 96 partof 65 2R:1731127-2080000 1 NULL:1984019 AT30445.5prime 568 633 1 1 0 2598929 137592 137396 1 0 0 0 99 partof 196 2R:1731127-2080000 1 NULL:1983517 RE26550.5prime 0 196 1 1 0 138305 137864 1 0 0 0 99 partof 441 2R:1731127-2080000 1 NULL:1983518 RE26550.5prime 196 639 1 1 0 2599586 212384 212007 1 0 0 0 99 partof 377 2R:1731127-2080000 1 NULL:1984021 AT15263.5prime 0 377 1 1 0 2599589 212413 212283 1 0 0 0 97 partof 130 2R:1731127-2080000 1 NULL:1984023 BE978736 0 130 1 1 0 212625 212483 1 0 0 0 99 partof 142 2R:1731127-2080000 1 NULL:1984024 BE978736 130 272 1 1 0 213039 212694 1 0 0 0 100 partof 345 2R:1731127-2080000 1 NULL:1984025 BE978736 272 617 1 1 0 2598933 137592 137400 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1983520 GH18759.5prime 0 192 1 1 0 138279 137864 1 0 0 0 99 partof 415 2R:1731127-2080000 1 NULL:1983521 GH18759.5prime 192 607 1 1 0 2598937 137592 137402 1 0 0 0 98 partof 190 2R:1731127-2080000 1 NULL:1983523 RH01237.5prime 0 188 1 1 0 138184 137864 1 0 0 0 99 partof 320 2R:1731127-2080000 1 NULL:1983524 RH01237.5prime 188 508 1 1 0 2599594 213542 212936 1 0 0 0 97 partof 606 2R:1731127-2080000 1 NULL:1984027 CK02196.3prime_revcomp 0 610 1 1 0 2599597 213117 213054 1 0 0 0 96 partof 63 2R:1731127-2080000 1 NULL:1984029 RH48695.5prime 0 63 1 1 0 213893 213388 1 0 0 0 99 partof 505 2R:1731127-2080000 1 NULL:1984030 RH48695.5prime 63 567 1 1 0 2598941 137592 137402 1 0 0 0 98 partof 190 2R:1731127-2080000 1 NULL:1983526 RH12314.5prime 0 188 1 1 0 138197 137864 1 0 0 0 99 partof 333 2R:1731127-2080000 1 NULL:1983527 RH12314.5prime 188 521 1 1 0 2598945 137592 137402 1 0 0 0 98 partof 190 2R:1731127-2080000 1 NULL:1983529 RH59176.5prime 0 188 1 1 0 138236 137864 1 0 0 0 99 partof 372 2R:1731127-2080000 1 NULL:1983530 RH59176.5prime 188 560 1 1 0 2598949 137592 137403 1 0 0 0 99 partof 189 2R:1731127-2080000 1 NULL:1983532 LD23740.5prime 0 188 1 1 0 138240 137864 1 0 0 0 99 partof 376 2R:1731127-2080000 1 NULL:1983533 LD23740.5prime 188 564 1 1 0 2598953 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983535 RH02420.5prime 0 187 1 1 0 138185 137864 1 0 0 0 98 partof 321 2R:1731127-2080000 1 NULL:1983536 RH02420.5prime 187 511 1 1 0 2598957 137592 137404 1 0 0 0 97 partof 188 2R:1731127-2080000 1 NULL:1983538 RH72046.5prime 0 188 1 1 0 138185 137864 1 0 0 0 97 partof 321 2R:1731127-2080000 1 NULL:1983539 RH72046.5prime 188 509 1 1 0 2599902 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984271 RE52558.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984272 RE52558.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984273 RE52558.5prime 203 395 1 1 0 326810 326705 1 0 0 0 100 partof 105 2R:1731127-2080000 1 NULL:1984274 RE52558.5prime 395 500 1 1 0 2599908 322552 322461 1 0 0 0 98 partof 91 2R:1731127-2080000 1 NULL:1984276 RE52954.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984277 RE52954.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984278 RE52954.5prime 203 395 1 1 0 326810 326705 1 0 0 0 99 partof 105 2R:1731127-2080000 1 NULL:1984279 RE52954.5prime 395 500 1 1 0 2598961 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983541 RH54763.5prime 0 187 1 1 0 138197 137864 1 0 0 0 99 partof 333 2R:1731127-2080000 1 NULL:1983542 RH54763.5prime 187 520 1 1 0 2598965 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983544 RH25786.5prime 0 188 1 1 0 138236 137864 1 0 0 0 100 partof 372 2R:1731127-2080000 1 NULL:1983545 RH25786.5prime 188 560 1 1 0 2598969 137592 137404 1 0 0 0 94 partof 188 2R:1731127-2080000 1 NULL:1983547 RE07187.5prime 0 182 1 1 0 138238 137864 1 0 0 0 100 partof 374 2R:1731127-2080000 1 NULL:1983548 RE07187.5prime 182 556 1 1 0 2600002 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984356 RE20717.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984357 RE20717.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984358 RE20717.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984359 RE20717.5prime 395 557 1 1 0 327018 326933 1 0 0 0 100 partof 85 2R:1731127-2080000 1 NULL:1984360 RE20717.5prime 557 642 1 1 0 2600009 322552 322461 1 0 0 0 98 partof 91 2R:1731127-2080000 1 NULL:1984362 RE51065.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984363 RE51065.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984364 RE51065.5prime 203 395 1 1 0 326867 326705 1 0 0 0 99 partof 162 2R:1731127-2080000 1 NULL:1984365 RE51065.5prime 395 557 1 1 0 327018 326933 1 0 0 0 100 partof 85 2R:1731127-2080000 1 NULL:1984366 RE51065.5prime 557 642 1 1 0 2599914 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984281 RE19268.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984282 RE19268.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984283 RE19268.5prime 203 395 1 1 0 326848 326705 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1984284 RE19268.5prime 395 538 1 1 0 2598973 137592 137404 1 0 0 0 97 partof 188 2R:1731127-2080000 1 NULL:1983550 RH69128.5prime 0 188 1 1 0 138238 137864 1 0 0 0 99 partof 374 2R:1731127-2080000 1 NULL:1983551 RH69128.5prime 188 562 1 1 0 2598977 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983553 RH50582.5prime 0 187 1 1 0 138271 137864 1 0 0 0 99 partof 407 2R:1731127-2080000 1 NULL:1983554 RH50582.5prime 187 594 1 1 0 2600016 322552 322461 1 0 0 0 98 partof 91 2R:1731127-2080000 1 NULL:1984368 RE73528.5prime 0 91 1 1 0 324259 324147 1 0 0 0 99 partof 112 2R:1731127-2080000 1 NULL:1984369 RE73528.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984370 RE73528.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984371 RE73528.5prime 395 557 1 1 0 327019 326933 1 0 0 0 100 partof 86 2R:1731127-2080000 1 NULL:1984372 RE73528.5prime 557 643 1 1 0 2599920 322552 322461 1 0 0 0 98 partof 91 2R:1731127-2080000 1 NULL:1984286 RE05301.5prime 0 92 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984287 RE05301.5prime 92 204 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984288 RE05301.5prime 204 396 1 1 0 326859 326705 1 0 0 0 99 partof 154 2R:1731127-2080000 1 NULL:1984289 RE05301.5prime 396 550 1 1 0 2599926 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984291 RE10090.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984292 RE10090.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984293 RE10090.5prime 203 395 1 1 0 326871 326705 1 0 0 0 97 partof 166 2R:1731127-2080000 1 NULL:1984294 RE10090.5prime 395 562 1 1 0 2598981 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983556 RH34034.5prime 0 188 1 1 0 138302 137864 1 0 0 0 100 partof 438 2R:1731127-2080000 1 NULL:1983557 RH34034.5prime 188 626 1 1 0 2598985 137592 137404 1 0 0 0 99 partof 188 2R:1731127-2080000 1 NULL:1983559 RH24825.5prime 0 188 1 1 0 138305 137864 1 0 0 0 99 partof 441 2R:1731127-2080000 1 NULL:1983560 RH24825.5prime 188 631 1 1 0 2598989 137592 137404 1 0 0 0 98 partof 188 2R:1731127-2080000 1 NULL:1983562 RH36087.5prime 0 188 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983563 RH36087.5prime 188 625 1 1 0 138398 138357 1 0 0 0 100 partof 41 2R:1731127-2080000 1 NULL:1983564 RH36087.5prime 625 666 1 1 0 2600023 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984374 RE51314.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984375 RE51314.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984376 RE51314.5prime 203 395 1 1 0 326867 326705 1 0 0 0 99 partof 162 2R:1731127-2080000 1 NULL:1984377 RE51314.5prime 395 558 1 1 0 327023 326933 1 0 0 0 100 partof 90 2R:1731127-2080000 1 NULL:1984378 RE51314.5prime 558 648 1 1 0 2599932 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984296 RE24359.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984297 RE24359.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984298 RE24359.5prime 203 395 1 1 0 326867 326705 1 0 0 0 98 partof 162 2R:1731127-2080000 1 NULL:1984299 RE24359.5prime 395 557 1 1 0 326980 326933 1 0 0 0 100 partof 47 2R:1731127-2080000 1 NULL:1984300 RE24359.5prime 557 604 1 1 0 2599939 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984302 RE71270.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984303 RE71270.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984304 RE71270.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984305 RE71270.5prime 395 557 1 1 0 326981 326933 1 0 0 0 95 partof 48 2R:1731127-2080000 1 NULL:1984306 RE71270.5prime 557 605 1 1 0 2598994 137592 137405 1 0 0 0 98 partof 187 2R:1731127-2080000 1 NULL:1983566 RE64936.5prime 0 186 1 1 0 138014 137864 1 0 0 0 96 partof 150 2R:1731127-2080000 1 NULL:1983567 RE64936.5prime 186 336 1 1 0 2598998 137592 137405 1 0 0 0 99 partof 187 2R:1731127-2080000 1 NULL:1983569 RE05741.5prime 0 187 1 1 0 138271 137864 1 0 0 0 100 partof 407 2R:1731127-2080000 1 NULL:1983570 RE05741.5prime 187 594 1 1 0 2600030 322552 322461 1 0 0 0 97 partof 91 2R:1731127-2080000 1 NULL:1984380 RE37323.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984381 RE37323.5prime 91 203 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984382 RE37323.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984383 RE37323.5prime 395 557 1 1 0 327024 326933 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984384 RE37323.5prime 557 648 1 1 0 2600037 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984386 RE38420.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984387 RE38420.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984388 RE38420.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984389 RE38420.5prime 395 557 1 1 0 327026 326933 1 0 0 0 97 partof 93 2R:1731127-2080000 1 NULL:1984390 RE38420.5prime 557 650 1 1 0 2599946 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984308 RE03911.5prime 0 91 1 1 0 324259 324147 1 0 0 0 98 partof 112 2R:1731127-2080000 1 NULL:1984309 RE03911.5prime 91 205 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984310 RE03911.5prime 205 397 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984311 RE03911.5prime 397 559 1 1 0 326983 326933 1 0 0 0 100 partof 50 2R:1731127-2080000 1 NULL:1984312 RE03911.5prime 559 609 1 1 0 2600044 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984392 RE60883.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984393 RE60883.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984394 RE60883.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984395 RE60883.5prime 395 557 1 1 0 327040 326933 1 0 0 0 99 partof 107 2R:1731127-2080000 1 NULL:1984396 RE60883.5prime 557 664 1 1 0 2599953 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984314 RE17840.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984315 RE17840.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984316 RE17840.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984317 RE17840.5prime 395 557 1 1 0 326983 326933 1 0 0 0 98 partof 50 2R:1731127-2080000 1 NULL:1984318 RE17840.5prime 557 607 1 1 0 2600051 322552 322463 1 0 0 0 100 partof 89 2R:1731127-2080000 1 NULL:1984398 GH05668:contig1 0 89 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984399 GH05668:contig1 89 201 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984400 GH05668:contig1 201 393 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984401 GH05668:contig1 393 555 1 1 0 326987 326933 1 0 0 0 98 partof 54 2R:1731127-2080000 1 NULL:1984402 GH05668:contig1 555 609 1 1 0 333156 332993 1 0 0 0 99 partof 163 2R:1731127-2080000 1 NULL:1984403 GH05668:contig2 609 772 1 1 0 333417 333222 1 0 0 0 100 partof 195 2R:1731127-2080000 1 NULL:1984404 GH05668:contig2 772 967 1 1 0 334031 333679 1 0 0 0 100 partof 352 2R:1731127-2080000 1 NULL:1984405 GH05668:contig2 967 1319 1 1 0 2599960 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984320 RE43950.5prime 0 91 1 1 0 324259 324153 1 0 0 0 100 partof 106 2R:1731127-2080000 1 NULL:1984321 RE43950.5prime 91 197 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984322 RE43950.5prime 197 389 1 1 0 326867 326705 1 0 0 0 99 partof 162 2R:1731127-2080000 1 NULL:1984323 RE43950.5prime 389 551 1 1 0 326985 326933 1 0 0 0 98 partof 52 2R:1731127-2080000 1 NULL:1984324 RE43950.5prime 551 604 1 1 0 2599967 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984326 RE49713.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984327 RE49713.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984328 RE49713.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984329 RE49713.5prime 395 557 1 1 0 326987 326933 1 0 0 0 98 partof 54 2R:1731127-2080000 1 NULL:1984330 RE49713.5prime 557 612 1 1 0 2600060 322552 322470 1 0 0 0 100 partof 82 2R:1731127-2080000 1 NULL:1984407 CK00403.contig 0 82 1 1 0 324259 324153 1 0 0 0 99 partof 106 2R:1731127-2080000 1 NULL:1984408 CK00403.contig 82 187 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984409 CK00403.contig 187 379 1 1 0 326867 326705 1 0 0 0 96 partof 162 2R:1731127-2080000 1 NULL:1984410 CK00403.contig 379 542 1 1 0 327128 326933 1 0 0 0 96 partof 195 2R:1731127-2080000 1 NULL:1984411 CK00403.contig 542 736 1 1 0 327748 327391 1 0 0 0 97 partof 357 2R:1731127-2080000 1 NULL:1984412 CK00403.contig 736 1094 1 1 0 2600068 322552 322472 1 0 0 0 96 partof 80 2R:1731127-2080000 1 NULL:1984414 GM13790.5prime 0 78 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984415 GM13790.5prime 78 190 1 1 0 326642 326450 1 0 0 0 97 partof 192 2R:1731127-2080000 1 NULL:1984416 GM13790.5prime 190 381 1 1 0 326867 326705 1 0 0 0 99 partof 162 2R:1731127-2080000 1 NULL:1984417 GM13790.5prime 381 543 1 1 0 326976 326933 1 0 0 0 95 partof 43 2R:1731127-2080000 1 NULL:1984418 GM13790.5prime 543 586 1 1 0 2599974 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984332 RE49414.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984333 RE49414.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984334 RE49414.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984335 RE49414.5prime 395 557 1 1 0 326989 326933 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1984336 RE49414.5prime 557 613 1 1 0 2600075 322552 322472 1 0 0 0 100 partof 80 2R:1731127-2080000 1 NULL:1984420 GH06231.5prime 0 80 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984421 GH06231.5prime 80 192 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984422 GH06231.5prime 192 384 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984423 GH06231.5prime 384 546 1 1 0 326989 326933 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1984424 GH06231.5prime 546 602 1 1 0 2599981 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984338 RE38520.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984339 RE38520.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984340 RE38520.5prime 203 395 1 1 0 326867 326705 1 0 0 0 99 partof 162 2R:1731127-2080000 1 NULL:1984341 RE38520.5prime 395 557 1 1 0 326989 326933 1 0 0 0 100 partof 56 2R:1731127-2080000 1 NULL:1984342 RE38520.5prime 557 613 1 1 0 2605300 208416 208213 1 0 0 0 99 partof 203 2R:1731127-2080000 -1 NULL:1988797 RH61281.5prime 0 204 1 1 0 208133 207820 1 0 0 0 100 partof 313 2R:1731127-2080000 -1 NULL:1988798 RH61281.5prime 204 517 1 1 0 2599988 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984344 RE73386.5prime 0 91 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984345 RE73386.5prime 91 203 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984346 RE73386.5prime 203 395 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984347 RE73386.5prime 395 557 1 1 0 326990 326933 1 0 0 0 100 partof 57 2R:1731127-2080000 1 NULL:1984348 RE73386.5prime 557 614 1 1 0 2605304 208675 208619 1 0 0 0 100 partof 56 2R:1731127-2080000 -1 NULL:1988800 GH08104.5prime 0 56 1 1 0 208133 207556 1 0 0 0 100 partof 577 2R:1731127-2080000 -1 NULL:1988801 GH08104.5prime 56 633 1 1 0 2605308 208683 207201 1 0 0 0 100 partof 1482 2R:1731127-2080000 -1 NULL:1988803 GH21896:contig1 0 1482 1 1 0 207137 206995 1 0 0 0 100 partof 142 2R:1731127-2080000 -1 NULL:1988804 GH21896:contig1 1482 1624 1 1 0 206508 206370 1 0 0 0 100 partof 138 2R:1731127-2080000 -1 NULL:1988805 GH21896:contig1 1624 1762 1 1 0 206301 205921 1 0 0 0 100 partof 380 2R:1731127-2080000 -1 NULL:1988806 GH21896:contig1 1762 2142 1 1 0 2600082 322552 322473 1 0 0 0 100 partof 79 2R:1731127-2080000 1 NULL:1984426 GH14139.5prime 0 79 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984427 GH14139.5prime 79 191 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984428 GH14139.5prime 191 383 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984429 GH14139.5prime 383 545 1 1 0 327050 326933 1 0 0 0 99 partof 117 2R:1731127-2080000 1 NULL:1984430 GH14139.5prime 545 662 1 1 0 2600089 322835 322481 1 0 0 0 100 partof 354 2R:1731127-2080000 1 NULL:1984432 GH17623:contig1 0 354 1 1 0 324083 322895 1 0 0 0 100 partof 1188 2R:1731127-2080000 1 NULL:1984433 GH17623:contig1 354 1542 1 1 0 2599995 326867 326705 1 0 0 0 98 partof 162 2R:1731127-2080000 1 NULL:1984353 RE39180.5prime 389 551 1 1 0 327000 326933 1 0 0 0 98 partof 67 2R:1731127-2080000 1 NULL:1984354 RE39180.5prime 551 619 1 1 0 322552 322461 1 0 0 0 100 partof 91 2R:1731127-2080000 1 NULL:1984350 RE39180.5prime 0 91 1 1 0 324259 324153 1 0 0 0 100 partof 106 2R:1731127-2080000 1 NULL:1984351 RE39180.5prime 91 197 1 1 0 326642 326450 1 0 0 0 99 partof 192 2R:1731127-2080000 1 NULL:1984352 RE39180.5prime 197 389 1 1 0 2605313 208698 208619 1 0 0 0 98 partof 79 2R:1731127-2080000 -1 NULL:1988808 RH55976.5prime 0 80 1 1 0 208133 207545 1 0 0 0 99 partof 588 2R:1731127-2080000 -1 NULL:1988809 RH55976.5prime 80 668 1 1 0 2605316 208698 208619 1 0 0 0 98 partof 79 2R:1731127-2080000 -1 NULL:1988811 RE28537.5prime 0 79 1 1 0 208133 207566 1 0 0 0 100 partof 567 2R:1731127-2080000 -1 NULL:1988812 RE28537.5prime 79 646 1 1 0 2599202 137592 137449 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983724 GH12740.5prime 0 143 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983725 GH12740.5prime 143 580 1 1 0 138427 138357 1 0 0 0 100 partof 70 2R:1731127-2080000 1 NULL:1983726 GH12740.5prime 580 650 1 1 0 2600092 322552 322482 1 0 0 0 100 partof 70 2R:1731127-2080000 1 NULL:1984435 GH04722.5prime 0 70 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984436 GH04722.5prime 70 182 1 1 0 326603 326450 1 0 0 0 98 partof 153 2R:1731127-2080000 1 NULL:1984437 GH04722.5prime 182 335 1 1 0 2599207 137592 137449 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983728 GH04059.5prime 0 143 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983729 GH04059.5prime 143 580 1 1 0 138459 138357 1 0 0 0 99 partof 102 2R:1731127-2080000 1 NULL:1983730 GH04059.5prime 580 683 1 1 0 2600097 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1984440 GH15378.5prime 70 182 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1984441 GH15378.5prime 182 374 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1984442 GH15378.5prime 374 536 1 1 0 327000 326933 1 0 0 0 100 partof 67 2R:1731127-2080000 1 NULL:1984443 GH15378.5prime 536 603 1 1 0 322552 322482 1 0 0 0 100 partof 70 2R:1731127-2080000 1 NULL:1984439 GH15378.5prime 0 70 1 1 0 2605320 208698 208619 1 0 0 0 98 partof 79 2R:1731127-2080000 -1 NULL:1988814 RE26283.5prime 0 79 1 1 0 208133 207576 1 0 0 0 100 partof 557 2R:1731127-2080000 -1 NULL:1988815 RE26283.5prime 79 636 1 1 0 2605324 208698 208619 1 0 0 0 98 partof 79 2R:1731127-2080000 -1 NULL:1988817 RH65980.5prime 0 80 1 1 0 208133 207652 1 0 0 0 100 partof 481 2R:1731127-2080000 -1 NULL:1988818 RH65980.5prime 80 561 1 1 0 2605328 208698 208619 1 0 0 0 98 partof 79 2R:1731127-2080000 -1 NULL:1988820 RH07638.5prime 0 80 1 1 0 208133 207989 1 0 0 0 99 partof 144 2R:1731127-2080000 -1 NULL:1988821 RH07638.5prime 80 224 1 1 0 2599212 137592 137450 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1983732 LD46288.5prime 0 142 1 1 0 138277 137864 1 0 0 0 100 partof 413 2R:1731127-2080000 1 NULL:1983733 LD46288.5prime 142 555 1 1 0 2599216 137592 137450 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1983735 GH27015.5prime 0 142 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983736 GH27015.5prime 142 579 1 1 0 138464 138357 1 0 0 0 99 partof 107 2R:1731127-2080000 1 NULL:1983737 GH27015.5prime 579 686 1 1 0 2605332 211842 211468 1 0 0 0 99 partof 374 2R:1731127-2080000 -1 NULL:1988823 AT18089.3prime_revcomp 0 374 1 1 0 2605335 218037 217835 1 0 0 0 100 partof 202 2R:1731127-2080000 -1 NULL:1988825 UNKNOWN_RE01906:contig1 0 202 1 1 0 217771 217629 1 0 0 0 100 partof 142 2R:1731127-2080000 -1 NULL:1988826 UNKNOWN_RE01906:contig1 202 344 1 1 0 217223 216406 1 0 0 0 99 partof 817 2R:1731127-2080000 -1 NULL:1988827 UNKNOWN_RE01906:contig1 344 1161 1 1 0 2599221 137592 137451 1 0 0 0 100 partof 141 2R:1731127-2080000 1 NULL:1983739 LD16520.5prime 0 141 1 1 0 138301 137864 1 0 0 0 98 partof 437 2R:1731127-2080000 1 NULL:1983740 LD16520.5prime 141 575 1 1 0 138383 138357 1 0 0 0 92 partof 26 2R:1731127-2080000 1 NULL:1983741 LD16520.5prime 575 603 1 1 0 2599226 137592 137464 1 0 0 0 100 partof 128 2R:1731127-2080000 1 NULL:1983743 RE73346.5prime 0 128 1 1 0 138236 137864 1 0 0 0 100 partof 372 2R:1731127-2080000 1 NULL:1983744 RE73346.5prime 128 500 1 1 0 2605340 255869 255476 1 0 0 0 96 partof 393 2R:1731127-2080000 -1 NULL:1988829 CK01046.3prime_revcomp 0 394 1 1 0 2605343 256524 255866 1 0 0 0 98 partof 658 2R:1731127-2080000 -1 NULL:1988831 RH11075.5prime 0 659 1 1 0 2605346 258657 258090 1 0 0 0 100 partof 567 2R:1731127-2080000 -1 NULL:1988833 SD09080:contig1 0 567 1 1 0 255920 255476 1 0 0 0 99 partof 444 2R:1731127-2080000 -1 NULL:1988834 SD09080:contig2 567 1011 1 1 0 2600401 342110 342033 1 0 0 0 98 partof 77 2R:1731127-2080000 1 NULL:1984686 RE24157.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984687 RE24157.5prime 77 161 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1984688 RE24157.5prime 161 524 1 1 0 347316 347209 1 0 0 0 100 partof 107 2R:1731127-2080000 1 NULL:1984689 RE24157.5prime 524 631 1 1 0 2600407 342110 342033 1 0 0 0 100 partof 77 2R:1731127-2080000 1 NULL:1984691 RE49313.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984692 RE49313.5prime 77 161 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984693 RE49313.5prime 161 524 1 1 0 347338 347209 1 0 0 0 98 partof 129 2R:1731127-2080000 1 NULL:1984694 RE49313.5prime 524 654 1 1 0 2599230 137592 137512 1 0 0 0 100 partof 80 2R:1731127-2080000 1 NULL:1983746 GH14836.5prime 0 80 1 1 0 138301 137864 1 0 0 0 100 partof 437 2R:1731127-2080000 1 NULL:1983747 GH14836.5prime 80 517 1 1 0 138375 138357 1 0 0 0 100 partof 18 2R:1731127-2080000 1 NULL:1983748 GH14836.5prime 517 535 1 1 0 2599235 138301 137875 1 0 0 0 100 partof 426 2R:1731127-2080000 1 NULL:1983750 GH26160.5prime 0 426 1 1 0 138608 138357 1 0 0 0 99 partof 251 2R:1731127-2080000 1 NULL:1983751 GH26160.5prime 426 677 1 1 0 2599239 138301 137969 1 0 0 0 100 partof 332 2R:1731127-2080000 1 NULL:1983753 GH09089.5prime 0 332 1 1 0 138645 138357 1 0 0 0 100 partof 288 2R:1731127-2080000 1 NULL:1983754 GH09089.5prime 332 620 1 1 0 2605351 261593 260657 1 0 0 0 100 partof 936 2R:1731127-2080000 -1 NULL:1988836 GH14660:contig1 0 936 1 1 0 258498 258283 1 0 0 0 99 partof 215 2R:1731127-2080000 -1 NULL:1988837 GH14660:contig2 936 1151 1 1 0 256596 256444 1 0 0 0 100 partof 152 2R:1731127-2080000 -1 NULL:1988838 GH14660:contig2 1151 1303 1 1 0 256073 255511 1 0 0 0 100 partof 562 2R:1731127-2080000 -1 NULL:1988839 GH14660:contig2 1303 1865 1 1 0 2605356 285147 284579 1 0 0 0 98 partof 568 2R:1731127-2080000 -1 NULL:1988841 RH41532.5prime 0 572 1 1 0 2605358 289375 288326 1 0 0 0 96 partof 1049 2R:1731127-2080000 -1 NULL:1988843 UNKNOWN_RH55627:contig1 0 1049 1 1 0 2600413 342110 342033 1 0 0 0 98 partof 77 2R:1731127-2080000 1 NULL:1984696 RE20588.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984697 RE20588.5prime 77 161 1 1 0 347150 346787 1 0 0 0 99 partof 363 2R:1731127-2080000 1 NULL:1984698 RE20588.5prime 161 525 1 1 0 347339 347209 1 0 0 0 100 partof 130 2R:1731127-2080000 1 NULL:1984699 RE20588.5prime 525 655 1 1 0 2600419 342110 342034 1 0 0 0 100 partof 76 2R:1731127-2080000 1 NULL:1984701 RE12641.5prime 0 76 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984702 RE12641.5prime 76 160 1 1 0 346906 346787 1 0 0 0 100 partof 119 2R:1731127-2080000 1 NULL:1984703 RE12641.5prime 160 279 1 1 0 2599243 140950 140794 1 0 0 0 98 partof 156 2R:1731127-2080000 1 NULL:1983756 RH58416:contig1 0 156 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983757 RH58416:contig1 156 338 1 1 0 142795 142555 1 0 0 0 100 partof 240 2R:1731127-2080000 1 NULL:1983758 RH58416:contig1 338 578 1 1 0 144599 144041 1 0 0 0 99 partof 558 2R:1731127-2080000 1 NULL:1983759 RH58416:contig2 578 1136 1 1 0 2605360 300887 300667 1 0 0 0 100 partof 220 2R:1731127-2080000 -1 NULL:1988845 AA433214 0 220 1 1 0 292870 292644 1 0 0 0 97 partof 226 2R:1731127-2080000 -1 NULL:1988846 AA433214 220 446 1 1 0 2605364 301319 300798 1 0 0 0 100 partof 521 2R:1731127-2080000 -1 NULL:1988848 LD28616:contig1 0 521 1 1 0 255687 255476 1 0 0 0 100 partof 211 2R:1731127-2080000 -1 NULL:1988849 LD28616:contig2 521 732 1 1 0 2605367 303043 302562 1 0 0 0 99 partof 481 2R:1731127-2080000 -1 NULL:1988851 GH27663:contig1 0 481 1 1 0 302504 301887 1 0 0 0 99 partof 617 2R:1731127-2080000 -1 NULL:1988852 GH27663:contig1 481 1098 1 1 0 2600424 342110 342034 1 0 0 0 100 partof 76 2R:1731127-2080000 1 NULL:1984705 RE06810.5prime 0 76 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984706 RE06810.5prime 76 160 1 1 0 347117 346787 1 0 0 0 100 partof 330 2R:1731127-2080000 1 NULL:1984707 RE06810.5prime 160 490 1 1 0 2600429 342110 342034 1 0 0 0 98 partof 76 2R:1731127-2080000 1 NULL:1984709 RE61794.5prime 0 77 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984710 RE61794.5prime 77 161 1 1 0 347121 346787 1 0 0 0 99 partof 334 2R:1731127-2080000 1 NULL:1984711 RE61794.5prime 161 495 1 1 0 2599250 140950 140795 1 0 0 0 97 partof 155 2R:1731127-2080000 1 NULL:1983761 RE51977.5prime 0 153 1 1 0 141840 141676 1 0 0 0 99 partof 164 2R:1731127-2080000 1 NULL:1983762 RE51977.5prime 153 318 1 1 0 2599254 140950 140795 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1983764 RH62978.5prime 0 155 1 1 0 141841 141676 1 0 0 0 96 partof 165 2R:1731127-2080000 1 NULL:1983765 RH62978.5prime 155 320 1 1 0 2599258 140950 140795 1 0 0 0 97 partof 155 2R:1731127-2080000 1 NULL:1983767 RE07879.5prime 0 156 1 1 0 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983768 RE07879.5prime 156 338 1 1 0 142762 142555 1 0 0 0 100 partof 207 2R:1731127-2080000 1 NULL:1983769 RE07879.5prime 338 545 1 1 0 2605371 303241 302623 1 0 0 0 98 partof 618 2R:1731127-2080000 -1 NULL:1988854 AT10063.5prime 0 618 1 1 0 2605374 303637 303246 1 0 0 0 98 partof 391 2R:1731127-2080000 -1 NULL:1988856 RE06341.5prime 0 392 1 1 0 2605377 303775 303293 1 0 0 0 100 partof 482 2R:1731127-2080000 -1 NULL:1988859 AT19905.5prime 25 507 1 1 0 304746 304721 1 0 0 0 96 partof 25 2R:1731127-2080000 -1 NULL:1988858 AT19905.5prime 0 25 1 1 0 2600434 342110 342034 1 0 0 0 100 partof 76 2R:1731127-2080000 1 NULL:1984713 RE54959.5prime 0 76 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1984714 RE54959.5prime 76 160 1 1 0 347150 346787 1 0 0 0 98 partof 363 2R:1731127-2080000 1 NULL:1984715 RE54959.5prime 160 526 1 1 0 347260 347209 1 0 0 0 100 partof 51 2R:1731127-2080000 1 NULL:1984716 RE54959.5prime 526 577 1 1 0 2599263 141858 141676 1 0 0 0 100 partof 182 2R:1731127-2080000 1 NULL:1983772 RH70711.5prime 156 338 1 1 0 142804 142555 1 0 0 0 99 partof 249 2R:1731127-2080000 1 NULL:1983773 RH70711.5prime 338 587 1 1 0 140950 140795 1 0 0 0 98 partof 155 2R:1731127-2080000 1 NULL:1983771 RH70711.5prime 0 156 1 1 0 blastx_masked 1.0 aa_SP.real.dros 1.0 2003-01-13 18:48:31 BLASTX Similarity to Fly genomic 2600595 137769 137529 1 0 0 0 108 partof MLATEARQILSRVGSLVARNQVSGVRGGPGLFWPRFQGRGGAGAQAAFV*CNYIRWKWGSRGSGIETPQISTRNA-LRNWG 240 2R:1731127-2080000 1 NULL:1984842 P21914 0 76 1 1 0 2600597 138302 137861 1 0 0 0 790 partof QMRAISNGTAQLEQQAQPKEAQEPQIKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 441 2R:1731127-2080000 1 NULL:1984844 P21914 20 167 1 1 0 138748 138355 1 0 0 0 707 partof RNEAGEKKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAALHK 393 2R:1731127-2080000 1 NULL:1984845 P21914 166 297 1 1 0 2605562 302505 302151 1 0 0 0 161 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAP-SAETSIPVEY 354 2R:1731127-2080000 -1 NULL:1989003 Q9V7G5 373 490 1 1 0 2605564 302508 302097 1 0 0 0 147 partof LETLRLHTPHPFLLRRATKE---FEVPGS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE-QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 411 2R:1731127-2080000 -1 NULL:1989005 Q9V6H1 376 515 1 1 0 2605566 302514 302172 1 0 0 0 190 partof FFLETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAE 342 2R:1731127-2080000 -1 NULL:1989007 Q9V559 376 489 1 1 0 2605568 302776 302566 1 0 0 0 134 partof DIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 210 2R:1731127-2080000 -1 NULL:1989009 Q9V675 303 372 1 1 0 2605570 302941 302563 1 0 0 0 143 partof FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIE-----------IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 378 2R:1731127-2080000 -1 NULL:1989011 Q27594 228 365 1 1 0 302505 302091 1 0 0 0 280 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989012 Q27594 365 504 1 1 0 2605573 302953 302563 1 0 0 0 163 partof LALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL-----------YS-NAEKPL---TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 390 2R:1731127-2080000 -1 NULL:1989014 Q9V776 233 377 1 1 0 2605575 303016 302563 1 0 0 0 162 partof NVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPL-----------TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 453 2R:1731127-2080000 -1 NULL:1989016 Q9V774 201 365 1 1 0 2605577 303019 302563 1 0 0 0 183 partof DNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPLQTFL--------QLYSNAE--KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 456 2R:1731127-2080000 -1 NULL:1989018 Q9VB31 201 367 1 1 0 302505 302091 1 0 0 0 288 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYD-NRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989019 Q9VB31 367 507 1 1 0 2605580 303088 302563 1 0 0 0 164 partof ISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA---YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD---RQPL-QTFLQLYSNA----EKPL----TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 525 2R:1731127-2080000 -1 NULL:1989021 Q9V674 178 369 1 1 0 2605582 303133 302563 1 0 0 0 189 partof RIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQKVALSQLQLH-----RRRDRQPLQTFLQL-YSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 570 2R:1731127-2080000 -1 NULL:1989023 Q9V773 158 362 1 1 0 2605584 303151 302566 1 0 0 0 160 partof LSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADF--RMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQT-FLQLYSNAEKPLTDIE------------IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEH-GGQVTPECLRELRYTKQVL 585 2R:1731127-2080000 -1 NULL:1989025 Q9VRB3 164 375 1 1 0 2605586 303175 302566 1 0 0 0 212 partof NMQKLLVRLSQISSRI---QRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQP---LQTFLQLYS-----NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1989027 Q9V771 143 361 1 1 0 302508 302085 1 0 0 0 284 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1989028 Q9V771 361 502 1 1 0 2605589 303175 302566 1 0 0 0 210 partof NMQKLLVRLSQISSRIQRDLGEKSL-QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFLQLYSN-----AEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1989030 Q9V770 142 360 1 1 0 2605591 303247 302563 1 0 0 0 189 partof NLLQLDGHKWRSLHAKSAEVF-TPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM-WQAYLAL-EFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFL---QLYSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 684 2R:1731127-2080000 -1 NULL:1989032 P82711 128 362 1 1 0 2605593 303253 302563 1 0 0 0 179 partof SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSQLQLHRRRDRQPLQTFLQLYSN--AEKPLTDIEI-AGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 690 2R:1731127-2080000 -1 NULL:1989034 Q9VRI9 136 383 1 1 0 2605595 303523 302569 1 0 0 0 220 partof YWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDG-HKWRSLHAKSAEVFTPANMQ-----KLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG---QDNVEFAKWTRNYW-ADFRMWQAYLALEF-PLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTF-LQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQV 954 2R:1731127-2080000 -1 NULL:1989036 Q9V676 23 354 1 1 0 302508 302106 1 0 0 0 155 partof LETLRLHTPHPFLLRRATKE----FEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERF-EEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 402 2R:1731127-2080000 -1 NULL:1989037 Q9V676 355 494 1 1 0 2605598 303523 302803 1 0 0 0 155 partof YWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK--GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSQLQLHRRRDRQPLQTFLQL 720 2R:1731127-2080000 -1 NULL:1989039 Q9VRI9 44 299 1 1 0 302505 302130 1 0 0 0 167 partof ETLRLHTPHPFLLRRATKE--FEV-P---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLL 375 2R:1731127-2080000 -1 NULL:1989040 Q9VRI9 383 514 1 1 0 2605601 303538 302566 1 0 0 0 259 partof KFSLGYWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACL-KPFILALDLKLVHQIIF-TDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----------VGQDNVEFAKWTRNYWADFRMW---QAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQ-VTPECLRELRYTKQVL 972 2R:1731127-2080000 -1 NULL:1989042 Q9VWR2 17 344 1 1 0 302508 302094 1 0 0 0 166 partof LETLRLHTPHPFLLRRATKEFEVP------GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989043 Q9VWR2 344 485 1 1 0 2605604 303544 302629 1 0 0 0 181 partof LVKFSLGYWKR---RGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL--------GEKSLQTINISELVGAYNTDVMASMAFGL-VGQ-DNVEFAKWTRNYWADFRMWQAYL----ALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD-RQP--LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALE 915 2R:1731127-2080000 -1 NULL:1989045 Q9V4I0 16 339 1 1 0 302505 302166 1 0 0 0 148 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETS 339 2R:1731127-2080000 -1 NULL:1989046 Q9V4I0 362 479 1 1 0 2605607 303556 302836 1 0 0 0 156 partof VVYALVKFSLGYWKRRGILHEKPKFLWGNIK-GVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS--RGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKL--LVRLSQISSR--IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG--QD-NVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPA-----TAYFQKVALSQLQLHRRR 720 2R:1731127-2080000 -1 NULL:1989048 Q9W130 15 267 1 1 0 2605609 303562 302878 1 0 0 0 301 partof LSVVYAL-VKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPAN---MQKLLVRLS-QISSRIQRDLGEKSLQ--TINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYF 684 2R:1731127-2080000 -1 NULL:1989050 Q9V4U7 11 250 1 1 0 302782 302563 1 0 0 0 141 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1989051 Q9V4U7 297 371 1 1 0 302505 302091 1 0 0 0 299 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989052 Q9V4U7 371 509 1 1 0 2605613 303565 302566 1 0 0 0 457 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT----INISELVGAYNTDVMASMAFGLV--GQDN--VEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQT-FLQLYSNAEK--PLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 999 2R:1731127-2080000 -1 NULL:1989054 Q9V769 10 354 1 1 0 302505 302082 1 0 0 0 251 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989055 Q9V769 355 497 1 1 0 2605616 303565 303028 1 0 0 0 178 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS-RGLYSNPSGEPLSHNLLQLDGH--------KWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1989057 Q9VG82 11 201 1 1 0 302466 302094 1 0 0 0 210 partof RRATKE--FEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSD--IKLSVER 372 2R:1731127-2080000 -1 NULL:1989058 Q9VG82 388 515 1 1 0 2605619 303565 302644 1 0 0 0 197 partof ALSVV-YALVKFSLGYWK---RRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQ-LDGHKWRSLHAKSAEVFTPANMQKLLVRLSQ-ISSRIQR-DLGEKSLQ-----TINISELVGAYNTDVMASMAFGLV--GQDNV--EFAKWTRN--YWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD-RQP--LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEI 921 2R:1731127-2080000 -1 NULL:1989060 Q9V4I1 8 334 1 1 0 302505 302169 1 0 0 0 134 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAET 336 2R:1731127-2080000 -1 NULL:1989061 Q9V4I1 362 478 1 1 0 2605622 303565 303028 1 0 0 0 168 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDA-LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHF----TSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1989063 Q9VQD2 14 201 1 1 0 2605624 303571 302836 1 0 0 0 258 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK---SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM-WQAYLAL-EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRR 735 2R:1731127-2080000 -1 NULL:1989065 P82711 8 263 1 1 0 302583 302091 1 0 0 0 274 partof IRSKSSMVSTKY*KAL-YSSNDFTFFLE-----TLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 492 2R:1731127-2080000 -1 NULL:1989066 P82711 330 500 1 1 0 2605627 303571 302764 1 0 0 0 258 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFA----KWTRNYWADF-RMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD---RQPLQTFLQLYSNAEKPLTDIEI 807 2R:1731127-2080000 -1 NULL:1989068 Q9VFP1 7 286 1 1 0 302797 302581 1 0 0 0 141 partof NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRY 216 2R:1731127-2080000 -1 NULL:1989069 Q9VFP1 293 365 1 1 0 302508 302094 1 0 0 0 185 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDI--KLSVER 414 2R:1731127-2080000 -1 NULL:1989070 Q9VFP1 370 508 1 1 0 2605631 303580 302803 1 0 0 0 264 partof LTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSG--KRHAQDA--LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRL----SQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRM---WQAYLA----LEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 777 2R:1731127-2080000 -1 NULL:1989072 Q9V776 9 282 1 1 0 302505 302124 1 0 0 0 202 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMP 381 2R:1731127-2080000 -1 NULL:1989073 Q9V776 377 505 1 1 0 2605634 303583 302788 1 0 0 0 294 partof LLTALGALSVVYALVKFSL----GYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQL--QLHRRRDRQP-LQTFLQLYSNAE 795 2R:1731127-2080000 -1 NULL:1989075 Q9V770 1 281 1 1 0 302508 302085 1 0 0 0 265 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1989076 Q9V770 360 501 1 1 0 2605637 303583 302737 1 0 0 0 328 partof LLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVL 846 2R:1731127-2080000 -1 NULL:1989078 Q9V774 6 295 1 1 0 302505 302091 1 0 0 0 282 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989079 Q9V774 365 504 1 1 0 2605640 303583 302803 1 0 0 0 277 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAY-KGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQT---INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQ--AYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 780 2R:1731127-2080000 -1 NULL:1989081 P33270 6 274 1 1 0 302941 302563 1 0 0 0 165 partof FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPLQTFL-QLYSNAEKPLT--------DI-EIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 378 2R:1731127-2080000 -1 NULL:1989082 P33270 229 367 1 1 0 302505 302091 1 0 0 0 270 partof ETLRLHTPHPFLLRRATKEFEVPG-SVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989083 P33270 367 506 1 1 0 2605644 303583 302875 1 0 0 0 200 partof LLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG--RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQ 708 2R:1731127-2080000 -1 NULL:1989085 Q9V9L1 2 248 1 1 0 302412 302091 1 0 0 0 178 partof GNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 321 2R:1731127-2080000 -1 NULL:1989086 Q9V9L1 398 505 1 1 0 2605647 303583 303028 1 0 0 0 266 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL---QTINISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1989088 Q9V773 4 193 1 1 0 302505 302091 1 0 0 0 278 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA-PSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989089 Q9V773 362 501 1 1 0 2605650 303583 302566 1 0 0 0 163 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGK-RHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL----GEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYF-QKVALSQLQLHRRRD-RQPLQTF------------LQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1017 2R:1731127-2080000 -1 NULL:1989091 Q9VJ71 2 338 1 1 0 302505 302094 1 0 0 0 150 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEE------QARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRL-LLMPKSDIKLSVER 411 2R:1731127-2080000 -1 NULL:1989092 Q9VJ71 339 483 1 1 0 2605653 303583 303028 1 0 0 0 167 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQIS-------SRIQRDL--GEKSLQTI-NISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1989094 Q9VRB3 7 204 1 1 0 302505 302097 1 0 0 0 173 partof ETLRLHTPHPFLLRRAT----KEFEV--PGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 408 2R:1731127-2080000 -1 NULL:1989095 Q9VRB3 376 518 1 1 0 2605656 303583 302635 1 0 0 0 189 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLW-GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS---RGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQ---DN----VEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKA 948 2R:1731127-2080000 -1 NULL:1989097 Q9VMT6 7 338 1 1 0 302505 302106 1 0 0 0 172 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ---ARRS-RPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 399 2R:1731127-2080000 -1 NULL:1989098 Q9VMT6 356 496 1 1 0 2605659 303583 302734 1 0 0 0 312 partof LLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ-LYSNAEKPLTDIEIAGQAFGFVLA 849 2R:1731127-2080000 -1 NULL:1989100 Q9V771 3 297 1 1 0 2605661 303586 302566 1 0 0 0 403 partof TLLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKR-HAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWAD---FRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD--RQPL-QTFLQLYSNAEKPLTDIE-IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1020 2R:1731127-2080000 -1 NULL:1989102 Q9V4U9 2 351 1 1 0 302505 302085 1 0 0 0 307 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 420 2R:1731127-2080000 -1 NULL:1989103 Q9V4U9 352 492 1 1 0 2605664 303586 302533 1 0 0 0 212 partof TLLTALGA-LSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTD--AGHFTSRGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTP---ANMQKLLVRLS-QISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGLVGQ---DN-VEFAKWTRNYWAD-FR-MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDR-QPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNGEYQILKSSL 1053 2R:1731127-2080000 -1 NULL:1989105 Q9VMT5 5 367 1 1 0 2605666 303586 302737 1 0 0 0 289 partof TLLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLG---EKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVL 849 2R:1731127-2080000 -1 NULL:1989107 Q27594 4 295 1 1 0 2605668 303595 302563 1 0 0 0 1779 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1032 2R:1731127-2080000 -1 NULL:1989109 Q9V979 0 344 1 1 0 302505 302082 1 0 0 0 724 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989110 Q9V979 344 485 1 1 0 2605671 303595 303028 1 0 0 0 221 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFL-WGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1989112 Q9VCW1 0 192 1 1 0 302505 302082 1 0 0 0 213 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV-ERVDKL 423 2R:1731127-2080000 -1 NULL:1989113 Q9VCW1 375 514 1 1 0 2605674 303595 302566 1 0 0 0 390 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGE---KSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM---WQAYLALEFPLIARL-LQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAE-KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1029 2R:1731127-2080000 -1 NULL:1989115 Q9VMN8 0 348 1 1 0 302505 302088 1 0 0 0 274 partof ETLRLHTPHPFLLRRATKEFEVP----GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA--PSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1989116 Q9VMN8 349 492 1 1 0 2605677 303595 303028 1 0 0 0 225 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT---INISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1989118 Q9W223 0 188 1 1 0 302508 302094 1 0 0 0 191 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989119 Q9W223 374 510 1 1 0 2605680 303595 302548 1 0 0 0 222 partof MHRTLLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRG---LYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTP-------ANMQKLLVRLSQISSRIQRDLGEKSLQTINIS-ELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALE--FPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTP-ECLRELRYTKQVLNGEYQI 1047 2R:1731127-2080000 -1 NULL:1989121 Q9VYT8 0 361 1 1 0 2605682 303598 302836 1 0 0 0 223 partof LMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYT--AYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL---GEKSLQTI--NISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA---YLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRR 762 2R:1731127-2080000 -1 NULL:1989123 Q9V674 1 267 1 1 0 302505 302082 1 0 0 0 179 partof ETLRLHTPHPFLLRR-ATKEFEVPGSV-----FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1989124 Q9V674 369 515 1 1 0 2605685 303604 302803 1 0 0 0 260 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQL 801 2R:1731127-2080000 -1 NULL:1989126 Q27593 0 274 1 1 0 302782 302563 1 0 0 0 171 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1989127 Q27593 294 367 1 1 0 302505 302091 1 0 0 0 302 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989128 Q27593 367 506 1 1 0 2605689 303604 303028 1 0 0 0 173 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEP---LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 576 2R:1731127-2080000 -1 NULL:1989130 Q9V419 0 197 1 1 0 302505 302091 1 0 0 0 185 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ--ARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1989131 Q9V419 362 505 1 1 0 2605692 303604 302731 1 0 0 0 232 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT-------INISELVGAYNTDVMASMAFGLVGQD----NVEFAKWTRNYWADFRMWQAY---LALEFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRDRQPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAG 873 2R:1731127-2080000 -1 NULL:1989133 Q9V675 0 303 1 1 0 302508 302094 1 0 0 0 238 partof LETLRLHTPHPFLLRRAT--KEFEV-P-GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1989134 Q9V675 372 514 1 1 0 2605695 303604 302833 1 0 0 0 304 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG-RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSQLQLHRRRD 771 2R:1731127-2080000 -1 NULL:1989136 Q9VB31 0 265 1 1 0 sim4 1.0 na_DGC.dros 1.0 2003-04-03 17:11:21 Fly cDNA Sequences DGC genomic 2597304 324081 323527 1 0 0 0 99 partof GGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCC-AAATAAAATGCCGAAATACCT 554 2R:1731127-2080000 1 NULL:1982065 LP01956.3prime_revcomp 0 555 1 1 0 2597307 333417 333374 1 0 0 0 100 partof CGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA 43 2R:1731127-2080000 1 NULL:1982067 GM15292.5prime 0 43 1 1 0 334038 333679 1 0 0 0 98 partof TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGC-AAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA 359 2R:1731127-2080000 1 NULL:1982068 GM15292.5prime 43 403 1 1 0 2597311 335037 334230 1 0 0 0 99 partof TCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTC 807 2R:1731127-2080000 1 NULL:1982070 GH04835:contig1 0 807 1 1 0 335244 335056 1 0 0 0 100 partof GTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTA 188 2R:1731127-2080000 1 NULL:1982071 GH04835:contig2 807 995 1 1 0 335473 335308 1 0 0 0 99 partof TACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCGTA 165 2R:1731127-2080000 1 NULL:1982072 GH04835:contig2 995 1160 1 1 0 335907 335545 1 0 0 0 100 partof TTCTCTTGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCCGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAACACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGTTAAGCCC 362 2R:1731127-2080000 1 NULL:1982073 GH04835:contig2 1160 1522 1 1 0 2597318 336407 336221 1 0 0 0 100 partof TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGTGTTTTTGGTA 186 2R:1731127-2080000 1 NULL:1982075 LP02831:contig1 0 186 1 1 0 337692 337500 1 0 0 0 100 partof ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCGGTA 192 2R:1731127-2080000 1 NULL:1982076 LP02831:contig1 186 378 1 1 0 338397 337755 1 0 0 0 100 partof TACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCAGGCCACATGCA 642 2R:1731127-2080000 1 NULL:1982077 LP02831:contig1 378 1020 1 1 0 2602498 1933 1282 1 0 0 0 100 partof CAGTAGAACTTGTCCATGAACTGCGCCAGAACGCCGCCATCGCGCGAGTATACCCTATAAGGCTGCAGTCCGGCTGCGGCCGCTCGAAGGTAGCGTTCATCCCCGCCGGAGTGCCAGTAGGCTCGTGCCAGCACTGAAATAGCGTGTCCCTGGCCCATGGCTGATATCCACCCCGGACGCAATTCGGCAAAGCCGTTGAGGCTGCGACGCACAGGATTGGTCCAGCCACCCGTCTTGGGGTCCTGGTTGTGGACGAACCACTCAGCCGCGTCGTAGAAGTGAGCCAGATGGTCACTGGTGGACAAGGTGATATTGTCGAAGAAGCCAAGGCCCAGAAAGCCAATAGATATTACCTCCAGATCGGAGCGCCGTATCTTTAGCGGCGAGCGTTTGTCACCCATGATGCCCTTTTGAAGGTCAATGTGCAGGTCTCGAGTGATGTGGCGCCACTTGTTCAGTGCCGAGCCTCCCAGACCGTAGTAGATGTTTGTATCCTGCACGCTCAGCAGCAGATCTGCGGGTATGTAGTGCAGGCTGTAGTTGTGACGGGTGTCCCGATTCTGAACGGTAATCATGAGACTACTGCTATTGGTTACCAGGAGCAGATCAACGCTGAGCAGAAGATCCAATGTCTGGTTTAGAGCAATGCTG 651 2R:1731127-2080000 -1 NULL:1986339 SD14112.5prime 0 651 1 1 0 1173 1114 1 0 0 0 100 partof GTGAATAGATAAAGCCGTTTAGCACATAAGAGGGTGGCGTGGTGGGGTACTCCTCGTACCTG 59 2R:1731127-2080000 -1 NULL:1986340 SD14112.5prime 651 710 1 1 0 2597323 342110 342030 1 0 0 0 100 partof ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTTAAAGTCGAAGGTA 80 2R:1731127-2080000 1 NULL:1982079 RE12209:contig1 0 80 1 1 0 342891 342807 1 0 0 0 100 partof ACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCGGTG 84 2R:1731127-2080000 1 NULL:1982080 RE12209:contig1 80 164 1 1 0 347117 346787 1 0 0 0 100 partof GTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGGTCTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTAT 330 2R:1731127-2080000 1 NULL:1982081 RE12209:contig1 164 494 1 1 0 348137 347502 1 0 0 0 100 partof CGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGAAATTTATGAATAAAGCATTTACTATGTATTTATATACC 635 2R:1731127-2080000 1 NULL:1982082 RE12209:contig2 494 1129 1 1 0 2602502 10161 9824 1 0 0 0 99 partof CTGGTAGCAGTTTTTTGAGGTAACCCGGATCCAAGGTGGGCGCCACGTCACGCTCCTCTATATTAGTGCCGTATTGGCATATATAATCAATCACTTCCTTGCCGTATTTGCGAAACTCTTCCACATCCATTTTCTCTAATTTACACTTTTCGTTTATCTTCTTGTTCAAATAAATTGCAGTCTATTAAGAAGTATCTGTTGGTGCTTGGTGCTTGTATCTCTAGTGCTCGGATACTAGGCTCTCACACGGTACACAGTAGCTTATCTCGATCACTTTCGAATCCCGGTTATCTCGCACCGCACACTCGTTGCAGGTCAGCTTCCTTGACGCGAATGT 337 2R:1731127-2080000 -1 NULL:1986342 RE04135:contig1 0 337 1 1 0 8836 8713 1 0 0 0 100 partof AGTTGCCCGAGGGGAAGTAGGCGAAGAACTTGGGGTGGTTCCAGTGCACCACGCCCGGCATGATCTTCTGCTCGAAGTCCTCGAGCACGTCCTTGAACGGCTCCGGCGACTGGGGAGCGTCGGCTG 123 2R:1731127-2080000 -1 NULL:1986343 RE04135:contig1 337 460 1 1 0 7375 6775 1 0 0 0 100 partof CCGTTGGATTGTGTTTGTATTTTTTAAAAACTTGCATAAAAAATGCCGAGATAATGTTTATAAATAAGTGCTTTTGTTCATGACAGTAACTTAAGGTAGCTAAACGGTATAAGCAGATGCAAATGAGTCTATCTTTAAATTACATGATATTCAGCAACAACTAAGGTCCTACTAGTACATAAATGGATGTTCTTAAATTCAAACTGAGCAATGTTAGTCGGTAGTCGATTGATTCATGCCTCATTTCAGCTCGACAACTAATACTAGGTAGAGGTAAATCCGCAAATCCCTTTTCGGGTCGACGCTCAGTTACTCGCCTCGTCCGTATCCACGTCTGATATATCTTTGAGTTTTACGTTGCCATTGCTGTTGTTCCTGTCATTGTCATCCGCCGCCTTTTGGAAGTTCTCCTGAAGAGTTTTGGGATCGACGACCAGGATGGGTGTGCACCCGTCCATTAGGTGCTCGCTCTGGCTCTGGTACTGCTCCCGCGAGATGCTGCGAGTGAAGGAGAATCGCAGCGACTTTGTCCTGGTCAGCCTCTTTTTGATGGGTGGCTTGCCCGCCACTGGAGCCAATGGCTCTGAGCTGGTCCGCTCT 600 2R:1731127-2080000 -1 NULL:1986344 RE04135:contig2 460 1060 1 1 0 2602508 26379 26114 1 0 0 0 100 partof CTTGGATTTTGTGCCTGGCCGGTTCCTACGCAATATGGTCGAGCCGTCAGCCATCTTCATGTTTCACCCGCTCGAAGACGCGATGATCCACAACGTCTGTGCCTACGCCTTGATGAGAAAATCACTGGCAGAAACTGAATGCTAGCCTGGTCCCTGCCCCGCGGGAGTCTCCGGATGTGGGATCCCTGCACCGTAGTATGCTGAGTGTATTCTACAGGAGCTGGCACATCGCTTGACAATTAATTGGCGTTTATCCTCCAAAACA 265 2R:1731127-2080000 -1 NULL:1986346 LD21194:contig1 0 265 1 1 0 26040 25666 1 0 0 0 100 partof CTGCTAGGGAAGTACTTGTTGCTGTTTAGCAGACAGGCGGCACCGTCCAGCGTGTGGCGTGTGTAGTCAATGGCCGGACATTCCTTGGGCGTCTTGTGCGCGGCGCACAGGAATATCCACTGGTCAGTGGCTGTCATCTGGGTGCACGTCGACGGCGAGCACTCCTTCTGCAGCCGCACTGCCAGGCCGTTCAGCTCCATGCAGAACTGGCGCAGGTGCTCGTACTTCCACACGCCCTCATCCTGGGCTTCGGGCATGGTCAGTATGAGTTCCACGTTGCTCGGGTCGCGCTTAATCAGCTGCTGTATGTACTGCTGCACCGCCAGCGTGCTGTCCATCTCCTCCAGGGGCTCGTCGGGCCAGCGACAGAAGTCCTG 374 2R:1731127-2080000 -1 NULL:1986347 LD21194:contig1 265 639 1 1 0 25606 24888 1 0 0 0 98 partof TGGCACAGATACGTCTCGGCCTCGAATTCGTCGAAAATGCGACGATGGTGAAAGTAGGCGTGCGAGAAGATGCGATACACCCGCCGACATACGGAGCCCAGCTTGGTTACCGACGACTCCTTGATGGAC-ACCCTG 718 2R:1731127-2080000 -1 NULL:1986348 LD21194:contig1 639 1357 1 1 0 2602513 45640 45068 1 0 0 0 100 partof CTCTTCGTCGAATTTGTTAGCTGTTGTTTTATGAATTTCTGCCGCCCGTCTTGCACAGTGGGATGAAATCGCTGTAGCACACGTCCAAATCAGCTGGCTTATATATGTATGTACGATTAGAATTGGTTGCGGGTGACACTCCAGAACGCCAAGTTGCCAAACACTCTTTATAGGCGATATTACGCACACTCAAGTTCCCGTGGAAAGTTATTATCTATCGGCTTCGCCCTGGGTCACGCCCACTGTACGGGAGTTTCGATTTTCTGCGGGGGAGGTGGGACAGTGACAACACCGCTCGGCGGCACAAGTTCAACAGAAAATGTGGGGCGACCGGAGGTCGTATAAACAAAAGCACAGTGCACCCGAGTGCGGAAATCGCGGCTGTAAGTGCTTCAAATGCACGCAGGAGTCGGGAATCGGGGAGGAACTTTCGATTCACCCAATCGCTGGATTTCAATTGATTACTTAACACGCTCTGTCGCGAGAAAAATAGGCTATCTCTACTGCCGCGGCCCTTAAAAATATAGAAAAGTCGTATAGTCCACCACACTAGCACCACACGTCCGTTCGCA 572 2R:1731127-2080000 -1 NULL:1986350 LD30953:contig1 0 572 1 1 0 30685 30656 1 0 0 0 100 partof CACCTGCCCGTATACTCGTATATGACGCCTGC 29 2R:1731127-2080000 -1 NULL:1986351 LD30953:contig2 572 601 1 1 0 30592 29995 1 0 0 0 100 partof ACGTTACATAGATTGTTGTTTATTGTATTCCCTTTAATTAATATTCGTACGAAATGTAAGGCAATTAAAACTATTTTTCTAAATTTTGTAAAGAAGACAATTGAGGGACCCGTTTGCACCTGGCAGTGATGCACTGCATTGATATTGATTGAAATTGAACAGTTTGTCTAGACAAAGATGCGGTTAGTAATTGCCCTAGTGCGGTAAGTATATGTTAGGTGTATATTGATACTTAGCTACGATTAGTCAAGTCAAGTATAGTCTTACAGGCTAGAGCTTAGGAATAGGCTTAGTTTCAGTTACAATTCTGCTCTGATTTTATGGCTGCAACACCATTTGACATAAGAAACTCGTTAACATTTAATGCTAGTCCATTATTATGCTACAGTTCGGATTTGTAGTACCTCCAGTTGCCTTCTACTTGCGGCGTTCAACAGTGCAATGTAAGTAACCTAGTGTAAAAGTTGAGCTTTTTTAGTCTCTAAGACATCACTATCACTCTCCTTAGGTGCTTTCTTTTCACAGAACTCGATCAGATACGAACAGACACCAGAGAGTGCGATAAATATTCCAGCATAATAGAAGGTGTCATCCCAT 597 2R:1731127-2080000 -1 NULL:1986352 LD30953:contig2 601 1198 1 1 0 2602519 47582 47103 1 0 0 0 100 partof GCCC-GTGCACAGCAGCATCTCCGCCAGAGCGAAGGGCGTCTTGACAAGCGAGCCGCATTCCTGGAGCGCTTCCACCACCTCGATCACCTCGGGCAGCATGTGCAGGAAGGTGGTGCAGATGAGCACACCGCCGCCGAAAAAGAGTAGGCACCGCACCACCAATGACGAGCGGGTTTCCTCCGGACTCGCCTTCGTCCAATGGAAGCACCTGTTCAGGACGTAGGGAAGGCTGCCGCAAAGCACGGTGATCACCACGAGCACCACCATGGAAACTATTTTGGCCACCAGCAGCGCATGGTGATCCACGTCTTGCGTTTGCTCTTGTGACATAGTTGCGGTAGCGCTCATCTTCACCTCCCGAGTTGATAGCTTCGACTGTGCTGGCTGGAACTCACAACCAGGCTAATGGTTTATATTTCCAGTCATATATCAGCGGGAGCCGATTGAAATCTGATCGCTGATTGATACGCGGATTCACT 479 2R:1731127-2080000 -1 NULL:1986354 RE15841:contig1 0 479 1 1 0 46722 46433 1 0 0 0 100 partof 289 2R:1731127-2080000 -1 NULL:1986355 RE15841:contig2 479 768 1 1 0 46357 46116 1 0 0 0 100 partof AAAGTAAAATATTGTCTCTTTTAATCCATATGGTTATTACATTTTTAATTATTTGCGTTGGATAAGATTTCTGAGAAACCTCTTTTGAAATTCTATTCGTATTTTATATAATAACTTTTACAGATCCCCAGGGAATCGTTTTGTATACTATTTTGTTGCTTCCTCTATAACTTGATAATACTGAAGTGGCGTCACACTGGCTAGGAACAGGTTAGGCTGTCATCACCCTCCGCTTCGTCAG 241 2R:1731127-2080000 -1 NULL:1986356 RE15841:contig2 768 1009 1 1 0 2602525 70444 69813 1 0 0 0 100 partof ACCAGAAAACGGCCACGTAATCCTTGTCGGCCAGGAGCTTCTCCAGCTGCTTGGCATTGACCTCCTCGATGACGGCCTCCGGCTCCGGAGGCGCCACTGGCTGCGAGCCCTTCTTGTTGTTGTTGTTGCCTGCACCACTCACATGTCCGGGAAAACTCAGGGCCAGCAGAGCACACACGAGCAGCGAGAGAGTCTTGAGGCGGGTGAAAGTCATCCTGCGATCGGTTACGGTTCTGATGTGCTTTAGGCCCTTAACGCGAACATGCGTGCGCGTGTCTGCTCGTTTTGGTGTGTTCTACAGTTTATAGTGTTATAATTGTATAATTGATTCGTTCTCGTCGTTTGGGGTCTTTCGTTATTAAAATTTGTATTCCTTTGAGAATCGGTCACTATTTTTAGTTGATAATGGTGTTTCTTCTTTCGCAATTTATTTTATGTATAACAACTTTTTGTTCACTGATACATATATACGGGGTTCGTATATGCACAGGCGAGATATATGTGGGGTATATACGAGAATAATTAGATTATATATGTGGTTTCTTGCTTCTATTAATTGAACGTTTTCCGCGGACTGTACTCTTTGCTCTTCAGATTTTGTTCCACTCCGTGCAGAGGTCCGCTCGCAACT 631 2R:1731127-2080000 -1 NULL:1986358 RE34119:contig1 0 631 1 1 0 68130 68069 1 0 0 0 100 partof TCATCGTCGATTTTCTCGAGTTCCGCTAAAACCTTATCACAGGTCACGCAGCTTCGCGCATCTG 61 2R:1731127-2080000 -1 NULL:1986359 RE34119:contig1 631 692 1 1 0 57304 56614 1 0 0 0 99 partof GAGTTGGATGGCTTTTATTAAATATTCTTACAATTTCATTCGGGAGCTATGTTTACAAAAGTGCTTTATGTCGATTTGCGTTTGATTTTTACGATCTGACAATTTCCATTTCGAAAATCTTGACTTATCAGCTGCTGTTCAACAAAATTTGTTTACATATATGTTGGATTTAGTTACAATTGCGTTTAGATTGGTAGGCTTTAGCTTAAGAAAACATAATGATAAAGATTTCTAATTCGATATTTTTCAAATACCGATAACAAAAACAACAGCGAGCGGTACAGAAATCGCTCTCAGAAGAAAACAAATGAAACAAAATGGCGAGCTACAATATGCGAGGCCATGTTCAGCGAGAAATATTGGATTTTCGATTCCATAACAAAATTAAGTATACGGCCTGTATGCTGCTGCAACATTTCTAAAAAGTTGTGGTTACAAATTATGGTTCCTCATGTTGTTATTATGAAAACTTATGAAAGTTGAAGGCTCTCATAGTTACACGTTTCAGTTAAATTAGCTAACAGTTGTGCACTGTCAGGTGTAAATTGTTTCAAAAAATATTTTATGCGTTTGTTCGTTCGTTTACTATGCTTTGGCCCTTGTTTAAATTAGACTAACTACATAAATGTAAATTGTATATTGCGACAAAAAGAAGTAGTATCAAAAAAGTTTAGGCGTTCGTTATTGACA 690 2R:1731127-2080000 -1 NULL:1986360 RE34119:contig2 692 1382 1 1 0 2602531 75644 75028 1 0 0 0 100 partof AACGCGGACCCCAGCGATCGGTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCCAATGTTTATGCTTGTCACGTG 616 2R:1731127-2080000 -1 NULL:1986362 AT06844.5prime 13 629 1 1 0 2602534 86795 86694 1 0 0 0 100 partof CTTGAGCAACCAGGATGCCCCCAGGTTCCGTCTTAGTATCATTGACATTCTAACGCTAATTTATTTTTGTTCTCTTTATTTAAGCTGATGATTGCAGTGTC 101 2R:1731127-2080000 -1 NULL:1986364 RE40412.5prime 0 101 1 1 0 86632 86487 1 0 0 0 100 partof CTTTGTCCAGGTGGATCTTGAAGGGGCGCTTGTCGAAGATCGTACCGTTCTCCTTTTGCAGAACGGCCGTTTGCTTATCCTCGAGCAGGTTACTGGGAATTGTTTTGGCCGAGTCCACCGGTTTTGCGCTGGAACTGTAGCATGCCTG 145 2R:1731127-2080000 -1 NULL:1986365 RE40412.5prime 101 246 1 1 0 86411 86317 1 0 0 0 100 partof CTCTGCTTGATCTTCAGGAACTCGTTCTTGTGCATTCCATCGCAGAGGGGCTGAGACTTGGACTTGCCGCACAGGCACCAGCTGTATGTTTTATCTG 94 2R:1731127-2080000 -1 NULL:1986366 RE40412.5prime 246 340 1 1 0 86256 86099 1 0 0 0 99 partof CACACGGGCAGGGCCCTACAACCAATCCTAAATCTATTTGACGGCGCTCTGGATGTGTGGCTGCTTGTGGGTGCCGTCACAGAAGGGTCTGTGGGTGGTCTGTTTGCAGTTGCAGAGCCAGTAGTCTCCCGACTTCTCCACCTTGAACCGAATGGGCCTG 157 2R:1731127-2080000 -1 NULL:1986367 RE40412.5prime 340 497 1 1 0 2602540 88661 88092 1 0 0 0 99 partof CCAGATCCACCAGCTTCTCCATCTCGCGCCAGGTGTCCAGATAGTCCACGTCCGTCAGCTCCAGGGTTCCGTGCACGTTGCTGTCATTGTGGAACTTCTGGCCCACCGGCATGTGCATCAGGTAGAGGTCTACGTATTCCAAACCCAGGTTGCTAAGGCTCAGGCGGCAGGCGCGCTCCACCAATGCAGGGTCGTGGTGGATTCCGCCTAGCTTGGTGGTCACGAAAACCTCCTCGCGTGTGACCACTCCCTCGGCGATCTTCTCGGAGATCGCCTGGCCCACCTCAGCCTCGTTCTCGTAGACGAAGGCGGTGTCCAGGTGCCGGTAGCCCACGTCGAGGGCGTGGCGCGTTGAGTGGTAGGCGTCCGACTCGAACGACTTCCAGGTGCCAAGGCCCAGAGTTGGCATCTCGCGCCCGTTGTTCAGCCGGATGGTGGGAGCCAGATTGGTCATCTTGTCGCTGGCGCTGATAATTAACGCTGTGCAAATTGGACGCTTCTAAGTCTAAACCAGTGCTACTACGCCTTTCTCGCGATCAAATCTCTATCTGTTCCAGCTCGTCGAAAG-C 569 2R:1731127-2080000 -1 NULL:1986369 LD24696:contig1 0 569 1 1 0 87870 87375 1 0 0 0 100 partof CTACGTAATATACTTTATTTTACAATACAAATACTACATATGCGGGGTGTCTTACGAACCTCTTCCAGTAAAATATTAAGGGGAATTAATGCACGGGTTTACTCGAAACCTTTTTAACTTTGAGTTAACAACTAAAACAAAACACCCCTCTTGGAATGCCACAGTCGTTTTGTTTGCATTCCTAGCCAATCCAATAACGGCGAAACCGATATTTCTGGGACACCCCTGAGCCCGTCTAGAACTCGTCGTTGAACGGGTAGTACTTATGGCCCGACATTCCCGAAAAGGGTACCGTGCGCTGCCCGGTGTGATACTGCTCCATGCCGGCGACGTCGTCTGGACTCAGCTCGAAGTCGAAGACGCGGAAGTTCTCCTCGATGCGGGCCTTGTTCGACGACTTGGGCAGTGGCACCACGCCTAGCTGGACCAGATAACGCAGGCAGATCTGTGCCGTGGTGCGGCCGTACTTCTTGGCCAGATTCTGGGCATGCTCGT 495 2R:1731127-2080000 -1 NULL:1986370 LD24696:contig2 569 1064 1 1 0 2602545 118781 118236 1 0 0 0 100 partof CAGAGGAGAATTCGCTGCTCTTTCCGCTGCAACCTTCCAGCAGATTTAATGAATGAAATCAACTTGAATTAAATTCCTCCATATTGCGGCTTTGTTTCTGGCTTTATTTGTTTACACACACTGCAGCTGTTGAATCACCAGAGAGGCGAGAAATGTGTTTTCGGCTGCCTTGCTTTGTTTCGCTTGGAAGGTAATAAATTTTTAACACAATTGCATTGCATAAACAATTTCAAAACTGCACTCGAAATGGGCCTGTTTACACTCCGTTGTCGTGTCGATTACATTTTTGGCCAATAGCCAAGCACTCAGATTTAACTGGTTTATTTCGACTTGGCGAACGCCCGCGCGCGAATCTTTCAGCACAGCCCACGCACTTTCTGCAGCATGGTTAACTTGAAGATACTCGAATCGCACAGGGAAACAGATACGGATGGGCTCCAATGGAGGTGATATAGAGGCGTAAACAGAGGCAGAGATTCAAACCGAACCGAACCAAACCGAACTGAACCTCTGGGCCAGCGATCGAGTTGTGCGCCGCTGGAGAG 545 2R:1731127-2080000 -1 NULL:1986372 GH01501:contig1 0 545 1 1 0 103561 103415 1 0 0 0 100 partof TCCCAGATGAGTCGAAAGTCCTGCTGCTCCACCCGCAGCAGCTCGCAGGTGGTCTTCGTCACTACGGTGCTGTCCCGCGGCAAGTCATGCAGTACGGACTCCCCGAATGTGGCACCCACGCCCAGGTTGCACAGAGTAACTGCGCTCTG 146 2R:1731127-2080000 -1 NULL:1986373 GH01501:contig1 545 691 1 1 0 99134 99082 1 0 0 0 98 partof CGTTCTTCAACTTGCAGTTGGTGAATATGTCATTCATTAACTCCTTGTTTTTCTG 52 2R:1731127-2080000 -1 NULL:1986374 GH01501:contig1 691 743 1 1 0 92430 91687 1 0 0 0 100 partof GTGTGTAAATAAATATTAATAAATGGTTTCGTATTTTATTTCCAAGTTGCCGTAAAAGGAGATGGGGTGACGGAATACCAAATGAAAATAAGATTGAAAACTATAAATAAAGTAACTTATCCGCTACGTAGCTTACTTGTTAATAACTAGCTGTAACTAGACTGTTTAATAGTTGGTTTTAGTTTAGGGTTTATAAAAATATAGATTCCATGCTCTCGAAAACGTTGTACAACTTTACAAATTATTCTACCAGCTCGCGCGGGATTTATAGAGTAATGGTTTGTGGGAAATTATGCTGTATAGTTGTGTTTGTTTTGATGTTGCCTCCTATAAATGTTTAGTATCACACACGTCCAAGTTTAGTTTTTATTCGTTTCGGTTTCCGCGGGGAATTGCCGAATTTCAAATTGTTTTCCATCTTTTCCATCGTTTTGTACTAAAGCAAAAAGTTTCTCGTTTGCATTAAAATGCGTTTGGGTTTCAGTTCATTAGAAGATTGAGATAGTTCCTAGTCGGGTCGTAGATATAGTACACTGTAGCTTAGGCTAATGCGGATGCGGATGCGGACGAAAGTTGGTCCGGGCTGTGGTGGCCGTGGCCCAATTGGCTTTCGGAAAGCAACAACAACCCGGCTAAGCTCATAACTGTGCAGCTAATTGCGGTTGATTAACACACACTAGGGTTAGACACTTAATACGCGCTACAGGCTAATTGGATGACAGCTCCACAAGGGCTTAGAGCTT 743 2R:1731127-2080000 -1 NULL:1986375 GH01501:contig2 743 1486 1 1 0 2602552 168702 168032 1 0 0 0 100 partof GATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGGCATTTCGAAACATGGCTCTATTTCATTTCAGTGTTTGTAATCCTATTTGCAAAAGGTAAGACTGCGAGTTAATTAATGCCGTGCATCATTGTCCATAATGCGGGCGAATTGGTCCACCGGCATACATAAATCATGTAGCCCAAGGTTGGTGCAACATTAGATACATATATTCCTCTTATGATGGCTCATACATGGGTGCTATTTACTAAAGTATCACTTTACTCTTTCCATCCTGCTAGTCGTCTTCGCTGCCGGACTCGAAGCCTGAATCCTCTTCGAGTTCGGCTAGAATGAAGGCTTCTATGGCCATCTGCAGGGCAAGGACGTCTCCTTCGCCAGGATCGGGTCCTTGCAGCATGGCCGTCGGTGGACCCGCGTAGTGGGAGAAGGCTTCGCGCTGCCTGCCCAAGGACCGCACCGCGAGCTGGTTGTCCCCTCCTCCGTCCATCTTAGTGGGTCCGGTGCAGGGCTATTGGTACCCGATCGGAGCTGGAAGTCGGCTGGAAACAAATGATGGCGCTTGGGCGCTGGGCTTGTGTTTTTTGGAATTTTGAGTATATGCTTTTCGATCGG 670 2R:1731127-2080000 -1 NULL:1986377 GH16767.5prime 0 670 1 1 0 2602555 202544 202308 1 0 0 0 100 partof TTTATCTATCACTCCACTCACTGGGGCCAGCGCATTCAGCGGGATTCAACTAGAGATTTTGCACACGACTCCGGCTGGAAACTTAAGGCACTTCTTTTCAGACTTTTCAGTCAGCAGAAAGACGGGACGAGTACAAAATGCCGACGAGAGCGCGCTGAGCATCTAAGAGCAAGTTCGACACTGTTGTTCGAGGCAAGTTGTTGATATCAGCGCAGTTCGCGTTCACGTTCACCGGG 236 2R:1731127-2080000 -1 NULL:1986379 LD37992:contig1 0 236 1 1 0 196716 196461 1 0 0 0 100 partof TTTGTTGTGTGGCAGGACGATGAAGGCTCCGCCGCCCGCCGACTCTACGATAATGGCCAGGAACTTGGGATTCACCGCGCAGAATGTGGAGTCCCAGCTGGACTTGGATACCCGTATGTTGTCGTAGCACTGCTCCCGCTTGAGAGCCTGTCCGTAGACGTGGCGGAACTTGGAGCTGCGCACTACGCGAAATGACATCTTGATGCTGCAGTGGCTTGGGTCAGCGATCAGTCCTGAGCTTCTCTACGTCTAGCTCTG 255 2R:1731127-2080000 -1 NULL:1986380 LD37992:contig1 236 491 1 1 0 195149 195032 1 0 0 0 100 partof CACACAGTCCTCTGAGCCGGAGGCGATCACGTTGTCGTTGTGGGGGCACCAGGCGATGTCCAGCACAGGACCCTTGTGACCGCCCACCAAAGGGTGGTCAGCCGCAATGCGACCAACCTG 117 2R:1731127-2080000 -1 NULL:1986381 LD37992:contig1 491 608 1 1 0 192419 191775 1 0 0 0 100 partof ATTAGCACCCAACTTCTTCTGGCATTGTATTTTGTTTTATTCCGTATCAAATTGTAAATTATTTGTATATAGAGTATTTATGTATGTATATGTATATAGTCTTCATTTTACAATGGTTGTGAATTACAAAATCGGTAGGTGTTTAATGACGCTGCTCTCGCCCTCGGTTCTCTAACAAAACTAATGAAAGTAAAATCAAATGAAAGAAAAGAAAAGTAAACAAATTTTTATAAAAATAGTTTCGATGGTTTCTTACTTTCTTTCTGATTTTGTTGCATTTATTGTTACTCTTATTATTTCAAAATACAGCTTATCATTAGTTTGAACAATAAAATTTTGATTACGAAAACGAATTAAGTCCGATGACCCCCATCACTTTCTTACTAAATTCGCTATGTTTGACACGACAATTTGCAGGGAAATGTGACTGATTAAGGGGGCCTCAGCTAGGATGAACAGTATCGATTCTATCAGCTATTGTCATGAAAACTTCCGGGACGTACAAATATACAGACGTTACAGAAAGGAGCTCGTACAAATTTGGTAGGTAGGTGTTAACTCTTAAGTGATTGAGGTTTAGTCTATGATTTGCCTTTGTTAAATTTACAACAATTTCATACTTGCGTAACAACAAGCCGATCAAA 644 2R:1731127-2080000 -1 NULL:1986382 LD37992:contig2 608 1252 1 1 0 2602562 208416 208213 1 0 0 0 100 partof CTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACT 203 2R:1731127-2080000 -1 NULL:1986384 RE31022:contig1 0 203 1 1 0 208133 207651 1 0 0 0 100 partof ATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTG 482 2R:1731127-2080000 -1 NULL:1986385 RE31022:contig1 203 685 1 1 0 207141 206995 1 0 0 0 97 partof CCGTGGCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTGTATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAAATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAGCT---GG 146 2R:1731127-2080000 -1 NULL:1986386 RE31022:contig2 685 831 1 1 0 206508 206370 1 0 0 0 99 partof TTCAAAACTTATTGATTCTTCCCGCAAACAAAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACATGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACATGACCATTCCTG 138 2R:1731127-2080000 -1 NULL:1986387 RE31022:contig2 831 969 1 1 0 206301 205927 1 0 0 0 100 partof AGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTAGTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGTTGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAACGTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATACCTG 374 2R:1731127-2080000 -1 NULL:1986388 RE31022:contig2 969 1343 1 1 0 2602570 208683 208126 1 0 0 0 100 partof CAGCAACCTGTAAGTATCCAAATCGACCGTGGATGAGGTGTGCTCGTTTTCATAAATTTATGTAATTGCAGTGTACTGATGAGTCACCTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACTGAATTCTCTCAGCGAGCGTACATTGTTTTTATACTCGCATATGCATATGTATTCCCCCACAAAACAATGATTTCTCTTCAGTTCGTGCTCCCAAACGGGTTTTTCTCTCGCCTGCCTTCGGTGTTCTCATTGATTTCACTCTTTACATCCATAATGCGTTTTCTTTCACTGGCTTTTTAAAGTCAAACTGCCGGATAACTCACCACATGGCACCAAACGATAATCCATACTCAGTAATTTTGCTTACAGTAAACCTAGTCTGCAAAG 557 2R:1731127-2080000 -1 NULL:1986390 GH21896:contig1 0 557 1 1 0 206146 205927 1 0 0 0 99 partof AGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTG 219 2R:1731127-2080000 -1 NULL:1986391 GH21896:contig2 557 776 1 1 0 2602575 208698 208619 1 0 0 0 99 partof CACATGGCACCAAACGATAATCCATACTCAGTAATTTTGCTTACAGTAAACCTAGTCTGCAAAGCGTACGTAATAGACT 79 2R:1731127-2080000 -1 NULL:1986393 RH55976.5prime 0 80 1 1 0 208133 207545 1 0 0 0 100 partof TGCCCTTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATACATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCCAATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTG 588 2R:1731127-2080000 -1 NULL:1986394 RH55976.5prime 80 668 1 1 0 2602579 261593 260657 1 0 0 0 100 partof CACATCGAACTTATAGCAAAAATGAGAAACCCAAAACCGCGTAAAGTTACTTCGGCAAGCACAAAATGATAAGGATACTTGCAAAGGTACAACAAAGTAGGAAAGTTTTCAAAATAAGGAATCAAAAACCAAAACCAAATAAACCCAAACAAATCAAAATCAAATTGAAACGAAACGAACCCGACAAAGAAGCCGGCCGGGGCGTAATGCACGGCTTGAGATGGGCATTGGCATTGGAAATGCTATTGGCGTGGTGGGGATTGGCTGGGGCATTGGAGCACACATATGGATGGGCGGGTGGTCGGTCACTGGCGGGCAACATCGATGGCCGGGCATTTGATGGTGATGAAGTGGTGGCTGGTAATGGTAATGACGATAGCGATGACGATGATAATGGCAAATGGCCGCGAGGTGATGACGGTGACAATGCCATTGTGGGCGTCTTGCACTGCGTGTGATTGGATGTGGCTGTCTGATTTTGGTTTGGCATTCTATGATTTGGATTCGGGTACGGGTCTGTGGATGCTGTTGCGGTTGCAAATGCAGATGCTGATGCAGTAATATTGGCGGCTTGTTGATTAGTGACATTACAGTTTCTGGTTTGGGGCGACTGTGGTGAGTGTTGCTGTTCTTGTGGTGCTTGCTGCTGCTGCTGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCTGCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCTAGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGCAGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCAGCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGCTGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTA 936 2R:1731127-2080000 -1 NULL:1986396 GH14660:contig1 0 936 1 1 0 258498 258283 1 0 0 0 100 partof CGTCAAAGTGTTGCTGCTGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCCTCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTTGGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCATTGAGCTGTGCAATTAGGTTCGGATTCGCCTTTGGCTGTGTCGGTGGCAGTGGGTGAGCATGTCCG 215 2R:1731127-2080000 -1 NULL:1986397 GH14660:contig2 936 1151 1 1 0 256596 256444 1 0 0 0 100 partof CAGGGCCTTGCTGTTGATGAGATTTCGCACGGCAAATGCTCGTCCAGACATTCCCTGCTTCGCCAGCTTCGCGTTGAGATTCTCGAGGAATTCGGCCTTGGTCTTGGCACGAATACTGCCAGTCTTTTCGATATTTGTGCTTGTGGCATAGTCTA 152 2R:1731127-2080000 -1 NULL:1986398 GH14660:contig2 1151 1303 1 1 0 256073 255511 1 0 0 0 100 partof TCGAGTGTTTGTTAAACTCATATTCATATGTATGTACATAAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATATCTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAAACATAAACATAACTGTCTTCCATATTGTATTCACTTAACAGAGAAAGCCTTTCGACACATTTTTGGGATACAGGAAATCAAGAAAGGTATTGATTAGTTCGATTTATGCTTAATGCTCCTGTTAAATATCGTATATCGAATATATATTATATATCGTAATCATATGTATTTAAGTTGTATGCTGTGTTTCGAGTTTTCAGTTTCAAACCAAACTCTGCAGAGCCCTGCAGTCGAGCAGGCGTCGGGCCTCATGATTATTCATAGATTAATTATTATGGTAATAAATATGCTGCTTCGCTTAGCCTATAGGTTAATTCAATGTATCTTGGGAGCGCTGCGATCGTTGATCTTCTGGTTACGCTTTAAGGTGGCTCCGCGCTTGATTTGATCCATCAGCGATTCGTGACAGATGCGAGGGTCCGGCTG 562 2R:1731127-2080000 -1 NULL:1986399 GH14660:contig2 1303 1865 1 1 0 2602586 301319 300798 1 0 0 0 100 partof TTCTAGCATTGCATTTCCAGGCGGCAAAAGCGCACACAAAGGATAGAAGCGGTTGTGAGTGCGAGCGGGGTGTATTCTCCCGTTATTCCCCTCTATTTCCTCTCTCTCCTTCTTACGCCCAGTTTCGTGTGCTTTGCTTTTGCATTTGCTTTTCTTTGCTTTGTTCAAACTCAAACAAACTACCCCAGAACCGTTGATCCTGACTGCCTTGTTGTTGCTGCTGCTGCTGTTGTTGTTGTTGTTTTGTTTTCTGTTATGTTATACACTCACAGACACACGTACACACACGCACACAGTGGGCTGGCAGACAGACGCTTAATTTTCCGTTTTCCTCGGGAAATCGCAAACAATTATTCGCTTATTTTTGCACCGAATCTGACACTTATATGCTCGCACTTCGAACTGCACTTCCAATTGGTTCGCGCATTCCTTTTCCGGTTAGAAAACAGTTAGAAGTTTGCCGCTGCAACCGCTATTTTCGCCAAGTCTACGACTGACTTTCCGAGCGCATTTTCGTTTTC 521 2R:1731127-2080000 -1 NULL:1986401 LD28616:contig1 0 521 1 1 0 255687 255476 1 0 0 0 100 partof ACGATAAATTCCATTTATTAGGCGTCAGATTAGTTTCGAGTGTTTGTTAAACTCATATTCATATGTATGTACATAAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATATCTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAAACATAAACATAACTGTCTTCCATATTGTATTCACTTA 211 2R:1731127-2080000 -1 NULL:1986402 LD28616:contig2 521 732 1 1 0 2602591 304761 304721 1 0 0 0 95 partof CTTGGGCAGCCGTAATTTGTTTTGTGAAAGTGAAATCGCA 40 2R:1731127-2080000 -1 NULL:1986404 SD07915:contig1 0 40 1 1 0 303775 303482 1 0 0 0 100 partof AACTTGGGCTTTTCGTGCAGGATCCCCCGCCGTTTCCAGTAGCCCAGACTGAACTTGACCAGGGCGTAGACCACTGACAGCGCACCCAGGGCGGTGAGCAGGGTGCGGTGCATTAGATCCATGCTCACTCAGCTGTCTTTTCCGGCTTTTACAATATGTTCGCGCTGTTTGATATGCTTAACAGCTGGCAGTAGCTGCTTGTCGAGGTTCTGGGGCTCAATGCCGCCGGTTTATCAGCGCCATTATCGTGCGGTCCGATTTAATAATTGATAAGGTCCATTGAGTATCGGCCG 293 2R:1731127-2080000 -1 NULL:1986405 SD07915:contig1 40 333 1 1 0 302448 301886 1 0 0 0 99 partof AACAACTAAATTATTTATTTGTTCACGTTGTTGAGCTTGGTGCAAAAGATTATAAAAGTCATCGTCAGCATTATCACACAAGTCCACAGCTTAGGAAAATCAACGAAAAAGGTGCATATACAAATATAAAAACAACTTAAACGCTTTGTAAAGCAAACAATACAAAATATGCGATGCTCCAGCAGAGCCTCCTTTAAAGCTTGTCCACCCGTTCCACACTGAGTTTGATGTCCGACTTGGGCATCAAGAGCAGTCTCCGGTTGTCGTACTCCACGGGAATCGAGGTCTCCGCAGAGGGAGCGTATCTGTGCTGCCTCAGCAGAGCCACCAGGCCCACCAGAAGCTGCTGCTCTGCAAAGCGAGCGGCAATGCATCCTCGCAGGCCATCGCCGAAAGGCAGGAACGCAGCTGCCGGGCGGGATCGCCTTGCCTGTTCCTCAAAGCGCTCCGGGTAGAACCGCTGGGGGTTTTCATAAATGCCAGGATCCATGTGTATCGCCGCCGTTGGTATCAGCACATTGTTGCCTTTGGCAATTACAAACACCGATCCGGGCACTTCGAA 562 2R:1731127-2080000 -1 NULL:1986406 SD07915:contig2 333 895 1 1 0 2602597 308255 307679 1 0 0 0 100 partof CCAGAATGCGAGACAGCTGGATATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATACTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATTGGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACTCCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGCAAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGATGGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGAGTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCCCGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTGTCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCT 576 2R:1731127-2080000 -1 NULL:1986408 SD10607:contig1 0 576 1 1 0 306046 305569 1 0 0 0 99 partof ATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTCCTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTCTAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAACTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTACAGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTCTCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAAAACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAAT 477 2R:1731127-2080000 -1 NULL:1986409 SD10607:contig2 576 1053 1 1 0 2597143 3592 3423 1 0 0 0 100 partof TCGGTGAGAAGGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAGGTG 169 2R:1731127-2080000 1 NULL:1981944 LD44494:contig1 0 169 1 1 0 3965 3648 1 0 0 0 100 partof ATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACCCACATATTCGCAGTG 317 2R:1731127-2080000 1 NULL:1981945 LD44494:contig1 169 486 1 1 0 4158 4035 1 0 0 0 98 partof CAGACGAGTCTCAACGGCTGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATG 123 2R:1731127-2080000 1 NULL:1981946 LD44494:contig1 486 609 1 1 0 4502 4264 1 0 0 0 99 partof ATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGAGTG 238 2R:1731127-2080000 1 NULL:1981947 LD44494:contig2 609 847 1 1 0 4836 4555 1 0 0 0 100 partof CTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACATAATAGAGACTTTATTACAACATTT 281 2R:1731127-2080000 1 NULL:1981948 LD44494:contig2 847 1128 1 1 0 2602602 312761 312176 1 0 0 0 99 partof TGCGCAGCACCTCGTAGTGATTGCGGCACCGCAGGACCTTCTGCACCACGTCCAGCATCTCGAGTGTGAACTTGTGGGGCAGGGCGTCAGATTTGCGAGTTGGGCCTATGGTCCGCTGGGCCTCGCCCTTCAGCCTCAGTCTCAAAATGATATTCTTTAGCTCCAGCAGCGCCATGATCTCATCGTGGTTCTGTAAGCCTTCCAGATCCTCGTTGATCTGCCTCAGAGCGTGCTCGTAGTGTCCCAGGCACAGGTCACTCACCACCTTGTCGACGCAGTGATGCCTCCTCGCCTGCAGGATTCCCATTGTGAAGTCGTCGTCCTCCAGTTCTTGGTTACTTTCTTCTCCTTCCCAGCAGCGTGAGAAGACAAAAAAGGATTCGTTTTTCTCTGTTCGTTTGCAAATTTTAAATTTTGGTTTGTTGTTCTGGGACAATCCACCGAGTTGGTGAATTTAACAAAGTGCTTTTGTATGTATATTAGAGGTAGCCGAAATAGTTTCGAACTAAGTTGACTGTATATGTATATGTAGCTGCAAACTTAAATACAAATTGACTTTCGCCAGTCAACATTTTGTATGTCAAC 585 2R:1731127-2080000 -1 NULL:1986411 AT29763:contig1 0 585 1 1 0 312040 311743 1 0 0 0 99 partof CCTGGTTAGCGTAAAACTGTAAGCAGGAGCGCCTGCGATGAAGTGCATGGTGACGAAGAGAAAAACCAGAGCAGCCACCACTCCGATGACGAGTTGCTGTGTTTGGTAGAGTGACTGCCTCTGGGGCATCCGCTGATTGGCCCCCCGATAAGGCCTTCTGAAAGCGGCTCCCAGATCGTTCCCATTTGCCTCATTGAATTCACTTTCCCCGCGATAATCCTTGTACTGCGAGGGATCCTGGTCGTGGCAGTCGCCCACTGCCGTTGCTATGTTGTACTCAATCCTTTTCTGGCAGTCC 297 2R:1731127-2080000 -1 NULL:1986412 AT29763:contig2 585 882 1 1 0 311684 311517 1 0 0 0 99 partof TCCAACTCCGCTCTTGCCTGCACTTATGTTTGAGGTCCGAGATGTAAACCTCCTCGATTTCTACTTCCAGTTCGGCCAACTGCTGTTCTGTGTACTTGGACAGAGTCGTCGGATTCATGTAGTAGGCAATGTGGTTCGTCCGACTGAGCCGTCGAGCGCTGTGGGTTCTG 167 2R:1731127-2080000 -1 NULL:1986413 AT29763:contig2 882 1049 1 1 0 311460 311220 1 0 0 0 100 partof ATTTTTAAAACTACTCTTTATTTACACCGTGCACTAATCCCTACATCTATCAATAGAAAAGTACAGAGTATCAGACTGGCACGTCCTGATTCAAAGACTCGTTCTCGAGCAACAGTCGACTGTGACCAGACTTTCCCAGCTGGAGCAACGCCTGGCAAGCGGGAGTGGACATCTGGCTGACATGCTGGAGCAACTTCTGGTCGTTGTTTCCCTGCCTCGCCCTGAGAAACAGATTATCCCCTG 240 2R:1731127-2080000 -1 NULL:1986414 AT29763:contig2 1049 1289 1 1 0 2602609 315484 315186 1 0 0 0 100 partof TCGCCATGTTTGCCGCCTTTGTTGATTATTCCGCTGCTGCTTCTTCCGTTTTTATGCTTTTCTGCTTTTCTTGCTCTGCGTTGGTTGCGATTCCAGGCACGTTGTATCACTGTTAGCTTGTAACAAACACTGCTGATAGGCTAATGACTGCTGCGCGCAACTGAACACATTTCACGGCTTTCTTTCAGTCGCGTCTCCGTTCAACTTCCGCAATATCCGTATAATTCGTATTATCCGTGTAATCCGTATTTTCCGAATCGCGTTCAGACGTTCACACCAACAACTGCAATTCTAGTGT 298 2R:1731127-2080000 -1 NULL:1986416 RE57156:contig1 0 298 1 1 0 308375 308136 1 0 0 0 99 partof CTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCTCGTGCTTATCGAAAAGTTTGGGGTCCTTCGTCGCCGAGATCTCGCAGAGCAAGTTGGTCGTGTTCGCCGGACTGACACTGGTCGTCTTCAGCTTTTCAATCAAATCGTCGATTTCAGCTGCTT 239 2R:1731127-2080000 -1 NULL:1986417 RE57156:contig1 298 537 1 1 0 305717 305059 1 0 0 0 100 partof GGTTTTCTCTTATTTCTCATGCATTTCAAATTTTATTTGAATTATTAAATGTACATTATTGTGTTTAGAGTTCATAAATATGTTTTCGCATTTATGTGTGTGGGTGTCTCAACGCTTTATATATTAACACCATTCCCCTTGAATTGTGTTCGTTTAATTTTTAGTTTTTGGTGACCAAACATTAGTACATCGTTTTTAATAATTGGTAAAATTTGTAGCACTCCATAAACTACGATTTGTAAAATTGAAATATTTGCATTATTGGTTTTCAACTATTTTCGGATTGCTGATTGTTACTGAGTTGCAGTTTTGTTAATGTTTTAAAGTTAGCTTAAAAATGCATTTTGGATAACTTCGCCGAGTTTTACAATAAATATATGGGATGCCGTTTGCAATATGTGTCTGTGCACCAATTAAAATACCTTAATTACGTCGTGCGTCTAAATGTTTTGTTATCTTCTCGTTTTTGGTTTGTGCCAGCAACGGTTTAAAAGAGGTCGATTGAAAATTATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTAT 658 2R:1731127-2080000 -1 NULL:1986418 RE57156:contig2 537 1195 1 1 0 2597151 5686 5601 1 0 0 0 98 partof TTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATATTTATTAAGGT 85 2R:1731127-2080000 1 NULL:1981950 RE35072:contig1 0 85 1 1 0 21600 21472 1 0 0 0 99 partof -ATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCATGTG 128 2R:1731127-2080000 1 NULL:1981951 RE35072:contig1 85 213 1 1 0 22011 21656 1 0 0 0 100 partof GTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAATAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGATACTATAGATGGGTA 355 2R:1731127-2080000 1 NULL:1981952 RE35072:contig1 213 568 1 1 0 22365 22067 1 0 0 0 97 partof CTTACAAAAGCCAAATACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATCCA 298 2R:1731127-2080000 1 NULL:1981953 RE35072:contig1 568 866 1 1 0 2597157 5686 5629 1 0 0 0 96 partof GCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATATTTATTAAGGT 57 2R:1731127-2080000 1 NULL:1981955 RE65722:contig1 0 57 1 1 0 21600 21472 1 0 0 0 99 partof -ATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCAT 128 2R:1731127-2080000 1 NULL:1981956 RE65722:contig1 57 185 1 1 0 21838 21656 1 0 0 0 99 partof AAGGTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTG 182 2R:1731127-2080000 1 NULL:1981957 RE65722:contig1 185 367 1 1 0 22011 21894 1 0 0 0 100 partof TGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGATACTATAGATGGGTA 117 2R:1731127-2080000 1 NULL:1981958 RE65722:contig1 367 484 1 1 0 22365 22067 1 0 0 0 100 partof CTTACAAAAGCCAAATACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAACGGA 298 2R:1731127-2080000 1 NULL:1981959 RE65722:contig1 484 782 1 1 0 2602615 335911 335545 1 0 0 0 99 partof TTCTCTTGCTGTGGCAACACGGGATACCAACAGTATGAAACCGTGCCCAGCTCCTGCTGCGGCTACAAGGATCGCACCAAGGTGTGCGAAGCGGAGATCTACAGCCAGCGACCTGGCTGCCGGCAGGAGTTCGTCGATTTCTGGGCCTCCAATACGGACCTGATTCGATGGAGCAGTCTGATCATCGCCCTCTTCGAGCTGGGCATCTTCATCATGTCGTGCTGCCTGGCCAGCGCGATGAGGAAGCGCTAGAGCCGAAGTCAGATACAATCCTTAGACGTAGCCCAGTTCATAGCATAAATCCAACACACGAATTCCTCACTCACTCACTCACCGTAAATAAACCAGAATAGGTTAAGCCCAATG 366 2R:1731127-2080000 -1 NULL:1986420 LP04610.3prime 203 569 1 1 0 335473 335308 1 0 0 0 100 partof TACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCCGTA 165 2R:1731127-2080000 -1 NULL:1986421 LP04610.3prime 38 203 1 1 0 335244 335206 1 0 0 0 100 partof GCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTA 38 2R:1731127-2080000 -1 NULL:1986422 LP04610.3prime 0 38 1 1 0 2597164 23427 23228 1 0 0 0 100 partof ACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGAGCGCGATGCTGGT 199 2R:1731127-2080000 1 NULL:1981961 GH02863:contig1 0 199 1 1 0 24962 23736 1 0 0 0 100 partof TA...CAGTACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTCAGGGTAAGA 1226 2R:1731127-2080000 1 NULL:1981962 GH02863:contig1 199 1425 1 1 0 2597168 26704 26559 1 0 0 0 100 partof AACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGACACAG 145 2R:1731127-2080000 1 NULL:1981964 GH01619:contig1 0 145 1 1 0 27350 27190 1 0 0 0 100 partof CAGGCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAGGTA 160 2R:1731127-2080000 1 NULL:1981965 GH01619:contig1 145 305 1 1 0 28160 27823 1 0 0 0 100 partof ATCTATCACACGCTCTTATTACCGCGGAGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATAC 337 2R:1731127-2080000 1 NULL:1981966 GH01619:contig1 305 642 1 1 0 28619 28220 1 0 0 0 100 partof GCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAACCAC 399 2R:1731127-2080000 1 NULL:1981967 GH01619:contig1 642 1041 1 1 0 2602620 341629 341366 1 0 0 0 99 partof CACAAACAGTATGTTGAATATGAACAGCACATATTTCACAAAAACGCCGCCGCAATCCATTGCTGAGATGTACTTGTGTATCACTTGTGTTCGATTTAAGAGTAAGACGTTCGATGCGATTTCGTTCGTGGTCCGCTTGATACTGAAAAAGTCTGATATATAACAATATTTTTATGAGCGCATTTCCTATCGCGAAAAGCTCTGTTAGATTTTAGCTCTGAATTTAGCGGCGATAAGAAAAGCGTTGCTGCAGTGGTAGAGAT 263 2R:1731127-2080000 -1 NULL:1986424 SD10395:contig1 0 263 1 1 0 340629 340437 1 0 0 0 98 partof CGAGGTCAGAGCACAGGAATTCTCGCGTATGGCGCCGCAGCATCCCATGAAGGCTACCAGGAAGACTACGCAGCCAAGGACCAGGATGATGATGGCCACGCTGTTTGCCGTGAAGGTCTCGCCAACGCCCGAGAAGTCCTTTATGGTGGACACCATGATGGAGCCGAAGGTGATAAGCAAAATGCCGCATATCTA 192 2R:1731127-2080000 -1 NULL:1986425 SD10395:contig1 263 455 1 1 0 340378 340206 1 0 0 0 99 partof CGATCGCTGCAGTGTGTCCATGAGGAGGGCATCGGTCTTGCGTTGATCCCATATGGTCTGGACGATCTTCTCCAAAGATTGCTGTATCTGCACATGGTCCACCCACACGTAGATAATGAGAGCTAGCTGACTAACCAACAGCACCAGCATGACCACAGAGTACTG 172 2R:1731127-2080000 -1 NULL:1986426 SD10395:contig1 455 627 1 1 0 340075 339877 1 0 0 0 100 partof CCATTGGAGGGCGAGTCGCAGCAGGAGGCGGGATACGTAATGCCGTAATCAGCGAAGCCGTTCAAGCCGCAGCACTTGAACTG 198 2R:1731127-2080000 -1 NULL:1986427 SD10395:contig1 627 825 1 1 0 339820 339634 1 0 0 0 97 partof ATATACAGTAAGCATGCGAAGCACTTTGTTTTATTTATTCATATTGACTTTATGACGTTAAAGAGGGTCGGGAGATAATCCTAATACTATGCTACTAATCATCGTTTCATCGTTTAGTAGTTCTGGCGTCTCTGCGAGTTGCGGGTCTGATTGGCCAGGCAGCAGGCGAAAATGAAGGCCACAAGCTG 186 2R:1731127-2080000 -1 NULL:1986428 SD10395:contig1 825 1011 1 1 0 2597174 71924 71669 1 0 0 0 100 partof ATTTGTGAGCACACACTTTAGTTTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCGATCTGTGACGCGGTTTAAACCAAGGTA 255 2R:1731127-2080000 1 NULL:1981969 GH08636:contig1 0 255 1 1 0 72544 72479 1 0 0 0 100 partof GCTGCACGACACTTCGAGGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGTA 65 2R:1731127-2080000 1 NULL:1981970 GH08636:contig1 255 320 1 1 0 72755 72615 1 0 0 0 100 partof GTACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAGGTG 140 2R:1731127-2080000 1 NULL:1981971 GH08636:contig1 320 460 1 1 0 73139 72811 1 0 0 0 100 partof GTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTAT 328 2R:1731127-2080000 1 NULL:1981972 GH08636:contig1 460 788 1 1 0 75626 75256 1 0 0 0 100 partof TTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCC 370 2R:1731127-2080000 1 NULL:1981973 GH08636:contig2 788 1158 1 1 0 2597182 76385 76160 1 0 0 0 100 partof ATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAGGTG 225 2R:1731127-2080000 1 NULL:1981975 RE27841:contig1 0 225 1 1 0 76698 76444 1 0 0 0 100 partof GAAAATGCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGGGTA 254 2R:1731127-2080000 1 NULL:1981976 RE27841:contig1 225 479 1 1 0 77109 77017 1 0 0 0 100 partof AACTGAGTGTTTGGTGGTGGCCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCGCTCAGGAGA 92 2R:1731127-2080000 1 NULL:1981977 RE27841:contig1 479 571 1 1 0 78729 78139 1 0 0 0 100 partof CGCGCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACACACATTTAAATGTATAATGTATAACAAAAC 590 2R:1731127-2080000 1 NULL:1981978 RE27841:contig2 571 1161 1 1 0 2597189 79164 78966 1 0 0 0 99 partof ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAG 198 2R:1731127-2080000 1 NULL:1981980 RE41364:contig1 0 198 1 1 0 82559 82406 1 0 0 0 100 partof G...CAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 153 2R:1731127-2080000 1 NULL:1981981 RE41364:contig1 198 351 1 1 0 82763 82617 1 0 0 0 100 partof GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 146 2R:1731127-2080000 1 NULL:1981982 RE41364:contig1 351 497 1 1 0 84110 83954 1 0 0 0 99 partof ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCG 156 2R:1731127-2080000 1 NULL:1981983 RE41364:contig1 497 653 1 1 0 85812 85155 1 0 0 0 99 partof GAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACAC 657 2R:1731127-2080000 1 NULL:1981984 RE41364:contig2 653 1310 1 1 0 2597197 79164 79011 1 0 0 0 100 partof CGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGGTG 153 2R:1731127-2080000 1 NULL:1981986 LD08743.5prime 0 153 1 1 0 82559 82406 1 0 0 0 100 partof TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 153 2R:1731127-2080000 1 NULL:1981987 LD08743.5prime 153 306 1 1 0 82768 82617 1 0 0 0 98 partof GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGT-ACA 151 2R:1731127-2080000 1 NULL:1981988 LD08743.5prime 306 458 1 1 0 2597202 79164 79026 1 0 0 0 99 partof GCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGGTG 138 2R:1731127-2080000 1 NULL:1981990 RH07059:contig1 0 138 1 1 0 82559 82406 1 0 0 0 100 partof TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAG 153 2R:1731127-2080000 1 NULL:1981991 RH07059:contig1 138 291 1 1 0 82763 82617 1 0 0 0 100 partof GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 146 2R:1731127-2080000 1 NULL:1981992 RH07059:contig1 291 437 1 1 0 83170 83001 1 0 0 0 98 partof ATCATTCCAGTTGATAAACTGATTAAGGGACGCTTTCAAGACAACTTTGAGTTCCTTCAATGGTTTAAAAAATTCTTCGACGCCAATTACGACGGTCGCGAGTACGACCCCGTGGCTCAGCGGGGCGGAGTCAAGCTGGGCAATGGCAACGGACACGG-CAGCAACGGAG 169 2R:1731127-2080000 1 NULL:1981993 RH07059:contig1 437 606 1 1 0 85806 85199 1 0 0 0 100 partof CACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCT 607 2R:1731127-2080000 1 NULL:1981994 RH07059:contig2 606 1213 1 1 0 2597210 137592 137403 1 0 0 0 99 partof CCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGGTG 189 2R:1731127-2080000 1 NULL:1981996 LD23740:contig1 0 189 1 1 0 138240 137864 1 0 0 0 100 partof ATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGG 376 2R:1731127-2080000 1 NULL:1981997 LD23740:contig1 189 565 1 1 0 138947 138471 1 0 0 0 97 partof CCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACC 476 2R:1731127-2080000 1 NULL:1981998 LD23740:contig2 565 1041 1 1 0 2597216 140950 140795 1 0 0 0 100 partof CATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAAGTA 155 2R:1731127-2080000 1 NULL:1982000 RE12054:contig1 0 155 1 1 0 141858 141676 1 0 0 0 100 partof GGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCA 182 2R:1731127-2080000 1 NULL:1982001 RE12054:contig1 155 337 1 1 0 142891 142555 1 0 0 0 99 partof CAGAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAA 336 2R:1731127-2080000 1 NULL:1982002 RE12054:contig1 337 673 1 1 0 144587 143971 1 0 0 0 100 partof CGTTCGCGATTGGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAAACATC 616 2R:1731127-2080000 1 NULL:1982003 RE12054:contig2 673 1289 1 1 0 2597223 158442 158132 1 0 0 0 99 partof AACAGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAACGTA 310 2R:1731127-2080000 1 NULL:1982005 RE34115:contig1 0 310 1 1 0 159667 159335 1 0 0 0 100 partof CAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAG 332 2R:1731127-2080000 1 NULL:1982006 RE34115:contig1 310 642 1 1 0 168135 167487 1 0 0 0 100 partof GTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGGCATTTC 648 2R:1731127-2080000 1 NULL:1982007 RE34115:contig2 642 1290 1 1 0 2597229 212413 211741 1 0 0 0 100 partof GGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAATTCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCAGGTACTTAATCAGGTA 672 2R:1731127-2080000 1 NULL:1982009 AT24862:contig1 0 672 1 1 0 212514 212483 1 0 0 0 100 partof CTGGGTATTACGGAAGTCTTCAGCGATAAGG 31 2R:1731127-2080000 1 NULL:1982010 AT24862:contig1 672 703 1 1 0 213182 212706 1 0 0 0 99 partof TACCC-ATGATGCTCAA-CATGAACAAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAACTT 476 2R:1731127-2080000 1 NULL:1982011 AT24862:contig2 703 1179 1 1 0 2597235 213117 213084 1 0 0 0 100 partof AGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTA 33 2R:1731127-2080000 1 NULL:1982013 GH04125:contig1 0 33 1 1 0 213942 213388 1 0 0 0 100 partof GCATTTTCCTGTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCC 554 2R:1731127-2080000 1 NULL:1982014 GH04125:contig1 33 587 1 1 0 214233 213965 1 0 0 0 100 partof CAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAATTTCGTGATGAACTCAAAGAGACCTTAGAGAAGGTA 268 2R:1731127-2080000 1 NULL:1982015 GH04125:contig2 587 855 1 1 0 214433 214291 1 0 0 0 100 partof CTGGGCATCCGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGGAGGGAGCGGAGGCCGCAGGTGCCACATGTA 142 2R:1731127-2080000 1 NULL:1982016 GH04125:contig2 855 997 1 1 0 214648 214503 1 0 0 0 99 partof CTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTT 145 2R:1731127-2080000 1 NULL:1982017 GH04125:contig2 997 1142 1 1 0 2597243 216199 216179 1 0 0 0 100 partof AGTTTTCCCAATCATGTCAGGTA 20 2R:1731127-2080000 1 NULL:1982019 RE02548:contig1 0 20 1 1 0 216830 216288 1 0 0 0 100 partof TCAAGGCCACGTGTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCTCCGGAATCTCTG 542 2R:1731127-2080000 1 NULL:1982020 RE02548:contig1 20 562 1 1 0 217223 216941 1 0 0 0 100 partof CGGAAGGTCAGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCGAGGAGGTG 282 2R:1731127-2080000 1 NULL:1982021 RE02548:contig2 562 844 1 1 0 217771 217629 1 0 0 0 100 partof TTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTGTA 142 2R:1731127-2080000 1 NULL:1982022 RE02548:contig2 844 986 1 1 0 218037 217835 1 0 0 0 100 partof TTATCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGC 202 2R:1731127-2080000 1 NULL:1982023 RE02548:contig2 986 1188 1 1 0 2597251 221698 221537 1 0 0 0 100 partof AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGGGTG 161 2R:1731127-2080000 1 NULL:1982025 RE28276:contig1 0 161 1 1 0 221801 221754 1 0 0 0 100 partof TTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCAGGTA 47 2R:1731127-2080000 1 NULL:1982026 RE28276:contig1 161 208 1 1 0 236063 235637 1 0 0 0 100 partof CTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCGCCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCTGTTCAAAACCTAC 426 2R:1731127-2080000 1 NULL:1982027 RE28276:contig1 208 634 1 1 0 252388 251782 1 0 0 0 100 partof AATGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCGTCCC 606 2R:1731127-2080000 1 NULL:1982028 RE28276:contig2 634 1240 1 1 0 2597258 253434 253220 1 0 0 0 100 partof GCTTGACTAGCTAACACCTGGCAATGCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATGGTA 214 2R:1731127-2080000 1 NULL:1982030 LD08659:contig1 0 214 1 1 0 254261 253654 1 0 0 0 100 partof AGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTC 607 2R:1731127-2080000 1 NULL:1982031 LD08659:contig1 214 821 1 1 0 254456 254327 1 0 0 0 100 partof CCAAGTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACATGCATTT 129 2R:1731127-2080000 1 NULL:1982032 LD08659:contig1 821 950 1 1 0 2597263 258432 257739 1 0 0 0 100 partof TGAGTCGCGTTCTGGCCAGTGGGCGGACGGGCCATCTTCTTGGGCATCGTGGCCGATGCACCGGCGGCGTAAATGGGCGGCGGTGGGGGATCCTCCAGAGGAGGCGGACAGGTGTAGTGCTGCTGCTGCGGCGGCTGGTGGTGCTGATGGGAATGAGCCTGTCTCATGTTCGGCGATTGCGCAGCTGCTGGATTTTTGGTAAACGAACTTGAGTAGATGGCCATGTCTTTGCTGTTAGCAACTGCTGCATTCGGCGGCTGAGGTGGCTGATAATGCGAACTGGCCGAGCCAGAGGTCGCTGCCGTTGTCGGTGGGGATGCGGATGAAGAGTTCGAGAATGAGCTGACTTTGGAGAGCAACGATGATGTGGATGAAGACAGGGGGAAGTGAGGCAATGCATTGAAAGAGGTGGTCGGTGTTAGAATGGACGGTTTAGTGCTGCTGTTGGCCGCATGAGCGGATGACATTGCTGATGATGAGGTGCCGAAACTAGCGTAAATTCTATGCTGTTGCTGGTGCTGCAGCTGGATTTGTTCAGATTTACCGTCAAAGTGTTGCTGCTGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCCTCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTTGGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCA 693 2R:1731127-2080000 1 NULL:1982034 RH38629:contig1 0 693 1 1 0 261827 261310 1 0 0 0 98 partof TGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCTGCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCTAGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGCAGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCAGCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGCTGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTACCGCCTGCTCACTGGGTGTTTTACCTCTTTGCGGGCTACCGCGTCCGAGGAGCTGCAACTGCTGCTCACTGGTGGCGCGAAACGAGGAGAGTCGCTGCTTGGCGGGCGCCACAGTTGCTGTTGGCGGTGCCTGGCCACCGGCAGAGTCCGGCGAGGAGTCCGGCGAACCGGCCAAATTGGCGGGCAACTGCTGCAGCTCGCGCATCTCGTGCAGCTGCAGCGCGTGGGGCTGCG 517 2R:1731127-2080000 1 NULL:1982035 RH38629:contig2 693 1210 1 1 0 2597268 287387 286742 1 0 0 0 99 partof CACGTTGAATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGTCAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATTCCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTGTCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGCAACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGGATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGAAATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTCGTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATCCGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAGACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCATGTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTAAGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTCAAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAG 645 2R:1731127-2080000 1 NULL:1982037 LD21171:contig1 0 645 1 1 0 288098 287596 1 0 0 0 100 partof CAAACCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCACTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAAGGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGACATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAATAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTGTTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAAAAGGTACAGGAAGACAACAAGATAACAGTTAAAACCAGATCAGGAAAAATTTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAAAAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGCTAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAAT 502 2R:1731127-2080000 1 NULL:1982038 LD21171:contig2 645 1147 1 1 0 2597271 288583 288100 1 0 0 0 100 partof AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAGTTAAGAAATACAAAAAGAAATACAAAAAAAACTATAAAAAAAATAATATAAAAAAATACAGATTATAAGAAATAAGAAATAAGAAATATAAAAAAATAAAAATATAAGTACACAAAATGTACCGTACCCCCACACACTACGTAGTCTTAGAACAACTTAGACGACCAGATATTTACGAATTGTCTTTTTGTAAGCGCGATTTCTGCATGCGGCGCAAATCCCGCTCACTGGACTGGCTGGGGTCGGCTTGGAAATGGGTAGCTGGATCTCCAGATGCTGCTGATTGGAACGCCGTCTTGGCCGCGCAAGCGACGGCTTCGAGGAACTGCAAAAACTGGAGGAGGCTAGCTGTATCCCTCGGCTACTGAAGTAACCAACGAGTGGTTAAGCAAGTCGACGATGGAATGCTCCTCCTGACCAACTTCAACGGAACTCTAAGAACG 483 2R:1731127-2080000 1 NULL:1982040 RH54175.5prime 0 483 1 1 0 2597273 311460 311220 1 0 0 0 100 partof ATTTTTAAAACTACTCTTTATTTACACCGTGCACTAATCCCTACATCTATCAATAGAAAAGTACAGAGTATCAGACTGGCACGTCCTGATTCAAAGACTCGTTCTCGAGCAACAGTCGACTGTGACCAGACTTTCCCAGCTGGAGCAACGCCTGGCAAGCGGGAGTGGACATCTGGCTGACATGCTGGAGCAACTTCTGGTCGTTGTTTCCCTGCCTCGCCCTGAGAAACAGATTATCCCCTG 240 2R:1731127-2080000 1 NULL:1982042 AT02529.3prime 375 614 1 1 0 311684 311517 1 0 0 0 100 partof TCCAACTCCGCTCTTGCCTGCACTTATGTTTGAGGTCCGAGATGTAAACCTCCTCGATTTCTACTTCCAGTTCGGCCAACTGCTGTTCTGTGTACTTGGACAGAGTCGTCGGATTCATGTAGTAGGCAATGTGGTTCGTCCGACTGAGCCGTCGAGCGCTGTGGGTTCTG 167 2R:1731127-2080000 1 NULL:1982043 AT02529.3prime 208 375 1 1 0 311951 311743 1 0 0 0 100 partof CTGGTTAGCGTAAAACTGTAAGCAGGAGCGCCTGCGATGAAGTGCATGGTGACGAAGAGAAAAACCAGAGCAGCCACCACTCCGATGACGAGTTGCTGTGTTTGGTAGAGTGACTGCCTCTGGGGCATCCGCTGATTGGCCCCCCGATAAGGCCTTCTGAAAGCGGCTCCCAGATCGTTCCCATTTGCCTCATTGAATTCACTTTCCC 208 2R:1731127-2080000 1 NULL:1982044 AT02529.3prime 0 208 1 1 0 2597278 316405 315854 1 0 0 0 100 partof CACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCCAAC 551 2R:1731127-2080000 1 NULL:1982046 LD41464:contig1 0 551 1 1 0 318040 317899 1 0 0 0 99 partof CACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAG 141 2R:1731127-2080000 1 NULL:1982047 LD41464:contig2 551 692 1 1 0 318697 318345 1 0 0 0 99 partof 352 2R:1731127-2080000 1 NULL:1982048 LD41464:contig2 692 1044 1 1 0 2597284 318408 317198 1 0 0 0 100 partof TTTTAAAATTCAACTGCAAATTGGCATTGGCTAAAGGTGCGATACAATCACCGATTGATCTGTTCTGCGGAGCTTTCGCTGTTCTTCTTGATTAACTGCTCGCTAACACTCCGTCCCGTTCATGAGAAATCCATTTCACTGCGCACACTAACCTCTAACAACACAGGCACACAACTTATGTTCATTTCGTTATTTGTTTACGATCGATTCGCAGAACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACAGTAAGCACCTCACTTGCAATACCAAGCCCGAGATCCTCCGTCGGAACGATCGCCAGATTCGTCAATTAAACCTCACTTTTCCTCTCTTCCAGAAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGGC 1210 2R:1731127-2080000 1 NULL:1982050 RH14346:contig1 0 1210 1 1 0 2597287 322552 322463 1 0 0 0 100 partof TTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTG 89 2R:1731127-2080000 1 NULL:1982052 GH05668:contig1 0 89 1 1 0 324259 324147 1 0 0 0 100 partof TTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGCTCTGTTCGGTG 112 2R:1731127-2080000 1 NULL:1982053 GH05668:contig1 89 201 1 1 0 326642 326450 1 0 0 0 100 partof ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGGTA 192 2R:1731127-2080000 1 NULL:1982054 GH05668:contig1 201 393 1 1 0 326867 326705 1 0 0 0 100 partof TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAGATCAGCGTA 162 2R:1731127-2080000 1 NULL:1982055 GH05668:contig1 393 555 1 1 0 326987 326933 1 0 0 0 98 partof ATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTC 54 2R:1731127-2080000 1 NULL:1982056 GH05668:contig1 555 609 1 1 0 333156 333133 1 0 0 0 100 partof ACATGGACGCGATTCAGATCAGCGTA 23 2R:1731127-2080000 1 NULL:1982057 GH05668:contig2 609 632 1 1 0 333417 333222 1 0 0 0 98 partof ATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAAGTA 195 2R:1731127-2080000 1 NULL:1982058 GH05668:contig2 632 827 1 1 0 334031 333679 1 0 0 0 100 partof TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTT 352 2R:1731127-2080000 1 NULL:1982059 GH05668:contig2 827 1179 1 1 0 2597298 322835 322481 1 0 0 0 100 partof CACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCCAAGTGGTAAAGTG 354 2R:1731127-2080000 1 NULL:1982061 GH17623:contig1 0 354 1 1 0 323221 322895 1 0 0 0 100 partof TTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCG 326 2R:1731127-2080000 1 NULL:1982062 GH17623:contig1 354 680 1 1 0 324081 323678 1 0 0 0 100 partof CATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCT 403 2R:1731127-2080000 1 NULL:1982063 GH17623:contig2 680 1083 1 1 0 blastx_masked 1.0 aa_SPTR.primate 1.0 2003-01-13 22:49:55 BLASTX Similarity to Other Species genomic 2597662 74969 74747 1 0 0 0 259 partof MVLAL-GFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHFRLNKVRNIKTWLSVRSYLK 222 2R:1731127-2080000 1 NULL:1982373 Q9BUP2 526 601 1 1 0 2597665 74969 74759 1 0 0 0 258 partof LGFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHFRLNKVRNIKTWLSVRSYLK 210 2R:1731127-2080000 1 NULL:1982375 Q9UMS5 531 601 1 1 0 75480 75027 1 0 0 0 286 partof KRGPQRSVDXXXXXXXXXXXXXXAFLSVEWLKDSAXXXXXXXX-EALIWSITIGIFLLRFMTLGQKIQHKYRSVSVLITEQINLYLQIEQKPKKKDELMVSNSVXXXXXXXXXXXXTPFKLSGLSANPYLFTTIKVVILSALSGVLSEVLGF 453 2R:1731127-2080000 1 NULL:1982376 Q9UMS5 601 753 1 1 0 2597669 76657 76423 1 0 0 0 189 partof LKSKLF*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGEEVV 234 2R:1731127-2080000 1 NULL:1982378 AAK49409 36 114 1 1 0 77909 77021 1 0 0 0 1111 partof ECLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 888 2R:1731127-2080000 1 NULL:1982379 AAK49409 129 409 1 1 0 78426 77952 1 0 0 0 617 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 474 2R:1731127-2080000 1 NULL:1982380 AAK49409 405 563 1 1 0 2597674 76657 76423 1 0 0 0 189 partof LKSKLF*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGEEVV 234 2R:1731127-2080000 1 NULL:1982382 Q9HCC0 36 114 1 1 0 77909 77021 1 0 0 0 1111 partof ECLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 888 2R:1731127-2080000 1 NULL:1982383 Q9HCC0 129 409 1 1 0 78426 77952 1 0 0 0 617 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 474 2R:1731127-2080000 1 NULL:1982384 Q9HCC0 405 563 1 1 0 2597679 77777 77285 1 0 0 0 395 partof AGGAYVPAMADESIIVKKQGTIF-----LAGPPL--VKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGH 492 2R:1731127-2080000 1 NULL:1982386 AAH14897 172 327 1 1 0 2597682 82561 82438 1 0 0 0 149 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982388 AAH07318 43 84 1 1 0 82766 82616 1 0 0 0 202 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982389 AAH07318 83 133 1 1 0 83124 82998 1 0 0 0 192 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982390 AAH07318 131 173 1 1 0 2597687 82561 82438 1 0 0 0 149 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982392 Q15555 43 84 1 1 0 82766 82616 1 0 0 0 202 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982393 Q15555 83 133 1 1 0 83124 82998 1 0 0 0 192 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982394 Q15555 131 173 1 1 0 2597692 82561 82438 1 0 0 0 166 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982396 Q15691 0 41 1 1 0 82766 82616 1 0 0 0 218 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982397 Q15691 40 90 1 1 0 83124 82998 1 0 0 0 207 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982398 Q15691 88 130 1 1 0 2597696 84083 83954 1 0 0 0 192 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREG 129 2R:1731127-2080000 1 NULL:1982400 Q9BZP8 91 134 1 1 0 2597698 84083 83954 1 0 0 0 192 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREG 129 2R:1731127-2080000 1 NULL:1982402 Q9UPY8 89 132 1 1 0 2603091 2496 1281 1 0 0 0 728 partof SSSGGEATAL--HDIECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLE---DGDGNQM-EWSTPKTSNMTRIWHHKFNTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKGI-MGDKRS--PLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSLN-GFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 1215 2R:1731127-2080000 -1 NULL:1986846 O94923 84 488 1 1 0 1172 809 1 0 0 0 445 partof YEEYPTTPPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 363 2R:1731127-2080000 -1 NULL:1986847 O94923 488 609 1 1 0 2603095 5318 4850 1 0 0 0 466 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986849 Q9BVK5 54 205 1 1 0 2603097 5318 4850 1 0 0 0 466 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986851 AAH08848 54 205 1 1 0 2603099 5318 4850 1 0 0 0 709 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986853 O43447 21 177 1 1 0 2597700 84218 83954 1 0 0 0 210 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVK---SLPGTAASGVSSSYRRGPSATTRPAMTSAVKPSM 264 2R:1731127-2080000 1 NULL:1982404 Q15691 89 179 1 1 0 2597702 138302 137936 1 0 0 0 522 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982406 Q9NQ12 38 160 1 1 0 138718 138373 1 0 0 0 521 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982407 Q9NQ12 163 278 1 1 0 2597706 138302 137936 1 0 0 0 522 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982409 AAH07840 38 160 1 1 0 138718 138373 1 0 0 0 521 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982410 AAH07840 163 278 1 1 0 2597710 138302 137936 1 0 0 0 518 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982412 P21912 38 160 1 1 0 138718 138373 1 0 0 0 521 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982413 P21912 163 278 1 1 0 2597713 146306 145466 1 0 0 0 284 partof RISLRVGELEPKESSGSSDAEVQIERLNREIAFIKLALSDKQAENADLHQSISNLKLGQEDLLERIQQHELSQDRRFHGLLAEIENKLSALNDSQFALLNKQIKLSLVEILGFKQSTAGGSAGQLD-DFDLQTWVRSMFVAKDY----LEQQLLELNKR--TNNNIRDEIERSSILLMSDISQRLK-REILLVVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 840 2R:1731127-2080000 1 NULL:1982415 Q9UH98 30 308 1 1 0 146504 146390 1 0 0 0 121 partof VLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVW 114 2R:1731127-2080000 1 NULL:1982416 Q9UH98 317 355 1 1 0 146768 146567 1 0 0 0 177 partof GLEQEKDQEPVLFGDYQFEDNGASLQYFAVQNLDIKRPYEIVELRIETNHGHPTYTCLYRFRVHGKP 201 2R:1731127-2080000 1 NULL:1982417 Q9UH98 355 422 1 1 0 2597718 146306 145466 1 0 0 0 284 partof RISLRVGELEPKESSGSSDAEVQIERLNREIAFIKLALSDKQAENADLHQSISNLKLGQEDLLERIQQHELSQDRRFHGLLAEIENKLSALNDSQFALLNKQIKLSLVEILGFKQSTAGGSAGQLD-DFDLQTWVRSMFVAKDY----LEQQLLELNKR--TNNNIRDEIERSSILLMSDISQRLK-REILLVVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 840 2R:1731127-2080000 1 NULL:1982419 O94901 430 708 1 1 0 146504 146390 1 0 0 0 121 partof VLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVW 114 2R:1731127-2080000 1 NULL:1982420 O94901 717 755 1 1 0 146768 146567 1 0 0 0 177 partof GLEQEKDQEPVLFGDYQFEDNGASLQYFAVQNLDIKRPYEIVELRIETNHGHPTYTCLYRFRVHGKP 201 2R:1731127-2080000 1 NULL:1982421 O94901 755 822 1 1 0 2597723 146306 145469 1 0 0 0 277 partof ISLRVGELEPKESSGSSDAEVQIE-RLNREIAFIKLALSDKQAENADLHQSISNLKLGQEDLLERIQQH--ELSQDRRFHGLLAEI---ENKLSALNDSQFALLNKQIKLSLVEILGFKQSTAGGSAGQLDDFDLQTWVRSMFVAKDYLEQQLLELNKRTNNNIRDEIERSSILLMSDISQRLKREILLVVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 837 2R:1731127-2080000 1 NULL:1982423 Q9UH99 51 325 1 1 0 146504 146369 1 0 0 0 99 partof PYSFLPTVLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVW 135 2R:1731127-2080000 1 NULL:1982424 Q9UH99 329 372 1 1 0 2597727 212407 211600 1 0 0 0 390 partof DALQQSKDPHINTVF-SPASVQSALTLAFMGASGSTAEELRNGLQL--------GPGDRHHIALNFG---EFWR--TSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADS-EGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQD--VEIFLPRMCIEYDVDLKQVL 807 2R:1731127-2080000 1 NULL:1982426 P29508 13 299 1 1 0 2597729 212407 211600 1 0 0 0 392 partof DALQQSKDPHINTVF-SPASVQSALTLAFMGASGSTAEELRNGLQLGP--------GDRHHIALNFG---EFWR--TSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADS-EGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQD--VEIFLPRMCIEYDVDLKQVL 807 2R:1731127-2080000 1 NULL:1982428 P48594 13 299 1 1 0 2597731 212407 211600 1 0 0 0 392 partof DALQQSKDPHINTVF-SPASVQSALTLAFMGASGSTAEELRNGLQLGP--------GDRHHIALNFG---EFWR--TSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADS-EGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQD--VEIFLPRMCIEYDVDLKQVL 807 2R:1731127-2080000 1 NULL:1982430 BAB21525 13 299 1 1 0 2597733 214275 213432 1 0 0 0 402 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP--SEDKEAVAARYGA------------LLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAA-ERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVA-------KE--VYLKLPKFKIEFRDELKETLEKVRLRQEKHGCATLT 843 2R:1731127-2080000 1 NULL:1982432 BAB21525 13 315 1 1 0 2597735 214275 213432 1 0 0 0 407 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP--SEDKEAVAARYGA------------LLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAA-ERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG-------FARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQEKHGCATLT 843 2R:1731127-2080000 1 NULL:1982434 AAH05224 13 315 1 1 0 2597737 214275 213432 1 0 0 0 407 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP--SEDKEAVAARYGA------------LLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAA-ERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG-------FARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQEKHGCATLT 843 2R:1731127-2080000 1 NULL:1982436 P29508 13 315 1 1 0 2597739 217139 216380 1 0 0 0 346 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXX--XTEVAEK--LDQL-LAKGQWEKA----SGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISS 759 2R:1731127-2080000 1 NULL:1982438 BAB21525 9 271 1 1 0 2597741 217139 216380 1 0 0 0 346 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXX--XTEVAEK--LDQL-LAKGQWEKA----SGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISS 759 2R:1731127-2080000 1 NULL:1982440 P48594 9 271 1 1 0 2597743 217139 216380 1 0 0 0 343 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKG-----QWEKA----SGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISS 759 2R:1731127-2080000 1 NULL:1982442 AAH05224 9 271 1 1 0 2597745 239902 239707 1 0 0 0 141 partof VDILDTSGDMQFPAMRRLSIATAHAFMLVYAATSAPSFQCVKQCFEEIREQRGDFQ------VSYRCSCSP 195 2R:1731127-2080000 1 NULL:1982444 AAH08065 56 127 1 1 0 2597747 253436 253253 1 0 0 0 162 partof DIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDG 183 2R:1731127-2080000 1 NULL:1982446 AAH07066 7 68 1 1 0 254067 253662 1 0 0 0 358 partof YTTVGTHPTRCEEFVPD-PEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKT 405 2R:1731127-2080000 1 NULL:1982447 AAH07066 70 202 1 1 0 2597751 253436 253253 1 0 0 0 162 partof DIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDG 183 2R:1731127-2080000 1 NULL:1982449 Q9BY40 7 68 1 1 0 254259 253662 1 0 0 0 548 partof YTTVGTHPTRCEEFVPD-PEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEPCQI 597 2R:1731127-2080000 1 NULL:1982450 Q9BY40 70 263 1 1 0 2603102 8846 7730 1 0 0 0 1048 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986855 AAH08366 40 414 1 1 0 7593 7422 1 0 0 0 96 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 171 2R:1731127-2080000 -1 NULL:1986856 AAH08366 419 476 1 1 0 2603105 8846 7730 1 0 0 0 1048 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986858 AAH00485 40 414 1 1 0 7593 7422 1 0 0 0 96 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 171 2R:1731127-2080000 -1 NULL:1986859 AAH00485 419 476 1 1 0 2603108 8846 7730 1 0 0 0 1048 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986861 P20711 40 414 1 1 0 7593 7422 1 0 0 0 96 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 171 2R:1731127-2080000 -1 NULL:1986862 P20711 419 476 1 1 0 2603111 18125 17777 1 0 0 0 364 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986864 AAH08366 33 145 1 1 0 17620 17149 1 0 0 0 316 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986865 AAH08366 144 298 1 1 0 17128 16870 1 0 0 0 285 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986866 AAH08366 289 376 1 1 0 15554 15332 1 0 0 0 172 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1986867 AAH08366 405 479 1 1 0 2603116 18125 17777 1 0 0 0 364 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986869 AAH00485 33 145 1 1 0 17620 17149 1 0 0 0 316 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986870 AAH00485 144 298 1 1 0 17128 16870 1 0 0 0 285 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986871 AAH00485 289 376 1 1 0 15554 15332 1 0 0 0 172 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1986872 AAH00485 405 479 1 1 0 2603121 18277 18121 1 0 0 0 158 partof MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLPRKPQK*PQN 156 2R:1731127-2080000 -1 NULL:1986874 P19113 1 53 1 1 0 18125 17771 1 0 0 0 369 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 354 2R:1731127-2080000 -1 NULL:1986875 P19113 34 149 1 1 0 17620 17182 1 0 0 0 342 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLK 438 2R:1731127-2080000 -1 NULL:1986876 P19113 146 291 1 1 0 17143 16870 1 0 0 0 260 partof GFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 273 2R:1731127-2080000 -1 NULL:1986877 P19113 287 376 1 1 0 2603126 26174 26114 1 0 0 0 74 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1986879 Q9Y3A3 0 20 1 1 0 26043 25665 1 0 0 0 583 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1986880 Q9Y3A3 19 145 1 1 0 25659 25410 1 0 0 0 314 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPI 249 2R:1731127-2080000 -1 NULL:1986881 Q9Y3A3 130 210 1 1 0 2603131 26174 26114 1 0 0 0 74 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1986883 Q9H5J1 0 20 1 1 0 26043 25665 1 0 0 0 581 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1986884 Q9H5J1 19 145 1 1 0 25659 25410 1 0 0 0 306 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPI 249 2R:1731127-2080000 -1 NULL:1986885 Q9H5J1 130 210 1 1 0 2603136 26174 26114 1 0 0 0 74 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1986887 Q9Y4T8 0 20 1 1 0 26043 25665 1 0 0 0 576 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1986888 Q9Y4T8 19 145 1 1 0 2603140 33769 33223 1 0 0 0 290 partof DGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 546 2R:1731127-2080000 -1 NULL:1986890 O15375 8 190 1 1 0 2603142 33772 33217 1 0 0 0 287 partof PDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMRDP 555 2R:1731127-2080000 -1 NULL:1986892 O95907 12 197 1 1 0 2603144 33778 33223 1 0 0 0 302 partof KMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 555 2R:1731127-2080000 -1 NULL:1986894 O15427 13 198 1 1 0 2603146 88534 87613 1 0 0 0 680 partof APTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQK-----FHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 921 2R:1731127-2080000 -1 NULL:1986896 P15121 0 315 1 1 0 2603148 88537 87613 1 0 0 0 682 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQK-----FHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 924 2R:1731127-2080000 -1 NULL:1986898 AAH00260 0 316 1 1 0 2603150 88537 87613 1 0 0 0 682 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQK-----FHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 924 2R:1731127-2080000 -1 NULL:1986900 AAH10391 0 316 1 1 0 2603152 93372 93243 1 0 0 0 126 partof TANLDVFLRRFNEVQYWIVTELVSTPSLSKRVGLVRKFIKLAA 129 2R:1731127-2080000 -1 NULL:1986902 Q92565 382 425 1 1 0 92957 92606 1 0 0 0 426 partof CKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSRSLG 351 2R:1731127-2080000 -1 NULL:1986903 Q92565 426 543 1 1 0 92535 92436 1 0 0 0 79 partof SPKSEGEVRSYISSFRVIDNQRVLTAMSQKVEP 99 2R:1731127-2080000 -1 NULL:1986904 Q92565 545 578 1 1 0 2603157 94119 93822 1 0 0 0 134 partof TSITYRKLNSAF*VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGP---ED-LVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDALV 297 2R:1731127-2080000 -1 NULL:1986906 Q9UHV5 99 199 1 1 0 92984 92609 1 0 0 0 393 partof KLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSRSL 375 2R:1731127-2080000 -1 NULL:1986907 Q9UHV5 294 415 1 1 0 2603161 96971 96824 1 0 0 0 208 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1986909 O95636 383 432 1 1 0 95888 95741 1 0 0 0 202 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERV 147 2R:1731127-2080000 -1 NULL:1986910 O95636 431 480 1 1 0 94080 93825 1 0 0 0 194 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDAL 255 2R:1731127-2080000 -1 NULL:1986911 O95636 669 751 1 1 0 93766 93595 1 0 0 0 177 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGK 171 2R:1731127-2080000 -1 NULL:1986912 O95636 751 808 1 1 0 92957 92615 1 0 0 0 466 partof CKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSR 342 2R:1731127-2080000 -1 NULL:1986913 O95636 853 967 1 1 0 92529 92430 1 0 0 0 90 partof KSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTR 99 2R:1731127-2080000 -1 NULL:1986914 O95636 977 1010 1 1 0 2603169 111141 109629 1 0 0 0 376 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRD-DPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERE--NFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYL-------NQVISGRCSV*ST---APR--GIVTG--FTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986916 P24557 35 530 1 1 0 2603172 111141 109629 1 0 0 0 372 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRD-DPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERE--NFKRNDFMNLLIELKQKGR-VTLDNGEVIEGM--DIG---ELAAQVFVFYVAGFETSSSTMSYC-LYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQ--VISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986918 Q9HD83 36 531 1 1 0 2603175 111141 109629 1 0 0 0 371 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRD-DPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERE--NFKRNDFMNLLIELKQKGR-VTLDNGEVIEGM--DIG---ELAAQVFVFYVAGFETSSSTMSYC-LYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQ--VISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986920 Q9HD77 36 531 1 1 0 2603178 140126 139976 1 0 0 0 199 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1986922 Q9BZL1 9 59 1 1 0 2603181 140126 139976 1 0 0 0 199 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1986924 AAH07053 9 59 1 1 0 2603184 194911 194350 1 0 0 0 224 partof CCLPPAPITR*ANANTSSEAHAYTLCIAKVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTA-ELESEAMCHEGSKATRAIFLRHG-LIFTTGFNRSSERQYSLRAPDAL-NEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMN-II*PKSHR 561 2R:1731127-2080000 -1 NULL:1986926 P57737 597 780 1 1 0 2603186 196650 196461 1 0 0 0 259 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 189 2R:1731127-2080000 -1 NULL:1986928 Q9ULV4 2 65 1 1 0 195158 194879 1 0 0 0 332 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986929 Q9ULV4 62 155 1 1 0 194836 194344 1 0 0 0 431 partof CIAKVVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 492 2R:1731127-2080000 -1 NULL:1986930 Q9ULV4 150 316 1 1 0 2603191 196650 196461 1 0 0 0 259 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 189 2R:1731127-2080000 -1 NULL:1986932 AAH02342 2 65 1 1 0 195158 194879 1 0 0 0 332 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986933 AAH02342 62 155 1 1 0 194836 194344 1 0 0 0 431 partof CIAKVVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 492 2R:1731127-2080000 -1 NULL:1986934 AAH02342 150 316 1 1 0 2603196 196659 196461 1 0 0 0 266 partof MSFR-VVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 198 2R:1731127-2080000 -1 NULL:1986936 Q9BR76 0 67 1 1 0 195158 194879 1 0 0 0 326 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986937 Q9BR76 64 157 1 1 0 194836 194344 1 0 0 0 418 partof CIAKVVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 492 2R:1731127-2080000 -1 NULL:1986938 Q9BR76 152 318 1 1 0 2603201 207846 207204 1 0 0 0 372 partof IAHSFHQVLAAYQ---DSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAAT-INNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQIT--QSLYETKVALKLPRFKAEFQVELSEVFQ 642 2R:1731127-2080000 -1 NULL:1986940 P29508 80 300 1 1 0 2603203 207846 207204 1 0 0 0 372 partof IAHSFHQVLAAYQ---DSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAAT-INNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQIT--QSLYETKVALKLPRFKAEFQVELSEVFQ 642 2R:1731127-2080000 -1 NULL:1986942 AAH05224 80 300 1 1 0 2603205 208026 207189 1 0 0 0 459 partof LALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLAS-SDPEQIAH--SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLP--ALDA----MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 837 2R:1731127-2080000 -1 NULL:1986944 Q99574 25 313 1 1 0 2603207 210340 209644 1 0 0 0 287 partof GSATAKEMDEGLRFGGL--EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGS--EQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLE--KVDVKIPSFTAEFQQELSQVL 696 2R:1731127-2080000 -1 NULL:1986946 P29508 67 299 1 1 0 209580 209466 1 0 0 0 90 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986947 P29508 301 338 1 1 0 2603210 210340 209644 1 0 0 0 287 partof GSATAKEMDEGLRFGGL--EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGS--EQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLE--KVDVKIPSFTAEFQQELSQVL 696 2R:1731127-2080000 -1 NULL:1986949 AAH05224 67 299 1 1 0 209580 209466 1 0 0 0 90 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986950 AAH05224 301 338 1 1 0 2603213 210469 209644 1 0 0 0 338 partof QGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGL---EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRP-TRVRMMHVCENFFFAVLP--MFEA----TALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 825 2R:1731127-2080000 -1 NULL:1986952 Q99574 23 307 1 1 0 209580 209466 1 0 0 0 82 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986953 Q99574 309 346 1 1 0 2603216 265938 265515 1 0 0 0 423 partof RVCLRHKAVETRLKTFTSTIMDCLVQPLQERIEDWKRTVATIDKDHAKEYKRCRSELKKRSSDTLRLQKKARKGQTDGLQSLMDSHMQDVTLRRAELEEVEKKSLRAAMVEERLRYCSFVHMLQPVVHEECEVMSELGHLQ 423 2R:1731127-2080000 -1 NULL:1986955 Q9BUA8 0 140 1 1 0 2603219 265971 265515 1 0 0 0 461 partof GASKEIGTALTRVCLRHKAVETRLKTFTSTIMDCLVQPLQERIEDWKRTVATIDKDHAKEYKRCRSELKKRSSDTLRLQKKARKGQTDGLQSLMDSHMQDVTLRRAELEEVEKKSLRAAMVEERLRYCSFVHMLQPVVHEECEVMSELGHLQ 456 2R:1731127-2080000 -1 NULL:1986957 AAF15947 69 220 1 1 0 2603222 303172 302563 1 0 0 0 118 partof MQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFG--LVGQDNVE--FAKWTRNYWA-DFRMWQAYLALEFPLIARLLQYKS---YAEPATAYFQK-VALSXXXXXXXXXXXPLQTFLQLYSN-------AEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 609 2R:1731127-2080000 -1 NULL:1986959 Q9HB55 144 361 1 1 0 302505 302088 1 0 0 0 214 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1986960 Q9HB55 361 497 1 1 0 2603225 303172 302563 1 0 0 0 118 partof MQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFG--LVGQDNVE--FAKWTRNYWA-DFRMWQAYLALEFPLIARLLQYKS---YAEPATAYFQK-VALSXXXXXXXXXXXPLQTFLQLYSN-------AEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 609 2R:1731127-2080000 -1 NULL:1986962 AAK38841 144 361 1 1 0 302505 302088 1 0 0 0 214 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1986963 AAK38841 361 497 1 1 0 2603228 303583 302563 1 0 0 0 177 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDA-GHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL---GEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVE-----FAKWTRNYWADFRMWQAYLALE-FPLIARL---LQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAE--------KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1020 2R:1731127-2080000 -1 NULL:1986965 P20815 12 361 1 1 0 302505 302088 1 0 0 0 222 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1986966 P20815 361 496 1 1 0 2603231 304557 304140 1 0 0 0 236 partof LEDPQGALTTPT-EGGRTLVTRGGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSDEILG-ELRSYFEKYQGFVAMGG 417 2R:1731127-2080000 -1 NULL:1986968 Q9NUQ7 260 401 1 1 0 2603234 304557 304140 1 0 0 0 236 partof LEDPQGALTTPT-EGGRTLVTRGGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSDEILG-ELRSYFEKYQGFVAMGG 417 2R:1731127-2080000 -1 NULL:1986970 AAH10493 260 401 1 1 0 2603237 307432 306874 1 0 0 0 267 partof DKFFNLFHFKTNYCTIVL----DDSMHYLYTT---PLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE*WQQPHAIRISNNICFSRETRTGVAEEQDSDRAAGAL 558 2R:1731127-2080000 -1 NULL:1986972 Q9BUW9 80 272 1 1 0 306687 306537 1 0 0 0 92 partof LANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYL-SQPSEAAQAQLLQ 150 2R:1731127-2080000 -1 NULL:1986973 Q9BUW9 284 335 1 1 0 2603241 308367 307467 1 0 0 0 201 partof IDDLIEKLKTTSVSPANTT-----NLLCEISATKDPKLFDKHE---LAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLL-RLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDXXXXXXXXXXXXTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 900 2R:1731127-2080000 -1 NULL:1986975 Q9NYM2 3 302 1 1 0 307432 306985 1 0 0 0 270 partof DKFFNLFHFKTNYCTIVL----DDSMHYLYTT---PLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE 447 2R:1731127-2080000 -1 NULL:1986976 Q9NYM2 280 435 1 1 0 306924 306762 1 0 0 0 107 partof ALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKG 162 2R:1731127-2080000 -1 NULL:1986977 Q9NYM2 436 490 1 1 0 2603246 308376 307467 1 0 0 0 201 partof AAEIDDLIEKLKTTSVSPANTT-----NLLCEISATKDPKLFDKHE---LAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLL-RLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDXXXXXXXXXXXXTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 909 2R:1731127-2080000 -1 NULL:1986979 Q9BUX6 1 303 1 1 0 307432 306874 1 0 0 0 267 partof DKFFNLFHFKTNYCTIVL----DDSMHYLYTT---PLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE*WQQPHAIRISNNICFSRETRTGVAEEQDSDRAAGAL 558 2R:1731127-2080000 -1 NULL:1986980 Q9BUX6 281 473 1 1 0 306687 306537 1 0 0 0 92 partof LANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYL-SQPSEAAQAQLLQ 150 2R:1731127-2080000 -1 NULL:1986981 Q9BUX6 485 536 1 1 0 2603251 312246 311835 1 0 0 0 190 partof FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYNIATAVGDCHDQDPSQYKDYRGE-SEFNEA---NGNDLGAAFRRPYRGANQRMPQRQSL---YQTQQ 411 2R:1731127-2080000 -1 NULL:1986983 Q9UBS3 9 145 1 1 0 2603253 312246 312012 1 0 0 0 181 partof FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYN 234 2R:1731127-2080000 -1 NULL:1986985 Q9NXW2 93 171 1 1 0 2597643 24843 23736 1 0 0 0 914 partof YTSASTVLSVGGVRQQFSLAENIEMSLFGYNFVVNGREHLGDVD-----LCYQPNGYLILASEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRT----VKFDT--------CVL---AAGAYSGQVARLAGIGDKEAKEASLS-VALPVEPRKRYVYVVST-QGKNCPGLATPLTVDPDGTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 1107 2R:1731127-2080000 1 NULL:1982357 Q9UKY9 102 486 1 1 0 2597645 24843 23736 1 0 0 0 912 partof YTSASTVLSVGGVRQQFSLAENIEMSLFGYNFVVNGREHLGDVD-----LCYQPNGYLILASEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRT----VKFDT--------CVL---AAGAYSGQVARLAGIGDKEAKEASLS-VALPVEPRKRYVYVVST-QGKNCPGLATPLTVDPDGTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 1107 2R:1731127-2080000 1 NULL:1982359 AAH13902 102 486 1 1 0 2597647 24843 23787 1 0 0 0 856 partof SLAENIEMSLFGYNFVVNGREHLGDVD-----LCYQPNGYLILASEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRT----VKFDT--------CVL---AAGAYSGQVARLAGIGDKEAKEASLS-VALPVEPRKRYVYVVST-QGKNCPGLATPLTVDPDGTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 1056 2R:1731127-2080000 1 NULL:1982361 Q9BU39 3 370 1 1 0 2597649 27351 27189 1 0 0 0 279 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982363 AAH08929 15 69 1 1 0 28172 27821 1 0 0 0 561 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982364 AAH08929 68 185 1 1 0 2597652 28166 27818 1 0 0 0 489 partof NRSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVR 348 2R:1731127-2080000 1 NULL:1982366 BAB55326 2 118 1 1 0 2597655 28172 27899 1 0 0 0 431 partof NHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 273 2R:1731127-2080000 1 NULL:1982368 O75546 0 91 1 1 0 2597658 74969 74675 1 0 0 0 255 partof LWEKSSASLFTLLGLAFGDSQWERMVLAL---GFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHFRLNKVRNIKTWLSVRSYLK 294 2R:1731127-2080000 1 NULL:1982370 Q9H099 486 586 1 1 0 75480 75240 1 0 0 0 184 partof SVSVLITEQINLYLQIEQKPKKKDELMVSNSVXXXXXXXXXXXXTPFKLSGLSANPYLFTTIKVVILSALSGVLSEVLGF 240 2R:1731127-2080000 1 NULL:1982371 Q9H099 606 686 1 1 0 blastx_masked 1.0 aa_SPTR.insect 1.0 2003-01-13 18:40:09 BLASTX Similarity to Other Species genomic 2604721 340629 340449 1 0 0 0 120 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1988340 Q9NB07 20 79 1 1 0 2598868 24840 24504 1 0 0 0 426 partof ETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNI 336 2R:1731127-2080000 1 NULL:1983460 O61468 1 113 1 1 0 2598871 27351 27186 1 0 0 0 171 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1983462 O16143 16 71 1 1 0 28130 27821 1 0 0 0 223 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKI 309 2R:1731127-2080000 1 NULL:1983463 O16143 70 173 1 1 0 2598874 28136 27839 1 0 0 0 164 partof YYRGAAGALLVYDITRRETFNHLTTWLEDA-RQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 297 2R:1731127-2080000 1 NULL:1983465 AAF15522 70 170 1 1 0 2598876 28136 27839 1 0 0 0 164 partof YYRGAAGALLVYDITRRETFNHLTTWLEDA-RQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 297 2R:1731127-2080000 1 NULL:1983467 AAF15521 70 170 1 1 0 2598878 212416 211549 1 0 0 0 381 partof QEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR---GPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVD-LADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 867 2R:1731127-2080000 1 NULL:1983469 Q25500 25 305 1 1 0 2598881 212407 211633 1 0 0 0 396 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHH-IALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1983471 Q9NFT5 34 289 1 1 0 2598883 212407 211633 1 0 0 0 396 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHH-IALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1983473 Q9NFT6 34 289 1 1 0 2598885 214248 213432 1 0 0 0 446 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSED-KEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 816 2R:1731127-2080000 1 NULL:1983475 Q9NFT6 21 296 1 1 0 2598887 214248 213432 1 0 0 0 446 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSED-KEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 816 2R:1731127-2080000 1 NULL:1983477 Q9NFT5 21 296 1 1 0 2598889 214275 213453 1 0 0 0 439 partof KSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEE-----KIVGFARP-LVAKEVYLKLPKFKIEFRDELKETLEKVRLRQEKHGCATLT 822 2R:1731127-2080000 1 NULL:1983479 P80034 25 302 1 1 0 2598891 217109 216299 1 0 0 0 348 partof CSXXXXXXXXXAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXX--XXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKN-FAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKL 810 2R:1731127-2080000 1 NULL:1983481 P22922 5 265 1 1 0 2598893 217145 216383 1 0 0 0 369 partof FASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTE-VAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 762 2R:1731127-2080000 1 NULL:1983483 Q9NFT6 18 265 1 1 0 217770 217629 1 0 0 0 126 partof LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGAT 141 2R:1731127-2080000 1 NULL:1983484 Q9NFT6 291 338 1 1 0 2598896 217145 216383 1 0 0 0 369 partof FASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTE-VAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 762 2R:1731127-2080000 1 NULL:1983486 Q9NFT5 18 265 1 1 0 217770 217629 1 0 0 0 126 partof LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGAT 141 2R:1731127-2080000 1 NULL:1983487 Q9NFT5 291 338 1 1 0 2604654 5318 4850 1 0 0 0 422 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1988280 P54985 14 164 1 1 0 2604656 5318 4913 1 0 0 0 402 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIEN 405 2R:1731127-2080000 -1 NULL:1988282 O44098 15 145 1 1 0 2604658 5318 4913 1 0 0 0 404 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIEN 405 2R:1731127-2080000 -1 NULL:1988284 O44099 15 145 1 1 0 2604660 8846 7730 1 0 0 0 989 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQ-TSVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1988286 Q95YG8 40 412 1 1 0 7605 7422 1 0 0 0 124 partof GDEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 183 2R:1731127-2080000 -1 NULL:1988287 Q95YG8 413 474 1 1 0 2604664 8846 7730 1 0 0 0 985 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQ-TSVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1988289 Q95YG9 40 412 1 1 0 7605 7422 1 0 0 0 124 partof GDEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 183 2R:1731127-2080000 -1 NULL:1988290 Q95YG9 413 474 1 1 0 2604668 8846 7730 1 0 0 0 1017 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGV-DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1988292 Q9NL84 40 412 1 1 0 7611 7422 1 0 0 0 101 partof RTGDEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 189 2R:1731127-2080000 -1 NULL:1988293 Q9NL84 411 474 1 1 0 2604672 17620 16990 1 0 0 0 435 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIG-------KQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKH 630 2R:1731127-2080000 -1 NULL:1988295 Q9Y1Q0 38 237 1 1 0 2604675 17897 17771 1 0 0 0 147 partof ASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 126 2R:1731127-2080000 -1 NULL:1988297 Q9Y1P9 0 41 1 1 0 17620 16972 1 0 0 0 421 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIG-----KQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAA 648 2R:1731127-2080000 -1 NULL:1988298 Q9Y1P9 38 241 1 1 0 2604679 18131 17771 1 0 0 0 394 partof TAEPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 360 2R:1731127-2080000 -1 NULL:1988300 Q9NL84 31 147 1 1 0 17620 17044 1 0 0 0 329 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADS--FNTNPNKWLLTNFDCSTLWVR 576 2R:1731127-2080000 -1 NULL:1988301 Q9NL84 144 334 1 1 0 15554 15338 1 0 0 0 168 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEK 216 2R:1731127-2080000 -1 NULL:1988302 Q9NL84 403 475 1 1 0 2604683 88531 87622 1 0 0 0 597 partof PTIRLNNGREMPTLGLGTWKSFESDAYHSTR---------HALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLAR--PQPARQWP-PFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQR-TVPFSGMSGHKYYPFN 909 2R:1731127-2080000 -1 NULL:1988304 Q9Y020 22 329 1 1 0 2604685 88585 87703 1 0 0 0 538 partof PICTALIISASDKMTNLAPTIRLNNGREMPTLGLGTWKSFE-SDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLA-RPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDV 882 2R:1731127-2080000 -1 NULL:1988306 AAL73387 6 294 1 1 0 2604687 111138 110205 1 0 0 0 864 partof NYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQD 933 2R:1731127-2080000 -1 NULL:1988308 Q9NGT2 26 333 1 1 0 2604690 111147 110106 1 0 0 0 849 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEE-QEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1988310 Q27703 23 363 1 1 0 110040 109620 1 0 0 0 424 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1988311 Q27703 362 502 1 1 0 2604693 111147 110106 1 0 0 0 845 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1988313 P90730 23 365 1 1 0 110040 109620 1 0 0 0 468 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1988314 P90730 364 504 1 1 0 2604696 208017 207195 1 0 0 0 475 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSD-PEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR-LTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVS 822 2R:1731127-2080000 -1 NULL:1988316 Q25492 31 306 1 1 0 2604699 208041 207204 1 0 0 0 550 partof EFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQ-IAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQ 837 2R:1731127-2080000 -1 NULL:1988318 Q9NFT5 10 290 1 1 0 2604701 208041 207204 1 0 0 0 550 partof EFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQ-IAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQ 837 2R:1731127-2080000 -1 NULL:1988320 Q9NFT6 10 290 1 1 0 2604703 210460 209644 1 0 0 0 342 partof EQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAES-FGVVLKSYEQCQV--LKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDI-SLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 816 2R:1731127-2080000 -1 NULL:1988322 Q25492 29 302 1 1 0 209586 209466 1 0 0 0 91 partof SQMGMNRIFS-GQAELGGMLQSEESLFVSQIVHKAFIEINE 120 2R:1731127-2080000 -1 NULL:1988323 Q25492 302 343 1 1 0 2604706 210484 209644 1 0 0 0 416 partof DEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ-VAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 840 2R:1731127-2080000 -1 NULL:1988325 Q9NFT5 8 289 1 1 0 209580 209466 1 0 0 0 109 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1988326 Q9NFT5 291 329 1 1 0 2604709 210484 209644 1 0 0 0 416 partof DEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ-VAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 840 2R:1731127-2080000 -1 NULL:1988328 Q9NFT6 8 289 1 1 0 209580 209466 1 0 0 0 109 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1988329 Q9NFT6 291 329 1 1 0 2604712 303571 302563 1 0 0 0 414 partof LGALS--VVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKL---LVRLSQI-SSRIQRDLGEKSL--QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLY-----SNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1008 2R:1731127-2080000 -1 NULL:1988331 Q27691 10 361 1 1 0 302505 302100 1 0 0 0 271 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV 405 2R:1731127-2080000 -1 NULL:1988332 Q27691 361 496 1 1 0 2604715 303583 302626 1 0 0 0 412 partof LLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKS--LQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQ---KVALSXXXXXXXXXXXPLQTFLQLYSNAEK-----PLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE 957 2R:1731127-2080000 -1 NULL:1988334 Q27703 6 341 1 1 0 302505 302091 1 0 0 0 243 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1988335 Q27703 363 502 1 1 0 2604718 302505 302091 1 0 0 0 251 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1988338 BAB43954 361 500 1 1 0 303583 302563 1 0 0 0 422 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGLVGQD--NVE--FAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKV---ALSXXXXXXXXXXXPLQTFLQLYSNAEKPL----TDIE-IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTP--ECLRELRYTKQVLN 1020 2R:1731127-2080000 -1 NULL:1988337 BAB43954 9 361 1 1 0 clonelocator 1.0 scaffoldBACs 1.0 2003-01-13 18:34:00 BAC Scaffold genomic 2601406 396828 222077 1 0 0 0 0 partof 174751 2R:1731127-2080000 -1 NULL:1985611 BACR36G11 0 174751 1 1 0 2596058 217982 36211 1 0 0 0 0 partof 181771 2R:1731127-2080000 1 NULL:1981212 BACR07J20 0 181771 1 1 0 2596061 237709 87122 1 0 0 0 0 partof 150587 2R:1731127-2080000 1 NULL:1981214 BACR04F03 0 150587 1 1 0 2596064 411787 245932 1 0 0 0 0 partof 165855 2R:1731127-2080000 1 NULL:1981216 BACR29G01 0 165855 1 1 0 2588354 44906 -128796 1 0 0 0 0 partof 173702 2R:1731127-2080000 1 NULL:1975147 BACR01C10 0 173702 1 1 0 trnascan-se 1.0 2003-01-14 22:45:01 tRNAscan-SE Gene Prediction Program genomic 278980 278907 1 0 0 160168,160095-AE003790.Feb-dummy-trnascan-se 0 0 2R:1731127-2080000 NULL:1985439 278980 278907 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985440 278980 278907 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985440 278131 278058 1 0 0 159319,159246-AE003790.Feb-dummy-trnascan-se 0 0 2R:1731127-2080000 NULL:1985441 278131 278058 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985442 278131 278058 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985442 277585 277512 1 0 0 158773,158700-AE003790.Feb-dummy-trnascan-se 0 0 2R:1731127-2080000 NULL:1985443 277585 277512 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985444 277585 277512 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985444 276655 276582 1 0 0 157843,157770-AE003790.Feb-dummy-trnascan-se 0 0 2R:1731127-2080000 NULL:1985445 276655 276582 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985446 276655 276582 1 0 0 1 0 80.47 partof 73 2R:1731127-2080000 -1 NULL:1985446 repeatmasker 1.0 2003-01-13 22:31:35 genomic 2604723 154020 153966 1 0 0 0 295 partof 54 2R:1731127-2080000 -1 NULL:1988342 - 3 57 1 1 0 2604725 257586 257470 1 0 0 0 249 partof 116 2R:1731127-2080000 -1 NULL:1988344 roo 1052 1163 1 1 0 2604727 259668 259608 1 0 0 0 299 partof 60 2R:1731127-2080000 -1 NULL:1988346 roo 1094 1154 1 1 0 2604729 261377 261278 1 0 0 0 277 partof 99 2R:1731127-2080000 -1 NULL:1988348 roo 1064 1163 1 1 0 2604731 262374 262290 1 0 0 0 257 partof 84 2R:1731127-2080000 -1 NULL:1988350 roo 1082 1157 1 1 0 2598899 136839 136784 1 0 0 0 401 partof 55 2R:1731127-2080000 1 NULL:1983489 - 0 56 1 1 0 2598901 137017 136969 1 0 0 0 259 partof 48 2R:1731127-2080000 1 NULL:1983491 - 516 569 1 1 0 2598903 165754 165653 1 0 0 0 233 partof 101 2R:1731127-2080000 1 NULL:1983493 roo 1060 1163 1 1 0 2598905 245007 244952 1 0 0 0 324 partof 55 2R:1731127-2080000 1 NULL:1983495 - 16 71 1 1 0 2598907 245275 245014 1 0 0 0 897 partof 261 2R:1731127-2080000 1 NULL:1983497 - 292 594 1 1 0 2598909 274259 274112 1 0 0 0 504 partof 147 2R:1731127-2080000 1 NULL:1983499 - 279 437 1 1 0 2598911 277027 276894 1 0 0 0 799 partof 133 2R:1731127-2080000 1 NULL:1983501 - 0 132 1 1 0 2598913 277091 277036 1 0 0 0 423 partof 55 2R:1731127-2080000 1 NULL:1983503 - 510 565 1 1 0 2598915 278748 278345 1 0 0 0 2196 partof 403 2R:1731127-2080000 1 NULL:1983505 - 168 594 1 1 0 2598917 289518 281995 1 0 0 0 70773 partof 7523 2R:1731127-2080000 1 NULL:1983507 yoyo 0 7521 1 1 0 2598919 320535 318902 1 0 0 0 11973 partof 1633 2R:1731127-2080000 1 NULL:1983509 X01748 0 1653 1 1 0 tblastx 1.0 na_unigene.rodent 1.0 2003-01-13 19:00:19 BLASTX Similarity to Other Species genomic blastx_masked 1.0 aa_SPTR.dros 1.0 2003-01-15 00:56:26 BLASTX Similarity to Fly genomic 2603781 210355 209644 1 0 0 0 336 partof MGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKS---Y-EQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVR--MMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 711 2R:1731127-2080000 -1 NULL:1987500 Q9V989 0 241 1 1 0 209586 209466 1 0 0 0 79 partof SQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 120 2R:1731127-2080000 -1 NULL:1987501 Q9V989 241 281 1 1 0 2603784 210406 209668 1 0 0 0 301 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG---SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEF 738 2R:1731127-2080000 -1 NULL:1987503 Q9V4I3 47 295 1 1 0 2603786 210406 209668 1 0 0 0 298 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG---SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEF 738 2R:1731127-2080000 -1 NULL:1987505 Q9U5W8 47 295 1 1 0 2603788 210409 209626 1 0 0 0 248 partof LNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLE----AQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLVS*N 783 2R:1731127-2080000 -1 NULL:1987507 Q9V5S3 32 297 1 1 0 2603790 210409 209626 1 0 0 0 248 partof LNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLE----AQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLVS*N 783 2R:1731127-2080000 -1 NULL:1987509 AAK92954 32 297 1 1 0 2603792 210430 209647 1 0 0 0 278 partof LCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVL---KSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQAAS-IINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 783 2R:1731127-2080000 -1 NULL:1987511 Q9VLZ8 43 301 1 1 0 2603794 210442 209644 1 0 0 0 336 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVL---KSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 798 2R:1731127-2080000 -1 NULL:1987513 Q9U1I8 20 284 1 1 0 209583 209466 1 0 0 0 85 partof QMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 117 2R:1731127-2080000 -1 NULL:1987514 Q9U1I8 285 324 1 1 0 2603797 210442 209635 1 0 0 0 327 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLV 807 2R:1731127-2080000 -1 NULL:1987516 Q9VII7 20 284 1 1 0 2603799 210442 209635 1 0 0 0 327 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLV 807 2R:1731127-2080000 -1 NULL:1987518 Q9U1I6 20 284 1 1 0 2604004 312471 311910 1 0 0 0 246 partof QARRHHCVDKVVSDLCLGHYEHALRQINEDLEGLQNHDEIMALL-ELKNIILRLRLKGEAQRTIGPTRKSDALPHK------------FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYNIATAVGDCHDQDPSQYKDYRGESEF-NEANGNDLG 561 2R:1731127-2080000 -1 NULL:1987720 Q9VFP0 6 201 1 1 0 2604006 340623 340440 1 0 0 0 162 partof GILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALT 183 2R:1731127-2080000 -1 NULL:1987722 Q9NB14 22 83 1 1 0 2604008 340629 340437 1 0 0 0 322 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTS 192 2R:1731127-2080000 -1 NULL:1987724 Q9U3V3 20 84 1 1 0 340108 339862 1 0 0 0 368 partof DSLTENIL*FQFKCCGLNGFADYGITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGVTAVEVRIAY 246 2R:1731127-2080000 -1 NULL:1987725 Q9U3V3 127 208 1 1 0 2604011 340629 340365 1 0 0 0 133 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTSVGAHDTCPAGCNI*IQLAPSCFQY 264 2R:1731127-2080000 -1 NULL:1987727 Q9NB13 20 104 1 1 0 340129 339889 1 0 0 0 117 partof LLFHIHKDSLTENIL*FQFKCCGLNGFADY---GITYPASCCDS-PSNGTCALTQV-MTRSSCLKAVDSFWDTNVSIIKYAGLGV 240 2R:1731127-2080000 -1 NULL:1987728 Q9NB13 119 203 1 1 0 2604014 340629 340449 1 0 0 0 153 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1987730 Q9NB15 20 80 1 1 0 2604016 340629 340449 1 0 0 0 153 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1987732 Q9U3V4 20 80 1 1 0 2603402 48843 48423 1 0 0 0 335 partof LRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQ 420 2R:1731127-2080000 -1 NULL:1987129 AAL48543 267 407 1 1 0 2603404 48843 48423 1 0 0 0 335 partof LRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQ 420 2R:1731127-2080000 -1 NULL:1987131 Q9VEX1 267 407 1 1 0 2603406 48843 48423 1 0 0 0 335 partof LRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQ 420 2R:1731127-2080000 -1 NULL:1987133 Q9GRW9 266 406 1 1 0 2603408 49230 48798 1 0 0 0 275 partof IPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLREVVTIKDAGEELRTEIVVQPEE----SPKEPNW-LRGLGIIVALSLHEL 432 2R:1731127-2080000 -1 NULL:1987135 Q9GRW9 71 216 1 1 0 2603410 49230 48798 1 0 0 0 275 partof IPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLREVVTIKDAGEELRTEIVVQPEE----SPKEPNW-LRGLGIIVALSLHEL 432 2R:1731127-2080000 -1 NULL:1987137 AAL48543 72 217 1 1 0 2603412 49230 48798 1 0 0 0 275 partof IPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLREVVTIKDAGEELRTEIVVQPEE----SPKEPNW-LRGLGIIVALSLHEL 432 2R:1731127-2080000 -1 NULL:1987139 Q9VEX1 72 217 1 1 0 2603414 49305 48867 1 0 0 0 290 partof VDQHXXXXXXXXXXXXXXXTLIFC-FIPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLRE--VVTIK-DAGEELRTEIVVQPE 438 2R:1731127-2080000 -1 NULL:1987141 Q9V9B2 14 164 1 1 0 48840 48414 1 0 0 0 347 partof RGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIAS 426 2R:1731127-2080000 -1 NULL:1987142 Q9V9B2 198 340 1 1 0 2603417 49305 48867 1 0 0 0 290 partof VDQHXXXXXXXXXXXXXXXTLIFC-FIPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLRE--VVTIK-DAGEELRTEIVVQPE 438 2R:1731127-2080000 -1 NULL:1987144 AAL48717 14 164 1 1 0 48840 48414 1 0 0 0 347 partof RGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIAS 426 2R:1731127-2080000 -1 NULL:1987145 AAL48717 198 340 1 1 0 2603420 49305 48867 1 0 0 0 290 partof VDQHXXXXXXXXXXXXXXXTLIFC-FIPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLRE--VVTIK-DAGEELRTEIVVQPE 438 2R:1731127-2080000 -1 NULL:1987147 Q9GRX0 8 158 1 1 0 48840 48414 1 0 0 0 347 partof RGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIAS 426 2R:1731127-2080000 -1 NULL:1987148 Q9GRX0 192 334 1 1 0 2603423 49308 48393 1 0 0 0 1206 partof MVDQHXXXXXXXXXXXXXXXTLIFCFIPYLLDRFYKWTQRPENNAREFKVVLCLLNFGGGVLIATTFIHMLPEVVEVVNALQDCRMLAPTPFGLPEVLLCTGFYLMYCIEETMHFXXXXXXXXXLREVVTIKDAGEELRTEIVVQPEESPKEPNWLRGLGIIVALSLHELFGGMAIGLEMSVSTVWFMTGAISVHKLVLAFCIGMEIMMAHTRWLLAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXACGTLIYVVFFEIVAKNHAGIRILLSSMVGFVLMFGLQIASKHTKKPK 915 2R:1731127-2080000 -1 NULL:1987150 Q9V9B1 0 305 1 1 0 2603425 53349 53070 1 0 0 0 295 partof LNYCILPAHTASTINHKXXXXXXXXXXXXXXXXXXXXXXXPERNGKQPAFCRSFCSPSSLKESNLXXXXXXXXXXXQFVQNYISRKRKRIEKQ 279 2R:1731127-2080000 -1 NULL:1987152 Q9N6X2 0 93 1 1 0 52684 52525 1 0 0 0 283 partof DARSCVTCDKVLAELEKIDDDTDSFGVDFVKINDKRLAKQYGIKNFPALTYFR 159 2R:1731127-2080000 -1 NULL:1987153 Q9N6X2 93 146 1 1 0 52471 52303 1 0 0 0 284 partof RNGNPLLFEGDLQNEQSVLEWLIDDDNRELADEIEEVNERMLDRLMAESTLLVVFF 168 2R:1731127-2080000 -1 NULL:1987154 Q9N6X2 145 201 1 1 0 52046 51857 1 0 0 0 303 partof TL*HFRKQVPVLYDGDLHQHDKVITWLTSQDVFEIKNEIEEVNRKMLDKLLEENEFLAVFFCE 189 2R:1731127-2080000 -1 NULL:1987155 Q9N6X2 248 311 1 1 0 51815 51617 1 0 0 0 323 partof VFYLDEHNQPDSTAALEKLENIDSETDNLDITFVKMADSRYAKKWGVTKLPAMVYFRRRFPSIYRG 198 2R:1731127-2080000 -1 NULL:1987156 Q9N6X2 306 371 1 1 0 51557 51368 1 0 0 0 279 partof QGDLLSEDEVLEWLRKNRFRQPELNIFMYALIALAVAFVVYTAFLLQCFKXXXXXXVQHPKQS 189 2R:1731127-2080000 -1 NULL:1987157 Q9N6X2 369 432 1 1 0 2603433 53795 53609 1 0 0 0 342 partof ADGCEQCTKVLEELENIDDDCDKHGITFVKTRDFSVADGYGVHEYPALVYFEGGIPNVFEGE 186 2R:1731127-2080000 -1 NULL:1987159 Q9V9A9 1260 1322 1 1 0 53563 53431 1 0 0 0 219 partof GELSEEEEVLQWLITQKTEDRIELITRQMLETMVEETQYLAVYF 132 2R:1731127-2080000 -1 NULL:1987160 Q9V9A9 1320 1364 1 1 0 52681 52525 1 0 0 0 277 partof KINCNICDQILEGLELIDDECDVFGIHMVKIQDPQLAKRYSIKTFPALVYFR 156 2R:1731127-2080000 -1 NULL:1987161 Q9V9A9 1365 1417 1 1 0 52471 52303 1 0 0 0 284 partof RNGNPLLFEGDLQNEQSVLEWLIDDDNRELADEIEEVNERMLDRLMAESTLLVVFF 168 2R:1731127-2080000 -1 NULL:1987162 Q9V9A9 1416 1472 1 1 0 52046 51857 1 0 0 0 303 partof TL*HFRKQVPVLYDGDLHQHDKVITWLTSQDVFEIKNEIEEVNRKMLDKLLEENEFLAVFFCE 189 2R:1731127-2080000 -1 NULL:1987163 Q9V9A9 1519 1582 1 1 0 51815 51617 1 0 0 0 323 partof VFYLDEHNQPDSTAALEKLENIDSETDNLDITFVKMADSRYAKKWGVTKLPAMVYFRRRFPSIYRG 198 2R:1731127-2080000 -1 NULL:1987164 Q9V9A9 1577 1642 1 1 0 51557 51368 1 0 0 0 279 partof QGDLLSEDEVLEWLRKNRFRQPELNIFMYALIALAVAFVVYTAFLLQCFKXXXXXXVQHPKQS 189 2R:1731127-2080000 -1 NULL:1987165 Q9V9A9 1640 1703 1 1 0 2603442 53804 53609 1 0 0 0 155 partof QSDADGCEQCTKVLEELENIDDDCDKHGITFVKTRDFSVADGYGVHEYPALVYFEGGIPNVFEGE 195 2R:1731127-2080000 -1 NULL:1987167 Q9N6X2 91 156 1 1 0 2603444 55415 55196 1 0 0 0 134 partof DSDECKQCPRVLAEVEHIDDEADKAGIDFVKIDDKQMAKEYGVFALPAIVFFKPTSKEPVIYAGRCPEFREVL 219 2R:1731127-2080000 -1 NULL:1987169 Q9N6X2 93 164 1 1 0 2603446 55776 55479 1 0 0 0 223 partof RVLRHIELIDDEAAEYGIYIVKMHDKLMAKKYGFRNPPGLTYFRKGKYINYDGDIDDEEEVLDWLTSPANMEMTDHIEQVNRKMFEKIRKNSDYVAVIF 297 2R:1731127-2080000 -1 NULL:1987171 Q9N6X2 102 201 1 1 0 2603448 62316 62013 1 0 0 0 271 partof CEHTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWITDDETLEIPGKIEEVNVKMLDKILAENDHVVVFF 303 2R:1731127-2080000 -1 NULL:1987173 Q9N6X2 100 201 1 1 0 2603450 63138 62115 1 0 0 0 305 partof SRYKLSKTAVC*SVNYIASNALQTIVKLSYEIIFADDK-DQKKSQKILAELENIDDECDQNDIAFVKIDDDKEAKEWGIDEIPSIVLFERGIPHIYEGDLMKEDELLGWLV---HQKRYSEIPEVTDEMKDKLVENTEHLAVIFCE*TTLLMYLRLCNHYHSLTXXXXXXXXXXXXXXXXXXXXXXXKEGIVIVRIDNAAEAKEYGLDHLPALIYFENKIPALYEGDL----MNEDEVLEWLLVQKKTATIEEVTDEILVTLINEHEYVVVFFTGPCEPGETCEHTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWI 1023 2R:1731127-2080000 -1 NULL:1987175 Q9N6X2 57 383 1 1 0 2603452 63658 63400 1 0 0 0 267 partof ECDALGITFVKIDNPEEAVEYGINKVPKLIYFEKGIPTIYEGNLEDEEKLLKWLTDQTSSDQIEDITDEMLDLIIEKMPHVAVLFC 258 2R:1731127-2080000 -1 NULL:1987177 Q9V9B0 179 265 1 1 0 63072 62718 1 0 0 0 609 partof QTIVKLSYEIIFADDKDQKKSQKILAELENIDDECDQNDIAFVKIDDDKEAKEWGIDEIPSIVLFERGIPHIYEGDLMKEDELLGWLVHQKRYSEIPEVTDEMKDKLVENTEHLAVIF 354 2R:1731127-2080000 -1 NULL:1987178 Q9V9B0 320 438 1 1 0 62589 62013 1 0 0 0 1000 partof KEGIVIVRIDNAAEAKEYGLDHLPALIYFENKIPALYEGDLMNEDEVLEWLLVQKKTATIEEVTDEILVTLINEHEYVVVFFTGPCEPGETCEHTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWITDDETLEIPGKIEEVNVKMLDKILAENDHVVVFF 576 2R:1731127-2080000 -1 NULL:1987179 Q9V9B0 461 653 1 1 0 61957 61771 1 0 0 0 326 partof AEGDKKAQKILNELENIDDECEEKDIDFVKTSDDDIDKEYDLPGLPALAFYRHKFRTIYTGE 186 2R:1731127-2080000 -1 NULL:1987180 Q9V9B0 654 716 1 1 0 61710 61572 1 0 0 0 231 partof GDLMKEEEILEWVIDLHESTADVIESVDRKTLQVLINDVEHLAVFF 138 2R:1731127-2080000 -1 NULL:1987181 Q9V9B0 714 760 1 1 0 61506 61317 1 0 0 0 244 partof DDECESCSXXXXXXXXXXXXXXKHGIQFVKSNDVKLAHEIGIFAFPALVYYETGVPIMYDGKL 189 2R:1731127-2080000 -1 NULL:1987182 Q9V9B0 761 824 1 1 0 56176 56026 1 0 0 0 232 partof ILQTGNIASNQDVFNWILEQKADQSIQLINRDQLFEYIGTKDFLAVVFCK 150 2R:1731127-2080000 -1 NULL:1987183 Q9V9B0 817 867 1 1 0 55800 55479 1 0 0 0 572 partof KEDDPDSPRVLRHIELIDDEAAEYGIYIVKMHDKLMAKKYGFRNPPGLTYFRKGKYINYDGDIDDEEEVLDWLTSPANMEMTDHIEQVNRKMFEKIRKNSDYVAVIF 321 2R:1731127-2080000 -1 NULL:1987184 Q9V9B0 866 973 1 1 0 55412 55196 1 0 0 0 335 partof SDECKQCPRVLAEVEHIDDEADKAGIDFVKIDDKQMAKEYGVFALPAIVFFKPTSKEPVIYAGRCPEFREVL 216 2R:1731127-2080000 -1 NULL:1987185 Q9V9B0 974 1046 1 1 0 55171 55030 1 0 0 0 240 partof AGDLYEEEQILTWLITQKDPSGDVIEDLEGERLVHLIEESGSIAVYF 141 2R:1731127-2080000 -1 NULL:1987186 Q9V9B0 1035 1082 1 1 0 53819 53609 1 0 0 0 351 partof STPL*QSDADGCEQCTKVLEELENIDDDCDKHGITFVKTRDFSVADGYGVHEYPALVYFEGGIPNVFEGE 210 2R:1731127-2080000 -1 NULL:1987187 Q9V9B0 1158 1228 1 1 0 53563 53431 1 0 0 0 219 partof GELSEEEEVLQWLITQKTEDRIELITRQMLETMVEETQYLAVYF 132 2R:1731127-2080000 -1 NULL:1987188 Q9V9B0 1226 1270 1 1 0 52681 52525 1 0 0 0 277 partof KINCNICDQILEGLELIDDECDVFGIHMVKIQDPQLAKRYSIKTFPALVYFR 156 2R:1731127-2080000 -1 NULL:1987189 Q9V9B0 1271 1323 1 1 0 52471 52081 1 0 0 0 525 partof RNGNPLLFEGDLQNEQSVLEWLIDDDNRELADEIEEVNERMLDRLMAESTLLVVFFCEYHSLNELQNGLKNSSHTYVXXXXXXXXXXXXXXXXXXXXXXXMFGIDFVKIASIQAAKKYEIVNIPSLVYFR 390 2R:1731127-2080000 -1 NULL:1987190 Q9V9B0 1322 1452 1 1 0 52046 51857 1 0 0 0 303 partof TL*HFRKQVPVLYDGDLHQHDKVITWLTSQDVFEIKNEIEEVNRKMLDKLLEENEFLAVFFCE 189 2R:1731127-2080000 -1 NULL:1987191 Q9V9B0 1446 1509 1 1 0 51815 51617 1 0 0 0 323 partof VFYLDEHNQPDSTAALEKLENIDSETDNLDITFVKMADSRYAKKWGVTKLPAMVYFRRRFPSIYRG 198 2R:1731127-2080000 -1 NULL:1987192 Q9V9B0 1504 1569 1 1 0 51557 51368 1 0 0 0 279 partof QGDLLSEDEVLEWLRKNRFRQPELNIFMYALIALAVAFVVYTAFLLQCFKXXXXXXVQHPKQS 189 2R:1731127-2080000 -1 NULL:1987193 Q9V9B0 1567 1630 1 1 0 2603471 63658 63403 1 0 0 0 185 partof ECDALGITFVKIDNPEEAVEYGINKVPKLIYFEKGIPTIYEGNLEDEEKLLKWLTDQTS---SDQIEDITDEMLDLIIEKMPHVAVLF 255 2R:1731127-2080000 -1 NULL:1987195 Q9N6X2 113 201 1 1 0 2603473 63966 63789 1 0 0 0 132 partof PAIVYFEKEIPNVYDGDLMDEEQILKWLLGQLER---DEIEDVTDEMLDTMIKEGRVIAVLF 177 2R:1731127-2080000 -1 NULL:1987197 Q9N6X2 139 201 1 1 0 2603475 65299 65128 1 0 0 0 276 partof MWPGSYHTDKFTDEATEINITYTQRRPEKRKLAENTFTNVVSPTQRNRGKGK--CKERA 171 2R:1731127-2080000 -1 NULL:1987199 Q9V9B0 0 59 1 1 0 64615 64501 1 0 0 0 203 partof LGIGFVKIHDEALADEYNLGNLPALVYYRHQTPIIYEG 114 2R:1731127-2080000 -1 NULL:1987200 Q9V9B0 74 112 1 1 0 64392 64230 1 0 0 0 239 partof YRTVSP----GELQREEDVLEWLVQNKSTGDEDDVIEDVTSKTLSTLISNIDNLVVLF 162 2R:1731127-2080000 -1 NULL:1987201 Q9V9B0 101 159 1 1 0 64165 64030 1 0 0 0 237 partof DHGNDDSMTVLEELEQIDDDCDKHGIQFVKIDDAKAAADYGIDSV 135 2R:1731127-2080000 -1 NULL:1987202 Q9V9B0 160 205 1 1 0 63969 63786 1 0 0 0 315 partof IPAIVYFEKEIPNVYDGDLMDEEQILKWLLGQLERDEIEDVTDEMLDTMIKEGRVIAVLFC 183 2R:1731127-2080000 -1 NULL:1987203 Q9V9B0 204 265 1 1 0 2603481 67985 67736 1 0 0 0 118 partof HLLQVGNSPTTNKTQDLIESNPYLENRREKEPIIYDGDLMDEEGVLDFLTSLEAMDLPDRIEEVNAKILQKIIEDTDFVAVLF 249 2R:1731127-2080000 -1 NULL:1987205 Q9N6X2 120 201 1 1 0 2603483 68128 67972 1 0 0 0 272 partof ARSCVTCDKVLAELEKIDDDTDSFGVDFVKINDKRLAKQYGIKNFPALTYFR 156 2R:1731127-2080000 -1 NULL:1987207 Q9V9A9 72 124 1 1 0 67934 67733 1 0 0 0 294 partof IESNPYLENRREKEPIIYDGDLMDEEGVLDFLTSLEAMDLPDRIEEVNAKILQKIIEDTDFVAVLFC 201 2R:1731127-2080000 -1 NULL:1987208 Q9V9A9 113 180 1 1 0 64615 64501 1 0 0 0 203 partof LGIGFVKIHDEALADEYNLGNLPALVYYRHQTPIIYEG 114 2R:1731127-2080000 -1 NULL:1987209 Q9V9A9 215 253 1 1 0 64392 64230 1 0 0 0 239 partof YRTVSP----GELQREEDVLEWLVQNKSTGDEDDVIEDVTSKTLSTLISNIDNLVVLF 162 2R:1731127-2080000 -1 NULL:1987210 Q9V9A9 242 300 1 1 0 64165 64030 1 0 0 0 237 partof DHGNDDSMTVLEELEQIDDDCDKHGIQFVKIDDAKAAADYGIDSV 135 2R:1731127-2080000 -1 NULL:1987211 Q9V9A9 301 346 1 1 0 63969 63789 1 0 0 0 306 partof IPAIVYFEKEIPNVYDGDLMDEEQILKWLLGQLERDEIEDVTDEMLDTMIKEGRVIAVLF 180 2R:1731127-2080000 -1 NULL:1987212 Q9V9A9 345 405 1 1 0 63658 63403 1 0 0 0 441 partof ECDALGITFVKIDNPEEAVEYGINKVPKLIYFEKGIPTIYEGNLEDEEKLLKWLTDQTSSDQIEDITDEMLDLIIEKMPHVAVLF 255 2R:1731127-2080000 -1 NULL:1987213 Q9V9A9 425 510 1 1 0 63090 62718 1 0 0 0 553 partof IASNALQTIV-KLSYEIIFADDKDQKKSQKILAELENIDDECDQNDIAFVKIDDDKEAKEWGIDEIPSIVLFERGIPHIYEGDLMKEDELLGWLVHQKRYSEIPEVTDEMKDKLVENTEHLAVIF 372 2R:1731127-2080000 -1 NULL:1987214 Q9V9A9 490 615 1 1 0 62589 62013 1 0 0 0 1000 partof KEGIVIVRIDNAAEAKEYGLDHLPALIYFENKIPALYEGDLMNEDEVLEWLLVQKKTATIEEVTDEILVTLINEHEYVVVFFTGPCEPGETCEHTLNALESIDDELDEAGIIFVTTEDTGIAKKYNVKTYPRLVFFRNRDPLHFTGDLDDEDEVLAWITDDETLEIPGKIEEVNVKMLDKILAENDHVVVFF 576 2R:1731127-2080000 -1 NULL:1987215 Q9V9A9 638 830 1 1 0 61957 61771 1 0 0 0 326 partof AEGDKKAQKILNELENIDDECEEKDIDFVKTSDDDIDKEYDLPGLPALAFYRHKFRTIYTGE 186 2R:1731127-2080000 -1 NULL:1987216 Q9V9A9 831 893 1 1 0 61710 61572 1 0 0 0 231 partof GDLMKEEEILEWVIDLHESTADVIESVDRKTLQVLINDVEHLAVFF 138 2R:1731127-2080000 -1 NULL:1987217 Q9V9A9 891 937 1 1 0 61506 61317 1 0 0 0 244 partof DDECESCSXXXXXXXXXXXXXXKHGIQFVKSNDVKLAHEIGIFAFPALVYYETGVPIMYDGKL 189 2R:1731127-2080000 -1 NULL:1987218 Q9V9A9 938 1001 1 1 0 56176 56026 1 0 0 0 232 partof ILQTGNIASNQDVFNWILEQKADQSIQLINRDQLFEYIGTKDFLAVVFCK 150 2R:1731127-2080000 -1 NULL:1987219 Q9V9A9 994 1044 1 1 0 55800 55479 1 0 0 0 572 partof KEDDPDSPRVLRHIELIDDEAAEYGIYIVKMHDKLMAKKYGFRNPPGLTYFRKGKYINYDGDIDDEEEVLDWLTSPANMEMTDHIEQVNRKMFEKIRKNSDYVAVIF 321 2R:1731127-2080000 -1 NULL:1987220 Q9V9A9 1043 1150 1 1 0 55412 55196 1 0 0 0 335 partof SDECKQCPRVLAEVEHIDDEADKAGIDFVKIDDKQMAKEYGVFALPAIVFFKPTSKEPVIYAGRCPEFREVL 216 2R:1731127-2080000 -1 NULL:1987221 Q9V9A9 1151 1223 1 1 0 55171 54967 1 0 0 0 241 partof AGDLYEEEQILTWLITQKDPSGDVIEDLEGERLVHLIEESGSIAVYFCKFATESTQ*FNR*IFNISED 204 2R:1731127-2080000 -1 NULL:1987222 Q9V9A9 1212 1280 1 1 0 2603801 210457 209641 1 0 0 0 334 partof QFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDV--KIPSFTAEFQQELSQVLM 816 2R:1731127-2080000 -1 NULL:1987520 Q9U1I7 15 283 1 1 0 209580 209466 1 0 0 0 71 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1987521 Q9U1I7 284 321 1 1 0 2603804 210457 209743 1 0 0 0 307 partof 714 2R:1731127-2080000 -1 NULL:1987523 Q9VLQ7 15 254 1 1 0 2603806 210463 209644 1 0 0 0 294 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQV--LKMANGLYVMKGLQ-VDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSD-RPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLS--DISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1987525 Q9U5W7 106 383 1 1 0 2603808 210463 209644 1 0 0 0 294 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQV--LKMANGLYVMKGLQ-VDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSD-RPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLS--DISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1987527 Q9V4I5 106 383 1 1 0 2603810 210466 209644 1 0 0 0 352 partof GLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKS--YEQCQ------VLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFG-SDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 822 2R:1731127-2080000 -1 NULL:1987529 Q9V987 12 294 1 1 0 2603812 210472 209641 1 0 0 0 195 partof AQGLEQFALCLHDHLCRA--SAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE-QCQVLKMAN--GLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT--RVRMMHVCENF-FFAVLPMFEATALRMNYSACN-LAMIILLPDEKSNLTSLEKKLSDISLEVV--------SSAMNLEKVDVKIPSFTAEFQQELSQVLM 831 2R:1731127-2080000 -1 NULL:1987531 Q9VWB3 64 353 1 1 0 2603814 210478 209644 1 0 0 0 394 partof EFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFF-GSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 834 2R:1731127-2080000 -1 NULL:1987533 Q9V3L3 6 284 1 1 0 209583 209466 1 0 0 0 111 partof QMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 117 2R:1731127-2080000 -1 NULL:1987534 Q9V3L3 285 324 1 1 0 2603817 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1987536 Q9U1I5 6 284 1 1 0 209589 209466 1 0 0 0 126 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 123 2R:1731127-2080000 -1 NULL:1987537 Q9U1I5 284 325 1 1 0 2603820 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1987539 Q9I7G5 6 284 1 1 0 209589 209466 1 0 0 0 133 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 123 2R:1731127-2080000 -1 NULL:1987540 Q9I7G5 284 325 1 1 0 2603823 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1987542 Q9I7G6 38 316 1 1 0 209589 209466 1 0 0 0 133 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 123 2R:1731127-2080000 -1 NULL:1987543 Q9I7G6 316 357 1 1 0 2603826 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1987545 Q9V991 45 323 1 1 0 209589 209466 1 0 0 0 133 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 123 2R:1731127-2080000 -1 NULL:1987546 Q9V991 323 364 1 1 0 2603829 210490 209632 1 0 0 0 1451 partof MKDEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLVS 858 2R:1731127-2080000 -1 NULL:1987548 Q9V990 0 286 1 1 0 2603831 210496 209701 1 0 0 0 208 partof FIMKDEEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFG-GLEAQQVAESFGVVLKSYE----QCQV-LKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQAASI--INKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSAC--NLAMIILLPDEKSNLTSLE--KKLSDISLEVVSSAMNLEKV 795 2R:1731127-2080000 -1 NULL:1987550 Q9VFC1 26 298 1 1 0 2603833 265998 265515 1 0 0 0 817 partof MIIRIPSIAGASKEIGTALTRVCLRHKAVETRLKTFTSTIMDCLVQPLQERIEDWKRTVATIDKDHAKEYKRCRSELKKRSSDTLRLQKKARKGQTDGLQSLMDSHMQDVTLRRAELEEVEKKSLRAAMVEERLRYCSFVHMLQPVVHEECEVMSELGHLQ 483 2R:1731127-2080000 -1 NULL:1987552 Q9V982 0 161 1 1 0 265461 265185 1 0 0 0 248 partof LQEAMQSIALVTKEPSVLPQASEELIHDAKASINLYPEXXXXXXXXXXXXXXXXXXXRKXXXXXXXXXXXXXXXXXPGHHHYPRSLSQVRHA 276 2R:1731127-2080000 -1 NULL:1987553 Q9V982 159 251 1 1 0 264859 264619 1 0 0 0 441 partof ANVSTWPPHSQDGVDTLPPTADRPHTISTAYEKGHQRPPLTVYTFQNPETIHESGSCLNNGTAAPNGQPLSGQATPATQK 240 2R:1731127-2080000 -1 NULL:1987554 Q9V982 255 335 1 1 0 263955 263841 1 0 0 0 203 partof RCSSLERPLSAQSNHRQGSGNNLLQRQCPSPIPAHITK 114 2R:1731127-2080000 -1 NULL:1987555 Q9V982 348 386 1 1 0 263703 262962 1 0 0 0 473 partof ELSAAHHAXXXXXXXXXXXXXXXXYVNMSELATMAALKQTNQQQKPSTPPLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIDSTVACGSLVXXXXXXXXXXXXXXXXXXXXXXXXXHYSPLLTNXXXXXXXXXXXXXXXXXXXXXXFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADETDERSRASVLQKASMFEKXXXXXXXXXXXXMQI 741 2R:1731127-2080000 -1 NULL:1987556 Q9V982 386 633 1 1 0 262425 260835 1 0 0 0 1716 partof ELDSFQREIDEGKVKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPATSNIEPCAISNQTNSSGCGTDISDTTSDELAGXXXXXXXXXXXXXXXLLGASDSELSRCYVSEXXXXXXXXXXXXYENPTFAHFAANANREDAVSLASDSVCLGQPRHAYVDTCSDSGSAVVVIYDHQIPNTPDIEFVKQNSEIVVLRTKDPQPHALXXXXXXXXXXXPANLXXXXXXXXXXXXXQAPPTATVAPAKQRLSSFRATSEQQLQLLGRGSPQRGKTPSEQAVQSRPXXXXXXXXXXXXXXGSSPPVELARRQLPPKPTSLSIFNGPVPTAGDRPVVPRKSDFKADLDAKIRRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPQSPQTRNCNVTNQQXXXXXXXXXXXXXXXXXXDPYPNPNHRMPNQNQTATSNHTQCKTPTMAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNARPSMLPASDRPPAHPYVCSNAPANPHHANSISNANAHLKPCITPRPASLSG 1590 2R:1731127-2080000 -1 NULL:1987557 Q9V982 652 1182 1 1 0 259888 259669 1 0 0 0 220 partof NYATQLQQQPQHATXXXXXXXXXXXXXXXXXXXXFMLDAMPQIPSSALKVSETVRALAAMRHQPASPVSLRRM 219 2R:1731127-2080000 -1 NULL:1987558 Q9V982 1217 1290 1 1 0 258653 257243 1 0 0 0 825 partof HATNTPSLTHIHDQTFRTSSPAAXXXXXXXIYAQPKLVNXXXXXXXXXXXPNGHAHPLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIEGIYGNQQAPGGESIYMRSXXXXXXXXXXXXFDGKSEXXXXXXXXXXRIYXXXXXXXXXXXXXXXXXXXTKPSILTPTTSFNAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHYXXXXXXNAAVANSKDMAIYSSSFTKNPAAAQSPNMRQAXXXXXXXXXXXXXXXXXXXXXXXXXXXIYAAGASATMPKKMARPPTGQNXXXXXXXXXXXXXXXLPKNMMXXXXXXXXXXXXXXPAXXXXXXXXXXXXQRPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPPIPSRHSSVQQKIFVSTNPFIQTTAVKFHSPSASPTCGSPVTGSLASIYATTSRGGXXXXXXXXXXXXXYYRD 1410 2R:1731127-2080000 -1 NULL:1987559 Q9V982 1368 1837 1 1 0 256601 256445 1 0 0 0 236 partof NRLCHKHKYRKDWQYSCQDQGRIPRESQREAGEAGNVWTSICRAKSHQQQGP 156 2R:1731127-2080000 -1 NULL:1987560 Q9V982 1852 1904 1 1 0 2603844 275194 274945 1 0 0 0 195 partof IVIMRTLMLFVFGFASSWAADYELLLEDPDIFSPCTEPPPGSIGFHDAFDIGDLVVDQDMDIIHLSESVTSIWDVEPTDRISV 249 2R:1731127-2080000 -1 NULL:1987562 Q9VIJ2 0 81 1 1 0 274889 274715 1 0 0 0 205 partof RFAIMHYNRGSWEPTVFSMATPDFCASMFDENQSWFKYWTKHISNRDEVMEKCFKTRG 174 2R:1731127-2080000 -1 NULL:1987563 Q9VIJ2 81 139 1 1 0 273815 273524 1 0 0 0 151 partof VAVAIKG--SDLTVFGSMVIMIFVXXXXXGVTSSWATDYELLLEDPDIFSTCTDGPPGSINIRQALNLDDIVIDQKGDILHVSGNATVVWDVQPTDRIT 291 2R:1731127-2080000 -1 NULL:1987564 Q9VIJ2 184 281 1 1 0 273458 273281 1 0 0 0 135 partof ARLDVFHFNRGTWEPTVFSMATQNFCSIMYDKNXXXXXXXXXXITNRHEVEKKCFRGPD 177 2R:1731127-2080000 -1 NULL:1987565 Q9VIJ2 281 340 1 1 0 273121 272962 1 0 0 0 123 partof TVLVHEPFDLILKFENFRGPLLRGRHKLVILFNALDERNIPRPNPICLEIIGE 159 2R:1731127-2080000 -1 NULL:1987566 Q9VIJ2 340 393 1 1 0 2603850 302514 302172 1 0 0 0 190 partof FFLETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAE 342 2R:1731127-2080000 -1 NULL:1987568 Q9V559 376 489 1 1 0 2603852 302953 302563 1 0 0 0 155 partof LALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQL-----------YS-NAEKPL---TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 390 2R:1731127-2080000 -1 NULL:1987570 Q9V776 233 377 1 1 0 2603854 303016 302563 1 0 0 0 154 partof NVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEKPL-----------TDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 453 2R:1731127-2080000 -1 NULL:1987572 Q9V774 201 365 1 1 0 2603856 303133 302563 1 0 0 0 175 partof RIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQL-------YSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 570 2R:1731127-2080000 -1 NULL:1987574 Q9V773 158 362 1 1 0 2603858 303151 302566 1 0 0 0 152 partof LSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADF--RMWQAYLALEFPLIARLLQYKSYAEPATAYFQKV---ALSXXXXXXXXXXXPLQTFLQLYSNAE-----KPLTDIE--IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEH-GGQVTPECLRELRYTKQVL 585 2R:1731127-2080000 -1 NULL:1987576 Q9VRB3 164 375 1 1 0 2603860 303175 302566 1 0 0 0 197 partof NMQKLLVRLSQISSRIQRDLGEKSL-QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVA---LSXXXXXXXXXXXPLQTFLQLYSN-----AEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1987578 Q9V770 142 360 1 1 0 2603862 303175 302566 1 0 0 0 199 partof NMQKLLVRLSQISSRI---QRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXP---LQTFLQLYS-----NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 609 2R:1731127-2080000 -1 NULL:1987580 Q9V771 143 361 1 1 0 2603864 303247 302563 1 0 0 0 176 partof NLLQLDGHKWRSLHAKSAEVF-TPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM-WQAYLAL-EFPLIARLLQYKSYAEPATAYFQKVA---LSXXXXXXXXXXXPLQTFL---QLYSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 684 2R:1731127-2080000 -1 NULL:1987582 P82711 128 362 1 1 0 2603866 303253 302563 1 0 0 0 176 partof SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSXXXXXXXXXXXPLQTFLQLYSN--AEKPLTDIEI-AGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 690 2R:1731127-2080000 -1 NULL:1987584 Q9VRI9 136 383 1 1 0 2603868 303385 302566 1 0 0 0 127 partof VGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAE-VFTPANMQKLLVRLSQISSRIQRDLGEKSLQT-INISELVGAYNTDVMASMAFGLV----GQD--NVEFAKWTRN-YWADFRMWQAYLALE----FPLIAR--LLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 819 2R:1731127-2080000 -1 NULL:1987586 Q9V7G5 87 372 1 1 0 302505 302151 1 0 0 0 161 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAP-SAETSIPVEY 354 2R:1731127-2080000 -1 NULL:1987587 Q9V7G5 373 490 1 1 0 2597754 3591 3477 1 0 0 0 203 partof AIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSA 114 2R:1731127-2080000 1 NULL:1982452 AAL39813 7 45 1 1 0 3974 3644 1 0 0 0 597 partof ADGLEIQEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFAVVCL 330 2R:1731127-2080000 1 NULL:1982453 AAL39813 44 154 1 1 0 4503 4035 1 0 0 0 829 partof TSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPLASLYYE 468 2R:1731127-2080000 1 NULL:1982454 AAL39813 151 307 1 1 0 2597759 3591 3477 1 0 0 0 203 partof AIVLLLGALVTACLASNGDRTQFFHNCRQNCERTNCSA 114 2R:1731127-2080000 1 NULL:1982456 Q9V9C0 7 45 1 1 0 3974 3644 1 0 0 0 597 partof ADGLEIQEQAVKFYQQSVFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFAVVCL 330 2R:1731127-2080000 1 NULL:1982457 Q9V9C0 44 154 1 1 0 4560 4035 1 0 0 0 930 partof TSLNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPLASLYYECVEILLYSNIATCVCILAS 525 2R:1731127-2080000 1 NULL:1982458 Q9V9C0 151 326 1 1 0 2603871 303523 302569 1 0 0 0 224 partof YWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDG-HKWRSLHAKSAEVFTPANMQ-----KLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG---QDNVEFAKWTRNYW-ADFRMWQAYLALEF-PLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTF-LQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQV 954 2R:1731127-2080000 -1 NULL:1987589 Q9V676 23 354 1 1 0 302508 302106 1 0 0 0 155 partof LETLRLHTPHPFLLRRATKE----FEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERF-EEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 402 2R:1731127-2080000 -1 NULL:1987590 Q9V676 355 494 1 1 0 2603874 303523 302803 1 0 0 0 152 partof YWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK--GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPA---NMQKLLVRLSQ-ISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQD--NVEFAKWTR-----NYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQK---VALSXXXXXXXXXXXPLQTFLQL 720 2R:1731127-2080000 -1 NULL:1987592 Q9VRI9 44 299 1 1 0 302505 302130 1 0 0 0 167 partof ETLRLHTPHPFLLRRATKE--FEV-P---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLL 375 2R:1731127-2080000 -1 NULL:1987593 Q9VRI9 383 514 1 1 0 2603877 303538 302566 1 0 0 0 257 partof KFSLGYWKRRGILHEKPKFLW---GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACL-KPFILALDLKLVHQIIF-TDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGL----------VGQDNVEFAKWTRNYWADFRMW---QAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQ-VTPECLRELRYTKQVL 972 2R:1731127-2080000 -1 NULL:1987595 Q9VWR2 17 344 1 1 0 302508 302094 1 0 0 0 166 partof LETLRLHTPHPFLLRRATKEFEVP------GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1987596 Q9VWR2 344 485 1 1 0 2597764 21627 21495 1 0 0 0 211 partof MHYRKAENVEKELSKSDLPFEDCMPKSQKDFLWMHVSSTNNVSN 132 2R:1731127-2080000 1 NULL:1982460 Q9V9B6 0 44 1 1 0 2597767 21836 21617 1 0 0 0 246 partof CFKSLPESIHFAKVKGGTKVSNVIEFAQEALNKGEHRCXXXXXXXXXXXKTISCAEVLKRSHPLYQVTRMAYT 219 2R:1731127-2080000 1 NULL:1982462 Q9V9B6 22 95 1 1 0 22012 21892 1 0 0 0 209 partof SVEEHWKPQMEGLEEIIVTRQIPTLHILMSLDELPDTIDG 120 2R:1731127-2080000 1 NULL:1982463 Q9V9B6 95 135 1 1 0 22278 22068 1 0 0 0 274 partof LQKPNTSTDFWDGGGAXXXXXXXXXXXXXXXXXKPGAGRGGRPNKRTRPGRNKPGQQPEKPAAEENLPAS 210 2R:1731127-2080000 1 NULL:1982464 Q9V9B6 135 205 1 1 0 2603880 303544 302629 1 0 0 0 165 partof LVKFSLGYWKR---RGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL--------GEKSLQTINISELVGAYNTDVMASMAFGL-VGQ-DNVEFAKWTRNYWADFRMWQAYL----ALEFPLIARLLQYKSYAEPATAYFQKV---ALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALE 915 2R:1731127-2080000 -1 NULL:1987598 Q9V4I0 16 339 1 1 0 302505 302166 1 0 0 0 148 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETS 339 2R:1731127-2080000 -1 NULL:1987599 Q9V4I0 362 479 1 1 0 2603883 303556 302914 1 0 0 0 154 partof VVYALVKFSLGYWKRRGILHEKPKFLWGNIK-GVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS--RGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKL--LVRLSQISSR--IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL-VG--QD-NVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQ 642 2R:1731127-2080000 -1 NULL:1987601 Q9W130 15 238 1 1 0 2603885 303562 302878 1 0 0 0 301 partof LSVVYAL-VKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPAN---MQKLLVRLS-QISSRIQRDLGEKSLQ--TINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYF 684 2R:1731127-2080000 -1 NULL:1987603 Q9V4U7 11 250 1 1 0 302782 302563 1 0 0 0 141 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEE-HGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1987604 Q9V4U7 297 371 1 1 0 302505 302091 1 0 0 0 299 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987605 Q9V4U7 371 509 1 1 0 2603889 303565 302566 1 0 0 0 444 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT----INISELVGAYNTDVMASMAFGLV--GQDN--VEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEK--PLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 999 2R:1731127-2080000 -1 NULL:1987607 Q9V769 10 354 1 1 0 302505 302082 1 0 0 0 251 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1987608 Q9V769 355 497 1 1 0 2597771 24843 23736 1 0 0 0 1957 partof YTSASTVLSVGGVRQQFSLAENIEMSLFGYNFVVNGREHLGDVDLCYQPNGYLILASEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRTVKFDTCVLAAGAYSGQVARLAGIGDKEAKEASLSVALPVEPRKRYVYVVSTQGKNCPGLATPLTVDPDGTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 1107 2R:1731127-2080000 1 NULL:1982466 Q9V9B5 71 440 1 1 0 2597774 24843 23736 1 0 0 0 1957 partof YTSASTVLSVGGVRQQFSLAENIEMSLFGYNFVVNGREHLGDVDLCYQPNGYLILASEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRTVKFDTCVLAAGAYSGQVARLAGIGDKEAKEASLSVALPVEPRKRYVYVVSTQGKNCPGLATPLTVDPDGTYFRRDGLCGNFLCGRSPNEDEEPECETLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHEVNIV 1107 2R:1731127-2080000 1 NULL:1982468 Q95U69 30 399 1 1 0 2597777 27351 27183 1 0 0 0 167 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1982470 AAL48702 14 70 1 1 0 28118 27821 1 0 0 0 237 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI 297 2R:1731127-2080000 1 NULL:1982471 AAL48702 69 167 1 1 0 2603892 303565 303028 1 0 0 0 178 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS-RGLYSNPSGEPLSHNLLQLDGH--------KWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1987610 Q9VG82 11 201 1 1 0 302466 302094 1 0 0 0 210 partof RRATKE--FEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSD--IKLSVER 372 2R:1731127-2080000 -1 NULL:1987611 Q9VG82 388 515 1 1 0 2603895 303565 302644 1 0 0 0 181 partof ALSVV-YALVKFSLGYWK---RRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQ-LDGHKWRSLHAKSAEVFTPANMQKLLVRLSQ-ISSRIQR-DLGEKSLQ-----TINISELVGAYNTDVMASMAFGLV--GQDNV--EFAKWTRN--YWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKV---ALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEI 921 2R:1731127-2080000 -1 NULL:1987613 Q9V4I1 8 334 1 1 0 302505 302169 1 0 0 0 134 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAET 336 2R:1731127-2080000 -1 NULL:1987614 Q9V4I1 362 478 1 1 0 2603898 303565 302644 1 0 0 0 181 partof ALSVV-YALVKFSLGYWK---RRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQ-LDGHKWRSLHAKSAEVFTPANMQKLLVRLSQ-ISSRIQR-DLGEKSLQ-----TINISELVGAYNTDVMASMAFGLV--GQDNV--EFAKWTRN--YWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKV---ALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEI 921 2R:1731127-2080000 -1 NULL:1987616 AAL13345 8 334 1 1 0 302505 302169 1 0 0 0 134 partof ETLRLHTPHPFLLRRATKEFEVP---GS-VFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAET 336 2R:1731127-2080000 -1 NULL:1987617 AAL13345 362 478 1 1 0 2597780 27351 27183 1 0 0 0 167 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1982473 Q9VM50 14 70 1 1 0 28118 27821 1 0 0 0 237 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI 297 2R:1731127-2080000 1 NULL:1982474 Q9VM50 69 167 1 1 0 2597783 27351 27183 1 0 0 0 123 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1982476 P25228 28 84 1 1 0 28142 27821 1 0 0 0 208 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGV 321 2R:1731127-2080000 1 NULL:1982477 P25228 83 190 1 1 0 2597786 27351 27183 1 0 0 0 123 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1982479 AAL25488 28 84 1 1 0 28142 27821 1 0 0 0 208 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGV 321 2R:1731127-2080000 1 NULL:1982480 AAL25488 83 190 1 1 0 2597789 27351 27183 1 0 0 0 181 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1982482 Q9V3L5 15 71 1 1 0 28148 27821 1 0 0 0 324 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFD 327 2R:1731127-2080000 1 NULL:1982483 Q9V3L5 70 179 1 1 0 2597792 27348 27186 1 0 0 0 116 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAF 162 2R:1731127-2080000 1 NULL:1982485 Q9V3I2 37 91 1 1 0 28118 27824 1 0 0 0 229 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI 294 2R:1731127-2080000 1 NULL:1982486 Q9V3I2 92 190 1 1 0 2597795 27351 27186 1 0 0 0 162 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982488 Q9W5X0 16 71 1 1 0 28124 27821 1 0 0 0 188 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVI-MLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYE 303 2R:1731127-2080000 1 NULL:1982489 Q9W5X0 70 170 1 1 0 2597798 27351 27186 1 0 0 0 127 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982491 O76742 16 71 1 1 0 28124 27821 1 0 0 0 139 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLED----ARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYE 303 2R:1731127-2080000 1 NULL:1982492 O76742 70 175 1 1 0 2598000 212416 211633 1 0 0 0 420 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 783 2R:1731127-2080000 1 NULL:1982687 Q9U1I8 32 287 1 1 0 2598002 212422 211633 1 0 0 0 317 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNY--GDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKF-RFAELPQLKARAVQLPYDYSN-IHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQVRY 789 2R:1731127-2080000 1 NULL:1982689 Q9VL44 29 293 1 1 0 2598004 212377 211669 1 0 0 0 192 partof LTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVND--SLELLTEFNEIAVDFFQS-----KAEATRFAD-SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHV-QVNMMYQEDKFRFAE-LPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL----ADIDAALTLQDVEIFLPR-MCI 708 2R:1731127-2080000 1 NULL:1982691 Q9VWB4 13 262 1 1 0 2598006 212416 211684 1 0 0 0 1267 partof MGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 732 2R:1731127-2080000 1 NULL:1982693 Q9V989 0 244 1 1 0 212624 212441 1 0 0 0 244 partof LCFNNNV-ISDIYSQLGITEVFSDKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVS 183 2R:1731127-2080000 1 NULL:1982694 Q9V989 228 290 1 1 0 212885 212690 1 0 0 0 256 partof SVMKIVPMMLNMNKKLFKADHPFVFYIRNPQAVFFAGRFSNPKXXXXXXXXXXXXXXFDANMYNV 195 2R:1731127-2080000 1 NULL:1982695 Q9V989 289 354 1 1 0 2598010 212416 211996 1 0 0 0 202 partof NLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFH-VDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 420 2R:1731127-2080000 1 NULL:1982697 Q9VA48 386 527 1 1 0 2598012 214236 213375 1 0 0 0 578 partof IPKLGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERI-NQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFAR-PLVAKEVYLKLPKFKIEFRDELKETLEKV 861 2R:1731127-2080000 1 NULL:1982699 Q9VLZ8 20 305 1 1 0 2598014 214227 213384 1 0 0 0 661 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETL 843 2R:1731127-2080000 1 NULL:1982701 Q9U1I7 3 282 1 1 0 2598016 214245 213384 1 0 0 0 687 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLR 861 2R:1731127-2080000 1 NULL:1982703 Q9U1I6 3 287 1 1 0 2598018 214245 213384 1 0 0 0 687 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLR 861 2R:1731127-2080000 1 NULL:1982705 Q9VII7 3 287 1 1 0 2598020 214281 213384 1 0 0 0 601 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFK--IEFRD-ELKETLEK--VRLRQEKHGCATLTLD 897 2R:1731127-2080000 1 NULL:1982707 Q9VLQ7 3 299 1 1 0 2598022 214248 213384 1 0 0 0 1413 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 864 2R:1731127-2080000 1 NULL:1982709 Q9U1I8 3 291 1 1 0 214619 214502 1 0 0 0 196 partof AVAVTNRAGFSTFLMADHPFAFVIRDANTIYFQGRVVSP 117 2R:1731127-2080000 1 NULL:1982710 Q9U1I8 333 372 1 1 0 2598025 214236 213405 1 0 0 0 274 partof TSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSE--DKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSG-KIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTAN-KSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSN-LSMTIFLPREVEGLSALEEKI----VGFARPLVAKE-VYLKLPKFKIEFRDELKETLEKV 831 2R:1731127-2080000 1 NULL:1982712 Q9VL44 7 291 1 1 0 2598027 214248 213420 1 0 0 0 491 partof QTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQ-----GQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGF-----ARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 828 2R:1731127-2080000 1 NULL:1982714 Q9V987 15 301 1 1 0 2598029 214059 213426 1 0 0 0 221 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP-SEDKEAVAARYG-ALLNDLQGQEEGPI-LKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGP-VAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPY 633 2R:1731127-2080000 1 NULL:1982716 Q9VFC1 41 252 1 1 0 2598031 214236 213426 1 0 0 0 460 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982718 Q9V3L3 15 287 1 1 0 2598033 214236 213426 1 0 0 0 390 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLND-LQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVA-----KEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982720 AAK92954 18 294 1 1 0 2598035 214236 213426 1 0 0 0 390 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLND-LQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVA-----KEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982722 Q9V5S3 18 294 1 1 0 2598037 214248 213426 1 0 0 0 373 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYS-LNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG--F-----ARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 822 2R:1731127-2080000 1 NULL:1982724 Q9V4I5 110 390 1 1 0 2598039 214248 213426 1 0 0 0 373 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYS-LNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG--F-----ARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 822 2R:1731127-2080000 1 NULL:1982726 Q9U5W7 110 390 1 1 0 2598041 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982728 Q9I7G6 48 320 1 1 0 214432 214288 1 0 0 0 80 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNXXXXXXXXXT 144 2R:1731127-2080000 1 NULL:1982729 Q9I7G6 318 366 1 1 0 2598044 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982731 Q9V991 55 327 1 1 0 214432 214288 1 0 0 0 80 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNXXXXXXXXXT 144 2R:1731127-2080000 1 NULL:1982732 Q9V991 325 373 1 1 0 2598047 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982734 Q9U1I5 16 288 1 1 0 214432 214288 1 0 0 0 77 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNXXXXXXXXXT 144 2R:1731127-2080000 1 NULL:1982735 Q9U1I5 286 334 1 1 0 2603500 68131 67972 1 0 0 0 150 partof DARSCVTCDKVLAELEKIDDDTDSFGVDFVKINDKRLAKQYGIKNFPALTYFR 159 2R:1731127-2080000 -1 NULL:1987224 Q9V9B0 50 103 1 1 0 2603502 68131 67972 1 0 0 0 158 partof 159 2R:1731127-2080000 -1 NULL:1987226 Q9N6X2 93 146 1 1 0 2603504 86526 86316 1 0 0 0 186 partof SSTSAP--SRSTWTKVLLRNRIVSVRREQ---VFT*-P-QLAIPTDKTYSWCLCGKSKSQPLCDGMHKNEFLKIKQR 210 2R:1731127-2080000 -1 NULL:1987228 Q9V9A5 17 94 1 1 0 86267 86135 1 0 0 0 240 partof VLSRPIRFKVEKSGDYWLCNCKQTTHRPFCDGTHKQPHIQSAVK 132 2R:1731127-2080000 -1 NULL:1987229 Q9V9A5 90 134 1 1 0 2603508 86526 86316 1 0 0 0 186 partof SSTSAP--SRSTWTKVLLRNRIVSVRREQ---VFT*-P-QLAIPTDKTYSWCLCGKSKSQPLCDGMHKNEFLKIKQR 210 2R:1731127-2080000 -1 NULL:1987231 AAL48998 19 96 1 1 0 86267 86135 1 0 0 0 240 partof VLSRPIRFKVEKSGDYWLCNCKQTTHRPFCDGTHKQPHIQSAVK 132 2R:1731127-2080000 -1 NULL:1987232 AAL48998 92 136 1 1 0 2598050 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1982737 Q9I7G5 16 288 1 1 0 214432 214288 1 0 0 0 80 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNXXXXXXXXXT 144 2R:1731127-2080000 1 NULL:1982738 Q9I7G5 286 334 1 1 0 2598053 214236 213432 1 0 0 0 341 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPV---AAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG---FAR--PLVAKEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1982740 Q9U5W8 34 306 1 1 0 2598055 214236 213432 1 0 0 0 338 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPV---AAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG---FAR--PLVAKEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1982742 Q9V4I3 34 306 1 1 0 2598057 214227 213435 1 0 0 0 326 partof IYQLLSKSHTNQNLVVSPVSIETILSMVFMG-AEGS-TAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVA-----KEVYLKLPKFKIEFRDELKETL 792 2R:1731127-2080000 1 NULL:1982744 Q9V990 16 282 1 1 0 2598059 214059 213444 1 0 0 0 240 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP-SEDKEAVAARYGA-LLNDLQGQEEGPI-LKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPY 615 2R:1731127-2080000 1 NULL:1982746 Q9U1I4 49 254 1 1 0 2603512 86638 86488 1 0 0 0 249 partof MQACYSSSAKPVDSAKTIPSNLLEDKQTAVLQKENGTIFDKRPFKIHLDK 150 2R:1731127-2080000 -1 NULL:1987234 Q9V9A5 12 62 1 1 0 2603514 86638 86488 1 0 0 0 249 partof MQACYSSSAKPVDSAKTIPSNLLEDKQTAVLQKENGTIFDKRPFKIHLDK 150 2R:1731127-2080000 -1 NULL:1987236 AAL48998 14 64 1 1 0 2603516 88525 87628 1 0 0 0 536 partof IRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNV----HGTLELTDV--DYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPA---------RQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYP 897 2R:1731127-2080000 -1 NULL:1987238 Q9VHX4 6 319 1 1 0 2603518 88531 87661 1 0 0 0 664 partof PTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHND---SNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARP-QP-ARQWPPFLYDE-HAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVP 870 2R:1731127-2080000 -1 NULL:1987240 Q9VTK9 3 299 1 1 0 2598061 214242 213447 1 0 0 0 231 partof LSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAAR-YGALLNDL-QGQEEGPILKLANRIYVNDQYSLN-QNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTS----DVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFR--DLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG-----FARPLVAKEVYLKLPKFKIEFRDELKETLEKVRL 795 2R:1731127-2080000 1 NULL:1982748 Q9V4I4 46 323 1 1 0 2598063 214245 213465 1 0 0 0 204 partof NQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAAR--YGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSV-PVQMMAQMGTFR-ANYFRDLDAQVIELPY-LNSNLSMTIFLPR------EVE------GLSALEEKIVGFA-RPLVAKEVYLKLPKFKIEFRDELKETLEKVRLR 780 2R:1731127-2080000 1 NULL:1982750 Q9VWB3 86 358 1 1 0 2598065 214248 213522 1 0 0 0 380 partof MGAEGSTAKELQSALGLPSEDKEAVAARYGALLN-DLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI--VGFA---RPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 726 2R:1731127-2080000 1 NULL:1982752 Q9V989 0 248 1 1 0 2598067 214242 213546 1 0 0 0 190 partof KELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAE-RINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPV---QMMAQMGTFRANYFRDLDAQVIELPYLNSNLS-MTIFLP--REVEGLSALE-----EKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRL 696 2R:1731127-2080000 1 NULL:1982754 Q9VLU4 65 303 1 1 0 2598069 217124 216332 1 0 0 0 303 partof AMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKAD--TAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDL 792 2R:1731127-2080000 1 NULL:1982756 Q9U5W8 15 272 1 1 0 2603520 88531 87688 1 0 0 0 625 partof PTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELT------DVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWP---PFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENF-RVFDFELSPDDVAGMEQ 843 2R:1731127-2080000 -1 NULL:1987242 Q9VTL0 3 293 1 1 0 2603522 88546 87613 1 0 0 0 1661 partof MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 933 2R:1731127-2080000 -1 NULL:1987244 Q9V9A4 0 311 1 1 0 2603524 88546 87613 1 0 0 0 909 partof MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNV-----HGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 933 2R:1731127-2080000 -1 NULL:1987246 Q9Y112 0 316 1 1 0 2603526 92972 92618 1 0 0 0 315 partof LSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGK---LQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTI-RFCRS 354 2R:1731127-2080000 -1 NULL:1987248 Q9VMF3 944 1065 1 1 0 2603528 92972 92618 1 0 0 0 315 partof LSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGK---LQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTI-RFCRS 354 2R:1731127-2080000 -1 NULL:1987250 Q95V18 944 1065 1 1 0 2598071 217124 216332 1 0 0 0 302 partof AMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKAD--TAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDL 792 2R:1731127-2080000 1 NULL:1982758 Q9V4I3 15 272 1 1 0 2598073 217226 216335 1 0 0 0 1309 partof MANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLXXXXXXXXXXXXXXXXXVPLQAALEEV 891 2R:1731127-2080000 1 NULL:1982760 Q9V987 0 297 1 1 0 217827 217620 1 0 0 0 238 partof LFQLGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSVRKHKYTNIFDSLYSF 207 2R:1731127-2080000 1 NULL:1982761 Q9V987 293 361 1 1 0 2598076 217034 216347 1 0 0 0 206 partof LN-YSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPY 687 2R:1731127-2080000 1 NULL:1982763 Q9VFC1 27 252 1 1 0 2598078 217145 216356 1 0 0 0 218 partof SKSPAGEA--QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVA-EKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLT--QTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLI-AP--ESL-DADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 789 2R:1731127-2080000 1 NULL:1982765 Q9V4I4 27 294 1 1 0 2603530 98799 98700 1 0 0 0 175 partof GFGPSVQATAAATSPTKRPLSPDHPNPALPITE 99 2R:1731127-2080000 -1 NULL:1987252 Q95U79 12 45 1 1 0 98443 98347 1 0 0 0 163 partof QTPSPAMNRMGWALRTLLVADNSSCLKDRKVS 96 2R:1731127-2080000 -1 NULL:1987253 Q95U79 44 76 1 1 0 98285 98099 1 0 0 0 246 partof VSGKLIRKCAPGTELVDWLVNLSPIVHTRAQAAGMWQALLEEGVLAHGKFHQTPRAQFPNRC 186 2R:1731127-2080000 -1 NULL:1987254 Q95U79 74 132 1 1 0 98090 97895 1 0 0 0 336 partof VNKEQPFKDKCFLYRFRIDEEGGTAAAGVPQAEDLGAANEHIREALSALFQRGPDATLRMILRKP 195 2R:1731127-2080000 -1 NULL:1987255 Q95U79 121 186 1 1 0 97346 97190 1 0 0 0 171 partof LIRSSHERTSXXXXXXXXXXXHIAALSHLSTSIKRELSSIFVFEAHAQAGTI 156 2R:1731127-2080000 -1 NULL:1987256 Q95U79 182 234 1 1 0 96971 96824 1 0 0 0 253 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1987257 Q95U79 234 283 1 1 0 95888 95708 1 0 0 0 305 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERVAKQRGQHSAFK 180 2R:1731127-2080000 -1 NULL:1987258 Q95U79 282 342 1 1 0 95474 95312 1 0 0 0 273 partof RYTVMSGTPAKMLEHLLETRLGQSVGGMDPFLDDFLLTHIVFMPVVQLVDELAN 162 2R:1731127-2080000 -1 NULL:1987259 Q95U79 341 395 1 1 0 94510 94150 1 0 0 0 648 partof FHCDAHEDAQTPEDREYIINFKKRVIQFMQKWVMAVRHAAFEEPSVCDFIEDLAAEVEADPDLNEETSIVHNVLTQMARYQEDRNQNAGQKWKLPPNGQPICLFSGNATPSKTVIRPDDD 360 2R:1731127-2080000 -1 NULL:1987260 Q95U79 396 516 1 1 0 94080 93801 1 0 0 0 446 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDALVSADQLGC 279 2R:1731127-2080000 -1 NULL:1987261 Q95U79 516 609 1 1 0 93766 93592 1 0 0 0 321 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGKV 174 2R:1731127-2080000 -1 NULL:1987262 Q95U79 601 659 1 1 0 93390 93243 1 0 0 0 221 partof HFHPQITANLDVFLRRFNEVQYWIVTELVSTPSLSKRVGLVRKFIKLAA 147 2R:1731127-2080000 -1 NULL:1987263 Q95U79 653 702 1 1 0 92984 92588 1 0 0 0 619 partof KLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSRSLGKTNKPP 396 2R:1731127-2080000 -1 NULL:1987264 Q95U79 695 824 1 1 0 92550 92424 1 0 0 0 209 partof GLEPPSPKSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTRKL 126 2R:1731127-2080000 -1 NULL:1987265 Q95U79 819 861 1 1 0 2598080 217034 216371 1 0 0 0 224 partof GEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVP-KLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPY 663 2R:1731127-2080000 1 NULL:1982767 Q9U1I4 38 254 1 1 0 2598082 217145 216371 1 0 0 0 292 partof GEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLG-AEGS-TADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 774 2R:1731127-2080000 1 NULL:1982769 Q9V990 8 258 1 1 0 2598084 217145 216371 1 0 0 0 354 partof GEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 774 2R:1731127-2080000 1 NULL:1982771 Q9V3L3 10 260 1 1 0 217770 217620 1 0 0 0 119 partof LFQLGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGAT 150 2R:1731127-2080000 1 NULL:1982772 Q9V3L3 283 333 1 1 0 2598087 217121 216374 1 0 0 0 294 partof EAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGID 747 2R:1731127-2080000 1 NULL:1982774 Q9VLZ8 32 275 1 1 0 2598089 217145 216374 1 0 0 0 214 partof EAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQ-QIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKV-SVDTMSQEDYF-RFGELTELKAKVVELPYT-GTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 771 2R:1731127-2080000 1 NULL:1982776 Q9VL44 10 264 1 1 0 2603545 99449 99080 1 0 0 0 535 partof MAAGRQRWSTQIVAGSERSPGVLLLRYRRHSGGDDQVXXXXXXXXXXXXXXXXXXXXVKWRRQLERGQMTRPQSTAFEMSNVMGIAELNQAETPNTNGHLRFPLQKNKELMNDIFTNCKLKNG 369 2R:1731127-2080000 -1 NULL:1987267 Q9V9A3 0 123 1 1 0 98799 98700 1 0 0 0 175 partof GFGPSVQATAAATSPTKRPLSPDHPNPALPITE 99 2R:1731127-2080000 -1 NULL:1987268 Q9V9A3 122 155 1 1 0 98443 98347 1 0 0 0 163 partof QTPSPAMNRMGWALRTLLVADNSSCLKDRKVS 96 2R:1731127-2080000 -1 NULL:1987269 Q9V9A3 154 186 1 1 0 98285 98099 1 0 0 0 246 partof VSGKLIRKCAPGTELVDWLVNLSPIVHTRAQAAGMWQALLEEGVLAHGKFHQTPRAQFPNRC 186 2R:1731127-2080000 -1 NULL:1987270 Q9V9A3 184 242 1 1 0 98090 97895 1 0 0 0 336 partof VNKEQPFKDKCFLYRFRIDEEGGTAAAGVPQAEDLGAANEHIREALSALFQRGPDATLRMILRKP 195 2R:1731127-2080000 -1 NULL:1987271 Q9V9A3 231 296 1 1 0 97346 97190 1 0 0 0 171 partof LIRSSHERTSXXXXXXXXXXXHIAALSHLSTSIKRELSSIFVFEAHAQAGTI 156 2R:1731127-2080000 -1 NULL:1987272 Q9V9A3 292 344 1 1 0 96971 96824 1 0 0 0 253 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1987273 Q9V9A3 344 393 1 1 0 95888 95708 1 0 0 0 305 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERVAKQRGQHSAFK 180 2R:1731127-2080000 -1 NULL:1987274 Q9V9A3 392 452 1 1 0 95474 95330 1 0 0 0 244 partof RYTVMSGTPAKMLEHLLETRLGQSVGGMDPFLDDFLLTHIVFMPVVQL 144 2R:1731127-2080000 -1 NULL:1987275 Q9V9A3 451 499 1 1 0 94489 94150 1 0 0 0 602 partof DAQTPEDREYIINFKKRVIQFMQKWVMAVRHAAFEEPSVCDFIEDLAAEVEADPDLNEETSIVHNVLTQMARYQEDRNQNAGQKWKLPPNGQPICLFSGNATPSKTVIRPDDD 339 2R:1731127-2080000 -1 NULL:1987276 Q9V9A3 499 612 1 1 0 94080 93801 1 0 0 0 446 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDALVSADQLGC 279 2R:1731127-2080000 -1 NULL:1987277 Q9V9A3 612 705 1 1 0 93766 93592 1 0 0 0 321 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGKV 174 2R:1731127-2080000 -1 NULL:1987278 Q9V9A3 697 755 1 1 0 93390 93243 1 0 0 0 221 partof HFHPQITANLDVFLRRFNEVQYWIVTELVSTPSLSKRVGLVRKFIKLAA 147 2R:1731127-2080000 -1 NULL:1987279 Q9V9A3 749 798 1 1 0 92984 92588 1 0 0 0 619 partof KLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSRSLGKTNKPP 396 2R:1731127-2080000 -1 NULL:1987280 Q9V9A3 791 920 1 1 0 92550 92424 1 0 0 0 209 partof GLEPPSPKSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTRKL 126 2R:1731127-2080000 -1 NULL:1987281 Q9V9A3 915 957 1 1 0 2598091 217145 216377 1 0 0 0 433 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 768 2R:1731127-2080000 1 NULL:1982778 Q9I7G6 45 293 1 1 0 217794 217620 1 0 0 0 133 partof LFQ-LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSVRKHK 174 2R:1731127-2080000 1 NULL:1982779 Q9I7G6 315 374 1 1 0 2598094 217145 216377 1 0 0 0 433 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 768 2R:1731127-2080000 1 NULL:1982781 Q9V991 52 300 1 1 0 217794 217620 1 0 0 0 133 partof LFQ-LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSVRKHK 174 2R:1731127-2080000 1 NULL:1982782 Q9V991 322 381 1 1 0 2598097 217145 216377 1 0 0 0 433 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 768 2R:1731127-2080000 1 NULL:1982784 Q9U1I5 13 261 1 1 0 217794 217620 1 0 0 0 132 partof LFQ-LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSVRKHK 174 2R:1731127-2080000 1 NULL:1982785 Q9U1I5 283 342 1 1 0 2603561 110994 110106 1 0 0 0 671 partof GFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSF-PKLASXXX-XXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 888 2R:1731127-2080000 -1 NULL:1987283 Q9VMN8 69 349 1 1 0 110040 109620 1 0 0 0 305 partof SETLRLYTLVPHLERKALNDYVVP---GHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987284 Q9VMN8 348 491 1 1 0 2603564 111003 110109 1 0 0 0 778 partof PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 894 2R:1731127-2080000 -1 NULL:1987286 Q95R69 23 315 1 1 0 110037 109620 1 0 0 0 313 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDT-TEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987287 Q95R69 316 455 1 1 0 2603567 111003 110103 1 0 0 0 725 partof PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISG 900 2R:1731127-2080000 -1 NULL:1987289 Q95RX9 20 314 1 1 0 2603569 111135 110106 1 0 0 0 899 partof YWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1029 2R:1731127-2080000 -1 NULL:1987291 AAL48149 27 365 1 1 0 110040 109620 1 0 0 0 477 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987292 AAL48149 364 504 1 1 0 2603572 111135 110106 1 0 0 0 899 partof YWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1029 2R:1731127-2080000 -1 NULL:1987294 Q9V774 27 365 1 1 0 110040 109620 1 0 0 0 477 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987295 Q9V774 364 504 1 1 0 2603575 111135 110031 1 0 0 0 294 partof YWNRRGVPHDAPHPLYGNMVGF--RKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADR--GQF--HNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLA----SXXXXXXMPEDVHQFFMRLVNDTIALRERENFK-RNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSET 1104 2R:1731127-2080000 -1 NULL:1987297 AAL48989 28 385 1 1 0 110058 109623 1 0 0 0 205 partof FTQHCSSETLRLYTLVPHLERKALNDYVVP-GHEK-LVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFS--PEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKY-SPMSIVL-GTVGGIYLRVER 435 2R:1731127-2080000 -1 NULL:1987298 AAL48989 358 506 1 1 0 2603578 111138 110106 1 0 0 0 504 partof NYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGF----PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRT-PVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIE-GMDI-GELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1032 2R:1731127-2080000 -1 NULL:1987300 Q9V776 27 377 1 1 0 110040 109686 1 0 0 0 268 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPL 354 2R:1731127-2080000 -1 NULL:1987301 Q9V776 376 492 1 1 0 2603581 111141 110106 1 0 0 0 827 partof FNYWNRRGVPHD-APHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987303 Q9V769 22 355 1 1 0 110040 109620 1 0 0 0 332 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987304 Q9V769 354 494 1 1 0 2603584 111141 110106 1 0 0 0 798 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAA--QNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIE---GMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEG-QLTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987306 Q9V4U7 22 371 1 1 0 110040 109620 1 0 0 0 389 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987307 Q9V4U7 370 509 1 1 0 2603587 111141 109851 1 0 0 0 476 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNG-RDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAV-LEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFK--RNDFMNLLIELKQKGRVTLDNGEVIE----GMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ-LTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFS 1290 2R:1731127-2080000 -1 NULL:1987309 Q9V6H1 25 442 1 1 0 109968 109626 1 0 0 0 146 partof GHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVE 342 2R:1731127-2080000 -1 NULL:1987310 Q9V6H1 403 515 1 1 0 2603590 111141 110109 1 0 0 0 565 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAV-LEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNG--------EVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1032 2R:1731127-2080000 -1 NULL:1987312 Q9VFP1 21 370 1 1 0 110058 109629 1 0 0 0 239 partof FTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 429 2R:1731127-2080000 -1 NULL:1987313 Q9VFP1 364 504 1 1 0 2603593 111141 109698 1 0 0 0 518 partof FNYWNRRGVPHDAPHPLYGN-----MVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFAD-RGQFHNGRDDP--LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLD-NGEVIEGMDIGE-----LAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQ-EGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTT 1443 2R:1731127-2080000 -1 NULL:1987315 Q9W130 24 493 1 1 0 2603595 111141 110106 1 0 0 0 399 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFN-LDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVI-----TEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ-LTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987317 Q9V4I0 24 362 1 1 0 110040 109698 1 0 0 0 198 partof SETLRLYTLVPHLERKALNDYVVPGHE--KLV-IEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTT 342 2R:1731127-2080000 -1 NULL:1987318 Q9V4I0 361 478 1 1 0 2603598 111141 110106 1 0 0 0 402 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFN-LDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVI-----TEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ-LTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987320 AAL48660 24 362 1 1 0 110040 109698 1 0 0 0 198 partof SETLRLYTLVPHLERKALNDYVVPGHE--KLV-IEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTT 342 2R:1731127-2080000 -1 NULL:1987321 AAL48660 361 478 1 1 0 2603901 303565 303028 1 0 0 0 168 partof ALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDA-LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHF----TSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 537 2R:1731127-2080000 -1 NULL:1987619 Q9VQD2 14 201 1 1 0 2603903 303571 303028 1 0 0 0 257 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK---SLQTINISELVGAYNTDVMASMAFGL 543 2R:1731127-2080000 -1 NULL:1987621 P82711 8 193 1 1 0 302583 302091 1 0 0 0 274 partof IRSKSSMVSTKY*KAL-YSSNDFTFFLE-----TLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 492 2R:1731127-2080000 -1 NULL:1987622 P82711 330 500 1 1 0 2603906 303571 303028 1 0 0 0 251 partof LGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 543 2R:1731127-2080000 -1 NULL:1987624 Q9VFP1 7 190 1 1 0 302797 302581 1 0 0 0 141 partof NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRY 216 2R:1731127-2080000 -1 NULL:1987625 Q9VFP1 293 365 1 1 0 302508 302094 1 0 0 0 185 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDI--KLSVER 414 2R:1731127-2080000 -1 NULL:1987626 Q9VFP1 370 508 1 1 0 2603910 303580 302803 1 0 0 0 256 partof LTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSG--KRHAQDA--LQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRL----SQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRM---WQAYLA----LEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQL 777 2R:1731127-2080000 -1 NULL:1987628 Q9V776 9 282 1 1 0 302505 302124 1 0 0 0 202 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMP 381 2R:1731127-2080000 -1 NULL:1987629 Q9V776 377 505 1 1 0 2603913 303583 302869 1 0 0 0 283 partof LLTALGALSVVYALVKFSL----GYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKV 714 2R:1731127-2080000 -1 NULL:1987631 Q9V770 1 251 1 1 0 302508 302085 1 0 0 0 265 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1987632 Q9V770 360 501 1 1 0 2603916 303583 302869 1 0 0 0 300 partof LLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA-PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA--YLALEFPLIARLLQYKSYAEPATAYFQKV 714 2R:1731127-2080000 -1 NULL:1987634 Q9V771 3 252 1 1 0 302508 302085 1 0 0 0 284 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 423 2R:1731127-2080000 -1 NULL:1987635 Q9V771 361 502 1 1 0 2603919 303583 302869 1 0 0 0 268 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAY-KGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQT---INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQ--AYLALEFPLIARLLQYKSYAEPATAYFQKV 714 2R:1731127-2080000 -1 NULL:1987637 P33270 6 253 1 1 0 302776 302563 1 0 0 0 159 partof DI-EIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 213 2R:1731127-2080000 -1 NULL:1987638 P33270 295 367 1 1 0 302505 302091 1 0 0 0 270 partof ETLRLHTPHPFLLRRATKEFEVPG-SVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987639 P33270 367 506 1 1 0 2597801 27348 27186 1 0 0 0 131 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAF 162 2R:1731127-2080000 1 NULL:1982494 Q9W2V3 15 69 1 1 0 28127 27824 1 0 0 0 190 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEK 303 2R:1731127-2080000 1 NULL:1982495 Q9W2V3 70 171 1 1 0 2597804 27351 27186 1 0 0 0 177 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982497 O18332 19 74 1 1 0 28130 27821 1 0 0 0 240 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKI 309 2R:1731127-2080000 1 NULL:1982498 O18332 73 176 1 1 0 2597807 27351 27186 1 0 0 0 138 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGK----QIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982500 O76901 25 84 1 1 0 28133 27821 1 0 0 0 183 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNS-NMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQ 312 2R:1731127-2080000 1 NULL:1982501 O76901 83 188 1 1 0 2603923 303583 302875 1 0 0 0 200 partof LLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG--RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWADFRMWQAYLALEF--PLIARLLQYKSYAEPATAYFQ 708 2R:1731127-2080000 -1 NULL:1987641 Q9V9L1 2 248 1 1 0 302412 302091 1 0 0 0 178 partof GNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 321 2R:1731127-2080000 -1 NULL:1987642 Q9V9L1 398 505 1 1 0 2603926 303583 302869 1 0 0 0 321 partof LLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKV 714 2R:1731127-2080000 -1 NULL:1987644 Q9V774 6 252 1 1 0 302505 302091 1 0 0 0 282 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987645 Q9V774 365 504 1 1 0 2603929 303583 303028 1 0 0 0 266 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRA--PFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL---QTINISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1987647 Q9V773 4 193 1 1 0 302505 302091 1 0 0 0 278 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA-PSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987648 Q9V773 362 501 1 1 0 2597810 27351 27186 1 0 0 0 138 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGK----QIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982503 Q95S31 19 78 1 1 0 28133 27821 1 0 0 0 183 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNS-NMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQ 312 2R:1731127-2080000 1 NULL:1982504 Q95S31 77 182 1 1 0 2597813 27351 27186 1 0 0 0 138 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGK----QIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982506 Q9W585 38 97 1 1 0 28133 27821 1 0 0 0 183 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNS-NMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQ 312 2R:1731127-2080000 1 NULL:1982507 Q9W585 96 201 1 1 0 2597816 27351 27186 1 0 0 0 158 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982509 AAL47999 19 74 1 1 0 28136 27821 1 0 0 0 272 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 315 2R:1731127-2080000 1 NULL:1982510 AAL47999 73 178 1 1 0 2597819 27351 27186 1 0 0 0 158 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982512 O18335 19 74 1 1 0 28136 27821 1 0 0 0 272 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 315 2R:1731127-2080000 1 NULL:1982513 O18335 73 178 1 1 0 2603932 303583 303028 1 0 0 0 167 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQIS-------SRIQRDL--GEKSLQTI-NISELVGAYNTDVMASMAFGL 555 2R:1731127-2080000 -1 NULL:1987650 Q9VRB3 7 204 1 1 0 302505 302097 1 0 0 0 173 partof ETLRLHTPHPFLLRRAT----KEFEV--PGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 408 2R:1731127-2080000 -1 NULL:1987651 Q9VRB3 376 518 1 1 0 2603935 303583 302635 1 0 0 0 171 partof LLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLW-GNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTS---RGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR-----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQ---DN----VEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKA 948 2R:1731127-2080000 -1 NULL:1987653 Q9VMT6 7 338 1 1 0 302505 302106 1 0 0 0 172 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ---ARRS-RPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 399 2R:1731127-2080000 -1 NULL:1987654 Q9VMT6 356 496 1 1 0 2603938 303586 302566 1 0 0 0 384 partof TLLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKR-HAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWAD---FRMWQAYLALEFPLIARLLQYKSYAEPATAYFQ---KVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIE-IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1020 2R:1731127-2080000 -1 NULL:1987656 AAK93147 2 351 1 1 0 302505 302085 1 0 0 0 307 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 420 2R:1731127-2080000 -1 NULL:1987657 AAK93147 352 492 1 1 0 2597822 27351 27186 1 0 0 0 147 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982515 O18337 13 68 1 1 0 28157 27821 1 0 0 0 220 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHS-NSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINN 336 2R:1731127-2080000 1 NULL:1982516 O18337 67 173 1 1 0 2597825 27351 27186 1 0 0 0 147 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982518 Q9W4A0 13 68 1 1 0 28157 27821 1 0 0 0 219 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHS-NSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINN 336 2R:1731127-2080000 1 NULL:1982519 Q9W4A0 67 173 1 1 0 2597828 27351 27186 1 0 0 0 147 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982521 AAL68196 13 68 1 1 0 28157 27821 1 0 0 0 219 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHS-NSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINN 336 2R:1731127-2080000 1 NULL:1982522 AAL68196 67 173 1 1 0 2603941 303586 302566 1 0 0 0 384 partof TLLTALGALSVV-YALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKR-HAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVG---QD-NVEFAKWTRNYWAD---FRMWQAYLALEFPLIARLLQYKSYAEPATAYFQ---KVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIE-IAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1020 2R:1731127-2080000 -1 NULL:1987659 Q9V4U9 2 351 1 1 0 302505 302085 1 0 0 0 307 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDK 420 2R:1731127-2080000 -1 NULL:1987660 Q9V4U9 352 492 1 1 0 2603944 303586 302737 1 0 0 0 280 partof TLLTALGALSVVYALVKF--SLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLG---EKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVL 849 2R:1731127-2080000 -1 NULL:1987662 Q27594 4 295 1 1 0 302505 302091 1 0 0 0 280 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987663 Q27594 365 504 1 1 0 2603947 303586 302548 1 0 0 0 190 partof TLLTALGA-LSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTD--AGHFTSRGLYSNPSGEP-LSHNLLQLDGHKWRSLHAKSAEVFTP---ANMQKLLVRLS-QISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGLVGQ---DN-VEFAKWTRNYWAD-FR-MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQT-FLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNGEYQI 1038 2R:1731127-2080000 -1 NULL:1987665 Q9VMT5 5 362 1 1 0 302505 302094 1 0 0 0 160 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAK---GNNVLIPTAAIHMDPGIYENPQRFYPERF---EEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLS-VER 411 2R:1731127-2080000 -1 NULL:1987666 Q9VMT5 357 501 1 1 0 2597831 27351 27186 1 0 0 0 126 partof AGVGKSCLLLQFTDKRFQ-PVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982524 Q95R32 198 254 1 1 0 28166 27821 1 0 0 0 268 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLD-SRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI----YEKIQEGVFDINNEVR 345 2R:1731127-2080000 1 NULL:1982525 Q95R32 253 373 1 1 0 2597834 27351 27186 1 0 0 0 162 partof AGVGKSCLLLQFTDKRFQPVHDL-TIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982527 Q9VP48 476 532 1 1 0 28166 27821 1 0 0 0 269 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLD-SRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI----YEKIQEGVFDINNEVR 345 2R:1731127-2080000 1 NULL:1982528 Q9VP48 531 651 1 1 0 2597837 27348 27186 1 0 0 0 155 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAF 162 2R:1731127-2080000 1 NULL:1982530 O15971 17 71 1 1 0 28172 27824 1 0 0 0 274 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 348 2R:1731127-2080000 1 NULL:1982531 O15971 72 187 1 1 0 2603950 303595 302563 1 0 0 0 1711 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQTINISELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1032 2R:1731127-2080000 -1 NULL:1987668 Q9V979 0 344 1 1 0 302505 302082 1 0 0 0 724 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1987669 Q9V979 344 485 1 1 0 2603953 303595 303028 1 0 0 0 221 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFL-WGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1987671 AAK93030 0 192 1 1 0 302505 302082 1 0 0 0 213 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV-ERVDKL 423 2R:1731127-2080000 -1 NULL:1987672 AAK93030 375 514 1 1 0 2603956 303595 303028 1 0 0 0 221 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFL-WGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1987674 Q9VCW1 0 192 1 1 0 302505 302082 1 0 0 0 213 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV-ERVDKL 423 2R:1731127-2080000 -1 NULL:1987675 Q9VCW1 375 514 1 1 0 2603959 303595 302566 1 0 0 0 367 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGE---KSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRM---WQAYLALEFPLIARL-LQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAE-KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 1029 2R:1731127-2080000 -1 NULL:1987677 Q9VMN8 0 348 1 1 0 302505 302088 1 0 0 0 274 partof ETLRLHTPHPFLLRRATKEFEVP----GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYA--PSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1987678 Q9VMN8 349 492 1 1 0 2597840 27351 27186 1 0 0 0 163 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982533 AAL39816 16 71 1 1 0 28175 27821 1 0 0 0 266 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRIH 354 2R:1731127-2080000 1 NULL:1982534 AAL39816 70 187 1 1 0 2597843 27351 27186 1 0 0 0 163 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982536 O18338 16 71 1 1 0 28175 27821 1 0 0 0 266 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRIH 354 2R:1731127-2080000 1 NULL:1982537 O18338 70 187 1 1 0 2597846 27351 27189 1 0 0 0 146 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982539 AAL48761 21 75 1 1 0 28100 27821 1 0 0 0 110 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSN---SNMVIMLIGNKSDLDS-RREVKKEEGEAFAREHGLV-FMETSARTAANVEEAFI 279 2R:1731127-2080000 1 NULL:1982540 AAL48761 74 172 1 1 0 2603962 303595 303028 1 0 0 0 225 partof MHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT---INISELVGAYNTDVMASMAFGL 567 2R:1731127-2080000 -1 NULL:1987680 Q9W223 0 188 1 1 0 302508 302094 1 0 0 0 191 partof LETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1987681 Q9W223 374 510 1 1 0 2603965 303595 302548 1 0 0 0 201 partof MHRTLLTALGAL-SVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRG---LYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTP-------ANMQKLLVRLSQISSRIQRDLGEKSLQTINIS-ELVGAYNTDVMASMAFGLVGQDNVEFAKWTRNYWADFRMWQAYLALE--FPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQ--LYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTP-ECLRELRYTKQVLNGEYQI 1047 2R:1731127-2080000 -1 NULL:1987683 Q9VYT8 0 361 1 1 0 2603967 303598 302902 1 0 0 0 217 partof LMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYT--AYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQL--DGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDL---GEKSLQTI--NISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQA---YLALEFPLIARLLQYKSY 696 2R:1731127-2080000 -1 NULL:1987685 Q9V674 1 246 1 1 0 302505 302082 1 0 0 0 179 partof ETLRLHTPHPFLLRR-ATKEFEVPGSV-----FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1987686 Q9V674 369 515 1 1 0 2597850 27351 27189 1 0 0 0 146 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982542 Q9VIW6 21 75 1 1 0 28100 27821 1 0 0 0 110 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSN---SNMVIMLIGNKSDLDS-RREVKKEEGEAFAREHGLV-FMETSARTAANVEEAFI 279 2R:1731127-2080000 1 NULL:1982543 Q9VIW6 74 172 1 1 0 2597853 27351 27189 1 0 0 0 155 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982545 AAL49022 30 84 1 1 0 28118 27821 1 0 0 0 235 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAR--EHGLVFMETSARTAANVEEAFINTAKEI 297 2R:1731127-2080000 1 NULL:1982546 AAL49022 83 184 1 1 0 2597856 27351 27189 1 0 0 0 155 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982548 O18339 30 84 1 1 0 28118 27821 1 0 0 0 235 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAR--EHGLVFMETSARTAANVEEAFINTAKEI 297 2R:1731127-2080000 1 NULL:1982549 O18339 83 184 1 1 0 2597859 27351 27189 1 0 0 0 162 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982551 Q9VZ47 16 70 1 1 0 28133 27821 1 0 0 0 219 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNK-SDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQ 312 2R:1731127-2080000 1 NULL:1982552 Q9VZ47 69 173 1 1 0 2603970 303604 302869 1 0 0 0 300 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKG-RAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT--INISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFRMWQAYLAL--EFPLIARLLQYKSYAEPATAYFQKV 735 2R:1731127-2080000 -1 NULL:1987688 Q9VB31 0 253 1 1 0 302788 302563 1 0 0 0 182 partof KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 225 2R:1731127-2080000 -1 NULL:1987689 Q9VB31 292 367 1 1 0 302505 302091 1 0 0 0 288 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYD-NRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987690 Q9VB31 367 507 1 1 0 2603974 303604 302563 1 0 0 0 282 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXP---LQTFLQLYSNAEKPLTDIEIA-GQAFGFVLAGLGPLNATLAFCL-YELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 1041 2R:1731127-2080000 -1 NULL:1987692 AAK71286 0 355 1 1 0 302505 302091 1 0 0 0 295 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987693 AAK71286 355 494 1 1 0 2603977 303604 302869 1 0 0 0 258 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKV 735 2R:1731127-2080000 -1 NULL:1987695 Q27593 0 253 1 1 0 302782 302563 1 0 0 0 171 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 219 2R:1731127-2080000 -1 NULL:1987696 Q27593 294 367 1 1 0 302505 302091 1 0 0 0 302 partof ETLRLHTPHPFLLRRATKEFEVPGSV-FVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987697 Q27593 367 506 1 1 0 2597862 27351 27189 1 0 0 0 192 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982554 AAL39708 20 74 1 1 0 28154 27821 1 0 0 0 369 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDIN 333 2R:1731127-2080000 1 NULL:1982555 AAL39708 73 184 1 1 0 2597865 27351 27189 1 0 0 0 192 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982557 O18336 20 74 1 1 0 28154 27821 1 0 0 0 374 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDIN 333 2R:1731127-2080000 1 NULL:1982558 O18336 73 184 1 1 0 2597868 27351 27189 1 0 0 0 282 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982560 O18333 15 69 1 1 0 28172 27821 1 0 0 0 575 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982561 O18333 68 185 1 1 0 2603981 303604 303028 1 0 0 0 173 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEP---LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 576 2R:1731127-2080000 -1 NULL:1987699 Q9V419 0 197 1 1 0 302505 302091 1 0 0 0 185 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ--ARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987700 Q9V419 362 505 1 1 0 2603984 303604 303028 1 0 0 0 173 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEP---LSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSR----IQRDLGEKSLQTINISELVGAYNTDVMASMAFGL 576 2R:1731127-2080000 -1 NULL:1987702 AAK92957 0 197 1 1 0 302505 302091 1 0 0 0 185 partof ETLRLHTPHPFLLRRATKEFEVP---GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQ--ARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1987703 AAK92957 362 505 1 1 0 2603987 303604 302872 1 0 0 0 228 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGR-APFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPL-SHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSLQT-------INISELVGAYNTDVMASMAFGLVGQD----NVEFAKWTRNYWADFRMWQAY---LALEFPLIARLLQYKSYAEPATAYFQK 732 2R:1731127-2080000 -1 NULL:1987705 Q9V675 0 257 1 1 0 302776 302566 1 0 0 0 134 partof DIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVL 210 2R:1731127-2080000 -1 NULL:1987706 Q9V675 303 372 1 1 0 302508 302094 1 0 0 0 238 partof LETLRLHTPHPFLLRRAT--KEFEV-P-GSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1987707 Q9V675 372 514 1 1 0 2597871 27351 27189 1 0 0 0 282 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982563 Q9U5D5 15 69 1 1 0 28172 27821 1 0 0 0 568 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982564 Q9U5D5 68 185 1 1 0 2597874 27351 27192 1 0 0 0 121 partof VGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 159 2R:1731127-2080000 1 NULL:1982566 O18334 22 75 1 1 0 28109 27821 1 0 0 0 218 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTA 288 2R:1731127-2080000 1 NULL:1982567 O18334 74 170 1 1 0 2597877 27351 27192 1 0 0 0 162 partof VGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI-DGKQIKLQIWDTAGQEAFR 159 2R:1731127-2080000 1 NULL:1982569 AAL48962 19 73 1 1 0 28145 27821 1 0 0 0 262 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNM-VIMLIGNKSDL---DSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVF 324 2R:1731127-2080000 1 NULL:1982570 AAL48962 72 184 1 1 0 2603991 303604 302869 1 0 0 0 258 partof MDLMHRTLLTALGALSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYK-GRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEK--SLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWADFR---MWQAYLALEFPLIARLLQYKSYAEPATAYFQKV 735 2R:1731127-2080000 -1 NULL:1987709 AAK77274 0 253 1 1 0 302782 302560 1 0 0 0 177 partof LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLNG 222 2R:1731127-2080000 -1 NULL:1987710 AAK77274 294 368 1 1 0 2603994 308376 307467 1 0 0 0 1434 partof AAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDXXXXXXXXXXXXTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 909 2R:1731127-2080000 -1 NULL:1987712 O44116 1 304 1 1 0 307378 306991 1 0 0 0 661 partof DDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQ 387 2R:1731127-2080000 -1 NULL:1987713 O44116 304 433 1 1 0 306933 306330 1 0 0 0 996 partof EKLALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADKIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCVNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 603 2R:1731127-2080000 -1 NULL:1987714 O44116 433 634 1 1 0 2603999 308376 307467 1 0 0 0 1437 partof AAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDXXXXXXXXXXXXTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 909 2R:1731127-2080000 -1 NULL:1987716 Q9V978 1 304 1 1 0 307378 306991 1 0 0 0 661 partof DDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQ 387 2R:1731127-2080000 -1 NULL:1987717 Q9V978 304 433 1 1 0 306933 306330 1 0 0 0 996 partof EKLALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADKIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCVNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 603 2R:1731127-2080000 -1 NULL:1987718 Q9V978 433 634 1 1 0 2597880 28124 27821 1 0 0 0 188 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVI-MLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYE 303 2R:1731127-2080000 1 NULL:1982572 Q95RH7 16 116 1 1 0 2597882 28139 27821 1 0 0 0 209 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEG 318 2R:1731127-2080000 1 NULL:1982574 Q9V3C2 69 175 1 1 0 2597884 28094 27824 1 0 0 0 140 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLED----ARQHSNSNMVIMLIGNKSDLDSRREVKK-EEGEAFAREHGLV-FMETSARTAANVEEA 270 2R:1731127-2080000 1 NULL:1982576 Q9I7E5 84 180 1 1 0 2597886 28118 27824 1 0 0 0 164 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRR-EVKKEEGEAFARE-HGLVFM--ETSARTAANVEEAFINTAKEI 294 2R:1731127-2080000 1 NULL:1982578 AAL49269 73 174 1 1 0 2597888 28136 27824 1 0 0 0 147 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMV-IMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 312 2R:1731127-2080000 1 NULL:1982580 P48555 73 178 1 1 0 2597890 28151 27824 1 0 0 0 145 partof SITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMV-IMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDI 327 2R:1731127-2080000 1 NULL:1982582 Q962I2 73 183 1 1 0 2597892 28118 27839 1 0 0 0 134 partof YYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMV-IMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI 279 2R:1731127-2080000 1 NULL:1982584 O96692 70 164 1 1 0 2597894 28118 27839 1 0 0 0 141 partof YYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIM-LIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEI 279 2R:1731127-2080000 1 NULL:1982586 P08646 70 163 1 1 0 2597896 28136 27839 1 0 0 0 164 partof YYRGAAGALLVYDITRRETFNHLTTWLEDA-RQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 297 2R:1731127-2080000 1 NULL:1982588 P08645 70 170 1 1 0 2597898 72781 72616 1 0 0 0 247 partof YQKRIGTYDKQEWEKTVEQRILDGFNSVNLKNTKLKTELIDVDLVRG-VFNLTDPK 165 2R:1731127-2080000 1 NULL:1982590 Q9V9A8 9 65 1 1 0 74313 72810 1 0 0 0 2021 partof GSTFPKAKPKQSLLTVIRLAILRYVLLPLYAQWWVKQTTPNAFGFILVLYLTQLTNWAIYVLHSSRIVPLDYEKPPNGTLLQXXXXXXXXXXXXXXXXXXXXXXXXXXXIPCAXXXXXXXXHSQIVATNTASGVSGGSSKNKLRRISASYLSDKAATXXXXXXXXXXXXXXXXSSFRNQILNSFFRVRQVEADLSQASSNISLPNRRTATSTIEVLPRPVTPLPSXXXXXXXXXXXXXXXXXXXXXIRRSTNEETYLTTTAISPLTQPLAAIDACYDLSRKAGGAAPESPKKRNVNWHTPIQIYATYELGEEPCSSRKVAEESAPESVGERLCSVKPDYQTRRNIGEDDGFESLNGKSSSGEDNNHSPLPNXXXXXXXXXXXQTNQLRLRLNTTNGVTASASPTEKKPQSRGNESSTSCAESDECDDADIMSSPASGCNQECTTSATDWLGVTTNSEDCSYTSDLDHSDGGLKHTAFSDEDPGELDITPTTILNPHSSLDR 1503 2R:1731127-2080000 1 NULL:1982591 Q9V9A8 55 540 1 1 0 74969 74369 1 0 0 0 1026 partof KVSCTIWDQRDAKKAQLSVLEIASCIIERVDSMGEANDYIYIGVVFSFLLTLIPIFCRLCEVCCREGFGGGDYLLLVKCTQVTLGSDAEKASEISYFNMPQLLWEKSSASLFTLLGLAFGDSQWERMVLALGFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHFRLNKVRNIKTWLSVRSYLK 600 2R:1731127-2080000 1 NULL:1982592 Q9V9A8 539 739 1 1 0 75480 75027 1 0 0 0 551 partof KRGPQRSVDXXXXXXXXXXXXXXAFLSVEWLKDSAXXXXXXXXEALIWSITIGIFLLRFMTLGQKIQHKYRSVSVLITEQINLYLQIEQKPKKKDELMVSNSVXXXXXXXXXXXXTPFKLSGLSANPYLFTTIKVVILSALSGVLSEVLGF 453 2R:1731127-2080000 1 NULL:1982593 Q9V9A8 739 890 1 1 0 2603255 2816 2717 1 0 0 0 166 partof MSKYLSSQRDALSAPALPVSRENREPPKFQGVK 99 2R:1731127-2080000 -1 NULL:1986987 Q9V9C1 0 33 1 1 0 2661 1281 1 0 0 0 2206 partof QREPLVFFIMRXXXXXXXXXXXXXXXXXXXXXYMRCAAFSFSPDFVRPLDRSARQSSSGGEATALHDIECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLEDGDGNQMEWSTPKTSNMTRIWHHKFNTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKGIMGDKRSPLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSLNGFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 1380 2R:1731127-2080000 -1 NULL:1986988 Q9V9C1 33 493 1 1 0 1181 809 1 0 0 0 650 partof FYRYEEYPTTPPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 372 2R:1731127-2080000 -1 NULL:1986989 Q9V9C1 490 614 1 1 0 2603260 5165 4850 1 0 0 0 311 partof MIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 315 2R:1731127-2080000 -1 NULL:1986991 Q9I7V3 0 105 1 1 0 2603262 5309 4850 1 0 0 0 427 partof GRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 459 2R:1731127-2080000 -1 NULL:1986993 Q9W227 42 190 1 1 0 2603264 5309 4886 1 0 0 0 269 partof GRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENF-TLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPN-NKP 423 2R:1731127-2080000 -1 NULL:1986995 Q960Q8 490 624 1 1 0 2603266 5312 4850 1 0 0 0 433 partof IGRMIFELFADTVPRTAENFRQFCTGEYR---PDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 462 2R:1731127-2080000 -1 NULL:1986997 Q9VAW1 25 182 1 1 0 2603268 5312 4850 1 0 0 0 372 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTL--KHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 462 2R:1731127-2080000 -1 NULL:1986999 P15425 39 191 1 1 0 2603270 5312 4868 1 0 0 0 308 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDE-NFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTI 444 2R:1731127-2080000 -1 NULL:1987001 AAL48597 28 168 1 1 0 2603272 5312 4886 1 0 0 0 297 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDE-NFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKP 426 2R:1731127-2080000 -1 NULL:1987003 Q9V7M9 287 421 1 1 0 2603274 5312 5003 1 0 0 0 335 partof IGRMIFELFADTVPRTAENFRQFCTGEYR---PDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFI 309 2R:1731127-2080000 -1 NULL:1987005 Q9VAW2 25 131 1 1 0 2603276 5315 4850 1 0 0 0 412 partof EIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 465 2R:1731127-2080000 -1 NULL:1987007 AAL28969 150 299 1 1 0 2603278 5315 4850 1 0 0 0 412 partof EIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 465 2R:1731127-2080000 -1 NULL:1987009 Q9V3G3 150 299 1 1 0 2598100 217145 216377 1 0 0 0 433 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 768 2R:1731127-2080000 1 NULL:1982787 Q9I7G5 13 261 1 1 0 217794 217620 1 0 0 0 133 partof LFQ-LGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSVRKHK 174 2R:1731127-2080000 1 NULL:1982788 Q9I7G5 283 342 1 1 0 2598103 217115 216380 1 0 0 0 361 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG 735 2R:1731127-2080000 1 NULL:1982790 Q9U1I7 15 253 1 1 0 2598105 217115 216380 1 0 0 0 363 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG 735 2R:1731127-2080000 1 NULL:1982792 Q9U1I6 15 252 1 1 0 2598107 217115 216380 1 0 0 0 363 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG 735 2R:1731127-2080000 1 NULL:1982794 Q9VII7 15 252 1 1 0 2598109 217118 216380 1 0 0 0 369 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGI 738 2R:1731127-2080000 1 NULL:1982796 Q9VLQ7 15 254 1 1 0 2603280 5318 4844 1 0 0 0 369 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPD--GVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGK-ETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM*H 474 2R:1731127-2080000 -1 NULL:1987011 Q9VT21 25 185 1 1 0 2603282 5318 4850 1 0 0 0 403 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1987013 P25007 15 165 1 1 0 2603284 5318 4850 1 0 0 0 415 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1987015 Q9VUD6 14 164 1 1 0 2603286 5357 4913 1 0 0 0 256 partof NLYIT-PPSNAFCVQE--IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDE-NFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVL-DGLLIMRKIEN 444 2R:1731127-2080000 -1 NULL:1987017 AAL48610 2 146 1 1 0 2603288 7602 7431 1 0 0 0 139 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEE 171 2R:1731127-2080000 -1 NULL:1987019 Q9V9B8 416 473 1 1 0 2598111 217145 216380 1 0 0 0 330 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFK-LTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG--IDLNEISSQL 765 2R:1731127-2080000 1 NULL:1982798 Q9V4I5 108 359 1 1 0 2598113 217145 216380 1 0 0 0 330 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFK-LTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG--IDLNEISSQL 765 2R:1731127-2080000 1 NULL:1982800 Q9U5W7 108 359 1 1 0 2598115 217115 216380 1 0 0 0 416 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG 735 2R:1731127-2080000 1 NULL:1982802 Q9U1I8 15 255 1 1 0 217782 217620 1 0 0 0 118 partof LFQLGIKKLFSPGANLSSLYQGSEPLRISEVKHKAIIEVNEKGTTASGATCKSV 162 2R:1731127-2080000 1 NULL:1982803 Q9U1I8 283 337 1 1 0 2598118 217142 216383 1 0 0 0 363 partof FASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQ 759 2R:1731127-2080000 1 NULL:1982805 AAK92954 17 266 1 1 0 2603290 8798 7739 1 0 0 0 238 partof LEDFEQKIMPGVVHWNHPKFF-AYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVF-LPSLIAYASREAHSSVEKATK-MALVKLRIIDA--DEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPL-YL-RHEHLTGVDYR--HYGIPLSRRFRALKLWFVF--RTYGIRGLQEYIRNHMALAKKFEMLVR-KDERFEVRNDVH-LGLVCF 1059 2R:1731127-2080000 -1 NULL:1987021 Q9VPH6 77 424 1 1 0 2603292 8807 7772 1 0 0 0 314 partof KDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEK-ATKMALVK--LRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHE---HLTGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEV 1035 2R:1731127-2080000 -1 NULL:1987023 AAL39897 145 484 1 1 0 2603294 8807 7772 1 0 0 0 314 partof KDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPSLIAYASREAHSSVEK-ATKMALVK--LRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHE---HLTGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEV 1035 2R:1731127-2080000 -1 NULL:1987025 Q24062 145 484 1 1 0 2603296 8834 7772 1 0 0 0 262 partof DAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLP-SLIAYASREAHSSVEKATKMALVKLR---IIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRV--FSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYL---RHEHLTGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAK-KFEMLVRKDERFEV 1062 2R:1731127-2080000 -1 NULL:1987027 P20228 73 420 1 1 0 2603298 8834 7772 1 0 0 0 268 partof DAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLP-SLIAYASREAHSSVEKATKMALVKLR---IIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRV--FSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYL---RHEHLTGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAK-KFEMLVRKDERFEV 1062 2R:1731127-2080000 -1 NULL:1987029 Q9VZI7 73 420 1 1 0 2598120 217142 216383 1 0 0 0 363 partof FASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQ 759 2R:1731127-2080000 1 NULL:1982807 Q9V5S3 17 266 1 1 0 2598122 217145 216482 1 0 0 0 315 partof LGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKAS--GDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 663 2R:1731127-2080000 1 NULL:1982809 Q9V989 0 217 1 1 0 2598124 217963 217846 1 0 0 0 198 partof SVESLTIGEEVFEFIADHPFFFAIKDAQNTLFLGHVSQL 117 2R:1731127-2080000 1 NULL:1982811 Q9V987 347 386 1 1 0 2598126 239875 239734 1 0 0 0 243 partof MQFPAMRRLSIATAHAFMLVYAATSAPSFQCVKQCFEEIREQRGDFQ 141 2R:1731127-2080000 1 NULL:1982813 Q9V986 0 47 1 1 0 240637 240523 1 0 0 0 199 partof QDIPIVIAGNKADLATTHREVKLEEVTDWVFCELPRLR 114 2R:1731127-2080000 1 NULL:1982814 Q9V986 46 84 1 1 0 2598130 253442 253280 1 0 0 0 274 partof MFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDGKL 162 2R:1731127-2080000 1 NULL:1982816 Q9V983 0 54 1 1 0 254259 253644 1 0 0 0 1101 partof SSTERIYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEPCQI 615 2R:1731127-2080000 1 NULL:1982817 Q9V983 48 253 1 1 0 254439 254319 1 0 0 0 190 partof RFSQVLESIAGIKQEPKEQLAALYYQNTLDLFFGTGESKE 120 2R:1731127-2080000 1 NULL:1982818 Q9V983 251 291 1 1 0 2598134 254136 253659 1 0 0 0 210 partof IYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNG--CSLKTDENAEVVRK---LPNDRIMLETDCPW 477 2R:1731127-2080000 1 NULL:1982820 Q9VDC1 91 246 1 1 0 2598136 279743 279506 1 0 0 0 179 partof PAWRHIKGKSLRKLFLINYLNIAQVFGQVYRLDKGTWQKTMFTASSNNFCKNMFDKNQYWYNFWTKYISNSDEIKEKCL 237 2R:1731127-2080000 1 NULL:1982822 Q9VIJ2 258 336 1 1 0 279968 279818 1 0 0 0 129 partof VLKYKDYELDLKT-SLNVPNLDGRYKLVVQIEAFDKRNVRRPVPICIEFRG 150 2R:1731127-2080000 1 NULL:1982823 Q9VIJ2 341 392 1 1 0 2598139 323619 322902 1 0 0 0 1249 partof MEAAKDFAVAKYQDLCNFLERDTRGSELAIYGTSAIMLAVAYAKRKPAYLVRQFKQPSHIPERLINERVMHTGKIAGVKQQEQDTLLMIQHRPLFPIFTSSKRLLPVKLPGVRVNANGYSWLQQCLIGREATFLPLKSAKGQDFVVCQLCLVHPPRGNRLLDVSETLLKLRFARFVQDAAAAVKKNGKYYQHLKKVEQTTAEKEAWLSWAAGYPYIWRRYNELRQRWLPKEKLLPELVR 717 2R:1731127-2080000 1 NULL:1982825 Q9V976 0 239 1 1 0 2598142 326708 326441 1 0 0 0 280 partof 267 2R:1731127-2080000 1 NULL:1982827 Q9NB15 17 102 1 1 0 327128 326909 1 0 0 0 374 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIAAIE 219 2R:1731127-2080000 1 NULL:1982828 Q9NB15 128 203 1 1 0 327460 327388 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1982829 Q9NB15 202 226 1 1 0 2598146 326708 326441 1 0 0 0 280 partof 267 2R:1731127-2080000 1 NULL:1982831 Q9U3V4 17 102 1 1 0 327128 326909 1 0 0 0 280 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIAAIE 219 2R:1731127-2080000 1 NULL:1982832 Q9U3V4 128 202 1 1 0 327460 327388 1 0 0 0 127 partof QFVGFVFACCLANSIRNYRRRAEY 72 2R:1731127-2080000 1 NULL:1982833 Q9U3V4 201 225 1 1 0 2603601 111141 110106 1 0 0 0 374 partof FNYWNRRGVPHDAPHPLYGNMVG--FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVI---TEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQK-VFTDMRHGKLLTMFVFS--FPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ-LTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987323 AAL13345 24 362 1 1 0 110040 109698 1 0 0 0 188 partof SETLRLYTLVPHLERKALNDYVVPGHE--KLVIEK-GTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTT 342 2R:1731127-2080000 -1 NULL:1987324 AAL13345 361 478 1 1 0 2603604 111141 110106 1 0 0 0 374 partof FNYWNRRGVPHDAPHPLYGNMVG--FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVI---TEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQK-VFTDMRHGKLLTMFVFS--FPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQ-LTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1987326 Q9V4I1 24 362 1 1 0 110040 109698 1 0 0 0 188 partof SETLRLYTLVPHLERKALNDYVVPGHE--KLVIEK-GTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTT 342 2R:1731127-2080000 -1 NULL:1987327 Q9V4I1 361 478 1 1 0 2603607 111141 110364 1 0 0 0 541 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSF-PKLASXXX-XXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQK 777 2R:1731127-2080000 -1 NULL:1987329 AAL48075 22 276 1 1 0 2603609 111144 110106 1 0 0 0 732 partof NFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFP-FVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1038 2R:1731127-2080000 -1 NULL:1987331 Q9V4U9 21 352 1 1 0 110040 109611 1 0 0 0 371 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI*PP 429 2R:1731127-2080000 -1 NULL:1987332 Q9V4U9 351 493 1 1 0 2598150 326711 326456 1 0 0 0 132 partof 255 2R:1731127-2080000 1 NULL:1982835 Q9NB14 22 105 1 1 0 327131 326912 1 0 0 0 133 partof DFLPLPQMKCCGRSGYTDYAYQGKFPPSCCS--D-TNNCRWETVYRR-GCKVTFVEFWDRNSDIIKYAGLVIAAIEV 219 2R:1731127-2080000 1 NULL:1982836 Q9NB14 133 206 1 1 0 2598153 326882 326705 1 0 0 0 279 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1982838 Q9NB15 84 143 1 1 0 2598155 326882 326705 1 0 0 0 279 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1982840 Q9U3V4 84 143 1 1 0 2598157 326882 326705 1 0 0 0 113 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDY-MDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1982842 Q9NB14 84 144 1 1 0 2598159 327131 326843 1 0 0 0 152 partof 288 2R:1731127-2080000 1 NULL:1982844 Q9U3V3 103 205 1 1 0 2603612 111144 110106 1 0 0 0 732 partof NFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFP-FVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1038 2R:1731127-2080000 -1 NULL:1987334 AAK93147 21 352 1 1 0 110040 109611 1 0 0 0 371 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI*PP 429 2R:1731127-2080000 -1 NULL:1987335 AAK93147 351 493 1 1 0 2603615 111144 110109 1 0 0 0 346 partof NFNYWNRRGVPHDAPHPLYGNMVGF--RKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHN---GRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERE-----NFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1035 2R:1731127-2080000 -1 NULL:1987337 AAK92957 22 361 1 1 0 110046 109620 1 0 0 0 269 partof CSSETLRLYTLVP-HLERKALNDYV-VPGHE--KLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERF-SPEKVAA-RESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 426 2R:1731127-2080000 -1 NULL:1987338 AAK92957 359 505 1 1 0 2603618 111144 110109 1 0 0 0 346 partof NFNYWNRRGVPHDAPHPLYGNMVGF--RKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHN---GRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERE-----NFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1035 2R:1731127-2080000 -1 NULL:1987340 Q9V419 22 361 1 1 0 110046 109620 1 0 0 0 269 partof CSSETLRLYTLVP-HLERKALNDYV-VPGHE--KLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERF-SPEKVAA-RESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 426 2R:1731127-2080000 -1 NULL:1987341 Q9V419 359 505 1 1 0 2598161 328962 328704 1 0 0 0 175 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1982846 Q9U3V3 0 86 1 1 0 329269 329020 1 0 0 0 78 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCC 249 2R:1731127-2080000 1 NULL:1982847 Q9U3V3 84 159 1 1 0 2598164 328956 328704 1 0 0 0 382 partof 252 2R:1731127-2080000 1 NULL:1982849 Q9NB14 0 84 1 1 0 329272 329020 1 0 0 0 290 partof 252 2R:1731127-2080000 1 NULL:1982850 Q9NB14 84 160 1 1 0 2598167 328950 328704 1 0 0 0 188 partof 246 2R:1731127-2080000 1 NULL:1982852 Q9NB13 0 82 1 1 0 329308 329020 1 0 0 0 88 partof 288 2R:1731127-2080000 1 NULL:1982853 Q9NB13 84 173 1 1 0 2603621 111144 110106 1 0 0 0 475 partof NFNYWNRRGVPHDAPHPLYGNMVG-FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFAD-RGQFHNGRDD-P------LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKV--FTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEG-QLTYESIKAMTYLNQVIS 1038 2R:1731127-2080000 -1 NULL:1987343 AAL13695 22 375 1 1 0 110040 109623 1 0 0 0 211 partof SETLRLYTLVPHLERKALND--YVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR-VER 417 2R:1731127-2080000 -1 NULL:1987344 AAL13695 374 515 1 1 0 2603624 111144 110106 1 0 0 0 475 partof NFNYWNRRGVPHDAPHPLYGNMVG-FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFAD-RGQFHNGRDD-P------LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKV--FTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEG-QLTYESIKAMTYLNQVIS 1038 2R:1731127-2080000 -1 NULL:1987346 Q9VG82 22 375 1 1 0 110040 109623 1 0 0 0 211 partof SETLRLYTLVPHLERKALND--YVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR-VER 417 2R:1731127-2080000 -1 NULL:1987347 Q9VG82 374 515 1 1 0 2603627 111144 110109 1 0 0 0 444 partof NFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMH-DFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPL-TQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMF-VFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEE-QEGQLTYESIKAMTYLNQVI 1035 2R:1731127-2080000 -1 NULL:1987349 AAL48867 41 382 1 1 0 110067 109632 1 0 0 0 269 partof VTG--FTQHCSSETLRLYTLVPHLER--KALNDY-VVP--GHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR 435 2R:1731127-2080000 -1 NULL:1987350 AAL48867 371 523 1 1 0 2598171 328962 328704 1 0 0 0 151 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1982855 Q9U3V4 0 86 1 1 0 329521 329230 1 0 0 0 148 partof 291 2R:1731127-2080000 1 NULL:1982856 Q9U3V4 129 224 1 1 0 2598174 328962 328704 1 0 0 0 151 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1982858 Q9NB15 0 86 1 1 0 329521 329230 1 0 0 0 176 partof DIYVSIPLQFSCCGNTGYQQYE---TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQ 291 2R:1731127-2080000 1 NULL:1982859 Q9NB15 129 225 1 1 0 2598177 329506 329242 1 0 0 0 463 partof SIPLQFSCCGNTGYQQYETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR 264 2R:1731127-2080000 1 NULL:1982861 Q9NB14 134 222 1 1 0 2598179 329500 329257 1 0 0 0 138 partof 243 2R:1731127-2080000 1 NULL:1982863 Q9U3V3 138 219 1 1 0 2603630 111144 110109 1 0 0 0 444 partof NFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMH-DFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPL-TQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMF-VFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEE-QEGQLTYESIKAMTYLNQVI 1035 2R:1731127-2080000 -1 NULL:1987352 Q9VRI9 41 382 1 1 0 110067 109632 1 0 0 0 269 partof VTG--FTQHCSSETLRLYTLVPHLER--KALNDY-VVP--GHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR 435 2R:1731127-2080000 -1 NULL:1987353 Q9VRI9 371 523 1 1 0 2603633 111144 110034 1 0 0 0 442 partof NFNYWNRRGVPHDAPHPLYGNMVG-FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFAD-RGQFHNGRDD-P------LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKV--FTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSE 1110 2R:1731127-2080000 -1 NULL:1987355 AAL68260 22 386 1 1 0 2603636 111144 110061 1 0 0 0 337 partof NFNYWNRRGVPHDAPHPLYGNM--VGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADR--GQFHNGRDDP-LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQ-VPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLL-TMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALREREN---FKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*ST--APRGIVT 1083 2R:1731127-2080000 -1 NULL:1987357 Q9VMT5 24 374 1 1 0 2603638 111144 110061 1 0 0 0 337 partof NFNYWNRRGVPHDAPHPLYGNM--VGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADR--GQFHNGRDDP-LTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQ-VPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLL-TMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALREREN---FKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*ST--APRGIVT 1083 2R:1731127-2080000 -1 NULL:1987359 AAL39321 24 374 1 1 0 2598181 329524 329257 1 0 0 0 220 partof FSCCGNTGYQQYE----TVPSSCCGYKDRTKVCEA-EIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQI 267 2R:1731127-2080000 1 NULL:1982865 Q9NB13 136 230 1 1 0 2598183 332997 332730 1 0 0 0 280 partof LPQICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMXXXXXXXXXXSWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQY 267 2R:1731127-2080000 1 NULL:1982867 Q9U3V4 17 102 1 1 0 2598185 332997 332730 1 0 0 0 280 partof LPQICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMXXXXXXXXXXSWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQY 267 2R:1731127-2080000 1 NULL:1982869 Q9NB15 17 102 1 1 0 2598187 333000 332745 1 0 0 0 132 partof GILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMXXXXXXXXXXSWFGCCGAIRESYCMSMTVEY*SC-IVPFILQFKMYSLWQYS 255 2R:1731127-2080000 1 NULL:1982871 Q9NB14 22 105 1 1 0 333420 333201 1 0 0 0 133 partof 219 2R:1731127-2080000 1 NULL:1982872 Q9NB14 133 206 1 1 0 2603640 111147 110109 1 0 0 0 854 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1038 2R:1731127-2080000 -1 NULL:1987361 Q9V771 20 361 1 1 0 110037 109620 1 0 0 0 368 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987362 Q9V771 362 500 1 1 0 2603643 111147 110109 1 0 0 0 855 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1038 2R:1731127-2080000 -1 NULL:1987364 AAL49218 20 361 1 1 0 110037 109620 1 0 0 0 368 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987365 AAL49218 362 500 1 1 0 2603646 111147 110106 1 0 0 0 769 partof RNFNYWNRRGVPHDAPHPLYGNMVG--FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1987367 P82711 20 362 1 1 0 110040 109620 1 0 0 0 315 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987368 P82711 361 500 1 1 0 2603649 111147 110106 1 0 0 0 864 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1987370 Q27594 23 365 1 1 0 110040 109620 1 0 0 0 483 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987371 Q27594 364 504 1 1 0 2598190 333171 332994 1 0 0 0 279 partof 177 2R:1731127-2080000 1 NULL:1982874 Q9U3V4 84 143 1 1 0 333417 333198 1 0 0 0 280 partof 219 2R:1731127-2080000 1 NULL:1982875 Q9U3V4 128 202 1 1 0 333748 333676 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1982876 Q9U3V4 201 225 1 1 0 2598194 333171 332994 1 0 0 0 279 partof 177 2R:1731127-2080000 1 NULL:1982878 Q9NB15 84 143 1 1 0 333417 333198 1 0 0 0 374 partof 219 2R:1731127-2080000 1 NULL:1982879 Q9NB15 128 203 1 1 0 333748 333676 1 0 0 0 127 partof QFVGFVFACCLANSIRNYRRRAEY 72 2R:1731127-2080000 1 NULL:1982880 Q9NB15 202 226 1 1 0 2598198 333420 333132 1 0 0 0 152 partof YMDAIQISVSI*GLPRTC-DPPSTDFLPLPQM----KCCGRSGYTDYAYQGKFPPSCCSDTNN--CRWETVYRRG-CKVTFVEFWDRNSDIIKYAGLVIAAIEV 288 2R:1731127-2080000 1 NULL:1982882 Q9U3V3 103 205 1 1 0 2603652 111147 110106 1 0 0 0 521 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGF---PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLT-QHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1987373 AAL39266 19 361 1 1 0 110040 109620 1 0 0 0 247 partof SETLRLYTLVPHLERKALND-----YVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987374 AAL39266 360 505 1 1 0 2603655 111147 110106 1 0 0 0 521 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGF---PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLT-QHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1041 2R:1731127-2080000 -1 NULL:1987376 Q9V9L1 19 361 1 1 0 110040 109620 1 0 0 0 247 partof SETLRLYTLVPHLERKALND-----YVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987377 Q9V9L1 360 505 1 1 0 2603658 111147 110109 1 0 0 0 830 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1038 2R:1731127-2080000 -1 NULL:1987379 AAL39235 19 360 1 1 0 110037 109620 1 0 0 0 359 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987380 AAL39235 361 499 1 1 0 2603661 111147 110109 1 0 0 0 830 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1038 2R:1731127-2080000 -1 NULL:1987382 Q9V770 19 360 1 1 0 110037 109620 1 0 0 0 359 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987383 Q9V770 361 499 1 1 0 2603664 111147 109623 1 0 0 0 619 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHG-KLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEV---------IEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQ----EGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVER 1524 2R:1731127-2080000 -1 NULL:1987385 Q9W223 19 510 1 1 0 2603666 111147 109623 1 0 0 0 378 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMH-DFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFM-FPTVIKVSEEFVKVITEQVPAAQNGAVLEI---KELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTD-----MRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEV-IEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTY-ESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALN--DY-VVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVER 1524 2R:1731127-2080000 -1 NULL:1987387 Q9V675 21 514 1 1 0 2603668 111147 110109 1 0 0 0 546 partof RNFNYWNRRGVPHDAPHPLYGNM-VGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLT-QHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFV-FSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1038 2R:1731127-2080000 -1 NULL:1987389 Q9V674 22 368 1 1 0 110037 109629 1 0 0 0 251 partof ETLRLYTLVPHLERKALN-----DYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 408 2R:1731127-2080000 -1 NULL:1987390 Q9V674 369 510 1 1 0 2603671 111147 109662 1 0 0 0 687 partof RNFNYWNRRGVPHDAPHPL-YGNMVG-FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEV-----------IEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIV 1485 2R:1731127-2080000 -1 NULL:1987392 Q9VCW1 20 498 1 1 0 2603673 111147 109662 1 0 0 0 687 partof RNFNYWNRRGVPHDAPHPL-YGNMVG-FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEV-----------IEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIV 1485 2R:1731127-2080000 -1 NULL:1987394 AAK93030 20 498 1 1 0 2603675 111147 109998 1 0 0 0 458 partof RNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGF---PFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPL-TQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVS---EEFVKVITEQVPA--AQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFT-DMRHGKLLTMFV-FSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQ-EGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSS-ETLRLYTLVPHLE 1149 2R:1731127-2080000 -1 NULL:1987396 Q9VRB3 23 408 1 1 0 2603677 111150 110109 1 0 0 0 859 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHD-FXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1041 2R:1731127-2080000 -1 NULL:1987398 Q9V773 19 361 1 1 0 110037 109620 1 0 0 0 313 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDT-TEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987399 Q9V773 362 501 1 1 0 2603680 111150 110109 1 0 0 0 953 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1041 2R:1731127-2080000 -1 NULL:1987401 Q27593 22 366 1 1 0 110037 109620 1 0 0 0 461 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987402 Q27593 367 506 1 1 0 2603683 111150 110109 1 0 0 0 890 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 1041 2R:1731127-2080000 -1 NULL:1987404 Q963E0 22 354 1 1 0 110037 109620 1 0 0 0 454 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 417 2R:1731127-2080000 -1 NULL:1987405 Q963E0 355 494 1 1 0 2603686 111150 110106 1 0 0 0 974 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1044 2R:1731127-2080000 -1 NULL:1987407 AAL48817 22 367 1 1 0 110040 109620 1 0 0 0 429 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMS-IVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987408 AAL48817 366 507 1 1 0 2603689 111150 110106 1 0 0 0 974 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1044 2R:1731127-2080000 -1 NULL:1987410 Q9VB31 22 367 1 1 0 110040 109620 1 0 0 0 429 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMS-IVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987411 Q9VB31 366 507 1 1 0 2603692 111150 110112 1 0 0 0 307 partof HRNFNYWNRRGVPHDAPH---PLYGNMVGFRKNRVMH-DFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDG-KKWKDMRQRLTPTFTSGKMK-FMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQV 1038 2R:1731127-2080000 -1 NULL:1987413 Q9V676 19 354 1 1 0 110037 109632 1 0 0 0 237 partof ETLRLYTLVPHLERK----ALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR 405 2R:1731127-2080000 -1 NULL:1987414 Q9V676 356 495 1 1 0 2603695 111150 110103 1 0 0 0 959 partof HRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISG 1047 2R:1731127-2080000 -1 NULL:1987416 Q961V2 22 368 1 1 0 2603697 111207 110106 1 0 0 0 1729 partof MFVXXXXXXXXXXXXXXXXHRNFNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1101 2R:1731127-2080000 -1 NULL:1987418 P33270 0 367 1 1 0 110040 109620 1 0 0 0 736 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1987419 P33270 366 506 1 1 0 2597904 76385 76259 1 0 0 0 125 partof MIRLNWLFXXXXXXXXXXXXXXXXGDANVLHSEVDKQSAEYK 126 2R:1731127-2080000 1 NULL:1982595 Q9V9A7 0 42 1 1 0 76663 76444 1 0 0 0 361 partof ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGEEVVNS 219 2R:1731127-2080000 1 NULL:1982596 Q9V9A7 42 115 1 1 0 77909 77018 1 0 0 0 1521 partof TECLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 891 2R:1731127-2080000 1 NULL:1982597 Q9V9A7 127 424 1 1 0 78426 77931 1 0 0 0 820 partof IMISIYVGFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 495 2R:1731127-2080000 1 NULL:1982598 Q9V9A7 413 578 1 1 0 2597910 82561 82438 1 0 0 0 216 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982600 Q9V9A6 0 41 1 1 0 82766 82616 1 0 0 0 261 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982601 Q9V9A6 40 90 1 1 0 83124 82998 1 0 0 0 200 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982602 Q9V9A6 88 130 1 1 0 2597914 82561 82438 1 0 0 0 216 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982604 Q9XZ57 0 41 1 1 0 82766 82616 1 0 0 0 261 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982605 Q9XZ57 40 90 1 1 0 83124 82998 1 0 0 0 200 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982606 Q9XZ57 88 130 1 1 0 2597918 82561 82438 1 0 0 0 216 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982608 AAL49002 0 41 1 1 0 82766 82616 1 0 0 0 261 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982609 AAL49002 40 90 1 1 0 83124 82998 1 0 0 0 200 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982610 AAL49002 88 130 1 1 0 2597922 84218 83954 1 0 0 0 450 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAASGVSSSYRRGPSATTRPAMTSAVKPSM 264 2R:1731127-2080000 1 NULL:1982612 Q9V9A6 89 177 1 1 0 84622 84472 1 0 0 0 176 partof PAVSKVLPRTNNAAPASRINACANSTGTXXXXXXXXXXXXQQIEEMSNQV 150 2R:1731127-2080000 1 NULL:1982613 Q9V9A6 174 224 1 1 0 84898 84820 1 0 0 0 127 partof CQEADDAEAHPIIQKILDILYATEVG 78 2R:1731127-2080000 1 NULL:1982614 Q9V9A6 251 277 1 1 0 2597926 84212 83954 1 0 0 0 448 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAASGVSSSYRRGPSATTRPAMTSAVKP 258 2R:1731127-2080000 1 NULL:1982616 Q9XZ57 89 175 1 1 0 84622 84469 1 0 0 0 169 partof IPAVSKVLPRTNNAAPASRINACANSTGTXXXXXXXXXXXXQQIEEMSNQV 153 2R:1731127-2080000 1 NULL:1982617 Q9XZ57 172 223 1 1 0 84898 84820 1 0 0 0 127 partof CQEADDAEAHPIIQKILDILYATEVG 78 2R:1731127-2080000 1 NULL:1982618 Q9XZ57 250 276 1 1 0 2597930 84218 83954 1 0 0 0 450 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPGTAASGVSSSYRRGPSATTRPAMTSAVKPSM 264 2R:1731127-2080000 1 NULL:1982620 AAL49002 89 177 1 1 0 84622 84472 1 0 0 0 176 partof PAVSKVLPRTNNAAPASRINACANSTGTXXXXXXXXXXXXQQIEEMSNQV 150 2R:1731127-2080000 1 NULL:1982621 AAL49002 174 224 1 1 0 84898 84820 1 0 0 0 127 partof CQEADDAEAHPIIQKILDILYATEVG 78 2R:1731127-2080000 1 NULL:1982622 AAL49002 251 277 1 1 0 2597934 138302 137861 1 0 0 0 695 partof QMRAISNGTXXXXXXXXXXXXXXXXIKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 441 2R:1731127-2080000 1 NULL:1982624 P21914 20 167 1 1 0 138748 138355 1 0 0 0 707 partof RNEAGEKKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAALHK 393 2R:1731127-2080000 1 NULL:1982625 P21914 166 297 1 1 0 2597937 138302 137936 1 0 0 0 525 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982627 Q9VWN3 147 266 1 1 0 138742 138349 1 0 0 0 502 partof LCRNEAGEKKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAAL 393 2R:1731127-2080000 1 NULL:1982628 Q9VWN3 262 393 1 1 0 2597940 141859 141703 1 0 0 0 282 partof MSENTYQIETRRRSRSKTPFLRSSCDHENCEHAGEEGHVHHLKRKSAAPNVQ 156 2R:1731127-2080000 1 NULL:1982630 Q9V997 0 52 1 1 0 142889 142595 1 0 0 0 281 partof KKTRAKAFAQLTSDYSSDDMTPDAKRKQNSITATVTSILTKRSGGATSTPRNRSQLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGEYW 294 2R:1731127-2080000 1 NULL:1982631 Q9V997 65 163 1 1 0 143482 142939 1 0 0 0 840 partof FCSKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLENHNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSWXXXXXXXXXXXXXXXXWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKIVQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKR 543 2R:1731127-2080000 1 NULL:1982632 Q9V997 161 342 1 1 0 144086 143807 1 0 0 0 491 partof AGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFESLRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV 279 2R:1731127-2080000 1 NULL:1982633 Q9V997 356 449 1 1 0 2597946 143482 143023 1 0 0 0 706 partof MPNMSRKSLENHNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVNYDSADELDATFGQQKQSWXXXXXXXXXXXXXXXXWSRVTNLSATETTAYQNYHAKRQQSQQVGLWWKIVQTIGGGLASLLRYLYVFIGSVLSLDTWLLRSSDAENKSKKR 459 2R:1731127-2080000 1 NULL:1982635 Q9I7G7 0 153 1 1 0 144086 143807 1 0 0 0 491 partof AGLFYYIHPNETFPPKSLSEYTFTLPELPKIDVKDYLNQEQFESLRSQAAEHAVRVRDWADDYVLYLRTIGQNVVNKGRQLFQGDDKVYYERV 279 2R:1731127-2080000 1 NULL:1982636 Q9I7G7 167 260 1 1 0 2597950 212416 211525 1 0 0 0 466 partof AQIEMSEPQEGRNQFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 891 2R:1731127-2080000 1 NULL:1982638 Q9V991 35 327 1 1 0 2597952 212416 211525 1 0 0 0 466 partof AQIEMSEPQEGRNQFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 891 2R:1731127-2080000 1 NULL:1982640 Q9I7G6 28 320 1 1 0 2597954 212416 211531 1 0 0 0 446 partof IEMSEPQEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEF-----WRTSCNYGDRG-PVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 885 2R:1731127-2080000 1 NULL:1982642 Q9V987 4 297 1 1 0 212624 212480 1 0 0 0 86 partof QLGITEVFSDKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVS 144 2R:1731127-2080000 1 NULL:1982643 Q9V987 295 343 1 1 0 2597957 212407 211552 1 0 0 0 261 partof EGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRG---PV-LKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRF-ADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY---------------DYSNIHMLILLPN-EVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 855 2R:1731127-2080000 1 NULL:1982645 Q9U1I4 37 331 1 1 0 2597959 212416 211552 1 0 0 0 180 partof EGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKIT-NLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHV-QVNMMYQEDKFRF-AELPQLKARAVQLPYDYSN-IHMLILLPNEVNGLQELEQQLNTVDLADIDAALTL--------QDVEIFLPRMCIEYDVDLKQVLNQV 864 2R:1731127-2080000 1 NULL:1982647 Q9VWB3 65 355 1 1 0 2597961 212416 211555 1 0 0 0 420 partof GRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 861 2R:1731127-2080000 1 NULL:1982649 Q9V3L3 10 287 1 1 0 2597963 212398 211558 1 0 0 0 394 partof RNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD--SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL-ADIDAALTLQDVEIFLPRMCIEYDVDLK 840 2R:1731127-2080000 1 NULL:1982651 Q9V4I3 28 300 1 1 0 2597965 212398 211558 1 0 0 0 391 partof RNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD--SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL-ADIDAALTLQDVEIFLPRMCIEYDVDLK 840 2R:1731127-2080000 1 NULL:1982653 Q9U5W8 28 300 1 1 0 2597967 212416 211561 1 0 0 0 230 partof NQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR-GPVLKSVNRLYVND--SLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNL-----LQSDAVNNETSALLINVLYFKGKWQKPFMP-ETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 855 2R:1731127-2080000 1 NULL:1982655 Q9V4I4 36 321 1 1 0 2597970 212416 211561 1 0 0 0 321 partof NQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR--GPVLKSVNRLYVNDSLELLTE-FNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNT--VDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 855 2R:1731127-2080000 1 NULL:1982657 Q9U5W7 107 386 1 1 0 2597972 212416 211561 1 0 0 0 321 partof NQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR--GPVLKSVNRLYVNDSLELLTE-FNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNT--VDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 855 2R:1731127-2080000 1 NULL:1982659 Q9V4I5 107 386 1 1 0 2597974 212416 211564 1 0 0 0 464 partof QFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 852 2R:1731127-2080000 1 NULL:1982661 Q9I7G5 7 288 1 1 0 2597976 212416 211564 1 0 0 0 464 partof QFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 852 2R:1731127-2080000 1 NULL:1982663 Q9U1I5 7 288 1 1 0 2597978 212416 211567 1 0 0 0 536 partof FARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 849 2R:1731127-2080000 1 NULL:1982665 Q9V5S3 17 294 1 1 0 212615 212480 1 0 0 0 89 partof QLGITEVF-SDKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAA 135 2R:1731127-2080000 1 NULL:1982666 Q9V5S3 292 338 1 1 0 212816 212699 1 0 0 0 92 partof KIVPMMLNMN--KKLFKADHPFVFYIRNPQAVFFAGRFSNP 117 2R:1731127-2080000 1 NULL:1982667 Q9V5S3 341 382 1 1 0 2597982 212416 211567 1 0 0 0 536 partof FARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 849 2R:1731127-2080000 1 NULL:1982669 AAK92954 17 294 1 1 0 212615 212480 1 0 0 0 89 partof QLGITEVF-SDKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAA 135 2R:1731127-2080000 1 NULL:1982670 AAK92954 292 338 1 1 0 212816 212699 1 0 0 0 92 partof KIVPMMLNMN--KKLFKADHPFVFYIRNPQAVFFAGRFSNP 117 2R:1731127-2080000 1 NULL:1982671 AAK92954 341 382 1 1 0 2603300 8846 7730 1 0 0 0 957 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDS-VFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1987031 P05031 75 446 1 1 0 7602 7428 1 0 0 0 92 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEI 174 2R:1731127-2080000 -1 NULL:1987032 P05031 448 506 1 1 0 2597986 212416 211615 1 0 0 0 353 partof SKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 801 2R:1731127-2080000 1 NULL:1982673 Q9VLZ8 45 305 1 1 0 2597988 212410 211624 1 0 0 0 247 partof PHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPG-DRHHIALNFGEFWRTSCNYGDRGPV-LKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYD--Y-------------SNIHMLILLPNEVN-GLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLN 786 2R:1731127-2080000 1 NULL:1982675 Q9VFC1 53 330 1 1 0 2603303 8846 7730 1 0 0 0 957 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDS-VFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1987034 Q95SL9 67 438 1 1 0 7602 7428 1 0 0 0 92 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEI 174 2R:1731127-2080000 -1 NULL:1987035 Q95SL9 440 498 1 1 0 2603306 8864 7736 1 0 0 0 896 partof PTACLSLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAF--VSDAPGSTGGGALQGSASECVLVSLITARARAISELK-GQTSVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEH--LTGV-DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFR 1128 2R:1731127-2080000 -1 NULL:1987037 P18486 34 412 1 1 0 2603308 8867 7730 1 0 0 0 1002 partof SPTACLSLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISEL-KGQTSVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1137 2R:1731127-2080000 -1 NULL:1987039 Q05733 33 413 1 1 0 7605 7311 1 0 0 0 136 partof GD-EPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPLAPVAGKPPIKKRL 294 2R:1731127-2080000 -1 NULL:1987040 Q05733 413 512 1 1 0 2597990 212407 211630 1 0 0 0 362 partof INTVFSPASVQSALTLAFMGAS-GS-TAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMP-ETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 777 2R:1731127-2080000 1 NULL:1982677 Q9V990 27 282 1 1 0 2597992 212299 211633 1 0 0 0 386 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQL 666 2R:1731127-2080000 1 NULL:1982679 Q9VLQ7 32 251 1 1 0 2597994 212407 211633 1 0 0 0 407 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1982681 Q9U1I7 32 282 1 1 0 2597996 212407 211633 1 0 0 0 394 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1982683 Q9VII7 32 281 1 1 0 2603311 8867 7730 1 0 0 0 999 partof SPTACLSLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISEL-KGQTSVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1137 2R:1731127-2080000 -1 NULL:1987042 Q9V5I3 33 413 1 1 0 7605 7311 1 0 0 0 136 partof GD-EPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPLAPVAGKPPIKKRL 294 2R:1731127-2080000 -1 NULL:1987043 Q9V5I3 413 512 1 1 0 2597998 212407 211633 1 0 0 0 394 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1982685 Q9U1I6 32 281 1 1 0 2603314 17131 16870 1 0 0 0 270 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 261 2R:1731127-2080000 -1 NULL:1987045 P05031 322 408 1 1 0 2603316 17131 16870 1 0 0 0 270 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 261 2R:1731127-2080000 -1 NULL:1987047 Q95SL9 314 400 1 1 0 2603318 17620 17038 1 0 0 0 284 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDR 582 2R:1731127-2080000 -1 NULL:1987049 P18486 144 336 1 1 0 2603320 18125 17708 1 0 0 0 372 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT*IFYRTTELSLVRYIDYKSEE 417 2R:1731127-2080000 -1 NULL:1987051 P05031 68 198 1 1 0 17620 17044 1 0 0 0 317 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADS--FNTNPNKWLLTNFDCSTLWVR 576 2R:1731127-2080000 -1 NULL:1987052 P05031 179 368 1 1 0 15554 15332 1 0 0 0 169 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1987053 P05031 437 510 1 1 0 2603324 18125 17708 1 0 0 0 372 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT*IFYRTTELSLVRYIDYKSEE 417 2R:1731127-2080000 -1 NULL:1987055 Q95SL9 60 190 1 1 0 17620 17044 1 0 0 0 317 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEYADS--FNTNPNKWLLTNFDCSTLWVR 576 2R:1731127-2080000 -1 NULL:1987056 Q95SL9 171 360 1 1 0 15554 15332 1 0 0 0 169 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1987057 Q95SL9 429 502 1 1 0 2603328 18125 17777 1 0 0 0 340 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1987059 P18486 33 145 1 1 0 17218 16912 1 0 0 0 202 partof SFICPELKPLLKVSGIPTARMANLTGFHS--QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYS-DAAI-DYRHWGVPLSRRFRSLKLW 306 2R:1731127-2080000 -1 NULL:1987060 P18486 257 363 1 1 0 2603331 18131 17771 1 0 0 0 573 partof TAEPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 360 2R:1731127-2080000 -1 NULL:1987062 Q9V9B8 31 148 1 1 0 17620 17149 1 0 0 0 687 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1987063 Q9V9B8 145 300 1 1 0 17131 16906 1 0 0 0 405 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYV 225 2R:1731127-2080000 -1 NULL:1987064 Q9V9B8 290 365 1 1 0 16560 16413 1 0 0 0 238 partof FVLRSYGISGLQHYIRHHIKLAKRFEELVLKDKRFEICNQVKVRHICFR 147 2R:1731127-2080000 -1 NULL:1987065 Q9V9B8 363 412 1 1 0 15554 15350 1 0 0 0 347 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANE 204 2R:1731127-2080000 -1 NULL:1987066 Q9V9B8 405 473 1 1 0 8841 8400 1 0 0 0 790 partof SSRRSPVAGAVQGRARGLRAEDHAGRGALEPPQVLRLLPLGQLFSIGPRRHAQQCHWFNWLQLGQLSGGCRAGDDRDELVRQGPWPAQGLCFGCPRQYRRRRPSGIRLRVRSRLSNHSPRPGHQRAKGSDQRSRQRLPAQPDRIRQP 441 2R:1731127-2080000 -1 NULL:1987067 Q9V9B8 471 618 1 1 0 2603338 18277 18148 1 0 0 0 148 partof MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLP 129 2R:1731127-2080000 -1 NULL:1987069 Q05733 0 43 1 1 0 18080 17771 1 0 0 0 378 partof APQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 309 2R:1731127-2080000 -1 NULL:1987070 Q05733 45 148 1 1 0 17620 17161 1 0 0 0 368 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTA 459 2R:1731127-2080000 -1 NULL:1987071 Q05733 145 295 1 1 0 17131 16876 1 0 0 0 234 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKAL 255 2R:1731127-2080000 -1 NULL:1987072 Q05733 289 373 1 1 0 2603343 18277 18148 1 0 0 0 148 partof MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLP 129 2R:1731127-2080000 -1 NULL:1987074 Q9V5I3 0 43 1 1 0 18080 17771 1 0 0 0 378 partof APQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 309 2R:1731127-2080000 -1 NULL:1987075 Q9V5I3 45 148 1 1 0 17620 17161 1 0 0 0 372 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTA 459 2R:1731127-2080000 -1 NULL:1987076 Q9V5I3 145 295 1 1 0 17131 16876 1 0 0 0 234 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKAL 255 2R:1731127-2080000 -1 NULL:1987077 Q9V5I3 289 373 1 1 0 2603348 18277 18121 1 0 0 0 233 partof MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLPRKPQK*PQN 156 2R:1731127-2080000 -1 NULL:1987079 Q9V9B8 0 52 1 1 0 2603350 26174 26114 1 0 0 0 101 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1987081 Q9V9B4 0 20 1 1 0 26043 25665 1 0 0 0 687 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1987082 Q9V9B4 19 145 1 1 0 25659 25404 1 0 0 0 365 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPINV 255 2R:1731127-2080000 -1 NULL:1987083 Q9V9B4 130 212 1 1 0 2603355 26174 26114 1 0 0 0 101 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1987085 AAL48009 0 20 1 1 0 26043 25665 1 0 0 0 687 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1987086 AAL48009 19 145 1 1 0 25659 25404 1 0 0 0 365 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPINV 255 2R:1731127-2080000 -1 NULL:1987087 AAL48009 130 212 1 1 0 2603360 30931 30655 1 0 0 0 345 partof IN*IYYLLYFSVCGASVFFMPLLITNYMGLMVMCVIXXXXXXXXXXXXXXILVSIVDLDDFTCAYGLVLLVQGVGMIAGPPIAGVIYEYTGR 276 2R:1731127-2080000 -1 NULL:1987089 AAL39716 756 847 1 1 0 2603362 30931 30655 1 0 0 0 345 partof IN*IYYLLYFSVCGASVFFMPLLITNYMGLMVMCVIXXXXXXXXXXXXXXILVSIVDLDDFTCAYGLVLLVQGVGMIAGPPIAGVIYEYTGR 276 2R:1731127-2080000 -1 NULL:1987091 Q9V9B3 662 753 1 1 0 2603364 33499 33223 1 0 0 0 154 partof FCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 276 2R:1731127-2080000 -1 NULL:1987093 Q9UB81 1 93 1 1 0 2603366 33772 32602 1 0 0 0 272 partof PDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMRDPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLLDTGIT---KEAVLDSLVTKNNTEANQQIDDPLDSALKRYRSEIFLPTFLSTQELDSICEVKSLSRRSLRHKEGEEAPSRENLL-SMSSGAGAYPPSTAVIGSPDDTLMGGIXXXXXXXXXXXYLASIETLSPSEKRSTGRTPNG----SLRSSDEGYLTQKHASSRYSLNENIFMAKHTT 1170 2R:1731127-2080000 -1 NULL:1987095 Q9V6Z1 43 424 1 1 0 2603368 33790 33223 1 0 0 0 395 partof KKTPKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 567 2R:1731127-2080000 -1 NULL:1987097 Q9W509 22 211 1 1 0 2603370 33796 33223 1 0 0 0 292 partof TEKKTPKM--PDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTA-WISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 573 2R:1731127-2080000 -1 NULL:1987099 Q9V623 215 409 1 1 0 2603372 33886 32161 1 0 0 0 2572 partof MTCLMNGNGQVKRRKRLXXXXXXXXXXXXXTEKKTPKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMRDPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLLDTGITKEAVLDSLVTKNNTEANQQIDDPLDSALKRYRSEIFLPTFLSTQELDSICEVKSLSRRSLRHKEGEEAPSRENLLSMSSGAGAYPPSTAVIGSPDDTLMGGIXXXXXXXXXXXYLASIETLSPSEKRSTGRTPNGSLRSSDEGYLTQKHASSRYSLNENIFMAKHTTPSISNLKVNGLRHNSVDILSEDMHCYYSKDETFALLEPSRRIRPTVIAIPEQEQSVNSELATRRARLDSITGIRRLSRSKKPSHHXXXXXXXXXXXXXXFLKDMRIHRNSIHYRGAMLNTHRYRLRASSCPNIYRNSMTTIAKEEED 1725 2R:1731127-2080000 -1 NULL:1987101 Q9V9B3 0 575 1 1 0 31697 31577 1 0 0 0 201 partof TWYDNFVDTMKSIFDFSLFLDMKFALFNLSTLFLFIW*VL 120 2R:1731127-2080000 -1 NULL:1987102 Q9V9B3 575 615 1 1 0 31145 30875 1 0 0 0 326 partof FIIPYLYLPDYMKQYKYDVSQSAELISDVGIAQTVGMIGLGYLGDLSWMNINICYSLCMLGECLDYVTFSIYQLNLLFIIFFSVRSVCVL 270 2R:1731127-2080000 -1 NULL:1987103 Q9V9B3 612 697 1 1 0 30594 30450 1 0 0 0 256 partof RWDDTFYYAGIFIALSGVCSYLIEFCEKKAPKESDSDVLETKKAQLLH 144 2R:1731127-2080000 -1 NULL:1987104 Q9V9B3 752 800 1 1 0 2603377 34168 32161 1 0 0 0 2811 partof MAKLATDPXXXXXXXXXXXXXXXXXXXXXXXXXXXXYQXXXXXXXXXXXXXHKAIKHDLFPEVTFCNLSVEELADGAGHSRVVRSSVIELEDGTMTCLMNGNGQVKRRKRLXXXXXXXXXXXXXTEKKTPKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMRDPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLLDTGITKEAVLDSLVTKNNTEANQQIDDPLDSALKRYRSEIFLPTFLSTQELDSICEVKSLSRRSLRHKEGEEAPSRENLLSMSSGAGAYPPSTAVIGSPDDTLMGGIXXXXXXXXXXXYLASIETLSPSEKRSTGRTPNGSLRSSDEGYLTQKHASSRYSLNENIFMAKHTTPSISNLKVNGLRHNSVDILSEDMHCYYSKDETFALLEPSRRIRPTVIAIPEQEQSVNSELATRRARLDSITGIRRLSRSKKPSHHXXXXXXXXXXXXXXFLKDMRIHRNSIHYRGAMLNTHRYRLRASSCPNIYRNSMTTIAKEEED 2007 2R:1731127-2080000 -1 NULL:1987106 AAL39716 0 669 1 1 0 31697 31577 1 0 0 0 201 partof TWYDNFVDTMKSIFDFSLFLDMKFALFNLSTLFLFIW*VL 120 2R:1731127-2080000 -1 NULL:1987107 AAL39716 669 709 1 1 0 31145 30875 1 0 0 0 326 partof FIIPYLYLPDYMKQYKYDVSQSAELISDVGIAQTVGMIGLGYLGDLSWMNINICYSLCMLGECLDYVTFSIYQLNLLFIIFFSVRSVCVL 270 2R:1731127-2080000 -1 NULL:1987108 AAL39716 706 791 1 1 0 30594 30450 1 0 0 0 256 partof RWDDTFYYAGIFIALSGVCSYLIEFCEKKAPKESDSDVLETKKAQLLH 144 2R:1731127-2080000 -1 NULL:1987109 AAL39716 846 894 1 1 0 2598200 333420 333228 1 0 0 0 125 partof CCGRSGYTDYAYQG-KFPPSCCS--DTN-NCRWETVY--RRGCKVTFVEFWDRNSDIIKYAGLVIAAIEV 192 2R:1731127-2080000 1 NULL:1982884 Q9NB13 138 208 1 1 0 2598202 335244 334992 1 0 0 0 382 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTI 252 2R:1731127-2080000 1 NULL:1982886 Q9NB14 0 84 1 1 0 335560 335308 1 0 0 0 290 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCG 252 2R:1731127-2080000 1 NULL:1982887 Q9NB14 84 160 1 1 0 2598205 335238 334992 1 0 0 0 188 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCT 246 2R:1731127-2080000 1 NULL:1982889 Q9NB13 0 82 1 1 0 335596 335308 1 0 0 0 88 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPS 288 2R:1731127-2080000 1 NULL:1982890 Q9NB13 84 173 1 1 0 2598208 335250 334992 1 0 0 0 175 partof 258 2R:1731127-2080000 1 NULL:1982892 Q9U3V3 0 86 1 1 0 335788 335545 1 0 0 0 138 partof FSCCGNTGYQQYE-TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMR 243 2R:1731127-2080000 1 NULL:1982893 Q9U3V3 138 219 1 1 0 2603382 47340 46962 1 0 0 0 331 partof CGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNP 378 2R:1731127-2080000 -1 NULL:1987111 AAL48543 69 188 1 1 0 46824 46425 1 0 0 0 383 partof HELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCEL 399 2R:1731127-2080000 -1 NULL:1987112 AAL48543 279 412 1 1 0 2603386 47340 46962 1 0 0 0 331 partof CGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNP 378 2R:1731127-2080000 -1 NULL:1987114 Q9VEX1 69 188 1 1 0 46824 46425 1 0 0 0 383 partof HELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCEL 399 2R:1731127-2080000 -1 NULL:1987115 Q9VEX1 279 412 1 1 0 2603389 47340 46962 1 0 0 0 331 partof CGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNP 378 2R:1731127-2080000 -1 NULL:1987117 Q9GRW9 68 187 1 1 0 46824 46425 1 0 0 0 383 partof HELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCEL 399 2R:1731127-2080000 -1 NULL:1987118 Q9GRW9 278 411 1 1 0 2598211 335605 335299 1 0 0 0 124 partof SFQYAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPSSCC 306 2R:1731127-2080000 1 NULL:1982895 Q9NB15 81 177 1 1 0 2598213 335809 335518 1 0 0 0 176 partof 291 2R:1731127-2080000 1 NULL:1982897 Q9NB15 129 225 1 1 0 2598215 335809 335518 1 0 0 0 148 partof DIYVSIPLQFSCCGNTGYQQYETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQ 291 2R:1731127-2080000 1 NULL:1982899 Q9U3V4 129 224 1 1 0 2598217 335794 335530 1 0 0 0 463 partof 264 2R:1731127-2080000 1 NULL:1982901 Q9NB14 134 222 1 1 0 2598219 335812 335545 1 0 0 0 220 partof 267 2R:1731127-2080000 1 NULL:1982903 Q9NB13 136 230 1 1 0 2603392 47409 46959 1 0 0 0 263 partof VDHHALXXXXXXXXXXXXXXXXXCGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNPQ 450 2R:1731127-2080000 -1 NULL:1987120 Q9V9B1 1 147 1 1 0 46824 46437 1 0 0 0 396 partof HELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQI 387 2R:1731127-2080000 -1 NULL:1987121 Q9V9B1 167 296 1 1 0 2603395 47433 46428 1 0 0 0 1205 partof MSQEQTQDVDHHALXXXXXXXXXXXXXXXXXCGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNPQAKEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCE 1005 2R:1731127-2080000 -1 NULL:1987123 Q9GRX0 0 335 1 1 0 2603397 47451 46428 1 0 0 0 1232 partof MSATATMSQEQTQDVDHHALXXXXXXXXXXXXXXXXXCGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNPQAKEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCE 1023 2R:1731127-2080000 -1 NULL:1987125 Q9V9B2 0 341 1 1 0 2603399 47451 46428 1 0 0 0 1232 partof MSATATMSQEQTQDVDHHALXXXXXXXXXXXXXXXXXCGSLPYVLNRCFHWTKASPEETRSSLVVRCLLFFGGGVLICTTFLHMLPXXXXXXXXXXECGSLVKTPFALAEMLLCTGFFLMYALDELMTSLVRHHQGKLSRKESVASLAFERGRSIRHSVLLNPQAKEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHELFEGMAIGLEGTVSTVWFMFGAVSAHKLVLAFCVGMELLVARTRSSLAILYLVTFXXXXXXXXXXXXXXXQQVAAGQPSLPSGVLQGIACGTLLYVVFFEILIESHAGWRALVAAVAGFALMFGLQILCE 1023 2R:1731127-2080000 -1 NULL:1987127 AAL48717 0 341 1 1 0 2598221 337692 337545 1 0 0 0 260 partof DLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGA 147 2R:1731127-2080000 1 NULL:1982905 Q9NB13 35 84 1 1 0 338199 337755 1 0 0 0 810 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVYA 444 2R:1731127-2080000 1 NULL:1982906 Q9NB13 84 232 1 1 0 2598224 338172 337746 1 0 0 0 207 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRS 426 2R:1731127-2080000 1 NULL:1982908 Q9NB15 81 219 1 1 0 2598226 338172 337746 1 0 0 0 187 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRS 426 2R:1731127-2080000 1 NULL:1982910 Q9U3V4 81 218 1 1 0 2598228 338175 337755 1 0 0 0 292 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTA---MGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQ 420 2R:1731127-2080000 1 NULL:1982912 Q9NB14 84 222 1 1 0 2598230 338196 337755 1 0 0 0 205 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH--DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVY 441 2R:1731127-2080000 1 NULL:1982914 Q9U3V3 84 227 1 1 0 2598232 347153 346886 1 0 0 0 163 partof MPIILISLGSIVVFISFLGCCGAIRESVCMTMSYAXXXXXXXXXXXXXXXXXXXHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 267 2R:1731127-2080000 1 NULL:1982916 Q9NB15 51 139 1 1 0 2598234 347153 346886 1 0 0 0 163 partof MPIILISLGSIVVFISFLGCCGAIRESVCMTMSYAXXXXXXXXXXXXXXXXXXXHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 267 2R:1731127-2080000 1 NULL:1982918 Q9U3V4 51 139 1 1 0 2603700 140126 139976 1 0 0 0 245 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1987421 Q9V998 9 59 1 1 0 2603703 168577 168436 1 0 0 0 248 partof MDGGGDNQLAVRSLGRQREAFSHYAGPPTAMLQGPDPGEGDVLALQM 141 2R:1731127-2080000 -1 NULL:1987423 Q9V994 0 47 1 1 0 2603706 195146 194918 1 0 0 0 167 partof GRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSA 228 2R:1731127-2080000 -1 NULL:1987425 Q9W3W1 65 141 1 1 0 194845 194383 1 0 0 0 287 partof YTLCIAKVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTA--ELESEAMCHEGSKATRAIFL--RHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTIL 462 2R:1731127-2080000 -1 NULL:1987426 Q9W3W1 145 301 1 1 0 2603709 196659 196458 1 0 0 0 349 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNKV 201 2R:1731127-2080000 -1 NULL:1987428 Q9V993 0 67 1 1 0 195152 194879 1 0 0 0 486 partof QVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 273 2R:1731127-2080000 -1 NULL:1987429 Q9V993 65 156 1 1 0 194827 194374 1 0 0 0 744 partof KVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMN 453 2R:1731127-2080000 -1 NULL:1987430 Q9V993 154 305 1 1 0 194349 194052 1 0 0 0 530 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLK 297 2R:1731127-2080000 -1 NULL:1987431 Q9V993 292 391 1 1 0 193314 193122 1 0 0 0 180 partof VQGGYVSSSVNKSLPAKKAGNILNKPRGDXXXXXXXXXXXXXXXXXXXXXXXXXEGGPPAAVLS 192 2R:1731127-2080000 -1 NULL:1987432 Q9V993 389 453 1 1 0 193064 192980 1 0 0 0 132 partof EKDLRTIQDEIRKLKAIIVKQENRIRAL 84 2R:1731127-2080000 -1 NULL:1987433 Q9V993 453 481 1 1 0 2603716 204626 204080 1 0 0 0 272 partof PP---GQRLLTSFSVVRNYHRLVEPYNSDFSRDVSFFDGFRVIGVFVVILGHTLMVFMTVPIENPEFFEQFLFRFETSIFQNGSLVIQIFFVMSGFLLYVKFTK-RQQIQPKTGTLEC--IAVYFRVFS-YRYFRLLPSLLALILFNGTLLVRLQNGPFWRHLTEAERVFCRANWWKNVFFVTNHMLED 546 2R:1731127-2080000 -1 NULL:1987435 Q9VF31 267 455 1 1 0 2603718 205388 204944 1 0 0 0 700 partof MPAXXXXXXXXXXXXNQAGTYCLVYVEILPNASSALWHQIDQVSQDSKHRFRHDRVFRGVCLESCKQRINHLSEFREYEKEEILDKELISYYDKVHRRDAMNSDRDLFNKEVVKGCLNQKFSEKFSLRTRSLIEYCVSASDKDLKMGK 444 2R:1731127-2080000 -1 NULL:1987437 Q9V992 0 148 1 1 0 204647 204068 1 0 0 0 968 partof SQVDFGMPPGQRLLTSFSVVRNYHRLVEPYNSDFSRDVSFFDGFRVIGVFVVILGHTLMVFMTVPIENPEFFEQFLFRFETSIFQNGSLVIQIFFVMSGFLLYVKFTKRQQIQPKTGTLECIAVYFRVFSYRYFRLLPSLLALILFNGTLLVRLQNGPFWRHLTEAERVFCRANWWKNVFFVTNHMLEDSVRY 579 2R:1731127-2080000 -1 NULL:1987438 Q9V992 137 330 1 1 0 2603721 207795 207198 1 0 0 0 229 partof LRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAA-TINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERT---VQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLP--NTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 597 2R:1731127-2080000 -1 NULL:1987440 Q9VLU4 97 301 1 1 0 2603723 207918 207189 1 0 0 0 424 partof LGAENETATQLDQGLGLASSDPEQIAHSFHQVLAA---YQD-SQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 729 2R:1731127-2080000 -1 NULL:1987442 Q9V989 0 247 1 1 0 2603725 208002 207198 1 0 0 0 362 partof YGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 804 2R:1731127-2080000 -1 NULL:1987444 Q9VLZ8 40 305 1 1 0 2603727 208005 207192 1 0 0 0 239 partof VYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLAS--SDPEQIAHSFHQVLAAYQ-DSQ-ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNH-LIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERF-RYADLPALDAMALELPYKDSD-LSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSF 813 2R:1731127-2080000 -1 NULL:1987446 Q9VL44 17 293 1 1 0 2603729 208014 207198 1 0 0 0 448 partof SINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 816 2R:1731127-2080000 -1 NULL:1987448 Q9U1I8 17 287 1 1 0 2603731 208017 207198 1 0 0 0 301 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLA-SSDPEQIAHSFHQVLAAYQDSQI----LRIANKIFVMDGY--QLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNS----ESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 819 2R:1731127-2080000 -1 NULL:1987450 Q9V4I4 38 321 1 1 0 2603733 208017 207198 1 0 0 0 240 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAY-----QDSQILRI--ANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYK---------------DSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYET---KVALKLPRFKAEFQVELSEVFQKV 819 2R:1731127-2080000 -1 NULL:1987452 Q9U1I4 42 334 1 1 0 2603735 208017 207210 1 0 0 0 412 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1987454 Q9U1I7 16 281 1 1 0 2603737 208017 207210 1 0 0 0 408 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1987456 Q9VII7 16 280 1 1 0 2603739 208017 207210 1 0 0 0 408 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1987458 Q9U1I6 16 280 1 1 0 2603741 208017 207210 1 0 0 0 248 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLA-SSDPEQIAHSFHQVLAAYQDS-------QILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAAT-INNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKD---------------SDLSMLIVLPNT-KTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1987460 Q9VFC1 40 328 1 1 0 2603743 208017 207213 1 0 0 0 366 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLA--AYQDSQILRIANKIFV---MDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTF-HLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTT--LSQITQSLYETKVALKLPRFKAEFQVELSE 804 2R:1731127-2080000 -1 NULL:1987462 Q9U5W7 109 381 1 1 0 2603745 208017 207213 1 0 0 0 366 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLA--AYQDSQILRIANKIFV---MDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTF-HLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTT--LSQITQSLYETKVALKLPRFKAEFQVELSE 804 2R:1731127-2080000 -1 NULL:1987464 Q9V4I5 109 381 1 1 0 2603747 208017 207279 1 0 0 0 225 partof FSINVYGKLSGQ--KPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQD--SQILRIAN--KIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIK-DLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLD-GERTVQVPMMSLKERFRY-ADLPALDAMALELPYKDSD-LSMLIVLPNTKTGLPALEEKLRLTTLSQITQSL 738 2R:1731127-2080000 -1 NULL:1987466 Q9VWB3 70 320 1 1 0 2603749 208017 207315 1 0 0 0 379 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKL 702 2R:1731127-2080000 -1 NULL:1987468 Q9VLQ7 16 251 1 1 0 2603751 208020 207198 1 0 0 0 354 partof LFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIA--H--SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 822 2R:1731127-2080000 -1 NULL:1987470 Q9V5S3 16 294 1 1 0 2603753 208020 207198 1 0 0 0 354 partof LFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIA--H--SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 822 2R:1731127-2080000 -1 NULL:1987472 AAK92954 16 294 1 1 0 2603755 208023 207198 1 0 0 0 515 partof ALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQ------DSQI--LRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 825 2R:1731127-2080000 -1 NULL:1987474 Q9V987 14 297 1 1 0 2603757 208041 207189 1 0 0 0 587 partof EFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 852 2R:1731127-2080000 -1 NULL:1987476 Q9V3L3 6 290 1 1 0 2603759 208044 207195 1 0 0 0 544 partof QEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETAT--QLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVS 849 2R:1731127-2080000 -1 NULL:1987478 Q9V990 3 286 1 1 0 2603761 208062 207189 1 0 0 0 1447 partof MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 873 2R:1731127-2080000 -1 NULL:1987480 Q9U1I5 0 291 1 1 0 207140 207026 1 0 0 0 178 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 114 2R:1731127-2080000 -1 NULL:1987481 Q9U1I5 286 324 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1987482 Q9U1I5 334 392 1 1 0 2603765 208062 207189 1 0 0 0 1447 partof MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 873 2R:1731127-2080000 -1 NULL:1987484 Q9I7G5 0 291 1 1 0 207140 207026 1 0 0 0 185 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 114 2R:1731127-2080000 -1 NULL:1987485 Q9I7G5 286 324 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1987486 Q9I7G5 334 392 1 1 0 2603769 208074 207198 1 0 0 0 393 partof ADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH---SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSK--NVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 876 2R:1731127-2080000 -1 NULL:1987488 Q9V4I3 12 306 1 1 0 2603771 208074 207198 1 0 0 0 397 partof ADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH---SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSK--NVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 876 2R:1731127-2080000 -1 NULL:1987490 Q9U5W8 12 306 1 1 0 2603773 208134 207189 1 0 0 0 1492 partof GCWXXXXXXXXXXXXXXVHTADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 945 2R:1731127-2080000 -1 NULL:1987492 Q9I7G6 8 323 1 1 0 207140 207026 1 0 0 0 185 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 114 2R:1731127-2080000 -1 NULL:1987493 Q9I7G6 318 356 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1987494 Q9I7G6 366 424 1 1 0 2603777 208179 207189 1 0 0 0 1575 partof MKTSTPHPRSIWILTGCWXXXXXXXXXXXXXXVHTADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 990 2R:1731127-2080000 -1 NULL:1987496 Q9V991 0 330 1 1 0 207140 207026 1 0 0 0 185 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 114 2R:1731127-2080000 -1 NULL:1987497 Q9V991 325 363 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1987498 Q9V991 373 431 1 1 0 sim4 1.0 na_pe.dros 1.0 2003-01-14 22:42:58 P Element genomic 2605700 301572 301303 1 0 0 0 99 partof 269 2R:1731127-2080000 -1 NULL:1989140 EP(2)2105 0 269 1 1 0 2600600 140232 140108 1 0 0 0 100 partof 124 2R:1731127-2080000 1 NULL:1984847 l(2)k16806 0 124 1 1 0 2600603 140877 140108 1 0 0 0 99 partof 769 2R:1731127-2080000 1 NULL:1984849 l(2)k03203 0 767 1 1 0 2600606 140791 140382 1 0 0 0 99 partof 409 2R:1731127-2080000 1 NULL:1984851 ms(2)09967 0 408 1 1 0 2600609 315995 315340 1 0 0 0 99 partof 655 2R:1731127-2080000 1 NULL:1984853 EP(2)2275 0 655 1 1 0 2600612 316197 315340 1 0 0 0 99 partof 857 2R:1731127-2080000 1 NULL:1984855 l(2)k16722 0 857 1 1 0 2605697 301572 301303 1 0 0 0 99 partof 269 2R:1731127-2080000 -1 NULL:1989138 EP(2)2303 0 269 1 1 0 blastx_masked 1.0 aa_TR.real.dros 1.0 2003-01-13 22:23:02 BLASTX Similarity to Fly genomic 2605709 207993 207198 1 0 0 0 250 partof LAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLG-LGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 795 2R:1731127-2080000 -1 NULL:1989146 Q9V3N1 84 350 1 1 0 2605711 208014 207198 1 0 0 0 448 partof SINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 816 2R:1731127-2080000 -1 NULL:1989148 Q9U1I8 17 287 1 1 0 2605713 208017 207210 1 0 0 0 408 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1989150 Q9U1I6 16 280 1 1 0 207146 206951 1 0 0 0 107 partof LLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGKWS--KSL----VFFGIHHP 195 2R:1731127-2080000 -1 NULL:1989151 Q9U1I6 280 350 1 1 0 2605716 208017 207210 1 0 0 0 408 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1989153 Q9VII7 16 280 1 1 0 207146 206951 1 0 0 0 110 partof LLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGKWS--KSL----VFFGIHHP 195 2R:1731127-2080000 -1 NULL:1989154 Q9VII7 280 350 1 1 0 2605719 208017 207315 1 0 0 0 379 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKL 702 2R:1731127-2080000 -1 NULL:1989156 Q9VLQ7 16 251 1 1 0 207137 206975 1 0 0 0 112 partof LGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATGKWSKSL 162 2R:1731127-2080000 -1 NULL:1989157 Q9VLQ7 251 302 1 1 0 2605722 208017 207213 1 0 0 0 366 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLA--AYQDSQILRIANKIFV---MDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTF-HLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTT--LSQITQSLYETKVALKLPRFKAEFQVELSE 804 2R:1731127-2080000 -1 NULL:1989159 Q9U5W7 109 381 1 1 0 207146 206996 1 0 0 0 101 partof LLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAAT 150 2R:1731127-2080000 -1 NULL:1989160 Q9U5W7 382 430 1 1 0 2605725 208017 207213 1 0 0 0 366 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLA--AYQDSQILRIANKIFV---MDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTF-HLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTT--LSQITQSLYETKVALKLPRFKAEFQVELSE 804 2R:1731127-2080000 -1 NULL:1989162 Q9V4I5 109 381 1 1 0 207146 206996 1 0 0 0 101 partof LLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAAT 150 2R:1731127-2080000 -1 NULL:1989163 Q9V4I5 382 430 1 1 0 2605728 208017 207198 1 0 0 0 240 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAY-----QDSQILRI--ANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYK---------------DSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYET---KVALKLPRFKAEFQVELSEVFQKV 819 2R:1731127-2080000 -1 NULL:1989165 Q9U1I4 42 334 1 1 0 2605730 208017 207198 1 0 0 0 242 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAY-----QDSQILRI--ANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDF-SKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYK---------------DSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYET---KVALKLPRFKAEFQVELSEVFQKV 819 2R:1731127-2080000 -1 NULL:1989167 Q9VFC2 42 334 1 1 0 2605732 208017 207210 1 0 0 0 412 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQ---ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1989169 Q9U1I7 16 281 1 1 0 2605734 208020 207189 1 0 0 0 439 partof LFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQ-IAHSFHQVLAAYQDSQ-ILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 831 2R:1731127-2080000 -1 NULL:1989171 Q9V3R7 28 305 1 1 0 2605736 208041 207189 1 0 0 0 587 partof EFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 852 2R:1731127-2080000 -1 NULL:1989173 Q9V3L3 6 290 1 1 0 2605738 208062 207189 1 0 0 0 1447 partof MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 873 2R:1731127-2080000 -1 NULL:1989175 Q9U1I5 0 291 1 1 0 207140 206993 1 0 0 0 231 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATG 147 2R:1731127-2080000 -1 NULL:1989176 Q9U1I5 286 335 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1989177 Q9U1I5 334 392 1 1 0 2605742 208062 207189 1 0 0 0 1447 partof MADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 873 2R:1731127-2080000 -1 NULL:1989179 Q9I7G5 0 291 1 1 0 207140 206993 1 0 0 0 238 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATG 147 2R:1731127-2080000 -1 NULL:1989180 Q9I7G5 286 335 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1989181 Q9I7G5 334 392 1 1 0 2605746 208074 207198 1 0 0 0 397 partof ADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH---SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSK--NVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 876 2R:1731127-2080000 -1 NULL:1989183 Q9U5W8 12 306 1 1 0 2605748 208074 207198 1 0 0 0 393 partof ADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH---SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSK--NVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 876 2R:1731127-2080000 -1 NULL:1989185 Q9V4I3 12 306 1 1 0 2600802 328962 328704 1 0 0 0 189 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1985042 Q9NB15 0 86 1 1 0 329521 329230 1 0 0 0 176 partof 291 2R:1731127-2080000 1 NULL:1985043 Q9NB15 129 225 1 1 0 2600805 328962 328830 1 0 0 0 108 partof FDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 132 2R:1731127-2080000 1 NULL:1985045 Q9I7D6 3 47 1 1 0 2600807 329506 329242 1 0 0 0 463 partof SIPLQFSCCGNTGYQQYETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR 264 2R:1731127-2080000 1 NULL:1985047 Q9NB14 134 222 1 1 0 2600809 329524 329257 1 0 0 0 220 partof 267 2R:1731127-2080000 1 NULL:1985049 Q9NB13 136 230 1 1 0 2605750 208134 207189 1 0 0 0 1583 partof GCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 945 2R:1731127-2080000 -1 NULL:1989187 Q9I7G6 8 323 1 1 0 207140 206993 1 0 0 0 238 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATG 147 2R:1731127-2080000 -1 NULL:1989188 Q9I7G6 318 367 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1989189 Q9I7G6 366 424 1 1 0 2605754 208179 207189 1 0 0 0 1666 partof MKTSTPHPRSIWILTGCWLLPLLGLALFPFPPVHTADVTMADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 990 2R:1731127-2080000 -1 NULL:1989191 Q9V991 0 330 1 1 0 207140 206993 1 0 0 0 238 partof QLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVNEEGTEAAAATG 147 2R:1731127-2080000 -1 NULL:1989192 Q9V991 325 374 1 1 0 206898 206724 1 0 0 0 306 partof GMAVRRKRAIMSPEEPIEFFADHPFTYVLVHQKDLPLFWGSVVRLEENTFASSEHDEL 174 2R:1731127-2080000 -1 NULL:1989193 Q9V991 373 431 1 1 0 2605758 210406 209668 1 0 0 0 298 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG---SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEF 738 2R:1731127-2080000 -1 NULL:1989195 Q9U5W8 47 295 1 1 0 2600811 333147 332727 1 0 0 0 131 partof SLPQICGILLIVFGALLFSKVRNMDDFAEALRTQQ--VPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQYSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAI 420 2R:1731127-2080000 1 NULL:1985051 Q9V3R4 16 154 1 1 0 2600813 332997 332730 1 0 0 0 332 partof 267 2R:1731127-2080000 1 NULL:1985053 Q9U3V4 17 102 1 1 0 333417 333198 1 0 0 0 280 partof 219 2R:1731127-2080000 1 NULL:1985054 Q9U3V4 128 202 1 1 0 333748 333676 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1985055 Q9U3V4 201 225 1 1 0 2600817 332997 332730 1 0 0 0 332 partof 267 2R:1731127-2080000 1 NULL:1985057 Q9NB15 17 102 1 1 0 333417 333198 1 0 0 0 374 partof 219 2R:1731127-2080000 1 NULL:1985058 Q9NB15 128 203 1 1 0 333748 333676 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1985059 Q9NB15 202 226 1 1 0 2605760 210406 209668 1 0 0 0 301 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG---SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEF 738 2R:1731127-2080000 -1 NULL:1989197 Q9V4I3 47 295 1 1 0 2605762 210418 209644 1 0 0 0 224 partof SAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ-VAESFGVVLKSYEQ----CQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGS-EQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 774 2R:1731127-2080000 -1 NULL:1989199 Q9V3N1 88 347 1 1 0 2605764 210442 209644 1 0 0 0 336 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVL---KSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 798 2R:1731127-2080000 -1 NULL:1989201 Q9U1I8 20 284 1 1 0 209583 209403 1 0 0 0 115 partof QMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKK-GSKTF 180 2R:1731127-2080000 -1 NULL:1989202 Q9U1I8 285 346 1 1 0 2605767 210442 209635 1 0 0 0 327 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLV 807 2R:1731127-2080000 -1 NULL:1989204 Q9VII7 20 284 1 1 0 209580 209439 1 0 0 0 91 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAAT 141 2R:1731127-2080000 -1 NULL:1989205 Q9VII7 283 329 1 1 0 2600821 333108 332739 1 0 0 0 157 partof ICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQYSILLFVLMIGQLALVIY-MWVQKDKYLEIMGDVVEKAW 369 2R:1731127-2080000 1 NULL:1985061 Q9U3V3 20 139 1 1 0 2600823 332979 332745 1 0 0 0 153 partof GILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SC-IVPFILQFKM 234 2R:1731127-2080000 1 NULL:1985063 Q9I7D5 22 99 1 1 0 2600825 333000 332745 1 0 0 0 162 partof 255 2R:1731127-2080000 1 NULL:1985065 Q9NB14 22 105 1 1 0 333420 333201 1 0 0 0 133 partof DFLPLPQMKCCGRSGYTDYAYQGKFPPSCCS--D-TNNCRWETVYRR-GCKVTFVEFWDRNSDIIKYAGLVIAAIEV 219 2R:1731127-2080000 1 NULL:1985066 Q9NB14 133 206 1 1 0 2600828 332997 332796 1 0 0 0 238 partof MDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQY 201 2R:1731127-2080000 1 NULL:1985068 Q9I7D6 0 63 1 1 0 2605770 210442 209635 1 0 0 0 327 partof LHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLV 807 2R:1731127-2080000 -1 NULL:1989207 Q9U1I6 20 284 1 1 0 209580 209439 1 0 0 0 88 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAAT 141 2R:1731127-2080000 -1 NULL:1989208 Q9U1I6 283 329 1 1 0 2605773 210454 209644 1 0 0 0 355 partof FALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ-VAESFGVVLKSYEQCQ-VLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSD-RPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 810 2R:1731127-2080000 -1 NULL:1989210 Q9V3R7 29 299 1 1 0 2605775 210457 209641 1 0 0 0 334 partof QFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDV--KIPSFTAEFQQELSQVLM 816 2R:1731127-2080000 -1 NULL:1989212 Q9U1I7 15 283 1 1 0 209580 209439 1 0 0 0 101 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAAT 141 2R:1731127-2080000 -1 NULL:1989213 Q9U1I7 284 330 1 1 0 2600830 333171 332994 1 0 0 0 279 partof 177 2R:1731127-2080000 1 NULL:1985070 Q9I7D6 45 104 1 1 0 2605778 210457 209743 1 0 0 0 307 partof QFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYE---QCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDI 714 2R:1731127-2080000 -1 NULL:1989215 Q9VLQ7 15 254 1 1 0 2600832 333171 332994 1 0 0 0 113 partof 177 2R:1731127-2080000 1 NULL:1985072 Q9NB14 84 144 1 1 0 2600834 333171 332994 1 0 0 0 279 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985074 Q9NB15 84 143 1 1 0 2600836 333171 332994 1 0 0 0 279 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985076 Q9U3V4 84 143 1 1 0 2600838 333420 333132 1 0 0 0 152 partof 288 2R:1731127-2080000 1 NULL:1985078 Q9U3V3 103 205 1 1 0 2605780 210463 209644 1 0 0 0 294 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQV--LKMANGLYVMKGLQ-VDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSD-RPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLS--DISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1989217 Q9U5W7 106 383 1 1 0 2605782 210463 209644 1 0 0 0 294 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQV--LKMANGLYVMKGLQ-VDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSD-RPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLS--DISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1989219 Q9V4I5 106 383 1 1 0 2605784 210469 209638 1 0 0 0 177 partof EGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRG---PV-LKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRF-ADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY---------------DYSNIHMLILLPN-EVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 831 2R:1731127-2080000 -1 NULL:1989221 Q9U1I4 37 331 1 1 0 2605786 210469 209698 1 0 0 0 176 partof QGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKM------ANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGS--EQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCENFFFAVLPMFEATALRMNYSAC--NLAMIILLPDEKSNLTS--LEKKLSDISLEVVSSAMNLEKVD 771 2R:1731127-2080000 -1 NULL:1989223 Q9VFC2 37 301 1 1 0 2600840 333357 333198 1 0 0 0 271 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVE 159 2R:1731127-2080000 1 NULL:1985080 Q9I7D6 89 144 1 1 0 333776 333677 1 0 0 0 173 partof 99 2R:1731127-2080000 1 NULL:1985081 Q9I7D6 163 196 1 1 0 2605788 210478 209644 1 0 0 0 394 partof EFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFF-GSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 834 2R:1731127-2080000 -1 NULL:1989225 Q9V3L3 6 284 1 1 0 209583 209436 1 0 0 0 152 partof QMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATG 147 2R:1731127-2080000 -1 NULL:1989226 Q9V3L3 285 334 1 1 0 2600843 335244 334992 1 0 0 0 435 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTI 252 2R:1731127-2080000 1 NULL:1985083 Q9I7D5 0 84 1 1 0 335359 335308 1 0 0 0 82 partof YAICMLILFGLQLALSI 51 2R:1731127-2080000 1 NULL:1985084 Q9I7D5 84 101 1 1 0 2600846 335244 334992 1 0 0 0 435 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTI 252 2R:1731127-2080000 1 NULL:1985086 Q9NB14 0 84 1 1 0 335560 335308 1 0 0 0 290 partof 252 2R:1731127-2080000 1 NULL:1985087 Q9NB14 84 160 1 1 0 2600849 335238 334992 1 0 0 0 228 partof 246 2R:1731127-2080000 1 NULL:1985089 Q9NB13 0 82 1 1 0 335596 335308 1 0 0 0 88 partof 288 2R:1731127-2080000 1 NULL:1985090 Q9NB13 84 173 1 1 0 2605791 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1989228 Q9U1I5 6 284 1 1 0 209589 209418 1 0 0 0 173 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKK 171 2R:1731127-2080000 -1 NULL:1989229 Q9U1I5 284 341 1 1 0 2605794 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1989231 Q9I7G5 6 284 1 1 0 209589 209418 1 0 0 0 180 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKK 171 2R:1731127-2080000 -1 NULL:1989232 Q9I7G5 284 341 1 1 0 2605797 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1989234 Q9I7G6 38 316 1 1 0 209589 209418 1 0 0 0 180 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKK 171 2R:1731127-2080000 -1 NULL:1989235 Q9I7G6 316 373 1 1 0 2600852 335253 334992 1 0 0 0 158 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDG--GVNTQTI-PICIIVIGSVTFVVAFFGCCGTIRENACCTTIVST 261 2R:1731127-2080000 1 NULL:1985092 Q9V3R4 0 89 1 1 0 335788 335503 1 0 0 0 108 partof H*FFPDIYVSIPLQFSCCGNTGYQQY----ETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMR 285 2R:1731127-2080000 1 NULL:1985093 Q9V3R4 127 220 1 1 0 2600855 335250 334992 1 0 0 0 210 partof 258 2R:1731127-2080000 1 NULL:1985095 Q9U3V3 0 86 1 1 0 335788 335545 1 0 0 0 138 partof 243 2R:1731127-2080000 1 NULL:1985096 Q9U3V3 138 219 1 1 0 2600858 335605 335299 1 0 0 0 124 partof SFQYAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPSSCC 306 2R:1731127-2080000 1 NULL:1985098 Q9NB15 81 177 1 1 0 2600860 335809 335518 1 0 0 0 176 partof DIYVSIPLQFSCCGNTGYQQYE---TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQ 291 2R:1731127-2080000 1 NULL:1985100 Q9NB15 129 225 1 1 0 2600862 335809 335518 1 0 0 0 148 partof DIYVSIPLQFSCCGNTGYQQYETVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQ 291 2R:1731127-2080000 1 NULL:1985102 Q9U3V4 129 224 1 1 0 2600864 335794 335530 1 0 0 0 463 partof 264 2R:1731127-2080000 1 NULL:1985104 Q9NB14 134 222 1 1 0 2600866 335812 335545 1 0 0 0 220 partof FSCCGNTGYQQYE----TVPSSCCGYKDRTKVCEA-EIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMRKR*SRSQI 267 2R:1731127-2080000 1 NULL:1985106 Q9NB13 136 230 1 1 0 2600868 336572 336347 1 0 0 0 115 partof MGCLSGIVNFILYIVNIVFLVSACRLSI*VKGINNVMRRVTIDQTLLGADPK*VPIMDN------FILSNYLCYNELPKNV 225 2R:1731127-2080000 1 NULL:1985108 Q9NB13 0 79 1 1 0 2600870 337686 337482 1 0 0 0 115 partof YSEYFQIVGILLIVLGSIMLSDLSRFDVAGSGTDP--NTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMT 204 2R:1731127-2080000 1 NULL:1985110 Q9V3R4 14 84 1 1 0 338196 337749 1 0 0 0 192 partof LQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDS-HDYTAMGV---LEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVY 447 2R:1731127-2080000 1 NULL:1985111 Q9V3R4 84 228 1 1 0 2600873 337701 337494 1 0 0 0 136 partof FQIVGILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGAVSL 207 2R:1731127-2080000 1 NULL:1985113 Q9U3V3 18 87 1 1 0 338196 337755 1 0 0 0 205 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH--DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVY 441 2R:1731127-2080000 1 NULL:1985114 Q9U3V3 84 227 1 1 0 2600876 337692 337494 1 0 0 0 329 partof FQIVGILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMTGA 198 2R:1731127-2080000 1 NULL:1985116 Q9NB13 18 84 1 1 0 338199 337755 1 0 0 0 810 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQNAGRQVYA 444 2R:1731127-2080000 1 NULL:1985117 Q9NB13 84 232 1 1 0 2600879 337686 337506 1 0 0 0 172 partof GILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMT 180 2R:1731127-2080000 1 NULL:1985119 Q9I7D5 22 82 1 1 0 2600881 337686 337506 1 0 0 0 172 partof GILLIVLGSIMLSDLSRFDVAGSGTDPNTIPICVTVLGGLIFVVSFFGCYGIFRQSVCMT 180 2R:1731127-2080000 1 NULL:1985121 Q9NB14 22 82 1 1 0 338175 337755 1 0 0 0 292 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTA---MGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQ 420 2R:1731127-2080000 1 NULL:1985122 Q9NB14 84 222 1 1 0 2600884 338064 337746 1 0 0 0 132 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEE 318 2R:1731127-2080000 1 NULL:1985124 Q9I7D6 42 144 1 1 0 2600886 338172 337746 1 0 0 0 207 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRS 426 2R:1731127-2080000 1 NULL:1985126 Q9NB15 81 219 1 1 0 2600888 338172 337746 1 0 0 0 187 partof ALQYTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSH----DYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRS 426 2R:1731127-2080000 1 NULL:1985128 Q9U3V4 81 218 1 1 0 2600890 347156 346742 1 0 0 0 205 partof VKTMSNPLFLFLRLQVI--GILGIVYGVLILKSIG-VVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSVS 414 2R:1731127-2080000 1 NULL:1985130 Q9NB14 3 141 1 1 0 2600892 347150 346748 1 0 0 0 173 partof TMSNPLFLFLRL-QVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKS 402 2R:1731127-2080000 1 NULL:1985132 Q9NB11 6 125 1 1 0 347413 347212 1 0 0 0 104 partof HCCGSSSALDYIG-K--GDLVPPSCCSG-SCLIPTNYYP-GCRGKFVELMTTGSDNAKYVGIGLIGIEVKII 201 2R:1731127-2080000 1 NULL:1985133 Q9NB11 126 198 1 1 0 2600896 347066 346763 1 0 0 0 155 partof LFLFLRLQVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFE 303 2R:1731127-2080000 1 NULL:1985135 Q9V4H5 13 100 1 1 0 2600899 347150 346763 1 0 0 0 198 partof LFLFLRLQVI-GILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKS 387 2R:1731127-2080000 1 NULL:1985137 Q9U3V3 11 138 1 1 0 2605800 210481 209647 1 0 0 0 538 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDF-FGSDRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQV 834 2R:1731127-2080000 -1 NULL:1989237 Q9V991 45 323 1 1 0 209589 209418 1 0 0 0 180 partof YSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINEVGTEAAAATGEPAKKK 171 2R:1731127-2080000 -1 NULL:1989238 Q9V991 323 380 1 1 0 2605803 258443 257642 1 0 0 0 128 partof AQLNARLSGKQQQHQQQQHIEGIYGNQQAPGGESIYMRSGLSMSQPQQ--QQHFDGKSEQIQLQHQQQHRI-YAS-FGTSSSAMSSAHAANSSTKPSILTPTTSFNA-LPHFPLSSSTSSLLSKVSSFSNS-SSASPPTTAATSG--SASSHYQPPQPPNAAVANSKDMAIYSSSFTKNPAAAQSPNMRQAHSHQHHQPPQQQHYTCPPPLEDPPPPPIYAAGASATMPKKMARPPTGQNATHSSAYAAASST---ATLPKNMMQQQQRLQHQQQYQQ 801 2R:1731127-2080000 -1 NULL:1989240 Q9VED3 656 920 1 1 0 2605805 258443 257642 1 0 0 0 128 partof AQLNARLSGKQQQHQQQQHIEGIYGNQQAPGGESIYMRSGLSMSQPQQ--QQHFDGKSEQIQLQHQQQHRI-YAS-FGTSSSAMSSAHAANSSTKPSILTPTTSFNA-LPHFPLSSSTSSLLSKVSSFSNS-SSASPPTTAATSG--SASSHYQPPQPPNAAVANSKDMAIYSSSFTKNPAAAQSPNMRQAHSHQHHQPPQQQHYTCPPPLEDPPPPPIYAAGASATMPKKMARPPTGQNATHSSAYAAASST---ATLPKNMMQQQQRLQHQQQYQQ 801 2R:1731127-2080000 -1 NULL:1989242 Q24163 650 914 1 1 0 2605807 263550 262947 1 0 0 0 127 partof QQQSSIDSTSSQHSNDSTGSHQLLQQQQQHHQSQQNHH-SATATRSHSISS-TASSLHSHPSIDSTVACGSLVGQHNHSTSTNTNTTSPSSGSSTPQNHYSPLLTNSPTSTAAGTPSGSSLGPGSGLGFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADETDERSRASVLQKASMFEKAAAAAAVSPPAPMQIASGSP 603 2R:1731127-2080000 -1 NULL:1989244 Q9VVM9 1590 1780 1 1 0 2605809 263685 262935 1 0 0 0 136 partof HAQQQQQQQNQQPQTPPTYVNMSELATMAALKQTNQQQKPSTPPLQQ---QSSIDSTSSQHSNDSTGSHQLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDSTVACGSLVGQHNHST-STNTNTTSPSSGSSTPQNHYSPLLTNSPT--STAAGTPSGSSLGPGSGLGFVYQVSSPTPPSS---EVLK-----ITEQAAAGQDQGPANSVADET-DERSRASVLQKASMF-EKAAAA---AAVSPPAPMQIASGSPASGG 750 2R:1731127-2080000 -1 NULL:1989246 Q9VYJ9 566 832 1 1 0 2605811 263697 262890 1 0 0 0 160 partof SAAHHAQQQQQQQNQQPQT-----PPTYVNMSELATMAALKQTNQQQK------PSTPP--LQQQSSIDSTSSQHSNDSTGSH-----QLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDSTVACGSLVGQHNHSTSTNTNTTSPSSGSSTPQNHYSPLLT-NSPTSTAAGTPSGSSLGPGSGLGFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADETDER---SRASVLQKASMFEKAAAAAAVSPPAPMQIASGSPASGGGTRRSEAEQQEMGKL 807 2R:1731127-2080000 -1 NULL:1989248 Q9W321 1277 1556 1 1 0 2605813 263706 262932 1 0 0 0 167 partof TELSAAHHAQQQQQQQNQQPQTPPTYVNMSELATMAALKQTNQQQKPSTPPLQQQSSIDSTSSQHSNDSTGSHQLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDS-TVACGS-LVG--QHNHSTSTNTNTTSPSSGSSTPQNHYSPLLTNSPTSTAAGTPSGSSLGPGSGLGFVYQVSSPTPPSSEVLKITEQAAAGQDQGPANSVADETDERSRASVLQKASMFEKAAAAAAVSPPAPMQIASGSPASGGG 774 2R:1731127-2080000 -1 NULL:1989250 O01368 1219 1463 1 1 0 2605815 263712 262935 1 0 0 0 132 partof PHTELSAAHHAQQQQQQQNQQPQTPPTYVNMSELATMAALKQTNQQ--QKPSTPPLQQQSSIDSTSSQHSNDSTGSHQLLQQQQQHHQSQQNHHSATATRSHSISSTASSLHSHPSIDSTVACGSLVGQHNHST-STNTNTTSPSSGSSTPQNHYSPLLTNSPT--STAAGTPSGSSLGPGSGLGFVYQVSSPTPPSS---EVLK-----ITEQAAAGQDQGPANSVADET-DERSRASVLQKASMF-EKAAAA---AAVSPPAPMQIASGSPASGG 777 2R:1731127-2080000 -1 NULL:1989252 Q9U4I2 434 693 1 1 0 2605817 308376 307467 1 0 0 0 1499 partof AAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDLLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 909 2R:1731127-2080000 -1 NULL:1989254 O44116 1 304 1 1 0 307378 306991 1 0 0 0 661 partof DDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQ 387 2R:1731127-2080000 -1 NULL:1989255 O44116 304 433 1 1 0 306933 306330 1 0 0 0 996 partof EKLALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADKIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCVNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 603 2R:1731127-2080000 -1 NULL:1989256 O44116 433 634 1 1 0 2605821 308376 307467 1 0 0 0 1502 partof AAEIDDLIEKLKTTSVSPANTTNLLCEISATKDPKLFDKHELAECFLGLTKCDDTNVRKEAAKCIAEITKSEVQRKKFTKRNIIAAFLECLRQVPTSDGSMELPIQICRALGNICYLNDEARDLILELEGDAVLLRLLDITTIEDVANAAQFIKVRGGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDLLLNTLPLLSILTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 909 2R:1731127-2080000 -1 NULL:1989258 Q9V978 1 304 1 1 0 307378 306991 1 0 0 0 661 partof DDSMHYLYTTPLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKDDVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQ 387 2R:1731127-2080000 -1 NULL:1989259 Q9V978 304 433 1 1 0 306933 306330 1 0 0 0 996 partof EKLALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKGDAPAEQIADKIPLTQDYDRSSLSEFLANEGTVEAMVSMLTAQHLVMQNEALIALCILSVVYLSQPSEAAQAQLLQDELVKCEVGKKLAELISKSSDTMTKEIVENLQNCVNLLKSSEQLVAHLEQHNINELLKSIPILTEYCTL 603 2R:1731127-2080000 -1 NULL:1989260 Q9V978 433 634 1 1 0 2605825 340114 339877 1 0 0 0 102 partof HKDSLTE--NIL*FQFKCCGLNGFADYGITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGVTAVE 237 2R:1731127-2080000 -1 NULL:1989262 Q9U3V4 123 202 1 1 0 339823 339751 1 0 0 0 82 partof QLVAFIFACCLANQTRNSQRRQNY 72 2R:1731127-2080000 -1 NULL:1989263 Q9U3V4 201 225 1 1 0 2605828 340623 340440 1 0 0 0 162 partof GILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALT 183 2R:1731127-2080000 -1 NULL:1989265 Q9I7D5 22 83 1 1 0 2605830 340623 340440 1 0 0 0 162 partof GILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALT 183 2R:1731127-2080000 -1 NULL:1989267 Q9NB14 22 83 1 1 0 2605832 340629 340437 1 0 0 0 322 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTS 192 2R:1731127-2080000 -1 NULL:1989269 Q9U3V3 20 84 1 1 0 340368 340206 1 0 0 0 265 partof YSVVMLVLLVSQLALIIYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRS 162 2R:1731127-2080000 -1 NULL:1989270 Q9U3V3 84 138 1 1 0 340108 339862 1 0 0 0 368 partof DSLTENIL*FQFKCCGLNGFADYGITYPASCCDSPSNGTCALTQVMTRSSCLKAVDSFWDTNVSIIKYAGLGVTAVEVRIAY 246 2R:1731127-2080000 -1 NULL:1989271 Q9U3V3 127 208 1 1 0 2605836 340629 340449 1 0 0 0 153 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1989273 Q9U3V4 20 80 1 1 0 340368 340203 1 0 0 0 108 partof YSVVMLVLLVSQLALIIYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRSV 165 2R:1731127-2080000 -1 NULL:1989274 Q9U3V4 84 139 1 1 0 2605839 340629 340449 1 0 0 0 153 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSC 180 2R:1731127-2080000 -1 NULL:1989276 Q9NB15 20 80 1 1 0 340368 340203 1 0 0 0 108 partof YSVVMLVLLVSQLALIIYVWVDHVQIQQSLEKIVQTIWDQRKTDALLMDTLQRSV 165 2R:1731127-2080000 -1 NULL:1989277 Q9NB15 84 139 1 1 0 2605842 340629 340299 1 0 0 0 139 partof ICGILLITFGSIMVSTIKDFSGVGETFTANSVAIIILVLGCVVFLVAFMGCCGAIRENSCALTSVGAHDTCPAGCNI*IQLAPSCFQYSVVMLVLLVSQLALIIYVWVDH 330 2R:1731127-2080000 -1 NULL:1989279 Q9NB13 20 125 1 1 0 2600901 347153 346763 1 0 0 0 237 partof LFLF-LRLQVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 390 2R:1731127-2080000 1 NULL:1985139 Q9NB15 11 139 1 1 0 2600903 347153 346763 1 0 0 0 237 partof LFLF-LRLQVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 390 2R:1731127-2080000 1 NULL:1985141 Q9U3V4 11 139 1 1 0 2600905 347153 346763 1 0 0 0 615 partof LFLFLRL-QVIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 390 2R:1731127-2080000 1 NULL:1985143 Q9V3R4 11 142 1 1 0 347404 347179 1 0 0 0 360 partof IYMTSQRNL*LHCCGSSSALDYIGKGDLVPPSCCSGSCLIPTNYYPGCRGKFVELMTTGSDNAKYVGIGLIGIEV 225 2R:1731127-2080000 1 NULL:1985144 Q9V3R4 133 206 1 1 0 347533 347464 1 0 0 0 126 partof LIGFIFACCLANNVRNYKRRNAY 69 2R:1731127-2080000 1 NULL:1985145 Q9V3R4 205 228 1 1 0 2600909 347135 346787 1 0 0 0 189 partof VIGILGIVYGVLILKSIGVVEVNGQVGFPIQALMPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKG-GVFD 348 2R:1731127-2080000 1 NULL:1985147 Q9NB13 20 134 1 1 0 347389 347215 1 0 0 0 99 partof CCGSSSALDYIGKGDLVPPSCCS-----GSCLIPTNYY--PGCRGKFVELMTTGSDNAKYVGIGL 174 2R:1731127-2080000 1 NULL:1985148 Q9NB13 138 203 1 1 0 2600912 347153 346886 1 0 0 0 212 partof MPIILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKSV 267 2R:1731127-2080000 1 NULL:1985150 Q9I7D6 12 100 1 1 0 2600914 347150 346895 1 0 0 0 164 partof ILISLGSIVVFISFLGCCGAIRESVCMTMSYATFLLILLILQLTFVVLLFTHREEFENAMGNVIENAWNSEHTYKGGVFDTIQKS 255 2R:1731127-2080000 1 NULL:1985152 Q9V4G9 8 89 1 1 0 347413 347212 1 0 0 0 104 partof HCCGSSSALDYIG-K--GDLVPPSCCSG-SCLIPTNYYP-GCRGKFVELMTTGSDNAKYVGIGLIGIEVKII 201 2R:1731127-2080000 1 NULL:1985153 Q9V4G9 90 162 1 1 0 2600918 347341 347146 1 0 0 0 102 partof IGKCFNNQ-ALSIYMTSQRNL*LHCCGSSSALDYIGKGDLVPPSCCS--GSCLIPTNYYPGCRGKFVE 195 2R:1731127-2080000 1 NULL:1985155 Q9I7D6 78 144 1 1 0 2600920 347533 347170 1 0 0 0 107 partof ALSIYMTSQRNL*LHCCGS--SSALDY-IGKGDLVPPSCCSGSCLIPTNYYP-GCRGKFVELMTTGSDNAKYVGIGLIGIEVKII----R*I*VSQAALLTKYPF*LIGFIFACCLANNVRNYKRRNAY 363 2R:1731127-2080000 1 NULL:1985157 Q9NB15 97 226 1 1 0 2600626 164443 163594 1 0 0 0 215 partof DDGDGNGNGDGDGDYSDPYRHESTTGKSTKVHKAARKVGKRHKHRKNQKNFNDYEVYHSQREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNY----NII---KQHKHEQQQQQLKIPQQLHQQQQQQNVAALGV------NHAA---KATHYQQAASTPLPTPPPPSEH--PQHSHHPHQQAHSSSKILNFPENLPALLYYDYKTEEHEHHQHQHHQQHLLHEKQRLLQQQQQQQQQQQQMVQQEALARQKASESASEPESRAGGTAEGGVEPSGDLAADKNSDEAETDSDILPEPP 849 2R:1731127-2080000 1 NULL:1984867 Q9VYJ9 21 314 1 1 0 2600628 164359 163687 1 0 0 0 173 partof HKAARKVGKRHKHRKNQKNFNDYEVYHSQREKQQQQQSDYKKSAIKQQLQMQQKHKSDKSGAGNYNIIKQHKHEQQQQQLKIPQQLHQQQQQQNVAALGVNH--AAKATHYQQAASTPLPTPPPPSEHPQHSHHPHQQAHSSSKILNFPENLPALLYYD---YKTEEHEHHQHQHHQQHL-LHEKQRLLQQQQQQQQQQQQMVQQEALAR----QKASESASEPESRAG-GTAEG 672 2R:1731127-2080000 1 NULL:1984869 Q9U4I2 41 264 1 1 0 2600630 164701 164287 1 0 0 0 103 partof ALARQKASESASEPESRAGGTAEGGVEPSGDLAADKNSDEAETDSDILPEPPTKQPRAAATQWPTPSSNSSARALMTSN-VASTSTAATTTTTKTSKTKTTTATTGRTTTTT--TATGTNEMVTSTLSGMEKSGATVAATD 414 2R:1731127-2080000 1 NULL:1984871 Q9U4I2 1055 1195 1 1 0 2600632 212416 211525 1 0 0 0 466 partof AQIEMSEPQEGRNQFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 891 2R:1731127-2080000 1 NULL:1984873 Q9V991 35 327 1 1 0 2600634 212416 211525 1 0 0 0 466 partof AQIEMSEPQEGRNQFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 891 2R:1731127-2080000 1 NULL:1984875 Q9I7G6 28 320 1 1 0 2600636 212407 211552 1 0 0 0 262 partof EGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRG---PV-LKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRF-ADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPY---------------DYSNIHMLILLPN-EVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 855 2R:1731127-2080000 1 NULL:1984877 Q9VFC2 37 331 1 1 0 2600638 212407 211552 1 0 0 0 261 partof 855 2R:1731127-2080000 1 NULL:1984879 Q9U1I4 37 331 1 1 0 2600640 212416 211555 1 0 0 0 420 partof GEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 861 2R:1731127-2080000 1 NULL:1984881 Q9V3L3 10 287 1 1 0 2600642 212398 211558 1 0 0 0 391 partof RNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD--SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL-ADIDAALTLQDVEIFLPRMCIEYDVDLK 840 2R:1731127-2080000 1 NULL:1984883 Q9U5W8 28 300 1 1 0 2600644 212398 211558 1 0 0 0 394 partof RNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD--SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL-ADIDAALTLQDVEIFLPRMCIEYDVDLK 840 2R:1731127-2080000 1 NULL:1984885 Q9V4I3 28 300 1 1 0 2600646 212416 211558 1 0 0 0 416 partof RNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGD-RHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 858 2R:1731127-2080000 1 NULL:1984887 Q9V3R7 26 302 1 1 0 212624 212480 1 0 0 0 100 partof QLGITEVFSDKAKLDGLFT-SQSGQKISAARHRGYIDVNEAGSEAAAVS 144 2R:1731127-2080000 1 NULL:1984888 Q9V3R7 300 349 1 1 0 212801 212705 1 0 0 0 95 partof VPMMLNMNKKLFKADHPFVFYIRNPQAVFFAG 96 2R:1731127-2080000 1 NULL:1984889 Q9V3R7 353 385 1 1 0 2600650 212416 211561 1 0 0 0 321 partof NQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR--GPVLKSVNRLYVNDSLELLTE-FNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNT--VDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 855 2R:1731127-2080000 1 NULL:1984891 Q9U5W7 107 386 1 1 0 2600652 212416 211561 1 0 0 0 321 partof NQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDR--GPVLKSVNRLYVNDSLELLTE-FNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNT--VDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 855 2R:1731127-2080000 1 NULL:1984893 Q9V4I5 107 386 1 1 0 2600654 212416 211564 1 0 0 0 464 partof QFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 852 2R:1731127-2080000 1 NULL:1984895 Q9I7G5 7 288 1 1 0 2600656 212416 211564 1 0 0 0 464 partof QFARNL--IDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 852 2R:1731127-2080000 1 NULL:1984897 Q9U1I5 7 288 1 1 0 2600658 212416 211612 1 0 0 0 263 partof QSKDPHINTVFSPASVQSALTLAF--MGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLK---SVN-RLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 804 2R:1731127-2080000 1 NULL:1984899 Q9V3N1 85 350 1 1 0 2600660 212299 211633 1 0 0 0 386 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQL 666 2R:1731127-2080000 1 NULL:1984901 Q9VLQ7 32 251 1 1 0 2600662 212407 211633 1 0 0 0 394 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1984903 Q9VII7 32 281 1 1 0 2600664 212407 211633 1 0 0 0 394 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1984905 Q9U1I6 32 281 1 1 0 2600666 212407 211633 1 0 0 0 407 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 774 2R:1731127-2080000 1 NULL:1984907 Q9U1I7 32 282 1 1 0 2600668 212416 211633 1 0 0 0 420 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 783 2R:1731127-2080000 1 NULL:1984909 Q9U1I8 32 287 1 1 0 2600670 214245 213384 1 0 0 0 687 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLR 861 2R:1731127-2080000 1 NULL:1984911 Q9U1I6 3 287 1 1 0 2600672 214245 213384 1 0 0 0 687 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLR 861 2R:1731127-2080000 1 NULL:1984913 Q9VII7 3 287 1 1 0 2600674 214281 213384 1 0 0 0 601 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFK--IEFRD-ELKETLEK--VRLRQEKHGCATLTLD 897 2R:1731127-2080000 1 NULL:1984915 Q9VLQ7 3 299 1 1 0 2600676 214248 213384 1 0 0 0 1413 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 864 2R:1731127-2080000 1 NULL:1984917 Q9U1I8 3 291 1 1 0 214432 214273 1 0 0 0 238 partof RSILFKLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 159 2R:1731127-2080000 1 NULL:1984918 Q9U1I8 280 333 1 1 0 214619 214502 1 0 0 0 196 partof AVAVTNRAGFSTFLMADHPFAFVIRDANTIYFQGRVVSP 117 2R:1731127-2080000 1 NULL:1984919 Q9U1I8 333 372 1 1 0 2600680 214227 213384 1 0 0 0 661 partof LGIFLWVTSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVAKEVYLKLPKFKIEFRDELKETL 843 2R:1731127-2080000 1 NULL:1984921 Q9U1I7 3 282 1 1 0 214432 214279 1 0 0 0 116 partof ILFKLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 153 2R:1731127-2080000 1 NULL:1984922 Q9U1I7 280 330 1 1 0 214619 214547 1 0 0 0 99 partof ADHPFAFVIRDANTIYFQGRVVSP 72 2R:1731127-2080000 1 NULL:1984923 Q9U1I7 349 373 1 1 0 2600684 214236 213426 1 0 0 0 460 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1984925 Q9V3L3 15 287 1 1 0 2600686 214248 213426 1 0 0 0 373 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYS-LNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG--F-----ARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 822 2R:1731127-2080000 1 NULL:1984927 Q9V4I5 110 390 1 1 0 2600688 214248 213426 1 0 0 0 373 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYS-LNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG--F-----ARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 822 2R:1731127-2080000 1 NULL:1984929 Q9U5W7 110 390 1 1 0 2600690 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1984931 Q9V991 55 327 1 1 0 214432 214288 1 0 0 0 117 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 144 2R:1731127-2080000 1 NULL:1984932 Q9V991 325 373 1 1 0 2600693 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1984934 Q9I7G6 48 320 1 1 0 214432 214288 1 0 0 0 117 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 144 2R:1731127-2080000 1 NULL:1984935 Q9I7G6 318 366 1 1 0 2600696 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1984937 Q9U1I5 16 288 1 1 0 214432 214288 1 0 0 0 114 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 144 2R:1731127-2080000 1 NULL:1984938 Q9U1I5 286 334 1 1 0 2600699 214236 213426 1 0 0 0 453 partof SKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKI-----VGFARPLVAKEVYLKLPKFKIEFRDELKETLEKV 810 2R:1731127-2080000 1 NULL:1984940 Q9I7G5 16 288 1 1 0 214432 214288 1 0 0 0 117 partof KLGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 144 2R:1731127-2080000 1 NULL:1984941 Q9I7G5 286 334 1 1 0 2600702 214236 213432 1 0 0 0 338 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPV---AAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG---FAR--PLVAKEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1984943 Q9V4I3 34 306 1 1 0 2600704 214236 213432 1 0 0 0 341 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPV---AAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG---FAR--PLVAKEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1984945 Q9U5W8 34 306 1 1 0 2600706 214236 213432 1 0 0 0 414 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPS-EDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQ-MMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFARPLVA-----KEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1984947 Q9V3R7 32 302 1 1 0 2600708 214059 213444 1 0 0 0 240 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP-SEDKEAVAARYGA-LLNDLQGQEEGPI-LKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPY 615 2R:1731127-2080000 1 NULL:1984949 Q9U1I4 49 254 1 1 0 2600710 214059 213444 1 0 0 0 240 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLP-SEDKEAVAARYGA-LLNDLQGQEEGPI-LKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPY 615 2R:1731127-2080000 1 NULL:1984951 Q9VFC2 49 254 1 1 0 2600712 214272 213444 1 0 0 0 267 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSA-LGLPSEDKEAVAARYGALLNDLQGQEE-GPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGF---ARPLVAKEVYLK--LPKFKIEFRDELKETLEKVRLRQEKHGCATL 828 2R:1731127-2080000 1 NULL:1984953 Q9V3N1 83 362 1 1 0 2600714 214432 214291 1 0 0 0 110 partof LGIRELFTDKSDLSGLFADKSGGKVSQVSHKAFLEVNEEGAEAAGAT 141 2R:1731127-2080000 1 NULL:1984955 Q9VLQ7 251 297 1 1 0 2600716 217226 216275 1 0 0 0 282 partof PCPAVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVP-KLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYT---------------GTDIVFLIILPQ-EEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 951 2R:1731127-2080000 1 NULL:1984957 Q9U1I4 12 334 1 1 0 2600718 217226 216275 1 0 0 0 282 partof PCPAVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVP-KLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNF-TQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYT---------------GTDIVFLIILPQ-EEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 951 2R:1731127-2080000 1 NULL:1984959 Q9VFC2 12 334 1 1 0 2600720 217226 216284 1 0 0 0 387 partof AVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKAD--TAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 942 2R:1731127-2080000 1 NULL:1984961 Q9V4I3 1 306 1 1 0 2600722 217226 216284 1 0 0 0 390 partof AVKATCSLLLLQGLNLAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKAD--TAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 942 2R:1731127-2080000 1 NULL:1984963 Q9U5W8 1 306 1 1 0 2600724 217226 216287 1 0 0 0 520 partof VKATCSLLLLQGLNL---AMANTLNYSKSPAGEAQFASQL-------FGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 939 2R:1731127-2080000 1 NULL:1984965 Q9I7G6 5 320 1 1 0 2600726 217226 216299 1 0 0 0 519 partof CSLLLLQGLNL---AMANTLNYSKSPAGEAQFASQL-------FGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 927 2R:1731127-2080000 1 NULL:1984967 Q9V991 16 327 1 1 0 2600728 217226 216371 1 0 0 0 405 partof 855 2R:1731127-2080000 1 NULL:1984969 Q9V3L3 10 287 1 1 0 2600730 217226 216377 1 0 0 0 515 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 849 2R:1731127-2080000 1 NULL:1984971 Q9U1I5 13 288 1 1 0 2600732 217226 216377 1 0 0 0 515 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 849 2R:1731127-2080000 1 NULL:1984973 Q9I7G5 13 288 1 1 0 2600734 217148 216380 1 0 0 0 395 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGI-DLNEISSQLR 768 2R:1731127-2080000 1 NULL:1984975 Q9VLQ7 15 265 1 1 0 2600736 217217 216380 1 0 0 0 416 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAAL 837 2R:1731127-2080000 1 NULL:1984977 Q9U1I7 15 282 1 1 0 2600738 217217 216380 1 0 0 0 419 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAAL 837 2R:1731127-2080000 1 NULL:1984979 Q9U1I6 15 281 1 1 0 2600740 217217 216380 1 0 0 0 419 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAAL 837 2R:1731127-2080000 1 NULL:1984981 Q9VII7 15 281 1 1 0 2600742 217226 216380 1 0 0 0 407 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFK-LTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG--IDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 846 2R:1731127-2080000 1 NULL:1984983 Q9V4I5 108 386 1 1 0 2600744 217226 216380 1 0 0 0 407 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFK-LTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG--IDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 846 2R:1731127-2080000 1 NULL:1984985 Q9U5W7 108 386 1 1 0 2600746 217226 216380 1 0 0 0 487 partof QFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGAGKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 846 2R:1731127-2080000 1 NULL:1984987 Q9U1I8 15 287 1 1 0 2600748 217226 216383 1 0 0 0 436 partof FASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADELKLGLGLEGA-GKTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQLRRRKVRVQLPKFKFEFDVPLQAALEEV 843 2R:1731127-2080000 1 NULL:1984989 Q9V3R7 29 302 1 1 0 2600750 217226 216407 1 0 0 0 236 partof 819 2R:1731127-2080000 1 NULL:1984991 Q9V3N1 84 350 1 1 0 2600752 326858 326438 1 0 0 0 131 partof 420 2R:1731127-2080000 1 NULL:1984993 Q9V3R4 16 154 1 1 0 2600754 326708 326441 1 0 0 0 332 partof LPQICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQY 267 2R:1731127-2080000 1 NULL:1984995 Q9NB15 17 102 1 1 0 327128 326909 1 0 0 0 374 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIAAIE 219 2R:1731127-2080000 1 NULL:1984996 Q9NB15 128 203 1 1 0 327460 327388 1 0 0 0 127 partof QFVGFVFACCLANSIRNYRRRAEY 72 2R:1731127-2080000 1 NULL:1984997 Q9NB15 202 226 1 1 0 2600758 326708 326441 1 0 0 0 332 partof LPQICGILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SCIVPFILQFKMYSLWQY 267 2R:1731127-2080000 1 NULL:1984999 Q9U3V4 17 102 1 1 0 327128 326909 1 0 0 0 280 partof TDFLPLPQ--MKCCGRSGYTDYAYQGKFPPSCCSDTNNCRWETVYRRGCKVTFVEFWDRNSDIIKYAGLVIAAIE 219 2R:1731127-2080000 1 NULL:1985000 Q9U3V4 128 202 1 1 0 327460 327388 1 0 0 0 127 partof 72 2R:1731127-2080000 1 NULL:1985001 Q9U3V4 201 225 1 1 0 2600762 326819 326450 1 0 0 0 157 partof 369 2R:1731127-2080000 1 NULL:1985003 Q9U3V3 20 139 1 1 0 2600764 326690 326456 1 0 0 0 153 partof 234 2R:1731127-2080000 1 NULL:1985005 Q9I7D5 22 99 1 1 0 2600767 326711 326456 1 0 0 0 162 partof GILLIVFGALLFSKVRNMDDFAEALRTQQVPVTMIILGTIILLISWFGCCGAIRESYCMSMTVEY*SC-IVPFILQFKMYSLWQYS 255 2R:1731127-2080000 1 NULL:1985007 Q9NB14 22 105 1 1 0 327131 326912 1 0 0 0 133 partof 219 2R:1731127-2080000 1 NULL:1985008 Q9NB14 133 206 1 1 0 2600770 326708 326507 1 0 0 0 238 partof 201 2R:1731127-2080000 1 NULL:1985010 Q9I7D6 0 63 1 1 0 327068 326909 1 0 0 0 271 partof 159 2R:1731127-2080000 1 NULL:1985011 Q9I7D6 89 144 1 1 0 327488 327389 1 0 0 0 173 partof SLWDSFSPVAWRTAFGTIDAVRNINRQRTKALH 99 2R:1731127-2080000 1 NULL:1985012 Q9I7D6 163 196 1 1 0 2600774 326882 326705 1 0 0 0 279 partof 177 2R:1731127-2080000 1 NULL:1985014 Q9NB15 84 143 1 1 0 2600776 326882 326705 1 0 0 0 279 partof 177 2R:1731127-2080000 1 NULL:1985016 Q9U3V4 84 143 1 1 0 2600778 326882 326705 1 0 0 0 279 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDYMDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985018 Q9I7D6 45 104 1 1 0 2600780 326882 326705 1 0 0 0 113 partof YSILLFVLMIGQLALVIYMWVQKDKYLEIMGDVVEKAWNHRTSRSDY-MDAIQISVSI*G 177 2R:1731127-2080000 1 NULL:1985020 Q9NB14 84 144 1 1 0 2600782 327131 326843 1 0 0 0 152 partof YMDAIQISVSI*GLPRTC-DPPSTDFLPLPQM----KCCGRSGYTDYAYQGKFPPSCCSDTNN--CRWETVYRRG-CKVTFVEFWDRNSDIIKYAGLVIAAIEV 288 2R:1731127-2080000 1 NULL:1985022 Q9U3V3 103 205 1 1 0 2600784 328956 328704 1 0 0 0 435 partof 252 2R:1731127-2080000 1 NULL:1985024 Q9I7D5 0 84 1 1 0 329071 329020 1 0 0 0 82 partof 51 2R:1731127-2080000 1 NULL:1985025 Q9I7D5 84 101 1 1 0 2600787 328956 328704 1 0 0 0 435 partof 252 2R:1731127-2080000 1 NULL:1985027 Q9NB14 0 84 1 1 0 329272 329020 1 0 0 0 290 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCG 252 2R:1731127-2080000 1 NULL:1985028 Q9NB14 84 160 1 1 0 2600790 328950 328704 1 0 0 0 228 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCT 246 2R:1731127-2080000 1 NULL:1985030 Q9NB13 0 82 1 1 0 329308 329020 1 0 0 0 88 partof YAICMLILFGLQLALSIWIFAANDKFLSSMGKAVDKAWDENNAAQGYPMDALQLAVSLSKFTIRCH*FFPDIYVSIPLQFSCCGNTGYQQYETVPS 288 2R:1731127-2080000 1 NULL:1985031 Q9NB13 84 173 1 1 0 2600793 328965 328704 1 0 0 0 158 partof 261 2R:1731127-2080000 1 NULL:1985033 Q9V3R4 0 89 1 1 0 329500 329215 1 0 0 0 108 partof 285 2R:1731127-2080000 1 NULL:1985034 Q9V3R4 127 220 1 1 0 2600796 328962 328704 1 0 0 0 210 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1985036 Q9U3V3 0 86 1 1 0 329500 329257 1 0 0 0 138 partof FSCCGNTGYQQYE-TVPSSCCGYKDRTKVCEAEIYSQRPGCRQEFVDFWASNTDLIRWSSLIIALFELGIFIMSCCLASAMR 243 2R:1731127-2080000 1 NULL:1985037 Q9U3V3 138 219 1 1 0 2600799 328962 328704 1 0 0 0 189 partof MNCLSAMFKYLLYLLNLVFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENACCTTIVS 258 2R:1731127-2080000 1 NULL:1985039 Q9U3V4 0 86 1 1 0 329521 329230 1 0 0 0 148 partof 291 2R:1731127-2080000 1 NULL:1985040 Q9U3V4 129 224 1 1 0 blastx_masked 1.0 aa_SPTR.worm 1.0 2003-01-15 03:34:31 BLASTX Similarity to Other Species genomic 2602804 204623 204080 1 0 0 0 203 partof PGQRLLTSFSVVRNYHRLVEPYNSDFSRDVSFFDGFRVIGVFVVILGHTLMVFMT-VPIEN--PEFFEQFLFRFETSIFQNGSLVIQIFFVMSGFLLYVKFTKRQQIQPKTGTLECIAVYFR---VFSY-RYFRLLPSLLALILFNGTLLVRLQNGPFWRHLTEAERVFCRANWWKNVFFVTNHMLED 543 2R:1731127-2080000 -1 NULL:1986584 Q09225 347 529 1 1 0 2602806 207969 207198 1 0 0 0 323 partof NIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQDSQI---LRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMS-LKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 771 2R:1731127-2080000 -1 NULL:1986586 O17365 23 276 1 1 0 2602808 207999 207198 1 0 0 0 335 partof GKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQV----LAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFR-YADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 801 2R:1731127-2080000 -1 NULL:1986588 Q19650 13 281 1 1 0 2602810 208062 207198 1 0 0 0 271 partof MADAAHQEFARRLALFSINVYGK--LSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQV----LAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLT-RPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKV 864 2R:1731127-2080000 -1 NULL:1986590 O01462 0 290 1 1 0 2602812 210406 209644 1 0 0 0 223 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQ--QVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCE-NFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 762 2R:1731127-2080000 -1 NULL:1986592 Q19650 23 278 1 1 0 209580 209466 1 0 0 0 79 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986593 Q19650 280 315 1 1 0 2602815 210406 209635 1 0 0 0 199 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGL--EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCE-NFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLV 771 2R:1731127-2080000 -1 NULL:1986595 O01462 32 290 1 1 0 2602817 210406 209644 1 0 0 0 229 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVAESFGVVLKSYEQCQ---VLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFG-SEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVR--MMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 762 2R:1731127-2080000 -1 NULL:1986597 O17365 23 273 1 1 0 2602819 302815 302566 1 0 0 0 102 partof FLQLYSNAEKP--LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQ-VTPECLRELRYTKQVL 249 2R:1731127-2080000 -1 NULL:1986599 O45219 280 366 1 1 0 302505 302172 1 0 0 0 173 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAE 333 2R:1731127-2080000 -1 NULL:1986600 O45219 367 476 1 1 0 2602822 302824 302569 1 0 0 0 112 partof LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQV 255 2R:1731127-2080000 -1 NULL:1986602 Q27476 301 384 1 1 0 302511 302106 1 0 0 0 159 partof FLETLRLHTP--HPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALL---RQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 405 2R:1731127-2080000 -1 NULL:1986603 Q27476 384 516 1 1 0 2602825 302824 302581 1 0 0 0 111 partof LQTFLQLYSNAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRY 243 2R:1731127-2080000 -1 NULL:1986605 Q27477 289 368 1 1 0 302511 302202 1 0 0 0 159 partof FLETLRLHTPHPFLLRRATKE-FEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALL 309 2R:1731127-2080000 -1 NULL:1986606 Q27477 372 473 1 1 0 2602828 303523 302911 1 0 0 0 129 partof YWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFY-ACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNP-SGEPLSH---NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL--QTINISELVGAYNTDVMASMAFGLVGQDNVE--FAKWTRNYWADFRMWQAYLALEFPLIARLLQY 612 2R:1731127-2080000 -1 NULL:1986608 Q09653 34 241 1 1 0 2602830 304560 304140 1 0 0 0 239 partof LLEDPQGALTTPTEGGRTLVTRGGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSD--EILGELRSYFEKYQGFVAMGG 420 2R:1731127-2080000 -1 NULL:1986610 Q94218 379 520 1 1 0 2597419 3914 3656 1 0 0 0 156 partof EIQEQAVKFYQQSVFDRLFQWSCAD--ECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRL---LG--MQEPASVIFSCLNFVVHLRLLRKFRR 258 2R:1731127-2080000 1 NULL:1982153 O61975 30 123 1 1 0 4485 4050 1 0 0 0 210 partof WIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRG---VITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRR----ILRFYILMALAMSLELLDFPPILWILDAHALWHLATIPL 435 2R:1731127-2080000 1 NULL:1982154 O61975 143 293 1 1 0 2597423 24420 23736 1 0 0 0 251 partof YTSASTVLSVGGVRQQFSLAENIEMSLFGYNFVVNGREHLGDVD-----LCYQPNGYLILA-SEKGAHILAKNSKLQNELGARNELLGPEALRQRFPWLSTEGVELGCHGIDKEGWFDPWALLMGYKKKARALGANFANGSVVGFEWNDSGGLSGAVVDAGDVLQRTVKFDTCVLAAGAYSGQVARLAGIGDKEAKEASLSVALPVE-PRKRYVYVVSTQGKNCPGLATPLTVDP 684 2R:1731127-2080000 1 NULL:1982156 Q21504 131 360 1 1 0 2597425 24831 24174 1 0 0 0 379 partof LSGAVV--DAGDVLQRTVKFDTCVLAAGAYSGQVARLAGIGDKEAKEASLSVALPVEPRKRYVYVVSTQGKNCPGLATPLTVDPD-GTYFRRDGLCGNFLCGRSPNEDEEPECE--TLDVDHGYFETDVWPTLANRVPAFESVKIQSSWAGFYDHNTFDANGVIGRHPHYSNLFIAAGFSGHGIQQTPAVGRAISELILDGKFTTLDLSRLGFERLVNQQPMHE 657 2R:1731127-2080000 1 NULL:1982158 Q21504 305 523 1 1 0 2597427 27351 27189 1 0 0 0 189 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982160 Q93874 20 74 1 1 0 28154 27821 1 0 0 0 377 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDIN 333 2R:1731127-2080000 1 NULL:1982161 Q93874 73 184 1 1 0 2597430 27351 27189 1 0 0 0 278 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982163 O01577 15 69 1 1 0 28172 27821 1 0 0 0 545 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982164 O01577 68 185 1 1 0 2597433 28169 27797 1 0 0 0 355 partof CDAKYFLNRSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRR 372 2R:1731127-2080000 1 NULL:1982166 O17788 62 183 1 1 0 2597435 76663 76438 1 0 0 0 196 partof F*ENAREMASLVGDLRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGHELYGEEVVNS 225 2R:1731127-2080000 1 NULL:1982168 P34385 86 161 1 1 0 77909 77024 1 0 0 0 1073 partof CLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 885 2R:1731127-2080000 1 NULL:1982169 P34385 175 454 1 1 0 78426 77952 1 0 0 0 579 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKAALNNAGQETKFGVFRM 474 2R:1731127-2080000 1 NULL:1982170 P34385 450 608 1 1 0 2597440 77906 77030 1 0 0 0 388 partof VVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGI-PQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALD-DEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGP-NLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNN-----GVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKL 876 2R:1731127-2080000 1 NULL:1982172 AAL65786 102 380 1 1 0 78354 77952 1 0 0 0 134 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQ 402 2R:1731127-2080000 1 NULL:1982173 AAL65786 377 496 1 1 0 2597444 77906 77030 1 0 0 0 388 partof VVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGI-PQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALD-DEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGP-NLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNN-----GVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKL 876 2R:1731127-2080000 1 NULL:1982175 Q20676 116 394 1 1 0 78354 77952 1 0 0 0 134 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQ 402 2R:1731127-2080000 1 NULL:1982176 Q20676 391 510 1 1 0 2597448 82561 82438 1 0 0 0 113 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982178 Q9XXA2 0 41 1 1 0 82763 82616 1 0 0 0 107 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1982179 Q9XXA2 40 88 1 1 0 83124 83004 1 0 0 0 115 partof IPVDKLIKGRFQDNFEFLQWFKKFFDANY--DGREYDPVAQR 120 2R:1731127-2080000 1 NULL:1982180 Q9XXA2 89 131 1 1 0 2597452 82561 82444 1 0 0 0 145 partof VNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 117 2R:1731127-2080000 1 NULL:1982182 Q9GRZ1 5 44 1 1 0 82766 82616 1 0 0 0 131 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982183 Q9GRZ1 43 93 1 1 0 83124 82998 1 0 0 0 197 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982184 Q9GRZ1 91 133 1 1 0 2597456 84215 83954 1 0 0 0 209 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVR--EGAPMGFGSGAVKSLPGTAASGVSSSYRRGPSATTR-PAMTSAVKPS 261 2R:1731127-2080000 1 NULL:1982186 Q9GRZ1 92 181 1 1 0 2597458 84218 83957 1 0 0 0 134 partof IPIDKLVKGRFQDNFEFLQWFKKFFDANY--DGRDYDASAVREGAPMGFGSGAVKSLPGTA-ASGVSSSY---RRGPSATTRPAMTSAVKPSM 261 2R:1731127-2080000 1 NULL:1982188 Q9XXA2 89 182 1 1 0 2597460 138302 137936 1 0 0 0 512 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982190 Q09545 52 174 1 1 0 138718 138379 1 0 0 0 480 partof GKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 339 2R:1731127-2080000 1 NULL:1982191 Q09545 179 292 1 1 0 2597463 138302 137936 1 0 0 0 512 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982193 O44075 51 173 1 1 0 138718 138379 1 0 0 0 480 partof GKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 339 2R:1731127-2080000 1 NULL:1982194 O44075 178 291 1 1 0 2597466 138302 138098 1 0 0 0 305 partof CREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 204 2R:1731127-2080000 1 NULL:1982196 Q26266 0 68 1 1 0 138643 138379 1 0 0 0 388 partof GKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTC 264 2R:1731127-2080000 1 NULL:1982197 Q26266 73 161 1 1 0 2597469 146636 145937 1 0 0 0 221 partof NIRDEIERSSIL------LMSDISQRLKREILLVVEAKHNESTKALK---GHIREEE--VRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQ---PGECWXXXXXXXXXXKSRVNSNC*NSPYSFLPTVLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVWV--SLTKGERKWCISNTTY----PSTQG-LEQEKDQEPVLFGDYQFEDN-GA 699 2R:1731127-2080000 1 NULL:1982199 Q9U476 858 1094 1 1 0 2597472 146636 145937 1 0 0 0 221 partof NIRDEIERSSIL------LMSDISQRLKREILLVVEAKHNESTKALK---GHIREEE--VRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQ---PGECWXXXXXXXXXXKSRVNSNC*NSPYSFLPTVLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVWV--SLTKGERKWCISNTTY----PSTQG-LEQEKDQEPVLFGDYQFEDN-GA 699 2R:1731127-2080000 1 NULL:1982201 Q20745 858 1094 1 1 0 2597475 212416 211624 1 0 0 0 268 partof PHINTV-FSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFR-FAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 792 2R:1731127-2080000 1 NULL:1982203 O17365 19 276 1 1 0 2597477 212416 211639 1 0 0 0 242 partof VFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFR-FAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 777 2R:1731127-2080000 1 NULL:1982205 O01462 34 290 1 1 0 2597479 212416 211642 1 0 0 0 254 partof FSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFR-FAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 774 2R:1731127-2080000 1 NULL:1982207 Q19650 26 281 1 1 0 2597481 214248 213420 1 0 0 0 369 partof QTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGL-SALE----EKIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 828 2R:1731127-2080000 1 NULL:1982209 O17365 7 280 1 1 0 2597483 214248 213441 1 0 0 0 307 partof QLLSKSHTNQ--NLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKL-ANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKF-DPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPRE----VEGLSALEE-KIVGFARPLVAKEVYLKLPKFKIEFRDELKETLEKVRLRQ 807 2R:1731127-2080000 1 NULL:1982211 O17362 17 287 1 1 0 2597485 214248 213444 1 0 0 0 328 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPRE----VEGLSALEEKIVGFARPLVAK-EVYLKLPKFKIEFRDELKETLEKVRLRQ 804 2R:1731127-2080000 1 NULL:1982213 Q19650 14 285 1 1 0 2597487 217145 216356 1 0 0 0 290 partof SKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVP-KLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTE-LKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 789 2R:1731127-2080000 1 NULL:1982215 O17365 1 249 1 1 0 2597489 217139 216398 1 0 0 0 264 partof FG-QLAKSQS-GRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTM-SQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISS 741 2R:1731127-2080000 1 NULL:1982217 O01462 19 261 1 1 0 2597491 217121 216401 1 0 0 0 293 partof GQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFR-FGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGID 720 2R:1731127-2080000 1 NULL:1982219 Q19650 13 243 1 1 0 2597493 254259 253659 1 0 0 0 234 partof IYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLK--TDENAEV-VR--KLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLID-GRCEPCQI 600 2R:1731127-2080000 1 NULL:1982221 O44160 60 253 1 1 0 2597495 254151 253665 1 0 0 0 203 partof TTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRT--KVRAVGECGLDYDRLHFCAQ--ETQRLYFEKQLDLAAEFKLPLFLHMRN-----AAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILA-FGGLYIGFNGCSLKTDENA--EVVRKLPNDRIMLETDCPWCGIRP 486 2R:1731127-2080000 1 NULL:1982223 Q9U2N7 258 425 1 1 0 2602723 2457 2031 1 0 0 0 243 partof ECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSK-------NLTEPAPRVRVLEDGDGNQMEW 426 2R:1731127-2080000 -1 NULL:1986514 P46555 81 223 1 1 0 1764 1281 1 0 0 0 300 partof YYGLGGSALNKWRHITRDLHIDLQKGIM-GDKRSP---LKIRRSDLEVISIGFLG-LGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSL-NGFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 483 2R:1731127-2080000 -1 NULL:1986515 P46555 338 503 1 1 0 1199 809 1 0 0 0 405 partof RNSFFGFYRYEEYPTTPPSYVLNGFIYSLLGLYDLNS----------TAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 390 2R:1731127-2080000 -1 NULL:1986516 P46555 493 632 1 1 0 2602728 5309 4850 1 0 0 0 440 partof GRMIFELFADTVPRTAENFRQFCTGEY-RPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 459 2R:1731127-2080000 -1 NULL:1986518 P52016 22 176 1 1 0 2602731 5309 4850 1 0 0 0 440 partof GRMIFELFADTVPRTAENFRQFCTGEY-RPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 459 2R:1731127-2080000 -1 NULL:1986520 Q95QQ0 22 176 1 1 0 2602734 5312 4850 1 0 0 0 649 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 462 2R:1731127-2080000 -1 NULL:1986522 P52018 29 183 1 1 0 2602737 8846 7730 1 0 0 0 1149 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTS-VHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLT-GVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986524 Q95ZS2 116 489 1 1 0 7602 7236 1 0 0 0 155 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPL-APVAGKPPIKKRLTRTKSLRFS-----FTRSISREQYQSQSEH 366 2R:1731127-2080000 -1 NULL:1986525 Q95ZS2 491 615 1 1 0 2602741 8846 7730 1 0 0 0 1149 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTS-VHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLT-GVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986527 Q21087 116 489 1 1 0 7602 7236 1 0 0 0 155 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLESSSVPTTPEGSERTSSEPL-APVAGKPPIKKRLTRTKSLRFS-----FTRSISREQYQSQSEH 366 2R:1731127-2080000 -1 NULL:1986528 Q21087 491 615 1 1 0 2602744 8849 7730 1 0 0 0 753 partof SLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTS-VHDSVFLPSLIAYASREAHSSVEK--ATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1119 2R:1731127-2080000 -1 NULL:1986530 P34751 306 671 1 1 0 2602746 18077 17693 1 0 0 0 213 partof PQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETI--------VLDWL-GKAIG-LPDHFLALK-EGSTGGGV----IQVT*IFYRTTELSLVRYIDYKSEEGRLSL 384 2R:1731127-2080000 -1 NULL:1986532 Q09945 46 188 1 1 0 17539 16888 1 0 0 0 324 partof PFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDD----DASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLK-VSGIPTARMANLTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWG 651 2R:1731127-2080000 -1 NULL:1986533 Q09945 164 380 1 1 0 2602750 18125 17777 1 0 0 0 413 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986535 Q21087 109 222 1 1 0 17620 17149 1 0 0 0 414 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986536 Q21087 221 375 1 1 0 17128 16906 1 0 0 0 347 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYV 222 2R:1731127-2080000 -1 NULL:1986537 Q21087 366 440 1 1 0 15554 15281 1 0 0 0 233 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQHDELSEIMNRKKQDTLA 273 2R:1731127-2080000 -1 NULL:1986538 Q21087 480 567 1 1 0 2602755 18125 17777 1 0 0 0 413 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986540 Q95ZS2 109 222 1 1 0 17620 17149 1 0 0 0 414 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986541 Q95ZS2 221 375 1 1 0 17128 16906 1 0 0 0 347 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYV 222 2R:1731127-2080000 -1 NULL:1986542 Q95ZS2 366 440 1 1 0 15554 15281 1 0 0 0 233 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQHDELSEIMNRKKQDTLA 273 2R:1731127-2080000 -1 NULL:1986543 Q95ZS2 480 567 1 1 0 2602760 25755 25410 1 0 0 0 281 partof PKECPAIDYTRHTLDGAACLLNSNK-----YFPSRYAGLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPI 345 2R:1731127-2080000 -1 NULL:1986545 P34349 131 248 1 1 0 2602763 26040 25665 1 0 0 0 504 partof DFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 375 2R:1731127-2080000 -1 NULL:1986547 P34349 58 183 1 1 0 2602765 33781 33067 1 0 0 0 259 partof PKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVC-GALMRDPDWL----IEENRLESRSQSVTTFSNSS-VCLEEIKKLLDTGITKEAVLDSLVTKN 714 2R:1731127-2080000 -1 NULL:1986549 Q9GYN2 80 323 1 1 0 2602767 33790 33232 1 0 0 0 284 partof KKTPKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGA 558 2R:1731127-2080000 -1 NULL:1986551 O17328 11 197 1 1 0 2602769 33790 33286 1 0 0 0 259 partof KKTPKMPDGGYGWVVVFASLVVSLIADGLSFSFGLINVELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWR 504 2R:1731127-2080000 -1 NULL:1986553 Q22109 8 176 1 1 0 2602771 88537 87613 1 0 0 0 585 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHND---SNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPA--RQW--PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSG-HKYYPFNDEF 924 2R:1731127-2080000 -1 NULL:1986555 Q9U2J6 0 316 1 1 0 2602773 88537 87613 1 0 0 0 573 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHND---SNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPA--RQW--PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSG-HKYYPFNDEF 924 2R:1731127-2080000 -1 NULL:1986557 Q9NAI5 0 316 1 1 0 2602775 88546 87640 1 0 0 0 531 partof MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVN-QVECHPGFQQRQLREHAKRHGLVICAYCPLARPQ------PARQ---WPPF---LYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGH 906 2R:1731127-2080000 -1 NULL:1986559 P91020 0 307 1 1 0 2602777 93017 92633 1 0 0 0 274 partof RNTHSSQRQSSKLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKL--QPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTI 384 2R:1731127-2080000 -1 NULL:1986561 Q95NL8 955 1084 1 1 0 2602779 93017 92633 1 0 0 0 274 partof RNTHSSQRQSSKLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKL--QPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTI 384 2R:1731127-2080000 -1 NULL:1986563 Q21218 955 1084 1 1 0 2602781 96971 96824 1 0 0 0 153 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1986565 P34578 598 646 1 1 0 92984 92615 1 0 0 0 334 partof KLASLSRYSCKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSR 369 2R:1731127-2080000 -1 NULL:1986566 P34578 1064 1186 1 1 0 2602785 111141 109683 1 0 0 0 331 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFV-GFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQH---LFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTL-RTPVSDF-RTMGQKVFTDMRH--------GKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENF---KRNDFMNLLIELKQKGRVTLDNGE--------VIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLE-RKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLY-PNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLK 1458 2R:1731127-2080000 -1 NULL:1986568 O17806 21 495 1 1 0 2602788 111141 109683 1 0 0 0 338 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQ---HLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFG-IECNTLRTPVSDF-RTM-GQK---VFTDMRH----GKLLTMFVFSFPKLASXXXXXXMPED---VHQFF-MRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGE--------VIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLY-PNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLK 1458 2R:1731127-2080000 -1 NULL:1986570 O17807 22 496 1 1 0 2602790 111150 110112 1 0 0 0 277 partof HRNFNYWNRRGVPHDAPHPLYGNM--VGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLF-NLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVF--TDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRN-----DFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQV 1038 2R:1731127-2080000 -1 NULL:1986572 Q27479 24 363 1 1 0 110037 109689 1 0 0 0 175 partof ETLRLYTLVPHL-ERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVC--DTTEIP 348 2R:1731127-2080000 -1 NULL:1986573 Q27479 365 480 1 1 0 2602793 140126 139976 1 0 0 0 202 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1986575 P91302 9 59 1 1 0 2602796 194863 194407 1 0 0 0 156 partof SSEAHAYTLCIAKVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAE--LESEAMCHEGSKATRAIFLRHG-LIFTTGFNRSSERQYSLRAPDALNEPIVMVE-LDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEV 456 2R:1731127-2080000 -1 NULL:1986577 Q9XTG9 689 845 1 1 0 2602798 196650 196458 1 0 0 0 184 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNKV 192 2R:1731127-2080000 -1 NULL:1986579 Q21624 2 65 1 1 0 195152 194885 1 0 0 0 289 partof QVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDN 267 2R:1731127-2080000 -1 NULL:1986580 Q21624 63 152 1 1 0 194818 194374 1 0 0 0 454 partof IWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMN 444 2R:1731127-2080000 -1 NULL:1986581 Q21624 155 303 1 1 0 194349 194070 1 0 0 0 247 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADP 279 2R:1731127-2080000 -1 NULL:1986582 Q21624 290 383 1 1 0 blastx_masked 1.0 aa_SP.hyp.dros 1.0 2003-01-15 00:40:12 BLASTX Similarity to Fly genomic sim4 1.0 na_users_i.dros 1.0 2003-01-13 21:26:49 BLASTX Similarity to Fly genomic 2605844 265998 265515 1 0 0 0 100 partof 483 2R:1731127-2080000 -1 NULL:1989281 FBgn0033118-u1 0 483 1 1 0 265455 265197 1 0 0 0 100 partof 258 2R:1731127-2080000 -1 NULL:1989282 FBgn0033118-u1 483 741 1 1 0 264883 264580 1 0 0 0 100 partof 303 2R:1731127-2080000 -1 NULL:1989283 FBgn0033118-u1 741 1044 1 1 0 263955 263840 1 0 0 0 100 partof 115 2R:1731127-2080000 -1 NULL:1989284 FBgn0033118-u1 1044 1159 1 1 0 263702 262898 1 0 0 0 100 partof 804 2R:1731127-2080000 -1 NULL:1989285 FBgn0033118-u1 1159 1963 1 1 0 262472 260837 1 0 0 0 100 partof 1635 2R:1731127-2080000 -1 NULL:1989286 FBgn0033118-u1 1963 3598 1 1 0 260145 260023 1 0 0 0 100 partof 122 2R:1731127-2080000 -1 NULL:1989287 FBgn0033118-u1 3598 3720 1 1 0 259873 259597 1 0 0 0 100 partof 276 2R:1731127-2080000 -1 NULL:1989288 FBgn0033118-u1 3720 3996 1 1 0 259048 258847 1 0 0 0 100 partof 201 2R:1731127-2080000 -1 NULL:1989289 FBgn0033118-u1 3996 4197 1 1 0 258611 257164 1 0 0 0 100 partof 1447 2R:1731127-2080000 -1 NULL:1989290 FBgn0033118-u1 4197 5644 1 1 0 256567 256444 1 0 0 0 100 partof 123 2R:1731127-2080000 -1 NULL:1989291 FBgn0033118-u1 5644 5767 1 1 0 256366 256255 1 0 0 0 100 partof 111 2R:1731127-2080000 -1 NULL:1989292 FBgn0033118-u1 5767 5878 1 1 0 2605857 341499 341366 1 0 0 0 100 partof 133 2R:1731127-2080000 -1 NULL:1989294 FBgn0029507-u1 0 133 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1989295 FBgn0029507-u1 133 325 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1989296 FBgn0029507-u1 325 487 1 1 0 340075 339877 1 0 0 0 100 partof 198 2R:1731127-2080000 -1 NULL:1989297 FBgn0029507-u1 487 685 1 1 0 339820 339647 1 0 0 0 99 partof 173 2R:1731127-2080000 -1 NULL:1989298 FBgn0029507-u1 685 858 1 1 0 2600922 164271 164232 1 0 0 0 89 partof 39 2R:1731127-2080000 1 NULL:1985159 FBgn0032330-u1 2191 2229 1 1 0 288136 288085 1 0 0 0 90 partof 51 2R:1731127-2080000 1 NULL:1985160 FBgn0032330-u1 4140 4193 1 1 0 2600925 322552 322463 1 0 0 0 100 partof 89 2R:1731127-2080000 1 NULL:1985162 FBgn0029508-u1 0 89 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1985163 FBgn0029508-u1 89 201 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1985164 FBgn0029508-u1 201 393 1 1 0 326867 326705 1 0 0 0 98 partof 162 2R:1731127-2080000 1 NULL:1985165 FBgn0029508-u1 393 555 1 1 0 327128 326933 1 0 0 0 100 partof 195 2R:1731127-2080000 1 NULL:1985166 FBgn0029508-u1 555 750 1 1 0 327750 327391 1 0 0 0 99 partof 359 2R:1731127-2080000 1 NULL:1985167 FBgn0029508-u1 750 1109 1 1 0 2600932 328956 328643 1 0 0 0 100 partof 313 2R:1731127-2080000 1 NULL:1985169 FBgn0042086-u1 0 313 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1985170 FBgn0042086-u1 313 478 1 1 0 329626 329257 1 0 0 0 100 partof 369 2R:1731127-2080000 1 NULL:1985171 FBgn0042086-u1 478 847 1 1 0 2600936 336407 336221 1 0 0 0 100 partof 186 2R:1731127-2080000 1 NULL:1985173 FBgn0033124-u1 0 186 1 1 0 337692 337500 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1985174 FBgn0033124-u1 186 378 1 1 0 338398 337755 1 0 0 0 100 partof 643 2R:1731127-2080000 1 NULL:1985175 FBgn0033124-u1 378 1021 1 1 0 blastx_masked 1.0 aa_SPTR.rodent 1.0 2003-01-14 22:54:32 BLASTX Similarity to Other Species genomic 2603006 96971 96824 1 0 0 0 208 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1986770 Q9Z1P0 365 414 1 1 0 95888 95741 1 0 0 0 202 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERV 147 2R:1731127-2080000 -1 NULL:1986771 Q9Z1P0 413 462 1 1 0 94080 93825 1 0 0 0 190 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDAL 255 2R:1731127-2080000 -1 NULL:1986772 Q9Z1P0 651 733 1 1 0 93766 93595 1 0 0 0 175 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGK 171 2R:1731127-2080000 -1 NULL:1986773 Q9Z1P0 733 790 1 1 0 92957 92615 1 0 0 0 462 partof CKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSR 342 2R:1731127-2080000 -1 NULL:1986774 Q9Z1P0 835 949 1 1 0 92529 92430 1 0 0 0 90 partof KSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTR 99 2R:1731127-2080000 -1 NULL:1986775 Q9Z1P0 959 992 1 1 0 2603013 97361 97190 1 0 0 0 114 partof HFLYSLIRSSHERTSXXXXXXXXXXXHIAALSHLSTSIKRELSSIFVFEAHAQAGTI 171 2R:1731127-2080000 -1 NULL:1986777 BAB72180 11 68 1 1 0 96971 96824 1 0 0 0 208 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1986778 BAB72180 68 117 1 1 0 95888 95741 1 0 0 0 202 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERV 147 2R:1731127-2080000 -1 NULL:1986779 BAB72180 116 165 1 1 0 94080 93825 1 0 0 0 190 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDAL 255 2R:1731127-2080000 -1 NULL:1986780 BAB72180 354 436 1 1 0 93766 93595 1 0 0 0 175 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGK 171 2R:1731127-2080000 -1 NULL:1986781 BAB72180 436 493 1 1 0 92957 92615 1 0 0 0 462 partof CKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSR 342 2R:1731127-2080000 -1 NULL:1986782 BAB72180 538 652 1 1 0 92529 92430 1 0 0 0 90 partof KSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTR 99 2R:1731127-2080000 -1 NULL:1986783 BAB72180 662 695 1 1 0 2603021 103564 103414 1 0 0 0 169 partof QSAVTLCNLGVGATFGESVLHDLPRDSTVVTKTTCELLRVEQQDFRLIWE 150 2R:1731127-2080000 -1 NULL:1986785 Q9CS95 98 148 1 1 0 2603024 111132 110106 1 0 0 0 350 partof WNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKD-FSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFT-DMRHGKLLTMFVFSF-PKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFK-RNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1026 2R:1731127-2080000 -1 NULL:1986787 P51538 32 361 1 1 0 110040 109662 1 0 0 0 263 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIV 378 2R:1731127-2080000 -1 NULL:1986788 P51538 360 483 1 1 0 2603027 111141 109629 1 0 0 0 385 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLT-QHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERE--NFKRNDFMNLLIELKQK-GRVTLDNGEVI-EGMDIGELAAQVF-----VFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPR--GIVTG--FTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986790 P36423 35 530 1 1 0 2603030 111141 109629 1 0 0 0 422 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPL-TQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERENF--KRNDFMNLLIELKQK-GRVTLDNGEVI-EGMD----IGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMT-YLNQVISGR-CSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986792 P49430 35 530 1 1 0 2603032 196659 196470 1 0 0 0 256 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLP 189 2R:1731127-2080000 -1 NULL:1986794 AAK98517 0 63 1 1 0 195158 194879 1 0 0 0 305 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986795 AAK98517 63 156 1 1 0 194824 194344 1 0 0 0 440 partof VVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMC-HEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 480 2R:1731127-2080000 -1 NULL:1986796 AAK98517 155 317 1 1 0 194349 194052 1 0 0 0 345 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLK 297 2R:1731127-2080000 -1 NULL:1986797 AAK98517 294 392 1 1 0 2603038 196659 196470 1 0 0 0 256 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLP 189 2R:1731127-2080000 -1 NULL:1986799 BAB64361 0 63 1 1 0 195158 194879 1 0 0 0 308 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986800 BAB64361 63 156 1 1 0 194824 194344 1 0 0 0 436 partof VVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESE-AMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 480 2R:1731127-2080000 -1 NULL:1986801 BAB64361 155 317 1 1 0 194349 194052 1 0 0 0 345 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLK 297 2R:1731127-2080000 -1 NULL:1986802 BAB64361 294 392 1 1 0 2603044 196659 196470 1 0 0 0 256 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLP 189 2R:1731127-2080000 -1 NULL:1986804 BAB64362 0 63 1 1 0 195158 194879 1 0 0 0 308 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986805 BAB64362 63 156 1 1 0 194824 194344 1 0 0 0 440 partof VVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMC-HEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 480 2R:1731127-2080000 -1 NULL:1986806 BAB64362 155 317 1 1 0 194349 194052 1 0 0 0 345 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLK 297 2R:1731127-2080000 -1 NULL:1986807 BAB64362 294 392 1 1 0 2603050 208017 207189 1 0 0 0 449 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLG---LASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLP--ALDA----MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 828 2R:1731127-2080000 -1 NULL:1986809 O35684 28 313 1 1 0 2603052 208017 207189 1 0 0 0 449 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLG---LASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLP--ALDA----MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 828 2R:1731127-2080000 -1 NULL:1986811 AAH06776 28 313 1 1 0 2603054 208026 207189 1 0 0 0 449 partof LALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLG---LASSDPEQIAHSFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLV-PADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLP--ALDA----MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 837 2R:1731127-2080000 -1 NULL:1986813 Q9JLD1 25 313 1 1 0 2603057 210463 209644 1 0 0 0 341 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ---VAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRP-TRVRMMHVCENFFFAVLP--MFEA----TALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1986815 AAH06776 25 307 1 1 0 209580 209466 1 0 0 0 75 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986816 AAH06776 309 346 1 1 0 2603060 210463 209644 1 0 0 0 341 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ---VAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRP-TRVRMMHVCENFFFAVLP--MFEA----TALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1986818 O35684 25 307 1 1 0 209580 209466 1 0 0 0 75 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986819 O35684 309 346 1 1 0 2603063 210463 209644 1 0 0 0 333 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ---VAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRP-TRVRMMHVCENFFFAVLP--MFEA----TALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1986821 Q9JLD1 25 307 1 1 0 209580 209466 1 0 0 0 83 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986822 Q9JLD1 309 346 1 1 0 2603066 302505 302082 1 0 0 0 222 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVDKL 423 2R:1731127-2080000 -1 NULL:1986824 Q64590 9 147 1 1 0 2603068 302797 302563 1 0 0 0 111 partof NAEKPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 234 2R:1731127-2080000 -1 NULL:1986826 Q64481 285 362 1 1 0 302505 302100 1 0 0 0 228 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV 405 2R:1731127-2080000 -1 NULL:1986827 Q64481 362 494 1 1 0 2603071 302932 302563 1 0 0 0 127 partof IARLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAE---------KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 369 2R:1731127-2080000 -1 NULL:1986829 P05183 231 362 1 1 0 302505 302100 1 0 0 0 225 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV 405 2R:1731127-2080000 -1 NULL:1986830 P05183 362 494 1 1 0 2603074 304557 304140 1 0 0 0 242 partof LEDPQGALTTPT-EGGRTLVTRGGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQG-SSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSSDEILG-ELRSYFEKYQGFVAMGG 417 2R:1731127-2080000 -1 NULL:1986832 Q99K23 252 393 1 1 0 2603077 304560 304086 1 0 0 0 253 partof LLEDPQGALTTPT-EGGRTLVTRGGFNYFHYGCDGHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKE---LSSDEILGELRSYFEKYQGFVAMGGLSDTASKAITGYHCSARG 474 2R:1731127-2080000 -1 NULL:1986834 Q9CZP0 10 166 1 1 0 2603080 307908 307467 1 0 0 0 98 partof GGLLSNYLLGGEGLAKRAMELGVMKKLQGIIDIGASNVEQHEDXXXXXXXXXXXXTENVSDLNFDSSLNIQLSRILAASTNPDLAEMCLELLHYQAESDEVKLILAKDGLCETIYNLLEKYKTLASTSEARALMKLACELIVLILTG 441 2R:1731127-2080000 -1 NULL:1986836 AAH11279 109 253 1 1 0 307378 306985 1 0 0 0 272 partof DDSMHYLYTT---PLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE 393 2R:1731127-2080000 -1 NULL:1986837 AAH11279 253 386 1 1 0 306924 306762 1 0 0 0 108 partof ALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKG 162 2R:1731127-2080000 -1 NULL:1986838 AAH11279 387 441 1 1 0 2603085 312246 311835 1 0 0 0 195 partof FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYNIA--TAVGDCHDQDPSQYKDYRGESEFNEANGNDLGAAFRRPYRGANQRMPQR-QSLYQTQQ 411 2R:1731127-2080000 -1 NULL:1986840 P97554 9 145 1 1 0 2603087 312246 312012 1 0 0 0 184 partof FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYN 234 2R:1731127-2080000 -1 NULL:1986842 Q9QYI4 94 172 1 1 0 2603089 312246 312012 1 0 0 0 204 partof FTLEMLDVVQKVLRCRNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYN 234 2R:1731127-2080000 -1 NULL:1986844 Q9CZJ9 65 143 1 1 0 2602936 2496 1281 1 0 0 0 731 partof SSSGGEATAL--HDIECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLE---DGDGN--QMEWSTPKTSNMTRIWHHKFNTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKGI-MGDKRS--PLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSLN-GFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 1215 2R:1731127-2080000 -1 NULL:1986707 Q99MM0 92 497 1 1 0 1172 809 1 0 0 0 439 partof YEEYPTTPPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 363 2R:1731127-2080000 -1 NULL:1986708 Q99MM0 497 618 1 1 0 2602940 2496 1281 1 0 0 0 731 partof SSSGGEATAL--HDIECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLE---DGDGN--QMEWSTPKTSNMTRIWHHKFNTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKGI-MGDKRS--PLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSLN-GFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 1215 2R:1731127-2080000 -1 NULL:1986710 Q9EPS3 92 497 1 1 0 1172 809 1 0 0 0 438 partof YEEYPTTPPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 363 2R:1731127-2080000 -1 NULL:1986711 Q9EPS3 497 618 1 1 0 2602944 5318 4850 1 0 0 0 462 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986713 O88541 46 197 1 1 0 2602946 5318 4850 1 0 0 0 709 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986715 Q9CQU7 21 177 1 1 0 2602949 5318 4901 1 0 0 0 598 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIE-NVPTG 417 2R:1731127-2080000 -1 NULL:1986717 Q9D868 21 161 1 1 0 2602952 8846 7730 1 0 0 0 1063 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TG--VDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986719 O88533 40 414 1 1 0 7602 7422 1 0 0 0 95 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 180 2R:1731127-2080000 -1 NULL:1986720 O88533 416 476 1 1 0 2602955 8849 7730 1 0 0 0 1055 partof SLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1119 2R:1731127-2080000 -1 NULL:1986722 Q62819 39 414 1 1 0 7593 7404 1 0 0 0 95 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLES 189 2R:1731127-2080000 -1 NULL:1986723 Q62819 419 482 1 1 0 2602958 8849 7730 1 0 0 0 1059 partof SLSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1119 2R:1731127-2080000 -1 NULL:1986725 P14173 39 414 1 1 0 7593 7422 1 0 0 0 94 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 171 2R:1731127-2080000 -1 NULL:1986726 P14173 419 476 1 1 0 2602961 18125 17771 1 0 0 0 370 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 354 2R:1731127-2080000 -1 NULL:1986728 Q9QWU3 41 156 1 1 0 17620 17182 1 0 0 0 347 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLK 438 2R:1731127-2080000 -1 NULL:1986729 Q9QWU3 153 298 1 1 0 17149 16870 1 0 0 0 269 partof LTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 279 2R:1731127-2080000 -1 NULL:1986730 Q9QWU3 292 383 1 1 0 15554 15329 1 0 0 0 150 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQH 225 2R:1731127-2080000 -1 NULL:1986731 Q9QWU3 412 485 1 1 0 2602966 18125 17771 1 0 0 0 370 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 354 2R:1731127-2080000 -1 NULL:1986733 P23738 41 156 1 1 0 17620 17182 1 0 0 0 348 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLK 438 2R:1731127-2080000 -1 NULL:1986734 P23738 153 298 1 1 0 17149 16870 1 0 0 0 269 partof LTGFHSQGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 279 2R:1731127-2080000 -1 NULL:1986735 P23738 292 383 1 1 0 15554 15329 1 0 0 0 150 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQH 225 2R:1731127-2080000 -1 NULL:1986736 P23738 412 485 1 1 0 2602971 18125 17777 1 0 0 0 374 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986738 O88533 33 145 1 1 0 17620 17149 1 0 0 0 324 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986739 O88533 144 298 1 1 0 17128 16870 1 0 0 0 284 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986740 O88533 289 376 1 1 0 15554 15332 1 0 0 0 181 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1986741 O88533 405 479 1 1 0 2602976 26174 26114 1 0 0 0 74 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1986743 Q9CX28 0 20 1 1 0 26043 25665 1 0 0 0 575 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1986744 Q9CX28 19 145 1 1 0 25659 25410 1 0 0 0 320 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPI 249 2R:1731127-2080000 -1 NULL:1986745 Q9CX28 130 210 1 1 0 2602981 26174 26114 1 0 0 0 74 partof MKMADGSTILRRNRPGTKSK 60 2R:1731127-2080000 -1 NULL:1986747 Q9QYW3 0 20 1 1 0 26043 25665 1 0 0 0 583 partof QDFCRWPDEPLEEMDSTLAVQQYIQQLIKRDPSNVELILTMPEAQDEGVWKYEHLRQFCMELNGLAVRLQKECSPSTCTQMTATDQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSR 378 2R:1731127-2080000 -1 NULL:1986748 Q9QYW3 19 145 1 1 0 25659 25410 1 0 0 0 314 partof GLATWLN*PHNKQSVSPRVSIKESSVTKLGSVCRRVYRIFSHAYFHHRRIFDEFEAETYLCHRFTHFVTKYNLMSKENLIVPI 249 2R:1731127-2080000 -1 NULL:1986749 Q9QYW3 130 210 1 1 0 2602986 33778 33223 1 0 0 0 302 partof KMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 555 2R:1731127-2080000 -1 NULL:1986751 O35910 13 198 1 1 0 2602988 33778 33223 1 0 0 0 301 partof KMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 555 2R:1731127-2080000 -1 NULL:1986753 P57787 13 198 1 1 0 2602990 33781 33115 1 0 0 0 295 partof PKMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR----DPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLLD 666 2R:1731127-2080000 -1 NULL:1986755 O70451 11 237 1 1 0 2602992 88534 87616 1 0 0 0 695 partof APTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDS---NVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDE 918 2R:1731127-2080000 -1 NULL:1986757 P07943 0 314 1 1 0 2602994 88537 87616 1 0 0 0 677 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDS---NVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDE 921 2R:1731127-2080000 -1 NULL:1986759 AAH21655 0 315 1 1 0 2602996 88537 87616 1 0 0 0 677 partof LAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDS---NVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDE 921 2R:1731127-2080000 -1 NULL:1986761 Q99KC9 0 315 1 1 0 2602998 96971 96824 1 0 0 0 208 partof VFNQGDEGRSWYILLKGSVDVVIHGKGTVATLKTGDDFGKLALINDAPR 147 2R:1731127-2080000 -1 NULL:1986763 Q9EQZ6 383 432 1 1 0 95888 95741 1 0 0 0 202 partof RAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERV 147 2R:1731127-2080000 -1 NULL:1986764 Q9EQZ6 431 480 1 1 0 94080 93825 1 0 0 0 190 partof VIFRVYCADHTYCTLRFPMHTTAELIKACAADKLQLNRGPEDLVLVEVKSNGERSVFKDNDVSIPTGLSLNGRLFVSVKDHLDAL 255 2R:1731127-2080000 -1 NULL:1986765 Q9EQZ6 669 751 1 1 0 93766 93595 1 0 0 0 175 partof TQLQEQECPTEGVDIDLEILSTKELAYHITLFEWDLFWAVHEYELLYHTFGRHHFGK 171 2R:1731127-2080000 -1 NULL:1986766 Q9EQZ6 751 808 1 1 0 92957 92615 1 0 0 0 462 partof CKEYQNLNAFFAVVMGLSNMAVSRLQQTWEKIPSKFRKIFQEFEALIDPSRNHRAYRVFVGKLQPPLIPFMPLLLKDMTFAHEGNKTSLDGLVNFEKMHMMAQTMRTIRFCRSR 342 2R:1731127-2080000 -1 NULL:1986767 Q9EQZ6 853 967 1 1 0 92529 92430 1 0 0 0 90 partof KSEGEVRSYISSFRVIDNQRVLTAMSQKVEPTR 99 2R:1731127-2080000 -1 NULL:1986768 Q9EQZ6 977 1010 1 1 0 2597565 27351 27189 1 0 0 0 279 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982289 P53994 15 69 1 1 0 28172 27821 1 0 0 0 561 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982290 P53994 68 185 1 1 0 2597568 27351 27189 1 0 0 0 276 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982292 P05712 15 69 1 1 0 28172 27821 1 0 0 0 561 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982293 P05712 68 185 1 1 0 2597571 27351 27189 1 0 0 0 273 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982295 Q9DB48 15 69 1 1 0 28172 27821 1 0 0 0 521 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982296 Q9DB48 68 185 1 1 0 2597574 72757 72616 1 0 0 0 134 partof YQKRIGTYDKQEWEKTVEQRILDGFNSVNLKNTKLKTELIDVDLVRG 141 2R:1731127-2080000 1 NULL:1982298 CAD24855 11 58 1 1 0 72939 72810 1 0 0 0 97 partof GSTFPKAKPKQSLLTVIRLAILRYVLLPLYAQWWVKQTTPNAF 129 2R:1731127-2080000 1 NULL:1982299 CAD24855 57 100 1 1 0 2597578 74969 74759 1 0 0 0 262 partof LGFVQRLCLTLILFIIFAVAERTFKQRFLYAKLFSHLTSSRRARKSNLPHFRLNKVRNIKTWLSVRSYLK 210 2R:1731127-2080000 1 NULL:1982301 Q9QZ09 530 600 1 1 0 75480 75027 1 0 0 0 285 partof KRGPQRSVDXXXXXXXXXXXXXXAFLSVEWLKDSAXXXXXXXX-EALIWSITIGIFLLRFMTLGQKIQHKYRSVSVLITEQINLYLQIEQKPKKKDELMVSNSVXXXXXXXXXXXXTPFKLSGLSANPYLFTTIKVVILSALSGVLSEVLGF 453 2R:1731127-2080000 1 NULL:1982302 Q9QZ09 600 752 1 1 0 2597582 76633 76480 1 0 0 0 110 partof LRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGH 153 2R:1731127-2080000 1 NULL:1982304 P07633 40 90 1 1 0 77906 77030 1 0 0 0 346 partof VVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQG-IPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALD-DEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGN-----NGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKL 876 2R:1731127-2080000 1 NULL:1982305 P07633 122 400 1 1 0 78351 77952 1 0 0 0 142 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTR 399 2R:1731127-2080000 1 NULL:1982306 P07633 397 514 1 1 0 2597587 76633 76504 1 0 0 0 106 partof LKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGH 129 2R:1731127-2080000 1 NULL:1982308 Q9DBG2 48 90 1 1 0 77906 77030 1 0 0 0 346 partof VVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQG-IPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALD-DEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGN-----NGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKL 876 2R:1731127-2080000 1 NULL:1982309 Q9DBG2 122 400 1 1 0 78351 77952 1 0 0 0 139 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTR 399 2R:1731127-2080000 1 NULL:1982310 Q9DBG2 397 514 1 1 0 2597592 77909 77372 1 0 0 0 593 partof VKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 537 2R:1731127-2080000 1 NULL:1982312 Q9D2F6 3 166 1 1 0 2597595 82561 82438 1 0 0 0 166 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982314 O35879 0 41 1 1 0 82763 82616 1 0 0 0 206 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1982315 O35879 40 89 1 1 0 2597598 82561 82438 1 0 0 0 166 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982317 Q61166 0 41 1 1 0 82766 82616 1 0 0 0 218 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982318 Q61166 40 90 1 1 0 83124 82998 1 0 0 0 210 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982319 Q61166 88 130 1 1 0 2597602 82766 82667 1 0 0 0 126 partof VKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 99 2R:1731127-2080000 1 NULL:1982321 Q61167 1 34 1 1 0 83124 82998 1 0 0 0 191 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982322 Q61167 32 74 1 1 0 2597605 84083 83954 1 0 0 0 192 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREG 129 2R:1731127-2080000 1 NULL:1982324 Q61167 33 76 1 1 0 2597607 84218 83954 1 0 0 0 209 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVK---SLPGTAASGVSSSYRRGPSATTRPAMTSAVKPSM 264 2R:1731127-2080000 1 NULL:1982326 Q61166 89 179 1 1 0 2597609 138302 137936 1 0 0 0 512 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982328 Q9DC91 40 162 1 1 0 138718 138373 1 0 0 0 523 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982329 Q9DC91 165 280 1 1 0 2597612 138302 137936 1 0 0 0 512 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982331 Q9CQA3 40 162 1 1 0 138718 138373 1 0 0 0 523 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982332 Q9CQA3 165 280 1 1 0 2597615 138302 137936 1 0 0 0 512 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982334 AAH13509 40 162 1 1 0 138718 138373 1 0 0 0 523 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982335 AAH13509 165 280 1 1 0 2597619 146306 145871 1 0 0 0 272 partof SMFVAKDYLEQQLLELNKRTNNNIRDEIERSSILLMSDISQRLKREILLVVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 435 2R:1731127-2080000 1 NULL:1982337 Q99P23 63 194 1 1 0 146504 146390 1 0 0 0 123 partof VLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVW 114 2R:1731127-2080000 1 NULL:1982338 Q99P23 203 241 1 1 0 146768 146567 1 0 0 0 166 partof GLEQEKDQEPVLFGDYQFEDNGASLQYF-AVQNLDIKRPYEIVELRIETNHGHPTYTCLYRFRVHGKP 201 2R:1731127-2080000 1 NULL:1982339 Q99P23 241 307 1 1 0 2597624 146306 145871 1 0 0 0 272 partof SMFVAKDYLEQQLLELNKRTNNNIRDEIERSSILLMSDISQRLKREILLVVEAKHNESTKALKGHIREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 435 2R:1731127-2080000 1 NULL:1982341 Q9D666 544 675 1 1 0 146504 146390 1 0 0 0 123 partof VLKLNSLVYVTGFTLEHIPKSLSPTGRIESAPRNFTVW 114 2R:1731127-2080000 1 NULL:1982342 Q9D666 684 722 1 1 0 146768 146567 1 0 0 0 162 partof GLEQEKDQEPVLFGDYQFEDNGASLQYF-AVQNLDIKRPYEIVELRIETNHGHPTYTCLYRFRVHGKP 201 2R:1731127-2080000 1 NULL:1982343 Q9D666 722 788 1 1 0 2597629 212416 211537 1 0 0 0 379 partof MSEPQEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQL-GPGDRHH-IALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFA-DSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLA--DIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 879 2R:1731127-2080000 1 NULL:1982345 AAB57815 0 286 1 1 0 2597632 212416 211537 1 0 0 0 412 partof MSEPQEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD-SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDL-ADIDAA-LTLQDVEIFLPRMCIEYDVDLKQVLNQV 879 2R:1731127-2080000 1 NULL:1982347 O08797 0 287 1 1 0 2597635 212407 211552 1 0 0 0 398 partof EGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQL----GPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADS-EGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNT---VDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVL 855 2R:1731127-2080000 1 NULL:1982349 AAB57819 5 288 1 1 0 2597637 214230 213432 1 0 0 0 415 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGL---------PSE---DKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAER-INQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEE-----KIVGF--ARPLVAKEVYLKLPKFKIEFRDELKETLE 798 2R:1731127-2080000 1 NULL:1982351 Q9D1Q5 13 297 1 1 0 2597639 214230 213432 1 0 0 0 395 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPS------------EDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAER-INQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEE-----KIVGFARP--LVAKEVYLKLPKFKIEFRDELKETLE 798 2R:1731127-2080000 1 NULL:1982353 Q9Z2G2 13 298 1 1 0 2597641 214236 213462 1 0 0 0 391 partof TNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEA---VAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAA-ERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALE-----EKIVGFAR--PLVAKEVYLKLPKFKIEFRDELKETLEKV 774 2R:1731127-2080000 1 NULL:1982355 AAH06766 22 291 1 1 0 sim4 1.0 na_affy_oligo.dros 1.0 2003-01-13 21:53:28 genomic 2602042 140008 139983 1 0 0 0 100 partof AGGCGAATCGGGTCCTTGAAGATTG 25 2R:1731127-2080000 -1 NULL:1986035 146694_at_158 0 25 1 1 0 2602045 140018 139993 1 0 0 0 100 partof GGTCCTTGAAGATTGTGTACCACTT 25 2R:1731127-2080000 -1 NULL:1986037 146694_at_148 0 25 1 1 0 2602048 140029 140004 1 0 0 0 100 partof ATTGTGTACCACTTCTTCAGGACAA 25 2R:1731127-2080000 -1 NULL:1986039 146694_at_137 0 25 1 1 0 2602051 140032 140007 1 0 0 0 100 partof GTGTACCACTTCTTCAGGACAATCT 25 2R:1731127-2080000 -1 NULL:1986041 146694_at_134 0 25 1 1 0 2602054 140041 140016 1 0 0 0 100 partof TTCTTCAGGACAATCTTCTCGTGCT 25 2R:1731127-2080000 -1 NULL:1986043 146694_at_125 0 25 1 1 0 2602057 140050 140025 1 0 0 0 100 partof ACAATCTTCTCGTGCTTTGTGCCCG 25 2R:1731127-2080000 -1 NULL:1986045 146694_at_116 0 25 1 1 0 2602060 140056 140031 1 0 0 0 100 partof TTCTCGTGCTTTGTGCCCGTTTGTG 25 2R:1731127-2080000 -1 NULL:1986047 146694_at_110 0 25 1 1 0 2602063 140063 140038 1 0 0 0 100 partof GCTTTGTGCCCGTTTGTGCCGCGAT 25 2R:1731127-2080000 -1 NULL:1986049 146694_at_103 0 25 1 1 0 2601409 982 957 1 0 0 0 100 partof CCCAGGCTCAGATGGCGCAGGTCGT 25 2R:1731127-2080000 -1 NULL:1985613 146683_at_1986 0 25 1 1 0 2602066 140067 140042 1 0 0 0 100 partof TGTGCCCGTTTGTGCCGCGATTAGT 25 2R:1731127-2080000 -1 NULL:1986051 146694_at_99 0 25 1 1 0 2602069 140074 140049 1 0 0 0 100 partof GTTTGTGCCGCGATTAGTTTCTTGA 25 2R:1731127-2080000 -1 NULL:1986053 146694_at_92 0 25 1 1 0 2601412 1007 982 1 0 0 0 100 partof AGCTGGTGCCGGAGCCAGTGTCAAA 25 2R:1731127-2080000 -1 NULL:1985615 146683_at_1961 0 25 1 1 0 2601415 1086 1061 1 0 0 0 100 partof CTCGCGGGCGATTTTTCCCGGGGCA 25 2R:1731127-2080000 -1 NULL:1985617 146683_at_1882 0 25 1 1 0 2602072 140089 140064 1 0 0 0 100 partof AGTTTCTTGAGGTCCCCAATCGTGT 25 2R:1731127-2080000 -1 NULL:1986055 146694_at_77 0 25 1 1 0 2601418 1150 1125 1 0 0 0 100 partof AAGCCGTTTAGCACATAAGAGGGTG 25 2R:1731127-2080000 -1 NULL:1985619 146683_at_1818 0 25 1 1 0 2602075 140094 140069 1 0 0 0 100 partof CTTGAGGTCCCCAATCGTGTCGTCC 25 2R:1731127-2080000 -1 NULL:1986057 146694_at_72 0 25 1 1 0 2602078 140096 140071 1 0 0 0 100 partof TGAGGTCCCCAATCGTGTCGTCCGG 25 2R:1731127-2080000 -1 NULL:1986059 146694_at_70 0 25 1 1 0 2601421 1313 1288 1 0 0 0 100 partof AACTTGTCCATGAACTGCGCCAGAA 25 2R:1731127-2080000 -1 NULL:1985621 146683_at_1764 0 25 1 1 0 2601424 1363 1338 1 0 0 0 100 partof ATAAGGCTGCAGTCCGGCTGCGGCC 25 2R:1731127-2080000 -1 NULL:1985623 146683_at_1714 0 25 1 1 0 2602081 168073 168048 1 0 0 0 100 partof CATCCCTGTGTTTAAATGGAATTTG 25 2R:1731127-2080000 -1 NULL:1986061 151151_at_618 0 25 1 1 0 2601427 1380 1355 1 0 0 0 100 partof CTGCGGCCGCTCGAAGGTAGCGTTC 25 2R:1731127-2080000 -1 NULL:1985625 146683_at_1697 0 25 1 1 0 2602084 168138 168113 1 0 0 0 100 partof CGAAACCCAACTAAGGCATTTCGAA 25 2R:1731127-2080000 -1 NULL:1986063 151151_at_553 0 25 1 1 0 2602087 168153 168128 1 0 0 0 100 partof GCATTTCGAAACATGGCTCTATTTC 25 2R:1731127-2080000 -1 NULL:1986065 151151_at_538 0 25 1 1 0 2601430 1385 1360 1 0 0 0 100 partof GCCGCTCGAAGGTAGCGTTCATCCC 25 2R:1731127-2080000 -1 NULL:1985627 146683_at_1692 0 25 1 1 0 2601433 1412 1387 1 0 0 0 100 partof CCGGAGTGCCAGTAGGCTCGTGCCA 25 2R:1731127-2080000 -1 NULL:1985629 146683_at_1665 0 25 1 1 0 2602090 168191 168166 1 0 0 0 100 partof TAATCCTATTTGCAAAAGGTAAGAC 25 2R:1731127-2080000 -1 NULL:1986067 151151_at_500 0 25 1 1 0 2601436 1452 1427 1 0 0 0 100 partof GTCCCTGGCCCATGGCTGATATCCA 25 2R:1731127-2080000 -1 NULL:1985631 146683_at_1625 0 25 1 1 0 2602093 168196 168171 1 0 0 0 100 partof CTATTTGCAAAAGGTAAGACTGCGA 25 2R:1731127-2080000 -1 NULL:1986069 151151_at_495 0 25 1 1 0 2601439 1478 1453 1 0 0 0 100 partof CCCGGACGCAATTCGGCAAAGCCGT 25 2R:1731127-2080000 -1 NULL:1985633 146683_at_1599 0 25 1 1 0 2602096 168223 168198 1 0 0 0 100 partof TAATTAATGCCGTGCATCATTGTCC 25 2R:1731127-2080000 -1 NULL:1986071 151151_at_468 0 25 1 1 0 2602099 168294 168269 1 0 0 0 100 partof CAAGGTTGGTGCAACATTAGATACA 25 2R:1731127-2080000 -1 NULL:1986073 151151_at_397 0 25 1 1 0 2601442 1493 1468 1 0 0 0 100 partof GCAAAGCCGTTGAGGCTGCGACGCA 25 2R:1731127-2080000 -1 NULL:1985635 146683_at_1584 0 25 1 1 0 2601445 1529 1504 1 0 0 0 100 partof CAGCCACCCGTCTTGGGGTCCTGGT 25 2R:1731127-2080000 -1 NULL:1985637 146683_at_1548 0 25 1 1 0 2601448 1546 1521 1 0 0 0 100 partof GTCCTGGTTGTGGACGAACCACTCA 25 2R:1731127-2080000 -1 NULL:1985639 146683_at_1531 0 25 1 1 0 2601451 4957 4932 1 0 0 0 100 partof ATGAGCAGTCCATCCAGAACCCGAC 25 2R:1731127-2080000 -1 NULL:1985641 146684_at_455 0 25 1 1 0 2601454 4982 4957 1 0 0 0 100 partof CGAACACCACGTGCTTTCCGTCTAA 25 2R:1731127-2080000 -1 NULL:1985643 146684_at_430 0 25 1 1 0 2601457 5025 5000 1 0 0 0 100 partof GGTGATAAAGAATTGGCAGCCGTTC 25 2R:1731127-2080000 -1 NULL:1985645 146684_at_387 0 25 1 1 0 2602402 302330 302305 1 0 0 0 100 partof GATCGCCTTGCCTGTTCCTCAAAGC 25 2R:1731127-2080000 -1 NULL:1986275 141721_at_1440 0 25 1 1 0 2602405 302345 302320 1 0 0 0 100 partof TCCTCAAAGCGCTCCGGGTAGAACC 25 2R:1731127-2080000 -1 NULL:1986277 141721_at_1425 0 25 1 1 0 2602408 302373 302348 1 0 0 0 100 partof GGGGGTTTTCATAAATGCCAGGATC 25 2R:1731127-2080000 -1 NULL:1986279 141721_at_1397 0 25 1 1 0 2601460 5044 5019 1 0 0 0 100 partof CCGTTCGTCTCCTTGCCACTGTTTG 25 2R:1731127-2080000 -1 NULL:1985647 146684_at_368 0 25 1 1 0 2601463 5061 5036 1 0 0 0 100 partof ACTGTTTGCCATGGAAAGGAGGCCG 25 2R:1731127-2080000 -1 NULL:1985649 146684_at_351 0 25 1 1 0 2601466 5087 5062 1 0 0 0 100 partof GCGAGTCGTGCTTCAGGGTAAAGTT 25 2R:1731127-2080000 -1 NULL:1985651 146684_at_325 0 25 1 1 0 2601469 5133 5108 1 0 0 0 100 partof GTATATGCTGGTCACGCCGGTGCCG 25 2R:1731127-2080000 -1 NULL:1985653 146684_at_279 0 25 1 1 0 2602411 302470 302445 1 0 0 0 100 partof GAATTCTTTGGTAGCCCGGCGTAGC 25 2R:1731127-2080000 -1 NULL:1986281 141721_at_1300 0 25 1 1 0 2602414 305660 305635 1 0 0 0 100 partof GTGCTCTTAAAAATCATGTAACAGA 25 2R:1731127-2080000 -1 NULL:1986283 141802_at_2863 0 25 1 1 0 2602417 305766 305741 1 0 0 0 100 partof TTGTGACTCCTTACTACATCGGATT 25 2R:1731127-2080000 -1 NULL:1986285 141802_at_2757 0 25 1 1 0 2601472 5197 5172 1 0 0 0 100 partof TTGATCACCCGATGGAAACTGGCGC 25 2R:1731127-2080000 -1 NULL:1985655 146684_at_215 0 25 1 1 0 2601475 5233 5208 1 0 0 0 100 partof ATGGGAACGCCATCCGGTCGGTACT 25 2R:1731127-2080000 -1 NULL:1985657 146684_at_179 0 25 1 1 0 2601478 5252 5227 1 0 0 0 100 partof GGTACTCGCCCGTGCAGAACTGCCG 25 2R:1731127-2080000 -1 NULL:1985659 146684_at_160 0 25 1 1 0 2596301 75415 75390 1 0 0 0 100 partof GGCCTTAGTGCCAATCCATATCTAT 25 2R:1731127-2080000 1 NULL:1981374 152190_at_2887 0 25 1 1 0 2596304 75433 75408 1 0 0 0 100 partof TATCTATTCACAACCATCAAGGTGG 25 2R:1731127-2080000 1 NULL:1981376 152190_at_2905 0 25 1 1 0 2596307 75504 75479 1 0 0 0 100 partof TAAACTGAAGCTGCATAAAATCAAG 25 2R:1731127-2080000 1 NULL:1981378 152190_at_2976 0 25 1 1 0 2602420 305806 305781 1 0 0 0 100 partof GTCAAAATACGCTTGCGTCTAAAAA 25 2R:1731127-2080000 -1 NULL:1986287 141802_at_2717 0 25 1 1 0 2602423 305832 305807 1 0 0 0 100 partof TACTTTCTGCTCCTCTCGTGTTCGC 25 2R:1731127-2080000 -1 NULL:1986289 141802_at_2691 0 25 1 1 0 2602426 305883 305858 1 0 0 0 100 partof CTGCTTAACTTGTGAATCTGCACTT 25 2R:1731127-2080000 -1 NULL:1986291 141802_at_2640 0 25 1 1 0 2602429 305922 305897 1 0 0 0 100 partof TACAGTCAAGTCTACATCTGAATCG 25 2R:1731127-2080000 -1 NULL:1986293 141802_at_2601 0 25 1 1 0 2601481 5271 5246 1 0 0 0 100 partof CTGCCGGAAGTTTTCCGCCGTGCGG 25 2R:1731127-2080000 -1 NULL:1985661 146684_at_141 0 25 1 1 0 2601484 5293 5268 1 0 0 0 100 partof CGGGGCACTGTGTCCGCAAAGAGTT 25 2R:1731127-2080000 -1 NULL:1985663 146684_at_119 0 25 1 1 0 2601487 5302 5277 1 0 0 0 100 partof GTGTCCGCAAAGAGTTCGAATATCA 25 2R:1731127-2080000 -1 NULL:1985665 146684_at_110 0 25 1 1 0 2596310 75523 75498 1 0 0 0 100 partof ATCAAGATCAAGTAACCTATGCAAG 25 2R:1731127-2080000 1 NULL:1981380 152190_at_2995 0 25 1 1 0 2596313 75550 75525 1 0 0 0 100 partof GCAGACCCATCATATTTTTGTAGTA 25 2R:1731127-2080000 1 NULL:1981382 152190_at_3022 0 25 1 1 0 2596316 75568 75543 1 0 0 0 100 partof TGTAGTACAACTTTTTAGAAACGCT 25 2R:1731127-2080000 1 NULL:1981384 152190_at_3040 0 25 1 1 0 2596319 78126 78101 1 0 0 0 100 partof GGCCTATTCGCCTCGTTTCCTATAC 25 2R:1731127-2080000 1 NULL:1981386 142557_at_1465 0 25 1 1 0 2602432 305936 305911 1 0 0 0 100 partof CATCTGAATCGTTGCTTTGGGGTGA 25 2R:1731127-2080000 -1 NULL:1986295 141802_at_2587 0 25 1 1 0 2602435 305962 305937 1 0 0 0 100 partof AACTACTATTTTCTCCGGTTCTGAG 25 2R:1731127-2080000 -1 NULL:1986297 141802_at_2561 0 25 1 1 0 2602438 305974 305949 1 0 0 0 100 partof CTCCGGTTCTGAGTGTGTCTGTGTG 25 2R:1731127-2080000 -1 NULL:1986299 141802_at_2549 0 25 1 1 0 2601490 5412 5387 1 0 0 0 100 partof GCCTACGGCAATGTCGAAGAAAACG 25 2R:1731127-2080000 -1 NULL:1985667 146684_at_66 0 25 1 1 0 2601493 7139 7114 1 0 0 0 100 partof ATATCTTTGAGTTTTACGTTGCCAT 25 2R:1731127-2080000 -1 NULL:1985669 146686_at_3156 0 25 1 1 0 2601496 7155 7130 1 0 0 0 100 partof CGTTGCCATTGCTGTTGTTCCTGTC 25 2R:1731127-2080000 -1 NULL:1985671 146686_at_3140 0 25 1 1 0 2601499 7189 7164 1 0 0 0 100 partof CGCCGCCTTTTGGAAGTTCTCCTGA 25 2R:1731127-2080000 -1 NULL:1985673 146686_at_3106 0 25 1 1 0 2596322 78228 78203 1 0 0 0 100 partof ACGCAAGCGAGCTGGCAAGGAGTTC 25 2R:1731127-2080000 1 NULL:1981388 142557_at_1567 0 25 1 1 0 2596325 78246 78221 1 0 0 0 100 partof GGAGTTCAGCGAGGAAGAAGCCCAA 25 2R:1731127-2080000 1 NULL:1981390 142557_at_1585 0 25 1 1 0 2596328 78261 78236 1 0 0 0 100 partof AGAAGCCCAAAAGCTGAAGGCTCCC 25 2R:1731127-2080000 1 NULL:1981392 142557_at_1600 0 25 1 1 0 2602441 306019 305994 1 0 0 0 100 partof TTTTAAAACATGCTCTAATAGTGGC 25 2R:1731127-2080000 -1 NULL:1986301 141802_at_2504 0 25 1 1 0 2602444 306078 306053 1 0 0 0 100 partof CGTCAGTGAATCTCAAGAGAGTGGA 25 2R:1731127-2080000 -1 NULL:1986303 141802_at_2445 0 25 1 1 0 2602447 306140 306115 1 0 0 0 100 partof AAGTGGAGTTTAGCACATTAGCGCA 25 2R:1731127-2080000 -1 NULL:1986305 141802_at_2383 0 25 1 1 0 2596331 78282 78257 1 0 0 0 100 partof TCCCATTGTGGAAATGTTTGAGGCG 25 2R:1731127-2080000 1 NULL:1981394 142557_at_1621 0 25 1 1 0 2596334 78307 78282 1 0 0 0 100 partof GAGGGTTCGCCCTACTACAGTACGG 25 2R:1731127-2080000 1 NULL:1981396 142557_at_1646 0 25 1 1 0 2596337 78367 78342 1 0 0 0 100 partof AACACCCGTCAGATCCTGGGCCTTA 25 2R:1731127-2080000 1 NULL:1981398 142557_at_1706 0 25 1 1 0 2602450 306152 306127 1 0 0 0 100 partof GCACATTAGCGCAACGTATTAATCT 25 2R:1731127-2080000 -1 NULL:1986307 141802_at_2371 0 25 1 1 0 2602453 306183 306158 1 0 0 0 100 partof CGTTACGAATAAGTATTGGCGTTTC 25 2R:1731127-2080000 -1 NULL:1986309 141802_at_2340 0 25 1 1 0 2602456 339998 339973 1 0 0 0 100 partof GACTTGGGTTAGTGCGCAGGTTCCA 25 2R:1731127-2080000 -1 NULL:1986311 146708_at_408 0 25 1 1 0 2602459 340045 340020 1 0 0 0 100 partof AGGCGGGATACGTAATGCCGTAATC 25 2R:1731127-2080000 -1 NULL:1986313 146708_at_361 0 25 1 1 0 2596340 78447 78422 1 0 0 0 100 partof CATGTAAATCCAATTTGTATGCTGG 25 2R:1731127-2080000 1 NULL:1981400 142557_at_1786 0 25 1 1 0 2596343 78479 78454 1 0 0 0 100 partof TAATCGGAGCGCATTTACAGGCATT 25 2R:1731127-2080000 1 NULL:1981402 142557_at_1818 0 25 1 1 0 2596346 78495 78470 1 0 0 0 100 partof ACAGGCATTTAATGCCTTTATTTCG 25 2R:1731127-2080000 1 NULL:1981404 142557_at_1834 0 25 1 1 0 2596349 78523 78498 1 0 0 0 100 partof CTGTTGCATTTATTAGCGTTAAGGC 25 2R:1731127-2080000 1 NULL:1981406 142557_at_1862 0 25 1 1 0 2601802 86350 86325 1 0 0 0 100 partof GATCTTCAGGAACTCGTTCTTGTGC 25 2R:1731127-2080000 -1 NULL:1985875 142715_at_261 0 25 1 1 0 2601805 86369 86344 1 0 0 0 100 partof TTGTGCATTCCATCGCAGAGGGGCT 25 2R:1731127-2080000 -1 NULL:1985877 142715_at_242 0 25 1 1 0 2602462 340070 340045 1 0 0 0 100 partof AGCGAAGCCGTTCAAGCCGCAGCAC 25 2R:1731127-2080000 -1 NULL:1986315 146708_at_336 0 25 1 1 0 2601808 86393 86368 1 0 0 0 100 partof TGAGACTTGGACTTGCCGCACAGGC 25 2R:1731127-2080000 -1 NULL:1985879 142715_at_218 0 25 1 1 0 2602465 340255 340230 1 0 0 0 100 partof GAGGGCATCGGTCTTGCGTTGATCC 25 2R:1731127-2080000 -1 NULL:1986317 146708_at_282 0 25 1 1 0 2602468 340288 340263 1 0 0 0 100 partof CTGGACGATCTTCTCCAAAGATTGC 25 2R:1731127-2080000 -1 NULL:1986319 146708_at_249 0 25 1 1 0 2596352 78588 78563 1 0 0 0 100 partof AACAGGCGTGTGAAATCGTTCAAAG 25 2R:1731127-2080000 1 NULL:1981408 142557_at_1927 0 25 1 1 0 2596355 78599 78574 1 0 0 0 100 partof GAAATCGTTCAAAGCTTACGAAACA 25 2R:1731127-2080000 1 NULL:1981410 142557_at_1938 0 25 1 1 0 2596358 78647 78622 1 0 0 0 100 partof TAATTCCTGTGCAATAGAACAAATG 25 2R:1731127-2080000 1 NULL:1981412 142557_at_1986 0 25 1 1 0 2601811 86406 86381 1 0 0 0 100 partof TGCCGCACAGGCACCAGCTGTATGT 25 2R:1731127-2080000 -1 NULL:1985881 142715_at_205 0 25 1 1 0 2601814 86532 86507 1 0 0 0 100 partof AAGGGGCGCTTGTCGAAGATCGTAC 25 2R:1731127-2080000 -1 NULL:1985883 142715_at_155 0 25 1 1 0 2602471 340297 340272 1 0 0 0 100 partof CTTCTCCAAAGATTGCTGTATCTGC 25 2R:1731127-2080000 -1 NULL:1986321 146708_at_240 0 25 1 1 0 2601817 86562 86537 1 0 0 0 100 partof TCCTTTTGCAGAACGGCCGTTTGCT 25 2R:1731127-2080000 -1 NULL:1985885 142715_at_125 0 25 1 1 0 2602474 340311 340286 1 0 0 0 100 partof GCTGTATCTGCACATGGTCCACCCA 25 2R:1731127-2080000 -1 NULL:1986323 146708_at_226 0 25 1 1 0 2602477 340330 340305 1 0 0 0 100 partof CACCCACACGTAGATAATGAGAGCT 25 2R:1731127-2080000 -1 NULL:1986325 146708_at_207 0 25 1 1 0 2596361 85220 85195 1 0 0 0 100 partof TCGCCACGTGATTAAATAGTTATTC 25 2R:1731127-2080000 1 NULL:1981414 142558_s_at_1262 0 25 1 1 0 2596364 85247 85222 1 0 0 0 100 partof CAAACATTTATTTGATACGAACGCG 25 2R:1731127-2080000 1 NULL:1981416 142558_s_at_1289 0 25 1 1 0 2596367 85276 85251 1 0 0 0 100 partof CGCTTAACAGATAGAGACGGGATTT 25 2R:1731127-2080000 1 NULL:1981418 142558_s_at_1318 0 25 1 1 0 2601820 86579 86554 1 0 0 0 100 partof CGTTTGCTTATCCTCGAGCAGGTTA 25 2R:1731127-2080000 -1 NULL:1985887 142715_at_108 0 25 1 1 0 2601823 86624 86599 1 0 0 0 100 partof GTCCACCGGTTTTGCGCTGGAACTG 25 2R:1731127-2080000 -1 NULL:1985889 142715_at_63 0 25 1 1 0 2602480 340359 340334 1 0 0 0 100 partof GACTAACCAACAGCACCAGCATGAC 25 2R:1731127-2080000 -1 NULL:1986327 146708_at_178 0 25 1 1 0 2601826 86729 86704 1 0 0 0 100 partof CAGGATGCCCCCAGGTTCCGTCTTA 25 2R:1731127-2080000 -1 NULL:1985891 142715_at_20 0 25 1 1 0 2602483 340468 340443 1 0 0 0 100 partof CAGAGCACAGGAATTCTCGCGTATG 25 2R:1731127-2080000 -1 NULL:1986329 146708_at_138 0 25 1 1 0 2601829 87446 87421 1 0 0 0 100 partof GTGTCTTACGAACCTCTTCCAGTAA 25 2R:1731127-2080000 -1 NULL:1985893 142716_at_1232 0 25 1 1 0 2602486 340472 340447 1 0 0 0 100 partof GCACAGGAATTCTCGCGTATGGCGC 25 2R:1731127-2080000 -1 NULL:1986331 146708_at_134 0 25 1 1 0 2602489 340492 340467 1 0 0 0 100 partof GGCGCCGCAGCATCCCATGAAGGCT 25 2R:1731127-2080000 -1 NULL:1986333 146708_at_114 0 25 1 1 0 2596370 85318 85293 1 0 0 0 100 partof TACCCACGATAATTTTGCTGATGTT 25 2R:1731127-2080000 1 NULL:1981420 142558_s_at_1360 0 25 1 1 0 2596373 85349 85324 1 0 0 0 100 partof GTGTGTGAACCATCAACCATTTCAT 25 2R:1731127-2080000 1 NULL:1981422 142558_s_at_1391 0 25 1 1 0 2596376 85397 85372 1 0 0 0 100 partof GGAATAAACGAACCAAATCTCGATA 25 2R:1731127-2080000 1 NULL:1981424 142558_s_at_1439 0 25 1 1 0 2596379 85424 85399 1 0 0 0 100 partof TAATGGAAAGCCAGCCTACCCTTTT 25 2R:1731127-2080000 1 NULL:1981426 142558_s_at_1466 0 25 1 1 0 2601832 87543 87518 1 0 0 0 100 partof ACCCCTCTTGGAATGCCACAGTCGT 25 2R:1731127-2080000 -1 NULL:1985895 142716_at_1135 0 25 1 1 0 2601835 87544 87519 1 0 0 0 100 partof CCCCTCTTGGAATGCCACAGTCGTT 25 2R:1731127-2080000 -1 NULL:1985897 142716_at_1134 0 25 1 1 0 2602492 340525 340500 1 0 0 0 100 partof GACTACGCAGCCAAGGACCAGGATG 25 2R:1731127-2080000 -1 NULL:1986335 146708_at_81 0 25 1 1 0 2601838 87575 87550 1 0 0 0 100 partof GCATTCCTAGCCAATCCAATAACGG 25 2R:1731127-2080000 -1 NULL:1985899 142716_at_1103 0 25 1 1 0 2602495 340574 340549 1 0 0 0 100 partof AAGGTCTCGCCAACGCCCGAGAAGT 25 2R:1731127-2080000 -1 NULL:1986337 146708_at_32 0 25 1 1 0 2596382 85461 85436 1 0 0 0 100 partof TTGAAAGGTTCACAGACTCGTAACT 25 2R:1731127-2080000 1 NULL:1981428 142558_s_at_1503 0 25 1 1 0 2596385 85501 85476 1 0 0 0 100 partof GCTCAGCTTGCAAATTTACTTTGAT 25 2R:1731127-2080000 1 NULL:1981430 142558_s_at_1543 0 25 1 1 0 2596388 85523 85498 1 0 0 0 100 partof GATTTAGATTAGCTCTTTGTATCAC 25 2R:1731127-2080000 1 NULL:1981432 142558_s_at_1565 0 25 1 1 0 2601841 87662 87637 1 0 0 0 100 partof CTTATGGCCCGACATTCCCGAAAAG 25 2R:1731127-2080000 -1 NULL:1985901 142716_at_1016 0 25 1 1 0 2601844 87678 87653 1 0 0 0 100 partof CCCGAAAAGGGTACCGTGCGCTGCC 25 2R:1731127-2080000 -1 NULL:1985903 142716_at_1000 0 25 1 1 0 2601847 87694 87669 1 0 0 0 100 partof TGCGCTGCCCGGTGTGATACTGCTC 25 2R:1731127-2080000 -1 NULL:1985905 142716_at_984 0 25 1 1 0 2596391 85537 85512 1 0 0 0 100 partof CTTTGTATCACATGGTTTACATGGT 25 2R:1731127-2080000 1 NULL:1981434 142558_s_at_1579 0 25 1 1 0 2596394 85608 85583 1 0 0 0 100 partof ACTTTTCACTAGCTGACTTTTGTCG 25 2R:1731127-2080000 1 NULL:1981436 142558_s_at_1650 0 25 1 1 0 2596397 85616 85591 1 0 0 0 100 partof CTAGCTGACTTTTGTCGTTTTGAGT 25 2R:1731127-2080000 1 NULL:1981438 142558_s_at_1658 0 25 1 1 0 2601850 87740 87715 1 0 0 0 100 partof ACTCAGCTCGAAGTCGAAGACGCGG 25 2R:1731127-2080000 -1 NULL:1985907 142716_at_938 0 25 1 1 0 2601853 87759 87734 1 0 0 0 100 partof ACGCGGAAGTTCTCCTCGATGCGGG 25 2R:1731127-2080000 -1 NULL:1985909 142716_at_919 0 25 1 1 0 2601856 87844 87819 1 0 0 0 100 partof TCTGTGCCGTGGTGCGGCCGTACTT 25 2R:1731127-2080000 -1 NULL:1985911 142716_at_834 0 25 1 1 0 2601859 87878 87853 1 0 0 0 100 partof ATTCTGGGCATGCTCGTCGTAGAGG 25 2R:1731127-2080000 -1 NULL:1985913 142716_at_800 0 25 1 1 0 2601862 87943 87918 1 0 0 0 100 partof GGCAGTAGGCGCAGATGACCAGTCC 25 2R:1731127-2080000 -1 NULL:1985915 142716_at_735 0 25 1 1 0 2601865 87981 87956 1 0 0 0 100 partof TGCTCCCGGAGCTGGCGCTGCTGAA 25 2R:1731127-2080000 -1 NULL:1985917 142716_at_697 0 25 1 1 0 2601868 87998 87973 1 0 0 0 100 partof CTGCTGAAAGCCTGGGTGGCACTCC 25 2R:1731127-2080000 -1 NULL:1985919 142716_at_680 0 25 1 1 0 2601871 91753 91728 1 0 0 0 100 partof CCAAGTTGCCGTAAAAGGAGATGGG 25 2R:1731127-2080000 -1 NULL:1985921 151791_at_4247 0 25 1 1 0 2601874 91819 91794 1 0 0 0 100 partof TAAAGTAACTTATCCGCTACGTAGC 25 2R:1731127-2080000 -1 NULL:1985923 151791_at_4181 0 25 1 1 0 2601877 91858 91833 1 0 0 0 100 partof CTAGCTGTAACTAGACTGTTTAATA 25 2R:1731127-2080000 -1 NULL:1985925 151791_at_4142 0 25 1 1 0 2596702 216892 216867 1 0 0 0 100 partof ACTTCAAGGCCGACTGGCAGAGCAG 25 2R:1731127-2080000 1 NULL:1981642 146702_at_545 0 25 1 1 0 2596705 216923 216898 1 0 0 0 100 partof TGATTACGCCACTTACGCCAGCGAC 25 2R:1731127-2080000 1 NULL:1981644 146702_at_576 0 25 1 1 0 2596708 217084 217059 1 0 0 0 100 partof TCATCCTGCCTCAGGAGGAGCAGGG 25 2R:1731127-2080000 1 NULL:1981646 146702_at_737 0 25 1 1 0 2601880 91911 91886 1 0 0 0 100 partof TATAGATTCCATGCTCTCGAAAACG 25 2R:1731127-2080000 -1 NULL:1985927 151791_at_4089 0 25 1 1 0 2601883 91965 91940 1 0 0 0 100 partof CTCGCGCGGGATTTATAGAGTAATG 25 2R:1731127-2080000 -1 NULL:1985929 151791_at_4035 0 25 1 1 0 2601886 92030 92005 1 0 0 0 100 partof TGTTGCCTCCTATAAATGTTTAGTA 25 2R:1731127-2080000 -1 NULL:1985931 151791_at_3970 0 25 1 1 0 2601889 92052 92027 1 0 0 0 100 partof GTATCACACACGTCCAAGTTTAGTT 25 2R:1731127-2080000 -1 NULL:1985933 151791_at_3948 0 25 1 1 0 2596711 217105 217080 1 0 0 0 100 partof AGGGACTGGCCATCGTCGAGGAAAA 25 2R:1731127-2080000 1 NULL:1981648 146702_at_758 0 25 1 1 0 2596714 217190 217165 1 0 0 0 100 partof GCAGCTGCCCAAATTCAAATTCGAA 25 2R:1731127-2080000 1 NULL:1981650 146702_at_843 0 25 1 1 0 2596717 217216 217191 1 0 0 0 100 partof TTGATGTCCCTCTACAGGCAGCCCT 25 2R:1731127-2080000 1 NULL:1981652 146702_at_869 0 25 1 1 0 2601892 92092 92067 1 0 0 0 100 partof TTCCGCGGGGAATTGCCGAATTTCA 25 2R:1731127-2080000 -1 NULL:1985935 151791_at_3908 0 25 1 1 0 2601895 92093 92068 1 0 0 0 100 partof TCCGCGGGGAATTGCCGAATTTCAA 25 2R:1731127-2080000 -1 NULL:1985937 151791_at_3907 0 25 1 1 0 2601898 92153 92128 1 0 0 0 100 partof GCAAAAAGTTTCTCGTTTGCATTAA 25 2R:1731127-2080000 -1 NULL:1985939 151791_at_3847 0 25 1 1 0 2596720 217659 217634 1 0 0 0 100 partof CATTAAGAAACTGTTCTCTCCTGGG 25 2R:1731127-2080000 1 NULL:1981654 146702_at_906 0 25 1 1 0 2596723 217727 217702 1 0 0 0 100 partof TCTCGGAGGTGAAGCACAAGGCGAT 25 2R:1731127-2080000 1 NULL:1981656 146702_at_974 0 25 1 1 0 2596726 217762 217737 1 0 0 0 100 partof AACGAAAAGGGCACTACGGCCAGTG 25 2R:1731127-2080000 1 NULL:1981658 146702_at_1009 0 25 1 1 0 2596729 217764 217739 1 0 0 0 100 partof CGAAAAGGGCACTACGGCCAGTGGA 25 2R:1731127-2080000 1 NULL:1981660 146702_at_1011 0 25 1 1 0 2596732 217865 217840 1 0 0 0 100 partof AAGGTCTCGGTGGAGTCGCTTACGA 25 2R:1731127-2080000 1 NULL:1981662 146702_at_1048 0 25 1 1 0 2596735 217868 217843 1 0 0 0 100 partof GTCTCGGTGGAGTCGCTTACGATTG 25 2R:1731127-2080000 1 NULL:1981664 146702_at_1051 0 25 1 1 0 2596738 217898 217873 1 0 0 0 100 partof GAAGTATTCGAGTTCATCGCGGATC 25 2R:1731127-2080000 1 NULL:1981666 146702_at_1081 0 25 1 1 0 2596741 239774 239749 1 0 0 0 100 partof ATGCGGCGCCTGTCCATCGCAACGG 25 2R:1731127-2080000 1 NULL:1981668 146703_at_28 0 25 1 1 0 2596744 239807 239782 1 0 0 0 100 partof TTCATGCTCGTCTACGCGGCCACAT 25 2R:1731127-2080000 1 NULL:1981670 146703_at_61 0 25 1 1 0 2596747 239833 239808 1 0 0 0 100 partof CGCGCCCAGCTTCCAGTGTGTGAAG 25 2R:1731127-2080000 1 NULL:1981672 146703_at_87 0 25 1 1 0 2596750 239834 239809 1 0 0 0 100 partof GCGCCCAGCTTCCAGTGTGTGAAGC 25 2R:1731127-2080000 1 NULL:1981674 146703_at_88 0 25 1 1 0 2596753 239837 239812 1 0 0 0 100 partof CCCAGCTTCCAGTGTGTGAAGCAGT 25 2R:1731127-2080000 1 NULL:1981676 146703_at_91 0 25 1 1 0 2596756 239840 239815 1 0 0 0 100 partof AGCTTCCAGTGTGTGAAGCAGTGCT 25 2R:1731127-2080000 1 NULL:1981678 146703_at_94 0 25 1 1 0 2596759 239841 239816 1 0 0 0 100 partof GCTTCCAGTGTGTGAAGCAGTGCTT 25 2R:1731127-2080000 1 NULL:1981680 146703_at_95 0 25 1 1 0 2596762 239843 239818 1 0 0 0 100 partof TTCCAGTGTGTGAAGCAGTGCTTCG 25 2R:1731127-2080000 1 NULL:1981682 146703_at_97 0 25 1 1 0 2596765 239858 239833 1 0 0 0 100 partof CAGTGCTTCGAGGAGATCCGCGAGC 25 2R:1731127-2080000 1 NULL:1981684 146703_at_112 0 25 1 1 0 2596768 240563 240538 1 0 0 0 100 partof GTGATCGCCGGGAACAAGGCCGACC 25 2R:1731127-2080000 1 NULL:1981686 146703_at_166 0 25 1 1 0 2596771 240566 240541 1 0 0 0 100 partof ATCGCCGGGAACAAGGCCGACCTGG 25 2R:1731127-2080000 1 NULL:1981688 146703_at_169 0 25 1 1 0 2596774 240567 240542 1 0 0 0 100 partof TCGCCGGGAACAAGGCCGACCTGGC 25 2R:1731127-2080000 1 NULL:1981690 146703_at_170 0 25 1 1 0 2596777 240595 240570 1 0 0 0 100 partof CACCCACAGAGAGGTCAAGCTGGAG 25 2R:1731127-2080000 1 NULL:1981692 146703_at_198 0 25 1 1 0 2596780 240597 240572 1 0 0 0 100 partof CCCACAGAGAGGTCAAGCTGGAGGA 25 2R:1731127-2080000 1 NULL:1981694 146703_at_200 0 25 1 1 0 2596783 244210 244185 1 0 0 0 100 partof GCACAAAAACTCTGTTTCGCATTGA 25 2R:1731127-2080000 1 NULL:1981696 151152_at_35 0 25 1 1 0 2596786 244446 244421 1 0 0 0 100 partof AGTGCTCCGCGAAGGAGGACAGCAA 25 2R:1731127-2080000 1 NULL:1981698 151152_at_86 0 25 1 1 0 2602102 168323 168298 1 0 0 0 100 partof TTCCTCTTATGATGGCTCATACATG 25 2R:1731127-2080000 -1 NULL:1986075 151151_at_368 0 25 1 1 0 2596789 244448 244423 1 0 0 0 100 partof TGCTCCGCGAAGGAGGACAGCAACG 25 2R:1731127-2080000 1 NULL:1981700 151152_at_88 0 25 1 1 0 2602105 168340 168315 1 0 0 0 100 partof CATACATGGGTGCTATTTACTAAAG 25 2R:1731127-2080000 -1 NULL:1986077 151151_at_351 0 25 1 1 0 2602108 168377 168352 1 0 0 0 100 partof CTTTCCATCCTGCTAGTCGTCTTCG 25 2R:1731127-2080000 -1 NULL:1986079 151151_at_314 0 25 1 1 0 2596792 244459 244434 1 0 0 0 100 partof GGAGGACAGCAACGTGACGGACCTC 25 2R:1731127-2080000 1 NULL:1981702 151152_at_99 0 25 1 1 0 2596795 244463 244438 1 0 0 0 100 partof GACAGCAACGTGACGGACCTCTTCA 25 2R:1731127-2080000 1 NULL:1981704 151152_at_103 0 25 1 1 0 2602111 168495 168470 1 0 0 0 100 partof TCGGGTCCTTGCAGCATGGCCGTCG 25 2R:1731127-2080000 -1 NULL:1986081 151151_at_196 0 25 1 1 0 2596798 244467 244442 1 0 0 0 100 partof GCAACGTGACGGACCTCTTCAAGTC 25 2R:1731127-2080000 1 NULL:1981706 151152_at_107 0 25 1 1 0 2602114 168540 168515 1 0 0 0 100 partof AAGGCTTCGCGCTGCCTGCCCAAGG 25 2R:1731127-2080000 -1 NULL:1986083 151151_at_151 0 25 1 1 0 2602117 168590 168565 1 0 0 0 100 partof TCCTCCGTCCATCTTAGTGGGTCCG 25 2R:1731127-2080000 -1 NULL:1986085 151151_at_101 0 25 1 1 0 2602120 168595 168570 1 0 0 0 100 partof CGTCCATCTTAGTGGGTCCGGTGCA 25 2R:1731127-2080000 -1 NULL:1986087 151151_at_96 0 25 1 1 0 2602123 192933 192908 1 0 0 0 100 partof AGACGTGGCTGCTCCCGCTGAAGCC 25 2R:1731127-2080000 -1 NULL:1986089 146698_at_1796 0 25 1 1 0 2602126 192952 192927 1 0 0 0 100 partof GAAGCCGGCGCAGCATCGCTTCCAT 25 2R:1731127-2080000 -1 NULL:1986091 146698_at_1777 0 25 1 1 0 2602129 192965 192940 1 0 0 0 100 partof CATCGCTTCCATTCTTGTTGCGGGC 25 2R:1731127-2080000 -1 NULL:1986093 146698_at_1764 0 25 1 1 0 2602132 192980 192955 1 0 0 0 100 partof TGTTGCGGGCGTCCTCCTTGGCCTC 25 2R:1731127-2080000 -1 NULL:1986095 146698_at_1749 0 25 1 1 0 2602135 192994 192969 1 0 0 0 100 partof TCCTTGGCCTCCAGAGCGCGGATGC 25 2R:1731127-2080000 -1 NULL:1986097 146698_at_1735 0 25 1 1 0 2602138 193059 193034 1 0 0 0 100 partof CTCGTCTTGTATGGTGCGCAGGTCC 25 2R:1731127-2080000 -1 NULL:1986099 146698_at_1670 0 25 1 1 0 2602141 193157 193132 1 0 0 0 100 partof GCTGCAGGCGGTCCACCTTCGCTAG 25 2R:1731127-2080000 -1 NULL:1986101 146698_at_1630 0 25 1 1 0 2602144 193181 193156 1 0 0 0 100 partof GCCTCATTGTTATTTCCGGACGCAA 25 2R:1731127-2080000 -1 NULL:1986103 146698_at_1606 0 25 1 1 0 2602147 193188 193163 1 0 0 0 100 partof TGTTATTTCCGGACGCAAAGTTGCC 25 2R:1731127-2080000 -1 NULL:1986105 146698_at_1599 0 25 1 1 0 2602150 193219 193194 1 0 0 0 100 partof CGCGCTGCTGCTCGTTGCACCGGAG 25 2R:1731127-2080000 -1 NULL:1986107 146698_at_1568 0 25 1 1 0 2602153 193302 193277 1 0 0 0 100 partof ATTTGTTTACCGACGAGGACACGTA 25 2R:1731127-2080000 -1 NULL:1986109 146698_at_1485 0 25 1 1 0 2602156 194086 194061 1 0 0 0 100 partof AAATGTGATCGGATCCGCATCCTTG 25 2R:1731127-2080000 -1 NULL:1986111 146698_at_1445 0 25 1 1 0 2602159 194087 194062 1 0 0 0 100 partof AATGTGATCGGATCCGCATCCTTGC 25 2R:1731127-2080000 -1 NULL:1986113 146698_at_1444 0 25 1 1 0 2601502 7295 7270 1 0 0 0 100 partof ATGCTGCGAGTGAAGGAGAATCGCA 25 2R:1731127-2080000 -1 NULL:1985675 146686_at_3000 0 25 1 1 0 2601505 7342 7317 1 0 0 0 100 partof CTTTTTGATGGGTGGCTTGCCCGCC 25 2R:1731127-2080000 -1 NULL:1985677 146686_at_2953 0 25 1 1 0 2602162 194113 194088 1 0 0 0 100 partof ATCGATCCACTCCTCCGCGGTGATG 25 2R:1731127-2080000 -1 NULL:1986115 146698_at_1418 0 25 1 1 0 2601508 7365 7340 1 0 0 0 100 partof CCACTGGAGCCAATGGCTCTGAGCT 25 2R:1731127-2080000 -1 NULL:1985679 146686_at_2930 0 25 1 1 0 2602165 204177 204152 1 0 0 0 100 partof CTCCGTAAGATGTCGCCAAAAGGGT 25 2R:1731127-2080000 -1 NULL:1986117 142388_at_894 0 25 1 1 0 2602168 204193 204168 1 0 0 0 100 partof CAAAAGGGTCCGTTTTGAAGGCGCA 25 2R:1731127-2080000 -1 NULL:1986119 142388_at_878 0 25 1 1 0 2601511 7394 7369 1 0 0 0 100 partof CGCTCTGAGCCTTCCGGCGTGGTTG 25 2R:1731127-2080000 -1 NULL:1985681 146686_at_2901 0 25 1 1 0 2601514 7415 7390 1 0 0 0 100 partof GTTGGCACGGAGCTGGACTCCAGCT 25 2R:1731127-2080000 -1 NULL:1985683 146686_at_2880 0 25 1 1 0 2602171 204228 204203 1 0 0 0 100 partof TCCATTGAACAGGATGAGAGCGAGA 25 2R:1731127-2080000 -1 NULL:1986121 142388_at_843 0 25 1 1 0 2601517 7503 7478 1 0 0 0 100 partof TCTCAGTGGCGTGCTCGTAGGTGAC 25 2R:1731127-2080000 -1 NULL:1985685 146686_at_2792 0 25 1 1 0 2602174 204253 204228 1 0 0 0 100 partof AGCGATGGCAGAAGTCTAAAGTATC 25 2R:1731127-2080000 -1 NULL:1986123 142388_at_818 0 25 1 1 0 2602177 204323 204298 1 0 0 0 100 partof CAGTCTTGGGTTGAATCTGTTGGCG 25 2R:1731127-2080000 -1 NULL:1986125 142388_at_748 0 25 1 1 0 2597002 318524 318499 1 0 0 0 100 partof CGCCTCCTGGTCAGCAGATGCATTA 25 2R:1731127-2080000 1 NULL:1981850 154950_at_1613 0 25 1 1 0 2597005 318554 318529 1 0 0 0 100 partof GGCGATTGTACTAGCCTCTAACCCC 25 2R:1731127-2080000 1 NULL:1981852 154950_at_1643 0 25 1 1 0 2597008 318583 318558 1 0 0 0 100 partof CCCTTTTGTCGCTACGGAACTCGCT 25 2R:1731127-2080000 1 NULL:1981854 154950_at_1672 0 25 1 1 0 2596067 4217 4192 1 0 0 0 100 partof GTGTTATCACGTTGGCATTCCTCTC 25 2R:1731127-2080000 1 NULL:1981218 155070_at_655 0 25 1 1 0 2601520 7518 7493 1 0 0 0 100 partof CGTAGGTGACGCAGAAGCGGATCAC 25 2R:1731127-2080000 -1 NULL:1985687 146686_at_2777 0 25 1 1 0 2601523 7578 7553 1 0 0 0 100 partof TCTTGCCCGAGTGGTTGATCTGGGC 25 2R:1731127-2080000 -1 NULL:1985689 146686_at_2717 0 25 1 1 0 2602180 204338 204313 1 0 0 0 100 partof TCTGTTGGCGTTTGGTGAATTTCAC 25 2R:1731127-2080000 -1 NULL:1986127 142388_at_733 0 25 1 1 0 2601526 7762 7737 1 0 0 0 100 partof CGGAAGCAAACTAGGCCAAGGTGAA 25 2R:1731127-2080000 -1 NULL:1985691 146686_at_2655 0 25 1 1 0 2602183 204339 204314 1 0 0 0 100 partof CTGTTGGCGTTTGGTGAATTTCACG 25 2R:1731127-2080000 -1 NULL:1986129 142388_at_732 0 25 1 1 0 2601529 7805 7780 1 0 0 0 100 partof ATCGTTCATCCTTGCGCACCAGCAT 25 2R:1731127-2080000 -1 NULL:1985693 146686_at_2612 0 25 1 1 0 2602186 204353 204328 1 0 0 0 100 partof TGAATTTCACGTAGAGAAGGAAGCC 25 2R:1731127-2080000 -1 NULL:1986131 142388_at_718 0 25 1 1 0 2602189 204362 204337 1 0 0 0 100 partof CGTAGAGAAGGAAGCCGCTCATAAC 25 2R:1731127-2080000 -1 NULL:1986133 142388_at_709 0 25 1 1 0 2597011 318599 318574 1 0 0 0 100 partof GAACTCGCTAACTGATATACTTACG 25 2R:1731127-2080000 1 NULL:1981856 154950_at_1688 0 25 1 1 0 2597014 318644 318619 1 0 0 0 100 partof CACTGACTACGCTTCCCACGTGAAG 25 2R:1731127-2080000 1 NULL:1981858 154950_at_1733 0 25 1 1 0 2597017 323510 323485 1 0 0 0 100 partof AGGTGGAGCAGACCACAGCGGAAAA 25 2R:1731127-2080000 1 NULL:1981860 152700_at_952 0 25 1 1 0 2596070 4252 4227 1 0 0 0 100 partof AACTACTTTGCCTACCTGAGCGTGG 25 2R:1731127-2080000 1 NULL:1981220 155070_at_690 0 25 1 1 0 2596073 4296 4271 1 0 0 0 100 partof CAACATGATGGTAAACGTGGCTACG 25 2R:1731127-2080000 1 NULL:1981222 155070_at_734 0 25 1 1 0 2596076 4342 4317 1 0 0 0 100 partof TGGTTCGTTTGGTGTCACTTTGTGC 25 2R:1731127-2080000 1 NULL:1981224 155070_at_780 0 25 1 1 0 2596079 4352 4327 1 0 0 0 100 partof GGTGTCACTTTGTGCGCACCCGCAG 25 2R:1731127-2080000 1 NULL:1981226 155070_at_790 0 25 1 1 0 2601532 7840 7815 1 0 0 0 100 partof TTAGCCAACGCCATATGATTTCGAA 25 2R:1731127-2080000 -1 NULL:1985695 146686_at_2577 0 25 1 1 0 2601535 25012 24987 1 0 0 0 100 partof CTGCCAGTAGTCAAGGGAATTTAGT 25 2R:1731127-2080000 -1 NULL:1985697 153993_at_1267 0 25 1 1 0 2602192 204388 204363 1 0 0 0 100 partof AAAAATATCTGGATGACCAGGCTGC 25 2R:1731127-2080000 -1 NULL:1986135 142388_at_683 0 25 1 1 0 2601538 25043 25018 1 0 0 0 100 partof TACGGGGATTTGACGTGGAATCAGC 25 2R:1731127-2080000 -1 NULL:1985699 153993_at_1236 0 25 1 1 0 2602195 204504 204479 1 0 0 0 100 partof GTGGCCCAAGATCACTACAAATACG 25 2R:1731127-2080000 -1 NULL:1986137 142388_at_567 0 25 1 1 0 2602198 204537 204512 1 0 0 0 100 partof CCGAAACCCGTCGAAAAAGCTCACA 25 2R:1731127-2080000 -1 NULL:1986139 142388_at_534 0 25 1 1 0 2597020 323519 323494 1 0 0 0 100 partof AGACCACAGCGGAAAAGGAGGCCTG 25 2R:1731127-2080000 1 NULL:1981862 152700_at_961 0 25 1 1 0 2597023 323572 323547 1 0 0 0 100 partof ATCTGGCGCCGCTACAACGAACTGA 25 2R:1731127-2080000 1 NULL:1981864 152700_at_1014 0 25 1 1 0 2597026 323588 323563 1 0 0 0 100 partof ACGAACTGAGGCAGCGCTGGTTGCC 25 2R:1731127-2080000 1 NULL:1981866 152700_at_1030 0 25 1 1 0 2597029 323612 323587 1 0 0 0 100 partof CCAAGGAGAAGCTGCTGCCGGAGCT 25 2R:1731127-2080000 1 NULL:1981868 152700_at_1054 0 25 1 1 0 2596082 4370 4345 1 0 0 0 100 partof CCCGCAGGCCCTACTTTAGAAGGAT 25 2R:1731127-2080000 1 NULL:1981228 155070_at_808 0 25 1 1 0 2596085 4494 4469 1 0 0 0 100 partof GGCAACAATTCCTCTGGCATCCCTA 25 2R:1731127-2080000 1 NULL:1981230 155070_at_932 0 25 1 1 0 2596088 4587 4562 1 0 0 0 100 partof ATAGAGGACTGTCGAACCCTGCGAA 25 2R:1731127-2080000 1 NULL:1981232 155070_at_972 0 25 1 1 0 2601541 25071 25046 1 0 0 0 100 partof GAGAAGGTCGTGTGCCTACATATAA 25 2R:1731127-2080000 -1 NULL:1985701 153993_at_1208 0 25 1 1 0 2601544 25129 25104 1 0 0 0 100 partof TATAACTTGCGAAATAATTGCTGAC 25 2R:1731127-2080000 -1 NULL:1985703 153993_at_1150 0 25 1 1 0 2601547 25146 25121 1 0 0 0 100 partof TTGCTGACTTAGGATCAGATGGGGC 25 2R:1731127-2080000 -1 NULL:1985705 153993_at_1133 0 25 1 1 0 2597032 323713 323688 1 0 0 0 100 partof GTTCCATGGCCAGCTACTCTCTATA 25 2R:1731127-2080000 1 NULL:1981870 152700_at_1155 0 25 1 1 0 2597035 323742 323717 1 0 0 0 100 partof TATTATGCCTGTTTACTAGCTTGTG 25 2R:1731127-2080000 1 NULL:1981872 152700_at_1184 0 25 1 1 0 2597038 323790 323765 1 0 0 0 100 partof CTATCTATTGTTATACGATTGGCAA 25 2R:1731127-2080000 1 NULL:1981874 152700_at_1232 0 25 1 1 0 2596091 4594 4569 1 0 0 0 100 partof ACTGTCGAACCCTGCGAAAGGAGAA 25 2R:1731127-2080000 1 NULL:1981234 155070_at_979 0 25 1 1 0 2596094 4627 4602 1 0 0 0 100 partof CGGGCGGCTATTCATTCTACAATTA 25 2R:1731127-2080000 1 NULL:1981236 155070_at_1012 0 25 1 1 0 2596097 4630 4605 1 0 0 0 100 partof GCGGCTATTCATTCTACAATTAGTA 25 2R:1731127-2080000 1 NULL:1981238 155070_at_1015 0 25 1 1 0 2601550 25198 25173 1 0 0 0 100 partof TTACTTAGTTATCGTTATGTAGCTC 25 2R:1731127-2080000 -1 NULL:1985707 153993_at_1081 0 25 1 1 0 2601553 25215 25190 1 0 0 0 100 partof TGTAGCTCTATGTGTATCTGACATC 25 2R:1731127-2080000 -1 NULL:1985709 153993_at_1064 0 25 1 1 0 2601556 25243 25218 1 0 0 0 100 partof ACTACATACAAGATCTGCATTAGAG 25 2R:1731127-2080000 -1 NULL:1985711 153993_at_1036 0 25 1 1 0 2601559 25311 25286 1 0 0 0 100 partof CAACTTGCAAGCTATTGGTAAATAT 25 2R:1731127-2080000 -1 NULL:1985713 153993_at_968 0 25 1 1 0 2597041 323836 323811 1 0 0 0 100 partof AGCATTTGTTTACAAACCCTCGAGC 25 2R:1731127-2080000 1 NULL:1981876 152700_at_1278 0 25 1 1 0 2597044 323875 323850 1 0 0 0 100 partof CAGTCTCAAAAGCTTATTAGTAAGG 25 2R:1731127-2080000 1 NULL:1981878 152700_at_1317 0 25 1 1 0 2597047 323903 323878 1 0 0 0 100 partof ATAGCTAGCGCGACTTGCCCAACGC 25 2R:1731127-2080000 1 NULL:1981880 152700_at_1345 0 25 1 1 0 2601562 25352 25327 1 0 0 0 100 partof AATGAGTGTTTCATGCGAGTCTGAC 25 2R:1731127-2080000 -1 NULL:1985715 153993_at_927 0 25 1 1 0 2601565 25364 25339 1 0 0 0 100 partof ATGCGAGTCTGACTAATCTGGGCGG 25 2R:1731127-2080000 -1 NULL:1985717 153993_at_915 0 25 1 1 0 2601568 25384 25359 1 0 0 0 100 partof GGCGGGCTCCTAAGCCTCGCTTTCG 25 2R:1731127-2080000 -1 NULL:1985719 153993_at_895 0 25 1 1 0 2597050 323970 323945 1 0 0 0 100 partof CACACCCAGTAGAGCCAAGAACGTC 25 2R:1731127-2080000 1 NULL:1981882 152700_at_1412 0 25 1 1 0 2597053 323981 323956 1 0 0 0 100 partof GAGCCAAGAACGTCAGCATTTTTTA 25 2R:1731127-2080000 1 NULL:1981884 152700_at_1423 0 25 1 1 0 2597056 324019 323994 1 0 0 0 100 partof GCGAAATGTTTTTACCACGGATGAC 25 2R:1731127-2080000 1 NULL:1981886 152700_at_1461 0 25 1 1 0 2597059 331283 331258 1 0 0 0 100 partof ATCTGAGCCGCTTCGATGTCGCGGG 25 2R:1731127-2080000 1 NULL:1981888 146707_at_23 0 25 1 1 0 2601571 25432 25407 1 0 0 0 100 partof GTTGATGGGCACGATCAGATTCTCC 25 2R:1731127-2080000 -1 NULL:1985721 153993_at_847 0 25 1 1 0 2601574 25479 25454 1 0 0 0 100 partof TGACGAAATGCGTGAAACGGTGGCA 25 2R:1731127-2080000 -1 NULL:1985723 153993_at_800 0 25 1 1 0 2601577 30143 30118 1 0 0 0 100 partof CAGTGATGCACTGCATTGATATTGA 25 2R:1731127-2080000 -1 NULL:1985725 154552_at_3002 0 25 1 1 0 2596400 85649 85624 1 0 0 0 100 partof TAGTGGATCACAAGAGCCGAACCAA 25 2R:1731127-2080000 1 NULL:1981440 142558_s_at_1691 0 25 1 1 0 2596403 87423 87398 1 0 0 0 100 partof AATACAAATACTACATATGCGGGGT 25 2R:1731127-2080000 1 NULL:1981442 142004_at_36 0 25 1 1 0 2596406 87443 87418 1 0 0 0 100 partof GGGGTGTCTTACGAACCTCTTCCAG 25 2R:1731127-2080000 1 NULL:1981444 142004_at_56 0 25 1 1 0 2597062 337625 337600 1 0 0 0 100 partof TCTGCGTCACCGTCCTGGGAGGCCT 25 2R:1731127-2080000 1 NULL:1981890 146707_at_77 0 25 1 1 0 2596409 87446 87421 1 0 0 0 100 partof GTGTCTTACGAACCTCTTCCAGTAA 25 2R:1731127-2080000 1 NULL:1981446 142004_at_59 0 25 1 1 0 2597065 337686 337661 1 0 0 0 100 partof TTTTCGGCAGAGTGTCTGCATGACC 25 2R:1731127-2080000 1 NULL:1981892 146707_at_138 0 25 1 1 0 2597068 337785 337760 1 0 0 0 100 partof CAGCATGGTTTTTGTGCTCTTTATC 25 2R:1731127-2080000 1 NULL:1981894 146707_at_174 0 25 1 1 0 2601580 30176 30151 1 0 0 0 100 partof GAACAGTTTGTCTAGACAAAGATGC 25 2R:1731127-2080000 -1 NULL:1985727 154552_at_2969 0 25 1 1 0 2601583 30213 30188 1 0 0 0 100 partof CCCTAGTGCGGTAAGTATATGTTAG 25 2R:1731127-2080000 -1 NULL:1985729 154552_at_2932 0 25 1 1 0 2601586 30243 30218 1 0 0 0 100 partof TATTGATACTTAGCTACGATTAGTC 25 2R:1731127-2080000 -1 NULL:1985731 154552_at_2902 0 25 1 1 0 2601589 30286 30261 1 0 0 0 100 partof CAGGCTAGAGCTTAGGAATAGGCTT 25 2R:1731127-2080000 -1 NULL:1985733 154552_at_2859 0 25 1 1 0 2596412 87486 87461 1 0 0 0 100 partof TAATGCACGGGTTTACTCGAAACCT 25 2R:1731127-2080000 1 NULL:1981448 142004_at_99 0 25 1 1 0 2596415 87543 87518 1 0 0 0 100 partof ACCCCTCTTGGAATGCCACAGTCGT 25 2R:1731127-2080000 1 NULL:1981450 142004_at_156 0 25 1 1 0 2597071 337949 337924 1 0 0 0 100 partof GTGATACGAGCTATACCAACTACAA 25 2R:1731127-2080000 1 NULL:1981896 146707_at_338 0 25 1 1 0 2596418 87549 87524 1 0 0 0 100 partof CTTGGAATGCCACAGTCGTTTTGTT 25 2R:1731127-2080000 1 NULL:1981452 142004_at_162 0 25 1 1 0 2597074 337966 337941 1 0 0 0 100 partof AACTACAACAACATCGGCCTTTCGG 25 2R:1731127-2080000 1 NULL:1981898 146707_at_355 0 25 1 1 0 2597077 337967 337942 1 0 0 0 100 partof ACTACAACAACATCGGCCTTTCGGT 25 2R:1731127-2080000 1 NULL:1981900 146707_at_356 0 25 1 1 0 2601592 30321 30296 1 0 0 0 100 partof ACAATTCTGCTCTGATTTTATGGCT 25 2R:1731127-2080000 -1 NULL:1985735 154552_at_2824 0 25 1 1 0 2601595 30343 30318 1 0 0 0 100 partof GCTGCAACACCATTTGACATAAGAA 25 2R:1731127-2080000 -1 NULL:1985737 154552_at_2802 0 25 1 1 0 2601598 30390 30365 1 0 0 0 100 partof TCCATTATTATGCTACAGTTCGGAT 25 2R:1731127-2080000 -1 NULL:1985739 154552_at_2755 0 25 1 1 0 2596421 87575 87550 1 0 0 0 100 partof GCATTCCTAGCCAATCCAATAACGG 25 2R:1731127-2080000 1 NULL:1981454 142004_at_188 0 25 1 1 0 2596424 87591 87566 1 0 0 0 100 partof CAATAACGGCGAAACCGATATTTCT 25 2R:1731127-2080000 1 NULL:1981456 142004_at_204 0 25 1 1 0 2597080 337989 337964 1 0 0 0 100 partof GGTTCCCGGAACCTGCTGCGGCTAC 25 2R:1731127-2080000 1 NULL:1981902 146707_at_378 0 25 1 1 0 2596427 87615 87590 1 0 0 0 100 partof TGGGACACCCCTGAGCCCGTCTAGA 25 2R:1731127-2080000 1 NULL:1981458 142004_at_228 0 25 1 1 0 2597083 338002 337977 1 0 0 0 100 partof TGCTGCGGCTACCTGGACCGCCAGG 25 2R:1731127-2080000 1 NULL:1981904 146707_at_391 0 25 1 1 0 2597086 338044 338019 1 0 0 0 100 partof TCGGTCTACCAGTCGAGGCCCGGCT 25 2R:1731127-2080000 1 NULL:1981906 146707_at_433 0 25 1 1 0 2597089 338046 338021 1 0 0 0 100 partof GGTCTACCAGTCGAGGCCCGGCTGC 25 2R:1731127-2080000 1 NULL:1981908 146707_at_435 0 25 1 1 0 2596430 87636 87611 1 0 0 0 100 partof TAGAACTCGTCGTTGAACGGGTAGT 25 2R:1731127-2080000 1 NULL:1981460 142004_at_249 0 25 1 1 0 2596433 87645 87620 1 0 0 0 100 partof TCGTTGAACGGGTAGTACTTATGGC 25 2R:1731127-2080000 1 NULL:1981462 142004_at_258 0 25 1 1 0 2596436 87664 87639 1 0 0 0 100 partof TATGGCCCGACATTCCCGAAAAGGG 25 2R:1731127-2080000 1 NULL:1981464 142004_at_277 0 25 1 1 0 2597092 338059 338034 1 0 0 0 100 partof AGGCCCGGCTGCAGCGCCAAGTTCG 25 2R:1731127-2080000 1 NULL:1981910 146707_at_448 0 25 1 1 0 2596439 87677 87652 1 0 0 0 100 partof TCCCGAAAAGGGTACCGTGCGCTGC 25 2R:1731127-2080000 1 NULL:1981466 142004_at_290 0 25 1 1 0 2597095 338102 338077 1 0 0 0 100 partof ACATGGACATCATCCGCTGGTCCGG 25 2R:1731127-2080000 1 NULL:1981912 146707_at_491 0 25 1 1 0 2597098 338129 338104 1 0 0 0 100 partof TCGGCCTCTGCATCTTCGACCTGGT 25 2R:1731127-2080000 1 NULL:1981914 146707_at_518 0 25 1 1 0 2596442 87694 87669 1 0 0 0 100 partof TGCGCTGCCCGGTGTGATACTGCTC 25 2R:1731127-2080000 1 NULL:1981468 142004_at_307 0 25 1 1 0 2596445 138279 138254 1 0 0 0 100 partof AACTTCTACGAGCAGTACCGCAACA 25 2R:1731127-2080000 1 NULL:1981470 154195_at_595 0 25 1 1 0 2596448 138403 138378 1 0 0 0 100 partof GGGCAAGGCCCAGTACCTGCAGTCC 25 2R:1731127-2080000 1 NULL:1981472 154195_at_663 0 25 1 1 0 2601901 92164 92139 1 0 0 0 100 partof CTCGTTTGCATTAAAATGCGTTTGG 25 2R:1731127-2080000 -1 NULL:1985941 151791_at_3836 0 25 1 1 0 2601904 92206 92181 1 0 0 0 100 partof GATTGAGATAGTTCCTAGTCGGGTC 25 2R:1731127-2080000 -1 NULL:1985943 151791_at_3794 0 25 1 1 0 2601907 92246 92221 1 0 0 0 100 partof TGTAGCTTAGGCTAATGCGGATGCG 25 2R:1731127-2080000 -1 NULL:1985945 151791_at_3754 0 25 1 1 0 2596451 138438 138413 1 0 0 0 100 partof GCTCCAAGTTGGACGGCCTGTACGA 25 2R:1731127-2080000 1 NULL:1981474 154195_at_698 0 25 1 1 0 2596454 138491 138466 1 0 0 0 100 partof TCGTGCCCCTCGTACTGGTGGAACG 25 2R:1731127-2080000 1 NULL:1981476 154195_at_751 0 25 1 1 0 2596457 138509 138484 1 0 0 0 100 partof TGGAACGCCGAGAAGTACCTGGGCC 25 2R:1731127-2080000 1 NULL:1981478 154195_at_769 0 25 1 1 0 2601910 92301 92276 1 0 0 0 100 partof TGGCCGTGGCCCAATTGGCTTTCGG 25 2R:1731127-2080000 -1 NULL:1985947 151791_at_3699 0 25 1 1 0 2601913 109630 109605 1 0 0 0 100 partof CGAATATGGAGGTTAGATGCGTTCC 25 2R:1731127-2080000 -1 NULL:1985949 143127_at_1544 0 25 1 1 0 2601916 109645 109620 1 0 0 0 100 partof GATGCGTTCCACTCGCAAGTAGATG 25 2R:1731127-2080000 -1 NULL:1985951 143127_at_1529 0 25 1 1 0 2601919 109673 109648 1 0 0 0 100 partof CCAACGGTGCCCAAAACTATGGACA 25 2R:1731127-2080000 -1 NULL:1985953 143127_at_1501 0 25 1 1 0 2596460 138550 138525 1 0 0 0 100 partof GGCCTACCGCTGGATCATCGACTCG 25 2R:1731127-2080000 1 NULL:1981480 154195_at_810 0 25 1 1 0 2596463 138641 138616 1 0 0 0 100 partof ACGATCATGAACTGCACGCGCACCT 25 2R:1731127-2080000 1 NULL:1981482 154195_at_901 0 25 1 1 0 2596466 138690 138665 1 0 0 0 100 partof GTGCCATCGCCGAGATCAAGAAGCT 25 2R:1731127-2080000 1 NULL:1981484 154195_at_950 0 25 1 1 0 2596469 138705 138680 1 0 0 0 100 partof TCAAGAAGCTGCTCTCGGGCCTGGC 25 2R:1731127-2080000 1 NULL:1981486 154195_at_965 0 25 1 1 0 2601922 109763 109738 1 0 0 0 100 partof TGAGCCAAACCGATGCGAGCCTGCA 25 2R:1731127-2080000 -1 NULL:1985955 143127_at_1411 0 25 1 1 0 2601925 109856 109831 1 0 0 0 100 partof CGGGCGGCCACTTTCTCCGGCGAGA 25 2R:1731127-2080000 -1 NULL:1985957 143127_at_1318 0 25 1 1 0 2601928 109859 109834 1 0 0 0 100 partof GCGGCCACTTTCTCCGGCGAGAAGC 25 2R:1731127-2080000 -1 NULL:1985959 143127_at_1315 0 25 1 1 0 2596472 138758 138733 1 0 0 0 100 partof GCGGCGCTGCACAAGTAGGGCCCAA 25 2R:1731127-2080000 1 NULL:1981488 154195_at_1018 0 25 1 1 0 2596475 138769 138744 1 0 0 0 100 partof CAAGTAGGGCCCAAGTCCTCTACTC 25 2R:1731127-2080000 1 NULL:1981490 154195_at_1029 0 25 1 1 0 2596478 138801 138776 1 0 0 0 100 partof GTCCCCTGCTGTCCTTAACCAGTGA 25 2R:1731127-2080000 1 NULL:1981492 154195_at_1061 0 25 1 1 0 2601931 109884 109859 1 0 0 0 100 partof GCTCCGGATCAAAGGTCTCCGGATT 25 2R:1731127-2080000 -1 NULL:1985961 143127_at_1290 0 25 1 1 0 2601934 109913 109888 1 0 0 0 100 partof TAAAGATCCTCGTCGCGGTGGTAGG 25 2R:1731127-2080000 -1 NULL:1985963 143127_at_1261 0 25 1 1 0 2601937 109938 109913 1 0 0 0 100 partof CGCAAGCGGGGATTATGACCTGTGT 25 2R:1731127-2080000 -1 NULL:1985965 143127_at_1236 0 25 1 1 0 2596481 138848 138823 1 0 0 0 100 partof TTGGAGACTCCTCCAGCCAACATGC 25 2R:1731127-2080000 1 NULL:1981494 154195_at_1108 0 25 1 1 0 2596484 138892 138867 1 0 0 0 100 partof TTAAGCCTAAAGTATCCGACACTTG 25 2R:1731127-2080000 1 NULL:1981496 154195_at_1152 0 25 1 1 0 2596487 143980 143955 1 0 0 0 100 partof CCGAGCATGCGGTCCGCGTTCGCGA 25 2R:1731127-2080000 1 NULL:1981498 146695_at_1390 0 25 1 1 0 2601940 109994 109969 1 0 0 0 100 partof GGCACCACGTAGTCGTTGAGGGCCT 25 2R:1731127-2080000 -1 NULL:1985967 143127_at_1180 0 25 1 1 0 2601943 110030 110005 1 0 0 0 100 partof TGGGGCACCAGTGTGTAGAGCCTCA 25 2R:1731127-2080000 -1 NULL:1985969 143127_at_1144 0 25 1 1 0 2601946 110136 110111 1 0 0 0 100 partof TGACCTGGTTCAAGTAGGTCATGGC 25 2R:1731127-2080000 -1 NULL:1985971 143127_at_1107 0 25 1 1 0 2601949 110165 110140 1 0 0 0 100 partof ATGGATTCGTACGTTAGCTGCCCCT 25 2R:1731127-2080000 -1 NULL:1985973 143127_at_1078 0 25 1 1 0 2596490 144066 144041 1 0 0 0 100 partof CGTCAGTTATTTCAGGGCGATGATA 25 2R:1731127-2080000 1 NULL:1981500 146695_at_1476 0 25 1 1 0 2596493 144109 144084 1 0 0 0 100 partof TGTAGGGAACATCTGCAATGGGCAG 25 2R:1731127-2080000 1 NULL:1981502 146695_at_1519 0 25 1 1 0 2596496 144159 144134 1 0 0 0 100 partof TGGTTGGGTGCAACGCCCCTTGCAC 25 2R:1731127-2080000 1 NULL:1981504 146695_at_1569 0 25 1 1 0 2596499 144179 144154 1 0 0 0 100 partof TGCACTTAGACAAATATGAGAAACT 25 2R:1731127-2080000 1 NULL:1981506 146695_at_1589 0 25 1 1 0 2601952 110189 110164 1 0 0 0 100 partof TCCTGTTCCTCCAGCACCGTTTGGA 25 2R:1731127-2080000 -1 NULL:1985975 143127_at_1054 0 25 1 1 0 2601955 121993 121968 1 0 0 0 100 partof GGGTACGCCGAGTAATCACTATCAA 25 2R:1731127-2080000 -1 NULL:1985977 146692_at_386 0 25 1 1 0 2601958 122017 121992 1 0 0 0 100 partof ATTATATTGCTCAGCACGCGCATTG 25 2R:1731127-2080000 -1 NULL:1985979 146692_at_362 0 25 1 1 0 2601961 122020 121995 1 0 0 0 100 partof ATATTGCTCAGCACGCGCATTGTCT 25 2R:1731127-2080000 -1 NULL:1985981 146692_at_359 0 25 1 1 0 2601964 122036 122011 1 0 0 0 100 partof GCATTGTCTCGCACTCTGCGCACGG 25 2R:1731127-2080000 -1 NULL:1985983 146692_at_343 0 25 1 1 0 2601967 122045 122020 1 0 0 0 100 partof CGCACTCTGCGCACGGCGGAATAGT 25 2R:1731127-2080000 -1 NULL:1985985 146692_at_334 0 25 1 1 0 2601970 122110 122085 1 0 0 0 100 partof CTTACCTTGCCATCGGCATCGGCGT 25 2R:1731127-2080000 -1 NULL:1985987 146692_at_269 0 25 1 1 0 2601973 122139 122114 1 0 0 0 100 partof ATGGTATCGCACCTCCAGCGATCCG 25 2R:1731127-2080000 -1 NULL:1985989 146692_at_240 0 25 1 1 0 2601976 122158 122133 1 0 0 0 100 partof GATCCGCCGAGCACTGCATACCAGA 25 2R:1731127-2080000 -1 NULL:1985991 146692_at_221 0 25 1 1 0 2601979 122170 122145 1 0 0 0 100 partof ACTGCATACCAGAAGCGTCCCTGCT 25 2R:1731127-2080000 -1 NULL:1985993 146692_at_209 0 25 1 1 0 2596801 244473 244448 1 0 0 0 100 partof TGACGGACCTCTTCAAGTCCCTGCT 25 2R:1731127-2080000 1 NULL:1981708 151152_at_113 0 25 1 1 0 2596804 244512 244487 1 0 0 0 100 partof TCCTGCCCGCCAGCAGTAGTGGGAG 25 2R:1731127-2080000 1 NULL:1981710 151152_at_152 0 25 1 1 0 2596807 244513 244488 1 0 0 0 100 partof CCTGCCCGCCAGCAGTAGTGGGAGC 25 2R:1731127-2080000 1 NULL:1981712 151152_at_153 0 25 1 1 0 2601982 122289 122264 1 0 0 0 100 partof TTCTCCAGGTCCTCATAGAATCCGC 25 2R:1731127-2080000 -1 NULL:1985995 146692_at_158 0 25 1 1 0 2601985 122319 122294 1 0 0 0 100 partof GCCAACTGCTGGAGCGCAGATCCCG 25 2R:1731127-2080000 -1 NULL:1985997 146692_at_128 0 25 1 1 0 2601988 122368 122343 1 0 0 0 100 partof GACGCAACCGGCACGAAATTAGCTC 25 2R:1731127-2080000 -1 NULL:1985999 146692_at_79 0 25 1 1 0 2596810 244565 244540 1 0 0 0 100 partof GCGCCCAGCGGTTTCAAGCGGCGTT 25 2R:1731127-2080000 1 NULL:1981714 151152_at_205 0 25 1 1 0 2596813 244569 244544 1 0 0 0 100 partof CCAGCGGTTTCAAGCGGCGTTCTTC 25 2R:1731127-2080000 1 NULL:1981716 151152_at_209 0 25 1 1 0 2596816 244576 244551 1 0 0 0 100 partof TTTCAAGCGGCGTTCTTCGGCCTAC 25 2R:1731127-2080000 1 NULL:1981718 151152_at_216 0 25 1 1 0 2596819 244580 244555 1 0 0 0 100 partof AAGCGGCGTTCTTCGGCCTACGTCA 25 2R:1731127-2080000 1 NULL:1981720 151152_at_220 0 25 1 1 0 2601991 122387 122362 1 0 0 0 100 partof TAGCTCCACATCACGCAGGTTCCGG 25 2R:1731127-2080000 -1 NULL:1986001 146692_at_60 0 25 1 1 0 2601994 122878 122853 1 0 0 0 100 partof CCTTGTATCTGATAGTGGATTATCT 25 2R:1731127-2080000 -1 NULL:1986003 146692_at_20 0 25 1 1 0 2601997 139054 139029 1 0 0 0 100 partof TGTCGTCGGCGGAGTAAAAGTCCTG 25 2R:1731127-2080000 -1 NULL:1986005 146693_at_301 0 25 1 1 0 2596822 244586 244561 1 0 0 0 100 partof CGTTCTTCGGCCTACGTCAGCGCAT 25 2R:1731127-2080000 1 NULL:1981722 151152_at_226 0 25 1 1 0 2596825 249887 249862 1 0 0 0 100 partof GACAAAAAGGGCTCCAGCCTCGTGG 25 2R:1731127-2080000 1 NULL:1981724 151153_at_55 0 25 1 1 0 2596828 249897 249872 1 0 0 0 100 partof GCTCCAGCCTCGTGGACGCCGTGGA 25 2R:1731127-2080000 1 NULL:1981726 151153_at_65 0 25 1 1 0 2596831 249900 249875 1 0 0 0 100 partof CCAGCCTCGTGGACGCCGTGGATGT 25 2R:1731127-2080000 1 NULL:1981728 151153_at_68 0 25 1 1 0 2596834 249930 249905 1 0 0 0 100 partof CCACCAGTGCGGAGGCCAAGCTGAA 25 2R:1731127-2080000 1 NULL:1981730 151153_at_98 0 25 1 1 0 2596837 249935 249910 1 0 0 0 100 partof AGTGCGGAGGCCAAGCTGAAGCCTC 25 2R:1731127-2080000 1 NULL:1981732 151153_at_103 0 25 1 1 0 2596840 250072 250047 1 0 0 0 100 partof TCATACGCCGTGCATCACGCAAGAC 25 2R:1731127-2080000 1 NULL:1981734 151153_at_140 0 25 1 1 0 2596843 250074 250049 1 0 0 0 100 partof ATACGCCGTGCATCACGCAAGACCA 25 2R:1731127-2080000 1 NULL:1981736 151153_at_142 0 25 1 1 0 2596846 250075 250050 1 0 0 0 100 partof TACGCCGTGCATCACGCAAGACCAA 25 2R:1731127-2080000 1 NULL:1981738 151153_at_143 0 25 1 1 0 2596849 250076 250051 1 0 0 0 100 partof ACGCCGTGCATCACGCAAGACCAAG 25 2R:1731127-2080000 1 NULL:1981740 151153_at_144 0 25 1 1 0 2596852 250080 250055 1 0 0 0 100 partof CGTGCATCACGCAAGACCAAGCAGC 25 2R:1731127-2080000 1 NULL:1981742 151153_at_148 0 25 1 1 0 2596855 250081 250056 1 0 0 0 100 partof GTGCATCACGCAAGACCAAGCAGCA 25 2R:1731127-2080000 1 NULL:1981744 151153_at_149 0 25 1 1 0 2596858 250084 250059 1 0 0 0 100 partof CATCACGCAAGACCAAGCAGCAAAT 25 2R:1731127-2080000 1 NULL:1981746 151153_at_152 0 25 1 1 0 2596861 250085 250060 1 0 0 0 100 partof ATCACGCAAGACCAAGCAGCAAATC 25 2R:1731127-2080000 1 NULL:1981748 151153_at_153 0 25 1 1 0 2596864 250088 250063 1 0 0 0 100 partof ACGCAAGACCAAGCAGCAAATCAAC 25 2R:1731127-2080000 1 NULL:1981750 151153_at_156 0 25 1 1 0 2596867 253773 253748 1 0 0 0 100 partof CAAGGCAAATCGAACCAAGGTGCGG 25 2R:1731127-2080000 1 NULL:1981752 153632_at_321 0 25 1 1 0 2596870 253806 253781 1 0 0 0 100 partof AGAATGTGGTCTAGACTACGATCGC 25 2R:1731127-2080000 1 NULL:1981754 153632_at_354 0 25 1 1 0 2596873 253963 253938 1 0 0 0 100 partof AATCGGAACAAGATCGAGGAGTGCG 25 2R:1731127-2080000 1 NULL:1981756 153632_at_511 0 25 1 1 0 2596876 253989 253964 1 0 0 0 100 partof CGGCGGAGTGGTGCACAGCTTTACA 25 2R:1731127-2080000 1 NULL:1981758 153632_at_537 0 25 1 1 0 2596879 254004 253979 1 0 0 0 100 partof CAGCTTTACAGGAACTTTGGAGGAG 25 2R:1731127-2080000 1 NULL:1981760 153632_at_552 0 25 1 1 0 2596882 254043 254018 1 0 0 0 100 partof CGCCTTCGGCGGTCTCTACATAGGC 25 2R:1731127-2080000 1 NULL:1981762 153632_at_591 0 25 1 1 0 2596885 254077 254052 1 0 0 0 100 partof TGCTCCCTAAAGACGGATGAAAACG 25 2R:1731127-2080000 1 NULL:1981764 153632_at_625 0 25 1 1 0 2602201 204614 204589 1 0 0 0 100 partof CCACTGAGAAGGATGTAAGGAGTCG 25 2R:1731127-2080000 -1 NULL:1986141 142388_at_457 0 25 1 1 0 2596888 254097 254072 1 0 0 0 100 partof AAACGCAGAAGTGGTGCGCAAGCTA 25 2R:1731127-2080000 1 NULL:1981766 153632_at_645 0 25 1 1 0 2602204 204983 204958 1 0 0 0 100 partof AGTCCTTATCCGAGGCCGAGACACA 25 2R:1731127-2080000 -1 NULL:1986143 142388_at_418 0 25 1 1 0 2602207 206827 206802 1 0 0 0 100 partof CTGATGCACAAGGACATAGGTGAAA 25 2R:1731127-2080000 -1 NULL:1986145 146699_at_1707 0 25 1 1 0 2596891 254191 254166 1 0 0 0 100 partof AAGCACGTGACCACCAAGTTTCCCA 25 2R:1731127-2080000 1 NULL:1981768 153632_at_739 0 25 1 1 0 2596894 254213 254188 1 0 0 0 100 partof CCACCGTCAAGAAGAAAGAGAAATG 25 2R:1731127-2080000 1 NULL:1981770 153632_at_761 0 25 1 1 0 2602210 206851 206826 1 0 0 0 100 partof AGGATGGTCGGCAAAGAACTCAATT 25 2R:1731127-2080000 -1 NULL:1986147 146699_at_1683 0 25 1 1 0 2596897 254233 254208 1 0 0 0 100 partof AAATGGACAGCTGAATCCCTAATAG 25 2R:1731127-2080000 1 NULL:1981772 153632_at_781 0 25 1 1 0 2602213 206891 206866 1 0 0 0 100 partof ATAATAGCGCGCTTCCTACGCACCG 25 2R:1731127-2080000 -1 NULL:1986149 146699_at_1643 0 25 1 1 0 2602216 207045 207020 1 0 0 0 100 partof CTCCTCGTTGACTTCAATGAAGGCC 25 2R:1731127-2080000 -1 NULL:1986151 146699_at_1587 0 25 1 1 0 2602219 207132 207107 1 0 0 0 100 partof CTGATCGGAGAACATCCTTGACATG 25 2R:1731127-2080000 -1 NULL:1986153 146699_at_1500 0 25 1 1 0 2596100 4667 4642 1 0 0 0 100 partof TTCTTAGCCCTTAAAGCACGCAAAG 25 2R:1731127-2080000 1 NULL:1981240 155070_at_1052 0 25 1 1 0 2596103 4698 4673 1 0 0 0 100 partof GGCAATTTTTCTGACATATTTCATG 25 2R:1731127-2080000 1 NULL:1981242 155070_at_1083 0 25 1 1 0 2596106 4767 4742 1 0 0 0 100 partof TCAAAGCGAAAACATCCTTTGACAG 25 2R:1731127-2080000 1 NULL:1981244 155070_at_1152 0 25 1 1 0 2596109 13546 13521 1 0 0 0 100 partof AGCTGCTGGCAATGAAGCGGCGATT 25 2R:1731127-2080000 1 NULL:1981246 146685_at_461 0 25 1 1 0 2602222 207232 207207 1 0 0 0 100 partof GAAAACCTCAGACAATTCCACTTGG 25 2R:1731127-2080000 -1 NULL:1986155 146699_at_1464 0 25 1 1 0 2602225 207304 207279 1 0 0 0 100 partof CAACGACTGCGTGATCTGCGAGAGG 25 2R:1731127-2080000 -1 NULL:1986157 146699_at_1392 0 25 1 1 0 2602228 207339 207314 1 0 0 0 100 partof GCAACTTCTCCTCCAGAGCGGGCAG 25 2R:1731127-2080000 -1 NULL:1986159 146699_at_1357 0 25 1 1 0 2596112 13573 13548 1 0 0 0 100 partof AAGAGTTGCAGCAGGTAGCAGGTAC 25 2R:1731127-2080000 1 NULL:1981248 146685_at_488 0 25 1 1 0 2596115 13611 13586 1 0 0 0 100 partof CCAGGATACCGTAGGCAGATTAAAG 25 2R:1731127-2080000 1 NULL:1981250 146685_at_526 0 25 1 1 0 2596118 13633 13608 1 0 0 0 100 partof AAGTAAATCCAATAGACAAGGATCC 25 2R:1731127-2080000 1 NULL:1981252 146685_at_548 0 25 1 1 0 2602231 207391 207366 1 0 0 0 100 partof CAGCATAGAGAGGTCTGAGTCCTTG 25 2R:1731127-2080000 -1 NULL:1986161 146699_at_1305 0 25 1 1 0 2602234 207417 207392 1 0 0 0 100 partof AGGGCAGTTCCAGAGCCATGGCATC 25 2R:1731127-2080000 -1 NULL:1986163 146699_at_1279 0 25 1 1 0 2602237 207431 207406 1 0 0 0 100 partof GCCATGGCATCTAGCGCCGGCAGAT 25 2R:1731127-2080000 -1 NULL:1986165 146699_at_1265 0 25 1 1 0 2596121 13654 13629 1 0 0 0 100 partof ATCCAGGGAAGTCAGCACAAAGTTA 25 2R:1731127-2080000 1 NULL:1981254 146685_at_569 0 25 1 1 0 2596124 13701 13676 1 0 0 0 100 partof ATTGAAAAGACGAGCCCACACTACT 25 2R:1731127-2080000 1 NULL:1981256 146685_at_616 0 25 1 1 0 2596127 13775 13750 1 0 0 0 100 partof AGCTCCTCCAGGAGCAACCCAAAAA 25 2R:1731127-2080000 1 NULL:1981258 146685_at_690 0 25 1 1 0 2602240 207455 207430 1 0 0 0 100 partof TCGGCGTAGCGGAACCGCTCCTTTA 25 2R:1731127-2080000 -1 NULL:1986167 146699_at_1241 0 25 1 1 0 2602243 207456 207431 1 0 0 0 100 partof CGGCGTAGCGGAACCGCTCCTTTAA 25 2R:1731127-2080000 -1 NULL:1986169 146699_at_1240 0 25 1 1 0 2602246 207511 207486 1 0 0 0 100 partof CCCATCCAGGTGAAAGGTGTCTGGG 25 2R:1731127-2080000 -1 NULL:1986171 146699_at_1185 0 25 1 1 0 2602249 209700 209675 1 0 0 0 100 partof GCTGTAAAGCTAGGAATCTTCACAT 25 2R:1731127-2080000 -1 NULL:1986173 146700_at_803 0 25 1 1 0 2596130 13874 13849 1 0 0 0 100 partof AGCGCAAAGTGCTCCCCGAAATTTA 25 2R:1731127-2080000 1 NULL:1981260 146685_at_789 0 25 1 1 0 2596133 13896 13871 1 0 0 0 100 partof TTATTGCATAAATCCGTAGTTGATC 25 2R:1731127-2080000 1 NULL:1981262 146685_at_811 0 25 1 1 0 2596136 13981 13956 1 0 0 0 100 partof TGGAATCGAAGTTGCGCGCGCCCAC 25 2R:1731127-2080000 1 NULL:1981264 146685_at_896 0 25 1 1 0 2596139 14000 13975 1 0 0 0 100 partof GCCCACCTATCTGAATTGGGACATG 25 2R:1731127-2080000 1 NULL:1981266 146685_at_915 0 25 1 1 0 2602252 209727 209702 1 0 0 0 100 partof ACTTTTTCCAGATTCATTGCTGATG 25 2R:1731127-2080000 -1 NULL:1986175 146700_at_776 0 25 1 1 0 2602255 209758 209733 1 0 0 0 100 partof CCTCTAGGGAAATATCACTAAGTTT 25 2R:1731127-2080000 -1 NULL:1986177 146700_at_745 0 25 1 1 0 2602258 209782 209757 1 0 0 0 100 partof TCTTTTCGAGGCTCGTGAGATTCGA 25 2R:1731127-2080000 -1 NULL:1986179 146700_at_721 0 25 1 1 0 2596142 14004 13979 1 0 0 0 100 partof ACCTATCTGAATTGGGACATGAAAA 25 2R:1731127-2080000 1 NULL:1981268 146685_at_919 0 25 1 1 0 2596145 14068 14043 1 0 0 0 100 partof CCTATTTGAACCAGTTGGTGAGAGT 25 2R:1731127-2080000 1 NULL:1981270 146685_at_983 0 25 1 1 0 2596148 14091 14066 1 0 0 0 100 partof GTGTTCGGGCGCAATTTGGATTTCA 25 2R:1731127-2080000 1 NULL:1981272 146685_at_1006 0 25 1 1 0 2601601 30403 30378 1 0 0 0 100 partof TACAGTTCGGATTTGTAGTACCTCC 25 2R:1731127-2080000 -1 NULL:1985741 154552_at_2742 0 25 1 1 0 2601604 30425 30400 1 0 0 0 100 partof TCCAGTTGCCTTCTACTTGCGGCGT 25 2R:1731127-2080000 -1 NULL:1985743 154552_at_2720 0 25 1 1 0 2602261 209878 209853 1 0 0 0 100 partof CGAACATGGGAAGTACGGCAAAAAA 25 2R:1731127-2080000 -1 NULL:1986181 146700_at_625 0 25 1 1 0 2601607 30454 30429 1 0 0 0 100 partof CAGTGCAATGTAAGTAACCTAGTGT 25 2R:1731127-2080000 -1 NULL:1985745 154552_at_2691 0 25 1 1 0 2602264 209902 209877 1 0 0 0 100 partof AGAAGTTCTCGCACACATGCATCAT 25 2R:1731127-2080000 -1 NULL:1986183 146700_at_601 0 25 1 1 0 2602267 209903 209878 1 0 0 0 100 partof GAAGTTCTCGCACACATGCATCATT 25 2R:1731127-2080000 -1 NULL:1986185 146700_at_600 0 25 1 1 0 2596151 21586 21561 1 0 0 0 100 partof TGCATGCCAAAGTCCCAAAAGGATT 25 2R:1731127-2080000 1 NULL:1981274 146687_at_82 0 25 1 1 0 2596154 21686 21661 1 0 0 0 100 partof AGGCGGTACCAAAGTGAGCAATGTG 25 2R:1731127-2080000 1 NULL:1981276 146687_at_126 0 25 1 1 0 2596157 21733 21708 1 0 0 0 100 partof TGAACAAGGGCGAGCACAGATGCGT 25 2R:1731127-2080000 1 NULL:1981278 146687_at_173 0 25 1 1 0 2601610 30536 30511 1 0 0 0 100 partof TTTTCACAGAACTCGATCAGATACG 25 2R:1731127-2080000 -1 NULL:1985747 154552_at_2609 0 25 1 1 0 2601613 30586 30561 1 0 0 0 100 partof TATTCCAGCATAATAGAAGGTGTCA 25 2R:1731127-2080000 -1 NULL:1985749 154552_at_2559 0 25 1 1 0 2602270 209953 209928 1 0 0 0 100 partof CGAAGAAATCCTCTTCGCGGGTTTC 25 2R:1731127-2080000 -1 NULL:1986187 146700_at_550 0 25 1 1 0 2601616 30686 30661 1 0 0 0 100 partof CGTATACTCGTATATGACGCCTGCA 25 2R:1731127-2080000 -1 NULL:1985751 154552_at_2523 0 25 1 1 0 2602273 209990 209965 1 0 0 0 100 partof ACTGATTGACCACTCACCCTTGAAG 25 2R:1731127-2080000 -1 NULL:1986189 146700_at_513 0 25 1 1 0 2601619 46477 46452 1 0 0 0 100 partof CATTAGAGCGAATCCCGCAACGGCG 25 2R:1731127-2080000 -1 NULL:1985753 146688_at_987 0 25 1 1 0 2602276 210082 210057 1 0 0 0 100 partof TCAGGTTGTTGGTCTGTGACTCCAC 25 2R:1731127-2080000 -1 NULL:1986191 146700_at_421 0 25 1 1 0 2602279 210102 210077 1 0 0 0 100 partof TCCACCCATTTGTTGATTATGCTGG 25 2R:1731127-2080000 -1 NULL:1986193 146700_at_401 0 25 1 1 0 2597101 347319 347294 1 0 0 0 100 partof TGATCCCGACTAACTACTACCCGGG 25 2R:1731127-2080000 1 NULL:1981916 146709_at_601 0 25 1 1 0 2597104 347353 347328 1 0 0 0 100 partof AAAGTTCGTCGAATTAATGACCACT 25 2R:1731127-2080000 1 NULL:1981918 146709_at_635 0 25 1 1 0 2597107 347394 347369 1 0 0 0 100 partof AATATGTGGGCATCGGCCTCATCGG 25 2R:1731127-2080000 1 NULL:1981920 146709_at_676 0 25 1 1 0 2596160 21784 21759 1 0 0 0 100 partof TGGTGAAGACCATATCCTGTGCCGA 25 2R:1731127-2080000 1 NULL:1981280 146687_at_224 0 25 1 1 0 2596163 21802 21777 1 0 0 0 100 partof GTGCCGAGGTCCTCAAGCGGAGCCA 25 2R:1731127-2080000 1 NULL:1981282 146687_at_242 0 25 1 1 0 2596166 21831 21806 1 0 0 0 100 partof CTCTACCAGGTGACGCGCATGGCCT 25 2R:1731127-2080000 1 NULL:1981284 146687_at_271 0 25 1 1 0 2596169 21924 21899 1 0 0 0 100 partof AGGAGCACTGGAAGCCGCAAATGGA 25 2R:1731127-2080000 1 NULL:1981286 146687_at_308 0 25 1 1 0 2601622 46519 46494 1 0 0 0 100 partof TCCGGCATGGCTCTCAATGAGGATC 25 2R:1731127-2080000 -1 NULL:1985755 146688_at_945 0 25 1 1 0 2601625 46569 46544 1 0 0 0 100 partof TTCCACAGGCGATGCCCTGGAGGAC 25 2R:1731127-2080000 -1 NULL:1985757 146688_at_895 0 25 1 1 0 2602282 210116 210091 1 0 0 0 100 partof GATTATGCTGGCAGCCTGCTCGCTG 25 2R:1731127-2080000 -1 NULL:1986195 146700_at_387 0 25 1 1 0 2601628 46619 46594 1 0 0 0 100 partof GCTGCCACCTGCTGGCTGATGCCGA 25 2R:1731127-2080000 -1 NULL:1985759 146688_at_845 0 25 1 1 0 2602285 210142 210117 1 0 0 0 100 partof CAAAGTCAATCTCCATTGGCTTGGA 25 2R:1731127-2080000 -1 NULL:1986197 146700_at_361 0 25 1 1 0 2602288 210225 210200 1 0 0 0 100 partof ACATATAGGCCGTTTGCCATTTTAA 25 2R:1731127-2080000 -1 NULL:1986199 146700_at_278 0 25 1 1 0 2597110 347505 347480 1 0 0 0 100 partof TTGCCTGCTGCCTGGCCAACAACGT 25 2R:1731127-2080000 1 NULL:1981922 146709_at_724 0 25 1 1 0 2597113 347554 347529 1 0 0 0 100 partof CTACTAAGCAATAGGTGTATCCATC 25 2R:1731127-2080000 1 NULL:1981924 146709_at_773 0 25 1 1 0 2597116 347566 347541 1 0 0 0 100 partof AGGTGTATCCATCAACTACATCTAG 25 2R:1731127-2080000 1 NULL:1981926 146709_at_785 0 25 1 1 0 2597119 347570 347545 1 0 0 0 100 partof GTATCCATCAACTACATCTAGAGGC 25 2R:1731127-2080000 1 NULL:1981928 146709_at_789 0 25 1 1 0 2596172 21959 21934 1 0 0 0 100 partof GAGATTATAGTCACACGCCAAATAC 25 2R:1731127-2080000 1 NULL:1981288 146687_at_343 0 25 1 1 0 2596175 22005 21980 1 0 0 0 100 partof GTCTGGACGAGCTGCCGGATACTAT 25 2R:1731127-2080000 1 NULL:1981290 146687_at_389 0 25 1 1 0 2596178 22100 22075 1 0 0 0 100 partof AGCCAAATACGTCCACTGATTTTTG 25 2R:1731127-2080000 1 NULL:1981292 146687_at_428 0 25 1 1 0 2601631 46726 46701 1 0 0 0 100 partof CAGAAGCTCCATACCCACGCAGAAG 25 2R:1731127-2080000 -1 NULL:1985761 146688_at_738 0 25 1 1 0 2601634 46768 46743 1 0 0 0 100 partof GGCGGAGACCGCTCCAAACATGAAC 25 2R:1731127-2080000 -1 NULL:1985763 146688_at_696 0 25 1 1 0 2602291 256356 256331 1 0 0 0 100 partof CTGGGTCGCGATAGTTTTTGCGGAT 25 2R:1731127-2080000 -1 NULL:1986201 146704_at_5736 0 25 1 1 0 2601637 46777 46752 1 0 0 0 100 partof CGCTCCAAACATGAACCACACAGTG 25 2R:1731127-2080000 -1 NULL:1985765 146688_at_687 0 25 1 1 0 2602294 256475 256450 1 0 0 0 100 partof CTTGCTGTTGATGAGATTTCGCACG 25 2R:1731127-2080000 -1 NULL:1986203 146704_at_5695 0 25 1 1 0 2602297 256560 256535 1 0 0 0 100 partof TCGGCCTTGGTCTTGGCACGAATAC 25 2R:1731127-2080000 -1 NULL:1986205 146704_at_5610 0 25 1 1 0 2597122 347585 347560 1 0 0 0 100 partof ATCTAGAGGCACACCCACATCCAGT 25 2R:1731127-2080000 1 NULL:1981930 146709_at_804 0 25 1 1 0 2597125 347589 347564 1 0 0 0 100 partof AGAGGCACACCCACATCCAGTAGCA 25 2R:1731127-2080000 1 NULL:1981932 146709_at_808 0 25 1 1 0 2597128 347631 347606 1 0 0 0 100 partof CATTAACTTTTACAGTCGTTGAACG 25 2R:1731127-2080000 1 NULL:1981934 146709_at_850 0 25 1 1 0 2596181 22111 22086 1 0 0 0 100 partof TCCACTGATTTTTGGGATGGCGGAG 25 2R:1731127-2080000 1 NULL:1981294 146687_at_439 0 25 1 1 0 2596184 22176 22151 1 0 0 0 100 partof TCAGCAGCAGCCACATAAACCAGGG 25 2R:1731127-2080000 1 NULL:1981296 146687_at_504 0 25 1 1 0 2596187 22180 22155 1 0 0 0 100 partof CAGCAGCCACATAAACCAGGGGCTG 25 2R:1731127-2080000 1 NULL:1981298 146687_at_508 0 25 1 1 0 2601640 46807 46782 1 0 0 0 100 partof AGTGCCCTCCAGACCAATGGCCATG 25 2R:1731127-2080000 -1 NULL:1985767 146688_at_657 0 25 1 1 0 2601643 46834 46809 1 0 0 0 100 partof CTCGAACAGTTCGTGGAGCGAAAGG 25 2R:1731127-2080000 -1 NULL:1985769 146688_at_630 0 25 1 1 0 2601646 46879 46854 1 0 0 0 100 partof CCTGGCAGAGGATCCATCGTCCGCT 25 2R:1731127-2080000 -1 NULL:1985771 146688_at_585 0 25 1 1 0 2601649 46891 46866 1 0 0 0 100 partof TCCATCGTCCGCTGGCACGGGCATG 25 2R:1731127-2080000 -1 NULL:1985773 146688_at_573 0 25 1 1 0 2597131 347654 347629 1 0 0 0 100 partof CGCACATACACAACGGGATACACAA 25 2R:1731127-2080000 1 NULL:1981936 146709_at_873 0 25 1 1 0 2597134 347667 347642 1 0 0 0 100 partof CGGGATACACAATAACACCTTGAAA 25 2R:1731127-2080000 1 NULL:1981938 146709_at_886 0 25 1 1 0 2597137 347668 347643 1 0 0 0 100 partof GGGATACACAATAACACCTTGAAAT 25 2R:1731127-2080000 1 NULL:1981940 146709_at_887 0 25 1 1 0 2596190 22224 22199 1 0 0 0 100 partof CAAACGGACCAGACCCGGACGCAAT 25 2R:1731127-2080000 1 NULL:1981300 146687_at_552 0 25 1 1 0 2596193 24442 24417 1 0 0 0 100 partof CCCGATGGCACCTACTTCAGGCGGG 25 2R:1731127-2080000 1 NULL:1981302 151882_at_907 0 25 1 1 0 2596196 24448 24423 1 0 0 0 100 partof GGCACCTACTTCAGGCGGGACGGTC 25 2R:1731127-2080000 1 NULL:1981304 151882_at_913 0 25 1 1 0 2596199 24462 24437 1 0 0 0 100 partof GCGGGACGGTCTTTGCGGCAACTTC 25 2R:1731127-2080000 1 NULL:1981306 151882_at_927 0 25 1 1 0 2601652 46930 46905 1 0 0 0 100 partof GTGATCCTTGTGTGGCTGCGGTTCC 25 2R:1731127-2080000 -1 NULL:1985775 146688_at_534 0 25 1 1 0 2601655 46939 46914 1 0 0 0 100 partof GTGTGGCTGCGGTTCCGTATCCTTA 25 2R:1731127-2080000 -1 NULL:1985777 146688_at_525 0 25 1 1 0 2601658 46966 46941 1 0 0 0 100 partof TTCCACTTCTTCCTTCGCCTGTGGA 25 2R:1731127-2080000 -1 NULL:1985779 146688_at_498 0 25 1 1 0 2597140 347797 347772 1 0 0 0 100 partof TCATGTTATACCTATCGAACGAACG 25 2R:1731127-2080000 1 NULL:1981942 146709_at_1016 0 25 1 1 0 2601661 48522 48497 1 0 0 0 100 partof CAATTTCAAAGAAGACCACGTAGAT 25 2R:1731127-2080000 -1 NULL:1985781 146689_at_799 0 25 1 1 0 2601664 48562 48537 1 0 0 0 100 partof CAGCCCCTGGAGGATTCCTGATACC 25 2R:1731127-2080000 -1 NULL:1985783 146689_at_759 0 25 1 1 0 2601667 48579 48554 1 0 0 0 100 partof CTGATACCGTGCTGGGCTGATTAGC 25 2R:1731127-2080000 -1 NULL:1985785 146689_at_742 0 25 1 1 0 2601670 48598 48573 1 0 0 0 100 partof ATTAGCCGCGGCAGATTCGCTAACT 25 2R:1731127-2080000 -1 NULL:1985787 146689_at_723 0 25 1 1 0 2601673 48616 48591 1 0 0 0 100 partof GCTAACTGCAATTCCGATGCCCACG 25 2R:1731127-2080000 -1 NULL:1985789 146689_at_705 0 25 1 1 0 2601676 48637 48612 1 0 0 0 100 partof CACGCCAATCGGAGTTACGATCGAG 25 2R:1731127-2080000 -1 NULL:1985791 146689_at_684 0 25 1 1 0 2601679 48645 48620 1 0 0 0 100 partof TCGGAGTTACGATCGAGAAGACGAG 25 2R:1731127-2080000 -1 NULL:1985793 146689_at_676 0 25 1 1 0 2596502 144248 144223 1 0 0 0 100 partof TTTTTGTCCGTCTGCTTGACCCGCA 25 2R:1731127-2080000 1 NULL:1981508 146695_at_1658 0 25 1 1 0 2596505 144278 144253 1 0 0 0 100 partof GCGCACTTACTTTATAGTTTTTCGT 25 2R:1731127-2080000 1 NULL:1981510 146695_at_1688 0 25 1 1 0 2596508 144371 144346 1 0 0 0 100 partof CAACAAAATGCAACATCACAGGCTG 25 2R:1731127-2080000 1 NULL:1981512 146695_at_1781 0 25 1 1 0 2601682 48656 48631 1 0 0 0 100 partof ATCGAGAAGACGAGGAGGTAAACCA 25 2R:1731127-2080000 -1 NULL:1985795 146689_at_665 0 25 1 1 0 2601685 48689 48664 1 0 0 0 100 partof AGCCAGCGGGTATGGGCCATCATGA 25 2R:1731127-2080000 -1 NULL:1985797 146689_at_632 0 25 1 1 0 2601688 48703 48678 1 0 0 0 100 partof GGCCATCATGATCTCCATGCCGATG 25 2R:1731127-2080000 -1 NULL:1985799 146689_at_618 0 25 1 1 0 2596511 144384 144359 1 0 0 0 100 partof CATCACAGGCTGATGGGAGAAGGAT 25 2R:1731127-2080000 1 NULL:1981514 146695_at_1794 0 25 1 1 0 2596514 144409 144384 1 0 0 0 100 partof AGAGCTCGCCGCTGTTCAAATTGTA 25 2R:1731127-2080000 1 NULL:1981516 146695_at_1819 0 25 1 1 0 2596517 144416 144391 1 0 0 0 100 partof GCCGCTGTTCAAATTGTAAAACTTT 25 2R:1731127-2080000 1 NULL:1981518 146695_at_1826 0 25 1 1 0 2601691 48760 48735 1 0 0 0 100 partof GGCTCCGGTCATGAACCACACCGTG 25 2R:1731127-2080000 -1 NULL:1985801 146689_at_561 0 25 1 1 0 2601694 48836 48811 1 0 0 0 100 partof GAGAGGGCCACGATTATTCCGAGGC 25 2R:1731127-2080000 -1 NULL:1985803 146689_at_485 0 25 1 1 0 2601697 48899 48874 1 0 0 0 100 partof TGGACCACAATCTCTGTCCGCAGCT 25 2R:1731127-2080000 -1 NULL:1985805 146689_at_422 0 25 1 1 0 2596520 144453 144428 1 0 0 0 100 partof CTTCATTCTTGTCCAACAATTAGGG 25 2R:1731127-2080000 1 NULL:1981520 146695_at_1863 0 25 1 1 0 2596523 144484 144459 1 0 0 0 100 partof TCCGTCTGGGTTAGTGCCCTAACTA 25 2R:1731127-2080000 1 NULL:1981522 146695_at_1894 0 25 1 1 0 2596526 144547 144522 1 0 0 0 100 partof GTGCACTGTTTGCTTTGTAATAGTC 25 2R:1731127-2080000 1 NULL:1981524 146695_at_1957 0 25 1 1 0 2596529 146101 146076 1 0 0 0 100 partof AGGAGGTGCGCCAGATAGTCAAGAC 25 2R:1731127-2080000 1 NULL:1981526 146696_at_1255 0 25 1 1 0 2596532 146140 146115 1 0 0 0 100 partof ACGATGCCGACAAGACGGGCCTGGT 25 2R:1731127-2080000 1 NULL:1981528 146696_at_1294 0 25 1 1 0 2596535 146152 146127 1 0 0 0 100 partof AGACGGGCCTGGTGGACTTCGCCCT 25 2R:1731127-2080000 1 NULL:1981530 146696_at_1306 0 25 1 1 0 2596538 146186 146161 1 0 0 0 100 partof GGGCGGCCAAATCCTTTCCACGCGT 25 2R:1731127-2080000 1 NULL:1981532 146696_at_1340 0 25 1 1 0 2596541 146256 146231 1 0 0 0 100 partof GGAATTCCACTCTGGTATCCCACCA 25 2R:1731127-2080000 1 NULL:1981534 146696_at_1410 0 25 1 1 0 2596544 146287 146262 1 0 0 0 100 partof CGCGGGTCGCCATTTCACCCAATGT 25 2R:1731127-2080000 1 NULL:1981536 146696_at_1441 0 25 1 1 0 2596547 146326 146301 1 0 0 0 100 partof GCTGGGCATTCCAAGGGTTTCCCGG 25 2R:1731127-2080000 1 NULL:1981538 146696_at_1480 0 25 1 1 0 2596550 146342 146317 1 0 0 0 100 partof GTTTCCCGGATTTCTAGGCAAGTCG 25 2R:1731127-2080000 1 NULL:1981540 146696_at_1496 0 25 1 1 0 2596553 146345 146320 1 0 0 0 100 partof TCCCGGATTTCTAGGCAAGTCGCGG 25 2R:1731127-2080000 1 NULL:1981542 146696_at_1499 0 25 1 1 0 2596556 146421 146396 1 0 0 0 100 partof AAGCTCAACTCGTTGGTGTACGTCA 25 2R:1731127-2080000 1 NULL:1981544 146696_at_1536 0 25 1 1 0 2596559 146461 146436 1 0 0 0 100 partof AGCACATACCGAAGAGTCTATCCCC 25 2R:1731127-2080000 1 NULL:1981546 146696_at_1576 0 25 1 1 0 2596562 146493 146468 1 0 0 0 100 partof AGAATAGAATCAGCTCCTCGCAACT 25 2R:1731127-2080000 1 NULL:1981548 146696_at_1608 0 25 1 1 0 2596565 146604 146579 1 0 0 0 100 partof GAGAAGGACCAGGAACCCGTATTGT 25 2R:1731127-2080000 1 NULL:1981550 146696_at_1656 0 25 1 1 0 2596568 146657 146632 1 0 0 0 100 partof TGCTTCCCTCCAGTACTTTGCCGTT 25 2R:1731127-2080000 1 NULL:1981552 146696_at_1709 0 25 1 1 0 2596571 164270 164245 1 0 0 0 100 partof CAGCAGCAACAGCAACAGCAGCAGC 25 2R:1731127-2080000 1 NULL:1981554 151224_f_at_40 0 25 1 1 0 2596573 165393 165368 1 0 0 0 100 partof CTCCATGGACGACAGCCTGGAGCGG 25 2R:1731127-2080000 1 NULL:1981556 146697_at_1797 0 25 1 1 0 2596576 165417 165392 1 0 0 0 100 partof GGAAACGCCGGCATCGACAATAATC 25 2R:1731127-2080000 1 NULL:1981558 146697_at_1821 0 25 1 1 0 2596579 165453 165428 1 0 0 0 100 partof CACGGCCAACAAGAGTGACAGGAGC 25 2R:1731127-2080000 1 NULL:1981560 146697_at_1857 0 25 1 1 0 2596582 165485 165460 1 0 0 0 100 partof GCATCGGTGGCATCGGCAAAGACAA 25 2R:1731127-2080000 1 NULL:1981562 146697_at_1889 0 25 1 1 0 2596585 165503 165478 1 0 0 0 100 partof AAGACAATGGCAACGACGCCGTCTT 25 2R:1731127-2080000 1 NULL:1981564 146697_at_1907 0 25 1 1 0 2596588 165564 165539 1 0 0 0 100 partof CAATGGGAGCGTTGTCAATATTGAC 25 2R:1731127-2080000 1 NULL:1981566 146697_at_1968 0 25 1 1 0 2596591 165583 165558 1 0 0 0 100 partof ATTGACATTACACTAACTGCAGTTG 25 2R:1731127-2080000 1 NULL:1981568 146697_at_1987 0 25 1 1 0 2596594 165638 165613 1 0 0 0 100 partof TTGCAAATGGCAACAGAACGTCAGG 25 2R:1731127-2080000 1 NULL:1981570 146697_at_2042 0 25 1 1 0 2596597 165675 165650 1 0 0 0 100 partof TGGCAACAGCTGTAGCAGCCAGGTT 25 2R:1731127-2080000 1 NULL:1981572 146697_at_2079 0 25 1 1 0 2596900 254255 254230 1 0 0 0 100 partof TAGACGGACGCTGTGAGCCTTGCCA 25 2R:1731127-2080000 1 NULL:1981774 153632_at_803 0 25 1 1 0 2596903 254357 254332 1 0 0 0 100 partof TTTTGGAGTCTATTGCCGGAATCAA 25 2R:1731127-2080000 1 NULL:1981776 153632_at_839 0 25 1 1 0 2596906 254407 254382 1 0 0 0 100 partof GCGTTATACTACCAAAACACATTGG 25 2R:1731127-2080000 1 NULL:1981778 153632_at_889 0 25 1 1 0 2596909 278304 278279 1 0 0 0 100 partof TCAGCTAGTGTGAATGCGAACGCGA 25 2R:1731127-2080000 1 NULL:1981780 154619_at_1845 0 25 1 1 0 2596911 281234 281209 1 0 0 0 100 partof AAGACATCGAATCCAAGGATCTCGA 25 2R:1731127-2080000 1 NULL:1981782 146706_at_1214 0 25 1 1 0 2596914 281246 281221 1 0 0 0 100 partof CCAAGGATCTCGATATTATGCTACA 25 2R:1731127-2080000 1 NULL:1981784 146706_at_1226 0 25 1 1 0 2596917 281266 281241 1 0 0 0 100 partof CTACATACCACATCGGCGGAAAGCG 25 2R:1731127-2080000 1 NULL:1981786 146706_at_1246 0 25 1 1 0 2596920 281291 281266 1 0 0 0 100 partof AGGTGCGAAATCTACCGGTAGCATA 25 2R:1731127-2080000 1 NULL:1981788 146706_at_1271 0 25 1 1 0 2596923 281326 281301 1 0 0 0 100 partof CGCTTCAGTGACGAAAACAATCTGC 25 2R:1731127-2080000 1 NULL:1981790 146706_at_1306 0 25 1 1 0 2596926 281430 281405 1 0 0 0 100 partof CCACCCAAGTCTTTGCCGACTTGAG 25 2R:1731127-2080000 1 NULL:1981792 146706_at_1347 0 25 1 1 0 2596929 281619 281594 1 0 0 0 100 partof TACCATCTTCAAAGTGTCTGACCAG 25 2R:1731127-2080000 1 NULL:1981794 146706_at_1536 0 25 1 1 0 2596932 281720 281695 1 0 0 0 100 partof TGACAACTACTCTGGCGAGAGGTTC 25 2R:1731127-2080000 1 NULL:1981796 146706_at_1572 0 25 1 1 0 2596935 281725 281700 1 0 0 0 100 partof ACTACTCTGGCGAGAGGTTCGAGCG 25 2R:1731127-2080000 1 NULL:1981798 146706_at_1577 0 25 1 1 0 2596938 281739 281714 1 0 0 0 100 partof AGGTTCGAGCGGACGCTGATCATCA 25 2R:1731127-2080000 1 NULL:1981800 146706_at_1591 0 25 1 1 0 2596941 281769 281744 1 0 0 0 100 partof CAAATTTCGAGGATGGGCATAAATC 25 2R:1731127-2080000 1 NULL:1981802 146706_at_1621 0 25 1 1 0 2596944 281788 281763 1 0 0 0 100 partof TAAATCGGCGGGTTGTATTCAGCAC 25 2R:1731127-2080000 1 NULL:1981804 146706_at_1640 0 25 1 1 0 2596947 281809 281784 1 0 0 0 100 partof GCACGGATCAGTTGATAATGTCGTT 25 2R:1731127-2080000 1 NULL:1981806 146706_at_1661 0 25 1 1 0 2596950 281825 281800 1 0 0 0 100 partof AATGTCGTTTGGTGGAGCCATTGGC 25 2R:1731127-2080000 1 NULL:1981808 146706_at_1677 0 25 1 1 0 2596953 282020 281995 1 0 0 0 100 partof AGTTAAGAACCCTCTTCTTGCGCTC 25 2R:1731127-2080000 1 NULL:1981810 152934_at_1915 0 25 1 1 0 2596955 282025 282000 1 0 0 0 100 partof AGAACCCTCTTCTTGCGCTCTTCGT 25 2R:1731127-2080000 1 NULL:1981812 152934_at_1920 0 25 1 1 0 2596957 282031 282006 1 0 0 0 100 partof CTCTTCTTGCGCTCTTCGTCAGGAC 25 2R:1731127-2080000 1 NULL:1981814 152934_at_1926 0 25 1 1 0 2596959 282038 282013 1 0 0 0 100 partof TGCGCTCTTCGTCAGGACTCACCAG 25 2R:1731127-2080000 1 NULL:1981816 152934_at_1933 0 25 1 1 0 2596961 282114 282089 1 0 0 0 100 partof CTAGTAACATGTTCGTGTAAGTTAC 25 2R:1731127-2080000 1 NULL:1981818 152934_at_2009 0 25 1 1 0 2596963 282118 282093 1 0 0 0 100 partof TAACATGTTCGTGTAAGTTACGAAC 25 2R:1731127-2080000 1 NULL:1981820 152934_at_2013 0 25 1 1 0 2596965 282121 282096 1 0 0 0 100 partof CATGTTCGTGTAAGTTACGAACCCT 25 2R:1731127-2080000 1 NULL:1981822 152934_at_2016 0 25 1 1 0 2596967 282128 282103 1 0 0 0 100 partof GTGTAAGTTACGAACCCTCTTCTTG 25 2R:1731127-2080000 1 NULL:1981824 152934_at_2023 0 25 1 1 0 2596969 282155 282130 1 0 0 0 100 partof ATCTTCGTCAGGACTCACCAGCGCT 25 2R:1731127-2080000 1 NULL:1981826 152934_at_2050 0 25 1 1 0 2596971 282243 282218 1 0 0 0 100 partof GTATGTGTGCATTCGGAACAAGTGC 25 2R:1731127-2080000 1 NULL:1981828 152934_at_2138 0 25 1 1 0 2596973 282262 282237 1 0 0 0 100 partof AAGTGCCGTTGGTCGCACTCAGGGT 25 2R:1731127-2080000 1 NULL:1981830 152934_at_2157 0 25 1 1 0 2596975 317797 317772 1 0 0 0 100 partof AGTGCTTCACATCAACCTCGACCAG 25 2R:1731127-2080000 1 NULL:1981832 154950_at_1191 0 25 1 1 0 2596978 317858 317833 1 0 0 0 100 partof GGCGGCAGCCTCTCGGTAAAGGCCT 25 2R:1731127-2080000 1 NULL:1981834 154950_at_1252 0 25 1 1 0 2596981 317931 317906 1 0 0 0 100 partof AGGTGAAGCACGACGGCCAGCCGCC 25 2R:1731127-2080000 1 NULL:1981836 154950_at_1325 0 25 1 1 0 2596984 317990 317965 1 0 0 0 100 partof GAGGGCGTCATCTTCAAGCCGCTGC 25 2R:1731127-2080000 1 NULL:1981838 154950_at_1384 0 25 1 1 0 2602300 257218 257193 1 0 0 0 100 partof GCATTGTGGTTATAGTAGGCAGCGC 25 2R:1731127-2080000 -1 NULL:1986207 146704_at_5549 0 25 1 1 0 2596987 318029 318004 1 0 0 0 100 partof TTGCACAGCAACGTGCTGCAGATAA 25 2R:1731127-2080000 1 NULL:1981840 154950_at_1423 0 25 1 1 0 2602303 257226 257201 1 0 0 0 100 partof GTTATAGTAGGCAGCGCCGCCGTTG 25 2R:1731127-2080000 -1 NULL:1986209 146704_at_5541 0 25 1 1 0 2602306 257262 257237 1 0 0 0 100 partof GGCAGCATCGCGATAGTAGTGCTGC 25 2R:1731127-2080000 -1 NULL:1986211 146704_at_5505 0 25 1 1 0 2602309 257263 257238 1 0 0 0 100 partof GCAGCATCGCGATAGTAGTGCTGCT 25 2R:1731127-2080000 -1 NULL:1986213 146704_at_5504 0 25 1 1 0 2596990 318376 318351 1 0 0 0 100 partof CCACAGAATCCGAAAACAGCGGGAA 25 2R:1731127-2080000 1 NULL:1981842 154950_at_1465 0 25 1 1 0 2596993 318415 318390 1 0 0 0 100 partof TATGCCCCTGGACGAGGTGGATCCG 25 2R:1731127-2080000 1 NULL:1981844 154950_at_1504 0 25 1 1 0 2596996 318438 318413 1 0 0 0 100 partof CGCCCACGAGCAGCAGTTGGCTCGG 25 2R:1731127-2080000 1 NULL:1981846 154950_at_1527 0 25 1 1 0 2602312 257319 257294 1 0 0 0 100 partof GCCGCCACGCGAGGTTGTGGCATAA 25 2R:1731127-2080000 -1 NULL:1986215 146704_at_5448 0 25 1 1 0 2596999 318467 318442 1 0 0 0 100 partof AGCTGGCGATGCTGCCTGGCCAGCC 25 2R:1731127-2080000 1 NULL:1981848 154950_at_1556 0 25 1 1 0 2602315 257353 257328 1 0 0 0 100 partof AAGGACCCAGTAACGGGCGAGCCGC 25 2R:1731127-2080000 -1 NULL:1986217 146704_at_5414 0 25 1 1 0 2602318 257396 257371 1 0 0 0 100 partof GCGAGTGAAACTTGACGGCCGTTGT 25 2R:1731127-2080000 -1 NULL:1986219 146704_at_5371 0 25 1 1 0 2596202 24501 24476 1 0 0 0 100 partof TCCAAACGAAGACGAGGAGCCGGAG 25 2R:1731127-2080000 1 NULL:1981308 151882_at_966 0 25 1 1 0 2596205 24524 24499 1 0 0 0 100 partof AGTGCGAAACGCTGGACGTGGACCA 25 2R:1731127-2080000 1 NULL:1981310 151882_at_989 0 25 1 1 0 2596208 24596 24571 1 0 0 0 100 partof CTGCTTTTGAGTCTGTGAAGATACA 25 2R:1731127-2080000 1 NULL:1981312 151882_at_1061 0 25 1 1 0 2602321 257414 257389 1 0 0 0 100 partof CCGTTGTCTGTATGAATGGATTCGT 25 2R:1731127-2080000 -1 NULL:1986221 146704_at_5353 0 25 1 1 0 2602324 257445 257420 1 0 0 0 100 partof GAATATCTTTTGCTGCACACTTGAG 25 2R:1731127-2080000 -1 NULL:1986223 146704_at_5322 0 25 1 1 0 2602327 257455 257430 1 0 0 0 100 partof TGCTGCACACTTGAGTGGCGTGAAG 25 2R:1731127-2080000 -1 NULL:1986225 146704_at_5312 0 25 1 1 0 2596211 24630 24605 1 0 0 0 100 partof GGCGGGCTTCTATGACCACAACACA 25 2R:1731127-2080000 1 NULL:1981314 151882_at_1095 0 25 1 1 0 2596214 24677 24652 1 0 0 0 100 partof GCAGGCATCCTCACTACAGCAATCT 25 2R:1731127-2080000 1 NULL:1981316 151882_at_1142 0 25 1 1 0 2596217 24691 24666 1 0 0 0 100 partof TACAGCAATCTCTTCATTGCCGCAG 25 2R:1731127-2080000 1 NULL:1981318 151882_at_1156 0 25 1 1 0 2602330 257578 257553 1 0 0 0 100 partof TGTGCAGCTCTAAGCTTCTGCTGGG 25 2R:1731127-2080000 -1 NULL:1986227 146704_at_5189 0 25 1 1 0 2602333 272999 272974 1 0 0 0 100 partof CTCCAAACAAATTGGGTTTGGGCGC 25 2R:1731127-2080000 -1 NULL:1986229 146705_at_1050 0 25 1 1 0 2602336 273025 273000 1 0 0 0 100 partof GTATATTCCTCTCATCTAGTGCGTT 25 2R:1731127-2080000 -1 NULL:1986231 146705_at_1024 0 25 1 1 0 2602339 273084 273059 1 0 0 0 100 partof AGAGGTCCACGAAAATTCTCAAATT 25 2R:1731127-2080000 -1 NULL:1986233 146705_at_965 0 25 1 1 0 2596220 24724 24699 1 0 0 0 100 partof GGGCACGGCATTCAGCAGACTCCCG 25 2R:1731127-2080000 1 NULL:1981320 151882_at_1189 0 25 1 1 0 2596223 24754 24729 1 0 0 0 100 partof GGTCGAGCCATTTCCGAACTAATCT 25 2R:1731127-2080000 1 NULL:1981322 151882_at_1219 0 25 1 1 0 2596226 24803 24778 1 0 0 0 100 partof ATCTGTCGCGCCTCGGCTTCGAACG 25 2R:1731127-2080000 1 NULL:1981324 151882_at_1268 0 25 1 1 0 2596229 24844 24819 1 0 0 0 100 partof CCTATGCACGAAGTGAATATCGTTT 25 2R:1731127-2080000 1 NULL:1981326 151882_at_1309 0 25 1 1 0 2602342 273112 273087 1 0 0 0 100 partof GTATGAGATCGAAGGGCTCGTGTAC 25 2R:1731127-2080000 -1 NULL:1986235 146705_at_937 0 25 1 1 0 2602345 273321 273296 1 0 0 0 100 partof GCACTTCTTTTCCACCTCATGGCGA 25 2R:1731127-2080000 -1 NULL:1986237 146705_at_888 0 25 1 1 0 2602348 273336 273311 1 0 0 0 100 partof CTCATGGCGATTGGTTATAAACCTT 25 2R:1731127-2080000 -1 NULL:1986239 146705_at_873 0 25 1 1 0 2596232 24867 24842 1 0 0 0 100 partof TTGACAAATTTATCACAGGAGGATC 25 2R:1731127-2080000 1 NULL:1981328 151882_at_1332 0 25 1 1 0 2596235 27970 27945 1 0 0 0 100 partof CGAACATGGTCATTATGCTGATAGG 25 2R:1731127-2080000 1 NULL:1981330 151803_at_416 0 25 1 1 0 2596238 28050 28025 1 0 0 0 100 partof TTCGCCCGCGAGCACGGACTGGTCT 25 2R:1731127-2080000 1 NULL:1981332 151803_at_496 0 25 1 1 0 2602351 273369 273344 1 0 0 0 100 partof CTTATACCAATACTGGTTCTTGTCG 25 2R:1731127-2080000 -1 NULL:1986241 146705_at_840 0 25 1 1 0 2602354 273430 273405 1 0 0 0 100 partof AAGACAGTGGGCTCCCAAGTGCCGC 25 2R:1731127-2080000 -1 NULL:1986243 146705_at_779 0 25 1 1 0 2602357 273452 273427 1 0 0 0 100 partof CGCGGTTGAAGTGAAAAACATCAAG 25 2R:1731127-2080000 -1 NULL:1986245 146705_at_757 0 25 1 1 0 2596241 28102 28077 1 0 0 0 100 partof CCAACGTAGAGGAGGCGTTCATAAA 25 2R:1731127-2080000 1 NULL:1981334 151803_at_548 0 25 1 1 0 2596244 28116 28091 1 0 0 0 100 partof GCGTTCATAAATACGGCCAAAGAGA 25 2R:1731127-2080000 1 NULL:1981336 151803_at_562 0 25 1 1 0 2596247 28125 28100 1 0 0 0 100 partof AATACGGCCAAAGAGATTTACGAGA 25 2R:1731127-2080000 1 NULL:1981338 151803_at_571 0 25 1 1 0 2601700 48957 48932 1 0 0 0 100 partof GTAGCTTCCTTTGCTGCCGCCGACG 25 2R:1731127-2080000 -1 NULL:1985807 146689_at_364 0 25 1 1 0 2601703 51423 51398 1 0 0 0 100 partof TGGCGCCGGCTTGAAGCACTGCAGC 25 2R:1731127-2080000 -1 NULL:1985809 146690_at_4848 0 25 1 1 0 2602360 273558 273533 1 0 0 0 100 partof ATCGGTGGGCTGCACATCCCACACG 25 2R:1731127-2080000 -1 NULL:1986247 146705_at_717 0 25 1 1 0 2601706 51446 51421 1 0 0 0 100 partof GCAGGAAGGCGGTGTAGACCACAAA 25 2R:1731127-2080000 -1 NULL:1985811 146690_at_4825 0 25 1 1 0 2602363 273638 273613 1 0 0 0 100 partof CGTCTAAGTTGAGTGCCTGGCGGAT 25 2R:1731127-2080000 -1 NULL:1986249 146705_at_637 0 25 1 1 0 2601709 51455 51430 1 0 0 0 100 partof CGGTGTAGACCACAAAGGCCACCGC 25 2R:1731127-2080000 -1 NULL:1985813 146690_at_4816 0 25 1 1 0 2602366 273667 273642 1 0 0 0 100 partof ATGGATCCGGGAGGACCATCAGTGC 25 2R:1731127-2080000 -1 NULL:1986251 146705_at_608 0 25 1 1 0 2602369 273725 273700 1 0 0 0 100 partof ATTCATAGTCTGTGGCCCAGGAACT 25 2R:1731127-2080000 -1 NULL:1986253 146705_at_550 0 25 1 1 0 2596250 28142 28117 1 0 0 0 100 partof TTACGAGAAGATCCAGGAAGGTGTC 25 2R:1731127-2080000 1 NULL:1981340 151803_at_588 0 25 1 1 0 2596253 28153 28128 1 0 0 0 100 partof TCCAGGAAGGTGTCTTCGACATCAA 25 2R:1731127-2080000 1 NULL:1981342 151803_at_599 0 25 1 1 0 2596256 28313 28288 1 0 0 0 100 partof AGCTGGAGCAGCAAACAGTGGCTGC 25 2R:1731127-2080000 1 NULL:1981344 151803_at_699 0 25 1 1 0 2596259 28334 28309 1 0 0 0 100 partof CTGCTGCTAGGAGTAAACCGCAGAT 25 2R:1731127-2080000 1 NULL:1981346 151803_at_720 0 25 1 1 0 2601712 51474 51449 1 0 0 0 100 partof CACCGCCAGAGCAATCAGAGCGTAC 25 2R:1731127-2080000 -1 NULL:1985815 146690_at_4797 0 25 1 1 0 2601715 51500 51475 1 0 0 0 100 partof TAAAGATGTTCAGCTCGGGCTGGCG 25 2R:1731127-2080000 -1 NULL:1985817 146690_at_4771 0 25 1 1 0 2602372 274560 274535 1 0 0 0 100 partof TCATCGACCGCCTCAAAGGTGACCA 25 2R:1731127-2080000 -1 NULL:1986255 146705_at_500 0 25 1 1 0 2601718 51524 51499 1 0 0 0 100 partof GGAAGCGGTTCTTGCGTAGCCACTC 25 2R:1731127-2080000 -1 NULL:1985819 146690_at_4747 0 25 1 1 0 2602375 301994 301969 1 0 0 0 100 partof CCACAGCTTAGGAAAATCAACGAAA 25 2R:1731127-2080000 -1 NULL:1986257 141721_at_1776 0 25 1 1 0 2602378 302063 302038 1 0 0 0 100 partof GCAAACAATACAAAATATGCGATGC 25 2R:1731127-2080000 -1 NULL:1986259 141721_at_1707 0 25 1 1 0 2596262 28374 28349 1 0 0 0 100 partof TGGGATAGGCGCAGCCGCTTCTGTA 25 2R:1731127-2080000 1 NULL:1981348 151803_at_760 0 25 1 1 0 2596265 28402 28377 1 0 0 0 100 partof GCTACTTTAGTGACTAACTAATAGA 25 2R:1731127-2080000 1 NULL:1981350 151803_at_788 0 25 1 1 0 2596268 28487 28462 1 0 0 0 100 partof TAGCTACCACTAATCTAGCAATTGG 25 2R:1731127-2080000 1 NULL:1981352 151803_at_873 0 25 1 1 0 2601721 51548 51523 1 0 0 0 100 partof CCAGCACTTCGTCCTCGGATAACAG 25 2R:1731127-2080000 -1 NULL:1985821 146690_at_4723 0 25 1 1 0 2601724 51650 51625 1 0 0 0 100 partof ATATGCTGGGAAACCGACGGCGGAA 25 2R:1731127-2080000 -1 NULL:1985823 146690_at_4687 0 25 1 1 0 2602381 302088 302063 1 0 0 0 100 partof TCCAGCAGAGCCTCCTTTAAAGCTT 25 2R:1731127-2080000 -1 NULL:1986261 141721_at_1682 0 25 1 1 0 2601727 51796 51771 1 0 0 0 100 partof GCTGCAGTACTGTCCGGCTGATTGT 25 2R:1731127-2080000 -1 NULL:1985825 146690_at_4541 0 25 1 1 0 2602384 302113 302088 1 0 0 0 100 partof GTCCACCCGTTCCACACTGAGTTTG 25 2R:1731127-2080000 -1 NULL:1986263 141721_at_1657 0 25 1 1 0 2602387 302197 302172 1 0 0 0 100 partof CTCCGCAGAGGGAGCGTATCTGTGC 25 2R:1731127-2080000 -1 NULL:1986265 141721_at_1573 0 25 1 1 0 2596271 28509 28484 1 0 0 0 100 partof TGGACACTAAGCTAAATGTTAAAAC 25 2R:1731127-2080000 1 NULL:1981354 151803_at_895 0 25 1 1 0 2596274 28525 28500 1 0 0 0 100 partof TGTTAAAACCATTAAGATCAGACAG 25 2R:1731127-2080000 1 NULL:1981356 151803_at_911 0 25 1 1 0 2596277 74955 74930 1 0 0 0 100 partof AACATCAAGACCTGGCTGAGCGTGA 25 2R:1731127-2080000 1 NULL:1981358 152190_at_2485 0 25 1 1 0 2601730 51900 51875 1 0 0 0 100 partof TAAGAACTCATTTTCCTCGAGTAGT 25 2R:1731127-2080000 -1 NULL:1985827 146690_at_4497 0 25 1 1 0 2601733 51913 51888 1 0 0 0 100 partof TCCTCGAGTAGTTTGTCGAGCATTT 25 2R:1731127-2080000 -1 NULL:1985829 146690_at_4484 0 25 1 1 0 2602390 302218 302193 1 0 0 0 100 partof GTGCTGCCTCAGCAGAGCCACCAGG 25 2R:1731127-2080000 -1 NULL:1986267 141721_at_1552 0 25 1 1 0 2601736 51962 51937 1 0 0 0 100 partof TTTTGATTTCGAATACGTCCTGTGA 25 2R:1731127-2080000 -1 NULL:1985831 146690_at_4435 0 25 1 1 0 2602393 302240 302215 1 0 0 0 100 partof AGGCCCACCAGAAGCTGCTGCTCTG 25 2R:1731127-2080000 -1 NULL:1986269 141721_at_1530 0 25 1 1 0 2601739 52023 51998 1 0 0 0 100 partof ATCGCCGTCGTAGAGGACGGGCACT 25 2R:1731127-2080000 -1 NULL:1985833 146690_at_4374 0 25 1 1 0 2602396 302275 302250 1 0 0 0 100 partof GGCAATGCATCCTCGCAGGCCATCG 25 2R:1731127-2080000 -1 NULL:1986271 141721_at_1495 0 25 1 1 0 2602399 302300 302275 1 0 0 0 100 partof CCGAAAGGCAGGAACGCAGCTGCCG 25 2R:1731127-2080000 -1 NULL:1986273 141721_at_1470 0 25 1 1 0 2596280 75057 75032 1 0 0 0 100 partof CGGACCCCAGCGATCGGTGGATATC 25 2R:1731127-2080000 1 NULL:1981360 152190_at_2529 0 25 1 1 0 2596283 75067 75042 1 0 0 0 100 partof CGATCGGTGGATATCATCGTTTCCG 25 2R:1731127-2080000 1 NULL:1981362 152190_at_2539 0 25 1 1 0 2596286 75093 75068 1 0 0 0 100 partof CGCCTTCATAGTAACCCTCCTGTTG 25 2R:1731127-2080000 1 NULL:1981364 152190_at_2565 0 25 1 1 0 2596289 75302 75277 1 0 0 0 100 partof ATCTGCAGATCGAGCAGAAGCCAAA 25 2R:1731127-2080000 1 NULL:1981366 152190_at_2774 0 25 1 1 0 2601742 52134 52109 1 0 0 0 100 partof ACTATCTCGTATTTCTTGGCTGCCT 25 2R:1731127-2080000 -1 NULL:1985835 146690_at_4316 0 25 1 1 0 2601745 67873 67848 1 0 0 0 100 partof AGCACTCCTTCCTCGTCCATGAGAT 25 2R:1731127-2080000 -1 NULL:1985837 146691_at_413 0 25 1 1 0 2601748 67891 67866 1 0 0 0 100 partof ATGAGATCCCCATCATATATGATGG 25 2R:1731127-2080000 -1 NULL:1985839 146691_at_395 0 25 1 1 0 2596292 75330 75305 1 0 0 0 100 partof AAAGGACGAGCTGATGGTGTCGAAC 25 2R:1731127-2080000 1 NULL:1981368 152190_at_2802 0 25 1 1 0 2596295 75351 75326 1 0 0 0 100 partof GAACAGCGTGCTCAAGCTGGCCGCC 25 2R:1731127-2080000 1 NULL:1981370 152190_at_2823 0 25 1 1 0 2596298 75372 75347 1 0 0 0 100 partof CGCCGATCTGCTAAAGGAACTCGAA 25 2R:1731127-2080000 1 NULL:1981372 152190_at_2844 0 25 1 1 0 2601751 67897 67872 1 0 0 0 100 partof TCCCCATCATATATGATGGGCTCCT 25 2R:1731127-2080000 -1 NULL:1985841 146691_at_389 0 25 1 1 0 2601754 68021 67996 1 0 0 0 100 partof GTTCTTGATGCCATACTGTTTGGCT 25 2R:1731127-2080000 -1 NULL:1985843 146691_at_336 0 25 1 1 0 2601757 68082 68057 1 0 0 0 100 partof AAGGAGTCGGTGTCATCGTCGATTT 25 2R:1731127-2080000 -1 NULL:1985845 146691_at_275 0 25 1 1 0 2601760 68098 68073 1 0 0 0 100 partof CGTCGATTTTCTCGAGTTCCGCTAA 25 2R:1731127-2080000 -1 NULL:1985847 146691_at_259 0 25 1 1 0 2601763 68101 68076 1 0 0 0 100 partof CGATTTTCTCGAGTTCCGCTAAAAC 25 2R:1731127-2080000 -1 NULL:1985849 146691_at_256 0 25 1 1 0 2601766 68117 68092 1 0 0 0 100 partof CGCTAAAACCTTATCACAGGTCACG 25 2R:1731127-2080000 -1 NULL:1985851 146691_at_240 0 25 1 1 0 2601769 68125 68100 1 0 0 0 100 partof CCTTATCACAGGTCACGCAGCTTCG 25 2R:1731127-2080000 -1 NULL:1985853 146691_at_232 0 25 1 1 0 2601772 69845 69820 1 0 0 0 100 partof AACGGCCACGTAATCCTTGTCGGCC 25 2R:1731127-2080000 -1 NULL:1985855 146691_at_195 0 25 1 1 0 2601775 69852 69827 1 0 0 0 100 partof ACGTAATCCTTGTCGGCCAGGAGCT 25 2R:1731127-2080000 -1 NULL:1985857 146691_at_188 0 25 1 1 0 2601778 69890 69865 1 0 0 0 100 partof GGCATTGACCTCCTCGATGACGGCC 25 2R:1731127-2080000 -1 NULL:1985859 146691_at_150 0 25 1 1 0 2596600 165716 165691 1 0 0 0 100 partof CAATGAACCCAGTGGCAGTCAGCAC 25 2R:1731127-2080000 1 NULL:1981574 146697_at_2120 0 25 1 1 0 2596603 165764 165739 1 0 0 0 100 partof ACAATCAGGATCAGCCTCAGCAGAG 25 2R:1731127-2080000 1 NULL:1981576 146697_at_2168 0 25 1 1 0 2596606 165782 165757 1 0 0 0 100 partof AGCAGAGCCCTGTTGTCCCGCCGTA 25 2R:1731127-2080000 1 NULL:1981578 146697_at_2186 0 25 1 1 0 2596609 165827 165802 1 0 0 0 100 partof CAACTGCGCCGATGGCACCAGGGCG 25 2R:1731127-2080000 1 NULL:1981580 146697_at_2231 0 25 1 1 0 2601781 69903 69878 1 0 0 0 100 partof TCGATGACGGCCTCCGGCTCCGGAG 25 2R:1731127-2080000 -1 NULL:1985861 146691_at_137 0 25 1 1 0 2601784 69957 69932 1 0 0 0 100 partof TTGTTGTTGCCTGCACCACTCACAT 25 2R:1731127-2080000 -1 NULL:1985863 146691_at_83 0 25 1 1 0 2601787 86131 86106 1 0 0 0 100 partof GCAGGGCCCTACAACCAATCCTAAA 25 2R:1731127-2080000 -1 NULL:1985865 142715_at_419 0 25 1 1 0 2596612 166340 166315 1 0 0 0 100 partof ATTGGTGACATTCTGCCGCAGGACA 25 2R:1731127-2080000 1 NULL:1981582 146697_at_2287 0 25 1 1 0 2596615 212158 212133 1 0 0 0 100 partof TCACGTGCAGGTGAATATGATGTAC 25 2R:1731127-2080000 1 NULL:1981584 146701_at_462 0 25 1 1 0 2596618 212173 212148 1 0 0 0 100 partof TATGATGTACCAAGAGGACAAGTTC 25 2R:1731127-2080000 1 NULL:1981586 146701_at_477 0 25 1 1 0 2601790 86152 86127 1 0 0 0 100 partof TAAATCTATTTGACGGCGCTCTGGA 25 2R:1731127-2080000 -1 NULL:1985867 142715_at_398 0 25 1 1 0 2601793 86183 86158 1 0 0 0 100 partof GCTGCTTGTGGGTGCCGTCACAGAA 25 2R:1731127-2080000 -1 NULL:1985869 142715_at_367 0 25 1 1 0 2601796 86218 86193 1 0 0 0 100 partof GTGGTCTGTTTGCAGTTGCAGAGCC 25 2R:1731127-2080000 -1 NULL:1985871 142715_at_332 0 25 1 1 0 2601799 86235 86210 1 0 0 0 100 partof GCAGAGCCAGTAGTCTCCCGACTTC 25 2R:1731127-2080000 -1 NULL:1985873 142715_at_315 0 25 1 1 0 2596621 212177 212152 1 0 0 0 100 partof ATGTACCAAGAGGACAAGTTCCGGT 25 2R:1731127-2080000 1 NULL:1981588 146701_at_481 0 25 1 1 0 2596624 212234 212209 1 0 0 0 100 partof GTGCAACTGCCCTATGATTACTCAA 25 2R:1731127-2080000 1 NULL:1981590 146701_at_538 0 25 1 1 0 2596627 212274 212249 1 0 0 0 100 partof TTCTGCTGCCCAACGAAGTAAACGG 25 2R:1731127-2080000 1 NULL:1981592 146701_at_578 0 25 1 1 0 2596630 212381 212356 1 0 0 0 100 partof TTTCTGCCCAGGATGTGCATAGAGT 25 2R:1731127-2080000 1 NULL:1981594 146701_at_685 0 25 1 1 0 2596633 212395 212370 1 0 0 0 100 partof GTGCATAGAGTACGACGTGGACCTC 25 2R:1731127-2080000 1 NULL:1981596 146701_at_699 0 25 1 1 0 2596636 212407 212382 1 0 0 0 100 partof CGACGTGGACCTCAAGCAGGTACTT 25 2R:1731127-2080000 1 NULL:1981598 146701_at_711 0 25 1 1 0 2596639 212513 212488 1 0 0 0 100 partof TATTACGGAAGTCTTCAGCGATAAG 25 2R:1731127-2080000 1 NULL:1981600 146701_at_747 0 25 1 1 0 2596642 212607 212582 1 0 0 0 100 partof ATCGACGTAAATGAGGCAGGATCGG 25 2R:1731127-2080000 1 NULL:1981602 146701_at_841 0 25 1 1 0 2596645 212724 212699 1 0 0 0 100 partof AAGATAGTACCCATGATGCTCAACA 25 2R:1731127-2080000 1 NULL:1981604 146701_at_889 0 25 1 1 0 2596648 212794 212769 1 0 0 0 100 partof TACGAAACCCGCAGGCCGTCTTCTT 25 2R:1731127-2080000 1 NULL:1981606 146701_at_959 0 25 1 1 0 2596651 212806 212781 1 0 0 0 100 partof AGGCCGTCTTCTTCGCCGGCCGATT 25 2R:1731127-2080000 1 NULL:1981608 146701_at_971 0 25 1 1 0 2596654 212823 212798 1 0 0 0 100 partof GGCCGATTCTCGAACCCCAAGTCTG 25 2R:1731127-2080000 1 NULL:1981610 146701_at_988 0 25 1 1 0 2596657 213893 213868 1 0 0 0 100 partof AGGCCTTGCTGGTGAACGCCATCTA 25 2R:1731127-2080000 1 NULL:1981612 151958_at_413 0 25 1 1 0 2596660 213927 213902 1 0 0 0 100 partof CCAGTGGGAGTCGAAGTTTGACCCA 25 2R:1731127-2080000 1 NULL:1981614 151958_at_447 0 25 1 1 0 2596663 213944 213919 1 0 0 0 100 partof TTGACCCAGCTAAGACCAGAGCCTC 25 2R:1731127-2080000 1 NULL:1981616 151958_at_464 0 25 1 1 0 2596666 214001 213976 1 0 0 0 100 partof CCGTCCAGATGATGGCGCAAATGGG 25 2R:1731127-2080000 1 NULL:1981618 151958_at_521 0 25 1 1 0 2596669 214070 214045 1 0 0 0 100 partof TCGAGCTGCCGTACCTTAACTCCAA 25 2R:1731127-2080000 1 NULL:1981620 151958_at_590 0 25 1 1 0 2596672 214097 214072 1 0 0 0 100 partof TGTCCATGACTATCTTTCTGCCCCG 25 2R:1731127-2080000 1 NULL:1981622 151958_at_617 0 25 1 1 0 2596675 214103 214078 1 0 0 0 100 partof TGACTATCTTTCTGCCCCGAGAAGT 25 2R:1731127-2080000 1 NULL:1981624 151958_at_623 0 25 1 1 0 2596678 214133 214108 1 0 0 0 100 partof GCTTGAGCGCCCTGGAAGAGAAGAT 25 2R:1731127-2080000 1 NULL:1981626 151958_at_653 0 25 1 1 0 2596681 214226 214201 1 0 0 0 100 partof TTCGTGATGAACTCAAAGAGACCTT 25 2R:1731127-2080000 1 NULL:1981628 151958_at_746 0 25 1 1 0 2596684 214321 214296 1 0 0 0 100 partof CATCCGAGAGCTATTCACCGACAAG 25 2R:1731127-2080000 1 NULL:1981630 151958_at_783 0 25 1 1 0 2602000 139071 139046 1 0 0 0 100 partof AAGTCCTGGGTTACCGGGATGACGC 25 2R:1731127-2080000 -1 NULL:1986007 146693_at_284 0 25 1 1 0 2596687 214402 214377 1 0 0 0 100 partof GCACAAGGCGTTTCTGGAGGTGAAC 25 2R:1731127-2080000 1 NULL:1981632 151958_at_864 0 25 1 1 0 2602003 139088 139063 1 0 0 0 100 partof GATGACGCGGTCGTTGGTCTCGTCA 25 2R:1731127-2080000 -1 NULL:1986009 146693_at_267 0 25 1 1 0 2602006 139090 139065 1 0 0 0 100 partof TGACGCGGTCGTTGGTCTCGTCATC 25 2R:1731127-2080000 -1 NULL:1986011 146693_at_265 0 25 1 1 0 2602009 139113 139088 1 0 0 0 100 partof TCCTCCTCATCGTGACTGTCCGTGT 25 2R:1731127-2080000 -1 NULL:1986013 146693_at_242 0 25 1 1 0 2596690 214533 214508 1 0 0 0 100 partof GCCGTCACAAATCGAGCGGGATTTT 25 2R:1731127-2080000 1 NULL:1981634 151958_at_925 0 25 1 1 0 2596693 214557 214532 1 0 0 0 100 partof TCTACGTTCCTCATGGCCGATCATC 25 2R:1731127-2080000 1 NULL:1981636 151958_at_949 0 25 1 1 0 2596696 214600 214575 1 0 0 0 100 partof GCGATGCGAACACCATATATTTCCA 25 2R:1731127-2080000 1 NULL:1981638 151958_at_992 0 25 1 1 0 2602012 139118 139093 1 0 0 0 100 partof CTCATCGTGACTGTCCGTGTCCTCG 25 2R:1731127-2080000 -1 NULL:1986015 146693_at_237 0 25 1 1 0 2596699 216868 216843 1 0 0 0 100 partof CGGCCATCCTGGTCAATGCCATCTA 25 2R:1731127-2080000 1 NULL:1981640 146702_at_521 0 25 1 1 0 2602015 139126 139101 1 0 0 0 100 partof GACTGTCCGTGTCCTCGCTGTCGTC 25 2R:1731127-2080000 -1 NULL:1986017 146693_at_229 0 25 1 1 0 2602018 139229 139204 1 0 0 0 100 partof CGTCGTCGGTCTCAATTCCGGGTAT 25 2R:1731127-2080000 -1 NULL:1986019 146693_at_193 0 25 1 1 0 2602021 139258 139233 1 0 0 0 100 partof AGCATTTTGCCCAGCGGCTGCAGAT 25 2R:1731127-2080000 -1 NULL:1986021 146693_at_164 0 25 1 1 0 2602024 139274 139249 1 0 0 0 100 partof GCTGCAGATCTGTGCCGGCCGTCTT 25 2R:1731127-2080000 -1 NULL:1986023 146693_at_148 0 25 1 1 0 2602027 139380 139355 1 0 0 0 100 partof TTTCATCCTCATAACGCCGCGTCTG 25 2R:1731127-2080000 -1 NULL:1986025 146693_at_100 0 25 1 1 0 2602030 139391 139366 1 0 0 0 100 partof TAACGCCGCGTCTGCGATTCTTCGT 25 2R:1731127-2080000 -1 NULL:1986027 146693_at_89 0 25 1 1 0 2602033 139400 139375 1 0 0 0 100 partof GTCTGCGATTCTTCGTTTACGGAGG 25 2R:1731127-2080000 -1 NULL:1986029 146693_at_80 0 25 1 1 0 2602036 139455 139430 1 0 0 0 100 partof CCACGGAGACTTTGAGCGTGGGAAA 25 2R:1731127-2080000 -1 NULL:1986031 146693_at_25 0 25 1 1 0 2602039 139905 139880 1 0 0 0 100 partof GTTCCAGATTCATGCCATCGTGAAT 25 2R:1731127-2080000 -1 NULL:1986033 146694_at_196 0 25 1 1 0 sim4 1.0 na_adh.cDNAs.dros 1.0 2003-01-13 21:14:12 Fly ESTs genomic blastx_masked 1.0 aa_SPTR.othvert 1.0 2003-01-15 00:28:37 BLASTX Similarity to Other Species genomic 2602833 2496 1281 1 0 0 0 731 partof SSSGGEATAL--HDIECSINQEYTVHCKRDENANEVYVPFSFLRNYFDVSGAVSTNSNEVAKFNWVHSTAKVNLPRGKYDARGVYMYFENYNVEVRDRVKCISAAEGVPVSTQWEKRGYFYPTQIAQFALSHYSKNLTEPAPRVRVLE---DGDGNQM--EWSTPKTSNMTRIWHHKFNTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKGI-MGDKRSPLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNPVRRSLN-GFAELRPGWISAMGQGHAISVLARAYWHSGGDERYLRAAAAGLQPYRVYSRDGGVLAQFMDKFYW 1215 2R:1731127-2080000 -1 NULL:1986612 O18756 91 496 1 1 0 1172 809 1 0 0 0 445 partof YEEYPTTPPSYVLNGFIYSLLGLYDLNSTAPGKIAREAGKLFAQGMHSLKKMLLLFDTGSGTSYDLRHLSLGVAPNLARWDYHATHVNQLLLLATIDSDPLIAQTAERWKGYMFGRRAKHN 363 2R:1731127-2080000 -1 NULL:1986613 O18756 496 617 1 1 0 2602837 5318 4841 1 0 0 0 440 partof QEIGRMIFELFADTVPRTAENFRQFCTGE--YRPD-GVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM*HG 477 2R:1731127-2080000 -1 NULL:1986615 P26882 26 187 1 1 0 2602839 5318 4850 1 0 0 0 456 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1986617 P80311 46 197 1 1 0 2602841 5318 4856 1 0 0 0 469 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCG 462 2R:1731127-2080000 -1 NULL:1986619 P24367 45 194 1 1 0 2602843 8846 7730 1 0 0 0 1005 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPF-FVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986621 P27718 40 414 1 1 0 7593 7395 1 0 0 0 88 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILRDHQLESSSV 198 2R:1731127-2080000 -1 NULL:1986622 P27718 419 485 1 1 0 2602846 8846 7730 1 0 0 0 1047 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986624 P22781 40 414 1 1 0 7593 7422 1 0 0 0 94 partof NHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEILR 171 2R:1731127-2080000 -1 NULL:1986625 P22781 419 476 1 1 0 2602849 8846 7730 1 0 0 0 1043 partof LSPADAPQSPEPFKDVLEDFEQKIMPGVVHWNHPKFFAYFPSGNSFPSVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQT-SVHDSVFLPSLIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHL-TGV--DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 1116 2R:1731127-2080000 -1 NULL:1986627 P80041 40 414 1 1 0 7602 7425 1 0 0 0 98 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQIKCFAEEIL 177 2R:1731127-2080000 -1 NULL:1986628 P80041 416 475 1 1 0 2602852 18125 17771 1 0 0 0 365 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 354 2R:1731127-2080000 -1 NULL:1986630 P27718 33 147 1 1 0 17620 17149 1 0 0 0 282 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPF-FVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986631 P27718 144 298 1 1 0 17128 16870 1 0 0 0 282 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986632 P27718 289 376 1 1 0 15554 15305 1 0 0 0 190 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQHDELSEIMN 249 2R:1731127-2080000 -1 NULL:1986633 P27718 405 487 1 1 0 2602857 18125 17777 1 0 0 0 367 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986635 P80041 33 145 1 1 0 17620 17149 1 0 0 0 325 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMAN 471 2R:1731127-2080000 -1 NULL:1986636 P80041 144 298 1 1 0 17128 16870 1 0 0 0 278 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986637 P80041 289 376 1 1 0 15554 15332 1 0 0 0 165 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1986638 P80041 405 479 1 1 0 2602862 18277 18124 1 0 0 0 148 partof MDSTEFRKRGMEMVEYICNYLETLNERRVTPSVEPGYLRHLLPRKPQK*PQ 153 2R:1731127-2080000 -1 NULL:1986640 P22781 0 51 1 1 0 18125 17777 1 0 0 0 372 partof EPGQFLPHHPSRTAEAPQEPEDWDQIMRDVEDKIMPGVTHWQHPRFHAYFPAGNSFPSILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQ 348 2R:1731127-2080000 -1 NULL:1986641 P22781 33 145 1 1 0 17620 17185 1 0 0 0 309 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLL 435 2R:1731127-2080000 -1 NULL:1986642 P22781 144 288 1 1 0 17128 16870 1 0 0 0 288 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAI--DYRHWGVPLSRRFRSLKLWYVACAIWGPKALDS 258 2R:1731127-2080000 -1 NULL:1986643 P22781 289 376 1 1 0 15554 15332 1 0 0 0 167 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAWDIIVDFANELLEKEQ 222 2R:1731127-2080000 -1 NULL:1986644 P22781 405 479 1 1 0 2602868 33778 33214 1 0 0 0 304 partof KMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMRDPD 564 2R:1731127-2080000 -1 NULL:1986646 Q90632 15 203 1 1 0 2602870 33778 33223 1 0 0 0 320 partof KMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 555 2R:1731127-2080000 -1 NULL:1986648 P57788 13 198 1 1 0 2602872 33781 33100 1 0 0 0 288 partof PKMPDGGYGWVVVFASLVVSLIADGLSFSFG-LINV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR----DPDWLIEENRLESRSQSVTTFSNSSVCLEEIKKLLDTGITK 681 2R:1731127-2080000 -1 NULL:1986650 P53988 11 242 1 1 0 2602874 88519 87613 1 0 0 0 680 partof LNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDS---NVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 906 2R:1731127-2080000 -1 NULL:1986652 P15122 5 315 1 1 0 2602876 88531 87613 1 0 0 0 682 partof PTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHND---SNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 918 2R:1731127-2080000 -1 NULL:1986654 Q90W83 3 317 1 1 0 2602878 88534 87613 1 0 0 0 654 partof APTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDS---NVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVL--ANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKYYPFNDEF 921 2R:1731127-2080000 -1 NULL:1986656 P16116 0 315 1 1 0 2602880 111132 110106 1 0 0 0 367 partof WNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKD-FSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFT-DMRHGKLLTMFVFSFP-KLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFK-RNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1026 2R:1731127-2080000 -1 NULL:1986658 P33268 32 361 1 1 0 110040 109626 1 0 0 0 243 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVE 414 2R:1731127-2080000 -1 NULL:1986659 P33268 360 494 1 1 0 2602883 111141 109629 1 0 0 0 416 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDD-PLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMFVFSFPKLASXXXXXXMP----EDVHQFFMRLVNDTIALRERE--NFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFT------QHCS------------SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRV 1512 2R:1731127-2080000 -1 NULL:1986661 P47787 35 531 1 1 0 2602886 111141 110106 1 0 0 0 390 partof FNYWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKD-FSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDF-RTMGQKVFTDMRHGKLLTMFVFSF-PKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFK-RNDFMNLLIEL-KQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1035 2R:1731127-2080000 -1 NULL:1986663 Q9PU44 29 367 1 1 0 110040 109665 1 0 0 0 268 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSI 375 2R:1731127-2080000 -1 NULL:1986664 Q9PU44 366 488 1 1 0 2602889 196650 196461 1 0 0 0 256 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 189 2R:1731127-2080000 -1 NULL:1986666 Q9PWG7 2 65 1 1 0 195146 194879 1 0 0 0 320 partof GRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 267 2R:1731127-2080000 -1 NULL:1986667 Q9PWG7 66 155 1 1 0 194836 194380 1 0 0 0 444 partof CIAKVVIWNVGTGEILVHI-DSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILH 456 2R:1731127-2080000 -1 NULL:1986668 Q9PWG7 150 303 1 1 0 194349 194052 1 0 0 0 342 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLK 297 2R:1731127-2080000 -1 NULL:1986669 Q9PWG7 293 391 1 1 0 2602894 196650 196461 1 0 0 0 259 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 189 2R:1731127-2080000 -1 NULL:1986671 Q9PWG8 2 65 1 1 0 195146 194879 1 0 0 0 326 partof GRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 267 2R:1731127-2080000 -1 NULL:1986672 Q9PWG8 66 155 1 1 0 194836 194344 1 0 0 0 438 partof CIAKVVIWNVGTGEILVHI-DSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 492 2R:1731127-2080000 -1 NULL:1986673 Q9PWG8 150 316 1 1 0 2602899 196659 196461 1 0 0 0 266 partof MSFR-VVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 198 2R:1731127-2080000 -1 NULL:1986675 Q9XS70 0 67 1 1 0 195158 194879 1 0 0 0 327 partof LFQVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 279 2R:1731127-2080000 -1 NULL:1986676 Q9XS70 64 157 1 1 0 194836 194344 1 0 0 0 417 partof CIAKVVIWNVGTGEILVHIDS-HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILHMNII*PKSHRTG 492 2R:1731127-2080000 -1 NULL:1986677 Q9XS70 152 318 1 1 0 2602903 208017 207216 1 0 0 0 376 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAHSFHQVLAAYQD----SQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSK-NVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNT----KTGLPALEEKLRLTTLSQITQ--SLYETKVALKLPRFKAEFQVELS 801 2R:1731127-2080000 -1 NULL:1986679 P80229 10 285 1 1 0 207158 207026 1 0 0 0 79 partof VNINLLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 132 2R:1731127-2080000 -1 NULL:1986680 P80229 283 326 1 1 0 2602906 208026 207189 1 0 0 0 434 partof LALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLAS-SDPEQIAH--SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLP--ALDA----MALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 837 2R:1731127-2080000 -1 NULL:1986682 Q90935 25 313 1 1 0 2602908 208041 207189 1 0 0 0 387 partof EFARRLALFSINVYGKLSGQK-PGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQI--AHSFHQVLAA--YQD---SQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAA-ATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQKVSFT 852 2R:1731127-2080000 -1 NULL:1986684 Q9W648 64 357 1 1 0 2602910 210463 209644 1 0 0 0 325 partof LEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGL---EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQA-ASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRP-TRVRMMHVCENFFFAVLP--MFEA----TALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 819 2R:1731127-2080000 -1 NULL:1986686 Q90935 25 307 1 1 0 209580 209466 1 0 0 0 81 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986687 Q90935 309 346 1 1 0 2602913 210472 209644 1 0 0 0 285 partof AQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQ--VAESFGVVLKSYEQ--CQV-LKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF-GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPT-RVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAM-NLEK--VDVKIPSFTAEFQQELSQVL 828 2R:1731127-2080000 -1 NULL:1986689 O54757 45 322 1 1 0 209580 209466 1 0 0 0 77 partof MGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 114 2R:1731127-2080000 -1 NULL:1986690 O54757 324 361 1 1 0 2602917 210481 209644 1 0 0 0 283 partof EEFAQGLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGL-EAQQVAESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF--GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPD----EKSNLTSLEKKLSDISLEVVSSAMNLE--KVDVKIPSFTAEFQQELSQVL 837 2R:1731127-2080000 -1 NULL:1986692 P80229 1 288 1 1 0 2602919 302502 302097 1 0 0 0 243 partof TLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 405 2R:1731127-2080000 -1 NULL:1986694 AAK58569 367 499 1 1 0 2602922 302505 302097 1 0 0 0 247 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVE 408 2R:1731127-2080000 -1 NULL:1986696 O42563 366 499 1 1 0 2602925 303124 302563 1 0 0 0 153 partof RDLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWA-DFRMWQAYLALEFPLIA---RLLQYKSYAEPATAYFQKVALSXXXXXXXXXXXPLQTFLQLYSNAE--------KPLTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 561 2R:1731127-2080000 -1 NULL:1986698 P24463 160 361 1 1 0 302505 302088 1 0 0 0 223 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERVD 417 2R:1731127-2080000 -1 NULL:1986699 P24463 361 497 1 1 0 2602928 307432 306985 1 0 0 0 264 partof DKFFNLFHFKTNYCTIVL----DDSMHYLYTTP---LLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE 447 2R:1731127-2080000 -1 NULL:1986701 Q04173 231 386 1 1 0 306924 306762 1 0 0 0 107 partof ALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKG 162 2R:1731127-2080000 -1 NULL:1986702 Q04173 387 441 1 1 0 2602932 307432 306985 1 0 0 0 274 partof DKFFNLFHFKTNYCTIVL----DDSMHYLYTT---PLLKNMVDWLDSTDIDLLTTGVLALGNFARTDSHCIYFVEQQTMNKLLEVLAKNNGVKD-DVRLQHALLSALRNLVIPKPNKNAVIQAGLVQTILPMLEIHQPPVVFKLLGTLRMTVDGQGE 447 2R:1731127-2080000 -1 NULL:1986704 O93614 280 435 1 1 0 306924 306762 1 0 0 0 104 partof ALELLKNKTLIEQLVHWSKSSDYAGVTGESLRLMAWLIKHAYLSKIAYALPRKG 162 2R:1731127-2080000 -1 NULL:1986705 O93614 436 490 1 1 0 2597498 27351 27186 1 0 0 0 158 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1982225 P22129 19 74 1 1 0 28136 27821 1 0 0 0 278 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 315 2R:1731127-2080000 1 NULL:1982226 P22129 73 178 1 1 0 2597501 27351 27189 1 0 0 0 279 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982228 Q90965 15 69 1 1 0 28172 27821 1 0 0 0 561 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982229 Q90965 68 185 1 1 0 2597504 27351 27189 1 0 0 0 279 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982231 Q01971 15 69 1 1 0 28172 27821 1 0 0 0 561 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982232 Q01971 68 185 1 1 0 2597507 76633 76480 1 0 0 0 109 partof LRNFTSQVLKGGGQKAIERHTSRGKLLARERINLLLDKGSPFLELSALAGH 153 2R:1731127-2080000 1 NULL:1982234 P79384 38 88 1 1 0 77906 77030 1 0 0 0 353 partof VVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQG-IPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALD-DEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLTKSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGN-----NGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKL 876 2R:1731127-2080000 1 NULL:1982235 P79384 120 398 1 1 0 78351 77952 1 0 0 0 141 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTR 399 2R:1731127-2080000 1 NULL:1982236 P79384 395 512 1 1 0 2597512 82561 82438 1 0 0 0 162 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982238 Q9W6M6 0 41 1 1 0 82766 82616 1 0 0 0 215 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982239 Q9W6M6 40 90 1 1 0 83124 82998 1 0 0 0 203 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982240 Q9W6M6 88 130 1 1 0 2597516 82561 82438 1 0 0 0 166 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982242 BAB84522 0 41 1 1 0 82766 82616 1 0 0 0 198 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982243 BAB84522 40 90 1 1 0 83124 82998 1 0 0 0 207 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982244 BAB84522 88 130 1 1 0 2597520 82561 82438 1 0 0 0 161 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982246 BAB84523 0 41 1 1 0 82766 82616 1 0 0 0 198 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982247 BAB84523 40 90 1 1 0 83124 82998 1 0 0 0 207 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982248 BAB84523 88 130 1 1 0 2597524 84125 83954 1 0 0 0 206 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREG---APMGFGSGAVKSLP 171 2R:1731127-2080000 1 NULL:1982250 BAB84523 89 149 1 1 0 2597526 84125 83954 1 0 0 0 206 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREG---APMGFGSGAVKSLP 171 2R:1731127-2080000 1 NULL:1982252 BAB84522 89 149 1 1 0 2597528 84212 83954 1 0 0 0 201 partof IIPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAP-MGFGSGAVKSLPGTAASGVSSSYRRGPSATTRPAMT--SAVKP 258 2R:1731127-2080000 1 NULL:1982254 Q9W6M6 89 177 1 1 0 2597530 138302 137936 1 0 0 0 520 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1982256 Q9YHT2 48 170 1 1 0 138718 138373 1 0 0 0 526 partof KKGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPA 345 2R:1731127-2080000 1 NULL:1982257 Q9YHT2 173 288 1 1 0 2597533 138302 138131 1 0 0 0 213 partof NIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 171 2R:1731127-2080000 1 NULL:1982259 O97650 0 57 1 1 0 138610 138379 1 0 0 0 370 partof GKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYR 231 2R:1731127-2080000 1 NULL:1982260 O97650 62 139 1 1 0 2597536 146306 145895 1 0 0 0 142 partof LEQQLLELNKRTNNNIRDEIERSSILLMS-DISQRLKREILLVVEAKHNESTKALK----GH--IREEEVRQIVKTVLAIYDADKTGLVDFALESAGGQILSTRCTESYQTKSAQISVFGIPLWYPTNTPRVAISPNVQPGECW 411 2R:1731127-2080000 1 NULL:1982262 BAB64478 0 144 1 1 0 146768 146558 1 0 0 0 139 partof STQGLEQEKDQEPVLFGDYQFEDNGASLQYFAVQNLDIKRPYEIVELRIETNHGHPTYTCLYRFRVHGKP 210 2R:1731127-2080000 1 NULL:1982263 BAB64478 188 257 1 1 0 2597540 212395 211603 1 0 0 0 361 partof ALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRG-P-VLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADS-EGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVN----GLQELEQQLNTVDLADIDAA--LTLQDVEIFLPRMCIEYDVDL 792 2R:1731127-2080000 1 NULL:1982265 P05619 17 284 1 1 0 212624 212477 1 0 0 0 78 partof SQLGITEVFS-DKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVS 147 2R:1731127-2080000 1 NULL:1982266 P05619 288 337 1 1 0 212816 212705 1 0 0 0 97 partof VPMMLNMNKKLFKADHPFVFYIR-NPQA-VFFAGRFSNP 111 2R:1731127-2080000 1 NULL:1982267 P05619 340 379 1 1 0 2597544 212407 211603 1 0 0 0 352 partof ALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGP-GDRHHI--ALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFAD-SEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVN----GLQELEQQLNTVDLADIDAA--LTLQDVEIFLPRMCIEYDVDLKQVL 804 2R:1731127-2080000 1 NULL:1982269 P80229 17 288 1 1 0 212624 212477 1 0 0 0 85 partof SQLGITEVFSDKAKLDGLFTSQSGQKISAARHRGYIDVNEAGSEAAAVS 147 2R:1731127-2080000 1 NULL:1982270 P80229 288 336 1 1 0 212816 212723 1 0 0 0 83 partof MNKKLFKADHPFVFYIR-NPQA-VFFAGRFSNP 93 2R:1731127-2080000 1 NULL:1982271 P80229 345 378 1 1 0 2597548 212416 211624 1 0 0 0 340 partof PHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFG-EFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 792 2R:1731127-2080000 1 NULL:1982273 Q9YIB8 85 346 1 1 0 2597551 214227 213432 1 0 0 0 372 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALG---LPSEDKEAVAARYGALLN------DLQGQEEGP----ILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISL-TNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALE-----EKIVGFARPLVAKEVYLK--LPKFKIEFRDELKETL 795 2R:1731127-2080000 1 NULL:1982275 P01012 12 297 1 1 0 2597553 214236 213432 1 0 0 0 403 partof EIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAER-INQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVE----GLSALE-----EKIVGFARP--LVAKEVYLKLPKFKIEFRDELKETLEKV 804 2R:1731127-2080000 1 NULL:1982277 P05619 13 291 1 1 0 2597555 214236 213465 1 0 0 0 373 partof NQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGL--PSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAER-INQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALE-----EKIVGFARPLVA--KEVYLKLPKFKIEFRDELKETLEKV 771 2R:1731127-2080000 1 NULL:1982279 O02739 23 290 1 1 0 2597557 217130 216368 1 0 0 0 317 partof AGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDF-VNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQ----EEQGLAIVEEKLMGIDLNE 762 2R:1731127-2080000 1 NULL:1982281 P80229 5 257 1 1 0 2597559 217130 216377 1 0 0 0 321 partof AQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTE--LKA----KVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNE 753 2R:1731127-2080000 1 NULL:1982283 Q90935 26 278 1 1 0 2597561 217145 216377 1 0 0 0 317 partof AQFASQLFGQLAKSQ-SGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAK-HINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 768 2R:1731127-2080000 1 NULL:1982285 Q9PTA8 74 328 1 1 0 2597563 239902 239707 1 0 0 0 142 partof VDILDTSGDMQFPAMRRLSIATAHAFMLVYAATSAPSFQCVKQCFEEIREQRGDFQ------VSYRCSCSP 195 2R:1731127-2080000 1 NULL:1982287 BAB60730 56 127 1 1 0 blastx_masked 1.0 aa_SPTR.othinv 1.0 2003-01-15 01:14:30 BLASTX Similarity to Other Species genomic 2604579 5312 4850 1 0 0 0 526 partof IGRMIFELFADTVPRTAENFRQFCTGE-YRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGN-TFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 462 2R:1731127-2080000 -1 NULL:1988212 O74729 17 173 1 1 0 2604582 5318 4850 1 0 0 0 672 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNT-FGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1988214 Q9GP41 28 185 1 1 0 2604585 5357 4850 1 0 0 0 516 partof NLYITPPSNAFCVQEI-------GRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDG--LLIMRKIENVPTGPN-NKPKLPVTISQCGQM 507 2R:1731127-2080000 -1 NULL:1988216 Q9U6U5 32 210 1 1 0 2604588 8252 7730 1 0 0 0 494 partof VVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGV-DYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 522 2R:1731127-2080000 -1 NULL:1988218 Q9GRB5 0 174 1 1 0 7602 7452 1 0 0 0 101 partof DEPNHMLLAQINHSGKMHMTPAKFNGRYVIRFCVTYEHATEKDILEAWTQ 150 2R:1731127-2080000 -1 NULL:1988219 Q9GRB5 176 226 1 1 0 2604591 8546 8075 1 0 0 0 191 partof GGGALQGSASECVLVSLITARARAISELKGQTSVHDSVF-LPSLIAYASREAHSSVEKATKMALVKLRI---IDADEHGRMRV-DLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADS 471 2R:1731127-2080000 -1 NULL:1988221 Q9XY41 24 179 1 1 0 2604593 17128 16906 1 0 0 0 254 partof GIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKHGYSDAAIDYRHWGVPLSRRFRSLKLWYV 222 2R:1731127-2080000 -1 NULL:1988223 Q9GRB5 51 125 1 1 0 15554 15377 1 0 0 0 158 partof LGLVCFRLKGSDKLNEKLLSIINESGKLHMVPASVGDRYIIRFCAVAQNATAEDIDYAW 177 2R:1731127-2080000 -1 NULL:1988224 Q9GRB5 165 224 1 1 0 2604596 33784 33223 1 0 0 0 270 partof TPKMPDGGYGWVVVFASLVVSLIADGLSFSFGL-INV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 561 2R:1731127-2080000 -1 NULL:1988226 O15894 11 196 1 1 0 2604598 33784 33223 1 0 0 0 270 partof TPKMPDGGYGWVVVFASLVVSLIADGLSFSFGL-INV---ELLEYFGESTSKTAWISSLFFSVPLLMGPIWSNLVDKYGCRKMTILGGVVSAFGFALSSFCNSIEMLMVTFXXXXXXXXXXXYVTAVVSIAFWFDKKRXXXXXXXXXXXXXXXXVYARLTSYLIESYGWRGATLILGGTMLNACVCGALMR 561 2R:1731127-2080000 -1 NULL:1988228 O15893 11 196 1 1 0 2598802 3968 3704 1 0 0 0 158 partof RLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPDSPCYMLTHIFAVV 264 2R:1731127-2080000 1 NULL:1983401 Q9P6N9 59 147 1 1 0 4500 4041 1 0 0 0 294 partof LNGWIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSL----FLRGVITLAFLSYYINYFAYLSVGRFNYAFNMMVNVATGVIAAVGWFVWCHFVRTRRPYFRRILRFYIL-MALAMSLELLDFPPILWILDAHALWHLATIPLASLYY 459 2R:1731127-2080000 1 NULL:1983402 Q9P6N9 148 306 1 1 0 2598806 27351 27189 1 0 0 0 243 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983404 Q9BHT6 16 70 1 1 0 28160 27821 1 0 0 0 410 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNE 339 2R:1731127-2080000 1 NULL:1983405 Q9BHT6 69 181 1 1 0 2598809 27351 27189 1 0 0 0 267 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983407 P36409 6 60 1 1 0 28160 27821 1 0 0 0 453 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNE 339 2R:1731127-2080000 1 NULL:1983408 P36409 59 172 1 1 0 2598813 27351 27189 1 0 0 0 279 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1983410 Q05975 15 69 1 1 0 28172 27821 1 0 0 0 555 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1983411 Q05975 68 185 1 1 0 2598816 76651 76537 1 0 0 0 119 partof HTSRGKLLARERINLLLDKGSPFLELSALAGHELYGEE 114 2R:1731127-2080000 1 NULL:1983413 Q95YY8 225 263 1 1 0 77909 77024 1 0 0 0 1012 partof CLVVANDATVKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADESIIVKKQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCKTSGVTDHYALDDEHALYLARQIVSNLNLSATNSYNDQLMHSSQVNFQTATPPSAVEEPRYDAEELYGIVGPNLT---KSFDVREVIARIVDGSRFTEFKKLYGETLVCGFAKLYGHTVGIVGNNGVLFSESALKGAHFIQLCAQRKIPLVFLQNITGKLI 885 2R:1731127-2080000 1 NULL:1983414 Q95YY8 287 572 1 1 0 78378 77952 1 0 0 0 430 partof GFMVGRDAEANGIAKNGAKMVTAVACANVPKFTVIIGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGGTQAANVMAQITEDQRKRAGKEFSEEEAQKLKAPIVEMFEAEGSPYYSTARLWDDGIIDPANTRQILGLSLKA 426 2R:1731127-2080000 1 NULL:1983415 Q95YY8 568 705 1 1 0 2598821 82561 82438 1 0 0 0 150 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1983417 O17509 0 41 1 1 0 82763 82616 1 0 0 0 166 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1983418 O17509 40 89 1 1 0 83124 83004 1 0 0 0 169 partof IPVDKLIKGRFQDNFEFLQWFKKFFDANY--DGREYDPVAQR 120 2R:1731127-2080000 1 NULL:1983419 O17509 90 132 1 1 0 2598825 82775 82616 1 0 0 0 109 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKVHMP 159 2R:1731127-2080000 1 NULL:1983421 Q10113 28 80 1 1 0 2598828 84212 83957 1 0 0 0 194 partof IPIDKLVKGRFQDNFEFLQWFKKFFDANY--DGRDYDASAVREGAPMGFGSGAVKSLPGTAASGVSSSYRRG-PSA---TTRPAMTSAVKP 255 2R:1731127-2080000 1 NULL:1983423 O17509 90 178 1 1 0 2598830 84215 83957 1 0 0 0 149 partof IPIDKLVKGRFQDNFEFLQWFKKFFDANYDGRDYDASAVREGAPMGFGSGAVKSLPG-TAASGVSSSYRRGPSATTRPAMTSAVKPS 258 2R:1731127-2080000 1 NULL:1983425 CAD19801 79 165 1 1 0 2598832 138302 137936 1 0 0 0 496 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1983427 Q25045 30 152 1 1 0 2598835 138302 137936 1 0 0 0 506 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQRK 366 2R:1731127-2080000 1 NULL:1983429 O44074 34 156 1 1 0 138739 138379 1 0 0 0 484 partof GKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAA 360 2R:1731127-2080000 1 NULL:1983430 O44074 161 280 1 1 0 2598838 138296 137939 1 0 0 0 508 partof KKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQ 357 2R:1731127-2080000 1 NULL:1983432 O42714 14 133 1 1 0 138685 138388 1 0 0 0 430 partof QYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIK 297 2R:1731127-2080000 1 NULL:1983433 O42714 140 239 1 1 0 2598842 212407 211618 1 0 0 0 354 partof KDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGP--VLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQL-INDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTL-QDVEIFLPRMCIEYDVDLKQVL 789 2R:1731127-2080000 1 NULL:1983435 Q9GP13 24 285 1 1 0 2598844 212416 211633 1 0 0 0 304 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGL-QLG-PGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIEYDVDLKQVLNQV 783 2R:1731127-2080000 1 NULL:1983437 Q9NH65 23 282 1 1 0 2598846 212416 211633 1 0 0 0 310 partof NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGP-G-DRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNE-IAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQLNTVDLADIDAALTLQDVEIFLPRMCIE--YDVDLKQVLNQV 783 2R:1731127-2080000 1 NULL:1983439 Q94823 65 329 1 1 0 2598848 214236 213405 1 0 0 0 349 partof TSVACQTSKEIYQLLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEE-GPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVGFAR-PLVAK----EVYLKLPKFKIEFRDELKETLEKV 831 2R:1731127-2080000 1 NULL:1983441 Q9NH65 2 282 1 1 0 2598850 214227 213426 1 0 0 0 392 partof SKEIYQLLSKS--HTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLT-NGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG------FARPLVAKEVYLKLPKFKIEFRDELKETL 801 2R:1731127-2080000 1 NULL:1983443 Q9GP13 12 285 1 1 0 2598852 214227 213444 1 0 0 0 379 partof LLSKSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLNSNLSMTIFLPREVEGLSALEEKIVG--FARPL-VAKEVYLKL--PKFKIEFRDELKETL 783 2R:1731127-2080000 1 NULL:1983445 Q9NLA5 12 275 1 1 0 2598854 217115 216356 1 0 0 0 273 partof SKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDF-VNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMG 759 2R:1731127-2080000 1 NULL:1983447 Q17158 25 269 1 1 0 2598856 217133 216383 1 0 0 0 336 partof FASQLFGQLAKS--QSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTAK-HINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEI 750 2R:1731127-2080000 1 NULL:1983449 Q9GP13 11 256 1 1 0 2598858 217145 216389 1 0 0 0 270 partof SQLFG-QLAKS-QSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXXXXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKNFAAAAENVNFTQKADTA-KHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVVELPYTGTDIVFLIILPQEEQGLAIVEEKLMGIDLNEISSQL 756 2R:1731127-2080000 1 NULL:1983451 Q27085 50 301 1 1 0 2598860 253427 253253 1 0 0 0 117 partof DIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELAS 174 2R:1731127-2080000 1 NULL:1983453 Q9UUF1 15 73 1 1 0 254253 253665 1 0 0 0 488 partof TTVGTHPTRCEEFVPDPEGYYDQL-RSRIKANRTK----VRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVK-KKEKWTAESLIDGRCEPC 588 2R:1731127-2080000 1 NULL:1983454 Q9UUF1 79 278 1 1 0 2598863 254253 253665 1 0 0 0 488 partof TTVGTHPTRCEEFVPDPEGYYDQL-RSRIKANRTK----VRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDFMGILERNRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVK-KKEKWTAESLIDGRCEPC 588 2R:1731127-2080000 1 NULL:1983456 O13630 25 224 1 1 0 2598865 254223 253734 1 0 0 0 362 partof LRSRIKANRTK---VRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEF--KLPLFLHMRNAAEDFMGILER----NRNKIEECGGGVVHSFTGTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAE 489 2R:1731127-2080000 1 NULL:1983458 Q9P3G1 170 338 1 1 0 2604600 88537 87634 1 0 0 0 535 partof LAPTIRLNNGREMPTLGLGTWKSFESDAY--HSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDV---DYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQRTVPFSGMSGHKY 903 2R:1731127-2080000 -1 NULL:1988230 CAD24968 1 300 1 1 0 2604603 88543 87670 1 0 0 0 514 partof TNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFH--NDSNVHG-------TLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQP--------ARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQYHTGQR 873 2R:1731127-2080000 -1 NULL:1988232 P87039 3 310 1 1 0 2604606 88558 87622 1 0 0 0 539 partof ASDKMTNLAPTIRLNNGREMPTLGLGTW------KSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELT-D--VDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARP-----QPAR--QWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDV---AGMEQYHTGQRTVPFS-GMSGHKYYPFN 936 2R:1731127-2080000 -1 NULL:1988234 Q968S3 3 333 1 1 0 2604609 110856 109716 1 0 0 0 282 partof LFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDF----RTMGQKVFTDMRHGKLLTM-FVFSFPKLASXXXXXXMPEDVHQFFMRLVNDT----IALRE-RENFKRNDFMNLLIELKQKGRVT-LDN--GEVI---EGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVL-EEQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRV 1140 2R:1731127-2080000 -1 NULL:1988236 Q9Y1T8 149 513 1 1 0 2604611 110976 109674 1 0 0 0 369 partof KPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLF-NLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVF-TDMRHGKLLTMFVFSFPKLASXXXXXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELKQKGRVTLDNGEVIEGMDIGELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLE-EQEGQLTYESIKAMTYLNQVISGRCSV*STAPRGIVTGFTQHCSSETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSP 1302 2R:1731127-2080000 -1 NULL:1988238 P98186 80 499 1 1 0 2604613 111138 110106 1 0 0 0 293 partof NYWNRRGVPHDAPHPLY-GNMVGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMR--HGKLLTMFVFSFPKLASXXX----XXXMPEDVHQFFMRLVNDTIALRERENFKRNDFMNLLIELK--QKGRVTLDNGEV-IEGM-DIG----ELAAQVFVFYVAGFETSSSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 1032 2R:1731127-2080000 -1 NULL:1988240 O16156 31 377 1 1 0 110040 109623 1 0 0 0 203 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGG-IYLRVER 417 2R:1731127-2080000 -1 NULL:1988241 O16156 376 511 1 1 0 2604616 140126 139976 1 0 0 0 179 partof INPQVRVKCNPDDTIGDLKKLIAAQTGTKHEKIVLKKWYTIFKDPIRLSD 150 2R:1731127-2080000 -1 NULL:1988243 O94650 9 59 1 1 0 2604619 196650 196467 1 0 0 0 194 partof RVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPH 183 2R:1731127-2080000 -1 NULL:1988245 P27133 2 63 1 1 0 195125 194888 1 0 0 0 193 partof PLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSD 237 2R:1731127-2080000 -1 NULL:1988246 P27133 72 151 1 1 0 194824 194380 1 0 0 0 337 partof VVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVSTSKSTILH 444 2R:1731127-2080000 -1 NULL:1988247 P27133 153 299 1 1 0 194349 194055 1 0 0 0 229 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSL 294 2R:1731127-2080000 -1 NULL:1988248 P27133 289 386 1 1 0 2604624 196659 196461 1 0 0 0 213 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNK 198 2R:1731127-2080000 -1 NULL:1988250 Q9GRB6 0 66 1 1 0 195152 194879 1 0 0 0 225 partof QVGRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTEPVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 273 2R:1731127-2080000 -1 NULL:1988251 Q9GRB6 65 156 1 1 0 194827 194404 1 0 0 0 268 partof KVVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHGLIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVS 423 2R:1731127-2080000 -1 NULL:1988252 Q9GRB6 154 294 1 1 0 194349 194055 1 0 0 0 266 partof QVTPEPPFVHYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNN-----GLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSL 294 2R:1731127-2080000 -1 NULL:1988253 Q9GRB6 291 394 1 1 0 2604629 196659 196443 1 0 0 0 191 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNKVSAPPD 216 2R:1731127-2080000 -1 NULL:1988255 O13923 0 72 1 1 0 195146 194879 1 0 0 0 172 partof GRIAADHPLVGGHKGPVLDIAWCPHNDNVIASGSEDCVVKVWQIPDGGLSRTLTE---PVVDLVFHQRRVGLVLWHPSALNVLLTAGSDNQV 267 2R:1731127-2080000 -1 NULL:1988256 O13923 67 159 1 1 0 194824 194410 1 0 0 0 268 partof VVIWNVGTGEILVHIDSHPDIV-YSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHGLIF-TTGFNRSSERQYSLRAPDALNEPIV-MVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFE 414 2R:1731127-2080000 -1 NULL:1988257 O13923 158 297 1 1 0 194322 194070 1 0 0 0 216 partof HYINTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADP 252 2R:1731127-2080000 -1 NULL:1988258 O13923 303 387 1 1 0 2604634 208017 207189 1 0 0 0 365 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSD--PEQIAHSFHQ---VLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAAT-INNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAE--FQVELSEVFQKVSFT 828 2R:1731127-2080000 -1 NULL:1988260 Q27085 53 333 1 1 0 2604636 208017 207210 1 0 0 0 413 partof FSINVYGKL--SGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH--SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNV-QAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETK-VALKLPRFKAEFQVELSEV 807 2R:1731127-2080000 -1 NULL:1988262 Q9GP13 11 284 1 1 0 2604638 208059 207204 1 0 0 0 393 partof ADAAHQEFARRLALFSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGL--ASSDPEQIAHSFHQ---VLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKN-VQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLRLTTLSQITQSLYETKVALKLPRFKAEFQVELSEVFQ 855 2R:1731127-2080000 -1 NULL:1988264 Q27086 30 318 1 1 0 2604640 210406 209644 1 0 0 0 269 partof NIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFG--GLEAQQVAESFGVVLKSYEQCQV---LKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQAA--SIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTRVRMMHVCENFF-FAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVL 762 2R:1731127-2080000 -1 NULL:1988266 Q94823 65 322 1 1 0 209592 209466 1 0 0 0 84 partof GYSQMGMNRIFSGQAELGGMLQSEESLFVSQIVHKAFIEINE 126 2R:1731127-2080000 -1 NULL:1988267 Q94823 324 365 1 1 0 2604643 210454 209644 1 0 0 0 281 partof FALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGG--LEAQQVAESF--GVVLKSYEQCQV-LKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF--GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDR-PTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAE--FQQELSQVL 810 2R:1731127-2080000 -1 NULL:1988269 Q27085 53 327 1 1 0 2604645 210481 209626 1 0 0 0 288 partof EEFAQGLEQFALCLHDHLCRA--SAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRF--GGLEAQQVAESFGV---VLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDF--GSEQAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGSDRPTR-VRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSDISLEVVSSAMNLEKVDVKIPSFTAEFQQELSQVLMLVS*N 855 2R:1731127-2080000 -1 NULL:1988271 Q27086 35 323 1 1 0 2604647 302505 302094 1 0 0 0 180 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSV-ER 411 2R:1731127-2080000 -1 NULL:1988273 P98186 379 516 1 1 0 2604649 302505 302157 1 0 0 0 164 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPV 348 2R:1731127-2080000 -1 NULL:1988275 O16156 377 491 1 1 0 2604651 303514 302569 1 0 0 0 146 partof RRGILHEKPKFLW--GNIKGVV--SGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQR--DLGEKSLQTINISELVGAYNTDVMASMAFGL----VGQDNVEFAKWTRNYWAD-----FRMWQAYLALEFPLIARLLQYKSYAEPAT---AYFQKVALSXXXXXXXXXXXPLQTFLQLYS---NAEKP-LTDIEIAGQAFGFVLAGLGPLNATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTP--ECLRELRYTKQV 945 2R:1731127-2080000 -1 NULL:1988277 O76345 29 353 1 1 0 302508 302094 1 0 0 0 200 partof LETLRLHTPHP-FLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVER 414 2R:1731127-2080000 -1 NULL:1988278 O76345 354 491 1 1 0 sim4 1.0 na_gb.dros 1.0 2003-01-13 21:24:55 Community Fly cDNA Sequences genomic 2598415 3592 3424 1 0 0 0 100 partof 168 2R:1731127-2080000 1 NULL:1983070 AY069668 0 168 1 1 0 3965 3648 1 0 0 0 100 partof 317 2R:1731127-2080000 1 NULL:1983071 AY069668 168 485 1 1 0 4502 4035 1 0 0 0 100 partof 467 2R:1731127-2080000 1 NULL:1983072 AY069668 485 952 1 1 0 4840 4555 1 0 0 0 99 partof 285 2R:1731127-2080000 1 NULL:1983073 AY069668 952 1236 1 1 0 2598421 5687 5601 1 0 0 0 97 partof 86 2R:1731127-2080000 1 NULL:1983075 AY089619 0 86 1 1 0 21600 21472 1 0 0 0 100 partof 128 2R:1731127-2080000 1 NULL:1983076 AY089619 86 214 1 1 0 22011 21656 1 0 0 0 99 partof 355 2R:1731127-2080000 1 NULL:1983077 AY089619 214 569 1 1 0 22369 22067 1 0 0 0 99 partof 302 2R:1731127-2080000 1 NULL:1983078 AY089619 569 871 1 1 0 2598427 23427 23228 1 0 0 0 100 partof 199 2R:1731127-2080000 1 NULL:1983080 AY058276 0 199 1 1 0 24959 23736 1 0 0 0 100 partof 1223 2R:1731127-2080000 1 NULL:1983081 AY058276 199 1422 1 1 0 2598431 26704 26518 1 0 0 0 99 partof 186 2R:1731127-2080000 1 NULL:1983083 AB035352 0 187 1 1 0 27350 27190 1 0 0 0 100 partof 160 2R:1731127-2080000 1 NULL:1983084 AB035352 187 347 1 1 0 28160 27823 1 0 0 0 99 partof 337 2R:1731127-2080000 1 NULL:1983085 AB035352 347 684 1 1 0 28475 28220 1 0 0 0 100 partof 255 2R:1731127-2080000 1 NULL:1983086 AB035352 684 939 1 1 0 2598437 26704 26561 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983088 D84313 0 143 1 1 0 27350 27190 1 0 0 0 100 partof 160 2R:1731127-2080000 1 NULL:1983089 D84313 143 303 1 1 0 28160 27823 1 0 0 0 100 partof 337 2R:1731127-2080000 1 NULL:1983090 D84313 303 640 1 1 0 29412 28220 1 0 0 0 99 partof 1192 2R:1731127-2080000 1 NULL:1983091 D84313 640 1833 1 1 0 29711 29447 1 0 0 0 98 partof 264 2R:1731127-2080000 1 NULL:1983092 D84313 1833 2100 1 1 0 2598444 71924 71669 1 0 0 0 100 partof 255 2R:1731127-2080000 1 NULL:1983094 AF181638 0 255 1 1 0 72544 72479 1 0 0 0 100 partof 65 2R:1731127-2080000 1 NULL:1983095 AF181638 255 320 1 1 0 72755 72615 1 0 0 0 100 partof 140 2R:1731127-2080000 1 NULL:1983096 AF181638 320 460 1 1 0 73319 72811 1 0 0 0 100 partof 508 2R:1731127-2080000 1 NULL:1983097 AF181638 460 968 1 1 0 74314 73367 1 0 0 0 100 partof 947 2R:1731127-2080000 1 NULL:1983098 AF181638 968 1915 1 1 0 74552 74373 1 0 0 0 100 partof 179 2R:1731127-2080000 1 NULL:1983099 AF181638 1915 2094 1 1 0 74969 74612 1 0 0 0 100 partof 357 2R:1731127-2080000 1 NULL:1983100 AF181638 2094 2451 1 1 0 75629 75027 1 0 0 0 99 partof 602 2R:1731127-2080000 1 NULL:1983101 AF181638 2451 3054 1 1 0 2598454 71924 71695 1 0 0 0 98 partof 229 2R:1731127-2080000 1 NULL:1983103 AJ242938 0 230 1 1 0 72544 72479 1 0 0 0 100 partof 65 2R:1731127-2080000 1 NULL:1983104 AJ242938 230 295 1 1 0 72755 72615 1 0 0 0 100 partof 140 2R:1731127-2080000 1 NULL:1983105 AJ242938 295 435 1 1 0 73319 72811 1 0 0 0 100 partof 508 2R:1731127-2080000 1 NULL:1983106 AJ242938 435 943 1 1 0 74314 73367 1 0 0 0 100 partof 947 2R:1731127-2080000 1 NULL:1983107 AJ242938 943 1890 1 1 0 74552 74373 1 0 0 0 100 partof 179 2R:1731127-2080000 1 NULL:1983108 AJ242938 1890 2069 1 1 0 74969 74612 1 0 0 0 100 partof 357 2R:1731127-2080000 1 NULL:1983109 AJ242938 2069 2426 1 1 0 75923 75027 1 0 0 0 99 partof 896 2R:1731127-2080000 1 NULL:1983110 AJ242938 2426 3321 1 1 0 2598464 76385 76160 1 0 0 0 100 partof 225 2R:1731127-2080000 1 NULL:1983112 AY084145 0 225 1 1 0 76698 76444 1 0 0 0 100 partof 254 2R:1731127-2080000 1 NULL:1983113 AY084145 225 479 1 1 0 77898 77017 1 0 0 0 99 partof 881 2R:1731127-2080000 1 NULL:1983114 AY084145 479 1360 1 1 0 78730 77953 1 0 0 0 100 partof 777 2R:1731127-2080000 1 NULL:1983115 AY084145 1360 2137 1 1 0 2598470 79158 77447 1 0 0 0 98 partof 1711 2R:1731127-2080000 1 NULL:1983117 AF006645 0 1718 1 1 0 2598473 78722 78146 1 0 0 0 99 partof 576 2R:1731127-2080000 1 NULL:1983119 AF006654 0 576 1 1 0 2598476 79164 78966 1 0 0 0 99 partof 198 2R:1731127-2080000 1 NULL:1983121 AY071380 0 197 1 1 0 82559 82406 1 0 0 0 100 partof 153 2R:1731127-2080000 1 NULL:1983122 AY071380 197 350 1 1 0 82763 82617 1 0 0 0 100 partof 146 2R:1731127-2080000 1 NULL:1983123 AY071380 350 496 1 1 0 84213 83954 1 0 0 0 100 partof 259 2R:1731127-2080000 1 NULL:1983124 AY071380 496 755 1 1 0 84619 84476 1 0 0 0 100 partof 143 2R:1731127-2080000 1 NULL:1983125 AY071380 755 898 1 1 0 84756 84673 1 0 0 0 100 partof 83 2R:1731127-2080000 1 NULL:1983126 AY071380 898 981 1 1 0 84892 84819 1 0 0 0 100 partof 73 2R:1731127-2080000 1 NULL:1983127 AY071380 981 1054 1 1 0 85814 84959 1 0 0 0 100 partof 855 2R:1731127-2080000 1 NULL:1983128 AY071380 1054 1909 1 1 0 2598486 79164 79008 1 0 0 0 100 partof 156 2R:1731127-2080000 1 NULL:1983130 AF132560 0 156 1 1 0 82559 82406 1 0 0 0 100 partof 153 2R:1731127-2080000 1 NULL:1983131 AF132560 156 309 1 1 0 82763 82617 1 0 0 0 100 partof 146 2R:1731127-2080000 1 NULL:1983132 AF132560 309 455 1 1 0 84213 83954 1 0 0 0 100 partof 259 2R:1731127-2080000 1 NULL:1983133 AF132560 455 714 1 1 0 84619 84479 1 0 0 0 100 partof 140 2R:1731127-2080000 1 NULL:1983134 AF132560 714 854 1 1 0 84756 84673 1 0 0 0 100 partof 83 2R:1731127-2080000 1 NULL:1983135 AF132560 854 937 1 1 0 84892 84819 1 0 0 0 100 partof 73 2R:1731127-2080000 1 NULL:1983136 AF132560 937 1010 1 1 0 85814 84959 1 0 0 0 100 partof 855 2R:1731127-2080000 1 NULL:1983137 AF132560 1010 1865 1 1 0 2598496 139255 136512 1 0 0 0 99 partof 2743 2R:1731127-2080000 1 NULL:1983139 L27705 0 2741 1 1 0 2598499 213117 212777 1 0 0 0 100 partof 340 2R:1731127-2080000 1 NULL:1983141 AJ251744 0 340 1 1 0 214233 213388 1 0 0 0 99 partof 845 2R:1731127-2080000 1 NULL:1983142 AJ251744 340 1185 1 1 0 214433 214291 1 0 0 0 100 partof 142 2R:1731127-2080000 1 NULL:1983143 AJ251744 1185 1327 1 1 0 214657 214503 1 0 0 0 93 partof 154 2R:1731127-2080000 1 NULL:1983144 AJ251744 1327 1491 1 1 0 2604212 10161 9824 1 0 0 0 99 partof 337 2R:1731127-2080000 -1 NULL:1987900 AY113382 0 337 1 1 0 8836 7731 1 0 0 0 100 partof 1105 2R:1731127-2080000 -1 NULL:1987901 AY113382 337 1442 1 1 0 7609 6770 1 0 0 0 99 partof 839 2R:1731127-2080000 -1 NULL:1987902 AY113382 1442 2280 1 1 0 2604217 26379 26114 1 0 0 0 100 partof 265 2R:1731127-2080000 -1 NULL:1987904 AY070538 0 265 1 1 0 26040 25666 1 0 0 0 100 partof 374 2R:1731127-2080000 -1 NULL:1987905 AY070538 265 639 1 1 0 25606 24890 1 0 0 0 100 partof 716 2R:1731127-2080000 -1 NULL:1987906 AY070538 639 1355 1 1 0 2604222 45640 44878 1 0 0 0 100 partof 762 2R:1731127-2080000 -1 NULL:1987908 AY069571 0 762 1 1 0 35973 35009 1 0 0 0 100 partof 964 2R:1731127-2080000 -1 NULL:1987909 AY069571 762 1726 1 1 0 34361 32161 1 0 0 0 100 partof 2200 2R:1731127-2080000 -1 NULL:1987910 AY069571 1726 3926 1 1 0 31697 31587 1 0 0 0 100 partof 110 2R:1731127-2080000 -1 NULL:1987911 AY069571 3926 4036 1 1 0 31146 30964 1 0 0 0 100 partof 182 2R:1731127-2080000 -1 NULL:1987912 AY069571 4036 4218 1 1 0 30897 30656 1 0 0 0 100 partof 241 2R:1731127-2080000 -1 NULL:1987913 AY069571 4218 4459 1 1 0 30592 29997 1 0 0 0 100 partof 595 2R:1731127-2080000 -1 NULL:1987914 AY069571 4459 5054 1 1 0 2604231 47446 46433 1 0 0 0 99 partof 1013 2R:1731127-2080000 -1 NULL:1987916 AJ401614 0 1013 1 1 0 46357 46116 1 0 0 0 100 partof 241 2R:1731127-2080000 -1 NULL:1987917 AJ401614 1013 1254 1 1 0 2604235 47582 46433 1 0 0 0 100 partof 1149 2R:1731127-2080000 -1 NULL:1987919 AY071095 0 1149 1 1 0 46357 46119 1 0 0 0 100 partof 238 2R:1731127-2080000 -1 NULL:1987920 AY071095 1149 1387 1 1 0 2604239 53349 53069 1 0 0 0 100 partof 280 2R:1731127-2080000 -1 NULL:1987922 AF216977 0 280 1 1 0 52683 52526 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987923 AF216977 280 437 1 1 0 52469 52302 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1987924 AF216977 437 604 1 1 0 52239 52082 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987925 AF216977 604 761 1 1 0 52029 51862 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1987926 AF216977 761 928 1 1 0 51802 51619 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987927 AF216977 928 1111 1 1 0 51553 50873 1 0 0 0 99 partof 680 2R:1731127-2080000 -1 NULL:1987928 AF216977 1111 1791 1 1 0 2604248 62065 62012 1 0 0 0 100 partof 53 2R:1731127-2080000 -1 NULL:1987930 AF216976 0 53 1 1 0 61959 61776 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987931 AF216976 53 236 1 1 0 61709 61571 1 0 0 0 100 partof 138 2R:1731127-2080000 -1 NULL:1987932 AF216976 236 374 1 1 0 61508 61325 1 0 0 0 99 partof 183 2R:1731127-2080000 -1 NULL:1987933 AF216976 374 557 1 1 0 56163 56031 1 0 0 0 100 partof 132 2R:1731127-2080000 -1 NULL:1987934 AF216976 557 689 1 1 0 55802 55478 1 0 0 0 100 partof 324 2R:1731127-2080000 -1 NULL:1987935 AF216976 689 1013 1 1 0 55414 55225 1 0 0 0 100 partof 189 2R:1731127-2080000 -1 NULL:1987936 AF216976 1013 1202 1 1 0 55167 55029 1 0 0 0 100 partof 138 2R:1731127-2080000 -1 NULL:1987937 AF216976 1202 1340 1 1 0 53797 53614 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987938 AF216976 1340 1523 1 1 0 53562 53430 1 0 0 0 100 partof 132 2R:1731127-2080000 -1 NULL:1987939 AF216976 1523 1655 1 1 0 52683 52526 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987940 AF216976 1655 1812 1 1 0 52469 52302 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1987941 AF216976 1812 1979 1 1 0 52239 52082 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987942 AF216976 1979 2136 1 1 0 52029 51890 1 0 0 0 99 partof 139 2R:1731127-2080000 -1 NULL:1987943 AF216976 2136 2275 1 1 0 2604264 70107 69813 1 0 0 0 99 partof 294 2R:1731127-2080000 -1 NULL:1987945 AF216975 0 294 1 1 0 68130 67973 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987946 AF216975 294 451 1 1 0 67902 67735 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1987947 AF216975 451 618 1 1 0 63032 62717 1 0 0 0 100 partof 315 2R:1731127-2080000 -1 NULL:1987948 AF216975 618 933 1 1 0 62657 62012 1 0 0 0 99 partof 645 2R:1731127-2080000 -1 NULL:1987949 AF216975 933 1578 1 1 0 61959 61776 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987950 AF216975 1578 1761 1 1 0 61709 61571 1 0 0 0 100 partof 138 2R:1731127-2080000 -1 NULL:1987951 AF216975 1761 1899 1 1 0 61508 61325 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987952 AF216975 1899 2082 1 1 0 61265 61214 1 0 0 0 100 partof 51 2R:1731127-2080000 -1 NULL:1987953 AF216975 2082 2133 1 1 0 58848 58365 1 0 0 0 99 partof 483 2R:1731127-2080000 -1 NULL:1987954 AF216975 2133 2616 1 1 0 58095 56603 1 0 0 0 98 partof 1492 2R:1731127-2080000 -1 NULL:1987955 AF216975 2616 4109 1 1 0 2604277 70419 69813 1 0 0 0 99 partof 606 2R:1731127-2080000 -1 NULL:1987957 AF216974 0 606 1 1 0 68130 67973 1 0 0 0 100 partof 157 2R:1731127-2080000 -1 NULL:1987958 AF216974 606 763 1 1 0 67902 67735 1 0 0 0 100 partof 167 2R:1731127-2080000 -1 NULL:1987959 AF216974 763 930 1 1 0 67304 67268 1 0 0 0 100 partof 36 2R:1731127-2080000 -1 NULL:1987960 AF216974 930 966 1 1 0 64686 64503 1 0 0 0 100 partof 183 2R:1731127-2080000 -1 NULL:1987961 AF216974 966 1149 1 1 0 64373 64229 1 0 0 0 100 partof 144 2R:1731127-2080000 -1 NULL:1987962 AF216974 1149 1293 1 1 0 64167 64033 1 0 0 0 100 partof 134 2R:1731127-2080000 -1 NULL:1987963 AF216974 1293 1427 1 1 0 63969 63788 1 0 0 0 100 partof 181 2R:1731127-2080000 -1 NULL:1987964 AF216974 1427 1608 1 1 0 63717 63402 1 0 0 0 100 partof 315 2R:1731127-2080000 -1 NULL:1987965 AF216974 1608 1923 1 1 0 63032 62864 1 0 0 0 100 partof 168 2R:1731127-2080000 -1 NULL:1987966 AF216974 1923 2091 1 1 0 2604289 71282 50490 1 0 0 0 99 partof 20792 2R:1731127-2080000 -1 NULL:1987968 AF216973 0 20796 1 1 0 2604292 86795 86694 1 0 0 0 100 partof 101 2R:1731127-2080000 -1 NULL:1987970 AY071376 0 101 1 1 0 86632 86487 1 0 0 0 100 partof 145 2R:1731127-2080000 -1 NULL:1987971 AY071376 101 246 1 1 0 86411 86317 1 0 0 0 100 partof 94 2R:1731127-2080000 -1 NULL:1987972 AY071376 246 340 1 1 0 86256 86064 1 0 0 0 98 partof 192 2R:1731127-2080000 -1 NULL:1987973 AY071376 340 532 1 1 0 2604298 88663 87370 1 0 0 0 99 partof 1293 2R:1731127-2080000 -1 NULL:1987975 AY118938 0 1292 1 1 0 2598505 289524 281980 1 0 0 0 99 partof 7544 2R:1731127-2080000 1 NULL:1983146 AF039416 13 7567 1 1 0 2598507 288122 286744 1 0 0 0 99 partof 1378 2R:1731127-2080000 1 NULL:1983148 AY058502 0 1378 1 1 0 2598509 289519 289138 1 0 0 0 99 partof 381 2R:1731127-2080000 1 NULL:1983150 AL035257 0 381 1 1 0 2598511 305439 305049 1 0 0 0 98 partof 390 2R:1731127-2080000 1 NULL:1983152 AF171836 42 431 1 1 0 2598514 320548 318892 1 0 0 0 90 partof 1656 2R:1731127-2080000 1 NULL:1983154 X01748 177 1854 1 1 0 2598516 322552 322462 1 0 0 0 100 partof 90 2R:1731127-2080000 1 NULL:1983156 AF220041 0 90 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1983157 AF220041 90 202 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1983158 AF220041 202 394 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1983159 AF220041 394 556 1 1 0 327128 326933 1 0 0 0 98 partof 195 2R:1731127-2080000 1 NULL:1983160 AF220041 556 748 1 1 0 327750 327391 1 0 0 0 99 partof 359 2R:1731127-2080000 1 NULL:1983161 AF220041 748 1107 1 1 0 2598524 322552 322463 1 0 0 0 100 partof 89 2R:1731127-2080000 1 NULL:1983163 AF274014 0 89 1 1 0 324259 324147 1 0 0 0 100 partof 112 2R:1731127-2080000 1 NULL:1983164 AF274014 89 201 1 1 0 326642 326450 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1983165 AF274014 201 393 1 1 0 326867 326705 1 0 0 0 100 partof 162 2R:1731127-2080000 1 NULL:1983166 AF274014 393 555 1 1 0 327128 326933 1 0 0 0 100 partof 195 2R:1731127-2080000 1 NULL:1983167 AF274014 555 750 1 1 0 327750 327391 1 0 0 0 99 partof 359 2R:1731127-2080000 1 NULL:1983168 AF274014 750 1109 1 1 0 2598532 328956 328643 1 0 0 0 100 partof 313 2R:1731127-2080000 1 NULL:1983170 AF274015 0 313 1 1 0 329185 329020 1 0 0 0 100 partof 165 2R:1731127-2080000 1 NULL:1983171 AF274015 313 478 1 1 0 329626 329257 1 0 0 0 100 partof 369 2R:1731127-2080000 1 NULL:1983172 AF274015 478 847 1 1 0 2598537 336407 336221 1 0 0 0 100 partof 186 2R:1731127-2080000 1 NULL:1983174 AF274016 0 186 1 1 0 337692 337500 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1983175 AF274016 186 378 1 1 0 338398 337755 1 0 0 0 100 partof 643 2R:1731127-2080000 1 NULL:1983176 AF274016 378 1021 1 1 0 2598542 342110 342060 1 0 0 0 100 partof 50 2R:1731127-2080000 1 NULL:1983178 AF220043 0 50 1 1 0 342891 342807 1 0 0 0 100 partof 84 2R:1731127-2080000 1 NULL:1983179 AF220043 50 134 1 1 0 347150 346787 1 0 0 0 100 partof 363 2R:1731127-2080000 1 NULL:1983180 AF220043 134 497 1 1 0 347401 347209 1 0 0 0 100 partof 192 2R:1731127-2080000 1 NULL:1983181 AF220043 497 689 1 1 0 348139 347464 1 0 0 0 100 partof 675 2R:1731127-2080000 1 NULL:1983182 AF220043 689 1364 1 1 0 2604301 110154 109989 1 0 0 0 98 partof 165 2R:1731127-2080000 -1 NULL:1987977 S81983 0 165 1 1 0 2604304 111471 110105 1 0 0 0 98 partof 1366 2R:1731127-2080000 -1 NULL:1987979 M88009_revcomp 0 1369 1 1 0 110036 108813 1 0 0 0 98 partof 1223 2R:1731127-2080000 -1 NULL:1987980 M88009_revcomp 1369 2599 1 1 0 108784 108534 1 0 0 0 99 partof 250 2R:1731127-2080000 -1 NULL:1987981 M88009_revcomp 2599 2848 1 1 0 2604309 112190 111207 1 0 0 0 98 partof 983 2R:1731127-2080000 -1 NULL:1987983 AF061083 0 985 1 1 0 2604312 112535 106790 1 0 0 0 99 partof 5745 2R:1731127-2080000 -1 NULL:1987985 U78088 0 5737 1 1 0 2604315 112535 111207 1 0 0 0 99 partof 1328 2R:1731127-2080000 -1 NULL:1987987 AF061082 0 1331 1 1 0 2604318 113512 111207 1 0 0 0 96 partof 2305 2R:1731127-2080000 -1 NULL:1987989 AF061081 0 2323 1 1 0 2604321 118781 118236 1 0 0 0 100 partof 545 2R:1731127-2080000 -1 NULL:1987991 AY058255 0 545 1 1 0 103561 103414 1 0 0 0 100 partof 147 2R:1731127-2080000 -1 NULL:1987992 AY058255 545 692 1 1 0 99134 99082 1 0 0 0 100 partof 52 2R:1731127-2080000 -1 NULL:1987993 AY058255 692 744 1 1 0 98798 98700 1 0 0 0 100 partof 98 2R:1731127-2080000 -1 NULL:1987994 AY058255 744 842 1 1 0 98440 98353 1 0 0 0 100 partof 87 2R:1731127-2080000 -1 NULL:1987995 AY058255 842 929 1 1 0 98285 98143 1 0 0 0 100 partof 142 2R:1731127-2080000 -1 NULL:1987996 AY058255 929 1071 1 1 0 98089 97896 1 0 0 0 100 partof 193 2R:1731127-2080000 -1 NULL:1987997 AY058255 1071 1264 1 1 0 97335 97189 1 0 0 0 100 partof 146 2R:1731127-2080000 -1 NULL:1987998 AY058255 1264 1410 1 1 0 96970 96825 1 0 0 0 100 partof 145 2R:1731127-2080000 -1 NULL:1987999 AY058255 1410 1555 1 1 0 95886 95709 1 0 0 0 100 partof 177 2R:1731127-2080000 -1 NULL:1988000 AY058255 1555 1732 1 1 0 95472 95310 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988001 AY058255 1732 1894 1 1 0 94511 94149 1 0 0 0 100 partof 362 2R:1731127-2080000 -1 NULL:1988002 AY058255 1894 2256 1 1 0 94079 93825 1 0 0 0 100 partof 254 2R:1731127-2080000 -1 NULL:1988003 AY058255 2256 2510 1 1 0 93766 93595 1 0 0 0 100 partof 171 2R:1731127-2080000 -1 NULL:1988004 AY058255 2510 2681 1 1 0 93375 93241 1 0 0 0 100 partof 134 2R:1731127-2080000 -1 NULL:1988005 AY058255 2681 2815 1 1 0 92958 92608 1 0 0 0 100 partof 350 2R:1731127-2080000 -1 NULL:1988006 AY058255 2815 3165 1 1 0 92549 91686 1 0 0 0 99 partof 863 2R:1731127-2080000 -1 NULL:1988007 AY058255 3165 4028 1 1 0 2604340 208417 208213 1 0 0 0 99 partof 204 2R:1731127-2080000 -1 NULL:1988009 AJ251747 127 331 1 1 0 208133 207201 1 0 0 0 99 partof 932 2R:1731127-2080000 -1 NULL:1988010 AJ251747 331 1263 1 1 0 207137 206995 1 0 0 0 97 partof 142 2R:1731127-2080000 -1 NULL:1988011 AJ251747 1263 1405 1 1 0 206897 206662 1 0 0 0 99 partof 235 2R:1731127-2080000 -1 NULL:1988012 AJ251747 1405 1640 1 1 0 2604346 315470 315186 1 0 0 0 98 partof 284 2R:1731127-2080000 -1 NULL:1988014 AF034421 0 285 1 1 0 308372 307466 1 0 0 0 99 partof 906 2R:1731127-2080000 -1 NULL:1988015 AF034421 285 1191 1 1 0 307377 306990 1 0 0 0 100 partof 387 2R:1731127-2080000 -1 NULL:1988016 AF034421 1191 1578 1 1 0 306932 305049 1 0 0 0 98 partof 1883 2R:1731127-2080000 -1 NULL:1988017 AF034421 1578 3458 1 1 0 2604352 341500 341366 1 0 0 0 100 partof 134 2R:1731127-2080000 -1 NULL:1988019 AF220042 0 134 1 1 0 340629 340437 1 0 0 0 100 partof 192 2R:1731127-2080000 -1 NULL:1988020 AF220042 134 326 1 1 0 340368 340206 1 0 0 0 100 partof 162 2R:1731127-2080000 -1 NULL:1988021 AF220042 326 488 1 1 0 340075 339877 1 0 0 0 100 partof 198 2R:1731127-2080000 -1 NULL:1988022 AF220042 488 686 1 1 0 339820 339647 1 0 0 0 99 partof 173 2R:1731127-2080000 -1 NULL:1988023 AF220042 686 859 1 1 0 tblastx 1.0 na_dbEST.insect 1.0 2003-01-14 22:26:33 BLASTX Similarity to Other Species genomic 2597330 27351 27189 1 0 0 0 276 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982084 BI511668 40 202 1 1 0 28082 27821 1 0 0 0 425 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAAN 261 2R:1731127-2080000 1 NULL:1982085 BI511668 199 460 1 1 0 2597334 27351 27189 1 0 0 0 276 partof GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 162 2R:1731127-2080000 1 NULL:1982087 BI514793 58 220 1 1 0 28133 27821 1 0 0 0 492 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQ 312 2R:1731127-2080000 1 NULL:1982088 BI514793 217 529 1 1 0 2597338 27351 27195 1 0 0 0 266 partof GKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 156 2R:1731127-2080000 1 NULL:1982090 BI515305 1 157 1 1 0 28172 27821 1 0 0 0 542 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINNEVRRI 351 2R:1731127-2080000 1 NULL:1982091 BI515305 154 505 1 1 0 2597341 77291 77051 1 0 0 0 352 partof VKGGSYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQADVFPDKLHFGRIFYNQANMSAQGIPQIAVVMGSCTAG 240 2R:1731127-2080000 1 NULL:1982093 BI517006 0 240 1 1 0 2597344 82561 82438 1 0 0 0 208 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982095 AV402055 20 143 1 1 0 82766 82616 1 0 0 0 245 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982096 AV402055 140 290 1 1 0 2597348 82561 82438 1 0 0 0 208 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982098 AI172663 115 238 1 1 0 82766 82616 1 0 0 0 244 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982099 AI172663 235 385 1 1 0 83124 82998 1 0 0 0 202 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982100 AI172663 379 505 1 1 0 2597353 82561 82438 1 0 0 0 208 partof MAVNVYSTNVTSENLSRHDMLAWVNDCLQSQFSKIEELCTG 123 2R:1731127-2080000 1 NULL:1982102 AV398352 132 255 1 1 0 82766 82616 1 0 0 0 244 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDKV 150 2R:1731127-2080000 1 NULL:1982103 AV398352 252 402 1 1 0 83124 82998 1 0 0 0 196 partof QIIPVDKLIKGRFQDNFEFLQWFKKFFDANYDGREYDPVAQR 126 2R:1731127-2080000 1 NULL:1982104 AV398352 396 522 1 1 0 2597358 138748 138358 1 0 0 0 538 partof NEAGEKKGK-AQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLSGLASKPAPKLETAALHK 390 2R:1731127-2080000 1 NULL:1982106 AU003987 28 415 1 1 0 2597361 143197 142939 1 0 0 0 258 partof FCSKTPKTDYTYSELSPHRRQLAPGIVAMPNMSRKSLENHNDRVNYMVQQNPAQEEFIRRRYQSKYTQQVN---YDSADELDATFGQQK 258 2R:1731127-2080000 1 NULL:1982108 AJ284492 121 388 1 1 0 2597364 212236 211549 1 0 0 0 260 partof QEGRNQFARNLIDVITKDALQQSKDPHINTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSVNRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSN 687 2R:1731127-2080000 1 NULL:1982110 AU005854 93 741 1 1 0 2597367 212260 211561 1 0 0 0 269 partof NQFARNLI-DVITKDALQQSKDPHI-----NTVFSPASVQSALTLAFMGASGSTAEELRNGLQLGPGDRHHIALNFGEFWRTSCNYGDRGPVLKSV-NRLYVNDSLELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLP 699 2R:1731127-2080000 1 NULL:1982112 AU001394 99 801 1 1 0 2597370 212299 211855 1 0 0 0 288 partof LELLTEFNEIAVDFFQSKAEATRFADSEGATQLINDWVEQETEHKITNLLQSDAVNNETSALLINVLYFKGKWQKPFMPETTSIDHFHVDRDTHVQVNMMYQEDKFRFAELPQLKARAVQLPYDYSNIHMLILLPNEVNGLQELEQQL 444 2R:1731127-2080000 1 NULL:1982114 BE015460 0 444 1 1 0 2597373 214032 213453 1 0 0 0 333 partof KSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDL 579 2R:1731127-2080000 1 NULL:1982116 AV402355 85 655 1 1 0 2597376 214032 213453 1 0 0 0 333 partof KSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDL 579 2R:1731127-2080000 1 NULL:1982118 AV405838 143 713 1 1 0 2597379 214065 213453 1 0 0 0 347 partof KSHTNQNLVVSPVSIETILSMVFMGAEGSTAKELQSALGLPSEDKEAVAARYGALLNDLQGQEEGPILKLANRIYVNDQYSLNQNYNLAVREPFKSEAESISLTNGPVAAERINQWVLDQTSGKIKGMIDPGSMTSDVKALLVNAIYFKGQWESKFDPAKTRASTFQVTANKSVPVQMMAQMGTFRANYFRDLDAQVIELPYLN 612 2R:1731127-2080000 1 NULL:1982120 AU005854 141 741 1 1 0 2597381 217007 216299 1 0 0 0 282 partof CSXXXXXXXXXAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXX--XXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKN-FAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTEL 708 2R:1731127-2080000 1 NULL:1982122 AV405838 35 713 1 1 0 2597383 217007 216299 1 0 0 0 280 partof CSXXXXXXXXXAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXX--XXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKN-FAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTEL 708 2R:1731127-2080000 1 NULL:1982124 AU004802 31 709 1 1 0 2597386 217094 216299 1 0 0 0 295 partof CSXXXXXXXXXAMANTLNYSKSPAGEAQFASQLFGQLAKSQSGRNIVFSPSSIRTGLALAYLGAEGSTADXXXXXXXX--XXXXXTEVAEKLDQLLAKGQWEKASGDEDVPKLKYANRIFVTQRFKLTQTYQDLVSKN-FAAAAENVNFTQKADTAKHINSWVEEQTHQQIKDLIAPESLDADTSAILVNAIYFKADWQSSFPDYATYASDFVNHGGRKVSVDTMSQEDYFRFGELTELKAKVV-ELPYTGTDIVF--LIILPQEEQGLAI 795 2R:1731127-2080000 1 NULL:1982126 AU005854 33 804 1 1 0 2597388 239875 239779 1 0 0 0 139 partof AFMLVYAATSAPSFQCVKQCFEEIREQRGDFQ 96 2R:1731127-2080000 1 NULL:1982128 BI505646 0 96 1 1 0 240637 240523 1 0 0 0 152 partof QDIPIVIAGNKADLATTHREVKLEEVTDWVFCELPRLR 114 2R:1731127-2080000 1 NULL:1982129 BI505646 93 207 1 1 0 2597392 253442 253253 1 0 0 0 210 partof DIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDGKL 189 2R:1731127-2080000 1 NULL:1982131 AV402242 270 459 1 1 0 253827 253698 1 0 0 0 126 partof EFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQE 129 2R:1731127-2080000 1 NULL:1982132 AV402242 493 622 1 1 0 2597396 253442 253274 1 0 0 0 158 partof DPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDGKL 168 2R:1731127-2080000 1 NULL:1982134 AJ285178 2 170 1 1 0 253920 253653 1 0 0 0 320 partof ERIYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAAEFKLPLFLHMRNAAEDF 267 2R:1731127-2080000 1 NULL:1982135 AJ285178 161 428 1 1 0 2597400 254259 253989 1 0 0 0 307 partof GTLEEAQRILAFGGLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTTKFPTVKKKEKWTAESLIDGRCEPCQI 270 2R:1731127-2080000 1 NULL:1982137 AJ283884 193 460 -1 1 0 254418 254325 1 0 0 0 92 partof SQVLESIAGIKQEPKEQLAALYYQNTLDLFF 93 2R:1731127-2080000 1 NULL:1982138 AJ283884 100 193 -1 1 0 2597404 286019 285311 1 0 0 0 362 partof IRTNTQDPIYAKSYPYPVNMRGEVERQIDELLQDGIIRPSNSPYNSPIWIVPKKPKPNGEKQYRMVVDFKRLNTVTIPDTYPIPDINATLASLGNAKYFTTLDLTSGFHQIHMKESDIPKTAFSTLNGKYEFLRLPFGLKNAPAIFQRMIDDILREHIGKVCYVYIDDIIVFSEDYDTHWKNLRLVLASLSKANLQVNLEKSHFLDTQVEFLGYIVTADGIKADPKKVRAISEMPP 708 2R:1731127-2080000 1 NULL:1982140 AV402520 1 688 -1 1 0 2597406 286127 285608 1 0 0 0 292 partof TTLDLTSGFHQIHMKESDIPKTAFSTLNGKYEFLRLPFGLKNAPAIFQRMIDDILREH-IGKVCYVYIDDIIVFSEDYDTHWKNLRLVLASLSKANLQVNLEKSHFLDTQVEFLGYIVTADGIKADPKKVRAISEMPPPTSVKELKRFLGMTSYYRKFIQDYAKVAKPLTNLTR 519 2R:1731127-2080000 1 NULL:1982142 AV404531 1 523 1 1 0 2597408 286460 285800 1 0 0 0 306 partof VYIDDIIVFSEDYDTHWKNLRLVLASLSKANLQVNLEKSHFLDTQVEFLGYIVTADGIKADPKKVRAISEMPPPTSVKELKRFLGMTSYYRKFIQDYAKVAKPLTNLTRGLYANIKSSQSSKVPITLDETALQSFNDLKSILCSSEILAFPCFTKPFHLTTDASNWAIGAVLSQDDQGRDRPIAYISRSLNKTEENYATIEKEMLAIIWSLDNLRAYLYG 660 2R:1731127-2080000 1 NULL:1982144 AV402517 6 618 1 1 0 2597410 328944 328704 1 0 0 0 118 partof MNCLSAMFKXXXXXXXXXFVAGGILLIVVGSIMLSTMGNFTAFDGGVNTQTIPICIIVIGSVTFVVAFFGCCGTIRENAC 240 2R:1731127-2080000 1 NULL:1982146 AV401663 59 299 1 1 0 338175 337755 1 0 0 0 131 partof YTSMVFVLFILQLVLTCWVFVNRSAFLGDMSNLVNLLWDSHDYTAMGVLEETFGCCGDTSYTNYNNIGLSVPGTCCGYLDRQATCNTPSVYQSRPGCSAKFEEFWNDNMDIIRWSGLGLCIFDLVVFLIAGALTNCMRSQ 420 2R:1731127-2080000 1 NULL:1982147 AV401663 311 701 1 1 0 2597414 328944 328770 1 0 0 0 109 partof GILLIVVGSIMLSTMGNFTAFDGGVNTQ-TI-PICIIVIGSVTFVVAFFGCCGTIRENAC 174 2R:1731127-2080000 1 NULL:1982149 BE015396 122 293 1 1 0 2597417 335232 335058 1 0 0 0 109 partof 174 2R:1731127-2080000 1 NULL:1982151 BE015396 122 293 1 1 0 2602627 1983 1389 1 0 0 0 308 partof NTSVVQFETAPGYEGVISIAXXXXXXXXXXXXXXXXXXXXXXMITVQNRDTRHNYSLHYIPADLLLSVQDTNIYYGLGGSALNKWRHITRDLHIDLQKG----IMGDKRSPLKIRRSDLEVISIGFLGLGFFDNITLSTSDHLAHFYDAAEWFVHNQDPKTGGWTNP-VRRSLNGFAELRPGWI-SAMGQGHAISVLARAYWHS 594 2R:1731127-2080000 -1 NULL:1986430 AI658400 1 604 1 1 0 2602630 5312 4847 1 0 0 0 447 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM* 465 2R:1731127-2080000 -1 NULL:1986432 BI515979 13 460 1 1 0 2602633 5312 4865 1 0 0 0 434 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTIS 447 2R:1731127-2080000 -1 NULL:1986434 AU005196 114 546 1 1 0 2602635 5312 4865 1 0 0 0 434 partof IGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTIS 447 2R:1731127-2080000 -1 NULL:1986436 AV401740 282 714 1 1 0 2602637 7994 7730 1 0 0 0 263 partof SALNVNPLYLRHEHL-TGVDYRHYGIPLSRRFRALKLWFVFRTYGIRGLQEYIRNHMALAKKFEMLVRKDERFEVRNDVHLGLVCFRMR 264 2R:1731127-2080000 -1 NULL:1986438 AJ280577 160 427 -1 1 0 2602640 8597 7940 1 0 0 0 493 partof KALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPS-LIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDITEIGKVCRQVSSIWLHVDGAYAGNSFILPEMRVFSAGLEYADSFNTNPNKLLLTNFDASALWVRDVMNLKSALNVNPLYLRHEHLTGV 657 2R:1731127-2080000 -1 NULL:1986440 AI638914 7 658 1 1 0 2602643 8705 8204 1 0 0 0 394 partof SVLGDMLSSAIGSIGFSWASCPAAAELETIVMNWYAKALGLPKAFVSDAPGSTGGGALQGSASECVLVSLITARARAISELKGQTSVHDSVFLPS-LIAYASREAHSSVEKATKMALVKLRIIDADEHGRMRVDLLRQAIQNDVNAGLTPFFVVATVGTTGGCAFDDI 501 2R:1731127-2080000 -1 NULL:1986442 BI512691 4 508 1 1 0 2602646 17131 16990 1 0 0 0 166 partof QGIEYADSFNTNPNKWLLTNFDCSTLWVRDRIRLTSALVVDPLYLKH 141 2R:1731127-2080000 -1 NULL:1986444 AI638914 502 643 1 1 0 2602648 17620 17044 1 0 0 0 342 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNLPEIGKQLQRFPGVWLHVDAAYAGNSFICPELKPLLKVSGIPTARMANLTGFHSQGIEY-ADSFNTNPNKWLLTNFDCSTLWVR 576 2R:1731127-2080000 -1 NULL:1986446 AI638914 70 640 1 1 0 2602650 17954 17771 1 0 0 0 229 partof SILGDMLGDGIGCIGFSWAASPACTELETIVLDWLGKAIGLPDHFLALKEGSTGGGVIQVT 183 2R:1731127-2080000 -1 NULL:1986448 BI512691 4 187 1 1 0 17620 17290 1 0 0 0 259 partof QTSASECVLVTMXXXXXXXXXXXXXXHPFVEEGHLLSKLMAYCSKEAHSCVEKAAMICFVKLRILEPDDDASLRGQTIYEAMEEDELQGLVPFFVSTTLGTTGSCAFDNL 330 2R:1731127-2080000 -1 NULL:1986449 BI512691 178 508 1 1 0 2602653 88435 87820 1 0 0 0 493 partof ALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHG--TLELTD-VDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQP--ARQWPPFLYDEHAQNL--AKKYGRTTAQ 615 2R:1731127-2080000 -1 NULL:1986451 BI505271 0 636 1 1 0 2602655 88447 87832 1 0 0 0 495 partof STRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQK-----FHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQW-----PPFLYDEHAQNLAKKYGR 615 2R:1731127-2080000 -1 NULL:1986453 AU003039 5 638 1 1 0 2602657 88537 87796 1 0 0 0 502 partof LAPTIRLNNGREMPTLGLGTWKSFES------DAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHNDSNVHGTLELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCP---LARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQ 741 2R:1731127-2080000 -1 NULL:1986455 AV405323 84 825 1 1 0 2602660 110223 110109 1 0 0 0 102 partof NQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVI 114 2R:1731127-2080000 -1 NULL:1986457 BI503528 2 113 1 1 0 110037 109632 1 0 0 0 327 partof ETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLR 405 2R:1731127-2080000 -1 NULL:1986458 BI503528 116 518 1 1 0 2602663 110247 110106 1 0 0 0 108 partof YCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 141 2R:1731127-2080000 -1 NULL:1986460 BE844462 459 600 -1 1 0 110040 109620 1 0 0 0 328 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1986461 BE844462 45 462 -1 1 0 2602666 110262 110106 1 0 0 0 126 partof SSTMSYCLYELAQNQDIQDRLRNEIQTVLEEQEGQLTYESIKAMTYLNQVIS 156 2R:1731127-2080000 -1 NULL:1986463 BE844331 0 156 1 1 0 110040 109620 1 0 0 0 328 partof SETLRLYTLVPHLERKALNDYVVPGHEKLVIEKGTQVIIPACAYHRDEDLYPNPETFDPERFSPEKVAARESVEWLPFGDGPRNCIGMRFGQMQARIGLAQIISRFRVSVCDTTEIPLKYSPMSIVLGTVGGIYLRVERI 420 2R:1731127-2080000 -1 NULL:1986464 BE844331 153 570 1 1 0 2602669 111135 110505 1 0 0 0 354 partof YWNRRGVPHDAPHPLYGNMVGFRKNRVMHDFXXXXXXXXXXS--GFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLT-QHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLLTMF-VFSFPKLA 630 2R:1731127-2080000 -1 NULL:1986466 BE844394 57 684 1 1 0 2602671 111141 110508 1 0 0 0 329 partof FNYWNRRGVPHDAPHPLYGNMVG--FRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHN-GRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTLRTPVSDFRTMGQKVFTDMRHGKLL---TMFVFSFPKL 633 2R:1731127-2080000 -1 NULL:1986468 BI504529 23 644 1 1 0 2602673 111141 110610 1 0 0 0 326 partof FNYWNRRGVPHDAPHPLYGNM--VGFRKNRVMHDFXXXXXXXXXXSGFPFVGFYFLHKPAAFIVDTQLAKNILIKDFSNFADRGQFHNGRDDPLTQHLFNLDGKKWKDMRQRLTPTFTSGKMKFMFPTVIKVSEEFVKVITEQVPAAQNGAVLEIKELMARFTTDVIGTCAFGIECNTL 531 2R:1731127-2080000 -1 NULL:1986470 BI505169 34 553 1 1 0 2602675 194238 194019 1 0 0 0 261 partof EVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDADPITFSLKVSG*GAEAAQT 219 2R:1731127-2080000 -1 NULL:1986472 AJ282062 0 216 1 1 0 2602678 194773 194404 1 0 0 0 213 partof HPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEA-MCHEGSKATRAIFLRHG-LIFTTGFNRSSERQYSLRAPDALNEPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFEVS 369 2R:1731127-2080000 -1 NULL:1986474 BI506088 28 403 1 1 0 2602680 194824 194551 1 0 0 0 265 partof VVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFL-RHGLIFTTGFNRSSERQYSL 273 2R:1731127-2080000 -1 NULL:1986476 BI510708 51 327 1 1 0 2602683 196635 196446 1 0 0 0 302 partof SKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNKVSAPP 189 2R:1731127-2080000 -1 NULL:1986478 BI515952 2 191 1 1 0 2602686 207158 207026 1 0 0 0 141 partof VNINLLQLGMSRMFSDQAEFGKMLQSPEPLKVSAIIHKAFIEVN 132 2R:1731127-2080000 -1 NULL:1986480 AJ282124 196 328 -1 1 0 2602689 207756 207312 1 0 0 0 351 partof QLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDAMALELPYKDSDLSMLIVLPNTKTGLPALEEKLR 444 2R:1731127-2080000 -1 NULL:1986482 BE015460 3 447 1 1 0 2602691 208017 207429 1 0 0 0 326 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH-SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYAD 588 2R:1731127-2080000 -1 NULL:1986484 AV402469 120 708 1 1 0 207420 207345 1 0 0 0 63 partof LDAMALELPYKDSDLSMLIVLPNTK 75 2R:1731127-2080000 -1 NULL:1986485 AV402469 716 791 1 1 0 2602695 208017 207411 1 0 0 0 326 partof FSINVYGKLSGQKPGENIVFSPFSIQTCAAMARLGAENETATQLDQGLGLASSDPEQIAH-SFHQVLAAYQDSQILRIANKIFVMDGYQLRQEFDQLLSKQFLSAAQSVDFSKNVQAAATINNWVEQRTNHLIKDLVPADVLNSESRLVLVNAIHFKGTWQHQFAKHLTRPDTFHLDGERTVQVPMMSLKERFRYADLPALDA 606 2R:1731127-2080000 -1 NULL:1986487 AU005854 111 717 1 1 0 2602697 210190 209746 1 0 0 0 260 partof LQVDEQFGHILEQKFRSKPMEIDFGSE-QAASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMHVCENFFFAVLPMFEATALRMNYSACNLAMIILLPDEKSNLTSLEKKLSD 444 2R:1731127-2080000 -1 NULL:1986489 BE015460 0 450 1 1 0 2602699 210466 209893 1 0 0 0 247 partof GLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVA-ESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMH 573 2R:1731127-2080000 -1 NULL:1986491 AU004356 108 681 1 1 0 2602702 210466 209893 1 0 0 0 247 partof GLEQFALCLHDHLCRASAGLNIIYSPLSIHISAAMLRMGTSEGSATAKEMDEGLRFGGLEAQQVA-ESFGVVLKSYEQCQVLKMANGLYVMKGLQVDEQFGHILEQKFRSKPMEIDFGSEQ-AASIINKWVESQTNNLIKDIIGPRVLTKDSRLCLVNGIHFKGEWSISFNEKETREEDFFGS-DRPTRVRMMH 573 2R:1731127-2080000 -1 NULL:1986493 AU004802 97 670 1 1 0 2602704 302505 302106 1 0 0 0 242 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKL 399 2R:1731127-2080000 -1 NULL:1986495 BI503528 116 515 1 1 0 2602706 302704 302563 1 0 0 0 79 partof FCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 141 2R:1731127-2080000 -1 NULL:1986497 BE844462 459 600 -1 1 0 302505 302091 1 0 0 0 236 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1986498 BE844462 45 459 -1 1 0 2602709 302719 302563 1 0 0 0 91 partof NATLAFCLYELARQPEVQDRTRLEINKALEEHGGQVTPECLRELRYTKQVLN 156 2R:1731127-2080000 -1 NULL:1986500 BE844331 0 156 1 1 0 302505 302091 1 0 0 0 236 partof ETLRLHTPHPFLLRRATKEFEVPGSVFVIAKGNNVLIPTAAIHMDPGIYENPQRFYPERFEEQARRSRPAAAFLPFGDGLRGCIAARFAEQQLLVGLVALLRQHRYAPSAETSIPVEYDNRRLLLMPKSDIKLSVERV 414 2R:1731127-2080000 -1 NULL:1986501 BE844331 156 570 1 1 0 2602712 303523 303028 1 0 0 0 221 partof YWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGE--KSLQTINISELVGAYNTDVMASMAFGL 495 2R:1731127-2080000 -1 NULL:1986503 BI504529 29 527 1 1 0 2602714 303553 303028 1 0 0 0 228 partof VYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSH-NLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLGEKSL----QTINISELVGAYNTDVMASMAFGL 525 2R:1731127-2080000 -1 NULL:1986505 BE844394 27 564 1 1 0 2602716 303562 303028 1 0 0 0 247 partof LSVVYALVKFSLGYWKRRGILHEKPKFLWGNIKGVVSGKRHAQDALQDIYTAYKGRAPFVGFYACLKPFILALDLKLVHQIIFTDAGHFTSRGLYSNPSGEPLSHNLLQLDGHKWRSLHAKSAEVFTPANMQKLLVRLSQISSRIQRDLG---EKSLQTINISELVGAYNTDVMASMAFGL 534 2R:1731127-2080000 -1 NULL:1986507 BI508390 36 570 1 1 0 2602718 304461 304074 1 0 0 0 260 partof GHQDAGWGCGYRTLQSAISWIQRRQGSSGHVPSIREIQQILVAIGDKGPEFVGSRDWIGTLEEFYVIDVLHQVPCKILHAKELSS-DEILGELRSYFEKYQGFVAMGGLSDTASKAITGYHCSARGRIFL 387 2R:1731127-2080000 -1 NULL:1986509 BI513035 1 391 1 1 0 304003 303892 1 0 0 0 78 partof DPHFVGVPSSRQHLIDLGYVRWVPVDEFAGST-YNLCL 111 2R:1731127-2080000 -1 NULL:1986510 BI513035 397 511 1 1 0 2602721 312201 312012 1 0 0 0 172 partof RNHYEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYN 189 2R:1731127-2080000 -1 NULL:1986512 BI516423 3 192 1 1 0 sim4 1.0 na_cDNA.dros 1.0 2003-04-03 17:16:46 Fly cDNA Sequences DGC genomic 2598612 140950 140795 1 0 0 0 100 partof CATTCGAATTTTTTCGCCGCTCGGAATAGACGTGATTTTGCCGTCGTGACGGTGGAGGCTATTTTTAAAACGGTCGCGGCGCTTGCAAACAAAATTCATATCCAGCTATTCAACGGAGGAATTCATTAGTACGGCAGTACAAGAAATATTACTAAGTA 155 2R:1731127-2080000 1 NULL:1983238 RE12054 0 155 1 1 0 141858 141676 1 0 0 0 100 partof GGCCCGAGCACTGGAGGGAATCTAATCATGAGCGAAAATACATACCAGATAGAAACGCGTCGGCGGTCGCGTTCCAAGACCCCCTTCCTGAGATCGAGCTGCGACCATGAGAACTGTGAGCACGCCGGAGAGGAGGGGCATGTGCACCACCTCAAAAGGAAATCGGCGGCCCCCAATGTGCA 182 2R:1731127-2080000 1 NULL:1983239 RE12054 155 337 1 1 0 142891 142555 1 0 0 0 100 partof CAGAACGATAATAGAGGAGCATATAGTGGAGTCGAGTATCAGTAAGAAAACCCGGGCAAAAGCGTTCGCCCAGCTGACCTCGGACTATTCGAGCGACGACATGACTCCGGATGCCAAACGCAAACAGAACTCGATCACGGCCACAGTCACGTCGATTCTCACCAAGCGATCCGGCGGCGCCACATCGACACCGCGGAACAGAAGCCAGCTGGAGACCACACAAAACACGCTGAATTCCGCCCAGGAAAAGCTAAACCAATCGAACGGTAACCTCAGCTCGGGAAATGTCAGCGATTATCTGGCCTACATCGAGTACAGGGATGCTGGTGAATACTGGAA 336 2R:1731127-2080000 1 NULL:1983240 RE12054 337 673 1 1 0 143528 142947 1 0 0 0 100 partof CAGGTCTGTTCTA 581 2R:1731127-2080000 1 NULL:1983241 RE12054 673 1254 1 1 0 144599 143811 1 0 0 0 99 partof TTACATACACCCCAATGAAACTTTCCCACCCAAATCCCTGTCCGAATACACATTCACCCTACCTGAGTTGCCCAAAATCGATGTGAAAGACTACCTGAACCA-GGAGCAGTTCGAATCGCTACGCTCTCAGGCCGCCGAGCATGCGGTCCGCGTTCGCGATTGGGCCGACGACTACGTTTTGTACTTGAGAACCATCGGTCAGAACGTGGTCAACAAGGGTCGTCAGTTATTTCAGGGCGATGATAAAGTCTATTATGAGCGTGTGTAGGGAACATCTGCAATGGGCAGGCTACAGCTACCAGATTTAGTGATCTGGTTGGGTGCAACGCCCCTTGCACTTAGACAAATATGAGAAACTTTCTTTATGAACAATATGAGTACAAAATAAAGCATTTGATCCGTTTTTTGTCCGTCTGCTTGACCCGCAGTTTTGCGCACTTACTTTATAGTTTTTCGTCCCGTCATTTACCCACTTCATAGGCAAACCCACCTCTCATACCCCACCATACTAACCGACACAATTCCCAACAAAATGCAACATCACAGGCTGATGGGAGAAGGATAGAGCTCGCCGCTGTTCAAATTGTAAAACTTTCGTAATCGTTAACTTCATTCTTGTCCAACAATTAGGGCCGTTATCCGTCTGGGTTAGTGCCCTAACTAAATCTTACTTGTTGTTAAACAACGTTTAATTGTAATTTGTGCACTGTTTGCTTTGTAATAGTCTATACAAAAATAAATCGCAAACAATTTCATATGAAACATCAAGTACAAAGAA 788 2R:1731127-2080000 1 NULL:1983242 RE12054 1254 2043 1 1 0 2598619 158442 158132 1 0 0 0 99 partof AACAGTGCCGTCGCAGTGCTGAGCGCAGAGTGTCGCAGGTCCAAGGACTCAGTCATCGCGTAGCCGCCGTGTGTGACGGACCGACGCCGCTTTGTGGCCGATTTAAAGCGAGTCTTGATGCGAGAAGTGCATTCAATTAACATAAAATGTAATTAGGGACCCTCTCTCCGCCTCTCTTAATCAAACGCAAACATCGGAAACTGAGCCGCGGAGGCAAAACGAATGCCATTAAAGCGCCTGCGAATAAATCACGGCATGCCAGTGCAGTCGAAACTCAATCAAGTTGAACGGAAATCGTCGAAAATTAAACGTA 310 2R:1731127-2080000 1 NULL:1983244 RE34115 0 310 1 1 0 159823 159335 1 0 0 0 100 partof CAGGCGCAGCACCGGCATTGTGAATGCAGCATACCACCGCCATTCTGTACATTCTAAAAATAACAAACAACTCGAGTGCGATAAAAACAGCCGTTCCTACCAAGGTATAAAGTGCTAGCGTAAACACAGCCGAAGAAGGAGCGCAAACAAACATCGGAGCCACCTAAAACGGCGAACAAACAGCGGCGAAGGTTCCTGTACTGTGCGGAATCCTCGCTGTGTCGGTGTATTGGTGTACCGGTGTACCGGTTTGTCGGTATATCGCTCTGTGTGTGTGCCAGTGTGTGTGGGCCAAAGGAGCCAAGCAAAGAGTCAGAGCAAAAATGTGCAAGTAAGGTGCAGCAAGCAAAGTGCAATGCCATCCGTGAAATCCGCCGAAAGTGAGATTCTTCTTGGGATTATAAGGAGCGACAGCATGACGAGCGGCAATTCCCTGAGGTCCTGCCTCCTGCTGGCCACCATCCTGGGATTACTCTGCCGGACGAAGGGTG 488 2R:1731127-2080000 1 NULL:1983245 RE34115 310 798 1 1 0 162706 162404 1 0 0 0 99 partof CTTTGCCCTTTGAGTATTTAGACGAGCACGAGGACTTCAACTACGACCTGGACACGGCGCAGTCCCAGGCCAAGTACGACGCCCGTCTGCTCTCGCAGCAGATGCTCAGCGATGCAGAGCTGCAGCGGCAGGGGCTGAGCGACGGCCAGGACAACGCCCTGGATGGCGACTCCGCGGCAGCTCAGGGGACTGGAGCAGGGTCCCACTTGGATGCGGTATCCTCTGTCCACGACGACCTGGAGCCGCACAGCAGGGCAGCGGCGTGCTTCACCAACGGGCACAAGTACACGCACGGACAGAAGGTA 302 2R:1731127-2080000 1 NULL:1983246 RE34115 798 1100 1 1 0 163462 163389 1 0 0 0 100 partof GTTCCGCGCCTGGATGCCTGCGAGGTGTGTCTCTGCATGGACGGCGAGATCTTCTGCTGGTGGGAGAAGTGCG 73 2R:1731127-2080000 1 NULL:1983247 RE34115 1100 1173 1 1 0 164701 163529 1 0 0 0 100 partof ATAAGGCCAATGTAAACAAGGCGAGGACGGCGGGGGACAACGCAGGACTTGGACTTGGTGTCGAGGACGACGGCGACGGCAATGGCAATGGCGATGGCGATGGTGACTATTCAGATCCATATCGCCACGAGAGCACAACGGGAAAGTCAACAAAAGTGCATAAAGCGGCGAGGAAAGTTGGCAAGCGGCATAAGCATCGCAAGAATCAAAAGAATTTTAATGACTACGAAGTTTACCACAGCCAGCGGGAGAAGCAGCAGCAGCAGCAGTCGGATTATAAAAAGTCCGCCATAAAGCAGCAGCTCCAGATGCAGCAAAAACACAAAAGCGACAAGAGCGGTGCTGGCAACTACAATATAATCAAGCAACACAAACACGAGCAGCAGCAGCAGCAGCTCAAAATACCGCAGCAGCTACATCAGCAACAGCAGCAACAGAATGTGGCAGCTTTGGGTGTTAATCACGCAGCAAAGGCAACGCATTATCAGCAGGCAGCTTCGACGCCCCTGCCAACTCCCCCACCCCCGTCGGAGCACCCGCAGCACAGCCACCACCCACACCAACAGGCGCACTCGTCCAGCAAAATCCTCAACTTCCCCGAGAACTTGCCAGCCCTGCTCTACTACGACTACAAGACGGAGGAGCACGAGCACCACCAGCACCAGCACCACCAGCAGCACTTGCTGCACGAAAAACAGCGCTTGCTGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGATGGTGCAGCAAGAGGCGTTGGCGCGACAAAAGGCATCTGAATCCGCATCTGAGCCCGAATCGCGGGCCGGAGGCACAGCAGAGGGAGGCGTTGAACCCAGCGGAGACTTGGCCGCTGATAAAAACTCTGATGAGGCGGAAACCGACAGCGATATTCTGCCAGAGCCGCCTACAAAGCAGCCCAGGGCAGCTGCCACACAATGGCCAACTCCATCTAGTAACAGCTCGGCCAGGGCGTTGATGACGAGCAACGTGGCATCCACATCCACGGCTGCGACAACGACAACGACAAAGACATCGAAAACGAAAACGACAACGGCGACAACGGGAAGGACGACGACGACGACAACGGCGACAGGCACAAATGAAATGGTGACAAGCACGCTGTCTGGAATGGAGAAGTCCGGGGCCACAGTTGCAGCCACAGATGTG 1172 2R:1731127-2080000 1 NULL:1983248 RE34115 1173 2345 1 1 0 165844 165267 1 0 0 0 100 partof CTTGGACAGATGCAACCCGATCGCCGTGGACCAGACGCGGAGCGAGACGACGCCTTCCACCGCTGGCTGACATCCACCGAGCTGAATGCTGACAACACAAACTCCATGGACGACAGCCTGGAGCGGGAAACGCCGGCATCGACAATAATCGATGATGTTGGCACGGCCAACAAGAGTGACAGGAGCATCGGCGGCATCGGTGGCATCGGCAAAGACAATGGCAACGACGCCGTCTTCTTTCGCAGCTCGTACAACGATTACAGCAGCGAATTCAATGGGAGCGTTGTCAATATTGACATTACACTAACTGCAGTTGATGTGCATCCCCGTCGCCAAACGGATTTAATTGCAAATGGCAACAGAACGTCAGGCGCTAACGACAATGGCAACAGCTGTAGCAGCCAGGTTGGAGCAGCAGGAACAACAATGAACCCAGTGGCAGTCAGCACCAGCAGCAGCACCAGGAGCAGCAACAATCAGGATCAGCCTCAGCAGAGCCCTGTTGTCCCGCCGTACACCCTGACAACGATTATAACAACTGCGCCGATGGCACCAGGGCGTATGTGCAATGTTTTGGGTA 577 2R:1731127-2080000 1 NULL:1983249 RE34115 2345 2922 1 1 0 168135 166301 1 0 0 0 99 partof GCAAACTGTATAAAATTGGTGACATTCTGCCGCAGGACACGGGCAACTGCCTGCAGTGCATTTGCACGGATGCCGTGACTCCCGACGAGATGCCGAGCGTCACCTGCAGTCCGCACAATTGCCCACCGCTGGTTCTTCCGGATCTGTTCGATGCGACTGGTTACTGAGGTTACGGGTTTGTGCTGTAAGTTGCTGCAACGGCAGGTGGCAAGTGGCAGGTAGCAGGTGGAACGCCCCTGCGGCATGAGCTGTGGGAGTTTTTGAATAGATCGAAGCGTGATTTAAATTTTGAAACCGAAAGCCACAACTGCAGCCAGCAAACGAAATAGAATCGAAACGAACGAACAAACGAACGAATCGAATCTAATCGAATCGATTCGAATCACACTCACAACAACTGCACTACAGAACTCACTCTTGAATTGCATGTCACGGTCTCAACTAACTCAACTCAATATGAATTGTATGGATTTCAGTGTAAAGCCCTCCCTATCACGAGTGCCCCAAGCACTCTCTAAAACGAAACCTATCAGCAGACATATATTATATTCGTACCAAACTATATAGTATCGATCCAAGCCGACCAGAGGGGAGAGAGGGGAATGAATAAAGAAGAAGAAGGAAATCGCAGTTGGCTCACAGTTTAGACTTTAAGCTGAATGTTTATGCATTTTATAAGAATCCGTATTCATCTCTCTCCGCAACAAAAATCCATTAATGTATACAGCAGTAGCAATCGTAAAGAATTTATAGATGTACCAAACAGAAGTATATAGTATATACAAACATATACGAGTATCTACTCTATATCTAAATCTAATATCTAAACCTATACCTGTGCGTAGCGAGTTCGGTGGGATCAGTTTGATTACTTAGATTATTTCCCGACTGAGAGGAAACCGTGTAGAGTTTTCAGTGTATTTATCAACGGAGAGCCCCAAGTGAAACGAGTAACTTATACAAATATAGGAAACTAAATCTAAACGAAAAAAACTGAACAATGACAAATAATGAACAACGTGTGTAACGTGTGTATTTTAATTTTGATATTAAAAGCAAACAACGTTCTCCTCATTTGCATGCATGTTATTGTTTCGCGCTTCTTTGGAAATTAAGCCATACGTAATCTATGAATCGAAAATTGACGTTAGGAGCAATGTATGGACATTGTTTAAACAAACACAAAGTTGGCAAGGAAAGACACCATATCGAGTAGCTATAACATTTTAAGGAATAATCCCCACTGTATTTAATATAAACTTAGAATTTCAAAAATTGCGGAGATTACCGAAAATCTATTTGTTTTGGTTTCTGGCGACAAAGACAGCATTTATTTCAAAGCAAGTTTAGGCGTGATAAACATTGATTTATTCGAAAGGGGTTAAAGCGGAATATATAATACTTGAAAAGTAGAAAACAATTTCGATTTTAAGGCAAATCAAAATACATTCGAGCGAGTTTTTTATAACCGAGCTCGAACAAAACTATACTCGTATGGGCATGTGAACCATGGAATCAAAATGCAAAATATACGTACATGCGAATATACCGATGCAGACAAACGTAAATATTTATTATTGATGTTGCACAAGAGAGCGTATGGTAAATTCGAAGAAAAATAGAAAAATTCATCTTGAACGAGCATATTAAAAATGTATACAAATATGCGTATTTATGTATGTGTAAAATAAATGTAACTACAACTCTCTACTAATCTGCAACTCGCACACAGATACAGATGCACCGGCATCCCTGTGTTTAAATGGAATTTGTGTTTGAAATCAAATTGAAATCAAATCGACATGAATAAACCGAAACCCAACTAAGGCATTTCGAA 1834 2R:1731127-2080000 1 NULL:1983250 RE34115 2922 4756 1 1 0 2598628 212413 211741 1 0 0 0 99 partof GGAGATCGCCATCACATAGCCCTAAACTTCGGAGAGTTCTGGCGCACGAGCTGTAACTACGGCGACAGGGGACCCGTGTTGAAGTCCGTGAACCGATTGTACGTCAACGATTCCTTGGAACTGCTTACCGAGTTCAACGAGATCGCCGTGGACTTCTTCCAGTCGAAGGCCGAGGCGACGAGGTTCGCCGATTCGGAGGGAGCTACGCAGCTGATCAACGACTGGGTGGAACAGGAGACGGAGCATAAGATCACCAACCTGCTTCAATCGGATGCCGTGAACAACGAAACGAGCGCCCTGCTCATCAATGTCTTGTACTTTAAGGGAAAGTGGCAGAAACCATTTATGCCAGAGACCACATCGATTGACCATTTCCACGTGGACCGGGACACTCACGTGCAGGTGAATATGATGTACCAAGAGGACAAGTTCCGGTTCGCAGAACTGCCACAGCTGAAGGCTCGAGCTGTGCAACTGCCCTATGATTACTCAAACATTCACATGCTAATTCTGCTGCCCAACGAAGTAAACGGTCTGCAGGAGTTAGAGCAGCAACTCAACACCGTGGATCTAGCCGATATTGACGCAGCGCTGACCTTGCAGGATGTCGAGATCTTTCTGCCCAGGATGTGCATAGAGTACGACGTGGACCTCAAGCAGGTACTTAATCAGGTA 672 2R:1731127-2080000 1 NULL:1983252 AT24862 0 672 1 1 0 212625 212483 1 0 0 0 100 partof CTGGGTATTACGGAAGTCTTCAGCGATAAGGCCAAGCTAGACGGGCTCTTTACCTCGCAAAGTGGCCAAAAAATCTCGGCAGCAAGGCACCGCGGCTACATCGACGTAAATGAGGCAGGATCGGAGGCAGCAGCAGTCAGTTGTA 142 2R:1731127-2080000 1 NULL:1983253 AT24862 672 814 1 1 0 213186 212694 1 0 0 0 99 partof TCATGAAGATAGTACCCATGATGCTCAACATGAACAAGAAGCTCTTCAAGGCGGATCACCCGTTCGTCTTTTACATACGAAACCCGCAGGCCGTCTTCTTCGCCGGCCGATTCTCGAACCCCAAGTCTGGATCTGGATCAGGAGAGGAGGGCTTGTCACGGGAAGGTTTCGATGCCAACATGTACAATGTCTAAGAACAGCAGTGAGACCGAATAGAACTCAGCTATGAAATCCCACTAGACGTCATTGGATTTCAATCCGAGAGAGCTGTGTGCGCAGTTCTCAGTAACGTAATGAAGTATCGCCAGTAGGTACATATATGTCCAGTGCATATATGAGCTCGTCTTGGCACTCGGCGCTCAGTTTACAGAGATACTTATCTCGGGGAAGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTAAGTGGCGATCGCTTATAGCCAGTGAATTAAAATACAAAGCAATAAATTACCTATAATAACTTATGATTT 492 2R:1731127-2080000 1 NULL:1983254 AT24862 814 1305 1 1 0 2598633 213117 213082 1 0 0 0 100 partof AGAGTTCGTTGTAGACGGTCAAATGTATTACTTGTGTA 35 2R:1731127-2080000 1 NULL:1983256 GH04125 0 35 1 1 0 214233 213388 1 0 0 0 100 partof GCATTTTCCTGTGGGTCACTTCAGTGGCATGTCAGACCTCCAAAGAGATCTACCAACTACTTTCCAAGAGCCATACAAACCAGAACCTCGTCGTCTCGCCCGTCTCCATAGAGACCATCCTTAGCATGGTCTTCATGGGCGCAGAAGGCTCGACGGCCAAGGAGCTGCAGAGCGCCTTAGGTTTACCATCGGAGGACAAAGAGGCGGTGGCAGCCAGGTACGGTGCTCTCCTCAACGATCTTCAGGGACAGGAGGAGGGACCCATACTAAAGCTCGCGAATCGCATCTACGTCAACGACCAGTACAGCCTGAATCAGAACTACAACCTCGCTGTGAGGGAACCCTTCAAGTCCGAGGCGGAGTCCATTAGTCTGACCAATGGCCCTGTGGCGGCCGAGAGAATCAACCAGTGGGTGCTGGATCAGACCAGTGGTAAAATCAAGGGCATGATCGATCCCGGCAGCATGACGTCCGACGTGAAGGCCTTGCTGGTGAACGCCATCTACTTTAAGGGCCAGTGGGAGTCGAAGTTTGACCCAGCTAAGACCAGAGCCTCCACCTTCCAAGTAACTGCGAACAAGAGTGTGCCCGTCCAGATGATGGCGCAAATGGGAACATTCAGGGCTAACTACTTCCGCGATCTAGATGCCCAAGTCATCGAGCTGCCGTACCTTAACTCCAACCTGTCCATGACTATCTTTCTGCCCCGAGAAGTGGAGGGCTTGAGCGCCCTGGAAGAGAAGATCGTTGGCTTCGCCAGGCCGCTGGTTGCCAAGGAGGTCTATCTTAAGCTGCCCAAGTTTAAAATCGAATTTCGTGATGAACTCAAAGAGACCTTAGAGAAGGTA 845 2R:1731127-2080000 1 NULL:1983257 GH04125 35 880 1 1 0 214433 214291 1 0 0 0 100 partof CTGGGCATCCGAGAGCTATTCACCGACAAGTCAGACTTAAGCGGCTTGTTCGCCGATAAGTCAGGCGGCAAAGTCAGTCAGGTCTCGCACAAGGCGTTTCTGGAGGTGAACGAGGAGGGAGCGGAGGCCGCAGGTGCCACATGTA 142 2R:1731127-2080000 1 NULL:1983258 GH04125 880 1022 1 1 0 214651 214503 1 0 0 0 100 partof CTGTGGCCGTCACAAATCGAGCGGGATTTTCTACGTTCCTCATGGCCGATCATCCCTTTGCCTTCGTCATTCGCGATGCGAACACCATATATTTCCAGGGGCGTGTTGTAAGCCCTTGAATAAATAAAAACAATATTTAAATTTTAAA 148 2R:1731127-2080000 1 NULL:1983259 GH04125 1022 1170 1 1 0 2598639 216199 216179 1 0 0 0 100 partof AGTTTTCCCAATCATGTCAGGTA 20 2R:1731127-2080000 1 NULL:1983261 RE02548 0 20 1 1 0 217223 216288 1 0 0 0 100 partof TCAAGGCCACGTGTTCACTTCTGCTGCTCCAGGGCTTGAATCTGGCCATGGCCAACACCCTTAACTACTCCAAAAGTCCCGCAGGCGAGGCTCAATTTGCCTCGCAGCTTTTTGGCCAGTTGGCCAAGTCCCAGTCCGGCCGGAACATCGTTTTCTCCCCATCTTCCATCCGGACGGGCTTGGCCCTAGCCTACCTGGGCGCCGAGGGGAGCACTGCCGACGAGTTGAAACTGGGATTGGGTCTGGAAGGAGCTGGAAAGACCGAGGTGGCCGAGAAATTGGACCAGTTGTTGGCCAAGGGACAGTGGGAGAAGGCTAGTGGGGACGAGGACGTGCCCAAATTGAAGTATGCCAATCGGATTTTCGTGACTCAGAGATTCAAACTGACCCAGACCTATCAGGATTTGGTGAGCAAGAACTTCGCAGCAGCTGCAGAGAATGTGAACTTTACCCAAAAAGCGGACACAGCCAAGCACATTAATTCCTGGGTGGAGGAGCAGACTCATCAGCAAATCAAGGACCTCATTGCTCCGGAATCTCTGGACGCAGATACTTCGGCCATCCTGGTCAATGCCATCTACTTCAAGGCCGACTGGCAGAGCAGCTTTCCTGATTACGCCACTTACGCCAGCGACTTCGTCAACCACGGAGGTCGGAAGGTCAGCGTGGATACTATGTCCCAAGAGGATTACTTTAGGTTCGGCGAACTGACCGAGTTGAAGGCCAAGGTCGTGGAACTGCCCTACACAGGCACAGATATCGTTTTCCTGATCATCCTGCCTCAGGAGGAGCAGGGACTGGCCATCGTCGAGGAAAAACTGATGGGCATAGACCTCAATGAAATAAGCTCCCAATTGAGAAGGCGAAAGGTACGCGTGCAGCTGCCCAAATTCAAATTCGAATTTGATGTCCCTCTACAGGCAGCCCTCGAGGAGGTG 935 2R:1731127-2080000 1 NULL:1983262 RE02548 20 955 1 1 0 217771 217629 1 0 0 0 100 partof TTGGGCATTAAGAAACTGTTCTCTCCTGGGGCAAATCTGAGCAGCCTGTACCAGGGATCGGAACCCCTACGCATCTCGGAGGTGAAGCACAAGGCGATCATCGAGGTTAACGAAAAGGGCACTACGGCCAGTGGAGCAACCTGTA 142 2R:1731127-2080000 1 NULL:1983263 RE02548 955 1097 1 1 0 218041 217835 1 0 0 0 99 partof TTATCAAGGTCTCGGTGGAGTCGCTTACGATTGGAGAGGAAGTATTCGAGTTCATCGCGGATCATCCCTTCTTCTTTGCCATCAAGGATGCCCAAAACACCTTATTCCTGGGCCACGTCAGTCAGTTGTGAGTCGGCGCTGGAATTCCCCAATATGATGTTTTGTCCGCATCCAATAAATGCCAGTTCACGATGTCAAGTGCACAA 206 2R:1731127-2080000 1 NULL:1983264 RE02548 1097 1303 1 1 0 2598645 221698 221537 1 0 0 0 100 partof AGTTCCCTGCTAGACAGCAACGCACGCGCTCCTCAGTGGAAACCCAGAGACTTTCGGCAGTGGATTACAAATTTTGGTTGAGGTGTCAGGAGCAACCGATGCTTCTGTCGTCCTAGTCCGTCGTCCGGTGGTGTTCAGAGTGTCTGTGGCTTTGTGTGCGGGTG 161 2R:1731127-2080000 1 NULL:1983266 RE28276 0 161 1 1 0 221801 221754 1 0 0 0 100 partof TTTACCACAGTTTCGTCGCTATTTCGGGGTGATTAAGTATACGCCAGGTA 47 2R:1731127-2080000 1 NULL:1983267 RE28276 161 208 1 1 0 236135 235637 1 0 0 0 99 partof CTTCGCACAACTTCGCGACTGGAAGCGGAAGTTGCCAGGCCGGAAATCTGGCTGCCTACTGCCGTCTGGCCCTGCAGTACTAGTGGCTATGGTGAAGGTGTACCTGGAACACTGAGCTCGCAGCGGAAATCGAGGAAGTGTTGGGACGTATGATGCCCCGACTCCGGCTTAAGCACACAAATCCGTCATAATGCAGCGCTGAGGCCAACGGAACAAGCAAATACAAGCCATCGCACTTGAAGGCCAACGCAGCTGAACAATCGCAGGACGAGGGTGCTCCACTTGACGACTAGCGATTTCCAAACAGGAGACGTCGACAAAGCCACCAGCGACATGGCGGACCTGGAGCGCATTCGCCTCGTCCTTCTGGGCGGCGCCGGCGTGGGCAAGAGCTCTATTGTGAAGCGCTTCCTGTTCAAAACCTACACGGACAAATATCGCGCCACCGTCGAGGATCTCTACAATCGCGAGTACGACCTGGGGGGCGTCACACTAAAGGTG 498 2R:1731127-2080000 1 NULL:1983268 RE28276 208 706 1 1 0 239875 239707 1 0 0 0 99 partof GTGGACATCCTGGACACGTCGGGTGACATGCAGTTCCCGGCCATGCGGCGCCTGTCCATCGCAACGGCACACGCCTTCATGCTCGTCTACGCGGCCACATCCGCGCCCAGCTTCCAGTGTGTGAAGCAGTGCTTCGAGGAGATCCGCGAGCAGCGTGGCGACTTTCAGGTG 168 2R:1731127-2080000 1 NULL:1983269 RE28276 706 874 1 1 0 240636 240526 1 0 0 0 100 partof GACATCCCCATTGTGATCGCCGGGAACAAGGCCGACCTGGCCACCACCCACAGAGAGGTCAAGCTGGAGGAGGTGACCGACTGGGTCTTCTGCGAACTGCCGCGCTTACGGTA 110 2R:1731127-2080000 1 NULL:1983270 RE28276 874 984 1 1 0 244598 244407 1 0 0 0 100 partof GGCGAAAGTGCTGGAGTGCTCCGCGAAGGAGGACAGCAACGTGACGGACCTCTTCAAGTCCCTGCTCTCCCTGTCCCGCTTCCTGCCCGCCAGCAGTAGTGGGAGCGGGGGCAGCGGGGGCGGCGGCGAGGCGGCGCCCAGCGGTTTCAAGCGGCGTTCTTCGGCCTACGTCAGCGCATCGTCCAGTCGCAGTA 191 2R:1731127-2080000 1 NULL:1983271 RE28276 984 1175 1 1 0 249942 249809 1 0 0 0 100 partof ATAAAAATCGGATGAACAGCCCGGCCCTGGGAGGCGCCGGCGGCAGTGGCGGTGACAAAAAGGGCTCCAGCCTCGTGGACGCCGTGGATGTGGCCACCACCAGTGCGGAGGCCAAGCTGAAGCCTCGTTCCAGGTG 133 2R:1731127-2080000 1 NULL:1983272 RE28276 1175 1308 1 1 0 252383 250042 1 0 0 0 99 partof ATCGCTCATACGCCGTGCATCACGCAAGACCAAGCAGCAAATCAACAACGCATCCGACGACTGCAACGTGCAGTAAACCATTATTTTGGCCGCCAGCGTCGAGCTTAATTATGTTATTTAGTTATTACGAGTATGTTGCCACAATGTGAATTAATAATGGACGCCAGTTAATTAGCGTGCATAAACAAGTGGCGCCGTATTTATGTTCGGTGCACTGAGCTGATTATTCTGATAAAGCTACCCAGTTCACAAAAACCTCTTGCTCAAGGGCACAAAAATTTCGATGAATTTGCTACGCGGCAAAACATTTTATAGTTTGTAACCACCAGAGCTTCGAAACGATGCCGTCATGACACTGGCCTCAGATTATATGATATTTCGTAAGCAACTCTGATTAGGTAAATTTATATTTCATTATGAATAGATATCCTAGCTTATAAGCCGTGAATCAAATCAAATTTCTTTAACAACACTATAAGTAAGTACGCTATAAGTACAGCAAAAGCAAACACAAATACTTATTCTGCGACATTTTAATCCAGTGTCATAGCGGCATAAAAGATAAGGTATTATTCCGACACTGAGCTGACTTGCGAGGCATTGTGCACACAAATCGATTTGAGTTGCGGTCATTAAGGTTGGAAGGGACCAGGTTTATTTAAATTTAAAATTAACTTTTATACGACAAACAATTTCGATTTTCGCAAACTTCAGTACAGCTCTGGGTGCCCGATTTGAATTTAATTTAGATGTCTCCCACGGGAGAAGGCATTTTGAAGACTCGTAGTGCCGTTCTCCTCGAAAGGAGTTCCTTTTGATGGCAAAATAATGGCTCAACGCGACTGAGTACGAGGTTTTTCGAGGCAGGACTAGGTTAAGCGCGTTTTCGACTGGCGGATTGTCATAATATTGTGACAGGTGGCATAGCCCTAAGGTACATTCTAGGATACTACTTTATGAATCTCTATCTGCACCCTTAGCCGACACCATGGTTAATATTTGAACGTTCCGTGTACACATCTATATATTAATACAGCTCCGATAAGAATGTTTATATTGGCCAAAGCCGAACTCGCTCCTTTCGAGTCGGCGAATACGAAAGGAATCGCAAGTTTTGCAAAAATAAGGCAATTTCGCGGCATTCTCCGCGGCTCCAGCCACGTAAAATAACAAGAACTTTGCCAGAGAGCACAGAGCAATTTACTATGCAAAAAACGTAATTGTAAAATAAATTTGGTGAGGGAAGGGAGGAGAGGAGGGTGCCGAATGCTTATCAAGGATAATACAGGGTGAACTTCTTATGCCAAAACGCCAAAATGCCAAATCAAATAGCCCACAATGCACATCCTGTTCGCAGGAGGCTTGCGGCAGCGAATAATCGATAAATCTGTTTTTAATACGCAACTTGTATCCATTCGCACAAGTTACACTTGCATCTGGGTGGGTGGTGCGTGGGTGTGCTCGCCAGTGTGTGATAAGAGAATCCTTTGTGTTTGTTCACCGGAATGTGCTTAGCAATAAGATTTATTTAAAAGACTACATTTAGGCGGTACCGAGTACGGCGGAGATATCTAAATGATCTGTAAATGGATGAAATACGGCATATGCAAAGTGAATTGTGATTAAACCAAATACATCTAGACACACGTGTGTGTGGCACTGTGTGCAAGCTGAAAAATGCAGCAAACAATGCACCCAGTGATTGCAGTAATGGATTCCAGCTACTGTAAACACCTGGGAAATGTCAGAGGCGTCTGAATGGCCCCAAAATAGTATTGAGTATTGTATTCGTCCATGGAGGATTGTAGTTATACATGCATACTTATGTGCGGCATTATAAACCGCTTACAGTACAGTTACATACGGATACATATAGTACACATAGTCAGTACCTAAACAAGTTTGTGTGTACAGTTTGGATGTTTGTTTTACAAGTAATACGTTGTTTATACATTGTTACTAGGTGTAGTTATTAACAACAAATCTGCTGACTAGTCGTCGCCACTCGCGTATATCATGAACCAATGGGAACACAAGGGTGCGGAGGATTCCACCCTATCCGCCCCATCGACGAGGGACCGCGAGATGCTCGATATCTTATCCGACCTACCCGATTTTAAATAAACATATTCGTCTACGTAGTTCGATTGATTGAGCGCACTTACACTTACCTACTCTACTGAATCGAAGGATCGTGGCCCATGGACTACACGTAGTCTAGGGAAACCCAAATTAACTCTCTAAGTGTGCGTATGTGTGTCATGTACTTGTAACTAATTGAATTTCAATTCAAATTGAATTATTGACAATTGTATTAGCCAGTTAAAATAAACCACAATGCGTC 2341 2R:1731127-2080000 1 NULL:1983273 RE28276 1308 3649 1 1 0 2598655 253434 253220 1 0 0 0 100 partof GCTTGACTAGCTAACACCTGGCAATGCTCCACAGACATTGGGGCCAACCTGACGGACCCCATGTTCCAGGGCTGCTACGGCGGAACCCAGAAGCACGAGCCCGACCTGCACATCGTCTTGGAGCGCGCGTGGCAACAGGGACTGCAGAAAGTCATCGTTACCGCCGGCTGCCTGAAGGATGTGGATGAGGCACTGGAACTGGCCTCCAAGGATGGTA 214 2R:1731127-2080000 1 NULL:1983275 LD08659 0 214 1 1 0 254261 253654 1 0 0 0 100 partof AGCGCATCTACACGACAGTGGGAACACATCCCACCCGGTGCGAGGAATTCGTACCAGACCCAGAGGGCTACTATGACCAGTTGCGATCCAGGATCAAGGCAAATCGAACCAAGGTGCGGGCCGTAGGAGAATGTGGTCTAGACTACGATCGCTTGCACTTCTGCGCCCAGGAAACCCAGCGTCTGTACTTCGAGAAGCAGCTGGACCTAGCGGCCGAGTTCAAACTGCCTCTCTTTCTGCACATGAGAAATGCTGCCGAGGACTTCATGGGCATCCTGGAAAGAAATCGGAACAAGATCGAGGAGTGCGGCGGCGGAGTGGTGCACAGCTTTACAGGAACTTTGGAGGAGGCCCAGCGCATCCTCGCCTTCGGCGGTCTCTACATAGGCTTCAATGGGTGCTCCCTAAAGACGGATGAAAACGCAGAAGTGGTGCGCAAGCTACCCAACGACAGGATAATGCTAGAAACCGACTGCCCGTGGTGTGGTATTCGACCCTCGCATGCTGGACACAAGCACGTGACCACCAAGTTTCCCACCGTCAAGAAGAAAGAGAAATGGACAGCTGAATCCCTAATAGACGGACGCTGTGAGCCTTGCCAAATCAGGTA 607 2R:1731127-2080000 1 NULL:1983276 LD08659 214 821 1 1 0 254459 254327 1 0 0 0 99 partof CCAAGTTTTGGAGTCTATTGCCGGAATCAAACAAGAGCCTAAAGAACAGCTGGCTGCGTTATACTACCAAAACACATTGGACTTGTTCTTCGGCACAGGAGAGAGTAAAGAATAAAACAACATGCATTTACATTC 132 2R:1731127-2080000 1 NULL:1983277 LD08659 821 953 1 1 0 2598660 288122 286744 1 0 0 0 99 partof CGTTGAATCTCCAATCAACGTTTTCAAGAATCAACTCATTTTTGACACAACCAGGTCAAAATACTTATGCGAGCACCCGTTCCCAGGTTATACTCGCCATCTGATTCCTCTCAAAGACGGATCACTTGCCGATTTAACCAACTCGTTACAATCGTGTCTACGACCTGTAATAATTAACGGCGTCAAAATCCCGGAAGCACATTTGCAACGCTTTCAGTCCATCTGCTTAGCGAATTTTCTTTTATACAAAATTCGGATAACGCAGCGCCTAGTGGCGGACGTGTCTGGCGCAGAGGAAATTTGTGAAATAATTGAAAAAGAACACCGTAGAGCACATAGGGGCCCTACGGAGATTCGTCTCCAACTTTTAGAAAAATATTATTTCCCGCGAATGTCCAGTACGATCCGTCTGCAAACTTCCTCATGTCAGTGTTGCAAACTCTACAAGTACGAGAGACACCCTAACAAACCAAACCTACAACCTACGCCAATTCCTAACTACCCATGTGAAATACTTCACATCGACATTTTTGCGCTCGAAAAAAGGTTATACCTAAGTTGTATTGACAAATTTAGCAAGTTTGCCAAACTTTTCCATCTGCAGTCAAAAGCATCTGTGCATTTGCGAGAAACTTTGGTGGAGGCCCTACATTACTTCACCGCCCCTAAGGTCTTGGTTTCGGATAACGAGCGAGGGTTGTTATGCCCCACAGTGCTCAACTATCTTCGGTCTCTAGATATCGATCTGTATTATGCTCCAACCCAGAAGAGCGAAGTAAATGGTCAAGTCGAGAGATTCCACTCTACGTTCCTAGAAATTTATCGTTGCCTTAAAGATGAGCTCCCTACCTTCAAACCCGTTGAGCTGGTACACATAGCAGTGGACCGCTACAACACTTCCGTTCACTCGGTAACGAATCGAAAACCAGCAGACGTTTTTTTCGACCGCTCGTCAAGGGTAAACTATCAGGGTCTGACAGATTTCCGGCGGCAGACTTTAGAGGACATCAAGGGCTTAATTGAGTATAAGCAAATTAGAGGTAATATGGCTCGGAATAAAAATAGGGACGAGCCAAAGTCTTATGGGCCGGGAGATGAAGTTTTTGTTGCAAATAAGCAAATAAAAACAAAGGAAAAAGCGAGGTTCAGATGCGAAAAGGTACAGGAAGACAACAAGATAACAGTTAAAACCAGATCAGGAAAAATTTTCCACAAATCTGATCTAAGAAATTGAGACGTGGCTTTCACATTTAAAAAAGAAACGCGAAAAAGAATAACGAAAGTAATAAAAGTACGTTGTGGCAGCTAATGAAATATTCCACCCATGCATACCCTATATAAAAAAAACATTAATAAAAAAAAAAAAAAAAAAAAAAAA 1378 2R:1731127-2080000 1 NULL:1983279 LD21171 0 1378 1 1 0 2598662 316551 315854 1 0 0 0 100 partof CACTCACTCAACAAATTGTTTACCACAAAAAACCGTGCTGAAAGTGAACGAAAATAAAGTGCAGCCCGGCGTCGAGCATTTGCAGTGATCCCAAGACGCCCAACCATTGATTCCCGTAGCGGTGTCCACCCGGATTCCAGCCCACCGCCACCAGCACGCCATTCCATTTGGGGAGCCTCTCGGTCGGTTCGGTCAAACAGTCGCGATTGCCCGGTCGTCCACGAACGCTTATAAAATTGGCAAGATAACTAAGCAGAGCACAAAGATGCCGCCAGCATCAGCGGTAAACAACAGCAACGCGGCCGCCCAGGCGGCGAAGGCCGAGCGGGCGGAGAAGCTGCGCGGGGCACTGAAGGGCTTCATCGTGGCGGACCGCCAGCGGCGCCAGGAGGAGTTCGAGGCTCAGTGCGAGGAGCAGCGGCTGCGACGGGAGCGCGAGGAGGTGGAGCGCCAGAACCAGGTGGCCCTGGATGACACACGCGGCCAGATAACCCGACTGGACGAGCAGCTGGCCGATCTGCACAGCCAGAAGCATCAGCTGACCGTCCAACTCAAGAAGGTGCTCAACGAGGACGAAACGCGCAAGAAGCTGGCCAAGGAGAACGAACTGTTCGCCATCCAGCAGGCGGCGGCCAGTAGCCCGGTCTTCCTGCCGCCCCTGCGCCTCCAACACCAGCACCATACGCTGATGCAGAAG 697 2R:1731127-2080000 1 NULL:1983281 LD41464 0 697 1 1 0 316708 316608 1 0 0 0 100 partof CAGCTCCCGTCCGGCGGACAGCCAGGAAAACGTGGCAGGAGTCCATCGCCGCCGAGTCAGCAGCAGGCTTACTACAAGAGCGCCGCCAGCTACGCCCAGCAGAGTA 100 2R:1731127-2080000 1 NULL:1983282 LD41464 697 797 1 1 0 317463 317412 1 0 0 0 100 partof AACACGATGACTACCGTCGTGCCGCTGACTATGCTAGATTATCATGGAACAGTA 51 2R:1731127-2080000 1 NULL:1983283 LD41464 797 848 1 1 0 318040 317555 1 0 0 0 100 partof AAACAGCGGCACAGTATCCGGGCACGGGAACGGTCTTCTACCAGACGGTCGCTCCTCCGCCGACGACACAGCACCAGGCGGACGCCCGCTTGCAGTCCATCTACAACTACAACCTTCCGTTGCGCCAGGCCTACCACGTGGACCTGCCCAGCGCCACGGTCAGCAAGCCGCCCGACTCGCAGTCGCCCAAGGCACCGTCGCAGTCGCAGCCCATGCAAGTGCTTCACATCAACCTCGACCAGCCGACCATTTCGCAGGCAGACCTGGTGGCTCAAGCCGGCGGCAGCCTCTCGGTAAAGGCCTCCCAGCCACACGTGACTATGGAGAAGCTACCGGACCGCTACCACATCGAGGTGAAGCACGACGGCCAGCCGCCGAGCCACGTCCCGCCTCCGCCACACCTGCTGCCGGAGGGCGTCATCTTCAAGCCGCTGCTCAACGAACTCTCATTGCACAGCAACGTGCTGCAGATAAGCAGCAGCCAGGTG 485 2R:1731127-2080000 1 NULL:1983284 LD41464 848 1333 1 1 0 318699 318345 1 0 0 0 99 partof TTTCCTCCACAGAATCCGAAAACAGCGGGAAGCATCACACAGGGCTATGCCCCTGGACGAGGTGGATCCGCCCACGAGCAGCAGTTGGCTCGGCAACAGCTGGCGATGCTGCCTGGCCAGCCGGGAGCACCGTCCGGATCCGGCTCCGCCCAGCCGCCTCCTGGTCAGCAGATGCATTACACGCGGCGATTGTACTAGCCTCTAACCCCTAACCCCTTTTGTCGCTACGGAACTCGCTAACTGATATACTTACGATTTTAAATAGACATTACAACACTGACTACGCTTCCCACGTGAAGTCGGATAAACGAAATAAAGCACACAACTATGGCGTCCCTATTTTCCAATCGACAA 354 2R:1731127-2080000 1 NULL:1983285 LD41464 1333 1687 1 1 0 2598669 322552 322463 1 0 0 0 100 partof TTAGCATTGTCAACTGCTCACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTG 89 2R:1731127-2080000 1 NULL:1983287 GH05668 0 89 1 1 0 324259 324147 1 0 0 0 100 partof TTGCAGTTCTTCATCCATCTCCACCAGCAATCTCTGGCAAAACTCAGGCAAAATGAGCTGCGGAATCTCCATGGTTAAATATATCCTATTTATATTTAATTTGCTCTGTTCGGTG 112 2R:1731127-2080000 1 NULL:1983288 GH05668 89 201 1 1 0 326642 326450 1 0 0 0 100 partof ATATGCGGCATATTGCTGATCGTATTCGGAGCTCTGCTGTTCAGCAAAGTCCGTAACATGGATGACTTCGCGGAAGCCCTGCGAACCCAGCAGGTGCCCGTAACGATGATCATCCTGGGCACCATCATCCTGCTGATTTCCTGGTTCGGCTGCTGCGGAGCCATTCGGGAATCCTACTGCATGTCCATGACGGTA 192 2R:1731127-2080000 1 NULL:1983289 GH05668 201 393 1 1 0 326867 326705 1 0 0 0 100 partof TACTCGATCTTGCTGTTCGTCCTGATGATTGGCCAACTGGCTTTGGTGATCTACATGTGGGTGCAGAAGGACAAGTACCTGGAGATCATGGGCGACGTGGTCGAGAAGGCCTGGAACCATCGCACCAGTCGTTCCGACTACATGGACGCGATTCAGATCAGCGTA 162 2R:1731127-2080000 1 NULL:1983290 GH05668 393 555 1 1 0 327128 326933 1 0 0 0 100 partof ATGAAATGCTGCGGACGCAGTGGCTACACCGACTACGCCTACCAGGGCAAGTTCCCTCCCTCCTGCTGCAGCGACACCAACAACTGCCGCTGGGAGACCGTCTACCGGCGGGGATGCAAGGTCACCTTCGTTGAGTTCTGGGACAGGAACAGCGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAAGTA 195 2R:1731127-2080000 1 NULL:1983291 GH05668 555 750 1 1 0 327750 327391 1 0 0 0 99 partof TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCAAATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA 359 2R:1731127-2080000 1 NULL:1983292 GH05668 750 1109 1 1 0 2598677 322835 322481 1 0 0 0 100 partof CACGAACGGTTCGAAAAGCGGAGCGCGCGTAAAATCATTCTGTAAATCATTCAAAAGGCGGAAAACTCAAGGTGTGTGTGTGGGTTTTGTTTTCAAATTCCGTGTGCTTGTGTGTGTGAGAGAGGGCGAGAGCGACAGTGTCGTAGCAGGCAGTGTTGTAAGGTGCCGAAACAGCGATCCCAACCGGCACACTAGTTGTCCTGCTCGCACTCCAGTGAGGCAAATGTCAAAGTCTGGTCAGTAGCAAAACAGAATTGCAGCCAAGAAAAGCGGAATCAGCGACAAAATTAGCCATTAGTTGGGTTTTACATATAGATTAGGCCAGCGAAACGACATAACGCTCCAAGTGGTAAAGTG 354 2R:1731127-2080000 1 NULL:1983294 GH17623 0 354 1 1 0 324083 322895 1 0 0 0 100 partof TTATCCAATGGAGGCGGCCAAGGATTTTGCGGTGGCCAAGTACCAGGACTTATGTAACTTCCTGGAGCGGGATACGCGCGGCAGTGAGCTGGCCATCTATGGCACCTCGGCCATCATGCTGGCCGTGGCCTATGCCAAACGGAAGCCGGCCTACCTGGTGCGCCAGTTTAAGCAGCCCTCGCACATCCCGGAGCGCCTGATCAACGAGCGCGTCATGCACACGGGCAAGATCGCCGGGGTCAAGCAGCAGGAGCAGGACACCCTGCTGATGATCCAGCACCGGCCGCTTTTCCCGATCTTCACTAGCAGCAAACGCCTGCTGCCCGTCAAACTGCCGGGCGTGCGCGTCAATGCCAACGGCTACTCCTGGCTGCAGCAGTGTCTCATTGGGCGCGAGGCCACCTTTCTGCCCCTTAAATCCGCCAAGGGACAGGACTTTGTTGTCTGCCAGCTGTGCCTGGTCCATCCGCCGAGGGGCAACCGCCTGCTGGACGTCTCGGAGACCCTGCTCAAGCTCCGCTTCGCCCGATTCGTGCAGGATGCCGCCGCCGCGGTTAAGAAGAACGGGAAGTACTACCAGCATCTGAAGAAGGTGGAGCAGACCACAGCGGAAAAGGAGGCCTGGCTCTCCTGGGCCGCCGGCTATCCCTACATCTGGCGCCGCTACAACGAACTGAGGCAGCGCTGGTTGCCCAAGGAGAAGCTGCTGCCGGAGCTAGTGCGCTGATTGCGATCTCCCCGTTCCTGCCTCGATGCTATTTACAGGGCTACCTAGCTCGCCACCATTAACTTAGTTCCATGGCCAGCTACTCTCTATATTTTTATTATGCCTGTTTACTAGCTTGTGCATTTGTGTCTTAGTGTTGCTTGCTATCTATTGTTATACGATTGGCAAATATCATATACGATATAAGACAGCATTTGTTTACAAACCCTCGAGCACAAGTACACAAGTCAGTCTCAAAAGCTTATTAGTAAGGGGAATAGCTAGCGCGACTTGCCCAACGCGACTTTCGATGCCCAGGCGGTACGTGATCGTGTGCTAATTTCCACACCCAGTAGAGCCAAGAACGTCAGCATTTTTTAAATATTCAAATAAGCGAAATGTTTTTACCACGGATGACATCAGTGCGTGTGCCTGTGTGTGTACGTGTGCGTGTTTCCCAAATAAAATGCCGAAATACCTAA 1188 2R:1731127-2080000 1 NULL:1983295 GH17623 354 1542 1 1 0 2598681 328956 327939 1 0 0 0 100 partof CAATCATTGGCTCTATTGACATATTTCCGTAGAACTAACCTATCAGAAGACTATATTTAGTTAGTTAGCTTTTTAGGGCTCAGACGAAATCTTATCTCCATTGAGCTATTTTATCTATGAAGGGCACATAGCCGTTTTGTGAATGTCAATGGGAAATTATTCCGCCGTGGAAACCCCAATAGTTGCCAAAATCTTGTTGAAGTTAGGCTGGGAGTGCACTCGCTAAAAGGTTTATTGCTCGATTGATAGTACATAAATCTAGGCGATAAGATCGGGGACTCACGGGGAAACGGACTCCAAGCAACGTAATATGTGAGTCAGCGTGCACCGCGTACTCTTGACTGGTGATAAGGCAAGGTGTGGAGGGTGTGAATGATTCATCTTATGAACGATCTAACGCCCCCAAGATGGAATCGCACGAGGGCTAGATAAAATTCCGCCACCAGCAGTTTGCACCTACCATTCGTTGAATGAATCATTGCGCCAAGGATGTAATTTCCCAGGTTCGGACCACCACAATGATCTGGTATCTCGTGGGTGCAAAGCGATTCACCAAGTACAAGTACATGGGCATCGGAGCTTCCAGCACAAGTACATACGGAATTTTATGGCCGAGATAAGAGCGCAGCCGATAAGATGAGGACTCCGAGTAAGCTTTAATAGCCGCGTTCTGTCCGAGGGCCCATTCAGTTAGACGAACATCGTCACATCGAACGAACGGATTATCCAGCTAGCCAACGAGAAACCCGAACAGAACCCAGCACCATGAACTGTCTATCCGCGATGTTCAAGTACCTGCTGTACTTGCTCAACCTGGTGTTCGTGGCCGGTGGCATCCTGCTCATTGTGGTGGGCTCCATCATGCTCTCCACGATGGGCAACTTTACGGCCTTCGACGGAGGCGTTAACACCCAGACCATCCCGATCTGCATTATCGTCATCGGAAGTGTCACCTTCGTAGTGGCCTTCTTCGGATGCTGCGGCACCATTCGCGAGAACGCCTGCTGCACCACCATCGTA 1017 2R:1731127-2080000 1 NULL:1983297 GH04835 0 1017 1 1 0 329185 329020 1 0 0 0 100 partof TACGCCATCTGCATGCTGATTCTGTTCGGCCTGCAACTGGCCCTCTCCATCTGGATCTTCGCGGCCAACGACAAGTTCCTGTCCAGCATGGGCAAGGCAGTGGACAAGGCGTGGGATGAGAACAATGCCGCCCAGGGATACCCCATGGATGCCCTCCAGTTGGCC 165 2R:1731127-2080000 1 NULL:1983298 GH04835 1017 1182 1 1 0 329626 329257 1 0 0 0 99 partof 369 2R:1731127-2080000 1 NULL:1983299 GH04835 1182 1551 1 1 0 2598686 333417 333374 1 0 0 0 100 partof CGACATCATCAAGTATGCCGGTCTGGTCATCGCCGCCATCGAA 43 2R:1731127-2080000 1 NULL:1983301 GM15292 0 43 1 1 0 334038 333679 1 0 0 0 98 partof TTTGTGGGATTCGTTTTCGCCTGTTGCTTGGCGAACAGCATTCGGAACTATAGACGCCGTGCGGAATATTAATCGACAAAGGACTAAGGCCTTGCACTAATTTTAATTGAAACCGAAAGTACGAATTATGTTGCCCAATTTTACGAATATTTACCTGATACAGATGGCCATTCAAATTTGCATAATCTCAAGCGTAAGCAGCA-AATGCAGCAAATCCAATGACGAATGCGTAACGATCACTTTTGTAAGATCGTTTGTTCAAAGTTACACTGAATGTGCTAATATGTTTAACTGTACAAAATAACTTATACTCCTGGAGATTGCAATAAACGGAGAAATTTATTTACAATTTACGAAAA 359 2R:1731127-2080000 1 NULL:1983302 GM15292 43 403 1 1 0 2598690 336407 336221 1 0 0 0 100 partof TCCAATCGAACGACAGTAAACGACGCGAGTGCGCGATAAAATCAGAGACACCGACAACTCCTTTGGATAAAACAATAGTGTTTATTTAATTCTACTAAATACAGGAGCAAACTATATACTTTCAAAATGGGTTGTCTATCGGGAATAGTCAACTTTATTTTATATATTGTCAATATCGTGTTTTTGGTA 186 2R:1731127-2080000 1 NULL:1983304 LP02831 0 186 1 1 0 337692 337500 1 0 0 0 100 partof ATCGTTGGCATCCTACTGATCGTGTTGGGCTCGATCATGCTGTCCGATCTGAGCCGCTTCGATGTCGCGGGGAGTGGGACGGACCCGAACACCATCCCCATCTGCGTCACCGTCCTGGGAGGCCTCATCTTCGTGGTGTCCTTCTTCGGGTGCTACGGCATTTTTCGGCAGAGTGTCTGCATGACCGGCGCGGTA 192 2R:1731127-2080000 1 NULL:1983305 LP02831 186 378 1 1 0 338398 337755 1 0 0 0 100 partof TACACCAGCATGGTTTTTGTGCTCTTTATCCTGCAACTGGTGCTTACGTGCTGGGTGTTCGTGAACCGATCTGCCTTCCTGGGCGATATGTCCAATCTGGTTAACTTGCTCTGGGACTCCCATGACTACACTGCCATGGGCGTTCTTGAGGAAACCTTCGGCTGCTGCGGTGATACGAGCTATACCAACTACAACAACATCGGCCTTTCGGTTCCCGGAACCTGCTGCGGCTACCTGGACCGCCAGGCCACATGCAACACCCCCTCGGTCTACCAGTCGAGGCCCGGCTGCAGCGCCAAGTTCGAGGAGTTCTGGAACGACAACATGGACATCATCCGCTGGTCCGGCCTCGGCCTCTGCATCTTCGACCTGGTCGTCTTCCTCATCGCCGGCGCCCTGACCAACTGCATGCGCAGCCAGAACGCAGGTCGCCAGGTGTACGCCTAAACTTGTGAGGAACAAGCCAAAGGCCAAAGGATCTACATATGTCTACTTATGTTACCATATAACAAACTGTTTTTCGAGCCGTGCCAATATTAATATATACGTCTACATTTCGCCTATTTATCAGTTACTACTTATGTTATTCTTTATACTCTTTTTGGAGCAATGCCAATATTAATATATACCGCTACAACATTTA 643 2R:1731127-2080000 1 NULL:1983306 LP02831 378 1021 1 1 0 2598695 342110 342030 1 0 0 0 100 partof ACTGACTAACAGAAAGCTGTTCGACTTGAACGGACGCGTATTTCGTTGGAATATAAATTGGTGATAATTTAAAGTCGAAGGTA 80 2R:1731127-2080000 1 NULL:1983308 RE12209 0 80 1 1 0 342891 342807 1 0 0 0 100 partof ACGGTACAGTAAAGCAACATCAAGATGGACTGCGGCACATCTATGGTCAAATACATCCTCTTCATATTCAACACCATTGTGTCGGTG 84 2R:1731127-2080000 1 NULL:1983309 RE12209 80 164 1 1 0 347150 346787 1 0 0 0 99 partof GTTATCGGCATCTTGGGCATTGTTTATGGCGTGCTGATTCTGAAGAGCATCGGTGTAGTTGAAGTTAATGGACAGGTGGGCTTCCCGATACAGGCTCTTATGCCGATCATTCTTATCAGCTTGGGCTCGATTGTGGTCTTCATTTCATTCCTGGGATGCTGCGGTGCCATTCGCGAATCCGTCTGCATGACCATGAGCTATGCCACCTTCTTGCTGATCCTGCTGATCCTGCAGCTGACGTTCGTTGTTCTGCTGTTTACCCACAGGGAAGAGTTTGAGAACGCAATGGGAAACGTTATCGAGAATGCATGGAATTCTGAACATACTTATAAGGGAGGTGTCTTCGACACCATTCAGAAATCG 363 2R:1731127-2080000 1 NULL:1983310 RE12209 164 527 1 1 0 347401 347209 1 0 0 0 100 partof TAGTTGCACTGCTGCGGATCAAGCTCTGCTCTGGACTACATCGGCAAGGGAGACTTGGTGCCCCCAAGTTGTTGCAGCGGTTCGTGCCTGATCCCGACTAACTACTACCCGGGATGCCGTGGAAAGTTCGTCGAATTAATGACCACTGGATCTGATAACGCTAAATATGTGGGCATCGGCCTCATCGGAATAGAG 192 2R:1731127-2080000 1 NULL:1983311 RE12209 527 719 1 1 0 348139 347464 1 0 0 0 99 partof TAGCTGATCGGCTTTATCTTTGCCTGCTGCCTGGCCAACAACGTGCGTAACTACAAGCGCCGGAACGCCTACTAAGCAATAGGTGTATCCATCAACTACATCTAGAGGCACACCCACATCCAGTAGCACACACACCTCACATTCTCATTAACTTTTACAGTCGTTGAACGCACATACACAACGGGATACACAATAACACCTTGAAATAAGCCATTTAAGTGGATATTTGTCACGGAAAAACAAGAAGAAGCTTAGTTTAAGGCGATATGAAATGCTTACATTTTTGATATCCTATGTATTTCTGGTAAAATTCATGTTATACCTATCGAACGAACGAGCAAACAAAGATATTTCCAAAGCCTTTGTACAAACGTTTTACTTGTTAAACCGAATCCCCACACATTAACAAAATAAACACGTTAATAATGATATATTTGTTCAAAATTAAGGATATAATCTATAAACTGTTGAGAGTCCCAATGCGAAAAGAAATATAAATTTGTAATAAACATATGTATATACTGGTATATATGTTTGTAAGTACATTGTTCATTCGATTCATATTTGTAAGGAGAATCTCCGGGAAAGATTTAAATTTGGAAGAAGCGTCAATAATCGAGAGCTCGAATTGCATAAGAAATTTATGAATAAAGCATTTACTATGTATTTATATACCAA 675 2R:1731127-2080000 1 NULL:1983312 RE12209 719 1394 1 1 0 2604401 88663 87370 1 0 0 0 99 partof ATCTTCTACGTAATATACTTTATTTTACAATACAAATACTACATATGCGGGGTGTCTTACGAACCTCTTCCAGTAAAATATTAAGGGGAATTAATGCACGGGTTTACTCGAAACCTTTTTAACTTTGAGTTAACAACTAAAACAAAACACCCCTCTTGGAATGCCACAGTCGTTTTGTTTGCATTCCTAGCCAATCCAATAACGGCGAAACCGATATTTCTGGGACACCCCTGAGCCCGTCTAGAACTCGTCGTTGAACGGGTAGTACTTATGGCCCGACATTCCCGAAAAGGGTACCGTGCGCTGCCCGGTGTGATACTGCTCCATGCCGGCGACGTCGTCTGGACTCAGCTCGAAGTCGAAGACGCGGAAGTTCTCCTCGATGCGGGCCTTGTTCGACGACTTGGGCAGTGGCACCACGCCTAGCTGGACCAGATAACGCAGGCAGATCTGTGCCGTGGTGCGGCCGTACTTCTTGGCCAGATTCTGGGCATGCTCGTCGTAGAGGAAGGGCGGCCACTGCCGAGCGGGCTGGGGACGTGCCAGGGGGCAGTAGGCGCAGATGACCAGTCCGTGGCGCTTGGCATGCTCCCGGAGCTGGCGCTGCTGAAAGCCTGGGTGGCACTCCACCTGGTTCACTACCGGCCGGATGCGGCAGTTGGCTAGCACTCGCTCCGTCTGCGCGGCGTTGAAGTTGGACAGGCCGATGCTGCGCGTCAGGCCCAGATCCACCAGCTTCTCCATCTCGCGCCAGGTGTCCAGATAGTCCACGTCCGTCAGCTCCAGGGTTCCGTGCACGTTGCTGTCATTGTGGAACTTCTGGCCCACCGGCATGTGCATCAGGTAGAGGTCTACGTATTCCAAACCCAGGTTGCTAAGGCTCAGGCGGCAGGCGCGCTCCACCAATGCAGGGTCGTGGTGGATTCCGCCTAGCTTGGTGGTCACGAAAACCTCCTCGCGTGTGACCACTCCCTCGGCGATCTTCTCGGAGATCGCCTGGCCCACCTCAGCCTCGTTCTCGTAGACGAAGGCGGTGTCCAGGTGCCGGTAGCCCACGTCGAGGGCGTGGCGCGTTGAGTGGTAGGCGTCCGACTCGAACGACTTCCAGGTGCCAAGGCCCAGAGTTGGCATCTCGCGCCCGTTGTTCAGCCGGATGGTGGGAGCCAGATTGGTCATCTTGTCGCTGGCGCTGATAATTAACGCTGTGCAAATTGGACGCTTCTAAGTCTAAACCAGTGCTACTACGCCTTTCTCGCGATCAAATCTCTATCTGTTCCAGCTCGTCGAAAGCTT 1293 2R:1731127-2080000 -1 NULL:1988061 LD24696 0 1292 1 1 0 2604404 118781 118236 1 0 0 0 100 partof CAGAGGAGAATTCGCTGCTCTTTCCGCTGCAACCTTCCAGCAGATTTAATGAATGAAATCAACTTGAATTAAATTCCTCCATATTGCGGCTTTGTTTCTGGCTTTATTTGTTTACACACACTGCAGCTGTTGAATCACCAGAGAGGCGAGAAATGTGTTTTCGGCTGCCTTGCTTTGTTTCGCTTGGAAGGTAATAAATTTTTAACACAATTGCATTGCATAAACAATTTCAAAACTGCACTCGAAATGGGCCTGTTTACACTCCGTTGTCGTGTCGATTACATTTTTGGCCAATAGCCAAGCACTCAGATTTAACTGGTTTATTTCGACTTGGCGAACGCCCGCGCGCGAATCTTTCAGCACAGCCCACGCACTTTCTGCAGCATGGTTAACTTGAAGATACTCGAATCGCACAGGGAAACAGATACGGATGGGCTCCAATGGAGGTGATATAGAGGCGTAAACAGAGGCAGAGATTCAAACCGAACCGAACCAAACCGAACTGAACCTCTGGGCCAGCGATCGAGTTGTGCGCCGCTGGAGAG 545 2R:1731127-2080000 -1 NULL:1988063 GH01501 0 545 1 1 0 103561 103414 1 0 0 0 100 partof CTCCCAGATGAGTCGAAAGTCCTGCTGCTCCACCCGCAGCAGCTCGCAGGTGGTCTTCGTCACTACGGTGCTGTCCCGCGGCAAGTCATGCAGTACGGACTCCCCGAATGTGGCACCCACGCCCAGGTTGCACAGAGTAACTGCGCT 147 2R:1731127-2080000 -1 NULL:1988064 GH01501 545 692 1 1 0 99134 99082 1 0 0 0 100 partof CGTTCTTCAACTTGCAGTTGGTGAATATGTCATTCATTAACTCCTTGTTTTTCTG 52 2R:1731127-2080000 -1 NULL:1988065 GH01501 692 744 1 1 0 98798 98700 1 0 0 0 100 partof CTCGGTGATGGGCAGCGCTGGGTTTGGGTGGTCGGGGCTGAGGGGTCGTTTCGTGGGCGATGTGGCTGCGGCTGTCGCTTGTACGCTCGGTCCAAAACCTG 98 2R:1731127-2080000 -1 NULL:1988066 GH01501 744 842 1 1 0 98440 98353 1 0 0 0 100 partof CTTGCGATCCTTCAGACAGCTCGAGTTGTCGGCGACGAGTAGTGTGCGTAGGGCCCAGCCCATGCGGTTCATAGCAGGACTCGGTGTCTG 87 2R:1731127-2080000 -1 NULL:1988067 GH01501 842 929 1 1 0 98285 98143 1 0 0 0 100 partof CGTGTGCGAGTACTCCTTCCTCGAGGAGCGCTTGCCACATGCCAGCCGCCTGGGCTCGGGTGTGGACGATGGGCGAGAGGTTGACCAGCCAGTCGACGAGCTCGGTGCCGGGGGCGCACTTACGGATTAGCTTGCCGGAGACCTA 142 2R:1731127-2080000 -1 NULL:1988068 GH01501 929 1071 1 1 0 98089 97896 1 0 0 0 100 partof GGTTTGCGCAATATCATACGCAGTGTGGCGTCCGGTCCGCGCTGGAAGAGTGCGCTGAGCGCCTCGCGGATGTGCTCGTTGGCCGCTCCGAGGTCCTCCGCCTGGGGCACGCCCGCTGCCGCCGTGCCGCCCTCCTCGTCGATGCGAAAGCGGTAGAGGAAGCACTTGTCCTTGAAGGGCTGCTCTTTGTTGACTG 193 2R:1731127-2080000 -1 NULL:1988069 GH01501 1071 1264 1 1 0 97335 97189 1 0 0 0 100 partof ATATTGTTCCCGCCTGGGCATGAGCCTCGAACACGAAAATCGACGACAGTTCCCGCTTTATGCTGGTCGACAAGTGGGAGAGTGCGGCAATGTGGACCAGTTCCTCGAAGACCAGCTCCAGCTCCTCCGATGTCCGTTCGTGAGAACTG 146 2R:1731127-2080000 -1 NULL:1988070 GH01501 1264 1410 1 1 0 96970 96825 1 0 0 0 100 partof CTGGGTGCGTCGTTTATCAAGGCCAGTTTCCCGAAATCATCCCCAGTCTTCAGAGTGGCAACAGTTCCCTTGCCGTGTATCACAACGTCTACCGATCCCTTGAGTAAGATGTACCAGGAGCGTCCTTCGTCGCCTTGATTGAATACTG 145 2R:1731127-2080000 -1 NULL:1988071 GH01501 1410 1555 1 1 0 95886 95709 1 0 0 0 100 partof TTAAATGCCGAATGCTGTCCACGTTGCTTAGCCACGCGCTCGAGCACTAAAACATCCTTGCCGTGCTCCTGCAATCTCAGAGTATTGGCCTCCACATCGCGCAGTATCCGGTTGAAGTGTTCCTTGTCCACGCGCAGCAAGTGGCAATTGTTCTCCTTCAGTACGATGGTAGCAGCTCTG 177 2R:1731127-2080000 -1 NULL:1988072 GH01501 1555 1732 1 1 0 95472 95310 1 0 0 0 100 partof TAATTGGCCAATTCATCAACCAGCTGAACGACGGGCATGAAAACGATGTGTGTGAGCAGGAAGTCGTCCAAGAACGGATCCATTCCACCCACGGACTGGCCCAGTCGCGTCTCCAGCAGGTGCTCCAGCATCTTGGCCGGAGTTCCCGACATCACCGTATATCTG 162 2R:1731127-2080000 -1 NULL:1988073 GH01501 1732 1894 1 1 0 94511 94149 1 0 0 0 100 partof TATCATCATCTGGTCGGATGACCGTCTTTGAAGGCGTCGCATTGCCACTGAAAAGGCAGATGGGCTGGCCGTTGGGCGGGAGCTTCCACTTCTGGCCGGCGTTCTGGTTGCGGTCCTCCTGGTAGCGCGCCATCTGGGTGAGCACGTTGTGCACTATGCTGGTCTCCTCGTTCAGGTCGGGATCGGCCTCCACCTCGGCGGCGAGGTCCTCGATAAAGTCGCACACGCTGGGCTCCTCGAAGGCCGCGTGGCGGACGGCCATGACCCACTTTTGCATGAACTGGATCACGCGCTTCTTAAAGTTGATTATATACTCCCGATCCTCGGGCGTTTGGGCGTCCTCATGGGCATCGCAGTGGAAGGTG 362 2R:1731127-2080000 -1 NULL:1988074 GH01501 1894 2256 1 1 0 94079 93825 1 0 0 0 100 partof TGACGGAGACGAAAAGGCGGCCGTTGAGCGACAGACCCGTGGGTATGCTGACATCGTTGTCCTTGAACACGGACCGCTCCCCGTTTGACTTGACCTCGACGAGGACGAGATCTTCGGGACCCCGATTTAGCTGCAGCTTGTCGGCGGCACACGCTTTGATGAGCTCCGCCGTGGTGTGCATGGGGAATCGCAGGGTACAGTAGGTGTGGTCGGCGCAGTAAACGCGGAAGATGACTT 254 2R:1731127-2080000 -1 NULL:1988075 GH01501 2256 2510 1 1 0 93766 93595 1 0 0 0 100 partof TACCAAGGCATCCAGGTGGTCCT 171 2R:1731127-2080000 -1 NULL:1988076 GH01501 2510 2681 1 1 0 93375 93241 1 0 0 0 100 partof G...TACTACGCGGCCAGCTTGATGAACTTCCGGACCAGACCGACGCGTTTGCTCAGACTGGGAGTGGACACCAGTTCGGTGACAATCCAGTACTGCACCTCGTTGAATCGGCGCAGGAACACATCCAAGTTGGCAGTGAT 134 2R:1731127-2080000 -1 NULL:1988077 GH01501 2681 2815 1 1 0 92958 92608 1 0 0 0 100 partof CCAGACTCCTGGAGCGACAAAAGCGGATGGTGCGCATCGTCTGGGCCATCATGTGCATCTTCTCGAAGTTCACCAGGCCGTCCAGGCTGGTCTTGTTGCCCTCATGGGCGAAGGTCATGTCCTTGAGCAGGAGCGGCATGAAGGGAATCAACGGCGGCTGCAGCTTGCCCACGAACACTCGGTACGCCCTGTGGTTGCGACTGGGGTCGATCAGGGCCTCGAACTCCTGGAAGATCTTCCTGAACTTCGACGGAATCTTTTCCCAGGTCTGTTGCAGCCTGGACACCGCCATGTTGGACAGACCCATTACCACAGCGAAGAAGGCGTTTAGGTTCTGGTACTCCTTGCAG 350 2R:1731127-2080000 -1 NULL:1988078 GH01501 2815 3165 1 1 0 92549 91686 1 0 0 0 99 partof TGTGTGTAAATAAATATTAATAAATGGTTTCGTATTTTATTTCCAAGTTGCCGTAAAAGGAGATGGGGTGACGGAATACCAAATGAAAATAAGATTGAAAACTATAAATAAAGTAACTTATCCGCTACGTAGCTTACTTGTTAATAACTAGCTGTAACTAGACTGTTTAATAGTTGGTTTTAGTTTAGGGTTTATAAAAATATAGATTCCATGCTCTCGAAAACGTTGTACAACTTTACAAATTATTCTACCAGCTCGCGCGGGATTTATAGAGTAATGGTTTGTGGGAAATTATGCTGTATAGTTGTGTTTGTTTTGATGTTGCCTCCTATAAATGTTTAGTATCACACACGTCCAAGTTTAGTTTTTATTCGTTTCGGTTTCCGCGGGGAATTGCCGAATTTCAAATTGTTTTCCATCTTTTCCATCGTTTTGTACTAAAGCAAAAAGTTTCTCGTTTGCATTAAAATGCGTTTGGGTTTCAGTTCATTAGAAGATTGAGATAGTTCCTAGTCGGGTCGTAGATATAGTACACTGTAGCTTAGGCTAATGCGGATGCGGATGCGGACGAAAGTTGGTCCGGGCTGTGGTGGCCGTGGCCCAATTGGCTTTCGGAAAGCAACAACAACCCGGCTAAGCTCATAACTGTGCAGCTAATTGCGGTTGATTAACACACACTAGGGTTAGACACTTAATACGCGCTACAGGCTAATTGGATGACAGCTCCACAAGGGCTTAGAGCTTCCTGGTGGGCTCCACCTTCTGGGACATGGCGGTGAGTACCCGCTGGTTGTCGATGACGCGGAAGCTGCTGATGTACGACCTCACCTCGCCCTCGCTCTTCGGGGACGGCGGCTCTAGTCCTG 863 2R:1731127-2080000 -1 NULL:1988079 GH01501 3165 4028 1 1 0 2604423 202544 202308 1 0 0 0 100 partof TTTATCTATCACTCCACTCACTGGGGCCAGCGCATTCAGCGGGATTCAACTAGAGATTTTGCACACGACTCCGGCTGGAAACTTAAGGCACTTCTTTTCAGACTTTTCAGTCAGCAGAAAGACGGGACGAGTACAAAATGCCGACGAGAGCGCGCTGAGCATCTAAGAGCAAGTTCGACACTGTTGTTCGAGGCAAGTTGTTGATATCAGCGCAGTTCGCGTTCACGTTCACCGGG 236 2R:1731127-2080000 -1 NULL:1988081 LD37992 0 236 1 1 0 196716 196461 1 0 0 0 100 partof TTTGTTGTGTGGCAGGACGATGAAGGCTCCGCCGCCCGCCGACTCTACGATAATGGCCAGGAACTTGGGATTCACCGCGCAGAATGTGGAGTCCCAGCTGGACTTGGATACCCGTATGTTGTCGTAGCACTGCTCCCGCTTGAGAGCCTGTCCGTAGACGTGGCGGAACTTGGAGCTGCGCACTACGCGAAATGACATCTTGATGCTGCAGTGGCTTGGGTCAGCGATCAGTCCTGAGCTTCTCTACGTCTAGCTCTG 255 2R:1731127-2080000 -1 NULL:1988082 LD37992 236 491 1 1 0 195149 194882 1 0 0 0 100 partof TT...CACCTGGTTATCGGAGCCGGCGGTAAGCAGCACGTTGAGCGCAGAGGGATGCCACAACACCAGACCCACGCGACGCTGGTGGAAAACCAGGTCGACCACGGGTTCGGTGAGTGTTCGCGACAGCCCGCCATCGGGGATCTGCCACACTTTGACCACACAGTCCTCTGAGCCGGAGGCGATCACGTTGTCGTTGTGGGGGCACCAGGCGATGTCCAGCACAGGACCCTTGTGACCGCCCACCAAAGGGTGGTCAGCCGCAATGCGACCAACCTG 267 2R:1731127-2080000 -1 NULL:1988083 LD37992 491 758 1 1 0 194824 194410 1 0 0 0 100 partof CTCGAAATACCGAATGACCGAGTCACCTTTTCCACACAAGTAGATCATGTTCGTGTCTGCGTCGTAAAGAGGGAACATTACGCCGTTGGACGTGTCCAGCTCCACCATGACAATGGGTTCGTTAAGGGCATCCGGTGCGCGCAGGGAGTACTGACGCTCCGAGCTACGGTTGAAGCCTGTGGTGAAGATCAGACCGTGACGTAGGAAAATGGCCCTCGTGGCCTTGGAGCCCTCATGACACATGGCTTCGCTCTCCAGCTCGGCAGTGCGCGGATCGTAGATGCGGATCTTTTTATCCTTGCAGGTGGTAACCAACTTAGAGCCATCCCAGTTGAAGCAGGCGCTGTAAACGATGTCCGGATGGGAGTCGATGTGCACGAGGATTTCACCAGTGCCCACGTTCCAAATCACGAC 414 2R:1731127-2080000 -1 NULL:1988084 LD37992 758 1172 1 1 0 194346 194052 1 0 0 0 100 partof TTTGAGCGAAAATGTGATCGGATCCGCATCCTTGCCATCGATCCACTCCTCCGCGGTGATGGCAGCGTCTTCCGCTAGCGTATCGGGGTAGAGATCCTCCTGGAAAAGATCCGATTTGCGCGGCACAGTCATCGAGATGACCTGACACAGACCGTTGTTGTTCATGCGATAGAACTTGGCGACCTCGCAGGTGGTCACATCACAGCCTCGCTTGGGCATCAGACCAATACCACGCTGCGGCTCTGTAGTCTGAAACGTGTTTATGTAGTGCACAAAAGGAGGTTCGGGCGTTACCTG 294 2R:1731127-2080000 -1 NULL:1988085 LD37992 1172 1466 1 1 0 193308 193122 1 0 0 0 100 partof CGATAAAACCGCTGCAGGCGGTCCACCTTCGCTAGCCTCATTGTTATTTCCGGACGCAAAGTTGCCGCCGCCCGCGCTGCTGCTCGTTGCACCGGAGCTAGCGCTGTCGCCTCTAGGCTTGTTCAGGATGTTGCCCGCCTTCTTCGCTGGTAGCGATTTGTTTACCGACGAGGACACGTAGCCACCCTG 186 2R:1731127-2080000 -1 NULL:1988086 LD37992 1466 1652 1 1 0 193064 191768 1 0 0 0 99 partof CTCCATTATTAGCACCCAACTTCTTCTGGCATTGTATTTTGTTTTATTCCGTATCAAATTGTAAATTATTTGTATATAGAGTATTTATGTATGTATATGTATATAGTCTTCATTTTACAATGGTTGTGAATTACAAAATCGGTAGGTGTTTAATGACGCTGCTCTCGCCCTCGGTTCTCTAACAAAACTAATGAAAGTAAAATCAAATGAAAGAAAAGAAAAGTAAACAAATTTTTATAAAAATAGTTTCGATGGTTTCTTACTTTCTTTCTGATTTTGTTGCATTTATTGTTACTCTTATTATTTCAAAATACAGCTTATCATTAGTTTGAACAATAAAATTTTGATTACGAAAACGAATTAAGTCCGATGACCCCCATCACTTTCTTACTAAATTCGCTATGTTTGACACGACAATTTGCAGGGAAATGTGACTGATTAAGGGGGCCTCAGCTAGGATGAACAGTATCGATTCTATCAGCTATTGTCATGAAAACTTCCGGGACGTACAAATATACAGACGTTACAGAAAGGAGCTCGTACAAATTTGGTAGGTAGGTGTTAACTCTTAAGTGATTGAGGTTTAGTCTATGATTTGCCTTTGTTAAATTTACAACAATTTCATACTTGCGTAACAACAAGCCGATCAAAGGGCCGAGTACCTGCCCTTCGCTCTGCTTGATTTTGGGCGCAAAATGTAGGTAGTTCGTTAGGTTTTTTATATATTTTTGGCAGGATGTAGTTTTATGTTATGTTTTATACGTTAAGCGTCCAGGTCTGCTCGGTTATGCTCGCTTAAGTTCGATTAGATGATTTAGCTCGGCATTCTCTAACCCTATCTGTGCCACACCCGCACTCAACTGATTTCGCTAATATTAAATTATAAAAAATAAATAATCGAAACCATAATGGTAATAGACAATAAGTTCTTTTTCAATTCGTCCTCAGCGCGCTTTGTTGCAATAGAGAAATTAAGCGTAGCTACGAGCTTCTACAAGCAGTTCTCTGTCTCTCCTCCAATCCATTCCGCCCATTTTTATCAGTTCAGTCCTCGTTTCATTGCTAGACCTAGTCCTCGTCCTTTGACGTTCCGGCTGATGTGGACGCGTGGTCGTTGGCACTTTCACTGGCTTTGCCGTCAGACGTGGCTGCTCCCGCTGAAGCCGGCGCAGCATCGCTTCCATTCTTGTTGCGGGCGTCCTCCTTGGCCTCCAGAGCGCGGATGCGGTTCTCTTGCTTGACGATGATCGCCTTAAGTTTGCGGATCTCGTCTTGTATGGTGCGCAGGTCCTTTTCCTT 1296 2R:1731127-2080000 -1 NULL:1988087 LD37992 1652 2945 1 1 0 2604432 208416 208213 1 0 0 0 100 partof CTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACT 203 2R:1731127-2080000 -1 NULL:1988089 RE31022 0 203 1 1 0 208133 207201 1 0 0 0 100 partof CTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTGGGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGAGAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGGTGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGTTCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTCCTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAAAGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCCTTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATACATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCCAATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTG 932 2R:1731127-2080000 -1 NULL:1988090 RE31022 203 1135 1 1 0 207137 206995 1 0 0 0 100 partof CCGTGGCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTGTATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAAATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAGCTG 142 2R:1731127-2080000 -1 NULL:1988091 RE31022 1135 1277 1 1 0 206508 206370 1 0 0 0 100 partof TTCAAAACTTATTGATTCTTCCCGCAAACAAAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACATGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACATGACCATTCCTG 138 2R:1731127-2080000 -1 NULL:1988092 RE31022 1277 1415 1 1 0 206301 205923 1 0 0 0 100 partof TTTTAGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTAGTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGTTGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAACGTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATACCTG 378 2R:1731127-2080000 -1 NULL:1988093 RE31022 1415 1793 1 1 0 2604439 208683 207201 1 0 0 0 100 partof TG...CACCTTCTGGAAAACCTCAGACAATTCCACTTGGAACTCTGCCTTGAACCTGGGCAATTTGAGCGCTACCTTTGTTTCGTACAACGACTGCGTGATCTGCGAGAGGGTCGTGAGGCGCAACTTCTCCTCCAGAGCGGGCAGACCCGTCTTGGTGTTGGGCAGTACGATCAGCATAGAGAGGTCTGAGTCCTTGTAGGGCAGTTCCAGAGCCATGGCATCTAGCGCCGGCAGATCGGCGTAGCGGAACCGCTCCTTTAAACTCATCATCGGAACCTGAACTGTTCGCTCCCCATCCAGGTGAAAGGTGTCTGGGCGGGTTAAGTGTTTGGCGAACTGGTGCTGCCAGGTGCCCTTGAAGTGAATGGCGTTCACAAGGACGAGTCGCGATTCGGAGTTCAATACATCAGCCGGCACAAGGTCCTTGATCAGATGGTTGGTGCGCTGCTCAACCCAATTGTTGATGGTGGCCGCTGCTTGTACATTTTTGGAAAAGTCCACGCTCTGAGCCGCCGAGAGGAACTGCTTGGATAACAGCTGATCAAACTCCTGGCGCAGCTGGTAGCCATCCATGACGAAAATCTTGTTGGCGATGCGCAAGATCTGACTGTCCTGGTAGGCGGCCAGCACCTGGTGAAAACTGTGTGCGATTTGCTCTGGGTCACTAGAGGCCAAGCCCAGTCCCTGGTCCAGCTGGGTAGCCGTCTCGTTTTCTGCACCCAGCCTGGCCATCGCCGCACAAGTCTGGATGGAAAAGGGCGAGAAGACGATGTTCTCGCCGGGCTTCTGCCCCGACAGCTTGCCGTACACGTTGATAGAGAAAAGGGCCAGCCGGCGGGCGAACTCCTGGTGGGCGGCGTCAGCCATGGTGACGTCAGCCGTGTGGACCGGTGGAAACGGGAAGAGGGCTAGGCCGAGCAGGGGGAGCAACCAGCAACCTGTAAGTATCCAAATCGACCGTGGATGAGGTGTGCTCGTTTTCATAAATTTATGTAATTGCAGTGTACTGATGAGTCACCTCCACAAACGGTGTTCACTATATCTCTCCGGTTGGCCGTTTCGCCGGGGATTCACTAGCTTGATTATCGGAAAGGGTAATTAACTGCCTGCTCCGACTGCTGGTACTGTTTTTCACCAGCGGCTTCGAGTGTGTAAATTAATTTCTTTTTATAAACCGGCTATCGCCCTCGACTTTTATAATGTGGCCTTTGAGCAACAACTGAATTCTCTCAGCGAGCGTACATTGTTTTTATACTCGCATATGCATATGTATTCCCCCACAAAACAATGATTTCTCTTCAGTTCGTGCTCCCAAACGGGTTTTTCTCTCGCCTGCCTTCGGTGTTCTCATTGATTTCACTCTTTACATCCATAATGCGTTTTCTTTCACTGGCTTTTTAAAGTCAAACTGCCGGATAACTCACCACATGGCACCAAACGATAATCCATACTCAGTAATTTTGCTTACAGTAAACCTAGTCTGCAAAG 1482 2R:1731127-2080000 -1 NULL:1988095 GH21896 0 1482 1 1 0 207137 206995 1 0 0 0 100 partof G...TACCCGTGGCGGCCGCAGCCTCCGTTCCCTCCTCGTTGACTTCAATGAAGGCCTTGTGTATGATGGCTGACACTTTCAATGGCTCCGGACTTTGTAGCATTTTTCCAAATTCAGCCTGATCGGAGAACATCCTTGACATGCCCAG 142 2R:1731127-2080000 -1 NULL:1988096 GH21896 1482 1624 1 1 0 206508 206370 1 0 0 0 100 partof TTCAAAACTTATTGATTCTTCCCGCAAACAAAATAGTAGAATCCTTATTGATAATGTAATAGTTAAATGGATGCTGGACATGGAATTGGACGGGCTGCGGTTCGAACGTGAGCATGGAGGCGTAGCACATGACCATTC 138 2R:1731127-2080000 -1 NULL:1988097 GH21896 1624 1762 1 1 0 206301 205923 1 0 0 0 99 partof TTTT-AGACATTTGCTTTTAGACTTTATTGAGGCTACGGCTACATGCTTGGTTAGTATAAAAATATTAAGTGTATATATAAGATCATCAATTGCGCACAGACTATAATTTTGTGAATCCTTATAGACAATGTAAAAGCTGAATATGCTCGTCAAGCCAGCAATATAGGACTGACCCGCTTGCACGTTAAATGAATACGAGACCCTCGAGTAACATTGTGGATTGGTTAGTATGTTTGCCTATTTAGAGTTTCTTTATGCTGCCAGCGAAGAGAGCGGTTGAGTCCTTGTTAAGGATGTAAAATGTAAATGGATGGTCGACATTGAAACGTATCGGATCCGGCTTCGGCATGGGCAGCGAAGTAAGGCTCATAAACATACCTG 378 2R:1731127-2080000 -1 NULL:1988098 GH21896 1762 2141 1 1 0 2604445 261593 258283 1 0 0 0 100 partof CGTCAAAGTGTTGCTGCTGTTGCGGCTGCGACATGGACAGGCCACTCCGCATGTAGATCGACTCTCCTCCGGGCGCCTGCTGGTTGCCGTAGATCCCCTCGATATGCTGCTGCTGTTGGTGCTGCTGCTGTTTGCCGCTGAGTCGTGCATTGAGCTGTGCAATTAGGTTCGGATTCGCCTTTGGCTGTGTCGGTGGCAGTGGGTGAGCATGTCCGTTGGGACTGGGGCTGCTGGTGCGGAAGCTGGACATGCTGTTGACCAGTTTGGGCTGGGCGTATATGCCGCCGCCACCCCCTCCGCCCGCGGCTGGTGATGAGGTGCGGAACGTCTGGTCGTGAATGTGTGTCAGTGATGGTGTGTTTGTGGCATGAGAGAAACGAGAAGAAGACGGGCACAAATTAAAAGTTAGCCAAAGCACGACCAAAGCTAAGCACTAGAGTAATCTATGACTATGGCATTACAACTAAGCTGGAAGGAGGGCAGTCGTGTTAGGCCAGAGAGGCGCTCCCAAAGACGCCTGTTAGTCTTGGTTAGTAGCCCGCGAGATACCCGCTGGTCACTTACGGCATCGACTTGGTAGACAGGCGGTTGCTGTGGCTGATGCAGATGCTGATGTTGCTGCTGGAGGGTAAAGCGTTGCTGGTTGGCCATCTGCTGACCGCCGGGCTGTTGGCCGCTGGCCAAGGCCTGGGCATAGGCGTGCAGATCCAAGTAGGAGTCGTAGTACACGGTCAGGTCCTCTTTGAGGGGGGAGTTGTGCGCAGACTACGTGGGGGATTGGGGTTTCGGTTTGTGTGTGGTAGTGGTGAAGCAAACGTAAGTTGAAATAAAATGAAATCATAAGTTGTAGAAGAAGATGGCTAAATTTCAAGGTGGCTCTAGACTCGTGCACTAGTTAGACCCAATGAATATTACCTAACTCTCACGCCGAACTATACTGGCTTTTGTTGGGGAATAAATGTCGAGTCTTCCAAGTCGTATTTCTATGCTCAATGAGCTCAAAGTATACCTACATTTGTAGGTAGAAAATGTATGGAACAAAGCTTATGCTTGTTTACCGGGGCTAGGCAACTAGAATCCCTACAGTTTACGATTAGTGATTAGCTTATTGTAGCTTTAAACTTTTTAGCCAGATATATGAATTTTCTAACTAAAGCCAAATACATCTTCATCTGGTTGCATAAATTTTTGGTCAGAAGCATAAACTACACATTAATAGTACCCAATTTGGGTTGTAAACTCAAATAGTCAGGTGAGAGTAGGAAATCAAACATTTTGGTACAAATGGAAACCGGATGCGAACCGAGCACACACCTGCAATAGGGGTTGCTGCTGCTGCACCTGTTGCTGCTGTTGCTGCTGAAGCTGCTGCTGCTGTTGCTGCTGCATGCGTCTGAGGGACACAGGTGATGCTGGCTGGTGCCGCATGGCTGCCAGGGCTCTTACCGTCTCCGATACCTTCAGCGCTGAGCTGGGAATCTGGGGCATGGCGTCCAGCATGAATGGCGGTGGCGGCGGTAAGTGCTCGCTGGAGCTGCTTAGTTGGTGATTCTGCTGCGACAGAGTCGCGTGCTGTGGTTGCTGCTGCAGCTGCGTTGCGTAATTAAATCATAAGTTAAAGAATAAAAGCATAGAGGAAACCAAAGAGTGTGTGACCCAGAGTGTGAACCCAGGCTTAGCGACTAGCTTAGATTAAGTGGCTAACTTAATTGGGTGTAGGTAATTGAAGGCTTAACTCACCCCGACCGAGGCATTGGGACTGGGGGTCACCGACGAACTGCGTCTGACTGGCGGCGGTGGCTTGGACTGATTAATGGACGATCGACGCCCGATGCGCGTGGAGCCACCGCCGGCTGCTCCTCCTGGGAAAAGTAAAAATCCTTGTTAGTGAGGCGGGCATTTTGATGATTTAGTCATTAATTTCTGCTGTTATTCACAGTAATGTACAGTTATCAGTTTATACACTTGGCACACAAAACACAGGACACCATCTAATACCAGTAGTTAGCGATAGACGCAGAGTTAGGATCTGCTGATCGAGAAAGTTATGAACGTTCTTGGTCTGCTGTGAATCATAATGATGACCCTGAAGCGAGTGGAAAAGCGTTAATGGCTGTGATGGCACTTTCGATACCACTTCATGTCGAAAAGACATTTCCCCTAATTTAAGCGATTTTGCAAAATGCAATTTTGTAAAAAAAATTTTGTAGTTACAAACGATCGAATCTGATTAGTGATTAAGCATTTAGCAGTTAGTGGCAGTATCATGCGGGTTTTGAGTTGTCTATTGATGATCTGAACTTAATGATTGTGACTTGATGGTATGAGCGTAGTGCTTAGCGAGAGAAACCAACTCCAATTTCAAAAAGGTTACCACATCGAACTTATAGCAAAAATGAGAAACCCAAAACCGCGTAAAGTTACTTCGGCAAGCACAAAATGATAAGGATACTTGCAAAGGTACAACAAAGTAGGAAAGTTTTCAAAATAAGGAATCAAAAACCAAAACCAAATAAACCCAAACAAATCAAAATCAAATTGAAACGAAACGAACCCGACAAAGAAGCCGGCCGGGGCGTAATGCACGGCTTGAGATGGGCATTGGCATTGGAAATGCTATTGGCGTGGTGGGGATTGGCTGGGGCATTGGAGCACACATATGGATGGGCGGGTGGTCGGTCACTGGCGGGCAACATCGATGGCCGGGCATTTGATGGTGATGAAGTGGTGGCTGGTAATGGTAATGACGATAGCGATGACGATGATAATGGCAAATGGCCGCGAGGTGATGACGGTGACAATGCCATTGTGGGCGTCTTGCACTGCGTGTGATTGGATGTGGCTGTCTGATTTTGGTTTGGCATTCTATGATTTGGATTCGGGTACGGGTCTGTGGATGCTGTTGCGGTTGCAAATGCAGATGCTGATGCAGTAATATTGGCGGCTTGTTGATTAGTGACATTACAGTTTCTGGTTTGGGGCGACTGTGGTGAGTGTTGCTGTTCTTGTGGTGCTTGCTGCTGCTGCTGCGTTTCTTGCTGCTCTTGCTGCTGTTGCTGCTGCTGCTGCTGCAACTGCTGTTTAACCTTCTGCTTTTGCCTGCGTATTTTAGCATCTAGATCAGCCTTAAAGTCCGACTTTCGCGGCACGACAGGCCTATCGCCCGCAGTGGGCACGGGGCCGTTAAAAATACTCAAACTGGTGGGCTTGGGGGGCAGCTGGCGCCTTGCAAGTTCTACTGGTGGACTACTGCCATCAATATCCTGCTGTTGTGTCTGTGGAAAATGCTGGTCCTGTGGCCTGCTTTGTA 3310 2R:1731127-2080000 -1 NULL:1988100 GH14660 0 3310 1 1 0 256596 256444 1 0 0 0 100 partof CAGGGCCTTGCTGTTGATGAGATTTCGCACGGCAAATGCTCGTCCAGACATTCCCTGCTTCGCCAGCTTCGCGTTGAGATTCTCGAGGAATTCGGCCTTGGTCTTGGCACGAATACTGCCAGTCTTTTCGATATTTGTGCTTGTGGCATAGTCTA 152 2R:1731127-2080000 -1 NULL:1988101 GH14660 3310 3462 1 1 0 256073 255472 1 0 0 0 99 partof ATGTACGATAAATTCCATTTATTAGGCGTCAGATTAGTTTCGAGTGTTTGTTAAACTCATATTCATATGTATGTACATAAATAAGCAAGGGAAATTATAAATACAGGAAATACATAAACATAAAATATCTTCAAACAAAGGTTCTCTAAAGATAAATTCGAGTTGCAGATATAAATAAACATAAACATAACTGTCTTCCATATTGTATTCACTTAACAGAGAAAGCCTTTCGACACATTTTTGGGATACAGGAAATCAAGAAAGGTATTGATTAGTTCGATTTATGCTTAATGCTCCTGTTAAATATCGTATATCGAATATATATTATATATCGTAATCATATGTATTTAAGTTGTATGCTGTGTTTCGAGTTTTCAGTTTCAAACCAAACTCTGCAGAGCCCTGCAGTCGAGCAGGCGTCGGGCCTCATGATTATTCATAGATTAATTATTATGGTAATAAATATGCTGCTTCGCTTAGCCTATAGGTTAATTCAATGTATCTTGGGAGCGCTGCGATCGTTGATCTTCTGGTTACGCTTTAAGGTGGCTCCGCGCTTGATTTGATCCATCAGCGATTCGTGACAGATGCGAGGGTCCGGCTG 601 2R:1731127-2080000 -1 NULL:1988102 GH14660 3462 4063 1 1 0 2604450 304761 304721 1 0 0 0 95 partof CTTGGGCAGCCGTAATTTGTTTTGTGAAAGTGAAATCGCA 40 2R:1731127-2080000 -1 NULL:1988104 SD07915 0 40 1 1 0 303775 302562 1 0 0 0 99 partof TA...CACCATTGAGGACTTGCTTCGTATACCTGAGCTCCCTTAGGCACTCCGGTGTCACTTGGCCACCATGCTCCTCCAGTGCCTTGTTAATCTCGAGCCTGGTTCGATCTTGCACCTCAGGCTGGCGGGCCAACTCGTAGAGGCAGAATGCTAGGGTGGCATTCAGGGGGCCCAAGCCAGCCAGAACGAAGCCGAAGGCTTGGCCCGCAATCTCGATGTCGGTGAGCGGCTTTTCTGCGTTGGAATATAGCTGCAGAAAGGTCTGGAGTGGCTGGCGATCCCTTCTTCGATGCAACTGCAACTGCGACAGGGCCACTTTTTGGAAGTAAGCTGTAGCAGGTTCTGCGTAGCTTTTGTACTGAAGAAGGCGAGCGATGAGCGGAAACTCAAGCGCCAGATAAGCCTGCCACATCCTAAAGTCCGCCCAGTAGTTGCGCGTCCACTTAGCGAACTCCACGTTATCCTGCCCTACTAGTCCAAAGGCCATTGACGCCATAACGTCCGTATTGTATGCACCCACGAGTTCGCTTATATTGATAGTTTGAAGGCTCTTTTCGCCCAGGTCCCTTTGAATTCTGGAGGAGATTTGCGACAGTCTGACCAGCAGCTTCTGCATGTTGGCCGGAGTGAAAACCTCTGCAGATTTGGCGTGCAGTGACCGCCACTTGTGACCGTCCAGCTGAAGGAGATTATGCGACAGCGGCTCTCCACTGGGATTACTATAAAGGCCTCGGGACGTAAAGTGTCCCGCGTCGGTGAAGATTATTTGGTGGACTAGCTTCAGGTCCAGCGCCAAGATGAACGGCTTGAGGCAGGCGTAGAATCCCACAAACGGCGCCCTGCCCTTGTATGCGGTGTAGATATCCTGCAAGGCGTCCTGGGCATGCCTCTTCCCGCTCACCACGCCCTTAATGTTGCCCCACAGGAACTTGGGCTTTTCGTGCAGGATCCCCCGCCGTTTCCAGTAGCCCAGACTGAACTTGACCAGGGCGTAGACCACTGACAGCGCACCCAGGGCGGTGAGCAGGGTGCGGTGCATTAGATCCATGCTCACTCAGCTGTCTTTTCCGGCTTTTACAATATGTTCGCGCTGTTTGATATGCTTAACAGCTGGCAGTAGCTGCTTGTCGAGGTTCTGGGGCTCAATGCCGCCGGTTTATCAGCGCCATTATCGTGCGGTCCGATTTAATAATTGATAAGGTCCATTGAGTATCGGCCGCTA 1213 2R:1731127-2080000 -1 NULL:1988105 SD07915 40 1253 1 1 0 302504 301889 1 0 0 0 99 partof AACTAAATTATTTATTTGTTCACGTTGTTGAGCTTGGTGCAAAAGATTATAAAAGTCATCGTCAGCATTATCACACAAGTCCACAGCTTAGGAAAATCAACGAAAAAGGTGCATATACAAATATAAAAACAACTTAAACGCTTTGTAAAGCAAACAATACAAAATATGCGATGCTCCAGCAGAGCCTCCTTTAAAGCTTGTCCACCCGTTCCACACTGAGTTTGATGTCCGACTTGGGCATCAAGAGCAGTCTCCGGTTGTCGTACTCCACGGGAATCGAGGTCTCCGCAGAGGGAGCGTATCTGTGCTGCCTCAGCAGAGCCACCAGGCCCACCAGAAGCTGCTGCTCTGCAAAGCGAGCGGCAATGCATCCTCGCAGGCCATCGCCGAAAGGCAGGAACGCAGCTGCCGGGCGGGATCGCCTTGCCTGTTCCTCAAAGCGCTCCGGGTAGAACCGCTGGGGGTTTTCATAAATGCCAGGATCCATGTGTATCGCCGCCGTTGGTATCAGCACATTGTTGCCTTTGGCAATTACAAACACCGATCCGGGCACTTCGAATTCTTTGGTAGCCCGGCGTAGCAGGAAGGGATGTGGAGTGTGCAGGCGAAGCGTTT 615 2R:1731127-2080000 -1 NULL:1988106 SD07915 1253 1868 1 1 0 2604455 308255 307466 1 0 0 0 99 partof CACCAGTAAGGATTAATACGATGAGTTCGCAGGCGAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACTTTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATAAGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACATCTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGATATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATACTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATTGGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACTCCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGCAAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGATGGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGAGTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCCCGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTGTCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCT 789 2R:1731127-2080000 -1 NULL:1988108 SD10607 0 789 1 1 0 307377 306990 1 0 0 0 99 partof CCTGTCCGTCGACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGTGTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACCGCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAGAGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCACCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGGCTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAGATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCGTGGTGTACAAATAGTGCATTGAGTCATCTA 387 2R:1731127-2080000 -1 NULL:1988109 SD10607 789 1176 1 1 0 306932 305568 1 0 0 0 99 partof TATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTCCTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTCTAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAACTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTACAGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTCTCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAAAACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTGCAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAATTGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAATCTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACACAGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTTCAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGGATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGAGAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGCGCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTTCTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGGCCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGGGCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCACAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCATGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAGCTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTCGGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGTAGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACGCCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGTCTTGTTCTTCAGCAACTCCAGTGCGAGTTTCT 1364 2R:1731127-2080000 -1 NULL:1988110 SD10607 1176 2540 1 1 0 2604460 315484 315186 1 0 0 0 99 partof TCGCCATGTTTGCCGCCTTTGTTGATTATTCCGCTGCTGCTTCTTCCGTTTTTATGCTTTTCTGCTTTTCTTGCTCTGCGTTGGTTGCGATTCCAGGCACGTTGTATCACTGTTAGCTTGTAACAAACACTGCTGATAGGCTAATGACTGCTGCGCGCAACTGAACACATTTCACGGCTTTCTTTCAGTCGCGTCTCCGTTCAACTTCCGCAATATCCGTATAATTCGTATTATCCGTGTAATCCGTATTTTCCGAATCGCGTTCAGACGTTCACACCAACAACTGCAATTCTAGTGT 298 2R:1731127-2080000 -1 NULL:1988112 RE57156 0 298 1 1 0 308375 307466 1 0 0 0 100 partof CACCAGTAAGGATTAATACGATGAGTTCGCAGGCGAGTTTCATCAACGCCCTGGCCTCACTTGTGCTGGCCAGAGTCTTGTACTTTTCCAGCAGGTTGTAGATGGTTTCGCACAGACCGTCCTTGGCCAAAATAAGCTTGACTTCGTCGCTCTCCGCCTGGTAATGGAGCAGCTCCAGGCACATCTCGGCAAGATCGGGATTCGTGGAAGCGGCCAGAATGCGAGACAGCTGGATATTCAGGGAAGAGTCGAAGTTCAGATCCGACACGTTCTCGGTGAGTATACTGAGCAGTGGAAGCGTGTTCAGCAGCAGATCCTCATGCTGTTCCACATTGGAGGCGCCAATGTCGATGATGCCTTGCAGCTTCTTCATCACGCCCAACTCCATGGCCCGCTTGGCCAAGCCCTCGCCTCCGAGCAAATAGTTGGACAGCAAGCCGCCGCGCACTTTGATGAATTGCGCCGCATTGGCCACGTCCTCGATGGTTGTGATGTCCAGCAGTCGCAGTAGAACAGCATCGCCCTCCAGCTCGAGTATTAAGTCCCTGGCTTCGTCGTTTAGGTAGCAGATATTGCCCAGTGCCCGACAAATCTGTATGGGCAGCTCCATACTGCCGTCGGACGTGGGCACTTGTCGCAAGCACTCCAGAAATGCGGCTATTATATTCCTCTTGGTGAACTTCTTGCGCTGCACCTCGGACTTGGTGATCTCCGCAATGCACTTGGCCGCCTCCTTGCGCACGTTTGTGTCGTCGCACTTGGTGAGGCCCAGAAAGCACTCTGCCAGCTCGTGCTTATCGAAAAGTTTGGGGTCCTTCGTCGCCGAGATCTCGCAGAGCAAGTTGGTCGTGTTCGCCGGACTGACACTGGTCGTCTTCAGCTTTTCAATCAAATCGTCGATTTCAGCTGCTT 909 2R:1731127-2080000 -1 NULL:1988113 RE57156 298 1207 1 1 0 307377 306990 1 0 0 0 100 partof CCTGTCCGTCGACGGTCATGCGAAGTGTGCCCAGCAGCTTGAAGACGACTGGTGGCTGGTGTATTTCGAGCATGGGAAGAATGGTCTGCACCAGGCCCGCCTGGATTACCGCGTTCTTGTTTGGCTTCGGGATGACCAGGTTGCGCAGCGCGGAGAGAAGAGCGTGCTGCAGGCGCACATCGTCCTTGACGCCGTTGTTCTTGGCCAGCACCTCGAGCAGCTTGTTCATGGTCTGCTGCTCCACAAAGTAGATGCAGTGGCTATCGGTGCGCGCAAAGTTGCCCAGGGCCAGCACGCCGGTGGTTAGCAGATCGATGTCCGTCGAGTCCAGCCAATCGACCATGTTCTTCAGCAGCGGCGTGGTGTACAAATAGTGCATTGAGTCATCTA 387 2R:1731127-2080000 -1 NULL:1988114 RE57156 1207 1594 1 1 0 306932 305056 1 0 0 0 99 partof TTTGGTTTTCTCTTATTTCTCATGCATTTCAAATTTTATTTGAATTATTAAATGTACATTATTGTGTTTAGAGTTCATAAATATGTTTTCGCATTTATGTGTGTGGGTGTCTCAACGCTTTATATATTAACACCATTCCCCTTGAATTGTGTTCGTTTAATTTTTAGTTTTTGGTGACCAAACATTAGTACATCGTTTTTAATAATTGGTAAAATTTGTAGCACTCCATAAACTACGATTTGTAAAATTGAAATATTTGCATTATTGGTTTTCAACTATTTTCGGATTGCTGATTGTTACTGAGTTGCAGTTTTGTTAATGTTTTAAAGTTAGCTTAAAAATGCATTTTGGATAACTTCGCCGAGTTTTACAATAAATATATGGGATGCCGTTTGCAATATGTGTCTGTGCACCAATTAAAATACCTTAATTACGTCGTGCGTCTAAATGTTTTGTTATCTTCTCGTTTTTGGTTTGTGCCAGCAACGGTTTAAAAGAGGTCGATTGAAAATTATAAGTACAATCATAAAATACATTTATTAAATATATTTAGCGATATCACCACGATTTGTTGTTATTGTGCTCTTAAAAATCATGTAACAGAAAAGATTAATATGCTAAATTATTAATATTATTATATTTATACGTATATGTTATGTATGTATGCTATAAATATTCATACGATTTGTGACTCCTTACTACATCGGATTCTCTTCATAAATGCAGTCAAAATACGCTTGCGTCTAAAAAATACTTTCTGCTCCTCTCGTGTTCGCGTGTTCCAGTGTGCTTAACTGATTAACTGCTTAACTTGTGAATCTGCACTTTCTTCTTACCAAACTACAGTCAAGTCTACATCTGAATCGTTGCTTTGGGGTGAAAACTACTATTTTCTCCGGTTCTGAGTGTGTCTGTGTGGCTAAGGGTGGGCTGATTTTTTTTAAAACATGCTCTAATAGTGGCAAACATTTATCTTTGGCTATTTGGAATCGTGCAACGTCAGTGAATCTCAAGAGAGTGGATTTAATTACAATTTAACAAAATTGTTATTAAGTAGTAAAGTGGAGTTTAGCACATTAGCGCAACGTATTAATCTTTGTATCGTTACGAATAAGTATTGGCGTTTCTCTTGGTAAGACCACACAGATAACTTCCAAAGATAACTGCTTACCCCTAAAGTATTTATGTTATGTTCAATCGTGCAAATCGACCCATCCCACTGTGAGGCATCCTGCGGTGCTGGGATAAATGCAATGACAGTCCCCGTTTTCTTACAAGGTGCAGTATTCGGTGAGAATGGGTATAGACTTCAGCAGCTCGTTGATGTTATGCTGTTCCAGATGCGCCACCAGCTGCTCGGAAGATTTGAGCAAGTTCACGCAGTTCTGCAGGTTCTCGACAATCTCCTTGGTCATCGTGTCCGACGACTTGCTGATGAGCTCGGCCAACTTCTTGCCGACCTCGCACTTGACCAGCTCGTCCTGCAGCAGCTGGGCCTGCGCCGCCTCGCTGGGCTGCGACAGGTACACCACGGACAGGATGCACAGGGCAATCAGCGCCTCGTTCTGCATGACCAGGTGCTGAGCTGTGAGCATGCTGACCATGGCCTCCACGGTGCCCTCGTTGGCAAGGAACTCGCTCAAGCTACTGCGATCGTAGTCTTGCGTTAGCGGAATCTTGTCGGCAATCTGTTCGGCGGGTGCATCGCCCTTGCGCGGCAGTGCGTATGCGATTTTGCTGAGGTAGGCGTGCTTGATCAGCCAGGCCATGAGGCGCAGAGACTCGCCGGTGACGCCCGCATAGTCCGACGATTTGCTCCAGTGCACCAGCTGCTCGATCAGAGTCTTGTTCTTCAGCAACTCCAGTGCGAGTTTCTCTG 1876 2R:1731127-2080000 -1 NULL:1988115 RE57156 1594 3470 1 1 0 2604466 341629 341366 1 0 0 0 98 partof CCACAAACAGTATGTTGAATATGAACAGCACATATTTCACAAAAACGCCGCCGCAATCCATTGCTGAGATGTACTTGTGTATCACTTGTGTTCGATTTAAGAGTAAGACGTTCGATGCGATTTCGTTCGTGGTCCGCTTGATACTGAAAAAGTCTGATATATAACAATATTTTTATGAGCGCATTTCCTATCGCGAAAAGCTCTGTTAGATTTTAGCTCTGAATTTAGCGGCGATAAGAAAAGCGTTGCTGCAGTGGTAGAGAT 263 2R:1731127-2080000 -1 NULL:1988117 SD10395 0 262 1 1 0 340629 340437 1 0 0 0 98 partof 192 2R:1731127-2080000 -1 NULL:1988118 SD10395 262 454 1 1 0 340368 340206 1 0 0 0 99 partof CGATCGCTGCAGTGTGTCCATGAGGAGGGCATCGGTCTTGCGTTGATCCCATATGGTCTGGACGATCTTCTCCAAAGATTGCTGTATCTGCACATGGTCCACCCACACGTAGATAATGAGAGCTAGCTGACTAACCAACAGCACCAGCATGACCACAGAGTA 162 2R:1731127-2080000 -1 NULL:1988119 SD10395 454 616 1 1 0 340075 339877 1 0 0 0 100 partof CTCAACAGCAGTCACACCCAGGCCAGCGTACTTGATGATGCTCACGTTGGTGTCCCAGAAGGAATCAACGGCCTTCAGGCAACTGGATCGCGTCATGACTTGGGTTAGTGCGCAGGTTCCATTGGAGGGCGAGTCGCAGCAGGAGGCGGGATACGTAATGCCGTAATCAGCGAAGCCGTTCAAGCCGCAGCACTTGAACTG 198 2R:1731127-2080000 -1 NULL:1988120 SD10395 616 814 1 1 0 339820 339632 1 0 0 0 97 partof TTATATACAGTAAGCATGCGAAGCACTTTGTTTTATTTATTCATATTGACTTTATGACGTTAAAGAGGGTCGGGAGATAATCCTAATACTATGCTACTAATTCATCGTTTCATCGTTTAGTAGTTCTGGCGTCTCTGCGAGTTGCGGGTCTGATTGGCCAGGCAGCAGGCGAAAATGAAGGCCACAAGCTG 188 2R:1731127-2080000 -1 NULL:1988121 SD10395 814 1000 1 1 0 2598549 3592 3424 1 0 0 0 100 partof CGGTGAGAAGGCGCGTTTAACTAGTTTTAGTAATGTCTAGTCGTAGTTTAAGTGCAATAGTCTTGCTCCTTGGGGCGTTAGTGACCGCCTGCCTCGCCTCCAACGGCGACCGCACACAGTTTTTTCACAATTGCCGACAGAACTGCGAGCGAACGAACTGCTCGGCAGGTG 168 2R:1731127-2080000 1 NULL:1983184 LD44494 0 168 1 1 0 3965 3648 1 0 0 0 100 partof ATGGACTGGAGATCCAGGAGCAGGCAGTCAAGTTTTACCAGCAGTCGGTGTTTGACCGGCTCTTCCAGTGGAGCTGCGCGGACGAGTGTCAGTATGGATGCATGTGGCGAACGGTGTTCGCCTTCTTTGAACGCGGTTGGCCGATTCCCCAGTTCTACGGCAAGTGGCCCTTTCTCCGCCTGCTGGGCATGCAGGAGCCGGCCTCAGTTATCTTCTCCTGCCTGAATTTTGTCGTTCACCTGCGCTTGTTACGCAAGTTCCGCCGAGAAGTGCGTCCGGACAGTCCCTGCTATATGCTGACCCACATATTCGCAGTG 317 2R:1731127-2080000 1 NULL:1983185 LD44494 168 485 1 1 0 4502 4035 1 0 0 0 100 partof ACGAGTCTCAACGGCTGGATCTGGTCCGCCATCTTTCACACAAGGGACTTTCCACTGACCGAGCTGCTGGACTACGCCTTTGCCTATTCCATCATCTTGTGCTCACTTTACGTCATGGTCATGCGGATGCTGCACCGCTACTCGCTGTTCCTACGGGGTGTTATCACGTTGGCATTCCTCTCCTACTACATTAACTACTTTGCCTACCTGAGCGTGGGACGGTTCAACTATGCGTTCAACATGATGGTAAACGTGGCTACGGGAGTTATAGCGGCAGTGGGATGGTTCGTTTGGTGTCACTTTGTGCGCACCCGCAGGCCCTACTTTAGAAGGATCCTGCGTTTCTATATTCTCATGGCGTTGGCTATGAGCCTTGAACTGCTTGACTTTCCGCCCATCCTCTGGATTCTGGATGCTCATGCTCTGTGGCACTTGGCAACAATTCCTCTGGCATCCCTATACTATGAGTG 467 2R:1731127-2080000 1 NULL:1983186 LD44494 485 952 1 1 0 4840 4555 1 0 0 0 99 partof CTTCATGATAGAGGACTGTCGAACCCTGCGAAAGGAGAAGGCTGCGGCGGGCGGCTATTCATTCTACAATTAGTATTATCTAAGTTATTCTTAGCCCTTAAAGCACGCAAAGCTATCTGGCAATTTTTCTGACATATTTCATGTAATTTGTAACAGAGCGAAAACATGTAATGTATTTTATTGAATGTCAAAGCGAAAACATCCTTTGACAGTAACCAGAACGGCAGGAAAACTAATAGCTTCGTTTAAAAAGACATAATAGAGACTTTATTACAACATTTAGAACTC 285 2R:1731127-2080000 1 NULL:1983187 LD44494 952 1236 1 1 0 2598555 5687 5601 1 0 0 0 97 partof TTATATCGATAGCACACGTGTGCCAAGTGCTTGTTTATATTTTGCTGTGCACATATTGGTGAAACTATTTAATAATATTTATTAAGGTG 86 2R:1731127-2080000 1 NULL:1983189 RE35072 0 86 1 1 0 21600 21472 1 0 0 0 100 partof ATTTTACGGAAGGCCTCAAAATGATGCACTACCGCAAGGCCGAGAATGTGGAGAAGGAGCTGAGCAAGAGCGATCTGCCATTCGAGGACTGCATGCCAAAGTCCCAAAAGGATTTTTTGTGGATGCATGTG 128 2R:1731127-2080000 1 NULL:1983190 RE35072 86 214 1 1 0 22011 21656 1 0 0 0 99 partof GTAAAAGGCGGTACCAAAGTGAGCAATGTGATTGAGTTTGCTCAGGAGGCGCTGAACAAGGGCGAGCACAGATGCGTGGTGTGGAGCGGATCCGGCGGAGGAGTGGTGAAGACCATATCCTGTGCCGAGGTCCTCAAGCGGAGCCACCCCCTCTACCAGGTGACGCGCATGGCCTACACCAGGTGAGTCGGCAATAAGCAGCCAATGTGCAATAACTTTTATAATGTACTACGCAAAGTGTGGAGGAGCACTGGAAGCCGCAAATGGAAGGCCTGGAGGAGATTATAGTCACACGCCAAATACCCACCCTGCACATCCTCATGAGTCTGGACGAGCTGCCGGATACTATAGATGGGTA 355 2R:1731127-2080000 1 NULL:1983191 RE35072 214 569 1 1 0 22369 22067 1 0 0 0 99 partof CTTACAAAAGCCAAATACGTCCACTGATTTTTGGGATGGCGGAGGAGCACAGCAACAGCCACATCCACGTTCCCAGCCCCGCCATCAGCAGCAGCCACATAAACCAGGGGCTGGGCGTGGGGGTCGGCCGAACAAACGGACCAGACCCGGACGCAATAAACCAGGCCAACAACCCGAAAAACCTGCCGCTGAAGAGAATTTACCCGCCAGTTAGAGTCAAGGTTGAGATAAGCGGACCATGCGAAGATTTTCTTATTTGCCCTTTGTAAGGATGTACAAATAAAGCCCAATTTATCACAAAA 302 2R:1731127-2080000 1 NULL:1983192 RE35072 569 871 1 1 0 2598561 23427 23228 1 0 0 0 100 partof ACGAGTTCTGCGATTGGGTGCACTGCGTCAGCTTCGCTCGTTAAGTGGCAAGCCGCAAGGCGATGTCCTTCCCGGGAGCTGCGGAGTCCTGATAATAGGTGGCGGTGGCATGGGCGCCTCCTCCGCTTTCTGGCTGAAGTCCCGGGCCCTGCAGCTGGGCCGCAAGCTCAATGTGCTGGTGGTGGAGCGCGATGCTGGT 199 2R:1731127-2080000 1 NULL:1983194 GH02863 0 199 1 1 0 24959 23736 1 0 0 0 100 partof TA...CAGTACACCAGCGCATCTACAGTGCTTTCTGTAGGCGGAGTGCGGCAGCAGTTCTCTTTGGCCGAGAACATAGAGATGTCGCTCTTCGGATACAACTTCGTGGTTAACGGCAGGGAGCATCTGGGCGACGTGGATCTGTGCTACCAGCCGAACGGCTACCTGATCCTTGCCTCCGAGAAGGGAGCCCACATCCTAGCAAAGAACTCAAAGCTACAGAACGAGCTGGGGGCCCGAAATGAGCTGCTAGGCCCGGAGGCACTGCGTCAGCGGTTTCCGTGGTTGTCCACAGAGGGCGTGGAGCTGGGATGCCACGGGATTGACAAGGAGGGATGGTTTGATCCGTGGGCCCTGCTCATGGGCTACAAGAAGAAGGCCCGTGCATTGGGGGCGAATTTCGCGAACGGTTCGGTAGTGGGTTTTGAGTGGAACGATTCGGGCGGCCTTTCTGGAGCTGTGGTCGACGCCGGAGATGTGTTGCAGCGCACGGTGAAGTTTGACACGTGCGTTCTGGCAGCGGGAGCGTACTCGGGTCAGGTGGCGCGTCTGGCAGGGATTGGTGATAAGGAAGCAAAGGAGGCTTCCCTGAGTGTAGCCCTGCCGGTGGAGCCTCGCAAGCGATACGTCTATGTGGTTAGCACTCAGGGTAAGAATTGTCCTGGGCTAGCCACACCTCTGACCGTTGATCCCGATGGCACCTACTTCAGGCGGGACGGTCTTTGCGGCAACTTCCTGTGCGGCCGCAGTCCAAACGAAGACGAGGAGCCGGAGTGCGAAACGCTGGACGTGGACCACGGGTACTTTGAAACGGATGTCTGGCCCACACTGGCGAACCGAGTTCCTGCTTTTGAGTCTGTGAAGATACAGAGCAGCTGGGCGGGCTTCTATGACCACAACACATTTGACGCAAACGGCGTCATCGGCAGGCATCCTCACTACAGCAATCTCTTCATTGCCGCAGGCTTCAGTGGGCACGGCATTCAGCAGACTCCCGCCGTGGGTCGAGCCATTTCCGAACTAATCTTGGACGGCAAGTTTACCACACTGGATCTGTCGCGCCTCGGCTTCGAACGCCTTGTAAACCAACAGCCTATGCACGAAGTGAATATCGTTTGACAAATTTATCACAGGAGGATCGTACTTGCCCTTGGTGTGTTTATGTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTC 1223 2R:1731127-2080000 1 NULL:1983195 GH02863 199 1422 1 1 0 2598565 26704 26559 1 0 0 0 100 partof AACAGATTGGAAAACGTACAAGAATTGCGTATTATCTGTGGCATTACGAGATCGTACTTTCTAAAAACTAGCTTACCGTAACCCCCGTCAGCTTAAAACATGTCCTACGCGTACTTGTTCAAATACATCATTATCGGAGACACAG 145 2R:1731127-2080000 1 NULL:1983197 GH01619 0 145 1 1 0 27350 27190 1 0 0 0 100 partof CAGGCGTGGGCAAGTCCTGTCTGCTGCTCCAGTTCACGGACAAGCGATTCCAGCCGGTGCACGACCTGACCATTGGCGTGGAGTTCGGAGCACGCATGATCACCATCGACGGCAAGCAGATCAAGCTTCAAATCTGGGACACGGCTGGGCAGGAGGCTTTCAGGTA 160 2R:1731127-2080000 1 NULL:1983198 GH01619 145 305 1 1 0 28160 27823 1 0 0 0 100 partof ATCTATCACACGCTCTTATTACCGCGGAGCTGCTGGCGCCTTGCTGGTGTACGACATCACGCGACGGGAGACCTTCAACCACCTGACCACCTGGCTGGAGGATGCGCGTCAGCACTCGAACTCGAACATGGTCATTATGCTGATAGGCAACAAGAGCGATTTGGATTCGCGGCGTGAGGTGAAGAAAGAGGAGGGCGAGGCCTTCGCCCGCGAGCACGGACTGGTCTTCATGGAGACTTCTGCGCGCACAGCTGCCAACGTAGAGGAGGCGTTCATAAATACGGCCAAAGAGATTTACGAGAAGATCCAGGAAGGTGTCTTCGACATCAACAATGAGGTA 337 2R:1731127-2080000 1 NULL:1983199 GH01619 305 642 1 1 0 28623 28220 1 0 0 0 99 partof GCAAACGGCATTAAGATCGGCCAACAGCACTCCCCCACAAACCCGTCGCTCCCAGGAGCCGGAGGAGCAGCTGGAGCAGCAAACAGTGGCTGCTGCTAGGAGTAAACCGCAGATGCCCGATTGCAATTCTGGGATAGGCGCAGCCGCTTCTGTAAAAGCTACTTTAGTGACTAACTAATAGAAGGTAGTTGAAGGAACAGATTTCTTGTTTTCTATCTCAACCGTAACTAACCACGTAAACATAGCTACCACTAATCTAGCAATTGGACACTAAGCTAAATGTTAAAACCATTAAGATCAGACAGTTACAAGAAACACATCTCCTTGTTCAGCTACGTTTTATTTTACCAAAAAAAACCAAAAGGAAGAAGTAACCAGAAATAAACCAAAACAAACCACATTTGTG 403 2R:1731127-2080000 1 NULL:1983200 GH01619 642 1044 1 1 0 2598571 71924 71669 1 0 0 0 100 partof ATTTGTGAGCACACACTTTAGTTTTTCGTTAGGAACGGGACGTTCGTTCTGTTGCGCACCAAATTTTTTCGGACCCAATGCAAATGCAAACGCTTTTGCGGCGTGTGTAGTGCATTCAAAATTACCAGATACCCAACGGGATCCAAAGTTCCCAGAGCAGTGGCACCGGAATCGATGCGACCAGCAGTCAGCGGAAGCGTAAGAAATTCGCGCCTAGGTGGACAAAAATCGATCTGTGACGCGGTTTAAACCAAGGTA 255 2R:1731127-2080000 1 NULL:1983202 GH08636 0 255 1 1 0 72544 72479 1 0 0 0 100 partof GCTGCACGACACTTCGAGGACTTTTATGTGATTATTACTATGAAATTGGATGAAATAGTTGCATGGTA 65 2R:1731127-2080000 1 NULL:1983203 GH08636 255 320 1 1 0 72755 72615 1 0 0 0 100 partof GTACCAGAAGAGAATCGGCACCTATGACAAGCAAGAATGGGAAAAGACCGTCGAACAGAGGATATTGGACGGCTTCAATAGTGTCAATTTAAAAAACACCAAGCTGAAGACGGAGCTAATCGATGTGGACTTGGTGCGAGGTG 140 2R:1731127-2080000 1 NULL:1983204 GH08636 320 460 1 1 0 73319 72811 1 0 0 0 100 partof GTTCCACGTTCCCTAAGGCCAAGCCCAAGCAGTCGTTACTCACTGTGATACGCCTGGCCATTCTGCGCTATGTCCTGCTGCCCCTCTATGCCCAGTGGTGGGTCAAGCAGACCACGCCAAACGCCTTCGGCTTCATCCTTGTGCTTTACCTCACACAGTTAACCAACTGGGCTATCTACGTGCTTCACAGCAGTCGCATAGTGCCCCTTGACTATGAGAAGCCGCCAAATGGAACCCTGCTTCAGGCAGAGGCAGATGGAGATGCCTCCGATAAGGATGCAGATAAGGAGTCCGAGGAACATGCCGCCCTCCTCAGTGCCCTGCTTATTCCGTGCGCCCTAAGCTTGCTGATCAGTCTCATCCACTCACAAATTGTAGCCACTAACACCGCCTCGGGTGTCTCTGGCGGGAGTAGCAAGAACAAGCTGCGTCGCATATCTGCAAGCTACTTAAGCGACAAAGCAGCAACCAGGGAGAACCGGGTGCGACGTCGCAAGAAGATTGTGCG 508 2R:1731127-2080000 1 NULL:1983205 GH08636 460 968 1 1 0 74314 73367 1 0 0 0 100 partof TAGAGTTCGACAAGTGGAGGCTGACTTGTCCCAGGCCAGCAGTAACATATCACTTCCAAACAGAAGAACCGCAACCAGCACAATCGAAGTTCTTCCCAGACCGGTCACGCCTTTGCCTTCACCAACAGTTACCTGTGCCACGGTGCCAGACCCCACCACGCCGACTACGCCTTCGCCATCTGTTATCAGGCGGAGCACCAACGAGGAGACCTATTTGACAACGACTGCAATCAGCCCACTAACGCAACCGCTGGCAGCCATAGACGCATGCTACGATCTCAGCAGAAAGGCAGGGGGAGCTGCTCCCGAAAGCCCCAAAAAGCGCAACGTCAACTGGCACACGCCTATTCAGATATACGCTACCTACGAGCTGGGCGAAGAGCCGTGCTCCAGCAGAAAAGTCGCAGAAGAAAGTGCGCCTGAGTCGGTTGGAGAAAGATTGTGTTCCGTCAAGCCAGACTACCAGACGCGTCGAAACATCGGGGAGGACGATGGCTTCGAGAGTCTGAATGGAAAGAGCTCAAGTGGAGAGGACAACAACCATTCGCCTTTGCCAAACGCGGTGGCTGTTGCGGCTCCACCAGCTCCTGTTCAGACCAATCAGTTGCGTCTGCGATTAAACACAACAAACGGTGTGACCGCCAGTGCTTCTCCAACCGAGAAGAAACCCCAGTCGCGCGGCAATGAATCCTCAACGAGTTGCGCCGAATCGGATGAGTGCGATGATGCCGACATTATGTCCAGTCCCGCCTCGGGCTGTAACCAAGAGTGCACCACTTCTGCCACCGACTGGCTGGGGGTGACGACAAATAGCGAAGACTGCAGTTACACCTCTGATCTGGATCACTCTGACGGGGGCTTGAAGCACACGGCCTTTAGCGACGAAGATCCTGGAGAGCTGGACATCACCCCTACCACTATACTAAATCCACATAGCAGCCTCGACCGTAGTA 947 2R:1731127-2080000 1 NULL:1983206 GH08636 968 1915 1 1 0 74552 74373 1 0 0 0 100 partof TTAGCTGCACCATTTGGGATCAGCGAGATGCCAAAAAGGCGCAGCTTTCCGTGCTGGAGATCGCGTCTTGCATAATCGAACGCGTGGACTCAATGGGCGAGGCCAACGACTACATCTACATAGGCGTGGTCTTCTCTTTCCTGCTCACATTGATTCCCATCTTCTGCCGTCTCTGCGAGGTA 179 2R:1731127-2080000 1 NULL:1983207 GH08636 1915 2094 1 1 0 74969 74612 1 0 0 0 100 partof GTCACACTCGGGAGCGATGCAGAGAAGGCCAGTGAGATTAGCTACTTTAACATGCCGCAGCTGCTGTGGGAGAAGTCATCGGCATCGCTCTTCACCCTGCTGGGCCTTGCCTTCGGCGACAGCCAGTGGGAGCGCATGGTATTGGCTCTGGGCTTTGTCCAACGCCTTTGCCTGACCCTCATACTGTTCATAATATTCGCCGTTGCAGAGCGCACCTTCAAGCAACGCTTCCTTTACGCCAAACTCTTCTCCCACCTAACTTCATCACGTAGGGCTCGAAAGTCAAATCTTCCCCACTTCCGTTTGAACAAGGTGCGTAACATCAAGACCTGGCTGAGCGTGAGGTCGTATTTGAAGGTA 357 2R:1731127-2080000 1 NULL:1983208 GH08636 2094 2451 1 1 0 75629 75027 1 0 0 0 99 partof AAACGCGGACCCCAGCGATCGGTGGATATCATCGTTTCCGCCGCCTTCATAGTAACCCTCCTGTTGCTGGCCTTCCTCAGCGTCGAGTGGCTGAAGGATTCGGCTCATCTGCACACACACCTTACCTTGGAGGCCCTAATCTGGTCCATAACAATCGGTATCTTTCTGCTGCGCTTCATGACCCTAGGTCAGAAGATACAGCACAAGTACCGCAGTGTGTCGGTGCTGATTACGGAGCAAATTAACTTGTATCTGCAGATCGAGCAGAAGCCAAAGAAAAAGGACGAGCTGATGGTGTCGAACAGCGTGCTCAAGCTGGCCGCCGATCTGCTAAAGGAACTCGAAACGCCATTCAAGCTCTCTGGCCTTAGTGCCAATCCATATCTATTCACAACCATCAAGGTGGTAATCCTGTCGGCCCTATCGGGCGTGCTTAGCGAAGTTTTAGGCTTTAAACTGAAGCTGCATAAAATCAAGATCAAGTAACCTATGCAAGGCGCAGACCCATCATATTTTTGTAGTACAACTTTTTAGAAACGCTTTAAGAGAAATCTAACACTACACTCTAAATTAGTTAAGTGAATAAATTTAAGCGAGCCAAT-GTT 602 2R:1731127-2080000 1 NULL:1983209 GH08636 2451 3054 1 1 0 2598581 76385 76160 1 0 0 0 100 partof ATCGTTATCAGTTCGGCCACCCACAACTGACGTAACTTTCGCCTCCACTCGCGTGGTAATTTTCGCATTTAGCTCCCTTAAAATCCCACCCCCCACAAAATGATCCGGCTTAATTGGCTATTCAGGAGCTCCTCGGTGCTGCTGCGCAGCCAGGTGCGACTGCTCCATGTGGGAGATGCCAATGTTTTGCATAGCGAGGTAGACAAGCAGTCCGCCGAGTACAAGGTG 225 2R:1731127-2080000 1 NULL:1983211 RE27841 0 225 1 1 0 76698 76444 1 0 0 0 100 partof GAAAATGCCAGAGAGATGGCCAGTTTGGTTGGAGATCTGCGGAACTTCACCAGCCAGGTGCTCAAGGGAGGCGGACAAAAGGCCATCGAGCGACACACATCGCGGGGTAAACTCTTAGCCAGGGAGCGCATCAACCTGCTCCTGGATAAAGGATCGCCCTTCCTAGAACTCAGTGCTTTGGCCGGACACGAGTTATATGGCGAAGAGGTGGTCAACTCCGGGGGAATCGTCACCGGAGTGGGACGCGTTTGCGGGTA 254 2R:1731127-2080000 1 NULL:1983212 RE27841 225 479 1 1 0 77898 77017 1 0 0 0 99 partof AACTGAGTGTTTGGTGGTGGCCAACGATGCCACTGTGAAGGGTGGAAGCTACTATCCCATTACCGTTAAGAAGCATTTGCGCGCTCAGGAGATTGCCCAAGAAAACCGCTTGCCCTGCATTTACCTTGTGGACTCGGGTGGCGCCAACCTTCCGCGCCAGGCGGATGTCTTTCCAGACAAACTGCACTTCGGACGCATCTTCTACAACCAGGCAAACATGTCGGCCCAGGGAATTCCTCAGATTGCTGTAGTTATGGGCAGCTGCACGGCCGGAGGAGCTTACGTACCGGCAATGGCCGATGAGAGCATCATTGTTAAGAAGCAGGGAACTATATTTCTTGCTGGGCCGCCGCTGGTGAAGGCGGCCACTGGAGAGGAAGTGTCTGCGGAAGATTTGGGTGGAGCAGACTTGCACTGCAAGACTTCTGGGGTCACCGACCACTATGCCTTAGACGACGAACACGCCTTGTATCTGGCCCGCCAGATTGTGAGCAACTTAAACTTGTCCGCCACTAATTCGTACAACGATCAGCTGATGCACTCCAGTCAAGTCAATTTCCAGACTGCTACTCCGCCGTCTGCCGTAGAAGAACCGCGCTACGACGCGGAAGAGCTGTACGGCATCGTAGGTCCCAATCTTACCAAAAGCTTTGACGTTCGCGAGGTGATTGCGCGCATCGTCGACGGAAGTCGCTTTACGGAGTTTAAGAAGCTATATGGTGAGACTTTGGTGTGCGGATTTGCGAAGCTATATGGCCACACAGTGGGAATAGTCGGAAACAATGGAGTCCTTTTCTCGGAGAGCGCACTCAAAGGCGCCCACTTCATTCAGTTGTGCGCACAGCGCAAGATACCGCTCGTTTTCCTGCAAAATATTACTGGTA 881 2R:1731127-2080000 1 NULL:1983213 RE27841 479 1360 1 1 0 78730 77953 1 0 0 0 100 partof GCTTCATGGTGGGGCGCGATGCCGAGGCCAATGGTATTGCCAAAAACGGAGCTAAGATGGTAACGGCCGTGGCCTGCGCTAATGTGCCCAAGTTCACGGTGATAATCGGCGGTTCCTACGGTGCGGGCAATTACGGCATGTGCGGTCGGGCCTATTCGCCTCGTTTCCTATACATGTGGCCAAATTCGCGCATCTCAGTGATGGGCGGAACTCAGGCAGCCAATGTTATGGCTCAGATCACCGAAGATCAACGCAAGCGAGCTGGCAAGGAGTTCAGCGAGGAAGAAGCCCAAAAGCTGAAGGCTCCCATTGTGGAAATGTTTGAGGCGGAGGGTTCGCCCTACTACAGTACGGCTCGTCTGTGGGACGACGGCATCATTGATCCGGCCAACACCCGTCAGATCCTGGGCCTTAGCTTGAAAGCAGCCTTGAACAACGCCGGTCAGGAGACCAAGTTTGGAGTCTTCCGCATGTAAATCCAATTTGTATGCTGGAGAAATTTAATCGGAGCGCATTTACAGGCATTTAATGCCTTTATTTCGAAACTGTTGCATTTATTAGCGTTAAGGCAATTGTTAACTGTGTAATGTACAACTGATTGTTTATTAGGAACAGGCGTGTGAAATCGTTCAAAGCTTACGAAACAACTTTTAAGTTGCTAAAATATTTTAATTCCTGTGCAATAGAACAAATGTTTATGTCAAAAAGTTACAGCTATTTAAGAAATACGGAAAACACAAAACACACACATTTAAATGTATAATGTATAACAAAACAATT 777 2R:1731127-2080000 1 NULL:1983214 RE27841 1360 2137 1 1 0 2598587 79164 78966 1 0 0 0 99 partof ATCGTTCATCTCTAGCGCCTATCGATAGACCTCCATGCGGACCTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAG 198 2R:1731127-2080000 1 NULL:1983216 RE41364 0 197 1 1 0 82559 82406 1 0 0 0 100 partof G...CAGTGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 153 2R:1731127-2080000 1 NULL:1983217 RE41364 197 350 1 1 0 82763 82617 1 0 0 0 100 partof GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 146 2R:1731127-2080000 1 NULL:1983218 RE41364 350 496 1 1 0 84213 83954 1 0 0 0 100 partof ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCAGTA 259 2R:1731127-2080000 1 NULL:1983219 RE41364 496 755 1 1 0 84619 84476 1 0 0 0 100 partof CAGTATCCAAGGTGCTGCCGCGCACGAACAACGCAGCCCCAGCGAGCAGAATAAACGCCTGTGCCAACAGCACGGGCACGGTCAAGAAGAACGACGTGAGCAATTCGGTCAACAATCAACAAATAGAAGAGATGTCAAATCAGGTG 143 2R:1731127-2080000 1 NULL:1983220 RE41364 755 898 1 1 0 84756 84673 1 0 0 0 100 partof GTGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTGTA 83 2R:1731127-2080000 1 NULL:1983221 RE41364 898 981 1 1 0 84892 84819 1 0 0 0 100 partof TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTA 73 2R:1731127-2080000 1 NULL:1983222 RE41364 981 1054 1 1 0 85814 84959 1 0 0 0 100 partof GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 855 2R:1731127-2080000 1 NULL:1983223 RE41364 1054 1909 1 1 0 2598597 79164 79008 1 0 0 0 100 partof CTGCGCTGGGCGGCCGATGCATCAGTGTACATTTTACATCCCTAGCGCTCGCTCGTTTAGCAGAAGACGGTTTTTCATAGAATTAACATTTCCTTGTTTAAAGCCAGGAATCATTTAGTTCTCCGTCGCCCCGAAGGATAACGACCAACTGATTAGGTG 156 2R:1731127-2080000 1 NULL:1983225 LD08743 0 156 1 1 0 82559 82406 1 0 0 0 100 partof TGCCGCTAACTAAACCAGAGGACACCACCAACATGGCTGTAAACGTCTACTCCACAAATGTGACGTCAGAGAATCTCTCGCGCCACGATATGCTAGCTTGGGTTAACGATTGCCTCCAGTCGCAATTCTCAAAAATCGAGGAGCTCTGCACAGGTA 153 2R:1731127-2080000 1 NULL:1983226 LD08743 156 309 1 1 0 82763 82617 1 0 0 0 100 partof GTGCAGCTTACTGTCAGTTCATGGACATGCTGTTTCCCAATTCAGTGCCAGTAAAGCGTGTCAAATTTCGTACCAATCTGGAGCACGAGTACATACAGAACTTCAAGATATTGCAGGCGGGCTTCAAGAAGATGTCTGTGGATAAGGTA 146 2R:1731127-2080000 1 NULL:1983227 LD08743 309 455 1 1 0 84213 83954 1 0 0 0 100 partof ATTATACCCATTGACAAATTAGTCAAGGGTCGCTTCCAAGACAATTTCGAGTTTTTGCAATGGTTTAAAAAGTTCTTCGATGCCAATTACGATGGCAGGGATTACGATGCCAGCGCGGTGCGCGAGGGAGCCCCAATGGGCTTCGGATCGGGAGCGGTAAAGTCACTGCCCGGCACGGCGGCAAGCGGCGTGTCCAGCAGCTATCGACGTGGCCCATCGGCAACGACACGCCCAGCAATGACGTCTGCAGTGAAGCCCA 259 2R:1731127-2080000 1 NULL:1983228 LD08743 455 714 1 1 0 84619 84479 1 0 0 0 100 partof CAGG 140 2R:1731127-2080000 1 NULL:1983229 LD08743 714 854 1 1 0 84756 84673 1 0 0 0 100 partof TGATGGATATGCGCATAAACCTGGAGGGATTGGAAAAGGAGCGAGACTTTTACTTCTCTAAGTTGCGGGATATTGAAATTCTGTA 83 2R:1731127-2080000 1 NULL:1983230 LD08743 854 937 1 1 0 84892 84819 1 0 0 0 100 partof TTGCCAAGAAGCCGATGACGCCGAGGCGCATCCGATCATACAAAAGATTTTGGACATCTTATATGCGACTGAGGTA 73 2R:1731127-2080000 1 NULL:1983231 LD08743 937 1010 1 1 0 85814 84959 1 0 0 0 100 partof GATGGTTTTGCGCCGCCTGACGATGCACCACCAGAGGACGAGGAGTATTAATTTGAAACGTGAACGAAAACCCACTAAATTCATTTGCTGCATACATATTCAAAACATAAGTCAAGAAGCATGATGAAGGGGACAGAGTTTATTATTTAGACAGAATCCAAGAAGACGTTAAGCAAAAACGAGAAGACTAACAAATGAAGAGTGTTTGATTTCCTAGGCCGAGGCTGACAGCAGGATCGCCACGTGATTAAATAGTTATTCTTCAAACATTTATTTGATACGAACGCGTCGTCGCTTAACAGATAGAGACGGGATTTTTTTCGATTCAAAATTGTACCCACGATAATTTTGCTGATGTTGCCGATGTGTGTGAACCATCAACCATTTCATATTTAAATTGTTTGTATATTAGCGGAATAAACGAACCAAATCTCGATATCTAATGGAAAGCCAGCCTACCCTTTTCAAAATTCTTTTTTGAAAGGTTCACAGACTCGTAACTAAGAAAATTTAGAATGCTCAGCTTGCAAATTTACTTTGATTTAGATTAGCTCTTTGTATCACATGGTTTACATGGTTGATTTATATCCTATTAAGCACATTTATAATTTTTGTTTAAGTAAAACTTTTCACTAGCTGACTTTTGTCGTTTTGAGTGTTGTATGTAGTGGATCACAAGAGCCGAACCAACGGTATTTTGTACTTTCGATTTCTATTTTTAAATAATTGGCTTCATAACAAAATGATTGTATAAAATAAGTGATTTTTGCTCTCAATTTTTTAAGTTCTATATTTATGTGTAAAACAGGCAGAACTCGTTAAAAAGTTTGAATAAAAGCGAACGTCTAAACACAA 855 2R:1731127-2080000 1 NULL:1983232 LD08743 1010 1865 1 1 0 2604359 10161 9824 1 0 0 0 99 partof CTGGTAGCAGTTTTTTGAGGTAACCCGGATCCAAGGTGGGCGCCACGTCACGCTCCTCTATATTAGTGCCGTATTGGCATATATAATCAATCACTTCCTTGCCGTATTTGCGAAACTCTTCCACATCCATTTTCTCTAATTTACACTTTTCGTTTATCTTCTTGTTCAAATAAATTGCAGTCTATTAAGAAGTATCTGTTGGTGCTTGGTGCTTGTATCTCTAGTGCTCGGATACTAGGCTCTCACACGGTACACAGTAGCTTATCTCGATCACTTTCGAATCCCGGTTATCTCGCACCGCACACTCGTTGCAGGTCAGCTTCCTTGACGCGAATGT 337 2R:1731127-2080000 -1 NULL:1988025 RE04135 0 337 1 1 0 8836 7731 1 0 0 0 100 partof CGCATTCGGAAGCAAACTAGGCCAAGGTGAACATCGTTGCGAACCTCAAATCGTTCATCCTTGCGCACCAGCATCTCAAACTTCTTAGCCAACGCCATATGATTTCGAATGTATTCCTGTAGGCCCCGAATGCCGTATGTCCGGAAGACGAACCACAGCTTGAGTGCCCGGAATCGGCGACTCAGGGGAATGCCGTAGTGGCGGTAGTCAACTCCGGTCAAGTGCTCGTGTCGTAGGTAGAGGGGATTCACGTTGAGCGCGCTCTTAAGGTTCATCACATCCCGCACCCACAGGGCAGAGGCATCGAAGTTCGTCAGCAGAAGCTTGTTGGGATTTGTGTTGAAGGAGTCGGCGTATTCGAGTCCTGCCGAAAAGACCCGCATCTCGGGCAGAATGAAGGAGTTTCCCGCATAGGCGCCGTCTACGTGCAGCCAAATGCTCGACACCTGGCGGCACACCTTTCCGATCTCCGTGATGTCGTCGAAAGCGCAGCCGCCGGTGGTACCCACAGTGGCCACTACAAAGAAGGGTGTCAAGCCGGCGTTCACATCGTTTTGAATTGCTTGGCGGAGTAGGTCAACGCGCATGCGTCCATGCTCGTCGGCATCGATTATCCGGAGCTTCACCAGGGCCATCTTGGTGGCCTTTTCCACGGAGGAGTGTGCCTCACGGCTGGCGTATGCGATCAGGCTGGGCAGGAAGACGCTGTCGTGAACGCTGGTCTGACCCTTTAGCTCGCTGATGGCCCGGGCGCGGGCTGTGATTAGAGAGACGAGAACGCACTCTGAGGCGGATCCCTGAAGGGCGCCGCCGCCTGTACTGCCTGGGGCATCCGAAACAAAGGCCTTGGGCAGGCCAAGGGCCTTGGCGTACCAGTTCATCACGATCGTCTCCAGCTCGGCAGCCGCCGGACAGCTGGCCCAGCTGAAGCCAATTGAACCAATGGCACTGCTGAGCATGTCGCCTAGGACCGATGGAAAAGAGTTGCCCGAGGGGAAGTAGGCGAAGAACTTGGGGTGGTTCCAGTGCACCACGCCCGGCATGATCTTCTGCTCGAAGTCCTCGAGCACGTCCTTGAACGGCTCCGGCGACTGGGGAGCGTCGGCTG 1105 2R:1731127-2080000 -1 NULL:1988026 RE04135 337 1442 1 1 0 7609 6770 1 0 0 0 99 partof ATTTTCCGTTGGATTGTGTTTGTATTTTTTAAAAACTTGCATAAAAAATGCCGAGATAATGTTTATAAATAAGTGCTTTTGTTCATGACAGTAACTTAAGGTAGCTAAACGGTATAAGCAGATGCAAATGAGTCTATCTTTAAATTACATGATATTCAGCAACAACTAAGGTCCTACTAGTACATAAATGGATGTTCTTAAATTCAAACTGAGCAATGTTAGTCGGTAGTCGATTGATTCATGCCTCATTTCAGCTCGACAACTAATACTAGGTAGAGGTAAATCCGCAAATCCCTTTTCGGGTCGACGCTCAGTTACTCGCCTCGTCCGTATCCACGTCTGATATATCTTTGAGTTTTACGTTGCCATTGCTGTTGTTCCTGTCATTGTCATCCGCCGCCTTTTGGAAGTTCTCCTGAAGAGTTTTGGGATCGACGACCAGGATGGGTGTGCACCCGTCCATTAGGTGCTCGCTCTGGCTCTGGTACTGCTCCCGCGAGATGCTGCGAGTGAAGGAGAATCGCAGCGACTTTGTCCTGGTCAGCCTCTTTTTGATGGGTGGCTTGCCCGCCACTGGAGCCAATGGCTCTGAGCTGGTCCGCTCTGAGCCTTCCGGCGTGGTTGGCACGGAGCTGGACTCCAGCTGGTGGTCCCGCAGTATTTCCTCAGCAAAGCACTTTATCTGGGTCCAAGCTTCCAGGATGTCCTTCTCAGTGGCGTGCTCGTAGGTGACGCAGAAGCGGATCACGTAGCGGCCGTTGAACTTGGCCGGCGTCATATGCATCTTGCCCGAGTGGTTGATCTGGGCGAGCAGCATGTGGTTGGGCTCGTCGCCAGTTCTG 839 2R:1731127-2080000 -1 NULL:1988027 RE04135 1442 2280 1 1 0 2604364 26379 26114 1 0 0 0 100 partof CTTGGATTTTGTGCCTGGCCGGTTCCTACGCAATATGGTCGAGCCGTCAGCCATCTTCATGTTTCACCCGCTCGAAGACGCGATGATCCACAACGTCTGTGCCTACGCCTTGATGAGAAAATCACTGGCAGAAACTGAATGCTAGCCTGGTCCCTGCCCCGCGGGAGTCTCCGGATGTGGGATCCCTGCACCGTAGTATGCTGAGTGTATTCTACAGGAGCTGGCACATCGCTTGACAATTAATTGGCGTTTATCCTCCAAAACA 265 2R:1731127-2080000 -1 NULL:1988029 LD21194 0 265 1 1 0 26040 25666 1 0 0 0 100 partof CTGCTAGGGAAGTACTTGTTGCTGTTTAGCAGACAGGCGGCACCGTCCAGCGTGTGGCGTGTGTAGTCAATGGCCGGACATTCCTTGGGCGTCTTGTGCGCGGCGCACAGGAATATCCACTGGTCAGTGGCTGTCATCTGGGTGCACGTCGACGGCGAGCACTCCTTCTGCAGCCGCACTGCCAGGCCGTTCAGCTCCATGCAGAACTGGCGCAGGTGCTCGTACTTCCACACGCCCTCATCCTGGGCTTCGGGCATGGTCAGTATGAGTTCCACGTTGCTCGGGTCGCGCTTAATCAGCTGCTGTATGTACTGCTGCACCGCCAGCGTGCTGTCCATCTCCTCCAGGGGCTCGTCGGGCCAGCGACAGAAGTCCTG 374 2R:1731127-2080000 -1 NULL:1988030 LD21194 265 639 1 1 0 25606 24890 1 0 0 0 100 partof GTATGTACTTCTTTTATTGCAATTTCTGTTGTGTATATAGTAATTTTGTATAGTAAAGTTCACGTTTTAGTCACGTACAGCTGTGTTGGTGTTTTGGCTGCCAGTAGTCAAGGGAATTTAGTTTAGTTTACGGGGATTTGACGTGGAATCAGCCACGAGAAGGTCGTGTGCCTACATATAATTTATTAAAATAAGGAGTTAAACATAATCGTAATATAACTTGCGAAATAATTGCTGACTTAGGATCAGATGGGGCGAGCGGGTTTGAGGGGGTCTGCCCTTGTTACTTAGTTATCGTTATGTAGCTCTATGTGTATCTGACATCTAAACTACATACAAGATCTGCATTAGAGTCGGGTCCGCGTGGAATCGTTTCCCTGTCAGGGTGAGCCAACCCAACTTGCAAGCTATTGGTAAATATAAATAGATGTATGTTGAATGAGTGTTTCATGCGAGTCTGACTAATCTGGGCGGGCTCCTAAGCCTCGCTTTCGCCAGGGGCCGCGTTTTCACCCACGTTGATGGGCACGATCAGATTCTCCTTCGACATCAGATTATATTTTGTGACGAAATGCGTGAAACGGTGGCACAGATACGTCTCGGCCTCGAATTCGTCGAAAATGCGACGATGGTGAAAGTAGGCGTGCGAGAAGATGCGATACACCCGCCGACATACGGAGCCCAGCTTGGTTACCGACGACTCCTTGATGGACACC 716 2R:1731127-2080000 -1 NULL:1988031 LD21194 639 1355 1 1 0 2604369 45640 44878 1 0 0 0 100 partof CTGATCACTCTGCTGAGTTGGTGAATTCGTGGCTTCTGGGCTAAATTGCAACCATTACTGGGAGTTGGTCCTGTGTCATTGCATTATCTTACATTATAGGCTGCACATTACAGTAAATGTAGTTGTTGGGCAGACGAGTATTACAAAAATACAATAAGCTCGCTCTCTCTTTCGTTTCTTTTGCGTATGCCTCTTCGTCGAATTTGTTAGCTGTTGTTTTATGAATTTCTGCCGCCCGTCTTGCACAGTGGGATGAAATCGCTGTAGCACACGTCCAAATCAGCTGGCTTATATATGTATGTACGATTAGAATTGGTTGCGGGTGACACTCCAGAACGCCAAGTTGCCAAACACTCTTTATAGGCGATATTACGCACACTCAAGTTCCCGTGGAAAGTTATTATCTATCGGCTTCGCCCTGGGTCACGCCCACTGTACGGGAGTTTCGATTTTCTGCGGGGGAGGTGGGACAGTGACAACACCGCTCGGCGGCACAAGTTCAACAGAAAATGTGGGGCGACCGGAGGTCGTATAAACAAAAGCACAGTGCACCCGAGTGCGGAAATCGCGGCTGTAAGTGCTTCAAATGCACGCAGGAGTCGGGAATCGGGGAGGAACTTTCGATTCACCCAATCGCTGGATTTCAATTGATTACTTAACACGCTCTGTCGCGAGAAAAATAGGCTATCTCTACTGCCGCGGCCCTTAAAAATATAGAAAAGTCGTATAGTCCACCACACTAGCACCACACGTCCGTTCGCA 762 2R:1731127-2080000 -1 NULL:1988033 LD30953 0 762 1 1 0 35973 35009 1 0 0 0 100 partof CCGATCGTAGTCCAGGCAATGCTCTCTCCGCACGCCAACAGCCAACTTTTGTTAACGAATAAATTGATTCGGTGATCTGCGGATTTTGCGGATATATTCTTAAGATTTCACTGGCACTAGTTTCACTGTTTCGGCACCACCGCCAATCAATTCACCATAATTGCACAGATCTTCAGTTATGTTTAGCTCGCTCAGGGTGCGATTCGAGTGTTTATTCAGGGTGGCGGTTTTGTTGAAAATTCTTAGGCGCGGATCGCGGGGTATGTAATGCAGGAACACCTTGTTCGACTTGCCGCTGTTGTTGTAAGTACGGGGATTGTTGTTCTGGCCCTTGTCGAACGACTTGGCGTTGGTGGTCGCGCCCGACGCGGATGCTGCAGATGTTGGTTTGCCTGCACGATAGAATGACTTGGACCGAAGGTCGTTCATTAAGAACGTTAGGGGGTTTATCACAGGCCAACGGAGAATATATTGAGCGATAATTGACGGCAACTGGCGGCAGTTGCTGGTGATGTTGCTGTTGTTGCTGTTGCAGTTGCAGATGCAGTTGTTGCAGTTTGTGCTGCCGGCTAGCAGATTTTGCCCTGGCAGCCACATGCGGTACTTTGTTTTCGCGGAAATCAAACACTTTTCGATTCGATGCCAACGATGCCAACTAGCGTGCCCGGCTAGCTCGAACAAGAAATAACAAACACAAATCGAACACAAGACTGGGCCTCACTGGCTTCTCCGGCTACTCTGCCGCTCCCCGTGTCAAGTGCGCGGCGCGTGGTGCGGAGGCGGATTCGCAGGCATTGTATATATGTATATCTTAGTATCGACGGAGGGACGACCAACGCGGCGTATGATTAATTCGTCTCTGGTGGTGCAACTCAATCGCTGCTGTCGCTGTGCTCGCCTCCTCGCTGGCGCCAGATAATGATTTATGATCCTCGTCCTCAATTAGCAGCCTTCAGTGCAAACGCTG 964 2R:1731127-2080000 -1 NULL:1988034 LD30953 762 1726 1 1 0 34361 32161 1 0 0 0 100 partof ATCTTCCTCCTCTTTGGCGATGGTGGTCATCGAGTTGCGGTAGATGTTGGGACAGGAGGAGGCGCGCAGCCGGTAGCGGTGCGTGTTCAGCATGGCCCCGCGGTAGTGGATCGAGTTGCGGTGAATGCGCATATCCTTAAGGAAGTTGGAGTTCCGGATCGAGATGTTGCGGCGGAGGTTCGATCGGTGGTGGCTGGGCTTCTTGGAGCGCGACAGCCGGCGGATTCCCGTGATGCTGTCCAGGCGTGCGCGACGGGTGGCCAGCTCGCTGTTCACCGACTGCTCCTGTTCCGGAATGGCGATGACGGTGGGCCTGATGCGCCTGCTCGGCTCCAGCAATGCGAAGGTCTCGTCCTTCGAGTAGTAGCAGTGCATGTCCTCGCTCAAGATGTCCACCGAATTGTGTCGCAGGCCATTCACCTTTAGGTTGGAGATTGATGGTGTTGTATGCTTGGCCATGAAGATGTTTTCGTTAAGCGAGTACCGGGAGCTGGCGTGCTTCTGCGTAAGGTAGCCTTCGTCCGAGGAGCGGAGCGAGCCATTGGGAGTCCTACCAGTGGAGCGCTTTTCCGATGGAGACAGCGTCTCGATGGAGGCCAGATAGGCCTTCTTTGCTTCCTCTGCCGCCTCGTGAGCTATTCCGCCCATTAGGGTATCATCTGGCGAGCCTATAACGGCCGTCGATGGGGGATAGGCACCTGCTCCTGAGGACATGGACAGCAGGTTCTCTCGTGACGGCGCCTCCTCACCCTCCTTGTGGCGTAGGGAGCGTCGGCTCAGGCTCTTAACCTCGCAGATGCTGTCAAGCTCCTGAGTGCTCAGGAAGGTGGGCAGGAAGATCTCGCTGCGGTAGCGCTTGAGAGCGGAGTCCAACGGATCGTCAATCTGCTGGTTGGCCTCCGTGTTGTTCTTGGTCACCAACGAGTCTAGCACAGCCTCCTTTGTGATGCCGGTGTCCAGCAGCTTTTTTATTTCCTCCAGGCAGACACTGGAGTTCGAGAAGGTGGTGACGCTTTGGGATCGACTCTCTAGACGGTTTTCCTCGATCAGCCAGTCGGGATCGCGCATGAGGGCGCCGCAAACGCATGCGTTGAGCATGGTGCCGCCAAGGATTAGAGTGGCTCCGCGCCAGCCGTACGATTCGATTAGATAGGAAGTAAGGCGGGCGTAGACAAAGGTCCCGATGCCGGTGCCCGATGCTCCGATGCCGGTCGCAAAGGTGCGCTTCTTGTCAAACCAGAATGCAATGGACACCACCGCGGTCACATACCCGATGCCTAGGCCCAGTCCCGAAATGATACCAAAGGTCACCATGAGCATCTCGATCGAGTTGCAAAACGAAGACAGAGCAAACCCAAAGGCAGAGACCACTCCGCCGAGGATGGTCATCTTTCGGCAGCCGTACTTGTCCACCAGATTGGACCAGATGGGTCCCATCAACAGGGGCACGGAGAAGAATAGCGAGGATATCCAGGCGGTCTTCGAAGTGGACTCTCCGAAGTATTCCAGCAGTTCCACGTTTATTAGGCCAAATGAGAAGCTCAGTCCGTCGGCTATAAGGGACACGACCAGAGAGGCGAACACCACCACCCACCCATATCCACCGTCGGGCATCTTGGGCGTTTTCTTCTCCGTGGAACTGGAGTCGATCGAGTCGCCGGACTCGTTCGAGATCAGGCGTTTGCGACGCTTCACCTGCCCATTTCCGTTCATCAGGCACGTCATGGTGCCGTCCTCCAGTTCGATGACACTGCTCCTTACCACACGGCTGTGTCCAGCCCCATCTGCGAGCTCCTCTACGGAGAGGTTGCAGAAGGTGACCTCCGGGAAGAGGTCGTGCTTGATGGCCTTGTGGAGTGGCGTGTTGGCCGGAGCAGGCGTAAGAGGCAGGGCCTGGTAATTGGAGGCGCCTCCGTTTTGGCTCTGGTTCTGGCCATTGTGGTTGTTGTTAACCGCCTCGCAGCTGTTGTTGTTGGAGGCGTTTGGATCCGTCGCTAGCTTGGCCATGTCGGAGTCCCAGTGATCGTGTTGTTGTGTAAAGGGTTCAGCTACGTCTATAAAAAGGTTTGTAAAATTTGCACTTTCTTGTCCAAGCGATTATTGGAAGTGAACACAATTTGCATTAGATTTCAGCATAAATTTTCTTAAGTAGGCGGTAGGTAAATATTCCCTCTCTCTGTTGGTCAACTGCAGTGCGTAG 2200 2R:1731127-2080000 -1 NULL:1988035 LD30953 1726 3926 1 1 0 31697 31587 1 0 0 0 100 partof CAAATGAACAAAAACAATGTAGAGAGATTGAAGAGGGCGAACTTCATGTCCAGAAAGAGTGAAAAGTCAAAGATGGACTTCATGGTGTCCACAAAGTTGTCATACCAGGTCTA 110 2R:1731127-2080000 -1 NULL:1988036 LD30953 3926 4036 1 1 0 31146 30964 1 0 0 0 100 partof CCAGCATGCACAGCGAGTAGCATATATTGATGTTCATCCAGGACAGATCCCCCAGATAGCCAAGTCCTATCATGCCCACCGTTTGGGCAATGCCGACATCCGAAATCAACTCGGCACTCTGGCTCACGTCGTACTTGTATTGCTTCATGTAATCGGGAAGGTACAGATAGGGGATAATGAACCTG 182 2R:1731127-2080000 -1 NULL:1988037 LD30953 4036 4218 1 1 0 30897 30656 1 0 0 0 100 partof CTGCCCGTATACTCGTATATGACGCCTGCAATAGGGGGTCCTGCGATCATTCCAACTCCCTGAACCAGCAGCACCAGACCGTAGGCACACGTGAAATCGTCCAGATCCACAATACTGACCAGAATGCTGGGCGTAAACGAGAAGGAGCTGGCGAACGTAAATCCGAAAATAACGCACATGACCATCAGGCCCATGTAGTTGGTAATCAGCAGGGGCATGAAGAACACAGACGCTCCGCACACTG 241 2R:1731127-2080000 -1 NULL:1988038 LD30953 4218 4459 1 1 0 30592 29997 1 0 0 0 100 partof GTTACATAGATTGTTGTTTATTGTATTCCCTTTAATTAATATTCGTACGAAATGTAAGGCAATTAAAACTATTTTTCTAAATTTTGTAAAGAAGACAATTGAGGGACCCGTTTGCACCTGGCAGTGATGCACTGCATTGATATTGATTGAAATTGAACAGTTTGTCTAGACAAAGATGCGGTTAGTAATTGCCCTAGTGCGGTAAGTATATGTTAGGTGTATATTGATACTTAGCTACGATTAGTCAAGTCAAGTATAGTCTTACAGGCTAGAGCTTAGGAATAGGCTTAGTTTCAGTTACAATTCTGCTCTGATTTTATGGCTGCAACACCATTTGACATAAGAAACTCGTTAACATTTAATGCTAGTCCATTATTATGCTACAGTTCGGATTTGTAGTACCTCCAGTTGCCTTCTACTTGCGGCGTTCAACAGTGCAATGTAAGTAACCTAGTGTAAAAGTTGAGCTTTTTTAGTCTCTAAGACATCACTATCACTCTCCTTAGGTGCTTTCTTTTCACAGAACTCGATCAGATACGAACAGACACCAGAGAGTGCGATAAATATTCCAGCATAATAGAAGGTGTCATCCCATCTG 595 2R:1731127-2080000 -1 NULL:1988039 LD30953 4459 5054 1 1 0 2604378 47582 46433 1 0 0 0 100 partof AAAGAATTTGAAGGCCAAACATTAGAGCGAATCCCGCAACGGCGGCCACAAGGGCCCTCCATCCGGCATGGCTCTCAATGAGGATCTCAAAGAAGACTACGTACAGCAAGGTTCCACAGGCGATGCCCTGGAGGACTCCGGATGGCAGACTGGGCTGACCCGCTGCCACCTGCTGGCTGATGCCGAGGCCAACACCGATACCGATGGGTGTAACAATGGAGAATGTCACCAGGTACAAGATGGCCAGCGAACTGCGTGTGCGGGCGACCAGAAGCTCCATACCCACGCAGAAGGCCAACACCAACTTGTGGGCGGAGACCGCTCCAAACATGAACCACACAGTGCTCACAGTGCCCTCCAGACCAATGGCCATGCCCTCGAACAGTTCGTGGAGCGAAAGGGCGAGGATAATGCCCAGCCCCCTGGCAGAGGATCCATCGTCCGCTGGCACGGGCATGTGCGAGTGGCCGTGGTGATCCTTGTGTGGCTGCGGTTCCGTATCCTTAACTTCCACTTCTTCCTTCGCCTGTGGATTGAGGAGAACACTGTGACGAATGCTGCGTCCTCTTTCGAAAGCCAGACTGGCCACCGACTCTTTCCGACTAAGCTTTCCCTGGTGGTGCCGCACGAGGCTGGTCATCAGCTCGTCCAACGCGTACATCAGGAAAAAGCCCGTGCACAGCAGCATCTCCGCCAGAGCGAAGGGCGTCTTGACAAGCGAGCCGCATTCCTGGAGCGCTTCCACCACCTCGATCACCTCGGGCAGCATGTGCAGGAAGGTGGTGCAGATGAGCACACCGCCGCCGAAAAAGAGTAGGCACCGCACCACCAATGACGAGCGGGTTTCCTCCGGACTCGCCTTCGTCCAATGGAAGCACCTGTTCAGGACGTAGGGAAGGCTGCCGCAAAGCACGGTGATCACCACGAGCACCACCATGGAAACTATTTTGGCCACCAGCAGCGCATGGTGATCCACGTCTTGCGTTTGCTCTTGTGACATAGTTGCGGTAGCGCTCATCTTCACCTCCCGAGTTGATAGCTTCGACTGTGCTGGCTGGAACTCACAACCAGGCTAATGGTTTATATTTCCAGTCATATATCAGCGGGAGCCGATTGAAATCTGATCGCTGATTGATACGCGGATTCACT 1149 2R:1731127-2080000 -1 NULL:1988041 RE15841 0 1149 1 1 0 46357 46119 1 0 0 0 100 partof GTAAAATATTGTCTCTTTTAATCCATATGGTTATTACATTTTTAATTATTTGCGTTGGATAAGATTTCTGAGAAACCTCTTTTGAAATTCTATTCGTATTTTATATAATAACTTTTACAGATCCCCAGGGAATCGTTTTGTATACTATTTTGTTGCTTCCTCTATAACTTGATAATACTGAAGTGGCGTCACACTGGCTAGGAACAGGTTAGGCTGTCATCACCCTCCGCTTCGTCAGCTG 238 2R:1731127-2080000 -1 NULL:1988042 RE15841 1149 1387 1 1 0 2604382 70444 69813 1 0 0 0 100 partof ACCAGAAAACGGCCACGTAATCCTTGTCGGCCAGGAGCTTCTCCAGCTGCTTGGCATTGACCTCCTCGATGACGGCCTCCGGCTCCGGAGGCGCCACTGGCTGCGAGCCCTTCTTGTTGTTGTTGTTGCCTGCACCACTCACATGTCCGGGAAAACTCAGGGCCAGCAGAGCACACACGAGCAGCGAGAGAGTCTTGAGGCGGGTGAAAGTCATCCTGCGATCGGTTACGGTTCTGATGTGCTTTAGGCCCTTAACGCGAACATGCGTGCGCGTGTCTGCTCGTTTTGGTGTGTTCTACAGTTTATAGTGTTATAATTGTATAATTGATTCGTTCTCGTCGTTTGGGGTCTTTCGTTATTAAAATTTGTATTCCTTTGAGAATCGGTCACTATTTTTAGTTGATAATGGTGTTTCTTCTTTCGCAATTTATTTTATGTATAACAACTTTTTGTTCACTGATACATATATACGGGGTTCGTATATGCACAGGCGAGATATATGTGGGGTATATACGAGAATAATTAGATTATATATGTGGTTTCTTGCTTCTATTAATTGAACGTTTTCCGCGGACTGTACTCTTTGCTCTTCAGATTTTGTTCCACTCCGTGCAGAGGTCCGCTCGCAACT 631 2R:1731127-2080000 -1 NULL:1988044 RE34119 0 631 1 1 0 68130 67973 1 0 0 0 100 partof CTGAAGTAGGTGAGGGCGGGGAAGTTCTTGATGCCATACTGTTTGGCTAGTCGTTTGTCGTTGATTTTCACGAAGTCCACACCGAAGGAGTCGGTGTCATCGTCGATTTTCTCGAGTTCCGCTAAAACCTTATCACAGGTCACGCAGCTTCGCGCATCTG 157 2R:1731127-2080000 -1 NULL:1988045 RE34119 631 788 1 1 0 67902 67735 1 0 0 0 100 partof G...TACAGAACAGAACGGCTACGAAGTCGGTGTCCTCGATGATCTTCTGCAATATCTTGGCATTGACCTCCTCGATGCGATCGGGCAAGTCCATGGCCTCCAAGGAGGTGAGGAAATCGAGCACTCCTTCCTCGTCCATGAGATCCCCATCATATATGATGGGCTCCTTTTCCCTG 167 2R:1731127-2080000 -1 NULL:1988046 RE34119 788 955 1 1 0 63032 62717 1 0 0 0 100 partof AGAATATAACCGCCAAGTGCTCGGTGTTCTCGACCAACTTGTCCTTCATCTCATCGGTGACCTCGGGAATTTCGGAATAGCGCTTCTGGTGCACCAACCAGCCAAGCAGCTCATCCTCTTTCATCAGATCACCCTCGTAGATGTGTGGAATTCCACGTTCAAAGAGTACAATCGATGGTATCTCATCGATACCCCATTCTTTGGCCTCCTTGTCATCATCGATCTTGACAAAGGCAATATCGTTCTGATCGCACTCATCGTCGATGTTTTCCAGTTCTGCGAGGATTTTCTGTGATTTCTTTTGGTCTTTGTCGT 315 2R:1731127-2080000 -1 NULL:1988047 RE34119 955 1270 1 1 0 62657 62012 1 0 0 0 99 partof AGAAGAATACGACAACGTGATCGTTTTCAGCCAAGATCTTGTCCAACATCTTCACATTGACCTCCTCAATTTTTCCGGGAATTTCAAGGGTCTCGTCGTCAGTAATCCAGGCCAACACCTCGTCCTCGTCGTCCAGATCACCGGTAAAGTGAAGTGGATCACGATTCCTGAAGAACACCAGACGTGGATAGGTCTTGACGTTGTATTTCTTGGCAATTCCGGTATCCTCAGTGGTAACAAAAATTATGCCAGCCTCATCCAATTCATCGTCGATGCTTTCCAGGGCGTTCAGAGTGTGCTCACAGGTCTCTCCGGGCTCGCAGGGACCCGTAAAGAAGACGACGACATATTCGTGTTCGTTGATCAGAGTGACCAGGATCTCATCGGTAACCTCCTCGATAGTAGCTGTCTTTTTCTGGACAAGAAGCCACTCGAGCACCTCATCCTCGTTCATCAGATCGCCTTCATAGAGGGCCGGGATCTTGTTTTCGAAGTAGATGAGGGCGGGCAAATGATCGAGACCATATTCCTTGGCCTCAGCGGCGTTATCAATGCGGACGATGACAATTCCCTCCTTCTCCAGCTCGTCATCAATGTTCTCCAGTTCGTTCAGGATGCGCATATCCTGCTTATCGTCCTTGTCGTCTG 645 2R:1731127-2080000 -1 NULL:1988048 RE34119 1270 1915 1 1 0 61959 61776 1 0 0 0 100 partof CGGTGTAAATTGTTCTAAACTTATGTCTATAAAATGCAAGTGCCGGCAGACCGGGCAGGTCGTACTCCTTATCAATATCGTCGTCGGATGTCTTTACAAAGTCAATGTCTTTTTCCTCGCATTCGTCATCGATGTTCTCCAGCTCGTTAAGGATCTTTTGGGCCTTCTTATCGCCCTCAGCGTCTG 183 2R:1731127-2080000 -1 NULL:1988049 RE34119 1915 2098 1 1 0 61709 61571 1 0 0 0 100 partof AGAAGAACACAGCCAGGTGCTCAACATCGTTGATCAAAACTTGCAGGGTCTTACGATCGACAGATTCAATGACATCAGCTGTGGACTCGTGCAAATCAATAACCCACTCGAGAATTTCCTCTTCCTTCATCAGGTCACCTT 138 2R:1731127-2080000 -1 NULL:1988050 RE34119 2098 2236 1 1 0 61508 61325 1 0 0 0 99 partof CATCATACATAATCGGGACGCCGGTCTCGTAGTAGACCAAAGCTGGAAATGCGAAAATGCCAATTTCATGAGCCAGCTTAACATCATTTGATTTGACAAATTGTATTCCGTGCTTGTCGGTGTCATCGTCGATGTTCTCCAACTCCTCCAAGATGTCGGAACACGATTCGCATTCATCGTCGTCTG 183 2R:1731127-2080000 -1 NULL:1988051 RE34119 2236 2419 1 1 0 61265 61214 1 0 0 0 100 partof TCTTTTGATTGACTAACCACTGCAGCACACGGTTTTCATTTTTGAGATTACCTA 51 2R:1731127-2080000 -1 NULL:1988052 RE34119 2419 2470 1 1 0 58848 58365 1 0 0 0 99 partof CGGATTTGACATTCAGTTTGCCGGACTTCTTCGCCGACTTCTGTTTGGATACCTTCTCCACCTCCTGGGACTGGTCGTCGTTGTCCTGGCCCTTGCCTACCGGCTTCTTGCCAGCCTGCGGCTTGTTGCTTCCTCCCGAGCGCTTGTTGGCATAGGAAACCTTGACCAGGGGCTTGTCCTCGTCGTCCTCATCGTCGTCATCGGTGTCCTTGGAGGGCTTGGCCTGCTTCTTGATGGCAGCTGGCTTGGTGGACGATTTGCTGGACGCCTGGTTGGCAAACTGGAAGTTGCCGCCGCTGGGACGCTTGCCCTGATCGCCTTCGCTATGCCCGATCCGCTGGGCGGTCATCTTAGGAACTTTCGTTGACTTCTCCAATTTGGTTGGACAGCATTGGAATGGTTTGTAATCGTTGGGCACGAAATTGTTGCCGCGCTTAGCTGAATGGCCGTCATGACCCAATCCAACATAGAAACATTCGTCATCTG 483 2R:1731127-2080000 -1 NULL:1988053 RE34119 2470 2952 1 1 0 58095 56608 1 0 0 0 99 partof TTTATTGAGTTGGATGGCTTTTATTAAATATTCTTACAATTTCATTCGGGAGCTATGTTTACAAAAGTGCTTTATGTCGATTTGCGTTTGATTTTTACGATCTGACAATTTCCATTTCGAAAATCTTGACTTATCAGCTGCTGTTCAACAAAATTTGTTTACATATATGTTGGATTTAGTTACAATTGCGTTTAGATTGGTAGGCTTTAGCTTAAGAAAACATAATGATAAAGATTTCTAATTCGATATTTTTCAAATACCGATAACAAAAACAACAGCGAGCGGTACAGAAATCGCTCTCAGAAGAAAACAAATGAAACAAAATGGCGAGCTACAATATGCGAGGCCATGTTCAGCGAGAAATATTGGATTTTCGATTCCATAACAAAATTAAGTATACGGCCTGTATGCTGCTGCAACATTTCTAAAAAGTTGTGGTTACAAATTATGGTTCCTCATGTTGTTATTATGAAAACTTATGAAAGTTGAAGGCTCTCATAGTTACACGTTTCAGTTAAATTAGCTAACAGTTGTGCACTGTCAGGTGTAAATTGTTTCAAAAAATATTTTATGCGTTTGTTCGTTCGTTTACTATGCTTTGGCCCTTGTTTAAATTAGACTAACTACATAAATGTAAATTGTATATTGCGACAAAAAGAAGTAGTATCAAAAAAGTTTAGGCGTTCGTTATTGACAAAAGACAATGTCCCATTAATTTGTTAATAACAAAGCTTGCTGACTAAATATACGAGCGAAAGTTCTCAGAAGTTTTATAGTTGTTTGTCGAAGTAATTGCTTTTAGTTTGAACAAAGTTTTTTGAAATCCGTTGGCAAAATGCAACAAATGTGTGGTTTAGTTAGTTATAGACCTGGGGACGACCTACACAGGTCGGCCCCTCTTGAAGAAAGTTAAAGCGAAAATATCAACAAAGTTTTAGTTAGTAGGTTTTCTTGATCATTATTCATTATTTCGGGTATCGTGTGATTCTGCTACTCGTGGATCTTCTTAACGTGGAACAACGCCCAAGGCTCGCTGCTTAAAAGTGTGGAGTAAGTTCTGATCTGACACAGAAGATGTATTGGTATTTAAGTCAATGTTTTTGTGCCAGACTGTTTAGGATTAGTGCGAGGAAACCTCAATTTTATGGACACACAGCCTGCGAATTCAGTTTTCAGTTGGTTCTTGTCATAGTTGTTGTCTTTTGCAGTCACACATATGTAGATGATGTACATTAATTATAGAAACCTGTCATTGAAGGTTCTTTTGCTGGCTATACAGGTTTGAGTTGGTTTTGTATTTTGTTTTGGTTTTGGTTTTGGGTTTGGTATTGGTTTTGGTTTGATAATTGTTCTATCAGTTGGCAACAGTGCGTATACGTGCTACTTTAGTATGGTATATCATTCAATCATACAATCAATCACTATCTAACTGTCTGTGGTTATCCACATTCAGTTAAACTGTTGCCTTACTCCCACAGAGAGATATCCTG 1487 2R:1731127-2080000 -1 NULL:1988054 RE34119 2952 4439 1 1 0 2604395 86795 86694 1 0 0 0 100 partof TG...TACCTTGAGCAACCAGGATGCCCCCAGGTTCCGTCTTAGTATCATTGACATTCTAACGCTAATTTATTTTTGTTCTCTTTATTTAAGCTGATGATTGCAGTGTC 101 2R:1731127-2080000 -1 NULL:1988056 RE40412 0 101 1 1 0 86632 86487 1 0 0 0 100 partof TACCTTTGTCCAGGTGGATCTTGAAGGGGCGCTTGTCGAAGATCGTACCGTTCTCCTTTTGCAGAACGGCCGTTTGCTTATCCTCGAGCAGGTTACTGGGAATTGTTTTGGCCGAGTCCACCGGTTTTGCGCTGGAACTGTAGCATGC 145 2R:1731127-2080000 -1 NULL:1988057 RE40412 101 246 1 1 0 86411 86317 1 0 0 0 100 partof CTCTGCTTGATCTTCAGGAACTCGTTCTTGTGCATTCCATCGCAGAGGGGCTGAGACTTGGACTTGCCGCACAGGCACCAGCTGTATGTTTTAT 94 2R:1731127-2080000 -1 NULL:1988058 RE40412 246 340 1 1 0 86256 86064 1 0 0 0 98 partof TTGCTTGATTCAAAATTAATGCATTTCTCTTTTCGCACACGGGCAGGGCCCTACAACCAATCCTAAATCTATTTGACGGCGCTCTGGATGTGTGGCTGCTTGTGGGTGCCGTCACAGAAGGGTCTGTGGGTGGTCTGTTTGCAGTTGCAGAGCCAGTAGTCTCCCGACTTCTCCACCTTGAACCGAATGGGC 192 2R:1731127-2080000 -1 NULL:1988059 RE40412 340 532 1 1 0 2598607 138301 137864 1 0 0 0 100 partof ATGCGCGCCATCAGCAATGGCACCGCCCAGCTGGAGCAGCAGGCGCAGCCCAAGGAGGCCCAGGAGCCGCAGATCAAGAAGTTCGAGATCTACCGCTGGAACCCGGACAACGCCGGCGAGAAGCCGTACATGCAGACCTACGAGGTGGACCTGCGCGAGTGCGGCCCCATGGTGCTGGACGCGCTGATCAAGATCAAGAACGAGATGGACCCCACGCTCACCTTTAGGCGCTCCTGTCGCGAGGGCATCTGCGGCTCCTGCGCCATGAACATCGGCGGCACCAACACGCTGGCCTGCATCAGCAAGATCGACATCAACACCTCCAAGTCGCTGAAGGTGTACCCGCTGCCCCATATGTACGTGGTGCGCGACCTGGTCCCGGACATGAACAACTTCTACGAGCAGTACCGCAACATCCAGCCCTGGCTGCAGCGCAAGTG 437 2R:1731127-2080000 1 NULL:1983235 LD23740 189 626 1 1 0 138948 138357 1 0 0 0 100 partof GAACGAAGCGGGCGAGAAGAAGGGCAAGGCCCAGTACCTGCAGTCCGTCGAGGATCGCTCCAAGTTGGACGGCCTGTACGAGTGCATCCTGTGCGCCTGCTGCTCCACCTCGTGCCCCTCGTACTGGTGGAACGCCGAGAAGTACCTGGGCCCCGCCGTGCTGATGCAGGCCTACCGCTGGATCATCGACTCGCGTGACGAGAACTCCGCCGAGCGTCTGAACAAGTTGAAGGACCCCTTCAGCGTCTACCGGTGCCACACGATCATGAACTGCACGCGCACCTGCCCCAAGGGGCTCAATCCCGGCCGTGCCATCGCCGAGATCAAGAAGCTGCTCTCGGGCCTGGCCTCCAAGCCGGCTCCGAAGCTGGAGACGGCGGCGCTGCACAAGTAGGGCCCAAGTCCTCTACTCCCAGTTCGTCCCCTGCTGTCCTTAACCAGTGAGCTAAGCCTCCGAAAATGTGTATTGGAGACTCCTCCAGCCAACATGCTTACTATGTTATAATTTATTTAAGCCTAAAGTATCCGACACTTGTTATTACAGTTTGTAAAGGGAACAAGACGCGAAAATAAATAATTGTGTATCCACCAGCC 591 2R:1731127-2080000 1 NULL:1983236 LD23740 626 1217 1 1 0 137592 137403 1 0 0 0 100 partof CCACACTGCACCCTCAGTTTCGTGCAACTTTTTGTACGCAAATAAGAAAAACATTAAATTTGCTCTCAGCAAATCGATAATTGCAAACGCAGTGCCGTTTCAATTGCAGCACAAACCGCAACGAAAATGTTGGCGACCGAGGCGAGACAGATCCTGAGCCGCGTGGGATCCCTGGTGGCCAGGAACCAGGTG 189 2R:1731127-2080000 1 NULL:1983234 LD23740 0 189 1 1 0 blastx_masked 1.0 aa_SPTR.yeast 1.0 2003-01-14 22:17:38 BLASTX Similarity to Other Species genomic 2598778 3929 3674 1 0 0 0 155 partof VKFYQQS-VFDRLFQWSCADECQYGCMWRTVFAFFERGWPIPQFYGKWPFLRLLGMQEPASVIFSCLNFVVHLRLLRKFRREVRPD 255 2R:1731127-2080000 1 NULL:1983380 P25625 57 143 1 1 0 4305 4050 1 0 0 0 114 partof WIWSAIFHTRDFPLTELLDYAFAYSIILCSLYVMVMRMLHRYSLFLRGVITLAFLSYYINYFAYLSVGR----FNYAFNMMVNVATGVI 255 2R:1731127-2080000 1 NULL:1983381 P25625 169 254 1 1 0 2598782 27351 27183 1 0 0 0 172 partof SAGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 168 2R:1731127-2080000 1 NULL:1983383 P01123 15 71 1 1 0 28136 27821 1 0 0 0 231 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQE 315 2R:1731127-2080000 1 NULL:1983384 P01123 70 175 1 1 0 2598785 27351 27186 1 0 0 0 174 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1983386 P07560 28 83 1 1 0 28130 27821 1 0 0 0 247 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKI 309 2R:1731127-2080000 1 NULL:1983387 P07560 82 184 1 1 0 2598788 27351 27186 1 0 0 0 160 partof AGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQEAFR 165 2R:1731127-2080000 1 NULL:1983389 P38555 21 76 1 1 0 28157 27821 1 0 0 0 254 partof RSITRSYYRGAAGALLVYDITRRETFNHLTTWLEDARQHSNSNMVIMLIGNKSDLDSRREVKKEEGEAFAREHGLVFMETSARTAANVEEAFINTAKEIYEKIQEGVFDINN 336 2R:1731127-2080000 1 NULL:1983390 P38555 75 187 1 1 0 2598791 82763 82616 1 0 0 0 121 partof GAAYCQFMDMLFPNSVPVKRVKFRTNLEHEYIQNFKILQAGFKKMSVDK 147 2R:1731127-2080000 1 NULL:1983392 P40013 32 80 1 1 0 2598793 138299 137936 1 0 0 0 516 partof IKKFEIYRWNPDNAGEKPYMQTYEVDLRECGPMVLDALIKIKNEMDPTLTFRRSCREGICGSCAMNIGGTNTLACISKIDINTSKSLKVYPLPHMYVVRDLVPDMNNFYEQYRNIQPWLQR 363 2R:1731127-2080000 1 NULL:1983394 P21801 32 153 1 1 0 138697 138376 1 0 0 0 456 partof KGKAQYLQSVEDRSKLDGLYECILCACCSTSCPSYWWNAEKYLGPAVLMQAYRWIIDSRDENSAERLNKLKDPFSVYRCHTIMNCTRTCPKGLNPGRAIAEIKKLLS 321 2R:1731127-2080000 1 NULL:1983395 P21801 157 264 1 1 0 2598797 253502 253253 1 0 0 0 135 partof DIGANLTDPMFQGCYGGTQKHEPDLHIVLERAWQQGLQKVIVTAGCLKDVDEALELASKDGKLTFRMFPLQIVL*IG-SPHCTS 249 2R:1731127-2080000 1 NULL:1983397 P34220 39 119 1 1 0 253938 253653 1 0 0 0 186 partof ERIYTTVGTHPTRCEEFVPDPEGYYDQLRSRIKANRTKVRAVGECGLDYDRLHFCAQETQRLYFEKQLDLAA-EFKL---PLFLHMRNAAEDFMGILER 285 2R:1731127-2080000 1 NULL:1983398 P34220 144 240 1 1 0 254277 253971 1 0 0 0 212 partof VVHSFTGTLEEAQRILAFG-GLYIGFNGCSLKTDENAEVVRKLPNDRIMLETDCPWCGIRPSHAGHKHVTT-------KFP---TVKKK---EKWTAESL--IDGRCEPCQIRYSLLI 306 2R:1731127-2080000 1 NULL:1983399 P34220 274 392 1 1 0 2604561 5309 4856 1 0 0 0 431 partof GRMIFELFADTVPRTAENFRQFCTG-----EYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGP-NNKPKLPVTISQCG 453 2R:1731127-2080000 -1 NULL:1988194 P53691 17 173 1 1 0 2604563 5315 4850 1 0 0 0 416 partof EIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 465 2R:1731127-2080000 -1 NULL:1988196 P25719 33 182 1 1 0 2604565 5318 4850 1 0 0 0 448 partof QEIGRMIFELFADTVPRTAENFRQFCTGEYRPDGVPIGYKGASFHRVIKDFMIQGGDFVQGDGTGVTSIYGNTFGDENFTLKHDSPGLLSMANSGKETNGCQFFITCAKCNFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVTISQCGQM 468 2R:1731127-2080000 -1 NULL:1988198 P14832 11 161 1 1 0 2604567 88519 87685 1 0 0 0 429 partof LNNGREMPTLGLGTWKSFE--SDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHHDPALVERACRLSLSNLGLEYVDLYLMHMPVG-QKFHNDSNVHG-----------TLELTDVDYLDTWREMEKL-VDLG--LTRSIGLSNFNAAQTERVLANCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDDVAGMEQY 834 2R:1731127-2080000 -1 NULL:1988200 P38115 26 312 1 1 0 2604569 88525 87706 1 0 0 0 443 partof IRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGI-HHDPALVERACRLSLSNLGLEYVDLYLMHMP--VGQKFHNDSNV-------HGT--LELTDVDYLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLANC--RIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDD 819 2R:1731127-2080000 -1 NULL:1988202 P14065 11 284 1 1 0 2604571 88546 87664 1 0 0 0 490 partof MTNLAPTIRLNNGREMPTLGLGTWKSFESDAYHSTRHALDVGYRHLDTAFVYENEAEVGQAISEKIAEGVVTREEVFVTTKLGGIHH-DPALVERACRLSLSNLGLEYVDLYLMHMPVGQKFHN--DSNVH--GTLE--LTDVD-----YLDTWREMEKLVDLGLTRSIGLSNFNAAQTERVLA--NCRIRPVVNQVECHPGFQQRQLREHAKRHGLVICAYCPLARPQPARQWPPFLYDEHAQNLAKKYGRTTAQICLRYLVQLGVVPLPKSSNKARIEENFRVFDFELSPDD---VAGMEQYHTGQRTV 882 2R:1731127-2080000 -1 NULL:1988204 Q12458 4 301 1 1 0 2604573 196659 196443 1 0 0 0 182 partof MSFRVVRSSKFRHVYGQALKREQCYDNIRVSKSSWDSTFCAVNPKFLAIIVESAGGGAFIVLPHNKVSAPPD 216 2R:1731127-2080000 -1 NULL:1988206 Q06440 0 72 1 1 0 194824 194410 1 0 0 0 253 partof VVIWNVGTGEILVHIDSHPDIVYSACFNWDGSKLVTTCKDKKIRIYDPRTAELESEAMCHEGSKATRAIFLRHG-LIFTTGFNRSSERQYSLRAPDALN----EPIVMVELDTSNGVMFPLYDADTNMIYLCGKGDSVIRYFE 414 2R:1731127-2080000 -1 NULL:1988207 Q06440 164 304 1 1 0 194316 194052 1 0 0 0 179 partof INTFQTTEPQRGIGLMPKRGCDVTTCEVAKFYRMNNNGLCQVISMTVPRKSDLFQEDLYPDTLAEDAAITAEEWIDGKDAD-PITFSLK 264 2R:1731127-2080000 -1 NULL:1988208 Q06440 312 401 1 1 0 2604577 312246 311901 1 0 0 0 174 partof FTLEMLDVVQKVLRCRNH--YEVLRISHHATYSEVKRAYHKLALRLHPDKNKSPGAEQAFRRISEAADCLTDCQKRIEYNIATAVGDCHDQDPSQYKDYRGESEFN-EANGNDLGAAF 345 2R:1731127-2080000 -1 NULL:1988210 P48353 2 115 1 1 0 chado-1.23/soi/SOI/Adapter.pm000644 000765 000024 00000126627 11256707645 015767 0ustar00cainstaff000000 000000 package SOI::Adapter; =head1 NAME SOI::Adapter =head1 SYNOPSIS =head1 USAGE my $ad = SOI::Adapter->new('Pg:chadodb@host'); OR my $ad = SOI::Adapter->new; $ad->dbh($dbh); OR my $ad = SOI::Adapter->get_adapter('Pg:chado@host' || $dbh); =head1 FEEDBACK Email sshu@fruitfly.org =cut use DBI; use Exporter; use SOI::Feature; use strict; use Carp; use base qw(Exporter); =head1 FUNCTIONS =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; my $dbh = $self->get_handle(@_); $self->dbh($dbh); return $self; } sub dbh { my $self = shift; if (@_) { $self->{dbh} = shift; } return $self->{dbh}; } =head2 get_adapter Usage - my $ad = SOI::Adapter->get_adapter("Pg:chadodbname\@host"); Usage - my $ad = SOI::Adapter->get_adapter($dbh); Returns - SOI::Adapter object Args - db, dbh Descr - another way to get this adapter obj with either db or dbh =cut sub get_adapter { my $class = shift; my $dbn = shift; my $dbh = $dbn; $dbh = $class->get_handle($dbn) unless (ref($dbh)); $class->dbh($dbh); return $class; } #ok, give up, want to know sequence ontology cv name sub SO_cv_name { my $self = shift; unless ($self->{SO_cv_name}) { my $so = shift || $ENV{SO_CV_NAME} || 'so'; my $hl = $self->_select_hashlist("select cv_id from cv where name = '$so'"); unless (@{$hl || []}) { confess("Invalid SO cv name: $so, which could be set via this adapter method: SO_cv_name or env SO_CV_NAME"); } $self->{SO_cv_name} = $so; } return $self->{SO_cv_name}; } sub get_feature { return shift @{shift->get_features(@_) || []}; } *get_f = \&get_feature; =head2 get_features Usage - my $features = $ad->get_features({range=>{src=>'3L',fmin=>10000,fmax=>20000}}) Returns - SOI::Feature object list Args - constraint in the form of hash ref, optional options in the form of hash ref valid constraint key: range, src/src_seq, value is a single value or hash ref (range) valid options key: type, values is a single SO type or an array ref of SO types default to [qw(gene transposable_element remark)] source_origin_feature_type, default to chromosome_arm. This is critical option when getting golden_path_region features in the range since your feature types is a feature that does not have src seq (most top level feature in a genome). This is true for getting any feature that is second level to most top feature in the genome (see soi tree, read readme for this) noauxillaries, not to get feature properties, dbxrefs, or ontology terms default 0 Description - get is_analysis false features and their children as a Feature tree =cut sub get_features { my $self = shift; my $constr = shift; my $opts = shift || {}; my $typelist = $opts->{type} || $opts->{types} || $opts->{feature_types} || [qw(gene transposable_element remark)]; my $f_src_origin_type = $opts->{source_origin_feature_type} || 'chromosome_arm'; unless (ref($typelist) eq 'ARRAY') { $typelist = [$typelist]; } my $tlist = join(",",map{sql_q($_)}@$typelist); my $where = $self->_get_where($constr, $opts); my $first_add_w = $where; my $fl_cols = join(", ",map{"fl.$_"}($self->_loc_attr)); my $special_cols = qq(src.uniquename as src_seq, $fl_cols); my $sp_from = qq( INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) ); #no src for chromosome_arm if (grep {$_ eq $f_src_origin_type}@$typelist) { $special_cols = qq(null as src_seq, null as srcfeature_id, null as fmin, null as fmax, null as strand); $special_cols .= ",".join (",", map{"null as $_"} grep{$_ ne 'srcfeature_id' && $_ ne 'fmin' && $_ ne 'fmax' && $_ ne 'strand'} ($self->_loc_attr)); my $opts2 = $opts; $opts2->{src_col} = 'f.uniquename'; $opts2->{chromosome_arm} = 1; $first_add_w = $self->_get_where($constr, $opts2); $sp_from = ""; } $first_add_w = " AND $first_add_w" if ($first_add_w); my $sec_where = $where; if ($sec_where) { $sec_where = " WHERE $sec_where AND f.is_analysis = 'f'"; } else { $sec_where = " WHERE f.is_analysis = 'f'"; } my $soi_children_sql = $self->_soi_children_select($typelist); my $so_cv = $self->SO_cv_name; my $sql = qq( select * FROM ((select f.*, $special_cols, q.name as type, 1 as depth, NULL as relationship_type, NULL as parent_id, 0 as orderrank FROM feature f INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (q.cv_id = cv.cv_id) $sp_from WHERE q.name in ($tlist) and cv.name = '$so_cv' and f.is_analysis = 'f' $first_add_w ) UNION (select f.*, src.uniquename as src_seq, $fl_cols, q.name as type, q.depth, frt.name as relationship_type, fr.object_id as parent_id, fr.rank as orderrank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join ($soi_children_sql) as q ON (f.type_id = q.cvterm_id) $sec_where )) as uf); $sql = sprintf("$sql %s", "order by depth, parent_id, orderrank, rank"); my $lfl; my %node_h = $self->_select_objhash($sql); return unless (scalar(keys %node_h)); #auxillaries can be optional my $opts2 = $opts; $opts2->{types} = $typelist; %node_h = $self->_get_auxillaries($constr, $opts2, \%node_h) unless ($opts->{noauxillaries}); #collect top level foreach my $id (keys %node_h) { my $nodes = $node_h{$id}; foreach my $node (@{$nodes || []}) { unless ($node->hash->{parent_id}) { push @$lfl, $node; } } } undef %node_h; return unless (scalar(@{$lfl || []})); $self->_get_organism($lfl); return $lfl; } *get_locatedfeature_list = \&get_features; *get_locatedfeatures = \&get_features; *get_lf_list = \&get_features; *lget_lf = \&get_features; =head2 get_analysis Usage - my $features = $ad->get_analysis() Returns - SOI::Feature object list Args - optional constraint in the form of hash ref, optional options in the form of hash ref valid constraint key: analysis, program, sourcename/database, value is either single val or arrayref Description - get feature holders (that will hold result feature from the computational analysis) =cut sub get_analysis { my $self = shift; my $constr = shift; my $opts = shift; my ($progs, $dbs) = $self->_get_progs_dbs($constr); my $prog_str = join(",", map{sql_q($_)}@{$progs || []}); my $wheres; push @$wheres, "an.program IN ($prog_str)" if ($prog_str); my $db_str = join(",", map{sql_q($_)}@{$dbs || []}); push @$wheres, "an.sourcename IN ($db_str)" if ($db_str); my $where = join(" AND ", @{$wheres || []}); $where = " WHERE $where" if $where; my $sql = qq(select an.*, t.name as type, ap.value FROM analysis an LEFT join analysisprop ap ON (an.analysis_id = ap.analysis_id) LEFT join cvterm t ON (t.cvterm_id = ap.type_id) $where); my %node_h; my $hl = $self->_select_hashlist($sql); foreach my $h (@{$hl || []}) { my $node = $node_h{$h->{analysis_id}}; my ($t,$v) = ($h->{type},$h->{value}); next if (!$t && $opts->{typed_analysis_only}); delete $h->{type}; delete $h->{value}; unless ($node) { $node = SOI::Feature->new($h); $node->hash->{type} = 'companalysis'; $node_h{$h->{analysis_id}} = $node; } $node->add_property({type=>$t,value=>$v}) if ($t); } return [values %node_h]; } sub _get_progs_dbs { my $self = shift; my $constr = shift; my (@progs, @dbs); if ($constr->{analysis}) { my $an = $constr->{analysis}; $an = [$an] unless (ref($an) eq 'ARRAY'); map { if ($_->isa("SOI::Feature")) { push @progs, $an->hash->{program}; push @progs, $an->hash->{sourcename}; } else { my ($prog, $db) = (split/\:/, $_); push @progs, $prog; push @dbs, $db; } }@{$an} } elsif ($constr->{program}) { my $prog = $constr->{program}; $prog = [$prog] unless (ref($prog) eq 'ARRAY'); map{push @progs, $_}@{$prog}; } my $db = $constr->{sourcename} || $constr->{database} || $constr->{dbname}; if ($db) { $db = [$db] unless (ref($db) eq 'ARRAY'); map{push @dbs, $_}@{$db}; } return (\@progs, \@dbs); } =head2 get_results Usage - my $features = $ad->get_results({range=>{src=>'3L',fmin=>10000,fmax=>20000}}) Returns - SOI::Feature object list Args - constraint in the form of hash ref, optional options in the form of hash ref valid constraint key: range, src/src_seq, value is a single value or hash ref (range) analysis, program, sourcename/database, value is either single val or arrayref valid options key: type, values is a single SO type or an array ref of SO types default to [qw(match mRNA transposable_element)] noresidues, not to get subject seq residues, default 0 (get them) BEWARE: without residues, you will not have subj seq len as $sec_loc->{seq}->{seqlen} Description - get is_analysis true features and their children as a Feature tree =cut sub get_results { my $self = shift; my $constr = shift; my $opts = shift || {}; my $tlist = $opts->{type} || $opts->{types} || $opts->{feature_types} || [qw(match mRNA transposable_element)]; my $tliststr = join(",", map{"'".$_."'"}@$tlist); my ($progs, $dbs) = $self->_get_progs_dbs($constr); my $where; #ok where clause is more complicated for analysi results. #can search query src seq and subj src seq, nor subject seq range yet!!! my $where = "f.is_analysis = 't'"; my $prog_str = join(",", map{sql_q($_)}@{$progs || []}); $where .= " AND an.program IN ($prog_str)" if ($prog_str); my $db_str = join(",", map{sql_q($_)}@{$dbs || []}); $where .= " AND an.sourcename IN ($db_str)" if ($db_str); if ($constr->{range}) { my $range = $constr->{range}; $where .= sprintf(" AND %s", "src.uniquename = ".sql_q($range->{src} || $range->{src_seq})); $where .= sprintf(" AND %s", "fl.fmin <= ".$range->{fmax}); $where .= sprintf(" AND %s", "fl.fmax >= ".$range->{fmin}); $where .= " AND fl.rank = 0"; } elsif ($constr->{src} || $constr->{src_seq}) { my $src = $constr->{src} || $constr->{src_seq}; $where .= sprintf(" AND src.uniquename = %s", sql_q($src)." AND fl.rank = 0"); } elsif ($constr->{subj} || $constr->{subj_seq}) { my $src = $constr->{subj} || $constr->{subj_seq}; $where .= sprintf(" AND src.uniquename = %s", sql_q($src)." AND fl.rank = 1"); } #soi children only my $soi_sql = $self->_soi_children_select($tlist); my $so_cv = $self->SO_cv_name; my $sub_select = qq(select DISTINCT feature_id, name, depth, object_id, rank, relationship_type FROM ((select f.feature_id, q.name, 1 as depth, null as object_id, null as rank, null as relationship_type FROM analysis an INNER join analysisfeature a2f ON (an.analysis_id = a2f.analysis_id) INNER join feature f ON (f.feature_id = a2f.feature_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm q ON (f.type_id = q.cvterm_id) INNER join cv ON (cv.cv_id = q.cv_id) WHERE cv.name = '$so_cv' AND q.name IN ($tliststr) and $where ) UNION (select f.feature_id, q.name, q.depth, fr.object_id, fr.rank as rank, frt.name as relationship_type FROM analysis an INNER join analysisfeature a2f ON (an.analysis_id = a2f.analysis_id) INNER join feature f ON (f.feature_id = a2f.feature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join cvterm frt ON (fr.type_id = frt.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join ($soi_sql) as q ON (f.type_id = q.cvterm_id) WHERE $where )) as uf); my $sql = qq(select f.*, af.*, fl.*, src.uniquename as src_seq, q.name as type, q.depth, q.object_id as parent_id, q.rank as orderrank, q.relationship_type FROM feature f INNER join analysisfeature AS af ON (af.feature_id = f.feature_id) INNER join featureloc fl ON (fl.feature_id = f.feature_id) INNER join feature AS src ON (src.feature_id = fl.srcfeature_id) INNER join ($sub_select) as q ON (f.feature_id = q.feature_id) order by depth, object_id, q.rank, fl.rank ); my %node_h = $self->_select_objhash($sql); my $lfl; # #collect top level # foreach my $id (keys %node_h) { # my $node = $node_h{$id}; # unless ($node->hash->{parent_id}) { # push @$lfl, $node; # } # } my (%parent_h, %sec_loc_h); #resultset (match) does not have entry in featureloc, do special thing here foreach my $id (keys %node_h) { my $nodes = $node_h{$id}; foreach my $node (@{$nodes || []}) { if (!$node->hash->{parent_id}) { $parent_h{$node->id} = $node; }elsif ($node->depth == 2) { #only second level may have subject span!!! map{push @{$sec_loc_h{$_->srcfeature_id}}, $_}@{$node->secondary_nodes || []}; my $parent = $parent_h{$node->parent_id}; unless ($parent) { my $pattr_h = {}; my $t = $node->type eq 'exon' ? 'mRNA' : 'match'; #hack $pattr_h = {feature_id => $node->parent_id, uniquename => $node->parent_id, analysis_id=> $node->hash->{analysis_id}, depth => 1, type => $t}; #only type top level SO type for analysis result? $parent = SOI::Feature->new($pattr_h); $parent_h{$parent->id} = $parent; } $parent->add_node($node); } } } undef %node_h; #get organism (genus, species) as one query my $sub_select2 = qq(select DISTINCT f.feature_id FROM analysis an INNER join analysisfeature a2f ON (an.analysis_id = a2f.analysis_id) INNER join feature f ON (f.feature_id = a2f.feature_id) INNER join feature_relationship fr ON (f.feature_id = fr.subject_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join ($soi_sql) as q ON (f.type_id = q.cvterm_id) WHERE $where AND fl.rank = 0 ); my $sql2 = qq(select DISTINCT src.*, org.genus, org.species, t.name as type, fp.value as description FROM feature f INNER join featureloc fl ON (fl.feature_id = f.feature_id) INNER join feature AS src ON (src.feature_id = fl.srcfeature_id) INNER join organism org ON (src.organism_id = org.organism_id) INNER join cvterm t ON (src.type_id = t.cvterm_id) INNER join featureprop fp ON (src.feature_id = fp.feature_id) INNER join cvterm fpt ON (fp.type_id = fpt.cvterm_id) INNER join ($sub_select2) as qo ON (f.feature_id = qo.feature_id) WHERE fl.rank > 0 AND fpt.name = 'description' ); my $hl = $self->_select_hashlist($sql2) unless ($opts->{noresidues}); foreach my $h (@{$hl || []}) { my $sec_locs = $sec_loc_h{$h->{feature_id}}; map{$_->sseq(SOI::Feature->new($h))}@{$sec_locs || []}; } undef %sec_loc_h; return [values %parent_h]; } =head2 get_features_by_typed_value Usage - my $features = $ad->get_features_by_type_value('gene', 'CG1234', {extend=>5000}) my ($range, $features) = $ad->get_features_by_type_value('gene', 'CG1234', {extend=>500}) Returns - a list of a range value in the form of has ref, e.g. {src=>NAME,fmin=>N1,fmax=>N2} and SOI::Feature object list in the range of this typed feature, Args - SO type, this typed feature ID, optional extending this feature bounds for the range valid options key: all valid option keys in get_features or get_results is_analysis, get is_analysis false features or is_analysis true featurs Description - help function for get_features[get_results]_by_$type =cut sub get_features_by_typed_value { my $self = shift; my $type = shift; my $value = shift; my $opts = shift || {}; my $extend = $opts->{extend} || 0; my $tlist = $opts->{type} || $opts->{feature_types} || $opts->{types}; my $where = "(f.name = '$value' OR f.uniquename = '$value')"; my $method = $opts->{is_analysis} ? 'results' : 'features'; $method = "get_".$method; my $sql = qq( select src.uniquename as src, fl.fmin, fl.fmax FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join cvterm type ON (type.cvterm_id = f.type_id) WHERE type.name = '$type' AND $where ); my $range; if ($type eq 'range') { $range = $value; #range hashref } else { my $hl = $self->_select_hashlist($sql); return unless (@{$hl || []}); my $h = $hl->[0]; $range = { src=>$h->{src},fmin=>$h->{fmin},fmax=>$h->{fmax} }; } if ($extend) { $range->{fmin} -= $extend; $range->{fmax} += $extend; } my $constr = {range=>$range}; if ($opts->{constraint}) { my $cnstr = $opts->{constraint}; map{$constr->{$_}=$cnstr->{$_}}keys %$cnstr; } return ($range, $self->$method($constr, $opts)); } =head2 get_features_by_gene Description - delegate to get_features_by_typed_value =cut sub get_features_by_gene { my $self = shift; my $gene = shift; my $opts = shift || {}; return ($self->get_features_by_typed_value('gene', $gene, $opts)); } =head2 get_features_by_scaffold Description - delegate to get_features_by_typed_value =cut sub get_features_by_scaffold { my $self = shift; my $scf = shift; my $opts = shift; return ($self->get_features_by_typed_value('golden_path_region', $scf, $opts)); } *get_features_by_accession = \&get_features_by_scaffold; =head2 get_features_by_range Description - delegate to get_features_by_typed_value =cut sub get_features_by_range { my $self = shift; my $range = shift; my $opts = shift; if ($range =~ /(\w+)\:(\d+)(\-|\:)(\d+)/) { my $range = {src=>$1,fmin=>$2,fmax=>$4}; return ($self->get_features_by_typed_value('range',$range,$opts)); } } =head2 get_features_by_cytoband Description - similar to get_features_by_typed_value, but use computational analysis result to get the range. one more option key (analysis), default to locator:cytology =cut sub get_features_by_cytoband { my $self = shift; my $band = shift; my $opts = shift || {}; my $analysis = $opts->{analysis} || 'locator:cytology'; my ($prog, $sn) = (split/\:/, $analysis); $band = sprintf("'band-%s-cyto'",$band);#special naming for cytoband in harvard chado!!! my $sql = qq (select f.name, min(cfl.fmin) as fmin, max(cfl.fmax) as fmax, src.uniquename as src FROM feature f INNER join feature_relationship fr ON (f.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join featureloc cfl ON (c.feature_id = cfl.feature_id) INNER join feature src ON (src.feature_id = cfl.srcfeature_id) INNER join analysisfeature af ON (f.feature_id = af.feature_id) INNER join analysis a ON (a.analysis_id = af.analysis_id) WHERE f.name = $band AND cfl.rank = 0 AND a.program = '$prog' AND a.sourcename = '$sn' group by f.name, src); my $hl = $self->_select_hashlist($sql); return unless (@{$hl || []}); my $h = $hl->[0]; my $range = { src=>$h->{src},fmin=>$h->{fmin},fmax=>$h->{fmax} }; return ($range, $self->get_features({range=>$range})); } *get_features_by_band = \&get_features_by_cytoband; =head2 get_results_by_gene Description - delegate to get_features_by_typed_value =cut sub get_results_by_gene { my $self = shift; my $gene = shift; my $opts = shift || {}; $opts->{is_analysis} = 1; return ($self->get_features_by_typed_value('gene', $gene, $opts)); } =head2 get_results_by_scaffold Description - delegate to get_features_by_typed_value =cut sub get_results_by_scaffold { my $self = shift; my $scf = shift; my $opts = shift; $opts->{is_analysis} = 1; return ($self->get_features_by_typed_value('golden_path_region', $scf, $opts)); } =head2 get_results_by_range Description - delegate to get_features_by_typed_value =cut sub get_results_by_range { my $self = shift; my $range = shift; my $opts = shift; $opts->{is_analysis} = 1; if ($range =~ /(\w+)\:(\d+)\-(\d+)/) { my $range = {src=>$1,fmin=>$2,fmax=>$3}; return ($self->get_features_by_typed_value('range',$range,$opts)); } } =head2 get_features_by_template Usage - my $features = $ad->get_features_by_template($templfile, $params_h, $option_h) Returns - SOI::Feature object list Args - template file, parameters hash ref, optional options hash ref parameters - template can has parameter (syntax: f.uniquename = &&gene&&, params_h will have to have {gene=>GENENAME}) or optional parameter (syntax: [AND type = &&type&&]) options - valid key: noauxillaries for not getting properties, dbxref, ont terms and no SQL for them in template Description - see typed_genes.soi under templates dir for general syntax of SOI::Adapter template =cut sub get_features_by_template { my $self = shift; my $templatef = shift; my $args = shift || {}; my $opts = shift || {}; my %sql_h; my $type = ""; my $sql; open(R, "< $templatef") or confess("can not open template file: $templatef"); while () { chomp; next unless ($_); next if ($_ =~ /^--/ || $_ =~ /\#/); my $line = $_; if ($line =~ /^SQL\:/) { $type = 'SQL'; } elsif ($line =~ /^(\w+)\-SQL\:/) { $type = $1; } elsif ($type) { $sql_h{$type} .= " $line"; } } close(R); $sql = $sql_h{'SQL'} or confess("did not find valid sql statement"); sub _translate { my $tsql = shift; my $args1 = shift; foreach my $k (keys %{$args1 || {}}) { my $vs = $args1->{$k}; $vs = [$vs] unless (ref($vs) eq 'ARRAY'); my $v = join(",",map{"'".$_."'"}@{$vs}); $v =~ s/\*/\%/g; $tsql =~ s/\&\&$k\&\&/$v/g; } $tsql =~ s/\[[^\[\]]+\&\&\S+\&\&[^\[\]]*\]//g; $tsql =~ s/\[//g; $tsql =~ s/\]//g; return $tsql; } my %node_h = $self->_select_objhash(_translate($sql, $args)); my $lfl; #collect top level foreach my $id (keys %node_h) { my $nodes = $node_h{$id}; foreach my $node (@{$nodes || []}) { unless ($node->hash->{parent_id}) { push @$lfl, $node; } } } return unless (scalar(@{$lfl || []})); #auxillaries can be optional if (scalar(keys %sql_h) > 1) { my $ont_sql = $sql_h{'ONTOLOGLY'}; $self->_get_ontologies(_translate($ont_sql, $args),\%node_h); my $prop_sql = $sql_h{'PROPERTY'}; $self->_get_properties(_translate($prop_sql, $args), \%node_h); my $dbx_sql = $sql_h{'DBXREF'}; $self->_get_dbxrefs(_translate($dbx_sql, $args), \%node_h); } else { $self->_get_auxillaries4features($lfl) unless ($opts->{noauxillaries}); } undef %node_h; $self->_get_organism($lfl); return $lfl; } sub _get_where { my $self = shift; my $constr = shift; my $opts = shift || {}; my $src_col = $opts->{src_col} || "src.uniquename"; my $fl_tbl = $opts->{featureloc_tbl} || "fl"; my $chr_arm = $opts->{chromosome_arm}; my $where; my $range = $constr->{range}; #constr will be RE-USED by caller, don't delete if ($range) { my ($src, $fmin, $fmax) = ($range->{src}, $range->{fmin}, $range->{fmax}); confess("Invalid range args $src, $fmin, $fmax") if (!$src || ($fmax-$fmin) <=0); $where = "$src_col = '$src' and $fl_tbl.fmin <= $fmax and $fl_tbl.fmax >= $fmin"; $where = "$src_col = '$src' and $fl_tbl.fmin >= $fmin and $fl_tbl.fmax <= $fmax" if ($opts->{within}); $where = "$src_col = '$src'" if ($chr_arm); } elsif ($constr->{src} || $constr->{src_seq}) { my $src = $constr->{src} || $constr->{src_seq}; $where = "$src_col = '$src'"; } elsif ($constr->{subj} || $constr->{subj_seq}) { my $src = $constr->{subj} || $constr->{subj_seq}; $where = "$src_col = '$src'"; } else { #confess("only support range and src seq name query"); warn("get whole genome!!!"); } return $where; } sub _loc_attr { return qw(srcfeature_id fmin fmax strand residue_info phase locgroup rank); } sub _soi_select { my $self = shift; my $tlist = shift || return; $tlist = [$tlist] unless (ref($tlist) eq 'ARRAY'); my $tliststr = join(",",map{sql_q($_)}@$tlist); my $so_cv = $self->SO_cv_name; my $soi = qq ((select c.name, c.cvterm_id, 1 as depth FROM cvterm c, cv WHERE c.cv_id = cv.cv_id and c.name IN ($tliststr) and cv.name = '$so_cv') UNION (select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name in ($tliststr) group by c.name, c.cvterm_id )); return $soi; } sub _soi_children_select { my $self = shift; my $tlist = shift || return; $tlist = [$tlist] unless (ref($tlist) eq 'ARRAY'); my $tliststr = join(",",map{sql_q($_)}@$tlist); my $soi = qq(select c.name, c.cvterm_id, max(pathdistance+1) as depth FROM cvterm c, cvtermpath path, cvterm p, cv WHERE c.cvterm_id = subject_id and p.cvterm_id = object_id and path.cv_id =cv.cv_id and cv.name = 'soi' and p.name in ($tliststr) group by c.name, c.cvterm_id ); return $soi; } sub _get_organism { my $self = shift; my $lfl = shift || return; #get organism; my %id_h = (); map{$id_h{$_->hash->{organism_id}}++}@$lfl; my $hl = $self->_select_hashlist ("select * from organism where organism_id in (".join(",",keys %id_h).")") if (keys %id_h); my %org_h; map{$org_h{$_->{organism_id}} = $_}@{$hl || []}; foreach my $l (@$lfl) { my $o_id = $l->hash->{organism_id}; $l->hash->{genus} = $org_h{$o_id}->{genus}; $l->hash->{species} = $org_h{$o_id}->{species}; } } sub _get_auxillaries { my $self = shift; my $constr = shift; my $opts = shift || {}; my $tlist = $opts->{type} || $opts->{types} || $opts->{feature_types}; my $href = shift; my %node_h = %{$href}; my ($sql, $where); my $soi = $self->_soi_select($tlist); ###########---NOTE----############################## # maybe using is_analysis will make it more speedy?? #################################################### #note: won't get chromosome's auxillary values #need to get is_current flag in feature_dbxref tabe!! #get dbxrefs $sql = qq( select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) INNER join ( $soi ) as q ON (f.type_id = q.cvterm_id) ); $where = $self->_get_where($constr, $opts); $sql = sprintf("$sql WHERE %s", $where) if ($where); $self->_get_dbxrefs($sql, \%node_h); #get properties $sql = qq ( select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) INNER join ( $soi ) as q ON (f.type_id = q.cvterm_id) ); $sql = sprintf("$sql WHERE %s", $where) if ($where); $self->_get_properties($sql, \%node_h); #get synonyms $sql = qq ( select f.feature_id, t.name as type, fs.name as value, fs.synonym_sgml FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_synonym fsym ON (fsym.feature_id = f.feature_id and fsym.is_current = 'f' AND fsym.is_internal = 'f') INNER join synonym fs ON (fs.synonym_id = fsym.synonym_id) INNER join cvterm t ON (t.cvterm_id = fs.type_id) INNER join ( $soi ) as q ON (f.type_id = q.cvterm_id) ); $sql = sprintf("$sql WHERE %s", $where) if ($where); $self->_get_synonyms($sql, \%node_h); #get ontology (GO or any ontology attached to feature $sql = qq( select f.feature_id, font.name, fontx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm font ON (font.cvterm_id = fcvt.cvterm_id) INNER join dbxref fontx ON (font.dbxref_id = fontx.dbxref_id) INNER join db ON (fontx.db_id = db.db_id) INNER join cv ON (font.cv_id = cv.cv_id) INNER join ( $soi ) as q ON (f.type_id = q.cvterm_id) ); $sql = sprintf("$sql WHERE %s", $where) if ($where); #use cvterm.dbxref_id # cvterm_dbxref cvtx ON (font.cvterm_id = cvtx.cvterm_id) # INNER join $self->_get_ontologies($sql, \%node_h); return %node_h; } sub _get_ontologies { my $self = shift; my $sql = shift || return; my $fhref = shift; my %node_h = %{$fhref}; my $hl = $self->_select_hashlist($sql); foreach my $h (@{$hl || []}) { my $nodes = $node_h{$h->{feature_id}}; foreach my $node (@{$nodes || []}) { $node->add_ontology($h); } } } sub _get_properties { my $self = shift; my $sql = shift || return; my $fhref = shift || {}; my %node_h = %{$fhref}; my $hl = $self->_select_hashlist($sql); foreach my $h (@{$hl || []}) { my $nodes = $node_h{$h->{feature_id}}; foreach my $node (@{$nodes}) { $node->add_property($h); } } } sub _get_synonyms { my $self = shift; my $sql = shift || return; my $fhref = shift || {}; my %node_h = %{$fhref}; my $hl = $self->_select_hashlist($sql); foreach my $h (@{$hl || []}) { my $nodes = $node_h{$h->{feature_id}}; foreach my $node (@{$nodes}) { $node->add_synonym($h); } } } sub _get_dbxrefs { my $self = shift; my $sql = shift || return; my $fhref = shift || {}; my %node_h = %{$fhref}; my $hl = $self->_select_hashlist($sql); foreach my $h (@{$hl || []}) { my $nodes = $node_h{$h->{feature_id}}; foreach my $node (@{$nodes || []}) { $node->add_dbxref($h); } } } sub _get_auxillaries4features { my $self = shift; my $lfl = shift; my $opts = shift || {}; my ($sql, $where); #get dbxref: assumption is dbxref on gene level feature my (%top_h, %node_h); #note: same feature_id can have >1 feature obj (e.g. sharing exons) map{$top_h{$_->id}++; push @{$node_h{$_->id}}, $_}@{$lfl || []}; my $f_ids = join(",",(keys %top_h)); $sql = qq(select f.feature_id, xref.accession, db.name as dbname FROM feature f INNER join feature_dbxref fxref ON (f.feature_id = fxref.feature_id) INNER join dbxref xref ON (fxref.dbxref_id = xref.dbxref_id) INNER join db ON (db.db_id = xref.db_id) WHERE f.feature_id IN ($f_ids) ); $self->_get_dbxrefs($sql) if ($f_ids, \%node_h); #get properties: assumption: on gene and transcript level #only add transcript to $node_h!! my %sec_h; map{map{$sec_h{$_->id}++; push @{$node_h{$_->id}}, $_}@{$_->nodes || []}}@{$lfl || []}; my $fp_ids = join(",",(keys %top_h, keys %sec_h)); $sql = qq(select f.feature_id, t.name as type, fp.value, fp.rank FROM feature f INNER join featureprop fp ON (fp.feature_id = f.feature_id) INNER join cvterm t ON (t.cvterm_id = fp.type_id) WHERE f.feature_id IN ($fp_ids) ); $self->_get_properties($sql, \%node_h) if ($fp_ids); #get synonyms: assumption: on gene level $sql = qq(select f.feature_id, t.name as type, fs.name as value, fs.synonym_sgml FROM feature f INNER join feature_synonym fsym ON (fsym.feature_id = f.feature_id AND fsym.is_current = 'f' AND fsym.is_internal = 'f') INNER join synonym fs ON (fs.synonym_id = fsym.synonym_id) INNER join cvterm t ON (t.cvterm_id = fs.type_id) WHERE f.feature_id IN ($f_ids) ); $self->_get_properties($sql, \%node_h) if ($f_ids); #get ontology (GO or any ontology attached to feature): assumption: on gene level $sql = qq( select f.feature_id, font.name, fontx.accession, db.name as dbname, cv.name as cv FROM feature f INNER join feature_cvterm fcvt ON (f.feature_id = fcvt.feature_id) INNER join cvterm font ON (font.cvterm_id = fcvt.cvterm_id) INNER join dbxref fontx ON (font.dbxref_id = fontx.dbxref_id) INNER join db ON (fontx.db_id = db.db_id) INNER join cv ON (font.cv_id = cv.cv_id) WHERE f.feature_id IN ($f_ids) ); #use cvterm.dbxref_id # cvterm_dbxref cvtx ON (font.cvterm_id = cvtx.cvterm_id) # INNER join $self->_get_ontologies($sql, \%node_h) if ($f_ids); return $lfl; } =head2 get_handle gets a DBI handle for a database. also sets up error tracing and logging depending on env variables LOGFILE amd DBI_TRACE_LEVEL and DBI_TRACE_FILE. =cut sub get_handle { my $self = shift; my $database_name = shift || confess("You must specify db name"); my $loc = name2locator($database_name); if ($loc) { $database_name = $loc; } my $dbms = "Pg"; if ($database_name =~ /:/) { ($dbms, $database_name) = split(/:/, $database_name); } $ENV{DBMS} = $dbms; my $dsn = "dbi:$dbms:$database_name"; my $dbn = $database_name; my $host; if ($database_name =~ /\@/) { ($dbn,$host) = split(/\@/, $database_name); $dsn = "dbi:$dbms:database=$dbn:host=$host"; } if ($dsn =~ /^dbi:pg/i) { $dsn =~ s/^dbi:pg/dbi:Pg/; $dsn =~ s/:database/:dbname/; $dsn =~ s/:host/;host/; if ($dsn !~ /:dbname/) { $dsn =~ s/^dbi:Pg:/dbi:Pg:dbname=/; } } if ($ENV{DBI_PROXY}) { $dsn = "DBI:Proxy:$ENV{DBI_PROXY};dsn=$dsn"; } my $opt_user= ''; my $opt_password= ''; my $dbh; eval { $dbh= DBI->connect($dsn,$opt_user,$opt_password) }; if ($@ || !$dbh) { my $err=$@; confess(-text=>"Can't connect to $dsn", -reason=>$err); } if ($dbh->{proxy_client}) { $dbh->{proxy_client}->{maxmessage} = 20000000; } $dbh->{private_database_name} = $database_name; $dbh->{private_dbms} = $dbms; $dbh->{private_dbhost} = $host; eval {$dbh->{AutoCommit} = 1}; $dbh->{private_dsn_str} = $dsn; # default behaviour should be to chop trailing blanks; # this behaviour is preferable as it makes the semantics free # of physical modelling issues # e.g. if we have some code that compares a user supplied string # with a database varchar, this code will break if the varchar # is changed to a char, unless we chop trailing blanks $dbh->{ChopBlanks} = 1; if ($ENV{DBI_TRACE_LEVEL}) { if ($ENV{DBI_TRACE_FILE}) { DBI->trace($ENV{DBI_TRACE_LEVEL}, $ENV{DBI_TRACE_FILE}); } else { DBI->trace($ENV{DBI_TRACE_LEVEL}); } } print STDERR "get_handle: $database_name\n" if ($ENV{DEBUG}); return $dbh; } sub name2locator { my $name = shift; my $loc; if (-f "/data/bioconf/bioresources.conf") { open(F, "/data/bioconf/bioresources.conf") || warn("cant open conf"); while() { chomp; next if /^\#/; s/^\!//; my @f=split(' ', $_); if ($f[0] && $f[0] eq $name && $f[1] eq "rdb") { $loc = $f[2]; last; } } close(F); } return $loc; } =head2 close_handle closes a database connection =cut sub close_handle { my $dbh = shift->dbh; $dbh->disconnect(); print STDERR "close_handle: $dbh->{private_database_name}\n" if ($ENV{SQL_TRACE}); } *disconnect = \&close_handle; sub commit { my $dbh = shift; if (!$ENV{DBMS} || $ENV{DBMS} ne "mysql") { $dbh->commit; print STDERR "commit\n"; } } =head2 set_isolation_level set the isolation level (must be ANSI standard) args: dbh, isolation level exceptions: SQL errors =cut sub set_isolation_level { my $dbh = shift; my $isolation_level = shift; if (!$ENV{DBMS} || $ENV{DBMS} ne "mysql") { my $sth = $dbh->prepare("set transaction isolation level $isolation_level") || confess $dbh->errstr; # if we are not in transaction mode, this # will issue a $sth->execute(); } } =head2 set_handle_readonly args: dbh =cut sub set_handle_readonly { my $dbh = shift; set_isolation_level($dbh, "read uncommitted"); # Use ANSI standard } =head2 set_handle_readwrite args: dbh =cut sub set_handle_readwrite { my $dbh = shift; set_isolation_level($dbh, "read committed"); # Use ANSI standard } sub sql_q { my $string = shift; # escape real quotes by double-quoting $string =~ s/\'/\'\'/g; return "'".$string."'"; } *sql_quote = \&sql_q; sub _select_hashlist { my $self = shift; my $dbh = $self->dbh; my $sql = shift; printf STDERR "SQL: %s\n", $sql if ($ENV{SQL_TRACE}); my $t = time; my $sth = $dbh->prepare($sql); my $hashr; my @hrows; $sth->execute() || confess $dbh->errstr; while ($hashr = $sth->fetchrow_hashref) { if ($hashr) { push @hrows, $hashr; } else { if ($sth->err) { confess($sth->err); } else { $sth->finish; } } } printf STDERR " SQLTime: %d\n", (time - $t) if ($ENV{SQL_TRACE}); return \@hrows; } sub _select_objhash { my $self = shift; my $dbh = $self->dbh; my $sql = shift; my $opts = shift || {}; printf STDERR "SQL: %s\n", $sql if ($ENV{SQL_TRACE}); my $sth = $dbh->prepare($sql); my $h; $sth->execute() || confess $dbh->errstr; my @sec_loc_attr = $self->_loc_attr; my %node_h; my %span_attr_h; while ($h = $sth->fetchrow_hashref) { if ($h) { confess("cycle") if ($h->{feature_id} eq $h->{parent_id}); #same feature_id obj has separate instance when having diff parent_id #need parent_id in obj for xml dump without asking parent my $k = sprintf("%d",$h->{feature_id}); my $nodes = $node_h{$k}; my $node; foreach my $n (@{$nodes || []}) { if ($h->{parent_id} == $n->hash->{parent_id}) { $node = $n; } } unless ($node) { $node = SOI::Feature->new($h); push @{$node_h{$k}}, $node; } #rank indicates secondary loc, another rank(renamed orderrank) for feature order if ($h->{rank}) { my %sec_loc_h; map {$sec_loc_h{$_} = $h->{$_}}('src_seq', @sec_loc_attr); $node->add_secondary_location({%sec_loc_h}); } my $parent = $node_h{$h->{parent_id}}; map{$_->add_node($node)}@{$parent || []}; } else { if ($sth->err) { confess($sth->err); } else { $sth->finish; } } } return %node_h; } 1; chado-1.23/soi/SOI/Feature.pm000644 000765 000024 00000041123 11256707645 015765 0ustar00cainstaff000000 000000 package SOI::Feature; =head1 NAME SOI::Feature =head1 SYNOPSIS =head1 USAGE my $feature = SOI::Feature->new($hashref) =cut =head1 FEEDBACK Email sshu@fruitfly.org =cut =head1 GENERAL DESCRIPTION For building feature tree, each SOI::Feature object has 0..m child SOI::Feature objects =cut =head2 chado feature table column method all chado feature table column names can be called, e.g. $feature->uniquename =cut =head2 non-chado feature table column method id, src/src_seq(=srcfeature.uniquename), nbeg, nend, start, end, symbol(=name), type(=SO type name), hash =cut =head2 coordinate system remapped to interbase 0 system (nbeg, nend) and base 1 system(start, end) from fmin, fmax and strand =cut =head2 multivalued attr/method properties, dbxrefs, and ontologies, all are a list of hash refs, nodes for child features =cut =head2 subject seq adapter by default get subject seq residues and all subject seq data are in $sec_loc->sseq (source seq), which will have subject seq length as $sec_loc->sseq->seqlen, if database has it. secondary_location will have rank, right now FlyBase use loc rank 1 to indicate span is subject =cut =head2 computating method transform, stitch_child_segments, see doc below for each method =cut =head2 GAME xml for apollo the following structure is expected chromosome_arm contig genes their children ... analyses result features their children and all features have to be mapped to contig using transform method and contig feature is made from overlapping segments (golden_path_region) for the specified range =cut =head2 XML formats chaos, soi, GAME. soi is nested structure, start/end tag are SO type, it is between chaos and GAME =cut use Exporter; use strict; use Carp; use SOI::Outputter qw(chaos_xml soi_xml game_xml gff3 fasta); use base qw(Exporter); use vars qw($AUTOLOAD); =head1 FUNCTIONS =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; $self->{hash} = {}; $self->hash(@_); return $self; } sub hash { my $self = shift; if (@_) { my $h = shift; confess("must be a hash ref") unless (ref($h) eq 'HASH'); $self->{hash} = $h; #take care of alias if ($h->{src}) { $h->{src_seq} = $h->{src}; } #do some compu: convert db fmin/fmax to nbeg/nend (directional interbase 0 system) $self->nbeg($h); $self->nend($h); } return $self->{hash}; } sub id { shift->hash->{feature_id}; } sub type { my $self = shift; $self->hash->{type} = shift if (@_); return $self->hash->{type}; } sub name { my $self = shift; $self->hash->{name} = shift if (@_); return $self->hash->{name}; } *symbol =\&name; sub uniquename { my $self = shift; $self->hash->{uniquename} = shift if (@_); return $self->hash->{uniquename} || $self->name; } sub src_seq { my $self = shift; if (@_) { $self->hash->{src_seq} = shift; } return $self->hash->{src_seq}; } *src = \&src_seq; sub nbeg { my $self = shift; if (@_) { my $h = shift; my $nbeg; if (ref($h)) { my $strand = $h->{strand} || 0; $nbeg = ($strand > 0) ? $h->{fmin} : $h->{fmax}; } else { $nbeg = $h; } $self->hash->{nbeg} = $nbeg; } return $self->hash->{nbeg}; } sub nend { my $self = shift; if (@_) { my $h = shift; my $nend; if (ref($h)) { my $strand = $h->{strand} || 0; $nend = ($strand > 0) ? $h->{fmax} : $h->{fmin} } else { $nend = $h; } $self->hash->{nend} = $nend; } return $self->hash->{nend}; } #it is genomic length (readonly), not seqlen sub length { my $self = shift; $self->{length} = shift if (@_); unless ($self->{length}) { if (defined($self->fmin) && defined($self->fmax)) { $self->{length} = $self->fmax - $self->fmin; } elsif (defined($self->nbeg) && defined($self->nend)) { my ($s, $e) = ($self->nbeg, $self->nend); if ($self->strand < 0) { ($s,$e) = ($e, $s); } $self->{length} = $e - $s; } } return $self->{length}; } #read only sub seqlen { my $self = shift; unless ($self->hash->{seqlen}) { $self->hash->{seqlen} = length($self->residues) if ($self->residues); } return $self->hash->{seqlen}; } sub strand { my $self = shift; $self->hash->{strand} = shift if (@_); return $self->hash->{strand}; } sub start { my $self = shift; $self->hash->{start} = shift if (@_); #support game parsing unless (defined($self->hash->{start})) { my $strand = $self->strand; $self->hash->{start} = ($strand > 0) ? $self->nbeg + 1 : $self->nbeg; } return $self->hash->{start}; } sub end { my $self = shift; $self->hash->{end} = shift if (@_); #support game parsing unless (defined($self->hash->{end})) { my $strand = $self->strand || ($self->nend - $self->nbeg); my $end = ($strand > 0) ? $self->nend : $self->nend + 1; $self->hash->{end} = $end; } return $self->hash->{end}; } sub nodes { my $self = shift; if (@_) { my $nodes = shift; unless (ref($nodes) eq 'ARRAY') { $nodes = [$nodes]; } $self->{nodes} = $nodes; } return $self->{nodes}; } sub add_node { my $self = shift; if (@_) { push @{$self->{nodes}}, shift; } } sub synonyms { my $self = shift; if (@_) { my $syn = shift; $syn = [$syn] unless (ref($syn) eq 'ARRAY'); $self->{synonyms} = $syn; } return $self->{synonyms}; } sub add_synonym { my $self = shift; if (@_) { push @{$self->{synonyms}}, shift; } } sub dbxrefs { my $self = shift; if (@_) { my $dbx = shift; $dbx = [$dbx] unless (ref($dbx) eq 'ARRAY'); $self->{dbxrefs} = $dbx; } return $self->{dbxrefs}; } sub add_dbxref { my $self = shift; if (@_) { push @{$self->{dbxrefs}}, shift; } } sub get_property { my $self = shift; my $k = shift; my @val; map{ if ($k eq $_->{type}) { push @val, $_->{value}; } }@{$self->properties || []}; return @val; } sub properties { my $self = shift; if (@_) { my $p = shift; $p = [$p] unless (ref($p) eq 'ARRAY'); $self->{properties} = $p; } return $self->{properties}; } sub add_property { my $self = shift; if (@_) { my $h = shift; unless (ref($h) eq 'HASH') { my $k = $h; $h = {type=>$k, value=>shift}; } push @{$self->{properties}}, $h; } } sub ontologies { my $self = shift; if (@_) { my $ont = shift; $ont = [$ont] unless (ref($ont) eq 'ARRAY'); $self->{ontologies} = $ont; } return $self->{ontologies}; } sub add_ontology { my $self = shift; if (@_) { push @{$self->{ontologies}}, shift; } } sub comments { my $self = shift; if (@_) { my $comments = shift; $comments = [$comments] unless (ref($comments) eq 'ARRAY'); $self->{comments} = $comments; } return $self->{comments}; } sub add_comment { my $self = shift; if (@_) { push @{$self->{comments}}, shift; } } #it has a sseq that is a Feature obj with a chado feature (name,residues,etc, plus SO-type,genus, species) sub secondary_locations { my $self = shift; if (@_) { my $loc = shift; $loc = [$loc] unless (ref($loc) eq 'ARRAY'); $self->{secondary_nodes} = [map{ref($self)->new($_)}@$loc]; } return [map{$_->hash}@{$self->secondary_nodes || []}]; } sub add_secondary_location { my $self = shift; if (@_) { push @{$self->{secondary_nodes}}, ref($self)->new(shift); } } #same as secondary_location but obj, as matter of fact, location stores internally as typeless SOI::Feature without property/dbxref/ontology sub secondary_nodes { my $self = shift; if (@_) { my $nodes = shift; $nodes = [$nodes] unless (ref($nodes) eq 'ARRAY'); $self->{secondary_nodes} = $nodes; } return $self->{secondary_nodes}; } sub add_secondary_node { my $self = shift; if (@_) { my $node = shift; push @{$self->{secondary_nodes}}, $node; } } sub secondary_node { my $nodes = shift->secondary_nodes; return $nodes->[0] if (@{$nodes || []}); } *secondary_loc =\&secondary_node; =head2 set_depth Usage - $feature->set_depth(0) Return - none Args - depth val Description - set depth and its children depth, change depth will change tree structure. mainly for finding intersection (see SOI::IntersectGraph) =cut sub set_depth { my $self = shift; my $d = shift; $self->depth($d); map{$_->set_depth($self->depth+1)}@{$self->nodes || []}; } =head2 transform Usage - $feature->transform($new_contig) Return - none Args - new contig(SOI::Feature) Description - map $feature and its children to $new_contig Prerequisite - both feature and new_contig are located on the same src_seq =cut sub transform { my $self = shift; my $new_f = shift; map{$_->transform($new_f)}@{$self->nodes || []}; $self->_transform($new_f); } sub _transform { my $self = shift; my $new_contig = shift || confess("must pass in Feature as arg"); if ($self->src_seq && $new_contig->name && $self->src_seq eq $new_contig->name) { #already transformed return; } if (!$new_contig->src_seq || !$self->src_seq || $new_contig->src_seq ne $self->src_seq) { #cant transform return; } #don't transform if this feature don't have coord, return unless (defined($self->nbeg)); my $delta = $new_contig->fmin; $self->hash->{src_seq} = $new_contig->uniquename; $self->hash->{srcfeature_id} = $self->src_seq; $self->hash->{fmin} = $self->fmin - $delta; $self->hash->{fmax} = $self->fmax - $delta; #make sure other coords will change as well delete $self->hash->{start}; delete $self->hash->{end}; $self->hash($self->hash); } =head2 stitch_child_segments Usage - my $contig = $arm->stich_child_segments($fmin, $fmax, $options) Returns - SOI::Feature object, and original segments (array ref) Args - arm (SOI::Feature) with overlapping segments (golden_path_region) that cover $fmin and $fmax fmin, fmax: the range of new contig optional options: {name=>'temp:blabla'}, {source_origin_feature_type=>'blabla'} the latter default to chromosome_arm Description - stitch all sequence from overlapping segments and cut to the range (fmin, fmax) Prerequisite - all segments on plus strand and overlap with neighbors =cut sub stitch_child_segments { my $self = shift; my @coords = (shift, shift); my $opts = shift || {}; my ($nbeg, $nend) = @coords; my @nodes = sort{$a->nbeg <=> $b->nbeg}@{$self->nodes || []}; return unless (@nodes); my ($seg_b,$seg_e) = ($nodes[0]->nbeg,$nodes[-1]->nend); unless (defined $nbeg && defined $nend) { ($nbeg, $nend) = ($seg_b,$seg_e); } my $most_top_type = $opts->{source_origin_feature_type} || 'chromosome_arm'; confess("ASSERTION ERROR: cutted segment, top level must be $most_top_type and range must be within range of children\n". "and requested ($nbeg, $nend) is NOT within ($seg_b, $seg_e)") unless ($nbeg >= $seg_b && $nend <= $seg_e && $self->type eq $most_top_type); my $residues = ""; my $last_e = 0; for (my $i = 0; $i < scalar(@nodes) - 1; $i++) { my $n = $nodes[$i]; $residues .= substr($n->residues, 0, $n->seqlen - ($n->nend - $nodes[$i+1]->nbeg)) } $residues .= $nodes[-1]->residues; #tested: stitching worked correctly # my ($arml, $armsl, $armasl) = ($self->seqlen, length($residues),length($self->residues)); # my $same = ($residues eq $self->residues); # printf STDERR "seqlen=%d stitched_reslen=%d actual reslen=%d seq same? %d\n",$arml,$armsl,$armasl, $same; my $offset = ($nbeg-$seg_b); $residues = substr($residues,$offset,($nend - $nbeg)); my $tmp = $opts->{name} || sprintf("%s:%d-%d",$nodes[0]->src_seq,$nbeg,$nend); my $new = SOI::Feature->new; my $nh = {feature_id=>$tmp, name=>$tmp, uniquename=>$tmp, fmin=>$nbeg, fmax=>$nbeg + CORE::length($residues), seqlen=>CORE::length($residues), strand=>1, is_analysis=>0, src_seq=>$nodes[0]->src_seq, srcfeature_id=>$nodes[0]->hash->{srcfeature_id}, residues=>$residues, type=>'contig' }; $new->hash($nh); $self->nodes([$new]); # $new->dbxrefs([]);$new->properties([]); return ([@nodes], $new); } sub _rsetup_coord { my $self = shift; $self->_setup_coord; map{$_->_rsetup_coord}@{$self->nodes || []}; } sub _setup_coord { my $self = shift; if ($self->hash->{start} && $self->hash->{end}) { my ($s, $e) = ($self->start, $self->end); $self->hash->{strand} = $s < $e ? 1 : -1; ($s, $e) = ($e, $s) if ($self->strand < 0); $self->fmin($s-1); $self->fmax($e); } unless (defined $self->nbeg && defined $self->nend) { my $h = $self->hash; $self->nbeg($h); $self->nend($h); } if (defined $self->nbeg && defined $self->nend) { $self->start; $self->end; } foreach my $loc (@{$self->secondary_nodes || []}) { $loc->_setup_coord; } } sub to_chaos_xml { my $self = shift; return if ($self->hash->{is_analysis} && !@{$self->nodes || []}); #detect cycle; my @c_ids = grep{$_->id}@{$self->nodes || []}; confess(sprintf("cycle detected; parent=%s", $self->hash->{name})) if (grep {$self->id eq $_}@c_ids); return chaos_xml($self, @_); } sub to_soi_xml { my $self = shift; #detect cycle; my @c_ids = grep{$_->id}@{$self->nodes || []}; confess(sprintf("cycle detected; parent=%s", $self->hash->{name})) if (grep {$self->id eq $_}@c_ids); $self->_setup_coord; return soi_xml($self, @_); } sub to_game_xml { my $self = shift; #detect cycle; my @c_ids = grep{$_->id}@{$self->nodes || []}; confess(sprintf("cycle detected; parent=%s", $self->hash->{name})) if (grep {$self->id eq $_}@c_ids); return game_xml($self, @_); } sub to_gff { my $self = shift; #detect cycle; my @c_ids = grep{$_->id}@{$self->nodes || []}; confess(sprintf("cycle detected; parent=%s", $self->hash->{name})) if (grep {$self->id eq $_}@c_ids); return gff3($self, @_); } *to_gff3 =\&to_gff; *to_GFF3 =\&to_gff; sub to_fasta { my $self = shift; return fasta($self, @_); } sub _min_attr { my $self = shift; unless ($self->{_min_attr}) { my %att_h; map{$att_h{$_}=1}keys %{$self->hash}; #some of them alread have method that is ok since it is for autoload method (see below) #sseq is diff from src_seq, latter is a name and former is feature obj map{$att_h{$_}=1}qw(type relationship_type depth name uniquename feature_id genus species residues seqlen md5checksum srcfeature_id src_seq sseq fmin fmax strand residue_info phase is_fmin_partial is_fmax_partial rank locgroup organism program database); #add game fields (seqtype: temp holder for sequence type as seq is feature type in GAME parsing) map{$att_h{$_}=1}qw(produces_seq focus seq author date timestamp version description score seqtype); $self->{_min_attr} = [keys %att_h]; } return $self->{_min_attr}; } sub DESTROY {} sub AUTOLOAD { no strict "refs"; my ($self, $newval) = @_; my $field = $AUTOLOAD; $field =~ s/.*://; # strip fully-qualified portion if (grep {$field eq $_}@{$self->_min_attr || []}) { #use autoload to install a method(with closure) #so next time it is called, the method is called instead of autoload for speed *{$field} = sub { my $self = shift; @_ ? $self->hash->{$field} = shift : $self->hash->{$field}; }; &$field(@_); } else { confess("Does not support $field"); } } #sub AUTOLOAD { # my $self = shift; # my $name = $AUTOLOAD; # $name =~ s/.*://; # strip fully-qualified portion # if ($name eq "DESTROY") { # return; # } # if (grep {$name eq $_}@{$self->_min_attr || []}) { # $self->hash->{$name} = shift if (@_); # return $self->hash->{$name}; # } else { # warn("Does not support $name") if ($ENV{DEBUG} || $self->hash->{DEBUGMODE}); # } #} 1; chado-1.23/soi/SOI/FeatureDecor.pm000644 000765 000024 00000033744 11256707645 016754 0ustar00cainstaff000000 000000 package SOI::FeatureDecor; =head1 NAME SOI::FeatureDecor =head1 SYNOPSIS =head1 USAGE =cut use Exporter; use SOI::Feature; use SOI::Visitor; use Bio::SeqFeatureI; use Bio::Graphics; use Carp; use base qw(Exporter SOI::Feature Bio::SeqFeatureI); use vars qw($AUTOLOAD); #@EXPORT_OK = qw(); %EXPORT_TAGS = (all=> [@EXPORT_OK]); use strict; =head1 FUNCTIONS =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; $self->feature(@_); return $self; } sub feature { my $self = shift; my $f = shift; if ($f) { confess("must be SOI::Feature") unless ($f->isa("SOI::Feature")); map{ map{ SOI::Visitor->set_loc($_); $_->_setup_coord; }@{$_->nodes || []}; }grep{$_->type eq 'companalysis'}@{$f->nodes || []}; #$f->_setup_coord; $self->_morph($f); $self->{_feature} = $f; } return $self->{_feature}; } sub _morph { my $self = shift; my $f = shift; my $class = ref($self); bless($f, $class); $self->_morph2($f); map{$self->_morph($_)}@{$f->nodes || []}; return $f; } sub _morph2 { my $self = shift; my $f = shift; my $class = ref($self); map{ my $sec = $_; my $sseq = $sec->sseq; if ($sseq && $sseq->isa("SOI::Feature")) { bless($sseq, $class); } bless($sec, $class); }@{$f->secondary_nodes || []}; } sub make_panel { my $self = shift; my $options = shift; my $feature = $self->feature; confess("no feature set and nothing to make from") unless ($feature); my ($contig) = grep{$_->type =~ /contig/}@{$feature->nodes || []}; unless ($contig) {#not mini-view arm feature $contig = SOI::Feature->new ({name=>'fake',src_seq=>$feature->src_seq,fmin=>$feature->fmin,fmax=>$feature->fmax,strand=>1}); $self->_morph($contig); $feature->transform($contig); } my $line = SOI::Feature->new({src=>$contig->src_seq,fmin=>0,fmax=>$contig->length,strand=>1}); $self->_morph($line); my $len = $line->length; my %keyed_h = (); my $panel = Bio::Graphics::Panel->new ( -offset => $options->{offset} || 0, -length=>$len, -width => $options->{width} || 1000, -pad_left => $options->{pad_left} || 50, -pad_right => $options->{pad_right} || 50, -key_style => $options->{key_style}, ); my @all_trs = (); foreach my $gene (grep{$_->type eq 'gene'}@{$feature->nodes || []}) { my @trs = @{$gene->nodes || []}; #all immediate children of gene push(@all_trs, @trs); } my @tes = (); @all_trs = grep { if ($_->type eq 'transposable_element') { push(@tes, $_); 0; } else { 1; } } @all_trs; unless (@all_trs) {#not mini-view feature? push @all_trs, grep{$_}@{$feature->nodes || []}; } my @analyses = grep{$_->type eq 'companalysis'}@{$feature->nodes || []}; ####################################### TO DO ##################################### # analysis glyph type and color need more work, better default and optionally set # and group analysis by type? ################################################################################### my %an_color = (); my @color_names = (); map { push @color_names, $_ if $_ ne 'yellow' && $_ ne 'steelblue' && $_ ne 'white' && $_ ne 'darkred' && $_ ne 'honeydew' && $_ ne 'red' }$panel->color_names; $an_color{'clonelocator:scaffoldBACs'} = 'honeydew'; $an_color{'clonelocator:BACs'} = 'honeydew'; $an_color{'tilingpath BAC'} = 'magenta'; # 'pink'; #'honeydew'; $an_color{'P Insertion'} = 'darkturquoise'; # 'turquoise'; #'red'; $an_color{'cDNA'} = 'mediumseagreen'; #'green'; $an_color{'Your BLAST hit'} = 'darkred'; $an_color{'Repeat'} = 'purple'; my $track = 0; my $middle_track; foreach my $strand (+1, -1) { my $meth = "unshift_track"; if ($strand == 1) { $meth = "unshift_track"; } $meth = "add_track"; if ($strand == -1) { # Add the scale in the middle using the "arrow" glyph $panel->$meth(arrow => [$line], -bump => 0, -tick=>1);#1->major tick, 2->major + minor ticks $middle_track = $track; $track++; } # draw analyses my $an_height = $options->{analysis_height} || 12; foreach my $analysis (@analyses) { my $ap = $analysis->program . ":" . $analysis->sourcename; my %uniquetypes = map {s/_/ /g;$_=>1}($analysis->get_property("type")); #$ap = join(" ",grep {$_} keys %uniquetypes) || $ap; my $an_type = $ap; my $color = $an_color{$an_type}; ## hard-coded color designations for evidence # blast if (lc($analysis->program) =~ /blastx/) { $color = 'darkorange'; } if (lc($analysis->program) =~ /sptr/) { $color = 'darkorange'; } # cDNA, DGC if (lc($analysis->sourcename) =~ /na_dgc/) { $color = 'mediumseagreen'; } if (lc($analysis->sourcename) =~ /na_cdna/) { $color = 'green'; } if (lc($analysis->sourcename) =~ /na_users/) { $color = 'green'; } if (lc($analysis->database) =~ /na_gb/) { $color = 'green'; } # tiling BACs if (lc($analysis->sourcename) =~ /bac/) { $color = 'lightslategray'; } if (lc($analysis->sourcename) =~ /clone/) { $color = 'lightslategray'; } if (lc($analysis->sourcename) =~ /all_nr/) { $color = 'black'; } # P elements if (lc($analysis->sourcename) =~ /na_pe.dros/) { $color = 'darkturquoise'; } # ESTs if (lc($analysis->database) =~ /est/) { $color = 'mediumaquamarine'; } # gene prediction if (lc($analysis->program) =~ /genscan/) { $color = 'lightskyblue'; } if (lc($analysis->program) =~ /genie/) { $color = 'lightskyblue'; } if (lc($analysis->program) =~ /trnascan/) { $color = 'lightskyblue'; } # affy oligo if (lc($analysis->database) =~ /na_affy_oligo.dros/) { $color = 'crimson'; } if ($options->{colormap}) { my $cmap = $options->{colormap}; my $c = $cmap->{$analysis->program .':'. $analysis->sourcename}; if (!$c) { $c = $cmap->{$analysis->sourcename}; } if (!$c) { $c = $cmap->{$analysis->program}; } if ($c) { $color = $c; } } my @rsets = @{$analysis->nodes || []}; my ($bump, $labelling) = (0, 0); if (defined($options->{bump_analyses})) { $bump = $options->{bump_analyses}; } $labelling = ($an_type =~ /scaffold bac/i) ? 0 : ($options->{label_analyses} || 0); if ($analysis->program eq "assembly" || $analysis->program eq "gulliver") { $bump = 1; $labelling = defined($options->{label_assembly}) ? $options->{label_assembly} : 1; } my @todraw = grep {$_->strand == $strand} @rsets; my $max = $options->{max_results_per_tier}; if (defined($max) && @rsets > $max) { $bump = 0; $an_type .= " (too many results - tier collapsed)"; } if (@todraw) { $panel->$meth([@todraw] =>$self->glyph_type($analysis), -bgcolor => $color, -fillcolor=> $color, -fgcolor => 'black', -bump => $bump, -key => ($keyed_h{$an_type} ? '' : $an_type), -height => $an_height, -label => $labelling ); $keyed_h{$an_type}++; $track++; } } # draw genes: actually transcript my $gene_height = $options->{gene_height} || 10; my @trs = grep {$_->strand == $strand} @all_trs; if (@trs) { $panel->$meth([@trs] =>'transcript', -fillcolor => 'blue', -bgcolor => 'blue', -fgcolor => 'black', -bump => 1, -key => ($keyed_h{annotation} ? '' : 'annotation'), -mark_cds => 1, -height => $gene_height, -label => $options->{label_annotations} || 1, ); $keyed_h{annotation}++; $track++; } if (@tes) { $panel->$meth([grep {$_->strand == $strand} @tes] =>'transcript', -fillcolor => 'red', -bgcolor => 'red', -fgcolor => 'black', -bump => 1, -key => ($keyed_h{te} ? '' : 'transposable element'), -mark_cds => 1, -height => $gene_height, -label => $options->{label_annotations} || 1, ); $keyed_h{te}++; $track++; } # draw overlapping segments my @segs = grep{$_->type eq 'golden_path_scaffold'}@{$feature->nodes || []}; if (@segs) { $panel->$meth([grep {$_->strand == $strand} @segs]=>'arrow', -fillcolor => 'yellow', -bgcolor => 'yellow', -fgcolor => 'black', -bump => 1, -key => ($keyed_h{segment} ? '' : 'segment'), -height => 10, -label => defined($options->{label_segments}) ? $options->{label_segments} : 1, ); $keyed_h{segment}++; $track++; } } # Panel object has no concept of being seperated into # 2 strands; lets do a vertical reverse on the negative strand my @rev = splice(@{$panel->{tracks}}, $middle_track+1); push(@{$panel->{tracks}}, reverse @rev); # imagemap my $map = ""; my @boxes = $panel->boxes; foreach my $box (@boxes) { my $f = shift @$box; my $coords = join(" ", @$box); my $alt_text = scalar(@{$f->secondary_locations || []}) ? $f->secondary_loc->src : $f->name; $alt_text =~ s/[\"\']//g; my $href = $f->{url} || "#"; $map .= qq[ ]; } $panel->{maptext} = $map; return $panel; } sub glyph_type { my $self = shift; my $an = shift; if (grep{lc($an->program) =~ /$_/i}('blastn', 'pinsertion') and !$an->sourcename) { return 'pinsertion'; } elsif (lc($an->program) eq 'blastn' && lc($an->sourcename) eq 'na_pe.dros') { return 'pinsertion'; } elsif (lc($an->program) eq "clonelocator") { return 'arrow'; } elsif ($an->sourcename =~ /(dgc|cdna|est)/i) { return "bdgp_ests"; } else { return 'segments'; } } #conform to Bio::FeatureI or Gadfly API for drawing sub seq_id {return shift->src} sub display_name { my $self = shift; return $self->name || $self->uniquename; } #only for drawing, mixed type and one of them span whole parent range? sub sub_SeqFeature { return grep{$_->type !~ 'protein' && $_->type !~ 'polypeptide' && $_->type !~ /cds/i && $_->type !~ /intron/i }@{shift->nodes || []}; } sub homol_sf { my $self = shift; if (@{$self->secondary_nodes || []}) { #check rank? my $homol = $self->secondary_nodes->[0]; $homol->src_seq(SOI::Feature->new({name=>$homol->src_seq})); return $homol; } } sub start_codon { my $self = shift; my ($sc) = grep{$_->type eq 'start_codon'}@{$self->nodes || []}; unless ($sc) { my ($p)= grep{$_->type =~ /protein/i or $_->type =~ /polypeptdie/}@{$self->nodes || []}; return unless ($p); #no junction in start/stop codon? my $fmin = ($p->strand > 0)?$p->fmin:$p->fmax; $sc = SOI::Feature->new({src_seq=>$p->src_seq,fmin=>$fmin,fmax=>$fmin+3,strand=>$p->strand}); } $sc->_setup_coord; $self->_morph($sc); return $sc; } sub stop_codon { my $self = shift; my ($sc) = grep{$_->type eq 'stop_codon'}@{$self->nodes || []}; unless ($sc) { my ($p)= grep{$_->type =~ /protein/i or $_->type =~ /polypeptdie/}@{$self->nodes || []}; return unless ($p); #no junction in start/stop codon? and protein feature end at stop codon start? my $fmin = ($p->strand > 0)?$p->fmax:$p->fmin; $sc = SOI::Feature->new({src_seq=>$p->src_seq,fmin=>$fmin,fmax=>$fmin+3,strand=>$p->strand}); } $sc->_setup_coord; $self->_morph($sc); return $sc; } sub stop {shift->end} 1; chado-1.23/soi/SOI/GAMEHandler.pm000644 000765 000024 00000026733 11256707645 016413 0ustar00cainstaff000000 000000 package SOI::GAMEHandler; =head1 NAME SOI::GAMEHandler =head1 SYNOPSIS perlSAX handler to parse GAME xml (WARNING: very alpha software!) =head1 USAGE =begin my $handler = SOI::SOIHandler->new([qw(your feature type list here)]); my $parser = XML::Parser::PerlSAX->new(Handler=>$handler); $parser->parse(Source => { SystemId =>$soixml_file}); my $feature = $handler->feature; #get SOI::Feature obj (feature tree) from soi xml =end =cut =head1 FEEDBACK Email sshu@fruitfly.org =cut use strict; use SOI::Feature; use FileHandle; use Carp; =head1 FUNCTIONS =cut sub new { my $class = shift; my $self = {}; bless $self, $class; #element tag becomes feature type, but overwritten by its type attr if any my $types = shift || [qw(game map_position seq annotation feature_set feature_span result_set result_span computational_analysis)]; #alias: synonym and output is also property, aspect is ontology my $mv_types = shift || [qw(property output dbxref ontology aspect comment)]; my $single2prop = shift || [qw(synonym)]; $types = [$types] unless (ref($types) eq 'ARRAY'); $mv_types = [$mv_types] unless (ref($mv_types) eq 'ARRAY'); $single2prop = [$single2prop] unless (ref($single2prop) eq 'ARRAY'); $self->{feature_types} = $types; $self->{multi_types} = $mv_types; $self->{single_types} = $single2prop; return $self; } =head2 start_element Called directly by SAX Parser. Do NOT call this directly. Adds element name string to stack. =cut sub start_element { my ($self, $element) = @_; my $name = $element->{Name}; my $feature = $self->_curr_feature; my $attrs = $element->{Attributes}; if (grep{$name eq $_}@{$self->{feature_types} || []}) { $feature = SOI::Feature->new({type=>$element->{Name}}); map{ my $m = $self->_field($_); $m = 'seqtype' if ($feature->type eq 'seq' && $_ eq 'type'); $m = 'seqlen' if ($feature->type eq 'seq' && $_ eq 'length'); $feature->$m($attrs->{$_}); }keys %{$attrs || {}}; $feature->depth(scalar(@{$self->{feature_stack} || []})); push @{$self->{feature_stack}}, $feature; push @{$self->{level_stack}}, "feature"; } elsif (grep{$name eq $_}@{$self->{multi_types} || []}) { push @{$self->{level_stack}}, $name; $self->start_multi($element); map{ $self->{hash}->{$_} = $attrs->{$_}; }keys %{$attrs || {}} } elsif (grep{$name eq $_}@{$self->{single_types} || []}) { push @{$self->{level_stack}}, $name; $self->start_single($element); } elsif (grep{$name eq $_}qw(seq_relationship span)) { #special handling if ($name eq 'span') { #simply contain start/end } else { my $type = $attrs->{type}; $feature = SOI::Feature->new(); push @{$self->{feature_stack}}, $feature; push @{$self->{level_stack}}, "feature"; $feature->src_seq($attrs->{seq}); $feature->hash->{seq_relationship} = $type; } } elsif (grep{$name eq $_}qw(gene)) { } else { undef $self->{cur_e_char}; if (keys %{$attrs || {}}) { my $level = $self->{level_stack}->[-1]; if ($level eq 'feature') { my $f = $self->_curr_feature; map{ my $m = $self->_field($_); $f->$m($attrs->{$_}); }keys %{$attrs || {}} } elsif (grep{$level eq $_}@{$self->{multi_types} || []}) { map{ $self->{hash}->{$_} = $attrs->{$_}; }keys %{$attrs || {}} } } } return 1; } =head2 end_element Called directly by SAX Parser. Do NOT call this directly. Removes element name string from stack. =cut sub end_element { my ($self, $element) = @_; my $name = $element->{Name}; my $feature = $self->_curr_feature; my $level = $self->{level_stack}->[-1]; if (grep{$name eq $_}@{$self->{feature_types} || []}) { pop @{$self->{level_stack}}; unless (@{$self->{feature_stack}} == 1) { my $child = pop @{$self->{feature_stack}}; my $parent = $self->_curr_feature; if ($child->type eq 'seq') { $self->{seq_hash}->{$child->uniquename || $child->name} = $child; } else { $parent->add_node($child); } } } elsif (grep{$name eq $_}@{$self->{multi_types} || []}) { pop @{$self->{level_stack}}; my $el_name = "end_multi"; $self->$el_name($element); } elsif (grep{$name eq $_}@{$self->{single_types} || []}) { pop @{$self->{level_stack}}; $self->end_single($element); } elsif (grep{$name eq $_}qw(seq_relationship span)) { #special handling if ($name eq 'span') { #simply contain start/end } else { pop @{$self->{level_stack}}; $feature = pop @{$self->{feature_stack}}; my $main_f = $self->_curr_feature; if ($feature->hash->{seq_relationship} eq 'subject') { $main_f->add_secondary_node($feature); delete $feature->hash->{seq_relationship}; } else { #query #$feature->_setup_coord; map{ my $m = $_; $main_f->$m($feature->$m) }keys %{$feature->hash}; delete $main_f->hash->{seq_relationship}; } } } elsif (grep{$name eq $_}qw(gene)) { } else { my $e_val = $self->{cur_e_char}; if ($e_val) { $e_val =~ s/^\s*//g; $e_val =~ s/\s*$//g; } if ($level eq 'feature') { my $m = $self->_field($name); $feature->$m($e_val); } else { $self->{hash}->{$name} = $e_val; } } return 1; } #multi to auxillary: property dbxref ontology comment sub start_multi { my ($self, $element) = @_; $self->{hash} = {}; } sub end_multi { my ($self, $element) = @_; my $name = $element->{Name}; $name =~ tr/A-Z/a-z/; my $feature = $self->_curr_feature; #alias tags!!! if ($name eq 'aspect') { $name = 'ontology'; } elsif ($name eq 'output') { $name = 'property'; } my $method = "add_$name"; confess("unsupported auxillary: $name") unless ($feature->can($method)); my $hs = $self->{hash}; #turn array of hash into one hash my $h; map{ my $k = $self->_field($_); $h->{$k}=$hs->{$_}; }keys %{$hs || {}}; $feature->$method($h); } #single to property (tag=type, val=val) sub start_single { my ($self, $element) = @_; undef $self->{cur_e_char}; #$self->{hash} = {}; } sub end_single { my ($self, $element) = @_; my $name = $element->{Name}; my $e_val = $self->{cur_e_char} || ""; $e_val =~ s/^\s*//g; $e_val =~ s/\s*$//g; $self->_curr_feature->add_property({type=>$name, value=>$e_val}); } sub start_document { my $self = shift; undef $self->{feature_stack}; undef $self->{level_stack}; } =head2 end_element Called directly by SAX Parser. Do NOT call this directly. The last method called by the Sax Parser. This returns the data in $self->data. =cut sub end_document { my $self = shift; } =head2 characters Called directly by SAX Parser. Do NOT call this directly. Calls method with the name of the current element with text as the first argument. =cut sub characters { my ($self, $characters) = @_; my $data = $characters->{Data}; return $self->{cur_e_char} .= $data; } =head2 feature usage: my $feature = $self->feature; returns: top node feature/apollo mini view feature =cut sub feature { my $self = shift; return unless (@{$self->{feature_stack} || []}); my $feature = $self->_curr_feature; $feature->type('chromosome_arm'); delete $feature->hash->{version}; my (@all, $contig); foreach my $sf (@{$feature->nodes || []}) { if ($sf->type eq 'tile') { $sf->type('contig'); $contig = $sf; } elsif ($sf->type eq 'gene') { $sf->_rsetup_coord; #do we have translation/polypeptide? foreach my $tr (@{$sf->nodes || []}) { my $seq = $self->{seq_hash}->{$tr->produces_seq}; delete $tr->hash->{produces_seq}; if ($seq) { my $res = $seq->residues; $res =~ s/\n//g; $res =~ s/\s+//g; $tr->residues($res); $tr->seqlen($seq->seqlen); $tr->md5checksum($seq->md5checksum); } my @prots = grep{$_->type eq 'translate offset'}@{$tr->nodes || []}; #only one foreach my $p (@prots) { my $seq = $self->{seq_hash}->{$p->produces_seq}; $p->uniquename($p->produces_seq); $p->type('protein'); delete $p->hash->{produces_seq}; if ($seq) { my $res = $seq->residues; my $res = $seq->residues; $res =~ s/\n//g; $res =~ s/\s+//g; $p->residues($res); $p->seqlen($seq->seqlen); $p->md5checksum($seq->md5checksum); } #$p->to_soi_xml; } } push @all, $sf; #$sf->to_soi_xml; } elsif ($sf->type eq 'computational_analysis') { $sf->_rsetup_coord; foreach my $rset (@{$sf->nodes || []}) { foreach my $span (@{$rset->nodes || []}) { my $seq = $span->secondary_node?$self->{seq_hash}->{$span->secondary_node->src_seq}:""; if ($seq) { my $res = $seq->residues; $res =~ s/\n//g; $res =~ s/\s+//g; $seq->residues($res); $span->secondary_node->sseq($seq); } } } push @all, $sf; #$sf->to_soi_xml; } } unless ($contig) { #fishing for contig (arm dump) my ($arm) = grep{$_->hash->{focus} eq 'true'}values %{$self->{seq_hash} || {}}; if ($arm) { $contig = SOI::Feature->new({type=>'contig'}); $contig->name($arm->name); $contig->src_seq($arm->name); $contig->seqlen($arm->seqlen); map{$contig->$_($arm->$_)}qw(length version md5checksum); } } my $seq = $self->{seq_hash}->{$contig->hash->{seq}}; if ($seq) { my $res = $seq->residues; $res =~ s/\n//g; $res =~ s/\s+//g; $contig->residues($res); $contig->name($seq->name); $contig->length($seq->length); } $feature->name($contig->src_seq); delete $contig->hash->{seq}; $feature->nodes([$contig, @all]); return $feature; } sub _curr_feature { my $self = shift; return unless (@{$self->{feature_stack} || []}); return $self->{feature_stack}->[-1]; } #field transform sub _field { my ($self, $field) = @_; my %map_h = (id => 'uniquename', arm => 'src_seq', alignment => 'residue_info', xref_db => 'dbname', db_xref_id => 'accession', ); return $map_h{$field} || $field; } 1; chado-1.23/soi/SOI/GFF3Parser.pm000644 000765 000024 00000014417 11256707645 016242 0ustar00cainstaff000000 000000 package SOI::GFF3Parser; =head1 NAME SOI::GFF3Parser =head1 SYNOPSIS perlSAX handler to parse soi xml =head1 USAGE =begin my $parser = SOI::GFF3Parser->new([qw(property_type_map2method)]); $parser->parse($yourGFF3File); my $feature = $parser->feature; #get SOI::Feature obj (feature tree) from soi xml =end =cut =head1 FEEDBACK Email sshu@fruitfly.org =cut use strict; use SOI::Feature; use FileHandle; use Carp; =head1 FUNCTIONS =cut sub new { my $class = shift; my $self = {}; bless $self, $class; my $file = shift; $self->file($file); my $types = shift; if ($types) { $types = [$types] unless (ref($types) eq 'ARRAY'); $self->{method_types} = $types; } return $self; } sub method_types { my $self = shift; if (@_) { my $types = shift; $types = [$types] unless (ref($types) eq 'ARRAY'); $self->{method_types} = $types; } return $self->{method_types}; } sub file { my $self = shift; my $file = shift; if ($file) { my $fh = FileHandle->new("<$file") || confess("Failed to open file $file: $!"); $self->fh($fh); $self->{file} = $file; undef $self->{top_features}; undef $self->{feature_h}; } return $self->{file}; } sub fh { my $self = shift; $self->{fh} = shift if (@_); return $self->{fh}; } sub parse { my $self = shift; my $f = shift; $self->file($f) if ($f); my $tops = $self->fetch_object(); #no object id, return top objects map{$_->set_depth(0)}@{$tops || []}; # return $tops; } #hard to implement get_next_object? sub fetch_object { my $self = shift; my $oid = shift; my $fh = $self->fh; return $self->_parse($fh, $oid); } sub _last_meta { my $self = shift; $self->{last_meta} = shift if (@_); return $self->{last_meta} || ""; } sub _parse { my $self = shift; my $fh = shift; my $oid = shift; #my (%seq_h, %feat_h, @tops); my @predefined = qw(ID Name Alias Parent Target Gap Note Dbxref Ontology_term); while (my $line = <$fh>) { chomp $line; next unless ($line); if ($line =~ /^\#\#/) { my $last_meta = $self->_last_meta || ""; $self->_last_meta($line); if ($line =~ /^\#{3}$/) { if ($last_meta =~ /^\#\#FASTA/) { #end of fasta seq } elsif ($oid) { last; #end of feature for the oid requested (### better be at right level) } } #rest meta NOT IMPLEMENTED next; } if ($self->_last_meta =~ /^\#\#FASTA/) { #get residue next; } #only able to handle tab-delimited file for now my @a = split/\t/, $line; map{undef $_ if ($_ eq '.')}@a; my $col9 = pop @a; my ($src_seq,$source,$type,$start,$end,$score,$strand,$phase) = @a; my (%magic_h, @props); map { my ($tag, $val) = split/\=/, $_; if (grep{$tag eq $_}@predefined) { my @v = (split/[,+]/, $val); $magic_h{$tag} = \@v; } else { push @props, {type=>$tag,value=>$val}; } }(split/\;\s*/, $col9); my ($id) = @{$magic_h{ID} || []}; confess("A feature must have ID and type") unless ($id && $type); my ($name) = @{$magic_h{Name} || []}; my $parent = $magic_h{Parent}; my $target = $magic_h{Target}; my ($gap) = @{$magic_h{Ga} || []}; push @props, {type=>'cigar',values=>$gap} if ($gap); my ($note) = @{$magic_h{Note} || []}; push @props, {type=>'note', value=>$note} if ($note); my $feature = SOI::Feature->new({uniquename=>$id,name=>$name,type=>$type}); confess("Feature ID: $id is duplicated") if (exists $self->{feature_h}->{$id}); $self->{feature_h}->{$id} = $feature; if ($parent) { map { my $p = $self->{feature_h}->{$_}; #parent must appear first!!! $p->add_node($feature); }@{$parent || []}; } else { push @{$self->{top_features}}, $feature; } if ($start && $end) { confess("Locatable feature must have src and coord including strand: $line") unless ($src_seq && $strand); my ($fmin, $fmax) = ($start - 1, $end); $feature->src_seq($src_seq); $feature->fmin($fmin); $feature->fmax($fmax); $feature->strand($strand); } if ($target) { my $sstrand = $target->[3] || 1; $feature->add_secondary_node(SOI::Feature->new({src_seq=>$target->[0], fmin=>$target->[1]-1, fmax=>$target->[2], strand=>$sstrand})); } &_set_synonyms($feature, $magic_h{Alias}); &_set_dbxrefs($feature, $magic_h{Dbxref}); &_set_ontology_terms($feature, $magic_h{Ontology_term}); $self->setup_properties($feature, \@props); } if ($oid) { return $self->{feature_h}->{$oid}; } return $self->{top_features}; } sub _set_synonyms { my $feature = shift; my $syns = shift || return; ##?? } sub _set_dbxrefs { my $feature = shift; my $dbxrefs = shift || return; my @a; map{my ($db, $acc) = (split/\:/);push @a, {dbname=>$db,accession=>$acc}}@$dbxrefs; $feature->dbxrefs(\@a); } sub _set_ontology_terms { my $feature = shift; my $terms = shift || return; my @a; map{my ($db, $acc) = (split/\:/);push @a, {dbname=>$db,accession=>$acc}}@$terms; $feature->ontologies(\@a); } sub setup_properties { my $self = shift; my $feature = shift; my $props = shift; my (@a, @m); foreach my $p (@{$props || []}) { if (grep{$p->{type} eq $_}@{$self->{method_types} || []}) { push @m, $p; } else { push @a, $p; } } $feature->properties(\@a) if (@a); foreach my $m (@m) { $feature->hash->{$m->{type}} = $m->{value}; } } =head2 feature usage: my $feature = $self->feature; returns: top node feature =cut sub feature { my $self = shift; return unless (@{$self->{top_features} || []}); return $self->{top_features}->[0]; } sub features { my $self = shift; return $self->{top_features}; } 1; chado-1.23/soi/SOI/IntersectGraph.pm000644 000765 000024 00000052113 11256707645 017315 0ustar00cainstaff000000 000000 package SOI::IntersectGraph; =head1 NAME SOI::IntersectGraph =head1 DESCRIPTION stores/finds the intersection graph between two sets of features. the algorithm (smaller/bigger (which is a Set) implies the number of elements): foreach I in smaller(Set1, Set2): foreach J in Set(J.range ov w I.range in bigger(Set1, Set2)): if ov(I, J): add to ov list it has O(N x k) instead of O(N^2). set i: smaller set, set j: bigger set. Both sets are sorted on fmin. J is from a set of item in set j and J index is between smallest index of set j whose range ov with the previous item of set i and that of set j whose range ov with current item of set i. for this to work efficiently, location intersection comparing node parent must have fmin and fmax and src_seq. because chado [early FlyBase version] did not have resultset located, you may have to manufacture its location: src_seq, fmin, and fmax from its spans/match_part (see Visitor module) soi tree has undeterministic depth and mixed types at one level, to find intersections, feature type must be specified (see property below). If no depth specified, top node (depth 0) is assumed. furthermore, 2 sets depth has the same sematics(same level has similar types of features): transcript vs transcript(resultset), NOT transcript vs exon(span/match_part), NOR translation vs exon although this is no enforced. API user should be clear on what is compared to when passing in 2 sets and options (hashref) as property (see below) to find intersection =cut =head2 property =over property can be set before call find_intersects or passed in as hashref (3rd arg) when call find_intersects =item query_type (required) feature type at the depth specified of query side (first arg in find_intersects) =item subject_type (required) feature type at the depth specified of subject side (2nd arg in find_intersects) NOTE: theoretically, mixed types at the same depth could work by passing in array ref of types =item depth feature depth for intersecting determination, without specifying depth, it will zigzag to go to right level (controlled by query_type, subject_type) to do comparison. =item query_depth, subject_depth feature depth for comparison can be different, but comparing feature at the same depth is much faster as it does not need to zigzag instead of diving into both graphs at the same time =item overlap min percentage overlaping (span length) to be intersecting =item overlap_length min overlap length to be intersecting per span =item attach_ov_coords add ov_fmin, ov_fmax as feature properties to subject feature =item same_strand on the same strand to be intersecting =item threshold min percentage overlaping (seq length) to be intersecting =item lt_threshold max percentage overlapping (seq length) to be intersecting, this is for getting set of not threshold WARNING: when specify threshold or lt_threshold, both sets of features have to be flatten ones like transcript or resultset (match). In other words, children of feature must be component_part_of, eg for gene, it may over-count overlaps since a gene may have >1 overlapping transcripts. =item query_compare default to primary location, only valid option is secondary_location =item subject_compare default to primary location, only valid option is secondary_location =back =head1 CREDITS Interface is similar to Gadfly IntersectionGraph.pm (Chris Mungall), but implementation is different =cut =head1 FEEDBACK Email sshu@fruitfly.org =cut use strict; use Carp; use Exporter; use SOI::Feature; use base qw(Exporter); #use vars qw($AUTOLOAD); =head1 FUNCTIONS =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; $self->_initialize; return $self; } # automatically called by new() sub _initialize { my $self = shift; $self->{arcs} = []; $self->{lookup} = {}; $self->{properties} = {}; } =head2 properties Usage - Returns - hashref Args - hashref =cut sub properties { my $self = shift; $self->{_properties} = shift if @_; return $self->{_properties}; } sub property_key_list { qw(boundary check depth query_depth subject_depth query_type subject_type both_type query_compare subject_compare overlap overlap_length attach_ov_coords has_overlaps same_strand profile n_comparisons threshold lt_threshold); } sub allowed_property { my $self = shift; my $p = shift; return 1 if grep {$p eq $_} $self->property_key_list; } =head2 set_property Usage - $sf->set_property("wibble", "on"); Returns - Args - property key, property scalar =cut sub set_property { my $self = shift; my $p = shift; my $v = shift; if (!$self->allowed_property($p)) { confess("$p not a valid property"); } if (!$self->properties) { $self->properties({}); } $self->properties->{$p} = $v; $v; } =head2 get_property Usage - Returns - Args - =cut sub get_property { my $self = shift; my $p = shift; if (!$self->allowed_property($p)) { confess("$p not a valid property"); } if (!$self->properties) { $self->properties({}); } $self->properties->{$p}; } =head2 has_intersects Usage - Returns - boolean Args - SOI::Feature listref, SOI::Feature listref =cut sub has_intersects { my $self = shift; $self->set_property("check", 1); $self->set_property("has_overlaps", 0); $self->find_intersects(@_); $self->set_property("check", 0); return $self->get_property("has_overlaps"); } *has_intersections =\&has_intersects; sub _qsec2sf_h { my $self = shift; my $sec = shift || confess('must pass in secondary loc'); if (@_) { my $sf = shift; $self->{_qsec2sf_h}->{$sec} = $sf; } return $self->{_qsec2sf_h}->{$sec}; } sub _ssec2sf_h { my $self = shift; my $sec = shift || confess('must pass in secondary loc'); if (@_) { my $sf = shift; $self->{_ssec2sf_h}->{$sec} = $sf; } return $self->{_ssec2sf_h}->{$sec}; } =head2 find_intersects Usage - Returns - Args - arrayref of features, arrayref of features, option (hashref) =cut sub find_intersects { my $self = shift; my $sfs1 = shift; my $sfs2 = shift; my $opts = shift; my %old = (); if ($opts) { my $p = $self->properties || {}; %old = %$p; $self->properties({}); map { if ($_ eq 'both_type') { $self->set_property('query_type', $opts->{$_}); $self->set_property('subject_type', $opts->{$_}); } else { $self->set_property($_, $opts->{$_}); } } keys %$opts; } unless ($self->get_property('query_type') && $self->get_property('subject_type')) { confess("must pass in query_type and subject_type in options hash"); } my %sfh1 = (); my %sfh2 = (); foreach (@$sfs1) { my $c = $_; if ($self->get_property('query_compare')|| "" eq 'secondary_location') { $c = $_->secondary_loc; $self->_qsec2sf_h($c, $_); } unless ($c->src_seq) { warn("no src seq: ".$c->name); next; } $sfh1{$c->src_seq} = [] unless $sfh1{$c->src_seq}; push(@{$sfh1{$c->src_seq}}, $c); } foreach (@$sfs2) { my $c = $_; if ($self->get_property('subject_compare')|| "" eq 'secondary_location') { $c = $_->secondary_loc; $self->_ssec2sf_h($c, $_); } next unless ($c->src_seq); $sfh2{$c->src_seq} = [] unless $sfh2{$c->src_seq}; push(@{$sfh2{$c->src_seq}}, $c); } $self->clear_overlaps; my $rv; # remember, there will be no intersections if # they dont share same seq! foreach my $k (keys %sfh1) { if ($sfh2{$k}) { $rv = $self->find_intersects_on_same_seq($sfh1{$k}, $sfh2{$k}) } } # unset temp properties if ($opts) { map {$self->set_property($_, $old{$_})} keys %$opts; } $self->overlap_list; } sub find_intersects_on_same_seq { my $self = shift; my $sfs1 = shift; my $sfs2 = shift; return [] unless (@{$sfs1 || []} && @{$sfs2 || []}); #use the flag to indicate I (smaller set) is first set of the args or not my $sets_order_flipped = 0; my ($small, $big) = ($sfs1, $sfs2); if (@{$sfs1} > @{$sfs2}) { ($small, $big) = ($sfs2, $sfs1); $sets_order_flipped = 1; } $small = [sort{$a->fmin <=> $b->fmin}@$small]; $big = [sort{$a->fmin <=> $b->fmin}@$big]; my @ovs = (); my $nc = 0; my $k = 0; for (my $i = 0; $i < scalar(@{$small}); $i++) { my $sf1 = $small->[$i]; #trace(sprintf("\nexamined one round: %s:%d-%d",$sf1->type." ".($sf1->secondary_loc?$sf1->secondary_loc->src_seq:$sf1->name),$sf1->fmin,$sf1->fmax)); my $pointer_moved; for (my $j = $k; $j < scalar(@{$big}); $j++) { my $sf2 = $big->[$j]; if ($sf2->fmax < $sf1->fmin) { #sf2 left of sf1: sf2 moves right next; } elsif ($sf1->fmin <= $sf2->fmax && $sf1->fmax >= $sf2->fmin) { unless ($pointer_moved) { $k = $j; $pointer_moved = 1; } } else { #sf2 right of sf1: no possible ov last; } #keep $sf1 straight by using alias because we have to swap sf in some cases! my ($c1, $c2) = ($sf1, $sf2); if ($sets_order_flipped) { ($c1, $c2) = ($sf2, $sf1); } if ($self->get_property('query_compare')|| "" eq 'secondary_location') { $c1 = $self->_qsec2sf_h($c1); } if ($self->get_property('subject_compare')|| "" eq 'secondary_location') { $c2 = $self->_ssec2sf_h($c2); } my $is_overlap = $self->_icheck($c1, $c2); $nc++; if ($is_overlap) { if ($self->get_property("check")) { # user doesn't care about list of # overlaps, use ig to find if overlap (has_overlaps)? $self->set_property("has_overlaps", 1); return; } trace(sprintf("%s:%d-%d %s ov %s:%d-%d %s",$sf1->src_seq,$sf1->fmin,$sf1->fmax,$c1->name || "", $sf2->src_seq,$sf2->fmin,$sf2->fmax, $c2->name || "")); push(@ovs, [$c1, $c2, $is_overlap]); } else { trace(sprintf("%s:%d-%d %s(d=%d) not ov %s:%d-%d %s(d=%d)",$sf1->src_seq,$sf1->fmin,$sf1->fmax,$c1->type,$c1->depth,$sf2->src_seq,$sf2->fmin,$sf2->fmax, $c2->type, $c2->depth)); } } } if ($self->get_property("profile")) { $self->set_property("n_comparisons", $nc); } foreach my $ov (@ovs) { $self->add_overlap($ov); } printf STDERR "EXAMINED ALL\n" if ($ENV{DEBUG}); trace('n overlaps = ', scalar(@ovs)); $self->overlap_list; } sub _icheck { my $self = shift; my $sf1 = shift; #must be from set of user's first arg my $sf2 = shift; local *sf_ov = sub { my $f1 = shift; my $f2 = shift; my $ov_lap = $self->overlaps($f1, $f2); my $is_overlap = $ov_lap->[0]; my $overlap = $self->get_property('overlap');#span overlap percentage my $ov_len = $self->get_property('overlap_length'); if ($overlap) { if ($is_overlap/($f2->length || 1) < $overlap) { $is_overlap = 0; } } elsif ($ov_len) { if ($is_overlap < $ov_len) { $is_overlap = 0; } } if ($is_overlap && $self->get_property('attach_ov_coords')) { my $ov_fmin_term = $self->get_property('subject_compare') eq 'secondary_location' ? 'ov_sec_loc_fmin' : 'ov_fmin'; my $ov_fmax_term = $self->get_property('subject_compare') eq 'secondary_location' ? 'ov_sec_loc_fmax' : 'ov_fmax'; $f2->add_property($ov_fmin_term, $ov_lap->[1]); $f2->add_property($ov_fmax_term, $ov_lap->[2]); } return $is_overlap; }; local *further_down = sub { my $leaf1 = shift; my $leaf2 = shift; my $f2 = shift; #parent of $leaf2 return unless (scalar(@{$leaf1 || []}) && scalar(@{$leaf2 || []})); # do a recursive check on next level nodes my $inner_ov = ref($self)->new; $inner_ov->properties({%{$self->properties}}); my $inovs = $inner_ov->find_intersects_on_same_seq($leaf1, $leaf2); # this assumes that both sf sets are flattened # eg it will work for transcripts (result set or match), but not genes #well, for genes, you may over-count overlaps as a gene may have >1 overlapping tr my $is_overlap = 0; #both flag and ov length (ov length is added up for next level node of $sf1, $sf2) foreach my $inov (@{$inovs || []}) { #arc (third item) is ov length $is_overlap += $inov->[2]; } my $thresh = $self->get_property("threshold"); my $ltthresh = $self->get_property("lt_threshold"); if ($thresh || $ltthresh) { my $seq_len = 0; my $types = $self->get_property('subject_type'); $types = [$types] unless (ref($types) eq 'ARRAY'); my @parts; map{my $p = $_; push @parts, $p if (grep{$p->type eq $_}@$types)}@{$leaf2}; map{$seq_len += $_->length}@parts; if ($ltthresh && $is_overlap / $seq_len >= $ltthresh) { print STDERR "NOT GETTING >= $ltthresh\n"; $is_overlap = 0; #filter out } else { if ($is_overlap / $seq_len < $thresh) { $is_overlap = 0; } } } return $is_overlap; }; #both sf are on the same src my $strand_test_passed = 1; if ($self->get_property("same_strand")) { $strand_test_passed = 0 unless ($sf1->strand == $sf2->strand); } if ($sf1->uniquename eq $sf2->uniquename || ($strand_test_passed)) { my $overlap; my $depth = $self->get_property('depth'); my ($qd, $sd) = ($self->get_property('query_depth'),$self->get_property('subject_depth')); #same depth of said types (a type can appear at diff level of the tree) if (defined($depth)) { if ($sf1->depth == $depth && $sf2->depth == $depth) { $overlap = sf_ov($sf1,$sf2); } else { # do a recursive check on next level nodes my $leaf1 = $sf1->nodes; my $leaf2 = $sf2->nodes; $overlap = further_down($leaf1,$leaf2,$sf2); } } #said depth of said types elsif (defined($qd) || defined($sd)) { confess("must specify both query and subject depth when a depth is specified") unless (defined($qd) && defined($sd)); if ($sf1->depth == $qd && $sf2->depth == $sd) { $overlap = sf_ov($sf1,$sf2); } elsif ($sf1->depth == $qd) { my $leaf2 = $sf2->nodes; $overlap = further_down([$sf1],$leaf2,$sf2); } elsif ($sf2->depth == $sd) { my $leaf1 = $sf1->nodes; $overlap = further_down($leaf1,[$sf2],$sf2); } else { # do a recursive check on next level nodes my $leaf1 = $sf1->nodes; my $leaf2 = $sf2->nodes; $overlap = further_down($leaf1,$leaf2,$sf2); } } #any depth of said types, the type must be unique in the tree #in other words, the type SHOULD NOT be at diff depth or you WILL get wrong answer else { my ($qtype, $stype) = ($self->get_property('query_type'),$self->get_property('subject_type')); $qtype = [$qtype] unless (ref($qtype) eq 'ARRAY'); $stype = [$stype] unless (ref($stype) eq 'ARRAY'); if (grep{$sf1->type eq $_}@$qtype and grep{$sf2->type eq $_}@$stype) { $overlap = sf_ov($sf1,$sf2); } elsif (grep{$sf1->type eq $_}@$qtype) { my $leaf2 = $sf2->nodes; $overlap = further_down([$sf1],$leaf2,$sf2); } elsif (grep{$sf2->type eq $_}@$stype) { my $leaf1 = $sf1->nodes; $overlap = further_down($leaf1,[$sf2],$sf2); } else { my $leaf1 = $sf1->nodes; my $leaf2 = $sf2->nodes; $overlap = further_down($leaf1,$leaf2,$sf2); } } return $overlap; } } #prerequisite: first arg is from query/user's first arg #return array ref: ov length, ov_fmin, ov_fmax sub overlaps { my $self = shift; my $sf1 = shift; my $sf2 = shift; my ($qtype, $stype) = ($self->get_property('query_type'),$self->get_property('subject_type')); $qtype = [$qtype] unless (ref($qtype) eq 'ARRAY'); $stype = [$stype] unless (ref($stype) eq 'ARRAY'); return unless (grep{$sf1->type eq $_}@$qtype and grep{$sf2->type eq $_}@$stype); #not right feature type if ($self->get_property('query_compare')|| "" eq 'secondary_location') { $sf1 = $sf1->secondary_loc; } if ($self->get_property('subject_compare')|| "" eq 'secondary_location') { $sf2 = $sf2->secondary_loc; } my ($ov, $fmin, $fmax); if ($sf1->fmin > $sf2->fmin) { ($sf2, $sf1) = ($sf1, $sf2); } elsif ($sf2->length > $sf1->length && $sf1->fmin == $sf2->fmin) { ($sf2, $sf1) = ($sf1, $sf2); } #$sf1 is smaller fmin (and longer if same fmin) if ($sf1->fmin <= $sf2->fmin && $sf1->fmax >= $sf2->fmax) { if ($sf1->length > $sf2->length) { ($fmin, $fmax) = ($sf2->fmin, $sf2->fmax); } else { ($fmin, $fmax) = ($sf1->fmin, $sf1->fmax); } } elsif ($sf1->fmax > $sf2->fmin && $sf1->fmax <= $sf2->fmax) { ($fmin, $fmax) = ($sf2->fmin, $sf1->fmax); } else { ; } if (defined($fmin) && defined($fmax)) { return [$fmax-$fmin, $fmin, $fmax]; } else { return [0,0,0] } } # an arc is stored as an arrayref # [0] - feature1 # [1] - feature2 # [2] - distance (optional) sub add_overlap { my $self = shift; my $ov = shift; $ov->[0]->isa("SOI::Feature") || confess; $ov->[1]->isa("SOI::Feature") || confess; push(@{$self->{arcs}}, $ov); my $lookup = $self->{lookup}; $lookup->{$ov->[0]->uniquename} = [] unless $lookup->{$ov->[0]->uniquename}; $lookup->{$ov->[1]->uniquename} = [] unless $lookup->{$ov->[1]->uniquename}; push(@{$lookup->{$ov->[0]->uniquename}}, $ov); push(@{$lookup->{$ov->[1]->uniquename}}, $ov);# unless ($ov->[0]->uniquename eq $ov->[1]->uniquename); 1; } =head2 overlap_list Usage - Returns - Args - =cut sub overlap_list { my $self = shift; if (@_) { $self->clear_overlaps; map {$self->add_overlap($_) } @{shift || []} } $self->{arcs}; } =head2 query_overlaps Usage - Returns - Args - returns list of SOI::Feature objects which came from the first set (query features) which overlap with some of 2nd set =cut sub query_overlaps { my $self = shift; my $p = shift; my $arcs = $self->overlap_list; my %u_h; map {my $o = $_->[0]; $u_h{$o} = $o } @$arcs; return [values %u_h]; } =head2 subject_overlaps Usage - Returns - Args - returns list of SOI::Feature objects which came from the second set (subject features) which overlap with some of first set =cut sub subject_overlaps { my $self = shift; my $arcs = $self->overlap_list; my %u_h; map { my $o = $_->[1]; $u_h{$o} = $o } @$arcs; return [values %u_h]; } =head2 overlap_count Usage - Returns - Args - =cut sub overlap_count { my $self = shift; scalar(@{$self->overlap_list}); } =head2 clear_overlaps Usage - Returns - Args - =cut sub clear_overlaps { my $self = shift; $self->{lookup} = {}; $self->{arcs} = []; } =head2 get_ilist Usage - Returns - Args - SOI::Feature returns all intersecting Features =cut sub get_ilist { my $self = shift; my $sf = shift; my $ovs = $self->{lookup}->{$sf->uniquename} || []; my @ilist = map { $_->[0]->uniquename eq $sf->uniquename ? $_->[1] : $_->[0] } @$ovs; return \@ilist; } =head2 get_distlist Usage - Returns - Args - SOI::Feature returns intersecting Features and their distance, as pairs eg [sfA, distA], [sfB, distC], [sfC, distC], =cut sub get_distlist { my $self = shift; my $sf = shift; my $ovs = $self->{lookup}->{$sf->uniquename} || []; my @ilist = map { $_->[0]->uniquename eq $sf->uniquename ? [$_->[1], $_->[2]] : [$_->[0], $_->[2]] } @$ovs; return \@ilist; } our $debug; sub debug { my $self = shift; $debug = shift; } sub trace { print STDERR join(" ", @_),"\n" if ($debug || $ENV{DEBUG}); } 1; chado-1.23/soi/SOI/Outputter.pm000644 000765 000024 00000057136 11256707645 016420 0ustar00cainstaff000000 000000 package SOI::Outputter; =head1 NAME SOI::Outputter =head1 SYNOPSIS =head1 USAGE =cut use Exporter; use SOI::Feature; use XML::Writer; use IO; use Carp; use base qw(Exporter); use vars qw($AUTOLOAD); @EXPORT_OK = qw(chaos_xml soi_xml game_xml gff3 fasta); %EXPORT_TAGS = (all=> [@EXPORT_OK]); use strict; =head1 FUNCTIONS =cut sub _out_params { return qw(relationship_type uniquename name symbol organism src_seq start end residues); } sub _analysis_params { return qw(description program programversion algorithm sourcename sourceversion sourceuri timeexecuted); } sub _chaos_hidden_params { return qw(analysis_id parent_id featureloc_id analysisfeature_id organism_id dbxref_id type_id nbeg nend start end fmin fmax depth timelastmodified timeaccessioned relationship_type rank locgroup); } #if not in the list, field value to property in gff3 sub _gff_hidden_prop_params { my @a1 = &_chaos_hidden_params; my @a2 = &_out_params; my %uniq; map{$uniq{$_}=1}(@a1, @a2, qw(srcfeature_id species genus is_analysis type strand rank phase feature_id seqlen orderrank md5checksum is_fmin_partial is_fmax_partial)); return keys %uniq; } sub _soi_hidden_params { return (grep{$_ ne 'fmin' && $_ ne 'fmax' && $_ ne 'relationship_type'}(_chaos_hidden_params), qw(feature_id srcfeature_id type md5checksum)); } sub chaos_xml { my $node = shift; my $output = shift; my $opath = $output; unless ($opath) { $opath ||= ">-"; #default to STDOUT } $output = new IO::File(">$opath") unless (ref($output)); my $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 2); $w->startTag('chaos'); if ($node->hash->{program}) { my $pt = 'property'; my $t = "companalysis"; $w->startTag($t); map{$w->dataElement($_,$node->hash->{$_}) if ($node->hash->{$_})}(_analysis_params); my @fp_params = qw(type value rank); map{ $w->startTag($pt); my $h = $_; map{ $w->dataElement($_, $h->{$_}) if (defined($h->{$_})); }@fp_params; $w->endTag($pt); }@{$node->properties || []}; map{_chaos_xml($_, $output, $w)}@{$node->nodes || []}; $w->endTag($t); } else { _chaos_xml($node, $output, $w); } $w->endTag('chaos'); } sub _chaos_xml { my $node = shift; my $output = shift; my $w = shift; $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 2) unless ($w); my $h = $node->hash; my ($ft, $flt, $fpt, $fxt, $frt, $fot) = ('feature', 'featureloc', 'featureprop', 'feature_dbxref', 'feature_relationship', 'feature_cvterm'); my @loc_params = qw(srcfeature_id src_seq nbeg nend strand phase residue_info rank locgroup ); $w->startTag($ft); foreach my $k (sort{$a cmp $b}keys %{$h || {}}) { next if (grep{$k eq $_}(_chaos_hidden_params, _analysis_params, @loc_params)); my ($t,$v) = ($k,$h->{$k}); $t = 'rank' if ($t eq 'orderrank'); $w->dataElement($t, $v) if (defined $v); } keys %{$h || {}}; if (scalar(@{$node->dbxrefs || []})) { $w->startTag($fxt); map{ $w->dataElement('dbxrefstr',sprintf("%s:%s",$_->{dbname},$_->{accession})); }@{$node->dbxrefs || []}; $w->endTag($fxt); } my @fp_params = qw(type value rank); map{ $w->startTag($fpt); my $h = $_; map{ $w->dataElement($_, $h->{$_}); }@fp_params; $w->endTag($fpt); }@{$node->properties || []}; $w->startTag($flt); $w->dataElement("srcfeature_id",$node->hash->{srcfeature_id}); $w->dataElement('nbeg',$node->nbeg); $w->dataElement('nend',$node->nend); $w->dataElement('rank',$node->hash->{rank}); $w->dataElement('locgroup',$node->hash->{locgroup}); $w->dataElement('phase',$node->hash->{phase}) if (defined($node->hash->{phase})); $w->endTag($flt); foreach my $h (@{$node->secondary_locations || []}) { $w->startTag($flt); $w->dataElement("srcfeature_id",$h->{srcfeature_id}); my ($nbeg, $nend) = ($h->{fmin},$h->{fmax}); if ($h->{strand} < 0) {($nbeg,$nend) = ($nend,$nbeg)}; $w->dataElement('nbeg',$nbeg); $w->dataElement('nend',$nend); $w->dataElement('strand',$h->{strand}); $w->dataElement('rank',$h->{rank}); $w->dataElement('locgroup',$h->{locgroup}); $w->dataElement('phase',$h->{phase}) if (defined($h->{phase})); $w->endTag($flt); } if (scalar(@{$node->ontologies || []})) { $w->startTag($fot); map{ $w->startTag('cvterm'); $w->dataElement('name',$_->{name}); $w->dataElement('dbxrefstr',sprintf("%s",$_->{accession})); $w->dataElement('cv', $_->{cv}); $w->endTag('cvterm'); }@{$node->ontologies || []}; $w->endTag($fot); } $w->endTag($ft); #recreate writer to write relationship outside feature $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 2); if ($node->hash->{parent_id}) { $w->startTag($frt); $w->dataElement('subject_id',$node->id); $w->dataElement('object_id', $node->hash->{parent_id}); $w->dataElement('type',$node->hash->{relationship_type}); $w->endTag($frt); } map{_chaos_xml($_, $output)}@{$node->nodes || []}; } sub soi_xml { my $node = shift; my $output = shift; my $w = shift; my $opath = $output; unless ($opath) { $opath ||= ">-"; #default to STDOUT } $output = new IO::File(">$opath") unless (ref($output)); undef $opath; my $h = $node->hash; $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 2) unless ($w); $node->_setup_coord; $w->startTag('soi'); $w->startTag($node->type); foreach my $k (sort{$a cmp $b}keys %{$h || {}}) { next if (grep{$k eq $_}(_soi_hidden_params)); my ($t,$v) = ($k,$h->{$k}); $t = 'rank' if ($t eq 'orderrank'); if ($t eq 'residues' and $v) { $v =~ s/(.{50})/$1\n/g; chomp $v; $v .= "\n"; $w->startTag('seq'); my $md5 = 'md5checksum'; $w->dataElement($md5,$h->{$md5}) if ($h->{$md5}); $w->dataElement($t, $v) if (defined($v)); $w->endTag('seq'); } else { $w->dataElement($t, $v) if (defined($v)); } } foreach my $h (@{$node->secondary_locations || []}) { $w->startTag("secondary_location"); $w->dataElement("src_seq",$h->{src_seq}); $w->dataElement('fmin',$h->{fmin}); $w->dataElement('fmax',$h->{fmax}); $w->dataElement('strand',$h->{strand}); $w->dataElement('rank',$h->{rank}) if (defined($h->{rank})); $w->dataElement('locgroup',$h->{locgroup}) if (defined($h->{locgroup})); $w->dataElement('phase',$h->{phase}) if (defined($h->{phase})); #subject seq data is hidden in soi and chaos?!! # my $subj_seq = $h->{seq}; # if ($subj_seq) { # foreach my $k (qw(seqlen)) { # my $t = "src_seq_$k"; # my $v = $subj_seq->{$k}; # $w->dataElement($t, $v) if (defined($v)); # } # } $w->endTag("secondary_location"); } #flatten synonym list??? map{ $w->dataElement($_->{type},$_->{value}); }@{$node->synonyms || []}; my ($dbxt, $pt, $cvt) = qw(dbxref property cvterm); map{ $w->startTag($dbxt); $w->dataElement($_->{dbname}, $_->{accession}); $w->endTag($dbxt); }@{$node->dbxrefs || []}; map{ $w->startTag($pt); $w->dataElement($_->{type}, $_->{value}); $w->endTag($pt); }@{$node->properties || []}; map{ $w->startTag($cvt); $w->startTag($_->{cv}); $w->dataElement('name',$_->{name}); $w->dataElement('dbxrefstr',$_->{accession}); $w->endTag($_->{cv}); $w->endTag($cvt); }@{$node->ontologies || []}; map{ $w->startTag('comment'); my $h = $_; map{$w->dataElement($_,$h->{$_})}keys %{$h}; $w->endTag('comment'); }@{$node->comments || []}; map{soi_xml($_, $output, $w)}@{$node->nodes || []}; $w->endTag($node->type); $w->endTag('soi'); } sub game_xml { my $node = shift; my $output = shift; my $w = shift; my $opath = $output; unless ($opath) { $opath ||= ">-"; #default to STDOUT } $output = new IO::File(">$opath") unless (ref($output)); undef $opath; my $h = $node->hash; $w = new XML::Writer(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 2) unless ($w); $w->startTag('game', version=>'1.2'); my ($g_node, @an_nodes, @o_nodes); foreach my $c (@{$node->nodes || []}) { if ($c->hash->{type} eq 'contig') { $g_node = $c; } elsif ($c->hash->{type} eq 'companalysis' || $c->hash->{program}) { push @an_nodes, $c; } else { push @o_nodes, $c; } } my %sec_seq_h; foreach my $an (@an_nodes) { foreach my $rset (@{$an->nodes || []}) { foreach my $span (@{$rset->nodes || []}) { foreach my $loc (@{$span->secondary_nodes || []}) { my $seq = $loc->sseq; my $seq_h = ref($seq) ? $seq->hash : ""; $sec_seq_h{$seq_h->{feature_id} || $seq_h->{name}} = $seq_h if ($seq_h); } } } } _genomic_seq_game_xml($g_node, $w, $node->name); _subject_seq_game_xml([values %sec_seq_h], $w); map{_game_xml($_, $w)}(@o_nodes); map{_an_game_xml($_, $w)}(@an_nodes); $w->endTag('game'); } sub _genomic_seq_game_xml { my $node = shift || return; my $w = shift; #XML writer my $arm = shift; $node->_setup_coord; $w->startTag('seq', id=>$node->uniquename, length=>$node->seqlen || $node->length, focus=>'true'); $w->dataElement('name', $node->name); my $residues = $node->hash->{residues} || ""; $residues =~ s/(.{50})/$1\n/g; chomp $residues; $residues = "\n$residues\n"; $w->dataElement('residues', $residues); $w->endTag('seq'); $w->startTag('map_position',type=>'tile',seq=>$node->name); $w->dataElement('arm', $arm); $w->startTag('span'); map{my $m=$_;$w->dataElement($m,$node->$m)}qw(start end); $w->endTag('span'); $w->endTag('map_position'); } sub _subject_seq_game_xml { my $seqs = shift || return; my $w = shift; #XML writer foreach my $seq_h (@{$seqs || []}) { $w->startTag('seq', id=>$seq_h->{uniquename}, length=>$seq_h->{seqlen} || length($seq_h->{residues}) || 0); $w->dataElement('name', $seq_h->{name}); my $residues = $seq_h->{residues} || ""; $residues =~ s/(.{50})/$1\n/g; chomp $residues; $residues = "\n$residues\n"; $w->dataElement('residues', $residues); $w->endTag('seq'); } } sub _game_xml { my $node = shift || return; my $w = shift; my @SO_game_fset = qw(mRNA pseudogene tRNA snRNA snoRNA rRNA ncRNA transcript); my @non_gene = qw(transposable_element remark); #only has top level my @so_polypep = qw(protein polypeptide); my %game_type_map = ('gene' => 'annotation', 'transposable_element' => 'annotation', 'remark' => 'annotation', 'exon' => 'feature_span', protein => 'feature_span', polypeptide => 'feature_span', ); $node->_setup_coord; my $h = $node->hash; #ok, treat transcript's protein node specially (output it in tr level) return if (grep{$node->type eq $_}@so_polypep); my $game_t = $game_type_map{$node->type} || ((grep{$_ eq $node->type}@SO_game_fset) ? 'feature_set' : $node->type); if ($game_t =~ /_set/) { $w->startTag($game_t, id=>$node->uniquename, produces_seq=>$node->uniquename); } else { $w->startTag($game_t, id=>$node->uniquename); } my $prot_node; #hard coded protein-producing feature!!! if (grep{$node->type eq $_}qw(mRNA transcript)) { foreach my $n (@{$node->nodes || []}) { if (grep{$n->type eq $_}@so_polypep) { $prot_node = $n; last; } } } #main attr $w->dataElement('name',$node->name); $w->dataElement('uniquename',$node->uniquename) if ($node->name && $game_t eq 'annotation'); my $v = $node->type;$v='transcript' if ($v eq 'mRNA'); if ($game_t eq 'annotation') { $v = $node->nodes->[0]->type if (@{$node->nodes || []}); $v = $node->type if (grep{$v eq $_}qw(mRNA transcript)); } $w->dataElement('type',$v); if ($game_t eq 'annotation') { $w->startTag('gene', association=>'IS'); $w->dataElement('name', $node->name); $w->endTag('gene'); unless (scalar(@{$node->nodes || []})) { #manufacture tr my $h; map{$h->{$_} = $node->hash->{$_}}keys %{$node->hash}; $h->{parent_id} = $node->id; $h->{feature_id} = $node->id.":1"; $h->{depth} = $node->depth + 1; $h->{type} = 'transcript'; my $n = SOI::Feature->new($h); $node->add_node($n); } } if ($game_t =~ /_set/) { unless (@{$node->nodes || []}) { #manufacture span my $h; map{$h->{$_} = $node->hash->{$_}}keys %{$node->hash}; $h->{parent_id} = $node->id; $h->{feature_id} = $node->id.":2"; $h->{depth} = $node->depth + 1; $h->{type} = 'exon'; my $n = SOI::Feature->new($h); $node->add_node($n); } } #primary loc, apollo can handle seq_relationship in annotation/feature_set but won't draw feature without span if ($game_t =~ /_span/) { $w->startTag('seq_relationship', type=>'query',seq=>$node->src_seq); $w->startTag('span'); map{my $m=$_;$w->dataElement($m,$node->$m)}qw(start end); $w->endTag('span'); $w->endTag('seq_relationship'); } #only analysis result has secondary loc?? foreach my $h (@{$node->secondary_locations || []}) { $w->startTag('seq_relationship', type=>'subject',seq=>$h->{src_seq}); $w->startTag('span'); map{my $m=$_;$w->dataElement($m,$h->{$m})}qw(start end); $w->endTag('span'); $w->endTag('seq_relationship'); } #flatten synonym list??? map{ $w->dataElement($_->{type},$_->{value}); }@{$node->synonyms || []}; my ($dbxt, $pt, $cvt) = qw(dbxref property aspect); map{ $w->startTag($pt); $w->dataElement('type',$_->{type}); $w->dataElement('valule', $_->{value}); $w->endTag($pt); }@{$node->properties || []}; map{ $w->startTag($dbxt); $w->dataElement('xref_db',$_->{dbname}); $w->dataElement('db_xref_id',$_->{accession}); $w->endTag($dbxt); }@{$node->dbxrefs || []}; map{ $w->startTag('comment'); my $h = $_; map{$w->dataElement($_,$h->{$_})}keys %{$h}; $w->endTag('comment'); }@{$node->comments || []}; map{ my $h = $_; $w->startTag($cvt); $w->startTag('dbxref'); $w->dataElement('xref_db',$h->{dbname}); $w->dataElement('db_xref_id',$h->{accession}); $w->endTag('dbxref'); if ($h->{cv} && $h->{name}) { $w->dataElement($h->{cv}, $h->{name});#coming from db } else { #coming from game xml my @others = grep{$_ ne 'dbname' && $_ ne 'accession'}keys %{$h || {}}; map{ $w->dataElement($_, $h->{$_}); }@others; } $w->endTag($cvt); }@{$node->ontologies || []}; if ($prot_node) { my $g_t = 'feature_span'; my $id = $prot_node->feature_id || sprintf("%s:tmp%d",$prot_node->uniquename,time); $w->startTag($g_t, id=>$id,produces_seq=>$prot_node->uniquename); $w->dataElement('type','translate offset'); $w->startTag('seq_relationship', type=>'query',seq=>$prot_node->src_seq); $w->startTag('span'); my $b = $prot_node->start; my $e = $b + 2; if ($prot_node->strand < 0) { $e = $b - 2; } $w->dataElement('start', $b); $w->dataElement('end', $e); $w->endTag('span'); $w->endTag('seq_relationship'); $w->endTag($g_t); } #out child before seq (work only for tr map{_game_xml($_, $w)}@{$node->nodes || []}; #sequence my @seq_nodes; push @seq_nodes, $node if ($node->hash->{residues}); push @seq_nodes, $prot_node if ($prot_node); foreach my $n (@seq_nodes) { my $t = 'residues'; my $v = $n->hash->{residues}; my $type = (grep{$n->type eq $_}@so_polypep) ? "aa" : "cdna"; $v =~ s/(.{50})/$1\n/g; chomp $v; $v = "\n$v\n"; my $md5 = 'md5checksum'; $w->startTag('seq',id=>$n->uniquename,length=>$n->seqlen,type=>$type,md5checksum=>$n->$md5); $w->dataElement($t, $v); $w->endTag('seq'); } #hmm so protein(polypeptide) can not out nest xml for children (see translate offset above) #already treat it specially, should not come down this far if protein node $w->endTag($game_t); } sub _an_game_xml { my $node = shift || return; my $w = shift; my @SO_game_fset = qw(match mRNA transposable_element); my %game_type_map = ('match_part' => 'result_span', 'exon' => 'result_span', ); $node->_setup_coord; my $h = $node->hash; my $game_t; if ($h->{type} eq 'companalysis' || $h->{program}) { $game_t = 'computational_analysis'; } else { $game_t = $game_type_map{$node->type} || ((grep{$_ eq $node->type}@SO_game_fset) ? 'result_set' : "unknown_set"); } if ($game_t =~ /_analysis/) { $w->startTag($game_t); $w->dataElement('program', $h->{program}); $w->dataElement('database', $h->{sourcename}) if ($h->{sourcename}); } elsif ($game_t =~ /_set/) { $w->startTag($game_t, id=>$node->uniquename); $w->dataElement('name',$node->name || $node->uniquename); unless (@{$node->nodes || []}) { #manufacture span my $h; map{$h->{$_} = $node->hash->{$_}}keys %{$node->hash}; $h->{parent_id} = $node->id; $h->{depth} = $node->depth + 1; $h->{type} = 'match_part'; my $n = SOI::Feature->new($h); $node->add_node($n); } } else { $w->startTag($game_t, id=>$node->uniquename); } #primary loc if ($game_t =~ /_span/) { foreach my $k (sort{$a cmp $b}keys %{$h || {}}) { next if (grep{$k eq $_}(_soi_hidden_params, qw(rank orderrank is_analysis strand fmin fmax is_fmin_partial is_fmax_partial src_seq seqlen start end residue_info relationship_type))); my ($t,$v) = ($k,$h->{$k}); $t = 'rank' if ($t eq 'orderrank'); $t = 'score' if ($t eq 'rawscore'); $t = 'name' if ($t eq 'uniquename' && !$h->{name}); $w->dataElement($t, $v) if (defined($v)); } $w->startTag('seq_relationship', type=>'query',seq=>$node->src_seq); $w->startTag('span'); map{my $m=$_;$w->dataElement($m,$node->$m)}qw(start end); $w->dataElement('alignment', $node->residue_info) if ($node->residue_info); $w->endTag('span'); $w->endTag('seq_relationship'); } #only analysis result has secondary loc?? foreach my $h (@{$node->secondary_locations || []}) { $w->startTag('seq_relationship', type=>'subject',seq=>$h->{src_seq}); $w->startTag('span'); map{my $m=$_;$w->dataElement($m,$h->{$m})}qw(start end); $w->dataElement('alignment', $h->{residue_info}) if ($h->{residue_info}); $w->endTag('span'); $w->endTag('seq_relationship'); } my ($dbxt, $pt, $cvt) = qw(dbxref property cvterm); $pt = 'output' if ($game_t =~ /_span/); map{ $w->startTag($pt); $w->dataElement('type',$_->{type}); $w->dataElement('value', $_->{value}); $w->endTag($pt); }@{$node->properties || []}; map{_an_game_xml($_, $w)}@{$node->nodes || []}; $w->endTag($game_t); } sub fasta { my $node = shift; my $fh = shift; my $opts = shift || {}; my $opath = $fh; unless ($opath) { $opath ||= ">-"; #default to STDOUT } $fh = new IO::File(">$opath") unless (ref($fh)); my $lw = $opts->{line_width} || $opts->{linewidth} || 50; my $res = $node->residues; $res =~ s/(.{$lw})/$1\n/g; chomp $res; printf $fh ">%s\n%s\n",$node->uniquename,$res; } sub gff3 { my $top = shift; my $fh = shift; my $opts = shift || {}; my $opath = $fh; unless ($opath) { $opath ||= ">-"; #default to STDOUT } $fh = new IO::File(">$opath") unless (ref($fh)); require SOI::Visitor; SOI::Visitor->set_loc($top); &_gff3($top,$fh, $opts); printf $fh "###EOF\n" if ($opts->{EOF}); $fh->close; } sub _gff3 { my $node = shift || return; my $fh = shift; my $opts = shift || {}; my $parent_id = shift; my $fasta_out= $opts->{fasta}; my $terminator_depth = $opts->{terminator_depth}; #use node type as parent ID is a hack here!!! my $id = $node->uniquename || $node->id || $node->type; my @magic9 = (); push @magic9, sprintf("ID=%s", $id); push @magic9, sprintf("Name=%s", $node->name) if ($node->name); push @magic9, sprintf("Parent=%s", $parent_id) if ($parent_id); my $secs = $node->secondary_nodes; push @magic9, sprintf("Target=%s",join(",",map{sprintf("%s+%d+%d",$_->src_seq,$_->start,$_->end)}@{$secs || []})) if (@{$secs || []}); #WARNING: property value HAS NOT BEEN URL escaped for the following characters: ",=;" and whitespace my $props = $node->properties; my $h = $node->hash; foreach my $k (keys %{$h || {}}) { unless (grep{$k eq $_}&_gff_hidden_prop_params) { push @{$props}, {type=>$k,value=>$h->{$k}} if (defined($h->{$k})); } } my ($s, $e) = ($node->fmin, $node->fmax); unless (defined($s) && $e) { if ($node->seqlen && !$node->src_seq) { push @{$props}, {type=>'seqlen',value=>$node->seqlen}; } } $s++ if (defined($s)); push @magic9, join(";", map{$_->{type}."=".$_->{value}}@{$props || []}) if (@{$props || []}); my $dbxrefs = $node->dbxrefs; push @magic9, sprintf("Dbxref=%s",join(",",map{$_->{dbname}.":".$_->{accession}}@{$dbxrefs || []})) if (@{$dbxrefs || []}); my $syns = $node->synonyms; push @magic9, sprintf("Alias=%s",join(",",map{$_->{type}."=".$_->{value}}@{$syns || []})) if (@{$syns || []}); my $onts = $node->ontologies; push @magic9, sprintf("Ontology_term=%s",join(",",map{$_->{dbname}.":".$_->{accession}}@{$onts || []})) if (@{$onts || []}); print $fh sprintf("%s\n",join("\t", ($node->src_seq || ".", ".", $node->type, $s || ".", $e || ".", ".", $node->strand || ".", ".", join(";",@magic9)))); #no homology (secondary_node) seq fasta?? if ($fasta_out) { my ($descr, $res) = (undef, $node->residues); ($descr) = $node->get_property('description'); if ($descr || $res) { print $fh "##FASTA\n"; printf $fh sprintf(">%s\n",$descr || $id); if ($res) { $res =~ s/(.{80})/$1\n/g; chomp $res; print $fh "$res\n"; } printf $fh "###\n"; } } map{_gff3($_, $fh, $opts, $id)}@{$node->nodes || []}; #terminator could be the end of FASTA or the end of a feature (complex feature) printf $fh "###\n" if ($terminator_depth && $terminator_depth == ($node->depth || -1)); #depth 0 is root } 1; chado-1.23/soi/SOI/SOIHandler.pm000644 000765 000024 00000010755 11256707645 016331 0ustar00cainstaff000000 000000 package SOI::SOIHandler; =head1 NAME SOI::SOIHandler =head1 SYNOPSIS perlSAX handler to parse soi xml =head1 USAGE =begin my $handler = SOI::SOIHandler->new([qw(your feature type list here)]); my $parser = XML::Parser::PerlSAX->new(Handler=>$handler); $parser->parse(Source => { SystemId =>$soixml_file}); my $feature = $handler->feature; #get SOI::Feature obj (feature tree) from soi xml =end =cut =head1 FEEDBACK Email sshu@fruitfly.org =cut use strict; use SOI::Feature; use FileHandle; use Carp; =head1 FUNCTIONS =cut sub new { my $class = shift; my $self = {}; # my $outfile = shift || ">-"; # $self->{fh} = new FileHandle ">$outfile"; bless $self, $class; #for now one arg (non-optional) my $types = shift || confess("must pass in feature types (arrayref)"); $types = [$types] unless (ref($types) eq 'ARRAY'); $self->{feature_types} = $types; return $self; } =head2 start_element Called directly by SAX Parser. Do NOT call this directly. Adds element name string to stack. =cut sub start_element { my ($self, $element) = @_; my $name = $element->{Name}; my $feature = $self->feature; my $method = "add_$name"; if (grep{$name eq $_}@{$self->{feature_types} || []}) { my $feature = SOI::Feature->new({type=>$element->{Name}}); $feature->depth(scalar(@{$self->{feature_stack} || []})); push @{$self->{feature_stack}}, $feature; push @{$self->{level_stack}}, "feature"; } # elsif (grep{$name eq $_}qw(property dbxref ontology secondary_location)) { elsif ($feature && $feature->can($method)) { push @{$self->{level_stack}}, $name; $self->start_auxillary($element); } else { undef $self->{cur_e_char}; } return 1; } =head2 end_element Called directly by SAX Parser. Do NOT call this directly. Removes element name string from stack. =cut sub end_element { my ($self, $element) = @_; my $name = $element->{Name}; my $feature = $self->feature; my $method = "add_$name"; my $level = $self->{level_stack}->[-1]; if (grep{$name eq $_}@{$self->{feature_types} || []}) { pop @{$self->{level_stack}}; unless (@{$self->{feature_stack}} == 1) { my $subf = pop @{$self->{feature_stack}}; my $curf = $self->feature; $curf->add_node($subf); } } # elsif (grep{$name eq $_}qw(property dbxref ontology secondary_location)) { elsif ($feature && $feature->can($method)) { pop @{$self->{level_stack}}; my $el_name = "end_auxillary"; $self->$el_name($element); } else { my $e_val = $self->{cur_e_char}; if ($e_val) { $e_val =~ s/^\s*//g; $e_val =~ s/\s*$//g; } if ($level eq 'feature') { $feature->hash->{$name} = $e_val; } else { if ($level eq 'secondary_location') { $self->{hash}->{$name} = $e_val; } else { $self->{hash} = {type=>$name, value=>$e_val}; } } } return 1; } sub start_auxillary { my ($self, $element) = @_; $self->{hash} = {}; } sub end_auxillary { my ($self, $element) = @_; my $name = $element->{Name}; $name =~ tr/A-Z/a-z/; my $feature = $self->feature; my $method = "add_$name"; confess("unsupported auxillary: $name") unless ($feature->can($method)); my $h = $self->{hash}; if ($name eq 'secondary_location') { my $locf = SOI::Feature->new($h); $feature->add_secondary_node($locf); } else { $feature->$method($h); } } sub start_document { my $self = shift; undef $self->{feature_stack}; undef $self->{level_stack}; } =head2 end_element Called directly by SAX Parser. Do NOT call this directly. The last method called by the Sax Parser. This returns the data in $self->data. =cut sub end_document { my $self = shift; # if ($self->{fh}) { # $self->{fh}->close; # } # return $self->{data}; } =head2 characters Called directly by SAX Parser. Do NOT call this directly. Calls method with the name of the current element with text as the first argument. =cut sub characters { my ($self, $characters) = @_; my $data = $characters->{Data}; return $self->{cur_e_char} .= $data; } =head2 feature usage: my $feature = $self->feature; returns: top node feature =cut sub feature { my $self = shift; return unless (@{$self->{feature_stack} || []}); return $self->{feature_stack}->[-1]; } 1; chado-1.23/soi/SOI/Visitor.pm000644 000765 000024 00000013403 11256707645 016031 0ustar00cainstaff000000 000000 package SOI::Visitor; =head1 NAME SOI::Visitor =head1 SYNOPSIS provide rare functions of SOI::Feature, which might include validation methods and set derived attribtues (more to come) to keep SOI::Feature lightweight, all these functions should be imported and used in client (script) =head1 FEEDBACK Email sshu@fruitfly.org =cut use Exporter; use SOI::Feature; use SOI::IntersectGraph; use Carp; use base qw(Exporter); use vars qw($AUTOLOAD); @EXPORT_OK = qw(set_location_from_component set_loc); %EXPORT_TAGS = (all=> [@EXPORT_OK]); use strict; #only relationship of part_of (may need to use more defined part_of, later) sub set_location_from_component { my $node = shift; if ($node->isa('SOI::Visitor')) { $node = shift; } return $node if (defined($node->fmax) && defined($node->strand)); #already set map{&set_loc($_)}@{$node->nodes || []}; my @children = grep{$_->relationship_type && ($_->relationship_type eq 'part_of' || $_->relationship_type eq 'partof')}@{$node->nodes || []}; return $node unless (@children); my $q_sec; @children = sort{$a->fmin <=> $b->fmin}@children; $node->fmin($children[0]->fmin); $node->strand($children[0]->strand); $q_sec = $children[0]->secondary_loc; @children = sort{$a->fmax <=> $b->fmax}@children; $node->fmax($children[-1]->fmax); $node->src_seq($children[0]->src_seq); if ($q_sec) { my $sec = ref($node)->new({src_seq=>$q_sec->src_seq,strand=>$q_sec->strand}); my @secs = map{$_->secondary_node}@{$node->nodes || []}; @secs = sort{$a->fmin <=> $b->fmin}@secs; $sec->fmin($secs[0]->fmin); $sec->strand($secs[0]->strand); @secs = sort{$a->fmax <=> $b->fmax}@secs; $sec->fmax($secs[-1]->fmax); my $node_sec = $node->secondary_node; $sec->_setup_coord; $node->add_secondary_node($sec) unless ($node_sec && $node_sec->src_seq eq $sec->src_seq && $node_sec->fmin == $sec->fmin); } return $node; } *set_loc = \&set_location_from_component; sub delete_property { my $node = shift; if ($node->isa('SOI::Visitor')) { $node = shift; } my $key = shift || return; my $props = $node->properties; my @remains = grep{$_->{type} ne $key}@{$props || []}; $node->properties(\@remains); } #must be mini-view feature sub remove_strand { my $node = shift; if ($node->isa('SOI::Visitor')) { $node = shift; } my $gone = shift || confess("must pass in strand that is to be removed"); my ($contig,@features); map{if ($_->type eq 'contig') {$contig = $_} else {push @features, $_}}@{$node->nodes || []}; my (@ans,@fs); map{if ($_->type eq 'companalysis') {push @ans, $_} else {push @fs, $_}}@features; my (@keep_ans, @keep_fs); foreach my $an (@ans) { my @rsets; map{ SOI::Visitor->set_loc($_); push @rsets, $_ if ($_->strand != $gone); }@{$an->nodes || []}; if (@rsets) { $an->nodes([@rsets]); push @keep_ans, $an; } } @keep_fs = grep{$_->strand != $gone}@fs; $node->nodes([$contig,@keep_ans,@keep_fs]); return $node; } sub make_CDS_feature { my $mRNA = shift; if ($mRNA->isa('SOI::Visitor')) { $mRNA = shift; } my ($protein) = grep{$_->type eq 'protein' or $_->type eq 'poly_peptide'}@{$mRNA->nodes || []}; my @exons = sort{$a->fmin <=> $b->fmin}grep{$_->type eq 'exon'}@{$mRNA->nodes || []}; my $ig = SOI::IntersectGraph->new; my ($startc_fmin, $stopc_fmin) = ($protein->fmin, $protein->fmax); if ($protein->strand < 0) { ($startc_fmin, $stopc_fmin) = ($protein->fmax-3, $protein->fmin-3); } my $start_codon = SOI::Feature->new({name=>$mRNA->name."_start_codon",type=>'codon',src_seq=>$mRNA->src,fmin=>$startc_fmin,fmax=>$startc_fmin+3, strand=>$protein->strand}); $ig->find_intersects([@exons],[$start_codon], {query_type=>'exon',subject_type=>'codon',same_strand=>1}); my $cds1exon = $ig->query_overlaps->[0]; my $cds_b = $start_codon->fmin - $cds1exon->fmin; if ($start_codon->strand < 0) { $cds_b = $cds1exon->fmax - $start_codon->fmax; } map{$cds_b += $_->length}@{&front_of($cds1exon, [@exons]) || []}; my $stop_codon = SOI::Feature->new({name=>$mRNA->name."_start_codon",type=>'codon',src=>$mRNA->src,fmin=>$stopc_fmin,fmax=>$stopc_fmin+3, strand=>$protein->strand}); $ig->find_intersects([@exons],[$stop_codon], {query_type=>'exon',subject_type=>'codon',same_strand=>1}); my $cdslastexon = $ig->query_overlaps->[0]; my $cds_e = $mRNA->seqlen - ($cdslastexon->fmax - $stop_codon->fmax); if ($stop_codon->strand < 0) { $cds_e = $mRNA->seqlen - ($stop_codon->fmin - $cdslastexon->fmin); } map{$cds_e -= $_->length}@{&behind_of($cdslastexon, [@exons]) || []}; printf STDERR "mRNA len: %d cds: $cds_b-$cds_e\n", $mRNA->seqlen if ($ENV{DEBUG}); my $res = substr($mRNA->residues, $cds_b, $cds_e - $cds_b); return SOI::Feature->new ({type=>'CDS',name=>$mRNA->name."_CDS", src_seq=>$protein->src, fmin=>$startc_fmin,fmax=>$stopc_fmin+3,strand=>$protein->strand, residues=>$res, seqlen=>length($res)} ); } sub front_of { my $it = shift; if ($it->strand > 0) { return &_smaller_than($it, @_); } else { return &_bigger_than($it, @_); } } sub _smaller_than { my $it = shift; my $all = shift; return [grep{$_->fmax < $it->fmin && $_->type eq $it->type}@{$all || []}]; } sub behind_of { my $it = shift; if ($it->strand > 0) { return &_bigger_than($it, @_); } else { return &_smaller_than($it, @_); } } sub _bigger_than { my $it = shift; my $all = shift; return [grep{$_->fmin > $it->fmax && $_->type eq $it->type}@{$all || []}]; } 1; chado-1.23/soi/scripts/dump_fasta.pl000755 000765 000024 00000007076 11723234763 017560 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # generegion_soi.pl # -------------------------------- # sshu@fruitfly.org # -------------------------------- use lib $ENV{GMOD_MODULE_PATH}; use FindBin qw($RealBin); use lib (($ENV{SOI_ROOT}) || (($INC[0]=~/^\./)?"$RealBin/$INC[0]":"$RealBin/..")); use Carp; use strict; use FileHandle; use SOI::Adapter; use SOI::Visitor; use Getopt::Long; my $argh = {}; GetOptions($argh, "dbname|d=s", "outfile|o=s", "idfile|file=s", "template=s", "args|arg=s%", "featuretype|type=s", "extend|e=s", "so_cv_name|so_cv|so=s", "help", ); if ($argh->{help}) { usage(); exit 0; } # set up the database adapter if (!$argh->{dbname}) { print STDERR "You MUST specify a database name; for example -d gadfly3\n\n"; usage(); exit 1; } my $ad; eval { $ad = SOI::Adapter->new($argh->{dbname}); }; if ($@) { print STDERR "There was an error connecting to $argh->dbname}\n\n"; print STDERR $@; exit 1; } if ($argh->{so_cv_name}) { $ad->SO_cv_name($argh->{so_cv_name}); } my @cgs = @ARGV; if ($argh->{template}) { my $features = $ad->get_features_by_template($argh->{template}, $argh->{args}); map{push @cgs, $_->uniquename}@{$features || []}; } if ($argh->{idfile}) { open(R, "<$argh->{idfile}") or die "can not open file: $argh->{idfile}"; while () { chomp; next unless ($_); next if (/^\#/); my @a = split/\s+/; push @cgs, @a; } } my $out = $argh->{outfile} || ">-"; my $fh = FileHandle->new(">$out"); my $type = $argh->{featuretype} || 'gene'; my $method = "get_features_by_$type"; foreach my $cg (@cgs) { my ($range,$genes) = $ad->$method($cg, {extend=>0}); if (!@{$genes || []}) { print "NO SUCH FEATURE: $cg\n"; next; } #test getting CDS seq my ($gene) = grep{$_->uniquename eq $cg}@$genes; my @mRNA = grep{$_->type eq 'mRNA'}@{$gene->nodes || []}; map{SOI::Visitor->make_CDS_feature($_)->to_fasta($fh)}@mRNA; next; #get around arm residues stored problem for speed my $GBs = $ad->get_f({range=>$range}, {feature_types=>'golden_path_region',noauxillaries=>1}); my $arm = SOI::Feature->new({type=>'chromosome_arm',name=>$range->{src}}); $arm->nodes($GBs); my ($fmin, $fmax) = ($range->{fmin},$range->{fmax}); my $new_f = $arm->stitch_child_segments($fmin,$fmax, {name=>"$cg-region"}); $arm->hash->{residues} = ""; $arm->nodes([$new_f,@{$genes}]); } print STDERR "Done!\n"; $ad->close_handle; sub usage { print <] [-extend|e NO OF BASES] [-template ] [-outfile|o filename to put xml in] [-format ] [-noresults] cg-list This script will export per-CG xml files. you can specify a list of CGs on the command line, or you can give it a file of CG ids (just CG ids, not gene symbols) If outfile is specified, only a single CG can be exported to the file. Default format is xml (soi). you can also get chaos xml: dump_generegion_soi.pl -d chado -format chaos CG6699 you can als get GAME xml: dump_generegion_soi.pl -d chado -format game CG6699 To get the gene region without evidence: dump_generegion_soi.pl -d chado -format chaos -noresults CG6699 to use template, here is one example (get genes whose protein has 2 mature_peptides): dump_generegion_soi.pl -d chado -format chaos -template ../templates/genes_by_child_count.soi -arg ptype=protein -arg ctype=mature_peptide -arg count=2 -arg operator='=' EOM } chado-1.23/soi/scripts/dump_segment.pl000755 000765 000024 00000004465 11723234774 020125 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use FindBin qw($RealBin); use lib (($ENV{SOI_ROOT}) || (($INC[0]=~/^\./)?"$RealBin/$INC[0]":"$RealBin/..")); use strict; use SOI::Adapter; use Getopt::Long; use Carp; use FileHandle; my ($ad); my $h = {}; GetOptions($h, "dbname|d=s", "program=s@", "sourcename=s@", "extend=s", "format=s", "debug", ); my $dbname = $h->{dbname}; my $type = 'scaffold'; eval { $ad = SOI::Adapter->new($dbname); }; if ($@) { print STDERR "There was an error\n"; print STDERR $@; exit 1; } foreach my $seg (@ARGV) { my ($features, $range, $t); ($range, $features) = &get_type_features($ad, $type, $seg); if (@{$features || []}) { my $arm = $ad->get_f({range=>$range}, {feature_types=>'chromosome_arm',noauxillaries=>1}); my ($fmin, $fmax) = ($range->{fmin},$range->{fmax}); my $new_f = $arm->stitch_child_segments($fmin,$fmax); $arm->hash->{residues} = ""; my $rset_constr = {range=>$range}; $rset_constr->{program} = $h->{program} if ($h->{program}); $rset_constr->{sourcename} = $h->{sourcename} if ($h->{sourcename}); my $rsets = $ad->get_results($rset_constr); map{$_->transform($new_f)}(@{$features},@{$rsets || []}); my $ans = $ad->get_analysis(); my %an_h; map{$an_h{$_->analysis_id}=$_}@{$ans || []}; foreach my $rset (@{$rsets || []}) { my $an = $an_h{$rset->analysis_id}; $an->add_node($rset) if ($an); } $arm->nodes([@{$arm->nodes || []},@{$features}, @{$ans || []}]); my $format = $h->{format} || "soi"; my $m = "to_$format"."_xml"; my $f; $f = "$seg.$format.xml" unless (scalar(@ARGV) == 1); $arm->$m($f); } else { printf STDERR "did not get any feature for %s=%s\n", $type, $seg } } $ad->close_handle; exit; sub get_type_features { my $ad = shift; my $by_type = shift; my $type = $by_type; my $val = shift; my $opts = {}; if ($by_type eq 'gene') { $opts->{extend} = $h->{extend} || 50000; } my $method = "get_features_by_$type"; if ($ad->can($method)) { return ($ad->$method($val, $opts)); } else { confess("can not do $method"); } } chado-1.23/soi/scripts/generegion.pl000755 000765 000024 00000010562 11723235004 017536 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # generegion_soi.pl # -------------------------------- # sshu@fruitfly.org # -------------------------------- use lib $ENV{GMOD_MODULE_PATH}; use FindBin qw($RealBin); use lib (($ENV{SOI_ROOT}) || (($INC[0]=~/^\./)?"$RealBin/$INC[0]":"$RealBin/..")); use Carp; use strict; use FileHandle; use SOI::Adapter; use SOI::FeatureDecor; use Getopt::Long; my $argh = {}; GetOptions($argh, "dbname|d=s", "outfile|o=s", "template=s", "args|arg=s%", "extend|e=s", "so_cv_name|so_cv|so=s", "dump", "display", "format|w=s", "noresults", "help", ); if ($argh->{help}) { usage(); exit 0; } # set up the database adapter if (!$argh->{dbname}) { print STDERR "You MUST specify a database name; for example -d gadfly3\n\n"; usage(); exit 1; } my $ad; eval { $ad = SOI::Adapter->new($argh->{dbname}); }; if ($@) { print STDERR "There was an error connecting to $argh->dbname}\n\n"; print STDERR $@; exit 1; } if ($argh->{so_cv_name}) { $ad->SO_cv_name($argh->{so_cv_name}); } my @cgs = @ARGV; if ($argh->{template}) { my $features = $ad->get_features_by_template($argh->{template}, $argh->{args}); map{push @cgs, $_->uniquename}@{$features || []}; } my $out = $argh->{outfile}; if (@cgs >1 && ($out || $argh->{display})) { die("can't combine multiple cgs into 1 file or display"); } my $ext =( $argh->{extend} ) || 5000; foreach my $cg (@cgs) { my ($range,$genes) = $ad->get_features_by_gene($cg, {extend=>$ext}); if (!@{$genes || []}) { print "NO SUCH GENE: $cg\n"; next; } #get around arm residues stored problem (wastefull & slow) my $GBs = $ad->get_f({range=>$range}, {feature_types=>'golden_path_region',noauxillaries=>1}); my $arm = SOI::Feature->new({type=>'chromosome_arm',name=>$range->{src}}); $arm->nodes($GBs); my ($fmin, $fmax) = ($range->{fmin},$range->{fmax}); my $new_f = $arm->stitch_child_segments($fmin,$fmax, {name=>"$cg-region-ext$ext"}); $arm->hash->{residues} = ""; my $ans; unless ($argh->{noresults}) { my $rsets = $ad->get_results({range=>$range}); map{$_->transform($new_f)}(@{$rsets || []}); $ans = $ad->get_analysis(); my %an_h; map{$an_h{$_->analysis_id}=$_}@{$ans || []}; foreach my $rset (@{$rsets || []}) { my $an = $an_h{$rset->analysis_id}; $an->add_node($rset) if ($an); } } map{$_->transform($new_f)}@{$genes}; $arm->nodes([$new_f,@{$genes}, @{$ans || []}]); unless ($argh->{display}) { my $format = $argh->{format} || 'soi'; $format =~ s/_xml//; my $method = sprintf("to_%s_xml", $format); unless ($arm->can($method)) { $method = "to_soi_xml"; $format = "soi"; } $out = ( $argh->{outfile} ) || "$cg.$format.xml"; $arm->$method("$out"); } else { my ($g) = grep{$_->name eq $cg}@{$genes}; SOI::Visitor->remove_strand($arm,-$g->strand); my $d = SOI::FeatureDecor->new($arm); my $p = $d->make_panel; my $tmpf = "./tmp$cg.gif"; open(F, ">$tmpf") or die; print F $p->gd->png; close(F); `xv $tmpf`; `rm -f $tmpf`; } } print STDERR "Done!\n"; $ad->close_handle; sub usage { print <] [-extend|e NO OF BASES] [-template ] [-outfile|o filename to put xml in] [-format ] [-noresults] cg-list This script will export per-CG xml files. you can specify a list of CGs on the command line, or you can give it a file of CG ids (just CG ids, not gene symbols) If outfile is specified, only a single CG can be exported to the file. Default format is xml (soi). you can also get chaos xml: dump_generegion_soi.pl -d chado -format chaos CG6699 you can als get GAME xml: dump_generegion_soi.pl -d chado -format game CG6699 To get the gene region without evidence: dump_generegion_soi.pl -d chado -format chaos -noresults CG6699 to use template, here is one example (get genes whose protein has 2 mature_peptides): dump_generegion_soi.pl -d chado -format chaos -template ../templates/genes_by_child_count.soi -arg ptype=protein -arg ctype=mature_peptide -arg count=2 -arg operator='=' EOM } chado-1.23/soi/cgi/get_xml.pl000755 000765 000024 00000006220 11723234744 016134 0ustar00cainstaff000000 000000 #!/usr/bin/env perl BEGIN{ eval{do "config.pl"}; } use FindBin qw($RealBin); use lib (($ENV{SOI_ROOT}) || (($INC[0]=~/^\./)?"$RealBin/$INC[0]":"$RealBin/..")); use strict; use SOI::Adapter; use Getopt::Long; use Carp; use FileHandle; use CGI; my ($cgi) = new CGI; my ($ad); my $dbname = $cgi->param('database') || $ENV{DBNAME} || "chado"; print $cgi->header(-type=>'text/plain'); my @params = $cgi->param(); my @type = grep{$_ eq 'gene' || $_ eq 'range' || $_ eq 'band' || $_ eq 'accession' || $_ eq 'scaffold'}@params; my $type = shift @type; if ($type) { my ($features, $range, $t); eval { $ad = SOI::Adapter->new($dbname); ($range, $features) = &get_type_features($ad, $type, $cgi->param($type)) if ($cgi->param($type)); }; if ($@) { print STDERR "There was an error\n"; print STDERR $@; exit 1; } if (@{$features || []}) { #get around arm residues stored problem (wastefull & slow) my $GBs = $ad->get_f({range=>$range}, {feature_types=>'golden_path_region',noauxillaries=>1}); my $arm = SOI::Feature->new({type=>'chromosome_arm',name=>$range->{src}}); $arm->nodes($GBs); my ($fmin, $fmax) = ($range->{fmin},$range->{fmax}); my ($segs, $new_f) = $arm->stitch_child_segments($fmin,$fmax); $arm->hash->{residues} = ""; my $rsets = $ad->get_results({range=>$range}); map{$_->transform($new_f)}(@{$features},@{$rsets || []}, @{$segs || []}); my $ans = $ad->get_analysis(); my %an_h; map{$an_h{$_->analysis_id}=$_}@{$ans || []}; foreach my $rset (@{$rsets || []}) { my $an = $an_h{$rset->analysis_id}; $an->add_node($rset) if ($an); } #golden_path is not an analysis in chado, manufacture one my $g_an = SOI::Feature->new({program=>'assembly',sourcename=>'path', type=>'companalysis'}); $g_an->nodes($segs); map{ my $g_path = $_; $g_path->residues(undef); $g_path->type('match'); my $span = SOI::Feature->new({%{$g_path->hash}}); $span->name($span->name.":1"); $span->uniquename($span->name); $span->type('match_part'); $g_path->nodes([$span]); $span->secondary_nodes([SOI::Feature->new({src_seq=>$g_path->name,fmin=>0,fmax=>$g_path->length,strand=>1})]); }@{$segs || []}; push @$ans, $g_an; $arm->nodes([@{$arm->nodes || []}, @{$features}, @{$ans || []}]); $arm->to_game_xml; } else { printf STDERR "did not get any feature for %s=%s\n", $type, $cgi->param($type); } $ad->close_handle; } else { printf STDERR "does not support type: %s\n",join(",",$cgi->param()); } exit; sub get_type_features { my $ad = shift; my $by_type = shift; my $type = $by_type; my $val = shift; my $opts = {}; if ($by_type eq 'gene') { $opts->{extend} = $cgi->param('window') || 50000; } my $method = "get_features_by_$type"; if ($ad->can($method)) { return ($ad->$method($val, $opts)); } else { confess("can not do $method"); } } chado-1.23/schemas/1/000755 000765 000024 00000000000 12061672375 014366 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.1/000755 000765 000024 00000000000 12061672376 014664 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.11/000755 000765 000024 00000000000 12061672376 014745 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.2/000755 000765 000024 00000000000 12061672376 014665 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.21/000755 000765 000024 00000000000 12061672376 014746 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.22/000755 000765 000024 00000000000 12061672375 014746 5ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.23/000755 000765 000024 00000000000 12061672375 014747 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.1/000755 000765 000024 00000000000 12061672375 014525 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.2/000755 000765 000024 00000000000 12061672375 015023 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.21/000755 000765 000024 00000000000 12061672376 015105 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.22/000755 000765 000024 00000000000 12061672375 015105 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.23/000755 000765 000024 00000000000 12061672376 015107 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.11/000755 000765 000024 00000000000 12061672376 014607 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.2/000755 000765 000024 00000000000 12061672376 015105 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.21/000755 000765 000024 00000000000 12061672376 015166 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.22/000755 000765 000024 00000000000 12061672375 015166 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.23/000755 000765 000024 00000000000 12061672376 015170 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.2/000755 000765 000024 00000000000 12061672376 014527 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.21/000755 000765 000024 00000000000 12061672376 015106 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.22/000755 000765 000024 00000000000 12061672375 015106 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.23/000755 000765 000024 00000000000 12061672376 015110 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.21-1.22/000755 000765 000024 00000000000 12061672376 015170 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.21-1.23/000755 000765 000024 00000000000 12061672375 015170 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.22-1.23/000755 000765 000024 00000000000 12061672375 015171 5ustar00cainstaff000000 000000 chado-1.23/schemas/1.22-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016616 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.21-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016615 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.21-1.22/diff.sql000644 000765 000024 00000000000 11661243501 016574 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016534 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.22/diff.sql000644 000765 000024 00000000000 11661243501 016513 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.2-1.21/diff.sql000644 000765 000024 00000000000 11660532136 016516 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.2/default_schema.sql000644 000765 000024 00010210753 11634146227 020221 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $1; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; -- ================================================ -- TABLE: cvprop -- ================================================ create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: chadoprop -- ================================================ create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL, CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3), CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) ); SET search_path = public,pg_catalog; -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql'; -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); --function to 'unshare' exons. It looks for exons that have the same fmin --and fmax and belong to the same gene and only keeps one. The other, --redundant exons are marked obsolete in the feature table. Nothing --is done with those features' entries in the featureprop, feature_dbxref, --feature_pub, or feature_cvterm tables. For the moment, I'm assuming --that any annotations that they have when this script is run are --identical to their non-obsoleted doppelgangers. If that's not the case, --they could be merged via query. -- --The bulk of this code was contributed by Robin Houston at --GeneDB/Sanger Centre. CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; /* Choose one of the shared exons to be the canonical representative. We pick the one with the smallest feature_id. */ CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; --This is an automatically generated file; do not edit it as changes will not --be saved. Instead, modify bin/create-so-bridge.pl, which creates this file. CREATE SCHEMA so; SET search_path=so,public,pg_catalog; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent greate *** --- *** r than zero. A nucleotide region is comp *** --- *** osed of bases and a polypeptide region i *** --- *** s composed of amino acids. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region'; --- ************************************************ --- *** relation: sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded sequence. *** --- ************************************************ --- CREATE VIEW sequence_secondary_structure AS SELECT feature_id AS sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure'; --- ************************************************ --- *** relation: g_quartet *** --- *** relation type: VIEW *** --- *** *** --- *** G-quartets are unusual nucleic acid stru *** --- *** ctures consisting of a planar arrangemen *** --- *** t where each guanine is hydrogen bonded *** --- *** by hoogsteen pairing to another guanine *** --- *** in the quartet. *** --- ************************************************ --- CREATE VIEW g_quartet AS SELECT feature_id AS g_quartet_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet'; --- ************************************************ --- *** relation: interior_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_coding_exon AS SELECT feature_id AS interior_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon'; --- ************************************************ --- *** relation: satellite_dna *** --- *** relation type: VIEW *** --- *** *** --- *** The many tandem repeats (identical or re *** --- *** lated) of a short basic repeating unit; *** --- *** many have a base composition or other pr *** --- *** operty different from the genome average *** --- *** that allows them to be separated from t *** --- *** he bulk (main band) genomic DNA. *** --- ************************************************ --- CREATE VIEW satellite_dna AS SELECT feature_id AS satellite_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** One of a pair of sequencing reads in whi *** --- *** ch the two members of the pair are relat *** --- *** ed by originating at either end of a clo *** --- *** ne insert. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding AS SELECT feature_id AS protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding'; --- ************************************************ --- *** relation: non_protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW non_protein_coding AS SELECT feature_id AS non_protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding'; --- ************************************************ --- *** relation: scrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of any one of sev *** --- *** eral small cytoplasmic RNA molecules pre *** --- *** sent in the cytoplasm and sometimes nucl *** --- *** eus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna_primary_transcript AS SELECT feature_id AS scrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA sequence, present *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: inr_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters required f *** --- *** or the correct positioning of the polyme *** --- *** rase for the start of transcription. Ove *** --- *** rlaps the TSS. The mammalian consensus s *** --- *** equence is YYAN(T|A)YY; the Drosophila c *** --- *** onsensus sequence is TCA(G|T)t(T|C). In *** --- *** each the A is at position +1 with respec *** --- *** t to the TSS. Functionally similar to th *** --- *** e TATA box element. *** --- ************************************************ --- CREATE VIEW inr_motif AS SELECT feature_id AS inr_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif'; --- ************************************************ --- *** relation: dpe_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters; Positione *** --- *** d from +28 to +32 with respect to the TS *** --- *** S (+1). Experimental results suggest tha *** --- *** t the DPE acts in conjunction with the I *** --- *** NR_motif to provide a binding site for T *** --- *** FIID in the absence of a TATA box to med *** --- *** iate transcription of TATA-less promoter *** --- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G *** --- *** |A|C). *** --- ************************************************ --- CREATE VIEW dpe_motif AS SELECT feature_id AS dpe_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE_motif'; --- ************************************************ --- *** relation: breu_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments at -37 to -32 with respect to the *** --- *** TSS (+1). Consensus sequence is (G|C)(G| *** --- *** C)(G|A)CGCC. Binds TFIIB. *** --- ************************************************ --- CREATE VIEW breu_motif AS SELECT feature_id AS breu_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREu_motif'; --- ************************************************ --- *** relation: pse_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of the *** --- *** promoters of snRNA genes transcribed by *** --- *** RNA polymerase II or by RNA polymerase *** --- *** III. Located between -45 and -60 relativ *** --- *** e to the TSS. The human PSE_motif consen *** --- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| *** --- *** G). *** --- ************************************************ --- CREATE VIEW pse_motif AS SELECT feature_id AS pse_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif'; --- ************************************************ --- *** relation: linkage_group *** --- *** relation type: VIEW *** --- *** *** --- *** A group of loci that can be grouped in a *** --- *** linear order representing the different *** --- *** degrees of linkage among the genes conc *** --- *** erned. *** --- ************************************************ --- CREATE VIEW linkage_group AS SELECT feature_id AS linkage_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linkage_group'; --- ************************************************ --- *** relation: rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A region of double stranded RNA where th *** --- *** e bases do not conform to WC base pairin *** --- *** g. The loop is closed on both sides by c *** --- *** anonical base pairing. If the interrupti *** --- *** on to base pairing occurs on one strand *** --- *** only, it is known as a bulge. *** --- ************************************************ --- CREATE VIEW rna_internal_loop AS SELECT feature_id AS rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_internal_loop'; --- ************************************************ --- *** relation: asymmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where one of the st *** --- *** rands includes more bases than the corre *** --- *** sponding region on the other strand. *** --- ************************************************ --- CREATE VIEW asymmetric_rna_internal_loop AS SELECT feature_id AS asymmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'asymmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: a_minor_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region forming a motif, composed of ad *** --- *** enines, where the minor groove edges are *** --- *** inserted into the minor groove of anoth *** --- *** er helix. *** --- ************************************************ --- CREATE VIEW a_minor_rna_motif AS SELECT feature_id AS a_minor_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_minor_RNA_motif'; --- ************************************************ --- *** relation: k_turn_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** The kink turn (K-turn) is an RNA structu *** --- *** ral motif that creates a sharp (~120 deg *** --- *** ree) bend between two continuous helices *** --- *** . *** --- ************************************************ --- CREATE VIEW k_turn_rna_motif AS SELECT feature_id AS k_turn_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif'; --- ************************************************ --- *** relation: sarcin_like_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A loop in ribosomal RNA containing the s *** --- *** ites of attack for ricin and sarcin. *** --- ************************************************ --- CREATE VIEW sarcin_like_rna_motif AS SELECT feature_id AS sarcin_like_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sarcin_like_RNA_motif'; --- ************************************************ --- *** relation: symmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where the extent of *** --- *** the loop on both stands is the same siz *** --- *** e. *** --- ************************************************ --- CREATE VIEW symmetric_rna_internal_loop AS SELECT feature_id AS symmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: rna_junction_loop *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_junction_loop AS SELECT feature_id AS rna_junction_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_junction_loop'; --- ************************************************ --- *** relation: rna_hook_turn *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_hook_turn AS SELECT feature_id AS rna_hook_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn'; --- ************************************************ --- *** relation: base_pair *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW base_pair AS SELECT feature_id AS base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'base_pair'; --- ************************************************ --- *** relation: wc_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical base pair, where two bases *** --- *** interact via WC edges, with glycosidic *** --- *** bonds oriented cis relative to the axis *** --- *** of orientation. *** --- ************************************************ --- CREATE VIEW wc_base_pair AS SELECT feature_id AS wc_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair'; --- ************************************************ --- *** relation: sugar_edge_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW sugar_edge_base_pair AS SELECT feature_id AS sugar_edge_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sugar_edge_base_pair'; --- ************************************************ --- *** relation: aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA or RNA molecules that have been sele *** --- *** cted from random pools based on their ab *** --- *** ility to bind other molecules. *** --- ************************************************ --- CREATE VIEW aptamer AS SELECT feature_id AS aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'aptamer'; --- ************************************************ --- *** relation: dna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW dna_aptamer AS SELECT feature_id AS dna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer'; --- ************************************************ --- *** relation: rna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** RNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW rna_aptamer AS SELECT feature_id AS rna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_aptamer'; --- ************************************************ --- *** relation: morpholino_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Morpholino oligos are synthesized from f *** --- *** our different Morpholino subunits, each *** --- *** of which contains one of the four geneti *** --- *** c bases (A, C, G, T) linked to a 6-membe *** --- *** red morpholine ring. Eighteen to 25 subu *** --- *** nits of these four subunit types are joi *** --- *** ned in a specific order by non-ionic pho *** --- *** sphorodiamidate intersubunit linkages to *** --- *** give a Morpholino. *** --- ************************************************ --- CREATE VIEW morpholino_oligo AS SELECT feature_id AS morpholino_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo'; --- ************************************************ --- *** relation: riboswitch *** --- *** relation type: VIEW *** --- *** *** --- *** A riboswitch is a part of an mRNA that c *** --- *** an act as a direct sensor of small molec *** --- *** ules to control their own expression. A *** --- *** riboswitch is a cis element in the 5' en *** --- *** d of an mRNA, that acts as a direct sens *** --- *** or of metabolites. *** --- ************************************************ --- CREATE VIEW riboswitch AS SELECT feature_id AS riboswitch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch'; --- ************************************************ --- *** relation: matrix_attachment_site *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that is required for the bi *** --- *** nding of chromatin to the nuclear matrix *** --- *** . *** --- ************************************************ --- CREATE VIEW matrix_attachment_site AS SELECT feature_id AS matrix_attachment_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site'; --- ************************************************ --- *** relation: locus_control_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that includes DNAse hyperse *** --- *** nsitive sites located 5' to a gene that *** --- *** confers the high-level, position-indepen *** --- *** dent, and copy number-dependent expressi *** --- *** on to that gene. *** --- ************************************************ --- CREATE VIEW locus_control_region AS SELECT feature_id AS locus_control_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast is a match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: genomic_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone of a DNA region of a genome. *** --- ************************************************ --- CREATE VIEW genomic_clone AS SELECT feature_id AS genomic_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone'; --- ************************************************ --- *** relation: processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene where by an mRNA was retrot *** --- *** ransposed. The mRNA sequence is transcri *** --- *** bed back into the genome, lacking intron *** --- *** s and promoters, but often including a p *** --- *** olyA tail. *** --- ************************************************ --- CREATE VIEW processed_pseudogene AS SELECT feature_id AS processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene'; --- ************************************************ --- *** relation: pseudogene_by_unequal_crossing_over *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene caused by unequal crossing *** --- *** over at recombination. *** --- ************************************************ --- CREATE VIEW pseudogene_by_unequal_crossing_over AS SELECT feature_id AS pseudogene_by_unequal_crossing_over_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over'; --- ************************************************ --- *** relation: probe *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence used experimentally to de *** --- *** tect the presence or absence of a comple *** --- *** mentary nucleic acid. *** --- ************************************************ --- CREATE VIEW probe AS SELECT feature_id AS probe_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo' OR cvterm.name = 'probe'; --- ************************************************ --- *** relation: aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW aneuploid AS SELECT feature_id AS aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'aneuploid'; --- ************************************************ --- *** relation: hyperploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as extra c *** --- *** hromosomes are present. *** --- ************************************************ --- CREATE VIEW hyperploid AS SELECT feature_id AS hyperploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid'; --- ************************************************ --- *** relation: hypoploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as some ch *** --- *** romosomes are missing. *** --- ************************************************ --- CREATE VIEW hypoploid AS SELECT feature_id AS hypoploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hypoploid'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind thereby *** --- *** effecting translation of genes in that *** --- *** operon. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: nuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, of a nucleotide mol *** --- *** ecule, that interacts selectively and no *** --- *** n-covalently with polypeptide residues o *** --- *** f a nuclease. *** --- ************************************************ --- CREATE VIEW nuclease_binding_site AS SELECT feature_id AS nuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_binding_site'; --- ************************************************ --- *** relation: compound_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome_arm AS SELECT feature_id AS compound_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm'; --- ************************************************ --- *** relation: restriction_enzyme_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** restriction enzyme. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_binding_site AS SELECT feature_id AS restriction_enzyme_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site'; --- ************************************************ --- *** relation: d_intrachr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_intrachr_transposition AS SELECT feature_id AS d_intrachr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition'; --- ************************************************ --- *** relation: d_interchr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_interchr_transposition AS SELECT feature_id AS d_interchr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition'; --- ************************************************ --- *** relation: free_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** an arm exists as an individual chromoso *** --- *** me element. *** --- ************************************************ --- CREATE VIEW free_chromosome_arm AS SELECT feature_id AS free_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm'; --- ************************************************ --- *** relation: gene_to_gene_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_to_gene_feature AS SELECT feature_id AS gene_to_gene_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'gene_to_gene_feature'; --- ************************************************ --- *** relation: overlapping *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that has *** --- *** a sequence that overlaps the sequence of *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW overlapping AS SELECT feature_id AS overlapping_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'overlapping'; --- ************************************************ --- *** relation: inside_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene. *** --- ************************************************ --- CREATE VIEW inside_intron AS SELECT feature_id AS inside_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'inside_intron'; --- ************************************************ --- *** relation: inside_intron_antiparallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the opposite strand. *** --- ************************************************ --- CREATE VIEW inside_intron_antiparallel AS SELECT feature_id AS inside_intron_antiparallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel'; --- ************************************************ --- *** relation: inside_intron_parallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the same strand. *** --- ************************************************ --- CREATE VIEW inside_intron_parallel AS SELECT feature_id AS inside_intron_parallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_parallel'; --- ************************************************ --- *** relation: five_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's 3' region. *** --- ************************************************ --- CREATE VIEW five_prime_three_prime_overlap AS SELECT feature_id AS five_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_three_prime_overlap'; --- ************************************************ --- *** relation: five_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's five prime region. *** --- ************************************************ --- CREATE VIEW five_prime_five_prime_overlap AS SELECT feature_id AS five_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_five_prime_overlap'; --- ************************************************ --- *** relation: three_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 3' region. *** --- ************************************************ --- CREATE VIEW three_prime_three_prime_overlap AS SELECT feature_id AS three_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_three_prime_overlap'; --- ************************************************ --- *** relation: three_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 5' region. *** --- ************************************************ --- CREATE VIEW three_prime_five_prime_overlap AS SELECT feature_id AS three_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_five_prime_overlap'; --- ************************************************ --- *** relation: antisense *** --- *** relation type: VIEW *** --- *** *** --- *** A region sequence that is complementary *** --- *** to a sequence of messenger RNA. *** --- ************************************************ --- CREATE VIEW antisense AS SELECT feature_id AS antisense_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense'; --- ************************************************ --- *** relation: polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is polycistronic. *** --- ************************************************ --- CREATE VIEW polycistronic_transcript AS SELECT feature_id AS polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_transcript'; --- ************************************************ --- *** relation: dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_transcript AS SELECT feature_id AS dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_transcript'; --- ************************************************ --- *** relation: operon_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW operon_member AS SELECT feature_id AS operon_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member'; --- ************************************************ --- *** relation: gene_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_array_member AS SELECT feature_id AS gene_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_array_member'; --- ************************************************ --- *** relation: macronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW macronuclear_sequence AS SELECT feature_id AS macronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence'; --- ************************************************ --- *** relation: micronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW micronuclear_sequence AS SELECT feature_id AS micronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_sequence'; --- ************************************************ --- *** relation: nuclear_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nuclear sequence. *** --- ************************************************ --- CREATE VIEW nuclear_gene AS SELECT feature_id AS nuclear_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene'; --- ************************************************ --- *** relation: mt_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in mitochondrial sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW mt_gene AS SELECT feature_id AS mt_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'mt_gene'; --- ************************************************ --- *** relation: kinetoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in kinetoplast sequence. *** --- ************************************************ --- CREATE VIEW kinetoplast_gene AS SELECT feature_id AS kinetoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'kinetoplast_gene'; --- ************************************************ --- *** relation: plastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plastid sequence. *** --- ************************************************ --- CREATE VIEW plastid_gene AS SELECT feature_id AS plastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'plastid_gene'; --- ************************************************ --- *** relation: apicoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from apicoplast sequence. *** --- ************************************************ --- CREATE VIEW apicoplast_gene AS SELECT feature_id AS apicoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene'; --- ************************************************ --- *** relation: ct_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chloroplast sequence. *** --- ************************************************ --- CREATE VIEW ct_gene AS SELECT feature_id AS ct_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ct_gene'; --- ************************************************ --- *** relation: chromoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chromoplast_sequence. *** --- ************************************************ --- CREATE VIEW chromoplast_gene AS SELECT feature_id AS chromoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_gene'; --- ************************************************ --- *** relation: cyanelle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from cyanelle sequence. *** --- ************************************************ --- CREATE VIEW cyanelle_gene AS SELECT feature_id AS cyanelle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_gene'; --- ************************************************ --- *** relation: leucoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A plastid gene from leucoplast sequence. *** --- ************************************************ --- CREATE VIEW leucoplast_gene AS SELECT feature_id AS leucoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_gene'; --- ************************************************ --- *** relation: proplastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proplastid sequence. *** --- ************************************************ --- CREATE VIEW proplastid_gene AS SELECT feature_id AS proplastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_gene'; --- ************************************************ --- *** relation: nucleomorph_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nucleomorph sequence. *** --- ************************************************ --- CREATE VIEW nucleomorph_gene AS SELECT feature_id AS nucleomorph_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorph_gene'; --- ************************************************ --- *** relation: plasmid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plasmid sequence. *** --- ************************************************ --- CREATE VIEW plasmid_gene AS SELECT feature_id AS plasmid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_gene'; --- ************************************************ --- *** relation: proviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proviral sequence. *** --- ************************************************ --- CREATE VIEW proviral_gene AS SELECT feature_id AS proviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'proviral_gene'; --- ************************************************ --- *** relation: endogenous_retroviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A proviral gene with origin endogenous r *** --- *** etrovirus. *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_gene AS SELECT feature_id AS endogenous_retroviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene'; --- ************************************************ --- *** relation: transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW transposable_element AS SELECT feature_id AS transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: clone_insert_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_end AS SELECT feature_id AS clone_insert_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversible denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the chromosome between the c *** --- *** entromere and the telomere. Human chromo *** --- *** somes have two arms, the p arm (short) a *** --- *** nd the q arm (long) which are separated *** --- *** from each other by the centromere. *** --- ************************************************ --- CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: sequencing_primer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequencing_primer AS SELECT feature_id AS sequencing_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer'; --- ************************************************ --- *** relation: mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_frameshift AS SELECT feature_id AS mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'mRNA_with_frameshift'; --- ************************************************ --- *** relation: sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** An extent of biological sequence. *** --- ************************************************ --- CREATE VIEW sequence_feature AS SELECT feature_id AS sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region' OR cvterm.name = 'junction' OR cvterm.name = 'sequence_alteration' OR cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_feature'; --- ************************************************ --- *** relation: transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoded within a transposable ele *** --- *** ment. For example gag, int, env and pol *** --- *** are the transposable element genes of th *** --- *** e TY element in yeast. *** --- ************************************************ --- CREATE VIEW transposable_element_gene AS SELECT feature_id AS transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'transposable_element_gene'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo to which new deoxyribonucleotid *** --- *** es can be added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'primer'; --- ************************************************ --- *** relation: proviral_region *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to a host genome. *** --- ************************************************ --- CREATE VIEW proviral_region AS SELECT feature_id AS proviral_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage' OR cvterm.name = 'proviral_region'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: edited *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is modified by editing. *** --- ************************************************ --- CREATE VIEW edited AS SELECT feature_id AS edited_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited'; --- ************************************************ --- *** relation: transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript with a translational frames *** --- *** hift. *** --- ************************************************ --- CREATE VIEW transcript_with_translational_frameshift AS SELECT feature_id AS transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a sequence that *** --- *** is regulated. *** --- ************************************************ --- CREATE VIEW regulated AS SELECT feature_id AS regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'regulated'; --- ************************************************ --- *** relation: protein_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW protein_coding_primary_transcript AS SELECT feature_id AS protein_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: forward_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW forward_primer AS SELECT feature_id AS forward_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward_primer'; --- ************************************************ --- *** relation: rna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_sequence_secondary_structure AS SELECT feature_id AS rna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'RNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: transcriptionally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated at transcription. *** --- ************************************************ --- CREATE VIEW transcriptionally_regulated AS SELECT feature_id AS transcriptionally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_regulated'; --- ************************************************ --- *** relation: transcriptionally_constitutive *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed in relatively constant amounts *** --- *** without regard to cellular environmenta *** --- *** l conditions such as the concentration o *** --- *** f a particular substrate. *** --- ************************************************ --- CREATE VIEW transcriptionally_constitutive AS SELECT feature_id AS transcriptionally_constitutive_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive'; --- ************************************************ --- *** relation: transcriptionally_induced *** --- *** relation type: VIEW *** --- *** *** --- *** An inducer molecule is required for tran *** --- *** scription to occur. *** --- ************************************************ --- CREATE VIEW transcriptionally_induced AS SELECT feature_id AS transcriptionally_induced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_induced'; --- ************************************************ --- *** relation: transcriptionally_repressed *** --- *** relation type: VIEW *** --- *** *** --- *** A repressor molecule is required for tra *** --- *** nscription to stop. *** --- ************************************************ --- CREATE VIEW transcriptionally_repressed AS SELECT feature_id AS transcriptionally_repressed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'transcriptionally_repressed'; --- ************************************************ --- *** relation: silenced_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced. *** --- ************************************************ --- CREATE VIEW silenced_gene AS SELECT feature_id AS silenced_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_gene'; --- ************************************************ --- *** relation: gene_silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA modificat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_modification AS SELECT feature_id AS gene_silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_DNA_modification'; --- ************************************************ --- *** relation: gene_silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA methylati *** --- *** on. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_methylation AS SELECT feature_id AS gene_silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: post_translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated after it has been translated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated AS SELECT feature_id AS post_translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'post_translationally_regulated'; --- ************************************************ --- *** relation: translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated as it is translated. *** --- ************************************************ --- CREATE VIEW translationally_regulated AS SELECT feature_id AS translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated'; --- ************************************************ --- *** relation: reverse_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW reverse_primer AS SELECT feature_id AS reverse_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_primer'; --- ************************************************ --- *** relation: epigenetically_modified *** --- *** relation type: VIEW *** --- *** *** --- *** This attribute describes a gene where he *** --- *** ritable changes other than those in the *** --- *** DNA sequence occur. These changes includ *** --- *** e: modification to the DNA (such as DNA *** --- *** methylation, the covalent modification o *** --- *** f cytosine), and post-translational modi *** --- *** fication of histones. *** --- ************************************************ --- CREATE VIEW epigenetically_modified AS SELECT feature_id AS epigenetically_modified_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'epigenetically_modified'; --- ************************************************ --- *** relation: imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** Imprinted genes are epigenetically modif *** --- *** ied genes that are expressed monoallelic *** --- *** ally according to their parent of origin *** --- *** . *** --- ************************************************ --- CREATE VIEW imprinted AS SELECT feature_id AS imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted'; --- ************************************************ --- *** relation: maternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The maternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW maternally_imprinted AS SELECT feature_id AS maternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted'; --- ************************************************ --- *** relation: paternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The paternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW paternally_imprinted AS SELECT feature_id AS paternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted'; --- ************************************************ --- *** relation: allelically_excluded *** --- *** relation type: VIEW *** --- *** *** --- *** Allelic exclusion is a process occurring *** --- *** in diploid organisms, where a gene is i *** --- *** nactivated and not expressed in that cel *** --- *** l. *** --- ************************************************ --- CREATE VIEW allelically_excluded AS SELECT feature_id AS allelically_excluded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded'; --- ************************************************ --- *** relation: gene_rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An epigenetically modified gene, rearran *** --- *** ged at the DNA level. *** --- ************************************************ --- CREATE VIEW gene_rearranged_at_dna_level AS SELECT feature_id AS gene_rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located within the fi *** --- *** ve prime end of an mRNA that causes prem *** --- *** ature termination of translation. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'terminator'; --- ************************************************ --- *** relation: dna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded DNA sequence. *** --- ************************************************ --- CREATE VIEW dna_sequence_secondary_structure AS SELECT feature_id AS dna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif' OR cvterm.name = 'DNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of known length which may be us *** --- *** ed to manufacture a longer region. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: recoded_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A codon that has been redefined at trans *** --- *** lation. The redefinition may be as a res *** --- *** ult of translational bypass, translation *** --- *** al frameshifting or stop codon readthrou *** --- *** gh. *** --- ************************************************ --- CREATE VIEW recoded_codon AS SELECT feature_id AS recoded_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'recoded_codon'; --- ************************************************ --- *** relation: capped *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing when a sequence, *** --- *** usually an mRNA is capped by the additi *** --- *** on of a modified guanine nucleotide at t *** --- *** he 5' end. *** --- ************************************************ --- CREATE VIEW capped AS SELECT feature_id AS capped_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the transcript sequence with *** --- *** in a gene which is not removed from the *** --- *** primary RNA transcript by RNA splicing. *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unavailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n a host bacterium or some other organis *** --- *** m. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'clone'; --- ************************************************ --- *** relation: yac *** --- *** relation type: VIEW *** --- *** *** --- *** Yeast Artificial Chromosome, a vector co *** --- *** nstructed from the telomeric, centromeri *** --- *** c, and replication origin sequences need *** --- *** ed for replication in yeast cells. *** --- ************************************************ --- CREATE VIEW yac AS SELECT feature_id AS yac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC'; --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Bacterial Artificial Chromosome, a cloni *** --- *** ng vector that can be propagated as mini *** --- *** -chromosomes in a bacterial host. *** --- ************************************************ --- CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: pac *** --- *** relation type: VIEW *** --- *** *** --- *** The P1-derived artificial chromosome are *** --- *** DNA constructs that are derived from th *** --- *** e DNA of P1 bacteriophage. They can carr *** --- *** y large amounts (about 100-300 kilobases *** --- *** ) of other sequences for a variety of bi *** --- *** oengineering purposes. It is one type of *** --- *** vector used to clone DNA fragments (100 *** --- *** - to 300-kb insert size; average, 150 kb *** --- *** ) in Escherichia coli cells. *** --- ************************************************ --- CREATE VIEW pac AS SELECT feature_id AS pac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC'; --- ************************************************ --- *** relation: plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A self replicating, using the hosts cell *** --- *** ular machinery, often circular nucleic a *** --- *** cid molecule that is distinct from a chr *** --- *** omosome in the organism. *** --- ************************************************ --- CREATE VIEW plasmid AS SELECT feature_id AS plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'plasmid'; --- ************************************************ --- *** relation: cosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that is a hybrid of lam *** --- *** bda phages and a plasmid that can be pro *** --- *** pagated as a plasmid or packaged as a ph *** --- *** age,since they retain the lambda cos sit *** --- *** es. *** --- ************************************************ --- CREATE VIEW cosmid AS SELECT feature_id AS cosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cosmid'; --- ************************************************ --- *** relation: phagemid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid which carries within its seque *** --- *** nce a bacteriophage replication origin. *** --- *** When the host bacterium is infected with *** --- *** "helper" phage, a phagemid is replicate *** --- *** d along with the phage DNA and packaged *** --- *** into phage capsids. *** --- ************************************************ --- CREATE VIEW phagemid AS SELECT feature_id AS phagemid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phagemid'; --- ************************************************ --- *** relation: fosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that utilizes the E. co *** --- *** li F factor. *** --- ************************************************ --- CREATE VIEW fosmid AS SELECT feature_id AS fosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fosmid'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The point at which one or more contiguou *** --- *** s nucleotides were excised. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which adenine has *** --- *** been methylated. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Consensus region of primary transcript b *** --- *** ordering junction of splicing. A region *** --- *** that overlaps exactly 2 base and adjacen *** --- *** t_to splice_junction. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: five_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 5' edge of the intron. A splice_ *** --- *** site that is downstream_adjacent_to exon *** --- *** and starts intron. *** --- ************************************************ --- CREATE VIEW five_prime_cis_splice_site AS SELECT feature_id AS five_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'five_prime_cis_splice_site'; --- ************************************************ --- *** relation: three_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 3' edge of the intron. A splice_ *** --- *** site that is upstream_adjacent_to exon a *** --- *** nd finishes intron. *** --- ************************************************ --- CREATE VIEW three_prime_cis_splice_site AS SELECT feature_id AS three_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'three_prime_cis_splice_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: enhancer_bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer bound by a factor. *** --- ************************************************ --- CREATE VIEW enhancer_bound_by_factor AS SELECT feature_id AS enhancer_bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region composed of the TSS( *** --- *** s) and binding sites for TF_complexes of *** --- *** the basal transcription machinery. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'promoter'; --- ************************************************ --- *** relation: rnapol_i_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase I binds, to begin trans *** --- *** cription. *** --- ************************************************ --- CREATE VIEW rnapol_i_promoter AS SELECT feature_id AS rnapol_i_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter'; --- ************************************************ --- *** relation: rnapol_ii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase II binds, to begin tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW rnapol_ii_promoter AS SELECT feature_id AS rnapol_ii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_II_promoter'; --- ************************************************ --- *** relation: rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase III binds, to begin tra *** --- *** nscription. *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter AS SELECT feature_id AS rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'RNApol_III_promoter'; --- ************************************************ --- *** relation: caat_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a conserved sequence located abo *** --- *** ut 75-bp upstream of the start point of *** --- *** eukaryotic transcription units which may *** --- *** be involved in RNA polymerase binding; *** --- *** consensus=GG(C|T)CAATCT. *** --- ************************************************ --- CREATE VIEW caat_signal AS SELECT feature_id AS caat_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CAAT_signal'; --- ************************************************ --- *** relation: gc_rich_promoter_region *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved GC-rich region located upstr *** --- *** eam of the start point of eukaryotic tra *** --- *** nscription units which may occur in mult *** --- *** iple copies or in either orientation; co *** --- *** nsensus=GGGCGG. *** --- ************************************************ --- CREATE VIEW gc_rich_promoter_region AS SELECT feature_id AS gc_rich_promoter_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region'; --- ************************************************ --- *** relation: tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved AT-rich septamer found about *** --- *** 25-bp before the start point of many eu *** --- *** karyotic RNA polymerase II transcript un *** --- *** its; may be involved in positioning the *** --- *** enzyme for correct initiation; consensus *** --- *** =TATA(A|T)A(A|T). *** --- ************************************************ --- CREATE VIEW tata_box AS SELECT feature_id AS tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'TATA_box'; --- ************************************************ --- *** relation: minus_10_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 10-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units which may be involved in bin *** --- *** ding RNA polymerase; consensus=TAtAaT. T *** --- *** his region is associated with sigma fact *** --- *** or 70. *** --- ************************************************ --- CREATE VIEW minus_10_signal AS SELECT feature_id AS minus_10_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_10_signal'; --- ************************************************ --- *** relation: minus_35_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved hexamer about 35-bp upstream *** --- *** of the start point of bacterial transcr *** --- *** iption units; consensus=TTGACa or TGTTGA *** --- *** CA. This region is associated with sigma *** --- *** factor 70. *** --- ************************************************ --- CREATE VIEW minus_35_signal AS SELECT feature_id AS minus_35_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_35_signal'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_insert_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_start AS SELECT feature_id AS clone_insert_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_start'; --- ************************************************ --- *** relation: retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is incorpora *** --- *** ted into a chromosome by a mechanism tha *** --- *** t requires reverse transcriptase. *** --- ************************************************ --- CREATE VIEW retrotransposon AS SELECT feature_id AS retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'retrotransposon'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: dna_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon where the mechanism of tran *** --- *** sposition is via a DNA intermediate. *** --- ************************************************ --- CREATE VIEW dna_transposon AS SELECT feature_id AS dna_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'DNA_transposon'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: u2_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A major type of spliceosomal intron spli *** --- *** ced by the U2 spliceosome, that includes *** --- *** U1, U2, U4/U6 and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u2_intron AS SELECT feature_id AS u2_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that in its initial state r *** --- *** equires modification to be functional. *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'primary_transcript'; --- ************************************************ --- *** relation: ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon flanked by long termin *** --- *** al repeat sequences. *** --- ************************************************ --- CREATE VIEW ltr_retrotransposon AS SELECT feature_id AS ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript that is *** --- *** transcribed, but removed from within th *** --- *** e transcript by splicing together the se *** --- *** quences (exons) on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'intron'; --- ************************************************ --- *** relation: non_ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon without long terminal *** --- *** repeat sequences. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon AS SELECT feature_id AS non_ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'non_LTR_retrotransposon'; --- ************************************************ --- *** relation: five_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_intron AS SELECT feature_id AS five_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron'; --- ************************************************ --- *** relation: interior_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_intron AS SELECT feature_id AS interior_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_intron'; --- ************************************************ --- *** relation: three_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_intron AS SELECT feature_id AS three_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_intron'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment used as a reagent to dete *** --- *** ct the polymorphic genomic loci by hybri *** --- *** dizing against the genomic DNA digested *** --- *** with a given restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: line_element *** --- *** relation type: VIEW *** --- *** *** --- *** A dispersed repeat family with many copi *** --- *** es, each from 1 to 6 kb long. New elemen *** --- *** ts are generated by retroposition of a t *** --- *** ranscribed copy. Typically the LINE cont *** --- *** ains 2 ORF's one of which is reverse tra *** --- *** nscriptase, and 3'and 5' direct repeats. *** --- ************************************************ --- CREATE VIEW line_element AS SELECT feature_id AS line_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element'; --- ************************************************ --- *** relation: coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon whereby at least one base is par *** --- *** t of a codon (here, 'codon' is inclusive *** --- *** of the stop_codon). *** --- ************************************************ --- CREATE VIEW coding_exon AS SELECT feature_id AS coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'coding_exon'; --- ************************************************ --- *** relation: five_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the five_prime_coding_ex *** --- *** on that codes for protein. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_coding_region AS SELECT feature_id AS five_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: three_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the three_prime_coding_e *** --- *** xon that codes for protein. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_coding_region AS SELECT feature_id AS three_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that does not contain any codons *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_exon AS SELECT feature_id AS noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'noncoding_exon'; --- ************************************************ --- *** relation: translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence that has *** --- *** translocated to a new position. *** --- ************************************************ --- CREATE VIEW translocation AS SELECT feature_id AS translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation'; --- ************************************************ --- *** relation: five_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' most coding exon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon AS SELECT feature_id AS five_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon'; --- ************************************************ --- *** relation: interior_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is bounded by 5' and 3' spl *** --- *** ice sites. *** --- ************************************************ --- CREATE VIEW interior_exon AS SELECT feature_id AS interior_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_exon'; --- ************************************************ --- *** relation: three_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The coding exon that is most 3-prime on *** --- *** a given transcript. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon AS SELECT feature_id AS three_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime or three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: sine_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element, a few hundred base *** --- *** pairs long, that is dispersed throughou *** --- *** t the genome. A common human SINE is the *** --- *** Alu element. *** --- ************************************************ --- CREATE VIEW sine_element AS SELECT feature_id AS sine_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SINE_element'; --- ************************************************ --- *** relation: simple_sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW simple_sequence_length_variation AS SELECT feature_id AS simple_sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation'; --- ************************************************ --- *** relation: terminal_inverted_repeat_element *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA transposable element defined as ha *** --- *** ving termini with perfect, or nearly per *** --- *** fect short inverted repeats, generally 1 *** --- *** 0 - 40 nucleotides long. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat_element AS SELECT feature_id AS terminal_inverted_repeat_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'terminal_inverted_repeat_element'; --- ************************************************ --- *** relation: rrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a ribosoma *** --- *** l RNA. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript AS SELECT feature_id AS rrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript'; --- ************************************************ --- *** relation: trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a transfer *** --- *** RNA (SO:0000253). *** --- ************************************************ --- CREATE VIEW trna_primary_transcript AS SELECT feature_id AS trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript'; --- ************************************************ --- *** relation: alanine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding alanyl tRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW alanine_trna_primary_transcript AS SELECT feature_id AS alanine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: arg_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding arginyl tR *** --- *** NA (SO:0000255). *** --- ************************************************ --- CREATE VIEW arg_trna_primary_transcript AS SELECT feature_id AS arg_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: asparagine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding asparaginy *** --- *** l tRNA (SO:0000256). *** --- ************************************************ --- CREATE VIEW asparagine_trna_primary_transcript AS SELECT feature_id AS asparagine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: aspartic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding aspartyl t *** --- *** RNA (SO:0000257). *** --- ************************************************ --- CREATE VIEW aspartic_acid_trna_primary_transcript AS SELECT feature_id AS aspartic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: cysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding cysteinyl *** --- *** tRNA (SO:0000258). *** --- ************************************************ --- CREATE VIEW cysteine_trna_primary_transcript AS SELECT feature_id AS cysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutaminyl *** --- *** tRNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamic_acid_trna_primary_transcript AS SELECT feature_id AS glutamic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutamyl t *** --- *** RNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamine_trna_primary_transcript AS SELECT feature_id AS glutamine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glycine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glycyl tRN *** --- *** A (SO:0000263). *** --- ************************************************ --- CREATE VIEW glycine_trna_primary_transcript AS SELECT feature_id AS glycine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: histidine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding histidyl t *** --- *** RNA (SO:0000262). *** --- ************************************************ --- CREATE VIEW histidine_trna_primary_transcript AS SELECT feature_id AS histidine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: isoleucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding isoleucyl *** --- *** tRNA (SO:0000263). *** --- ************************************************ --- CREATE VIEW isoleucine_trna_primary_transcript AS SELECT feature_id AS isoleucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: leucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding leucyl tRN *** --- *** A (SO:0000264). *** --- ************************************************ --- CREATE VIEW leucine_trna_primary_transcript AS SELECT feature_id AS leucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: lysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding lysyl tRNA *** --- *** (SO:0000265). *** --- ************************************************ --- CREATE VIEW lysine_trna_primary_transcript AS SELECT feature_id AS lysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: methionine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding methionyl *** --- *** tRNA (SO:0000266). *** --- ************************************************ --- CREATE VIEW methionine_trna_primary_transcript AS SELECT feature_id AS methionine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: phe_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding phenylalan *** --- *** yl tRNA (SO:0000267). *** --- ************************************************ --- CREATE VIEW phe_trna_primary_transcript AS SELECT feature_id AS phe_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: proline_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding prolyl tRN *** --- *** A (SO:0000268). *** --- ************************************************ --- CREATE VIEW proline_trna_primary_transcript AS SELECT feature_id AS proline_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline_tRNA_primary_transcript'; --- ************************************************ --- *** relation: serine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW serine_trna_primary_transcript AS SELECT feature_id AS serine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: thr_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding threonyl t *** --- *** RNA (SO:000270). *** --- ************************************************ --- CREATE VIEW thr_trna_primary_transcript AS SELECT feature_id AS thr_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: try_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tryptophan *** --- *** yl tRNA (SO:000271). *** --- ************************************************ --- CREATE VIEW try_trna_primary_transcript AS SELECT feature_id AS try_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan_tRNA_primary_transcript'; --- ************************************************ --- *** relation: tyrosine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tyrosyl tR *** --- *** NA (SO:000272). *** --- ************************************************ --- CREATE VIEW tyrosine_trna_primary_transcript AS SELECT feature_id AS tyrosine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: valine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding valyl tRNA *** --- *** (SO:000273). *** --- ************************************************ --- CREATE VIEW valine_trna_primary_transcript AS SELECT feature_id AS valine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: snrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** clear RNA (SO:0000274). *** --- ************************************************ --- CREATE VIEW snrna_primary_transcript AS SELECT feature_id AS snrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_primary_transcript'; --- ************************************************ --- *** relation: snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar mRNA (SO:0000275). *** --- ************************************************ --- CREATE VIEW snorna_primary_transcript AS SELECT feature_id AS snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript'; --- ************************************************ --- *** relation: mature_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone the nec *** --- *** essary modifications, if any, for its fu *** --- *** nction. In eukaryotes this includes, for *** --- *** example, processing of introns, cleavag *** --- *** e, base modification, and modifications *** --- *** to the 5' and/or the 3' ends, other than *** --- *** addition of bases. In bacteria function *** --- *** al mRNAs are usually not modified. *** --- ************************************************ --- CREATE VIEW mature_transcript AS SELECT feature_id AS mature_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'mature_transcript'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not co *** --- *** ntain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a nucleotide molecule that b *** --- *** inds a Transcription Factor or Transcrip *** --- *** tion Factor complex [GO:0005667]. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The in-frame interval between the stop c *** --- *** odons of a reading frame which when read *** --- *** as sequential triplets, has the potenti *** --- *** al of encoding a sequential string of am *** --- *** ino acids. TER(NNN)nTER. *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'ORF'; --- ************************************************ --- *** relation: transcript_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transcript_attribute AS SELECT feature_id AS transcript_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'transcript_attribute'; --- ************************************************ --- *** relation: foldback_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element with extensive se *** --- *** condary structure, characterized by larg *** --- *** e modular imperfect long inverted repeat *** --- *** s. *** --- ************************************************ --- CREATE VIEW foldback_element AS SELECT feature_id AS foldback_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foldback_element'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequences extending on either side o *** --- *** f a specific region. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: chromosome_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_variation AS SELECT feature_id AS chromosome_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_variation'; --- ************************************************ --- *** relation: internal_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR bordered by the terminal and initi *** --- *** al codons of two CDSs in a polycistronic *** --- *** transcript. Every UTR is either 5', 3' *** --- *** or internal. *** --- ************************************************ --- CREATE VIEW internal_utr AS SELECT feature_id AS internal_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_UTR'; --- ************************************************ --- *** relation: untranslated_region_polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The untranslated sequence separating the *** --- *** 'cistrons' of multicistronic mRNA. *** --- ************************************************ --- CREATE VIEW untranslated_region_polycistronic_mrna AS SELECT feature_id AS untranslated_region_polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'untranslated_region_polycistronic_mRNA'; --- ************************************************ --- *** relation: internal_ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence element that recruits a ribosom *** --- *** al subunit to internal mRNA for translat *** --- *** ion initiation. *** --- ************************************************ --- CREATE VIEW internal_ribosome_entry_site AS SELECT feature_id AS internal_ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'internal_ribosome_entry_site'; --- ************************************************ --- *** relation: polyadenylated *** --- *** relation type: VIEW *** --- *** *** --- *** A attribute describing the addition of a *** --- *** poly A tail to the 3' end of a mRNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW polyadenylated AS SELECT feature_id AS polyadenylated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated'; --- ************************************************ --- *** relation: sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_length_variation AS SELECT feature_id AS sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'sequence_length_variation'; --- ************************************************ --- *** relation: modified_rna_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post_transcriptionally modified base. *** --- ************************************************ --- CREATE VIEW modified_rna_base_feature AS SELECT feature_id AS modified_rna_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_RNA_base_feature'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. Transfer R *** --- *** NAs have two regions of fundamental func *** --- *** tional importance: the anti-codon, which *** --- *** is responsible for specific mRNA codon *** --- *** recognition, and the 3' end, to which th *** --- *** e tRNA's corresponding amino acid is att *** --- *** ached (by aminoacyl-tRNA synthetases). T *** --- *** ransfer RNAs cope with the degeneracy of *** --- *** the genetic code in two manners: having *** --- *** more than one tRNA (with a specific ant *** --- *** i-codon) for a particular amino acid; an *** --- *** d 'wobble' base-pairing, i.e. permitting *** --- *** non-standard base-pairing at the 3rd an *** --- *** ti-codon position. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: alanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an alanine anti *** --- *** codon, and a 3' alanine binding region. *** --- ************************************************ --- CREATE VIEW alanyl_trna AS SELECT feature_id AS alanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA'; --- ************************************************ --- *** relation: rrna_small_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_small_subunit_primary_transcript AS SELECT feature_id AS rrna_small_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript'; --- ************************************************ --- *** relation: asparaginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an asparagine a *** --- *** nticodon, and a 3' asparagine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW asparaginyl_trna AS SELECT feature_id AS asparaginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparaginyl_tRNA'; --- ************************************************ --- *** relation: aspartyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an aspartic aci *** --- *** d anticodon, and a 3' aspartic acid bind *** --- *** ing region. *** --- ************************************************ --- CREATE VIEW aspartyl_trna AS SELECT feature_id AS aspartyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartyl_tRNA'; --- ************************************************ --- *** relation: cysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a cysteine anti *** --- *** codon, and a 3' cysteine binding region. *** --- ************************************************ --- CREATE VIEW cysteinyl_trna AS SELECT feature_id AS cysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteinyl_tRNA'; --- ************************************************ --- *** relation: glutaminyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamine ant *** --- *** icodon, and a 3' glutamine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW glutaminyl_trna AS SELECT feature_id AS glutaminyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutaminyl_tRNA'; --- ************************************************ --- *** relation: glutamyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamic acid *** --- *** anticodon, and a 3' glutamic acid bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW glutamyl_trna AS SELECT feature_id AS glutamyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamyl_tRNA'; --- ************************************************ --- *** relation: glycyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glycine antic *** --- *** odon, and a 3' glycine binding region. *** --- ************************************************ --- CREATE VIEW glycyl_trna AS SELECT feature_id AS glycyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycyl_tRNA'; --- ************************************************ --- *** relation: histidyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a histidine ant *** --- *** icodon, and a 3' histidine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW histidyl_trna AS SELECT feature_id AS histidyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidyl_tRNA'; --- ************************************************ --- *** relation: isoleucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an isoleucine a *** --- *** nticodon, and a 3' isoleucine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW isoleucyl_trna AS SELECT feature_id AS isoleucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucyl_tRNA'; --- ************************************************ --- *** relation: leucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a leucine antic *** --- *** odon, and a 3' leucine binding region. *** --- ************************************************ --- CREATE VIEW leucyl_trna AS SELECT feature_id AS leucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucyl_tRNA'; --- ************************************************ --- *** relation: lysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a lysine antico *** --- *** don, and a 3' lysine binding region. *** --- ************************************************ --- CREATE VIEW lysyl_trna AS SELECT feature_id AS lysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysyl_tRNA'; --- ************************************************ --- *** relation: methionyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a methionine an *** --- *** ticodon, and a 3' methionine binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW methionyl_trna AS SELECT feature_id AS methionyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionyl_tRNA'; --- ************************************************ --- *** relation: phenylalanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a phenylalanine *** --- *** anticodon, and a 3' phenylalanine bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW phenylalanyl_trna AS SELECT feature_id AS phenylalanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanyl_tRNA'; --- ************************************************ --- *** relation: prolyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a proline antic *** --- *** odon, and a 3' proline binding region. *** --- ************************************************ --- CREATE VIEW prolyl_trna AS SELECT feature_id AS prolyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prolyl_tRNA'; --- ************************************************ --- *** relation: seryl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a serine antico *** --- *** don, and a 3' serine binding region. *** --- ************************************************ --- CREATE VIEW seryl_trna AS SELECT feature_id AS seryl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seryl_tRNA'; --- ************************************************ --- *** relation: threonyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a threonine ant *** --- *** icodon, and a 3' threonine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW threonyl_trna AS SELECT feature_id AS threonyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonyl_tRNA'; --- ************************************************ --- *** relation: tryptophanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tryptophan an *** --- *** ticodon, and a 3' tryptophan binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW tryptophanyl_trna AS SELECT feature_id AS tryptophanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophanyl_tRNA'; --- ************************************************ --- *** relation: tyrosyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tyrosine anti *** --- *** codon, and a 3' tyrosine binding region. *** --- ************************************************ --- CREATE VIEW tyrosyl_trna AS SELECT feature_id AS tyrosyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosyl_tRNA'; --- ************************************************ --- *** relation: valyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a valine antico *** --- *** don, and a 3' valine binding region. *** --- ************************************************ --- CREATE VIEW valyl_trna AS SELECT feature_id AS valyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valyl_tRNA'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small nuclear RNA molecule involved in *** --- *** pre-mRNA splicing and processing. *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA (small nucleolar RNA) is any on *** --- *** e of a class of small RNAs that are asso *** --- *** ciated with the eukaryotic nucleus as co *** --- *** mponents of small nucleolar ribonucleopr *** --- *** oteins. They participate in the processi *** --- *** ng or modifications of many RNAs, mostly *** --- *** ribosomal RNAs (rRNAs) though snoRNAs a *** --- *** re also known to target other classes of *** --- *** RNA, including spliceosomal RNAs, tRNAs *** --- *** , and mRNAs via a stretch of sequence th *** --- *** at is complementary to a sequence in the *** --- *** targeted RNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. M *** --- *** icro RNAs are produced from precursor mo *** --- *** lecules (SO:0000647) that can form local *** --- *** hairpin structures, which ordinarily ar *** --- *** e processed (via the Dicer pathway) such *** --- *** that a single miRNA molecule accumulate *** --- *** s from one arm of a hairpin precursor mo *** --- *** lecule. Micro RNAs may trigger the cleav *** --- *** age of their target molecules or act as *** --- *** translational repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by another molecule. *** --- ************************************************ --- CREATE VIEW bound_by_factor AS SELECT feature_id AS bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'bound_by_factor'; --- ************************************************ --- *** relation: transcript_bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a nucleic *** --- *** acid. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_nucleic_acid AS SELECT feature_id AS transcript_bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_nucleic_acid'; --- ************************************************ --- *** relation: transcript_bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a protein. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_protein AS SELECT feature_id AS transcript_bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_protein'; --- ************************************************ --- *** relation: engineered_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_gene AS SELECT feature_id AS engineered_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_gene'; --- ************************************************ --- *** relation: engineered_foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_gene AS SELECT feature_id AS engineered_foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene'; --- ************************************************ --- *** relation: mrna_with_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a minus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_1_frameshift AS SELECT feature_id AS mrna_with_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element_gene AS SELECT feature_id AS engineered_foreign_transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene'; --- ************************************************ --- *** relation: foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_gene AS SELECT feature_id AS foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'foreign_gene'; --- ************************************************ --- *** relation: long_terminal_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence directly repeated at both end *** --- *** s of a defined sequence, of the sort typ *** --- *** ically found in retroviruses. *** --- ************************************************ --- CREATE VIEW long_terminal_repeat AS SELECT feature_id AS long_terminal_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'long_terminal_repeat'; --- ************************************************ --- *** relation: fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is a fusion. *** --- ************************************************ --- CREATE VIEW fusion_gene AS SELECT feature_id AS fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'fusion_gene'; --- ************************************************ --- *** relation: engineered_fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A fusion gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_fusion_gene AS SELECT feature_id AS engineered_fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat_region containing repeat_units *** --- *** (2 to 4 bp) that is repeated multiple ti *** --- *** mes in tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: dinucleotide_repeat_microsatellite_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dinucleotide_repeat_microsatellite_feature AS SELECT feature_id AS dinucleotide_repeat_microsatellite_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: trinuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trinuc_repeat_microsat AS SELECT feature_id AS trinuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: engineered_foreign_repetitive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element that is engineered *** --- *** and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_repetitive_element AS SELECT feature_id AS engineered_foreign_repetitive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_repetitive_element'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. It is a palindr *** --- *** ome, and it may, or may not be hyphenate *** --- *** d. Examples: GCTGATCAGC, or GCTGA-----TC *** --- *** AGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: u12_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A type of spliceosomal intron spliced by *** --- *** the U12 spliceosome, that includes U11, *** --- *** U12, U4atac/U6atac and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u12_intron AS SELECT feature_id AS u12_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_intron'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: d_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Displacement loop; a region within mitoc *** --- *** hondrial DNA in which a short stretch of *** --- *** RNA is paired with one strand of DNA, d *** --- *** isplacing the original partner DNA stran *** --- *** d in this region; also used to describe *** --- *** the displacement of a region of one stra *** --- *** nd of duplex DNA by a single stranded in *** --- *** vader in the reaction catalyzed by RecA *** --- *** protein. *** --- ************************************************ --- CREATE VIEW d_loop AS SELECT feature_id AS d_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop'; --- ************************************************ --- *** relation: recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature AS SELECT feature_id AS recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'recombination_feature'; --- ************************************************ --- *** relation: specific_recombination_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW specific_recombination_site AS SELECT feature_id AS specific_recombination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'specific_recombination_site'; --- ************************************************ --- *** relation: recombination_feature_of_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature_of_rearranged_gene AS SELECT feature_id AS recombination_feature_of_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'recombination_feature_of_rearranged_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature'; --- ************************************************ --- *** relation: j_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including J-heptame *** --- *** r, J-spacer and J-nonamer in 5' of J-reg *** --- *** ion of a J-gene or J-sequence. *** --- ************************************************ --- CREATE VIEW j_gene_recombination_feature AS SELECT feature_id AS j_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G. *** --- ************************************************ --- CREATE VIEW modified_base AS SELECT feature_id AS modified_base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'modified_base'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: experimentally_determined *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that has *** --- *** been experimentally verified. *** --- ************************************************ --- CREATE VIEW experimentally_determined AS SELECT feature_id AS experimentally_determined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined'; --- ************************************************ --- *** relation: stem_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A double-helical region of nucleic acid *** --- *** formed by base-pairing between adjacent *** --- *** (inverted) complementary sequences. *** --- ************************************************ --- CREATE VIEW stem_loop AS SELECT feature_id AS stem_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop' OR cvterm.name = 'stem_loop'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: tss *** --- *** relation type: VIEW *** --- *** *** --- *** The first base where RNA polymerase begi *** --- *** ns to synthesize the RNA transcript. *** --- ************************************************ --- CREATE VIEW tss AS SELECT feature_id AS tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'TSS'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS'; --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Complementary DNA; A piece of DNA copied *** --- *** from an mRNA and spliced into a vector *** --- *** for propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** First codon to be translated by a riboso *** --- *** me. *** --- ************************************************ --- CREATE VIEW start_codon AS SELECT feature_id AS start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'start_codon'; --- ************************************************ --- *** relation: stop_codon *** --- *** relation type: VIEW *** --- *** *** --- *** In mRNA, a set of three nucleotides that *** --- *** indicates the end of information for pr *** --- *** otein synthesis. *** --- ************************************************ --- CREATE VIEW stop_codon AS SELECT feature_id AS stop_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon'; --- ************************************************ --- *** relation: intronic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Sequences within the intron that modulat *** --- *** e splice site selection for some introns *** --- *** . *** --- ************************************************ --- CREATE VIEW intronic_splice_enhancer AS SELECT feature_id AS intronic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer'; --- ************************************************ --- *** relation: mrna_with_plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_1_frameshift AS SELECT feature_id AS mrna_with_plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_1_frameshift'; --- ************************************************ --- *** relation: nuclease_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclease_hypersensitive_site AS SELECT feature_id AS nuclease_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_hypersensitive_site'; --- ************************************************ --- *** relation: coding_start *** --- *** relation type: VIEW *** --- *** *** --- *** The first base to be translated into pro *** --- *** tein. *** --- ************************************************ --- CREATE VIEW coding_start AS SELECT feature_id AS coding_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna_large_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a large ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_large_subunit_primary_transcript AS SELECT feature_id AS rrna_large_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_large_subunit_primary_transcript'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: coding_end *** --- *** relation type: VIEW *** --- *** *** --- *** The last base to be translated into prot *** --- *** ein. It does not include the stop codon. *** --- ************************************************ --- CREATE VIEW coding_end AS SELECT feature_id AS coding_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_end'; --- ************************************************ --- *** relation: microarray_oligo *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW microarray_oligo AS SELECT feature_id AS microarray_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo'; --- ************************************************ --- *** relation: mrna_with_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_2_frameshift AS SELECT feature_id AS mrna_with_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_2_frameshift'; --- ************************************************ --- *** relation: conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of sequence similarity by descent *** --- *** from a common ancestor. *** --- ************************************************ --- CREATE VIEW conserved_region AS SELECT feature_id AS conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'conserved_region'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: coding_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Coding region of sequence similarity by *** --- *** descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW coding_conserved_region AS SELECT feature_id AS coding_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: nc_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding region of sequence similarity *** --- *** by descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW nc_conserved_region AS SELECT feature_id AS nc_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_conserved_region'; --- ************************************************ --- *** relation: mrna_with_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mRNA with a minus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_2_frameshift AS SELECT feature_id AS mrna_with_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_2_frameshift'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: mite *** --- *** relation type: VIEW *** --- *** *** --- *** A highly repetitive and short (100-500 b *** --- *** ase pair) transposable element with term *** --- *** inal inverted repeats (TIR) and target s *** --- *** ite duplication (TSD). MITEs do not enco *** --- *** de proteins. *** --- ************************************************ --- CREATE VIEW mite AS SELECT feature_id AS mite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE'; --- ************************************************ --- *** relation: recombination_hotspot *** --- *** relation type: VIEW *** --- *** *** --- *** A region in a genome which promotes reco *** --- *** mbination. *** --- ************************************************ --- CREATE VIEW recombination_hotspot AS SELECT feature_id AS recombination_hotspot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a nucleic ac *** --- *** id molecule which controls its own repli *** --- *** cation through the interaction of specif *** --- *** ic proteins at one or more origins of re *** --- *** plication. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** A cytologically distinguishable feature *** --- *** of a chromosome, often made visible by s *** --- *** taining, and usually alternating light a *** --- *** nd dark. *** --- ************************************************ --- CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: site_specific_recombination_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW site_specific_recombination_target_region AS SELECT feature_id AS site_specific_recombination_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'site_specific_recombination_target_region'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'match'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a cDNA clone or PCR product; t *** --- *** ypically a few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'EST'; --- ************************************************ --- *** relation: loxp_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loxp_site AS SELECT feature_id AS loxp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to repeating *** --- *** units. The forms found in nature are deo *** --- *** xyribonucleic acid (DNA), where the repe *** --- *** ating units are 2-deoxy-D-ribose rings c *** --- *** onnected to a phosphate backbone, and ri *** --- *** bonucleic acid (RNA), where the repeatin *** --- *** g units are D-ribose rings connected to *** --- *** a phosphate backbone. *** --- ************************************************ --- CREATE VIEW nucleic_acid AS SELECT feature_id AS nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'nucleic_acid'; --- ************************************************ --- *** relation: protein_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW protein_match AS SELECT feature_id AS protein_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: frt_site *** --- *** relation type: VIEW *** --- *** *** --- *** An inversion site found on the Saccharom *** --- *** yces cerevisiae 2 micron plasmid. *** --- ************************************************ --- CREATE VIEW frt_site AS SELECT feature_id AS frt_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site'; --- ************************************************ --- *** relation: synthetic_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to decide a sequence of nuc *** --- *** leotides, nucleotide analogs, or amino a *** --- *** cids that has been designed by an experi *** --- *** menter and which may, or may not, corres *** --- *** pond with any natural sequence. *** --- ************************************************ --- CREATE VIEW synthetic_sequence AS SELECT feature_id AS synthetic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'synthetic_sequence'; --- ************************************************ --- *** relation: dna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a 2-deoxy-D-ribose ring c *** --- *** onnected to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW dna AS SELECT feature_id AS dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'DNA'; --- ************************************************ --- *** relation: sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW sequence_assembly AS SELECT feature_id AS sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'sequence_assembly'; --- ************************************************ --- *** relation: group_1_intron_homing_endonuclease_target_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of intronic nucleotide sequence *** --- *** targeted by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW group_1_intron_homing_endonuclease_target_region AS SELECT feature_id AS group_1_intron_homing_endonuclease_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_1_intron_homing_endonuclease_target_region'; --- ************************************************ --- *** relation: haplotype_block *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome which is co-inher *** --- *** ited as the result of the lack of histor *** --- *** ic recombination within it. *** --- ************************************************ --- CREATE VIEW haplotype_block AS SELECT feature_id AS haplotype_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype_block'; --- ************************************************ --- *** relation: rna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a D-ribose ring connected *** --- *** to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW rna AS SELECT feature_id AS rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA'; --- ************************************************ --- *** relation: flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region that is *** --- *** bounded either side by a particular kin *** --- *** d of region. *** --- ************************************************ --- CREATE VIEW flanked AS SELECT feature_id AS flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'flanked'; --- ************************************************ --- *** relation: floxed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence that is *** --- *** flanked by Lox-P sites. *** --- ************************************************ --- CREATE VIEW floxed AS SELECT feature_id AS floxed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er code for a unique amino acid or the t *** --- *** ermination of translation and are contai *** --- *** ned within the CDS. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'codon'; --- ************************************************ --- *** relation: frt_flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe sequence that i *** --- *** s flanked by the FLP recombinase recogni *** --- *** tion site, FRT. *** --- ************************************************ --- CREATE VIEW frt_flanked AS SELECT feature_id AS frt_flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_flanked'; --- ************************************************ --- *** relation: invalidated_by_chimeric_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone constructed from more than *** --- *** one mRNA. Usually an experimental artifa *** --- *** ct. *** --- ************************************************ --- CREATE VIEW invalidated_by_chimeric_cdna AS SELECT feature_id AS invalidated_by_chimeric_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA'; --- ************************************************ --- *** relation: floxed_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene that is floxed. *** --- ************************************************ --- CREATE VIEW floxed_gene AS SELECT feature_id AS floxed_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene'; --- ************************************************ --- *** relation: transposable_element_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence surrounding a tra *** --- *** nsposable element. *** --- ************************************************ --- CREATE VIEW transposable_element_flanking_region AS SELECT feature_id AS transposable_element_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region'; --- ************************************************ --- *** relation: integron *** --- *** relation type: VIEW *** --- *** *** --- *** A region encoding an integrase which act *** --- *** s at a site adjacent to it (attI_site) t *** --- *** o insert DNA which must include but is n *** --- *** ot limited to an attC_site. *** --- ************************************************ --- CREATE VIEW integron AS SELECT feature_id AS integron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integron'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: atti_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an integron, adjacent to *** --- *** an integrase, at which site specific re *** --- *** combination involving an attC_site takes *** --- *** place. *** --- ************************************************ --- CREATE VIEW atti_site AS SELECT feature_id AS atti_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site'; --- ************************************************ --- *** relation: transposable_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW transposable_element_insertion_site AS SELECT feature_id AS transposable_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that encodes function requi *** --- *** red for conjugation. *** --- ************************************************ --- CREATE VIEW conjugative_transposon AS SELECT feature_id AS conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conjugative_transposon'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA sequence that has catalytic activ *** --- *** ity with or without an associated ribonu *** --- *** cleoprotein. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme' OR cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: recombinationally_inverted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene by i *** --- *** nversion. *** --- ************************************************ --- CREATE VIEW recombinationally_inverted_gene AS SELECT feature_id AS recombinationally_inverted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5_8S ribosomal RNA (5. 8S rRNA) is a com *** --- *** ponent of the large subunit of the eukar *** --- *** yotic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurs *** --- *** or that also contains 18S and 28S rRNA. *** --- *** Functionally, it is thought that 5.8S rR *** --- *** NA may be involved in ribosome transloca *** --- *** tion. It is also known to form covalent *** --- *** linkage to the p53 tumour suppressor pro *** --- *** tein. 5_8S rRNA is also found in archaea *** --- *** . *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S'; --- ************************************************ --- *** relation: rna_6s *** --- *** relation type: VIEW *** --- *** *** --- *** A small (184-nt in E. coli) RNA that for *** --- *** ms a hairpin type structure. 6S RNA asso *** --- *** ciates with RNA polymerase in a highly s *** --- *** pecific manner. 6S RNA represses express *** --- *** ion from a sigma70-dependent promoter du *** --- *** ring stationary phase. *** --- ************************************************ --- CREATE VIEW rna_6s AS SELECT feature_id AS rna_6s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_6S'; --- ************************************************ --- *** relation: csrb_rsmb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An enterobacterial RNA that binds the Cs *** --- *** rA protein. The CsrB RNAs contain a cons *** --- *** erved motif CAGGXXG that is found in up *** --- *** to 18 copies and has been suggested to b *** --- *** ind CsrA. The Csr regulatory system has *** --- *** a strong negative regulatory effect on g *** --- *** lycogen biosynthesis, glyconeogenesis an *** --- *** d glycogen catabolism and a positive reg *** --- *** ulatory effect on glycolysis. In other b *** --- *** acteria such as Erwinia caratovara the R *** --- *** smA protein has been shown to regulate t *** --- *** he production of virulence determinants, *** --- *** such extracellular enzymes. RsmA binds *** --- *** to RsmB regulatory RNA which is also a m *** --- *** ember of this family. *** --- ************************************************ --- CREATE VIEW csrb_rsmb_rna AS SELECT feature_id AS csrb_rsmb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CsrB_RsmB_RNA'; --- ************************************************ --- *** relation: dsra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** DsrA RNA regulates both transcription, b *** --- *** y overcoming transcriptional silencing b *** --- *** y the nucleoid-associated H-NS protein, *** --- *** and translation, by promoting efficient *** --- *** translation of the stress sigma factor, *** --- *** RpoS. These two activities of DsrA can b *** --- *** e separated by mutation: the first of th *** --- *** ree stem-loops of the 85 nucleotide RNA *** --- *** is necessary for RpoS translation but no *** --- *** t for anti-H-NS action, while the second *** --- *** stem-loop is essential for antisilencin *** --- *** g and less critical for RpoS translation *** --- *** . The third stem-loop, which behaves as *** --- *** a transcription terminator, can be subst *** --- *** ituted by the trp transcription terminat *** --- *** or without loss of either DsrA function. *** --- *** The sequence of the first stem-loop of *** --- *** DsrA is complementary with the upstream *** --- *** leader portion of RpoS messenger RNA, su *** --- *** ggesting that pairing of DsrA with the R *** --- *** poS message might be important for trans *** --- *** lational regulation. *** --- ************************************************ --- CREATE VIEW dsra_rna AS SELECT feature_id AS dsra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA' OR cvterm.name = 'DsrA_RNA'; --- ************************************************ --- *** relation: gcvb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA involved in exp *** --- *** ression of the dipeptide and oligopeptid *** --- *** e transport systems in Escherichia coli. *** --- ************************************************ --- CREATE VIEW gcvb_rna AS SELECT feature_id AS gcvb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: group_iia_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iia_intron AS SELECT feature_id AS group_iia_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron'; --- ************************************************ --- *** relation: group_iib_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iib_intron AS SELECT feature_id AS group_iib_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIB_intron'; --- ************************************************ --- *** relation: micf_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-translated 93 nt antisense RNA tha *** --- *** t binds its target ompF mRNA and regulat *** --- *** es ompF expression by inhibiting transla *** --- *** tion and inducing degradation of the mes *** --- *** sage. *** --- ************************************************ --- CREATE VIEW micf_rna AS SELECT feature_id AS micf_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA'; --- ************************************************ --- *** relation: oxys_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA which is induce *** --- *** d in response to oxidative stress in Esc *** --- *** herichia coli. Acts as a global regulato *** --- *** r to activate or repress the expression *** --- *** of as many as 40 genes, including the fh *** --- *** lA-encoded transcriptional activator and *** --- *** the rpoS-encoded sigma(s) subunit of RN *** --- *** A polymerase. OxyS is bound by the Hfq p *** --- *** rotein, that increases the OxyS RNA inte *** --- *** raction with its target messages. *** --- ************************************************ --- CREATE VIEW oxys_rna AS SELECT feature_id AS oxys_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'OxyS_RNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterized activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: rpra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Translational regulation of the stationa *** --- *** ry phase sigma factor RpoS is mediated b *** --- *** y the formation of a double-stranded RNA *** --- *** stem-loop structure in the upstream reg *** --- *** ion of the rpoS messenger RNA, occluding *** --- *** the translation initiation site. Clones *** --- *** carrying rprA (RpoS regulator RNA) incr *** --- *** eased the translation of RpoS. The rprA *** --- *** gene encodes a 106 nucleotide regulatory *** --- *** RNA. As with DsrA Rfam:RF00014, RprA is *** --- *** predicted to form three stem-loops. Thu *** --- *** s, at least two small RNAs, DsrA and Rpr *** --- *** A, participate in the positive regulatio *** --- *** n of RpoS translation. Unlike DsrA, RprA *** --- *** does not have an extensive region of co *** --- *** mplementarity to the RpoS leader, leavin *** --- *** g its mechanism of action unclear. RprA *** --- *** is non-essential. *** --- ************************************************ --- CREATE VIEW rpra_rna AS SELECT feature_id AS rpra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RprA_RNA'; --- ************************************************ --- *** relation: rre_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The Rev response element (RRE) is encode *** --- *** d within the HIV-env gene. Rev is an ess *** --- *** ential regulatory protein of HIV that bi *** --- *** nds an internal loop of the RRE leading, *** --- *** encouraging further Rev-RRE binding. Th *** --- *** is RNP complex is critical for mRNA expo *** --- *** rt and hence for expression of the HIV s *** --- *** tructural proteins. *** --- ************************************************ --- CREATE VIEW rre_rna AS SELECT feature_id AS rre_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RRE_RNA'; --- ************************************************ --- *** relation: spot_42_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A 109-nucleotide RNA of E. coli that see *** --- *** ms to have a regulatory role on the gala *** --- *** ctose operon. Changes in Spot 42 levels *** --- *** are implicated in affecting DNA polymera *** --- *** se I levels. *** --- ************************************************ --- CREATE VIEW spot_42_rna AS SELECT feature_id AS spot_42_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spot_42_RNA'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesizes telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA is an snRNA required for th *** --- *** e splicing of the minor U12-dependent cl *** --- *** ass of eukaryotic nuclear introns. It fo *** --- *** rms a base paired complex with U4atac_sn *** --- *** RNA (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: sequence_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describes a quality of sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW sequence_attribute AS SELECT feature_id AS sequence_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymer_attribute' OR cvterm.name = 'feature_attribute' OR cvterm.name = 'sequence_location' OR cvterm.name = 'variant_quality' OR cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'sequence_attribute'; --- ************************************************ --- *** relation: gene_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_attribute AS SELECT feature_id AS gene_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'gene_attribute'; --- ************************************************ --- *** relation: u14_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snorna AS SELECT feature_id AS u14_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonucleoprotein comp *** --- *** lex. The complex consists of a major vau *** --- *** lt protein (MVP), two minor vault protei *** --- *** ns (VPARP and TEP1), and several small u *** --- *** ntranslated RNA molecules. It has been s *** --- *** uggested that the vault complex is invol *** --- *** ved in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: twintron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron within an intron. Twintrons ar *** --- *** e group II or III introns, into which an *** --- *** other group II or III intron has been tr *** --- *** ansposed. *** --- ************************************************ --- CREATE VIEW twintron AS SELECT feature_id AS twintron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'twintron'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in eukaryotes, wh *** --- *** ich functions as the small subunit of th *** --- *** e ribosome. *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region of sequence that, in *** --- *** the molecule, interacts selectively and *** --- *** non-covalently with other molecules. A *** --- *** region on the surface of a molecule that *** --- *** may interact with another molecule. Whe *** --- *** n applied to polypeptides: Amino acids i *** --- *** nvolved in binding or interactions. It c *** --- *** an also apply to an amino acid bond whic *** --- *** h is represented by the positions of the *** --- *** two flanking amino acids. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith polypeptide molecules. *** --- ************************************************ --- CREATE VIEW protein_binding_site AS SELECT feature_id AS protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'protein_binding_site'; --- ************************************************ --- *** relation: rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that rescues. *** --- ************************************************ --- CREATE VIEW rescue_region AS SELECT feature_id AS rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'rescue_region'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polynucleotide sequence prod *** --- *** uced by digestion with a restriction end *** --- *** onuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment' OR cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequence differs from *** --- *** that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: invalidated_by_genomic_contamination *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to genomic contaminat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_contamination AS SELECT feature_id AS invalidated_by_genomic_contamination_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_contamination'; --- ************************************************ --- *** relation: invalidated_by_genomic_polya_primed_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to polyA priming. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_polya_primed_cdna AS SELECT feature_id AS invalidated_by_genomic_polya_primed_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA'; --- ************************************************ --- *** relation: invalidated_by_partial_processing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to partial processing *** --- *** . *** --- ************************************************ --- CREATE VIEW invalidated_by_partial_processing AS SELECT feature_id AS invalidated_by_partial_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_partial_processing'; --- ************************************************ --- *** relation: polypeptide_domain *** --- *** relation type: VIEW *** --- *** *** --- *** A structurally or functionally defined p *** --- *** rotein region. In proteins with multiple *** --- *** domains, the combination of the domains *** --- *** determines the function of the protein. *** --- *** A region which has been shown to recur *** --- *** throughout evolution. *** --- ************************************************ --- CREATE VIEW polypeptide_domain AS SELECT feature_id AS polypeptide_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The signal_peptide is a short region of *** --- *** the peptide located at the N-terminus th *** --- *** at directs the protein to be secreted or *** --- *** part of membrane components. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: mature_protein_region *** --- *** relation type: VIEW *** --- *** *** --- *** The polypeptide sequence that remains wh *** --- *** en the cleaved peptide regions have been *** --- *** cleaved from the immature peptide. *** --- ************************************************ --- CREATE VIEW mature_protein_region AS SELECT feature_id AS mature_protein_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide' OR cvterm.name = 'mature_protein_region'; --- ************************************************ --- *** relation: five_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_terminal_inverted_repeat AS SELECT feature_id AS five_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: three_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_terminal_inverted_repeat AS SELECT feature_id AS three_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: u5_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_ltr_region AS SELECT feature_id AS u5_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U5_LTR_region'; --- ************************************************ --- *** relation: r_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_ltr_region AS SELECT feature_id AS r_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'R_LTR_region'; --- ************************************************ --- *** relation: u3_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_ltr_region AS SELECT feature_id AS u3_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'U3_LTR_region'; --- ************************************************ --- *** relation: five_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr AS SELECT feature_id AS five_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR'; --- ************************************************ --- *** relation: three_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr AS SELECT feature_id AS three_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_LTR'; --- ************************************************ --- *** relation: r_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_five_prime_ltr_region AS SELECT feature_id AS r_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region'; --- ************************************************ --- *** relation: u5_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_five_prime_ltr_region AS SELECT feature_id AS u5_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region'; --- ************************************************ --- *** relation: u3_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_five_prime_ltr_region AS SELECT feature_id AS u3_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region'; --- ************************************************ --- *** relation: r_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_three_prime_ltr_region AS SELECT feature_id AS r_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region'; --- ************************************************ --- *** relation: u3_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_three_prime_ltr_region AS SELECT feature_id AS u3_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_three_prime_LTR_region'; --- ************************************************ --- *** relation: u5_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_three_prime_ltr_region AS SELECT feature_id AS u5_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_three_prime_LTR_region'; --- ************************************************ --- *** relation: non_ltr_retrotransposon_polymeric_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polymeric tract, such as poly(dA), wit *** --- *** hin a non_LTR_retrotransposon. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon_polymeric_tract AS SELECT feature_id AS non_ltr_retrotransposon_polymeric_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract'; --- ************************************************ --- *** relation: target_site_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of the target DNA that is dup *** --- *** licated when a transposable element or p *** --- *** hage inserts; usually found at each end *** --- *** the insertion. *** --- ************************************************ --- CREATE VIEW target_site_duplication AS SELECT feature_id AS target_site_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication'; --- ************************************************ --- *** relation: rr_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polypurine tract within an LTR_retrotr *** --- *** ansposon. *** --- ************************************************ --- CREATE VIEW rr_tract AS SELECT feature_id AS rr_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: inverted_ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_ring_chromosome AS SELECT feature_id AS inverted_ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome'; --- ************************************************ --- *** relation: vector_replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A replicon that has been modified to act *** --- *** as a vector for foreign sequence. *** --- ************************************************ --- CREATE VIEW vector_replicon AS SELECT feature_id AS vector_replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'vector_replicon'; --- ************************************************ --- *** relation: ss_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ss_oligo AS SELECT feature_id AS ss_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'ss_oligo'; --- ************************************************ --- *** relation: ds_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ds_oligo AS SELECT feature_id AS ds_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'ds_oligo'; --- ************************************************ --- *** relation: polymer_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the kind of bio *** --- *** logical sequence. *** --- ************************************************ --- CREATE VIEW polymer_attribute AS SELECT feature_id AS polymer_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'polymer_attribute'; --- ************************************************ --- *** relation: three_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_noncoding_exon AS SELECT feature_id AS three_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon'; --- ************************************************ --- *** relation: five_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_noncoding_exon AS SELECT feature_id AS five_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_noncoding_exon'; --- ************************************************ --- *** relation: utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Intron located in the untranslated regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW utr_intron AS SELECT feature_id AS utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'UTR_intron'; --- ************************************************ --- *** relation: five_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_intron AS SELECT feature_id AS five_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron'; --- ************************************************ --- *** relation: three_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_intron AS SELECT feature_id AS three_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR_intron'; --- ************************************************ --- *** relation: random_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides or amino acids *** --- *** which, by design, has a "random" order *** --- *** of components, given a predetermined inp *** --- *** ut frequency of these components. *** --- ************************************************ --- CREATE VIEW random_sequence AS SELECT feature_id AS random_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence'; --- ************************************************ --- *** relation: interband *** --- *** relation type: VIEW *** --- *** *** --- *** A light region between two darkly staini *** --- *** ng bands in a polytene chromosome. *** --- ************************************************ --- CREATE VIEW interband AS SELECT feature_id AS interband_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interband'; --- ************************************************ --- *** relation: gene_with_polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polyadenylated mRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW gene_with_polyadenylated_mrna AS SELECT feature_id AS gene_with_polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA'; --- ************************************************ --- *** relation: chromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant whereby a *** --- *** region of a chromosome has been transfe *** --- *** rred to another position. Among interchr *** --- *** omosomal rearrangements, the term transp *** --- *** osition is reserved for that class in wh *** --- *** ich the telomeres of the chromosomes inv *** --- *** olved are coupled (that is to say, form *** --- *** the two ends of a single DNA molecule) a *** --- *** s in wild-type. *** --- ************************************************ --- CREATE VIEW chromosomal_transposition AS SELECT feature_id AS chromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'chromosomal_transposition'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A 17-28-nt, small interfering RNA derive *** --- *** d from transcripts of repetitive element *** --- *** s. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: gene_with_mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA with a frame *** --- *** shift. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_with_frameshift AS SELECT feature_id AS gene_with_mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_with_frameshift'; --- ************************************************ --- *** relation: recombinationally_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is recombinationally rearran *** --- *** ged. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_gene AS SELECT feature_id AS recombinationally_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'recombinationally_rearranged_gene'; --- ************************************************ --- *** relation: interchromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving an in *** --- *** sertion from another chromosome. *** --- ************************************************ --- CREATE VIEW interchromosomal_duplication AS SELECT feature_id AS interchromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication'; --- ************************************************ --- *** relation: d_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including D-region *** --- *** with 5' UTR and 3' UTR, also designated *** --- *** as D-segment. *** --- ************************************************ --- CREATE VIEW d_gene AS SELECT feature_id AS d_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene'; --- ************************************************ --- *** relation: gene_with_trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a transcript that is trans-s *** --- *** pliced. *** --- ************************************************ --- CREATE VIEW gene_with_trans_spliced_transcript AS SELECT feature_id AS gene_with_trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_trans_spliced_transcript'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment'; --- ************************************************ --- *** relation: inversion_derived_bipartite_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at each *** --- *** end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_deficiency AS SELECT feature_id AS inversion_derived_bipartite_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: encodes_alternately_spliced_transcripts *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes more than one transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW encodes_alternately_spliced_transcripts AS SELECT feature_id AS encodes_alternately_spliced_transcripts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_alternately_spliced_transcripts'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendant of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome deletion whereby a chromoso *** --- *** me is generated by recombination between *** --- *** two inversions; there is a deficiency a *** --- *** t one end of the inversion and a duplica *** --- *** tion at the other end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_duplication AS SELECT feature_id AS inversion_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: v_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including L-part1, *** --- *** V-intron and V-exon, with the 5' UTR and *** --- *** 3' UTR. *** --- ************************************************ --- CREATE VIEW v_gene AS SELECT feature_id AS v_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_stability *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is regulated *** --- *** by the stability of the resulting prote *** --- *** in. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_stability AS SELECT feature_id AS post_translationally_regulated_by_protein_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is modified *** --- *** to regulate it. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_modification AS SELECT feature_id AS post_translationally_regulated_by_protein_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_modification'; --- ************************************************ --- *** relation: j_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA of an immunoglobuli *** --- *** n/T-cell receptor gene including J-regio *** --- *** n with 5' UTR (SO:0000204) and 3' UTR (S *** --- *** O:0000205), also designated as J-segment *** --- *** . *** --- ************************************************ --- CREATE VIEW j_gene AS SELECT feature_id AS j_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene'; --- ************************************************ --- *** relation: autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation. *** --- ************************************************ --- CREATE VIEW autoregulated AS SELECT feature_id AS autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'autoregulated'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: negatively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation where it decr *** --- *** eases transcription. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated AS SELECT feature_id AS negatively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path (SO:0000472). *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone' OR cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: positively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation, where it inc *** --- *** reases transcription. *** --- ************************************************ --- CREATE VIEW positively_autoregulated AS SELECT feature_id AS positively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated'; --- ************************************************ --- *** relation: contig_read *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequencer read which is part of a *** --- *** contig. *** --- ************************************************ --- CREATE VIEW contig_read AS SELECT feature_id AS contig_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read'; --- ************************************************ --- *** relation: c_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including C-region (and intro *** --- *** ns if present) with 5' UTR (SO:0000204) *** --- *** and 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW c_gene AS SELECT feature_id AS c_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_gene'; --- ************************************************ --- *** relation: trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_transcript AS SELECT feature_id AS trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'trans_spliced_transcript'; --- ************************************************ --- *** relation: tiling_path_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone which is part of a tiling path. *** --- *** A tiling path is a set of sequencing sub *** --- *** strates, typically clones, which have be *** --- *** en selected in order to efficiently cove *** --- *** r a region of the genome in preparation *** --- *** for sequencing and assembly. *** --- ************************************************ --- CREATE VIEW tiling_path_clone AS SELECT feature_id AS tiling_path_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone'; --- ************************************************ --- *** relation: terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An inverted repeat (SO:0000294) occurrin *** --- *** g at the termini of a DNA transposon. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat AS SELECT feature_id AS terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'terminal_inverted_repeat'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_gene_cluster AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: three_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 3' exon that is not *** --- *** coding. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_noncoding_region AS SELECT feature_id AS three_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene, and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW dj_j_cluster AS SELECT feature_id AS dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster'; --- ************************************************ --- *** relation: five_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 5' exon preceding th *** --- *** e start codon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_noncoding_region AS SELECT feature_id AS five_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene, one J-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW vdj_j_c_cluster AS SELECT feature_id AS vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_j_cluster AS SELECT feature_id AS vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_cluster'; --- ************************************************ --- *** relation: vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_c_cluster AS SELECT feature_id AS vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_C_cluster'; --- ************************************************ --- *** relation: vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene, one J-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW vj_j_c_cluster AS SELECT feature_id AS vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_C_cluster'; --- ************************************************ --- *** relation: vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one J- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_j_cluster AS SELECT feature_id AS vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_cluster'; --- ************************************************ --- *** relation: d_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_gene_recombination_feature AS SELECT feature_id AS d_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'D_gene_recombination_feature'; --- ************************************************ --- *** relation: three_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site like CAC *** --- *** AGTG, part of a 3' D-recombination signa *** --- *** l sequence of an immunoglobulin/T-cell r *** --- *** eceptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_heptamer AS SELECT feature_id AS three_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer'; --- ************************************************ --- *** relation: three_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** A 9 nucleotide recombination site (e.g. *** --- *** ACAAAAACC), part of a 3' D-recombination *** --- *** signal sequence of an immunoglobulin/T- *** --- *** cell receptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_nonamer AS SELECT feature_id AS three_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer'; --- ************************************************ --- *** relation: three_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** A 12 or 23 nucleotide spacer between the *** --- *** 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-R *** --- *** S. *** --- ************************************************ --- CREATE VIEW three_prime_d_spacer AS SELECT feature_id AS three_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer'; --- ************************************************ --- *** relation: five_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CTGTG), part of a 5' D-recombination sig *** --- *** nal sequence (SO:0000556) of an immunogl *** --- *** obulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_heptamer AS SELECT feature_id AS five_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_heptamer'; --- ************************************************ --- *** relation: five_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a five_prime_D-recombi *** --- *** nation signal sequence (SO:0000556) of a *** --- *** n immunoglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_nonamer AS SELECT feature_id AS five_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_nonamer'; --- ************************************************ --- *** relation: five_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the 5 *** --- *** ' D-heptamer (SO:0000496) and 5' D-nonam *** --- *** er (SO:0000497) of a 5' D-recombination *** --- *** signal sequence (SO:0000556) of an immun *** --- *** oglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_spacer AS SELECT feature_id AS five_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_spacer'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous piece of sequence similar t *** --- *** o the 'virtual contig' concept of the En *** --- *** sembl database. *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. Th *** --- *** is is less energetically favourable than *** --- *** watson crick base pairing. Hoogsteen GC *** --- *** base pairs only have two hydrogen bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW hoogsteen_base_pair AS SELECT feature_id AS hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Hoogsteen_base_pair'; --- ************************************************ --- *** relation: reverse_hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW reverse_hoogsteen_base_pair AS SELECT feature_id AS reverse_hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_Hoogsteen_base_pair'; --- ************************************************ --- *** relation: d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_c_cluster AS SELECT feature_id AS d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_C_cluster'; --- ************************************************ --- *** relation: d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW d_dj_cluster AS SELECT feature_id AS d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_cluster'; --- ************************************************ --- *** relation: d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_c_cluster AS SELECT feature_id AS d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of an exon, *** --- *** part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, and one J-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_cluster AS SELECT feature_id AS d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_cluster'; --- ************************************************ --- *** relation: d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW d_j_c_cluster AS SELECT feature_id AS d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster'; --- ************************************************ --- *** relation: vd_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including L-part1, V-intron and V *** --- *** -D-exon, with the 5' UTR (SO:0000204) an *** --- *** d 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vd_gene AS SELECT feature_id AS vd_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene'; --- ************************************************ --- *** relation: j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one J-gene and one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW j_c_cluster AS SELECT feature_id AS j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at one e *** --- *** nd and presumed to have a deficiency or *** --- *** duplication at the other end of the inve *** --- *** rsion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_aneuploid AS SELECT feature_id AS inversion_derived_deficiency_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_aneuploid'; --- ************************************************ --- *** relation: j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one J-gene. *** --- ************************************************ --- CREATE VIEW j_cluster AS SELECT feature_id AS j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_cluster'; --- ************************************************ --- *** relation: j_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a J-gene recombination *** --- *** feature of an immunoglobulin/T-cell rec *** --- *** eptor gene. *** --- ************************************************ --- CREATE VIEW j_nonamer AS SELECT feature_id AS j_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_nonamer'; --- ************************************************ --- *** relation: j_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of a J-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW j_heptamer AS SELECT feature_id AS j_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_heptamer'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of a transcr *** --- *** ipt, part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: j_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the J *** --- *** -nonamer and the J-heptamer of a J-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW j_spacer AS SELECT feature_id AS j_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_spacer'; --- ************************************************ --- *** relation: v_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_dj_cluster AS SELECT feature_id AS v_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_cluster'; --- ************************************************ --- *** relation: v_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_cluster AS SELECT feature_id AS v_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_cluster'; --- ************************************************ --- *** relation: v_vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_c_cluster AS SELECT feature_id AS v_vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_C_cluster'; --- ************************************************ --- *** relation: v_vdj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VDJ *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW v_vdj_cluster AS SELECT feature_id AS v_vdj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_cluster'; --- ************************************************ --- *** relation: v_vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_cluster AS SELECT feature_id AS v_vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_cluster'; --- ************************************************ --- *** relation: v_vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_c_cluster AS SELECT feature_id AS v_vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_C_cluster'; --- ************************************************ --- *** relation: v_vj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_vj_cluster AS SELECT feature_id AS v_vj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_cluster'; --- ************************************************ --- *** relation: v_vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_cluster AS SELECT feature_id AS v_vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_cluster'; --- ************************************************ --- *** relation: v_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one V-gene. *** --- ************************************************ --- CREATE VIEW v_cluster AS SELECT feature_id AS v_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_cluster'; --- ************************************************ --- *** relation: v_d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_c_cluster AS SELECT feature_id AS v_d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_cluster AS SELECT feature_id AS v_d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene, one J-gene and one C-gene *** --- *** . *** --- ************************************************ --- CREATE VIEW v_d_dj_j_c_cluster AS SELECT feature_id AS v_d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_j_cluster AS SELECT feature_id AS v_d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_cluster'; --- ************************************************ --- *** relation: v_d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_c_cluster AS SELECT feature_id AS v_d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_C_cluster'; --- ************************************************ --- *** relation: v_d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_cluster AS SELECT feature_id AS v_d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_cluster'; --- ************************************************ --- *** relation: v_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of V-gene recombination fea *** --- *** ture of an immunoglobulin/T-cell recepto *** --- *** r gene. *** --- ************************************************ --- CREATE VIEW v_heptamer AS SELECT feature_id AS v_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_heptamer'; --- ************************************************ --- *** relation: v_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW v_j_cluster AS SELECT feature_id AS v_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_cluster'; --- ************************************************ --- *** relation: v_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW v_j_c_cluster AS SELECT feature_id AS v_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_C_cluster'; --- ************************************************ --- *** relation: v_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. AC *** --- *** AAAAACC), part of V-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW v_nonamer AS SELECT feature_id AS v_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_nonamer'; --- ************************************************ --- *** relation: v_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the V *** --- *** -heptamer and the V-nonamer of a V-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_spacer AS SELECT feature_id AS v_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_spacer'; --- ************************************************ --- *** relation: v_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including V-heptame *** --- *** r, V-spacer and V-nonamer in 3' of V-reg *** --- *** ion of a V-gene or V-sequence of an immu *** --- *** noglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_gene_recombination_feature AS SELECT feature_id AS v_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene_recombination_feature'; --- ************************************************ --- *** relation: dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW dj_c_cluster AS SELECT feature_id AS dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_C_cluster'; --- ************************************************ --- *** relation: dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA in rearranged configuration *** --- *** including at least one D-J-GENE, one J-G *** --- *** ENE and one C-GENE. *** --- ************************************************ --- CREATE VIEW dj_j_c_cluster AS SELECT feature_id AS dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one C *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_c_cluster AS SELECT feature_id AS vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_C_cluster'; --- ************************************************ --- *** relation: v_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_c_cluster AS SELECT feature_id AS v_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_C_cluster'; --- ************************************************ --- *** relation: helitron *** --- *** relation type: VIEW *** --- *** *** --- *** A rolling circle transposon. Autonomous *** --- *** helitrons encode a 5'-to-3' DNA helicase *** --- *** and nuclease/ligase similar to those en *** --- *** coded by known rolling-circle replicons. *** --- ************************************************ --- CREATE VIEW helitron AS SELECT feature_id AS helitron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helitron'; --- ************************************************ --- *** relation: recoding_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** The pseudoknots involved in recoding are *** --- *** unique in that, as they play their role *** --- *** as a structure, they are immediately un *** --- *** folded and their now linear sequence ser *** --- *** ves as a template for decoding. *** --- ************************************************ --- CREATE VIEW recoding_pseudoknot AS SELECT feature_id AS recoding_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot'; --- ************************************************ --- *** relation: designed_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW designed_sequence AS SELECT feature_id AS designed_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'designed_sequence'; --- ************************************************ --- *** relation: inversion_derived_bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a dupli *** --- *** cation at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_duplication AS SELECT feature_id AS inversion_derived_bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_duplication'; --- ************************************************ --- *** relation: gene_with_edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript that is *** --- *** edited. *** --- ************************************************ --- CREATE VIEW gene_with_edited_transcript AS SELECT feature_id AS gene_with_edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_edited_transcript'; --- ************************************************ --- *** relation: inversion_derived_duplication_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a duplicatio *** --- *** n at one end and presumed to have a defi *** --- *** ciency or duplication at the other end o *** --- *** f the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_duplication_plus_aneuploid AS SELECT feature_id AS inversion_derived_duplication_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_duplication_plus_aneuploid'; --- ************************************************ --- *** relation: aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structural variation whereb *** --- *** y either a chromosome exists in addition *** --- *** to the normal chromosome complement or *** --- *** is lacking. *** --- ************************************************ --- CREATE VIEW aneuploid_chromosome AS SELECT feature_id AS aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'aneuploid_chromosome'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region in the 5' UTR that pairs with t *** --- *** he 16S rRNA during formation of the prei *** --- *** nitiation complex. *** --- ************************************************ --- CREATE VIEW shine_dalgarno_sequence AS SELECT feature_id AS shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. The bound *** --- *** ary between the UTR and the polyA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: five_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 5' most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW five_prime_clip AS SELECT feature_id AS five_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip'; --- ************************************************ --- *** relation: five_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 5' *** --- *** D-nonamer (SO:0000497), 5' D-spacer (SO *** --- *** :0000498), and 5' D-heptamer (SO:0000396 *** --- *** ) in 5' of the D-region of a D-gene, or *** --- *** in 5' of the D-region of DJ-gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_recombination_signal_sequence AS SELECT feature_id AS five_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: three_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 3'-most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW three_prime_clip AS SELECT feature_id AS three_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_clip'; --- ************************************************ --- *** relation: c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including more than one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW c_cluster AS SELECT feature_id AS c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_cluster'; --- ************************************************ --- *** relation: d_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one D-gene. *** --- ************************************************ --- CREATE VIEW d_cluster AS SELECT feature_id AS d_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_cluster'; --- ************************************************ --- *** relation: d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW d_j_cluster AS SELECT feature_id AS d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_cluster'; --- ************************************************ --- *** relation: heptamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Seven nucleotide recombination site (e.g *** --- *** . CACAGTG), part of V-gene, D-gene or J- *** --- *** gene recombination feature of an immunog *** --- *** lobulin or T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW heptamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS heptamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: nonamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nonamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS nonamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_spacer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_spacer AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer'; --- ************************************************ --- *** relation: v_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_c_cluster AS SELECT feature_id AS v_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_c_cluster AS SELECT feature_id AS v_vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_c_cluster AS SELECT feature_id AS v_vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome may be generated by recombi *** --- *** nation between two inversions; presumed *** --- *** to have a deficiency or duplication at e *** --- *** ach end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_aneuploid_chromosome AS SELECT feature_id AS inversion_derived_aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome'; --- ************************************************ --- *** relation: bidirectional_promoter *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bidirectional_promoter AS SELECT feature_id AS bidirectional_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter'; --- ************************************************ --- *** relation: retrotransposed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of a feature that occurred *** --- *** as the product of a reverse transcriptas *** --- *** e mediated event. *** --- ************************************************ --- CREATE VIEW retrotransposed AS SELECT feature_id AS retrotransposed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposed'; --- ************************************************ --- *** relation: three_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 3' *** --- *** D-heptamer (SO:0000493), 3' D-spacer, a *** --- *** nd 3' D-nonamer (SO:0000494) in 3' of th *** --- *** e D-region of a D-gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_recombination_signal_sequence AS SELECT feature_id AS three_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: mirna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_encoding AS SELECT feature_id AS mirna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding'; --- ************************************************ --- *** relation: dj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including D-J-region with 5' UTR *** --- *** and 3' UTR, also designated as D-J-segme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW dj_gene AS SELECT feature_id AS dj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_gene'; --- ************************************************ --- *** relation: rrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rrna_encoding AS SELECT feature_id AS rrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_encoding'; --- ************************************************ --- *** relation: vdj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-D-J-exon, with the 5'UTR *** --- *** (SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vdj_gene AS SELECT feature_id AS vdj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_gene'; --- ************************************************ --- *** relation: scrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_encoding AS SELECT feature_id AS scrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_encoding'; --- ************************************************ --- *** relation: vj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-J-exon, with the 5'UTR ( *** --- *** SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vj_gene AS SELECT feature_id AS vj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_gene'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'centromere'; --- ************************************************ --- *** relation: snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_encoding AS SELECT feature_id AS snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'snoRNA_encoding'; --- ************************************************ --- *** relation: edited_transcript_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable feature on a transcript that *** --- *** is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript_feature AS SELECT feature_id AS edited_transcript_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'edited_transcript_feature'; --- ************************************************ --- *** relation: methylation_guide_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a methylat *** --- *** ion guide small nucleolar RNA. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna_primary_transcript AS SELECT feature_id AS methylation_guide_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: rrna_cleavage_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding an rRNA cl *** --- *** eavage snoRNA. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_snorna_primary_transcript AS SELECT feature_id AS rrna_cleavage_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: pre_edited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a transcript that will be *** --- *** edited. *** --- ************************************************ --- CREATE VIEW pre_edited_region AS SELECT feature_id AS pre_edited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region'; --- ************************************************ --- *** relation: tmrna *** --- *** relation type: VIEW *** --- *** *** --- *** A tmRNA liberates a mRNA from a stalled *** --- *** ribosome. To accomplish this part of the *** --- *** tmRNA is used as a reading frame that e *** --- *** nds in a translation stop signal. The br *** --- *** oken mRNA is replaced in the ribosome by *** --- *** the tmRNA and translation of the tmRNA *** --- *** leads to addition of a proteolysis tag t *** --- *** o the incomplete protein enabling recogn *** --- *** ition by a protease. Recently a number o *** --- *** f permuted tmRNAs genes have been found *** --- *** encoded in two parts. TmRNAs have been i *** --- *** dentified in eubacteria and some chlorop *** --- *** lasts but are absent from archeal and Eu *** --- *** karyote nuclear genomes. *** --- ************************************************ --- CREATE VIEW tmrna AS SELECT feature_id AS tmrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_encoding AS SELECT feature_id AS c_d_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding'; --- ************************************************ --- *** relation: tmrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tmRNA (S *** --- *** O:0000584). *** --- ************************************************ --- CREATE VIEW tmrna_primary_transcript AS SELECT feature_id AS tmrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_primary_transcript'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyze their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: autocatalytically_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW autocatalytically_spliced_intron AS SELECT feature_id AS autocatalytically_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: srp_rna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a signal r *** --- *** ecognition particle RNA. *** --- ************************************************ --- CREATE VIEW srp_rna_primary_transcript AS SELECT feature_id AS srp_rna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_primary_transcript'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A tertiary structure in RNA where nucleo *** --- *** tides in a loop form base pairs with a r *** --- *** egion of RNA downstream of the loop. *** --- ************************************************ --- CREATE VIEW pseudoknot AS SELECT feature_id AS pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'pseudoknot'; --- ************************************************ --- *** relation: h_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudoknot which contains two stems an *** --- *** d at least two loops. *** --- ************************************************ --- CREATE VIEW h_pseudoknot AS SELECT feature_id AS h_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_pseudoknot'; --- ************************************************ --- *** relation: c_d_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Most box C/D snoRNAs also contain long ( *** --- *** >10 nt) sequences complementary to rRNA. *** --- *** Boxes C and D, as well as boxes C' and *** --- *** D', are usually located in close proximi *** --- *** ty, and form a structure known as the bo *** --- *** x C/D motif. This motif is important for *** --- *** snoRNA stability, processing, nucleolar *** --- *** targeting and function. A small number *** --- *** of box C/D snoRNAs are involved in rRNA *** --- *** processing; most, however, are known or *** --- *** predicted to serve as guide RNAs in ribo *** --- *** se methylation of rRNA. Targeting involv *** --- *** es direct base pairing of the snoRNA at *** --- *** the rRNA site to be modified and selecti *** --- *** on of a rRNA nucleotide a fixed distance *** --- *** from box D or D'. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna AS SELECT feature_id AS c_d_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'C_D_box_snoRNA'; --- ************************************************ --- *** relation: h_aca_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Members of the box H/ACA family contain *** --- *** an ACA triplet, exactly 3 nt upstream fr *** --- *** om the 3' end and an H-box in a hinge re *** --- *** gion that links two structurally similar *** --- *** functional domains of the molecule. Bot *** --- *** h boxes are important for snoRNA biosynt *** --- *** hesis and function. A few box H/ACA snoR *** --- *** NAs are involved in rRNA processing; mos *** --- *** t others are known or predicted to parti *** --- *** cipate in selection of uridine nucleosid *** --- *** es in rRNA to be converted to pseudourid *** --- *** ines. Site selection is mediated by dire *** --- *** ct base pairing of the snoRNA with rRNA *** --- *** through one or both targeting domains. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna AS SELECT feature_id AS h_aca_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box C/D family. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_primary_transcript AS SELECT feature_id AS c_d_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: h_aca_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box H/ACA family. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_primary_transcript AS SELECT feature_id AS h_aca_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a duplex (except for its post-transcript *** --- *** ionally added oligo_U tail (SO:0000609)) *** --- *** with a stretch of mature edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: editing_block *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by a singl *** --- *** e guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW editing_block AS SELECT feature_id AS editing_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_block'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing or overlapping no ge *** --- *** nes that is bounded on either side by a *** --- *** gene, or bounded by a gene and the end o *** --- *** f the chromosome. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: editing_domain *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by two or *** --- *** more overlapping guide RNAs (SO:0000602) *** --- *** . *** --- ************************************************ --- CREATE VIEW editing_domain AS SELECT feature_id AS editing_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_domain'; --- ************************************************ --- *** relation: unedited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an edited transcript that *** --- *** will not be edited. *** --- ************************************************ --- CREATE VIEW unedited_region AS SELECT feature_id AS unedited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unedited_region'; --- ************************************************ --- *** relation: h_aca_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_encoding AS SELECT feature_id AS h_aca_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_encoding'; --- ************************************************ --- *** relation: oligo_u_tail *** --- *** relation type: VIEW *** --- *** *** --- *** The string of non-encoded U's at the 3' *** --- *** end of a guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW oligo_u_tail AS SELECT feature_id AS oligo_u_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo_U_tail'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which bacterial RNA po *** --- *** lymerase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter AS SELECT feature_id AS bacterial_rnapol_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'bacterial_RNApol_promoter'; --- ************************************************ --- *** relation: bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for bacterial transc *** --- *** ription. *** --- ************************************************ --- CREATE VIEW bacterial_terminator AS SELECT feature_id AS bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'bacterial_terminator'; --- ************************************************ --- *** relation: terminator_of_type_2_rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for RNA polymerase I *** --- *** II transcription. *** --- ************************************************ --- CREATE VIEW terminator_of_type_2_rnapol_iii_promoter AS SELECT feature_id AS terminator_of_type_2_rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter'; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The base where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_1 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_1 AS SELECT feature_id AS rnapol_iii_promoter_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_2 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_2 AS SELECT feature_id AS rnapol_iii_promoter_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_2'; --- ************************************************ --- *** relation: a_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence TGGCnnAGTGG. *** --- ************************************************ --- CREATE VIEW a_box AS SELECT feature_id AS a_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'A_box'; --- ************************************************ --- *** relation: b_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence AGGTTCCAnnCC. *** --- ************************************************ --- CREATE VIEW b_box AS SELECT feature_id AS b_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'B_box'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_3 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_3 AS SELECT feature_id AS rnapol_iii_promoter_type_3_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_3'; --- ************************************************ --- *** relation: c_box *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA polymerase III type 1 promoter wi *** --- *** th consensus sequence CAnnCCn. *** --- ************************************************ --- CREATE VIEW c_box AS SELECT feature_id AS c_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_box'; --- ************************************************ --- *** relation: snrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_encoding AS SELECT feature_id AS snrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_encoding'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenance of the end. *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region which upon binding o *** --- *** f transcription factors, suppress the tr *** --- *** anscription of the gene or genes they co *** --- *** ntrol. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: chromosomal_regulatory_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_regulatory_element AS SELECT feature_id AS chromosomal_regulatory_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'chromosomal_regulatory_element'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional cis regulatory region *** --- *** that when located between a CM and a gen *** --- *** e's promoter prevents the CRM from modul *** --- *** ating that genes expression. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: five_prime_open_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_open_reading_frame AS SELECT feature_id AS five_prime_open_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_open_reading_frame'; --- ************************************************ --- *** relation: upstream_aug_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon upstream of the ORF. *** --- ************************************************ --- CREATE VIEW upstream_aug_codon AS SELECT feature_id AS upstream_aug_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon'; --- ************************************************ --- *** relation: polycistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for more t *** --- *** han one gene product. *** --- ************************************************ --- CREATE VIEW polycistronic_primary_transcript AS SELECT feature_id AS polycistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for one ge *** --- *** ne product. *** --- ************************************************ --- CREATE VIEW monocistronic_primary_transcript AS SELECT feature_id AS monocistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with either a single protein pro *** --- *** duct, or for which the regions encoding *** --- *** all its protein products overlap. *** --- ************************************************ --- CREATE VIEW monocistronic_mrna AS SELECT feature_id AS monocistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_mRNA'; --- ************************************************ --- *** relation: polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that encodes multiple proteins f *** --- *** rom at least two non-overlapping regions *** --- *** . *** --- ************************************************ --- CREATE VIEW polycistronic_mrna AS SELECT feature_id AS polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA'; --- ************************************************ --- *** relation: mini_exon_donor_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that donates the sp *** --- *** liced leader to other mRNA. *** --- ************************************************ --- CREATE VIEW mini_exon_donor_rna AS SELECT feature_id AS mini_exon_donor_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_exon_donor_RNA'; --- ************************************************ --- *** relation: spliced_leader_rna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW spliced_leader_rna AS SELECT feature_id AS spliced_leader_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliced_leader_RNA'; --- ************************************************ --- *** relation: engineered_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_plasmid AS SELECT feature_id AS engineered_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_plasmid'; --- ************************************************ --- *** relation: transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Part of an rRNA transcription unit that *** --- *** is transcribed but discarded during matu *** --- *** ration, not giving rise to any part of r *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW transcribed_spacer_region AS SELECT feature_id AS transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'transcribed_spacer_region'; --- ************************************************ --- *** relation: internal_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA sequence that *** --- *** separate genes coding for the 28S, 5.8S, *** --- *** and 18S ribosomal RNAs. *** --- ************************************************ --- CREATE VIEW internal_transcribed_spacer_region AS SELECT feature_id AS internal_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region'; --- ************************************************ --- *** relation: external_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA that precede t *** --- *** he sequence that codes for the ribosomal *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW external_transcribed_spacer_region AS SELECT feature_id AS external_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'external_transcribed_spacer_region'; --- ************************************************ --- *** relation: tetranuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tetranuc_repeat_microsat AS SELECT feature_id AS tetranuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetranucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: srp_rna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_encoding AS SELECT feature_id AS srp_rna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_encoding'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region containing tandemly repe *** --- *** ated sequences having a unit length of 1 *** --- *** 0 to 40 bp. *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA' OR cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small RNA molecule that is the product *** --- *** of a longer exogenous or endogenous dsR *** --- *** NA, which is either a bimolecular duplex *** --- *** or very long hairpin, processed (via th *** --- *** e Dicer pathway) such that numerous siRN *** --- *** As accumulate from both strands of the d *** --- *** sRNA. SRNAs trigger the cleavage of thei *** --- *** r target molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: mirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a micro RN *** --- *** A. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript AS SELECT feature_id AS mirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript'; --- ************************************************ --- *** relation: strna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small te *** --- *** mporal mRNA (SO:0000649). *** --- ************************************************ --- CREATE VIEW strna_primary_transcript AS SELECT feature_id AS strna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: small_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the small subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW small_subunit_rrna AS SELECT feature_id AS small_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'small_subunit_rRNA'; --- ************************************************ --- *** relation: large_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the large subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW large_subunit_rrna AS SELECT feature_id AS large_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'large_subunit_rRNA'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilizes 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: maxicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mitochondrial gene located in a maxici *** --- *** rcle. *** --- ************************************************ --- CREATE VIEW maxicircle_gene AS SELECT feature_id AS maxicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'maxicircle_gene'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA transcript that does not encode f *** --- *** or a protein rather the RNA molecule is *** --- *** the gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: strna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_encoding AS SELECT feature_id AS strna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_encoding'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: tmrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_encoding AS SELECT feature_id AS tmrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_encoding'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: trna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_encoding AS SELECT feature_id AS trna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_encoding'; --- ************************************************ --- *** relation: introgressed_chromosome_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW introgressed_chromosome_region AS SELECT feature_id AS introgressed_chromosome_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'introgressed_chromosome_region'; --- ************************************************ --- *** relation: monocistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is monocistronic. *** --- ************************************************ --- CREATE VIEW monocistronic_transcript AS SELECT feature_id AS monocistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'monocistronic_transcript'; --- ************************************************ --- *** relation: mobile_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron (mitochondrial, chloroplast, n *** --- *** uclear or prokaryotic) that encodes a do *** --- *** uble strand sequence specific endonuclea *** --- *** se allowing for mobility. *** --- ************************************************ --- CREATE VIEW mobile_intron AS SELECT feature_id AS mobile_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of one or more nucleotides *** --- *** added between two adjacent nucleotides i *** --- *** n the sequence. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'insertion'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: sequence_rearrangement_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_rearrangement_feature AS SELECT feature_id AS sequence_rearrangement_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'sequence_rearrangement_feature'; --- ************************************************ --- *** relation: chromosome_breakage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence within the micronuclear DNA o *** --- *** f ciliates at which chromosome breakage *** --- *** and telomere addition occurs during nucl *** --- *** ear differentiation. *** --- ************************************************ --- CREATE VIEW chromosome_breakage_sequence AS SELECT feature_id AS chromosome_breakage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_breakage_sequence'; --- ************************************************ --- *** relation: internal_eliminated_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence eliminated from the genome of *** --- *** ciliates during nuclear differentiation *** --- *** . *** --- ************************************************ --- CREATE VIEW internal_eliminated_sequence AS SELECT feature_id AS internal_eliminated_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_eliminated_sequence'; --- ************************************************ --- *** relation: macronucleus_destined_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that is conserved, although r *** --- *** earranged relative to the micronucleus, *** --- *** in the macronucleus of a ciliate genome. *** --- ************************************************ --- CREATE VIEW macronucleus_destined_segment AS SELECT feature_id AS macronucleus_destined_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronucleus_destined_segment'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcript'; --- ************************************************ --- *** relation: canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 3' splice site has the seq *** --- *** uence "AG". *** --- ************************************************ --- CREATE VIEW canonical_three_prime_splice_site AS SELECT feature_id AS canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 5' splice site has the seq *** --- *** uence "GT". *** --- ************************************************ --- CREATE VIEW canonical_five_prime_splice_site AS SELECT feature_id AS canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 3' splice site that does not have the *** --- *** sequence "AG". *** --- ************************************************ --- CREATE VIEW non_canonical_three_prime_splice_site AS SELECT feature_id AS non_canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 5' splice site which does not have the *** --- *** sequence "GT". *** --- ************************************************ --- CREATE VIEW non_canonical_five_prime_splice_site AS SELECT feature_id AS non_canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon that is not the usual AUG *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW non_canonical_start_codon AS SELECT feature_id AS non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'non_canonical_start_codon'; --- ************************************************ --- *** relation: aberrant_processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been processed "in *** --- *** correctly", for example by the failure o *** --- *** f splicing of one or more exons. *** --- ************************************************ --- CREATE VIEW aberrant_processed_transcript AS SELECT feature_id AS aberrant_processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aberrant_processed_transcript'; --- ************************************************ --- *** relation: exonic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Exonic splicing enhancers (ESEs) facilit *** --- *** ate exon definition by assisting in the *** --- *** recruitment of splicing factors to the a *** --- *** djacent intron. *** --- ************************************************ --- CREATE VIEW exonic_splice_enhancer AS SELECT feature_id AS exonic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exonic_splice_enhancer'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targeted *** --- *** by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: dnasei_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dnasei_hypersensitive_site AS SELECT feature_id AS dnasei_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site'; --- ************************************************ --- *** relation: translocation_element *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** chromosomes carrying non-homologous cent *** --- *** romeres may be recovered independently. *** --- *** These chromosomes are described as trans *** --- *** location elements. This occurs for some *** --- *** translocations, particularly but not exc *** --- *** lusively, reciprocal translocations. *** --- ************************************************ --- CREATE VIEW translocation_element AS SELECT feature_id AS translocation_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occurred. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: gene_with_polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW gene_with_polycistronic_transcript AS SELECT feature_id AS gene_with_polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_polycistronic_transcript'; --- ************************************************ --- *** relation: cleaved_initiator_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** The initiator methionine that has been c *** --- *** leaved from a mature polypeptide sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW cleaved_initiator_methionine AS SELECT feature_id AS cleaved_initiator_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine'; --- ************************************************ --- *** relation: gene_with_dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_transcript AS SELECT feature_id AS gene_with_dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_dicistronic_transcript'; --- ************************************************ --- *** relation: gene_with_recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA that is reco *** --- *** ded. *** --- ************************************************ --- CREATE VIEW gene_with_recoded_mrna AS SELECT feature_id AS gene_with_recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_recoded_mRNA'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives exist in normal individuals *** --- *** in some population(s), wherein the least *** --- *** frequent variant has an abundance of 1% *** --- *** or greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'oligo'; --- ************************************************ --- *** relation: gene_with_stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript with st *** --- *** op codon readthrough. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_read_through AS SELECT feature_id AS gene_with_stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_stop_codon_read_through'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as pyrrolysine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent of zer *** --- *** o. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'junction'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'remark'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A region (or regions) that includes all *** --- *** of the sequence elements necessary to en *** --- *** code a functional transcript. A gene may *** --- *** include regulatory regions, transcribed *** --- *** regions and/or other functional sequenc *** --- *** e regions. *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjcent copies of a region ( *** --- *** of length greater than 1). *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 3' splice site of the acceptor prima *** --- *** ry transcript. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: trans_splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' five prime splice site region of *** --- *** the donor RNA. *** --- ************************************************ --- CREATE VIEW trans_splice_donor_site AS SELECT feature_id AS trans_splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_donor_site'; --- ************************************************ --- *** relation: sl1_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL1 RNA leader sequence to *** --- *** the 5' end of most mRNAs. *** --- ************************************************ --- CREATE VIEW sl1_acceptor_site AS SELECT feature_id AS sl1_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site'; --- ************************************************ --- *** relation: sl2_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL2 RNA leader sequence to *** --- *** the 5' end of mRNAs. SL2 acceptor sites *** --- *** occur in genes in internal segments of *** --- *** polycistronic transcripts. *** --- ************************************************ --- CREATE VIEW sl2_acceptor_site AS SELECT feature_id AS sl2_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'SL2_acceptor_site'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as selenocysteine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: gene_with_mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with mRNA recoded by translationa *** --- *** l bypass. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_recoded_by_translational_bypass AS SELECT feature_id AS gene_with_mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: gene_with_transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding a transcript that has a *** --- *** translational frameshift. *** --- ************************************************ --- CREATE VIEW gene_with_transcript_with_translational_frameshift AS SELECT feature_id AS gene_with_transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: dna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in the DNA form o *** --- *** f the sequence. *** --- ************************************************ --- CREATE VIEW dna_motif AS SELECT feature_id AS dna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'DNA_motif'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_motif AS SELECT feature_id AS rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_motif'; --- ************************************************ --- *** relation: dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that has the quality dicistronic *** --- *** . *** --- ************************************************ --- CREATE VIEW dicistronic_mrna AS SELECT feature_id AS dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It need not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: blocked_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A reading_frame that is interrupted by o *** --- *** ne or more stop codons; usually identifi *** --- *** ed through intergenomic sequence compari *** --- *** sons. *** --- ************************************************ --- CREATE VIEW blocked_reading_frame AS SELECT feature_id AS blocked_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blocked_reading_frame'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_transposable_element AS SELECT feature_id AS foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'foreign_transposable_element'; --- ************************************************ --- *** relation: gene_with_dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic primar *** --- *** y transcript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_primary_transcript AS SELECT feature_id AS gene_with_dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript'; --- ************************************************ --- *** relation: gene_with_dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic mRNA *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_mrna AS SELECT feature_id AS gene_with_dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_mRNA'; --- ************************************************ --- *** relation: idna *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic sequence removed from the genome *** --- *** , as a normal event, by a process of rec *** --- *** ombination. *** --- ************************************************ --- CREATE VIEW idna AS SELECT feature_id AS idna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iDNA'; --- ************************************************ --- *** relation: orit *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule where transfe *** --- *** r is initiated during the process of con *** --- *** jugation or mobilization. *** --- ************************************************ --- CREATE VIEW orit AS SELECT feature_id AS orit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriT'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The transit_peptide is a short region at *** --- *** the N-terminus of the peptide that dire *** --- *** cts the protein to an organelle (chlorop *** --- *** last, mitochondrion, microbody or cyanel *** --- *** le). *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: repeat_unit *** --- *** relation type: VIEW *** --- *** *** --- *** The simplest repeated component of a rep *** --- *** eat region. A single repeat. *** --- ************************************************ --- CREATE VIEW repeat_unit AS SELECT feature_id AS repeat_unit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_unit'; --- ************************************************ --- *** relation: crm *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region where more than 1 TF *** --- *** _binding_site together are regulatorily *** --- *** active. *** --- ************************************************ --- CREATE VIEW crm AS SELECT feature_id AS crm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'CRM'; --- ************************************************ --- *** relation: intein *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is able to ex *** --- *** cise itself and rejoin the remaining por *** --- *** tions with a peptide bond. *** --- ************************************************ --- CREATE VIEW intein AS SELECT feature_id AS intein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein'; --- ************************************************ --- *** relation: intein_containing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of protein-coding genes whe *** --- *** re the initial protein product contains *** --- *** an intein. *** --- ************************************************ --- CREATE VIEW intein_containing AS SELECT feature_id AS intein_containing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** he unknown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: fragmentary *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is incomplete. *** --- ************************************************ --- CREATE VIEW fragmentary AS SELECT feature_id AS fragmentary_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary'; --- ************************************************ --- *** relation: predicted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an unverified re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW predicted AS SELECT feature_id AS predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'predicted'; --- ************************************************ --- *** relation: feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a located_sequen *** --- *** ce_feature. *** --- ************************************************ --- CREATE VIEW feature_attribute AS SELECT feature_id AS feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'feature_attribute'; --- ************************************************ --- *** relation: exemplar_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An exemplar is a representative cDNA seq *** --- *** uence for each gene. The exemplar approa *** --- *** ch is a method that usually involves som *** --- *** e initial clustering into gene groups an *** --- *** d the subsequent selection of a represen *** --- *** tative from each gene group. *** --- ************************************************ --- CREATE VIEW exemplar_mrna AS SELECT feature_id AS exemplar_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar_mRNA'; --- ************************************************ --- *** relation: sequence_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_location AS SELECT feature_id AS sequence_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_location'; --- ************************************************ --- *** relation: organelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW organelle_sequence AS SELECT feature_id AS organelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'organelle_sequence'; --- ************************************************ --- *** relation: mitochondrial_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_sequence AS SELECT feature_id AS mitochondrial_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'mitochondrial_sequence'; --- ************************************************ --- *** relation: nuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclear_sequence AS SELECT feature_id AS nuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_sequence'; --- ************************************************ --- *** relation: nucleomorphic_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nucleomorphic_sequence AS SELECT feature_id AS nucleomorphic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_sequence'; --- ************************************************ --- *** relation: plastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plastid_sequence AS SELECT feature_id AS plastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'plastid_sequence'; --- ************************************************ --- *** relation: kinetoplast *** --- *** relation type: VIEW *** --- *** *** --- *** A kinetoplast is an interlocked network *** --- *** of thousands of minicircles and tens of *** --- *** maxi circles, located near the base of t *** --- *** he flagellum of some protozoan species. *** --- ************************************************ --- CREATE VIEW kinetoplast AS SELECT feature_id AS kinetoplast_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast'; --- ************************************************ --- *** relation: maxicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle is a replicon, part of a ki *** --- *** netoplast, that contains open reading fr *** --- *** ames and replicates via a rolling circle *** --- *** method. *** --- ************************************************ --- CREATE VIEW maxicircle AS SELECT feature_id AS maxicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle'; --- ************************************************ --- *** relation: apicoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW apicoplast_sequence AS SELECT feature_id AS apicoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence'; --- ************************************************ --- *** relation: chromoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromoplast_sequence AS SELECT feature_id AS chromoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_sequence'; --- ************************************************ --- *** relation: chloroplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_sequence AS SELECT feature_id AS chloroplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'chloroplast_sequence'; --- ************************************************ --- *** relation: cyanelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cyanelle_sequence AS SELECT feature_id AS cyanelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_sequence'; --- ************************************************ --- *** relation: leucoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucoplast_sequence AS SELECT feature_id AS leucoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_sequence'; --- ************************************************ --- *** relation: proplastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proplastid_sequence AS SELECT feature_id AS proplastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_sequence'; --- ************************************************ --- *** relation: plasmid_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_location AS SELECT feature_id AS plasmid_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_location'; --- ************************************************ --- *** relation: amplification_origin *** --- *** relation type: VIEW *** --- *** *** --- *** An origin_of_replication that is used fo *** --- *** r the amplification of a chromosomal nuc *** --- *** leic acid sequence. *** --- ************************************************ --- CREATE VIEW amplification_origin AS SELECT feature_id AS amplification_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amplification_origin'; --- ************************************************ --- *** relation: proviral_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proviral_location AS SELECT feature_id AS proviral_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'proviral_location'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: clone_insert *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence that has been ins *** --- *** erted and is being propagated by the clo *** --- *** ne. *** --- ************************************************ --- CREATE VIEW clone_insert AS SELECT feature_id AS clone_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'clone_insert'; --- ************************************************ --- *** relation: lambda_vector *** --- *** relation type: VIEW *** --- *** *** --- *** The lambda bacteriophage is the vector f *** --- *** or the linear lambda clone. The genes in *** --- *** volved in the lysogenic pathway are remo *** --- *** ved from the from the viral DNA. Up to 2 *** --- *** 5 kb of foreign DNA can then be inserted *** --- *** into the lambda genome. *** --- ************************************************ --- CREATE VIEW lambda_vector AS SELECT feature_id AS lambda_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lambda_vector'; --- ************************************************ --- *** relation: plasmid_vector *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_vector AS SELECT feature_id AS plasmid_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_vector'; --- ************************************************ --- *** relation: cdna *** --- *** relation type: VIEW *** --- *** *** --- *** DNA synthesized by reverse transcriptase *** --- *** using RNA as a template. *** --- ************************************************ --- CREATE VIEW cdna AS SELECT feature_id AS cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'cDNA'; --- ************************************************ --- *** relation: single_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single_stranded_cdna AS SELECT feature_id AS single_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA'; --- ************************************************ --- *** relation: double_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double_stranded_cdna AS SELECT feature_id AS double_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_cDNA'; --- ************************************************ --- *** relation: pyrrolysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a pyrrolysine a *** --- *** nticodon, and a 3' pyrrolysine binding r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW pyrrolysyl_trna AS SELECT feature_id AS pyrrolysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysyl_tRNA'; --- ************************************************ --- *** relation: episome *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that may integrate with a chro *** --- *** mosome. *** --- ************************************************ --- CREATE VIEW episome AS SELECT feature_id AS episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'episome'; --- ************************************************ --- *** relation: tmrna_coding_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a two-piece tmRNA that bea *** --- *** rs the reading frame encoding the proteo *** --- *** lysis tag. The tmRNA gene undergoes circ *** --- *** ular permutation in some groups of bacte *** --- *** ria. Processing of the transcripts from *** --- *** such a gene leaves the mature tmRNA in t *** --- *** wo pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_coding_piece AS SELECT feature_id AS tmrna_coding_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece'; --- ************************************************ --- *** relation: tmrna_acceptor_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The acceptor region of a two-piece tmRNA *** --- *** that when mature is charged at its 3' e *** --- *** nd with alanine. The tmRNA gene undergoe *** --- *** s circular permutation in some groups of *** --- *** bacteria; processing of the transcripts *** --- *** from such a gene leaves the mature tmRN *** --- *** A in two pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_acceptor_piece AS SELECT feature_id AS tmrna_acceptor_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_acceptor_piece'; --- ************************************************ --- *** relation: qtl *** --- *** relation type: VIEW *** --- *** *** --- *** A quantitative trait locus (QTL) is a po *** --- *** lymorphic locus which contains alleles t *** --- *** hat differentially affect the expression *** --- *** of a continuously distributed phenotypi *** --- *** c trait. Usually it is a marker describe *** --- *** d by statistical association to quantita *** --- *** tive variation in the particular phenoty *** --- *** pic trait that is thought to be controll *** --- *** ed by the cumulative action of alleles a *** --- *** t multiple loci. *** --- ************************************************ --- CREATE VIEW qtl AS SELECT feature_id AS qtl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'QTL'; --- ************************************************ --- *** relation: genomic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A genomic island is an integrated mobile *** --- *** genetic element, characterized by size *** --- *** (over 10 Kb). It that has features that *** --- *** suggest a foreign origin. These can incl *** --- *** ude nucleotide distribution (oligonucleo *** --- *** tides signature, CG content etc.) that d *** --- *** iffers from the bulk of the chromosome a *** --- *** nd/or genes suggesting DNA mobility. *** --- ************************************************ --- CREATE VIEW genomic_island AS SELECT feature_id AS genomic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'genomic_island'; --- ************************************************ --- *** relation: pathogenic_island *** --- *** relation type: VIEW *** --- *** *** --- *** Mobile genetic elements that contribute *** --- *** to rapid changes in virulence potential. *** --- *** They are present on the genomes of path *** --- *** ogenic strains but absent from the genom *** --- *** es of non pathogenic members of the same *** --- *** or related species. *** --- ************************************************ --- CREATE VIEW pathogenic_island AS SELECT feature_id AS pathogenic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island'; --- ************************************************ --- *** relation: metabolic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in metabolism, analogous to th *** --- *** e pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW metabolic_island AS SELECT feature_id AS metabolic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'metabolic_island'; --- ************************************************ --- *** relation: adaptive_island *** --- *** relation type: VIEW *** --- *** *** --- *** An adaptive island is a genomic island t *** --- *** hat provides an adaptive advantage to th *** --- *** e host. *** --- ************************************************ --- CREATE VIEW adaptive_island AS SELECT feature_id AS adaptive_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'adaptive_island'; --- ************************************************ --- *** relation: symbiosis_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in symbiosis, analogous to the *** --- *** pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW symbiosis_island AS SELECT feature_id AS symbiosis_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symbiosis_island'; --- ************************************************ --- *** relation: pseudogenic_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of an rRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_rrna AS SELECT feature_id AS pseudogenic_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_rRNA'; --- ************************************************ --- *** relation: pseudogenic_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of a tRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_trna AS SELECT feature_id AS pseudogenic_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_tRNA'; --- ************************************************ --- *** relation: engineered_episome *** --- *** relation type: VIEW *** --- *** *** --- *** An episome that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_episome AS SELECT feature_id AS engineered_episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome'; --- ************************************************ --- *** relation: transgenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence that has b *** --- *** een integrated with foreign sequence. *** --- ************************************************ --- CREATE VIEW transgenic AS SELECT feature_id AS transgenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic'; --- ************************************************ --- *** relation: so_natural *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that o *** --- *** ccurs in nature. *** --- ************************************************ --- CREATE VIEW so_natural AS SELECT feature_id AS so_natural_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural'; --- ************************************************ --- *** relation: engineered *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region that w *** --- *** as modified in vitro. *** --- ************************************************ --- CREATE VIEW engineered AS SELECT feature_id AS engineered_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered'; --- ************************************************ --- *** relation: so_foreign *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region from a *** --- *** nother species. *** --- ************************************************ --- CREATE VIEW so_foreign AS SELECT feature_id AS so_foreign_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foreign'; --- ************************************************ --- *** relation: cloned_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cloned_region AS SELECT feature_id AS cloned_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_region'; --- ************************************************ --- *** relation: validated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been proven. *** --- ************************************************ --- CREATE VIEW validated AS SELECT feature_id AS validated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined' OR cvterm.name = 'validated'; --- ************************************************ --- *** relation: invalidated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s invalidated. *** --- ************************************************ --- CREATE VIEW invalidated AS SELECT feature_id AS invalidated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'invalidated'; --- ************************************************ --- *** relation: engineered_rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A rescue region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_rescue_region AS SELECT feature_id AS engineered_rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region'; --- ************************************************ --- *** relation: rescue_mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mini_gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_mini_gene AS SELECT feature_id AS rescue_mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene'; --- ************************************************ --- *** relation: transgenic_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified in vitro, incl *** --- *** uding insertion of DNA derived from a so *** --- *** urce other than the originating TE. *** --- ************************************************ --- CREATE VIEW transgenic_transposable_element AS SELECT feature_id AS transgenic_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_transposable_element'; --- ************************************************ --- *** relation: natural_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that exists (or existed) in nature. *** --- ************************************************ --- CREATE VIEW natural_transposable_element AS SELECT feature_id AS natural_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element'; --- ************************************************ --- *** relation: engineered_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified by manipulatio *** --- *** ns in vitro. *** --- ************************************************ --- CREATE VIEW engineered_transposable_element AS SELECT feature_id AS engineered_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_transposable_element'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element AS SELECT feature_id AS engineered_foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element'; --- ************************************************ --- *** relation: assortment_derived_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome duplication aberratio *** --- *** n generated by reassortment of other abe *** --- *** rration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_duplication AS SELECT feature_id AS assortment_derived_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency an *** --- *** d a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency_plus_duplication AS SELECT feature_id AS assortment_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome deficiency aberration *** --- *** generated by reassortment of other aber *** --- *** ration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency AS SELECT feature_id AS assortment_derived_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency'; --- ************************************************ --- *** relation: assortment_derived_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency or *** --- *** a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_aneuploid AS SELECT feature_id AS assortment_derived_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_aneuploid'; --- ************************************************ --- *** relation: engineered_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_region AS SELECT feature_id AS engineered_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_region'; --- ************************************************ --- *** relation: engineered_foreign_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_region AS SELECT feature_id AS engineered_foreign_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_region'; --- ************************************************ --- *** relation: fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fusion AS SELECT feature_id AS fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fusion'; --- ************************************************ --- *** relation: engineered_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A tag that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_tag AS SELECT feature_id AS engineered_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_tag'; --- ************************************************ --- *** relation: validated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that has been validated. *** --- ************************************************ --- CREATE VIEW validated_cdna_clone AS SELECT feature_id AS validated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone'; --- ************************************************ --- *** relation: invalidated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that is invalid. *** --- ************************************************ --- CREATE VIEW invalidated_cdna_clone AS SELECT feature_id AS invalidated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone'; --- ************************************************ --- *** relation: chimeric_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated because it is c *** --- *** himeric. *** --- ************************************************ --- CREATE VIEW chimeric_cdna_clone AS SELECT feature_id AS chimeric_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone'; --- ************************************************ --- *** relation: genomically_contaminated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by genomic cont *** --- *** amination. *** --- ************************************************ --- CREATE VIEW genomically_contaminated_cdna_clone AS SELECT feature_id AS genomically_contaminated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomically_contaminated_cDNA_clone'; --- ************************************************ --- *** relation: polya_primed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by polyA primin *** --- *** g. *** --- ************************************************ --- CREATE VIEW polya_primed_cdna_clone AS SELECT feature_id AS polya_primed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_primed_cDNA_clone'; --- ************************************************ --- *** relation: partially_processed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA invalidated clone by partial proc *** --- *** essing. *** --- ************************************************ --- CREATE VIEW partially_processed_cdna_clone AS SELECT feature_id AS partially_processed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_processed_cDNA_clone'; --- ************************************************ --- *** relation: rescue *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region's abili *** --- *** ty, when introduced to a mutant organism *** --- *** , to re-establish (rescue) a phenotype. *** --- ************************************************ --- CREATE VIEW rescue AS SELECT feature_id AS rescue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue'; --- ************************************************ --- *** relation: mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** By definition, minigenes are short open- *** --- *** reading frames (ORF), usually encoding a *** --- *** pproximately 9 to 20 amino acids, which *** --- *** are expressed in vivo (as distinct from *** --- *** being synthesized as peptide or protein *** --- *** ex vivo and subsequently injected). The *** --- *** in vivo synthesis confers a distinct adv *** --- *** antage: the expressed sequences can ente *** --- *** r both antigen presentation pathways, MH *** --- *** C I (inducing CD8+ T- cells, which are u *** --- *** sually cytotoxic T-lymphocytes (CTL)) an *** --- *** d MHC II (inducing CD4+ T-cells, usually *** --- *** 'T-helpers' (Th)); and can encounter B- *** --- *** cells, inducing antibody responses. Thre *** --- *** e main vector approaches have been used *** --- *** to deliver minigenes: viral vectors, bac *** --- *** terial vectors and plasmid DNA. *** --- ************************************************ --- CREATE VIEW mini_gene AS SELECT feature_id AS mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'mini_gene'; --- ************************************************ --- *** relation: rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_gene AS SELECT feature_id AS rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'rescue_gene'; --- ************************************************ --- *** relation: wild_type *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence with th *** --- *** e genotype found in nature and/or standa *** --- *** rd laboratory stock. *** --- ************************************************ --- CREATE VIEW wild_type AS SELECT feature_id AS wild_type_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type'; --- ************************************************ --- *** relation: wild_type_rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW wild_type_rescue_gene AS SELECT feature_id AS wild_type_rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene'; --- ************************************************ --- *** relation: mitochondrial_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a mitochondr *** --- *** ia. *** --- ************************************************ --- CREATE VIEW mitochondrial_chromosome AS SELECT feature_id AS mitochondrial_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome'; --- ************************************************ --- *** relation: chloroplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chloroplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chloroplast_chromosome AS SELECT feature_id AS chloroplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_chromosome'; --- ************************************************ --- *** relation: chromoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chromoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chromoplast_chromosome AS SELECT feature_id AS chromoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_chromosome'; --- ************************************************ --- *** relation: cyanelle_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a cyanelle. *** --- ************************************************ --- CREATE VIEW cyanelle_chromosome AS SELECT feature_id AS cyanelle_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_chromosome'; --- ************************************************ --- *** relation: leucoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome with origin in a leucoplast *** --- *** . *** --- ************************************************ --- CREATE VIEW leucoplast_chromosome AS SELECT feature_id AS leucoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_chromosome'; --- ************************************************ --- *** relation: macronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a macronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW macronuclear_chromosome AS SELECT feature_id AS macronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_chromosome'; --- ************************************************ --- *** relation: micronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a micronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW micronuclear_chromosome AS SELECT feature_id AS micronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_chromosome'; --- ************************************************ --- *** relation: nuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_chromosome AS SELECT feature_id AS nuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_chromosome'; --- ************************************************ --- *** relation: nucleomorphic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleomorp *** --- *** h. *** --- ************************************************ --- CREATE VIEW nucleomorphic_chromosome AS SELECT feature_id AS nucleomorphic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_chromosome'; --- ************************************************ --- *** relation: chromosome_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_part AS SELECT feature_id AS chromosome_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosome_part'; --- ************************************************ --- *** relation: gene_member_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a gene. *** --- ************************************************ --- CREATE VIEW gene_member_region AS SELECT feature_id AS gene_member_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'gene_member_region'; --- ************************************************ --- *** relation: transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a transcript. *** --- ************************************************ --- CREATE VIEW transcript_region AS SELECT feature_id AS transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'transcript_region'; --- ************************************************ --- *** relation: mature_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a mature transcript. *** --- ************************************************ --- CREATE VIEW mature_transcript_region AS SELECT feature_id AS mature_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'mature_transcript_region'; --- ************************************************ --- *** relation: primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a primary transcript. *** --- ************************************************ --- CREATE VIEW primary_transcript_region AS SELECT feature_id AS primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'primary_transcript_region'; --- ************************************************ --- *** relation: mrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an mRNA. *** --- ************************************************ --- CREATE VIEW mrna_region AS SELECT feature_id AS mrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'mRNA_region'; --- ************************************************ --- *** relation: utr_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of UTR. *** --- ************************************************ --- CREATE VIEW utr_region AS SELECT feature_id AS utr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'UTR_region'; --- ************************************************ --- *** relation: rrna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an rRNA primary transcript. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript_region AS SELECT feature_id AS rrna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'rRNA_primary_transcript_region'; --- ************************************************ --- *** relation: polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Biological sequence region that can be a *** --- *** ssigned to a specific subsequence of a p *** --- *** olypeptide. *** --- ************************************************ --- CREATE VIEW polypeptide_region AS SELECT feature_id AS polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_region'; --- ************************************************ --- *** relation: repeat_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a repeated sequence. *** --- ************************************************ --- CREATE VIEW repeat_component AS SELECT feature_id AS repeat_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'repeat_component'; --- ************************************************ --- *** relation: spliceosomal_intron_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an intron. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron_region AS SELECT feature_id AS spliceosomal_intron_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'spliceosomal_intron_region'; --- ************************************************ --- *** relation: gene_component_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_component_region AS SELECT feature_id AS gene_component_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_component_region'; --- ************************************************ --- *** relation: tmrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tmRNA. *** --- ************************************************ --- CREATE VIEW tmrna_region AS SELECT feature_id AS tmrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'tmRNA_region'; --- ************************************************ --- *** relation: ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ltr_component AS SELECT feature_id AS ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'LTR_component'; --- ************************************************ --- *** relation: three_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr_component AS SELECT feature_id AS three_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'three_prime_LTR_component'; --- ************************************************ --- *** relation: five_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr_component AS SELECT feature_id AS five_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'five_prime_LTR_component'; --- ************************************************ --- *** relation: cds_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a CDS. *** --- ************************************************ --- CREATE VIEW cds_region AS SELECT feature_id AS cds_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'CDS_region'; --- ************************************************ --- *** relation: exon_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an exon. *** --- ************************************************ --- CREATE VIEW exon_region AS SELECT feature_id AS exon_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'exon_region'; --- ************************************************ --- *** relation: homologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is homologous to another r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW homologous_region AS SELECT feature_id AS homologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'homologous_region'; --- ************************************************ --- *** relation: paralogous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is paralogous t *** --- *** o another region. *** --- ************************************************ --- CREATE VIEW paralogous_region AS SELECT feature_id AS paralogous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region'; --- ************************************************ --- *** relation: orthologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is orthologous *** --- *** to another region. *** --- ************************************************ --- CREATE VIEW orthologous_region AS SELECT feature_id AS orthologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous_region'; --- ************************************************ --- *** relation: conserved *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW conserved AS SELECT feature_id AS conserved_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'conserved'; --- ************************************************ --- *** relation: homologous *** --- *** relation type: VIEW *** --- *** *** --- *** Similarity due to common ancestry. *** --- ************************************************ --- CREATE VIEW homologous AS SELECT feature_id AS homologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'homologous'; --- ************************************************ --- *** relation: orthologous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occured after a spec *** --- *** iation event. *** --- ************************************************ --- CREATE VIEW orthologous AS SELECT feature_id AS orthologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous'; --- ************************************************ --- *** relation: paralogous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occurred after a dup *** --- *** lication event. *** --- ************************************************ --- CREATE VIEW paralogous AS SELECT feature_id AS paralogous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous'; --- ************************************************ --- *** relation: syntenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence regions oc *** --- *** curring in same order on chromosome of d *** --- *** ifferent species. *** --- ************************************************ --- CREATE VIEW syntenic AS SELECT feature_id AS syntenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic'; --- ************************************************ --- *** relation: capped_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is capped. *** --- ************************************************ --- CREATE VIEW capped_primary_transcript AS SELECT feature_id AS capped_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_primary_transcript'; --- ************************************************ --- *** relation: capped_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is capped. *** --- ************************************************ --- CREATE VIEW capped_mrna AS SELECT feature_id AS capped_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_mRNA'; --- ************************************************ --- *** relation: mrna_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA feature. *** --- ************************************************ --- CREATE VIEW mrna_attribute AS SELECT feature_id AS mrna_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'mRNA_attribute'; --- ************************************************ --- *** relation: exemplar *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence is re *** --- *** presentative of a class of similar seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW exemplar AS SELECT feature_id AS exemplar_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar'; --- ************************************************ --- *** relation: frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains a mutation involving the deleti *** --- *** on or insertion of one or more bases, wh *** --- *** ere this number is not divisible by 3. *** --- ************************************************ --- CREATE VIEW frameshift AS SELECT feature_id AS frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'frameshift'; --- ************************************************ --- *** relation: minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting one base *** --- *** . *** --- ************************************************ --- CREATE VIEW minus_1_frameshift AS SELECT feature_id AS minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift'; --- ************************************************ --- *** relation: minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting two base *** --- *** s. *** --- ************************************************ --- CREATE VIEW minus_2_frameshift AS SELECT feature_id AS minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift'; --- ************************************************ --- *** relation: plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting one bas *** --- *** e. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift AS SELECT feature_id AS plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift'; --- ************************************************ --- *** relation: plus_2_framshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting two bas *** --- *** es. *** --- ************************************************ --- CREATE VIEW plus_2_framshift AS SELECT feature_id AS plus_2_framshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_framshift'; --- ************************************************ --- *** relation: trans_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing transcript seque *** --- *** nce that is created by splicing exons fr *** --- *** om diferent genes. *** --- ************************************************ --- CREATE VIEW trans_spliced AS SELECT feature_id AS trans_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced'; --- ************************************************ --- *** relation: polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is polyadenylated. *** --- ************************************************ --- CREATE VIEW polyadenylated_mrna AS SELECT feature_id AS polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated_mRNA'; --- ************************************************ --- *** relation: trans_spliced_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_mrna AS SELECT feature_id AS trans_spliced_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA'; --- ************************************************ --- *** relation: edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript AS SELECT feature_id AS edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript'; --- ************************************************ --- *** relation: edited_transcript_by_a_to_i_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been edited by A t *** --- *** o I substitution. *** --- ************************************************ --- CREATE VIEW edited_transcript_by_a_to_i_substitution AS SELECT feature_id AS edited_transcript_by_a_to_i_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution'; --- ************************************************ --- *** relation: bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a protein. *** --- ************************************************ --- CREATE VIEW bound_by_protein AS SELECT feature_id AS bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein'; --- ************************************************ --- *** relation: bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a nucleic acid. *** --- ************************************************ --- CREATE VIEW bound_by_nucleic_acid AS SELECT feature_id AS bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_nucleic_acid'; --- ************************************************ --- *** relation: alternatively_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a situation wher *** --- *** e a gene may encode for more than 1 tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW alternatively_spliced AS SELECT feature_id AS alternatively_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced'; --- ************************************************ --- *** relation: monocistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for one gene product. *** --- ************************************************ --- CREATE VIEW monocistronic AS SELECT feature_id AS monocistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic'; --- ************************************************ --- *** relation: dicistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for two gene products. *** --- ************************************************ --- CREATE VIEW dicistronic AS SELECT feature_id AS dicistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic'; --- ************************************************ --- *** relation: polycistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for more than one gene *** --- *** product. *** --- ************************************************ --- CREATE VIEW polycistronic AS SELECT feature_id AS polycistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic' OR cvterm.name = 'polycistronic'; --- ************************************************ --- *** relation: recoded *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA sequence *** --- *** that has been reprogrammed at translati *** --- *** on, causing localized alterations. *** --- ************************************************ --- CREATE VIEW recoded AS SELECT feature_id AS recoded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'recoded'; --- ************************************************ --- *** relation: codon_redefined *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the alteration o *** --- *** f codon meaning. *** --- ************************************************ --- CREATE VIEW codon_redefined AS SELECT feature_id AS codon_redefined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined'; --- ************************************************ --- *** relation: stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be a new amino *** --- *** acid. *** --- ************************************************ --- CREATE VIEW stop_codon_read_through AS SELECT feature_id AS stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'stop_codon_read_through'; --- ************************************************ --- *** relation: stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, pyrrolysine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, selenocysteine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** Recoded mRNA where a block of nucleotide *** --- *** s is not translated. *** --- ************************************************ --- CREATE VIEW recoded_by_translational_bypass AS SELECT feature_id AS recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_by_translational_bypass'; --- ************************************************ --- *** relation: translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** Recoding by frameshifting a particular s *** --- *** ite. *** --- ************************************************ --- CREATE VIEW translationally_frameshifted AS SELECT feature_id AS translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'translationally_frameshifted'; --- ************************************************ --- *** relation: maternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is maternally_imprinted. *** --- ************************************************ --- CREATE VIEW maternally_imprinted_gene AS SELECT feature_id AS maternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted_gene'; --- ************************************************ --- *** relation: paternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is paternally imprinted. *** --- ************************************************ --- CREATE VIEW paternally_imprinted_gene AS SELECT feature_id AS paternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is post translationally regu *** --- *** lated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_gene AS SELECT feature_id AS post_translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_gene'; --- ************************************************ --- *** relation: negatively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is negatively autoreguated. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated_gene AS SELECT feature_id AS negatively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated_gene'; --- ************************************************ --- *** relation: positively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is positively autoregulated. *** --- ************************************************ --- CREATE VIEW positively_autoregulated_gene AS SELECT feature_id AS positively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated_gene'; --- ************************************************ --- *** relation: silenced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated at tra *** --- *** nscriptional or translational level. *** --- ************************************************ --- CREATE VIEW silenced AS SELECT feature_id AS silenced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced'; --- ************************************************ --- *** relation: silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** modifications, resulting in repression *** --- *** of transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_modification AS SELECT feature_id AS silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_DNA_modification'; --- ************************************************ --- *** relation: silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** methylation, resulting in repression of *** --- *** transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_methylation AS SELECT feature_id AS silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is translationally regulated *** --- *** . *** --- ************************************************ --- CREATE VIEW translationally_regulated_gene AS SELECT feature_id AS translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated_gene'; --- ************************************************ --- *** relation: allelically_excluded_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is allelically_excluded. *** --- ************************************************ --- CREATE VIEW allelically_excluded_gene AS SELECT feature_id AS allelically_excluded_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded_gene'; --- ************************************************ --- *** relation: epigenetically_modified_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is epigenetically modified. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_gene AS SELECT feature_id AS epigenetically_modified_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'epigenetically_modified_gene'; --- ************************************************ --- *** relation: transgene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene is a gene that has been tran *** --- *** sferred naturally or by any of a number *** --- *** of genetic engineering techniques from o *** --- *** ne organism to another. *** --- ************************************************ --- CREATE VIEW transgene AS SELECT feature_id AS transgene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene' OR cvterm.name = 'transgene'; --- ************************************************ --- *** relation: endogenous_retroviral_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_sequence AS SELECT feature_id AS endogenous_retroviral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence'; --- ************************************************ --- *** relation: rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the sequence of *** --- *** a feature, where the DNA is rearranged. *** --- ************************************************ --- CREATE VIEW rearranged_at_dna_level AS SELECT feature_id AS rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rearranged_at_DNA_level'; --- ************************************************ --- *** relation: status *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the status of a *** --- *** feature, based on the available evidence *** --- *** . *** --- ************************************************ --- CREATE VIEW status AS SELECT feature_id AS status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'status'; --- ************************************************ --- *** relation: independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that is *** --- *** independently known - not predicted. *** --- ************************************************ --- CREATE VIEW independently_known AS SELECT feature_id AS independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'independently_known'; --- ************************************************ --- *** relation: supported_by_sequence_similarity *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity techniques. *** --- ************************************************ --- CREATE VIEW supported_by_sequence_similarity AS SELECT feature_id AS supported_by_sequence_similarity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'supported_by_sequence_similarity'; --- ************************************************ --- *** relation: supported_by_domain_match *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity of a known domain. *** --- ************************************************ --- CREATE VIEW supported_by_domain_match AS SELECT feature_id AS supported_by_domain_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match'; --- ************************************************ --- *** relation: supported_by_est_or_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity to EST or cDNA data. *** --- ************************************************ --- CREATE VIEW supported_by_est_or_cdna AS SELECT feature_id AS supported_by_est_or_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_EST_or_cDNA'; --- ************************************************ --- *** relation: orphan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW orphan AS SELECT feature_id AS orphan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan'; --- ************************************************ --- *** relation: predicted_by_ab_initio_computation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s predicted by a computer program that d *** --- *** id not rely on sequence similarity. *** --- ************************************************ --- CREATE VIEW predicted_by_ab_initio_computation AS SELECT feature_id AS predicted_by_ab_initio_computation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_by_ab_initio_computation'; --- ************************************************ --- *** relation: asx_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Asp *** --- *** artate or Asparagine (Asx), the side-cha *** --- *** in O of residue(i) is H-bonded to the ma *** --- *** in-chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW asx_turn AS SELECT feature_id AS asx_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'asx_turn'; --- ************************************************ --- *** relation: cloned_cdna_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from cDNA. *** --- ************************************************ --- CREATE VIEW cloned_cdna_insert AS SELECT feature_id AS cloned_cdna_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert'; --- ************************************************ --- *** relation: cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from genomic DNA. *** --- ************************************************ --- CREATE VIEW cloned_genomic_insert AS SELECT feature_id AS cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'cloned_genomic_insert'; --- ************************************************ --- *** relation: engineered_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_insert AS SELECT feature_id AS engineered_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_insert'; --- ************************************************ --- *** relation: edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is edited. *** --- ************************************************ --- CREATE VIEW edited_mrna AS SELECT feature_id AS edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_mRNA'; --- ************************************************ --- *** relation: guide_rna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of guide RNA. *** --- ************************************************ --- CREATE VIEW guide_rna_region AS SELECT feature_id AS guide_rna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'guide_RNA_region'; --- ************************************************ --- *** relation: anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that base-pairs *** --- *** to a target mRNA. *** --- ************************************************ --- CREATE VIEW anchor_region AS SELECT feature_id AS anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region'; --- ************************************************ --- *** relation: pre_edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pre_edited_mrna AS SELECT feature_id AS pre_edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA'; --- ************************************************ --- *** relation: intermediate *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature betwe *** --- *** en stages of processing. *** --- ************************************************ --- CREATE VIEW intermediate AS SELECT feature_id AS intermediate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate'; --- ************************************************ --- *** relation: mirna_target_site *** --- *** relation type: VIEW *** --- *** *** --- *** A miRNA target site is a binding site wh *** --- *** ere the molecule is a micro RNA. *** --- ************************************************ --- CREATE VIEW mirna_target_site AS SELECT feature_id AS mirna_target_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site'; --- ************************************************ --- *** relation: edited_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is edited. *** --- ************************************************ --- CREATE VIEW edited_cds AS SELECT feature_id AS edited_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment'; --- ************************************************ --- *** relation: vertebrate_ig_t_cell_receptor_rearranged_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_ig_t_cell_receptor_rearranged_gene_cluster AS SELECT feature_id AS vertebrate_ig_t_cell_receptor_rearranged_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_signal_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_signal_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_signal_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature'; --- ************************************************ --- *** relation: recombinationally_rearranged *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged AS SELECT feature_id AS recombinationally_rearranged_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged'; --- ************************************************ --- *** relation: recombinationally_rearranged_vertebrate_immune_system_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene of t *** --- *** he vertebrate immune system. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_vertebrate_immune_system_gene AS SELECT feature_id AS recombinationally_rearranged_vertebrate_immune_system_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: attp_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a phage *** --- *** chromosome at which a recombinase acts t *** --- *** o insert the phage DNA at a cognate inte *** --- *** gration/excision site on a bacterial chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW attp_site AS SELECT feature_id AS attp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attP_site'; --- ************************************************ --- *** relation: attb_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a bacter *** --- *** ial chromosome at which a recombinase ac *** --- *** ts to insert foreign DNA containing a co *** --- *** gnate integration/excision site. *** --- ************************************************ --- CREATE VIEW attb_site AS SELECT feature_id AS attb_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attB_site'; --- ************************************************ --- *** relation: attl_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attB_site and th *** --- *** e 3' portion of attP_site. *** --- ************************************************ --- CREATE VIEW attl_site AS SELECT feature_id AS attl_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attL_site'; --- ************************************************ --- *** relation: attr_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attP_site and th *** --- *** e 3' portion of attB_site. *** --- ************************************************ --- CREATE VIEW attr_site AS SELECT feature_id AS attr_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attR_site'; --- ************************************************ --- *** relation: integration_excision_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inserts or removes anot *** --- *** her region marked by a distinct cognate *** --- *** integration/excision site. *** --- ************************************************ --- CREATE VIEW integration_excision_site AS SELECT feature_id AS integration_excision_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'integration_excision_site'; --- ************************************************ --- *** relation: resolution_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which separates a physically *** --- *** contiguous circle of DNA into two physic *** --- *** ally separate circles. *** --- ************************************************ --- CREATE VIEW resolution_site AS SELECT feature_id AS resolution_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'resolution_site'; --- ************************************************ --- *** relation: inversion_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inverts the region flan *** --- *** ked by a pair of sites. *** --- ************************************************ --- CREATE VIEW inversion_site AS SELECT feature_id AS inversion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site' OR cvterm.name = 'inversion_site'; --- ************************************************ --- *** relation: dif_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site at which replicated bacterial cir *** --- *** cular chromosomes are decatenated by sit *** --- *** e specific resolvase. *** --- ************************************************ --- CREATE VIEW dif_site AS SELECT feature_id AS dif_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dif_site'; --- ************************************************ --- *** relation: attc_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attC site is a sequence required for *** --- *** the integration of a DNA of an integron. *** --- ************************************************ --- CREATE VIEW attc_site AS SELECT feature_id AS attc_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attC_site'; --- ************************************************ --- *** relation: eukaryotic_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW eukaryotic_terminator AS SELECT feature_id AS eukaryotic_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'eukaryotic_terminator'; --- ************************************************ --- *** relation: oriv *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of vegetative replication in p *** --- *** lasmids and phages. *** --- ************************************************ --- CREATE VIEW oriv AS SELECT feature_id AS oriv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriV'; --- ************************************************ --- *** relation: oric *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of bacterial chromosome replic *** --- *** ation. *** --- ************************************************ --- CREATE VIEW oric AS SELECT feature_id AS oric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriC'; --- ************************************************ --- *** relation: dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, DNA molecule. *** --- ************************************************ --- CREATE VIEW dna_chromosome AS SELECT feature_id AS dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'DNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_dna_chromosome AS SELECT feature_id AS double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_dna_chromosome AS SELECT feature_id AS single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_dna_chromosome AS SELECT feature_id AS linear_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_dna_chromosome AS SELECT feature_id AS circular_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_dna_chromosome AS SELECT feature_id AS linear_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_dna_chromosome AS SELECT feature_id AS circular_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, RNA molecule. *** --- ************************************************ --- CREATE VIEW rna_chromosome AS SELECT feature_id AS rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_rna_chromosome AS SELECT feature_id AS single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_rna_chromosome AS SELECT feature_id AS linear_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_rna_chromosome AS SELECT feature_id AS linear_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_rna_chromosome AS SELECT feature_id AS double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_rna_chromosome AS SELECT feature_id AS circular_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular RNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_rna_chromosome AS SELECT feature_id AS circular_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: insertion_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal_inverted_repeat_element that *** --- *** is bacterial and only encodes the functi *** --- *** ons required for its transposition betwe *** --- *** en these inverted repeats. *** --- ************************************************ --- CREATE VIEW insertion_sequence AS SELECT feature_id AS insertion_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_sequence'; --- ************************************************ --- *** relation: minicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minicircle_gene AS SELECT feature_id AS minicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle_gene'; --- ************************************************ --- *** relation: cryptic *** --- *** relation type: VIEW *** --- *** *** --- *** A feature_attribute describing a feature *** --- *** that is not manifest under normal condi *** --- *** tions. *** --- ************************************************ --- CREATE VIEW cryptic AS SELECT feature_id AS cryptic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic'; --- ************************************************ --- *** relation: anchor_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW anchor_binding_site AS SELECT feature_id AS anchor_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_binding_site'; --- ************************************************ --- *** relation: template_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that specifies t *** --- *** he insertions and deletions of bases in *** --- *** the editing of a target mRNA. *** --- ************************************************ --- CREATE VIEW template_region AS SELECT feature_id AS template_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'template_region'; --- ************************************************ --- *** relation: grna_encoding *** --- *** relation type: VIEW *** --- *** *** --- *** A non-protein_coding gene that encodes a *** --- *** guide_RNA. *** --- ************************************************ --- CREATE VIEW grna_encoding AS SELECT feature_id AS grna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_encoding'; --- ************************************************ --- *** relation: minicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A minicircle is a replicon, part of a ki *** --- *** netoplast, that encodes for guide RNAs. *** --- ************************************************ --- CREATE VIEW minicircle AS SELECT feature_id AS minicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle'; --- ************************************************ --- *** relation: rho_dependent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_dependent_bacterial_terminator AS SELECT feature_id AS rho_dependent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator'; --- ************************************************ --- *** relation: rho_independent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_independent_bacterial_terminator AS SELECT feature_id AS rho_independent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_independent_bacterial_terminator'; --- ************************************************ --- *** relation: strand_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strand_attribute AS SELECT feature_id AS strand_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute'; --- ************************************************ --- *** relation: single *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single AS SELECT feature_id AS single_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single'; --- ************************************************ --- *** relation: double *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double AS SELECT feature_id AS double_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double'; --- ************************************************ --- *** relation: topology_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW topology_attribute AS SELECT feature_id AS topology_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute'; --- ************************************************ --- *** relation: linear *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as a 3'-terminal residue and a 5'-termin *** --- *** al residue. *** --- ************************************************ --- CREATE VIEW linear AS SELECT feature_id AS linear_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear'; --- ************************************************ --- *** relation: circular *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as no terminal nucleotide residues. *** --- ************************************************ --- CREATE VIEW circular AS SELECT feature_id AS circular_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular'; --- ************************************************ --- *** relation: class_ii_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (59-60 nt long) con *** --- *** taining 5' and 3' ends that are predicte *** --- *** d to come together to form a stem struct *** --- *** ure. Identified in the social amoeba Dic *** --- *** tyostelium discoideum and localized in t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW class_ii_rna AS SELECT feature_id AS class_ii_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_II_RNA'; --- ************************************************ --- *** relation: class_i_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (55-65 nt long) con *** --- *** taining highly conserved 5' and 3' ends *** --- *** (16 and 8 nt, respectively) that are pre *** --- *** dicted to come together to form a stem s *** --- *** tructure. Identified in the social amoeb *** --- *** a Dictyostelium discoideum and localized *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW class_i_rna AS SELECT feature_id AS class_i_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_I_RNA'; --- ************************************************ --- *** relation: genomic_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW genomic_dna AS SELECT feature_id AS genomic_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_DNA'; --- ************************************************ --- *** relation: bac_cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bac_cloned_genomic_insert AS SELECT feature_id AS bac_cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert'; --- ************************************************ --- *** relation: consensus *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus AS SELECT feature_id AS consensus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus'; --- ************************************************ --- *** relation: consensus_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_region AS SELECT feature_id AS consensus_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region'; --- ************************************************ --- *** relation: consensus_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_mrna AS SELECT feature_id AS consensus_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA'; --- ************************************************ --- *** relation: predicted_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW predicted_gene AS SELECT feature_id AS predicted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_gene'; --- ************************************************ --- *** relation: gene_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_fragment AS SELECT feature_id AS gene_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fragment'; --- ************************************************ --- *** relation: recursive_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A recursive splice site is a splice site *** --- *** which subdivides a large intron. Recurs *** --- *** ive splicing is a mechanism that splices *** --- *** large introns by sub dividing the intro *** --- *** n at non exonic elements and alternate e *** --- *** xons. *** --- ************************************************ --- CREATE VIEW recursive_splice_site AS SELECT feature_id AS recursive_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recursive_splice_site'; --- ************************************************ --- *** relation: bac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a B *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW bac_end AS SELECT feature_id AS bac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_end'; --- ************************************************ --- *** relation: rrna_16s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the small sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_16s AS SELECT feature_id AS rrna_16s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_16S'; --- ************************************************ --- *** relation: rrna_23s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the large sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_23s AS SELECT feature_id AS rrna_23s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_23S'; --- ************************************************ --- *** relation: rrna_25s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide which functions a *** --- *** s part of the large subunit of the ribos *** --- *** ome in some eukaryotes. *** --- ************************************************ --- CREATE VIEW rrna_25s AS SELECT feature_id AS rrna_25s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_25S'; --- ************************************************ --- *** relation: solo_ltr *** --- *** relation type: VIEW *** --- *** *** --- *** A recombination product between the 2 LT *** --- *** R of the same element. *** --- ************************************************ --- CREATE VIEW solo_ltr AS SELECT feature_id AS solo_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'solo_LTR'; --- ************************************************ --- *** relation: low_complexity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity AS SELECT feature_id AS low_complexity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity'; --- ************************************************ --- *** relation: low_complexity_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity_region AS SELECT feature_id AS low_complexity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity_region'; --- ************************************************ --- *** relation: prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A phage genome after it has established *** --- *** in the host genome in a latent/immune st *** --- *** ate either as a plasmid or as an integra *** --- *** ted "island". *** --- ************************************************ --- CREATE VIEW prophage AS SELECT feature_id AS prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage'; --- ************************************************ --- *** relation: cryptic_prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A remnant of an integrated prophage in t *** --- *** he host genome or an "island" in the hos *** --- *** t genome that includes phage like-genes. *** --- ************************************************ --- CREATE VIEW cryptic_prophage AS SELECT feature_id AS cryptic_prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_prophage'; --- ************************************************ --- *** relation: tetraloop *** --- *** relation type: VIEW *** --- *** *** --- *** A base-paired stem with loop of 4 non-hy *** --- *** drogen bonded nucleotides. *** --- ************************************************ --- CREATE VIEW tetraloop AS SELECT feature_id AS tetraloop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop'; --- ************************************************ --- *** relation: dna_constraint_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A double-stranded DNA used to control ma *** --- *** cromolecular structure and function. *** --- ************************************************ --- CREATE VIEW dna_constraint_sequence AS SELECT feature_id AS dna_constraint_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_constraint_sequence'; --- ************************************************ --- *** relation: i_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A cytosine rich domain whereby strands a *** --- *** ssociate both inter- and intramolecularl *** --- *** y at moderately acidic pH. *** --- ************************************************ --- CREATE VIEW i_motif AS SELECT feature_id AS i_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif'; --- ************************************************ --- *** relation: pna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Peptide nucleic acid, is a chemical not *** --- *** known to occur naturally but is artifici *** --- *** ally synthesized and used in some biolog *** --- *** ical research and medical treatments. Th *** --- *** e PNA backbone is composed of repeating *** --- *** N-(2-aminoethyl)-glycine units linked by *** --- *** peptide bonds. The purine and pyrimidin *** --- *** e bases are linked to the backbone by me *** --- *** thylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna_oligo AS SELECT feature_id AS pna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA_oligo'; --- ************************************************ --- *** relation: dnazyme *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence with catalytic activity. *** --- ************************************************ --- CREATE VIEW dnazyme AS SELECT feature_id AS dnazyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAzyme'; --- ************************************************ --- *** relation: mnp *** --- *** relation type: VIEW *** --- *** *** --- *** A multiple nucleotide polymorphism with *** --- *** alleles of common length > 1, for exampl *** --- *** e AAA/TTT. *** --- ************************************************ --- CREATE VIEW mnp AS SELECT feature_id AS mnp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP'; --- ************************************************ --- *** relation: intron_domain *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intron_domain AS SELECT feature_id AS intron_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain'; --- ************************************************ --- *** relation: wobble_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base pairing, mo *** --- *** st commonly between G and U, which is im *** --- *** portant for the secondary structure of R *** --- *** NAs. It has similar thermodynamic stabil *** --- *** ity to the Watson-Crick pairing. Wobble *** --- *** base pairs only have two hydrogen bonds. *** --- *** Other wobble base pair possibilities ar *** --- *** e I-A, I-U and I-C. *** --- ************************************************ --- CREATE VIEW wobble_base_pair AS SELECT feature_id AS wobble_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wobble_base_pair'; --- ************************************************ --- *** relation: internal_guide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A purine-rich sequence in the group I in *** --- *** trons which determines the locations of *** --- *** the splice sites in group I intron splic *** --- *** ing and has catalytic activity. *** --- ************************************************ --- CREATE VIEW internal_guide_sequence AS SELECT feature_id AS internal_guide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence'; --- ************************************************ --- *** relation: silent_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that does not affect *** --- *** protein function. Silent mutations may o *** --- *** ccur in genic ( CDS, UTR, intron etc) an *** --- *** d intergenic regions. Silent mutations m *** --- *** ay have affects on processes such as spl *** --- *** icing and regulation. *** --- ************************************************ --- CREATE VIEW silent_mutation AS SELECT feature_id AS silent_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation'; --- ************************************************ --- *** relation: epitope *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith antibodies, B cells or T cells. *** --- ************************************************ --- CREATE VIEW epitope AS SELECT feature_id AS epitope_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epitope'; --- ************************************************ --- *** relation: copy_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A variation that increases or decreases *** --- *** the copy number of a given region. *** --- ************************************************ --- CREATE VIEW copy_number_variation AS SELECT feature_id AS copy_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'copy_number_variation'; --- ************************************************ --- *** relation: chromosome_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_breakpoint AS SELECT feature_id AS chromosome_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint'; --- ************************************************ --- *** relation: inversion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where an i *** --- *** nversion begins or ends. *** --- ************************************************ --- CREATE VIEW inversion_breakpoint AS SELECT feature_id AS inversion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint'; --- ************************************************ --- *** relation: allele *** --- *** relation type: VIEW *** --- *** *** --- *** An allele is one of a set of coexisting *** --- *** sequence variants of a gene. *** --- ************************************************ --- CREATE VIEW allele AS SELECT feature_id AS allele_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'allele'; --- ************************************************ --- *** relation: haplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A haplotype is one of a set of coexistin *** --- *** g sequence variants of a haplotype block *** --- *** . *** --- ************************************************ --- CREATE VIEW haplotype AS SELECT feature_id AS haplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype'; --- ************************************************ --- *** relation: polymorphic_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that is segregating i *** --- *** n one or more natural populations of a s *** --- *** pecies. *** --- ************************************************ --- CREATE VIEW polymorphic_sequence_variant AS SELECT feature_id AS polymorphic_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant'; --- ************************************************ --- *** relation: genome *** --- *** relation type: VIEW *** --- *** *** --- *** A genome is the sum of genetic material *** --- *** within a cell or virion. *** --- ************************************************ --- CREATE VIEW genome AS SELECT feature_id AS genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'genome'; --- ************************************************ --- *** relation: so_genotype *** --- *** relation type: VIEW *** --- *** *** --- *** A genotype is a variant genome, complete *** --- *** or incomplete. *** --- ************************************************ --- CREATE VIEW so_genotype AS SELECT feature_id AS so_genotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genotype'; --- ************************************************ --- *** relation: diplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A diplotype is a pair of haplotypes from *** --- *** a given individual. It is a genotype wh *** --- *** ere the phase is known. *** --- ************************************************ --- CREATE VIEW diplotype AS SELECT feature_id AS diplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype'; --- ************************************************ --- *** relation: direction_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direction_attribute AS SELECT feature_id AS direction_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'direction_attribute'; --- ************************************************ --- *** relation: forward *** --- *** relation type: VIEW *** --- *** *** --- *** Forward is an attribute of the feature, *** --- *** where the feature is in the 5' to 3' dir *** --- *** ection. *** --- ************************************************ --- CREATE VIEW forward AS SELECT feature_id AS forward_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward'; --- ************************************************ --- *** relation: reverse *** --- *** relation type: VIEW *** --- *** *** --- *** Reverse is an attribute of the feature, *** --- *** where the feature is in the 3' to 5' dir *** --- *** ection. Again could be applied to primer *** --- *** . *** --- ************************************************ --- CREATE VIEW reverse AS SELECT feature_id AS reverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse'; --- ************************************************ --- *** relation: mitochondrial_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_dna AS SELECT feature_id AS mitochondrial_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA'; --- ************************************************ --- *** relation: chloroplast_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_dna AS SELECT feature_id AS chloroplast_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA'; --- ************************************************ --- *** relation: mirtron *** --- *** relation type: VIEW *** --- *** *** --- *** A de-branched intron which mimics the st *** --- *** ructure of pre-miRNA and enters the miRN *** --- *** A processing pathway without Drosha medi *** --- *** ated cleavage. *** --- ************************************************ --- CREATE VIEW mirtron AS SELECT feature_id AS mirtron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mirtron'; --- ************************************************ --- *** relation: pirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA, part of a silenc *** --- *** ing system that prevents the spreading o *** --- *** f selfish genetic elements. *** --- ************************************************ --- CREATE VIEW pirna AS SELECT feature_id AS pirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA'; --- ************************************************ --- *** relation: arginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an arginine ant *** --- *** icodon, and a 3' arginine binding region *** --- *** . *** --- ************************************************ --- CREATE VIEW arginyl_trna AS SELECT feature_id AS arginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginyl_tRNA'; --- ************************************************ --- *** relation: mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide region with either intra-ge *** --- *** nome or intracellular moblity, of varyin *** --- *** g length, which often carry the informat *** --- *** ion necessary for transfer and recombina *** --- *** tion with the host genome. *** --- ************************************************ --- CREATE VIEW mobile_genetic_element AS SELECT feature_id AS mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'mobile_genetic_element'; --- ************************************************ --- *** relation: extrachromosomal_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is not integrated into the h *** --- *** ost chromosome. *** --- ************************************************ --- CREATE VIEW extrachromosomal_mobile_genetic_element AS SELECT feature_id AS extrachromosomal_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'extrachromosomal_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is integrated into the host *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW integrated_mobile_genetic_element AS SELECT feature_id AS integrated_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'integrated_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid sequence that is integrated wi *** --- *** thin the host chromosome. *** --- ************************************************ --- CREATE VIEW integrated_plasmid AS SELECT feature_id AS integrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_plasmid'; --- ************************************************ --- *** relation: viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The region of nucleotide sequence of a v *** --- *** irus, a submicroscopic particle that rep *** --- *** licates by infecting a host cell. *** --- ************************************************ --- CREATE VIEW viral_sequence AS SELECT feature_id AS viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'viral_sequence'; --- ************************************************ --- *** relation: phage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide sequence of a virus that *** --- *** infects bacteria. *** --- ************************************************ --- CREATE VIEW phage_sequence AS SELECT feature_id AS phage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence'; --- ************************************************ --- *** relation: attctn_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attachment site located on a conjugat *** --- *** ive transposon and used for site-specifi *** --- *** c integration of a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW attctn_site AS SELECT feature_id AS attctn_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attCtn_site'; --- ************************************************ --- *** relation: nuclear_mt_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A nuclear pseudogene of either coding or *** --- *** non-coding mitochondria derived sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW nuclear_mt_pseudogene AS SELECT feature_id AS nuclear_mt_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_mt_pseudogene'; --- ************************************************ --- *** relation: cointegrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A MGE region consisting of two fused pla *** --- *** smids resulting from a replicative trans *** --- *** position event. *** --- ************************************************ --- CREATE VIEW cointegrated_plasmid AS SELECT feature_id AS cointegrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cointegrated_plasmid'; --- ************************************************ --- *** relation: irlinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the left of a region susceptible to s *** --- *** ite-specific inversion. *** --- ************************************************ --- CREATE VIEW irlinv_site AS SELECT feature_id AS irlinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site'; --- ************************************************ --- *** relation: irrinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the right of a region susceptible to *** --- *** site-specific inversion. *** --- ************************************************ --- CREATE VIEW irrinv_site AS SELECT feature_id AS irrinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRRinv_site'; --- ************************************************ --- *** relation: inversion_site_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region located within an inversion sit *** --- *** e. *** --- ************************************************ --- CREATE VIEW inversion_site_part AS SELECT feature_id AS inversion_site_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'inversion_site_part'; --- ************************************************ --- *** relation: defective_conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** An island that contains genes for integr *** --- *** ation/excision and the gene and site for *** --- *** the initiation of intercellular transfe *** --- *** r by conjugation. It can be complemented *** --- *** for transfer by a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW defective_conjugative_transposon AS SELECT feature_id AS defective_conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'defective_conjugative_transposon'; --- ************************************************ --- *** relation: repeat_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a repeat, interrupted by th *** --- *** e insertion of another element. *** --- ************************************************ --- CREATE VIEW repeat_fragment AS SELECT feature_id AS repeat_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_fragment'; --- ************************************************ --- *** relation: transposon_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a transposon, interrupted b *** --- *** y the insertion of another element. *** --- ************************************************ --- CREATE VIEW transposon_fragment AS SELECT feature_id AS transposon_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposon_fragment'; --- ************************************************ --- *** relation: transcriptional_cis_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates the t *** --- *** ranscription of a gene or genes. *** --- ************************************************ --- CREATE VIEW transcriptional_cis_regulatory_region AS SELECT feature_id AS transcriptional_cis_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'transcriptional_cis_regulatory_region'; --- ************************************************ --- *** relation: splicing_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates splic *** --- *** ing. *** --- ************************************************ --- CREATE VIEW splicing_regulatory_region AS SELECT feature_id AS splicing_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splicing_regulatory_region'; --- ************************************************ --- *** relation: promoter_targeting_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional_cis_regulatory_region *** --- *** that restricts the activity of a CRM to *** --- *** a single promoter and which functions on *** --- *** ly when both itself and an insulator are *** --- *** located between the CRM and the promote *** --- *** r. *** --- ************************************************ --- CREATE VIEW promoter_targeting_sequence AS SELECT feature_id AS promoter_targeting_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_targeting_sequence'; --- ************************************************ --- *** relation: sequence_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_alteration is a sequence_feat *** --- *** ure whose extent is the deviation from a *** --- *** nother sequence. *** --- ************************************************ --- CREATE VIEW sequence_alteration AS SELECT feature_id AS sequence_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_alteration'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant is a non exact copy o *** --- *** f a sequence_feature or genome exhibitin *** --- *** g one or more sequence_alteration. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'functional_variant' OR cvterm.name = 'structural_variant' OR cvterm.name = 'loss_of_heterozygosity' OR cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: propeptide_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** The propeptide_cleavage_site is the argi *** --- *** nine/lysine boundary on a propeptide whe *** --- *** re cleavage occurs. *** --- ************************************************ --- CREATE VIEW propeptide_cleavage_site AS SELECT feature_id AS propeptide_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide_cleavage_site'; --- ************************************************ --- *** relation: propeptide *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a peptide chain which is cleaved *** --- *** off during the formation of the mature *** --- *** protein. *** --- ************************************************ --- CREATE VIEW propeptide AS SELECT feature_id AS propeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide'; --- ************************************************ --- *** relation: immature_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** An immature_peptide_region is the extent *** --- *** of the peptide after it has been transl *** --- *** ated and before any processing occurs. *** --- ************************************************ --- CREATE VIEW immature_peptide_region AS SELECT feature_id AS immature_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'immature_peptide_region'; --- ************************************************ --- *** relation: active_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Active peptides are proteins which are b *** --- *** iologically active, released from a prec *** --- *** ursor molecule. *** --- ************************************************ --- CREATE VIEW active_peptide AS SELECT feature_id AS active_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide'; --- ************************************************ --- *** relation: compositionally_biased_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is rich in a par *** --- *** ticular amino acid or homopolymeric and *** --- *** greater than three residues in length. *** --- ************************************************ --- CREATE VIEW compositionally_biased_region_of_peptide AS SELECT feature_id AS compositionally_biased_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compositionally_biased_region_of_peptide'; --- ************************************************ --- *** relation: polypeptide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a short (up to 20 am *** --- *** ino acids) region of biological interest *** --- *** . Such motifs, although they are too sho *** --- *** rt to constitute functional domains, sha *** --- *** re sequence similarities and are conserv *** --- *** ed in different proteins. They display a *** --- *** common function (protein-binding, subce *** --- *** llular location etc.). *** --- ************************************************ --- CREATE VIEW polypeptide_motif AS SELECT feature_id AS polypeptide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_motif'; --- ************************************************ --- *** relation: polypeptide_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide_repeat is a single copy of *** --- *** an internal sequence repetition. *** --- ************************************************ --- CREATE VIEW polypeptide_repeat AS SELECT feature_id AS polypeptide_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_repeat'; --- ************************************************ --- *** relation: polypeptide_structural_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of polypeptide with a given struc *** --- *** tural property. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_region AS SELECT feature_id AS polypeptide_structural_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_region'; --- ************************************************ --- *** relation: membrane_structure *** --- *** relation type: VIEW *** --- *** *** --- *** Arrangement of the polypeptide with resp *** --- *** ect to the lipid bilayer. *** --- ************************************************ --- CREATE VIEW membrane_structure AS SELECT feature_id AS membrane_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_structure'; --- ************************************************ --- *** relation: extramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer. *** --- ************************************************ --- CREATE VIEW extramembrane_polypeptide_region AS SELECT feature_id AS extramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'extramembrane_polypeptide_region'; --- ************************************************ --- *** relation: cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized ins *** --- *** ide the cytoplasm. *** --- ************************************************ --- CREATE VIEW cytoplasmic_polypeptide_region AS SELECT feature_id AS cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: non_cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer and outside of t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW non_cytoplasmic_polypeptide_region AS SELECT feature_id AS non_cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: intramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region present in the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW intramembrane_polypeptide_region AS SELECT feature_id AS intramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region'; --- ************************************************ --- *** relation: membrane_peptide_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region localized within the *** --- *** lipid bilayer where both ends traverse t *** --- *** he same membrane. *** --- ************************************************ --- CREATE VIEW membrane_peptide_loop AS SELECT feature_id AS membrane_peptide_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop'; --- ************************************************ --- *** relation: transmembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region traversing the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW transmembrane_polypeptide_region AS SELECT feature_id AS transmembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transmembrane_polypeptide_region'; --- ************************************************ --- *** relation: polypeptide_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide with secondary struc *** --- *** ture has hydrogen bonding along the pept *** --- *** ide chain that causes a defined conforma *** --- *** tion of the chain. *** --- ************************************************ --- CREATE VIEW polypeptide_secondary_structure AS SELECT feature_id AS polypeptide_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_secondary_structure'; --- ************************************************ --- *** relation: polypeptide_structural_motif *** --- *** relation type: VIEW *** --- *** *** --- *** Motif is a three-dimensional structural *** --- *** element within the chain, which appears *** --- *** also in a variety of other molecules. Un *** --- *** like a domain, a motif does not need to *** --- *** form a stable globular unit. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_motif AS SELECT feature_id AS polypeptide_structural_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_motif'; --- ************************************************ --- *** relation: coiled_coil *** --- *** relation type: VIEW *** --- *** *** --- *** A coiled coil is a structural motif in p *** --- *** roteins, in which alpha-helices are coil *** --- *** ed together like the strands of a rope. *** --- ************************************************ --- CREATE VIEW coiled_coil AS SELECT feature_id AS coiled_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil'; --- ************************************************ --- *** relation: helix_turn_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A motif comprising two helices separated *** --- *** by a turn. *** --- ************************************************ --- CREATE VIEW helix_turn_helix AS SELECT feature_id AS helix_turn_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helix_turn_helix'; --- ************************************************ --- *** relation: polypeptide_sequencing_information *** --- *** relation type: VIEW *** --- *** *** --- *** Incompatibility in the sequence due to s *** --- *** ome experimental problem. *** --- ************************************************ --- CREATE VIEW polypeptide_sequencing_information AS SELECT feature_id AS polypeptide_sequencing_information_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'polypeptide_sequencing_information'; --- ************************************************ --- *** relation: non_adjacent_residues *** --- *** relation type: VIEW *** --- *** *** --- *** Indicates that two consecutive residues *** --- *** in a fragment sequence are not consecuti *** --- *** ve in the full-length protein and that t *** --- *** here are a number of unsequenced residue *** --- *** s between them. *** --- ************************************************ --- CREATE VIEW non_adjacent_residues AS SELECT feature_id AS non_adjacent_residues_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues'; --- ************************************************ --- *** relation: non_terminal_residue *** --- *** relation type: VIEW *** --- *** *** --- *** The residue at an extremity of the seque *** --- *** nce is not the terminal residue. *** --- ************************************************ --- CREATE VIEW non_terminal_residue AS SELECT feature_id AS non_terminal_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_terminal_residue'; --- ************************************************ --- *** relation: sequence_conflict *** --- *** relation type: VIEW *** --- *** *** --- *** Different sources report differing seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW sequence_conflict AS SELECT feature_id AS sequence_conflict_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection' OR cvterm.name = 'sequence_conflict'; --- ************************************************ --- *** relation: sequence_uncertainty *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the positions in a sequence wh *** --- *** ere the authors are unsure about the seq *** --- *** uence assignment. *** --- ************************************************ --- CREATE VIEW sequence_uncertainty AS SELECT feature_id AS sequence_uncertainty_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_uncertainty'; --- ************************************************ --- *** relation: post_translationally_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region where a transformation occurs i *** --- *** n a protein after it has been synthesize *** --- *** d. This which may regulate, stabilize, c *** --- *** rosslink or introduce new chemical funct *** --- *** ionalities in the protein. *** --- ************************************************ --- CREATE VIEW post_translationally_modified_region AS SELECT feature_id AS post_translationally_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'post_translationally_modified_region'; --- ************************************************ --- *** relation: polypeptide_metal_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with metal ions. *** --- ************************************************ --- CREATE VIEW polypeptide_metal_contact AS SELECT feature_id AS polypeptide_metal_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_metal_contact'; --- ************************************************ --- *** relation: protein_protein_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the protein mole *** --- *** cule, interacts selectively and non-cova *** --- *** lently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW protein_protein_contact AS SELECT feature_id AS protein_protein_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact'; --- ************************************************ --- *** relation: polypeptide_calcium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with calcium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_calcium_ion_contact_site AS SELECT feature_id AS polypeptide_calcium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_cobalt_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with cobalt ions. *** --- ************************************************ --- CREATE VIEW polypeptide_cobalt_ion_contact_site AS SELECT feature_id AS polypeptide_cobalt_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_cobalt_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_copper_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with copper ions. *** --- ************************************************ --- CREATE VIEW polypeptide_copper_ion_contact_site AS SELECT feature_id AS polypeptide_copper_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_copper_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_iron_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with iron ions. *** --- ************************************************ --- CREATE VIEW polypeptide_iron_ion_contact_site AS SELECT feature_id AS polypeptide_iron_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_iron_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_magnesium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with magnesium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_magnesium_ion_contact_site AS SELECT feature_id AS polypeptide_magnesium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_magnesium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_manganese_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with manganese ions. *** --- ************************************************ --- CREATE VIEW polypeptide_manganese_ion_contact_site AS SELECT feature_id AS polypeptide_manganese_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_manganese_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_molybdenum_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with molybdenum ions. *** --- ************************************************ --- CREATE VIEW polypeptide_molybdenum_ion_contact_site AS SELECT feature_id AS polypeptide_molybdenum_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_molybdenum_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_nickel_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with nickel ions. *** --- ************************************************ --- CREATE VIEW polypeptide_nickel_ion_contact_site AS SELECT feature_id AS polypeptide_nickel_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nickel_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_tungsten_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with tungsten ions. *** --- ************************************************ --- CREATE VIEW polypeptide_tungsten_ion_contact_site AS SELECT feature_id AS polypeptide_tungsten_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_tungsten_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_zinc_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with zinc ions. *** --- ************************************************ --- CREATE VIEW polypeptide_zinc_ion_contact_site AS SELECT feature_id AS polypeptide_zinc_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_zinc_ion_contact_site'; --- ************************************************ --- *** relation: catalytic_residue *** --- *** relation type: VIEW *** --- *** *** --- *** Amino acid involved in the activity of a *** --- *** n enzyme. *** --- ************************************************ --- CREATE VIEW catalytic_residue AS SELECT feature_id AS catalytic_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue'; --- ************************************************ --- *** relation: polypeptide_ligand_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues which interact with a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_ligand_contact AS SELECT feature_id AS polypeptide_ligand_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact'; --- ************************************************ --- *** relation: asx_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: Residue(i) is Asp *** --- *** artate or Asparagine (Asx), side-chain O *** --- *** of residue(i) is H-bonded to the main-c *** --- *** hain NH of residue(i+2) or (i+3), main-c *** --- *** hain CO of residue(i) is H-bonded to the *** --- *** main-chain NH of residue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW asx_motif AS SELECT feature_id AS asx_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif'; --- ************************************************ --- *** relation: beta_bulge *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet in which the main chains of two co *** --- *** nsecutive residues are H-bonded to that *** --- *** of the third, and in which the dihedral *** --- *** angles are as follows: Residue(i): -140 *** --- *** degrees < phi(l) -20 degrees , -90 degre *** --- *** es < psi(l) < 40 degrees. Residue (i+1): *** --- *** -180 degrees < phi < -25 degrees or +12 *** --- *** 0 degrees < phi < +180 degrees, +40 degr *** --- *** ees < psi < +180 degrees or -180 degrees *** --- *** < psi < -120 degrees. *** --- ************************************************ --- CREATE VIEW beta_bulge AS SELECT feature_id AS beta_bulge_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge'; --- ************************************************ --- *** relation: beta_bulge_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds. Beta bu *** --- *** lge loops often occur at the loop ends o *** --- *** f beta-hairpins. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop AS SELECT feature_id AS beta_bulge_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'beta_bulge_loop'; --- ************************************************ --- *** relation: beta_bulge_loop_five *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 4), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +3), these loops have an RL nest at resi *** --- *** dues i+2 and i+3. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_five AS SELECT feature_id AS beta_bulge_loop_five_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five'; --- ************************************************ --- *** relation: beta_bulge_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 5), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +4), these loops have an RL nest at resi *** --- *** dues i+3 and i+4. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_six AS SELECT feature_id AS beta_bulge_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_six'; --- ************************************************ --- *** relation: beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A beta strand describes a single length *** --- *** of polypeptide chain that forms part of *** --- *** a beta sheet. A single continuous stretc *** --- *** h of amino acids adopting an extended co *** --- *** nformation of hydrogen bonds between the *** --- *** N-O and the C=O of another part of the *** --- *** peptide. This forms a secondary protein *** --- *** structure in which two or more extended *** --- *** polypeptide regions are hydrogen-bonded *** --- *** to one another in a planar array. *** --- ************************************************ --- CREATE VIEW beta_strand AS SELECT feature_id AS beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'beta_strand'; --- ************************************************ --- *** relation: antiparallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (one running N-term *** --- *** inal to C-terminal and one running C-ter *** --- *** minal to N-terminal). Hydrogen bonding o *** --- *** ccurs between every other C=O from one s *** --- *** trand to every other N-H on the adjacent *** --- *** strand. In this case, if two atoms C-al *** --- *** pha (i) and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then t *** --- *** hey form two mutual backbone hydrogen bo *** --- *** nds to each other's flanking peptide gro *** --- *** ups; this is known as a close pair of hy *** --- *** drogen bonds. The peptide backbone dihed *** --- *** ral angles (phi, psi) are about (-140 de *** --- *** grees, 135 degrees) in antiparallel shee *** --- *** ts. *** --- ************************************************ --- CREATE VIEW antiparallel_beta_strand AS SELECT feature_id AS antiparallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand'; --- ************************************************ --- *** relation: parallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (both running N-ter *** --- *** minal to C-terminal). This orientation i *** --- *** s slightly less stable because it introd *** --- *** uces nonplanarity in the inter-strand hy *** --- *** drogen bonding pattern. Hydrogen bonding *** --- *** occurs between every other C=O from one *** --- *** strand to every other N-H on the adjace *** --- *** nt strand. In this case, if two atoms C- *** --- *** alpha (i)and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then *** --- *** they do not hydrogen bond to each other; *** --- *** rather, one residue forms hydrogen bond *** --- *** s to the residues that flank the other ( *** --- *** but not vice versa). For example, residu *** --- *** e i may form hydrogen bonds to residues *** --- *** j - 1 and j + 1; this is known as a wide *** --- *** pair of hydrogen bonds. By contrast, re *** --- *** sidue j may hydrogen-bond to different r *** --- *** esidues altogether, or to none at all. T *** --- *** he dihedral angles (phi, psi) are about *** --- *** (-120 degrees, 115 degrees) in parallel *** --- *** sheets. *** --- ************************************************ --- CREATE VIEW parallel_beta_strand AS SELECT feature_id AS parallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'parallel_beta_strand'; --- ************************************************ --- *** relation: peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A helix is a secondary_structure conform *** --- *** ation where the peptide backbone forms a *** --- *** coil. *** --- ************************************************ --- CREATE VIEW peptide_helix AS SELECT feature_id AS peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'peptide_helix'; --- ************************************************ --- *** relation: left_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A left handed helix is a region of pepti *** --- *** de where the coiled conformation turns i *** --- *** n an anticlockwise, left handed screw. *** --- ************************************************ --- CREATE VIEW left_handed_peptide_helix AS SELECT feature_id AS left_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix'; --- ************************************************ --- *** relation: right_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A right handed helix is a region of pept *** --- *** ide where the coiled conformation turns *** --- *** in a clockwise, right handed screw. *** --- ************************************************ --- CREATE VIEW right_handed_peptide_helix AS SELECT feature_id AS right_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'right_handed_peptide_helix'; --- ************************************************ --- *** relation: alpha_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The helix has 3.6 residues per turn whic *** --- *** h corersponds to a translation of 1.5 an *** --- *** gstroms (= 0.15 nm) along the helical ax *** --- *** is. Every backbone N-H group donates a h *** --- *** ydrogen bond to the backbone C=O group o *** --- *** f the amino acid four residues earlier. *** --- ************************************************ --- CREATE VIEW alpha_helix AS SELECT feature_id AS alpha_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix'; --- ************************************************ --- *** relation: pi_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The pi helix has 4.1 residues per turn a *** --- *** nd a translation of 1.15 (=0.115 nm) al *** --- *** ong the helical axis. The N-H group of a *** --- *** n amino acid forms a hydrogen bond with *** --- *** the C=O group of the amino acid five res *** --- *** idues earlier. *** --- ************************************************ --- CREATE VIEW pi_helix AS SELECT feature_id AS pi_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pi_helix'; --- ************************************************ --- *** relation: three_ten_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The 3-10 helix has 3 residues per turn w *** --- *** ith a translation of 2.0 angstroms (=0.2 *** --- *** nm) along the helical axis. The N-H gro *** --- *** up of an amino acid forms a hydrogen bon *** --- *** d with the C=O group of the amino acid t *** --- *** hree residues earlier. *** --- ************************************************ --- CREATE VIEW three_ten_helix AS SELECT feature_id AS three_ten_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_ten_helix'; --- ************************************************ --- *** relation: polypeptide_nest_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles. Nest should not have P *** --- *** roline as any residue. Nests frequently *** --- *** occur as parts of other motifs such as S *** --- *** chellman loops. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_motif AS SELECT feature_id AS polypeptide_nest_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'polypeptide_nest_motif'; --- ************************************************ --- *** relation: polypeptide_nest_left_right_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): +20 degree *** --- *** s < phi < +140 degrees, -40 degrees < ps *** --- *** i < +90 degrees. Residue(i+1): -140 degr *** --- *** ees < phi < -20 degrees, -90 degrees < p *** --- *** si < +40 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_left_right_motif AS SELECT feature_id AS polypeptide_nest_left_right_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif'; --- ************************************************ --- *** relation: polypeptide_nest_right_left_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): -140 degre *** --- *** es < phi < -20 degrees, -90 degrees < ps *** --- *** i < +40 degrees. Residue(i+1): +20 degre *** --- *** es < phi < +140 degrees, -40 degrees < p *** --- *** si < +90 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_right_left_motif AS SELECT feature_id AS polypeptide_nest_right_left_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_right_left_motif'; --- ************************************************ --- *** relation: schellmann_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of six or seven consecutive resi *** --- *** dues that contains two H-bonds. *** --- ************************************************ --- CREATE VIEW schellmann_loop AS SELECT feature_id AS schellmann_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'schellmann_loop'; --- ************************************************ --- *** relation: schellmann_loop_seven *** --- *** relation type: VIEW *** --- *** *** --- *** Wild type: A motif of seven consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+6), the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of res *** --- *** idue(i+5). *** --- ************************************************ --- CREATE VIEW schellmann_loop_seven AS SELECT feature_id AS schellmann_loop_seven_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven'; --- ************************************************ --- *** relation: schellmann_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** Common Type: A motif of six consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+5) the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of resi *** --- *** due(i+4). *** --- ************************************************ --- CREATE VIEW schellmann_loop_six AS SELECT feature_id AS schellmann_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_six'; --- ************************************************ --- *** relation: serine_threonine_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two hydrogen bonds in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain O of residue(i) is H-bonded to t *** --- *** he main-chain NH of residue(i+2) or (i+3 *** --- *** ) , the main-chain CO group of residue(i *** --- *** ) is H-bonded to the main-chain NH of re *** --- *** sidue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW serine_threonine_motif AS SELECT feature_id AS serine_threonine_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_motif'; --- ************************************************ --- *** relation: serine_threonine_staple_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four or five consecutive resi *** --- *** dues and one H-bond in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain OH of residue(i) is H-bonded to *** --- *** the main-chain CO of residue(i3) or (i4) *** --- *** , Phi angles of residues(i1), (i2) and ( *** --- *** i3) are negative. *** --- ************************************************ --- CREATE VIEW serine_threonine_staple_motif AS SELECT feature_id AS serine_threonine_staple_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_staple_motif'; --- ************************************************ --- *** relation: polypeptide_turn_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A reversal in the direction of the backb *** --- *** one of a protein that is stabilized by h *** --- *** ydrogen bond between backbone NH and CO *** --- *** groups, involving no more than 4 amino a *** --- *** cid residues. *** --- ************************************************ --- CREATE VIEW polypeptide_turn_motif AS SELECT feature_id AS polypeptide_turn_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_turn_motif'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I (dihedral angles):- R *** --- *** esidue(i): -140 degrees < chi (1) -120 d *** --- *** egrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1) *** --- *** : -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_one AS SELECT feature_id AS asx_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < psi *** --- *** +120 degrees < +180 degrees. Residue(i+ *** --- *** 1): +20 degrees < phi < +140 degrees, -4 *** --- *** 0 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_two AS SELECT feature_id AS asx_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < ps *** --- *** i +120 degrees < +180 degrees. Residue(i *** --- *** +1): +20 degrees < phi < +140 degrees, - *** --- *** 40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_two AS SELECT feature_id AS asx_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1 *** --- *** ): -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_one AS SELECT feature_id AS asx_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive residues tha *** --- *** t may contain one H-bond, which, if pres *** --- *** ent, is between the main-chain CO of the *** --- *** first residue and the main-chain NH of *** --- *** the fourth. It is characterized by the d *** --- *** ihedral angles of the second and third r *** --- *** esidues, which are the basis for sub-cat *** --- *** egorization. *** --- ************************************************ --- CREATE VIEW beta_turn AS SELECT feature_id AS beta_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I:A motif of four conse *** --- *** cutive residues that may contain one H-b *** --- *** ond, which, if present, is between the m *** --- *** ain-chain CO of the first residue and th *** --- *** e main-chain NH of the fourth. It is cha *** --- *** racterized by the dihedral angles:- Resi *** --- *** due(i+1): -140 degrees > phi > -20 degre *** --- *** es, -90 degrees > psi > +40 degrees. Res *** --- *** idue(i+2): -140 degrees > phi > -20 degr *** --- *** ees, -90 degrees > psi > +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_one AS SELECT feature_id AS beta_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II: A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees > phi > -20 degr *** --- *** ees, +80 degrees > psi > +180 degrees. R *** --- *** esidue(i+2): +20 degrees > phi > +140 de *** --- *** grees, -40 degrees > psi > +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_two AS SELECT feature_id AS beta_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_two'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I:A motif of four cons *** --- *** ecutive residues that may contain one H- *** --- *** bond, which, if present, is between the *** --- *** main-chain CO of the first residue and t *** --- *** he main-chain NH of the fourth. It is ch *** --- *** aracterized by the dihedral angles: Resi *** --- *** due(i+1): -140 degrees < phi < -20 degre *** --- *** es, -90 degrees < psi < +40 degrees. Res *** --- *** idue(i+2): -140 degrees < phi < -20 degr *** --- *** ees, -90 degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_one AS SELECT feature_id AS beta_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II:A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees < phi < -20 degr *** --- *** ees, +80 degrees < psi < +180 degrees. R *** --- *** esidue(i+2): +20 degrees < phi < +140 de *** --- *** grees, -40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_two AS SELECT feature_id AS beta_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_two'; --- ************************************************ --- *** relation: gamma_turn *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i,( *** --- *** i+1),( i+2) if a hydrogen bond exists be *** --- *** tween residues i and i+2 and the phi and *** --- *** psi angles of residue i+1 fall within 4 *** --- *** 0 degrees. *** --- ************************************************ --- CREATE VIEW gamma_turn AS SELECT feature_id AS gamma_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'gamma_turn'; --- ************************************************ --- *** relation: gamma_turn_classic *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=75.0 - psi(i+1)=-64.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_classic AS SELECT feature_id AS gamma_turn_classic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic'; --- ************************************************ --- *** relation: gamma_turn_inverse *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=-79.0 - psi(i+1)=69.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_inverse AS SELECT feature_id AS gamma_turn_inverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_inverse'; --- ************************************************ --- *** relation: serine_threonine_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Ser *** --- *** ine (S) or Threonine (T), the side-chain *** --- *** O of residue(i) is H-bonded to the main *** --- *** -chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW serine_threonine_turn AS SELECT feature_id AS serine_threonine_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'serine_threonine_turn'; --- ************************************************ --- *** relation: st_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** -90 degrees psi +120 degrees < +40 degr *** --- *** ees, residue(i+1): -140 degrees < phi < *** --- *** -20 degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_one AS SELECT feature_id AS st_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one'; --- ************************************************ --- *** relation: st_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** +80 degrees psi +120 degrees < +180 deg *** --- *** rees, residue(i+1): +20 degrees < phi < *** --- *** +140 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_two AS SELECT feature_id AS st_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_two'; --- ************************************************ --- *** relation: st_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, -9 *** --- *** 0 degrees psi +120 degrees < +40 degrees *** --- *** , residue(i+1): -140 degrees < phi < -20 *** --- *** degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_one AS SELECT feature_id AS st_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_one'; --- ************************************************ --- *** relation: st_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, +8 *** --- *** 0 degrees psi +120 degrees < +180 degree *** --- *** s, residue(i+1): +20 degrees < phi < +14 *** --- *** 0 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_two AS SELECT feature_id AS st_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_two'; --- ************************************************ --- *** relation: polypeptide_variation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site of sequence variation (alteration *** --- *** ). Alternative sequence due to naturally *** --- *** occuring events such as polymorphisms a *** --- *** nd altermatve splicing or experimental m *** --- *** ethods such as site directed mutagenesis *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_variation_site AS SELECT feature_id AS polypeptide_variation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'polypeptide_variation_site'; --- ************************************************ --- *** relation: natural_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the natural sequence variants *** --- *** due to polymorphisms, disease-associated *** --- *** mutations, RNA editing and variations b *** --- *** etween strains, isolates or cultivars. *** --- ************************************************ --- CREATE VIEW natural_variant_site AS SELECT feature_id AS natural_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site'; --- ************************************************ --- *** relation: mutated_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Site which has been experimentally alter *** --- *** ed. *** --- ************************************************ --- CREATE VIEW mutated_variant_site AS SELECT feature_id AS mutated_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutated_variant_site'; --- ************************************************ --- *** relation: alternate_sequence_site *** --- *** relation type: VIEW *** --- *** *** --- *** Description of sequence variants produce *** --- *** d by alternative splicing, alternative p *** --- *** romoter usage, alternative initiation an *** --- *** d ribosomal frameshifting. *** --- ************************************************ --- CREATE VIEW alternate_sequence_site AS SELECT feature_id AS alternate_sequence_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternate_sequence_site'; --- ************************************************ --- *** relation: beta_turn_type_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** des of type VIa or type VIb and where th *** --- *** e i+2 residue is cis-proline. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six AS SELECT feature_id AS beta_turn_type_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six'; --- ************************************************ --- *** relation: beta_turn_type_six_a *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -60 degrees, psi ~ 120 degrees. Re *** --- *** sidue(i+2): phi ~ -90 degrees, psi ~ 0 d *** --- *** egrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a AS SELECT feature_id AS beta_turn_type_six_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six_a'; --- ************************************************ --- *** relation: beta_turn_type_six_a_one *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_one AS SELECT feature_id AS beta_turn_type_six_a_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one'; --- ************************************************ --- *** relation: beta_turn_type_six_a_two *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_two AS SELECT feature_id AS beta_turn_type_six_a_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_two'; --- ************************************************ --- *** relation: beta_turn_type_six_b *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -120 degrees, psi ~ 120 degrees. R *** --- *** esidue(i+2): phi ~ -60 degrees, psi ~ 0 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_b AS SELECT feature_id AS beta_turn_type_six_b_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_b'; --- ************************************************ --- *** relation: beta_turn_type_eight *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues that may contain one H-bond, which, *** --- *** if present, is between the main-chain C *** --- *** O of the first residue and the main-chai *** --- *** n NH of the fourth and is characterized *** --- *** by the dihedral angles: Residue(i+1): ph *** --- *** i ~ -60 degrees, psi ~ -30 degrees. Resi *** --- *** due(i+2): phi ~ -120 degrees, psi ~ 120 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_eight AS SELECT feature_id AS beta_turn_type_eight_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_eight'; --- ************************************************ --- *** relation: dre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -10 and -60 relative to t *** --- *** he TSS. Consensus sequence is WATCGATW. *** --- ************************************************ --- CREATE VIEW dre_motif AS SELECT feature_id AS dre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DRE_motif'; --- ************************************************ --- *** relation: dmv4_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments with respect to the TSS (+1). Cons *** --- *** ensus sequence is YGGTCACACTR. Marked sp *** --- *** atial preference within core promoter; t *** --- *** end to occur near the TSS, although not *** --- *** as tightly as INR (SO:0000014). *** --- ************************************************ --- CREATE VIEW dmv4_motif AS SELECT feature_id AS dmv4_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv4_motif'; --- ************************************************ --- *** relation: e_box_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and +1 relative to th *** --- *** e TSS. Consensus sequence is AWCAGCTGWT. *** --- *** Tends to co-occur with DMv2 (SO:0001161 *** --- *** ). Tends to not occur with DPE motif (SO *** --- *** :0000015). *** --- ************************************************ --- CREATE VIEW e_box_motif AS SELECT feature_id AS e_box_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'E_box_motif'; --- ************************************************ --- *** relation: dmv5_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -50 and -10 relative to t *** --- *** he TSS. Consensus sequence is KTYRGTATWT *** --- *** TT. Tends to co-occur with DMv4 (SO:0001 *** --- *** 157) . Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv5_motif AS SELECT feature_id AS dmv5_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv5_motif'; --- ************************************************ --- *** relation: dmv3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -30 and +15 relative to t *** --- *** he TSS. Consensus sequence is KNNCAKCNCT *** --- *** RNY. Tends to co-occur with DMv2 (SO:000 *** --- *** 1161). Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (0001162). *** --- ************************************************ --- CREATE VIEW dmv3_motif AS SELECT feature_id AS dmv3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv3_motif'; --- ************************************************ --- *** relation: dmv2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and -45 relative to t *** --- *** he TSS. Consensus sequence is MKSYGGCARC *** --- *** GSYSS. Tends to co-occur with DMv3 (SO:0 *** --- *** 001160). Tends to not occur with DPE mot *** --- *** if (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv2_motif AS SELECT feature_id AS dmv2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv2_motif'; --- ************************************************ --- *** relation: mte *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between +20 and +30 relative to t *** --- *** he TSS. Consensus sequence is CSARCSSAAC *** --- *** GS. Tends to co-occur with INR motif (SO *** --- *** :0000014). Tends to not occur with DPE m *** --- *** otif (SO:0000015) or DMv5 (SO:0001159). *** --- ************************************************ --- CREATE VIEW mte AS SELECT feature_id AS mte_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MTE'; --- ************************************************ --- *** relation: inr1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** TCATTCG. *** --- ************************************************ --- CREATE VIEW inr1_motif AS SELECT feature_id AS inr1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR1_motif'; --- ************************************************ --- *** relation: dpe1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CGGACGT. *** --- ************************************************ --- CREATE VIEW dpe1_motif AS SELECT feature_id AS dpe1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE1_motif'; --- ************************************************ --- *** relation: dmv1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CARCCCT. *** --- ************************************************ --- CREATE VIEW dmv1_motif AS SELECT feature_id AS dmv1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv1_motif'; --- ************************************************ --- *** relation: gaga_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAGAGCG. *** --- ************************************************ --- CREATE VIEW gaga_motif AS SELECT feature_id AS gaga_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GAGA_motif'; --- ************************************************ --- *** relation: ndm2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus CGMYGYCR. *** --- ************************************************ --- CREATE VIEW ndm2_motif AS SELECT feature_id AS ndm2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM2_motif'; --- ************************************************ --- *** relation: ndm3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAAAGCT. *** --- ************************************************ --- CREATE VIEW ndm3_motif AS SELECT feature_id AS ndm3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM3_motif'; --- ************************************************ --- *** relation: ds_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded RNA. *** --- ************************************************ --- CREATE VIEW ds_rna_viral_sequence AS SELECT feature_id AS ds_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_RNA_viral_sequence'; --- ************************************************ --- *** relation: polinton *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of DNA transposon that populates *** --- *** the genomes of protists, fungi, and anim *** --- *** als, characterized by a unique set of pr *** --- *** oteins necessary for their transposition *** --- *** , including a protein-primed DNA polymer *** --- *** ase B, retroviral integrase, cysteine pr *** --- *** otease, and ATPase. Polintons are charac *** --- *** terized by 6-bp target site duplications *** --- *** , terminal-inverted repeats that are sev *** --- *** eral hundred nucleotides long, and 5'-AG *** --- *** and TC-3' termini. Polintons exist as a *** --- *** utonomous and nonautonomous elements. *** --- ************************************************ --- CREATE VIEW polinton AS SELECT feature_id AS polinton_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polinton'; --- ************************************************ --- *** relation: rrna_21s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it in mitochondrial rRNA. *** --- ************************************************ --- CREATE VIEW rrna_21s AS SELECT feature_id AS rrna_21s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_21S'; --- ************************************************ --- *** relation: trna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tRNA. *** --- ************************************************ --- CREATE VIEW trna_region AS SELECT feature_id AS trna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'tRNA_region'; --- ************************************************ --- *** relation: anticodon_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of seven nucleotide bases in *** --- *** tRNA which contains the anticodon. It ha *** --- *** s the sequence 5'-pyrimidine-purine-anti *** --- *** codon-modified purine-any base-3. *** --- ************************************************ --- CREATE VIEW anticodon_loop AS SELECT feature_id AS anticodon_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop'; --- ************************************************ --- *** relation: anticodon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of three nucleotide bases in *** --- *** tRNA which recognizes a codon in mRNA. *** --- ************************************************ --- CREATE VIEW anticodon AS SELECT feature_id AS anticodon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon'; --- ************************************************ --- *** relation: cca_tail *** --- *** relation type: VIEW *** --- *** *** --- *** Base sequence at the 3' end of a tRNA. T *** --- *** he 3'-hydroxyl group on the terminal ade *** --- *** nosine is the attachment point for the a *** --- *** mino acid. *** --- ************************************************ --- CREATE VIEW cca_tail AS SELECT feature_id AS cca_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CCA_tail'; --- ************************************************ --- *** relation: dhu_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of nucleotide b *** --- *** ases in tRNA. It contains several dihydr *** --- *** ouracil residues. *** --- ************************************************ --- CREATE VIEW dhu_loop AS SELECT feature_id AS dhu_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DHU_loop'; --- ************************************************ --- *** relation: t_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of three nucleo *** --- *** tide bases in tRNA. It has sequence T-Ps *** --- *** i-C. *** --- ************************************************ --- CREATE VIEW t_loop AS SELECT feature_id AS t_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_loop'; --- ************************************************ --- *** relation: pyrrolysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding pyrrolysyl *** --- *** tRNA (SO:0000766). *** --- ************************************************ --- CREATE VIEW pyrrolysine_trna_primary_transcript AS SELECT feature_id AS pyrrolysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: u3_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U3 snoRNA is a member of the box C/D cla *** --- *** ss of small nucleolar RNAs. The U3 snoRN *** --- *** A secondary structure is characterised b *** --- *** y a small 5' domain (with boxes A and A' *** --- *** ), and a larger 3' domain (with boxes B, *** --- *** C, C', and D), the two domains being li *** --- *** nked by a single-stranded hinge. Boxes B *** --- *** and C form the B/C motif, which appears *** --- *** to be exclusive to U3 snoRNAs, and boxe *** --- *** s C' and D form the C'/D motif. The latt *** --- *** er is functionally similar to the C/D mo *** --- *** tifs found in other snoRNAs. The 5' doma *** --- *** in and the hinge region act as a pre-rRN *** --- *** A-binding domain. The 3' domain has cons *** --- *** erved protein-binding sites. Both the bo *** --- *** x B/C and box C'/D motifs are sufficient *** --- *** for nuclear retention of U3 snoRNA. The *** --- *** box C'/D motif is also necessary for nu *** --- *** cleolar localization, stability and hype *** --- *** rmethylation of U3 snoRNA. Both box B/C *** --- *** and C'/D motifs are involved in specific *** --- *** protein interactions and are necessary *** --- *** for the rRNA processing functions of U3 *** --- *** snoRNA. *** --- ************************************************ --- CREATE VIEW u3_snorna AS SELECT feature_id AS u3_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_snoRNA'; --- ************************************************ --- *** relation: au_rich_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is rich in AUUUA pen *** --- *** tamers. Messenger RNAs bearing multiple *** --- *** AU-rich elements are often unstable. *** --- ************************************************ --- CREATE VIEW au_rich_element AS SELECT feature_id AS au_rich_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'AU_rich_element'; --- ************************************************ --- *** relation: bruno_response_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is bound by the Dros *** --- *** ophila Bruno protein and its homologs. *** --- ************************************************ --- CREATE VIEW bruno_response_element AS SELECT feature_id AS bruno_response_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Bruno_response_element'; --- ************************************************ --- *** relation: iron_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory sequence found in the 5' an *** --- *** d 3' UTRs of many mRNAs which encode iro *** --- *** n-binding proteins. It has a hairpin str *** --- *** ucture and is recognized by trans-acting *** --- *** proteins known as iron-regulatory prote *** --- *** ins. *** --- ************************************************ --- CREATE VIEW iron_responsive_element AS SELECT feature_id AS iron_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iron_responsive_element'; --- ************************************************ --- *** relation: morpholino_backbone *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of nucleobases bound to a morpholino *** --- *** backbone. A morpholino backbone consist *** --- *** s of morpholine (CHEBI:34856) rings conn *** --- *** ected by phosphorodiamidate linkages. *** --- ************************************************ --- CREATE VIEW morpholino_backbone AS SELECT feature_id AS morpholino_backbone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_backbone'; --- ************************************************ --- *** relation: pna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of peptide nucleic acid (CHEBI:48021 *** --- *** ), a chemical consisting of nucleobases *** --- *** bound to a backbone composed of repeatin *** --- *** g N-(2-aminoethyl)-glycine units linked *** --- *** by peptide bonds. The purine and pyrimid *** --- *** ine bases are linked to the backbone by *** --- *** methylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna AS SELECT feature_id AS pna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA'; --- ************************************************ --- *** relation: enzymatic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** with or without an associated ribonucle *** --- *** oprotein. *** --- ************************************************ --- CREATE VIEW enzymatic AS SELECT feature_id AS enzymatic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic' OR cvterm.name = 'enzymatic'; --- ************************************************ --- *** relation: ribozymic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** even without an associated ribonucleopr *** --- *** otein. *** --- ************************************************ --- CREATE VIEW ribozymic AS SELECT feature_id AS ribozymic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic'; --- ************************************************ --- *** relation: pseudouridylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of pseu *** --- *** douridylation in an RNA molecule by base *** --- *** pairing with a short sequence around th *** --- *** e target residue. *** --- ************************************************ --- CREATE VIEW pseudouridylation_guide_snorna AS SELECT feature_id AS pseudouridylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA'; --- ************************************************ --- *** relation: lna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of 'locked' deoxyribose r *** --- *** ings connected to a phosphate backbone. *** --- *** The deoxyribose unit's conformation is ' *** --- *** locked' by a 2'-C,4'-C-oxymethylene link *** --- *** . *** --- ************************************************ --- CREATE VIEW lna AS SELECT feature_id AS lna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA'; --- ************************************************ --- *** relation: lna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of LNA residues. *** --- ************************************************ --- CREATE VIEW lna_oligo AS SELECT feature_id AS lna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA_oligo'; --- ************************************************ --- *** relation: tna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of threose rings connecte *** --- *** d to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW tna AS SELECT feature_id AS tna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA'; --- ************************************************ --- *** relation: tna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of TNA residues. *** --- ************************************************ --- CREATE VIEW tna_oligo AS SELECT feature_id AS tna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA_oligo'; --- ************************************************ --- *** relation: gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of an acyclic three-carbo *** --- *** n propylene glycol connected to a phosph *** --- *** ate backbone. It has two enantiomeric fo *** --- *** rms, (R)-GNA and (S)-GNA. *** --- ************************************************ --- CREATE VIEW gna AS SELECT feature_id AS gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'GNA'; --- ************************************************ --- *** relation: gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of GNA residues. *** --- ************************************************ --- CREATE VIEW gna_oligo AS SELECT feature_id AS gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'GNA_oligo'; --- ************************************************ --- *** relation: r_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (R)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW r_gna AS SELECT feature_id AS r_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA'; --- ************************************************ --- *** relation: r_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (R)-GNA residues. *** --- ************************************************ --- CREATE VIEW r_gna_oligo AS SELECT feature_id AS r_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo'; --- ************************************************ --- *** relation: s_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (S)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW s_gna AS SELECT feature_id AS s_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA'; --- ************************************************ --- *** relation: s_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (S)-GNA residues. *** --- ************************************************ --- CREATE VIEW s_gna_oligo AS SELECT feature_id AS s_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA_oligo'; --- ************************************************ --- *** relation: ds_dna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_DNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded DNA. *** --- ************************************************ --- CREATE VIEW ds_dna_viral_sequence AS SELECT feature_id AS ds_dna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_DNA_viral_sequence'; --- ************************************************ --- *** relation: ss_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ss_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as single stranded RNA. *** --- ************************************************ --- CREATE VIEW ss_rna_viral_sequence AS SELECT feature_id AS ss_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence'; --- ************************************************ --- *** relation: negative_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A negative_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** is complementary to mRNA and must be con *** --- *** verted to positive sense RNA by RNA poly *** --- *** merase before translation. *** --- ************************************************ --- CREATE VIEW negative_sense_ssrna_viral_sequence AS SELECT feature_id AS negative_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: positive_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A positive_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** can be immediately translated by the hos *** --- *** t. *** --- ************************************************ --- CREATE VIEW positive_sense_ssrna_viral_sequence AS SELECT feature_id AS positive_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positive_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: ambisense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ambisense_RNA_virus is a ss_RNA_viral_ *** --- *** sequence that is the sequence of a singl *** --- *** e stranded RNA virus with both messenger *** --- *** and anti messenger polarity. *** --- ************************************************ --- CREATE VIEW ambisense_ssrna_viral_sequence AS SELECT feature_id AS ambisense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ambisense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which RNA polymerase b *** --- *** inds, to begin transcription. *** --- ************************************************ --- CREATE VIEW rna_polymerase_promoter AS SELECT feature_id AS rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'RNA_polymerase_promoter'; --- ************************************************ --- *** relation: phage_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which Bacteriophage RN *** --- *** A polymerase binds, to begin transcripti *** --- *** on. *** --- ************************************************ --- CREATE VIEW phage_rna_polymerase_promoter AS SELECT feature_id AS phage_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: sp6_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the SP6 RNA poly *** --- *** merase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW sp6_rna_polymerase_promoter AS SELECT feature_id AS sp6_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t3_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which the T3 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t3_rna_polymerase_promoter AS SELECT feature_id AS t3_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T3_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t7_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the T7 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t7_rna_polymerase_promoter AS SELECT feature_id AS t7_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T7_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: five_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 5' end of a transcr *** --- *** ipt that usually codes for a protein. Th *** --- *** ese regions tend to be conserved across *** --- *** species and do not change much within a *** --- *** gene family. *** --- ************************************************ --- CREATE VIEW five_prime_est AS SELECT feature_id AS five_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST'; --- ************************************************ --- *** relation: three_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 3' end of a transcr *** --- *** ipt. They are more likely to fall within *** --- *** non-coding, or untranslated regions(UTR *** --- *** s). *** --- ************************************************ --- CREATE VIEW three_prime_est AS SELECT feature_id AS three_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_EST'; --- ************************************************ --- *** relation: translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA (not divisible by 3 b *** --- *** ases) that is skipped during the process *** --- *** of translational frameshifting (GO:0006 *** --- *** 452), causing the reading frame to be di *** --- *** fferent. *** --- ************************************************ --- CREATE VIEW translational_frameshift AS SELECT feature_id AS translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'translational_frameshift'; --- ************************************************ --- *** relation: plus_1_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 1 base long that is s *** --- *** kipped during the process of translation *** --- *** al frameshifting (GO:0006452), causing t *** --- *** he reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_1_translational_frameshift AS SELECT feature_id AS plus_1_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift'; --- ************************************************ --- *** relation: plus_2_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 2 bases long that is *** --- *** skipped during the process of translatio *** --- *** nal frameshifting (GO:0006452), causing *** --- *** the reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_2_translational_frameshift AS SELECT feature_id AS plus_2_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_translational_frameshift'; --- ************************************************ --- *** relation: group_iii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group III introns are introns found in t *** --- *** he mRNA of the plastids of euglenoid pro *** --- *** tists. They are spliced by a two step tr *** --- *** ansesterification with bulged adenosine *** --- *** as initiating nucleophile. *** --- ************************************************ --- CREATE VIEW group_iii_intron AS SELECT feature_id AS group_iii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_III_intron'; --- ************************************************ --- *** relation: noncoding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The maximal intersection of exon and UTR *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_region_of_exon AS SELECT feature_id AS noncoding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'noncoding_region_of_exon'; --- ************************************************ --- *** relation: coding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an exon that encodes for p *** --- *** rotein sequence. *** --- ************************************************ --- CREATE VIEW coding_region_of_exon AS SELECT feature_id AS coding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'coding_region_of_exon'; --- ************************************************ --- *** relation: endonuclease_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron that spliced via endonucleolyt *** --- *** ic cleavage and ligation rather than tra *** --- *** nsesterification. *** --- ************************************************ --- CREATE VIEW endonuclease_spliced_intron AS SELECT feature_id AS endonuclease_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'endonuclease_spliced_intron'; --- ************************************************ --- *** relation: protein_coding_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding_gene AS SELECT feature_id AS protein_coding_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'protein_coding_gene'; --- ************************************************ --- *** relation: transgenic_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** An insertion that derives from another o *** --- *** rganism, via the use of recombinant DNA *** --- *** technology. *** --- ************************************************ --- CREATE VIEW transgenic_insertion AS SELECT feature_id AS transgenic_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion'; --- ************************************************ --- *** relation: retrogene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW retrogene AS SELECT feature_id AS retrogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrogene'; --- ************************************************ --- *** relation: silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by RNA *** --- *** interference. *** --- ************************************************ --- CREATE VIEW silenced_by_rna_interference AS SELECT feature_id AS silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_RNA_interference'; --- ************************************************ --- *** relation: silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone modification. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_modification AS SELECT feature_id AS silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_by_histone_modification'; --- ************************************************ --- *** relation: silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone methylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_methylation AS SELECT feature_id AS silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation'; --- ************************************************ --- *** relation: silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone deacetylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_deacetylation AS SELECT feature_id AS silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: gene_silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by RNA interfere *** --- *** nce. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_rna_interference AS SELECT feature_id AS gene_silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_RNA_interference'; --- ************************************************ --- *** relation: gene_silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone modif *** --- *** ication. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_modification AS SELECT feature_id AS gene_silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'gene_silenced_by_histone_modification'; --- ************************************************ --- *** relation: gene_silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone methy *** --- *** lation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_methylation AS SELECT feature_id AS gene_silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation'; --- ************************************************ --- *** relation: gene_silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone deace *** --- *** tylation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_deacetylation AS SELECT feature_id AS gene_silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: dihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5,6-dih *** --- *** ydrouracil is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW dihydrouridine AS SELECT feature_id AS dihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine'; --- ************************************************ --- *** relation: pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5- posi *** --- *** tion of the uracil is bound to the ribos *** --- *** e ring instead of the 4- position. *** --- ************************************************ --- CREATE VIEW pseudouridine AS SELECT feature_id AS pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridine'; --- ************************************************ --- *** relation: inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which hypoxanthin *** --- *** e is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW inosine AS SELECT feature_id AS inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'inosine'; --- ************************************************ --- *** relation: seven_methylguanine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which guanine is *** --- *** methylated at the 7- position. *** --- ************************************************ --- CREATE VIEW seven_methylguanine AS SELECT feature_id AS seven_methylguanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanine'; --- ************************************************ --- *** relation: ribothymidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which thymine is *** --- *** bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW ribothymidine AS SELECT feature_id AS ribothymidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribothymidine'; --- ************************************************ --- *** relation: methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which methylhypox *** --- *** anthine is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW methylinosine AS SELECT feature_id AS methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine'; --- ************************************************ --- *** relation: mobile *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that h *** --- *** as either intra-genome or intracellular *** --- *** mobility. *** --- ************************************************ --- CREATE VIEW mobile AS SELECT feature_id AS mobile_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile'; --- ************************************************ --- *** relation: replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing at least one unique *** --- *** origin of replication and a unique termi *** --- *** nation site. *** --- ************************************************ --- CREATE VIEW replicon AS SELECT feature_id AS replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'replicon'; --- ************************************************ --- *** relation: base *** --- *** relation type: VIEW *** --- *** *** --- *** A base is a sequence feature that corres *** --- *** ponds to a single unit of a nucleotide p *** --- *** olymer. *** --- ************************************************ --- CREATE VIEW base AS SELECT feature_id AS base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'base'; --- ************************************************ --- *** relation: amino_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence feature that corresponds to a *** --- *** single amino acid residue in a polypept *** --- *** ide. *** --- ************************************************ --- CREATE VIEW amino_acid AS SELECT feature_id AS amino_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'amino_acid'; --- ************************************************ --- *** relation: major_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW major_tss AS SELECT feature_id AS major_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS'; --- ************************************************ --- *** relation: minor_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minor_tss AS SELECT feature_id AS minor_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minor_TSS'; --- ************************************************ --- *** relation: tss_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a gene from the 5' most TS *** --- *** S to the 3' TSS. *** --- ************************************************ --- CREATE VIEW tss_region AS SELECT feature_id AS tss_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TSS_region'; --- ************************************************ --- *** relation: encodes_alternate_transcription_start_sites *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW encodes_alternate_transcription_start_sites AS SELECT feature_id AS encodes_alternate_transcription_start_sites_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_alternate_transcription_start_sites'; --- ************************************************ --- *** relation: mirna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of an miRNA primary_transcript. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript_region AS SELECT feature_id AS mirna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'miRNA_primary_transcript_region'; --- ************************************************ --- *** relation: pre_mirna *** --- *** relation type: VIEW *** --- *** *** --- *** The 60-70 nucleotide region remain after *** --- *** Drosha processing of the primary transc *** --- *** ript, that folds back upon itself to for *** --- *** m a hairpin sructure. *** --- ************************************************ --- CREATE VIEW pre_mirna AS SELECT feature_id AS pre_mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA'; --- ************************************************ --- *** relation: mirna_stem *** --- *** relation type: VIEW *** --- *** *** --- *** The stem of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_stem AS SELECT feature_id AS mirna_stem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_stem'; --- ************************************************ --- *** relation: mirna_loop *** --- *** relation type: VIEW *** --- *** *** --- *** The loop of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_loop AS SELECT feature_id AS mirna_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_loop'; --- ************************************************ --- *** relation: synthetic_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of synthetic nucleotid *** --- *** es. *** --- ************************************************ --- CREATE VIEW synthetic_oligo AS SELECT feature_id AS synthetic_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'synthetic_oligo'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome of known length t *** --- *** hat is composed by ordering and aligning *** --- *** two or more different regions. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'assembly'; --- ************************************************ --- *** relation: fragment_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A fragment assembly is a genome assembly *** --- *** that orders overlapping fragments of th *** --- *** e genome based on landmark sequences. Th *** --- *** e base pair distance between the landmar *** --- *** ks is known allowing additivity of lengt *** --- *** hs. *** --- ************************************************ --- CREATE VIEW fragment_assembly AS SELECT feature_id AS fragment_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'fragment_assembly'; --- ************************************************ --- *** relation: fingerprint_map *** --- *** relation type: VIEW *** --- *** *** --- *** A fingerprint_map is a physical map comp *** --- *** osed of restriction fragments. *** --- ************************************************ --- CREATE VIEW fingerprint_map AS SELECT feature_id AS fingerprint_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map'; --- ************************************************ --- *** relation: sts_map *** --- *** relation type: VIEW *** --- *** *** --- *** An STS map is a physical map organized b *** --- *** y the unique STS landmarks. *** --- ************************************************ --- CREATE VIEW sts_map AS SELECT feature_id AS sts_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS_map'; --- ************************************************ --- *** relation: rh_map *** --- *** relation type: VIEW *** --- *** *** --- *** A radiation hybrid map is a physical map *** --- *** . *** --- ************************************************ --- CREATE VIEW rh_map AS SELECT feature_id AS rh_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RH_map'; --- ************************************************ --- *** relation: sonicate_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment generated by sonication. *** --- *** Sonication is a technique used to sheer *** --- *** DNA into smaller fragments. *** --- ************************************************ --- CREATE VIEW sonicate_fragment AS SELECT feature_id AS sonicate_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sonicate_fragment'; --- ************************************************ --- *** relation: polyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is an exact multi *** --- *** ple of the haploid number and is greater *** --- *** than the diploid number. *** --- ************************************************ --- CREATE VIEW polyploid AS SELECT feature_id AS polyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'polyploid'; --- ************************************************ --- *** relation: autopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from the same organism *** --- *** . *** --- ************************************************ --- CREATE VIEW autopolyploid AS SELECT feature_id AS autopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid'; --- ************************************************ --- *** relation: allopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from a different organ *** --- *** ism. *** --- ************************************************ --- CREATE VIEW allopolyploid AS SELECT feature_id AS allopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allopolyploid'; --- ************************************************ --- *** relation: homing_endonuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The binding site (recognition site) of a *** --- *** homing endonuclease. The binding site i *** --- *** s typically large. *** --- ************************************************ --- CREATE VIEW homing_endonuclease_binding_site AS SELECT feature_id AS homing_endonuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homing_endonuclease_binding_site'; --- ************************************************ --- *** relation: octamer_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters with seque *** --- *** nce ATTGCAT that binds Pou-domain transc *** --- *** ription factors. *** --- ************************************************ --- CREATE VIEW octamer_motif AS SELECT feature_id AS octamer_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'octamer_motif'; --- ************************************************ --- *** relation: apicoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in an apicoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW apicoplast_chromosome AS SELECT feature_id AS apicoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_chromosome'; --- ************************************************ --- *** relation: sequence_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of discontinuous sequences. *** --- ************************************************ --- CREATE VIEW sequence_collection AS SELECT feature_id AS sequence_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'genome' OR cvterm.name = 'contig_collection' OR cvterm.name = 'peptide_collection' OR cvterm.name = 'variant_collection' OR cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'sequence_collection'; --- ************************************************ --- *** relation: overlapping_feature_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous region of sequence composed *** --- *** of the overlapping of multiple sequence *** --- *** _features, which ultimately provides evi *** --- *** dence for another sequence_feature. *** --- ************************************************ --- CREATE VIEW overlapping_feature_set AS SELECT feature_id AS overlapping_feature_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'overlapping_feature_set'; --- ************************************************ --- *** relation: overlapping_est_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continous experimental result region e *** --- *** xtending the length of multiple overlapp *** --- *** ing EST's. *** --- ************************************************ --- CREATE VIEW overlapping_est_set AS SELECT feature_id AS overlapping_est_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set'; --- ************************************************ --- *** relation: ncrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ncrna_gene AS SELECT feature_id AS ncrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'ncRNA_gene'; --- ************************************************ --- *** relation: grna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW grna_gene AS SELECT feature_id AS grna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene'; --- ************************************************ --- *** relation: mirna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_gene AS SELECT feature_id AS mirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_gene'; --- ************************************************ --- *** relation: scrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_gene AS SELECT feature_id AS scrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_gene'; --- ************************************************ --- *** relation: snorna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_gene AS SELECT feature_id AS snorna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA_gene'; --- ************************************************ --- *** relation: snrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_gene AS SELECT feature_id AS snrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_gene'; --- ************************************************ --- *** relation: srp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_gene AS SELECT feature_id AS srp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_gene'; --- ************************************************ --- *** relation: strna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_gene AS SELECT feature_id AS strna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_gene'; --- ************************************************ --- *** relation: tmrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_gene AS SELECT feature_id AS tmrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_gene'; --- ************************************************ --- *** relation: trna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_gene AS SELECT feature_id AS trna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_gene'; --- ************************************************ --- *** relation: modified_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified adenine is an adenine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_adenosine AS SELECT feature_id AS modified_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'modified_adenosine'; --- ************************************************ --- *** relation: modified_inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified inosine is an inosine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_inosine AS SELECT feature_id AS modified_inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'modified_inosine'; --- ************************************************ --- *** relation: modified_cytidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified cytidine is a cytidine base f *** --- *** eature which has been altered. *** --- ************************************************ --- CREATE VIEW modified_cytidine AS SELECT feature_id AS modified_cytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'modified_cytidine'; --- ************************************************ --- *** relation: modified_guanosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_guanosine AS SELECT feature_id AS modified_guanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'modified_guanosine'; --- ************************************************ --- *** relation: modified_uridine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_uridine AS SELECT feature_id AS modified_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_uridine'; --- ************************************************ --- *** relation: one_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1-methylinosine is a modified insosine. *** --- ************************************************ --- CREATE VIEW one_methylinosine AS SELECT feature_id AS one_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylinosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethylinosine is a modified ino *** --- *** sine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylinosine AS SELECT feature_id AS one_two_prime_o_dimethylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylinosine'; --- ************************************************ --- *** relation: two_prime_o_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylinosine is a modified inosine *** --- *** . *** --- ************************************************ --- CREATE VIEW two_prime_o_methylinosine AS SELECT feature_id AS two_prime_o_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylinosine'; --- ************************************************ --- *** relation: three_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 3-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW three_methylcytidine AS SELECT feature_id AS three_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine'; --- ************************************************ --- *** relation: five_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_methylcytidine AS SELECT feature_id AS five_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylcytidine'; --- ************************************************ --- *** relation: two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylcytidine is a modified cytidi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylcytidine AS SELECT feature_id AS two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: two_thiocytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2-thiocytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW two_thiocytidine AS SELECT feature_id AS two_thiocytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiocytidine'; --- ************************************************ --- *** relation: n4_acetylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_acetylcytidine AS SELECT feature_id AS n4_acetylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetylcytidine'; --- ************************************************ --- *** relation: five_formylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_formylcytidine AS SELECT feature_id AS five_formylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formylcytidine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5,2'-O-dimethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethylcytidine AS SELECT feature_id AS five_two_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: n4_acetyl_2_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetyl-2'-O-methylcytidine is a modif *** --- *** ied cytidine. *** --- ************************************************ --- CREATE VIEW n4_acetyl_2_prime_o_methylcytidine AS SELECT feature_id AS n4_acetyl_2_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine'; --- ************************************************ --- *** relation: lysidine *** --- *** relation type: VIEW *** --- *** *** --- *** Lysidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW lysidine AS SELECT feature_id AS lysidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysidine'; --- ************************************************ --- *** relation: n4_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-methylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_methylcytidine AS SELECT feature_id AS n4_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_methylcytidine'; --- ************************************************ --- *** relation: n4_2_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4,2'-O-dimethylcytidine is a modified c *** --- *** ytidine. *** --- ************************************************ --- CREATE VIEW n4_2_prime_o_dimethylcytidine AS SELECT feature_id AS n4_2_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_2_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: five_hydroxymethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-hydroxymethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_hydroxymethylcytidine AS SELECT feature_id AS five_hydroxymethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxymethylcytidine'; --- ************************************************ --- *** relation: five_formyl_two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formyl-2'-O-methylcytidine is a modifi *** --- *** ed cytidine. *** --- ************************************************ --- CREATE VIEW five_formyl_two_prime_o_methylcytidine AS SELECT feature_id AS five_formyl_two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formyl_two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: n4_n4_2_prime_o_trimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4_N4_2_prime_O_trimethylcytidine is a m *** --- *** odified cytidine. *** --- ************************************************ --- CREATE VIEW n4_n4_2_prime_o_trimethylcytidine AS SELECT feature_id AS n4_n4_2_prime_o_trimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine'; --- ************************************************ --- *** relation: one_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW one_methyladenosine AS SELECT feature_id AS one_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine'; --- ************************************************ --- *** relation: two_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW two_methyladenosine AS SELECT feature_id AS two_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methyladenosine'; --- ************************************************ --- *** relation: n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_methyladenosine AS SELECT feature_id AS n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyladenosine'; --- ************************************************ --- *** relation: two_prime_o_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyladenosine AS SELECT feature_id AS two_prime_o_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_methyladenosine is a mod *** --- *** ified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_methyladenosine AS SELECT feature_id AS two_methylthio_n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_methyladenosine'; --- ************************************************ --- *** relation: n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_isopentenyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_isopentenyladenosine AS SELECT feature_id AS n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_isopentenyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_isopentenyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_isopentenyladenosine AS SELECT feature_id AS two_methylthio_n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_isopentenyladenosine'; --- ************************************************ --- *** relation: n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_cis_hydroxyisopentenyl_adenosine is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_cis_hydroxyisopentenyl_a *** --- *** denosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS two_methylthio_n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: n6_glycinylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_glycinylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_glycinylcarbamoyladenosine AS SELECT feature_id AS n6_glycinylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_glycinylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_threonylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_threonyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_threonyl_carbamoyladenos *** --- *** ine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_threonyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_threonyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine'; --- ************************************************ --- *** relation: n6_methyl_n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyl_N6_threonylcarbamoyladenosine *** --- *** is a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_methyl_n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_methyl_n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_hydroxynorvalylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_hydroxynorvalylcarbamoyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_hydroxynorvalylcarbamoyladenosine AS SELECT feature_id AS n6_hydroxynorvalylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_hydroxynorvalyl_carbamoy *** --- *** ladenosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine'; --- ************************************************ --- *** relation: two_prime_o_riboA_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosyladenosine_phosphate is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_riboA_phosphate AS SELECT feature_id AS two_prime_o_riboA_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosyladenosine_phosphate'; --- ************************************************ --- *** relation: n6_n6_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_dimethyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_n6_dimethyladenosine AS SELECT feature_id AS n6_n6_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_dimethyladenosine'; --- ************************************************ --- *** relation: n6_2_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_2prime_O_dimethyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_2_prime_o_dimethyladenosine AS SELECT feature_id AS n6_2_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_2_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_n6_2_prime_o_trimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_2prime_O_trimethyladenosine is a m *** --- *** odified adenosine. *** --- ************************************************ --- CREATE VIEW n6_n6_2_prime_o_trimethyladenosine AS SELECT feature_id AS n6_n6_2_prime_o_trimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethyladenosine AS SELECT feature_id AS one_two_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_acetyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_acetyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_acetyladenosine AS SELECT feature_id AS n6_acetyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_acetyladenosine'; --- ************************************************ --- *** relation: seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7-deazaguanosine is a moddified guanosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW seven_deazaguanosine AS SELECT feature_id AS seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'seven_deazaguanosine'; --- ************************************************ --- *** relation: queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Queuosine is a modified 7-deazoguanosine *** --- *** . *** --- ************************************************ --- CREATE VIEW queuosine AS SELECT feature_id AS queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine'; --- ************************************************ --- *** relation: epoxyqueuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Epoxyqueuosine is a modified 7-deazoguan *** --- *** osine. *** --- ************************************************ --- CREATE VIEW epoxyqueuosine AS SELECT feature_id AS epoxyqueuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epoxyqueuosine'; --- ************************************************ --- *** relation: galactosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Galactosyl_queuosine is a modified 7-dea *** --- *** zoguanosine. *** --- ************************************************ --- CREATE VIEW galactosyl_queuosine AS SELECT feature_id AS galactosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'galactosyl_queuosine'; --- ************************************************ --- *** relation: mannosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Mannosyl_queuosine is a modified 7-deazo *** --- *** guanosine. *** --- ************************************************ --- CREATE VIEW mannosyl_queuosine AS SELECT feature_id AS mannosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mannosyl_queuosine'; --- ************************************************ --- *** relation: seven_cyano_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_cyano_7_deazaguanosine is a modified 7 *** --- *** -deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_cyano_seven_deazaguanosine AS SELECT feature_id AS seven_cyano_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_cyano_seven_deazaguanosine'; --- ************************************************ --- *** relation: seven_aminomethyl_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_aminomethyl_7_deazaguanosine is a modi *** --- *** fied 7-deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_aminomethyl_seven_deazaguanosine AS SELECT feature_id AS seven_aminomethyl_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_aminomethyl_seven_deazaguanosine'; --- ************************************************ --- *** relation: archaeosine *** --- *** relation type: VIEW *** --- *** *** --- *** Archaeosine is a modified 7-deazoguanosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW archaeosine AS SELECT feature_id AS archaeosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeosine'; --- ************************************************ --- *** relation: one_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW one_methylguanosine AS SELECT feature_id AS one_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylguanosine'; --- ************************************************ --- *** relation: n2_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_methylguanosine is a modified guanosi *** --- *** ne base feature. *** --- ************************************************ --- CREATE VIEW n2_methylguanosine AS SELECT feature_id AS n2_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_methylguanosine'; --- ************************************************ --- *** relation: seven_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW seven_methylguanosine AS SELECT feature_id AS seven_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanosine'; --- ************************************************ --- *** relation: two_prime_o_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylguanosine is a modified g *** --- *** uanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylguanosine AS SELECT feature_id AS two_prime_o_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylguanosine'; --- ************************************************ --- *** relation: n2_n2_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_dimethylguanosine is a modified gu *** --- *** anosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_dimethylguanosine AS SELECT feature_id AS n2_n2_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_dimethylguanosine'; --- ************************************************ --- *** relation: n2_2_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_2prime_O_dimethylguanosine is a modif *** --- *** ied guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_2_prime_o_dimethylguanosine AS SELECT feature_id AS n2_2_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_2_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_2_prime_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_2prime_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_2_prime_o_trimethylguanosine AS SELECT feature_id AS n2_n2_2_prime_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine'; --- ************************************************ --- *** relation: two_prime_o_ribosylguanosine_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosylguanosine_phosphate is a *** --- *** modified guanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_ribosylguanosine_phosphate AS SELECT feature_id AS two_prime_o_ribosylguanosine_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosylguanosine_phosphate'; --- ************************************************ --- *** relation: wybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wybutosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW wybutosine AS SELECT feature_id AS wybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wybutosine'; --- ************************************************ --- *** relation: peroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Peroxywybutosine is a modified guanosine *** --- *** base feature. *** --- ************************************************ --- CREATE VIEW peroxywybutosine AS SELECT feature_id AS peroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peroxywybutosine'; --- ************************************************ --- *** relation: hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Hydroxywybutosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW hydroxywybutosine AS SELECT feature_id AS hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydroxywybutosine'; --- ************************************************ --- *** relation: undermodified_hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Undermodified_hydroxywybutosine is a mod *** --- *** ified guanosine base feature. *** --- ************************************************ --- CREATE VIEW undermodified_hydroxywybutosine AS SELECT feature_id AS undermodified_hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'undermodified_hydroxywybutosine'; --- ************************************************ --- *** relation: wyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wyosine is a modified guanosine base fea *** --- *** ture. *** --- ************************************************ --- CREATE VIEW wyosine AS SELECT feature_id AS wyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wyosine'; --- ************************************************ --- *** relation: methylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Methylwyosine is a modified guanosine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW methylwyosine AS SELECT feature_id AS methylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylwyosine'; --- ************************************************ --- *** relation: n2_7_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_dimethylguanosine is a modified gua *** --- *** nosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_dimethylguanosine AS SELECT feature_id AS n2_7_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_7_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_7_trimethylguanosine is a modified *** --- *** guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_7_trimethylguanosine AS SELECT feature_id AS n2_n2_7_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_7_trimethylguanosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_2prime_O_dimethylguanosine is a modifi *** --- *** ed guanosine base feature. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylguanosine AS SELECT feature_id AS one_two_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: four_demethylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_demethylwyosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW four_demethylwyosine AS SELECT feature_id AS four_demethylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_demethylwyosine'; --- ************************************************ --- *** relation: isowyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Isowyosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW isowyosine AS SELECT feature_id AS isowyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isowyosine'; --- ************************************************ --- *** relation: n2_7_2prirme_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_2prirme_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_2prirme_o_trimethylguanosine AS SELECT feature_id AS n2_7_2prirme_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_2prirme_O_trimethylguanosine'; --- ************************************************ --- *** relation: five_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW five_methyluridine AS SELECT feature_id AS five_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyluridine'; --- ************************************************ --- *** relation: two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyluridine AS SELECT feature_id AS two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_2_prime_O_dimethyluridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethyluridine AS SELECT feature_id AS five_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: one_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW one_methylpseudouridine AS SELECT feature_id AS one_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylpseudouridine'; --- ************************************************ --- *** relation: two_prime_o_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylpseudouridine is a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylpseudouridine AS SELECT feature_id AS two_prime_o_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylpseudouridine'; --- ************************************************ --- *** relation: two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW two_thiouridine AS SELECT feature_id AS two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiouridine'; --- ************************************************ --- *** relation: four_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW four_thiouridine AS SELECT feature_id AS four_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_thiouridine'; --- ************************************************ --- *** relation: five_methyl_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyl_2_thiouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyl_2_thiouridine AS SELECT feature_id AS five_methyl_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyl_2_thiouridine'; --- ************************************************ --- *** relation: two_thio_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thio_2prime_O_methyluridine is a modif *** --- *** ied uridine base feature. *** --- ************************************************ --- CREATE VIEW two_thio_two_prime_o_methyluridine AS SELECT feature_id AS two_thio_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thio_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: three_three_amino_three_carboxypropyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_3_amino_3_carboxypropyl_uridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW three_three_amino_three_carboxypropyl_uridine AS SELECT feature_id AS three_three_amino_three_carboxypropyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_three_amino_three_carboxypropyl_uridine'; --- ************************************************ --- *** relation: five_hydroxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_hydroxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_hydroxyuridine AS SELECT feature_id AS five_hydroxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxyuridine'; --- ************************************************ --- *** relation: five_methoxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_methoxyuridine AS SELECT feature_id AS five_methoxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxyuridine'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid AS SELECT feature_id AS uridine_five_oxyacetic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid_methyl_ester is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid_methyl_ester AS SELECT feature_id AS uridine_five_oxyacetic_acid_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine is a modi *** --- *** fied uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine_methyl_es *** --- *** ter is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine_methyl_ester AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyluridine AS SELECT feature_id AS five_methoxycarbonylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyluridine'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_methoxycarbonylmethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_mcm_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxycarbonylmethyl_2_thiouridine is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mcm_2_thiouridine AS SELECT feature_id AS five_mcm_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_aminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_aminomethyl_2_thiouridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_aminomethyl_two_thiouridine AS SELECT feature_id AS five_aminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_aminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyluridine AS SELECT feature_id AS five_methylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyluridine'; --- ************************************************ --- *** relation: five_mam_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_thiouridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mam_2_thiouridine AS SELECT feature_id AS five_mam_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyl_two_selenouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_selenouridine is a *** --- *** modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyl_two_selenouridine AS SELECT feature_id AS five_methylaminomethyl_two_selenouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_selenouridine'; --- ************************************************ --- *** relation: five_carbamoylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyluridine is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW five_carbamoylmethyluridine AS SELECT feature_id AS five_carbamoylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyluridine'; --- ************************************************ --- *** relation: five_cm_2_prime_o_methU *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyl_2_prime_O_methyluridin *** --- *** e is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_cm_2_prime_o_methU AS SELECT feature_id AS five_cm_2_prime_o_methU_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyluridine AS SELECT feature_id AS five_carboxymethylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_thiouridine *** --- *** is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_thiouridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: three_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW three_methyluridine AS SELECT feature_id AS three_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methyluridine'; --- ************************************************ --- *** relation: one_methyl_3_3_amino_three_carboxypropyl_pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyl_3_3_amino_3_carboxypropyl_pseud *** --- *** ouridine is a modified uridine base feat *** --- *** ure. *** --- ************************************************ --- CREATE VIEW one_methyl_3_3_amino_three_carboxypropyl_pseudouridine AS SELECT feature_id AS one_methyl_3_3_amino_three_carboxypropyl_pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine'; --- ************************************************ --- *** relation: five_carboxymethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethyluridine AS SELECT feature_id AS five_carboxymethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethyluridine'; --- ************************************************ --- *** relation: three_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_2prime_O_dimethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW three_two_prime_o_dimethyluridine AS SELECT feature_id AS three_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: five_methyldihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyldihydrouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyldihydrouridine AS SELECT feature_id AS five_methyldihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyldihydrouridine'; --- ************************************************ --- *** relation: three_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW three_methylpseudouridine AS SELECT feature_id AS three_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylpseudouridine'; --- ************************************************ --- *** relation: five_taurinomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyluridine AS SELECT feature_id AS five_taurinomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyluridine'; --- ************************************************ --- *** relation: five_taurinomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyl_2_thiouridineis a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyl_two_thiouridine AS SELECT feature_id AS five_taurinomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_uridine is a mo *** --- *** dified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_uridine AS SELECT feature_id AS five_isopentenylaminomethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_uridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2_thiouridine i *** --- *** s a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_thiouridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2prime_O_methyl *** --- *** uridine is a modified uridine base featu *** --- *** re. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: histone_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** histone. *** --- ************************************************ --- CREATE VIEW histone_binding_site AS SELECT feature_id AS histone_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_binding_site'; --- ************************************************ --- *** relation: cds_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cds_fragment AS SELECT feature_id AS cds_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_fragment'; --- ************************************************ --- *** relation: modified_amino_acid_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified amino ac *** --- *** id feature. *** --- ************************************************ --- CREATE VIEW modified_amino_acid_feature AS SELECT feature_id AS modified_amino_acid_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'modified_amino_acid_feature'; --- ************************************************ --- *** relation: modified_glycine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glycine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_glycine AS SELECT feature_id AS modified_glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine'; --- ************************************************ --- *** relation: modified_l_alanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified alanine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_alanine AS SELECT feature_id AS modified_l_alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_alanine'; --- ************************************************ --- *** relation: modified_l_asparagine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified asparagi *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_asparagine AS SELECT feature_id AS modified_l_asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_asparagine'; --- ************************************************ --- *** relation: modified_l_aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified aspartic *** --- *** acid amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_aspartic_acid AS SELECT feature_id AS modified_l_aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_aspartic_acid'; --- ************************************************ --- *** relation: modified_l_cysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified cysteine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_cysteine AS SELECT feature_id AS modified_l_cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_cysteine'; --- ************************************************ --- *** relation: modified_l_glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_l_glutamic_acid AS SELECT feature_id AS modified_l_glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamic_acid'; --- ************************************************ --- *** relation: modified_l_threonine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified threonin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_threonine AS SELECT feature_id AS modified_l_threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_threonine'; --- ************************************************ --- *** relation: modified_l_tryptophan *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tryptoph *** --- *** an amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tryptophan AS SELECT feature_id AS modified_l_tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tryptophan'; --- ************************************************ --- *** relation: modified_l_glutamine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glutamin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_glutamine AS SELECT feature_id AS modified_l_glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamine'; --- ************************************************ --- *** relation: modified_l_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified methioni *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_methionine AS SELECT feature_id AS modified_l_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_methionine'; --- ************************************************ --- *** relation: modified_l_isoleucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified isoleuci *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_isoleucine AS SELECT feature_id AS modified_l_isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_isoleucine'; --- ************************************************ --- *** relation: modified_l_phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified phenylal *** --- *** anine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_phenylalanine AS SELECT feature_id AS modified_l_phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_phenylalanine'; --- ************************************************ --- *** relation: modified_l_histidine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified histidie *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_histidine AS SELECT feature_id AS modified_l_histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_histidine'; --- ************************************************ --- *** relation: modified_l_serine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified serine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_serine AS SELECT feature_id AS modified_l_serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_serine'; --- ************************************************ --- *** relation: modified_l_lysine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified lysine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_lysine AS SELECT feature_id AS modified_l_lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_lysine'; --- ************************************************ --- *** relation: modified_l_leucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified leucine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_leucine AS SELECT feature_id AS modified_l_leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_leucine'; --- ************************************************ --- *** relation: modified_l_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified selenocy *** --- *** steine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_selenocysteine AS SELECT feature_id AS modified_l_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_selenocysteine'; --- ************************************************ --- *** relation: modified_l_valine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified valine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_valine AS SELECT feature_id AS modified_l_valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_valine'; --- ************************************************ --- *** relation: modified_l_proline *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified proline *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_proline AS SELECT feature_id AS modified_l_proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_proline'; --- ************************************************ --- *** relation: modified_l_tyrosine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tyrosine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tyrosine AS SELECT feature_id AS modified_l_tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tyrosine'; --- ************************************************ --- *** relation: modified_l_arginine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified arginine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_arginine AS SELECT feature_id AS modified_l_arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_arginine'; --- ************************************************ --- *** relation: peptidyl *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the nature of a *** --- *** proteinaceous polymer, where by the amin *** --- *** o acid units are joined by peptide bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW peptidyl AS SELECT feature_id AS peptidyl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptidyl'; --- ************************************************ --- *** relation: cleaved_for_gpi_anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** The C-terminal residues of a polypeptide *** --- *** which are exchanged for a GPI-anchor. *** --- ************************************************ --- CREATE VIEW cleaved_for_gpi_anchor_region AS SELECT feature_id AS cleaved_for_gpi_anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_for_gpi_anchor_region'; --- ************************************************ --- *** relation: biomaterial_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is intended for use in an *** --- *** experiment. *** --- ************************************************ --- CREATE VIEW biomaterial_region AS SELECT feature_id AS biomaterial_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'biomaterial_region'; --- ************************************************ --- *** relation: experimental_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is the result of some arb *** --- *** itrary experimental procedure. The proce *** --- *** dure may be carried out with biological *** --- *** material or inside a computer. *** --- ************************************************ --- CREATE VIEW experimental_feature AS SELECT feature_id AS experimental_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimental_feature'; --- ************************************************ --- *** relation: biological_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by its disposition to b *** --- *** e involved in a biological process. *** --- ************************************************ --- CREATE VIEW biological_region AS SELECT feature_id AS biological_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'biological_region'; --- ************************************************ --- *** relation: topologically_defined_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is defined according to it *** --- *** s relations with other regions within th *** --- *** e same sequence. *** --- ************************************************ --- CREATE VIEW topologically_defined_region AS SELECT feature_id AS topologically_defined_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'topologically_defined_region'; --- ************************************************ --- *** relation: translocation_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a tr *** --- *** anslocation begins or ends. *** --- ************************************************ --- CREATE VIEW translocation_breakpoint AS SELECT feature_id AS translocation_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_breakpoint'; --- ************************************************ --- *** relation: insertion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a in *** --- *** sertion begins or ends. *** --- ************************************************ --- CREATE VIEW insertion_breakpoint AS SELECT feature_id AS insertion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_breakpoint'; --- ************************************************ --- *** relation: deletion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a de *** --- *** letion begins or ends. *** --- ************************************************ --- CREATE VIEW deletion_breakpoint AS SELECT feature_id AS deletion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_breakpoint'; --- ************************************************ --- *** relation: five_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located five prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW five_prime_flanking_region AS SELECT feature_id AS five_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_flanking_region'; --- ************************************************ --- *** relation: three_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located three prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW three_prime_flanking_region AS SELECT feature_id AS three_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_flanking_region'; --- ************************************************ --- *** relation: transcribed_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region, defined by a til *** --- *** ing array experiment to be transcribed a *** --- *** t some level. *** --- ************************************************ --- CREATE VIEW transcribed_fragment AS SELECT feature_id AS transcribed_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_fragment'; --- ************************************************ --- *** relation: cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering exon. A s *** --- *** plice_site that adjacent_to exon and ove *** --- *** rlaps intron. *** --- ************************************************ --- CREATE VIEW cis_splice_site AS SELECT feature_id AS cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'cis_splice_site'; --- ************************************************ --- *** relation: trans_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Primary transcript region bordering tran *** --- *** s-splice junction. *** --- ************************************************ --- CREATE VIEW trans_splice_site AS SELECT feature_id AS trans_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_site'; --- ************************************************ --- *** relation: splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between an intron and an ex *** --- *** on. *** --- ************************************************ --- CREATE VIEW splice_junction AS SELECT feature_id AS splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_junction'; --- ************************************************ --- *** relation: conformational_switch *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a polypeptide, involved in t *** --- *** he transition from one conformational st *** --- *** ate to another. *** --- ************************************************ --- CREATE VIEW conformational_switch AS SELECT feature_id AS conformational_switch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_switch'; --- ************************************************ --- *** relation: dye_terminator_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the dye terminator me *** --- *** thod of sequencing. *** --- ************************************************ --- CREATE VIEW dye_terminator_read AS SELECT feature_id AS dye_terminator_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dye_terminator_read'; --- ************************************************ --- *** relation: pyrosequenced_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by pyrosequencing techno *** --- *** logy. *** --- ************************************************ --- CREATE VIEW pyrosequenced_read AS SELECT feature_id AS pyrosequenced_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrosequenced_read'; --- ************************************************ --- *** relation: ligation_based_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by ligation based sequen *** --- *** cing technologies. *** --- ************************************************ --- CREATE VIEW ligation_based_read AS SELECT feature_id AS ligation_based_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ligation_based_read'; --- ************************************************ --- *** relation: polymerase_synthesis_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the polymerase based *** --- *** sequence by synthesis method. *** --- ************************************************ --- CREATE VIEW polymerase_synthesis_read AS SELECT feature_id AS polymerase_synthesis_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymerase_synthesis_read'; --- ************************************************ --- *** relation: cis_regulatory_frameshift_element *** --- *** relation type: VIEW *** --- *** *** --- *** A structural region in an RNA molecule w *** --- *** hich promotes ribosomal frameshifting of *** --- *** cis coding sequence. *** --- ************************************************ --- CREATE VIEW cis_regulatory_frameshift_element AS SELECT feature_id AS cis_regulatory_frameshift_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_regulatory_frameshift_element'; --- ************************************************ --- *** relation: expressed_sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence assembly derived from express *** --- *** ed sequences. *** --- ************************************************ --- CREATE VIEW expressed_sequence_assembly AS SELECT feature_id AS expressed_sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_assembly'; --- ************************************************ --- *** relation: dna_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith DNA. *** --- ************************************************ --- CREATE VIEW dna_binding_site AS SELECT feature_id AS dna_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'DNA_binding_site'; --- ************************************************ --- *** relation: cryptic_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is not transcribed under nor *** --- *** mal conditions and is not critical to no *** --- *** rmal cellular functioning. *** --- ************************************************ --- CREATE VIEW cryptic_gene AS SELECT feature_id AS cryptic_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'cryptic_gene'; --- ************************************************ --- *** relation: three_prime_race_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A three prime RACE (Rapid Amplification *** --- *** of cDNA Ends) clone is a cDNA clone copi *** --- *** ed from the 3' end of an mRNA (using a p *** --- *** oly-dT primer to capture the polyA tail *** --- *** and a gene-specific or randomly primed 5 *** --- *** ' primer), and spliced into a vector for *** --- *** propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW three_prime_race_clone AS SELECT feature_id AS three_prime_race_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RACE_clone'; --- ************************************************ --- *** relation: cassette_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A cassette pseudogene is a kind of gene *** --- *** in an inactive form which may recombine *** --- *** at a telomeric locus to form a functiona *** --- *** l copy. *** --- ************************************************ --- CREATE VIEW cassette_pseudogene AS SELECT feature_id AS cassette_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_pseudogene'; --- ************************************************ --- *** relation: alanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alanine AS SELECT feature_id AS alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine'; --- ************************************************ --- *** relation: valine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW valine AS SELECT feature_id AS valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine'; --- ************************************************ --- *** relation: leucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucine AS SELECT feature_id AS leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine'; --- ************************************************ --- *** relation: isoleucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW isoleucine AS SELECT feature_id AS isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine'; --- ************************************************ --- *** relation: proline *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proline AS SELECT feature_id AS proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline'; --- ************************************************ --- *** relation: tryptophan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tryptophan AS SELECT feature_id AS tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan'; --- ************************************************ --- *** relation: phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW phenylalanine AS SELECT feature_id AS phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine'; --- ************************************************ --- *** relation: methionine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW methionine AS SELECT feature_id AS methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine'; --- ************************************************ --- *** relation: glycine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glycine AS SELECT feature_id AS glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine'; --- ************************************************ --- *** relation: serine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW serine AS SELECT feature_id AS serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine'; --- ************************************************ --- *** relation: threonine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW threonine AS SELECT feature_id AS threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine'; --- ************************************************ --- *** relation: tyrosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tyrosine AS SELECT feature_id AS tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine'; --- ************************************************ --- *** relation: cysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cysteine AS SELECT feature_id AS cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine'; --- ************************************************ --- *** relation: glutamine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamine AS SELECT feature_id AS glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine'; --- ************************************************ --- *** relation: asparagine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW asparagine AS SELECT feature_id AS asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine'; --- ************************************************ --- *** relation: lysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lysine AS SELECT feature_id AS lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine'; --- ************************************************ --- *** relation: arginine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW arginine AS SELECT feature_id AS arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine'; --- ************************************************ --- *** relation: histidine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW histidine AS SELECT feature_id AS histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine'; --- ************************************************ --- *** relation: aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aspartic_acid AS SELECT feature_id AS aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid'; --- ************************************************ --- *** relation: glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamic_acid AS SELECT feature_id AS glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid'; --- ************************************************ --- *** relation: selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW selenocysteine AS SELECT feature_id AS selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine'; --- ************************************************ --- *** relation: pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pyrrolysine AS SELECT feature_id AS pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine'; --- ************************************************ --- *** relation: transcribed_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by a set of transcribed *** --- *** sequences from the same gene or express *** --- *** ed pseudogene. *** --- ************************************************ --- CREATE VIEW transcribed_cluster AS SELECT feature_id AS transcribed_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster' OR cvterm.name = 'transcribed_cluster'; --- ************************************************ --- *** relation: unigene_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of transcribed_cluster defined by *** --- *** a set of transcribed sequences from the *** --- *** a unique gene. *** --- ************************************************ --- CREATE VIEW unigene_cluster AS SELECT feature_id AS unigene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster'; --- ************************************************ --- *** relation: crispr *** --- *** relation type: VIEW *** --- *** *** --- *** Clustered Palindromic Repeats interspers *** --- *** ed with bacteriophage derived spacer seq *** --- *** uences. *** --- ************************************************ --- CREATE VIEW crispr AS SELECT feature_id AS crispr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CRISPR'; --- ************************************************ --- *** relation: insulator_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in an insulator reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW insulator_binding_site AS SELECT feature_id AS insulator_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator_binding_site'; --- ************************************************ --- *** relation: enhancer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the enhancer reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW enhancer_binding_site AS SELECT feature_id AS enhancer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_binding_site'; --- ************************************************ --- *** relation: contig_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of contigs. *** --- ************************************************ --- CREATE VIEW contig_collection AS SELECT feature_id AS contig_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection'; --- ************************************************ --- *** relation: lincrna *** --- *** relation type: VIEW *** --- *** *** --- *** A multiexonic non-coding RNA transcribed *** --- *** by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW lincrna AS SELECT feature_id AS lincrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA'; --- ************************************************ --- *** relation: ust *** --- *** relation type: VIEW *** --- *** *** --- *** An EST spanning part or all of the untra *** --- *** nslated regions of a protein-coding tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW ust AS SELECT feature_id AS ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'UST'; --- ************************************************ --- *** relation: three_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** A UST located in the 3'UTR of a protein- *** --- *** coding transcript. *** --- ************************************************ --- CREATE VIEW three_prime_ust AS SELECT feature_id AS three_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST'; --- ************************************************ --- *** relation: five_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** An UST located in the 5'UTR of a protein *** --- *** -coding transcript. *** --- ************************************************ --- CREATE VIEW five_prime_ust AS SELECT feature_id AS five_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UST'; --- ************************************************ --- *** relation: rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a RACE product; typically a fe *** --- *** w hundred base pairs long. *** --- ************************************************ --- CREATE VIEW rst AS SELECT feature_id AS rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'RST'; --- ************************************************ --- *** relation: three_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 3'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW three_prime_rst AS SELECT feature_id AS three_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST'; --- ************************************************ --- *** relation: five_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 5'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW five_prime_rst AS SELECT feature_id AS five_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_RST'; --- ************************************************ --- *** relation: ust_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an UST sequence. *** --- ************************************************ --- CREATE VIEW ust_match AS SELECT feature_id AS ust_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UST_match'; --- ************************************************ --- *** relation: rst_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an RST sequence. *** --- ************************************************ --- CREATE VIEW rst_match AS SELECT feature_id AS rst_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RST_match'; --- ************************************************ --- *** relation: primer_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match to a primer sequence. *** --- ************************************************ --- CREATE VIEW primer_match AS SELECT feature_id AS primer_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_match'; --- ************************************************ --- *** relation: mirna_antiguide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the pri miRNA that basepairs *** --- *** with the guide to form the hairpin. *** --- ************************************************ --- CREATE VIEW mirna_antiguide AS SELECT feature_id AS mirna_antiguide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_antiguide'; --- ************************************************ --- *** relation: trans_splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the spliced leader *** --- *** and the first exon of the mRNA. *** --- ************************************************ --- CREATE VIEW trans_splice_junction AS SELECT feature_id AS trans_splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_junction'; --- ************************************************ --- *** relation: outron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript, that i *** --- *** s removed via trans splicing. *** --- ************************************************ --- CREATE VIEW outron AS SELECT feature_id AS outron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'outron'; --- ************************************************ --- *** relation: natural_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that occurs naturally. *** --- ************************************************ --- CREATE VIEW natural_plasmid AS SELECT feature_id AS natural_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_plasmid'; --- ************************************************ --- *** relation: gene_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A gene trap construct is a type of engin *** --- *** eered plasmid which is designed to integ *** --- *** rate into a genome and produce a fusion *** --- *** transcript between exons of the gene int *** --- *** o which it inserts and a reporter elemen *** --- *** t in the construct. Gene traps contain a *** --- *** splice acceptor, do not contain promote *** --- *** r elements for the reporter, and are mut *** --- *** agenic. Gene traps may be bicistronic wi *** --- *** th the second cassette containing a prom *** --- *** oter driving an a selectable marker. *** --- ************************************************ --- CREATE VIEW gene_trap_construct AS SELECT feature_id AS gene_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_trap_construct'; --- ************************************************ --- *** relation: promoter_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter trap construct is a type of e *** --- *** ngineered plasmid which is designed to i *** --- *** ntegrate into a genome and express a rep *** --- *** orter when inserted in close proximity t *** --- *** o a promoter element. Promoter traps typ *** --- *** ically do not contain promoter elements *** --- *** and are mutagenic. *** --- ************************************************ --- CREATE VIEW promoter_trap_construct AS SELECT feature_id AS promoter_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_trap_construct'; --- ************************************************ --- *** relation: enhancer_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer trap construct is a type of *** --- *** engineered plasmid which is designed to *** --- *** integrate into a genome and express a re *** --- *** porter when the expression from a basic *** --- *** minimal promoter is enhanced by genomic *** --- *** enhancer elements. Enhancer traps contai *** --- *** n promoter elements and are not usually *** --- *** mutagenic. *** --- ************************************************ --- CREATE VIEW enhancer_trap_construct AS SELECT feature_id AS enhancer_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_trap_construct'; --- ************************************************ --- *** relation: pac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a P *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW pac_end AS SELECT feature_id AS pac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC_end'; --- ************************************************ --- *** relation: rapd *** --- *** relation type: VIEW *** --- *** *** --- *** RAPD is a 'PCR product' where a sequence *** --- *** variant is identified through the use o *** --- *** f PCR with random primers. *** --- ************************************************ --- CREATE VIEW rapd AS SELECT feature_id AS rapd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD'; --- ************************************************ --- *** relation: shadow_enhancer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW shadow_enhancer AS SELECT feature_id AS shadow_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'shadow_enhancer'; --- ************************************************ --- *** relation: snv *** --- *** relation type: VIEW *** --- *** *** --- *** SNVs are single nucleotide positions in *** --- *** genomic DNA at which different sequence *** --- *** alternatives exist. *** --- ************************************************ --- CREATE VIEW snv AS SELECT feature_id AS snv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'SNV'; --- ************************************************ --- *** relation: x_element_combinatorial_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An X element combinatorial repeat is a r *** --- *** epeat region located between the X eleme *** --- *** nt and the telomere or adjacent Y' eleme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW x_element_combinatorial_repeat AS SELECT feature_id AS x_element_combinatorial_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element_combinatorial_repeat'; --- ************************************************ --- *** relation: y_prime_element *** --- *** relation type: VIEW *** --- *** *** --- *** A Y' element is a repeat region (SO:0000 *** --- *** 657) located adjacent to telomeric repea *** --- *** ts or X element combinatorial repeats, e *** --- *** ither as a single copy or tandem repeat *** --- *** of two to four copies. *** --- ************************************************ --- CREATE VIEW y_prime_element AS SELECT feature_id AS y_prime_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_prime_element'; --- ************************************************ --- *** relation: standard_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the data is minimally filtered or u *** --- *** n-filtered, from any number of sequencin *** --- *** g platforms, and is assembled into conti *** --- *** gs. Genome sequence of this quality may *** --- *** harbour regions of poor quality and can *** --- *** be relatively incomplete. *** --- ************************************************ --- CREATE VIEW standard_draft AS SELECT feature_id AS standard_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft'; --- ************************************************ --- *** relation: high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here overall coverage represents at leas *** --- *** t 90 percent of the genome. *** --- ************************************************ --- CREATE VIEW high_quality_draft AS SELECT feature_id AS high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_quality_draft'; --- ************************************************ --- *** relation: improved_high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here additional work has been performed, *** --- *** using either manual or automated method *** --- *** s, such as gap resolution. *** --- ************************************************ --- CREATE VIEW improved_high_quality_draft AS SELECT feature_id AS improved_high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'improved_high_quality_draft'; --- ************************************************ --- *** relation: annotation_directed_improved_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence,wh *** --- *** ere annotation, and verification of codi *** --- *** ng regions has occurred. *** --- ************************************************ --- CREATE VIEW annotation_directed_improved_draft AS SELECT feature_id AS annotation_directed_improved_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'annotation_directed_improved_draft'; --- ************************************************ --- *** relation: noncontiguous_finished *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the assembly is high quality, closu *** --- *** re approaches have been successful for m *** --- *** ost gaps, misassemblies and low quality *** --- *** regions. *** --- ************************************************ --- CREATE VIEW noncontiguous_finished AS SELECT feature_id AS noncontiguous_finished_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncontiguous_finished'; --- ************************************************ --- *** relation: finished_genome *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** ith less than 1 error per 100,000 base p *** --- *** airs. *** --- ************************************************ --- CREATE VIEW finished_genome AS SELECT feature_id AS finished_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'finished_genome'; --- ************************************************ --- *** relation: intronic_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is part of an i *** --- *** ntron. *** --- ************************************************ --- CREATE VIEW intronic_regulatory_region AS SELECT feature_id AS intronic_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_regulatory_region'; --- ************************************************ --- *** relation: centromere_dna_element_i *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region compos *** --- *** ed of 8-11bp which enables binding by th *** --- *** e centromere binding factor 1(Cbf1p). *** --- ************************************************ --- CREATE VIEW centromere_dna_element_i AS SELECT feature_id AS centromere_dna_element_i_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_I'; --- ************************************************ --- *** relation: centromere_dna_element_ii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element II (CDEII) is p *** --- *** art a conserved region of the centromere *** --- *** , consisting of a consensus region that *** --- *** is AT-rich and ~ 75-100 bp in length. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_ii AS SELECT feature_id AS centromere_dna_element_ii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_II'; --- ************************************************ --- *** relation: centromere_dna_element_iii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region that c *** --- *** onsists of a 25-bp which enables binding *** --- *** by the centromere DNA binding factor 3 *** --- *** (CBF3) complex. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_iii AS SELECT feature_id AS centromere_dna_element_iii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_III'; --- ************************************************ --- *** relation: telomeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The telomeric repeat is a repeat region, *** --- *** part of the chromosome, which in yeast, *** --- *** is a G-rich terminal sequence of the fo *** --- *** rm (TG(1-3))n or more precisely ((TG)(1- *** --- *** 6)TG(2-3))n. *** --- ************************************************ --- CREATE VIEW telomeric_repeat AS SELECT feature_id AS telomeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomeric_repeat'; --- ************************************************ --- *** relation: x_element *** --- *** relation type: VIEW *** --- *** *** --- *** The X element is a conserved region, of *** --- *** the telomere, of ~475 bp that contains a *** --- *** n ARS sequence and in most cases an Abf1 *** --- *** p binding site. *** --- ************************************************ --- CREATE VIEW x_element AS SELECT feature_id AS x_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element'; --- ************************************************ --- *** relation: yac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a Y *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW yac_end AS SELECT feature_id AS yac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC_end'; --- ************************************************ --- *** relation: whole_genome_sequence_status *** --- *** relation type: VIEW *** --- *** *** --- *** The status of whole genome sequence. *** --- ************************************************ --- CREATE VIEW whole_genome_sequence_status AS SELECT feature_id AS whole_genome_sequence_status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'whole_genome_sequence_status'; --- ************************************************ --- *** relation: heritable_phenotypic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region characterized as a s *** --- *** ingle heritable trait in a phenotype scr *** --- *** een. The heritable phenotype may be mapp *** --- *** ed to a chromosome but generally has not *** --- *** been characterized to a specific gene l *** --- *** ocus. *** --- ************************************************ --- CREATE VIEW heritable_phenotypic_marker AS SELECT feature_id AS heritable_phenotypic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker'; --- ************************************************ --- *** relation: peptide_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of peptide sequences. *** --- ************************************************ --- CREATE VIEW peptide_collection AS SELECT feature_id AS peptide_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_collection'; --- ************************************************ --- *** relation: high_identity_region *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature with high sequen *** --- *** ce identity to another sequence. *** --- ************************************************ --- CREATE VIEW high_identity_region AS SELECT feature_id AS high_identity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_identity_region'; --- ************************************************ --- *** relation: processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript for which no open reading f *** --- *** rame has been identified and for which n *** --- *** o other function has been determined. *** --- ************************************************ --- CREATE VIEW processed_transcript AS SELECT feature_id AS processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_transcript'; --- ************************************************ --- *** relation: assortment_derived_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome variation derived from an e *** --- *** vent during meiosis. *** --- ************************************************ --- CREATE VIEW assortment_derived_variation AS SELECT feature_id AS assortment_derived_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'assortment_derived_variation'; --- ************************************************ --- *** relation: reference_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) taken as the standard for a given *** --- *** organism and genome assembly. *** --- ************************************************ --- CREATE VIEW reference_genome AS SELECT feature_id AS reference_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reference_genome'; --- ************************************************ --- *** relation: variant_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) of an individual. *** --- ************************************************ --- CREATE VIEW variant_genome AS SELECT feature_id AS variant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'variant_genome'; --- ************************************************ --- *** relation: variant_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of one or more sequences of *** --- *** an individual. *** --- ************************************************ --- CREATE VIEW variant_collection AS SELECT feature_id AS variant_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'variant_collection'; --- ************************************************ --- *** relation: alteration_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alteration_attribute AS SELECT feature_id AS alteration_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'alteration_attribute'; --- ************************************************ --- *** relation: chromosomal_variation_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_variation_attribute AS SELECT feature_id AS chromosomal_variation_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'chromosomal_variation_attribute'; --- ************************************************ --- *** relation: intrachromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal AS SELECT feature_id AS intrachromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal'; --- ************************************************ --- *** relation: interchromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal AS SELECT feature_id AS interchromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal'; --- ************************************************ --- *** relation: insertion_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a chromosomal insertion,. *** --- ************************************************ --- CREATE VIEW insertion_attribute AS SELECT feature_id AS insertion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'insertion_attribute'; --- ************************************************ --- *** relation: tandem *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tandem AS SELECT feature_id AS tandem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem'; --- ************************************************ --- *** relation: direct *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is not in a cytologically inverted or *** --- *** ientation. *** --- ************************************************ --- CREATE VIEW direct AS SELECT feature_id AS direct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct'; --- ************************************************ --- *** relation: inverted *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is in a cytologically inverted orient *** --- *** ation. *** --- ************************************************ --- CREATE VIEW inverted AS SELECT feature_id AS inverted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted'; --- ************************************************ --- *** relation: free *** --- *** relation type: VIEW *** --- *** *** --- *** The quality of a duplication where the n *** --- *** ew region exists independently of the or *** --- *** iginal. *** --- ************************************************ --- CREATE VIEW free AS SELECT feature_id AS free_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free'; --- ************************************************ --- *** relation: inversion_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inversion_attribute AS SELECT feature_id AS inversion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'inversion_attribute'; --- ************************************************ --- *** relation: pericentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pericentric AS SELECT feature_id AS pericentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric'; --- ************************************************ --- *** relation: paracentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paracentric AS SELECT feature_id AS paracentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric'; --- ************************************************ --- *** relation: translocaton_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW translocaton_attribute AS SELECT feature_id AS translocaton_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'translocaton_attribute'; --- ************************************************ --- *** relation: reciprocal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW reciprocal AS SELECT feature_id AS reciprocal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal'; --- ************************************************ --- *** relation: insertional *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW insertional AS SELECT feature_id AS insertional_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertional'; --- ************************************************ --- *** relation: duplication_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW duplication_attribute AS SELECT feature_id AS duplication_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free' OR cvterm.name = 'duplication_attribute'; --- ************************************************ --- *** relation: chromosomally_aberrant_genome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomally_aberrant_genome AS SELECT feature_id AS chromosomally_aberrant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome'; --- ************************************************ --- *** relation: assembly_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment differs from the orig *** --- *** inal assembly due to an improvement that *** --- *** replaces a mistake. *** --- ************************************************ --- CREATE VIEW assembly_error_correction AS SELECT feature_id AS assembly_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assembly_error_correction'; --- ************************************************ --- *** relation: base_call_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment is different from tha *** --- *** t given by the base caller due to an imp *** --- *** rovement that replaces a mistake. *** --- ************************************************ --- CREATE VIEW base_call_error_correction AS SELECT feature_id AS base_call_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'base_call_error_correction'; --- ************************************************ --- *** relation: peptide_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide sequence used to tar *** --- *** get the polypeptide molecule to a specif *** --- *** ic organelle. *** --- ************************************************ --- CREATE VIEW peptide_localization_signal AS SELECT feature_id AS peptide_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'peptide_localization_signal'; --- ************************************************ --- *** relation: nuclear_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_localization_signal AS SELECT feature_id AS nuclear_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_localization_signal'; --- ************************************************ --- *** relation: endosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the endosome. *** --- ************************************************ --- CREATE VIEW endosomal_localization_signal AS SELECT feature_id AS endosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endosomal_localization_signal'; --- ************************************************ --- *** relation: lysosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the lysosome. *** --- ************************************************ --- CREATE VIEW lysosomal_localization_signal AS SELECT feature_id AS lysosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysosomal_localization_signal'; --- ************************************************ --- *** relation: nuclear_export_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to he cytoplasm. *** --- ************************************************ --- CREATE VIEW nuclear_export_signal AS SELECT feature_id AS nuclear_export_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_export_signal'; --- ************************************************ --- *** relation: recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region recognized by a recombinase. *** --- ************************************************ --- CREATE VIEW recombination_signal_sequence AS SELECT feature_id AS recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_signal_sequence'; --- ************************************************ --- *** relation: cryptic_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A splice site that is in part of the tra *** --- *** nscript not normally spliced. They occur *** --- *** via mutation or transcriptional error. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site AS SELECT feature_id AS cryptic_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site'; --- ************************************************ --- *** relation: nuclear_rim_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nuclear rim. *** --- ************************************************ --- CREATE VIEW nuclear_rim_localization_signal AS SELECT feature_id AS nuclear_rim_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_rim_localization_signal'; --- ************************************************ --- *** relation: p_element *** --- *** relation type: VIEW *** --- *** *** --- *** A P_element is a DNA transposon responsi *** --- *** ble for hybrid dysgenesis. *** --- ************************************************ --- CREATE VIEW p_element AS SELECT feature_id AS p_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'p_element'; --- ************************************************ --- *** relation: functional_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which the function *** --- *** of a gene product is altered with respe *** --- *** ct to a reference. *** --- ************************************************ --- CREATE VIEW functional_variant AS SELECT feature_id AS functional_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'functional_variant'; --- ************************************************ --- *** relation: structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes one or m *** --- *** ore sequence features. *** --- ************************************************ --- CREATE VIEW structural_variant AS SELECT feature_id AS structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'structural_variant'; --- ************************************************ --- *** relation: transcript_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the func *** --- *** tioning of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcript_function_variant AS SELECT feature_id AS transcript_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcript_function_variant'; --- ************************************************ --- *** relation: translational_product_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the func *** --- *** tioning of a translational product with *** --- *** respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_function_variant AS SELECT feature_id AS translational_product_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'translational_product_function_variant'; --- ************************************************ --- *** relation: level_of_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the leve *** --- *** l of a transcript. *** --- ************************************************ --- CREATE VIEW level_of_transcript_variant AS SELECT feature_id AS level_of_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'level_of_transcript_variant'; --- ************************************************ --- *** relation: decreased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_level_variant AS SELECT feature_id AS decreased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant'; --- ************************************************ --- *** relation: increased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_level_variant AS SELECT feature_id AS increased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_level_variant'; --- ************************************************ --- *** relation: transcript_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the post *** --- *** transcriptional processing of a transcr *** --- *** ipt with respect to a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW transcript_processing_variant AS SELECT feature_id AS transcript_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'transcript_processing_variant'; --- ************************************************ --- *** relation: editing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** the process of editing is disrupted with *** --- *** respect to the reference. *** --- ************************************************ --- CREATE VIEW editing_variant AS SELECT feature_id AS editing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant'; --- ************************************************ --- *** relation: polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes polyaden *** --- *** ylation with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polyadenylation_variant AS SELECT feature_id AS polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'polyadenylation_variant'; --- ************************************************ --- *** relation: transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes the stability of *** --- *** a transcript with respect to a reference *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW transcript_stability_variant AS SELECT feature_id AS transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'transcript_stability_variant'; --- ************************************************ --- *** relation: decreased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_stability_variant AS SELECT feature_id AS decreased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant'; --- ************************************************ --- *** relation: increased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_stability_variant AS SELECT feature_id AS increased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_stability_variant'; --- ************************************************ --- *** relation: transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes alters the transc *** --- *** ription of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcription_variant AS SELECT feature_id AS transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcription_variant'; --- ************************************************ --- *** relation: rate_of_transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the rate *** --- *** of transcription with respect to a refe *** --- *** rence sequence. *** --- ************************************************ --- CREATE VIEW rate_of_transcription_variant AS SELECT feature_id AS rate_of_transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'rate_of_transcription_variant'; --- ************************************************ --- *** relation: increased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcription_rate_variant AS SELECT feature_id AS increased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant'; --- ************************************************ --- *** relation: decreased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcription_rate_variant AS SELECT feature_id AS decreased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcription_rate_variant'; --- ************************************************ --- *** relation: translational_product_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A functional variant that changes the tr *** --- *** anslational product level with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_level_variant AS SELECT feature_id AS translational_product_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'translational_product_level_variant'; --- ************************************************ --- *** relation: polypeptide_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes polypep *** --- *** tide functioning with respect to a refer *** --- *** ence sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_function_variant AS SELECT feature_id AS polypeptide_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_function_variant'; --- ************************************************ --- *** relation: decreased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which decreases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_translational_product_level AS SELECT feature_id AS decreased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level'; --- ************************************************ --- *** relation: increased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which increases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_translational_product_level AS SELECT feature_id AS increased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_translational_product_level'; --- ************************************************ --- *** relation: polypeptide_gain_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes gain of *** --- *** polypeptide function with respect to a r *** --- *** eference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_gain_of_function_variant AS SELECT feature_id AS polypeptide_gain_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant'; --- ************************************************ --- *** relation: polypeptide_localization_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes the loc *** --- *** alization of a polypeptide with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_localization_variant AS SELECT feature_id AS polypeptide_localization_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_localization_variant'; --- ************************************************ --- *** relation: polypeptide_loss_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the loss *** --- *** of a polypeptide function with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_loss_of_function_variant AS SELECT feature_id AS polypeptide_loss_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_loss_of_function_variant'; --- ************************************************ --- *** relation: inactive_ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a ligand binding site with re *** --- *** spect to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_ligand_binding_site AS SELECT feature_id AS inactive_ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'inactive_ligand_binding_site'; --- ************************************************ --- *** relation: polypeptide_partial_loss_of_function *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes some but *** --- *** not all loss of polypeptide function wit *** --- *** h respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_partial_loss_of_function AS SELECT feature_id AS polypeptide_partial_loss_of_function_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_partial_loss_of_function'; --- ************************************************ --- *** relation: polypeptide_post_translational_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** in post translational processing of the *** --- *** peptide with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polypeptide_post_translational_processing_variant AS SELECT feature_id AS polypeptide_post_translational_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_post_translational_processing_variant'; --- ************************************************ --- *** relation: copy_number_change *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where copies of a fea *** --- *** ture (CNV) are either increased or decre *** --- *** ased. *** --- ************************************************ --- CREATE VIEW copy_number_change AS SELECT feature_id AS copy_number_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_change'; --- ************************************************ --- *** relation: gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where the structure o *** --- *** f the gene is changed. *** --- ************************************************ --- CREATE VIEW gene_variant AS SELECT feature_id AS gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'gene_variant'; --- ************************************************ --- *** relation: gene_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a two genes h *** --- *** ave become joined. *** --- ************************************************ --- CREATE VIEW gene_fusion AS SELECT feature_id AS gene_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion'; --- ************************************************ --- *** relation: regulatory_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a regu *** --- *** latory region. *** --- ************************************************ --- CREATE VIEW regulatory_region_variant AS SELECT feature_id AS regulatory_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant' OR cvterm.name = 'regulatory_region_variant'; --- ************************************************ --- *** relation: stop_retained_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se in the terminator codon is changed, b *** --- *** ut the terminator remains. *** --- ************************************************ --- CREATE VIEW stop_retained_variant AS SELECT feature_id AS stop_retained_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant'; --- ************************************************ --- *** relation: splicing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the proc *** --- *** ess of splicing. *** --- ************************************************ --- CREATE VIEW splicing_variant AS SELECT feature_id AS splicing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'splicing_variant'; --- ************************************************ --- *** relation: cryptic_splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a new (functi *** --- *** onal) splice site. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site_variant AS SELECT feature_id AS cryptic_splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'cryptic_splice_site_variant'; --- ************************************************ --- *** relation: cryptic_splice_acceptor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new acceptor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_acceptor AS SELECT feature_id AS cryptic_splice_acceptor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor'; --- ************************************************ --- *** relation: cryptic_splice_donor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new donor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_donor AS SELECT feature_id AS cryptic_splice_donor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_donor'; --- ************************************************ --- *** relation: exon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an exon is lo *** --- *** st from the transcript. *** --- ************************************************ --- CREATE VIEW exon_loss AS SELECT feature_id AS exon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_loss'; --- ************************************************ --- *** relation: intron_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an intron is *** --- *** gained by the processed transcript; usua *** --- *** lly a result of an alteration of the don *** --- *** or or acceptor. *** --- ************************************************ --- CREATE VIEW intron_gain AS SELECT feature_id AS intron_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intron_gain'; --- ************************************************ --- *** relation: splice_acceptor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the 2 base *** --- *** region at the 3' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_acceptor_variant AS SELECT feature_id AS splice_acceptor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant'; --- ************************************************ --- *** relation: splice_donor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the2 base *** --- *** region at the 5' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_donor_variant AS SELECT feature_id AS splice_donor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_variant'; --- ************************************************ --- *** relation: transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the stru *** --- *** cture of the transcript. *** --- ************************************************ --- CREATE VIEW transcript_variant AS SELECT feature_id AS transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'transcript_variant'; --- ************************************************ --- *** relation: complex_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant with a complex INDE *** --- *** L- Insertion or deletion that spans an e *** --- *** xon/intron border or a coding sequence/U *** --- *** TR border. *** --- ************************************************ --- CREATE VIEW complex_change_in_transcript AS SELECT feature_id AS complex_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript'; --- ************************************************ --- *** relation: stop_lost *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the terminator codon (stop) is cha *** --- *** nged, resulting in an elongated transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW stop_lost AS SELECT feature_id AS stop_lost_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_lost'; --- ************************************************ --- *** relation: coding_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the codi *** --- *** ng sequence. *** --- ************************************************ --- CREATE VIEW coding_sequence_variant AS SELECT feature_id AS coding_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'coding_sequence_variant'; --- ************************************************ --- *** relation: codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes at least *** --- *** one base in a codon. *** --- ************************************************ --- CREATE VIEW codon_variant AS SELECT feature_id AS codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'codon_variant'; --- ************************************************ --- *** relation: initiator_codon_change *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the first codon of a transcrip *** --- *** t. *** --- ************************************************ --- CREATE VIEW initiator_codon_change AS SELECT feature_id AS initiator_codon_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change'; --- ************************************************ --- *** relation: non_synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid or stop codon. *** --- ************************************************ --- CREATE VIEW non_synonymous_codon AS SELECT feature_id AS non_synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'non_synonymous_codon'; --- ************************************************ --- *** relation: conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different but *** --- *** similar amino acid. These variants may *** --- *** or may not be deleterious. *** --- ************************************************ --- CREATE VIEW conservative_missense_codon AS SELECT feature_id AS conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon'; --- ************************************************ --- *** relation: non_conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for an amino acid w *** --- *** ith different biochemical properties. *** --- ************************************************ --- CREATE VIEW non_conservative_missense_codon AS SELECT feature_id AS non_conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_missense_codon'; --- ************************************************ --- *** relation: stop_gained *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed, resulting in *** --- *** a premature stop codon, leading to a sh *** --- *** ortened transcript. *** --- ************************************************ --- CREATE VIEW stop_gained AS SELECT feature_id AS stop_gained_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained'; --- ************************************************ --- *** relation: synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a base of a c *** --- *** odon is changed, but there is no resulti *** --- *** ng change to the encoded amino acid. *** --- ************************************************ --- CREATE VIEW synonymous_codon AS SELECT feature_id AS synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'synonymous_codon'; --- ************************************************ --- *** relation: frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** because the number of nucleotides inser *** --- *** ted or deleted is not a multiple of thre *** --- *** e. *** --- ************************************************ --- CREATE VIEW frameshift_variant AS SELECT feature_id AS frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'frameshift_variant'; --- ************************************************ --- *** relation: terminator_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** of the bases in the terminator codon is *** --- *** changed. *** --- ************************************************ --- CREATE VIEW terminator_codon_variant AS SELECT feature_id AS terminator_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminator_codon_variant'; --- ************************************************ --- *** relation: frame_restoring_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that reverts the sequ *** --- *** ence of a previous frameshift mutation b *** --- *** ack to the initial frame. *** --- ************************************************ --- CREATE VIEW frame_restoring_variant AS SELECT feature_id AS frame_restoring_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant'; --- ************************************************ --- *** relation: minus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base ahead. *** --- ************************************************ --- CREATE VIEW minus_1_frameshift_variant AS SELECT feature_id AS minus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift_variant'; --- ************************************************ --- *** relation: minus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minus_2_frameshift_variant AS SELECT feature_id AS minus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift_variant'; --- ************************************************ --- *** relation: plus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base backward. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift_variant AS SELECT feature_id AS plus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift_variant'; --- ************************************************ --- *** relation: plus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plus_2_frameshift_variant AS SELECT feature_id AS plus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_frameshift variant'; --- ************************************************ --- *** relation: transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a transcript t *** --- *** hat changes the secondary structure of t *** --- *** he RNA product. *** --- ************************************************ --- CREATE VIEW transcript_secondary_structure_variant AS SELECT feature_id AS transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: compensatory_transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A secondary structure variant that compe *** --- *** nsate for the change made by a previous *** --- *** variant. *** --- ************************************************ --- CREATE VIEW compensatory_transcript_secondary_structure_variant AS SELECT feature_id AS compensatory_transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: translational_product_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within the transcript *** --- *** that changes the structure of the trans *** --- *** lational product. *** --- ************************************************ --- CREATE VIEW translational_product_structure_variant AS SELECT feature_id AS translational_product_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'translational_product_structure_variant'; --- ************************************************ --- *** relation: threed_polypeptide_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW threed_polypeptide_structure_variant AS SELECT feature_id AS threed_polypeptide_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = '3D_polypeptide_structure_variant'; --- ************************************************ --- *** relation: complex_3d_structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW complex_3d_structural_variant AS SELECT feature_id AS complex_3d_structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant'; --- ************************************************ --- *** relation: conformational_change_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in the CDS region tha *** --- *** t causes a conformational change in the *** --- *** resulting polypeptide sequence. *** --- ************************************************ --- CREATE VIEW conformational_change_variant AS SELECT feature_id AS conformational_change_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_change_variant'; --- ************************************************ --- *** relation: complex_change_of_translational_product_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW complex_change_of_translational_product_variant AS SELECT feature_id AS complex_change_of_translational_product_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_of_translational_product_variant'; --- ************************************************ --- *** relation: polypeptide_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes a change in the resulting polypep *** --- *** tide sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_sequence_variant AS SELECT feature_id AS polypeptide_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'polypeptide_sequence_variant'; --- ************************************************ --- *** relation: amino_acid_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the loss of an amino acid from the *** --- *** resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_deletion AS SELECT feature_id AS amino_acid_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion'; --- ************************************************ --- *** relation: amino_acid_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the gain of an amino acid to the re *** --- *** sulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_insertion AS SELECT feature_id AS amino_acid_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_insertion'; --- ************************************************ --- *** relation: amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon resulting *** --- *** in the substitution of one amino acid fo *** --- *** r another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_substitution AS SELECT feature_id AS amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'amino_acid_substitution'; --- ************************************************ --- *** relation: conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a similar amino acid f *** --- *** or another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW conservative_amino_acid_substitution AS SELECT feature_id AS conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: non_conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a non conservative ami *** --- *** no acid for another in the resulting pol *** --- *** ypeptide. *** --- ************************************************ --- CREATE VIEW non_conservative_amino_acid_substitution AS SELECT feature_id AS non_conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: elongated_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide AS SELECT feature_id AS elongated_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide'; --- ************************************************ --- *** relation: elongated_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the C terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_c_terminal AS SELECT feature_id AS elongated_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the N terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_n_terminal AS SELECT feature_id AS elongated_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the C termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_in_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the C te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the N termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_n_terminal_elongation AS SELECT feature_id AS elongated_in_frame_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the N te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_n_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal'; --- ************************************************ --- *** relation: polypeptide_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a fusion *** --- *** of two polypeptide sequences. *** --- ************************************************ --- CREATE VIEW polypeptide_fusion AS SELECT feature_id AS polypeptide_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_fusion'; --- ************************************************ --- *** relation: polypeptide_truncation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of the CD that causes *** --- *** a truncation of the resulting polypepti *** --- *** de. *** --- ************************************************ --- CREATE VIEW polypeptide_truncation AS SELECT feature_id AS polypeptide_truncation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_truncation'; --- ************************************************ --- *** relation: inactive_catalytic_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a catalytic site with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_catalytic_site AS SELECT feature_id AS inactive_catalytic_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site'; --- ************************************************ --- *** relation: nc_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant of a non coding RNA *** --- *** gene. *** --- ************************************************ --- CREATE VIEW nc_transcript_variant AS SELECT feature_id AS nc_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant' OR cvterm.name = 'nc_transcript_variant'; --- ************************************************ --- *** relation: mature_mirna_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant located with the se *** --- *** quence of the mature miRNA. *** --- ************************************************ --- CREATE VIEW mature_mirna_variant AS SELECT feature_id AS mature_mirna_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant'; --- ************************************************ --- *** relation: nmd_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant in a transcript that is the ta *** --- *** rget of NMD. *** --- ************************************************ --- CREATE VIEW nmd_transcript_variant AS SELECT feature_id AS nmd_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NMD_transcript_variant'; --- ************************************************ --- *** relation: utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant that is located wit *** --- *** hin the UTR. *** --- ************************************************ --- CREATE VIEW utr_variant AS SELECT feature_id AS utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'UTR_variant'; --- ************************************************ --- *** relation: five_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_variant AS SELECT feature_id AS five_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant'; --- ************************************************ --- *** relation: three_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_variant AS SELECT feature_id AS three_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3_prime_UTR_variant'; --- ************************************************ --- *** relation: terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the last codon of the transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW terminal_codon_variant AS SELECT feature_id AS terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminal_codon_variant'; --- ************************************************ --- *** relation: incomplete_terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the final codon of an incompletely *** --- *** annotated transcript is changed. *** --- ************************************************ --- CREATE VIEW incomplete_terminal_codon_variant AS SELECT feature_id AS incomplete_terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'incomplete_terminal_codon_variant'; --- ************************************************ --- *** relation: intron_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant occurring within an *** --- *** intron. *** --- ************************************************ --- CREATE VIEW intron_variant AS SELECT feature_id AS intron_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'intron_variant'; --- ************************************************ --- *** relation: intergenic_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located in the interg *** --- *** enic region, between genes. *** --- ************************************************ --- CREATE VIEW intergenic_variant AS SELECT feature_id AS intergenic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_variant'; --- ************************************************ --- *** relation: splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the firs *** --- *** t two or last two bases of an intron, or *** --- *** the 5th base from the start of the intr *** --- *** on in the orientation of the transcript. *** --- ************************************************ --- CREATE VIEW splice_site_variant AS SELECT feature_id AS splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'splice_site_variant'; --- ************************************************ --- *** relation: splice_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which a change has *** --- *** occurred within the region of the splic *** --- *** e site, either within 1-3 bases of the e *** --- *** xon or 3-8 bases of the intron. *** --- ************************************************ --- CREATE VIEW splice_region_variant AS SELECT feature_id AS splice_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_region_variant'; --- ************************************************ --- *** relation: upstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 5' of a gene. *** --- ************************************************ --- CREATE VIEW upstream_gene_variant AS SELECT feature_id AS upstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = 'upstream_gene_variant'; --- ************************************************ --- *** relation: downstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 3' of a gene. *** --- ************************************************ --- CREATE VIEW downstream_gene_variant AS SELECT feature_id AS downstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'downstream_gene_variant'; --- ************************************************ --- *** relation: fivekb_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5 KB o *** --- *** f the end of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_downstream_variant AS SELECT feature_id AS fivekb_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant' OR cvterm.name = '5KB_downstream_variant'; --- ************************************************ --- *** relation: fivehundred_b_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a half *** --- *** KB of the end of a gene. *** --- ************************************************ --- CREATE VIEW fivehundred_b_downstream_variant AS SELECT feature_id AS fivehundred_b_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant'; --- ************************************************ --- *** relation: fivekb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_upstream_variant AS SELECT feature_id AS fivekb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_upstream_variant'; --- ************************************************ --- *** relation: twokb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 2KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW twokb_upstream_variant AS SELECT feature_id AS twokb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant'; --- ************************************************ --- *** relation: rrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for ribosomal RNA. *** --- ************************************************ --- CREATE VIEW rrna_gene AS SELECT feature_id AS rrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_gene'; --- ************************************************ --- *** relation: pirna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for an piwi associat *** --- *** ed RNA. *** --- ************************************************ --- CREATE VIEW pirna_gene AS SELECT feature_id AS pirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA_gene'; --- ************************************************ --- *** relation: rnase_p_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an RNase P RNA. *** --- ************************************************ --- CREATE VIEW rnase_p_rna_gene AS SELECT feature_id AS rnase_p_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA_gene'; --- ************************************************ --- *** relation: rnase_mrp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a RNase_MRP_RNA. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna_gene AS SELECT feature_id AS rnase_mrp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA_gene'; --- ************************************************ --- *** relation: lincrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes large intervening no *** --- *** n-coding RNA. *** --- ************************************************ --- CREATE VIEW lincrna_gene AS SELECT feature_id AS lincrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA_gene'; --- ************************************************ --- *** relation: mathematically_defined_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A mathematically defined repeat (MDR) is *** --- *** a experimental feature that is determin *** --- *** ed by querying overlapping oligomers of *** --- *** length k against a database of shotgun s *** --- *** equence data and identifying regions in *** --- *** the query sequence that exceed a statist *** --- *** ically determined threshold of repetitiv *** --- *** eness. *** --- ************************************************ --- CREATE VIEW mathematically_defined_repeat AS SELECT feature_id AS mathematically_defined_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mathematically_defined_repeat'; --- ************************************************ --- *** relation: telomerase_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A telomerase RNA gene is a non coding RN *** --- *** A gene the RNA product of which is a com *** --- *** ponent of telomerase. *** --- ************************************************ --- CREATE VIEW telomerase_rna_gene AS SELECT feature_id AS telomerase_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA_gene'; --- ************************************************ --- *** relation: targeting_vector *** --- *** relation type: VIEW *** --- *** *** --- *** An engineered vector that is able to tak *** --- *** e part in homologous recombination in a *** --- *** host with the intent of introducing site *** --- *** specific genomic modifications. *** --- ************************************************ --- CREATE VIEW targeting_vector AS SELECT feature_id AS targeting_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'targeting_vector'; --- ************************************************ --- *** relation: genetic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A measurable sequence feature that varie *** --- *** s within a population. *** --- ************************************************ --- CREATE VIEW genetic_marker AS SELECT feature_id AS genetic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'genetic_marker'; --- ************************************************ --- *** relation: dart_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A genetic marker, discovered using Diver *** --- *** sity Arrays Technology (DArT) technology *** --- *** . *** --- ************************************************ --- CREATE VIEW dart_marker AS SELECT feature_id AS dart_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DArT_marker'; --- ************************************************ --- *** relation: kozak_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of ribosome entry site, specific *** --- *** to Eukaryotic organisms that overlaps pa *** --- *** rt of both 5' UTR and CDS sequence. *** --- ************************************************ --- CREATE VIEW kozak_sequence AS SELECT feature_id AS kozak_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kozak_sequence'; --- ************************************************ --- *** relation: nested_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that is disrupted by the in *** --- *** sertion of another element. *** --- ************************************************ --- CREATE VIEW nested_transposon AS SELECT feature_id AS nested_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_transposon'; --- ************************************************ --- *** relation: nested_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is disrupted by the insert *** --- *** ion of another element. *** --- ************************************************ --- CREATE VIEW nested_repeat AS SELECT feature_id AS nested_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'nested_repeat'; --- ************************************************ --- *** relation: inframe_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which does not cause *** --- *** a disruption of the translational readin *** --- *** g frame. *** --- ************************************************ --- CREATE VIEW inframe_variant AS SELECT feature_id AS inframe_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'inframe_variant'; --- ************************************************ --- *** relation: inframe_codon_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which gains a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_gain AS SELECT feature_id AS inframe_codon_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain'; --- ************************************************ --- *** relation: inframe_codon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which loses a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_loss AS SELECT feature_id AS inframe_codon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_loss'; --- ************************************************ --- *** relation: retinoic_acid_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transcription factor binding site of v *** --- *** ariable direct repeats of the sequence P *** --- *** uGGTCA spaced by five nucleotides (DR5) *** --- *** found in the promoters of retinoic acid- *** --- *** responsive genes, to which retinoic acid *** --- *** receptors bind. *** --- ************************************************ --- CREATE VIEW retinoic_acid_responsive_element AS SELECT feature_id AS retinoic_acid_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retinoic_acid_responsive_element'; --- ************************************************ --- *** relation: nucleotide_to_protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_to_protein_binding_site AS SELECT feature_id AS nucleotide_to_protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nucleotide_to_protein_binding_site'; --- ************************************************ --- *** relation: nucleotide_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith nucleotide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_binding_site AS SELECT feature_id AS nucleotide_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nucleotide_binding_site'; --- ************************************************ --- *** relation: metal_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith metal ions. *** --- ************************************************ --- CREATE VIEW metal_binding_site AS SELECT feature_id AS metal_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'metal_binding_site'; --- ************************************************ --- *** relation: ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith a small molecule such as a drug, or *** --- *** hormone. *** --- ************************************************ --- CREATE VIEW ligand_binding_site AS SELECT feature_id AS ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'ligand_binding_site'; --- ************************************************ --- *** relation: nested_tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An NTR is a nested repeat of two distinc *** --- *** t tandem motifs interspersed with each o *** --- *** ther. *** --- ************************************************ --- CREATE VIEW nested_tandem_repeat AS SELECT feature_id AS nested_tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat'; --- ************************************************ --- *** relation: promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW promoter_element AS SELECT feature_id AS promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'promoter_element'; --- ************************************************ --- *** relation: core_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW core_promoter_element AS SELECT feature_id AS core_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'core_promoter_element'; --- ************************************************ --- *** relation: rna_polymerase_ii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW rna_polymerase_ii_tata_box AS SELECT feature_id AS rna_polymerase_ii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box'; --- ************************************************ --- *** relation: rna_polymerase_iii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase III. *** --- ************************************************ --- CREATE VIEW rna_polymerase_iii_tata_box AS SELECT feature_id AS rna_polymerase_iii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_III_TATA_box'; --- ************************************************ --- *** relation: bred_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A core TRNA polymerase II promoter eleme *** --- *** nt with consensus (G/A)T(T/G/A)(T/A)(G/T *** --- *** )(T/G)(T/G). *** --- ************************************************ --- CREATE VIEW bred_motif AS SELECT feature_id AS bred_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREd_motif'; --- ************************************************ --- *** relation: dce *** --- *** relation type: VIEW *** --- *** *** --- *** A discontinuous core element of RNA poly *** --- *** merase II transcribed genes, situated do *** --- *** wnstream of the TSS. It is composed of t *** --- *** hree sub elements: SI, SII and SIII. *** --- ************************************************ --- CREATE VIEW dce AS SELECT feature_id AS dce_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE'; --- ************************************************ --- *** relation: dce_si *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement, with consensus sequence CTTC. *** --- ************************************************ --- CREATE VIEW dce_si AS SELECT feature_id AS dce_si_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SI'; --- ************************************************ --- *** relation: dce_sii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence CTGT. *** --- ************************************************ --- CREATE VIEW dce_sii AS SELECT feature_id AS dce_sii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SII'; --- ************************************************ --- *** relation: dce_siii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence AGC. *** --- ************************************************ --- CREATE VIEW dce_siii AS SELECT feature_id AS dce_siii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SIII'; --- ************************************************ --- *** relation: proximal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proximal_promoter_element AS SELECT feature_id AS proximal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element'; --- ************************************************ --- *** relation: rnapol_ii_core_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** The minimal portion of the promoter requ *** --- *** ired to properly initiate transcription *** --- *** in RNA polymerase II transcribed genes. *** --- ************************************************ --- CREATE VIEW rnapol_ii_core_promoter AS SELECT feature_id AS rnapol_ii_core_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter'; --- ************************************************ --- *** relation: distal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW distal_promoter_element AS SELECT feature_id AS distal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distal_promoter_element'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma_70 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma_70 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma_70_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma54 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma54 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma54_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma54'; --- ************************************************ --- *** relation: minus_12_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_12_signal AS SELECT feature_id AS minus_12_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_12_signal'; --- ************************************************ --- *** relation: minus_24_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_24_signal AS SELECT feature_id AS minus_24_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_24_signal'; --- ************************************************ --- *** relation: a_box_type_1 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 1 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_1 AS SELECT feature_id AS a_box_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1'; --- ************************************************ --- *** relation: a_box_type_2 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 2 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_2 AS SELECT feature_id AS a_box_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_2'; --- ************************************************ --- *** relation: intermediate_element *** --- *** relation type: VIEW *** --- *** *** --- *** A core promoter region of RNA polymerase *** --- *** III type 1 promoters. *** --- ************************************************ --- CREATE VIEW intermediate_element AS SELECT feature_id AS intermediate_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate_element'; --- ************************************************ --- *** relation: regulatory_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter element that is not part of t *** --- *** he core promoter, but provides the promo *** --- *** ter with a specific regulatory region. *** --- ************************************************ --- CREATE VIEW regulatory_promoter_element AS SELECT feature_id AS regulatory_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'regulatory_promoter_element'; --- ************************************************ --- *** relation: transcription_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of transcript *** --- *** ion. *** --- ************************************************ --- CREATE VIEW transcription_regulatory_region AS SELECT feature_id AS transcription_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'transcription_regulatory_region'; --- ************************************************ --- *** relation: translation_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of translatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW translation_regulatory_region AS SELECT feature_id AS translation_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator' OR cvterm.name = 'translation_regulatory_region'; --- ************************************************ --- *** relation: recombination_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of recombinat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW recombination_regulatory_region AS SELECT feature_id AS recombination_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_regulatory_region'; --- ************************************************ --- *** relation: replication_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of nucleotide *** --- *** replication. *** --- ************************************************ --- CREATE VIEW replication_regulatory_region AS SELECT feature_id AS replication_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'replication_regulatory_region'; --- ************************************************ --- *** relation: sequence_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a nucleotide or amin *** --- *** o-acid sequence pattern that may have bi *** --- *** ological significance. *** --- ************************************************ --- CREATE VIEW sequence_motif AS SELECT feature_id AS sequence_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'sequence_motif'; --- ************************************************ --- *** relation: experimental_feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of an experimentally derive *** --- *** d feature. *** --- ************************************************ --- CREATE VIEW experimental_feature_attribute AS SELECT feature_id AS experimental_feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'experimental_feature_attribute'; --- ************************************************ --- *** relation: score *** --- *** relation type: VIEW *** --- *** *** --- *** The score of an experimentally derived f *** --- *** eature such as a p-value. *** --- ************************************************ --- CREATE VIEW score AS SELECT feature_id AS score_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score'; --- ************************************************ --- *** relation: quality_value *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature attribute that d *** --- *** efines the quality of the feature in a q *** --- *** uantitative way, such as a phred quality *** --- *** score. *** --- ************************************************ --- CREATE VIEW quality_value AS SELECT feature_id AS quality_value_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quality_value'; --- ************************************************ --- *** relation: restriction_enzyme_recognition_site *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide region (usually a palindr *** --- *** ome) that is recognized by a restriction *** --- *** enzyme. This may or may not be equal to *** --- *** the restriction enzyme binding site. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_recognition_site AS SELECT feature_id AS restriction_enzyme_recognition_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'restriction_enzyme_recognition_site'; --- ************************************************ --- *** relation: restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary at which a restriction enzy *** --- *** me breaks the nucleotide sequence. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_cleavage_junction AS SELECT feature_id AS restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: five_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The restriction enzyme cleavage junction *** --- *** on the 5' strand of the nucleotide sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW five_prime_restriction_enzyme_junction AS SELECT feature_id AS five_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: three_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_restriction_enzyme_junction AS SELECT feature_id AS three_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: sticky_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sticky_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS sticky_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** both strands are cut at the same positi *** --- *** on. *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_junction AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: single_strand_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** by only one strand is cut. *** --- ************************************************ --- CREATE VIEW single_strand_restriction_enzyme_cleavage_site AS SELECT feature_id AS single_strand_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: restriction_enzyme_single_strand_overhang *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal region of DNA sequence where *** --- *** the end of the region is not blunt ended *** --- *** . *** --- ************************************************ --- CREATE VIEW restriction_enzyme_single_strand_overhang AS SELECT feature_id AS restriction_enzyme_single_strand_overhang_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_single_strand_overhang'; --- ************************************************ --- *** relation: experimentally_defined_binding_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that has been implicated in bin *** --- *** ding although the exact coordinates of b *** --- *** inding may be unknown. *** --- ************************************************ --- CREATE VIEW experimentally_defined_binding_region AS SELECT feature_id AS experimentally_defined_binding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimentally_defined_binding_region'; --- ************************************************ --- *** relation: chip_seq_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence identified by CHiP *** --- *** seq technology to contain a protein bind *** --- *** ing site. *** --- ************************************************ --- CREATE VIEW chip_seq_region AS SELECT feature_id AS chip_seq_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region'; --- ************************************************ --- *** relation: aspe_primer *** --- *** relation type: VIEW *** --- *** *** --- *** "A primer containing an SNV at the 3' en *** --- *** d for accurate genotyping. *** --- ************************************************ --- CREATE VIEW aspe_primer AS SELECT feature_id AS aspe_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ASPE_primer'; --- ************************************************ --- *** relation: dcaps_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A primer with one or more mis-matches to *** --- *** the DNA template corresponding to a pos *** --- *** ition within a restriction enzyme recogn *** --- *** ition site. *** --- ************************************************ --- CREATE VIEW dcaps_primer AS SELECT feature_id AS dcaps_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dCAPS_primer'; --- ************************************************ --- *** relation: histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** Histone modification is a post translati *** --- *** onally modified region whereby residues *** --- *** of the histone protein are modified by m *** --- *** ethylation, acetylation, phosphorylation *** --- *** , ubiquitination, sumoylation, citrullin *** --- *** ation, or ADP-ribosylation. *** --- ************************************************ --- CREATE VIEW histone_modification AS SELECT feature_id AS histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_modification'; --- ************************************************ --- *** relation: histone_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where the mo *** --- *** dification is the methylation of the res *** --- *** idue. *** --- ************************************************ --- CREATE VIEW histone_methylation_site AS SELECT feature_id AS histone_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'histone_methylation_site'; --- ************************************************ --- *** relation: histone_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification where the modific *** --- *** ation is the acylation of the residue. *** --- ************************************************ --- CREATE VIEW histone_acetylation_site AS SELECT feature_id AS histone_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'histone_acetylation_site'; --- ************************************************ --- *** relation: h3k9_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h3k9_acetylation_site AS SELECT feature_id AS h3k9_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site'; --- ************************************************ --- *** relation: h3k14_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k14_acetylation_site AS SELECT feature_id AS h3k14_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K14_acetylation_site'; --- ************************************************ --- *** relation: h3k4_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is mono-methylated. *** --- ************************************************ --- CREATE VIEW h3k4_monomethylation_site AS SELECT feature_id AS h3k4_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site'; --- ************************************************ --- *** relation: h3k4_trimethylation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 protein is tri-methyla *** --- *** ted. *** --- ************************************************ --- CREATE VIEW h3k4_trimethylation AS SELECT feature_id AS h3k4_trimethylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_trimethylation'; --- ************************************************ --- *** relation: h3k9_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is tri *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k9_trimethylation_site AS SELECT feature_id AS h3k9_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site'; --- ************************************************ --- *** relation: h3k27_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_monomethylation_site AS SELECT feature_id AS h3k27_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site'; --- ************************************************ --- *** relation: h3k27_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_trimethylation_site AS SELECT feature_id AS h3k27_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_trimethylation_site'; --- ************************************************ --- *** relation: h3k79_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no- methylated. *** --- ************************************************ --- CREATE VIEW h3k79_monomethylation_site AS SELECT feature_id AS h3k79_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site'; --- ************************************************ --- *** relation: h3k79_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k79_dimethylation_site AS SELECT feature_id AS h3k79_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_dimethylation_site'; --- ************************************************ --- *** relation: h3k79_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k79_trimethylation_site AS SELECT feature_id AS h3k79_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_trimethylation_site'; --- ************************************************ --- *** relation: h4k20_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 20th residue (a lysine), from t *** --- *** he start of the H34histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h4k20_monomethylation_site AS SELECT feature_id AS h4k20_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site'; --- ************************************************ --- *** relation: h2bk5_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H2B protein is methylated *** --- *** . *** --- ************************************************ --- CREATE VIEW h2bk5_monomethylation_site AS SELECT feature_id AS h2bk5_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2BK5_monomethylation_site'; --- ************************************************ --- *** relation: isre *** --- *** relation type: VIEW *** --- *** *** --- *** An ISRE is a transcriptional cis regulat *** --- *** ory region, containing the consensus reg *** --- *** ion: YAGTTTC(A/T)YTTTYCC, responsible fo *** --- *** r increased transcription via interferon *** --- *** binding. *** --- ************************************************ --- CREATE VIEW isre AS SELECT feature_id AS isre_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ISRE'; --- ************************************************ --- *** relation: histone_ubiqitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where ubiqui *** --- *** tin may be added. *** --- ************************************************ --- CREATE VIEW histone_ubiqitination_site AS SELECT feature_id AS histone_ubiqitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'histone_ubiqitination_site'; --- ************************************************ --- *** relation: h2b_ubiquitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site on H2B where *** --- *** ubiquitin may be added. *** --- ************************************************ --- CREATE VIEW h2b_ubiquitination_site AS SELECT feature_id AS h2b_ubiquitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site'; --- ************************************************ --- *** relation: h3k18_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k18_acetylation_site AS SELECT feature_id AS h3k18_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K18_acetylation_site'; --- ************************************************ --- *** relation: h3k23_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 23rd residue (a lysine), from the st *** --- *** art of the H3 histone protein is acylate *** --- *** d. *** --- ************************************************ --- CREATE VIEW h3k23_acylation_site AS SELECT feature_id AS h3k23_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K23_acylation site'; --- ************************************************ --- *** relation: epigenetically_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A biological region implicated in inheri *** --- *** ted changes caused by mechanisms other t *** --- *** han changes in the underlying DNA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_region AS SELECT feature_id AS epigenetically_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'epigenetically_modified_region'; --- ************************************************ --- *** relation: h3k27_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k27_acylation_site AS SELECT feature_id AS h3k27_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_acylation_site'; --- ************************************************ --- *** relation: h3k36_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_monomethylation_site AS SELECT feature_id AS h3k36_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site'; --- ************************************************ --- *** relation: h3k36_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k36_dimethylation_site AS SELECT feature_id AS h3k36_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_dimethylation_site'; --- ************************************************ --- *** relation: h3k36_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_trimethylation_site AS SELECT feature_id AS h3k36_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_trimethylation_site'; --- ************************************************ --- *** relation: h3k4_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 histone protein is di- *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k4_dimethylation_site AS SELECT feature_id AS h3k4_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_dimethylation_site'; --- ************************************************ --- *** relation: h3k27_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k27_dimethylation_site AS SELECT feature_id AS h3k27_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_dimethylation_site'; --- ************************************************ --- *** relation: h3k9_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is mon *** --- *** o-methylated. *** --- ************************************************ --- CREATE VIEW h3k9_monomethylation_site AS SELECT feature_id AS h3k9_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_monomethylation_site'; --- ************************************************ --- *** relation: h3k9_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein may be *** --- *** dimethylated. *** --- ************************************************ --- CREATE VIEW h3k9_dimethylation_site AS SELECT feature_id AS h3k9_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_dimethylation_site'; --- ************************************************ --- *** relation: h4k16_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 16th residue (a lysine), from t *** --- *** he start of the H4 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h4k16_acylation_site AS SELECT feature_id AS h4k16_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K16_acylation_site'; --- ************************************************ --- *** relation: h4k5_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k5_acylation_site AS SELECT feature_id AS h4k5_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K5_acylation_site'; --- ************************************************ --- *** relation: h4k8_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 8th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k8_acylation_site AS SELECT feature_id AS h4k8_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K8_acylation site'; --- ************************************************ --- *** relation: h3k27_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k27_methylation_site AS SELECT feature_id AS h3k27_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K27_methylation_site'; --- ************************************************ --- *** relation: h3k36_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k36_methylation_site AS SELECT feature_id AS h3k36_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K36_methylation_site'; --- ************************************************ --- *** relation: h3k4_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is methylated. *** --- ************************************************ --- CREATE VIEW h3k4_methylation_site AS SELECT feature_id AS h3k4_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K4_methylation_site'; --- ************************************************ --- *** relation: h3k79_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k79_methylation_site AS SELECT feature_id AS h3k79_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K79_methylation_site'; --- ************************************************ --- *** relation: h3k9_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is met *** --- *** hylated. *** --- ************************************************ --- CREATE VIEW h3k9_methylation_site AS SELECT feature_id AS h3k9_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_methylation_site'; --- ************************************************ --- *** relation: histone_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification, whereby the hist *** --- *** one protein is acylated at multiple site *** --- *** s in a region. *** --- ************************************************ --- CREATE VIEW histone_acylation_region AS SELECT feature_id AS histone_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_acylation_region'; --- ************************************************ --- *** relation: h4k_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the H4 histone whereby multi *** --- *** ple lysines are acylated. *** --- ************************************************ --- CREATE VIEW h4k_acylation_region AS SELECT feature_id AS h4k_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region'; --- ************************************************ --- *** relation: gene_with_non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a start codon other than AUG *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_non_canonical_start_codon AS SELECT feature_id AS gene_with_non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene_with_non_canonical_start_codon'; --- ************************************************ --- *** relation: gene_with_start_codon_cug *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a translational start codon *** --- *** of CUG. *** --- ************************************************ --- CREATE VIEW gene_with_start_codon_cug AS SELECT feature_id AS gene_with_start_codon_cug_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG'; --- ************************************************ --- *** relation: pseudogenic_gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene segment which when incorporated b *** --- *** y somatic recombination in the final gen *** --- *** e transcript results in a nonfunctional *** --- *** product. *** --- ************************************************ --- CREATE VIEW pseudogenic_gene_segment AS SELECT feature_id AS pseudogenic_gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment'; --- ************************************************ --- *** relation: copy_number_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given regions is greater than *** --- *** the reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_gain AS SELECT feature_id AS copy_number_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain'; --- ************************************************ --- *** relation: copy_number_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given region is less than the *** --- *** reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_loss AS SELECT feature_id AS copy_number_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_loss'; --- ************************************************ --- *** relation: upd *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from one parent and no copies of the *** --- *** same chromosome or region from the other *** --- *** parent. *** --- ************************************************ --- CREATE VIEW upd AS SELECT feature_id AS upd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'UPD'; --- ************************************************ --- *** relation: maternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the mother and no copies of the *** --- *** same chromosome or region from the fathe *** --- *** r. *** --- ************************************************ --- CREATE VIEW maternal_uniparental_disomy AS SELECT feature_id AS maternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy'; --- ************************************************ --- *** relation: paternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the father and no copies of the *** --- *** same chromosome or region from the mothe *** --- *** r. *** --- ************************************************ --- CREATE VIEW paternal_uniparental_disomy AS SELECT feature_id AS paternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_uniparental_disomy'; --- ************************************************ --- *** relation: open_chromatin_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that in the normal state *** --- *** of the chromosome corresponds to an unfo *** --- *** lded, un-complexed stretch of double-str *** --- *** anded DNA. *** --- ************************************************ --- CREATE VIEW open_chromatin_region AS SELECT feature_id AS open_chromatin_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'open_chromatin_region'; --- ************************************************ --- *** relation: sl3_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 3 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL3 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl3_acceptor_site AS SELECT feature_id AS sl3_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site'; --- ************************************************ --- *** relation: sl4_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 4 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL4 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl4_acceptor_site AS SELECT feature_id AS sl4_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL4_acceptor_site'; --- ************************************************ --- *** relation: sl5_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 5 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL5 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl5_acceptor_site AS SELECT feature_id AS sl5_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL5_acceptor_site'; --- ************************************************ --- *** relation: sl6_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 6 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL6 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl6_acceptor_site AS SELECT feature_id AS sl6_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL6_acceptor_site'; --- ************************************************ --- *** relation: sl7_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 7 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL7 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl7_acceptor_site AS SELECT feature_id AS sl7_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL7_acceptor_site'; --- ************************************************ --- *** relation: sl8_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 8 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL8 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl8_acceptor_site AS SELECT feature_id AS sl8_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL8_acceptor_site'; --- ************************************************ --- *** relation: sl9_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 9 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL9 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl9_acceptor_site AS SELECT feature_id AS sl9_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL9_acceptor_site'; --- ************************************************ --- *** relation: sl10_accceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 10 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL10 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl10_accceptor_site AS SELECT feature_id AS sl10_accceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL10_accceptor_site'; --- ************************************************ --- *** relation: sl11_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 11 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL11 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl11_acceptor_site AS SELECT feature_id AS sl11_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL11_acceptor_site'; --- ************************************************ --- *** relation: sl12_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 12 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL12 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl12_acceptor_site AS SELECT feature_id AS sl12_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL12_acceptor_site'; --- ************************************************ --- *** relation: duplicated_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose via gene duplica *** --- *** tion. Generally duplicated pseudogenes h *** --- *** ave the same structure as the original g *** --- *** ene, including intron-exon structure and *** --- *** some regulatory sequence. *** --- ************************************************ --- CREATE VIEW duplicated_pseudogene AS SELECT feature_id AS duplicated_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'duplicated_pseudogene'; --- ************************************************ --- *** relation: unitary_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene, deactivated from original *** --- *** state by mutation, fixed in a population *** --- *** . *** --- ************************************************ --- CREATE VIEW unitary_pseudogene AS SELECT feature_id AS unitary_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unitary_pseudogene'; --- ************************************************ --- *** relation: non_processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose from a means oth *** --- *** er than retrotransposition. *** --- ************************************************ --- CREATE VIEW non_processed_pseudogene AS SELECT feature_id AS non_processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'non_processed_pseudogene'; --- ************************************************ --- *** relation: variant_quality *** --- *** relation type: VIEW *** --- *** *** --- *** A dependent entity that inheres in a bea *** --- *** rer, a sequence variant. *** --- ************************************************ --- CREATE VIEW variant_quality AS SELECT feature_id AS variant_quality_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_quality'; --- ************************************************ --- *** relation: variant_origin *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its origin. *** --- ************************************************ --- CREATE VIEW variant_origin AS SELECT feature_id AS variant_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'variant_origin'; --- ************************************************ --- *** relation: variant_frequency *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW variant_frequency AS SELECT feature_id AS variant_frequency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'variant_frequency'; --- ************************************************ --- *** relation: unique_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW unique_variant AS SELECT feature_id AS unique_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant'; --- ************************************************ --- *** relation: rare_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rare_variant AS SELECT feature_id AS rare_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rare_variant'; --- ************************************************ --- *** relation: polymorphic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW polymorphic_variant AS SELECT feature_id AS polymorphic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_variant'; --- ************************************************ --- *** relation: common_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW common_variant AS SELECT feature_id AS common_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'common_variant'; --- ************************************************ --- *** relation: fixed_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fixed_variant AS SELECT feature_id AS fixed_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fixed_variant'; --- ************************************************ --- *** relation: variant_phenotype *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its phenotype. *** --- ************************************************ --- CREATE VIEW variant_phenotype AS SELECT feature_id AS variant_phenotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_phenotype'; --- ************************************************ --- *** relation: benign_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW benign_variant AS SELECT feature_id AS benign_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant'; --- ************************************************ --- *** relation: disease_associated_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_associated_variant AS SELECT feature_id AS disease_associated_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_associated_variant'; --- ************************************************ --- *** relation: disease_causing_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_causing_variant AS SELECT feature_id AS disease_causing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_causing_variant'; --- ************************************************ --- *** relation: lethal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lethal_variant AS SELECT feature_id AS lethal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lethal_variant'; --- ************************************************ --- *** relation: quantitative_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW quantitative_variant AS SELECT feature_id AS quantitative_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quantitative_variant'; --- ************************************************ --- *** relation: maternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW maternal_variant AS SELECT feature_id AS maternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant'; --- ************************************************ --- *** relation: paternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paternal_variant AS SELECT feature_id AS paternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_variant'; --- ************************************************ --- *** relation: somatic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW somatic_variant AS SELECT feature_id AS somatic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'somatic_variant'; --- ************************************************ --- *** relation: germline_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW germline_variant AS SELECT feature_id AS germline_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'germline_variant'; --- ************************************************ --- *** relation: pedigree_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pedigree_specific_variant AS SELECT feature_id AS pedigree_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pedigree_specific_variant'; --- ************************************************ --- *** relation: population_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW population_specific_variant AS SELECT feature_id AS population_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'population_specific_variant'; --- ************************************************ --- *** relation: de_novo_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW de_novo_variant AS SELECT feature_id AS de_novo_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'de_novo_variant'; --- ************************************************ --- *** relation: tf_binding_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a tran *** --- *** scription factor binding site. *** --- ************************************************ --- CREATE VIEW tf_binding_site_variant AS SELECT feature_id AS tf_binding_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant'; --- ************************************************ --- *** relation: missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid. *** --- ************************************************ --- CREATE VIEW missense_codon AS SELECT feature_id AS missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'missense_codon'; --- ************************************************ --- *** relation: complex_structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A structural sequence alteration where t *** --- *** here are multiple equally plausible expl *** --- *** anations for the change. *** --- ************************************************ --- CREATE VIEW complex_structural_alteration AS SELECT feature_id AS complex_structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration'; --- ************************************************ --- *** relation: structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW structural_alteration AS SELECT feature_id AS structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'structural_alteration'; --- ************************************************ --- *** relation: loss_of_heterozygosity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loss_of_heterozygosity AS SELECT feature_id AS loss_of_heterozygosity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loss_of_heterozygosity'; --- ************************************************ --- *** relation: splice_donor_5th_base_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** at the 5th base pair after the start of *** --- *** the intron in the orientation of the tra *** --- *** nscript. *** --- ************************************************ --- CREATE VIEW splice_donor_5th_base_variant AS SELECT feature_id AS splice_donor_5th_base_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_5th_base_variant'; --- ************************************************ --- *** relation: u_box *** --- *** relation type: VIEW *** --- *** *** --- *** An U-box is a conserved T-rich region up *** --- *** stream of a retroviral polypurine tract *** --- *** that is involved in PPT primer creation *** --- *** during reverse transcription. *** --- ************************************************ --- CREATE VIEW u_box AS SELECT feature_id AS u_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U_box'; --- ************************************************ --- *** relation: mating_type_region *** --- *** relation type: VIEW *** --- *** *** --- *** A specialized region in the genomes of s *** --- *** ome yeast and fungi, the genes of which *** --- *** regulate mating type. *** --- ************************************************ --- CREATE VIEW mating_type_region AS SELECT feature_id AS mating_type_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mating_type_region'; --- ************************************************ --- *** relation: paired_end_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An assembly region that has been sequenc *** --- *** ed from both ends resulting in a read_pa *** --- *** ir (mate_pair). *** --- ************************************************ --- CREATE VIEW paired_end_fragment AS SELECT feature_id AS paired_end_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paired_end_fragment'; --- ************************************************ --- *** relation: exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes exon seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW exon_variant AS SELECT feature_id AS exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'exon_variant'; --- ************************************************ --- *** relation: non_coding_exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes non-codi *** --- *** ng exon sequence. *** --- ************************************************ --- CREATE VIEW non_coding_exon_variant AS SELECT feature_id AS non_coding_exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_coding_exon_variant'; --- ************************************************ --- *** relation: clone_end *** --- *** relation type: VIEW *** --- *** *** --- *** A read from an end of the clone sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW clone_end AS SELECT feature_id AS clone_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_end'; --- ************************************************ --- *** relation: point_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A point centromere is a relatively small *** --- *** centromere (about 125 bp DNA) in discre *** --- *** te sequence, found in some yeast includi *** --- *** ng S. cerevisiae. *** --- ************************************************ --- CREATE VIEW point_centromere AS SELECT feature_id AS point_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere'; --- ************************************************ --- *** relation: regional_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A regional centromere is a large modular *** --- *** centromere found in fission yeast and h *** --- *** igher eukaryotes. It consist of a centra *** --- *** l core region flanked by inverted inner *** --- *** and outer repeat regions. *** --- ************************************************ --- CREATE VIEW regional_centromere AS SELECT feature_id AS regional_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere'; --- ************************************************ --- *** relation: regional_centromere_central_core *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region within the central re *** --- *** gion of a modular centromere, where the *** --- *** kinetochore is formed. *** --- ************************************************ --- CREATE VIEW regional_centromere_central_core AS SELECT feature_id AS regional_centromere_central_core_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_central_core'; --- ************************************************ --- *** relation: centromeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region found within the modular *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW centromeric_repeat AS SELECT feature_id AS centromeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'centromeric_repeat'; --- ************************************************ --- *** relation: regional_centromere_inner_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The inner repeat region of a modular cen *** --- *** tromere. This region is adjacent to the *** --- *** central core, on each chromosome arm. *** --- ************************************************ --- CREATE VIEW regional_centromere_inner_repeat_region AS SELECT feature_id AS regional_centromere_inner_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region'; --- ************************************************ --- *** relation: regional_centromere_outer_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The heterochromatic outer repeat region *** --- *** of a modular centromere. These repeats e *** --- *** xist in tandem arrays on both chromosome *** --- *** arms. *** --- ************************************************ --- CREATE VIEW regional_centromere_outer_repeat_region AS SELECT feature_id AS regional_centromere_outer_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_outer_repeat_region'; --- ************************************************ --- *** relation: tasirna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a 21 nucleotide double s *** --- *** tranded, polyadenylated non coding RNA, *** --- *** transcribed from the TAS gene. *** --- ************************************************ --- CREATE VIEW tasirna AS SELECT feature_id AS tasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA'; --- ************************************************ --- *** relation: tasirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tasiRNA. *** --- ************************************************ --- CREATE VIEW tasirna_primary_transcript AS SELECT feature_id AS tasirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA_primary_transcript'; --- ************************************************ --- *** relation: increased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is increased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW increased_polyadenylation_variant AS SELECT feature_id AS increased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant'; --- ************************************************ --- *** relation: decreased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is decreased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW decreased_polyadenylation_variant AS SELECT feature_id AS decreased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_polyadenylation_variant'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence that is involved in *** --- *** the control of a biological process. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: u14_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of an evolutionar *** --- *** ily conserved eukaryotic low molecular w *** --- *** eight RNA capable of intermolecular hybr *** --- *** idization with both homologous and heter *** --- *** ologous 18S rRNA. *** --- ************************************************ --- CREATE VIEW u14_snorna_primary_transcript AS SELECT feature_id AS u14_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: methylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of 2'-O *** --- *** -ribose methylation in an RNA molecule b *** --- *** y base pairing with a short sequence aro *** --- *** und the target residue. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna AS SELECT feature_id AS methylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA'; --- ************************************************ --- *** relation: rrna_cleavage_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An ncRNA that is part of a ribonucleopro *** --- *** tein that cleaves the primary pre-rRNA t *** --- *** ranscript in the process of producing ma *** --- *** ture rRNA molecules. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_rna AS SELECT feature_id AS rrna_cleavage_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_RNA'; --- ************************************************ --- *** relation: exon_of_single_exon_gene *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is the only exon in a gene. *** --- ************************************************ --- CREATE VIEW exon_of_single_exon_gene AS SELECT feature_id AS exon_of_single_exon_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_of_single_exon_gene'; --- ************************************************ --- *** relation: cassette_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cassette_array_member AS SELECT feature_id AS cassette_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member'; --- ************************************************ --- *** relation: gene_cassette_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_cassette_member AS SELECT feature_id AS gene_cassette_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member'; --- ************************************************ --- *** relation: gene_subarray_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_subarray_member AS SELECT feature_id AS gene_subarray_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray_member'; --- ************************************************ --- *** relation: primer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** Non-covalent primer binding site for ini *** --- *** tiation of replication, transcription, o *** --- *** r reverse transcription. *** --- ************************************************ --- CREATE VIEW primer_binding_site AS SELECT feature_id AS primer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_binding_site'; --- ************************************************ --- *** relation: gene_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array includes two or more genes, or *** --- *** two or more gene subarrays, contiguously *** --- *** arranged where the individual genes, or *** --- *** subarrays, are either identical in sequ *** --- *** ence, or essentially so. *** --- ************************************************ --- CREATE VIEW gene_array AS SELECT feature_id AS gene_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_array'; --- ************************************************ --- *** relation: gene_subarray *** --- *** relation type: VIEW *** --- *** *** --- *** A subarray is, by defintition, a member *** --- *** of a gene array (SO:0005851); the member *** --- *** s of a subarray may differ substantially *** --- *** in sequence, but are closely related in *** --- *** function. *** --- ************************************************ --- CREATE VIEW gene_subarray AS SELECT feature_id AS gene_subarray_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray'; --- ************************************************ --- *** relation: gene_cassette *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that can be substituted for a rel *** --- *** ated gene at a different site in the gen *** --- *** ome. *** --- ************************************************ --- CREATE VIEW gene_cassette AS SELECT feature_id AS gene_cassette_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette'; --- ************************************************ --- *** relation: gene_cassette_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array of non-functional genes whose m *** --- *** embers, when captured by recombination f *** --- *** orm functional genes. *** --- ************************************************ --- CREATE VIEW gene_cassette_array AS SELECT feature_id AS gene_cassette_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette_array'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: selenocysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW selenocysteine_trna_primary_transcript AS SELECT feature_id AS selenocysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: selenocysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a selenocystein *** --- *** e anticodon, and a 3' selenocysteine bin *** --- *** ding region. *** --- ************************************************ --- CREATE VIEW selenocysteinyl_trna AS SELECT feature_id AS selenocysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteinyl_tRNA'; --- ************************************************ --- *** relation: syntenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region in which two or more pairs of h *** --- *** omologous markers occur on the same chro *** --- *** mosome in two or more species. *** --- ************************************************ --- CREATE VIEW syntenic_region AS SELECT feature_id AS syntenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic_region'; --- ************************************************ --- *** relation: biochemical_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is involved i *** --- *** n a biochemical function. *** --- ************************************************ --- CREATE VIEW biochemical_region_of_peptide AS SELECT feature_id AS biochemical_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide'; --- ************************************************ --- *** relation: molecular_contact_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is involved a contact with *** --- *** another molecule. *** --- ************************************************ --- CREATE VIEW molecular_contact_region AS SELECT feature_id AS molecular_contact_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region'; --- ************************************************ --- *** relation: intrinsically_unstructured_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polypeptide chain with high *** --- *** conformational flexibility. *** --- ************************************************ --- CREATE VIEW intrinsically_unstructured_polypeptide_region AS SELECT feature_id AS intrinsically_unstructured_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region'; --- ************************************************ --- *** relation: catmat_left_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_three AS SELECT feature_id AS catmat_left_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_three'; --- ************************************************ --- *** relation: catmat_left_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i psi -10 boun *** --- *** ds -50 to 30, res i+1: phi -90 bounds -1 *** --- *** 20 to -60, res i+1: psi -10 bounds -50 t *** --- *** o 30, res i+2: phi -75 bounds -100 to -5 *** --- *** 0, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_four AS SELECT feature_id AS catmat_left_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_four'; --- ************************************************ --- *** relation: catmat_right_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_three AS SELECT feature_id AS catmat_right_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_three'; --- ************************************************ --- *** relation: catmat_right_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -90 bounds - *** --- *** 120 to -60, res i+1: psi -10 bounds -50 *** --- *** to 30, res i+2: phi -75 bounds -100 to - *** --- *** 50, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_four AS SELECT feature_id AS catmat_right_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_four'; --- ************************************************ --- *** relation: alpha_beta_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: H-bond between CO *** --- *** of residue(i) and NH of residue(i+4), H *** --- *** -bond between CO of residue(i) and NH of *** --- *** residue(i+3),Phi angles of residues(i+1 *** --- *** ), (i+2) and (i+3) are negative. *** --- ************************************************ --- CREATE VIEW alpha_beta_motif AS SELECT feature_id AS alpha_beta_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_beta_motif'; --- ************************************************ --- *** relation: lipoprotein_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide that acts as a signal for both *** --- *** membrane translocation and lipid attach *** --- *** ment in prokaryotes. *** --- ************************************************ --- CREATE VIEW lipoprotein_signal_peptide AS SELECT feature_id AS lipoprotein_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lipoprotein_signal_peptide'; --- ************************************************ --- *** relation: no_output *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region wherean analysis *** --- *** has been run and not produced any annota *** --- *** tion. *** --- ************************************************ --- CREATE VIEW no_output AS SELECT feature_id AS no_output_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'no_output'; --- ************************************************ --- *** relation: cleaved_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** The cleaved_peptide_regon is the a regio *** --- *** n of peptide sequence that is cleaved du *** --- *** ring maturation. *** --- ************************************************ --- CREATE VIEW cleaved_peptide_region AS SELECT feature_id AS cleaved_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'cleaved_peptide_region'; --- ************************************************ --- *** relation: peptide_coil *** --- *** relation type: VIEW *** --- *** *** --- *** Irregular, unstructured regions of a pro *** --- *** tein's backbone, as distinct from the re *** --- *** gular region (namely alpha helix and bet *** --- *** a strand - characterised by specific pat *** --- *** terns of main-chain hydrogen bonds). *** --- ************************************************ --- CREATE VIEW peptide_coil AS SELECT feature_id AS peptide_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_coil'; --- ************************************************ --- *** relation: hydrophobic_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Hydrophobic regions are regions with a l *** --- *** ow affinity for water. *** --- ************************************************ --- CREATE VIEW hydrophobic_region_of_peptide AS SELECT feature_id AS hydrophobic_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydrophobic_region_of_peptide'; --- ************************************************ --- *** relation: n_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The amino-terminal positively-charged re *** --- *** gion of a signal peptide (approx 1-5 aa) *** --- *** . *** --- ************************************************ --- CREATE VIEW n_terminal_region AS SELECT feature_id AS n_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'n_terminal_region'; --- ************************************************ --- *** relation: c_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The more polar, carboxy-terminal region *** --- *** of the signal peptide (approx 3-7 aa). *** --- ************************************************ --- CREATE VIEW c_terminal_region AS SELECT feature_id AS c_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'c_terminal_region'; --- ************************************************ --- *** relation: central_hydrophobic_region_of_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The central, hydrophobic region of the s *** --- *** ignal peptide (approx 7-15 aa). *** --- ************************************************ --- CREATE VIEW central_hydrophobic_region_of_signal_peptide AS SELECT feature_id AS central_hydrophobic_region_of_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'central_hydrophobic_region_of_signal_peptide'; --- ************************************************ --- *** relation: polypeptide_conserved_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved motif is a short (up to 20 a *** --- *** mino acids) region of biological interes *** --- *** t that is conserved in different protein *** --- *** s. They may or may not have functional o *** --- *** r structural significance within the pro *** --- *** teins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_motif AS SELECT feature_id AS polypeptide_conserved_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_conserved_motif'; --- ************************************************ --- *** relation: polypeptide_binding_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide binding motif is a short ( *** --- *** up to 20 amino acids) polypeptide region *** --- *** of biological interest that contains on *** --- *** e or more amino acids experimentally sho *** --- *** wn to bind to a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_binding_motif AS SELECT feature_id AS polypeptide_binding_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_binding_motif'; --- ************************************************ --- *** relation: polypeptide_catalytic_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide catalytic motif is a short *** --- *** (up to 20 amino acids) polypeptide regi *** --- *** on that contains one or more active site *** --- *** residues. *** --- ************************************************ --- CREATE VIEW polypeptide_catalytic_motif AS SELECT feature_id AS polypeptide_catalytic_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_catalytic_motif'; --- ************************************************ --- *** relation: polypeptide_dna_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with DNA. *** --- ************************************************ --- CREATE VIEW polypeptide_dna_contact AS SELECT feature_id AS polypeptide_dna_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact'; --- ************************************************ --- *** relation: polypeptide_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** A subsection of sequence with biological *** --- *** interest that is conserved in different *** --- *** proteins. They may or may not have func *** --- *** tional or structural significance within *** --- *** the proteins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_region AS SELECT feature_id AS polypeptide_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_conserved_region'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration where the length o *** --- *** f the change in the variant is the same *** --- *** as that of the reference. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'substitution'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A single nucleotide change which has occ *** --- *** urred at the same position of a correspo *** --- *** nding nucleotide in a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: transition *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into an other pyrimidine nucleotide, *** --- *** or change of a purine nucleotide, A or G *** --- *** , into an other purine nucleotide. *** --- ************************************************ --- CREATE VIEW transition AS SELECT feature_id AS transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'transition'; --- ************************************************ --- *** relation: pyrimidine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a pyrimidine, C or T, *** --- *** for another pyrimidine. *** --- ************************************************ --- CREATE VIEW pyrimidine_transition AS SELECT feature_id AS pyrimidine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'pyrimidine_transition'; --- ************************************************ --- *** relation: c_to_t_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a cytidine to a thymine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition AS SELECT feature_id AS c_to_t_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'C_to_T_transition'; --- ************************************************ --- *** relation: c_to_t_transition_at_pcpg_site *** --- *** relation type: VIEW *** --- *** *** --- *** The transition of cytidine to thymine oc *** --- *** curring at a pCpG site as a consequence *** --- *** of the spontaneous deamination of 5'-met *** --- *** hylcytidine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition_at_pcpg_site AS SELECT feature_id AS c_to_t_transition_at_pcpg_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site'; --- ************************************************ --- *** relation: t_to_c_transition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW t_to_c_transition AS SELECT feature_id AS t_to_c_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_C_transition'; --- ************************************************ --- *** relation: purine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a purine, A or G, for *** --- *** another purine. *** --- ************************************************ --- CREATE VIEW purine_transition AS SELECT feature_id AS purine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'purine_transition'; --- ************************************************ --- *** relation: a_to_g_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of an adenine to a guanine. *** --- ************************************************ --- CREATE VIEW a_to_g_transition AS SELECT feature_id AS a_to_g_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition'; --- ************************************************ --- *** relation: g_to_a_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a guanine to an adenine. *** --- ************************************************ --- CREATE VIEW g_to_a_transition AS SELECT feature_id AS g_to_a_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_A_transition'; --- ************************************************ --- *** relation: transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G, or *** --- *** vice versa. *** --- ************************************************ --- CREATE VIEW transversion AS SELECT feature_id AS transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'transversion'; --- ************************************************ --- *** relation: pyrimidine_to_purine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G. *** --- ************************************************ --- CREATE VIEW pyrimidine_to_purine_transversion AS SELECT feature_id AS pyrimidine_to_purine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'pyrimidine_to_purine_transversion'; --- ************************************************ --- *** relation: c_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from cytidine to adenine. *** --- ************************************************ --- CREATE VIEW c_to_a_transversion AS SELECT feature_id AS c_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion'; --- ************************************************ --- *** relation: c_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_to_g_transversion AS SELECT feature_id AS c_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_G_transversion'; --- ************************************************ --- *** relation: t_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to A. *** --- ************************************************ --- CREATE VIEW t_to_a_transversion AS SELECT feature_id AS t_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_A_transversion'; --- ************************************************ --- *** relation: t_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to G. *** --- ************************************************ --- CREATE VIEW t_to_g_transversion AS SELECT feature_id AS t_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_G_transversion'; --- ************************************************ --- *** relation: purine_to_pyrimidine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a purine nucleotide, A or G , *** --- *** into a pyrimidine nucleotide C or T. *** --- ************************************************ --- CREATE VIEW purine_to_pyrimidine_transversion AS SELECT feature_id AS purine_to_pyrimidine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion'; --- ************************************************ --- *** relation: a_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to cytidine. *** --- ************************************************ --- CREATE VIEW a_to_c_transversion AS SELECT feature_id AS a_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion'; --- ************************************************ --- *** relation: a_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to thymine. *** --- ************************************************ --- CREATE VIEW a_to_t_transversion AS SELECT feature_id AS a_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_T_transversion'; --- ************************************************ --- *** relation: g_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to cytidine. *** --- ************************************************ --- CREATE VIEW g_to_c_transversion AS SELECT feature_id AS g_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_C_transversion'; --- ************************************************ --- *** relation: g_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to thymine. *** --- ************************************************ --- CREATE VIEW g_to_t_transversion AS SELECT feature_id AS g_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_T_transversion'; --- ************************************************ --- *** relation: intrachromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation within *** --- *** a single chromosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_mutation AS SELECT feature_id AS intrachromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'intrachromosomal_mutation'; --- ************************************************ --- *** relation: chromosomal_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** An incomplete chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_deletion AS SELECT feature_id AS chromosomal_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_deletion'; --- ************************************************ --- *** relation: chromosomal_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation where a reg *** --- *** ion of the chromosome is inverted with r *** --- *** espect to wild type. *** --- ************************************************ --- CREATE VIEW chromosomal_inversion AS SELECT feature_id AS chromosomal_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_inversion'; --- ************************************************ --- *** relation: interchromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation whereb *** --- *** y more than one chromosome is involved. *** --- ************************************************ --- CREATE VIEW interchromosomal_mutation AS SELECT feature_id AS interchromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_mutation'; --- ************************************************ --- *** relation: indel *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration which included an *** --- *** insertion and a deletion, affecting 2 or *** --- *** more bases. *** --- ************************************************ --- CREATE VIEW indel AS SELECT feature_id AS indel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'indel'; --- ************************************************ --- *** relation: duplication *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce; the inserted sequence derives from, *** --- *** or is identical in sequence to, nucleoti *** --- *** des adjacent to insertion point. *** --- ************************************************ --- CREATE VIEW duplication AS SELECT feature_id AS duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'duplication'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: chromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An extra chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_duplication AS SELECT feature_id AS chromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_duplication'; --- ************************************************ --- *** relation: intrachromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication that occurred within a chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_duplication AS SELECT feature_id AS intrachromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_duplication'; --- ************************************************ --- *** relation: direct_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are in the same orientation. *** --- ************************************************ --- CREATE VIEW direct_tandem_duplication AS SELECT feature_id AS direct_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication'; --- ************************************************ --- *** relation: inverted_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are not in the same orientatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW inverted_tandem_duplication AS SELECT feature_id AS inverted_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_tandem_duplication'; --- ************************************************ --- *** relation: intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred within a chrom *** --- *** osome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_transposition AS SELECT feature_id AS intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_transposition'; --- ************************************************ --- *** relation: compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant where a m *** --- *** onocentric element is caused by the fusi *** --- *** on of two chromosome arms. *** --- ************************************************ --- CREATE VIEW compound_chromosome AS SELECT feature_id AS compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'compound_chromosome'; --- ************************************************ --- *** relation: robertsonian_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A non reciprocal translocation whereby t *** --- *** he participating chromosomes break at th *** --- *** eir centromeres and the long arms fuse t *** --- *** o form a single chromosome with a single *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW robertsonian_fusion AS SELECT feature_id AS robertsonian_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Robertsonian_fusion'; --- ************************************************ --- *** relation: chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation. Rearrangem *** --- *** ents that alter the pairing of telomeres *** --- *** are classified as translocations. *** --- ************************************************ --- CREATE VIEW chromosomal_translocation AS SELECT feature_id AS chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_translocation'; --- ************************************************ --- *** relation: ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome is a chromosome whose *** --- *** arms have fused together to form a ring, *** --- *** often with the loss of the ends of the *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW ring_chromosome AS SELECT feature_id AS ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'ring_chromosome'; --- ************************************************ --- *** relation: pericentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that includes th *** --- *** e centromere. *** --- ************************************************ --- CREATE VIEW pericentric_inversion AS SELECT feature_id AS pericentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric_inversion'; --- ************************************************ --- *** relation: paracentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that does not in *** --- *** clude the centromere. *** --- ************************************************ --- CREATE VIEW paracentric_inversion AS SELECT feature_id AS paracentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric_inversion'; --- ************************************************ --- *** relation: reciprocal_chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation with two bre *** --- *** aks; two chromosome segments have simply *** --- *** been exchanged. *** --- ************************************************ --- CREATE VIEW reciprocal_chromosomal_translocation AS SELECT feature_id AS reciprocal_chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal_chromosomal_translocation'; --- ************************************************ --- *** relation: autosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome is the aneupl *** --- *** oid product of recombination between a p *** --- *** ericentric inversion and a cytologically *** --- *** wild-type chromosome. *** --- ************************************************ --- CREATE VIEW autosynaptic_chromosome AS SELECT feature_id AS autosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'autosynaptic_chromosome'; --- ************************************************ --- *** relation: homo_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two copies *** --- *** of the same chromosomal arm attached to *** --- *** a common centromere. The chromosome is *** --- *** diploid for the arm involved. *** --- ************************************************ --- CREATE VIEW homo_compound_chromosome AS SELECT feature_id AS homo_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homo_compound_chromosome'; --- ************************************************ --- *** relation: hetero_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two arms f *** --- *** rom different chromosomes are connected *** --- *** through the centromere of one of them. *** --- ************************************************ --- CREATE VIEW hetero_compound_chromosome AS SELECT feature_id AS hetero_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hetero_compound_chromosome'; --- ************************************************ --- *** relation: chromosome_fission *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome that occurred by the divisi *** --- *** on of a larger chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_fission AS SELECT feature_id AS chromosome_fission_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_fission'; --- ************************************************ --- *** relation: dexstrosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome carrying the *** --- *** two right (D = dextro) telomeres. *** --- ************************************************ --- CREATE VIEW dexstrosynaptic_chromosome AS SELECT feature_id AS dexstrosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome'; --- ************************************************ --- *** relation: laevosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** LS is an autosynaptic chromosome carryin *** --- *** g the two left (L = levo) telomeres. *** --- ************************************************ --- CREATE VIEW laevosynaptic_chromosome AS SELECT feature_id AS laevosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'laevosynaptic_chromosome'; --- ************************************************ --- *** relation: free_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** the duplicated sequences are carried as *** --- *** a free centric element. *** --- ************************************************ --- CREATE VIEW free_duplication AS SELECT feature_id AS free_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication' OR cvterm.name = 'free_duplication'; --- ************************************************ --- *** relation: free_ring_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome which is a copy of ano *** --- *** ther chromosome. *** --- ************************************************ --- CREATE VIEW free_ring_duplication AS SELECT feature_id AS free_ring_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication'; --- ************************************************ --- *** relation: complex_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant with 4 or *** --- *** more breakpoints. *** --- ************************************************ --- CREATE VIEW complex_chromosomal_mutation AS SELECT feature_id AS complex_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a translo *** --- *** cation occurs in which one of the four b *** --- *** roken ends loses a segment before re-joi *** --- *** ning. *** --- ************************************************ --- CREATE VIEW deficient_translocation AS SELECT feature_id AS deficient_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_translocation'; --- ************************************************ --- *** relation: inversion_cum_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** first two breaks are in the same chromos *** --- *** ome, and the region between them is rejo *** --- *** ined in inverted order to the other side *** --- *** of the first break, such that both side *** --- *** s of break one are present on the same c *** --- *** hromosome. The remaining free ends are j *** --- *** oined as a translocation with those resu *** --- *** lting from the third break. *** --- ************************************************ --- CREATE VIEW inversion_cum_translocation AS SELECT feature_id AS inversion_cum_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_cum_translocation'; --- ************************************************ --- *** relation: bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation whereby the *** --- *** (large) region between the first two br *** --- *** eaks listed is lost, and the two flankin *** --- *** g segments (one of them centric) are joi *** --- *** ned as a translocation to the free ends *** --- *** resulting from the third break. *** --- ************************************************ --- CREATE VIEW bipartite_duplication AS SELECT feature_id AS bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_duplication'; --- ************************************************ --- *** relation: cyclic_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby thre *** --- *** e breaks occurred in three different chr *** --- *** omosomes. The centric segment resulting *** --- *** from the first break listed is joined to *** --- *** the acentric segment resulting from the *** --- *** second, rather than the third. *** --- ************************************************ --- CREATE VIEW cyclic_translocation AS SELECT feature_id AS cyclic_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyclic_translocation'; --- ************************************************ --- *** relation: bipartite_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion caused by three *** --- *** breaks in the same chromosome; both cent *** --- *** ral segments are inverted in place (i.e. *** --- *** , they are not transposed). *** --- ************************************************ --- CREATE VIEW bipartite_inversion AS SELECT feature_id AS bipartite_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_inversion'; --- ************************************************ --- *** relation: uninvert_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically the *** --- *** same orientation as its flanking segmen *** --- *** ts. *** --- ************************************************ --- CREATE VIEW uninvert_insert_dup AS SELECT feature_id AS uninvert_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication'; --- ************************************************ --- *** relation: inverted_insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically inv *** --- *** erted orientation with respect to its fl *** --- *** anking segments. *** --- ************************************************ --- CREATE VIEW inverted_insertional_duplication AS SELECT feature_id AS inverted_insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_insertional_duplication'; --- ************************************************ --- *** relation: insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving the i *** --- *** nsertion of a duplicated region (as oppo *** --- *** sed to a free duplication). *** --- ************************************************ --- CREATE VIEW insertional_duplication AS SELECT feature_id AS insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'insertional_duplication'; --- ************************************************ --- *** relation: interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred between chromo *** --- *** somes. *** --- ************************************************ --- CREATE VIEW interchromosomal_transposition AS SELECT feature_id AS interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally inverted orientation with respect *** --- *** to its flanking segment. *** --- ************************************************ --- CREATE VIEW invert_inter_transposition AS SELECT feature_id AS invert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transition where the *** --- *** segment between the first two breaks li *** --- *** sted is removed and inserted at the thir *** --- *** d break; the insertion is in cytological *** --- *** ly the same orientation as its flanking *** --- *** segments. *** --- ************************************************ --- CREATE VIEW uninvert_inter_transposition AS SELECT feature_id AS uninvert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically inverted orientation with respec *** --- *** t to its flanking segments. *** --- ************************************************ --- CREATE VIEW invert_intra_transposition AS SELECT feature_id AS invert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically the same orientation as its flan *** --- *** king segments. *** --- ************************************************ --- CREATE VIEW uninvert_intra_transposition AS SELECT feature_id AS uninvert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: unorient_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the orientation of the insertion with *** --- *** respect to its flanking segments is not *** --- *** recorded. *** --- ************************************************ --- CREATE VIEW unorient_insert_dup AS SELECT feature_id AS unorient_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_insertional_duplication'; --- ************************************************ --- *** relation: unoriented_interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the orientation of the inser *** --- *** tion with respect to its flanking segmen *** --- *** ts is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_interchromosomal_transposition AS SELECT feature_id AS unoriented_interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_interchromosomal_transposition'; --- ************************************************ --- *** relation: unoriented_intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the orientation of the ins *** --- *** ertion with respect to its flanking segm *** --- *** ents is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_intrachromosomal_transposition AS SELECT feature_id AS unoriented_intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uncharacterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uncharacterised_chromosomal_mutation AS SELECT feature_id AS uncharacterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby three bre *** --- *** aks occur in the same chromosome; one ce *** --- *** ntral region is lost, and the other is i *** --- *** nverted. *** --- ************************************************ --- CREATE VIEW deficient_inversion AS SELECT feature_id AS deficient_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_inversion'; --- ************************************************ --- *** relation: tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication consisting of 2 identical *** --- *** adjacent regions. *** --- ************************************************ --- CREATE VIEW tandem_duplication AS SELECT feature_id AS tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'tandem_duplication'; --- ************************************************ --- *** relation: partially_characterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW partially_characterised_chromosomal_mutation AS SELECT feature_id AS partially_characterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation'; --- ************************************************ --- *** relation: chromosome_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW chromosome_number_variation AS SELECT feature_id AS chromosome_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'chromosome_number_variation'; --- ************************************************ --- *** relation: chromosome_structure_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_structure_variation AS SELECT feature_id AS chromosome_structure_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_structure_variation'; --- ************************************************ --- *** relation: alternatively_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is alternatively splic *** --- *** ed. *** --- ************************************************ --- CREATE VIEW alternatively_spliced_transcript AS SELECT feature_id AS alternatively_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced_transcript'; --- ************************************************ --- *** relation: encodes_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, but *** --- *** encodes only one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_1_polypeptide AS SELECT feature_id AS encodes_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide'; --- ************************************************ --- *** relation: encodes_greater_than_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_greater_than_1_polypeptide AS SELECT feature_id AS encodes_greater_than_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_greater_than_1_polypeptide'; --- ************************************************ --- *** relation: encodes_different_polypeptides_different_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different stop codons. *** --- ************************************************ --- CREATE VIEW encodes_different_polypeptides_different_stop AS SELECT feature_id AS encodes_different_polypeptides_different_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides_different_start *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides_different_start AS SELECT feature_id AS encodes_overlapping_peptides_different_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_peptides_different_start'; --- ************************************************ --- *** relation: encodes_disjoint_polypeptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** do not have overlapping peptide sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW encodes_disjoint_polypeptides AS SELECT feature_id AS encodes_disjoint_polypeptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides'; --- ************************************************ --- *** relation: encodes_overlapping_polypeptides_different_start_and_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start and stop codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_polypeptides_different_start_and_stop AS SELECT feature_id AS encodes_overlapping_polypeptides_different_start_and_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides AS SELECT feature_id AS encodes_overlapping_peptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_overlapping_peptides'; --- ************************************************ --- *** relation: cryptogene *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle gene so extensively edited *** --- *** that it cannot be matched to its edited *** --- *** mRNA sequence. *** --- ************************************************ --- CREATE VIEW cryptogene AS SELECT feature_id AS cryptogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene'; --- ************************************************ --- *** relation: dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that has the qualit *** --- *** y dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_primary_transcript AS SELECT feature_id AS dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript'; --- ************************************************ --- *** relation: member_of_regulon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW member_of_regulon AS SELECT feature_id AS member_of_regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'member_of_regulon'; --- ************************************************ --- *** relation: cds_independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS with the evidence status of being *** --- *** independently known. *** --- ************************************************ --- CREATE VIEW cds_independently_known AS SELECT feature_id AS cds_independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_independently_known'; --- ************************************************ --- *** relation: orphan_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS whose predicted amino acid sequenc *** --- *** e is unsupported by any experimental evi *** --- *** dence or by any match with any other kno *** --- *** wn sequence. *** --- ************************************************ --- CREATE VIEW orphan_cds AS SELECT feature_id AS orphan_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS'; --- ************************************************ --- *** relation: cds_supported_by_domain_match_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by domain simila *** --- *** rity. *** --- ************************************************ --- CREATE VIEW cds_supported_by_domain_match_data AS SELECT feature_id AS cds_supported_by_domain_match_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data'; --- ************************************************ --- *** relation: cds_supported_by_sequence_similarity_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by sequence simi *** --- *** larity data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_sequence_similarity_data AS SELECT feature_id AS cds_supported_by_sequence_similarity_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data'; --- ************************************************ --- *** relation: cds_predicted *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is predicted. *** --- ************************************************ --- CREATE VIEW cds_predicted AS SELECT feature_id AS cds_predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_predicted'; --- ************************************************ --- *** relation: cds_supported_by_est_or_cdna_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by similarity to *** --- *** EST or cDNA data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_est_or_cdna_data AS SELECT feature_id AS cds_supported_by_est_or_cdna_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_EST_or_cDNA_data'; --- ************************************************ --- *** relation: internal_shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A Shine-Dalgarno sequence that stimulate *** --- *** s recoding through interactions with the *** --- *** anti-Shine-Dalgarno in the RNA of small *** --- *** ribosomal subunits of translating ribos *** --- *** omes. The signal is only operative in Ba *** --- *** cteria. *** --- ************************************************ --- CREATE VIEW internal_shine_dalgarno_sequence AS SELECT feature_id AS internal_shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a mature mRNA transcript *** --- *** , modified before translation or during *** --- *** translation, usually by special cis-acti *** --- *** ng signals. *** --- ************************************************ --- CREATE VIEW recoded_mrna AS SELECT feature_id AS recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'recoded_mRNA'; --- ************************************************ --- *** relation: minus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of -1. *** --- ************************************************ --- CREATE VIEW minus_1_translationally_frameshifted AS SELECT feature_id AS minus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: plus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of +1. *** --- ************************************************ --- CREATE VIEW plus_1_translationally_frameshifted AS SELECT feature_id AS plus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA where translation was sus *** --- *** pended at a particular codon and resumed *** --- *** at a particular non-overlapping downstr *** --- *** eam codon. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_translational_bypass AS SELECT feature_id AS mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: mrna_recoded_by_codon_redefinition *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA that was modified by an a *** --- *** lteration of codon meaning. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_codon_redefinition AS SELECT feature_id AS mrna_recoded_by_codon_redefinition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_codon_redefinition'; --- ************************************************ --- *** relation: recoding_stimulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A site in an mRNA sequence that stimulat *** --- *** es the recoding of a region in the same *** --- *** mRNA. *** --- ************************************************ --- CREATE VIEW recoding_stimulatory_region AS SELECT feature_id AS recoding_stimulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'recoding_stimulatory_region'; --- ************************************************ --- *** relation: four_bp_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon with 4 base *** --- *** pairs. *** --- ************************************************ --- CREATE VIEW four_bp_start_codon AS SELECT feature_id AS four_bp_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon'; --- ************************************************ --- *** relation: archaeal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron characteristic of Archaeal tRN *** --- *** A and rRNA genes, where intron transcrip *** --- *** t generates a bulge-helix-bulge motif th *** --- *** at is recognised by a splicing endoribon *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW archaeal_intron AS SELECT feature_id AS archaeal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron'; --- ************************************************ --- *** relation: trna_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron found in tRNA that is spliced *** --- *** via endonucleolytic cleavage and ligatio *** --- *** n rather than transesterification. *** --- ************************************************ --- CREATE VIEW trna_intron AS SELECT feature_id AS trna_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_intron'; --- ************************************************ --- *** relation: ctg_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon of sequence *** --- *** CTG. *** --- ************************************************ --- CREATE VIEW ctg_start_codon AS SELECT feature_id AS ctg_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CTG_start_codon'; --- ************************************************ --- *** relation: secis_element *** --- *** relation type: VIEW *** --- *** *** --- *** The incorporation of selenocysteine into *** --- *** a protein sequence is directed by an in *** --- *** -frame UGA codon (usually a stop codon) *** --- *** within the coding region of the mRNA. Se *** --- *** lenoprotein mRNAs contain a conserved se *** --- *** condary structure in the 3' UTR that is *** --- *** required for the distinction of UGA stop *** --- *** from UGA selenocysteine. The selenocyst *** --- *** eine insertion sequence (SECIS) is aroun *** --- *** d 60 nt in length and adopts a hairpin s *** --- *** tructure which is sufficiently well-defi *** --- *** ned and conserved to act as a computatio *** --- *** nal screen for selenoprotein genes. *** --- ************************************************ --- CREATE VIEW secis_element AS SELECT feature_id AS secis_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SECIS_element'; --- ************************************************ --- *** relation: retron *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence coding for a short, single-stra *** --- *** nded, DNA sequence via a retrotransposed *** --- *** RNA intermediate; characteristic of som *** --- *** e microbial genomes. *** --- ************************************************ --- CREATE VIEW retron AS SELECT feature_id AS retron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retron'; --- ************************************************ --- *** relation: three_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** downstream of the recoding site. *** --- ************************************************ --- CREATE VIEW three_prime_recoding_site AS SELECT feature_id AS three_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'three_prime_recoding_site'; --- ************************************************ --- *** relation: three_prime_stem_loop_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory region, the stem- *** --- *** loop secondary structural element is dow *** --- *** nstream of the redefined region. *** --- ************************************************ --- CREATE VIEW three_prime_stem_loop_structure AS SELECT feature_id AS three_prime_stem_loop_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure'; --- ************************************************ --- *** relation: five_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** upstream of the recoding site. *** --- ************************************************ --- CREATE VIEW five_prime_recoding_site AS SELECT feature_id AS five_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_recoding_site'; --- ************************************************ --- *** relation: flanking_three_prime_quadruplet_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Four base pair sequence immediately down *** --- *** stream of the redefined region. The rede *** --- *** fined region is a frameshift site. The q *** --- *** uadruplet is 2 overlapping codons. *** --- ************************************************ --- CREATE VIEW flanking_three_prime_quadruplet_recoding_signal AS SELECT feature_id AS flanking_three_prime_quadruplet_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal'; --- ************************************************ --- *** relation: uag_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAG stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uag_stop_codon_signal AS SELECT feature_id AS uag_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal'; --- ************************************************ --- *** relation: uaa_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uaa_stop_codon_signal AS SELECT feature_id AS uaa_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAA_stop_codon_signal'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: uga_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UGA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uga_stop_codon_signal AS SELECT feature_id AS uga_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UGA_stop_codon_signal'; --- ************************************************ --- *** relation: three_prime_repeat_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal, downstrea *** --- *** m sequence important for recoding that c *** --- *** ontains repetitive elements. *** --- ************************************************ --- CREATE VIEW three_prime_repeat_recoding_signal AS SELECT feature_id AS three_prime_repeat_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_repeat_recoding_signal'; --- ************************************************ --- *** relation: distant_three_prime_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding signal that is found many hun *** --- *** dreds of nucleotides 3' of a redefined s *** --- *** top codon. *** --- ************************************************ --- CREATE VIEW distant_three_prime_recoding_signal AS SELECT feature_id AS distant_three_prime_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distant_three_prime_recoding_signal'; --- ************************************************ --- *** relation: stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal that is a *** --- *** stop codon and has effect on efficiency *** --- *** of recoding. *** --- ************************************************ --- CREATE VIEW stop_codon_signal AS SELECT feature_id AS stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'stop_codon_signal'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene component region which acts as a *** --- *** recombinational unit of a gene whose fun *** --- *** ctional form is generated through somati *** --- *** c recombination. *** --- ************************************************ --- CREATE VIEW gene_segment AS SELECT feature_id AS gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_segment'; CREATE TABLE sequence_cv_lookup_table (sequence_cv_lookup_table_id serial not null, primary key(sequence_cv_lookup_table_id), original_cvterm_name varchar(1024), relation_name varchar(128)); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_variant','transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helitron','helitron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_initiator_methionine','cleaved_initiator_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epoxyqueuosine','epoxyqueuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4atac_snrna','u4atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast','kinetoplast'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_n_terminal','elongated_out_of_frame_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shadow_enhancer','shadow_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered','engineered'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_ii_tata_box','rna_polymerase_ii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_aminomethyl_seven_deazaguanosine','seven_aminomethyl_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_motif','sequence_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity','low_complexity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est_match','est_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_nonamer','v_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_c_cluster','d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_21s','rrna_21s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_factor','bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethyluridine','five_carboxymethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dinucleotide_repeat_microsatellite_feature','dinucleotide_repeat_microsatellite_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_methyladenosine','two_methylthio_n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_mrna','trans_spliced_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_c_transversion','g_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heptamer_of_recombination_feature_of_vertebrate_immune_system_gene','heptamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genotype','so_genotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_region','cloned_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_coding_piece','tmrna_coding_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_6s','rna_6s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element','x_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle','minicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_encoding','grna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endonuclease_spliced_intron','endonuclease_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional_duplication','insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('databank_entry','databank_entry'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine','glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_phenotype','variant_phenotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_cluster','v_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl12_acceptor_site','sl12_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nickel_ion_contact_site','polypeptide_nickel_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_rna_chromosome','circular_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wc_base_pair','wc_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pcr_product','pcr_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3_prime_utr_variant','three_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_three_amino_three_carboxypropyl_uridine','three_three_amino_three_carboxypropyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('site_specific_recombination_target_region','site_specific_recombination_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polycistronic_transcript','gene_with_polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue','rescue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_hypersensitive_site','nuclease_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_gene_variant','upstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_loop','mirna_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_cdna','double_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_post_translational_processing_variant','polypeptide_post_translational_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('2kb_upstream_variant','twokb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_domain_match','supported_by_domain_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylpseudouridine','one_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n_terminal_region','n_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_site','blunt_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_result_region','experimental_result_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine_trna_primary_transcript','methionine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr','utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_terminal_residue','non_terminal_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('member_of_regulon','member_of_regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine_trna_primary_transcript','thr_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_sequence_similarity_data','cds_supported_by_sequence_similarity_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_region','polypeptide_structural_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_gene','trna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_tungsten_ion_contact_site','polypeptide_tungsten_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_six','beta_bulge_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_c_cluster','d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_location','sequence_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_right_left_motif','polypeptide_nest_right_left_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_polypeptides_different_start_and_stop','encodes_overlapping_polypeptides_different_start_and_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_gene','leucoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_rna','y_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_transcript','trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted','inverted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_regulatory_region','splicing_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('branch_site','branch_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_five','beta_bulge_loop_five'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakpoint','chromosome_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_uncertainty','sequence_uncertainty'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyl_n6_threonylcarbamoyladenosine','n6_methyl_n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_with_frameshift','gene_with_mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compositionally_biased_region_of_peptide','compositionally_biased_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_c_cluster','vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna','pirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_hoogsteen_base_pair','reverse_hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophanyl_trna','tryptophanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_primed_cdna_clone','polya_primed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_chromosome','leucoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('status','status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_retrotransposon','ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna','rnase_p_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conjugative_transposon','conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('improved_high_quality_draft','improved_high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_gain','copy_number_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linkage_group','linkage_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_trans_spliced_transcript','gene_with_trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl8_acceptor_site','sl8_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_coil','peptide_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine_trna_primary_transcript','pyrrolysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_c_cluster','v_vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_sequence','phage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_methylation_site','h3k79_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded','recoded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposon_fragment','transposon_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_c_cluster','vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_domain','editing_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyluridine','five_methylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_ii','centromere_dna_element_ii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alteration_attribute','alteration_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon_polymeric_tract','non_ltr_retrotransposon_polymeric_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transversion','transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan','tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recursive_splice_site','recursive_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_fusion','polypeptide_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator_binding_site','insulator_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_polyadenylation_variant','increased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline_trna_primary_transcript','proline_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_fragment','repeat_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blocked_reading_frame','blocked_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_snorna_primary_transcript','rrna_cleavage_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_isopentenyladenosine','n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_arginine','modified_l_arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_motif','polypeptide_conserved_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric','paracentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t3_rna_polymerase_promoter','t3_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_duplication','inversion_derived_bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_acceptor_site','trans_splice_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_2','a_box_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rre_rna','rre_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosyladenosine_phosphate','two_prime_o_riboA_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac_end','pac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extramembrane_polypeptide_region','extramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_change','copy_number_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein','intein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endosomal_localization_signal','endosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('twintron','twintron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_primary_transcript','scrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_prime_o_methyluridine','five_carboxymethylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('somatic_variant','somatic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication','duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_encoding','tmrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_cobalt_ion_contact_site','polypeptide_cobalt_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanked','flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion','inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ctg_start_codon','ctg_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine_trna_primary_transcript','tyrosine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('eukaryotic_terminator','eukaryotic_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_flanked','frt_flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron_region','spliceosomal_intron_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_region_of_exon','coding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_cdna_insert','cloned_cdna_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcription_rate_variant','decreased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_c_cluster','v_vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna_gene','rnase_p_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated','translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidyl_trna','histidyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sonicate_fragment','sonicate_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_recoded_mrna','gene_with_recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyluridine','two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cosmid','cosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_rna_interference','silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_missense_codon','non_conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna','snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript','mature_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridylation_guide_snorna','pseudouridylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_gene','c_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_transcript','processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed_gene','floxed_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spot_42_rna','spot_42_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_clone','cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site','cryptic_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_gene_segment','pseudogenic_gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr','three_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_ii_intron','group_ii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna_gene','rnase_mrp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_alteration','structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna_oligo','pna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_sequence','insertion_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('junction','junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous','paralogous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna','tna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_thiouridine','five_isopentenylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_tandem_repeat','nested_tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift','minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_three_prime_splice_site','non_canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_non_canonical_start_codon','gene_with_non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_rrna','pseudogenic_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_turn','serine_threonine_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene','j_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_trimethylation_site','h3k27_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_primary_transcript','strna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_eliminated_sequence','internal_eliminated_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded_gene','allelically_excluded_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('qtl','qtl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_est','three_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bred_motif','bred_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse','reverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_encoding','mirna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_2_prime_o_trimethylguanosine','n2_n2_2_prime_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_function_variant','translational_product_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternate_transcription_start_sites','encodes_alternate_transcription_start_sites'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array','gene_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetranucleotide_repeat_microsatellite_feature','tetranuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_aminomethyl_two_thiouridine','five_aminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_primary_transcript','monocistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snv','snv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct','direct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_genetic_element','mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_ligand_contact','polypeptide_ligand_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biomaterial_region','biomaterial_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_flanking_region','transposable_element_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symmetric_rna_internal_loop','symmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_1_frameshift','mrna_with_plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_regulated','transcriptionally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_intron','five_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_feature','vertebrate_immune_system_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine_methyl_ester','five_carboxyhydroxymethyl_uridine_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_transposition','chromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_gene','proplastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_trna_primary_transcript','serine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attp_site','attp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense','antisense'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat_element','terminal_inverted_repeat_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coiled_coil','coiled_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_cluster','v_vdj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_by_a_to_i_substitution','edited_transcript_by_a_to_i_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_primary_transcript','protein_coding_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mite','mite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site_variant','cryptic_splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion','insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('secis_element','secis_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle','maxicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss','tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pedigree_specific_variant','pedigree_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine','cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribothymidine','ribothymidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_adjacent_residues','non_adjacent_residues'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_modification','histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_ribosome_entry_site','internal_ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('outron','outron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_repeat','polypeptide_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_start','clone_insert_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attr_site','attr_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv3_motif','dmv3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_mrna','capped_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_rearrangement_feature','sequence_rearrangement_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_chromosome','apicoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_two','beta_turn_type_six_a_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated','invalidated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine','valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated_gene','translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_insertion','amino_acid_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_targeting_sequence','promoter_targeting_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polinton','polinton'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_tag','engineered_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_coding_exon_variant','non_coding_exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylcytidine','five_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl5_acceptor_site','sl5_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated','positively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridine','pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amplification_origin','amplification_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_insertional_duplication','unorient_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_constitutive','transcriptionally_constitutive'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extrachromosomal_mobile_genetic_element','extrachromosomal_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_origin','variant_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_region','utr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna','mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine','tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr1_motif','inr1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2b_ubiquitination_site','h2b_ubiquitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_acetyladenosine','n6_acetyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_splice_site','cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed','floxed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_two','beta_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_variant','utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_terminal_region','c_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_regulatory_region','transcription_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_leucine','modified_l_leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr_component','five_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acylation_region','histone_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_c_cluster','vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_part','chromosome_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptional_cis_regulatory_region','transcriptional_cis_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanyl_trna','phenylalanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_site','insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gc_rich_promoter_region','gc_rich_promoter_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_est_set','overlapping_est_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_two','asx_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon_loop','anticodon_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv5_motif','dmv5_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl1_acceptor_site','sl1_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_region','cds_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region_variant','regulatory_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_dimethylation_site','h3k9_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_gained','stop_gained'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna_gene','telomerase_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_c_cluster','v_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_insert','engineered_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_inverted_gene','recombinationally_inverted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microarray_oligo','microarray_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_array_member','cassette_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift_variant','plus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_snrna','u12_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_est_or_cdna','supported_by_est_or_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_10_signal','minus_10_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_end','clone_insert_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr_motif','inr_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_stem_loop_structure','three_prime_stem_loop_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rflp_fragment','rflp_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_rna_polymerase_promoter','phage_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_transition','pyrimidine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrinsically_unstructured_polypeptide_region','intrinsically_unstructured_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_2_prime_o_dimethylguanosine','n2_2_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_loss','exon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeal_intron','archaeal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna','lna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_junction','exon_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t7_rna_polymerase_promoter','t7_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_interchromosomal_transposition','invert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('episome','episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_insertional_duplication','uninvert_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free','free'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_difference','sequence_difference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k5_acylation_site','h4k5_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_c_cluster','v_d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_conflict','sequence_conflict'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nmd_transcript_variant','nmd_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_clone','tiling_path_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iii_intron','group_iii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_glycine','modified_glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_alteration','sequence_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyploid','polyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mathematically_defined_repeat','mathematically_defined_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_modification','gene_silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_cluster','v_vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine_trna_primary_transcript','isoleucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_small_subunit_primary_transcript','rrna_small_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_component','ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_framshift','plus_2_framshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_structure_variant','translational_product_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid_trna_primary_transcript','glutamic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_rearranged_at_dna_level','gene_rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript','edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_partial_processing','invalidated_by_partial_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_stability_variant','increased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequencing_primer','sequencing_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_for_gpi_anchor_region','cleaved_for_gpi_anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_cysteine','modified_l_cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr','five_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_recognition_site','restriction_enzyme_recognition_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_site','frt_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat','terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_i','centromere_dna_element_i'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transition','transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_junction','deletion_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_one','beta_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosylguanosine_phosphate','two_prime_o_ribosylguanosine_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyl_two_prime_o_methyluridine','five_cm_2_prime_o_methU'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_transcribed_spacer_region','internal_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic','dicistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_sequence_similarity','supported_by_sequence_similarity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_primer','reverse_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_three_prime_ltr_region','u3_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine_trna_primary_transcript','glutamine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_promoter','rnapol_ii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping','overlapping'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_beta_motif','alpha_beta_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_transposable_element','engineered_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward_primer','forward_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attctn_site','attctn_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_recombination_signal_sequence','five_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6_snrna','u6_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_gene','recombinationally_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_threonylcarbamoyladenosine','n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyluridine','five_carbamoylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_fragment','cds_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genome','genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_translational_product_level','increased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_level_variant','translational_product_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter','promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_gene','protein_coding_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_snrna','u5_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wybutosine','wybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylwyosine','methylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('large_subunit_rrna','large_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomally_aberrant_genome','chromosomally_aberrant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_2_prime_o_dimethylcytidine','n4_2_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition','c_to_t_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bidirectional_promoter','bidirectional_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated_cdna_clone','validated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('k_turn_rna_motif','k_turn_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_fragment','transcribed_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ust','five_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr_intron','three_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrogene','retrogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_to_purine_transversion','pyrimidine_to_purine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sine_element','sine_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_rst','five_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_intron','utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_transposition','interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_sequence_secondary_structure','rna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_in_transcript','complex_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element','engineered_foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_rna_viral_sequence','ds_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fosmid','fosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_substitution','complex_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated','validated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_snrna','u2_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication_attribute','duplication_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('caat_signal','caat_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_cluster','c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_region','consensus_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_spacer','vertebrate_immune_system_gene_recombination_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_restriction_enzyme_junction','three_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_trap_construct','gene_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_aptamer','rna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_induced','transcriptionally_induced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal','intrachromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_localization_signal','nuclear_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_region','rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site_part','inversion_site_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_frameshift variant','plus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('origin_of_replication','origin_of_replication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('standard_draft','standard_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_dimethylation_site','h3k79_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_internal_loop','rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ultracontig','ultracontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptidyl','peptidyl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_region','polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_region','epigenetically_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_insertion','transgenic_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_antiguide','mirna_antiguide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rearranged_at_dna_level','rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_variant','intergenic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_spacer','v_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strand_attribute','strand_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_lost','stop_lost'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced','alternatively_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formyl_two_prime_o_methylcytidine','five_formyl_two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_location','plasmid_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_bp_start_codon','four_bp_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcription_rate_variant','increased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged','recombinationally_rearranged'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_3d_structural_variant','complex_3d_structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chimeric_cdna_clone','chimeric_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna_primary_transcript','tasirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_transcript','gene_with_dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr_component','three_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retron','retron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autopolyploid','autopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine','phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translation_regulatory_region','translation_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transit_peptide','transit_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_deletion','amino_acid_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_28s','rrna_28s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylinosine','one_two_prime_o_dimethylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine','threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_minor_rna_motif','a_minor_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_cluster','j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce','dce'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quantitative_variant','quantitative_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysosomal_localization_signal','lysosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_cluster','d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_arm','chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast_gene','kinetoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('line_element','line_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('solo_ltr','solo_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('external_transcribed_spacer_region','external_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_transcribed_region','non_transcribed_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_stem','mirna_stem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_c_cluster','dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hyperploid','hyperploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic','cryptic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_acetylation_site','h3k9_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_helix','alpha_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion','fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_cluster','vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isowyosine','isowyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric_inversion','paracentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homing_endonuclease_binding_site','homing_endonuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna_oligo','tna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_gene','mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_fragment','restriction_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_pair','base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_antiparallel','inside_intron_antiparallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_binding_site','dna_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_cytidine','modified_cytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydrophobic_region_of_peptide','hydrophobic_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_primary_transcript','polycistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_proline','modified_l_proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_feature_set','overlapping_feature_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_two','asx_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_duplication','interchromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_loss','inframe_codon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('substitution','substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine','isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('functional_variant','functional_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_recoding_site','three_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_stability_variant','transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_upstream_variant','fivekb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_of_type_2_rnapol_iii_promoter','terminator_of_type_2_rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine_trna_primary_transcript','glycine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_variant','intron_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_outer_repeat_region','regional_centromere_outer_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replication_regulatory_region','replication_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mating_type_region','mating_type_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_heptamer','v_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dispersed_repeat','dispersed_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer','primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_domain','polypeptide_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type','wild_type'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion_gene','fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_function_variant','transcript_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_member_region','gene_member_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginyl_trna','arginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compensatory_transcript_secondary_structure_variant','compensatory_transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_base_feature','methylated_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_intrachromosomal_transposition','uninvert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_gene','scrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_18s','rrna_18s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_1','rnapol_iii_promoter_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_mutation','point_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudoknot','pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_quartet','g_quartet'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop','schellmann_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_selenocysteine','modified_l_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna','pna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon','three_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_gene','endogenous_retroviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_segment','vertebrate_immunoglobulin_t_cell_receptor_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_translational_bypass','mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_region','engineered_foreign_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_encoding','snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_est','five_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foldback_element','foldback_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_encoding','srp_rna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_c_cluster','d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_c_cluster','dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_ubiqitination_site','histone_ubiqitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_structural_alteration','complex_structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_encoding','rrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_codon_redefinition','mrna_recoded_by_codon_redefinition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyluridine','five_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_sequence','polya_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metabolic_island','metabolic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous','homologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('immature_peptide_region','immature_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2bk5_monomethylation_site','h2bk5_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_attribute','sequence_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sirna','sirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dart_marker','dart_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_motif','nucleotide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translationally_frameshifted','plus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_intron','trna_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_noncoding_exon','five_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_motif','dna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_strand','beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_oligo','ds_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyladenosine','one_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oxys_rna','oxys_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_motif','asx_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxyuridine','five_hydroxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_exon','coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translational_frameshift','plus_1_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formylcytidine','five_formylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_dimethylation_site','h3k27_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliced_leader_rna','spliced_leader_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_chromosome','mitochondrial_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fragment','gene_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_2prirme_o_trimethylguanosine','n2_7_2prirme_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift','frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide_cleavage_site','propeptide_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyldihydrouridine','five_methyldihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid','amino_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_breakpoint','translocation_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5_8s','rrna_5_8s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helix_turn_helix','helix_turn_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('simple_sequence_length_variation','simple_sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine','methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_loss_of_function_variant','polypeptide_loss_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_gene','transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('whole_genome_sequence_status','whole_genome_sequence_status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_island','genomic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_segment','gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_gene','snrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_region','engineered_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('common_variant','common_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptogene','cryptogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_noncoding_region','three_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_rna_interference','gene_silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_interchromosomal_transposition','d_interchr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_variant_site','natural_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly','assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('major_tss','major_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna','trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides','encodes_overlapping_peptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_conserved_region','nc_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('locus_control_region','locus_control_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna_oligo','s_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_chromosome','dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_b','beta_turn_type_six_b'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loss_of_heterozygosity','loss_of_heterozygosity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_gene','engineered_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wobble_base_pair','wobble_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_amino_acid_feature','modified_amino_acid_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_c_transition','t_to_c_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocaton_attribute','translocaton_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_sequence','apicoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_codon_variant','terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irlinv_site','irlinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_sequence','synthetic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_1_polypeptide','encodes_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iia_intron','group_iia_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomere','telomere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_intron','interior_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_mrna','edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_three','catmat_right_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_duplication','tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_gene','tmrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_region','pre_edited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_hydroxynorvalylcarbamoyladenosine','n6_hydroxynorvalylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_chromosome','nucleomorphic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragmentary','fragmentary'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single','single'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('binding_site','binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanine','seven_methylguanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('target_site_duplication','target_site_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_gene','vdj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_nucleic_acid','bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_localization_signal','peptide_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_four','catmat_right_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_acylation_site','h3k27_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome','compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_end','coding_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gap','gap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligand_binding_site','ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_aug_codon','upstream_aug_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_transcript','pseudogenic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('satellite_dna','satellite_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency_plus_duplication','assortment_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element','transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_sequence','endogenous_retroviral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microsatellite','microsatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_different_polypeptides_different_stop','encodes_different_polypeptides_different_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript','primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_mrna','consensus_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_peptide_loop','membrane_peptide_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign','so_foreign'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_independent_bacterial_terminator','rho_independent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u_box','u_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_deacetylation','gene_silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_c_cluster','vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cpg_island','cpg_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype','haplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylinosine','two_prime_o_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna','dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_rna_chromosome','circular_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_protein_region','mature_protein_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('b_box','b_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_zinc_ion_contact_site','polypeptide_zinc_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray_member','gene_subarray_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette','gene_cassette'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oric','oric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_breakpoint','deletion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_attribute','insertion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_2_frameshift','mrna_with_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chip_seq_region','chip_seq_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_one','asx_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_cluster','transcribed_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosyl_trna','tyrosyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous','orthologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna','s_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_three_prime_splice_site','canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_exon','noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lethal_variant','lethal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minor_tss','minor_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethylcytidine','five_two_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_trimethylation_site','h3k36_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_chromosome','macronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_translocation','deficient_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read_pair','read_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_with_translational_frameshift','transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('finished_genome','finished_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_3','rnapol_iii_promoter_type_3'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_transposon','dna_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orf','orf'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('right_handed_peptide_helix','right_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_left_right_motif','polypeptide_nest_left_right_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topology_attribute','topology_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirtron','mirtron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_motif','polypeptide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl9_acceptor_site','sl9_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_sequence','proplastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated_gene','negatively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retinoic_acid_responsive_element','retinoic_acid_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_encoding','c_d_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_assembly','sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_gene','chromoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dcaps_primer','dcaps_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_clip','five_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path','golden_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_acceptor_variant','splice_acceptor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine','alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_peptide_region','cleaved_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_cluster','v_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_region','pseudogenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_codon_variant','terminator_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna','methylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_c_cluster','v_vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_start_codon','non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_recoded_by_translational_bypass','gene_with_mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_turn_motif','polypeptide_turn_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autocatalytically_spliced_intron','autocatalytically_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile','mobile'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem','tandem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron','intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clip','clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dye_terminator_read','dye_terminator_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv4_motif','dmv4_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('au_rich_element','au_rich_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_breakpoint','inversion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_siii','dce_siii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_recoding_site','five_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_protein_coding','non_protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_intron','mobile_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment','vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_one','st_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna','rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_parallel','inside_intron_parallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron','spliceosomal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phagemid','phagemid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_block','editing_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragment_assembly','fragment_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_acceptor_piece','tmrna_acceptor_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six','beta_turn_type_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_rst','three_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine_trna_primary_transcript','cysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_gene','post_translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_repressed','transcriptionally_repressed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crm','crm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cointegrated_plasmid','cointegrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequencing_information','polypeptide_sequencing_information'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_spacer','three_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_fragment','tiling_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural','so_natural'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pi_helix','pi_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_base_call_error','possible_base_call_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_truncation','polypeptide_truncation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k14_acetylation_site','h3k14_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('adaptive_island','adaptive_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid','uridine_five_oxyacetic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl7_acceptor_site','sl7_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_translational_frameshift','plus_2_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_retained_variant','stop_retained_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous_region','homologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('500b_downstream_variant','fivehundred_b_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_utr','internal_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_cytoplasmic_polypeptide_region','non_cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature','experimental_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_chromosome','nuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar','exemplar'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_core_promoter','rnapol_ii_core_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_methylation_site','h3k9_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine_trna_primary_transcript','alanine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_variation','assortment_derived_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_dimethylguanosine','n2_n2_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_hook_turn','rna_hook_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_spacer_region','transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_gene','plasmid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna','u14_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('galactosyl_queuosine','galactosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_gene','cyanelle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type_rescue_gene','wild_type_rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_intron','u12_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aptamer','aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_mrna','recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_transposon','nested_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site_variant','tf_binding_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_sequence','macronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust','ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine','selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_c_terminal','elongated_out_of_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_mrna','gene_with_dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match_part','match_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_sequence','nucleomorphic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_gene','apicoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulon','regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_vector','plasmid_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tryptophan','modified_l_tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_chromosome_arm','free_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_primary_transcript','srp_rna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn','asx_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_binding_site','anchor_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript','rrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reading_frame','reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k23_acylation site','h3k23_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_variant','maternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dhu_loop','dhu_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetylcytidine','n4_acetylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature_attribute','experimental_feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_gene','silenced_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_genomic_insert','cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_gain','intron_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_sequence_secondary_structure','dna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_match','cdna_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_flanking_region','five_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysyl_trna','pyrrolysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_cis_hydroxyisopentenyl_adenosine','two_methylthio_n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_component','repeat_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyl_three_three_amino_three_carboxypropyl_pseudouridine','one_methyl_3_3_amino_three_carboxypropyl_pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rpra_rna','rpra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_sensitive_site','nuclease_sensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_amino_acid_substitution','conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_noncoding_region','five_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter','rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan_trna_primary_transcript','try_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncontiguous_finished','noncontiguous_finished'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('region','region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site','tf_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attl_site','attl_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_plasmid','natural_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upd','upd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_missense_codon','conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_dimethyladenosine','n6_n6_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('laevosynaptic_chromosome','laevosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_structural_element','chromosomal_structural_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_array','gene_cassette_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_gene_cluster','vertebrate_immunoglobulin_t_cell_receptor_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_five_prime_splice_site','canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_protein','bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts_map','sts_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnazyme','dnazyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silent_mutation','silent_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_cluster','v_d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distal_promoter_element','distal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_duplication','bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydroxywybutosine','hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dihydrouridine','dihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_coding_region','five_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_one','beta_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_trimethylation','h3k4_trimethylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_codon','recoded_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted','predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('resolution_site','resolution_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_cyano_seven_deazaguanosine','seven_cyano_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_associated_variant','disease_associated_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_switch','conformational_switch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulated','regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_repeat','inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_a_transversion','t_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attc_site','attc_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methyladenosine','two_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cross_genome_match','cross_genome_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_repeat','tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_loss','copy_number_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_primary_transcript','antisense_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_collection','sequence_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polyadenylated_mrna','gene_with_polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_i_promoter','rnapol_i_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methyluridine','three_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('start_codon','start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposon','retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_c_terminal','elongated_in_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene','v_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_dna','chloroplast_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negative_sense_ssrna_viral_sequence','negative_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_binding_site','primer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_box','c_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid','plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biological_region','biological_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_a_transition','g_to_a_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_five_prime_splice_site','non_canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_primary_transcript','c_d_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_region','trna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_cis_hydroxyisopentenyl_adenosine','n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_sequence','chloroplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_frequency','variant_frequency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_region','exon_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_five_prime_ltr_region','r_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_c_cluster','v_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_three_prime_ltr_region','r_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna','snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylinosine','one_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_gain','inframe_codon_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene_recombination_feature','j_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_motif','polypeptide_structural_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved_region','conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl3_acceptor_site','sl3_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('remark','remark'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fixed_variant','fixed_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_dna_contact','polypeptide_dna_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon','codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_23s','rrna_23s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_gain_of_function_variant','polypeptide_gain_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna','mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycyl_trna','glycyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_sequence','cyanelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_independently_known','cds_independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator','insulator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positive_sense_ssrna_viral_sequence','positive_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sticky_end_restriction_enzyme_cleavage_site','sticky_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_match','expressed_sequence_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_assembly_error','possible_assembly_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_snorna','u3_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_manganese_ion_contact_site','polypeptide_manganese_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k16_acylation_site','h4k16_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_t_transversion','g_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature_of_rearranged_gene','recombination_feature_of_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_coding_region','three_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_primary_transcript','tmrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_cdna','single_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_determined','experimentally_determined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_exon','pseudogenic_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_intron','u2_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome','chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternately_spliced_transcripts','encodes_alternately_spliced_transcripts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aberrant_processed_transcript','aberrant_processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_of_translational_product_variant','complex_change_of_translational_product_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna','gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dsra_rna','dsra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_domain','intron_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_predicted','cds_predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_asparagine','modified_l_asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_variant','inframe_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_nonamer','five_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl2_acceptor_site','sl2_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_localization_variant','polypeptide_localization_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_si','dce_si'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_primary_transcript','snrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation','translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_methylation_site','h3k27_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_phenylalanine','modified_l_phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna','lincrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_valine','modified_l_valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac','yac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('signal_peptide','signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_ltr_region','r_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_gene','srp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_n_terminal','elongated_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_hotspot','recombination_hotspot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_c_cluster','v_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('viral_sequence','viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_terminal_inverted_repeat','five_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_thiouridine','five_mcm_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited','edited'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('breu_motif','breu_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_start','coding_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_monomethylation_site','h3k9_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr','three_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe1_motif','dpe1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tyrosine','modified_l_tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_c_cluster','v_d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_methylation','silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_inversion','deficient_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_level_variant','decreased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiouridine','two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylation_variant','polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_iii_tata_box','rna_polymerase_iii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thio_two_prime_o_methyluridine','two_thio_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k18_acetylation_site','h3k18_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_sequence','leucoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds','cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_signal_sequence','polya_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_sequence','micronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamyl_trna','glutamyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_monomethylation_site','h3k27_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift_variant','minus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_gene','strna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted_gene','paternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_chromosome','rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm3_motif','ndm3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u1_snrna','u1_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxymethylcytidine','five_hydroxymethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature','recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_disjoint_polypeptides','encodes_disjoint_polypeptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated','post_translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_fusion_gene','engineered_fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_recombination_signal_sequence','three_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate','intermediate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_calcium_ion_contact_site','polypeptide_calcium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic_region','syntenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_collection','variant_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_donor','cryptic_splice_donor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_error_correction','assembly_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sugar_edge_base_pair','sugar_edge_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_gene','engineered_foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_monomethylation_site','h3k4_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetyl_2_prime_o_methylcytidine','n4_acetyl_2_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_by_ab_initio_computation','predicted_by_ab_initio_computation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_secondary_structure','polypeptide_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna_gene','ncrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_junction_loop','rna_junction_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype_block','haplotype_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oriv','oriv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_collection','peptide_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ambisense_ssrna_viral_sequence','ambisense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_oligo','morpholino_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere','centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_gene','epigenetically_modified_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_inversion','chromosomal_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_35_signal','minus_35_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_two_prime_o_dimethyluridine','three_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_thiouridine','four_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_end_site','transcription_end_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna_gene','pirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_mirna','pre_mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteinyl_trna','cysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_three','catmat_left_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_acceptor','cryptic_splice_acceptor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_seven','schellmann_loop_seven'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_c_cluster','v_vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_insertion_site','transposable_element_insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_element','translocation_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript_region','mirna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan_cds','orphan_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_mrna','monocistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_transposable_element','natural_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path_fragment','golden_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lipoprotein_signal_peptide','lipoprotein_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine','arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_rna_chromosome','linear_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k8_acylation site','h4k8_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_large_subunit_primary_transcript','rrna_large_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irrinv_site','irrinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_sequence','plastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_call_error_correction','base_call_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_plasmid','integrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_methionine','modified_l_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_rna_chromosome','linear_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_sequence','chromoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proximal_promoter_element','proximal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_read','contig_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_trap_construct','promoter_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_selenocysteine','stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanosine','seven_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn','gamma_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna','tmrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionyl_trna','methionyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synonymous_codon','synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna','cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl4_acceptor_site','sl4_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_binding_site','nuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid_methyl_ester','uridine_five_oxyacetic_acid_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_race_clone','three_prime_race_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_dna_chromosome','circular_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus','consensus'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated_gene','positively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss_region','tss_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_histidine','modified_l_histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unitary_pseudogene','unitary_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_metal_contact','polypeptide_metal_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integron','integron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_loop','d_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decayed_exon','decayed_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_signal_sequence','recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_inosine','modified_inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_three_prime_overlap','three_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_cluster','v_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_five_prime_overlap','three_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_regulatory_region','recombination_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop','beta_bulge_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_cleavage_junction','restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_junction','blunt_end_restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_region','intergenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv2_motif','dmv2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_mutation','intrachromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_rna','antisense_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_feature','sequence_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_glycinylcarbamoyladenosine','n6_glycinylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_classic','gamma_turn_classic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_cis_splice_site','three_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rapd','rapd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_ring_chromosome','inverted_ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cca_tail','cca_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_dna_chromosome','linear_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_five_prime_ltr_region','u5_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bruno_response_element','bruno_response_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_g_transversion','t_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_a_transversion','c_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronucleus_destined_segment','macronucleus_destined_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distant_three_prime_recoding_signal','distant_three_prime_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_mrna','pre_edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('p_element','p_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac','pac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fusion','gene_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base','base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_redefined','codon_redefined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_mrna','polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_variant','codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_prime_o_methyluridine','five_methoxycarbonylmethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match','match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_read_through','gene_with_stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparaginyl_trna','asparaginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonyl_trna','threonyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_five_prime_ltr_region','u3_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr','five_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_gene','vj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_dependent_bacterial_terminator','rho_dependent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_methylguanosine','n2_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_flanking_region','three_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomically_contaminated_cdna_clone','genomically_contaminated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_guide_sequence','internal_guide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_target_site','mirna_target_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_three_prime_ltr_region','u5_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('undermodified_hydroxywybutosine','undermodified_hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('introgressed_chromosome_region','introgressed_chromosome_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_frameshifted','translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced','trans_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna_primary_transcript','methylation_guide_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine','leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_deletion','chromosomal_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_uridine','five_isopentenylaminomethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon','stop_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_threonyl_carbamoyladenosine','two_methylthio_n6_threonyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_polyadenylation_variant','decreased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biochemical_region_of_peptide','biochemical_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interband','interband'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_constraint_sequence','dna_constraint_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert','clone_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snp','snp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_chromosome','chromoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_25s','rrna_25s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tata_box','tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_gene','plastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_one','asx_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_uridine','modified_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_sii','dce_sii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intramembrane_polypeptide_region','intramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysyl_trna','lysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rr_tract','rr_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript_region','rrna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k20_monomethylation_site','h4k20_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_dna_viral_sequence','ds_dna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced_transcript','alternatively_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_copper_ion_contact_site','polypeptide_copper_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_encoding','scrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_duplication','chromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone','clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_isoleucine','modified_l_isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray','gene_subarray'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hetero_compound_chromosome','hetero_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_transcript','dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_ligand_binding_site','inactive_ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_methylation','silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl6_acceptor_site','sl6_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_loop','t_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('targeting_vector','targeting_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiocytidine','two_thiocytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_serine','modified_l_serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna','srp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_repeat_recoding_signal','three_prime_repeat_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rate_of_transcription_variant','rate_of_transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylguanosine','two_prime_o_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_binding_motif','polypeptide_binding_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_vertebrate_immune_system_gene','recombinationally_rearranged_vertebrate_immune_system_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box','a_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_variant','splicing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylguanosine','one_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamine','modified_l_glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant','sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_length_variation','sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_encoding','strna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift','plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topologically_defined_region','topologically_defined_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_cds','edited_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_modification','gene_silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('e_box_motif','e_box_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_uniparental_disomy','paternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_subunit_rrna','small_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnasei_hypersensitive_site','dnasei_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_c_cluster','v_d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome_arm','compound_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('score','score'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('feature_attribute','feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_match','protein_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('downstream_gene_variant','downstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl10_accceptor_site','sl10_accceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_variation','chromosome_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_motif','serine_threonine_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_1','a_box_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded','allelically_excluded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_aneuploid','assortment_derived_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rare_variant','rare_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_prime_o_methyluridine','five_isopentenylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_central_core','regional_centromere_central_core'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna_oligo','gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_transcript_variant','nc_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_variation','copy_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced','silenced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylcytidine','three_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dexstrosynaptic_chromosome','dexstrosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_insertional_duplication','inverted_insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_mini_gene','rescue_mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_four','catmat_left_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternate_sequence_site','alternate_sequence_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_iron_ion_contact_site','polypeptide_iron_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition_at_pcpg_site','c_to_t_transition_at_pcpg_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_molybdenum_ion_contact_site','polypeptide_molybdenum_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine_trna_primary_transcript','phe_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_translational_product_level','decreased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_primary_transcript','h_aca_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna','r_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_sequence_variant','coding_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_partial_loss_of_function','polypeptide_partial_loss_of_function'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_restriction_enzyme_junction','five_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_transposition','intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_a','methylated_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_16s','rrna_16s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_causing_variant','disease_causing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_methylcytidine','n4_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('riboswitch','riboswitch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplicated_pseudogene','duplicated_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_duplication','assortment_derived_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_regulatory_element','chromosomal_regulatory_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_five_prime_overlap','five_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_function_variant','polypeptide_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozymic','ribozymic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_deficiency','inversion_derived_bipartite_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_contamination','invalidated_by_genomic_contamination'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_genome','variant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_cluster','vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_number_variation','chromosome_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_attribute','gene_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uag_stop_codon_signal','uag_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_match','nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_mirna_variant','mature_mirna_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_two','st_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified','epigenetically_modified'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_duplication','inversion_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_selenouridine','five_methylaminomethyl_two_selenouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid_trna_primary_transcript','aspartic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_mt_pseudogene','nuclear_mt_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exonic_splice_enhancer','exonic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4_snrna','u4_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('csrb_rsmb_rna','csrb_rsmb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_1_intron_homing_endonuclease_target_region','group_1_intron_homing_endonuclease_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crispr','crispr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_gene','snorna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_junction','trans_splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_three_prime_quadruplet_recoding_signal','flanking_three_prime_quadruplet_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_cluster','v_vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_pseudogene','cassette_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('incomplete_terminal_codon_variant','incomplete_terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_modification','silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_gene','proviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine','five_carboxyhydroxymethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mt_gene','mt_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_rna_chromosome','single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_stimulatory_region','recoding_stimulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyluridine','five_taurinomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_threonine','modified_l_threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_cluster','v_d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_oligo','synthetic_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_to_pyrimidine_transversion','purine_to_pyrimidine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_variant','editing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antiparallel_beta_strand','antiparallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('central_hydrophobic_region_of_signal_peptide','central_hydrophobic_region_of_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_mobile_genetic_element','integrated_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('parallel_beta_strand','parallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_cluster','v_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dre_motif','dre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon','non_ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna_oligo','r_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autoregulated','autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_lysine','modified_l_lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_end','bac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine','pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_quality_draft','high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine','lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide','elongated_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unique_variant','unique_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_protein_contact','protein_protein_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_attribute','inversion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_binding_site','nucleotide_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site','splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_synonymous_codon','non_synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_downstream_variant','fivekb_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_translocation','chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epitope','epitope'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allele','allele'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_n4_2_prime_o_trimethylcytidine','n4_n4_2_prime_o_trimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_ltr_region','u5_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paired_end_fragment','paired_end_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_gene','rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_transposable_element','transgenic_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_region','polypeptide_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts','sts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_c_transversion','a_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_ii_rna','class_ii_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nonamer_of_recombination_feature_of_vertebrate_immune_system_gene','nonamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unedited_region','unedited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lambda_vector','lambda_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene','gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanyl_trna','alanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_substitution','amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('virtual_sequence','virtual_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iib_intron','group_iib_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposed','retrotransposed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_2_frameshift','mrna_with_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymer_attribute','polymer_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autosynaptic_chromosome','autosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_helix','peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_processed_cdna_clone','partially_processed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst_match','rst_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted','paternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_gene','predicted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element_combinatorial_repeat','x_element_combinatorial_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('robertsonian_fusion','robertsonian_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylpseudouridine','two_prime_o_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric_inversion','pericentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartyl_trna','aspartyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna','strna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_intron','three_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear','linear'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_nonamer','j_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_t_transversion','a_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('idna','idna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_7_trimethylguanosine','n2_n2_7_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_chromosomal_mutation','complex_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_aneuploid','inversion_derived_deficiency_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_methylation_site','h3k4_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asymmetric_rna_internal_loop','asymmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion','deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_monomethylation_site','h3k79_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyclic_translocation','cyclic_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ars','ars'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutaminyl_trna','glutaminyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allopolyploid','allopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replicon','replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylcytidine','two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere','regional_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_one','st_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous_region','paralogous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript_region','mature_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_frameshift','mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reference_genome','reference_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_interchromosomal_transposition','unoriented_interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_cluster','d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle_gene','maxicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_two','st_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_encoding','snrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('annotation_directed_improved_draft','annotation_directed_improved_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_spacer','five_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read','read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine_trna_primary_transcript','arg_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo_u_tail','oligo_u_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_pseudoknot','recoding_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_thiouridine','five_mam_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic','monocistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3d_polypeptide_structure_variant','threed_polypeptide_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transmembrane_polypeptide_region','transmembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_processing_variant','transcript_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vector_replicon','vector_replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_uniparental_disomy','maternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrosequenced_read','pyrosequenced_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site_variant','splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_magnesium_ion_contact_site','polypeptide_magnesium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_transcript','polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_site','polya_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_variation_attribute','chromosomal_variation_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_duplication','free_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_structure_variation','chromosome_structure_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_rna_base_feature','modified_rna_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutated_variant_site','mutated_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gaga_motif','gaga_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromeric_repeat','centromeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_gene','rrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_mutation','interchromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prophage','prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic','syntenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_repetitive_element','engineered_foreign_repetitive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translated_nucleotide_match','translated_nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_variant','exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna','h_aca_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vault_rna','vault_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan','orphan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_dna_chromosome','linear_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomeric_repeat','telomeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_greater_than_1_polypeptide','encodes_greater_than_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('atti_site','atti_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_start_codon_cug','gene_with_start_codon_cug'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_deacetylation','silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reagent','reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_fission','chromosome_fission'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ct_gene','ct_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_primary_transcript','capped_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylinosine','methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_spacer','j_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine','glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_guanosine','modified_guanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_dimethylguanosine','n2_7_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_trimethylation_site','h3k79_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_heptamer','three_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_cdna_clone','invalidated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator','terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stem_loop','stem_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr_intron','five_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_intrachromosomal_transposition','unoriented_intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_band','chromosome_band'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_exon_donor_rna','mini_exon_donor_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid','aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyl_2_thiouridine','five_methyl_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_methylation','gene_silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element_gene','engineered_foreign_transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_pseudogene','processed_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supercontig','supercontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_encoding','trna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal_chromosomal_translocation','reciprocal_chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna','tasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hoogsteen_base_pair','hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_inner_repeat_region','regional_centromere_inner_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac_end','yac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_transition','purine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna','c_d_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_primary_transcript','snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_cluster','v_vj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_regulatory_region','intronic_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_ltr_region','u3_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attenuator','attenuator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_noncoding_exon','three_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna_primary_transcript','u14_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene_recombination_feature','d_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mte','mte'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gcvb_rna','gcvb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst','rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operator','operator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ring_chromosome','ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm2_motif','ndm2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_dimethylation_site','h3k4_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine_trna_primary_transcript','selenocysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_feature','edited_transcript_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_pyrrolysine','stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homo_compound_chromosome','homo_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_gene','foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_demethylwyosine','four_demethylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna','guide_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylpseudouridine','three_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_aneuploid_chromosome','inversion_derived_aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_stability_variant','decreased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna_gene','lincrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('specific_recombination_site','specific_recombination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inosine','inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_transposable_element','foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene','d_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_inversion','bipartite_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_plasmid','engineered_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group_regulatory_region','gene_group_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vd_gene','vd_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region','regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl11_acceptor_site','sl11_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna_region','guide_rna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_base','modified_base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_c_terminal','elongated_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_ten_helix','three_ten_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_n_terminal_elongation','elongated_in_frame_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sarcin_like_rna_motif','sarcin_like_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_translationally_frameshifted','minus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_alanine','modified_l_alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_cum_translocation','inversion_cum_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tag','tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_interchromosomal_transposition','uninvert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_gene','cryptic_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric','pericentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic','transgenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_clone','genomic_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakage_sequence','chromosome_breakage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_cluster','d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_one','beta_turn_type_six_a_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribosome_entry_site','ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('left_handed_peptide_helix','left_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_aptamer','dna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('i_motif','i_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_intrachromosomal_transposition','d_intrachr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_dna_chromosome','single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_c','methylated_c'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_end','clone_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligation_based_read','ligation_based_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_assembly','expressed_sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethyluridine','five_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine_trna_primary_transcript','histidine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous_region','orthologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine_trna_primary_transcript','valine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon_member','operon_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('missense_codon','missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma54','bacterial_rnapol_promoter_sigma54'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group','gene_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_regulatory_ncrna','small_regulatory_ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_duplication','intrachromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_amino_acid_substitution','non_conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uaa_stop_codon_signal','uaa_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_methylation_site','h3k36_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_variant','transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift','minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('organelle_sequence','organelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('initiator_codon_change','initiator_codon_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_prophage','cryptic_prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micf_rna','micf_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_tandem_duplication','direct_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved','conserved'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna','telomerase_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6atac_snrna','u6atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attb_site','attb_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array_member','gene_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated_mrna','polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symbiosis_island','symbiosis_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_variant','polymorphic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_junction','splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fingerprint_map','fingerprint_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_strand_restriction_enzyme_cleavage_site','single_strand_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wyosine','wyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uga_stop_codon_signal','uga_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_24_signal','minus_24_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cytoplasmic_polypeptide_region','cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k_acylation_region','h4k_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylguanosine','one_two_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rh_map','rh_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_modification','silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_catalytic_site','inactive_catalytic_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon','anticodon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_deazaguanosine','seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine','asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('probe','probe'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('defective_conjugative_transposon','defective_conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeosine','archaeosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('molecular_contact_region','molecular_contact_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_repeat','nested_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_structure','membrane_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_collection','contig_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetraloop','tetraloop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_conserved_region','coding_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('long_terminal_repeat','long_terminal_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_signal_feature','vertebrate_immune_system_gene_recombination_signal_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('untranslated_region_polycistronic_mrna','untranslated_region_polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine_trna_primary_transcript','leucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_identity_region','high_identity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_dna_chromosome','circular_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_rim_localization_signal','nuclear_rim_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucyl_trna','isoleucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_breakpoint','insertion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5_prime_utr_variant','five_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgene','transgene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_region','mrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_attribute','transcript_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_staple_motif','serine_threonine_staple_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding','protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_bound_by_factor','enhancer_bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_by_translational_bypass','recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon','operon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_transcript','monocistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal','reciprocal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated','polyadenylated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unigene_cluster','unigene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_gene_cluster','vertebrate_ig_t_cell_receptor_rearranged_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_member','gene_cassette_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_read_through','stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_transcript_with_translational_frameshift','gene_with_transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_quality','variant_quality'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mnp','mnp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid','glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_prime_element','y_prime_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn','beta_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pathogenic_island','pathogenic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust_match','ust_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_protein','transcript_bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyladenosine','n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_chromosome','cyanelle_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orit','orit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted','maternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_chromosome','chloroplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle_gene','minicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_catalytic_motif','polypeptide_catalytic_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_2','rnapol_iii_promoter_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('no_output','no_output'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_coding_exon','interior_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyl_two_thiouridine','five_taurinomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_trimethylation_site','h3k9_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_secondary_structure_variant','transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide','polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_5th_base_variant','splice_donor_5th_base_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymerase_synthesis_read','polymerase_synthesis_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_binding_site','enhancer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_to_protein_binding_site','nucleotide_to_protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_two','beta_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_polya_primed_cdna','invalidated_by_genomic_polya_primed_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_edited_transcript','gene_with_edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv1_motif','dmv1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_12_signal','minus_12_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_modified_region','post_translationally_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline','proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_region','flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_isopentenyladenosine','two_methylthio_n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypyrimidine_tract','polypyrimidine_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxyuridine','five_methoxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_to_gene_feature','gene_to_gene_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_cloned_genomic_insert','bac_cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_heptamer','j_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ust','three_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_2_prime_o_dimethyladenosine','n6_2_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_site','trans_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('de_novo_variant','de_novo_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_rescue_region','engineered_rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorph_gene','nucleomorph_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_attribute','mrna_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_three_prime_overlap','five_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_i_intron','group_i_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_cluster','d_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('open_chromatin_region','open_chromatin_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_dna','genomic_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron','inside_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hammerhead_ribozyme','hammerhead_ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_heptamer','five_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_splice_enhancer','intronic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_adenosine','modified_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyluridine','five_carboxymethylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_region','repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_unit','repeat_unit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_dna_chromosome','double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heritable_phenotypic_marker','heritable_phenotypic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('template_region','template_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript_region','primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_dna','mitochondrial_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_region','transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acetylation_site','histone_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozyme','ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('matrix_attachment_site','matrix_attachment_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('imprinted','imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequence_variant','polypeptide_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est','est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_motif','rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_variation_site','polypeptide_variation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_i_rna','class_i_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo','oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_signal','stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hypoploid','hypoploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar_mrna','exemplar_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_defined_binding_region','experimentally_defined_binding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_g_transversion','c_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('active_peptide','active_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mannosyl_queuosine','mannosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_pyrrolysine','gene_with_stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('queuosine','queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna_oligo','lna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('independently_known','independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_region','proviral_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped','capped'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift_variant','minus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direction_attribute','direction_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_chromosome','micronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene_by_unequal_crossing_over','pseudogene_by_unequal_crossing_over'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethyladenosine','one_two_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe_motif','dpe_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frame_restoring_variant','frame_restoring_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seryl_trna','seryl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_variant','structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_promoter_element','regulatory_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integration_excision_site','integration_excision_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_region_of_exon','noncoding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna','rnase_mrp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_export_signal','nuclear_export_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyluridine','five_methoxycarbonylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_of_single_exon_gene','exon_of_single_exon_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_primary_transcript','gene_with_dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_secondary_structure','sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma_70','bacterial_rnapol_promoter_sigma_70'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path','tiling_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_sequence','nuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig','contig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quality_value','quality_value'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kozak_sequence','kozak_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('population_specific_variant','population_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catalytic_residue','catalytic_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site','inversion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid','aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dif_site','dif_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_gene','mirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valyl_trna','valyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_tandem_duplication','inverted_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_regulatory_frameshift_element','cis_regulatory_frameshift_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minisatellite','minisatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_component','assembly_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity_region','low_complexity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_backbone','morpholino_backbone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('designed_sequence','designed_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_2_prime_o_trimethyladenosine','n6_n6_2_prime_o_trimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_promoter','rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene_recombination_feature','v_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_thiouridine','five_carboxymethylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_ring_duplication','free_ring_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_centromere','point_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_mrna','dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal','interchromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_chromosomal_mutation','uncharacterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_cis_splice_site','five_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('octamer_motif','octamer_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides_different_start','encodes_overlapping_peptides_different_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_rna_viral_sequence','ss_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('indel','indel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_primary_transcript','dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_binding_site','protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic','polycistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine_trna_primary_transcript','asparagine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_enhancer','splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid_chromosome','aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peroxywybutosine','peroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_aspartic_acid','modified_l_aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_episome','engineered_episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnai_reagent','rnai_reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rasirna','rasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_region','tmrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_level_variant','increased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter','bacterial_rnapol_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_sequence','mitochondrial_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trinucleotide_repeat_microsatellite_feature','trinuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_stability','post_translationally_regulated_by_protein_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_primary_transcript','nc_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('iron_responsive_element','iron_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_cluster','v_d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward','forward'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_location','proviral_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_binding_site','histone_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_element','promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pse_motif','pse_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_eight','beta_turn_type_eight'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double','double'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_est_or_cdna_data','cds_supported_by_est_or_cdna_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_rna_chromosome','double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamic_acid','modified_l_glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_motif','polypeptide_nest_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_frameshift','translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_terminal_inverted_repeat','three_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_trna','pseudogenic_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cap','cap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon','five_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic','enzymatic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_exon','interior_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genetic_marker','genetic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_g_transition','a_to_g_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine','two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isre','isre'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted_gene','maternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular','circular'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_pseudoknot','h_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate_element','intermediate_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript','transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene','pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_repeat','direct_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_terminator','bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('diplotype','diplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metal_binding_site','metal_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_gene','dj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyladenosine','two_prime_o_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_region_variant','splice_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspe_primer','aspe_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_binding_site','restriction_enzyme_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac','bac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_cluster','dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_dimethylation_site','h3k36_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_donor_site','trans_splice_donor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_variant','gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_change_variant','conformational_change_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_monomethylation_site','h3k36_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleic_acid','nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_chimeric_cdna','invalidated_by_chimeric_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine','histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_component_region','gene_component_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_match','primer_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_primary_transcript','trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loxp_site','loxp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine','serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide','propeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_open_reading_frame','five_prime_open_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_six','schellmann_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shine_dalgarno_sequence','shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sp6_rna_polymerase_promoter','sp6_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_iii','centromere_dna_element_iii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine_trna_primary_transcript','lysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_c_cluster','j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency','assortment_derived_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript','mirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5s','rrna_5s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucyl_trna','leucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_intrachromosomal_transposition','invert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic_rna','enzymatic_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('germline_variant','germline_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated','negatively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('benign_variant','benign_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_region','anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon','exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a','beta_turn_type_six_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('random_sequence','random_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_chromosomal_mutation','partially_characterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna','rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('core_promoter_element','core_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_single_strand_overhang','restriction_enzyme_single_strand_overhang'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_oligo','ss_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_methylation_site','histone_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_duplication_plus_aneuploid','inversion_derived_duplication_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_nucleic_acid','transcript_bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein_containing','intein_containing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_encoding','h_aca_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_rna','rrna_cleavage_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_trap_construct','enhancer_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_inverse','gamma_turn_inverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_nonamer','three_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_variant','paternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('level_of_transcript_variant','level_of_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteinyl_trna','selenocysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_methylation','gene_silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u11_snrna','u11_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna','scrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_selenocysteine','gene_with_stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silencer','silencer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sage_tag','sage_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_1_frameshift','mrna_with_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_gene','nuclear_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_domain_match_data','cds_supported_by_domain_match_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_shine_dalgarno_sequence','internal_shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prolyl_trna','prolyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysidine','lysidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge','beta_bulge'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_modification','post_translationally_regulated_by_protein_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_variant','splice_donor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna','ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_gene','grna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer','enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_sequence_variant','polymorphic_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_clip','three_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift_variant','frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional','insertional'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_processed_pseudogene','non_processed_pseudogene'); CREATE INDEX sequence_cv_lookup_table_idx ON sequence_cv_lookup_table (original_cvterm_name); SET search_path=public,pg_catalog; -- DEPENDENCY: -- chado/modules/bridges/sofa-bridge.sql -- The standard Chado pattern for protein coding genes -- is a feature of type 'gene' with 'mRNA' features as parts -- REQUIRES: 'mrna' view from so-bridge.sql CREATE OR REPLACE VIEW protein_coding_gene AS SELECT DISTINCT gene.* FROM feature AS gene INNER JOIN feature_relationship AS fr ON (gene.feature_id=fr.object_id) INNER JOIN so.mrna ON (mrna.feature_id=fr.subject_id); -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE SCHEMA frange; SET search_path = frange,public,pg_catalog; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public,pg_catalog; --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- 05-31-2011 -- added 'name' column to phenotype. non-unique human readable field. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, name TEXT default null, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- changes 2011-05-31 -- added type_id to genotype (can be null for backward compatibility) -- added genotypeprop table -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- ================================================ -- TABLE: genotypeprop -- ================================================ create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import contact from contact -- ================================================================= -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; -- ================================================ -- TABLE: projectprop -- ================================================ CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from project -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_cvterm -- ================================================ CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id integer not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_cvtermprop -- ================================================ create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- ================================================ -- TABLE: stock_dbxrefprop -- ================================================ create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; --replaced with Rob B's improved view CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, COALESCE(gffdbx.accession,'.'::varchar(255)), cv.name, fl.fmin+1, fl.fmax, COALESCE(CAST(af.significance AS text), '.'), CASE WHEN fl.strand=-1 THEN '-' WHEN fl.strand=1 THEN '+' ELSE '.' END, COALESCE(CAST(fl.phase AS text), '.'), f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''Ontology_term'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''Dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id UNION SELECT feature_id, ''Alias'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255),organism_id integer -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- -- OR, you could execute this command (the materialized view tool has been -- updated to allow this all to be supplied on the command line): -- -- (yes, it's all one really long line, to make copy and pasting easier) -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer" --sql_query "SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "create index all_feature_names_lower_name on all_feature_names (lower(name))" --yes -- -- -- OR, even more complicated, you could use this command to create a materialized view -- for use with full text searching on PostgreSQL 8.4 or better: -- -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer,searchable_name tsvector" --sql_query "SELECT feature_id, CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255)) AS name, organism_id, to_tsvector('english', CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM feature UNION SELECT feature_id, name, organism_id, to_tsvector('english', name) AS searchable_name FROM feature WHERE name IS NOT NULL UNION SELECT fs.feature_id, s.name, f.organism_id, to_tsvector('english', s.name) AS searchable_name FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255)) AS name, f.organism_id, to_tsvector('english',CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id,to_tsvector('english',d.accession) AS searchable_name FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "CREATE INDEX searchable_all_feature_names_idx ON all_feature_names USING gin(searchable_name)" --yes -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1.11-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016614 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.22/diff.sql000644 000765 000024 00000000000 11661243501 016573 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.11-1.21/diff.sql000644 000765 000024 00000065732 11660532044 016623 0ustar00cainstaff000000 000000 create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1.11-1.2/diff.sql000644 000765 000024 00000065732 11627534663 016556 0ustar00cainstaff000000 000000 create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1.11/default_schema.sql000644 000765 000024 00007167677 11554343252 020325 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $1; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) ); SET search_path = public,pg_catalog; -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql'; -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); --function to 'unshare' exons. It looks for exons that have the same fmin --and fmax and belong to the same gene and only keeps one. The other, --redundant exons are marked obsolete in the feature table. Nothing --is done with those features' entries in the featureprop, feature_dbxref, --feature_pub, or feature_cvterm tables. For the moment, I'm assuming --that any annotations that they have when this script is run are --identical to their non-obsoleted doppelgangers. If that's not the case, --they could be merged via query. -- --The bulk of this code was contributed by Robin Houston at --GeneDB/Sanger Centre. CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; /* Choose one of the shared exons to be the canonical representative. We pick the one with the smallest feature_id. */ CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; --This is an automatically generated file; do not edit it as changes will not --be saved. Instead, modify bin/create-so-bridge.pl, which creates this file. CREATE SCHEMA so; SET search_path=so,public,pg_catalog; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent greate *** --- *** r than zero. A nucleotide region is comp *** --- *** osed of bases and a polypeptide region i *** --- *** s composed of amino acids. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region'; --- ************************************************ --- *** relation: sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded sequence. *** --- ************************************************ --- CREATE VIEW sequence_secondary_structure AS SELECT feature_id AS sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure'; --- ************************************************ --- *** relation: g_quartet *** --- *** relation type: VIEW *** --- *** *** --- *** G-quartets are unusual nucleic acid stru *** --- *** ctures consisting of a planar arrangemen *** --- *** t where each guanine is hydrogen bonded *** --- *** by hoogsteen pairing to another guanine *** --- *** in the quartet. *** --- ************************************************ --- CREATE VIEW g_quartet AS SELECT feature_id AS g_quartet_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet'; --- ************************************************ --- *** relation: interior_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_coding_exon AS SELECT feature_id AS interior_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon'; --- ************************************************ --- *** relation: satellite_dna *** --- *** relation type: VIEW *** --- *** *** --- *** The many tandem repeats (identical or re *** --- *** lated) of a short basic repeating unit; *** --- *** many have a base composition or other pr *** --- *** operty different from the genome average *** --- *** that allows them to be separated from t *** --- *** he bulk (main band) genomic DNA. *** --- ************************************************ --- CREATE VIEW satellite_dna AS SELECT feature_id AS satellite_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A pair of sequencing reads in which the *** --- *** two members of the pair are related by o *** --- *** riginating at either end of a clone inse *** --- *** rt. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding AS SELECT feature_id AS protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding'; --- ************************************************ --- *** relation: non_protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW non_protein_coding AS SELECT feature_id AS non_protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding'; --- ************************************************ --- *** relation: scrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of any one of sev *** --- *** eral small cytoplasmic RNA molecules pre *** --- *** sent in the cytoplasm and sometimes nucl *** --- *** eus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna_primary_transcript AS SELECT feature_id AS scrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** Any one of several small cytoplasmic RNA *** --- *** molecules present in the cytoplasm and *** --- *** sometimes nucleus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: inr_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters required f *** --- *** or the correct positioning of the polyme *** --- *** rase for the start of transcription. Ove *** --- *** rlaps the TSS. The mammalian consensus s *** --- *** equence is YYAN(T|A)YY; the Drosophila c *** --- *** onsensus sequence is TCA(G|T)t(T|C). In *** --- *** each the A is at position +1 with respec *** --- *** t to the TSS. Functionally similar to th *** --- *** e TATA box element. *** --- ************************************************ --- CREATE VIEW inr_motif AS SELECT feature_id AS inr_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif'; --- ************************************************ --- *** relation: dpe_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters; Positione *** --- *** d from +28 to +32 with respect to the TS *** --- *** S (+1). Experimental results suggest tha *** --- *** t the DPE acts in conjunction with the I *** --- *** NR_motif to provide a binding site for T *** --- *** FIID in the absence of a TATA box to med *** --- *** iate transcription of TATA-less promoter *** --- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G *** --- *** |A|C). *** --- ************************************************ --- CREATE VIEW dpe_motif AS SELECT feature_id AS dpe_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE_motif'; --- ************************************************ --- *** relation: bre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments at -37 to -32 with respect to the *** --- *** TSS (+1). Consensus sequence is (G|C)(G| *** --- *** C)(G|A)CGCC. Binds TFIIB. *** --- ************************************************ --- CREATE VIEW bre_motif AS SELECT feature_id AS bre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BRE_motif'; --- ************************************************ --- *** relation: pse_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of the *** --- *** promoters of snRNA genes transcribed by *** --- *** RNA polymerase II or by RNA polymerase *** --- *** III. Located between -45 and -60 relativ *** --- *** e to the TSS. The human PSE_motif consen *** --- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| *** --- *** G). *** --- ************************************************ --- CREATE VIEW pse_motif AS SELECT feature_id AS pse_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif'; --- ************************************************ --- *** relation: linkage_group *** --- *** relation type: VIEW *** --- *** *** --- *** A group of loci that can be grouped in a *** --- *** linear order representing the different *** --- *** degrees of linkage among the genes conc *** --- *** erned. *** --- ************************************************ --- CREATE VIEW linkage_group AS SELECT feature_id AS linkage_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linkage_group'; --- ************************************************ --- *** relation: rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A region of double stranded RNA where th *** --- *** e bases do not conform to WC base pairin *** --- *** g. The loop is closed on both sides by c *** --- *** anonical base pairing. If the interrupti *** --- *** on to base pairing occurs on one strand *** --- *** only, it is known as a bulge. *** --- ************************************************ --- CREATE VIEW rna_internal_loop AS SELECT feature_id AS rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_internal_loop'; --- ************************************************ --- *** relation: asymmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where one of the st *** --- *** rands includes more bases than the corre *** --- *** sponding region on the other strand. *** --- ************************************************ --- CREATE VIEW asymmetric_rna_internal_loop AS SELECT feature_id AS asymmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'asymmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: a_minor_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region forming a motif, composed of ad *** --- *** enines, where the minor groove edges are *** --- *** inserted into the minor groove of anoth *** --- *** er helix. *** --- ************************************************ --- CREATE VIEW a_minor_rna_motif AS SELECT feature_id AS a_minor_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_minor_RNA_motif'; --- ************************************************ --- *** relation: k_turn_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** The kink turn (K-turn) is an RNA structu *** --- *** ral motif that creates a sharp (~120 deg *** --- *** ree) bend between two continuous helices *** --- *** . *** --- ************************************************ --- CREATE VIEW k_turn_rna_motif AS SELECT feature_id AS k_turn_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif'; --- ************************************************ --- *** relation: sarcin_like_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A loop in ribosomal RNA containing the s *** --- *** ites of attack for ricin and sarcin. *** --- ************************************************ --- CREATE VIEW sarcin_like_rna_motif AS SELECT feature_id AS sarcin_like_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sarcin_like_RNA_motif'; --- ************************************************ --- *** relation: symmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where the extent of *** --- *** the loop on both stands is the same siz *** --- *** e. *** --- ************************************************ --- CREATE VIEW symmetric_rna_internal_loop AS SELECT feature_id AS symmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: rna_junction_loop *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_junction_loop AS SELECT feature_id AS rna_junction_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_junction_loop'; --- ************************************************ --- *** relation: rna_hook_turn *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_hook_turn AS SELECT feature_id AS rna_hook_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn'; --- ************************************************ --- *** relation: base_pair *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW base_pair AS SELECT feature_id AS base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'base_pair'; --- ************************************************ --- *** relation: wc_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical base pair, where two bases *** --- *** interact via WC edges, with glycosidic *** --- *** bonds oriented cis relative to the axis *** --- *** of orientation. *** --- ************************************************ --- CREATE VIEW wc_base_pair AS SELECT feature_id AS wc_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair'; --- ************************************************ --- *** relation: sugar_edge_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW sugar_edge_base_pair AS SELECT feature_id AS sugar_edge_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sugar_edge_base_pair'; --- ************************************************ --- *** relation: aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA or RNA molecules that have been sele *** --- *** cted from random pools based on their ab *** --- *** ility to bind other molecules. *** --- ************************************************ --- CREATE VIEW aptamer AS SELECT feature_id AS aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'aptamer'; --- ************************************************ --- *** relation: dna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW dna_aptamer AS SELECT feature_id AS dna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer'; --- ************************************************ --- *** relation: rna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** RNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW rna_aptamer AS SELECT feature_id AS rna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_aptamer'; --- ************************************************ --- *** relation: morpholino_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Morpholino oligos are synthesized from f *** --- *** our different Morpholino subunits, each *** --- *** of which contains one of the four geneti *** --- *** c bases (A, C, G, T) linked to a 6-membe *** --- *** red morpholine ring. Eighteen to 25 subu *** --- *** nits of these four subunit types are joi *** --- *** ned in a specific order by non-ionic pho *** --- *** sphorodiamidate intersubunit linkages to *** --- *** give a Morpholino. *** --- ************************************************ --- CREATE VIEW morpholino_oligo AS SELECT feature_id AS morpholino_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo'; --- ************************************************ --- *** relation: riboswitch *** --- *** relation type: VIEW *** --- *** *** --- *** A riboswitch is a part of an mRNA that c *** --- *** an act as a direct sensor of small molec *** --- *** ules to control their own expression. A *** --- *** riboswitch is a cis element in the 5' en *** --- *** d of an mRNA, that acts as a direct sens *** --- *** or of metabolites. *** --- ************************************************ --- CREATE VIEW riboswitch AS SELECT feature_id AS riboswitch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch'; --- ************************************************ --- *** relation: matrix_attachment_site *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that is required for the bi *** --- *** nding of chromatin to the nuclear matrix *** --- *** . *** --- ************************************************ --- CREATE VIEW matrix_attachment_site AS SELECT feature_id AS matrix_attachment_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site'; --- ************************************************ --- *** relation: locus_control_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that includes DNAse hyperse *** --- *** nsitive sites located 5' to a gene that *** --- *** confers the high-level, position-indepen *** --- *** dent, and copy number-dependent expressi *** --- *** on to that gene. *** --- ************************************************ --- CREATE VIEW locus_control_region AS SELECT feature_id AS locus_control_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast is a match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: genomic_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone of a DNA region of a genome. *** --- ************************************************ --- CREATE VIEW genomic_clone AS SELECT feature_id AS genomic_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone'; --- ************************************************ --- *** relation: processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene where by an mRNA was retrot *** --- *** ransposed. The mRNA sequence is transcri *** --- *** bed back into the genome, lacking intron *** --- *** s and promotors, but often including a p *** --- *** olyA tail. *** --- ************************************************ --- CREATE VIEW processed_pseudogene AS SELECT feature_id AS processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene'; --- ************************************************ --- *** relation: pseudogene_by_unequal_crossing_over *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene caused by unequal crossing *** --- *** over at recombination. *** --- ************************************************ --- CREATE VIEW pseudogene_by_unequal_crossing_over AS SELECT feature_id AS pseudogene_by_unequal_crossing_over_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over'; --- ************************************************ --- *** relation: probe *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence used experimentally to de *** --- *** tect the presence or absence of a comple *** --- *** mentary nucleic acid. *** --- ************************************************ --- CREATE VIEW probe AS SELECT feature_id AS probe_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo' OR cvterm.name = 'probe'; --- ************************************************ --- *** relation: sequence_variant_affecting_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect which changes *** --- *** the regulatory region of a gene. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_regulatory_region AS SELECT feature_id AS sequence_variant_affecting_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_regulatory_region'; --- ************************************************ --- *** relation: aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW aneuploid AS SELECT feature_id AS aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'aneuploid'; --- ************************************************ --- *** relation: hyperploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as extra c *** --- *** hromosomes are present. *** --- ************************************************ --- CREATE VIEW hyperploid AS SELECT feature_id AS hyperploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid'; --- ************************************************ --- *** relation: hypoploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as some ch *** --- *** romosomes are missing. *** --- ************************************************ --- CREATE VIEW hypoploid AS SELECT feature_id AS hypoploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hypoploid'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind thereby *** --- *** effecting translation of genes in that *** --- *** operon. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: nuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a n *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW nuclease_binding_site AS SELECT feature_id AS nuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_binding_site'; --- ************************************************ --- *** relation: compound_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome_arm AS SELECT feature_id AS compound_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm'; --- ************************************************ --- *** relation: restriction_enzyme_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a r *** --- *** estriction enzyme. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_binding_site AS SELECT feature_id AS restriction_enzyme_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site'; --- ************************************************ --- *** relation: d_intrachr_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_intrachr_transposition AS SELECT feature_id AS d_intrachr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition'; --- ************************************************ --- *** relation: d_interchr_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_interchr_transposition AS SELECT feature_id AS d_interchr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition'; --- ************************************************ --- *** relation: free_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_chromosome_arm AS SELECT feature_id AS free_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm'; --- ************************************************ --- *** relation: gene_to_gene_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_to_gene_feature AS SELECT feature_id AS gene_to_gene_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'gene_to_gene_feature'; --- ************************************************ --- *** relation: overlapping *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that has *** --- *** a sequence that overlaps the sequence of *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW overlapping AS SELECT feature_id AS overlapping_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'overlapping'; --- ************************************************ --- *** relation: inside_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene. *** --- ************************************************ --- CREATE VIEW inside_intron AS SELECT feature_id AS inside_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'inside_intron'; --- ************************************************ --- *** relation: inside_intron_antiparallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the opposite strand. *** --- ************************************************ --- CREATE VIEW inside_intron_antiparallel AS SELECT feature_id AS inside_intron_antiparallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel'; --- ************************************************ --- *** relation: inside_intron_parallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the same strand. *** --- ************************************************ --- CREATE VIEW inside_intron_parallel AS SELECT feature_id AS inside_intron_parallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_parallel'; --- ************************************************ --- *** relation: five_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's 3' region. *** --- ************************************************ --- CREATE VIEW five_prime_three_prime_overlap AS SELECT feature_id AS five_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_three_prime_overlap'; --- ************************************************ --- *** relation: five_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's five prime region. *** --- ************************************************ --- CREATE VIEW five_prime_five_prime_overlap AS SELECT feature_id AS five_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_five_prime_overlap'; --- ************************************************ --- *** relation: three_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 3' region. *** --- ************************************************ --- CREATE VIEW three_prime_three_prime_overlap AS SELECT feature_id AS three_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_three_prime_overlap'; --- ************************************************ --- *** relation: three_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 5' region. *** --- ************************************************ --- CREATE VIEW three_prime_five_prime_overlap AS SELECT feature_id AS three_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_five_prime_overlap'; --- ************************************************ --- *** relation: antisense *** --- *** relation type: VIEW *** --- *** *** --- *** A region sequence that is complementary *** --- *** to a sequence of messenger RNA. *** --- ************************************************ --- CREATE VIEW antisense AS SELECT feature_id AS antisense_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense'; --- ************************************************ --- *** relation: polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is polycistronic. *** --- ************************************************ --- CREATE VIEW polycistronic_transcript AS SELECT feature_id AS polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_transcript'; --- ************************************************ --- *** relation: dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_transcript AS SELECT feature_id AS dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_transcript'; --- ************************************************ --- *** relation: operon_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW operon_member AS SELECT feature_id AS operon_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member'; --- ************************************************ --- *** relation: gene_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_array_member AS SELECT feature_id AS gene_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_array_member'; --- ************************************************ --- *** relation: macronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW macronuclear_sequence AS SELECT feature_id AS macronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence'; --- ************************************************ --- *** relation: micronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW micronuclear_sequence AS SELECT feature_id AS micronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_sequence'; --- ************************************************ --- *** relation: nuclear_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nuclear sequence. *** --- ************************************************ --- CREATE VIEW nuclear_gene AS SELECT feature_id AS nuclear_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene'; --- ************************************************ --- *** relation: mt_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in mitochondrial sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW mt_gene AS SELECT feature_id AS mt_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'mt_gene'; --- ************************************************ --- *** relation: kinetoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in kinetoplast sequence. *** --- ************************************************ --- CREATE VIEW kinetoplast_gene AS SELECT feature_id AS kinetoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'kinetoplast_gene'; --- ************************************************ --- *** relation: plastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plastid sequence. *** --- ************************************************ --- CREATE VIEW plastid_gene AS SELECT feature_id AS plastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'plastid_gene'; --- ************************************************ --- *** relation: apicoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from apicoplast sequence. *** --- ************************************************ --- CREATE VIEW apicoplast_gene AS SELECT feature_id AS apicoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene'; --- ************************************************ --- *** relation: ct_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chloroplast sequence. *** --- ************************************************ --- CREATE VIEW ct_gene AS SELECT feature_id AS ct_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ct_gene'; --- ************************************************ --- *** relation: chromoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chromoplast_sequence. *** --- ************************************************ --- CREATE VIEW chromoplast_gene AS SELECT feature_id AS chromoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_gene'; --- ************************************************ --- *** relation: cyanelle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from cyanelle sequence. *** --- ************************************************ --- CREATE VIEW cyanelle_gene AS SELECT feature_id AS cyanelle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_gene'; --- ************************************************ --- *** relation: leucoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A plastid gene from leucoplast sequence. *** --- ************************************************ --- CREATE VIEW leucoplast_gene AS SELECT feature_id AS leucoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_gene'; --- ************************************************ --- *** relation: proplastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proplastid sequence. *** --- ************************************************ --- CREATE VIEW proplastid_gene AS SELECT feature_id AS proplastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_gene'; --- ************************************************ --- *** relation: nucleomorph_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nucleomorph sequence. *** --- ************************************************ --- CREATE VIEW nucleomorph_gene AS SELECT feature_id AS nucleomorph_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorph_gene'; --- ************************************************ --- *** relation: plasmid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plasmid sequence. *** --- ************************************************ --- CREATE VIEW plasmid_gene AS SELECT feature_id AS plasmid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_gene'; --- ************************************************ --- *** relation: proviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proviral sequence. *** --- ************************************************ --- CREATE VIEW proviral_gene AS SELECT feature_id AS proviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'proviral_gene'; --- ************************************************ --- *** relation: endogenous_retroviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A proviral gene with origin endogenous r *** --- *** etrovirus. *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_gene AS SELECT feature_id AS endogenous_retroviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene'; --- ************************************************ --- *** relation: transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW transposable_element AS SELECT feature_id AS transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: clone_insert_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_end AS SELECT feature_id AS clone_insert_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversible denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the chromosome between the c *** --- *** entromere and the telomere. Human chromo *** --- *** somes have two arms, the p arm (short) a *** --- *** nd the q arm (long) which are separated *** --- *** from each other by the centromere. *** --- ************************************************ --- CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: sequencing_primer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequencing_primer AS SELECT feature_id AS sequencing_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer'; --- ************************************************ --- *** relation: mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_frameshift AS SELECT feature_id AS mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'mRNA_with_frameshift'; --- ************************************************ --- *** relation: sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** An extent of biological sequence. *** --- ************************************************ --- CREATE VIEW sequence_feature AS SELECT feature_id AS sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region' OR cvterm.name = 'junction' OR cvterm.name = 'sequence_alteration' OR cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'polyA_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'substitution' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'sequence_feature'; --- ************************************************ --- *** relation: transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoded within a transposable ele *** --- *** ment. For example gag, int, env and pol *** --- *** are the transposable element genes of th *** --- *** e TY element in yeast. *** --- ************************************************ --- CREATE VIEW transposable_element_gene AS SELECT feature_id AS transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'transposable_element_gene'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** A short preexisting polynucleotide chain *** --- *** to which new deoxyribonucleotides can b *** --- *** e added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'primer'; --- ************************************************ --- *** relation: proviral_region *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to a host genome. *** --- ************************************************ --- CREATE VIEW proviral_region AS SELECT feature_id AS proviral_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage' OR cvterm.name = 'proviral_region'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: edited *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is modified by editing. *** --- ************************************************ --- CREATE VIEW edited AS SELECT feature_id AS edited_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited'; --- ************************************************ --- *** relation: transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript with a translational frames *** --- *** hift. *** --- ************************************************ --- CREATE VIEW transcript_with_translational_frameshift AS SELECT feature_id AS transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a sequence that *** --- *** is regulated. *** --- ************************************************ --- CREATE VIEW regulated AS SELECT feature_id AS regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'regulated'; --- ************************************************ --- *** relation: protein_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW protein_coding_primary_transcript AS SELECT feature_id AS protein_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: forward_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW forward_primer AS SELECT feature_id AS forward_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward_primer'; --- ************************************************ --- *** relation: rna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_sequence_secondary_structure AS SELECT feature_id AS rna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'RNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: transcriptionally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated at transcription. *** --- ************************************************ --- CREATE VIEW transcriptionally_regulated AS SELECT feature_id AS transcriptionally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_regulated'; --- ************************************************ --- *** relation: transcriptionally_constitutive *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed in relatively constant amounts *** --- *** without regard to cellular environmenta *** --- *** l conditions such as the concentration o *** --- *** f a particular substrate. *** --- ************************************************ --- CREATE VIEW transcriptionally_constitutive AS SELECT feature_id AS transcriptionally_constitutive_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive'; --- ************************************************ --- *** relation: transcriptionally_induced *** --- *** relation type: VIEW *** --- *** *** --- *** An inducer molecule is required for tran *** --- *** scription to occur. *** --- ************************************************ --- CREATE VIEW transcriptionally_induced AS SELECT feature_id AS transcriptionally_induced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_induced'; --- ************************************************ --- *** relation: transcriptionally_repressed *** --- *** relation type: VIEW *** --- *** *** --- *** A repressor molecule is required for tra *** --- *** nscription to stop. *** --- ************************************************ --- CREATE VIEW transcriptionally_repressed AS SELECT feature_id AS transcriptionally_repressed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'transcriptionally_repressed'; --- ************************************************ --- *** relation: silenced_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced. *** --- ************************************************ --- CREATE VIEW silenced_gene AS SELECT feature_id AS silenced_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_gene'; --- ************************************************ --- *** relation: gene_silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA modificat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_modification AS SELECT feature_id AS gene_silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_DNA_modification'; --- ************************************************ --- *** relation: gene_silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA methylati *** --- *** on. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_methylation AS SELECT feature_id AS gene_silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: post_translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated after it has been translated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated AS SELECT feature_id AS post_translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'post_translationally_regulated'; --- ************************************************ --- *** relation: translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated as it is translated. *** --- ************************************************ --- CREATE VIEW translationally_regulated AS SELECT feature_id AS translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated'; --- ************************************************ --- *** relation: reverse_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW reverse_primer AS SELECT feature_id AS reverse_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_primer'; --- ************************************************ --- *** relation: epigenetically_modified *** --- *** relation type: VIEW *** --- *** *** --- *** This attribute describes a gene where he *** --- *** ritable changes other than those in the *** --- *** DNA sequence occur. These changes includ *** --- *** e: modification to the DNA (such as DNA *** --- *** methylation, the covalent modification o *** --- *** f cytosine), and post-translational modi *** --- *** fication of histones. *** --- ************************************************ --- CREATE VIEW epigenetically_modified AS SELECT feature_id AS epigenetically_modified_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'epigenetically_modified'; --- ************************************************ --- *** relation: imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** Imprinted genes are epigenetically modif *** --- *** ied genes that are expressed monoallelic *** --- *** ally according to their parent of origin *** --- *** . *** --- ************************************************ --- CREATE VIEW imprinted AS SELECT feature_id AS imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted'; --- ************************************************ --- *** relation: maternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The maternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW maternally_imprinted AS SELECT feature_id AS maternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted'; --- ************************************************ --- *** relation: paternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The paternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW paternally_imprinted AS SELECT feature_id AS paternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted'; --- ************************************************ --- *** relation: allelically_excluded *** --- *** relation type: VIEW *** --- *** *** --- *** Allelic exclusion is a process occuring *** --- *** in diploid organisms, where a gene is in *** --- *** activated and not expressed in that cell *** --- *** . *** --- ************************************************ --- CREATE VIEW allelically_excluded AS SELECT feature_id AS allelically_excluded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded'; --- ************************************************ --- *** relation: gene_rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An epigenetically modified gene, rearran *** --- *** ged at the DNA level. *** --- ************************************************ --- CREATE VIEW gene_rearranged_at_dna_level AS SELECT feature_id AS gene_rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located within the fi *** --- *** ve prime end of an mRNA that causes prem *** --- *** ature termination of translation. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'terminator'; --- ************************************************ --- *** relation: dna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded DNA sequence. *** --- ************************************************ --- CREATE VIEW dna_sequence_secondary_structure AS SELECT feature_id AS dna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif' OR cvterm.name = 'DNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of known length which may be us *** --- *** ed to manufacture a longer region. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: recoded_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A codon that has been redefined at trans *** --- *** lation. The redefinition may be as a res *** --- *** ult of translational bypass, translation *** --- *** al frameshifting or stop codon readthrou *** --- *** gh. *** --- ************************************************ --- CREATE VIEW recoded_codon AS SELECT feature_id AS recoded_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'recoded_codon'; --- ************************************************ --- *** relation: capped *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing when a sequence, *** --- *** usually an mRNA is capped by the additi *** --- *** on of a modified guanine nucleotide at t *** --- *** he 5' end. *** --- ************************************************ --- CREATE VIEW capped AS SELECT feature_id AS capped_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the transcript sequence with *** --- *** in a gene which is not removed from the *** --- *** primary RNA transcript by RNA splicing. *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unvailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n a host bacterium or some other organis *** --- *** m. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'clone'; --- ************************************************ --- *** relation: yac *** --- *** relation type: VIEW *** --- *** *** --- *** Yeast Artificial Chromosome, a vector co *** --- *** nstructed from the telomeric, centromeri *** --- *** c, and replication origin sequences need *** --- *** ed for replication in yeast cells. *** --- ************************************************ --- CREATE VIEW yac AS SELECT feature_id AS yac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC'; --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Bacterial Artificial Chromosome, a cloni *** --- *** ng vector that can be propagated as mini *** --- *** -chromosomes in a bacterial host. *** --- ************************************************ --- CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: pac *** --- *** relation type: VIEW *** --- *** *** --- *** The P1-derived artificial chromosome are *** --- *** DNA constructs that are derived from th *** --- *** e DNA of P1 bacteriophage. They can carr *** --- *** y large amounts (about 100-300 kilobases *** --- *** ) of other sequences for a variety of bi *** --- *** oengineering purposes. It is one type of *** --- *** vector used to clone DNA fragments (100 *** --- *** - to 300-kb insert size; average, 150 kb *** --- *** ) in Escherichia coli cells. *** --- ************************************************ --- CREATE VIEW pac AS SELECT feature_id AS pac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC'; --- ************************************************ --- *** relation: plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A self replicating, using the hosts cell *** --- *** ular machinery, often circular nucleic a *** --- *** cid molecule that is distinct from a chr *** --- *** omosome in the organism. *** --- ************************************************ --- CREATE VIEW plasmid AS SELECT feature_id AS plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'plasmid'; --- ************************************************ --- *** relation: cosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that is a hybrid of lam *** --- *** bda phages and a plasmid that can be pro *** --- *** pagated as a plasmid or packaged as a ph *** --- *** age,since they retain the lambda cos sit *** --- *** es. *** --- ************************************************ --- CREATE VIEW cosmid AS SELECT feature_id AS cosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cosmid'; --- ************************************************ --- *** relation: phagemid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid which carries within its seque *** --- *** nce a bacteriophage replication origin. *** --- *** When the host bacterium is infected with *** --- *** "helper" phage, a phagemid is replicate *** --- *** d along with the phage DNA and packaged *** --- *** into phage capsids. *** --- ************************************************ --- CREATE VIEW phagemid AS SELECT feature_id AS phagemid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phagemid'; --- ************************************************ --- *** relation: fosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that utilises the E. co *** --- *** li F factor. *** --- ************************************************ --- CREATE VIEW fosmid AS SELECT feature_id AS fosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fosmid'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The point at which a deletion occured. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which adenine has *** --- *** been methylated. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Consensus region of primary transcript b *** --- *** ordering junction of splicing. A region *** --- *** that overlaps exactly 2 base and adjacen *** --- *** t_to splice_junction. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: five_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 5' edge of the intron. A splice_ *** --- *** site that is downstream_adjacent_to exon *** --- *** and starts intron. *** --- ************************************************ --- CREATE VIEW five_prime_cis_splice_site AS SELECT feature_id AS five_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'five_prime_cis_splice_site'; --- ************************************************ --- *** relation: three_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 3' edge of the intron. A splice_ *** --- *** site that is upstream_adjacent_to exon a *** --- *** nd finishes intron. *** --- ************************************************ --- CREATE VIEW three_prime_cis_splice_site AS SELECT feature_id AS three_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'three_prime_cis_splice_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: enhancer_bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer bound by a factor. *** --- ************************************************ --- CREATE VIEW enhancer_bound_by_factor AS SELECT feature_id AS enhancer_bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region composed of the TSS( *** --- *** s) and binding sites for TF_complexes of *** --- *** the basal transcription machinery. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'promoter'; --- ************************************************ --- *** relation: rnapol_i_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase I binds, to begin trans *** --- *** cription. *** --- ************************************************ --- CREATE VIEW rnapol_i_promoter AS SELECT feature_id AS rnapol_i_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter'; --- ************************************************ --- *** relation: rnapol_ii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase II binds, to begin tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW rnapol_ii_promoter AS SELECT feature_id AS rnapol_ii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_promoter'; --- ************************************************ --- *** relation: rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase III binds, to begin tra *** --- *** nscription. *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter AS SELECT feature_id AS rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'RNApol_III_promoter'; --- ************************************************ --- *** relation: caat_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a conserved sequence located abo *** --- *** ut 75-bp upstream of the start point of *** --- *** eukaryotic transcription units which may *** --- *** be involved in RNA polymerase binding; *** --- *** consensus=GG(C|T)CAATCT. *** --- ************************************************ --- CREATE VIEW caat_signal AS SELECT feature_id AS caat_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CAAT_signal'; --- ************************************************ --- *** relation: gc_rich_promoter_region *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved GC-rich region located upstr *** --- *** eam of the start point of eukaryotic tra *** --- *** nscription units which may occur in mult *** --- *** iple copies or in either orientation; co *** --- *** nsensus=GGGCGG. *** --- ************************************************ --- CREATE VIEW gc_rich_promoter_region AS SELECT feature_id AS gc_rich_promoter_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region'; --- ************************************************ --- *** relation: tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved AT-rich septamer found about *** --- *** 25-bp before the start point of many eu *** --- *** karyotic RNA polymerase II transcript un *** --- *** its; may be involved in positioning the *** --- *** enzyme for correct initiation; consensus *** --- *** =TATA(A|T)A(A|T). *** --- ************************************************ --- CREATE VIEW tata_box AS SELECT feature_id AS tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TATA_box'; --- ************************************************ --- *** relation: minus_10_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 10-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units which may be involved in bin *** --- *** ding RNA polymerase; consensus=TAtAaT. *** --- ************************************************ --- CREATE VIEW minus_10_signal AS SELECT feature_id AS minus_10_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_10_signal'; --- ************************************************ --- *** relation: minus_35_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved hexamer about 35-bp upstream *** --- *** of the start point of bacterial transcr *** --- *** iption units; consensus=TTGACa or TGTTGA *** --- *** CA. *** --- ************************************************ --- CREATE VIEW minus_35_signal AS SELECT feature_id AS minus_35_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_35_signal'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_insert_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_start AS SELECT feature_id AS clone_insert_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_start'; --- ************************************************ --- *** relation: retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is incorpora *** --- *** ted into a chromosome by a mechanism tha *** --- *** t requires reverse transcriptase. *** --- ************************************************ --- CREATE VIEW retrotransposon AS SELECT feature_id AS retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'retrotransposon'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: dna_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon where the mechanism of tran *** --- *** sposition is via a DNA intermediate. *** --- ************************************************ --- CREATE VIEW dna_transposon AS SELECT feature_id AS dna_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'DNA_transposon'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: u2_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A major type of spliceosomal intron spli *** --- *** ced by the U2 spliceosome, that includes *** --- *** U1, U2, U4/U6 and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u2_intron AS SELECT feature_id AS u2_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that in its initial state r *** --- *** equires modification to be functional. *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'primary_transcript'; --- ************************************************ --- *** relation: ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon flanked by long termin *** --- *** al repeat sequences. *** --- ************************************************ --- CREATE VIEW ltr_retrotransposon AS SELECT feature_id AS ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract' OR cvterm.name = 'LTR_retrotransposon'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A segment of DNA that is transcribed, bu *** --- *** t removed from within the transcript by *** --- *** splicing together the sequences (exons) *** --- *** on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'intron'; --- ************************************************ --- *** relation: non_ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon without long terminal *** --- *** repeat sequences. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon AS SELECT feature_id AS non_ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'non_LTR_retrotransposon'; --- ************************************************ --- *** relation: five_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_intron AS SELECT feature_id AS five_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron'; --- ************************************************ --- *** relation: interior_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_intron AS SELECT feature_id AS interior_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_intron'; --- ************************************************ --- *** relation: three_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_intron AS SELECT feature_id AS three_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_intron'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment used as a reagent to dete *** --- *** ct the polymorphic genomic loci by hybri *** --- *** dizing against the genomic DNA digested *** --- *** with a given restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: line_element *** --- *** relation type: VIEW *** --- *** *** --- *** A dispersed repeat family with many copi *** --- *** es, each from 1 to 6 kb long. New elemen *** --- *** ts are generated by retroposition of a t *** --- *** ranscribed copy. Typically the LINE cont *** --- *** ains 2 ORF's one of which is reverse tra *** --- *** nscriptase, and 3'and 5' direct repeats. *** --- ************************************************ --- CREATE VIEW line_element AS SELECT feature_id AS line_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element'; --- ************************************************ --- *** relation: coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon whereby at least one base is par *** --- *** t of a codon (here, 'codon'nis inclusive *** --- *** of the stop_codon). *** --- ************************************************ --- CREATE VIEW coding_exon AS SELECT feature_id AS coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'coding_exon'; --- ************************************************ --- *** relation: five_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the five_prime_coding_ex *** --- *** on that codes for protein. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_coding_region AS SELECT feature_id AS five_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: three_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the three_prime_coding_e *** --- *** xon that codes for protein. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_coding_region AS SELECT feature_id AS three_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding exon_coding_region'; --- ************************************************ --- *** relation: noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that does not contain any codons *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_exon AS SELECT feature_id AS noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'noncoding_exon'; --- ************************************************ --- *** relation: translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence that has *** --- *** translocated to a new position. *** --- ************************************************ --- CREATE VIEW translocation AS SELECT feature_id AS translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation'; --- ************************************************ --- *** relation: five_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' most coding exon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon AS SELECT feature_id AS five_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon'; --- ************************************************ --- *** relation: interior_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is bounded by 5' and 3' spl *** --- *** ice sites. *** --- ************************************************ --- CREATE VIEW interior_exon AS SELECT feature_id AS interior_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_exon'; --- ************************************************ --- *** relation: three_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The coding exon that is most 3-prime on *** --- *** a given transcript. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon AS SELECT feature_id AS three_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime or three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: sine_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element, a few hundred base *** --- *** pairs long, that is dispersed throughou *** --- *** t the genome. A common human SINE is the *** --- *** Alu element. *** --- ************************************************ --- CREATE VIEW sine_element AS SELECT feature_id AS sine_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SINE_element'; --- ************************************************ --- *** relation: simple_sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW simple_sequence_length_variation AS SELECT feature_id AS simple_sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation'; --- ************************************************ --- *** relation: terminal_inverted_repeat_element *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA transposable element defined as ha *** --- *** ving termini with perfect, or nearly per *** --- *** fect short inverted repeats, generally 1 *** --- *** 0 - 40 nucleotides long. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat_element AS SELECT feature_id AS terminal_inverted_repeat_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'terminal_inverted_repeat_element'; --- ************************************************ --- *** relation: rrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a ribosoma *** --- *** l RNA. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript AS SELECT feature_id AS rrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript'; --- ************************************************ --- *** relation: trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a transfer *** --- *** RNA (SO:0000253). *** --- ************************************************ --- CREATE VIEW trna_primary_transcript AS SELECT feature_id AS trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript'; --- ************************************************ --- *** relation: alanine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding alanyl tRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW alanine_trna_primary_transcript AS SELECT feature_id AS alanine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: arg_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding arginyl tR *** --- *** NA (SO:0000255). *** --- ************************************************ --- CREATE VIEW arg_trna_primary_transcript AS SELECT feature_id AS arg_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: asparagine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding asparaginy *** --- *** l tRNA (SO:0000256). *** --- ************************************************ --- CREATE VIEW asparagine_trna_primary_transcript AS SELECT feature_id AS asparagine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: aspartic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding aspartyl t *** --- *** RNA (SO:0000257). *** --- ************************************************ --- CREATE VIEW aspartic_acid_trna_primary_transcript AS SELECT feature_id AS aspartic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: cysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding cysteinyl *** --- *** tRNA (SO:0000258). *** --- ************************************************ --- CREATE VIEW cysteine_trna_primary_transcript AS SELECT feature_id AS cysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutaminyl *** --- *** tRNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamic_acid_trna_primary_transcript AS SELECT feature_id AS glutamic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutamyl t *** --- *** RNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamine_trna_primary_transcript AS SELECT feature_id AS glutamine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glycine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glycyl tRN *** --- *** A (SO:0000263). *** --- ************************************************ --- CREATE VIEW glycine_trna_primary_transcript AS SELECT feature_id AS glycine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: histidine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding histidyl t *** --- *** RNA (SO:0000262). *** --- ************************************************ --- CREATE VIEW histidine_trna_primary_transcript AS SELECT feature_id AS histidine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: isoleucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding isoleucyl *** --- *** tRNA (SO:0000263). *** --- ************************************************ --- CREATE VIEW isoleucine_trna_primary_transcript AS SELECT feature_id AS isoleucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: leucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding leucyl tRN *** --- *** A (SO:0000264). *** --- ************************************************ --- CREATE VIEW leucine_trna_primary_transcript AS SELECT feature_id AS leucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: lysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding lysyl tRNA *** --- *** (SO:0000265). *** --- ************************************************ --- CREATE VIEW lysine_trna_primary_transcript AS SELECT feature_id AS lysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: methionine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding methionyl *** --- *** tRNA (SO:0000266). *** --- ************************************************ --- CREATE VIEW methionine_trna_primary_transcript AS SELECT feature_id AS methionine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: phe_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding phenylalan *** --- *** yl tRNA (SO:0000267). *** --- ************************************************ --- CREATE VIEW phe_trna_primary_transcript AS SELECT feature_id AS phe_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: proline_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding prolyl tRN *** --- *** A (SO:0000268). *** --- ************************************************ --- CREATE VIEW proline_trna_primary_transcript AS SELECT feature_id AS proline_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline_tRNA_primary_transcript'; --- ************************************************ --- *** relation: serine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW serine_trna_primary_transcript AS SELECT feature_id AS serine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: thr_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding threonyl t *** --- *** RNA (SO:000270). *** --- ************************************************ --- CREATE VIEW thr_trna_primary_transcript AS SELECT feature_id AS thr_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: try_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tryptophan *** --- *** yl tRNA (SO:000271). *** --- ************************************************ --- CREATE VIEW try_trna_primary_transcript AS SELECT feature_id AS try_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan_tRNA_primary_transcript'; --- ************************************************ --- *** relation: tyrosine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tyrosyl tR *** --- *** NA (SO:000272). *** --- ************************************************ --- CREATE VIEW tyrosine_trna_primary_transcript AS SELECT feature_id AS tyrosine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: valine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding valyl tRNA *** --- *** (SO:000273). *** --- ************************************************ --- CREATE VIEW valine_trna_primary_transcript AS SELECT feature_id AS valine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: snrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** clear RNA (SO:0000274). *** --- ************************************************ --- CREATE VIEW snrna_primary_transcript AS SELECT feature_id AS snrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_primary_transcript'; --- ************************************************ --- *** relation: snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar mRNA (SO:0000275). *** --- ************************************************ --- CREATE VIEW snorna_primary_transcript AS SELECT feature_id AS snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript'; --- ************************************************ --- *** relation: mature_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone the nec *** --- *** essary modifications, if any, for its fu *** --- *** nction. In eukaryotes this includes, for *** --- *** example, processing of introns, cleavag *** --- *** e, base modification, and modifications *** --- *** to the 5' and/or the 3' ends, other than *** --- *** addition of bases. In bacteria function *** --- *** al mRNAs are usually not modified. *** --- ************************************************ --- CREATE VIEW mature_transcript AS SELECT feature_id AS mature_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'mature_transcript'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not co *** --- *** ntain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds a TF c *** --- *** omplex [GO:0005667]. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The inframe interval between the stop co *** --- *** dons of a reading frame which when read *** --- *** as sequential triplets, has the potentia *** --- *** l of encoding a sequential string of ami *** --- *** no acids. TER(NNN)nTER. *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'ORF'; --- ************************************************ --- *** relation: transcript_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transcript_attribute AS SELECT feature_id AS transcript_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'transcript_attribute'; --- ************************************************ --- *** relation: foldback_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element with extensive se *** --- *** condary structure, characterised by larg *** --- *** e modular imperfect long inverted repeat *** --- *** s. *** --- ************************************************ --- CREATE VIEW foldback_element AS SELECT feature_id AS foldback_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foldback_element'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequences extending on either side o *** --- *** f a specific region. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: chromosome_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_variation AS SELECT feature_id AS chromosome_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_variation'; --- ************************************************ --- *** relation: internal_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR bordered by the terminal and initi *** --- *** al codons of two CDSs in a polycistronic *** --- *** transcript. Every UTR is either 5', 3' *** --- *** or internal. *** --- ************************************************ --- CREATE VIEW internal_utr AS SELECT feature_id AS internal_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_UTR'; --- ************************************************ --- *** relation: untranslated_region_polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The untranslated sequence separating the *** --- *** 'cistrons' of multicistronic mRNA. *** --- ************************************************ --- CREATE VIEW untranslated_region_polycistronic_mrna AS SELECT feature_id AS untranslated_region_polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'untranslated_region_polycistronic_mRNA'; --- ************************************************ --- *** relation: internal_ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence element that recruits a ribosom *** --- *** al subunit to internal mRNA for translat *** --- *** ion initiation. *** --- ************************************************ --- CREATE VIEW internal_ribosome_entry_site AS SELECT feature_id AS internal_ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'internal_ribosome_entry_site'; --- ************************************************ --- *** relation: polyadenylated *** --- *** relation type: VIEW *** --- *** *** --- *** A attribute describing the addition of a *** --- *** poly A tail to the 3' end of a mRNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW polyadenylated AS SELECT feature_id AS polyadenylated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated'; --- ************************************************ --- *** relation: sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_length_variation AS SELECT feature_id AS sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'sequence_length_variation'; --- ************************************************ --- *** relation: modified_rna_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post_transcriptionally modified base. *** --- ************************************************ --- CREATE VIEW modified_rna_base_feature AS SELECT feature_id AS modified_rna_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_RNA_base_feature'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. Transfer R *** --- *** NAs have two regions of fundamental func *** --- *** tional importance: the anti-codon, which *** --- *** is responsible for specific mRNA codon *** --- *** recognition, and the 3' end, to which th *** --- *** e tRNA's corresponding amino acid is att *** --- *** ached (by aminoacyl-tRNA synthetases). T *** --- *** ransfer RNAs cope with the degeneracy of *** --- *** the genetic code in two manners: having *** --- *** more than one tRNA (with a specific ant *** --- *** i-codon) for a particular amino acid; an *** --- *** d 'wobble' base-pairing, i.e. permitting *** --- *** non-standard base-pairing at the 3rd an *** --- *** ti-codon position. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: alanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an alanine anti *** --- *** codon, and a 3' alanine binding region. *** --- ************************************************ --- CREATE VIEW alanyl_trna AS SELECT feature_id AS alanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA'; --- ************************************************ --- *** relation: rrna_small_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_small_subunit_primary_transcript AS SELECT feature_id AS rrna_small_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript'; --- ************************************************ --- *** relation: asparaginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an asparagine a *** --- *** nticodon, and a 3' asparagine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW asparaginyl_trna AS SELECT feature_id AS asparaginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparaginyl_tRNA'; --- ************************************************ --- *** relation: aspartyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an aspartic aci *** --- *** d anticodon, and a 3' aspartic acid bind *** --- *** ing region. *** --- ************************************************ --- CREATE VIEW aspartyl_trna AS SELECT feature_id AS aspartyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartyl_tRNA'; --- ************************************************ --- *** relation: cysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a cysteine anti *** --- *** codon, and a 3' cysteine binding region. *** --- ************************************************ --- CREATE VIEW cysteinyl_trna AS SELECT feature_id AS cysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteinyl_tRNA'; --- ************************************************ --- *** relation: glutaminyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamine ant *** --- *** icodon, and a 3' glutamine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW glutaminyl_trna AS SELECT feature_id AS glutaminyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutaminyl_tRNA'; --- ************************************************ --- *** relation: glutamyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamic acid *** --- *** anticodon, and a 3' glutamic acid bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW glutamyl_trna AS SELECT feature_id AS glutamyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamyl_tRNA'; --- ************************************************ --- *** relation: glycyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glycine antic *** --- *** odon, and a 3' glycine binding region. *** --- ************************************************ --- CREATE VIEW glycyl_trna AS SELECT feature_id AS glycyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycyl_tRNA'; --- ************************************************ --- *** relation: histidyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a histidine ant *** --- *** icodon, and a 3' histidine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW histidyl_trna AS SELECT feature_id AS histidyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidyl_tRNA'; --- ************************************************ --- *** relation: isoleucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an isoleucine a *** --- *** nticodon, and a 3' isoleucine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW isoleucyl_trna AS SELECT feature_id AS isoleucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucyl_tRNA'; --- ************************************************ --- *** relation: leucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a leucine antic *** --- *** odon, and a 3' leucine binding region. *** --- ************************************************ --- CREATE VIEW leucyl_trna AS SELECT feature_id AS leucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucyl_tRNA'; --- ************************************************ --- *** relation: lysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a lysine antico *** --- *** don, and a 3' lysine binding region. *** --- ************************************************ --- CREATE VIEW lysyl_trna AS SELECT feature_id AS lysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysyl_tRNA'; --- ************************************************ --- *** relation: methionyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a methionine an *** --- *** ticodon, and a 3' methionine binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW methionyl_trna AS SELECT feature_id AS methionyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionyl_tRNA'; --- ************************************************ --- *** relation: phenylalanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a phenylalanine *** --- *** anticodon, and a 3' phenylalanine bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW phenylalanyl_trna AS SELECT feature_id AS phenylalanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanyl_tRNA'; --- ************************************************ --- *** relation: prolyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a proline antic *** --- *** odon, and a 3' proline binding region. *** --- ************************************************ --- CREATE VIEW prolyl_trna AS SELECT feature_id AS prolyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prolyl_tRNA'; --- ************************************************ --- *** relation: seryl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a serine antico *** --- *** don, and a 3' serine binding region. *** --- ************************************************ --- CREATE VIEW seryl_trna AS SELECT feature_id AS seryl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seryl_tRNA'; --- ************************************************ --- *** relation: threonyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a threonine ant *** --- *** icodon, and a 3' threonine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW threonyl_trna AS SELECT feature_id AS threonyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonyl_tRNA'; --- ************************************************ --- *** relation: tryptophanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tryptophan an *** --- *** ticodon, and a 3' tryptophan binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW tryptophanyl_trna AS SELECT feature_id AS tryptophanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophanyl_tRNA'; --- ************************************************ --- *** relation: tyrosyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tyrosine anti *** --- *** codon, and a 3' tyrosine binding region. *** --- ************************************************ --- CREATE VIEW tyrosyl_trna AS SELECT feature_id AS tyrosyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosyl_tRNA'; --- ************************************************ --- *** relation: valyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a valine antico *** --- *** don, and a 3' valine binding region. *** --- ************************************************ --- CREATE VIEW valyl_trna AS SELECT feature_id AS valyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valyl_tRNA'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small nuclear RNA molecule involved in *** --- *** pre-mRNA splicing and processing. *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA (small nucleolar RNA) is any on *** --- *** e of a class of small RNAs that are asso *** --- *** ciated with the eukaryotic nucleus as co *** --- *** mponents of small nucleolar ribonucleopr *** --- *** oteins. They participate in the processi *** --- *** ng or modifications of many RNAs, mostly *** --- *** ribosomal RNAs (rRNAs) though snoRNAs a *** --- *** re also known to target other classes of *** --- *** RNA, including spliceosomal RNAs, tRNAs *** --- *** , and mRNAs via a stretch of sequence th *** --- *** at is complementary to a sequence in the *** --- *** targeted RNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. M *** --- *** icro RNAs are produced from precursor mo *** --- *** lecules (SO:0000647) that can form local *** --- *** hairpin structures, which ordinarily ar *** --- *** e processed (via the Dicer pathway) such *** --- *** that a single miRNA molecule accumulate *** --- *** s from one arm of a hairpin precursor mo *** --- *** lecule. Micro RNAs may trigger the cleav *** --- *** age of their target molecules or act as *** --- *** translational repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by another molecule. *** --- ************************************************ --- CREATE VIEW bound_by_factor AS SELECT feature_id AS bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'bound_by_factor'; --- ************************************************ --- *** relation: transcript_bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a nucleic *** --- *** acid. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_nucleic_acid AS SELECT feature_id AS transcript_bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_nucleic_acid'; --- ************************************************ --- *** relation: transcript_bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a protein. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_protein AS SELECT feature_id AS transcript_bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_protein'; --- ************************************************ --- *** relation: engineered_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_gene AS SELECT feature_id AS engineered_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_gene'; --- ************************************************ --- *** relation: engineered_foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_gene AS SELECT feature_id AS engineered_foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene'; --- ************************************************ --- *** relation: mrna_with_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a minus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_1_frameshift AS SELECT feature_id AS mrna_with_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transposible_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element_gene AS SELECT feature_id AS engineered_foreign_transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene'; --- ************************************************ --- *** relation: foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_gene AS SELECT feature_id AS foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'foreign_gene'; --- ************************************************ --- *** relation: long_terminal_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence directly repeated at both end *** --- *** s of a defined sequence, of the sort typ *** --- *** ically found in retroviruses. *** --- ************************************************ --- CREATE VIEW long_terminal_repeat AS SELECT feature_id AS long_terminal_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'long_terminal_repeat'; --- ************************************************ --- *** relation: fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is a fusion. *** --- ************************************************ --- CREATE VIEW fusion_gene AS SELECT feature_id AS fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'fusion_gene'; --- ************************************************ --- *** relation: engineered_fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A fusion gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_fusion_gene AS SELECT feature_id AS engineered_fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat_region containing repeat_units *** --- *** (2 to 4 bp) that is repeated multiple ti *** --- *** mes in tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: dinucleotide_repeat_microsatellite_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dinucleotide_repeat_microsatellite_feature AS SELECT feature_id AS dinucleotide_repeat_microsatellite_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: trinuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trinuc_repeat_microsat AS SELECT feature_id AS trinuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: engineered_foreign_repetitive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element that is engineered *** --- *** and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_repetitive_element AS SELECT feature_id AS engineered_foreign_repetitive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_repetitive_element'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. It is a palindr *** --- *** ome, and it may, or may not be hyphenate *** --- *** d. Examples: GCTGATCAGC, or GCTGA-----TC *** --- *** AGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: u12_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A type of spliceosomal intron spliced by *** --- *** the U12 spliceosome, that includes U11, *** --- *** U12, U4atac/U6atac and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u12_intron AS SELECT feature_id AS u12_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_intron'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: d_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Displacement loop; a region within mitoc *** --- *** hondrial DNA in which a short stretch of *** --- *** RNA is paired with one strand of DNA, d *** --- *** isplacing the original partner DNA stran *** --- *** d in this region; also used to describe *** --- *** the displacement of a region of one stra *** --- *** nd of duplex DNA by a single stranded in *** --- *** vader in the reaction catalyzed by RecA *** --- *** protein. *** --- ************************************************ --- CREATE VIEW d_loop AS SELECT feature_id AS d_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop'; --- ************************************************ --- *** relation: recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature AS SELECT feature_id AS recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'recombination_feature'; --- ************************************************ --- *** relation: specific_recombination_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW specific_recombination_site AS SELECT feature_id AS specific_recombination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'specific_recombination_site'; --- ************************************************ --- *** relation: recombination_feature_of_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature_of_rearranged_gene AS SELECT feature_id AS recombination_feature_of_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'recombination_feature_of_rearranged_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature'; --- ************************************************ --- *** relation: j_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including J-heptame *** --- *** r, J-spacer and J-nonamer in 5' of J-reg *** --- *** ion of a J-gene or J-sequence. *** --- ************************************************ --- CREATE VIEW j_gene_recombination_feature AS SELECT feature_id AS j_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base_site *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G or (in RNA) U. *** --- ************************************************ --- CREATE VIEW modified_base_site AS SELECT feature_id AS modified_base_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'modified_base_site'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: experimentally_determined *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that has *** --- *** been experiemntally verified. *** --- ************************************************ --- CREATE VIEW experimentally_determined AS SELECT feature_id AS experimentally_determined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined'; --- ************************************************ --- *** relation: stem_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A double-helical region of nucleic acid *** --- *** formed by base-pairing between adjacent *** --- *** (inverted) complementary sequences. *** --- ************************************************ --- CREATE VIEW stem_loop AS SELECT feature_id AS stem_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop' OR cvterm.name = 'stem_loop'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: tss *** --- *** relation type: VIEW *** --- *** *** --- *** The first base where RNA polymerase begi *** --- *** ns to synthesize the RNA transcript. *** --- ************************************************ --- CREATE VIEW tss AS SELECT feature_id AS tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'TSS'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS'; --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Complementary DNA; A piece of DNA copied *** --- *** from an mRNA and spliced into a vector *** --- *** for propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** First codon to be translated by a riboso *** --- *** me. *** --- ************************************************ --- CREATE VIEW start_codon AS SELECT feature_id AS start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'start_codon'; --- ************************************************ --- *** relation: stop_codon *** --- *** relation type: VIEW *** --- *** *** --- *** In mRNA, a set of three nucleotides that *** --- *** indicates the end of information for pr *** --- *** otein synthesis. *** --- ************************************************ --- CREATE VIEW stop_codon AS SELECT feature_id AS stop_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon'; --- ************************************************ --- *** relation: intronic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Sequences within the intron that modulat *** --- *** e splice site selection for some introns *** --- *** . *** --- ************************************************ --- CREATE VIEW intronic_splice_enhancer AS SELECT feature_id AS intronic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer'; --- ************************************************ --- *** relation: mrna_with_plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_1_frameshift AS SELECT feature_id AS mrna_with_plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_1_frameshift'; --- ************************************************ --- *** relation: nuclease_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclease_hypersensitive_site AS SELECT feature_id AS nuclease_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_hypersensitive_site'; --- ************************************************ --- *** relation: coding_start *** --- *** relation type: VIEW *** --- *** *** --- *** The first base to be translated into pro *** --- *** tein. *** --- ************************************************ --- CREATE VIEW coding_start AS SELECT feature_id AS coding_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna_large_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a large ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_large_subunit_primary_transcript AS SELECT feature_id AS rrna_large_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_large_subunit_primary_transcript'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: coding_end *** --- *** relation type: VIEW *** --- *** *** --- *** The last base to be translated into prot *** --- *** ein. It does not include the stop codon. *** --- ************************************************ --- CREATE VIEW coding_end AS SELECT feature_id AS coding_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_end'; --- ************************************************ --- *** relation: microarray_oligo *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW microarray_oligo AS SELECT feature_id AS microarray_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo'; --- ************************************************ --- *** relation: mrna_with_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_2_frameshift AS SELECT feature_id AS mrna_with_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_2_frameshift'; --- ************************************************ --- *** relation: conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of sequence similarity by descent *** --- *** from a common ancestor. *** --- ************************************************ --- CREATE VIEW conserved_region AS SELECT feature_id AS conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'conserved_region'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: coding_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Coding region of sequence similarity by *** --- *** descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW coding_conserved_region AS SELECT feature_id AS coding_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: nc_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding region of sequence similarity *** --- *** by descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW nc_conserved_region AS SELECT feature_id AS nc_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_conserved_region'; --- ************************************************ --- *** relation: mrna_with_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mRNA with a minus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_2_frameshift AS SELECT feature_id AS mrna_with_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_2_frameshift'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: mite *** --- *** relation type: VIEW *** --- *** *** --- *** A highly repetitive and short (100-500 b *** --- *** ase pair) transposable element with term *** --- *** inal inverted repeats (TIR) and target s *** --- *** ite duplication (TSD). MITEs do not enco *** --- *** de proteins. *** --- ************************************************ --- CREATE VIEW mite AS SELECT feature_id AS mite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE'; --- ************************************************ --- *** relation: recombination_hotspot *** --- *** relation type: VIEW *** --- *** *** --- *** A region in a genome which promotes reco *** --- *** mbination. *** --- ************************************************ --- CREATE VIEW recombination_hotspot AS SELECT feature_id AS recombination_hotspot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a nucleic ac *** --- *** id molecule which controls its own repli *** --- *** cation through the interaction of specif *** --- *** ic proteins at one or more origins of re *** --- *** plication. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** A cytologically distinguishable feature *** --- *** of a chromosome, often made visible by s *** --- *** taining, and usually alternating light a *** --- *** nd dark. *** --- ************************************************ --- CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: site_specific_recombination_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW site_specific_recombination_target_region AS SELECT feature_id AS site_specific_recombination_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'site_specific_recombination_target_region'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'match'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a cDNA clone or PCR product; t *** --- *** ypically a few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'EST'; --- ************************************************ --- *** relation: loxp_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loxp_site AS SELECT feature_id AS loxp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to repeating *** --- *** units. The forms found in nature are deo *** --- *** xyribonucleic acid (DNA), where the repe *** --- *** ating units are 2-deoxy-D-ribose rings c *** --- *** onnected to a phosphate backbone, and ri *** --- *** bonucleic acid (RNA), where the repeatin *** --- *** g units are D-ribose rings connected to *** --- *** a phosphate backbone. *** --- ************************************************ --- CREATE VIEW nucleic_acid AS SELECT feature_id AS nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'nucleic_acid'; --- ************************************************ --- *** relation: protein_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW protein_match AS SELECT feature_id AS protein_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: frt_site *** --- *** relation type: VIEW *** --- *** *** --- *** An inversion site found on the Saccharom *** --- *** yces cerevisiae 2 micron plasmid. *** --- ************************************************ --- CREATE VIEW frt_site AS SELECT feature_id AS frt_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site'; --- ************************************************ --- *** relation: synthetic_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to decide a sequence of nuc *** --- *** leotides, nucleotide analogs, or amino a *** --- *** cids that has been designed by an experi *** --- *** menter and which may, or may not, corres *** --- *** pond with any natural sequence. *** --- ************************************************ --- CREATE VIEW synthetic_sequence AS SELECT feature_id AS synthetic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'synthetic_sequence'; --- ************************************************ --- *** relation: dna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a 2-deoxy-D-ribose ring c *** --- *** onnected to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW dna AS SELECT feature_id AS dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'DNA'; --- ************************************************ --- *** relation: sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW sequence_assembly AS SELECT feature_id AS sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'sequence_assembly'; --- ************************************************ --- *** relation: group_1_intron_homing_endonuclease_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_1_intron_homing_endonuclease_target_region AS SELECT feature_id AS group_1_intron_homing_endonuclease_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_1_intron_homing_endonuclease_target_region'; --- ************************************************ --- *** relation: haplotype_block *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome which is co-inher *** --- *** ited as the result of the lack of histor *** --- *** ic recombination within it. *** --- ************************************************ --- CREATE VIEW haplotype_block AS SELECT feature_id AS haplotype_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype_block'; --- ************************************************ --- *** relation: rna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a D-ribose ring connected *** --- *** to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW rna AS SELECT feature_id AS rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA'; --- ************************************************ --- *** relation: flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region that is *** --- *** bounded either side by a paricular kind *** --- *** of region. *** --- ************************************************ --- CREATE VIEW flanked AS SELECT feature_id AS flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'flanked'; --- ************************************************ --- *** relation: floxed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence that is *** --- *** flanked by Lox-P sites. *** --- ************************************************ --- CREATE VIEW floxed AS SELECT feature_id AS floxed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er code for a unique amino acid or the t *** --- *** ermination of translation and are contai *** --- *** ned within the CDS. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'codon'; --- ************************************************ --- *** relation: frt_flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe sequence that i *** --- *** s flanked by the FLP recombinase recogni *** --- *** tion site, FRT. *** --- ************************************************ --- CREATE VIEW frt_flanked AS SELECT feature_id AS frt_flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_flanked'; --- ************************************************ --- *** relation: invalidated_by_chimeric_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone constructed from more than *** --- *** one mRNA. Usually an experimental artifa *** --- *** ct. *** --- ************************************************ --- CREATE VIEW invalidated_by_chimeric_cdna AS SELECT feature_id AS invalidated_by_chimeric_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA'; --- ************************************************ --- *** relation: floxed_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene that is floxed. *** --- ************************************************ --- CREATE VIEW floxed_gene AS SELECT feature_id AS floxed_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene'; --- ************************************************ --- *** relation: transposable_element_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence surrounding a tra *** --- *** nsposible element. *** --- ************************************************ --- CREATE VIEW transposable_element_flanking_region AS SELECT feature_id AS transposable_element_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region'; --- ************************************************ --- *** relation: integron *** --- *** relation type: VIEW *** --- *** *** --- *** A region encoding an integrase which act *** --- *** s at a site adjacent to it (attI_site) t *** --- *** o insert DNA which must include but is n *** --- *** ot limited to an attC_site. *** --- ************************************************ --- CREATE VIEW integron AS SELECT feature_id AS integron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integron'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: atti_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an integron, adjacent to *** --- *** an integrase, at which site specific re *** --- *** combination involving an attC_site takes *** --- *** place. *** --- ************************************************ --- CREATE VIEW atti_site AS SELECT feature_id AS atti_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site'; --- ************************************************ --- *** relation: transposable_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW transposable_element_insertion_site AS SELECT feature_id AS transposable_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that encodes function requi *** --- *** red for conjugation. *** --- ************************************************ --- CREATE VIEW conjugative_transposon AS SELECT feature_id AS conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conjugative_transposon'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA sequence that has catalytic activ *** --- *** ity with or without an associated ribonu *** --- *** cleoprotein. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme' OR cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: recombinationally_inverted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene by i *** --- *** nversion. *** --- ************************************************ --- CREATE VIEW recombinationally_inverted_gene AS SELECT feature_id AS recombinationally_inverted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5_8S ribosomal RNA (5. 8S rRNA) is a com *** --- *** ponent of the large subunit of the eukar *** --- *** yotic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurs *** --- *** or that also contains 18S and 28S rRNA. *** --- *** Functionally, it is thought that 5.8S rR *** --- *** NA may be involved in ribosome transloca *** --- *** tion. It is also known to form covalent *** --- *** linkage to the p53 tumour suppressor pro *** --- *** tein. 5_8S rRNA is also found in archaea *** --- *** . *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S'; --- ************************************************ --- *** relation: rna_6s *** --- *** relation type: VIEW *** --- *** *** --- *** A small (184-nt in E. coli) RNA that for *** --- *** ms a hairpin type structure. 6S RNA asso *** --- *** ciates with RNA polymerase in a highly s *** --- *** pecific manner. 6S RNA represses express *** --- *** ion from a sigma70-dependent promoter du *** --- *** ring stationary phase. *** --- ************************************************ --- CREATE VIEW rna_6s AS SELECT feature_id AS rna_6s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_6S'; --- ************************************************ --- *** relation: csrb_rsmb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An enterobacterial RNA that binds the Cs *** --- *** rA protein. The CsrB RNAs contain a cons *** --- *** erved motif CAGGXXG that is found in up *** --- *** to 18 copies and has been suggested to b *** --- *** ind CsrA. The Csr regulatory system has *** --- *** a strong negative regulatory effect on g *** --- *** lycogen biosynthesis, glyconeogenesis an *** --- *** d glycogen catabolism and a positive reg *** --- *** ulatory effect on glycolysis. In other b *** --- *** acteria such as Erwinia caratovara the R *** --- *** smA protein has been shown to regulate t *** --- *** he production of virulence determinants, *** --- *** such extracellular enzymes. RsmA binds *** --- *** to RsmB regulatory RNA which is also a m *** --- *** ember of this family. *** --- ************************************************ --- CREATE VIEW csrb_rsmb_rna AS SELECT feature_id AS csrb_rsmb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CsrB_RsmB_RNA'; --- ************************************************ --- *** relation: dsra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** DsrA RNA regulates both transcription, b *** --- *** y overcoming transcriptional silencing b *** --- *** y the nucleoid-associated H-NS protein, *** --- *** and translation, by promoting efficient *** --- *** translation of the stress sigma factor, *** --- *** RpoS. These two activities of DsrA can b *** --- *** e separated by mutation: the first of th *** --- *** ree stem-loops of the 85 nucleotide RNA *** --- *** is necessary for RpoS translation but no *** --- *** t for anti-H-NS action, while the second *** --- *** stem-loop is essential for antisilencin *** --- *** g and less critical for RpoS translation *** --- *** . The third stem-loop, which behaves as *** --- *** a transcription terminator, can be subst *** --- *** ituted by the trp transcription terminat *** --- *** or without loss of either DsrA function. *** --- *** The sequence of the first stem-loop of *** --- *** DsrA is complementary with the upstream *** --- *** leader portion of RpoS messenger RNA, su *** --- *** ggesting that pairing of DsrA with the R *** --- *** poS message might be important for trans *** --- *** lational regulation. *** --- ************************************************ --- CREATE VIEW dsra_rna AS SELECT feature_id AS dsra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA' OR cvterm.name = 'DsrA_RNA'; --- ************************************************ --- *** relation: gcvb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA involved in exp *** --- *** ression of the dipeptide and oligopeptid *** --- *** e transport systems in Escherichia coli. *** --- ************************************************ --- CREATE VIEW gcvb_rna AS SELECT feature_id AS gcvb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: group_iia_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iia_intron AS SELECT feature_id AS group_iia_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron'; --- ************************************************ --- *** relation: group_iib_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iib_intron AS SELECT feature_id AS group_iib_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIB_intron'; --- ************************************************ --- *** relation: micf_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-translated 93 nt antisense RNA tha *** --- *** t binds its target ompF mRNA and regulat *** --- *** es ompF expression by inhibiting transla *** --- *** tion and inducing degradation of the mes *** --- *** sage. *** --- ************************************************ --- CREATE VIEW micf_rna AS SELECT feature_id AS micf_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA'; --- ************************************************ --- *** relation: oxys_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA which is induce *** --- *** d in response to oxidative stress in Esc *** --- *** herichia coli. Acts as a global regulato *** --- *** r to activate or repress the expression *** --- *** of as many as 40 genes, including the fh *** --- *** lA-encoded transcriptional activator and *** --- *** the rpoS-encoded sigma(s) subunit of RN *** --- *** A polymerase. OxyS is bound by the Hfq p *** --- *** rotein, that increases the OxyS RNA inte *** --- *** raction with its target messages. *** --- ************************************************ --- CREATE VIEW oxys_rna AS SELECT feature_id AS oxys_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'OxyS_RNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterised activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: rpra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Translational regulation of the stationa *** --- *** ry phase sigma factor RpoS is mediated b *** --- *** y the formation of a double-stranded RNA *** --- *** stem-loop structure in the upstream reg *** --- *** ion of the rpoS messenger RNA, occluding *** --- *** the translation initiation site. Clones *** --- *** carrying rprA (RpoS regulator RNA) incr *** --- *** eased the translation of RpoS. The rprA *** --- *** gene encodes a 106 nucleotide regulatory *** --- *** RNA. As with DsrA Rfam:RF00014, RprA is *** --- *** predicted to form three stem-loops. Thu *** --- *** s, at least two small RNAs, DsrA and Rpr *** --- *** A, participate in the positive regulatio *** --- *** n of RpoS translation. Unlike DsrA, RprA *** --- *** does not have an extensive region of co *** --- *** mplementarity to the RpoS leader, leavin *** --- *** g its mechanism of action unclear. RprA *** --- *** is non-essential. *** --- ************************************************ --- CREATE VIEW rpra_rna AS SELECT feature_id AS rpra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RprA_RNA'; --- ************************************************ --- *** relation: rre_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The Rev response element (RRE) is encode *** --- *** d within the HIV-env gene. Rev is an ess *** --- *** ential regulatory protein of HIV that bi *** --- *** nds an internal loop of the RRE leading, *** --- *** encouraging further Rev-RRE binding. Th *** --- *** is RNP complex is critical for mRNA expo *** --- *** rt and hence for expression of the HIV s *** --- *** tructural proteins. *** --- ************************************************ --- CREATE VIEW rre_rna AS SELECT feature_id AS rre_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RRE_RNA'; --- ************************************************ --- *** relation: spot_42_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A 109-nucleotide RNA of E. coli that see *** --- *** ms to have a regulatory role on the gala *** --- *** ctose operon. Changes in Spot 42 levels *** --- *** are implicated in affecting DNA polymera *** --- *** se I levels. *** --- ************************************************ --- CREATE VIEW spot_42_rna AS SELECT feature_id AS spot_42_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spot_42_RNA'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesises telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA is an snRNA required for th *** --- *** e splicing of the minor U12-dependent cl *** --- *** ass of eukaryotic nuclear introns. It fo *** --- *** rms a base paired complex with U4atac_sn *** --- *** RNA (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: sequence_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describes a quality of sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW sequence_attribute AS SELECT feature_id AS sequence_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymer_attribute' OR cvterm.name = 'feature_attribute' OR cvterm.name = 'sequence_location' OR cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_attribute'; --- ************************************************ --- *** relation: gene_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_attribute AS SELECT feature_id AS gene_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'gene_attribute'; --- ************************************************ --- *** relation: u14_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snorna AS SELECT feature_id AS u14_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonucleoprotein comp *** --- *** lex. The complex consists of a major vau *** --- *** lt protein (MVP), two minor vault protei *** --- *** ns (VPARP and TEP1), and several small u *** --- *** ntranslated RNA molecules. It has been s *** --- *** uggested that the vault complex is invol *** --- *** ved in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: twintron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron within an intron. Twintrons ar *** --- *** e group II or III introns, into which an *** --- *** other group II or III intron has been tr *** --- *** ansposed. *** --- ************************************************ --- CREATE VIEW twintron AS SELECT feature_id AS twintron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'twintron'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in eukaryotes, wh *** --- *** ich functions as the small subunit of th *** --- *** e ribosome. *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region on the surface of a molecule th *** --- *** at may interact with another molecule. W *** --- *** hen applied to polypeptides: Amino acids *** --- *** involved in binding or interactions. It *** --- *** can also apply to an amino acid bond wh *** --- *** ich is represented by the positions of t *** --- *** he two flanking amino acids. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a p *** --- *** rotein. *** --- ************************************************ --- CREATE VIEW protein_binding_site AS SELECT feature_id AS protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'protein_binding_site'; --- ************************************************ --- *** relation: rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that rescues. *** --- ************************************************ --- CREATE VIEW rescue_region AS SELECT feature_id AS rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'rescue_region'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polynucleotide sequence prod *** --- *** uced by digestion with a restriction end *** --- *** onuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment' OR cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequence differs from *** --- *** that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: invalidated_by_genomic_contamination *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to genomic contaminat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_contamination AS SELECT feature_id AS invalidated_by_genomic_contamination_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_contamination'; --- ************************************************ --- *** relation: invalidated_by_genomic_polya_primed_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to polyA priming. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_polya_primed_cdna AS SELECT feature_id AS invalidated_by_genomic_polya_primed_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA'; --- ************************************************ --- *** relation: invalidated_by_partial_processing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to partial processing *** --- *** . *** --- ************************************************ --- CREATE VIEW invalidated_by_partial_processing AS SELECT feature_id AS invalidated_by_partial_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_partial_processing'; --- ************************************************ --- *** relation: polypeptide_domain *** --- *** relation type: VIEW *** --- *** *** --- *** A structurally or functionally defined p *** --- *** rotein region. In proteins with multiple *** --- *** domains, the combination of the domains *** --- *** determines the function of the protein. *** --- *** A region which has been shown to recur *** --- *** throughout evolution. *** --- ************************************************ --- CREATE VIEW polypeptide_domain AS SELECT feature_id AS polypeptide_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The signal_peptide is a short region of *** --- *** the peptide located at the N-terminus th *** --- *** at directs the protein to be secreted or *** --- *** part of membrane components. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: mature_protein_region *** --- *** relation type: VIEW *** --- *** *** --- *** The polypeptide sequence that remains wh *** --- *** en the cleaved peptide regions have been *** --- *** cleaved from the immature peptide. *** --- ************************************************ --- CREATE VIEW mature_protein_region AS SELECT feature_id AS mature_protein_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide' OR cvterm.name = 'mature_protein_region'; --- ************************************************ --- *** relation: five_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_terminal_inverted_repeat AS SELECT feature_id AS five_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: three_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_terminal_inverted_repeat AS SELECT feature_id AS three_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: u5_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_ltr_region AS SELECT feature_id AS u5_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U5_LTR_region'; --- ************************************************ --- *** relation: r_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_ltr_region AS SELECT feature_id AS r_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'R_LTR_region'; --- ************************************************ --- *** relation: u3_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_ltr_region AS SELECT feature_id AS u3_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'U3_LTR_region'; --- ************************************************ --- *** relation: five_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr AS SELECT feature_id AS five_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR'; --- ************************************************ --- *** relation: three_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr AS SELECT feature_id AS three_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_LTR'; --- ************************************************ --- *** relation: r_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_five_prime_ltr_region AS SELECT feature_id AS r_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region'; --- ************************************************ --- *** relation: u5_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_five_prime_ltr_region AS SELECT feature_id AS u5_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region'; --- ************************************************ --- *** relation: u3_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_five_prime_ltr_region AS SELECT feature_id AS u3_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region'; --- ************************************************ --- *** relation: r_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_three_prime_ltr_region AS SELECT feature_id AS r_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region'; --- ************************************************ --- *** relation: u3_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_three_prime_ltr_region AS SELECT feature_id AS u3_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_three_prime_LTR_region'; --- ************************************************ --- *** relation: u5_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_three_prime_ltr_region AS SELECT feature_id AS u5_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_three_prime_LTR_region'; --- ************************************************ --- *** relation: non_ltr_retrotransposon_polymeric_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polymeric tract, such as poly(dA), wit *** --- *** hin a non_LTR_retrotransposon. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon_polymeric_tract AS SELECT feature_id AS non_ltr_retrotransposon_polymeric_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract'; --- ************************************************ --- *** relation: target_site_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of the target DNA that is dup *** --- *** licated when a transposable element or p *** --- *** hage inserts; usually found at each end *** --- *** the insertion. *** --- ************************************************ --- CREATE VIEW target_site_duplication AS SELECT feature_id AS target_site_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication'; --- ************************************************ --- *** relation: rr_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polypurine tract within an LTR_retrotr *** --- *** ansposon. *** --- ************************************************ --- CREATE VIEW rr_tract AS SELECT feature_id AS rr_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: inverted_ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_ring_chromosome AS SELECT feature_id AS inverted_ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome'; --- ************************************************ --- *** relation: vector_replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A replicon that has been modified to act *** --- *** as a vector for foreign sequence. *** --- ************************************************ --- CREATE VIEW vector_replicon AS SELECT feature_id AS vector_replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'vector_replicon'; --- ************************************************ --- *** relation: ss_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ss_oligo AS SELECT feature_id AS ss_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ss_oligo'; --- ************************************************ --- *** relation: ds_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ds_oligo AS SELECT feature_id AS ds_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'ds_oligo'; --- ************************************************ --- *** relation: polymer_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the kind of bio *** --- *** logical sequence. *** --- ************************************************ --- CREATE VIEW polymer_attribute AS SELECT feature_id AS polymer_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'polymer_attribute'; --- ************************************************ --- *** relation: three_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_noncoding_exon AS SELECT feature_id AS three_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon'; --- ************************************************ --- *** relation: five_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_noncoding_exon AS SELECT feature_id AS five_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_noncoding_exon'; --- ************************************************ --- *** relation: utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Intron located in the untranslated regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW utr_intron AS SELECT feature_id AS utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'UTR_intron'; --- ************************************************ --- *** relation: five_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_intron AS SELECT feature_id AS five_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron'; --- ************************************************ --- *** relation: three_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_intron AS SELECT feature_id AS three_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR_intron'; --- ************************************************ --- *** relation: random_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides or amino acids *** --- *** which, by design, has a "random" order *** --- *** of components, given a predetermined inp *** --- *** ut frequency of these components. *** --- ************************************************ --- CREATE VIEW random_sequence AS SELECT feature_id AS random_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence'; --- ************************************************ --- *** relation: interband *** --- *** relation type: VIEW *** --- *** *** --- *** A light region between two darkly staini *** --- *** ng bands in a polytene chromosome. *** --- ************************************************ --- CREATE VIEW interband AS SELECT feature_id AS interband_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interband'; --- ************************************************ --- *** relation: gene_with_polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polyadenylated mRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW gene_with_polyadenylated_mrna AS SELECT feature_id AS gene_with_polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA'; --- ************************************************ --- *** relation: transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transposition AS SELECT feature_id AS transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'transposition'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small, 17-28-nt, small interfering RNA *** --- *** derived from transcripts of repetitive *** --- *** elements. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: gene_with_mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA with a frame *** --- *** shift. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_with_frameshift AS SELECT feature_id AS gene_with_mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_with_frameshift'; --- ************************************************ --- *** relation: recombinationally_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is recombinationally rearran *** --- *** ged. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_gene AS SELECT feature_id AS recombinationally_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'recombinationally_rearranged_gene'; --- ************************************************ --- *** relation: interchromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving an in *** --- *** sertion from another chromosome. *** --- ************************************************ --- CREATE VIEW interchromosomal_duplication AS SELECT feature_id AS interchromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication'; --- ************************************************ --- *** relation: d_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including D-region *** --- *** with 5' UTR and 3' UTR, also designated *** --- *** as D-segment. *** --- ************************************************ --- CREATE VIEW d_gene AS SELECT feature_id AS d_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene'; --- ************************************************ --- *** relation: gene_with_trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a transcript that is trans-s *** --- *** pliced. *** --- ************************************************ --- CREATE VIEW gene_with_trans_spliced_transcript AS SELECT feature_id AS gene_with_trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_trans_spliced_transcript'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment'; --- ************************************************ --- *** relation: inversion_derived_bipartite_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a deficiency *** --- *** at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_deficiency AS SELECT feature_id AS inversion_derived_bipartite_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: encodes_alternately_spliced_transcripts *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes more than one transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW encodes_alternately_spliced_transcripts AS SELECT feature_id AS encodes_alternately_spliced_transcripts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_alternately_spliced_transcripts'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendant of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a defic *** --- *** iency at one end of the inversion and a *** --- *** duplication at the other end of the inve *** --- *** rsion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_duplication AS SELECT feature_id AS inversion_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: v_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including L-part1, *** --- *** V-intron and V-exon, with the 5' UTR and *** --- *** 3' UTR. *** --- ************************************************ --- CREATE VIEW v_gene AS SELECT feature_id AS v_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_stability *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is regulated *** --- *** by the stability of the resulting prote *** --- *** in. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_stability AS SELECT feature_id AS post_translationally_regulated_by_protein_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is modified *** --- *** to regulate it. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_modification AS SELECT feature_id AS post_translationally_regulated_by_protein_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_modification'; --- ************************************************ --- *** relation: j_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA of an immunoglobuli *** --- *** n/T-cell receptor gene including J-regio *** --- *** n with 5' UTR (SO:0000204) and 3' UTR (S *** --- *** O:0000205), also designated as J-segment *** --- *** . *** --- ************************************************ --- CREATE VIEW j_gene AS SELECT feature_id AS j_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene'; --- ************************************************ --- *** relation: autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation. *** --- ************************************************ --- CREATE VIEW autoregulated AS SELECT feature_id AS autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'autoregulated'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: negatively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation where it decr *** --- *** eases transcription. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated AS SELECT feature_id AS negatively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path (SO:0000472). *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone' OR cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: positively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation, where it inc *** --- *** reases transcription. *** --- ************************************************ --- CREATE VIEW positively_autoregulated AS SELECT feature_id AS positively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated'; --- ************************************************ --- *** relation: contig_read *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequencer read which is part of a *** --- *** contig. *** --- ************************************************ --- CREATE VIEW contig_read AS SELECT feature_id AS contig_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read'; --- ************************************************ --- *** relation: c_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including C-region (and intro *** --- *** ns if present) with 5' UTR (SO:0000204) *** --- *** and 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW c_gene AS SELECT feature_id AS c_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_gene'; --- ************************************************ --- *** relation: trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_transcript AS SELECT feature_id AS trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'trans_spliced_transcript'; --- ************************************************ --- *** relation: tiling_path_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone which is part of a tiling path. *** --- *** A tiling path is a set of sequencing sub *** --- *** strates, typically clones, which have be *** --- *** en selected in order to efficiently cove *** --- *** r a region of the genome in preparation *** --- *** for sequencing and assembly. *** --- ************************************************ --- CREATE VIEW tiling_path_clone AS SELECT feature_id AS tiling_path_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone'; --- ************************************************ --- *** relation: terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An inverted repeat (SO:0000294) occuring *** --- *** at the termini of a DNA transposon. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat AS SELECT feature_id AS terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'terminal_inverted_repeat'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_gene_cluster AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: three_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 3' exon that is not *** --- *** coding. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_noncoding_region AS SELECT feature_id AS three_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene, and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW dj_j_cluster AS SELECT feature_id AS dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster'; --- ************************************************ --- *** relation: five_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 5' exon preceding th *** --- *** e start codon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_noncoding_region AS SELECT feature_id AS five_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene, one J-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW vdj_j_c_cluster AS SELECT feature_id AS vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_j_cluster AS SELECT feature_id AS vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_cluster'; --- ************************************************ --- *** relation: vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_c_cluster AS SELECT feature_id AS vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_C_cluster'; --- ************************************************ --- *** relation: vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene, one J-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW vj_j_c_cluster AS SELECT feature_id AS vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_C_cluster'; --- ************************************************ --- *** relation: vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one J- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_j_cluster AS SELECT feature_id AS vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_cluster'; --- ************************************************ --- *** relation: d_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_gene_recombination_feature AS SELECT feature_id AS d_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'D_gene_recombination_feature'; --- ************************************************ --- *** relation: three_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site like CAC *** --- *** AGTG, part of a 3' D-recombination signa *** --- *** l sequence of an immunoglobulin/T-cell r *** --- *** eceptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_heptamer AS SELECT feature_id AS three_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer'; --- ************************************************ --- *** relation: three_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** A 9 nucleotide recombination site (e.g. *** --- *** ACAAAAACC), part of a 3' D-recombination *** --- *** signal sequence of an immunoglobulin/T- *** --- *** cell receptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_nonamer AS SELECT feature_id AS three_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer'; --- ************************************************ --- *** relation: three_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** A 12 or 23 nucleotide spacer between the *** --- *** 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-R *** --- *** S. *** --- ************************************************ --- CREATE VIEW three_prime_d_spacer AS SELECT feature_id AS three_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer'; --- ************************************************ --- *** relation: five_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CTGTG), part of a 5' D-recombination sig *** --- *** nal sequence (SO:0000556) of an immunogl *** --- *** obulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_heptamer AS SELECT feature_id AS five_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_heptamer'; --- ************************************************ --- *** relation: five_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a five_prime_D-recombi *** --- *** nation signal sequence (SO:0000556) of a *** --- *** n immunoglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_nonamer AS SELECT feature_id AS five_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_nonamer'; --- ************************************************ --- *** relation: five_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the 5 *** --- *** ' D-heptamer (SO:0000496) and 5' D-nonam *** --- *** er (SO:0000497) of a 5' D-recombination *** --- *** signal sequence (SO:0000556) of an immun *** --- *** oglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_spacer AS SELECT feature_id AS five_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_spacer'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous piece of sequence similar t *** --- *** o the 'virtual contig' concept of the En *** --- *** sembl database. *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. Th *** --- *** is is less energetically favourable than *** --- *** watson crick base pairing. Hoogsteen GC *** --- *** base pairs only have two hydrogen bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW hoogsteen_base_pair AS SELECT feature_id AS hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Hoogsteen_base_pair'; --- ************************************************ --- *** relation: reverse_hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW reverse_hoogsteen_base_pair AS SELECT feature_id AS reverse_hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_Hoogsteen_base_pair'; --- ************************************************ --- *** relation: d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_c_cluster AS SELECT feature_id AS d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_C_cluster'; --- ************************************************ --- *** relation: d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW d_dj_cluster AS SELECT feature_id AS d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_cluster'; --- ************************************************ --- *** relation: d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_c_cluster AS SELECT feature_id AS d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of an exon, *** --- *** part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, and one J-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_cluster AS SELECT feature_id AS d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_cluster'; --- ************************************************ --- *** relation: d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW d_j_c_cluster AS SELECT feature_id AS d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster'; --- ************************************************ --- *** relation: vd_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including L-part1, V-intron and V *** --- *** -D-exon, with the 5' UTR (SO:0000204) an *** --- *** d 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vd_gene AS SELECT feature_id AS vd_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene'; --- ************************************************ --- *** relation: j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one J-gene and one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW j_c_cluster AS SELECT feature_id AS j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a deficiency *** --- *** at one end and presumed to have a defic *** --- *** iency or duplication at the other end of *** --- *** the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_aneuploid AS SELECT feature_id AS inversion_derived_deficiency_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_aneuploid'; --- ************************************************ --- *** relation: j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one J-gene. *** --- ************************************************ --- CREATE VIEW j_cluster AS SELECT feature_id AS j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_cluster'; --- ************************************************ --- *** relation: j_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a J-gene recombination *** --- *** feature of an immunoglobulin/T-cell rec *** --- *** eptor gene. *** --- ************************************************ --- CREATE VIEW j_nonamer AS SELECT feature_id AS j_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_nonamer'; --- ************************************************ --- *** relation: j_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of a J-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW j_heptamer AS SELECT feature_id AS j_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_heptamer'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of a transcr *** --- *** ipt, part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: j_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the J *** --- *** -nonamer and the J-heptamer of a J-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW j_spacer AS SELECT feature_id AS j_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_spacer'; --- ************************************************ --- *** relation: v_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_dj_cluster AS SELECT feature_id AS v_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_cluster'; --- ************************************************ --- *** relation: v_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_cluster AS SELECT feature_id AS v_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_cluster'; --- ************************************************ --- *** relation: v_vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_c_cluster AS SELECT feature_id AS v_vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_C_cluster'; --- ************************************************ --- *** relation: v_vdj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VDJ *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW v_vdj_cluster AS SELECT feature_id AS v_vdj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_cluster'; --- ************************************************ --- *** relation: v_vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_cluster AS SELECT feature_id AS v_vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_cluster'; --- ************************************************ --- *** relation: v_vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_c_cluster AS SELECT feature_id AS v_vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_C_cluster'; --- ************************************************ --- *** relation: v_vj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_vj_cluster AS SELECT feature_id AS v_vj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_cluster'; --- ************************************************ --- *** relation: v_vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_cluster AS SELECT feature_id AS v_vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_cluster'; --- ************************************************ --- *** relation: v_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one V-gene. *** --- ************************************************ --- CREATE VIEW v_cluster AS SELECT feature_id AS v_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_cluster'; --- ************************************************ --- *** relation: v_d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_c_cluster AS SELECT feature_id AS v_d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_cluster AS SELECT feature_id AS v_d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene, one J-gene and one C-gene *** --- *** . *** --- ************************************************ --- CREATE VIEW v_d_dj_j_c_cluster AS SELECT feature_id AS v_d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_j_cluster AS SELECT feature_id AS v_d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_cluster'; --- ************************************************ --- *** relation: v_d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_c_cluster AS SELECT feature_id AS v_d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_C_cluster'; --- ************************************************ --- *** relation: v_d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_cluster AS SELECT feature_id AS v_d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_cluster'; --- ************************************************ --- *** relation: v_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of V-gene recombination fea *** --- *** ture of an immunoglobulin/T-cell recepto *** --- *** r gene. *** --- ************************************************ --- CREATE VIEW v_heptamer AS SELECT feature_id AS v_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_heptamer'; --- ************************************************ --- *** relation: v_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW v_j_cluster AS SELECT feature_id AS v_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_cluster'; --- ************************************************ --- *** relation: v_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW v_j_c_cluster AS SELECT feature_id AS v_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_C_cluster'; --- ************************************************ --- *** relation: v_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. AC *** --- *** AAAAACC), part of V-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW v_nonamer AS SELECT feature_id AS v_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_nonamer'; --- ************************************************ --- *** relation: v_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the V *** --- *** -heptamer and the V-nonamer of a V-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_spacer AS SELECT feature_id AS v_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_spacer'; --- ************************************************ --- *** relation: v_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including V-heptame *** --- *** r, V-spacer and V-nonamer in 3' of V-reg *** --- *** ion of a V-gene or V-sequence of an immu *** --- *** noglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_gene_recombination_feature AS SELECT feature_id AS v_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene_recombination_feature'; --- ************************************************ --- *** relation: dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW dj_c_cluster AS SELECT feature_id AS dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_C_cluster'; --- ************************************************ --- *** relation: dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA in rearranged configuration *** --- *** including at least one D-J-GENE, one J-G *** --- *** ENE and one C-GENE. *** --- ************************************************ --- CREATE VIEW dj_j_c_cluster AS SELECT feature_id AS dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one C *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_c_cluster AS SELECT feature_id AS vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_C_cluster'; --- ************************************************ --- *** relation: v_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_c_cluster AS SELECT feature_id AS v_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_C_cluster'; --- ************************************************ --- *** relation: helitron *** --- *** relation type: VIEW *** --- *** *** --- *** A rolling circle transposon. Autonomous *** --- *** helitrons encode a 5'-to-3' DNA helicase *** --- *** and nuclease/ligase similar to those en *** --- *** coded by known rolling-circle replicons. *** --- ************************************************ --- CREATE VIEW helitron AS SELECT feature_id AS helitron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helitron'; --- ************************************************ --- *** relation: recoding_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** The pseudoknots involved in recoding are *** --- *** unique in that, as they play their role *** --- *** as a structure, they are immediately un *** --- *** folded and their now linear sequence ser *** --- *** ves as a template for decoding. *** --- ************************************************ --- CREATE VIEW recoding_pseudoknot AS SELECT feature_id AS recoding_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot'; --- ************************************************ --- *** relation: designed_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW designed_sequence AS SELECT feature_id AS designed_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'designed_sequence'; --- ************************************************ --- *** relation: inversion_derived_bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a dupli *** --- *** cation at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_duplication AS SELECT feature_id AS inversion_derived_bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_duplication'; --- ************************************************ --- *** relation: gene_with_edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript that is *** --- *** edited. *** --- ************************************************ --- CREATE VIEW gene_with_edited_transcript AS SELECT feature_id AS gene_with_edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_edited_transcript'; --- ************************************************ --- *** relation: inversion_derived_duplication_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a duplicatio *** --- *** n at one end and presumed to have a defi *** --- *** ciency or duplication at the other end o *** --- *** f the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_duplication_plus_aneuploid AS SELECT feature_id AS inversion_derived_duplication_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_duplication_plus_aneuploid'; --- ************************************************ --- *** relation: aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aneuploid_chromosome AS SELECT feature_id AS aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'aneuploid_chromosome'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Region in 5' UTR where ribosome assemble *** --- *** s on mRNA. *** --- ************************************************ --- CREATE VIEW shine_dalgarno_sequence AS SELECT feature_id AS shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: five_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 5' most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW five_prime_clip AS SELECT feature_id AS five_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip'; --- ************************************************ --- *** relation: five_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 5' *** --- *** D-nonamer (SO:0000497), 5' D-spacer (SO *** --- *** :0000498), and 5' D-heptamer (SO:0000396 *** --- *** ) in 5' of the D-region of a D-gene, or *** --- *** in 5' of the D-region of DJ-gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_recombination_signal_sequence AS SELECT feature_id AS five_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: three_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 3'-most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW three_prime_clip AS SELECT feature_id AS three_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_clip'; --- ************************************************ --- *** relation: c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including more than one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW c_cluster AS SELECT feature_id AS c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_cluster'; --- ************************************************ --- *** relation: d_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one D-gene. *** --- ************************************************ --- CREATE VIEW d_cluster AS SELECT feature_id AS d_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_cluster'; --- ************************************************ --- *** relation: d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW d_j_cluster AS SELECT feature_id AS d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_cluster'; --- ************************************************ --- *** relation: heptamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Seven nucleotide recombination site (e.g *** --- *** . CACAGTG), part of V-gene, D-gene or J- *** --- *** gene recombination feature of an immunog *** --- *** lobulin or T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW heptamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS heptamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: nonamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nonamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS nonamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_spacer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_spacer AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer'; --- ************************************************ --- *** relation: v_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_c_cluster AS SELECT feature_id AS v_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_c_cluster AS SELECT feature_id AS v_vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_c_cluster AS SELECT feature_id AS v_vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome may be generated by recombi *** --- *** nation between two inverversions; presum *** --- *** ed to have a deficiency or duplication a *** --- *** t each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_aneuploid_chromosome AS SELECT feature_id AS inversion_derived_aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome'; --- ************************************************ --- *** relation: bidirectional_promoter *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bidirectional_promoter AS SELECT feature_id AS bidirectional_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter'; --- ************************************************ --- *** relation: retrotransposed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of a feature that occured a *** --- *** s the product of a reverse transcriptase *** --- *** mediated event. *** --- ************************************************ --- CREATE VIEW retrotransposed AS SELECT feature_id AS retrotransposed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposed'; --- ************************************************ --- *** relation: three_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 3' *** --- *** D-heptamer (SO:0000493), 3' D-spacer, a *** --- *** nd 3' D-nonamer (SO:0000494) in 3' of th *** --- *** e D-region of a D-gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_recombination_signal_sequence AS SELECT feature_id AS three_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: mirna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_encoding AS SELECT feature_id AS mirna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding'; --- ************************************************ --- *** relation: dj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including D-J-region with 5' UTR *** --- *** and 3' UTR, also designated as D-J-segme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW dj_gene AS SELECT feature_id AS dj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_gene'; --- ************************************************ --- *** relation: rrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rrna_encoding AS SELECT feature_id AS rrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_encoding'; --- ************************************************ --- *** relation: vdj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-D-J-exon, with the 5'UTR *** --- *** (SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vdj_gene AS SELECT feature_id AS vdj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_gene'; --- ************************************************ --- *** relation: scrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_encoding AS SELECT feature_id AS scrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_encoding'; --- ************************************************ --- *** relation: vj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-J-exon, with the 5'UTR ( *** --- *** SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vj_gene AS SELECT feature_id AS vj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_gene'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere'; --- ************************************************ --- *** relation: snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_encoding AS SELECT feature_id AS snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'snoRNA_encoding'; --- ************************************************ --- *** relation: edited_transcript_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable feature on a transcript that *** --- *** is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript_feature AS SELECT feature_id AS edited_transcript_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'edited_transcript_feature'; --- ************************************************ --- *** relation: methylation_guide_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a methylat *** --- *** ion guide small nucleolar RNA. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna_primary_transcript AS SELECT feature_id AS methylation_guide_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: rrna_cleavage_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding an rRNA cl *** --- *** eavage snoRNA. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_snorna_primary_transcript AS SELECT feature_id AS rrna_cleavage_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: pre_edited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a transcript that will be *** --- *** edited. *** --- ************************************************ --- CREATE VIEW pre_edited_region AS SELECT feature_id AS pre_edited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region'; --- ************************************************ --- *** relation: tmrna *** --- *** relation type: VIEW *** --- *** *** --- *** A tmRNA liberates a mRNA from a stalled *** --- *** ribosome. To accomplish this part of the *** --- *** tmRNA is used as a reading frame that e *** --- *** nds in a translation stop signal. The br *** --- *** oken mRNA is replaced in the ribosome by *** --- *** the tmRNA and translation of the tmRNA *** --- *** leads to addition of a proteolysis tag t *** --- *** o the incomplete protein enabling recogn *** --- *** ition by a protease. Recently a number o *** --- *** f permuted tmRNAs genes have been found *** --- *** encoded in two parts. TmRNAs have been i *** --- *** dentified in eubacteria and some chlorop *** --- *** lasts but are absent from archeal and eu *** --- *** karyote nuclear genomes. *** --- ************************************************ --- CREATE VIEW tmrna AS SELECT feature_id AS tmrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_encoding AS SELECT feature_id AS c_d_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding'; --- ************************************************ --- *** relation: tmrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tmRNA (S *** --- *** O:0000584). *** --- ************************************************ --- CREATE VIEW tmrna_primary_transcript AS SELECT feature_id AS tmrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_primary_transcript'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyse their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: autocatalytically_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW autocatalytically_spliced_intron AS SELECT feature_id AS autocatalytically_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: srp_rna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a signal r *** --- *** ecognition particle RNA. *** --- ************************************************ --- CREATE VIEW srp_rna_primary_transcript AS SELECT feature_id AS srp_rna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_primary_transcript'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A tertiary structure in RNA where nucleo *** --- *** tides in a loop form base pairs with a r *** --- *** egion of RNA downstream of the loop. *** --- ************************************************ --- CREATE VIEW pseudoknot AS SELECT feature_id AS pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'pseudoknot'; --- ************************************************ --- *** relation: h_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudoknot which contains two stems an *** --- *** d at least two loops. *** --- ************************************************ --- CREATE VIEW h_pseudoknot AS SELECT feature_id AS h_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_pseudoknot'; --- ************************************************ --- *** relation: c_d_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Most box C/D snoRNAs also contain long ( *** --- *** >10 nt) sequences complementary to rRNA. *** --- *** Boxes C and D, as well as boxes C' and *** --- *** D', are usually located in close proximi *** --- *** ty, and form a structure known as the bo *** --- *** x C/D motif. This motif is important for *** --- *** snoRNA stability, processing, nucleolar *** --- *** targeting and function. A small number *** --- *** of box C/D snoRNAs are involved in rRNA *** --- *** processing; most, however, are known or *** --- *** predicted to serve as guide RNAs in ribo *** --- *** se methylation of rRNA. Targeting involv *** --- *** es direct base pairing of the snoRNA at *** --- *** the rRNA site to be modified and selecti *** --- *** on of a rRNA nucleotide a fixed distance *** --- *** from box D or D'. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna AS SELECT feature_id AS c_d_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'C_D_box_snoRNA'; --- ************************************************ --- *** relation: h_aca_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Members of the box H/ACA family contain *** --- *** an ACA triplet, exactly 3 nt upstream fr *** --- *** om the 3' end and an H-box in a hinge re *** --- *** gion that links two structurally similar *** --- *** functional domains of the molecule. Bot *** --- *** h boxes are important for snoRNA biosynt *** --- *** hesis and function. A few box H/ACA snoR *** --- *** NAs are involved in rRNA processing; mos *** --- *** t others are known or predicted to parti *** --- *** cipate in selection of uridine nucleosid *** --- *** es in rRNA to be converted to pseudourid *** --- *** ines. Site selection is mediated by dire *** --- *** ct base pairing of the snoRNA with rRNA *** --- *** through one or both targeting domains. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna AS SELECT feature_id AS h_aca_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box C/D family. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_primary_transcript AS SELECT feature_id AS c_d_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: h_aca_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box H/ACA family. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_primary_transcript AS SELECT feature_id AS h_aca_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a duplex (except for its post-transcript *** --- *** ionally added oligo_U tail (SO:0000609)) *** --- *** with a stretch of mature edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: editing_block *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by a singl *** --- *** e guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW editing_block AS SELECT feature_id AS editing_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_block'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing or overlapping no ge *** --- *** nes that is bounded on either side by a *** --- *** gene, or bounded by a gene and the end o *** --- *** f the chromosome. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: editing_domain *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by two or *** --- *** more overlapping guide RNAs (SO:0000602) *** --- *** . *** --- ************************************************ --- CREATE VIEW editing_domain AS SELECT feature_id AS editing_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_domain'; --- ************************************************ --- *** relation: unedited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an edited transcript that *** --- *** will not be edited. *** --- ************************************************ --- CREATE VIEW unedited_region AS SELECT feature_id AS unedited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unedited_region'; --- ************************************************ --- *** relation: h_aca_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_encoding AS SELECT feature_id AS h_aca_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_encoding'; --- ************************************************ --- *** relation: oligo_u_tail *** --- *** relation type: VIEW *** --- *** *** --- *** The string of non-encoded U's at the 3' *** --- *** end of a guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW oligo_u_tail AS SELECT feature_id AS oligo_u_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo_U_tail'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which bacterial RNA po *** --- *** lymerase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter AS SELECT feature_id AS bacterial_rnapol_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter'; --- ************************************************ --- *** relation: bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for bacterial transc *** --- *** ription. *** --- ************************************************ --- CREATE VIEW bacterial_terminator AS SELECT feature_id AS bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'bacterial_terminator'; --- ************************************************ --- *** relation: terminator_of_type_2_rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for RNA polymerase I *** --- *** II transcription. *** --- ************************************************ --- CREATE VIEW terminator_of_type_2_rnapol_iii_promoter AS SELECT feature_id AS terminator_of_type_2_rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter'; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The base where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_1 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_1 AS SELECT feature_id AS rnapol_iii_promoter_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_2 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_2 AS SELECT feature_id AS rnapol_iii_promoter_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_2'; --- ************************************************ --- *** relation: a_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognised by TFIIIC, with consensus s *** --- *** equence TGGCnnAGTGG. *** --- ************************************************ --- CREATE VIEW a_box AS SELECT feature_id AS a_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box'; --- ************************************************ --- *** relation: b_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognised by TFIIIC, with consensus s *** --- *** equence AGGTTCCAnnCC. *** --- ************************************************ --- CREATE VIEW b_box AS SELECT feature_id AS b_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'B_box'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_3 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_3 AS SELECT feature_id AS rnapol_iii_promoter_type_3_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_3'; --- ************************************************ --- *** relation: c_box *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA polymerase III type 1 promoter wi *** --- *** th consensus sequence CAnnCCn. *** --- ************************************************ --- CREATE VIEW c_box AS SELECT feature_id AS c_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_box'; --- ************************************************ --- *** relation: snrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_encoding AS SELECT feature_id AS snrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_encoding'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenance of the end. *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region which upon binding o *** --- *** f transcription factors, suppress the tr *** --- *** anscription of the gene or genes they co *** --- *** ntrol. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: chromosomal_regulatory_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_regulatory_element AS SELECT feature_id AS chromosomal_regulatory_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'chromosomal_regulatory_element'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** A trancriptional cis regulatory region t *** --- *** hat when located between a CM and a gene *** --- *** 's promoter prevents the CRM from modula *** --- *** ting that genes expression. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: five_prime_open_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_open_reading_frame AS SELECT feature_id AS five_prime_open_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_open_reading_frame'; --- ************************************************ --- *** relation: upstream_aug_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon upstream of the ORF. *** --- ************************************************ --- CREATE VIEW upstream_aug_codon AS SELECT feature_id AS upstream_aug_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon'; --- ************************************************ --- *** relation: polycistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for more t *** --- *** han one gene product. *** --- ************************************************ --- CREATE VIEW polycistronic_primary_transcript AS SELECT feature_id AS polycistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for one ge *** --- *** ne product. *** --- ************************************************ --- CREATE VIEW monocistronic_primary_transcript AS SELECT feature_id AS monocistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with either a single protein pro *** --- *** duct, or for which the regions encoding *** --- *** all its protein products overlap. *** --- ************************************************ --- CREATE VIEW monocistronic_mrna AS SELECT feature_id AS monocistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_mRNA'; --- ************************************************ --- *** relation: polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that encodes multiple proteins f *** --- *** rom at least two non-overlapping regions *** --- *** . *** --- ************************************************ --- CREATE VIEW polycistronic_mrna AS SELECT feature_id AS polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA'; --- ************************************************ --- *** relation: mini_exon_donor_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that donates the sp *** --- *** liced leader to other mRNA. *** --- ************************************************ --- CREATE VIEW mini_exon_donor_rna AS SELECT feature_id AS mini_exon_donor_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_exon_donor_RNA'; --- ************************************************ --- *** relation: spliced_leader_rna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW spliced_leader_rna AS SELECT feature_id AS spliced_leader_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliced_leader_RNA'; --- ************************************************ --- *** relation: engineered_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_plasmid AS SELECT feature_id AS engineered_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_plasmid'; --- ************************************************ --- *** relation: transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Part of an rRNA transcription unit that *** --- *** is transcribed but discarded during matu *** --- *** ration, not giving rise to any part of r *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW transcribed_spacer_region AS SELECT feature_id AS transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'transcribed_spacer_region'; --- ************************************************ --- *** relation: internal_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA sequence that *** --- *** separate genes coding for the 28S, 5.8S, *** --- *** and 18S ribosomal RNAs. *** --- ************************************************ --- CREATE VIEW internal_transcribed_spacer_region AS SELECT feature_id AS internal_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region'; --- ************************************************ --- *** relation: external_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA that precede t *** --- *** he sequence that codes for the ribosomal *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW external_transcribed_spacer_region AS SELECT feature_id AS external_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'external_transcribed_spacer_region'; --- ************************************************ --- *** relation: tetranuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tetranuc_repeat_microsat AS SELECT feature_id AS tetranuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetranucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: srp_rna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_encoding AS SELECT feature_id AS srp_rna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_encoding'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region containing tandemly repe *** --- *** ated sequences having a unit length of 1 *** --- *** 0 to 40 bp. *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA' OR cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small RNA molecule that is the product *** --- *** of a longer exogenous or endogenous dsR *** --- *** NA, which is either a bimolecular duplex *** --- *** or very long hairpin, processed (via th *** --- *** e Dicer pathway) such that numerous siRN *** --- *** As accumulate from both strands of the d *** --- *** sRNA. SRNAs trigger the cleavage of thei *** --- *** r target molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: mirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a micro RN *** --- *** A. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript AS SELECT feature_id AS mirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript'; --- ************************************************ --- *** relation: strna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small te *** --- *** mporal mRNA (SO:0000649). *** --- ************************************************ --- CREATE VIEW strna_primary_transcript AS SELECT feature_id AS strna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: small_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the small subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW small_subunit_rrna AS SELECT feature_id AS small_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'small_subunit_rRNA'; --- ************************************************ --- *** relation: large_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the large subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW large_subunit_rrna AS SELECT feature_id AS large_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'large_subunit_rRNA'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilises 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: maxicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mitochondrial gene located in a maxici *** --- *** rcle. *** --- ************************************************ --- CREATE VIEW maxicircle_gene AS SELECT feature_id AS maxicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'maxicircle_gene'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA transcript that does not encode f *** --- *** or a protein rather the RNA molecule is *** --- *** the gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: strna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_encoding AS SELECT feature_id AS strna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_encoding'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: tmrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_encoding AS SELECT feature_id AS tmrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_encoding'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: trna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_encoding AS SELECT feature_id AS trna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_encoding'; --- ************************************************ --- *** relation: introgressed_chromosome_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW introgressed_chromosome_region AS SELECT feature_id AS introgressed_chromosome_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'introgressed_chromosome_region'; --- ************************************************ --- *** relation: monocistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is monocistronic. *** --- ************************************************ --- CREATE VIEW monocistronic_transcript AS SELECT feature_id AS monocistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'monocistronic_transcript'; --- ************************************************ --- *** relation: mobile_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron (mitochondrial, chloroplast, n *** --- *** uclear or prokaryotic) that encodes a do *** --- *** uble strand sequence specific endonuclea *** --- *** se allowing for mobility. *** --- ************************************************ --- CREATE VIEW mobile_intron AS SELECT feature_id AS mobile_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence that has been inser *** --- *** ted. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion' OR cvterm.name = 'insertion'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: sequence_rearrangement_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_rearrangement_feature AS SELECT feature_id AS sequence_rearrangement_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'sequence_rearrangement_feature'; --- ************************************************ --- *** relation: chromosome_breakage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence within the micronuclear DNA o *** --- *** f ciliates at which chromosome breakage *** --- *** and telomere addition occurs during nucl *** --- *** ear differentiation. *** --- ************************************************ --- CREATE VIEW chromosome_breakage_sequence AS SELECT feature_id AS chromosome_breakage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_breakage_sequence'; --- ************************************************ --- *** relation: internal_eliminated_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence eliminated from the genome of *** --- *** ciliates during nuclear differentiation *** --- *** . *** --- ************************************************ --- CREATE VIEW internal_eliminated_sequence AS SELECT feature_id AS internal_eliminated_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_eliminated_sequence'; --- ************************************************ --- *** relation: macronucleus_destined_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that is conserved, although r *** --- *** earranged relative to the micronucleus, *** --- *** in the macronucleus of a ciliate genome. *** --- ************************************************ --- CREATE VIEW macronucleus_destined_segment AS SELECT feature_id AS macronucleus_destined_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronucleus_destined_segment'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'transcript'; --- ************************************************ --- *** relation: canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 3' splice site has the seq *** --- *** uence "AG". *** --- ************************************************ --- CREATE VIEW canonical_three_prime_splice_site AS SELECT feature_id AS canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 5' splice site has the seq *** --- *** uence "GT". *** --- ************************************************ --- CREATE VIEW canonical_five_prime_splice_site AS SELECT feature_id AS canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 3' splice site that does not have the *** --- *** sequence "AG". *** --- ************************************************ --- CREATE VIEW non_canonical_three_prime_splice_site AS SELECT feature_id AS non_canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 5' splice site which does not have the *** --- *** sequence "GT". *** --- ************************************************ --- CREATE VIEW non_canonical_five_prime_splice_site AS SELECT feature_id AS non_canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon that is not the usual AUG *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW non_canonical_start_codon AS SELECT feature_id AS non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'non_canonical_start_codon'; --- ************************************************ --- *** relation: aberrant_processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been processed "in *** --- *** correctly", for example by the failure o *** --- *** f splicing of one or more exons. *** --- ************************************************ --- CREATE VIEW aberrant_processed_transcript AS SELECT feature_id AS aberrant_processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aberrant_processed_transcript'; --- ************************************************ --- *** relation: exonic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Exonic splicing enhancers (ESEs) facilit *** --- *** ate exon definition by assisting in the *** --- *** recruitment of splicing factors to the a *** --- *** djacent intron. *** --- ************************************************ --- CREATE VIEW exonic_splice_enhancer AS SELECT feature_id AS exonic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exonic_splice_enhancer'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targeted *** --- *** by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: dnasei_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dnasei_hypersensitive_site AS SELECT feature_id AS dnasei_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site'; --- ************************************************ --- *** relation: translocation_element *** --- *** relation type: VIEW *** --- *** *** --- *** For some translocations, particularly bu *** --- *** t not exclusively, reciprocal translocat *** --- *** ions, the chromosomes carrying non-homol *** --- *** ogous centromeres may be recovered indep *** --- *** endently. These chromosomes are describe *** --- *** d as translocation elements. *** --- ************************************************ --- CREATE VIEW translocation_element AS SELECT feature_id AS translocation_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occurred. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: gene_with_polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW gene_with_polycistronic_transcript AS SELECT feature_id AS gene_with_polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_polycistronic_transcript'; --- ************************************************ --- *** relation: cleaved_initiator_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** The initiator methionine that has been c *** --- *** leaved from a mature polypeptide sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW cleaved_initiator_methionine AS SELECT feature_id AS cleaved_initiator_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine'; --- ************************************************ --- *** relation: gene_with_dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_transcript AS SELECT feature_id AS gene_with_dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_dicistronic_transcript'; --- ************************************************ --- *** relation: gene_with_recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA that is reco *** --- *** ded. *** --- ************************************************ --- CREATE VIEW gene_with_recoded_mrna AS SELECT feature_id AS gene_with_recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_recoded_mRNA'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives (alleles) exist in normal in *** --- *** dividuals in some population(s), wherein *** --- *** the least frequent allele has an abunda *** --- *** nce of 1% or greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'oligo'; --- ************************************************ --- *** relation: gene_with_stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript with st *** --- *** op codon readthrough. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_read_through AS SELECT feature_id AS gene_with_stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_stop_codon_read_through'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as pyrrolysine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent of zer *** --- *** o. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'polyA_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'junction'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'remark'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A region (or regions) that includes all *** --- *** of the sequence elements necessary to en *** --- *** code a functional transcript. A gene may *** --- *** include regulatory regions, transcribed *** --- *** regions and/or other functional sequenc *** --- *** e regions. *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjcent copies of a region ( *** --- *** of length greater than 1). *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 3' splice site of the acceptor prima *** --- *** ry transcript. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: trans_splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' five prime splice site region of *** --- *** the donor RNA. *** --- ************************************************ --- CREATE VIEW trans_splice_donor_site AS SELECT feature_id AS trans_splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_donor_site'; --- ************************************************ --- *** relation: sl1_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sl1_acceptor_site AS SELECT feature_id AS sl1_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site'; --- ************************************************ --- *** relation: sl2_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sl2_acceptor_site AS SELECT feature_id AS sl2_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL2_acceptor_site'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as selenocysteine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: gene_with_mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with mRNA recoded by translationa *** --- *** l bypass. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_recoded_by_translational_bypass AS SELECT feature_id AS gene_with_mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: gene_with_transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding a transcript that has a *** --- *** translational frameshift. *** --- ************************************************ --- CREATE VIEW gene_with_transcript_with_translational_frameshift AS SELECT feature_id AS gene_with_transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: dna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in the DNA form o *** --- *** f the sequence. *** --- ************************************************ --- CREATE VIEW dna_motif AS SELECT feature_id AS dna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'DNA_motif'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_motif AS SELECT feature_id AS rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_motif'; --- ************************************************ --- *** relation: dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that has the quality dicistronic *** --- *** . *** --- ************************************************ --- CREATE VIEW dicistronic_mrna AS SELECT feature_id AS dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It need not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: blocked_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A reading_frame that is interrupted by o *** --- *** ne or more stop codons; usually identifi *** --- *** ed through intergenomic sequence compari *** --- *** sons. *** --- ************************************************ --- CREATE VIEW blocked_reading_frame AS SELECT feature_id AS blocked_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blocked_reading_frame'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_transposable_element AS SELECT feature_id AS foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'foreign_transposable_element'; --- ************************************************ --- *** relation: gene_with_dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic primar *** --- *** y transcript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_primary_transcript AS SELECT feature_id AS gene_with_dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript'; --- ************************************************ --- *** relation: gene_with_dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic mRNA *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_mrna AS SELECT feature_id AS gene_with_dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_mRNA'; --- ************************************************ --- *** relation: idna *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic sequence removed from the genome *** --- *** , as a normal event, by a process of rec *** --- *** ombination. *** --- ************************************************ --- CREATE VIEW idna AS SELECT feature_id AS idna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iDNA'; --- ************************************************ --- *** relation: orit *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule where transfe *** --- *** r is initiated during the process of con *** --- *** jugation or mobilization. *** --- ************************************************ --- CREATE VIEW orit AS SELECT feature_id AS orit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriT'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The transit_peptide is a short region at *** --- *** the N-terminus of the peptide that dire *** --- *** cts the protein to an organelle (chlorop *** --- *** last, mitochondrion, microbody or cyanel *** --- *** le). *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: repeat_unit *** --- *** relation type: VIEW *** --- *** *** --- *** The simplest repeated component of a rep *** --- *** eat region. A single repeat. *** --- ************************************************ --- CREATE VIEW repeat_unit AS SELECT feature_id AS repeat_unit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_unit'; --- ************************************************ --- *** relation: crm *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region where more than 1 TF *** --- *** _binding_site together are regulatorily *** --- *** active. *** --- ************************************************ --- CREATE VIEW crm AS SELECT feature_id AS crm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'CRM'; --- ************************************************ --- *** relation: intein *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is able to ex *** --- *** cise itself and rejoin the remaining por *** --- *** tions with a peptide bond. *** --- ************************************************ --- CREATE VIEW intein AS SELECT feature_id AS intein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein'; --- ************************************************ --- *** relation: intein_containing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of protein-coding genes whe *** --- *** re the initial protein product contains *** --- *** an intein. *** --- ************************************************ --- CREATE VIEW intein_containing AS SELECT feature_id AS intein_containing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** he unknown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: fragmentary *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is incomplete. *** --- ************************************************ --- CREATE VIEW fragmentary AS SELECT feature_id AS fragmentary_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary'; --- ************************************************ --- *** relation: predicted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an unverified re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW predicted AS SELECT feature_id AS predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'predicted'; --- ************************************************ --- *** relation: feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a located_sequen *** --- *** ce_feature. *** --- ************************************************ --- CREATE VIEW feature_attribute AS SELECT feature_id AS feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'feature_attribute'; --- ************************************************ --- *** relation: exemplar_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An exemplar is a representative cDNA seq *** --- *** uence for each gene. The exemplar approa *** --- *** ch is a method that usually involves som *** --- *** e initial clustering into gene groups an *** --- *** d the subsequent selection of a represen *** --- *** tative from each gene group. *** --- ************************************************ --- CREATE VIEW exemplar_mrna AS SELECT feature_id AS exemplar_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar_mRNA'; --- ************************************************ --- *** relation: sequence_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_location AS SELECT feature_id AS sequence_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_location'; --- ************************************************ --- *** relation: organelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW organelle_sequence AS SELECT feature_id AS organelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'organelle_sequence'; --- ************************************************ --- *** relation: mitochondrial_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_sequence AS SELECT feature_id AS mitochondrial_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'mitochondrial_sequence'; --- ************************************************ --- *** relation: nuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclear_sequence AS SELECT feature_id AS nuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_sequence'; --- ************************************************ --- *** relation: nucleomorphic_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nucleomorphic_sequence AS SELECT feature_id AS nucleomorphic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_sequence'; --- ************************************************ --- *** relation: plastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plastid_sequence AS SELECT feature_id AS plastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'plastid_sequence'; --- ************************************************ --- *** relation: kinetoplast *** --- *** relation type: VIEW *** --- *** *** --- *** A kinetoplast is an interlocked network *** --- *** of thousands of minicircles and tens of *** --- *** maxi circles, located near the base of t *** --- *** he flagellum of some protozoan species. *** --- ************************************************ --- CREATE VIEW kinetoplast AS SELECT feature_id AS kinetoplast_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast'; --- ************************************************ --- *** relation: maxicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle is a replicon, part of a ki *** --- *** netoplast, that contains open reading fr *** --- *** ames and replicates via a rolling circle *** --- *** method. *** --- ************************************************ --- CREATE VIEW maxicircle AS SELECT feature_id AS maxicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle'; --- ************************************************ --- *** relation: apicoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW apicoplast_sequence AS SELECT feature_id AS apicoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence'; --- ************************************************ --- *** relation: chromoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromoplast_sequence AS SELECT feature_id AS chromoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_sequence'; --- ************************************************ --- *** relation: chloroplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_sequence AS SELECT feature_id AS chloroplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'chloroplast_sequence'; --- ************************************************ --- *** relation: cyanelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cyanelle_sequence AS SELECT feature_id AS cyanelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_sequence'; --- ************************************************ --- *** relation: leucoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucoplast_sequence AS SELECT feature_id AS leucoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_sequence'; --- ************************************************ --- *** relation: proplastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proplastid_sequence AS SELECT feature_id AS proplastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_sequence'; --- ************************************************ --- *** relation: plasmid_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_location AS SELECT feature_id AS plasmid_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_location'; --- ************************************************ --- *** relation: amplification_origin *** --- *** relation type: VIEW *** --- *** *** --- *** An origin_of_replication that is used fo *** --- *** r the amplification of a chromosomal nuc *** --- *** leic acid sequence. *** --- ************************************************ --- CREATE VIEW amplification_origin AS SELECT feature_id AS amplification_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amplification_origin'; --- ************************************************ --- *** relation: proviral_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proviral_location AS SELECT feature_id AS proviral_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'proviral_location'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: clone_insert *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence that has been ins *** --- *** erted and is being propogated by the clo *** --- *** ne. *** --- ************************************************ --- CREATE VIEW clone_insert AS SELECT feature_id AS clone_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'clone_insert'; --- ************************************************ --- *** relation: lambda_vector *** --- *** relation type: VIEW *** --- *** *** --- *** The lambda bacteriophage is the vector f *** --- *** or the linear lambda clone. The genes in *** --- *** volved in the lysogenic pathway are remo *** --- *** ved from the from the viral DNA. Up to 2 *** --- *** 5 kb of foreign DNA can then be inserted *** --- *** into the lambda genome. *** --- ************************************************ --- CREATE VIEW lambda_vector AS SELECT feature_id AS lambda_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lambda_vector'; --- ************************************************ --- *** relation: plasmid_vector *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_vector AS SELECT feature_id AS plasmid_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_vector'; --- ************************************************ --- *** relation: cdna *** --- *** relation type: VIEW *** --- *** *** --- *** DNA synthesized by reverse transcriptase *** --- *** using RNA as a template. *** --- ************************************************ --- CREATE VIEW cdna AS SELECT feature_id AS cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'cDNA'; --- ************************************************ --- *** relation: single_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single_stranded_cdna AS SELECT feature_id AS single_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA'; --- ************************************************ --- *** relation: double_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double_stranded_cdna AS SELECT feature_id AS double_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_cDNA'; --- ************************************************ --- *** relation: pyrrolysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a pyrrolysine a *** --- *** nticodon, and a 3' pyrrolysine binding r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW pyrrolysyl_trna AS SELECT feature_id AS pyrrolysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysyl_tRNA'; --- ************************************************ --- *** relation: episome *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that may integrate with a chro *** --- *** mosome. *** --- ************************************************ --- CREATE VIEW episome AS SELECT feature_id AS episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'episome'; --- ************************************************ --- *** relation: tmrna_coding_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a two-piece tmRNA that bea *** --- *** rs the reading frame encoding the proteo *** --- *** lysis tag. The tmRNA gene undergoes circ *** --- *** ular permutation in some groups of bacte *** --- *** ria. Processing of the transcripts from *** --- *** such a gene leaves the mature tmRNA in t *** --- *** wo pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_coding_piece AS SELECT feature_id AS tmrna_coding_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece'; --- ************************************************ --- *** relation: tmrna_acceptor_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The acceptor region of a two-piece tmRNA *** --- *** that when mature is charged at its 3' e *** --- *** nd with alanine. The tmRNA gene undergoe *** --- *** s circular permutation in some groups of *** --- *** bacteria; processing of the transcripts *** --- *** from such a gene leaves the mature tmRN *** --- *** A in two pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_acceptor_piece AS SELECT feature_id AS tmrna_acceptor_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_acceptor_piece'; --- ************************************************ --- *** relation: qtl *** --- *** relation type: VIEW *** --- *** *** --- *** A quantitative trait locus (QTL) is a po *** --- *** lymorphic locus which contains alleles t *** --- *** hat differentially affect the expression *** --- *** of a continuously distributed phenotypi *** --- *** c trait. Usually it is a marker describe *** --- *** d by statistical association to quantita *** --- *** tive variation in the particular phenoty *** --- *** pic trait that is thought to be controll *** --- *** ed by the cumulative action of alleles a *** --- *** t multiple loci. *** --- ************************************************ --- CREATE VIEW qtl AS SELECT feature_id AS qtl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'QTL'; --- ************************************************ --- *** relation: genomic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A genomic island is an integrated mobile *** --- *** genetic element, characterized by size *** --- *** (over 10 Kb). It that has features that *** --- *** suggest a foreign origin. These can incl *** --- *** ude nucleotide distribution (oligonucleo *** --- *** tides signature, CG content etc.) that d *** --- *** iffers from the bulk of the chromosome a *** --- *** nd/or genes suggesting DNA mobility. *** --- ************************************************ --- CREATE VIEW genomic_island AS SELECT feature_id AS genomic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'genomic_island'; --- ************************************************ --- *** relation: pathogenic_island *** --- *** relation type: VIEW *** --- *** *** --- *** Mobile genetic elements that contribute *** --- *** to rapid changes in virulence potential. *** --- *** They are present on the genomes of path *** --- *** ogenic strains but absent from the genom *** --- *** es of non pathogenic members of the same *** --- *** or related species. *** --- ************************************************ --- CREATE VIEW pathogenic_island AS SELECT feature_id AS pathogenic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island'; --- ************************************************ --- *** relation: metabolic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in metabolism, analogous to th *** --- *** e pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW metabolic_island AS SELECT feature_id AS metabolic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'metabolic_island'; --- ************************************************ --- *** relation: adaptive_island *** --- *** relation type: VIEW *** --- *** *** --- *** An adaptive island is a genomic island t *** --- *** hat provides an adaptive advantage to th *** --- *** e host. *** --- ************************************************ --- CREATE VIEW adaptive_island AS SELECT feature_id AS adaptive_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'adaptive_island'; --- ************************************************ --- *** relation: symbiosis_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in symbiosis, analogous to the *** --- *** pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW symbiosis_island AS SELECT feature_id AS symbiosis_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symbiosis_island'; --- ************************************************ --- *** relation: pseudogenic_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of an rRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_rrna AS SELECT feature_id AS pseudogenic_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_rRNA'; --- ************************************************ --- *** relation: pseudogenic_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of a tRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_trna AS SELECT feature_id AS pseudogenic_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_tRNA'; --- ************************************************ --- *** relation: engineered_episome *** --- *** relation type: VIEW *** --- *** *** --- *** An episome that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_episome AS SELECT feature_id AS engineered_episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome'; --- ************************************************ --- *** relation: transgenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence that has b *** --- *** een integrated with foreign sequence. *** --- ************************************************ --- CREATE VIEW transgenic AS SELECT feature_id AS transgenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic'; --- ************************************************ --- *** relation: so_natural *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that o *** --- *** ccurs in nature. *** --- ************************************************ --- CREATE VIEW so_natural AS SELECT feature_id AS so_natural_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural'; --- ************************************************ --- *** relation: engineered *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region that w *** --- *** as modified in vitro. *** --- ************************************************ --- CREATE VIEW engineered AS SELECT feature_id AS engineered_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered'; --- ************************************************ --- *** relation: so_foreign *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region from a *** --- *** nother species. *** --- ************************************************ --- CREATE VIEW so_foreign AS SELECT feature_id AS so_foreign_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foreign'; --- ************************************************ --- *** relation: cloned_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cloned_region AS SELECT feature_id AS cloned_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_region'; --- ************************************************ --- *** relation: validated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been proven. *** --- ************************************************ --- CREATE VIEW validated AS SELECT feature_id AS validated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined' OR cvterm.name = 'validated'; --- ************************************************ --- *** relation: invalidated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s invalidated. *** --- ************************************************ --- CREATE VIEW invalidated AS SELECT feature_id AS invalidated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'invalidated'; --- ************************************************ --- *** relation: engineered_rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A rescue region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_rescue_region AS SELECT feature_id AS engineered_rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region'; --- ************************************************ --- *** relation: rescue_mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mini_gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_mini_gene AS SELECT feature_id AS rescue_mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene'; --- ************************************************ --- *** relation: transgenic_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified in vitro, incl *** --- *** uding insertion of DNA derived from a so *** --- *** urce other than the originating TE. *** --- ************************************************ --- CREATE VIEW transgenic_transposable_element AS SELECT feature_id AS transgenic_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_transposable_element'; --- ************************************************ --- *** relation: natural_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that exists (or existed) in nature. *** --- ************************************************ --- CREATE VIEW natural_transposable_element AS SELECT feature_id AS natural_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element'; --- ************************************************ --- *** relation: engineered_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified by manipulatio *** --- *** ns in vitro. *** --- ************************************************ --- CREATE VIEW engineered_transposable_element AS SELECT feature_id AS engineered_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_transposable_element'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element AS SELECT feature_id AS engineered_foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element'; --- ************************************************ --- *** relation: assortment_derived_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome duplication aberratio *** --- *** n generated by reassortment of other abe *** --- *** rration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_duplication AS SELECT feature_id AS assortment_derived_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency an *** --- *** d a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency_plus_duplication AS SELECT feature_id AS assortment_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome deficiency aberration *** --- *** generated by reassortment of other aber *** --- *** ration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency AS SELECT feature_id AS assortment_derived_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency'; --- ************************************************ --- *** relation: assortment_derived_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency or *** --- *** a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_aneuploid AS SELECT feature_id AS assortment_derived_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_aneuploid'; --- ************************************************ --- *** relation: engineered_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_region AS SELECT feature_id AS engineered_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_region'; --- ************************************************ --- *** relation: engineered_foreign_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_region AS SELECT feature_id AS engineered_foreign_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_region'; --- ************************************************ --- *** relation: fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fusion AS SELECT feature_id AS fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fusion'; --- ************************************************ --- *** relation: engineered_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A tag that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_tag AS SELECT feature_id AS engineered_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_tag'; --- ************************************************ --- *** relation: validated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that has been validated. *** --- ************************************************ --- CREATE VIEW validated_cdna_clone AS SELECT feature_id AS validated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone'; --- ************************************************ --- *** relation: invalidated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that is invalid. *** --- ************************************************ --- CREATE VIEW invalidated_cdna_clone AS SELECT feature_id AS invalidated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone'; --- ************************************************ --- *** relation: chimeric_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated because it is c *** --- *** himeric. *** --- ************************************************ --- CREATE VIEW chimeric_cdna_clone AS SELECT feature_id AS chimeric_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone'; --- ************************************************ --- *** relation: genomically_contaminated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by genomic cont *** --- *** amination. *** --- ************************************************ --- CREATE VIEW genomically_contaminated_cdna_clone AS SELECT feature_id AS genomically_contaminated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomically_contaminated_cDNA_clone'; --- ************************************************ --- *** relation: polya_primed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by polyA primin *** --- *** g. *** --- ************************************************ --- CREATE VIEW polya_primed_cdna_clone AS SELECT feature_id AS polya_primed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_primed_cDNA_clone'; --- ************************************************ --- *** relation: partially_processed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA invalidated clone by partial proc *** --- *** essing. *** --- ************************************************ --- CREATE VIEW partially_processed_cdna_clone AS SELECT feature_id AS partially_processed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_processed_cDNA_clone'; --- ************************************************ --- *** relation: rescue *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region's abili *** --- *** ty, when introduced to a mutant organism *** --- *** , to re-establish (rescue) a phenotype. *** --- ************************************************ --- CREATE VIEW rescue AS SELECT feature_id AS rescue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue'; --- ************************************************ --- *** relation: mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** By definition, minigenes are short open- *** --- *** reading frames (ORF), usually encoding a *** --- *** pproximately 9 to 20 amino acids, which *** --- *** are expressed in vivo (as distinct from *** --- *** being synthesized as peptide or protein *** --- *** ex vivo and subsequently injected). The *** --- *** in vivo synthesis confers a distinct adv *** --- *** antage: the expressed sequences can ente *** --- *** r both antigen presentation pathways, MH *** --- *** C I (inducing CD8+ T- cells, which are u *** --- *** sually cytotoxic T-lymphocytes (CTL)) an *** --- *** d MHC II (inducing CD4+ T-cells, usually *** --- *** 'T-helpers' (Th)); and can encounter B- *** --- *** cells, inducing antibody responses. Thre *** --- *** e main vector approaches have been used *** --- *** to deliver minigenes: viral vectors, bac *** --- *** terial vectors and plasmid DNA. *** --- ************************************************ --- CREATE VIEW mini_gene AS SELECT feature_id AS mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'mini_gene'; --- ************************************************ --- *** relation: rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_gene AS SELECT feature_id AS rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'rescue_gene'; --- ************************************************ --- *** relation: wild_type *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence with th *** --- *** e genotype found in nature and/or standa *** --- *** rd laboratory stock. *** --- ************************************************ --- CREATE VIEW wild_type AS SELECT feature_id AS wild_type_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type'; --- ************************************************ --- *** relation: wild_type_rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW wild_type_rescue_gene AS SELECT feature_id AS wild_type_rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene'; --- ************************************************ --- *** relation: mitochondrial_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a mitochondr *** --- *** ia. *** --- ************************************************ --- CREATE VIEW mitochondrial_chromosome AS SELECT feature_id AS mitochondrial_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome'; --- ************************************************ --- *** relation: chloroplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chloroplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chloroplast_chromosome AS SELECT feature_id AS chloroplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_chromosome'; --- ************************************************ --- *** relation: chromoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chromoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chromoplast_chromosome AS SELECT feature_id AS chromoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_chromosome'; --- ************************************************ --- *** relation: cyanelle_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a cyanelle. *** --- ************************************************ --- CREATE VIEW cyanelle_chromosome AS SELECT feature_id AS cyanelle_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_chromosome'; --- ************************************************ --- *** relation: leucoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome with origin in a leucoplast *** --- *** . *** --- ************************************************ --- CREATE VIEW leucoplast_chromosome AS SELECT feature_id AS leucoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_chromosome'; --- ************************************************ --- *** relation: macronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a macronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW macronuclear_chromosome AS SELECT feature_id AS macronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_chromosome'; --- ************************************************ --- *** relation: micronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a micronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW micronuclear_chromosome AS SELECT feature_id AS micronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_chromosome'; --- ************************************************ --- *** relation: nuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_chromosome AS SELECT feature_id AS nuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_chromosome'; --- ************************************************ --- *** relation: nucleomorphic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleomorp *** --- *** h. *** --- ************************************************ --- CREATE VIEW nucleomorphic_chromosome AS SELECT feature_id AS nucleomorphic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_chromosome'; --- ************************************************ --- *** relation: chromosome_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_part AS SELECT feature_id AS chromosome_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'chromosome_part'; --- ************************************************ --- *** relation: gene_member_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a gene. *** --- ************************************************ --- CREATE VIEW gene_member_region AS SELECT feature_id AS gene_member_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'gene_member_region'; --- ************************************************ --- *** relation: transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a transcript. *** --- ************************************************ --- CREATE VIEW transcript_region AS SELECT feature_id AS transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'transcript_region'; --- ************************************************ --- *** relation: mature_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a mature transcript. *** --- ************************************************ --- CREATE VIEW mature_transcript_region AS SELECT feature_id AS mature_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'mature_transcript_region'; --- ************************************************ --- *** relation: primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a primary transcript. *** --- ************************************************ --- CREATE VIEW primary_transcript_region AS SELECT feature_id AS primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'primary_transcript_region'; --- ************************************************ --- *** relation: mrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an mRNA. *** --- ************************************************ --- CREATE VIEW mrna_region AS SELECT feature_id AS mrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'mRNA_region'; --- ************************************************ --- *** relation: utr_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of UTR. *** --- ************************************************ --- CREATE VIEW utr_region AS SELECT feature_id AS utr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'UTR_region'; --- ************************************************ --- *** relation: rrna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an rRNA primary transcript. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript_region AS SELECT feature_id AS rrna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'rRNA_primary_transcript_region'; --- ************************************************ --- *** relation: polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Biological sequence region that can be a *** --- *** ssigned to a specific subsequence of a p *** --- *** olypeptide. *** --- ************************************************ --- CREATE VIEW polypeptide_region AS SELECT feature_id AS polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_region'; --- ************************************************ --- *** relation: repeat_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a repeated sequence. *** --- ************************************************ --- CREATE VIEW repeat_component AS SELECT feature_id AS repeat_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'repeat_component'; --- ************************************************ --- *** relation: spliceosomal_intron_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an intron. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron_region AS SELECT feature_id AS spliceosomal_intron_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'spliceosomal_intron_region'; --- ************************************************ --- *** relation: gene_component_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_component_region AS SELECT feature_id AS gene_component_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'gene_component_region'; --- ************************************************ --- *** relation: tmrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tmRNA. *** --- ************************************************ --- CREATE VIEW tmrna_region AS SELECT feature_id AS tmrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'tmRNA_region'; --- ************************************************ --- *** relation: ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ltr_component AS SELECT feature_id AS ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'LTR_component'; --- ************************************************ --- *** relation: three_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr_component AS SELECT feature_id AS three_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'three_prime_LTR_component'; --- ************************************************ --- *** relation: five_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr_component AS SELECT feature_id AS five_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'five_prime_LTR_component'; --- ************************************************ --- *** relation: cds_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a CDS. *** --- ************************************************ --- CREATE VIEW cds_region AS SELECT feature_id AS cds_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'CDS_region'; --- ************************************************ --- *** relation: exon_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an exon. *** --- ************************************************ --- CREATE VIEW exon_region AS SELECT feature_id AS exon_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'exon_region'; --- ************************************************ --- *** relation: homologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is homologous to another r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW homologous_region AS SELECT feature_id AS homologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'homologous_region'; --- ************************************************ --- *** relation: paralogous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is paralogous t *** --- *** o another region. *** --- ************************************************ --- CREATE VIEW paralogous_region AS SELECT feature_id AS paralogous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region'; --- ************************************************ --- *** relation: orthologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is orthologous *** --- *** to another region. *** --- ************************************************ --- CREATE VIEW orthologous_region AS SELECT feature_id AS orthologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous_region'; --- ************************************************ --- *** relation: conserved *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW conserved AS SELECT feature_id AS conserved_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'conserved'; --- ************************************************ --- *** relation: homologous *** --- *** relation type: VIEW *** --- *** *** --- *** Similarity due to common ancestry. *** --- ************************************************ --- CREATE VIEW homologous AS SELECT feature_id AS homologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'homologous'; --- ************************************************ --- *** relation: orthologous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occured after a spec *** --- *** iation event. *** --- ************************************************ --- CREATE VIEW orthologous AS SELECT feature_id AS orthologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous'; --- ************************************************ --- *** relation: paralogous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occurred after a dup *** --- *** lication event. *** --- ************************************************ --- CREATE VIEW paralogous AS SELECT feature_id AS paralogous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous'; --- ************************************************ --- *** relation: syntenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence regions oc *** --- *** curring in same order on chromosome of d *** --- *** ifferent species. *** --- ************************************************ --- CREATE VIEW syntenic AS SELECT feature_id AS syntenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic'; --- ************************************************ --- *** relation: capped_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is capped. *** --- ************************************************ --- CREATE VIEW capped_primary_transcript AS SELECT feature_id AS capped_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_primary_transcript'; --- ************************************************ --- *** relation: capped_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is capped. *** --- ************************************************ --- CREATE VIEW capped_mrna AS SELECT feature_id AS capped_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_mRNA'; --- ************************************************ --- *** relation: mrna_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA feature. *** --- ************************************************ --- CREATE VIEW mrna_attribute AS SELECT feature_id AS mrna_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'mRNA_attribute'; --- ************************************************ --- *** relation: exemplar *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence is re *** --- *** presentative of a class of similar seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW exemplar AS SELECT feature_id AS exemplar_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar'; --- ************************************************ --- *** relation: frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains a mutation involving the deleti *** --- *** on or insertion of one or more bases, wh *** --- *** ere this number is not divisible by 3. *** --- ************************************************ --- CREATE VIEW frameshift AS SELECT feature_id AS frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'frameshift'; --- ************************************************ --- *** relation: minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting one base *** --- *** . *** --- ************************************************ --- CREATE VIEW minus_1_frameshift AS SELECT feature_id AS minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift'; --- ************************************************ --- *** relation: minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting two base *** --- *** s. *** --- ************************************************ --- CREATE VIEW minus_2_frameshift AS SELECT feature_id AS minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift'; --- ************************************************ --- *** relation: plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting one bas *** --- *** e. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift AS SELECT feature_id AS plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift'; --- ************************************************ --- *** relation: plus_2_framshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting two bas *** --- *** es. *** --- ************************************************ --- CREATE VIEW plus_2_framshift AS SELECT feature_id AS plus_2_framshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_framshift'; --- ************************************************ --- *** relation: trans_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing transcript seque *** --- *** nce that is created by splicing exons fr *** --- *** om diferent genes. *** --- ************************************************ --- CREATE VIEW trans_spliced AS SELECT feature_id AS trans_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced'; --- ************************************************ --- *** relation: polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is polyadenylated. *** --- ************************************************ --- CREATE VIEW polyadenylated_mrna AS SELECT feature_id AS polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated_mRNA'; --- ************************************************ --- *** relation: trans_spliced_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_mrna AS SELECT feature_id AS trans_spliced_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA'; --- ************************************************ --- *** relation: edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript AS SELECT feature_id AS edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_transcript'; --- ************************************************ --- *** relation: edited_transcript_by_a_to_i_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been edited by A t *** --- *** o I substitution. *** --- ************************************************ --- CREATE VIEW edited_transcript_by_a_to_i_substitution AS SELECT feature_id AS edited_transcript_by_a_to_i_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution'; --- ************************************************ --- *** relation: bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a protein. *** --- ************************************************ --- CREATE VIEW bound_by_protein AS SELECT feature_id AS bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein'; --- ************************************************ --- *** relation: bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a nucleic acid. *** --- ************************************************ --- CREATE VIEW bound_by_nucleic_acid AS SELECT feature_id AS bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_nucleic_acid'; --- ************************************************ --- *** relation: alternatively_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a situation wher *** --- *** e a gene may encode for more than 1 tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW alternatively_spliced AS SELECT feature_id AS alternatively_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced'; --- ************************************************ --- *** relation: monocistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for one gene product. *** --- ************************************************ --- CREATE VIEW monocistronic AS SELECT feature_id AS monocistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic'; --- ************************************************ --- *** relation: dicistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for two gene products. *** --- ************************************************ --- CREATE VIEW dicistronic AS SELECT feature_id AS dicistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic'; --- ************************************************ --- *** relation: polycistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for more than one gene *** --- *** product. *** --- ************************************************ --- CREATE VIEW polycistronic AS SELECT feature_id AS polycistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic' OR cvterm.name = 'polycistronic'; --- ************************************************ --- *** relation: recoded *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA sequence *** --- *** that has been reprogrammed at translati *** --- *** on, causing localized alterations. *** --- ************************************************ --- CREATE VIEW recoded AS SELECT feature_id AS recoded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'recoded'; --- ************************************************ --- *** relation: codon_redefined *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the alteration o *** --- *** f codon meaning. *** --- ************************************************ --- CREATE VIEW codon_redefined AS SELECT feature_id AS codon_redefined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined'; --- ************************************************ --- *** relation: stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be a new amino *** --- *** acid. *** --- ************************************************ --- CREATE VIEW stop_codon_read_through AS SELECT feature_id AS stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'stop_codon_read_through'; --- ************************************************ --- *** relation: stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, pyrrolysine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, selenocysteine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** Recoded mRNA where a block of nucleotide *** --- *** s is not translated. *** --- ************************************************ --- CREATE VIEW recoded_by_translational_bypass AS SELECT feature_id AS recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_by_translational_bypass'; --- ************************************************ --- *** relation: translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** Recoding by frameshifting a particular s *** --- *** ite. *** --- ************************************************ --- CREATE VIEW translationally_frameshifted AS SELECT feature_id AS translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'translationally_frameshifted'; --- ************************************************ --- *** relation: maternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is maternally_imprinted. *** --- ************************************************ --- CREATE VIEW maternally_imprinted_gene AS SELECT feature_id AS maternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted_gene'; --- ************************************************ --- *** relation: paternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is paternally imprinted. *** --- ************************************************ --- CREATE VIEW paternally_imprinted_gene AS SELECT feature_id AS paternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is post translationally regu *** --- *** lated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_gene AS SELECT feature_id AS post_translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_gene'; --- ************************************************ --- *** relation: negatively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is negatively autoreguated. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated_gene AS SELECT feature_id AS negatively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated_gene'; --- ************************************************ --- *** relation: positively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is positively autoregulated. *** --- ************************************************ --- CREATE VIEW positively_autoregulated_gene AS SELECT feature_id AS positively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated_gene'; --- ************************************************ --- *** relation: silenced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated at tra *** --- *** nscriptional or translational level. *** --- ************************************************ --- CREATE VIEW silenced AS SELECT feature_id AS silenced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced'; --- ************************************************ --- *** relation: silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** modifications, resulting in repression *** --- *** of transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_modification AS SELECT feature_id AS silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_DNA_modification'; --- ************************************************ --- *** relation: silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** methylation, resulting in repression of *** --- *** transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_methylation AS SELECT feature_id AS silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is translationally regulated *** --- *** . *** --- ************************************************ --- CREATE VIEW translationally_regulated_gene AS SELECT feature_id AS translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated_gene'; --- ************************************************ --- *** relation: allelically_excluded_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is allelically_excluded. *** --- ************************************************ --- CREATE VIEW allelically_excluded_gene AS SELECT feature_id AS allelically_excluded_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded_gene'; --- ************************************************ --- *** relation: epigenetically_modified_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is epigenetically modified. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_gene AS SELECT feature_id AS epigenetically_modified_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'epigenetically_modified_gene'; --- ************************************************ --- *** relation: transgene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is transgenic. *** --- ************************************************ --- CREATE VIEW transgene AS SELECT feature_id AS transgene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene' OR cvterm.name = 'transgene'; --- ************************************************ --- *** relation: endogenous_retroviral_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_sequence AS SELECT feature_id AS endogenous_retroviral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence'; --- ************************************************ --- *** relation: rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the sequence of *** --- *** a feature, where the DNA is rearranged. *** --- ************************************************ --- CREATE VIEW rearranged_at_dna_level AS SELECT feature_id AS rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rearranged_at_DNA_level'; --- ************************************************ --- *** relation: status *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the status of a *** --- *** feature, based on the available evidence *** --- *** . *** --- ************************************************ --- CREATE VIEW status AS SELECT feature_id AS status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'status'; --- ************************************************ --- *** relation: independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that is *** --- *** independently known - not predicted. *** --- ************************************************ --- CREATE VIEW independently_known AS SELECT feature_id AS independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'independently_known'; --- ************************************************ --- *** relation: supported_by_sequence_similarity *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity techniques. *** --- ************************************************ --- CREATE VIEW supported_by_sequence_similarity AS SELECT feature_id AS supported_by_sequence_similarity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'supported_by_sequence_similarity'; --- ************************************************ --- *** relation: supported_by_domain_match *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity of a known domain. *** --- ************************************************ --- CREATE VIEW supported_by_domain_match AS SELECT feature_id AS supported_by_domain_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match'; --- ************************************************ --- *** relation: supported_by_est_or_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity to EST or cDNA data. *** --- ************************************************ --- CREATE VIEW supported_by_est_or_cdna AS SELECT feature_id AS supported_by_est_or_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_EST_or_cDNA'; --- ************************************************ --- *** relation: orphan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW orphan AS SELECT feature_id AS orphan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan'; --- ************************************************ --- *** relation: predicted_by_ab_initio_computation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s predicted by a computer program that d *** --- *** id not rely on sequence similarity. *** --- ************************************************ --- CREATE VIEW predicted_by_ab_initio_computation AS SELECT feature_id AS predicted_by_ab_initio_computation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_by_ab_initio_computation'; --- ************************************************ --- *** relation: asx_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Asp *** --- *** artate or Asparagine (Asx), the side-cha *** --- *** in O of residue(i) is H-bonded to the ma *** --- *** in-chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW asx_turn AS SELECT feature_id AS asx_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'asx_turn'; --- ************************************************ --- *** relation: cloned_cdna_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from cDNA. *** --- ************************************************ --- CREATE VIEW cloned_cdna_insert AS SELECT feature_id AS cloned_cdna_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert'; --- ************************************************ --- *** relation: cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from genomic DNA. *** --- ************************************************ --- CREATE VIEW cloned_genomic_insert AS SELECT feature_id AS cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'cloned_genomic_insert'; --- ************************************************ --- *** relation: engineered_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_insert AS SELECT feature_id AS engineered_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_insert'; --- ************************************************ --- *** relation: edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is edited. *** --- ************************************************ --- CREATE VIEW edited_mrna AS SELECT feature_id AS edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA'; --- ************************************************ --- *** relation: guide_rna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of guide RNA. *** --- ************************************************ --- CREATE VIEW guide_rna_region AS SELECT feature_id AS guide_rna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'guide_RNA_region'; --- ************************************************ --- *** relation: anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that base-pairs *** --- *** to a target mRNA. *** --- ************************************************ --- CREATE VIEW anchor_region AS SELECT feature_id AS anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region'; --- ************************************************ --- *** relation: pre_edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pre_edited_mrna AS SELECT feature_id AS pre_edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA'; --- ************************************************ --- *** relation: intermediate *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature betwe *** --- *** en stages of processing. *** --- ************************************************ --- CREATE VIEW intermediate AS SELECT feature_id AS intermediate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate'; --- ************************************************ --- *** relation: mirna_target_site *** --- *** relation type: VIEW *** --- *** *** --- *** A miRNA target site is a binding site wh *** --- *** ere the molecule is a micro RNA. *** --- ************************************************ --- CREATE VIEW mirna_target_site AS SELECT feature_id AS mirna_target_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site'; --- ************************************************ --- *** relation: edited_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is edited. *** --- ************************************************ --- CREATE VIEW edited_cds AS SELECT feature_id AS edited_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment'; --- ************************************************ --- *** relation: vertebrate_ig_t_cell_receptor_rearranged_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_ig_t_cell_receptor_rearranged_gene_cluster AS SELECT feature_id AS vertebrate_ig_t_cell_receptor_rearranged_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_signal_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_signal_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_signal_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature'; --- ************************************************ --- *** relation: recombinationally_rearranged *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged AS SELECT feature_id AS recombinationally_rearranged_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged'; --- ************************************************ --- *** relation: recombinationally_rearranged_vertebrate_immune_system_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene of t *** --- *** he vertebrate immune system. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_vertebrate_immune_system_gene AS SELECT feature_id AS recombinationally_rearranged_vertebrate_immune_system_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: attp_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a phage *** --- *** chromosome at which a recombinase acts t *** --- *** o insert the phage DNA at a cognate inte *** --- *** gration/excision site on a bacterial chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW attp_site AS SELECT feature_id AS attp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attP_site'; --- ************************************************ --- *** relation: attb_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a bacter *** --- *** ial chromosome at which a recombinase ac *** --- *** ts to insert foreign DNA containing a co *** --- *** gnate integration/excision site. *** --- ************************************************ --- CREATE VIEW attb_site AS SELECT feature_id AS attb_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attB_site'; --- ************************************************ --- *** relation: attl_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attB_site and th *** --- *** e 3' portion of attP_site. *** --- ************************************************ --- CREATE VIEW attl_site AS SELECT feature_id AS attl_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attL_site'; --- ************************************************ --- *** relation: attr_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attP_site and th *** --- *** e 3' portion of attB_site. *** --- ************************************************ --- CREATE VIEW attr_site AS SELECT feature_id AS attr_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attR_site'; --- ************************************************ --- *** relation: integration_excision_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inserts or removes anot *** --- *** her region marked by a distinct cognate *** --- *** integration/excision site. *** --- ************************************************ --- CREATE VIEW integration_excision_site AS SELECT feature_id AS integration_excision_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'integration_excision_site'; --- ************************************************ --- *** relation: resolution_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which separates a physically *** --- *** contiguous circle of DNA into two physic *** --- *** ally separate circles. *** --- ************************************************ --- CREATE VIEW resolution_site AS SELECT feature_id AS resolution_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'resolution_site'; --- ************************************************ --- *** relation: inversion_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inverts the region flan *** --- *** ked by a pair of sites. *** --- ************************************************ --- CREATE VIEW inversion_site AS SELECT feature_id AS inversion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site' OR cvterm.name = 'inversion_site'; --- ************************************************ --- *** relation: dif_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site at which replicated bacterial cir *** --- *** cular chromosomes are decatenated by sit *** --- *** e specific resolvase. *** --- ************************************************ --- CREATE VIEW dif_site AS SELECT feature_id AS dif_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dif_site'; --- ************************************************ --- *** relation: attc_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attC site is a sequence required for *** --- *** the integration of a DNA of an integron. *** --- ************************************************ --- CREATE VIEW attc_site AS SELECT feature_id AS attc_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attC_site'; --- ************************************************ --- *** relation: eukaryotic_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW eukaryotic_terminator AS SELECT feature_id AS eukaryotic_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'eukaryotic_terminator'; --- ************************************************ --- *** relation: oriv *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of vegetative replication in p *** --- *** lasmids and phages. *** --- ************************************************ --- CREATE VIEW oriv AS SELECT feature_id AS oriv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriV'; --- ************************************************ --- *** relation: oric *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of bacterial chromosome replic *** --- *** ation. *** --- ************************************************ --- CREATE VIEW oric AS SELECT feature_id AS oric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriC'; --- ************************************************ --- *** relation: dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, DNA molecule. *** --- ************************************************ --- CREATE VIEW dna_chromosome AS SELECT feature_id AS dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'DNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_dna_chromosome AS SELECT feature_id AS double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_dna_chromosome AS SELECT feature_id AS single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_dna_chromosome AS SELECT feature_id AS linear_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_dna_chromosome AS SELECT feature_id AS circular_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_dna_chromosome AS SELECT feature_id AS linear_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_dna_chromosome AS SELECT feature_id AS circular_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, RNA molecule. *** --- ************************************************ --- CREATE VIEW rna_chromosome AS SELECT feature_id AS rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_rna_chromosome AS SELECT feature_id AS single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_rna_chromosome AS SELECT feature_id AS linear_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_rna_chromosome AS SELECT feature_id AS linear_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_rna_chromosome AS SELECT feature_id AS double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_rna_chromosome AS SELECT feature_id AS circular_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular RNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_rna_chromosome AS SELECT feature_id AS circular_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: insertion_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal_inverted_repeat_element that *** --- *** is bacterial and only encodes the functi *** --- *** ons required for its transposition betwe *** --- *** en these inverted repeats. *** --- ************************************************ --- CREATE VIEW insertion_sequence AS SELECT feature_id AS insertion_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_sequence'; --- ************************************************ --- *** relation: minicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minicircle_gene AS SELECT feature_id AS minicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle_gene'; --- ************************************************ --- *** relation: cryptic *** --- *** relation type: VIEW *** --- *** *** --- *** A feature_attribute describing a feature *** --- *** that is not manifest under normal condi *** --- *** tions. *** --- ************************************************ --- CREATE VIEW cryptic AS SELECT feature_id AS cryptic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic'; --- ************************************************ --- *** relation: anchor_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW anchor_binding_site AS SELECT feature_id AS anchor_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_binding_site'; --- ************************************************ --- *** relation: template_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that specifies t *** --- *** he insertions and deletions of bases in *** --- *** the editing of a target mRNA. *** --- ************************************************ --- CREATE VIEW template_region AS SELECT feature_id AS template_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'template_region'; --- ************************************************ --- *** relation: grna_encoding *** --- *** relation type: VIEW *** --- *** *** --- *** A non-protein_coding gene that encodes a *** --- *** guide_RNA. *** --- ************************************************ --- CREATE VIEW grna_encoding AS SELECT feature_id AS grna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_encoding'; --- ************************************************ --- *** relation: minicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A minicircle is a replicon, part of a ki *** --- *** netoplast, that encodes for guide RNAs. *** --- ************************************************ --- CREATE VIEW minicircle AS SELECT feature_id AS minicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle'; --- ************************************************ --- *** relation: rho_dependent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_dependent_bacterial_terminator AS SELECT feature_id AS rho_dependent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator'; --- ************************************************ --- *** relation: rho_independent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_independent_bacterial_terminator AS SELECT feature_id AS rho_independent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_independent_bacterial_terminator'; --- ************************************************ --- *** relation: strand_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strand_attribute AS SELECT feature_id AS strand_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute'; --- ************************************************ --- *** relation: single *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single AS SELECT feature_id AS single_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single'; --- ************************************************ --- *** relation: double *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double AS SELECT feature_id AS double_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double'; --- ************************************************ --- *** relation: topology_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW topology_attribute AS SELECT feature_id AS topology_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute'; --- ************************************************ --- *** relation: linear *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as a 3'-terminal residue and a 5'-termin *** --- *** al residue. *** --- ************************************************ --- CREATE VIEW linear AS SELECT feature_id AS linear_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear'; --- ************************************************ --- *** relation: circular *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as no terminal nucleotide residues. *** --- ************************************************ --- CREATE VIEW circular AS SELECT feature_id AS circular_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular'; --- ************************************************ --- *** relation: class_ii_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (59-60 nt long) con *** --- *** taining 5' and 3' ends that are predicte *** --- *** d to come together to form a stem struct *** --- *** ure. Identified in the social amoeba Dic *** --- *** tyostelium discoideum and localized in t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW class_ii_rna AS SELECT feature_id AS class_ii_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_II_RNA'; --- ************************************************ --- *** relation: class_i_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (55-65 nt long) con *** --- *** taining highly conserved 5' and 3' ends *** --- *** (16 and 8 nt, respectively) that are pre *** --- *** dicted to come together to form a stem s *** --- *** tructure. Identified in the social amoeb *** --- *** a Dictyostelium discoideum and localized *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW class_i_rna AS SELECT feature_id AS class_i_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_I_RNA'; --- ************************************************ --- *** relation: genomic_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW genomic_dna AS SELECT feature_id AS genomic_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_DNA'; --- ************************************************ --- *** relation: bac_cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bac_cloned_genomic_insert AS SELECT feature_id AS bac_cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert'; --- ************************************************ --- *** relation: consensus *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus AS SELECT feature_id AS consensus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus'; --- ************************************************ --- *** relation: consensus_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_region AS SELECT feature_id AS consensus_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region'; --- ************************************************ --- *** relation: consensus_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_mrna AS SELECT feature_id AS consensus_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA'; --- ************************************************ --- *** relation: predicted_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW predicted_gene AS SELECT feature_id AS predicted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_gene'; --- ************************************************ --- *** relation: gene_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_fragment AS SELECT feature_id AS gene_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fragment'; --- ************************************************ --- *** relation: recursive_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A recursive splice site is a splice site *** --- *** which subdivides a large intron. Recurs *** --- *** ive splicing is a mechanism that splices *** --- *** large introns by sub dividing the intro *** --- *** n at non exonic elements and alternate e *** --- *** xons. *** --- ************************************************ --- CREATE VIEW recursive_splice_site AS SELECT feature_id AS recursive_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recursive_splice_site'; --- ************************************************ --- *** relation: bac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a B *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW bac_end AS SELECT feature_id AS bac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_end'; --- ************************************************ --- *** relation: rrna_16s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the small sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_16s AS SELECT feature_id AS rrna_16s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_16S'; --- ************************************************ --- *** relation: rrna_23s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the large sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_23s AS SELECT feature_id AS rrna_23s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_23S'; --- ************************************************ --- *** relation: rrna_25s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide which functions a *** --- *** s part of the large subunit of the ribos *** --- *** ome in some eukaryotes. *** --- ************************************************ --- CREATE VIEW rrna_25s AS SELECT feature_id AS rrna_25s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_25S'; --- ************************************************ --- *** relation: solo_ltr *** --- *** relation type: VIEW *** --- *** *** --- *** A recombination product between the 2 LT *** --- *** R of the same element. *** --- ************************************************ --- CREATE VIEW solo_ltr AS SELECT feature_id AS solo_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'solo_LTR'; --- ************************************************ --- *** relation: low_complexity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity AS SELECT feature_id AS low_complexity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity'; --- ************************************************ --- *** relation: low_complexity_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity_region AS SELECT feature_id AS low_complexity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity_region'; --- ************************************************ --- *** relation: prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A phage genome after it has established *** --- *** in the host genome in a latent/immune st *** --- *** ate either as a plasmid or as an integra *** --- *** ted "island". *** --- ************************************************ --- CREATE VIEW prophage AS SELECT feature_id AS prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage'; --- ************************************************ --- *** relation: cryptic_prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A remnant of an integrated prophage in t *** --- *** he host genome or an "island" in the hos *** --- *** t genome that includes phage like-genes. *** --- ************************************************ --- CREATE VIEW cryptic_prophage AS SELECT feature_id AS cryptic_prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_prophage'; --- ************************************************ --- *** relation: tetraloop *** --- *** relation type: VIEW *** --- *** *** --- *** A base-paired stem with loop of 4 non-hy *** --- *** drogen bonded nucleotides. *** --- ************************************************ --- CREATE VIEW tetraloop AS SELECT feature_id AS tetraloop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop'; --- ************************************************ --- *** relation: dna_constraint_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A double-stranded DNA used to control ma *** --- *** cromolecular structure and function. *** --- ************************************************ --- CREATE VIEW dna_constraint_sequence AS SELECT feature_id AS dna_constraint_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_constraint_sequence'; --- ************************************************ --- *** relation: i_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A cytosine rich domain whereby strands a *** --- *** ssociate both inter- and intramolecularl *** --- *** y at moderately acidic pH. *** --- ************************************************ --- CREATE VIEW i_motif AS SELECT feature_id AS i_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif'; --- ************************************************ --- *** relation: pna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Peptide nucleic acid, is a chemical not *** --- *** known to occur naturally but is artifici *** --- *** ally synthesized and used in some biolog *** --- *** ical research and medical treatments. Th *** --- *** e PNA backbone is composed of repeating *** --- *** N-(2-aminoethyl)-glycine units linked by *** --- *** peptide bonds. The purine and pyrimidin *** --- *** e bases are linked to the backbone by me *** --- *** thylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna_oligo AS SELECT feature_id AS pna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA_oligo'; --- ************************************************ --- *** relation: dnazyme *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence with catalytic activity. *** --- ************************************************ --- CREATE VIEW dnazyme AS SELECT feature_id AS dnazyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAzyme'; --- ************************************************ --- *** relation: mnp *** --- *** relation type: VIEW *** --- *** *** --- *** A multiple nucleotide polymorphism with *** --- *** alleles of common length > 1, for exampl *** --- *** e AAA/TTT. *** --- ************************************************ --- CREATE VIEW mnp AS SELECT feature_id AS mnp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP'; --- ************************************************ --- *** relation: intron_domain *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intron_domain AS SELECT feature_id AS intron_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain'; --- ************************************************ --- *** relation: wobble_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base pairing, mo *** --- *** st commonly between G and U, which is im *** --- *** portant for the secondary structure of R *** --- *** NAs. It has similar thermodynamic stabil *** --- *** ity to the Watson-Crick pairing. Wobble *** --- *** base pairs only have two hydrogen bonds. *** --- *** Other wobble base pair possibilities ar *** --- *** e I-A, I-U and I-C. *** --- ************************************************ --- CREATE VIEW wobble_base_pair AS SELECT feature_id AS wobble_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wobble_base_pair'; --- ************************************************ --- *** relation: internal_guide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A purine-rich sequence in the group I in *** --- *** trons which determines the locations of *** --- *** the splice sites in group I intron splic *** --- *** ing and has catalytic activity. *** --- ************************************************ --- CREATE VIEW internal_guide_sequence AS SELECT feature_id AS internal_guide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence'; --- ************************************************ --- *** relation: silent_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW silent_mutation AS SELECT feature_id AS silent_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation'; --- ************************************************ --- *** relation: epitope *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a macromolecule that is reco *** --- *** gnized by the immune system. *** --- ************************************************ --- CREATE VIEW epitope AS SELECT feature_id AS epitope_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epitope'; --- ************************************************ --- *** relation: copy_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A variation that increases or decreases *** --- *** the copy number of a given region. *** --- ************************************************ --- CREATE VIEW copy_number_variation AS SELECT feature_id AS copy_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_variation'; --- ************************************************ --- *** relation: sequence_variant_affecting_copy_number *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_copy_number AS SELECT feature_id AS sequence_variant_affecting_copy_number_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_copy_number'; --- ************************************************ --- *** relation: chromosome_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_breakpoint AS SELECT feature_id AS chromosome_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint'; --- ************************************************ --- *** relation: inversion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where an i *** --- *** nversion begins or ends. *** --- ************************************************ --- CREATE VIEW inversion_breakpoint AS SELECT feature_id AS inversion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint'; --- ************************************************ --- *** relation: allele *** --- *** relation type: VIEW *** --- *** *** --- *** An allele is one of a set of coexisting *** --- *** sequence variants of a gene. *** --- ************************************************ --- CREATE VIEW allele AS SELECT feature_id AS allele_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allele'; --- ************************************************ --- *** relation: haplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A haplotype is one of a set of coexistin *** --- *** g sequence variants of a haplotype block *** --- *** . *** --- ************************************************ --- CREATE VIEW haplotype AS SELECT feature_id AS haplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype'; --- ************************************************ --- *** relation: polymorphic_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that is segregating i *** --- *** n one or more natural populations of a s *** --- *** pecies. *** --- ************************************************ --- CREATE VIEW polymorphic_sequence_variant AS SELECT feature_id AS polymorphic_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant'; --- ************************************************ --- *** relation: genome *** --- *** relation type: VIEW *** --- *** *** --- *** A genome is the sum of genetic material *** --- *** within a cell or virion. *** --- ************************************************ --- CREATE VIEW genome AS SELECT feature_id AS genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genome'; --- ************************************************ --- *** relation: genotype *** --- *** relation type: VIEW *** --- *** *** --- *** A genotype is a variant genome, complete *** --- *** or incomplete. *** --- ************************************************ --- CREATE VIEW genotype AS SELECT feature_id AS genotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype' OR cvterm.name = 'genotype'; --- ************************************************ --- *** relation: diplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A diplotype is a pair of haplotypes from *** --- *** a given individual. It is a genotype wh *** --- *** ere the phase is known. *** --- ************************************************ --- CREATE VIEW diplotype AS SELECT feature_id AS diplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype'; --- ************************************************ --- *** relation: direction_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direction_attribute AS SELECT feature_id AS direction_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'direction_attribute'; --- ************************************************ --- *** relation: forward *** --- *** relation type: VIEW *** --- *** *** --- *** Forward is an attribute of the feature, *** --- *** where the feature is in the 5' to 3' dir *** --- *** ection. *** --- ************************************************ --- CREATE VIEW forward AS SELECT feature_id AS forward_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward'; --- ************************************************ --- *** relation: reverse *** --- *** relation type: VIEW *** --- *** *** --- *** Reverse is an attribute of the feature, *** --- *** where the feature is in the 3' to 5' dir *** --- *** ection. Again could be applied to primer *** --- *** . *** --- ************************************************ --- CREATE VIEW reverse AS SELECT feature_id AS reverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse'; --- ************************************************ --- *** relation: mitochondrial_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_dna AS SELECT feature_id AS mitochondrial_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA'; --- ************************************************ --- *** relation: chloroplast_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_dna AS SELECT feature_id AS chloroplast_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA'; --- ************************************************ --- *** relation: mirtron *** --- *** relation type: VIEW *** --- *** *** --- *** A debranched intron which mimics the str *** --- *** ucture of pre-miRNA and enters the miRNA *** --- *** processing pathway without Drosha media *** --- *** ted cleavage. *** --- ************************************************ --- CREATE VIEW mirtron AS SELECT feature_id AS mirtron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mirtron'; --- ************************************************ --- *** relation: pirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA, part of a silenc *** --- *** ing system that prevents the spreading o *** --- *** f selfish genetic elements. *** --- ************************************************ --- CREATE VIEW pirna AS SELECT feature_id AS pirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA'; --- ************************************************ --- *** relation: arginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an arginine ant *** --- *** icodon, and a 3' arginine binding region *** --- *** . *** --- ************************************************ --- CREATE VIEW arginyl_trna AS SELECT feature_id AS arginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginyl_tRNA'; --- ************************************************ --- *** relation: mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide region with either intra-ge *** --- *** nome or intracellular moblity, of varyin *** --- *** g length, which often carry the informat *** --- *** ion necessary for transfer and recombina *** --- *** tion with the host genome. *** --- ************************************************ --- CREATE VIEW mobile_genetic_element AS SELECT feature_id AS mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'mobile_genetic_element'; --- ************************************************ --- *** relation: extrachromosomal_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is not integrated into the h *** --- *** ost chromosome. *** --- ************************************************ --- CREATE VIEW extrachromosomal_mobile_genetic_element AS SELECT feature_id AS extrachromosomal_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'extrachromosomal_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is integrated into the host *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW integrated_mobile_genetic_element AS SELECT feature_id AS integrated_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'integrated_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid sequence that is integrated wi *** --- *** thin the host chromosome. *** --- ************************************************ --- CREATE VIEW integrated_plasmid AS SELECT feature_id AS integrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_plasmid'; --- ************************************************ --- *** relation: viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The region of nucleotide sequence of a v *** --- *** irus, a submicroscopic particle that rep *** --- *** licates by infecting a host cell. *** --- ************************************************ --- CREATE VIEW viral_sequence AS SELECT feature_id AS viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'viral_sequence'; --- ************************************************ --- *** relation: phage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide sequence of a virus that *** --- *** infects bacteria. *** --- ************************************************ --- CREATE VIEW phage_sequence AS SELECT feature_id AS phage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence'; --- ************************************************ --- *** relation: attctn_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attachment site located on a conjugat *** --- *** ive transposon and used for site-specifi *** --- *** c integration of a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW attctn_site AS SELECT feature_id AS attctn_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attCtn_site'; --- ************************************************ --- *** relation: nuclear_mt_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A nuclear pseudogene of a mitochndrial g *** --- *** ene. *** --- ************************************************ --- CREATE VIEW nuclear_mt_pseudogene AS SELECT feature_id AS nuclear_mt_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_mt_pseudogene'; --- ************************************************ --- *** relation: cointegrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A MGE region consisting of two fused pla *** --- *** smids resulting from a replicative trans *** --- *** position event. *** --- ************************************************ --- CREATE VIEW cointegrated_plasmid AS SELECT feature_id AS cointegrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cointegrated_plasmid'; --- ************************************************ --- *** relation: irlinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the left of a region susceptible to s *** --- *** ite-specific inversion. *** --- ************************************************ --- CREATE VIEW irlinv_site AS SELECT feature_id AS irlinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site'; --- ************************************************ --- *** relation: irrinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the right of a region susceptible to *** --- *** site-specific inversion. *** --- ************************************************ --- CREATE VIEW irrinv_site AS SELECT feature_id AS irrinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRRinv_site'; --- ************************************************ --- *** relation: inversion_site_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region located within an inversion sit *** --- *** e. *** --- ************************************************ --- CREATE VIEW inversion_site_part AS SELECT feature_id AS inversion_site_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'inversion_site_part'; --- ************************************************ --- *** relation: defective_conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** An island that contains genes for integr *** --- *** ation/excision and the gene and site for *** --- *** the initiation of intercellular transfe *** --- *** r by conjugation. It can be complemented *** --- *** for transfer by a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW defective_conjugative_transposon AS SELECT feature_id AS defective_conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'defective_conjugative_transposon'; --- ************************************************ --- *** relation: repeat_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a repeat, interrupted by th *** --- *** e insertion of another element. *** --- ************************************************ --- CREATE VIEW repeat_fragment AS SELECT feature_id AS repeat_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_fragment'; --- ************************************************ --- *** relation: transposon_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transposon_fragment AS SELECT feature_id AS transposon_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposon_fragment'; --- ************************************************ --- *** relation: transcriptional_cis_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates the t *** --- *** ranscription of a gene or genes. *** --- ************************************************ --- CREATE VIEW transcriptional_cis_regulatory_region AS SELECT feature_id AS transcriptional_cis_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'transcriptional_cis_regulatory_region'; --- ************************************************ --- *** relation: splicing_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates splic *** --- *** ing. *** --- ************************************************ --- CREATE VIEW splicing_regulatory_region AS SELECT feature_id AS splicing_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splicing_regulatory_region'; --- ************************************************ --- *** relation: promoter_targeting_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional_cis_regulatory_region *** --- *** that restricts the activity of a CRM to *** --- *** a single promoter and which functions on *** --- *** ly when both itself and an insulator are *** --- *** located between the CRM and the promote *** --- *** r. *** --- ************************************************ --- CREATE VIEW promoter_targeting_sequence AS SELECT feature_id AS promoter_targeting_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_targeting_sequence'; --- ************************************************ --- *** relation: sequence_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_alteration is a sequence_feat *** --- *** ure whose extent is the deviation from a *** --- *** nother sequence. *** --- ************************************************ --- CREATE VIEW sequence_alteration AS SELECT feature_id AS sequence_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'substitution' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'sequence_alteration'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant is a non exact copy o *** --- *** f a sequence_feature or genome exhibitin *** --- *** g one or more sequence_alteration. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: propeptide_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** The propeptide_cleavage_site is the argi *** --- *** nine/lysine boundary on a propeptide whe *** --- *** re cleavage occurs. *** --- ************************************************ --- CREATE VIEW propeptide_cleavage_site AS SELECT feature_id AS propeptide_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide_cleavage_site'; --- ************************************************ --- *** relation: propeptide *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a peptide chain which is cleaved *** --- *** off during the formation of the mature *** --- *** protein. *** --- ************************************************ --- CREATE VIEW propeptide AS SELECT feature_id AS propeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide'; --- ************************************************ --- *** relation: immature_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** An immature_peptide_region is the extent *** --- *** of the peptide after it has been transl *** --- *** ated and before any processing occurs. *** --- ************************************************ --- CREATE VIEW immature_peptide_region AS SELECT feature_id AS immature_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'immature_peptide_region'; --- ************************************************ --- *** relation: active_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Active peptides are proteins which are b *** --- *** iologically active, released from a prec *** --- *** ursor molecule. *** --- ************************************************ --- CREATE VIEW active_peptide AS SELECT feature_id AS active_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide'; --- ************************************************ --- *** relation: compositionally_biased_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is rich in a par *** --- *** ticular amino acid or homopolymeric and *** --- *** greater than three residues in length. *** --- ************************************************ --- CREATE VIEW compositionally_biased_region_of_peptide AS SELECT feature_id AS compositionally_biased_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compositionally_biased_region_of_peptide'; --- ************************************************ --- *** relation: polypeptide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a short (up to 20 am *** --- *** ino acids) region of biological interest *** --- *** . Such motifs, although they are too sho *** --- *** rt to constitute functional domains, sha *** --- *** re sequence similarities and are conserv *** --- *** ed in different proteins. They display a *** --- *** common function (protein-binding, subce *** --- *** llular location etc.). *** --- ************************************************ --- CREATE VIEW polypeptide_motif AS SELECT feature_id AS polypeptide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_motif'; --- ************************************************ --- *** relation: polypeptide_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide_repeat is a single copy of *** --- *** an internal sequence repetition. *** --- ************************************************ --- CREATE VIEW polypeptide_repeat AS SELECT feature_id AS polypeptide_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_repeat'; --- ************************************************ --- *** relation: polypeptide_structural_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of polypeptide with a given struc *** --- *** tural property. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_region AS SELECT feature_id AS polypeptide_structural_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_region'; --- ************************************************ --- *** relation: membrane_structure *** --- *** relation type: VIEW *** --- *** *** --- *** Arrangement of the polypeptide with resp *** --- *** ect to the lipid bilayer. *** --- ************************************************ --- CREATE VIEW membrane_structure AS SELECT feature_id AS membrane_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_structure'; --- ************************************************ --- *** relation: extramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer. *** --- ************************************************ --- CREATE VIEW extramembrane_polypeptide_region AS SELECT feature_id AS extramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'extramembrane_polypeptide_region'; --- ************************************************ --- *** relation: cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized ins *** --- *** ide the cytoplasm. *** --- ************************************************ --- CREATE VIEW cytoplasmic_polypeptide_region AS SELECT feature_id AS cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: non_cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer and outside of t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW non_cytoplasmic_polypeptide_region AS SELECT feature_id AS non_cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: intramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region present in the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW intramembrane_polypeptide_region AS SELECT feature_id AS intramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region'; --- ************************************************ --- *** relation: membrane_peptide_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region localized within the *** --- *** lipid bilayer where both ends traverse t *** --- *** he same membrane. *** --- ************************************************ --- CREATE VIEW membrane_peptide_loop AS SELECT feature_id AS membrane_peptide_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop'; --- ************************************************ --- *** relation: transmembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region traversing the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW transmembrane_polypeptide_region AS SELECT feature_id AS transmembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transmembrane_polypeptide_region'; --- ************************************************ --- *** relation: polypeptide_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide with secondary struc *** --- *** ture has hydrogen bonding along the pept *** --- *** ide chain that causes a defined conforma *** --- *** tion of the chain. *** --- ************************************************ --- CREATE VIEW polypeptide_secondary_structure AS SELECT feature_id AS polypeptide_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_secondary_structure'; --- ************************************************ --- *** relation: polypeptide_structural_motif *** --- *** relation type: VIEW *** --- *** *** --- *** Motif is a three-dimensional structural *** --- *** element within the chain, which appears *** --- *** also in a variety of other molecules. Un *** --- *** like a domain, a motif does not need to *** --- *** form a stable globular unit. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_motif AS SELECT feature_id AS polypeptide_structural_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_motif'; --- ************************************************ --- *** relation: coiled_coil *** --- *** relation type: VIEW *** --- *** *** --- *** A coiled coil is a structural motif in p *** --- *** roteins, in which alpha-helices are coil *** --- *** ed together like the strands of a rope. *** --- ************************************************ --- CREATE VIEW coiled_coil AS SELECT feature_id AS coiled_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil'; --- ************************************************ --- *** relation: helix_turn_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A motif comprising two helices separated *** --- *** by a turn. *** --- ************************************************ --- CREATE VIEW helix_turn_helix AS SELECT feature_id AS helix_turn_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helix_turn_helix'; --- ************************************************ --- *** relation: polypeptide_sequencing_information *** --- *** relation type: VIEW *** --- *** *** --- *** Incompatibility in the sequence due to s *** --- *** ome experimental problem. *** --- ************************************************ --- CREATE VIEW polypeptide_sequencing_information AS SELECT feature_id AS polypeptide_sequencing_information_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'polypeptide_sequencing_information'; --- ************************************************ --- *** relation: non_adjacent_residues *** --- *** relation type: VIEW *** --- *** *** --- *** Indicates that two consecutive residues *** --- *** in a fragment sequence are not consecuti *** --- *** ve in the full-length protein and that t *** --- *** here are a number of unsequenced residue *** --- *** s between them. *** --- ************************************************ --- CREATE VIEW non_adjacent_residues AS SELECT feature_id AS non_adjacent_residues_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues'; --- ************************************************ --- *** relation: non_terminal_residue *** --- *** relation type: VIEW *** --- *** *** --- *** The residue at an extremity of the seque *** --- *** nce is not the terminal residue. *** --- ************************************************ --- CREATE VIEW non_terminal_residue AS SELECT feature_id AS non_terminal_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_terminal_residue'; --- ************************************************ --- *** relation: sequence_conflict *** --- *** relation type: VIEW *** --- *** *** --- *** Different sources report differing seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW sequence_conflict AS SELECT feature_id AS sequence_conflict_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_conflict'; --- ************************************************ --- *** relation: sequence_uncertainty *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the positions in a sequence wh *** --- *** ere the authors are unsure about the seq *** --- *** uence assignment. *** --- ************************************************ --- CREATE VIEW sequence_uncertainty AS SELECT feature_id AS sequence_uncertainty_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_uncertainty'; --- ************************************************ --- *** relation: post_translationally_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region where a transformation occurs i *** --- *** n a protein after it has been synthesize *** --- *** d. This which may regulate, stabilize, c *** --- *** rosslink or introduce new chemical funct *** --- *** ionalities in the protein. *** --- ************************************************ --- CREATE VIEW post_translationally_modified_region AS SELECT feature_id AS post_translationally_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region'; --- ************************************************ --- *** relation: polypeptide_metal_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residue is part of a binding site for a *** --- *** metal ion. *** --- ************************************************ --- CREATE VIEW polypeptide_metal_contact AS SELECT feature_id AS polypeptide_metal_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_metal_contact'; --- ************************************************ --- *** relation: protein_protein_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues involved in protein-protein int *** --- *** eractions. *** --- ************************************************ --- CREATE VIEW protein_protein_contact AS SELECT feature_id AS protein_protein_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact'; --- ************************************************ --- *** relation: polypeptide_calcium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with calcium *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_calcium_ion_contact_site AS SELECT feature_id AS polypeptide_calcium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_cobalt_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with cobalt. *** --- ************************************************ --- CREATE VIEW polypeptide_cobalt_ion_contact_site AS SELECT feature_id AS polypeptide_cobalt_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_cobalt_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_copper_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with copper. *** --- ************************************************ --- CREATE VIEW polypeptide_copper_ion_contact_site AS SELECT feature_id AS polypeptide_copper_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_copper_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_iron_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with iron. *** --- ************************************************ --- CREATE VIEW polypeptide_iron_ion_contact_site AS SELECT feature_id AS polypeptide_iron_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_iron_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_magnesium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with magnesi *** --- *** um. *** --- ************************************************ --- CREATE VIEW polypeptide_magnesium_ion_contact_site AS SELECT feature_id AS polypeptide_magnesium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_magnesium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_manganese_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with mangane *** --- *** se. *** --- ************************************************ --- CREATE VIEW polypeptide_manganese_ion_contact_site AS SELECT feature_id AS polypeptide_manganese_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_manganese_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_molybdenum_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with molybde *** --- *** num. *** --- ************************************************ --- CREATE VIEW polypeptide_molybdenum_ion_contact_site AS SELECT feature_id AS polypeptide_molybdenum_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_molybdenum_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_nickel_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with nickel. *** --- ************************************************ --- CREATE VIEW polypeptide_nickel_ion_contact_site AS SELECT feature_id AS polypeptide_nickel_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nickel_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_tungsten_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with tungste *** --- *** n. *** --- ************************************************ --- CREATE VIEW polypeptide_tungsten_ion_contact_site AS SELECT feature_id AS polypeptide_tungsten_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_tungsten_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_zinc_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with zinc. *** --- ************************************************ --- CREATE VIEW polypeptide_zinc_ion_contact_site AS SELECT feature_id AS polypeptide_zinc_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_zinc_ion_contact_site'; --- ************************************************ --- *** relation: catalytic_residue *** --- *** relation type: VIEW *** --- *** *** --- *** Amino acid involved in the activity of a *** --- *** n enzyme. *** --- ************************************************ --- CREATE VIEW catalytic_residue AS SELECT feature_id AS catalytic_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue'; --- ************************************************ --- *** relation: polypeptide_ligand_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues which interact with a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_ligand_contact AS SELECT feature_id AS polypeptide_ligand_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact'; --- ************************************************ --- *** relation: asx_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: Residue(i) is Asp *** --- *** artate or Asparagine (Asx), side-chain O *** --- *** of residue(i) is H-bonded to the main-c *** --- *** hain NH of residue(i+2) or (i+3), main-c *** --- *** hain CO of residue(i) is H-bonded to the *** --- *** main-chain NH of residue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW asx_motif AS SELECT feature_id AS asx_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif'; --- ************************************************ --- *** relation: beta_bulge *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet in which the main chains of two co *** --- *** nsecutive residues are H-bonded to that *** --- *** of the third, and in which the dihedral *** --- *** angles are as follows: Residue(i): -140 *** --- *** degrees < phi(l) -20 degrees , -90 degre *** --- *** es < psi(l) < 40 degrees. Residue (i+1): *** --- *** -180 degrees < phi < -25 degrees or +12 *** --- *** 0 degrees < phi < +180 degrees, +40 degr *** --- *** ees < psi < +180 degrees or -180 degrees *** --- *** < psi < -120 degrees. *** --- ************************************************ --- CREATE VIEW beta_bulge AS SELECT feature_id AS beta_bulge_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge'; --- ************************************************ --- *** relation: beta_bulge_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds. Beta bu *** --- *** lge loops often occur at the loop ends o *** --- *** f beta-hairpins. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop AS SELECT feature_id AS beta_bulge_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'beta_bulge_loop'; --- ************************************************ --- *** relation: beta_bulge_loop_five *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 4), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +3), these loops have an RL nest at resi *** --- *** dues i+2 and i+3. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_five AS SELECT feature_id AS beta_bulge_loop_five_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five'; --- ************************************************ --- *** relation: beta_bulge_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 5), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +4), these loops have an RL nest at resi *** --- *** dues i+3 and i+4. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_six AS SELECT feature_id AS beta_bulge_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_six'; --- ************************************************ --- *** relation: beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A beta strand describes a single length *** --- *** of polypeptide chain that forms part of *** --- *** a beta sheet. A single continuous stretc *** --- *** h of amino acids adopting an extended co *** --- *** nformation of hydrogen bonds between the *** --- *** N-O and the C=O of another part of the *** --- *** peptide. This forms a secondary protein *** --- *** structure in which two or more extended *** --- *** polypeptide regions are hydrogen-bonded *** --- *** to one another in a planar array. *** --- ************************************************ --- CREATE VIEW beta_strand AS SELECT feature_id AS beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'beta_strand'; --- ************************************************ --- *** relation: antiparallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (one running N-term *** --- *** inal to C-terminal and one running C-ter *** --- *** minal to N-terminal). Hydrogen bonding o *** --- *** ccurs between every other C=O from one s *** --- *** trand to every other N-H on the adjacent *** --- *** strand. In this case, if two atoms C-al *** --- *** pha (i) and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then t *** --- *** hey form two mutual backbone hydrogen bo *** --- *** nds to each other's flanking peptide gro *** --- *** ups; this is known as a close pair of hy *** --- *** drogen bonds. The peptide backbone dihed *** --- *** ral angles (phi, psi) are about (-140 de *** --- *** grees, 135 degrees) in antiparallel shee *** --- *** ts. *** --- ************************************************ --- CREATE VIEW antiparallel_beta_strand AS SELECT feature_id AS antiparallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand'; --- ************************************************ --- *** relation: parallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (both running N-ter *** --- *** minal to C-terminal). This orientation i *** --- *** s slightly less stable because it introd *** --- *** uces nonplanarity in the inter-strand hy *** --- *** drogen bonding pattern. Hydrogen bonding *** --- *** occurs between every other C=O from one *** --- *** strand to every other N-H on the adjace *** --- *** nt strand. In this case, if two atoms C- *** --- *** alpha (i)and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then *** --- *** they do not hydrogen bond to each other; *** --- *** rather, one residue forms hydrogen bond *** --- *** s to the residues that flank the other ( *** --- *** but not vice versa). For example, residu *** --- *** e i may form hydrogen bonds to residues *** --- *** j - 1 and j + 1; this is known as a wide *** --- *** pair of hydrogen bonds. By contrast, re *** --- *** sidue j may hydrogen-bond to different r *** --- *** esidues altogether, or to none at all. T *** --- *** he dihedral angles (phi, psi) are about *** --- *** (-120 degrees, 115 degrees) in parallel *** --- *** sheets. *** --- ************************************************ --- CREATE VIEW parallel_beta_strand AS SELECT feature_id AS parallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'parallel_beta_strand'; --- ************************************************ --- *** relation: peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A helix is a secondary_structure conform *** --- *** ation where the peptide backbone forms a *** --- *** coil. *** --- ************************************************ --- CREATE VIEW peptide_helix AS SELECT feature_id AS peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'peptide_helix'; --- ************************************************ --- *** relation: left_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A left handed helix is a region of pepti *** --- *** de where the coiled conformation turns i *** --- *** n an anticlockwise, left handed screw. *** --- ************************************************ --- CREATE VIEW left_handed_peptide_helix AS SELECT feature_id AS left_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix'; --- ************************************************ --- *** relation: right_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A right handed helix is a region of pept *** --- *** ide where the coiled conformation turns *** --- *** in a clockwise, right handed screw. *** --- ************************************************ --- CREATE VIEW right_handed_peptide_helix AS SELECT feature_id AS right_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'right_handed_peptide_helix'; --- ************************************************ --- *** relation: alpha_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The helix has 3.6 residues per turn whic *** --- *** h corersponds to a translation of 1.5 an *** --- *** gstroms (= 0.15 nm) along the helical ax *** --- *** is. Every backbone N-H group donates a h *** --- *** ydrogen bond to the backbone C=O group o *** --- *** f the amino acid four residues earlier. *** --- ************************************************ --- CREATE VIEW alpha_helix AS SELECT feature_id AS alpha_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix'; --- ************************************************ --- *** relation: pi_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The pi helix has 4.1 residues per turn a *** --- *** nd a translation of 1.15 (=0.115 nm) al *** --- *** ong the helical axis. The N-H group of a *** --- *** n amino acid forms a hydrogen bond with *** --- *** the C=O group of the amino acid five res *** --- *** idues earlier. *** --- ************************************************ --- CREATE VIEW pi_helix AS SELECT feature_id AS pi_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pi_helix'; --- ************************************************ --- *** relation: three_ten_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The 3-10 helix has 3 residues per turn w *** --- *** ith a translation of 2.0 angstroms (=0.2 *** --- *** nm) along the helical axis. The N-H gro *** --- *** up of an amino acid forms a hydrogen bon *** --- *** d with the C=O group of the amino acid t *** --- *** hree residues earlier. *** --- ************************************************ --- CREATE VIEW three_ten_helix AS SELECT feature_id AS three_ten_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_ten_helix'; --- ************************************************ --- *** relation: polypeptide_nest_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles. Nest should not have P *** --- *** roline as any residue. Nests frequently *** --- *** occur as parts of other motifs such as S *** --- *** chellman loops. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_motif AS SELECT feature_id AS polypeptide_nest_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'polypeptide_nest_motif'; --- ************************************************ --- *** relation: polypeptide_nest_left_right_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): +20 degree *** --- *** s < phi < +140 degrees, -40 degrees < ps *** --- *** i < +90 degrees. Residue(i+1): -140 degr *** --- *** ees < phi < -20 degrees, -90 degrees < p *** --- *** si < +40 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_left_right_motif AS SELECT feature_id AS polypeptide_nest_left_right_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif'; --- ************************************************ --- *** relation: polypeptide_nest_right_left_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): -140 degre *** --- *** es < phi < -20 degrees, -90 degrees < ps *** --- *** i < +40 degrees. Residue(i+1): +20 degre *** --- *** es < phi < +140 degrees, -40 degrees < p *** --- *** si < +90 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_right_left_motif AS SELECT feature_id AS polypeptide_nest_right_left_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_right_left_motif'; --- ************************************************ --- *** relation: schellmann_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of six or seven consecutive resi *** --- *** dues that contains two H-bonds. *** --- ************************************************ --- CREATE VIEW schellmann_loop AS SELECT feature_id AS schellmann_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'schellmann_loop'; --- ************************************************ --- *** relation: schellmann_loop_seven *** --- *** relation type: VIEW *** --- *** *** --- *** Wild type: A motif of seven consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+6), the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of res *** --- *** idue(i+5). *** --- ************************************************ --- CREATE VIEW schellmann_loop_seven AS SELECT feature_id AS schellmann_loop_seven_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven'; --- ************************************************ --- *** relation: schellmann_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** Common Type: A motif of six consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+5) the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of resi *** --- *** due(i+4). *** --- ************************************************ --- CREATE VIEW schellmann_loop_six AS SELECT feature_id AS schellmann_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_six'; --- ************************************************ --- *** relation: serine_threonine_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two hydrogen bonds in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain O of residue(i) is H-bonded to t *** --- *** he main-chain NH of residue(i+2) or (i+3 *** --- *** ) , the main-chain CO group of residue(i *** --- *** ) is H-bonded to the main-chain NH of re *** --- *** sidue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW serine_threonine_motif AS SELECT feature_id AS serine_threonine_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_motif'; --- ************************************************ --- *** relation: serine_threonine_staple_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four or five consecutive resi *** --- *** dues and one H-bond in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain OH of residue(i) is H-bonded to *** --- *** the main-chain CO of residue(i3) or (i4) *** --- *** , Phi angles of residues(i1), (i2) and ( *** --- *** i3) are negative. *** --- ************************************************ --- CREATE VIEW serine_threonine_staple_motif AS SELECT feature_id AS serine_threonine_staple_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_staple_motif'; --- ************************************************ --- *** relation: polypeptide_turn_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A reversal in the direction of the backb *** --- *** one of a protein that is stabilized by h *** --- *** ydrogen bond between backbone NH and CO *** --- *** groups, involving no more than 4 amino a *** --- *** cid residues. *** --- ************************************************ --- CREATE VIEW polypeptide_turn_motif AS SELECT feature_id AS polypeptide_turn_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_turn_motif'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I (dihedral angles):- R *** --- *** esidue(i): -140 degrees < chi (1) -120 d *** --- *** egrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1) *** --- *** : -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_one AS SELECT feature_id AS asx_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < psi *** --- *** +120 degrees < +180 degrees. Residue(i+ *** --- *** 1): +20 degrees < phi < +140 degrees, -4 *** --- *** 0 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_two AS SELECT feature_id AS asx_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < ps *** --- *** i +120 degrees < +180 degrees. Residue(i *** --- *** +1): +20 degrees < phi < +140 degrees, - *** --- *** 40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_two AS SELECT feature_id AS asx_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1 *** --- *** ): -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_one AS SELECT feature_id AS asx_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive residues tha *** --- *** t may contain one H-bond, which, if pres *** --- *** ent, is between the main-chain CO of the *** --- *** first residue and the main-chain NH of *** --- *** the fourth. It is characterized by the d *** --- *** ihedral angles of the second and third r *** --- *** esidues, which are the basis for sub-cat *** --- *** egorization. *** --- ************************************************ --- CREATE VIEW beta_turn AS SELECT feature_id AS beta_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I:A motif of four conse *** --- *** cutive residues that may contain one H-b *** --- *** ond, which, if present, is between the m *** --- *** ain-chain CO of the first residue and th *** --- *** e main-chain NH of the fourth. It is cha *** --- *** racterized by the dihedral angles:- Resi *** --- *** due(i+1): -140 degrees > phi > -20 degre *** --- *** es, -90 degrees > psi > +40 degrees. Res *** --- *** idue(i+2): -140 degrees > phi > -20 degr *** --- *** ees, -90 degrees > psi > +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_one AS SELECT feature_id AS beta_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II: A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees > phi > -20 degr *** --- *** ees, +80 degrees > psi > +180 degrees. R *** --- *** esidue(i+2): +20 degrees > phi > +140 de *** --- *** grees, -40 degrees > psi > +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_two AS SELECT feature_id AS beta_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_two'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I:A motif of four cons *** --- *** ecutive residues that may contain one H- *** --- *** bond, which, if present, is between the *** --- *** main-chain CO of the first residue and t *** --- *** he main-chain NH of the fourth. It is ch *** --- *** aracterized by the dihedral angles: Resi *** --- *** due(i+1): -140 degrees < phi < -20 degre *** --- *** es, -90 degrees < psi < +40 degrees. Res *** --- *** idue(i+2): -140 degrees < phi < -20 degr *** --- *** ees, -90 degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_one AS SELECT feature_id AS beta_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II:A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees < phi < -20 degr *** --- *** ees, +80 degrees < psi < +180 degrees. R *** --- *** esidue(i+2): +20 degrees < phi < +140 de *** --- *** grees, -40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_two AS SELECT feature_id AS beta_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_two'; --- ************************************************ --- *** relation: gamma_turn *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees. *** --- ************************************************ --- CREATE VIEW gamma_turn AS SELECT feature_id AS gamma_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'gamma_turn'; --- ************************************************ --- *** relation: gamma_turn_classic *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=75.0 - psi(i+1)=-64.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_classic AS SELECT feature_id AS gamma_turn_classic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic'; --- ************************************************ --- *** relation: gamma_turn_inverse *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=-79.0 - psi(i+1)=69.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_inverse AS SELECT feature_id AS gamma_turn_inverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_inverse'; --- ************************************************ --- *** relation: serine_threonine_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Ser *** --- *** ine (S) or Threonine (T), the side-chain *** --- *** O of residue(i) is H-bonded to the main *** --- *** -chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW serine_threonine_turn AS SELECT feature_id AS serine_threonine_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'serine_threonine_turn'; --- ************************************************ --- *** relation: st_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** -90 degrees psi +120 degrees < +40 degr *** --- *** ees, residue(i+1): -140 degrees < phi < *** --- *** -20 degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_one AS SELECT feature_id AS st_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one'; --- ************************************************ --- *** relation: st_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** +80 degrees psi +120 degrees < +180 deg *** --- *** rees, residue(i+1): +20 degrees < phi < *** --- *** +140 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_two AS SELECT feature_id AS st_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_two'; --- ************************************************ --- *** relation: st_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, -9 *** --- *** 0 degrees psi +120 degrees < +40 degrees *** --- *** , residue(i+1): -140 degrees < phi < -20 *** --- *** degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_one AS SELECT feature_id AS st_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_one'; --- ************************************************ --- *** relation: st_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, +8 *** --- *** 0 degrees psi +120 degrees < +180 degree *** --- *** s, residue(i+1): +20 degrees < phi < +14 *** --- *** 0 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_two AS SELECT feature_id AS st_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_two'; --- ************************************************ --- *** relation: polypeptide_variation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site of sequence variation (alteration *** --- *** ). Alternative sequence due to naturally *** --- *** occuring events such as polymorphisms a *** --- *** nd altermatve splicing or experimental m *** --- *** ethods such as site directed mutagenesis *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_variation_site AS SELECT feature_id AS polypeptide_variation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'polypeptide_variation_site'; --- ************************************************ --- *** relation: natural_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the natural sequence variants *** --- *** due to polymorphisms, disease-associated *** --- *** mutations, RNA editing and variations b *** --- *** etween strains, isolates or cultivars. *** --- ************************************************ --- CREATE VIEW natural_variant_site AS SELECT feature_id AS natural_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site'; --- ************************************************ --- *** relation: mutated_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Site which has been experimentally alter *** --- *** ed. *** --- ************************************************ --- CREATE VIEW mutated_variant_site AS SELECT feature_id AS mutated_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutated_variant_site'; --- ************************************************ --- *** relation: alternate_sequence_site *** --- *** relation type: VIEW *** --- *** *** --- *** Description of sequence variants produce *** --- *** d by alternative splicing, alternative p *** --- *** romoter usage, alternative initiation an *** --- *** d ribosomal frameshifting. *** --- ************************************************ --- CREATE VIEW alternate_sequence_site AS SELECT feature_id AS alternate_sequence_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternate_sequence_site'; --- ************************************************ --- *** relation: beta_turn_type_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** des of type VIa or type VIb and where th *** --- *** e i+2 residue is cis-proline. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six AS SELECT feature_id AS beta_turn_type_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six'; --- ************************************************ --- *** relation: beta_turn_type_six_a *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -60 degrees, psi ~ 120 degrees. Re *** --- *** sidue(i+2): phi ~ -90 degrees, psi ~ 0 d *** --- *** egrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a AS SELECT feature_id AS beta_turn_type_six_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six_a'; --- ************************************************ --- *** relation: beta_turn_type_six_a_one *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_one AS SELECT feature_id AS beta_turn_type_six_a_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one'; --- ************************************************ --- *** relation: beta_turn_type_six_a_two *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_two AS SELECT feature_id AS beta_turn_type_six_a_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_two'; --- ************************************************ --- *** relation: beta_turn_type_six_b *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -120 degrees, psi ~ 120 degrees. R *** --- *** esidue(i+2): phi ~ -60 degrees, psi ~ 0 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_b AS SELECT feature_id AS beta_turn_type_six_b_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_b'; --- ************************************************ --- *** relation: beta_turn_type_eight *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues that may contain one H-bond, which, *** --- *** if present, is between the main-chain C *** --- *** O of the first residue and the main-chai *** --- *** n NH of the fourth and is characterized *** --- *** by the dihedral angles: Residue(i+1): ph *** --- *** i ~ -60 degrees, psi ~ -30 degrees. Resi *** --- *** due(i+2): phi ~ -120 degrees, psi ~ 120 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_eight AS SELECT feature_id AS beta_turn_type_eight_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_eight'; --- ************************************************ --- *** relation: dre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -10 and -60 relative to t *** --- *** he TSS. Consensus sequence is WATCGATW. *** --- ************************************************ --- CREATE VIEW dre_motif AS SELECT feature_id AS dre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DRE_motif'; --- ************************************************ --- *** relation: dmv4_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments with respect to the TSS (+1). Cons *** --- *** ensus sequence is YGGTCACACTR. Marked sp *** --- *** atial preference within core promoter; t *** --- *** end to occur near the TSS, although not *** --- *** as tightly as INR (SO:0000014). *** --- ************************************************ --- CREATE VIEW dmv4_motif AS SELECT feature_id AS dmv4_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv4_motif'; --- ************************************************ --- *** relation: e_box_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and +1 relative to th *** --- *** e TSS. Consensus sequence is AWCAGCTGWT. *** --- *** Tends to co-occur with DMv2 (SO:0001161 *** --- *** ). Tends to not occur with DPE motif (SO *** --- *** :0000015). *** --- ************************************************ --- CREATE VIEW e_box_motif AS SELECT feature_id AS e_box_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'E_box_motif'; --- ************************************************ --- *** relation: dmv5_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -50 and -10 relative to t *** --- *** he TSS. Consensus sequence is KTYRGTATWT *** --- *** TT. Tends to co-occur with DMv4 (SO:0001 *** --- *** 157) . Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv5_motif AS SELECT feature_id AS dmv5_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv5_motif'; --- ************************************************ --- *** relation: dmv3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -30 and +15 relative to t *** --- *** he TSS. Consensus sequence is KNNCAKCNCT *** --- *** RNY. Tends to co-occur with DMv2 (SO:000 *** --- *** 1161). Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (0001162). *** --- ************************************************ --- CREATE VIEW dmv3_motif AS SELECT feature_id AS dmv3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv3_motif'; --- ************************************************ --- *** relation: dmv2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and -45 relative to t *** --- *** he TSS. Consensus sequence is MKSYGGCARC *** --- *** GSYSS. Tends to co-occur with DMv3 (SO:0 *** --- *** 001160). Tends to not occur with DPE mot *** --- *** if (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv2_motif AS SELECT feature_id AS dmv2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv2_motif'; --- ************************************************ --- *** relation: mte *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between +20 and +30 relative to t *** --- *** he TSS. Consensus sequence is CSARCSSAAC *** --- *** GS. Tends to co-occur with INR motif (SO *** --- *** :0000014). Tends to not occur with DPE m *** --- *** otif (SO:0000015) or DMv5 (SO:0001159). *** --- ************************************************ --- CREATE VIEW mte AS SELECT feature_id AS mte_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MTE'; --- ************************************************ --- *** relation: inr1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** TCATTCG. *** --- ************************************************ --- CREATE VIEW inr1_motif AS SELECT feature_id AS inr1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR1_motif'; --- ************************************************ --- *** relation: dpe1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CGGACGT. *** --- ************************************************ --- CREATE VIEW dpe1_motif AS SELECT feature_id AS dpe1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE1_motif'; --- ************************************************ --- *** relation: dmv1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CARCCCT. *** --- ************************************************ --- CREATE VIEW dmv1_motif AS SELECT feature_id AS dmv1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv1_motif'; --- ************************************************ --- *** relation: gaga_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAGAGCG. *** --- ************************************************ --- CREATE VIEW gaga_motif AS SELECT feature_id AS gaga_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GAGA_motif'; --- ************************************************ --- *** relation: ndm2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus CGMYGYCR. *** --- ************************************************ --- CREATE VIEW ndm2_motif AS SELECT feature_id AS ndm2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM2_motif'; --- ************************************************ --- *** relation: ndm3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAAAGCT. *** --- ************************************************ --- CREATE VIEW ndm3_motif AS SELECT feature_id AS ndm3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM3_motif'; --- ************************************************ --- *** relation: ds_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded RNA. *** --- ************************************************ --- CREATE VIEW ds_rna_viral_sequence AS SELECT feature_id AS ds_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_RNA_viral_sequence'; --- ************************************************ --- *** relation: polinton *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of DNA transposon that populates *** --- *** the genomes of protists, fungi, and anim *** --- *** als, characterized by a unique set of pr *** --- *** oteins necessary for their transposition *** --- *** , including a protein-primed DNA polymer *** --- *** ase B, retroviral integrase, cysteine pr *** --- *** otease, and ATPase. Polintons are charac *** --- *** terized by 6-bp target site duplications *** --- *** , terminal-inverted repeats that are sev *** --- *** eral hundred nucleotides long, and 5'-AG *** --- *** and TC-3' termini. Polintons exist as a *** --- *** utonomous and nonautonomous elements. *** --- ************************************************ --- CREATE VIEW polinton AS SELECT feature_id AS polinton_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polinton'; --- ************************************************ --- *** relation: rrna_21s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it in mitochondrial rRNA. *** --- ************************************************ --- CREATE VIEW rrna_21s AS SELECT feature_id AS rrna_21s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_21S'; --- ************************************************ --- *** relation: trna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tRNA. *** --- ************************************************ --- CREATE VIEW trna_region AS SELECT feature_id AS trna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'tRNA_region'; --- ************************************************ --- *** relation: anticodon_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of seven nucleotide bases in *** --- *** tRNA which contains the anticodon. It ha *** --- *** s the sequence 5'-pyrimidine-purine-anti *** --- *** codon-modified purine-any base-3. *** --- ************************************************ --- CREATE VIEW anticodon_loop AS SELECT feature_id AS anticodon_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop'; --- ************************************************ --- *** relation: anticodon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of three nucleotide bases in *** --- *** tRNA which recognizes a codon in mRNA. *** --- ************************************************ --- CREATE VIEW anticodon AS SELECT feature_id AS anticodon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon'; --- ************************************************ --- *** relation: cca_tail *** --- *** relation type: VIEW *** --- *** *** --- *** Base sequence at the 3' end of a tRNA. T *** --- *** he 3'-hydroxyl group on the terminal ade *** --- *** nosine is the attachment point for the a *** --- *** mino acid. *** --- ************************************************ --- CREATE VIEW cca_tail AS SELECT feature_id AS cca_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CCA_tail'; --- ************************************************ --- *** relation: dhu_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of nucleotide b *** --- *** ases in tRNA. It contains several dihydr *** --- *** ouracil residues. *** --- ************************************************ --- CREATE VIEW dhu_loop AS SELECT feature_id AS dhu_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DHU_loop'; --- ************************************************ --- *** relation: t_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of three nucleo *** --- *** tide bases in tRNA. It has sequence T-Ps *** --- *** i-C. *** --- ************************************************ --- CREATE VIEW t_loop AS SELECT feature_id AS t_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_loop'; --- ************************************************ --- *** relation: pyrrolysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding pyrrolysyl *** --- *** tRNA (SO:0000766). *** --- ************************************************ --- CREATE VIEW pyrrolysine_trna_primary_transcript AS SELECT feature_id AS pyrrolysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: u3_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U3 snoRNA is a member of the box C/D cla *** --- *** ss of small nucleolar RNAs. The U3 snoRN *** --- *** A secondary structure is characterised b *** --- *** y a small 5' domain (with boxes A and A' *** --- *** ), and a larger 3' domain (with boxes B, *** --- *** C, C', and D), the two domains being li *** --- *** nked by a single-stranded hinge. Boxes B *** --- *** and C form the B/C motif, which appears *** --- *** to be exclusive to U3 snoRNAs, and boxe *** --- *** s C' and D form the C'/D motif. The latt *** --- *** er is functionally similar to the C/D mo *** --- *** tifs found in other snoRNAs. The 5' doma *** --- *** in and the hinge region act as a pre-rRN *** --- *** A-binding domain. The 3' domain has cons *** --- *** erved protein-binding sites. Both the bo *** --- *** x B/C and box C'/D motifs are sufficient *** --- *** for nuclear retention of U3 snoRNA. The *** --- *** box C'/D motif is also necessary for nu *** --- *** cleolar localization, stability and hype *** --- *** rmethylation of U3 snoRNA. Both box B/C *** --- *** and C'/D motifs are involved in specific *** --- *** protein interactions and are necessary *** --- *** for the rRNA processing functions of U3 *** --- *** snoRNA. *** --- ************************************************ --- CREATE VIEW u3_snorna AS SELECT feature_id AS u3_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_snoRNA'; --- ************************************************ --- *** relation: au_rich_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is rich in AUUUA pen *** --- *** tamers. Messenger RNAs bearing multiple *** --- *** AU-rich elements are often unstable. *** --- ************************************************ --- CREATE VIEW au_rich_element AS SELECT feature_id AS au_rich_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'AU_rich_element'; --- ************************************************ --- *** relation: bruno_response_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is bound by the Dros *** --- *** ophila Bruno protein and its homologs. *** --- ************************************************ --- CREATE VIEW bruno_response_element AS SELECT feature_id AS bruno_response_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Bruno_response_element'; --- ************************************************ --- *** relation: iron_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory sequence found in the 5' an *** --- *** d 3' UTRs of many mRNAs which encode iro *** --- *** n-binding proteins. It has a hairpin str *** --- *** ucture and is recognized by trans-acting *** --- *** proteins known as iron-regulatory prote *** --- *** ins. *** --- ************************************************ --- CREATE VIEW iron_responsive_element AS SELECT feature_id AS iron_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iron_responsive_element'; --- ************************************************ --- *** relation: morpholino *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of nucleobases bound to a morpholino *** --- *** backbone. A morpholino backbone consist *** --- *** s of morpholine (CHEBI:34856) rings conn *** --- *** ected by phosphorodiamidate linkages. *** --- ************************************************ --- CREATE VIEW morpholino AS SELECT feature_id AS morpholino_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino'; --- ************************************************ --- *** relation: pna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of peptide nucleic acid (CHEBI:48021 *** --- *** ), a chemical consisting of nucleobases *** --- *** bound to a backbone composed of repeatin *** --- *** g N-(2-aminoethyl)-glycine units linked *** --- *** by peptide bonds. The purine and pyrimid *** --- *** ine bases are linked to the backbone by *** --- *** methylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna AS SELECT feature_id AS pna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA'; --- ************************************************ --- *** relation: enzymatic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** with or without an associated ribonucle *** --- *** oprotein. *** --- ************************************************ --- CREATE VIEW enzymatic AS SELECT feature_id AS enzymatic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic' OR cvterm.name = 'enzymatic'; --- ************************************************ --- *** relation: ribozymic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** even without an associated ribonucleopr *** --- *** otein. *** --- ************************************************ --- CREATE VIEW ribozymic AS SELECT feature_id AS ribozymic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic'; --- ************************************************ --- *** relation: pseudouridylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of pseu *** --- *** douridylation in an RNA molecule by base *** --- *** pairing with a short sequence around th *** --- *** e target residue. *** --- ************************************************ --- CREATE VIEW pseudouridylation_guide_snorna AS SELECT feature_id AS pseudouridylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA'; --- ************************************************ --- *** relation: lna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of 'locked' deoxyribose r *** --- *** ings connected to a phosphate backbone. *** --- *** The deoxyribose unit's conformation is ' *** --- *** locked' by a 2'-C,4'-C-oxymethylene link *** --- *** . *** --- ************************************************ --- CREATE VIEW lna AS SELECT feature_id AS lna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA'; --- ************************************************ --- *** relation: lna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of LNA residues. *** --- ************************************************ --- CREATE VIEW lna_oligo AS SELECT feature_id AS lna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA_oligo'; --- ************************************************ --- *** relation: tna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of threose rings connecte *** --- *** d to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW tna AS SELECT feature_id AS tna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA'; --- ************************************************ --- *** relation: tna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of TNA residues. *** --- ************************************************ --- CREATE VIEW tna_oligo AS SELECT feature_id AS tna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA_oligo'; --- ************************************************ --- *** relation: gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of an acyclic three-carbo *** --- *** n propylene glycol connected to a phosph *** --- *** ate backbone. It has two enantiomeric fo *** --- *** rms, (R)-GNA and (S)-GNA. *** --- ************************************************ --- CREATE VIEW gna AS SELECT feature_id AS gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'GNA'; --- ************************************************ --- *** relation: gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of GNA residues. *** --- ************************************************ --- CREATE VIEW gna_oligo AS SELECT feature_id AS gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'GNA_oligo'; --- ************************************************ --- *** relation: r_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (R)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW r_gna AS SELECT feature_id AS r_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA'; --- ************************************************ --- *** relation: r_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (R)-GNA residues. *** --- ************************************************ --- CREATE VIEW r_gna_oligo AS SELECT feature_id AS r_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo'; --- ************************************************ --- *** relation: s_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (S)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW s_gna AS SELECT feature_id AS s_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA'; --- ************************************************ --- *** relation: s_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (S)-GNA residues. *** --- ************************************************ --- CREATE VIEW s_gna_oligo AS SELECT feature_id AS s_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA_oligo'; --- ************************************************ --- *** relation: ds_dna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_DNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded DNA. *** --- ************************************************ --- CREATE VIEW ds_dna_viral_sequence AS SELECT feature_id AS ds_dna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_DNA_viral_sequence'; --- ************************************************ --- *** relation: ss_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ss_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as single stranded RNA. *** --- ************************************************ --- CREATE VIEW ss_rna_viral_sequence AS SELECT feature_id AS ss_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence'; --- ************************************************ --- *** relation: negative_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A negative_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** is complementary to mRNA and must be con *** --- *** verted to positive sense RNA by RNA poly *** --- *** merase before translation. *** --- ************************************************ --- CREATE VIEW negative_sense_ssrna_viral_sequence AS SELECT feature_id AS negative_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: positive_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A positive_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** can be immediately translated by the hos *** --- *** t. *** --- ************************************************ --- CREATE VIEW positive_sense_ssrna_viral_sequence AS SELECT feature_id AS positive_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positive_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: ambisense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ambisense_RNA_virus is a ss_RNA_viral_ *** --- *** sequence that is the sequence of a singl *** --- *** e stranded RNA virus with both messenger *** --- *** and anti messenger polarity. *** --- ************************************************ --- CREATE VIEW ambisense_ssrna_viral_sequence AS SELECT feature_id AS ambisense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ambisense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which RNA polymerase b *** --- *** inds, to begin transcription. *** --- ************************************************ --- CREATE VIEW rna_polymerase_promoter AS SELECT feature_id AS rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'RNA_polymerase_promoter'; --- ************************************************ --- *** relation: phage_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which Bacteriophage RN *** --- *** A polymerase binds, to begin transcripti *** --- *** on. *** --- ************************************************ --- CREATE VIEW phage_rna_polymerase_promoter AS SELECT feature_id AS phage_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: sp6_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the SP6 RNA poly *** --- *** merase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW sp6_rna_polymerase_promoter AS SELECT feature_id AS sp6_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t3_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which the T3 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t3_rna_polymerase_promoter AS SELECT feature_id AS t3_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T3_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t7_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the T7 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t7_rna_polymerase_promoter AS SELECT feature_id AS t7_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T7_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: five_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 5' end of a transcr *** --- *** ipt that usually codes for a protein. Th *** --- *** ese regions tend to be conserved across *** --- *** species and do not change much within a *** --- *** gene family. *** --- ************************************************ --- CREATE VIEW five_prime_est AS SELECT feature_id AS five_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST'; --- ************************************************ --- *** relation: three_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 3' end of a transcr *** --- *** ipt. They are more likely to fall within *** --- *** non-coding, or untranslated regions(UTR *** --- *** s). *** --- ************************************************ --- CREATE VIEW three_prime_est AS SELECT feature_id AS three_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_EST'; --- ************************************************ --- *** relation: translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA (not divisible by 3 b *** --- *** ases) that is skipped during the process *** --- *** of translational frameshifting (GO:0006 *** --- *** 452), causing the reading frame to be di *** --- *** fferent. *** --- ************************************************ --- CREATE VIEW translational_frameshift AS SELECT feature_id AS translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'translational_frameshift'; --- ************************************************ --- *** relation: plus_1_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 1 base long that is s *** --- *** kipped during the process of translation *** --- *** al frameshifting (GO:0006452), causing t *** --- *** he reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_1_translational_frameshift AS SELECT feature_id AS plus_1_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift'; --- ************************************************ --- *** relation: plus_2_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 2 bases long that is *** --- *** skipped during the process of translatio *** --- *** nal frameshifting (GO:0006452), causing *** --- *** the reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_2_translational_frameshift AS SELECT feature_id AS plus_2_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_translational_frameshift'; --- ************************************************ --- *** relation: group_iii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group III introns are introns found in t *** --- *** he mRNA of the plastids of euglenoid pro *** --- *** tists. They are spliced by a two step tr *** --- *** ansesterification with bulged adenosine *** --- *** as initiating nucleophile. *** --- ************************************************ --- CREATE VIEW group_iii_intron AS SELECT feature_id AS group_iii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_III_intron'; --- ************************************************ --- *** relation: noncoding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The maximal intersection of exon and UTR *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_region_of_exon AS SELECT feature_id AS noncoding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'noncoding_region_of_exon'; --- ************************************************ --- *** relation: coding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an exon that encodes for p *** --- *** rotein sequence. *** --- ************************************************ --- CREATE VIEW coding_region_of_exon AS SELECT feature_id AS coding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'coding_region_of_exon'; --- ************************************************ --- *** relation: endonuclease_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron that spliced via endonucleolyt *** --- *** ic cleavage and ligation rather than tra *** --- *** nsesterification. *** --- ************************************************ --- CREATE VIEW endonuclease_spliced_intron AS SELECT feature_id AS endonuclease_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'endonuclease_spliced_intron'; --- ************************************************ --- *** relation: protein_coding_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding_gene AS SELECT feature_id AS protein_coding_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'protein_coding_gene'; --- ************************************************ --- *** relation: transgenic_insertion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transgenic_insertion AS SELECT feature_id AS transgenic_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion'; --- ************************************************ --- *** relation: retrogene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW retrogene AS SELECT feature_id AS retrogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrogene'; --- ************************************************ --- *** relation: silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by RNA *** --- *** interference. *** --- ************************************************ --- CREATE VIEW silenced_by_rna_interference AS SELECT feature_id AS silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_RNA_interference'; --- ************************************************ --- *** relation: silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone modification. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_modification AS SELECT feature_id AS silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_by_histone_modification'; --- ************************************************ --- *** relation: silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone methylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_methylation AS SELECT feature_id AS silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation'; --- ************************************************ --- *** relation: silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone deacetylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_deacetylation AS SELECT feature_id AS silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: gene_silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by RNA interfere *** --- *** nce. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_rna_interference AS SELECT feature_id AS gene_silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_RNA_interference'; --- ************************************************ --- *** relation: gene_silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone modif *** --- *** ication. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_modification AS SELECT feature_id AS gene_silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'gene_silenced_by_histone_modification'; --- ************************************************ --- *** relation: gene_silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone methy *** --- *** lation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_methylation AS SELECT feature_id AS gene_silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation'; --- ************************************************ --- *** relation: gene_silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone deace *** --- *** tylation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_deacetylation AS SELECT feature_id AS gene_silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: dihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5,6-dih *** --- *** ydrouracil is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW dihydrouridine AS SELECT feature_id AS dihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine'; --- ************************************************ --- *** relation: pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5- posi *** --- *** tion of the uracil is bound to the ribos *** --- *** e ring instead of the 4- position. *** --- ************************************************ --- CREATE VIEW pseudouridine AS SELECT feature_id AS pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridine'; --- ************************************************ --- *** relation: inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which hypoxanthin *** --- *** e is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW inosine AS SELECT feature_id AS inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'inosine'; --- ************************************************ --- *** relation: seven_methylguanine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which guanine is *** --- *** methylated at the 7- position. *** --- ************************************************ --- CREATE VIEW seven_methylguanine AS SELECT feature_id AS seven_methylguanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanine'; --- ************************************************ --- *** relation: ribothymidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which thymine is *** --- *** bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW ribothymidine AS SELECT feature_id AS ribothymidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribothymidine'; --- ************************************************ --- *** relation: methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which methylhypox *** --- *** anthine is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW methylinosine AS SELECT feature_id AS methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine'; --- ************************************************ --- *** relation: mobile *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that h *** --- *** as either intra-genome or intracellular *** --- *** mobility. *** --- ************************************************ --- CREATE VIEW mobile AS SELECT feature_id AS mobile_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile'; --- ************************************************ --- *** relation: replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing at least one unique *** --- *** origin of replication and a unique termi *** --- *** nation site. *** --- ************************************************ --- CREATE VIEW replicon AS SELECT feature_id AS replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'replicon'; --- ************************************************ --- *** relation: base *** --- *** relation type: VIEW *** --- *** *** --- *** A base is a sequence feature that corres *** --- *** ponds to a single unit of a nucleotide p *** --- *** olymer. *** --- ************************************************ --- CREATE VIEW base AS SELECT feature_id AS base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'base'; --- ************************************************ --- *** relation: amino_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence feature that corresponds to a *** --- *** single amino acid residue in a polypept *** --- *** ide. *** --- ************************************************ --- CREATE VIEW amino_acid AS SELECT feature_id AS amino_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'amino_acid'; --- ************************************************ --- *** relation: major_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW major_tss AS SELECT feature_id AS major_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS'; --- ************************************************ --- *** relation: minor_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minor_tss AS SELECT feature_id AS minor_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minor_TSS'; --- ************************************************ --- *** relation: tss_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a gene from the 5' most TS *** --- *** S to the 3' TSS. *** --- ************************************************ --- CREATE VIEW tss_region AS SELECT feature_id AS tss_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TSS_region'; --- ************************************************ --- *** relation: encodes_alternate_transcription_start_sites *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW encodes_alternate_transcription_start_sites AS SELECT feature_id AS encodes_alternate_transcription_start_sites_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_alternate_transcription_start_sites'; --- ************************************************ --- *** relation: mirna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of an miRNA primary_transcript. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript_region AS SELECT feature_id AS mirna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'miRNA_primary_transcript_region'; --- ************************************************ --- *** relation: pre_mirna *** --- *** relation type: VIEW *** --- *** *** --- *** The 60-70 nucleotide region remain after *** --- *** Drosha processing of the primary transc *** --- *** ript, that folds back upon itself to for *** --- *** m a hairpin sructure. *** --- ************************************************ --- CREATE VIEW pre_mirna AS SELECT feature_id AS pre_mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA'; --- ************************************************ --- *** relation: mirna_stem *** --- *** relation type: VIEW *** --- *** *** --- *** The stem of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_stem AS SELECT feature_id AS mirna_stem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_stem'; --- ************************************************ --- *** relation: mirna_loop *** --- *** relation type: VIEW *** --- *** *** --- *** The loop of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_loop AS SELECT feature_id AS mirna_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_loop'; --- ************************************************ --- *** relation: synthetic_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of synthetic nucleotid *** --- *** es. *** --- ************************************************ --- CREATE VIEW synthetic_oligo AS SELECT feature_id AS synthetic_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'synthetic_oligo'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome of known length t *** --- *** hat is composed by ordering and aligning *** --- *** two or more different regions. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'assembly'; --- ************************************************ --- *** relation: fragment_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A fragment assembly is a genome assembly *** --- *** that orders overlapping fragments of th *** --- *** e genome based on landmark sequences. Th *** --- *** e base pair distance between the landmar *** --- *** ks is known allowing additivity of lengt *** --- *** hs. *** --- ************************************************ --- CREATE VIEW fragment_assembly AS SELECT feature_id AS fragment_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'fragment_assembly'; --- ************************************************ --- *** relation: fingerprint_map *** --- *** relation type: VIEW *** --- *** *** --- *** A fingerprint_map is a physical map comp *** --- *** osed of restriction fragments. *** --- ************************************************ --- CREATE VIEW fingerprint_map AS SELECT feature_id AS fingerprint_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map'; --- ************************************************ --- *** relation: sts_map *** --- *** relation type: VIEW *** --- *** *** --- *** An STS map is a physical map organized b *** --- *** y the unique STS landmarks. *** --- ************************************************ --- CREATE VIEW sts_map AS SELECT feature_id AS sts_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS_map'; --- ************************************************ --- *** relation: rh_map *** --- *** relation type: VIEW *** --- *** *** --- *** A radiation hybrid map is a physical map *** --- *** . *** --- ************************************************ --- CREATE VIEW rh_map AS SELECT feature_id AS rh_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RH_map'; --- ************************************************ --- *** relation: sonicate_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment generated by sonication. *** --- *** Sonication is a technique used to sheer *** --- *** DNA into smaller fragments. *** --- ************************************************ --- CREATE VIEW sonicate_fragment AS SELECT feature_id AS sonicate_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sonicate_fragment'; --- ************************************************ --- *** relation: polyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is an exact multi *** --- *** ple of the haploid number and is greater *** --- *** than the diploid number. *** --- ************************************************ --- CREATE VIEW polyploid AS SELECT feature_id AS polyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'polyploid'; --- ************************************************ --- *** relation: autopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from the same organism *** --- *** . *** --- ************************************************ --- CREATE VIEW autopolyploid AS SELECT feature_id AS autopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid'; --- ************************************************ --- *** relation: allopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from a different organ *** --- *** ism. *** --- ************************************************ --- CREATE VIEW allopolyploid AS SELECT feature_id AS allopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allopolyploid'; --- ************************************************ --- *** relation: homing_endonuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The binding site (recognition site) of a *** --- *** homing endonuclease. The binding site i *** --- *** s typically large. *** --- ************************************************ --- CREATE VIEW homing_endonuclease_binding_site AS SELECT feature_id AS homing_endonuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homing_endonuclease_binding_site'; --- ************************************************ --- *** relation: octamer_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters with seque *** --- *** nce ATTGCAT that binds Pou-domain transc *** --- *** ription factors. *** --- ************************************************ --- CREATE VIEW octamer_motif AS SELECT feature_id AS octamer_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'octamer_motif'; --- ************************************************ --- *** relation: apicoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in an apicoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW apicoplast_chromosome AS SELECT feature_id AS apicoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_chromosome'; --- ************************************************ --- *** relation: sequence_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of discontinuous sequences. *** --- ************************************************ --- CREATE VIEW sequence_collection AS SELECT feature_id AS sequence_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'genome' OR cvterm.name = 'contig_collection' OR cvterm.name = 'sequence_collection'; --- ************************************************ --- *** relation: overlapping_feature_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous region of sequence composed *** --- *** of the overlapping of multiple sequence *** --- *** _features, which ultimately provides evi *** --- *** dence for another sequence_feature. *** --- ************************************************ --- CREATE VIEW overlapping_feature_set AS SELECT feature_id AS overlapping_feature_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'overlapping_feature_set'; --- ************************************************ --- *** relation: overlapping_est_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continous experimental result region e *** --- *** xtending the length of multiple overlapp *** --- *** ing EST's. *** --- ************************************************ --- CREATE VIEW overlapping_est_set AS SELECT feature_id AS overlapping_est_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set'; --- ************************************************ --- *** relation: ncrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ncrna_gene AS SELECT feature_id AS ncrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'ncRNA_gene'; --- ************************************************ --- *** relation: grna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW grna_gene AS SELECT feature_id AS grna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene'; --- ************************************************ --- *** relation: mirna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_gene AS SELECT feature_id AS mirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_gene'; --- ************************************************ --- *** relation: scrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_gene AS SELECT feature_id AS scrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_gene'; --- ************************************************ --- *** relation: snorna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_gene AS SELECT feature_id AS snorna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA_gene'; --- ************************************************ --- *** relation: snrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_gene AS SELECT feature_id AS snrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_gene'; --- ************************************************ --- *** relation: srp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_gene AS SELECT feature_id AS srp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_gene'; --- ************************************************ --- *** relation: strna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_gene AS SELECT feature_id AS strna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_gene'; --- ************************************************ --- *** relation: tmrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_gene AS SELECT feature_id AS tmrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_gene'; --- ************************************************ --- *** relation: trna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_gene AS SELECT feature_id AS trna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_gene'; --- ************************************************ --- *** relation: modified_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified adenine is an adenine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_adenosine AS SELECT feature_id AS modified_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'modified_adenosine'; --- ************************************************ --- *** relation: modified_inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified inosine is an inosine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_inosine AS SELECT feature_id AS modified_inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'modified_inosine'; --- ************************************************ --- *** relation: modified_cytidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified cytidine is a cytidine base f *** --- *** eature which has been altered. *** --- ************************************************ --- CREATE VIEW modified_cytidine AS SELECT feature_id AS modified_cytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'modified_cytidine'; --- ************************************************ --- *** relation: modified_guanosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_guanosine AS SELECT feature_id AS modified_guanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'modified_guanosine'; --- ************************************************ --- *** relation: modified_uridine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_uridine AS SELECT feature_id AS modified_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_uridine'; --- ************************************************ --- *** relation: one_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1-methylinosine is a modified insosine. *** --- ************************************************ --- CREATE VIEW one_methylinosine AS SELECT feature_id AS one_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylinosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethylinosine is a modified ino *** --- *** sine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylinosine AS SELECT feature_id AS one_two_prime_o_dimethylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylinosine'; --- ************************************************ --- *** relation: two_prime_o_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylinosine is a modified inosine *** --- *** . *** --- ************************************************ --- CREATE VIEW two_prime_o_methylinosine AS SELECT feature_id AS two_prime_o_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylinosine'; --- ************************************************ --- *** relation: three_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 3-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW three_methylcytidine AS SELECT feature_id AS three_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine'; --- ************************************************ --- *** relation: five_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_methylcytidine AS SELECT feature_id AS five_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylcytidine'; --- ************************************************ --- *** relation: two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylcytidine is a modified cytidi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylcytidine AS SELECT feature_id AS two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: two_thiocytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2-thiocytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW two_thiocytidine AS SELECT feature_id AS two_thiocytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiocytidine'; --- ************************************************ --- *** relation: n4_acetylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_acetylcytidine AS SELECT feature_id AS n4_acetylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetylcytidine'; --- ************************************************ --- *** relation: five_formylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_formylcytidine AS SELECT feature_id AS five_formylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formylcytidine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5,2'-O-dimethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethylcytidine AS SELECT feature_id AS five_two_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: n4_acetyl_2_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetyl-2'-O-methylcytidine is a modif *** --- *** ied cytidine. *** --- ************************************************ --- CREATE VIEW n4_acetyl_2_prime_o_methylcytidine AS SELECT feature_id AS n4_acetyl_2_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine'; --- ************************************************ --- *** relation: lysidine *** --- *** relation type: VIEW *** --- *** *** --- *** Lysidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW lysidine AS SELECT feature_id AS lysidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysidine'; --- ************************************************ --- *** relation: n4_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-methylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_methylcytidine AS SELECT feature_id AS n4_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_methylcytidine'; --- ************************************************ --- *** relation: n4_2_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4,2'-O-dimethylcytidine is a modified c *** --- *** ytidine. *** --- ************************************************ --- CREATE VIEW n4_2_prime_o_dimethylcytidine AS SELECT feature_id AS n4_2_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_2_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: five_hydroxymethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-hydroxymethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_hydroxymethylcytidine AS SELECT feature_id AS five_hydroxymethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxymethylcytidine'; --- ************************************************ --- *** relation: five_formyl_two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formyl-2'-O-methylcytidine is a modifi *** --- *** ed cytidine. *** --- ************************************************ --- CREATE VIEW five_formyl_two_prime_o_methylcytidine AS SELECT feature_id AS five_formyl_two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formyl_two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: n4_n4_2_prime_o_trimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4_N4_2_prime_O_trimethylcytidine is a m *** --- *** odified cytidine. *** --- ************************************************ --- CREATE VIEW n4_n4_2_prime_o_trimethylcytidine AS SELECT feature_id AS n4_n4_2_prime_o_trimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine'; --- ************************************************ --- *** relation: one_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW one_methyladenosine AS SELECT feature_id AS one_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine'; --- ************************************************ --- *** relation: two_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW two_methyladenosine AS SELECT feature_id AS two_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methyladenosine'; --- ************************************************ --- *** relation: n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_methyladenosine AS SELECT feature_id AS n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyladenosine'; --- ************************************************ --- *** relation: two_prime_o_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyladenosine AS SELECT feature_id AS two_prime_o_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_methyladenosine is a mod *** --- *** ified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_methyladenosine AS SELECT feature_id AS two_methylthio_n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_methyladenosine'; --- ************************************************ --- *** relation: n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_isopentenyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_isopentenyladenosine AS SELECT feature_id AS n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_isopentenyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_isopentenyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_isopentenyladenosine AS SELECT feature_id AS two_methylthio_n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_isopentenyladenosine'; --- ************************************************ --- *** relation: n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_cis_hydroxyisopentenyl_adenosine is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_cis_hydroxyisopentenyl_a *** --- *** denosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS two_methylthio_n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: n6_glycinylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_glycinylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_glycinylcarbamoyladenosine AS SELECT feature_id AS n6_glycinylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_glycinylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_threonylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_threonyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_threonyl_carbamoyladenos *** --- *** ine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_threonyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_threonyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine'; --- ************************************************ --- *** relation: n6_methyl_n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyl_N6_threonylcarbamoyladenosine *** --- *** is a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_methyl_n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_methyl_n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_hydroxynorvalylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_hydroxynorvalylcarbamoyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_hydroxynorvalylcarbamoyladenosine AS SELECT feature_id AS n6_hydroxynorvalylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_hydroxynorvalyl_carbamoy *** --- *** ladenosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine'; --- ************************************************ --- *** relation: two_prime_o_riboA_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosyladenosine_phosphate is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_riboA_phosphate AS SELECT feature_id AS two_prime_o_riboA_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosyladenosine_phosphate'; --- ************************************************ --- *** relation: n6_n6_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_dimethyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_n6_dimethyladenosine AS SELECT feature_id AS n6_n6_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_dimethyladenosine'; --- ************************************************ --- *** relation: n6_2_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_2prime_O_dimethyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_2_prime_o_dimethyladenosine AS SELECT feature_id AS n6_2_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_2_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_n6_2_prime_o_trimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_2prime_O_trimethyladenosine is a m *** --- *** odified adenosine. *** --- ************************************************ --- CREATE VIEW n6_n6_2_prime_o_trimethyladenosine AS SELECT feature_id AS n6_n6_2_prime_o_trimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethyladenosine AS SELECT feature_id AS one_two_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_acetyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_acetyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_acetyladenosine AS SELECT feature_id AS n6_acetyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_acetyladenosine'; --- ************************************************ --- *** relation: seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7-deazaguanosine is a moddified guanosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW seven_deazaguanosine AS SELECT feature_id AS seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'seven_deazaguanosine'; --- ************************************************ --- *** relation: queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Queuosine is a modified 7-deazoguanosine *** --- *** . *** --- ************************************************ --- CREATE VIEW queuosine AS SELECT feature_id AS queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine'; --- ************************************************ --- *** relation: epoxyqueuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Epoxyqueuosine is a modified 7-deazoguan *** --- *** osine. *** --- ************************************************ --- CREATE VIEW epoxyqueuosine AS SELECT feature_id AS epoxyqueuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epoxyqueuosine'; --- ************************************************ --- *** relation: galactosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Galactosyl_queuosine is a modified 7-dea *** --- *** zoguanosine. *** --- ************************************************ --- CREATE VIEW galactosyl_queuosine AS SELECT feature_id AS galactosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'galactosyl_queuosine'; --- ************************************************ --- *** relation: mannosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Mannosyl_queuosine is a modified 7-deazo *** --- *** guanosine. *** --- ************************************************ --- CREATE VIEW mannosyl_queuosine AS SELECT feature_id AS mannosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mannosyl_queuosine'; --- ************************************************ --- *** relation: seven_cyano_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_cyano_7_deazaguanosine is a modified 7 *** --- *** -deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_cyano_seven_deazaguanosine AS SELECT feature_id AS seven_cyano_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_cyano_seven_deazaguanosine'; --- ************************************************ --- *** relation: seven_aminomethyl_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_aminomethyl_7_deazaguanosine is a modi *** --- *** fied 7-deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_aminomethyl_seven_deazaguanosine AS SELECT feature_id AS seven_aminomethyl_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_aminomethyl_seven_deazaguanosine'; --- ************************************************ --- *** relation: archaeosine *** --- *** relation type: VIEW *** --- *** *** --- *** Archaeosine is a modified 7-deazoguanosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW archaeosine AS SELECT feature_id AS archaeosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeosine'; --- ************************************************ --- *** relation: one_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW one_methylguanosine AS SELECT feature_id AS one_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylguanosine'; --- ************************************************ --- *** relation: n2_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_methylguanosine is a modified guanosi *** --- *** ne base feature. *** --- ************************************************ --- CREATE VIEW n2_methylguanosine AS SELECT feature_id AS n2_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_methylguanosine'; --- ************************************************ --- *** relation: seven_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW seven_methylguanosine AS SELECT feature_id AS seven_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanosine'; --- ************************************************ --- *** relation: two_prime_o_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylguanosine is a modified g *** --- *** uanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylguanosine AS SELECT feature_id AS two_prime_o_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylguanosine'; --- ************************************************ --- *** relation: n2_n2_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_dimethylguanosine is a modified gu *** --- *** anosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_dimethylguanosine AS SELECT feature_id AS n2_n2_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_dimethylguanosine'; --- ************************************************ --- *** relation: n2_2_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_2prime_O_dimethylguanosine is a modif *** --- *** ied guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_2_prime_o_dimethylguanosine AS SELECT feature_id AS n2_2_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_2_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_2_prime_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_2prime_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_2_prime_o_trimethylguanosine AS SELECT feature_id AS n2_n2_2_prime_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine'; --- ************************************************ --- *** relation: two_prime_o_ribosylguanosine_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosylguanosine_phosphate is a *** --- *** modified guanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_ribosylguanosine_phosphate AS SELECT feature_id AS two_prime_o_ribosylguanosine_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosylguanosine_phosphate'; --- ************************************************ --- *** relation: wybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wybutosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW wybutosine AS SELECT feature_id AS wybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wybutosine'; --- ************************************************ --- *** relation: peroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Peroxywybutosine is a modified guanosine *** --- *** base feature. *** --- ************************************************ --- CREATE VIEW peroxywybutosine AS SELECT feature_id AS peroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peroxywybutosine'; --- ************************************************ --- *** relation: hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Hydroxywybutosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW hydroxywybutosine AS SELECT feature_id AS hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydroxywybutosine'; --- ************************************************ --- *** relation: undermodified_hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Undermodified_hydroxywybutosine is a mod *** --- *** ified guanosine base feature. *** --- ************************************************ --- CREATE VIEW undermodified_hydroxywybutosine AS SELECT feature_id AS undermodified_hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'undermodified_hydroxywybutosine'; --- ************************************************ --- *** relation: wyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wyosine is a modified guanosine base fea *** --- *** ture. *** --- ************************************************ --- CREATE VIEW wyosine AS SELECT feature_id AS wyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wyosine'; --- ************************************************ --- *** relation: methylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Methylwyosine is a modified guanosine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW methylwyosine AS SELECT feature_id AS methylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylwyosine'; --- ************************************************ --- *** relation: n2_7_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_dimethylguanosine is a modified gua *** --- *** nosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_dimethylguanosine AS SELECT feature_id AS n2_7_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_7_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_7_trimethylguanosine is a modified *** --- *** guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_7_trimethylguanosine AS SELECT feature_id AS n2_n2_7_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_7_trimethylguanosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_2prime_O_dimethylguanosine is a modifi *** --- *** ed guanosine base feature. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylguanosine AS SELECT feature_id AS one_two_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: four_demethylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_demethylwyosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW four_demethylwyosine AS SELECT feature_id AS four_demethylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_demethylwyosine'; --- ************************************************ --- *** relation: isowyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Isowyosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW isowyosine AS SELECT feature_id AS isowyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isowyosine'; --- ************************************************ --- *** relation: n2_7_2prirme_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_2prirme_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_2prirme_o_trimethylguanosine AS SELECT feature_id AS n2_7_2prirme_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_2prirme_O_trimethylguanosine'; --- ************************************************ --- *** relation: five_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW five_methyluridine AS SELECT feature_id AS five_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyluridine'; --- ************************************************ --- *** relation: two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyluridine AS SELECT feature_id AS two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_2_prime_O_dimethyluridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethyluridine AS SELECT feature_id AS five_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: one_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW one_methylpseudouridine AS SELECT feature_id AS one_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylpseudouridine'; --- ************************************************ --- *** relation: two_prime_o_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylpseudouridine is a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylpseudouridine AS SELECT feature_id AS two_prime_o_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylpseudouridine'; --- ************************************************ --- *** relation: two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW two_thiouridine AS SELECT feature_id AS two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiouridine'; --- ************************************************ --- *** relation: four_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW four_thiouridine AS SELECT feature_id AS four_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_thiouridine'; --- ************************************************ --- *** relation: five_methyl_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyl_2_thiouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyl_2_thiouridine AS SELECT feature_id AS five_methyl_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyl_2_thiouridine'; --- ************************************************ --- *** relation: two_thio_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thio_2prime_O_methyluridine is a modif *** --- *** ied uridine base feature. *** --- ************************************************ --- CREATE VIEW two_thio_two_prime_o_methyluridine AS SELECT feature_id AS two_thio_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thio_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: three_three_amino_three_carboxypropyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_3_amino_3_carboxypropyl_uridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW three_three_amino_three_carboxypropyl_uridine AS SELECT feature_id AS three_three_amino_three_carboxypropyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_three_amino_three_carboxypropyl_uridine'; --- ************************************************ --- *** relation: five_hydroxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_hydroxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_hydroxyuridine AS SELECT feature_id AS five_hydroxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxyuridine'; --- ************************************************ --- *** relation: five_methoxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_methoxyuridine AS SELECT feature_id AS five_methoxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxyuridine'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid AS SELECT feature_id AS uridine_five_oxyacetic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid_methyl_ester is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid_methyl_ester AS SELECT feature_id AS uridine_five_oxyacetic_acid_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine is a modi *** --- *** fied uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine_methyl_es *** --- *** ter is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine_methyl_ester AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyluridine AS SELECT feature_id AS five_methoxycarbonylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyluridine'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_methoxycarbonylmethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_mcm_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxycarbonylmethyl_2_thiouridine is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mcm_2_thiouridine AS SELECT feature_id AS five_mcm_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_aminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_aminomethyl_2_thiouridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_aminomethyl_two_thiouridine AS SELECT feature_id AS five_aminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_aminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyluridine AS SELECT feature_id AS five_methylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyluridine'; --- ************************************************ --- *** relation: five_mam_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_thiouridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mam_2_thiouridine AS SELECT feature_id AS five_mam_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyl_two_selenouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_selenouridine is a *** --- *** modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyl_two_selenouridine AS SELECT feature_id AS five_methylaminomethyl_two_selenouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_selenouridine'; --- ************************************************ --- *** relation: five_carbamoylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyluridine is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW five_carbamoylmethyluridine AS SELECT feature_id AS five_carbamoylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyluridine'; --- ************************************************ --- *** relation: five_cm_2_prime_o_methU *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyl_2_prime_O_methyluridin *** --- *** e is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_cm_2_prime_o_methU AS SELECT feature_id AS five_cm_2_prime_o_methU_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyluridine AS SELECT feature_id AS five_carboxymethylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_thiouridine *** --- *** is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_thiouridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: three_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW three_methyluridine AS SELECT feature_id AS three_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methyluridine'; --- ************************************************ --- *** relation: one_methyl_3_3_amino_three_carboxypropyl_pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyl_3_3_amino_3_carboxypropyl_pseud *** --- *** ouridine is a modified uridine base feat *** --- *** ure. *** --- ************************************************ --- CREATE VIEW one_methyl_3_3_amino_three_carboxypropyl_pseudouridine AS SELECT feature_id AS one_methyl_3_3_amino_three_carboxypropyl_pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine'; --- ************************************************ --- *** relation: five_carboxymethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethyluridine AS SELECT feature_id AS five_carboxymethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethyluridine'; --- ************************************************ --- *** relation: three_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_2prime_O_dimethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW three_two_prime_o_dimethyluridine AS SELECT feature_id AS three_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: five_methyldihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyldihydrouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyldihydrouridine AS SELECT feature_id AS five_methyldihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyldihydrouridine'; --- ************************************************ --- *** relation: three_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW three_methylpseudouridine AS SELECT feature_id AS three_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylpseudouridine'; --- ************************************************ --- *** relation: five_taurinomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyluridine AS SELECT feature_id AS five_taurinomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyluridine'; --- ************************************************ --- *** relation: five_taurinomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyl_2_thiouridineis a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyl_two_thiouridine AS SELECT feature_id AS five_taurinomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_uridine is a mo *** --- *** dified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_uridine AS SELECT feature_id AS five_isopentenylaminomethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_uridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2_thiouridine i *** --- *** s a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_thiouridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2prime_O_methyl *** --- *** uridine is a modified uridine base featu *** --- *** re. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: histone_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule that is bound *** --- *** by a histone. *** --- ************************************************ --- CREATE VIEW histone_binding_site AS SELECT feature_id AS histone_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_binding_site'; --- ************************************************ --- *** relation: cds_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cds_fragment AS SELECT feature_id AS cds_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_fragment'; --- ************************************************ --- *** relation: modified_amino_acid_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified amino ac *** --- *** id feature. *** --- ************************************************ --- CREATE VIEW modified_amino_acid_feature AS SELECT feature_id AS modified_amino_acid_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'modified_amino_acid_feature'; --- ************************************************ --- *** relation: modified_glycine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glycine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_glycine AS SELECT feature_id AS modified_glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine'; --- ************************************************ --- *** relation: modified_l_alanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified alanine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_alanine AS SELECT feature_id AS modified_l_alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_alanine'; --- ************************************************ --- *** relation: modified_l_asparagine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified asparagi *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_asparagine AS SELECT feature_id AS modified_l_asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_asparagine'; --- ************************************************ --- *** relation: modified_l_aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified aspartic *** --- *** acid amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_aspartic_acid AS SELECT feature_id AS modified_l_aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_aspartic_acid'; --- ************************************************ --- *** relation: modified_l_cysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified cysteine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_cysteine AS SELECT feature_id AS modified_l_cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_cysteine'; --- ************************************************ --- *** relation: modified_l_glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_l_glutamic_acid AS SELECT feature_id AS modified_l_glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamic_acid'; --- ************************************************ --- *** relation: modified_l_threonine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified threonin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_threonine AS SELECT feature_id AS modified_l_threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_threonine'; --- ************************************************ --- *** relation: modified_l_tryptophan *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tryptoph *** --- *** an amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tryptophan AS SELECT feature_id AS modified_l_tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tryptophan'; --- ************************************************ --- *** relation: modified_l_glutamine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glutamin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_glutamine AS SELECT feature_id AS modified_l_glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamine'; --- ************************************************ --- *** relation: modified_l_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified methioni *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_methionine AS SELECT feature_id AS modified_l_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_methionine'; --- ************************************************ --- *** relation: modified_l_isoleucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified isoleuci *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_isoleucine AS SELECT feature_id AS modified_l_isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_isoleucine'; --- ************************************************ --- *** relation: modified_l_phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified phenylal *** --- *** anine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_phenylalanine AS SELECT feature_id AS modified_l_phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_phenylalanine'; --- ************************************************ --- *** relation: modified_l_histidine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified histidie *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_histidine AS SELECT feature_id AS modified_l_histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_histidine'; --- ************************************************ --- *** relation: modified_l_serine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified serine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_serine AS SELECT feature_id AS modified_l_serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_serine'; --- ************************************************ --- *** relation: modified_l_lysine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified lysine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_lysine AS SELECT feature_id AS modified_l_lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_lysine'; --- ************************************************ --- *** relation: modified_l_leucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified leucine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_leucine AS SELECT feature_id AS modified_l_leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_leucine'; --- ************************************************ --- *** relation: modified_l_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified selenocy *** --- *** steine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_selenocysteine AS SELECT feature_id AS modified_l_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_selenocysteine'; --- ************************************************ --- *** relation: modified_l_valine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified valine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_valine AS SELECT feature_id AS modified_l_valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_valine'; --- ************************************************ --- *** relation: modified_l_proline *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified proline *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_proline AS SELECT feature_id AS modified_l_proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_proline'; --- ************************************************ --- *** relation: modified_l_tyrosine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tyrosine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tyrosine AS SELECT feature_id AS modified_l_tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tyrosine'; --- ************************************************ --- *** relation: modified_l_arginine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified arginine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_arginine AS SELECT feature_id AS modified_l_arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_arginine'; --- ************************************************ --- *** relation: peptidyl *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the nature of a *** --- *** proteinaceous polymer, where by the amin *** --- *** o acid units are joined by peptide bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW peptidyl AS SELECT feature_id AS peptidyl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptidyl'; --- ************************************************ --- *** relation: cleaved_for_gpi_anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** The C-terminal residues of a polypeptide *** --- *** which are exchanged for a GPI-anchor. *** --- ************************************************ --- CREATE VIEW cleaved_for_gpi_anchor_region AS SELECT feature_id AS cleaved_for_gpi_anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_for_gpi_anchor_region'; --- ************************************************ --- *** relation: biomaterial_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is intended for use in an *** --- *** experiment. *** --- ************************************************ --- CREATE VIEW biomaterial_region AS SELECT feature_id AS biomaterial_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'biomaterial_region'; --- ************************************************ --- *** relation: experimental_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is the result of some arb *** --- *** itrary experimental procedure. The proce *** --- *** dure may be carried out with biological *** --- *** material or inside a computer. *** --- ************************************************ --- CREATE VIEW experimental_feature AS SELECT feature_id AS experimental_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'experimental_feature'; --- ************************************************ --- *** relation: biological_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by its disposition to b *** --- *** e involved in a biological process. *** --- ************************************************ --- CREATE VIEW biological_region AS SELECT feature_id AS biological_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'biological_region'; --- ************************************************ --- *** relation: topologically_defined_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is defined according to it *** --- *** s relations with other regions within th *** --- *** e same sequence. *** --- ************************************************ --- CREATE VIEW topologically_defined_region AS SELECT feature_id AS topologically_defined_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'topologically_defined_region'; --- ************************************************ --- *** relation: translocation_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a tr *** --- *** anslocation begins or ends. *** --- ************************************************ --- CREATE VIEW translocation_breakpoint AS SELECT feature_id AS translocation_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_breakpoint'; --- ************************************************ --- *** relation: insertion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a in *** --- *** sertion begins or ends. *** --- ************************************************ --- CREATE VIEW insertion_breakpoint AS SELECT feature_id AS insertion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_breakpoint'; --- ************************************************ --- *** relation: deletion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a de *** --- *** letion begins or ends. *** --- ************************************************ --- CREATE VIEW deletion_breakpoint AS SELECT feature_id AS deletion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_breakpoint'; --- ************************************************ --- *** relation: five_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located five prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW five_prime_flanking_region AS SELECT feature_id AS five_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_flanking_region'; --- ************************************************ --- *** relation: three_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located three prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW three_prime_flanking_region AS SELECT feature_id AS three_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_flanking_region'; --- ************************************************ --- *** relation: transcribed_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region, defined by a til *** --- *** ing array experiment to be transcribed a *** --- *** t some level. *** --- ************************************************ --- CREATE VIEW transcribed_fragment AS SELECT feature_id AS transcribed_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_fragment'; --- ************************************************ --- *** relation: cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering exon. A s *** --- *** plice_site that adjacent_to exon and ove *** --- *** rlaps intron. *** --- ************************************************ --- CREATE VIEW cis_splice_site AS SELECT feature_id AS cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'cis_splice_site'; --- ************************************************ --- *** relation: trans_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Primary transcript region bordering tran *** --- *** s-splice junction. *** --- ************************************************ --- CREATE VIEW trans_splice_site AS SELECT feature_id AS trans_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'trans_splice_site'; --- ************************************************ --- *** relation: splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between an intron and an ex *** --- *** on. *** --- ************************************************ --- CREATE VIEW splice_junction AS SELECT feature_id AS splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_junction'; --- ************************************************ --- *** relation: conformational_switch *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a polypeptide, involved in t *** --- *** he transition from one conformational st *** --- *** ate to another. *** --- ************************************************ --- CREATE VIEW conformational_switch AS SELECT feature_id AS conformational_switch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_switch'; --- ************************************************ --- *** relation: dye_terminator_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the dye terminator me *** --- *** thod of sequencing. *** --- ************************************************ --- CREATE VIEW dye_terminator_read AS SELECT feature_id AS dye_terminator_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dye_terminator_read'; --- ************************************************ --- *** relation: pyrosequenced_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by pyrosequencing techno *** --- *** logy. *** --- ************************************************ --- CREATE VIEW pyrosequenced_read AS SELECT feature_id AS pyrosequenced_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrosequenced_read'; --- ************************************************ --- *** relation: ligation_based_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by ligation based sequen *** --- *** cing technologies. *** --- ************************************************ --- CREATE VIEW ligation_based_read AS SELECT feature_id AS ligation_based_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ligation_based_read'; --- ************************************************ --- *** relation: polymerase_synthesis_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the polymerase based *** --- *** sequence by synthesis method. *** --- ************************************************ --- CREATE VIEW polymerase_synthesis_read AS SELECT feature_id AS polymerase_synthesis_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymerase_synthesis_read'; --- ************************************************ --- *** relation: cis_regulatory_frameshift_element *** --- *** relation type: VIEW *** --- *** *** --- *** A structural region in an RNA molecule w *** --- *** hich promotes ribosomal frameshifting of *** --- *** cis coding sequence. *** --- ************************************************ --- CREATE VIEW cis_regulatory_frameshift_element AS SELECT feature_id AS cis_regulatory_frameshift_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_regulatory_frameshift_element'; --- ************************************************ --- *** relation: expressed_sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence assembly derived from express *** --- *** ed sequences. *** --- ************************************************ --- CREATE VIEW expressed_sequence_assembly AS SELECT feature_id AS expressed_sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_assembly'; --- ************************************************ --- *** relation: dna_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to DNA *** --- *** . *** --- ************************************************ --- CREATE VIEW dna_binding_site AS SELECT feature_id AS dna_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_binding_site'; --- ************************************************ --- *** relation: polya_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the UTR and the pol *** --- *** yA sequence. *** --- ************************************************ --- CREATE VIEW polya_junction AS SELECT feature_id AS polya_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_junction'; --- ************************************************ --- *** relation: cryptic_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is not transcribed under nor *** --- *** mal conditions and is not critical to no *** --- *** rmal cellular functioning. *** --- ************************************************ --- CREATE VIEW cryptic_gene AS SELECT feature_id AS cryptic_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'cryptic_gene'; --- ************************************************ --- *** relation: sequence_variant_affecting_polyadenylation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polyadenylation AS SELECT feature_id AS sequence_variant_affecting_polyadenylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_polyadenylation'; --- ************************************************ --- *** relation: three_prime_race_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A three prime RACE (Rapid Amplification *** --- *** of cDNA Ends) clone is a cDNA clone copi *** --- *** ed from the 3' end of an mRNA (using a p *** --- *** oly-dT primer to capture the polyA tail *** --- *** and a gene-specific or randomly primed 5 *** --- *** ' primer), and spliced into a vector for *** --- *** propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW three_prime_race_clone AS SELECT feature_id AS three_prime_race_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RACE_clone'; --- ************************************************ --- *** relation: cassette_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A cassette pseudogene is a kind of gene *** --- *** in an innactive form which may recombine *** --- *** at a telomeric locus to form a function *** --- *** al copy. *** --- ************************************************ --- CREATE VIEW cassette_pseudogene AS SELECT feature_id AS cassette_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_pseudogene'; --- ************************************************ --- *** relation: alanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alanine AS SELECT feature_id AS alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine'; --- ************************************************ --- *** relation: valine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW valine AS SELECT feature_id AS valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine'; --- ************************************************ --- *** relation: leucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucine AS SELECT feature_id AS leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine'; --- ************************************************ --- *** relation: isoleucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW isoleucine AS SELECT feature_id AS isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine'; --- ************************************************ --- *** relation: proline *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proline AS SELECT feature_id AS proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline'; --- ************************************************ --- *** relation: tryptophan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tryptophan AS SELECT feature_id AS tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan'; --- ************************************************ --- *** relation: phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW phenylalanine AS SELECT feature_id AS phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine'; --- ************************************************ --- *** relation: methionine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW methionine AS SELECT feature_id AS methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine'; --- ************************************************ --- *** relation: glycine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glycine AS SELECT feature_id AS glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine'; --- ************************************************ --- *** relation: serine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW serine AS SELECT feature_id AS serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine'; --- ************************************************ --- *** relation: threonine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW threonine AS SELECT feature_id AS threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine'; --- ************************************************ --- *** relation: tyrosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tyrosine AS SELECT feature_id AS tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine'; --- ************************************************ --- *** relation: cysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cysteine AS SELECT feature_id AS cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine'; --- ************************************************ --- *** relation: glutamine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamine AS SELECT feature_id AS glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine'; --- ************************************************ --- *** relation: asparagine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW asparagine AS SELECT feature_id AS asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine'; --- ************************************************ --- *** relation: lysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lysine AS SELECT feature_id AS lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine'; --- ************************************************ --- *** relation: argenine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW argenine AS SELECT feature_id AS argenine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'argenine'; --- ************************************************ --- *** relation: histidine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW histidine AS SELECT feature_id AS histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine'; --- ************************************************ --- *** relation: aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aspartic_acid AS SELECT feature_id AS aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid'; --- ************************************************ --- *** relation: glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamic_acid AS SELECT feature_id AS glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid'; --- ************************************************ --- *** relation: selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW selenocysteine AS SELECT feature_id AS selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine'; --- ************************************************ --- *** relation: pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pyrrolysine AS SELECT feature_id AS pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine'; --- ************************************************ --- *** relation: transcribed_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by a set of transcribed *** --- *** sequences from the same gene or express *** --- *** ed pseudogene. *** --- ************************************************ --- CREATE VIEW transcribed_cluster AS SELECT feature_id AS transcribed_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster' OR cvterm.name = 'transcribed_cluster'; --- ************************************************ --- *** relation: unigene_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of transcribed_cluster defined by *** --- *** a set of transcribed sequences from the *** --- *** a unique gene. *** --- ************************************************ --- CREATE VIEW unigene_cluster AS SELECT feature_id AS unigene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster'; --- ************************************************ --- *** relation: crispr *** --- *** relation type: VIEW *** --- *** *** --- *** Clustered Palindromic Repeats interspers *** --- *** ed with bacteriophage derived spacer seq *** --- *** uences. *** --- ************************************************ --- CREATE VIEW crispr AS SELECT feature_id AS crispr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CRISPR'; --- ************************************************ --- *** relation: insulator_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A protein_binding_site located within an *** --- *** insulator. *** --- ************************************************ --- CREATE VIEW insulator_binding_site AS SELECT feature_id AS insulator_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator_binding_site'; --- ************************************************ --- *** relation: enhancer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A protein_binding_site located within an *** --- *** enhancer. *** --- ************************************************ --- CREATE VIEW enhancer_binding_site AS SELECT feature_id AS enhancer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_binding_site'; --- ************************************************ --- *** relation: contig_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of contigs. *** --- ************************************************ --- CREATE VIEW contig_collection AS SELECT feature_id AS contig_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection'; --- ************************************************ --- *** relation: lincrna *** --- *** relation type: VIEW *** --- *** *** --- *** A multiexonic non-coding RNA transcribed *** --- *** by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW lincrna AS SELECT feature_id AS lincrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA'; --- ************************************************ --- *** relation: ust *** --- *** relation type: VIEW *** --- *** *** --- *** An EST spanning part or all of the untra *** --- *** nslated regions of a protein-coding tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW ust AS SELECT feature_id AS ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'UST'; --- ************************************************ --- *** relation: three_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** A UST located in the 3'UTR of a protein- *** --- *** coding transcript. *** --- ************************************************ --- CREATE VIEW three_prime_ust AS SELECT feature_id AS three_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST'; --- ************************************************ --- *** relation: five_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** An UST located in the 5'UTR of a protein *** --- *** -coding transcript. *** --- ************************************************ --- CREATE VIEW five_prime_ust AS SELECT feature_id AS five_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UST'; --- ************************************************ --- *** relation: rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a RACE product; typically a fe *** --- *** w hundred base pairs long. *** --- ************************************************ --- CREATE VIEW rst AS SELECT feature_id AS rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'RST'; --- ************************************************ --- *** relation: three_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 3'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW three_prime_rst AS SELECT feature_id AS three_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST'; --- ************************************************ --- *** relation: five_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 5'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW five_prime_rst AS SELECT feature_id AS five_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_RST'; --- ************************************************ --- *** relation: ust_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an UST sequence. *** --- ************************************************ --- CREATE VIEW ust_match AS SELECT feature_id AS ust_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UST_match'; --- ************************************************ --- *** relation: rst_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an RST sequence. *** --- ************************************************ --- CREATE VIEW rst_match AS SELECT feature_id AS rst_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RST_match'; --- ************************************************ --- *** relation: primer_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match to a primer sequence. *** --- ************************************************ --- CREATE VIEW primer_match AS SELECT feature_id AS primer_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_match'; --- ************************************************ --- *** relation: mirna_antiguide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the pri miRNA that basepairs *** --- *** with the guide to form the hairpin. *** --- ************************************************ --- CREATE VIEW mirna_antiguide AS SELECT feature_id AS mirna_antiguide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_antiguide'; --- ************************************************ --- *** relation: trans_splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the spliced leader *** --- *** and the first exon of the mRNA. *** --- ************************************************ --- CREATE VIEW trans_splice_junction AS SELECT feature_id AS trans_splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_junction'; --- ************************************************ --- *** relation: outron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript, that i *** --- *** s removed via trans splicing. *** --- ************************************************ --- CREATE VIEW outron AS SELECT feature_id AS outron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'outron'; --- ************************************************ --- *** relation: natural_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that occurs naturally. *** --- ************************************************ --- CREATE VIEW natural_plasmid AS SELECT feature_id AS natural_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element' OR cvterm.name = 'natural_plasmid'; --- ************************************************ --- *** relation: gene_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A gene trap construct is a type of engin *** --- *** eered plasmid which is designed to integ *** --- *** rate into a genome and produce a fusion *** --- *** transcript between exons of the gene int *** --- *** o which it inserts and a reporter elemen *** --- *** t in the construct. Gene traps contain a *** --- *** splice acceptor, do not contain promote *** --- *** r elements for the reporter, and are mut *** --- *** agenic. Gene traps may be bicistronic wi *** --- *** th the second cassette containing a prom *** --- *** oter driving an a selectable marker. *** --- ************************************************ --- CREATE VIEW gene_trap_construct AS SELECT feature_id AS gene_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_trap_construct'; --- ************************************************ --- *** relation: promoter_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter trap construct is a type of e *** --- *** ngineered plasmid which is designed to i *** --- *** ntegrate into a genome and express a rep *** --- *** orter when inserted in close proximity t *** --- *** o a promoter element. Promoter traps typ *** --- *** ically do not contain promoter elements *** --- *** and are mutagenic. *** --- ************************************************ --- CREATE VIEW promoter_trap_construct AS SELECT feature_id AS promoter_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_trap_construct'; --- ************************************************ --- *** relation: enhancer_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer trap construct is a type of *** --- *** engineered plasmid which is designed to *** --- *** integrate into a genome and express a re *** --- *** porter when the expression from a basic *** --- *** minimal promoter is enhanced by genomic *** --- *** enhancer elements. Enhancer traps contai *** --- *** n promoter elements and are not usually *** --- *** mutagenic. *** --- ************************************************ --- CREATE VIEW enhancer_trap_construct AS SELECT feature_id AS enhancer_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_trap_construct'; --- ************************************************ --- *** relation: pac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a P *** --- *** AC clone that may provide anhighly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW pac_end AS SELECT feature_id AS pac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC_end'; --- ************************************************ --- *** relation: rapd *** --- *** relation type: VIEW *** --- *** *** --- *** RAPD is a 'PCR product' where a sequence *** --- *** variant is identified through the use o *** --- *** f PCR with random primers. *** --- ************************************************ --- CREATE VIEW rapd AS SELECT feature_id AS rapd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD'; --- ************************************************ --- *** relation: shadow_enhancer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW shadow_enhancer AS SELECT feature_id AS shadow_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'shadow_enhancer'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that controls the express *** --- *** ion of a gene. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: u14_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of an evolutionar *** --- *** ily conserved eukaryotic low molecular w *** --- *** eight RNA capable of intermolecular hybr *** --- *** idization with both homologous and heter *** --- *** ologous 18S rRNA. *** --- ************************************************ --- CREATE VIEW u14_snorna_primary_transcript AS SELECT feature_id AS u14_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: methylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of 2'-O *** --- *** -ribose methylation in an RNA molecule b *** --- *** y base pairing with a short sequence aro *** --- *** und the target residue. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna AS SELECT feature_id AS methylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA'; --- ************************************************ --- *** relation: rrna_cleavage_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An ncRNA that is part of a ribonucleopro *** --- *** tein that cleaves the primary pre-rRNA t *** --- *** ranscript in the process of producing ma *** --- *** ture rRNA molecules. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_rna AS SELECT feature_id AS rrna_cleavage_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_RNA'; --- ************************************************ --- *** relation: exon_of_single_exon_gene *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is the only exon in a gene. *** --- ************************************************ --- CREATE VIEW exon_of_single_exon_gene AS SELECT feature_id AS exon_of_single_exon_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_of_single_exon_gene'; --- ************************************************ --- *** relation: cassette_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cassette_array_member AS SELECT feature_id AS cassette_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member'; --- ************************************************ --- *** relation: gene_cassette_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_cassette_member AS SELECT feature_id AS gene_cassette_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member'; --- ************************************************ --- *** relation: gene_subarray_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_subarray_member AS SELECT feature_id AS gene_subarray_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray_member'; --- ************************************************ --- *** relation: primer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** Non-covalent primer binding site for ini *** --- *** tiation of replication, transcription, o *** --- *** r reverse transcription. *** --- ************************************************ --- CREATE VIEW primer_binding_site AS SELECT feature_id AS primer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_binding_site'; --- ************************************************ --- *** relation: gene_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array includes two or more genes, or *** --- *** two or more gene subarrays, contiguously *** --- *** arranged where the individual genes, or *** --- *** subarrays, are either identical in sequ *** --- *** ence, or essentially so. *** --- ************************************************ --- CREATE VIEW gene_array AS SELECT feature_id AS gene_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_array'; --- ************************************************ --- *** relation: gene_subarray *** --- *** relation type: VIEW *** --- *** *** --- *** A subarray is, by defintition, a member *** --- *** of a gene array (SO:0005851); the member *** --- *** s of a subarray may differ substantially *** --- *** in sequence, but are closely related in *** --- *** function. *** --- ************************************************ --- CREATE VIEW gene_subarray AS SELECT feature_id AS gene_subarray_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray'; --- ************************************************ --- *** relation: gene_cassette *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that can be substituted for a rel *** --- *** ated gene at a different site in the gen *** --- *** ome. *** --- ************************************************ --- CREATE VIEW gene_cassette AS SELECT feature_id AS gene_cassette_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette'; --- ************************************************ --- *** relation: gene_cassette_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array of non-functional genes whose m *** --- *** embers, when captured by recombination f *** --- *** orm functional genes. *** --- ************************************************ --- CREATE VIEW gene_cassette_array AS SELECT feature_id AS gene_cassette_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette_array'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: selenocysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW selenocysteine_trna_primary_transcript AS SELECT feature_id AS selenocysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: selenocysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a selenocystein *** --- *** e anticodon, and a 3' selenocysteine bin *** --- *** ding region. *** --- ************************************************ --- CREATE VIEW selenocysteinyl_trna AS SELECT feature_id AS selenocysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteinyl_tRNA'; --- ************************************************ --- *** relation: syntenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region in which two or more pairs of h *** --- *** omologous markers occur on the same chro *** --- *** mosome in two or more species. *** --- ************************************************ --- CREATE VIEW syntenic_region AS SELECT feature_id AS syntenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic_region'; --- ************************************************ --- *** relation: biochemical_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is involved i *** --- *** n a biochemical function. *** --- ************************************************ --- CREATE VIEW biochemical_region_of_peptide AS SELECT feature_id AS biochemical_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide'; --- ************************************************ --- *** relation: molecular_contact_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is involved a contact with *** --- *** another molecule. *** --- ************************************************ --- CREATE VIEW molecular_contact_region AS SELECT feature_id AS molecular_contact_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region'; --- ************************************************ --- *** relation: intrinsically_unstructured_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polypeptide chain with high *** --- *** conformational flexibility. *** --- ************************************************ --- CREATE VIEW intrinsically_unstructured_polypeptide_region AS SELECT feature_id AS intrinsically_unstructured_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region'; --- ************************************************ --- *** relation: catmat_left_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_three AS SELECT feature_id AS catmat_left_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_three'; --- ************************************************ --- *** relation: catmat_left_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i psi -10 boun *** --- *** ds -50 to 30, res i+1: phi -90 bounds -1 *** --- *** 20 to -60, res i+1: psi -10 bounds -50 t *** --- *** o 30, res i+2: phi -75 bounds -100 to -5 *** --- *** 0, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_four AS SELECT feature_id AS catmat_left_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_four'; --- ************************************************ --- *** relation: catmat_right_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_three AS SELECT feature_id AS catmat_right_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_three'; --- ************************************************ --- *** relation: catmat_right_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -90 bounds - *** --- *** 120 to -60, res i+1: psi -10 bounds -50 *** --- *** to 30, res i+2: phi -75 bounds -100 to - *** --- *** 50, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_four AS SELECT feature_id AS catmat_right_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_four'; --- ************************************************ --- *** relation: alpha_beta_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: H-bond between CO *** --- *** of residue(i) and NH of residue(i+4), H *** --- *** -bond between CO of residue(i) and NH of *** --- *** residue(i+3),Phi angles of residues(i+1 *** --- *** ), (i+2) and (i+3) are negative. *** --- ************************************************ --- CREATE VIEW alpha_beta_motif AS SELECT feature_id AS alpha_beta_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_beta_motif'; --- ************************************************ --- *** relation: lipoprotein_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide that acts as a signal for both *** --- *** membrane translocation and lipid attach *** --- *** ment in prokaryotes. *** --- ************************************************ --- CREATE VIEW lipoprotein_signal_peptide AS SELECT feature_id AS lipoprotein_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lipoprotein_signal_peptide'; --- ************************************************ --- *** relation: no_output *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region wherean analysis *** --- *** has been run and not produced any annota *** --- *** tion. *** --- ************************************************ --- CREATE VIEW no_output AS SELECT feature_id AS no_output_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'no_output'; --- ************************************************ --- *** relation: cleaved_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** The cleaved_peptide_regon is the a regio *** --- *** n of peptide sequence that is cleaved du *** --- *** ring maturation. *** --- ************************************************ --- CREATE VIEW cleaved_peptide_region AS SELECT feature_id AS cleaved_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'cleaved_peptide_region'; --- ************************************************ --- *** relation: peptide_coil *** --- *** relation type: VIEW *** --- *** *** --- *** Irregular, unstructured regions of a pro *** --- *** tein's backbone, as distinct from the re *** --- *** gular region (namely alpha helix and bet *** --- *** a strand - characterised by specific pat *** --- *** terns of main-chain hydrogen bonds). *** --- ************************************************ --- CREATE VIEW peptide_coil AS SELECT feature_id AS peptide_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_coil'; --- ************************************************ --- *** relation: hydrophobic_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Hydrophobic regions are regions with a l *** --- *** ow affinity for water. *** --- ************************************************ --- CREATE VIEW hydrophobic_region_of_peptide AS SELECT feature_id AS hydrophobic_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydrophobic_region_of_peptide'; --- ************************************************ --- *** relation: n_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The amino-terminal positively-charged re *** --- *** gion of a signal peptide (approx 1-5 aa) *** --- *** . *** --- ************************************************ --- CREATE VIEW n_terminal_region AS SELECT feature_id AS n_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'n_terminal_region'; --- ************************************************ --- *** relation: c_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The more polar, carboxy-terminal region *** --- *** of the signal peptide (approx 3-7 aa). *** --- ************************************************ --- CREATE VIEW c_terminal_region AS SELECT feature_id AS c_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'c_terminal_region'; --- ************************************************ --- *** relation: central_hydrophobic_region_of_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The central, hydrophobic region of the s *** --- *** ignal peptide (approx 7-15 aa). *** --- ************************************************ --- CREATE VIEW central_hydrophobic_region_of_signal_peptide AS SELECT feature_id AS central_hydrophobic_region_of_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'central_hydrophobic_region_of_signal_peptide'; --- ************************************************ --- *** relation: polypeptide_conserved_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved motif is a short (up to 20 a *** --- *** mino acids) region of biological interes *** --- *** t that is conserved in different protein *** --- *** s. They may or may not have functional o *** --- *** r structural significance within the pro *** --- *** teins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_motif AS SELECT feature_id AS polypeptide_conserved_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_conserved_motif'; --- ************************************************ --- *** relation: polypeptide_binding_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide binding motif is a short ( *** --- *** up to 20 amino acids) polypeptide region *** --- *** of biological interest that contains on *** --- *** e or more amino acids experimentally sho *** --- *** wn to bind to a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_binding_motif AS SELECT feature_id AS polypeptide_binding_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_binding_motif'; --- ************************************************ --- *** relation: polypeptide_catalytic_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide catalytic motif is a short *** --- *** (up to 20 amino acids) polypeptide regi *** --- *** on that contains one or more active site *** --- *** residues. *** --- ************************************************ --- CREATE VIEW polypeptide_catalytic_motif AS SELECT feature_id AS polypeptide_catalytic_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_catalytic_motif'; --- ************************************************ --- *** relation: polypeptide_dna_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues involved in interactions with D *** --- *** NA. *** --- ************************************************ --- CREATE VIEW polypeptide_dna_contact AS SELECT feature_id AS polypeptide_dna_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact'; --- ************************************************ --- *** relation: polypeptide_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** A subsection of sequence with biological *** --- *** interest that is conserved in different *** --- *** proteins. They may or may not have func *** --- *** tional or structural significance within *** --- *** the proteins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_region AS SELECT feature_id AS polypeptide_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_conserved_region'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** Any change in genomic DNA caused by a si *** --- *** ngle event. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'substitution'; --- ************************************************ --- *** relation: partially_characterised_change_in_dna_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is only *** --- *** partially characterised. *** --- ************************************************ --- CREATE VIEW partially_characterised_change_in_dna_sequence AS SELECT feature_id AS partially_characterised_change_in_dna_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_change_in_DNA_sequence'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP' OR cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: uncharacterised_change_in_nucleotide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is eith *** --- *** er uncharacterised or only partially cha *** --- *** racterised. *** --- ************************************************ --- CREATE VIEW uncharacterised_change_in_nucleotide_sequence AS SELECT feature_id AS uncharacterised_change_in_nucleotide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A single nucleotide change which has occ *** --- *** urred at the same position of a correspo *** --- *** nding nucleotide in a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: transition *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into an other pyrimidine nucleotide, *** --- *** or change of a purine nucleotide, A or G *** --- *** , into an other purine nucleotide. *** --- ************************************************ --- CREATE VIEW transition AS SELECT feature_id AS transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'transition'; --- ************************************************ --- *** relation: pyrimidine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a pyrimidine, C or T, *** --- *** for another pyrimidine. *** --- ************************************************ --- CREATE VIEW pyrimidine_transition AS SELECT feature_id AS pyrimidine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'pyrimidine_transition'; --- ************************************************ --- *** relation: c_to_t_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a cytidine to a thymine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition AS SELECT feature_id AS c_to_t_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'C_to_T_transition'; --- ************************************************ --- *** relation: c_to_t_transition_at_pcpg_site *** --- *** relation type: VIEW *** --- *** *** --- *** The transition of cytidine to thymine oc *** --- *** curring at a pCpG site as a consequence *** --- *** of the spontaneous deamination of 5'-met *** --- *** hylcytidine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition_at_pcpg_site AS SELECT feature_id AS c_to_t_transition_at_pcpg_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site'; --- ************************************************ --- *** relation: t_to_c_transition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW t_to_c_transition AS SELECT feature_id AS t_to_c_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_C_transition'; --- ************************************************ --- *** relation: purine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a purine, A or G, for *** --- *** another purine. *** --- ************************************************ --- CREATE VIEW purine_transition AS SELECT feature_id AS purine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'purine_transition'; --- ************************************************ --- *** relation: a_to_g_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of an adenine to a guanine. *** --- ************************************************ --- CREATE VIEW a_to_g_transition AS SELECT feature_id AS a_to_g_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition'; --- ************************************************ --- *** relation: g_to_a_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a guanine to an adenine. *** --- ************************************************ --- CREATE VIEW g_to_a_transition AS SELECT feature_id AS g_to_a_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_A_transition'; --- ************************************************ --- *** relation: transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G, or *** --- *** vice versa. *** --- ************************************************ --- CREATE VIEW transversion AS SELECT feature_id AS transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'transversion'; --- ************************************************ --- *** relation: pyrimidine_to_purine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G. *** --- ************************************************ --- CREATE VIEW pyrimidine_to_purine_transversion AS SELECT feature_id AS pyrimidine_to_purine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'pyrimidine_to_purine_transversion'; --- ************************************************ --- *** relation: c_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from cytidine to adenine. *** --- ************************************************ --- CREATE VIEW c_to_a_transversion AS SELECT feature_id AS c_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion'; --- ************************************************ --- *** relation: c_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_to_g_transversion AS SELECT feature_id AS c_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_G_transversion'; --- ************************************************ --- *** relation: t_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to A. *** --- ************************************************ --- CREATE VIEW t_to_a_transversion AS SELECT feature_id AS t_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_A_transversion'; --- ************************************************ --- *** relation: t_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to G. *** --- ************************************************ --- CREATE VIEW t_to_g_transversion AS SELECT feature_id AS t_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_G_transversion'; --- ************************************************ --- *** relation: purine_to_pyrimidine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a purine nucleotide, A or G , *** --- *** into a pyrimidine nucleotide C or T. *** --- ************************************************ --- CREATE VIEW purine_to_pyrimidine_transversion AS SELECT feature_id AS purine_to_pyrimidine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion'; --- ************************************************ --- *** relation: a_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to cytidine. *** --- ************************************************ --- CREATE VIEW a_to_c_transversion AS SELECT feature_id AS a_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion'; --- ************************************************ --- *** relation: a_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to thymine. *** --- ************************************************ --- CREATE VIEW a_to_t_transversion AS SELECT feature_id AS a_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_T_transversion'; --- ************************************************ --- *** relation: g_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to cytidine. *** --- ************************************************ --- CREATE VIEW g_to_c_transversion AS SELECT feature_id AS g_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_C_transversion'; --- ************************************************ --- *** relation: g_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to thymine. *** --- ************************************************ --- CREATE VIEW g_to_t_transversion AS SELECT feature_id AS g_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_T_transversion'; --- ************************************************ --- *** relation: intrachromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_mutation AS SELECT feature_id AS intrachromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'intrachromosomal_mutation'; --- ************************************************ --- *** relation: chromosomal_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** An incomplete chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_deletion AS SELECT feature_id AS chromosomal_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_deletion'; --- ************************************************ --- *** relation: chromosomal_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_inversion AS SELECT feature_id AS chromosomal_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_inversion'; --- ************************************************ --- *** relation: interchromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal_mutation AS SELECT feature_id AS interchromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_mutation'; --- ************************************************ --- *** relation: indel *** --- *** relation type: VIEW *** --- *** *** --- *** A hybrid term (insertion/deletion) to de *** --- *** scribe sequence length change when the d *** --- *** irection of the change is unspecified. *** --- ************************************************ --- CREATE VIEW indel AS SELECT feature_id AS indel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'indel'; --- ************************************************ --- *** relation: nucleotide_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** One or more continuous nucleotides are e *** --- *** xcised from the sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_deletion AS SELECT feature_id AS nucleotide_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_deletion'; --- ************************************************ --- *** relation: nucleotide_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW nucleotide_insertion AS SELECT feature_id AS nucleotide_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'nucleotide_insertion'; --- ************************************************ --- *** relation: nucleotide_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce; the inserted sequence derives from, *** --- *** or is identical in sequence to, nucleoti *** --- *** des adjacent to insertion point. *** --- ************************************************ --- CREATE VIEW nucleotide_duplication AS SELECT feature_id AS nucleotide_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_duplication'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: chromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An extra chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_duplication AS SELECT feature_id AS chromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_duplication'; --- ************************************************ --- *** relation: intrachromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_duplication AS SELECT feature_id AS intrachromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'intrachromosomal_duplication'; --- ************************************************ --- *** relation: direct_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direct_tandem_duplication AS SELECT feature_id AS direct_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication'; --- ************************************************ --- *** relation: inverted_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_tandem_duplication AS SELECT feature_id AS inverted_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_tandem_duplication'; --- ************************************************ --- *** relation: intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_transposition AS SELECT feature_id AS intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_transposition'; --- ************************************************ --- *** relation: compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome AS SELECT feature_id AS compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'compound_chromosome'; --- ************************************************ --- *** relation: robertsonian_fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW robertsonian_fusion AS SELECT feature_id AS robertsonian_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Robertsonian_fusion'; --- ************************************************ --- *** relation: chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_translocation AS SELECT feature_id AS chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'chromosomal_translocation'; --- ************************************************ --- *** relation: ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ring_chromosome AS SELECT feature_id AS ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'ring_chromosome'; --- ************************************************ --- *** relation: pericentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pericentric_inversion AS SELECT feature_id AS pericentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric_inversion'; --- ************************************************ --- *** relation: paracentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paracentric_inversion AS SELECT feature_id AS paracentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric_inversion'; --- ************************************************ --- *** relation: reciprocal_chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW reciprocal_chromosomal_translocation AS SELECT feature_id AS reciprocal_chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal_chromosomal_translocation'; --- ************************************************ --- *** relation: sequence_variation_affecting_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** Any change in mature, spliced and proces *** --- *** sed, RNA that results from a change in t *** --- *** he corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_transcript AS SELECT feature_id AS sequence_variation_affecting_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_transcription' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_no_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** No effect on the state of the RNA. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_no_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_complex_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_complex_change_in_transcript AS SELECT feature_id AS sequence_variation_affecting_complex_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_coding_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Any of the amino acid coding triplets of *** --- *** a gene are affected by the DNA mutation *** --- *** . *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_coding_sequence AS SELECT feature_id AS sequence_variation_affecting_coding_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variation_affecting_coding_sequence'; --- ************************************************ --- *** relation: sequence_variant_causing_initiator_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The DNA mutation changes, usually destro *** --- *** ys, the first coding triplet of a gene. *** --- *** Usually prevents translation although an *** --- *** other initiator codon may be used. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_initiator_codon_change_in_trans AS SELECT feature_id AS sequence_variant_causing_initiator_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_amino_acid_coding_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The DNA mutation affects the amino acid *** --- *** coding sequence of a gene; this region i *** --- *** ncludes both the initiator and terminato *** --- *** r codons. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_amino_acid_coding_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_amino_acid_coding_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_synonymous_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The changed codon has the same translati *** --- *** on product as the original codon. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_synonymous_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_synonymous_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_non_synonymous_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA point mutation that causes a subst *** --- *** itution of an amino acid by an other. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_non_synonymous_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_non_synonymous_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_missense_codon_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon leads *** --- *** to a new codon coding for a new amino a *** --- *** cid. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_missense_codon_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_missense_codon_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_var_causing_conservative_missense_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The amino acid change following from the *** --- *** codon change does not change the gross *** --- *** properties (size, charge, hydrophobicity *** --- *** ) of the amino acid at that position. *** --- ************************************************ --- CREATE VIEW seq_var_causing_conservative_missense_codon_change_in_trans AS SELECT feature_id AS seq_var_causing_conservative_missense_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_var_causing_nonconserv_missense_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The amino acid change following from the *** --- *** codon change changes the gross properti *** --- *** es (size, charge, hydrophobicity) of the *** --- *** amino acid in that position. *** --- ************************************************ --- CREATE VIEW seq_var_causing_nonconserv_missense_codon_change_in_trans AS SELECT feature_id AS seq_var_causing_nonconserv_missense_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_nonsense_codon_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon tripl *** --- *** et creates a terminator codon. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_nonsense_codon_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_nonsense_codon_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_terminator_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon tripl *** --- *** et changes the stop codon, causing an el *** --- *** ongated transcript sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_terminator_codon_change_in_trans AS SELECT feature_id AS sequence_variant_causing_terminator_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** An umbrella term for terms describing an *** --- *** effect of a sequence variation on the f *** --- *** rame of translation. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_reading_frame AS SELECT feature_id AS sequence_variation_affecting_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variation_affecting_reading_frame'; --- ************************************************ --- *** relation: frameshift_sequence_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, because the *** --- *** number of nucleotides inserted or delete *** --- *** d is not a multiple of three. *** --- ************************************************ --- CREATE VIEW frameshift_sequence_variation AS SELECT feature_id AS frameshift_sequence_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'frameshift_sequence_variation'; --- ************************************************ --- *** relation: sequence_variant_causing_plus_1_frameshift_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the i *** --- *** nsertion of a nucleotide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_plus_1_frameshift_mutation AS SELECT feature_id AS sequence_variant_causing_plus_1_frameshift_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation'; --- ************************************************ --- *** relation: sequence_variant_causing_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the d *** --- *** eletion of a nucleotide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_minus_1_frameshift AS SELECT feature_id AS sequence_variant_causing_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_minus_1_frameshift'; --- ************************************************ --- *** relation: sequence_variant_causing_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the i *** --- *** nsertion of two nucleotides. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_plus_2_frameshift AS SELECT feature_id AS sequence_variant_causing_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_2_frameshift'; --- ************************************************ --- *** relation: sequence_variant_causing_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the d *** --- *** eletion of two nucleotides. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_minus_2_frameshift AS SELECT feature_id AS sequence_variant_causing_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_minus_2_frameshift'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_processing *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the way in whic *** --- *** h the primary transcriptional product is *** --- *** processed to form the mature transcript *** --- *** . *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_processing AS SELECT feature_id AS sequence_variant_affecting_transcript_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_affecting_transcript_processing'; --- ************************************************ --- *** relation: sequence_variant_affecting_splicing *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect where the way *** --- *** in which the primary transcriptional pro *** --- *** duct is processed to form the mature tra *** --- *** nscript, specifically by the removal (sp *** --- *** licing) of intron sequences is changed. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splicing AS SELECT feature_id AS sequence_variant_affecting_splicing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_donor' OR cvterm.name = 'sequence_variant_affecting_splice_acceptor' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation' OR cvterm.name = 'sequence_variant_causes_exon_loss' OR cvterm.name = 'sequence_variant_causes_intron_gain' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_affecting_splicing'; --- ************************************************ --- *** relation: sequence_variant_affecting_splice_donor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he splice donor sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splice_donor AS SELECT feature_id AS sequence_variant_affecting_splice_donor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_donor'; --- ************************************************ --- *** relation: sequence_variant_affecting_splice_acceptor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he splice acceptor sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splice_acceptor AS SELECT feature_id AS sequence_variant_affecting_splice_acceptor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_acceptor'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_activation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a new (functi *** --- *** onal) splice site. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation'; --- ************************************************ --- *** relation: sequence_variant_affecting_editing *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the editing of *** --- *** the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_editing AS SELECT feature_id AS sequence_variant_affecting_editing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_editing'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** Mutation affects the process of transcri *** --- *** ption, its initiation, progression or te *** --- *** rmination. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcription AS SELECT feature_id AS sequence_variant_affecting_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_affecting_transcription'; --- ************************************************ --- *** relation: sequence_variant_decreasing_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that decreases the *** --- *** rate a which transcription of the sequen *** --- *** ce occurs. *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_rate_of_transcription AS SELECT feature_id AS sequence_variant_decreasing_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variation_affecting_transcript_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_transcript_sequence AS SELECT feature_id AS sequence_variation_affecting_transcript_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence'; --- ************************************************ --- *** relation: sequence_variant_increasing_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_rate_of_transcription AS SELECT feature_id AS sequence_variant_increasing_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variant_affecting_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that alters the rate a which *** --- *** transcription of the sequence occurs. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_rate_of_transcription AS SELECT feature_id AS sequence_variant_affecting_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the stability o *** --- *** f the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_stability AS SELECT feature_id AS sequence_variant_affecting_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence variant_affecting_transcript_stability'; --- ************************************************ --- *** relation: sequence_variant_increasing_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant increases the stability *** --- *** (half-life) of the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_transcript_stability AS SELECT feature_id AS sequence_variant_increasing_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_transcript_stability'; --- ************************************************ --- *** relation: sequence_variant_decreasing_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant decreases the stability *** --- *** (half-life) of the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_transcript_stability AS SELECT feature_id AS sequence_variant_decreasing_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_transcript_stability'; --- ************************************************ --- *** relation: sequence_variation_affecting_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that causes a chang *** --- *** e in the level of mature, spliced and pr *** --- *** ocessed RNA, resulting from a change in *** --- *** the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_level_of_transcript AS SELECT feature_id AS sequence_variation_affecting_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variation_decreasing_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that causes a decre *** --- *** ase in the level of mature, spliced and *** --- *** processed RNA, resulting from a change i *** --- *** n the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_decreasing_level_of_transcript AS SELECT feature_id AS sequence_variation_decreasing_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_decreasing_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variation_increasing_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variation that causes an incr *** --- *** ease in the level of mature, spliced and *** --- *** processed RNA, resulting from a change *** --- *** in the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_increasing_level_of_transcript AS SELECT feature_id AS sequence_variation_increasing_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_increasing_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variant_affecting_translational_product *** --- *** relation type: VIEW *** --- *** *** --- *** Mutation causes a change in primary tran *** --- *** slation product of a transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_translational_product AS SELECT feature_id AS sequence_variant_affecting_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_affecting_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_no_change_of_translational_product *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence variant at RNA level does n *** --- *** ot lead to any change in polypeptide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_change_of_translational_product AS SELECT feature_id AS sequence_variant_causing_no_change_of_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_uncharacterised_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing an uncharacte *** --- *** rized change of translational product. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_uncharacterised_change_of_product AS SELECT feature_id AS sequence_variant_causing_uncharacterised_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product'; --- ************************************************ --- *** relation: seq_variant_causing_partly_characterised_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a partially u *** --- *** ncharacterised change in translational p *** --- *** roduct. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_partly_characterised_change_of_product AS SELECT feature_id AS seq_variant_causing_partly_characterised_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_complex_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** Any sequence variant effect that is know *** --- *** n at nucleotide level but cannot be expl *** --- *** ained by using other key terms. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_complex_change_of_product AS SELECT feature_id AS sequence_variant_causing_complex_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** The replacement of a single amino acid b *** --- *** y another. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_substitution AS SELECT feature_id AS sequence_variant_causing_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_conservative_amino_acid_sub *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_conservative_amino_acid_sub AS SELECT feature_id AS sequence_variant_causing_conservative_amino_acid_sub_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_nonconservative_amino_acid_sub *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_nonconservative_amino_acid_sub AS SELECT feature_id AS sequence_variant_causing_nonconservative_amino_acid_sub_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** The insertion of one or more amino acids *** --- *** from the polypeptide, without affecting *** --- *** the surrounding sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_insertion AS SELECT feature_id AS sequence_variant_causing_amino_acid_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_insertion'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The deletion of one or more amino acids *** --- *** from the polypeptide, without affecting *** --- *** the surrounding sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_deletion AS SELECT feature_id AS sequence_variant_causing_amino_acid_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_deletion'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_truncation *** --- *** relation type: VIEW *** --- *** *** --- *** The translational product is truncated a *** --- *** t its C-terminus, usually a result of a *** --- *** nonsense codon change in transcript (SO: *** --- *** 1000062). *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_truncation AS SELECT feature_id AS sequence_variant_causing_polypeptide_truncation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_truncation'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** The extension of the translational produ *** --- *** ct at either (or both) the N-terminus an *** --- *** d/or the C-terminus. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_elongation AS SELECT feature_id AS sequence_variant_causing_polypeptide_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation'; --- ************************************************ --- *** relation: mutation_causing_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** . *** --- ************************************************ --- CREATE VIEW mutation_causing_polypeptide_n_terminal_elongation AS SELECT feature_id AS mutation_causing_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_polypeptide_c_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** . *** --- ************************************************ --- CREATE VIEW mutation_causing_polypeptide_c_terminal_elongation AS SELECT feature_id AS mutation_causing_polypeptide_c_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: sequence_variant_affecting_level_of_translational_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_level_of_translational_product AS SELECT feature_id AS sequence_variant_affecting_level_of_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_decreasing_level_of_translation_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_level_of_translation_product AS SELECT feature_id AS sequence_variant_decreasing_level_of_translation_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_level_of_translation_product'; --- ************************************************ --- *** relation: sequence_variant_increasing_level_of_translation_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_level_of_translation_product AS SELECT feature_id AS sequence_variant_increasing_level_of_translation_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_level_of_translation_product'; --- ************************************************ --- *** relation: sequence_variant_affecting_polypeptide_amino_acid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polypeptide_amino_acid_sequence AS SELECT feature_id AS sequence_variant_affecting_polypeptide_amino_acid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence'; --- ************************************************ --- *** relation: mutation_causing_inframe_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_inframe_polypeptide_n_terminal_elongation AS SELECT feature_id AS mutation_causing_inframe_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_out_of_frame_polypeptide_n_terminal_elong *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_out_of_frame_polypeptide_n_terminal_elong AS SELECT feature_id AS mutation_causing_out_of_frame_polypeptide_n_terminal_elong_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutaton_causing_inframe_polypeptide_c_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutaton_causing_inframe_polypeptide_c_terminal_elongation AS SELECT feature_id AS mutaton_causing_inframe_polypeptide_c_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_out_of_frame_polypeptide_c_terminal_elong *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_out_of_frame_polypeptide_c_terminal_elong AS SELECT feature_id AS mutation_causing_out_of_frame_polypeptide_c_terminal_elong_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: frame_restoring_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that reverts the sequence of *** --- *** a previous frameshift mutation back to t *** --- *** he initial frame. *** --- ************************************************ --- CREATE VIEW frame_restoring_sequence_variant AS SELECT feature_id AS frame_restoring_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_sequence_variant'; --- ************************************************ --- *** relation: sequence_variant_affecting_3d_structure_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that changes the amino acid s *** --- *** equence of the peptide in such a way tha *** --- *** t it changes the 3D structure of the mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_3d_structure_of_polypeptide AS SELECT feature_id AS sequence_variant_affecting_3d_structure_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_no_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_3d_structural_change AS SELECT feature_id AS sequence_variant_causing_no_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_3D_structural_change'; --- ************************************************ --- *** relation: seq_variant_causing_uncharacterised_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_uncharacterised_3d_structural_change AS SELECT feature_id AS seq_variant_causing_uncharacterised_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change'; --- ************************************************ --- *** relation: seq_var_causing_partly_characterised_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_var_causing_partly_characterised_3d_structural_change AS SELECT feature_id AS seq_var_causing_partly_characterised_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change'; --- ************************************************ --- *** relation: sequence_variant_causing_complex_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_complex_3d_structural_change AS SELECT feature_id AS sequence_variant_causing_complex_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_complex_3D_structural_change'; --- ************************************************ --- *** relation: sequence_variant_causing_conformational_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_conformational_change AS SELECT feature_id AS sequence_variant_causing_conformational_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conformational_change'; --- ************************************************ --- *** relation: sequence_variant_affecting_polypeptide_function *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polypeptide_function AS SELECT feature_id AS sequence_variant_affecting_polypeptide_function_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function'; --- ************************************************ --- *** relation: sequence_variant_causing_loss_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_loss_of_function_of_polypeptide AS SELECT feature_id AS sequence_variant_causing_loss_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_inactive_ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_inactive_ligand_binding_site AS SELECT feature_id AS sequence_variant_causing_inactive_ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site'; --- ************************************************ --- *** relation: sequence_variant_causing_inactive_catalytic_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_inactive_catalytic_site AS SELECT feature_id AS sequence_variant_causing_inactive_catalytic_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_catalytic_site'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_localization_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_localization_change AS SELECT feature_id AS sequence_variant_causing_polypeptide_localization_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_localization_change'; --- ************************************************ --- *** relation: seq_variant_causing_polypeptide_post_trans_processing_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_polypeptide_post_trans_processing_change AS SELECT feature_id AS seq_variant_causing_polypeptide_post_trans_processing_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change'; --- ************************************************ --- *** relation: seq_variant_causing_part_loss_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_part_loss_of_function_of_polypeptide AS SELECT feature_id AS seq_variant_causing_part_loss_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_gain_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_gain_of_function_of_polypeptide AS SELECT feature_id AS sequence_variant_causing_gain_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the seco *** --- *** ndary structure (folding) of the RNA tra *** --- *** nscript molecule. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_secondary_structure AS SELECT feature_id AS sequence_variant_affecting_transcript_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure'; --- ************************************************ --- *** relation: seq_variant_caus_compensatory_trans_secondary_structure_mut *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_caus_compensatory_trans_secondary_structure_mut AS SELECT feature_id AS seq_variant_caus_compensatory_trans_secondary_structure_mut_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation'; --- ************************************************ --- *** relation: sequence_variant_effect *** --- *** relation type: VIEW *** --- *** *** --- *** The effect of a change in nucleotide seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW sequence_variant_effect AS SELECT feature_id AS sequence_variant_effect_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_regulatory_region' OR cvterm.name = 'silent_mutation' OR cvterm.name = 'sequence_variant_affecting_copy_number' OR cvterm.name = 'sequence_variation_affecting_transcript' OR cvterm.name = 'sequence_variant_affecting_splicing' OR cvterm.name = 'sequence_variant_affecting_translational_product' OR cvterm.name = 'sequence_variant_affecting_gene_structure' OR cvterm.name = 'sequence_variant_causing_no_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_transcription' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_splice_donor' OR cvterm.name = 'sequence_variant_affecting_splice_acceptor' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation' OR cvterm.name = 'sequence_variant_causes_exon_loss' OR cvterm.name = 'sequence_variant_causes_intron_gain' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_causing_no_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_gene_fusion' OR cvterm.name = 'sequence_variant_effect'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_fusion AS SELECT feature_id AS sequence_variant_causing_polypeptide_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_fusion'; --- ************************************************ --- *** relation: autosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW autosynaptic_chromosome AS SELECT feature_id AS autosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'autosynaptic_chromosome'; --- ************************************************ --- *** relation: homo_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW homo_compound_chromosome AS SELECT feature_id AS homo_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homo_compound_chromosome'; --- ************************************************ --- *** relation: hetero_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW hetero_compound_chromosome AS SELECT feature_id AS hetero_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hetero_compound_chromosome'; --- ************************************************ --- *** relation: chromosome_fission *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_fission AS SELECT feature_id AS chromosome_fission_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_fission'; --- ************************************************ --- *** relation: dexstrosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dexstrosynaptic_chromosome AS SELECT feature_id AS dexstrosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome'; --- ************************************************ --- *** relation: laevosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW laevosynaptic_chromosome AS SELECT feature_id AS laevosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'laevosynaptic_chromosome'; --- ************************************************ --- *** relation: free_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_duplication AS SELECT feature_id AS free_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication' OR cvterm.name = 'free_duplication'; --- ************************************************ --- *** relation: free_ring_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_ring_duplication AS SELECT feature_id AS free_ring_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication'; --- ************************************************ --- *** relation: complex_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW complex_chromosomal_mutation AS SELECT feature_id AS complex_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A translocation in which one of the four *** --- *** broken ends loses a segment before re-j *** --- *** oining. *** --- ************************************************ --- CREATE VIEW deficient_translocation AS SELECT feature_id AS deficient_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_translocation'; --- ************************************************ --- *** relation: inversion_cum_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** The first two breaks are in the same chr *** --- *** omosome, and the region between them is *** --- *** rejoined in inverted order to the other *** --- *** side of the first break, such that both *** --- *** sides of break one are present on the sa *** --- *** me chromosome. The remaining free ends a *** --- *** re joined as a translocation with those *** --- *** resulting from the third break. *** --- ************************************************ --- CREATE VIEW inversion_cum_translocation AS SELECT feature_id AS inversion_cum_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_cum_translocation'; --- ************************************************ --- *** relation: bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** The (large) region between the first two *** --- *** breaks listed is lost, and the two flan *** --- *** king segments (one of them centric) are *** --- *** joined as a translocation to the free en *** --- *** ds resulting from the third break. *** --- ************************************************ --- CREATE VIEW bipartite_duplication AS SELECT feature_id AS bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_duplication'; --- ************************************************ --- *** relation: cyclic_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in three different chromoso *** --- *** mes. The centric segment resulting from *** --- *** the first break listed is joined to the *** --- *** acentric segment resulting from the seco *** --- *** nd, rather than the third. *** --- ************************************************ --- CREATE VIEW cyclic_translocation AS SELECT feature_id AS cyclic_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyclic_translocation'; --- ************************************************ --- *** relation: bipartite_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in the same chromosome; bot *** --- *** h central segments are inverted in place *** --- *** (i.e., they are not transposed). *** --- ************************************************ --- CREATE VIEW bipartite_inversion AS SELECT feature_id AS bipartite_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_inversion'; --- ************************************************ --- *** relation: uninvert_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the insertion is in cytologica *** --- *** lly the same orientation as its flanking *** --- *** segments. *** --- ************************************************ --- CREATE VIEW uninvert_insert_dup AS SELECT feature_id AS uninvert_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication'; --- ************************************************ --- *** relation: inverted_insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the insertion is in cytologica *** --- *** lly inverted orientation with respect to *** --- *** its flanking segments. *** --- ************************************************ --- CREATE VIEW inverted_insertional_duplication AS SELECT feature_id AS inverted_insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_insertional_duplication'; --- ************************************************ --- *** relation: insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving the i *** --- *** nsertion of a duplicated region. *** --- ************************************************ --- CREATE VIEW insertional_duplication AS SELECT feature_id AS insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'insertional_duplication'; --- ************************************************ --- *** relation: interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal_transposition AS SELECT feature_id AS interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW invert_inter_transposition AS SELECT feature_id AS invert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uninvert_inter_transposition AS SELECT feature_id AS uninvert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally inverted orientation with respect *** --- *** to its flanking segments. *** --- ************************************************ --- CREATE VIEW invert_intra_transposition AS SELECT feature_id AS invert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally the same orientation as its flanki *** --- *** ng segments. *** --- ************************************************ --- CREATE VIEW uninvert_intra_transposition AS SELECT feature_id AS uninvert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: unorient_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the orientation of the inserti *** --- *** on with respect to its flanking segments *** --- *** is not recorded. *** --- ************************************************ --- CREATE VIEW unorient_insert_dup AS SELECT feature_id AS unorient_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_insertional_duplication'; --- ************************************************ --- *** relation: unorient_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW unorient_inter_transposition AS SELECT feature_id AS unorient_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unorientated_interchromosomal_transposition'; --- ************************************************ --- *** relation: unorient_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the orientation of the inser *** --- *** tion with respect to its flanking segmen *** --- *** ts is not recorded. *** --- ************************************************ --- CREATE VIEW unorient_intra_transposition AS SELECT feature_id AS unorient_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unorientated_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uncharacterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uncharacterised_chromosomal_mutation AS SELECT feature_id AS uncharacterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in the same chromosome; one *** --- *** central region lost, the other inverted *** --- *** . *** --- ************************************************ --- CREATE VIEW deficient_inversion AS SELECT feature_id AS deficient_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_inversion'; --- ************************************************ --- *** relation: tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tandem_duplication AS SELECT feature_id AS tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'tandem_duplication'; --- ************************************************ --- *** relation: partially_characterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW partially_characterised_chromosomal_mutation AS SELECT feature_id AS partially_characterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation'; --- ************************************************ --- *** relation: seq_variant_causing_uncharacterised_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is eith *** --- *** er uncharacterised or only partially cha *** --- *** racterised. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_uncharacterised_change_in_transcript AS SELECT feature_id AS seq_variant_causing_uncharacterised_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_partly_characterised_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is only *** --- *** partially characterised. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_partly_characterised_change_in_trans AS SELECT feature_id AS seq_variant_causing_partly_characterised_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_affecting_gene_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he gene structure. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_gene_structure AS SELECT feature_id AS sequence_variant_affecting_gene_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gene_fusion' OR cvterm.name = 'sequence_variant_affecting_gene_structure'; --- ************************************************ --- *** relation: sequence_variant_causing_gene_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he gene structure by causing a fusion to *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_gene_fusion AS SELECT feature_id AS sequence_variant_causing_gene_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gene_fusion'; --- ************************************************ --- *** relation: chromosome_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW chromosome_number_variation AS SELECT feature_id AS chromosome_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'chromosome_number_variation'; --- ************************************************ --- *** relation: chromosome_structure_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_structure_variation AS SELECT feature_id AS chromosome_structure_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_structure_variation'; --- ************************************************ --- *** relation: sequence_variant_causes_exon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant affecting splicing an *** --- *** d causes an exon loss. *** --- ************************************************ --- CREATE VIEW sequence_variant_causes_exon_loss AS SELECT feature_id AS sequence_variant_causes_exon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causes_exon_loss'; --- ************************************************ --- *** relation: sequence_variant_causes_intron_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant effect, causing an in *** --- *** tron to be gained by the processed trans *** --- *** cript; usually a result of a donor accep *** --- *** tor mutation (SO:1000072). *** --- ************************************************ --- CREATE VIEW sequence_variant_causes_intron_gain AS SELECT feature_id AS sequence_variant_causes_intron_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causes_intron_gain'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_donor_activation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_donor_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_donor_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_acceptor_activation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_acceptor_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_acceptor_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation'; --- ************************************************ --- *** relation: alternatively_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is alternatively splic *** --- *** ed. *** --- ************************************************ --- CREATE VIEW alternatively_spliced_transcript AS SELECT feature_id AS alternatively_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced_transcript'; --- ************************************************ --- *** relation: encodes_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, but *** --- *** encodes only one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_1_polypeptide AS SELECT feature_id AS encodes_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide'; --- ************************************************ --- *** relation: encodes_greater_than_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_greater_than_1_polypeptide AS SELECT feature_id AS encodes_greater_than_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_greater_than_1_polypeptide'; --- ************************************************ --- *** relation: encodes_different_polypeptides_different_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different stop codons. *** --- ************************************************ --- CREATE VIEW encodes_different_polypeptides_different_stop AS SELECT feature_id AS encodes_different_polypeptides_different_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides_different_start *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides_different_start AS SELECT feature_id AS encodes_overlapping_peptides_different_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_peptides_different_start'; --- ************************************************ --- *** relation: encodes_disjoint_polypeptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** do not have overlapping peptide sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW encodes_disjoint_polypeptides AS SELECT feature_id AS encodes_disjoint_polypeptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides'; --- ************************************************ --- *** relation: encodes_overlapping_polypeptides_different_start_and_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start and stop codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_polypeptides_different_start_and_stop AS SELECT feature_id AS encodes_overlapping_polypeptides_different_start_and_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides AS SELECT feature_id AS encodes_overlapping_peptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_overlapping_peptides'; --- ************************************************ --- *** relation: cryptogene *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle gene so extensively edited *** --- *** that it cannot be matched to its edited *** --- *** mRNA sequence. *** --- ************************************************ --- CREATE VIEW cryptogene AS SELECT feature_id AS cryptogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene'; --- ************************************************ --- *** relation: dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that has the qualit *** --- *** y dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_primary_transcript AS SELECT feature_id AS dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript'; --- ************************************************ --- *** relation: member_of_regulon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW member_of_regulon AS SELECT feature_id AS member_of_regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'member_of_regulon'; --- ************************************************ --- *** relation: cds_independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS with the evidence status of being *** --- *** independently known. *** --- ************************************************ --- CREATE VIEW cds_independently_known AS SELECT feature_id AS cds_independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_independently_known'; --- ************************************************ --- *** relation: orphan_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS whose predicted amino acid sequenc *** --- *** e is unsupported by any experimental evi *** --- *** dence or by any match with any other kno *** --- *** wn sequence. *** --- ************************************************ --- CREATE VIEW orphan_cds AS SELECT feature_id AS orphan_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS'; --- ************************************************ --- *** relation: cds_supported_by_domain_match_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by domain simila *** --- *** rity. *** --- ************************************************ --- CREATE VIEW cds_supported_by_domain_match_data AS SELECT feature_id AS cds_supported_by_domain_match_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data'; --- ************************************************ --- *** relation: cds_supported_by_sequence_similarity_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by sequence simi *** --- *** larity data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_sequence_similarity_data AS SELECT feature_id AS cds_supported_by_sequence_similarity_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data'; --- ************************************************ --- *** relation: cds_predicted *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is predicted. *** --- ************************************************ --- CREATE VIEW cds_predicted AS SELECT feature_id AS cds_predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_predicted'; --- ************************************************ --- *** relation: cds_supported_by_est_or_cdna_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by similarity to *** --- *** EST or cDNA data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_est_or_cdna_data AS SELECT feature_id AS cds_supported_by_est_or_cdna_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_EST_or_cDNA_data'; --- ************************************************ --- *** relation: internal_shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A Shine-Dalgarno sequence that stimulate *** --- *** s recoding through interactions with the *** --- *** anti-Shine-Dalgarno in the RNA of small *** --- *** ribosomal subunits of translating ribos *** --- *** omes. The signal is only operative in Ba *** --- *** cteria. *** --- ************************************************ --- CREATE VIEW internal_shine_dalgarno_sequence AS SELECT feature_id AS internal_shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a mature mRNA transcript *** --- *** , modified before translation or during *** --- *** translation, usually by special cis-acti *** --- *** ng signals. *** --- ************************************************ --- CREATE VIEW recoded_mrna AS SELECT feature_id AS recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'recoded_mRNA'; --- ************************************************ --- *** relation: minus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of -1. *** --- ************************************************ --- CREATE VIEW minus_1_translationally_frameshifted AS SELECT feature_id AS minus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: plus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of +1. *** --- ************************************************ --- CREATE VIEW plus_1_translationally_frameshifted AS SELECT feature_id AS plus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA where translation was sus *** --- *** pended at a particular codon and resumed *** --- *** at a particular non-overlapping downstr *** --- *** eam codon. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_translational_bypass AS SELECT feature_id AS mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: mrna_recoded_by_codon_redefinition *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA that was modified by an a *** --- *** lteration of codon meaning. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_codon_redefinition AS SELECT feature_id AS mrna_recoded_by_codon_redefinition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_codon_redefinition'; --- ************************************************ --- *** relation: recoding_stimulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A site in an mRNA sequence that stimulat *** --- *** es the recoding of a region in the same *** --- *** mRNA. *** --- ************************************************ --- CREATE VIEW recoding_stimulatory_region AS SELECT feature_id AS recoding_stimulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'recoding_stimulatory_region'; --- ************************************************ --- *** relation: four_bp_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon with 4 base *** --- *** pairs. *** --- ************************************************ --- CREATE VIEW four_bp_start_codon AS SELECT feature_id AS four_bp_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon'; --- ************************************************ --- *** relation: archaeal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron characteristic of Archaeal tRN *** --- *** A and rRNA genes, where intron transcrip *** --- *** t generates a bulge-helix-bulge motif th *** --- *** at is recognised by a splicing endoribon *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW archaeal_intron AS SELECT feature_id AS archaeal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron'; --- ************************************************ --- *** relation: trna_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron found in tRNA that is spliced *** --- *** via endonucleolytic cleavage and ligatio *** --- *** n rather than transesterification. *** --- ************************************************ --- CREATE VIEW trna_intron AS SELECT feature_id AS trna_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_intron'; --- ************************************************ --- *** relation: ctg_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon of sequence *** --- *** CTG. *** --- ************************************************ --- CREATE VIEW ctg_start_codon AS SELECT feature_id AS ctg_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CTG_start_codon'; --- ************************************************ --- *** relation: secis_element *** --- *** relation type: VIEW *** --- *** *** --- *** The incorporation of selenocysteine into *** --- *** a protein sequence is directed by an in *** --- *** -frame UGA codon (usually a stop codon) *** --- *** within the coding region of the mRNA. Se *** --- *** lenoprotein mRNAs contain a conserved se *** --- *** condary structure in the 3' UTR that is *** --- *** required for the distinction of UGA stop *** --- *** from UGA selenocysteine. The selenocyst *** --- *** eine insertion sequence (SECIS) is aroun *** --- *** d 60 nt in length and adopts a hairpin s *** --- *** tructure which is sufficiently well-defi *** --- *** ned and conserved to act as a computatio *** --- *** nal screen for selenoprotein genes. *** --- ************************************************ --- CREATE VIEW secis_element AS SELECT feature_id AS secis_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SECIS_element'; --- ************************************************ --- *** relation: retron *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence coding for a short, single-stra *** --- *** nded, DNA sequence via a retrotransposed *** --- *** RNA intermediate; characteristic of som *** --- *** e microbial genomes. *** --- ************************************************ --- CREATE VIEW retron AS SELECT feature_id AS retron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retron'; --- ************************************************ --- *** relation: three_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** downstream of the recoding site. *** --- ************************************************ --- CREATE VIEW three_prime_recoding_site AS SELECT feature_id AS three_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'three_prime_recoding_site'; --- ************************************************ --- *** relation: three_prime_stem_loop_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory region, the stem- *** --- *** loop secondary structural element is dow *** --- *** nstream of the redefined region. *** --- ************************************************ --- CREATE VIEW three_prime_stem_loop_structure AS SELECT feature_id AS three_prime_stem_loop_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure'; --- ************************************************ --- *** relation: five_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** upstream of the recoding site. *** --- ************************************************ --- CREATE VIEW five_prime_recoding_site AS SELECT feature_id AS five_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_recoding_site'; --- ************************************************ --- *** relation: flanking_three_prime_quadruplet_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Four base pair sequence immediately down *** --- *** stream of the redefined region. The rede *** --- *** fined region is a frameshift site. The q *** --- *** uadruplet is 2 overlapping codons. *** --- ************************************************ --- CREATE VIEW flanking_three_prime_quadruplet_recoding_signal AS SELECT feature_id AS flanking_three_prime_quadruplet_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal'; --- ************************************************ --- *** relation: uag_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAG stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uag_stop_codon_signal AS SELECT feature_id AS uag_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal'; --- ************************************************ --- *** relation: uaa_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uaa_stop_codon_signal AS SELECT feature_id AS uaa_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAA_stop_codon_signal'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: uga_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UGA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uga_stop_codon_signal AS SELECT feature_id AS uga_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UGA_stop_codon_signal'; --- ************************************************ --- *** relation: three_prime_repeat_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal, downstrea *** --- *** m sequence important for recoding that c *** --- *** ontains repetitive elements. *** --- ************************************************ --- CREATE VIEW three_prime_repeat_recoding_signal AS SELECT feature_id AS three_prime_repeat_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_repeat_recoding_signal'; --- ************************************************ --- *** relation: distant_three_prime_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding signal that is found many hun *** --- *** dreds of nucleotides 3' of a redefined s *** --- *** top codon. *** --- ************************************************ --- CREATE VIEW distant_three_prime_recoding_signal AS SELECT feature_id AS distant_three_prime_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distant_three_prime_recoding_signal'; --- ************************************************ --- *** relation: stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal that is a *** --- *** stop codon and has effect on efficiency *** --- *** of recoding. *** --- ************************************************ --- CREATE VIEW stop_codon_signal AS SELECT feature_id AS stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'stop_codon_signal'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene component region which acts as a *** --- *** recombinational unit of a gene whose fun *** --- *** ctional form is generated through somati *** --- *** c recombination. *** --- ************************************************ --- CREATE VIEW gene_segment AS SELECT feature_id AS gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_segment'; CREATE TABLE sequence_cv_lookup_table (sequence_cv_lookup_table_id serial not null, primary key(sequence_cv_lookup_table_id), original_cvterm_name varchar(1024), relation_name varchar(128)); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helitron','helitron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_initiator_methionine','cleaved_initiator_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epoxyqueuosine','epoxyqueuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4atac_snrna','u4atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast','kinetoplast'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shadow_enhancer','shadow_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered','engineered'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_aminomethyl_seven_deazaguanosine','seven_aminomethyl_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity','low_complexity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est_match','est_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_nonamer','v_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_21s','rrna_21s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_c_cluster','d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethyluridine','five_carboxymethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_factor','bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_methyladenosine','two_methylthio_n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dinucleotide_repeat_microsatellite_feature','dinucleotide_repeat_microsatellite_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_mrna','trans_spliced_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_c_transversion','g_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heptamer_of_recombination_feature_of_vertebrate_immune_system_gene','heptamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genotype','genotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_region','cloned_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_coding_piece','tmrna_coding_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_6s','rna_6s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle','minicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_encoding','grna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endonuclease_spliced_intron','endonuclease_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional_duplication','insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('databank_entry','databank_entry'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine','glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_cluster','v_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nickel_ion_contact_site','polypeptide_nickel_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_rna_chromosome','circular_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wc_base_pair','wc_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pcr_product','pcr_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_three_amino_three_carboxypropyl_uridine','three_three_amino_three_carboxypropyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('site_specific_recombination_target_region','site_specific_recombination_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polycistronic_transcript','gene_with_polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue','rescue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_hypersensitive_site','nuclease_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_loop','mirna_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_cdna','double_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_domain_match','supported_by_domain_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylpseudouridine','one_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n_terminal_region','n_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_result_region','experimental_result_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine_trna_primary_transcript','methionine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr','utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_terminal_residue','non_terminal_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('member_of_regulon','member_of_regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine_trna_primary_transcript','thr_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_sequence_similarity_data','cds_supported_by_sequence_similarity_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_region','polypeptide_structural_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_gene','trna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_six','beta_bulge_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_tungsten_ion_contact_site','polypeptide_tungsten_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_polypeptides_different_start_and_stop','encodes_overlapping_polypeptides_different_start_and_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_right_left_motif','polypeptide_nest_right_left_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_location','sequence_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_c_cluster','d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_transcript','trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_rna','y_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_gene','leucoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_regulatory_region','splicing_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('branch_site','branch_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_five','beta_bulge_loop_five'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakpoint','chromosome_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_uncertainty','sequence_uncertainty'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyl_n6_threonylcarbamoyladenosine','n6_methyl_n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_with_frameshift','gene_with_mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compositionally_biased_region_of_peptide','compositionally_biased_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_c_cluster','vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splice_acceptor','sequence_variant_affecting_splice_acceptor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna','pirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_hoogsteen_base_pair','reverse_hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophanyl_trna','tryptophanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_primed_cdna_clone','polya_primed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_chromosome','leucoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('status','status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_retrotransposon','ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna','rnase_p_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conjugative_transposon','conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linkage_group','linkage_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_trans_spliced_transcript','gene_with_trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_coil','peptide_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine_trna_primary_transcript','pyrrolysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_c_cluster','v_vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_sequence','phage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded','recoded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposon_fragment','transposon_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_c_cluster','vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_domain','editing_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyluridine','five_methylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_insertion','nucleotide_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutaton_causing_inframe_polypeptide_c_terminal_elongation','mutaton_causing_inframe_polypeptide_c_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon_polymeric_tract','non_ltr_retrotransposon_polymeric_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transversion','transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan','tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recursive_splice_site','recursive_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator_binding_site','insulator_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline_trna_primary_transcript','proline_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_fragment','repeat_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blocked_reading_frame','blocked_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_snorna_primary_transcript','rrna_cleavage_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_isopentenyladenosine','n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_arginine','modified_l_arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_motif','polypeptide_conserved_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t3_rna_polymerase_promoter','t3_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_duplication','inversion_derived_bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_acceptor_site','trans_splice_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosyladenosine_phosphate','two_prime_o_riboA_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rre_rna','rre_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac_end','pac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extramembrane_polypeptide_region','extramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein','intein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('twintron','twintron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_prime_o_methyluridine','five_carboxymethylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_primary_transcript','scrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_cobalt_ion_contact_site','polypeptide_cobalt_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_encoding','tmrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanked','flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ctg_start_codon','ctg_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion','inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('eukaryotic_terminator','eukaryotic_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine_trna_primary_transcript','tyrosine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_region_of_exon','coding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron_region','spliceosomal_intron_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_flanked','frt_flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_cdna_insert','cloned_cdna_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_c_cluster','v_vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated','translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_reading_frame','sequence_variation_affecting_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_minus_1_frameshift','sequence_variant_causing_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidyl_trna','histidyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sonicate_fragment','sonicate_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_recoded_mrna','gene_with_recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyluridine','two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cosmid','cosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_rna_interference','silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna','snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript','mature_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridylation_guide_snorna','pseudouridylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_gene','c_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed_gene','floxed_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spot_42_rna','spot_42_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_clone','cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr','three_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_ii_intron','group_ii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna_oligo','pna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_sequence','insertion_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('junction','junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous','paralogous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna','tna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_thiouridine','five_isopentenylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift','minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_gene_structure','sequence_variant_affecting_gene_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_three_prime_splice_site','non_canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_rrna','pseudogenic_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_turn','serine_threonine_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene','j_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_primary_transcript','strna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_eliminated_sequence','internal_eliminated_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded_gene','allelically_excluded_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('qtl','qtl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_est','three_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse','reverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_encoding','mirna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_2_prime_o_trimethylguanosine','n2_n2_2_prime_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternate_transcription_start_sites','encodes_alternate_transcription_start_sites'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array','gene_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetranucleotide_repeat_microsatellite_feature','tetranuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_aminomethyl_two_thiouridine','five_aminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_primary_transcript','monocistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_acceptor_activation','sequence_variant_causing_cryptic_splice_acceptor_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_genetic_element','mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_ligand_contact','polypeptide_ligand_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biomaterial_region','biomaterial_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_flanking_region','transposable_element_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symmetric_rna_internal_loop','symmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_1_frameshift','mrna_with_plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_regulated','transcriptionally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_intron','five_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_feature','vertebrate_immune_system_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine_methyl_ester','five_carboxyhydroxymethyl_uridine_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_gene','proplastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_trna_primary_transcript','serine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attp_site','attp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense','antisense'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat_element','terminal_inverted_repeat_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coiled_coil','coiled_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_cluster','v_vdj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_by_a_to_i_substitution','edited_transcript_by_a_to_i_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_primary_transcript','protein_coding_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mite','mite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion','insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('secis_element','secis_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle','maxicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss','tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine','cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribothymidine','ribothymidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_adjacent_residues','non_adjacent_residues'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_ribosome_entry_site','internal_ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('outron','outron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_repeat','polypeptide_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_start','clone_insert_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attr_site','attr_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv3_motif','dmv3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_mrna','capped_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_non_synonymous_codon_change_in_transcript','seq_variant_causing_non_synonymous_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_rearrangement_feature','sequence_rearrangement_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_chromosome','apicoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_two','beta_turn_type_six_a_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated','invalidated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_junction','polya_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partial_loss_of_function_of_polypeptide','seq_variant_causing_part_loss_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine','valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated_gene','translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_targeting_sequence','promoter_targeting_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polinton','polinton'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_tag','engineered_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylcytidine','five_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridine','pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated','positively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amplification_origin','amplification_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_insertional_duplication','unorient_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extrachromosomal_mobile_genetic_element','extrachromosomal_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_constitutive','transcriptionally_constitutive'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_fusion','sequence_variant_causing_polypeptide_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_region','utr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine','tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna','mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr1_motif','inr1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_acetyladenosine','n6_acetyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_splice_site','cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_two','beta_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed','floxed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_terminal_region','c_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_leucine','modified_l_leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_complex_change_in_transcript','sequence_variation_affecting_complex_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr_component','five_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_c_cluster','vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptional_cis_regulatory_region','transcriptional_cis_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_part','chromosome_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_site','insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanyl_trna','phenylalanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_est_set','overlapping_est_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gc_rich_promoter_region','gc_rich_promoter_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_two','asx_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon_loop','anticodon_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_change_in_dna_sequence','partially_characterised_change_in_dna_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv5_motif','dmv5_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl1_acceptor_site','sl1_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_region','cds_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_c_cluster','v_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_insert','engineered_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_inverted_gene','recombinationally_inverted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_array_member','cassette_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microarray_oligo','microarray_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_snrna','u12_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_est_or_cdna','supported_by_est_or_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_10_signal','minus_10_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_end','clone_insert_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr_motif','inr_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_inactive_ligand_binding_site','sequence_variant_causing_inactive_ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_stem_loop_structure','three_prime_stem_loop_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_level_of_translation_product','sequence_variant_decreasing_level_of_translation_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rflp_fragment','rflp_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_rna_polymerase_promoter','phage_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_transition','pyrimidine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrinsically_unstructured_polypeptide_region','intrinsically_unstructured_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_2_prime_o_dimethylguanosine','n2_2_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeal_intron','archaeal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna','lna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_junction','exon_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t7_rna_polymerase_promoter','t7_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_interchromosomal_transposition','invert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('episome','episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_insertional_duplication','uninvert_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_difference','sequence_difference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_c_cluster','v_d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_conflict','sequence_conflict'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_gene_fusion','sequence_variant_causing_gene_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_clone','tiling_path_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iii_intron','group_iii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_glycine','modified_glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_alteration','sequence_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyploid','polyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_modification','gene_silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_cluster','v_vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine_trna_primary_transcript','isoleucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_small_subunit_primary_transcript','rrna_small_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_component','ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_framshift','plus_2_framshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid_trna_primary_transcript','glutamic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_rearranged_at_dna_level','gene_rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript','edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_partial_processing','invalidated_by_partial_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequencing_primer','sequencing_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_for_gpi_anchor_region','cleaved_for_gpi_anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift_sequence_variation','frameshift_sequence_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_cysteine','modified_l_cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr','five_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_site','frt_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat','terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transition','transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_junction','deletion_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_one','beta_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosylguanosine_phosphate','two_prime_o_ribosylguanosine_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyl_two_prime_o_methyluridine','five_cm_2_prime_o_methU'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_transcribed_spacer_region','internal_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic','dicistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_sequence_similarity','supported_by_sequence_similarity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_primer','reverse_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_three_prime_ltr_region','u3_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine_trna_primary_transcript','glutamine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_promoter','rnapol_ii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping','overlapping'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_beta_motif','alpha_beta_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_transposable_element','engineered_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward_primer','forward_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attctn_site','attctn_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_recombination_signal_sequence','five_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conservative_amino_acid_substitution','sequence_variant_causing_conservative_amino_acid_sub'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6_snrna','u6_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_gene','recombinationally_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_threonylcarbamoyladenosine','n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyluridine','five_carbamoylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_fragment','cds_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genome','genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter','promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_gene','protein_coding_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_snrna','u5_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wybutosine','wybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylwyosine','methylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('large_subunit_rrna','large_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_substitution','sequence_variant_causing_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_2_prime_o_dimethylcytidine','n4_2_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition','c_to_t_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_transcript_sequence','sequence_variation_affecting_transcript_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bidirectional_promoter','bidirectional_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_change_of_translational_product','seq_variant_causing_partly_characterised_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated_cdna_clone','validated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('k_turn_rna_motif','k_turn_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_fragment','transcribed_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ust','five_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr_intron','three_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrogene','retrogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_to_purine_transversion','pyrimidine_to_purine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sine_element','sine_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_rst','five_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding exon_coding_region','three_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_intron','utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_3d_structural_change','sequence_variant_causing_no_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_transposition','interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_sequence_secondary_structure','rna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element','engineered_foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_rna_viral_sequence','ds_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fosmid','fosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_substitution','complex_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated','validated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_snrna','u2_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('caat_signal','caat_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_cluster','c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_region','consensus_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_spacer','vertebrate_immune_system_gene_recombination_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_trap_construct','gene_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_aptamer','rna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_induced','transcriptionally_induced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_region','rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site_part','inversion_site_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('origin_of_replication','origin_of_replication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_out_of_frame_polypeptide_c_terminal_elongation','mutation_causing_out_of_frame_polypeptide_c_terminal_elong'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_internal_loop','rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ultracontig','ultracontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptidyl','peptidyl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_region','polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_insertion','transgenic_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_antiguide','mirna_antiguide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rearranged_at_dna_level','rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_spacer','v_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strand_attribute','strand_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_increasing_level_of_transcript','sequence_variation_increasing_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced','alternatively_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formyl_two_prime_o_methylcytidine','five_formyl_two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_location','plasmid_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_bp_start_codon','four_bp_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged','recombinationally_rearranged'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chimeric_cdna_clone','chimeric_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_transcript','gene_with_dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr_component','three_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retron','retron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autopolyploid','autopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine','phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transit_peptide','transit_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_28s','rrna_28s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylinosine','one_two_prime_o_dimethylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine','threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_minor_rna_motif','a_minor_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_cluster','j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_cluster','d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_activation','sequence_variant_causing_cryptic_splice_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_arm','chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast_gene','kinetoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('line_element','line_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('solo_ltr','solo_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('external_transcribed_spacer_region','external_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_transcribed_region','non_transcribed_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_stem','mirna_stem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_c_cluster','dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hyperploid','hyperploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic','cryptic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_helix','alpha_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion','fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_cluster','vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isowyosine','isowyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric_inversion','paracentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_inframe_polypeptide_n_terminal_elongation','mutation_causing_inframe_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homing_endonuclease_binding_site','homing_endonuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna_oligo','tna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_gene','mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_fragment','restriction_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_pair','base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_antiparallel','inside_intron_antiparallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcription','sequence_variant_affecting_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_binding_site','dna_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_cytidine','modified_cytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydrophobic_region_of_peptide','hydrophobic_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_primary_transcript','polycistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_proline','modified_l_proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_feature_set','overlapping_feature_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_two','asx_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_duplication','interchromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('substitution','substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine','isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_recoding_site','three_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_of_type_2_rnapol_iii_promoter','terminator_of_type_2_rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine_trna_primary_transcript','glycine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_polypeptide_c_terminal_elongation','mutation_causing_polypeptide_c_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_heptamer','v_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dispersed_repeat','dispersed_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer','primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_transcript','sequence_variation_affecting_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type','wild_type'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_domain','polypeptide_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_synonymous_codon_change_in_transcript','seq_variant_causing_synonymous_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion_gene','fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginyl_trna','arginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_member_region','gene_member_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_intrachromosomal_transposition','uninvert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_translational_product','sequence_variant_affecting_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_base_feature','methylated_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_gene','scrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_18s','rrna_18s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_elongation','sequence_variant_causing_polypeptide_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_1','rnapol_iii_promoter_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_mutation','point_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_3d_structure_of_polypeptide','sequence_variant_affecting_3d_structure_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudoknot','pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_quartet','g_quartet'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_selenocysteine','modified_l_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop','schellmann_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna','pna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon','three_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_gene','endogenous_retroviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_segment','vertebrate_immunoglobulin_t_cell_receptor_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_translational_bypass','mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_region','engineered_foreign_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_encoding','snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_est','five_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_encoding','srp_rna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foldback_element','foldback_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_c_cluster','d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_c_cluster','dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_encoding','rrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_codon_redefinition','mrna_recoded_by_codon_redefinition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyluridine','five_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('immature_peptide_region','immature_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous','homologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metabolic_island','metabolic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_sequence','polya_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sirna','sirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_attribute','sequence_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_intron','trna_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translationally_frameshifted','plus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_motif','nucleotide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_motif','dna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_noncoding_exon','five_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_strand','beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyladenosine','one_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_oligo','ds_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_motif','asx_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oxys_rna','oxys_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxyuridine','five_hydroxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formylcytidine','five_formylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translational_frameshift','plus_1_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_exon','coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliced_leader_rna','spliced_leader_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_2prirme_o_trimethylguanosine','n2_7_2prirme_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fragment','gene_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_chromosome','mitochondrial_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyldihydrouridine','five_methyldihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide_cleavage_site','propeptide_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift','frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid','amino_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_breakpoint','translocation_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_compensatory_transcript_secondary_structure_mutation','seq_variant_caus_compensatory_trans_secondary_structure_mut'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helix_turn_helix','helix_turn_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5_8s','rrna_5_8s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('simple_sequence_length_variation','simple_sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine','methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_gene','transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_island','genomic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_segment','gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_gene','snrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_region','engineered_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptogene','cryptogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_noncoding_region','three_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_rna_interference','gene_silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_interchromosomal_transposition','d_interchr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_variant_site','natural_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly','assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_minus_2_frameshift','sequence_variant_causing_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('major_tss','major_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_missense_codon_change_in_transcript','sequence_variant_causing_missense_codon_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna','trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides','encodes_overlapping_peptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_conserved_region','nc_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('locus_control_region','locus_control_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna_oligo','s_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_chromosome','dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_b','beta_turn_type_six_b'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_gene','engineered_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wobble_base_pair','wobble_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_amino_acid_feature','modified_amino_acid_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_c_transition','t_to_c_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_sequence','apicoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irlinv_site','irlinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_sequence','synthetic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_1_polypeptide','encodes_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_transcript_stability','sequence_variant_decreasing_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iia_intron','group_iia_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomere','telomere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_intron','interior_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_mrna','edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_three','catmat_right_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_effect','sequence_variant_effect'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_duplication','tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_gene','tmrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_region','pre_edited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_hydroxynorvalylcarbamoyladenosine','n6_hydroxynorvalylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_chromosome','nucleomorphic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragmentary','fragmentary'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single','single'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('binding_site','binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanine','seven_methylguanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('target_site_duplication','target_site_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_gene','vdj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_loss_of_function_of_polypeptide','sequence_variant_causing_loss_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_nucleic_acid','bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_four','catmat_right_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome','compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_end','coding_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gap','gap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_aug_codon','upstream_aug_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_transcript','pseudogenic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('satellite_dna','satellite_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency_plus_duplication','assortment_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element','transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_sequence','endogenous_retroviral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_level_of_transcript','sequence_variation_affecting_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microsatellite','microsatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_different_polypeptides_different_stop','encodes_different_polypeptides_different_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript','primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_mrna','consensus_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_peptide_loop','membrane_peptide_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_complex_3d_structural_change','sequence_variant_causing_complex_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign','so_foreign'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_deletion','nucleotide_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_independent_bacterial_terminator','rho_independent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_deacetylation','gene_silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_c_cluster','vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cpg_island','cpg_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype','haplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylinosine','two_prime_o_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna','dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_rna_chromosome','circular_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_protein_region','mature_protein_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('b_box','b_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_zinc_ion_contact_site','polypeptide_zinc_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray_member','gene_subarray_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette','gene_cassette'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oric','oric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_breakpoint','deletion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_2_frameshift','mrna_with_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_one','asx_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_cluster','transcribed_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_decreasing_level_of_transcript','sequence_variation_decreasing_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosyl_trna','tyrosyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous','orthologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna','s_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_three_prime_splice_site','canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_exon','noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minor_tss','minor_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethylcytidine','five_two_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_chromosome','macronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_translocation','deficient_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read_pair','read_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_with_translational_frameshift','transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_3','rnapol_iii_promoter_type_3'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_transposon','dna_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orf','orf'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('right_handed_peptide_helix','right_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_left_right_motif','polypeptide_nest_left_right_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splice_donor','sequence_variant_affecting_splice_donor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topology_attribute','topology_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirtron','mirtron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_motif','polypeptide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_sequence','proplastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated_gene','negatively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_base_site','modified_base_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_encoding','c_d_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_assembly','sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bre_motif','bre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_gene','chromoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_clip','five_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path','golden_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine','alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_peptide_region','cleaved_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_cluster','v_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_region','pseudogenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna','methylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_c_cluster','v_vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_start_codon','non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_recoded_by_translational_bypass','gene_with_mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_turn_motif','polypeptide_turn_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autocatalytically_spliced_intron','autocatalytically_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile','mobile'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron','intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clip','clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dye_terminator_read','dye_terminator_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('argenine','argenine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv4_motif','dmv4_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_post_translational_processing_change','seq_variant_causing_polypeptide_post_trans_processing_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('au_rich_element','au_rich_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_breakpoint','inversion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_recoding_site','five_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_protein_coding','non_protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_intron','mobile_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment','vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_one','st_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna','rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_parallel','inside_intron_parallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron','spliceosomal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phagemid','phagemid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_block','editing_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragment_assembly','fragment_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_acceptor_piece','tmrna_acceptor_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six','beta_turn_type_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_rst','three_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine_trna_primary_transcript','cysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_gene','post_translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_repressed','transcriptionally_repressed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crm','crm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cointegrated_plasmid','cointegrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequencing_information','polypeptide_sequencing_information'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_spacer','three_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_fragment','tiling_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural','so_natural'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pi_helix','pi_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_base_call_error','possible_base_call_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('adaptive_island','adaptive_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid','uridine_five_oxyacetic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_translational_frameshift','plus_2_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous_region','homologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_utr','internal_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_level_of_translational_product','sequence_variant_affecting_level_of_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_cytoplasmic_polypeptide_region','non_cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature','experimental_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_chromosome','nuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar','exemplar'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine_trna_primary_transcript','alanine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_dimethylguanosine','n2_n2_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_hook_turn','rna_hook_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_spacer_region','transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_gene','plasmid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna','u14_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('galactosyl_queuosine','galactosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_gene','cyanelle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type_rescue_gene','wild_type_rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_intron','u12_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aptamer','aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_mrna','recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_sequence','macronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust','ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine','selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_mrna','gene_with_dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match_part','match_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_sequence','nucleomorphic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_gene','apicoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulon','regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_vector','plasmid_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tryptophan','modified_l_tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_coding_codon_change_in_transcript','seq_variant_causing_amino_acid_coding_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_chromosome_arm','free_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_primary_transcript','srp_rna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn','asx_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_binding_site','anchor_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript','rrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reading_frame','reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dhu_loop','dhu_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetylcytidine','n4_acetylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polypeptide_function','sequence_variant_affecting_polypeptide_function'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_gene','silenced_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_genomic_insert','cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_sequence_secondary_structure','dna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_match','cdna_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_flanking_region','five_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysyl_trna','pyrrolysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_cis_hydroxyisopentenyl_adenosine','two_methylthio_n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_component','repeat_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyl_three_three_amino_three_carboxypropyl_pseudouridine','one_methyl_3_3_amino_three_carboxypropyl_pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rpra_rna','rpra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_sensitive_site','nuclease_sensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_noncoding_region','five_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter','rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan_trna_primary_transcript','try_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('region','region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site','tf_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attl_site','attl_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_plasmid','natural_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_dimethyladenosine','n6_n6_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('laevosynaptic_chromosome','laevosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_structural_element','chromosomal_structural_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_array','gene_cassette_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_gene_cluster','vertebrate_immunoglobulin_t_cell_receptor_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_five_prime_splice_site','canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_protein','bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts_map','sts_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnazyme','dnazyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silent_mutation','silent_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_cluster','v_d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_duplication','bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydroxywybutosine','hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dihydrouridine','dihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_rate_of_transcription','sequence_variant_affecting_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_coding_region','five_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_one','beta_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_codon','recoded_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted','predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('resolution_site','resolution_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_cyano_seven_deazaguanosine','seven_cyano_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conformational_change','sequence_variant_causing_conformational_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_switch','conformational_switch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulated','regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_repeat','inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_a_transversion','t_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attc_site','attc_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methyladenosine','two_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cross_genome_match','cross_genome_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_repeat','tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_primary_transcript','antisense_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polyadenylation','sequence_variant_affecting_polyadenylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_collection','sequence_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polyadenylated_mrna','gene_with_polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_i_promoter','rnapol_i_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methyluridine','three_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('start_codon','start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposon','retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene','v_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_dna','chloroplast_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negative_sense_ssrna_viral_sequence','negative_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_binding_site','primer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_box','c_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid','plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biological_region','biological_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_a_transition','g_to_a_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_five_prime_splice_site','non_canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_primary_transcript','c_d_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_region','trna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_change_in_nucleotide_sequence','uncharacterised_change_in_nucleotide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_cis_hydroxyisopentenyl_adenosine','n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_sequence','chloroplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_region','exon_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_five_prime_ltr_region','r_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_c_cluster','v_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_three_prime_ltr_region','r_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna','snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylinosine','one_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene_recombination_feature','j_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_motif','polypeptide_structural_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved_region','conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('remark','remark'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_dna_contact','polypeptide_dna_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon','codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_23s','rrna_23s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna','mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycyl_trna','glycyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_sequence','cyanelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_independently_known','cds_independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator','insulator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positive_sense_ssrna_viral_sequence','positive_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_match','expressed_sequence_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_assembly_error','possible_assembly_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_snorna','u3_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unorientated_interchromosomal_transposition','unorient_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_manganese_ion_contact_site','polypeptide_manganese_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_t_transversion','g_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature_of_rearranged_gene','recombination_feature_of_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_primary_transcript','tmrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_cdna','single_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_determined','experimentally_determined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_exon','pseudogenic_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_intron','u2_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome','chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternately_spliced_transcripts','encodes_alternately_spliced_transcripts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aberrant_processed_transcript','aberrant_processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna','gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dsra_rna','dsra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_domain','intron_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_predicted','cds_predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_asparagine','modified_l_asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_nonamer','five_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl2_acceptor_site','sl2_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_primary_transcript','snrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation','translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_phenylalanine','modified_l_phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna','lincrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_valine','modified_l_valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac','yac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('signal_peptide','signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_ltr_region','r_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_gene','srp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcript_processing','sequence_variant_affecting_transcript_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_hotspot','recombination_hotspot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_c_cluster','v_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('viral_sequence','viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_terminal_inverted_repeat','five_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_thiouridine','five_mcm_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited','edited'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_start','coding_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr','three_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe1_motif','dpe1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tyrosine','modified_l_tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_c_cluster','v_d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unorientated_intrachromosomal_transposition','unorient_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_methylation','silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_inversion','deficient_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiouridine','two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thio_two_prime_o_methyluridine','two_thio_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_sequence','leucoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds','cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_polypeptide_n_terminal_elongation','mutation_causing_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_signal_sequence','polya_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_sequence','micronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamyl_trna','glutamyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_gene','strna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted_gene','paternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_chromosome','rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm3_motif','ndm3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u1_snrna','u1_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxymethylcytidine','five_hydroxymethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature','recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_disjoint_polypeptides','encodes_disjoint_polypeptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated','post_translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_fusion_gene','engineered_fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_recombination_signal_sequence','three_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causes_exon_loss','sequence_variant_causes_exon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate','intermediate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_calcium_ion_contact_site','polypeptide_calcium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic_region','syntenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sugar_edge_base_pair','sugar_edge_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_gene','engineered_foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetyl_2_prime_o_methylcytidine','n4_acetyl_2_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_by_ab_initio_computation','predicted_by_ab_initio_computation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_secondary_structure','polypeptide_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna_gene','ncrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_junction_loop','rna_junction_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype_block','haplotype_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oriv','oriv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ambisense_ssrna_viral_sequence','ambisense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_oligo','morpholino_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere','centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_gene','epigenetically_modified_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_inversion','chromosomal_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_35_signal','minus_35_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_two_prime_o_dimethyluridine','three_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_thiouridine','four_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_end_site','transcription_end_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_mirna','pre_mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteinyl_trna','cysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_three','catmat_left_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_seven','schellmann_loop_seven'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_c_cluster','v_vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_insertion_site','transposable_element_insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_element','translocation_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript_region','mirna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan_cds','orphan_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_mrna','monocistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_transposable_element','natural_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path_fragment','golden_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lipoprotein_signal_peptide','lipoprotein_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_large_subunit_primary_transcript','rrna_large_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_rna_chromosome','linear_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_rate_of_transcription','sequence_variant_increasing_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_sequence','plastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irrinv_site','irrinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_plasmid','integrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_methionine','modified_l_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_sequence','chromoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_rna_chromosome','linear_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_trap_construct','promoter_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_read','contig_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanosine','seven_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_selenocysteine','stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn','gamma_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionyl_trna','methionyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna','tmrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna','cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_binding_site','nuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid_methyl_ester','uridine_five_oxyacetic_acid_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_race_clone','three_prime_race_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_dna_chromosome','circular_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_histidine','modified_l_histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss_region','tss_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated_gene','positively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus','consensus'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integron','integron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_metal_contact','polypeptide_metal_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_loop','d_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decayed_exon','decayed_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_inosine','modified_inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_three_prime_overlap','three_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_five_prime_overlap','three_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_cluster','v_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop','beta_bulge_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_mutation','intrachromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv2_motif','dmv2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_region','intergenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_glycinylcarbamoyladenosine','n6_glycinylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_feature','sequence_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_rna','antisense_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_cis_splice_site','three_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_classic','gamma_turn_classic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rapd','rapd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cca_tail','cca_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_ring_chromosome','inverted_ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_dna_chromosome','linear_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_g_transversion','t_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bruno_response_element','bruno_response_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_five_prime_ltr_region','u5_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_a_transversion','c_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distant_three_prime_recoding_signal','distant_three_prime_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronucleus_destined_segment','macronucleus_destined_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_mrna','pre_edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac','pac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base','base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_mrna','polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_redefined','codon_redefined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_prime_o_methyluridine','five_methoxycarbonylmethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match','match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_read_through','gene_with_stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparaginyl_trna','asparaginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonyl_trna','threonyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_five_prime_ltr_region','u3_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr','five_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_gene','vj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_methylguanosine','n2_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_dependent_bacterial_terminator','rho_dependent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_flanking_region','three_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomically_contaminated_cdna_clone','genomically_contaminated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_target_site','mirna_target_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_guide_sequence','internal_guide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_three_prime_ltr_region','u5_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_out_of_frame_polypeptide_n_terminal_elongation','mutation_causing_out_of_frame_polypeptide_n_terminal_elong'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('undermodified_hydroxywybutosine','undermodified_hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('introgressed_chromosome_region','introgressed_chromosome_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_frameshifted','translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_deletion','chromosomal_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine','leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna_primary_transcript','methylation_guide_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced','trans_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_uridine','five_isopentenylaminomethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_threonyl_carbamoyladenosine','two_methylthio_n6_threonyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon','stop_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_change_of_translational_product','sequence_variant_causing_no_change_of_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biochemical_region_of_peptide','biochemical_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interband','interband'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert','clone_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_constraint_sequence','dna_constraint_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snp','snp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_chromosome','chromoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tata_box','tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_25s','rrna_25s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_gene','plastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_one','asx_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_transcript_stability','sequence_variant_increasing_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_uridine','modified_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysyl_trna','lysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intramembrane_polypeptide_region','intramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rr_tract','rr_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript_region','rrna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced_transcript','alternatively_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_dna_viral_sequence','ds_dna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_duplication','chromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_encoding','scrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_copper_ion_contact_site','polypeptide_copper_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_isoleucine','modified_l_isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone','clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hetero_compound_chromosome','hetero_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray','gene_subarray'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_transcript','dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_methylation','silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_change_in_transcript','seq_variant_causing_partly_characterised_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_loop','t_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_serine','modified_l_serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiocytidine','two_thiocytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_repeat_recoding_signal','three_prime_repeat_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna','srp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_binding_motif','polypeptide_binding_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylguanosine','two_prime_o_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_truncation','sequence_variant_causing_polypeptide_truncation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box','a_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_vertebrate_immune_system_gene','recombinationally_rearranged_vertebrate_immune_system_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylguanosine','one_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamine','modified_l_glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant','sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_length_variation','sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_encoding','strna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift','plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topologically_defined_region','topologically_defined_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_cds','edited_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_modification','gene_silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('e_box_motif','e_box_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_subunit_rrna','small_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnasei_hypersensitive_site','dnasei_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_c_cluster','v_d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome_arm','compound_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('feature_attribute','feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_match','protein_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splicing','sequence_variant_affecting_splicing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_variation','chromosome_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_motif','serine_threonine_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded','allelically_excluded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_aneuploid','assortment_derived_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino','morpholino'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_prime_o_methyluridine','five_isopentenylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna_oligo','gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_variation','copy_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced','silenced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylcytidine','three_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dexstrosynaptic_chromosome','dexstrosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_insertional_duplication','inverted_insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_mini_gene','rescue_mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_four','catmat_left_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternate_sequence_site','alternate_sequence_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_iron_ion_contact_site','polypeptide_iron_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition_at_pcpg_site','c_to_t_transition_at_pcpg_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_molybdenum_ion_contact_site','polypeptide_molybdenum_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine_trna_primary_transcript','phe_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_primary_transcript','h_aca_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna','r_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_transposition','intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_localization_change','sequence_variant_causing_polypeptide_localization_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_a','methylated_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_16s','rrna_16s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_methylcytidine','n4_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('riboswitch','riboswitch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_duplication','assortment_derived_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_regulatory_element','chromosomal_regulatory_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_3d_structural_change','seq_var_causing_partly_characterised_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_five_prime_overlap','five_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozymic','ribozymic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_deficiency','inversion_derived_bipartite_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_contamination','invalidated_by_genomic_contamination'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_cluster','vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_change_of_translational_product','sequence_variant_causing_uncharacterised_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_number_variation','chromosome_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_attribute','gene_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uag_stop_codon_signal','uag_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_match','nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified','epigenetically_modified'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_two','st_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_duplication','inversion_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_selenouridine','five_methylaminomethyl_two_selenouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid_trna_primary_transcript','aspartic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_mt_pseudogene','nuclear_mt_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exonic_splice_enhancer','exonic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4_snrna','u4_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('csrb_rsmb_rna','csrb_rsmb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_1_intron_homing_endonuclease_target_region','group_1_intron_homing_endonuclease_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crispr','crispr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_change_in_transcript','sequence_variant_causing_no_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_gene','snorna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_junction','trans_splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_three_prime_quadruplet_recoding_signal','flanking_three_prime_quadruplet_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_cluster','v_vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_pseudogene','cassette_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_modification','silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_gene','proviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine','five_carboxyhydroxymethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mt_gene','mt_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_rna_chromosome','single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_stimulatory_region','recoding_stimulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyluridine','five_taurinomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_threonine','modified_l_threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_cluster','v_d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_oligo','synthetic_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_to_pyrimidine_transversion','purine_to_pyrimidine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonsense_codon_change_in_transcript','sequence_variant_causing_nonsense_codon_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antiparallel_beta_strand','antiparallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('central_hydrophobic_region_of_signal_peptide','central_hydrophobic_region_of_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_mobile_genetic_element','integrated_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('parallel_beta_strand','parallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_cluster','v_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dre_motif','dre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon','non_ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna_oligo','r_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autoregulated','autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_lysine','modified_l_lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_end','bac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine','pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine','lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_protein_contact','protein_protein_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site','splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_translocation','chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epitope','epitope'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allele','allele'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_n4_2_prime_o_trimethylcytidine','n4_n4_2_prime_o_trimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_ltr_region','u5_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_gene','rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_transposable_element','transgenic_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_region','polypeptide_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts','sts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_c_transversion','a_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_ii_rna','class_ii_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nonamer_of_recombination_feature_of_vertebrate_immune_system_gene','nonamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unedited_region','unedited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_level_of_translation_product','sequence_variant_increasing_level_of_translation_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lambda_vector','lambda_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene','gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanyl_trna','alanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('virtual_sequence','virtual_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iib_intron','group_iib_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposed','retrotransposed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_2_frameshift','mrna_with_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymer_attribute','polymer_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autosynaptic_chromosome','autosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_helix','peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_processed_cdna_clone','partially_processed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst_match','rst_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted','paternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_gene','predicted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('robertsonian_fusion','robertsonian_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylpseudouridine','two_prime_o_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric_inversion','pericentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartyl_trna','aspartyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna','strna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_intron','three_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear','linear'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_nonamer','j_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_t_transversion','a_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('idna','idna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_7_trimethylguanosine','n2_n2_7_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_chromosomal_mutation','complex_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_aneuploid','inversion_derived_deficiency_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asymmetric_rna_internal_loop','asymmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion','deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyclic_translocation','cyclic_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ars','ars'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutaminyl_trna','glutaminyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allopolyploid','allopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replicon','replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylcytidine','two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_one','st_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous_region','paralogous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript_region','mature_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_frameshift','mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_cluster','d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle_gene','maxicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_two','st_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_encoding','snrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_spacer','five_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read','read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine_trna_primary_transcript','arg_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo_u_tail','oligo_u_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_pseudoknot','recoding_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_thiouridine','five_mam_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic','monocistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frame_restoring_sequence_variant','frame_restoring_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transmembrane_polypeptide_region','transmembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vector_replicon','vector_replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrosequenced_read','pyrosequenced_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_magnesium_ion_contact_site','polypeptide_magnesium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_transcript','polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_site','polya_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_duplication','free_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_structure_variation','chromosome_structure_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_rna_base_feature','modified_rna_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutated_variant_site','mutated_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gaga_motif','gaga_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_mutation','interchromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prophage','prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic','syntenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_repetitive_element','engineered_foreign_repetitive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translated_nucleotide_match','translated_nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna','h_aca_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vault_rna','vault_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan','orphan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_dna_chromosome','linear_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_greater_than_1_polypeptide','encodes_greater_than_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('atti_site','atti_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_deacetylation','silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reagent','reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_fission','chromosome_fission'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ct_gene','ct_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_primary_transcript','capped_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_initiator_codon_change_in_transcript','sequence_variant_causing_initiator_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylinosine','methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_spacer','j_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine','glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_guanosine','modified_guanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_dimethylguanosine','n2_7_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonconservative_amino_acid_substitution','sequence_variant_causing_nonconservative_amino_acid_sub'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_heptamer','three_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_cdna_clone','invalidated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator','terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stem_loop','stem_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr_intron','five_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_plus_2_frameshift','sequence_variant_causing_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_band','chromosome_band'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_exon_donor_rna','mini_exon_donor_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid','aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyl_2_thiouridine','five_methyl_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_methylation','gene_silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element_gene','engineered_foreign_transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_pseudogene','processed_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supercontig','supercontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_encoding','trna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal_chromosomal_translocation','reciprocal_chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hoogsteen_base_pair','hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_transition','purine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna','c_d_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_primary_transcript','snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_cluster','v_vj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_ltr_region','u3_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attenuator','attenuator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_noncoding_exon','three_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna_primary_transcript','u14_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene_recombination_feature','d_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mte','mte'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_coding_sequence','sequence_variation_affecting_coding_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gcvb_rna','gcvb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst','rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operator','operator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ring_chromosome','ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm2_motif','ndm2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine_trna_primary_transcript','selenocysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_feature','edited_transcript_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_pyrrolysine','stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homo_compound_chromosome','homo_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_gene','foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_demethylwyosine','four_demethylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna','guide_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylpseudouridine','three_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_aneuploid_chromosome','inversion_derived_aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('specific_recombination_site','specific_recombination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inosine','inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_transposable_element','foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene','d_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_inversion','bipartite_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_plasmid','engineered_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group_regulatory_region','gene_group_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vd_gene','vd_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region','regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_rate_of_transcription','sequence_variant_decreasing_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna_region','guide_rna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence variant_affecting_transcript_stability','sequence_variant_affecting_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_ten_helix','three_ten_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sarcin_like_rna_motif','sarcin_like_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_translationally_frameshifted','minus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_alanine','modified_l_alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_deletion','sequence_variant_causing_amino_acid_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_cum_translocation','inversion_cum_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tag','tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_interchromosomal_transposition','uninvert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_gene','cryptic_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic','transgenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_clone','genomic_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakage_sequence','chromosome_breakage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_cluster','d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_one','beta_turn_type_six_a_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribosome_entry_site','ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('left_handed_peptide_helix','left_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_aptamer','dna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('i_motif','i_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_intrachromosomal_transposition','d_intrachr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_dna_chromosome','single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_c','methylated_c'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligation_based_read','ligation_based_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_assembly','expressed_sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethyluridine','five_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine_trna_primary_transcript','histidine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous_region','orthologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine_trna_primary_transcript','valine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon_member','operon_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group','gene_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposition','transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_regulatory_ncrna','small_regulatory_ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_duplication','intrachromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uaa_stop_codon_signal','uaa_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift','minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('organelle_sequence','organelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_prophage','cryptic_prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micf_rna','micf_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_tandem_duplication','direct_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved','conserved'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna','telomerase_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6atac_snrna','u6atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attb_site','attb_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array_member','gene_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated_mrna','polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symbiosis_island','symbiosis_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_junction','splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fingerprint_map','fingerprint_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wyosine','wyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uga_stop_codon_signal','uga_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cytoplasmic_polypeptide_region','cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylguanosine','one_two_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rh_map','rh_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_modification','silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon','anticodon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_deazaguanosine','seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine','asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('probe','probe'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('defective_conjugative_transposon','defective_conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeosine','archaeosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('molecular_contact_region','molecular_contact_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_structure','membrane_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_collection','contig_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetraloop','tetraloop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_conserved_region','coding_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('long_terminal_repeat','long_terminal_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_signal_feature','vertebrate_immune_system_gene_recombination_signal_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('untranslated_region_polycistronic_mrna','untranslated_region_polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine_trna_primary_transcript','leucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_dna_chromosome','circular_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucyl_trna','isoleucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_breakpoint','insertion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgene','transgene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_region','mrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_attribute','transcript_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_staple_motif','serine_threonine_staple_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding','protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_bound_by_factor','enhancer_bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_by_translational_bypass','recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon','operon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_transcript','monocistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_insertion','sequence_variant_causing_amino_acid_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated','polyadenylated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unigene_cluster','unigene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_gene_cluster','vertebrate_ig_t_cell_receptor_rearranged_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_member','gene_cassette_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_read_through','stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_transcript_with_translational_frameshift','gene_with_transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mnp','mnp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid','glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polypeptide_amino_acid_sequence','sequence_variant_affecting_polypeptide_amino_acid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn','beta_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pathogenic_island','pathogenic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust_match','ust_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conservative_missense_codon_change_in_transcript','seq_var_causing_conservative_missense_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_protein','transcript_bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyladenosine','n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_chromosome','cyanelle_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orit','orit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted','maternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_chromosome','chloroplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle_gene','minicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_catalytic_motif','polypeptide_catalytic_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_2','rnapol_iii_promoter_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('no_output','no_output'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_coding_exon','interior_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyl_two_thiouridine','five_taurinomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide','polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymerase_synthesis_read','polymerase_synthesis_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_binding_site','enhancer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_two','beta_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_polya_primed_cdna','invalidated_by_genomic_polya_primed_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_edited_transcript','gene_with_edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv1_motif','dmv1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_modified_region','post_translationally_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline','proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_region','flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_isopentenyladenosine','two_methylthio_n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypyrimidine_tract','polypyrimidine_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxyuridine','five_methoxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_to_gene_feature','gene_to_gene_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_cloned_genomic_insert','bac_cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_heptamer','j_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ust','three_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_2_prime_o_dimethyladenosine','n6_2_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_site','trans_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_rescue_region','engineered_rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorph_gene','nucleomorph_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_attribute','mrna_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_three_prime_overlap','five_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_i_intron','group_i_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_cluster','d_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_dna','genomic_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron','inside_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hammerhead_ribozyme','hammerhead_ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_heptamer','five_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_splice_enhancer','intronic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_adenosine','modified_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyluridine','five_carboxymethylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_region','repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_unit','repeat_unit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_dna_chromosome','double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('template_region','template_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript_region','primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_dna','mitochondrial_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_region','transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozyme','ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('matrix_attachment_site','matrix_attachment_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('imprinted','imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est','est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_motif','rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_variation_site','polypeptide_variation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_i_rna','class_i_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo','oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_signal','stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hypoploid','hypoploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar_mrna','exemplar_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_g_transversion','c_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('active_peptide','active_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mannosyl_queuosine','mannosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_pyrrolysine','gene_with_stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('queuosine','queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna_oligo','lna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('independently_known','independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causes_intron_gain','sequence_variant_causes_intron_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_region','proviral_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped','capped'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direction_attribute','direction_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_chromosome','micronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene_by_unequal_crossing_over','pseudogene_by_unequal_crossing_over'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethyladenosine','one_two_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe_motif','dpe_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seryl_trna','seryl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integration_excision_site','integration_excision_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_region_of_exon','noncoding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna','rnase_mrp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyluridine','five_methoxycarbonylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_of_single_exon_gene','exon_of_single_exon_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_primary_transcript','gene_with_dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_secondary_structure','sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path','tiling_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_sequence','nuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig','contig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catalytic_residue','catalytic_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site','inversion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid','aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dif_site','dif_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_gene','mirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valyl_trna','valyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_tandem_duplication','inverted_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_regulatory_frameshift_element','cis_regulatory_frameshift_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minisatellite','minisatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_component','assembly_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity_region','low_complexity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('designed_sequence','designed_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_2_prime_o_trimethyladenosine','n6_n6_2_prime_o_trimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_promoter','rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene_recombination_feature','v_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_thiouridine','five_carboxymethylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_ring_duplication','free_ring_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_mrna','dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_chromosomal_mutation','uncharacterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_cis_splice_site','five_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('octamer_motif','octamer_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides_different_start','encodes_overlapping_peptides_different_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_rna_viral_sequence','ss_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('indel','indel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_primary_transcript','dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_binding_site','protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic','polycistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine_trna_primary_transcript','asparagine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_enhancer','splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid_chromosome','aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peroxywybutosine','peroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_aspartic_acid','modified_l_aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_episome','engineered_episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnai_reagent','rnai_reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rasirna','rasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_region','tmrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_gain_of_function_of_polypeptide','sequence_variant_causing_gain_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter','bacterial_rnapol_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_sequence','mitochondrial_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trinucleotide_repeat_microsatellite_feature','trinuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_stability','post_translationally_regulated_by_protein_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_primary_transcript','nc_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_donor_activation','sequence_variant_causing_cryptic_splice_donor_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('iron_responsive_element','iron_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_cluster','v_d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward','forward'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_location','proviral_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_binding_site','histone_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pse_motif','pse_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_eight','beta_turn_type_eight'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double','double'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonconservative_missense_codon_change_in_transcript','seq_var_causing_nonconserv_missense_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_complex_change_of_translational_product','sequence_variant_causing_complex_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_est_or_cdna_data','cds_supported_by_est_or_cdna_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_rna_chromosome','double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamic_acid','modified_l_glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_motif','polypeptide_nest_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_frameshift','translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_terminal_inverted_repeat','three_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_trna','pseudogenic_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cap','cap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon','five_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic','enzymatic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_exon','interior_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_g_transition','a_to_g_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_inactive_catalytic_site','sequence_variant_causing_inactive_catalytic_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine','two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted_gene','maternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_terminator_codon_change_in_transcript','sequence_variant_causing_terminator_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular','circular'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_pseudoknot','h_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript','transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene','pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_duplication','nucleotide_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_repeat','direct_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_terminator','bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('diplotype','diplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_3d_structural_change','seq_variant_causing_uncharacterised_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_gene','dj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyladenosine','two_prime_o_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_plus_1_frameshift_mutation','sequence_variant_causing_plus_1_frameshift_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_binding_site','restriction_enzyme_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac','bac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_cluster','dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_donor_site','trans_splice_donor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleic_acid','nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_chimeric_cdna','invalidated_by_chimeric_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine','histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_component_region','gene_component_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_match','primer_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_primary_transcript','trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loxp_site','loxp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine','serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide','propeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_open_reading_frame','five_prime_open_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_six','schellmann_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shine_dalgarno_sequence','shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sp6_rna_polymerase_promoter','sp6_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_editing','sequence_variant_affecting_editing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_regulatory_region','sequence_variant_affecting_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine_trna_primary_transcript','lysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_c_cluster','j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency','assortment_derived_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript','mirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5s','rrna_5s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucyl_trna','leucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_intrachromosomal_transposition','invert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic_rna','enzymatic_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated','negatively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_region','anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon','exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a','beta_turn_type_six_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('random_sequence','random_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_chromosomal_mutation','partially_characterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna','rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcript_secondary_structure','sequence_variant_affecting_transcript_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_oligo','ss_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_duplication_plus_aneuploid','inversion_derived_duplication_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_nucleic_acid','transcript_bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein_containing','intein_containing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_encoding','h_aca_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_rna','rrna_cleavage_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_trap_construct','enhancer_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_change_in_transcript','seq_variant_causing_uncharacterised_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_inverse','gamma_turn_inverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_nonamer','three_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteinyl_trna','selenocysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_methylation','gene_silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u11_snrna','u11_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna','scrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_copy_number','sequence_variant_affecting_copy_number'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_selenocysteine','gene_with_stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silencer','silencer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sage_tag','sage_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_1_frameshift','mrna_with_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_gene','nuclear_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_domain_match_data','cds_supported_by_domain_match_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_shine_dalgarno_sequence','internal_shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prolyl_trna','prolyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysidine','lysidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge','beta_bulge'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_modification','post_translationally_regulated_by_protein_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna','ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_gene','grna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer','enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_sequence_variant','polymorphic_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_clip','three_prime_clip'); CREATE INDEX sequence_cv_lookup_table_idx ON sequence_cv_lookup_table (original_cvterm_name); SET search_path=public,pg_catalog; -- DEPENDENCY: -- chado/modules/bridges/sofa-bridge.sql -- The standard Chado pattern for protein coding genes -- is a feature of type 'gene' with 'mRNA' features as parts -- REQUIRES: 'mrna' view from so-bridge.sql CREATE OR REPLACE VIEW protein_coding_gene AS SELECT DISTINCT gene.* FROM feature AS gene INNER JOIN feature_relationship AS fr ON (gene.feature_id=fr.object_id) INNER JOIN so.mrna ON (mrna.feature_id=fr.subject_id); -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE SCHEMA frange; SET search_path = frange,public,pg_catalog; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public,pg_catalog; --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from general -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id int not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'cvterm' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id --SELECT feature_id, 'expression' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.expression_id = s.expression_id --UNION ALL --SELECT fg.feature_id, 'genotype' AS type, g.uniquename||': '||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE g.gcontext_id = fg.gcontext_id --UNION ALL --SELECT feature_id, 'genotype' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.genotype_id = s.genotype_id --UNION ALL --SELECT feature_id, 'phenotype' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.phenotype_id = s.phenotype_id UNION ALL SELECT feature_id, 'synonym' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of') UNION ALL SELECT fr.subject_id as feature_id, 'Derived_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from') UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; --replaced with Rob B's improved view CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''cvterm'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id --UNION --SELECT feature_id, ''expression'' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id --UNION --SELECT fg.feature_id, ''genotype'' AS type, g.uniquename||'': ''||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id --UNION --SELECT feature_id, ''genotype'' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id --UNION --SELECT feature_id, ''phenotype'' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id UNION SELECT feature_id, ''synonym'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255),organism_id integer -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); chado-1.23/schemas/1.1-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016533 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.22/diff.sql000644 000765 000024 00000000000 11661243501 016512 0ustar00cainstaff000000 000000 chado-1.23/schemas/1.1-1.21/diff.sql000644 000765 000024 00000065732 11660531775 016554 0ustar00cainstaff000000 000000 create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1.1-1.2/diff.sql000644 000765 000024 00000065732 11627534717 016475 0ustar00cainstaff000000 000000 create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1.1/default_schema.sql000644 000765 000024 00007167677 11554343216 020244 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $1; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) ); SET search_path = public,pg_catalog; -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql'; -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); --function to 'unshare' exons. It looks for exons that have the same fmin --and fmax and belong to the same gene and only keeps one. The other, --redundant exons are marked obsolete in the feature table. Nothing --is done with those features' entries in the featureprop, feature_dbxref, --feature_pub, or feature_cvterm tables. For the moment, I'm assuming --that any annotations that they have when this script is run are --identical to their non-obsoleted doppelgangers. If that's not the case, --they could be merged via query. -- --The bulk of this code was contributed by Robin Houston at --GeneDB/Sanger Centre. CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; /* Choose one of the shared exons to be the canonical representative. We pick the one with the smallest feature_id. */ CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; --This is an automatically generated file; do not edit it as changes will not --be saved. Instead, modify bin/create-so-bridge.pl, which creates this file. CREATE SCHEMA so; SET search_path=so,public,pg_catalog; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent greate *** --- *** r than zero. A nucleotide region is comp *** --- *** osed of bases and a polypeptide region i *** --- *** s composed of amino acids. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region'; --- ************************************************ --- *** relation: sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded sequence. *** --- ************************************************ --- CREATE VIEW sequence_secondary_structure AS SELECT feature_id AS sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure'; --- ************************************************ --- *** relation: g_quartet *** --- *** relation type: VIEW *** --- *** *** --- *** G-quartets are unusual nucleic acid stru *** --- *** ctures consisting of a planar arrangemen *** --- *** t where each guanine is hydrogen bonded *** --- *** by hoogsteen pairing to another guanine *** --- *** in the quartet. *** --- ************************************************ --- CREATE VIEW g_quartet AS SELECT feature_id AS g_quartet_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet'; --- ************************************************ --- *** relation: interior_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_coding_exon AS SELECT feature_id AS interior_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon'; --- ************************************************ --- *** relation: satellite_dna *** --- *** relation type: VIEW *** --- *** *** --- *** The many tandem repeats (identical or re *** --- *** lated) of a short basic repeating unit; *** --- *** many have a base composition or other pr *** --- *** operty different from the genome average *** --- *** that allows them to be separated from t *** --- *** he bulk (main band) genomic DNA. *** --- ************************************************ --- CREATE VIEW satellite_dna AS SELECT feature_id AS satellite_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A pair of sequencing reads in which the *** --- *** two members of the pair are related by o *** --- *** riginating at either end of a clone inse *** --- *** rt. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding AS SELECT feature_id AS protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding'; --- ************************************************ --- *** relation: non_protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW non_protein_coding AS SELECT feature_id AS non_protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding'; --- ************************************************ --- *** relation: scrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of any one of sev *** --- *** eral small cytoplasmic RNA molecules pre *** --- *** sent in the cytoplasm and sometimes nucl *** --- *** eus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna_primary_transcript AS SELECT feature_id AS scrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** Any one of several small cytoplasmic RNA *** --- *** molecules present in the cytoplasm and *** --- *** sometimes nucleus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: inr_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters required f *** --- *** or the correct positioning of the polyme *** --- *** rase for the start of transcription. Ove *** --- *** rlaps the TSS. The mammalian consensus s *** --- *** equence is YYAN(T|A)YY; the Drosophila c *** --- *** onsensus sequence is TCA(G|T)t(T|C). In *** --- *** each the A is at position +1 with respec *** --- *** t to the TSS. Functionally similar to th *** --- *** e TATA box element. *** --- ************************************************ --- CREATE VIEW inr_motif AS SELECT feature_id AS inr_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif'; --- ************************************************ --- *** relation: dpe_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters; Positione *** --- *** d from +28 to +32 with respect to the TS *** --- *** S (+1). Experimental results suggest tha *** --- *** t the DPE acts in conjunction with the I *** --- *** NR_motif to provide a binding site for T *** --- *** FIID in the absence of a TATA box to med *** --- *** iate transcription of TATA-less promoter *** --- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G *** --- *** |A|C). *** --- ************************************************ --- CREATE VIEW dpe_motif AS SELECT feature_id AS dpe_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE_motif'; --- ************************************************ --- *** relation: bre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments at -37 to -32 with respect to the *** --- *** TSS (+1). Consensus sequence is (G|C)(G| *** --- *** C)(G|A)CGCC. Binds TFIIB. *** --- ************************************************ --- CREATE VIEW bre_motif AS SELECT feature_id AS bre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BRE_motif'; --- ************************************************ --- *** relation: pse_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of the *** --- *** promoters of snRNA genes transcribed by *** --- *** RNA polymerase II or by RNA polymerase *** --- *** III. Located between -45 and -60 relativ *** --- *** e to the TSS. The human PSE_motif consen *** --- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| *** --- *** G). *** --- ************************************************ --- CREATE VIEW pse_motif AS SELECT feature_id AS pse_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif'; --- ************************************************ --- *** relation: linkage_group *** --- *** relation type: VIEW *** --- *** *** --- *** A group of loci that can be grouped in a *** --- *** linear order representing the different *** --- *** degrees of linkage among the genes conc *** --- *** erned. *** --- ************************************************ --- CREATE VIEW linkage_group AS SELECT feature_id AS linkage_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linkage_group'; --- ************************************************ --- *** relation: rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A region of double stranded RNA where th *** --- *** e bases do not conform to WC base pairin *** --- *** g. The loop is closed on both sides by c *** --- *** anonical base pairing. If the interrupti *** --- *** on to base pairing occurs on one strand *** --- *** only, it is known as a bulge. *** --- ************************************************ --- CREATE VIEW rna_internal_loop AS SELECT feature_id AS rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_internal_loop'; --- ************************************************ --- *** relation: asymmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where one of the st *** --- *** rands includes more bases than the corre *** --- *** sponding region on the other strand. *** --- ************************************************ --- CREATE VIEW asymmetric_rna_internal_loop AS SELECT feature_id AS asymmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'asymmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: a_minor_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region forming a motif, composed of ad *** --- *** enines, where the minor groove edges are *** --- *** inserted into the minor groove of anoth *** --- *** er helix. *** --- ************************************************ --- CREATE VIEW a_minor_rna_motif AS SELECT feature_id AS a_minor_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_minor_RNA_motif'; --- ************************************************ --- *** relation: k_turn_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** The kink turn (K-turn) is an RNA structu *** --- *** ral motif that creates a sharp (~120 deg *** --- *** ree) bend between two continuous helices *** --- *** . *** --- ************************************************ --- CREATE VIEW k_turn_rna_motif AS SELECT feature_id AS k_turn_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif'; --- ************************************************ --- *** relation: sarcin_like_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A loop in ribosomal RNA containing the s *** --- *** ites of attack for ricin and sarcin. *** --- ************************************************ --- CREATE VIEW sarcin_like_rna_motif AS SELECT feature_id AS sarcin_like_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sarcin_like_RNA_motif'; --- ************************************************ --- *** relation: symmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where the extent of *** --- *** the loop on both stands is the same siz *** --- *** e. *** --- ************************************************ --- CREATE VIEW symmetric_rna_internal_loop AS SELECT feature_id AS symmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: rna_junction_loop *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_junction_loop AS SELECT feature_id AS rna_junction_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_junction_loop'; --- ************************************************ --- *** relation: rna_hook_turn *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_hook_turn AS SELECT feature_id AS rna_hook_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn'; --- ************************************************ --- *** relation: base_pair *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW base_pair AS SELECT feature_id AS base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'base_pair'; --- ************************************************ --- *** relation: wc_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical base pair, where two bases *** --- *** interact via WC edges, with glycosidic *** --- *** bonds oriented cis relative to the axis *** --- *** of orientation. *** --- ************************************************ --- CREATE VIEW wc_base_pair AS SELECT feature_id AS wc_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair'; --- ************************************************ --- *** relation: sugar_edge_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW sugar_edge_base_pair AS SELECT feature_id AS sugar_edge_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sugar_edge_base_pair'; --- ************************************************ --- *** relation: aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA or RNA molecules that have been sele *** --- *** cted from random pools based on their ab *** --- *** ility to bind other molecules. *** --- ************************************************ --- CREATE VIEW aptamer AS SELECT feature_id AS aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'aptamer'; --- ************************************************ --- *** relation: dna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW dna_aptamer AS SELECT feature_id AS dna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer'; --- ************************************************ --- *** relation: rna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** RNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW rna_aptamer AS SELECT feature_id AS rna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_aptamer'; --- ************************************************ --- *** relation: morpholino_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Morpholino oligos are synthesized from f *** --- *** our different Morpholino subunits, each *** --- *** of which contains one of the four geneti *** --- *** c bases (A, C, G, T) linked to a 6-membe *** --- *** red morpholine ring. Eighteen to 25 subu *** --- *** nits of these four subunit types are joi *** --- *** ned in a specific order by non-ionic pho *** --- *** sphorodiamidate intersubunit linkages to *** --- *** give a Morpholino. *** --- ************************************************ --- CREATE VIEW morpholino_oligo AS SELECT feature_id AS morpholino_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo'; --- ************************************************ --- *** relation: riboswitch *** --- *** relation type: VIEW *** --- *** *** --- *** A riboswitch is a part of an mRNA that c *** --- *** an act as a direct sensor of small molec *** --- *** ules to control their own expression. A *** --- *** riboswitch is a cis element in the 5' en *** --- *** d of an mRNA, that acts as a direct sens *** --- *** or of metabolites. *** --- ************************************************ --- CREATE VIEW riboswitch AS SELECT feature_id AS riboswitch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch'; --- ************************************************ --- *** relation: matrix_attachment_site *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that is required for the bi *** --- *** nding of chromatin to the nuclear matrix *** --- *** . *** --- ************************************************ --- CREATE VIEW matrix_attachment_site AS SELECT feature_id AS matrix_attachment_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site'; --- ************************************************ --- *** relation: locus_control_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that includes DNAse hyperse *** --- *** nsitive sites located 5' to a gene that *** --- *** confers the high-level, position-indepen *** --- *** dent, and copy number-dependent expressi *** --- *** on to that gene. *** --- ************************************************ --- CREATE VIEW locus_control_region AS SELECT feature_id AS locus_control_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast is a match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: genomic_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone of a DNA region of a genome. *** --- ************************************************ --- CREATE VIEW genomic_clone AS SELECT feature_id AS genomic_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone'; --- ************************************************ --- *** relation: processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene where by an mRNA was retrot *** --- *** ransposed. The mRNA sequence is transcri *** --- *** bed back into the genome, lacking intron *** --- *** s and promotors, but often including a p *** --- *** olyA tail. *** --- ************************************************ --- CREATE VIEW processed_pseudogene AS SELECT feature_id AS processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene'; --- ************************************************ --- *** relation: pseudogene_by_unequal_crossing_over *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene caused by unequal crossing *** --- *** over at recombination. *** --- ************************************************ --- CREATE VIEW pseudogene_by_unequal_crossing_over AS SELECT feature_id AS pseudogene_by_unequal_crossing_over_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over'; --- ************************************************ --- *** relation: probe *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence used experimentally to de *** --- *** tect the presence or absence of a comple *** --- *** mentary nucleic acid. *** --- ************************************************ --- CREATE VIEW probe AS SELECT feature_id AS probe_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo' OR cvterm.name = 'probe'; --- ************************************************ --- *** relation: sequence_variant_affecting_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect which changes *** --- *** the regulatory region of a gene. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_regulatory_region AS SELECT feature_id AS sequence_variant_affecting_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_regulatory_region'; --- ************************************************ --- *** relation: aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW aneuploid AS SELECT feature_id AS aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'aneuploid'; --- ************************************************ --- *** relation: hyperploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as extra c *** --- *** hromosomes are present. *** --- ************************************************ --- CREATE VIEW hyperploid AS SELECT feature_id AS hyperploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid'; --- ************************************************ --- *** relation: hypoploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as some ch *** --- *** romosomes are missing. *** --- ************************************************ --- CREATE VIEW hypoploid AS SELECT feature_id AS hypoploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hypoploid'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind thereby *** --- *** effecting translation of genes in that *** --- *** operon. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: nuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a n *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW nuclease_binding_site AS SELECT feature_id AS nuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_binding_site'; --- ************************************************ --- *** relation: compound_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome_arm AS SELECT feature_id AS compound_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm'; --- ************************************************ --- *** relation: restriction_enzyme_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a r *** --- *** estriction enzyme. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_binding_site AS SELECT feature_id AS restriction_enzyme_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site'; --- ************************************************ --- *** relation: d_intrachr_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_intrachr_transposition AS SELECT feature_id AS d_intrachr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition'; --- ************************************************ --- *** relation: d_interchr_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_interchr_transposition AS SELECT feature_id AS d_interchr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition'; --- ************************************************ --- *** relation: free_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_chromosome_arm AS SELECT feature_id AS free_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm'; --- ************************************************ --- *** relation: gene_to_gene_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_to_gene_feature AS SELECT feature_id AS gene_to_gene_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'gene_to_gene_feature'; --- ************************************************ --- *** relation: overlapping *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that has *** --- *** a sequence that overlaps the sequence of *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW overlapping AS SELECT feature_id AS overlapping_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'overlapping'; --- ************************************************ --- *** relation: inside_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene. *** --- ************************************************ --- CREATE VIEW inside_intron AS SELECT feature_id AS inside_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'inside_intron'; --- ************************************************ --- *** relation: inside_intron_antiparallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the opposite strand. *** --- ************************************************ --- CREATE VIEW inside_intron_antiparallel AS SELECT feature_id AS inside_intron_antiparallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel'; --- ************************************************ --- *** relation: inside_intron_parallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the same strand. *** --- ************************************************ --- CREATE VIEW inside_intron_parallel AS SELECT feature_id AS inside_intron_parallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_parallel'; --- ************************************************ --- *** relation: five_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's 3' region. *** --- ************************************************ --- CREATE VIEW five_prime_three_prime_overlap AS SELECT feature_id AS five_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_three_prime_overlap'; --- ************************************************ --- *** relation: five_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's five prime region. *** --- ************************************************ --- CREATE VIEW five_prime_five_prime_overlap AS SELECT feature_id AS five_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_five_prime_overlap'; --- ************************************************ --- *** relation: three_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 3' region. *** --- ************************************************ --- CREATE VIEW three_prime_three_prime_overlap AS SELECT feature_id AS three_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_three_prime_overlap'; --- ************************************************ --- *** relation: three_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 5' region. *** --- ************************************************ --- CREATE VIEW three_prime_five_prime_overlap AS SELECT feature_id AS three_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_five_prime_overlap'; --- ************************************************ --- *** relation: antisense *** --- *** relation type: VIEW *** --- *** *** --- *** A region sequence that is complementary *** --- *** to a sequence of messenger RNA. *** --- ************************************************ --- CREATE VIEW antisense AS SELECT feature_id AS antisense_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense'; --- ************************************************ --- *** relation: polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is polycistronic. *** --- ************************************************ --- CREATE VIEW polycistronic_transcript AS SELECT feature_id AS polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_transcript'; --- ************************************************ --- *** relation: dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_transcript AS SELECT feature_id AS dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_transcript'; --- ************************************************ --- *** relation: operon_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW operon_member AS SELECT feature_id AS operon_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member'; --- ************************************************ --- *** relation: gene_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_array_member AS SELECT feature_id AS gene_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_array_member'; --- ************************************************ --- *** relation: macronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW macronuclear_sequence AS SELECT feature_id AS macronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence'; --- ************************************************ --- *** relation: micronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW micronuclear_sequence AS SELECT feature_id AS micronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_sequence'; --- ************************************************ --- *** relation: nuclear_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nuclear sequence. *** --- ************************************************ --- CREATE VIEW nuclear_gene AS SELECT feature_id AS nuclear_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene'; --- ************************************************ --- *** relation: mt_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in mitochondrial sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW mt_gene AS SELECT feature_id AS mt_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'mt_gene'; --- ************************************************ --- *** relation: kinetoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in kinetoplast sequence. *** --- ************************************************ --- CREATE VIEW kinetoplast_gene AS SELECT feature_id AS kinetoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'kinetoplast_gene'; --- ************************************************ --- *** relation: plastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plastid sequence. *** --- ************************************************ --- CREATE VIEW plastid_gene AS SELECT feature_id AS plastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'plastid_gene'; --- ************************************************ --- *** relation: apicoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from apicoplast sequence. *** --- ************************************************ --- CREATE VIEW apicoplast_gene AS SELECT feature_id AS apicoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene'; --- ************************************************ --- *** relation: ct_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chloroplast sequence. *** --- ************************************************ --- CREATE VIEW ct_gene AS SELECT feature_id AS ct_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ct_gene'; --- ************************************************ --- *** relation: chromoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chromoplast_sequence. *** --- ************************************************ --- CREATE VIEW chromoplast_gene AS SELECT feature_id AS chromoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_gene'; --- ************************************************ --- *** relation: cyanelle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from cyanelle sequence. *** --- ************************************************ --- CREATE VIEW cyanelle_gene AS SELECT feature_id AS cyanelle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_gene'; --- ************************************************ --- *** relation: leucoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A plastid gene from leucoplast sequence. *** --- ************************************************ --- CREATE VIEW leucoplast_gene AS SELECT feature_id AS leucoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_gene'; --- ************************************************ --- *** relation: proplastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proplastid sequence. *** --- ************************************************ --- CREATE VIEW proplastid_gene AS SELECT feature_id AS proplastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_gene'; --- ************************************************ --- *** relation: nucleomorph_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nucleomorph sequence. *** --- ************************************************ --- CREATE VIEW nucleomorph_gene AS SELECT feature_id AS nucleomorph_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorph_gene'; --- ************************************************ --- *** relation: plasmid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plasmid sequence. *** --- ************************************************ --- CREATE VIEW plasmid_gene AS SELECT feature_id AS plasmid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_gene'; --- ************************************************ --- *** relation: proviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proviral sequence. *** --- ************************************************ --- CREATE VIEW proviral_gene AS SELECT feature_id AS proviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'proviral_gene'; --- ************************************************ --- *** relation: endogenous_retroviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A proviral gene with origin endogenous r *** --- *** etrovirus. *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_gene AS SELECT feature_id AS endogenous_retroviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene'; --- ************************************************ --- *** relation: transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW transposable_element AS SELECT feature_id AS transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: clone_insert_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_end AS SELECT feature_id AS clone_insert_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversible denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the chromosome between the c *** --- *** entromere and the telomere. Human chromo *** --- *** somes have two arms, the p arm (short) a *** --- *** nd the q arm (long) which are separated *** --- *** from each other by the centromere. *** --- ************************************************ --- CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: sequencing_primer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequencing_primer AS SELECT feature_id AS sequencing_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer'; --- ************************************************ --- *** relation: mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_frameshift AS SELECT feature_id AS mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'mRNA_with_frameshift'; --- ************************************************ --- *** relation: sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** An extent of biological sequence. *** --- ************************************************ --- CREATE VIEW sequence_feature AS SELECT feature_id AS sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region' OR cvterm.name = 'junction' OR cvterm.name = 'sequence_alteration' OR cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'polyA_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'substitution' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'sequence_feature'; --- ************************************************ --- *** relation: transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoded within a transposable ele *** --- *** ment. For example gag, int, env and pol *** --- *** are the transposable element genes of th *** --- *** e TY element in yeast. *** --- ************************************************ --- CREATE VIEW transposable_element_gene AS SELECT feature_id AS transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'transposable_element_gene'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** A short preexisting polynucleotide chain *** --- *** to which new deoxyribonucleotides can b *** --- *** e added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'primer'; --- ************************************************ --- *** relation: proviral_region *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to a host genome. *** --- ************************************************ --- CREATE VIEW proviral_region AS SELECT feature_id AS proviral_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage' OR cvterm.name = 'proviral_region'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: edited *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is modified by editing. *** --- ************************************************ --- CREATE VIEW edited AS SELECT feature_id AS edited_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited'; --- ************************************************ --- *** relation: transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript with a translational frames *** --- *** hift. *** --- ************************************************ --- CREATE VIEW transcript_with_translational_frameshift AS SELECT feature_id AS transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a sequence that *** --- *** is regulated. *** --- ************************************************ --- CREATE VIEW regulated AS SELECT feature_id AS regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'regulated'; --- ************************************************ --- *** relation: protein_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW protein_coding_primary_transcript AS SELECT feature_id AS protein_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: forward_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW forward_primer AS SELECT feature_id AS forward_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward_primer'; --- ************************************************ --- *** relation: rna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_sequence_secondary_structure AS SELECT feature_id AS rna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'RNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: transcriptionally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated at transcription. *** --- ************************************************ --- CREATE VIEW transcriptionally_regulated AS SELECT feature_id AS transcriptionally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_regulated'; --- ************************************************ --- *** relation: transcriptionally_constitutive *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed in relatively constant amounts *** --- *** without regard to cellular environmenta *** --- *** l conditions such as the concentration o *** --- *** f a particular substrate. *** --- ************************************************ --- CREATE VIEW transcriptionally_constitutive AS SELECT feature_id AS transcriptionally_constitutive_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive'; --- ************************************************ --- *** relation: transcriptionally_induced *** --- *** relation type: VIEW *** --- *** *** --- *** An inducer molecule is required for tran *** --- *** scription to occur. *** --- ************************************************ --- CREATE VIEW transcriptionally_induced AS SELECT feature_id AS transcriptionally_induced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_induced'; --- ************************************************ --- *** relation: transcriptionally_repressed *** --- *** relation type: VIEW *** --- *** *** --- *** A repressor molecule is required for tra *** --- *** nscription to stop. *** --- ************************************************ --- CREATE VIEW transcriptionally_repressed AS SELECT feature_id AS transcriptionally_repressed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'transcriptionally_repressed'; --- ************************************************ --- *** relation: silenced_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced. *** --- ************************************************ --- CREATE VIEW silenced_gene AS SELECT feature_id AS silenced_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_gene'; --- ************************************************ --- *** relation: gene_silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA modificat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_modification AS SELECT feature_id AS gene_silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_DNA_modification'; --- ************************************************ --- *** relation: gene_silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA methylati *** --- *** on. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_methylation AS SELECT feature_id AS gene_silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: post_translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated after it has been translated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated AS SELECT feature_id AS post_translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'post_translationally_regulated'; --- ************************************************ --- *** relation: translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated as it is translated. *** --- ************************************************ --- CREATE VIEW translationally_regulated AS SELECT feature_id AS translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated'; --- ************************************************ --- *** relation: reverse_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW reverse_primer AS SELECT feature_id AS reverse_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_primer'; --- ************************************************ --- *** relation: epigenetically_modified *** --- *** relation type: VIEW *** --- *** *** --- *** This attribute describes a gene where he *** --- *** ritable changes other than those in the *** --- *** DNA sequence occur. These changes includ *** --- *** e: modification to the DNA (such as DNA *** --- *** methylation, the covalent modification o *** --- *** f cytosine), and post-translational modi *** --- *** fication of histones. *** --- ************************************************ --- CREATE VIEW epigenetically_modified AS SELECT feature_id AS epigenetically_modified_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'epigenetically_modified'; --- ************************************************ --- *** relation: imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** Imprinted genes are epigenetically modif *** --- *** ied genes that are expressed monoallelic *** --- *** ally according to their parent of origin *** --- *** . *** --- ************************************************ --- CREATE VIEW imprinted AS SELECT feature_id AS imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted'; --- ************************************************ --- *** relation: maternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The maternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW maternally_imprinted AS SELECT feature_id AS maternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted'; --- ************************************************ --- *** relation: paternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The paternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW paternally_imprinted AS SELECT feature_id AS paternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted'; --- ************************************************ --- *** relation: allelically_excluded *** --- *** relation type: VIEW *** --- *** *** --- *** Allelic exclusion is a process occuring *** --- *** in diploid organisms, where a gene is in *** --- *** activated and not expressed in that cell *** --- *** . *** --- ************************************************ --- CREATE VIEW allelically_excluded AS SELECT feature_id AS allelically_excluded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded'; --- ************************************************ --- *** relation: gene_rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An epigenetically modified gene, rearran *** --- *** ged at the DNA level. *** --- ************************************************ --- CREATE VIEW gene_rearranged_at_dna_level AS SELECT feature_id AS gene_rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located within the fi *** --- *** ve prime end of an mRNA that causes prem *** --- *** ature termination of translation. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'terminator'; --- ************************************************ --- *** relation: dna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded DNA sequence. *** --- ************************************************ --- CREATE VIEW dna_sequence_secondary_structure AS SELECT feature_id AS dna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif' OR cvterm.name = 'DNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of known length which may be us *** --- *** ed to manufacture a longer region. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: recoded_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A codon that has been redefined at trans *** --- *** lation. The redefinition may be as a res *** --- *** ult of translational bypass, translation *** --- *** al frameshifting or stop codon readthrou *** --- *** gh. *** --- ************************************************ --- CREATE VIEW recoded_codon AS SELECT feature_id AS recoded_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'recoded_codon'; --- ************************************************ --- *** relation: capped *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing when a sequence, *** --- *** usually an mRNA is capped by the additi *** --- *** on of a modified guanine nucleotide at t *** --- *** he 5' end. *** --- ************************************************ --- CREATE VIEW capped AS SELECT feature_id AS capped_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the transcript sequence with *** --- *** in a gene which is not removed from the *** --- *** primary RNA transcript by RNA splicing. *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unvailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n a host bacterium or some other organis *** --- *** m. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'clone'; --- ************************************************ --- *** relation: yac *** --- *** relation type: VIEW *** --- *** *** --- *** Yeast Artificial Chromosome, a vector co *** --- *** nstructed from the telomeric, centromeri *** --- *** c, and replication origin sequences need *** --- *** ed for replication in yeast cells. *** --- ************************************************ --- CREATE VIEW yac AS SELECT feature_id AS yac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC'; --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Bacterial Artificial Chromosome, a cloni *** --- *** ng vector that can be propagated as mini *** --- *** -chromosomes in a bacterial host. *** --- ************************************************ --- CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: pac *** --- *** relation type: VIEW *** --- *** *** --- *** The P1-derived artificial chromosome are *** --- *** DNA constructs that are derived from th *** --- *** e DNA of P1 bacteriophage. They can carr *** --- *** y large amounts (about 100-300 kilobases *** --- *** ) of other sequences for a variety of bi *** --- *** oengineering purposes. It is one type of *** --- *** vector used to clone DNA fragments (100 *** --- *** - to 300-kb insert size; average, 150 kb *** --- *** ) in Escherichia coli cells. *** --- ************************************************ --- CREATE VIEW pac AS SELECT feature_id AS pac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC'; --- ************************************************ --- *** relation: plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A self replicating, using the hosts cell *** --- *** ular machinery, often circular nucleic a *** --- *** cid molecule that is distinct from a chr *** --- *** omosome in the organism. *** --- ************************************************ --- CREATE VIEW plasmid AS SELECT feature_id AS plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'plasmid'; --- ************************************************ --- *** relation: cosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that is a hybrid of lam *** --- *** bda phages and a plasmid that can be pro *** --- *** pagated as a plasmid or packaged as a ph *** --- *** age,since they retain the lambda cos sit *** --- *** es. *** --- ************************************************ --- CREATE VIEW cosmid AS SELECT feature_id AS cosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cosmid'; --- ************************************************ --- *** relation: phagemid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid which carries within its seque *** --- *** nce a bacteriophage replication origin. *** --- *** When the host bacterium is infected with *** --- *** "helper" phage, a phagemid is replicate *** --- *** d along with the phage DNA and packaged *** --- *** into phage capsids. *** --- ************************************************ --- CREATE VIEW phagemid AS SELECT feature_id AS phagemid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phagemid'; --- ************************************************ --- *** relation: fosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that utilises the E. co *** --- *** li F factor. *** --- ************************************************ --- CREATE VIEW fosmid AS SELECT feature_id AS fosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fosmid'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The point at which a deletion occured. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which adenine has *** --- *** been methylated. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Consensus region of primary transcript b *** --- *** ordering junction of splicing. A region *** --- *** that overlaps exactly 2 base and adjacen *** --- *** t_to splice_junction. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: five_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 5' edge of the intron. A splice_ *** --- *** site that is downstream_adjacent_to exon *** --- *** and starts intron. *** --- ************************************************ --- CREATE VIEW five_prime_cis_splice_site AS SELECT feature_id AS five_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'five_prime_cis_splice_site'; --- ************************************************ --- *** relation: three_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 3' edge of the intron. A splice_ *** --- *** site that is upstream_adjacent_to exon a *** --- *** nd finishes intron. *** --- ************************************************ --- CREATE VIEW three_prime_cis_splice_site AS SELECT feature_id AS three_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'three_prime_cis_splice_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: enhancer_bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer bound by a factor. *** --- ************************************************ --- CREATE VIEW enhancer_bound_by_factor AS SELECT feature_id AS enhancer_bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region composed of the TSS( *** --- *** s) and binding sites for TF_complexes of *** --- *** the basal transcription machinery. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'promoter'; --- ************************************************ --- *** relation: rnapol_i_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase I binds, to begin trans *** --- *** cription. *** --- ************************************************ --- CREATE VIEW rnapol_i_promoter AS SELECT feature_id AS rnapol_i_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter'; --- ************************************************ --- *** relation: rnapol_ii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase II binds, to begin tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW rnapol_ii_promoter AS SELECT feature_id AS rnapol_ii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_promoter'; --- ************************************************ --- *** relation: rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase III binds, to begin tra *** --- *** nscription. *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter AS SELECT feature_id AS rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'RNApol_III_promoter'; --- ************************************************ --- *** relation: caat_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a conserved sequence located abo *** --- *** ut 75-bp upstream of the start point of *** --- *** eukaryotic transcription units which may *** --- *** be involved in RNA polymerase binding; *** --- *** consensus=GG(C|T)CAATCT. *** --- ************************************************ --- CREATE VIEW caat_signal AS SELECT feature_id AS caat_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CAAT_signal'; --- ************************************************ --- *** relation: gc_rich_promoter_region *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved GC-rich region located upstr *** --- *** eam of the start point of eukaryotic tra *** --- *** nscription units which may occur in mult *** --- *** iple copies or in either orientation; co *** --- *** nsensus=GGGCGG. *** --- ************************************************ --- CREATE VIEW gc_rich_promoter_region AS SELECT feature_id AS gc_rich_promoter_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region'; --- ************************************************ --- *** relation: tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved AT-rich septamer found about *** --- *** 25-bp before the start point of many eu *** --- *** karyotic RNA polymerase II transcript un *** --- *** its; may be involved in positioning the *** --- *** enzyme for correct initiation; consensus *** --- *** =TATA(A|T)A(A|T). *** --- ************************************************ --- CREATE VIEW tata_box AS SELECT feature_id AS tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TATA_box'; --- ************************************************ --- *** relation: minus_10_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 10-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units which may be involved in bin *** --- *** ding RNA polymerase; consensus=TAtAaT. *** --- ************************************************ --- CREATE VIEW minus_10_signal AS SELECT feature_id AS minus_10_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_10_signal'; --- ************************************************ --- *** relation: minus_35_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved hexamer about 35-bp upstream *** --- *** of the start point of bacterial transcr *** --- *** iption units; consensus=TTGACa or TGTTGA *** --- *** CA. *** --- ************************************************ --- CREATE VIEW minus_35_signal AS SELECT feature_id AS minus_35_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_35_signal'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_insert_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_start AS SELECT feature_id AS clone_insert_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_start'; --- ************************************************ --- *** relation: retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is incorpora *** --- *** ted into a chromosome by a mechanism tha *** --- *** t requires reverse transcriptase. *** --- ************************************************ --- CREATE VIEW retrotransposon AS SELECT feature_id AS retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'retrotransposon'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: dna_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon where the mechanism of tran *** --- *** sposition is via a DNA intermediate. *** --- ************************************************ --- CREATE VIEW dna_transposon AS SELECT feature_id AS dna_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'DNA_transposon'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: u2_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A major type of spliceosomal intron spli *** --- *** ced by the U2 spliceosome, that includes *** --- *** U1, U2, U4/U6 and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u2_intron AS SELECT feature_id AS u2_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that in its initial state r *** --- *** equires modification to be functional. *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'primary_transcript'; --- ************************************************ --- *** relation: ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon flanked by long termin *** --- *** al repeat sequences. *** --- ************************************************ --- CREATE VIEW ltr_retrotransposon AS SELECT feature_id AS ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract' OR cvterm.name = 'LTR_retrotransposon'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A segment of DNA that is transcribed, bu *** --- *** t removed from within the transcript by *** --- *** splicing together the sequences (exons) *** --- *** on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'intron'; --- ************************************************ --- *** relation: non_ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon without long terminal *** --- *** repeat sequences. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon AS SELECT feature_id AS non_ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'non_LTR_retrotransposon'; --- ************************************************ --- *** relation: five_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_intron AS SELECT feature_id AS five_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron'; --- ************************************************ --- *** relation: interior_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_intron AS SELECT feature_id AS interior_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_intron'; --- ************************************************ --- *** relation: three_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_intron AS SELECT feature_id AS three_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_intron'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment used as a reagent to dete *** --- *** ct the polymorphic genomic loci by hybri *** --- *** dizing against the genomic DNA digested *** --- *** with a given restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: line_element *** --- *** relation type: VIEW *** --- *** *** --- *** A dispersed repeat family with many copi *** --- *** es, each from 1 to 6 kb long. New elemen *** --- *** ts are generated by retroposition of a t *** --- *** ranscribed copy. Typically the LINE cont *** --- *** ains 2 ORF's one of which is reverse tra *** --- *** nscriptase, and 3'and 5' direct repeats. *** --- ************************************************ --- CREATE VIEW line_element AS SELECT feature_id AS line_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element'; --- ************************************************ --- *** relation: coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon whereby at least one base is par *** --- *** t of a codon (here, 'codon'nis inclusive *** --- *** of the stop_codon). *** --- ************************************************ --- CREATE VIEW coding_exon AS SELECT feature_id AS coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'coding_exon'; --- ************************************************ --- *** relation: five_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the five_prime_coding_ex *** --- *** on that codes for protein. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_coding_region AS SELECT feature_id AS five_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: three_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the three_prime_coding_e *** --- *** xon that codes for protein. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_coding_region AS SELECT feature_id AS three_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding exon_coding_region'; --- ************************************************ --- *** relation: noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that does not contain any codons *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_exon AS SELECT feature_id AS noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'noncoding_exon'; --- ************************************************ --- *** relation: translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence that has *** --- *** translocated to a new position. *** --- ************************************************ --- CREATE VIEW translocation AS SELECT feature_id AS translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation'; --- ************************************************ --- *** relation: five_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' most coding exon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon AS SELECT feature_id AS five_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon'; --- ************************************************ --- *** relation: interior_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is bounded by 5' and 3' spl *** --- *** ice sites. *** --- ************************************************ --- CREATE VIEW interior_exon AS SELECT feature_id AS interior_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_exon'; --- ************************************************ --- *** relation: three_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The coding exon that is most 3-prime on *** --- *** a given transcript. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon AS SELECT feature_id AS three_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime or three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: sine_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element, a few hundred base *** --- *** pairs long, that is dispersed throughou *** --- *** t the genome. A common human SINE is the *** --- *** Alu element. *** --- ************************************************ --- CREATE VIEW sine_element AS SELECT feature_id AS sine_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SINE_element'; --- ************************************************ --- *** relation: simple_sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW simple_sequence_length_variation AS SELECT feature_id AS simple_sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation'; --- ************************************************ --- *** relation: terminal_inverted_repeat_element *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA transposable element defined as ha *** --- *** ving termini with perfect, or nearly per *** --- *** fect short inverted repeats, generally 1 *** --- *** 0 - 40 nucleotides long. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat_element AS SELECT feature_id AS terminal_inverted_repeat_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'terminal_inverted_repeat_element'; --- ************************************************ --- *** relation: rrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a ribosoma *** --- *** l RNA. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript AS SELECT feature_id AS rrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript'; --- ************************************************ --- *** relation: trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a transfer *** --- *** RNA (SO:0000253). *** --- ************************************************ --- CREATE VIEW trna_primary_transcript AS SELECT feature_id AS trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript'; --- ************************************************ --- *** relation: alanine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding alanyl tRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW alanine_trna_primary_transcript AS SELECT feature_id AS alanine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: arg_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding arginyl tR *** --- *** NA (SO:0000255). *** --- ************************************************ --- CREATE VIEW arg_trna_primary_transcript AS SELECT feature_id AS arg_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: asparagine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding asparaginy *** --- *** l tRNA (SO:0000256). *** --- ************************************************ --- CREATE VIEW asparagine_trna_primary_transcript AS SELECT feature_id AS asparagine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: aspartic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding aspartyl t *** --- *** RNA (SO:0000257). *** --- ************************************************ --- CREATE VIEW aspartic_acid_trna_primary_transcript AS SELECT feature_id AS aspartic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: cysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding cysteinyl *** --- *** tRNA (SO:0000258). *** --- ************************************************ --- CREATE VIEW cysteine_trna_primary_transcript AS SELECT feature_id AS cysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutaminyl *** --- *** tRNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamic_acid_trna_primary_transcript AS SELECT feature_id AS glutamic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutamyl t *** --- *** RNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamine_trna_primary_transcript AS SELECT feature_id AS glutamine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glycine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glycyl tRN *** --- *** A (SO:0000263). *** --- ************************************************ --- CREATE VIEW glycine_trna_primary_transcript AS SELECT feature_id AS glycine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: histidine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding histidyl t *** --- *** RNA (SO:0000262). *** --- ************************************************ --- CREATE VIEW histidine_trna_primary_transcript AS SELECT feature_id AS histidine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: isoleucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding isoleucyl *** --- *** tRNA (SO:0000263). *** --- ************************************************ --- CREATE VIEW isoleucine_trna_primary_transcript AS SELECT feature_id AS isoleucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: leucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding leucyl tRN *** --- *** A (SO:0000264). *** --- ************************************************ --- CREATE VIEW leucine_trna_primary_transcript AS SELECT feature_id AS leucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: lysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding lysyl tRNA *** --- *** (SO:0000265). *** --- ************************************************ --- CREATE VIEW lysine_trna_primary_transcript AS SELECT feature_id AS lysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: methionine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding methionyl *** --- *** tRNA (SO:0000266). *** --- ************************************************ --- CREATE VIEW methionine_trna_primary_transcript AS SELECT feature_id AS methionine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: phe_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding phenylalan *** --- *** yl tRNA (SO:0000267). *** --- ************************************************ --- CREATE VIEW phe_trna_primary_transcript AS SELECT feature_id AS phe_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: proline_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding prolyl tRN *** --- *** A (SO:0000268). *** --- ************************************************ --- CREATE VIEW proline_trna_primary_transcript AS SELECT feature_id AS proline_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline_tRNA_primary_transcript'; --- ************************************************ --- *** relation: serine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW serine_trna_primary_transcript AS SELECT feature_id AS serine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: thr_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding threonyl t *** --- *** RNA (SO:000270). *** --- ************************************************ --- CREATE VIEW thr_trna_primary_transcript AS SELECT feature_id AS thr_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: try_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tryptophan *** --- *** yl tRNA (SO:000271). *** --- ************************************************ --- CREATE VIEW try_trna_primary_transcript AS SELECT feature_id AS try_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan_tRNA_primary_transcript'; --- ************************************************ --- *** relation: tyrosine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tyrosyl tR *** --- *** NA (SO:000272). *** --- ************************************************ --- CREATE VIEW tyrosine_trna_primary_transcript AS SELECT feature_id AS tyrosine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: valine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding valyl tRNA *** --- *** (SO:000273). *** --- ************************************************ --- CREATE VIEW valine_trna_primary_transcript AS SELECT feature_id AS valine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: snrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** clear RNA (SO:0000274). *** --- ************************************************ --- CREATE VIEW snrna_primary_transcript AS SELECT feature_id AS snrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_primary_transcript'; --- ************************************************ --- *** relation: snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar mRNA (SO:0000275). *** --- ************************************************ --- CREATE VIEW snorna_primary_transcript AS SELECT feature_id AS snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript'; --- ************************************************ --- *** relation: mature_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone the nec *** --- *** essary modifications, if any, for its fu *** --- *** nction. In eukaryotes this includes, for *** --- *** example, processing of introns, cleavag *** --- *** e, base modification, and modifications *** --- *** to the 5' and/or the 3' ends, other than *** --- *** addition of bases. In bacteria function *** --- *** al mRNAs are usually not modified. *** --- ************************************************ --- CREATE VIEW mature_transcript AS SELECT feature_id AS mature_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'mature_transcript'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not co *** --- *** ntain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds a TF c *** --- *** omplex [GO:0005667]. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The inframe interval between the stop co *** --- *** dons of a reading frame which when read *** --- *** as sequential triplets, has the potentia *** --- *** l of encoding a sequential string of ami *** --- *** no acids. TER(NNN)nTER. *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'ORF'; --- ************************************************ --- *** relation: transcript_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transcript_attribute AS SELECT feature_id AS transcript_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'transcript_attribute'; --- ************************************************ --- *** relation: foldback_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element with extensive se *** --- *** condary structure, characterised by larg *** --- *** e modular imperfect long inverted repeat *** --- *** s. *** --- ************************************************ --- CREATE VIEW foldback_element AS SELECT feature_id AS foldback_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foldback_element'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequences extending on either side o *** --- *** f a specific region. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: chromosome_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_variation AS SELECT feature_id AS chromosome_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_variation'; --- ************************************************ --- *** relation: internal_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR bordered by the terminal and initi *** --- *** al codons of two CDSs in a polycistronic *** --- *** transcript. Every UTR is either 5', 3' *** --- *** or internal. *** --- ************************************************ --- CREATE VIEW internal_utr AS SELECT feature_id AS internal_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_UTR'; --- ************************************************ --- *** relation: untranslated_region_polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The untranslated sequence separating the *** --- *** 'cistrons' of multicistronic mRNA. *** --- ************************************************ --- CREATE VIEW untranslated_region_polycistronic_mrna AS SELECT feature_id AS untranslated_region_polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'untranslated_region_polycistronic_mRNA'; --- ************************************************ --- *** relation: internal_ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence element that recruits a ribosom *** --- *** al subunit to internal mRNA for translat *** --- *** ion initiation. *** --- ************************************************ --- CREATE VIEW internal_ribosome_entry_site AS SELECT feature_id AS internal_ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'internal_ribosome_entry_site'; --- ************************************************ --- *** relation: polyadenylated *** --- *** relation type: VIEW *** --- *** *** --- *** A attribute describing the addition of a *** --- *** poly A tail to the 3' end of a mRNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW polyadenylated AS SELECT feature_id AS polyadenylated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated'; --- ************************************************ --- *** relation: sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_length_variation AS SELECT feature_id AS sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'sequence_length_variation'; --- ************************************************ --- *** relation: modified_rna_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post_transcriptionally modified base. *** --- ************************************************ --- CREATE VIEW modified_rna_base_feature AS SELECT feature_id AS modified_rna_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_RNA_base_feature'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. Transfer R *** --- *** NAs have two regions of fundamental func *** --- *** tional importance: the anti-codon, which *** --- *** is responsible for specific mRNA codon *** --- *** recognition, and the 3' end, to which th *** --- *** e tRNA's corresponding amino acid is att *** --- *** ached (by aminoacyl-tRNA synthetases). T *** --- *** ransfer RNAs cope with the degeneracy of *** --- *** the genetic code in two manners: having *** --- *** more than one tRNA (with a specific ant *** --- *** i-codon) for a particular amino acid; an *** --- *** d 'wobble' base-pairing, i.e. permitting *** --- *** non-standard base-pairing at the 3rd an *** --- *** ti-codon position. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: alanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an alanine anti *** --- *** codon, and a 3' alanine binding region. *** --- ************************************************ --- CREATE VIEW alanyl_trna AS SELECT feature_id AS alanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA'; --- ************************************************ --- *** relation: rrna_small_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_small_subunit_primary_transcript AS SELECT feature_id AS rrna_small_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript'; --- ************************************************ --- *** relation: asparaginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an asparagine a *** --- *** nticodon, and a 3' asparagine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW asparaginyl_trna AS SELECT feature_id AS asparaginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparaginyl_tRNA'; --- ************************************************ --- *** relation: aspartyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an aspartic aci *** --- *** d anticodon, and a 3' aspartic acid bind *** --- *** ing region. *** --- ************************************************ --- CREATE VIEW aspartyl_trna AS SELECT feature_id AS aspartyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartyl_tRNA'; --- ************************************************ --- *** relation: cysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a cysteine anti *** --- *** codon, and a 3' cysteine binding region. *** --- ************************************************ --- CREATE VIEW cysteinyl_trna AS SELECT feature_id AS cysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteinyl_tRNA'; --- ************************************************ --- *** relation: glutaminyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamine ant *** --- *** icodon, and a 3' glutamine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW glutaminyl_trna AS SELECT feature_id AS glutaminyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutaminyl_tRNA'; --- ************************************************ --- *** relation: glutamyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamic acid *** --- *** anticodon, and a 3' glutamic acid bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW glutamyl_trna AS SELECT feature_id AS glutamyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamyl_tRNA'; --- ************************************************ --- *** relation: glycyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glycine antic *** --- *** odon, and a 3' glycine binding region. *** --- ************************************************ --- CREATE VIEW glycyl_trna AS SELECT feature_id AS glycyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycyl_tRNA'; --- ************************************************ --- *** relation: histidyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a histidine ant *** --- *** icodon, and a 3' histidine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW histidyl_trna AS SELECT feature_id AS histidyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidyl_tRNA'; --- ************************************************ --- *** relation: isoleucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an isoleucine a *** --- *** nticodon, and a 3' isoleucine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW isoleucyl_trna AS SELECT feature_id AS isoleucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucyl_tRNA'; --- ************************************************ --- *** relation: leucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a leucine antic *** --- *** odon, and a 3' leucine binding region. *** --- ************************************************ --- CREATE VIEW leucyl_trna AS SELECT feature_id AS leucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucyl_tRNA'; --- ************************************************ --- *** relation: lysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a lysine antico *** --- *** don, and a 3' lysine binding region. *** --- ************************************************ --- CREATE VIEW lysyl_trna AS SELECT feature_id AS lysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysyl_tRNA'; --- ************************************************ --- *** relation: methionyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a methionine an *** --- *** ticodon, and a 3' methionine binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW methionyl_trna AS SELECT feature_id AS methionyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionyl_tRNA'; --- ************************************************ --- *** relation: phenylalanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a phenylalanine *** --- *** anticodon, and a 3' phenylalanine bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW phenylalanyl_trna AS SELECT feature_id AS phenylalanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanyl_tRNA'; --- ************************************************ --- *** relation: prolyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a proline antic *** --- *** odon, and a 3' proline binding region. *** --- ************************************************ --- CREATE VIEW prolyl_trna AS SELECT feature_id AS prolyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prolyl_tRNA'; --- ************************************************ --- *** relation: seryl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a serine antico *** --- *** don, and a 3' serine binding region. *** --- ************************************************ --- CREATE VIEW seryl_trna AS SELECT feature_id AS seryl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seryl_tRNA'; --- ************************************************ --- *** relation: threonyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a threonine ant *** --- *** icodon, and a 3' threonine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW threonyl_trna AS SELECT feature_id AS threonyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonyl_tRNA'; --- ************************************************ --- *** relation: tryptophanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tryptophan an *** --- *** ticodon, and a 3' tryptophan binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW tryptophanyl_trna AS SELECT feature_id AS tryptophanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophanyl_tRNA'; --- ************************************************ --- *** relation: tyrosyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tyrosine anti *** --- *** codon, and a 3' tyrosine binding region. *** --- ************************************************ --- CREATE VIEW tyrosyl_trna AS SELECT feature_id AS tyrosyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosyl_tRNA'; --- ************************************************ --- *** relation: valyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a valine antico *** --- *** don, and a 3' valine binding region. *** --- ************************************************ --- CREATE VIEW valyl_trna AS SELECT feature_id AS valyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valyl_tRNA'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small nuclear RNA molecule involved in *** --- *** pre-mRNA splicing and processing. *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA (small nucleolar RNA) is any on *** --- *** e of a class of small RNAs that are asso *** --- *** ciated with the eukaryotic nucleus as co *** --- *** mponents of small nucleolar ribonucleopr *** --- *** oteins. They participate in the processi *** --- *** ng or modifications of many RNAs, mostly *** --- *** ribosomal RNAs (rRNAs) though snoRNAs a *** --- *** re also known to target other classes of *** --- *** RNA, including spliceosomal RNAs, tRNAs *** --- *** , and mRNAs via a stretch of sequence th *** --- *** at is complementary to a sequence in the *** --- *** targeted RNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. M *** --- *** icro RNAs are produced from precursor mo *** --- *** lecules (SO:0000647) that can form local *** --- *** hairpin structures, which ordinarily ar *** --- *** e processed (via the Dicer pathway) such *** --- *** that a single miRNA molecule accumulate *** --- *** s from one arm of a hairpin precursor mo *** --- *** lecule. Micro RNAs may trigger the cleav *** --- *** age of their target molecules or act as *** --- *** translational repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by another molecule. *** --- ************************************************ --- CREATE VIEW bound_by_factor AS SELECT feature_id AS bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'bound_by_factor'; --- ************************************************ --- *** relation: transcript_bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a nucleic *** --- *** acid. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_nucleic_acid AS SELECT feature_id AS transcript_bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_nucleic_acid'; --- ************************************************ --- *** relation: transcript_bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a protein. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_protein AS SELECT feature_id AS transcript_bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_protein'; --- ************************************************ --- *** relation: engineered_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_gene AS SELECT feature_id AS engineered_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_gene'; --- ************************************************ --- *** relation: engineered_foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_gene AS SELECT feature_id AS engineered_foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene'; --- ************************************************ --- *** relation: mrna_with_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a minus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_1_frameshift AS SELECT feature_id AS mrna_with_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transposible_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element_gene AS SELECT feature_id AS engineered_foreign_transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene'; --- ************************************************ --- *** relation: foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_gene AS SELECT feature_id AS foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'foreign_gene'; --- ************************************************ --- *** relation: long_terminal_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence directly repeated at both end *** --- *** s of a defined sequence, of the sort typ *** --- *** ically found in retroviruses. *** --- ************************************************ --- CREATE VIEW long_terminal_repeat AS SELECT feature_id AS long_terminal_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'long_terminal_repeat'; --- ************************************************ --- *** relation: fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is a fusion. *** --- ************************************************ --- CREATE VIEW fusion_gene AS SELECT feature_id AS fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'fusion_gene'; --- ************************************************ --- *** relation: engineered_fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A fusion gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_fusion_gene AS SELECT feature_id AS engineered_fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat_region containing repeat_units *** --- *** (2 to 4 bp) that is repeated multiple ti *** --- *** mes in tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: dinucleotide_repeat_microsatellite_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dinucleotide_repeat_microsatellite_feature AS SELECT feature_id AS dinucleotide_repeat_microsatellite_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: trinuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trinuc_repeat_microsat AS SELECT feature_id AS trinuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: engineered_foreign_repetitive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element that is engineered *** --- *** and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_repetitive_element AS SELECT feature_id AS engineered_foreign_repetitive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_repetitive_element'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. It is a palindr *** --- *** ome, and it may, or may not be hyphenate *** --- *** d. Examples: GCTGATCAGC, or GCTGA-----TC *** --- *** AGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: u12_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A type of spliceosomal intron spliced by *** --- *** the U12 spliceosome, that includes U11, *** --- *** U12, U4atac/U6atac and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u12_intron AS SELECT feature_id AS u12_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_intron'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: d_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Displacement loop; a region within mitoc *** --- *** hondrial DNA in which a short stretch of *** --- *** RNA is paired with one strand of DNA, d *** --- *** isplacing the original partner DNA stran *** --- *** d in this region; also used to describe *** --- *** the displacement of a region of one stra *** --- *** nd of duplex DNA by a single stranded in *** --- *** vader in the reaction catalyzed by RecA *** --- *** protein. *** --- ************************************************ --- CREATE VIEW d_loop AS SELECT feature_id AS d_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop'; --- ************************************************ --- *** relation: recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature AS SELECT feature_id AS recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'recombination_feature'; --- ************************************************ --- *** relation: specific_recombination_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW specific_recombination_site AS SELECT feature_id AS specific_recombination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'specific_recombination_site'; --- ************************************************ --- *** relation: recombination_feature_of_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature_of_rearranged_gene AS SELECT feature_id AS recombination_feature_of_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'recombination_feature_of_rearranged_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature'; --- ************************************************ --- *** relation: j_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including J-heptame *** --- *** r, J-spacer and J-nonamer in 5' of J-reg *** --- *** ion of a J-gene or J-sequence. *** --- ************************************************ --- CREATE VIEW j_gene_recombination_feature AS SELECT feature_id AS j_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base_site *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G or (in RNA) U. *** --- ************************************************ --- CREATE VIEW modified_base_site AS SELECT feature_id AS modified_base_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'modified_base_site'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: experimentally_determined *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that has *** --- *** been experiemntally verified. *** --- ************************************************ --- CREATE VIEW experimentally_determined AS SELECT feature_id AS experimentally_determined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined'; --- ************************************************ --- *** relation: stem_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A double-helical region of nucleic acid *** --- *** formed by base-pairing between adjacent *** --- *** (inverted) complementary sequences. *** --- ************************************************ --- CREATE VIEW stem_loop AS SELECT feature_id AS stem_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop' OR cvterm.name = 'stem_loop'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: tss *** --- *** relation type: VIEW *** --- *** *** --- *** The first base where RNA polymerase begi *** --- *** ns to synthesize the RNA transcript. *** --- ************************************************ --- CREATE VIEW tss AS SELECT feature_id AS tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'TSS'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS'; --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Complementary DNA; A piece of DNA copied *** --- *** from an mRNA and spliced into a vector *** --- *** for propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** First codon to be translated by a riboso *** --- *** me. *** --- ************************************************ --- CREATE VIEW start_codon AS SELECT feature_id AS start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'start_codon'; --- ************************************************ --- *** relation: stop_codon *** --- *** relation type: VIEW *** --- *** *** --- *** In mRNA, a set of three nucleotides that *** --- *** indicates the end of information for pr *** --- *** otein synthesis. *** --- ************************************************ --- CREATE VIEW stop_codon AS SELECT feature_id AS stop_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon'; --- ************************************************ --- *** relation: intronic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Sequences within the intron that modulat *** --- *** e splice site selection for some introns *** --- *** . *** --- ************************************************ --- CREATE VIEW intronic_splice_enhancer AS SELECT feature_id AS intronic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer'; --- ************************************************ --- *** relation: mrna_with_plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_1_frameshift AS SELECT feature_id AS mrna_with_plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_1_frameshift'; --- ************************************************ --- *** relation: nuclease_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclease_hypersensitive_site AS SELECT feature_id AS nuclease_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_hypersensitive_site'; --- ************************************************ --- *** relation: coding_start *** --- *** relation type: VIEW *** --- *** *** --- *** The first base to be translated into pro *** --- *** tein. *** --- ************************************************ --- CREATE VIEW coding_start AS SELECT feature_id AS coding_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna_large_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a large ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_large_subunit_primary_transcript AS SELECT feature_id AS rrna_large_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_large_subunit_primary_transcript'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: coding_end *** --- *** relation type: VIEW *** --- *** *** --- *** The last base to be translated into prot *** --- *** ein. It does not include the stop codon. *** --- ************************************************ --- CREATE VIEW coding_end AS SELECT feature_id AS coding_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_end'; --- ************************************************ --- *** relation: microarray_oligo *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW microarray_oligo AS SELECT feature_id AS microarray_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo'; --- ************************************************ --- *** relation: mrna_with_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_2_frameshift AS SELECT feature_id AS mrna_with_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_2_frameshift'; --- ************************************************ --- *** relation: conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of sequence similarity by descent *** --- *** from a common ancestor. *** --- ************************************************ --- CREATE VIEW conserved_region AS SELECT feature_id AS conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'conserved_region'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: coding_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Coding region of sequence similarity by *** --- *** descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW coding_conserved_region AS SELECT feature_id AS coding_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: nc_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding region of sequence similarity *** --- *** by descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW nc_conserved_region AS SELECT feature_id AS nc_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_conserved_region'; --- ************************************************ --- *** relation: mrna_with_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mRNA with a minus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_2_frameshift AS SELECT feature_id AS mrna_with_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_2_frameshift'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: mite *** --- *** relation type: VIEW *** --- *** *** --- *** A highly repetitive and short (100-500 b *** --- *** ase pair) transposable element with term *** --- *** inal inverted repeats (TIR) and target s *** --- *** ite duplication (TSD). MITEs do not enco *** --- *** de proteins. *** --- ************************************************ --- CREATE VIEW mite AS SELECT feature_id AS mite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE'; --- ************************************************ --- *** relation: recombination_hotspot *** --- *** relation type: VIEW *** --- *** *** --- *** A region in a genome which promotes reco *** --- *** mbination. *** --- ************************************************ --- CREATE VIEW recombination_hotspot AS SELECT feature_id AS recombination_hotspot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a nucleic ac *** --- *** id molecule which controls its own repli *** --- *** cation through the interaction of specif *** --- *** ic proteins at one or more origins of re *** --- *** plication. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** A cytologically distinguishable feature *** --- *** of a chromosome, often made visible by s *** --- *** taining, and usually alternating light a *** --- *** nd dark. *** --- ************************************************ --- CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: site_specific_recombination_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW site_specific_recombination_target_region AS SELECT feature_id AS site_specific_recombination_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'site_specific_recombination_target_region'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'match'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a cDNA clone or PCR product; t *** --- *** ypically a few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'EST'; --- ************************************************ --- *** relation: loxp_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loxp_site AS SELECT feature_id AS loxp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to repeating *** --- *** units. The forms found in nature are deo *** --- *** xyribonucleic acid (DNA), where the repe *** --- *** ating units are 2-deoxy-D-ribose rings c *** --- *** onnected to a phosphate backbone, and ri *** --- *** bonucleic acid (RNA), where the repeatin *** --- *** g units are D-ribose rings connected to *** --- *** a phosphate backbone. *** --- ************************************************ --- CREATE VIEW nucleic_acid AS SELECT feature_id AS nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'nucleic_acid'; --- ************************************************ --- *** relation: protein_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW protein_match AS SELECT feature_id AS protein_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: frt_site *** --- *** relation type: VIEW *** --- *** *** --- *** An inversion site found on the Saccharom *** --- *** yces cerevisiae 2 micron plasmid. *** --- ************************************************ --- CREATE VIEW frt_site AS SELECT feature_id AS frt_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site'; --- ************************************************ --- *** relation: synthetic_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to decide a sequence of nuc *** --- *** leotides, nucleotide analogs, or amino a *** --- *** cids that has been designed by an experi *** --- *** menter and which may, or may not, corres *** --- *** pond with any natural sequence. *** --- ************************************************ --- CREATE VIEW synthetic_sequence AS SELECT feature_id AS synthetic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'synthetic_sequence'; --- ************************************************ --- *** relation: dna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a 2-deoxy-D-ribose ring c *** --- *** onnected to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW dna AS SELECT feature_id AS dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'DNA'; --- ************************************************ --- *** relation: sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW sequence_assembly AS SELECT feature_id AS sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'sequence_assembly'; --- ************************************************ --- *** relation: group_1_intron_homing_endonuclease_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_1_intron_homing_endonuclease_target_region AS SELECT feature_id AS group_1_intron_homing_endonuclease_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_1_intron_homing_endonuclease_target_region'; --- ************************************************ --- *** relation: haplotype_block *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome which is co-inher *** --- *** ited as the result of the lack of histor *** --- *** ic recombination within it. *** --- ************************************************ --- CREATE VIEW haplotype_block AS SELECT feature_id AS haplotype_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype_block'; --- ************************************************ --- *** relation: rna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a D-ribose ring connected *** --- *** to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW rna AS SELECT feature_id AS rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA'; --- ************************************************ --- *** relation: flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region that is *** --- *** bounded either side by a paricular kind *** --- *** of region. *** --- ************************************************ --- CREATE VIEW flanked AS SELECT feature_id AS flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'flanked'; --- ************************************************ --- *** relation: floxed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence that is *** --- *** flanked by Lox-P sites. *** --- ************************************************ --- CREATE VIEW floxed AS SELECT feature_id AS floxed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er code for a unique amino acid or the t *** --- *** ermination of translation and are contai *** --- *** ned within the CDS. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'codon'; --- ************************************************ --- *** relation: frt_flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe sequence that i *** --- *** s flanked by the FLP recombinase recogni *** --- *** tion site, FRT. *** --- ************************************************ --- CREATE VIEW frt_flanked AS SELECT feature_id AS frt_flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_flanked'; --- ************************************************ --- *** relation: invalidated_by_chimeric_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone constructed from more than *** --- *** one mRNA. Usually an experimental artifa *** --- *** ct. *** --- ************************************************ --- CREATE VIEW invalidated_by_chimeric_cdna AS SELECT feature_id AS invalidated_by_chimeric_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA'; --- ************************************************ --- *** relation: floxed_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene that is floxed. *** --- ************************************************ --- CREATE VIEW floxed_gene AS SELECT feature_id AS floxed_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene'; --- ************************************************ --- *** relation: transposable_element_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence surrounding a tra *** --- *** nsposible element. *** --- ************************************************ --- CREATE VIEW transposable_element_flanking_region AS SELECT feature_id AS transposable_element_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region'; --- ************************************************ --- *** relation: integron *** --- *** relation type: VIEW *** --- *** *** --- *** A region encoding an integrase which act *** --- *** s at a site adjacent to it (attI_site) t *** --- *** o insert DNA which must include but is n *** --- *** ot limited to an attC_site. *** --- ************************************************ --- CREATE VIEW integron AS SELECT feature_id AS integron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integron'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: atti_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an integron, adjacent to *** --- *** an integrase, at which site specific re *** --- *** combination involving an attC_site takes *** --- *** place. *** --- ************************************************ --- CREATE VIEW atti_site AS SELECT feature_id AS atti_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site'; --- ************************************************ --- *** relation: transposable_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW transposable_element_insertion_site AS SELECT feature_id AS transposable_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that encodes function requi *** --- *** red for conjugation. *** --- ************************************************ --- CREATE VIEW conjugative_transposon AS SELECT feature_id AS conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conjugative_transposon'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA sequence that has catalytic activ *** --- *** ity with or without an associated ribonu *** --- *** cleoprotein. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme' OR cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: recombinationally_inverted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene by i *** --- *** nversion. *** --- ************************************************ --- CREATE VIEW recombinationally_inverted_gene AS SELECT feature_id AS recombinationally_inverted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5_8S ribosomal RNA (5. 8S rRNA) is a com *** --- *** ponent of the large subunit of the eukar *** --- *** yotic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurs *** --- *** or that also contains 18S and 28S rRNA. *** --- *** Functionally, it is thought that 5.8S rR *** --- *** NA may be involved in ribosome transloca *** --- *** tion. It is also known to form covalent *** --- *** linkage to the p53 tumour suppressor pro *** --- *** tein. 5_8S rRNA is also found in archaea *** --- *** . *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S'; --- ************************************************ --- *** relation: rna_6s *** --- *** relation type: VIEW *** --- *** *** --- *** A small (184-nt in E. coli) RNA that for *** --- *** ms a hairpin type structure. 6S RNA asso *** --- *** ciates with RNA polymerase in a highly s *** --- *** pecific manner. 6S RNA represses express *** --- *** ion from a sigma70-dependent promoter du *** --- *** ring stationary phase. *** --- ************************************************ --- CREATE VIEW rna_6s AS SELECT feature_id AS rna_6s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_6S'; --- ************************************************ --- *** relation: csrb_rsmb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An enterobacterial RNA that binds the Cs *** --- *** rA protein. The CsrB RNAs contain a cons *** --- *** erved motif CAGGXXG that is found in up *** --- *** to 18 copies and has been suggested to b *** --- *** ind CsrA. The Csr regulatory system has *** --- *** a strong negative regulatory effect on g *** --- *** lycogen biosynthesis, glyconeogenesis an *** --- *** d glycogen catabolism and a positive reg *** --- *** ulatory effect on glycolysis. In other b *** --- *** acteria such as Erwinia caratovara the R *** --- *** smA protein has been shown to regulate t *** --- *** he production of virulence determinants, *** --- *** such extracellular enzymes. RsmA binds *** --- *** to RsmB regulatory RNA which is also a m *** --- *** ember of this family. *** --- ************************************************ --- CREATE VIEW csrb_rsmb_rna AS SELECT feature_id AS csrb_rsmb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CsrB_RsmB_RNA'; --- ************************************************ --- *** relation: dsra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** DsrA RNA regulates both transcription, b *** --- *** y overcoming transcriptional silencing b *** --- *** y the nucleoid-associated H-NS protein, *** --- *** and translation, by promoting efficient *** --- *** translation of the stress sigma factor, *** --- *** RpoS. These two activities of DsrA can b *** --- *** e separated by mutation: the first of th *** --- *** ree stem-loops of the 85 nucleotide RNA *** --- *** is necessary for RpoS translation but no *** --- *** t for anti-H-NS action, while the second *** --- *** stem-loop is essential for antisilencin *** --- *** g and less critical for RpoS translation *** --- *** . The third stem-loop, which behaves as *** --- *** a transcription terminator, can be subst *** --- *** ituted by the trp transcription terminat *** --- *** or without loss of either DsrA function. *** --- *** The sequence of the first stem-loop of *** --- *** DsrA is complementary with the upstream *** --- *** leader portion of RpoS messenger RNA, su *** --- *** ggesting that pairing of DsrA with the R *** --- *** poS message might be important for trans *** --- *** lational regulation. *** --- ************************************************ --- CREATE VIEW dsra_rna AS SELECT feature_id AS dsra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA' OR cvterm.name = 'DsrA_RNA'; --- ************************************************ --- *** relation: gcvb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA involved in exp *** --- *** ression of the dipeptide and oligopeptid *** --- *** e transport systems in Escherichia coli. *** --- ************************************************ --- CREATE VIEW gcvb_rna AS SELECT feature_id AS gcvb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: group_iia_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iia_intron AS SELECT feature_id AS group_iia_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron'; --- ************************************************ --- *** relation: group_iib_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iib_intron AS SELECT feature_id AS group_iib_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIB_intron'; --- ************************************************ --- *** relation: micf_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-translated 93 nt antisense RNA tha *** --- *** t binds its target ompF mRNA and regulat *** --- *** es ompF expression by inhibiting transla *** --- *** tion and inducing degradation of the mes *** --- *** sage. *** --- ************************************************ --- CREATE VIEW micf_rna AS SELECT feature_id AS micf_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA'; --- ************************************************ --- *** relation: oxys_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA which is induce *** --- *** d in response to oxidative stress in Esc *** --- *** herichia coli. Acts as a global regulato *** --- *** r to activate or repress the expression *** --- *** of as many as 40 genes, including the fh *** --- *** lA-encoded transcriptional activator and *** --- *** the rpoS-encoded sigma(s) subunit of RN *** --- *** A polymerase. OxyS is bound by the Hfq p *** --- *** rotein, that increases the OxyS RNA inte *** --- *** raction with its target messages. *** --- ************************************************ --- CREATE VIEW oxys_rna AS SELECT feature_id AS oxys_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'OxyS_RNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterised activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: rpra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Translational regulation of the stationa *** --- *** ry phase sigma factor RpoS is mediated b *** --- *** y the formation of a double-stranded RNA *** --- *** stem-loop structure in the upstream reg *** --- *** ion of the rpoS messenger RNA, occluding *** --- *** the translation initiation site. Clones *** --- *** carrying rprA (RpoS regulator RNA) incr *** --- *** eased the translation of RpoS. The rprA *** --- *** gene encodes a 106 nucleotide regulatory *** --- *** RNA. As with DsrA Rfam:RF00014, RprA is *** --- *** predicted to form three stem-loops. Thu *** --- *** s, at least two small RNAs, DsrA and Rpr *** --- *** A, participate in the positive regulatio *** --- *** n of RpoS translation. Unlike DsrA, RprA *** --- *** does not have an extensive region of co *** --- *** mplementarity to the RpoS leader, leavin *** --- *** g its mechanism of action unclear. RprA *** --- *** is non-essential. *** --- ************************************************ --- CREATE VIEW rpra_rna AS SELECT feature_id AS rpra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RprA_RNA'; --- ************************************************ --- *** relation: rre_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The Rev response element (RRE) is encode *** --- *** d within the HIV-env gene. Rev is an ess *** --- *** ential regulatory protein of HIV that bi *** --- *** nds an internal loop of the RRE leading, *** --- *** encouraging further Rev-RRE binding. Th *** --- *** is RNP complex is critical for mRNA expo *** --- *** rt and hence for expression of the HIV s *** --- *** tructural proteins. *** --- ************************************************ --- CREATE VIEW rre_rna AS SELECT feature_id AS rre_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RRE_RNA'; --- ************************************************ --- *** relation: spot_42_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A 109-nucleotide RNA of E. coli that see *** --- *** ms to have a regulatory role on the gala *** --- *** ctose operon. Changes in Spot 42 levels *** --- *** are implicated in affecting DNA polymera *** --- *** se I levels. *** --- ************************************************ --- CREATE VIEW spot_42_rna AS SELECT feature_id AS spot_42_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spot_42_RNA'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesises telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA is an snRNA required for th *** --- *** e splicing of the minor U12-dependent cl *** --- *** ass of eukaryotic nuclear introns. It fo *** --- *** rms a base paired complex with U4atac_sn *** --- *** RNA (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: sequence_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describes a quality of sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW sequence_attribute AS SELECT feature_id AS sequence_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymer_attribute' OR cvterm.name = 'feature_attribute' OR cvterm.name = 'sequence_location' OR cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_attribute'; --- ************************************************ --- *** relation: gene_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_attribute AS SELECT feature_id AS gene_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'gene_attribute'; --- ************************************************ --- *** relation: u14_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snorna AS SELECT feature_id AS u14_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonucleoprotein comp *** --- *** lex. The complex consists of a major vau *** --- *** lt protein (MVP), two minor vault protei *** --- *** ns (VPARP and TEP1), and several small u *** --- *** ntranslated RNA molecules. It has been s *** --- *** uggested that the vault complex is invol *** --- *** ved in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: twintron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron within an intron. Twintrons ar *** --- *** e group II or III introns, into which an *** --- *** other group II or III intron has been tr *** --- *** ansposed. *** --- ************************************************ --- CREATE VIEW twintron AS SELECT feature_id AS twintron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'twintron'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in eukaryotes, wh *** --- *** ich functions as the small subunit of th *** --- *** e ribosome. *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region on the surface of a molecule th *** --- *** at may interact with another molecule. W *** --- *** hen applied to polypeptides: Amino acids *** --- *** involved in binding or interactions. It *** --- *** can also apply to an amino acid bond wh *** --- *** ich is represented by the positions of t *** --- *** he two flanking amino acids. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a p *** --- *** rotein. *** --- ************************************************ --- CREATE VIEW protein_binding_site AS SELECT feature_id AS protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'protein_binding_site'; --- ************************************************ --- *** relation: rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that rescues. *** --- ************************************************ --- CREATE VIEW rescue_region AS SELECT feature_id AS rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'rescue_region'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polynucleotide sequence prod *** --- *** uced by digestion with a restriction end *** --- *** onuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment' OR cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequence differs from *** --- *** that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: invalidated_by_genomic_contamination *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to genomic contaminat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_contamination AS SELECT feature_id AS invalidated_by_genomic_contamination_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_contamination'; --- ************************************************ --- *** relation: invalidated_by_genomic_polya_primed_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to polyA priming. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_polya_primed_cdna AS SELECT feature_id AS invalidated_by_genomic_polya_primed_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA'; --- ************************************************ --- *** relation: invalidated_by_partial_processing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to partial processing *** --- *** . *** --- ************************************************ --- CREATE VIEW invalidated_by_partial_processing AS SELECT feature_id AS invalidated_by_partial_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_partial_processing'; --- ************************************************ --- *** relation: polypeptide_domain *** --- *** relation type: VIEW *** --- *** *** --- *** A structurally or functionally defined p *** --- *** rotein region. In proteins with multiple *** --- *** domains, the combination of the domains *** --- *** determines the function of the protein. *** --- *** A region which has been shown to recur *** --- *** throughout evolution. *** --- ************************************************ --- CREATE VIEW polypeptide_domain AS SELECT feature_id AS polypeptide_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The signal_peptide is a short region of *** --- *** the peptide located at the N-terminus th *** --- *** at directs the protein to be secreted or *** --- *** part of membrane components. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: mature_protein_region *** --- *** relation type: VIEW *** --- *** *** --- *** The polypeptide sequence that remains wh *** --- *** en the cleaved peptide regions have been *** --- *** cleaved from the immature peptide. *** --- ************************************************ --- CREATE VIEW mature_protein_region AS SELECT feature_id AS mature_protein_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide' OR cvterm.name = 'mature_protein_region'; --- ************************************************ --- *** relation: five_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_terminal_inverted_repeat AS SELECT feature_id AS five_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: three_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_terminal_inverted_repeat AS SELECT feature_id AS three_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: u5_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_ltr_region AS SELECT feature_id AS u5_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U5_LTR_region'; --- ************************************************ --- *** relation: r_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_ltr_region AS SELECT feature_id AS r_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'R_LTR_region'; --- ************************************************ --- *** relation: u3_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_ltr_region AS SELECT feature_id AS u3_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'U3_LTR_region'; --- ************************************************ --- *** relation: five_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr AS SELECT feature_id AS five_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR'; --- ************************************************ --- *** relation: three_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr AS SELECT feature_id AS three_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_LTR'; --- ************************************************ --- *** relation: r_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_five_prime_ltr_region AS SELECT feature_id AS r_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region'; --- ************************************************ --- *** relation: u5_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_five_prime_ltr_region AS SELECT feature_id AS u5_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region'; --- ************************************************ --- *** relation: u3_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_five_prime_ltr_region AS SELECT feature_id AS u3_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region'; --- ************************************************ --- *** relation: r_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_three_prime_ltr_region AS SELECT feature_id AS r_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region'; --- ************************************************ --- *** relation: u3_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_three_prime_ltr_region AS SELECT feature_id AS u3_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_three_prime_LTR_region'; --- ************************************************ --- *** relation: u5_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_three_prime_ltr_region AS SELECT feature_id AS u5_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_three_prime_LTR_region'; --- ************************************************ --- *** relation: non_ltr_retrotransposon_polymeric_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polymeric tract, such as poly(dA), wit *** --- *** hin a non_LTR_retrotransposon. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon_polymeric_tract AS SELECT feature_id AS non_ltr_retrotransposon_polymeric_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract'; --- ************************************************ --- *** relation: target_site_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of the target DNA that is dup *** --- *** licated when a transposable element or p *** --- *** hage inserts; usually found at each end *** --- *** the insertion. *** --- ************************************************ --- CREATE VIEW target_site_duplication AS SELECT feature_id AS target_site_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication'; --- ************************************************ --- *** relation: rr_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polypurine tract within an LTR_retrotr *** --- *** ansposon. *** --- ************************************************ --- CREATE VIEW rr_tract AS SELECT feature_id AS rr_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: inverted_ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_ring_chromosome AS SELECT feature_id AS inverted_ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome'; --- ************************************************ --- *** relation: vector_replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A replicon that has been modified to act *** --- *** as a vector for foreign sequence. *** --- ************************************************ --- CREATE VIEW vector_replicon AS SELECT feature_id AS vector_replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'vector_replicon'; --- ************************************************ --- *** relation: ss_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ss_oligo AS SELECT feature_id AS ss_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ss_oligo'; --- ************************************************ --- *** relation: ds_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ds_oligo AS SELECT feature_id AS ds_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'ds_oligo'; --- ************************************************ --- *** relation: polymer_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the kind of bio *** --- *** logical sequence. *** --- ************************************************ --- CREATE VIEW polymer_attribute AS SELECT feature_id AS polymer_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'polymer_attribute'; --- ************************************************ --- *** relation: three_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_noncoding_exon AS SELECT feature_id AS three_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon'; --- ************************************************ --- *** relation: five_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_noncoding_exon AS SELECT feature_id AS five_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_noncoding_exon'; --- ************************************************ --- *** relation: utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Intron located in the untranslated regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW utr_intron AS SELECT feature_id AS utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'UTR_intron'; --- ************************************************ --- *** relation: five_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_intron AS SELECT feature_id AS five_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron'; --- ************************************************ --- *** relation: three_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_intron AS SELECT feature_id AS three_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR_intron'; --- ************************************************ --- *** relation: random_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides or amino acids *** --- *** which, by design, has a "random" order *** --- *** of components, given a predetermined inp *** --- *** ut frequency of these components. *** --- ************************************************ --- CREATE VIEW random_sequence AS SELECT feature_id AS random_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence'; --- ************************************************ --- *** relation: interband *** --- *** relation type: VIEW *** --- *** *** --- *** A light region between two darkly staini *** --- *** ng bands in a polytene chromosome. *** --- ************************************************ --- CREATE VIEW interband AS SELECT feature_id AS interband_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interband'; --- ************************************************ --- *** relation: gene_with_polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polyadenylated mRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW gene_with_polyadenylated_mrna AS SELECT feature_id AS gene_with_polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA'; --- ************************************************ --- *** relation: transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transposition AS SELECT feature_id AS transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'transposition'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small, 17-28-nt, small interfering RNA *** --- *** derived from transcripts of repetitive *** --- *** elements. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: gene_with_mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA with a frame *** --- *** shift. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_with_frameshift AS SELECT feature_id AS gene_with_mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_with_frameshift'; --- ************************************************ --- *** relation: recombinationally_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is recombinationally rearran *** --- *** ged. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_gene AS SELECT feature_id AS recombinationally_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'recombinationally_rearranged_gene'; --- ************************************************ --- *** relation: interchromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving an in *** --- *** sertion from another chromosome. *** --- ************************************************ --- CREATE VIEW interchromosomal_duplication AS SELECT feature_id AS interchromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication'; --- ************************************************ --- *** relation: d_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including D-region *** --- *** with 5' UTR and 3' UTR, also designated *** --- *** as D-segment. *** --- ************************************************ --- CREATE VIEW d_gene AS SELECT feature_id AS d_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene'; --- ************************************************ --- *** relation: gene_with_trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a transcript that is trans-s *** --- *** pliced. *** --- ************************************************ --- CREATE VIEW gene_with_trans_spliced_transcript AS SELECT feature_id AS gene_with_trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_trans_spliced_transcript'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment'; --- ************************************************ --- *** relation: inversion_derived_bipartite_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a deficiency *** --- *** at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_deficiency AS SELECT feature_id AS inversion_derived_bipartite_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: encodes_alternately_spliced_transcripts *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes more than one transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW encodes_alternately_spliced_transcripts AS SELECT feature_id AS encodes_alternately_spliced_transcripts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_alternately_spliced_transcripts'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendant of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a defic *** --- *** iency at one end of the inversion and a *** --- *** duplication at the other end of the inve *** --- *** rsion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_duplication AS SELECT feature_id AS inversion_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: v_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including L-part1, *** --- *** V-intron and V-exon, with the 5' UTR and *** --- *** 3' UTR. *** --- ************************************************ --- CREATE VIEW v_gene AS SELECT feature_id AS v_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_stability *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is regulated *** --- *** by the stability of the resulting prote *** --- *** in. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_stability AS SELECT feature_id AS post_translationally_regulated_by_protein_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is modified *** --- *** to regulate it. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_modification AS SELECT feature_id AS post_translationally_regulated_by_protein_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_modification'; --- ************************************************ --- *** relation: j_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA of an immunoglobuli *** --- *** n/T-cell receptor gene including J-regio *** --- *** n with 5' UTR (SO:0000204) and 3' UTR (S *** --- *** O:0000205), also designated as J-segment *** --- *** . *** --- ************************************************ --- CREATE VIEW j_gene AS SELECT feature_id AS j_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene'; --- ************************************************ --- *** relation: autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation. *** --- ************************************************ --- CREATE VIEW autoregulated AS SELECT feature_id AS autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'autoregulated'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: negatively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation where it decr *** --- *** eases transcription. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated AS SELECT feature_id AS negatively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path (SO:0000472). *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone' OR cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: positively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation, where it inc *** --- *** reases transcription. *** --- ************************************************ --- CREATE VIEW positively_autoregulated AS SELECT feature_id AS positively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated'; --- ************************************************ --- *** relation: contig_read *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequencer read which is part of a *** --- *** contig. *** --- ************************************************ --- CREATE VIEW contig_read AS SELECT feature_id AS contig_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read'; --- ************************************************ --- *** relation: c_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including C-region (and intro *** --- *** ns if present) with 5' UTR (SO:0000204) *** --- *** and 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW c_gene AS SELECT feature_id AS c_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_gene'; --- ************************************************ --- *** relation: trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_transcript AS SELECT feature_id AS trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'trans_spliced_transcript'; --- ************************************************ --- *** relation: tiling_path_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone which is part of a tiling path. *** --- *** A tiling path is a set of sequencing sub *** --- *** strates, typically clones, which have be *** --- *** en selected in order to efficiently cove *** --- *** r a region of the genome in preparation *** --- *** for sequencing and assembly. *** --- ************************************************ --- CREATE VIEW tiling_path_clone AS SELECT feature_id AS tiling_path_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone'; --- ************************************************ --- *** relation: terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An inverted repeat (SO:0000294) occuring *** --- *** at the termini of a DNA transposon. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat AS SELECT feature_id AS terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'terminal_inverted_repeat'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_gene_cluster AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: three_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 3' exon that is not *** --- *** coding. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_noncoding_region AS SELECT feature_id AS three_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene, and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW dj_j_cluster AS SELECT feature_id AS dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster'; --- ************************************************ --- *** relation: five_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 5' exon preceding th *** --- *** e start codon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_noncoding_region AS SELECT feature_id AS five_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene, one J-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW vdj_j_c_cluster AS SELECT feature_id AS vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_j_cluster AS SELECT feature_id AS vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_cluster'; --- ************************************************ --- *** relation: vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_c_cluster AS SELECT feature_id AS vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_C_cluster'; --- ************************************************ --- *** relation: vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene, one J-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW vj_j_c_cluster AS SELECT feature_id AS vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_C_cluster'; --- ************************************************ --- *** relation: vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one J- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_j_cluster AS SELECT feature_id AS vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_cluster'; --- ************************************************ --- *** relation: d_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_gene_recombination_feature AS SELECT feature_id AS d_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'D_gene_recombination_feature'; --- ************************************************ --- *** relation: three_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site like CAC *** --- *** AGTG, part of a 3' D-recombination signa *** --- *** l sequence of an immunoglobulin/T-cell r *** --- *** eceptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_heptamer AS SELECT feature_id AS three_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer'; --- ************************************************ --- *** relation: three_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** A 9 nucleotide recombination site (e.g. *** --- *** ACAAAAACC), part of a 3' D-recombination *** --- *** signal sequence of an immunoglobulin/T- *** --- *** cell receptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_nonamer AS SELECT feature_id AS three_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer'; --- ************************************************ --- *** relation: three_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** A 12 or 23 nucleotide spacer between the *** --- *** 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-R *** --- *** S. *** --- ************************************************ --- CREATE VIEW three_prime_d_spacer AS SELECT feature_id AS three_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer'; --- ************************************************ --- *** relation: five_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CTGTG), part of a 5' D-recombination sig *** --- *** nal sequence (SO:0000556) of an immunogl *** --- *** obulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_heptamer AS SELECT feature_id AS five_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_heptamer'; --- ************************************************ --- *** relation: five_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a five_prime_D-recombi *** --- *** nation signal sequence (SO:0000556) of a *** --- *** n immunoglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_nonamer AS SELECT feature_id AS five_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_nonamer'; --- ************************************************ --- *** relation: five_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the 5 *** --- *** ' D-heptamer (SO:0000496) and 5' D-nonam *** --- *** er (SO:0000497) of a 5' D-recombination *** --- *** signal sequence (SO:0000556) of an immun *** --- *** oglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_spacer AS SELECT feature_id AS five_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_spacer'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous piece of sequence similar t *** --- *** o the 'virtual contig' concept of the En *** --- *** sembl database. *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. Th *** --- *** is is less energetically favourable than *** --- *** watson crick base pairing. Hoogsteen GC *** --- *** base pairs only have two hydrogen bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW hoogsteen_base_pair AS SELECT feature_id AS hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Hoogsteen_base_pair'; --- ************************************************ --- *** relation: reverse_hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW reverse_hoogsteen_base_pair AS SELECT feature_id AS reverse_hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_Hoogsteen_base_pair'; --- ************************************************ --- *** relation: d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_c_cluster AS SELECT feature_id AS d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_C_cluster'; --- ************************************************ --- *** relation: d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW d_dj_cluster AS SELECT feature_id AS d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_cluster'; --- ************************************************ --- *** relation: d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_c_cluster AS SELECT feature_id AS d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of an exon, *** --- *** part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, and one J-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_cluster AS SELECT feature_id AS d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_cluster'; --- ************************************************ --- *** relation: d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW d_j_c_cluster AS SELECT feature_id AS d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster'; --- ************************************************ --- *** relation: vd_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including L-part1, V-intron and V *** --- *** -D-exon, with the 5' UTR (SO:0000204) an *** --- *** d 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vd_gene AS SELECT feature_id AS vd_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene'; --- ************************************************ --- *** relation: j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one J-gene and one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW j_c_cluster AS SELECT feature_id AS j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a deficiency *** --- *** at one end and presumed to have a defic *** --- *** iency or duplication at the other end of *** --- *** the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_aneuploid AS SELECT feature_id AS inversion_derived_deficiency_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_aneuploid'; --- ************************************************ --- *** relation: j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one J-gene. *** --- ************************************************ --- CREATE VIEW j_cluster AS SELECT feature_id AS j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_cluster'; --- ************************************************ --- *** relation: j_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a J-gene recombination *** --- *** feature of an immunoglobulin/T-cell rec *** --- *** eptor gene. *** --- ************************************************ --- CREATE VIEW j_nonamer AS SELECT feature_id AS j_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_nonamer'; --- ************************************************ --- *** relation: j_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of a J-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW j_heptamer AS SELECT feature_id AS j_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_heptamer'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of a transcr *** --- *** ipt, part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: j_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the J *** --- *** -nonamer and the J-heptamer of a J-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW j_spacer AS SELECT feature_id AS j_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_spacer'; --- ************************************************ --- *** relation: v_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_dj_cluster AS SELECT feature_id AS v_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_cluster'; --- ************************************************ --- *** relation: v_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_cluster AS SELECT feature_id AS v_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_cluster'; --- ************************************************ --- *** relation: v_vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_c_cluster AS SELECT feature_id AS v_vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_C_cluster'; --- ************************************************ --- *** relation: v_vdj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VDJ *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW v_vdj_cluster AS SELECT feature_id AS v_vdj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_cluster'; --- ************************************************ --- *** relation: v_vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_cluster AS SELECT feature_id AS v_vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_cluster'; --- ************************************************ --- *** relation: v_vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_c_cluster AS SELECT feature_id AS v_vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_C_cluster'; --- ************************************************ --- *** relation: v_vj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_vj_cluster AS SELECT feature_id AS v_vj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_cluster'; --- ************************************************ --- *** relation: v_vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_cluster AS SELECT feature_id AS v_vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_cluster'; --- ************************************************ --- *** relation: v_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one V-gene. *** --- ************************************************ --- CREATE VIEW v_cluster AS SELECT feature_id AS v_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_cluster'; --- ************************************************ --- *** relation: v_d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_c_cluster AS SELECT feature_id AS v_d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_cluster AS SELECT feature_id AS v_d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene, one J-gene and one C-gene *** --- *** . *** --- ************************************************ --- CREATE VIEW v_d_dj_j_c_cluster AS SELECT feature_id AS v_d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_j_cluster AS SELECT feature_id AS v_d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_cluster'; --- ************************************************ --- *** relation: v_d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_c_cluster AS SELECT feature_id AS v_d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_C_cluster'; --- ************************************************ --- *** relation: v_d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_cluster AS SELECT feature_id AS v_d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_cluster'; --- ************************************************ --- *** relation: v_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of V-gene recombination fea *** --- *** ture of an immunoglobulin/T-cell recepto *** --- *** r gene. *** --- ************************************************ --- CREATE VIEW v_heptamer AS SELECT feature_id AS v_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_heptamer'; --- ************************************************ --- *** relation: v_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW v_j_cluster AS SELECT feature_id AS v_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_cluster'; --- ************************************************ --- *** relation: v_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW v_j_c_cluster AS SELECT feature_id AS v_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_C_cluster'; --- ************************************************ --- *** relation: v_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. AC *** --- *** AAAAACC), part of V-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW v_nonamer AS SELECT feature_id AS v_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_nonamer'; --- ************************************************ --- *** relation: v_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the V *** --- *** -heptamer and the V-nonamer of a V-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_spacer AS SELECT feature_id AS v_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_spacer'; --- ************************************************ --- *** relation: v_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including V-heptame *** --- *** r, V-spacer and V-nonamer in 3' of V-reg *** --- *** ion of a V-gene or V-sequence of an immu *** --- *** noglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_gene_recombination_feature AS SELECT feature_id AS v_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene_recombination_feature'; --- ************************************************ --- *** relation: dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW dj_c_cluster AS SELECT feature_id AS dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_C_cluster'; --- ************************************************ --- *** relation: dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA in rearranged configuration *** --- *** including at least one D-J-GENE, one J-G *** --- *** ENE and one C-GENE. *** --- ************************************************ --- CREATE VIEW dj_j_c_cluster AS SELECT feature_id AS dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one C *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_c_cluster AS SELECT feature_id AS vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_C_cluster'; --- ************************************************ --- *** relation: v_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_c_cluster AS SELECT feature_id AS v_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_C_cluster'; --- ************************************************ --- *** relation: helitron *** --- *** relation type: VIEW *** --- *** *** --- *** A rolling circle transposon. Autonomous *** --- *** helitrons encode a 5'-to-3' DNA helicase *** --- *** and nuclease/ligase similar to those en *** --- *** coded by known rolling-circle replicons. *** --- ************************************************ --- CREATE VIEW helitron AS SELECT feature_id AS helitron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helitron'; --- ************************************************ --- *** relation: recoding_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** The pseudoknots involved in recoding are *** --- *** unique in that, as they play their role *** --- *** as a structure, they are immediately un *** --- *** folded and their now linear sequence ser *** --- *** ves as a template for decoding. *** --- ************************************************ --- CREATE VIEW recoding_pseudoknot AS SELECT feature_id AS recoding_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot'; --- ************************************************ --- *** relation: designed_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW designed_sequence AS SELECT feature_id AS designed_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'designed_sequence'; --- ************************************************ --- *** relation: inversion_derived_bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a dupli *** --- *** cation at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_duplication AS SELECT feature_id AS inversion_derived_bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_duplication'; --- ************************************************ --- *** relation: gene_with_edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript that is *** --- *** edited. *** --- ************************************************ --- CREATE VIEW gene_with_edited_transcript AS SELECT feature_id AS gene_with_edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_edited_transcript'; --- ************************************************ --- *** relation: inversion_derived_duplication_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a duplicatio *** --- *** n at one end and presumed to have a defi *** --- *** ciency or duplication at the other end o *** --- *** f the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_duplication_plus_aneuploid AS SELECT feature_id AS inversion_derived_duplication_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_duplication_plus_aneuploid'; --- ************************************************ --- *** relation: aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aneuploid_chromosome AS SELECT feature_id AS aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'aneuploid_chromosome'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Region in 5' UTR where ribosome assemble *** --- *** s on mRNA. *** --- ************************************************ --- CREATE VIEW shine_dalgarno_sequence AS SELECT feature_id AS shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: five_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 5' most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW five_prime_clip AS SELECT feature_id AS five_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip'; --- ************************************************ --- *** relation: five_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 5' *** --- *** D-nonamer (SO:0000497), 5' D-spacer (SO *** --- *** :0000498), and 5' D-heptamer (SO:0000396 *** --- *** ) in 5' of the D-region of a D-gene, or *** --- *** in 5' of the D-region of DJ-gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_recombination_signal_sequence AS SELECT feature_id AS five_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: three_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 3'-most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW three_prime_clip AS SELECT feature_id AS three_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_clip'; --- ************************************************ --- *** relation: c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including more than one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW c_cluster AS SELECT feature_id AS c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_cluster'; --- ************************************************ --- *** relation: d_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one D-gene. *** --- ************************************************ --- CREATE VIEW d_cluster AS SELECT feature_id AS d_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_cluster'; --- ************************************************ --- *** relation: d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW d_j_cluster AS SELECT feature_id AS d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_cluster'; --- ************************************************ --- *** relation: heptamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Seven nucleotide recombination site (e.g *** --- *** . CACAGTG), part of V-gene, D-gene or J- *** --- *** gene recombination feature of an immunog *** --- *** lobulin or T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW heptamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS heptamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: nonamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nonamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS nonamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_spacer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_spacer AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer'; --- ************************************************ --- *** relation: v_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_c_cluster AS SELECT feature_id AS v_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_c_cluster AS SELECT feature_id AS v_vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_c_cluster AS SELECT feature_id AS v_vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome may be generated by recombi *** --- *** nation between two inverversions; presum *** --- *** ed to have a deficiency or duplication a *** --- *** t each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_aneuploid_chromosome AS SELECT feature_id AS inversion_derived_aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome'; --- ************************************************ --- *** relation: bidirectional_promoter *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bidirectional_promoter AS SELECT feature_id AS bidirectional_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter'; --- ************************************************ --- *** relation: retrotransposed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of a feature that occured a *** --- *** s the product of a reverse transcriptase *** --- *** mediated event. *** --- ************************************************ --- CREATE VIEW retrotransposed AS SELECT feature_id AS retrotransposed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposed'; --- ************************************************ --- *** relation: three_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 3' *** --- *** D-heptamer (SO:0000493), 3' D-spacer, a *** --- *** nd 3' D-nonamer (SO:0000494) in 3' of th *** --- *** e D-region of a D-gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_recombination_signal_sequence AS SELECT feature_id AS three_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: mirna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_encoding AS SELECT feature_id AS mirna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding'; --- ************************************************ --- *** relation: dj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including D-J-region with 5' UTR *** --- *** and 3' UTR, also designated as D-J-segme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW dj_gene AS SELECT feature_id AS dj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_gene'; --- ************************************************ --- *** relation: rrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rrna_encoding AS SELECT feature_id AS rrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_encoding'; --- ************************************************ --- *** relation: vdj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-D-J-exon, with the 5'UTR *** --- *** (SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vdj_gene AS SELECT feature_id AS vdj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_gene'; --- ************************************************ --- *** relation: scrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_encoding AS SELECT feature_id AS scrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_encoding'; --- ************************************************ --- *** relation: vj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-J-exon, with the 5'UTR ( *** --- *** SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vj_gene AS SELECT feature_id AS vj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_gene'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere'; --- ************************************************ --- *** relation: snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_encoding AS SELECT feature_id AS snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'snoRNA_encoding'; --- ************************************************ --- *** relation: edited_transcript_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable feature on a transcript that *** --- *** is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript_feature AS SELECT feature_id AS edited_transcript_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'edited_transcript_feature'; --- ************************************************ --- *** relation: methylation_guide_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a methylat *** --- *** ion guide small nucleolar RNA. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna_primary_transcript AS SELECT feature_id AS methylation_guide_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: rrna_cleavage_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding an rRNA cl *** --- *** eavage snoRNA. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_snorna_primary_transcript AS SELECT feature_id AS rrna_cleavage_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: pre_edited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a transcript that will be *** --- *** edited. *** --- ************************************************ --- CREATE VIEW pre_edited_region AS SELECT feature_id AS pre_edited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region'; --- ************************************************ --- *** relation: tmrna *** --- *** relation type: VIEW *** --- *** *** --- *** A tmRNA liberates a mRNA from a stalled *** --- *** ribosome. To accomplish this part of the *** --- *** tmRNA is used as a reading frame that e *** --- *** nds in a translation stop signal. The br *** --- *** oken mRNA is replaced in the ribosome by *** --- *** the tmRNA and translation of the tmRNA *** --- *** leads to addition of a proteolysis tag t *** --- *** o the incomplete protein enabling recogn *** --- *** ition by a protease. Recently a number o *** --- *** f permuted tmRNAs genes have been found *** --- *** encoded in two parts. TmRNAs have been i *** --- *** dentified in eubacteria and some chlorop *** --- *** lasts but are absent from archeal and eu *** --- *** karyote nuclear genomes. *** --- ************************************************ --- CREATE VIEW tmrna AS SELECT feature_id AS tmrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_encoding AS SELECT feature_id AS c_d_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding'; --- ************************************************ --- *** relation: tmrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tmRNA (S *** --- *** O:0000584). *** --- ************************************************ --- CREATE VIEW tmrna_primary_transcript AS SELECT feature_id AS tmrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_primary_transcript'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyse their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: autocatalytically_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW autocatalytically_spliced_intron AS SELECT feature_id AS autocatalytically_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: srp_rna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a signal r *** --- *** ecognition particle RNA. *** --- ************************************************ --- CREATE VIEW srp_rna_primary_transcript AS SELECT feature_id AS srp_rna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_primary_transcript'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A tertiary structure in RNA where nucleo *** --- *** tides in a loop form base pairs with a r *** --- *** egion of RNA downstream of the loop. *** --- ************************************************ --- CREATE VIEW pseudoknot AS SELECT feature_id AS pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'pseudoknot'; --- ************************************************ --- *** relation: h_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudoknot which contains two stems an *** --- *** d at least two loops. *** --- ************************************************ --- CREATE VIEW h_pseudoknot AS SELECT feature_id AS h_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_pseudoknot'; --- ************************************************ --- *** relation: c_d_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Most box C/D snoRNAs also contain long ( *** --- *** >10 nt) sequences complementary to rRNA. *** --- *** Boxes C and D, as well as boxes C' and *** --- *** D', are usually located in close proximi *** --- *** ty, and form a structure known as the bo *** --- *** x C/D motif. This motif is important for *** --- *** snoRNA stability, processing, nucleolar *** --- *** targeting and function. A small number *** --- *** of box C/D snoRNAs are involved in rRNA *** --- *** processing; most, however, are known or *** --- *** predicted to serve as guide RNAs in ribo *** --- *** se methylation of rRNA. Targeting involv *** --- *** es direct base pairing of the snoRNA at *** --- *** the rRNA site to be modified and selecti *** --- *** on of a rRNA nucleotide a fixed distance *** --- *** from box D or D'. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna AS SELECT feature_id AS c_d_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'C_D_box_snoRNA'; --- ************************************************ --- *** relation: h_aca_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Members of the box H/ACA family contain *** --- *** an ACA triplet, exactly 3 nt upstream fr *** --- *** om the 3' end and an H-box in a hinge re *** --- *** gion that links two structurally similar *** --- *** functional domains of the molecule. Bot *** --- *** h boxes are important for snoRNA biosynt *** --- *** hesis and function. A few box H/ACA snoR *** --- *** NAs are involved in rRNA processing; mos *** --- *** t others are known or predicted to parti *** --- *** cipate in selection of uridine nucleosid *** --- *** es in rRNA to be converted to pseudourid *** --- *** ines. Site selection is mediated by dire *** --- *** ct base pairing of the snoRNA with rRNA *** --- *** through one or both targeting domains. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna AS SELECT feature_id AS h_aca_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box C/D family. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_primary_transcript AS SELECT feature_id AS c_d_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: h_aca_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box H/ACA family. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_primary_transcript AS SELECT feature_id AS h_aca_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a duplex (except for its post-transcript *** --- *** ionally added oligo_U tail (SO:0000609)) *** --- *** with a stretch of mature edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: editing_block *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by a singl *** --- *** e guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW editing_block AS SELECT feature_id AS editing_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_block'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing or overlapping no ge *** --- *** nes that is bounded on either side by a *** --- *** gene, or bounded by a gene and the end o *** --- *** f the chromosome. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: editing_domain *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by two or *** --- *** more overlapping guide RNAs (SO:0000602) *** --- *** . *** --- ************************************************ --- CREATE VIEW editing_domain AS SELECT feature_id AS editing_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_domain'; --- ************************************************ --- *** relation: unedited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an edited transcript that *** --- *** will not be edited. *** --- ************************************************ --- CREATE VIEW unedited_region AS SELECT feature_id AS unedited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unedited_region'; --- ************************************************ --- *** relation: h_aca_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_encoding AS SELECT feature_id AS h_aca_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_encoding'; --- ************************************************ --- *** relation: oligo_u_tail *** --- *** relation type: VIEW *** --- *** *** --- *** The string of non-encoded U's at the 3' *** --- *** end of a guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW oligo_u_tail AS SELECT feature_id AS oligo_u_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo_U_tail'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which bacterial RNA po *** --- *** lymerase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter AS SELECT feature_id AS bacterial_rnapol_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter'; --- ************************************************ --- *** relation: bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for bacterial transc *** --- *** ription. *** --- ************************************************ --- CREATE VIEW bacterial_terminator AS SELECT feature_id AS bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'bacterial_terminator'; --- ************************************************ --- *** relation: terminator_of_type_2_rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for RNA polymerase I *** --- *** II transcription. *** --- ************************************************ --- CREATE VIEW terminator_of_type_2_rnapol_iii_promoter AS SELECT feature_id AS terminator_of_type_2_rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter'; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The base where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_1 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_1 AS SELECT feature_id AS rnapol_iii_promoter_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_2 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_2 AS SELECT feature_id AS rnapol_iii_promoter_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_2'; --- ************************************************ --- *** relation: a_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognised by TFIIIC, with consensus s *** --- *** equence TGGCnnAGTGG. *** --- ************************************************ --- CREATE VIEW a_box AS SELECT feature_id AS a_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box'; --- ************************************************ --- *** relation: b_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognised by TFIIIC, with consensus s *** --- *** equence AGGTTCCAnnCC. *** --- ************************************************ --- CREATE VIEW b_box AS SELECT feature_id AS b_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'B_box'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_3 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_3 AS SELECT feature_id AS rnapol_iii_promoter_type_3_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_3'; --- ************************************************ --- *** relation: c_box *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA polymerase III type 1 promoter wi *** --- *** th consensus sequence CAnnCCn. *** --- ************************************************ --- CREATE VIEW c_box AS SELECT feature_id AS c_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_box'; --- ************************************************ --- *** relation: snrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_encoding AS SELECT feature_id AS snrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_encoding'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenance of the end. *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region which upon binding o *** --- *** f transcription factors, suppress the tr *** --- *** anscription of the gene or genes they co *** --- *** ntrol. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: chromosomal_regulatory_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_regulatory_element AS SELECT feature_id AS chromosomal_regulatory_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'chromosomal_regulatory_element'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** A trancriptional cis regulatory region t *** --- *** hat when located between a CM and a gene *** --- *** 's promoter prevents the CRM from modula *** --- *** ting that genes expression. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: five_prime_open_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_open_reading_frame AS SELECT feature_id AS five_prime_open_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_open_reading_frame'; --- ************************************************ --- *** relation: upstream_aug_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon upstream of the ORF. *** --- ************************************************ --- CREATE VIEW upstream_aug_codon AS SELECT feature_id AS upstream_aug_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon'; --- ************************************************ --- *** relation: polycistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for more t *** --- *** han one gene product. *** --- ************************************************ --- CREATE VIEW polycistronic_primary_transcript AS SELECT feature_id AS polycistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for one ge *** --- *** ne product. *** --- ************************************************ --- CREATE VIEW monocistronic_primary_transcript AS SELECT feature_id AS monocistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with either a single protein pro *** --- *** duct, or for which the regions encoding *** --- *** all its protein products overlap. *** --- ************************************************ --- CREATE VIEW monocistronic_mrna AS SELECT feature_id AS monocistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_mRNA'; --- ************************************************ --- *** relation: polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that encodes multiple proteins f *** --- *** rom at least two non-overlapping regions *** --- *** . *** --- ************************************************ --- CREATE VIEW polycistronic_mrna AS SELECT feature_id AS polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA'; --- ************************************************ --- *** relation: mini_exon_donor_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that donates the sp *** --- *** liced leader to other mRNA. *** --- ************************************************ --- CREATE VIEW mini_exon_donor_rna AS SELECT feature_id AS mini_exon_donor_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_exon_donor_RNA'; --- ************************************************ --- *** relation: spliced_leader_rna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW spliced_leader_rna AS SELECT feature_id AS spliced_leader_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliced_leader_RNA'; --- ************************************************ --- *** relation: engineered_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_plasmid AS SELECT feature_id AS engineered_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_plasmid'; --- ************************************************ --- *** relation: transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Part of an rRNA transcription unit that *** --- *** is transcribed but discarded during matu *** --- *** ration, not giving rise to any part of r *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW transcribed_spacer_region AS SELECT feature_id AS transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'transcribed_spacer_region'; --- ************************************************ --- *** relation: internal_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA sequence that *** --- *** separate genes coding for the 28S, 5.8S, *** --- *** and 18S ribosomal RNAs. *** --- ************************************************ --- CREATE VIEW internal_transcribed_spacer_region AS SELECT feature_id AS internal_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region'; --- ************************************************ --- *** relation: external_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA that precede t *** --- *** he sequence that codes for the ribosomal *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW external_transcribed_spacer_region AS SELECT feature_id AS external_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'external_transcribed_spacer_region'; --- ************************************************ --- *** relation: tetranuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tetranuc_repeat_microsat AS SELECT feature_id AS tetranuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetranucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: srp_rna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_encoding AS SELECT feature_id AS srp_rna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_encoding'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region containing tandemly repe *** --- *** ated sequences having a unit length of 1 *** --- *** 0 to 40 bp. *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA' OR cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small RNA molecule that is the product *** --- *** of a longer exogenous or endogenous dsR *** --- *** NA, which is either a bimolecular duplex *** --- *** or very long hairpin, processed (via th *** --- *** e Dicer pathway) such that numerous siRN *** --- *** As accumulate from both strands of the d *** --- *** sRNA. SRNAs trigger the cleavage of thei *** --- *** r target molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: mirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a micro RN *** --- *** A. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript AS SELECT feature_id AS mirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript'; --- ************************************************ --- *** relation: strna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small te *** --- *** mporal mRNA (SO:0000649). *** --- ************************************************ --- CREATE VIEW strna_primary_transcript AS SELECT feature_id AS strna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: small_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the small subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW small_subunit_rrna AS SELECT feature_id AS small_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'small_subunit_rRNA'; --- ************************************************ --- *** relation: large_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the large subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW large_subunit_rrna AS SELECT feature_id AS large_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'large_subunit_rRNA'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilises 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: maxicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mitochondrial gene located in a maxici *** --- *** rcle. *** --- ************************************************ --- CREATE VIEW maxicircle_gene AS SELECT feature_id AS maxicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'maxicircle_gene'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA transcript that does not encode f *** --- *** or a protein rather the RNA molecule is *** --- *** the gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: strna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_encoding AS SELECT feature_id AS strna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_encoding'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: tmrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_encoding AS SELECT feature_id AS tmrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_encoding'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: trna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_encoding AS SELECT feature_id AS trna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_encoding'; --- ************************************************ --- *** relation: introgressed_chromosome_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW introgressed_chromosome_region AS SELECT feature_id AS introgressed_chromosome_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'introgressed_chromosome_region'; --- ************************************************ --- *** relation: monocistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is monocistronic. *** --- ************************************************ --- CREATE VIEW monocistronic_transcript AS SELECT feature_id AS monocistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'monocistronic_transcript'; --- ************************************************ --- *** relation: mobile_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron (mitochondrial, chloroplast, n *** --- *** uclear or prokaryotic) that encodes a do *** --- *** uble strand sequence specific endonuclea *** --- *** se allowing for mobility. *** --- ************************************************ --- CREATE VIEW mobile_intron AS SELECT feature_id AS mobile_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence that has been inser *** --- *** ted. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion' OR cvterm.name = 'insertion'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: sequence_rearrangement_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_rearrangement_feature AS SELECT feature_id AS sequence_rearrangement_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'sequence_rearrangement_feature'; --- ************************************************ --- *** relation: chromosome_breakage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence within the micronuclear DNA o *** --- *** f ciliates at which chromosome breakage *** --- *** and telomere addition occurs during nucl *** --- *** ear differentiation. *** --- ************************************************ --- CREATE VIEW chromosome_breakage_sequence AS SELECT feature_id AS chromosome_breakage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_breakage_sequence'; --- ************************************************ --- *** relation: internal_eliminated_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence eliminated from the genome of *** --- *** ciliates during nuclear differentiation *** --- *** . *** --- ************************************************ --- CREATE VIEW internal_eliminated_sequence AS SELECT feature_id AS internal_eliminated_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_eliminated_sequence'; --- ************************************************ --- *** relation: macronucleus_destined_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that is conserved, although r *** --- *** earranged relative to the micronucleus, *** --- *** in the macronucleus of a ciliate genome. *** --- ************************************************ --- CREATE VIEW macronucleus_destined_segment AS SELECT feature_id AS macronucleus_destined_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronucleus_destined_segment'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'transcript'; --- ************************************************ --- *** relation: canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 3' splice site has the seq *** --- *** uence "AG". *** --- ************************************************ --- CREATE VIEW canonical_three_prime_splice_site AS SELECT feature_id AS canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 5' splice site has the seq *** --- *** uence "GT". *** --- ************************************************ --- CREATE VIEW canonical_five_prime_splice_site AS SELECT feature_id AS canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 3' splice site that does not have the *** --- *** sequence "AG". *** --- ************************************************ --- CREATE VIEW non_canonical_three_prime_splice_site AS SELECT feature_id AS non_canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 5' splice site which does not have the *** --- *** sequence "GT". *** --- ************************************************ --- CREATE VIEW non_canonical_five_prime_splice_site AS SELECT feature_id AS non_canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon that is not the usual AUG *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW non_canonical_start_codon AS SELECT feature_id AS non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'non_canonical_start_codon'; --- ************************************************ --- *** relation: aberrant_processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been processed "in *** --- *** correctly", for example by the failure o *** --- *** f splicing of one or more exons. *** --- ************************************************ --- CREATE VIEW aberrant_processed_transcript AS SELECT feature_id AS aberrant_processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aberrant_processed_transcript'; --- ************************************************ --- *** relation: exonic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Exonic splicing enhancers (ESEs) facilit *** --- *** ate exon definition by assisting in the *** --- *** recruitment of splicing factors to the a *** --- *** djacent intron. *** --- ************************************************ --- CREATE VIEW exonic_splice_enhancer AS SELECT feature_id AS exonic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exonic_splice_enhancer'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targeted *** --- *** by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: dnasei_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dnasei_hypersensitive_site AS SELECT feature_id AS dnasei_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site'; --- ************************************************ --- *** relation: translocation_element *** --- *** relation type: VIEW *** --- *** *** --- *** For some translocations, particularly bu *** --- *** t not exclusively, reciprocal translocat *** --- *** ions, the chromosomes carrying non-homol *** --- *** ogous centromeres may be recovered indep *** --- *** endently. These chromosomes are describe *** --- *** d as translocation elements. *** --- ************************************************ --- CREATE VIEW translocation_element AS SELECT feature_id AS translocation_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occurred. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: gene_with_polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW gene_with_polycistronic_transcript AS SELECT feature_id AS gene_with_polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_polycistronic_transcript'; --- ************************************************ --- *** relation: cleaved_initiator_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** The initiator methionine that has been c *** --- *** leaved from a mature polypeptide sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW cleaved_initiator_methionine AS SELECT feature_id AS cleaved_initiator_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine'; --- ************************************************ --- *** relation: gene_with_dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_transcript AS SELECT feature_id AS gene_with_dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_dicistronic_transcript'; --- ************************************************ --- *** relation: gene_with_recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA that is reco *** --- *** ded. *** --- ************************************************ --- CREATE VIEW gene_with_recoded_mrna AS SELECT feature_id AS gene_with_recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_recoded_mRNA'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives (alleles) exist in normal in *** --- *** dividuals in some population(s), wherein *** --- *** the least frequent allele has an abunda *** --- *** nce of 1% or greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'oligo'; --- ************************************************ --- *** relation: gene_with_stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript with st *** --- *** op codon readthrough. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_read_through AS SELECT feature_id AS gene_with_stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_stop_codon_read_through'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as pyrrolysine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent of zer *** --- *** o. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'polyA_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'junction'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'remark'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A region (or regions) that includes all *** --- *** of the sequence elements necessary to en *** --- *** code a functional transcript. A gene may *** --- *** include regulatory regions, transcribed *** --- *** regions and/or other functional sequenc *** --- *** e regions. *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjcent copies of a region ( *** --- *** of length greater than 1). *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 3' splice site of the acceptor prima *** --- *** ry transcript. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: trans_splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' five prime splice site region of *** --- *** the donor RNA. *** --- ************************************************ --- CREATE VIEW trans_splice_donor_site AS SELECT feature_id AS trans_splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_donor_site'; --- ************************************************ --- *** relation: sl1_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sl1_acceptor_site AS SELECT feature_id AS sl1_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site'; --- ************************************************ --- *** relation: sl2_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sl2_acceptor_site AS SELECT feature_id AS sl2_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL2_acceptor_site'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as selenocysteine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: gene_with_mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with mRNA recoded by translationa *** --- *** l bypass. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_recoded_by_translational_bypass AS SELECT feature_id AS gene_with_mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: gene_with_transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding a transcript that has a *** --- *** translational frameshift. *** --- ************************************************ --- CREATE VIEW gene_with_transcript_with_translational_frameshift AS SELECT feature_id AS gene_with_transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: dna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in the DNA form o *** --- *** f the sequence. *** --- ************************************************ --- CREATE VIEW dna_motif AS SELECT feature_id AS dna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'DNA_motif'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_motif AS SELECT feature_id AS rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_motif'; --- ************************************************ --- *** relation: dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that has the quality dicistronic *** --- *** . *** --- ************************************************ --- CREATE VIEW dicistronic_mrna AS SELECT feature_id AS dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It need not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: blocked_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A reading_frame that is interrupted by o *** --- *** ne or more stop codons; usually identifi *** --- *** ed through intergenomic sequence compari *** --- *** sons. *** --- ************************************************ --- CREATE VIEW blocked_reading_frame AS SELECT feature_id AS blocked_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blocked_reading_frame'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_transposable_element AS SELECT feature_id AS foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'foreign_transposable_element'; --- ************************************************ --- *** relation: gene_with_dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic primar *** --- *** y transcript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_primary_transcript AS SELECT feature_id AS gene_with_dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript'; --- ************************************************ --- *** relation: gene_with_dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic mRNA *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_mrna AS SELECT feature_id AS gene_with_dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_mRNA'; --- ************************************************ --- *** relation: idna *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic sequence removed from the genome *** --- *** , as a normal event, by a process of rec *** --- *** ombination. *** --- ************************************************ --- CREATE VIEW idna AS SELECT feature_id AS idna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iDNA'; --- ************************************************ --- *** relation: orit *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule where transfe *** --- *** r is initiated during the process of con *** --- *** jugation or mobilization. *** --- ************************************************ --- CREATE VIEW orit AS SELECT feature_id AS orit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriT'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The transit_peptide is a short region at *** --- *** the N-terminus of the peptide that dire *** --- *** cts the protein to an organelle (chlorop *** --- *** last, mitochondrion, microbody or cyanel *** --- *** le). *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: repeat_unit *** --- *** relation type: VIEW *** --- *** *** --- *** The simplest repeated component of a rep *** --- *** eat region. A single repeat. *** --- ************************************************ --- CREATE VIEW repeat_unit AS SELECT feature_id AS repeat_unit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_unit'; --- ************************************************ --- *** relation: crm *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region where more than 1 TF *** --- *** _binding_site together are regulatorily *** --- *** active. *** --- ************************************************ --- CREATE VIEW crm AS SELECT feature_id AS crm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'CRM'; --- ************************************************ --- *** relation: intein *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is able to ex *** --- *** cise itself and rejoin the remaining por *** --- *** tions with a peptide bond. *** --- ************************************************ --- CREATE VIEW intein AS SELECT feature_id AS intein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein'; --- ************************************************ --- *** relation: intein_containing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of protein-coding genes whe *** --- *** re the initial protein product contains *** --- *** an intein. *** --- ************************************************ --- CREATE VIEW intein_containing AS SELECT feature_id AS intein_containing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** he unknown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: fragmentary *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is incomplete. *** --- ************************************************ --- CREATE VIEW fragmentary AS SELECT feature_id AS fragmentary_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary'; --- ************************************************ --- *** relation: predicted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an unverified re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW predicted AS SELECT feature_id AS predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'predicted'; --- ************************************************ --- *** relation: feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a located_sequen *** --- *** ce_feature. *** --- ************************************************ --- CREATE VIEW feature_attribute AS SELECT feature_id AS feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'feature_attribute'; --- ************************************************ --- *** relation: exemplar_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An exemplar is a representative cDNA seq *** --- *** uence for each gene. The exemplar approa *** --- *** ch is a method that usually involves som *** --- *** e initial clustering into gene groups an *** --- *** d the subsequent selection of a represen *** --- *** tative from each gene group. *** --- ************************************************ --- CREATE VIEW exemplar_mrna AS SELECT feature_id AS exemplar_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar_mRNA'; --- ************************************************ --- *** relation: sequence_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_location AS SELECT feature_id AS sequence_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_location'; --- ************************************************ --- *** relation: organelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW organelle_sequence AS SELECT feature_id AS organelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'organelle_sequence'; --- ************************************************ --- *** relation: mitochondrial_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_sequence AS SELECT feature_id AS mitochondrial_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'mitochondrial_sequence'; --- ************************************************ --- *** relation: nuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclear_sequence AS SELECT feature_id AS nuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_sequence'; --- ************************************************ --- *** relation: nucleomorphic_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nucleomorphic_sequence AS SELECT feature_id AS nucleomorphic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_sequence'; --- ************************************************ --- *** relation: plastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plastid_sequence AS SELECT feature_id AS plastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'plastid_sequence'; --- ************************************************ --- *** relation: kinetoplast *** --- *** relation type: VIEW *** --- *** *** --- *** A kinetoplast is an interlocked network *** --- *** of thousands of minicircles and tens of *** --- *** maxi circles, located near the base of t *** --- *** he flagellum of some protozoan species. *** --- ************************************************ --- CREATE VIEW kinetoplast AS SELECT feature_id AS kinetoplast_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast'; --- ************************************************ --- *** relation: maxicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle is a replicon, part of a ki *** --- *** netoplast, that contains open reading fr *** --- *** ames and replicates via a rolling circle *** --- *** method. *** --- ************************************************ --- CREATE VIEW maxicircle AS SELECT feature_id AS maxicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle'; --- ************************************************ --- *** relation: apicoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW apicoplast_sequence AS SELECT feature_id AS apicoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence'; --- ************************************************ --- *** relation: chromoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromoplast_sequence AS SELECT feature_id AS chromoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_sequence'; --- ************************************************ --- *** relation: chloroplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_sequence AS SELECT feature_id AS chloroplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'chloroplast_sequence'; --- ************************************************ --- *** relation: cyanelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cyanelle_sequence AS SELECT feature_id AS cyanelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_sequence'; --- ************************************************ --- *** relation: leucoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucoplast_sequence AS SELECT feature_id AS leucoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_sequence'; --- ************************************************ --- *** relation: proplastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proplastid_sequence AS SELECT feature_id AS proplastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_sequence'; --- ************************************************ --- *** relation: plasmid_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_location AS SELECT feature_id AS plasmid_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_location'; --- ************************************************ --- *** relation: amplification_origin *** --- *** relation type: VIEW *** --- *** *** --- *** An origin_of_replication that is used fo *** --- *** r the amplification of a chromosomal nuc *** --- *** leic acid sequence. *** --- ************************************************ --- CREATE VIEW amplification_origin AS SELECT feature_id AS amplification_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amplification_origin'; --- ************************************************ --- *** relation: proviral_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proviral_location AS SELECT feature_id AS proviral_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'proviral_location'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: clone_insert *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence that has been ins *** --- *** erted and is being propogated by the clo *** --- *** ne. *** --- ************************************************ --- CREATE VIEW clone_insert AS SELECT feature_id AS clone_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'clone_insert'; --- ************************************************ --- *** relation: lambda_vector *** --- *** relation type: VIEW *** --- *** *** --- *** The lambda bacteriophage is the vector f *** --- *** or the linear lambda clone. The genes in *** --- *** volved in the lysogenic pathway are remo *** --- *** ved from the from the viral DNA. Up to 2 *** --- *** 5 kb of foreign DNA can then be inserted *** --- *** into the lambda genome. *** --- ************************************************ --- CREATE VIEW lambda_vector AS SELECT feature_id AS lambda_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lambda_vector'; --- ************************************************ --- *** relation: plasmid_vector *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_vector AS SELECT feature_id AS plasmid_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_vector'; --- ************************************************ --- *** relation: cdna *** --- *** relation type: VIEW *** --- *** *** --- *** DNA synthesized by reverse transcriptase *** --- *** using RNA as a template. *** --- ************************************************ --- CREATE VIEW cdna AS SELECT feature_id AS cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'cDNA'; --- ************************************************ --- *** relation: single_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single_stranded_cdna AS SELECT feature_id AS single_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA'; --- ************************************************ --- *** relation: double_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double_stranded_cdna AS SELECT feature_id AS double_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_cDNA'; --- ************************************************ --- *** relation: pyrrolysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a pyrrolysine a *** --- *** nticodon, and a 3' pyrrolysine binding r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW pyrrolysyl_trna AS SELECT feature_id AS pyrrolysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysyl_tRNA'; --- ************************************************ --- *** relation: episome *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that may integrate with a chro *** --- *** mosome. *** --- ************************************************ --- CREATE VIEW episome AS SELECT feature_id AS episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'episome'; --- ************************************************ --- *** relation: tmrna_coding_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a two-piece tmRNA that bea *** --- *** rs the reading frame encoding the proteo *** --- *** lysis tag. The tmRNA gene undergoes circ *** --- *** ular permutation in some groups of bacte *** --- *** ria. Processing of the transcripts from *** --- *** such a gene leaves the mature tmRNA in t *** --- *** wo pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_coding_piece AS SELECT feature_id AS tmrna_coding_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece'; --- ************************************************ --- *** relation: tmrna_acceptor_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The acceptor region of a two-piece tmRNA *** --- *** that when mature is charged at its 3' e *** --- *** nd with alanine. The tmRNA gene undergoe *** --- *** s circular permutation in some groups of *** --- *** bacteria; processing of the transcripts *** --- *** from such a gene leaves the mature tmRN *** --- *** A in two pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_acceptor_piece AS SELECT feature_id AS tmrna_acceptor_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_acceptor_piece'; --- ************************************************ --- *** relation: qtl *** --- *** relation type: VIEW *** --- *** *** --- *** A quantitative trait locus (QTL) is a po *** --- *** lymorphic locus which contains alleles t *** --- *** hat differentially affect the expression *** --- *** of a continuously distributed phenotypi *** --- *** c trait. Usually it is a marker describe *** --- *** d by statistical association to quantita *** --- *** tive variation in the particular phenoty *** --- *** pic trait that is thought to be controll *** --- *** ed by the cumulative action of alleles a *** --- *** t multiple loci. *** --- ************************************************ --- CREATE VIEW qtl AS SELECT feature_id AS qtl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'QTL'; --- ************************************************ --- *** relation: genomic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A genomic island is an integrated mobile *** --- *** genetic element, characterized by size *** --- *** (over 10 Kb). It that has features that *** --- *** suggest a foreign origin. These can incl *** --- *** ude nucleotide distribution (oligonucleo *** --- *** tides signature, CG content etc.) that d *** --- *** iffers from the bulk of the chromosome a *** --- *** nd/or genes suggesting DNA mobility. *** --- ************************************************ --- CREATE VIEW genomic_island AS SELECT feature_id AS genomic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'genomic_island'; --- ************************************************ --- *** relation: pathogenic_island *** --- *** relation type: VIEW *** --- *** *** --- *** Mobile genetic elements that contribute *** --- *** to rapid changes in virulence potential. *** --- *** They are present on the genomes of path *** --- *** ogenic strains but absent from the genom *** --- *** es of non pathogenic members of the same *** --- *** or related species. *** --- ************************************************ --- CREATE VIEW pathogenic_island AS SELECT feature_id AS pathogenic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island'; --- ************************************************ --- *** relation: metabolic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in metabolism, analogous to th *** --- *** e pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW metabolic_island AS SELECT feature_id AS metabolic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'metabolic_island'; --- ************************************************ --- *** relation: adaptive_island *** --- *** relation type: VIEW *** --- *** *** --- *** An adaptive island is a genomic island t *** --- *** hat provides an adaptive advantage to th *** --- *** e host. *** --- ************************************************ --- CREATE VIEW adaptive_island AS SELECT feature_id AS adaptive_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'adaptive_island'; --- ************************************************ --- *** relation: symbiosis_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in symbiosis, analogous to the *** --- *** pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW symbiosis_island AS SELECT feature_id AS symbiosis_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symbiosis_island'; --- ************************************************ --- *** relation: pseudogenic_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of an rRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_rrna AS SELECT feature_id AS pseudogenic_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_rRNA'; --- ************************************************ --- *** relation: pseudogenic_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of a tRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_trna AS SELECT feature_id AS pseudogenic_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_tRNA'; --- ************************************************ --- *** relation: engineered_episome *** --- *** relation type: VIEW *** --- *** *** --- *** An episome that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_episome AS SELECT feature_id AS engineered_episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome'; --- ************************************************ --- *** relation: transgenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence that has b *** --- *** een integrated with foreign sequence. *** --- ************************************************ --- CREATE VIEW transgenic AS SELECT feature_id AS transgenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic'; --- ************************************************ --- *** relation: so_natural *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that o *** --- *** ccurs in nature. *** --- ************************************************ --- CREATE VIEW so_natural AS SELECT feature_id AS so_natural_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural'; --- ************************************************ --- *** relation: engineered *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region that w *** --- *** as modified in vitro. *** --- ************************************************ --- CREATE VIEW engineered AS SELECT feature_id AS engineered_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered'; --- ************************************************ --- *** relation: so_foreign *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region from a *** --- *** nother species. *** --- ************************************************ --- CREATE VIEW so_foreign AS SELECT feature_id AS so_foreign_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foreign'; --- ************************************************ --- *** relation: cloned_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cloned_region AS SELECT feature_id AS cloned_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_region'; --- ************************************************ --- *** relation: validated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been proven. *** --- ************************************************ --- CREATE VIEW validated AS SELECT feature_id AS validated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined' OR cvterm.name = 'validated'; --- ************************************************ --- *** relation: invalidated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s invalidated. *** --- ************************************************ --- CREATE VIEW invalidated AS SELECT feature_id AS invalidated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'invalidated'; --- ************************************************ --- *** relation: engineered_rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A rescue region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_rescue_region AS SELECT feature_id AS engineered_rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region'; --- ************************************************ --- *** relation: rescue_mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mini_gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_mini_gene AS SELECT feature_id AS rescue_mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene'; --- ************************************************ --- *** relation: transgenic_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified in vitro, incl *** --- *** uding insertion of DNA derived from a so *** --- *** urce other than the originating TE. *** --- ************************************************ --- CREATE VIEW transgenic_transposable_element AS SELECT feature_id AS transgenic_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_transposable_element'; --- ************************************************ --- *** relation: natural_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that exists (or existed) in nature. *** --- ************************************************ --- CREATE VIEW natural_transposable_element AS SELECT feature_id AS natural_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element'; --- ************************************************ --- *** relation: engineered_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified by manipulatio *** --- *** ns in vitro. *** --- ************************************************ --- CREATE VIEW engineered_transposable_element AS SELECT feature_id AS engineered_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_transposable_element'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element AS SELECT feature_id AS engineered_foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element'; --- ************************************************ --- *** relation: assortment_derived_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome duplication aberratio *** --- *** n generated by reassortment of other abe *** --- *** rration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_duplication AS SELECT feature_id AS assortment_derived_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency an *** --- *** d a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency_plus_duplication AS SELECT feature_id AS assortment_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome deficiency aberration *** --- *** generated by reassortment of other aber *** --- *** ration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency AS SELECT feature_id AS assortment_derived_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency'; --- ************************************************ --- *** relation: assortment_derived_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency or *** --- *** a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_aneuploid AS SELECT feature_id AS assortment_derived_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_aneuploid'; --- ************************************************ --- *** relation: engineered_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_region AS SELECT feature_id AS engineered_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_region'; --- ************************************************ --- *** relation: engineered_foreign_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_region AS SELECT feature_id AS engineered_foreign_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_region'; --- ************************************************ --- *** relation: fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fusion AS SELECT feature_id AS fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fusion'; --- ************************************************ --- *** relation: engineered_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A tag that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_tag AS SELECT feature_id AS engineered_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_tag'; --- ************************************************ --- *** relation: validated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that has been validated. *** --- ************************************************ --- CREATE VIEW validated_cdna_clone AS SELECT feature_id AS validated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone'; --- ************************************************ --- *** relation: invalidated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that is invalid. *** --- ************************************************ --- CREATE VIEW invalidated_cdna_clone AS SELECT feature_id AS invalidated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone'; --- ************************************************ --- *** relation: chimeric_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated because it is c *** --- *** himeric. *** --- ************************************************ --- CREATE VIEW chimeric_cdna_clone AS SELECT feature_id AS chimeric_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone'; --- ************************************************ --- *** relation: genomically_contaminated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by genomic cont *** --- *** amination. *** --- ************************************************ --- CREATE VIEW genomically_contaminated_cdna_clone AS SELECT feature_id AS genomically_contaminated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomically_contaminated_cDNA_clone'; --- ************************************************ --- *** relation: polya_primed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by polyA primin *** --- *** g. *** --- ************************************************ --- CREATE VIEW polya_primed_cdna_clone AS SELECT feature_id AS polya_primed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_primed_cDNA_clone'; --- ************************************************ --- *** relation: partially_processed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA invalidated clone by partial proc *** --- *** essing. *** --- ************************************************ --- CREATE VIEW partially_processed_cdna_clone AS SELECT feature_id AS partially_processed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_processed_cDNA_clone'; --- ************************************************ --- *** relation: rescue *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region's abili *** --- *** ty, when introduced to a mutant organism *** --- *** , to re-establish (rescue) a phenotype. *** --- ************************************************ --- CREATE VIEW rescue AS SELECT feature_id AS rescue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue'; --- ************************************************ --- *** relation: mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** By definition, minigenes are short open- *** --- *** reading frames (ORF), usually encoding a *** --- *** pproximately 9 to 20 amino acids, which *** --- *** are expressed in vivo (as distinct from *** --- *** being synthesized as peptide or protein *** --- *** ex vivo and subsequently injected). The *** --- *** in vivo synthesis confers a distinct adv *** --- *** antage: the expressed sequences can ente *** --- *** r both antigen presentation pathways, MH *** --- *** C I (inducing CD8+ T- cells, which are u *** --- *** sually cytotoxic T-lymphocytes (CTL)) an *** --- *** d MHC II (inducing CD4+ T-cells, usually *** --- *** 'T-helpers' (Th)); and can encounter B- *** --- *** cells, inducing antibody responses. Thre *** --- *** e main vector approaches have been used *** --- *** to deliver minigenes: viral vectors, bac *** --- *** terial vectors and plasmid DNA. *** --- ************************************************ --- CREATE VIEW mini_gene AS SELECT feature_id AS mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'mini_gene'; --- ************************************************ --- *** relation: rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_gene AS SELECT feature_id AS rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'rescue_gene'; --- ************************************************ --- *** relation: wild_type *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence with th *** --- *** e genotype found in nature and/or standa *** --- *** rd laboratory stock. *** --- ************************************************ --- CREATE VIEW wild_type AS SELECT feature_id AS wild_type_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type'; --- ************************************************ --- *** relation: wild_type_rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW wild_type_rescue_gene AS SELECT feature_id AS wild_type_rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene'; --- ************************************************ --- *** relation: mitochondrial_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a mitochondr *** --- *** ia. *** --- ************************************************ --- CREATE VIEW mitochondrial_chromosome AS SELECT feature_id AS mitochondrial_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome'; --- ************************************************ --- *** relation: chloroplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chloroplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chloroplast_chromosome AS SELECT feature_id AS chloroplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_chromosome'; --- ************************************************ --- *** relation: chromoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chromoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chromoplast_chromosome AS SELECT feature_id AS chromoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_chromosome'; --- ************************************************ --- *** relation: cyanelle_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a cyanelle. *** --- ************************************************ --- CREATE VIEW cyanelle_chromosome AS SELECT feature_id AS cyanelle_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_chromosome'; --- ************************************************ --- *** relation: leucoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome with origin in a leucoplast *** --- *** . *** --- ************************************************ --- CREATE VIEW leucoplast_chromosome AS SELECT feature_id AS leucoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_chromosome'; --- ************************************************ --- *** relation: macronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a macronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW macronuclear_chromosome AS SELECT feature_id AS macronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_chromosome'; --- ************************************************ --- *** relation: micronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a micronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW micronuclear_chromosome AS SELECT feature_id AS micronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_chromosome'; --- ************************************************ --- *** relation: nuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_chromosome AS SELECT feature_id AS nuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_chromosome'; --- ************************************************ --- *** relation: nucleomorphic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleomorp *** --- *** h. *** --- ************************************************ --- CREATE VIEW nucleomorphic_chromosome AS SELECT feature_id AS nucleomorphic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_chromosome'; --- ************************************************ --- *** relation: chromosome_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_part AS SELECT feature_id AS chromosome_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'chromosome_part'; --- ************************************************ --- *** relation: gene_member_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a gene. *** --- ************************************************ --- CREATE VIEW gene_member_region AS SELECT feature_id AS gene_member_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'gene_member_region'; --- ************************************************ --- *** relation: transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a transcript. *** --- ************************************************ --- CREATE VIEW transcript_region AS SELECT feature_id AS transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'transcript_region'; --- ************************************************ --- *** relation: mature_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a mature transcript. *** --- ************************************************ --- CREATE VIEW mature_transcript_region AS SELECT feature_id AS mature_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'mature_transcript_region'; --- ************************************************ --- *** relation: primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a primary transcript. *** --- ************************************************ --- CREATE VIEW primary_transcript_region AS SELECT feature_id AS primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'primary_transcript_region'; --- ************************************************ --- *** relation: mrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an mRNA. *** --- ************************************************ --- CREATE VIEW mrna_region AS SELECT feature_id AS mrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'mRNA_region'; --- ************************************************ --- *** relation: utr_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of UTR. *** --- ************************************************ --- CREATE VIEW utr_region AS SELECT feature_id AS utr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'UTR_region'; --- ************************************************ --- *** relation: rrna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an rRNA primary transcript. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript_region AS SELECT feature_id AS rrna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'rRNA_primary_transcript_region'; --- ************************************************ --- *** relation: polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Biological sequence region that can be a *** --- *** ssigned to a specific subsequence of a p *** --- *** olypeptide. *** --- ************************************************ --- CREATE VIEW polypeptide_region AS SELECT feature_id AS polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_region'; --- ************************************************ --- *** relation: repeat_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a repeated sequence. *** --- ************************************************ --- CREATE VIEW repeat_component AS SELECT feature_id AS repeat_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'repeat_component'; --- ************************************************ --- *** relation: spliceosomal_intron_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an intron. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron_region AS SELECT feature_id AS spliceosomal_intron_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'spliceosomal_intron_region'; --- ************************************************ --- *** relation: gene_component_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_component_region AS SELECT feature_id AS gene_component_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'gene_component_region'; --- ************************************************ --- *** relation: tmrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tmRNA. *** --- ************************************************ --- CREATE VIEW tmrna_region AS SELECT feature_id AS tmrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'tmRNA_region'; --- ************************************************ --- *** relation: ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ltr_component AS SELECT feature_id AS ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'LTR_component'; --- ************************************************ --- *** relation: three_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr_component AS SELECT feature_id AS three_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'three_prime_LTR_component'; --- ************************************************ --- *** relation: five_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr_component AS SELECT feature_id AS five_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'five_prime_LTR_component'; --- ************************************************ --- *** relation: cds_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a CDS. *** --- ************************************************ --- CREATE VIEW cds_region AS SELECT feature_id AS cds_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'CDS_region'; --- ************************************************ --- *** relation: exon_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an exon. *** --- ************************************************ --- CREATE VIEW exon_region AS SELECT feature_id AS exon_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'exon_region'; --- ************************************************ --- *** relation: homologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is homologous to another r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW homologous_region AS SELECT feature_id AS homologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'homologous_region'; --- ************************************************ --- *** relation: paralogous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is paralogous t *** --- *** o another region. *** --- ************************************************ --- CREATE VIEW paralogous_region AS SELECT feature_id AS paralogous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region'; --- ************************************************ --- *** relation: orthologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is orthologous *** --- *** to another region. *** --- ************************************************ --- CREATE VIEW orthologous_region AS SELECT feature_id AS orthologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous_region'; --- ************************************************ --- *** relation: conserved *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW conserved AS SELECT feature_id AS conserved_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'conserved'; --- ************************************************ --- *** relation: homologous *** --- *** relation type: VIEW *** --- *** *** --- *** Similarity due to common ancestry. *** --- ************************************************ --- CREATE VIEW homologous AS SELECT feature_id AS homologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'homologous'; --- ************************************************ --- *** relation: orthologous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occured after a spec *** --- *** iation event. *** --- ************************************************ --- CREATE VIEW orthologous AS SELECT feature_id AS orthologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous'; --- ************************************************ --- *** relation: paralogous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occurred after a dup *** --- *** lication event. *** --- ************************************************ --- CREATE VIEW paralogous AS SELECT feature_id AS paralogous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous'; --- ************************************************ --- *** relation: syntenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence regions oc *** --- *** curring in same order on chromosome of d *** --- *** ifferent species. *** --- ************************************************ --- CREATE VIEW syntenic AS SELECT feature_id AS syntenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic'; --- ************************************************ --- *** relation: capped_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is capped. *** --- ************************************************ --- CREATE VIEW capped_primary_transcript AS SELECT feature_id AS capped_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_primary_transcript'; --- ************************************************ --- *** relation: capped_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is capped. *** --- ************************************************ --- CREATE VIEW capped_mrna AS SELECT feature_id AS capped_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_mRNA'; --- ************************************************ --- *** relation: mrna_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA feature. *** --- ************************************************ --- CREATE VIEW mrna_attribute AS SELECT feature_id AS mrna_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'mRNA_attribute'; --- ************************************************ --- *** relation: exemplar *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence is re *** --- *** presentative of a class of similar seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW exemplar AS SELECT feature_id AS exemplar_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar'; --- ************************************************ --- *** relation: frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains a mutation involving the deleti *** --- *** on or insertion of one or more bases, wh *** --- *** ere this number is not divisible by 3. *** --- ************************************************ --- CREATE VIEW frameshift AS SELECT feature_id AS frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'frameshift'; --- ************************************************ --- *** relation: minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting one base *** --- *** . *** --- ************************************************ --- CREATE VIEW minus_1_frameshift AS SELECT feature_id AS minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift'; --- ************************************************ --- *** relation: minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting two base *** --- *** s. *** --- ************************************************ --- CREATE VIEW minus_2_frameshift AS SELECT feature_id AS minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift'; --- ************************************************ --- *** relation: plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting one bas *** --- *** e. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift AS SELECT feature_id AS plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift'; --- ************************************************ --- *** relation: plus_2_framshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting two bas *** --- *** es. *** --- ************************************************ --- CREATE VIEW plus_2_framshift AS SELECT feature_id AS plus_2_framshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_framshift'; --- ************************************************ --- *** relation: trans_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing transcript seque *** --- *** nce that is created by splicing exons fr *** --- *** om diferent genes. *** --- ************************************************ --- CREATE VIEW trans_spliced AS SELECT feature_id AS trans_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced'; --- ************************************************ --- *** relation: polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is polyadenylated. *** --- ************************************************ --- CREATE VIEW polyadenylated_mrna AS SELECT feature_id AS polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated_mRNA'; --- ************************************************ --- *** relation: trans_spliced_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_mrna AS SELECT feature_id AS trans_spliced_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA'; --- ************************************************ --- *** relation: edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript AS SELECT feature_id AS edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_transcript'; --- ************************************************ --- *** relation: edited_transcript_by_a_to_i_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been edited by A t *** --- *** o I substitution. *** --- ************************************************ --- CREATE VIEW edited_transcript_by_a_to_i_substitution AS SELECT feature_id AS edited_transcript_by_a_to_i_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution'; --- ************************************************ --- *** relation: bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a protein. *** --- ************************************************ --- CREATE VIEW bound_by_protein AS SELECT feature_id AS bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein'; --- ************************************************ --- *** relation: bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a nucleic acid. *** --- ************************************************ --- CREATE VIEW bound_by_nucleic_acid AS SELECT feature_id AS bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_nucleic_acid'; --- ************************************************ --- *** relation: alternatively_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a situation wher *** --- *** e a gene may encode for more than 1 tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW alternatively_spliced AS SELECT feature_id AS alternatively_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced'; --- ************************************************ --- *** relation: monocistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for one gene product. *** --- ************************************************ --- CREATE VIEW monocistronic AS SELECT feature_id AS monocistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic'; --- ************************************************ --- *** relation: dicistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for two gene products. *** --- ************************************************ --- CREATE VIEW dicistronic AS SELECT feature_id AS dicistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic'; --- ************************************************ --- *** relation: polycistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for more than one gene *** --- *** product. *** --- ************************************************ --- CREATE VIEW polycistronic AS SELECT feature_id AS polycistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic' OR cvterm.name = 'polycistronic'; --- ************************************************ --- *** relation: recoded *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA sequence *** --- *** that has been reprogrammed at translati *** --- *** on, causing localized alterations. *** --- ************************************************ --- CREATE VIEW recoded AS SELECT feature_id AS recoded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'recoded'; --- ************************************************ --- *** relation: codon_redefined *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the alteration o *** --- *** f codon meaning. *** --- ************************************************ --- CREATE VIEW codon_redefined AS SELECT feature_id AS codon_redefined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined'; --- ************************************************ --- *** relation: stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be a new amino *** --- *** acid. *** --- ************************************************ --- CREATE VIEW stop_codon_read_through AS SELECT feature_id AS stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'stop_codon_read_through'; --- ************************************************ --- *** relation: stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, pyrrolysine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, selenocysteine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** Recoded mRNA where a block of nucleotide *** --- *** s is not translated. *** --- ************************************************ --- CREATE VIEW recoded_by_translational_bypass AS SELECT feature_id AS recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_by_translational_bypass'; --- ************************************************ --- *** relation: translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** Recoding by frameshifting a particular s *** --- *** ite. *** --- ************************************************ --- CREATE VIEW translationally_frameshifted AS SELECT feature_id AS translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'translationally_frameshifted'; --- ************************************************ --- *** relation: maternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is maternally_imprinted. *** --- ************************************************ --- CREATE VIEW maternally_imprinted_gene AS SELECT feature_id AS maternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted_gene'; --- ************************************************ --- *** relation: paternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is paternally imprinted. *** --- ************************************************ --- CREATE VIEW paternally_imprinted_gene AS SELECT feature_id AS paternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is post translationally regu *** --- *** lated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_gene AS SELECT feature_id AS post_translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_gene'; --- ************************************************ --- *** relation: negatively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is negatively autoreguated. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated_gene AS SELECT feature_id AS negatively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated_gene'; --- ************************************************ --- *** relation: positively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is positively autoregulated. *** --- ************************************************ --- CREATE VIEW positively_autoregulated_gene AS SELECT feature_id AS positively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated_gene'; --- ************************************************ --- *** relation: silenced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated at tra *** --- *** nscriptional or translational level. *** --- ************************************************ --- CREATE VIEW silenced AS SELECT feature_id AS silenced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced'; --- ************************************************ --- *** relation: silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** modifications, resulting in repression *** --- *** of transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_modification AS SELECT feature_id AS silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_DNA_modification'; --- ************************************************ --- *** relation: silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** methylation, resulting in repression of *** --- *** transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_methylation AS SELECT feature_id AS silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is translationally regulated *** --- *** . *** --- ************************************************ --- CREATE VIEW translationally_regulated_gene AS SELECT feature_id AS translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated_gene'; --- ************************************************ --- *** relation: allelically_excluded_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is allelically_excluded. *** --- ************************************************ --- CREATE VIEW allelically_excluded_gene AS SELECT feature_id AS allelically_excluded_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded_gene'; --- ************************************************ --- *** relation: epigenetically_modified_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is epigenetically modified. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_gene AS SELECT feature_id AS epigenetically_modified_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'epigenetically_modified_gene'; --- ************************************************ --- *** relation: transgene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is transgenic. *** --- ************************************************ --- CREATE VIEW transgene AS SELECT feature_id AS transgene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene' OR cvterm.name = 'transgene'; --- ************************************************ --- *** relation: endogenous_retroviral_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_sequence AS SELECT feature_id AS endogenous_retroviral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence'; --- ************************************************ --- *** relation: rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the sequence of *** --- *** a feature, where the DNA is rearranged. *** --- ************************************************ --- CREATE VIEW rearranged_at_dna_level AS SELECT feature_id AS rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rearranged_at_DNA_level'; --- ************************************************ --- *** relation: status *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the status of a *** --- *** feature, based on the available evidence *** --- *** . *** --- ************************************************ --- CREATE VIEW status AS SELECT feature_id AS status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'status'; --- ************************************************ --- *** relation: independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that is *** --- *** independently known - not predicted. *** --- ************************************************ --- CREATE VIEW independently_known AS SELECT feature_id AS independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'independently_known'; --- ************************************************ --- *** relation: supported_by_sequence_similarity *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity techniques. *** --- ************************************************ --- CREATE VIEW supported_by_sequence_similarity AS SELECT feature_id AS supported_by_sequence_similarity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'supported_by_sequence_similarity'; --- ************************************************ --- *** relation: supported_by_domain_match *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity of a known domain. *** --- ************************************************ --- CREATE VIEW supported_by_domain_match AS SELECT feature_id AS supported_by_domain_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match'; --- ************************************************ --- *** relation: supported_by_est_or_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity to EST or cDNA data. *** --- ************************************************ --- CREATE VIEW supported_by_est_or_cdna AS SELECT feature_id AS supported_by_est_or_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_EST_or_cDNA'; --- ************************************************ --- *** relation: orphan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW orphan AS SELECT feature_id AS orphan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan'; --- ************************************************ --- *** relation: predicted_by_ab_initio_computation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s predicted by a computer program that d *** --- *** id not rely on sequence similarity. *** --- ************************************************ --- CREATE VIEW predicted_by_ab_initio_computation AS SELECT feature_id AS predicted_by_ab_initio_computation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_by_ab_initio_computation'; --- ************************************************ --- *** relation: asx_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Asp *** --- *** artate or Asparagine (Asx), the side-cha *** --- *** in O of residue(i) is H-bonded to the ma *** --- *** in-chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW asx_turn AS SELECT feature_id AS asx_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'asx_turn'; --- ************************************************ --- *** relation: cloned_cdna_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from cDNA. *** --- ************************************************ --- CREATE VIEW cloned_cdna_insert AS SELECT feature_id AS cloned_cdna_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert'; --- ************************************************ --- *** relation: cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from genomic DNA. *** --- ************************************************ --- CREATE VIEW cloned_genomic_insert AS SELECT feature_id AS cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'cloned_genomic_insert'; --- ************************************************ --- *** relation: engineered_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_insert AS SELECT feature_id AS engineered_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_insert'; --- ************************************************ --- *** relation: edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is edited. *** --- ************************************************ --- CREATE VIEW edited_mrna AS SELECT feature_id AS edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA'; --- ************************************************ --- *** relation: guide_rna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of guide RNA. *** --- ************************************************ --- CREATE VIEW guide_rna_region AS SELECT feature_id AS guide_rna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'guide_RNA_region'; --- ************************************************ --- *** relation: anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that base-pairs *** --- *** to a target mRNA. *** --- ************************************************ --- CREATE VIEW anchor_region AS SELECT feature_id AS anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region'; --- ************************************************ --- *** relation: pre_edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pre_edited_mrna AS SELECT feature_id AS pre_edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA'; --- ************************************************ --- *** relation: intermediate *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature betwe *** --- *** en stages of processing. *** --- ************************************************ --- CREATE VIEW intermediate AS SELECT feature_id AS intermediate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate'; --- ************************************************ --- *** relation: mirna_target_site *** --- *** relation type: VIEW *** --- *** *** --- *** A miRNA target site is a binding site wh *** --- *** ere the molecule is a micro RNA. *** --- ************************************************ --- CREATE VIEW mirna_target_site AS SELECT feature_id AS mirna_target_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site'; --- ************************************************ --- *** relation: edited_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is edited. *** --- ************************************************ --- CREATE VIEW edited_cds AS SELECT feature_id AS edited_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment'; --- ************************************************ --- *** relation: vertebrate_ig_t_cell_receptor_rearranged_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_ig_t_cell_receptor_rearranged_gene_cluster AS SELECT feature_id AS vertebrate_ig_t_cell_receptor_rearranged_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_signal_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_signal_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_signal_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature'; --- ************************************************ --- *** relation: recombinationally_rearranged *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged AS SELECT feature_id AS recombinationally_rearranged_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged'; --- ************************************************ --- *** relation: recombinationally_rearranged_vertebrate_immune_system_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene of t *** --- *** he vertebrate immune system. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_vertebrate_immune_system_gene AS SELECT feature_id AS recombinationally_rearranged_vertebrate_immune_system_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: attp_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a phage *** --- *** chromosome at which a recombinase acts t *** --- *** o insert the phage DNA at a cognate inte *** --- *** gration/excision site on a bacterial chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW attp_site AS SELECT feature_id AS attp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attP_site'; --- ************************************************ --- *** relation: attb_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a bacter *** --- *** ial chromosome at which a recombinase ac *** --- *** ts to insert foreign DNA containing a co *** --- *** gnate integration/excision site. *** --- ************************************************ --- CREATE VIEW attb_site AS SELECT feature_id AS attb_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attB_site'; --- ************************************************ --- *** relation: attl_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attB_site and th *** --- *** e 3' portion of attP_site. *** --- ************************************************ --- CREATE VIEW attl_site AS SELECT feature_id AS attl_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attL_site'; --- ************************************************ --- *** relation: attr_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attP_site and th *** --- *** e 3' portion of attB_site. *** --- ************************************************ --- CREATE VIEW attr_site AS SELECT feature_id AS attr_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attR_site'; --- ************************************************ --- *** relation: integration_excision_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inserts or removes anot *** --- *** her region marked by a distinct cognate *** --- *** integration/excision site. *** --- ************************************************ --- CREATE VIEW integration_excision_site AS SELECT feature_id AS integration_excision_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'integration_excision_site'; --- ************************************************ --- *** relation: resolution_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which separates a physically *** --- *** contiguous circle of DNA into two physic *** --- *** ally separate circles. *** --- ************************************************ --- CREATE VIEW resolution_site AS SELECT feature_id AS resolution_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'resolution_site'; --- ************************************************ --- *** relation: inversion_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inverts the region flan *** --- *** ked by a pair of sites. *** --- ************************************************ --- CREATE VIEW inversion_site AS SELECT feature_id AS inversion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site' OR cvterm.name = 'inversion_site'; --- ************************************************ --- *** relation: dif_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site at which replicated bacterial cir *** --- *** cular chromosomes are decatenated by sit *** --- *** e specific resolvase. *** --- ************************************************ --- CREATE VIEW dif_site AS SELECT feature_id AS dif_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dif_site'; --- ************************************************ --- *** relation: attc_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attC site is a sequence required for *** --- *** the integration of a DNA of an integron. *** --- ************************************************ --- CREATE VIEW attc_site AS SELECT feature_id AS attc_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attC_site'; --- ************************************************ --- *** relation: eukaryotic_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW eukaryotic_terminator AS SELECT feature_id AS eukaryotic_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'eukaryotic_terminator'; --- ************************************************ --- *** relation: oriv *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of vegetative replication in p *** --- *** lasmids and phages. *** --- ************************************************ --- CREATE VIEW oriv AS SELECT feature_id AS oriv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriV'; --- ************************************************ --- *** relation: oric *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of bacterial chromosome replic *** --- *** ation. *** --- ************************************************ --- CREATE VIEW oric AS SELECT feature_id AS oric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriC'; --- ************************************************ --- *** relation: dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, DNA molecule. *** --- ************************************************ --- CREATE VIEW dna_chromosome AS SELECT feature_id AS dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'DNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_dna_chromosome AS SELECT feature_id AS double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_dna_chromosome AS SELECT feature_id AS single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_dna_chromosome AS SELECT feature_id AS linear_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_dna_chromosome AS SELECT feature_id AS circular_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_dna_chromosome AS SELECT feature_id AS linear_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_dna_chromosome AS SELECT feature_id AS circular_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, RNA molecule. *** --- ************************************************ --- CREATE VIEW rna_chromosome AS SELECT feature_id AS rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_rna_chromosome AS SELECT feature_id AS single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_rna_chromosome AS SELECT feature_id AS linear_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_rna_chromosome AS SELECT feature_id AS linear_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_rna_chromosome AS SELECT feature_id AS double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_rna_chromosome AS SELECT feature_id AS circular_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular RNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_rna_chromosome AS SELECT feature_id AS circular_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: insertion_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal_inverted_repeat_element that *** --- *** is bacterial and only encodes the functi *** --- *** ons required for its transposition betwe *** --- *** en these inverted repeats. *** --- ************************************************ --- CREATE VIEW insertion_sequence AS SELECT feature_id AS insertion_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_sequence'; --- ************************************************ --- *** relation: minicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minicircle_gene AS SELECT feature_id AS minicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle_gene'; --- ************************************************ --- *** relation: cryptic *** --- *** relation type: VIEW *** --- *** *** --- *** A feature_attribute describing a feature *** --- *** that is not manifest under normal condi *** --- *** tions. *** --- ************************************************ --- CREATE VIEW cryptic AS SELECT feature_id AS cryptic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic'; --- ************************************************ --- *** relation: anchor_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW anchor_binding_site AS SELECT feature_id AS anchor_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_binding_site'; --- ************************************************ --- *** relation: template_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that specifies t *** --- *** he insertions and deletions of bases in *** --- *** the editing of a target mRNA. *** --- ************************************************ --- CREATE VIEW template_region AS SELECT feature_id AS template_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'template_region'; --- ************************************************ --- *** relation: grna_encoding *** --- *** relation type: VIEW *** --- *** *** --- *** A non-protein_coding gene that encodes a *** --- *** guide_RNA. *** --- ************************************************ --- CREATE VIEW grna_encoding AS SELECT feature_id AS grna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_encoding'; --- ************************************************ --- *** relation: minicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A minicircle is a replicon, part of a ki *** --- *** netoplast, that encodes for guide RNAs. *** --- ************************************************ --- CREATE VIEW minicircle AS SELECT feature_id AS minicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle'; --- ************************************************ --- *** relation: rho_dependent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_dependent_bacterial_terminator AS SELECT feature_id AS rho_dependent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator'; --- ************************************************ --- *** relation: rho_independent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_independent_bacterial_terminator AS SELECT feature_id AS rho_independent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_independent_bacterial_terminator'; --- ************************************************ --- *** relation: strand_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strand_attribute AS SELECT feature_id AS strand_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute'; --- ************************************************ --- *** relation: single *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single AS SELECT feature_id AS single_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single'; --- ************************************************ --- *** relation: double *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double AS SELECT feature_id AS double_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double'; --- ************************************************ --- *** relation: topology_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW topology_attribute AS SELECT feature_id AS topology_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute'; --- ************************************************ --- *** relation: linear *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as a 3'-terminal residue and a 5'-termin *** --- *** al residue. *** --- ************************************************ --- CREATE VIEW linear AS SELECT feature_id AS linear_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear'; --- ************************************************ --- *** relation: circular *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as no terminal nucleotide residues. *** --- ************************************************ --- CREATE VIEW circular AS SELECT feature_id AS circular_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular'; --- ************************************************ --- *** relation: class_ii_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (59-60 nt long) con *** --- *** taining 5' and 3' ends that are predicte *** --- *** d to come together to form a stem struct *** --- *** ure. Identified in the social amoeba Dic *** --- *** tyostelium discoideum and localized in t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW class_ii_rna AS SELECT feature_id AS class_ii_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_II_RNA'; --- ************************************************ --- *** relation: class_i_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (55-65 nt long) con *** --- *** taining highly conserved 5' and 3' ends *** --- *** (16 and 8 nt, respectively) that are pre *** --- *** dicted to come together to form a stem s *** --- *** tructure. Identified in the social amoeb *** --- *** a Dictyostelium discoideum and localized *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW class_i_rna AS SELECT feature_id AS class_i_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_I_RNA'; --- ************************************************ --- *** relation: genomic_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW genomic_dna AS SELECT feature_id AS genomic_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_DNA'; --- ************************************************ --- *** relation: bac_cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bac_cloned_genomic_insert AS SELECT feature_id AS bac_cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert'; --- ************************************************ --- *** relation: consensus *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus AS SELECT feature_id AS consensus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus'; --- ************************************************ --- *** relation: consensus_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_region AS SELECT feature_id AS consensus_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region'; --- ************************************************ --- *** relation: consensus_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_mrna AS SELECT feature_id AS consensus_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA'; --- ************************************************ --- *** relation: predicted_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW predicted_gene AS SELECT feature_id AS predicted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_gene'; --- ************************************************ --- *** relation: gene_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_fragment AS SELECT feature_id AS gene_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fragment'; --- ************************************************ --- *** relation: recursive_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A recursive splice site is a splice site *** --- *** which subdivides a large intron. Recurs *** --- *** ive splicing is a mechanism that splices *** --- *** large introns by sub dividing the intro *** --- *** n at non exonic elements and alternate e *** --- *** xons. *** --- ************************************************ --- CREATE VIEW recursive_splice_site AS SELECT feature_id AS recursive_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recursive_splice_site'; --- ************************************************ --- *** relation: bac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a B *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW bac_end AS SELECT feature_id AS bac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_end'; --- ************************************************ --- *** relation: rrna_16s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the small sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_16s AS SELECT feature_id AS rrna_16s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_16S'; --- ************************************************ --- *** relation: rrna_23s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the large sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_23s AS SELECT feature_id AS rrna_23s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_23S'; --- ************************************************ --- *** relation: rrna_25s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide which functions a *** --- *** s part of the large subunit of the ribos *** --- *** ome in some eukaryotes. *** --- ************************************************ --- CREATE VIEW rrna_25s AS SELECT feature_id AS rrna_25s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_25S'; --- ************************************************ --- *** relation: solo_ltr *** --- *** relation type: VIEW *** --- *** *** --- *** A recombination product between the 2 LT *** --- *** R of the same element. *** --- ************************************************ --- CREATE VIEW solo_ltr AS SELECT feature_id AS solo_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'solo_LTR'; --- ************************************************ --- *** relation: low_complexity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity AS SELECT feature_id AS low_complexity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity'; --- ************************************************ --- *** relation: low_complexity_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity_region AS SELECT feature_id AS low_complexity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity_region'; --- ************************************************ --- *** relation: prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A phage genome after it has established *** --- *** in the host genome in a latent/immune st *** --- *** ate either as a plasmid or as an integra *** --- *** ted "island". *** --- ************************************************ --- CREATE VIEW prophage AS SELECT feature_id AS prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage'; --- ************************************************ --- *** relation: cryptic_prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A remnant of an integrated prophage in t *** --- *** he host genome or an "island" in the hos *** --- *** t genome that includes phage like-genes. *** --- ************************************************ --- CREATE VIEW cryptic_prophage AS SELECT feature_id AS cryptic_prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_prophage'; --- ************************************************ --- *** relation: tetraloop *** --- *** relation type: VIEW *** --- *** *** --- *** A base-paired stem with loop of 4 non-hy *** --- *** drogen bonded nucleotides. *** --- ************************************************ --- CREATE VIEW tetraloop AS SELECT feature_id AS tetraloop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop'; --- ************************************************ --- *** relation: dna_constraint_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A double-stranded DNA used to control ma *** --- *** cromolecular structure and function. *** --- ************************************************ --- CREATE VIEW dna_constraint_sequence AS SELECT feature_id AS dna_constraint_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_constraint_sequence'; --- ************************************************ --- *** relation: i_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A cytosine rich domain whereby strands a *** --- *** ssociate both inter- and intramolecularl *** --- *** y at moderately acidic pH. *** --- ************************************************ --- CREATE VIEW i_motif AS SELECT feature_id AS i_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif'; --- ************************************************ --- *** relation: pna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Peptide nucleic acid, is a chemical not *** --- *** known to occur naturally but is artifici *** --- *** ally synthesized and used in some biolog *** --- *** ical research and medical treatments. Th *** --- *** e PNA backbone is composed of repeating *** --- *** N-(2-aminoethyl)-glycine units linked by *** --- *** peptide bonds. The purine and pyrimidin *** --- *** e bases are linked to the backbone by me *** --- *** thylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna_oligo AS SELECT feature_id AS pna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA_oligo'; --- ************************************************ --- *** relation: dnazyme *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence with catalytic activity. *** --- ************************************************ --- CREATE VIEW dnazyme AS SELECT feature_id AS dnazyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAzyme'; --- ************************************************ --- *** relation: mnp *** --- *** relation type: VIEW *** --- *** *** --- *** A multiple nucleotide polymorphism with *** --- *** alleles of common length > 1, for exampl *** --- *** e AAA/TTT. *** --- ************************************************ --- CREATE VIEW mnp AS SELECT feature_id AS mnp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP'; --- ************************************************ --- *** relation: intron_domain *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intron_domain AS SELECT feature_id AS intron_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain'; --- ************************************************ --- *** relation: wobble_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base pairing, mo *** --- *** st commonly between G and U, which is im *** --- *** portant for the secondary structure of R *** --- *** NAs. It has similar thermodynamic stabil *** --- *** ity to the Watson-Crick pairing. Wobble *** --- *** base pairs only have two hydrogen bonds. *** --- *** Other wobble base pair possibilities ar *** --- *** e I-A, I-U and I-C. *** --- ************************************************ --- CREATE VIEW wobble_base_pair AS SELECT feature_id AS wobble_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wobble_base_pair'; --- ************************************************ --- *** relation: internal_guide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A purine-rich sequence in the group I in *** --- *** trons which determines the locations of *** --- *** the splice sites in group I intron splic *** --- *** ing and has catalytic activity. *** --- ************************************************ --- CREATE VIEW internal_guide_sequence AS SELECT feature_id AS internal_guide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence'; --- ************************************************ --- *** relation: silent_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW silent_mutation AS SELECT feature_id AS silent_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation'; --- ************************************************ --- *** relation: epitope *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a macromolecule that is reco *** --- *** gnized by the immune system. *** --- ************************************************ --- CREATE VIEW epitope AS SELECT feature_id AS epitope_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epitope'; --- ************************************************ --- *** relation: copy_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A variation that increases or decreases *** --- *** the copy number of a given region. *** --- ************************************************ --- CREATE VIEW copy_number_variation AS SELECT feature_id AS copy_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_variation'; --- ************************************************ --- *** relation: sequence_variant_affecting_copy_number *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_copy_number AS SELECT feature_id AS sequence_variant_affecting_copy_number_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_copy_number'; --- ************************************************ --- *** relation: chromosome_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_breakpoint AS SELECT feature_id AS chromosome_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint'; --- ************************************************ --- *** relation: inversion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where an i *** --- *** nversion begins or ends. *** --- ************************************************ --- CREATE VIEW inversion_breakpoint AS SELECT feature_id AS inversion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint'; --- ************************************************ --- *** relation: allele *** --- *** relation type: VIEW *** --- *** *** --- *** An allele is one of a set of coexisting *** --- *** sequence variants of a gene. *** --- ************************************************ --- CREATE VIEW allele AS SELECT feature_id AS allele_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allele'; --- ************************************************ --- *** relation: haplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A haplotype is one of a set of coexistin *** --- *** g sequence variants of a haplotype block *** --- *** . *** --- ************************************************ --- CREATE VIEW haplotype AS SELECT feature_id AS haplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype'; --- ************************************************ --- *** relation: polymorphic_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that is segregating i *** --- *** n one or more natural populations of a s *** --- *** pecies. *** --- ************************************************ --- CREATE VIEW polymorphic_sequence_variant AS SELECT feature_id AS polymorphic_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant'; --- ************************************************ --- *** relation: genome *** --- *** relation type: VIEW *** --- *** *** --- *** A genome is the sum of genetic material *** --- *** within a cell or virion. *** --- ************************************************ --- CREATE VIEW genome AS SELECT feature_id AS genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genome'; --- ************************************************ --- *** relation: genotype *** --- *** relation type: VIEW *** --- *** *** --- *** A genotype is a variant genome, complete *** --- *** or incomplete. *** --- ************************************************ --- CREATE VIEW genotype AS SELECT feature_id AS genotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype' OR cvterm.name = 'genotype'; --- ************************************************ --- *** relation: diplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A diplotype is a pair of haplotypes from *** --- *** a given individual. It is a genotype wh *** --- *** ere the phase is known. *** --- ************************************************ --- CREATE VIEW diplotype AS SELECT feature_id AS diplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype'; --- ************************************************ --- *** relation: direction_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direction_attribute AS SELECT feature_id AS direction_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'direction_attribute'; --- ************************************************ --- *** relation: forward *** --- *** relation type: VIEW *** --- *** *** --- *** Forward is an attribute of the feature, *** --- *** where the feature is in the 5' to 3' dir *** --- *** ection. *** --- ************************************************ --- CREATE VIEW forward AS SELECT feature_id AS forward_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward'; --- ************************************************ --- *** relation: reverse *** --- *** relation type: VIEW *** --- *** *** --- *** Reverse is an attribute of the feature, *** --- *** where the feature is in the 3' to 5' dir *** --- *** ection. Again could be applied to primer *** --- *** . *** --- ************************************************ --- CREATE VIEW reverse AS SELECT feature_id AS reverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse'; --- ************************************************ --- *** relation: mitochondrial_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_dna AS SELECT feature_id AS mitochondrial_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA'; --- ************************************************ --- *** relation: chloroplast_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_dna AS SELECT feature_id AS chloroplast_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA'; --- ************************************************ --- *** relation: mirtron *** --- *** relation type: VIEW *** --- *** *** --- *** A debranched intron which mimics the str *** --- *** ucture of pre-miRNA and enters the miRNA *** --- *** processing pathway without Drosha media *** --- *** ted cleavage. *** --- ************************************************ --- CREATE VIEW mirtron AS SELECT feature_id AS mirtron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mirtron'; --- ************************************************ --- *** relation: pirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA, part of a silenc *** --- *** ing system that prevents the spreading o *** --- *** f selfish genetic elements. *** --- ************************************************ --- CREATE VIEW pirna AS SELECT feature_id AS pirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA'; --- ************************************************ --- *** relation: arginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an arginine ant *** --- *** icodon, and a 3' arginine binding region *** --- *** . *** --- ************************************************ --- CREATE VIEW arginyl_trna AS SELECT feature_id AS arginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginyl_tRNA'; --- ************************************************ --- *** relation: mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide region with either intra-ge *** --- *** nome or intracellular moblity, of varyin *** --- *** g length, which often carry the informat *** --- *** ion necessary for transfer and recombina *** --- *** tion with the host genome. *** --- ************************************************ --- CREATE VIEW mobile_genetic_element AS SELECT feature_id AS mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'mobile_genetic_element'; --- ************************************************ --- *** relation: extrachromosomal_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is not integrated into the h *** --- *** ost chromosome. *** --- ************************************************ --- CREATE VIEW extrachromosomal_mobile_genetic_element AS SELECT feature_id AS extrachromosomal_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'extrachromosomal_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is integrated into the host *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW integrated_mobile_genetic_element AS SELECT feature_id AS integrated_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'integrated_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid sequence that is integrated wi *** --- *** thin the host chromosome. *** --- ************************************************ --- CREATE VIEW integrated_plasmid AS SELECT feature_id AS integrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_plasmid'; --- ************************************************ --- *** relation: viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The region of nucleotide sequence of a v *** --- *** irus, a submicroscopic particle that rep *** --- *** licates by infecting a host cell. *** --- ************************************************ --- CREATE VIEW viral_sequence AS SELECT feature_id AS viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'viral_sequence'; --- ************************************************ --- *** relation: phage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide sequence of a virus that *** --- *** infects bacteria. *** --- ************************************************ --- CREATE VIEW phage_sequence AS SELECT feature_id AS phage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence'; --- ************************************************ --- *** relation: attctn_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attachment site located on a conjugat *** --- *** ive transposon and used for site-specifi *** --- *** c integration of a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW attctn_site AS SELECT feature_id AS attctn_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attCtn_site'; --- ************************************************ --- *** relation: nuclear_mt_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A nuclear pseudogene of a mitochndrial g *** --- *** ene. *** --- ************************************************ --- CREATE VIEW nuclear_mt_pseudogene AS SELECT feature_id AS nuclear_mt_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_mt_pseudogene'; --- ************************************************ --- *** relation: cointegrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A MGE region consisting of two fused pla *** --- *** smids resulting from a replicative trans *** --- *** position event. *** --- ************************************************ --- CREATE VIEW cointegrated_plasmid AS SELECT feature_id AS cointegrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cointegrated_plasmid'; --- ************************************************ --- *** relation: irlinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the left of a region susceptible to s *** --- *** ite-specific inversion. *** --- ************************************************ --- CREATE VIEW irlinv_site AS SELECT feature_id AS irlinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site'; --- ************************************************ --- *** relation: irrinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the right of a region susceptible to *** --- *** site-specific inversion. *** --- ************************************************ --- CREATE VIEW irrinv_site AS SELECT feature_id AS irrinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRRinv_site'; --- ************************************************ --- *** relation: inversion_site_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region located within an inversion sit *** --- *** e. *** --- ************************************************ --- CREATE VIEW inversion_site_part AS SELECT feature_id AS inversion_site_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'inversion_site_part'; --- ************************************************ --- *** relation: defective_conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** An island that contains genes for integr *** --- *** ation/excision and the gene and site for *** --- *** the initiation of intercellular transfe *** --- *** r by conjugation. It can be complemented *** --- *** for transfer by a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW defective_conjugative_transposon AS SELECT feature_id AS defective_conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'defective_conjugative_transposon'; --- ************************************************ --- *** relation: repeat_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a repeat, interrupted by th *** --- *** e insertion of another element. *** --- ************************************************ --- CREATE VIEW repeat_fragment AS SELECT feature_id AS repeat_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_fragment'; --- ************************************************ --- *** relation: transposon_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transposon_fragment AS SELECT feature_id AS transposon_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposon_fragment'; --- ************************************************ --- *** relation: transcriptional_cis_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates the t *** --- *** ranscription of a gene or genes. *** --- ************************************************ --- CREATE VIEW transcriptional_cis_regulatory_region AS SELECT feature_id AS transcriptional_cis_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'transcriptional_cis_regulatory_region'; --- ************************************************ --- *** relation: splicing_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates splic *** --- *** ing. *** --- ************************************************ --- CREATE VIEW splicing_regulatory_region AS SELECT feature_id AS splicing_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splicing_regulatory_region'; --- ************************************************ --- *** relation: promoter_targeting_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional_cis_regulatory_region *** --- *** that restricts the activity of a CRM to *** --- *** a single promoter and which functions on *** --- *** ly when both itself and an insulator are *** --- *** located between the CRM and the promote *** --- *** r. *** --- ************************************************ --- CREATE VIEW promoter_targeting_sequence AS SELECT feature_id AS promoter_targeting_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_targeting_sequence'; --- ************************************************ --- *** relation: sequence_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_alteration is a sequence_feat *** --- *** ure whose extent is the deviation from a *** --- *** nother sequence. *** --- ************************************************ --- CREATE VIEW sequence_alteration AS SELECT feature_id AS sequence_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'substitution' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'sequence_alteration'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant is a non exact copy o *** --- *** f a sequence_feature or genome exhibitin *** --- *** g one or more sequence_alteration. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: propeptide_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** The propeptide_cleavage_site is the argi *** --- *** nine/lysine boundary on a propeptide whe *** --- *** re cleavage occurs. *** --- ************************************************ --- CREATE VIEW propeptide_cleavage_site AS SELECT feature_id AS propeptide_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide_cleavage_site'; --- ************************************************ --- *** relation: propeptide *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a peptide chain which is cleaved *** --- *** off during the formation of the mature *** --- *** protein. *** --- ************************************************ --- CREATE VIEW propeptide AS SELECT feature_id AS propeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide'; --- ************************************************ --- *** relation: immature_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** An immature_peptide_region is the extent *** --- *** of the peptide after it has been transl *** --- *** ated and before any processing occurs. *** --- ************************************************ --- CREATE VIEW immature_peptide_region AS SELECT feature_id AS immature_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'immature_peptide_region'; --- ************************************************ --- *** relation: active_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Active peptides are proteins which are b *** --- *** iologically active, released from a prec *** --- *** ursor molecule. *** --- ************************************************ --- CREATE VIEW active_peptide AS SELECT feature_id AS active_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide'; --- ************************************************ --- *** relation: compositionally_biased_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is rich in a par *** --- *** ticular amino acid or homopolymeric and *** --- *** greater than three residues in length. *** --- ************************************************ --- CREATE VIEW compositionally_biased_region_of_peptide AS SELECT feature_id AS compositionally_biased_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compositionally_biased_region_of_peptide'; --- ************************************************ --- *** relation: polypeptide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a short (up to 20 am *** --- *** ino acids) region of biological interest *** --- *** . Such motifs, although they are too sho *** --- *** rt to constitute functional domains, sha *** --- *** re sequence similarities and are conserv *** --- *** ed in different proteins. They display a *** --- *** common function (protein-binding, subce *** --- *** llular location etc.). *** --- ************************************************ --- CREATE VIEW polypeptide_motif AS SELECT feature_id AS polypeptide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_motif'; --- ************************************************ --- *** relation: polypeptide_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide_repeat is a single copy of *** --- *** an internal sequence repetition. *** --- ************************************************ --- CREATE VIEW polypeptide_repeat AS SELECT feature_id AS polypeptide_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_repeat'; --- ************************************************ --- *** relation: polypeptide_structural_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of polypeptide with a given struc *** --- *** tural property. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_region AS SELECT feature_id AS polypeptide_structural_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_region'; --- ************************************************ --- *** relation: membrane_structure *** --- *** relation type: VIEW *** --- *** *** --- *** Arrangement of the polypeptide with resp *** --- *** ect to the lipid bilayer. *** --- ************************************************ --- CREATE VIEW membrane_structure AS SELECT feature_id AS membrane_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_structure'; --- ************************************************ --- *** relation: extramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer. *** --- ************************************************ --- CREATE VIEW extramembrane_polypeptide_region AS SELECT feature_id AS extramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'extramembrane_polypeptide_region'; --- ************************************************ --- *** relation: cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized ins *** --- *** ide the cytoplasm. *** --- ************************************************ --- CREATE VIEW cytoplasmic_polypeptide_region AS SELECT feature_id AS cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: non_cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer and outside of t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW non_cytoplasmic_polypeptide_region AS SELECT feature_id AS non_cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: intramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region present in the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW intramembrane_polypeptide_region AS SELECT feature_id AS intramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region'; --- ************************************************ --- *** relation: membrane_peptide_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region localized within the *** --- *** lipid bilayer where both ends traverse t *** --- *** he same membrane. *** --- ************************************************ --- CREATE VIEW membrane_peptide_loop AS SELECT feature_id AS membrane_peptide_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop'; --- ************************************************ --- *** relation: transmembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region traversing the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW transmembrane_polypeptide_region AS SELECT feature_id AS transmembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transmembrane_polypeptide_region'; --- ************************************************ --- *** relation: polypeptide_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide with secondary struc *** --- *** ture has hydrogen bonding along the pept *** --- *** ide chain that causes a defined conforma *** --- *** tion of the chain. *** --- ************************************************ --- CREATE VIEW polypeptide_secondary_structure AS SELECT feature_id AS polypeptide_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_secondary_structure'; --- ************************************************ --- *** relation: polypeptide_structural_motif *** --- *** relation type: VIEW *** --- *** *** --- *** Motif is a three-dimensional structural *** --- *** element within the chain, which appears *** --- *** also in a variety of other molecules. Un *** --- *** like a domain, a motif does not need to *** --- *** form a stable globular unit. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_motif AS SELECT feature_id AS polypeptide_structural_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_motif'; --- ************************************************ --- *** relation: coiled_coil *** --- *** relation type: VIEW *** --- *** *** --- *** A coiled coil is a structural motif in p *** --- *** roteins, in which alpha-helices are coil *** --- *** ed together like the strands of a rope. *** --- ************************************************ --- CREATE VIEW coiled_coil AS SELECT feature_id AS coiled_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil'; --- ************************************************ --- *** relation: helix_turn_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A motif comprising two helices separated *** --- *** by a turn. *** --- ************************************************ --- CREATE VIEW helix_turn_helix AS SELECT feature_id AS helix_turn_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helix_turn_helix'; --- ************************************************ --- *** relation: polypeptide_sequencing_information *** --- *** relation type: VIEW *** --- *** *** --- *** Incompatibility in the sequence due to s *** --- *** ome experimental problem. *** --- ************************************************ --- CREATE VIEW polypeptide_sequencing_information AS SELECT feature_id AS polypeptide_sequencing_information_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'polypeptide_sequencing_information'; --- ************************************************ --- *** relation: non_adjacent_residues *** --- *** relation type: VIEW *** --- *** *** --- *** Indicates that two consecutive residues *** --- *** in a fragment sequence are not consecuti *** --- *** ve in the full-length protein and that t *** --- *** here are a number of unsequenced residue *** --- *** s between them. *** --- ************************************************ --- CREATE VIEW non_adjacent_residues AS SELECT feature_id AS non_adjacent_residues_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues'; --- ************************************************ --- *** relation: non_terminal_residue *** --- *** relation type: VIEW *** --- *** *** --- *** The residue at an extremity of the seque *** --- *** nce is not the terminal residue. *** --- ************************************************ --- CREATE VIEW non_terminal_residue AS SELECT feature_id AS non_terminal_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_terminal_residue'; --- ************************************************ --- *** relation: sequence_conflict *** --- *** relation type: VIEW *** --- *** *** --- *** Different sources report differing seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW sequence_conflict AS SELECT feature_id AS sequence_conflict_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_conflict'; --- ************************************************ --- *** relation: sequence_uncertainty *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the positions in a sequence wh *** --- *** ere the authors are unsure about the seq *** --- *** uence assignment. *** --- ************************************************ --- CREATE VIEW sequence_uncertainty AS SELECT feature_id AS sequence_uncertainty_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_uncertainty'; --- ************************************************ --- *** relation: post_translationally_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region where a transformation occurs i *** --- *** n a protein after it has been synthesize *** --- *** d. This which may regulate, stabilize, c *** --- *** rosslink or introduce new chemical funct *** --- *** ionalities in the protein. *** --- ************************************************ --- CREATE VIEW post_translationally_modified_region AS SELECT feature_id AS post_translationally_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region'; --- ************************************************ --- *** relation: polypeptide_metal_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residue is part of a binding site for a *** --- *** metal ion. *** --- ************************************************ --- CREATE VIEW polypeptide_metal_contact AS SELECT feature_id AS polypeptide_metal_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_metal_contact'; --- ************************************************ --- *** relation: protein_protein_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues involved in protein-protein int *** --- *** eractions. *** --- ************************************************ --- CREATE VIEW protein_protein_contact AS SELECT feature_id AS protein_protein_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact'; --- ************************************************ --- *** relation: polypeptide_calcium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with calcium *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_calcium_ion_contact_site AS SELECT feature_id AS polypeptide_calcium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_cobalt_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with cobalt. *** --- ************************************************ --- CREATE VIEW polypeptide_cobalt_ion_contact_site AS SELECT feature_id AS polypeptide_cobalt_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_cobalt_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_copper_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with copper. *** --- ************************************************ --- CREATE VIEW polypeptide_copper_ion_contact_site AS SELECT feature_id AS polypeptide_copper_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_copper_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_iron_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with iron. *** --- ************************************************ --- CREATE VIEW polypeptide_iron_ion_contact_site AS SELECT feature_id AS polypeptide_iron_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_iron_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_magnesium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with magnesi *** --- *** um. *** --- ************************************************ --- CREATE VIEW polypeptide_magnesium_ion_contact_site AS SELECT feature_id AS polypeptide_magnesium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_magnesium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_manganese_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with mangane *** --- *** se. *** --- ************************************************ --- CREATE VIEW polypeptide_manganese_ion_contact_site AS SELECT feature_id AS polypeptide_manganese_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_manganese_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_molybdenum_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with molybde *** --- *** num. *** --- ************************************************ --- CREATE VIEW polypeptide_molybdenum_ion_contact_site AS SELECT feature_id AS polypeptide_molybdenum_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_molybdenum_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_nickel_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with nickel. *** --- ************************************************ --- CREATE VIEW polypeptide_nickel_ion_contact_site AS SELECT feature_id AS polypeptide_nickel_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nickel_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_tungsten_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with tungste *** --- *** n. *** --- ************************************************ --- CREATE VIEW polypeptide_tungsten_ion_contact_site AS SELECT feature_id AS polypeptide_tungsten_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_tungsten_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_zinc_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** Residue involved in contact with zinc. *** --- ************************************************ --- CREATE VIEW polypeptide_zinc_ion_contact_site AS SELECT feature_id AS polypeptide_zinc_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_zinc_ion_contact_site'; --- ************************************************ --- *** relation: catalytic_residue *** --- *** relation type: VIEW *** --- *** *** --- *** Amino acid involved in the activity of a *** --- *** n enzyme. *** --- ************************************************ --- CREATE VIEW catalytic_residue AS SELECT feature_id AS catalytic_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue'; --- ************************************************ --- *** relation: polypeptide_ligand_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues which interact with a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_ligand_contact AS SELECT feature_id AS polypeptide_ligand_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact'; --- ************************************************ --- *** relation: asx_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: Residue(i) is Asp *** --- *** artate or Asparagine (Asx), side-chain O *** --- *** of residue(i) is H-bonded to the main-c *** --- *** hain NH of residue(i+2) or (i+3), main-c *** --- *** hain CO of residue(i) is H-bonded to the *** --- *** main-chain NH of residue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW asx_motif AS SELECT feature_id AS asx_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif'; --- ************************************************ --- *** relation: beta_bulge *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet in which the main chains of two co *** --- *** nsecutive residues are H-bonded to that *** --- *** of the third, and in which the dihedral *** --- *** angles are as follows: Residue(i): -140 *** --- *** degrees < phi(l) -20 degrees , -90 degre *** --- *** es < psi(l) < 40 degrees. Residue (i+1): *** --- *** -180 degrees < phi < -25 degrees or +12 *** --- *** 0 degrees < phi < +180 degrees, +40 degr *** --- *** ees < psi < +180 degrees or -180 degrees *** --- *** < psi < -120 degrees. *** --- ************************************************ --- CREATE VIEW beta_bulge AS SELECT feature_id AS beta_bulge_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge'; --- ************************************************ --- *** relation: beta_bulge_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds. Beta bu *** --- *** lge loops often occur at the loop ends o *** --- *** f beta-hairpins. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop AS SELECT feature_id AS beta_bulge_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'beta_bulge_loop'; --- ************************************************ --- *** relation: beta_bulge_loop_five *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 4), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +3), these loops have an RL nest at resi *** --- *** dues i+2 and i+3. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_five AS SELECT feature_id AS beta_bulge_loop_five_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five'; --- ************************************************ --- *** relation: beta_bulge_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 5), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +4), these loops have an RL nest at resi *** --- *** dues i+3 and i+4. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_six AS SELECT feature_id AS beta_bulge_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_six'; --- ************************************************ --- *** relation: beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A beta strand describes a single length *** --- *** of polypeptide chain that forms part of *** --- *** a beta sheet. A single continuous stretc *** --- *** h of amino acids adopting an extended co *** --- *** nformation of hydrogen bonds between the *** --- *** N-O and the C=O of another part of the *** --- *** peptide. This forms a secondary protein *** --- *** structure in which two or more extended *** --- *** polypeptide regions are hydrogen-bonded *** --- *** to one another in a planar array. *** --- ************************************************ --- CREATE VIEW beta_strand AS SELECT feature_id AS beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'beta_strand'; --- ************************************************ --- *** relation: antiparallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (one running N-term *** --- *** inal to C-terminal and one running C-ter *** --- *** minal to N-terminal). Hydrogen bonding o *** --- *** ccurs between every other C=O from one s *** --- *** trand to every other N-H on the adjacent *** --- *** strand. In this case, if two atoms C-al *** --- *** pha (i) and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then t *** --- *** hey form two mutual backbone hydrogen bo *** --- *** nds to each other's flanking peptide gro *** --- *** ups; this is known as a close pair of hy *** --- *** drogen bonds. The peptide backbone dihed *** --- *** ral angles (phi, psi) are about (-140 de *** --- *** grees, 135 degrees) in antiparallel shee *** --- *** ts. *** --- ************************************************ --- CREATE VIEW antiparallel_beta_strand AS SELECT feature_id AS antiparallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand'; --- ************************************************ --- *** relation: parallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (both running N-ter *** --- *** minal to C-terminal). This orientation i *** --- *** s slightly less stable because it introd *** --- *** uces nonplanarity in the inter-strand hy *** --- *** drogen bonding pattern. Hydrogen bonding *** --- *** occurs between every other C=O from one *** --- *** strand to every other N-H on the adjace *** --- *** nt strand. In this case, if two atoms C- *** --- *** alpha (i)and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then *** --- *** they do not hydrogen bond to each other; *** --- *** rather, one residue forms hydrogen bond *** --- *** s to the residues that flank the other ( *** --- *** but not vice versa). For example, residu *** --- *** e i may form hydrogen bonds to residues *** --- *** j - 1 and j + 1; this is known as a wide *** --- *** pair of hydrogen bonds. By contrast, re *** --- *** sidue j may hydrogen-bond to different r *** --- *** esidues altogether, or to none at all. T *** --- *** he dihedral angles (phi, psi) are about *** --- *** (-120 degrees, 115 degrees) in parallel *** --- *** sheets. *** --- ************************************************ --- CREATE VIEW parallel_beta_strand AS SELECT feature_id AS parallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'parallel_beta_strand'; --- ************************************************ --- *** relation: peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A helix is a secondary_structure conform *** --- *** ation where the peptide backbone forms a *** --- *** coil. *** --- ************************************************ --- CREATE VIEW peptide_helix AS SELECT feature_id AS peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'peptide_helix'; --- ************************************************ --- *** relation: left_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A left handed helix is a region of pepti *** --- *** de where the coiled conformation turns i *** --- *** n an anticlockwise, left handed screw. *** --- ************************************************ --- CREATE VIEW left_handed_peptide_helix AS SELECT feature_id AS left_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix'; --- ************************************************ --- *** relation: right_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A right handed helix is a region of pept *** --- *** ide where the coiled conformation turns *** --- *** in a clockwise, right handed screw. *** --- ************************************************ --- CREATE VIEW right_handed_peptide_helix AS SELECT feature_id AS right_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'right_handed_peptide_helix'; --- ************************************************ --- *** relation: alpha_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The helix has 3.6 residues per turn whic *** --- *** h corersponds to a translation of 1.5 an *** --- *** gstroms (= 0.15 nm) along the helical ax *** --- *** is. Every backbone N-H group donates a h *** --- *** ydrogen bond to the backbone C=O group o *** --- *** f the amino acid four residues earlier. *** --- ************************************************ --- CREATE VIEW alpha_helix AS SELECT feature_id AS alpha_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix'; --- ************************************************ --- *** relation: pi_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The pi helix has 4.1 residues per turn a *** --- *** nd a translation of 1.15 (=0.115 nm) al *** --- *** ong the helical axis. The N-H group of a *** --- *** n amino acid forms a hydrogen bond with *** --- *** the C=O group of the amino acid five res *** --- *** idues earlier. *** --- ************************************************ --- CREATE VIEW pi_helix AS SELECT feature_id AS pi_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pi_helix'; --- ************************************************ --- *** relation: three_ten_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The 3-10 helix has 3 residues per turn w *** --- *** ith a translation of 2.0 angstroms (=0.2 *** --- *** nm) along the helical axis. The N-H gro *** --- *** up of an amino acid forms a hydrogen bon *** --- *** d with the C=O group of the amino acid t *** --- *** hree residues earlier. *** --- ************************************************ --- CREATE VIEW three_ten_helix AS SELECT feature_id AS three_ten_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_ten_helix'; --- ************************************************ --- *** relation: polypeptide_nest_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles. Nest should not have P *** --- *** roline as any residue. Nests frequently *** --- *** occur as parts of other motifs such as S *** --- *** chellman loops. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_motif AS SELECT feature_id AS polypeptide_nest_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'polypeptide_nest_motif'; --- ************************************************ --- *** relation: polypeptide_nest_left_right_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): +20 degree *** --- *** s < phi < +140 degrees, -40 degrees < ps *** --- *** i < +90 degrees. Residue(i+1): -140 degr *** --- *** ees < phi < -20 degrees, -90 degrees < p *** --- *** si < +40 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_left_right_motif AS SELECT feature_id AS polypeptide_nest_left_right_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif'; --- ************************************************ --- *** relation: polypeptide_nest_right_left_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): -140 degre *** --- *** es < phi < -20 degrees, -90 degrees < ps *** --- *** i < +40 degrees. Residue(i+1): +20 degre *** --- *** es < phi < +140 degrees, -40 degrees < p *** --- *** si < +90 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_right_left_motif AS SELECT feature_id AS polypeptide_nest_right_left_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_right_left_motif'; --- ************************************************ --- *** relation: schellmann_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of six or seven consecutive resi *** --- *** dues that contains two H-bonds. *** --- ************************************************ --- CREATE VIEW schellmann_loop AS SELECT feature_id AS schellmann_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'schellmann_loop'; --- ************************************************ --- *** relation: schellmann_loop_seven *** --- *** relation type: VIEW *** --- *** *** --- *** Wild type: A motif of seven consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+6), the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of res *** --- *** idue(i+5). *** --- ************************************************ --- CREATE VIEW schellmann_loop_seven AS SELECT feature_id AS schellmann_loop_seven_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven'; --- ************************************************ --- *** relation: schellmann_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** Common Type: A motif of six consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+5) the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of resi *** --- *** due(i+4). *** --- ************************************************ --- CREATE VIEW schellmann_loop_six AS SELECT feature_id AS schellmann_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_six'; --- ************************************************ --- *** relation: serine_threonine_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two hydrogen bonds in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain O of residue(i) is H-bonded to t *** --- *** he main-chain NH of residue(i+2) or (i+3 *** --- *** ) , the main-chain CO group of residue(i *** --- *** ) is H-bonded to the main-chain NH of re *** --- *** sidue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW serine_threonine_motif AS SELECT feature_id AS serine_threonine_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_motif'; --- ************************************************ --- *** relation: serine_threonine_staple_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four or five consecutive resi *** --- *** dues and one H-bond in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain OH of residue(i) is H-bonded to *** --- *** the main-chain CO of residue(i3) or (i4) *** --- *** , Phi angles of residues(i1), (i2) and ( *** --- *** i3) are negative. *** --- ************************************************ --- CREATE VIEW serine_threonine_staple_motif AS SELECT feature_id AS serine_threonine_staple_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_staple_motif'; --- ************************************************ --- *** relation: polypeptide_turn_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A reversal in the direction of the backb *** --- *** one of a protein that is stabilized by h *** --- *** ydrogen bond between backbone NH and CO *** --- *** groups, involving no more than 4 amino a *** --- *** cid residues. *** --- ************************************************ --- CREATE VIEW polypeptide_turn_motif AS SELECT feature_id AS polypeptide_turn_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_turn_motif'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I (dihedral angles):- R *** --- *** esidue(i): -140 degrees < chi (1) -120 d *** --- *** egrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1) *** --- *** : -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_one AS SELECT feature_id AS asx_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < psi *** --- *** +120 degrees < +180 degrees. Residue(i+ *** --- *** 1): +20 degrees < phi < +140 degrees, -4 *** --- *** 0 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_two AS SELECT feature_id AS asx_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < ps *** --- *** i +120 degrees < +180 degrees. Residue(i *** --- *** +1): +20 degrees < phi < +140 degrees, - *** --- *** 40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_two AS SELECT feature_id AS asx_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1 *** --- *** ): -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_one AS SELECT feature_id AS asx_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive residues tha *** --- *** t may contain one H-bond, which, if pres *** --- *** ent, is between the main-chain CO of the *** --- *** first residue and the main-chain NH of *** --- *** the fourth. It is characterized by the d *** --- *** ihedral angles of the second and third r *** --- *** esidues, which are the basis for sub-cat *** --- *** egorization. *** --- ************************************************ --- CREATE VIEW beta_turn AS SELECT feature_id AS beta_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I:A motif of four conse *** --- *** cutive residues that may contain one H-b *** --- *** ond, which, if present, is between the m *** --- *** ain-chain CO of the first residue and th *** --- *** e main-chain NH of the fourth. It is cha *** --- *** racterized by the dihedral angles:- Resi *** --- *** due(i+1): -140 degrees > phi > -20 degre *** --- *** es, -90 degrees > psi > +40 degrees. Res *** --- *** idue(i+2): -140 degrees > phi > -20 degr *** --- *** ees, -90 degrees > psi > +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_one AS SELECT feature_id AS beta_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II: A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees > phi > -20 degr *** --- *** ees, +80 degrees > psi > +180 degrees. R *** --- *** esidue(i+2): +20 degrees > phi > +140 de *** --- *** grees, -40 degrees > psi > +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_two AS SELECT feature_id AS beta_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_two'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I:A motif of four cons *** --- *** ecutive residues that may contain one H- *** --- *** bond, which, if present, is between the *** --- *** main-chain CO of the first residue and t *** --- *** he main-chain NH of the fourth. It is ch *** --- *** aracterized by the dihedral angles: Resi *** --- *** due(i+1): -140 degrees < phi < -20 degre *** --- *** es, -90 degrees < psi < +40 degrees. Res *** --- *** idue(i+2): -140 degrees < phi < -20 degr *** --- *** ees, -90 degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_one AS SELECT feature_id AS beta_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II:A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees < phi < -20 degr *** --- *** ees, +80 degrees < psi < +180 degrees. R *** --- *** esidue(i+2): +20 degrees < phi < +140 de *** --- *** grees, -40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_two AS SELECT feature_id AS beta_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_two'; --- ************************************************ --- *** relation: gamma_turn *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees. *** --- ************************************************ --- CREATE VIEW gamma_turn AS SELECT feature_id AS gamma_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'gamma_turn'; --- ************************************************ --- *** relation: gamma_turn_classic *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=75.0 - psi(i+1)=-64.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_classic AS SELECT feature_id AS gamma_turn_classic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic'; --- ************************************************ --- *** relation: gamma_turn_inverse *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=-79.0 - psi(i+1)=69.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_inverse AS SELECT feature_id AS gamma_turn_inverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_inverse'; --- ************************************************ --- *** relation: serine_threonine_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Ser *** --- *** ine (S) or Threonine (T), the side-chain *** --- *** O of residue(i) is H-bonded to the main *** --- *** -chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW serine_threonine_turn AS SELECT feature_id AS serine_threonine_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'serine_threonine_turn'; --- ************************************************ --- *** relation: st_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** -90 degrees psi +120 degrees < +40 degr *** --- *** ees, residue(i+1): -140 degrees < phi < *** --- *** -20 degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_one AS SELECT feature_id AS st_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one'; --- ************************************************ --- *** relation: st_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** +80 degrees psi +120 degrees < +180 deg *** --- *** rees, residue(i+1): +20 degrees < phi < *** --- *** +140 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_two AS SELECT feature_id AS st_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_two'; --- ************************************************ --- *** relation: st_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, -9 *** --- *** 0 degrees psi +120 degrees < +40 degrees *** --- *** , residue(i+1): -140 degrees < phi < -20 *** --- *** degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_one AS SELECT feature_id AS st_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_one'; --- ************************************************ --- *** relation: st_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, +8 *** --- *** 0 degrees psi +120 degrees < +180 degree *** --- *** s, residue(i+1): +20 degrees < phi < +14 *** --- *** 0 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_two AS SELECT feature_id AS st_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_two'; --- ************************************************ --- *** relation: polypeptide_variation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site of sequence variation (alteration *** --- *** ). Alternative sequence due to naturally *** --- *** occuring events such as polymorphisms a *** --- *** nd altermatve splicing or experimental m *** --- *** ethods such as site directed mutagenesis *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_variation_site AS SELECT feature_id AS polypeptide_variation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'polypeptide_variation_site'; --- ************************************************ --- *** relation: natural_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the natural sequence variants *** --- *** due to polymorphisms, disease-associated *** --- *** mutations, RNA editing and variations b *** --- *** etween strains, isolates or cultivars. *** --- ************************************************ --- CREATE VIEW natural_variant_site AS SELECT feature_id AS natural_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site'; --- ************************************************ --- *** relation: mutated_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Site which has been experimentally alter *** --- *** ed. *** --- ************************************************ --- CREATE VIEW mutated_variant_site AS SELECT feature_id AS mutated_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutated_variant_site'; --- ************************************************ --- *** relation: alternate_sequence_site *** --- *** relation type: VIEW *** --- *** *** --- *** Description of sequence variants produce *** --- *** d by alternative splicing, alternative p *** --- *** romoter usage, alternative initiation an *** --- *** d ribosomal frameshifting. *** --- ************************************************ --- CREATE VIEW alternate_sequence_site AS SELECT feature_id AS alternate_sequence_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternate_sequence_site'; --- ************************************************ --- *** relation: beta_turn_type_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** des of type VIa or type VIb and where th *** --- *** e i+2 residue is cis-proline. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six AS SELECT feature_id AS beta_turn_type_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six'; --- ************************************************ --- *** relation: beta_turn_type_six_a *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -60 degrees, psi ~ 120 degrees. Re *** --- *** sidue(i+2): phi ~ -90 degrees, psi ~ 0 d *** --- *** egrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a AS SELECT feature_id AS beta_turn_type_six_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six_a'; --- ************************************************ --- *** relation: beta_turn_type_six_a_one *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_one AS SELECT feature_id AS beta_turn_type_six_a_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one'; --- ************************************************ --- *** relation: beta_turn_type_six_a_two *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_two AS SELECT feature_id AS beta_turn_type_six_a_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_two'; --- ************************************************ --- *** relation: beta_turn_type_six_b *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -120 degrees, psi ~ 120 degrees. R *** --- *** esidue(i+2): phi ~ -60 degrees, psi ~ 0 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_b AS SELECT feature_id AS beta_turn_type_six_b_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_b'; --- ************************************************ --- *** relation: beta_turn_type_eight *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues that may contain one H-bond, which, *** --- *** if present, is between the main-chain C *** --- *** O of the first residue and the main-chai *** --- *** n NH of the fourth and is characterized *** --- *** by the dihedral angles: Residue(i+1): ph *** --- *** i ~ -60 degrees, psi ~ -30 degrees. Resi *** --- *** due(i+2): phi ~ -120 degrees, psi ~ 120 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_eight AS SELECT feature_id AS beta_turn_type_eight_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_eight'; --- ************************************************ --- *** relation: dre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -10 and -60 relative to t *** --- *** he TSS. Consensus sequence is WATCGATW. *** --- ************************************************ --- CREATE VIEW dre_motif AS SELECT feature_id AS dre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DRE_motif'; --- ************************************************ --- *** relation: dmv4_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments with respect to the TSS (+1). Cons *** --- *** ensus sequence is YGGTCACACTR. Marked sp *** --- *** atial preference within core promoter; t *** --- *** end to occur near the TSS, although not *** --- *** as tightly as INR (SO:0000014). *** --- ************************************************ --- CREATE VIEW dmv4_motif AS SELECT feature_id AS dmv4_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv4_motif'; --- ************************************************ --- *** relation: e_box_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and +1 relative to th *** --- *** e TSS. Consensus sequence is AWCAGCTGWT. *** --- *** Tends to co-occur with DMv2 (SO:0001161 *** --- *** ). Tends to not occur with DPE motif (SO *** --- *** :0000015). *** --- ************************************************ --- CREATE VIEW e_box_motif AS SELECT feature_id AS e_box_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'E_box_motif'; --- ************************************************ --- *** relation: dmv5_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -50 and -10 relative to t *** --- *** he TSS. Consensus sequence is KTYRGTATWT *** --- *** TT. Tends to co-occur with DMv4 (SO:0001 *** --- *** 157) . Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv5_motif AS SELECT feature_id AS dmv5_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv5_motif'; --- ************************************************ --- *** relation: dmv3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -30 and +15 relative to t *** --- *** he TSS. Consensus sequence is KNNCAKCNCT *** --- *** RNY. Tends to co-occur with DMv2 (SO:000 *** --- *** 1161). Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (0001162). *** --- ************************************************ --- CREATE VIEW dmv3_motif AS SELECT feature_id AS dmv3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv3_motif'; --- ************************************************ --- *** relation: dmv2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and -45 relative to t *** --- *** he TSS. Consensus sequence is MKSYGGCARC *** --- *** GSYSS. Tends to co-occur with DMv3 (SO:0 *** --- *** 001160). Tends to not occur with DPE mot *** --- *** if (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv2_motif AS SELECT feature_id AS dmv2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv2_motif'; --- ************************************************ --- *** relation: mte *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between +20 and +30 relative to t *** --- *** he TSS. Consensus sequence is CSARCSSAAC *** --- *** GS. Tends to co-occur with INR motif (SO *** --- *** :0000014). Tends to not occur with DPE m *** --- *** otif (SO:0000015) or DMv5 (SO:0001159). *** --- ************************************************ --- CREATE VIEW mte AS SELECT feature_id AS mte_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MTE'; --- ************************************************ --- *** relation: inr1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** TCATTCG. *** --- ************************************************ --- CREATE VIEW inr1_motif AS SELECT feature_id AS inr1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR1_motif'; --- ************************************************ --- *** relation: dpe1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CGGACGT. *** --- ************************************************ --- CREATE VIEW dpe1_motif AS SELECT feature_id AS dpe1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE1_motif'; --- ************************************************ --- *** relation: dmv1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CARCCCT. *** --- ************************************************ --- CREATE VIEW dmv1_motif AS SELECT feature_id AS dmv1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv1_motif'; --- ************************************************ --- *** relation: gaga_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAGAGCG. *** --- ************************************************ --- CREATE VIEW gaga_motif AS SELECT feature_id AS gaga_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GAGA_motif'; --- ************************************************ --- *** relation: ndm2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus CGMYGYCR. *** --- ************************************************ --- CREATE VIEW ndm2_motif AS SELECT feature_id AS ndm2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM2_motif'; --- ************************************************ --- *** relation: ndm3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAAAGCT. *** --- ************************************************ --- CREATE VIEW ndm3_motif AS SELECT feature_id AS ndm3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM3_motif'; --- ************************************************ --- *** relation: ds_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded RNA. *** --- ************************************************ --- CREATE VIEW ds_rna_viral_sequence AS SELECT feature_id AS ds_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_RNA_viral_sequence'; --- ************************************************ --- *** relation: polinton *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of DNA transposon that populates *** --- *** the genomes of protists, fungi, and anim *** --- *** als, characterized by a unique set of pr *** --- *** oteins necessary for their transposition *** --- *** , including a protein-primed DNA polymer *** --- *** ase B, retroviral integrase, cysteine pr *** --- *** otease, and ATPase. Polintons are charac *** --- *** terized by 6-bp target site duplications *** --- *** , terminal-inverted repeats that are sev *** --- *** eral hundred nucleotides long, and 5'-AG *** --- *** and TC-3' termini. Polintons exist as a *** --- *** utonomous and nonautonomous elements. *** --- ************************************************ --- CREATE VIEW polinton AS SELECT feature_id AS polinton_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polinton'; --- ************************************************ --- *** relation: rrna_21s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it in mitochondrial rRNA. *** --- ************************************************ --- CREATE VIEW rrna_21s AS SELECT feature_id AS rrna_21s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_21S'; --- ************************************************ --- *** relation: trna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tRNA. *** --- ************************************************ --- CREATE VIEW trna_region AS SELECT feature_id AS trna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'tRNA_region'; --- ************************************************ --- *** relation: anticodon_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of seven nucleotide bases in *** --- *** tRNA which contains the anticodon. It ha *** --- *** s the sequence 5'-pyrimidine-purine-anti *** --- *** codon-modified purine-any base-3. *** --- ************************************************ --- CREATE VIEW anticodon_loop AS SELECT feature_id AS anticodon_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop'; --- ************************************************ --- *** relation: anticodon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of three nucleotide bases in *** --- *** tRNA which recognizes a codon in mRNA. *** --- ************************************************ --- CREATE VIEW anticodon AS SELECT feature_id AS anticodon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon'; --- ************************************************ --- *** relation: cca_tail *** --- *** relation type: VIEW *** --- *** *** --- *** Base sequence at the 3' end of a tRNA. T *** --- *** he 3'-hydroxyl group on the terminal ade *** --- *** nosine is the attachment point for the a *** --- *** mino acid. *** --- ************************************************ --- CREATE VIEW cca_tail AS SELECT feature_id AS cca_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CCA_tail'; --- ************************************************ --- *** relation: dhu_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of nucleotide b *** --- *** ases in tRNA. It contains several dihydr *** --- *** ouracil residues. *** --- ************************************************ --- CREATE VIEW dhu_loop AS SELECT feature_id AS dhu_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DHU_loop'; --- ************************************************ --- *** relation: t_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of three nucleo *** --- *** tide bases in tRNA. It has sequence T-Ps *** --- *** i-C. *** --- ************************************************ --- CREATE VIEW t_loop AS SELECT feature_id AS t_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_loop'; --- ************************************************ --- *** relation: pyrrolysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding pyrrolysyl *** --- *** tRNA (SO:0000766). *** --- ************************************************ --- CREATE VIEW pyrrolysine_trna_primary_transcript AS SELECT feature_id AS pyrrolysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: u3_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U3 snoRNA is a member of the box C/D cla *** --- *** ss of small nucleolar RNAs. The U3 snoRN *** --- *** A secondary structure is characterised b *** --- *** y a small 5' domain (with boxes A and A' *** --- *** ), and a larger 3' domain (with boxes B, *** --- *** C, C', and D), the two domains being li *** --- *** nked by a single-stranded hinge. Boxes B *** --- *** and C form the B/C motif, which appears *** --- *** to be exclusive to U3 snoRNAs, and boxe *** --- *** s C' and D form the C'/D motif. The latt *** --- *** er is functionally similar to the C/D mo *** --- *** tifs found in other snoRNAs. The 5' doma *** --- *** in and the hinge region act as a pre-rRN *** --- *** A-binding domain. The 3' domain has cons *** --- *** erved protein-binding sites. Both the bo *** --- *** x B/C and box C'/D motifs are sufficient *** --- *** for nuclear retention of U3 snoRNA. The *** --- *** box C'/D motif is also necessary for nu *** --- *** cleolar localization, stability and hype *** --- *** rmethylation of U3 snoRNA. Both box B/C *** --- *** and C'/D motifs are involved in specific *** --- *** protein interactions and are necessary *** --- *** for the rRNA processing functions of U3 *** --- *** snoRNA. *** --- ************************************************ --- CREATE VIEW u3_snorna AS SELECT feature_id AS u3_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_snoRNA'; --- ************************************************ --- *** relation: au_rich_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is rich in AUUUA pen *** --- *** tamers. Messenger RNAs bearing multiple *** --- *** AU-rich elements are often unstable. *** --- ************************************************ --- CREATE VIEW au_rich_element AS SELECT feature_id AS au_rich_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'AU_rich_element'; --- ************************************************ --- *** relation: bruno_response_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is bound by the Dros *** --- *** ophila Bruno protein and its homologs. *** --- ************************************************ --- CREATE VIEW bruno_response_element AS SELECT feature_id AS bruno_response_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Bruno_response_element'; --- ************************************************ --- *** relation: iron_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory sequence found in the 5' an *** --- *** d 3' UTRs of many mRNAs which encode iro *** --- *** n-binding proteins. It has a hairpin str *** --- *** ucture and is recognized by trans-acting *** --- *** proteins known as iron-regulatory prote *** --- *** ins. *** --- ************************************************ --- CREATE VIEW iron_responsive_element AS SELECT feature_id AS iron_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iron_responsive_element'; --- ************************************************ --- *** relation: morpholino *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of nucleobases bound to a morpholino *** --- *** backbone. A morpholino backbone consist *** --- *** s of morpholine (CHEBI:34856) rings conn *** --- *** ected by phosphorodiamidate linkages. *** --- ************************************************ --- CREATE VIEW morpholino AS SELECT feature_id AS morpholino_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino'; --- ************************************************ --- *** relation: pna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of peptide nucleic acid (CHEBI:48021 *** --- *** ), a chemical consisting of nucleobases *** --- *** bound to a backbone composed of repeatin *** --- *** g N-(2-aminoethyl)-glycine units linked *** --- *** by peptide bonds. The purine and pyrimid *** --- *** ine bases are linked to the backbone by *** --- *** methylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna AS SELECT feature_id AS pna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA'; --- ************************************************ --- *** relation: enzymatic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** with or without an associated ribonucle *** --- *** oprotein. *** --- ************************************************ --- CREATE VIEW enzymatic AS SELECT feature_id AS enzymatic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic' OR cvterm.name = 'enzymatic'; --- ************************************************ --- *** relation: ribozymic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** even without an associated ribonucleopr *** --- *** otein. *** --- ************************************************ --- CREATE VIEW ribozymic AS SELECT feature_id AS ribozymic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic'; --- ************************************************ --- *** relation: pseudouridylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of pseu *** --- *** douridylation in an RNA molecule by base *** --- *** pairing with a short sequence around th *** --- *** e target residue. *** --- ************************************************ --- CREATE VIEW pseudouridylation_guide_snorna AS SELECT feature_id AS pseudouridylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA'; --- ************************************************ --- *** relation: lna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of 'locked' deoxyribose r *** --- *** ings connected to a phosphate backbone. *** --- *** The deoxyribose unit's conformation is ' *** --- *** locked' by a 2'-C,4'-C-oxymethylene link *** --- *** . *** --- ************************************************ --- CREATE VIEW lna AS SELECT feature_id AS lna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA'; --- ************************************************ --- *** relation: lna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of LNA residues. *** --- ************************************************ --- CREATE VIEW lna_oligo AS SELECT feature_id AS lna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA_oligo'; --- ************************************************ --- *** relation: tna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of threose rings connecte *** --- *** d to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW tna AS SELECT feature_id AS tna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA'; --- ************************************************ --- *** relation: tna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of TNA residues. *** --- ************************************************ --- CREATE VIEW tna_oligo AS SELECT feature_id AS tna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA_oligo'; --- ************************************************ --- *** relation: gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of an acyclic three-carbo *** --- *** n propylene glycol connected to a phosph *** --- *** ate backbone. It has two enantiomeric fo *** --- *** rms, (R)-GNA and (S)-GNA. *** --- ************************************************ --- CREATE VIEW gna AS SELECT feature_id AS gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'GNA'; --- ************************************************ --- *** relation: gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of GNA residues. *** --- ************************************************ --- CREATE VIEW gna_oligo AS SELECT feature_id AS gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'GNA_oligo'; --- ************************************************ --- *** relation: r_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (R)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW r_gna AS SELECT feature_id AS r_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA'; --- ************************************************ --- *** relation: r_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (R)-GNA residues. *** --- ************************************************ --- CREATE VIEW r_gna_oligo AS SELECT feature_id AS r_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo'; --- ************************************************ --- *** relation: s_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (S)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW s_gna AS SELECT feature_id AS s_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA'; --- ************************************************ --- *** relation: s_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (S)-GNA residues. *** --- ************************************************ --- CREATE VIEW s_gna_oligo AS SELECT feature_id AS s_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA_oligo'; --- ************************************************ --- *** relation: ds_dna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_DNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded DNA. *** --- ************************************************ --- CREATE VIEW ds_dna_viral_sequence AS SELECT feature_id AS ds_dna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_DNA_viral_sequence'; --- ************************************************ --- *** relation: ss_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ss_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as single stranded RNA. *** --- ************************************************ --- CREATE VIEW ss_rna_viral_sequence AS SELECT feature_id AS ss_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence'; --- ************************************************ --- *** relation: negative_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A negative_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** is complementary to mRNA and must be con *** --- *** verted to positive sense RNA by RNA poly *** --- *** merase before translation. *** --- ************************************************ --- CREATE VIEW negative_sense_ssrna_viral_sequence AS SELECT feature_id AS negative_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: positive_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A positive_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** can be immediately translated by the hos *** --- *** t. *** --- ************************************************ --- CREATE VIEW positive_sense_ssrna_viral_sequence AS SELECT feature_id AS positive_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positive_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: ambisense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ambisense_RNA_virus is a ss_RNA_viral_ *** --- *** sequence that is the sequence of a singl *** --- *** e stranded RNA virus with both messenger *** --- *** and anti messenger polarity. *** --- ************************************************ --- CREATE VIEW ambisense_ssrna_viral_sequence AS SELECT feature_id AS ambisense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ambisense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which RNA polymerase b *** --- *** inds, to begin transcription. *** --- ************************************************ --- CREATE VIEW rna_polymerase_promoter AS SELECT feature_id AS rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'RNA_polymerase_promoter'; --- ************************************************ --- *** relation: phage_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which Bacteriophage RN *** --- *** A polymerase binds, to begin transcripti *** --- *** on. *** --- ************************************************ --- CREATE VIEW phage_rna_polymerase_promoter AS SELECT feature_id AS phage_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: sp6_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the SP6 RNA poly *** --- *** merase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW sp6_rna_polymerase_promoter AS SELECT feature_id AS sp6_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t3_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which the T3 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t3_rna_polymerase_promoter AS SELECT feature_id AS t3_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T3_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t7_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the T7 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t7_rna_polymerase_promoter AS SELECT feature_id AS t7_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T7_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: five_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 5' end of a transcr *** --- *** ipt that usually codes for a protein. Th *** --- *** ese regions tend to be conserved across *** --- *** species and do not change much within a *** --- *** gene family. *** --- ************************************************ --- CREATE VIEW five_prime_est AS SELECT feature_id AS five_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST'; --- ************************************************ --- *** relation: three_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 3' end of a transcr *** --- *** ipt. They are more likely to fall within *** --- *** non-coding, or untranslated regions(UTR *** --- *** s). *** --- ************************************************ --- CREATE VIEW three_prime_est AS SELECT feature_id AS three_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_EST'; --- ************************************************ --- *** relation: translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA (not divisible by 3 b *** --- *** ases) that is skipped during the process *** --- *** of translational frameshifting (GO:0006 *** --- *** 452), causing the reading frame to be di *** --- *** fferent. *** --- ************************************************ --- CREATE VIEW translational_frameshift AS SELECT feature_id AS translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'translational_frameshift'; --- ************************************************ --- *** relation: plus_1_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 1 base long that is s *** --- *** kipped during the process of translation *** --- *** al frameshifting (GO:0006452), causing t *** --- *** he reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_1_translational_frameshift AS SELECT feature_id AS plus_1_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift'; --- ************************************************ --- *** relation: plus_2_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 2 bases long that is *** --- *** skipped during the process of translatio *** --- *** nal frameshifting (GO:0006452), causing *** --- *** the reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_2_translational_frameshift AS SELECT feature_id AS plus_2_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_translational_frameshift'; --- ************************************************ --- *** relation: group_iii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group III introns are introns found in t *** --- *** he mRNA of the plastids of euglenoid pro *** --- *** tists. They are spliced by a two step tr *** --- *** ansesterification with bulged adenosine *** --- *** as initiating nucleophile. *** --- ************************************************ --- CREATE VIEW group_iii_intron AS SELECT feature_id AS group_iii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_III_intron'; --- ************************************************ --- *** relation: noncoding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The maximal intersection of exon and UTR *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_region_of_exon AS SELECT feature_id AS noncoding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'noncoding_region_of_exon'; --- ************************************************ --- *** relation: coding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an exon that encodes for p *** --- *** rotein sequence. *** --- ************************************************ --- CREATE VIEW coding_region_of_exon AS SELECT feature_id AS coding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'coding_region_of_exon'; --- ************************************************ --- *** relation: endonuclease_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron that spliced via endonucleolyt *** --- *** ic cleavage and ligation rather than tra *** --- *** nsesterification. *** --- ************************************************ --- CREATE VIEW endonuclease_spliced_intron AS SELECT feature_id AS endonuclease_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'endonuclease_spliced_intron'; --- ************************************************ --- *** relation: protein_coding_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding_gene AS SELECT feature_id AS protein_coding_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'protein_coding_gene'; --- ************************************************ --- *** relation: transgenic_insertion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transgenic_insertion AS SELECT feature_id AS transgenic_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion'; --- ************************************************ --- *** relation: retrogene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW retrogene AS SELECT feature_id AS retrogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrogene'; --- ************************************************ --- *** relation: silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by RNA *** --- *** interference. *** --- ************************************************ --- CREATE VIEW silenced_by_rna_interference AS SELECT feature_id AS silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_RNA_interference'; --- ************************************************ --- *** relation: silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone modification. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_modification AS SELECT feature_id AS silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_by_histone_modification'; --- ************************************************ --- *** relation: silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone methylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_methylation AS SELECT feature_id AS silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation'; --- ************************************************ --- *** relation: silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone deacetylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_deacetylation AS SELECT feature_id AS silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: gene_silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by RNA interfere *** --- *** nce. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_rna_interference AS SELECT feature_id AS gene_silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_RNA_interference'; --- ************************************************ --- *** relation: gene_silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone modif *** --- *** ication. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_modification AS SELECT feature_id AS gene_silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'gene_silenced_by_histone_modification'; --- ************************************************ --- *** relation: gene_silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone methy *** --- *** lation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_methylation AS SELECT feature_id AS gene_silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation'; --- ************************************************ --- *** relation: gene_silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone deace *** --- *** tylation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_deacetylation AS SELECT feature_id AS gene_silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: dihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5,6-dih *** --- *** ydrouracil is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW dihydrouridine AS SELECT feature_id AS dihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine'; --- ************************************************ --- *** relation: pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5- posi *** --- *** tion of the uracil is bound to the ribos *** --- *** e ring instead of the 4- position. *** --- ************************************************ --- CREATE VIEW pseudouridine AS SELECT feature_id AS pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridine'; --- ************************************************ --- *** relation: inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which hypoxanthin *** --- *** e is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW inosine AS SELECT feature_id AS inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'inosine'; --- ************************************************ --- *** relation: seven_methylguanine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which guanine is *** --- *** methylated at the 7- position. *** --- ************************************************ --- CREATE VIEW seven_methylguanine AS SELECT feature_id AS seven_methylguanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanine'; --- ************************************************ --- *** relation: ribothymidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which thymine is *** --- *** bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW ribothymidine AS SELECT feature_id AS ribothymidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribothymidine'; --- ************************************************ --- *** relation: methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which methylhypox *** --- *** anthine is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW methylinosine AS SELECT feature_id AS methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine'; --- ************************************************ --- *** relation: mobile *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that h *** --- *** as either intra-genome or intracellular *** --- *** mobility. *** --- ************************************************ --- CREATE VIEW mobile AS SELECT feature_id AS mobile_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile'; --- ************************************************ --- *** relation: replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing at least one unique *** --- *** origin of replication and a unique termi *** --- *** nation site. *** --- ************************************************ --- CREATE VIEW replicon AS SELECT feature_id AS replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'replicon'; --- ************************************************ --- *** relation: base *** --- *** relation type: VIEW *** --- *** *** --- *** A base is a sequence feature that corres *** --- *** ponds to a single unit of a nucleotide p *** --- *** olymer. *** --- ************************************************ --- CREATE VIEW base AS SELECT feature_id AS base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'base'; --- ************************************************ --- *** relation: amino_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence feature that corresponds to a *** --- *** single amino acid residue in a polypept *** --- *** ide. *** --- ************************************************ --- CREATE VIEW amino_acid AS SELECT feature_id AS amino_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'amino_acid'; --- ************************************************ --- *** relation: major_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW major_tss AS SELECT feature_id AS major_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS'; --- ************************************************ --- *** relation: minor_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minor_tss AS SELECT feature_id AS minor_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minor_TSS'; --- ************************************************ --- *** relation: tss_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a gene from the 5' most TS *** --- *** S to the 3' TSS. *** --- ************************************************ --- CREATE VIEW tss_region AS SELECT feature_id AS tss_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TSS_region'; --- ************************************************ --- *** relation: encodes_alternate_transcription_start_sites *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW encodes_alternate_transcription_start_sites AS SELECT feature_id AS encodes_alternate_transcription_start_sites_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_alternate_transcription_start_sites'; --- ************************************************ --- *** relation: mirna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of an miRNA primary_transcript. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript_region AS SELECT feature_id AS mirna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'miRNA_primary_transcript_region'; --- ************************************************ --- *** relation: pre_mirna *** --- *** relation type: VIEW *** --- *** *** --- *** The 60-70 nucleotide region remain after *** --- *** Drosha processing of the primary transc *** --- *** ript, that folds back upon itself to for *** --- *** m a hairpin sructure. *** --- ************************************************ --- CREATE VIEW pre_mirna AS SELECT feature_id AS pre_mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA'; --- ************************************************ --- *** relation: mirna_stem *** --- *** relation type: VIEW *** --- *** *** --- *** The stem of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_stem AS SELECT feature_id AS mirna_stem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_stem'; --- ************************************************ --- *** relation: mirna_loop *** --- *** relation type: VIEW *** --- *** *** --- *** The loop of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_loop AS SELECT feature_id AS mirna_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_loop'; --- ************************************************ --- *** relation: synthetic_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of synthetic nucleotid *** --- *** es. *** --- ************************************************ --- CREATE VIEW synthetic_oligo AS SELECT feature_id AS synthetic_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'synthetic_oligo'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome of known length t *** --- *** hat is composed by ordering and aligning *** --- *** two or more different regions. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'assembly'; --- ************************************************ --- *** relation: fragment_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A fragment assembly is a genome assembly *** --- *** that orders overlapping fragments of th *** --- *** e genome based on landmark sequences. Th *** --- *** e base pair distance between the landmar *** --- *** ks is known allowing additivity of lengt *** --- *** hs. *** --- ************************************************ --- CREATE VIEW fragment_assembly AS SELECT feature_id AS fragment_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'fragment_assembly'; --- ************************************************ --- *** relation: fingerprint_map *** --- *** relation type: VIEW *** --- *** *** --- *** A fingerprint_map is a physical map comp *** --- *** osed of restriction fragments. *** --- ************************************************ --- CREATE VIEW fingerprint_map AS SELECT feature_id AS fingerprint_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map'; --- ************************************************ --- *** relation: sts_map *** --- *** relation type: VIEW *** --- *** *** --- *** An STS map is a physical map organized b *** --- *** y the unique STS landmarks. *** --- ************************************************ --- CREATE VIEW sts_map AS SELECT feature_id AS sts_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS_map'; --- ************************************************ --- *** relation: rh_map *** --- *** relation type: VIEW *** --- *** *** --- *** A radiation hybrid map is a physical map *** --- *** . *** --- ************************************************ --- CREATE VIEW rh_map AS SELECT feature_id AS rh_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RH_map'; --- ************************************************ --- *** relation: sonicate_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment generated by sonication. *** --- *** Sonication is a technique used to sheer *** --- *** DNA into smaller fragments. *** --- ************************************************ --- CREATE VIEW sonicate_fragment AS SELECT feature_id AS sonicate_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sonicate_fragment'; --- ************************************************ --- *** relation: polyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is an exact multi *** --- *** ple of the haploid number and is greater *** --- *** than the diploid number. *** --- ************************************************ --- CREATE VIEW polyploid AS SELECT feature_id AS polyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'polyploid'; --- ************************************************ --- *** relation: autopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from the same organism *** --- *** . *** --- ************************************************ --- CREATE VIEW autopolyploid AS SELECT feature_id AS autopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid'; --- ************************************************ --- *** relation: allopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from a different organ *** --- *** ism. *** --- ************************************************ --- CREATE VIEW allopolyploid AS SELECT feature_id AS allopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allopolyploid'; --- ************************************************ --- *** relation: homing_endonuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The binding site (recognition site) of a *** --- *** homing endonuclease. The binding site i *** --- *** s typically large. *** --- ************************************************ --- CREATE VIEW homing_endonuclease_binding_site AS SELECT feature_id AS homing_endonuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homing_endonuclease_binding_site'; --- ************************************************ --- *** relation: octamer_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters with seque *** --- *** nce ATTGCAT that binds Pou-domain transc *** --- *** ription factors. *** --- ************************************************ --- CREATE VIEW octamer_motif AS SELECT feature_id AS octamer_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'octamer_motif'; --- ************************************************ --- *** relation: apicoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in an apicoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW apicoplast_chromosome AS SELECT feature_id AS apicoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_chromosome'; --- ************************************************ --- *** relation: sequence_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of discontinuous sequences. *** --- ************************************************ --- CREATE VIEW sequence_collection AS SELECT feature_id AS sequence_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'genome' OR cvterm.name = 'contig_collection' OR cvterm.name = 'sequence_collection'; --- ************************************************ --- *** relation: overlapping_feature_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous region of sequence composed *** --- *** of the overlapping of multiple sequence *** --- *** _features, which ultimately provides evi *** --- *** dence for another sequence_feature. *** --- ************************************************ --- CREATE VIEW overlapping_feature_set AS SELECT feature_id AS overlapping_feature_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'overlapping_feature_set'; --- ************************************************ --- *** relation: overlapping_est_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continous experimental result region e *** --- *** xtending the length of multiple overlapp *** --- *** ing EST's. *** --- ************************************************ --- CREATE VIEW overlapping_est_set AS SELECT feature_id AS overlapping_est_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set'; --- ************************************************ --- *** relation: ncrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ncrna_gene AS SELECT feature_id AS ncrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'ncRNA_gene'; --- ************************************************ --- *** relation: grna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW grna_gene AS SELECT feature_id AS grna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene'; --- ************************************************ --- *** relation: mirna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_gene AS SELECT feature_id AS mirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_gene'; --- ************************************************ --- *** relation: scrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_gene AS SELECT feature_id AS scrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_gene'; --- ************************************************ --- *** relation: snorna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_gene AS SELECT feature_id AS snorna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA_gene'; --- ************************************************ --- *** relation: snrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_gene AS SELECT feature_id AS snrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_gene'; --- ************************************************ --- *** relation: srp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_gene AS SELECT feature_id AS srp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_gene'; --- ************************************************ --- *** relation: strna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_gene AS SELECT feature_id AS strna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_gene'; --- ************************************************ --- *** relation: tmrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_gene AS SELECT feature_id AS tmrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_gene'; --- ************************************************ --- *** relation: trna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_gene AS SELECT feature_id AS trna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_gene'; --- ************************************************ --- *** relation: modified_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified adenine is an adenine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_adenosine AS SELECT feature_id AS modified_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'modified_adenosine'; --- ************************************************ --- *** relation: modified_inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified inosine is an inosine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_inosine AS SELECT feature_id AS modified_inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'modified_inosine'; --- ************************************************ --- *** relation: modified_cytidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified cytidine is a cytidine base f *** --- *** eature which has been altered. *** --- ************************************************ --- CREATE VIEW modified_cytidine AS SELECT feature_id AS modified_cytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'modified_cytidine'; --- ************************************************ --- *** relation: modified_guanosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_guanosine AS SELECT feature_id AS modified_guanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'modified_guanosine'; --- ************************************************ --- *** relation: modified_uridine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_uridine AS SELECT feature_id AS modified_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_uridine'; --- ************************************************ --- *** relation: one_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1-methylinosine is a modified insosine. *** --- ************************************************ --- CREATE VIEW one_methylinosine AS SELECT feature_id AS one_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylinosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethylinosine is a modified ino *** --- *** sine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylinosine AS SELECT feature_id AS one_two_prime_o_dimethylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylinosine'; --- ************************************************ --- *** relation: two_prime_o_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylinosine is a modified inosine *** --- *** . *** --- ************************************************ --- CREATE VIEW two_prime_o_methylinosine AS SELECT feature_id AS two_prime_o_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylinosine'; --- ************************************************ --- *** relation: three_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 3-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW three_methylcytidine AS SELECT feature_id AS three_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine'; --- ************************************************ --- *** relation: five_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_methylcytidine AS SELECT feature_id AS five_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylcytidine'; --- ************************************************ --- *** relation: two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylcytidine is a modified cytidi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylcytidine AS SELECT feature_id AS two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: two_thiocytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2-thiocytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW two_thiocytidine AS SELECT feature_id AS two_thiocytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiocytidine'; --- ************************************************ --- *** relation: n4_acetylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_acetylcytidine AS SELECT feature_id AS n4_acetylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetylcytidine'; --- ************************************************ --- *** relation: five_formylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_formylcytidine AS SELECT feature_id AS five_formylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formylcytidine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5,2'-O-dimethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethylcytidine AS SELECT feature_id AS five_two_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: n4_acetyl_2_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetyl-2'-O-methylcytidine is a modif *** --- *** ied cytidine. *** --- ************************************************ --- CREATE VIEW n4_acetyl_2_prime_o_methylcytidine AS SELECT feature_id AS n4_acetyl_2_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine'; --- ************************************************ --- *** relation: lysidine *** --- *** relation type: VIEW *** --- *** *** --- *** Lysidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW lysidine AS SELECT feature_id AS lysidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysidine'; --- ************************************************ --- *** relation: n4_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-methylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_methylcytidine AS SELECT feature_id AS n4_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_methylcytidine'; --- ************************************************ --- *** relation: n4_2_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4,2'-O-dimethylcytidine is a modified c *** --- *** ytidine. *** --- ************************************************ --- CREATE VIEW n4_2_prime_o_dimethylcytidine AS SELECT feature_id AS n4_2_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_2_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: five_hydroxymethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-hydroxymethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_hydroxymethylcytidine AS SELECT feature_id AS five_hydroxymethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxymethylcytidine'; --- ************************************************ --- *** relation: five_formyl_two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formyl-2'-O-methylcytidine is a modifi *** --- *** ed cytidine. *** --- ************************************************ --- CREATE VIEW five_formyl_two_prime_o_methylcytidine AS SELECT feature_id AS five_formyl_two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formyl_two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: n4_n4_2_prime_o_trimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4_N4_2_prime_O_trimethylcytidine is a m *** --- *** odified cytidine. *** --- ************************************************ --- CREATE VIEW n4_n4_2_prime_o_trimethylcytidine AS SELECT feature_id AS n4_n4_2_prime_o_trimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine'; --- ************************************************ --- *** relation: one_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW one_methyladenosine AS SELECT feature_id AS one_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine'; --- ************************************************ --- *** relation: two_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW two_methyladenosine AS SELECT feature_id AS two_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methyladenosine'; --- ************************************************ --- *** relation: n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_methyladenosine AS SELECT feature_id AS n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyladenosine'; --- ************************************************ --- *** relation: two_prime_o_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyladenosine AS SELECT feature_id AS two_prime_o_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_methyladenosine is a mod *** --- *** ified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_methyladenosine AS SELECT feature_id AS two_methylthio_n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_methyladenosine'; --- ************************************************ --- *** relation: n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_isopentenyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_isopentenyladenosine AS SELECT feature_id AS n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_isopentenyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_isopentenyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_isopentenyladenosine AS SELECT feature_id AS two_methylthio_n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_isopentenyladenosine'; --- ************************************************ --- *** relation: n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_cis_hydroxyisopentenyl_adenosine is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_cis_hydroxyisopentenyl_a *** --- *** denosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS two_methylthio_n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: n6_glycinylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_glycinylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_glycinylcarbamoyladenosine AS SELECT feature_id AS n6_glycinylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_glycinylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_threonylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_threonyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_threonyl_carbamoyladenos *** --- *** ine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_threonyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_threonyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine'; --- ************************************************ --- *** relation: n6_methyl_n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyl_N6_threonylcarbamoyladenosine *** --- *** is a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_methyl_n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_methyl_n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_hydroxynorvalylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_hydroxynorvalylcarbamoyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_hydroxynorvalylcarbamoyladenosine AS SELECT feature_id AS n6_hydroxynorvalylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_hydroxynorvalyl_carbamoy *** --- *** ladenosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine'; --- ************************************************ --- *** relation: two_prime_o_riboA_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosyladenosine_phosphate is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_riboA_phosphate AS SELECT feature_id AS two_prime_o_riboA_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosyladenosine_phosphate'; --- ************************************************ --- *** relation: n6_n6_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_dimethyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_n6_dimethyladenosine AS SELECT feature_id AS n6_n6_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_dimethyladenosine'; --- ************************************************ --- *** relation: n6_2_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_2prime_O_dimethyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_2_prime_o_dimethyladenosine AS SELECT feature_id AS n6_2_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_2_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_n6_2_prime_o_trimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_2prime_O_trimethyladenosine is a m *** --- *** odified adenosine. *** --- ************************************************ --- CREATE VIEW n6_n6_2_prime_o_trimethyladenosine AS SELECT feature_id AS n6_n6_2_prime_o_trimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethyladenosine AS SELECT feature_id AS one_two_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_acetyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_acetyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_acetyladenosine AS SELECT feature_id AS n6_acetyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_acetyladenosine'; --- ************************************************ --- *** relation: seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7-deazaguanosine is a moddified guanosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW seven_deazaguanosine AS SELECT feature_id AS seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'seven_deazaguanosine'; --- ************************************************ --- *** relation: queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Queuosine is a modified 7-deazoguanosine *** --- *** . *** --- ************************************************ --- CREATE VIEW queuosine AS SELECT feature_id AS queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine'; --- ************************************************ --- *** relation: epoxyqueuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Epoxyqueuosine is a modified 7-deazoguan *** --- *** osine. *** --- ************************************************ --- CREATE VIEW epoxyqueuosine AS SELECT feature_id AS epoxyqueuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epoxyqueuosine'; --- ************************************************ --- *** relation: galactosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Galactosyl_queuosine is a modified 7-dea *** --- *** zoguanosine. *** --- ************************************************ --- CREATE VIEW galactosyl_queuosine AS SELECT feature_id AS galactosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'galactosyl_queuosine'; --- ************************************************ --- *** relation: mannosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Mannosyl_queuosine is a modified 7-deazo *** --- *** guanosine. *** --- ************************************************ --- CREATE VIEW mannosyl_queuosine AS SELECT feature_id AS mannosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mannosyl_queuosine'; --- ************************************************ --- *** relation: seven_cyano_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_cyano_7_deazaguanosine is a modified 7 *** --- *** -deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_cyano_seven_deazaguanosine AS SELECT feature_id AS seven_cyano_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_cyano_seven_deazaguanosine'; --- ************************************************ --- *** relation: seven_aminomethyl_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_aminomethyl_7_deazaguanosine is a modi *** --- *** fied 7-deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_aminomethyl_seven_deazaguanosine AS SELECT feature_id AS seven_aminomethyl_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_aminomethyl_seven_deazaguanosine'; --- ************************************************ --- *** relation: archaeosine *** --- *** relation type: VIEW *** --- *** *** --- *** Archaeosine is a modified 7-deazoguanosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW archaeosine AS SELECT feature_id AS archaeosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeosine'; --- ************************************************ --- *** relation: one_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW one_methylguanosine AS SELECT feature_id AS one_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylguanosine'; --- ************************************************ --- *** relation: n2_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_methylguanosine is a modified guanosi *** --- *** ne base feature. *** --- ************************************************ --- CREATE VIEW n2_methylguanosine AS SELECT feature_id AS n2_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_methylguanosine'; --- ************************************************ --- *** relation: seven_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW seven_methylguanosine AS SELECT feature_id AS seven_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanosine'; --- ************************************************ --- *** relation: two_prime_o_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylguanosine is a modified g *** --- *** uanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylguanosine AS SELECT feature_id AS two_prime_o_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylguanosine'; --- ************************************************ --- *** relation: n2_n2_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_dimethylguanosine is a modified gu *** --- *** anosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_dimethylguanosine AS SELECT feature_id AS n2_n2_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_dimethylguanosine'; --- ************************************************ --- *** relation: n2_2_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_2prime_O_dimethylguanosine is a modif *** --- *** ied guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_2_prime_o_dimethylguanosine AS SELECT feature_id AS n2_2_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_2_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_2_prime_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_2prime_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_2_prime_o_trimethylguanosine AS SELECT feature_id AS n2_n2_2_prime_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine'; --- ************************************************ --- *** relation: two_prime_o_ribosylguanosine_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosylguanosine_phosphate is a *** --- *** modified guanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_ribosylguanosine_phosphate AS SELECT feature_id AS two_prime_o_ribosylguanosine_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosylguanosine_phosphate'; --- ************************************************ --- *** relation: wybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wybutosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW wybutosine AS SELECT feature_id AS wybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wybutosine'; --- ************************************************ --- *** relation: peroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Peroxywybutosine is a modified guanosine *** --- *** base feature. *** --- ************************************************ --- CREATE VIEW peroxywybutosine AS SELECT feature_id AS peroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peroxywybutosine'; --- ************************************************ --- *** relation: hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Hydroxywybutosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW hydroxywybutosine AS SELECT feature_id AS hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydroxywybutosine'; --- ************************************************ --- *** relation: undermodified_hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Undermodified_hydroxywybutosine is a mod *** --- *** ified guanosine base feature. *** --- ************************************************ --- CREATE VIEW undermodified_hydroxywybutosine AS SELECT feature_id AS undermodified_hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'undermodified_hydroxywybutosine'; --- ************************************************ --- *** relation: wyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wyosine is a modified guanosine base fea *** --- *** ture. *** --- ************************************************ --- CREATE VIEW wyosine AS SELECT feature_id AS wyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wyosine'; --- ************************************************ --- *** relation: methylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Methylwyosine is a modified guanosine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW methylwyosine AS SELECT feature_id AS methylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylwyosine'; --- ************************************************ --- *** relation: n2_7_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_dimethylguanosine is a modified gua *** --- *** nosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_dimethylguanosine AS SELECT feature_id AS n2_7_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_7_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_7_trimethylguanosine is a modified *** --- *** guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_7_trimethylguanosine AS SELECT feature_id AS n2_n2_7_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_7_trimethylguanosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_2prime_O_dimethylguanosine is a modifi *** --- *** ed guanosine base feature. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylguanosine AS SELECT feature_id AS one_two_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: four_demethylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_demethylwyosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW four_demethylwyosine AS SELECT feature_id AS four_demethylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_demethylwyosine'; --- ************************************************ --- *** relation: isowyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Isowyosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW isowyosine AS SELECT feature_id AS isowyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isowyosine'; --- ************************************************ --- *** relation: n2_7_2prirme_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_2prirme_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_2prirme_o_trimethylguanosine AS SELECT feature_id AS n2_7_2prirme_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_2prirme_O_trimethylguanosine'; --- ************************************************ --- *** relation: five_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW five_methyluridine AS SELECT feature_id AS five_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyluridine'; --- ************************************************ --- *** relation: two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyluridine AS SELECT feature_id AS two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_2_prime_O_dimethyluridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethyluridine AS SELECT feature_id AS five_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: one_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW one_methylpseudouridine AS SELECT feature_id AS one_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylpseudouridine'; --- ************************************************ --- *** relation: two_prime_o_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylpseudouridine is a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylpseudouridine AS SELECT feature_id AS two_prime_o_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylpseudouridine'; --- ************************************************ --- *** relation: two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW two_thiouridine AS SELECT feature_id AS two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiouridine'; --- ************************************************ --- *** relation: four_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW four_thiouridine AS SELECT feature_id AS four_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_thiouridine'; --- ************************************************ --- *** relation: five_methyl_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyl_2_thiouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyl_2_thiouridine AS SELECT feature_id AS five_methyl_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyl_2_thiouridine'; --- ************************************************ --- *** relation: two_thio_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thio_2prime_O_methyluridine is a modif *** --- *** ied uridine base feature. *** --- ************************************************ --- CREATE VIEW two_thio_two_prime_o_methyluridine AS SELECT feature_id AS two_thio_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thio_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: three_three_amino_three_carboxypropyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_3_amino_3_carboxypropyl_uridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW three_three_amino_three_carboxypropyl_uridine AS SELECT feature_id AS three_three_amino_three_carboxypropyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_three_amino_three_carboxypropyl_uridine'; --- ************************************************ --- *** relation: five_hydroxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_hydroxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_hydroxyuridine AS SELECT feature_id AS five_hydroxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxyuridine'; --- ************************************************ --- *** relation: five_methoxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_methoxyuridine AS SELECT feature_id AS five_methoxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxyuridine'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid AS SELECT feature_id AS uridine_five_oxyacetic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid_methyl_ester is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid_methyl_ester AS SELECT feature_id AS uridine_five_oxyacetic_acid_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine is a modi *** --- *** fied uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine_methyl_es *** --- *** ter is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine_methyl_ester AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyluridine AS SELECT feature_id AS five_methoxycarbonylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyluridine'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_methoxycarbonylmethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_mcm_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxycarbonylmethyl_2_thiouridine is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mcm_2_thiouridine AS SELECT feature_id AS five_mcm_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_aminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_aminomethyl_2_thiouridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_aminomethyl_two_thiouridine AS SELECT feature_id AS five_aminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_aminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyluridine AS SELECT feature_id AS five_methylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyluridine'; --- ************************************************ --- *** relation: five_mam_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_thiouridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mam_2_thiouridine AS SELECT feature_id AS five_mam_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyl_two_selenouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_selenouridine is a *** --- *** modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyl_two_selenouridine AS SELECT feature_id AS five_methylaminomethyl_two_selenouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_selenouridine'; --- ************************************************ --- *** relation: five_carbamoylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyluridine is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW five_carbamoylmethyluridine AS SELECT feature_id AS five_carbamoylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyluridine'; --- ************************************************ --- *** relation: five_cm_2_prime_o_methU *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyl_2_prime_O_methyluridin *** --- *** e is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_cm_2_prime_o_methU AS SELECT feature_id AS five_cm_2_prime_o_methU_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyluridine AS SELECT feature_id AS five_carboxymethylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_thiouridine *** --- *** is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_thiouridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: three_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW three_methyluridine AS SELECT feature_id AS three_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methyluridine'; --- ************************************************ --- *** relation: one_methyl_3_3_amino_three_carboxypropyl_pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyl_3_3_amino_3_carboxypropyl_pseud *** --- *** ouridine is a modified uridine base feat *** --- *** ure. *** --- ************************************************ --- CREATE VIEW one_methyl_3_3_amino_three_carboxypropyl_pseudouridine AS SELECT feature_id AS one_methyl_3_3_amino_three_carboxypropyl_pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine'; --- ************************************************ --- *** relation: five_carboxymethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethyluridine AS SELECT feature_id AS five_carboxymethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethyluridine'; --- ************************************************ --- *** relation: three_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_2prime_O_dimethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW three_two_prime_o_dimethyluridine AS SELECT feature_id AS three_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: five_methyldihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyldihydrouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyldihydrouridine AS SELECT feature_id AS five_methyldihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyldihydrouridine'; --- ************************************************ --- *** relation: three_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW three_methylpseudouridine AS SELECT feature_id AS three_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylpseudouridine'; --- ************************************************ --- *** relation: five_taurinomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyluridine AS SELECT feature_id AS five_taurinomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyluridine'; --- ************************************************ --- *** relation: five_taurinomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyl_2_thiouridineis a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyl_two_thiouridine AS SELECT feature_id AS five_taurinomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_uridine is a mo *** --- *** dified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_uridine AS SELECT feature_id AS five_isopentenylaminomethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_uridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2_thiouridine i *** --- *** s a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_thiouridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2prime_O_methyl *** --- *** uridine is a modified uridine base featu *** --- *** re. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: histone_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule that is bound *** --- *** by a histone. *** --- ************************************************ --- CREATE VIEW histone_binding_site AS SELECT feature_id AS histone_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_binding_site'; --- ************************************************ --- *** relation: cds_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cds_fragment AS SELECT feature_id AS cds_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_fragment'; --- ************************************************ --- *** relation: modified_amino_acid_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified amino ac *** --- *** id feature. *** --- ************************************************ --- CREATE VIEW modified_amino_acid_feature AS SELECT feature_id AS modified_amino_acid_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'modified_amino_acid_feature'; --- ************************************************ --- *** relation: modified_glycine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glycine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_glycine AS SELECT feature_id AS modified_glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine'; --- ************************************************ --- *** relation: modified_l_alanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified alanine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_alanine AS SELECT feature_id AS modified_l_alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_alanine'; --- ************************************************ --- *** relation: modified_l_asparagine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified asparagi *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_asparagine AS SELECT feature_id AS modified_l_asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_asparagine'; --- ************************************************ --- *** relation: modified_l_aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified aspartic *** --- *** acid amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_aspartic_acid AS SELECT feature_id AS modified_l_aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_aspartic_acid'; --- ************************************************ --- *** relation: modified_l_cysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified cysteine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_cysteine AS SELECT feature_id AS modified_l_cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_cysteine'; --- ************************************************ --- *** relation: modified_l_glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_l_glutamic_acid AS SELECT feature_id AS modified_l_glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamic_acid'; --- ************************************************ --- *** relation: modified_l_threonine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified threonin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_threonine AS SELECT feature_id AS modified_l_threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_threonine'; --- ************************************************ --- *** relation: modified_l_tryptophan *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tryptoph *** --- *** an amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tryptophan AS SELECT feature_id AS modified_l_tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tryptophan'; --- ************************************************ --- *** relation: modified_l_glutamine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glutamin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_glutamine AS SELECT feature_id AS modified_l_glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamine'; --- ************************************************ --- *** relation: modified_l_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified methioni *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_methionine AS SELECT feature_id AS modified_l_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_methionine'; --- ************************************************ --- *** relation: modified_l_isoleucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified isoleuci *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_isoleucine AS SELECT feature_id AS modified_l_isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_isoleucine'; --- ************************************************ --- *** relation: modified_l_phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified phenylal *** --- *** anine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_phenylalanine AS SELECT feature_id AS modified_l_phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_phenylalanine'; --- ************************************************ --- *** relation: modified_l_histidine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified histidie *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_histidine AS SELECT feature_id AS modified_l_histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_histidine'; --- ************************************************ --- *** relation: modified_l_serine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified serine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_serine AS SELECT feature_id AS modified_l_serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_serine'; --- ************************************************ --- *** relation: modified_l_lysine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified lysine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_lysine AS SELECT feature_id AS modified_l_lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_lysine'; --- ************************************************ --- *** relation: modified_l_leucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified leucine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_leucine AS SELECT feature_id AS modified_l_leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_leucine'; --- ************************************************ --- *** relation: modified_l_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified selenocy *** --- *** steine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_selenocysteine AS SELECT feature_id AS modified_l_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_selenocysteine'; --- ************************************************ --- *** relation: modified_l_valine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified valine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_valine AS SELECT feature_id AS modified_l_valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_valine'; --- ************************************************ --- *** relation: modified_l_proline *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified proline *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_proline AS SELECT feature_id AS modified_l_proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_proline'; --- ************************************************ --- *** relation: modified_l_tyrosine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tyrosine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tyrosine AS SELECT feature_id AS modified_l_tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tyrosine'; --- ************************************************ --- *** relation: modified_l_arginine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified arginine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_arginine AS SELECT feature_id AS modified_l_arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_arginine'; --- ************************************************ --- *** relation: peptidyl *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the nature of a *** --- *** proteinaceous polymer, where by the amin *** --- *** o acid units are joined by peptide bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW peptidyl AS SELECT feature_id AS peptidyl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptidyl'; --- ************************************************ --- *** relation: cleaved_for_gpi_anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** The C-terminal residues of a polypeptide *** --- *** which are exchanged for a GPI-anchor. *** --- ************************************************ --- CREATE VIEW cleaved_for_gpi_anchor_region AS SELECT feature_id AS cleaved_for_gpi_anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_for_gpi_anchor_region'; --- ************************************************ --- *** relation: biomaterial_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is intended for use in an *** --- *** experiment. *** --- ************************************************ --- CREATE VIEW biomaterial_region AS SELECT feature_id AS biomaterial_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'biomaterial_region'; --- ************************************************ --- *** relation: experimental_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is the result of some arb *** --- *** itrary experimental procedure. The proce *** --- *** dure may be carried out with biological *** --- *** material or inside a computer. *** --- ************************************************ --- CREATE VIEW experimental_feature AS SELECT feature_id AS experimental_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'QTL' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'homologous_region' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'experimental_feature'; --- ************************************************ --- *** relation: biological_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by its disposition to b *** --- *** e involved in a biological process. *** --- ************************************************ --- CREATE VIEW biological_region AS SELECT feature_id AS biological_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'epitope' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'pseudogene' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'codon' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'RR_tract' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'modified_base_site' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'argenine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'biological_region'; --- ************************************************ --- *** relation: topologically_defined_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is defined according to it *** --- *** s relations with other regions within th *** --- *** e same sequence. *** --- ************************************************ --- CREATE VIEW topologically_defined_region AS SELECT feature_id AS topologically_defined_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_region' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'topologically_defined_region'; --- ************************************************ --- *** relation: translocation_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a tr *** --- *** anslocation begins or ends. *** --- ************************************************ --- CREATE VIEW translocation_breakpoint AS SELECT feature_id AS translocation_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_breakpoint'; --- ************************************************ --- *** relation: insertion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a in *** --- *** sertion begins or ends. *** --- ************************************************ --- CREATE VIEW insertion_breakpoint AS SELECT feature_id AS insertion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_breakpoint'; --- ************************************************ --- *** relation: deletion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a de *** --- *** letion begins or ends. *** --- ************************************************ --- CREATE VIEW deletion_breakpoint AS SELECT feature_id AS deletion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_breakpoint'; --- ************************************************ --- *** relation: five_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located five prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW five_prime_flanking_region AS SELECT feature_id AS five_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_flanking_region'; --- ************************************************ --- *** relation: three_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located three prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW three_prime_flanking_region AS SELECT feature_id AS three_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_flanking_region'; --- ************************************************ --- *** relation: transcribed_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region, defined by a til *** --- *** ing array experiment to be transcribed a *** --- *** t some level. *** --- ************************************************ --- CREATE VIEW transcribed_fragment AS SELECT feature_id AS transcribed_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_fragment'; --- ************************************************ --- *** relation: cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering exon. A s *** --- *** plice_site that adjacent_to exon and ove *** --- *** rlaps intron. *** --- ************************************************ --- CREATE VIEW cis_splice_site AS SELECT feature_id AS cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'cis_splice_site'; --- ************************************************ --- *** relation: trans_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Primary transcript region bordering tran *** --- *** s-splice junction. *** --- ************************************************ --- CREATE VIEW trans_splice_site AS SELECT feature_id AS trans_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'trans_splice_site'; --- ************************************************ --- *** relation: splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between an intron and an ex *** --- *** on. *** --- ************************************************ --- CREATE VIEW splice_junction AS SELECT feature_id AS splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_junction'; --- ************************************************ --- *** relation: conformational_switch *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a polypeptide, involved in t *** --- *** he transition from one conformational st *** --- *** ate to another. *** --- ************************************************ --- CREATE VIEW conformational_switch AS SELECT feature_id AS conformational_switch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_switch'; --- ************************************************ --- *** relation: dye_terminator_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the dye terminator me *** --- *** thod of sequencing. *** --- ************************************************ --- CREATE VIEW dye_terminator_read AS SELECT feature_id AS dye_terminator_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dye_terminator_read'; --- ************************************************ --- *** relation: pyrosequenced_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by pyrosequencing techno *** --- *** logy. *** --- ************************************************ --- CREATE VIEW pyrosequenced_read AS SELECT feature_id AS pyrosequenced_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrosequenced_read'; --- ************************************************ --- *** relation: ligation_based_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by ligation based sequen *** --- *** cing technologies. *** --- ************************************************ --- CREATE VIEW ligation_based_read AS SELECT feature_id AS ligation_based_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ligation_based_read'; --- ************************************************ --- *** relation: polymerase_synthesis_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the polymerase based *** --- *** sequence by synthesis method. *** --- ************************************************ --- CREATE VIEW polymerase_synthesis_read AS SELECT feature_id AS polymerase_synthesis_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymerase_synthesis_read'; --- ************************************************ --- *** relation: cis_regulatory_frameshift_element *** --- *** relation type: VIEW *** --- *** *** --- *** A structural region in an RNA molecule w *** --- *** hich promotes ribosomal frameshifting of *** --- *** cis coding sequence. *** --- ************************************************ --- CREATE VIEW cis_regulatory_frameshift_element AS SELECT feature_id AS cis_regulatory_frameshift_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_regulatory_frameshift_element'; --- ************************************************ --- *** relation: expressed_sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence assembly derived from express *** --- *** ed sequences. *** --- ************************************************ --- CREATE VIEW expressed_sequence_assembly AS SELECT feature_id AS expressed_sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_assembly'; --- ************************************************ --- *** relation: dna_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to DNA *** --- *** . *** --- ************************************************ --- CREATE VIEW dna_binding_site AS SELECT feature_id AS dna_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_binding_site'; --- ************************************************ --- *** relation: polya_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the UTR and the pol *** --- *** yA sequence. *** --- ************************************************ --- CREATE VIEW polya_junction AS SELECT feature_id AS polya_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_junction'; --- ************************************************ --- *** relation: cryptic_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is not transcribed under nor *** --- *** mal conditions and is not critical to no *** --- *** rmal cellular functioning. *** --- ************************************************ --- CREATE VIEW cryptic_gene AS SELECT feature_id AS cryptic_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'cryptic_gene'; --- ************************************************ --- *** relation: sequence_variant_affecting_polyadenylation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polyadenylation AS SELECT feature_id AS sequence_variant_affecting_polyadenylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_polyadenylation'; --- ************************************************ --- *** relation: three_prime_race_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A three prime RACE (Rapid Amplification *** --- *** of cDNA Ends) clone is a cDNA clone copi *** --- *** ed from the 3' end of an mRNA (using a p *** --- *** oly-dT primer to capture the polyA tail *** --- *** and a gene-specific or randomly primed 5 *** --- *** ' primer), and spliced into a vector for *** --- *** propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW three_prime_race_clone AS SELECT feature_id AS three_prime_race_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RACE_clone'; --- ************************************************ --- *** relation: cassette_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A cassette pseudogene is a kind of gene *** --- *** in an innactive form which may recombine *** --- *** at a telomeric locus to form a function *** --- *** al copy. *** --- ************************************************ --- CREATE VIEW cassette_pseudogene AS SELECT feature_id AS cassette_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_pseudogene'; --- ************************************************ --- *** relation: alanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alanine AS SELECT feature_id AS alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine'; --- ************************************************ --- *** relation: valine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW valine AS SELECT feature_id AS valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine'; --- ************************************************ --- *** relation: leucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucine AS SELECT feature_id AS leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine'; --- ************************************************ --- *** relation: isoleucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW isoleucine AS SELECT feature_id AS isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine'; --- ************************************************ --- *** relation: proline *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proline AS SELECT feature_id AS proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline'; --- ************************************************ --- *** relation: tryptophan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tryptophan AS SELECT feature_id AS tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan'; --- ************************************************ --- *** relation: phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW phenylalanine AS SELECT feature_id AS phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine'; --- ************************************************ --- *** relation: methionine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW methionine AS SELECT feature_id AS methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine'; --- ************************************************ --- *** relation: glycine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glycine AS SELECT feature_id AS glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine'; --- ************************************************ --- *** relation: serine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW serine AS SELECT feature_id AS serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine'; --- ************************************************ --- *** relation: threonine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW threonine AS SELECT feature_id AS threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine'; --- ************************************************ --- *** relation: tyrosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tyrosine AS SELECT feature_id AS tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine'; --- ************************************************ --- *** relation: cysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cysteine AS SELECT feature_id AS cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine'; --- ************************************************ --- *** relation: glutamine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamine AS SELECT feature_id AS glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine'; --- ************************************************ --- *** relation: asparagine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW asparagine AS SELECT feature_id AS asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine'; --- ************************************************ --- *** relation: lysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lysine AS SELECT feature_id AS lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine'; --- ************************************************ --- *** relation: argenine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW argenine AS SELECT feature_id AS argenine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'argenine'; --- ************************************************ --- *** relation: histidine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW histidine AS SELECT feature_id AS histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine'; --- ************************************************ --- *** relation: aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aspartic_acid AS SELECT feature_id AS aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid'; --- ************************************************ --- *** relation: glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamic_acid AS SELECT feature_id AS glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid'; --- ************************************************ --- *** relation: selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW selenocysteine AS SELECT feature_id AS selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine'; --- ************************************************ --- *** relation: pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pyrrolysine AS SELECT feature_id AS pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine'; --- ************************************************ --- *** relation: transcribed_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by a set of transcribed *** --- *** sequences from the same gene or express *** --- *** ed pseudogene. *** --- ************************************************ --- CREATE VIEW transcribed_cluster AS SELECT feature_id AS transcribed_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster' OR cvterm.name = 'transcribed_cluster'; --- ************************************************ --- *** relation: unigene_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of transcribed_cluster defined by *** --- *** a set of transcribed sequences from the *** --- *** a unique gene. *** --- ************************************************ --- CREATE VIEW unigene_cluster AS SELECT feature_id AS unigene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster'; --- ************************************************ --- *** relation: crispr *** --- *** relation type: VIEW *** --- *** *** --- *** Clustered Palindromic Repeats interspers *** --- *** ed with bacteriophage derived spacer seq *** --- *** uences. *** --- ************************************************ --- CREATE VIEW crispr AS SELECT feature_id AS crispr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CRISPR'; --- ************************************************ --- *** relation: insulator_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A protein_binding_site located within an *** --- *** insulator. *** --- ************************************************ --- CREATE VIEW insulator_binding_site AS SELECT feature_id AS insulator_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator_binding_site'; --- ************************************************ --- *** relation: enhancer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A protein_binding_site located within an *** --- *** enhancer. *** --- ************************************************ --- CREATE VIEW enhancer_binding_site AS SELECT feature_id AS enhancer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_binding_site'; --- ************************************************ --- *** relation: contig_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of contigs. *** --- ************************************************ --- CREATE VIEW contig_collection AS SELECT feature_id AS contig_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection'; --- ************************************************ --- *** relation: lincrna *** --- *** relation type: VIEW *** --- *** *** --- *** A multiexonic non-coding RNA transcribed *** --- *** by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW lincrna AS SELECT feature_id AS lincrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA'; --- ************************************************ --- *** relation: ust *** --- *** relation type: VIEW *** --- *** *** --- *** An EST spanning part or all of the untra *** --- *** nslated regions of a protein-coding tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW ust AS SELECT feature_id AS ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'UST'; --- ************************************************ --- *** relation: three_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** A UST located in the 3'UTR of a protein- *** --- *** coding transcript. *** --- ************************************************ --- CREATE VIEW three_prime_ust AS SELECT feature_id AS three_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST'; --- ************************************************ --- *** relation: five_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** An UST located in the 5'UTR of a protein *** --- *** -coding transcript. *** --- ************************************************ --- CREATE VIEW five_prime_ust AS SELECT feature_id AS five_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UST'; --- ************************************************ --- *** relation: rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a RACE product; typically a fe *** --- *** w hundred base pairs long. *** --- ************************************************ --- CREATE VIEW rst AS SELECT feature_id AS rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'RST'; --- ************************************************ --- *** relation: three_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 3'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW three_prime_rst AS SELECT feature_id AS three_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST'; --- ************************************************ --- *** relation: five_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 5'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW five_prime_rst AS SELECT feature_id AS five_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_RST'; --- ************************************************ --- *** relation: ust_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an UST sequence. *** --- ************************************************ --- CREATE VIEW ust_match AS SELECT feature_id AS ust_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UST_match'; --- ************************************************ --- *** relation: rst_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an RST sequence. *** --- ************************************************ --- CREATE VIEW rst_match AS SELECT feature_id AS rst_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RST_match'; --- ************************************************ --- *** relation: primer_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match to a primer sequence. *** --- ************************************************ --- CREATE VIEW primer_match AS SELECT feature_id AS primer_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_match'; --- ************************************************ --- *** relation: mirna_antiguide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the pri miRNA that basepairs *** --- *** with the guide to form the hairpin. *** --- ************************************************ --- CREATE VIEW mirna_antiguide AS SELECT feature_id AS mirna_antiguide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_antiguide'; --- ************************************************ --- *** relation: trans_splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the spliced leader *** --- *** and the first exon of the mRNA. *** --- ************************************************ --- CREATE VIEW trans_splice_junction AS SELECT feature_id AS trans_splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_junction'; --- ************************************************ --- *** relation: outron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript, that i *** --- *** s removed via trans splicing. *** --- ************************************************ --- CREATE VIEW outron AS SELECT feature_id AS outron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'outron'; --- ************************************************ --- *** relation: natural_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that occurs naturally. *** --- ************************************************ --- CREATE VIEW natural_plasmid AS SELECT feature_id AS natural_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element' OR cvterm.name = 'natural_plasmid'; --- ************************************************ --- *** relation: gene_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A gene trap construct is a type of engin *** --- *** eered plasmid which is designed to integ *** --- *** rate into a genome and produce a fusion *** --- *** transcript between exons of the gene int *** --- *** o which it inserts and a reporter elemen *** --- *** t in the construct. Gene traps contain a *** --- *** splice acceptor, do not contain promote *** --- *** r elements for the reporter, and are mut *** --- *** agenic. Gene traps may be bicistronic wi *** --- *** th the second cassette containing a prom *** --- *** oter driving an a selectable marker. *** --- ************************************************ --- CREATE VIEW gene_trap_construct AS SELECT feature_id AS gene_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_trap_construct'; --- ************************************************ --- *** relation: promoter_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter trap construct is a type of e *** --- *** ngineered plasmid which is designed to i *** --- *** ntegrate into a genome and express a rep *** --- *** orter when inserted in close proximity t *** --- *** o a promoter element. Promoter traps typ *** --- *** ically do not contain promoter elements *** --- *** and are mutagenic. *** --- ************************************************ --- CREATE VIEW promoter_trap_construct AS SELECT feature_id AS promoter_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_trap_construct'; --- ************************************************ --- *** relation: enhancer_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer trap construct is a type of *** --- *** engineered plasmid which is designed to *** --- *** integrate into a genome and express a re *** --- *** porter when the expression from a basic *** --- *** minimal promoter is enhanced by genomic *** --- *** enhancer elements. Enhancer traps contai *** --- *** n promoter elements and are not usually *** --- *** mutagenic. *** --- ************************************************ --- CREATE VIEW enhancer_trap_construct AS SELECT feature_id AS enhancer_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_trap_construct'; --- ************************************************ --- *** relation: pac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a P *** --- *** AC clone that may provide anhighly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW pac_end AS SELECT feature_id AS pac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC_end'; --- ************************************************ --- *** relation: rapd *** --- *** relation type: VIEW *** --- *** *** --- *** RAPD is a 'PCR product' where a sequence *** --- *** variant is identified through the use o *** --- *** f PCR with random primers. *** --- ************************************************ --- CREATE VIEW rapd AS SELECT feature_id AS rapd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD'; --- ************************************************ --- *** relation: shadow_enhancer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW shadow_enhancer AS SELECT feature_id AS shadow_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'shadow_enhancer'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that controls the express *** --- *** ion of a gene. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BRE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'MTE' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: u14_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of an evolutionar *** --- *** ily conserved eukaryotic low molecular w *** --- *** eight RNA capable of intermolecular hybr *** --- *** idization with both homologous and heter *** --- *** ologous 18S rRNA. *** --- ************************************************ --- CREATE VIEW u14_snorna_primary_transcript AS SELECT feature_id AS u14_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: methylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of 2'-O *** --- *** -ribose methylation in an RNA molecule b *** --- *** y base pairing with a short sequence aro *** --- *** und the target residue. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna AS SELECT feature_id AS methylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA'; --- ************************************************ --- *** relation: rrna_cleavage_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An ncRNA that is part of a ribonucleopro *** --- *** tein that cleaves the primary pre-rRNA t *** --- *** ranscript in the process of producing ma *** --- *** ture rRNA molecules. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_rna AS SELECT feature_id AS rrna_cleavage_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_RNA'; --- ************************************************ --- *** relation: exon_of_single_exon_gene *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is the only exon in a gene. *** --- ************************************************ --- CREATE VIEW exon_of_single_exon_gene AS SELECT feature_id AS exon_of_single_exon_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_of_single_exon_gene'; --- ************************************************ --- *** relation: cassette_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cassette_array_member AS SELECT feature_id AS cassette_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member'; --- ************************************************ --- *** relation: gene_cassette_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_cassette_member AS SELECT feature_id AS gene_cassette_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member'; --- ************************************************ --- *** relation: gene_subarray_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_subarray_member AS SELECT feature_id AS gene_subarray_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray_member'; --- ************************************************ --- *** relation: primer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** Non-covalent primer binding site for ini *** --- *** tiation of replication, transcription, o *** --- *** r reverse transcription. *** --- ************************************************ --- CREATE VIEW primer_binding_site AS SELECT feature_id AS primer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_binding_site'; --- ************************************************ --- *** relation: gene_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array includes two or more genes, or *** --- *** two or more gene subarrays, contiguously *** --- *** arranged where the individual genes, or *** --- *** subarrays, are either identical in sequ *** --- *** ence, or essentially so. *** --- ************************************************ --- CREATE VIEW gene_array AS SELECT feature_id AS gene_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_array'; --- ************************************************ --- *** relation: gene_subarray *** --- *** relation type: VIEW *** --- *** *** --- *** A subarray is, by defintition, a member *** --- *** of a gene array (SO:0005851); the member *** --- *** s of a subarray may differ substantially *** --- *** in sequence, but are closely related in *** --- *** function. *** --- ************************************************ --- CREATE VIEW gene_subarray AS SELECT feature_id AS gene_subarray_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray'; --- ************************************************ --- *** relation: gene_cassette *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that can be substituted for a rel *** --- *** ated gene at a different site in the gen *** --- *** ome. *** --- ************************************************ --- CREATE VIEW gene_cassette AS SELECT feature_id AS gene_cassette_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette'; --- ************************************************ --- *** relation: gene_cassette_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array of non-functional genes whose m *** --- *** embers, when captured by recombination f *** --- *** orm functional genes. *** --- ************************************************ --- CREATE VIEW gene_cassette_array AS SELECT feature_id AS gene_cassette_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette_array'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: selenocysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW selenocysteine_trna_primary_transcript AS SELECT feature_id AS selenocysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: selenocysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a selenocystein *** --- *** e anticodon, and a 3' selenocysteine bin *** --- *** ding region. *** --- ************************************************ --- CREATE VIEW selenocysteinyl_trna AS SELECT feature_id AS selenocysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteinyl_tRNA'; --- ************************************************ --- *** relation: syntenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region in which two or more pairs of h *** --- *** omologous markers occur on the same chro *** --- *** mosome in two or more species. *** --- ************************************************ --- CREATE VIEW syntenic_region AS SELECT feature_id AS syntenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic_region'; --- ************************************************ --- *** relation: biochemical_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is involved i *** --- *** n a biochemical function. *** --- ************************************************ --- CREATE VIEW biochemical_region_of_peptide AS SELECT feature_id AS biochemical_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide'; --- ************************************************ --- *** relation: molecular_contact_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is involved a contact with *** --- *** another molecule. *** --- ************************************************ --- CREATE VIEW molecular_contact_region AS SELECT feature_id AS molecular_contact_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region'; --- ************************************************ --- *** relation: intrinsically_unstructured_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polypeptide chain with high *** --- *** conformational flexibility. *** --- ************************************************ --- CREATE VIEW intrinsically_unstructured_polypeptide_region AS SELECT feature_id AS intrinsically_unstructured_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region'; --- ************************************************ --- *** relation: catmat_left_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_three AS SELECT feature_id AS catmat_left_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_three'; --- ************************************************ --- *** relation: catmat_left_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i psi -10 boun *** --- *** ds -50 to 30, res i+1: phi -90 bounds -1 *** --- *** 20 to -60, res i+1: psi -10 bounds -50 t *** --- *** o 30, res i+2: phi -75 bounds -100 to -5 *** --- *** 0, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_four AS SELECT feature_id AS catmat_left_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_four'; --- ************************************************ --- *** relation: catmat_right_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_three AS SELECT feature_id AS catmat_right_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_three'; --- ************************************************ --- *** relation: catmat_right_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -90 bounds - *** --- *** 120 to -60, res i+1: psi -10 bounds -50 *** --- *** to 30, res i+2: phi -75 bounds -100 to - *** --- *** 50, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_four AS SELECT feature_id AS catmat_right_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_four'; --- ************************************************ --- *** relation: alpha_beta_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: H-bond between CO *** --- *** of residue(i) and NH of residue(i+4), H *** --- *** -bond between CO of residue(i) and NH of *** --- *** residue(i+3),Phi angles of residues(i+1 *** --- *** ), (i+2) and (i+3) are negative. *** --- ************************************************ --- CREATE VIEW alpha_beta_motif AS SELECT feature_id AS alpha_beta_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_beta_motif'; --- ************************************************ --- *** relation: lipoprotein_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide that acts as a signal for both *** --- *** membrane translocation and lipid attach *** --- *** ment in prokaryotes. *** --- ************************************************ --- CREATE VIEW lipoprotein_signal_peptide AS SELECT feature_id AS lipoprotein_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lipoprotein_signal_peptide'; --- ************************************************ --- *** relation: no_output *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region wherean analysis *** --- *** has been run and not produced any annota *** --- *** tion. *** --- ************************************************ --- CREATE VIEW no_output AS SELECT feature_id AS no_output_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'no_output'; --- ************************************************ --- *** relation: cleaved_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** The cleaved_peptide_regon is the a regio *** --- *** n of peptide sequence that is cleaved du *** --- *** ring maturation. *** --- ************************************************ --- CREATE VIEW cleaved_peptide_region AS SELECT feature_id AS cleaved_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'cleaved_peptide_region'; --- ************************************************ --- *** relation: peptide_coil *** --- *** relation type: VIEW *** --- *** *** --- *** Irregular, unstructured regions of a pro *** --- *** tein's backbone, as distinct from the re *** --- *** gular region (namely alpha helix and bet *** --- *** a strand - characterised by specific pat *** --- *** terns of main-chain hydrogen bonds). *** --- ************************************************ --- CREATE VIEW peptide_coil AS SELECT feature_id AS peptide_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_coil'; --- ************************************************ --- *** relation: hydrophobic_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Hydrophobic regions are regions with a l *** --- *** ow affinity for water. *** --- ************************************************ --- CREATE VIEW hydrophobic_region_of_peptide AS SELECT feature_id AS hydrophobic_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydrophobic_region_of_peptide'; --- ************************************************ --- *** relation: n_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The amino-terminal positively-charged re *** --- *** gion of a signal peptide (approx 1-5 aa) *** --- *** . *** --- ************************************************ --- CREATE VIEW n_terminal_region AS SELECT feature_id AS n_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'n_terminal_region'; --- ************************************************ --- *** relation: c_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The more polar, carboxy-terminal region *** --- *** of the signal peptide (approx 3-7 aa). *** --- ************************************************ --- CREATE VIEW c_terminal_region AS SELECT feature_id AS c_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'c_terminal_region'; --- ************************************************ --- *** relation: central_hydrophobic_region_of_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The central, hydrophobic region of the s *** --- *** ignal peptide (approx 7-15 aa). *** --- ************************************************ --- CREATE VIEW central_hydrophobic_region_of_signal_peptide AS SELECT feature_id AS central_hydrophobic_region_of_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'central_hydrophobic_region_of_signal_peptide'; --- ************************************************ --- *** relation: polypeptide_conserved_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved motif is a short (up to 20 a *** --- *** mino acids) region of biological interes *** --- *** t that is conserved in different protein *** --- *** s. They may or may not have functional o *** --- *** r structural significance within the pro *** --- *** teins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_motif AS SELECT feature_id AS polypeptide_conserved_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_conserved_motif'; --- ************************************************ --- *** relation: polypeptide_binding_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide binding motif is a short ( *** --- *** up to 20 amino acids) polypeptide region *** --- *** of biological interest that contains on *** --- *** e or more amino acids experimentally sho *** --- *** wn to bind to a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_binding_motif AS SELECT feature_id AS polypeptide_binding_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_binding_motif'; --- ************************************************ --- *** relation: polypeptide_catalytic_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide catalytic motif is a short *** --- *** (up to 20 amino acids) polypeptide regi *** --- *** on that contains one or more active site *** --- *** residues. *** --- ************************************************ --- CREATE VIEW polypeptide_catalytic_motif AS SELECT feature_id AS polypeptide_catalytic_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_catalytic_motif'; --- ************************************************ --- *** relation: polypeptide_dna_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues involved in interactions with D *** --- *** NA. *** --- ************************************************ --- CREATE VIEW polypeptide_dna_contact AS SELECT feature_id AS polypeptide_dna_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact'; --- ************************************************ --- *** relation: polypeptide_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** A subsection of sequence with biological *** --- *** interest that is conserved in different *** --- *** proteins. They may or may not have func *** --- *** tional or structural significance within *** --- *** the proteins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_region AS SELECT feature_id AS polypeptide_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_conserved_region'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** Any change in genomic DNA caused by a si *** --- *** ngle event. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'point_mutation' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'substitution'; --- ************************************************ --- *** relation: partially_characterised_change_in_dna_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is only *** --- *** partially characterised. *** --- ************************************************ --- CREATE VIEW partially_characterised_change_in_dna_sequence AS SELECT feature_id AS partially_characterised_change_in_dna_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_change_in_DNA_sequence'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP' OR cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: uncharacterised_change_in_nucleotide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is eith *** --- *** er uncharacterised or only partially cha *** --- *** racterised. *** --- ************************************************ --- CREATE VIEW uncharacterised_change_in_nucleotide_sequence AS SELECT feature_id AS uncharacterised_change_in_nucleotide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_change_in_DNA_sequence' OR cvterm.name = 'uncharacterised_change_in_nucleotide_sequence'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A single nucleotide change which has occ *** --- *** urred at the same position of a correspo *** --- *** nding nucleotide in a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: transition *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into an other pyrimidine nucleotide, *** --- *** or change of a purine nucleotide, A or G *** --- *** , into an other purine nucleotide. *** --- ************************************************ --- CREATE VIEW transition AS SELECT feature_id AS transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'transition'; --- ************************************************ --- *** relation: pyrimidine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a pyrimidine, C or T, *** --- *** for another pyrimidine. *** --- ************************************************ --- CREATE VIEW pyrimidine_transition AS SELECT feature_id AS pyrimidine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'pyrimidine_transition'; --- ************************************************ --- *** relation: c_to_t_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a cytidine to a thymine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition AS SELECT feature_id AS c_to_t_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'C_to_T_transition'; --- ************************************************ --- *** relation: c_to_t_transition_at_pcpg_site *** --- *** relation type: VIEW *** --- *** *** --- *** The transition of cytidine to thymine oc *** --- *** curring at a pCpG site as a consequence *** --- *** of the spontaneous deamination of 5'-met *** --- *** hylcytidine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition_at_pcpg_site AS SELECT feature_id AS c_to_t_transition_at_pcpg_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site'; --- ************************************************ --- *** relation: t_to_c_transition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW t_to_c_transition AS SELECT feature_id AS t_to_c_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_C_transition'; --- ************************************************ --- *** relation: purine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a purine, A or G, for *** --- *** another purine. *** --- ************************************************ --- CREATE VIEW purine_transition AS SELECT feature_id AS purine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'purine_transition'; --- ************************************************ --- *** relation: a_to_g_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of an adenine to a guanine. *** --- ************************************************ --- CREATE VIEW a_to_g_transition AS SELECT feature_id AS a_to_g_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition'; --- ************************************************ --- *** relation: g_to_a_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a guanine to an adenine. *** --- ************************************************ --- CREATE VIEW g_to_a_transition AS SELECT feature_id AS g_to_a_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_A_transition'; --- ************************************************ --- *** relation: transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G, or *** --- *** vice versa. *** --- ************************************************ --- CREATE VIEW transversion AS SELECT feature_id AS transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'transversion'; --- ************************************************ --- *** relation: pyrimidine_to_purine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G. *** --- ************************************************ --- CREATE VIEW pyrimidine_to_purine_transversion AS SELECT feature_id AS pyrimidine_to_purine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'pyrimidine_to_purine_transversion'; --- ************************************************ --- *** relation: c_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from cytidine to adenine. *** --- ************************************************ --- CREATE VIEW c_to_a_transversion AS SELECT feature_id AS c_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion'; --- ************************************************ --- *** relation: c_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_to_g_transversion AS SELECT feature_id AS c_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_G_transversion'; --- ************************************************ --- *** relation: t_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to A. *** --- ************************************************ --- CREATE VIEW t_to_a_transversion AS SELECT feature_id AS t_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_A_transversion'; --- ************************************************ --- *** relation: t_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to G. *** --- ************************************************ --- CREATE VIEW t_to_g_transversion AS SELECT feature_id AS t_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_G_transversion'; --- ************************************************ --- *** relation: purine_to_pyrimidine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a purine nucleotide, A or G , *** --- *** into a pyrimidine nucleotide C or T. *** --- ************************************************ --- CREATE VIEW purine_to_pyrimidine_transversion AS SELECT feature_id AS purine_to_pyrimidine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion'; --- ************************************************ --- *** relation: a_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to cytidine. *** --- ************************************************ --- CREATE VIEW a_to_c_transversion AS SELECT feature_id AS a_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion'; --- ************************************************ --- *** relation: a_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to thymine. *** --- ************************************************ --- CREATE VIEW a_to_t_transversion AS SELECT feature_id AS a_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_T_transversion'; --- ************************************************ --- *** relation: g_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to cytidine. *** --- ************************************************ --- CREATE VIEW g_to_c_transversion AS SELECT feature_id AS g_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_C_transversion'; --- ************************************************ --- *** relation: g_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to thymine. *** --- ************************************************ --- CREATE VIEW g_to_t_transversion AS SELECT feature_id AS g_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_T_transversion'; --- ************************************************ --- *** relation: intrachromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_mutation AS SELECT feature_id AS intrachromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'intrachromosomal_mutation'; --- ************************************************ --- *** relation: chromosomal_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** An incomplete chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_deletion AS SELECT feature_id AS chromosomal_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_deletion'; --- ************************************************ --- *** relation: chromosomal_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_inversion AS SELECT feature_id AS chromosomal_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_inversion'; --- ************************************************ --- *** relation: interchromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal_mutation AS SELECT feature_id AS interchromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_mutation'; --- ************************************************ --- *** relation: indel *** --- *** relation type: VIEW *** --- *** *** --- *** A hybrid term (insertion/deletion) to de *** --- *** scribe sequence length change when the d *** --- *** irection of the change is unspecified. *** --- ************************************************ --- CREATE VIEW indel AS SELECT feature_id AS indel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_deletion' OR cvterm.name = 'nucleotide_insertion' OR cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'indel'; --- ************************************************ --- *** relation: nucleotide_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** One or more continuous nucleotides are e *** --- *** xcised from the sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_deletion AS SELECT feature_id AS nucleotide_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_deletion'; --- ************************************************ --- *** relation: nucleotide_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW nucleotide_insertion AS SELECT feature_id AS nucleotide_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_duplication' OR cvterm.name = 'nucleotide_insertion'; --- ************************************************ --- *** relation: nucleotide_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce; the inserted sequence derives from, *** --- *** or is identical in sequence to, nucleoti *** --- *** des adjacent to insertion point. *** --- ************************************************ --- CREATE VIEW nucleotide_duplication AS SELECT feature_id AS nucleotide_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_duplication'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: chromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An extra chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_duplication AS SELECT feature_id AS chromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_duplication'; --- ************************************************ --- *** relation: intrachromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_duplication AS SELECT feature_id AS intrachromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'intrachromosomal_duplication'; --- ************************************************ --- *** relation: direct_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direct_tandem_duplication AS SELECT feature_id AS direct_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication'; --- ************************************************ --- *** relation: inverted_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_tandem_duplication AS SELECT feature_id AS inverted_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_tandem_duplication'; --- ************************************************ --- *** relation: intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal_transposition AS SELECT feature_id AS intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_transposition'; --- ************************************************ --- *** relation: compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome AS SELECT feature_id AS compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'compound_chromosome'; --- ************************************************ --- *** relation: robertsonian_fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW robertsonian_fusion AS SELECT feature_id AS robertsonian_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Robertsonian_fusion'; --- ************************************************ --- *** relation: chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_translocation AS SELECT feature_id AS chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'chromosomal_translocation'; --- ************************************************ --- *** relation: ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ring_chromosome AS SELECT feature_id AS ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'ring_chromosome'; --- ************************************************ --- *** relation: pericentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pericentric_inversion AS SELECT feature_id AS pericentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric_inversion'; --- ************************************************ --- *** relation: paracentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paracentric_inversion AS SELECT feature_id AS paracentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric_inversion'; --- ************************************************ --- *** relation: reciprocal_chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW reciprocal_chromosomal_translocation AS SELECT feature_id AS reciprocal_chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal_chromosomal_translocation'; --- ************************************************ --- *** relation: sequence_variation_affecting_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** Any change in mature, spliced and proces *** --- *** sed, RNA that results from a change in t *** --- *** he corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_transcript AS SELECT feature_id AS sequence_variation_affecting_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_transcription' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_no_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** No effect on the state of the RNA. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_no_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_complex_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_complex_change_in_transcript AS SELECT feature_id AS sequence_variation_affecting_complex_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_coding_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Any of the amino acid coding triplets of *** --- *** a gene are affected by the DNA mutation *** --- *** . *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_coding_sequence AS SELECT feature_id AS sequence_variation_affecting_coding_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variation_affecting_coding_sequence'; --- ************************************************ --- *** relation: sequence_variant_causing_initiator_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The DNA mutation changes, usually destro *** --- *** ys, the first coding triplet of a gene. *** --- *** Usually prevents translation although an *** --- *** other initiator codon may be used. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_initiator_codon_change_in_trans AS SELECT feature_id AS sequence_variant_causing_initiator_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_amino_acid_coding_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The DNA mutation affects the amino acid *** --- *** coding sequence of a gene; this region i *** --- *** ncludes both the initiator and terminato *** --- *** r codons. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_amino_acid_coding_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_amino_acid_coding_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_synonymous_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The changed codon has the same translati *** --- *** on product as the original codon. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_synonymous_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_synonymous_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_non_synonymous_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA point mutation that causes a subst *** --- *** itution of an amino acid by an other. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_non_synonymous_codon_change_in_trans AS SELECT feature_id AS seq_variant_causing_non_synonymous_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_missense_codon_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon leads *** --- *** to a new codon coding for a new amino a *** --- *** cid. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_missense_codon_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_missense_codon_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_var_causing_conservative_missense_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The amino acid change following from the *** --- *** codon change does not change the gross *** --- *** properties (size, charge, hydrophobicity *** --- *** ) of the amino acid at that position. *** --- ************************************************ --- CREATE VIEW seq_var_causing_conservative_missense_codon_change_in_trans AS SELECT feature_id AS seq_var_causing_conservative_missense_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: seq_var_causing_nonconserv_missense_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The amino acid change following from the *** --- *** codon change changes the gross properti *** --- *** es (size, charge, hydrophobicity) of the *** --- *** amino acid in that position. *** --- ************************************************ --- CREATE VIEW seq_var_causing_nonconserv_missense_codon_change_in_trans AS SELECT feature_id AS seq_var_causing_nonconserv_missense_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_nonsense_codon_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon tripl *** --- *** et creates a terminator codon. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_nonsense_codon_change_in_transcript AS SELECT feature_id AS sequence_variant_causing_nonsense_codon_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_causing_terminator_codon_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide change in the codon tripl *** --- *** et changes the stop codon, causing an el *** --- *** ongated transcript sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_terminator_codon_change_in_trans AS SELECT feature_id AS sequence_variant_causing_terminator_codon_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variation_affecting_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** An umbrella term for terms describing an *** --- *** effect of a sequence variation on the f *** --- *** rame of translation. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_reading_frame AS SELECT feature_id AS sequence_variation_affecting_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variation_affecting_reading_frame'; --- ************************************************ --- *** relation: frameshift_sequence_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, because the *** --- *** number of nucleotides inserted or delete *** --- *** d is not a multiple of three. *** --- ************************************************ --- CREATE VIEW frameshift_sequence_variation AS SELECT feature_id AS frameshift_sequence_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'frameshift_sequence_variation'; --- ************************************************ --- *** relation: sequence_variant_causing_plus_1_frameshift_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the i *** --- *** nsertion of a nucleotide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_plus_1_frameshift_mutation AS SELECT feature_id AS sequence_variant_causing_plus_1_frameshift_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation'; --- ************************************************ --- *** relation: sequence_variant_causing_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the d *** --- *** eletion of a nucleotide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_minus_1_frameshift AS SELECT feature_id AS sequence_variant_causing_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_minus_1_frameshift'; --- ************************************************ --- *** relation: sequence_variant_causing_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the i *** --- *** nsertion of two nucleotides. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_plus_2_frameshift AS SELECT feature_id AS sequence_variant_causing_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_plus_2_frameshift'; --- ************************************************ --- *** relation: sequence_variant_causing_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation causing a disruption of the t *** --- *** ranslational reading frame, due to the d *** --- *** eletion of two nucleotides. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_minus_2_frameshift AS SELECT feature_id AS sequence_variant_causing_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_minus_2_frameshift'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_processing *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the way in whic *** --- *** h the primary transcriptional product is *** --- *** processed to form the mature transcript *** --- *** . *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_processing AS SELECT feature_id AS sequence_variant_affecting_transcript_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_affecting_transcript_processing'; --- ************************************************ --- *** relation: sequence_variant_affecting_splicing *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect where the way *** --- *** in which the primary transcriptional pro *** --- *** duct is processed to form the mature tra *** --- *** nscript, specifically by the removal (sp *** --- *** licing) of intron sequences is changed. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splicing AS SELECT feature_id AS sequence_variant_affecting_splicing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_donor' OR cvterm.name = 'sequence_variant_affecting_splice_acceptor' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation' OR cvterm.name = 'sequence_variant_causes_exon_loss' OR cvterm.name = 'sequence_variant_causes_intron_gain' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_affecting_splicing'; --- ************************************************ --- *** relation: sequence_variant_affecting_splice_donor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he splice donor sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splice_donor AS SELECT feature_id AS sequence_variant_affecting_splice_donor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_donor'; --- ************************************************ --- *** relation: sequence_variant_affecting_splice_acceptor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he splice acceptor sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_splice_acceptor AS SELECT feature_id AS sequence_variant_affecting_splice_acceptor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_splice_acceptor'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_activation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a new (functi *** --- *** onal) splice site. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation'; --- ************************************************ --- *** relation: sequence_variant_affecting_editing *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the editing of *** --- *** the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_editing AS SELECT feature_id AS sequence_variant_affecting_editing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_editing'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** Mutation affects the process of transcri *** --- *** ption, its initiation, progression or te *** --- *** rmination. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcription AS SELECT feature_id AS sequence_variant_affecting_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_affecting_transcription'; --- ************************************************ --- *** relation: sequence_variant_decreasing_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that decreases the *** --- *** rate a which transcription of the sequen *** --- *** ce occurs. *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_rate_of_transcription AS SELECT feature_id AS sequence_variant_decreasing_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variation_affecting_transcript_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_transcript_sequence AS SELECT feature_id AS sequence_variation_affecting_transcript_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence'; --- ************************************************ --- *** relation: sequence_variant_increasing_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_rate_of_transcription AS SELECT feature_id AS sequence_variant_increasing_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variant_affecting_rate_of_transcription *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that alters the rate a which *** --- *** transcription of the sequence occurs. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_rate_of_transcription AS SELECT feature_id AS sequence_variant_affecting_rate_of_transcription_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant affects the stability o *** --- *** f the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_stability AS SELECT feature_id AS sequence_variant_affecting_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence variant_affecting_transcript_stability'; --- ************************************************ --- *** relation: sequence_variant_increasing_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant increases the stability *** --- *** (half-life) of the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_transcript_stability AS SELECT feature_id AS sequence_variant_increasing_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_transcript_stability'; --- ************************************************ --- *** relation: sequence_variant_decreasing_transcript_stability *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence variant decreases the stability *** --- *** (half-life) of the transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_transcript_stability AS SELECT feature_id AS sequence_variant_decreasing_transcript_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_transcript_stability'; --- ************************************************ --- *** relation: sequence_variation_affecting_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that causes a chang *** --- *** e in the level of mature, spliced and pr *** --- *** ocessed RNA, resulting from a change in *** --- *** the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_affecting_level_of_transcript AS SELECT feature_id AS sequence_variation_affecting_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variation_decreasing_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variation that causes a decre *** --- *** ase in the level of mature, spliced and *** --- *** processed RNA, resulting from a change i *** --- *** n the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_decreasing_level_of_transcript AS SELECT feature_id AS sequence_variation_decreasing_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_decreasing_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variation_increasing_level_of_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variation that causes an incr *** --- *** ease in the level of mature, spliced and *** --- *** processed RNA, resulting from a change *** --- *** in the corresponding DNA sequence. *** --- ************************************************ --- CREATE VIEW sequence_variation_increasing_level_of_transcript AS SELECT feature_id AS sequence_variation_increasing_level_of_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variation_increasing_level_of_transcript'; --- ************************************************ --- *** relation: sequence_variant_affecting_translational_product *** --- *** relation type: VIEW *** --- *** *** --- *** Mutation causes a change in primary tran *** --- *** slation product of a transcript. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_translational_product AS SELECT feature_id AS sequence_variant_affecting_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_affecting_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_no_change_of_translational_product *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence variant at RNA level does n *** --- *** ot lead to any change in polypeptide. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_change_of_translational_product AS SELECT feature_id AS sequence_variant_causing_no_change_of_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_uncharacterised_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing an uncharacte *** --- *** rized change of translational product. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_uncharacterised_change_of_product AS SELECT feature_id AS sequence_variant_causing_uncharacterised_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product'; --- ************************************************ --- *** relation: seq_variant_causing_partly_characterised_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a partially u *** --- *** ncharacterised change in translational p *** --- *** roduct. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_partly_characterised_change_of_product AS SELECT feature_id AS seq_variant_causing_partly_characterised_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_complex_change_of_product *** --- *** relation type: VIEW *** --- *** *** --- *** Any sequence variant effect that is know *** --- *** n at nucleotide level but cannot be expl *** --- *** ained by using other key terms. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_complex_change_of_product AS SELECT feature_id AS sequence_variant_causing_complex_change_of_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** The replacement of a single amino acid b *** --- *** y another. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_substitution AS SELECT feature_id AS sequence_variant_causing_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_conservative_amino_acid_sub *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_conservative_amino_acid_sub AS SELECT feature_id AS sequence_variant_causing_conservative_amino_acid_sub_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_nonconservative_amino_acid_sub *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_nonconservative_amino_acid_sub AS SELECT feature_id AS sequence_variant_causing_nonconservative_amino_acid_sub_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** The insertion of one or more amino acids *** --- *** from the polypeptide, without affecting *** --- *** the surrounding sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_insertion AS SELECT feature_id AS sequence_variant_causing_amino_acid_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_insertion'; --- ************************************************ --- *** relation: sequence_variant_causing_amino_acid_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The deletion of one or more amino acids *** --- *** from the polypeptide, without affecting *** --- *** the surrounding sequence. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_amino_acid_deletion AS SELECT feature_id AS sequence_variant_causing_amino_acid_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_deletion'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_truncation *** --- *** relation type: VIEW *** --- *** *** --- *** The translational product is truncated a *** --- *** t its C-terminus, usually a result of a *** --- *** nonsense codon change in transcript (SO: *** --- *** 1000062). *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_truncation AS SELECT feature_id AS sequence_variant_causing_polypeptide_truncation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_truncation'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** The extension of the translational produ *** --- *** ct at either (or both) the N-terminus an *** --- *** d/or the C-terminus. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_elongation AS SELECT feature_id AS sequence_variant_causing_polypeptide_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation'; --- ************************************************ --- *** relation: mutation_causing_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** . *** --- ************************************************ --- CREATE VIEW mutation_causing_polypeptide_n_terminal_elongation AS SELECT feature_id AS mutation_causing_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_polypeptide_c_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** . *** --- ************************************************ --- CREATE VIEW mutation_causing_polypeptide_c_terminal_elongation AS SELECT feature_id AS mutation_causing_polypeptide_c_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: sequence_variant_affecting_level_of_translational_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_level_of_translational_product AS SELECT feature_id AS sequence_variant_affecting_level_of_translational_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product'; --- ************************************************ --- *** relation: sequence_variant_decreasing_level_of_translation_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_decreasing_level_of_translation_product AS SELECT feature_id AS sequence_variant_decreasing_level_of_translation_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_decreasing_level_of_translation_product'; --- ************************************************ --- *** relation: sequence_variant_increasing_level_of_translation_product *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_increasing_level_of_translation_product AS SELECT feature_id AS sequence_variant_increasing_level_of_translation_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_increasing_level_of_translation_product'; --- ************************************************ --- *** relation: sequence_variant_affecting_polypeptide_amino_acid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polypeptide_amino_acid_sequence AS SELECT feature_id AS sequence_variant_affecting_polypeptide_amino_acid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence'; --- ************************************************ --- *** relation: mutation_causing_inframe_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_inframe_polypeptide_n_terminal_elongation AS SELECT feature_id AS mutation_causing_inframe_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_out_of_frame_polypeptide_n_terminal_elong *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_out_of_frame_polypeptide_n_terminal_elong AS SELECT feature_id AS mutation_causing_out_of_frame_polypeptide_n_terminal_elong_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: mutaton_causing_inframe_polypeptide_c_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutaton_causing_inframe_polypeptide_c_terminal_elongation AS SELECT feature_id AS mutaton_causing_inframe_polypeptide_c_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: mutation_causing_out_of_frame_polypeptide_c_terminal_elong *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mutation_causing_out_of_frame_polypeptide_c_terminal_elong AS SELECT feature_id AS mutation_causing_out_of_frame_polypeptide_c_terminal_elong_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation'; --- ************************************************ --- *** relation: frame_restoring_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that reverts the sequence of *** --- *** a previous frameshift mutation back to t *** --- *** he initial frame. *** --- ************************************************ --- CREATE VIEW frame_restoring_sequence_variant AS SELECT feature_id AS frame_restoring_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_sequence_variant'; --- ************************************************ --- *** relation: sequence_variant_affecting_3d_structure_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation that changes the amino acid s *** --- *** equence of the peptide in such a way tha *** --- *** t it changes the 3D structure of the mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_3d_structure_of_polypeptide AS SELECT feature_id AS sequence_variant_affecting_3d_structure_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_no_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_no_3d_structural_change AS SELECT feature_id AS sequence_variant_causing_no_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_no_3D_structural_change'; --- ************************************************ --- *** relation: seq_variant_causing_uncharacterised_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_uncharacterised_3d_structural_change AS SELECT feature_id AS seq_variant_causing_uncharacterised_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change'; --- ************************************************ --- *** relation: seq_var_causing_partly_characterised_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_var_causing_partly_characterised_3d_structural_change AS SELECT feature_id AS seq_var_causing_partly_characterised_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change'; --- ************************************************ --- *** relation: sequence_variant_causing_complex_3d_structural_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_complex_3d_structural_change AS SELECT feature_id AS sequence_variant_causing_complex_3d_structural_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_complex_3D_structural_change'; --- ************************************************ --- *** relation: sequence_variant_causing_conformational_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_conformational_change AS SELECT feature_id AS sequence_variant_causing_conformational_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_conformational_change'; --- ************************************************ --- *** relation: sequence_variant_affecting_polypeptide_function *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_polypeptide_function AS SELECT feature_id AS sequence_variant_affecting_polypeptide_function_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function'; --- ************************************************ --- *** relation: sequence_variant_causing_loss_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_loss_of_function_of_polypeptide AS SELECT feature_id AS sequence_variant_causing_loss_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_inactive_ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_inactive_ligand_binding_site AS SELECT feature_id AS sequence_variant_causing_inactive_ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site'; --- ************************************************ --- *** relation: sequence_variant_causing_inactive_catalytic_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_inactive_catalytic_site AS SELECT feature_id AS sequence_variant_causing_inactive_catalytic_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_inactive_catalytic_site'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_localization_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_localization_change AS SELECT feature_id AS sequence_variant_causing_polypeptide_localization_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_localization_change'; --- ************************************************ --- *** relation: seq_variant_causing_polypeptide_post_trans_processing_change *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_polypeptide_post_trans_processing_change AS SELECT feature_id AS seq_variant_causing_polypeptide_post_trans_processing_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change'; --- ************************************************ --- *** relation: seq_variant_causing_part_loss_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_causing_part_loss_of_function_of_polypeptide AS SELECT feature_id AS seq_variant_causing_part_loss_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_causing_gain_of_function_of_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_gain_of_function_of_polypeptide AS SELECT feature_id AS sequence_variant_causing_gain_of_function_of_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide'; --- ************************************************ --- *** relation: sequence_variant_affecting_transcript_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the seco *** --- *** ndary structure (folding) of the RNA tra *** --- *** nscript molecule. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_transcript_secondary_structure AS SELECT feature_id AS sequence_variant_affecting_transcript_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure'; --- ************************************************ --- *** relation: seq_variant_caus_compensatory_trans_secondary_structure_mut *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW seq_variant_caus_compensatory_trans_secondary_structure_mut AS SELECT feature_id AS seq_variant_caus_compensatory_trans_secondary_structure_mut_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation'; --- ************************************************ --- *** relation: sequence_variant_effect *** --- *** relation type: VIEW *** --- *** *** --- *** The effect of a change in nucleotide seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW sequence_variant_effect AS SELECT feature_id AS sequence_variant_effect_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_affecting_regulatory_region' OR cvterm.name = 'silent_mutation' OR cvterm.name = 'sequence_variant_affecting_copy_number' OR cvterm.name = 'sequence_variation_affecting_transcript' OR cvterm.name = 'sequence_variant_affecting_splicing' OR cvterm.name = 'sequence_variant_affecting_translational_product' OR cvterm.name = 'sequence_variant_affecting_gene_structure' OR cvterm.name = 'sequence_variant_causing_no_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_complex_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_transcription' OR cvterm.name = 'sequence_variation_affecting_transcript_sequence' OR cvterm.name = 'sequence_variation_affecting_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_rate_of_transcription' OR cvterm.name = 'sequence_variant_decreasing_rate_of_transcription' OR cvterm.name = 'sequence_variant_increasing_rate_of_transcription' OR cvterm.name = 'sequence_variation_affecting_coding_sequence' OR cvterm.name = 'sequence_variant_affecting_transcript_processing' OR cvterm.name = 'sequence variant_affecting_transcript_stability' OR cvterm.name = 'sequence_variant_affecting_transcript_secondary_structure' OR cvterm.name = 'sequence_variant_causing_amino_acid_coding_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_terminator_codon_change_in_transcript' OR cvterm.name = 'sequence_variation_affecting_reading_frame' OR cvterm.name = 'sequence_variant_causing_initiator_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_non_synonymous_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonsense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_conservative_missense_codon_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_nonconservative_missense_codon_change_in_transcript' OR cvterm.name = 'frameshift_sequence_variation' OR cvterm.name = 'sequence_variant_causing_plus_1_frameshift_mutation' OR cvterm.name = 'sequence_variant_causing_minus_1_frameshift' OR cvterm.name = 'sequence_variant_causing_plus_2_frameshift' OR cvterm.name = 'sequence_variant_causing_minus_2_frameshift' OR cvterm.name = 'frame_restoring_sequence_variant' OR cvterm.name = 'sequence_variant_affecting_polyadenylation' OR cvterm.name = 'sequence_variant_affecting_editing' OR cvterm.name = 'sequence_variant_increasing_transcript_stability' OR cvterm.name = 'sequence_variant_decreasing_transcript_stability' OR cvterm.name = 'sequence_variant_causing_compensatory_transcript_secondary_structure_mutation' OR cvterm.name = 'sequence_variation_decreasing_level_of_transcript' OR cvterm.name = 'sequence_variation_increasing_level_of_transcript' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variant_affecting_splice_donor' OR cvterm.name = 'sequence_variant_affecting_splice_acceptor' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_activation' OR cvterm.name = 'sequence_variant_causes_exon_loss' OR cvterm.name = 'sequence_variant_causes_intron_gain' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation' OR cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation' OR cvterm.name = 'sequence_variant_causing_no_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_causing_complex_change_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_level_of_translational_product' OR cvterm.name = 'sequence_variant_affecting_polypeptide_amino_acid_sequence' OR cvterm.name = 'sequence_variant_affecting_3D_structure_of_polypeptide' OR cvterm.name = 'sequence_variant_affecting_polypeptide_function' OR cvterm.name = 'sequence_variant_causing_partially_characterised_change_of_translational_product' OR cvterm.name = 'sequence_variant_decreasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_increasing_level_of_translation_product' OR cvterm.name = 'sequence_variant_causing_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_amino_acid_insertion' OR cvterm.name = 'sequence_variant_causing_amino_acid_deletion' OR cvterm.name = 'sequence_variant_causing_polypeptide_truncation' OR cvterm.name = 'sequence_variant_causing_polypeptide_elongation' OR cvterm.name = 'sequence_variant_causing_polypeptide_fusion' OR cvterm.name = 'sequence_variant_causing_conservative_amino_acid_substitution' OR cvterm.name = 'sequence_variant_causing_nonconservative_amino_acid_substitution' OR cvterm.name = 'mutation_causing_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_inframe_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'mutaton_causing_inframe_polypeptide_C_terminal_elongation' OR cvterm.name = 'mutation_causing_out_of_frame_polypeptide_C_terminal_elongation' OR cvterm.name = 'sequence_variant_causing_no_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_uncharacterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_complex_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_conformational_change' OR cvterm.name = 'sequence_variant_causing_partially_characterised_3D_structural_change' OR cvterm.name = 'sequence_variant_causing_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_polypeptide_localization_change' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_gain_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_ligand_binding_site' OR cvterm.name = 'sequence_variant_causing_polypeptide_post_translational_processing_change' OR cvterm.name = 'sequence_variant_causing_partial_loss_of_function_of_polypeptide' OR cvterm.name = 'sequence_variant_causing_inactive_catalytic_site' OR cvterm.name = 'sequence_variant_causing_gene_fusion' OR cvterm.name = 'sequence_variant_effect'; --- ************************************************ --- *** relation: sequence_variant_causing_polypeptide_fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_polypeptide_fusion AS SELECT feature_id AS sequence_variant_causing_polypeptide_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_polypeptide_fusion'; --- ************************************************ --- *** relation: autosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW autosynaptic_chromosome AS SELECT feature_id AS autosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'autosynaptic_chromosome'; --- ************************************************ --- *** relation: homo_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW homo_compound_chromosome AS SELECT feature_id AS homo_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homo_compound_chromosome'; --- ************************************************ --- *** relation: hetero_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW hetero_compound_chromosome AS SELECT feature_id AS hetero_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hetero_compound_chromosome'; --- ************************************************ --- *** relation: chromosome_fission *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_fission AS SELECT feature_id AS chromosome_fission_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_fission'; --- ************************************************ --- *** relation: dexstrosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dexstrosynaptic_chromosome AS SELECT feature_id AS dexstrosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome'; --- ************************************************ --- *** relation: laevosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW laevosynaptic_chromosome AS SELECT feature_id AS laevosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'laevosynaptic_chromosome'; --- ************************************************ --- *** relation: free_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_duplication AS SELECT feature_id AS free_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication' OR cvterm.name = 'free_duplication'; --- ************************************************ --- *** relation: free_ring_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW free_ring_duplication AS SELECT feature_id AS free_ring_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication'; --- ************************************************ --- *** relation: complex_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW complex_chromosomal_mutation AS SELECT feature_id AS complex_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A translocation in which one of the four *** --- *** broken ends loses a segment before re-j *** --- *** oining. *** --- ************************************************ --- CREATE VIEW deficient_translocation AS SELECT feature_id AS deficient_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_translocation'; --- ************************************************ --- *** relation: inversion_cum_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** The first two breaks are in the same chr *** --- *** omosome, and the region between them is *** --- *** rejoined in inverted order to the other *** --- *** side of the first break, such that both *** --- *** sides of break one are present on the sa *** --- *** me chromosome. The remaining free ends a *** --- *** re joined as a translocation with those *** --- *** resulting from the third break. *** --- ************************************************ --- CREATE VIEW inversion_cum_translocation AS SELECT feature_id AS inversion_cum_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_cum_translocation'; --- ************************************************ --- *** relation: bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** The (large) region between the first two *** --- *** breaks listed is lost, and the two flan *** --- *** king segments (one of them centric) are *** --- *** joined as a translocation to the free en *** --- *** ds resulting from the third break. *** --- ************************************************ --- CREATE VIEW bipartite_duplication AS SELECT feature_id AS bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_duplication'; --- ************************************************ --- *** relation: cyclic_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in three different chromoso *** --- *** mes. The centric segment resulting from *** --- *** the first break listed is joined to the *** --- *** acentric segment resulting from the seco *** --- *** nd, rather than the third. *** --- ************************************************ --- CREATE VIEW cyclic_translocation AS SELECT feature_id AS cyclic_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyclic_translocation'; --- ************************************************ --- *** relation: bipartite_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in the same chromosome; bot *** --- *** h central segments are inverted in place *** --- *** (i.e., they are not transposed). *** --- ************************************************ --- CREATE VIEW bipartite_inversion AS SELECT feature_id AS bipartite_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_inversion'; --- ************************************************ --- *** relation: uninvert_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the insertion is in cytologica *** --- *** lly the same orientation as its flanking *** --- *** segments. *** --- ************************************************ --- CREATE VIEW uninvert_insert_dup AS SELECT feature_id AS uninvert_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication'; --- ************************************************ --- *** relation: inverted_insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the insertion is in cytologica *** --- *** lly inverted orientation with respect to *** --- *** its flanking segments. *** --- ************************************************ --- CREATE VIEW inverted_insertional_duplication AS SELECT feature_id AS inverted_insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_insertional_duplication'; --- ************************************************ --- *** relation: insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving the i *** --- *** nsertion of a duplicated region. *** --- ************************************************ --- CREATE VIEW insertional_duplication AS SELECT feature_id AS insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'insertional_duplication'; --- ************************************************ --- *** relation: interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal_transposition AS SELECT feature_id AS interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW invert_inter_transposition AS SELECT feature_id AS invert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uninvert_inter_transposition AS SELECT feature_id AS uninvert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally inverted orientation with respect *** --- *** to its flanking segments. *** --- ************************************************ --- CREATE VIEW invert_intra_transposition AS SELECT feature_id AS invert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally the same orientation as its flanki *** --- *** ng segments. *** --- ************************************************ --- CREATE VIEW uninvert_intra_transposition AS SELECT feature_id AS uninvert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: unorient_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** A copy of the segment between the first *** --- *** two breaks listed is inserted at the thi *** --- *** rd break; the orientation of the inserti *** --- *** on with respect to its flanking segments *** --- *** is not recorded. *** --- ************************************************ --- CREATE VIEW unorient_insert_dup AS SELECT feature_id AS unorient_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_insertional_duplication'; --- ************************************************ --- *** relation: unorient_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW unorient_inter_transposition AS SELECT feature_id AS unorient_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unorientated_interchromosomal_transposition'; --- ************************************************ --- *** relation: unorient_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** The segment between the first two breaks *** --- *** listed is removed and inserted at the t *** --- *** hird break; the orientation of the inser *** --- *** tion with respect to its flanking segmen *** --- *** ts is not recorded. *** --- ************************************************ --- CREATE VIEW unorient_intra_transposition AS SELECT feature_id AS unorient_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unorientated_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uncharacterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uncharacterised_chromosomal_mutation AS SELECT feature_id AS uncharacterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** Three breaks in the same chromosome; one *** --- *** central region lost, the other inverted *** --- *** . *** --- ************************************************ --- CREATE VIEW deficient_inversion AS SELECT feature_id AS deficient_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_inversion'; --- ************************************************ --- *** relation: tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tandem_duplication AS SELECT feature_id AS tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'tandem_duplication'; --- ************************************************ --- *** relation: partially_characterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW partially_characterised_chromosomal_mutation AS SELECT feature_id AS partially_characterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation'; --- ************************************************ --- *** relation: seq_variant_causing_uncharacterised_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is eith *** --- *** er uncharacterised or only partially cha *** --- *** racterised. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_uncharacterised_change_in_transcript AS SELECT feature_id AS seq_variant_causing_uncharacterised_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript' OR cvterm.name = 'sequence_variant_causing_uncharacterised_change_in_transcript'; --- ************************************************ --- *** relation: seq_variant_causing_partly_characterised_change_in_trans *** --- *** relation type: VIEW *** --- *** *** --- *** The nature of the mutation event is only *** --- *** partially characterised. *** --- ************************************************ --- CREATE VIEW seq_variant_causing_partly_characterised_change_in_trans AS SELECT feature_id AS seq_variant_causing_partly_characterised_change_in_trans_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_partially_characterised_change_in_transcript'; --- ************************************************ --- *** relation: sequence_variant_affecting_gene_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he gene structure. *** --- ************************************************ --- CREATE VIEW sequence_variant_affecting_gene_structure AS SELECT feature_id AS sequence_variant_affecting_gene_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gene_fusion' OR cvterm.name = 'sequence_variant_affecting_gene_structure'; --- ************************************************ --- *** relation: sequence_variant_causing_gene_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant_effect that changes t *** --- *** he gene structure by causing a fusion to *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_gene_fusion AS SELECT feature_id AS sequence_variant_causing_gene_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_gene_fusion'; --- ************************************************ --- *** relation: chromosome_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW chromosome_number_variation AS SELECT feature_id AS chromosome_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'chromosome_number_variation'; --- ************************************************ --- *** relation: chromosome_structure_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_structure_variation AS SELECT feature_id AS chromosome_structure_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unorientated_intrachromosomal_transposition' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unorientated_interchromosomal_transposition' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_structure_variation'; --- ************************************************ --- *** relation: sequence_variant_causes_exon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant affecting splicing an *** --- *** d causes an exon loss. *** --- ************************************************ --- CREATE VIEW sequence_variant_causes_exon_loss AS SELECT feature_id AS sequence_variant_causes_exon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causes_exon_loss'; --- ************************************************ --- *** relation: sequence_variant_causes_intron_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant effect, causing an in *** --- *** tron to be gained by the processed trans *** --- *** cript; usually a result of a donor accep *** --- *** tor mutation (SO:1000072). *** --- ************************************************ --- CREATE VIEW sequence_variant_causes_intron_gain AS SELECT feature_id AS sequence_variant_causes_intron_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causes_intron_gain'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_donor_activation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_donor_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_donor_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_donor_activation'; --- ************************************************ --- *** relation: sequence_variant_causing_cryptic_splice_acceptor_activation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_variant_causing_cryptic_splice_acceptor_activation AS SELECT feature_id AS sequence_variant_causing_cryptic_splice_acceptor_activation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant_causing_cryptic_splice_acceptor_activation'; --- ************************************************ --- *** relation: alternatively_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is alternatively splic *** --- *** ed. *** --- ************************************************ --- CREATE VIEW alternatively_spliced_transcript AS SELECT feature_id AS alternatively_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced_transcript'; --- ************************************************ --- *** relation: encodes_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, but *** --- *** encodes only one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_1_polypeptide AS SELECT feature_id AS encodes_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide'; --- ************************************************ --- *** relation: encodes_greater_than_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_greater_than_1_polypeptide AS SELECT feature_id AS encodes_greater_than_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_greater_than_1_polypeptide'; --- ************************************************ --- *** relation: encodes_different_polypeptides_different_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different stop codons. *** --- ************************************************ --- CREATE VIEW encodes_different_polypeptides_different_stop AS SELECT feature_id AS encodes_different_polypeptides_different_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides_different_start *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides_different_start AS SELECT feature_id AS encodes_overlapping_peptides_different_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_peptides_different_start'; --- ************************************************ --- *** relation: encodes_disjoint_polypeptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** do not have overlapping peptide sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW encodes_disjoint_polypeptides AS SELECT feature_id AS encodes_disjoint_polypeptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides'; --- ************************************************ --- *** relation: encodes_overlapping_polypeptides_different_start_and_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start and stop codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_polypeptides_different_start_and_stop AS SELECT feature_id AS encodes_overlapping_polypeptides_different_start_and_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides AS SELECT feature_id AS encodes_overlapping_peptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_overlapping_peptides'; --- ************************************************ --- *** relation: cryptogene *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle gene so extensively edited *** --- *** that it cannot be matched to its edited *** --- *** mRNA sequence. *** --- ************************************************ --- CREATE VIEW cryptogene AS SELECT feature_id AS cryptogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene'; --- ************************************************ --- *** relation: dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that has the qualit *** --- *** y dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_primary_transcript AS SELECT feature_id AS dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript'; --- ************************************************ --- *** relation: member_of_regulon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW member_of_regulon AS SELECT feature_id AS member_of_regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'member_of_regulon'; --- ************************************************ --- *** relation: cds_independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS with the evidence status of being *** --- *** independently known. *** --- ************************************************ --- CREATE VIEW cds_independently_known AS SELECT feature_id AS cds_independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_independently_known'; --- ************************************************ --- *** relation: orphan_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS whose predicted amino acid sequenc *** --- *** e is unsupported by any experimental evi *** --- *** dence or by any match with any other kno *** --- *** wn sequence. *** --- ************************************************ --- CREATE VIEW orphan_cds AS SELECT feature_id AS orphan_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS'; --- ************************************************ --- *** relation: cds_supported_by_domain_match_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by domain simila *** --- *** rity. *** --- ************************************************ --- CREATE VIEW cds_supported_by_domain_match_data AS SELECT feature_id AS cds_supported_by_domain_match_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data'; --- ************************************************ --- *** relation: cds_supported_by_sequence_similarity_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by sequence simi *** --- *** larity data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_sequence_similarity_data AS SELECT feature_id AS cds_supported_by_sequence_similarity_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data'; --- ************************************************ --- *** relation: cds_predicted *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is predicted. *** --- ************************************************ --- CREATE VIEW cds_predicted AS SELECT feature_id AS cds_predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_predicted'; --- ************************************************ --- *** relation: cds_supported_by_est_or_cdna_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by similarity to *** --- *** EST or cDNA data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_est_or_cdna_data AS SELECT feature_id AS cds_supported_by_est_or_cdna_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_EST_or_cDNA_data'; --- ************************************************ --- *** relation: internal_shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A Shine-Dalgarno sequence that stimulate *** --- *** s recoding through interactions with the *** --- *** anti-Shine-Dalgarno in the RNA of small *** --- *** ribosomal subunits of translating ribos *** --- *** omes. The signal is only operative in Ba *** --- *** cteria. *** --- ************************************************ --- CREATE VIEW internal_shine_dalgarno_sequence AS SELECT feature_id AS internal_shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a mature mRNA transcript *** --- *** , modified before translation or during *** --- *** translation, usually by special cis-acti *** --- *** ng signals. *** --- ************************************************ --- CREATE VIEW recoded_mrna AS SELECT feature_id AS recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'recoded_mRNA'; --- ************************************************ --- *** relation: minus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of -1. *** --- ************************************************ --- CREATE VIEW minus_1_translationally_frameshifted AS SELECT feature_id AS minus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: plus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of +1. *** --- ************************************************ --- CREATE VIEW plus_1_translationally_frameshifted AS SELECT feature_id AS plus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA where translation was sus *** --- *** pended at a particular codon and resumed *** --- *** at a particular non-overlapping downstr *** --- *** eam codon. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_translational_bypass AS SELECT feature_id AS mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: mrna_recoded_by_codon_redefinition *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA that was modified by an a *** --- *** lteration of codon meaning. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_codon_redefinition AS SELECT feature_id AS mrna_recoded_by_codon_redefinition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_codon_redefinition'; --- ************************************************ --- *** relation: recoding_stimulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A site in an mRNA sequence that stimulat *** --- *** es the recoding of a region in the same *** --- *** mRNA. *** --- ************************************************ --- CREATE VIEW recoding_stimulatory_region AS SELECT feature_id AS recoding_stimulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'recoding_stimulatory_region'; --- ************************************************ --- *** relation: four_bp_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon with 4 base *** --- *** pairs. *** --- ************************************************ --- CREATE VIEW four_bp_start_codon AS SELECT feature_id AS four_bp_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon'; --- ************************************************ --- *** relation: archaeal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron characteristic of Archaeal tRN *** --- *** A and rRNA genes, where intron transcrip *** --- *** t generates a bulge-helix-bulge motif th *** --- *** at is recognised by a splicing endoribon *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW archaeal_intron AS SELECT feature_id AS archaeal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron'; --- ************************************************ --- *** relation: trna_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron found in tRNA that is spliced *** --- *** via endonucleolytic cleavage and ligatio *** --- *** n rather than transesterification. *** --- ************************************************ --- CREATE VIEW trna_intron AS SELECT feature_id AS trna_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_intron'; --- ************************************************ --- *** relation: ctg_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon of sequence *** --- *** CTG. *** --- ************************************************ --- CREATE VIEW ctg_start_codon AS SELECT feature_id AS ctg_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CTG_start_codon'; --- ************************************************ --- *** relation: secis_element *** --- *** relation type: VIEW *** --- *** *** --- *** The incorporation of selenocysteine into *** --- *** a protein sequence is directed by an in *** --- *** -frame UGA codon (usually a stop codon) *** --- *** within the coding region of the mRNA. Se *** --- *** lenoprotein mRNAs contain a conserved se *** --- *** condary structure in the 3' UTR that is *** --- *** required for the distinction of UGA stop *** --- *** from UGA selenocysteine. The selenocyst *** --- *** eine insertion sequence (SECIS) is aroun *** --- *** d 60 nt in length and adopts a hairpin s *** --- *** tructure which is sufficiently well-defi *** --- *** ned and conserved to act as a computatio *** --- *** nal screen for selenoprotein genes. *** --- ************************************************ --- CREATE VIEW secis_element AS SELECT feature_id AS secis_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SECIS_element'; --- ************************************************ --- *** relation: retron *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence coding for a short, single-stra *** --- *** nded, DNA sequence via a retrotransposed *** --- *** RNA intermediate; characteristic of som *** --- *** e microbial genomes. *** --- ************************************************ --- CREATE VIEW retron AS SELECT feature_id AS retron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retron'; --- ************************************************ --- *** relation: three_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** downstream of the recoding site. *** --- ************************************************ --- CREATE VIEW three_prime_recoding_site AS SELECT feature_id AS three_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'three_prime_recoding_site'; --- ************************************************ --- *** relation: three_prime_stem_loop_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory region, the stem- *** --- *** loop secondary structural element is dow *** --- *** nstream of the redefined region. *** --- ************************************************ --- CREATE VIEW three_prime_stem_loop_structure AS SELECT feature_id AS three_prime_stem_loop_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure'; --- ************************************************ --- *** relation: five_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** upstream of the recoding site. *** --- ************************************************ --- CREATE VIEW five_prime_recoding_site AS SELECT feature_id AS five_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_recoding_site'; --- ************************************************ --- *** relation: flanking_three_prime_quadruplet_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Four base pair sequence immediately down *** --- *** stream of the redefined region. The rede *** --- *** fined region is a frameshift site. The q *** --- *** uadruplet is 2 overlapping codons. *** --- ************************************************ --- CREATE VIEW flanking_three_prime_quadruplet_recoding_signal AS SELECT feature_id AS flanking_three_prime_quadruplet_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal'; --- ************************************************ --- *** relation: uag_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAG stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uag_stop_codon_signal AS SELECT feature_id AS uag_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal'; --- ************************************************ --- *** relation: uaa_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uaa_stop_codon_signal AS SELECT feature_id AS uaa_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAA_stop_codon_signal'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: uga_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UGA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uga_stop_codon_signal AS SELECT feature_id AS uga_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UGA_stop_codon_signal'; --- ************************************************ --- *** relation: three_prime_repeat_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal, downstrea *** --- *** m sequence important for recoding that c *** --- *** ontains repetitive elements. *** --- ************************************************ --- CREATE VIEW three_prime_repeat_recoding_signal AS SELECT feature_id AS three_prime_repeat_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_repeat_recoding_signal'; --- ************************************************ --- *** relation: distant_three_prime_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding signal that is found many hun *** --- *** dreds of nucleotides 3' of a redefined s *** --- *** top codon. *** --- ************************************************ --- CREATE VIEW distant_three_prime_recoding_signal AS SELECT feature_id AS distant_three_prime_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distant_three_prime_recoding_signal'; --- ************************************************ --- *** relation: stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal that is a *** --- *** stop codon and has effect on efficiency *** --- *** of recoding. *** --- ************************************************ --- CREATE VIEW stop_codon_signal AS SELECT feature_id AS stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'stop_codon_signal'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene component region which acts as a *** --- *** recombinational unit of a gene whose fun *** --- *** ctional form is generated through somati *** --- *** c recombination. *** --- ************************************************ --- CREATE VIEW gene_segment AS SELECT feature_id AS gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_segment'; CREATE TABLE sequence_cv_lookup_table (sequence_cv_lookup_table_id serial not null, primary key(sequence_cv_lookup_table_id), original_cvterm_name varchar(1024), relation_name varchar(128)); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helitron','helitron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_initiator_methionine','cleaved_initiator_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epoxyqueuosine','epoxyqueuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4atac_snrna','u4atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast','kinetoplast'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shadow_enhancer','shadow_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered','engineered'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_aminomethyl_seven_deazaguanosine','seven_aminomethyl_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity','low_complexity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est_match','est_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_nonamer','v_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_21s','rrna_21s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_c_cluster','d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethyluridine','five_carboxymethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_factor','bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_methyladenosine','two_methylthio_n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dinucleotide_repeat_microsatellite_feature','dinucleotide_repeat_microsatellite_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_mrna','trans_spliced_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_c_transversion','g_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heptamer_of_recombination_feature_of_vertebrate_immune_system_gene','heptamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genotype','genotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_region','cloned_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_coding_piece','tmrna_coding_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_6s','rna_6s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle','minicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_encoding','grna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endonuclease_spliced_intron','endonuclease_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional_duplication','insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('databank_entry','databank_entry'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine','glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_cluster','v_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nickel_ion_contact_site','polypeptide_nickel_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_rna_chromosome','circular_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wc_base_pair','wc_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pcr_product','pcr_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_three_amino_three_carboxypropyl_uridine','three_three_amino_three_carboxypropyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('site_specific_recombination_target_region','site_specific_recombination_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polycistronic_transcript','gene_with_polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue','rescue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_hypersensitive_site','nuclease_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_loop','mirna_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_cdna','double_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_domain_match','supported_by_domain_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylpseudouridine','one_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n_terminal_region','n_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_result_region','experimental_result_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine_trna_primary_transcript','methionine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr','utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_terminal_residue','non_terminal_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('member_of_regulon','member_of_regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine_trna_primary_transcript','thr_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_sequence_similarity_data','cds_supported_by_sequence_similarity_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_region','polypeptide_structural_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_gene','trna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_six','beta_bulge_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_tungsten_ion_contact_site','polypeptide_tungsten_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_polypeptides_different_start_and_stop','encodes_overlapping_polypeptides_different_start_and_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_right_left_motif','polypeptide_nest_right_left_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_location','sequence_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_c_cluster','d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_transcript','trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_rna','y_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_gene','leucoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_regulatory_region','splicing_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('branch_site','branch_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_five','beta_bulge_loop_five'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakpoint','chromosome_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_uncertainty','sequence_uncertainty'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyl_n6_threonylcarbamoyladenosine','n6_methyl_n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_with_frameshift','gene_with_mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compositionally_biased_region_of_peptide','compositionally_biased_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_c_cluster','vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splice_acceptor','sequence_variant_affecting_splice_acceptor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna','pirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_hoogsteen_base_pair','reverse_hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophanyl_trna','tryptophanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_primed_cdna_clone','polya_primed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_chromosome','leucoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('status','status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_retrotransposon','ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna','rnase_p_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conjugative_transposon','conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linkage_group','linkage_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_trans_spliced_transcript','gene_with_trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_coil','peptide_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine_trna_primary_transcript','pyrrolysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_c_cluster','v_vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_sequence','phage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded','recoded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposon_fragment','transposon_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_c_cluster','vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_domain','editing_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyluridine','five_methylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_insertion','nucleotide_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutaton_causing_inframe_polypeptide_c_terminal_elongation','mutaton_causing_inframe_polypeptide_c_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon_polymeric_tract','non_ltr_retrotransposon_polymeric_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transversion','transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan','tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recursive_splice_site','recursive_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator_binding_site','insulator_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline_trna_primary_transcript','proline_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_fragment','repeat_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blocked_reading_frame','blocked_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_snorna_primary_transcript','rrna_cleavage_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_isopentenyladenosine','n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_arginine','modified_l_arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_motif','polypeptide_conserved_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t3_rna_polymerase_promoter','t3_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_duplication','inversion_derived_bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_acceptor_site','trans_splice_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosyladenosine_phosphate','two_prime_o_riboA_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rre_rna','rre_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac_end','pac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extramembrane_polypeptide_region','extramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein','intein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('twintron','twintron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_prime_o_methyluridine','five_carboxymethylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_primary_transcript','scrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_cobalt_ion_contact_site','polypeptide_cobalt_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_encoding','tmrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanked','flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ctg_start_codon','ctg_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion','inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('eukaryotic_terminator','eukaryotic_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine_trna_primary_transcript','tyrosine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_region_of_exon','coding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron_region','spliceosomal_intron_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_flanked','frt_flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_cdna_insert','cloned_cdna_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_c_cluster','v_vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated','translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_reading_frame','sequence_variation_affecting_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_minus_1_frameshift','sequence_variant_causing_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidyl_trna','histidyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sonicate_fragment','sonicate_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_recoded_mrna','gene_with_recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyluridine','two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cosmid','cosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_rna_interference','silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna','snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript','mature_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridylation_guide_snorna','pseudouridylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_gene','c_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed_gene','floxed_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spot_42_rna','spot_42_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_clone','cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr','three_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_ii_intron','group_ii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna_oligo','pna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_sequence','insertion_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('junction','junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous','paralogous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna','tna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_thiouridine','five_isopentenylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift','minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_gene_structure','sequence_variant_affecting_gene_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_three_prime_splice_site','non_canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_rrna','pseudogenic_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_turn','serine_threonine_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene','j_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_primary_transcript','strna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_eliminated_sequence','internal_eliminated_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded_gene','allelically_excluded_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('qtl','qtl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_est','three_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse','reverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_encoding','mirna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_2_prime_o_trimethylguanosine','n2_n2_2_prime_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternate_transcription_start_sites','encodes_alternate_transcription_start_sites'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array','gene_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetranucleotide_repeat_microsatellite_feature','tetranuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_aminomethyl_two_thiouridine','five_aminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_primary_transcript','monocistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_acceptor_activation','sequence_variant_causing_cryptic_splice_acceptor_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_genetic_element','mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_ligand_contact','polypeptide_ligand_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biomaterial_region','biomaterial_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_flanking_region','transposable_element_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symmetric_rna_internal_loop','symmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_1_frameshift','mrna_with_plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_regulated','transcriptionally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_intron','five_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_feature','vertebrate_immune_system_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine_methyl_ester','five_carboxyhydroxymethyl_uridine_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_gene','proplastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_trna_primary_transcript','serine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attp_site','attp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense','antisense'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat_element','terminal_inverted_repeat_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coiled_coil','coiled_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_cluster','v_vdj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_by_a_to_i_substitution','edited_transcript_by_a_to_i_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_primary_transcript','protein_coding_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mite','mite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion','insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('secis_element','secis_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle','maxicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss','tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine','cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribothymidine','ribothymidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_adjacent_residues','non_adjacent_residues'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_ribosome_entry_site','internal_ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('outron','outron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_repeat','polypeptide_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_start','clone_insert_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attr_site','attr_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv3_motif','dmv3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_mrna','capped_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_non_synonymous_codon_change_in_transcript','seq_variant_causing_non_synonymous_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_rearrangement_feature','sequence_rearrangement_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_chromosome','apicoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_two','beta_turn_type_six_a_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated','invalidated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_junction','polya_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partial_loss_of_function_of_polypeptide','seq_variant_causing_part_loss_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine','valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated_gene','translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_targeting_sequence','promoter_targeting_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polinton','polinton'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_tag','engineered_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylcytidine','five_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridine','pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated','positively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amplification_origin','amplification_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_insertional_duplication','unorient_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extrachromosomal_mobile_genetic_element','extrachromosomal_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_constitutive','transcriptionally_constitutive'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_fusion','sequence_variant_causing_polypeptide_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_region','utr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine','tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna','mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr1_motif','inr1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_acetyladenosine','n6_acetyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_splice_site','cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_two','beta_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed','floxed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_terminal_region','c_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_leucine','modified_l_leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_complex_change_in_transcript','sequence_variation_affecting_complex_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr_component','five_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_c_cluster','vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptional_cis_regulatory_region','transcriptional_cis_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_part','chromosome_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_site','insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanyl_trna','phenylalanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_est_set','overlapping_est_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gc_rich_promoter_region','gc_rich_promoter_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_two','asx_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon_loop','anticodon_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_change_in_dna_sequence','partially_characterised_change_in_dna_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv5_motif','dmv5_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl1_acceptor_site','sl1_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_region','cds_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_c_cluster','v_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_insert','engineered_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_inverted_gene','recombinationally_inverted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_array_member','cassette_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microarray_oligo','microarray_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_snrna','u12_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_est_or_cdna','supported_by_est_or_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_10_signal','minus_10_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_end','clone_insert_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr_motif','inr_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_inactive_ligand_binding_site','sequence_variant_causing_inactive_ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_stem_loop_structure','three_prime_stem_loop_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_level_of_translation_product','sequence_variant_decreasing_level_of_translation_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rflp_fragment','rflp_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_rna_polymerase_promoter','phage_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_transition','pyrimidine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrinsically_unstructured_polypeptide_region','intrinsically_unstructured_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_2_prime_o_dimethylguanosine','n2_2_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeal_intron','archaeal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna','lna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_junction','exon_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t7_rna_polymerase_promoter','t7_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_interchromosomal_transposition','invert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('episome','episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_insertional_duplication','uninvert_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_difference','sequence_difference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_c_cluster','v_d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_conflict','sequence_conflict'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_gene_fusion','sequence_variant_causing_gene_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_clone','tiling_path_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iii_intron','group_iii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_glycine','modified_glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_alteration','sequence_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyploid','polyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_modification','gene_silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_cluster','v_vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine_trna_primary_transcript','isoleucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_small_subunit_primary_transcript','rrna_small_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_component','ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_framshift','plus_2_framshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid_trna_primary_transcript','glutamic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_rearranged_at_dna_level','gene_rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript','edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_partial_processing','invalidated_by_partial_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequencing_primer','sequencing_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_for_gpi_anchor_region','cleaved_for_gpi_anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift_sequence_variation','frameshift_sequence_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_cysteine','modified_l_cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr','five_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_site','frt_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat','terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transition','transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_junction','deletion_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_one','beta_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosylguanosine_phosphate','two_prime_o_ribosylguanosine_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyl_two_prime_o_methyluridine','five_cm_2_prime_o_methU'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_transcribed_spacer_region','internal_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic','dicistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_sequence_similarity','supported_by_sequence_similarity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_primer','reverse_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_three_prime_ltr_region','u3_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine_trna_primary_transcript','glutamine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_promoter','rnapol_ii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping','overlapping'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_beta_motif','alpha_beta_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_transposable_element','engineered_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward_primer','forward_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attctn_site','attctn_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_recombination_signal_sequence','five_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conservative_amino_acid_substitution','sequence_variant_causing_conservative_amino_acid_sub'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6_snrna','u6_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_gene','recombinationally_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_threonylcarbamoyladenosine','n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyluridine','five_carbamoylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_fragment','cds_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genome','genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter','promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_gene','protein_coding_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_snrna','u5_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wybutosine','wybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylwyosine','methylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('large_subunit_rrna','large_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_substitution','sequence_variant_causing_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_2_prime_o_dimethylcytidine','n4_2_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition','c_to_t_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_transcript_sequence','sequence_variation_affecting_transcript_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bidirectional_promoter','bidirectional_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_change_of_translational_product','seq_variant_causing_partly_characterised_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated_cdna_clone','validated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('k_turn_rna_motif','k_turn_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_fragment','transcribed_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ust','five_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr_intron','three_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrogene','retrogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_to_purine_transversion','pyrimidine_to_purine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sine_element','sine_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_rst','five_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding exon_coding_region','three_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_intron','utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_3d_structural_change','sequence_variant_causing_no_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_transposition','interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_sequence_secondary_structure','rna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element','engineered_foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_rna_viral_sequence','ds_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fosmid','fosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_substitution','complex_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated','validated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_snrna','u2_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('caat_signal','caat_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_cluster','c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_region','consensus_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_spacer','vertebrate_immune_system_gene_recombination_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_trap_construct','gene_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_aptamer','rna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_induced','transcriptionally_induced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_region','rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site_part','inversion_site_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('origin_of_replication','origin_of_replication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_out_of_frame_polypeptide_c_terminal_elongation','mutation_causing_out_of_frame_polypeptide_c_terminal_elong'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_internal_loop','rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ultracontig','ultracontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptidyl','peptidyl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_region','polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_insertion','transgenic_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_antiguide','mirna_antiguide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rearranged_at_dna_level','rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_spacer','v_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strand_attribute','strand_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_increasing_level_of_transcript','sequence_variation_increasing_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced','alternatively_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formyl_two_prime_o_methylcytidine','five_formyl_two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_location','plasmid_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_bp_start_codon','four_bp_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged','recombinationally_rearranged'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chimeric_cdna_clone','chimeric_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_transcript','gene_with_dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr_component','three_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retron','retron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autopolyploid','autopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine','phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transit_peptide','transit_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_28s','rrna_28s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylinosine','one_two_prime_o_dimethylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine','threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_minor_rna_motif','a_minor_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_cluster','j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_cluster','d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_activation','sequence_variant_causing_cryptic_splice_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_arm','chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast_gene','kinetoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('line_element','line_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('solo_ltr','solo_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('external_transcribed_spacer_region','external_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_transcribed_region','non_transcribed_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_stem','mirna_stem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_c_cluster','dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hyperploid','hyperploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic','cryptic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_helix','alpha_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion','fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_cluster','vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isowyosine','isowyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric_inversion','paracentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_inframe_polypeptide_n_terminal_elongation','mutation_causing_inframe_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homing_endonuclease_binding_site','homing_endonuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna_oligo','tna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_gene','mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_fragment','restriction_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_pair','base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_antiparallel','inside_intron_antiparallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcription','sequence_variant_affecting_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_binding_site','dna_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_cytidine','modified_cytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydrophobic_region_of_peptide','hydrophobic_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_primary_transcript','polycistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_proline','modified_l_proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_feature_set','overlapping_feature_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_two','asx_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_duplication','interchromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('substitution','substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine','isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_recoding_site','three_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_of_type_2_rnapol_iii_promoter','terminator_of_type_2_rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine_trna_primary_transcript','glycine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_polypeptide_c_terminal_elongation','mutation_causing_polypeptide_c_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_heptamer','v_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dispersed_repeat','dispersed_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer','primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_transcript','sequence_variation_affecting_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type','wild_type'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_domain','polypeptide_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_synonymous_codon_change_in_transcript','seq_variant_causing_synonymous_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion_gene','fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginyl_trna','arginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_member_region','gene_member_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_intrachromosomal_transposition','uninvert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_translational_product','sequence_variant_affecting_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_base_feature','methylated_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_gene','scrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_18s','rrna_18s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_elongation','sequence_variant_causing_polypeptide_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_1','rnapol_iii_promoter_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_mutation','point_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_3d_structure_of_polypeptide','sequence_variant_affecting_3d_structure_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudoknot','pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_quartet','g_quartet'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_selenocysteine','modified_l_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop','schellmann_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna','pna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon','three_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_gene','endogenous_retroviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_segment','vertebrate_immunoglobulin_t_cell_receptor_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_translational_bypass','mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_region','engineered_foreign_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_encoding','snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_est','five_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_encoding','srp_rna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foldback_element','foldback_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_c_cluster','d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_c_cluster','dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_encoding','rrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_codon_redefinition','mrna_recoded_by_codon_redefinition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyluridine','five_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('immature_peptide_region','immature_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous','homologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metabolic_island','metabolic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_sequence','polya_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sirna','sirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_attribute','sequence_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_intron','trna_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translationally_frameshifted','plus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_motif','nucleotide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_motif','dna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_noncoding_exon','five_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_strand','beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyladenosine','one_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_oligo','ds_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_motif','asx_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oxys_rna','oxys_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxyuridine','five_hydroxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formylcytidine','five_formylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translational_frameshift','plus_1_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_exon','coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliced_leader_rna','spliced_leader_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_2prirme_o_trimethylguanosine','n2_7_2prirme_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fragment','gene_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_chromosome','mitochondrial_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyldihydrouridine','five_methyldihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide_cleavage_site','propeptide_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift','frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid','amino_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_breakpoint','translocation_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_compensatory_transcript_secondary_structure_mutation','seq_variant_caus_compensatory_trans_secondary_structure_mut'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helix_turn_helix','helix_turn_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5_8s','rrna_5_8s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('simple_sequence_length_variation','simple_sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine','methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_gene','transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_island','genomic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_segment','gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_gene','snrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_region','engineered_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptogene','cryptogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_noncoding_region','three_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_rna_interference','gene_silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_interchromosomal_transposition','d_interchr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_variant_site','natural_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly','assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_minus_2_frameshift','sequence_variant_causing_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('major_tss','major_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_missense_codon_change_in_transcript','sequence_variant_causing_missense_codon_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna','trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides','encodes_overlapping_peptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_conserved_region','nc_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('locus_control_region','locus_control_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna_oligo','s_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_chromosome','dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_b','beta_turn_type_six_b'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_gene','engineered_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wobble_base_pair','wobble_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_amino_acid_feature','modified_amino_acid_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_c_transition','t_to_c_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_sequence','apicoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irlinv_site','irlinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_sequence','synthetic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_1_polypeptide','encodes_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_transcript_stability','sequence_variant_decreasing_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iia_intron','group_iia_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomere','telomere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_intron','interior_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_mrna','edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_three','catmat_right_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_effect','sequence_variant_effect'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_duplication','tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_gene','tmrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_region','pre_edited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_hydroxynorvalylcarbamoyladenosine','n6_hydroxynorvalylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_chromosome','nucleomorphic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragmentary','fragmentary'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single','single'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('binding_site','binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanine','seven_methylguanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('target_site_duplication','target_site_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_gene','vdj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_loss_of_function_of_polypeptide','sequence_variant_causing_loss_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_nucleic_acid','bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_four','catmat_right_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome','compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_end','coding_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gap','gap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_aug_codon','upstream_aug_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_transcript','pseudogenic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('satellite_dna','satellite_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency_plus_duplication','assortment_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element','transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_sequence','endogenous_retroviral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_level_of_transcript','sequence_variation_affecting_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microsatellite','microsatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_different_polypeptides_different_stop','encodes_different_polypeptides_different_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript','primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_mrna','consensus_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_peptide_loop','membrane_peptide_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_complex_3d_structural_change','sequence_variant_causing_complex_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign','so_foreign'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_deletion','nucleotide_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_independent_bacterial_terminator','rho_independent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_deacetylation','gene_silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_c_cluster','vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cpg_island','cpg_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype','haplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylinosine','two_prime_o_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna','dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_rna_chromosome','circular_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_protein_region','mature_protein_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('b_box','b_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_zinc_ion_contact_site','polypeptide_zinc_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray_member','gene_subarray_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette','gene_cassette'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oric','oric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_breakpoint','deletion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_2_frameshift','mrna_with_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_one','asx_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_cluster','transcribed_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_decreasing_level_of_transcript','sequence_variation_decreasing_level_of_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosyl_trna','tyrosyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous','orthologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna','s_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_three_prime_splice_site','canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_exon','noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minor_tss','minor_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethylcytidine','five_two_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_chromosome','macronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_translocation','deficient_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read_pair','read_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_with_translational_frameshift','transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_3','rnapol_iii_promoter_type_3'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_transposon','dna_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orf','orf'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('right_handed_peptide_helix','right_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_left_right_motif','polypeptide_nest_left_right_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splice_donor','sequence_variant_affecting_splice_donor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topology_attribute','topology_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirtron','mirtron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_motif','polypeptide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_sequence','proplastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated_gene','negatively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_base_site','modified_base_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_encoding','c_d_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_assembly','sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bre_motif','bre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_gene','chromoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_clip','five_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path','golden_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine','alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_peptide_region','cleaved_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_cluster','v_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_region','pseudogenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna','methylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_c_cluster','v_vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_start_codon','non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_recoded_by_translational_bypass','gene_with_mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_turn_motif','polypeptide_turn_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autocatalytically_spliced_intron','autocatalytically_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile','mobile'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron','intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clip','clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dye_terminator_read','dye_terminator_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('argenine','argenine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv4_motif','dmv4_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_post_translational_processing_change','seq_variant_causing_polypeptide_post_trans_processing_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('au_rich_element','au_rich_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_breakpoint','inversion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_recoding_site','five_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_protein_coding','non_protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_intron','mobile_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment','vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_one','st_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna','rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_parallel','inside_intron_parallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron','spliceosomal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phagemid','phagemid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_block','editing_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragment_assembly','fragment_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_acceptor_piece','tmrna_acceptor_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six','beta_turn_type_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_rst','three_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine_trna_primary_transcript','cysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_gene','post_translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_repressed','transcriptionally_repressed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crm','crm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cointegrated_plasmid','cointegrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequencing_information','polypeptide_sequencing_information'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_spacer','three_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_fragment','tiling_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural','so_natural'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pi_helix','pi_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_base_call_error','possible_base_call_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('adaptive_island','adaptive_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid','uridine_five_oxyacetic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_translational_frameshift','plus_2_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous_region','homologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_utr','internal_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_level_of_translational_product','sequence_variant_affecting_level_of_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_cytoplasmic_polypeptide_region','non_cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature','experimental_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_chromosome','nuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar','exemplar'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine_trna_primary_transcript','alanine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_dimethylguanosine','n2_n2_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_hook_turn','rna_hook_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_spacer_region','transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_gene','plasmid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna','u14_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('galactosyl_queuosine','galactosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_gene','cyanelle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type_rescue_gene','wild_type_rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_intron','u12_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aptamer','aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_mrna','recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_sequence','macronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust','ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine','selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_mrna','gene_with_dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match_part','match_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_sequence','nucleomorphic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_gene','apicoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulon','regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_vector','plasmid_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tryptophan','modified_l_tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_coding_codon_change_in_transcript','seq_variant_causing_amino_acid_coding_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_chromosome_arm','free_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_primary_transcript','srp_rna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn','asx_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_binding_site','anchor_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript','rrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reading_frame','reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dhu_loop','dhu_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetylcytidine','n4_acetylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polypeptide_function','sequence_variant_affecting_polypeptide_function'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_gene','silenced_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_genomic_insert','cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_sequence_secondary_structure','dna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_match','cdna_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_flanking_region','five_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysyl_trna','pyrrolysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_cis_hydroxyisopentenyl_adenosine','two_methylthio_n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_component','repeat_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyl_three_three_amino_three_carboxypropyl_pseudouridine','one_methyl_3_3_amino_three_carboxypropyl_pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rpra_rna','rpra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_sensitive_site','nuclease_sensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_noncoding_region','five_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter','rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan_trna_primary_transcript','try_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('region','region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site','tf_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attl_site','attl_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_plasmid','natural_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_dimethyladenosine','n6_n6_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('laevosynaptic_chromosome','laevosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_structural_element','chromosomal_structural_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_array','gene_cassette_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_gene_cluster','vertebrate_immunoglobulin_t_cell_receptor_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_five_prime_splice_site','canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_protein','bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts_map','sts_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnazyme','dnazyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silent_mutation','silent_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_cluster','v_d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_duplication','bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydroxywybutosine','hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dihydrouridine','dihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_rate_of_transcription','sequence_variant_affecting_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_coding_region','five_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_one','beta_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_codon','recoded_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted','predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('resolution_site','resolution_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_cyano_seven_deazaguanosine','seven_cyano_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conformational_change','sequence_variant_causing_conformational_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_switch','conformational_switch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulated','regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_repeat','inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_a_transversion','t_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attc_site','attc_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methyladenosine','two_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cross_genome_match','cross_genome_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_repeat','tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_primary_transcript','antisense_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polyadenylation','sequence_variant_affecting_polyadenylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_collection','sequence_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polyadenylated_mrna','gene_with_polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_i_promoter','rnapol_i_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methyluridine','three_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('start_codon','start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposon','retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene','v_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_dna','chloroplast_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negative_sense_ssrna_viral_sequence','negative_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_binding_site','primer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_box','c_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid','plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biological_region','biological_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_a_transition','g_to_a_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_five_prime_splice_site','non_canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_primary_transcript','c_d_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_region','trna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_change_in_nucleotide_sequence','uncharacterised_change_in_nucleotide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_cis_hydroxyisopentenyl_adenosine','n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_sequence','chloroplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_region','exon_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_five_prime_ltr_region','r_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_c_cluster','v_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_three_prime_ltr_region','r_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna','snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylinosine','one_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene_recombination_feature','j_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_motif','polypeptide_structural_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved_region','conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('remark','remark'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_dna_contact','polypeptide_dna_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon','codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_23s','rrna_23s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna','mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycyl_trna','glycyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_sequence','cyanelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_independently_known','cds_independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator','insulator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positive_sense_ssrna_viral_sequence','positive_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_match','expressed_sequence_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_assembly_error','possible_assembly_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_snorna','u3_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unorientated_interchromosomal_transposition','unorient_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_manganese_ion_contact_site','polypeptide_manganese_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_t_transversion','g_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature_of_rearranged_gene','recombination_feature_of_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_primary_transcript','tmrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_cdna','single_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_determined','experimentally_determined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_exon','pseudogenic_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_intron','u2_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome','chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternately_spliced_transcripts','encodes_alternately_spliced_transcripts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aberrant_processed_transcript','aberrant_processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna','gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dsra_rna','dsra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_domain','intron_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_predicted','cds_predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_asparagine','modified_l_asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_nonamer','five_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl2_acceptor_site','sl2_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_primary_transcript','snrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation','translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_phenylalanine','modified_l_phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna','lincrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_valine','modified_l_valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac','yac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('signal_peptide','signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_ltr_region','r_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_gene','srp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcript_processing','sequence_variant_affecting_transcript_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_hotspot','recombination_hotspot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_c_cluster','v_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('viral_sequence','viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_terminal_inverted_repeat','five_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_thiouridine','five_mcm_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited','edited'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_start','coding_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr','three_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe1_motif','dpe1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tyrosine','modified_l_tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_c_cluster','v_d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unorientated_intrachromosomal_transposition','unorient_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_methylation','silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_inversion','deficient_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiouridine','two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thio_two_prime_o_methyluridine','two_thio_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_sequence','leucoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds','cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_polypeptide_n_terminal_elongation','mutation_causing_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_signal_sequence','polya_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_sequence','micronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamyl_trna','glutamyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_gene','strna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted_gene','paternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_chromosome','rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm3_motif','ndm3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u1_snrna','u1_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxymethylcytidine','five_hydroxymethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature','recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_disjoint_polypeptides','encodes_disjoint_polypeptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated','post_translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_fusion_gene','engineered_fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_recombination_signal_sequence','three_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causes_exon_loss','sequence_variant_causes_exon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate','intermediate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_calcium_ion_contact_site','polypeptide_calcium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic_region','syntenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sugar_edge_base_pair','sugar_edge_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_gene','engineered_foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetyl_2_prime_o_methylcytidine','n4_acetyl_2_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_by_ab_initio_computation','predicted_by_ab_initio_computation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_secondary_structure','polypeptide_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna_gene','ncrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_junction_loop','rna_junction_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype_block','haplotype_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oriv','oriv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ambisense_ssrna_viral_sequence','ambisense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_oligo','morpholino_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere','centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_gene','epigenetically_modified_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_inversion','chromosomal_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_35_signal','minus_35_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_two_prime_o_dimethyluridine','three_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_thiouridine','four_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_end_site','transcription_end_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_mirna','pre_mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteinyl_trna','cysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_three','catmat_left_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_seven','schellmann_loop_seven'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_c_cluster','v_vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_insertion_site','transposable_element_insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_element','translocation_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript_region','mirna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan_cds','orphan_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_mrna','monocistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_transposable_element','natural_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path_fragment','golden_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lipoprotein_signal_peptide','lipoprotein_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_large_subunit_primary_transcript','rrna_large_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_rna_chromosome','linear_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_rate_of_transcription','sequence_variant_increasing_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_sequence','plastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irrinv_site','irrinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_plasmid','integrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_methionine','modified_l_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_sequence','chromoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_rna_chromosome','linear_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_trap_construct','promoter_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_read','contig_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanosine','seven_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_selenocysteine','stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn','gamma_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionyl_trna','methionyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna','tmrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna','cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_binding_site','nuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid_methyl_ester','uridine_five_oxyacetic_acid_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_race_clone','three_prime_race_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_dna_chromosome','circular_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_histidine','modified_l_histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss_region','tss_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated_gene','positively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus','consensus'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integron','integron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_metal_contact','polypeptide_metal_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_loop','d_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decayed_exon','decayed_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_inosine','modified_inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_three_prime_overlap','three_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_five_prime_overlap','three_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_cluster','v_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop','beta_bulge_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_mutation','intrachromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv2_motif','dmv2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_region','intergenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_glycinylcarbamoyladenosine','n6_glycinylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_feature','sequence_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_rna','antisense_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_cis_splice_site','three_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_classic','gamma_turn_classic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rapd','rapd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cca_tail','cca_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_ring_chromosome','inverted_ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_dna_chromosome','linear_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_g_transversion','t_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bruno_response_element','bruno_response_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_five_prime_ltr_region','u5_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_a_transversion','c_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distant_three_prime_recoding_signal','distant_three_prime_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronucleus_destined_segment','macronucleus_destined_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_mrna','pre_edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac','pac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base','base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_mrna','polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_redefined','codon_redefined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_prime_o_methyluridine','five_methoxycarbonylmethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match','match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_read_through','gene_with_stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparaginyl_trna','asparaginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonyl_trna','threonyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_five_prime_ltr_region','u3_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr','five_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_gene','vj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_methylguanosine','n2_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_dependent_bacterial_terminator','rho_dependent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_flanking_region','three_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomically_contaminated_cdna_clone','genomically_contaminated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_target_site','mirna_target_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_guide_sequence','internal_guide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_three_prime_ltr_region','u5_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutation_causing_out_of_frame_polypeptide_n_terminal_elongation','mutation_causing_out_of_frame_polypeptide_n_terminal_elong'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('undermodified_hydroxywybutosine','undermodified_hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('introgressed_chromosome_region','introgressed_chromosome_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_frameshifted','translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_deletion','chromosomal_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine','leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna_primary_transcript','methylation_guide_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced','trans_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_uridine','five_isopentenylaminomethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_threonyl_carbamoyladenosine','two_methylthio_n6_threonyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon','stop_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_change_of_translational_product','sequence_variant_causing_no_change_of_translational_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biochemical_region_of_peptide','biochemical_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interband','interband'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert','clone_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_constraint_sequence','dna_constraint_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snp','snp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_chromosome','chromoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tata_box','tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_25s','rrna_25s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_gene','plastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_one','asx_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_transcript_stability','sequence_variant_increasing_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_uridine','modified_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysyl_trna','lysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intramembrane_polypeptide_region','intramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rr_tract','rr_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript_region','rrna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced_transcript','alternatively_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_dna_viral_sequence','ds_dna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_duplication','chromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_encoding','scrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_copper_ion_contact_site','polypeptide_copper_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_isoleucine','modified_l_isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone','clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hetero_compound_chromosome','hetero_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray','gene_subarray'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_transcript','dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_methylation','silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_change_in_transcript','seq_variant_causing_partly_characterised_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_loop','t_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_serine','modified_l_serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiocytidine','two_thiocytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_repeat_recoding_signal','three_prime_repeat_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna','srp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_binding_motif','polypeptide_binding_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylguanosine','two_prime_o_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_truncation','sequence_variant_causing_polypeptide_truncation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box','a_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_vertebrate_immune_system_gene','recombinationally_rearranged_vertebrate_immune_system_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylguanosine','one_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamine','modified_l_glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant','sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_length_variation','sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_encoding','strna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift','plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topologically_defined_region','topologically_defined_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_cds','edited_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_modification','gene_silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('e_box_motif','e_box_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_subunit_rrna','small_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnasei_hypersensitive_site','dnasei_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_c_cluster','v_d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome_arm','compound_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('feature_attribute','feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_match','protein_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_splicing','sequence_variant_affecting_splicing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_variation','chromosome_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_motif','serine_threonine_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded','allelically_excluded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_aneuploid','assortment_derived_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino','morpholino'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_prime_o_methyluridine','five_isopentenylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna_oligo','gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_variation','copy_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced','silenced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylcytidine','three_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dexstrosynaptic_chromosome','dexstrosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_insertional_duplication','inverted_insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_mini_gene','rescue_mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_four','catmat_left_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternate_sequence_site','alternate_sequence_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_iron_ion_contact_site','polypeptide_iron_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition_at_pcpg_site','c_to_t_transition_at_pcpg_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_molybdenum_ion_contact_site','polypeptide_molybdenum_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine_trna_primary_transcript','phe_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_primary_transcript','h_aca_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna','r_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_transposition','intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_polypeptide_localization_change','sequence_variant_causing_polypeptide_localization_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_a','methylated_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_16s','rrna_16s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_methylcytidine','n4_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('riboswitch','riboswitch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_duplication','assortment_derived_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_regulatory_element','chromosomal_regulatory_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_partially_characterised_3d_structural_change','seq_var_causing_partly_characterised_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_five_prime_overlap','five_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozymic','ribozymic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_deficiency','inversion_derived_bipartite_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_contamination','invalidated_by_genomic_contamination'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_cluster','vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_change_of_translational_product','sequence_variant_causing_uncharacterised_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_number_variation','chromosome_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_attribute','gene_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uag_stop_codon_signal','uag_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_match','nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified','epigenetically_modified'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_two','st_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_duplication','inversion_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_selenouridine','five_methylaminomethyl_two_selenouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid_trna_primary_transcript','aspartic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_mt_pseudogene','nuclear_mt_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exonic_splice_enhancer','exonic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4_snrna','u4_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('csrb_rsmb_rna','csrb_rsmb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_1_intron_homing_endonuclease_target_region','group_1_intron_homing_endonuclease_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crispr','crispr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_no_change_in_transcript','sequence_variant_causing_no_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_gene','snorna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_junction','trans_splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_three_prime_quadruplet_recoding_signal','flanking_three_prime_quadruplet_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_cluster','v_vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_pseudogene','cassette_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_modification','silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_gene','proviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine','five_carboxyhydroxymethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mt_gene','mt_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_rna_chromosome','single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_stimulatory_region','recoding_stimulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyluridine','five_taurinomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_threonine','modified_l_threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_cluster','v_d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_oligo','synthetic_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_to_pyrimidine_transversion','purine_to_pyrimidine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonsense_codon_change_in_transcript','sequence_variant_causing_nonsense_codon_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antiparallel_beta_strand','antiparallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('central_hydrophobic_region_of_signal_peptide','central_hydrophobic_region_of_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_mobile_genetic_element','integrated_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('parallel_beta_strand','parallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_cluster','v_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dre_motif','dre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon','non_ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna_oligo','r_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autoregulated','autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_lysine','modified_l_lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_end','bac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine','pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine','lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_protein_contact','protein_protein_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site','splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_translocation','chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epitope','epitope'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allele','allele'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_n4_2_prime_o_trimethylcytidine','n4_n4_2_prime_o_trimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_ltr_region','u5_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_gene','rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_transposable_element','transgenic_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_region','polypeptide_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts','sts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_c_transversion','a_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_ii_rna','class_ii_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nonamer_of_recombination_feature_of_vertebrate_immune_system_gene','nonamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unedited_region','unedited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_increasing_level_of_translation_product','sequence_variant_increasing_level_of_translation_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lambda_vector','lambda_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene','gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanyl_trna','alanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('virtual_sequence','virtual_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iib_intron','group_iib_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposed','retrotransposed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_2_frameshift','mrna_with_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymer_attribute','polymer_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autosynaptic_chromosome','autosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_helix','peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_processed_cdna_clone','partially_processed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst_match','rst_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted','paternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_gene','predicted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('robertsonian_fusion','robertsonian_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylpseudouridine','two_prime_o_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric_inversion','pericentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartyl_trna','aspartyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna','strna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_intron','three_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear','linear'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_nonamer','j_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_t_transversion','a_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('idna','idna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_7_trimethylguanosine','n2_n2_7_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_chromosomal_mutation','complex_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_aneuploid','inversion_derived_deficiency_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asymmetric_rna_internal_loop','asymmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion','deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyclic_translocation','cyclic_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ars','ars'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutaminyl_trna','glutaminyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allopolyploid','allopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replicon','replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylcytidine','two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_one','st_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous_region','paralogous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript_region','mature_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_frameshift','mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_cluster','d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle_gene','maxicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_two','st_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_encoding','snrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_spacer','five_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read','read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine_trna_primary_transcript','arg_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo_u_tail','oligo_u_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_pseudoknot','recoding_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_thiouridine','five_mam_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic','monocistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frame_restoring_sequence_variant','frame_restoring_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transmembrane_polypeptide_region','transmembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vector_replicon','vector_replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrosequenced_read','pyrosequenced_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_magnesium_ion_contact_site','polypeptide_magnesium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_transcript','polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_site','polya_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_duplication','free_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_structure_variation','chromosome_structure_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_rna_base_feature','modified_rna_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutated_variant_site','mutated_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gaga_motif','gaga_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_mutation','interchromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prophage','prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic','syntenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_repetitive_element','engineered_foreign_repetitive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translated_nucleotide_match','translated_nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna','h_aca_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vault_rna','vault_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan','orphan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_dna_chromosome','linear_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_greater_than_1_polypeptide','encodes_greater_than_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('atti_site','atti_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_deacetylation','silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reagent','reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_fission','chromosome_fission'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ct_gene','ct_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_primary_transcript','capped_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_initiator_codon_change_in_transcript','sequence_variant_causing_initiator_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylinosine','methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_spacer','j_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine','glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_guanosine','modified_guanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_dimethylguanosine','n2_7_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonconservative_amino_acid_substitution','sequence_variant_causing_nonconservative_amino_acid_sub'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_heptamer','three_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_cdna_clone','invalidated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator','terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stem_loop','stem_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr_intron','five_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_plus_2_frameshift','sequence_variant_causing_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_band','chromosome_band'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_exon_donor_rna','mini_exon_donor_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid','aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyl_2_thiouridine','five_methyl_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_methylation','gene_silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element_gene','engineered_foreign_transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_pseudogene','processed_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supercontig','supercontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_encoding','trna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal_chromosomal_translocation','reciprocal_chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hoogsteen_base_pair','hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_transition','purine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna','c_d_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_primary_transcript','snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_cluster','v_vj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_ltr_region','u3_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attenuator','attenuator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_noncoding_exon','three_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna_primary_transcript','u14_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene_recombination_feature','d_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mte','mte'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variation_affecting_coding_sequence','sequence_variation_affecting_coding_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gcvb_rna','gcvb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst','rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operator','operator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ring_chromosome','ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm2_motif','ndm2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine_trna_primary_transcript','selenocysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_feature','edited_transcript_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_pyrrolysine','stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homo_compound_chromosome','homo_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_gene','foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_demethylwyosine','four_demethylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna','guide_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylpseudouridine','three_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_aneuploid_chromosome','inversion_derived_aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('specific_recombination_site','specific_recombination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inosine','inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_transposable_element','foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene','d_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_inversion','bipartite_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_plasmid','engineered_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group_regulatory_region','gene_group_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vd_gene','vd_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region','regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_decreasing_rate_of_transcription','sequence_variant_decreasing_rate_of_transcription'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna_region','guide_rna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence variant_affecting_transcript_stability','sequence_variant_affecting_transcript_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_ten_helix','three_ten_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sarcin_like_rna_motif','sarcin_like_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_translationally_frameshifted','minus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_alanine','modified_l_alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_deletion','sequence_variant_causing_amino_acid_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_cum_translocation','inversion_cum_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tag','tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_interchromosomal_transposition','uninvert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_gene','cryptic_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic','transgenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_clone','genomic_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakage_sequence','chromosome_breakage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_cluster','d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_one','beta_turn_type_six_a_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribosome_entry_site','ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('left_handed_peptide_helix','left_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_aptamer','dna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('i_motif','i_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_intrachromosomal_transposition','d_intrachr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_dna_chromosome','single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_c','methylated_c'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligation_based_read','ligation_based_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_assembly','expressed_sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethyluridine','five_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine_trna_primary_transcript','histidine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous_region','orthologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine_trna_primary_transcript','valine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon_member','operon_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group','gene_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposition','transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_regulatory_ncrna','small_regulatory_ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_duplication','intrachromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uaa_stop_codon_signal','uaa_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift','minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('organelle_sequence','organelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_prophage','cryptic_prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micf_rna','micf_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_tandem_duplication','direct_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved','conserved'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna','telomerase_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6atac_snrna','u6atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attb_site','attb_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array_member','gene_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated_mrna','polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symbiosis_island','symbiosis_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_junction','splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fingerprint_map','fingerprint_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wyosine','wyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uga_stop_codon_signal','uga_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cytoplasmic_polypeptide_region','cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylguanosine','one_two_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rh_map','rh_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_modification','silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon','anticodon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_deazaguanosine','seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine','asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('probe','probe'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('defective_conjugative_transposon','defective_conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeosine','archaeosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('molecular_contact_region','molecular_contact_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_structure','membrane_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_collection','contig_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetraloop','tetraloop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_conserved_region','coding_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('long_terminal_repeat','long_terminal_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_signal_feature','vertebrate_immune_system_gene_recombination_signal_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('untranslated_region_polycistronic_mrna','untranslated_region_polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine_trna_primary_transcript','leucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_dna_chromosome','circular_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucyl_trna','isoleucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_breakpoint','insertion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgene','transgene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_region','mrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_attribute','transcript_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_staple_motif','serine_threonine_staple_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding','protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_bound_by_factor','enhancer_bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_by_translational_bypass','recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon','operon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_transcript','monocistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_amino_acid_insertion','sequence_variant_causing_amino_acid_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated','polyadenylated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unigene_cluster','unigene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_gene_cluster','vertebrate_ig_t_cell_receptor_rearranged_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_member','gene_cassette_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_read_through','stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_transcript_with_translational_frameshift','gene_with_transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mnp','mnp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid','glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_polypeptide_amino_acid_sequence','sequence_variant_affecting_polypeptide_amino_acid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn','beta_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pathogenic_island','pathogenic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust_match','ust_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_conservative_missense_codon_change_in_transcript','seq_var_causing_conservative_missense_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_protein','transcript_bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyladenosine','n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_chromosome','cyanelle_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orit','orit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted','maternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_chromosome','chloroplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle_gene','minicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_catalytic_motif','polypeptide_catalytic_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_2','rnapol_iii_promoter_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('no_output','no_output'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_coding_exon','interior_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyl_two_thiouridine','five_taurinomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide','polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymerase_synthesis_read','polymerase_synthesis_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_binding_site','enhancer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_two','beta_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_polya_primed_cdna','invalidated_by_genomic_polya_primed_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_edited_transcript','gene_with_edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv1_motif','dmv1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_modified_region','post_translationally_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline','proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_region','flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_isopentenyladenosine','two_methylthio_n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypyrimidine_tract','polypyrimidine_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxyuridine','five_methoxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_to_gene_feature','gene_to_gene_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_cloned_genomic_insert','bac_cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_heptamer','j_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ust','three_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_2_prime_o_dimethyladenosine','n6_2_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_site','trans_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_rescue_region','engineered_rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorph_gene','nucleomorph_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_attribute','mrna_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_three_prime_overlap','five_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_i_intron','group_i_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_cluster','d_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_dna','genomic_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron','inside_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hammerhead_ribozyme','hammerhead_ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_heptamer','five_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_splice_enhancer','intronic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_adenosine','modified_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyluridine','five_carboxymethylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_region','repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_unit','repeat_unit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_dna_chromosome','double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('template_region','template_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript_region','primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_dna','mitochondrial_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_region','transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozyme','ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('matrix_attachment_site','matrix_attachment_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('imprinted','imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est','est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_motif','rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_variation_site','polypeptide_variation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_i_rna','class_i_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo','oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_signal','stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hypoploid','hypoploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar_mrna','exemplar_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_g_transversion','c_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('active_peptide','active_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mannosyl_queuosine','mannosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_pyrrolysine','gene_with_stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('queuosine','queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna_oligo','lna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('independently_known','independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causes_intron_gain','sequence_variant_causes_intron_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_region','proviral_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped','capped'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direction_attribute','direction_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_chromosome','micronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene_by_unequal_crossing_over','pseudogene_by_unequal_crossing_over'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethyladenosine','one_two_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe_motif','dpe_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seryl_trna','seryl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integration_excision_site','integration_excision_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_region_of_exon','noncoding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna','rnase_mrp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyluridine','five_methoxycarbonylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_of_single_exon_gene','exon_of_single_exon_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_primary_transcript','gene_with_dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_secondary_structure','sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path','tiling_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_sequence','nuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig','contig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catalytic_residue','catalytic_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site','inversion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid','aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dif_site','dif_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_gene','mirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valyl_trna','valyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_tandem_duplication','inverted_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_regulatory_frameshift_element','cis_regulatory_frameshift_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minisatellite','minisatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_component','assembly_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity_region','low_complexity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('designed_sequence','designed_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_2_prime_o_trimethyladenosine','n6_n6_2_prime_o_trimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_promoter','rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene_recombination_feature','v_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_thiouridine','five_carboxymethylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_ring_duplication','free_ring_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_mrna','dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_chromosomal_mutation','uncharacterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_cis_splice_site','five_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('octamer_motif','octamer_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides_different_start','encodes_overlapping_peptides_different_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_rna_viral_sequence','ss_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('indel','indel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_primary_transcript','dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_binding_site','protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic','polycistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine_trna_primary_transcript','asparagine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_enhancer','splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid_chromosome','aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peroxywybutosine','peroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_aspartic_acid','modified_l_aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_episome','engineered_episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnai_reagent','rnai_reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rasirna','rasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_region','tmrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_gain_of_function_of_polypeptide','sequence_variant_causing_gain_of_function_of_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter','bacterial_rnapol_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_sequence','mitochondrial_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trinucleotide_repeat_microsatellite_feature','trinuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_stability','post_translationally_regulated_by_protein_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_primary_transcript','nc_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_cryptic_splice_donor_activation','sequence_variant_causing_cryptic_splice_donor_activation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('iron_responsive_element','iron_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_cluster','v_d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward','forward'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_location','proviral_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_binding_site','histone_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pse_motif','pse_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_eight','beta_turn_type_eight'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double','double'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_nonconservative_missense_codon_change_in_transcript','seq_var_causing_nonconserv_missense_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_complex_change_of_translational_product','sequence_variant_causing_complex_change_of_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_est_or_cdna_data','cds_supported_by_est_or_cdna_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_rna_chromosome','double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamic_acid','modified_l_glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_motif','polypeptide_nest_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_frameshift','translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_terminal_inverted_repeat','three_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_trna','pseudogenic_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cap','cap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon','five_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic','enzymatic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_exon','interior_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_g_transition','a_to_g_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_inactive_catalytic_site','sequence_variant_causing_inactive_catalytic_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine','two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted_gene','maternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_terminator_codon_change_in_transcript','sequence_variant_causing_terminator_codon_change_in_trans'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular','circular'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_pseudoknot','h_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript','transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene','pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_duplication','nucleotide_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_repeat','direct_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_terminator','bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('diplotype','diplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_3d_structural_change','seq_variant_causing_uncharacterised_3d_structural_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_gene','dj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyladenosine','two_prime_o_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_plus_1_frameshift_mutation','sequence_variant_causing_plus_1_frameshift_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_binding_site','restriction_enzyme_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac','bac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_cluster','dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_donor_site','trans_splice_donor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleic_acid','nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_chimeric_cdna','invalidated_by_chimeric_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine','histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_component_region','gene_component_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_match','primer_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_primary_transcript','trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loxp_site','loxp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine','serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide','propeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_open_reading_frame','five_prime_open_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_six','schellmann_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shine_dalgarno_sequence','shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sp6_rna_polymerase_promoter','sp6_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_editing','sequence_variant_affecting_editing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_regulatory_region','sequence_variant_affecting_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine_trna_primary_transcript','lysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_c_cluster','j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency','assortment_derived_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript','mirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5s','rrna_5s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucyl_trna','leucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_intrachromosomal_transposition','invert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic_rna','enzymatic_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated','negatively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_region','anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon','exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a','beta_turn_type_six_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('random_sequence','random_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_chromosomal_mutation','partially_characterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna','rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_transcript_secondary_structure','sequence_variant_affecting_transcript_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_oligo','ss_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_duplication_plus_aneuploid','inversion_derived_duplication_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_nucleic_acid','transcript_bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein_containing','intein_containing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_encoding','h_aca_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_rna','rrna_cleavage_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_trap_construct','enhancer_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_causing_uncharacterised_change_in_transcript','seq_variant_causing_uncharacterised_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_inverse','gamma_turn_inverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_nonamer','three_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteinyl_trna','selenocysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_methylation','gene_silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u11_snrna','u11_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna','scrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant_affecting_copy_number','sequence_variant_affecting_copy_number'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_selenocysteine','gene_with_stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silencer','silencer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sage_tag','sage_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_1_frameshift','mrna_with_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_gene','nuclear_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_domain_match_data','cds_supported_by_domain_match_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_shine_dalgarno_sequence','internal_shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prolyl_trna','prolyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysidine','lysidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge','beta_bulge'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_modification','post_translationally_regulated_by_protein_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna','ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_gene','grna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer','enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_sequence_variant','polymorphic_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_clip','three_prime_clip'); CREATE INDEX sequence_cv_lookup_table_idx ON sequence_cv_lookup_table (original_cvterm_name); SET search_path=public,pg_catalog; -- DEPENDENCY: -- chado/modules/bridges/sofa-bridge.sql -- The standard Chado pattern for protein coding genes -- is a feature of type 'gene' with 'mRNA' features as parts -- REQUIRES: 'mrna' view from so-bridge.sql CREATE OR REPLACE VIEW protein_coding_gene AS SELECT DISTINCT gene.* FROM feature AS gene INNER JOIN feature_relationship AS fr ON (gene.feature_id=fr.object_id) INNER JOIN so.mrna ON (mrna.feature_id=fr.subject_id); -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE SCHEMA frange; SET search_path = frange,public,pg_catalog; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public,pg_catalog; --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from general -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id int not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'cvterm' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id --SELECT feature_id, 'expression' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.expression_id = s.expression_id --UNION ALL --SELECT fg.feature_id, 'genotype' AS type, g.uniquename||': '||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE g.gcontext_id = fg.gcontext_id --UNION ALL --SELECT feature_id, 'genotype' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.genotype_id = s.genotype_id --UNION ALL --SELECT feature_id, 'phenotype' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.phenotype_id = s.phenotype_id UNION ALL SELECT feature_id, 'synonym' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of') UNION ALL SELECT fr.subject_id as feature_id, 'Derived_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from') UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; --replaced with Rob B's improved view CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''cvterm'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id --UNION --SELECT feature_id, ''expression'' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id --UNION --SELECT fg.feature_id, ''genotype'' AS type, g.uniquename||'': ''||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id --UNION --SELECT feature_id, ''genotype'' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id --UNION --SELECT feature_id, ''phenotype'' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id UNION SELECT feature_id, ''synonym'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255),organism_id integer -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); chado-1.23/schemas/1-1.23/diff.sql000644 000765 000024 00000000000 11665754254 016374 0ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.22/diff.sql000644 000765 000024 00000000000 11661243501 016353 0ustar00cainstaff000000 000000 chado-1.23/schemas/1-1.21/diff.sql000644 000765 000024 00000126226 11660531725 016404 0ustar00cainstaff000000 000000 --Note that the so schema is left out of this diff ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; ALTER TABLE feature_synonym ALTER COLUMN is_current SET DEFAULT 'false'; CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; ALTER TABLE analysisprop ADD COLUMN rank int not null default 0; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); ALTER TABLE phenotype_comparison_cvterm ADD CONSTRAINT phenotype_comparison_cvterm_pub_id_fkey FOREIGN KEY (pub_id) REFERENCES pub(pub_id) ON DELETE CASCADE; create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; --start 1.11-1.2 diff create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1-1.2/diff.sql000644 000765 000024 00000126226 11627536455 016333 0ustar00cainstaff000000 000000 --Note that the so schema is left out of this diff ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; ALTER TABLE feature_synonym ALTER COLUMN is_current SET DEFAULT 'false'; CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; ALTER TABLE analysisprop ADD COLUMN rank int not null default 0; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); ALTER TABLE phenotype_comparison_cvterm ADD CONSTRAINT phenotype_comparison_cvterm_pub_id_fkey FOREIGN KEY (pub_id) REFERENCES pub(pub_id) ON DELETE CASCADE; create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; --start 1.11-1.2 diff create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; ALTER TABLE genetic_code.gencode_startcodon ADD CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ); ALTER TABLE phenotype ADD COLUMN name TEXT default null; ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL; ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE; create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; ALTER TABLE stock alter organism_id drop not null; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; alter table stock_cvterm add column is_not boolean not null default false; alter table stock_cvterm add column rank integer not null default 0; alter table stock_cvterm drop constraint stock_cvterm_c1; alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ; create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/schemas/1-1.11/diff.sql000644 000765 000024 00000040246 11554362152 016376 0ustar00cainstaff000000 000000 --Note that the so schema is left out of this diff ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; ALTER TABLE feature_synonym ALTER COLUMN is_current SET DEFAULT 'false'; CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; ALTER TABLE analysisprop ADD COLUMN rank int not null default 0; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); ALTER TABLE phenotype_comparison_cvterm ADD CONSTRAINT phenotype_comparison_cvterm_pub_id_fkey FOREIGN KEY (pub_id) REFERENCES pub(pub_id) ON DELETE CASCADE; create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; chado-1.23/schemas/1-1.1/diff.sql000644 000765 000024 00000040246 11554360246 016317 0ustar00cainstaff000000 000000 --Note that the so schema is left out of this diff ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; ALTER TABLE feature_synonym ALTER COLUMN is_current SET DEFAULT 'false'; CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; ALTER TABLE analysisprop ADD COLUMN rank int not null default 0; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); ALTER TABLE phenotype_comparison_cvterm ADD CONSTRAINT phenotype_comparison_cvterm_pub_id_fkey FOREIGN KEY (pub_id) REFERENCES pub(pub_id) ON DELETE CASCADE; create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, gffdbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; chado-1.23/schemas/1/default_schema.sql000644 000765 000024 00000761603 11554343135 020063 0ustar00cainstaff000000 000000 -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $1; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) ); SET search_path = public; -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql'; -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE SCHEMA frange; SET search_path = frange,public; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public; --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, constraint analysisprop_c1 unique (analysis_id,type_id,value) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado phenotype module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( pub_id INT NOT NULL, phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from general -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id int not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- $Id: default_schema.sql,v 1.53 2008-03-28 16:05:24 scottcain Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'cvterm' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id --SELECT feature_id, 'expression' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.expression_id = s.expression_id --UNION ALL --SELECT fg.feature_id, 'genotype' AS type, g.uniquename||': '||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE g.gcontext_id = fg.gcontext_id --UNION ALL --SELECT feature_id, 'genotype' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.genotype_id = s.genotype_id --UNION ALL --SELECT feature_id, 'phenotype' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.phenotype_id = s.phenotype_id UNION ALL SELECT feature_id, 'synonym' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of') UNION ALL SELECT fr.subject_id as feature_id, 'Derived_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from') UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, dbx.accession, cv.name, fl.fmin+1, fl.fmax, af.significance, fl.strand, fl.phase, f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN feature_dbxref fd ON (f.feature_id = fd.feature_id) LEFT JOIN dbxref dbx ON (dbx.dbxref_id = fd.dbxref_id AND dbx.db_id IN (select db_id from db where db.name = 'GFF_source')) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''cvterm'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id --UNION --SELECT feature_id, ''expression'' AS type, s.description AS attribute --FROM expression s, feature_expression fs --WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id --UNION --SELECT fg.feature_id, ''genotype'' AS type, g.uniquename||'': ''||g.description AS attribute --FROM gcontext g, feature_gcontext fg --WHERE fg.feature_id= $1 AND g.gcontext_id = fg.gcontext_id --UNION --SELECT feature_id, ''genotype'' AS type, s.description AS attribute --FROM genotype s, feature_genotype fs --WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id --UNION --SELECT feature_id, ''phenotype'' AS type, s.description AS attribute --FROM phenotype s, feature_phenotype fs --WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id UNION SELECT feature_id, ''synonym'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255) -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name FROM feature UNION SELECT feature_id, name FROM feature where name is not null UNION SELECT fs.feature_id,s.name FROM feature_synonym fs, synonym s WHERE fs.synonym_id = s.synonym_id ; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); chado-1.23/modules/audit/000755 000765 000024 00000000000 12061672376 015362 5ustar00cainstaff000000 000000 chado-1.23/modules/bin/000755 000765 000024 00000000000 12061672375 015023 5ustar00cainstaff000000 000000 chado-1.23/modules/cell_line/000755 000765 000024 00000000000 12061672375 016201 5ustar00cainstaff000000 000000 chado-1.23/modules/companalysis/000755 000765 000024 00000000000 12061672376 016756 5ustar00cainstaff000000 000000 chado-1.23/modules/contact/000755 000765 000024 00000000000 12061672376 015707 5ustar00cainstaff000000 000000 chado-1.23/modules/cv/000755 000765 000024 00000000000 12061672376 014664 5ustar00cainstaff000000 000000 chado-1.23/modules/default_nofuncs.sql000644 000765 000024 00000574720 11634146122 020161 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; -- ================================================ -- TABLE: cvprop -- ================================================ create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: chadoprop -- ================================================ create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL, CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3), CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) ); SET search_path = public,pg_catalog; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- 05-31-2011 -- added 'name' column to phenotype. non-unique human readable field. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, name TEXT default null, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- changes 2011-05-31 -- added type_id to genotype (can be null for backward compatibility) -- added genotypeprop table -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- ================================================ -- TABLE: genotypeprop -- ================================================ create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import contact from contact -- ================================================================= -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; -- ================================================ -- TABLE: projectprop -- ================================================ CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from project -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_cvterm -- ================================================ CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id integer not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_cvtermprop -- ================================================ create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- ================================================ -- TABLE: stock_dbxrefprop -- ================================================ create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/modules/default_schema.sql000644 000765 000024 00010210753 11635706630 017747 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $2; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; -- ================================================ -- TABLE: cvprop -- ================================================ create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: chadoprop -- ================================================ create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL, CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3), CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) ); SET search_path = public,pg_catalog; -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql'; -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); --function to 'unshare' exons. It looks for exons that have the same fmin --and fmax and belong to the same gene and only keeps one. The other, --redundant exons are marked obsolete in the feature table. Nothing --is done with those features' entries in the featureprop, feature_dbxref, --feature_pub, or feature_cvterm tables. For the moment, I'm assuming --that any annotations that they have when this script is run are --identical to their non-obsoleted doppelgangers. If that's not the case, --they could be merged via query. -- --The bulk of this code was contributed by Robin Houston at --GeneDB/Sanger Centre. CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; /* Choose one of the shared exons to be the canonical representative. We pick the one with the smallest feature_id. */ CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; --This is an automatically generated file; do not edit it as changes will not --be saved. Instead, modify bin/create-so-bridge.pl, which creates this file. CREATE SCHEMA so; SET search_path=so,public,pg_catalog; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent greate *** --- *** r than zero. A nucleotide region is comp *** --- *** osed of bases and a polypeptide region i *** --- *** s composed of amino acids. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region'; --- ************************************************ --- *** relation: sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded sequence. *** --- ************************************************ --- CREATE VIEW sequence_secondary_structure AS SELECT feature_id AS sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure'; --- ************************************************ --- *** relation: g_quartet *** --- *** relation type: VIEW *** --- *** *** --- *** G-quartets are unusual nucleic acid stru *** --- *** ctures consisting of a planar arrangemen *** --- *** t where each guanine is hydrogen bonded *** --- *** by hoogsteen pairing to another guanine *** --- *** in the quartet. *** --- ************************************************ --- CREATE VIEW g_quartet AS SELECT feature_id AS g_quartet_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet'; --- ************************************************ --- *** relation: interior_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_coding_exon AS SELECT feature_id AS interior_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon'; --- ************************************************ --- *** relation: satellite_dna *** --- *** relation type: VIEW *** --- *** *** --- *** The many tandem repeats (identical or re *** --- *** lated) of a short basic repeating unit; *** --- *** many have a base composition or other pr *** --- *** operty different from the genome average *** --- *** that allows them to be separated from t *** --- *** he bulk (main band) genomic DNA. *** --- ************************************************ --- CREATE VIEW satellite_dna AS SELECT feature_id AS satellite_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** One of a pair of sequencing reads in whi *** --- *** ch the two members of the pair are relat *** --- *** ed by originating at either end of a clo *** --- *** ne insert. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding AS SELECT feature_id AS protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding'; --- ************************************************ --- *** relation: non_protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW non_protein_coding AS SELECT feature_id AS non_protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding'; --- ************************************************ --- *** relation: scrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of any one of sev *** --- *** eral small cytoplasmic RNA molecules pre *** --- *** sent in the cytoplasm and sometimes nucl *** --- *** eus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna_primary_transcript AS SELECT feature_id AS scrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA sequence, present *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: inr_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters required f *** --- *** or the correct positioning of the polyme *** --- *** rase for the start of transcription. Ove *** --- *** rlaps the TSS. The mammalian consensus s *** --- *** equence is YYAN(T|A)YY; the Drosophila c *** --- *** onsensus sequence is TCA(G|T)t(T|C). In *** --- *** each the A is at position +1 with respec *** --- *** t to the TSS. Functionally similar to th *** --- *** e TATA box element. *** --- ************************************************ --- CREATE VIEW inr_motif AS SELECT feature_id AS inr_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif'; --- ************************************************ --- *** relation: dpe_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters; Positione *** --- *** d from +28 to +32 with respect to the TS *** --- *** S (+1). Experimental results suggest tha *** --- *** t the DPE acts in conjunction with the I *** --- *** NR_motif to provide a binding site for T *** --- *** FIID in the absence of a TATA box to med *** --- *** iate transcription of TATA-less promoter *** --- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G *** --- *** |A|C). *** --- ************************************************ --- CREATE VIEW dpe_motif AS SELECT feature_id AS dpe_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE_motif'; --- ************************************************ --- *** relation: breu_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments at -37 to -32 with respect to the *** --- *** TSS (+1). Consensus sequence is (G|C)(G| *** --- *** C)(G|A)CGCC. Binds TFIIB. *** --- ************************************************ --- CREATE VIEW breu_motif AS SELECT feature_id AS breu_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREu_motif'; --- ************************************************ --- *** relation: pse_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of the *** --- *** promoters of snRNA genes transcribed by *** --- *** RNA polymerase II or by RNA polymerase *** --- *** III. Located between -45 and -60 relativ *** --- *** e to the TSS. The human PSE_motif consen *** --- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| *** --- *** G). *** --- ************************************************ --- CREATE VIEW pse_motif AS SELECT feature_id AS pse_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif'; --- ************************************************ --- *** relation: linkage_group *** --- *** relation type: VIEW *** --- *** *** --- *** A group of loci that can be grouped in a *** --- *** linear order representing the different *** --- *** degrees of linkage among the genes conc *** --- *** erned. *** --- ************************************************ --- CREATE VIEW linkage_group AS SELECT feature_id AS linkage_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linkage_group'; --- ************************************************ --- *** relation: rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A region of double stranded RNA where th *** --- *** e bases do not conform to WC base pairin *** --- *** g. The loop is closed on both sides by c *** --- *** anonical base pairing. If the interrupti *** --- *** on to base pairing occurs on one strand *** --- *** only, it is known as a bulge. *** --- ************************************************ --- CREATE VIEW rna_internal_loop AS SELECT feature_id AS rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_internal_loop'; --- ************************************************ --- *** relation: asymmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where one of the st *** --- *** rands includes more bases than the corre *** --- *** sponding region on the other strand. *** --- ************************************************ --- CREATE VIEW asymmetric_rna_internal_loop AS SELECT feature_id AS asymmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'asymmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: a_minor_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region forming a motif, composed of ad *** --- *** enines, where the minor groove edges are *** --- *** inserted into the minor groove of anoth *** --- *** er helix. *** --- ************************************************ --- CREATE VIEW a_minor_rna_motif AS SELECT feature_id AS a_minor_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_minor_RNA_motif'; --- ************************************************ --- *** relation: k_turn_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** The kink turn (K-turn) is an RNA structu *** --- *** ral motif that creates a sharp (~120 deg *** --- *** ree) bend between two continuous helices *** --- *** . *** --- ************************************************ --- CREATE VIEW k_turn_rna_motif AS SELECT feature_id AS k_turn_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif'; --- ************************************************ --- *** relation: sarcin_like_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A loop in ribosomal RNA containing the s *** --- *** ites of attack for ricin and sarcin. *** --- ************************************************ --- CREATE VIEW sarcin_like_rna_motif AS SELECT feature_id AS sarcin_like_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sarcin_like_RNA_motif'; --- ************************************************ --- *** relation: symmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where the extent of *** --- *** the loop on both stands is the same siz *** --- *** e. *** --- ************************************************ --- CREATE VIEW symmetric_rna_internal_loop AS SELECT feature_id AS symmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: rna_junction_loop *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_junction_loop AS SELECT feature_id AS rna_junction_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_junction_loop'; --- ************************************************ --- *** relation: rna_hook_turn *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_hook_turn AS SELECT feature_id AS rna_hook_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn'; --- ************************************************ --- *** relation: base_pair *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW base_pair AS SELECT feature_id AS base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'base_pair'; --- ************************************************ --- *** relation: wc_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical base pair, where two bases *** --- *** interact via WC edges, with glycosidic *** --- *** bonds oriented cis relative to the axis *** --- *** of orientation. *** --- ************************************************ --- CREATE VIEW wc_base_pair AS SELECT feature_id AS wc_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair'; --- ************************************************ --- *** relation: sugar_edge_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW sugar_edge_base_pair AS SELECT feature_id AS sugar_edge_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sugar_edge_base_pair'; --- ************************************************ --- *** relation: aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA or RNA molecules that have been sele *** --- *** cted from random pools based on their ab *** --- *** ility to bind other molecules. *** --- ************************************************ --- CREATE VIEW aptamer AS SELECT feature_id AS aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'aptamer'; --- ************************************************ --- *** relation: dna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW dna_aptamer AS SELECT feature_id AS dna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer'; --- ************************************************ --- *** relation: rna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** RNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW rna_aptamer AS SELECT feature_id AS rna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_aptamer'; --- ************************************************ --- *** relation: morpholino_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Morpholino oligos are synthesized from f *** --- *** our different Morpholino subunits, each *** --- *** of which contains one of the four geneti *** --- *** c bases (A, C, G, T) linked to a 6-membe *** --- *** red morpholine ring. Eighteen to 25 subu *** --- *** nits of these four subunit types are joi *** --- *** ned in a specific order by non-ionic pho *** --- *** sphorodiamidate intersubunit linkages to *** --- *** give a Morpholino. *** --- ************************************************ --- CREATE VIEW morpholino_oligo AS SELECT feature_id AS morpholino_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo'; --- ************************************************ --- *** relation: riboswitch *** --- *** relation type: VIEW *** --- *** *** --- *** A riboswitch is a part of an mRNA that c *** --- *** an act as a direct sensor of small molec *** --- *** ules to control their own expression. A *** --- *** riboswitch is a cis element in the 5' en *** --- *** d of an mRNA, that acts as a direct sens *** --- *** or of metabolites. *** --- ************************************************ --- CREATE VIEW riboswitch AS SELECT feature_id AS riboswitch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch'; --- ************************************************ --- *** relation: matrix_attachment_site *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that is required for the bi *** --- *** nding of chromatin to the nuclear matrix *** --- *** . *** --- ************************************************ --- CREATE VIEW matrix_attachment_site AS SELECT feature_id AS matrix_attachment_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site'; --- ************************************************ --- *** relation: locus_control_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that includes DNAse hyperse *** --- *** nsitive sites located 5' to a gene that *** --- *** confers the high-level, position-indepen *** --- *** dent, and copy number-dependent expressi *** --- *** on to that gene. *** --- ************************************************ --- CREATE VIEW locus_control_region AS SELECT feature_id AS locus_control_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast is a match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: genomic_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone of a DNA region of a genome. *** --- ************************************************ --- CREATE VIEW genomic_clone AS SELECT feature_id AS genomic_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone'; --- ************************************************ --- *** relation: processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene where by an mRNA was retrot *** --- *** ransposed. The mRNA sequence is transcri *** --- *** bed back into the genome, lacking intron *** --- *** s and promoters, but often including a p *** --- *** olyA tail. *** --- ************************************************ --- CREATE VIEW processed_pseudogene AS SELECT feature_id AS processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene'; --- ************************************************ --- *** relation: pseudogene_by_unequal_crossing_over *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene caused by unequal crossing *** --- *** over at recombination. *** --- ************************************************ --- CREATE VIEW pseudogene_by_unequal_crossing_over AS SELECT feature_id AS pseudogene_by_unequal_crossing_over_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over'; --- ************************************************ --- *** relation: probe *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence used experimentally to de *** --- *** tect the presence or absence of a comple *** --- *** mentary nucleic acid. *** --- ************************************************ --- CREATE VIEW probe AS SELECT feature_id AS probe_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo' OR cvterm.name = 'probe'; --- ************************************************ --- *** relation: aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW aneuploid AS SELECT feature_id AS aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'aneuploid'; --- ************************************************ --- *** relation: hyperploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as extra c *** --- *** hromosomes are present. *** --- ************************************************ --- CREATE VIEW hyperploid AS SELECT feature_id AS hyperploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid'; --- ************************************************ --- *** relation: hypoploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as some ch *** --- *** romosomes are missing. *** --- ************************************************ --- CREATE VIEW hypoploid AS SELECT feature_id AS hypoploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hypoploid'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind thereby *** --- *** effecting translation of genes in that *** --- *** operon. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: nuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, of a nucleotide mol *** --- *** ecule, that interacts selectively and no *** --- *** n-covalently with polypeptide residues o *** --- *** f a nuclease. *** --- ************************************************ --- CREATE VIEW nuclease_binding_site AS SELECT feature_id AS nuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_binding_site'; --- ************************************************ --- *** relation: compound_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome_arm AS SELECT feature_id AS compound_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm'; --- ************************************************ --- *** relation: restriction_enzyme_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** restriction enzyme. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_binding_site AS SELECT feature_id AS restriction_enzyme_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site'; --- ************************************************ --- *** relation: d_intrachr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_intrachr_transposition AS SELECT feature_id AS d_intrachr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition'; --- ************************************************ --- *** relation: d_interchr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_interchr_transposition AS SELECT feature_id AS d_interchr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition'; --- ************************************************ --- *** relation: free_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** an arm exists as an individual chromoso *** --- *** me element. *** --- ************************************************ --- CREATE VIEW free_chromosome_arm AS SELECT feature_id AS free_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm'; --- ************************************************ --- *** relation: gene_to_gene_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_to_gene_feature AS SELECT feature_id AS gene_to_gene_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'gene_to_gene_feature'; --- ************************************************ --- *** relation: overlapping *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that has *** --- *** a sequence that overlaps the sequence of *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW overlapping AS SELECT feature_id AS overlapping_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'overlapping'; --- ************************************************ --- *** relation: inside_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene. *** --- ************************************************ --- CREATE VIEW inside_intron AS SELECT feature_id AS inside_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'inside_intron'; --- ************************************************ --- *** relation: inside_intron_antiparallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the opposite strand. *** --- ************************************************ --- CREATE VIEW inside_intron_antiparallel AS SELECT feature_id AS inside_intron_antiparallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel'; --- ************************************************ --- *** relation: inside_intron_parallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the same strand. *** --- ************************************************ --- CREATE VIEW inside_intron_parallel AS SELECT feature_id AS inside_intron_parallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_parallel'; --- ************************************************ --- *** relation: five_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's 3' region. *** --- ************************************************ --- CREATE VIEW five_prime_three_prime_overlap AS SELECT feature_id AS five_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_three_prime_overlap'; --- ************************************************ --- *** relation: five_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's five prime region. *** --- ************************************************ --- CREATE VIEW five_prime_five_prime_overlap AS SELECT feature_id AS five_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_five_prime_overlap'; --- ************************************************ --- *** relation: three_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 3' region. *** --- ************************************************ --- CREATE VIEW three_prime_three_prime_overlap AS SELECT feature_id AS three_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_three_prime_overlap'; --- ************************************************ --- *** relation: three_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 5' region. *** --- ************************************************ --- CREATE VIEW three_prime_five_prime_overlap AS SELECT feature_id AS three_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_five_prime_overlap'; --- ************************************************ --- *** relation: antisense *** --- *** relation type: VIEW *** --- *** *** --- *** A region sequence that is complementary *** --- *** to a sequence of messenger RNA. *** --- ************************************************ --- CREATE VIEW antisense AS SELECT feature_id AS antisense_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense'; --- ************************************************ --- *** relation: polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is polycistronic. *** --- ************************************************ --- CREATE VIEW polycistronic_transcript AS SELECT feature_id AS polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_transcript'; --- ************************************************ --- *** relation: dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_transcript AS SELECT feature_id AS dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_transcript'; --- ************************************************ --- *** relation: operon_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW operon_member AS SELECT feature_id AS operon_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member'; --- ************************************************ --- *** relation: gene_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_array_member AS SELECT feature_id AS gene_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_array_member'; --- ************************************************ --- *** relation: macronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW macronuclear_sequence AS SELECT feature_id AS macronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence'; --- ************************************************ --- *** relation: micronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW micronuclear_sequence AS SELECT feature_id AS micronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_sequence'; --- ************************************************ --- *** relation: nuclear_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nuclear sequence. *** --- ************************************************ --- CREATE VIEW nuclear_gene AS SELECT feature_id AS nuclear_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene'; --- ************************************************ --- *** relation: mt_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in mitochondrial sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW mt_gene AS SELECT feature_id AS mt_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'mt_gene'; --- ************************************************ --- *** relation: kinetoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in kinetoplast sequence. *** --- ************************************************ --- CREATE VIEW kinetoplast_gene AS SELECT feature_id AS kinetoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'kinetoplast_gene'; --- ************************************************ --- *** relation: plastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plastid sequence. *** --- ************************************************ --- CREATE VIEW plastid_gene AS SELECT feature_id AS plastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'plastid_gene'; --- ************************************************ --- *** relation: apicoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from apicoplast sequence. *** --- ************************************************ --- CREATE VIEW apicoplast_gene AS SELECT feature_id AS apicoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene'; --- ************************************************ --- *** relation: ct_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chloroplast sequence. *** --- ************************************************ --- CREATE VIEW ct_gene AS SELECT feature_id AS ct_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ct_gene'; --- ************************************************ --- *** relation: chromoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chromoplast_sequence. *** --- ************************************************ --- CREATE VIEW chromoplast_gene AS SELECT feature_id AS chromoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_gene'; --- ************************************************ --- *** relation: cyanelle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from cyanelle sequence. *** --- ************************************************ --- CREATE VIEW cyanelle_gene AS SELECT feature_id AS cyanelle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_gene'; --- ************************************************ --- *** relation: leucoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A plastid gene from leucoplast sequence. *** --- ************************************************ --- CREATE VIEW leucoplast_gene AS SELECT feature_id AS leucoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_gene'; --- ************************************************ --- *** relation: proplastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proplastid sequence. *** --- ************************************************ --- CREATE VIEW proplastid_gene AS SELECT feature_id AS proplastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_gene'; --- ************************************************ --- *** relation: nucleomorph_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nucleomorph sequence. *** --- ************************************************ --- CREATE VIEW nucleomorph_gene AS SELECT feature_id AS nucleomorph_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorph_gene'; --- ************************************************ --- *** relation: plasmid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plasmid sequence. *** --- ************************************************ --- CREATE VIEW plasmid_gene AS SELECT feature_id AS plasmid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_gene'; --- ************************************************ --- *** relation: proviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proviral sequence. *** --- ************************************************ --- CREATE VIEW proviral_gene AS SELECT feature_id AS proviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'proviral_gene'; --- ************************************************ --- *** relation: endogenous_retroviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A proviral gene with origin endogenous r *** --- *** etrovirus. *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_gene AS SELECT feature_id AS endogenous_retroviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene'; --- ************************************************ --- *** relation: transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW transposable_element AS SELECT feature_id AS transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: clone_insert_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_end AS SELECT feature_id AS clone_insert_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversible denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the chromosome between the c *** --- *** entromere and the telomere. Human chromo *** --- *** somes have two arms, the p arm (short) a *** --- *** nd the q arm (long) which are separated *** --- *** from each other by the centromere. *** --- ************************************************ --- CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: sequencing_primer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequencing_primer AS SELECT feature_id AS sequencing_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer'; --- ************************************************ --- *** relation: mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_frameshift AS SELECT feature_id AS mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'mRNA_with_frameshift'; --- ************************************************ --- *** relation: sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** An extent of biological sequence. *** --- ************************************************ --- CREATE VIEW sequence_feature AS SELECT feature_id AS sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region' OR cvterm.name = 'junction' OR cvterm.name = 'sequence_alteration' OR cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_feature'; --- ************************************************ --- *** relation: transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoded within a transposable ele *** --- *** ment. For example gag, int, env and pol *** --- *** are the transposable element genes of th *** --- *** e TY element in yeast. *** --- ************************************************ --- CREATE VIEW transposable_element_gene AS SELECT feature_id AS transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'transposable_element_gene'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo to which new deoxyribonucleotid *** --- *** es can be added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'primer'; --- ************************************************ --- *** relation: proviral_region *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to a host genome. *** --- ************************************************ --- CREATE VIEW proviral_region AS SELECT feature_id AS proviral_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage' OR cvterm.name = 'proviral_region'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: edited *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is modified by editing. *** --- ************************************************ --- CREATE VIEW edited AS SELECT feature_id AS edited_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited'; --- ************************************************ --- *** relation: transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript with a translational frames *** --- *** hift. *** --- ************************************************ --- CREATE VIEW transcript_with_translational_frameshift AS SELECT feature_id AS transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a sequence that *** --- *** is regulated. *** --- ************************************************ --- CREATE VIEW regulated AS SELECT feature_id AS regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'regulated'; --- ************************************************ --- *** relation: protein_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW protein_coding_primary_transcript AS SELECT feature_id AS protein_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: forward_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW forward_primer AS SELECT feature_id AS forward_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward_primer'; --- ************************************************ --- *** relation: rna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_sequence_secondary_structure AS SELECT feature_id AS rna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'RNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: transcriptionally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated at transcription. *** --- ************************************************ --- CREATE VIEW transcriptionally_regulated AS SELECT feature_id AS transcriptionally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_regulated'; --- ************************************************ --- *** relation: transcriptionally_constitutive *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed in relatively constant amounts *** --- *** without regard to cellular environmenta *** --- *** l conditions such as the concentration o *** --- *** f a particular substrate. *** --- ************************************************ --- CREATE VIEW transcriptionally_constitutive AS SELECT feature_id AS transcriptionally_constitutive_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive'; --- ************************************************ --- *** relation: transcriptionally_induced *** --- *** relation type: VIEW *** --- *** *** --- *** An inducer molecule is required for tran *** --- *** scription to occur. *** --- ************************************************ --- CREATE VIEW transcriptionally_induced AS SELECT feature_id AS transcriptionally_induced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_induced'; --- ************************************************ --- *** relation: transcriptionally_repressed *** --- *** relation type: VIEW *** --- *** *** --- *** A repressor molecule is required for tra *** --- *** nscription to stop. *** --- ************************************************ --- CREATE VIEW transcriptionally_repressed AS SELECT feature_id AS transcriptionally_repressed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'transcriptionally_repressed'; --- ************************************************ --- *** relation: silenced_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced. *** --- ************************************************ --- CREATE VIEW silenced_gene AS SELECT feature_id AS silenced_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_gene'; --- ************************************************ --- *** relation: gene_silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA modificat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_modification AS SELECT feature_id AS gene_silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_DNA_modification'; --- ************************************************ --- *** relation: gene_silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA methylati *** --- *** on. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_methylation AS SELECT feature_id AS gene_silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: post_translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated after it has been translated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated AS SELECT feature_id AS post_translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'post_translationally_regulated'; --- ************************************************ --- *** relation: translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated as it is translated. *** --- ************************************************ --- CREATE VIEW translationally_regulated AS SELECT feature_id AS translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated'; --- ************************************************ --- *** relation: reverse_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW reverse_primer AS SELECT feature_id AS reverse_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_primer'; --- ************************************************ --- *** relation: epigenetically_modified *** --- *** relation type: VIEW *** --- *** *** --- *** This attribute describes a gene where he *** --- *** ritable changes other than those in the *** --- *** DNA sequence occur. These changes includ *** --- *** e: modification to the DNA (such as DNA *** --- *** methylation, the covalent modification o *** --- *** f cytosine), and post-translational modi *** --- *** fication of histones. *** --- ************************************************ --- CREATE VIEW epigenetically_modified AS SELECT feature_id AS epigenetically_modified_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'epigenetically_modified'; --- ************************************************ --- *** relation: imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** Imprinted genes are epigenetically modif *** --- *** ied genes that are expressed monoallelic *** --- *** ally according to their parent of origin *** --- *** . *** --- ************************************************ --- CREATE VIEW imprinted AS SELECT feature_id AS imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted'; --- ************************************************ --- *** relation: maternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The maternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW maternally_imprinted AS SELECT feature_id AS maternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted'; --- ************************************************ --- *** relation: paternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The paternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW paternally_imprinted AS SELECT feature_id AS paternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted'; --- ************************************************ --- *** relation: allelically_excluded *** --- *** relation type: VIEW *** --- *** *** --- *** Allelic exclusion is a process occurring *** --- *** in diploid organisms, where a gene is i *** --- *** nactivated and not expressed in that cel *** --- *** l. *** --- ************************************************ --- CREATE VIEW allelically_excluded AS SELECT feature_id AS allelically_excluded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded'; --- ************************************************ --- *** relation: gene_rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An epigenetically modified gene, rearran *** --- *** ged at the DNA level. *** --- ************************************************ --- CREATE VIEW gene_rearranged_at_dna_level AS SELECT feature_id AS gene_rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located within the fi *** --- *** ve prime end of an mRNA that causes prem *** --- *** ature termination of translation. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'terminator'; --- ************************************************ --- *** relation: dna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded DNA sequence. *** --- ************************************************ --- CREATE VIEW dna_sequence_secondary_structure AS SELECT feature_id AS dna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif' OR cvterm.name = 'DNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of known length which may be us *** --- *** ed to manufacture a longer region. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: recoded_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A codon that has been redefined at trans *** --- *** lation. The redefinition may be as a res *** --- *** ult of translational bypass, translation *** --- *** al frameshifting or stop codon readthrou *** --- *** gh. *** --- ************************************************ --- CREATE VIEW recoded_codon AS SELECT feature_id AS recoded_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'recoded_codon'; --- ************************************************ --- *** relation: capped *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing when a sequence, *** --- *** usually an mRNA is capped by the additi *** --- *** on of a modified guanine nucleotide at t *** --- *** he 5' end. *** --- ************************************************ --- CREATE VIEW capped AS SELECT feature_id AS capped_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the transcript sequence with *** --- *** in a gene which is not removed from the *** --- *** primary RNA transcript by RNA splicing. *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unavailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n a host bacterium or some other organis *** --- *** m. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'clone'; --- ************************************************ --- *** relation: yac *** --- *** relation type: VIEW *** --- *** *** --- *** Yeast Artificial Chromosome, a vector co *** --- *** nstructed from the telomeric, centromeri *** --- *** c, and replication origin sequences need *** --- *** ed for replication in yeast cells. *** --- ************************************************ --- CREATE VIEW yac AS SELECT feature_id AS yac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC'; --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Bacterial Artificial Chromosome, a cloni *** --- *** ng vector that can be propagated as mini *** --- *** -chromosomes in a bacterial host. *** --- ************************************************ --- CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: pac *** --- *** relation type: VIEW *** --- *** *** --- *** The P1-derived artificial chromosome are *** --- *** DNA constructs that are derived from th *** --- *** e DNA of P1 bacteriophage. They can carr *** --- *** y large amounts (about 100-300 kilobases *** --- *** ) of other sequences for a variety of bi *** --- *** oengineering purposes. It is one type of *** --- *** vector used to clone DNA fragments (100 *** --- *** - to 300-kb insert size; average, 150 kb *** --- *** ) in Escherichia coli cells. *** --- ************************************************ --- CREATE VIEW pac AS SELECT feature_id AS pac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC'; --- ************************************************ --- *** relation: plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A self replicating, using the hosts cell *** --- *** ular machinery, often circular nucleic a *** --- *** cid molecule that is distinct from a chr *** --- *** omosome in the organism. *** --- ************************************************ --- CREATE VIEW plasmid AS SELECT feature_id AS plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'plasmid'; --- ************************************************ --- *** relation: cosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that is a hybrid of lam *** --- *** bda phages and a plasmid that can be pro *** --- *** pagated as a plasmid or packaged as a ph *** --- *** age,since they retain the lambda cos sit *** --- *** es. *** --- ************************************************ --- CREATE VIEW cosmid AS SELECT feature_id AS cosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cosmid'; --- ************************************************ --- *** relation: phagemid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid which carries within its seque *** --- *** nce a bacteriophage replication origin. *** --- *** When the host bacterium is infected with *** --- *** "helper" phage, a phagemid is replicate *** --- *** d along with the phage DNA and packaged *** --- *** into phage capsids. *** --- ************************************************ --- CREATE VIEW phagemid AS SELECT feature_id AS phagemid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phagemid'; --- ************************************************ --- *** relation: fosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that utilizes the E. co *** --- *** li F factor. *** --- ************************************************ --- CREATE VIEW fosmid AS SELECT feature_id AS fosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fosmid'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The point at which one or more contiguou *** --- *** s nucleotides were excised. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which adenine has *** --- *** been methylated. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Consensus region of primary transcript b *** --- *** ordering junction of splicing. A region *** --- *** that overlaps exactly 2 base and adjacen *** --- *** t_to splice_junction. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: five_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 5' edge of the intron. A splice_ *** --- *** site that is downstream_adjacent_to exon *** --- *** and starts intron. *** --- ************************************************ --- CREATE VIEW five_prime_cis_splice_site AS SELECT feature_id AS five_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'five_prime_cis_splice_site'; --- ************************************************ --- *** relation: three_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 3' edge of the intron. A splice_ *** --- *** site that is upstream_adjacent_to exon a *** --- *** nd finishes intron. *** --- ************************************************ --- CREATE VIEW three_prime_cis_splice_site AS SELECT feature_id AS three_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'three_prime_cis_splice_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: enhancer_bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer bound by a factor. *** --- ************************************************ --- CREATE VIEW enhancer_bound_by_factor AS SELECT feature_id AS enhancer_bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region composed of the TSS( *** --- *** s) and binding sites for TF_complexes of *** --- *** the basal transcription machinery. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'promoter'; --- ************************************************ --- *** relation: rnapol_i_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase I binds, to begin trans *** --- *** cription. *** --- ************************************************ --- CREATE VIEW rnapol_i_promoter AS SELECT feature_id AS rnapol_i_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter'; --- ************************************************ --- *** relation: rnapol_ii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase II binds, to begin tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW rnapol_ii_promoter AS SELECT feature_id AS rnapol_ii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_II_promoter'; --- ************************************************ --- *** relation: rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase III binds, to begin tra *** --- *** nscription. *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter AS SELECT feature_id AS rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'RNApol_III_promoter'; --- ************************************************ --- *** relation: caat_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a conserved sequence located abo *** --- *** ut 75-bp upstream of the start point of *** --- *** eukaryotic transcription units which may *** --- *** be involved in RNA polymerase binding; *** --- *** consensus=GG(C|T)CAATCT. *** --- ************************************************ --- CREATE VIEW caat_signal AS SELECT feature_id AS caat_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CAAT_signal'; --- ************************************************ --- *** relation: gc_rich_promoter_region *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved GC-rich region located upstr *** --- *** eam of the start point of eukaryotic tra *** --- *** nscription units which may occur in mult *** --- *** iple copies or in either orientation; co *** --- *** nsensus=GGGCGG. *** --- ************************************************ --- CREATE VIEW gc_rich_promoter_region AS SELECT feature_id AS gc_rich_promoter_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region'; --- ************************************************ --- *** relation: tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved AT-rich septamer found about *** --- *** 25-bp before the start point of many eu *** --- *** karyotic RNA polymerase II transcript un *** --- *** its; may be involved in positioning the *** --- *** enzyme for correct initiation; consensus *** --- *** =TATA(A|T)A(A|T). *** --- ************************************************ --- CREATE VIEW tata_box AS SELECT feature_id AS tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'TATA_box'; --- ************************************************ --- *** relation: minus_10_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 10-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units which may be involved in bin *** --- *** ding RNA polymerase; consensus=TAtAaT. T *** --- *** his region is associated with sigma fact *** --- *** or 70. *** --- ************************************************ --- CREATE VIEW minus_10_signal AS SELECT feature_id AS minus_10_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_10_signal'; --- ************************************************ --- *** relation: minus_35_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved hexamer about 35-bp upstream *** --- *** of the start point of bacterial transcr *** --- *** iption units; consensus=TTGACa or TGTTGA *** --- *** CA. This region is associated with sigma *** --- *** factor 70. *** --- ************************************************ --- CREATE VIEW minus_35_signal AS SELECT feature_id AS minus_35_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_35_signal'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_insert_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_start AS SELECT feature_id AS clone_insert_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_start'; --- ************************************************ --- *** relation: retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is incorpora *** --- *** ted into a chromosome by a mechanism tha *** --- *** t requires reverse transcriptase. *** --- ************************************************ --- CREATE VIEW retrotransposon AS SELECT feature_id AS retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'retrotransposon'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: dna_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon where the mechanism of tran *** --- *** sposition is via a DNA intermediate. *** --- ************************************************ --- CREATE VIEW dna_transposon AS SELECT feature_id AS dna_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'DNA_transposon'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: u2_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A major type of spliceosomal intron spli *** --- *** ced by the U2 spliceosome, that includes *** --- *** U1, U2, U4/U6 and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u2_intron AS SELECT feature_id AS u2_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that in its initial state r *** --- *** equires modification to be functional. *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'primary_transcript'; --- ************************************************ --- *** relation: ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon flanked by long termin *** --- *** al repeat sequences. *** --- ************************************************ --- CREATE VIEW ltr_retrotransposon AS SELECT feature_id AS ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript that is *** --- *** transcribed, but removed from within th *** --- *** e transcript by splicing together the se *** --- *** quences (exons) on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'intron'; --- ************************************************ --- *** relation: non_ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon without long terminal *** --- *** repeat sequences. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon AS SELECT feature_id AS non_ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'non_LTR_retrotransposon'; --- ************************************************ --- *** relation: five_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_intron AS SELECT feature_id AS five_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron'; --- ************************************************ --- *** relation: interior_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_intron AS SELECT feature_id AS interior_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_intron'; --- ************************************************ --- *** relation: three_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_intron AS SELECT feature_id AS three_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_intron'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment used as a reagent to dete *** --- *** ct the polymorphic genomic loci by hybri *** --- *** dizing against the genomic DNA digested *** --- *** with a given restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: line_element *** --- *** relation type: VIEW *** --- *** *** --- *** A dispersed repeat family with many copi *** --- *** es, each from 1 to 6 kb long. New elemen *** --- *** ts are generated by retroposition of a t *** --- *** ranscribed copy. Typically the LINE cont *** --- *** ains 2 ORF's one of which is reverse tra *** --- *** nscriptase, and 3'and 5' direct repeats. *** --- ************************************************ --- CREATE VIEW line_element AS SELECT feature_id AS line_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element'; --- ************************************************ --- *** relation: coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon whereby at least one base is par *** --- *** t of a codon (here, 'codon' is inclusive *** --- *** of the stop_codon). *** --- ************************************************ --- CREATE VIEW coding_exon AS SELECT feature_id AS coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'coding_exon'; --- ************************************************ --- *** relation: five_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the five_prime_coding_ex *** --- *** on that codes for protein. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_coding_region AS SELECT feature_id AS five_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: three_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the three_prime_coding_e *** --- *** xon that codes for protein. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_coding_region AS SELECT feature_id AS three_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that does not contain any codons *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_exon AS SELECT feature_id AS noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'noncoding_exon'; --- ************************************************ --- *** relation: translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence that has *** --- *** translocated to a new position. *** --- ************************************************ --- CREATE VIEW translocation AS SELECT feature_id AS translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation'; --- ************************************************ --- *** relation: five_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' most coding exon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon AS SELECT feature_id AS five_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon'; --- ************************************************ --- *** relation: interior_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is bounded by 5' and 3' spl *** --- *** ice sites. *** --- ************************************************ --- CREATE VIEW interior_exon AS SELECT feature_id AS interior_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_exon'; --- ************************************************ --- *** relation: three_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The coding exon that is most 3-prime on *** --- *** a given transcript. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon AS SELECT feature_id AS three_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime or three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: sine_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element, a few hundred base *** --- *** pairs long, that is dispersed throughou *** --- *** t the genome. A common human SINE is the *** --- *** Alu element. *** --- ************************************************ --- CREATE VIEW sine_element AS SELECT feature_id AS sine_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SINE_element'; --- ************************************************ --- *** relation: simple_sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW simple_sequence_length_variation AS SELECT feature_id AS simple_sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation'; --- ************************************************ --- *** relation: terminal_inverted_repeat_element *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA transposable element defined as ha *** --- *** ving termini with perfect, or nearly per *** --- *** fect short inverted repeats, generally 1 *** --- *** 0 - 40 nucleotides long. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat_element AS SELECT feature_id AS terminal_inverted_repeat_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'terminal_inverted_repeat_element'; --- ************************************************ --- *** relation: rrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a ribosoma *** --- *** l RNA. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript AS SELECT feature_id AS rrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript'; --- ************************************************ --- *** relation: trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a transfer *** --- *** RNA (SO:0000253). *** --- ************************************************ --- CREATE VIEW trna_primary_transcript AS SELECT feature_id AS trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript'; --- ************************************************ --- *** relation: alanine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding alanyl tRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW alanine_trna_primary_transcript AS SELECT feature_id AS alanine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: arg_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding arginyl tR *** --- *** NA (SO:0000255). *** --- ************************************************ --- CREATE VIEW arg_trna_primary_transcript AS SELECT feature_id AS arg_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: asparagine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding asparaginy *** --- *** l tRNA (SO:0000256). *** --- ************************************************ --- CREATE VIEW asparagine_trna_primary_transcript AS SELECT feature_id AS asparagine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: aspartic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding aspartyl t *** --- *** RNA (SO:0000257). *** --- ************************************************ --- CREATE VIEW aspartic_acid_trna_primary_transcript AS SELECT feature_id AS aspartic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: cysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding cysteinyl *** --- *** tRNA (SO:0000258). *** --- ************************************************ --- CREATE VIEW cysteine_trna_primary_transcript AS SELECT feature_id AS cysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutaminyl *** --- *** tRNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamic_acid_trna_primary_transcript AS SELECT feature_id AS glutamic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutamyl t *** --- *** RNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamine_trna_primary_transcript AS SELECT feature_id AS glutamine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glycine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glycyl tRN *** --- *** A (SO:0000263). *** --- ************************************************ --- CREATE VIEW glycine_trna_primary_transcript AS SELECT feature_id AS glycine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: histidine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding histidyl t *** --- *** RNA (SO:0000262). *** --- ************************************************ --- CREATE VIEW histidine_trna_primary_transcript AS SELECT feature_id AS histidine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: isoleucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding isoleucyl *** --- *** tRNA (SO:0000263). *** --- ************************************************ --- CREATE VIEW isoleucine_trna_primary_transcript AS SELECT feature_id AS isoleucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: leucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding leucyl tRN *** --- *** A (SO:0000264). *** --- ************************************************ --- CREATE VIEW leucine_trna_primary_transcript AS SELECT feature_id AS leucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: lysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding lysyl tRNA *** --- *** (SO:0000265). *** --- ************************************************ --- CREATE VIEW lysine_trna_primary_transcript AS SELECT feature_id AS lysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: methionine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding methionyl *** --- *** tRNA (SO:0000266). *** --- ************************************************ --- CREATE VIEW methionine_trna_primary_transcript AS SELECT feature_id AS methionine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: phe_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding phenylalan *** --- *** yl tRNA (SO:0000267). *** --- ************************************************ --- CREATE VIEW phe_trna_primary_transcript AS SELECT feature_id AS phe_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: proline_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding prolyl tRN *** --- *** A (SO:0000268). *** --- ************************************************ --- CREATE VIEW proline_trna_primary_transcript AS SELECT feature_id AS proline_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline_tRNA_primary_transcript'; --- ************************************************ --- *** relation: serine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW serine_trna_primary_transcript AS SELECT feature_id AS serine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: thr_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding threonyl t *** --- *** RNA (SO:000270). *** --- ************************************************ --- CREATE VIEW thr_trna_primary_transcript AS SELECT feature_id AS thr_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: try_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tryptophan *** --- *** yl tRNA (SO:000271). *** --- ************************************************ --- CREATE VIEW try_trna_primary_transcript AS SELECT feature_id AS try_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan_tRNA_primary_transcript'; --- ************************************************ --- *** relation: tyrosine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tyrosyl tR *** --- *** NA (SO:000272). *** --- ************************************************ --- CREATE VIEW tyrosine_trna_primary_transcript AS SELECT feature_id AS tyrosine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: valine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding valyl tRNA *** --- *** (SO:000273). *** --- ************************************************ --- CREATE VIEW valine_trna_primary_transcript AS SELECT feature_id AS valine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: snrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** clear RNA (SO:0000274). *** --- ************************************************ --- CREATE VIEW snrna_primary_transcript AS SELECT feature_id AS snrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_primary_transcript'; --- ************************************************ --- *** relation: snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar mRNA (SO:0000275). *** --- ************************************************ --- CREATE VIEW snorna_primary_transcript AS SELECT feature_id AS snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript'; --- ************************************************ --- *** relation: mature_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone the nec *** --- *** essary modifications, if any, for its fu *** --- *** nction. In eukaryotes this includes, for *** --- *** example, processing of introns, cleavag *** --- *** e, base modification, and modifications *** --- *** to the 5' and/or the 3' ends, other than *** --- *** addition of bases. In bacteria function *** --- *** al mRNAs are usually not modified. *** --- ************************************************ --- CREATE VIEW mature_transcript AS SELECT feature_id AS mature_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'mature_transcript'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not co *** --- *** ntain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a nucleotide molecule that b *** --- *** inds a Transcription Factor or Transcrip *** --- *** tion Factor complex [GO:0005667]. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The in-frame interval between the stop c *** --- *** odons of a reading frame which when read *** --- *** as sequential triplets, has the potenti *** --- *** al of encoding a sequential string of am *** --- *** ino acids. TER(NNN)nTER. *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'ORF'; --- ************************************************ --- *** relation: transcript_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transcript_attribute AS SELECT feature_id AS transcript_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'transcript_attribute'; --- ************************************************ --- *** relation: foldback_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element with extensive se *** --- *** condary structure, characterized by larg *** --- *** e modular imperfect long inverted repeat *** --- *** s. *** --- ************************************************ --- CREATE VIEW foldback_element AS SELECT feature_id AS foldback_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foldback_element'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequences extending on either side o *** --- *** f a specific region. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: chromosome_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_variation AS SELECT feature_id AS chromosome_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_variation'; --- ************************************************ --- *** relation: internal_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR bordered by the terminal and initi *** --- *** al codons of two CDSs in a polycistronic *** --- *** transcript. Every UTR is either 5', 3' *** --- *** or internal. *** --- ************************************************ --- CREATE VIEW internal_utr AS SELECT feature_id AS internal_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_UTR'; --- ************************************************ --- *** relation: untranslated_region_polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The untranslated sequence separating the *** --- *** 'cistrons' of multicistronic mRNA. *** --- ************************************************ --- CREATE VIEW untranslated_region_polycistronic_mrna AS SELECT feature_id AS untranslated_region_polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'untranslated_region_polycistronic_mRNA'; --- ************************************************ --- *** relation: internal_ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence element that recruits a ribosom *** --- *** al subunit to internal mRNA for translat *** --- *** ion initiation. *** --- ************************************************ --- CREATE VIEW internal_ribosome_entry_site AS SELECT feature_id AS internal_ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'internal_ribosome_entry_site'; --- ************************************************ --- *** relation: polyadenylated *** --- *** relation type: VIEW *** --- *** *** --- *** A attribute describing the addition of a *** --- *** poly A tail to the 3' end of a mRNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW polyadenylated AS SELECT feature_id AS polyadenylated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated'; --- ************************************************ --- *** relation: sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_length_variation AS SELECT feature_id AS sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'sequence_length_variation'; --- ************************************************ --- *** relation: modified_rna_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post_transcriptionally modified base. *** --- ************************************************ --- CREATE VIEW modified_rna_base_feature AS SELECT feature_id AS modified_rna_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_RNA_base_feature'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. Transfer R *** --- *** NAs have two regions of fundamental func *** --- *** tional importance: the anti-codon, which *** --- *** is responsible for specific mRNA codon *** --- *** recognition, and the 3' end, to which th *** --- *** e tRNA's corresponding amino acid is att *** --- *** ached (by aminoacyl-tRNA synthetases). T *** --- *** ransfer RNAs cope with the degeneracy of *** --- *** the genetic code in two manners: having *** --- *** more than one tRNA (with a specific ant *** --- *** i-codon) for a particular amino acid; an *** --- *** d 'wobble' base-pairing, i.e. permitting *** --- *** non-standard base-pairing at the 3rd an *** --- *** ti-codon position. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: alanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an alanine anti *** --- *** codon, and a 3' alanine binding region. *** --- ************************************************ --- CREATE VIEW alanyl_trna AS SELECT feature_id AS alanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA'; --- ************************************************ --- *** relation: rrna_small_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_small_subunit_primary_transcript AS SELECT feature_id AS rrna_small_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript'; --- ************************************************ --- *** relation: asparaginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an asparagine a *** --- *** nticodon, and a 3' asparagine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW asparaginyl_trna AS SELECT feature_id AS asparaginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparaginyl_tRNA'; --- ************************************************ --- *** relation: aspartyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an aspartic aci *** --- *** d anticodon, and a 3' aspartic acid bind *** --- *** ing region. *** --- ************************************************ --- CREATE VIEW aspartyl_trna AS SELECT feature_id AS aspartyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartyl_tRNA'; --- ************************************************ --- *** relation: cysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a cysteine anti *** --- *** codon, and a 3' cysteine binding region. *** --- ************************************************ --- CREATE VIEW cysteinyl_trna AS SELECT feature_id AS cysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteinyl_tRNA'; --- ************************************************ --- *** relation: glutaminyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamine ant *** --- *** icodon, and a 3' glutamine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW glutaminyl_trna AS SELECT feature_id AS glutaminyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutaminyl_tRNA'; --- ************************************************ --- *** relation: glutamyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamic acid *** --- *** anticodon, and a 3' glutamic acid bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW glutamyl_trna AS SELECT feature_id AS glutamyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamyl_tRNA'; --- ************************************************ --- *** relation: glycyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glycine antic *** --- *** odon, and a 3' glycine binding region. *** --- ************************************************ --- CREATE VIEW glycyl_trna AS SELECT feature_id AS glycyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycyl_tRNA'; --- ************************************************ --- *** relation: histidyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a histidine ant *** --- *** icodon, and a 3' histidine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW histidyl_trna AS SELECT feature_id AS histidyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidyl_tRNA'; --- ************************************************ --- *** relation: isoleucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an isoleucine a *** --- *** nticodon, and a 3' isoleucine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW isoleucyl_trna AS SELECT feature_id AS isoleucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucyl_tRNA'; --- ************************************************ --- *** relation: leucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a leucine antic *** --- *** odon, and a 3' leucine binding region. *** --- ************************************************ --- CREATE VIEW leucyl_trna AS SELECT feature_id AS leucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucyl_tRNA'; --- ************************************************ --- *** relation: lysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a lysine antico *** --- *** don, and a 3' lysine binding region. *** --- ************************************************ --- CREATE VIEW lysyl_trna AS SELECT feature_id AS lysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysyl_tRNA'; --- ************************************************ --- *** relation: methionyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a methionine an *** --- *** ticodon, and a 3' methionine binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW methionyl_trna AS SELECT feature_id AS methionyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionyl_tRNA'; --- ************************************************ --- *** relation: phenylalanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a phenylalanine *** --- *** anticodon, and a 3' phenylalanine bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW phenylalanyl_trna AS SELECT feature_id AS phenylalanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanyl_tRNA'; --- ************************************************ --- *** relation: prolyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a proline antic *** --- *** odon, and a 3' proline binding region. *** --- ************************************************ --- CREATE VIEW prolyl_trna AS SELECT feature_id AS prolyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prolyl_tRNA'; --- ************************************************ --- *** relation: seryl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a serine antico *** --- *** don, and a 3' serine binding region. *** --- ************************************************ --- CREATE VIEW seryl_trna AS SELECT feature_id AS seryl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seryl_tRNA'; --- ************************************************ --- *** relation: threonyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a threonine ant *** --- *** icodon, and a 3' threonine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW threonyl_trna AS SELECT feature_id AS threonyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonyl_tRNA'; --- ************************************************ --- *** relation: tryptophanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tryptophan an *** --- *** ticodon, and a 3' tryptophan binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW tryptophanyl_trna AS SELECT feature_id AS tryptophanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophanyl_tRNA'; --- ************************************************ --- *** relation: tyrosyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tyrosine anti *** --- *** codon, and a 3' tyrosine binding region. *** --- ************************************************ --- CREATE VIEW tyrosyl_trna AS SELECT feature_id AS tyrosyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosyl_tRNA'; --- ************************************************ --- *** relation: valyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a valine antico *** --- *** don, and a 3' valine binding region. *** --- ************************************************ --- CREATE VIEW valyl_trna AS SELECT feature_id AS valyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valyl_tRNA'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small nuclear RNA molecule involved in *** --- *** pre-mRNA splicing and processing. *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA (small nucleolar RNA) is any on *** --- *** e of a class of small RNAs that are asso *** --- *** ciated with the eukaryotic nucleus as co *** --- *** mponents of small nucleolar ribonucleopr *** --- *** oteins. They participate in the processi *** --- *** ng or modifications of many RNAs, mostly *** --- *** ribosomal RNAs (rRNAs) though snoRNAs a *** --- *** re also known to target other classes of *** --- *** RNA, including spliceosomal RNAs, tRNAs *** --- *** , and mRNAs via a stretch of sequence th *** --- *** at is complementary to a sequence in the *** --- *** targeted RNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. M *** --- *** icro RNAs are produced from precursor mo *** --- *** lecules (SO:0000647) that can form local *** --- *** hairpin structures, which ordinarily ar *** --- *** e processed (via the Dicer pathway) such *** --- *** that a single miRNA molecule accumulate *** --- *** s from one arm of a hairpin precursor mo *** --- *** lecule. Micro RNAs may trigger the cleav *** --- *** age of their target molecules or act as *** --- *** translational repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by another molecule. *** --- ************************************************ --- CREATE VIEW bound_by_factor AS SELECT feature_id AS bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'bound_by_factor'; --- ************************************************ --- *** relation: transcript_bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a nucleic *** --- *** acid. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_nucleic_acid AS SELECT feature_id AS transcript_bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_nucleic_acid'; --- ************************************************ --- *** relation: transcript_bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a protein. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_protein AS SELECT feature_id AS transcript_bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_protein'; --- ************************************************ --- *** relation: engineered_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_gene AS SELECT feature_id AS engineered_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_gene'; --- ************************************************ --- *** relation: engineered_foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_gene AS SELECT feature_id AS engineered_foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene'; --- ************************************************ --- *** relation: mrna_with_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a minus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_1_frameshift AS SELECT feature_id AS mrna_with_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element_gene AS SELECT feature_id AS engineered_foreign_transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene'; --- ************************************************ --- *** relation: foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_gene AS SELECT feature_id AS foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'foreign_gene'; --- ************************************************ --- *** relation: long_terminal_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence directly repeated at both end *** --- *** s of a defined sequence, of the sort typ *** --- *** ically found in retroviruses. *** --- ************************************************ --- CREATE VIEW long_terminal_repeat AS SELECT feature_id AS long_terminal_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'long_terminal_repeat'; --- ************************************************ --- *** relation: fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is a fusion. *** --- ************************************************ --- CREATE VIEW fusion_gene AS SELECT feature_id AS fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'fusion_gene'; --- ************************************************ --- *** relation: engineered_fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A fusion gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_fusion_gene AS SELECT feature_id AS engineered_fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat_region containing repeat_units *** --- *** (2 to 4 bp) that is repeated multiple ti *** --- *** mes in tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: dinucleotide_repeat_microsatellite_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dinucleotide_repeat_microsatellite_feature AS SELECT feature_id AS dinucleotide_repeat_microsatellite_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: trinuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trinuc_repeat_microsat AS SELECT feature_id AS trinuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: engineered_foreign_repetitive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element that is engineered *** --- *** and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_repetitive_element AS SELECT feature_id AS engineered_foreign_repetitive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_repetitive_element'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. It is a palindr *** --- *** ome, and it may, or may not be hyphenate *** --- *** d. Examples: GCTGATCAGC, or GCTGA-----TC *** --- *** AGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: u12_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A type of spliceosomal intron spliced by *** --- *** the U12 spliceosome, that includes U11, *** --- *** U12, U4atac/U6atac and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u12_intron AS SELECT feature_id AS u12_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_intron'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: d_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Displacement loop; a region within mitoc *** --- *** hondrial DNA in which a short stretch of *** --- *** RNA is paired with one strand of DNA, d *** --- *** isplacing the original partner DNA stran *** --- *** d in this region; also used to describe *** --- *** the displacement of a region of one stra *** --- *** nd of duplex DNA by a single stranded in *** --- *** vader in the reaction catalyzed by RecA *** --- *** protein. *** --- ************************************************ --- CREATE VIEW d_loop AS SELECT feature_id AS d_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop'; --- ************************************************ --- *** relation: recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature AS SELECT feature_id AS recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'recombination_feature'; --- ************************************************ --- *** relation: specific_recombination_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW specific_recombination_site AS SELECT feature_id AS specific_recombination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'specific_recombination_site'; --- ************************************************ --- *** relation: recombination_feature_of_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature_of_rearranged_gene AS SELECT feature_id AS recombination_feature_of_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'recombination_feature_of_rearranged_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature'; --- ************************************************ --- *** relation: j_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including J-heptame *** --- *** r, J-spacer and J-nonamer in 5' of J-reg *** --- *** ion of a J-gene or J-sequence. *** --- ************************************************ --- CREATE VIEW j_gene_recombination_feature AS SELECT feature_id AS j_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G. *** --- ************************************************ --- CREATE VIEW modified_base AS SELECT feature_id AS modified_base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'modified_base'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: experimentally_determined *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that has *** --- *** been experimentally verified. *** --- ************************************************ --- CREATE VIEW experimentally_determined AS SELECT feature_id AS experimentally_determined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined'; --- ************************************************ --- *** relation: stem_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A double-helical region of nucleic acid *** --- *** formed by base-pairing between adjacent *** --- *** (inverted) complementary sequences. *** --- ************************************************ --- CREATE VIEW stem_loop AS SELECT feature_id AS stem_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop' OR cvterm.name = 'stem_loop'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: tss *** --- *** relation type: VIEW *** --- *** *** --- *** The first base where RNA polymerase begi *** --- *** ns to synthesize the RNA transcript. *** --- ************************************************ --- CREATE VIEW tss AS SELECT feature_id AS tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'TSS'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS'; --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Complementary DNA; A piece of DNA copied *** --- *** from an mRNA and spliced into a vector *** --- *** for propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** First codon to be translated by a riboso *** --- *** me. *** --- ************************************************ --- CREATE VIEW start_codon AS SELECT feature_id AS start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'start_codon'; --- ************************************************ --- *** relation: stop_codon *** --- *** relation type: VIEW *** --- *** *** --- *** In mRNA, a set of three nucleotides that *** --- *** indicates the end of information for pr *** --- *** otein synthesis. *** --- ************************************************ --- CREATE VIEW stop_codon AS SELECT feature_id AS stop_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon'; --- ************************************************ --- *** relation: intronic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Sequences within the intron that modulat *** --- *** e splice site selection for some introns *** --- *** . *** --- ************************************************ --- CREATE VIEW intronic_splice_enhancer AS SELECT feature_id AS intronic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer'; --- ************************************************ --- *** relation: mrna_with_plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_1_frameshift AS SELECT feature_id AS mrna_with_plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_1_frameshift'; --- ************************************************ --- *** relation: nuclease_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclease_hypersensitive_site AS SELECT feature_id AS nuclease_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_hypersensitive_site'; --- ************************************************ --- *** relation: coding_start *** --- *** relation type: VIEW *** --- *** *** --- *** The first base to be translated into pro *** --- *** tein. *** --- ************************************************ --- CREATE VIEW coding_start AS SELECT feature_id AS coding_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna_large_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a large ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_large_subunit_primary_transcript AS SELECT feature_id AS rrna_large_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_large_subunit_primary_transcript'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: coding_end *** --- *** relation type: VIEW *** --- *** *** --- *** The last base to be translated into prot *** --- *** ein. It does not include the stop codon. *** --- ************************************************ --- CREATE VIEW coding_end AS SELECT feature_id AS coding_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_end'; --- ************************************************ --- *** relation: microarray_oligo *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW microarray_oligo AS SELECT feature_id AS microarray_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo'; --- ************************************************ --- *** relation: mrna_with_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_2_frameshift AS SELECT feature_id AS mrna_with_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_2_frameshift'; --- ************************************************ --- *** relation: conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of sequence similarity by descent *** --- *** from a common ancestor. *** --- ************************************************ --- CREATE VIEW conserved_region AS SELECT feature_id AS conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'conserved_region'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: coding_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Coding region of sequence similarity by *** --- *** descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW coding_conserved_region AS SELECT feature_id AS coding_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: nc_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding region of sequence similarity *** --- *** by descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW nc_conserved_region AS SELECT feature_id AS nc_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_conserved_region'; --- ************************************************ --- *** relation: mrna_with_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mRNA with a minus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_2_frameshift AS SELECT feature_id AS mrna_with_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_2_frameshift'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: mite *** --- *** relation type: VIEW *** --- *** *** --- *** A highly repetitive and short (100-500 b *** --- *** ase pair) transposable element with term *** --- *** inal inverted repeats (TIR) and target s *** --- *** ite duplication (TSD). MITEs do not enco *** --- *** de proteins. *** --- ************************************************ --- CREATE VIEW mite AS SELECT feature_id AS mite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE'; --- ************************************************ --- *** relation: recombination_hotspot *** --- *** relation type: VIEW *** --- *** *** --- *** A region in a genome which promotes reco *** --- *** mbination. *** --- ************************************************ --- CREATE VIEW recombination_hotspot AS SELECT feature_id AS recombination_hotspot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a nucleic ac *** --- *** id molecule which controls its own repli *** --- *** cation through the interaction of specif *** --- *** ic proteins at one or more origins of re *** --- *** plication. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** A cytologically distinguishable feature *** --- *** of a chromosome, often made visible by s *** --- *** taining, and usually alternating light a *** --- *** nd dark. *** --- ************************************************ --- CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: site_specific_recombination_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW site_specific_recombination_target_region AS SELECT feature_id AS site_specific_recombination_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'site_specific_recombination_target_region'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'match'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a cDNA clone or PCR product; t *** --- *** ypically a few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'EST'; --- ************************************************ --- *** relation: loxp_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loxp_site AS SELECT feature_id AS loxp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to repeating *** --- *** units. The forms found in nature are deo *** --- *** xyribonucleic acid (DNA), where the repe *** --- *** ating units are 2-deoxy-D-ribose rings c *** --- *** onnected to a phosphate backbone, and ri *** --- *** bonucleic acid (RNA), where the repeatin *** --- *** g units are D-ribose rings connected to *** --- *** a phosphate backbone. *** --- ************************************************ --- CREATE VIEW nucleic_acid AS SELECT feature_id AS nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'nucleic_acid'; --- ************************************************ --- *** relation: protein_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW protein_match AS SELECT feature_id AS protein_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: frt_site *** --- *** relation type: VIEW *** --- *** *** --- *** An inversion site found on the Saccharom *** --- *** yces cerevisiae 2 micron plasmid. *** --- ************************************************ --- CREATE VIEW frt_site AS SELECT feature_id AS frt_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site'; --- ************************************************ --- *** relation: synthetic_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to decide a sequence of nuc *** --- *** leotides, nucleotide analogs, or amino a *** --- *** cids that has been designed by an experi *** --- *** menter and which may, or may not, corres *** --- *** pond with any natural sequence. *** --- ************************************************ --- CREATE VIEW synthetic_sequence AS SELECT feature_id AS synthetic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'synthetic_sequence'; --- ************************************************ --- *** relation: dna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a 2-deoxy-D-ribose ring c *** --- *** onnected to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW dna AS SELECT feature_id AS dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'DNA'; --- ************************************************ --- *** relation: sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW sequence_assembly AS SELECT feature_id AS sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'sequence_assembly'; --- ************************************************ --- *** relation: group_1_intron_homing_endonuclease_target_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of intronic nucleotide sequence *** --- *** targeted by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW group_1_intron_homing_endonuclease_target_region AS SELECT feature_id AS group_1_intron_homing_endonuclease_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_1_intron_homing_endonuclease_target_region'; --- ************************************************ --- *** relation: haplotype_block *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome which is co-inher *** --- *** ited as the result of the lack of histor *** --- *** ic recombination within it. *** --- ************************************************ --- CREATE VIEW haplotype_block AS SELECT feature_id AS haplotype_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype_block'; --- ************************************************ --- *** relation: rna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a D-ribose ring connected *** --- *** to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW rna AS SELECT feature_id AS rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA'; --- ************************************************ --- *** relation: flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region that is *** --- *** bounded either side by a particular kin *** --- *** d of region. *** --- ************************************************ --- CREATE VIEW flanked AS SELECT feature_id AS flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'flanked'; --- ************************************************ --- *** relation: floxed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence that is *** --- *** flanked by Lox-P sites. *** --- ************************************************ --- CREATE VIEW floxed AS SELECT feature_id AS floxed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er code for a unique amino acid or the t *** --- *** ermination of translation and are contai *** --- *** ned within the CDS. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'codon'; --- ************************************************ --- *** relation: frt_flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe sequence that i *** --- *** s flanked by the FLP recombinase recogni *** --- *** tion site, FRT. *** --- ************************************************ --- CREATE VIEW frt_flanked AS SELECT feature_id AS frt_flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_flanked'; --- ************************************************ --- *** relation: invalidated_by_chimeric_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone constructed from more than *** --- *** one mRNA. Usually an experimental artifa *** --- *** ct. *** --- ************************************************ --- CREATE VIEW invalidated_by_chimeric_cdna AS SELECT feature_id AS invalidated_by_chimeric_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA'; --- ************************************************ --- *** relation: floxed_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene that is floxed. *** --- ************************************************ --- CREATE VIEW floxed_gene AS SELECT feature_id AS floxed_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene'; --- ************************************************ --- *** relation: transposable_element_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence surrounding a tra *** --- *** nsposable element. *** --- ************************************************ --- CREATE VIEW transposable_element_flanking_region AS SELECT feature_id AS transposable_element_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region'; --- ************************************************ --- *** relation: integron *** --- *** relation type: VIEW *** --- *** *** --- *** A region encoding an integrase which act *** --- *** s at a site adjacent to it (attI_site) t *** --- *** o insert DNA which must include but is n *** --- *** ot limited to an attC_site. *** --- ************************************************ --- CREATE VIEW integron AS SELECT feature_id AS integron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integron'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: atti_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an integron, adjacent to *** --- *** an integrase, at which site specific re *** --- *** combination involving an attC_site takes *** --- *** place. *** --- ************************************************ --- CREATE VIEW atti_site AS SELECT feature_id AS atti_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site'; --- ************************************************ --- *** relation: transposable_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW transposable_element_insertion_site AS SELECT feature_id AS transposable_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that encodes function requi *** --- *** red for conjugation. *** --- ************************************************ --- CREATE VIEW conjugative_transposon AS SELECT feature_id AS conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conjugative_transposon'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA sequence that has catalytic activ *** --- *** ity with or without an associated ribonu *** --- *** cleoprotein. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme' OR cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: recombinationally_inverted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene by i *** --- *** nversion. *** --- ************************************************ --- CREATE VIEW recombinationally_inverted_gene AS SELECT feature_id AS recombinationally_inverted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5_8S ribosomal RNA (5. 8S rRNA) is a com *** --- *** ponent of the large subunit of the eukar *** --- *** yotic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurs *** --- *** or that also contains 18S and 28S rRNA. *** --- *** Functionally, it is thought that 5.8S rR *** --- *** NA may be involved in ribosome transloca *** --- *** tion. It is also known to form covalent *** --- *** linkage to the p53 tumour suppressor pro *** --- *** tein. 5_8S rRNA is also found in archaea *** --- *** . *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S'; --- ************************************************ --- *** relation: rna_6s *** --- *** relation type: VIEW *** --- *** *** --- *** A small (184-nt in E. coli) RNA that for *** --- *** ms a hairpin type structure. 6S RNA asso *** --- *** ciates with RNA polymerase in a highly s *** --- *** pecific manner. 6S RNA represses express *** --- *** ion from a sigma70-dependent promoter du *** --- *** ring stationary phase. *** --- ************************************************ --- CREATE VIEW rna_6s AS SELECT feature_id AS rna_6s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_6S'; --- ************************************************ --- *** relation: csrb_rsmb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An enterobacterial RNA that binds the Cs *** --- *** rA protein. The CsrB RNAs contain a cons *** --- *** erved motif CAGGXXG that is found in up *** --- *** to 18 copies and has been suggested to b *** --- *** ind CsrA. The Csr regulatory system has *** --- *** a strong negative regulatory effect on g *** --- *** lycogen biosynthesis, glyconeogenesis an *** --- *** d glycogen catabolism and a positive reg *** --- *** ulatory effect on glycolysis. In other b *** --- *** acteria such as Erwinia caratovara the R *** --- *** smA protein has been shown to regulate t *** --- *** he production of virulence determinants, *** --- *** such extracellular enzymes. RsmA binds *** --- *** to RsmB regulatory RNA which is also a m *** --- *** ember of this family. *** --- ************************************************ --- CREATE VIEW csrb_rsmb_rna AS SELECT feature_id AS csrb_rsmb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CsrB_RsmB_RNA'; --- ************************************************ --- *** relation: dsra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** DsrA RNA regulates both transcription, b *** --- *** y overcoming transcriptional silencing b *** --- *** y the nucleoid-associated H-NS protein, *** --- *** and translation, by promoting efficient *** --- *** translation of the stress sigma factor, *** --- *** RpoS. These two activities of DsrA can b *** --- *** e separated by mutation: the first of th *** --- *** ree stem-loops of the 85 nucleotide RNA *** --- *** is necessary for RpoS translation but no *** --- *** t for anti-H-NS action, while the second *** --- *** stem-loop is essential for antisilencin *** --- *** g and less critical for RpoS translation *** --- *** . The third stem-loop, which behaves as *** --- *** a transcription terminator, can be subst *** --- *** ituted by the trp transcription terminat *** --- *** or without loss of either DsrA function. *** --- *** The sequence of the first stem-loop of *** --- *** DsrA is complementary with the upstream *** --- *** leader portion of RpoS messenger RNA, su *** --- *** ggesting that pairing of DsrA with the R *** --- *** poS message might be important for trans *** --- *** lational regulation. *** --- ************************************************ --- CREATE VIEW dsra_rna AS SELECT feature_id AS dsra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA' OR cvterm.name = 'DsrA_RNA'; --- ************************************************ --- *** relation: gcvb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA involved in exp *** --- *** ression of the dipeptide and oligopeptid *** --- *** e transport systems in Escherichia coli. *** --- ************************************************ --- CREATE VIEW gcvb_rna AS SELECT feature_id AS gcvb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: group_iia_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iia_intron AS SELECT feature_id AS group_iia_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron'; --- ************************************************ --- *** relation: group_iib_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iib_intron AS SELECT feature_id AS group_iib_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIB_intron'; --- ************************************************ --- *** relation: micf_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-translated 93 nt antisense RNA tha *** --- *** t binds its target ompF mRNA and regulat *** --- *** es ompF expression by inhibiting transla *** --- *** tion and inducing degradation of the mes *** --- *** sage. *** --- ************************************************ --- CREATE VIEW micf_rna AS SELECT feature_id AS micf_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA'; --- ************************************************ --- *** relation: oxys_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA which is induce *** --- *** d in response to oxidative stress in Esc *** --- *** herichia coli. Acts as a global regulato *** --- *** r to activate or repress the expression *** --- *** of as many as 40 genes, including the fh *** --- *** lA-encoded transcriptional activator and *** --- *** the rpoS-encoded sigma(s) subunit of RN *** --- *** A polymerase. OxyS is bound by the Hfq p *** --- *** rotein, that increases the OxyS RNA inte *** --- *** raction with its target messages. *** --- ************************************************ --- CREATE VIEW oxys_rna AS SELECT feature_id AS oxys_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'OxyS_RNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterized activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: rpra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Translational regulation of the stationa *** --- *** ry phase sigma factor RpoS is mediated b *** --- *** y the formation of a double-stranded RNA *** --- *** stem-loop structure in the upstream reg *** --- *** ion of the rpoS messenger RNA, occluding *** --- *** the translation initiation site. Clones *** --- *** carrying rprA (RpoS regulator RNA) incr *** --- *** eased the translation of RpoS. The rprA *** --- *** gene encodes a 106 nucleotide regulatory *** --- *** RNA. As with DsrA Rfam:RF00014, RprA is *** --- *** predicted to form three stem-loops. Thu *** --- *** s, at least two small RNAs, DsrA and Rpr *** --- *** A, participate in the positive regulatio *** --- *** n of RpoS translation. Unlike DsrA, RprA *** --- *** does not have an extensive region of co *** --- *** mplementarity to the RpoS leader, leavin *** --- *** g its mechanism of action unclear. RprA *** --- *** is non-essential. *** --- ************************************************ --- CREATE VIEW rpra_rna AS SELECT feature_id AS rpra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RprA_RNA'; --- ************************************************ --- *** relation: rre_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The Rev response element (RRE) is encode *** --- *** d within the HIV-env gene. Rev is an ess *** --- *** ential regulatory protein of HIV that bi *** --- *** nds an internal loop of the RRE leading, *** --- *** encouraging further Rev-RRE binding. Th *** --- *** is RNP complex is critical for mRNA expo *** --- *** rt and hence for expression of the HIV s *** --- *** tructural proteins. *** --- ************************************************ --- CREATE VIEW rre_rna AS SELECT feature_id AS rre_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RRE_RNA'; --- ************************************************ --- *** relation: spot_42_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A 109-nucleotide RNA of E. coli that see *** --- *** ms to have a regulatory role on the gala *** --- *** ctose operon. Changes in Spot 42 levels *** --- *** are implicated in affecting DNA polymera *** --- *** se I levels. *** --- ************************************************ --- CREATE VIEW spot_42_rna AS SELECT feature_id AS spot_42_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spot_42_RNA'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesizes telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA is an snRNA required for th *** --- *** e splicing of the minor U12-dependent cl *** --- *** ass of eukaryotic nuclear introns. It fo *** --- *** rms a base paired complex with U4atac_sn *** --- *** RNA (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: sequence_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describes a quality of sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW sequence_attribute AS SELECT feature_id AS sequence_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymer_attribute' OR cvterm.name = 'feature_attribute' OR cvterm.name = 'sequence_location' OR cvterm.name = 'variant_quality' OR cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'sequence_attribute'; --- ************************************************ --- *** relation: gene_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_attribute AS SELECT feature_id AS gene_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'gene_attribute'; --- ************************************************ --- *** relation: u14_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snorna AS SELECT feature_id AS u14_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonucleoprotein comp *** --- *** lex. The complex consists of a major vau *** --- *** lt protein (MVP), two minor vault protei *** --- *** ns (VPARP and TEP1), and several small u *** --- *** ntranslated RNA molecules. It has been s *** --- *** uggested that the vault complex is invol *** --- *** ved in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: twintron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron within an intron. Twintrons ar *** --- *** e group II or III introns, into which an *** --- *** other group II or III intron has been tr *** --- *** ansposed. *** --- ************************************************ --- CREATE VIEW twintron AS SELECT feature_id AS twintron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'twintron'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in eukaryotes, wh *** --- *** ich functions as the small subunit of th *** --- *** e ribosome. *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region of sequence that, in *** --- *** the molecule, interacts selectively and *** --- *** non-covalently with other molecules. A *** --- *** region on the surface of a molecule that *** --- *** may interact with another molecule. Whe *** --- *** n applied to polypeptides: Amino acids i *** --- *** nvolved in binding or interactions. It c *** --- *** an also apply to an amino acid bond whic *** --- *** h is represented by the positions of the *** --- *** two flanking amino acids. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith polypeptide molecules. *** --- ************************************************ --- CREATE VIEW protein_binding_site AS SELECT feature_id AS protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'protein_binding_site'; --- ************************************************ --- *** relation: rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that rescues. *** --- ************************************************ --- CREATE VIEW rescue_region AS SELECT feature_id AS rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'rescue_region'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polynucleotide sequence prod *** --- *** uced by digestion with a restriction end *** --- *** onuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment' OR cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequence differs from *** --- *** that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: invalidated_by_genomic_contamination *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to genomic contaminat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_contamination AS SELECT feature_id AS invalidated_by_genomic_contamination_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_contamination'; --- ************************************************ --- *** relation: invalidated_by_genomic_polya_primed_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to polyA priming. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_polya_primed_cdna AS SELECT feature_id AS invalidated_by_genomic_polya_primed_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA'; --- ************************************************ --- *** relation: invalidated_by_partial_processing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to partial processing *** --- *** . *** --- ************************************************ --- CREATE VIEW invalidated_by_partial_processing AS SELECT feature_id AS invalidated_by_partial_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_partial_processing'; --- ************************************************ --- *** relation: polypeptide_domain *** --- *** relation type: VIEW *** --- *** *** --- *** A structurally or functionally defined p *** --- *** rotein region. In proteins with multiple *** --- *** domains, the combination of the domains *** --- *** determines the function of the protein. *** --- *** A region which has been shown to recur *** --- *** throughout evolution. *** --- ************************************************ --- CREATE VIEW polypeptide_domain AS SELECT feature_id AS polypeptide_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The signal_peptide is a short region of *** --- *** the peptide located at the N-terminus th *** --- *** at directs the protein to be secreted or *** --- *** part of membrane components. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: mature_protein_region *** --- *** relation type: VIEW *** --- *** *** --- *** The polypeptide sequence that remains wh *** --- *** en the cleaved peptide regions have been *** --- *** cleaved from the immature peptide. *** --- ************************************************ --- CREATE VIEW mature_protein_region AS SELECT feature_id AS mature_protein_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide' OR cvterm.name = 'mature_protein_region'; --- ************************************************ --- *** relation: five_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_terminal_inverted_repeat AS SELECT feature_id AS five_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: three_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_terminal_inverted_repeat AS SELECT feature_id AS three_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: u5_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_ltr_region AS SELECT feature_id AS u5_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U5_LTR_region'; --- ************************************************ --- *** relation: r_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_ltr_region AS SELECT feature_id AS r_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'R_LTR_region'; --- ************************************************ --- *** relation: u3_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_ltr_region AS SELECT feature_id AS u3_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'U3_LTR_region'; --- ************************************************ --- *** relation: five_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr AS SELECT feature_id AS five_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR'; --- ************************************************ --- *** relation: three_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr AS SELECT feature_id AS three_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_LTR'; --- ************************************************ --- *** relation: r_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_five_prime_ltr_region AS SELECT feature_id AS r_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region'; --- ************************************************ --- *** relation: u5_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_five_prime_ltr_region AS SELECT feature_id AS u5_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region'; --- ************************************************ --- *** relation: u3_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_five_prime_ltr_region AS SELECT feature_id AS u3_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region'; --- ************************************************ --- *** relation: r_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_three_prime_ltr_region AS SELECT feature_id AS r_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region'; --- ************************************************ --- *** relation: u3_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_three_prime_ltr_region AS SELECT feature_id AS u3_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_three_prime_LTR_region'; --- ************************************************ --- *** relation: u5_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_three_prime_ltr_region AS SELECT feature_id AS u5_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_three_prime_LTR_region'; --- ************************************************ --- *** relation: non_ltr_retrotransposon_polymeric_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polymeric tract, such as poly(dA), wit *** --- *** hin a non_LTR_retrotransposon. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon_polymeric_tract AS SELECT feature_id AS non_ltr_retrotransposon_polymeric_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract'; --- ************************************************ --- *** relation: target_site_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of the target DNA that is dup *** --- *** licated when a transposable element or p *** --- *** hage inserts; usually found at each end *** --- *** the insertion. *** --- ************************************************ --- CREATE VIEW target_site_duplication AS SELECT feature_id AS target_site_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication'; --- ************************************************ --- *** relation: rr_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polypurine tract within an LTR_retrotr *** --- *** ansposon. *** --- ************************************************ --- CREATE VIEW rr_tract AS SELECT feature_id AS rr_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: inverted_ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_ring_chromosome AS SELECT feature_id AS inverted_ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome'; --- ************************************************ --- *** relation: vector_replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A replicon that has been modified to act *** --- *** as a vector for foreign sequence. *** --- ************************************************ --- CREATE VIEW vector_replicon AS SELECT feature_id AS vector_replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'vector_replicon'; --- ************************************************ --- *** relation: ss_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ss_oligo AS SELECT feature_id AS ss_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'ss_oligo'; --- ************************************************ --- *** relation: ds_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ds_oligo AS SELECT feature_id AS ds_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'ds_oligo'; --- ************************************************ --- *** relation: polymer_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the kind of bio *** --- *** logical sequence. *** --- ************************************************ --- CREATE VIEW polymer_attribute AS SELECT feature_id AS polymer_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'polymer_attribute'; --- ************************************************ --- *** relation: three_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_noncoding_exon AS SELECT feature_id AS three_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon'; --- ************************************************ --- *** relation: five_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_noncoding_exon AS SELECT feature_id AS five_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_noncoding_exon'; --- ************************************************ --- *** relation: utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Intron located in the untranslated regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW utr_intron AS SELECT feature_id AS utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'UTR_intron'; --- ************************************************ --- *** relation: five_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_intron AS SELECT feature_id AS five_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron'; --- ************************************************ --- *** relation: three_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_intron AS SELECT feature_id AS three_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR_intron'; --- ************************************************ --- *** relation: random_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides or amino acids *** --- *** which, by design, has a "random" order *** --- *** of components, given a predetermined inp *** --- *** ut frequency of these components. *** --- ************************************************ --- CREATE VIEW random_sequence AS SELECT feature_id AS random_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence'; --- ************************************************ --- *** relation: interband *** --- *** relation type: VIEW *** --- *** *** --- *** A light region between two darkly staini *** --- *** ng bands in a polytene chromosome. *** --- ************************************************ --- CREATE VIEW interband AS SELECT feature_id AS interband_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interband'; --- ************************************************ --- *** relation: gene_with_polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polyadenylated mRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW gene_with_polyadenylated_mrna AS SELECT feature_id AS gene_with_polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA'; --- ************************************************ --- *** relation: chromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant whereby a *** --- *** region of a chromosome has been transfe *** --- *** rred to another position. Among interchr *** --- *** omosomal rearrangements, the term transp *** --- *** osition is reserved for that class in wh *** --- *** ich the telomeres of the chromosomes inv *** --- *** olved are coupled (that is to say, form *** --- *** the two ends of a single DNA molecule) a *** --- *** s in wild-type. *** --- ************************************************ --- CREATE VIEW chromosomal_transposition AS SELECT feature_id AS chromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'chromosomal_transposition'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A 17-28-nt, small interfering RNA derive *** --- *** d from transcripts of repetitive element *** --- *** s. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: gene_with_mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA with a frame *** --- *** shift. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_with_frameshift AS SELECT feature_id AS gene_with_mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_with_frameshift'; --- ************************************************ --- *** relation: recombinationally_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is recombinationally rearran *** --- *** ged. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_gene AS SELECT feature_id AS recombinationally_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'recombinationally_rearranged_gene'; --- ************************************************ --- *** relation: interchromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving an in *** --- *** sertion from another chromosome. *** --- ************************************************ --- CREATE VIEW interchromosomal_duplication AS SELECT feature_id AS interchromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication'; --- ************************************************ --- *** relation: d_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including D-region *** --- *** with 5' UTR and 3' UTR, also designated *** --- *** as D-segment. *** --- ************************************************ --- CREATE VIEW d_gene AS SELECT feature_id AS d_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene'; --- ************************************************ --- *** relation: gene_with_trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a transcript that is trans-s *** --- *** pliced. *** --- ************************************************ --- CREATE VIEW gene_with_trans_spliced_transcript AS SELECT feature_id AS gene_with_trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_trans_spliced_transcript'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment'; --- ************************************************ --- *** relation: inversion_derived_bipartite_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at each *** --- *** end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_deficiency AS SELECT feature_id AS inversion_derived_bipartite_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: encodes_alternately_spliced_transcripts *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes more than one transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW encodes_alternately_spliced_transcripts AS SELECT feature_id AS encodes_alternately_spliced_transcripts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_alternately_spliced_transcripts'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendant of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome deletion whereby a chromoso *** --- *** me is generated by recombination between *** --- *** two inversions; there is a deficiency a *** --- *** t one end of the inversion and a duplica *** --- *** tion at the other end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_duplication AS SELECT feature_id AS inversion_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: v_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including L-part1, *** --- *** V-intron and V-exon, with the 5' UTR and *** --- *** 3' UTR. *** --- ************************************************ --- CREATE VIEW v_gene AS SELECT feature_id AS v_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_stability *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is regulated *** --- *** by the stability of the resulting prote *** --- *** in. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_stability AS SELECT feature_id AS post_translationally_regulated_by_protein_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is modified *** --- *** to regulate it. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_modification AS SELECT feature_id AS post_translationally_regulated_by_protein_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_modification'; --- ************************************************ --- *** relation: j_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA of an immunoglobuli *** --- *** n/T-cell receptor gene including J-regio *** --- *** n with 5' UTR (SO:0000204) and 3' UTR (S *** --- *** O:0000205), also designated as J-segment *** --- *** . *** --- ************************************************ --- CREATE VIEW j_gene AS SELECT feature_id AS j_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene'; --- ************************************************ --- *** relation: autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation. *** --- ************************************************ --- CREATE VIEW autoregulated AS SELECT feature_id AS autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'autoregulated'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: negatively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation where it decr *** --- *** eases transcription. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated AS SELECT feature_id AS negatively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path (SO:0000472). *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone' OR cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: positively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation, where it inc *** --- *** reases transcription. *** --- ************************************************ --- CREATE VIEW positively_autoregulated AS SELECT feature_id AS positively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated'; --- ************************************************ --- *** relation: contig_read *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequencer read which is part of a *** --- *** contig. *** --- ************************************************ --- CREATE VIEW contig_read AS SELECT feature_id AS contig_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read'; --- ************************************************ --- *** relation: c_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including C-region (and intro *** --- *** ns if present) with 5' UTR (SO:0000204) *** --- *** and 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW c_gene AS SELECT feature_id AS c_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_gene'; --- ************************************************ --- *** relation: trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_transcript AS SELECT feature_id AS trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'trans_spliced_transcript'; --- ************************************************ --- *** relation: tiling_path_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone which is part of a tiling path. *** --- *** A tiling path is a set of sequencing sub *** --- *** strates, typically clones, which have be *** --- *** en selected in order to efficiently cove *** --- *** r a region of the genome in preparation *** --- *** for sequencing and assembly. *** --- ************************************************ --- CREATE VIEW tiling_path_clone AS SELECT feature_id AS tiling_path_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone'; --- ************************************************ --- *** relation: terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An inverted repeat (SO:0000294) occurrin *** --- *** g at the termini of a DNA transposon. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat AS SELECT feature_id AS terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'terminal_inverted_repeat'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_gene_cluster AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: three_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 3' exon that is not *** --- *** coding. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_noncoding_region AS SELECT feature_id AS three_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene, and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW dj_j_cluster AS SELECT feature_id AS dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster'; --- ************************************************ --- *** relation: five_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 5' exon preceding th *** --- *** e start codon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_noncoding_region AS SELECT feature_id AS five_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene, one J-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW vdj_j_c_cluster AS SELECT feature_id AS vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_j_cluster AS SELECT feature_id AS vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_cluster'; --- ************************************************ --- *** relation: vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_c_cluster AS SELECT feature_id AS vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_C_cluster'; --- ************************************************ --- *** relation: vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene, one J-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW vj_j_c_cluster AS SELECT feature_id AS vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_C_cluster'; --- ************************************************ --- *** relation: vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one J- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_j_cluster AS SELECT feature_id AS vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_cluster'; --- ************************************************ --- *** relation: d_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_gene_recombination_feature AS SELECT feature_id AS d_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'D_gene_recombination_feature'; --- ************************************************ --- *** relation: three_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site like CAC *** --- *** AGTG, part of a 3' D-recombination signa *** --- *** l sequence of an immunoglobulin/T-cell r *** --- *** eceptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_heptamer AS SELECT feature_id AS three_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer'; --- ************************************************ --- *** relation: three_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** A 9 nucleotide recombination site (e.g. *** --- *** ACAAAAACC), part of a 3' D-recombination *** --- *** signal sequence of an immunoglobulin/T- *** --- *** cell receptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_nonamer AS SELECT feature_id AS three_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer'; --- ************************************************ --- *** relation: three_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** A 12 or 23 nucleotide spacer between the *** --- *** 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-R *** --- *** S. *** --- ************************************************ --- CREATE VIEW three_prime_d_spacer AS SELECT feature_id AS three_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer'; --- ************************************************ --- *** relation: five_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CTGTG), part of a 5' D-recombination sig *** --- *** nal sequence (SO:0000556) of an immunogl *** --- *** obulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_heptamer AS SELECT feature_id AS five_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_heptamer'; --- ************************************************ --- *** relation: five_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a five_prime_D-recombi *** --- *** nation signal sequence (SO:0000556) of a *** --- *** n immunoglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_nonamer AS SELECT feature_id AS five_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_nonamer'; --- ************************************************ --- *** relation: five_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the 5 *** --- *** ' D-heptamer (SO:0000496) and 5' D-nonam *** --- *** er (SO:0000497) of a 5' D-recombination *** --- *** signal sequence (SO:0000556) of an immun *** --- *** oglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_spacer AS SELECT feature_id AS five_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_spacer'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous piece of sequence similar t *** --- *** o the 'virtual contig' concept of the En *** --- *** sembl database. *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. Th *** --- *** is is less energetically favourable than *** --- *** watson crick base pairing. Hoogsteen GC *** --- *** base pairs only have two hydrogen bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW hoogsteen_base_pair AS SELECT feature_id AS hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Hoogsteen_base_pair'; --- ************************************************ --- *** relation: reverse_hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW reverse_hoogsteen_base_pair AS SELECT feature_id AS reverse_hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_Hoogsteen_base_pair'; --- ************************************************ --- *** relation: d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_c_cluster AS SELECT feature_id AS d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_C_cluster'; --- ************************************************ --- *** relation: d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW d_dj_cluster AS SELECT feature_id AS d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_cluster'; --- ************************************************ --- *** relation: d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_c_cluster AS SELECT feature_id AS d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of an exon, *** --- *** part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, and one J-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_cluster AS SELECT feature_id AS d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_cluster'; --- ************************************************ --- *** relation: d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW d_j_c_cluster AS SELECT feature_id AS d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster'; --- ************************************************ --- *** relation: vd_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including L-part1, V-intron and V *** --- *** -D-exon, with the 5' UTR (SO:0000204) an *** --- *** d 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vd_gene AS SELECT feature_id AS vd_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene'; --- ************************************************ --- *** relation: j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one J-gene and one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW j_c_cluster AS SELECT feature_id AS j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at one e *** --- *** nd and presumed to have a deficiency or *** --- *** duplication at the other end of the inve *** --- *** rsion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_aneuploid AS SELECT feature_id AS inversion_derived_deficiency_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_aneuploid'; --- ************************************************ --- *** relation: j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one J-gene. *** --- ************************************************ --- CREATE VIEW j_cluster AS SELECT feature_id AS j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_cluster'; --- ************************************************ --- *** relation: j_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a J-gene recombination *** --- *** feature of an immunoglobulin/T-cell rec *** --- *** eptor gene. *** --- ************************************************ --- CREATE VIEW j_nonamer AS SELECT feature_id AS j_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_nonamer'; --- ************************************************ --- *** relation: j_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of a J-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW j_heptamer AS SELECT feature_id AS j_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_heptamer'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of a transcr *** --- *** ipt, part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: j_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the J *** --- *** -nonamer and the J-heptamer of a J-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW j_spacer AS SELECT feature_id AS j_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_spacer'; --- ************************************************ --- *** relation: v_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_dj_cluster AS SELECT feature_id AS v_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_cluster'; --- ************************************************ --- *** relation: v_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_cluster AS SELECT feature_id AS v_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_cluster'; --- ************************************************ --- *** relation: v_vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_c_cluster AS SELECT feature_id AS v_vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_C_cluster'; --- ************************************************ --- *** relation: v_vdj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VDJ *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW v_vdj_cluster AS SELECT feature_id AS v_vdj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_cluster'; --- ************************************************ --- *** relation: v_vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_cluster AS SELECT feature_id AS v_vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_cluster'; --- ************************************************ --- *** relation: v_vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_c_cluster AS SELECT feature_id AS v_vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_C_cluster'; --- ************************************************ --- *** relation: v_vj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_vj_cluster AS SELECT feature_id AS v_vj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_cluster'; --- ************************************************ --- *** relation: v_vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_cluster AS SELECT feature_id AS v_vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_cluster'; --- ************************************************ --- *** relation: v_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one V-gene. *** --- ************************************************ --- CREATE VIEW v_cluster AS SELECT feature_id AS v_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_cluster'; --- ************************************************ --- *** relation: v_d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_c_cluster AS SELECT feature_id AS v_d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_cluster AS SELECT feature_id AS v_d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene, one J-gene and one C-gene *** --- *** . *** --- ************************************************ --- CREATE VIEW v_d_dj_j_c_cluster AS SELECT feature_id AS v_d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_j_cluster AS SELECT feature_id AS v_d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_cluster'; --- ************************************************ --- *** relation: v_d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_c_cluster AS SELECT feature_id AS v_d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_C_cluster'; --- ************************************************ --- *** relation: v_d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_cluster AS SELECT feature_id AS v_d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_cluster'; --- ************************************************ --- *** relation: v_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of V-gene recombination fea *** --- *** ture of an immunoglobulin/T-cell recepto *** --- *** r gene. *** --- ************************************************ --- CREATE VIEW v_heptamer AS SELECT feature_id AS v_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_heptamer'; --- ************************************************ --- *** relation: v_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW v_j_cluster AS SELECT feature_id AS v_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_cluster'; --- ************************************************ --- *** relation: v_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW v_j_c_cluster AS SELECT feature_id AS v_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_C_cluster'; --- ************************************************ --- *** relation: v_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. AC *** --- *** AAAAACC), part of V-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW v_nonamer AS SELECT feature_id AS v_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_nonamer'; --- ************************************************ --- *** relation: v_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the V *** --- *** -heptamer and the V-nonamer of a V-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_spacer AS SELECT feature_id AS v_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_spacer'; --- ************************************************ --- *** relation: v_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including V-heptame *** --- *** r, V-spacer and V-nonamer in 3' of V-reg *** --- *** ion of a V-gene or V-sequence of an immu *** --- *** noglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_gene_recombination_feature AS SELECT feature_id AS v_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene_recombination_feature'; --- ************************************************ --- *** relation: dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW dj_c_cluster AS SELECT feature_id AS dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_C_cluster'; --- ************************************************ --- *** relation: dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA in rearranged configuration *** --- *** including at least one D-J-GENE, one J-G *** --- *** ENE and one C-GENE. *** --- ************************************************ --- CREATE VIEW dj_j_c_cluster AS SELECT feature_id AS dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one C *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_c_cluster AS SELECT feature_id AS vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_C_cluster'; --- ************************************************ --- *** relation: v_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_c_cluster AS SELECT feature_id AS v_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_C_cluster'; --- ************************************************ --- *** relation: helitron *** --- *** relation type: VIEW *** --- *** *** --- *** A rolling circle transposon. Autonomous *** --- *** helitrons encode a 5'-to-3' DNA helicase *** --- *** and nuclease/ligase similar to those en *** --- *** coded by known rolling-circle replicons. *** --- ************************************************ --- CREATE VIEW helitron AS SELECT feature_id AS helitron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helitron'; --- ************************************************ --- *** relation: recoding_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** The pseudoknots involved in recoding are *** --- *** unique in that, as they play their role *** --- *** as a structure, they are immediately un *** --- *** folded and their now linear sequence ser *** --- *** ves as a template for decoding. *** --- ************************************************ --- CREATE VIEW recoding_pseudoknot AS SELECT feature_id AS recoding_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot'; --- ************************************************ --- *** relation: designed_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW designed_sequence AS SELECT feature_id AS designed_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'designed_sequence'; --- ************************************************ --- *** relation: inversion_derived_bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a dupli *** --- *** cation at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_duplication AS SELECT feature_id AS inversion_derived_bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_duplication'; --- ************************************************ --- *** relation: gene_with_edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript that is *** --- *** edited. *** --- ************************************************ --- CREATE VIEW gene_with_edited_transcript AS SELECT feature_id AS gene_with_edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_edited_transcript'; --- ************************************************ --- *** relation: inversion_derived_duplication_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a duplicatio *** --- *** n at one end and presumed to have a defi *** --- *** ciency or duplication at the other end o *** --- *** f the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_duplication_plus_aneuploid AS SELECT feature_id AS inversion_derived_duplication_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_duplication_plus_aneuploid'; --- ************************************************ --- *** relation: aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structural variation whereb *** --- *** y either a chromosome exists in addition *** --- *** to the normal chromosome complement or *** --- *** is lacking. *** --- ************************************************ --- CREATE VIEW aneuploid_chromosome AS SELECT feature_id AS aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'aneuploid_chromosome'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region in the 5' UTR that pairs with t *** --- *** he 16S rRNA during formation of the prei *** --- *** nitiation complex. *** --- ************************************************ --- CREATE VIEW shine_dalgarno_sequence AS SELECT feature_id AS shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. The bound *** --- *** ary between the UTR and the polyA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: five_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 5' most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW five_prime_clip AS SELECT feature_id AS five_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip'; --- ************************************************ --- *** relation: five_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 5' *** --- *** D-nonamer (SO:0000497), 5' D-spacer (SO *** --- *** :0000498), and 5' D-heptamer (SO:0000396 *** --- *** ) in 5' of the D-region of a D-gene, or *** --- *** in 5' of the D-region of DJ-gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_recombination_signal_sequence AS SELECT feature_id AS five_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: three_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 3'-most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW three_prime_clip AS SELECT feature_id AS three_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_clip'; --- ************************************************ --- *** relation: c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including more than one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW c_cluster AS SELECT feature_id AS c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_cluster'; --- ************************************************ --- *** relation: d_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one D-gene. *** --- ************************************************ --- CREATE VIEW d_cluster AS SELECT feature_id AS d_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_cluster'; --- ************************************************ --- *** relation: d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW d_j_cluster AS SELECT feature_id AS d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_cluster'; --- ************************************************ --- *** relation: heptamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Seven nucleotide recombination site (e.g *** --- *** . CACAGTG), part of V-gene, D-gene or J- *** --- *** gene recombination feature of an immunog *** --- *** lobulin or T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW heptamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS heptamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: nonamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nonamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS nonamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_spacer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_spacer AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer'; --- ************************************************ --- *** relation: v_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_c_cluster AS SELECT feature_id AS v_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_c_cluster AS SELECT feature_id AS v_vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_c_cluster AS SELECT feature_id AS v_vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome may be generated by recombi *** --- *** nation between two inversions; presumed *** --- *** to have a deficiency or duplication at e *** --- *** ach end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_aneuploid_chromosome AS SELECT feature_id AS inversion_derived_aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome'; --- ************************************************ --- *** relation: bidirectional_promoter *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bidirectional_promoter AS SELECT feature_id AS bidirectional_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter'; --- ************************************************ --- *** relation: retrotransposed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of a feature that occurred *** --- *** as the product of a reverse transcriptas *** --- *** e mediated event. *** --- ************************************************ --- CREATE VIEW retrotransposed AS SELECT feature_id AS retrotransposed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposed'; --- ************************************************ --- *** relation: three_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 3' *** --- *** D-heptamer (SO:0000493), 3' D-spacer, a *** --- *** nd 3' D-nonamer (SO:0000494) in 3' of th *** --- *** e D-region of a D-gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_recombination_signal_sequence AS SELECT feature_id AS three_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: mirna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_encoding AS SELECT feature_id AS mirna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding'; --- ************************************************ --- *** relation: dj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including D-J-region with 5' UTR *** --- *** and 3' UTR, also designated as D-J-segme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW dj_gene AS SELECT feature_id AS dj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_gene'; --- ************************************************ --- *** relation: rrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rrna_encoding AS SELECT feature_id AS rrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_encoding'; --- ************************************************ --- *** relation: vdj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-D-J-exon, with the 5'UTR *** --- *** (SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vdj_gene AS SELECT feature_id AS vdj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_gene'; --- ************************************************ --- *** relation: scrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_encoding AS SELECT feature_id AS scrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_encoding'; --- ************************************************ --- *** relation: vj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-J-exon, with the 5'UTR ( *** --- *** SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vj_gene AS SELECT feature_id AS vj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_gene'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'centromere'; --- ************************************************ --- *** relation: snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_encoding AS SELECT feature_id AS snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'snoRNA_encoding'; --- ************************************************ --- *** relation: edited_transcript_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable feature on a transcript that *** --- *** is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript_feature AS SELECT feature_id AS edited_transcript_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'edited_transcript_feature'; --- ************************************************ --- *** relation: methylation_guide_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a methylat *** --- *** ion guide small nucleolar RNA. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna_primary_transcript AS SELECT feature_id AS methylation_guide_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: rrna_cleavage_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding an rRNA cl *** --- *** eavage snoRNA. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_snorna_primary_transcript AS SELECT feature_id AS rrna_cleavage_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: pre_edited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a transcript that will be *** --- *** edited. *** --- ************************************************ --- CREATE VIEW pre_edited_region AS SELECT feature_id AS pre_edited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region'; --- ************************************************ --- *** relation: tmrna *** --- *** relation type: VIEW *** --- *** *** --- *** A tmRNA liberates a mRNA from a stalled *** --- *** ribosome. To accomplish this part of the *** --- *** tmRNA is used as a reading frame that e *** --- *** nds in a translation stop signal. The br *** --- *** oken mRNA is replaced in the ribosome by *** --- *** the tmRNA and translation of the tmRNA *** --- *** leads to addition of a proteolysis tag t *** --- *** o the incomplete protein enabling recogn *** --- *** ition by a protease. Recently a number o *** --- *** f permuted tmRNAs genes have been found *** --- *** encoded in two parts. TmRNAs have been i *** --- *** dentified in eubacteria and some chlorop *** --- *** lasts but are absent from archeal and Eu *** --- *** karyote nuclear genomes. *** --- ************************************************ --- CREATE VIEW tmrna AS SELECT feature_id AS tmrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_encoding AS SELECT feature_id AS c_d_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding'; --- ************************************************ --- *** relation: tmrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tmRNA (S *** --- *** O:0000584). *** --- ************************************************ --- CREATE VIEW tmrna_primary_transcript AS SELECT feature_id AS tmrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_primary_transcript'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyze their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: autocatalytically_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW autocatalytically_spliced_intron AS SELECT feature_id AS autocatalytically_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: srp_rna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a signal r *** --- *** ecognition particle RNA. *** --- ************************************************ --- CREATE VIEW srp_rna_primary_transcript AS SELECT feature_id AS srp_rna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_primary_transcript'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A tertiary structure in RNA where nucleo *** --- *** tides in a loop form base pairs with a r *** --- *** egion of RNA downstream of the loop. *** --- ************************************************ --- CREATE VIEW pseudoknot AS SELECT feature_id AS pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'pseudoknot'; --- ************************************************ --- *** relation: h_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudoknot which contains two stems an *** --- *** d at least two loops. *** --- ************************************************ --- CREATE VIEW h_pseudoknot AS SELECT feature_id AS h_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_pseudoknot'; --- ************************************************ --- *** relation: c_d_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Most box C/D snoRNAs also contain long ( *** --- *** >10 nt) sequences complementary to rRNA. *** --- *** Boxes C and D, as well as boxes C' and *** --- *** D', are usually located in close proximi *** --- *** ty, and form a structure known as the bo *** --- *** x C/D motif. This motif is important for *** --- *** snoRNA stability, processing, nucleolar *** --- *** targeting and function. A small number *** --- *** of box C/D snoRNAs are involved in rRNA *** --- *** processing; most, however, are known or *** --- *** predicted to serve as guide RNAs in ribo *** --- *** se methylation of rRNA. Targeting involv *** --- *** es direct base pairing of the snoRNA at *** --- *** the rRNA site to be modified and selecti *** --- *** on of a rRNA nucleotide a fixed distance *** --- *** from box D or D'. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna AS SELECT feature_id AS c_d_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'C_D_box_snoRNA'; --- ************************************************ --- *** relation: h_aca_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Members of the box H/ACA family contain *** --- *** an ACA triplet, exactly 3 nt upstream fr *** --- *** om the 3' end and an H-box in a hinge re *** --- *** gion that links two structurally similar *** --- *** functional domains of the molecule. Bot *** --- *** h boxes are important for snoRNA biosynt *** --- *** hesis and function. A few box H/ACA snoR *** --- *** NAs are involved in rRNA processing; mos *** --- *** t others are known or predicted to parti *** --- *** cipate in selection of uridine nucleosid *** --- *** es in rRNA to be converted to pseudourid *** --- *** ines. Site selection is mediated by dire *** --- *** ct base pairing of the snoRNA with rRNA *** --- *** through one or both targeting domains. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna AS SELECT feature_id AS h_aca_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box C/D family. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_primary_transcript AS SELECT feature_id AS c_d_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: h_aca_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box H/ACA family. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_primary_transcript AS SELECT feature_id AS h_aca_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a duplex (except for its post-transcript *** --- *** ionally added oligo_U tail (SO:0000609)) *** --- *** with a stretch of mature edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: editing_block *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by a singl *** --- *** e guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW editing_block AS SELECT feature_id AS editing_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_block'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing or overlapping no ge *** --- *** nes that is bounded on either side by a *** --- *** gene, or bounded by a gene and the end o *** --- *** f the chromosome. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: editing_domain *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by two or *** --- *** more overlapping guide RNAs (SO:0000602) *** --- *** . *** --- ************************************************ --- CREATE VIEW editing_domain AS SELECT feature_id AS editing_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_domain'; --- ************************************************ --- *** relation: unedited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an edited transcript that *** --- *** will not be edited. *** --- ************************************************ --- CREATE VIEW unedited_region AS SELECT feature_id AS unedited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unedited_region'; --- ************************************************ --- *** relation: h_aca_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_encoding AS SELECT feature_id AS h_aca_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_encoding'; --- ************************************************ --- *** relation: oligo_u_tail *** --- *** relation type: VIEW *** --- *** *** --- *** The string of non-encoded U's at the 3' *** --- *** end of a guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW oligo_u_tail AS SELECT feature_id AS oligo_u_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo_U_tail'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which bacterial RNA po *** --- *** lymerase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter AS SELECT feature_id AS bacterial_rnapol_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'bacterial_RNApol_promoter'; --- ************************************************ --- *** relation: bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for bacterial transc *** --- *** ription. *** --- ************************************************ --- CREATE VIEW bacterial_terminator AS SELECT feature_id AS bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'bacterial_terminator'; --- ************************************************ --- *** relation: terminator_of_type_2_rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for RNA polymerase I *** --- *** II transcription. *** --- ************************************************ --- CREATE VIEW terminator_of_type_2_rnapol_iii_promoter AS SELECT feature_id AS terminator_of_type_2_rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter'; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The base where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_1 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_1 AS SELECT feature_id AS rnapol_iii_promoter_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_2 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_2 AS SELECT feature_id AS rnapol_iii_promoter_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_2'; --- ************************************************ --- *** relation: a_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence TGGCnnAGTGG. *** --- ************************************************ --- CREATE VIEW a_box AS SELECT feature_id AS a_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'A_box'; --- ************************************************ --- *** relation: b_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence AGGTTCCAnnCC. *** --- ************************************************ --- CREATE VIEW b_box AS SELECT feature_id AS b_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'B_box'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_3 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_3 AS SELECT feature_id AS rnapol_iii_promoter_type_3_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_3'; --- ************************************************ --- *** relation: c_box *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA polymerase III type 1 promoter wi *** --- *** th consensus sequence CAnnCCn. *** --- ************************************************ --- CREATE VIEW c_box AS SELECT feature_id AS c_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_box'; --- ************************************************ --- *** relation: snrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_encoding AS SELECT feature_id AS snrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_encoding'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenance of the end. *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region which upon binding o *** --- *** f transcription factors, suppress the tr *** --- *** anscription of the gene or genes they co *** --- *** ntrol. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: chromosomal_regulatory_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_regulatory_element AS SELECT feature_id AS chromosomal_regulatory_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'chromosomal_regulatory_element'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional cis regulatory region *** --- *** that when located between a CM and a gen *** --- *** e's promoter prevents the CRM from modul *** --- *** ating that genes expression. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: five_prime_open_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_open_reading_frame AS SELECT feature_id AS five_prime_open_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_open_reading_frame'; --- ************************************************ --- *** relation: upstream_aug_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon upstream of the ORF. *** --- ************************************************ --- CREATE VIEW upstream_aug_codon AS SELECT feature_id AS upstream_aug_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon'; --- ************************************************ --- *** relation: polycistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for more t *** --- *** han one gene product. *** --- ************************************************ --- CREATE VIEW polycistronic_primary_transcript AS SELECT feature_id AS polycistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for one ge *** --- *** ne product. *** --- ************************************************ --- CREATE VIEW monocistronic_primary_transcript AS SELECT feature_id AS monocistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with either a single protein pro *** --- *** duct, or for which the regions encoding *** --- *** all its protein products overlap. *** --- ************************************************ --- CREATE VIEW monocistronic_mrna AS SELECT feature_id AS monocistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_mRNA'; --- ************************************************ --- *** relation: polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that encodes multiple proteins f *** --- *** rom at least two non-overlapping regions *** --- *** . *** --- ************************************************ --- CREATE VIEW polycistronic_mrna AS SELECT feature_id AS polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA'; --- ************************************************ --- *** relation: mini_exon_donor_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that donates the sp *** --- *** liced leader to other mRNA. *** --- ************************************************ --- CREATE VIEW mini_exon_donor_rna AS SELECT feature_id AS mini_exon_donor_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_exon_donor_RNA'; --- ************************************************ --- *** relation: spliced_leader_rna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW spliced_leader_rna AS SELECT feature_id AS spliced_leader_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliced_leader_RNA'; --- ************************************************ --- *** relation: engineered_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_plasmid AS SELECT feature_id AS engineered_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_plasmid'; --- ************************************************ --- *** relation: transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Part of an rRNA transcription unit that *** --- *** is transcribed but discarded during matu *** --- *** ration, not giving rise to any part of r *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW transcribed_spacer_region AS SELECT feature_id AS transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'transcribed_spacer_region'; --- ************************************************ --- *** relation: internal_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA sequence that *** --- *** separate genes coding for the 28S, 5.8S, *** --- *** and 18S ribosomal RNAs. *** --- ************************************************ --- CREATE VIEW internal_transcribed_spacer_region AS SELECT feature_id AS internal_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region'; --- ************************************************ --- *** relation: external_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA that precede t *** --- *** he sequence that codes for the ribosomal *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW external_transcribed_spacer_region AS SELECT feature_id AS external_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'external_transcribed_spacer_region'; --- ************************************************ --- *** relation: tetranuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tetranuc_repeat_microsat AS SELECT feature_id AS tetranuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetranucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: srp_rna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_encoding AS SELECT feature_id AS srp_rna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_encoding'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region containing tandemly repe *** --- *** ated sequences having a unit length of 1 *** --- *** 0 to 40 bp. *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA' OR cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small RNA molecule that is the product *** --- *** of a longer exogenous or endogenous dsR *** --- *** NA, which is either a bimolecular duplex *** --- *** or very long hairpin, processed (via th *** --- *** e Dicer pathway) such that numerous siRN *** --- *** As accumulate from both strands of the d *** --- *** sRNA. SRNAs trigger the cleavage of thei *** --- *** r target molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: mirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a micro RN *** --- *** A. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript AS SELECT feature_id AS mirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript'; --- ************************************************ --- *** relation: strna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small te *** --- *** mporal mRNA (SO:0000649). *** --- ************************************************ --- CREATE VIEW strna_primary_transcript AS SELECT feature_id AS strna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: small_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the small subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW small_subunit_rrna AS SELECT feature_id AS small_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'small_subunit_rRNA'; --- ************************************************ --- *** relation: large_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the large subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW large_subunit_rrna AS SELECT feature_id AS large_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'large_subunit_rRNA'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilizes 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: maxicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mitochondrial gene located in a maxici *** --- *** rcle. *** --- ************************************************ --- CREATE VIEW maxicircle_gene AS SELECT feature_id AS maxicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'maxicircle_gene'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA transcript that does not encode f *** --- *** or a protein rather the RNA molecule is *** --- *** the gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: strna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_encoding AS SELECT feature_id AS strna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_encoding'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: tmrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_encoding AS SELECT feature_id AS tmrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_encoding'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: trna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_encoding AS SELECT feature_id AS trna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_encoding'; --- ************************************************ --- *** relation: introgressed_chromosome_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW introgressed_chromosome_region AS SELECT feature_id AS introgressed_chromosome_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'introgressed_chromosome_region'; --- ************************************************ --- *** relation: monocistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is monocistronic. *** --- ************************************************ --- CREATE VIEW monocistronic_transcript AS SELECT feature_id AS monocistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'monocistronic_transcript'; --- ************************************************ --- *** relation: mobile_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron (mitochondrial, chloroplast, n *** --- *** uclear or prokaryotic) that encodes a do *** --- *** uble strand sequence specific endonuclea *** --- *** se allowing for mobility. *** --- ************************************************ --- CREATE VIEW mobile_intron AS SELECT feature_id AS mobile_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of one or more nucleotides *** --- *** added between two adjacent nucleotides i *** --- *** n the sequence. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'insertion'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: sequence_rearrangement_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_rearrangement_feature AS SELECT feature_id AS sequence_rearrangement_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'sequence_rearrangement_feature'; --- ************************************************ --- *** relation: chromosome_breakage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence within the micronuclear DNA o *** --- *** f ciliates at which chromosome breakage *** --- *** and telomere addition occurs during nucl *** --- *** ear differentiation. *** --- ************************************************ --- CREATE VIEW chromosome_breakage_sequence AS SELECT feature_id AS chromosome_breakage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_breakage_sequence'; --- ************************************************ --- *** relation: internal_eliminated_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence eliminated from the genome of *** --- *** ciliates during nuclear differentiation *** --- *** . *** --- ************************************************ --- CREATE VIEW internal_eliminated_sequence AS SELECT feature_id AS internal_eliminated_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_eliminated_sequence'; --- ************************************************ --- *** relation: macronucleus_destined_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that is conserved, although r *** --- *** earranged relative to the micronucleus, *** --- *** in the macronucleus of a ciliate genome. *** --- ************************************************ --- CREATE VIEW macronucleus_destined_segment AS SELECT feature_id AS macronucleus_destined_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronucleus_destined_segment'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcript'; --- ************************************************ --- *** relation: canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 3' splice site has the seq *** --- *** uence "AG". *** --- ************************************************ --- CREATE VIEW canonical_three_prime_splice_site AS SELECT feature_id AS canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 5' splice site has the seq *** --- *** uence "GT". *** --- ************************************************ --- CREATE VIEW canonical_five_prime_splice_site AS SELECT feature_id AS canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 3' splice site that does not have the *** --- *** sequence "AG". *** --- ************************************************ --- CREATE VIEW non_canonical_three_prime_splice_site AS SELECT feature_id AS non_canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 5' splice site which does not have the *** --- *** sequence "GT". *** --- ************************************************ --- CREATE VIEW non_canonical_five_prime_splice_site AS SELECT feature_id AS non_canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon that is not the usual AUG *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW non_canonical_start_codon AS SELECT feature_id AS non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'non_canonical_start_codon'; --- ************************************************ --- *** relation: aberrant_processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been processed "in *** --- *** correctly", for example by the failure o *** --- *** f splicing of one or more exons. *** --- ************************************************ --- CREATE VIEW aberrant_processed_transcript AS SELECT feature_id AS aberrant_processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aberrant_processed_transcript'; --- ************************************************ --- *** relation: exonic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Exonic splicing enhancers (ESEs) facilit *** --- *** ate exon definition by assisting in the *** --- *** recruitment of splicing factors to the a *** --- *** djacent intron. *** --- ************************************************ --- CREATE VIEW exonic_splice_enhancer AS SELECT feature_id AS exonic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exonic_splice_enhancer'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targeted *** --- *** by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: dnasei_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dnasei_hypersensitive_site AS SELECT feature_id AS dnasei_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site'; --- ************************************************ --- *** relation: translocation_element *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** chromosomes carrying non-homologous cent *** --- *** romeres may be recovered independently. *** --- *** These chromosomes are described as trans *** --- *** location elements. This occurs for some *** --- *** translocations, particularly but not exc *** --- *** lusively, reciprocal translocations. *** --- ************************************************ --- CREATE VIEW translocation_element AS SELECT feature_id AS translocation_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occurred. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: gene_with_polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW gene_with_polycistronic_transcript AS SELECT feature_id AS gene_with_polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_polycistronic_transcript'; --- ************************************************ --- *** relation: cleaved_initiator_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** The initiator methionine that has been c *** --- *** leaved from a mature polypeptide sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW cleaved_initiator_methionine AS SELECT feature_id AS cleaved_initiator_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine'; --- ************************************************ --- *** relation: gene_with_dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_transcript AS SELECT feature_id AS gene_with_dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_dicistronic_transcript'; --- ************************************************ --- *** relation: gene_with_recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA that is reco *** --- *** ded. *** --- ************************************************ --- CREATE VIEW gene_with_recoded_mrna AS SELECT feature_id AS gene_with_recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_recoded_mRNA'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives exist in normal individuals *** --- *** in some population(s), wherein the least *** --- *** frequent variant has an abundance of 1% *** --- *** or greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'oligo'; --- ************************************************ --- *** relation: gene_with_stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript with st *** --- *** op codon readthrough. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_read_through AS SELECT feature_id AS gene_with_stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_stop_codon_read_through'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as pyrrolysine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent of zer *** --- *** o. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'junction'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'remark'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A region (or regions) that includes all *** --- *** of the sequence elements necessary to en *** --- *** code a functional transcript. A gene may *** --- *** include regulatory regions, transcribed *** --- *** regions and/or other functional sequenc *** --- *** e regions. *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjcent copies of a region ( *** --- *** of length greater than 1). *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 3' splice site of the acceptor prima *** --- *** ry transcript. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: trans_splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' five prime splice site region of *** --- *** the donor RNA. *** --- ************************************************ --- CREATE VIEW trans_splice_donor_site AS SELECT feature_id AS trans_splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_donor_site'; --- ************************************************ --- *** relation: sl1_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL1 RNA leader sequence to *** --- *** the 5' end of most mRNAs. *** --- ************************************************ --- CREATE VIEW sl1_acceptor_site AS SELECT feature_id AS sl1_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site'; --- ************************************************ --- *** relation: sl2_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL2 RNA leader sequence to *** --- *** the 5' end of mRNAs. SL2 acceptor sites *** --- *** occur in genes in internal segments of *** --- *** polycistronic transcripts. *** --- ************************************************ --- CREATE VIEW sl2_acceptor_site AS SELECT feature_id AS sl2_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'SL2_acceptor_site'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as selenocysteine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: gene_with_mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with mRNA recoded by translationa *** --- *** l bypass. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_recoded_by_translational_bypass AS SELECT feature_id AS gene_with_mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: gene_with_transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding a transcript that has a *** --- *** translational frameshift. *** --- ************************************************ --- CREATE VIEW gene_with_transcript_with_translational_frameshift AS SELECT feature_id AS gene_with_transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: dna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in the DNA form o *** --- *** f the sequence. *** --- ************************************************ --- CREATE VIEW dna_motif AS SELECT feature_id AS dna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'DNA_motif'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_motif AS SELECT feature_id AS rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_motif'; --- ************************************************ --- *** relation: dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that has the quality dicistronic *** --- *** . *** --- ************************************************ --- CREATE VIEW dicistronic_mrna AS SELECT feature_id AS dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It need not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: blocked_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A reading_frame that is interrupted by o *** --- *** ne or more stop codons; usually identifi *** --- *** ed through intergenomic sequence compari *** --- *** sons. *** --- ************************************************ --- CREATE VIEW blocked_reading_frame AS SELECT feature_id AS blocked_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blocked_reading_frame'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_transposable_element AS SELECT feature_id AS foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'foreign_transposable_element'; --- ************************************************ --- *** relation: gene_with_dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic primar *** --- *** y transcript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_primary_transcript AS SELECT feature_id AS gene_with_dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript'; --- ************************************************ --- *** relation: gene_with_dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic mRNA *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_mrna AS SELECT feature_id AS gene_with_dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_mRNA'; --- ************************************************ --- *** relation: idna *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic sequence removed from the genome *** --- *** , as a normal event, by a process of rec *** --- *** ombination. *** --- ************************************************ --- CREATE VIEW idna AS SELECT feature_id AS idna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iDNA'; --- ************************************************ --- *** relation: orit *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule where transfe *** --- *** r is initiated during the process of con *** --- *** jugation or mobilization. *** --- ************************************************ --- CREATE VIEW orit AS SELECT feature_id AS orit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriT'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The transit_peptide is a short region at *** --- *** the N-terminus of the peptide that dire *** --- *** cts the protein to an organelle (chlorop *** --- *** last, mitochondrion, microbody or cyanel *** --- *** le). *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: repeat_unit *** --- *** relation type: VIEW *** --- *** *** --- *** The simplest repeated component of a rep *** --- *** eat region. A single repeat. *** --- ************************************************ --- CREATE VIEW repeat_unit AS SELECT feature_id AS repeat_unit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_unit'; --- ************************************************ --- *** relation: crm *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region where more than 1 TF *** --- *** _binding_site together are regulatorily *** --- *** active. *** --- ************************************************ --- CREATE VIEW crm AS SELECT feature_id AS crm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'CRM'; --- ************************************************ --- *** relation: intein *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is able to ex *** --- *** cise itself and rejoin the remaining por *** --- *** tions with a peptide bond. *** --- ************************************************ --- CREATE VIEW intein AS SELECT feature_id AS intein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein'; --- ************************************************ --- *** relation: intein_containing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of protein-coding genes whe *** --- *** re the initial protein product contains *** --- *** an intein. *** --- ************************************************ --- CREATE VIEW intein_containing AS SELECT feature_id AS intein_containing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** he unknown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: fragmentary *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is incomplete. *** --- ************************************************ --- CREATE VIEW fragmentary AS SELECT feature_id AS fragmentary_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary'; --- ************************************************ --- *** relation: predicted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an unverified re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW predicted AS SELECT feature_id AS predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'predicted'; --- ************************************************ --- *** relation: feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a located_sequen *** --- *** ce_feature. *** --- ************************************************ --- CREATE VIEW feature_attribute AS SELECT feature_id AS feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'feature_attribute'; --- ************************************************ --- *** relation: exemplar_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An exemplar is a representative cDNA seq *** --- *** uence for each gene. The exemplar approa *** --- *** ch is a method that usually involves som *** --- *** e initial clustering into gene groups an *** --- *** d the subsequent selection of a represen *** --- *** tative from each gene group. *** --- ************************************************ --- CREATE VIEW exemplar_mrna AS SELECT feature_id AS exemplar_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar_mRNA'; --- ************************************************ --- *** relation: sequence_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_location AS SELECT feature_id AS sequence_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_location'; --- ************************************************ --- *** relation: organelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW organelle_sequence AS SELECT feature_id AS organelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'organelle_sequence'; --- ************************************************ --- *** relation: mitochondrial_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_sequence AS SELECT feature_id AS mitochondrial_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'mitochondrial_sequence'; --- ************************************************ --- *** relation: nuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclear_sequence AS SELECT feature_id AS nuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_sequence'; --- ************************************************ --- *** relation: nucleomorphic_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nucleomorphic_sequence AS SELECT feature_id AS nucleomorphic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_sequence'; --- ************************************************ --- *** relation: plastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plastid_sequence AS SELECT feature_id AS plastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'plastid_sequence'; --- ************************************************ --- *** relation: kinetoplast *** --- *** relation type: VIEW *** --- *** *** --- *** A kinetoplast is an interlocked network *** --- *** of thousands of minicircles and tens of *** --- *** maxi circles, located near the base of t *** --- *** he flagellum of some protozoan species. *** --- ************************************************ --- CREATE VIEW kinetoplast AS SELECT feature_id AS kinetoplast_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast'; --- ************************************************ --- *** relation: maxicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle is a replicon, part of a ki *** --- *** netoplast, that contains open reading fr *** --- *** ames and replicates via a rolling circle *** --- *** method. *** --- ************************************************ --- CREATE VIEW maxicircle AS SELECT feature_id AS maxicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle'; --- ************************************************ --- *** relation: apicoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW apicoplast_sequence AS SELECT feature_id AS apicoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence'; --- ************************************************ --- *** relation: chromoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromoplast_sequence AS SELECT feature_id AS chromoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_sequence'; --- ************************************************ --- *** relation: chloroplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_sequence AS SELECT feature_id AS chloroplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'chloroplast_sequence'; --- ************************************************ --- *** relation: cyanelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cyanelle_sequence AS SELECT feature_id AS cyanelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_sequence'; --- ************************************************ --- *** relation: leucoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucoplast_sequence AS SELECT feature_id AS leucoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_sequence'; --- ************************************************ --- *** relation: proplastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proplastid_sequence AS SELECT feature_id AS proplastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_sequence'; --- ************************************************ --- *** relation: plasmid_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_location AS SELECT feature_id AS plasmid_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_location'; --- ************************************************ --- *** relation: amplification_origin *** --- *** relation type: VIEW *** --- *** *** --- *** An origin_of_replication that is used fo *** --- *** r the amplification of a chromosomal nuc *** --- *** leic acid sequence. *** --- ************************************************ --- CREATE VIEW amplification_origin AS SELECT feature_id AS amplification_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amplification_origin'; --- ************************************************ --- *** relation: proviral_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proviral_location AS SELECT feature_id AS proviral_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'proviral_location'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: clone_insert *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence that has been ins *** --- *** erted and is being propagated by the clo *** --- *** ne. *** --- ************************************************ --- CREATE VIEW clone_insert AS SELECT feature_id AS clone_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'clone_insert'; --- ************************************************ --- *** relation: lambda_vector *** --- *** relation type: VIEW *** --- *** *** --- *** The lambda bacteriophage is the vector f *** --- *** or the linear lambda clone. The genes in *** --- *** volved in the lysogenic pathway are remo *** --- *** ved from the from the viral DNA. Up to 2 *** --- *** 5 kb of foreign DNA can then be inserted *** --- *** into the lambda genome. *** --- ************************************************ --- CREATE VIEW lambda_vector AS SELECT feature_id AS lambda_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lambda_vector'; --- ************************************************ --- *** relation: plasmid_vector *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_vector AS SELECT feature_id AS plasmid_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_vector'; --- ************************************************ --- *** relation: cdna *** --- *** relation type: VIEW *** --- *** *** --- *** DNA synthesized by reverse transcriptase *** --- *** using RNA as a template. *** --- ************************************************ --- CREATE VIEW cdna AS SELECT feature_id AS cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'cDNA'; --- ************************************************ --- *** relation: single_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single_stranded_cdna AS SELECT feature_id AS single_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA'; --- ************************************************ --- *** relation: double_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double_stranded_cdna AS SELECT feature_id AS double_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_cDNA'; --- ************************************************ --- *** relation: pyrrolysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a pyrrolysine a *** --- *** nticodon, and a 3' pyrrolysine binding r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW pyrrolysyl_trna AS SELECT feature_id AS pyrrolysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysyl_tRNA'; --- ************************************************ --- *** relation: episome *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that may integrate with a chro *** --- *** mosome. *** --- ************************************************ --- CREATE VIEW episome AS SELECT feature_id AS episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'episome'; --- ************************************************ --- *** relation: tmrna_coding_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a two-piece tmRNA that bea *** --- *** rs the reading frame encoding the proteo *** --- *** lysis tag. The tmRNA gene undergoes circ *** --- *** ular permutation in some groups of bacte *** --- *** ria. Processing of the transcripts from *** --- *** such a gene leaves the mature tmRNA in t *** --- *** wo pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_coding_piece AS SELECT feature_id AS tmrna_coding_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece'; --- ************************************************ --- *** relation: tmrna_acceptor_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The acceptor region of a two-piece tmRNA *** --- *** that when mature is charged at its 3' e *** --- *** nd with alanine. The tmRNA gene undergoe *** --- *** s circular permutation in some groups of *** --- *** bacteria; processing of the transcripts *** --- *** from such a gene leaves the mature tmRN *** --- *** A in two pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_acceptor_piece AS SELECT feature_id AS tmrna_acceptor_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_acceptor_piece'; --- ************************************************ --- *** relation: qtl *** --- *** relation type: VIEW *** --- *** *** --- *** A quantitative trait locus (QTL) is a po *** --- *** lymorphic locus which contains alleles t *** --- *** hat differentially affect the expression *** --- *** of a continuously distributed phenotypi *** --- *** c trait. Usually it is a marker describe *** --- *** d by statistical association to quantita *** --- *** tive variation in the particular phenoty *** --- *** pic trait that is thought to be controll *** --- *** ed by the cumulative action of alleles a *** --- *** t multiple loci. *** --- ************************************************ --- CREATE VIEW qtl AS SELECT feature_id AS qtl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'QTL'; --- ************************************************ --- *** relation: genomic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A genomic island is an integrated mobile *** --- *** genetic element, characterized by size *** --- *** (over 10 Kb). It that has features that *** --- *** suggest a foreign origin. These can incl *** --- *** ude nucleotide distribution (oligonucleo *** --- *** tides signature, CG content etc.) that d *** --- *** iffers from the bulk of the chromosome a *** --- *** nd/or genes suggesting DNA mobility. *** --- ************************************************ --- CREATE VIEW genomic_island AS SELECT feature_id AS genomic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'genomic_island'; --- ************************************************ --- *** relation: pathogenic_island *** --- *** relation type: VIEW *** --- *** *** --- *** Mobile genetic elements that contribute *** --- *** to rapid changes in virulence potential. *** --- *** They are present on the genomes of path *** --- *** ogenic strains but absent from the genom *** --- *** es of non pathogenic members of the same *** --- *** or related species. *** --- ************************************************ --- CREATE VIEW pathogenic_island AS SELECT feature_id AS pathogenic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island'; --- ************************************************ --- *** relation: metabolic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in metabolism, analogous to th *** --- *** e pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW metabolic_island AS SELECT feature_id AS metabolic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'metabolic_island'; --- ************************************************ --- *** relation: adaptive_island *** --- *** relation type: VIEW *** --- *** *** --- *** An adaptive island is a genomic island t *** --- *** hat provides an adaptive advantage to th *** --- *** e host. *** --- ************************************************ --- CREATE VIEW adaptive_island AS SELECT feature_id AS adaptive_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'adaptive_island'; --- ************************************************ --- *** relation: symbiosis_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in symbiosis, analogous to the *** --- *** pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW symbiosis_island AS SELECT feature_id AS symbiosis_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symbiosis_island'; --- ************************************************ --- *** relation: pseudogenic_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of an rRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_rrna AS SELECT feature_id AS pseudogenic_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_rRNA'; --- ************************************************ --- *** relation: pseudogenic_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of a tRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_trna AS SELECT feature_id AS pseudogenic_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_tRNA'; --- ************************************************ --- *** relation: engineered_episome *** --- *** relation type: VIEW *** --- *** *** --- *** An episome that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_episome AS SELECT feature_id AS engineered_episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome'; --- ************************************************ --- *** relation: transgenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence that has b *** --- *** een integrated with foreign sequence. *** --- ************************************************ --- CREATE VIEW transgenic AS SELECT feature_id AS transgenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic'; --- ************************************************ --- *** relation: so_natural *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that o *** --- *** ccurs in nature. *** --- ************************************************ --- CREATE VIEW so_natural AS SELECT feature_id AS so_natural_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural'; --- ************************************************ --- *** relation: engineered *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region that w *** --- *** as modified in vitro. *** --- ************************************************ --- CREATE VIEW engineered AS SELECT feature_id AS engineered_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered'; --- ************************************************ --- *** relation: so_foreign *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region from a *** --- *** nother species. *** --- ************************************************ --- CREATE VIEW so_foreign AS SELECT feature_id AS so_foreign_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foreign'; --- ************************************************ --- *** relation: cloned_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cloned_region AS SELECT feature_id AS cloned_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_region'; --- ************************************************ --- *** relation: validated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been proven. *** --- ************************************************ --- CREATE VIEW validated AS SELECT feature_id AS validated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined' OR cvterm.name = 'validated'; --- ************************************************ --- *** relation: invalidated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s invalidated. *** --- ************************************************ --- CREATE VIEW invalidated AS SELECT feature_id AS invalidated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'invalidated'; --- ************************************************ --- *** relation: engineered_rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A rescue region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_rescue_region AS SELECT feature_id AS engineered_rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region'; --- ************************************************ --- *** relation: rescue_mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mini_gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_mini_gene AS SELECT feature_id AS rescue_mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene'; --- ************************************************ --- *** relation: transgenic_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified in vitro, incl *** --- *** uding insertion of DNA derived from a so *** --- *** urce other than the originating TE. *** --- ************************************************ --- CREATE VIEW transgenic_transposable_element AS SELECT feature_id AS transgenic_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_transposable_element'; --- ************************************************ --- *** relation: natural_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that exists (or existed) in nature. *** --- ************************************************ --- CREATE VIEW natural_transposable_element AS SELECT feature_id AS natural_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element'; --- ************************************************ --- *** relation: engineered_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified by manipulatio *** --- *** ns in vitro. *** --- ************************************************ --- CREATE VIEW engineered_transposable_element AS SELECT feature_id AS engineered_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_transposable_element'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element AS SELECT feature_id AS engineered_foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element'; --- ************************************************ --- *** relation: assortment_derived_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome duplication aberratio *** --- *** n generated by reassortment of other abe *** --- *** rration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_duplication AS SELECT feature_id AS assortment_derived_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency an *** --- *** d a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency_plus_duplication AS SELECT feature_id AS assortment_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome deficiency aberration *** --- *** generated by reassortment of other aber *** --- *** ration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency AS SELECT feature_id AS assortment_derived_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency'; --- ************************************************ --- *** relation: assortment_derived_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency or *** --- *** a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_aneuploid AS SELECT feature_id AS assortment_derived_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_aneuploid'; --- ************************************************ --- *** relation: engineered_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_region AS SELECT feature_id AS engineered_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_region'; --- ************************************************ --- *** relation: engineered_foreign_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_region AS SELECT feature_id AS engineered_foreign_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_region'; --- ************************************************ --- *** relation: fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fusion AS SELECT feature_id AS fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fusion'; --- ************************************************ --- *** relation: engineered_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A tag that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_tag AS SELECT feature_id AS engineered_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_tag'; --- ************************************************ --- *** relation: validated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that has been validated. *** --- ************************************************ --- CREATE VIEW validated_cdna_clone AS SELECT feature_id AS validated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone'; --- ************************************************ --- *** relation: invalidated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that is invalid. *** --- ************************************************ --- CREATE VIEW invalidated_cdna_clone AS SELECT feature_id AS invalidated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone'; --- ************************************************ --- *** relation: chimeric_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated because it is c *** --- *** himeric. *** --- ************************************************ --- CREATE VIEW chimeric_cdna_clone AS SELECT feature_id AS chimeric_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone'; --- ************************************************ --- *** relation: genomically_contaminated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by genomic cont *** --- *** amination. *** --- ************************************************ --- CREATE VIEW genomically_contaminated_cdna_clone AS SELECT feature_id AS genomically_contaminated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomically_contaminated_cDNA_clone'; --- ************************************************ --- *** relation: polya_primed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by polyA primin *** --- *** g. *** --- ************************************************ --- CREATE VIEW polya_primed_cdna_clone AS SELECT feature_id AS polya_primed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_primed_cDNA_clone'; --- ************************************************ --- *** relation: partially_processed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA invalidated clone by partial proc *** --- *** essing. *** --- ************************************************ --- CREATE VIEW partially_processed_cdna_clone AS SELECT feature_id AS partially_processed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_processed_cDNA_clone'; --- ************************************************ --- *** relation: rescue *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region's abili *** --- *** ty, when introduced to a mutant organism *** --- *** , to re-establish (rescue) a phenotype. *** --- ************************************************ --- CREATE VIEW rescue AS SELECT feature_id AS rescue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue'; --- ************************************************ --- *** relation: mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** By definition, minigenes are short open- *** --- *** reading frames (ORF), usually encoding a *** --- *** pproximately 9 to 20 amino acids, which *** --- *** are expressed in vivo (as distinct from *** --- *** being synthesized as peptide or protein *** --- *** ex vivo and subsequently injected). The *** --- *** in vivo synthesis confers a distinct adv *** --- *** antage: the expressed sequences can ente *** --- *** r both antigen presentation pathways, MH *** --- *** C I (inducing CD8+ T- cells, which are u *** --- *** sually cytotoxic T-lymphocytes (CTL)) an *** --- *** d MHC II (inducing CD4+ T-cells, usually *** --- *** 'T-helpers' (Th)); and can encounter B- *** --- *** cells, inducing antibody responses. Thre *** --- *** e main vector approaches have been used *** --- *** to deliver minigenes: viral vectors, bac *** --- *** terial vectors and plasmid DNA. *** --- ************************************************ --- CREATE VIEW mini_gene AS SELECT feature_id AS mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'mini_gene'; --- ************************************************ --- *** relation: rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_gene AS SELECT feature_id AS rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'rescue_gene'; --- ************************************************ --- *** relation: wild_type *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence with th *** --- *** e genotype found in nature and/or standa *** --- *** rd laboratory stock. *** --- ************************************************ --- CREATE VIEW wild_type AS SELECT feature_id AS wild_type_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type'; --- ************************************************ --- *** relation: wild_type_rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW wild_type_rescue_gene AS SELECT feature_id AS wild_type_rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene'; --- ************************************************ --- *** relation: mitochondrial_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a mitochondr *** --- *** ia. *** --- ************************************************ --- CREATE VIEW mitochondrial_chromosome AS SELECT feature_id AS mitochondrial_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome'; --- ************************************************ --- *** relation: chloroplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chloroplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chloroplast_chromosome AS SELECT feature_id AS chloroplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_chromosome'; --- ************************************************ --- *** relation: chromoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chromoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chromoplast_chromosome AS SELECT feature_id AS chromoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_chromosome'; --- ************************************************ --- *** relation: cyanelle_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a cyanelle. *** --- ************************************************ --- CREATE VIEW cyanelle_chromosome AS SELECT feature_id AS cyanelle_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_chromosome'; --- ************************************************ --- *** relation: leucoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome with origin in a leucoplast *** --- *** . *** --- ************************************************ --- CREATE VIEW leucoplast_chromosome AS SELECT feature_id AS leucoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_chromosome'; --- ************************************************ --- *** relation: macronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a macronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW macronuclear_chromosome AS SELECT feature_id AS macronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_chromosome'; --- ************************************************ --- *** relation: micronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a micronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW micronuclear_chromosome AS SELECT feature_id AS micronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_chromosome'; --- ************************************************ --- *** relation: nuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_chromosome AS SELECT feature_id AS nuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_chromosome'; --- ************************************************ --- *** relation: nucleomorphic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleomorp *** --- *** h. *** --- ************************************************ --- CREATE VIEW nucleomorphic_chromosome AS SELECT feature_id AS nucleomorphic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_chromosome'; --- ************************************************ --- *** relation: chromosome_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_part AS SELECT feature_id AS chromosome_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosome_part'; --- ************************************************ --- *** relation: gene_member_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a gene. *** --- ************************************************ --- CREATE VIEW gene_member_region AS SELECT feature_id AS gene_member_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'gene_member_region'; --- ************************************************ --- *** relation: transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a transcript. *** --- ************************************************ --- CREATE VIEW transcript_region AS SELECT feature_id AS transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'transcript_region'; --- ************************************************ --- *** relation: mature_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a mature transcript. *** --- ************************************************ --- CREATE VIEW mature_transcript_region AS SELECT feature_id AS mature_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'mature_transcript_region'; --- ************************************************ --- *** relation: primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a primary transcript. *** --- ************************************************ --- CREATE VIEW primary_transcript_region AS SELECT feature_id AS primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'primary_transcript_region'; --- ************************************************ --- *** relation: mrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an mRNA. *** --- ************************************************ --- CREATE VIEW mrna_region AS SELECT feature_id AS mrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'mRNA_region'; --- ************************************************ --- *** relation: utr_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of UTR. *** --- ************************************************ --- CREATE VIEW utr_region AS SELECT feature_id AS utr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'UTR_region'; --- ************************************************ --- *** relation: rrna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an rRNA primary transcript. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript_region AS SELECT feature_id AS rrna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'rRNA_primary_transcript_region'; --- ************************************************ --- *** relation: polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Biological sequence region that can be a *** --- *** ssigned to a specific subsequence of a p *** --- *** olypeptide. *** --- ************************************************ --- CREATE VIEW polypeptide_region AS SELECT feature_id AS polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_region'; --- ************************************************ --- *** relation: repeat_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a repeated sequence. *** --- ************************************************ --- CREATE VIEW repeat_component AS SELECT feature_id AS repeat_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'repeat_component'; --- ************************************************ --- *** relation: spliceosomal_intron_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an intron. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron_region AS SELECT feature_id AS spliceosomal_intron_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'spliceosomal_intron_region'; --- ************************************************ --- *** relation: gene_component_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_component_region AS SELECT feature_id AS gene_component_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_component_region'; --- ************************************************ --- *** relation: tmrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tmRNA. *** --- ************************************************ --- CREATE VIEW tmrna_region AS SELECT feature_id AS tmrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'tmRNA_region'; --- ************************************************ --- *** relation: ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ltr_component AS SELECT feature_id AS ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'LTR_component'; --- ************************************************ --- *** relation: three_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr_component AS SELECT feature_id AS three_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'three_prime_LTR_component'; --- ************************************************ --- *** relation: five_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr_component AS SELECT feature_id AS five_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'five_prime_LTR_component'; --- ************************************************ --- *** relation: cds_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a CDS. *** --- ************************************************ --- CREATE VIEW cds_region AS SELECT feature_id AS cds_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'CDS_region'; --- ************************************************ --- *** relation: exon_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an exon. *** --- ************************************************ --- CREATE VIEW exon_region AS SELECT feature_id AS exon_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'exon_region'; --- ************************************************ --- *** relation: homologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is homologous to another r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW homologous_region AS SELECT feature_id AS homologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'homologous_region'; --- ************************************************ --- *** relation: paralogous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is paralogous t *** --- *** o another region. *** --- ************************************************ --- CREATE VIEW paralogous_region AS SELECT feature_id AS paralogous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region'; --- ************************************************ --- *** relation: orthologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is orthologous *** --- *** to another region. *** --- ************************************************ --- CREATE VIEW orthologous_region AS SELECT feature_id AS orthologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous_region'; --- ************************************************ --- *** relation: conserved *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW conserved AS SELECT feature_id AS conserved_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'conserved'; --- ************************************************ --- *** relation: homologous *** --- *** relation type: VIEW *** --- *** *** --- *** Similarity due to common ancestry. *** --- ************************************************ --- CREATE VIEW homologous AS SELECT feature_id AS homologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'homologous'; --- ************************************************ --- *** relation: orthologous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occured after a spec *** --- *** iation event. *** --- ************************************************ --- CREATE VIEW orthologous AS SELECT feature_id AS orthologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous'; --- ************************************************ --- *** relation: paralogous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occurred after a dup *** --- *** lication event. *** --- ************************************************ --- CREATE VIEW paralogous AS SELECT feature_id AS paralogous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous'; --- ************************************************ --- *** relation: syntenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence regions oc *** --- *** curring in same order on chromosome of d *** --- *** ifferent species. *** --- ************************************************ --- CREATE VIEW syntenic AS SELECT feature_id AS syntenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic'; --- ************************************************ --- *** relation: capped_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is capped. *** --- ************************************************ --- CREATE VIEW capped_primary_transcript AS SELECT feature_id AS capped_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_primary_transcript'; --- ************************************************ --- *** relation: capped_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is capped. *** --- ************************************************ --- CREATE VIEW capped_mrna AS SELECT feature_id AS capped_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_mRNA'; --- ************************************************ --- *** relation: mrna_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA feature. *** --- ************************************************ --- CREATE VIEW mrna_attribute AS SELECT feature_id AS mrna_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'mRNA_attribute'; --- ************************************************ --- *** relation: exemplar *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence is re *** --- *** presentative of a class of similar seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW exemplar AS SELECT feature_id AS exemplar_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar'; --- ************************************************ --- *** relation: frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains a mutation involving the deleti *** --- *** on or insertion of one or more bases, wh *** --- *** ere this number is not divisible by 3. *** --- ************************************************ --- CREATE VIEW frameshift AS SELECT feature_id AS frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'frameshift'; --- ************************************************ --- *** relation: minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting one base *** --- *** . *** --- ************************************************ --- CREATE VIEW minus_1_frameshift AS SELECT feature_id AS minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift'; --- ************************************************ --- *** relation: minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting two base *** --- *** s. *** --- ************************************************ --- CREATE VIEW minus_2_frameshift AS SELECT feature_id AS minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift'; --- ************************************************ --- *** relation: plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting one bas *** --- *** e. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift AS SELECT feature_id AS plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift'; --- ************************************************ --- *** relation: plus_2_framshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting two bas *** --- *** es. *** --- ************************************************ --- CREATE VIEW plus_2_framshift AS SELECT feature_id AS plus_2_framshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_framshift'; --- ************************************************ --- *** relation: trans_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing transcript seque *** --- *** nce that is created by splicing exons fr *** --- *** om diferent genes. *** --- ************************************************ --- CREATE VIEW trans_spliced AS SELECT feature_id AS trans_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced'; --- ************************************************ --- *** relation: polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is polyadenylated. *** --- ************************************************ --- CREATE VIEW polyadenylated_mrna AS SELECT feature_id AS polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated_mRNA'; --- ************************************************ --- *** relation: trans_spliced_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_mrna AS SELECT feature_id AS trans_spliced_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA'; --- ************************************************ --- *** relation: edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript AS SELECT feature_id AS edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript'; --- ************************************************ --- *** relation: edited_transcript_by_a_to_i_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been edited by A t *** --- *** o I substitution. *** --- ************************************************ --- CREATE VIEW edited_transcript_by_a_to_i_substitution AS SELECT feature_id AS edited_transcript_by_a_to_i_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution'; --- ************************************************ --- *** relation: bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a protein. *** --- ************************************************ --- CREATE VIEW bound_by_protein AS SELECT feature_id AS bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein'; --- ************************************************ --- *** relation: bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a nucleic acid. *** --- ************************************************ --- CREATE VIEW bound_by_nucleic_acid AS SELECT feature_id AS bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_nucleic_acid'; --- ************************************************ --- *** relation: alternatively_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a situation wher *** --- *** e a gene may encode for more than 1 tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW alternatively_spliced AS SELECT feature_id AS alternatively_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced'; --- ************************************************ --- *** relation: monocistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for one gene product. *** --- ************************************************ --- CREATE VIEW monocistronic AS SELECT feature_id AS monocistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic'; --- ************************************************ --- *** relation: dicistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for two gene products. *** --- ************************************************ --- CREATE VIEW dicistronic AS SELECT feature_id AS dicistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic'; --- ************************************************ --- *** relation: polycistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for more than one gene *** --- *** product. *** --- ************************************************ --- CREATE VIEW polycistronic AS SELECT feature_id AS polycistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic' OR cvterm.name = 'polycistronic'; --- ************************************************ --- *** relation: recoded *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA sequence *** --- *** that has been reprogrammed at translati *** --- *** on, causing localized alterations. *** --- ************************************************ --- CREATE VIEW recoded AS SELECT feature_id AS recoded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'recoded'; --- ************************************************ --- *** relation: codon_redefined *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the alteration o *** --- *** f codon meaning. *** --- ************************************************ --- CREATE VIEW codon_redefined AS SELECT feature_id AS codon_redefined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined'; --- ************************************************ --- *** relation: stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be a new amino *** --- *** acid. *** --- ************************************************ --- CREATE VIEW stop_codon_read_through AS SELECT feature_id AS stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'stop_codon_read_through'; --- ************************************************ --- *** relation: stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, pyrrolysine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, selenocysteine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** Recoded mRNA where a block of nucleotide *** --- *** s is not translated. *** --- ************************************************ --- CREATE VIEW recoded_by_translational_bypass AS SELECT feature_id AS recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_by_translational_bypass'; --- ************************************************ --- *** relation: translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** Recoding by frameshifting a particular s *** --- *** ite. *** --- ************************************************ --- CREATE VIEW translationally_frameshifted AS SELECT feature_id AS translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'translationally_frameshifted'; --- ************************************************ --- *** relation: maternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is maternally_imprinted. *** --- ************************************************ --- CREATE VIEW maternally_imprinted_gene AS SELECT feature_id AS maternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted_gene'; --- ************************************************ --- *** relation: paternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is paternally imprinted. *** --- ************************************************ --- CREATE VIEW paternally_imprinted_gene AS SELECT feature_id AS paternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is post translationally regu *** --- *** lated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_gene AS SELECT feature_id AS post_translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_gene'; --- ************************************************ --- *** relation: negatively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is negatively autoreguated. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated_gene AS SELECT feature_id AS negatively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated_gene'; --- ************************************************ --- *** relation: positively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is positively autoregulated. *** --- ************************************************ --- CREATE VIEW positively_autoregulated_gene AS SELECT feature_id AS positively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated_gene'; --- ************************************************ --- *** relation: silenced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated at tra *** --- *** nscriptional or translational level. *** --- ************************************************ --- CREATE VIEW silenced AS SELECT feature_id AS silenced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced'; --- ************************************************ --- *** relation: silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** modifications, resulting in repression *** --- *** of transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_modification AS SELECT feature_id AS silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_DNA_modification'; --- ************************************************ --- *** relation: silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** methylation, resulting in repression of *** --- *** transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_methylation AS SELECT feature_id AS silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is translationally regulated *** --- *** . *** --- ************************************************ --- CREATE VIEW translationally_regulated_gene AS SELECT feature_id AS translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated_gene'; --- ************************************************ --- *** relation: allelically_excluded_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is allelically_excluded. *** --- ************************************************ --- CREATE VIEW allelically_excluded_gene AS SELECT feature_id AS allelically_excluded_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded_gene'; --- ************************************************ --- *** relation: epigenetically_modified_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is epigenetically modified. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_gene AS SELECT feature_id AS epigenetically_modified_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'epigenetically_modified_gene'; --- ************************************************ --- *** relation: transgene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene is a gene that has been tran *** --- *** sferred naturally or by any of a number *** --- *** of genetic engineering techniques from o *** --- *** ne organism to another. *** --- ************************************************ --- CREATE VIEW transgene AS SELECT feature_id AS transgene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene' OR cvterm.name = 'transgene'; --- ************************************************ --- *** relation: endogenous_retroviral_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_sequence AS SELECT feature_id AS endogenous_retroviral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence'; --- ************************************************ --- *** relation: rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the sequence of *** --- *** a feature, where the DNA is rearranged. *** --- ************************************************ --- CREATE VIEW rearranged_at_dna_level AS SELECT feature_id AS rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rearranged_at_DNA_level'; --- ************************************************ --- *** relation: status *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the status of a *** --- *** feature, based on the available evidence *** --- *** . *** --- ************************************************ --- CREATE VIEW status AS SELECT feature_id AS status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'status'; --- ************************************************ --- *** relation: independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that is *** --- *** independently known - not predicted. *** --- ************************************************ --- CREATE VIEW independently_known AS SELECT feature_id AS independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'independently_known'; --- ************************************************ --- *** relation: supported_by_sequence_similarity *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity techniques. *** --- ************************************************ --- CREATE VIEW supported_by_sequence_similarity AS SELECT feature_id AS supported_by_sequence_similarity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'supported_by_sequence_similarity'; --- ************************************************ --- *** relation: supported_by_domain_match *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity of a known domain. *** --- ************************************************ --- CREATE VIEW supported_by_domain_match AS SELECT feature_id AS supported_by_domain_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match'; --- ************************************************ --- *** relation: supported_by_est_or_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity to EST or cDNA data. *** --- ************************************************ --- CREATE VIEW supported_by_est_or_cdna AS SELECT feature_id AS supported_by_est_or_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_EST_or_cDNA'; --- ************************************************ --- *** relation: orphan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW orphan AS SELECT feature_id AS orphan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan'; --- ************************************************ --- *** relation: predicted_by_ab_initio_computation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s predicted by a computer program that d *** --- *** id not rely on sequence similarity. *** --- ************************************************ --- CREATE VIEW predicted_by_ab_initio_computation AS SELECT feature_id AS predicted_by_ab_initio_computation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_by_ab_initio_computation'; --- ************************************************ --- *** relation: asx_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Asp *** --- *** artate or Asparagine (Asx), the side-cha *** --- *** in O of residue(i) is H-bonded to the ma *** --- *** in-chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW asx_turn AS SELECT feature_id AS asx_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'asx_turn'; --- ************************************************ --- *** relation: cloned_cdna_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from cDNA. *** --- ************************************************ --- CREATE VIEW cloned_cdna_insert AS SELECT feature_id AS cloned_cdna_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert'; --- ************************************************ --- *** relation: cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from genomic DNA. *** --- ************************************************ --- CREATE VIEW cloned_genomic_insert AS SELECT feature_id AS cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'cloned_genomic_insert'; --- ************************************************ --- *** relation: engineered_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_insert AS SELECT feature_id AS engineered_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_insert'; --- ************************************************ --- *** relation: edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is edited. *** --- ************************************************ --- CREATE VIEW edited_mrna AS SELECT feature_id AS edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_mRNA'; --- ************************************************ --- *** relation: guide_rna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of guide RNA. *** --- ************************************************ --- CREATE VIEW guide_rna_region AS SELECT feature_id AS guide_rna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'guide_RNA_region'; --- ************************************************ --- *** relation: anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that base-pairs *** --- *** to a target mRNA. *** --- ************************************************ --- CREATE VIEW anchor_region AS SELECT feature_id AS anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region'; --- ************************************************ --- *** relation: pre_edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pre_edited_mrna AS SELECT feature_id AS pre_edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA'; --- ************************************************ --- *** relation: intermediate *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature betwe *** --- *** en stages of processing. *** --- ************************************************ --- CREATE VIEW intermediate AS SELECT feature_id AS intermediate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate'; --- ************************************************ --- *** relation: mirna_target_site *** --- *** relation type: VIEW *** --- *** *** --- *** A miRNA target site is a binding site wh *** --- *** ere the molecule is a micro RNA. *** --- ************************************************ --- CREATE VIEW mirna_target_site AS SELECT feature_id AS mirna_target_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site'; --- ************************************************ --- *** relation: edited_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is edited. *** --- ************************************************ --- CREATE VIEW edited_cds AS SELECT feature_id AS edited_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment'; --- ************************************************ --- *** relation: vertebrate_ig_t_cell_receptor_rearranged_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_ig_t_cell_receptor_rearranged_gene_cluster AS SELECT feature_id AS vertebrate_ig_t_cell_receptor_rearranged_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_signal_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_signal_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_signal_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature'; --- ************************************************ --- *** relation: recombinationally_rearranged *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged AS SELECT feature_id AS recombinationally_rearranged_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged'; --- ************************************************ --- *** relation: recombinationally_rearranged_vertebrate_immune_system_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene of t *** --- *** he vertebrate immune system. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_vertebrate_immune_system_gene AS SELECT feature_id AS recombinationally_rearranged_vertebrate_immune_system_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: attp_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a phage *** --- *** chromosome at which a recombinase acts t *** --- *** o insert the phage DNA at a cognate inte *** --- *** gration/excision site on a bacterial chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW attp_site AS SELECT feature_id AS attp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attP_site'; --- ************************************************ --- *** relation: attb_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a bacter *** --- *** ial chromosome at which a recombinase ac *** --- *** ts to insert foreign DNA containing a co *** --- *** gnate integration/excision site. *** --- ************************************************ --- CREATE VIEW attb_site AS SELECT feature_id AS attb_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attB_site'; --- ************************************************ --- *** relation: attl_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attB_site and th *** --- *** e 3' portion of attP_site. *** --- ************************************************ --- CREATE VIEW attl_site AS SELECT feature_id AS attl_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attL_site'; --- ************************************************ --- *** relation: attr_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attP_site and th *** --- *** e 3' portion of attB_site. *** --- ************************************************ --- CREATE VIEW attr_site AS SELECT feature_id AS attr_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attR_site'; --- ************************************************ --- *** relation: integration_excision_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inserts or removes anot *** --- *** her region marked by a distinct cognate *** --- *** integration/excision site. *** --- ************************************************ --- CREATE VIEW integration_excision_site AS SELECT feature_id AS integration_excision_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'integration_excision_site'; --- ************************************************ --- *** relation: resolution_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which separates a physically *** --- *** contiguous circle of DNA into two physic *** --- *** ally separate circles. *** --- ************************************************ --- CREATE VIEW resolution_site AS SELECT feature_id AS resolution_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'resolution_site'; --- ************************************************ --- *** relation: inversion_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inverts the region flan *** --- *** ked by a pair of sites. *** --- ************************************************ --- CREATE VIEW inversion_site AS SELECT feature_id AS inversion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site' OR cvterm.name = 'inversion_site'; --- ************************************************ --- *** relation: dif_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site at which replicated bacterial cir *** --- *** cular chromosomes are decatenated by sit *** --- *** e specific resolvase. *** --- ************************************************ --- CREATE VIEW dif_site AS SELECT feature_id AS dif_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dif_site'; --- ************************************************ --- *** relation: attc_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attC site is a sequence required for *** --- *** the integration of a DNA of an integron. *** --- ************************************************ --- CREATE VIEW attc_site AS SELECT feature_id AS attc_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attC_site'; --- ************************************************ --- *** relation: eukaryotic_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW eukaryotic_terminator AS SELECT feature_id AS eukaryotic_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'eukaryotic_terminator'; --- ************************************************ --- *** relation: oriv *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of vegetative replication in p *** --- *** lasmids and phages. *** --- ************************************************ --- CREATE VIEW oriv AS SELECT feature_id AS oriv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriV'; --- ************************************************ --- *** relation: oric *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of bacterial chromosome replic *** --- *** ation. *** --- ************************************************ --- CREATE VIEW oric AS SELECT feature_id AS oric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriC'; --- ************************************************ --- *** relation: dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, DNA molecule. *** --- ************************************************ --- CREATE VIEW dna_chromosome AS SELECT feature_id AS dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'DNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_dna_chromosome AS SELECT feature_id AS double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_dna_chromosome AS SELECT feature_id AS single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_dna_chromosome AS SELECT feature_id AS linear_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_dna_chromosome AS SELECT feature_id AS circular_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_dna_chromosome AS SELECT feature_id AS linear_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_dna_chromosome AS SELECT feature_id AS circular_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, RNA molecule. *** --- ************************************************ --- CREATE VIEW rna_chromosome AS SELECT feature_id AS rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_rna_chromosome AS SELECT feature_id AS single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_rna_chromosome AS SELECT feature_id AS linear_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_rna_chromosome AS SELECT feature_id AS linear_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_rna_chromosome AS SELECT feature_id AS double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_rna_chromosome AS SELECT feature_id AS circular_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular RNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_rna_chromosome AS SELECT feature_id AS circular_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: insertion_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal_inverted_repeat_element that *** --- *** is bacterial and only encodes the functi *** --- *** ons required for its transposition betwe *** --- *** en these inverted repeats. *** --- ************************************************ --- CREATE VIEW insertion_sequence AS SELECT feature_id AS insertion_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_sequence'; --- ************************************************ --- *** relation: minicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minicircle_gene AS SELECT feature_id AS minicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle_gene'; --- ************************************************ --- *** relation: cryptic *** --- *** relation type: VIEW *** --- *** *** --- *** A feature_attribute describing a feature *** --- *** that is not manifest under normal condi *** --- *** tions. *** --- ************************************************ --- CREATE VIEW cryptic AS SELECT feature_id AS cryptic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic'; --- ************************************************ --- *** relation: anchor_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW anchor_binding_site AS SELECT feature_id AS anchor_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_binding_site'; --- ************************************************ --- *** relation: template_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that specifies t *** --- *** he insertions and deletions of bases in *** --- *** the editing of a target mRNA. *** --- ************************************************ --- CREATE VIEW template_region AS SELECT feature_id AS template_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'template_region'; --- ************************************************ --- *** relation: grna_encoding *** --- *** relation type: VIEW *** --- *** *** --- *** A non-protein_coding gene that encodes a *** --- *** guide_RNA. *** --- ************************************************ --- CREATE VIEW grna_encoding AS SELECT feature_id AS grna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_encoding'; --- ************************************************ --- *** relation: minicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A minicircle is a replicon, part of a ki *** --- *** netoplast, that encodes for guide RNAs. *** --- ************************************************ --- CREATE VIEW minicircle AS SELECT feature_id AS minicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle'; --- ************************************************ --- *** relation: rho_dependent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_dependent_bacterial_terminator AS SELECT feature_id AS rho_dependent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator'; --- ************************************************ --- *** relation: rho_independent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_independent_bacterial_terminator AS SELECT feature_id AS rho_independent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_independent_bacterial_terminator'; --- ************************************************ --- *** relation: strand_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strand_attribute AS SELECT feature_id AS strand_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute'; --- ************************************************ --- *** relation: single *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single AS SELECT feature_id AS single_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single'; --- ************************************************ --- *** relation: double *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double AS SELECT feature_id AS double_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double'; --- ************************************************ --- *** relation: topology_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW topology_attribute AS SELECT feature_id AS topology_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute'; --- ************************************************ --- *** relation: linear *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as a 3'-terminal residue and a 5'-termin *** --- *** al residue. *** --- ************************************************ --- CREATE VIEW linear AS SELECT feature_id AS linear_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear'; --- ************************************************ --- *** relation: circular *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as no terminal nucleotide residues. *** --- ************************************************ --- CREATE VIEW circular AS SELECT feature_id AS circular_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular'; --- ************************************************ --- *** relation: class_ii_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (59-60 nt long) con *** --- *** taining 5' and 3' ends that are predicte *** --- *** d to come together to form a stem struct *** --- *** ure. Identified in the social amoeba Dic *** --- *** tyostelium discoideum and localized in t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW class_ii_rna AS SELECT feature_id AS class_ii_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_II_RNA'; --- ************************************************ --- *** relation: class_i_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (55-65 nt long) con *** --- *** taining highly conserved 5' and 3' ends *** --- *** (16 and 8 nt, respectively) that are pre *** --- *** dicted to come together to form a stem s *** --- *** tructure. Identified in the social amoeb *** --- *** a Dictyostelium discoideum and localized *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW class_i_rna AS SELECT feature_id AS class_i_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_I_RNA'; --- ************************************************ --- *** relation: genomic_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW genomic_dna AS SELECT feature_id AS genomic_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_DNA'; --- ************************************************ --- *** relation: bac_cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bac_cloned_genomic_insert AS SELECT feature_id AS bac_cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert'; --- ************************************************ --- *** relation: consensus *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus AS SELECT feature_id AS consensus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus'; --- ************************************************ --- *** relation: consensus_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_region AS SELECT feature_id AS consensus_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region'; --- ************************************************ --- *** relation: consensus_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_mrna AS SELECT feature_id AS consensus_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA'; --- ************************************************ --- *** relation: predicted_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW predicted_gene AS SELECT feature_id AS predicted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_gene'; --- ************************************************ --- *** relation: gene_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_fragment AS SELECT feature_id AS gene_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fragment'; --- ************************************************ --- *** relation: recursive_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A recursive splice site is a splice site *** --- *** which subdivides a large intron. Recurs *** --- *** ive splicing is a mechanism that splices *** --- *** large introns by sub dividing the intro *** --- *** n at non exonic elements and alternate e *** --- *** xons. *** --- ************************************************ --- CREATE VIEW recursive_splice_site AS SELECT feature_id AS recursive_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recursive_splice_site'; --- ************************************************ --- *** relation: bac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a B *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW bac_end AS SELECT feature_id AS bac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_end'; --- ************************************************ --- *** relation: rrna_16s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the small sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_16s AS SELECT feature_id AS rrna_16s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_16S'; --- ************************************************ --- *** relation: rrna_23s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the large sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_23s AS SELECT feature_id AS rrna_23s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_23S'; --- ************************************************ --- *** relation: rrna_25s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide which functions a *** --- *** s part of the large subunit of the ribos *** --- *** ome in some eukaryotes. *** --- ************************************************ --- CREATE VIEW rrna_25s AS SELECT feature_id AS rrna_25s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_25S'; --- ************************************************ --- *** relation: solo_ltr *** --- *** relation type: VIEW *** --- *** *** --- *** A recombination product between the 2 LT *** --- *** R of the same element. *** --- ************************************************ --- CREATE VIEW solo_ltr AS SELECT feature_id AS solo_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'solo_LTR'; --- ************************************************ --- *** relation: low_complexity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity AS SELECT feature_id AS low_complexity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity'; --- ************************************************ --- *** relation: low_complexity_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity_region AS SELECT feature_id AS low_complexity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity_region'; --- ************************************************ --- *** relation: prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A phage genome after it has established *** --- *** in the host genome in a latent/immune st *** --- *** ate either as a plasmid or as an integra *** --- *** ted "island". *** --- ************************************************ --- CREATE VIEW prophage AS SELECT feature_id AS prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage'; --- ************************************************ --- *** relation: cryptic_prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A remnant of an integrated prophage in t *** --- *** he host genome or an "island" in the hos *** --- *** t genome that includes phage like-genes. *** --- ************************************************ --- CREATE VIEW cryptic_prophage AS SELECT feature_id AS cryptic_prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_prophage'; --- ************************************************ --- *** relation: tetraloop *** --- *** relation type: VIEW *** --- *** *** --- *** A base-paired stem with loop of 4 non-hy *** --- *** drogen bonded nucleotides. *** --- ************************************************ --- CREATE VIEW tetraloop AS SELECT feature_id AS tetraloop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop'; --- ************************************************ --- *** relation: dna_constraint_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A double-stranded DNA used to control ma *** --- *** cromolecular structure and function. *** --- ************************************************ --- CREATE VIEW dna_constraint_sequence AS SELECT feature_id AS dna_constraint_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_constraint_sequence'; --- ************************************************ --- *** relation: i_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A cytosine rich domain whereby strands a *** --- *** ssociate both inter- and intramolecularl *** --- *** y at moderately acidic pH. *** --- ************************************************ --- CREATE VIEW i_motif AS SELECT feature_id AS i_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif'; --- ************************************************ --- *** relation: pna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Peptide nucleic acid, is a chemical not *** --- *** known to occur naturally but is artifici *** --- *** ally synthesized and used in some biolog *** --- *** ical research and medical treatments. Th *** --- *** e PNA backbone is composed of repeating *** --- *** N-(2-aminoethyl)-glycine units linked by *** --- *** peptide bonds. The purine and pyrimidin *** --- *** e bases are linked to the backbone by me *** --- *** thylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna_oligo AS SELECT feature_id AS pna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA_oligo'; --- ************************************************ --- *** relation: dnazyme *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence with catalytic activity. *** --- ************************************************ --- CREATE VIEW dnazyme AS SELECT feature_id AS dnazyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAzyme'; --- ************************************************ --- *** relation: mnp *** --- *** relation type: VIEW *** --- *** *** --- *** A multiple nucleotide polymorphism with *** --- *** alleles of common length > 1, for exampl *** --- *** e AAA/TTT. *** --- ************************************************ --- CREATE VIEW mnp AS SELECT feature_id AS mnp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP'; --- ************************************************ --- *** relation: intron_domain *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intron_domain AS SELECT feature_id AS intron_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain'; --- ************************************************ --- *** relation: wobble_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base pairing, mo *** --- *** st commonly between G and U, which is im *** --- *** portant for the secondary structure of R *** --- *** NAs. It has similar thermodynamic stabil *** --- *** ity to the Watson-Crick pairing. Wobble *** --- *** base pairs only have two hydrogen bonds. *** --- *** Other wobble base pair possibilities ar *** --- *** e I-A, I-U and I-C. *** --- ************************************************ --- CREATE VIEW wobble_base_pair AS SELECT feature_id AS wobble_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wobble_base_pair'; --- ************************************************ --- *** relation: internal_guide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A purine-rich sequence in the group I in *** --- *** trons which determines the locations of *** --- *** the splice sites in group I intron splic *** --- *** ing and has catalytic activity. *** --- ************************************************ --- CREATE VIEW internal_guide_sequence AS SELECT feature_id AS internal_guide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence'; --- ************************************************ --- *** relation: silent_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that does not affect *** --- *** protein function. Silent mutations may o *** --- *** ccur in genic ( CDS, UTR, intron etc) an *** --- *** d intergenic regions. Silent mutations m *** --- *** ay have affects on processes such as spl *** --- *** icing and regulation. *** --- ************************************************ --- CREATE VIEW silent_mutation AS SELECT feature_id AS silent_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation'; --- ************************************************ --- *** relation: epitope *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith antibodies, B cells or T cells. *** --- ************************************************ --- CREATE VIEW epitope AS SELECT feature_id AS epitope_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epitope'; --- ************************************************ --- *** relation: copy_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A variation that increases or decreases *** --- *** the copy number of a given region. *** --- ************************************************ --- CREATE VIEW copy_number_variation AS SELECT feature_id AS copy_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'copy_number_variation'; --- ************************************************ --- *** relation: chromosome_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_breakpoint AS SELECT feature_id AS chromosome_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint'; --- ************************************************ --- *** relation: inversion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where an i *** --- *** nversion begins or ends. *** --- ************************************************ --- CREATE VIEW inversion_breakpoint AS SELECT feature_id AS inversion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint'; --- ************************************************ --- *** relation: allele *** --- *** relation type: VIEW *** --- *** *** --- *** An allele is one of a set of coexisting *** --- *** sequence variants of a gene. *** --- ************************************************ --- CREATE VIEW allele AS SELECT feature_id AS allele_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'allele'; --- ************************************************ --- *** relation: haplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A haplotype is one of a set of coexistin *** --- *** g sequence variants of a haplotype block *** --- *** . *** --- ************************************************ --- CREATE VIEW haplotype AS SELECT feature_id AS haplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype'; --- ************************************************ --- *** relation: polymorphic_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that is segregating i *** --- *** n one or more natural populations of a s *** --- *** pecies. *** --- ************************************************ --- CREATE VIEW polymorphic_sequence_variant AS SELECT feature_id AS polymorphic_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant'; --- ************************************************ --- *** relation: genome *** --- *** relation type: VIEW *** --- *** *** --- *** A genome is the sum of genetic material *** --- *** within a cell or virion. *** --- ************************************************ --- CREATE VIEW genome AS SELECT feature_id AS genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'genome'; --- ************************************************ --- *** relation: so_genotype *** --- *** relation type: VIEW *** --- *** *** --- *** A genotype is a variant genome, complete *** --- *** or incomplete. *** --- ************************************************ --- CREATE VIEW so_genotype AS SELECT feature_id AS so_genotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genotype'; --- ************************************************ --- *** relation: diplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A diplotype is a pair of haplotypes from *** --- *** a given individual. It is a genotype wh *** --- *** ere the phase is known. *** --- ************************************************ --- CREATE VIEW diplotype AS SELECT feature_id AS diplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype'; --- ************************************************ --- *** relation: direction_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direction_attribute AS SELECT feature_id AS direction_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'direction_attribute'; --- ************************************************ --- *** relation: forward *** --- *** relation type: VIEW *** --- *** *** --- *** Forward is an attribute of the feature, *** --- *** where the feature is in the 5' to 3' dir *** --- *** ection. *** --- ************************************************ --- CREATE VIEW forward AS SELECT feature_id AS forward_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward'; --- ************************************************ --- *** relation: reverse *** --- *** relation type: VIEW *** --- *** *** --- *** Reverse is an attribute of the feature, *** --- *** where the feature is in the 3' to 5' dir *** --- *** ection. Again could be applied to primer *** --- *** . *** --- ************************************************ --- CREATE VIEW reverse AS SELECT feature_id AS reverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse'; --- ************************************************ --- *** relation: mitochondrial_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_dna AS SELECT feature_id AS mitochondrial_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA'; --- ************************************************ --- *** relation: chloroplast_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_dna AS SELECT feature_id AS chloroplast_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA'; --- ************************************************ --- *** relation: mirtron *** --- *** relation type: VIEW *** --- *** *** --- *** A de-branched intron which mimics the st *** --- *** ructure of pre-miRNA and enters the miRN *** --- *** A processing pathway without Drosha medi *** --- *** ated cleavage. *** --- ************************************************ --- CREATE VIEW mirtron AS SELECT feature_id AS mirtron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mirtron'; --- ************************************************ --- *** relation: pirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA, part of a silenc *** --- *** ing system that prevents the spreading o *** --- *** f selfish genetic elements. *** --- ************************************************ --- CREATE VIEW pirna AS SELECT feature_id AS pirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA'; --- ************************************************ --- *** relation: arginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an arginine ant *** --- *** icodon, and a 3' arginine binding region *** --- *** . *** --- ************************************************ --- CREATE VIEW arginyl_trna AS SELECT feature_id AS arginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginyl_tRNA'; --- ************************************************ --- *** relation: mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide region with either intra-ge *** --- *** nome or intracellular moblity, of varyin *** --- *** g length, which often carry the informat *** --- *** ion necessary for transfer and recombina *** --- *** tion with the host genome. *** --- ************************************************ --- CREATE VIEW mobile_genetic_element AS SELECT feature_id AS mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'mobile_genetic_element'; --- ************************************************ --- *** relation: extrachromosomal_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is not integrated into the h *** --- *** ost chromosome. *** --- ************************************************ --- CREATE VIEW extrachromosomal_mobile_genetic_element AS SELECT feature_id AS extrachromosomal_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'extrachromosomal_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is integrated into the host *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW integrated_mobile_genetic_element AS SELECT feature_id AS integrated_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'integrated_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid sequence that is integrated wi *** --- *** thin the host chromosome. *** --- ************************************************ --- CREATE VIEW integrated_plasmid AS SELECT feature_id AS integrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_plasmid'; --- ************************************************ --- *** relation: viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The region of nucleotide sequence of a v *** --- *** irus, a submicroscopic particle that rep *** --- *** licates by infecting a host cell. *** --- ************************************************ --- CREATE VIEW viral_sequence AS SELECT feature_id AS viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'viral_sequence'; --- ************************************************ --- *** relation: phage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide sequence of a virus that *** --- *** infects bacteria. *** --- ************************************************ --- CREATE VIEW phage_sequence AS SELECT feature_id AS phage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence'; --- ************************************************ --- *** relation: attctn_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attachment site located on a conjugat *** --- *** ive transposon and used for site-specifi *** --- *** c integration of a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW attctn_site AS SELECT feature_id AS attctn_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attCtn_site'; --- ************************************************ --- *** relation: nuclear_mt_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A nuclear pseudogene of either coding or *** --- *** non-coding mitochondria derived sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW nuclear_mt_pseudogene AS SELECT feature_id AS nuclear_mt_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_mt_pseudogene'; --- ************************************************ --- *** relation: cointegrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A MGE region consisting of two fused pla *** --- *** smids resulting from a replicative trans *** --- *** position event. *** --- ************************************************ --- CREATE VIEW cointegrated_plasmid AS SELECT feature_id AS cointegrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cointegrated_plasmid'; --- ************************************************ --- *** relation: irlinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the left of a region susceptible to s *** --- *** ite-specific inversion. *** --- ************************************************ --- CREATE VIEW irlinv_site AS SELECT feature_id AS irlinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site'; --- ************************************************ --- *** relation: irrinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the right of a region susceptible to *** --- *** site-specific inversion. *** --- ************************************************ --- CREATE VIEW irrinv_site AS SELECT feature_id AS irrinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRRinv_site'; --- ************************************************ --- *** relation: inversion_site_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region located within an inversion sit *** --- *** e. *** --- ************************************************ --- CREATE VIEW inversion_site_part AS SELECT feature_id AS inversion_site_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'inversion_site_part'; --- ************************************************ --- *** relation: defective_conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** An island that contains genes for integr *** --- *** ation/excision and the gene and site for *** --- *** the initiation of intercellular transfe *** --- *** r by conjugation. It can be complemented *** --- *** for transfer by a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW defective_conjugative_transposon AS SELECT feature_id AS defective_conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'defective_conjugative_transposon'; --- ************************************************ --- *** relation: repeat_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a repeat, interrupted by th *** --- *** e insertion of another element. *** --- ************************************************ --- CREATE VIEW repeat_fragment AS SELECT feature_id AS repeat_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_fragment'; --- ************************************************ --- *** relation: transposon_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a transposon, interrupted b *** --- *** y the insertion of another element. *** --- ************************************************ --- CREATE VIEW transposon_fragment AS SELECT feature_id AS transposon_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposon_fragment'; --- ************************************************ --- *** relation: transcriptional_cis_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates the t *** --- *** ranscription of a gene or genes. *** --- ************************************************ --- CREATE VIEW transcriptional_cis_regulatory_region AS SELECT feature_id AS transcriptional_cis_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'transcriptional_cis_regulatory_region'; --- ************************************************ --- *** relation: splicing_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates splic *** --- *** ing. *** --- ************************************************ --- CREATE VIEW splicing_regulatory_region AS SELECT feature_id AS splicing_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splicing_regulatory_region'; --- ************************************************ --- *** relation: promoter_targeting_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional_cis_regulatory_region *** --- *** that restricts the activity of a CRM to *** --- *** a single promoter and which functions on *** --- *** ly when both itself and an insulator are *** --- *** located between the CRM and the promote *** --- *** r. *** --- ************************************************ --- CREATE VIEW promoter_targeting_sequence AS SELECT feature_id AS promoter_targeting_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_targeting_sequence'; --- ************************************************ --- *** relation: sequence_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_alteration is a sequence_feat *** --- *** ure whose extent is the deviation from a *** --- *** nother sequence. *** --- ************************************************ --- CREATE VIEW sequence_alteration AS SELECT feature_id AS sequence_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_alteration'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant is a non exact copy o *** --- *** f a sequence_feature or genome exhibitin *** --- *** g one or more sequence_alteration. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'functional_variant' OR cvterm.name = 'structural_variant' OR cvterm.name = 'loss_of_heterozygosity' OR cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: propeptide_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** The propeptide_cleavage_site is the argi *** --- *** nine/lysine boundary on a propeptide whe *** --- *** re cleavage occurs. *** --- ************************************************ --- CREATE VIEW propeptide_cleavage_site AS SELECT feature_id AS propeptide_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide_cleavage_site'; --- ************************************************ --- *** relation: propeptide *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a peptide chain which is cleaved *** --- *** off during the formation of the mature *** --- *** protein. *** --- ************************************************ --- CREATE VIEW propeptide AS SELECT feature_id AS propeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide'; --- ************************************************ --- *** relation: immature_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** An immature_peptide_region is the extent *** --- *** of the peptide after it has been transl *** --- *** ated and before any processing occurs. *** --- ************************************************ --- CREATE VIEW immature_peptide_region AS SELECT feature_id AS immature_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'immature_peptide_region'; --- ************************************************ --- *** relation: active_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Active peptides are proteins which are b *** --- *** iologically active, released from a prec *** --- *** ursor molecule. *** --- ************************************************ --- CREATE VIEW active_peptide AS SELECT feature_id AS active_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide'; --- ************************************************ --- *** relation: compositionally_biased_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is rich in a par *** --- *** ticular amino acid or homopolymeric and *** --- *** greater than three residues in length. *** --- ************************************************ --- CREATE VIEW compositionally_biased_region_of_peptide AS SELECT feature_id AS compositionally_biased_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compositionally_biased_region_of_peptide'; --- ************************************************ --- *** relation: polypeptide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a short (up to 20 am *** --- *** ino acids) region of biological interest *** --- *** . Such motifs, although they are too sho *** --- *** rt to constitute functional domains, sha *** --- *** re sequence similarities and are conserv *** --- *** ed in different proteins. They display a *** --- *** common function (protein-binding, subce *** --- *** llular location etc.). *** --- ************************************************ --- CREATE VIEW polypeptide_motif AS SELECT feature_id AS polypeptide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_motif'; --- ************************************************ --- *** relation: polypeptide_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide_repeat is a single copy of *** --- *** an internal sequence repetition. *** --- ************************************************ --- CREATE VIEW polypeptide_repeat AS SELECT feature_id AS polypeptide_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_repeat'; --- ************************************************ --- *** relation: polypeptide_structural_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of polypeptide with a given struc *** --- *** tural property. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_region AS SELECT feature_id AS polypeptide_structural_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_region'; --- ************************************************ --- *** relation: membrane_structure *** --- *** relation type: VIEW *** --- *** *** --- *** Arrangement of the polypeptide with resp *** --- *** ect to the lipid bilayer. *** --- ************************************************ --- CREATE VIEW membrane_structure AS SELECT feature_id AS membrane_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_structure'; --- ************************************************ --- *** relation: extramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer. *** --- ************************************************ --- CREATE VIEW extramembrane_polypeptide_region AS SELECT feature_id AS extramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'extramembrane_polypeptide_region'; --- ************************************************ --- *** relation: cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized ins *** --- *** ide the cytoplasm. *** --- ************************************************ --- CREATE VIEW cytoplasmic_polypeptide_region AS SELECT feature_id AS cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: non_cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer and outside of t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW non_cytoplasmic_polypeptide_region AS SELECT feature_id AS non_cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: intramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region present in the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW intramembrane_polypeptide_region AS SELECT feature_id AS intramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region'; --- ************************************************ --- *** relation: membrane_peptide_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region localized within the *** --- *** lipid bilayer where both ends traverse t *** --- *** he same membrane. *** --- ************************************************ --- CREATE VIEW membrane_peptide_loop AS SELECT feature_id AS membrane_peptide_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop'; --- ************************************************ --- *** relation: transmembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region traversing the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW transmembrane_polypeptide_region AS SELECT feature_id AS transmembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transmembrane_polypeptide_region'; --- ************************************************ --- *** relation: polypeptide_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide with secondary struc *** --- *** ture has hydrogen bonding along the pept *** --- *** ide chain that causes a defined conforma *** --- *** tion of the chain. *** --- ************************************************ --- CREATE VIEW polypeptide_secondary_structure AS SELECT feature_id AS polypeptide_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_secondary_structure'; --- ************************************************ --- *** relation: polypeptide_structural_motif *** --- *** relation type: VIEW *** --- *** *** --- *** Motif is a three-dimensional structural *** --- *** element within the chain, which appears *** --- *** also in a variety of other molecules. Un *** --- *** like a domain, a motif does not need to *** --- *** form a stable globular unit. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_motif AS SELECT feature_id AS polypeptide_structural_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_motif'; --- ************************************************ --- *** relation: coiled_coil *** --- *** relation type: VIEW *** --- *** *** --- *** A coiled coil is a structural motif in p *** --- *** roteins, in which alpha-helices are coil *** --- *** ed together like the strands of a rope. *** --- ************************************************ --- CREATE VIEW coiled_coil AS SELECT feature_id AS coiled_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil'; --- ************************************************ --- *** relation: helix_turn_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A motif comprising two helices separated *** --- *** by a turn. *** --- ************************************************ --- CREATE VIEW helix_turn_helix AS SELECT feature_id AS helix_turn_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helix_turn_helix'; --- ************************************************ --- *** relation: polypeptide_sequencing_information *** --- *** relation type: VIEW *** --- *** *** --- *** Incompatibility in the sequence due to s *** --- *** ome experimental problem. *** --- ************************************************ --- CREATE VIEW polypeptide_sequencing_information AS SELECT feature_id AS polypeptide_sequencing_information_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'polypeptide_sequencing_information'; --- ************************************************ --- *** relation: non_adjacent_residues *** --- *** relation type: VIEW *** --- *** *** --- *** Indicates that two consecutive residues *** --- *** in a fragment sequence are not consecuti *** --- *** ve in the full-length protein and that t *** --- *** here are a number of unsequenced residue *** --- *** s between them. *** --- ************************************************ --- CREATE VIEW non_adjacent_residues AS SELECT feature_id AS non_adjacent_residues_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues'; --- ************************************************ --- *** relation: non_terminal_residue *** --- *** relation type: VIEW *** --- *** *** --- *** The residue at an extremity of the seque *** --- *** nce is not the terminal residue. *** --- ************************************************ --- CREATE VIEW non_terminal_residue AS SELECT feature_id AS non_terminal_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_terminal_residue'; --- ************************************************ --- *** relation: sequence_conflict *** --- *** relation type: VIEW *** --- *** *** --- *** Different sources report differing seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW sequence_conflict AS SELECT feature_id AS sequence_conflict_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection' OR cvterm.name = 'sequence_conflict'; --- ************************************************ --- *** relation: sequence_uncertainty *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the positions in a sequence wh *** --- *** ere the authors are unsure about the seq *** --- *** uence assignment. *** --- ************************************************ --- CREATE VIEW sequence_uncertainty AS SELECT feature_id AS sequence_uncertainty_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_uncertainty'; --- ************************************************ --- *** relation: post_translationally_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region where a transformation occurs i *** --- *** n a protein after it has been synthesize *** --- *** d. This which may regulate, stabilize, c *** --- *** rosslink or introduce new chemical funct *** --- *** ionalities in the protein. *** --- ************************************************ --- CREATE VIEW post_translationally_modified_region AS SELECT feature_id AS post_translationally_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'post_translationally_modified_region'; --- ************************************************ --- *** relation: polypeptide_metal_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with metal ions. *** --- ************************************************ --- CREATE VIEW polypeptide_metal_contact AS SELECT feature_id AS polypeptide_metal_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_metal_contact'; --- ************************************************ --- *** relation: protein_protein_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the protein mole *** --- *** cule, interacts selectively and non-cova *** --- *** lently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW protein_protein_contact AS SELECT feature_id AS protein_protein_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact'; --- ************************************************ --- *** relation: polypeptide_calcium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with calcium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_calcium_ion_contact_site AS SELECT feature_id AS polypeptide_calcium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_cobalt_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with cobalt ions. *** --- ************************************************ --- CREATE VIEW polypeptide_cobalt_ion_contact_site AS SELECT feature_id AS polypeptide_cobalt_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_cobalt_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_copper_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with copper ions. *** --- ************************************************ --- CREATE VIEW polypeptide_copper_ion_contact_site AS SELECT feature_id AS polypeptide_copper_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_copper_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_iron_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with iron ions. *** --- ************************************************ --- CREATE VIEW polypeptide_iron_ion_contact_site AS SELECT feature_id AS polypeptide_iron_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_iron_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_magnesium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with magnesium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_magnesium_ion_contact_site AS SELECT feature_id AS polypeptide_magnesium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_magnesium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_manganese_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with manganese ions. *** --- ************************************************ --- CREATE VIEW polypeptide_manganese_ion_contact_site AS SELECT feature_id AS polypeptide_manganese_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_manganese_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_molybdenum_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with molybdenum ions. *** --- ************************************************ --- CREATE VIEW polypeptide_molybdenum_ion_contact_site AS SELECT feature_id AS polypeptide_molybdenum_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_molybdenum_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_nickel_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with nickel ions. *** --- ************************************************ --- CREATE VIEW polypeptide_nickel_ion_contact_site AS SELECT feature_id AS polypeptide_nickel_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nickel_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_tungsten_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with tungsten ions. *** --- ************************************************ --- CREATE VIEW polypeptide_tungsten_ion_contact_site AS SELECT feature_id AS polypeptide_tungsten_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_tungsten_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_zinc_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with zinc ions. *** --- ************************************************ --- CREATE VIEW polypeptide_zinc_ion_contact_site AS SELECT feature_id AS polypeptide_zinc_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_zinc_ion_contact_site'; --- ************************************************ --- *** relation: catalytic_residue *** --- *** relation type: VIEW *** --- *** *** --- *** Amino acid involved in the activity of a *** --- *** n enzyme. *** --- ************************************************ --- CREATE VIEW catalytic_residue AS SELECT feature_id AS catalytic_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue'; --- ************************************************ --- *** relation: polypeptide_ligand_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues which interact with a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_ligand_contact AS SELECT feature_id AS polypeptide_ligand_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact'; --- ************************************************ --- *** relation: asx_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: Residue(i) is Asp *** --- *** artate or Asparagine (Asx), side-chain O *** --- *** of residue(i) is H-bonded to the main-c *** --- *** hain NH of residue(i+2) or (i+3), main-c *** --- *** hain CO of residue(i) is H-bonded to the *** --- *** main-chain NH of residue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW asx_motif AS SELECT feature_id AS asx_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif'; --- ************************************************ --- *** relation: beta_bulge *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet in which the main chains of two co *** --- *** nsecutive residues are H-bonded to that *** --- *** of the third, and in which the dihedral *** --- *** angles are as follows: Residue(i): -140 *** --- *** degrees < phi(l) -20 degrees , -90 degre *** --- *** es < psi(l) < 40 degrees. Residue (i+1): *** --- *** -180 degrees < phi < -25 degrees or +12 *** --- *** 0 degrees < phi < +180 degrees, +40 degr *** --- *** ees < psi < +180 degrees or -180 degrees *** --- *** < psi < -120 degrees. *** --- ************************************************ --- CREATE VIEW beta_bulge AS SELECT feature_id AS beta_bulge_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge'; --- ************************************************ --- *** relation: beta_bulge_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds. Beta bu *** --- *** lge loops often occur at the loop ends o *** --- *** f beta-hairpins. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop AS SELECT feature_id AS beta_bulge_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'beta_bulge_loop'; --- ************************************************ --- *** relation: beta_bulge_loop_five *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 4), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +3), these loops have an RL nest at resi *** --- *** dues i+2 and i+3. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_five AS SELECT feature_id AS beta_bulge_loop_five_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five'; --- ************************************************ --- *** relation: beta_bulge_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 5), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +4), these loops have an RL nest at resi *** --- *** dues i+3 and i+4. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_six AS SELECT feature_id AS beta_bulge_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_six'; --- ************************************************ --- *** relation: beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A beta strand describes a single length *** --- *** of polypeptide chain that forms part of *** --- *** a beta sheet. A single continuous stretc *** --- *** h of amino acids adopting an extended co *** --- *** nformation of hydrogen bonds between the *** --- *** N-O and the C=O of another part of the *** --- *** peptide. This forms a secondary protein *** --- *** structure in which two or more extended *** --- *** polypeptide regions are hydrogen-bonded *** --- *** to one another in a planar array. *** --- ************************************************ --- CREATE VIEW beta_strand AS SELECT feature_id AS beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'beta_strand'; --- ************************************************ --- *** relation: antiparallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (one running N-term *** --- *** inal to C-terminal and one running C-ter *** --- *** minal to N-terminal). Hydrogen bonding o *** --- *** ccurs between every other C=O from one s *** --- *** trand to every other N-H on the adjacent *** --- *** strand. In this case, if two atoms C-al *** --- *** pha (i) and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then t *** --- *** hey form two mutual backbone hydrogen bo *** --- *** nds to each other's flanking peptide gro *** --- *** ups; this is known as a close pair of hy *** --- *** drogen bonds. The peptide backbone dihed *** --- *** ral angles (phi, psi) are about (-140 de *** --- *** grees, 135 degrees) in antiparallel shee *** --- *** ts. *** --- ************************************************ --- CREATE VIEW antiparallel_beta_strand AS SELECT feature_id AS antiparallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand'; --- ************************************************ --- *** relation: parallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (both running N-ter *** --- *** minal to C-terminal). This orientation i *** --- *** s slightly less stable because it introd *** --- *** uces nonplanarity in the inter-strand hy *** --- *** drogen bonding pattern. Hydrogen bonding *** --- *** occurs between every other C=O from one *** --- *** strand to every other N-H on the adjace *** --- *** nt strand. In this case, if two atoms C- *** --- *** alpha (i)and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then *** --- *** they do not hydrogen bond to each other; *** --- *** rather, one residue forms hydrogen bond *** --- *** s to the residues that flank the other ( *** --- *** but not vice versa). For example, residu *** --- *** e i may form hydrogen bonds to residues *** --- *** j - 1 and j + 1; this is known as a wide *** --- *** pair of hydrogen bonds. By contrast, re *** --- *** sidue j may hydrogen-bond to different r *** --- *** esidues altogether, or to none at all. T *** --- *** he dihedral angles (phi, psi) are about *** --- *** (-120 degrees, 115 degrees) in parallel *** --- *** sheets. *** --- ************************************************ --- CREATE VIEW parallel_beta_strand AS SELECT feature_id AS parallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'parallel_beta_strand'; --- ************************************************ --- *** relation: peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A helix is a secondary_structure conform *** --- *** ation where the peptide backbone forms a *** --- *** coil. *** --- ************************************************ --- CREATE VIEW peptide_helix AS SELECT feature_id AS peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'peptide_helix'; --- ************************************************ --- *** relation: left_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A left handed helix is a region of pepti *** --- *** de where the coiled conformation turns i *** --- *** n an anticlockwise, left handed screw. *** --- ************************************************ --- CREATE VIEW left_handed_peptide_helix AS SELECT feature_id AS left_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix'; --- ************************************************ --- *** relation: right_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A right handed helix is a region of pept *** --- *** ide where the coiled conformation turns *** --- *** in a clockwise, right handed screw. *** --- ************************************************ --- CREATE VIEW right_handed_peptide_helix AS SELECT feature_id AS right_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'right_handed_peptide_helix'; --- ************************************************ --- *** relation: alpha_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The helix has 3.6 residues per turn whic *** --- *** h corersponds to a translation of 1.5 an *** --- *** gstroms (= 0.15 nm) along the helical ax *** --- *** is. Every backbone N-H group donates a h *** --- *** ydrogen bond to the backbone C=O group o *** --- *** f the amino acid four residues earlier. *** --- ************************************************ --- CREATE VIEW alpha_helix AS SELECT feature_id AS alpha_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix'; --- ************************************************ --- *** relation: pi_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The pi helix has 4.1 residues per turn a *** --- *** nd a translation of 1.15 (=0.115 nm) al *** --- *** ong the helical axis. The N-H group of a *** --- *** n amino acid forms a hydrogen bond with *** --- *** the C=O group of the amino acid five res *** --- *** idues earlier. *** --- ************************************************ --- CREATE VIEW pi_helix AS SELECT feature_id AS pi_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pi_helix'; --- ************************************************ --- *** relation: three_ten_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The 3-10 helix has 3 residues per turn w *** --- *** ith a translation of 2.0 angstroms (=0.2 *** --- *** nm) along the helical axis. The N-H gro *** --- *** up of an amino acid forms a hydrogen bon *** --- *** d with the C=O group of the amino acid t *** --- *** hree residues earlier. *** --- ************************************************ --- CREATE VIEW three_ten_helix AS SELECT feature_id AS three_ten_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_ten_helix'; --- ************************************************ --- *** relation: polypeptide_nest_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles. Nest should not have P *** --- *** roline as any residue. Nests frequently *** --- *** occur as parts of other motifs such as S *** --- *** chellman loops. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_motif AS SELECT feature_id AS polypeptide_nest_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'polypeptide_nest_motif'; --- ************************************************ --- *** relation: polypeptide_nest_left_right_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): +20 degree *** --- *** s < phi < +140 degrees, -40 degrees < ps *** --- *** i < +90 degrees. Residue(i+1): -140 degr *** --- *** ees < phi < -20 degrees, -90 degrees < p *** --- *** si < +40 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_left_right_motif AS SELECT feature_id AS polypeptide_nest_left_right_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif'; --- ************************************************ --- *** relation: polypeptide_nest_right_left_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): -140 degre *** --- *** es < phi < -20 degrees, -90 degrees < ps *** --- *** i < +40 degrees. Residue(i+1): +20 degre *** --- *** es < phi < +140 degrees, -40 degrees < p *** --- *** si < +90 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_right_left_motif AS SELECT feature_id AS polypeptide_nest_right_left_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_right_left_motif'; --- ************************************************ --- *** relation: schellmann_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of six or seven consecutive resi *** --- *** dues that contains two H-bonds. *** --- ************************************************ --- CREATE VIEW schellmann_loop AS SELECT feature_id AS schellmann_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'schellmann_loop'; --- ************************************************ --- *** relation: schellmann_loop_seven *** --- *** relation type: VIEW *** --- *** *** --- *** Wild type: A motif of seven consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+6), the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of res *** --- *** idue(i+5). *** --- ************************************************ --- CREATE VIEW schellmann_loop_seven AS SELECT feature_id AS schellmann_loop_seven_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven'; --- ************************************************ --- *** relation: schellmann_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** Common Type: A motif of six consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+5) the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of resi *** --- *** due(i+4). *** --- ************************************************ --- CREATE VIEW schellmann_loop_six AS SELECT feature_id AS schellmann_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_six'; --- ************************************************ --- *** relation: serine_threonine_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two hydrogen bonds in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain O of residue(i) is H-bonded to t *** --- *** he main-chain NH of residue(i+2) or (i+3 *** --- *** ) , the main-chain CO group of residue(i *** --- *** ) is H-bonded to the main-chain NH of re *** --- *** sidue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW serine_threonine_motif AS SELECT feature_id AS serine_threonine_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_motif'; --- ************************************************ --- *** relation: serine_threonine_staple_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four or five consecutive resi *** --- *** dues and one H-bond in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain OH of residue(i) is H-bonded to *** --- *** the main-chain CO of residue(i3) or (i4) *** --- *** , Phi angles of residues(i1), (i2) and ( *** --- *** i3) are negative. *** --- ************************************************ --- CREATE VIEW serine_threonine_staple_motif AS SELECT feature_id AS serine_threonine_staple_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_staple_motif'; --- ************************************************ --- *** relation: polypeptide_turn_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A reversal in the direction of the backb *** --- *** one of a protein that is stabilized by h *** --- *** ydrogen bond between backbone NH and CO *** --- *** groups, involving no more than 4 amino a *** --- *** cid residues. *** --- ************************************************ --- CREATE VIEW polypeptide_turn_motif AS SELECT feature_id AS polypeptide_turn_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_turn_motif'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I (dihedral angles):- R *** --- *** esidue(i): -140 degrees < chi (1) -120 d *** --- *** egrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1) *** --- *** : -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_one AS SELECT feature_id AS asx_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < psi *** --- *** +120 degrees < +180 degrees. Residue(i+ *** --- *** 1): +20 degrees < phi < +140 degrees, -4 *** --- *** 0 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_two AS SELECT feature_id AS asx_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < ps *** --- *** i +120 degrees < +180 degrees. Residue(i *** --- *** +1): +20 degrees < phi < +140 degrees, - *** --- *** 40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_two AS SELECT feature_id AS asx_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1 *** --- *** ): -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_one AS SELECT feature_id AS asx_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive residues tha *** --- *** t may contain one H-bond, which, if pres *** --- *** ent, is between the main-chain CO of the *** --- *** first residue and the main-chain NH of *** --- *** the fourth. It is characterized by the d *** --- *** ihedral angles of the second and third r *** --- *** esidues, which are the basis for sub-cat *** --- *** egorization. *** --- ************************************************ --- CREATE VIEW beta_turn AS SELECT feature_id AS beta_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I:A motif of four conse *** --- *** cutive residues that may contain one H-b *** --- *** ond, which, if present, is between the m *** --- *** ain-chain CO of the first residue and th *** --- *** e main-chain NH of the fourth. It is cha *** --- *** racterized by the dihedral angles:- Resi *** --- *** due(i+1): -140 degrees > phi > -20 degre *** --- *** es, -90 degrees > psi > +40 degrees. Res *** --- *** idue(i+2): -140 degrees > phi > -20 degr *** --- *** ees, -90 degrees > psi > +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_one AS SELECT feature_id AS beta_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II: A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees > phi > -20 degr *** --- *** ees, +80 degrees > psi > +180 degrees. R *** --- *** esidue(i+2): +20 degrees > phi > +140 de *** --- *** grees, -40 degrees > psi > +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_two AS SELECT feature_id AS beta_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_two'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I:A motif of four cons *** --- *** ecutive residues that may contain one H- *** --- *** bond, which, if present, is between the *** --- *** main-chain CO of the first residue and t *** --- *** he main-chain NH of the fourth. It is ch *** --- *** aracterized by the dihedral angles: Resi *** --- *** due(i+1): -140 degrees < phi < -20 degre *** --- *** es, -90 degrees < psi < +40 degrees. Res *** --- *** idue(i+2): -140 degrees < phi < -20 degr *** --- *** ees, -90 degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_one AS SELECT feature_id AS beta_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II:A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees < phi < -20 degr *** --- *** ees, +80 degrees < psi < +180 degrees. R *** --- *** esidue(i+2): +20 degrees < phi < +140 de *** --- *** grees, -40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_two AS SELECT feature_id AS beta_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_two'; --- ************************************************ --- *** relation: gamma_turn *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i,( *** --- *** i+1),( i+2) if a hydrogen bond exists be *** --- *** tween residues i and i+2 and the phi and *** --- *** psi angles of residue i+1 fall within 4 *** --- *** 0 degrees. *** --- ************************************************ --- CREATE VIEW gamma_turn AS SELECT feature_id AS gamma_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'gamma_turn'; --- ************************************************ --- *** relation: gamma_turn_classic *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=75.0 - psi(i+1)=-64.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_classic AS SELECT feature_id AS gamma_turn_classic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic'; --- ************************************************ --- *** relation: gamma_turn_inverse *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=-79.0 - psi(i+1)=69.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_inverse AS SELECT feature_id AS gamma_turn_inverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_inverse'; --- ************************************************ --- *** relation: serine_threonine_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Ser *** --- *** ine (S) or Threonine (T), the side-chain *** --- *** O of residue(i) is H-bonded to the main *** --- *** -chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW serine_threonine_turn AS SELECT feature_id AS serine_threonine_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'serine_threonine_turn'; --- ************************************************ --- *** relation: st_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** -90 degrees psi +120 degrees < +40 degr *** --- *** ees, residue(i+1): -140 degrees < phi < *** --- *** -20 degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_one AS SELECT feature_id AS st_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one'; --- ************************************************ --- *** relation: st_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** +80 degrees psi +120 degrees < +180 deg *** --- *** rees, residue(i+1): +20 degrees < phi < *** --- *** +140 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_two AS SELECT feature_id AS st_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_two'; --- ************************************************ --- *** relation: st_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, -9 *** --- *** 0 degrees psi +120 degrees < +40 degrees *** --- *** , residue(i+1): -140 degrees < phi < -20 *** --- *** degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_one AS SELECT feature_id AS st_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_one'; --- ************************************************ --- *** relation: st_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, +8 *** --- *** 0 degrees psi +120 degrees < +180 degree *** --- *** s, residue(i+1): +20 degrees < phi < +14 *** --- *** 0 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_two AS SELECT feature_id AS st_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_two'; --- ************************************************ --- *** relation: polypeptide_variation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site of sequence variation (alteration *** --- *** ). Alternative sequence due to naturally *** --- *** occuring events such as polymorphisms a *** --- *** nd altermatve splicing or experimental m *** --- *** ethods such as site directed mutagenesis *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_variation_site AS SELECT feature_id AS polypeptide_variation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'polypeptide_variation_site'; --- ************************************************ --- *** relation: natural_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the natural sequence variants *** --- *** due to polymorphisms, disease-associated *** --- *** mutations, RNA editing and variations b *** --- *** etween strains, isolates or cultivars. *** --- ************************************************ --- CREATE VIEW natural_variant_site AS SELECT feature_id AS natural_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site'; --- ************************************************ --- *** relation: mutated_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Site which has been experimentally alter *** --- *** ed. *** --- ************************************************ --- CREATE VIEW mutated_variant_site AS SELECT feature_id AS mutated_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutated_variant_site'; --- ************************************************ --- *** relation: alternate_sequence_site *** --- *** relation type: VIEW *** --- *** *** --- *** Description of sequence variants produce *** --- *** d by alternative splicing, alternative p *** --- *** romoter usage, alternative initiation an *** --- *** d ribosomal frameshifting. *** --- ************************************************ --- CREATE VIEW alternate_sequence_site AS SELECT feature_id AS alternate_sequence_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternate_sequence_site'; --- ************************************************ --- *** relation: beta_turn_type_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** des of type VIa or type VIb and where th *** --- *** e i+2 residue is cis-proline. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six AS SELECT feature_id AS beta_turn_type_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six'; --- ************************************************ --- *** relation: beta_turn_type_six_a *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -60 degrees, psi ~ 120 degrees. Re *** --- *** sidue(i+2): phi ~ -90 degrees, psi ~ 0 d *** --- *** egrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a AS SELECT feature_id AS beta_turn_type_six_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six_a'; --- ************************************************ --- *** relation: beta_turn_type_six_a_one *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_one AS SELECT feature_id AS beta_turn_type_six_a_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one'; --- ************************************************ --- *** relation: beta_turn_type_six_a_two *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_two AS SELECT feature_id AS beta_turn_type_six_a_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_two'; --- ************************************************ --- *** relation: beta_turn_type_six_b *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -120 degrees, psi ~ 120 degrees. R *** --- *** esidue(i+2): phi ~ -60 degrees, psi ~ 0 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_b AS SELECT feature_id AS beta_turn_type_six_b_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_b'; --- ************************************************ --- *** relation: beta_turn_type_eight *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues that may contain one H-bond, which, *** --- *** if present, is between the main-chain C *** --- *** O of the first residue and the main-chai *** --- *** n NH of the fourth and is characterized *** --- *** by the dihedral angles: Residue(i+1): ph *** --- *** i ~ -60 degrees, psi ~ -30 degrees. Resi *** --- *** due(i+2): phi ~ -120 degrees, psi ~ 120 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_eight AS SELECT feature_id AS beta_turn_type_eight_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_eight'; --- ************************************************ --- *** relation: dre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -10 and -60 relative to t *** --- *** he TSS. Consensus sequence is WATCGATW. *** --- ************************************************ --- CREATE VIEW dre_motif AS SELECT feature_id AS dre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DRE_motif'; --- ************************************************ --- *** relation: dmv4_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments with respect to the TSS (+1). Cons *** --- *** ensus sequence is YGGTCACACTR. Marked sp *** --- *** atial preference within core promoter; t *** --- *** end to occur near the TSS, although not *** --- *** as tightly as INR (SO:0000014). *** --- ************************************************ --- CREATE VIEW dmv4_motif AS SELECT feature_id AS dmv4_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv4_motif'; --- ************************************************ --- *** relation: e_box_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and +1 relative to th *** --- *** e TSS. Consensus sequence is AWCAGCTGWT. *** --- *** Tends to co-occur with DMv2 (SO:0001161 *** --- *** ). Tends to not occur with DPE motif (SO *** --- *** :0000015). *** --- ************************************************ --- CREATE VIEW e_box_motif AS SELECT feature_id AS e_box_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'E_box_motif'; --- ************************************************ --- *** relation: dmv5_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -50 and -10 relative to t *** --- *** he TSS. Consensus sequence is KTYRGTATWT *** --- *** TT. Tends to co-occur with DMv4 (SO:0001 *** --- *** 157) . Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv5_motif AS SELECT feature_id AS dmv5_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv5_motif'; --- ************************************************ --- *** relation: dmv3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -30 and +15 relative to t *** --- *** he TSS. Consensus sequence is KNNCAKCNCT *** --- *** RNY. Tends to co-occur with DMv2 (SO:000 *** --- *** 1161). Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (0001162). *** --- ************************************************ --- CREATE VIEW dmv3_motif AS SELECT feature_id AS dmv3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv3_motif'; --- ************************************************ --- *** relation: dmv2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and -45 relative to t *** --- *** he TSS. Consensus sequence is MKSYGGCARC *** --- *** GSYSS. Tends to co-occur with DMv3 (SO:0 *** --- *** 001160). Tends to not occur with DPE mot *** --- *** if (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv2_motif AS SELECT feature_id AS dmv2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv2_motif'; --- ************************************************ --- *** relation: mte *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between +20 and +30 relative to t *** --- *** he TSS. Consensus sequence is CSARCSSAAC *** --- *** GS. Tends to co-occur with INR motif (SO *** --- *** :0000014). Tends to not occur with DPE m *** --- *** otif (SO:0000015) or DMv5 (SO:0001159). *** --- ************************************************ --- CREATE VIEW mte AS SELECT feature_id AS mte_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MTE'; --- ************************************************ --- *** relation: inr1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** TCATTCG. *** --- ************************************************ --- CREATE VIEW inr1_motif AS SELECT feature_id AS inr1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR1_motif'; --- ************************************************ --- *** relation: dpe1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CGGACGT. *** --- ************************************************ --- CREATE VIEW dpe1_motif AS SELECT feature_id AS dpe1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE1_motif'; --- ************************************************ --- *** relation: dmv1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CARCCCT. *** --- ************************************************ --- CREATE VIEW dmv1_motif AS SELECT feature_id AS dmv1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv1_motif'; --- ************************************************ --- *** relation: gaga_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAGAGCG. *** --- ************************************************ --- CREATE VIEW gaga_motif AS SELECT feature_id AS gaga_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GAGA_motif'; --- ************************************************ --- *** relation: ndm2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus CGMYGYCR. *** --- ************************************************ --- CREATE VIEW ndm2_motif AS SELECT feature_id AS ndm2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM2_motif'; --- ************************************************ --- *** relation: ndm3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAAAGCT. *** --- ************************************************ --- CREATE VIEW ndm3_motif AS SELECT feature_id AS ndm3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM3_motif'; --- ************************************************ --- *** relation: ds_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded RNA. *** --- ************************************************ --- CREATE VIEW ds_rna_viral_sequence AS SELECT feature_id AS ds_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_RNA_viral_sequence'; --- ************************************************ --- *** relation: polinton *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of DNA transposon that populates *** --- *** the genomes of protists, fungi, and anim *** --- *** als, characterized by a unique set of pr *** --- *** oteins necessary for their transposition *** --- *** , including a protein-primed DNA polymer *** --- *** ase B, retroviral integrase, cysteine pr *** --- *** otease, and ATPase. Polintons are charac *** --- *** terized by 6-bp target site duplications *** --- *** , terminal-inverted repeats that are sev *** --- *** eral hundred nucleotides long, and 5'-AG *** --- *** and TC-3' termini. Polintons exist as a *** --- *** utonomous and nonautonomous elements. *** --- ************************************************ --- CREATE VIEW polinton AS SELECT feature_id AS polinton_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polinton'; --- ************************************************ --- *** relation: rrna_21s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it in mitochondrial rRNA. *** --- ************************************************ --- CREATE VIEW rrna_21s AS SELECT feature_id AS rrna_21s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_21S'; --- ************************************************ --- *** relation: trna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tRNA. *** --- ************************************************ --- CREATE VIEW trna_region AS SELECT feature_id AS trna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'tRNA_region'; --- ************************************************ --- *** relation: anticodon_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of seven nucleotide bases in *** --- *** tRNA which contains the anticodon. It ha *** --- *** s the sequence 5'-pyrimidine-purine-anti *** --- *** codon-modified purine-any base-3. *** --- ************************************************ --- CREATE VIEW anticodon_loop AS SELECT feature_id AS anticodon_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop'; --- ************************************************ --- *** relation: anticodon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of three nucleotide bases in *** --- *** tRNA which recognizes a codon in mRNA. *** --- ************************************************ --- CREATE VIEW anticodon AS SELECT feature_id AS anticodon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon'; --- ************************************************ --- *** relation: cca_tail *** --- *** relation type: VIEW *** --- *** *** --- *** Base sequence at the 3' end of a tRNA. T *** --- *** he 3'-hydroxyl group on the terminal ade *** --- *** nosine is the attachment point for the a *** --- *** mino acid. *** --- ************************************************ --- CREATE VIEW cca_tail AS SELECT feature_id AS cca_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CCA_tail'; --- ************************************************ --- *** relation: dhu_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of nucleotide b *** --- *** ases in tRNA. It contains several dihydr *** --- *** ouracil residues. *** --- ************************************************ --- CREATE VIEW dhu_loop AS SELECT feature_id AS dhu_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DHU_loop'; --- ************************************************ --- *** relation: t_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of three nucleo *** --- *** tide bases in tRNA. It has sequence T-Ps *** --- *** i-C. *** --- ************************************************ --- CREATE VIEW t_loop AS SELECT feature_id AS t_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_loop'; --- ************************************************ --- *** relation: pyrrolysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding pyrrolysyl *** --- *** tRNA (SO:0000766). *** --- ************************************************ --- CREATE VIEW pyrrolysine_trna_primary_transcript AS SELECT feature_id AS pyrrolysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: u3_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U3 snoRNA is a member of the box C/D cla *** --- *** ss of small nucleolar RNAs. The U3 snoRN *** --- *** A secondary structure is characterised b *** --- *** y a small 5' domain (with boxes A and A' *** --- *** ), and a larger 3' domain (with boxes B, *** --- *** C, C', and D), the two domains being li *** --- *** nked by a single-stranded hinge. Boxes B *** --- *** and C form the B/C motif, which appears *** --- *** to be exclusive to U3 snoRNAs, and boxe *** --- *** s C' and D form the C'/D motif. The latt *** --- *** er is functionally similar to the C/D mo *** --- *** tifs found in other snoRNAs. The 5' doma *** --- *** in and the hinge region act as a pre-rRN *** --- *** A-binding domain. The 3' domain has cons *** --- *** erved protein-binding sites. Both the bo *** --- *** x B/C and box C'/D motifs are sufficient *** --- *** for nuclear retention of U3 snoRNA. The *** --- *** box C'/D motif is also necessary for nu *** --- *** cleolar localization, stability and hype *** --- *** rmethylation of U3 snoRNA. Both box B/C *** --- *** and C'/D motifs are involved in specific *** --- *** protein interactions and are necessary *** --- *** for the rRNA processing functions of U3 *** --- *** snoRNA. *** --- ************************************************ --- CREATE VIEW u3_snorna AS SELECT feature_id AS u3_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_snoRNA'; --- ************************************************ --- *** relation: au_rich_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is rich in AUUUA pen *** --- *** tamers. Messenger RNAs bearing multiple *** --- *** AU-rich elements are often unstable. *** --- ************************************************ --- CREATE VIEW au_rich_element AS SELECT feature_id AS au_rich_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'AU_rich_element'; --- ************************************************ --- *** relation: bruno_response_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is bound by the Dros *** --- *** ophila Bruno protein and its homologs. *** --- ************************************************ --- CREATE VIEW bruno_response_element AS SELECT feature_id AS bruno_response_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Bruno_response_element'; --- ************************************************ --- *** relation: iron_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory sequence found in the 5' an *** --- *** d 3' UTRs of many mRNAs which encode iro *** --- *** n-binding proteins. It has a hairpin str *** --- *** ucture and is recognized by trans-acting *** --- *** proteins known as iron-regulatory prote *** --- *** ins. *** --- ************************************************ --- CREATE VIEW iron_responsive_element AS SELECT feature_id AS iron_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iron_responsive_element'; --- ************************************************ --- *** relation: morpholino_backbone *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of nucleobases bound to a morpholino *** --- *** backbone. A morpholino backbone consist *** --- *** s of morpholine (CHEBI:34856) rings conn *** --- *** ected by phosphorodiamidate linkages. *** --- ************************************************ --- CREATE VIEW morpholino_backbone AS SELECT feature_id AS morpholino_backbone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_backbone'; --- ************************************************ --- *** relation: pna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of peptide nucleic acid (CHEBI:48021 *** --- *** ), a chemical consisting of nucleobases *** --- *** bound to a backbone composed of repeatin *** --- *** g N-(2-aminoethyl)-glycine units linked *** --- *** by peptide bonds. The purine and pyrimid *** --- *** ine bases are linked to the backbone by *** --- *** methylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna AS SELECT feature_id AS pna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA'; --- ************************************************ --- *** relation: enzymatic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** with or without an associated ribonucle *** --- *** oprotein. *** --- ************************************************ --- CREATE VIEW enzymatic AS SELECT feature_id AS enzymatic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic' OR cvterm.name = 'enzymatic'; --- ************************************************ --- *** relation: ribozymic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** even without an associated ribonucleopr *** --- *** otein. *** --- ************************************************ --- CREATE VIEW ribozymic AS SELECT feature_id AS ribozymic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic'; --- ************************************************ --- *** relation: pseudouridylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of pseu *** --- *** douridylation in an RNA molecule by base *** --- *** pairing with a short sequence around th *** --- *** e target residue. *** --- ************************************************ --- CREATE VIEW pseudouridylation_guide_snorna AS SELECT feature_id AS pseudouridylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA'; --- ************************************************ --- *** relation: lna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of 'locked' deoxyribose r *** --- *** ings connected to a phosphate backbone. *** --- *** The deoxyribose unit's conformation is ' *** --- *** locked' by a 2'-C,4'-C-oxymethylene link *** --- *** . *** --- ************************************************ --- CREATE VIEW lna AS SELECT feature_id AS lna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA'; --- ************************************************ --- *** relation: lna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of LNA residues. *** --- ************************************************ --- CREATE VIEW lna_oligo AS SELECT feature_id AS lna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA_oligo'; --- ************************************************ --- *** relation: tna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of threose rings connecte *** --- *** d to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW tna AS SELECT feature_id AS tna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA'; --- ************************************************ --- *** relation: tna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of TNA residues. *** --- ************************************************ --- CREATE VIEW tna_oligo AS SELECT feature_id AS tna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA_oligo'; --- ************************************************ --- *** relation: gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of an acyclic three-carbo *** --- *** n propylene glycol connected to a phosph *** --- *** ate backbone. It has two enantiomeric fo *** --- *** rms, (R)-GNA and (S)-GNA. *** --- ************************************************ --- CREATE VIEW gna AS SELECT feature_id AS gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'GNA'; --- ************************************************ --- *** relation: gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of GNA residues. *** --- ************************************************ --- CREATE VIEW gna_oligo AS SELECT feature_id AS gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'GNA_oligo'; --- ************************************************ --- *** relation: r_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (R)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW r_gna AS SELECT feature_id AS r_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA'; --- ************************************************ --- *** relation: r_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (R)-GNA residues. *** --- ************************************************ --- CREATE VIEW r_gna_oligo AS SELECT feature_id AS r_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo'; --- ************************************************ --- *** relation: s_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (S)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW s_gna AS SELECT feature_id AS s_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA'; --- ************************************************ --- *** relation: s_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (S)-GNA residues. *** --- ************************************************ --- CREATE VIEW s_gna_oligo AS SELECT feature_id AS s_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA_oligo'; --- ************************************************ --- *** relation: ds_dna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_DNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded DNA. *** --- ************************************************ --- CREATE VIEW ds_dna_viral_sequence AS SELECT feature_id AS ds_dna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_DNA_viral_sequence'; --- ************************************************ --- *** relation: ss_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ss_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as single stranded RNA. *** --- ************************************************ --- CREATE VIEW ss_rna_viral_sequence AS SELECT feature_id AS ss_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence'; --- ************************************************ --- *** relation: negative_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A negative_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** is complementary to mRNA and must be con *** --- *** verted to positive sense RNA by RNA poly *** --- *** merase before translation. *** --- ************************************************ --- CREATE VIEW negative_sense_ssrna_viral_sequence AS SELECT feature_id AS negative_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: positive_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A positive_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** can be immediately translated by the hos *** --- *** t. *** --- ************************************************ --- CREATE VIEW positive_sense_ssrna_viral_sequence AS SELECT feature_id AS positive_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positive_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: ambisense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ambisense_RNA_virus is a ss_RNA_viral_ *** --- *** sequence that is the sequence of a singl *** --- *** e stranded RNA virus with both messenger *** --- *** and anti messenger polarity. *** --- ************************************************ --- CREATE VIEW ambisense_ssrna_viral_sequence AS SELECT feature_id AS ambisense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ambisense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which RNA polymerase b *** --- *** inds, to begin transcription. *** --- ************************************************ --- CREATE VIEW rna_polymerase_promoter AS SELECT feature_id AS rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'RNA_polymerase_promoter'; --- ************************************************ --- *** relation: phage_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which Bacteriophage RN *** --- *** A polymerase binds, to begin transcripti *** --- *** on. *** --- ************************************************ --- CREATE VIEW phage_rna_polymerase_promoter AS SELECT feature_id AS phage_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: sp6_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the SP6 RNA poly *** --- *** merase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW sp6_rna_polymerase_promoter AS SELECT feature_id AS sp6_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t3_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which the T3 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t3_rna_polymerase_promoter AS SELECT feature_id AS t3_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T3_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t7_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the T7 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t7_rna_polymerase_promoter AS SELECT feature_id AS t7_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T7_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: five_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 5' end of a transcr *** --- *** ipt that usually codes for a protein. Th *** --- *** ese regions tend to be conserved across *** --- *** species and do not change much within a *** --- *** gene family. *** --- ************************************************ --- CREATE VIEW five_prime_est AS SELECT feature_id AS five_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST'; --- ************************************************ --- *** relation: three_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 3' end of a transcr *** --- *** ipt. They are more likely to fall within *** --- *** non-coding, or untranslated regions(UTR *** --- *** s). *** --- ************************************************ --- CREATE VIEW three_prime_est AS SELECT feature_id AS three_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_EST'; --- ************************************************ --- *** relation: translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA (not divisible by 3 b *** --- *** ases) that is skipped during the process *** --- *** of translational frameshifting (GO:0006 *** --- *** 452), causing the reading frame to be di *** --- *** fferent. *** --- ************************************************ --- CREATE VIEW translational_frameshift AS SELECT feature_id AS translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'translational_frameshift'; --- ************************************************ --- *** relation: plus_1_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 1 base long that is s *** --- *** kipped during the process of translation *** --- *** al frameshifting (GO:0006452), causing t *** --- *** he reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_1_translational_frameshift AS SELECT feature_id AS plus_1_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift'; --- ************************************************ --- *** relation: plus_2_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 2 bases long that is *** --- *** skipped during the process of translatio *** --- *** nal frameshifting (GO:0006452), causing *** --- *** the reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_2_translational_frameshift AS SELECT feature_id AS plus_2_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_translational_frameshift'; --- ************************************************ --- *** relation: group_iii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group III introns are introns found in t *** --- *** he mRNA of the plastids of euglenoid pro *** --- *** tists. They are spliced by a two step tr *** --- *** ansesterification with bulged adenosine *** --- *** as initiating nucleophile. *** --- ************************************************ --- CREATE VIEW group_iii_intron AS SELECT feature_id AS group_iii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_III_intron'; --- ************************************************ --- *** relation: noncoding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The maximal intersection of exon and UTR *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_region_of_exon AS SELECT feature_id AS noncoding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'noncoding_region_of_exon'; --- ************************************************ --- *** relation: coding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an exon that encodes for p *** --- *** rotein sequence. *** --- ************************************************ --- CREATE VIEW coding_region_of_exon AS SELECT feature_id AS coding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'coding_region_of_exon'; --- ************************************************ --- *** relation: endonuclease_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron that spliced via endonucleolyt *** --- *** ic cleavage and ligation rather than tra *** --- *** nsesterification. *** --- ************************************************ --- CREATE VIEW endonuclease_spliced_intron AS SELECT feature_id AS endonuclease_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'endonuclease_spliced_intron'; --- ************************************************ --- *** relation: protein_coding_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding_gene AS SELECT feature_id AS protein_coding_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'protein_coding_gene'; --- ************************************************ --- *** relation: transgenic_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** An insertion that derives from another o *** --- *** rganism, via the use of recombinant DNA *** --- *** technology. *** --- ************************************************ --- CREATE VIEW transgenic_insertion AS SELECT feature_id AS transgenic_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion'; --- ************************************************ --- *** relation: retrogene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW retrogene AS SELECT feature_id AS retrogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrogene'; --- ************************************************ --- *** relation: silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by RNA *** --- *** interference. *** --- ************************************************ --- CREATE VIEW silenced_by_rna_interference AS SELECT feature_id AS silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_RNA_interference'; --- ************************************************ --- *** relation: silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone modification. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_modification AS SELECT feature_id AS silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_by_histone_modification'; --- ************************************************ --- *** relation: silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone methylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_methylation AS SELECT feature_id AS silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation'; --- ************************************************ --- *** relation: silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone deacetylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_deacetylation AS SELECT feature_id AS silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: gene_silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by RNA interfere *** --- *** nce. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_rna_interference AS SELECT feature_id AS gene_silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_RNA_interference'; --- ************************************************ --- *** relation: gene_silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone modif *** --- *** ication. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_modification AS SELECT feature_id AS gene_silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'gene_silenced_by_histone_modification'; --- ************************************************ --- *** relation: gene_silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone methy *** --- *** lation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_methylation AS SELECT feature_id AS gene_silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation'; --- ************************************************ --- *** relation: gene_silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone deace *** --- *** tylation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_deacetylation AS SELECT feature_id AS gene_silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: dihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5,6-dih *** --- *** ydrouracil is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW dihydrouridine AS SELECT feature_id AS dihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine'; --- ************************************************ --- *** relation: pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5- posi *** --- *** tion of the uracil is bound to the ribos *** --- *** e ring instead of the 4- position. *** --- ************************************************ --- CREATE VIEW pseudouridine AS SELECT feature_id AS pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridine'; --- ************************************************ --- *** relation: inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which hypoxanthin *** --- *** e is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW inosine AS SELECT feature_id AS inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'inosine'; --- ************************************************ --- *** relation: seven_methylguanine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which guanine is *** --- *** methylated at the 7- position. *** --- ************************************************ --- CREATE VIEW seven_methylguanine AS SELECT feature_id AS seven_methylguanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanine'; --- ************************************************ --- *** relation: ribothymidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which thymine is *** --- *** bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW ribothymidine AS SELECT feature_id AS ribothymidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribothymidine'; --- ************************************************ --- *** relation: methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which methylhypox *** --- *** anthine is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW methylinosine AS SELECT feature_id AS methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine'; --- ************************************************ --- *** relation: mobile *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that h *** --- *** as either intra-genome or intracellular *** --- *** mobility. *** --- ************************************************ --- CREATE VIEW mobile AS SELECT feature_id AS mobile_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile'; --- ************************************************ --- *** relation: replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing at least one unique *** --- *** origin of replication and a unique termi *** --- *** nation site. *** --- ************************************************ --- CREATE VIEW replicon AS SELECT feature_id AS replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'replicon'; --- ************************************************ --- *** relation: base *** --- *** relation type: VIEW *** --- *** *** --- *** A base is a sequence feature that corres *** --- *** ponds to a single unit of a nucleotide p *** --- *** olymer. *** --- ************************************************ --- CREATE VIEW base AS SELECT feature_id AS base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'base'; --- ************************************************ --- *** relation: amino_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence feature that corresponds to a *** --- *** single amino acid residue in a polypept *** --- *** ide. *** --- ************************************************ --- CREATE VIEW amino_acid AS SELECT feature_id AS amino_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'amino_acid'; --- ************************************************ --- *** relation: major_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW major_tss AS SELECT feature_id AS major_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS'; --- ************************************************ --- *** relation: minor_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minor_tss AS SELECT feature_id AS minor_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minor_TSS'; --- ************************************************ --- *** relation: tss_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a gene from the 5' most TS *** --- *** S to the 3' TSS. *** --- ************************************************ --- CREATE VIEW tss_region AS SELECT feature_id AS tss_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TSS_region'; --- ************************************************ --- *** relation: encodes_alternate_transcription_start_sites *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW encodes_alternate_transcription_start_sites AS SELECT feature_id AS encodes_alternate_transcription_start_sites_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_alternate_transcription_start_sites'; --- ************************************************ --- *** relation: mirna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of an miRNA primary_transcript. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript_region AS SELECT feature_id AS mirna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'miRNA_primary_transcript_region'; --- ************************************************ --- *** relation: pre_mirna *** --- *** relation type: VIEW *** --- *** *** --- *** The 60-70 nucleotide region remain after *** --- *** Drosha processing of the primary transc *** --- *** ript, that folds back upon itself to for *** --- *** m a hairpin sructure. *** --- ************************************************ --- CREATE VIEW pre_mirna AS SELECT feature_id AS pre_mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA'; --- ************************************************ --- *** relation: mirna_stem *** --- *** relation type: VIEW *** --- *** *** --- *** The stem of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_stem AS SELECT feature_id AS mirna_stem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_stem'; --- ************************************************ --- *** relation: mirna_loop *** --- *** relation type: VIEW *** --- *** *** --- *** The loop of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_loop AS SELECT feature_id AS mirna_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_loop'; --- ************************************************ --- *** relation: synthetic_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of synthetic nucleotid *** --- *** es. *** --- ************************************************ --- CREATE VIEW synthetic_oligo AS SELECT feature_id AS synthetic_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'synthetic_oligo'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome of known length t *** --- *** hat is composed by ordering and aligning *** --- *** two or more different regions. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'assembly'; --- ************************************************ --- *** relation: fragment_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A fragment assembly is a genome assembly *** --- *** that orders overlapping fragments of th *** --- *** e genome based on landmark sequences. Th *** --- *** e base pair distance between the landmar *** --- *** ks is known allowing additivity of lengt *** --- *** hs. *** --- ************************************************ --- CREATE VIEW fragment_assembly AS SELECT feature_id AS fragment_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'fragment_assembly'; --- ************************************************ --- *** relation: fingerprint_map *** --- *** relation type: VIEW *** --- *** *** --- *** A fingerprint_map is a physical map comp *** --- *** osed of restriction fragments. *** --- ************************************************ --- CREATE VIEW fingerprint_map AS SELECT feature_id AS fingerprint_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map'; --- ************************************************ --- *** relation: sts_map *** --- *** relation type: VIEW *** --- *** *** --- *** An STS map is a physical map organized b *** --- *** y the unique STS landmarks. *** --- ************************************************ --- CREATE VIEW sts_map AS SELECT feature_id AS sts_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS_map'; --- ************************************************ --- *** relation: rh_map *** --- *** relation type: VIEW *** --- *** *** --- *** A radiation hybrid map is a physical map *** --- *** . *** --- ************************************************ --- CREATE VIEW rh_map AS SELECT feature_id AS rh_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RH_map'; --- ************************************************ --- *** relation: sonicate_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment generated by sonication. *** --- *** Sonication is a technique used to sheer *** --- *** DNA into smaller fragments. *** --- ************************************************ --- CREATE VIEW sonicate_fragment AS SELECT feature_id AS sonicate_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sonicate_fragment'; --- ************************************************ --- *** relation: polyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is an exact multi *** --- *** ple of the haploid number and is greater *** --- *** than the diploid number. *** --- ************************************************ --- CREATE VIEW polyploid AS SELECT feature_id AS polyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'polyploid'; --- ************************************************ --- *** relation: autopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from the same organism *** --- *** . *** --- ************************************************ --- CREATE VIEW autopolyploid AS SELECT feature_id AS autopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid'; --- ************************************************ --- *** relation: allopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from a different organ *** --- *** ism. *** --- ************************************************ --- CREATE VIEW allopolyploid AS SELECT feature_id AS allopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allopolyploid'; --- ************************************************ --- *** relation: homing_endonuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The binding site (recognition site) of a *** --- *** homing endonuclease. The binding site i *** --- *** s typically large. *** --- ************************************************ --- CREATE VIEW homing_endonuclease_binding_site AS SELECT feature_id AS homing_endonuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homing_endonuclease_binding_site'; --- ************************************************ --- *** relation: octamer_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters with seque *** --- *** nce ATTGCAT that binds Pou-domain transc *** --- *** ription factors. *** --- ************************************************ --- CREATE VIEW octamer_motif AS SELECT feature_id AS octamer_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'octamer_motif'; --- ************************************************ --- *** relation: apicoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in an apicoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW apicoplast_chromosome AS SELECT feature_id AS apicoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_chromosome'; --- ************************************************ --- *** relation: sequence_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of discontinuous sequences. *** --- ************************************************ --- CREATE VIEW sequence_collection AS SELECT feature_id AS sequence_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'genome' OR cvterm.name = 'contig_collection' OR cvterm.name = 'peptide_collection' OR cvterm.name = 'variant_collection' OR cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'sequence_collection'; --- ************************************************ --- *** relation: overlapping_feature_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous region of sequence composed *** --- *** of the overlapping of multiple sequence *** --- *** _features, which ultimately provides evi *** --- *** dence for another sequence_feature. *** --- ************************************************ --- CREATE VIEW overlapping_feature_set AS SELECT feature_id AS overlapping_feature_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'overlapping_feature_set'; --- ************************************************ --- *** relation: overlapping_est_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continous experimental result region e *** --- *** xtending the length of multiple overlapp *** --- *** ing EST's. *** --- ************************************************ --- CREATE VIEW overlapping_est_set AS SELECT feature_id AS overlapping_est_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set'; --- ************************************************ --- *** relation: ncrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ncrna_gene AS SELECT feature_id AS ncrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'ncRNA_gene'; --- ************************************************ --- *** relation: grna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW grna_gene AS SELECT feature_id AS grna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene'; --- ************************************************ --- *** relation: mirna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_gene AS SELECT feature_id AS mirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_gene'; --- ************************************************ --- *** relation: scrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_gene AS SELECT feature_id AS scrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_gene'; --- ************************************************ --- *** relation: snorna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_gene AS SELECT feature_id AS snorna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA_gene'; --- ************************************************ --- *** relation: snrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_gene AS SELECT feature_id AS snrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_gene'; --- ************************************************ --- *** relation: srp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_gene AS SELECT feature_id AS srp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_gene'; --- ************************************************ --- *** relation: strna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_gene AS SELECT feature_id AS strna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_gene'; --- ************************************************ --- *** relation: tmrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_gene AS SELECT feature_id AS tmrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_gene'; --- ************************************************ --- *** relation: trna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_gene AS SELECT feature_id AS trna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_gene'; --- ************************************************ --- *** relation: modified_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified adenine is an adenine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_adenosine AS SELECT feature_id AS modified_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'modified_adenosine'; --- ************************************************ --- *** relation: modified_inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified inosine is an inosine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_inosine AS SELECT feature_id AS modified_inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'modified_inosine'; --- ************************************************ --- *** relation: modified_cytidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified cytidine is a cytidine base f *** --- *** eature which has been altered. *** --- ************************************************ --- CREATE VIEW modified_cytidine AS SELECT feature_id AS modified_cytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'modified_cytidine'; --- ************************************************ --- *** relation: modified_guanosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_guanosine AS SELECT feature_id AS modified_guanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'modified_guanosine'; --- ************************************************ --- *** relation: modified_uridine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_uridine AS SELECT feature_id AS modified_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_uridine'; --- ************************************************ --- *** relation: one_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1-methylinosine is a modified insosine. *** --- ************************************************ --- CREATE VIEW one_methylinosine AS SELECT feature_id AS one_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylinosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethylinosine is a modified ino *** --- *** sine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylinosine AS SELECT feature_id AS one_two_prime_o_dimethylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylinosine'; --- ************************************************ --- *** relation: two_prime_o_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylinosine is a modified inosine *** --- *** . *** --- ************************************************ --- CREATE VIEW two_prime_o_methylinosine AS SELECT feature_id AS two_prime_o_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylinosine'; --- ************************************************ --- *** relation: three_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 3-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW three_methylcytidine AS SELECT feature_id AS three_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine'; --- ************************************************ --- *** relation: five_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_methylcytidine AS SELECT feature_id AS five_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylcytidine'; --- ************************************************ --- *** relation: two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylcytidine is a modified cytidi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylcytidine AS SELECT feature_id AS two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: two_thiocytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2-thiocytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW two_thiocytidine AS SELECT feature_id AS two_thiocytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiocytidine'; --- ************************************************ --- *** relation: n4_acetylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_acetylcytidine AS SELECT feature_id AS n4_acetylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetylcytidine'; --- ************************************************ --- *** relation: five_formylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_formylcytidine AS SELECT feature_id AS five_formylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formylcytidine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5,2'-O-dimethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethylcytidine AS SELECT feature_id AS five_two_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: n4_acetyl_2_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetyl-2'-O-methylcytidine is a modif *** --- *** ied cytidine. *** --- ************************************************ --- CREATE VIEW n4_acetyl_2_prime_o_methylcytidine AS SELECT feature_id AS n4_acetyl_2_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine'; --- ************************************************ --- *** relation: lysidine *** --- *** relation type: VIEW *** --- *** *** --- *** Lysidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW lysidine AS SELECT feature_id AS lysidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysidine'; --- ************************************************ --- *** relation: n4_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-methylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_methylcytidine AS SELECT feature_id AS n4_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_methylcytidine'; --- ************************************************ --- *** relation: n4_2_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4,2'-O-dimethylcytidine is a modified c *** --- *** ytidine. *** --- ************************************************ --- CREATE VIEW n4_2_prime_o_dimethylcytidine AS SELECT feature_id AS n4_2_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_2_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: five_hydroxymethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-hydroxymethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_hydroxymethylcytidine AS SELECT feature_id AS five_hydroxymethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxymethylcytidine'; --- ************************************************ --- *** relation: five_formyl_two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formyl-2'-O-methylcytidine is a modifi *** --- *** ed cytidine. *** --- ************************************************ --- CREATE VIEW five_formyl_two_prime_o_methylcytidine AS SELECT feature_id AS five_formyl_two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formyl_two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: n4_n4_2_prime_o_trimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4_N4_2_prime_O_trimethylcytidine is a m *** --- *** odified cytidine. *** --- ************************************************ --- CREATE VIEW n4_n4_2_prime_o_trimethylcytidine AS SELECT feature_id AS n4_n4_2_prime_o_trimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine'; --- ************************************************ --- *** relation: one_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW one_methyladenosine AS SELECT feature_id AS one_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine'; --- ************************************************ --- *** relation: two_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW two_methyladenosine AS SELECT feature_id AS two_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methyladenosine'; --- ************************************************ --- *** relation: n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_methyladenosine AS SELECT feature_id AS n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyladenosine'; --- ************************************************ --- *** relation: two_prime_o_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyladenosine AS SELECT feature_id AS two_prime_o_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_methyladenosine is a mod *** --- *** ified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_methyladenosine AS SELECT feature_id AS two_methylthio_n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_methyladenosine'; --- ************************************************ --- *** relation: n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_isopentenyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_isopentenyladenosine AS SELECT feature_id AS n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_isopentenyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_isopentenyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_isopentenyladenosine AS SELECT feature_id AS two_methylthio_n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_isopentenyladenosine'; --- ************************************************ --- *** relation: n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_cis_hydroxyisopentenyl_adenosine is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_cis_hydroxyisopentenyl_a *** --- *** denosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS two_methylthio_n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: n6_glycinylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_glycinylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_glycinylcarbamoyladenosine AS SELECT feature_id AS n6_glycinylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_glycinylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_threonylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_threonyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_threonyl_carbamoyladenos *** --- *** ine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_threonyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_threonyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine'; --- ************************************************ --- *** relation: n6_methyl_n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyl_N6_threonylcarbamoyladenosine *** --- *** is a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_methyl_n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_methyl_n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_hydroxynorvalylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_hydroxynorvalylcarbamoyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_hydroxynorvalylcarbamoyladenosine AS SELECT feature_id AS n6_hydroxynorvalylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_hydroxynorvalyl_carbamoy *** --- *** ladenosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine'; --- ************************************************ --- *** relation: two_prime_o_riboA_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosyladenosine_phosphate is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_riboA_phosphate AS SELECT feature_id AS two_prime_o_riboA_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosyladenosine_phosphate'; --- ************************************************ --- *** relation: n6_n6_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_dimethyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_n6_dimethyladenosine AS SELECT feature_id AS n6_n6_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_dimethyladenosine'; --- ************************************************ --- *** relation: n6_2_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_2prime_O_dimethyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_2_prime_o_dimethyladenosine AS SELECT feature_id AS n6_2_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_2_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_n6_2_prime_o_trimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_2prime_O_trimethyladenosine is a m *** --- *** odified adenosine. *** --- ************************************************ --- CREATE VIEW n6_n6_2_prime_o_trimethyladenosine AS SELECT feature_id AS n6_n6_2_prime_o_trimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethyladenosine AS SELECT feature_id AS one_two_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_acetyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_acetyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_acetyladenosine AS SELECT feature_id AS n6_acetyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_acetyladenosine'; --- ************************************************ --- *** relation: seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7-deazaguanosine is a moddified guanosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW seven_deazaguanosine AS SELECT feature_id AS seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'seven_deazaguanosine'; --- ************************************************ --- *** relation: queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Queuosine is a modified 7-deazoguanosine *** --- *** . *** --- ************************************************ --- CREATE VIEW queuosine AS SELECT feature_id AS queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine'; --- ************************************************ --- *** relation: epoxyqueuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Epoxyqueuosine is a modified 7-deazoguan *** --- *** osine. *** --- ************************************************ --- CREATE VIEW epoxyqueuosine AS SELECT feature_id AS epoxyqueuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epoxyqueuosine'; --- ************************************************ --- *** relation: galactosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Galactosyl_queuosine is a modified 7-dea *** --- *** zoguanosine. *** --- ************************************************ --- CREATE VIEW galactosyl_queuosine AS SELECT feature_id AS galactosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'galactosyl_queuosine'; --- ************************************************ --- *** relation: mannosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Mannosyl_queuosine is a modified 7-deazo *** --- *** guanosine. *** --- ************************************************ --- CREATE VIEW mannosyl_queuosine AS SELECT feature_id AS mannosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mannosyl_queuosine'; --- ************************************************ --- *** relation: seven_cyano_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_cyano_7_deazaguanosine is a modified 7 *** --- *** -deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_cyano_seven_deazaguanosine AS SELECT feature_id AS seven_cyano_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_cyano_seven_deazaguanosine'; --- ************************************************ --- *** relation: seven_aminomethyl_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_aminomethyl_7_deazaguanosine is a modi *** --- *** fied 7-deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_aminomethyl_seven_deazaguanosine AS SELECT feature_id AS seven_aminomethyl_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_aminomethyl_seven_deazaguanosine'; --- ************************************************ --- *** relation: archaeosine *** --- *** relation type: VIEW *** --- *** *** --- *** Archaeosine is a modified 7-deazoguanosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW archaeosine AS SELECT feature_id AS archaeosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeosine'; --- ************************************************ --- *** relation: one_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW one_methylguanosine AS SELECT feature_id AS one_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylguanosine'; --- ************************************************ --- *** relation: n2_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_methylguanosine is a modified guanosi *** --- *** ne base feature. *** --- ************************************************ --- CREATE VIEW n2_methylguanosine AS SELECT feature_id AS n2_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_methylguanosine'; --- ************************************************ --- *** relation: seven_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW seven_methylguanosine AS SELECT feature_id AS seven_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanosine'; --- ************************************************ --- *** relation: two_prime_o_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylguanosine is a modified g *** --- *** uanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylguanosine AS SELECT feature_id AS two_prime_o_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylguanosine'; --- ************************************************ --- *** relation: n2_n2_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_dimethylguanosine is a modified gu *** --- *** anosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_dimethylguanosine AS SELECT feature_id AS n2_n2_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_dimethylguanosine'; --- ************************************************ --- *** relation: n2_2_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_2prime_O_dimethylguanosine is a modif *** --- *** ied guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_2_prime_o_dimethylguanosine AS SELECT feature_id AS n2_2_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_2_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_2_prime_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_2prime_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_2_prime_o_trimethylguanosine AS SELECT feature_id AS n2_n2_2_prime_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine'; --- ************************************************ --- *** relation: two_prime_o_ribosylguanosine_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosylguanosine_phosphate is a *** --- *** modified guanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_ribosylguanosine_phosphate AS SELECT feature_id AS two_prime_o_ribosylguanosine_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosylguanosine_phosphate'; --- ************************************************ --- *** relation: wybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wybutosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW wybutosine AS SELECT feature_id AS wybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wybutosine'; --- ************************************************ --- *** relation: peroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Peroxywybutosine is a modified guanosine *** --- *** base feature. *** --- ************************************************ --- CREATE VIEW peroxywybutosine AS SELECT feature_id AS peroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peroxywybutosine'; --- ************************************************ --- *** relation: hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Hydroxywybutosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW hydroxywybutosine AS SELECT feature_id AS hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydroxywybutosine'; --- ************************************************ --- *** relation: undermodified_hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Undermodified_hydroxywybutosine is a mod *** --- *** ified guanosine base feature. *** --- ************************************************ --- CREATE VIEW undermodified_hydroxywybutosine AS SELECT feature_id AS undermodified_hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'undermodified_hydroxywybutosine'; --- ************************************************ --- *** relation: wyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wyosine is a modified guanosine base fea *** --- *** ture. *** --- ************************************************ --- CREATE VIEW wyosine AS SELECT feature_id AS wyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wyosine'; --- ************************************************ --- *** relation: methylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Methylwyosine is a modified guanosine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW methylwyosine AS SELECT feature_id AS methylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylwyosine'; --- ************************************************ --- *** relation: n2_7_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_dimethylguanosine is a modified gua *** --- *** nosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_dimethylguanosine AS SELECT feature_id AS n2_7_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_7_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_7_trimethylguanosine is a modified *** --- *** guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_7_trimethylguanosine AS SELECT feature_id AS n2_n2_7_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_7_trimethylguanosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_2prime_O_dimethylguanosine is a modifi *** --- *** ed guanosine base feature. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylguanosine AS SELECT feature_id AS one_two_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: four_demethylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_demethylwyosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW four_demethylwyosine AS SELECT feature_id AS four_demethylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_demethylwyosine'; --- ************************************************ --- *** relation: isowyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Isowyosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW isowyosine AS SELECT feature_id AS isowyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isowyosine'; --- ************************************************ --- *** relation: n2_7_2prirme_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_2prirme_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_2prirme_o_trimethylguanosine AS SELECT feature_id AS n2_7_2prirme_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_2prirme_O_trimethylguanosine'; --- ************************************************ --- *** relation: five_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW five_methyluridine AS SELECT feature_id AS five_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyluridine'; --- ************************************************ --- *** relation: two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyluridine AS SELECT feature_id AS two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_2_prime_O_dimethyluridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethyluridine AS SELECT feature_id AS five_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: one_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW one_methylpseudouridine AS SELECT feature_id AS one_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylpseudouridine'; --- ************************************************ --- *** relation: two_prime_o_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylpseudouridine is a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylpseudouridine AS SELECT feature_id AS two_prime_o_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylpseudouridine'; --- ************************************************ --- *** relation: two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW two_thiouridine AS SELECT feature_id AS two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiouridine'; --- ************************************************ --- *** relation: four_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW four_thiouridine AS SELECT feature_id AS four_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_thiouridine'; --- ************************************************ --- *** relation: five_methyl_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyl_2_thiouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyl_2_thiouridine AS SELECT feature_id AS five_methyl_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyl_2_thiouridine'; --- ************************************************ --- *** relation: two_thio_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thio_2prime_O_methyluridine is a modif *** --- *** ied uridine base feature. *** --- ************************************************ --- CREATE VIEW two_thio_two_prime_o_methyluridine AS SELECT feature_id AS two_thio_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thio_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: three_three_amino_three_carboxypropyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_3_amino_3_carboxypropyl_uridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW three_three_amino_three_carboxypropyl_uridine AS SELECT feature_id AS three_three_amino_three_carboxypropyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_three_amino_three_carboxypropyl_uridine'; --- ************************************************ --- *** relation: five_hydroxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_hydroxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_hydroxyuridine AS SELECT feature_id AS five_hydroxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxyuridine'; --- ************************************************ --- *** relation: five_methoxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_methoxyuridine AS SELECT feature_id AS five_methoxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxyuridine'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid AS SELECT feature_id AS uridine_five_oxyacetic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid_methyl_ester is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid_methyl_ester AS SELECT feature_id AS uridine_five_oxyacetic_acid_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine is a modi *** --- *** fied uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine_methyl_es *** --- *** ter is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine_methyl_ester AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyluridine AS SELECT feature_id AS five_methoxycarbonylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyluridine'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_methoxycarbonylmethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_mcm_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxycarbonylmethyl_2_thiouridine is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mcm_2_thiouridine AS SELECT feature_id AS five_mcm_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_aminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_aminomethyl_2_thiouridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_aminomethyl_two_thiouridine AS SELECT feature_id AS five_aminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_aminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyluridine AS SELECT feature_id AS five_methylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyluridine'; --- ************************************************ --- *** relation: five_mam_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_thiouridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mam_2_thiouridine AS SELECT feature_id AS five_mam_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyl_two_selenouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_selenouridine is a *** --- *** modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyl_two_selenouridine AS SELECT feature_id AS five_methylaminomethyl_two_selenouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_selenouridine'; --- ************************************************ --- *** relation: five_carbamoylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyluridine is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW five_carbamoylmethyluridine AS SELECT feature_id AS five_carbamoylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyluridine'; --- ************************************************ --- *** relation: five_cm_2_prime_o_methU *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyl_2_prime_O_methyluridin *** --- *** e is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_cm_2_prime_o_methU AS SELECT feature_id AS five_cm_2_prime_o_methU_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyluridine AS SELECT feature_id AS five_carboxymethylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_thiouridine *** --- *** is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_thiouridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: three_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW three_methyluridine AS SELECT feature_id AS three_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methyluridine'; --- ************************************************ --- *** relation: one_methyl_3_3_amino_three_carboxypropyl_pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyl_3_3_amino_3_carboxypropyl_pseud *** --- *** ouridine is a modified uridine base feat *** --- *** ure. *** --- ************************************************ --- CREATE VIEW one_methyl_3_3_amino_three_carboxypropyl_pseudouridine AS SELECT feature_id AS one_methyl_3_3_amino_three_carboxypropyl_pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine'; --- ************************************************ --- *** relation: five_carboxymethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethyluridine AS SELECT feature_id AS five_carboxymethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethyluridine'; --- ************************************************ --- *** relation: three_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_2prime_O_dimethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW three_two_prime_o_dimethyluridine AS SELECT feature_id AS three_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: five_methyldihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyldihydrouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyldihydrouridine AS SELECT feature_id AS five_methyldihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyldihydrouridine'; --- ************************************************ --- *** relation: three_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW three_methylpseudouridine AS SELECT feature_id AS three_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylpseudouridine'; --- ************************************************ --- *** relation: five_taurinomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyluridine AS SELECT feature_id AS five_taurinomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyluridine'; --- ************************************************ --- *** relation: five_taurinomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyl_2_thiouridineis a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyl_two_thiouridine AS SELECT feature_id AS five_taurinomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_uridine is a mo *** --- *** dified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_uridine AS SELECT feature_id AS five_isopentenylaminomethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_uridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2_thiouridine i *** --- *** s a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_thiouridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2prime_O_methyl *** --- *** uridine is a modified uridine base featu *** --- *** re. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: histone_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** histone. *** --- ************************************************ --- CREATE VIEW histone_binding_site AS SELECT feature_id AS histone_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_binding_site'; --- ************************************************ --- *** relation: cds_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cds_fragment AS SELECT feature_id AS cds_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_fragment'; --- ************************************************ --- *** relation: modified_amino_acid_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified amino ac *** --- *** id feature. *** --- ************************************************ --- CREATE VIEW modified_amino_acid_feature AS SELECT feature_id AS modified_amino_acid_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'modified_amino_acid_feature'; --- ************************************************ --- *** relation: modified_glycine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glycine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_glycine AS SELECT feature_id AS modified_glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine'; --- ************************************************ --- *** relation: modified_l_alanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified alanine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_alanine AS SELECT feature_id AS modified_l_alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_alanine'; --- ************************************************ --- *** relation: modified_l_asparagine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified asparagi *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_asparagine AS SELECT feature_id AS modified_l_asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_asparagine'; --- ************************************************ --- *** relation: modified_l_aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified aspartic *** --- *** acid amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_aspartic_acid AS SELECT feature_id AS modified_l_aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_aspartic_acid'; --- ************************************************ --- *** relation: modified_l_cysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified cysteine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_cysteine AS SELECT feature_id AS modified_l_cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_cysteine'; --- ************************************************ --- *** relation: modified_l_glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_l_glutamic_acid AS SELECT feature_id AS modified_l_glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamic_acid'; --- ************************************************ --- *** relation: modified_l_threonine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified threonin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_threonine AS SELECT feature_id AS modified_l_threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_threonine'; --- ************************************************ --- *** relation: modified_l_tryptophan *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tryptoph *** --- *** an amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tryptophan AS SELECT feature_id AS modified_l_tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tryptophan'; --- ************************************************ --- *** relation: modified_l_glutamine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glutamin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_glutamine AS SELECT feature_id AS modified_l_glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamine'; --- ************************************************ --- *** relation: modified_l_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified methioni *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_methionine AS SELECT feature_id AS modified_l_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_methionine'; --- ************************************************ --- *** relation: modified_l_isoleucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified isoleuci *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_isoleucine AS SELECT feature_id AS modified_l_isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_isoleucine'; --- ************************************************ --- *** relation: modified_l_phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified phenylal *** --- *** anine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_phenylalanine AS SELECT feature_id AS modified_l_phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_phenylalanine'; --- ************************************************ --- *** relation: modified_l_histidine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified histidie *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_histidine AS SELECT feature_id AS modified_l_histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_histidine'; --- ************************************************ --- *** relation: modified_l_serine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified serine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_serine AS SELECT feature_id AS modified_l_serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_serine'; --- ************************************************ --- *** relation: modified_l_lysine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified lysine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_lysine AS SELECT feature_id AS modified_l_lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_lysine'; --- ************************************************ --- *** relation: modified_l_leucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified leucine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_leucine AS SELECT feature_id AS modified_l_leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_leucine'; --- ************************************************ --- *** relation: modified_l_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified selenocy *** --- *** steine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_selenocysteine AS SELECT feature_id AS modified_l_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_selenocysteine'; --- ************************************************ --- *** relation: modified_l_valine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified valine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_valine AS SELECT feature_id AS modified_l_valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_valine'; --- ************************************************ --- *** relation: modified_l_proline *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified proline *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_proline AS SELECT feature_id AS modified_l_proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_proline'; --- ************************************************ --- *** relation: modified_l_tyrosine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tyrosine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tyrosine AS SELECT feature_id AS modified_l_tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tyrosine'; --- ************************************************ --- *** relation: modified_l_arginine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified arginine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_arginine AS SELECT feature_id AS modified_l_arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_arginine'; --- ************************************************ --- *** relation: peptidyl *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the nature of a *** --- *** proteinaceous polymer, where by the amin *** --- *** o acid units are joined by peptide bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW peptidyl AS SELECT feature_id AS peptidyl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptidyl'; --- ************************************************ --- *** relation: cleaved_for_gpi_anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** The C-terminal residues of a polypeptide *** --- *** which are exchanged for a GPI-anchor. *** --- ************************************************ --- CREATE VIEW cleaved_for_gpi_anchor_region AS SELECT feature_id AS cleaved_for_gpi_anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_for_gpi_anchor_region'; --- ************************************************ --- *** relation: biomaterial_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is intended for use in an *** --- *** experiment. *** --- ************************************************ --- CREATE VIEW biomaterial_region AS SELECT feature_id AS biomaterial_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'biomaterial_region'; --- ************************************************ --- *** relation: experimental_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is the result of some arb *** --- *** itrary experimental procedure. The proce *** --- *** dure may be carried out with biological *** --- *** material or inside a computer. *** --- ************************************************ --- CREATE VIEW experimental_feature AS SELECT feature_id AS experimental_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimental_feature'; --- ************************************************ --- *** relation: biological_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by its disposition to b *** --- *** e involved in a biological process. *** --- ************************************************ --- CREATE VIEW biological_region AS SELECT feature_id AS biological_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'biological_region'; --- ************************************************ --- *** relation: topologically_defined_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is defined according to it *** --- *** s relations with other regions within th *** --- *** e same sequence. *** --- ************************************************ --- CREATE VIEW topologically_defined_region AS SELECT feature_id AS topologically_defined_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'topologically_defined_region'; --- ************************************************ --- *** relation: translocation_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a tr *** --- *** anslocation begins or ends. *** --- ************************************************ --- CREATE VIEW translocation_breakpoint AS SELECT feature_id AS translocation_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_breakpoint'; --- ************************************************ --- *** relation: insertion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a in *** --- *** sertion begins or ends. *** --- ************************************************ --- CREATE VIEW insertion_breakpoint AS SELECT feature_id AS insertion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_breakpoint'; --- ************************************************ --- *** relation: deletion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a de *** --- *** letion begins or ends. *** --- ************************************************ --- CREATE VIEW deletion_breakpoint AS SELECT feature_id AS deletion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_breakpoint'; --- ************************************************ --- *** relation: five_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located five prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW five_prime_flanking_region AS SELECT feature_id AS five_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_flanking_region'; --- ************************************************ --- *** relation: three_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located three prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW three_prime_flanking_region AS SELECT feature_id AS three_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_flanking_region'; --- ************************************************ --- *** relation: transcribed_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region, defined by a til *** --- *** ing array experiment to be transcribed a *** --- *** t some level. *** --- ************************************************ --- CREATE VIEW transcribed_fragment AS SELECT feature_id AS transcribed_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_fragment'; --- ************************************************ --- *** relation: cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering exon. A s *** --- *** plice_site that adjacent_to exon and ove *** --- *** rlaps intron. *** --- ************************************************ --- CREATE VIEW cis_splice_site AS SELECT feature_id AS cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'cis_splice_site'; --- ************************************************ --- *** relation: trans_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Primary transcript region bordering tran *** --- *** s-splice junction. *** --- ************************************************ --- CREATE VIEW trans_splice_site AS SELECT feature_id AS trans_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_site'; --- ************************************************ --- *** relation: splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between an intron and an ex *** --- *** on. *** --- ************************************************ --- CREATE VIEW splice_junction AS SELECT feature_id AS splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_junction'; --- ************************************************ --- *** relation: conformational_switch *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a polypeptide, involved in t *** --- *** he transition from one conformational st *** --- *** ate to another. *** --- ************************************************ --- CREATE VIEW conformational_switch AS SELECT feature_id AS conformational_switch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_switch'; --- ************************************************ --- *** relation: dye_terminator_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the dye terminator me *** --- *** thod of sequencing. *** --- ************************************************ --- CREATE VIEW dye_terminator_read AS SELECT feature_id AS dye_terminator_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dye_terminator_read'; --- ************************************************ --- *** relation: pyrosequenced_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by pyrosequencing techno *** --- *** logy. *** --- ************************************************ --- CREATE VIEW pyrosequenced_read AS SELECT feature_id AS pyrosequenced_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrosequenced_read'; --- ************************************************ --- *** relation: ligation_based_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by ligation based sequen *** --- *** cing technologies. *** --- ************************************************ --- CREATE VIEW ligation_based_read AS SELECT feature_id AS ligation_based_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ligation_based_read'; --- ************************************************ --- *** relation: polymerase_synthesis_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the polymerase based *** --- *** sequence by synthesis method. *** --- ************************************************ --- CREATE VIEW polymerase_synthesis_read AS SELECT feature_id AS polymerase_synthesis_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymerase_synthesis_read'; --- ************************************************ --- *** relation: cis_regulatory_frameshift_element *** --- *** relation type: VIEW *** --- *** *** --- *** A structural region in an RNA molecule w *** --- *** hich promotes ribosomal frameshifting of *** --- *** cis coding sequence. *** --- ************************************************ --- CREATE VIEW cis_regulatory_frameshift_element AS SELECT feature_id AS cis_regulatory_frameshift_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_regulatory_frameshift_element'; --- ************************************************ --- *** relation: expressed_sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence assembly derived from express *** --- *** ed sequences. *** --- ************************************************ --- CREATE VIEW expressed_sequence_assembly AS SELECT feature_id AS expressed_sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_assembly'; --- ************************************************ --- *** relation: dna_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith DNA. *** --- ************************************************ --- CREATE VIEW dna_binding_site AS SELECT feature_id AS dna_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'DNA_binding_site'; --- ************************************************ --- *** relation: cryptic_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is not transcribed under nor *** --- *** mal conditions and is not critical to no *** --- *** rmal cellular functioning. *** --- ************************************************ --- CREATE VIEW cryptic_gene AS SELECT feature_id AS cryptic_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'cryptic_gene'; --- ************************************************ --- *** relation: three_prime_race_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A three prime RACE (Rapid Amplification *** --- *** of cDNA Ends) clone is a cDNA clone copi *** --- *** ed from the 3' end of an mRNA (using a p *** --- *** oly-dT primer to capture the polyA tail *** --- *** and a gene-specific or randomly primed 5 *** --- *** ' primer), and spliced into a vector for *** --- *** propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW three_prime_race_clone AS SELECT feature_id AS three_prime_race_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RACE_clone'; --- ************************************************ --- *** relation: cassette_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A cassette pseudogene is a kind of gene *** --- *** in an inactive form which may recombine *** --- *** at a telomeric locus to form a functiona *** --- *** l copy. *** --- ************************************************ --- CREATE VIEW cassette_pseudogene AS SELECT feature_id AS cassette_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_pseudogene'; --- ************************************************ --- *** relation: alanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alanine AS SELECT feature_id AS alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine'; --- ************************************************ --- *** relation: valine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW valine AS SELECT feature_id AS valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine'; --- ************************************************ --- *** relation: leucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucine AS SELECT feature_id AS leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine'; --- ************************************************ --- *** relation: isoleucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW isoleucine AS SELECT feature_id AS isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine'; --- ************************************************ --- *** relation: proline *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proline AS SELECT feature_id AS proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline'; --- ************************************************ --- *** relation: tryptophan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tryptophan AS SELECT feature_id AS tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan'; --- ************************************************ --- *** relation: phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW phenylalanine AS SELECT feature_id AS phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine'; --- ************************************************ --- *** relation: methionine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW methionine AS SELECT feature_id AS methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine'; --- ************************************************ --- *** relation: glycine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glycine AS SELECT feature_id AS glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine'; --- ************************************************ --- *** relation: serine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW serine AS SELECT feature_id AS serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine'; --- ************************************************ --- *** relation: threonine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW threonine AS SELECT feature_id AS threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine'; --- ************************************************ --- *** relation: tyrosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tyrosine AS SELECT feature_id AS tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine'; --- ************************************************ --- *** relation: cysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cysteine AS SELECT feature_id AS cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine'; --- ************************************************ --- *** relation: glutamine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamine AS SELECT feature_id AS glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine'; --- ************************************************ --- *** relation: asparagine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW asparagine AS SELECT feature_id AS asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine'; --- ************************************************ --- *** relation: lysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lysine AS SELECT feature_id AS lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine'; --- ************************************************ --- *** relation: arginine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW arginine AS SELECT feature_id AS arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine'; --- ************************************************ --- *** relation: histidine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW histidine AS SELECT feature_id AS histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine'; --- ************************************************ --- *** relation: aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aspartic_acid AS SELECT feature_id AS aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid'; --- ************************************************ --- *** relation: glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamic_acid AS SELECT feature_id AS glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid'; --- ************************************************ --- *** relation: selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW selenocysteine AS SELECT feature_id AS selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine'; --- ************************************************ --- *** relation: pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pyrrolysine AS SELECT feature_id AS pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine'; --- ************************************************ --- *** relation: transcribed_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by a set of transcribed *** --- *** sequences from the same gene or express *** --- *** ed pseudogene. *** --- ************************************************ --- CREATE VIEW transcribed_cluster AS SELECT feature_id AS transcribed_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster' OR cvterm.name = 'transcribed_cluster'; --- ************************************************ --- *** relation: unigene_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of transcribed_cluster defined by *** --- *** a set of transcribed sequences from the *** --- *** a unique gene. *** --- ************************************************ --- CREATE VIEW unigene_cluster AS SELECT feature_id AS unigene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster'; --- ************************************************ --- *** relation: crispr *** --- *** relation type: VIEW *** --- *** *** --- *** Clustered Palindromic Repeats interspers *** --- *** ed with bacteriophage derived spacer seq *** --- *** uences. *** --- ************************************************ --- CREATE VIEW crispr AS SELECT feature_id AS crispr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CRISPR'; --- ************************************************ --- *** relation: insulator_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in an insulator reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW insulator_binding_site AS SELECT feature_id AS insulator_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator_binding_site'; --- ************************************************ --- *** relation: enhancer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the enhancer reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW enhancer_binding_site AS SELECT feature_id AS enhancer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_binding_site'; --- ************************************************ --- *** relation: contig_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of contigs. *** --- ************************************************ --- CREATE VIEW contig_collection AS SELECT feature_id AS contig_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection'; --- ************************************************ --- *** relation: lincrna *** --- *** relation type: VIEW *** --- *** *** --- *** A multiexonic non-coding RNA transcribed *** --- *** by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW lincrna AS SELECT feature_id AS lincrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA'; --- ************************************************ --- *** relation: ust *** --- *** relation type: VIEW *** --- *** *** --- *** An EST spanning part or all of the untra *** --- *** nslated regions of a protein-coding tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW ust AS SELECT feature_id AS ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'UST'; --- ************************************************ --- *** relation: three_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** A UST located in the 3'UTR of a protein- *** --- *** coding transcript. *** --- ************************************************ --- CREATE VIEW three_prime_ust AS SELECT feature_id AS three_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST'; --- ************************************************ --- *** relation: five_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** An UST located in the 5'UTR of a protein *** --- *** -coding transcript. *** --- ************************************************ --- CREATE VIEW five_prime_ust AS SELECT feature_id AS five_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UST'; --- ************************************************ --- *** relation: rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a RACE product; typically a fe *** --- *** w hundred base pairs long. *** --- ************************************************ --- CREATE VIEW rst AS SELECT feature_id AS rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'RST'; --- ************************************************ --- *** relation: three_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 3'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW three_prime_rst AS SELECT feature_id AS three_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST'; --- ************************************************ --- *** relation: five_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 5'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW five_prime_rst AS SELECT feature_id AS five_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_RST'; --- ************************************************ --- *** relation: ust_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an UST sequence. *** --- ************************************************ --- CREATE VIEW ust_match AS SELECT feature_id AS ust_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UST_match'; --- ************************************************ --- *** relation: rst_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an RST sequence. *** --- ************************************************ --- CREATE VIEW rst_match AS SELECT feature_id AS rst_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RST_match'; --- ************************************************ --- *** relation: primer_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match to a primer sequence. *** --- ************************************************ --- CREATE VIEW primer_match AS SELECT feature_id AS primer_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_match'; --- ************************************************ --- *** relation: mirna_antiguide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the pri miRNA that basepairs *** --- *** with the guide to form the hairpin. *** --- ************************************************ --- CREATE VIEW mirna_antiguide AS SELECT feature_id AS mirna_antiguide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_antiguide'; --- ************************************************ --- *** relation: trans_splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the spliced leader *** --- *** and the first exon of the mRNA. *** --- ************************************************ --- CREATE VIEW trans_splice_junction AS SELECT feature_id AS trans_splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_junction'; --- ************************************************ --- *** relation: outron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript, that i *** --- *** s removed via trans splicing. *** --- ************************************************ --- CREATE VIEW outron AS SELECT feature_id AS outron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'outron'; --- ************************************************ --- *** relation: natural_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that occurs naturally. *** --- ************************************************ --- CREATE VIEW natural_plasmid AS SELECT feature_id AS natural_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_plasmid'; --- ************************************************ --- *** relation: gene_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A gene trap construct is a type of engin *** --- *** eered plasmid which is designed to integ *** --- *** rate into a genome and produce a fusion *** --- *** transcript between exons of the gene int *** --- *** o which it inserts and a reporter elemen *** --- *** t in the construct. Gene traps contain a *** --- *** splice acceptor, do not contain promote *** --- *** r elements for the reporter, and are mut *** --- *** agenic. Gene traps may be bicistronic wi *** --- *** th the second cassette containing a prom *** --- *** oter driving an a selectable marker. *** --- ************************************************ --- CREATE VIEW gene_trap_construct AS SELECT feature_id AS gene_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_trap_construct'; --- ************************************************ --- *** relation: promoter_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter trap construct is a type of e *** --- *** ngineered plasmid which is designed to i *** --- *** ntegrate into a genome and express a rep *** --- *** orter when inserted in close proximity t *** --- *** o a promoter element. Promoter traps typ *** --- *** ically do not contain promoter elements *** --- *** and are mutagenic. *** --- ************************************************ --- CREATE VIEW promoter_trap_construct AS SELECT feature_id AS promoter_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_trap_construct'; --- ************************************************ --- *** relation: enhancer_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer trap construct is a type of *** --- *** engineered plasmid which is designed to *** --- *** integrate into a genome and express a re *** --- *** porter when the expression from a basic *** --- *** minimal promoter is enhanced by genomic *** --- *** enhancer elements. Enhancer traps contai *** --- *** n promoter elements and are not usually *** --- *** mutagenic. *** --- ************************************************ --- CREATE VIEW enhancer_trap_construct AS SELECT feature_id AS enhancer_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_trap_construct'; --- ************************************************ --- *** relation: pac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a P *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW pac_end AS SELECT feature_id AS pac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC_end'; --- ************************************************ --- *** relation: rapd *** --- *** relation type: VIEW *** --- *** *** --- *** RAPD is a 'PCR product' where a sequence *** --- *** variant is identified through the use o *** --- *** f PCR with random primers. *** --- ************************************************ --- CREATE VIEW rapd AS SELECT feature_id AS rapd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD'; --- ************************************************ --- *** relation: shadow_enhancer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW shadow_enhancer AS SELECT feature_id AS shadow_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'shadow_enhancer'; --- ************************************************ --- *** relation: snv *** --- *** relation type: VIEW *** --- *** *** --- *** SNVs are single nucleotide positions in *** --- *** genomic DNA at which different sequence *** --- *** alternatives exist. *** --- ************************************************ --- CREATE VIEW snv AS SELECT feature_id AS snv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'SNV'; --- ************************************************ --- *** relation: x_element_combinatorial_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An X element combinatorial repeat is a r *** --- *** epeat region located between the X eleme *** --- *** nt and the telomere or adjacent Y' eleme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW x_element_combinatorial_repeat AS SELECT feature_id AS x_element_combinatorial_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element_combinatorial_repeat'; --- ************************************************ --- *** relation: y_prime_element *** --- *** relation type: VIEW *** --- *** *** --- *** A Y' element is a repeat region (SO:0000 *** --- *** 657) located adjacent to telomeric repea *** --- *** ts or X element combinatorial repeats, e *** --- *** ither as a single copy or tandem repeat *** --- *** of two to four copies. *** --- ************************************************ --- CREATE VIEW y_prime_element AS SELECT feature_id AS y_prime_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_prime_element'; --- ************************************************ --- *** relation: standard_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the data is minimally filtered or u *** --- *** n-filtered, from any number of sequencin *** --- *** g platforms, and is assembled into conti *** --- *** gs. Genome sequence of this quality may *** --- *** harbour regions of poor quality and can *** --- *** be relatively incomplete. *** --- ************************************************ --- CREATE VIEW standard_draft AS SELECT feature_id AS standard_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft'; --- ************************************************ --- *** relation: high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here overall coverage represents at leas *** --- *** t 90 percent of the genome. *** --- ************************************************ --- CREATE VIEW high_quality_draft AS SELECT feature_id AS high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_quality_draft'; --- ************************************************ --- *** relation: improved_high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here additional work has been performed, *** --- *** using either manual or automated method *** --- *** s, such as gap resolution. *** --- ************************************************ --- CREATE VIEW improved_high_quality_draft AS SELECT feature_id AS improved_high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'improved_high_quality_draft'; --- ************************************************ --- *** relation: annotation_directed_improved_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence,wh *** --- *** ere annotation, and verification of codi *** --- *** ng regions has occurred. *** --- ************************************************ --- CREATE VIEW annotation_directed_improved_draft AS SELECT feature_id AS annotation_directed_improved_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'annotation_directed_improved_draft'; --- ************************************************ --- *** relation: noncontiguous_finished *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the assembly is high quality, closu *** --- *** re approaches have been successful for m *** --- *** ost gaps, misassemblies and low quality *** --- *** regions. *** --- ************************************************ --- CREATE VIEW noncontiguous_finished AS SELECT feature_id AS noncontiguous_finished_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncontiguous_finished'; --- ************************************************ --- *** relation: finished_genome *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** ith less than 1 error per 100,000 base p *** --- *** airs. *** --- ************************************************ --- CREATE VIEW finished_genome AS SELECT feature_id AS finished_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'finished_genome'; --- ************************************************ --- *** relation: intronic_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is part of an i *** --- *** ntron. *** --- ************************************************ --- CREATE VIEW intronic_regulatory_region AS SELECT feature_id AS intronic_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_regulatory_region'; --- ************************************************ --- *** relation: centromere_dna_element_i *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region compos *** --- *** ed of 8-11bp which enables binding by th *** --- *** e centromere binding factor 1(Cbf1p). *** --- ************************************************ --- CREATE VIEW centromere_dna_element_i AS SELECT feature_id AS centromere_dna_element_i_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_I'; --- ************************************************ --- *** relation: centromere_dna_element_ii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element II (CDEII) is p *** --- *** art a conserved region of the centromere *** --- *** , consisting of a consensus region that *** --- *** is AT-rich and ~ 75-100 bp in length. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_ii AS SELECT feature_id AS centromere_dna_element_ii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_II'; --- ************************************************ --- *** relation: centromere_dna_element_iii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region that c *** --- *** onsists of a 25-bp which enables binding *** --- *** by the centromere DNA binding factor 3 *** --- *** (CBF3) complex. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_iii AS SELECT feature_id AS centromere_dna_element_iii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_III'; --- ************************************************ --- *** relation: telomeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The telomeric repeat is a repeat region, *** --- *** part of the chromosome, which in yeast, *** --- *** is a G-rich terminal sequence of the fo *** --- *** rm (TG(1-3))n or more precisely ((TG)(1- *** --- *** 6)TG(2-3))n. *** --- ************************************************ --- CREATE VIEW telomeric_repeat AS SELECT feature_id AS telomeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomeric_repeat'; --- ************************************************ --- *** relation: x_element *** --- *** relation type: VIEW *** --- *** *** --- *** The X element is a conserved region, of *** --- *** the telomere, of ~475 bp that contains a *** --- *** n ARS sequence and in most cases an Abf1 *** --- *** p binding site. *** --- ************************************************ --- CREATE VIEW x_element AS SELECT feature_id AS x_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element'; --- ************************************************ --- *** relation: yac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a Y *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW yac_end AS SELECT feature_id AS yac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC_end'; --- ************************************************ --- *** relation: whole_genome_sequence_status *** --- *** relation type: VIEW *** --- *** *** --- *** The status of whole genome sequence. *** --- ************************************************ --- CREATE VIEW whole_genome_sequence_status AS SELECT feature_id AS whole_genome_sequence_status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'whole_genome_sequence_status'; --- ************************************************ --- *** relation: heritable_phenotypic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region characterized as a s *** --- *** ingle heritable trait in a phenotype scr *** --- *** een. The heritable phenotype may be mapp *** --- *** ed to a chromosome but generally has not *** --- *** been characterized to a specific gene l *** --- *** ocus. *** --- ************************************************ --- CREATE VIEW heritable_phenotypic_marker AS SELECT feature_id AS heritable_phenotypic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker'; --- ************************************************ --- *** relation: peptide_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of peptide sequences. *** --- ************************************************ --- CREATE VIEW peptide_collection AS SELECT feature_id AS peptide_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_collection'; --- ************************************************ --- *** relation: high_identity_region *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature with high sequen *** --- *** ce identity to another sequence. *** --- ************************************************ --- CREATE VIEW high_identity_region AS SELECT feature_id AS high_identity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_identity_region'; --- ************************************************ --- *** relation: processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript for which no open reading f *** --- *** rame has been identified and for which n *** --- *** o other function has been determined. *** --- ************************************************ --- CREATE VIEW processed_transcript AS SELECT feature_id AS processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_transcript'; --- ************************************************ --- *** relation: assortment_derived_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome variation derived from an e *** --- *** vent during meiosis. *** --- ************************************************ --- CREATE VIEW assortment_derived_variation AS SELECT feature_id AS assortment_derived_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'assortment_derived_variation'; --- ************************************************ --- *** relation: reference_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) taken as the standard for a given *** --- *** organism and genome assembly. *** --- ************************************************ --- CREATE VIEW reference_genome AS SELECT feature_id AS reference_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reference_genome'; --- ************************************************ --- *** relation: variant_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) of an individual. *** --- ************************************************ --- CREATE VIEW variant_genome AS SELECT feature_id AS variant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'variant_genome'; --- ************************************************ --- *** relation: variant_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of one or more sequences of *** --- *** an individual. *** --- ************************************************ --- CREATE VIEW variant_collection AS SELECT feature_id AS variant_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'variant_collection'; --- ************************************************ --- *** relation: alteration_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alteration_attribute AS SELECT feature_id AS alteration_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'alteration_attribute'; --- ************************************************ --- *** relation: chromosomal_variation_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_variation_attribute AS SELECT feature_id AS chromosomal_variation_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'chromosomal_variation_attribute'; --- ************************************************ --- *** relation: intrachromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal AS SELECT feature_id AS intrachromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal'; --- ************************************************ --- *** relation: interchromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal AS SELECT feature_id AS interchromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal'; --- ************************************************ --- *** relation: insertion_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a chromosomal insertion,. *** --- ************************************************ --- CREATE VIEW insertion_attribute AS SELECT feature_id AS insertion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'insertion_attribute'; --- ************************************************ --- *** relation: tandem *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tandem AS SELECT feature_id AS tandem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem'; --- ************************************************ --- *** relation: direct *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is not in a cytologically inverted or *** --- *** ientation. *** --- ************************************************ --- CREATE VIEW direct AS SELECT feature_id AS direct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct'; --- ************************************************ --- *** relation: inverted *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is in a cytologically inverted orient *** --- *** ation. *** --- ************************************************ --- CREATE VIEW inverted AS SELECT feature_id AS inverted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted'; --- ************************************************ --- *** relation: free *** --- *** relation type: VIEW *** --- *** *** --- *** The quality of a duplication where the n *** --- *** ew region exists independently of the or *** --- *** iginal. *** --- ************************************************ --- CREATE VIEW free AS SELECT feature_id AS free_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free'; --- ************************************************ --- *** relation: inversion_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inversion_attribute AS SELECT feature_id AS inversion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'inversion_attribute'; --- ************************************************ --- *** relation: pericentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pericentric AS SELECT feature_id AS pericentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric'; --- ************************************************ --- *** relation: paracentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paracentric AS SELECT feature_id AS paracentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric'; --- ************************************************ --- *** relation: translocaton_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW translocaton_attribute AS SELECT feature_id AS translocaton_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'translocaton_attribute'; --- ************************************************ --- *** relation: reciprocal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW reciprocal AS SELECT feature_id AS reciprocal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal'; --- ************************************************ --- *** relation: insertional *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW insertional AS SELECT feature_id AS insertional_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertional'; --- ************************************************ --- *** relation: duplication_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW duplication_attribute AS SELECT feature_id AS duplication_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free' OR cvterm.name = 'duplication_attribute'; --- ************************************************ --- *** relation: chromosomally_aberrant_genome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomally_aberrant_genome AS SELECT feature_id AS chromosomally_aberrant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome'; --- ************************************************ --- *** relation: assembly_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment differs from the orig *** --- *** inal assembly due to an improvement that *** --- *** replaces a mistake. *** --- ************************************************ --- CREATE VIEW assembly_error_correction AS SELECT feature_id AS assembly_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assembly_error_correction'; --- ************************************************ --- *** relation: base_call_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment is different from tha *** --- *** t given by the base caller due to an imp *** --- *** rovement that replaces a mistake. *** --- ************************************************ --- CREATE VIEW base_call_error_correction AS SELECT feature_id AS base_call_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'base_call_error_correction'; --- ************************************************ --- *** relation: peptide_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide sequence used to tar *** --- *** get the polypeptide molecule to a specif *** --- *** ic organelle. *** --- ************************************************ --- CREATE VIEW peptide_localization_signal AS SELECT feature_id AS peptide_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'peptide_localization_signal'; --- ************************************************ --- *** relation: nuclear_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_localization_signal AS SELECT feature_id AS nuclear_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_localization_signal'; --- ************************************************ --- *** relation: endosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the endosome. *** --- ************************************************ --- CREATE VIEW endosomal_localization_signal AS SELECT feature_id AS endosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endosomal_localization_signal'; --- ************************************************ --- *** relation: lysosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the lysosome. *** --- ************************************************ --- CREATE VIEW lysosomal_localization_signal AS SELECT feature_id AS lysosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysosomal_localization_signal'; --- ************************************************ --- *** relation: nuclear_export_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to he cytoplasm. *** --- ************************************************ --- CREATE VIEW nuclear_export_signal AS SELECT feature_id AS nuclear_export_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_export_signal'; --- ************************************************ --- *** relation: recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region recognized by a recombinase. *** --- ************************************************ --- CREATE VIEW recombination_signal_sequence AS SELECT feature_id AS recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_signal_sequence'; --- ************************************************ --- *** relation: cryptic_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A splice site that is in part of the tra *** --- *** nscript not normally spliced. They occur *** --- *** via mutation or transcriptional error. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site AS SELECT feature_id AS cryptic_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site'; --- ************************************************ --- *** relation: nuclear_rim_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nuclear rim. *** --- ************************************************ --- CREATE VIEW nuclear_rim_localization_signal AS SELECT feature_id AS nuclear_rim_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_rim_localization_signal'; --- ************************************************ --- *** relation: p_element *** --- *** relation type: VIEW *** --- *** *** --- *** A P_element is a DNA transposon responsi *** --- *** ble for hybrid dysgenesis. *** --- ************************************************ --- CREATE VIEW p_element AS SELECT feature_id AS p_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'p_element'; --- ************************************************ --- *** relation: functional_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which the function *** --- *** of a gene product is altered with respe *** --- *** ct to a reference. *** --- ************************************************ --- CREATE VIEW functional_variant AS SELECT feature_id AS functional_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'functional_variant'; --- ************************************************ --- *** relation: structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes one or m *** --- *** ore sequence features. *** --- ************************************************ --- CREATE VIEW structural_variant AS SELECT feature_id AS structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'structural_variant'; --- ************************************************ --- *** relation: transcript_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the func *** --- *** tioning of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcript_function_variant AS SELECT feature_id AS transcript_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcript_function_variant'; --- ************************************************ --- *** relation: translational_product_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the func *** --- *** tioning of a translational product with *** --- *** respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_function_variant AS SELECT feature_id AS translational_product_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'translational_product_function_variant'; --- ************************************************ --- *** relation: level_of_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the leve *** --- *** l of a transcript. *** --- ************************************************ --- CREATE VIEW level_of_transcript_variant AS SELECT feature_id AS level_of_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'level_of_transcript_variant'; --- ************************************************ --- *** relation: decreased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_level_variant AS SELECT feature_id AS decreased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant'; --- ************************************************ --- *** relation: increased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_level_variant AS SELECT feature_id AS increased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_level_variant'; --- ************************************************ --- *** relation: transcript_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the post *** --- *** transcriptional processing of a transcr *** --- *** ipt with respect to a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW transcript_processing_variant AS SELECT feature_id AS transcript_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'transcript_processing_variant'; --- ************************************************ --- *** relation: editing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** the process of editing is disrupted with *** --- *** respect to the reference. *** --- ************************************************ --- CREATE VIEW editing_variant AS SELECT feature_id AS editing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant'; --- ************************************************ --- *** relation: polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes polyaden *** --- *** ylation with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polyadenylation_variant AS SELECT feature_id AS polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'polyadenylation_variant'; --- ************************************************ --- *** relation: transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes the stability of *** --- *** a transcript with respect to a reference *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW transcript_stability_variant AS SELECT feature_id AS transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'transcript_stability_variant'; --- ************************************************ --- *** relation: decreased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_stability_variant AS SELECT feature_id AS decreased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant'; --- ************************************************ --- *** relation: increased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_stability_variant AS SELECT feature_id AS increased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_stability_variant'; --- ************************************************ --- *** relation: transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes alters the transc *** --- *** ription of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcription_variant AS SELECT feature_id AS transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcription_variant'; --- ************************************************ --- *** relation: rate_of_transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the rate *** --- *** of transcription with respect to a refe *** --- *** rence sequence. *** --- ************************************************ --- CREATE VIEW rate_of_transcription_variant AS SELECT feature_id AS rate_of_transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'rate_of_transcription_variant'; --- ************************************************ --- *** relation: increased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcription_rate_variant AS SELECT feature_id AS increased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant'; --- ************************************************ --- *** relation: decreased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcription_rate_variant AS SELECT feature_id AS decreased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcription_rate_variant'; --- ************************************************ --- *** relation: translational_product_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A functional variant that changes the tr *** --- *** anslational product level with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_level_variant AS SELECT feature_id AS translational_product_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'translational_product_level_variant'; --- ************************************************ --- *** relation: polypeptide_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes polypep *** --- *** tide functioning with respect to a refer *** --- *** ence sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_function_variant AS SELECT feature_id AS polypeptide_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_function_variant'; --- ************************************************ --- *** relation: decreased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which decreases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_translational_product_level AS SELECT feature_id AS decreased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level'; --- ************************************************ --- *** relation: increased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which increases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_translational_product_level AS SELECT feature_id AS increased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_translational_product_level'; --- ************************************************ --- *** relation: polypeptide_gain_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes gain of *** --- *** polypeptide function with respect to a r *** --- *** eference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_gain_of_function_variant AS SELECT feature_id AS polypeptide_gain_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant'; --- ************************************************ --- *** relation: polypeptide_localization_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes the loc *** --- *** alization of a polypeptide with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_localization_variant AS SELECT feature_id AS polypeptide_localization_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_localization_variant'; --- ************************************************ --- *** relation: polypeptide_loss_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the loss *** --- *** of a polypeptide function with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_loss_of_function_variant AS SELECT feature_id AS polypeptide_loss_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_loss_of_function_variant'; --- ************************************************ --- *** relation: inactive_ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a ligand binding site with re *** --- *** spect to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_ligand_binding_site AS SELECT feature_id AS inactive_ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'inactive_ligand_binding_site'; --- ************************************************ --- *** relation: polypeptide_partial_loss_of_function *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes some but *** --- *** not all loss of polypeptide function wit *** --- *** h respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_partial_loss_of_function AS SELECT feature_id AS polypeptide_partial_loss_of_function_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_partial_loss_of_function'; --- ************************************************ --- *** relation: polypeptide_post_translational_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** in post translational processing of the *** --- *** peptide with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polypeptide_post_translational_processing_variant AS SELECT feature_id AS polypeptide_post_translational_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_post_translational_processing_variant'; --- ************************************************ --- *** relation: copy_number_change *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where copies of a fea *** --- *** ture (CNV) are either increased or decre *** --- *** ased. *** --- ************************************************ --- CREATE VIEW copy_number_change AS SELECT feature_id AS copy_number_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_change'; --- ************************************************ --- *** relation: gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where the structure o *** --- *** f the gene is changed. *** --- ************************************************ --- CREATE VIEW gene_variant AS SELECT feature_id AS gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'gene_variant'; --- ************************************************ --- *** relation: gene_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a two genes h *** --- *** ave become joined. *** --- ************************************************ --- CREATE VIEW gene_fusion AS SELECT feature_id AS gene_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion'; --- ************************************************ --- *** relation: regulatory_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a regu *** --- *** latory region. *** --- ************************************************ --- CREATE VIEW regulatory_region_variant AS SELECT feature_id AS regulatory_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant' OR cvterm.name = 'regulatory_region_variant'; --- ************************************************ --- *** relation: stop_retained_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se in the terminator codon is changed, b *** --- *** ut the terminator remains. *** --- ************************************************ --- CREATE VIEW stop_retained_variant AS SELECT feature_id AS stop_retained_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant'; --- ************************************************ --- *** relation: splicing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the proc *** --- *** ess of splicing. *** --- ************************************************ --- CREATE VIEW splicing_variant AS SELECT feature_id AS splicing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'splicing_variant'; --- ************************************************ --- *** relation: cryptic_splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a new (functi *** --- *** onal) splice site. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site_variant AS SELECT feature_id AS cryptic_splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'cryptic_splice_site_variant'; --- ************************************************ --- *** relation: cryptic_splice_acceptor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new acceptor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_acceptor AS SELECT feature_id AS cryptic_splice_acceptor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor'; --- ************************************************ --- *** relation: cryptic_splice_donor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new donor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_donor AS SELECT feature_id AS cryptic_splice_donor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_donor'; --- ************************************************ --- *** relation: exon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an exon is lo *** --- *** st from the transcript. *** --- ************************************************ --- CREATE VIEW exon_loss AS SELECT feature_id AS exon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_loss'; --- ************************************************ --- *** relation: intron_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an intron is *** --- *** gained by the processed transcript; usua *** --- *** lly a result of an alteration of the don *** --- *** or or acceptor. *** --- ************************************************ --- CREATE VIEW intron_gain AS SELECT feature_id AS intron_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intron_gain'; --- ************************************************ --- *** relation: splice_acceptor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the 2 base *** --- *** region at the 3' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_acceptor_variant AS SELECT feature_id AS splice_acceptor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant'; --- ************************************************ --- *** relation: splice_donor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the2 base *** --- *** region at the 5' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_donor_variant AS SELECT feature_id AS splice_donor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_variant'; --- ************************************************ --- *** relation: transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the stru *** --- *** cture of the transcript. *** --- ************************************************ --- CREATE VIEW transcript_variant AS SELECT feature_id AS transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'transcript_variant'; --- ************************************************ --- *** relation: complex_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant with a complex INDE *** --- *** L- Insertion or deletion that spans an e *** --- *** xon/intron border or a coding sequence/U *** --- *** TR border. *** --- ************************************************ --- CREATE VIEW complex_change_in_transcript AS SELECT feature_id AS complex_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript'; --- ************************************************ --- *** relation: stop_lost *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the terminator codon (stop) is cha *** --- *** nged, resulting in an elongated transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW stop_lost AS SELECT feature_id AS stop_lost_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_lost'; --- ************************************************ --- *** relation: coding_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the codi *** --- *** ng sequence. *** --- ************************************************ --- CREATE VIEW coding_sequence_variant AS SELECT feature_id AS coding_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'coding_sequence_variant'; --- ************************************************ --- *** relation: codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes at least *** --- *** one base in a codon. *** --- ************************************************ --- CREATE VIEW codon_variant AS SELECT feature_id AS codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'codon_variant'; --- ************************************************ --- *** relation: initiator_codon_change *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the first codon of a transcrip *** --- *** t. *** --- ************************************************ --- CREATE VIEW initiator_codon_change AS SELECT feature_id AS initiator_codon_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change'; --- ************************************************ --- *** relation: non_synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid or stop codon. *** --- ************************************************ --- CREATE VIEW non_synonymous_codon AS SELECT feature_id AS non_synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'non_synonymous_codon'; --- ************************************************ --- *** relation: conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different but *** --- *** similar amino acid. These variants may *** --- *** or may not be deleterious. *** --- ************************************************ --- CREATE VIEW conservative_missense_codon AS SELECT feature_id AS conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon'; --- ************************************************ --- *** relation: non_conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for an amino acid w *** --- *** ith different biochemical properties. *** --- ************************************************ --- CREATE VIEW non_conservative_missense_codon AS SELECT feature_id AS non_conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_missense_codon'; --- ************************************************ --- *** relation: stop_gained *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed, resulting in *** --- *** a premature stop codon, leading to a sh *** --- *** ortened transcript. *** --- ************************************************ --- CREATE VIEW stop_gained AS SELECT feature_id AS stop_gained_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained'; --- ************************************************ --- *** relation: synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a base of a c *** --- *** odon is changed, but there is no resulti *** --- *** ng change to the encoded amino acid. *** --- ************************************************ --- CREATE VIEW synonymous_codon AS SELECT feature_id AS synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'synonymous_codon'; --- ************************************************ --- *** relation: frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** because the number of nucleotides inser *** --- *** ted or deleted is not a multiple of thre *** --- *** e. *** --- ************************************************ --- CREATE VIEW frameshift_variant AS SELECT feature_id AS frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'frameshift_variant'; --- ************************************************ --- *** relation: terminator_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** of the bases in the terminator codon is *** --- *** changed. *** --- ************************************************ --- CREATE VIEW terminator_codon_variant AS SELECT feature_id AS terminator_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminator_codon_variant'; --- ************************************************ --- *** relation: frame_restoring_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that reverts the sequ *** --- *** ence of a previous frameshift mutation b *** --- *** ack to the initial frame. *** --- ************************************************ --- CREATE VIEW frame_restoring_variant AS SELECT feature_id AS frame_restoring_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant'; --- ************************************************ --- *** relation: minus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base ahead. *** --- ************************************************ --- CREATE VIEW minus_1_frameshift_variant AS SELECT feature_id AS minus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift_variant'; --- ************************************************ --- *** relation: minus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minus_2_frameshift_variant AS SELECT feature_id AS minus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift_variant'; --- ************************************************ --- *** relation: plus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base backward. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift_variant AS SELECT feature_id AS plus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift_variant'; --- ************************************************ --- *** relation: plus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plus_2_frameshift_variant AS SELECT feature_id AS plus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_frameshift variant'; --- ************************************************ --- *** relation: transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a transcript t *** --- *** hat changes the secondary structure of t *** --- *** he RNA product. *** --- ************************************************ --- CREATE VIEW transcript_secondary_structure_variant AS SELECT feature_id AS transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: compensatory_transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A secondary structure variant that compe *** --- *** nsate for the change made by a previous *** --- *** variant. *** --- ************************************************ --- CREATE VIEW compensatory_transcript_secondary_structure_variant AS SELECT feature_id AS compensatory_transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: translational_product_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within the transcript *** --- *** that changes the structure of the trans *** --- *** lational product. *** --- ************************************************ --- CREATE VIEW translational_product_structure_variant AS SELECT feature_id AS translational_product_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'translational_product_structure_variant'; --- ************************************************ --- *** relation: threed_polypeptide_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW threed_polypeptide_structure_variant AS SELECT feature_id AS threed_polypeptide_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = '3D_polypeptide_structure_variant'; --- ************************************************ --- *** relation: complex_3d_structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW complex_3d_structural_variant AS SELECT feature_id AS complex_3d_structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant'; --- ************************************************ --- *** relation: conformational_change_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in the CDS region tha *** --- *** t causes a conformational change in the *** --- *** resulting polypeptide sequence. *** --- ************************************************ --- CREATE VIEW conformational_change_variant AS SELECT feature_id AS conformational_change_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_change_variant'; --- ************************************************ --- *** relation: complex_change_of_translational_product_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW complex_change_of_translational_product_variant AS SELECT feature_id AS complex_change_of_translational_product_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_of_translational_product_variant'; --- ************************************************ --- *** relation: polypeptide_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes a change in the resulting polypep *** --- *** tide sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_sequence_variant AS SELECT feature_id AS polypeptide_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'polypeptide_sequence_variant'; --- ************************************************ --- *** relation: amino_acid_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the loss of an amino acid from the *** --- *** resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_deletion AS SELECT feature_id AS amino_acid_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion'; --- ************************************************ --- *** relation: amino_acid_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the gain of an amino acid to the re *** --- *** sulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_insertion AS SELECT feature_id AS amino_acid_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_insertion'; --- ************************************************ --- *** relation: amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon resulting *** --- *** in the substitution of one amino acid fo *** --- *** r another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_substitution AS SELECT feature_id AS amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'amino_acid_substitution'; --- ************************************************ --- *** relation: conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a similar amino acid f *** --- *** or another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW conservative_amino_acid_substitution AS SELECT feature_id AS conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: non_conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a non conservative ami *** --- *** no acid for another in the resulting pol *** --- *** ypeptide. *** --- ************************************************ --- CREATE VIEW non_conservative_amino_acid_substitution AS SELECT feature_id AS non_conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: elongated_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide AS SELECT feature_id AS elongated_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide'; --- ************************************************ --- *** relation: elongated_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the C terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_c_terminal AS SELECT feature_id AS elongated_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the N terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_n_terminal AS SELECT feature_id AS elongated_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the C termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_in_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the C te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the N termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_n_terminal_elongation AS SELECT feature_id AS elongated_in_frame_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the N te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_n_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal'; --- ************************************************ --- *** relation: polypeptide_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a fusion *** --- *** of two polypeptide sequences. *** --- ************************************************ --- CREATE VIEW polypeptide_fusion AS SELECT feature_id AS polypeptide_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_fusion'; --- ************************************************ --- *** relation: polypeptide_truncation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of the CD that causes *** --- *** a truncation of the resulting polypepti *** --- *** de. *** --- ************************************************ --- CREATE VIEW polypeptide_truncation AS SELECT feature_id AS polypeptide_truncation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_truncation'; --- ************************************************ --- *** relation: inactive_catalytic_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a catalytic site with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_catalytic_site AS SELECT feature_id AS inactive_catalytic_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site'; --- ************************************************ --- *** relation: nc_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant of a non coding RNA *** --- *** gene. *** --- ************************************************ --- CREATE VIEW nc_transcript_variant AS SELECT feature_id AS nc_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant' OR cvterm.name = 'nc_transcript_variant'; --- ************************************************ --- *** relation: mature_mirna_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant located with the se *** --- *** quence of the mature miRNA. *** --- ************************************************ --- CREATE VIEW mature_mirna_variant AS SELECT feature_id AS mature_mirna_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant'; --- ************************************************ --- *** relation: nmd_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant in a transcript that is the ta *** --- *** rget of NMD. *** --- ************************************************ --- CREATE VIEW nmd_transcript_variant AS SELECT feature_id AS nmd_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NMD_transcript_variant'; --- ************************************************ --- *** relation: utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant that is located wit *** --- *** hin the UTR. *** --- ************************************************ --- CREATE VIEW utr_variant AS SELECT feature_id AS utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'UTR_variant'; --- ************************************************ --- *** relation: five_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_variant AS SELECT feature_id AS five_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant'; --- ************************************************ --- *** relation: three_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_variant AS SELECT feature_id AS three_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3_prime_UTR_variant'; --- ************************************************ --- *** relation: terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the last codon of the transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW terminal_codon_variant AS SELECT feature_id AS terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminal_codon_variant'; --- ************************************************ --- *** relation: incomplete_terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the final codon of an incompletely *** --- *** annotated transcript is changed. *** --- ************************************************ --- CREATE VIEW incomplete_terminal_codon_variant AS SELECT feature_id AS incomplete_terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'incomplete_terminal_codon_variant'; --- ************************************************ --- *** relation: intron_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant occurring within an *** --- *** intron. *** --- ************************************************ --- CREATE VIEW intron_variant AS SELECT feature_id AS intron_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'intron_variant'; --- ************************************************ --- *** relation: intergenic_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located in the interg *** --- *** enic region, between genes. *** --- ************************************************ --- CREATE VIEW intergenic_variant AS SELECT feature_id AS intergenic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_variant'; --- ************************************************ --- *** relation: splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the firs *** --- *** t two or last two bases of an intron, or *** --- *** the 5th base from the start of the intr *** --- *** on in the orientation of the transcript. *** --- ************************************************ --- CREATE VIEW splice_site_variant AS SELECT feature_id AS splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'splice_site_variant'; --- ************************************************ --- *** relation: splice_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which a change has *** --- *** occurred within the region of the splic *** --- *** e site, either within 1-3 bases of the e *** --- *** xon or 3-8 bases of the intron. *** --- ************************************************ --- CREATE VIEW splice_region_variant AS SELECT feature_id AS splice_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_region_variant'; --- ************************************************ --- *** relation: upstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 5' of a gene. *** --- ************************************************ --- CREATE VIEW upstream_gene_variant AS SELECT feature_id AS upstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = 'upstream_gene_variant'; --- ************************************************ --- *** relation: downstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 3' of a gene. *** --- ************************************************ --- CREATE VIEW downstream_gene_variant AS SELECT feature_id AS downstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'downstream_gene_variant'; --- ************************************************ --- *** relation: fivekb_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5 KB o *** --- *** f the end of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_downstream_variant AS SELECT feature_id AS fivekb_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant' OR cvterm.name = '5KB_downstream_variant'; --- ************************************************ --- *** relation: fivehundred_b_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a half *** --- *** KB of the end of a gene. *** --- ************************************************ --- CREATE VIEW fivehundred_b_downstream_variant AS SELECT feature_id AS fivehundred_b_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant'; --- ************************************************ --- *** relation: fivekb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_upstream_variant AS SELECT feature_id AS fivekb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_upstream_variant'; --- ************************************************ --- *** relation: twokb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 2KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW twokb_upstream_variant AS SELECT feature_id AS twokb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant'; --- ************************************************ --- *** relation: rrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for ribosomal RNA. *** --- ************************************************ --- CREATE VIEW rrna_gene AS SELECT feature_id AS rrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_gene'; --- ************************************************ --- *** relation: pirna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for an piwi associat *** --- *** ed RNA. *** --- ************************************************ --- CREATE VIEW pirna_gene AS SELECT feature_id AS pirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA_gene'; --- ************************************************ --- *** relation: rnase_p_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an RNase P RNA. *** --- ************************************************ --- CREATE VIEW rnase_p_rna_gene AS SELECT feature_id AS rnase_p_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA_gene'; --- ************************************************ --- *** relation: rnase_mrp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a RNase_MRP_RNA. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna_gene AS SELECT feature_id AS rnase_mrp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA_gene'; --- ************************************************ --- *** relation: lincrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes large intervening no *** --- *** n-coding RNA. *** --- ************************************************ --- CREATE VIEW lincrna_gene AS SELECT feature_id AS lincrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA_gene'; --- ************************************************ --- *** relation: mathematically_defined_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A mathematically defined repeat (MDR) is *** --- *** a experimental feature that is determin *** --- *** ed by querying overlapping oligomers of *** --- *** length k against a database of shotgun s *** --- *** equence data and identifying regions in *** --- *** the query sequence that exceed a statist *** --- *** ically determined threshold of repetitiv *** --- *** eness. *** --- ************************************************ --- CREATE VIEW mathematically_defined_repeat AS SELECT feature_id AS mathematically_defined_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mathematically_defined_repeat'; --- ************************************************ --- *** relation: telomerase_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A telomerase RNA gene is a non coding RN *** --- *** A gene the RNA product of which is a com *** --- *** ponent of telomerase. *** --- ************************************************ --- CREATE VIEW telomerase_rna_gene AS SELECT feature_id AS telomerase_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA_gene'; --- ************************************************ --- *** relation: targeting_vector *** --- *** relation type: VIEW *** --- *** *** --- *** An engineered vector that is able to tak *** --- *** e part in homologous recombination in a *** --- *** host with the intent of introducing site *** --- *** specific genomic modifications. *** --- ************************************************ --- CREATE VIEW targeting_vector AS SELECT feature_id AS targeting_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'targeting_vector'; --- ************************************************ --- *** relation: genetic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A measurable sequence feature that varie *** --- *** s within a population. *** --- ************************************************ --- CREATE VIEW genetic_marker AS SELECT feature_id AS genetic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'genetic_marker'; --- ************************************************ --- *** relation: dart_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A genetic marker, discovered using Diver *** --- *** sity Arrays Technology (DArT) technology *** --- *** . *** --- ************************************************ --- CREATE VIEW dart_marker AS SELECT feature_id AS dart_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DArT_marker'; --- ************************************************ --- *** relation: kozak_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of ribosome entry site, specific *** --- *** to Eukaryotic organisms that overlaps pa *** --- *** rt of both 5' UTR and CDS sequence. *** --- ************************************************ --- CREATE VIEW kozak_sequence AS SELECT feature_id AS kozak_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kozak_sequence'; --- ************************************************ --- *** relation: nested_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that is disrupted by the in *** --- *** sertion of another element. *** --- ************************************************ --- CREATE VIEW nested_transposon AS SELECT feature_id AS nested_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_transposon'; --- ************************************************ --- *** relation: nested_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is disrupted by the insert *** --- *** ion of another element. *** --- ************************************************ --- CREATE VIEW nested_repeat AS SELECT feature_id AS nested_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'nested_repeat'; --- ************************************************ --- *** relation: inframe_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which does not cause *** --- *** a disruption of the translational readin *** --- *** g frame. *** --- ************************************************ --- CREATE VIEW inframe_variant AS SELECT feature_id AS inframe_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'inframe_variant'; --- ************************************************ --- *** relation: inframe_codon_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which gains a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_gain AS SELECT feature_id AS inframe_codon_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain'; --- ************************************************ --- *** relation: inframe_codon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which loses a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_loss AS SELECT feature_id AS inframe_codon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_loss'; --- ************************************************ --- *** relation: retinoic_acid_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transcription factor binding site of v *** --- *** ariable direct repeats of the sequence P *** --- *** uGGTCA spaced by five nucleotides (DR5) *** --- *** found in the promoters of retinoic acid- *** --- *** responsive genes, to which retinoic acid *** --- *** receptors bind. *** --- ************************************************ --- CREATE VIEW retinoic_acid_responsive_element AS SELECT feature_id AS retinoic_acid_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retinoic_acid_responsive_element'; --- ************************************************ --- *** relation: nucleotide_to_protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_to_protein_binding_site AS SELECT feature_id AS nucleotide_to_protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nucleotide_to_protein_binding_site'; --- ************************************************ --- *** relation: nucleotide_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith nucleotide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_binding_site AS SELECT feature_id AS nucleotide_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nucleotide_binding_site'; --- ************************************************ --- *** relation: metal_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith metal ions. *** --- ************************************************ --- CREATE VIEW metal_binding_site AS SELECT feature_id AS metal_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'metal_binding_site'; --- ************************************************ --- *** relation: ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith a small molecule such as a drug, or *** --- *** hormone. *** --- ************************************************ --- CREATE VIEW ligand_binding_site AS SELECT feature_id AS ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'ligand_binding_site'; --- ************************************************ --- *** relation: nested_tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An NTR is a nested repeat of two distinc *** --- *** t tandem motifs interspersed with each o *** --- *** ther. *** --- ************************************************ --- CREATE VIEW nested_tandem_repeat AS SELECT feature_id AS nested_tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat'; --- ************************************************ --- *** relation: promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW promoter_element AS SELECT feature_id AS promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'promoter_element'; --- ************************************************ --- *** relation: core_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW core_promoter_element AS SELECT feature_id AS core_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'core_promoter_element'; --- ************************************************ --- *** relation: rna_polymerase_ii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW rna_polymerase_ii_tata_box AS SELECT feature_id AS rna_polymerase_ii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box'; --- ************************************************ --- *** relation: rna_polymerase_iii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase III. *** --- ************************************************ --- CREATE VIEW rna_polymerase_iii_tata_box AS SELECT feature_id AS rna_polymerase_iii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_III_TATA_box'; --- ************************************************ --- *** relation: bred_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A core TRNA polymerase II promoter eleme *** --- *** nt with consensus (G/A)T(T/G/A)(T/A)(G/T *** --- *** )(T/G)(T/G). *** --- ************************************************ --- CREATE VIEW bred_motif AS SELECT feature_id AS bred_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREd_motif'; --- ************************************************ --- *** relation: dce *** --- *** relation type: VIEW *** --- *** *** --- *** A discontinuous core element of RNA poly *** --- *** merase II transcribed genes, situated do *** --- *** wnstream of the TSS. It is composed of t *** --- *** hree sub elements: SI, SII and SIII. *** --- ************************************************ --- CREATE VIEW dce AS SELECT feature_id AS dce_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE'; --- ************************************************ --- *** relation: dce_si *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement, with consensus sequence CTTC. *** --- ************************************************ --- CREATE VIEW dce_si AS SELECT feature_id AS dce_si_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SI'; --- ************************************************ --- *** relation: dce_sii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence CTGT. *** --- ************************************************ --- CREATE VIEW dce_sii AS SELECT feature_id AS dce_sii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SII'; --- ************************************************ --- *** relation: dce_siii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence AGC. *** --- ************************************************ --- CREATE VIEW dce_siii AS SELECT feature_id AS dce_siii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SIII'; --- ************************************************ --- *** relation: proximal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proximal_promoter_element AS SELECT feature_id AS proximal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element'; --- ************************************************ --- *** relation: rnapol_ii_core_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** The minimal portion of the promoter requ *** --- *** ired to properly initiate transcription *** --- *** in RNA polymerase II transcribed genes. *** --- ************************************************ --- CREATE VIEW rnapol_ii_core_promoter AS SELECT feature_id AS rnapol_ii_core_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter'; --- ************************************************ --- *** relation: distal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW distal_promoter_element AS SELECT feature_id AS distal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distal_promoter_element'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma_70 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma_70 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma_70_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma54 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma54 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma54_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma54'; --- ************************************************ --- *** relation: minus_12_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_12_signal AS SELECT feature_id AS minus_12_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_12_signal'; --- ************************************************ --- *** relation: minus_24_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_24_signal AS SELECT feature_id AS minus_24_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_24_signal'; --- ************************************************ --- *** relation: a_box_type_1 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 1 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_1 AS SELECT feature_id AS a_box_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1'; --- ************************************************ --- *** relation: a_box_type_2 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 2 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_2 AS SELECT feature_id AS a_box_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_2'; --- ************************************************ --- *** relation: intermediate_element *** --- *** relation type: VIEW *** --- *** *** --- *** A core promoter region of RNA polymerase *** --- *** III type 1 promoters. *** --- ************************************************ --- CREATE VIEW intermediate_element AS SELECT feature_id AS intermediate_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate_element'; --- ************************************************ --- *** relation: regulatory_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter element that is not part of t *** --- *** he core promoter, but provides the promo *** --- *** ter with a specific regulatory region. *** --- ************************************************ --- CREATE VIEW regulatory_promoter_element AS SELECT feature_id AS regulatory_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'regulatory_promoter_element'; --- ************************************************ --- *** relation: transcription_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of transcript *** --- *** ion. *** --- ************************************************ --- CREATE VIEW transcription_regulatory_region AS SELECT feature_id AS transcription_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'transcription_regulatory_region'; --- ************************************************ --- *** relation: translation_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of translatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW translation_regulatory_region AS SELECT feature_id AS translation_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator' OR cvterm.name = 'translation_regulatory_region'; --- ************************************************ --- *** relation: recombination_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of recombinat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW recombination_regulatory_region AS SELECT feature_id AS recombination_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_regulatory_region'; --- ************************************************ --- *** relation: replication_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of nucleotide *** --- *** replication. *** --- ************************************************ --- CREATE VIEW replication_regulatory_region AS SELECT feature_id AS replication_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'replication_regulatory_region'; --- ************************************************ --- *** relation: sequence_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a nucleotide or amin *** --- *** o-acid sequence pattern that may have bi *** --- *** ological significance. *** --- ************************************************ --- CREATE VIEW sequence_motif AS SELECT feature_id AS sequence_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'sequence_motif'; --- ************************************************ --- *** relation: experimental_feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of an experimentally derive *** --- *** d feature. *** --- ************************************************ --- CREATE VIEW experimental_feature_attribute AS SELECT feature_id AS experimental_feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'experimental_feature_attribute'; --- ************************************************ --- *** relation: score *** --- *** relation type: VIEW *** --- *** *** --- *** The score of an experimentally derived f *** --- *** eature such as a p-value. *** --- ************************************************ --- CREATE VIEW score AS SELECT feature_id AS score_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score'; --- ************************************************ --- *** relation: quality_value *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature attribute that d *** --- *** efines the quality of the feature in a q *** --- *** uantitative way, such as a phred quality *** --- *** score. *** --- ************************************************ --- CREATE VIEW quality_value AS SELECT feature_id AS quality_value_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quality_value'; --- ************************************************ --- *** relation: restriction_enzyme_recognition_site *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide region (usually a palindr *** --- *** ome) that is recognized by a restriction *** --- *** enzyme. This may or may not be equal to *** --- *** the restriction enzyme binding site. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_recognition_site AS SELECT feature_id AS restriction_enzyme_recognition_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'restriction_enzyme_recognition_site'; --- ************************************************ --- *** relation: restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary at which a restriction enzy *** --- *** me breaks the nucleotide sequence. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_cleavage_junction AS SELECT feature_id AS restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: five_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The restriction enzyme cleavage junction *** --- *** on the 5' strand of the nucleotide sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW five_prime_restriction_enzyme_junction AS SELECT feature_id AS five_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: three_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_restriction_enzyme_junction AS SELECT feature_id AS three_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: sticky_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sticky_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS sticky_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** both strands are cut at the same positi *** --- *** on. *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_junction AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: single_strand_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** by only one strand is cut. *** --- ************************************************ --- CREATE VIEW single_strand_restriction_enzyme_cleavage_site AS SELECT feature_id AS single_strand_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: restriction_enzyme_single_strand_overhang *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal region of DNA sequence where *** --- *** the end of the region is not blunt ended *** --- *** . *** --- ************************************************ --- CREATE VIEW restriction_enzyme_single_strand_overhang AS SELECT feature_id AS restriction_enzyme_single_strand_overhang_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_single_strand_overhang'; --- ************************************************ --- *** relation: experimentally_defined_binding_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that has been implicated in bin *** --- *** ding although the exact coordinates of b *** --- *** inding may be unknown. *** --- ************************************************ --- CREATE VIEW experimentally_defined_binding_region AS SELECT feature_id AS experimentally_defined_binding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimentally_defined_binding_region'; --- ************************************************ --- *** relation: chip_seq_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence identified by CHiP *** --- *** seq technology to contain a protein bind *** --- *** ing site. *** --- ************************************************ --- CREATE VIEW chip_seq_region AS SELECT feature_id AS chip_seq_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region'; --- ************************************************ --- *** relation: aspe_primer *** --- *** relation type: VIEW *** --- *** *** --- *** "A primer containing an SNV at the 3' en *** --- *** d for accurate genotyping. *** --- ************************************************ --- CREATE VIEW aspe_primer AS SELECT feature_id AS aspe_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ASPE_primer'; --- ************************************************ --- *** relation: dcaps_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A primer with one or more mis-matches to *** --- *** the DNA template corresponding to a pos *** --- *** ition within a restriction enzyme recogn *** --- *** ition site. *** --- ************************************************ --- CREATE VIEW dcaps_primer AS SELECT feature_id AS dcaps_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dCAPS_primer'; --- ************************************************ --- *** relation: histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** Histone modification is a post translati *** --- *** onally modified region whereby residues *** --- *** of the histone protein are modified by m *** --- *** ethylation, acetylation, phosphorylation *** --- *** , ubiquitination, sumoylation, citrullin *** --- *** ation, or ADP-ribosylation. *** --- ************************************************ --- CREATE VIEW histone_modification AS SELECT feature_id AS histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_modification'; --- ************************************************ --- *** relation: histone_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where the mo *** --- *** dification is the methylation of the res *** --- *** idue. *** --- ************************************************ --- CREATE VIEW histone_methylation_site AS SELECT feature_id AS histone_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'histone_methylation_site'; --- ************************************************ --- *** relation: histone_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification where the modific *** --- *** ation is the acylation of the residue. *** --- ************************************************ --- CREATE VIEW histone_acetylation_site AS SELECT feature_id AS histone_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'histone_acetylation_site'; --- ************************************************ --- *** relation: h3k9_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h3k9_acetylation_site AS SELECT feature_id AS h3k9_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site'; --- ************************************************ --- *** relation: h3k14_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k14_acetylation_site AS SELECT feature_id AS h3k14_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K14_acetylation_site'; --- ************************************************ --- *** relation: h3k4_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is mono-methylated. *** --- ************************************************ --- CREATE VIEW h3k4_monomethylation_site AS SELECT feature_id AS h3k4_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site'; --- ************************************************ --- *** relation: h3k4_trimethylation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 protein is tri-methyla *** --- *** ted. *** --- ************************************************ --- CREATE VIEW h3k4_trimethylation AS SELECT feature_id AS h3k4_trimethylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_trimethylation'; --- ************************************************ --- *** relation: h3k9_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is tri *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k9_trimethylation_site AS SELECT feature_id AS h3k9_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site'; --- ************************************************ --- *** relation: h3k27_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_monomethylation_site AS SELECT feature_id AS h3k27_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site'; --- ************************************************ --- *** relation: h3k27_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_trimethylation_site AS SELECT feature_id AS h3k27_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_trimethylation_site'; --- ************************************************ --- *** relation: h3k79_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no- methylated. *** --- ************************************************ --- CREATE VIEW h3k79_monomethylation_site AS SELECT feature_id AS h3k79_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site'; --- ************************************************ --- *** relation: h3k79_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k79_dimethylation_site AS SELECT feature_id AS h3k79_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_dimethylation_site'; --- ************************************************ --- *** relation: h3k79_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k79_trimethylation_site AS SELECT feature_id AS h3k79_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_trimethylation_site'; --- ************************************************ --- *** relation: h4k20_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 20th residue (a lysine), from t *** --- *** he start of the H34histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h4k20_monomethylation_site AS SELECT feature_id AS h4k20_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site'; --- ************************************************ --- *** relation: h2bk5_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H2B protein is methylated *** --- *** . *** --- ************************************************ --- CREATE VIEW h2bk5_monomethylation_site AS SELECT feature_id AS h2bk5_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2BK5_monomethylation_site'; --- ************************************************ --- *** relation: isre *** --- *** relation type: VIEW *** --- *** *** --- *** An ISRE is a transcriptional cis regulat *** --- *** ory region, containing the consensus reg *** --- *** ion: YAGTTTC(A/T)YTTTYCC, responsible fo *** --- *** r increased transcription via interferon *** --- *** binding. *** --- ************************************************ --- CREATE VIEW isre AS SELECT feature_id AS isre_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ISRE'; --- ************************************************ --- *** relation: histone_ubiqitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where ubiqui *** --- *** tin may be added. *** --- ************************************************ --- CREATE VIEW histone_ubiqitination_site AS SELECT feature_id AS histone_ubiqitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'histone_ubiqitination_site'; --- ************************************************ --- *** relation: h2b_ubiquitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site on H2B where *** --- *** ubiquitin may be added. *** --- ************************************************ --- CREATE VIEW h2b_ubiquitination_site AS SELECT feature_id AS h2b_ubiquitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site'; --- ************************************************ --- *** relation: h3k18_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k18_acetylation_site AS SELECT feature_id AS h3k18_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K18_acetylation_site'; --- ************************************************ --- *** relation: h3k23_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 23rd residue (a lysine), from the st *** --- *** art of the H3 histone protein is acylate *** --- *** d. *** --- ************************************************ --- CREATE VIEW h3k23_acylation_site AS SELECT feature_id AS h3k23_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K23_acylation site'; --- ************************************************ --- *** relation: epigenetically_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A biological region implicated in inheri *** --- *** ted changes caused by mechanisms other t *** --- *** han changes in the underlying DNA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_region AS SELECT feature_id AS epigenetically_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'epigenetically_modified_region'; --- ************************************************ --- *** relation: h3k27_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k27_acylation_site AS SELECT feature_id AS h3k27_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_acylation_site'; --- ************************************************ --- *** relation: h3k36_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_monomethylation_site AS SELECT feature_id AS h3k36_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site'; --- ************************************************ --- *** relation: h3k36_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k36_dimethylation_site AS SELECT feature_id AS h3k36_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_dimethylation_site'; --- ************************************************ --- *** relation: h3k36_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_trimethylation_site AS SELECT feature_id AS h3k36_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_trimethylation_site'; --- ************************************************ --- *** relation: h3k4_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 histone protein is di- *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k4_dimethylation_site AS SELECT feature_id AS h3k4_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_dimethylation_site'; --- ************************************************ --- *** relation: h3k27_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k27_dimethylation_site AS SELECT feature_id AS h3k27_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_dimethylation_site'; --- ************************************************ --- *** relation: h3k9_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is mon *** --- *** o-methylated. *** --- ************************************************ --- CREATE VIEW h3k9_monomethylation_site AS SELECT feature_id AS h3k9_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_monomethylation_site'; --- ************************************************ --- *** relation: h3k9_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein may be *** --- *** dimethylated. *** --- ************************************************ --- CREATE VIEW h3k9_dimethylation_site AS SELECT feature_id AS h3k9_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_dimethylation_site'; --- ************************************************ --- *** relation: h4k16_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 16th residue (a lysine), from t *** --- *** he start of the H4 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h4k16_acylation_site AS SELECT feature_id AS h4k16_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K16_acylation_site'; --- ************************************************ --- *** relation: h4k5_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k5_acylation_site AS SELECT feature_id AS h4k5_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K5_acylation_site'; --- ************************************************ --- *** relation: h4k8_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 8th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k8_acylation_site AS SELECT feature_id AS h4k8_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K8_acylation site'; --- ************************************************ --- *** relation: h3k27_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k27_methylation_site AS SELECT feature_id AS h3k27_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K27_methylation_site'; --- ************************************************ --- *** relation: h3k36_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k36_methylation_site AS SELECT feature_id AS h3k36_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K36_methylation_site'; --- ************************************************ --- *** relation: h3k4_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is methylated. *** --- ************************************************ --- CREATE VIEW h3k4_methylation_site AS SELECT feature_id AS h3k4_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K4_methylation_site'; --- ************************************************ --- *** relation: h3k79_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k79_methylation_site AS SELECT feature_id AS h3k79_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K79_methylation_site'; --- ************************************************ --- *** relation: h3k9_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is met *** --- *** hylated. *** --- ************************************************ --- CREATE VIEW h3k9_methylation_site AS SELECT feature_id AS h3k9_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_methylation_site'; --- ************************************************ --- *** relation: histone_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification, whereby the hist *** --- *** one protein is acylated at multiple site *** --- *** s in a region. *** --- ************************************************ --- CREATE VIEW histone_acylation_region AS SELECT feature_id AS histone_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_acylation_region'; --- ************************************************ --- *** relation: h4k_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the H4 histone whereby multi *** --- *** ple lysines are acylated. *** --- ************************************************ --- CREATE VIEW h4k_acylation_region AS SELECT feature_id AS h4k_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region'; --- ************************************************ --- *** relation: gene_with_non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a start codon other than AUG *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_non_canonical_start_codon AS SELECT feature_id AS gene_with_non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene_with_non_canonical_start_codon'; --- ************************************************ --- *** relation: gene_with_start_codon_cug *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a translational start codon *** --- *** of CUG. *** --- ************************************************ --- CREATE VIEW gene_with_start_codon_cug AS SELECT feature_id AS gene_with_start_codon_cug_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG'; --- ************************************************ --- *** relation: pseudogenic_gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene segment which when incorporated b *** --- *** y somatic recombination in the final gen *** --- *** e transcript results in a nonfunctional *** --- *** product. *** --- ************************************************ --- CREATE VIEW pseudogenic_gene_segment AS SELECT feature_id AS pseudogenic_gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment'; --- ************************************************ --- *** relation: copy_number_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given regions is greater than *** --- *** the reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_gain AS SELECT feature_id AS copy_number_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain'; --- ************************************************ --- *** relation: copy_number_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given region is less than the *** --- *** reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_loss AS SELECT feature_id AS copy_number_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_loss'; --- ************************************************ --- *** relation: upd *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from one parent and no copies of the *** --- *** same chromosome or region from the other *** --- *** parent. *** --- ************************************************ --- CREATE VIEW upd AS SELECT feature_id AS upd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'UPD'; --- ************************************************ --- *** relation: maternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the mother and no copies of the *** --- *** same chromosome or region from the fathe *** --- *** r. *** --- ************************************************ --- CREATE VIEW maternal_uniparental_disomy AS SELECT feature_id AS maternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy'; --- ************************************************ --- *** relation: paternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the father and no copies of the *** --- *** same chromosome or region from the mothe *** --- *** r. *** --- ************************************************ --- CREATE VIEW paternal_uniparental_disomy AS SELECT feature_id AS paternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_uniparental_disomy'; --- ************************************************ --- *** relation: open_chromatin_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that in the normal state *** --- *** of the chromosome corresponds to an unfo *** --- *** lded, un-complexed stretch of double-str *** --- *** anded DNA. *** --- ************************************************ --- CREATE VIEW open_chromatin_region AS SELECT feature_id AS open_chromatin_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'open_chromatin_region'; --- ************************************************ --- *** relation: sl3_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 3 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL3 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl3_acceptor_site AS SELECT feature_id AS sl3_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site'; --- ************************************************ --- *** relation: sl4_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 4 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL4 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl4_acceptor_site AS SELECT feature_id AS sl4_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL4_acceptor_site'; --- ************************************************ --- *** relation: sl5_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 5 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL5 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl5_acceptor_site AS SELECT feature_id AS sl5_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL5_acceptor_site'; --- ************************************************ --- *** relation: sl6_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 6 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL6 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl6_acceptor_site AS SELECT feature_id AS sl6_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL6_acceptor_site'; --- ************************************************ --- *** relation: sl7_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 7 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL7 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl7_acceptor_site AS SELECT feature_id AS sl7_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL7_acceptor_site'; --- ************************************************ --- *** relation: sl8_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 8 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL8 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl8_acceptor_site AS SELECT feature_id AS sl8_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL8_acceptor_site'; --- ************************************************ --- *** relation: sl9_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 9 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL9 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl9_acceptor_site AS SELECT feature_id AS sl9_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL9_acceptor_site'; --- ************************************************ --- *** relation: sl10_accceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 10 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL10 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl10_accceptor_site AS SELECT feature_id AS sl10_accceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL10_accceptor_site'; --- ************************************************ --- *** relation: sl11_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 11 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL11 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl11_acceptor_site AS SELECT feature_id AS sl11_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL11_acceptor_site'; --- ************************************************ --- *** relation: sl12_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 12 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL12 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl12_acceptor_site AS SELECT feature_id AS sl12_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL12_acceptor_site'; --- ************************************************ --- *** relation: duplicated_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose via gene duplica *** --- *** tion. Generally duplicated pseudogenes h *** --- *** ave the same structure as the original g *** --- *** ene, including intron-exon structure and *** --- *** some regulatory sequence. *** --- ************************************************ --- CREATE VIEW duplicated_pseudogene AS SELECT feature_id AS duplicated_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'duplicated_pseudogene'; --- ************************************************ --- *** relation: unitary_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene, deactivated from original *** --- *** state by mutation, fixed in a population *** --- *** . *** --- ************************************************ --- CREATE VIEW unitary_pseudogene AS SELECT feature_id AS unitary_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unitary_pseudogene'; --- ************************************************ --- *** relation: non_processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose from a means oth *** --- *** er than retrotransposition. *** --- ************************************************ --- CREATE VIEW non_processed_pseudogene AS SELECT feature_id AS non_processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'non_processed_pseudogene'; --- ************************************************ --- *** relation: variant_quality *** --- *** relation type: VIEW *** --- *** *** --- *** A dependent entity that inheres in a bea *** --- *** rer, a sequence variant. *** --- ************************************************ --- CREATE VIEW variant_quality AS SELECT feature_id AS variant_quality_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_quality'; --- ************************************************ --- *** relation: variant_origin *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its origin. *** --- ************************************************ --- CREATE VIEW variant_origin AS SELECT feature_id AS variant_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'variant_origin'; --- ************************************************ --- *** relation: variant_frequency *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW variant_frequency AS SELECT feature_id AS variant_frequency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'variant_frequency'; --- ************************************************ --- *** relation: unique_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW unique_variant AS SELECT feature_id AS unique_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant'; --- ************************************************ --- *** relation: rare_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rare_variant AS SELECT feature_id AS rare_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rare_variant'; --- ************************************************ --- *** relation: polymorphic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW polymorphic_variant AS SELECT feature_id AS polymorphic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_variant'; --- ************************************************ --- *** relation: common_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW common_variant AS SELECT feature_id AS common_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'common_variant'; --- ************************************************ --- *** relation: fixed_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fixed_variant AS SELECT feature_id AS fixed_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fixed_variant'; --- ************************************************ --- *** relation: variant_phenotype *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its phenotype. *** --- ************************************************ --- CREATE VIEW variant_phenotype AS SELECT feature_id AS variant_phenotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_phenotype'; --- ************************************************ --- *** relation: benign_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW benign_variant AS SELECT feature_id AS benign_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant'; --- ************************************************ --- *** relation: disease_associated_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_associated_variant AS SELECT feature_id AS disease_associated_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_associated_variant'; --- ************************************************ --- *** relation: disease_causing_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_causing_variant AS SELECT feature_id AS disease_causing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_causing_variant'; --- ************************************************ --- *** relation: lethal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lethal_variant AS SELECT feature_id AS lethal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lethal_variant'; --- ************************************************ --- *** relation: quantitative_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW quantitative_variant AS SELECT feature_id AS quantitative_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quantitative_variant'; --- ************************************************ --- *** relation: maternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW maternal_variant AS SELECT feature_id AS maternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant'; --- ************************************************ --- *** relation: paternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paternal_variant AS SELECT feature_id AS paternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_variant'; --- ************************************************ --- *** relation: somatic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW somatic_variant AS SELECT feature_id AS somatic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'somatic_variant'; --- ************************************************ --- *** relation: germline_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW germline_variant AS SELECT feature_id AS germline_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'germline_variant'; --- ************************************************ --- *** relation: pedigree_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pedigree_specific_variant AS SELECT feature_id AS pedigree_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pedigree_specific_variant'; --- ************************************************ --- *** relation: population_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW population_specific_variant AS SELECT feature_id AS population_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'population_specific_variant'; --- ************************************************ --- *** relation: de_novo_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW de_novo_variant AS SELECT feature_id AS de_novo_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'de_novo_variant'; --- ************************************************ --- *** relation: tf_binding_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a tran *** --- *** scription factor binding site. *** --- ************************************************ --- CREATE VIEW tf_binding_site_variant AS SELECT feature_id AS tf_binding_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant'; --- ************************************************ --- *** relation: missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid. *** --- ************************************************ --- CREATE VIEW missense_codon AS SELECT feature_id AS missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'missense_codon'; --- ************************************************ --- *** relation: complex_structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A structural sequence alteration where t *** --- *** here are multiple equally plausible expl *** --- *** anations for the change. *** --- ************************************************ --- CREATE VIEW complex_structural_alteration AS SELECT feature_id AS complex_structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration'; --- ************************************************ --- *** relation: structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW structural_alteration AS SELECT feature_id AS structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'structural_alteration'; --- ************************************************ --- *** relation: loss_of_heterozygosity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loss_of_heterozygosity AS SELECT feature_id AS loss_of_heterozygosity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loss_of_heterozygosity'; --- ************************************************ --- *** relation: splice_donor_5th_base_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** at the 5th base pair after the start of *** --- *** the intron in the orientation of the tra *** --- *** nscript. *** --- ************************************************ --- CREATE VIEW splice_donor_5th_base_variant AS SELECT feature_id AS splice_donor_5th_base_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_5th_base_variant'; --- ************************************************ --- *** relation: u_box *** --- *** relation type: VIEW *** --- *** *** --- *** An U-box is a conserved T-rich region up *** --- *** stream of a retroviral polypurine tract *** --- *** that is involved in PPT primer creation *** --- *** during reverse transcription. *** --- ************************************************ --- CREATE VIEW u_box AS SELECT feature_id AS u_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U_box'; --- ************************************************ --- *** relation: mating_type_region *** --- *** relation type: VIEW *** --- *** *** --- *** A specialized region in the genomes of s *** --- *** ome yeast and fungi, the genes of which *** --- *** regulate mating type. *** --- ************************************************ --- CREATE VIEW mating_type_region AS SELECT feature_id AS mating_type_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mating_type_region'; --- ************************************************ --- *** relation: paired_end_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An assembly region that has been sequenc *** --- *** ed from both ends resulting in a read_pa *** --- *** ir (mate_pair). *** --- ************************************************ --- CREATE VIEW paired_end_fragment AS SELECT feature_id AS paired_end_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paired_end_fragment'; --- ************************************************ --- *** relation: exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes exon seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW exon_variant AS SELECT feature_id AS exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'exon_variant'; --- ************************************************ --- *** relation: non_coding_exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes non-codi *** --- *** ng exon sequence. *** --- ************************************************ --- CREATE VIEW non_coding_exon_variant AS SELECT feature_id AS non_coding_exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_coding_exon_variant'; --- ************************************************ --- *** relation: clone_end *** --- *** relation type: VIEW *** --- *** *** --- *** A read from an end of the clone sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW clone_end AS SELECT feature_id AS clone_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_end'; --- ************************************************ --- *** relation: point_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A point centromere is a relatively small *** --- *** centromere (about 125 bp DNA) in discre *** --- *** te sequence, found in some yeast includi *** --- *** ng S. cerevisiae. *** --- ************************************************ --- CREATE VIEW point_centromere AS SELECT feature_id AS point_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere'; --- ************************************************ --- *** relation: regional_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A regional centromere is a large modular *** --- *** centromere found in fission yeast and h *** --- *** igher eukaryotes. It consist of a centra *** --- *** l core region flanked by inverted inner *** --- *** and outer repeat regions. *** --- ************************************************ --- CREATE VIEW regional_centromere AS SELECT feature_id AS regional_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere'; --- ************************************************ --- *** relation: regional_centromere_central_core *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region within the central re *** --- *** gion of a modular centromere, where the *** --- *** kinetochore is formed. *** --- ************************************************ --- CREATE VIEW regional_centromere_central_core AS SELECT feature_id AS regional_centromere_central_core_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_central_core'; --- ************************************************ --- *** relation: centromeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region found within the modular *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW centromeric_repeat AS SELECT feature_id AS centromeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'centromeric_repeat'; --- ************************************************ --- *** relation: regional_centromere_inner_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The inner repeat region of a modular cen *** --- *** tromere. This region is adjacent to the *** --- *** central core, on each chromosome arm. *** --- ************************************************ --- CREATE VIEW regional_centromere_inner_repeat_region AS SELECT feature_id AS regional_centromere_inner_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region'; --- ************************************************ --- *** relation: regional_centromere_outer_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The heterochromatic outer repeat region *** --- *** of a modular centromere. These repeats e *** --- *** xist in tandem arrays on both chromosome *** --- *** arms. *** --- ************************************************ --- CREATE VIEW regional_centromere_outer_repeat_region AS SELECT feature_id AS regional_centromere_outer_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_outer_repeat_region'; --- ************************************************ --- *** relation: tasirna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a 21 nucleotide double s *** --- *** tranded, polyadenylated non coding RNA, *** --- *** transcribed from the TAS gene. *** --- ************************************************ --- CREATE VIEW tasirna AS SELECT feature_id AS tasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA'; --- ************************************************ --- *** relation: tasirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tasiRNA. *** --- ************************************************ --- CREATE VIEW tasirna_primary_transcript AS SELECT feature_id AS tasirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA_primary_transcript'; --- ************************************************ --- *** relation: increased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is increased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW increased_polyadenylation_variant AS SELECT feature_id AS increased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant'; --- ************************************************ --- *** relation: decreased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is decreased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW decreased_polyadenylation_variant AS SELECT feature_id AS decreased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_polyadenylation_variant'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence that is involved in *** --- *** the control of a biological process. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: u14_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of an evolutionar *** --- *** ily conserved eukaryotic low molecular w *** --- *** eight RNA capable of intermolecular hybr *** --- *** idization with both homologous and heter *** --- *** ologous 18S rRNA. *** --- ************************************************ --- CREATE VIEW u14_snorna_primary_transcript AS SELECT feature_id AS u14_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: methylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of 2'-O *** --- *** -ribose methylation in an RNA molecule b *** --- *** y base pairing with a short sequence aro *** --- *** und the target residue. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna AS SELECT feature_id AS methylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA'; --- ************************************************ --- *** relation: rrna_cleavage_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An ncRNA that is part of a ribonucleopro *** --- *** tein that cleaves the primary pre-rRNA t *** --- *** ranscript in the process of producing ma *** --- *** ture rRNA molecules. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_rna AS SELECT feature_id AS rrna_cleavage_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_RNA'; --- ************************************************ --- *** relation: exon_of_single_exon_gene *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is the only exon in a gene. *** --- ************************************************ --- CREATE VIEW exon_of_single_exon_gene AS SELECT feature_id AS exon_of_single_exon_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_of_single_exon_gene'; --- ************************************************ --- *** relation: cassette_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cassette_array_member AS SELECT feature_id AS cassette_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member'; --- ************************************************ --- *** relation: gene_cassette_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_cassette_member AS SELECT feature_id AS gene_cassette_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member'; --- ************************************************ --- *** relation: gene_subarray_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_subarray_member AS SELECT feature_id AS gene_subarray_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray_member'; --- ************************************************ --- *** relation: primer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** Non-covalent primer binding site for ini *** --- *** tiation of replication, transcription, o *** --- *** r reverse transcription. *** --- ************************************************ --- CREATE VIEW primer_binding_site AS SELECT feature_id AS primer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_binding_site'; --- ************************************************ --- *** relation: gene_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array includes two or more genes, or *** --- *** two or more gene subarrays, contiguously *** --- *** arranged where the individual genes, or *** --- *** subarrays, are either identical in sequ *** --- *** ence, or essentially so. *** --- ************************************************ --- CREATE VIEW gene_array AS SELECT feature_id AS gene_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_array'; --- ************************************************ --- *** relation: gene_subarray *** --- *** relation type: VIEW *** --- *** *** --- *** A subarray is, by defintition, a member *** --- *** of a gene array (SO:0005851); the member *** --- *** s of a subarray may differ substantially *** --- *** in sequence, but are closely related in *** --- *** function. *** --- ************************************************ --- CREATE VIEW gene_subarray AS SELECT feature_id AS gene_subarray_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray'; --- ************************************************ --- *** relation: gene_cassette *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that can be substituted for a rel *** --- *** ated gene at a different site in the gen *** --- *** ome. *** --- ************************************************ --- CREATE VIEW gene_cassette AS SELECT feature_id AS gene_cassette_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette'; --- ************************************************ --- *** relation: gene_cassette_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array of non-functional genes whose m *** --- *** embers, when captured by recombination f *** --- *** orm functional genes. *** --- ************************************************ --- CREATE VIEW gene_cassette_array AS SELECT feature_id AS gene_cassette_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette_array'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: selenocysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW selenocysteine_trna_primary_transcript AS SELECT feature_id AS selenocysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: selenocysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a selenocystein *** --- *** e anticodon, and a 3' selenocysteine bin *** --- *** ding region. *** --- ************************************************ --- CREATE VIEW selenocysteinyl_trna AS SELECT feature_id AS selenocysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteinyl_tRNA'; --- ************************************************ --- *** relation: syntenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region in which two or more pairs of h *** --- *** omologous markers occur on the same chro *** --- *** mosome in two or more species. *** --- ************************************************ --- CREATE VIEW syntenic_region AS SELECT feature_id AS syntenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic_region'; --- ************************************************ --- *** relation: biochemical_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is involved i *** --- *** n a biochemical function. *** --- ************************************************ --- CREATE VIEW biochemical_region_of_peptide AS SELECT feature_id AS biochemical_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide'; --- ************************************************ --- *** relation: molecular_contact_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is involved a contact with *** --- *** another molecule. *** --- ************************************************ --- CREATE VIEW molecular_contact_region AS SELECT feature_id AS molecular_contact_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region'; --- ************************************************ --- *** relation: intrinsically_unstructured_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polypeptide chain with high *** --- *** conformational flexibility. *** --- ************************************************ --- CREATE VIEW intrinsically_unstructured_polypeptide_region AS SELECT feature_id AS intrinsically_unstructured_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region'; --- ************************************************ --- *** relation: catmat_left_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_three AS SELECT feature_id AS catmat_left_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_three'; --- ************************************************ --- *** relation: catmat_left_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i psi -10 boun *** --- *** ds -50 to 30, res i+1: phi -90 bounds -1 *** --- *** 20 to -60, res i+1: psi -10 bounds -50 t *** --- *** o 30, res i+2: phi -75 bounds -100 to -5 *** --- *** 0, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_four AS SELECT feature_id AS catmat_left_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_four'; --- ************************************************ --- *** relation: catmat_right_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_three AS SELECT feature_id AS catmat_right_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_three'; --- ************************************************ --- *** relation: catmat_right_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -90 bounds - *** --- *** 120 to -60, res i+1: psi -10 bounds -50 *** --- *** to 30, res i+2: phi -75 bounds -100 to - *** --- *** 50, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_four AS SELECT feature_id AS catmat_right_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_four'; --- ************************************************ --- *** relation: alpha_beta_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: H-bond between CO *** --- *** of residue(i) and NH of residue(i+4), H *** --- *** -bond between CO of residue(i) and NH of *** --- *** residue(i+3),Phi angles of residues(i+1 *** --- *** ), (i+2) and (i+3) are negative. *** --- ************************************************ --- CREATE VIEW alpha_beta_motif AS SELECT feature_id AS alpha_beta_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_beta_motif'; --- ************************************************ --- *** relation: lipoprotein_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide that acts as a signal for both *** --- *** membrane translocation and lipid attach *** --- *** ment in prokaryotes. *** --- ************************************************ --- CREATE VIEW lipoprotein_signal_peptide AS SELECT feature_id AS lipoprotein_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lipoprotein_signal_peptide'; --- ************************************************ --- *** relation: no_output *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region wherean analysis *** --- *** has been run and not produced any annota *** --- *** tion. *** --- ************************************************ --- CREATE VIEW no_output AS SELECT feature_id AS no_output_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'no_output'; --- ************************************************ --- *** relation: cleaved_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** The cleaved_peptide_regon is the a regio *** --- *** n of peptide sequence that is cleaved du *** --- *** ring maturation. *** --- ************************************************ --- CREATE VIEW cleaved_peptide_region AS SELECT feature_id AS cleaved_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'cleaved_peptide_region'; --- ************************************************ --- *** relation: peptide_coil *** --- *** relation type: VIEW *** --- *** *** --- *** Irregular, unstructured regions of a pro *** --- *** tein's backbone, as distinct from the re *** --- *** gular region (namely alpha helix and bet *** --- *** a strand - characterised by specific pat *** --- *** terns of main-chain hydrogen bonds). *** --- ************************************************ --- CREATE VIEW peptide_coil AS SELECT feature_id AS peptide_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_coil'; --- ************************************************ --- *** relation: hydrophobic_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Hydrophobic regions are regions with a l *** --- *** ow affinity for water. *** --- ************************************************ --- CREATE VIEW hydrophobic_region_of_peptide AS SELECT feature_id AS hydrophobic_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydrophobic_region_of_peptide'; --- ************************************************ --- *** relation: n_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The amino-terminal positively-charged re *** --- *** gion of a signal peptide (approx 1-5 aa) *** --- *** . *** --- ************************************************ --- CREATE VIEW n_terminal_region AS SELECT feature_id AS n_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'n_terminal_region'; --- ************************************************ --- *** relation: c_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The more polar, carboxy-terminal region *** --- *** of the signal peptide (approx 3-7 aa). *** --- ************************************************ --- CREATE VIEW c_terminal_region AS SELECT feature_id AS c_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'c_terminal_region'; --- ************************************************ --- *** relation: central_hydrophobic_region_of_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The central, hydrophobic region of the s *** --- *** ignal peptide (approx 7-15 aa). *** --- ************************************************ --- CREATE VIEW central_hydrophobic_region_of_signal_peptide AS SELECT feature_id AS central_hydrophobic_region_of_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'central_hydrophobic_region_of_signal_peptide'; --- ************************************************ --- *** relation: polypeptide_conserved_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved motif is a short (up to 20 a *** --- *** mino acids) region of biological interes *** --- *** t that is conserved in different protein *** --- *** s. They may or may not have functional o *** --- *** r structural significance within the pro *** --- *** teins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_motif AS SELECT feature_id AS polypeptide_conserved_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_conserved_motif'; --- ************************************************ --- *** relation: polypeptide_binding_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide binding motif is a short ( *** --- *** up to 20 amino acids) polypeptide region *** --- *** of biological interest that contains on *** --- *** e or more amino acids experimentally sho *** --- *** wn to bind to a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_binding_motif AS SELECT feature_id AS polypeptide_binding_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_binding_motif'; --- ************************************************ --- *** relation: polypeptide_catalytic_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide catalytic motif is a short *** --- *** (up to 20 amino acids) polypeptide regi *** --- *** on that contains one or more active site *** --- *** residues. *** --- ************************************************ --- CREATE VIEW polypeptide_catalytic_motif AS SELECT feature_id AS polypeptide_catalytic_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_catalytic_motif'; --- ************************************************ --- *** relation: polypeptide_dna_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with DNA. *** --- ************************************************ --- CREATE VIEW polypeptide_dna_contact AS SELECT feature_id AS polypeptide_dna_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact'; --- ************************************************ --- *** relation: polypeptide_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** A subsection of sequence with biological *** --- *** interest that is conserved in different *** --- *** proteins. They may or may not have func *** --- *** tional or structural significance within *** --- *** the proteins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_region AS SELECT feature_id AS polypeptide_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_conserved_region'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration where the length o *** --- *** f the change in the variant is the same *** --- *** as that of the reference. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'substitution'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A single nucleotide change which has occ *** --- *** urred at the same position of a correspo *** --- *** nding nucleotide in a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: transition *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into an other pyrimidine nucleotide, *** --- *** or change of a purine nucleotide, A or G *** --- *** , into an other purine nucleotide. *** --- ************************************************ --- CREATE VIEW transition AS SELECT feature_id AS transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'transition'; --- ************************************************ --- *** relation: pyrimidine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a pyrimidine, C or T, *** --- *** for another pyrimidine. *** --- ************************************************ --- CREATE VIEW pyrimidine_transition AS SELECT feature_id AS pyrimidine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'pyrimidine_transition'; --- ************************************************ --- *** relation: c_to_t_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a cytidine to a thymine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition AS SELECT feature_id AS c_to_t_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'C_to_T_transition'; --- ************************************************ --- *** relation: c_to_t_transition_at_pcpg_site *** --- *** relation type: VIEW *** --- *** *** --- *** The transition of cytidine to thymine oc *** --- *** curring at a pCpG site as a consequence *** --- *** of the spontaneous deamination of 5'-met *** --- *** hylcytidine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition_at_pcpg_site AS SELECT feature_id AS c_to_t_transition_at_pcpg_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site'; --- ************************************************ --- *** relation: t_to_c_transition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW t_to_c_transition AS SELECT feature_id AS t_to_c_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_C_transition'; --- ************************************************ --- *** relation: purine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a purine, A or G, for *** --- *** another purine. *** --- ************************************************ --- CREATE VIEW purine_transition AS SELECT feature_id AS purine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'purine_transition'; --- ************************************************ --- *** relation: a_to_g_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of an adenine to a guanine. *** --- ************************************************ --- CREATE VIEW a_to_g_transition AS SELECT feature_id AS a_to_g_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition'; --- ************************************************ --- *** relation: g_to_a_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a guanine to an adenine. *** --- ************************************************ --- CREATE VIEW g_to_a_transition AS SELECT feature_id AS g_to_a_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_A_transition'; --- ************************************************ --- *** relation: transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G, or *** --- *** vice versa. *** --- ************************************************ --- CREATE VIEW transversion AS SELECT feature_id AS transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'transversion'; --- ************************************************ --- *** relation: pyrimidine_to_purine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G. *** --- ************************************************ --- CREATE VIEW pyrimidine_to_purine_transversion AS SELECT feature_id AS pyrimidine_to_purine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'pyrimidine_to_purine_transversion'; --- ************************************************ --- *** relation: c_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from cytidine to adenine. *** --- ************************************************ --- CREATE VIEW c_to_a_transversion AS SELECT feature_id AS c_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion'; --- ************************************************ --- *** relation: c_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_to_g_transversion AS SELECT feature_id AS c_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_G_transversion'; --- ************************************************ --- *** relation: t_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to A. *** --- ************************************************ --- CREATE VIEW t_to_a_transversion AS SELECT feature_id AS t_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_A_transversion'; --- ************************************************ --- *** relation: t_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to G. *** --- ************************************************ --- CREATE VIEW t_to_g_transversion AS SELECT feature_id AS t_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_G_transversion'; --- ************************************************ --- *** relation: purine_to_pyrimidine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a purine nucleotide, A or G , *** --- *** into a pyrimidine nucleotide C or T. *** --- ************************************************ --- CREATE VIEW purine_to_pyrimidine_transversion AS SELECT feature_id AS purine_to_pyrimidine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion'; --- ************************************************ --- *** relation: a_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to cytidine. *** --- ************************************************ --- CREATE VIEW a_to_c_transversion AS SELECT feature_id AS a_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion'; --- ************************************************ --- *** relation: a_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to thymine. *** --- ************************************************ --- CREATE VIEW a_to_t_transversion AS SELECT feature_id AS a_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_T_transversion'; --- ************************************************ --- *** relation: g_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to cytidine. *** --- ************************************************ --- CREATE VIEW g_to_c_transversion AS SELECT feature_id AS g_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_C_transversion'; --- ************************************************ --- *** relation: g_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to thymine. *** --- ************************************************ --- CREATE VIEW g_to_t_transversion AS SELECT feature_id AS g_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_T_transversion'; --- ************************************************ --- *** relation: intrachromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation within *** --- *** a single chromosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_mutation AS SELECT feature_id AS intrachromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'intrachromosomal_mutation'; --- ************************************************ --- *** relation: chromosomal_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** An incomplete chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_deletion AS SELECT feature_id AS chromosomal_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_deletion'; --- ************************************************ --- *** relation: chromosomal_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation where a reg *** --- *** ion of the chromosome is inverted with r *** --- *** espect to wild type. *** --- ************************************************ --- CREATE VIEW chromosomal_inversion AS SELECT feature_id AS chromosomal_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_inversion'; --- ************************************************ --- *** relation: interchromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation whereb *** --- *** y more than one chromosome is involved. *** --- ************************************************ --- CREATE VIEW interchromosomal_mutation AS SELECT feature_id AS interchromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_mutation'; --- ************************************************ --- *** relation: indel *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration which included an *** --- *** insertion and a deletion, affecting 2 or *** --- *** more bases. *** --- ************************************************ --- CREATE VIEW indel AS SELECT feature_id AS indel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'indel'; --- ************************************************ --- *** relation: duplication *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce; the inserted sequence derives from, *** --- *** or is identical in sequence to, nucleoti *** --- *** des adjacent to insertion point. *** --- ************************************************ --- CREATE VIEW duplication AS SELECT feature_id AS duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'duplication'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: chromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An extra chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_duplication AS SELECT feature_id AS chromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_duplication'; --- ************************************************ --- *** relation: intrachromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication that occurred within a chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_duplication AS SELECT feature_id AS intrachromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_duplication'; --- ************************************************ --- *** relation: direct_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are in the same orientation. *** --- ************************************************ --- CREATE VIEW direct_tandem_duplication AS SELECT feature_id AS direct_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication'; --- ************************************************ --- *** relation: inverted_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are not in the same orientatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW inverted_tandem_duplication AS SELECT feature_id AS inverted_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_tandem_duplication'; --- ************************************************ --- *** relation: intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred within a chrom *** --- *** osome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_transposition AS SELECT feature_id AS intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_transposition'; --- ************************************************ --- *** relation: compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant where a m *** --- *** onocentric element is caused by the fusi *** --- *** on of two chromosome arms. *** --- ************************************************ --- CREATE VIEW compound_chromosome AS SELECT feature_id AS compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'compound_chromosome'; --- ************************************************ --- *** relation: robertsonian_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A non reciprocal translocation whereby t *** --- *** he participating chromosomes break at th *** --- *** eir centromeres and the long arms fuse t *** --- *** o form a single chromosome with a single *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW robertsonian_fusion AS SELECT feature_id AS robertsonian_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Robertsonian_fusion'; --- ************************************************ --- *** relation: chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation. Rearrangem *** --- *** ents that alter the pairing of telomeres *** --- *** are classified as translocations. *** --- ************************************************ --- CREATE VIEW chromosomal_translocation AS SELECT feature_id AS chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_translocation'; --- ************************************************ --- *** relation: ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome is a chromosome whose *** --- *** arms have fused together to form a ring, *** --- *** often with the loss of the ends of the *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW ring_chromosome AS SELECT feature_id AS ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'ring_chromosome'; --- ************************************************ --- *** relation: pericentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that includes th *** --- *** e centromere. *** --- ************************************************ --- CREATE VIEW pericentric_inversion AS SELECT feature_id AS pericentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric_inversion'; --- ************************************************ --- *** relation: paracentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that does not in *** --- *** clude the centromere. *** --- ************************************************ --- CREATE VIEW paracentric_inversion AS SELECT feature_id AS paracentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric_inversion'; --- ************************************************ --- *** relation: reciprocal_chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation with two bre *** --- *** aks; two chromosome segments have simply *** --- *** been exchanged. *** --- ************************************************ --- CREATE VIEW reciprocal_chromosomal_translocation AS SELECT feature_id AS reciprocal_chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal_chromosomal_translocation'; --- ************************************************ --- *** relation: autosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome is the aneupl *** --- *** oid product of recombination between a p *** --- *** ericentric inversion and a cytologically *** --- *** wild-type chromosome. *** --- ************************************************ --- CREATE VIEW autosynaptic_chromosome AS SELECT feature_id AS autosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'autosynaptic_chromosome'; --- ************************************************ --- *** relation: homo_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two copies *** --- *** of the same chromosomal arm attached to *** --- *** a common centromere. The chromosome is *** --- *** diploid for the arm involved. *** --- ************************************************ --- CREATE VIEW homo_compound_chromosome AS SELECT feature_id AS homo_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homo_compound_chromosome'; --- ************************************************ --- *** relation: hetero_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two arms f *** --- *** rom different chromosomes are connected *** --- *** through the centromere of one of them. *** --- ************************************************ --- CREATE VIEW hetero_compound_chromosome AS SELECT feature_id AS hetero_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hetero_compound_chromosome'; --- ************************************************ --- *** relation: chromosome_fission *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome that occurred by the divisi *** --- *** on of a larger chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_fission AS SELECT feature_id AS chromosome_fission_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_fission'; --- ************************************************ --- *** relation: dexstrosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome carrying the *** --- *** two right (D = dextro) telomeres. *** --- ************************************************ --- CREATE VIEW dexstrosynaptic_chromosome AS SELECT feature_id AS dexstrosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome'; --- ************************************************ --- *** relation: laevosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** LS is an autosynaptic chromosome carryin *** --- *** g the two left (L = levo) telomeres. *** --- ************************************************ --- CREATE VIEW laevosynaptic_chromosome AS SELECT feature_id AS laevosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'laevosynaptic_chromosome'; --- ************************************************ --- *** relation: free_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** the duplicated sequences are carried as *** --- *** a free centric element. *** --- ************************************************ --- CREATE VIEW free_duplication AS SELECT feature_id AS free_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication' OR cvterm.name = 'free_duplication'; --- ************************************************ --- *** relation: free_ring_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome which is a copy of ano *** --- *** ther chromosome. *** --- ************************************************ --- CREATE VIEW free_ring_duplication AS SELECT feature_id AS free_ring_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication'; --- ************************************************ --- *** relation: complex_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant with 4 or *** --- *** more breakpoints. *** --- ************************************************ --- CREATE VIEW complex_chromosomal_mutation AS SELECT feature_id AS complex_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a translo *** --- *** cation occurs in which one of the four b *** --- *** roken ends loses a segment before re-joi *** --- *** ning. *** --- ************************************************ --- CREATE VIEW deficient_translocation AS SELECT feature_id AS deficient_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_translocation'; --- ************************************************ --- *** relation: inversion_cum_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** first two breaks are in the same chromos *** --- *** ome, and the region between them is rejo *** --- *** ined in inverted order to the other side *** --- *** of the first break, such that both side *** --- *** s of break one are present on the same c *** --- *** hromosome. The remaining free ends are j *** --- *** oined as a translocation with those resu *** --- *** lting from the third break. *** --- ************************************************ --- CREATE VIEW inversion_cum_translocation AS SELECT feature_id AS inversion_cum_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_cum_translocation'; --- ************************************************ --- *** relation: bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation whereby the *** --- *** (large) region between the first two br *** --- *** eaks listed is lost, and the two flankin *** --- *** g segments (one of them centric) are joi *** --- *** ned as a translocation to the free ends *** --- *** resulting from the third break. *** --- ************************************************ --- CREATE VIEW bipartite_duplication AS SELECT feature_id AS bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_duplication'; --- ************************************************ --- *** relation: cyclic_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby thre *** --- *** e breaks occurred in three different chr *** --- *** omosomes. The centric segment resulting *** --- *** from the first break listed is joined to *** --- *** the acentric segment resulting from the *** --- *** second, rather than the third. *** --- ************************************************ --- CREATE VIEW cyclic_translocation AS SELECT feature_id AS cyclic_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyclic_translocation'; --- ************************************************ --- *** relation: bipartite_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion caused by three *** --- *** breaks in the same chromosome; both cent *** --- *** ral segments are inverted in place (i.e. *** --- *** , they are not transposed). *** --- ************************************************ --- CREATE VIEW bipartite_inversion AS SELECT feature_id AS bipartite_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_inversion'; --- ************************************************ --- *** relation: uninvert_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically the *** --- *** same orientation as its flanking segmen *** --- *** ts. *** --- ************************************************ --- CREATE VIEW uninvert_insert_dup AS SELECT feature_id AS uninvert_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication'; --- ************************************************ --- *** relation: inverted_insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically inv *** --- *** erted orientation with respect to its fl *** --- *** anking segments. *** --- ************************************************ --- CREATE VIEW inverted_insertional_duplication AS SELECT feature_id AS inverted_insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_insertional_duplication'; --- ************************************************ --- *** relation: insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving the i *** --- *** nsertion of a duplicated region (as oppo *** --- *** sed to a free duplication). *** --- ************************************************ --- CREATE VIEW insertional_duplication AS SELECT feature_id AS insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'insertional_duplication'; --- ************************************************ --- *** relation: interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred between chromo *** --- *** somes. *** --- ************************************************ --- CREATE VIEW interchromosomal_transposition AS SELECT feature_id AS interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally inverted orientation with respect *** --- *** to its flanking segment. *** --- ************************************************ --- CREATE VIEW invert_inter_transposition AS SELECT feature_id AS invert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transition where the *** --- *** segment between the first two breaks li *** --- *** sted is removed and inserted at the thir *** --- *** d break; the insertion is in cytological *** --- *** ly the same orientation as its flanking *** --- *** segments. *** --- ************************************************ --- CREATE VIEW uninvert_inter_transposition AS SELECT feature_id AS uninvert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically inverted orientation with respec *** --- *** t to its flanking segments. *** --- ************************************************ --- CREATE VIEW invert_intra_transposition AS SELECT feature_id AS invert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically the same orientation as its flan *** --- *** king segments. *** --- ************************************************ --- CREATE VIEW uninvert_intra_transposition AS SELECT feature_id AS uninvert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: unorient_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the orientation of the insertion with *** --- *** respect to its flanking segments is not *** --- *** recorded. *** --- ************************************************ --- CREATE VIEW unorient_insert_dup AS SELECT feature_id AS unorient_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_insertional_duplication'; --- ************************************************ --- *** relation: unoriented_interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the orientation of the inser *** --- *** tion with respect to its flanking segmen *** --- *** ts is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_interchromosomal_transposition AS SELECT feature_id AS unoriented_interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_interchromosomal_transposition'; --- ************************************************ --- *** relation: unoriented_intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the orientation of the ins *** --- *** ertion with respect to its flanking segm *** --- *** ents is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_intrachromosomal_transposition AS SELECT feature_id AS unoriented_intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uncharacterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uncharacterised_chromosomal_mutation AS SELECT feature_id AS uncharacterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby three bre *** --- *** aks occur in the same chromosome; one ce *** --- *** ntral region is lost, and the other is i *** --- *** nverted. *** --- ************************************************ --- CREATE VIEW deficient_inversion AS SELECT feature_id AS deficient_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_inversion'; --- ************************************************ --- *** relation: tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication consisting of 2 identical *** --- *** adjacent regions. *** --- ************************************************ --- CREATE VIEW tandem_duplication AS SELECT feature_id AS tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'tandem_duplication'; --- ************************************************ --- *** relation: partially_characterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW partially_characterised_chromosomal_mutation AS SELECT feature_id AS partially_characterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation'; --- ************************************************ --- *** relation: chromosome_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW chromosome_number_variation AS SELECT feature_id AS chromosome_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'chromosome_number_variation'; --- ************************************************ --- *** relation: chromosome_structure_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_structure_variation AS SELECT feature_id AS chromosome_structure_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_structure_variation'; --- ************************************************ --- *** relation: alternatively_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is alternatively splic *** --- *** ed. *** --- ************************************************ --- CREATE VIEW alternatively_spliced_transcript AS SELECT feature_id AS alternatively_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced_transcript'; --- ************************************************ --- *** relation: encodes_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, but *** --- *** encodes only one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_1_polypeptide AS SELECT feature_id AS encodes_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide'; --- ************************************************ --- *** relation: encodes_greater_than_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_greater_than_1_polypeptide AS SELECT feature_id AS encodes_greater_than_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_greater_than_1_polypeptide'; --- ************************************************ --- *** relation: encodes_different_polypeptides_different_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different stop codons. *** --- ************************************************ --- CREATE VIEW encodes_different_polypeptides_different_stop AS SELECT feature_id AS encodes_different_polypeptides_different_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides_different_start *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides_different_start AS SELECT feature_id AS encodes_overlapping_peptides_different_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_peptides_different_start'; --- ************************************************ --- *** relation: encodes_disjoint_polypeptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** do not have overlapping peptide sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW encodes_disjoint_polypeptides AS SELECT feature_id AS encodes_disjoint_polypeptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides'; --- ************************************************ --- *** relation: encodes_overlapping_polypeptides_different_start_and_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start and stop codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_polypeptides_different_start_and_stop AS SELECT feature_id AS encodes_overlapping_polypeptides_different_start_and_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides AS SELECT feature_id AS encodes_overlapping_peptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_overlapping_peptides'; --- ************************************************ --- *** relation: cryptogene *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle gene so extensively edited *** --- *** that it cannot be matched to its edited *** --- *** mRNA sequence. *** --- ************************************************ --- CREATE VIEW cryptogene AS SELECT feature_id AS cryptogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene'; --- ************************************************ --- *** relation: dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that has the qualit *** --- *** y dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_primary_transcript AS SELECT feature_id AS dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript'; --- ************************************************ --- *** relation: member_of_regulon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW member_of_regulon AS SELECT feature_id AS member_of_regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'member_of_regulon'; --- ************************************************ --- *** relation: cds_independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS with the evidence status of being *** --- *** independently known. *** --- ************************************************ --- CREATE VIEW cds_independently_known AS SELECT feature_id AS cds_independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_independently_known'; --- ************************************************ --- *** relation: orphan_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS whose predicted amino acid sequenc *** --- *** e is unsupported by any experimental evi *** --- *** dence or by any match with any other kno *** --- *** wn sequence. *** --- ************************************************ --- CREATE VIEW orphan_cds AS SELECT feature_id AS orphan_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS'; --- ************************************************ --- *** relation: cds_supported_by_domain_match_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by domain simila *** --- *** rity. *** --- ************************************************ --- CREATE VIEW cds_supported_by_domain_match_data AS SELECT feature_id AS cds_supported_by_domain_match_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data'; --- ************************************************ --- *** relation: cds_supported_by_sequence_similarity_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by sequence simi *** --- *** larity data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_sequence_similarity_data AS SELECT feature_id AS cds_supported_by_sequence_similarity_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data'; --- ************************************************ --- *** relation: cds_predicted *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is predicted. *** --- ************************************************ --- CREATE VIEW cds_predicted AS SELECT feature_id AS cds_predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_predicted'; --- ************************************************ --- *** relation: cds_supported_by_est_or_cdna_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by similarity to *** --- *** EST or cDNA data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_est_or_cdna_data AS SELECT feature_id AS cds_supported_by_est_or_cdna_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_EST_or_cDNA_data'; --- ************************************************ --- *** relation: internal_shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A Shine-Dalgarno sequence that stimulate *** --- *** s recoding through interactions with the *** --- *** anti-Shine-Dalgarno in the RNA of small *** --- *** ribosomal subunits of translating ribos *** --- *** omes. The signal is only operative in Ba *** --- *** cteria. *** --- ************************************************ --- CREATE VIEW internal_shine_dalgarno_sequence AS SELECT feature_id AS internal_shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a mature mRNA transcript *** --- *** , modified before translation or during *** --- *** translation, usually by special cis-acti *** --- *** ng signals. *** --- ************************************************ --- CREATE VIEW recoded_mrna AS SELECT feature_id AS recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'recoded_mRNA'; --- ************************************************ --- *** relation: minus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of -1. *** --- ************************************************ --- CREATE VIEW minus_1_translationally_frameshifted AS SELECT feature_id AS minus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: plus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of +1. *** --- ************************************************ --- CREATE VIEW plus_1_translationally_frameshifted AS SELECT feature_id AS plus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA where translation was sus *** --- *** pended at a particular codon and resumed *** --- *** at a particular non-overlapping downstr *** --- *** eam codon. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_translational_bypass AS SELECT feature_id AS mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: mrna_recoded_by_codon_redefinition *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA that was modified by an a *** --- *** lteration of codon meaning. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_codon_redefinition AS SELECT feature_id AS mrna_recoded_by_codon_redefinition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_codon_redefinition'; --- ************************************************ --- *** relation: recoding_stimulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A site in an mRNA sequence that stimulat *** --- *** es the recoding of a region in the same *** --- *** mRNA. *** --- ************************************************ --- CREATE VIEW recoding_stimulatory_region AS SELECT feature_id AS recoding_stimulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'recoding_stimulatory_region'; --- ************************************************ --- *** relation: four_bp_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon with 4 base *** --- *** pairs. *** --- ************************************************ --- CREATE VIEW four_bp_start_codon AS SELECT feature_id AS four_bp_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon'; --- ************************************************ --- *** relation: archaeal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron characteristic of Archaeal tRN *** --- *** A and rRNA genes, where intron transcrip *** --- *** t generates a bulge-helix-bulge motif th *** --- *** at is recognised by a splicing endoribon *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW archaeal_intron AS SELECT feature_id AS archaeal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron'; --- ************************************************ --- *** relation: trna_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron found in tRNA that is spliced *** --- *** via endonucleolytic cleavage and ligatio *** --- *** n rather than transesterification. *** --- ************************************************ --- CREATE VIEW trna_intron AS SELECT feature_id AS trna_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_intron'; --- ************************************************ --- *** relation: ctg_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon of sequence *** --- *** CTG. *** --- ************************************************ --- CREATE VIEW ctg_start_codon AS SELECT feature_id AS ctg_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CTG_start_codon'; --- ************************************************ --- *** relation: secis_element *** --- *** relation type: VIEW *** --- *** *** --- *** The incorporation of selenocysteine into *** --- *** a protein sequence is directed by an in *** --- *** -frame UGA codon (usually a stop codon) *** --- *** within the coding region of the mRNA. Se *** --- *** lenoprotein mRNAs contain a conserved se *** --- *** condary structure in the 3' UTR that is *** --- *** required for the distinction of UGA stop *** --- *** from UGA selenocysteine. The selenocyst *** --- *** eine insertion sequence (SECIS) is aroun *** --- *** d 60 nt in length and adopts a hairpin s *** --- *** tructure which is sufficiently well-defi *** --- *** ned and conserved to act as a computatio *** --- *** nal screen for selenoprotein genes. *** --- ************************************************ --- CREATE VIEW secis_element AS SELECT feature_id AS secis_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SECIS_element'; --- ************************************************ --- *** relation: retron *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence coding for a short, single-stra *** --- *** nded, DNA sequence via a retrotransposed *** --- *** RNA intermediate; characteristic of som *** --- *** e microbial genomes. *** --- ************************************************ --- CREATE VIEW retron AS SELECT feature_id AS retron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retron'; --- ************************************************ --- *** relation: three_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** downstream of the recoding site. *** --- ************************************************ --- CREATE VIEW three_prime_recoding_site AS SELECT feature_id AS three_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'three_prime_recoding_site'; --- ************************************************ --- *** relation: three_prime_stem_loop_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory region, the stem- *** --- *** loop secondary structural element is dow *** --- *** nstream of the redefined region. *** --- ************************************************ --- CREATE VIEW three_prime_stem_loop_structure AS SELECT feature_id AS three_prime_stem_loop_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure'; --- ************************************************ --- *** relation: five_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** upstream of the recoding site. *** --- ************************************************ --- CREATE VIEW five_prime_recoding_site AS SELECT feature_id AS five_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_recoding_site'; --- ************************************************ --- *** relation: flanking_three_prime_quadruplet_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Four base pair sequence immediately down *** --- *** stream of the redefined region. The rede *** --- *** fined region is a frameshift site. The q *** --- *** uadruplet is 2 overlapping codons. *** --- ************************************************ --- CREATE VIEW flanking_three_prime_quadruplet_recoding_signal AS SELECT feature_id AS flanking_three_prime_quadruplet_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal'; --- ************************************************ --- *** relation: uag_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAG stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uag_stop_codon_signal AS SELECT feature_id AS uag_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal'; --- ************************************************ --- *** relation: uaa_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uaa_stop_codon_signal AS SELECT feature_id AS uaa_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAA_stop_codon_signal'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: uga_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UGA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uga_stop_codon_signal AS SELECT feature_id AS uga_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UGA_stop_codon_signal'; --- ************************************************ --- *** relation: three_prime_repeat_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal, downstrea *** --- *** m sequence important for recoding that c *** --- *** ontains repetitive elements. *** --- ************************************************ --- CREATE VIEW three_prime_repeat_recoding_signal AS SELECT feature_id AS three_prime_repeat_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_repeat_recoding_signal'; --- ************************************************ --- *** relation: distant_three_prime_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding signal that is found many hun *** --- *** dreds of nucleotides 3' of a redefined s *** --- *** top codon. *** --- ************************************************ --- CREATE VIEW distant_three_prime_recoding_signal AS SELECT feature_id AS distant_three_prime_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distant_three_prime_recoding_signal'; --- ************************************************ --- *** relation: stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal that is a *** --- *** stop codon and has effect on efficiency *** --- *** of recoding. *** --- ************************************************ --- CREATE VIEW stop_codon_signal AS SELECT feature_id AS stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'stop_codon_signal'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene component region which acts as a *** --- *** recombinational unit of a gene whose fun *** --- *** ctional form is generated through somati *** --- *** c recombination. *** --- ************************************************ --- CREATE VIEW gene_segment AS SELECT feature_id AS gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_segment'; CREATE TABLE sequence_cv_lookup_table (sequence_cv_lookup_table_id serial not null, primary key(sequence_cv_lookup_table_id), original_cvterm_name varchar(1024), relation_name varchar(128)); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_variant','transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helitron','helitron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_initiator_methionine','cleaved_initiator_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epoxyqueuosine','epoxyqueuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4atac_snrna','u4atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast','kinetoplast'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_n_terminal','elongated_out_of_frame_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shadow_enhancer','shadow_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered','engineered'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_ii_tata_box','rna_polymerase_ii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_aminomethyl_seven_deazaguanosine','seven_aminomethyl_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_motif','sequence_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity','low_complexity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est_match','est_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_nonamer','v_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_c_cluster','d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_21s','rrna_21s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_factor','bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethyluridine','five_carboxymethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dinucleotide_repeat_microsatellite_feature','dinucleotide_repeat_microsatellite_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_methyladenosine','two_methylthio_n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_mrna','trans_spliced_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_c_transversion','g_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heptamer_of_recombination_feature_of_vertebrate_immune_system_gene','heptamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genotype','so_genotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_region','cloned_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_coding_piece','tmrna_coding_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_6s','rna_6s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element','x_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle','minicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_encoding','grna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endonuclease_spliced_intron','endonuclease_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional_duplication','insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('databank_entry','databank_entry'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine','glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_phenotype','variant_phenotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_cluster','v_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl12_acceptor_site','sl12_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nickel_ion_contact_site','polypeptide_nickel_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_rna_chromosome','circular_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wc_base_pair','wc_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pcr_product','pcr_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3_prime_utr_variant','three_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_three_amino_three_carboxypropyl_uridine','three_three_amino_three_carboxypropyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('site_specific_recombination_target_region','site_specific_recombination_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polycistronic_transcript','gene_with_polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue','rescue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_hypersensitive_site','nuclease_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_gene_variant','upstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_loop','mirna_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_cdna','double_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_post_translational_processing_variant','polypeptide_post_translational_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('2kb_upstream_variant','twokb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_domain_match','supported_by_domain_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylpseudouridine','one_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n_terminal_region','n_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_site','blunt_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_result_region','experimental_result_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine_trna_primary_transcript','methionine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr','utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_terminal_residue','non_terminal_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('member_of_regulon','member_of_regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine_trna_primary_transcript','thr_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_sequence_similarity_data','cds_supported_by_sequence_similarity_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_region','polypeptide_structural_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_gene','trna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_tungsten_ion_contact_site','polypeptide_tungsten_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_six','beta_bulge_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_c_cluster','d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_location','sequence_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_right_left_motif','polypeptide_nest_right_left_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_polypeptides_different_start_and_stop','encodes_overlapping_polypeptides_different_start_and_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_gene','leucoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_rna','y_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_transcript','trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted','inverted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_regulatory_region','splicing_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('branch_site','branch_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_five','beta_bulge_loop_five'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakpoint','chromosome_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_uncertainty','sequence_uncertainty'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyl_n6_threonylcarbamoyladenosine','n6_methyl_n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_with_frameshift','gene_with_mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compositionally_biased_region_of_peptide','compositionally_biased_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_c_cluster','vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna','pirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_hoogsteen_base_pair','reverse_hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophanyl_trna','tryptophanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_primed_cdna_clone','polya_primed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_chromosome','leucoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('status','status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_retrotransposon','ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna','rnase_p_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conjugative_transposon','conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('improved_high_quality_draft','improved_high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_gain','copy_number_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linkage_group','linkage_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_trans_spliced_transcript','gene_with_trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl8_acceptor_site','sl8_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_coil','peptide_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine_trna_primary_transcript','pyrrolysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_c_cluster','v_vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_sequence','phage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_methylation_site','h3k79_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded','recoded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposon_fragment','transposon_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_c_cluster','vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_domain','editing_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyluridine','five_methylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_ii','centromere_dna_element_ii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alteration_attribute','alteration_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon_polymeric_tract','non_ltr_retrotransposon_polymeric_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transversion','transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan','tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recursive_splice_site','recursive_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_fusion','polypeptide_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator_binding_site','insulator_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_polyadenylation_variant','increased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline_trna_primary_transcript','proline_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_fragment','repeat_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blocked_reading_frame','blocked_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_snorna_primary_transcript','rrna_cleavage_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_isopentenyladenosine','n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_arginine','modified_l_arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_motif','polypeptide_conserved_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric','paracentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t3_rna_polymerase_promoter','t3_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_duplication','inversion_derived_bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_acceptor_site','trans_splice_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_2','a_box_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rre_rna','rre_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosyladenosine_phosphate','two_prime_o_riboA_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac_end','pac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extramembrane_polypeptide_region','extramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_change','copy_number_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein','intein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endosomal_localization_signal','endosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('twintron','twintron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_primary_transcript','scrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_prime_o_methyluridine','five_carboxymethylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('somatic_variant','somatic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication','duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_encoding','tmrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_cobalt_ion_contact_site','polypeptide_cobalt_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanked','flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion','inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ctg_start_codon','ctg_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine_trna_primary_transcript','tyrosine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('eukaryotic_terminator','eukaryotic_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_flanked','frt_flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron_region','spliceosomal_intron_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_region_of_exon','coding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_cdna_insert','cloned_cdna_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcription_rate_variant','decreased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_c_cluster','v_vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna_gene','rnase_p_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated','translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidyl_trna','histidyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sonicate_fragment','sonicate_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_recoded_mrna','gene_with_recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyluridine','two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cosmid','cosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_rna_interference','silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_missense_codon','non_conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna','snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript','mature_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridylation_guide_snorna','pseudouridylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_gene','c_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_transcript','processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed_gene','floxed_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spot_42_rna','spot_42_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_clone','cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site','cryptic_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_gene_segment','pseudogenic_gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr','three_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_ii_intron','group_ii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna_gene','rnase_mrp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_alteration','structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna_oligo','pna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_sequence','insertion_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('junction','junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous','paralogous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna','tna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_thiouridine','five_isopentenylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_tandem_repeat','nested_tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift','minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_three_prime_splice_site','non_canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_non_canonical_start_codon','gene_with_non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_rrna','pseudogenic_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_turn','serine_threonine_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene','j_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_trimethylation_site','h3k27_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_primary_transcript','strna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_eliminated_sequence','internal_eliminated_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded_gene','allelically_excluded_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('qtl','qtl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_est','three_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bred_motif','bred_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse','reverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_encoding','mirna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_2_prime_o_trimethylguanosine','n2_n2_2_prime_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_function_variant','translational_product_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternate_transcription_start_sites','encodes_alternate_transcription_start_sites'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array','gene_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetranucleotide_repeat_microsatellite_feature','tetranuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_aminomethyl_two_thiouridine','five_aminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_primary_transcript','monocistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snv','snv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct','direct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_genetic_element','mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_ligand_contact','polypeptide_ligand_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biomaterial_region','biomaterial_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_flanking_region','transposable_element_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symmetric_rna_internal_loop','symmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_1_frameshift','mrna_with_plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_regulated','transcriptionally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_intron','five_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_feature','vertebrate_immune_system_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine_methyl_ester','five_carboxyhydroxymethyl_uridine_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_transposition','chromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_gene','proplastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_trna_primary_transcript','serine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attp_site','attp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense','antisense'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat_element','terminal_inverted_repeat_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coiled_coil','coiled_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_cluster','v_vdj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_by_a_to_i_substitution','edited_transcript_by_a_to_i_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_primary_transcript','protein_coding_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mite','mite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site_variant','cryptic_splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion','insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('secis_element','secis_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle','maxicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss','tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pedigree_specific_variant','pedigree_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine','cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribothymidine','ribothymidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_adjacent_residues','non_adjacent_residues'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_modification','histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_ribosome_entry_site','internal_ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('outron','outron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_repeat','polypeptide_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_start','clone_insert_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attr_site','attr_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv3_motif','dmv3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_mrna','capped_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_rearrangement_feature','sequence_rearrangement_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_chromosome','apicoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_two','beta_turn_type_six_a_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated','invalidated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine','valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated_gene','translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_insertion','amino_acid_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_targeting_sequence','promoter_targeting_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polinton','polinton'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_tag','engineered_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_coding_exon_variant','non_coding_exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylcytidine','five_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl5_acceptor_site','sl5_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated','positively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridine','pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amplification_origin','amplification_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_insertional_duplication','unorient_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_constitutive','transcriptionally_constitutive'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extrachromosomal_mobile_genetic_element','extrachromosomal_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_origin','variant_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_region','utr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna','mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine','tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr1_motif','inr1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2b_ubiquitination_site','h2b_ubiquitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_acetyladenosine','n6_acetyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_splice_site','cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed','floxed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_two','beta_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_variant','utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_terminal_region','c_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_regulatory_region','transcription_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_leucine','modified_l_leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr_component','five_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acylation_region','histone_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_c_cluster','vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_part','chromosome_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptional_cis_regulatory_region','transcriptional_cis_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanyl_trna','phenylalanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_site','insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gc_rich_promoter_region','gc_rich_promoter_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_est_set','overlapping_est_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_two','asx_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon_loop','anticodon_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv5_motif','dmv5_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl1_acceptor_site','sl1_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_region','cds_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region_variant','regulatory_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_dimethylation_site','h3k9_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_gained','stop_gained'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna_gene','telomerase_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_c_cluster','v_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_insert','engineered_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_inverted_gene','recombinationally_inverted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microarray_oligo','microarray_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_array_member','cassette_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift_variant','plus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_snrna','u12_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_est_or_cdna','supported_by_est_or_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_10_signal','minus_10_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_end','clone_insert_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr_motif','inr_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_stem_loop_structure','three_prime_stem_loop_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rflp_fragment','rflp_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_rna_polymerase_promoter','phage_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_transition','pyrimidine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrinsically_unstructured_polypeptide_region','intrinsically_unstructured_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_2_prime_o_dimethylguanosine','n2_2_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_loss','exon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeal_intron','archaeal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna','lna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_junction','exon_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t7_rna_polymerase_promoter','t7_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_interchromosomal_transposition','invert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('episome','episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_insertional_duplication','uninvert_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free','free'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_difference','sequence_difference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k5_acylation_site','h4k5_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_c_cluster','v_d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_conflict','sequence_conflict'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nmd_transcript_variant','nmd_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_clone','tiling_path_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iii_intron','group_iii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_glycine','modified_glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_alteration','sequence_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyploid','polyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mathematically_defined_repeat','mathematically_defined_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_modification','gene_silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_cluster','v_vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine_trna_primary_transcript','isoleucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_small_subunit_primary_transcript','rrna_small_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_component','ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_framshift','plus_2_framshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_structure_variant','translational_product_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid_trna_primary_transcript','glutamic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_rearranged_at_dna_level','gene_rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript','edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_partial_processing','invalidated_by_partial_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_stability_variant','increased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequencing_primer','sequencing_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_for_gpi_anchor_region','cleaved_for_gpi_anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_cysteine','modified_l_cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr','five_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_recognition_site','restriction_enzyme_recognition_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_site','frt_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat','terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_i','centromere_dna_element_i'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transition','transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_junction','deletion_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_one','beta_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosylguanosine_phosphate','two_prime_o_ribosylguanosine_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyl_two_prime_o_methyluridine','five_cm_2_prime_o_methU'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_transcribed_spacer_region','internal_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic','dicistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_sequence_similarity','supported_by_sequence_similarity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_primer','reverse_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_three_prime_ltr_region','u3_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine_trna_primary_transcript','glutamine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_promoter','rnapol_ii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping','overlapping'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_beta_motif','alpha_beta_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_transposable_element','engineered_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward_primer','forward_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attctn_site','attctn_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_recombination_signal_sequence','five_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6_snrna','u6_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_gene','recombinationally_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_threonylcarbamoyladenosine','n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyluridine','five_carbamoylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_fragment','cds_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genome','genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_translational_product_level','increased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_level_variant','translational_product_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter','promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_gene','protein_coding_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_snrna','u5_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wybutosine','wybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylwyosine','methylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('large_subunit_rrna','large_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomally_aberrant_genome','chromosomally_aberrant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_2_prime_o_dimethylcytidine','n4_2_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition','c_to_t_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bidirectional_promoter','bidirectional_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated_cdna_clone','validated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('k_turn_rna_motif','k_turn_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_fragment','transcribed_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ust','five_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr_intron','three_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrogene','retrogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_to_purine_transversion','pyrimidine_to_purine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sine_element','sine_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_rst','five_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_intron','utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_transposition','interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_sequence_secondary_structure','rna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_in_transcript','complex_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element','engineered_foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_rna_viral_sequence','ds_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fosmid','fosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_substitution','complex_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated','validated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_snrna','u2_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication_attribute','duplication_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('caat_signal','caat_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_cluster','c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_region','consensus_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_spacer','vertebrate_immune_system_gene_recombination_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_restriction_enzyme_junction','three_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_trap_construct','gene_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_aptamer','rna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_induced','transcriptionally_induced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal','intrachromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_localization_signal','nuclear_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_region','rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site_part','inversion_site_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_frameshift variant','plus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('origin_of_replication','origin_of_replication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('standard_draft','standard_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_dimethylation_site','h3k79_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_internal_loop','rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ultracontig','ultracontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptidyl','peptidyl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_region','polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_region','epigenetically_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_insertion','transgenic_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_antiguide','mirna_antiguide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rearranged_at_dna_level','rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_variant','intergenic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_spacer','v_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strand_attribute','strand_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_lost','stop_lost'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced','alternatively_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formyl_two_prime_o_methylcytidine','five_formyl_two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_location','plasmid_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_bp_start_codon','four_bp_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcription_rate_variant','increased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged','recombinationally_rearranged'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_3d_structural_variant','complex_3d_structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chimeric_cdna_clone','chimeric_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna_primary_transcript','tasirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_transcript','gene_with_dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr_component','three_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retron','retron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autopolyploid','autopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine','phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translation_regulatory_region','translation_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transit_peptide','transit_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_deletion','amino_acid_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_28s','rrna_28s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylinosine','one_two_prime_o_dimethylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine','threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_minor_rna_motif','a_minor_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_cluster','j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce','dce'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quantitative_variant','quantitative_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysosomal_localization_signal','lysosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_cluster','d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_arm','chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast_gene','kinetoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('line_element','line_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('solo_ltr','solo_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('external_transcribed_spacer_region','external_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_transcribed_region','non_transcribed_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_stem','mirna_stem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_c_cluster','dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hyperploid','hyperploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic','cryptic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_acetylation_site','h3k9_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_helix','alpha_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion','fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_cluster','vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isowyosine','isowyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric_inversion','paracentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homing_endonuclease_binding_site','homing_endonuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna_oligo','tna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_gene','mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_fragment','restriction_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_pair','base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_antiparallel','inside_intron_antiparallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_binding_site','dna_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_cytidine','modified_cytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydrophobic_region_of_peptide','hydrophobic_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_primary_transcript','polycistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_proline','modified_l_proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_feature_set','overlapping_feature_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_two','asx_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_duplication','interchromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_loss','inframe_codon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('substitution','substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine','isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('functional_variant','functional_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_recoding_site','three_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_stability_variant','transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_upstream_variant','fivekb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_of_type_2_rnapol_iii_promoter','terminator_of_type_2_rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine_trna_primary_transcript','glycine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_variant','intron_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_outer_repeat_region','regional_centromere_outer_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replication_regulatory_region','replication_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mating_type_region','mating_type_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_heptamer','v_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dispersed_repeat','dispersed_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer','primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_domain','polypeptide_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type','wild_type'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion_gene','fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_function_variant','transcript_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_member_region','gene_member_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginyl_trna','arginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compensatory_transcript_secondary_structure_variant','compensatory_transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_base_feature','methylated_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_intrachromosomal_transposition','uninvert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_gene','scrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_18s','rrna_18s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_1','rnapol_iii_promoter_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_mutation','point_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudoknot','pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_quartet','g_quartet'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop','schellmann_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_selenocysteine','modified_l_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna','pna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon','three_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_gene','endogenous_retroviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_segment','vertebrate_immunoglobulin_t_cell_receptor_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_translational_bypass','mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_region','engineered_foreign_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_encoding','snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_est','five_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foldback_element','foldback_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_encoding','srp_rna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_c_cluster','d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_c_cluster','dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_ubiqitination_site','histone_ubiqitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_structural_alteration','complex_structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_encoding','rrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_codon_redefinition','mrna_recoded_by_codon_redefinition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyluridine','five_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_sequence','polya_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metabolic_island','metabolic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous','homologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('immature_peptide_region','immature_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2bk5_monomethylation_site','h2bk5_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_attribute','sequence_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sirna','sirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dart_marker','dart_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_motif','nucleotide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translationally_frameshifted','plus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_intron','trna_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_noncoding_exon','five_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_motif','dna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_strand','beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_oligo','ds_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyladenosine','one_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oxys_rna','oxys_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_motif','asx_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxyuridine','five_hydroxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_exon','coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translational_frameshift','plus_1_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formylcytidine','five_formylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_dimethylation_site','h3k27_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliced_leader_rna','spliced_leader_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_chromosome','mitochondrial_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fragment','gene_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_2prirme_o_trimethylguanosine','n2_7_2prirme_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift','frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide_cleavage_site','propeptide_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyldihydrouridine','five_methyldihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid','amino_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_breakpoint','translocation_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5_8s','rrna_5_8s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helix_turn_helix','helix_turn_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('simple_sequence_length_variation','simple_sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine','methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_loss_of_function_variant','polypeptide_loss_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_gene','transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('whole_genome_sequence_status','whole_genome_sequence_status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_island','genomic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_segment','gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_gene','snrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_region','engineered_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('common_variant','common_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptogene','cryptogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_noncoding_region','three_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_rna_interference','gene_silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_interchromosomal_transposition','d_interchr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_variant_site','natural_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly','assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('major_tss','major_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna','trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides','encodes_overlapping_peptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_conserved_region','nc_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('locus_control_region','locus_control_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna_oligo','s_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_chromosome','dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_b','beta_turn_type_six_b'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loss_of_heterozygosity','loss_of_heterozygosity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_gene','engineered_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wobble_base_pair','wobble_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_amino_acid_feature','modified_amino_acid_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_c_transition','t_to_c_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocaton_attribute','translocaton_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_sequence','apicoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_codon_variant','terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irlinv_site','irlinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_sequence','synthetic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_1_polypeptide','encodes_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iia_intron','group_iia_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomere','telomere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_intron','interior_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_mrna','edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_three','catmat_right_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_duplication','tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_gene','tmrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_region','pre_edited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_hydroxynorvalylcarbamoyladenosine','n6_hydroxynorvalylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_chromosome','nucleomorphic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragmentary','fragmentary'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single','single'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('binding_site','binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanine','seven_methylguanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('target_site_duplication','target_site_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_gene','vdj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_nucleic_acid','bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_localization_signal','peptide_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_four','catmat_right_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_acylation_site','h3k27_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome','compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_end','coding_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gap','gap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligand_binding_site','ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_aug_codon','upstream_aug_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_transcript','pseudogenic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('satellite_dna','satellite_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency_plus_duplication','assortment_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element','transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_sequence','endogenous_retroviral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microsatellite','microsatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_different_polypeptides_different_stop','encodes_different_polypeptides_different_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript','primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_mrna','consensus_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_peptide_loop','membrane_peptide_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign','so_foreign'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_independent_bacterial_terminator','rho_independent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u_box','u_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_deacetylation','gene_silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_c_cluster','vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cpg_island','cpg_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype','haplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylinosine','two_prime_o_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna','dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_rna_chromosome','circular_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_protein_region','mature_protein_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('b_box','b_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_zinc_ion_contact_site','polypeptide_zinc_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray_member','gene_subarray_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette','gene_cassette'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oric','oric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_breakpoint','deletion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_attribute','insertion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_2_frameshift','mrna_with_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chip_seq_region','chip_seq_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_one','asx_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_cluster','transcribed_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosyl_trna','tyrosyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous','orthologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna','s_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_three_prime_splice_site','canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_exon','noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lethal_variant','lethal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minor_tss','minor_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethylcytidine','five_two_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_trimethylation_site','h3k36_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_chromosome','macronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_translocation','deficient_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read_pair','read_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_with_translational_frameshift','transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('finished_genome','finished_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_3','rnapol_iii_promoter_type_3'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_transposon','dna_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orf','orf'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('right_handed_peptide_helix','right_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_left_right_motif','polypeptide_nest_left_right_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topology_attribute','topology_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirtron','mirtron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_motif','polypeptide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl9_acceptor_site','sl9_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_sequence','proplastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated_gene','negatively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retinoic_acid_responsive_element','retinoic_acid_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_encoding','c_d_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_assembly','sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_gene','chromoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dcaps_primer','dcaps_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_clip','five_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path','golden_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_acceptor_variant','splice_acceptor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine','alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_peptide_region','cleaved_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_cluster','v_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_region','pseudogenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_codon_variant','terminator_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna','methylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_c_cluster','v_vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_start_codon','non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_recoded_by_translational_bypass','gene_with_mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_turn_motif','polypeptide_turn_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autocatalytically_spliced_intron','autocatalytically_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile','mobile'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem','tandem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron','intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clip','clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dye_terminator_read','dye_terminator_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv4_motif','dmv4_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('au_rich_element','au_rich_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_breakpoint','inversion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_siii','dce_siii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_recoding_site','five_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_protein_coding','non_protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_intron','mobile_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment','vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_one','st_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna','rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_parallel','inside_intron_parallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron','spliceosomal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phagemid','phagemid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_block','editing_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragment_assembly','fragment_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_acceptor_piece','tmrna_acceptor_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six','beta_turn_type_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_rst','three_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine_trna_primary_transcript','cysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_gene','post_translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_repressed','transcriptionally_repressed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crm','crm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cointegrated_plasmid','cointegrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequencing_information','polypeptide_sequencing_information'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_spacer','three_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_fragment','tiling_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural','so_natural'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pi_helix','pi_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_base_call_error','possible_base_call_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_truncation','polypeptide_truncation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k14_acetylation_site','h3k14_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('adaptive_island','adaptive_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid','uridine_five_oxyacetic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl7_acceptor_site','sl7_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_translational_frameshift','plus_2_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_retained_variant','stop_retained_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous_region','homologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('500b_downstream_variant','fivehundred_b_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_utr','internal_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_cytoplasmic_polypeptide_region','non_cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature','experimental_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_chromosome','nuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar','exemplar'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_core_promoter','rnapol_ii_core_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_methylation_site','h3k9_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine_trna_primary_transcript','alanine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_variation','assortment_derived_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_dimethylguanosine','n2_n2_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_hook_turn','rna_hook_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_spacer_region','transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_gene','plasmid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna','u14_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('galactosyl_queuosine','galactosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_gene','cyanelle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type_rescue_gene','wild_type_rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_intron','u12_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aptamer','aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_mrna','recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_transposon','nested_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site_variant','tf_binding_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_sequence','macronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust','ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine','selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_c_terminal','elongated_out_of_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_mrna','gene_with_dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match_part','match_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_sequence','nucleomorphic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_gene','apicoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulon','regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_vector','plasmid_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tryptophan','modified_l_tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_chromosome_arm','free_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_primary_transcript','srp_rna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn','asx_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_binding_site','anchor_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript','rrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reading_frame','reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k23_acylation site','h3k23_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_variant','maternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dhu_loop','dhu_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetylcytidine','n4_acetylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature_attribute','experimental_feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_gene','silenced_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_genomic_insert','cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_gain','intron_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_sequence_secondary_structure','dna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_match','cdna_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_flanking_region','five_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysyl_trna','pyrrolysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_cis_hydroxyisopentenyl_adenosine','two_methylthio_n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_component','repeat_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyl_three_three_amino_three_carboxypropyl_pseudouridine','one_methyl_3_3_amino_three_carboxypropyl_pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rpra_rna','rpra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_sensitive_site','nuclease_sensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_amino_acid_substitution','conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_noncoding_region','five_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter','rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan_trna_primary_transcript','try_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncontiguous_finished','noncontiguous_finished'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('region','region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site','tf_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attl_site','attl_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_plasmid','natural_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upd','upd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_missense_codon','conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_dimethyladenosine','n6_n6_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('laevosynaptic_chromosome','laevosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_structural_element','chromosomal_structural_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_array','gene_cassette_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_gene_cluster','vertebrate_immunoglobulin_t_cell_receptor_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_five_prime_splice_site','canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_protein','bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts_map','sts_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnazyme','dnazyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silent_mutation','silent_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_cluster','v_d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distal_promoter_element','distal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_duplication','bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydroxywybutosine','hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dihydrouridine','dihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_coding_region','five_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_one','beta_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_trimethylation','h3k4_trimethylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_codon','recoded_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted','predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('resolution_site','resolution_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_cyano_seven_deazaguanosine','seven_cyano_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_associated_variant','disease_associated_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_switch','conformational_switch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulated','regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_repeat','inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_a_transversion','t_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attc_site','attc_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methyladenosine','two_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cross_genome_match','cross_genome_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_repeat','tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_loss','copy_number_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_primary_transcript','antisense_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_collection','sequence_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polyadenylated_mrna','gene_with_polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_i_promoter','rnapol_i_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methyluridine','three_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('start_codon','start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposon','retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_c_terminal','elongated_in_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene','v_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_dna','chloroplast_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negative_sense_ssrna_viral_sequence','negative_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_binding_site','primer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_box','c_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid','plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biological_region','biological_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_a_transition','g_to_a_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_five_prime_splice_site','non_canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_primary_transcript','c_d_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_region','trna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_cis_hydroxyisopentenyl_adenosine','n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_sequence','chloroplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_frequency','variant_frequency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_region','exon_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_five_prime_ltr_region','r_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_c_cluster','v_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_three_prime_ltr_region','r_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna','snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylinosine','one_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_gain','inframe_codon_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene_recombination_feature','j_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_motif','polypeptide_structural_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved_region','conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl3_acceptor_site','sl3_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('remark','remark'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fixed_variant','fixed_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_dna_contact','polypeptide_dna_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon','codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_23s','rrna_23s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_gain_of_function_variant','polypeptide_gain_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna','mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycyl_trna','glycyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_sequence','cyanelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_independently_known','cds_independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator','insulator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positive_sense_ssrna_viral_sequence','positive_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sticky_end_restriction_enzyme_cleavage_site','sticky_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_match','expressed_sequence_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_assembly_error','possible_assembly_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_snorna','u3_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_manganese_ion_contact_site','polypeptide_manganese_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k16_acylation_site','h4k16_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_t_transversion','g_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature_of_rearranged_gene','recombination_feature_of_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_coding_region','three_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_primary_transcript','tmrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_cdna','single_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_determined','experimentally_determined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_exon','pseudogenic_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_intron','u2_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome','chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternately_spliced_transcripts','encodes_alternately_spliced_transcripts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aberrant_processed_transcript','aberrant_processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_of_translational_product_variant','complex_change_of_translational_product_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna','gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dsra_rna','dsra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_domain','intron_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_predicted','cds_predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_asparagine','modified_l_asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_variant','inframe_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_nonamer','five_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl2_acceptor_site','sl2_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_localization_variant','polypeptide_localization_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_si','dce_si'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_primary_transcript','snrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation','translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_methylation_site','h3k27_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_phenylalanine','modified_l_phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna','lincrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_valine','modified_l_valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac','yac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('signal_peptide','signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_ltr_region','r_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_gene','srp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_n_terminal','elongated_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_hotspot','recombination_hotspot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_c_cluster','v_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('viral_sequence','viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_terminal_inverted_repeat','five_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_thiouridine','five_mcm_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited','edited'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('breu_motif','breu_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_start','coding_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_monomethylation_site','h3k9_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr','three_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe1_motif','dpe1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tyrosine','modified_l_tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_c_cluster','v_d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_methylation','silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_inversion','deficient_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_level_variant','decreased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiouridine','two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylation_variant','polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_iii_tata_box','rna_polymerase_iii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thio_two_prime_o_methyluridine','two_thio_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k18_acetylation_site','h3k18_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_sequence','leucoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds','cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_signal_sequence','polya_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_sequence','micronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamyl_trna','glutamyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_monomethylation_site','h3k27_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift_variant','minus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_gene','strna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted_gene','paternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_chromosome','rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm3_motif','ndm3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u1_snrna','u1_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxymethylcytidine','five_hydroxymethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature','recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_disjoint_polypeptides','encodes_disjoint_polypeptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated','post_translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_fusion_gene','engineered_fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_recombination_signal_sequence','three_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate','intermediate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_calcium_ion_contact_site','polypeptide_calcium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic_region','syntenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_collection','variant_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_donor','cryptic_splice_donor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_error_correction','assembly_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sugar_edge_base_pair','sugar_edge_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_gene','engineered_foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_monomethylation_site','h3k4_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetyl_2_prime_o_methylcytidine','n4_acetyl_2_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_by_ab_initio_computation','predicted_by_ab_initio_computation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_secondary_structure','polypeptide_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna_gene','ncrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_junction_loop','rna_junction_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype_block','haplotype_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oriv','oriv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_collection','peptide_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ambisense_ssrna_viral_sequence','ambisense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_oligo','morpholino_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere','centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_gene','epigenetically_modified_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_inversion','chromosomal_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_35_signal','minus_35_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_two_prime_o_dimethyluridine','three_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_thiouridine','four_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_end_site','transcription_end_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna_gene','pirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_mirna','pre_mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteinyl_trna','cysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_three','catmat_left_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_acceptor','cryptic_splice_acceptor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_seven','schellmann_loop_seven'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_c_cluster','v_vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_insertion_site','transposable_element_insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_element','translocation_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript_region','mirna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan_cds','orphan_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_mrna','monocistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_transposable_element','natural_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path_fragment','golden_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lipoprotein_signal_peptide','lipoprotein_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine','arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_rna_chromosome','linear_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k8_acylation site','h4k8_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_large_subunit_primary_transcript','rrna_large_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irrinv_site','irrinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_sequence','plastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_call_error_correction','base_call_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_plasmid','integrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_methionine','modified_l_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_rna_chromosome','linear_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_sequence','chromoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proximal_promoter_element','proximal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_read','contig_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_trap_construct','promoter_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_selenocysteine','stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanosine','seven_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn','gamma_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna','tmrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionyl_trna','methionyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synonymous_codon','synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna','cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl4_acceptor_site','sl4_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_binding_site','nuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid_methyl_ester','uridine_five_oxyacetic_acid_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_race_clone','three_prime_race_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_dna_chromosome','circular_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus','consensus'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated_gene','positively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss_region','tss_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_histidine','modified_l_histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unitary_pseudogene','unitary_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_metal_contact','polypeptide_metal_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integron','integron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_loop','d_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decayed_exon','decayed_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_signal_sequence','recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_inosine','modified_inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_three_prime_overlap','three_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_cluster','v_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_five_prime_overlap','three_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_regulatory_region','recombination_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop','beta_bulge_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_cleavage_junction','restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_junction','blunt_end_restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_region','intergenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv2_motif','dmv2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_mutation','intrachromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_rna','antisense_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_feature','sequence_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_glycinylcarbamoyladenosine','n6_glycinylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_classic','gamma_turn_classic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_cis_splice_site','three_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rapd','rapd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_ring_chromosome','inverted_ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cca_tail','cca_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_dna_chromosome','linear_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_five_prime_ltr_region','u5_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bruno_response_element','bruno_response_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_g_transversion','t_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_a_transversion','c_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronucleus_destined_segment','macronucleus_destined_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distant_three_prime_recoding_signal','distant_three_prime_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_mrna','pre_edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('p_element','p_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac','pac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fusion','gene_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base','base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_redefined','codon_redefined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_mrna','polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_variant','codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_prime_o_methyluridine','five_methoxycarbonylmethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match','match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_read_through','gene_with_stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparaginyl_trna','asparaginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonyl_trna','threonyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_five_prime_ltr_region','u3_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr','five_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_gene','vj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_dependent_bacterial_terminator','rho_dependent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_methylguanosine','n2_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_flanking_region','three_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomically_contaminated_cdna_clone','genomically_contaminated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_guide_sequence','internal_guide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_target_site','mirna_target_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_three_prime_ltr_region','u5_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('undermodified_hydroxywybutosine','undermodified_hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('introgressed_chromosome_region','introgressed_chromosome_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_frameshifted','translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced','trans_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna_primary_transcript','methylation_guide_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine','leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_deletion','chromosomal_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_uridine','five_isopentenylaminomethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon','stop_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_threonyl_carbamoyladenosine','two_methylthio_n6_threonyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_polyadenylation_variant','decreased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biochemical_region_of_peptide','biochemical_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interband','interband'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_constraint_sequence','dna_constraint_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert','clone_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snp','snp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_chromosome','chromoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_25s','rrna_25s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tata_box','tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_gene','plastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_one','asx_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_uridine','modified_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_sii','dce_sii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intramembrane_polypeptide_region','intramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysyl_trna','lysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rr_tract','rr_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript_region','rrna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k20_monomethylation_site','h4k20_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_dna_viral_sequence','ds_dna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced_transcript','alternatively_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_copper_ion_contact_site','polypeptide_copper_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_encoding','scrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_duplication','chromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone','clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_isoleucine','modified_l_isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray','gene_subarray'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hetero_compound_chromosome','hetero_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_transcript','dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_ligand_binding_site','inactive_ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_methylation','silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl6_acceptor_site','sl6_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_loop','t_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('targeting_vector','targeting_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiocytidine','two_thiocytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_serine','modified_l_serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna','srp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_repeat_recoding_signal','three_prime_repeat_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rate_of_transcription_variant','rate_of_transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylguanosine','two_prime_o_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_binding_motif','polypeptide_binding_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_vertebrate_immune_system_gene','recombinationally_rearranged_vertebrate_immune_system_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box','a_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_variant','splicing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylguanosine','one_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamine','modified_l_glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant','sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_length_variation','sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_encoding','strna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift','plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topologically_defined_region','topologically_defined_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_cds','edited_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_modification','gene_silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('e_box_motif','e_box_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_uniparental_disomy','paternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_subunit_rrna','small_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnasei_hypersensitive_site','dnasei_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_c_cluster','v_d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome_arm','compound_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('score','score'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('feature_attribute','feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_match','protein_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('downstream_gene_variant','downstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl10_accceptor_site','sl10_accceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_variation','chromosome_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_motif','serine_threonine_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_1','a_box_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded','allelically_excluded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_aneuploid','assortment_derived_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rare_variant','rare_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_prime_o_methyluridine','five_isopentenylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_central_core','regional_centromere_central_core'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna_oligo','gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_transcript_variant','nc_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_variation','copy_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced','silenced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylcytidine','three_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dexstrosynaptic_chromosome','dexstrosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_insertional_duplication','inverted_insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_mini_gene','rescue_mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_four','catmat_left_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternate_sequence_site','alternate_sequence_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_iron_ion_contact_site','polypeptide_iron_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition_at_pcpg_site','c_to_t_transition_at_pcpg_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_molybdenum_ion_contact_site','polypeptide_molybdenum_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine_trna_primary_transcript','phe_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_translational_product_level','decreased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_primary_transcript','h_aca_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna','r_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_sequence_variant','coding_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_partial_loss_of_function','polypeptide_partial_loss_of_function'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_restriction_enzyme_junction','five_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_transposition','intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_a','methylated_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_16s','rrna_16s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_causing_variant','disease_causing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_methylcytidine','n4_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('riboswitch','riboswitch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplicated_pseudogene','duplicated_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_duplication','assortment_derived_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_regulatory_element','chromosomal_regulatory_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_five_prime_overlap','five_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_function_variant','polypeptide_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozymic','ribozymic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_deficiency','inversion_derived_bipartite_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_contamination','invalidated_by_genomic_contamination'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_genome','variant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_cluster','vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_number_variation','chromosome_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_attribute','gene_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uag_stop_codon_signal','uag_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_match','nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_mirna_variant','mature_mirna_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_two','st_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified','epigenetically_modified'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_duplication','inversion_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_selenouridine','five_methylaminomethyl_two_selenouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid_trna_primary_transcript','aspartic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_mt_pseudogene','nuclear_mt_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exonic_splice_enhancer','exonic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4_snrna','u4_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('csrb_rsmb_rna','csrb_rsmb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_1_intron_homing_endonuclease_target_region','group_1_intron_homing_endonuclease_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crispr','crispr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_gene','snorna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_junction','trans_splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_three_prime_quadruplet_recoding_signal','flanking_three_prime_quadruplet_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_cluster','v_vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_pseudogene','cassette_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('incomplete_terminal_codon_variant','incomplete_terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_modification','silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_gene','proviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine','five_carboxyhydroxymethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mt_gene','mt_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_rna_chromosome','single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_stimulatory_region','recoding_stimulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyluridine','five_taurinomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_threonine','modified_l_threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_cluster','v_d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_oligo','synthetic_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_to_pyrimidine_transversion','purine_to_pyrimidine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_variant','editing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antiparallel_beta_strand','antiparallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('central_hydrophobic_region_of_signal_peptide','central_hydrophobic_region_of_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_mobile_genetic_element','integrated_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('parallel_beta_strand','parallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_cluster','v_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dre_motif','dre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon','non_ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna_oligo','r_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autoregulated','autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_lysine','modified_l_lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_end','bac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine','pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_quality_draft','high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine','lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide','elongated_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unique_variant','unique_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_protein_contact','protein_protein_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_attribute','inversion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_binding_site','nucleotide_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site','splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_synonymous_codon','non_synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_downstream_variant','fivekb_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_translocation','chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epitope','epitope'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allele','allele'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_n4_2_prime_o_trimethylcytidine','n4_n4_2_prime_o_trimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_ltr_region','u5_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paired_end_fragment','paired_end_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_gene','rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_transposable_element','transgenic_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_region','polypeptide_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts','sts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_c_transversion','a_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_ii_rna','class_ii_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nonamer_of_recombination_feature_of_vertebrate_immune_system_gene','nonamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unedited_region','unedited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lambda_vector','lambda_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene','gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanyl_trna','alanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_substitution','amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('virtual_sequence','virtual_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iib_intron','group_iib_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposed','retrotransposed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_2_frameshift','mrna_with_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymer_attribute','polymer_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autosynaptic_chromosome','autosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_helix','peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_processed_cdna_clone','partially_processed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst_match','rst_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted','paternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_gene','predicted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element_combinatorial_repeat','x_element_combinatorial_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('robertsonian_fusion','robertsonian_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylpseudouridine','two_prime_o_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric_inversion','pericentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartyl_trna','aspartyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna','strna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_intron','three_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear','linear'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_nonamer','j_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_t_transversion','a_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('idna','idna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_7_trimethylguanosine','n2_n2_7_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_chromosomal_mutation','complex_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_aneuploid','inversion_derived_deficiency_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_methylation_site','h3k4_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asymmetric_rna_internal_loop','asymmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion','deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_monomethylation_site','h3k79_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyclic_translocation','cyclic_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ars','ars'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutaminyl_trna','glutaminyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allopolyploid','allopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replicon','replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylcytidine','two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere','regional_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_one','st_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous_region','paralogous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript_region','mature_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_frameshift','mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reference_genome','reference_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_interchromosomal_transposition','unoriented_interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_cluster','d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle_gene','maxicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_two','st_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_encoding','snrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('annotation_directed_improved_draft','annotation_directed_improved_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_spacer','five_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read','read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine_trna_primary_transcript','arg_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo_u_tail','oligo_u_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_pseudoknot','recoding_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_thiouridine','five_mam_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic','monocistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3d_polypeptide_structure_variant','threed_polypeptide_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transmembrane_polypeptide_region','transmembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_processing_variant','transcript_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vector_replicon','vector_replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_uniparental_disomy','maternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrosequenced_read','pyrosequenced_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site_variant','splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_magnesium_ion_contact_site','polypeptide_magnesium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_transcript','polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_site','polya_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_variation_attribute','chromosomal_variation_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_duplication','free_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_structure_variation','chromosome_structure_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_rna_base_feature','modified_rna_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutated_variant_site','mutated_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gaga_motif','gaga_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromeric_repeat','centromeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_gene','rrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_mutation','interchromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prophage','prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic','syntenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_repetitive_element','engineered_foreign_repetitive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translated_nucleotide_match','translated_nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_variant','exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna','h_aca_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vault_rna','vault_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan','orphan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_dna_chromosome','linear_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomeric_repeat','telomeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_greater_than_1_polypeptide','encodes_greater_than_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('atti_site','atti_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_start_codon_cug','gene_with_start_codon_cug'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_deacetylation','silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reagent','reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_fission','chromosome_fission'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ct_gene','ct_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_primary_transcript','capped_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylinosine','methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_spacer','j_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine','glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_guanosine','modified_guanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_dimethylguanosine','n2_7_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_trimethylation_site','h3k79_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_heptamer','three_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_cdna_clone','invalidated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator','terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stem_loop','stem_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr_intron','five_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_intrachromosomal_transposition','unoriented_intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_band','chromosome_band'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_exon_donor_rna','mini_exon_donor_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid','aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyl_2_thiouridine','five_methyl_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_methylation','gene_silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element_gene','engineered_foreign_transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_pseudogene','processed_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supercontig','supercontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_encoding','trna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal_chromosomal_translocation','reciprocal_chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna','tasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hoogsteen_base_pair','hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_inner_repeat_region','regional_centromere_inner_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac_end','yac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_transition','purine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna','c_d_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_primary_transcript','snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_cluster','v_vj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_regulatory_region','intronic_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_ltr_region','u3_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attenuator','attenuator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_noncoding_exon','three_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna_primary_transcript','u14_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene_recombination_feature','d_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mte','mte'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gcvb_rna','gcvb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst','rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operator','operator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ring_chromosome','ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm2_motif','ndm2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_dimethylation_site','h3k4_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine_trna_primary_transcript','selenocysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_feature','edited_transcript_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_pyrrolysine','stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homo_compound_chromosome','homo_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_gene','foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_demethylwyosine','four_demethylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna','guide_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylpseudouridine','three_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_aneuploid_chromosome','inversion_derived_aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_stability_variant','decreased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna_gene','lincrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('specific_recombination_site','specific_recombination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inosine','inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_transposable_element','foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene','d_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_inversion','bipartite_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_plasmid','engineered_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group_regulatory_region','gene_group_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vd_gene','vd_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region','regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl11_acceptor_site','sl11_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna_region','guide_rna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_base','modified_base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_c_terminal','elongated_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_ten_helix','three_ten_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_n_terminal_elongation','elongated_in_frame_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sarcin_like_rna_motif','sarcin_like_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_translationally_frameshifted','minus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_alanine','modified_l_alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_cum_translocation','inversion_cum_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tag','tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_interchromosomal_transposition','uninvert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_gene','cryptic_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric','pericentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic','transgenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_clone','genomic_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakage_sequence','chromosome_breakage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_cluster','d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_one','beta_turn_type_six_a_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribosome_entry_site','ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('left_handed_peptide_helix','left_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_aptamer','dna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('i_motif','i_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_intrachromosomal_transposition','d_intrachr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_dna_chromosome','single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_c','methylated_c'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_end','clone_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligation_based_read','ligation_based_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_assembly','expressed_sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethyluridine','five_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine_trna_primary_transcript','histidine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous_region','orthologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine_trna_primary_transcript','valine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon_member','operon_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('missense_codon','missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma54','bacterial_rnapol_promoter_sigma54'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group','gene_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_regulatory_ncrna','small_regulatory_ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_duplication','intrachromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_amino_acid_substitution','non_conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uaa_stop_codon_signal','uaa_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_methylation_site','h3k36_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_variant','transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift','minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('organelle_sequence','organelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('initiator_codon_change','initiator_codon_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_prophage','cryptic_prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micf_rna','micf_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_tandem_duplication','direct_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved','conserved'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna','telomerase_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6atac_snrna','u6atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attb_site','attb_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array_member','gene_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated_mrna','polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symbiosis_island','symbiosis_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_variant','polymorphic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_junction','splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fingerprint_map','fingerprint_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_strand_restriction_enzyme_cleavage_site','single_strand_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wyosine','wyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uga_stop_codon_signal','uga_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_24_signal','minus_24_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cytoplasmic_polypeptide_region','cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k_acylation_region','h4k_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylguanosine','one_two_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rh_map','rh_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_modification','silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_catalytic_site','inactive_catalytic_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon','anticodon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_deazaguanosine','seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine','asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('probe','probe'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('defective_conjugative_transposon','defective_conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeosine','archaeosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('molecular_contact_region','molecular_contact_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_repeat','nested_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_structure','membrane_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_collection','contig_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetraloop','tetraloop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_conserved_region','coding_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('long_terminal_repeat','long_terminal_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_signal_feature','vertebrate_immune_system_gene_recombination_signal_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('untranslated_region_polycistronic_mrna','untranslated_region_polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine_trna_primary_transcript','leucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_identity_region','high_identity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_dna_chromosome','circular_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_rim_localization_signal','nuclear_rim_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucyl_trna','isoleucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_breakpoint','insertion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5_prime_utr_variant','five_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgene','transgene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_region','mrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_attribute','transcript_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_staple_motif','serine_threonine_staple_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding','protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_bound_by_factor','enhancer_bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_by_translational_bypass','recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon','operon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_transcript','monocistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal','reciprocal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated','polyadenylated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unigene_cluster','unigene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_gene_cluster','vertebrate_ig_t_cell_receptor_rearranged_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_member','gene_cassette_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_read_through','stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_transcript_with_translational_frameshift','gene_with_transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_quality','variant_quality'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mnp','mnp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid','glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_prime_element','y_prime_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn','beta_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pathogenic_island','pathogenic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust_match','ust_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_protein','transcript_bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyladenosine','n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_chromosome','cyanelle_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orit','orit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted','maternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_chromosome','chloroplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle_gene','minicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_catalytic_motif','polypeptide_catalytic_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_2','rnapol_iii_promoter_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('no_output','no_output'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_coding_exon','interior_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyl_two_thiouridine','five_taurinomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_trimethylation_site','h3k9_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_secondary_structure_variant','transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide','polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_5th_base_variant','splice_donor_5th_base_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymerase_synthesis_read','polymerase_synthesis_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_binding_site','enhancer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_to_protein_binding_site','nucleotide_to_protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_two','beta_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_polya_primed_cdna','invalidated_by_genomic_polya_primed_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_edited_transcript','gene_with_edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv1_motif','dmv1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_12_signal','minus_12_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_modified_region','post_translationally_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline','proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_region','flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_isopentenyladenosine','two_methylthio_n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypyrimidine_tract','polypyrimidine_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxyuridine','five_methoxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_to_gene_feature','gene_to_gene_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_cloned_genomic_insert','bac_cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_heptamer','j_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ust','three_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_2_prime_o_dimethyladenosine','n6_2_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_site','trans_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('de_novo_variant','de_novo_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_rescue_region','engineered_rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorph_gene','nucleomorph_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_attribute','mrna_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_three_prime_overlap','five_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_i_intron','group_i_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_cluster','d_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('open_chromatin_region','open_chromatin_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_dna','genomic_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron','inside_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hammerhead_ribozyme','hammerhead_ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_heptamer','five_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_splice_enhancer','intronic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_adenosine','modified_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyluridine','five_carboxymethylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_region','repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_unit','repeat_unit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_dna_chromosome','double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heritable_phenotypic_marker','heritable_phenotypic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('template_region','template_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript_region','primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_dna','mitochondrial_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_region','transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acetylation_site','histone_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozyme','ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('matrix_attachment_site','matrix_attachment_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('imprinted','imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequence_variant','polypeptide_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est','est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_motif','rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_variation_site','polypeptide_variation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_i_rna','class_i_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo','oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_signal','stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hypoploid','hypoploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar_mrna','exemplar_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_defined_binding_region','experimentally_defined_binding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_g_transversion','c_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('active_peptide','active_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mannosyl_queuosine','mannosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_pyrrolysine','gene_with_stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('queuosine','queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna_oligo','lna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('independently_known','independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_region','proviral_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped','capped'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift_variant','minus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direction_attribute','direction_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_chromosome','micronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene_by_unequal_crossing_over','pseudogene_by_unequal_crossing_over'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethyladenosine','one_two_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe_motif','dpe_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frame_restoring_variant','frame_restoring_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seryl_trna','seryl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_variant','structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_promoter_element','regulatory_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integration_excision_site','integration_excision_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_region_of_exon','noncoding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna','rnase_mrp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_export_signal','nuclear_export_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyluridine','five_methoxycarbonylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_of_single_exon_gene','exon_of_single_exon_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_primary_transcript','gene_with_dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_secondary_structure','sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma_70','bacterial_rnapol_promoter_sigma_70'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path','tiling_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_sequence','nuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig','contig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quality_value','quality_value'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kozak_sequence','kozak_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('population_specific_variant','population_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catalytic_residue','catalytic_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site','inversion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid','aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dif_site','dif_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_gene','mirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valyl_trna','valyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_tandem_duplication','inverted_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_regulatory_frameshift_element','cis_regulatory_frameshift_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minisatellite','minisatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_component','assembly_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity_region','low_complexity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_backbone','morpholino_backbone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('designed_sequence','designed_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_2_prime_o_trimethyladenosine','n6_n6_2_prime_o_trimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_promoter','rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene_recombination_feature','v_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_thiouridine','five_carboxymethylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_ring_duplication','free_ring_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_centromere','point_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_mrna','dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal','interchromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_chromosomal_mutation','uncharacterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_cis_splice_site','five_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('octamer_motif','octamer_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides_different_start','encodes_overlapping_peptides_different_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_rna_viral_sequence','ss_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('indel','indel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_primary_transcript','dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_binding_site','protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic','polycistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine_trna_primary_transcript','asparagine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_enhancer','splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid_chromosome','aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peroxywybutosine','peroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_aspartic_acid','modified_l_aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_episome','engineered_episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnai_reagent','rnai_reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rasirna','rasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_region','tmrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_level_variant','increased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter','bacterial_rnapol_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_sequence','mitochondrial_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trinucleotide_repeat_microsatellite_feature','trinuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_stability','post_translationally_regulated_by_protein_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_primary_transcript','nc_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('iron_responsive_element','iron_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_cluster','v_d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward','forward'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_location','proviral_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_binding_site','histone_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_element','promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pse_motif','pse_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_eight','beta_turn_type_eight'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double','double'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_est_or_cdna_data','cds_supported_by_est_or_cdna_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_rna_chromosome','double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamic_acid','modified_l_glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_motif','polypeptide_nest_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_frameshift','translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_terminal_inverted_repeat','three_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_trna','pseudogenic_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cap','cap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon','five_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic','enzymatic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_exon','interior_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genetic_marker','genetic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_g_transition','a_to_g_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine','two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isre','isre'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted_gene','maternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular','circular'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_pseudoknot','h_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate_element','intermediate_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript','transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene','pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_repeat','direct_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_terminator','bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('diplotype','diplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metal_binding_site','metal_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_gene','dj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyladenosine','two_prime_o_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_region_variant','splice_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspe_primer','aspe_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_binding_site','restriction_enzyme_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac','bac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_cluster','dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_dimethylation_site','h3k36_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_donor_site','trans_splice_donor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_variant','gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_change_variant','conformational_change_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_monomethylation_site','h3k36_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleic_acid','nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_chimeric_cdna','invalidated_by_chimeric_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine','histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_component_region','gene_component_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_match','primer_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_primary_transcript','trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loxp_site','loxp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine','serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide','propeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_open_reading_frame','five_prime_open_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_six','schellmann_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shine_dalgarno_sequence','shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sp6_rna_polymerase_promoter','sp6_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_iii','centromere_dna_element_iii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine_trna_primary_transcript','lysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_c_cluster','j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency','assortment_derived_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript','mirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5s','rrna_5s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucyl_trna','leucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_intrachromosomal_transposition','invert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic_rna','enzymatic_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('germline_variant','germline_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated','negatively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('benign_variant','benign_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_region','anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon','exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a','beta_turn_type_six_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('random_sequence','random_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_chromosomal_mutation','partially_characterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna','rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('core_promoter_element','core_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_single_strand_overhang','restriction_enzyme_single_strand_overhang'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_oligo','ss_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_methylation_site','histone_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_duplication_plus_aneuploid','inversion_derived_duplication_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_nucleic_acid','transcript_bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein_containing','intein_containing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_encoding','h_aca_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_rna','rrna_cleavage_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_trap_construct','enhancer_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_inverse','gamma_turn_inverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_nonamer','three_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_variant','paternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('level_of_transcript_variant','level_of_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteinyl_trna','selenocysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_methylation','gene_silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u11_snrna','u11_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna','scrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_selenocysteine','gene_with_stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silencer','silencer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sage_tag','sage_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_1_frameshift','mrna_with_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_gene','nuclear_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_domain_match_data','cds_supported_by_domain_match_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_shine_dalgarno_sequence','internal_shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prolyl_trna','prolyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysidine','lysidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge','beta_bulge'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_modification','post_translationally_regulated_by_protein_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_variant','splice_donor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna','ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_gene','grna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer','enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_sequence_variant','polymorphic_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_clip','three_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift_variant','frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional','insertional'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_processed_pseudogene','non_processed_pseudogene'); CREATE INDEX sequence_cv_lookup_table_idx ON sequence_cv_lookup_table (original_cvterm_name); SET search_path=public,pg_catalog; -- DEPENDENCY: -- chado/modules/bridges/sofa-bridge.sql -- The standard Chado pattern for protein coding genes -- is a feature of type 'gene' with 'mRNA' features as parts -- REQUIRES: 'mrna' view from so-bridge.sql CREATE OR REPLACE VIEW protein_coding_gene AS SELECT DISTINCT gene.* FROM feature AS gene INNER JOIN feature_relationship AS fr ON (gene.feature_id=fr.object_id) INNER JOIN so.mrna ON (mrna.feature_id=fr.subject_id); -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE SCHEMA frange; SET search_path = frange,public,pg_catalog; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public,pg_catalog; --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- 05-31-2011 -- added 'name' column to phenotype. non-unique human readable field. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, name TEXT default null, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- changes 2011-05-31 -- added type_id to genotype (can be null for backward compatibility) -- added genotypeprop table -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- ================================================ -- TABLE: genotypeprop -- ================================================ create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import contact from contact -- ================================================================= -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; -- ================================================ -- TABLE: projectprop -- ================================================ CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from project -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_cvterm -- ================================================ CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id integer not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_cvtermprop -- ================================================ create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- ================================================ -- TABLE: stock_dbxrefprop -- ================================================ create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; --replaced with Rob B's improved view CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, COALESCE(gffdbx.accession,'.'::varchar(255)), cv.name, fl.fmin+1, fl.fmax, COALESCE(CAST(af.significance AS text), '.'), CASE WHEN fl.strand=-1 THEN '-' WHEN fl.strand=1 THEN '+' ELSE '.' END, COALESCE(CAST(fl.phase AS text), '.'), f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''Ontology_term'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''Dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id UNION SELECT feature_id, ''Alias'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255),organism_id integer -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- -- OR, you could execute this command (the materialized view tool has been -- updated to allow this all to be supplied on the command line): -- -- (yes, it's all one really long line, to make copy and pasting easier) -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer" --sql_query "SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "create index all_feature_names_lower_name on all_feature_names (lower(name))" --yes -- -- -- OR, even more complicated, you could use this command to create a materialized view -- for use with full text searching on PostgreSQL 8.4 or better: -- -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer,searchable_name tsvector" --sql_query "SELECT feature_id, CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255)) AS name, organism_id, to_tsvector('english', CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM feature UNION SELECT feature_id, name, organism_id, to_tsvector('english', name) AS searchable_name FROM feature WHERE name IS NOT NULL UNION SELECT fs.feature_id, s.name, f.organism_id, to_tsvector('english', s.name) AS searchable_name FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255)) AS name, f.organism_id, to_tsvector('english',CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id,to_tsvector('english',d.accession) AS searchable_name FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "CREATE INDEX searchable_all_feature_names_idx ON all_feature_names USING gin(searchable_name)" --yes -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/modules/expression/000755 000765 000024 00000000000 12061672375 016452 5ustar00cainstaff000000 000000 chado-1.23/modules/extension.modules000644 000765 000024 00000000247 11256710154 017655 0ustar00cainstaff000000 000000 contact/contact.sql expression/rad.sql expression/rad.views sequence/gff-bridge/sequence-gff-views.sql #sequence/bdgp/bdgp-views.sql #pathway/pathway.sql #www/www.sql chado-1.23/modules/function.modules000644 000765 000024 00000000270 11256710154 017462 0ustar00cainstaff000000 000000 sequence/gff-bridge/sequence-gff-funcs.pgsql sequence/functions/feature_subalignments.plpgsql sequence/functions/get_sub_feature_ids.plpgsql sequence/apollo-bridge/apollo-triggers.sql chado-1.23/modules/general/000755 000765 000024 00000000000 12061672375 015670 5ustar00cainstaff000000 000000 chado-1.23/modules/genetic/000755 000765 000024 00000000000 12061672375 015671 5ustar00cainstaff000000 000000 chado-1.23/modules/idb-full.modules000644 000765 000024 00000000302 11256710154 017327 0ustar00cainstaff000000 000000 general/general.sql cv/cv.sql organism/organism.sql pub/pub.sql sequence/sequence.sql genetic/genetic.sql companalysis/companalysis.sql expression/expression.sql map/map.sql library/library.sql chado-1.23/modules/library/000755 000765 000024 00000000000 12061672376 015720 5ustar00cainstaff000000 000000 chado-1.23/modules/mage/000755 000765 000024 00000000000 12061672375 015164 5ustar00cainstaff000000 000000 chado-1.23/modules/map/000755 000765 000024 00000000000 12061672376 015031 5ustar00cainstaff000000 000000 chado-1.23/modules/module-tables.json000644 000765 000024 00000011407 11477500723 017703 0ustar00cainstaff000000 000000 { "modules" : [ { "module" : "General", "tables" : [ "tableinfo", "db", "dbxref", "dbxrefprop" ] }, { "module" : "CV", "tables" : [ "cv", "cvterm", "cvterm_relationship", "cvtermpath", "cvtermsynonym", "cvterm_dbxref", "cvtermprop" ] }, { "module" : "Publication", "tables" : [ "pub", "pub_relationship", "pub_dbxref", "pubauthor", "pubprop" ] }, { "module" : "Organism", "tables" : [ "organism", "organism_dbxref", "organismprop" ] }, { "module" : "Sequence", "tables" : [ "feature", "featureloc", "featureloc_pub", "feature_pub", "feature_pubprop", "featureprop", "featureprop_pub", "feature_dbxref", "feature_relationship", "feature_relationship_pub", "feature_relationshipprop", "feature_relationshipprop_pub", "feature_cvterm", "feature_cvtermprop", "feature_cvterm_dbxref", "feature_cvterm_pub", "featuregroup", "synonym", "feature_synonym", "gencode", "gencode_codon_aa", "gencode_startcodon" ] }, { "module" : "Companalysis", "tables" : [ "analysis", "analysisprop", "analysisfeature", "analysisfeatureprop" ] }, { "module" : "Cell Line", "tables" : [ "cell_line", "cell_line_relationship", "cell_line_synonym", "cell_line_cvterm", "cell_line_dbxref", "cell_lineprop", "cell_lineprop_pub", "cell_line_feature", "cell_line_cvtermprop", "cell_line_pub", "cell_line_library" ] }, { "module" : "Contact", "tables" : [ "contact", "contact_relationship" ] }, { "module" : "Expression", "tables" : [ "expression", "expression_cvterm", "expression_cvtermprop", "expressionprop", "expression_pub", "feature_expression", "feature_expressionprop", "eimage", "expression_image" ] }, { "module" : "Genetic", "tables" : [ "genotype", "feature_genotype", "environment", "environment_cvterm", "phenstatement", "phendesc", "phenotype_comparison", "phenotype_comparison_cvterm" ] }, { "module" : "Library", "tables" : [ "library", "library_synonym", "library_pub", "libraryprop", "libraryprop_pub", "library_cvterm", "library_feature", "library_dbxref" ] }, { "module" : "Mage", "tables" : [ "mageml", "magedocumentation", "protocol", "protocolparam", "channel", "arraydesign", "arraydesignprop", "assay", "assayprop", "assay_project", "biomaterial", "biomaterial_relationship", "biomaterialprop", "biomaterial_dbxref", "treatment", "biomaterial_treatment", "assay_biomaterial", "acquisition", "acquisitionprop", "acquisition_relationship", "quantification", "quantificationprop", "quantification_relationship", "control", "element", "elementresult", "element_relationship", "elementresult_relationship", "study", "study_assay", "studydesign", "studydesignprop", "studyfactor", "studyfactorvalue", "studyprop", "studyprop_feature" ] }, { "module" : "Map", "tables" : [ "featuremap", "featurerange", "featurepos", "featuremap_pub" ] }, { "module" : "Natural Diversity", "tables" : [ "nd_geolocation", "nd_experiment", "nd_experiment_project", "nd_experimentprop", "nd_experiment_pub", "nd_geolocationprop", "nd_protocol", "nd_reagent", "nd_protocol_reagent", "nd_protocolprop", "nd_experiment_stock", "nd_experiment_protocol", "nd_experiment_phenotype", "nd_experiment_genotype", "nd_reagent_relationship", "nd_reagentprop", "nd_experiment_stockprop", "nd_experiment_stock_dbxref", "nd_experiment_dbxref", "nd_experiment_contact" ] }, { "module" : "Phenotype", "tables" : [ "phenotype", "phenotype_cvterm", "feature_phenotype" ] }, { "module" : "Phylogeny", "tables" : [ "phylotree", "phylotree_pub", "phylonode", "phylonode_dbxref", "phylonode_pub", "phylonode_organism", "phylonodeprop", "phylonode_relationship" ] }, { "module" : "Project", "tables" : [ "project", "projectprop", "project_relationship", "project_pub", "project_contact" ] }, { "module" : "Stock", "tables" : [ "stock", "stock_pub", "stockprop", "stockprop_pub", "stock_relationship", "stock_relationship_cvterm", "stock_relationship_pub", "stock_dbxref", "stock_cvterm", "stock_genotype", "stockcollection", "stockcollectionprop", "stockcollection_stock", "stock_dbxrefprop" ] }, { "module" : "Internal", "tables" : [ "materialized_view", "sequence_cv_lookup_table" ] } ] }chado-1.23/modules/natural_diversity/000755 000765 000024 00000000000 12061672375 020023 5ustar00cainstaff000000 000000 chado-1.23/modules/nofuncs.html000644 000765 000024 00002432031 11634146576 016625 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

tableinfo
db
dbxref
cv
cvterm
cvterm_relationship
cvtermpath
cvtermsynonym
cvterm_dbxref
cvtermprop
dbxrefprop
cvprop
chadoprop
pub
pub_relationship
pub_dbxref
pubauthor
pubprop
organism
organism_dbxref
organismprop
feature
featureloc
featureloc_pub
feature_pub
feature_pubprop
featureprop
featureprop_pub
feature_dbxref
feature_relationship
feature_relationship_pub
feature_relationshipprop
feature_relationshipprop_pub
feature_cvterm
feature_cvtermprop
feature_cvterm_dbxref
feature_cvterm_pub
synonym
feature_synonym
analysis
analysisprop
analysisfeature
analysisfeatureprop
phenotype
phenotype_cvterm
feature_phenotype
genotype
feature_genotype
environment
environment_cvterm
phenstatement
phendesc
phenotype_comparison
phenotype_comparison_cvterm
genotypeprop
featuremap
featurerange
featurepos
featuremap_pub
phylotree
phylotree_pub
phylonode
phylonode_dbxref
phylonode_pub
phylonode_organism
phylonodeprop
phylonode_relationship
contact
contact_relationship
expression
expression_cvterm
expression_cvtermprop
expressionprop
expression_pub
feature_expression
feature_expressionprop
eimage
expression_image
project
projectprop
project_relationship
project_pub
project_contact
mageml
magedocumentation
protocol
protocolparam
channel
arraydesign
arraydesignprop
assay
assayprop
assay_project
biomaterial
biomaterial_relationship
biomaterialprop
biomaterial_dbxref
treatment
biomaterial_treatment
assay_biomaterial
acquisition
acquisitionprop
acquisition_relationship
quantification
quantificationprop
quantification_relationship
control
element
elementresult
element_relationship
elementresult_relationship
study
study_assay
studydesign
studydesignprop
studyfactor
studyfactorvalue
studyprop
studyprop_feature
stock
stock_pub
stockprop
stockprop_pub
stock_relationship
stock_relationship_cvterm
stock_relationship_pub
stock_dbxref
stock_cvterm
stock_cvtermprop
stock_genotype
stockcollection
stockcollectionprop
stockcollection_stock
stock_dbxrefprop
library
library_synonym
library_pub
libraryprop
libraryprop_pub
library_cvterm
library_feature
library_dbxref
cell_line
cell_line_relationship
cell_line_synonym
cell_line_cvterm
cell_line_dbxref
cell_lineprop
cell_lineprop_pub
cell_line_feature
cell_line_cvtermprop
cell_line_pub
cell_line_library
nd_geolocation
nd_experiment
nd_experiment_project
nd_experimentprop
nd_experiment_pub
nd_geolocationprop
nd_protocol
nd_reagent
nd_protocol_reagent
nd_protocolprop
nd_experiment_stock
nd_experiment_protocol
nd_experiment_phenotype
nd_experiment_genotype
nd_reagent_relationship
nd_reagentprop
nd_experiment_stockprop
nd_experiment_stock_dbxref
nd_experiment_dbxref
nd_experiment_contact

tableinfo

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$Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $
==========================================
Chado general module
================================================
TABLE: tableinfo
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
tableinfo_id integer 11 PRIMARY KEY, NOT NULL
name varchar 30 UNIQUE, NOT NULL
primary_key_column varchar 30 NULL
is_view integer 10 0 NOT NULL
view_on_table_id integer 10 NULL
superclass_table_id integer 10 NULL
is_updateable integer 10 1 NOT NULL
modification_date date 0 now() NOT NULL

Constraints

Type Fields
NOT NULL tableinfo_id
NOT NULL name
NOT NULL is_view
NOT NULL is_updateable
NOT NULL modification_date
UNIQUE name

db

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================================================
TABLE: db
================================================
A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.
Field Name Data Type Size Default Value Other Foreign Key
db_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL contact_id int,
urlprefix varchar 255 NULL
url varchar 255 NULL

Constraints

Type Fields
NOT NULL db_id
NOT NULL name
UNIQUE name

dbxref

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================================================
TABLE: dbxref
================================================
A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.
Field Name Data Type Size Default Value Other Foreign Key
dbxref_id integer 11 PRIMARY KEY, NOT NULL
db_id integer 10 UNIQUE, NOT NULL db.db_id
accession varchar 255 UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version varchar 255 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
dbxref_idx1 db_id
dbxref_idx2 accession
dbxref_idx3 version

Constraints

Type Fields
NOT NULL dbxref_id
NOT NULL db_id
FOREIGN KEY db_id
NOT NULL accession
NOT NULL version
UNIQUE db_id, accession, version

cv

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Comments:

$Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $
==========================================
Chado cv module
=================================================================
Dependencies:
:import dbxref from general
=================================================================
================================================
TABLE: cv
================================================
A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.
Field Name Data Type Size Default Value Other Foreign Key
cv_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.
definition text 64000 A text description of the criteria for membership of this ontology.

Constraints

Type Fields
NOT NULL cv_id
NOT NULL name
UNIQUE name

cvterm

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================================================
TABLE: cvterm
================================================
A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_id integer 11 PRIMARY KEY, NOT NULL
cv_id integer 10 UNIQUE, NOT NULL, The cv or ontology or namespace to which this cvterm belongs. cv.cv_id
name varchar 1024 UNIQUE, NOT NULL, A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.
definition text 64000 A human-readable text definition.
dbxref_id integer 10 UNIQUE, NOT NULL, Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref. dbxref.dbxref_id
is_obsolete integer 10 0 UNIQUE, NOT NULL, Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.
is_relationshiptype integer 10 0 NOT NULL, Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.

Indices

Name Fields
cvterm_idx1 cv_id
cvterm_idx2 name
cvterm_idx3 dbxref_id

Constraints

Type Fields
NOT NULL cvterm_id
NOT NULL cv_id
FOREIGN KEY cv_id
NOT NULL name
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_obsolete
NOT NULL is_relationshiptype
UNIQUE name, cv_id, is_obsolete
UNIQUE dbxref_id

cvterm_relationship

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Comments:

A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.
The OBO identifier is globally unique.
================================================
TABLE: cvterm_relationship
================================================
A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".
Field Name Data Type Size Default Value Other Foreign Key
cvterm_relationship_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node. cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node. cvterm.cvterm_id

Indices

Name Fields
cvterm_relationship_idx1 type_id
cvterm_relationship_idx2 subject_id
cvterm_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL cvterm_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

cvtermpath

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================================================
TABLE: cvtermpath
================================================
The reflexive transitive closure of the cvterm_relationship relation.
Field Name Data Type Size Default Value Other Foreign Key
cvtermpath_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
cv_id integer 10 NOT NULL, Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm. cv.cv_id
pathdistance integer 10 UNIQUE, The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).

Indices

Name Fields
cvtermpath_idx1 type_id
cvtermpath_idx2 subject_id
cvtermpath_idx3 object_id
cvtermpath_idx4 cv_id

Constraints

Type Fields
NOT NULL cvtermpath_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL cv_id
FOREIGN KEY cv_id
UNIQUE subject_id, object_id, type_id, pathdistance

cvtermsynonym

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================================================
TABLE: cvtermsynonym
================================================
A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".
Field Name Data Type Size Default Value Other Foreign Key
cvtermsynonym_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
synonym varchar 1024 UNIQUE, NOT NULL
type_id integer 10 A synonym can be exact, narrower, or broader than. cvterm.cvterm_id

Indices

Name Fields
cvtermsynonym_idx1 cvterm_id

Constraints

Type Fields
NOT NULL cvtermsynonym_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL synonym
FOREIGN KEY type_id
UNIQUE cvterm_id, synonym

cvterm_dbxref

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================================================
TABLE: cvterm_dbxref
================================================
In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_dbxref_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_for_definition integer 10 0 NOT NULL, A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.

Indices

Name Fields
cvterm_dbxref_idx1 cvterm_id
cvterm_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL cvterm_dbxref_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_for_definition
UNIQUE cvterm_id, dbxref_id

cvtermprop

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================================================
TABLE: cvtermprop
================================================
Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
Field Name Data Type Size Default Value Other Foreign Key
cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL, The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
cvtermprop_idx1 cvterm_id
cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL cvtermprop_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE cvterm_id, type_id, value, rank

dbxrefprop

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================================================
TABLE: dbxrefprop
================================================
Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.
Field Name Data Type Size Default Value Other Foreign Key
dbxrefprop_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
dbxrefprop_idx1 dbxref_id
dbxrefprop_idx2 type_id

Constraints

Type Fields
NOT NULL dbxrefprop_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE dbxref_id, type_id, rank

cvprop

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================================================
TABLE: cvprop
================================================
Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version
Field Name Data Type Size Default Value Other Foreign Key
cvprop_id integer 11 PRIMARY KEY, NOT NULL
cv_id integer 10 UNIQUE, NOT NULL cv.cv_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULL cvprop_id
NOT NULL cv_id
FOREIGN KEY cv_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cv_id, type_id, rank

chadoprop

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================================================
TABLE: chadoprop
================================================
This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version
Field Name Data Type Size Default Value Other Foreign Key
chadoprop_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULL chadoprop_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE type_id, rank

pub

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Comments:

$Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $
==========================================
Chado pub module
=================================================================
Dependencies:
:import cvterm from cv
:import dbxref from general
=================================================================
================================================
TABLE: pub
================================================
A documented provenance artefact - publications, documents, personal communication.
Field Name Data Type Size Default Value Other Foreign Key
pub_id integer 11 PRIMARY KEY, NOT NULL
title text 64000 Descriptive general heading.
volumetitle text 64000 Title of part if one of a series.
volume varchar 255
series_name varchar 255 Full name of (journal) series.
issue varchar 255
pyear varchar 255
pages varchar 255 Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 10 NOT NULL, The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. cvterm.cvterm_id
is_obsolete boolean 0 false
publisher varchar 255
pubplace varchar 255

Indices

Name Fields
pub_idx1 type_id

Constraints

Type Fields
NOT NULL pub_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE uniquename

pub_relationship

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================================================
TABLE: pub_relationship
================================================
Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.
Field Name Data Type Size Default Value Other Foreign Key
pub_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL pub.pub_id
object_id integer 10 UNIQUE, NOT NULL pub.pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
pub_relationship_idx1 subject_id
pub_relationship_idx2 object_id
pub_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL pub_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_id, object_id, type_id

pub_dbxref

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================================================
TABLE: pub_dbxref
================================================
Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...
Field Name Data Type Size Default Value Other Foreign Key
pub_dbxref_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
pub_dbxref_idx1 pub_id
pub_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL pub_dbxref_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE pub_id, dbxref_id

pubauthor

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================================================
TABLE: pubauthor
================================================
An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.
Field Name Data Type Size Default Value Other Foreign Key
pubauthor_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
rank integer 10 UNIQUE, NOT NULL, Order of author in author list for this pub - order is important.
editor boolean 0 false Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.
surname varchar 100 NOT NULL
givennames varchar 100 First name, initials
suffix varchar 100 Jr., Sr., etc

Indices

Name Fields
pubauthor_idx2 pub_id

Constraints

Type Fields
NOT NULL pubauthor_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
NOT NULL surname
UNIQUE pub_id, rank

pubprop

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================================================
TABLE: pubprop
================================================
Property-value pairs for a pub. Follows standard chado pattern.
Field Name Data Type Size Default Value Other Foreign Key
pubprop_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 UNIQUE

Indices

Name Fields
pubprop_idx1 pub_id
pubprop_idx2 type_id

Constraints

Type Fields
NOT NULL pubprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
UNIQUE pub_id, type_id, rank

organism

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$Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $
==========================================
Chado organism module
============
DEPENDENCIES
============
:import cvterm from cv
:import dbxref from general
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: organism
================================================
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
Field Name Data Type Size Default Value Other Foreign Key
organism_id integer 11 PRIMARY KEY, NOT NULL
abbreviation varchar 255 NULL
genus varchar 255 UNIQUE, NOT NULL
species varchar 255 UNIQUE, NOT NULL, A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.
common_name varchar 255 NULL
comment text 64000 NULL

Constraints

Type Fields
NOT NULL organism_id
NOT NULL genus
NOT NULL species
UNIQUE genus, species

organism_dbxref

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TABLE: organism_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
organism_dbxref_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
organism_dbxref_idx1 organism_id
organism_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL organism_dbxref_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE organism_id, dbxref_id

organismprop

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TABLE: organismprop
================================================
Tag-value properties - follows standard chado model.
Field Name Data Type Size Default Value Other Foreign Key
organismprop_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
organismprop_idx1 organism_id
organismprop_idx2 type_id

Constraints

Type Fields
NOT NULL organismprop_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE organism_id, type_id, rank

feature

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$Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $
==========================================
Chado sequence module
=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from general
=================================================================
================================================
TABLE: feature
================================================
A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.
Field Name Data Type Size Default Value Other Foreign Key
feature_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref. dbxref.dbxref_id
organism_id integer 10 UNIQUE, NOT NULL, The organism to which this feature belongs. This column is mandatory. organism.organism_id
name varchar 255 The optional human-readable common name for a feature, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.
residues text 64000 A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.
seqlen integer 10 The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.
md5checksum char 32 The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.
type_id integer 10 UNIQUE, NOT NULL, A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table. cvterm.cvterm_id
is_analysis boolean 0 false NOT NULL, Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.
is_obsolete boolean 0 false NOT NULL, Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.
timeaccessioned timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.
timelastmodified timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.

Indices

Name Fields
feature_name_ind1 name
feature_idx1 dbxref_id
feature_idx2 organism_id
feature_idx3 type_id
feature_idx4 uniquename

Constraints

Type Fields
NOT NULL feature_id
FOREIGN KEY dbxref_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_analysis
NOT NULL is_obsolete
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE organism_id, uniquename, type_id

featureloc

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COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified
by the combination of organism, uniquename and feature type';
================================================
TABLE: featureloc
================================================
The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL, The feature that is being located. Any feature can have zero or more featurelocs. feature.feature_id
srcfeature_id integer 10 The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph. feature.feature_id
fmin integer 10 The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.
is_fmin_partial boolean 0 false NOT NULL, This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.
fmax integer 10 The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).
is_fmax_partial boolean 0 false NOT NULL, This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.
strand integer 5 The orientation/directionality of the location. Should be 0, -1 or +1.
phase integer 10 Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.
residue_info text 64000 Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.
locgroup integer 10 0 UNIQUE, NOT NULL, This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).
rank integer 10 0 UNIQUE, NOT NULL, Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.

Indices

Name Fields
featureloc_idx1 feature_id
featureloc_idx2 srcfeature_id
featureloc_idx3 srcfeature_id, fmin, fmax

Constraints

Type Fields
NOT NULL featureloc_id
NOT NULL feature_id
FOREIGN KEY feature_id
FOREIGN KEY srcfeature_id
NOT NULL is_fmin_partial
NOT NULL is_fmax_partial
NOT NULL locgroup
NOT NULL rank
UNIQUE feature_id, locgroup, rank
CHECK

featureloc_pub

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COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely
partition locations for any one feature';
================================================
TABLE: featureloc_pub
================================================
Provenance of featureloc. Linking table between featurelocs and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_pub_id integer 11 PRIMARY KEY, NOT NULL
featureloc_id integer 10 UNIQUE, NOT NULL featureloc.featureloc_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureloc_pub_idx1 featureloc_id
featureloc_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featureloc_pub_id
NOT NULL featureloc_id
FOREIGN KEY featureloc_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE featureloc_id, pub_id

feature_pub

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TABLE: feature_pub
================================================
Provenance. Linking table between features and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
feature_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_pub_idx1 feature_id
feature_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_pub_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_id, pub_id

feature_pubprop

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================================================
TABLE: feature_pubprop
================================================
Property or attribute of a feature_pub link.
Field Name Data Type Size Default Value Other Foreign Key
feature_pubprop_id integer 11 PRIMARY KEY, NOT NULL
feature_pub_id integer 10 UNIQUE, NOT NULL feature_pub.feature_pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_pubprop_idx1 feature_pub_id

Constraints

Type Fields
NOT NULL feature_pubprop_id
NOT NULL feature_pub_id
FOREIGN KEY feature_pub_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_pub_id, type_id, rank

featureprop

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================================================
TABLE: featureprop
================================================
A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used

Indices

Name Fields
featureprop_idx1 feature_id
featureprop_idx2 type_id

Constraints

Type Fields
NOT NULL featureprop_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_id, type_id, rank

featureprop_pub

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Comments:

For any one feature, multivalued property-value pairs must be differentiated by rank.
================================================
TABLE: featureprop_pub
================================================
Provenance. Any featureprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_pub_id integer 11 PRIMARY KEY, NOT NULL
featureprop_id integer 10 UNIQUE, NOT NULL featureprop.featureprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureprop_pub_idx1 featureprop_id
featureprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featureprop_pub_id
NOT NULL featureprop_id
FOREIGN KEY featureprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE featureprop_id, pub_id

feature_dbxref

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TABLE: feature_dbxref
================================================
Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.
Field Name Data Type Size Default Value Other Foreign Key
feature_dbxref_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false

Indices

Name Fields
feature_dbxref_idx1 feature_id
feature_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL feature_dbxref_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE feature_id, dbxref_id

feature_relationship

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================================================
TABLE: feature_relationship
================================================
Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. This is typically the subfeature. feature.feature_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. This is typically the container feature. feature.feature_id
type_id integer 10 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology. cvterm.cvterm_id
value text 64000 NULL Additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.

Indices

Name Fields
feature_relationship_idx1 subject_id
feature_relationship_idx2 object_id
feature_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL feature_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

feature_relationship_pub

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Comments:

================================================
TABLE: feature_relationship_pub
================================================
Provenance. Attach optional evidence to a feature_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_relationship_id integer 10 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationship_pub_idx1 feature_relationship_id
feature_relationship_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_relationship_pub_id
NOT NULL feature_relationship_id
FOREIGN KEY feature_relationship_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_relationship_id, pub_id

feature_relationshipprop

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Comments:

================================================
TABLE: feature_relationshipprop
================================================
Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_id integer 11 PRIMARY KEY, NOT NULL
feature_relationship_id integer 10 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_relationshipprop_idx1 feature_relationship_id
feature_relationshipprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_relationshipprop_id
NOT NULL feature_relationship_id
FOREIGN KEY feature_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_relationship_id, type_id, rank

feature_relationshipprop_pub

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Comments:

================================================
TABLE: feature_relationshipprop_pub
================================================
Provenance for feature_relationshipprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_relationshipprop_id integer 10 UNIQUE, NOT NULL feature_relationshipprop.feature_relationshipprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationshipprop_pub_idx1 feature_relationshipprop_id
feature_relationshipprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_relationshipprop_pub_id
NOT NULL feature_relationshipprop_id
FOREIGN KEY feature_relationshipprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_relationshipprop_id, pub_id

feature_cvterm

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Comments:

================================================
TABLE: feature_cvterm
================================================
Associate a term from a cv with a feature, for example, GO annotation.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL, Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref. pub.pub_id
is_not boolean 0 false NOT NULL, If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_cvterm_idx1 feature_id
feature_cvterm_idx2 cvterm_id
feature_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_cvterm_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_not
NOT NULL rank
UNIQUE feature_id, cvterm_id, pub_id, rank

feature_cvtermprop

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Comments:

================================================
TABLE: feature_cvtermprop
================================================
Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_cvtermprop_idx1 feature_cvterm_id
feature_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_cvtermprop_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_cvterm_id, type_id, rank

feature_cvterm_dbxref

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Comments:

================================================
TABLE: feature_cvterm_dbxref
================================================
Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_dbxref_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
feature_cvterm_dbxref_idx1 feature_cvterm_id
feature_cvterm_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL feature_cvterm_dbxref_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE feature_cvterm_id, dbxref_id

feature_cvterm_pub

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Comments:

================================================
TABLE: feature_cvterm_pub
================================================
Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_cvterm_pub_idx1 feature_cvterm_id
feature_cvterm_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_cvterm_pub_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_cvterm_id, pub_id

synonym

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Comments:

================================================
TABLE: synonym
================================================
A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.
Field Name Data Type Size Default Value Other Foreign Key
synonym_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The synonym itself. Should be human-readable machine-searchable ascii text.
type_id integer 10 UNIQUE, NOT NULL, Types would be symbol and fullname for now. cvterm.cvterm_id
synonym_sgml varchar 255 NOT NULL, The fully specified synonym, with any non-ascii characters encoded in SGML.

Indices

Name Fields
synonym_idx1 type_id

Constraints

Type Fields
NOT NULL synonym_id
NOT NULL name
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL synonym_sgml
UNIQUE name, type_id

feature_synonym

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Comments:

================================================
TABLE: feature_synonym
================================================
Linking table between feature and synonym.
Field Name Data Type Size Default Value Other Foreign Key
feature_synonym_id integer 11 PRIMARY KEY, NOT NULL
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 false NOT NULL, The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
feature_synonym_idx1 synonym_id
feature_synonym_idx2 feature_id
feature_synonym_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_synonym_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, feature_id, pub_id

analysis

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Comments:

$Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado companalysis module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
=================================================================
================================================
TABLE: analysis
================================================
An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.
Field Name Data Type Size Default Value Other Foreign Key
analysis_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.
description text 64000
program varchar 255 UNIQUE, NOT NULL, Program name, e.g. blastx, blastp, sim4, genscan.
programversion varchar 255 UNIQUE, NOT NULL, Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].
algorithm varchar 255 Algorithm name, e.g. blast.
sourcename varchar 255 UNIQUE, Source name, e.g. cDNA, SwissProt.
sourceversion varchar 255
sourceuri text 64000 This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).
timeexecuted timestamp 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULL analysis_id
NOT NULL program
NOT NULL programversion
NOT NULL timeexecuted
UNIQUE program, programversion, sourcename

analysisprop

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Comments:

================================================
TABLE: analysisprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
analysisprop_id integer 11 PRIMARY KEY, NOT NULL
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
analysisprop_idx1 analysis_id
analysisprop_idx2 type_id

Constraints

Type Fields
NOT NULL analysisprop_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE analysis_id, type_id, rank

analysisfeature

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Comments:

================================================
TABLE: analysisfeature
================================================
Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject
Field Name Data Type Size Default Value Other Foreign Key
analysisfeature_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
rawscore float 20 This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.
normscore float 20 This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.
significance float 20 This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.
identity float 20 Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.

Indices

Name Fields
analysisfeature_idx1 feature_id
analysisfeature_idx2 analysis_id

Constraints

Type Fields
NOT NULL analysisfeature_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
UNIQUE feature_id, analysis_id

analysisfeatureprop

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Field Name Data Type Size Default Value Other Foreign Key
analysisfeatureprop_id integer 11 PRIMARY KEY, NOT NULL
analysisfeature_id integer 10 UNIQUE, NOT NULL analysisfeature.analysisfeature_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL analysisfeature_id
FOREIGN KEY analysisfeature_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE analysisfeature_id, type_id, rank
FOREIGN KEY analysisfeature_id
FOREIGN KEY type_id

phenotype

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Comments:

$Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $
==========================================
Chado phenotype module
05-31-2011
added 'name' column to phenotype. non-unique human readable field.
=================================================================
Dependencies:
:import cvterm from cv
:import feature from sequence
=================================================================
================================================
TABLE: phenotype
================================================
A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
name text 64000 null
observable_id integer 10 The entity: e.g. anatomy_part, biological_process. cvterm.cvterm_id
attr_id integer 10 Phenotypic attribute (quality, property, attribute, character) - drawn from PATO. cvterm.cvterm_id
value text 64000 Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
cvalue_id integer 10 Phenotype attribute value (state). cvterm.cvterm_id
assay_id integer 10 Evidence type. cvterm.cvterm_id

Indices

Name Fields
phenotype_idx1 cvalue_id
phenotype_idx2 observable_id
phenotype_idx3 attr_id

Constraints

Type Fields
NOT NULL phenotype_id
NOT NULL uniquename
FOREIGN KEY observable_id
FOREIGN KEY attr_id
FOREIGN KEY cvalue_id
FOREIGN KEY assay_id
UNIQUE uniquename

phenotype_cvterm

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Comments:

================================================
TABLE: phenotype_cvterm
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
phenotype_cvterm_id integer 11 PRIMARY KEY, NOT NULL
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
phenotype_cvterm_idx1 phenotype_id
phenotype_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL phenotype_cvterm_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL rank
UNIQUE phenotype_id, cvterm_id, rank

feature_phenotype

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Comments:

================================================
TABLE: feature_phenotype
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
feature_phenotype_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id

Indices

Name Fields
feature_phenotype_idx1 feature_id
feature_phenotype_idx2 phenotype_id

Constraints

Type Fields
NOT NULL feature_phenotype_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
UNIQUE feature_id, phenotype_id

genotype

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Comments:

$Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $
==========================================
Chado genetics module
changes 2011-05-31
added type_id to genotype (can be null for backward compatibility)
added genotypeprop table
2006-04-11
split out phenotype tables into phenotype module
redesigned 2003-10-28
changes 2003-11-10:
incorporating suggestions to make everything a gcontext; use
gcontext_relationship to make some gcontexts derivable from others. we
would incorporate environment this way - just add the environment
descriptors as properties of the child gcontext
changes 2004-06 (Documented by DE: 10-MAR-2005):
Many, including rename of gcontext to genotype, split
phenstatement into phenstatement & phenotype, created environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
============
DEPENDENCIES
============
:import feature from sequence
:import phenotype from phenotype
:import cvterm from cv
:import pub from pub
:import dbxref from general
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: genotype
================================================
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
Field Name Data Type Size Default Value Other Foreign Key
genotype_id integer 11 PRIMARY KEY, NOT NULL
name text 64000 Optional alternative name for a genotype, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a genotype; typically derived from the features making up the genotype.
description varchar 255
type_id integer 10 NOT NULL cvterm.cvterm_id

Indices

Name Fields
genotype_idx1 uniquename
genotype_idx2 name

Constraints

Type Fields
NOT NULL genotype_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE uniquename

feature_genotype

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Comments:

===============================================
TABLE: feature_genotype
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
feature_genotype_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
chromosome_id integer 10 UNIQUE, A feature of SO type "chromosome". feature.feature_id
rank integer 10 UNIQUE, NOT NULL, rank can be used for n-ploid organisms or to preserve order.
cgroup integer 10 UNIQUE, NOT NULL, Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
feature_genotype_idx1 feature_id
feature_genotype_idx2 genotype_id

Constraints

Type Fields
NOT NULL feature_genotype_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
FOREIGN KEY chromosome_id
NOT NULL rank
NOT NULL cgroup
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
UNIQUE feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup

environment

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Comments:

================================================
TABLE: environment
================================================
The environmental component of a phenotype description.
Field Name Data Type Size Default Value Other Foreign Key
environment_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
environment_idx1 uniquename

Constraints

Type Fields
NOT NULL environment_id
NOT NULL uniquename
UNIQUE uniquename

environment_cvterm

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Comments:

================================================
TABLE: environment_cvterm
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
environment_cvterm_id integer 11 PRIMARY KEY, NOT NULL
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
environment_cvterm_idx1 environment_id
environment_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL environment_cvterm_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
UNIQUE environment_id, cvterm_id

phenstatement

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Comments:

================================================
TABLE: phenstatement
================================================
Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.
Field Name Data Type Size Default Value Other Foreign Key
phenstatement_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phenstatement_idx1 genotype_id
phenstatement_idx2 phenotype_id

Constraints

Type Fields
NOT NULL phenstatement_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE genotype_id, phenotype_id, environment_id, type_id, pub_id

phendesc

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Comments:

================================================
TABLE: phendesc
================================================
A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
Field Name Data Type Size Default Value Other Foreign Key
phendesc_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
description text 64000 NOT NULL
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phendesc_idx1 genotype_id
phendesc_idx2 environment_id
phendesc_idx3 pub_id

Constraints

Type Fields
NOT NULL phendesc_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL description
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE genotype_id, environment_id, type_id, pub_id

phenotype_comparison

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Comments:

================================================
TABLE: phenotype_comparison
================================================
Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_id integer 11 PRIMARY KEY, NOT NULL
genotype1_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment1_id integer 10 UNIQUE, NOT NULL environment.environment_id
genotype2_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment2_id integer 10 UNIQUE, NOT NULL environment.environment_id
phenotype1_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
phenotype2_id integer 10 phenotype.phenotype_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
organism_id integer 10 NOT NULL organism.organism_id

Indices

Name Fields
phenotype_comparison_idx1 genotype1_id
phenotype_comparison_idx2 genotype2_id
phenotype_comparison_idx4 pub_id

Constraints

Type Fields
NOT NULL phenotype_comparison_id
NOT NULL genotype1_id
FOREIGN KEY genotype1_id
NOT NULL environment1_id
FOREIGN KEY environment1_id
NOT NULL genotype2_id
FOREIGN KEY genotype2_id
NOT NULL environment2_id
FOREIGN KEY environment2_id
NOT NULL phenotype1_id
FOREIGN KEY phenotype1_id
FOREIGN KEY phenotype2_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL organism_id
FOREIGN KEY organism_id
UNIQUE genotype1_id, environment1_id, genotype2_id, environment2_id, phenotype1_id, pub_id

phenotype_comparison_cvterm

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Comments:

================================================
TABLE: phenotype_comparison_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_cvterm_id integer 11 PRIMARY KEY, NOT NULL
phenotype_comparison_id integer 10 UNIQUE, NOT NULL phenotype_comparison.phenotype_comparison_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 NOT NULL pub.pub_id
rank integer 10 0 NOT NULL

Indices

Name Fields
phenotype_comparison_cvterm_idx1 phenotype_comparison_id
phenotype_comparison_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL phenotype_comparison_cvterm_id
NOT NULL phenotype_comparison_id
FOREIGN KEY phenotype_comparison_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
UNIQUE phenotype_comparison_id, cvterm_id

genotypeprop

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Comments:

================================================
TABLE: genotypeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
genotypeprop_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
genotypeprop_idx1 genotype_id
genotypeprop_idx2 type_id

Constraints

Type Fields
NOT NULL genotypeprop_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE genotype_id, type_id, rank

featuremap

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Comments:

$Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado map module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
=================================================================
================================================
TABLE: featuremap
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE
description text 64000
unittype_id integer 10 NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL featuremap_id
FOREIGN KEY unittype_id
UNIQUE name

featurerange

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Comments:

================================================
TABLE: featurerange
================================================
In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.
Field Name Data Type Size Default Value Other Foreign Key
featurerange_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 10 NOT NULL, featuremap_id is the id of the feature being mapped. featuremap.featuremap_id
feature_id integer 10 NOT NULL feature.feature_id
leftstartf_id integer 10 NOT NULL feature.feature_id
leftendf_id integer 10 feature.feature_id
rightstartf_id integer 10 feature.feature_id
rightendf_id integer 10 NOT NULL feature.feature_id
rangestr varchar 255

Indices

Name Fields
featurerange_idx1 featuremap_id
featurerange_idx2 feature_id
featurerange_idx3 leftstartf_id
featurerange_idx4 leftendf_id
featurerange_idx5 rightstartf_id
featurerange_idx6 rightendf_id

Constraints

Type Fields
NOT NULL featurerange_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL leftstartf_id
FOREIGN KEY leftstartf_id
FOREIGN KEY leftendf_id
FOREIGN KEY rightstartf_id
NOT NULL rightendf_id
FOREIGN KEY rightendf_id

featurepos

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Comments:

================================================
TABLE: featurepos
================================================
Field Name Data Type Size Default Value Other Foreign Key
featurepos_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 11 NOT NULL featuremap.featuremap_id
feature_id integer 10 NOT NULL feature.feature_id
map_feature_id integer 10 NOT NULL, map_feature_id links to the feature (map) upon which the feature is being localized. feature.feature_id
mappos float 20 NOT NULL

Indices

Name Fields
featurepos_idx1 featuremap_id
featurepos_idx2 feature_id
featurepos_idx3 map_feature_id

Constraints

Type Fields
NOT NULL featurepos_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL map_feature_id
FOREIGN KEY map_feature_id
NOT NULL mappos

featuremap_pub

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Comments:

================================================
TABLE: featuremap_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_pub_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 10 NOT NULL featuremap.featuremap_id
pub_id integer 10 NOT NULL pub.pub_id

Indices

Name Fields
featuremap_pub_idx1 featuremap_id
featuremap_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featuremap_pub_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL pub_id
FOREIGN KEY pub_id

phylotree

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Comments:

$Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $
==========================================
Chado phylogenetics module
Richard Bruskiewich
Chris Mungall
Initial design: 2004-05-27
============
DEPENDENCIES
============
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from general
:import analysis from companalysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: phylotree
================================================
Global anchor for phylogenetic tree.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_id integer 11 PRIMARY KEY, UNIQUE, NOT NULL
dbxref_id integer 10 NOT NULL dbxref.dbxref_id
name varchar 255 NULL
type_id integer 10 Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". cvterm.cvterm_id
analysis_id integer 10 NULL analysis.analysis_id
comment text 64000 NULL

Indices

Name Fields
phylotree_idx1 phylotree_id

Constraints

Type Fields
NOT NULL phylotree_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY type_id
FOREIGN KEY analysis_id
UNIQUE phylotree_id

phylotree_pub

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Comments:

================================================
TABLE: phylotree_pub
================================================
Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_pub_id integer 11 PRIMARY KEY, NOT NULL
phylotree_id integer 10 UNIQUE, NOT NULL phylotree.phylotree_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylotree_pub_idx1 phylotree_id
phylotree_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL phylotree_pub_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE phylotree_id, pub_id

phylonode

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Comments:

================================================
TABLE: phylonode
================================================
Bootstrap float null.
This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_id integer 11 PRIMARY KEY, NOT NULL
phylotree_id integer 10 UNIQUE, NOT NULL phylotree.phylotree_id
parent_phylonode_id integer 10 NULL Root phylonode can have null parent_phylonode_id value. phylonode.phylonode_id
left_idx integer 10 UNIQUE, NOT NULL
right_idx integer 10 UNIQUE, NOT NULL
type_id integer 10 Type: e.g. root, interior, leaf. cvterm.cvterm_id
feature_id integer 10 Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it. feature.feature_id
label varchar 255 NULL
distance float 20 NULL

Constraints

Type Fields
NOT NULL phylonode_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
FOREIGN KEY parent_phylonode_id
NOT NULL left_idx
NOT NULL right_idx
FOREIGN KEY type_id
FOREIGN KEY feature_id
UNIQUE phylotree_id, left_idx
UNIQUE phylotree_id, right_idx

phylonode_dbxref

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Comments:

================================================
TABLE: phylonode_dbxref
================================================
For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_dbxref_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
phylonode_dbxref_idx1 phylonode_id
phylonode_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL phylonode_dbxref_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE phylonode_id, dbxref_id

phylonode_pub

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Comments:

================================================
TABLE: phylonode_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonode_pub_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylonode_pub_idx1 phylonode_id
phylonode_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL phylonode_pub_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE phylonode_id, pub_id

phylonode_organism

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Comments:

================================================
TABLE: phylonode_organism
================================================
This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).
Field Name Data Type Size Default Value Other Foreign Key
phylonode_organism_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL, One phylonode cannot refer to >1 organism. phylonode.phylonode_id
organism_id integer 10 NOT NULL organism.organism_id

Indices

Name Fields
phylonode_organism_idx1 phylonode_id
phylonode_organism_idx2 organism_id

Constraints

Type Fields
NOT NULL phylonode_organism_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL organism_id
FOREIGN KEY organism_id
UNIQUE phylonode_id

phylonodeprop

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Comments:

================================================
TABLE: phylonodeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonodeprop_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 10 UNIQUE, NOT NULL, type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL
rank integer 10 0 UNIQUE, NOT NULL, It is not clear how useful the rank concept is here, leave it in for now.

Indices

Name Fields
phylonodeprop_idx1 phylonode_id
phylonodeprop_idx2 type_id

Constraints

Type Fields
NOT NULL phylonodeprop_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE phylonode_id, type_id, value, rank

phylonode_relationship

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Comments:

================================================
TABLE: phylonode_relationship
================================================
This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
object_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10
phylotree_id integer 10 NOT NULL phylotree.phylotree_id

Indices

Name Fields
phylonode_relationship_idx1 subject_id
phylonode_relationship_idx2 object_id
phylonode_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL phylonode_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
UNIQUE subject_id, object_id, type_id

contact

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Comments:

$Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $
==========================================
Chado contact module
=================================================================
Dependencies:
:import cvterm from cv
=================================================================
================================================
TABLE: contact
================================================
Model persons, institutes, groups, organizations, etc.
Field Name Data Type Size Default Value Other Foreign Key
contact_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NULL What type of contact is this? E.g. "person", "lab". cvterm.cvterm_id
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL

Constraints

Type Fields
NOT NULL contact_id
FOREIGN KEY type_id
NOT NULL name
UNIQUE name

contact_relationship

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Comments:

================================================
TABLE: contact_relationship
================================================
Model relationships between contacts
Field Name Data Type Size Default Value Other Foreign Key
contact_relationship_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node. contact.contact_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node. contact.contact_id

Indices

Name Fields
contact_relationship_idx1 type_id
contact_relationship_idx2 subject_id
contact_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL contact_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

expression

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Comments:

$Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado expression module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
=================================================================
================================================
TABLE: expression
================================================
The expression table is essentially a bridge table.
Field Name Data Type Size Default Value Other Foreign Key
expression_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
md5checksum char 32
description text 64000

Constraints

Type Fields
NOT NULL expression_id
NOT NULL uniquename
UNIQUE uniquename

expression_cvterm

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Comments:

================================================
TABLE: expression_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_cvterm_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 NOT NULL
cvterm_type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
expression_cvterm_idx1 expression_id
expression_cvterm_idx2 cvterm_id
expression_cvterm_idx3 cvterm_type_id

Constraints

Type Fields
NOT NULL expression_cvterm_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL rank
NOT NULL cvterm_type_id
FOREIGN KEY cvterm_type_id
UNIQUE expression_id, cvterm_id, cvterm_type_id

expression_cvtermprop

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Comments:

================================================
TABLE: expression_cvtermprop
================================================
Extensible properties for expression to cvterm associations. Examples: qualifiers.
Field Name Data Type Size Default Value Other Foreign Key
expression_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
expression_cvterm_id integer 10 UNIQUE, NOT NULL expression_cvterm.expression_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
expression_cvtermprop_idx1 expression_cvterm_id
expression_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL expression_cvtermprop_id
NOT NULL expression_cvterm_id
FOREIGN KEY expression_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE expression_cvterm_id, type_id, rank

expressionprop

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Comments:

================================================
TABLE: expressionprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
expressionprop_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
expressionprop_idx1 expression_id
expressionprop_idx2 type_id

Constraints

Type Fields
NOT NULL expressionprop_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE expression_id, type_id, rank

expression_pub

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Comments:

================================================
TABLE: expression_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_pub_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
expression_pub_idx1 expression_id
expression_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL expression_pub_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE expression_id, pub_id

feature_expression

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Comments:

================================================
TABLE: feature_expression
================================================
Field Name Data Type Size Default Value Other Foreign Key
feature_expression_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_expression_idx1 expression_id
feature_expression_idx2 feature_id
feature_expression_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_expression_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE expression_id, feature_id, pub_id

feature_expressionprop

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Comments:

================================================
TABLE: feature_expressionprop
================================================
Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_expressionprop_id integer 11 PRIMARY KEY, NOT NULL
feature_expression_id integer 10 UNIQUE, NOT NULL feature_expression.feature_expression_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_expressionprop_idx1 feature_expression_id
feature_expressionprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_expressionprop_id
NOT NULL feature_expression_id
FOREIGN KEY feature_expression_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_expression_id, type_id, rank

eimage

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Comments:

================================================
TABLE: eimage
================================================
Field Name Data Type Size Default Value Other Foreign Key
eimage_id integer 11 PRIMARY KEY, NOT NULL
eimage_data text 64000 We expect images in eimage_data (e.g. JPEGs) to be uuencoded.
eimage_type varchar 255 NOT NULL, Describes the type of data in eimage_data.
image_uri varchar 255

Constraints

Type Fields
NOT NULL eimage_id
NOT NULL eimage_type

expression_image

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Comments:

================================================
TABLE: expression_image
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_image_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
eimage_id integer 10 UNIQUE, NOT NULL eimage.eimage_id

Indices

Name Fields
expression_image_idx1 expression_id
expression_image_idx2 eimage_id

Constraints

Type Fields
NOT NULL expression_image_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL eimage_id
FOREIGN KEY eimage_id
UNIQUE expression_id, eimage_id

project

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Comments:

=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import contact from contact
=================================================================
================================================
TABLE: project
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
project_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NOT NULL

Constraints

Type Fields
NOT NULL project_id
NOT NULL name
NOT NULL description
UNIQUE name

projectprop

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Comments:

================================================
TABLE: projectprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
projectprop_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL projectprop_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE project_id, type_id, rank

project_relationship

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Comments:

================================================
TABLE: project_relationship
================================================
A project can be composed of several smaller scale projects
Field Name Data Type Size Default Value Other Foreign Key
project_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_project_id integer 10 UNIQUE, NOT NULL project.project_id
object_project_id integer 10 UNIQUE, NOT NULL project.project_id
type_id integer 10 UNIQUE, NOT NULL, The type of relationship being stated, such as "is part of". cvterm.cvterm_id

Constraints

Type Fields
NOT NULL project_relationship_id
NOT NULL subject_project_id
FOREIGN KEY subject_project_id
NOT NULL object_project_id
FOREIGN KEY object_project_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_project_id, object_project_id, type_id

project_pub

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Comments:

Linking project(s) to publication(s)
Field Name Data Type Size Default Value Other Foreign Key
project_pub_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
project_pub_idx1 project_id
project_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL project_pub_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE project_id, pub_id

project_contact

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Comments:

Linking project(s) to contact(s)
Field Name Data Type Size Default Value Other Foreign Key
project_contact_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
contact_id integer 10 UNIQUE, NOT NULL contact.contact_id

Indices

Name Fields
project_contact_idx1 project_id
project_contact_idx2 contact_id

Constraints

Type Fields
NOT NULL project_contact_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL contact_id
FOREIGN KEY contact_id
UNIQUE project_id, contact_id

mageml

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Comments:

$Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $
==========================================
Chado mage module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import contact from contact
:import dbxref from general
:import tableinfo from general
:import project from project
:import analysis from companalysis
=================================================================
================================================
TABLE: mageml
================================================
This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.
Field Name Data Type Size Default Value Other Foreign Key
mageml_id integer 11 PRIMARY KEY, NOT NULL
mage_package text 64000 NOT NULL
mage_ml text 64000 NOT NULL

Constraints

Type Fields
NOT NULL mageml_id
NOT NULL mage_package
NOT NULL mage_ml

magedocumentation

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Comments:

================================================
TABLE: magedocumentation
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
magedocumentation_id integer 11 PRIMARY KEY, NOT NULL
mageml_id integer 10 NOT NULL mageml.mageml_id
tableinfo_id integer 10 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
mageidentifier text 64000 NOT NULL

Indices

Name Fields
magedocumentation_idx1 mageml_id
magedocumentation_idx2 tableinfo_id
magedocumentation_idx3 row_id

Constraints

Type Fields
NOT NULL magedocumentation_id
NOT NULL mageml_id
FOREIGN KEY mageml_id
NOT NULL tableinfo_id
FOREIGN KEY tableinfo_id
NOT NULL row_id
NOT NULL mageidentifier

protocol

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Comments:

================================================
TABLE: protocol
================================================
Procedural notes on how data was prepared and processed.
Field Name Data Type Size Default Value Other Foreign Key
protocol_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NOT NULL cvterm.cvterm_id
pub_id integer 10 NULL pub.pub_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
uri text 64000 NULL
protocoldescription text 64000 NULL
hardwaredescription text 64000 NULL
softwaredescription text 64000 NULL

Indices

Name Fields
protocol_idx1 type_id
protocol_idx2 pub_id
protocol_idx3 dbxref_id

Constraints

Type Fields
NOT NULL protocol_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY pub_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

protocolparam

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Comments:

================================================
TABLE: protocolparam
================================================
Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.
Field Name Data Type Size Default Value Other Foreign Key
protocolparam_id integer 11 PRIMARY KEY, NOT NULL
protocol_id integer 10 NOT NULL protocol.protocol_id
name text 64000 NOT NULL
datatype_id integer 10 NULL cvterm.cvterm_id
unittype_id integer 10 NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
protocolparam_idx1 protocol_id
protocolparam_idx2 datatype_id
protocolparam_idx3 unittype_id

Constraints

Type Fields
NOT NULL protocolparam_id
NOT NULL protocol_id
FOREIGN KEY protocol_id
NOT NULL name
FOREIGN KEY datatype_id
FOREIGN KEY unittype_id
NOT NULL rank

channel

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Comments:

================================================
TABLE: channel
================================================
Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).
Field Name Data Type Size Default Value Other Foreign Key
channel_id integer 11 PRIMARY KEY, NOT NULL
name text 64000 UNIQUE, NOT NULL
definition text 64000 NOT NULL

Constraints

Type Fields
NOT NULL channel_id
NOT NULL name
NOT NULL definition
UNIQUE name

arraydesign

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Comments:

================================================
TABLE: arraydesign
================================================
General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).
Field Name Data Type Size Default Value Other Foreign Key
arraydesign_id integer 11 PRIMARY KEY, NOT NULL
manufacturer_id integer 10 NOT NULL contact.contact_id
platformtype_id integer 10 NOT NULL cvterm.cvterm_id
substratetype_id integer 10 NULL cvterm.cvterm_id
protocol_id integer 10 NULL protocol.protocol_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
version text 64000 NULL
description text 64000 NULL
array_dimensions text 64000 NULL
element_dimensions text 64000 NULL
num_of_elements integer 10 NULL
num_array_columns integer 10 NULL
num_array_rows integer 10 NULL
num_grid_columns integer 10 NULL
num_grid_rows integer 10 NULL
num_sub_columns integer 10 NULL
num_sub_rows integer 10 NULL

Indices

Name Fields
arraydesign_idx1 manufacturer_id
arraydesign_idx2 platformtype_id
arraydesign_idx3 substratetype_id
arraydesign_idx4 protocol_id
arraydesign_idx5 dbxref_id

Constraints

Type Fields
NOT NULL arraydesign_id
NOT NULL manufacturer_id
FOREIGN KEY manufacturer_id
NOT NULL platformtype_id
FOREIGN KEY platformtype_id
FOREIGN KEY substratetype_id
FOREIGN KEY protocol_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

arraydesignprop

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Comments:

================================================
TABLE: arraydesignprop
================================================
Extra array design properties that are not accounted for in arraydesign.
Field Name Data Type Size Default Value Other Foreign Key
arraydesignprop_id integer 11 PRIMARY KEY, NOT NULL
arraydesign_id integer 10 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
arraydesignprop_idx1 arraydesign_id
arraydesignprop_idx2 type_id

Constraints

Type Fields
NOT NULL arraydesignprop_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE arraydesign_id, type_id, rank

assay

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Comments:

================================================
TABLE: assay
================================================
An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.
Field Name Data Type Size Default Value Other Foreign Key
assay_id integer 11 PRIMARY KEY, NOT NULL
arraydesign_id integer 10 NOT NULL arraydesign.arraydesign_id
protocol_id integer 10 NULL protocol.protocol_id
assaydate timestamp 0 current_timestamp
arrayidentifier text 64000 NULL
arraybatchidentifier text 64000 NULL
operator_id integer 10 NOT NULL contact.contact_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
assay_idx1 arraydesign_id
assay_idx2 protocol_id
assay_idx3 operator_id
assay_idx4 dbxref_id

Constraints

Type Fields
NOT NULL assay_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
FOREIGN KEY protocol_id
NOT NULL operator_id
FOREIGN KEY operator_id
FOREIGN KEY dbxref_id
UNIQUE name

assayprop

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Comments:

================================================
TABLE: assayprop
================================================
Extra assay properties that are not accounted for in assay.
Field Name Data Type Size Default Value Other Foreign Key
assayprop_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assayprop_idx1 assay_id
assayprop_idx2 type_id

Constraints

Type Fields
NOT NULL assayprop_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE assay_id, type_id, rank

assay_project

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Comments:

================================================
TABLE: assay_project
================================================
Link assays to projects.
Field Name Data Type Size Default Value Other Foreign Key
assay_project_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
project_id integer 10 UNIQUE, NOT NULL project.project_id

Indices

Name Fields
assay_project_idx1 assay_id
assay_project_idx2 project_id

Constraints

Type Fields
NOT NULL assay_project_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL project_id
FOREIGN KEY project_id
UNIQUE assay_id, project_id

biomaterial

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Comments:

================================================
TABLE: biomaterial
================================================
A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_id integer 11 PRIMARY KEY, NOT NULL
taxon_id integer 10 NULL organism.organism_id
biosourceprovider_id integer 10 NULL contact.contact_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
biomaterial_idx1 taxon_id
biomaterial_idx2 biosourceprovider_id
biomaterial_idx3 dbxref_id

Constraints

Type Fields
NOT NULL biomaterial_id
FOREIGN KEY taxon_id
FOREIGN KEY biosourceprovider_id
FOREIGN KEY dbxref_id
UNIQUE name

biomaterial_relationship

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Comments:

================================================
TABLE: biomaterial_relationship
================================================
Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id

Indices

Name Fields
biomaterial_relationship_idx1 subject_id
biomaterial_relationship_idx2 object_id
biomaterial_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL biomaterial_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

biomaterialprop

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Comments:

================================================
TABLE: biomaterialprop
================================================
Extra biomaterial properties that are not accounted for in biomaterial.
Field Name Data Type Size Default Value Other Foreign Key
biomaterialprop_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
biomaterialprop_idx1 biomaterial_id
biomaterialprop_idx2 type_id

Constraints

Type Fields
NOT NULL biomaterialprop_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE biomaterial_id, type_id, rank

biomaterial_dbxref

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Comments:

================================================
TABLE: biomaterial_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_dbxref_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
biomaterial_dbxref_idx1 biomaterial_id
biomaterial_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL biomaterial_dbxref_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE biomaterial_id, dbxref_id

treatment

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Comments:

================================================
TABLE: treatment
================================================
A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.
Field Name Data Type Size Default Value Other Foreign Key
treatment_id integer 11 PRIMARY KEY, NOT NULL
rank integer 10 0 NOT NULL
biomaterial_id integer 10 NOT NULL biomaterial.biomaterial_id
type_id integer 10 NOT NULL cvterm.cvterm_id
protocol_id integer 10 NULL protocol.protocol_id
name text 64000 NULL

Indices

Name Fields
treatment_idx1 biomaterial_id
treatment_idx2 type_id
treatment_idx3 protocol_id

Constraints

Type Fields
NOT NULL treatment_id
NOT NULL rank
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY protocol_id

biomaterial_treatment

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Comments:

================================================
TABLE: biomaterial_treatment
================================================
Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_treatment_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
treatment_id integer 10 UNIQUE, NOT NULL treatment.treatment_id
unittype_id integer 10 NULL cvterm.cvterm_id
value float 15 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
biomaterial_treatment_idx1 biomaterial_id
biomaterial_treatment_idx2 treatment_id
biomaterial_treatment_idx3 unittype_id

Constraints

Type Fields
NOT NULL biomaterial_treatment_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL treatment_id
FOREIGN KEY treatment_id
FOREIGN KEY unittype_id
NOT NULL rank
UNIQUE biomaterial_id, treatment_id

assay_biomaterial

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Comments:

================================================
TABLE: assay_biomaterial
================================================
A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).
Field Name Data Type Size Default Value Other Foreign Key
assay_biomaterial_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
channel_id integer 10 NULL UNIQUE channel.channel_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assay_biomaterial_idx1 assay_id
assay_biomaterial_idx2 biomaterial_id
assay_biomaterial_idx3 channel_id

Constraints

Type Fields
NOT NULL assay_biomaterial_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
FOREIGN KEY channel_id
NOT NULL rank
UNIQUE assay_id, biomaterial_id, channel_id, rank

acquisition

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Comments:

================================================
TABLE: acquisition
================================================
This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 NOT NULL assay.assay_id
protocol_id integer 10 NULL protocol.protocol_id
channel_id integer 10 NULL channel.channel_id
acquisitiondate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
acquisition_idx1 assay_id
acquisition_idx2 protocol_id
acquisition_idx3 channel_id

Constraints

Type Fields
NOT NULL acquisition_id
NOT NULL assay_id
FOREIGN KEY assay_id
FOREIGN KEY protocol_id
FOREIGN KEY channel_id
UNIQUE name

acquisitionprop

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Comments:

================================================
TABLE: acquisitionprop
================================================
Parameters associated with image acquisition.
Field Name Data Type Size Default Value Other Foreign Key
acquisitionprop_id integer 11 PRIMARY KEY, NOT NULL
acquisition_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisitionprop_idx1 acquisition_id
acquisitionprop_idx2 type_id

Constraints

Type Fields
NOT NULL acquisitionprop_id
NOT NULL acquisition_id
FOREIGN KEY acquisition_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE acquisition_id, type_id, rank

acquisition_relationship

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Comments:

================================================
TABLE: acquisition_relationship
================================================
Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisition_relationship_idx1 subject_id
acquisition_relationship_idx2 type_id
acquisition_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL acquisition_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

quantification

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Comments:

================================================
TABLE: quantification
================================================
Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.
Field Name Data Type Size Default Value Other Foreign Key
quantification_id integer 11 PRIMARY KEY, NOT NULL
acquisition_id integer 10 NOT NULL acquisition.acquisition_id
operator_id integer 10 NULL contact.contact_id
protocol_id integer 10 NULL protocol.protocol_id
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
quantificationdate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
quantification_idx1 acquisition_id
quantification_idx2 operator_id
quantification_idx3 protocol_id
quantification_idx4 analysis_id

Constraints

Type Fields
NOT NULL quantification_id
NOT NULL acquisition_id
FOREIGN KEY acquisition_id
FOREIGN KEY operator_id
FOREIGN KEY protocol_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
UNIQUE name, analysis_id

quantificationprop

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Comments:

================================================
TABLE: quantificationprop
================================================
Extra quantification properties that are not accounted for in quantification.
Field Name Data Type Size Default Value Other Foreign Key
quantificationprop_id integer 11 PRIMARY KEY, NOT NULL
quantification_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
quantificationprop_idx1 quantification_id
quantificationprop_idx2 type_id

Constraints

Type Fields
NOT NULL quantificationprop_id
NOT NULL quantification_id
FOREIGN KEY quantification_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE quantification_id, type_id, rank

quantification_relationship

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Comments:

================================================
TABLE: quantification_relationship
================================================
There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.
Field Name Data Type Size Default Value Other Foreign Key
quantification_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL quantification.quantification_id

Indices

Name Fields
quantification_relationship_idx1 subject_id
quantification_relationship_idx2 type_id
quantification_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL quantification_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

control

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Comments:

================================================
TABLE: control
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
control_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NOT NULL cvterm.cvterm_id
assay_id integer 10 NOT NULL assay.assay_id
tableinfo_id integer 10 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
name text 64000 NULL
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
control_idx1 type_id
control_idx2 assay_id
control_idx3 tableinfo_id
control_idx4 row_id

Constraints

Type Fields
NOT NULL control_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL tableinfo_id
FOREIGN KEY tableinfo_id
NOT NULL row_id
NOT NULL rank

element

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Comments:

================================================
TABLE: element
================================================
Represents a feature of the array. This is typically a region of the array coated or bound to DNA.
Field Name Data Type Size Default Value Other Foreign Key
element_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 NULL UNIQUE feature.feature_id
arraydesign_id integer 10 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 10 NULL cvterm.cvterm_id
dbxref_id integer 10 NULL dbxref.dbxref_id

Indices

Name Fields
element_idx1 feature_id
element_idx2 arraydesign_id
element_idx3 type_id
element_idx4 dbxref_id

Constraints

Type Fields
NOT NULL element_id
FOREIGN KEY feature_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
FOREIGN KEY type_id
FOREIGN KEY dbxref_id
UNIQUE feature_id, arraydesign_id

elementresult

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Comments:

================================================
TABLE: element_result
================================================
An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_id integer 11 PRIMARY KEY, NOT NULL
element_id integer 10 UNIQUE, NOT NULL element.element_id
quantification_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
signal float 20 NOT NULL

Indices

Name Fields
elementresult_idx1 element_id
elementresult_idx2 quantification_id
elementresult_idx3 signal

Constraints

Type Fields
NOT NULL elementresult_id
NOT NULL element_id
FOREIGN KEY element_id
NOT NULL quantification_id
FOREIGN KEY quantification_id
NOT NULL signal
UNIQUE element_id, quantification_id

element_relationship

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Comments:

================================================
TABLE: element_relationship
================================================
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Field Name Data Type Size Default Value Other Foreign Key
element_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL element.element_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL element.element_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
element_relationship_idx1 subject_id
element_relationship_idx2 type_id
element_relationship_idx3 object_id
element_relationship_idx4 value

Constraints

Type Fields
NOT NULL element_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

elementresult_relationship

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Comments:

================================================
TABLE: elementresult_relationship
================================================
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL elementresult.elementresult_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL elementresult.elementresult_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
elementresult_relationship_idx1 subject_id
elementresult_relationship_idx2 type_id
elementresult_relationship_idx3 object_id
elementresult_relationship_idx4 value

Constraints

Type Fields
NOT NULL elementresult_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

study

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Comments:

================================================
TABLE: study
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_id integer 11 PRIMARY KEY, NOT NULL
contact_id integer 10 NOT NULL contact.contact_id
pub_id integer 10 NULL pub.pub_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
description text 64000 NULL

Indices

Name Fields
study_idx1 contact_id
study_idx2 pub_id
study_idx3 dbxref_id

Constraints

Type Fields
NOT NULL study_id
NOT NULL contact_id
FOREIGN KEY contact_id
FOREIGN KEY pub_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

study_assay

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Comments:

================================================
TABLE: study_assay
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_assay_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 UNIQUE, NOT NULL study.study_id
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id

Indices

Name Fields
study_assay_idx1 study_id
study_assay_idx2 assay_id

Constraints

Type Fields
NOT NULL study_assay_id
NOT NULL study_id
FOREIGN KEY study_id
NOT NULL assay_id
FOREIGN KEY assay_id
UNIQUE study_id, assay_id

studydesign

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Comments:

================================================
TABLE: studydesign
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesign_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 NOT NULL study.study_id
description text 64000 NULL

Indices

Name Fields
studydesign_idx1 study_id

Constraints

Type Fields
NOT NULL studydesign_id
NOT NULL study_id
FOREIGN KEY study_id

studydesignprop

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Comments:

================================================
TABLE: studydesignprop
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesignprop_id integer 11 PRIMARY KEY, NOT NULL
studydesign_id integer 10 UNIQUE, NOT NULL studydesign.studydesign_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studydesignprop_idx1 studydesign_id
studydesignprop_idx2 type_id

Constraints

Type Fields
NOT NULL studydesignprop_id
NOT NULL studydesign_id
FOREIGN KEY studydesign_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE studydesign_id, type_id, rank

studyfactor

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Comments:

================================================
TABLE: studyfactor
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactor_id integer 11 PRIMARY KEY, NOT NULL
studydesign_id integer 10 NOT NULL studydesign.studydesign_id
type_id integer 10 NULL cvterm.cvterm_id
name text 64000 NOT NULL
description text 64000 NULL

Indices

Name Fields
studyfactor_idx1 studydesign_id
studyfactor_idx2 type_id

Constraints

Type Fields
NOT NULL studyfactor_id
NOT NULL studydesign_id
FOREIGN KEY studydesign_id
FOREIGN KEY type_id
NOT NULL name

studyfactorvalue

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Comments:

================================================
TABLE: studyfactorvalue
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactorvalue_id integer 11 PRIMARY KEY, NOT NULL
studyfactor_id integer 10 NOT NULL studyfactor.studyfactor_id
assay_id integer 10 NOT NULL assay.assay_id
factorvalue text 64000 NULL
name text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
studyfactorvalue_idx1 studyfactor_id
studyfactorvalue_idx2 assay_id

Constraints

Type Fields
NOT NULL studyfactorvalue_id
NOT NULL studyfactor_id
FOREIGN KEY studyfactor_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL rank

studyprop

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Comments:

studyprop and studyprop_feature added for Kara Dolinski's group
Here is her description of it:
Both of the tables are used for our YFGdb project
(http://yfgdb.princeton.edu/), which uses chado.
Here is how we use those tables, using the following example:
http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969
The above data set is represented as a row in the STUDY table. We have
lots of attributes that we want to store about each STUDY (status, etc)
and in the official schema, the only prop table we could use was the
STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN
table when we often have no real data to store in that table (small
percent of our collection use MAGE-ML unfortunately, and even fewer
provide all the data in the MAGE model, of which STUDYDESIGN is a vestige).
So, we created a STUDYPROP table. I'd think this table would be
generally useful to people storing various types of data sets via the
STUDY table.
The other new table is STUDYPROP_FEATURE. This basically allows us to
group features together per study. For example, we can store microarray
clustering results by saying that the STUDYPROP type is 'cluster' (via
type_id -> CVTERM of course), the value is 'cluster id 123', and then
that cluster would be associated with all the features that are in that
cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is
fine by us!
studyprop
Field Name Data Type Size Default Value Other Foreign Key
studyprop_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 UNIQUE, NOT NULL study.study_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studyprop_idx1 study_id
studyprop_idx2 type_id

Constraints

Type Fields
NOT NULL studyprop_id
NOT NULL study_id
FOREIGN KEY study_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE study_id, type_id, rank

studyprop_feature

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Comments:

studyprop_feature
Field Name Data Type Size Default Value Other Foreign Key
studyprop_feature_id integer 11 PRIMARY KEY, NOT NULL
studyprop_id integer 10 UNIQUE, NOT NULL studyprop.studyprop_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
type_id integer 10 cvterm.cvterm_id

Indices

Name Fields
studyprop_feature_idx1 studyprop_id
studyprop_feature_idx2 feature_id

Constraints

Type Fields
NOT NULL studyprop_feature_id
NOT NULL studyprop_id
FOREIGN KEY studyprop_id
NOT NULL feature_id
FOREIGN KEY feature_id
FOREIGN KEY type_id
UNIQUE studyprop_id, feature_id

stock

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Comments:

$Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $
==========================================
Chado stock module
DEPENDENCIES
============
:import cvterm from cv
:import pub from pub
:import dbxref from general
:import organism from organism
:import genotype from genetic
:import contact from contact
================================================
TABLE: stock
================================================
Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
Field Name Data Type Size Default Value Other Foreign Key
stock_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. dbxref.dbxref_id
organism_id integer 10 UNIQUE, The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. organism.organism_id
name varchar 255 The name is a human-readable local name for a stock.
uniquename text 64000 UNIQUE, NOT NULL
description text 64000 The description is the genetic description provided in the stock list.
type_id integer 10 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm. cvterm.cvterm_id
is_obsolete boolean 0 false NOT NULL

Indices

Name Fields
stock_name_ind1 name
stock_idx1 dbxref_id
stock_idx2 organism_id
stock_idx3 type_id
stock_idx4 uniquename

Constraints

Type Fields
NOT NULL stock_id
FOREIGN KEY dbxref_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_obsolete
UNIQUE organism_id, uniquename, type_id

stock_pub

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Comments:

================================================
TABLE: stock_pub
================================================
Provenance. Linking table between stocks and, for example, a stocklist computer file.
Field Name Data Type Size Default Value Other Foreign Key
stock_pub_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_pub_idx1 stock_id
stock_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stock_pub_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stock_id, pub_id

stockprop

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Comments:

================================================
TABLE: stockprop
================================================
A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockprop_idx1 stock_id
stockprop_idx2 type_id

Constraints

Type Fields
NOT NULL stockprop_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_id, type_id, rank

stockprop_pub

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Comments:

================================================
TABLE: stockprop_pub
================================================
Provenance. Any stockprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_pub_id integer 11 PRIMARY KEY, NOT NULL
stockprop_id integer 10 UNIQUE, NOT NULL stockprop.stockprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stockprop_pub_idx1 stockprop_id
stockprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stockprop_pub_id
NOT NULL stockprop_id
FOREIGN KEY stockprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stockprop_id, pub_id

stock_relationship

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Comments:

================================================
TABLE: stock_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL, stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock. stock.stock_id
object_id integer 10 UNIQUE, NOT NULL, stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock. stock.stock_id
type_id integer 10 UNIQUE, NOT NULL, stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
value text 64000 NULL stock_relationship.value is for additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.

Indices

Name Fields
stock_relationship_idx1 subject_id
stock_relationship_idx2 object_id
stock_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL stock_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

stock_relationship_cvterm

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Comments:

================================================
TABLE: stock_relationship_cvterm
================================================
For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_cvterm_id integer 11 PRIMARY KEY, NOT NULL
stock_relationship_id integer 10 NOT NULL stock_relationship.stock_relationship_id
cvterm_id integer 10 NOT NULL cvterm.cvterm_id
pub_id integer 10 pub.pub_id

Constraints

Type Fields
NOT NULL stock_relationship_cvterm_id
NOT NULL stock_relationship_id
FOREIGN KEY stock_relationship_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
FOREIGN KEY pub_id

stock_relationship_pub

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Comments:

================================================
TABLE: stock_relationship_pub
================================================
Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_pub_id integer 11 PRIMARY KEY, NOT NULL
stock_relationship_id integer 10 UNIQUE, NOT NULL stock_relationship.stock_relationship_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_relationship_pub_idx1 stock_relationship_id
stock_relationship_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stock_relationship_pub_id
NOT NULL stock_relationship_id
FOREIGN KEY stock_relationship_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stock_relationship_id, pub_id

stock_dbxref

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Comments:

================================================
TABLE: stock_dbxref
================================================
stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxref_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.

Indices

Name Fields
stock_dbxref_idx1 stock_id
stock_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL stock_dbxref_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE stock_id, dbxref_id

stock_cvterm

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Comments:

================================================
TABLE: stock_cvterm
================================================
stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvterm_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
is_not boolean 0 false NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_cvterm_idx1 stock_id
stock_cvterm_idx2 cvterm_id
stock_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL stock_cvterm_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_not
NOT NULL rank
UNIQUE stock_id, cvterm_id, pub_id, rank

stock_cvtermprop

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Comments:

================================================
TABLE: stock_cvtermprop
================================================
Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
stock_cvterm_id integer 10 UNIQUE, NOT NULL stock_cvterm.stock_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
stock_cvtermprop_idx1 stock_cvterm_id
stock_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL stock_cvtermprop_id
NOT NULL stock_cvterm_id
FOREIGN KEY stock_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_cvterm_id, type_id, rank

stock_genotype

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Comments:

================================================
TABLE: stock_genotype
================================================
Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
Field Name Data Type Size Default Value Other Foreign Key
stock_genotype_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id

Indices

Name Fields
stock_genotype_idx1 stock_id
stock_genotype_idx2 genotype_id

Constraints

Type Fields
NOT NULL stock_genotype_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
UNIQUE stock_id, genotype_id

stockcollection

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Comments:

================================================
TABLE: stockcollection
================================================
The lab or stock center distributing the stocks in their collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, type_id is the collection type cv. cvterm.cvterm_id
contact_id integer 10 NULL contact_id links to the contact information for the collection. contact.contact_id
name varchar 255 name is the collection.
uniquename text 64000 UNIQUE, NOT NULL, uniqename is the value of the collection cv.

Indices

Name Fields
stockcollection_name_ind1 name
stockcollection_idx1 contact_id
stockcollection_idx2 type_id
stockcollection_idx3 uniquename

Constraints

Type Fields
NOT NULL stockcollection_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY contact_id
NOT NULL uniquename
UNIQUE uniquename, type_id

stockcollectionprop

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Comments:

================================================
TABLE: stockcollectionprop
================================================
The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
Field Name Data Type Size Default Value Other Foreign Key
stockcollectionprop_id integer 11 PRIMARY KEY, NOT NULL
stockcollection_id integer 10 UNIQUE, NOT NULL stockcollection.stockcollection_id
type_id integer 10 UNIQUE, NOT NULL, The cv for the type_id is "stockcollection property type". cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockcollectionprop_idx1 stockcollection_id
stockcollectionprop_idx2 type_id

Constraints

Type Fields
NOT NULL stockcollectionprop_id
NOT NULL stockcollection_id
FOREIGN KEY stockcollection_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stockcollection_id, type_id, rank

stockcollection_stock

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Comments:

================================================
TABLE: stockcollection_stock
================================================
stockcollection_stock links a stock collection to the stocks which are contained in the collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_stock_id integer 11 PRIMARY KEY, NOT NULL
stockcollection_id integer 10 UNIQUE, NOT NULL stockcollection.stockcollection_id
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id

Indices

Name Fields
stockcollection_stock_idx1 stockcollection_id
stockcollection_stock_idx2 stock_id

Constraints

Type Fields
NOT NULL stockcollection_stock_id
NOT NULL stockcollection_id
FOREIGN KEY stockcollection_id
NOT NULL stock_id
FOREIGN KEY stock_id
UNIQUE stockcollection_id, stock_id

stock_dbxrefprop

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Comments:

================================================
TABLE: stock_dbxrefprop
================================================
A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxrefprop_id integer 11 PRIMARY KEY, NOT NULL
stock_dbxref_id integer 10 UNIQUE, NOT NULL stock_dbxref.stock_dbxref_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_dbxrefprop_idx1 stock_dbxref_id
stock_dbxrefprop_idx2 type_id

Constraints

Type Fields
NOT NULL stock_dbxrefprop_id
NOT NULL stock_dbxref_id
FOREIGN KEY stock_dbxref_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_dbxref_id, type_id, rank

library

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Comments:

$Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $
=================================================================
Dependencies:
:import feature from sequence
:import synonym from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
=================================================================
================================================
TABLE: library
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
name varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" cvterm.cvterm_id
is_obsolete integer 10 0 NOT NULL
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Indices

Name Fields
library_name_ind1 name
library_idx1 organism_id
library_idx2 type_id
library_idx3 uniquename

Constraints

Type Fields
NOT NULL library_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_obsolete
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE organism_id, uniquename, type_id

library_synonym

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Comments:

================================================
TABLE: library_synonym
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_synonym_id integer 11 PRIMARY KEY, NOT NULL
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 true NOT NULL, The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
library_synonym_idx1 synonym_id
library_synonym_idx2 library_id
library_synonym_idx3 pub_id

Constraints

Type Fields
NOT NULL library_synonym_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, library_id, pub_id

library_pub

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Comments:

================================================
TABLE: library_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_pub_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_pub_idx1 library_id
library_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL library_pub_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, pub_id

libraryprop

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Comments:

================================================
TABLE: libraryprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
libraryprop_idx1 library_id
libraryprop_idx2 type_id

Constraints

Type Fields
NOT NULL libraryprop_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE library_id, type_id, rank

libraryprop_pub

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Comments:

================================================
TABLE: libraryprop_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_pub_id integer 11 PRIMARY KEY, NOT NULL
libraryprop_id integer 10 UNIQUE, NOT NULL libraryprop.libraryprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
libraryprop_pub_idx1 libraryprop_id
libraryprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL libraryprop_pub_id
NOT NULL libraryprop_id
FOREIGN KEY libraryprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE libraryprop_id, pub_id

library_cvterm

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Comments:

================================================
TABLE: library_cvterm
================================================
The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
Field Name Data Type Size Default Value Other Foreign Key
library_cvterm_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_cvterm_idx1 library_id
library_cvterm_idx2 cvterm_id
library_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL library_cvterm_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, cvterm_id, pub_id

library_feature

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Comments:

================================================
TABLE: library_feature
================================================
library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
Field Name Data Type Size Default Value Other Foreign Key
library_feature_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id

Indices

Name Fields
library_feature_idx1 library_id
library_feature_idx2 feature_id

Constraints

Type Fields
NOT NULL library_feature_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL feature_id
FOREIGN KEY feature_id
UNIQUE library_id, feature_id

library_dbxref

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Comments:

================================================
TABLE: library_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_dbxref_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
library_dbxref_idx1 library_id
library_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL library_dbxref_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE library_id, dbxref_id

cell_line

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Comments:

==========================================
Chado cell line module
============
DEPENDENCIES
============
:import feature from sequence
:import synonym from sequence
:import library from library
:import cvterm from cv
:import dbxref from general
:import pub from pub
:import organism from organism
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: cell_line
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 NULL
uniquename varchar 255 UNIQUE, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULL cell_line_id
NOT NULL uniquename
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE uniquename, organism_id

cell_line_relationship

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Comments:

================================================
TABLE: cell_line_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
object_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL cell_line_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_id, object_id, type_id

cell_line_synonym

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Comments:

================================================
TABLE: cell_line_synonym
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_synonym_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
is_current boolean 0 false NOT NULL
is_internal boolean 0 false NOT NULL

Constraints

Type Fields
NOT NULL cell_line_synonym_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, cell_line_id, pub_id

cell_line_cvterm

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Comments:

================================================
TABLE: cell_line_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvterm_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_line_cvterm_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
UNIQUE cell_line_id, cvterm_id, pub_id, rank

cell_line_dbxref

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Comments:

================================================
TABLE: cell_line_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_dbxref_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Constraints

Type Fields
NOT NULL cell_line_dbxref_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE cell_line_id, dbxref_id

cell_lineprop

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Comments:

================================================
TABLE: cell_lineprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_lineprop_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cell_line_id, type_id, rank

cell_lineprop_pub

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Comments:

================================================
TABLE: cell_lineprop_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_pub_id integer 11 PRIMARY KEY, NOT NULL
cell_lineprop_id integer 10 UNIQUE, NOT NULL cell_lineprop.cell_lineprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_lineprop_pub_id
NOT NULL cell_lineprop_id
FOREIGN KEY cell_lineprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_lineprop_id, pub_id

cell_line_feature

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Comments:

================================================
TABLE: cell_line_feature
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_feature_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_feature_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, feature_id, pub_id

cell_line_cvtermprop

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Comments:

================================================
TABLE: cell_line_cvtermprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
cell_line_cvterm_id integer 10 UNIQUE, NOT NULL cell_line_cvterm.cell_line_cvterm_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_line_cvtermprop_id
NOT NULL cell_line_cvterm_id
FOREIGN KEY cell_line_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cell_line_cvterm_id, type_id, rank

cell_line_pub

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Comments:

================================================
TABLE: cell_line_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_pub_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_pub_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, pub_id

cell_line_library

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Comments:

================================================
TABLE: cell_line_library
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_library_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_library_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, library_id, pub_id

nd_geolocation

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Comments:

=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import phenotype from phenotype
:import organism from organism
:import genotype from genetic
:import contact from contact
:import project from project
:import stock from stock
:import synonym
=================================================================
this probably needs some work, depending on how cross-database we
want to be. In Postgres, at least, there are much better ways to
represent geo information.
The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocation_id integer 11 PRIMARY KEY, NOT NULL
description varchar 255 A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.
latitude real 10 The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.
longitude real 10 The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.
geodetic_datum varchar 32 The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.
altitude real 10 The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.

Constraints

Type Fields
NOT NULL nd_geolocation_id

nd_experiment

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Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_id integer 11 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 10 NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_experiment_id
NOT NULL nd_geolocation_id
FOREIGN KEY nd_geolocation_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_geolocation_id
FOREIGN KEY type_id

nd_experiment_project

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Comments:

used to be nd_diversityexperiment_project
then was nd_assay_project
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_project_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 NOT NULL project.project_id
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id

Constraints

Type Fields
NOT NULL nd_experiment_project_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY project_id
FOREIGN KEY nd_experiment_id

nd_experimentprop

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Field Name Data Type Size Default Value Other Foreign Key
nd_experimentprop_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL nd_experimentprop_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_experiment_id, type_id, rank
FOREIGN KEY nd_experiment_id
FOREIGN KEY type_id

nd_experiment_pub

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Comments:

Linking nd_experiment(s) to publication(s)
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_pub_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
nd_experiment_pub_idx1 nd_experiment_id
nd_experiment_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL nd_experiment_pub_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE nd_experiment_id, pub_id

nd_geolocationprop

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Comments:

Property/value associations for geolocations. This table can store the properties such as location and environment
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocationprop_id integer 11 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 10 UNIQUE, NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_geolocationprop_id
NOT NULL nd_geolocation_id
FOREIGN KEY nd_geolocation_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_geolocation_id, type_id, rank
FOREIGN KEY nd_geolocation_id
FOREIGN KEY type_id

nd_protocol

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Comments:

A protocol can be anything that is done as part of the experiment.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The protocol name.
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_protocol_id
NOT NULL name
UNIQUE name
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY type_id

nd_reagent

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Comments:

A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_id integer 11 PRIMARY KEY, NOT NULL
name varchar 80 NOT NULL, The name of the reagent. The name should be unique for a given type.
type_id integer 10 NOT NULL, The type of the reagent, for example linker oligomer, or forward primer. cvterm.cvterm_id
feature_id integer 10 If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.

Constraints

Type Fields
NOT NULL nd_reagent_id
NOT NULL name
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY type_id

nd_protocol_reagent

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Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_reagent_id integer 11 PRIMARY KEY, NOT NULL
nd_protocol_id integer 10 NOT NULL nd_protocol.nd_protocol_id
reagent_id integer 10 NOT NULL nd_reagent.nd_reagent_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_protocol_reagent_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
NOT NULL reagent_id
FOREIGN KEY reagent_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_protocol_id
FOREIGN KEY reagent_id
FOREIGN KEY type_id

nd_protocolprop

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Comments:

Property/value associations for protocol.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocolprop_id integer 11 PRIMARY KEY, NOT NULL
nd_protocol_id integer 10 UNIQUE, NOT NULL, The protocol to which the property applies. nd_protocol.nd_protocol_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_protocolprop_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_protocol_id, type_id, rank
FOREIGN KEY nd_protocol_id
FOREIGN KEY type_id

nd_experiment_stock

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Comments:

Part of a stock or a clone of a stock that is used in an experiment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
stock_id integer 10 NOT NULL, stock used in the extraction or the corresponding stock for the clone stock.stock_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_experiment_stock_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY stock_id
FOREIGN KEY type_id

nd_experiment_protocol

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Comments:

Linking table: experiments to the protocols they involve.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_protocol_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
nd_protocol_id integer 10 NOT NULL nd_protocol.nd_protocol_id

Constraints

Type Fields
NOT NULL nd_experiment_protocol_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY nd_protocol_id

nd_experiment_phenotype

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Comments:

Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_phenotype_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id

Constraints

Type Fields
NOT NULL nd_experiment_phenotype_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
UNIQUE nd_experiment_id, phenotype_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY phenotype_id

nd_experiment_genotype

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Comments:

Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_genotype_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id

Constraints

Type Fields
NOT NULL nd_experiment_genotype_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
UNIQUE nd_experiment_id, genotype_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY genotype_id

nd_reagent_relationship

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Comments:

Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_reagent_id integer 10 NOT NULL, The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. nd_reagent.nd_reagent_id
object_reagent_id integer 10 NOT NULL, The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. nd_reagent.nd_reagent_id
type_id integer 10 NOT NULL, The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_reagent_relationship_id
NOT NULL subject_reagent_id
FOREIGN KEY subject_reagent_id
NOT NULL object_reagent_id
FOREIGN KEY object_reagent_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY subject_reagent_id
FOREIGN KEY object_reagent_id
FOREIGN KEY type_id

nd_reagentprop

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Field Name Data Type Size Default Value Other Foreign Key
nd_reagentprop_id integer 11 PRIMARY KEY, NOT NULL
nd_reagent_id integer 10 UNIQUE, NOT NULL nd_reagent.nd_reagent_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL nd_reagentprop_id
NOT NULL nd_reagent_id
FOREIGN KEY nd_reagent_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_reagent_id, type_id, rank
FOREIGN KEY nd_reagent_id
FOREIGN KEY type_id

nd_experiment_stockprop

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Comments:

Property/value associations for experiment_stocks. This table can store the properties such as treatment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stockprop_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 10 UNIQUE, NOT NULL, The experiment_stock to which the property applies. nd_experiment_stock.nd_experiment_stock_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_experiment_stockprop_id
NOT NULL nd_experiment_stock_id
FOREIGN KEY nd_experiment_stock_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_experiment_stock_id, type_id, rank
FOREIGN KEY nd_experiment_stock_id
FOREIGN KEY type_id

nd_experiment_stock_dbxref

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Comments:

Cross-reference experiment_stock to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_dbxref_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 10 NOT NULL nd_experiment_stock.nd_experiment_stock_id
dbxref_id integer 10 NOT NULL dbxref.dbxref_id

Constraints

Type Fields
NOT NULL nd_experiment_stock_dbxref_id
NOT NULL nd_experiment_stock_id
FOREIGN KEY nd_experiment_stock_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY nd_experiment_stock_id
FOREIGN KEY dbxref_id

nd_experiment_dbxref

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Comments:

Cross-reference experiment to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_dbxref_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
dbxref_id integer 10 NOT NULL dbxref.dbxref_id

Constraints

Type Fields
NOT NULL nd_experiment_dbxref_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY dbxref_id

nd_experiment_contact

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Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_contact_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
contact_id integer 10 NOT NULL contact.contact_id

Constraints

Type Fields
NOT NULL nd_experiment_contact_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL contact_id
FOREIGN KEY contact_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY contact_id
Created by SQL::Translator 0.11003 chado-1.23/modules/nofuncs.sql000644 000765 000024 00000574720 12061672320 016454 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; -- ================================================ -- TABLE: cvprop -- ================================================ create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: chadoprop -- ================================================ create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL, CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3), CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) ); SET search_path = public,pg_catalog; -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- 05-31-2011 -- added 'name' column to phenotype. non-unique human readable field. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, name TEXT default null, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- changes 2011-05-31 -- added type_id to genotype (can be null for backward compatibility) -- added genotypeprop table -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- ================================================ -- TABLE: genotypeprop -- ================================================ create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import contact from contact -- ================================================================= -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS NULL; -- ================================================ -- TABLE: projectprop -- ================================================ CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects'; COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)'; -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from project -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_cvterm -- ================================================ CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id integer not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_cvtermprop -- ================================================ create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- ================================================ -- TABLE: stock_dbxrefprop -- ================================================ create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/modules/organism/000755 000765 000024 00000000000 12061672376 016073 5ustar00cainstaff000000 000000 chado-1.23/modules/phenotype/000755 000765 000024 00000000000 12061672375 016266 5ustar00cainstaff000000 000000 chado-1.23/modules/phylogeny/000755 000765 000024 00000000000 12061672376 016272 5ustar00cainstaff000000 000000 chado-1.23/modules/project/000755 000765 000024 00000000000 12061672376 015722 5ustar00cainstaff000000 000000 chado-1.23/modules/pub/000755 000765 000024 00000000000 12061672376 015042 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/000755 000765 000024 00000000000 12061672376 016064 5ustar00cainstaff000000 000000 chado-1.23/modules/stock/000755 000765 000024 00000000000 12061672376 015377 5ustar00cainstaff000000 000000 chado-1.23/modules/stock/stock.html000644 000765 000024 00000162423 11634146500 017406 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

stock
stock_pub
stockprop
stockprop_pub
stock_relationship
stock_relationship_cvterm
stock_relationship_pub
stock_dbxref
stock_cvterm
stock_cvtermprop
stock_genotype
stockcollection
stockcollectionprop
stockcollection_stock
stock_dbxrefprop

stock

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Comments:

$Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $
==========================================
Chado stock module
DEPENDENCIES
============
:import cvterm from cv
:import pub from pub
:import dbxref from general
:import organism from organism
:import genotype from genetic
:import contact from contact
================================================
TABLE: stock
================================================
Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
Field Name Data Type Size Default Value Other Foreign Key
stock_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. dbxref.dbxref_id
organism_id integer 10 UNIQUE, The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. organism.organism_id
name varchar 255 The name is a human-readable local name for a stock.
uniquename text 64000 UNIQUE, NOT NULL
description text 64000 The description is the genetic description provided in the stock list.
type_id integer 10 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm. cvterm.cvterm_id
is_obsolete boolean 0 false NOT NULL

Indices

Name Fields
stock_name_ind1 name
stock_idx1 dbxref_id
stock_idx2 organism_id
stock_idx3 type_id
stock_idx4 uniquename

Constraints

Type Fields
NOT NULL stock_id
FOREIGN KEY dbxref_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_obsolete
UNIQUE organism_id, uniquename, type_id

stock_pub

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Comments:

================================================
TABLE: stock_pub
================================================
Provenance. Linking table between stocks and, for example, a stocklist computer file.
Field Name Data Type Size Default Value Other Foreign Key
stock_pub_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_pub_idx1 stock_id
stock_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stock_pub_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stock_id, pub_id

stockprop

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Comments:

================================================
TABLE: stockprop
================================================
A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockprop_idx1 stock_id
stockprop_idx2 type_id

Constraints

Type Fields
NOT NULL stockprop_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_id, type_id, rank

stockprop_pub

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Comments:

================================================
TABLE: stockprop_pub
================================================
Provenance. Any stockprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_pub_id integer 11 PRIMARY KEY, NOT NULL
stockprop_id integer 10 UNIQUE, NOT NULL stockprop.stockprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stockprop_pub_idx1 stockprop_id
stockprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stockprop_pub_id
NOT NULL stockprop_id
FOREIGN KEY stockprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stockprop_id, pub_id

stock_relationship

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Comments:

================================================
TABLE: stock_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL, stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock. stock.stock_id
object_id integer 10 UNIQUE, NOT NULL, stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock. stock.stock_id
type_id integer 10 UNIQUE, NOT NULL, stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
value text 64000 NULL stock_relationship.value is for additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.

Indices

Name Fields
stock_relationship_idx1 subject_id
stock_relationship_idx2 object_id
stock_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL stock_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

stock_relationship_cvterm

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TABLE: stock_relationship_cvterm
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For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_cvterm_id integer 11 PRIMARY KEY, NOT NULL
stock_relationship_id integer 10 NOT NULL stock_relationship.stock_relationship_id
cvterm_id integer 10 NOT NULL cvterm.cvterm_id
pub_id integer 10 pub.pub_id

Constraints

Type Fields
NOT NULL stock_relationship_cvterm_id
NOT NULL stock_relationship_id
FOREIGN KEY stock_relationship_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
FOREIGN KEY pub_id

stock_relationship_pub

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TABLE: stock_relationship_pub
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Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_pub_id integer 11 PRIMARY KEY, NOT NULL
stock_relationship_id integer 10 UNIQUE, NOT NULL stock_relationship.stock_relationship_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_relationship_pub_idx1 stock_relationship_id
stock_relationship_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL stock_relationship_pub_id
NOT NULL stock_relationship_id
FOREIGN KEY stock_relationship_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE stock_relationship_id, pub_id

stock_dbxref

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TABLE: stock_dbxref
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stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxref_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.

Indices

Name Fields
stock_dbxref_idx1 stock_id
stock_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL stock_dbxref_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE stock_id, dbxref_id

stock_cvterm

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TABLE: stock_cvterm
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stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvterm_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
is_not boolean 0 false NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_cvterm_idx1 stock_id
stock_cvterm_idx2 cvterm_id
stock_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL stock_cvterm_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_not
NOT NULL rank
UNIQUE stock_id, cvterm_id, pub_id, rank

stock_cvtermprop

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TABLE: stock_cvtermprop
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Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
stock_cvterm_id integer 10 UNIQUE, NOT NULL stock_cvterm.stock_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
stock_cvtermprop_idx1 stock_cvterm_id
stock_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL stock_cvtermprop_id
NOT NULL stock_cvterm_id
FOREIGN KEY stock_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_cvterm_id, type_id, rank

stock_genotype

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TABLE: stock_genotype
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Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
Field Name Data Type Size Default Value Other Foreign Key
stock_genotype_id integer 11 PRIMARY KEY, NOT NULL
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id

Indices

Name Fields
stock_genotype_idx1 stock_id
stock_genotype_idx2 genotype_id

Constraints

Type Fields
NOT NULL stock_genotype_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
UNIQUE stock_id, genotype_id

stockcollection

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TABLE: stockcollection
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The lab or stock center distributing the stocks in their collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, type_id is the collection type cv. cvterm.cvterm_id
contact_id integer 10 NULL contact_id links to the contact information for the collection. contact.contact_id
name varchar 255 name is the collection.
uniquename text 64000 UNIQUE, NOT NULL, uniqename is the value of the collection cv.

Indices

Name Fields
stockcollection_name_ind1 name
stockcollection_idx1 contact_id
stockcollection_idx2 type_id
stockcollection_idx3 uniquename

Constraints

Type Fields
NOT NULL stockcollection_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY contact_id
NOT NULL uniquename
UNIQUE uniquename, type_id

stockcollectionprop

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TABLE: stockcollectionprop
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The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
Field Name Data Type Size Default Value Other Foreign Key
stockcollectionprop_id integer 11 PRIMARY KEY, NOT NULL
stockcollection_id integer 10 UNIQUE, NOT NULL stockcollection.stockcollection_id
type_id integer 10 UNIQUE, NOT NULL, The cv for the type_id is "stockcollection property type". cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockcollectionprop_idx1 stockcollection_id
stockcollectionprop_idx2 type_id

Constraints

Type Fields
NOT NULL stockcollectionprop_id
NOT NULL stockcollection_id
FOREIGN KEY stockcollection_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stockcollection_id, type_id, rank

stockcollection_stock

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TABLE: stockcollection_stock
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stockcollection_stock links a stock collection to the stocks which are contained in the collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_stock_id integer 11 PRIMARY KEY, NOT NULL
stockcollection_id integer 10 UNIQUE, NOT NULL stockcollection.stockcollection_id
stock_id integer 10 UNIQUE, NOT NULL stock.stock_id

Indices

Name Fields
stockcollection_stock_idx1 stockcollection_id
stockcollection_stock_idx2 stock_id

Constraints

Type Fields
NOT NULL stockcollection_stock_id
NOT NULL stockcollection_id
FOREIGN KEY stockcollection_id
NOT NULL stock_id
FOREIGN KEY stock_id
UNIQUE stockcollection_id, stock_id

stock_dbxrefprop

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TABLE: stock_dbxrefprop
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A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxrefprop_id integer 11 PRIMARY KEY, NOT NULL
stock_dbxref_id integer 10 UNIQUE, NOT NULL stock_dbxref.stock_dbxref_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_dbxrefprop_idx1 stock_dbxref_id
stock_dbxrefprop_idx2 type_id

Constraints

Type Fields
NOT NULL stock_dbxrefprop_id
NOT NULL stock_dbxref_id
FOREIGN KEY stock_dbxref_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE stock_dbxref_id, type_id, rank
Created by SQL::Translator 0.11003 chado-1.23/modules/stock/stock.sql000644 000765 000024 00000044066 11634146053 017246 0ustar00cainstaff000000 000000 -- $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ -- ========================================== -- Chado stock module -- -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- ================================================ -- TABLE: stock -- ================================================ create table stock ( stock_id serial not null, primary key (stock_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, description text, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean not null default 'false', constraint stock_c1 unique (organism_id,uniquename,type_id) ); create index stock_name_ind1 on stock (name); create index stock_idx1 on stock (dbxref_id); create index stock_idx2 on stock (organism_id); create index stock_idx3 on stock (type_id); create index stock_idx4 on stock (uniquename); COMMENT ON TABLE stock IS 'Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.'; COMMENT ON COLUMN stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.'; COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.'; COMMENT ON COLUMN stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.'; COMMENT ON COLUMN stock.description IS 'The description is the genetic description provided in the stock list.'; COMMENT ON COLUMN stock.name IS 'The name is a human-readable local name for a stock.'; -- ================================================ -- TABLE: stock_pub -- ================================================ create table stock_pub ( stock_pub_id serial not null, primary key (stock_pub_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_pub_c1 unique (stock_id,pub_id) ); create index stock_pub_idx1 on stock_pub (stock_id); create index stock_pub_idx2 on stock_pub (pub_id); COMMENT ON TABLE stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.'; -- ================================================ -- TABLE: stockprop -- ================================================ create table stockprop ( stockprop_id serial not null, primary key (stockprop_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stockprop_c1 unique (stock_id,type_id,rank) ); create index stockprop_idx1 on stockprop (stock_id); create index stockprop_idx2 on stockprop (type_id); COMMENT ON TABLE stockprop IS 'A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: stockprop_pub -- ================================================ create table stockprop_pub ( stockprop_pub_id serial not null, primary key (stockprop_pub_id), stockprop_id int not null, foreign key (stockprop_id) references stockprop (stockprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stockprop_pub_c1 unique (stockprop_id,pub_id) ); create index stockprop_pub_idx1 on stockprop_pub (stockprop_id); create index stockprop_pub_idx2 on stockprop_pub (pub_id); COMMENT ON TABLE stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: stock_relationship -- ================================================ create table stock_relationship ( stock_relationship_id serial not null, primary key (stock_relationship_id), subject_id int not null, foreign key (subject_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index stock_relationship_idx1 on stock_relationship (subject_id); create index stock_relationship_idx2 on stock_relationship (object_id); create index stock_relationship_idx3 on stock_relationship (type_id); COMMENT ON COLUMN stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.'; COMMENT ON COLUMN stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.'; COMMENT ON COLUMN stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; COMMENT ON COLUMN stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.'; COMMENT ON COLUMN stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.'; -- ================================================ -- TABLE: stock_relationship_cvterm -- ================================================ CREATE TABLE stock_relationship_cvterm ( stock_relationship_cvterm_id SERIAL NOT NULL, PRIMARY KEY (stock_relationship_cvterm_id), stock_relationship_id integer NOT NULL, FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED, cvterm_id integer NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, pub_id integer, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT ); COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm'; -- ================================================ -- TABLE: stock_relationship_pub -- ================================================ create table stock_relationship_pub ( stock_relationship_pub_id serial not null, primary key (stock_relationship_pub_id), stock_relationship_id integer not null, foreign key (stock_relationship_id) references stock_relationship (stock_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint stock_relationship_pub_c1 unique (stock_relationship_id,pub_id) ); create index stock_relationship_pub_idx1 on stock_relationship_pub (stock_relationship_id); create index stock_relationship_pub_idx2 on stock_relationship_pub (pub_id); COMMENT ON TABLE stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.'; -- ================================================ -- TABLE: stock_dbxref -- ================================================ create table stock_dbxref ( stock_dbxref_id serial not null, primary key (stock_dbxref_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint stock_dbxref_c1 unique (stock_id,dbxref_id) ); create index stock_dbxref_idx1 on stock_dbxref (stock_id); create index stock_dbxref_idx2 on stock_dbxref (dbxref_id); COMMENT ON TABLE stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.'; COMMENT ON COLUMN stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.'; -- ================================================ -- TABLE: stock_cvterm -- ================================================ create table stock_cvterm ( stock_cvterm_id serial not null, primary key (stock_cvterm_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank) ); create index stock_cvterm_idx1 on stock_cvterm (stock_id); create index stock_cvterm_idx2 on stock_cvterm (cvterm_id); create index stock_cvterm_idx3 on stock_cvterm (pub_id); COMMENT ON TABLE stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.'; -- ================================================ -- TABLE: stock_cvtermprop -- ================================================ create table stock_cvtermprop ( stock_cvtermprop_id serial not null, primary key (stock_cvtermprop_id), stock_cvterm_id int not null, foreign key (stock_cvterm_id) references stock_cvterm (stock_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank) ); create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id); create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id); COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for stock to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the stockprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN stock_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN stock_cvtermprop.rank IS 'Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: stock_genotype -- ================================================ create table stock_genotype ( stock_genotype_id serial not null, primary key (stock_genotype_id), stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, constraint stock_genotype_c1 unique (stock_id, genotype_id) ); create index stock_genotype_idx1 on stock_genotype (stock_id); create index stock_genotype_idx2 on stock_genotype (genotype_id); COMMENT ON TABLE stock_genotype IS 'Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.'; -- ================================================ -- TABLE: stockcollection -- ================================================ create table stockcollection ( stockcollection_id serial not null, primary key (stockcollection_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, contact_id int null, foreign key (contact_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, name varchar(255), uniquename text not null, constraint stockcollection_c1 unique (uniquename,type_id) ); create index stockcollection_name_ind1 on stockcollection (name); create index stockcollection_idx1 on stockcollection (contact_id); create index stockcollection_idx2 on stockcollection (type_id); create index stockcollection_idx3 on stockcollection (uniquename); COMMENT ON TABLE stockcollection IS 'The lab or stock center distributing the stocks in their collection.'; COMMENT ON COLUMN stockcollection.uniquename IS 'uniqename is the value of the collection cv.'; COMMENT ON COLUMN stockcollection.type_id IS 'type_id is the collection type cv.'; COMMENT ON COLUMN stockcollection.name IS 'name is the collection.'; COMMENT ON COLUMN stockcollection.contact_id IS 'contact_id links to the contact information for the collection.'; -- ================================================ -- TABLE: stockcollectionprop -- ================================================ create table stockcollectionprop ( stockcollectionprop_id serial not null, primary key (stockcollectionprop_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint stockcollectionprop_c1 unique (stockcollection_id,type_id,rank) ); create index stockcollectionprop_idx1 on stockcollectionprop (stockcollection_id); create index stockcollectionprop_idx2 on stockcollectionprop (type_id); COMMENT ON TABLE stockcollectionprop IS 'The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.'; COMMENT ON COLUMN stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".'; -- ================================================ -- TABLE: stockcollection_stock -- ================================================ create table stockcollection_stock ( stockcollection_stock_id serial not null, primary key (stockcollection_stock_id), stockcollection_id int not null, foreign key (stockcollection_id) references stockcollection (stockcollection_id) on delete cascade INITIALLY DEFERRED, stock_id int not null, foreign key (stock_id) references stock (stock_id) on delete cascade INITIALLY DEFERRED, constraint stockcollection_stock_c1 unique (stockcollection_id,stock_id) ); create index stockcollection_stock_idx1 on stockcollection_stock (stockcollection_id); create index stockcollection_stock_idx2 on stockcollection_stock (stock_id); COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links a stock collection to the stocks which are contained in the collection.'; -- ================================================ -- TABLE: stock_dbxrefprop -- ================================================ create table stock_dbxrefprop ( stock_dbxrefprop_id serial not null, primary key (stock_dbxrefprop_id), stock_dbxref_id int not null, foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank) ); create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id); create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id); COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; chado-1.23/modules/sequence/apollo-bridge/000755 000765 000024 00000000000 12061672376 020604 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/bdgp/000755 000765 000024 00000000000 12061672375 016777 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/bridges/000755 000765 000024 00000000000 12061672376 017503 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/functions/000755 000765 000024 00000000000 12061672376 020074 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/gencode/000755 000765 000024 00000000000 12061672376 017470 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/gff-bridge/000755 000765 000024 00000000000 12061672376 020060 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/sequence-dbapi.sqli000644 000765 000024 00000061277 11256710150 021644 0ustar00cainstaff000000 000000 -- $Id: sequence-dbapi.sqli,v 1.2 2005-03-15 21:28:15 sshu Exp $ -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- sequence-dbapi.sqli -- -- STATUS: alpha -- -- this interface describes the functions implemented by -- a chado database over the sequence module -- -- [at this time, this API specifies functions some of which do not -- yet have an implementation - a default impl will be -- provided soon] -- -- the interface is specified in pseudo-SQL function syntax -- it is intended as formal documentation for DB Admins and -- application programmers. It is not intended to be used -- directly by the DB. The DB should implement these functions -- using a language pertinent to the DBMS implementing policies -- pertinent to the policy chosen by the MOD and DB Admin. -- -- a default postgresql implementation will be provided, in -- the functions/ directory. hopefully it should not be difficult -- to port these to other DBMS systems -- -- the DB API contains granual 'atomic' functions; that is, -- functions that neither accept not return complex datatypes -- such as objects, XML or other data structures. -- The API accepts/returns primitive values and relations. -- As such, the DB API is perhaps mostly useful for applications that -- modify the database. The API is intended to be complementary -- to APIs that accept or return complex datatypes, such as ChadoXML -- -- CONVENTIONS: -- functions are generally named _ -- the noun phrase typically refers to a chado table name, -- a type in some ontology such as SO, or an emergent -- table/type, such as "gene model" -- -- TODO: Document possible exceptions raised -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- ************************************************************ -- ** Data Modification Functions ** -- ** ** -- ** Calling any of these functions can result in data ** -- ** being modified ** -- ** ** -- ** Each function should note in the comments which ** -- ** tables are affected ** -- ** [d] - may result in deletion ** -- ** [u] - may result in update ** -- ** [i] - may result in insertion ** -- ** Cascading deletes are not explicitly noted; ** -- ** (ie if table 'feature' can be deleted then ** -- ** 'featureloc' may be deleted as a consequence) ** -- ************************************************************ -- ============================================================ -- FUNCTION: delete_gene_model -- ============================================================ -- + different chado instances may have different policies -- + simple policy: blow away gene and subfeatures -- + integrated-db policy: remove exons and all featurelocs -- (preserves data attached to features) -- + undecided: additional tracking? obsoletion property? -- TABLES AFFECTED: feature[d] DECLARE FUNCTION delete_gene_model(gene_feature_id integer NOT NULL); DECLARE FUNCTION delete_gene_model(uniquename varchar NOT NULL, organism_id integer NOT NULL); -- ============================================================ -- FUNCTION: delete_transcript_model -- ============================================================ -- + see delete_gene_model -- TABLES AFFECTED: feature[d] DECLARE FUNCTION delete_transcript_model(transcript_feature_id integer NOT NULL); DECLARE FUNCTION delete_transcript_model(uniquename varchar NOT NULL, organism_id integer NOT NULL); -- ============================================================ -- remove exon from transcript -- ============================================================ -- + deletes feature_relationship -- + will delete feature if this is the only exon on this transcript -- TABLES AFFECTED: feature[d] feature_relationship[d] DECLARE FUNCTION remove_exon_from_transcript(transcript_feature_id integer NOT NULL, exon_fmin integer NOT NULL, exon_fmax integer NOT NULL) RETURNS remaining_transcript_exon_count integer NOT NULL; -- ============================================================ -- FUNCTION: add_exon_to_transcript -- ============================================================ -- + adds feature_relationship -- + will create exon feature if this is the first exon on this transcript -- + will generate a name for the new exon if required -- TABLES AFFECTED: feature[i] featureloc[i] feature_relationship[i] DELCARE add_exon_to_transcript(transcript_feature_id integer NOT NULL, exon_fmin integer NOT NULL, exon_fmax integer NOT NULL, exon_strand integer NOT NULL) RETURNS remaining_transcript_exon_count integer NOT NULL; -- ============================================================ -- FUNCTION: change_exonloc_for_transcript -- ============================================================ -- + changes exon coordinates within a transcript -- + coordinates are relative to genomic -- + if a transcript has >1 exon, this will split the exon -- UNLESS the new coordinates match an existing exon -- + will generate a name for the new exon if required -- TABLES AFFECTED: feature[idu] featureloc[idu] feature_relationship[id] DECLARE FUNCTION change_exonloc_for_transcript(transcript_feature_id integer NOT NULL, exon_fmin_old integer NOT NULL, exon_fmax_old integer NOT NULL, exon_fmin_new integer NOT NULL, exon_fmax_new integer NOT NULL) RETURNS remaining_transcript_exon_count integer NOT NULL; -- ============================================================ -- FUNCTION: set_feature_residues -- ============================================================ -- convenience method for setting feature.residues -- [should this be handled by triggers?] -- + also sets feature.seqlen -- + also sets feature.md5checksum -- -- setting residues to NULL will *NOT* clear seqlen or md5checksum -- -- is this too onerous for the DB to implement? the MD5 calculation -- will require using the pg foreign language interface -- TABLES AFFECTED: feature[u] DECLARE FUNCTION set_feature_residues(feature_id integer NOT NULL, residues text); -- ============================================================ -- FUNCTION: new_feature -- ============================================================ -- inserts a new feature -- + ftype - feature type (SO cv assumed) -- + root_feature_id - root of the feature graph (eg gene) -- + if the feature does not have a name or uniquename, this -- will generated based on the type and root_feature -- (root_feature_id and uniquename cannot BOTH be null) -- [this allows centralization of naming policy] -- + organism_id MUST be set UNLESS set_default_organism has been called -- TABLES AFFECTED: feature[i] dbxref[iu] DECLARE FUNCTION new_basic_analysis_feature(name varchar, uniquename varchar, dbxref_id integer, ftype varchar NOT NULL, residues text, root_feature_id integer rank_by_root integer NOT NULL) RETURNS feature_id integer NOT NULL; -- ============================================================ -- FUNCTION: new_basic_analysis_feature -- ============================================================ -- inserts a new analysis feature. adds featureloc for convenience -- basic analysis features typically have zero or one parent -- TABLES AFFECTED: feature[i] dbxref[iu] featureloc[i] -- feature_relationship[id] analysisfeature[i] DECLARE FUNCTION new_basic_analysis_feature(srcfeature_name varchar NOT NULL, program varchar NOT NULL, sourcename varchar, organism_id integer, ftype varchar DEFAULT 'match', fmin integer NOT NULL, fmax integer NOT NULL, strand integer NOT NULL, score float, frame integer, parent_feature_id integer, rank_by_root integer) RETURNS feature_id integer NOT NULL; -- ============================================================ -- FUNCTION: new_basic_match_feature -- ============================================================ -- inserts a new analysis feature. adds BOTH featurelocs for convenience -- basic match features typically have zero or one parent -- (zero if Hit, 1 if HSP) -- TABLES AFFECTED: feature[i] dbxref[iu] featureloc[i] -- feature_relationship[id] analysisfeature[i] DECLARE FUNCTION new_basic_analysis_feature(srcfeature_name varchar NOT NULL, program varchar NOT NULL, sourcename varchar, organism_id integer, fmin integer NOT NULL, fmax integer NOT NULL, strand integer NOT NULL, target_fmin integer NOT NULL, target_fmax integer NOT NULL, score float, frame integer, cigar varchar, parent_feature_id integer, rank_by_root integer) RETURNS feature_id integer NOT NULL; -- ************************************************************ -- ** Non-modifying Functions ** -- ************************************************************ -- The functions below have no side-effects (ie they never -- result in update/delete/insert of any data) -- ============================================================ -- FUNCTION: synthesize_feature_uniquename -- ============================================================ -- synthesizes the name of a feature using DB-specific naming policy -- + ftype - feature type (SO cv assumed) -- + root_feature_id - root of the feature graph (eg gene) -- + rank_by_root - eg exon number within gene DECLARE FUNCTION synthesize_feature_uniquename(ftype varchar NOT NULL, root_feature_id integer NOT NULL, rank_by_root integer NOT NULL) RETURNS uniquename varchar NOT NULL; -- ============================================================ -- FUNCTION: get_sub_feature_ids -- ============================================================ -- return feature's child feature_id and their child feature_id -- all way down to leaf nodes -- + root_feature_id - root of the feature graph (eg gene) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_sub_feature_ids(root_feature_id integer not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_sub_feature_ids -- ============================================================ -- return feature's child feature_id and their child feature_id -- all way down to leaf nodes, with depth -- + root_feature_id - root of the feature graph (eg gene) -- + depth - graph depth (eg 1) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_sub_feature_ids(root_feature_id integer not null, depth integer not null) RETURNS setof feature_id, depth; -- ============================================================ -- FUNCTION: get_sub_feature_ids -- ============================================================ -- return feature (specified with sql arg) child feature_id -- and their child feature_id all way down to leaf nodes -- NOTE: sql must be like 'select distinct feature_id from ...' -- + sql - to get root_feature_id of the feature graph (eg gene) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_sub_feature_ids(sql text not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_up_feature_ids -- ============================================================ -- return feature's parent feature_id and their parent feature_id -- all way up to root -- + leaf_feature_id - leaf of the feature graph (e.g. exon) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_up_feature_ids(leaf_feature_id integer not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_up_feature_ids -- ============================================================ -- return feature's parent feature_id and their parent feature_id -- all way up to root, with depth value (in reverse order, leaf node smallest depth) -- + leaf_feature_id - leaf of the feature graph (e.g. exon) -- + depth - reversed graph depth -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_up_feature_ids(leaf_feature_id integer not null, depth integer not null) RETURNS setof feature_id, depth; -- ============================================================ -- FUNCTION: get_up_feature_ids -- ============================================================ -- return feature (specified with sql arg) parent feature_id -- and their parent feature_id all way up to root -- NOTE: sql must be like 'select distinct feature_id from ...' -- + sql - to get leaf_feature_id of the feature graph (eg exon) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_up_feature_ids(sql text not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids -- ============================================================ -- return all feature ids of the feature graph that feature_id -- is in -- + feature_id - feature id of the feature graph (e.g. mRNA) -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids(feature_id integer not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids -- ============================================================ -- return all feature ids of the feature graph that feature_id -- (specified with sql arg) is in -- NOTE: sql must be like 'select distinct feature_id from ...' -- + sql - get feature_id of a feature graph -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids(sql text not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_sub_feature_ids_by_type_src -- ============================================================ -- return child feature_id and their child feature_id of feature -- specified by the feature type and the feature's src feature name -- all way down to leaf nodes -- + feature_type -- + src - feature name that returned features are locateded on -- + is_analysis -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_sub_feature_ids_by_type_src(feature_type varchar not null src varchar not null, is_analysis char(1) not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_type -- ============================================================ -- return all feature ids of the feature graph, some of which are -- of the feature type and is_analysis value -- + feature_type - SO term -- + is_analysis -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_type(feature_type varchar not null, is_analysis char(1) not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_type_src -- ============================================================ -- return all feature ids of the feature graph, some of which are -- of the feature type and is_analysis value -- + feature_type - SO term -- + src - feature name that returned features are locateded on -- + is_analysis -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_type(feature_type varchar not null, src varchar not null, is_analysis char(1) not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_type_name -- ============================================================ -- return all feature ids of the feature graph, some of which are -- of the specified type and have the feature name -- + feature_type - SO term -- + feature_name - feature name, sql wild card (%) is allowed -- + is_analysis -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_type_name(feature_type varchar not null, feature_name varchar not null, is_analysis char(1) not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_ont -- ============================================================ -- return all feature ids of the feature graph, some of which have -- assignment of the cvterm of the aspect -- + aspect - cv.name -- + cvterm_name -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_ont(aspect varchar not null, cvterm_name varchar not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_ont_root -- ============================================================ -- return all feature ids of the feature graph, some of which have -- assignment of the cvterm of the aspect or have assignment of -- cvterms that are sub nodes of the cvterm of the aspect -- + aspect - cv.name -- + cvterm_name -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_ont_root(aspect varchar not null, cvterm_name varchar not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_propval -- ============================================================ -- return all feature ids of the feature graph, some of which have -- the property value -- + property_val -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_propval(property_val varchar not null) RETURNS setof feature_id; -- ============================================================ -- FUNCTION: get_feature_ids_by_child_count -- ============================================================ -- return all feature ids of the feature graph, some of which -- are of the feature type (parent_feature_type) who has -- the specified number of child features of the feature type -- (child_feature_type) -- + parent_feature_type - SO term -- + child_feature_type - SO term -- + number -- + operator - sql comparison operator string (eg >=, =, <, etc) -- + is_analysis -- impl: see functions/feature_ids_fx.plpgsql DECLARE FUNCTION get_feature_ids_by_child_count(parent_feature_type varchar not null, child_feature_type varchar not null, number integer not null, operator varchar not null, is_analysis char(1) not null) RETURNS setof feature_id; -- ************************************************************ -- ** Configuration Management ** -- ************************************************************ -- ============================================================ -- FUNCTION: set_default_organism_id -- ============================================================ -- In some chado instances it is desirable to have a default -- organism; when calling the methods above, the organism column -- may be left blank, in which case the deafult is used -- [NOTE: THIS SHOULD BE MOVED TO ORGANISM MODULE] -- this will update a 'private' table (in seperate postgresql schemaspace?) set_default_organism_id(organism_id integer NOT NULL); -- ============================================================ -- FUNCTION: set_default_organism -- ============================================================ -- [NOTE: THIS SHOULD BE MOVED TO ORGANISM MODULE] -- will NOT create organism if not present DECLARE FUNCTION set_default_organism_id(genus varchar NOT NULL, species varchar NOT NULL) RETURNS organism_id integer NOT NULL; -- ************************************************************ -- Mereological spatial relations -- -- This is a declaration of relations which may be implemented -- as either views or tables (typically only the latter in -- a denormalized warehouse DB) -- -- a RELATION declaration is stating that either a TABLE or VIEW -- exists. The relation is not necessarily updateable (ie it -- may be a view) -- -- default VIEW implementations will be provided; -- DB Admins may wish to materialize these views (eg in a report db) -- ************************************************************ -- identical strand (ST) DECLARE RELATION feature_on_same_strand_as_feature(subject_id, object_id, overlaplen); -- at least 1bp of overlap (S!T) DECLARE RELATION feature_overlaps_feature(subject_id, object_id, overlaplen); -- overlaps AND on same strand (S!T) DECLARE RELATION feature_overlaps_feature_on_same_strand(subject_id, object_id, overlaplen); -- feature overlaps and completely contains the other feature (!ST) DECLARE RELATION feature_contains_feature(subject_id, object_id); -- inverse of above (!ST) DECLARE RELATION feature_contained_by_feature(subject_id, object_id); -- identity (ST) DECLARE RELATION feature_same_loc_as_feature(subject_id, object_id); -- edges touch but no overlap; distance=0 (S!T) DECLARE RELATION feature_adjacent_to_feature(subject_id, object_id); -- edges touch, subj upstream of obj (!S!T) DECLARE RELATION feature_adjacent_upstream_of_feature(subject_id, object_id); -- edges touch, subj downstream of obj (!S!T) DECLARE RELATION feature_adjacent_downstream_of_feature(subject_id, object_id); -- opposite of overlap (S!T) DECLARE RELATION feature_disjoint_from_feature(subject_id, object_id, distance); -- upstream and no overlap (!ST) DECLARE RELATION feature_upstream_of_feature(subject_id, object_id, distance); -- downstream and no overlap (!ST) DECLARE RELATION feature_downstream_of_feature(subject_id, object_id, distance); -- distance between features, -ve number indicates degree of overlap DECLARE RELATION feature_distance(subject_id, object_id, distance); -- part_of (!ST) DECLARE RELATION feature_part_of_feature(subject_id, object_id); chado-1.23/modules/sequence/sequence.html000644 000765 000024 00000246321 11256710150 020556 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

feature
featureloc
featureloc_pub
feature_pub
feature_pubprop
featureprop
featureprop_pub
feature_dbxref
feature_relationship
feature_relationship_pub
feature_relationshipprop
feature_relationshipprop_pub
feature_cvterm
feature_cvtermprop
feature_cvterm_dbxref
feature_cvterm_pub
synonym
feature_synonym

feature

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Comments:

$Id: sequence.html,v 1.10 2009-08-28 19:42:15 scottcain Exp $
==========================================
Chado sequence module
=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from general
=================================================================
================================================
TABLE: feature
================================================
A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.
Field Name Data Type Size Default Value Other Foreign Key
feature_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref. dbxref.dbxref_id
organism_id integer 10 UNIQUE, NOT NULL, The organism to which this feature belongs. This column is mandatory. organism.organism_id
name varchar 255 The optional human-readable common name for a feature, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.
residues text 64000 A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.
seqlen integer 10 The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.
md5checksum char 32 The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.
type_id integer 10 UNIQUE, NOT NULL, A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table. cvterm.cvterm_id
is_analysis boolean 0 false NOT NULL, Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.
is_obsolete boolean 0 false NOT NULL, Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.
timeaccessioned timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.
timelastmodified timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.

Indices

Name Fields
feature_name_ind1 name
feature_idx1 dbxref_id
feature_idx2 organism_id
feature_idx3 type_id
feature_idx4 uniquename

Constraints

Type Fields
NOT NULL feature_id
FOREIGN KEY dbxref_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_analysis
NOT NULL is_obsolete
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE organism_id, uniquename, type_id

featureloc

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Comments:

COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified
by the combination of organism, uniquename and feature type';
================================================
TABLE: featureloc
================================================
The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL, The feature that is being located. Any feature can have zero or more featurelocs. feature.feature_id
srcfeature_id integer 10 The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph. feature.feature_id
fmin integer 10 The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.
is_fmin_partial boolean 0 false NOT NULL, This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.
fmax integer 10 The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).
is_fmax_partial boolean 0 false NOT NULL, This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.
strand integer 5 The orientation/directionality of the location. Should be 0, -1 or +1.
phase integer 10 Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.
residue_info text 64000 Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.
locgroup integer 10 0 UNIQUE, NOT NULL, This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).
rank integer 10 0 UNIQUE, NOT NULL, Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.

Indices

Name Fields
featureloc_idx1 feature_id
featureloc_idx2 srcfeature_id
featureloc_idx3 srcfeature_id, fmin, fmax

Constraints

Type Fields
NOT NULL featureloc_id
NOT NULL feature_id
FOREIGN KEY feature_id
FOREIGN KEY srcfeature_id
NOT NULL is_fmin_partial
NOT NULL is_fmax_partial
NOT NULL locgroup
NOT NULL rank
UNIQUE feature_id, locgroup, rank
CHECK

featureloc_pub

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Comments:

COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely
partition locations for any one feature';
================================================
TABLE: featureloc_pub
================================================
Provenance of featureloc. Linking table between featurelocs and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_pub_id integer 11 PRIMARY KEY, NOT NULL
featureloc_id integer 10 UNIQUE, NOT NULL featureloc.featureloc_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureloc_pub_idx1 featureloc_id
featureloc_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featureloc_pub_id
NOT NULL featureloc_id
FOREIGN KEY featureloc_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE featureloc_id, pub_id

feature_pub

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Comments:

================================================
TABLE: feature_pub
================================================
Provenance. Linking table between features and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
feature_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_pub_idx1 feature_id
feature_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_pub_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_id, pub_id

feature_pubprop

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Comments:

================================================
TABLE: feature_pubprop
================================================
Property or attribute of a feature_pub link.
Field Name Data Type Size Default Value Other Foreign Key
feature_pubprop_id integer 11 PRIMARY KEY, NOT NULL
feature_pub_id integer 10 UNIQUE, NOT NULL feature_pub.feature_pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_pubprop_idx1 feature_pub_id

Constraints

Type Fields
NOT NULL feature_pubprop_id
NOT NULL feature_pub_id
FOREIGN KEY feature_pub_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_pub_id, type_id, rank

featureprop

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Comments:

================================================
TABLE: featureprop
================================================
A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used

Indices

Name Fields
featureprop_idx1 feature_id
featureprop_idx2 type_id

Constraints

Type Fields
NOT NULL featureprop_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_id, type_id, rank

featureprop_pub

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For any one feature, multivalued property-value pairs must be differentiated by rank.
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TABLE: featureprop_pub
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Provenance. Any featureprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_pub_id integer 11 PRIMARY KEY, NOT NULL
featureprop_id integer 10 UNIQUE, NOT NULL featureprop.featureprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureprop_pub_idx1 featureprop_id
featureprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featureprop_pub_id
NOT NULL featureprop_id
FOREIGN KEY featureprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE featureprop_id, pub_id

feature_dbxref

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TABLE: feature_dbxref
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Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.
Field Name Data Type Size Default Value Other Foreign Key
feature_dbxref_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false

Indices

Name Fields
feature_dbxref_idx1 feature_id
feature_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL feature_dbxref_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE feature_id, dbxref_id

feature_relationship

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TABLE: feature_relationship
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Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. This is typically the subfeature. feature.feature_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. This is typically the container feature. feature.feature_id
type_id integer 10 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology. cvterm.cvterm_id
value text 64000 NULL Additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.

Indices

Name Fields
feature_relationship_idx1 subject_id
feature_relationship_idx2 object_id
feature_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL feature_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

feature_relationship_pub

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TABLE: feature_relationship_pub
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Provenance. Attach optional evidence to a feature_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_relationship_id integer 10 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationship_pub_idx1 feature_relationship_id
feature_relationship_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_relationship_pub_id
NOT NULL feature_relationship_id
FOREIGN KEY feature_relationship_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_relationship_id, pub_id

feature_relationshipprop

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TABLE: feature_relationshipprop
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Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_id integer 11 PRIMARY KEY, NOT NULL
feature_relationship_id integer 10 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_relationshipprop_idx1 feature_relationship_id
feature_relationshipprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_relationshipprop_id
NOT NULL feature_relationship_id
FOREIGN KEY feature_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_relationship_id, type_id, rank

feature_relationshipprop_pub

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TABLE: feature_relationshipprop_pub
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Provenance for feature_relationshipprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_relationshipprop_id integer 10 UNIQUE, NOT NULL feature_relationshipprop.feature_relationshipprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationshipprop_pub_idx1 feature_relationshipprop_id
feature_relationshipprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_relationshipprop_pub_id
NOT NULL feature_relationshipprop_id
FOREIGN KEY feature_relationshipprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_relationshipprop_id, pub_id

feature_cvterm

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TABLE: feature_cvterm
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Associate a term from a cv with a feature, for example, GO annotation.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL, Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref. pub.pub_id
is_not boolean 0 false NOT NULL, If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_cvterm_idx1 feature_id
feature_cvterm_idx2 cvterm_id
feature_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_cvterm_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_not
NOT NULL rank
UNIQUE feature_id, cvterm_id, pub_id, rank

feature_cvtermprop

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TABLE: feature_cvtermprop
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Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_cvtermprop_idx1 feature_cvterm_id
feature_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_cvtermprop_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_cvterm_id, type_id, rank

feature_cvterm_dbxref

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TABLE: feature_cvterm_dbxref
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Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_dbxref_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
feature_cvterm_dbxref_idx1 feature_cvterm_id
feature_cvterm_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL feature_cvterm_dbxref_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE feature_cvterm_id, dbxref_id

feature_cvterm_pub

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TABLE: feature_cvterm_pub
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Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_pub_id integer 11 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 10 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_cvterm_pub_idx1 feature_cvterm_id
feature_cvterm_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL feature_cvterm_pub_id
NOT NULL feature_cvterm_id
FOREIGN KEY feature_cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE feature_cvterm_id, pub_id

synonym

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TABLE: synonym
================================================
A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.
Field Name Data Type Size Default Value Other Foreign Key
synonym_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The synonym itself. Should be human-readable machine-searchable ascii text.
type_id integer 10 UNIQUE, NOT NULL, Types would be symbol and fullname for now. cvterm.cvterm_id
synonym_sgml varchar 255 NOT NULL, The fully specified synonym, with any non-ascii characters encoded in SGML.

Indices

Name Fields
synonym_idx1 type_id

Constraints

Type Fields
NOT NULL synonym_id
NOT NULL name
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL synonym_sgml
UNIQUE name, type_id

feature_synonym

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TABLE: feature_synonym
================================================
Linking table between feature and synonym.
Field Name Data Type Size Default Value Other Foreign Key
feature_synonym_id integer 11 PRIMARY KEY, NOT NULL
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 false NOT NULL, The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
feature_synonym_idx1 synonym_id
feature_synonym_idx2 feature_id
feature_synonym_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_synonym_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, feature_id, pub_id
Created by SQL::Translator 0.10 chado-1.23/modules/sequence/sequence.pgfunc000644 000765 000024 00000032443 11256710150 021072 0ustar00cainstaff000000 000000 --- =========================== --- store_feature (accession) --- Returns: feature_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: accession CREATE FUNCTION store_feature (varchar) RETURNS int AS ' DECLARE paccession ALIAS FOR $1; pkeyid INTEGER; BEGIN SELECT INTO pkeyid feature_id FROM feature WHERE feature.accession = paccession; IF NOT FOUND THEN INSERT INTO feature (accession) VALUES (paccession); RETURN currval(''feature_pk_seq''); END IF; UPDATE feature SET WHERE feature.accession = paccession RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_feature (accession) --- =========================== --- store_feature (name, accession, fmin, fmax, fstrand, residues, seqlen, md5checksum, type_id) --- Returns: feature_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: name, accession, fmin, fmax, fstrand, residues, seqlen, md5checksum, type_id CREATE FUNCTION store_feature (varchar, varchar, INTEGER, INTEGER, INTEGER, TEXT, INTEGER, char, INTEGER) RETURNS int AS ' DECLARE pname ALIAS FOR $1; paccession ALIAS FOR $2; pfmin ALIAS FOR $3; pfmax ALIAS FOR $4; pfstrand ALIAS FOR $5; presidues ALIAS FOR $6; pseqlen ALIAS FOR $7; pmd5checksum ALIAS FOR $8; ptype_id ALIAS FOR $9; pkeyid INTEGER; BEGIN SELECT INTO pkeyid feature_id FROM feature WHERE feature.name = pname AND feature.accession = paccession AND feature.fmin = pfmin AND feature.fmax = pfmax AND feature.fstrand = pfstrand AND feature.residues = presidues AND feature.seqlen = pseqlen AND feature.md5checksum = pmd5checksum AND feature.type_id = ptype_id; IF NOT FOUND THEN INSERT INTO feature (name, accession, fmin, fmax, fstrand, residues, seqlen, md5checksum, type_id) VALUES (pname, paccession, pfmin, pfmax, pfstrand, presidues, pseqlen, pmd5checksum, ptype_id); RETURN currval(''feature_pk_seq''); END IF; UPDATE feature SET WHERE feature.name = pname AND feature.accession = paccession AND feature.fmin = pfmin AND feature.fmax = pfmax AND feature.fstrand = pfstrand AND feature.residues = presidues AND feature.seqlen = pseqlen AND feature.md5checksum = pmd5checksum AND feature.type_id = ptype_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_feature (name, accession, fmin, fmax, fstrand, residues, seqlen, md5checksum, type_id) --- =========================== --- store_featureprop (feature_id, pkey_id, pval, prank) --- Returns: featureprop_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: feature_id, pkey_id, pval, prank CREATE FUNCTION store_featureprop (INTEGER, INTEGER, TEXT, INTEGER) RETURNS int AS ' DECLARE pfeature_id ALIAS FOR $1; ppkey_id ALIAS FOR $2; ppval ALIAS FOR $3; pprank ALIAS FOR $4; pkeyid INTEGER; BEGIN SELECT INTO pkeyid featureprop_id FROM featureprop WHERE featureprop.feature_id = pfeature_id AND featureprop.pkey_id = ppkey_id AND featureprop.pval = ppval AND featureprop.prank = pprank; IF NOT FOUND THEN INSERT INTO featureprop (feature_id, pkey_id, pval, prank) VALUES (pfeature_id, ppkey_id, ppval, pprank); RETURN currval(''featureprop_pk_seq''); END IF; UPDATE featureprop SET WHERE featureprop.feature_id = pfeature_id AND featureprop.pkey_id = ppkey_id AND featureprop.pval = ppval AND featureprop.prank = pprank RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_featureprop (feature_id, pkey_id, pval, prank) --- =========================== --- store_featureprop_pub (featureprop_id, pub_id) --- Returns: 0 (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: featureprop_id, pub_id CREATE FUNCTION store_featureprop_pub (INTEGER, INTEGER) RETURNS int AS ' DECLARE pfeatureprop_id ALIAS FOR $1; ppub_id ALIAS FOR $2; pkeyid INTEGER; BEGIN SELECT INTO pkeyid 0 FROM featureprop_pub WHERE featureprop_pub.featureprop_id = pfeatureprop_id AND featureprop_pub.pub_id = ppub_id; IF NOT FOUND THEN INSERT INTO featureprop_pub (featureprop_id, pub_id) VALUES (pfeatureprop_id, ppub_id); RETURN currval(''0''); END IF; UPDATE featureprop_pub SET WHERE featureprop_pub.featureprop_id = pfeatureprop_id AND featureprop_pub.pub_id = ppub_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_featureprop_pub (featureprop_id, pub_id) --- =========================== --- store_feature_dbxref (dbxref_id) --- Returns: feature_dbxref_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: feature_dbxref_id, dbxref_id CREATE FUNCTION store_feature_dbxref (INTEGER) RETURNS int AS ' DECLARE pdbxref_id ALIAS FOR $1; pkeyid INTEGER; BEGIN SELECT INTO pkeyid feature_dbxref_id FROM feature_dbxref WHERE feature_dbxref.feature_dbxref_id = pfeature_dbxref_id AND feature_dbxref.dbxref_id = pdbxref_id; IF NOT FOUND THEN INSERT INTO feature_dbxref (dbxref_id) VALUES (pdbxref_id); RETURN currval(''feature_dbxref_pk_seq''); END IF; UPDATE feature_dbxref SET WHERE feature_dbxref.feature_dbxref_id = pfeature_dbxref_id AND feature_dbxref.dbxref_id = pdbxref_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_feature_dbxref (dbxref_id) --- =========================== --- store_feature_relationship (subj_feature_id, obj_feature_id, type_id) --- Returns: feature_relationship_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: subj_feature_id, obj_feature_id, type_id CREATE FUNCTION store_feature_relationship (INTEGER, INTEGER, INTEGER) RETURNS int AS ' DECLARE psubj_feature_id ALIAS FOR $1; pobj_feature_id ALIAS FOR $2; ptype_id ALIAS FOR $3; pkeyid INTEGER; BEGIN SELECT INTO pkeyid feature_relationship_id FROM feature_relationship WHERE feature_relationship.subj_feature_id = psubj_feature_id AND feature_relationship.obj_feature_id = pobj_feature_id AND feature_relationship.type_id = ptype_id; IF NOT FOUND THEN INSERT INTO feature_relationship (subj_feature_id, obj_feature_id, type_id) VALUES (psubj_feature_id, pobj_feature_id, ptype_id); RETURN currval(''feature_relationship_pk_seq''); END IF; UPDATE feature_relationship SET WHERE feature_relationship.subj_feature_id = psubj_feature_id AND feature_relationship.obj_feature_id = pobj_feature_id AND feature_relationship.type_id = ptype_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_feature_relationship (subj_feature_id, obj_feature_id, type_id) --- =========================== --- store_feature_cvterm (feature_id, cvterm_id, pub_id) --- Returns: feature_cvterm_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: feature_id, cvterm_id, pub_id CREATE FUNCTION store_feature_cvterm (INTEGER, INTEGER, INTEGER) RETURNS int AS ' DECLARE pfeature_id ALIAS FOR $1; pcvterm_id ALIAS FOR $2; ppub_id ALIAS FOR $3; pkeyid INTEGER; BEGIN SELECT INTO pkeyid feature_cvterm_id FROM feature_cvterm WHERE feature_cvterm.feature_id = pfeature_id AND feature_cvterm.cvterm_id = pcvterm_id AND feature_cvterm.pub_id = ppub_id; IF NOT FOUND THEN INSERT INTO feature_cvterm (feature_id, cvterm_id, pub_id) VALUES (pfeature_id, pcvterm_id, ppub_id); RETURN currval(''feature_cvterm_pk_seq''); END IF; UPDATE feature_cvterm SET WHERE feature_cvterm.feature_id = pfeature_id AND feature_cvterm.cvterm_id = pcvterm_id AND feature_cvterm.pub_id = ppub_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_feature_cvterm (feature_id, cvterm_id, pub_id) --- =========================== --- store_gene (name) --- Returns: gene_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: name CREATE FUNCTION store_gene (varchar) RETURNS int AS ' DECLARE pname ALIAS FOR $1; pkeyid INTEGER; BEGIN SELECT INTO pkeyid gene_id FROM gene WHERE gene.name = pname; IF NOT FOUND THEN INSERT INTO gene (name) VALUES (pname); RETURN currval(''gene_pk_seq''); END IF; UPDATE gene SET WHERE gene.name = pname RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_gene (name) --- =========================== --- store_gene (accession) --- Returns: gene_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: accession CREATE FUNCTION store_gene (varchar) RETURNS int AS ' DECLARE paccession ALIAS FOR $1; pkeyid INTEGER; BEGIN SELECT INTO pkeyid gene_id FROM gene WHERE gene.accession = paccession; IF NOT FOUND THEN INSERT INTO gene (accession) VALUES (paccession); RETURN currval(''gene_pk_seq''); END IF; UPDATE gene SET WHERE gene.accession = paccession RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_gene (accession) --- =========================== --- store_genesynonym (gsynonym) --- Returns: genesynonym_id (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: gsynonym CREATE FUNCTION store_genesynonym (varchar) RETURNS int AS ' DECLARE pgsynonym ALIAS FOR $1; pkeyid INTEGER; BEGIN SELECT INTO pkeyid genesynonym_id FROM genesynonym WHERE genesynonym.gsynonym = pgsynonym; IF NOT FOUND THEN INSERT INTO genesynonym (gsynonym) VALUES (pgsynonym); RETURN currval(''genesynonym_pk_seq''); END IF; UPDATE genesynonym SET WHERE genesynonym.gsynonym = pgsynonym RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_genesynonym (gsynonym) --- =========================== --- store_gene_genesynonym (genesynonym_id, gene_id, pub_id) --- Returns: 0 (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: genesynonym_id, gene_id, pub_id CREATE FUNCTION store_gene_genesynonym (INTEGER, INTEGER, INTEGER) RETURNS int AS ' DECLARE pgenesynonym_id ALIAS FOR $1; pgene_id ALIAS FOR $2; ppub_id ALIAS FOR $3; pkeyid INTEGER; BEGIN SELECT INTO pkeyid 0 FROM gene_genesynonym WHERE gene_genesynonym.genesynonym_id = pgenesynonym_id AND gene_genesynonym.gene_id = pgene_id AND gene_genesynonym.pub_id = ppub_id; IF NOT FOUND THEN INSERT INTO gene_genesynonym (genesynonym_id, gene_id, pub_id) VALUES (pgenesynonym_id, pgene_id, ppub_id); RETURN currval(''0''); END IF; UPDATE gene_genesynonym SET WHERE gene_genesynonym.genesynonym_id = pgenesynonym_id AND gene_genesynonym.gene_id = pgene_id AND gene_genesynonym.pub_id = ppub_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_gene_genesynonym (genesynonym_id, gene_id, pub_id) --- =========================== --- store_gene_feature (gene_id, feature_id) --- Returns: 0 (primary key) --- --- --- stores (updates or inserts) --- based on unique columns: gene_id, feature_id CREATE FUNCTION store_gene_feature (INTEGER, INTEGER) RETURNS int AS ' DECLARE pgene_id ALIAS FOR $1; pfeature_id ALIAS FOR $2; pkeyid INTEGER; BEGIN SELECT INTO pkeyid 0 FROM gene_feature WHERE gene_feature.gene_id = pgene_id AND gene_feature.feature_id = pfeature_id; IF NOT FOUND THEN INSERT INTO gene_feature (gene_id, feature_id) VALUES (pgene_id, pfeature_id); RETURN currval(''0''); END IF; UPDATE gene_feature SET WHERE gene_feature.gene_id = pgene_id AND gene_feature.feature_id = pfeature_id RETURN pkeyid; END; ' LANGUAGE 'plpgsql'; --- end of function store_gene_feature (gene_id, feature_id) chado-1.23/modules/sequence/sequence.sql000644 000765 000024 00000103744 11256710150 020412 0ustar00cainstaff000000 000000 -- $Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $ -- ========================================== -- Chado sequence module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: feature -- ================================================ create table feature ( feature_id serial not null, primary key (feature_id), dbxref_id int, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, name varchar(255), uniquename text not null, residues text, seqlen int, md5checksum char(32), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_analysis boolean not null default 'false', is_obsolete boolean not null default 'false', timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint feature_c1 unique (organism_id,uniquename,type_id) ); create sequence feature_uniquename_seq; create index feature_name_ind1 on feature(name); create index feature_idx1 on feature (dbxref_id); create index feature_idx2 on feature (organism_id); create index feature_idx3 on feature (type_id); create index feature_idx4 on feature (uniquename); create index feature_idx5 on feature (lower(name)); ALTER TABLE feature ALTER residues SET STORAGE EXTERNAL; COMMENT ON TABLE feature IS 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.'; COMMENT ON COLUMN feature.dbxref_id IS 'An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.'; COMMENT ON COLUMN feature.organism_id IS 'The organism to which this feature belongs. This column is mandatory.'; COMMENT ON COLUMN feature.name IS 'The optional human-readable common name for a feature, for display purposes.'; COMMENT ON COLUMN feature.uniquename IS 'The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'; COMMENT ON COLUMN feature.residues IS 'A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.'; COMMENT ON COLUMN feature.seqlen IS 'The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'; COMMENT ON COLUMN feature.md5checksum IS 'The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.'; COMMENT ON COLUMN feature.type_id IS 'A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.'; COMMENT ON COLUMN feature.is_analysis IS 'Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.'; COMMENT ON COLUMN feature.is_obsolete IS 'Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'; COMMENT ON COLUMN feature.timeaccessioned IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; COMMENT ON COLUMN feature.timelastmodified IS 'For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.'; --- COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified --- by the combination of organism, uniquename and feature type'; -- ================================================ -- TABLE: featureloc -- ================================================ create table featureloc ( featureloc_id serial not null, primary key (featureloc_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int, foreign key (srcfeature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, fmin int, is_fmin_partial boolean not null default 'false', fmax int, is_fmax_partial boolean not null default 'false', strand smallint, phase int, residue_info text, locgroup int not null default 0, rank int not null default 0, constraint featureloc_c1 unique (feature_id,locgroup,rank), constraint featureloc_c2 check (fmin <= fmax) ); create index featureloc_idx1 on featureloc (feature_id); create index featureloc_idx2 on featureloc (srcfeature_id); create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax); COMMENT ON TABLE featureloc IS 'The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.'; COMMENT ON COLUMN featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.'; COMMENT ON COLUMN featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.'; COMMENT ON COLUMN featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.'; COMMENT ON COLUMN featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).'; COMMENT ON COLUMN featureloc.strand IS 'The orientation/directionality of the location. Should be 0, -1 or +1.'; COMMENT ON COLUMN featureloc.rank IS 'Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.'; COMMENT ON COLUMN featureloc.locgroup IS 'This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).'; COMMENT ON COLUMN featureloc.residue_info IS 'Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.'; COMMENT ON COLUMN featureloc.phase IS 'Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.'; COMMENT ON COLUMN featureloc.is_fmin_partial IS 'This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.'; COMMENT ON COLUMN featureloc.is_fmax_partial IS 'This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.'; --- COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely --- partition locations for any one feature'; -- ================================================ -- TABLE: featureloc_pub -- ================================================ create table featureloc_pub ( featureloc_pub_id serial not null, primary key (featureloc_pub_id), featureloc_id int not null, foreign key (featureloc_id) references featureloc (featureloc_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureloc_pub_c1 unique (featureloc_id,pub_id) ); create index featureloc_pub_idx1 on featureloc_pub (featureloc_id); create index featureloc_pub_idx2 on featureloc_pub (pub_id); COMMENT ON TABLE featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.'; -- ================================================ -- TABLE: feature_pub -- ================================================ create table feature_pub ( feature_pub_id serial not null, primary key (feature_pub_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_pub_c1 unique (feature_id,pub_id) ); create index feature_pub_idx1 on feature_pub (feature_id); create index feature_pub_idx2 on feature_pub (pub_id); COMMENT ON TABLE feature_pub IS 'Provenance. Linking table between features and publications that mention them.'; -- ================================================ -- TABLE: feature_pubprop -- ================================================ create table feature_pubprop ( feature_pubprop_id serial not null, primary key (feature_pubprop_id), feature_pub_id int not null, foreign key (feature_pub_id) references feature_pub (feature_pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_pubprop_c1 unique (feature_pub_id,type_id,rank) ); create index feature_pubprop_idx1 on feature_pubprop (feature_pub_id); COMMENT ON TABLE feature_pubprop IS 'Property or attribute of a feature_pub link.'; -- ================================================ -- TABLE: featureprop -- ================================================ create table featureprop ( featureprop_id serial not null, primary key (featureprop_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint featureprop_c1 unique (feature_id,type_id,rank) ); create index featureprop_idx1 on featureprop (feature_id); create index featureprop_idx2 on featureprop (type_id); COMMENT ON TABLE featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.'; COMMENT ON COLUMN featureprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology.'; COMMENT ON COLUMN featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN featureprop.rank IS 'Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used'; COMMENT ON INDEX featureprop_c1 IS 'For any one feature, multivalued property-value pairs must be differentiated by rank.'; -- ================================================ -- TABLE: featureprop_pub -- ================================================ create table featureprop_pub ( featureprop_pub_id serial not null, primary key (featureprop_pub_id), featureprop_id int not null, foreign key (featureprop_id) references featureprop (featureprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint featureprop_pub_c1 unique (featureprop_id,pub_id) ); create index featureprop_pub_idx1 on featureprop_pub (featureprop_id); create index featureprop_pub_idx2 on featureprop_pub (pub_id); COMMENT ON TABLE featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.'; -- ================================================ -- TABLE: feature_dbxref -- ================================================ create table feature_dbxref ( feature_dbxref_id serial not null, primary key (feature_dbxref_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint feature_dbxref_c1 unique (feature_id,dbxref_id) ); create index feature_dbxref_idx1 on feature_dbxref (feature_id); create index feature_dbxref_idx2 on feature_dbxref (dbxref_id); COMMENT ON TABLE feature_dbxref IS 'Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.'; COMMENT ON COLUMN feature_dbxref.is_current IS 'True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false'; -- ================================================ -- TABLE: feature_relationship -- ================================================ create table feature_relationship ( feature_relationship_id serial not null, primary key (feature_relationship_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index feature_relationship_idx1 on feature_relationship (subject_id); create index feature_relationship_idx2 on feature_relationship (object_id); create index feature_relationship_idx3 on feature_relationship (type_id); COMMENT ON TABLE feature_relationship IS 'Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.'; COMMENT ON COLUMN feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.'; COMMENT ON COLUMN feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.'; COMMENT ON COLUMN feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.'; COMMENT ON COLUMN feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.'; COMMENT ON COLUMN feature_relationship.value IS 'Additional notes or comments.'; -- ================================================ -- TABLE: feature_relationship_pub -- ================================================ create table feature_relationship_pub ( feature_relationship_pub_id serial not null, primary key (feature_relationship_pub_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationship_pub_c1 unique (feature_relationship_id,pub_id) ); create index feature_relationship_pub_idx1 on feature_relationship_pub (feature_relationship_id); create index feature_relationship_pub_idx2 on feature_relationship_pub (pub_id); COMMENT ON TABLE feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.'; -- ================================================ -- TABLE: feature_relationshipprop -- ================================================ create table feature_relationshipprop ( feature_relationshipprop_id serial not null, primary key (feature_relationshipprop_id), feature_relationship_id int not null, foreign key (feature_relationship_id) references feature_relationship (feature_relationship_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_relationshipprop_c1 unique (feature_relationship_id,type_id,rank) ); create index feature_relationshipprop_idx1 on feature_relationshipprop (feature_relationship_id); create index feature_relationshipprop_idx2 on feature_relationshipprop (type_id); COMMENT ON TABLE feature_relationshipprop IS 'Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.'; COMMENT ON COLUMN feature_relationshipprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types.'; COMMENT ON COLUMN feature_relationshipprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_relationshipprop.rank IS 'Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_relationshipprop_pub -- ================================================ create table feature_relationshipprop_pub ( feature_relationshipprop_pub_id serial not null, primary key (feature_relationshipprop_pub_id), feature_relationshipprop_id int not null, foreign key (feature_relationshipprop_id) references feature_relationshipprop (feature_relationshipprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_relationshipprop_pub_c1 unique (feature_relationshipprop_id,pub_id) ); create index feature_relationshipprop_pub_idx1 on feature_relationshipprop_pub (feature_relationshipprop_id); create index feature_relationshipprop_pub_idx2 on feature_relationshipprop_pub (pub_id); COMMENT ON TABLE feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.'; -- ================================================ -- TABLE: feature_cvterm -- ================================================ create table feature_cvterm ( feature_cvterm_id serial not null, primary key (feature_cvterm_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_not boolean not null default false, rank integer not null default 0, constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank) ); create index feature_cvterm_idx1 on feature_cvterm (feature_id); create index feature_cvterm_idx2 on feature_cvterm (cvterm_id); create index feature_cvterm_idx3 on feature_cvterm (pub_id); COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.'; COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.'; COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.'; -- ================================================ -- TABLE: feature_cvtermprop -- ================================================ create table feature_cvtermprop ( feature_cvtermprop_id serial not null, primary key (feature_cvtermprop_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank) ); create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id); create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id); COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.'; COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv.'; COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: feature_cvterm_dbxref -- ================================================ create table feature_cvterm_dbxref ( feature_cvterm_dbxref_id serial not null, primary key (feature_cvterm_dbxref_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id) ); create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id); create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id); COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.'; -- ================================================ -- TABLE: feature_cvterm_pub -- ================================================ create table feature_cvterm_pub ( feature_cvterm_pub_id serial not null, primary key (feature_cvterm_pub_id), feature_cvterm_id int not null, foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id) ); create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id); create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id); COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.'; -- ================================================ -- TABLE: synonym -- ================================================ create table synonym ( synonym_id serial not null, primary key (synonym_id), name varchar(255) not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym_sgml varchar(255) not null, constraint synonym_c1 unique (name,type_id) ); create index synonym_idx1 on synonym (type_id); create index synonym_idx2 on synonym ((lower(synonym_sgml))); COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.'; COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.'; COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.'; COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.'; -- ================================================ -- TABLE: feature_synonym -- ================================================ create table feature_synonym ( feature_synonym_id serial not null, primary key (feature_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id) ); create index feature_synonym_idx1 on feature_synonym (synonym_id); create index feature_synonym_idx2 on feature_synonym (feature_id); create index feature_synonym_idx3 on feature_synonym (pub_id); COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.'; COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.'; COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.'; chado-1.23/modules/sequence/sequence_opt.xml000644 000765 000024 00000001036 11256710150 021264 0ustar00cainstaff000000 000000 chado-1.23/modules/sequence/sequence_views.sql000644 000765 000024 00000016515 11406436230 021627 0ustar00cainstaff000000 000000 -------------------------------- ---- all_feature_names --------- -------------------------------- -- This is a view to replace the denormaliziation of the synonym -- table. It contains names and uniquenames from feature and -- synonym.names from the synonym table, so that GBrowse has one -- place to search for names. -- -- To materialize this view, run gmod_materialized_view_tool.pl -c and -- answer the questions with these responses: -- -- all_feature_names -- -- public.all_feature_names -- -- y (yes, replace the existing view) -- -- (some update frequency, I chose daily) -- -- feature_id integer,name varchar(255),organism_id integer -- -- (the select part of the view below, all on one line) -- -- feature_id,name -- -- create index all_feature_names_lower_name on all_feature_names (lower(name)) -- -- y -- -- OR, you could execute this command (the materialized view tool has been -- updated to allow this all to be supplied on the command line): -- -- (yes, it's all one really long line, to make copy and pasting easier) -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer" --sql_query "SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "create index all_feature_names_lower_name on all_feature_names (lower(name))" --yes -- -- -- OR, even more complicated, you could use this command to create a materialized view -- for use with full text searching on PostgreSQL 8.4 or better: -- -- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer,searchable_name tsvector" --sql_query "SELECT feature_id, CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255)) AS name, organism_id, to_tsvector('english', CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM feature UNION SELECT feature_id, name, organism_id, to_tsvector('english', name) AS searchable_name FROM feature WHERE name IS NOT NULL UNION SELECT fs.feature_id, s.name, f.organism_id, to_tsvector('english', s.name) AS searchable_name FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255)) AS name, f.organism_id, to_tsvector('english',CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id,to_tsvector('english',d.accession) AS searchable_name FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "CREATE INDEX searchable_all_feature_names_idx ON all_feature_names USING gin(searchable_name)" --yes -- CREATE OR REPLACE VIEW all_feature_names ( feature_id, name, organism_id ) AS SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id; -------------------------------- ---- dfeatureloc --------------- -------------------------------- -- dfeatureloc is meant as an alternate representation of -- the data in featureloc (see the descrption of featureloc -- in sequence.sql). In dfeatureloc, fmin and fmax are -- replaced with nbeg and nend. Whereas fmin and fmax -- are absolute coordinates relative to the parent feature, nbeg -- and nend are the beginning and ending coordinates -- relative to the feature itself. For example, nbeg would -- mark the 5' end of a gene and nend would mark the 3' end. CREATE OR REPLACE VIEW dfeatureloc ( featureloc_id, feature_id, srcfeature_id, nbeg, is_nbeg_partial, nend, is_nend_partial, strand, phase, residue_info, locgroup, rank ) AS SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand < 0 or phase < 0) UNION SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial, fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank FROM featureloc WHERE (strand is NULL or strand >= 0 or phase >= 0) ; -------------------------------- ---- f_type -------------------- -------------------------------- CREATE OR REPLACE VIEW f_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f, cvterm c WHERE f.type_id = c.cvterm_id; -------------------------------- ---- fnr_type ------------------ -------------------------------- CREATE OR REPLACE VIEW fnr_type AS SELECT f.feature_id, f.name, f.dbxref_id, c.name AS type, f.residues, f.seqlen, f.md5checksum, f.type_id, f.timeaccessioned, f.timelastmodified FROM feature f left outer join analysisfeature af on (f.feature_id = af.feature_id), cvterm c WHERE f.type_id = c.cvterm_id and af.feature_id is null; -------------------------------- ---- f_loc --------------------- -------------------------------- -- Note from Scott: I changed this view to depend on dfeatureloc, -- since I don't know what it is used for. The change should -- be transparent. I also changed dbxrefstr to dbxref_id since -- dbxrefstr is no longer in feature CREATE OR REPLACE VIEW f_loc AS SELECT f.feature_id, f.name, f.dbxref_id, fl.nbeg, fl.nend, fl.strand FROM dfeatureloc fl, f_type f WHERE f.feature_id = fl.feature_id; -------------------------------- ---- fp_key ------------------- -------------------------------- CREATE OR REPLACE VIEW fp_key AS SELECT fp.feature_id, c.name AS pkey, fp.value FROM featureprop fp, cvterm c WHERE fp.featureprop_id = c.cvterm_id; chado-1.23/modules/sequence/views/000755 000765 000024 00000000000 12061672376 017221 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/views/exon-views.sql000644 000765 000024 00000000573 11256710150 022037 0ustar00cainstaff000000 000000 -- requires: so-views CREATE OR REPLACE VIEW unshared_exon AS SELECT FROM exon AS exon1 INNER JOIN featureloc AS fl1 USING (feature_id), exon AS exon2 INNER JOIN featureloc AS fl2 USING (feature_id) WHERE exon1.feature_id != exon2.feature_id AND fl1.srcfeature_id = fl2.srcfeature_id AND fl1.fmin = fl2.fmin AND fl1.fmax = fl2.fmax AND fl1.strand = fl2.strand; chado-1.23/modules/sequence/views/implicit-feature-views.sql000644 000765 000024 00000004203 11256710150 024323 0ustar00cainstaff000000 000000 -- DEPENDENCY: -- chado/modules/bridges/sofa-bridge.sql -- The standard Chado pattern for protein coding genes -- is a feature of type 'gene' with 'mRNA' features as parts -- REQUIRES: 'mrna' view from so-bridge.sql CREATE OR REPLACE VIEW protein_coding_gene AS SELECT DISTINCT gene.* FROM feature AS gene INNER JOIN feature_relationship AS fr ON (gene.feature_id=fr.object_id) INNER JOIN so.mrna ON (mrna.feature_id=fr.subject_id); -- introns are implicit from surrounding exons -- combines intron features with location and parent transcript -- the same intron appearing in multiple transcripts will appear -- multiple times CREATE VIEW intron_combined_view AS SELECT x1.feature_id AS exon1_id, x2.feature_id AS exon2_id, CASE WHEN l1.strand=-1 THEN l2.fmax ELSE l1.fmax END AS fmin, CASE WHEN l1.strand=-1 THEN l1.fmin ELSE l2.fmin END AS fmax, l1.strand AS strand, l1.srcfeature_id AS srcfeature_id, r1.rank AS intron_rank, r1.object_id AS transcript_id FROM cvterm INNER JOIN feature AS x1 ON (x1.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r1 ON (x1.feature_id=r1.subject_id) INNER JOIN featureloc AS l1 ON (x1.feature_id=l1.feature_id) INNER JOIN feature AS x2 ON (x2.type_id=cvterm.cvterm_id) INNER JOIN feature_relationship AS r2 ON (x2.feature_id=r2.subject_id) INNER JOIN featureloc AS l2 ON (x2.feature_id=l2.feature_id) WHERE cvterm.name='exon' AND (r2.rank - r1.rank) = 1 AND r1.object_id=r2.object_id AND l1.strand = l2.strand AND l1.srcfeature_id = l2.srcfeature_id AND l1.locgroup=0 AND l2.locgroup=0; -- intron locations. intron IDs are the (exon1,exon2) ID pair -- this means that introns may be counted twice if the start of -- the 5' exon or the end of the 3' exon vary -- introns shared by transcripts will not appear twice CREATE VIEW intronloc_view AS SELECT DISTINCT exon1_id, exon2_id, fmin, fmax, strand, srcfeature_id FROM intron_combined_view; chado-1.23/modules/sequence/views/range-views.sql000644 000765 000024 00000012037 11256710150 022160 0ustar00cainstaff000000 000000 -- [symmetric,reflexive] -- intervals have at least one interbase point in common -- (i.e. overlap OR abut) -- EXAMPLE QUERY: -- (features of same type that overlap) -- SELECT r.* -- FROM feature AS x -- INNER JOIN feature_meets AS r ON (x.feature_id=r.subject_id) -- INNER JOIN feature AS y ON (y.feature_id=r.object_id) -- WHERE x.type_id=y.type_id CREATE OR REPLACE VIEW feature_meets ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets IS 'intervals have at least one interbase point in common (ie overlap OR abut). symmetric,reflexive'; -- [symmetric,reflexive] -- as above, strands match CREATE OR REPLACE VIEW feature_meets_on_same_strand ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND x.strand = y.strand AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_meets_on_same_strand IS 'as feature_meets, but featurelocs must be on the same strand. symmetric,reflexive'; -- [symmetric] -- intervals have no interbase points in common and do not abut CREATE OR REPLACE VIEW feature_disjoint ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax < y.fmin AND x.fmin > y.fmax ); COMMENT ON VIEW feature_disjoint IS 'featurelocs do not meet. symmetric'; -- 4-ary relation CREATE OR REPLACE VIEW feature_union AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN x.fmax ELSE y.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_intersection AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fminy.fmax THEN y.fmax ELSE x.fmax END AS fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ); COMMENT ON VIEW feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation -- subtract object interval from subject interval -- (may leave zero, one or two intervals) CREATE OR REPLACE VIEW feature_difference ( subject_id, object_id, srcfeature_id, fmin, fmax, strand ) AS -- left interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, x.fmin, y.fmin FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmin < y.fmin AND x.fmax >= y.fmax ) UNION -- right interval SELECT x.feature_id, y.feature_id, x.strand, x.srcfeature_id, y.fmax, x.fmax FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND (x.fmax > y.fmax AND x.fmin <= y.fmin ); COMMENT ON VIEW feature_difference IS 'set-distance on interval defined by featureloc. featurelocs must meet'; -- 4-ary relation CREATE OR REPLACE VIEW feature_distance AS SELECT x.feature_id AS subject_id, y.feature_id AS object_id, x.srcfeature_id, x.strand AS subject_strand, y.strand AS object_strand, CASE WHEN x.fmax <= y.fmin THEN (x.fmax-y.fmin) ELSE (y.fmax-x.fmin) END AS distance FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( x.fmax <= y.fmin OR x.fmin >= y.fmax ); COMMENT ON VIEW feature_difference IS 'size of gap between two features. must be abutting or disjoint'; -- [transitive,reflexive] -- (should this be made non-reflexive?) -- subject intervals contains (or is same as) object interval CREATE OR REPLACE VIEW feature_contains ( subject_id, object_id ) AS SELECT x.feature_id, y.feature_id FROM featureloc AS x, featureloc AS y WHERE x.srcfeature_id=y.srcfeature_id AND ( y.fmin >= x.fmin AND y.fmin <= x.fmax ); COMMENT ON VIEW feature_contains IS 'subject intervals contains (or is same as) object interval. transitive,reflexive'; -- featureset relations: -- a featureset relation is true between any two features x and y -- if the relation is true for any x' and y' where x' and y' are -- subfeatures of x and y -- see feature_meets -- example: two transcripts meet if any of their exons or CDSs overlap -- or abut CREATE OR REPLACE VIEW featureset_meets ( subject_id, object_id ) AS SELECT x.object_id, y.object_id FROM feature_meets AS r INNER JOIN feature_relationship AS x ON (r.subject_id = x.subject_id) INNER JOIN feature_relationship AS y ON (r.object_id = y.subject_id); chado-1.23/modules/sequence/views/sequence-cv-views.sql000644 000765 000024 00000000362 11256710150 023300 0ustar00cainstaff000000 000000 CREATE VIEW cv_for_feature AS SELECT * FROM cv WHERE name='sequence'; CREATE VIEW cv_for_featureprop AS SELECT * FROM cv WHERE name='feature_property'; CREATE VIEW cv_for_feature_relationship AS SELECT * FROM cv WHERE name='relationship'; chado-1.23/modules/sequence/views/sequence-report.sql000644 000765 000024 00000000361 11256710150 023047 0ustar00cainstaff000000 000000 CREATE VIEW type_feature_count AS SELECT t.name AS type,count(*) AS num_features FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id) GROUP BY t.name; COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts'; chado-1.23/modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql000644 000765 000024 00000006314 11464332272 025146 0ustar00cainstaff000000 000000 -- FUNCTION gfffeatureatts (integer) is a function to get -- data in the same format as the gffatts view so that -- it can be easily converted to GFF attributes. CREATE FUNCTION gfffeatureatts (integer) RETURNS SETOF gffatts AS ' SELECT feature_id, ''Ontology_term'' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id UNION SELECT feature_id, ''Dbxref'' AS type, d.name || '':'' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id UNION SELECT feature_id, ''Alias'' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id UNION SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id UNION SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id ' LANGUAGE SQL; -- -- functions for creating coordinate based functions -- -- create a point CREATE OR REPLACE FUNCTION featureslice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; --uses the gff3atts to create a GFF3 compliant attribute string CREATE OR REPLACE FUNCTION gffattstring (integer) RETURNS varchar AS 'DECLARE return_string varchar; f_id ALIAS FOR $1; atts_view gffatts%ROWTYPE; feature_row feature%ROWTYPE; name varchar; uniquename varchar; parent varchar; escape_loc int; BEGIN --Get name from feature.name --Get ID from feature.uniquename SELECT INTO feature_row * FROM feature WHERE feature_id = f_id; name = feature_row.name; return_string = ''ID='' || feature_row.uniquename; IF name IS NOT NULL AND name != '''' THEN return_string = return_string ||'';'' || ''Name='' || name; END IF; --Get Parent from feature_relationship SELECT INTO feature_row * FROM feature f, feature_relationship fr WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id; IF FOUND THEN return_string = return_string||'';''||''Parent=''||feature_row.uniquename; END IF; FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id LOOP escape_loc = position('';'' in atts_view.attribute); IF escape_loc > 0 THEN atts_view.attribute = replace(atts_view.attribute, '';'', ''%3B''); END IF; return_string = return_string || '';'' || atts_view.type || ''='' || atts_view.attribute; END LOOP; RETURN return_string; END; ' LANGUAGE plpgsql; --creates a view that is suitable for creating a GFF3 string --CREATE OR REPLACE VIEW gff3view ( --REMOVED and RECREATED in sequence-gff-views.sql to avoid --using the function above chado-1.23/modules/sequence/gff-bridge/sequence-gff-views.sql000644 000765 000024 00000010406 11466536265 024311 0ustar00cainstaff000000 000000 -- VIEW gffatts: a view to get feature attributes in a format that -- will make it easy to convert them to GFF attributes CREATE OR REPLACE VIEW gffatts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, s.name AS attribute FROM cvterm s, feature_cvterm fs WHERE fs.cvterm_id = s.cvterm_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs WHERE fs.synonym_id = s.synonym_id UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id; --creates a view that can be used to assemble a GFF3 compliant attribute string CREATE OR REPLACE VIEW gff3atts ( feature_id, type, attribute ) AS SELECT feature_id, 'Ontology_term' AS type, CASE WHEN db.name like '%Gene Ontology%' THEN 'GO:'|| dbx.accession WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession ELSE CAST(db.name||':'|| dbx.accession AS varchar) END FROM cvterm s, dbxref dbx, feature_cvterm fs, db WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and db.db_id = dbx.db_id UNION ALL SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and d.name != 'GFF_source' UNION ALL SELECT f.feature_id, 'Alias' AS type, s.name AS attribute FROM synonym s, feature_synonym fs, feature f WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and f.name != s.name and f.uniquename != s.name UNION ALL SELECT fp.feature_id,cv.name,fp.value FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id UNION ALL SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute FROM pub s, feature_pub fs WHERE fs.pub_id = s.pub_id UNION ALL SELECT fr.subject_id as feature_id, 'Parent' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='part_of' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fr.subject_id as feature_id, 'Derives_from' as type, parent.uniquename as attribute FROM feature_relationship fr, feature parent WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id FROM cv WHERE name='relationship')) UNION ALL SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1 || ' ' || fl.fmax || ' ' || fl.strand as attribute FROM featureloc fl, feature target WHERE fl.srcfeature_id=target.feature_id AND fl.rank != 0 UNION ALL SELECT feature_id, 'ID' as type, uniquename as attribute FROM feature WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS') UNION ALL SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS varchar) as attribute FROM feature UNION ALL SELECT feature_id, 'Name' as type, name as attribute FROM feature; --replaced with Rob B's improved view CREATE OR REPLACE VIEW gff3view ( feature_id, ref, source, type, fstart, fend, score, strand, phase, seqlen, name, organism_id ) AS SELECT f.feature_id, sf.name, COALESCE(gffdbx.accession,'.'::varchar(255)), cv.name, fl.fmin+1, fl.fmax, COALESCE(CAST(af.significance AS text), '.'), CASE WHEN fl.strand=-1 THEN '-' WHEN fl.strand=1 THEN '+' ELSE '.' END, COALESCE(CAST(fl.phase AS text), '.'), f.seqlen, f.name, f.organism_id FROM feature f LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id) LEFT JOIN feature sf ON (fl.srcfeature_id = sf.feature_id) LEFT JOIN ( SELECT fd.feature_id, d.accession FROM feature_dbxref fd JOIN dbxref d using(dbxref_id) JOIN db using(db_id) WHERE db.name = 'GFF_source' ) as gffdbx ON (f.feature_id=gffdbx.feature_id) LEFT JOIN cvterm cv ON (f.type_id = cv.cvterm_id) LEFT JOIN analysisfeature af ON (f.feature_id = af.feature_id); chado-1.23/modules/sequence/gencode/gencode.sql000644 000765 000024 00000001433 11551351443 021606 0ustar00cainstaff000000 000000 CREATE SCHEMA genetic_code; SET search_path = genetic_code,public,pg_catalog; CREATE TABLE gencode ( gencode_id INTEGER PRIMARY KEY NOT NULL, organismstr VARCHAR(512) NOT NULL ); CREATE TABLE gencode_codon_aa ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3) NOT NULL, aa CHAR(1) NOT NULL, CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon ) ); CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa); CREATE TABLE gencode_startcodon ( gencode_id INTEGER NOT NULL REFERENCES gencode(gencode_id), codon CHAR(3), CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon ) ); SET search_path = public,pg_catalog; chado-1.23/modules/sequence/gencode/gencode_data.sql000644 000765 000024 00000246033 11256710122 022601 0ustar00cainstaff000000 000000 -- autogenerated by gencode2sql.pl from NCBI gencode.dmp SET search_path=public,genetic_code; INSERT INTO gencode (gencode_id,organismstr) VALUES (0,'Unspecified'); INSERT INTO gencode (gencode_id,organismstr) VALUES (1,'Standard'); INSERT INTO gencode (gencode_id,organismstr) VALUES (2,'Vertebrate Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (3,'Yeast Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (4,'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma'); INSERT INTO gencode (gencode_id,organismstr) VALUES (5,'Invertebrate Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (6,'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear'); INSERT INTO gencode (gencode_id,organismstr) VALUES (9,'Echinoderm Mitochondrial; Flatworm Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (10,'Euplotid Nuclear'); INSERT INTO gencode (gencode_id,organismstr) VALUES (11,'Bacterial and Plant Plastid'); INSERT INTO gencode (gencode_id,organismstr) VALUES (12,'Alternative Yeast Nuclear'); INSERT INTO gencode (gencode_id,organismstr) VALUES (13,'Ascidian Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (14,'Alternative Flatworm Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (15,'Blepharisma Macronuclear'); INSERT INTO gencode (gencode_id,organismstr) VALUES (16,'Chlorophycean Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (21,'Trematode Mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (22,'Scenedesmus obliquus mitochondrial'); INSERT INTO gencode (gencode_id,organismstr) VALUES (23,'Thraustochytrium mitochondrial code'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (1,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ATA','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'AGG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (2,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CTT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CTC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CTA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CTG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ATA','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (3,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (4,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ATA','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AGA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'AGG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (5,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (6,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AAA','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AGA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'AGG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (9,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TGA','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (10,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (11,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CTG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (12,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ATA','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'AGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (13,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TAA','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AAA','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AGA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'AGG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (14,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (15,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TAG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (16,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TGA','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ATA','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AAA','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AGA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'AGG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (21,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TCA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TAG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (22,'GGG','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TTT','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TTC','F'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TTA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TCT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TCC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TCA','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TCG','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TAT','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TAC','Y'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TAA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TAG','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TGT','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TGC','C'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TGA','*'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'TGG','W'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CTT','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CTC','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CTA','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CTG','L'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CCT','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CCC','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CCA','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CCG','P'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CAT','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CAC','H'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CAA','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CAG','Q'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CGT','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CGC','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'CGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ATT','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ATC','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ATA','I'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ATG','M'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ACT','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ACC','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ACA','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'ACG','T'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AAT','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AAC','N'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AAA','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AAG','K'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AGT','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AGC','S'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AGA','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'AGG','R'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GTT','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GTC','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GTA','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GTG','V'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GCT','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GCC','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GCA','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GCG','A'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GAT','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GAC','D'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GAA','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GAG','E'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GGT','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GGC','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GGA','G'); INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (23,'GGG','G'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (1,'TTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (1,'CTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (1,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (2,'ATT'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (2,'ATC'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (2,'ATA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (2,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (2,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (3,'ATA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (3,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'TTA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'TTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'CTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'ATT'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'ATC'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'ATA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (4,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'TTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'ATT'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'ATC'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'ATA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (5,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (6,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (9,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (9,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (10,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'TTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'CTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'ATT'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'ATC'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'ATA'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (11,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (12,'CTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (12,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (13,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (14,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (15,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (16,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (21,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (21,'GTG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (22,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (23,'ATT'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (23,'ATG'); INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (23,'GTG'); chado-1.23/modules/sequence/functions/create_soi.plpgsql000644 000765 000024 00000015105 11256710124 023604 0ustar00cainstaff000000 000000 --- create ontology that has instantiated located_sequence_feature part of SO --- way as it is written, the function can not be execute more than once in one connection --- when you get error like ERROR: relation with OID NNNNN does not exist --- as this is not meant to execute >1 times in one session so it should never happen --- except at testing and test failed --- disconnect and try again, in other words, it can NOT be executed >1 time in one connection --- if using EXECUTE, we can avoid this problem but code is hard to write and read (lots of ', escape char) --NOTE: private, don't call directly as relying on having temp table tmpcvtr --DROP TYPE soi_type CASCADE; CREATE TYPE soi_type AS ( type_id INT, subject_id INT, object_id INT ); CREATE OR REPLACE FUNCTION _fill_cvtermpath4soinode(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm soi_type%ROWTYPE; exist_c int; BEGIN --RAISE NOTICE ''depth=% o=%, root=%, cv=%, t=%'', depth,origin,child_id,cvid,typeid; SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; --- longest path IF (exist_c > 0) THEN UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id; ELSE INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4soi(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm soi_type%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE name = ''isa''; --RAISE NOTICE ''got ttype %'',ttype; PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; --- use tmpcvtr to temp store soi (virtural ontology) --- using tmp tables is faster than using recursive function to create feature type relationship --- since it gets feature type rel set by set instead of one by one --- and getting feature type rel is very expensive --- call _fillcvtermpath4soi to create path for the virtual ontology CREATE OR REPLACE FUNCTION create_soi() RETURNS INTEGER AS ' DECLARE parent soi_type%ROWTYPE; isa_id cvterm.cvterm_id%TYPE; soi_term TEXT := ''soi''; soi_def TEXT := ''ontology of SO feature instantiated in database''; soi_cvid INTEGER; soiterm_id INTEGER; pcount INTEGER; count INTEGER := 0; cquery TEXT; BEGIN SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = ''isa''; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; IF (soi_cvid > 0) THEN DELETE FROM cvtermpath WHERE cv_id = soi_cvid; DELETE FROM cvterm WHERE cv_id = soi_cvid; ELSE INSERT INTO cv (name, definition) VALUES(soi_term, soi_def); END IF; SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term; INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid); SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term; CREATE TEMP TABLE tmpcvtr (tmp_type INT, type_id INT, subject_id INT, object_id INT); CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id); INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t WHERE f.type_id = t.cvterm_id AND f.type_id > 0; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature %'',pcount; --- do it hard way, delete any child feature type from above (NOT IN clause did not work) FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id AND subject_id = parent.subject_id; END LOOP; EXECUTE ''select * from tmpcvtr where type_id = '' || soiterm_id || '';''; get diagnostics pcount = row_count; raise notice ''all types in feature after delete child %'',pcount; --- create feature type relationship (store in tmpcvtr) CREATE TEMP TABLE tmproot (cv_id INTEGER not null, cvterm_id INTEGER not null, status INTEGER DEFAULT 0); cquery := ''SELECT * FROM tmproot tmp WHERE tmp.status = 0;''; ---temp use tmpcvtr to hold instantiated SO relationship for speed ---use soterm_id as type_id, will delete from tmpcvtr ---us tmproot for this as well INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c WHERE c.object_id = soiterm_id; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; WHILE (pcount > 0) LOOP RAISE NOTICE ''num child temp (to be inserted) in tmpcvtr: %'',pcount; INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id) SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr, tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0; UPDATE tmproot SET status = 1 WHERE status = 0; INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr, tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1; UPDATE tmproot SET status = 2 WHERE status = 1; EXECUTE cquery; GET DIAGNOSTICS pcount = ROW_COUNT; END LOOP; DELETE FROM tmproot; ---get transitive closure for soi PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid); DROP TABLE tmpcvtr; DROP TABLE tmproot; RETURN 1; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/delete-trigger.plpgsql000644 000765 000024 00000003715 11256710124 024376 0ustar00cainstaff000000 000000 --This is a fairly simple trigger to delete child features of features that --are being deleted as long as the child features dont have other parents --(that is, they are orphan features). Items to consider/improve: -- -- * the relationship type isnt considered; you may want to only delete -- part_of, or only delete part_of and derives_from but not other -- relationships. -- * as written, it will infintely recurse, that is, it doesnt care how -- many levels of relationships you have (typically you will have -- three: gene, transcript, and exon); maybe you dont want that -- --To install this trigger in your database, execute this on the command line: -- -- psql DATABASENAME < delete-trigger.plpgsql -- --replacing DATABASENAME with the name of your database. DROP TRIGGER tr_feature_del ON feature; CREATE OR REPLACE function fn_feature_del() RETURNS TRIGGER AS ' DECLARE id_count int; old_f_id feature.feature_id%TYPE; feat_rel_row feature_relationship%ROWTYPE; BEGIN RAISE NOTICE ''enter f_d, feature uniquename:%, type_id:%'',OLD.uniquename, OLD.type_id; old_f_id:=OLD.feature_id; --look for children of the feature to be deleted FOR feat_rel_row IN SELECT * FROM feature_relationship WHERE object_id = old_f_id LOOP --see if it has any other parents SELECT INTO id_count count(object_id) FROM feature_relationship WHERE subject_id = feat_rel_row.subject_id and object_id != old_f_id; --if not, delete it (which will cause this trigger to be called again IF id_count > 0 THEN --dont delete anything RETURN OLD; ELSE --no other parents DELETE FROM feature WHERE feature_id = feat_rel_row.subject_id; END IF; END LOOP; RAISE NOTICE ''leave f_d ....''; RETURN OLD; END; 'LANGUAGE 'plpgsql'; GRANT ALL ON FUNCTION fn_feature_del() TO PUBLIC; CREATE TRIGGER tr_feature_del BEFORE DELETE ON feature for EACH ROW EXECUTE PROCEDURE fn_feature_del(); chado-1.23/modules/sequence/functions/feature.plpgsql000644 000765 000024 00000000423 11256710124 023117 0ustar00cainstaff000000 000000 -- depends on sequence-cv-helper CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS ' SELECT feature_id FROM feature WHERE uniquename=$1 AND type_id=get_feature_type_id($2) AND organism_id=get_organism_id($3) ' LANGUAGE 'sql'; chado-1.23/modules/sequence/functions/feature.sqlapi000644 000765 000024 00000001046 11256710124 022730 0ustar00cainstaff000000 000000 IMPORT get_organism_id(TEXT) FROM organism; IMPORT get_feature_type_id(TEXT) FROM 'sequence-cv-helper'; DECLARE FUNCTION get_feature_id(uniquename VARCHAR, type VARCHAR, organism VARCHAR) RETURNS INT; COMMENT ON FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) IS 'returns feature_id based on uniquename type organism. Type is assumed to be from sequence ontology. Organism is a binomial string'; EXAMPLE SELECT get_feature_id('2L','chromosome_arm','Drosophila melanogaster'); chado-1.23/modules/sequence/functions/feature_ids_fx.plpgsql000644 000765 000024 00000034227 11256710124 024464 0ustar00cainstaff000000 000000 ---bad precedence: change customed type name ---drop here to remove old function --DROP TYPE feature_by_cvt_type CASCADE; --DROP TYPE fxgsfids_type CASCADE; --DROP TYPE feature_by_fx_type CASCADE; CREATE TYPE feature_by_fx_type AS ( feature_id INTEGER, depth INT ); CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS ' DECLARE sql alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; myrc3 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN EXECUTE sql LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc3; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE root alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- depth is reversed and meanless when union with results from get_sub_feature_ids CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS ' DECLARE leaf alias for $1; depth alias for $2; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP RETURN NEXT myrc; FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP RETURN NEXT myrc2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- children feature ids only (not include itself--parent) for SO type and range (src) CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query text; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- by SO type, usefull for tRNA, ncRNA, etc CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; is_an alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '' || quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; src alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(gtype, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id) WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE gtype alias for $1; name alias for $2; is_an alias for $3; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name) || '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; IF (STRPOS(name, ''%'') > 0) THEN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name) || '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature that has an ontology term (say GO function) CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS ' DECLARE aspect alias for $1; term alias for $2; query TEXT; subquery TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';''; IF (STRPOS(term, ''%'') > 0) THEN subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';''; END IF; query := ''SELECT DISTINCT fcvt.feature_id FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);''; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property (type, val) CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_type alias for $1; p_val alias for $2; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' || quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --- get all feature ids (including children) for feature with the property val CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS ' DECLARE p_val alias for $1; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type%ROWTYPE; BEGIN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';''; IF (STRPOS(p_val, ''%'') > 0) THEN query := ''SELECT DISTINCT fprop.feature_id FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';''; END IF; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis ---get feature ids for any node with type = ptype whose child node type = ctype ---and child node feature count comparing (using operator) to ccount CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS ' DECLARE ptype alias for $1; ctype alias for $2; ccount alias for $3; operator alias for $4; is_an alias for $5; query TEXT; myrc feature_by_fx_type%ROWTYPE; myrc2 feature_by_fx_type %ROWTYPE; BEGIN query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id) INNER join cvterm ct ON (c.type_id = ct.cvterm_id) WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype) || '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';''; ---RAISE NOTICE ''%'', query; FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP RETURN NEXT myrc; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/feature_subalignments.plpgsql000644 000765 000024 00000003523 11256710124 026056 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS ' DECLARE return_data featureloc%ROWTYPE; f_id ALIAS FOR $1; feature_data feature%rowtype; featureloc_data featureloc%rowtype; s text; fmin integer; slen integer; BEGIN --RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id; SELECT INTO feature_data * FROM feature WHERE feature_id = f_id; FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP --RAISE NOTICE ''fmin is %'', featureloc_data.fmin; return_data.feature_id = f_id; return_data.srcfeature_id = featureloc_data.srcfeature_id; return_data.is_fmin_partial = featureloc_data.is_fmin_partial; return_data.is_fmax_partial = featureloc_data.is_fmax_partial; return_data.strand = featureloc_data.strand; return_data.phase = featureloc_data.phase; return_data.residue_info = featureloc_data.residue_info; return_data.locgroup = featureloc_data.locgroup; return_data.rank = featureloc_data.rank; s = feature_data.residues; fmin = featureloc_data.fmin; slen = char_length(s); WHILE char_length(s) LOOP --RAISE NOTICE ''residues is %'', s; --trim off leading match s = trim(leading ''|ATCGNatcgn'' from s); --if leading match detected IF slen > char_length(s) THEN return_data.fmin = fmin; return_data.fmax = featureloc_data.fmin + (slen - char_length(s)); --if the string started with a match, return it, --otherwise, trim the gaps first (ie do not return this iteration) RETURN NEXT return_data; END IF; --trim off leading gap s = trim(leading ''-'' from s); fmin = featureloc_data.fmin + (slen - char_length(s)); END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/frange.plpgsql000644 000765 000024 00000023574 11256710124 022742 0ustar00cainstaff000000 000000 CREATE SCHEMA frange; SET search_path = frange,public,pg_catalog; CREATE TABLE featuregroup ( featuregroup_id serial not null, primary key (featuregroup_id), subject_id int not null, foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, group_id int not null, foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, srcfeature_id int null, foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, fmin int null, fmax int null, strand int null, is_root int not null default 0, constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand) ); CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id); CREATE INDEX featuregroup_idx2 ON featuregroup (object_id); CREATE INDEX featuregroup_idx3 ON featuregroup (group_id); CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id); CREATE INDEX featuregroup_idx5 ON featuregroup (strand); CREATE INDEX featuregroup_idx6 ON featuregroup (is_root); CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT g2.* FROM featuregroup g1, featuregroup g2 WHERE g1.is_root = 1 AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL ) AND g1.group_id = g2.group_id AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3) AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin <= $1 AND fmax >= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin >= $1 AND fmax <= $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS ' SELECT * FROM groupoverlaps($1,$2,$3) WHERE fmin = $1 AND fmax = $2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS ' SELECT * FROM featuregroup WHERE is_root = 1 AND boxquery($1, $2) @ boxrange(fmin,fmax) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin <= mins[i] AND fmax >= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin >= mins[i] AND fmax <= maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS ' DECLARE mins alias for $1; maxs alias for $2; srcs alias for $3; f featuregroup%ROWTYPE; i int; s int; BEGIN i := 1; FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i]; FOR f IN SELECT * FROM featuregroup WHERE group_id IN ( SELECT group_id FROM featuregroup WHERE (srcfeature_id = s OR srcfeature_id IS NULL) AND fmin = mins[i] AND fmax = maxs[i] AND group_id IN ( SELECT group_id FROM groupoverlaps( mins[i], maxs[i] ) WHERE srcfeature_id = s ) ) LOOP RETURN NEXT f; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; --functional index that depends on the above functions CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1; CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE groupid alias for $1; parentid alias for $2; g featuregroup%ROWTYPE; BEGIN FOR g IN SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0 FROM feature_relationship AS fr, featureloc AS fl WHERE fr.object_id = parentid AND fr.subject_id = fl.feature_id LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0); PERFORM _fill_featuregroup(groupid,g.subject_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS ' DECLARE p featuregroup%ROWTYPE; l featureloc%ROWTYPE; isa int; c int; BEGIN TRUNCATE featuregroup; SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); -- Recursion is the biggest performance killer for this function. -- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach. -- Luckily, most feature graphs are only 2 levels deep, so most recursion is -- avoidable. RAISE NOTICE ''Loading root and singleton features.''; FOR p IN SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1 FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1); END LOOP; RAISE NOTICE ''Loading child features. If your database contains grandchild''; RAISE NOTICE ''features, they will be loaded recursively and may take a long time.''; FOR p IN SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id) FROM feature_relationship AS fr0 LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id), featureloc AS fl WHERE fr0.subject_id = fl.feature_id AND fr0.object_id IN ( SELECT f.feature_id FROM feature AS f LEFT JOIN feature_relationship ON (f.feature_id = object_id) LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id) WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship ) AND f.feature_id IN ( SELECT object_id FROM feature_relationship ) AND srcfeature_id IS NOT NULL ) GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand LOOP INSERT INTO featuregroup (subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root) VALUES (p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0); IF ( p.is_root > 0 ) THEN PERFORM _fill_featuregroup(p.subject_id,p.subject_id); END IF; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; SET search_path = public,pg_catalog; chado-1.23/modules/sequence/functions/locgraph.plpgsql000644 000765 000024 00000005466 11256710124 023277 0ustar00cainstaff000000 000000 -- down the graph: eg from chromosome to contig CREATE OR REPLACE FUNCTION project_point_up(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 -- rev strand ELSE $1-$2 -- fwd strand END AS p' LANGUAGE 'sql'; -- down the graph: eg from contig to chromosome CREATE OR REPLACE FUNCTION project_point_down(int,int,int,int) RETURNS int AS 'SELECT CASE WHEN $4<0 THEN $3-$1 ELSE $1+$2 END AS p' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION project_featureloc_up(int,int) RETURNS featureloc AS ' DECLARE in_featureloc_id alias for $1; up_srcfeature_id alias for $2; in_featureloc featureloc%ROWTYPE; up_featureloc featureloc%ROWTYPE; nu_featureloc featureloc%ROWTYPE; nu_fmin INT; nu_fmax INT; nu_strand INT; BEGIN SELECT INTO in_featureloc featureloc.* FROM featureloc WHERE featureloc_id = in_featureloc_id; SELECT INTO up_featureloc up_fl.* FROM featureloc AS in_fl INNER JOIN featureloc AS up_fl ON (in_fl.srcfeature_id = up_fl.feature_id) WHERE in_fl.featureloc_id = in_featureloc_id AND up_fl.srcfeature_id = up_srcfeature_id; IF up_featureloc.strand IS NULL THEN RETURN NULL; END IF; IF up_featureloc.strand < 0 THEN nu_fmin = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,-1); nu_fmax = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,-1); nu_strand = -in_featureloc.strand; ELSE nu_fmin = project_point_up(in_featureloc.fmin, up_featureloc.fmin,up_featureloc.fmax,1); nu_fmax = project_point_up(in_featureloc.fmax, up_featureloc.fmin,up_featureloc.fmax,1); nu_strand = in_featureloc.strand; END IF; in_featureloc.fmin = nu_fmin; in_featureloc.fmax = nu_fmax; in_featureloc.strand = nu_strand; in_featureloc.srcfeature_id = up_featureloc.srcfeature_id; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int) RETURNS INT AS ' DECLARE in_p alias for $1; srcf_id alias for $2; t_id alias for $3; e_floc featureloc%ROWTYPE; out_p INT; exon_cvterm_id INT; BEGIN SELECT INTO exon_cvterm_id get_feature_type_id(''exon''); SELECT INTO out_p CASE WHEN strand<0 THEN fmax-p ELSE p-fmin END AS p FROM featureloc INNER JOIN feature USING (feature_id) INNER JOIN feature_relationship ON (feature.feature_id=subject_id) WHERE object_id = t_id AND feature.type_id = exon_cvterm_id AND featureloc.srcfeature_id = srcf_id AND in_p >= fmin AND in_p <= fmax; RETURN in_featureloc; END ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/locgraph.sqlapi000644 000765 000024 00000001377 11256710124 023103 0ustar00cainstaff000000 000000 COMMENT ON FUNCTION project_point_up(INT,INT,INT,INT) IS '(p,fmin,fmax,strand). p is relative to some feature f; fmin and fmax are also relative to this feature. p will be relocated relative to fmin/fmax (eg fmin/fmax may be for some contig, the desired behaviour is to project p from the chromosome onto the contig)'; COMMENT ON FUNCTION project_point_down(INT,INT,INT,INT) IS '(p,fmin,fmax,strand). p is relative to fmin/fmax. p will be relocated from fmin/fmax (eg fmin/fmax may be for some contig, the desired behaviour is to project p from the contig onto the chromosme)'; COMMENT ON FUNCTION project_featureloc_up(INT,INT) IS '(in_featureloc_id,up_srcfeature_id). will return a new featureloc (with the same featureloc_id) projected up the featureloc graph'; chado-1.23/modules/sequence/functions/range.plpgsql000644 000765 000024 00000007103 11256710124 022562 0ustar00cainstaff000000 000000 -- -- functions operating on featureloc ranges -- -- create a point CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS 'SELECT point ($1, $2)' LANGUAGE 'sql'; -- create a range box -- (make this immutable so we can index it) CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS 'SELECT box (create_point(0, $1), create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $2))' LANGUAGE 'sql' IMMUTABLE; --functional index that depends on the above functions CREATE INDEX binloc_boxrange ON featureloc USING RTREE (boxrange(fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS setof featureloc AS 'SELECT * from featureloc where boxquery($1, $2) @ boxrange(fmin,fmax)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int) RETURNS setof featureloc AS 'SELECT featureloc.* FROM featureloc INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id) WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcf.name = $1 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($2, $3) @ boxrange(fmin,fmax) AND srcfeature_id = $1 ' LANGUAGE 'sql'; -- can we not just do these as views? CREATE OR REPLACE FUNCTION feature_overlaps(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION feature_disjoint_from(int) RETURNS setof feature AS 'SELECT feature.* FROM feature INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id) INNER JOIN featureloc AS y ON (y.feature_id = $1) WHERE x.srcfeature_id = y.srcfeature_id AND ( x.fmax < y.fmin OR x.fmin > y.fmax ) ' LANGUAGE 'sql'; --Evolution of the methods found in range.plpgsql (C. Pommier) --Goal : increase performances of segment fetching -- Implies to optimise featureloc_slice --Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed. -- To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results. -- The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs : -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax)) -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax)) CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1,$3))' LANGUAGE 'sql' IMMUTABLE; -- create a query box CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS 'SELECT box (create_point($1, $2), create_point($1, $3))' LANGUAGE 'sql' IMMUTABLE; CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcfeature_id,fmin, fmax)); CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int) RETURNS setof featureloc AS 'SELECT * FROM featureloc WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)' LANGUAGE 'sql';chado-1.23/modules/sequence/functions/range.sqlapi000644 000765 000024 00000001707 11256710124 022375 0ustar00cainstaff000000 000000 -- -- functions operating on featureloc ranges -- DECLARE FUNCTION featureloc_slice( fmin INTEGER, fmax INTEGER) RETURNS SETOF featureloc; COMMENT ON FUNCTION featureloc_slice(INT,INT) IS ' returns all featurelocs with coordinates that intersect fmin and fmax '; DECLARE FUNCTION featureloc_slice( srcfeature_name VARCHAR, fmin INTEGER, fmax INTEGER) RETURNS SETOF featureloc; COMMENT ON FUNCTION featureloc_slice(VARCHAR,INT,INT) IS ' returns all featurelocs with coordinates that intersect fmin and fmax and located relative to srcfeature (specified by srcfeature.name) '; DECLARE FUNCTION featureloc_slice( srcfeature_id INTEGER, fmin INTEGER, fmax INTEGER) RETURNS SETOF featureloc; COMMENT ON FUNCTION featureloc_slice(INT,INT,INT) IS ' returns all featurelocs with coordinates that intersect fmin and fmax and located relative to srcfeature (specified by id) '; chado-1.23/modules/sequence/functions/sequence-cv-helper.plpgsql000644 000765 000024 00000002047 11256710124 025163 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''sequence'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''feature_property'' ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT AS ' SELECT cvterm_id FROM cv INNER JOIN cvterm USING (cv_id) WHERE cvterm.name=$1 AND cv.name=''relationship'' ' LANGUAGE 'sql'; chado-1.23/modules/sequence/functions/sequence-cv-helper.sqlapi000644 000765 000024 00000001126 11256710124 024767 0ustar00cainstaff000000 000000 COMMENT ON FUNCTION get_cv_id_for_feature() IS 'return cv_id for SO'; COMMENT ON FUNCTION get_cv_id_for_featureprop() IS 'return cv_id for SOFP'; COMMENT ON FUNCTION get_cv_id_for_feature_relationship() IS 'return cv_id for OBO_REL'; COMMENT ON FUNCTION get_feature_type_id(VARCHAR) IS 'gets cvterm_id for a feature type by name - eg exon'; COMMENT ON FUNCTION get_featureprop_type_id(VARCHAR) IS 'gets cvterm_id for a featureprop type by name - eg anticodon'; COMMENT ON FUNCTION get_feature_relationship_type_id(VARCHAR) IS 'gets cvterm_id for a feature_relationship type by name - eg part_of'; chado-1.23/modules/sequence/functions/sequence-loading.plpgsql000644 000765 000024 00000012242 11256710124 024711 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURNS INT AS 'DECLARE v_srcfeature_id ALIAS FOR $1; v_fmin ALIAS FOR $2; v_fmax ALIAS FOR $3; v_strand ALIAS FOR $4; v_dbxref_id ALIAS FOR $5; v_organism_id ALIAS FOR $6; v_name ALIAS FOR $7; v_uniquename ALIAS FOR $8; v_type_id ALIAS FOR $9; v_is_analysis ALIAS FOR $10; v_feature_id INT; v_featureloc_id INT; BEGIN IF v_dbxref_id IS NULL THEN SELECT INTO v_feature_id feature_id FROM feature WHERE uniquename=v_uniquename AND organism_id=v_organism_id AND type_id=v_type_id; ELSE SELECT INTO v_feature_id feature_id FROM feature WHERE dbxref_id=v_dbxref_id; END IF; IF NOT FOUND THEN INSERT INTO feature ( dbxref_id , organism_id , name , uniquename , type_id , is_analysis ) VALUES ( v_dbxref_id , v_organism_id , v_name , v_uniquename , v_type_id , v_is_analysis ); v_feature_id = currval(''feature_feature_id_seq''); ELSE UPDATE feature SET dbxref_id = v_dbxref_id , organism_id = v_organism_id , name = v_name , uniquename = v_uniquename , type_id = v_type_id , is_analysis = v_is_analysis WHERE feature_id=v_feature_id; END IF; PERFORM store_featureloc(v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, 0, 0); RETURN v_feature_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_srcfeature_id ALIAS FOR $2; v_fmin ALIAS FOR $3; v_fmax ALIAS FOR $4; v_strand ALIAS FOR $5; v_rank ALIAS FOR $6; v_locgroup ALIAS FOR $7; v_featureloc_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_featureloc_id featureloc_id FROM featureloc WHERE feature_id=v_feature_id AND rank=v_rank AND locgroup=v_locgroup; IF NOT FOUND THEN INSERT INTO featureloc ( feature_id, srcfeature_id, fmin, fmax, strand, rank, locgroup) VALUES ( v_feature_id, v_srcfeature_id, v_fmin, v_fmax, v_strand, v_rank, v_locgroup); v_featureloc_id = currval(''featureloc_featureloc_id_seq''); ELSE UPDATE featureloc SET feature_id = v_feature_id, srcfeature_id = v_srcfeature_id, fmin = v_fmin, fmax = v_fmax, strand = v_strand, rank = v_rank, locgroup = v_locgroup WHERE featureloc_id=v_featureloc_id; END IF; RETURN v_featureloc_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT AS 'DECLARE v_feature_id ALIAS FOR $1; v_syn ALIAS FOR $2; v_type_id ALIAS FOR $3; v_is_current ALIAS FOR $4; v_is_internal ALIAS FOR $5; v_pub_id ALIAS FOR $6; v_synonym_id INT; v_feature_synonym_id INT; BEGIN IF v_feature_id IS NULL THEN RAISE EXCEPTION ''feature_id cannot be null''; END IF; SELECT INTO v_synonym_id synonym_id FROM synonym WHERE name=v_syn AND type_id=v_type_id; IF NOT FOUND THEN INSERT INTO synonym ( name, synonym_sgml, type_id) VALUES ( v_syn, v_syn, v_type_id); v_synonym_id = currval(''synonym_synonym_id_seq''); END IF; SELECT INTO v_feature_synonym_id feature_synonym_id FROM feature_synonym WHERE feature_id=v_feature_id AND synonym_id=v_synonym_id AND pub_id=v_pub_id; IF NOT FOUND THEN INSERT INTO feature_synonym ( feature_id, synonym_id, pub_id, is_current, is_internal) VALUES ( v_feature_id, v_synonym_id, v_pub_id, v_is_current, v_is_internal); v_feature_synonym_id = currval(''feature_synonym_feature_synonym_id_seq''); ELSE UPDATE feature_synonym SET is_current=v_is_current, is_internal=v_is_internal WHERE feature_synonym_id=v_feature_synonym_id; END IF; RETURN v_feature_synonym_id; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/sequence-loading.sqlapi000644 000765 000024 00000003250 11256710124 024517 0ustar00cainstaff000000 000000 DECLARE FUNCTION store_feature ( srcfeature_id INT, fmin INT, fmax INT, strand INT, dbxref_id INT, organism_id INT, name VARCHAR, uniquename VARCHAR, type_id INT, is_analysis BOOLEAN) RETURNS INT; COMMENT ON FUNCTION store_feature (INT,INT,INT,INT, INT,INT,VARCHAR,VARCHAR,INT,BOOLEAN) RETURN INT IS 'stores a feature and its featureloc. The featureloc is assumed to be primary (rank and locgroup=0). Performs UPDATE on feature if either (dbxref_id) or (uniquename,organism_id,type_id) correspond to a row in the database, INSERTs otherwise. Will replace any existing primary featureloc'; DECLARE FUNCTION store_featureloc ( feature_id INT, srcfeature_id INT, fmin INT, fmax INT, strand INT, rank INT, locgroup INT); RETURNS INT; COMMENT ON FUNCTION store_featureloc (INT,INT,INT,INT,INT,INT,INT) RETURNS INT AS 'stores the featureloc for a given feature. If a featureloc with the same (feature_id,rank,locgroup) exists, will replace - otherwise inserts new featureloc'; DECLARE FUNCTION store_feature_synonym ( feature_id INT, syn VARCHAR, type_id INT, is_current BOOLEAN, is_internal BOOLEAN, pub_id INT) RETURN INT; COMMENT ON FUNCTION store_feature_synonym (INT,VARCHAR,INT,BOOLEAN,BOOLEAN,INT) RETURNS INT IS 'stores a synonym and feature_synonym link for a given feature. inserts new synonym if not present. if feature_synonym link exists for this synonym, will update the boolean flags'; chado-1.23/modules/sequence/functions/sequtil.plpgsql000644 000765 000024 00000023020 11256710124 023150 0ustar00cainstaff000000 000000 -- reverse_string CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS ' DECLARE reversed_string TEXT; incoming ALIAS FOR $1; BEGIN reversed_string = ''''; FOR i IN REVERSE char_length(incoming)..1 loop reversed_string = reversed_string || substring(incoming FROM i FOR 1); END loop; RETURN reversed_string; END' language plpgsql; -- complements DNA CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS 'SELECT (translate($1, ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'', ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))' LANGUAGE 'sql'; -- revcomp CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS 'SELECT reverse_string(complement_residues($1))' LANGUAGE 'sql'; -- DNA to AA CREATE OR REPLACE FUNCTION translate_dna(TEXT,INT) RETURNS TEXT AS ' DECLARE dnaseq ALIAS FOR $1; gcode ALIAS FOR $2; translation TEXT; dnaseqlen INT; codon CHAR(3); aa CHAR(1); i INT; BEGIN translation = ''''; dnaseqlen = char_length(dnaseq); i=1; WHILE i+1 < dnaseqlen loop codon = substring(dnaseq,i,3); aa = translate_codon(codon,gcode); translation = translation || aa; i = i+3; END loop; RETURN translation; END' language plpgsql; -- DNA to AA, default genetic code CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS 'SELECT translate_dna($1,1)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION translate_codon(TEXT,INT) RETURNS CHAR AS 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS 'SELECT $1 || $2' LANGUAGE 'sql'; CREATE AGGREGATE concat ( sfunc = concat_pair, basetype = text, stype = text, initcond = '' ); --function to 'unshare' exons. It looks for exons that have the same fmin --and fmax and belong to the same gene and only keeps one. The other, --redundant exons are marked obsolete in the feature table. Nothing --is done with those features' entries in the featureprop, feature_dbxref, --feature_pub, or feature_cvterm tables. For the moment, I'm assuming --that any annotations that they have when this script is run are --identical to their non-obsoleted doppelgangers. If that's not the case, --they could be merged via query. -- --The bulk of this code was contributed by Robin Houston at --GeneDB/Sanger Centre. CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS ' DECLARE BEGIN /* Generate a table of shared exons */ CREATE temporary TABLE shared_exons AS SELECT gene.feature_id as gene_feature_id , gene.uniquename as gene_uniquename , transcript1.uniquename as transcript1 , exon1.feature_id as exon1_feature_id , exon1.uniquename as exon1_uniquename , transcript2.uniquename as transcript2 , exon2.feature_id as exon2_feature_id , exon2.uniquename as exon2_uniquename , exon1_loc.fmin /* = exon2_loc.fmin */ , exon1_loc.fmax /* = exon2_loc.fmax */ FROM feature gene JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id JOIN cv gene_type_cv USING (cv_id) JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id WHERE gene_type_cv.name = ''sequence'' AND gene_type.name = ''gene'' AND transcript1_type_cv.name = ''sequence'' AND transcript1_type.name = ''mRNA'' AND transcript2_type_cv.name = ''sequence'' AND transcript2_type.name = ''mRNA'' AND exon1_type_cv.name = ''sequence'' AND exon1_type.name = ''exon'' AND exon2_type_cv.name = ''sequence'' AND exon2_type.name = ''exon'' AND exon1.feature_id < exon2.feature_id AND exon1_loc.rank = 0 AND exon2_loc.rank = 0 AND exon1_loc.fmin = exon2_loc.fmin AND exon1_loc.fmax = exon2_loc.fmax ; /* Choose one of the shared exons to be the canonical representative. We pick the one with the smallest feature_id. */ CREATE temporary TABLE canonical_exon_representatives AS SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin FROM shared_exons GROUP BY gene_feature_id,fmin ; CREATE temporary TABLE exon_replacements AS SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id , canonical_exon_representatives.canonical_feature_id , canonical_exon_representatives.fmin FROM shared_exons JOIN canonical_exon_representatives USING (gene_feature_id) WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id AND shared_exons.fmin = canonical_exon_representatives.fmin ; UPDATE feature_relationship SET subject_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE subject_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature_relationship SET object_id = ( SELECT canonical_feature_id FROM exon_replacements WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id) WHERE object_id IN ( SELECT actual_feature_id FROM exon_replacements ); UPDATE feature SET is_obsolete = true WHERE feature_id IN ( SELECT actual_feature_id FROM exon_replacements ); END; ' LANGUAGE 'plpgsql'; --This is a function to seek out exons of transcripts and orders them, --using feature_relationship.rank, in "transcript order" numbering --from 0, taking strand into account. It will not touch transcripts that --already have their exons ordered (in case they have a non-obvious --ordering due to trans splicing). It takes as an argument the --feature.type_id of the parent transcript type (typically, mRNA, although --non coding transcript types should work too). CREATE OR REPLACE FUNCTION order_exons (integer) RETURNS void AS ' DECLARE parent_type ALIAS FOR $1; exon_id int; part_of int; exon_type int; strand int; arow RECORD; order_by varchar; rowcount int; exon_count int; ordered_exons int; transcript_id int; transcript_row feature%ROWTYPE; BEGIN SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of'' AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship''); --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon'' -- AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence''); --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type; FOR transcript_row IN SELECT * FROM feature WHERE type_id = parent_type LOOP transcript_id = transcript_row.feature_id; SELECT INTO rowcount count(*) FROM feature_relationship WHERE object_id = transcript_id AND rank = 0; --Dont modify this transcript if there are already numbered exons or --if there is only one exon IF rowcount = 1 THEN --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount; CONTINUE; END IF; --need to reverse the order if the strand is negative SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id; IF strand > 0 THEN order_by = ''fl.fmin''; ELSE order_by = ''fl.fmax desc''; END IF; exon_count = 0; FOR arow IN EXECUTE ''SELECT fr.*, fl.fmin, fl.fmax FROM feature_relationship fr, featureloc fl WHERE fr.object_id = ''||transcript_id||'' AND fr.subject_id = fl.feature_id AND fr.type_id = ''||part_of||'' ORDER BY ''||order_by LOOP --number the exons for a given transcript UPDATE feature_relationship SET rank = exon_count WHERE feature_relationship_id = arow.feature_relationship_id; exon_count = exon_count + 1; END LOOP; END LOOP; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/sequence/functions/sequtil.sqlapi000644 000765 000024 00000004100 11256710124 022755 0ustar00cainstaff000000 000000 -- -- functions for bio sequences -- DECLARE FUNCTION reverse_complement( residues TEXT) RETURNS TEXT; COMMENT ON FUNCTION reverse_complement(TEXT) IS ' Calculates the reverse complement of a DNA sequence. The value of the argument must an an IUPAC compliant string '; -- Requires: gencode module; see modules/sequence/gencode DECLARE FUNCTION translate_dna( residues TEXT) RETURNS TEXT; COMMENT ON FUNCTION translate_dna(TEXT) IS ' Translates a DNA sequence to AA sequence based on standard genetic code '; -- Requires: gencode schema; see modules/sequence/gencode DECLARE FUNCTION translate_dna( residues TEXT, gencode_id INT) RETURNS TEXT; COMMENT ON FUNCTION translate_dna(TEXT,INT) IS ' Translates a DNA sequence to AA sequence based on NCBI genetic code ID (1=standard). See gencode schema module for details '; DECLARE FUNCTION share_exons() RETURNS void; COMMENT ON FUNCTION share_exons() IS ' This is a function to 'unshare' exons. It looks for exons that have the same fmin and fmax and belong to the same gene and only keeps one. The other, redundant exons are marked obsolete in the feature table. Nothing is done with those features' entries in the featureprop, feature_dbxref, feature_pub, or feature_cvterm tables. For the moment, I'm assuming that any annotations that they have when this script is run are identical to their non-obsoleted doppelgangers. If that's not the case, they could be merged via query. The bulk of this code was contributed by Robin Houston at GeneDB/Sanger Centre. ' DECLARE FUNCTION order_exons( parent_type_id INT) RETURNS void; COMMENT ON FUNCTION order_exons(INT) IS ' This is a function to seek out exons of transcripts and orders them, using feature_relationship.rank, in "transcript order" numbering from 0, taking strand into account. It will not touch transcripts that already have their exons ordered (in case they have a non-obvious ordering due to trans splicing). It takes as an argument the feature.type_id of the parent transcript type (typically, mRNA, although non coding transcript types should work too). '; chado-1.23/modules/sequence/functions/subsequence.plpgsql000644 000765 000024 00000007704 11256710124 024017 0ustar00cainstaff000000 000000 -- dependency_on: [sequtil,sequence-cv-helper] CREATE OR REPLACE FUNCTION subsequence(INT,INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN $4<0 THEN reverse_complement(substring(srcf.residues,$2+1,($3-$2))) ELSE substring(residues,$2+1,($3-$2)) END AS residues FROM feature AS srcf WHERE srcf.feature_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_featureloc(INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc_id=$1' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT,INT,INT) RETURNS TEXT AS 'SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) WHERE featureloc.feature_id=$1 AND featureloc.rank=$2 AND featureloc.locgroup=$3' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_feature(INT) RETURNS TEXT AS 'SELECT subsequence_by_feature($1,0,0)' LANGUAGE 'sql'; -- based on subfeature sets: -- constrained by feature_relationship.type_id -- (allows user to construct queries that only get subsequences of -- part_of subfeatures) CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_rtype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=featureloc.feature_id) WHERE fr.object_id=v_feature_id AND fr.type_id=v_rtype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT) RETURNS TEXT AS ' SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0) ' LANGUAGE 'sql'; -- constrained by subfeature.type_id (eg exons of a transcript) CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) RETURNS TEXT AS ' DECLARE v_feature_id ALIAS FOR $1; DECLARE v_ftype_id ALIAS FOR $2; DECLARE v_rank ALIAS FOR $3; DECLARE v_locgroup ALIAS FOR $4; DECLARE subseq TEXT; DECLARE seqrow RECORD; BEGIN subseq = ''''; FOR seqrow IN SELECT CASE WHEN strand<0 THEN reverse_complement(substring(srcf.residues,fmin+1,(fmax-fmin))) ELSE substring(srcf.residues,fmin+1,(fmax-fmin)) END AS residues FROM feature AS srcf INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id) INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id) INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id) WHERE fr.object_id=v_feature_id AND subf.type_id=v_ftype_id AND featureloc.rank=v_rank AND featureloc.locgroup=v_locgroup ORDER BY fr.rank LOOP subseq = subseq || seqrow.residues; END LOOP; RETURN subseq; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT) RETURNS TEXT AS 'SELECT subsequence_by_typed_subfeatures($1,$2,0,0)' LANGUAGE 'sql'; chado-1.23/modules/sequence/functions/subsequence.sqlapi000644 000765 000024 00000010151 11256710124 023614 0ustar00cainstaff000000 000000 IMPORT reverse_complement(TEXT) FROM sequtil; IMPORT get_feature_relationship_type_id(TEXT) sequence-cv-helper; ----------------------------------- -- basic subsequencing functions -- ----------------------------------- DECLARE FUNCTION subsequence( srcfeature_id INT REFERENCES feature(feature_id), fmin INT, fmax INT, strand INT ) RETURNS TEXT; COMMENT ON FUNCTION subsequence(INT,INT,INT,INT) IS 'extracts a subsequence, reverse complementing if range <1'; DECLARE FUNCTION subsequence_by_feature ( feature_id INT REFERENCES feature(feature_id) ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_by_feature(INT) IS 'extracts a subsequence for a feature, using featureloc (rank,group=0). The subsequence will be extracted from the featureloc.srcfeature from fmin to fmax, revcomping if required'; DECLARE FUNCTION subsequence_by_feature ( feature_id INT REFERENCES feature(feature_id), rank INT, locgroup INT ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_by_feature(INT) IS 'extracts a subsequence for a feature, using featureloc (rank,group=0)'; ------------------------------------------------------- -- subsequences based on discontiguous featurelocs --- ------------------------------------------------------- -- a feature can contain subfeatures (eg transcripts -- containing exons and polypeptides) -- these functions automatically extract the concatenated -- sequence of the multiple featurelocs defined by the -- subfeatures of any containing feature -- ** typed relations ** -- here subfeatures are constrained by the type of the relationship -- between subfeature and container feature DECLARE FUNCTION subsequence_by_subfeatures( feature_id INT REFERENCES feature(feature_id), type_id INT REFERENCES cvterm(cvterm_id) ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_by_subfeatures(INT,INT) IS 'extracts a subsequence for a featureset. a featureset contains subfeatures, as defined by feature_relationship (the set is the object of the relation, the subfeature is the subject). the subfeatures are constrained by the type_id of the feature_relationship (this allows you to get the subsequence of a feature based on part_of featurelocs only). The rank and locgroup are set to 0'; DECLARE FUNCTION subsequence_by_subfeatures( feature_id INT REFERENCES feature(feature_id) ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_set_by_subfeatures(INT,INT,INT,INT) IS 'See the 2-arg version of this function; the feature_relationship type is set to part_of'; DECLARE FUNCTION subsequence_set_by_subfeatures( feature_id INT REFERENCES feature(feature_id), type_id INT REFERENCES cvterm(cvterm_id), rank INT, locgroup INT ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_set_by_subfeatures(INT,INT,INT,INT) IS 'See the 2-arg version of this function; this allows the featurelocs to be constrained by rank and locgroup'; -- ** typed subfeatures ** -- here subfeatures are constrained by their type; eg exon DECLARE FUNCTION subsequence_by_typed_subfeatures( feature_id INT REFERENCES feature(feature_id), type_id INT REFERENCES cvterm(cvterm_id) ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_set_by_typed_subfeatures(INT,INT) IS 'extracts a subsequence for a featureset. a featureset contains subfeatures, as defined by feature_relationship (the set is the object of the relation, the subfeature is the subject). the subfeatures are constrained by a type_id (this allows you to get the subsequence of a transcript based on exon featurelocs only). The rank and locgroup are set to 0'; DECLARE FUNCTION subsequence_by_typed_subfeatures( feature_id INT REFERENCES feature(feature_id), type_id INT REFERENCES cvterm(cvterm_id), rank INT, locgroup INT ) RETURNS TEXT; COMMENT ON FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT) IS 'See the 2-arg version of this function; this allows the featurelocs to be constrained by rank and locgroup'; chado-1.23/modules/sequence/bridges/bin/000755 000765 000024 00000000000 12061672375 020252 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/bridges/chaos-bridge.sql.xml000644 000765 000024 00000003555 11256710112 023344 0ustar00cainstaff000000 000000 Chaos is a simplified view layer over Chado. To activate, SET search_path=chaos,public,pg_catalog; Be warned - this rewrites standard chado tables like feature table name clash - be sure to prefix with schema name SELECT dbxref.*, db.name AS dbname, db.name || ':' || accession AS dbxrefstr FROM public.dbxref INNER JOIN public.db USING (db_id); table name clash - be sure to prefix with schema name SELECT *, genus || ' ' || species || ' (' || common_name || ')' AS organismstr FROM organism table name clash - be sure to prefix with schema name SELECT feature_id, f.name, uniquename, type_id, f.dbxref_id, t.name AS type, organismstr, dbxrefstr, residues, seqlen, md5checksum FROM public.feature AS f LEFT OUTER JOIN chaos.dbxref USING (dbxref_id) INNER JOIN chaos.organism USING (organism_id) INNER JOIN cvterm AS t ON (t.cvterm_id=type_id) table name clash - be sure to prefix with schema name SELECT feature_id, t.name AS type, value FROM public.featureprop INNER JOIN cvterm AS t ON (t.cvterm_id=type_id) table name clash - be sure to prefix with schema name chado-1.23/modules/sequence/bridges/gadfly-bridge.sql.xml000644 000765 000024 00000013727 11256710112 023517 0ustar00cainstaff000000 000000 Bridge layer for GadFly Database schema - allows chado to "masquerade" as a GadFly Schema, which means we can use (legacy) GadFly software; GadFly is still in use at the BDGP/DHGP Activate this to make this bridge take precedence SET SEARCH_PATH TO gadfly,public; (note that placing gadfly first in the search path means that gadfly.dbxref takes precedence over public.dbxref) SELECT feature_id AS id, 0 AS created, feature.name AS name, NULL AS molecule_type, NULL AS last_modified, residues, NULL AS description, seqlen AS length, 0 AS major_version, md5checksum FROM feature; SELECT produced_by_sf_id AS subject_id, produces_sf_id AS object_id FROM feature_relationship; SELECT exon_sf_id AS subject_id, transcript_sf_id AS object_id, rank FROM feature_relationship; SELECT analysis_id AS id, name, program, sourcename AS dbname, NULL AS descrption, 0 AS created, 0 AS last_modified FROM analysis; SELECT analysis_id, feature_id AS seq_feature_id, 0 AS job_id FROM analysisfeature; SELECT feature_id AS seq_feature_id, t.name AS p_key, value AS p_val FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id); SELECT feature_id AS seq_feature_id, 0 AS is_internal, value AS comment FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id) WHERE t.name='comment'; SELECT feature_id AS seq_feature_id, 0 AS is_internal, value AS comment FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id) WHERE t.name='description'; SELECT result_span_id AS seq_feature_id, t.name AS param_key, value AS param_value FROM featureprop INNER JOIN cvterm AS t ON (cvterm_id=type_id) SELECT feature_id AS seq_id, dbxref_id FROM feature_dbxref; SELECT feature_id AS seq_id, organism_id FROM feature; SELECT feature_id AS feature_id, dbxref_id FROM feature_dbxref; SELECT feature_id AS feature_id, organism_id FROM feature; table name clash - be sure to prefix with schema name SELECT dbxref_id AS id, db.name AS dbname, dbxref.accession AS accession, CAST(NULL AS VARCHAR) AS accessiontype, dbxref.description AS description FROM public.dbxref INNER JOIN public.db USING (db_id); CREATE INDEX dbxref_idx1 ON gadfly.dbxref (id); CREATE INDEX dbxref_idx2 ON gadfly.dbxref (dbname); CREATE INDEX dbxref_idx3 ON gadfly.dbxref (accession); CREATE INDEX dbxref_idx4 ON gadfly.dbxref (accessiontype); CREATE INDEX dbxref_idx5 ON gadfly.dbxref (description); SELECT organism_id AS id, 0 AS parent_taxon_id, genus, species, common_name, '' AS taxon_code, '' AS embl_code FROM organism; chado-1.23/modules/sequence/bridges/so-bridge.sql000644 000765 000024 00007100571 11610544526 022104 0ustar00cainstaff000000 000000 --This is an automatically generated file; do not edit it as changes will not --be saved. Instead, modify bin/create-so-bridge.pl, which creates this file. CREATE SCHEMA so; SET search_path=so,public,pg_catalog; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent greate *** --- *** r than zero. A nucleotide region is comp *** --- *** osed of bases and a polypeptide region i *** --- *** s composed of amino acids. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region'; --- ************************************************ --- *** relation: sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded sequence. *** --- ************************************************ --- CREATE VIEW sequence_secondary_structure AS SELECT feature_id AS sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure'; --- ************************************************ --- *** relation: g_quartet *** --- *** relation type: VIEW *** --- *** *** --- *** G-quartets are unusual nucleic acid stru *** --- *** ctures consisting of a planar arrangemen *** --- *** t where each guanine is hydrogen bonded *** --- *** by hoogsteen pairing to another guanine *** --- *** in the quartet. *** --- ************************************************ --- CREATE VIEW g_quartet AS SELECT feature_id AS g_quartet_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_quartet'; --- ************************************************ --- *** relation: interior_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_coding_exon AS SELECT feature_id AS interior_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon'; --- ************************************************ --- *** relation: satellite_dna *** --- *** relation type: VIEW *** --- *** *** --- *** The many tandem repeats (identical or re *** --- *** lated) of a short basic repeating unit; *** --- *** many have a base composition or other pr *** --- *** operty different from the genome average *** --- *** that allows them to be separated from t *** --- *** he bulk (main band) genomic DNA. *** --- ************************************************ --- CREATE VIEW satellite_dna AS SELECT feature_id AS satellite_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** One of a pair of sequencing reads in whi *** --- *** ch the two members of the pair are relat *** --- *** ed by originating at either end of a clo *** --- *** ne insert. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding AS SELECT feature_id AS protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding'; --- ************************************************ --- *** relation: non_protein_coding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW non_protein_coding AS SELECT feature_id AS non_protein_coding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding'; --- ************************************************ --- *** relation: scrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of any one of sev *** --- *** eral small cytoplasmic RNA molecules pre *** --- *** sent in the cytoplasm and sometimes nucl *** --- *** eus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna_primary_transcript AS SELECT feature_id AS scrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA sequence, present *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: inr_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters required f *** --- *** or the correct positioning of the polyme *** --- *** rase for the start of transcription. Ove *** --- *** rlaps the TSS. The mammalian consensus s *** --- *** equence is YYAN(T|A)YY; the Drosophila c *** --- *** onsensus sequence is TCA(G|T)t(T|C). In *** --- *** each the A is at position +1 with respec *** --- *** t to the TSS. Functionally similar to th *** --- *** e TATA box element. *** --- ************************************************ --- CREATE VIEW inr_motif AS SELECT feature_id AS inr_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif'; --- ************************************************ --- *** relation: dpe_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters; Positione *** --- *** d from +28 to +32 with respect to the TS *** --- *** S (+1). Experimental results suggest tha *** --- *** t the DPE acts in conjunction with the I *** --- *** NR_motif to provide a binding site for T *** --- *** FIID in the absence of a TATA box to med *** --- *** iate transcription of TATA-less promoter *** --- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G *** --- *** |A|C). *** --- ************************************************ --- CREATE VIEW dpe_motif AS SELECT feature_id AS dpe_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE_motif'; --- ************************************************ --- *** relation: breu_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments at -37 to -32 with respect to the *** --- *** TSS (+1). Consensus sequence is (G|C)(G| *** --- *** C)(G|A)CGCC. Binds TFIIB. *** --- ************************************************ --- CREATE VIEW breu_motif AS SELECT feature_id AS breu_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREu_motif'; --- ************************************************ --- *** relation: pse_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of the *** --- *** promoters of snRNA genes transcribed by *** --- *** RNA polymerase II or by RNA polymerase *** --- *** III. Located between -45 and -60 relativ *** --- *** e to the TSS. The human PSE_motif consen *** --- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| *** --- *** G). *** --- ************************************************ --- CREATE VIEW pse_motif AS SELECT feature_id AS pse_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif'; --- ************************************************ --- *** relation: linkage_group *** --- *** relation type: VIEW *** --- *** *** --- *** A group of loci that can be grouped in a *** --- *** linear order representing the different *** --- *** degrees of linkage among the genes conc *** --- *** erned. *** --- ************************************************ --- CREATE VIEW linkage_group AS SELECT feature_id AS linkage_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linkage_group'; --- ************************************************ --- *** relation: rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A region of double stranded RNA where th *** --- *** e bases do not conform to WC base pairin *** --- *** g. The loop is closed on both sides by c *** --- *** anonical base pairing. If the interrupti *** --- *** on to base pairing occurs on one strand *** --- *** only, it is known as a bulge. *** --- ************************************************ --- CREATE VIEW rna_internal_loop AS SELECT feature_id AS rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_internal_loop'; --- ************************************************ --- *** relation: asymmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where one of the st *** --- *** rands includes more bases than the corre *** --- *** sponding region on the other strand. *** --- ************************************************ --- CREATE VIEW asymmetric_rna_internal_loop AS SELECT feature_id AS asymmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'asymmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: a_minor_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region forming a motif, composed of ad *** --- *** enines, where the minor groove edges are *** --- *** inserted into the minor groove of anoth *** --- *** er helix. *** --- ************************************************ --- CREATE VIEW a_minor_rna_motif AS SELECT feature_id AS a_minor_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_minor_RNA_motif'; --- ************************************************ --- *** relation: k_turn_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** The kink turn (K-turn) is an RNA structu *** --- *** ral motif that creates a sharp (~120 deg *** --- *** ree) bend between two continuous helices *** --- *** . *** --- ************************************************ --- CREATE VIEW k_turn_rna_motif AS SELECT feature_id AS k_turn_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'K_turn_RNA_motif'; --- ************************************************ --- *** relation: sarcin_like_rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A loop in ribosomal RNA containing the s *** --- *** ites of attack for ricin and sarcin. *** --- ************************************************ --- CREATE VIEW sarcin_like_rna_motif AS SELECT feature_id AS sarcin_like_rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sarcin_like_RNA_motif'; --- ************************************************ --- *** relation: symmetric_rna_internal_loop *** --- *** relation type: VIEW *** --- *** *** --- *** An internal RNA loop where the extent of *** --- *** the loop on both stands is the same siz *** --- *** e. *** --- ************************************************ --- CREATE VIEW symmetric_rna_internal_loop AS SELECT feature_id AS symmetric_rna_internal_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symmetric_RNA_internal_loop'; --- ************************************************ --- *** relation: rna_junction_loop *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_junction_loop AS SELECT feature_id AS rna_junction_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_junction_loop'; --- ************************************************ --- *** relation: rna_hook_turn *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rna_hook_turn AS SELECT feature_id AS rna_hook_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_hook_turn'; --- ************************************************ --- *** relation: base_pair *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW base_pair AS SELECT feature_id AS base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'base_pair'; --- ************************************************ --- *** relation: wc_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical base pair, where two bases *** --- *** interact via WC edges, with glycosidic *** --- *** bonds oriented cis relative to the axis *** --- *** of orientation. *** --- ************************************************ --- CREATE VIEW wc_base_pair AS SELECT feature_id AS wc_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'WC_base_pair'; --- ************************************************ --- *** relation: sugar_edge_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW sugar_edge_base_pair AS SELECT feature_id AS sugar_edge_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sugar_edge_base_pair'; --- ************************************************ --- *** relation: aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA or RNA molecules that have been sele *** --- *** cted from random pools based on their ab *** --- *** ility to bind other molecules. *** --- ************************************************ --- CREATE VIEW aptamer AS SELECT feature_id AS aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'aptamer'; --- ************************************************ --- *** relation: dna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** DNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW dna_aptamer AS SELECT feature_id AS dna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_aptamer'; --- ************************************************ --- *** relation: rna_aptamer *** --- *** relation type: VIEW *** --- *** *** --- *** RNA molecules that have been selected fr *** --- *** om random pools based on their ability t *** --- *** o bind other molecules. *** --- ************************************************ --- CREATE VIEW rna_aptamer AS SELECT feature_id AS rna_aptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_aptamer'; --- ************************************************ --- *** relation: morpholino_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Morpholino oligos are synthesized from f *** --- *** our different Morpholino subunits, each *** --- *** of which contains one of the four geneti *** --- *** c bases (A, C, G, T) linked to a 6-membe *** --- *** red morpholine ring. Eighteen to 25 subu *** --- *** nits of these four subunit types are joi *** --- *** ned in a specific order by non-ionic pho *** --- *** sphorodiamidate intersubunit linkages to *** --- *** give a Morpholino. *** --- ************************************************ --- CREATE VIEW morpholino_oligo AS SELECT feature_id AS morpholino_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo'; --- ************************************************ --- *** relation: riboswitch *** --- *** relation type: VIEW *** --- *** *** --- *** A riboswitch is a part of an mRNA that c *** --- *** an act as a direct sensor of small molec *** --- *** ules to control their own expression. A *** --- *** riboswitch is a cis element in the 5' en *** --- *** d of an mRNA, that acts as a direct sens *** --- *** or of metabolites. *** --- ************************************************ --- CREATE VIEW riboswitch AS SELECT feature_id AS riboswitch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch'; --- ************************************************ --- *** relation: matrix_attachment_site *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that is required for the bi *** --- *** nding of chromatin to the nuclear matrix *** --- *** . *** --- ************************************************ --- CREATE VIEW matrix_attachment_site AS SELECT feature_id AS matrix_attachment_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site'; --- ************************************************ --- *** relation: locus_control_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA region that includes DNAse hyperse *** --- *** nsitive sites located 5' to a gene that *** --- *** confers the high-level, position-indepen *** --- *** dent, and copy number-dependent expressi *** --- *** on to that gene. *** --- ************************************************ --- CREATE VIEW locus_control_region AS SELECT feature_id AS locus_control_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast is a match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: genomic_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone of a DNA region of a genome. *** --- ************************************************ --- CREATE VIEW genomic_clone AS SELECT feature_id AS genomic_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone'; --- ************************************************ --- *** relation: processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene where by an mRNA was retrot *** --- *** ransposed. The mRNA sequence is transcri *** --- *** bed back into the genome, lacking intron *** --- *** s and promoters, but often including a p *** --- *** olyA tail. *** --- ************************************************ --- CREATE VIEW processed_pseudogene AS SELECT feature_id AS processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene'; --- ************************************************ --- *** relation: pseudogene_by_unequal_crossing_over *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene caused by unequal crossing *** --- *** over at recombination. *** --- ************************************************ --- CREATE VIEW pseudogene_by_unequal_crossing_over AS SELECT feature_id AS pseudogene_by_unequal_crossing_over_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over'; --- ************************************************ --- *** relation: probe *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence used experimentally to de *** --- *** tect the presence or absence of a comple *** --- *** mentary nucleic acid. *** --- ************************************************ --- CREATE VIEW probe AS SELECT feature_id AS probe_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo' OR cvterm.name = 'probe'; --- ************************************************ --- *** relation: aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW aneuploid AS SELECT feature_id AS aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'aneuploid'; --- ************************************************ --- *** relation: hyperploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as extra c *** --- *** hromosomes are present. *** --- ************************************************ --- CREATE VIEW hyperploid AS SELECT feature_id AS hyperploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hyperploid'; --- ************************************************ --- *** relation: hypoploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number as some ch *** --- *** romosomes are missing. *** --- ************************************************ --- CREATE VIEW hypoploid AS SELECT feature_id AS hypoploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hypoploid'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind thereby *** --- *** effecting translation of genes in that *** --- *** operon. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: nuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, of a nucleotide mol *** --- *** ecule, that interacts selectively and no *** --- *** n-covalently with polypeptide residues o *** --- *** f a nuclease. *** --- ************************************************ --- CREATE VIEW nuclease_binding_site AS SELECT feature_id AS nuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_binding_site'; --- ************************************************ --- *** relation: compound_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW compound_chromosome_arm AS SELECT feature_id AS compound_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm'; --- ************************************************ --- *** relation: restriction_enzyme_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** restriction enzyme. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_binding_site AS SELECT feature_id AS restriction_enzyme_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_binding_site'; --- ************************************************ --- *** relation: d_intrachr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_intrachr_transposition AS SELECT feature_id AS d_intrachr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition'; --- ************************************************ --- *** relation: d_interchr_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a translocation in which one of the fo *** --- *** ur broken ends loses a segment before re *** --- *** -joining. *** --- ************************************************ --- CREATE VIEW d_interchr_transposition AS SELECT feature_id AS d_interchr_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition'; --- ************************************************ --- *** relation: free_chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** an arm exists as an individual chromoso *** --- *** me element. *** --- ************************************************ --- CREATE VIEW free_chromosome_arm AS SELECT feature_id AS free_chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm'; --- ************************************************ --- *** relation: gene_to_gene_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_to_gene_feature AS SELECT feature_id AS gene_to_gene_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'gene_to_gene_feature'; --- ************************************************ --- *** relation: overlapping *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that has *** --- *** a sequence that overlaps the sequence of *** --- *** another gene. *** --- ************************************************ --- CREATE VIEW overlapping AS SELECT feature_id AS overlapping_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'overlapping'; --- ************************************************ --- *** relation: inside_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene. *** --- ************************************************ --- CREATE VIEW inside_intron AS SELECT feature_id AS inside_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'inside_intron'; --- ************************************************ --- *** relation: inside_intron_antiparallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the opposite strand. *** --- ************************************************ --- CREATE VIEW inside_intron_antiparallel AS SELECT feature_id AS inside_intron_antiparallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_antiparallel'; --- ************************************************ --- *** relation: inside_intron_parallel *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when it *** --- *** is located within the intron of another *** --- *** gene and on the same strand. *** --- ************************************************ --- CREATE VIEW inside_intron_parallel AS SELECT feature_id AS inside_intron_parallel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inside_intron_parallel'; --- ************************************************ --- *** relation: five_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's 3' region. *** --- ************************************************ --- CREATE VIEW five_prime_three_prime_overlap AS SELECT feature_id AS five_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_three_prime_overlap'; --- ************************************************ --- *** relation: five_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** five prime region overlaps with another *** --- *** gene's five prime region. *** --- ************************************************ --- CREATE VIEW five_prime_five_prime_overlap AS SELECT feature_id AS five_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_five_prime_overlap'; --- ************************************************ --- *** relation: three_prime_three_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 3' region. *** --- ************************************************ --- CREATE VIEW three_prime_three_prime_overlap AS SELECT feature_id AS three_prime_three_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_three_prime_overlap'; --- ************************************************ --- *** relation: three_prime_five_prime_overlap *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a gene when the *** --- *** 3' region overlaps with another gene's *** --- *** 5' region. *** --- ************************************************ --- CREATE VIEW three_prime_five_prime_overlap AS SELECT feature_id AS three_prime_five_prime_overlap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_five_prime_overlap'; --- ************************************************ --- *** relation: antisense *** --- *** relation type: VIEW *** --- *** *** --- *** A region sequence that is complementary *** --- *** to a sequence of messenger RNA. *** --- ************************************************ --- CREATE VIEW antisense AS SELECT feature_id AS antisense_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense'; --- ************************************************ --- *** relation: polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is polycistronic. *** --- ************************************************ --- CREATE VIEW polycistronic_transcript AS SELECT feature_id AS polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_transcript'; --- ************************************************ --- *** relation: dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_transcript AS SELECT feature_id AS dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_transcript'; --- ************************************************ --- *** relation: operon_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW operon_member AS SELECT feature_id AS operon_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member'; --- ************************************************ --- *** relation: gene_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_array_member AS SELECT feature_id AS gene_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_array_member'; --- ************************************************ --- *** relation: macronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW macronuclear_sequence AS SELECT feature_id AS macronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence'; --- ************************************************ --- *** relation: micronuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW micronuclear_sequence AS SELECT feature_id AS micronuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_sequence'; --- ************************************************ --- *** relation: nuclear_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nuclear sequence. *** --- ************************************************ --- CREATE VIEW nuclear_gene AS SELECT feature_id AS nuclear_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene'; --- ************************************************ --- *** relation: mt_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in mitochondrial sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW mt_gene AS SELECT feature_id AS mt_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'mt_gene'; --- ************************************************ --- *** relation: kinetoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene located in kinetoplast sequence. *** --- ************************************************ --- CREATE VIEW kinetoplast_gene AS SELECT feature_id AS kinetoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'kinetoplast_gene'; --- ************************************************ --- *** relation: plastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plastid sequence. *** --- ************************************************ --- CREATE VIEW plastid_gene AS SELECT feature_id AS plastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'plastid_gene'; --- ************************************************ --- *** relation: apicoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from apicoplast sequence. *** --- ************************************************ --- CREATE VIEW apicoplast_gene AS SELECT feature_id AS apicoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_gene'; --- ************************************************ --- *** relation: ct_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chloroplast sequence. *** --- ************************************************ --- CREATE VIEW ct_gene AS SELECT feature_id AS ct_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ct_gene'; --- ************************************************ --- *** relation: chromoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from chromoplast_sequence. *** --- ************************************************ --- CREATE VIEW chromoplast_gene AS SELECT feature_id AS chromoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_gene'; --- ************************************************ --- *** relation: cyanelle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from cyanelle sequence. *** --- ************************************************ --- CREATE VIEW cyanelle_gene AS SELECT feature_id AS cyanelle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_gene'; --- ************************************************ --- *** relation: leucoplast_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A plastid gene from leucoplast sequence. *** --- ************************************************ --- CREATE VIEW leucoplast_gene AS SELECT feature_id AS leucoplast_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_gene'; --- ************************************************ --- *** relation: proplastid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proplastid sequence. *** --- ************************************************ --- CREATE VIEW proplastid_gene AS SELECT feature_id AS proplastid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_gene'; --- ************************************************ --- *** relation: nucleomorph_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from nucleomorph sequence. *** --- ************************************************ --- CREATE VIEW nucleomorph_gene AS SELECT feature_id AS nucleomorph_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorph_gene'; --- ************************************************ --- *** relation: plasmid_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from plasmid sequence. *** --- ************************************************ --- CREATE VIEW plasmid_gene AS SELECT feature_id AS plasmid_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_gene'; --- ************************************************ --- *** relation: proviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene from proviral sequence. *** --- ************************************************ --- CREATE VIEW proviral_gene AS SELECT feature_id AS proviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'proviral_gene'; --- ************************************************ --- *** relation: endogenous_retroviral_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A proviral gene with origin endogenous r *** --- *** etrovirus. *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_gene AS SELECT feature_id AS endogenous_retroviral_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_gene'; --- ************************************************ --- *** relation: transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW transposable_element AS SELECT feature_id AS transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: clone_insert_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_end AS SELECT feature_id AS clone_insert_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversible denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the chromosome between the c *** --- *** entromere and the telomere. Human chromo *** --- *** somes have two arms, the p arm (short) a *** --- *** nd the q arm (long) which are separated *** --- *** from each other by the centromere. *** --- ************************************************ --- CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: sequencing_primer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequencing_primer AS SELECT feature_id AS sequencing_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer'; --- ************************************************ --- *** relation: mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_frameshift AS SELECT feature_id AS mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'mRNA_with_frameshift'; --- ************************************************ --- *** relation: sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** An extent of biological sequence. *** --- ************************************************ --- CREATE VIEW sequence_feature AS SELECT feature_id AS sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region' OR cvterm.name = 'junction' OR cvterm.name = 'sequence_alteration' OR cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_feature'; --- ************************************************ --- *** relation: transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoded within a transposable ele *** --- *** ment. For example gag, int, env and pol *** --- *** are the transposable element genes of th *** --- *** e TY element in yeast. *** --- ************************************************ --- CREATE VIEW transposable_element_gene AS SELECT feature_id AS transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'transposable_element_gene'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo to which new deoxyribonucleotid *** --- *** es can be added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'primer'; --- ************************************************ --- *** relation: proviral_region *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to a host genome. *** --- ************************************************ --- CREATE VIEW proviral_region AS SELECT feature_id AS proviral_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage' OR cvterm.name = 'proviral_region'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: edited *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is modified by editing. *** --- ************************************************ --- CREATE VIEW edited AS SELECT feature_id AS edited_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited'; --- ************************************************ --- *** relation: transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript with a translational frames *** --- *** hift. *** --- ************************************************ --- CREATE VIEW transcript_with_translational_frameshift AS SELECT feature_id AS transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a sequence that *** --- *** is regulated. *** --- ************************************************ --- CREATE VIEW regulated AS SELECT feature_id AS regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'regulated'; --- ************************************************ --- *** relation: protein_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW protein_coding_primary_transcript AS SELECT feature_id AS protein_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: forward_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW forward_primer AS SELECT feature_id AS forward_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward_primer'; --- ************************************************ --- *** relation: rna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_sequence_secondary_structure AS SELECT feature_id AS rna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'RNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: transcriptionally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated at transcription. *** --- ************************************************ --- CREATE VIEW transcriptionally_regulated AS SELECT feature_id AS transcriptionally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_regulated'; --- ************************************************ --- *** relation: transcriptionally_constitutive *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed in relatively constant amounts *** --- *** without regard to cellular environmenta *** --- *** l conditions such as the concentration o *** --- *** f a particular substrate. *** --- ************************************************ --- CREATE VIEW transcriptionally_constitutive AS SELECT feature_id AS transcriptionally_constitutive_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcriptionally_constitutive'; --- ************************************************ --- *** relation: transcriptionally_induced *** --- *** relation type: VIEW *** --- *** *** --- *** An inducer molecule is required for tran *** --- *** scription to occur. *** --- ************************************************ --- CREATE VIEW transcriptionally_induced AS SELECT feature_id AS transcriptionally_induced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated' OR cvterm.name = 'transcriptionally_induced'; --- ************************************************ --- *** relation: transcriptionally_repressed *** --- *** relation type: VIEW *** --- *** *** --- *** A repressor molecule is required for tra *** --- *** nscription to stop. *** --- ************************************************ --- CREATE VIEW transcriptionally_repressed AS SELECT feature_id AS transcriptionally_repressed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'transcriptionally_repressed'; --- ************************************************ --- *** relation: silenced_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced. *** --- ************************************************ --- CREATE VIEW silenced_gene AS SELECT feature_id AS silenced_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_gene'; --- ************************************************ --- *** relation: gene_silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA modificat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_modification AS SELECT feature_id AS gene_silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_DNA_modification'; --- ************************************************ --- *** relation: gene_silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by DNA methylati *** --- *** on. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_dna_methylation AS SELECT feature_id AS gene_silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: post_translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated after it has been translated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated AS SELECT feature_id AS post_translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'post_translationally_regulated'; --- ************************************************ --- *** relation: translationally_regulated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene that is r *** --- *** egulated as it is translated. *** --- ************************************************ --- CREATE VIEW translationally_regulated AS SELECT feature_id AS translationally_regulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated'; --- ************************************************ --- *** relation: reverse_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligo used for polymer *** --- *** ase chain reaction. *** --- ************************************************ --- CREATE VIEW reverse_primer AS SELECT feature_id AS reverse_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_primer'; --- ************************************************ --- *** relation: epigenetically_modified *** --- *** relation type: VIEW *** --- *** *** --- *** This attribute describes a gene where he *** --- *** ritable changes other than those in the *** --- *** DNA sequence occur. These changes includ *** --- *** e: modification to the DNA (such as DNA *** --- *** methylation, the covalent modification o *** --- *** f cytosine), and post-translational modi *** --- *** fication of histones. *** --- ************************************************ --- CREATE VIEW epigenetically_modified AS SELECT feature_id AS epigenetically_modified_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'epigenetically_modified'; --- ************************************************ --- *** relation: imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** Imprinted genes are epigenetically modif *** --- *** ied genes that are expressed monoallelic *** --- *** ally according to their parent of origin *** --- *** . *** --- ************************************************ --- CREATE VIEW imprinted AS SELECT feature_id AS imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted'; --- ************************************************ --- *** relation: maternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The maternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW maternally_imprinted AS SELECT feature_id AS maternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted'; --- ************************************************ --- *** relation: paternally_imprinted *** --- *** relation type: VIEW *** --- *** *** --- *** The paternal copy of the gene is modifie *** --- *** d, rendering it transcriptionally silent *** --- *** . *** --- ************************************************ --- CREATE VIEW paternally_imprinted AS SELECT feature_id AS paternally_imprinted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted'; --- ************************************************ --- *** relation: allelically_excluded *** --- *** relation type: VIEW *** --- *** *** --- *** Allelic exclusion is a process occurring *** --- *** in diploid organisms, where a gene is i *** --- *** nactivated and not expressed in that cel *** --- *** l. *** --- ************************************************ --- CREATE VIEW allelically_excluded AS SELECT feature_id AS allelically_excluded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded'; --- ************************************************ --- *** relation: gene_rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An epigenetically modified gene, rearran *** --- *** ged at the DNA level. *** --- ************************************************ --- CREATE VIEW gene_rearranged_at_dna_level AS SELECT feature_id AS gene_rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located within the fi *** --- *** ve prime end of an mRNA that causes prem *** --- *** ature termination of translation. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'terminator'; --- ************************************************ --- *** relation: dna_sequence_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A folded DNA sequence. *** --- ************************************************ --- CREATE VIEW dna_sequence_secondary_structure AS SELECT feature_id AS dna_sequence_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif' OR cvterm.name = 'DNA_sequence_secondary_structure'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of known length which may be us *** --- *** ed to manufacture a longer region. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: recoded_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A codon that has been redefined at trans *** --- *** lation. The redefinition may be as a res *** --- *** ult of translational bypass, translation *** --- *** al frameshifting or stop codon readthrou *** --- *** gh. *** --- ************************************************ --- CREATE VIEW recoded_codon AS SELECT feature_id AS recoded_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'recoded_codon'; --- ************************************************ --- *** relation: capped *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing when a sequence, *** --- *** usually an mRNA is capped by the additi *** --- *** on of a modified guanine nucleotide at t *** --- *** he 5' end. *** --- ************************************************ --- CREATE VIEW capped AS SELECT feature_id AS capped_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the transcript sequence with *** --- *** in a gene which is not removed from the *** --- *** primary RNA transcript by RNA splicing. *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unavailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n a host bacterium or some other organis *** --- *** m. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'clone'; --- ************************************************ --- *** relation: yac *** --- *** relation type: VIEW *** --- *** *** --- *** Yeast Artificial Chromosome, a vector co *** --- *** nstructed from the telomeric, centromeri *** --- *** c, and replication origin sequences need *** --- *** ed for replication in yeast cells. *** --- ************************************************ --- CREATE VIEW yac AS SELECT feature_id AS yac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC'; --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Bacterial Artificial Chromosome, a cloni *** --- *** ng vector that can be propagated as mini *** --- *** -chromosomes in a bacterial host. *** --- ************************************************ --- CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: pac *** --- *** relation type: VIEW *** --- *** *** --- *** The P1-derived artificial chromosome are *** --- *** DNA constructs that are derived from th *** --- *** e DNA of P1 bacteriophage. They can carr *** --- *** y large amounts (about 100-300 kilobases *** --- *** ) of other sequences for a variety of bi *** --- *** oengineering purposes. It is one type of *** --- *** vector used to clone DNA fragments (100 *** --- *** - to 300-kb insert size; average, 150 kb *** --- *** ) in Escherichia coli cells. *** --- ************************************************ --- CREATE VIEW pac AS SELECT feature_id AS pac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC'; --- ************************************************ --- *** relation: plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A self replicating, using the hosts cell *** --- *** ular machinery, often circular nucleic a *** --- *** cid molecule that is distinct from a chr *** --- *** omosome in the organism. *** --- ************************************************ --- CREATE VIEW plasmid AS SELECT feature_id AS plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'plasmid'; --- ************************************************ --- *** relation: cosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that is a hybrid of lam *** --- *** bda phages and a plasmid that can be pro *** --- *** pagated as a plasmid or packaged as a ph *** --- *** age,since they retain the lambda cos sit *** --- *** es. *** --- ************************************************ --- CREATE VIEW cosmid AS SELECT feature_id AS cosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cosmid'; --- ************************************************ --- *** relation: phagemid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid which carries within its seque *** --- *** nce a bacteriophage replication origin. *** --- *** When the host bacterium is infected with *** --- *** "helper" phage, a phagemid is replicate *** --- *** d along with the phage DNA and packaged *** --- *** into phage capsids. *** --- ************************************************ --- CREATE VIEW phagemid AS SELECT feature_id AS phagemid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phagemid'; --- ************************************************ --- *** relation: fosmid *** --- *** relation type: VIEW *** --- *** *** --- *** A cloning vector that utilizes the E. co *** --- *** li F factor. *** --- ************************************************ --- CREATE VIEW fosmid AS SELECT feature_id AS fosmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fosmid'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The point at which one or more contiguou *** --- *** s nucleotides were excised. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which adenine has *** --- *** been methylated. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Consensus region of primary transcript b *** --- *** ordering junction of splicing. A region *** --- *** that overlaps exactly 2 base and adjacen *** --- *** t_to splice_junction. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: five_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 5' edge of the intron. A splice_ *** --- *** site that is downstream_adjacent_to exon *** --- *** and starts intron. *** --- ************************************************ --- CREATE VIEW five_prime_cis_splice_site AS SELECT feature_id AS five_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'five_prime_cis_splice_site'; --- ************************************************ --- *** relation: three_prime_cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering the exon, *** --- *** at the 3' edge of the intron. A splice_ *** --- *** site that is upstream_adjacent_to exon a *** --- *** nd finishes intron. *** --- ************************************************ --- CREATE VIEW three_prime_cis_splice_site AS SELECT feature_id AS three_prime_cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'three_prime_cis_splice_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: enhancer_bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer bound by a factor. *** --- ************************************************ --- CREATE VIEW enhancer_bound_by_factor AS SELECT feature_id AS enhancer_bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_bound_by_factor'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region composed of the TSS( *** --- *** s) and binding sites for TF_complexes of *** --- *** the basal transcription machinery. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'promoter'; --- ************************************************ --- *** relation: rnapol_i_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase I binds, to begin trans *** --- *** cription. *** --- ************************************************ --- CREATE VIEW rnapol_i_promoter AS SELECT feature_id AS rnapol_i_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter'; --- ************************************************ --- *** relation: rnapol_ii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase II binds, to begin tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW rnapol_ii_promoter AS SELECT feature_id AS rnapol_ii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_II_promoter'; --- ************************************************ --- *** relation: rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence in eukaryotic DNA to whic *** --- *** h RNA polymerase III binds, to begin tra *** --- *** nscription. *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter AS SELECT feature_id AS rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'RNApol_III_promoter'; --- ************************************************ --- *** relation: caat_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a conserved sequence located abo *** --- *** ut 75-bp upstream of the start point of *** --- *** eukaryotic transcription units which may *** --- *** be involved in RNA polymerase binding; *** --- *** consensus=GG(C|T)CAATCT. *** --- ************************************************ --- CREATE VIEW caat_signal AS SELECT feature_id AS caat_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CAAT_signal'; --- ************************************************ --- *** relation: gc_rich_promoter_region *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved GC-rich region located upstr *** --- *** eam of the start point of eukaryotic tra *** --- *** nscription units which may occur in mult *** --- *** iple copies or in either orientation; co *** --- *** nsensus=GGGCGG. *** --- ************************************************ --- CREATE VIEW gc_rich_promoter_region AS SELECT feature_id AS gc_rich_promoter_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region'; --- ************************************************ --- *** relation: tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved AT-rich septamer found about *** --- *** 25-bp before the start point of many eu *** --- *** karyotic RNA polymerase II transcript un *** --- *** its; may be involved in positioning the *** --- *** enzyme for correct initiation; consensus *** --- *** =TATA(A|T)A(A|T). *** --- ************************************************ --- CREATE VIEW tata_box AS SELECT feature_id AS tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'TATA_box'; --- ************************************************ --- *** relation: minus_10_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 10-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units which may be involved in bin *** --- *** ding RNA polymerase; consensus=TAtAaT. T *** --- *** his region is associated with sigma fact *** --- *** or 70. *** --- ************************************************ --- CREATE VIEW minus_10_signal AS SELECT feature_id AS minus_10_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_10_signal'; --- ************************************************ --- *** relation: minus_35_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved hexamer about 35-bp upstream *** --- *** of the start point of bacterial transcr *** --- *** iption units; consensus=TTGACa or TGTTGA *** --- *** CA. This region is associated with sigma *** --- *** factor 70. *** --- ************************************************ --- CREATE VIEW minus_35_signal AS SELECT feature_id AS minus_35_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_35_signal'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_insert_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_insert_start AS SELECT feature_id AS clone_insert_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_start'; --- ************************************************ --- *** relation: retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is incorpora *** --- *** ted into a chromosome by a mechanism tha *** --- *** t requires reverse transcriptase. *** --- ************************************************ --- CREATE VIEW retrotransposon AS SELECT feature_id AS retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'retrotransposon'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: dna_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon where the mechanism of tran *** --- *** sposition is via a DNA intermediate. *** --- ************************************************ --- CREATE VIEW dna_transposon AS SELECT feature_id AS dna_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'DNA_transposon'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: u2_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A major type of spliceosomal intron spli *** --- *** ced by the U2 spliceosome, that includes *** --- *** U1, U2, U4/U6 and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u2_intron AS SELECT feature_id AS u2_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that in its initial state r *** --- *** equires modification to be functional. *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'primary_transcript'; --- ************************************************ --- *** relation: ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon flanked by long termin *** --- *** al repeat sequences. *** --- ************************************************ --- CREATE VIEW ltr_retrotransposon AS SELECT feature_id AS ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LTR_retrotransposon'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript that is *** --- *** transcribed, but removed from within th *** --- *** e transcript by splicing together the se *** --- *** quences (exons) on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'intron'; --- ************************************************ --- *** relation: non_ltr_retrotransposon *** --- *** relation type: VIEW *** --- *** *** --- *** A retrotransposon without long terminal *** --- *** repeat sequences. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon AS SELECT feature_id AS non_ltr_retrotransposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'non_LTR_retrotransposon'; --- ************************************************ --- *** relation: five_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_intron AS SELECT feature_id AS five_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_intron'; --- ************************************************ --- *** relation: interior_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interior_intron AS SELECT feature_id AS interior_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_intron'; --- ************************************************ --- *** relation: three_prime_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_intron AS SELECT feature_id AS three_prime_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_intron'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment used as a reagent to dete *** --- *** ct the polymorphic genomic loci by hybri *** --- *** dizing against the genomic DNA digested *** --- *** with a given restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: line_element *** --- *** relation type: VIEW *** --- *** *** --- *** A dispersed repeat family with many copi *** --- *** es, each from 1 to 6 kb long. New elemen *** --- *** ts are generated by retroposition of a t *** --- *** ranscribed copy. Typically the LINE cont *** --- *** ains 2 ORF's one of which is reverse tra *** --- *** nscriptase, and 3'and 5' direct repeats. *** --- ************************************************ --- CREATE VIEW line_element AS SELECT feature_id AS line_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LINE_element'; --- ************************************************ --- *** relation: coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon whereby at least one base is par *** --- *** t of a codon (here, 'codon' is inclusive *** --- *** of the stop_codon). *** --- ************************************************ --- CREATE VIEW coding_exon AS SELECT feature_id AS coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'coding_exon'; --- ************************************************ --- *** relation: five_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the five_prime_coding_ex *** --- *** on that codes for protein. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_coding_region AS SELECT feature_id AS five_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: three_prime_coding_exon_coding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the three_prime_coding_e *** --- *** xon that codes for protein. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_coding_region AS SELECT feature_id AS three_prime_coding_exon_coding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_coding_region'; --- ************************************************ --- *** relation: noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that does not contain any codons *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_exon AS SELECT feature_id AS noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'noncoding_exon'; --- ************************************************ --- *** relation: translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence that has *** --- *** translocated to a new position. *** --- ************************************************ --- CREATE VIEW translocation AS SELECT feature_id AS translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation'; --- ************************************************ --- *** relation: five_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' most coding exon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon AS SELECT feature_id AS five_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon'; --- ************************************************ --- *** relation: interior_exon *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is bounded by 5' and 3' spl *** --- *** ice sites. *** --- ************************************************ --- CREATE VIEW interior_exon AS SELECT feature_id AS interior_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interior_exon'; --- ************************************************ --- *** relation: three_prime_coding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The coding exon that is most 3-prime on *** --- *** a given transcript. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon AS SELECT feature_id AS three_prime_coding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime or three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: sine_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element, a few hundred base *** --- *** pairs long, that is dispersed throughou *** --- *** t the genome. A common human SINE is the *** --- *** Alu element. *** --- ************************************************ --- CREATE VIEW sine_element AS SELECT feature_id AS sine_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SINE_element'; --- ************************************************ --- *** relation: simple_sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW simple_sequence_length_variation AS SELECT feature_id AS simple_sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation'; --- ************************************************ --- *** relation: terminal_inverted_repeat_element *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA transposable element defined as ha *** --- *** ving termini with perfect, or nearly per *** --- *** fect short inverted repeats, generally 1 *** --- *** 0 - 40 nucleotides long. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat_element AS SELECT feature_id AS terminal_inverted_repeat_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'terminal_inverted_repeat_element'; --- ************************************************ --- *** relation: rrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a ribosoma *** --- *** l RNA. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript AS SELECT feature_id AS rrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript'; --- ************************************************ --- *** relation: trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a transfer *** --- *** RNA (SO:0000253). *** --- ************************************************ --- CREATE VIEW trna_primary_transcript AS SELECT feature_id AS trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript'; --- ************************************************ --- *** relation: alanine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding alanyl tRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW alanine_trna_primary_transcript AS SELECT feature_id AS alanine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: arg_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding arginyl tR *** --- *** NA (SO:0000255). *** --- ************************************************ --- CREATE VIEW arg_trna_primary_transcript AS SELECT feature_id AS arg_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: asparagine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding asparaginy *** --- *** l tRNA (SO:0000256). *** --- ************************************************ --- CREATE VIEW asparagine_trna_primary_transcript AS SELECT feature_id AS asparagine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: aspartic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding aspartyl t *** --- *** RNA (SO:0000257). *** --- ************************************************ --- CREATE VIEW aspartic_acid_trna_primary_transcript AS SELECT feature_id AS aspartic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: cysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding cysteinyl *** --- *** tRNA (SO:0000258). *** --- ************************************************ --- CREATE VIEW cysteine_trna_primary_transcript AS SELECT feature_id AS cysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamic_acid_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutaminyl *** --- *** tRNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamic_acid_trna_primary_transcript AS SELECT feature_id AS glutamic_acid_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glutamine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glutamyl t *** --- *** RNA (SO:0000260). *** --- ************************************************ --- CREATE VIEW glutamine_trna_primary_transcript AS SELECT feature_id AS glutamine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: glycine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding glycyl tRN *** --- *** A (SO:0000263). *** --- ************************************************ --- CREATE VIEW glycine_trna_primary_transcript AS SELECT feature_id AS glycine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: histidine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding histidyl t *** --- *** RNA (SO:0000262). *** --- ************************************************ --- CREATE VIEW histidine_trna_primary_transcript AS SELECT feature_id AS histidine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: isoleucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding isoleucyl *** --- *** tRNA (SO:0000263). *** --- ************************************************ --- CREATE VIEW isoleucine_trna_primary_transcript AS SELECT feature_id AS isoleucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: leucine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding leucyl tRN *** --- *** A (SO:0000264). *** --- ************************************************ --- CREATE VIEW leucine_trna_primary_transcript AS SELECT feature_id AS leucine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: lysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding lysyl tRNA *** --- *** (SO:0000265). *** --- ************************************************ --- CREATE VIEW lysine_trna_primary_transcript AS SELECT feature_id AS lysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: methionine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding methionyl *** --- *** tRNA (SO:0000266). *** --- ************************************************ --- CREATE VIEW methionine_trna_primary_transcript AS SELECT feature_id AS methionine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: phe_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding phenylalan *** --- *** yl tRNA (SO:0000267). *** --- ************************************************ --- CREATE VIEW phe_trna_primary_transcript AS SELECT feature_id AS phe_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: proline_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding prolyl tRN *** --- *** A (SO:0000268). *** --- ************************************************ --- CREATE VIEW proline_trna_primary_transcript AS SELECT feature_id AS proline_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline_tRNA_primary_transcript'; --- ************************************************ --- *** relation: serine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW serine_trna_primary_transcript AS SELECT feature_id AS serine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: thr_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding threonyl t *** --- *** RNA (SO:000270). *** --- ************************************************ --- CREATE VIEW thr_trna_primary_transcript AS SELECT feature_id AS thr_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: try_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tryptophan *** --- *** yl tRNA (SO:000271). *** --- ************************************************ --- CREATE VIEW try_trna_primary_transcript AS SELECT feature_id AS try_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan_tRNA_primary_transcript'; --- ************************************************ --- *** relation: tyrosine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding tyrosyl tR *** --- *** NA (SO:000272). *** --- ************************************************ --- CREATE VIEW tyrosine_trna_primary_transcript AS SELECT feature_id AS tyrosine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: valine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding valyl tRNA *** --- *** (SO:000273). *** --- ************************************************ --- CREATE VIEW valine_trna_primary_transcript AS SELECT feature_id AS valine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: snrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** clear RNA (SO:0000274). *** --- ************************************************ --- CREATE VIEW snrna_primary_transcript AS SELECT feature_id AS snrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_primary_transcript'; --- ************************************************ --- *** relation: snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar mRNA (SO:0000275). *** --- ************************************************ --- CREATE VIEW snorna_primary_transcript AS SELECT feature_id AS snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript'; --- ************************************************ --- *** relation: mature_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone the nec *** --- *** essary modifications, if any, for its fu *** --- *** nction. In eukaryotes this includes, for *** --- *** example, processing of introns, cleavag *** --- *** e, base modification, and modifications *** --- *** to the 5' and/or the 3' ends, other than *** --- *** addition of bases. In bacteria function *** --- *** al mRNAs are usually not modified. *** --- ************************************************ --- CREATE VIEW mature_transcript AS SELECT feature_id AS mature_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'mature_transcript'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not co *** --- *** ntain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a nucleotide molecule that b *** --- *** inds a Transcription Factor or Transcrip *** --- *** tion Factor complex [GO:0005667]. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The in-frame interval between the stop c *** --- *** odons of a reading frame which when read *** --- *** as sequential triplets, has the potenti *** --- *** al of encoding a sequential string of am *** --- *** ino acids. TER(NNN)nTER. *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'ORF'; --- ************************************************ --- *** relation: transcript_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW transcript_attribute AS SELECT feature_id AS transcript_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'transcript_attribute'; --- ************************************************ --- *** relation: foldback_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element with extensive se *** --- *** condary structure, characterized by larg *** --- *** e modular imperfect long inverted repeat *** --- *** s. *** --- ************************************************ --- CREATE VIEW foldback_element AS SELECT feature_id AS foldback_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foldback_element'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequences extending on either side o *** --- *** f a specific region. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: chromosome_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_variation AS SELECT feature_id AS chromosome_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_variation'; --- ************************************************ --- *** relation: internal_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR bordered by the terminal and initi *** --- *** al codons of two CDSs in a polycistronic *** --- *** transcript. Every UTR is either 5', 3' *** --- *** or internal. *** --- ************************************************ --- CREATE VIEW internal_utr AS SELECT feature_id AS internal_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_UTR'; --- ************************************************ --- *** relation: untranslated_region_polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The untranslated sequence separating the *** --- *** 'cistrons' of multicistronic mRNA. *** --- ************************************************ --- CREATE VIEW untranslated_region_polycistronic_mrna AS SELECT feature_id AS untranslated_region_polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'untranslated_region_polycistronic_mRNA'; --- ************************************************ --- *** relation: internal_ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence element that recruits a ribosom *** --- *** al subunit to internal mRNA for translat *** --- *** ion initiation. *** --- ************************************************ --- CREATE VIEW internal_ribosome_entry_site AS SELECT feature_id AS internal_ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'internal_ribosome_entry_site'; --- ************************************************ --- *** relation: polyadenylated *** --- *** relation type: VIEW *** --- *** *** --- *** A attribute describing the addition of a *** --- *** poly A tail to the 3' end of a mRNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW polyadenylated AS SELECT feature_id AS polyadenylated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated'; --- ************************************************ --- *** relation: sequence_length_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_length_variation AS SELECT feature_id AS sequence_length_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'sequence_length_variation'; --- ************************************************ --- *** relation: modified_rna_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post_transcriptionally modified base. *** --- ************************************************ --- CREATE VIEW modified_rna_base_feature AS SELECT feature_id AS modified_rna_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_RNA_base_feature'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. Transfer R *** --- *** NAs have two regions of fundamental func *** --- *** tional importance: the anti-codon, which *** --- *** is responsible for specific mRNA codon *** --- *** recognition, and the 3' end, to which th *** --- *** e tRNA's corresponding amino acid is att *** --- *** ached (by aminoacyl-tRNA synthetases). T *** --- *** ransfer RNAs cope with the degeneracy of *** --- *** the genetic code in two manners: having *** --- *** more than one tRNA (with a specific ant *** --- *** i-codon) for a particular amino acid; an *** --- *** d 'wobble' base-pairing, i.e. permitting *** --- *** non-standard base-pairing at the 3rd an *** --- *** ti-codon position. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: alanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an alanine anti *** --- *** codon, and a 3' alanine binding region. *** --- ************************************************ --- CREATE VIEW alanyl_trna AS SELECT feature_id AS alanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanyl_tRNA'; --- ************************************************ --- *** relation: rrna_small_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_small_subunit_primary_transcript AS SELECT feature_id AS rrna_small_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_small_subunit_primary_transcript'; --- ************************************************ --- *** relation: asparaginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an asparagine a *** --- *** nticodon, and a 3' asparagine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW asparaginyl_trna AS SELECT feature_id AS asparaginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparaginyl_tRNA'; --- ************************************************ --- *** relation: aspartyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an aspartic aci *** --- *** d anticodon, and a 3' aspartic acid bind *** --- *** ing region. *** --- ************************************************ --- CREATE VIEW aspartyl_trna AS SELECT feature_id AS aspartyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartyl_tRNA'; --- ************************************************ --- *** relation: cysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a cysteine anti *** --- *** codon, and a 3' cysteine binding region. *** --- ************************************************ --- CREATE VIEW cysteinyl_trna AS SELECT feature_id AS cysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteinyl_tRNA'; --- ************************************************ --- *** relation: glutaminyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamine ant *** --- *** icodon, and a 3' glutamine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW glutaminyl_trna AS SELECT feature_id AS glutaminyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutaminyl_tRNA'; --- ************************************************ --- *** relation: glutamyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glutamic acid *** --- *** anticodon, and a 3' glutamic acid bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW glutamyl_trna AS SELECT feature_id AS glutamyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamyl_tRNA'; --- ************************************************ --- *** relation: glycyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a glycine antic *** --- *** odon, and a 3' glycine binding region. *** --- ************************************************ --- CREATE VIEW glycyl_trna AS SELECT feature_id AS glycyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycyl_tRNA'; --- ************************************************ --- *** relation: histidyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a histidine ant *** --- *** icodon, and a 3' histidine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW histidyl_trna AS SELECT feature_id AS histidyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidyl_tRNA'; --- ************************************************ --- *** relation: isoleucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an isoleucine a *** --- *** nticodon, and a 3' isoleucine binding re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW isoleucyl_trna AS SELECT feature_id AS isoleucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucyl_tRNA'; --- ************************************************ --- *** relation: leucyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a leucine antic *** --- *** odon, and a 3' leucine binding region. *** --- ************************************************ --- CREATE VIEW leucyl_trna AS SELECT feature_id AS leucyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucyl_tRNA'; --- ************************************************ --- *** relation: lysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a lysine antico *** --- *** don, and a 3' lysine binding region. *** --- ************************************************ --- CREATE VIEW lysyl_trna AS SELECT feature_id AS lysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysyl_tRNA'; --- ************************************************ --- *** relation: methionyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a methionine an *** --- *** ticodon, and a 3' methionine binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW methionyl_trna AS SELECT feature_id AS methionyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionyl_tRNA'; --- ************************************************ --- *** relation: phenylalanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a phenylalanine *** --- *** anticodon, and a 3' phenylalanine bindi *** --- *** ng region. *** --- ************************************************ --- CREATE VIEW phenylalanyl_trna AS SELECT feature_id AS phenylalanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanyl_tRNA'; --- ************************************************ --- *** relation: prolyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a proline antic *** --- *** odon, and a 3' proline binding region. *** --- ************************************************ --- CREATE VIEW prolyl_trna AS SELECT feature_id AS prolyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prolyl_tRNA'; --- ************************************************ --- *** relation: seryl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a serine antico *** --- *** don, and a 3' serine binding region. *** --- ************************************************ --- CREATE VIEW seryl_trna AS SELECT feature_id AS seryl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seryl_tRNA'; --- ************************************************ --- *** relation: threonyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a threonine ant *** --- *** icodon, and a 3' threonine binding regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW threonyl_trna AS SELECT feature_id AS threonyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonyl_tRNA'; --- ************************************************ --- *** relation: tryptophanyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tryptophan an *** --- *** ticodon, and a 3' tryptophan binding reg *** --- *** ion. *** --- ************************************************ --- CREATE VIEW tryptophanyl_trna AS SELECT feature_id AS tryptophanyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophanyl_tRNA'; --- ************************************************ --- *** relation: tyrosyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a tyrosine anti *** --- *** codon, and a 3' tyrosine binding region. *** --- ************************************************ --- CREATE VIEW tyrosyl_trna AS SELECT feature_id AS tyrosyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosyl_tRNA'; --- ************************************************ --- *** relation: valyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a valine antico *** --- *** don, and a 3' valine binding region. *** --- ************************************************ --- CREATE VIEW valyl_trna AS SELECT feature_id AS valyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valyl_tRNA'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** A small nuclear RNA molecule involved in *** --- *** pre-mRNA splicing and processing. *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA (small nucleolar RNA) is any on *** --- *** e of a class of small RNAs that are asso *** --- *** ciated with the eukaryotic nucleus as co *** --- *** mponents of small nucleolar ribonucleopr *** --- *** oteins. They participate in the processi *** --- *** ng or modifications of many RNAs, mostly *** --- *** ribosomal RNAs (rRNAs) though snoRNAs a *** --- *** re also known to target other classes of *** --- *** RNA, including spliceosomal RNAs, tRNAs *** --- *** , and mRNAs via a stretch of sequence th *** --- *** at is complementary to a sequence in the *** --- *** targeted RNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. M *** --- *** icro RNAs are produced from precursor mo *** --- *** lecules (SO:0000647) that can form local *** --- *** hairpin structures, which ordinarily ar *** --- *** e processed (via the Dicer pathway) such *** --- *** that a single miRNA molecule accumulate *** --- *** s from one arm of a hairpin precursor mo *** --- *** lecule. Micro RNAs may trigger the cleav *** --- *** age of their target molecules or act as *** --- *** translational repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: bound_by_factor *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by another molecule. *** --- ************************************************ --- CREATE VIEW bound_by_factor AS SELECT feature_id AS bound_by_factor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'bound_by_factor'; --- ************************************************ --- *** relation: transcript_bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a nucleic *** --- *** acid. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_nucleic_acid AS SELECT feature_id AS transcript_bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_nucleic_acid'; --- ************************************************ --- *** relation: transcript_bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is bound by a protein. *** --- ************************************************ --- CREATE VIEW transcript_bound_by_protein AS SELECT feature_id AS transcript_bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_bound_by_protein'; --- ************************************************ --- *** relation: engineered_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_gene AS SELECT feature_id AS engineered_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_gene'; --- ************************************************ --- *** relation: engineered_foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_gene AS SELECT feature_id AS engineered_foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene'; --- ************************************************ --- *** relation: mrna_with_minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a minus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_1_frameshift AS SELECT feature_id AS mrna_with_minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_1_frameshift'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element_gene AS SELECT feature_id AS engineered_foreign_transposable_element_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element_gene'; --- ************************************************ --- *** relation: foreign_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_gene AS SELECT feature_id AS foreign_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'foreign_gene'; --- ************************************************ --- *** relation: long_terminal_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence directly repeated at both end *** --- *** s of a defined sequence, of the sort typ *** --- *** ically found in retroviruses. *** --- ************************************************ --- CREATE VIEW long_terminal_repeat AS SELECT feature_id AS long_terminal_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'long_terminal_repeat'; --- ************************************************ --- *** relation: fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is a fusion. *** --- ************************************************ --- CREATE VIEW fusion_gene AS SELECT feature_id AS fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'fusion_gene'; --- ************************************************ --- *** relation: engineered_fusion_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A fusion gene that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_fusion_gene AS SELECT feature_id AS engineered_fusion_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_fusion_gene'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat_region containing repeat_units *** --- *** (2 to 4 bp) that is repeated multiple ti *** --- *** mes in tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: dinucleotide_repeat_microsatellite_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dinucleotide_repeat_microsatellite_feature AS SELECT feature_id AS dinucleotide_repeat_microsatellite_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: trinuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trinuc_repeat_microsat AS SELECT feature_id AS trinuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trinucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: engineered_foreign_repetitive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive element that is engineered *** --- *** and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_repetitive_element AS SELECT feature_id AS engineered_foreign_repetitive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_repetitive_element'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. It is a palindr *** --- *** ome, and it may, or may not be hyphenate *** --- *** d. Examples: GCTGATCAGC, or GCTGA-----TC *** --- *** AGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: u12_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A type of spliceosomal intron spliced by *** --- *** the U12 spliceosome, that includes U11, *** --- *** U12, U4atac/U6atac and U5 snRNAs. *** --- ************************************************ --- CREATE VIEW u12_intron AS SELECT feature_id AS u12_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_intron'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: d_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Displacement loop; a region within mitoc *** --- *** hondrial DNA in which a short stretch of *** --- *** RNA is paired with one strand of DNA, d *** --- *** isplacing the original partner DNA stran *** --- *** d in this region; also used to describe *** --- *** the displacement of a region of one stra *** --- *** nd of duplex DNA by a single stranded in *** --- *** vader in the reaction catalyzed by RecA *** --- *** protein. *** --- ************************************************ --- CREATE VIEW d_loop AS SELECT feature_id AS d_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_loop'; --- ************************************************ --- *** relation: recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature AS SELECT feature_id AS recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'recombination_feature'; --- ************************************************ --- *** relation: specific_recombination_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW specific_recombination_site AS SELECT feature_id AS specific_recombination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'specific_recombination_site'; --- ************************************************ --- *** relation: recombination_feature_of_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombination_feature_of_rearranged_gene AS SELECT feature_id AS recombination_feature_of_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'recombination_feature_of_rearranged_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature'; --- ************************************************ --- *** relation: j_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including J-heptame *** --- *** r, J-spacer and J-nonamer in 5' of J-reg *** --- *** ion of a J-gene or J-sequence. *** --- ************************************************ --- CREATE VIEW j_gene_recombination_feature AS SELECT feature_id AS j_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G. *** --- ************************************************ --- CREATE VIEW modified_base AS SELECT feature_id AS modified_base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'modified_base'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: experimentally_determined *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that has *** --- *** been experimentally verified. *** --- ************************************************ --- CREATE VIEW experimentally_determined AS SELECT feature_id AS experimentally_determined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined'; --- ************************************************ --- *** relation: stem_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A double-helical region of nucleic acid *** --- *** formed by base-pairing between adjacent *** --- *** (inverted) complementary sequences. *** --- ************************************************ --- CREATE VIEW stem_loop AS SELECT feature_id AS stem_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop' OR cvterm.name = 'stem_loop'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: tss *** --- *** relation type: VIEW *** --- *** *** --- *** The first base where RNA polymerase begi *** --- *** ns to synthesize the RNA transcript. *** --- ************************************************ --- CREATE VIEW tss AS SELECT feature_id AS tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'TSS'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS'; --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Complementary DNA; A piece of DNA copied *** --- *** from an mRNA and spliced into a vector *** --- *** for propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** First codon to be translated by a riboso *** --- *** me. *** --- ************************************************ --- CREATE VIEW start_codon AS SELECT feature_id AS start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'start_codon'; --- ************************************************ --- *** relation: stop_codon *** --- *** relation type: VIEW *** --- *** *** --- *** In mRNA, a set of three nucleotides that *** --- *** indicates the end of information for pr *** --- *** otein synthesis. *** --- ************************************************ --- CREATE VIEW stop_codon AS SELECT feature_id AS stop_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon'; --- ************************************************ --- *** relation: intronic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Sequences within the intron that modulat *** --- *** e splice site selection for some introns *** --- *** . *** --- ************************************************ --- CREATE VIEW intronic_splice_enhancer AS SELECT feature_id AS intronic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer'; --- ************************************************ --- *** relation: mrna_with_plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 1 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_1_frameshift AS SELECT feature_id AS mrna_with_plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_1_frameshift'; --- ************************************************ --- *** relation: nuclease_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclease_hypersensitive_site AS SELECT feature_id AS nuclease_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_hypersensitive_site'; --- ************************************************ --- *** relation: coding_start *** --- *** relation type: VIEW *** --- *** *** --- *** The first base to be translated into pro *** --- *** tein. *** --- ************************************************ --- CREATE VIEW coding_start AS SELECT feature_id AS coding_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna_large_subunit_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a large ri *** --- *** bosomal subunit RNA. *** --- ************************************************ --- CREATE VIEW rrna_large_subunit_primary_transcript AS SELECT feature_id AS rrna_large_subunit_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_large_subunit_primary_transcript'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: coding_end *** --- *** relation type: VIEW *** --- *** *** --- *** The last base to be translated into prot *** --- *** ein. It does not include the stop codon. *** --- ************************************************ --- CREATE VIEW coding_end AS SELECT feature_id AS coding_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_end'; --- ************************************************ --- *** relation: microarray_oligo *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW microarray_oligo AS SELECT feature_id AS microarray_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microarray_oligo'; --- ************************************************ --- *** relation: mrna_with_plus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with a plus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_plus_2_frameshift AS SELECT feature_id AS mrna_with_plus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_plus_2_frameshift'; --- ************************************************ --- *** relation: conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of sequence similarity by descent *** --- *** from a common ancestor. *** --- ************************************************ --- CREATE VIEW conserved_region AS SELECT feature_id AS conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'conserved_region'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: coding_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Coding region of sequence similarity by *** --- *** descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW coding_conserved_region AS SELECT feature_id AS coding_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_conserved_region'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: nc_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding region of sequence similarity *** --- *** by descent from a common ancestor. *** --- ************************************************ --- CREATE VIEW nc_conserved_region AS SELECT feature_id AS nc_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_conserved_region'; --- ************************************************ --- *** relation: mrna_with_minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A mRNA with a minus 2 frameshift. *** --- ************************************************ --- CREATE VIEW mrna_with_minus_2_frameshift AS SELECT feature_id AS mrna_with_minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_with_minus_2_frameshift'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: mite *** --- *** relation type: VIEW *** --- *** *** --- *** A highly repetitive and short (100-500 b *** --- *** ase pair) transposable element with term *** --- *** inal inverted repeats (TIR) and target s *** --- *** ite duplication (TSD). MITEs do not enco *** --- *** de proteins. *** --- ************************************************ --- CREATE VIEW mite AS SELECT feature_id AS mite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MITE'; --- ************************************************ --- *** relation: recombination_hotspot *** --- *** relation type: VIEW *** --- *** *** --- *** A region in a genome which promotes reco *** --- *** mbination. *** --- ************************************************ --- CREATE VIEW recombination_hotspot AS SELECT feature_id AS recombination_hotspot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_hotspot'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a nucleic ac *** --- *** id molecule which controls its own repli *** --- *** cation through the interaction of specif *** --- *** ic proteins at one or more origins of re *** --- *** plication. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** A cytologically distinguishable feature *** --- *** of a chromosome, often made visible by s *** --- *** taining, and usually alternating light a *** --- *** nd dark. *** --- ************************************************ --- CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: site_specific_recombination_target_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW site_specific_recombination_target_region AS SELECT feature_id AS site_specific_recombination_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'site_specific_recombination_target_region'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'match'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a cDNA clone or PCR product; t *** --- *** ypically a few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'EST'; --- ************************************************ --- *** relation: loxp_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loxp_site AS SELECT feature_id AS loxp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to repeating *** --- *** units. The forms found in nature are deo *** --- *** xyribonucleic acid (DNA), where the repe *** --- *** ating units are 2-deoxy-D-ribose rings c *** --- *** onnected to a phosphate backbone, and ri *** --- *** bonucleic acid (RNA), where the repeatin *** --- *** g units are D-ribose rings connected to *** --- *** a phosphate backbone. *** --- ************************************************ --- CREATE VIEW nucleic_acid AS SELECT feature_id AS nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'nucleic_acid'; --- ************************************************ --- *** relation: protein_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW protein_match AS SELECT feature_id AS protein_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: frt_site *** --- *** relation type: VIEW *** --- *** *** --- *** An inversion site found on the Saccharom *** --- *** yces cerevisiae 2 micron plasmid. *** --- ************************************************ --- CREATE VIEW frt_site AS SELECT feature_id AS frt_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site'; --- ************************************************ --- *** relation: synthetic_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to decide a sequence of nuc *** --- *** leotides, nucleotide analogs, or amino a *** --- *** cids that has been designed by an experi *** --- *** menter and which may, or may not, corres *** --- *** pond with any natural sequence. *** --- ************************************************ --- CREATE VIEW synthetic_sequence AS SELECT feature_id AS synthetic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'synthetic_sequence'; --- ************************************************ --- *** relation: dna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a 2-deoxy-D-ribose ring c *** --- *** onnected to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW dna AS SELECT feature_id AS dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'DNA'; --- ************************************************ --- *** relation: sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW sequence_assembly AS SELECT feature_id AS sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'sequence_assembly'; --- ************************************************ --- *** relation: group_1_intron_homing_endonuclease_target_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of intronic nucleotide sequence *** --- *** targeted by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW group_1_intron_homing_endonuclease_target_region AS SELECT feature_id AS group_1_intron_homing_endonuclease_target_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_1_intron_homing_endonuclease_target_region'; --- ************************************************ --- *** relation: haplotype_block *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome which is co-inher *** --- *** ited as the result of the lack of histor *** --- *** ic recombination within it. *** --- ************************************************ --- CREATE VIEW haplotype_block AS SELECT feature_id AS haplotype_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype_block'; --- ************************************************ --- *** relation: rna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases bound to a repeatin *** --- *** g unit made of a D-ribose ring connected *** --- *** to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW rna AS SELECT feature_id AS rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA'; --- ************************************************ --- *** relation: flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region that is *** --- *** bounded either side by a particular kin *** --- *** d of region. *** --- ************************************************ --- CREATE VIEW flanked AS SELECT feature_id AS flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'flanked'; --- ************************************************ --- *** relation: floxed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence that is *** --- *** flanked by Lox-P sites. *** --- ************************************************ --- CREATE VIEW floxed AS SELECT feature_id AS floxed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er code for a unique amino acid or the t *** --- *** ermination of translation and are contai *** --- *** ned within the CDS. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'codon'; --- ************************************************ --- *** relation: frt_flanked *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe sequence that i *** --- *** s flanked by the FLP recombinase recogni *** --- *** tion site, FRT. *** --- ************************************************ --- CREATE VIEW frt_flanked AS SELECT feature_id AS frt_flanked_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_flanked'; --- ************************************************ --- *** relation: invalidated_by_chimeric_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone constructed from more than *** --- *** one mRNA. Usually an experimental artifa *** --- *** ct. *** --- ************************************************ --- CREATE VIEW invalidated_by_chimeric_cdna AS SELECT feature_id AS invalidated_by_chimeric_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA'; --- ************************************************ --- *** relation: floxed_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene that is floxed. *** --- ************************************************ --- CREATE VIEW floxed_gene AS SELECT feature_id AS floxed_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene'; --- ************************************************ --- *** relation: transposable_element_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence surrounding a tra *** --- *** nsposable element. *** --- ************************************************ --- CREATE VIEW transposable_element_flanking_region AS SELECT feature_id AS transposable_element_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_flanking_region'; --- ************************************************ --- *** relation: integron *** --- *** relation type: VIEW *** --- *** *** --- *** A region encoding an integrase which act *** --- *** s at a site adjacent to it (attI_site) t *** --- *** o insert DNA which must include but is n *** --- *** ot limited to an attC_site. *** --- ************************************************ --- CREATE VIEW integron AS SELECT feature_id AS integron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integron'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: atti_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an integron, adjacent to *** --- *** an integrase, at which site specific re *** --- *** combination involving an attC_site takes *** --- *** place. *** --- ************************************************ --- CREATE VIEW atti_site AS SELECT feature_id AS atti_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site'; --- ************************************************ --- *** relation: transposable_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW transposable_element_insertion_site AS SELECT feature_id AS transposable_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that encodes function requi *** --- *** red for conjugation. *** --- ************************************************ --- CREATE VIEW conjugative_transposon AS SELECT feature_id AS conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conjugative_transposon'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA sequence that has catalytic activ *** --- *** ity with or without an associated ribonu *** --- *** cleoprotein. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme' OR cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: recombinationally_inverted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene by i *** --- *** nversion. *** --- ************************************************ --- CREATE VIEW recombinationally_inverted_gene AS SELECT feature_id AS recombinationally_inverted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5_8S ribosomal RNA (5. 8S rRNA) is a com *** --- *** ponent of the large subunit of the eukar *** --- *** yotic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurs *** --- *** or that also contains 18S and 28S rRNA. *** --- *** Functionally, it is thought that 5.8S rR *** --- *** NA may be involved in ribosome transloca *** --- *** tion. It is also known to form covalent *** --- *** linkage to the p53 tumour suppressor pro *** --- *** tein. 5_8S rRNA is also found in archaea *** --- *** . *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S'; --- ************************************************ --- *** relation: rna_6s *** --- *** relation type: VIEW *** --- *** *** --- *** A small (184-nt in E. coli) RNA that for *** --- *** ms a hairpin type structure. 6S RNA asso *** --- *** ciates with RNA polymerase in a highly s *** --- *** pecific manner. 6S RNA represses express *** --- *** ion from a sigma70-dependent promoter du *** --- *** ring stationary phase. *** --- ************************************************ --- CREATE VIEW rna_6s AS SELECT feature_id AS rna_6s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_6S'; --- ************************************************ --- *** relation: csrb_rsmb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An enterobacterial RNA that binds the Cs *** --- *** rA protein. The CsrB RNAs contain a cons *** --- *** erved motif CAGGXXG that is found in up *** --- *** to 18 copies and has been suggested to b *** --- *** ind CsrA. The Csr regulatory system has *** --- *** a strong negative regulatory effect on g *** --- *** lycogen biosynthesis, glyconeogenesis an *** --- *** d glycogen catabolism and a positive reg *** --- *** ulatory effect on glycolysis. In other b *** --- *** acteria such as Erwinia caratovara the R *** --- *** smA protein has been shown to regulate t *** --- *** he production of virulence determinants, *** --- *** such extracellular enzymes. RsmA binds *** --- *** to RsmB regulatory RNA which is also a m *** --- *** ember of this family. *** --- ************************************************ --- CREATE VIEW csrb_rsmb_rna AS SELECT feature_id AS csrb_rsmb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CsrB_RsmB_RNA'; --- ************************************************ --- *** relation: dsra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** DsrA RNA regulates both transcription, b *** --- *** y overcoming transcriptional silencing b *** --- *** y the nucleoid-associated H-NS protein, *** --- *** and translation, by promoting efficient *** --- *** translation of the stress sigma factor, *** --- *** RpoS. These two activities of DsrA can b *** --- *** e separated by mutation: the first of th *** --- *** ree stem-loops of the 85 nucleotide RNA *** --- *** is necessary for RpoS translation but no *** --- *** t for anti-H-NS action, while the second *** --- *** stem-loop is essential for antisilencin *** --- *** g and less critical for RpoS translation *** --- *** . The third stem-loop, which behaves as *** --- *** a transcription terminator, can be subst *** --- *** ituted by the trp transcription terminat *** --- *** or without loss of either DsrA function. *** --- *** The sequence of the first stem-loop of *** --- *** DsrA is complementary with the upstream *** --- *** leader portion of RpoS messenger RNA, su *** --- *** ggesting that pairing of DsrA with the R *** --- *** poS message might be important for trans *** --- *** lational regulation. *** --- ************************************************ --- CREATE VIEW dsra_rna AS SELECT feature_id AS dsra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA' OR cvterm.name = 'DsrA_RNA'; --- ************************************************ --- *** relation: gcvb_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA involved in exp *** --- *** ression of the dipeptide and oligopeptid *** --- *** e transport systems in Escherichia coli. *** --- ************************************************ --- CREATE VIEW gcvb_rna AS SELECT feature_id AS gcvb_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GcvB_RNA'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: group_iia_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iia_intron AS SELECT feature_id AS group_iia_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron'; --- ************************************************ --- *** relation: group_iib_intron *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW group_iib_intron AS SELECT feature_id AS group_iib_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIB_intron'; --- ************************************************ --- *** relation: micf_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-translated 93 nt antisense RNA tha *** --- *** t binds its target ompF mRNA and regulat *** --- *** es ompF expression by inhibiting transla *** --- *** tion and inducing degradation of the mes *** --- *** sage. *** --- ************************************************ --- CREATE VIEW micf_rna AS SELECT feature_id AS micf_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA'; --- ************************************************ --- *** relation: oxys_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A small untranslated RNA which is induce *** --- *** d in response to oxidative stress in Esc *** --- *** herichia coli. Acts as a global regulato *** --- *** r to activate or repress the expression *** --- *** of as many as 40 genes, including the fh *** --- *** lA-encoded transcriptional activator and *** --- *** the rpoS-encoded sigma(s) subunit of RN *** --- *** A polymerase. OxyS is bound by the Hfq p *** --- *** rotein, that increases the OxyS RNA inte *** --- *** raction with its target messages. *** --- ************************************************ --- CREATE VIEW oxys_rna AS SELECT feature_id AS oxys_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'OxyS_RNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterized activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: rpra_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Translational regulation of the stationa *** --- *** ry phase sigma factor RpoS is mediated b *** --- *** y the formation of a double-stranded RNA *** --- *** stem-loop structure in the upstream reg *** --- *** ion of the rpoS messenger RNA, occluding *** --- *** the translation initiation site. Clones *** --- *** carrying rprA (RpoS regulator RNA) incr *** --- *** eased the translation of RpoS. The rprA *** --- *** gene encodes a 106 nucleotide regulatory *** --- *** RNA. As with DsrA Rfam:RF00014, RprA is *** --- *** predicted to form three stem-loops. Thu *** --- *** s, at least two small RNAs, DsrA and Rpr *** --- *** A, participate in the positive regulatio *** --- *** n of RpoS translation. Unlike DsrA, RprA *** --- *** does not have an extensive region of co *** --- *** mplementarity to the RpoS leader, leavin *** --- *** g its mechanism of action unclear. RprA *** --- *** is non-essential. *** --- ************************************************ --- CREATE VIEW rpra_rna AS SELECT feature_id AS rpra_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RprA_RNA'; --- ************************************************ --- *** relation: rre_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The Rev response element (RRE) is encode *** --- *** d within the HIV-env gene. Rev is an ess *** --- *** ential regulatory protein of HIV that bi *** --- *** nds an internal loop of the RRE leading, *** --- *** encouraging further Rev-RRE binding. Th *** --- *** is RNP complex is critical for mRNA expo *** --- *** rt and hence for expression of the HIV s *** --- *** tructural proteins. *** --- ************************************************ --- CREATE VIEW rre_rna AS SELECT feature_id AS rre_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RRE_RNA'; --- ************************************************ --- *** relation: spot_42_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A 109-nucleotide RNA of E. coli that see *** --- *** ms to have a regulatory role on the gala *** --- *** ctose operon. Changes in Spot 42 levels *** --- *** are implicated in affecting DNA polymera *** --- *** se I levels. *** --- ************************************************ --- CREATE VIEW spot_42_rna AS SELECT feature_id AS spot_42_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spot_42_RNA'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesizes telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA is an snRNA required for th *** --- *** e splicing of the minor U12-dependent cl *** --- *** ass of eukaryotic nuclear introns. It fo *** --- *** rms a base paired complex with U4atac_sn *** --- *** RNA (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: sequence_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describes a quality of sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW sequence_attribute AS SELECT feature_id AS sequence_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymer_attribute' OR cvterm.name = 'feature_attribute' OR cvterm.name = 'sequence_location' OR cvterm.name = 'variant_quality' OR cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'sequence_attribute'; --- ************************************************ --- *** relation: gene_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_attribute AS SELECT feature_id AS gene_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'gene_attribute'; --- ************************************************ --- *** relation: u14_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snorna AS SELECT feature_id AS u14_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonucleoprotein comp *** --- *** lex. The complex consists of a major vau *** --- *** lt protein (MVP), two minor vault protei *** --- *** ns (VPARP and TEP1), and several small u *** --- *** ntranslated RNA molecules. It has been s *** --- *** uggested that the vault complex is invol *** --- *** ved in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: twintron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron within an intron. Twintrons ar *** --- *** e group II or III introns, into which an *** --- *** other group II or III intron has been tr *** --- *** ansposed. *** --- ************************************************ --- CREATE VIEW twintron AS SELECT feature_id AS twintron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'twintron'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in eukaryotes, wh *** --- *** ich functions as the small subunit of th *** --- *** e ribosome. *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region of sequence that, in *** --- *** the molecule, interacts selectively and *** --- *** non-covalently with other molecules. A *** --- *** region on the surface of a molecule that *** --- *** may interact with another molecule. Whe *** --- *** n applied to polypeptides: Amino acids i *** --- *** nvolved in binding or interactions. It c *** --- *** an also apply to an amino acid bond whic *** --- *** h is represented by the positions of the *** --- *** two flanking amino acids. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith polypeptide molecules. *** --- ************************************************ --- CREATE VIEW protein_binding_site AS SELECT feature_id AS protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'protein_binding_site'; --- ************************************************ --- *** relation: rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that rescues. *** --- ************************************************ --- CREATE VIEW rescue_region AS SELECT feature_id AS rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'rescue_region'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polynucleotide sequence prod *** --- *** uced by digestion with a restriction end *** --- *** onuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment' OR cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequence differs from *** --- *** that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: invalidated_by_genomic_contamination *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to genomic contaminat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_contamination AS SELECT feature_id AS invalidated_by_genomic_contamination_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_contamination'; --- ************************************************ --- *** relation: invalidated_by_genomic_polya_primed_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to polyA priming. *** --- ************************************************ --- CREATE VIEW invalidated_by_genomic_polya_primed_cdna AS SELECT feature_id AS invalidated_by_genomic_polya_primed_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA'; --- ************************************************ --- *** relation: invalidated_by_partial_processing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is invalidated due to partial processing *** --- *** . *** --- ************************************************ --- CREATE VIEW invalidated_by_partial_processing AS SELECT feature_id AS invalidated_by_partial_processing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_partial_processing'; --- ************************************************ --- *** relation: polypeptide_domain *** --- *** relation type: VIEW *** --- *** *** --- *** A structurally or functionally defined p *** --- *** rotein region. In proteins with multiple *** --- *** domains, the combination of the domains *** --- *** determines the function of the protein. *** --- *** A region which has been shown to recur *** --- *** throughout evolution. *** --- ************************************************ --- CREATE VIEW polypeptide_domain AS SELECT feature_id AS polypeptide_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The signal_peptide is a short region of *** --- *** the peptide located at the N-terminus th *** --- *** at directs the protein to be secreted or *** --- *** part of membrane components. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: mature_protein_region *** --- *** relation type: VIEW *** --- *** *** --- *** The polypeptide sequence that remains wh *** --- *** en the cleaved peptide regions have been *** --- *** cleaved from the immature peptide. *** --- ************************************************ --- CREATE VIEW mature_protein_region AS SELECT feature_id AS mature_protein_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide' OR cvterm.name = 'mature_protein_region'; --- ************************************************ --- *** relation: five_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_terminal_inverted_repeat AS SELECT feature_id AS five_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: three_prime_terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_terminal_inverted_repeat AS SELECT feature_id AS three_prime_terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_terminal_inverted_repeat'; --- ************************************************ --- *** relation: u5_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_ltr_region AS SELECT feature_id AS u5_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U5_LTR_region'; --- ************************************************ --- *** relation: r_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_ltr_region AS SELECT feature_id AS r_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'R_LTR_region'; --- ************************************************ --- *** relation: u3_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_ltr_region AS SELECT feature_id AS u3_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'U3_LTR_region'; --- ************************************************ --- *** relation: five_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr AS SELECT feature_id AS five_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_LTR'; --- ************************************************ --- *** relation: three_prime_ltr *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr AS SELECT feature_id AS three_prime_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_LTR'; --- ************************************************ --- *** relation: r_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_five_prime_ltr_region AS SELECT feature_id AS r_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region'; --- ************************************************ --- *** relation: u5_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_five_prime_ltr_region AS SELECT feature_id AS u5_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_five_prime_LTR_region'; --- ************************************************ --- *** relation: u3_five_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_five_prime_ltr_region AS SELECT feature_id AS u3_five_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_five_prime_LTR_region'; --- ************************************************ --- *** relation: r_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW r_three_prime_ltr_region AS SELECT feature_id AS r_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region'; --- ************************************************ --- *** relation: u3_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u3_three_prime_ltr_region AS SELECT feature_id AS u3_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_three_prime_LTR_region'; --- ************************************************ --- *** relation: u5_three_prime_ltr_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW u5_three_prime_ltr_region AS SELECT feature_id AS u5_three_prime_ltr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_three_prime_LTR_region'; --- ************************************************ --- *** relation: non_ltr_retrotransposon_polymeric_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polymeric tract, such as poly(dA), wit *** --- *** hin a non_LTR_retrotransposon. *** --- ************************************************ --- CREATE VIEW non_ltr_retrotransposon_polymeric_tract AS SELECT feature_id AS non_ltr_retrotransposon_polymeric_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract'; --- ************************************************ --- *** relation: target_site_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of the target DNA that is dup *** --- *** licated when a transposable element or p *** --- *** hage inserts; usually found at each end *** --- *** the insertion. *** --- ************************************************ --- CREATE VIEW target_site_duplication AS SELECT feature_id AS target_site_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'target_site_duplication'; --- ************************************************ --- *** relation: rr_tract *** --- *** relation type: VIEW *** --- *** *** --- *** A polypurine tract within an LTR_retrotr *** --- *** ansposon. *** --- ************************************************ --- CREATE VIEW rr_tract AS SELECT feature_id AS rr_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RR_tract'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: inverted_ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inverted_ring_chromosome AS SELECT feature_id AS inverted_ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome'; --- ************************************************ --- *** relation: vector_replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A replicon that has been modified to act *** --- *** as a vector for foreign sequence. *** --- ************************************************ --- CREATE VIEW vector_replicon AS SELECT feature_id AS vector_replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'vector_replicon'; --- ************************************************ --- *** relation: ss_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A single stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ss_oligo AS SELECT feature_id AS ss_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'ss_oligo'; --- ************************************************ --- *** relation: ds_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded oligonucleotide. *** --- ************************************************ --- CREATE VIEW ds_oligo AS SELECT feature_id AS ds_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'ds_oligo'; --- ************************************************ --- *** relation: polymer_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the kind of bio *** --- *** logical sequence. *** --- ************************************************ --- CREATE VIEW polymer_attribute AS SELECT feature_id AS polymer_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleic_acid' OR cvterm.name = 'synthetic_sequence' OR cvterm.name = 'topology_attribute' OR cvterm.name = 'peptidyl' OR cvterm.name = 'DNA' OR cvterm.name = 'RNA' OR cvterm.name = 'morpholino_backbone' OR cvterm.name = 'PNA' OR cvterm.name = 'LNA' OR cvterm.name = 'TNA' OR cvterm.name = 'GNA' OR cvterm.name = 'cDNA' OR cvterm.name = 'genomic_DNA' OR cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'random_sequence' OR cvterm.name = 'designed_sequence' OR cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'polymer_attribute'; --- ************************************************ --- *** relation: three_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_noncoding_exon AS SELECT feature_id AS three_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_noncoding_exon'; --- ************************************************ --- *** relation: five_prime_noncoding_exon *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding exon in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_noncoding_exon AS SELECT feature_id AS five_prime_noncoding_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_noncoding_exon'; --- ************************************************ --- *** relation: utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Intron located in the untranslated regio *** --- *** n. *** --- ************************************************ --- CREATE VIEW utr_intron AS SELECT feature_id AS utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'UTR_intron'; --- ************************************************ --- *** relation: five_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_intron AS SELECT feature_id AS five_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR_intron'; --- ************************************************ --- *** relation: three_prime_utr_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron located in the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_intron AS SELECT feature_id AS three_prime_utr_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR_intron'; --- ************************************************ --- *** relation: random_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides or amino acids *** --- *** which, by design, has a "random" order *** --- *** of components, given a predetermined inp *** --- *** ut frequency of these components. *** --- ************************************************ --- CREATE VIEW random_sequence AS SELECT feature_id AS random_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'random_sequence'; --- ************************************************ --- *** relation: interband *** --- *** relation type: VIEW *** --- *** *** --- *** A light region between two darkly staini *** --- *** ng bands in a polytene chromosome. *** --- ************************************************ --- CREATE VIEW interband AS SELECT feature_id AS interband_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interband'; --- ************************************************ --- *** relation: gene_with_polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polyadenylated mRN *** --- *** A. *** --- ************************************************ --- CREATE VIEW gene_with_polyadenylated_mrna AS SELECT feature_id AS gene_with_polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA'; --- ************************************************ --- *** relation: chromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant whereby a *** --- *** region of a chromosome has been transfe *** --- *** rred to another position. Among interchr *** --- *** omosomal rearrangements, the term transp *** --- *** osition is reserved for that class in wh *** --- *** ich the telomeres of the chromosomes inv *** --- *** olved are coupled (that is to say, form *** --- *** the two ends of a single DNA molecule) a *** --- *** s in wild-type. *** --- ************************************************ --- CREATE VIEW chromosomal_transposition AS SELECT feature_id AS chromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'chromosomal_transposition'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A 17-28-nt, small interfering RNA derive *** --- *** d from transcripts of repetitive element *** --- *** s. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: gene_with_mrna_with_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA with a frame *** --- *** shift. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_with_frameshift AS SELECT feature_id AS gene_with_mrna_with_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_with_frameshift'; --- ************************************************ --- *** relation: recombinationally_rearranged_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is recombinationally rearran *** --- *** ged. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_gene AS SELECT feature_id AS recombinationally_rearranged_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'recombinationally_rearranged_gene'; --- ************************************************ --- *** relation: interchromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving an in *** --- *** sertion from another chromosome. *** --- ************************************************ --- CREATE VIEW interchromosomal_duplication AS SELECT feature_id AS interchromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication'; --- ************************************************ --- *** relation: d_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including D-region *** --- *** with 5' UTR and 3' UTR, also designated *** --- *** as D-segment. *** --- ************************************************ --- CREATE VIEW d_gene AS SELECT feature_id AS d_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene'; --- ************************************************ --- *** relation: gene_with_trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a transcript that is trans-s *** --- *** pliced. *** --- ************************************************ --- CREATE VIEW gene_with_trans_spliced_transcript AS SELECT feature_id AS gene_with_trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_trans_spliced_transcript'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment'; --- ************************************************ --- *** relation: inversion_derived_bipartite_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at each *** --- *** end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_deficiency AS SELECT feature_id AS inversion_derived_bipartite_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_deficiency'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: encodes_alternately_spliced_transcripts *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes more than one transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW encodes_alternately_spliced_transcripts AS SELECT feature_id AS encodes_alternately_spliced_transcripts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_alternately_spliced_transcripts'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendant of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome deletion whereby a chromoso *** --- *** me is generated by recombination between *** --- *** two inversions; there is a deficiency a *** --- *** t one end of the inversion and a duplica *** --- *** tion at the other end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_duplication AS SELECT feature_id AS inversion_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: v_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA including L-part1, *** --- *** V-intron and V-exon, with the 5' UTR and *** --- *** 3' UTR. *** --- ************************************************ --- CREATE VIEW v_gene AS SELECT feature_id AS v_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_stability *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is regulated *** --- *** by the stability of the resulting prote *** --- *** in. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_stability AS SELECT feature_id AS post_translationally_regulated_by_protein_stability_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_stability'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: post_translationally_regulated_by_protein_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a gene sequence *** --- *** where the resulting protein is modified *** --- *** to regulate it. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_by_protein_modification AS SELECT feature_id AS post_translationally_regulated_by_protein_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_by_protein_modification'; --- ************************************************ --- *** relation: j_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Germline genomic DNA of an immunoglobuli *** --- *** n/T-cell receptor gene including J-regio *** --- *** n with 5' UTR (SO:0000204) and 3' UTR (S *** --- *** O:0000205), also designated as J-segment *** --- *** . *** --- ************************************************ --- CREATE VIEW j_gene AS SELECT feature_id AS j_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene'; --- ************************************************ --- *** relation: autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation. *** --- ************************************************ --- CREATE VIEW autoregulated AS SELECT feature_id AS autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'autoregulated'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: negatively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation where it decr *** --- *** eases transcription. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated AS SELECT feature_id AS negatively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path (SO:0000472). *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone' OR cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: positively_autoregulated *** --- *** relation type: VIEW *** --- *** *** --- *** The gene product is involved in its own *** --- *** transcriptional regulation, where it inc *** --- *** reases transcription. *** --- ************************************************ --- CREATE VIEW positively_autoregulated AS SELECT feature_id AS positively_autoregulated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated'; --- ************************************************ --- *** relation: contig_read *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequencer read which is part of a *** --- *** contig. *** --- ************************************************ --- CREATE VIEW contig_read AS SELECT feature_id AS contig_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_read'; --- ************************************************ --- *** relation: c_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including C-region (and intro *** --- *** ns if present) with 5' UTR (SO:0000204) *** --- *** and 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW c_gene AS SELECT feature_id AS c_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_gene'; --- ************************************************ --- *** relation: trans_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_transcript AS SELECT feature_id AS trans_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'trans_spliced_transcript'; --- ************************************************ --- *** relation: tiling_path_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A clone which is part of a tiling path. *** --- *** A tiling path is a set of sequencing sub *** --- *** strates, typically clones, which have be *** --- *** en selected in order to efficiently cove *** --- *** r a region of the genome in preparation *** --- *** for sequencing and assembly. *** --- ************************************************ --- CREATE VIEW tiling_path_clone AS SELECT feature_id AS tiling_path_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_clone'; --- ************************************************ --- *** relation: terminal_inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An inverted repeat (SO:0000294) occurrin *** --- *** g at the termini of a DNA transposon. *** --- ************************************************ --- CREATE VIEW terminal_inverted_repeat AS SELECT feature_id AS terminal_inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'terminal_inverted_repeat'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_gene_cluster AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: three_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 3' exon that is not *** --- *** coding. *** --- ************************************************ --- CREATE VIEW three_prime_coding_exon_noncoding_region AS SELECT feature_id AS three_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene, and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW dj_j_cluster AS SELECT feature_id AS dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster'; --- ************************************************ --- *** relation: five_prime_coding_exon_noncoding_region *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of the 5' exon preceding th *** --- *** e start codon. *** --- ************************************************ --- CREATE VIEW five_prime_coding_exon_noncoding_region AS SELECT feature_id AS five_prime_coding_exon_noncoding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_noncoding_region'; --- ************************************************ --- *** relation: vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene, one J-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW vdj_j_c_cluster AS SELECT feature_id AS vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one J *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_j_cluster AS SELECT feature_id AS vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_J_cluster'; --- ************************************************ --- *** relation: vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_c_cluster AS SELECT feature_id AS vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_C_cluster'; --- ************************************************ --- *** relation: vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene, one J-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW vj_j_c_cluster AS SELECT feature_id AS vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_C_cluster'; --- ************************************************ --- *** relation: vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VJ-gene and one J- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW vj_j_cluster AS SELECT feature_id AS vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_J_cluster'; --- ************************************************ --- *** relation: d_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW d_gene_recombination_feature AS SELECT feature_id AS d_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'D_gene_recombination_feature'; --- ************************************************ --- *** relation: three_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site like CAC *** --- *** AGTG, part of a 3' D-recombination signa *** --- *** l sequence of an immunoglobulin/T-cell r *** --- *** eceptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_heptamer AS SELECT feature_id AS three_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer'; --- ************************************************ --- *** relation: three_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** A 9 nucleotide recombination site (e.g. *** --- *** ACAAAAACC), part of a 3' D-recombination *** --- *** signal sequence of an immunoglobulin/T- *** --- *** cell receptor gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_nonamer AS SELECT feature_id AS three_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer'; --- ************************************************ --- *** relation: three_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** A 12 or 23 nucleotide spacer between the *** --- *** 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-R *** --- *** S. *** --- ************************************************ --- CREATE VIEW three_prime_d_spacer AS SELECT feature_id AS three_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer'; --- ************************************************ --- *** relation: five_prime_d_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CTGTG), part of a 5' D-recombination sig *** --- *** nal sequence (SO:0000556) of an immunogl *** --- *** obulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_heptamer AS SELECT feature_id AS five_prime_d_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_heptamer'; --- ************************************************ --- *** relation: five_prime_d_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a five_prime_D-recombi *** --- *** nation signal sequence (SO:0000556) of a *** --- *** n immunoglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_nonamer AS SELECT feature_id AS five_prime_d_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_nonamer'; --- ************************************************ --- *** relation: five_prime_d_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the 5 *** --- *** ' D-heptamer (SO:0000496) and 5' D-nonam *** --- *** er (SO:0000497) of a 5' D-recombination *** --- *** signal sequence (SO:0000556) of an immun *** --- *** oglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_spacer AS SELECT feature_id AS five_prime_d_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_spacer'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous piece of sequence similar t *** --- *** o the 'virtual contig' concept of the En *** --- *** sembl database. *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. Th *** --- *** is is less energetically favourable than *** --- *** watson crick base pairing. Hoogsteen GC *** --- *** base pairs only have two hydrogen bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW hoogsteen_base_pair AS SELECT feature_id AS hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Hoogsteen_base_pair'; --- ************************************************ --- *** relation: reverse_hoogsteen_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base-pairing. *** --- ************************************************ --- CREATE VIEW reverse_hoogsteen_base_pair AS SELECT feature_id AS reverse_hoogsteen_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse_Hoogsteen_base_pair'; --- ************************************************ --- *** relation: d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_c_cluster AS SELECT feature_id AS d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_C_cluster'; --- ************************************************ --- *** relation: d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW d_dj_cluster AS SELECT feature_id AS d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_cluster'; --- ************************************************ --- *** relation: d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_c_cluster AS SELECT feature_id AS d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of an exon, *** --- *** part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one D-gene, one DJ-gen *** --- *** e, and one J-gene. *** --- ************************************************ --- CREATE VIEW d_dj_j_cluster AS SELECT feature_id AS d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_DJ_J_cluster'; --- ************************************************ --- *** relation: d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW d_j_c_cluster AS SELECT feature_id AS d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_C_cluster'; --- ************************************************ --- *** relation: vd_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including L-part1, V-intron and V *** --- *** -D-exon, with the 5' UTR (SO:0000204) an *** --- *** d 3' UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vd_gene AS SELECT feature_id AS vd_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene'; --- ************************************************ --- *** relation: j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one J-gene and one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW j_c_cluster AS SELECT feature_id AS j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_deficiency_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a chromos *** --- *** ome generated by recombination between t *** --- *** wo inversions; has a deficiency at one e *** --- *** nd and presumed to have a deficiency or *** --- *** duplication at the other end of the inve *** --- *** rsion. *** --- ************************************************ --- CREATE VIEW inversion_derived_deficiency_plus_aneuploid AS SELECT feature_id AS inversion_derived_deficiency_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_aneuploid'; --- ************************************************ --- *** relation: j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one J-gene. *** --- ************************************************ --- CREATE VIEW j_cluster AS SELECT feature_id AS j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_cluster'; --- ************************************************ --- *** relation: j_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. GG *** --- *** TTTTTGT), part of a J-gene recombination *** --- *** feature of an immunoglobulin/T-cell rec *** --- *** eptor gene. *** --- ************************************************ --- CREATE VIEW j_nonamer AS SELECT feature_id AS j_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_nonamer'; --- ************************************************ --- *** relation: j_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of a J-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW j_heptamer AS SELECT feature_id AS j_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_heptamer'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendant of a transcr *** --- *** ipt, part of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: j_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the J *** --- *** -nonamer and the J-heptamer of a J-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW j_spacer AS SELECT feature_id AS j_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_spacer'; --- ************************************************ --- *** relation: v_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one DJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_dj_cluster AS SELECT feature_id AS v_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_cluster'; --- ************************************************ --- *** relation: v_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_cluster AS SELECT feature_id AS v_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_cluster'; --- ************************************************ --- *** relation: v_vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_c_cluster AS SELECT feature_id AS v_vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_C_cluster'; --- ************************************************ --- *** relation: v_vdj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VDJ *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW v_vdj_cluster AS SELECT feature_id AS v_vdj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_cluster'; --- ************************************************ --- *** relation: v_vdj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_cluster AS SELECT feature_id AS v_vdj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_cluster'; --- ************************************************ --- *** relation: v_vj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_c_cluster AS SELECT feature_id AS v_vj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_C_cluster'; --- ************************************************ --- *** relation: v_vj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene and one VJ- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW v_vj_cluster AS SELECT feature_id AS v_vj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_cluster'; --- ************************************************ --- *** relation: v_vj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e and one J-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_cluster AS SELECT feature_id AS v_vj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_cluster'; --- ************************************************ --- *** relation: v_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one V-gene. *** --- ************************************************ --- CREATE VIEW v_cluster AS SELECT feature_id AS v_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_cluster'; --- ************************************************ --- *** relation: v_d_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_c_cluster AS SELECT feature_id AS v_d_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_cluster AS SELECT feature_id AS v_d_dj_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene, one J-gene and one C-gene *** --- *** . *** --- ************************************************ --- CREATE VIEW v_d_dj_j_c_cluster AS SELECT feature_id AS v_d_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_d_dj_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one D-gene *** --- *** , one DJ-gene and one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_dj_j_cluster AS SELECT feature_id AS v_d_dj_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_DJ_J_cluster'; --- ************************************************ --- *** relation: v_d_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_c_cluster AS SELECT feature_id AS v_d_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_C_cluster'; --- ************************************************ --- *** relation: v_d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one D-gene a *** --- *** nd one J-gene. *** --- ************************************************ --- CREATE VIEW v_d_j_cluster AS SELECT feature_id AS v_d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_D_J_cluster'; --- ************************************************ --- *** relation: v_heptamer *** --- *** relation type: VIEW *** --- *** *** --- *** 7 nucleotide recombination site (e.g. CA *** --- *** CAGTG), part of V-gene recombination fea *** --- *** ture of an immunoglobulin/T-cell recepto *** --- *** r gene. *** --- ************************************************ --- CREATE VIEW v_heptamer AS SELECT feature_id AS v_heptamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_heptamer'; --- ************************************************ --- *** relation: v_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW v_j_cluster AS SELECT feature_id AS v_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_cluster'; --- ************************************************ --- *** relation: v_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one V-gene, one J-gene a *** --- *** nd one C-gene. *** --- ************************************************ --- CREATE VIEW v_j_c_cluster AS SELECT feature_id AS v_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_J_C_cluster'; --- ************************************************ --- *** relation: v_nonamer *** --- *** relation type: VIEW *** --- *** *** --- *** 9 nucleotide recombination site (e.g. AC *** --- *** AAAAACC), part of V-gene recombination f *** --- *** eature of an immunoglobulin/T-cell recep *** --- *** tor gene. *** --- ************************************************ --- CREATE VIEW v_nonamer AS SELECT feature_id AS v_nonamer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_nonamer'; --- ************************************************ --- *** relation: v_spacer *** --- *** relation type: VIEW *** --- *** *** --- *** 12 or 23 nucleotide spacer between the V *** --- *** -heptamer and the V-nonamer of a V-gene *** --- *** recombination feature of an immunoglobul *** --- *** in/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_spacer AS SELECT feature_id AS v_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_spacer'; --- ************************************************ --- *** relation: v_gene_recombination_feature *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal including V-heptame *** --- *** r, V-spacer and V-nonamer in 3' of V-reg *** --- *** ion of a V-gene or V-sequence of an immu *** --- *** noglobulin/T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW v_gene_recombination_feature AS SELECT feature_id AS v_gene_recombination_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_gene_recombination_feature'; --- ************************************************ --- *** relation: dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one DJ-gene and one C- *** --- *** gene. *** --- ************************************************ --- CREATE VIEW dj_c_cluster AS SELECT feature_id AS dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_C_cluster'; --- ************************************************ --- *** relation: dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA in rearranged configuration *** --- *** including at least one D-J-GENE, one J-G *** --- *** ENE and one C-GENE. *** --- ************************************************ --- CREATE VIEW dj_j_c_cluster AS SELECT feature_id AS dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_C_cluster'; --- ************************************************ --- *** relation: vdj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one VDJ-gene and one C *** --- *** -gene. *** --- ************************************************ --- CREATE VIEW vdj_c_cluster AS SELECT feature_id AS vdj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_C_cluster'; --- ************************************************ --- *** relation: v_dj_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_c_cluster AS SELECT feature_id AS v_dj_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_C_cluster'; --- ************************************************ --- *** relation: helitron *** --- *** relation type: VIEW *** --- *** *** --- *** A rolling circle transposon. Autonomous *** --- *** helitrons encode a 5'-to-3' DNA helicase *** --- *** and nuclease/ligase similar to those en *** --- *** coded by known rolling-circle replicons. *** --- ************************************************ --- CREATE VIEW helitron AS SELECT feature_id AS helitron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helitron'; --- ************************************************ --- *** relation: recoding_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** The pseudoknots involved in recoding are *** --- *** unique in that, as they play their role *** --- *** as a structure, they are immediately un *** --- *** folded and their now linear sequence ser *** --- *** ves as a template for decoding. *** --- ************************************************ --- CREATE VIEW recoding_pseudoknot AS SELECT feature_id AS recoding_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot'; --- ************************************************ --- *** relation: designed_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW designed_sequence AS SELECT feature_id AS designed_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'designed_sequence'; --- ************************************************ --- *** relation: inversion_derived_bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; there is a dupli *** --- *** cation at each end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_bipartite_duplication AS SELECT feature_id AS inversion_derived_bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_bipartite_duplication'; --- ************************************************ --- *** relation: gene_with_edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript that is *** --- *** edited. *** --- ************************************************ --- CREATE VIEW gene_with_edited_transcript AS SELECT feature_id AS gene_with_edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_edited_transcript'; --- ************************************************ --- *** relation: inversion_derived_duplication_plus_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome generated by recombination *** --- *** between two inversions; has a duplicatio *** --- *** n at one end and presumed to have a defi *** --- *** ciency or duplication at the other end o *** --- *** f the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_duplication_plus_aneuploid AS SELECT feature_id AS inversion_derived_duplication_plus_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_duplication_plus_aneuploid'; --- ************************************************ --- *** relation: aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structural variation whereb *** --- *** y either a chromosome exists in addition *** --- *** to the normal chromosome complement or *** --- *** is lacking. *** --- ************************************************ --- CREATE VIEW aneuploid_chromosome AS SELECT feature_id AS aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'aneuploid_chromosome'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region in the 5' UTR that pairs with t *** --- *** he 16S rRNA during formation of the prei *** --- *** nitiation complex. *** --- ************************************************ --- CREATE VIEW shine_dalgarno_sequence AS SELECT feature_id AS shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. The bound *** --- *** ary between the UTR and the polyA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: five_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 5' most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW five_prime_clip AS SELECT feature_id AS five_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_clip'; --- ************************************************ --- *** relation: five_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 5' *** --- *** D-nonamer (SO:0000497), 5' D-spacer (SO *** --- *** :0000498), and 5' D-heptamer (SO:0000396 *** --- *** ) in 5' of the D-region of a D-gene, or *** --- *** in 5' of the D-region of DJ-gene. *** --- ************************************************ --- CREATE VIEW five_prime_d_recombination_signal_sequence AS SELECT feature_id AS five_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: three_prime_clip *** --- *** relation type: VIEW *** --- *** *** --- *** 3'-most region of a precursor transcript *** --- *** that is clipped off during processing. *** --- ************************************************ --- CREATE VIEW three_prime_clip AS SELECT feature_id AS three_prime_clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_clip'; --- ************************************************ --- *** relation: c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene including more than one C-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW c_cluster AS SELECT feature_id AS c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_cluster'; --- ************************************************ --- *** relation: d_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding more than one D-gene. *** --- ************************************************ --- CREATE VIEW d_cluster AS SELECT feature_id AS d_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_cluster'; --- ************************************************ --- *** relation: d_j_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in germline configuration inc *** --- *** luding at least one D-gene and one J-gen *** --- *** e. *** --- ************************************************ --- CREATE VIEW d_j_cluster AS SELECT feature_id AS d_j_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'D_J_cluster'; --- ************************************************ --- *** relation: heptamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Seven nucleotide recombination site (e.g *** --- *** . CACAGTG), part of V-gene, D-gene or J- *** --- *** gene recombination feature of an immunog *** --- *** lobulin or T-cell receptor gene. *** --- ************************************************ --- CREATE VIEW heptamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS heptamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: nonamer_of_recombination_feature_of_vertebrate_im_sys_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nonamer_of_recombination_feature_of_vertebrate_im_sys_gene AS SELECT feature_id AS nonamer_of_recombination_feature_of_vertebrate_im_sys_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_spacer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_spacer AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_spacer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer'; --- ************************************************ --- *** relation: v_dj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one DJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_dj_j_c_cluster AS SELECT feature_id AS v_dj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_DJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vdj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VDJ-ge *** --- *** ne, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vdj_j_c_cluster AS SELECT feature_id AS v_vdj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VDJ_J_C_cluster'; --- ************************************************ --- *** relation: v_vj_j_c_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in rearranged configuration i *** --- *** ncluding at least one V-gene, one VJ-gen *** --- *** e, one J-gene and one C-gene. *** --- ************************************************ --- CREATE VIEW v_vj_j_c_cluster AS SELECT feature_id AS v_vj_j_c_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'V_VJ_J_C_cluster'; --- ************************************************ --- *** relation: inversion_derived_aneuploid_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome may be generated by recombi *** --- *** nation between two inversions; presumed *** --- *** to have a deficiency or duplication at e *** --- *** ach end of the inversion. *** --- ************************************************ --- CREATE VIEW inversion_derived_aneuploid_chromosome AS SELECT feature_id AS inversion_derived_aneuploid_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_aneuploid_chromosome'; --- ************************************************ --- *** relation: bidirectional_promoter *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bidirectional_promoter AS SELECT feature_id AS bidirectional_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bidirectional_promoter'; --- ************************************************ --- *** relation: retrotransposed *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of a feature that occurred *** --- *** as the product of a reverse transcriptas *** --- *** e mediated event. *** --- ************************************************ --- CREATE VIEW retrotransposed AS SELECT feature_id AS retrotransposed_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrotransposed'; --- ************************************************ --- *** relation: three_prime_d_recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Recombination signal of an immunoglobuli *** --- *** n/T-cell receptor gene, including the 3' *** --- *** D-heptamer (SO:0000493), 3' D-spacer, a *** --- *** nd 3' D-nonamer (SO:0000494) in 3' of th *** --- *** e D-region of a D-gene. *** --- ************************************************ --- CREATE VIEW three_prime_d_recombination_signal_sequence AS SELECT feature_id AS three_prime_d_recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_D_recombination_signal_sequence'; --- ************************************************ --- *** relation: mirna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_encoding AS SELECT feature_id AS mirna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_encoding'; --- ************************************************ --- *** relation: dj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic DNA of immunoglobulin/T-cell rec *** --- *** eptor gene in partially rearranged genom *** --- *** ic DNA including D-J-region with 5' UTR *** --- *** and 3' UTR, also designated as D-J-segme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW dj_gene AS SELECT feature_id AS dj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_gene'; --- ************************************************ --- *** relation: rrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rrna_encoding AS SELECT feature_id AS rrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_encoding'; --- ************************************************ --- *** relation: vdj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-D-J-exon, with the 5'UTR *** --- *** (SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vdj_gene AS SELECT feature_id AS vdj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VDJ_gene'; --- ************************************************ --- *** relation: scrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_encoding AS SELECT feature_id AS scrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_encoding'; --- ************************************************ --- *** relation: vj_gene *** --- *** relation type: VIEW *** --- *** *** --- *** Rearranged genomic DNA of immunoglobulin *** --- *** /T-cell receptor gene including L-part1, *** --- *** V-intron and V-J-exon, with the 5'UTR ( *** --- *** SO:0000204) and 3'UTR (SO:0000205). *** --- ************************************************ --- CREATE VIEW vj_gene AS SELECT feature_id AS vj_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VJ_gene'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'centromere'; --- ************************************************ --- *** relation: snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_encoding AS SELECT feature_id AS snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'snoRNA_encoding'; --- ************************************************ --- *** relation: edited_transcript_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable feature on a transcript that *** --- *** is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript_feature AS SELECT feature_id AS edited_transcript_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'edited_transcript_feature'; --- ************************************************ --- *** relation: methylation_guide_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a methylat *** --- *** ion guide small nucleolar RNA. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna_primary_transcript AS SELECT feature_id AS methylation_guide_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: rrna_cleavage_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding an rRNA cl *** --- *** eavage snoRNA. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_snorna_primary_transcript AS SELECT feature_id AS rrna_cleavage_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: pre_edited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a transcript that will be *** --- *** edited. *** --- ************************************************ --- CREATE VIEW pre_edited_region AS SELECT feature_id AS pre_edited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_region'; --- ************************************************ --- *** relation: tmrna *** --- *** relation type: VIEW *** --- *** *** --- *** A tmRNA liberates a mRNA from a stalled *** --- *** ribosome. To accomplish this part of the *** --- *** tmRNA is used as a reading frame that e *** --- *** nds in a translation stop signal. The br *** --- *** oken mRNA is replaced in the ribosome by *** --- *** the tmRNA and translation of the tmRNA *** --- *** leads to addition of a proteolysis tag t *** --- *** o the incomplete protein enabling recogn *** --- *** ition by a protease. Recently a number o *** --- *** f permuted tmRNAs genes have been found *** --- *** encoded in two parts. TmRNAs have been i *** --- *** dentified in eubacteria and some chlorop *** --- *** lasts but are absent from archeal and Eu *** --- *** karyote nuclear genomes. *** --- ************************************************ --- CREATE VIEW tmrna AS SELECT feature_id AS tmrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_encoding AS SELECT feature_id AS c_d_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_encoding'; --- ************************************************ --- *** relation: tmrna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tmRNA (S *** --- *** O:0000584). *** --- ************************************************ --- CREATE VIEW tmrna_primary_transcript AS SELECT feature_id AS tmrna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_primary_transcript'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyze their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: autocatalytically_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW autocatalytically_spliced_intron AS SELECT feature_id AS autocatalytically_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: srp_rna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a signal r *** --- *** ecognition particle RNA. *** --- ************************************************ --- CREATE VIEW srp_rna_primary_transcript AS SELECT feature_id AS srp_rna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_primary_transcript'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A tertiary structure in RNA where nucleo *** --- *** tides in a loop form base pairs with a r *** --- *** egion of RNA downstream of the loop. *** --- ************************************************ --- CREATE VIEW pseudoknot AS SELECT feature_id AS pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'pseudoknot'; --- ************************************************ --- *** relation: h_pseudoknot *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudoknot which contains two stems an *** --- *** d at least two loops. *** --- ************************************************ --- CREATE VIEW h_pseudoknot AS SELECT feature_id AS h_pseudoknot_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_pseudoknot'; --- ************************************************ --- *** relation: c_d_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Most box C/D snoRNAs also contain long ( *** --- *** >10 nt) sequences complementary to rRNA. *** --- *** Boxes C and D, as well as boxes C' and *** --- *** D', are usually located in close proximi *** --- *** ty, and form a structure known as the bo *** --- *** x C/D motif. This motif is important for *** --- *** snoRNA stability, processing, nucleolar *** --- *** targeting and function. A small number *** --- *** of box C/D snoRNAs are involved in rRNA *** --- *** processing; most, however, are known or *** --- *** predicted to serve as guide RNAs in ribo *** --- *** se methylation of rRNA. Targeting involv *** --- *** es direct base pairing of the snoRNA at *** --- *** the rRNA site to be modified and selecti *** --- *** on of a rRNA nucleotide a fixed distance *** --- *** from box D or D'. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna AS SELECT feature_id AS c_d_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'C_D_box_snoRNA'; --- ************************************************ --- *** relation: h_aca_box_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Members of the box H/ACA family contain *** --- *** an ACA triplet, exactly 3 nt upstream fr *** --- *** om the 3' end and an H-box in a hinge re *** --- *** gion that links two structurally similar *** --- *** functional domains of the molecule. Bot *** --- *** h boxes are important for snoRNA biosynt *** --- *** hesis and function. A few box H/ACA snoR *** --- *** NAs are involved in rRNA processing; mos *** --- *** t others are known or predicted to parti *** --- *** cipate in selection of uridine nucleosid *** --- *** es in rRNA to be converted to pseudourid *** --- *** ines. Site selection is mediated by dire *** --- *** ct base pairing of the snoRNA with rRNA *** --- *** through one or both targeting domains. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna AS SELECT feature_id AS h_aca_box_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA'; --- ************************************************ --- *** relation: c_d_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box C/D family. *** --- ************************************************ --- CREATE VIEW c_d_box_snorna_primary_transcript AS SELECT feature_id AS c_d_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_D_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: h_aca_box_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small nu *** --- *** cleolar RNA of the box H/ACA family. *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_primary_transcript AS SELECT feature_id AS h_aca_box_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a duplex (except for its post-transcript *** --- *** ionally added oligo_U tail (SO:0000609)) *** --- *** with a stretch of mature edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: editing_block *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by a singl *** --- *** e guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW editing_block AS SELECT feature_id AS editing_block_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_block'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing or overlapping no ge *** --- *** nes that is bounded on either side by a *** --- *** gene, or bounded by a gene and the end o *** --- *** f the chromosome. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: editing_domain *** --- *** relation type: VIEW *** --- *** *** --- *** Edited mRNA sequence mediated by two or *** --- *** more overlapping guide RNAs (SO:0000602) *** --- *** . *** --- ************************************************ --- CREATE VIEW editing_domain AS SELECT feature_id AS editing_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_domain'; --- ************************************************ --- *** relation: unedited_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an edited transcript that *** --- *** will not be edited. *** --- ************************************************ --- CREATE VIEW unedited_region AS SELECT feature_id AS unedited_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unedited_region'; --- ************************************************ --- *** relation: h_aca_box_snorna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW h_aca_box_snorna_encoding AS SELECT feature_id AS h_aca_box_snorna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H_ACA_box_snoRNA_encoding'; --- ************************************************ --- *** relation: oligo_u_tail *** --- *** relation type: VIEW *** --- *** *** --- *** The string of non-encoded U's at the 3' *** --- *** end of a guide RNA (SO:0000602). *** --- ************************************************ --- CREATE VIEW oligo_u_tail AS SELECT feature_id AS oligo_u_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo_U_tail'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which bacterial RNA po *** --- *** lymerase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter AS SELECT feature_id AS bacterial_rnapol_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'bacterial_RNApol_promoter'; --- ************************************************ --- *** relation: bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for bacterial transc *** --- *** ription. *** --- ************************************************ --- CREATE VIEW bacterial_terminator AS SELECT feature_id AS bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'bacterial_terminator'; --- ************************************************ --- *** relation: terminator_of_type_2_rnapol_iii_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A terminator signal for RNA polymerase I *** --- *** II transcription. *** --- ************************************************ --- CREATE VIEW terminator_of_type_2_rnapol_iii_promoter AS SELECT feature_id AS terminator_of_type_2_rnapol_iii_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter'; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The base where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_1 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_1 AS SELECT feature_id AS rnapol_iii_promoter_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_1'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_2 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_2 AS SELECT feature_id AS rnapol_iii_promoter_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_2'; --- ************************************************ --- *** relation: a_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence TGGCnnAGTGG. *** --- ************************************************ --- CREATE VIEW a_box AS SELECT feature_id AS a_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'A_box'; --- ************************************************ --- *** relation: b_box *** --- *** relation type: VIEW *** --- *** *** --- *** A variably distant linear promoter regio *** --- *** n recognized by TFIIIC, with consensus s *** --- *** equence AGGTTCCAnnCC. *** --- ************************************************ --- CREATE VIEW b_box AS SELECT feature_id AS b_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'B_box'; --- ************************************************ --- *** relation: rnapol_iii_promoter_type_3 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rnapol_iii_promoter_type_3 AS SELECT feature_id AS rnapol_iii_promoter_type_3_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_III_promoter_type_3'; --- ************************************************ --- *** relation: c_box *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA polymerase III type 1 promoter wi *** --- *** th consensus sequence CAnnCCn. *** --- ************************************************ --- CREATE VIEW c_box AS SELECT feature_id AS c_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_box'; --- ************************************************ --- *** relation: snrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_encoding AS SELECT feature_id AS snrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_encoding'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenance of the end. *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region which upon binding o *** --- *** f transcription factors, suppress the tr *** --- *** anscription of the gene or genes they co *** --- *** ntrol. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: chromosomal_regulatory_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_regulatory_element AS SELECT feature_id AS chromosomal_regulatory_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'chromosomal_regulatory_element'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional cis regulatory region *** --- *** that when located between a CM and a gen *** --- *** e's promoter prevents the CRM from modul *** --- *** ating that genes expression. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: five_prime_open_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_open_reading_frame AS SELECT feature_id AS five_prime_open_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_open_reading_frame'; --- ************************************************ --- *** relation: upstream_aug_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon upstream of the ORF. *** --- ************************************************ --- CREATE VIEW upstream_aug_codon AS SELECT feature_id AS upstream_aug_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon'; --- ************************************************ --- *** relation: polycistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for more t *** --- *** han one gene product. *** --- ************************************************ --- CREATE VIEW polycistronic_primary_transcript AS SELECT feature_id AS polycistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding for one ge *** --- *** ne product. *** --- ************************************************ --- CREATE VIEW monocistronic_primary_transcript AS SELECT feature_id AS monocistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript'; --- ************************************************ --- *** relation: monocistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA with either a single protein pro *** --- *** duct, or for which the regions encoding *** --- *** all its protein products overlap. *** --- ************************************************ --- CREATE VIEW monocistronic_mrna AS SELECT feature_id AS monocistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_mRNA'; --- ************************************************ --- *** relation: polycistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that encodes multiple proteins f *** --- *** rom at least two non-overlapping regions *** --- *** . *** --- ************************************************ --- CREATE VIEW polycistronic_mrna AS SELECT feature_id AS polycistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA'; --- ************************************************ --- *** relation: mini_exon_donor_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that donates the sp *** --- *** liced leader to other mRNA. *** --- ************************************************ --- CREATE VIEW mini_exon_donor_rna AS SELECT feature_id AS mini_exon_donor_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mini_exon_donor_RNA'; --- ************************************************ --- *** relation: spliced_leader_rna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW spliced_leader_rna AS SELECT feature_id AS spliced_leader_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliced_leader_RNA'; --- ************************************************ --- *** relation: engineered_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_plasmid AS SELECT feature_id AS engineered_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_plasmid'; --- ************************************************ --- *** relation: transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Part of an rRNA transcription unit that *** --- *** is transcribed but discarded during matu *** --- *** ration, not giving rise to any part of r *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW transcribed_spacer_region AS SELECT feature_id AS transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'transcribed_spacer_region'; --- ************************************************ --- *** relation: internal_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA sequence that *** --- *** separate genes coding for the 28S, 5.8S, *** --- *** and 18S ribosomal RNAs. *** --- ************************************************ --- CREATE VIEW internal_transcribed_spacer_region AS SELECT feature_id AS internal_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_transcribed_spacer_region'; --- ************************************************ --- *** relation: external_transcribed_spacer_region *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding regions of DNA that precede t *** --- *** he sequence that codes for the ribosomal *** --- *** RNA. *** --- ************************************************ --- CREATE VIEW external_transcribed_spacer_region AS SELECT feature_id AS external_transcribed_spacer_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'external_transcribed_spacer_region'; --- ************************************************ --- *** relation: tetranuc_repeat_microsat *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tetranuc_repeat_microsat AS SELECT feature_id AS tetranuc_repeat_microsat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetranucleotide_repeat_microsatellite_feature'; --- ************************************************ --- *** relation: srp_rna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_encoding AS SELECT feature_id AS srp_rna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_encoding'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region containing tandemly repe *** --- *** ated sequences having a unit length of 1 *** --- *** 0 to 40 bp. *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MicF_RNA' OR cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small RNA molecule that is the product *** --- *** of a longer exogenous or endogenous dsR *** --- *** NA, which is either a bimolecular duplex *** --- *** or very long hairpin, processed (via th *** --- *** e Dicer pathway) such that numerous siRN *** --- *** As accumulate from both strands of the d *** --- *** sRNA. SRNAs trigger the cleavage of thei *** --- *** r target molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: mirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a micro RN *** --- *** A. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript AS SELECT feature_id AS mirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript'; --- ************************************************ --- *** relation: strna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a small te *** --- *** mporal mRNA (SO:0000649). *** --- ************************************************ --- CREATE VIEW strna_primary_transcript AS SELECT feature_id AS strna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_primary_transcript'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: small_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the small subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW small_subunit_rrna AS SELECT feature_id AS small_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'small_subunit_rRNA'; --- ************************************************ --- *** relation: large_subunit_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** Ribosomal RNA transcript that structures *** --- *** the large subunit of the ribosome. *** --- ************************************************ --- CREATE VIEW large_subunit_rrna AS SELECT feature_id AS large_subunit_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'large_subunit_rRNA'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilizes 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: maxicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mitochondrial gene located in a maxici *** --- *** rcle. *** --- ************************************************ --- CREATE VIEW maxicircle_gene AS SELECT feature_id AS maxicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'maxicircle_gene'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA transcript that does not encode f *** --- *** or a protein rather the RNA molecule is *** --- *** the gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: strna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_encoding AS SELECT feature_id AS strna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_encoding'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: tmrna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_encoding AS SELECT feature_id AS tmrna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_encoding'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: trna_encoding *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_encoding AS SELECT feature_id AS trna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_encoding'; --- ************************************************ --- *** relation: introgressed_chromosome_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW introgressed_chromosome_region AS SELECT feature_id AS introgressed_chromosome_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'introgressed_chromosome_region'; --- ************************************************ --- *** relation: monocistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is monocistronic. *** --- ************************************************ --- CREATE VIEW monocistronic_transcript AS SELECT feature_id AS monocistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'monocistronic_transcript'; --- ************************************************ --- *** relation: mobile_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron (mitochondrial, chloroplast, n *** --- *** uclear or prokaryotic) that encodes a do *** --- *** uble strand sequence specific endonuclea *** --- *** se allowing for mobility. *** --- ************************************************ --- CREATE VIEW mobile_intron AS SELECT feature_id AS mobile_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of one or more nucleotides *** --- *** added between two adjacent nucleotides i *** --- *** n the sequence. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'insertion'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: sequence_rearrangement_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_rearrangement_feature AS SELECT feature_id AS sequence_rearrangement_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'sequence_rearrangement_feature'; --- ************************************************ --- *** relation: chromosome_breakage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence within the micronuclear DNA o *** --- *** f ciliates at which chromosome breakage *** --- *** and telomere addition occurs during nucl *** --- *** ear differentiation. *** --- ************************************************ --- CREATE VIEW chromosome_breakage_sequence AS SELECT feature_id AS chromosome_breakage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_breakage_sequence'; --- ************************************************ --- *** relation: internal_eliminated_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence eliminated from the genome of *** --- *** ciliates during nuclear differentiation *** --- *** . *** --- ************************************************ --- CREATE VIEW internal_eliminated_sequence AS SELECT feature_id AS internal_eliminated_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_eliminated_sequence'; --- ************************************************ --- *** relation: macronucleus_destined_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that is conserved, although r *** --- *** earranged relative to the micronucleus, *** --- *** in the macronucleus of a ciliate genome. *** --- ************************************************ --- CREATE VIEW macronucleus_destined_segment AS SELECT feature_id AS macronucleus_destined_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronucleus_destined_segment'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcript'; --- ************************************************ --- *** relation: canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 3' splice site has the seq *** --- *** uence "AG". *** --- ************************************************ --- CREATE VIEW canonical_three_prime_splice_site AS SELECT feature_id AS canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The canonical 5' splice site has the seq *** --- *** uence "GT". *** --- ************************************************ --- CREATE VIEW canonical_five_prime_splice_site AS SELECT feature_id AS canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_three_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 3' splice site that does not have the *** --- *** sequence "AG". *** --- ************************************************ --- CREATE VIEW non_canonical_three_prime_splice_site AS SELECT feature_id AS non_canonical_three_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_three_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_five_prime_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A 5' splice site which does not have the *** --- *** sequence "GT". *** --- ************************************************ --- CREATE VIEW non_canonical_five_prime_splice_site AS SELECT feature_id AS non_canonical_five_prime_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_canonical_five_prime_splice_site'; --- ************************************************ --- *** relation: non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A start codon that is not the usual AUG *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW non_canonical_start_codon AS SELECT feature_id AS non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'non_canonical_start_codon'; --- ************************************************ --- *** relation: aberrant_processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been processed "in *** --- *** correctly", for example by the failure o *** --- *** f splicing of one or more exons. *** --- ************************************************ --- CREATE VIEW aberrant_processed_transcript AS SELECT feature_id AS aberrant_processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aberrant_processed_transcript'; --- ************************************************ --- *** relation: exonic_splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Exonic splicing enhancers (ESEs) facilit *** --- *** ate exon definition by assisting in the *** --- *** recruitment of splicing factors to the a *** --- *** djacent intron. *** --- ************************************************ --- CREATE VIEW exonic_splice_enhancer AS SELECT feature_id AS exonic_splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exonic_splice_enhancer'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targeted *** --- *** by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: dnasei_hypersensitive_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW dnasei_hypersensitive_site AS SELECT feature_id AS dnasei_hypersensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAseI_hypersensitive_site'; --- ************************************************ --- *** relation: translocation_element *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** chromosomes carrying non-homologous cent *** --- *** romeres may be recovered independently. *** --- *** These chromosomes are described as trans *** --- *** location elements. This occurs for some *** --- *** translocations, particularly but not exc *** --- *** lusively, reciprocal translocations. *** --- ************************************************ --- CREATE VIEW translocation_element AS SELECT feature_id AS translocation_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occurred. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: gene_with_polycistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW gene_with_polycistronic_transcript AS SELECT feature_id AS gene_with_polycistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_polycistronic_transcript'; --- ************************************************ --- *** relation: cleaved_initiator_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** The initiator methionine that has been c *** --- *** leaved from a mature polypeptide sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW cleaved_initiator_methionine AS SELECT feature_id AS cleaved_initiator_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine'; --- ************************************************ --- *** relation: gene_with_dicistronic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic transc *** --- *** ript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_transcript AS SELECT feature_id AS gene_with_dicistronic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'gene_with_dicistronic_transcript'; --- ************************************************ --- *** relation: gene_with_recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an mRNA that is reco *** --- *** ded. *** --- ************************************************ --- CREATE VIEW gene_with_recoded_mrna AS SELECT feature_id AS gene_with_recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_recoded_mRNA'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives exist in normal individuals *** --- *** in some population(s), wherein the least *** --- *** frequent variant has an abundance of 1% *** --- *** or greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'oligo'; --- ************************************************ --- *** relation: gene_with_stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a transcript with st *** --- *** op codon readthrough. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_read_through AS SELECT feature_id AS gene_with_stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gene_with_stop_codon_read_through'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as pyrrolysine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_feature with an extent of zer *** --- *** o. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_insert_end' OR cvterm.name = 'clone_insert_start' OR cvterm.name = 'exon_junction' OR cvterm.name = 'insertion_site' OR cvterm.name = 'polyA_site' OR cvterm.name = 'deletion_junction' OR cvterm.name = 'chromosome_breakpoint' OR cvterm.name = 'splice_junction' OR cvterm.name = 'trans_splice_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction' OR cvterm.name = 'transposable_element_insertion_site' OR cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'junction'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'remark'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A region (or regions) that includes all *** --- *** of the sequence elements necessary to en *** --- *** code a functional transcript. A gene may *** --- *** include regulatory regions, transcribed *** --- *** regions and/or other functional sequenc *** --- *** e regions. *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjcent copies of a region ( *** --- *** of length greater than 1). *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 3' splice site of the acceptor prima *** --- *** ry transcript. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: trans_splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The 5' five prime splice site region of *** --- *** the donor RNA. *** --- ************************************************ --- CREATE VIEW trans_splice_donor_site AS SELECT feature_id AS trans_splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_donor_site'; --- ************************************************ --- *** relation: sl1_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL1 RNA leader sequence to *** --- *** the 5' end of most mRNAs. *** --- ************************************************ --- CREATE VIEW sl1_acceptor_site AS SELECT feature_id AS sl1_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL1_acceptor_site'; --- ************************************************ --- *** relation: sl2_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A trans_splicing_acceptor_site which app *** --- *** ends the 22nt SL2 RNA leader sequence to *** --- *** the 5' end of mRNAs. SL2 acceptor sites *** --- *** occur in genes in internal segments of *** --- *** polycistronic transcripts. *** --- ************************************************ --- CREATE VIEW sl2_acceptor_site AS SELECT feature_id AS sl2_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'SL2_acceptor_site'; --- ************************************************ --- *** relation: gene_with_stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding an mRNA that has the sto *** --- *** p codon redefined as selenocysteine. *** --- ************************************************ --- CREATE VIEW gene_with_stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS gene_with_stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: gene_with_mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with mRNA recoded by translationa *** --- *** l bypass. *** --- ************************************************ --- CREATE VIEW gene_with_mrna_recoded_by_translational_bypass AS SELECT feature_id AS gene_with_mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: gene_with_transcript_with_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A gene encoding a transcript that has a *** --- *** translational frameshift. *** --- ************************************************ --- CREATE VIEW gene_with_transcript_with_translational_frameshift AS SELECT feature_id AS gene_with_transcript_with_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_transcript_with_translational_frameshift'; --- ************************************************ --- *** relation: dna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in the DNA form o *** --- *** f the sequence. *** --- ************************************************ --- CREATE VIEW dna_motif AS SELECT feature_id AS dna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'DNA_motif'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: rna_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif that is active in RNA sequence. *** --- ************************************************ --- CREATE VIEW rna_motif AS SELECT feature_id AS rna_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'RNA_motif'; --- ************************************************ --- *** relation: dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that has the quality dicistronic *** --- *** . *** --- ************************************************ --- CREATE VIEW dicistronic_mrna AS SELECT feature_id AS dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_mRNA'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It need not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: blocked_reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A reading_frame that is interrupted by o *** --- *** ne or more stop codons; usually identifi *** --- *** ed through intergenomic sequence compari *** --- *** sons. *** --- ************************************************ --- CREATE VIEW blocked_reading_frame AS SELECT feature_id AS blocked_reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blocked_reading_frame'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable element that is foreign. *** --- ************************************************ --- CREATE VIEW foreign_transposable_element AS SELECT feature_id AS foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'foreign_transposable_element'; --- ************************************************ --- *** relation: gene_with_dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a dicistronic primar *** --- *** y transcript. *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_primary_transcript AS SELECT feature_id AS gene_with_dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_primary_transcript'; --- ************************************************ --- *** relation: gene_with_dicistronic_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a polycistronic mRNA *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_dicistronic_mrna AS SELECT feature_id AS gene_with_dicistronic_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_dicistronic_mRNA'; --- ************************************************ --- *** relation: idna *** --- *** relation type: VIEW *** --- *** *** --- *** Genomic sequence removed from the genome *** --- *** , as a normal event, by a process of rec *** --- *** ombination. *** --- ************************************************ --- CREATE VIEW idna AS SELECT feature_id AS idna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iDNA'; --- ************************************************ --- *** relation: orit *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule where transfe *** --- *** r is initiated during the process of con *** --- *** jugation or mobilization. *** --- ************************************************ --- CREATE VIEW orit AS SELECT feature_id AS orit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriT'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The transit_peptide is a short region at *** --- *** the N-terminus of the peptide that dire *** --- *** cts the protein to an organelle (chlorop *** --- *** last, mitochondrion, microbody or cyanel *** --- *** le). *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: repeat_unit *** --- *** relation type: VIEW *** --- *** *** --- *** The simplest repeated component of a rep *** --- *** eat region. A single repeat. *** --- ************************************************ --- CREATE VIEW repeat_unit AS SELECT feature_id AS repeat_unit_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_unit'; --- ************************************************ --- *** relation: crm *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region where more than 1 TF *** --- *** _binding_site together are regulatorily *** --- *** active. *** --- ************************************************ --- CREATE VIEW crm AS SELECT feature_id AS crm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'CRM'; --- ************************************************ --- *** relation: intein *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is able to ex *** --- *** cise itself and rejoin the remaining por *** --- *** tions with a peptide bond. *** --- ************************************************ --- CREATE VIEW intein AS SELECT feature_id AS intein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein'; --- ************************************************ --- *** relation: intein_containing *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of protein-coding genes whe *** --- *** re the initial protein product contains *** --- *** an intein. *** --- ************************************************ --- CREATE VIEW intein_containing AS SELECT feature_id AS intein_containing_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intein_containing'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** he unknown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: fragmentary *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** is incomplete. *** --- ************************************************ --- CREATE VIEW fragmentary AS SELECT feature_id AS fragmentary_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary'; --- ************************************************ --- *** relation: predicted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an unverified re *** --- *** gion. *** --- ************************************************ --- CREATE VIEW predicted AS SELECT feature_id AS predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'predicted'; --- ************************************************ --- *** relation: feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a located_sequen *** --- *** ce_feature. *** --- ************************************************ --- CREATE VIEW feature_attribute AS SELECT feature_id AS feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_attribute' OR cvterm.name = 'bound_by_factor' OR cvterm.name = 'flanked' OR cvterm.name = 'gene_attribute' OR cvterm.name = 'retrotransposed' OR cvterm.name = 'transgenic' OR cvterm.name = 'natural' OR cvterm.name = 'engineered' OR cvterm.name = 'foreign' OR cvterm.name = 'fusion' OR cvterm.name = 'rescue' OR cvterm.name = 'wild_type' OR cvterm.name = 'conserved' OR cvterm.name = 'status' OR cvterm.name = 'intermediate' OR cvterm.name = 'recombinationally_rearranged' OR cvterm.name = 'cryptic' OR cvterm.name = 'strand_attribute' OR cvterm.name = 'direction_attribute' OR cvterm.name = 'enzymatic' OR cvterm.name = 'mobile' OR cvterm.name = 'alteration_attribute' OR cvterm.name = 'experimental_feature_attribute' OR cvterm.name = 'edited' OR cvterm.name = 'capped' OR cvterm.name = 'mRNA_attribute' OR cvterm.name = 'trans_spliced' OR cvterm.name = 'alternatively_spliced' OR cvterm.name = 'monocistronic' OR cvterm.name = 'polycistronic' OR cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'dicistronic' OR cvterm.name = 'bound_by_protein' OR cvterm.name = 'bound_by_nucleic_acid' OR cvterm.name = 'floxed' OR cvterm.name = 'FRT_flanked' OR cvterm.name = 'protein_coding' OR cvterm.name = 'non_protein_coding' OR cvterm.name = 'gene_to_gene_feature' OR cvterm.name = 'gene_array_member' OR cvterm.name = 'regulated' OR cvterm.name = 'epigenetically_modified' OR cvterm.name = 'encodes_alternately_spliced_transcripts' OR cvterm.name = 'encodes_alternate_transcription_start_sites' OR cvterm.name = 'intein_containing' OR cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'overlapping' OR cvterm.name = 'inside_intron' OR cvterm.name = 'five_prime_three_prime_overlap' OR cvterm.name = 'five_prime_five_prime_overlap' OR cvterm.name = 'three_prime_three_prime_overlap' OR cvterm.name = 'three_prime_five_prime_overlap' OR cvterm.name = 'antisense' OR cvterm.name = 'inside_intron_antiparallel' OR cvterm.name = 'inside_intron_parallel' OR cvterm.name = 'operon_member' OR cvterm.name = 'gene_cassette_member' OR cvterm.name = 'gene_subarray_member' OR cvterm.name = 'member_of_regulon' OR cvterm.name = 'cassette_array_member' OR cvterm.name = 'transcriptionally_regulated' OR cvterm.name = 'post_translationally_regulated' OR cvterm.name = 'translationally_regulated' OR cvterm.name = 'imprinted' OR cvterm.name = 'transcriptionally_constitutive' OR cvterm.name = 'transcriptionally_induced' OR cvterm.name = 'transcriptionally_repressed' OR cvterm.name = 'autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'silenced' OR cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'negatively_autoregulated' OR cvterm.name = 'positively_autoregulated' OR cvterm.name = 'post_translationally_regulated_by_protein_stability' OR cvterm.name = 'post_translationally_regulated_by_protein_modification' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'imprinted' OR cvterm.name = 'allelically_excluded' OR cvterm.name = 'rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted' OR cvterm.name = 'paternally_imprinted' OR cvterm.name = 'encodes_1_polypeptide' OR cvterm.name = 'encodes_greater_than_1_polypeptide' OR cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'ribozymic' OR cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'feature_attribute'; --- ************************************************ --- *** relation: exemplar_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An exemplar is a representative cDNA seq *** --- *** uence for each gene. The exemplar approa *** --- *** ch is a method that usually involves som *** --- *** e initial clustering into gene groups an *** --- *** d the subsequent selection of a represen *** --- *** tative from each gene group. *** --- ************************************************ --- CREATE VIEW exemplar_mrna AS SELECT feature_id AS exemplar_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar_mRNA'; --- ************************************************ --- *** relation: sequence_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_location AS SELECT feature_id AS sequence_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'organelle_sequence' OR cvterm.name = 'plasmid_location' OR cvterm.name = 'proviral_location' OR cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'sequence_location'; --- ************************************************ --- *** relation: organelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW organelle_sequence AS SELECT feature_id AS organelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_sequence' OR cvterm.name = 'micronuclear_sequence' OR cvterm.name = 'mitochondrial_sequence' OR cvterm.name = 'nuclear_sequence' OR cvterm.name = 'nucleomorphic_sequence' OR cvterm.name = 'plastid_sequence' OR cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'organelle_sequence'; --- ************************************************ --- *** relation: mitochondrial_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_sequence AS SELECT feature_id AS mitochondrial_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA' OR cvterm.name = 'mitochondrial_sequence'; --- ************************************************ --- *** relation: nuclear_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nuclear_sequence AS SELECT feature_id AS nuclear_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_sequence'; --- ************************************************ --- *** relation: nucleomorphic_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW nucleomorphic_sequence AS SELECT feature_id AS nucleomorphic_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_sequence'; --- ************************************************ --- *** relation: plastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plastid_sequence AS SELECT feature_id AS plastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence' OR cvterm.name = 'chromoplast_sequence' OR cvterm.name = 'chloroplast_sequence' OR cvterm.name = 'cyanelle_sequence' OR cvterm.name = 'leucoplast_sequence' OR cvterm.name = 'proplastid_sequence' OR cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'plastid_sequence'; --- ************************************************ --- *** relation: kinetoplast *** --- *** relation type: VIEW *** --- *** *** --- *** A kinetoplast is an interlocked network *** --- *** of thousands of minicircles and tens of *** --- *** maxi circles, located near the base of t *** --- *** he flagellum of some protozoan species. *** --- ************************************************ --- CREATE VIEW kinetoplast AS SELECT feature_id AS kinetoplast_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast'; --- ************************************************ --- *** relation: maxicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle is a replicon, part of a ki *** --- *** netoplast, that contains open reading fr *** --- *** ames and replicates via a rolling circle *** --- *** method. *** --- ************************************************ --- CREATE VIEW maxicircle AS SELECT feature_id AS maxicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maxicircle'; --- ************************************************ --- *** relation: apicoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW apicoplast_sequence AS SELECT feature_id AS apicoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_sequence'; --- ************************************************ --- *** relation: chromoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromoplast_sequence AS SELECT feature_id AS chromoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_sequence'; --- ************************************************ --- *** relation: chloroplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_sequence AS SELECT feature_id AS chloroplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA' OR cvterm.name = 'chloroplast_sequence'; --- ************************************************ --- *** relation: cyanelle_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cyanelle_sequence AS SELECT feature_id AS cyanelle_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_sequence'; --- ************************************************ --- *** relation: leucoplast_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucoplast_sequence AS SELECT feature_id AS leucoplast_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_sequence'; --- ************************************************ --- *** relation: proplastid_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proplastid_sequence AS SELECT feature_id AS proplastid_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proplastid_sequence'; --- ************************************************ --- *** relation: plasmid_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_location AS SELECT feature_id AS plasmid_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_location'; --- ************************************************ --- *** relation: amplification_origin *** --- *** relation type: VIEW *** --- *** *** --- *** An origin_of_replication that is used fo *** --- *** r the amplification of a chromosomal nuc *** --- *** leic acid sequence. *** --- ************************************************ --- CREATE VIEW amplification_origin AS SELECT feature_id AS amplification_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amplification_origin'; --- ************************************************ --- *** relation: proviral_location *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proviral_location AS SELECT feature_id AS proviral_location_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence' OR cvterm.name = 'proviral_location'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: clone_insert *** --- *** relation type: VIEW *** --- *** *** --- *** The region of sequence that has been ins *** --- *** erted and is being propagated by the clo *** --- *** ne. *** --- ************************************************ --- CREATE VIEW clone_insert AS SELECT feature_id AS clone_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'clone_insert'; --- ************************************************ --- *** relation: lambda_vector *** --- *** relation type: VIEW *** --- *** *** --- *** The lambda bacteriophage is the vector f *** --- *** or the linear lambda clone. The genes in *** --- *** volved in the lysogenic pathway are remo *** --- *** ved from the from the viral DNA. Up to 2 *** --- *** 5 kb of foreign DNA can then be inserted *** --- *** into the lambda genome. *** --- ************************************************ --- CREATE VIEW lambda_vector AS SELECT feature_id AS lambda_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lambda_vector'; --- ************************************************ --- *** relation: plasmid_vector *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plasmid_vector AS SELECT feature_id AS plasmid_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid_vector'; --- ************************************************ --- *** relation: cdna *** --- *** relation type: VIEW *** --- *** *** --- *** DNA synthesized by reverse transcriptase *** --- *** using RNA as a template. *** --- ************************************************ --- CREATE VIEW cdna AS SELECT feature_id AS cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA' OR cvterm.name = 'double_stranded_cDNA' OR cvterm.name = 'cDNA'; --- ************************************************ --- *** relation: single_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single_stranded_cdna AS SELECT feature_id AS single_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_cDNA'; --- ************************************************ --- *** relation: double_stranded_cdna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double_stranded_cdna AS SELECT feature_id AS double_stranded_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_cDNA'; --- ************************************************ --- *** relation: pyrrolysyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a pyrrolysine a *** --- *** nticodon, and a 3' pyrrolysine binding r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW pyrrolysyl_trna AS SELECT feature_id AS pyrrolysyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysyl_tRNA'; --- ************************************************ --- *** relation: episome *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that may integrate with a chro *** --- *** mosome. *** --- ************************************************ --- CREATE VIEW episome AS SELECT feature_id AS episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome' OR cvterm.name = 'episome'; --- ************************************************ --- *** relation: tmrna_coding_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a two-piece tmRNA that bea *** --- *** rs the reading frame encoding the proteo *** --- *** lysis tag. The tmRNA gene undergoes circ *** --- *** ular permutation in some groups of bacte *** --- *** ria. Processing of the transcripts from *** --- *** such a gene leaves the mature tmRNA in t *** --- *** wo pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_coding_piece AS SELECT feature_id AS tmrna_coding_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece'; --- ************************************************ --- *** relation: tmrna_acceptor_piece *** --- *** relation type: VIEW *** --- *** *** --- *** The acceptor region of a two-piece tmRNA *** --- *** that when mature is charged at its 3' e *** --- *** nd with alanine. The tmRNA gene undergoe *** --- *** s circular permutation in some groups of *** --- *** bacteria; processing of the transcripts *** --- *** from such a gene leaves the mature tmRN *** --- *** A in two pieces, base-paired together. *** --- ************************************************ --- CREATE VIEW tmrna_acceptor_piece AS SELECT feature_id AS tmrna_acceptor_piece_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_acceptor_piece'; --- ************************************************ --- *** relation: qtl *** --- *** relation type: VIEW *** --- *** *** --- *** A quantitative trait locus (QTL) is a po *** --- *** lymorphic locus which contains alleles t *** --- *** hat differentially affect the expression *** --- *** of a continuously distributed phenotypi *** --- *** c trait. Usually it is a marker describe *** --- *** d by statistical association to quantita *** --- *** tive variation in the particular phenoty *** --- *** pic trait that is thought to be controll *** --- *** ed by the cumulative action of alleles a *** --- *** t multiple loci. *** --- ************************************************ --- CREATE VIEW qtl AS SELECT feature_id AS qtl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'QTL'; --- ************************************************ --- *** relation: genomic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A genomic island is an integrated mobile *** --- *** genetic element, characterized by size *** --- *** (over 10 Kb). It that has features that *** --- *** suggest a foreign origin. These can incl *** --- *** ude nucleotide distribution (oligonucleo *** --- *** tides signature, CG content etc.) that d *** --- *** iffers from the bulk of the chromosome a *** --- *** nd/or genes suggesting DNA mobility. *** --- ************************************************ --- CREATE VIEW genomic_island AS SELECT feature_id AS genomic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'genomic_island'; --- ************************************************ --- *** relation: pathogenic_island *** --- *** relation type: VIEW *** --- *** *** --- *** Mobile genetic elements that contribute *** --- *** to rapid changes in virulence potential. *** --- *** They are present on the genomes of path *** --- *** ogenic strains but absent from the genom *** --- *** es of non pathogenic members of the same *** --- *** or related species. *** --- ************************************************ --- CREATE VIEW pathogenic_island AS SELECT feature_id AS pathogenic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pathogenic_island'; --- ************************************************ --- *** relation: metabolic_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in metabolism, analogous to th *** --- *** e pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW metabolic_island AS SELECT feature_id AS metabolic_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'metabolic_island'; --- ************************************************ --- *** relation: adaptive_island *** --- *** relation type: VIEW *** --- *** *** --- *** An adaptive island is a genomic island t *** --- *** hat provides an adaptive advantage to th *** --- *** e host. *** --- ************************************************ --- CREATE VIEW adaptive_island AS SELECT feature_id AS adaptive_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'adaptive_island'; --- ************************************************ --- *** relation: symbiosis_island *** --- *** relation type: VIEW *** --- *** *** --- *** A transmissible element containing genes *** --- *** involved in symbiosis, analogous to the *** --- *** pathogenicity islands of gram negative *** --- *** bacteria. *** --- ************************************************ --- CREATE VIEW symbiosis_island AS SELECT feature_id AS symbiosis_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'symbiosis_island'; --- ************************************************ --- *** relation: pseudogenic_rrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of an rRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_rrna AS SELECT feature_id AS pseudogenic_rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_rRNA'; --- ************************************************ --- *** relation: pseudogenic_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A non functional descendent of a tRNA. *** --- ************************************************ --- CREATE VIEW pseudogenic_trna AS SELECT feature_id AS pseudogenic_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_tRNA'; --- ************************************************ --- *** relation: engineered_episome *** --- *** relation type: VIEW *** --- *** *** --- *** An episome that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_episome AS SELECT feature_id AS engineered_episome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_episome'; --- ************************************************ --- *** relation: transgenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence that has b *** --- *** een integrated with foreign sequence. *** --- ************************************************ --- CREATE VIEW transgenic AS SELECT feature_id AS transgenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic'; --- ************************************************ --- *** relation: so_natural *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that o *** --- *** ccurs in nature. *** --- ************************************************ --- CREATE VIEW so_natural AS SELECT feature_id AS so_natural_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural'; --- ************************************************ --- *** relation: engineered *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region that w *** --- *** as modified in vitro. *** --- ************************************************ --- CREATE VIEW engineered AS SELECT feature_id AS engineered_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered'; --- ************************************************ --- *** relation: so_foreign *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a region from a *** --- *** nother species. *** --- ************************************************ --- CREATE VIEW so_foreign AS SELECT feature_id AS so_foreign_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'foreign'; --- ************************************************ --- *** relation: cloned_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cloned_region AS SELECT feature_id AS cloned_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_region'; --- ************************************************ --- *** relation: validated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been proven. *** --- ************************************************ --- CREATE VIEW validated AS SELECT feature_id AS validated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimentally_determined' OR cvterm.name = 'validated'; --- ************************************************ --- *** relation: invalidated *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s invalidated. *** --- ************************************************ --- CREATE VIEW invalidated AS SELECT feature_id AS invalidated_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'invalidated'; --- ************************************************ --- *** relation: engineered_rescue_region *** --- *** relation type: VIEW *** --- *** *** --- *** A rescue region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_rescue_region AS SELECT feature_id AS engineered_rescue_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_rescue_region'; --- ************************************************ --- *** relation: rescue_mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A mini_gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_mini_gene AS SELECT feature_id AS rescue_mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene'; --- ************************************************ --- *** relation: transgenic_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified in vitro, incl *** --- *** uding insertion of DNA derived from a so *** --- *** urce other than the originating TE. *** --- ************************************************ --- CREATE VIEW transgenic_transposable_element AS SELECT feature_id AS transgenic_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_transposable_element'; --- ************************************************ --- *** relation: natural_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that exists (or existed) in nature. *** --- ************************************************ --- CREATE VIEW natural_transposable_element AS SELECT feature_id AS natural_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element'; --- ************************************************ --- *** relation: engineered_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** TE that has been modified by manipulatio *** --- *** ns in vitro. *** --- ************************************************ --- CREATE VIEW engineered_transposable_element AS SELECT feature_id AS engineered_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_transposable_element'; --- ************************************************ --- *** relation: engineered_foreign_transposable_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposable_element that is engineere *** --- *** d and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_transposable_element AS SELECT feature_id AS engineered_foreign_transposable_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_transposable_element'; --- ************************************************ --- *** relation: assortment_derived_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome duplication aberratio *** --- *** n generated by reassortment of other abe *** --- *** rration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_duplication AS SELECT feature_id AS assortment_derived_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency_plus_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency an *** --- *** d a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency_plus_duplication AS SELECT feature_id AS assortment_derived_deficiency_plus_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency_plus_duplication'; --- ************************************************ --- *** relation: assortment_derived_deficiency *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome deficiency aberration *** --- *** generated by reassortment of other aber *** --- *** ration components. *** --- ************************************************ --- CREATE VIEW assortment_derived_deficiency AS SELECT feature_id AS assortment_derived_deficiency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_deficiency'; --- ************************************************ --- *** relation: assortment_derived_aneuploid *** --- *** relation type: VIEW *** --- *** *** --- *** A multi-chromosome aberration generated *** --- *** by reassortment of other aberration comp *** --- *** onents; presumed to have a deficiency or *** --- *** a duplication. *** --- ************************************************ --- CREATE VIEW assortment_derived_aneuploid AS SELECT feature_id AS assortment_derived_aneuploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_aneuploid'; --- ************************************************ --- *** relation: engineered_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_region AS SELECT feature_id AS engineered_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_region'; --- ************************************************ --- *** relation: engineered_foreign_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is engineered and foreign. *** --- ************************************************ --- CREATE VIEW engineered_foreign_region AS SELECT feature_id AS engineered_foreign_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_region'; --- ************************************************ --- *** relation: fusion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fusion AS SELECT feature_id AS fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fusion'; --- ************************************************ --- *** relation: engineered_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A tag that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_tag AS SELECT feature_id AS engineered_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_tag'; --- ************************************************ --- *** relation: validated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that has been validated. *** --- ************************************************ --- CREATE VIEW validated_cdna_clone AS SELECT feature_id AS validated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'validated_cDNA_clone'; --- ************************************************ --- *** relation: invalidated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone that is invalid. *** --- ************************************************ --- CREATE VIEW invalidated_cdna_clone AS SELECT feature_id AS invalidated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone'; --- ************************************************ --- *** relation: chimeric_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated because it is c *** --- *** himeric. *** --- ************************************************ --- CREATE VIEW chimeric_cdna_clone AS SELECT feature_id AS chimeric_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chimeric_cDNA_clone'; --- ************************************************ --- *** relation: genomically_contaminated_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by genomic cont *** --- *** amination. *** --- ************************************************ --- CREATE VIEW genomically_contaminated_cdna_clone AS SELECT feature_id AS genomically_contaminated_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomically_contaminated_cDNA_clone'; --- ************************************************ --- *** relation: polya_primed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA clone invalidated by polyA primin *** --- *** g. *** --- ************************************************ --- CREATE VIEW polya_primed_cdna_clone AS SELECT feature_id AS polya_primed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_primed_cDNA_clone'; --- ************************************************ --- *** relation: partially_processed_cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A cDNA invalidated clone by partial proc *** --- *** essing. *** --- ************************************************ --- CREATE VIEW partially_processed_cdna_clone AS SELECT feature_id AS partially_processed_cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_processed_cDNA_clone'; --- ************************************************ --- *** relation: rescue *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a region's abili *** --- *** ty, when introduced to a mutant organism *** --- *** , to re-establish (rescue) a phenotype. *** --- ************************************************ --- CREATE VIEW rescue AS SELECT feature_id AS rescue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue'; --- ************************************************ --- *** relation: mini_gene *** --- *** relation type: VIEW *** --- *** *** --- *** By definition, minigenes are short open- *** --- *** reading frames (ORF), usually encoding a *** --- *** pproximately 9 to 20 amino acids, which *** --- *** are expressed in vivo (as distinct from *** --- *** being synthesized as peptide or protein *** --- *** ex vivo and subsequently injected). The *** --- *** in vivo synthesis confers a distinct adv *** --- *** antage: the expressed sequences can ente *** --- *** r both antigen presentation pathways, MH *** --- *** C I (inducing CD8+ T- cells, which are u *** --- *** sually cytotoxic T-lymphocytes (CTL)) an *** --- *** d MHC II (inducing CD4+ T-cells, usually *** --- *** 'T-helpers' (Th)); and can encounter B- *** --- *** cells, inducing antibody responses. Thre *** --- *** e main vector approaches have been used *** --- *** to deliver minigenes: viral vectors, bac *** --- *** terial vectors and plasmid DNA. *** --- ************************************************ --- CREATE VIEW mini_gene AS SELECT feature_id AS mini_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'mini_gene'; --- ************************************************ --- *** relation: rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW rescue_gene AS SELECT feature_id AS rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'rescue_gene'; --- ************************************************ --- *** relation: wild_type *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing sequence with th *** --- *** e genotype found in nature and/or standa *** --- *** rd laboratory stock. *** --- ************************************************ --- CREATE VIEW wild_type AS SELECT feature_id AS wild_type_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type'; --- ************************************************ --- *** relation: wild_type_rescue_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that rescues. *** --- ************************************************ --- CREATE VIEW wild_type_rescue_gene AS SELECT feature_id AS wild_type_rescue_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wild_type_rescue_gene'; --- ************************************************ --- *** relation: mitochondrial_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a mitochondr *** --- *** ia. *** --- ************************************************ --- CREATE VIEW mitochondrial_chromosome AS SELECT feature_id AS mitochondrial_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_chromosome'; --- ************************************************ --- *** relation: chloroplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chloroplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chloroplast_chromosome AS SELECT feature_id AS chloroplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_chromosome'; --- ************************************************ --- *** relation: chromoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a chromoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW chromoplast_chromosome AS SELECT feature_id AS chromoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromoplast_chromosome'; --- ************************************************ --- *** relation: cyanelle_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a cyanelle. *** --- ************************************************ --- CREATE VIEW cyanelle_chromosome AS SELECT feature_id AS cyanelle_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyanelle_chromosome'; --- ************************************************ --- *** relation: leucoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome with origin in a leucoplast *** --- *** . *** --- ************************************************ --- CREATE VIEW leucoplast_chromosome AS SELECT feature_id AS leucoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucoplast_chromosome'; --- ************************************************ --- *** relation: macronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a macronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW macronuclear_chromosome AS SELECT feature_id AS macronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'macronuclear_chromosome'; --- ************************************************ --- *** relation: micronuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a micronucle *** --- *** us. *** --- ************************************************ --- CREATE VIEW micronuclear_chromosome AS SELECT feature_id AS micronuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'micronuclear_chromosome'; --- ************************************************ --- *** relation: nuclear_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_chromosome AS SELECT feature_id AS nuclear_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_chromosome'; --- ************************************************ --- *** relation: nucleomorphic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in a nucleomorp *** --- *** h. *** --- ************************************************ --- CREATE VIEW nucleomorphic_chromosome AS SELECT feature_id AS nucleomorphic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleomorphic_chromosome'; --- ************************************************ --- *** relation: chromosome_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_part AS SELECT feature_id AS chromosome_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'chromosome_part'; --- ************************************************ --- *** relation: gene_member_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a gene. *** --- ************************************************ --- CREATE VIEW gene_member_region AS SELECT feature_id AS gene_member_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'gene_member_region'; --- ************************************************ --- *** relation: transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a transcript. *** --- ************************************************ --- CREATE VIEW transcript_region AS SELECT feature_id AS transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'transcript_region'; --- ************************************************ --- *** relation: mature_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a mature transcript. *** --- ************************************************ --- CREATE VIEW mature_transcript_region AS SELECT feature_id AS mature_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'mature_transcript_region'; --- ************************************************ --- *** relation: primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a primary transcript. *** --- ************************************************ --- CREATE VIEW primary_transcript_region AS SELECT feature_id AS primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'primary_transcript_region'; --- ************************************************ --- *** relation: mrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an mRNA. *** --- ************************************************ --- CREATE VIEW mrna_region AS SELECT feature_id AS mrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'mRNA_region'; --- ************************************************ --- *** relation: utr_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of UTR. *** --- ************************************************ --- CREATE VIEW utr_region AS SELECT feature_id AS utr_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'UTR_region'; --- ************************************************ --- *** relation: rrna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an rRNA primary transcript. *** --- ************************************************ --- CREATE VIEW rrna_primary_transcript_region AS SELECT feature_id AS rrna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'rRNA_primary_transcript_region'; --- ************************************************ --- *** relation: polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Biological sequence region that can be a *** --- *** ssigned to a specific subsequence of a p *** --- *** olypeptide. *** --- ************************************************ --- CREATE VIEW polypeptide_region AS SELECT feature_id AS polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_region'; --- ************************************************ --- *** relation: repeat_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a repeated sequence. *** --- ************************************************ --- CREATE VIEW repeat_component AS SELECT feature_id AS repeat_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'repeat_component'; --- ************************************************ --- *** relation: spliceosomal_intron_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region within an intron. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron_region AS SELECT feature_id AS spliceosomal_intron_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'spliceosomal_intron_region'; --- ************************************************ --- *** relation: gene_component_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_component_region AS SELECT feature_id AS gene_component_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_component_region'; --- ************************************************ --- *** relation: tmrna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tmRNA. *** --- ************************************************ --- CREATE VIEW tmrna_region AS SELECT feature_id AS tmrna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'tmRNA_region'; --- ************************************************ --- *** relation: ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ltr_component AS SELECT feature_id AS ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'LTR_component'; --- ************************************************ --- *** relation: three_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_ltr_component AS SELECT feature_id AS three_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'three_prime_LTR_component'; --- ************************************************ --- *** relation: five_prime_ltr_component *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW five_prime_ltr_component AS SELECT feature_id AS five_prime_ltr_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'five_prime_LTR_component'; --- ************************************************ --- *** relation: cds_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a CDS. *** --- ************************************************ --- CREATE VIEW cds_region AS SELECT feature_id AS cds_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'CDS_region'; --- ************************************************ --- *** relation: exon_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of an exon. *** --- ************************************************ --- CREATE VIEW exon_region AS SELECT feature_id AS exon_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'exon_region'; --- ************************************************ --- *** relation: homologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is homologous to another r *** --- *** egion. *** --- ************************************************ --- CREATE VIEW homologous_region AS SELECT feature_id AS homologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'homologous_region'; --- ************************************************ --- *** relation: paralogous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is paralogous t *** --- *** o another region. *** --- ************************************************ --- CREATE VIEW paralogous_region AS SELECT feature_id AS paralogous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous_region'; --- ************************************************ --- *** relation: orthologous_region *** --- *** relation type: VIEW *** --- *** *** --- *** A homologous_region that is orthologous *** --- *** to another region. *** --- ************************************************ --- CREATE VIEW orthologous_region AS SELECT feature_id AS orthologous_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous_region'; --- ************************************************ --- *** relation: conserved *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW conserved AS SELECT feature_id AS conserved_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homologous' OR cvterm.name = 'syntenic' OR cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'conserved'; --- ************************************************ --- *** relation: homologous *** --- *** relation type: VIEW *** --- *** *** --- *** Similarity due to common ancestry. *** --- ************************************************ --- CREATE VIEW homologous AS SELECT feature_id AS homologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous' OR cvterm.name = 'paralogous' OR cvterm.name = 'homologous'; --- ************************************************ --- *** relation: orthologous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occured after a spec *** --- *** iation event. *** --- ************************************************ --- CREATE VIEW orthologous AS SELECT feature_id AS orthologous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orthologous'; --- ************************************************ --- *** relation: paralogous *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a kind of homolo *** --- *** gy where divergence occurred after a dup *** --- *** lication event. *** --- ************************************************ --- CREATE VIEW paralogous AS SELECT feature_id AS paralogous_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paralogous'; --- ************************************************ --- *** relation: syntenic *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute describing sequence regions oc *** --- *** curring in same order on chromosome of d *** --- *** ifferent species. *** --- ************************************************ --- CREATE VIEW syntenic AS SELECT feature_id AS syntenic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic'; --- ************************************************ --- *** relation: capped_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is capped. *** --- ************************************************ --- CREATE VIEW capped_primary_transcript AS SELECT feature_id AS capped_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_primary_transcript'; --- ************************************************ --- *** relation: capped_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is capped. *** --- ************************************************ --- CREATE VIEW capped_mrna AS SELECT feature_id AS capped_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'capped_mRNA'; --- ************************************************ --- *** relation: mrna_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA feature. *** --- ************************************************ --- CREATE VIEW mrna_attribute AS SELECT feature_id AS mrna_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated' OR cvterm.name = 'exemplar' OR cvterm.name = 'frameshift' OR cvterm.name = 'recoded' OR cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'mRNA_attribute'; --- ************************************************ --- *** relation: exemplar *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence is re *** --- *** presentative of a class of similar seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW exemplar AS SELECT feature_id AS exemplar_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exemplar'; --- ************************************************ --- *** relation: frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains a mutation involving the deleti *** --- *** on or insertion of one or more bases, wh *** --- *** ere this number is not divisible by 3. *** --- ************************************************ --- CREATE VIEW frameshift AS SELECT feature_id AS frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift' OR cvterm.name = 'minus_2_frameshift' OR cvterm.name = 'plus_1_frameshift' OR cvterm.name = 'plus_2_framshift' OR cvterm.name = 'frameshift'; --- ************************************************ --- *** relation: minus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting one base *** --- *** . *** --- ************************************************ --- CREATE VIEW minus_1_frameshift AS SELECT feature_id AS minus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift'; --- ************************************************ --- *** relation: minus_2_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by deleting two base *** --- *** s. *** --- ************************************************ --- CREATE VIEW minus_2_frameshift AS SELECT feature_id AS minus_2_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift'; --- ************************************************ --- *** relation: plus_1_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting one bas *** --- *** e. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift AS SELECT feature_id AS plus_1_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift'; --- ************************************************ --- *** relation: plus_2_framshift *** --- *** relation type: VIEW *** --- *** *** --- *** A frameshift caused by inserting two bas *** --- *** es. *** --- ************************************************ --- CREATE VIEW plus_2_framshift AS SELECT feature_id AS plus_2_framshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_framshift'; --- ************************************************ --- *** relation: trans_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing transcript seque *** --- *** nce that is created by splicing exons fr *** --- *** om diferent genes. *** --- ************************************************ --- CREATE VIEW trans_spliced AS SELECT feature_id AS trans_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced'; --- ************************************************ --- *** relation: polyadenylated_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is polyadenylated. *** --- ************************************************ --- CREATE VIEW polyadenylated_mrna AS SELECT feature_id AS polyadenylated_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyadenylated_mRNA'; --- ************************************************ --- *** relation: trans_spliced_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is trans-spliced. *** --- ************************************************ --- CREATE VIEW trans_spliced_mrna AS SELECT feature_id AS trans_spliced_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_spliced_mRNA'; --- ************************************************ --- *** relation: edited_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is edited. *** --- ************************************************ --- CREATE VIEW edited_transcript AS SELECT feature_id AS edited_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'edited_transcript'; --- ************************************************ --- *** relation: edited_transcript_by_a_to_i_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that has been edited by A t *** --- *** o I substitution. *** --- ************************************************ --- CREATE VIEW edited_transcript_by_a_to_i_substitution AS SELECT feature_id AS edited_transcript_by_a_to_i_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_transcript_by_A_to_I_substitution'; --- ************************************************ --- *** relation: bound_by_protein *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a protein. *** --- ************************************************ --- CREATE VIEW bound_by_protein AS SELECT feature_id AS bound_by_protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_protein'; --- ************************************************ --- *** relation: bound_by_nucleic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** is bound by a nucleic acid. *** --- ************************************************ --- CREATE VIEW bound_by_nucleic_acid AS SELECT feature_id AS bound_by_nucleic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bound_by_nucleic_acid'; --- ************************************************ --- *** relation: alternatively_spliced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a situation wher *** --- *** e a gene may encode for more than 1 tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW alternatively_spliced AS SELECT feature_id AS alternatively_spliced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced'; --- ************************************************ --- *** relation: monocistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for one gene product. *** --- ************************************************ --- CREATE VIEW monocistronic AS SELECT feature_id AS monocistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'monocistronic'; --- ************************************************ --- *** relation: dicistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for two gene products. *** --- ************************************************ --- CREATE VIEW dicistronic AS SELECT feature_id AS dicistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic'; --- ************************************************ --- *** relation: polycistronic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence that *** --- *** contains the code for more than one gene *** --- *** product. *** --- ************************************************ --- CREATE VIEW polycistronic AS SELECT feature_id AS polycistronic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic' OR cvterm.name = 'polycistronic'; --- ************************************************ --- *** relation: recoded *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an mRNA sequence *** --- *** that has been reprogrammed at translati *** --- *** on, causing localized alterations. *** --- ************************************************ --- CREATE VIEW recoded AS SELECT feature_id AS recoded_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined' OR cvterm.name = 'recoded_by_translational_bypass' OR cvterm.name = 'translationally_frameshifted' OR cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'recoded'; --- ************************************************ --- *** relation: codon_redefined *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the alteration o *** --- *** f codon meaning. *** --- ************************************************ --- CREATE VIEW codon_redefined AS SELECT feature_id AS codon_redefined_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_redefined'; --- ************************************************ --- *** relation: stop_codon_read_through *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be a new amino *** --- *** acid. *** --- ************************************************ --- CREATE VIEW stop_codon_read_through AS SELECT feature_id AS stop_codon_read_through_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'stop_codon_read_through'; --- ************************************************ --- *** relation: stop_codon_redefined_as_pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, pyrrolysine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_pyrrolysine AS SELECT feature_id AS stop_codon_redefined_as_pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_pyrrolysine'; --- ************************************************ --- *** relation: stop_codon_redefined_as_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon redefined to be the new ami *** --- *** no acid, selenocysteine. *** --- ************************************************ --- CREATE VIEW stop_codon_redefined_as_selenocysteine AS SELECT feature_id AS stop_codon_redefined_as_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_codon_redefined_as_selenocysteine'; --- ************************************************ --- *** relation: recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** Recoded mRNA where a block of nucleotide *** --- *** s is not translated. *** --- ************************************************ --- CREATE VIEW recoded_by_translational_bypass AS SELECT feature_id AS recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recoded_by_translational_bypass'; --- ************************************************ --- *** relation: translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** Recoding by frameshifting a particular s *** --- *** ite. *** --- ************************************************ --- CREATE VIEW translationally_frameshifted AS SELECT feature_id AS translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted' OR cvterm.name = 'plus_1_translationally_frameshifted' OR cvterm.name = 'translationally_frameshifted'; --- ************************************************ --- *** relation: maternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is maternally_imprinted. *** --- ************************************************ --- CREATE VIEW maternally_imprinted_gene AS SELECT feature_id AS maternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternally_imprinted_gene'; --- ************************************************ --- *** relation: paternally_imprinted_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is paternally imprinted. *** --- ************************************************ --- CREATE VIEW paternally_imprinted_gene AS SELECT feature_id AS paternally_imprinted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternally_imprinted_gene'; --- ************************************************ --- *** relation: post_translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is post translationally regu *** --- *** lated. *** --- ************************************************ --- CREATE VIEW post_translationally_regulated_gene AS SELECT feature_id AS post_translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_regulated_gene'; --- ************************************************ --- *** relation: negatively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is negatively autoreguated. *** --- ************************************************ --- CREATE VIEW negatively_autoregulated_gene AS SELECT feature_id AS negatively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negatively_autoregulated_gene'; --- ************************************************ --- *** relation: positively_autoregulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is positively autoregulated. *** --- ************************************************ --- CREATE VIEW positively_autoregulated_gene AS SELECT feature_id AS positively_autoregulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positively_autoregulated_gene'; --- ************************************************ --- *** relation: silenced *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated at tra *** --- *** nscriptional or translational level. *** --- ************************************************ --- CREATE VIEW silenced AS SELECT feature_id AS silenced_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_modification' OR cvterm.name = 'silenced_by_RNA_interference' OR cvterm.name = 'silenced_by_histone_modification' OR cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced'; --- ************************************************ --- *** relation: silenced_by_dna_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** modifications, resulting in repression *** --- *** of transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_modification AS SELECT feature_id AS silenced_by_dna_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation' OR cvterm.name = 'silenced_by_DNA_modification'; --- ************************************************ --- *** relation: silenced_by_dna_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by DNA *** --- *** methylation, resulting in repression of *** --- *** transcription. *** --- ************************************************ --- CREATE VIEW silenced_by_dna_methylation AS SELECT feature_id AS silenced_by_dna_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_DNA_methylation'; --- ************************************************ --- *** relation: translationally_regulated_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is translationally regulated *** --- *** . *** --- ************************************************ --- CREATE VIEW translationally_regulated_gene AS SELECT feature_id AS translationally_regulated_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translationally_regulated_gene'; --- ************************************************ --- *** relation: allelically_excluded_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is allelically_excluded. *** --- ************************************************ --- CREATE VIEW allelically_excluded_gene AS SELECT feature_id AS allelically_excluded_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allelically_excluded_gene'; --- ************************************************ --- *** relation: epigenetically_modified_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is epigenetically modified. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_gene AS SELECT feature_id AS epigenetically_modified_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'epigenetically_modified_gene'; --- ************************************************ --- *** relation: transgene *** --- *** relation type: VIEW *** --- *** *** --- *** A transgene is a gene that has been tran *** --- *** sferred naturally or by any of a number *** --- *** of genetic engineering techniques from o *** --- *** ne organism to another. *** --- ************************************************ --- CREATE VIEW transgene AS SELECT feature_id AS transgene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'floxed_gene' OR cvterm.name = 'transgene'; --- ************************************************ --- *** relation: endogenous_retroviral_sequence *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW endogenous_retroviral_sequence AS SELECT feature_id AS endogenous_retroviral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endogenous_retroviral_sequence'; --- ************************************************ --- *** relation: rearranged_at_dna_level *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe the sequence of *** --- *** a feature, where the DNA is rearranged. *** --- ************************************************ --- CREATE VIEW rearranged_at_dna_level AS SELECT feature_id AS rearranged_at_dna_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rearranged_at_DNA_level'; --- ************************************************ --- *** relation: status *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the status of a *** --- *** feature, based on the available evidence *** --- *** . *** --- ************************************************ --- CREATE VIEW status AS SELECT feature_id AS status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fragmentary' OR cvterm.name = 'predicted' OR cvterm.name = 'validated' OR cvterm.name = 'invalidated' OR cvterm.name = 'independently_known' OR cvterm.name = 'consensus' OR cvterm.name = 'low_complexity' OR cvterm.name = 'whole_genome_sequence_status' OR cvterm.name = 'supported_by_sequence_similarity' OR cvterm.name = 'orphan' OR cvterm.name = 'predicted_by_ab_initio_computation' OR cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'experimentally_determined' OR cvterm.name = 'invalidated_by_chimeric_cDNA' OR cvterm.name = 'invalidated_by_genomic_contamination' OR cvterm.name = 'invalidated_by_genomic_polyA_primed_cDNA' OR cvterm.name = 'invalidated_by_partial_processing' OR cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'status'; --- ************************************************ --- *** relation: independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** Attribute to describe a feature that is *** --- *** independently known - not predicted. *** --- ************************************************ --- CREATE VIEW independently_known AS SELECT feature_id AS independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'independently_known'; --- ************************************************ --- *** relation: supported_by_sequence_similarity *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity techniques. *** --- ************************************************ --- CREATE VIEW supported_by_sequence_similarity AS SELECT feature_id AS supported_by_sequence_similarity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match' OR cvterm.name = 'supported_by_EST_or_cDNA' OR cvterm.name = 'supported_by_sequence_similarity'; --- ************************************************ --- *** relation: supported_by_domain_match *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity of a known domain. *** --- ************************************************ --- CREATE VIEW supported_by_domain_match AS SELECT feature_id AS supported_by_domain_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_domain_match'; --- ************************************************ --- *** relation: supported_by_est_or_cdna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature that *** --- *** has been predicted using sequence simila *** --- *** rity to EST or cDNA data. *** --- ************************************************ --- CREATE VIEW supported_by_est_or_cdna AS SELECT feature_id AS supported_by_est_or_cdna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supported_by_EST_or_cDNA'; --- ************************************************ --- *** relation: orphan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW orphan AS SELECT feature_id AS orphan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan'; --- ************************************************ --- *** relation: predicted_by_ab_initio_computation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that i *** --- *** s predicted by a computer program that d *** --- *** id not rely on sequence similarity. *** --- ************************************************ --- CREATE VIEW predicted_by_ab_initio_computation AS SELECT feature_id AS predicted_by_ab_initio_computation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_by_ab_initio_computation'; --- ************************************************ --- *** relation: asx_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Asp *** --- *** artate or Asparagine (Asx), the side-cha *** --- *** in O of residue(i) is H-bonded to the ma *** --- *** in-chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW asx_turn AS SELECT feature_id AS asx_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'asx_turn'; --- ************************************************ --- *** relation: cloned_cdna_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from cDNA. *** --- ************************************************ --- CREATE VIEW cloned_cdna_insert AS SELECT feature_id AS cloned_cdna_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cloned_cDNA_insert'; --- ************************************************ --- *** relation: cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert made from genomic DNA. *** --- ************************************************ --- CREATE VIEW cloned_genomic_insert AS SELECT feature_id AS cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'cloned_genomic_insert'; --- ************************************************ --- *** relation: engineered_insert *** --- *** relation type: VIEW *** --- *** *** --- *** A clone insert that is engineered. *** --- ************************************************ --- CREATE VIEW engineered_insert AS SELECT feature_id AS engineered_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'engineered_insert'; --- ************************************************ --- *** relation: edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA that is edited. *** --- ************************************************ --- CREATE VIEW edited_mrna AS SELECT feature_id AS edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_mRNA'; --- ************************************************ --- *** relation: guide_rna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of guide RNA. *** --- ************************************************ --- CREATE VIEW guide_rna_region AS SELECT feature_id AS guide_rna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'guide_RNA_region'; --- ************************************************ --- *** relation: anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that base-pairs *** --- *** to a target mRNA. *** --- ************************************************ --- CREATE VIEW anchor_region AS SELECT feature_id AS anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_region'; --- ************************************************ --- *** relation: pre_edited_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pre_edited_mrna AS SELECT feature_id AS pre_edited_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_edited_mRNA'; --- ************************************************ --- *** relation: intermediate *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute to describe a feature betwe *** --- *** en stages of processing. *** --- ************************************************ --- CREATE VIEW intermediate AS SELECT feature_id AS intermediate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate'; --- ************************************************ --- *** relation: mirna_target_site *** --- *** relation type: VIEW *** --- *** *** --- *** A miRNA target site is a binding site wh *** --- *** ere the molecule is a micro RNA. *** --- ************************************************ --- CREATE VIEW mirna_target_site AS SELECT feature_id AS mirna_target_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site'; --- ************************************************ --- *** relation: edited_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is edited. *** --- ************************************************ --- CREATE VIEW edited_cds AS SELECT feature_id AS edited_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'edited_CDS'; --- ************************************************ --- *** relation: vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment AS SELECT feature_id AS vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment'; --- ************************************************ --- *** relation: vertebrate_ig_t_cell_receptor_rearranged_gene_cluster *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_ig_t_cell_receptor_rearranged_gene_cluster AS SELECT feature_id AS vertebrate_ig_t_cell_receptor_rearranged_gene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster'; --- ************************************************ --- *** relation: vertebrate_immune_system_gene_recombination_signal_feature *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW vertebrate_immune_system_gene_recombination_signal_feature AS SELECT feature_id AS vertebrate_immune_system_gene_recombination_signal_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature'; --- ************************************************ --- *** relation: recombinationally_rearranged *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged AS SELECT feature_id AS recombinationally_rearranged_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged'; --- ************************************************ --- *** relation: recombinationally_rearranged_vertebrate_immune_system_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A recombinationally rearranged gene of t *** --- *** he vertebrate immune system. *** --- ************************************************ --- CREATE VIEW recombinationally_rearranged_vertebrate_immune_system_gene AS SELECT feature_id AS recombinationally_rearranged_vertebrate_immune_system_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene'; --- ************************************************ --- *** relation: attp_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a phage *** --- *** chromosome at which a recombinase acts t *** --- *** o insert the phage DNA at a cognate inte *** --- *** gration/excision site on a bacterial chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW attp_site AS SELECT feature_id AS attp_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attP_site'; --- ************************************************ --- *** relation: attb_site *** --- *** relation type: VIEW *** --- *** *** --- *** An integration/excision site of a bacter *** --- *** ial chromosome at which a recombinase ac *** --- *** ts to insert foreign DNA containing a co *** --- *** gnate integration/excision site. *** --- ************************************************ --- CREATE VIEW attb_site AS SELECT feature_id AS attb_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attB_site'; --- ************************************************ --- *** relation: attl_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attB_site and th *** --- *** e 3' portion of attP_site. *** --- ************************************************ --- CREATE VIEW attl_site AS SELECT feature_id AS attl_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attL_site'; --- ************************************************ --- *** relation: attr_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region that results from recombination *** --- *** between attP_site and attB_site, compos *** --- *** ed of the 5' portion of attP_site and th *** --- *** e 3' portion of attB_site. *** --- ************************************************ --- CREATE VIEW attr_site AS SELECT feature_id AS attr_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attR_site'; --- ************************************************ --- *** relation: integration_excision_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inserts or removes anot *** --- *** her region marked by a distinct cognate *** --- *** integration/excision site. *** --- ************************************************ --- CREATE VIEW integration_excision_site AS SELECT feature_id AS integration_excision_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'integration_excision_site'; --- ************************************************ --- *** relation: resolution_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which separates a physically *** --- *** contiguous circle of DNA into two physic *** --- *** ally separate circles. *** --- ************************************************ --- CREATE VIEW resolution_site AS SELECT feature_id AS resolution_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'resolution_site'; --- ************************************************ --- *** relation: inversion_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region specifically recognised by a re *** --- *** combinase, which inverts the region flan *** --- *** ked by a pair of sites. *** --- ************************************************ --- CREATE VIEW inversion_site AS SELECT feature_id AS inversion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'FRT_site' OR cvterm.name = 'inversion_site'; --- ************************************************ --- *** relation: dif_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site at which replicated bacterial cir *** --- *** cular chromosomes are decatenated by sit *** --- *** e specific resolvase. *** --- ************************************************ --- CREATE VIEW dif_site AS SELECT feature_id AS dif_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dif_site'; --- ************************************************ --- *** relation: attc_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attC site is a sequence required for *** --- *** the integration of a DNA of an integron. *** --- ************************************************ --- CREATE VIEW attc_site AS SELECT feature_id AS attc_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attC_site'; --- ************************************************ --- *** relation: eukaryotic_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW eukaryotic_terminator AS SELECT feature_id AS eukaryotic_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'eukaryotic_terminator'; --- ************************************************ --- *** relation: oriv *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of vegetative replication in p *** --- *** lasmids and phages. *** --- ************************************************ --- CREATE VIEW oriv AS SELECT feature_id AS oriv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriV'; --- ************************************************ --- *** relation: oric *** --- *** relation type: VIEW *** --- *** *** --- *** An origin of bacterial chromosome replic *** --- *** ation. *** --- ************************************************ --- CREATE VIEW oric AS SELECT feature_id AS oric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oriC'; --- ************************************************ --- *** relation: dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, DNA molecule. *** --- ************************************************ --- CREATE VIEW dna_chromosome AS SELECT feature_id AS dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'DNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_dna_chromosome AS SELECT feature_id AS double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded DNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_dna_chromosome AS SELECT feature_id AS single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_dna_chromosome AS SELECT feature_id AS linear_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_dna_chromosome AS SELECT feature_id AS circular_double_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear DNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_dna_chromosome AS SELECT feature_id AS linear_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_dna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_dna_chromosome AS SELECT feature_id AS circular_single_stranded_dna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_DNA_chromosome'; --- ************************************************ --- *** relation: rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, RNA molecule. *** --- ************************************************ --- CREATE VIEW rna_chromosome AS SELECT feature_id AS rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome'; --- ************************************************ --- *** relation: single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW single_stranded_rna_chromosome AS SELECT feature_id AS single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_single_stranded_rna_chromosome AS SELECT feature_id AS linear_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: linear_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, linear RNA mole *** --- *** cule. *** --- ************************************************ --- CREATE VIEW linear_double_stranded_rna_chromosome AS SELECT feature_id AS linear_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded RNA molecule. *** --- ************************************************ --- CREATE VIEW double_stranded_rna_chromosome AS SELECT feature_id AS double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_single_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, single-stranded, circular DNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_single_stranded_rna_chromosome AS SELECT feature_id AS circular_single_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: circular_double_stranded_rna_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of a self-repli *** --- *** cating, double-stranded, circular RNA mo *** --- *** lecule. *** --- ************************************************ --- CREATE VIEW circular_double_stranded_rna_chromosome AS SELECT feature_id AS circular_double_stranded_rna_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome'; --- ************************************************ --- *** relation: insertion_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal_inverted_repeat_element that *** --- *** is bacterial and only encodes the functi *** --- *** ons required for its transposition betwe *** --- *** en these inverted repeats. *** --- ************************************************ --- CREATE VIEW insertion_sequence AS SELECT feature_id AS insertion_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_sequence'; --- ************************************************ --- *** relation: minicircle_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minicircle_gene AS SELECT feature_id AS minicircle_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle_gene'; --- ************************************************ --- *** relation: cryptic *** --- *** relation type: VIEW *** --- *** *** --- *** A feature_attribute describing a feature *** --- *** that is not manifest under normal condi *** --- *** tions. *** --- ************************************************ --- CREATE VIEW cryptic AS SELECT feature_id AS cryptic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic'; --- ************************************************ --- *** relation: anchor_binding_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW anchor_binding_site AS SELECT feature_id AS anchor_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anchor_binding_site'; --- ************************************************ --- *** relation: template_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a guide_RNA that specifies t *** --- *** he insertions and deletions of bases in *** --- *** the editing of a target mRNA. *** --- ************************************************ --- CREATE VIEW template_region AS SELECT feature_id AS template_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'template_region'; --- ************************************************ --- *** relation: grna_encoding *** --- *** relation type: VIEW *** --- *** *** --- *** A non-protein_coding gene that encodes a *** --- *** guide_RNA. *** --- ************************************************ --- CREATE VIEW grna_encoding AS SELECT feature_id AS grna_encoding_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_encoding'; --- ************************************************ --- *** relation: minicircle *** --- *** relation type: VIEW *** --- *** *** --- *** A minicircle is a replicon, part of a ki *** --- *** netoplast, that encodes for guide RNAs. *** --- ************************************************ --- CREATE VIEW minicircle AS SELECT feature_id AS minicircle_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minicircle'; --- ************************************************ --- *** relation: rho_dependent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_dependent_bacterial_terminator AS SELECT feature_id AS rho_dependent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_dependent_bacterial_terminator'; --- ************************************************ --- *** relation: rho_independent_bacterial_terminator *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rho_independent_bacterial_terminator AS SELECT feature_id AS rho_independent_bacterial_terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rho_independent_bacterial_terminator'; --- ************************************************ --- *** relation: strand_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strand_attribute AS SELECT feature_id AS strand_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute'; --- ************************************************ --- *** relation: single *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW single AS SELECT feature_id AS single_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'single'; --- ************************************************ --- *** relation: double *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW double AS SELECT feature_id AS double_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'double'; --- ************************************************ --- *** relation: topology_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW topology_attribute AS SELECT feature_id AS topology_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute'; --- ************************************************ --- *** relation: linear *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as a 3'-terminal residue and a 5'-termin *** --- *** al residue. *** --- ************************************************ --- CREATE VIEW linear AS SELECT feature_id AS linear_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'linear'; --- ************************************************ --- *** relation: circular *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a nucleotide polymer that h *** --- *** as no terminal nucleotide residues. *** --- ************************************************ --- CREATE VIEW circular AS SELECT feature_id AS circular_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'circular'; --- ************************************************ --- *** relation: class_ii_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (59-60 nt long) con *** --- *** taining 5' and 3' ends that are predicte *** --- *** d to come together to form a stem struct *** --- *** ure. Identified in the social amoeba Dic *** --- *** tyostelium discoideum and localized in t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW class_ii_rna AS SELECT feature_id AS class_ii_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_II_RNA'; --- ************************************************ --- *** relation: class_i_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA (55-65 nt long) con *** --- *** taining highly conserved 5' and 3' ends *** --- *** (16 and 8 nt, respectively) that are pre *** --- *** dicted to come together to form a stem s *** --- *** tructure. Identified in the social amoeb *** --- *** a Dictyostelium discoideum and localized *** --- *** in the cytoplasm. *** --- ************************************************ --- CREATE VIEW class_i_rna AS SELECT feature_id AS class_i_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'class_I_RNA'; --- ************************************************ --- *** relation: genomic_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW genomic_dna AS SELECT feature_id AS genomic_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genomic_DNA'; --- ************************************************ --- *** relation: bac_cloned_genomic_insert *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bac_cloned_genomic_insert AS SELECT feature_id AS bac_cloned_genomic_insert_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_cloned_genomic_insert'; --- ************************************************ --- *** relation: consensus *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus AS SELECT feature_id AS consensus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus'; --- ************************************************ --- *** relation: consensus_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_region AS SELECT feature_id AS consensus_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region'; --- ************************************************ --- *** relation: consensus_mrna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW consensus_mrna AS SELECT feature_id AS consensus_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'consensus_mRNA'; --- ************************************************ --- *** relation: predicted_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW predicted_gene AS SELECT feature_id AS predicted_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'predicted_gene'; --- ************************************************ --- *** relation: gene_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_fragment AS SELECT feature_id AS gene_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fragment'; --- ************************************************ --- *** relation: recursive_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A recursive splice site is a splice site *** --- *** which subdivides a large intron. Recurs *** --- *** ive splicing is a mechanism that splices *** --- *** large introns by sub dividing the intro *** --- *** n at non exonic elements and alternate e *** --- *** xons. *** --- ************************************************ --- CREATE VIEW recursive_splice_site AS SELECT feature_id AS recursive_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recursive_splice_site'; --- ************************************************ --- *** relation: bac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a B *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW bac_end AS SELECT feature_id AS bac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC_end'; --- ************************************************ --- *** relation: rrna_16s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the small sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_16s AS SELECT feature_id AS rrna_16s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_16S'; --- ************************************************ --- *** relation: rrna_23s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide in Bacteria and A *** --- *** rchaea, which functions as the large sub *** --- *** unit of the ribosome. *** --- ************************************************ --- CREATE VIEW rrna_23s AS SELECT feature_id AS rrna_23s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_23S'; --- ************************************************ --- *** relation: rrna_25s *** --- *** relation type: VIEW *** --- *** *** --- *** A large polynucleotide which functions a *** --- *** s part of the large subunit of the ribos *** --- *** ome in some eukaryotes. *** --- ************************************************ --- CREATE VIEW rrna_25s AS SELECT feature_id AS rrna_25s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_25S'; --- ************************************************ --- *** relation: solo_ltr *** --- *** relation type: VIEW *** --- *** *** --- *** A recombination product between the 2 LT *** --- *** R of the same element. *** --- ************************************************ --- CREATE VIEW solo_ltr AS SELECT feature_id AS solo_ltr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'solo_LTR'; --- ************************************************ --- *** relation: low_complexity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity AS SELECT feature_id AS low_complexity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity'; --- ************************************************ --- *** relation: low_complexity_region *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW low_complexity_region AS SELECT feature_id AS low_complexity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'low_complexity_region'; --- ************************************************ --- *** relation: prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A phage genome after it has established *** --- *** in the host genome in a latent/immune st *** --- *** ate either as a plasmid or as an integra *** --- *** ted "island". *** --- ************************************************ --- CREATE VIEW prophage AS SELECT feature_id AS prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'prophage'; --- ************************************************ --- *** relation: cryptic_prophage *** --- *** relation type: VIEW *** --- *** *** --- *** A remnant of an integrated prophage in t *** --- *** he host genome or an "island" in the hos *** --- *** t genome that includes phage like-genes. *** --- ************************************************ --- CREATE VIEW cryptic_prophage AS SELECT feature_id AS cryptic_prophage_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_prophage'; --- ************************************************ --- *** relation: tetraloop *** --- *** relation type: VIEW *** --- *** *** --- *** A base-paired stem with loop of 4 non-hy *** --- *** drogen bonded nucleotides. *** --- ************************************************ --- CREATE VIEW tetraloop AS SELECT feature_id AS tetraloop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tetraloop'; --- ************************************************ --- *** relation: dna_constraint_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A double-stranded DNA used to control ma *** --- *** cromolecular structure and function. *** --- ************************************************ --- CREATE VIEW dna_constraint_sequence AS SELECT feature_id AS dna_constraint_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNA_constraint_sequence'; --- ************************************************ --- *** relation: i_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A cytosine rich domain whereby strands a *** --- *** ssociate both inter- and intramolecularl *** --- *** y at moderately acidic pH. *** --- ************************************************ --- CREATE VIEW i_motif AS SELECT feature_id AS i_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'i_motif'; --- ************************************************ --- *** relation: pna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** Peptide nucleic acid, is a chemical not *** --- *** known to occur naturally but is artifici *** --- *** ally synthesized and used in some biolog *** --- *** ical research and medical treatments. Th *** --- *** e PNA backbone is composed of repeating *** --- *** N-(2-aminoethyl)-glycine units linked by *** --- *** peptide bonds. The purine and pyrimidin *** --- *** e bases are linked to the backbone by me *** --- *** thylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna_oligo AS SELECT feature_id AS pna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA_oligo'; --- ************************************************ --- *** relation: dnazyme *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence with catalytic activity. *** --- ************************************************ --- CREATE VIEW dnazyme AS SELECT feature_id AS dnazyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DNAzyme'; --- ************************************************ --- *** relation: mnp *** --- *** relation type: VIEW *** --- *** *** --- *** A multiple nucleotide polymorphism with *** --- *** alleles of common length > 1, for exampl *** --- *** e AAA/TTT. *** --- ************************************************ --- CREATE VIEW mnp AS SELECT feature_id AS mnp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MNP'; --- ************************************************ --- *** relation: intron_domain *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intron_domain AS SELECT feature_id AS intron_domain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain'; --- ************************************************ --- *** relation: wobble_base_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A type of non-canonical base pairing, mo *** --- *** st commonly between G and U, which is im *** --- *** portant for the secondary structure of R *** --- *** NAs. It has similar thermodynamic stabil *** --- *** ity to the Watson-Crick pairing. Wobble *** --- *** base pairs only have two hydrogen bonds. *** --- *** Other wobble base pair possibilities ar *** --- *** e I-A, I-U and I-C. *** --- ************************************************ --- CREATE VIEW wobble_base_pair AS SELECT feature_id AS wobble_base_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wobble_base_pair'; --- ************************************************ --- *** relation: internal_guide_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A purine-rich sequence in the group I in *** --- *** trons which determines the locations of *** --- *** the splice sites in group I intron splic *** --- *** ing and has catalytic activity. *** --- ************************************************ --- CREATE VIEW internal_guide_sequence AS SELECT feature_id AS internal_guide_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_guide_sequence'; --- ************************************************ --- *** relation: silent_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that does not affect *** --- *** protein function. Silent mutations may o *** --- *** ccur in genic ( CDS, UTR, intron etc) an *** --- *** d intergenic regions. Silent mutations m *** --- *** ay have affects on processes such as spl *** --- *** icing and regulation. *** --- ************************************************ --- CREATE VIEW silent_mutation AS SELECT feature_id AS silent_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation'; --- ************************************************ --- *** relation: epitope *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith antibodies, B cells or T cells. *** --- ************************************************ --- CREATE VIEW epitope AS SELECT feature_id AS epitope_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epitope'; --- ************************************************ --- *** relation: copy_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A variation that increases or decreases *** --- *** the copy number of a given region. *** --- ************************************************ --- CREATE VIEW copy_number_variation AS SELECT feature_id AS copy_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'copy_number_variation'; --- ************************************************ --- *** relation: chromosome_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_breakpoint AS SELECT feature_id AS chromosome_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint'; --- ************************************************ --- *** relation: inversion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where an i *** --- *** nversion begins or ends. *** --- ************************************************ --- CREATE VIEW inversion_breakpoint AS SELECT feature_id AS inversion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_breakpoint'; --- ************************************************ --- *** relation: allele *** --- *** relation type: VIEW *** --- *** *** --- *** An allele is one of a set of coexisting *** --- *** sequence variants of a gene. *** --- ************************************************ --- CREATE VIEW allele AS SELECT feature_id AS allele_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'allele'; --- ************************************************ --- *** relation: haplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A haplotype is one of a set of coexistin *** --- *** g sequence variants of a haplotype block *** --- *** . *** --- ************************************************ --- CREATE VIEW haplotype AS SELECT feature_id AS haplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'haplotype'; --- ************************************************ --- *** relation: polymorphic_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that is segregating i *** --- *** n one or more natural populations of a s *** --- *** pecies. *** --- ************************************************ --- CREATE VIEW polymorphic_sequence_variant AS SELECT feature_id AS polymorphic_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_sequence_variant'; --- ************************************************ --- *** relation: genome *** --- *** relation type: VIEW *** --- *** *** --- *** A genome is the sum of genetic material *** --- *** within a cell or virion. *** --- ************************************************ --- CREATE VIEW genome AS SELECT feature_id AS genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'genome'; --- ************************************************ --- *** relation: so_genotype *** --- *** relation type: VIEW *** --- *** *** --- *** A genotype is a variant genome, complete *** --- *** or incomplete. *** --- ************************************************ --- CREATE VIEW so_genotype AS SELECT feature_id AS so_genotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'genotype'; --- ************************************************ --- *** relation: diplotype *** --- *** relation type: VIEW *** --- *** *** --- *** A diplotype is a pair of haplotypes from *** --- *** a given individual. It is a genotype wh *** --- *** ere the phase is known. *** --- ************************************************ --- CREATE VIEW diplotype AS SELECT feature_id AS diplotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'diplotype'; --- ************************************************ --- *** relation: direction_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW direction_attribute AS SELECT feature_id AS direction_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward' OR cvterm.name = 'reverse' OR cvterm.name = 'direction_attribute'; --- ************************************************ --- *** relation: forward *** --- *** relation type: VIEW *** --- *** *** --- *** Forward is an attribute of the feature, *** --- *** where the feature is in the 5' to 3' dir *** --- *** ection. *** --- ************************************************ --- CREATE VIEW forward AS SELECT feature_id AS forward_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'forward'; --- ************************************************ --- *** relation: reverse *** --- *** relation type: VIEW *** --- *** *** --- *** Reverse is an attribute of the feature, *** --- *** where the feature is in the 3' to 5' dir *** --- *** ection. Again could be applied to primer *** --- *** . *** --- ************************************************ --- CREATE VIEW reverse AS SELECT feature_id AS reverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reverse'; --- ************************************************ --- *** relation: mitochondrial_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mitochondrial_dna AS SELECT feature_id AS mitochondrial_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mitochondrial_DNA'; --- ************************************************ --- *** relation: chloroplast_dna *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chloroplast_dna AS SELECT feature_id AS chloroplast_dna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chloroplast_DNA'; --- ************************************************ --- *** relation: mirtron *** --- *** relation type: VIEW *** --- *** *** --- *** A de-branched intron which mimics the st *** --- *** ructure of pre-miRNA and enters the miRN *** --- *** A processing pathway without Drosha medi *** --- *** ated cleavage. *** --- ************************************************ --- CREATE VIEW mirtron AS SELECT feature_id AS mirtron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mirtron'; --- ************************************************ --- *** relation: pirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small non coding RNA, part of a silenc *** --- *** ing system that prevents the spreading o *** --- *** f selfish genetic elements. *** --- ************************************************ --- CREATE VIEW pirna AS SELECT feature_id AS pirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA'; --- ************************************************ --- *** relation: arginyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has an arginine ant *** --- *** icodon, and a 3' arginine binding region *** --- *** . *** --- ************************************************ --- CREATE VIEW arginyl_trna AS SELECT feature_id AS arginyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginyl_tRNA'; --- ************************************************ --- *** relation: mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide region with either intra-ge *** --- *** nome or intracellular moblity, of varyin *** --- *** g length, which often carry the informat *** --- *** ion necessary for transfer and recombina *** --- *** tion with the host genome. *** --- ************************************************ --- CREATE VIEW mobile_genetic_element AS SELECT feature_id AS mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'mobile_genetic_element'; --- ************************************************ --- *** relation: extrachromosomal_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is not integrated into the h *** --- *** ost chromosome. *** --- ************************************************ --- CREATE VIEW extrachromosomal_mobile_genetic_element AS SELECT feature_id AS extrachromosomal_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'extrachromosomal_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_mobile_genetic_element *** --- *** relation type: VIEW *** --- *** *** --- *** An MGE that is integrated into the host *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW integrated_mobile_genetic_element AS SELECT feature_id AS integrated_mobile_genetic_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'integrated_mobile_genetic_element'; --- ************************************************ --- *** relation: integrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid sequence that is integrated wi *** --- *** thin the host chromosome. *** --- ************************************************ --- CREATE VIEW integrated_plasmid AS SELECT feature_id AS integrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_plasmid'; --- ************************************************ --- *** relation: viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The region of nucleotide sequence of a v *** --- *** irus, a submicroscopic particle that rep *** --- *** licates by infecting a host cell. *** --- ************************************************ --- CREATE VIEW viral_sequence AS SELECT feature_id AS viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'viral_sequence'; --- ************************************************ --- *** relation: phage_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide sequence of a virus that *** --- *** infects bacteria. *** --- ************************************************ --- CREATE VIEW phage_sequence AS SELECT feature_id AS phage_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phage_sequence'; --- ************************************************ --- *** relation: attctn_site *** --- *** relation type: VIEW *** --- *** *** --- *** An attachment site located on a conjugat *** --- *** ive transposon and used for site-specifi *** --- *** c integration of a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW attctn_site AS SELECT feature_id AS attctn_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attCtn_site'; --- ************************************************ --- *** relation: nuclear_mt_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A nuclear pseudogene of either coding or *** --- *** non-coding mitochondria derived sequenc *** --- *** e. *** --- ************************************************ --- CREATE VIEW nuclear_mt_pseudogene AS SELECT feature_id AS nuclear_mt_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_mt_pseudogene'; --- ************************************************ --- *** relation: cointegrated_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A MGE region consisting of two fused pla *** --- *** smids resulting from a replicative trans *** --- *** position event. *** --- ************************************************ --- CREATE VIEW cointegrated_plasmid AS SELECT feature_id AS cointegrated_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cointegrated_plasmid'; --- ************************************************ --- *** relation: irlinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the left of a region susceptible to s *** --- *** ite-specific inversion. *** --- ************************************************ --- CREATE VIEW irlinv_site AS SELECT feature_id AS irlinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site'; --- ************************************************ --- *** relation: irrinv_site *** --- *** relation type: VIEW *** --- *** *** --- *** Component of the inversion site located *** --- *** at the right of a region susceptible to *** --- *** site-specific inversion. *** --- ************************************************ --- CREATE VIEW irrinv_site AS SELECT feature_id AS irrinv_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRRinv_site'; --- ************************************************ --- *** relation: inversion_site_part *** --- *** relation type: VIEW *** --- *** *** --- *** A region located within an inversion sit *** --- *** e. *** --- ************************************************ --- CREATE VIEW inversion_site_part AS SELECT feature_id AS inversion_site_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'inversion_site_part'; --- ************************************************ --- *** relation: defective_conjugative_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** An island that contains genes for integr *** --- *** ation/excision and the gene and site for *** --- *** the initiation of intercellular transfe *** --- *** r by conjugation. It can be complemented *** --- *** for transfer by a conjugative transposo *** --- *** n. *** --- ************************************************ --- CREATE VIEW defective_conjugative_transposon AS SELECT feature_id AS defective_conjugative_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'defective_conjugative_transposon'; --- ************************************************ --- *** relation: repeat_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a repeat, interrupted by th *** --- *** e insertion of another element. *** --- ************************************************ --- CREATE VIEW repeat_fragment AS SELECT feature_id AS repeat_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_fragment'; --- ************************************************ --- *** relation: transposon_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A portion of a transposon, interrupted b *** --- *** y the insertion of another element. *** --- ************************************************ --- CREATE VIEW transposon_fragment AS SELECT feature_id AS transposon_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposon_fragment'; --- ************************************************ --- *** relation: transcriptional_cis_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates the t *** --- *** ranscription of a gene or genes. *** --- ************************************************ --- CREATE VIEW transcriptional_cis_regulatory_region AS SELECT feature_id AS transcriptional_cis_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'transcriptional_cis_regulatory_region'; --- ************************************************ --- *** relation: splicing_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory_region that modulates splic *** --- *** ing. *** --- ************************************************ --- CREATE VIEW splicing_regulatory_region AS SELECT feature_id AS splicing_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'splicing_regulatory_region'; --- ************************************************ --- *** relation: promoter_targeting_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A transcriptional_cis_regulatory_region *** --- *** that restricts the activity of a CRM to *** --- *** a single promoter and which functions on *** --- *** ly when both itself and an insulator are *** --- *** located between the CRM and the promote *** --- *** r. *** --- ************************************************ --- CREATE VIEW promoter_targeting_sequence AS SELECT feature_id AS promoter_targeting_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_targeting_sequence'; --- ************************************************ --- *** relation: sequence_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_alteration is a sequence_feat *** --- *** ure whose extent is the deviation from a *** --- *** nother sequence. *** --- ************************************************ --- CREATE VIEW sequence_alteration AS SELECT feature_id AS sequence_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion' OR cvterm.name = 'translocation' OR cvterm.name = 'insertion' OR cvterm.name = 'copy_number_variation' OR cvterm.name = 'UPD' OR cvterm.name = 'structural_alteration' OR cvterm.name = 'substitution' OR cvterm.name = 'indel' OR cvterm.name = 'inversion' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'sequence_alteration'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence_variant is a non exact copy o *** --- *** f a sequence_feature or genome exhibitin *** --- *** g one or more sequence_alteration. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'functional_variant' OR cvterm.name = 'structural_variant' OR cvterm.name = 'loss_of_heterozygosity' OR cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: propeptide_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** The propeptide_cleavage_site is the argi *** --- *** nine/lysine boundary on a propeptide whe *** --- *** re cleavage occurs. *** --- ************************************************ --- CREATE VIEW propeptide_cleavage_site AS SELECT feature_id AS propeptide_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide_cleavage_site'; --- ************************************************ --- *** relation: propeptide *** --- *** relation type: VIEW *** --- *** *** --- *** Part of a peptide chain which is cleaved *** --- *** off during the formation of the mature *** --- *** protein. *** --- ************************************************ --- CREATE VIEW propeptide AS SELECT feature_id AS propeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'propeptide'; --- ************************************************ --- *** relation: immature_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** An immature_peptide_region is the extent *** --- *** of the peptide after it has been transl *** --- *** ated and before any processing occurs. *** --- ************************************************ --- CREATE VIEW immature_peptide_region AS SELECT feature_id AS immature_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'immature_peptide_region'; --- ************************************************ --- *** relation: active_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Active peptides are proteins which are b *** --- *** iologically active, released from a prec *** --- *** ursor molecule. *** --- ************************************************ --- CREATE VIEW active_peptide AS SELECT feature_id AS active_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'active_peptide'; --- ************************************************ --- *** relation: compositionally_biased_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is rich in a par *** --- *** ticular amino acid or homopolymeric and *** --- *** greater than three residues in length. *** --- ************************************************ --- CREATE VIEW compositionally_biased_region_of_peptide AS SELECT feature_id AS compositionally_biased_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compositionally_biased_region_of_peptide'; --- ************************************************ --- *** relation: polypeptide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a short (up to 20 am *** --- *** ino acids) region of biological interest *** --- *** . Such motifs, although they are too sho *** --- *** rt to constitute functional domains, sha *** --- *** re sequence similarities and are conserv *** --- *** ed in different proteins. They display a *** --- *** common function (protein-binding, subce *** --- *** llular location etc.). *** --- ************************************************ --- CREATE VIEW polypeptide_motif AS SELECT feature_id AS polypeptide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_motif'; --- ************************************************ --- *** relation: polypeptide_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide_repeat is a single copy of *** --- *** an internal sequence repetition. *** --- ************************************************ --- CREATE VIEW polypeptide_repeat AS SELECT feature_id AS polypeptide_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_repeat'; --- ************************************************ --- *** relation: polypeptide_structural_region *** --- *** relation type: VIEW *** --- *** *** --- *** Region of polypeptide with a given struc *** --- *** tural property. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_region AS SELECT feature_id AS polypeptide_structural_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_region'; --- ************************************************ --- *** relation: membrane_structure *** --- *** relation type: VIEW *** --- *** *** --- *** Arrangement of the polypeptide with resp *** --- *** ect to the lipid bilayer. *** --- ************************************************ --- CREATE VIEW membrane_structure AS SELECT feature_id AS membrane_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_structure'; --- ************************************************ --- *** relation: extramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer. *** --- ************************************************ --- CREATE VIEW extramembrane_polypeptide_region AS SELECT feature_id AS extramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'extramembrane_polypeptide_region'; --- ************************************************ --- *** relation: cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized ins *** --- *** ide the cytoplasm. *** --- ************************************************ --- CREATE VIEW cytoplasmic_polypeptide_region AS SELECT feature_id AS cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: non_cytoplasmic_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region that is localized out *** --- *** side of a lipid bilayer and outside of t *** --- *** he cytoplasm. *** --- ************************************************ --- CREATE VIEW non_cytoplasmic_polypeptide_region AS SELECT feature_id AS non_cytoplasmic_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_cytoplasmic_polypeptide_region'; --- ************************************************ --- *** relation: intramembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region present in the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW intramembrane_polypeptide_region AS SELECT feature_id AS intramembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region'; --- ************************************************ --- *** relation: membrane_peptide_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region localized within the *** --- *** lipid bilayer where both ends traverse t *** --- *** he same membrane. *** --- ************************************************ --- CREATE VIEW membrane_peptide_loop AS SELECT feature_id AS membrane_peptide_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'membrane_peptide_loop'; --- ************************************************ --- *** relation: transmembrane_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** Polypeptide region traversing the lipid *** --- *** bilayer. *** --- ************************************************ --- CREATE VIEW transmembrane_polypeptide_region AS SELECT feature_id AS transmembrane_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transmembrane_polypeptide_region'; --- ************************************************ --- *** relation: polypeptide_secondary_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide with secondary struc *** --- *** ture has hydrogen bonding along the pept *** --- *** ide chain that causes a defined conforma *** --- *** tion of the chain. *** --- ************************************************ --- CREATE VIEW polypeptide_secondary_structure AS SELECT feature_id AS polypeptide_secondary_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_secondary_structure'; --- ************************************************ --- *** relation: polypeptide_structural_motif *** --- *** relation type: VIEW *** --- *** *** --- *** Motif is a three-dimensional structural *** --- *** element within the chain, which appears *** --- *** also in a variety of other molecules. Un *** --- *** like a domain, a motif does not need to *** --- *** form a stable globular unit. *** --- ************************************************ --- CREATE VIEW polypeptide_structural_motif AS SELECT feature_id AS polypeptide_structural_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'polypeptide_structural_motif'; --- ************************************************ --- *** relation: coiled_coil *** --- *** relation type: VIEW *** --- *** *** --- *** A coiled coil is a structural motif in p *** --- *** roteins, in which alpha-helices are coil *** --- *** ed together like the strands of a rope. *** --- ************************************************ --- CREATE VIEW coiled_coil AS SELECT feature_id AS coiled_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coiled_coil'; --- ************************************************ --- *** relation: helix_turn_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A motif comprising two helices separated *** --- *** by a turn. *** --- ************************************************ --- CREATE VIEW helix_turn_helix AS SELECT feature_id AS helix_turn_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'helix_turn_helix'; --- ************************************************ --- *** relation: polypeptide_sequencing_information *** --- *** relation type: VIEW *** --- *** *** --- *** Incompatibility in the sequence due to s *** --- *** ome experimental problem. *** --- ************************************************ --- CREATE VIEW polypeptide_sequencing_information AS SELECT feature_id AS polypeptide_sequencing_information_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'polypeptide_sequencing_information'; --- ************************************************ --- *** relation: non_adjacent_residues *** --- *** relation type: VIEW *** --- *** *** --- *** Indicates that two consecutive residues *** --- *** in a fragment sequence are not consecuti *** --- *** ve in the full-length protein and that t *** --- *** here are a number of unsequenced residue *** --- *** s between them. *** --- ************************************************ --- CREATE VIEW non_adjacent_residues AS SELECT feature_id AS non_adjacent_residues_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_adjacent_residues'; --- ************************************************ --- *** relation: non_terminal_residue *** --- *** relation type: VIEW *** --- *** *** --- *** The residue at an extremity of the seque *** --- *** nce is not the terminal residue. *** --- ************************************************ --- CREATE VIEW non_terminal_residue AS SELECT feature_id AS non_terminal_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_terminal_residue'; --- ************************************************ --- *** relation: sequence_conflict *** --- *** relation type: VIEW *** --- *** *** --- *** Different sources report differing seque *** --- *** nces. *** --- ************************************************ --- CREATE VIEW sequence_conflict AS SELECT feature_id AS sequence_conflict_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection' OR cvterm.name = 'sequence_conflict'; --- ************************************************ --- *** relation: sequence_uncertainty *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the positions in a sequence wh *** --- *** ere the authors are unsure about the seq *** --- *** uence assignment. *** --- ************************************************ --- CREATE VIEW sequence_uncertainty AS SELECT feature_id AS sequence_uncertainty_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_uncertainty'; --- ************************************************ --- *** relation: post_translationally_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region where a transformation occurs i *** --- *** n a protein after it has been synthesize *** --- *** d. This which may regulate, stabilize, c *** --- *** rosslink or introduce new chemical funct *** --- *** ionalities in the protein. *** --- ************************************************ --- CREATE VIEW post_translationally_modified_region AS SELECT feature_id AS post_translationally_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'post_translationally_modified_region'; --- ************************************************ --- *** relation: polypeptide_metal_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with metal ions. *** --- ************************************************ --- CREATE VIEW polypeptide_metal_contact AS SELECT feature_id AS polypeptide_metal_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_metal_contact'; --- ************************************************ --- *** relation: protein_protein_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the protein mole *** --- *** cule, interacts selectively and non-cova *** --- *** lently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW protein_protein_contact AS SELECT feature_id AS protein_protein_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_protein_contact'; --- ************************************************ --- *** relation: polypeptide_calcium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with calcium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_calcium_ion_contact_site AS SELECT feature_id AS polypeptide_calcium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_calcium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_cobalt_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with cobalt ions. *** --- ************************************************ --- CREATE VIEW polypeptide_cobalt_ion_contact_site AS SELECT feature_id AS polypeptide_cobalt_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_cobalt_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_copper_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with copper ions. *** --- ************************************************ --- CREATE VIEW polypeptide_copper_ion_contact_site AS SELECT feature_id AS polypeptide_copper_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_copper_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_iron_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with iron ions. *** --- ************************************************ --- CREATE VIEW polypeptide_iron_ion_contact_site AS SELECT feature_id AS polypeptide_iron_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_iron_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_magnesium_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with magnesium ions. *** --- ************************************************ --- CREATE VIEW polypeptide_magnesium_ion_contact_site AS SELECT feature_id AS polypeptide_magnesium_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_magnesium_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_manganese_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with manganese ions. *** --- ************************************************ --- CREATE VIEW polypeptide_manganese_ion_contact_site AS SELECT feature_id AS polypeptide_manganese_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_manganese_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_molybdenum_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with molybdenum ions. *** --- ************************************************ --- CREATE VIEW polypeptide_molybdenum_ion_contact_site AS SELECT feature_id AS polypeptide_molybdenum_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_molybdenum_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_nickel_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with nickel ions. *** --- ************************************************ --- CREATE VIEW polypeptide_nickel_ion_contact_site AS SELECT feature_id AS polypeptide_nickel_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nickel_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_tungsten_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with tungsten ions. *** --- ************************************************ --- CREATE VIEW polypeptide_tungsten_ion_contact_site AS SELECT feature_id AS polypeptide_tungsten_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_tungsten_ion_contact_site'; --- ************************************************ --- *** relation: polypeptide_zinc_ion_contact_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with zinc ions. *** --- ************************************************ --- CREATE VIEW polypeptide_zinc_ion_contact_site AS SELECT feature_id AS polypeptide_zinc_ion_contact_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_zinc_ion_contact_site'; --- ************************************************ --- *** relation: catalytic_residue *** --- *** relation type: VIEW *** --- *** *** --- *** Amino acid involved in the activity of a *** --- *** n enzyme. *** --- ************************************************ --- CREATE VIEW catalytic_residue AS SELECT feature_id AS catalytic_residue_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue'; --- ************************************************ --- *** relation: polypeptide_ligand_contact *** --- *** relation type: VIEW *** --- *** *** --- *** Residues which interact with a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_ligand_contact AS SELECT feature_id AS polypeptide_ligand_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact'; --- ************************************************ --- *** relation: asx_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: Residue(i) is Asp *** --- *** artate or Asparagine (Asx), side-chain O *** --- *** of residue(i) is H-bonded to the main-c *** --- *** hain NH of residue(i+2) or (i+3), main-c *** --- *** hain CO of residue(i) is H-bonded to the *** --- *** main-chain NH of residue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW asx_motif AS SELECT feature_id AS asx_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_motif'; --- ************************************************ --- *** relation: beta_bulge *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet in which the main chains of two co *** --- *** nsecutive residues are H-bonded to that *** --- *** of the third, and in which the dihedral *** --- *** angles are as follows: Residue(i): -140 *** --- *** degrees < phi(l) -20 degrees , -90 degre *** --- *** es < psi(l) < 40 degrees. Residue (i+1): *** --- *** -180 degrees < phi < -25 degrees or +12 *** --- *** 0 degrees < phi < +180 degrees, +40 degr *** --- *** ees < psi < +180 degrees or -180 degrees *** --- *** < psi < -120 degrees. *** --- ************************************************ --- CREATE VIEW beta_bulge AS SELECT feature_id AS beta_bulge_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge'; --- ************************************************ --- *** relation: beta_bulge_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds. Beta bu *** --- *** lge loops often occur at the loop ends o *** --- *** f beta-hairpins. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop AS SELECT feature_id AS beta_bulge_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'beta_bulge_loop'; --- ************************************************ --- *** relation: beta_bulge_loop_five *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 4), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +3), these loops have an RL nest at resi *** --- *** dues i+2 and i+3. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_five AS SELECT feature_id AS beta_bulge_loop_five_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_five'; --- ************************************************ --- *** relation: beta_bulge_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three residues within a beta- *** --- *** sheet consisting of two H-bonds in which *** --- *** : the main-chain NH of residue(i) is H-b *** --- *** onded to the main-chain CO of residue(i+ *** --- *** 5), the main-chain CO of residue i is H- *** --- *** bonded to the main-chain NH of residue(i *** --- *** +4), these loops have an RL nest at resi *** --- *** dues i+3 and i+4. *** --- ************************************************ --- CREATE VIEW beta_bulge_loop_six AS SELECT feature_id AS beta_bulge_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_bulge_loop_six'; --- ************************************************ --- *** relation: beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A beta strand describes a single length *** --- *** of polypeptide chain that forms part of *** --- *** a beta sheet. A single continuous stretc *** --- *** h of amino acids adopting an extended co *** --- *** nformation of hydrogen bonds between the *** --- *** N-O and the C=O of another part of the *** --- *** peptide. This forms a secondary protein *** --- *** structure in which two or more extended *** --- *** polypeptide regions are hydrogen-bonded *** --- *** to one another in a planar array. *** --- ************************************************ --- CREATE VIEW beta_strand AS SELECT feature_id AS beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'beta_strand'; --- ************************************************ --- *** relation: antiparallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (one running N-term *** --- *** inal to C-terminal and one running C-ter *** --- *** minal to N-terminal). Hydrogen bonding o *** --- *** ccurs between every other C=O from one s *** --- *** trand to every other N-H on the adjacent *** --- *** strand. In this case, if two atoms C-al *** --- *** pha (i) and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then t *** --- *** hey form two mutual backbone hydrogen bo *** --- *** nds to each other's flanking peptide gro *** --- *** ups; this is known as a close pair of hy *** --- *** drogen bonds. The peptide backbone dihed *** --- *** ral angles (phi, psi) are about (-140 de *** --- *** grees, 135 degrees) in antiparallel shee *** --- *** ts. *** --- ************************************************ --- CREATE VIEW antiparallel_beta_strand AS SELECT feature_id AS antiparallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antiparallel_beta_strand'; --- ************************************************ --- *** relation: parallel_beta_strand *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide region which hydrogen bonded t *** --- *** o another region of peptide running in t *** --- *** he oposite direction (both running N-ter *** --- *** minal to C-terminal). This orientation i *** --- *** s slightly less stable because it introd *** --- *** uces nonplanarity in the inter-strand hy *** --- *** drogen bonding pattern. Hydrogen bonding *** --- *** occurs between every other C=O from one *** --- *** strand to every other N-H on the adjace *** --- *** nt strand. In this case, if two atoms C- *** --- *** alpha (i)and C-alpha (j) are adjacent in *** --- *** two hydrogen-bonded beta strands, then *** --- *** they do not hydrogen bond to each other; *** --- *** rather, one residue forms hydrogen bond *** --- *** s to the residues that flank the other ( *** --- *** but not vice versa). For example, residu *** --- *** e i may form hydrogen bonds to residues *** --- *** j - 1 and j + 1; this is known as a wide *** --- *** pair of hydrogen bonds. By contrast, re *** --- *** sidue j may hydrogen-bond to different r *** --- *** esidues altogether, or to none at all. T *** --- *** he dihedral angles (phi, psi) are about *** --- *** (-120 degrees, 115 degrees) in parallel *** --- *** sheets. *** --- ************************************************ --- CREATE VIEW parallel_beta_strand AS SELECT feature_id AS parallel_beta_strand_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'parallel_beta_strand'; --- ************************************************ --- *** relation: peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A helix is a secondary_structure conform *** --- *** ation where the peptide backbone forms a *** --- *** coil. *** --- ************************************************ --- CREATE VIEW peptide_helix AS SELECT feature_id AS peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'peptide_helix'; --- ************************************************ --- *** relation: left_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A left handed helix is a region of pepti *** --- *** de where the coiled conformation turns i *** --- *** n an anticlockwise, left handed screw. *** --- ************************************************ --- CREATE VIEW left_handed_peptide_helix AS SELECT feature_id AS left_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'left_handed_peptide_helix'; --- ************************************************ --- *** relation: right_handed_peptide_helix *** --- *** relation type: VIEW *** --- *** *** --- *** A right handed helix is a region of pept *** --- *** ide where the coiled conformation turns *** --- *** in a clockwise, right handed screw. *** --- ************************************************ --- CREATE VIEW right_handed_peptide_helix AS SELECT feature_id AS right_handed_peptide_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'right_handed_peptide_helix'; --- ************************************************ --- *** relation: alpha_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The helix has 3.6 residues per turn whic *** --- *** h corersponds to a translation of 1.5 an *** --- *** gstroms (= 0.15 nm) along the helical ax *** --- *** is. Every backbone N-H group donates a h *** --- *** ydrogen bond to the backbone C=O group o *** --- *** f the amino acid four residues earlier. *** --- ************************************************ --- CREATE VIEW alpha_helix AS SELECT feature_id AS alpha_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_helix'; --- ************************************************ --- *** relation: pi_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The pi helix has 4.1 residues per turn a *** --- *** nd a translation of 1.15 (=0.115 nm) al *** --- *** ong the helical axis. The N-H group of a *** --- *** n amino acid forms a hydrogen bond with *** --- *** the C=O group of the amino acid five res *** --- *** idues earlier. *** --- ************************************************ --- CREATE VIEW pi_helix AS SELECT feature_id AS pi_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pi_helix'; --- ************************************************ --- *** relation: three_ten_helix *** --- *** relation type: VIEW *** --- *** *** --- *** The 3-10 helix has 3 residues per turn w *** --- *** ith a translation of 2.0 angstroms (=0.2 *** --- *** nm) along the helical axis. The N-H gro *** --- *** up of an amino acid forms a hydrogen bon *** --- *** d with the C=O group of the amino acid t *** --- *** hree residues earlier. *** --- ************************************************ --- CREATE VIEW three_ten_helix AS SELECT feature_id AS three_ten_helix_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_ten_helix'; --- ************************************************ --- *** relation: polypeptide_nest_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles. Nest should not have P *** --- *** roline as any residue. Nests frequently *** --- *** occur as parts of other motifs such as S *** --- *** chellman loops. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_motif AS SELECT feature_id AS polypeptide_nest_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'polypeptide_nest_motif'; --- ************************************************ --- *** relation: polypeptide_nest_left_right_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): +20 degree *** --- *** s < phi < +140 degrees, -40 degrees < ps *** --- *** i < +90 degrees. Residue(i+1): -140 degr *** --- *** ees < phi < -20 degrees, -90 degrees < p *** --- *** si < +40 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_left_right_motif AS SELECT feature_id AS polypeptide_nest_left_right_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_left_right_motif'; --- ************************************************ --- *** relation: polypeptide_nest_right_left_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of two consecutive residues with *** --- *** dihedral angles: Residue(i): -140 degre *** --- *** es < phi < -20 degrees, -90 degrees < ps *** --- *** i < +40 degrees. Residue(i+1): +20 degre *** --- *** es < phi < +140 degrees, -40 degrees < p *** --- *** si < +90 degrees. *** --- ************************************************ --- CREATE VIEW polypeptide_nest_right_left_motif AS SELECT feature_id AS polypeptide_nest_right_left_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_nest_right_left_motif'; --- ************************************************ --- *** relation: schellmann_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of six or seven consecutive resi *** --- *** dues that contains two H-bonds. *** --- ************************************************ --- CREATE VIEW schellmann_loop AS SELECT feature_id AS schellmann_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'schellmann_loop'; --- ************************************************ --- *** relation: schellmann_loop_seven *** --- *** relation type: VIEW *** --- *** *** --- *** Wild type: A motif of seven consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+6), the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of res *** --- *** idue(i+5). *** --- ************************************************ --- CREATE VIEW schellmann_loop_seven AS SELECT feature_id AS schellmann_loop_seven_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_seven'; --- ************************************************ --- *** relation: schellmann_loop_six *** --- *** relation type: VIEW *** --- *** *** --- *** Common Type: A motif of six consecutive *** --- *** residues that contains two H-bonds in wh *** --- *** ich: the main-chain CO of residue(i) is *** --- *** H-bonded to the main-chain NH of residue *** --- *** (i+5) the main-chain CO of residue(i+1) *** --- *** is H-bonded to the main-chain NH of resi *** --- *** due(i+4). *** --- ************************************************ --- CREATE VIEW schellmann_loop_six AS SELECT feature_id AS schellmann_loop_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'schellmann_loop_six'; --- ************************************************ --- *** relation: serine_threonine_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two hydrogen bonds in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain O of residue(i) is H-bonded to t *** --- *** he main-chain NH of residue(i+2) or (i+3 *** --- *** ) , the main-chain CO group of residue(i *** --- *** ) is H-bonded to the main-chain NH of re *** --- *** sidue(i+3) or (i+4). *** --- ************************************************ --- CREATE VIEW serine_threonine_motif AS SELECT feature_id AS serine_threonine_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_motif'; --- ************************************************ --- *** relation: serine_threonine_staple_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four or five consecutive resi *** --- *** dues and one H-bond in which: residue(i) *** --- *** is Serine (S) or Threonine (T), the sid *** --- *** e-chain OH of residue(i) is H-bonded to *** --- *** the main-chain CO of residue(i3) or (i4) *** --- *** , Phi angles of residues(i1), (i2) and ( *** --- *** i3) are negative. *** --- ************************************************ --- CREATE VIEW serine_threonine_staple_motif AS SELECT feature_id AS serine_threonine_staple_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine_threonine_staple_motif'; --- ************************************************ --- *** relation: polypeptide_turn_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A reversal in the direction of the backb *** --- *** one of a protein that is stabilized by h *** --- *** ydrogen bond between backbone NH and CO *** --- *** groups, involving no more than 4 amino a *** --- *** cid residues. *** --- ************************************************ --- CREATE VIEW polypeptide_turn_motif AS SELECT feature_id AS polypeptide_turn_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'polypeptide_turn_motif'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I (dihedral angles):- R *** --- *** esidue(i): -140 degrees < chi (1) -120 d *** --- *** egrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1) *** --- *** : -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_one AS SELECT feature_id AS asx_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_one'; --- ************************************************ --- *** relation: asx_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < psi *** --- *** +120 degrees < +180 degrees. Residue(i+ *** --- *** 1): +20 degrees < phi < +140 degrees, -4 *** --- *** 0 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_left_handed_type_two AS SELECT feature_id AS asx_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_left_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, +80 degrees < ps *** --- *** i +120 degrees < +180 degrees. Residue(i *** --- *** +1): +20 degrees < phi < +140 degrees, - *** --- *** 40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_two AS SELECT feature_id AS asx_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_two'; --- ************************************************ --- *** relation: asx_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I (dihedral angles):- *** --- *** Residue(i): -140 degrees < chi (1) -120 *** --- *** degrees < -20 degrees, -90 degrees < psi *** --- *** +120 degrees < +40 degrees. Residue(i+1 *** --- *** ): -140 degrees < phi < -20 degrees, -90 *** --- *** degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW asx_turn_right_handed_type_one AS SELECT feature_id AS asx_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asx_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive residues tha *** --- *** t may contain one H-bond, which, if pres *** --- *** ent, is between the main-chain CO of the *** --- *** first residue and the main-chain NH of *** --- *** the fourth. It is characterized by the d *** --- *** ihedral angles of the second and third r *** --- *** esidues, which are the basis for sub-cat *** --- *** egorization. *** --- ************************************************ --- CREATE VIEW beta_turn AS SELECT feature_id AS beta_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type I:A motif of four conse *** --- *** cutive residues that may contain one H-b *** --- *** ond, which, if present, is between the m *** --- *** ain-chain CO of the first residue and th *** --- *** e main-chain NH of the fourth. It is cha *** --- *** racterized by the dihedral angles:- Resi *** --- *** due(i+1): -140 degrees > phi > -20 degre *** --- *** es, -90 degrees > psi > +40 degrees. Res *** --- *** idue(i+2): -140 degrees > phi > -20 degr *** --- *** ees, -90 degrees > psi > +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_one AS SELECT feature_id AS beta_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Left handed type II: A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees > phi > -20 degr *** --- *** ees, +80 degrees > psi > +180 degrees. R *** --- *** esidue(i+2): +20 degrees > phi > +140 de *** --- *** grees, -40 degrees > psi > +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_left_handed_type_two AS SELECT feature_id AS beta_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_left_handed_type_two'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type I:A motif of four cons *** --- *** ecutive residues that may contain one H- *** --- *** bond, which, if present, is between the *** --- *** main-chain CO of the first residue and t *** --- *** he main-chain NH of the fourth. It is ch *** --- *** aracterized by the dihedral angles: Resi *** --- *** due(i+1): -140 degrees < phi < -20 degre *** --- *** es, -90 degrees < psi < +40 degrees. Res *** --- *** idue(i+2): -140 degrees < phi < -20 degr *** --- *** ees, -90 degrees < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_one AS SELECT feature_id AS beta_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_one'; --- ************************************************ --- *** relation: beta_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** Right handed type II:A motif of four con *** --- *** secutive residues that may contain one H *** --- *** -bond, which, if present, is between the *** --- *** main-chain CO of the first residue and *** --- *** the main-chain NH of the fourth. It is c *** --- *** haracterized by the dihedral angles: Res *** --- *** idue(i+1): -140 degrees < phi < -20 degr *** --- *** ees, +80 degrees < psi < +180 degrees. R *** --- *** esidue(i+2): +20 degrees < phi < +140 de *** --- *** grees, -40 degrees < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_right_handed_type_two AS SELECT feature_id AS beta_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_right_handed_type_two'; --- ************************************************ --- *** relation: gamma_turn *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i,( *** --- *** i+1),( i+2) if a hydrogen bond exists be *** --- *** tween residues i and i+2 and the phi and *** --- *** psi angles of residue i+1 fall within 4 *** --- *** 0 degrees. *** --- ************************************************ --- CREATE VIEW gamma_turn AS SELECT feature_id AS gamma_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'gamma_turn'; --- ************************************************ --- *** relation: gamma_turn_classic *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=75.0 - psi(i+1)=-64.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_classic AS SELECT feature_id AS gamma_turn_classic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_classic'; --- ************************************************ --- *** relation: gamma_turn_inverse *** --- *** relation type: VIEW *** --- *** *** --- *** Gamma turns, defined for 3 residues i, i *** --- *** +1, i+2 if a hydrogen bond exists betwee *** --- *** n residues i and i+2 and the phi and psi *** --- *** angles of residue i+1 fall within 40 de *** --- *** grees: phi(i+1)=-79.0 - psi(i+1)=69.0. *** --- ************************************************ --- CREATE VIEW gamma_turn_inverse AS SELECT feature_id AS gamma_turn_inverse_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gamma_turn_inverse'; --- ************************************************ --- *** relation: serine_threonine_turn *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of three consecutive residues an *** --- *** d one H-bond in which: residue(i) is Ser *** --- *** ine (S) or Threonine (T), the side-chain *** --- *** O of residue(i) is H-bonded to the main *** --- *** -chain NH of residue(i+2). *** --- ************************************************ --- CREATE VIEW serine_threonine_turn AS SELECT feature_id AS serine_threonine_turn_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'serine_threonine_turn'; --- ************************************************ --- *** relation: st_turn_left_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** -90 degrees psi +120 degrees < +40 degr *** --- *** ees, residue(i+1): -140 degrees < phi < *** --- *** -20 degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_one AS SELECT feature_id AS st_turn_left_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_one'; --- ************************************************ --- *** relation: st_turn_left_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an anticlockwise, *** --- *** left handed manner. The dihedral angles *** --- *** for this turn are: Residue(i): -140 degr *** --- *** ees < chi(1) -120 degrees < -20 degrees, *** --- *** +80 degrees psi +120 degrees < +180 deg *** --- *** rees, residue(i+1): +20 degrees < phi < *** --- *** +140 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_left_handed_type_two AS SELECT feature_id AS st_turn_left_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_left_handed_type_two'; --- ************************************************ --- *** relation: st_turn_right_handed_type_one *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, -9 *** --- *** 0 degrees psi +120 degrees < +40 degrees *** --- *** , residue(i+1): -140 degrees < phi < -20 *** --- *** degrees, -90 < psi < +40 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_one AS SELECT feature_id AS st_turn_right_handed_type_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_one'; --- ************************************************ --- *** relation: st_turn_right_handed_type_two *** --- *** relation type: VIEW *** --- *** *** --- *** The peptide twists in an clockwise, righ *** --- *** t handed manner. The dihedral angles for *** --- *** this turn are: Residue(i): -140 degrees *** --- *** < chi(1) -120 degrees < -20 degrees, +8 *** --- *** 0 degrees psi +120 degrees < +180 degree *** --- *** s, residue(i+1): +20 degrees < phi < +14 *** --- *** 0 degrees, -40 < psi < +90 degrees. *** --- ************************************************ --- CREATE VIEW st_turn_right_handed_type_two AS SELECT feature_id AS st_turn_right_handed_type_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'st_turn_right_handed_type_two'; --- ************************************************ --- *** relation: polypeptide_variation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A site of sequence variation (alteration *** --- *** ). Alternative sequence due to naturally *** --- *** occuring events such as polymorphisms a *** --- *** nd altermatve splicing or experimental m *** --- *** ethods such as site directed mutagenesis *** --- *** . *** --- ************************************************ --- CREATE VIEW polypeptide_variation_site AS SELECT feature_id AS polypeptide_variation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'polypeptide_variation_site'; --- ************************************************ --- *** relation: natural_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Describes the natural sequence variants *** --- *** due to polymorphisms, disease-associated *** --- *** mutations, RNA editing and variations b *** --- *** etween strains, isolates or cultivars. *** --- ************************************************ --- CREATE VIEW natural_variant_site AS SELECT feature_id AS natural_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_variant_site'; --- ************************************************ --- *** relation: mutated_variant_site *** --- *** relation type: VIEW *** --- *** *** --- *** Site which has been experimentally alter *** --- *** ed. *** --- ************************************************ --- CREATE VIEW mutated_variant_site AS SELECT feature_id AS mutated_variant_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mutated_variant_site'; --- ************************************************ --- *** relation: alternate_sequence_site *** --- *** relation type: VIEW *** --- *** *** --- *** Description of sequence variants produce *** --- *** d by alternative splicing, alternative p *** --- *** romoter usage, alternative initiation an *** --- *** d ribosomal frameshifting. *** --- ************************************************ --- CREATE VIEW alternate_sequence_site AS SELECT feature_id AS alternate_sequence_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternate_sequence_site'; --- ************************************************ --- *** relation: beta_turn_type_six *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** des of type VIa or type VIb and where th *** --- *** e i+2 residue is cis-proline. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six AS SELECT feature_id AS beta_turn_type_six_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six'; --- ************************************************ --- *** relation: beta_turn_type_six_a *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -60 degrees, psi ~ 120 degrees. Re *** --- *** sidue(i+2): phi ~ -90 degrees, psi ~ 0 d *** --- *** egrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a AS SELECT feature_id AS beta_turn_type_six_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'beta_turn_type_six_a'; --- ************************************************ --- *** relation: beta_turn_type_six_a_one *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_one AS SELECT feature_id AS beta_turn_type_six_a_one_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_one'; --- ************************************************ --- *** relation: beta_turn_type_six_a_two *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_a_two AS SELECT feature_id AS beta_turn_type_six_a_two_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_a_two'; --- ************************************************ --- *** relation: beta_turn_type_six_b *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues, of which the i+2 residue is prolin *** --- *** e, and that may contain one H-bond, whic *** --- *** h, if present, is between the main-chain *** --- *** CO of the first residue and the main-ch *** --- *** ain NH of the fourth and is characterize *** --- *** d by the dihedral angles: Residue(i+1): *** --- *** phi ~ -120 degrees, psi ~ 120 degrees. R *** --- *** esidue(i+2): phi ~ -60 degrees, psi ~ 0 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_six_b AS SELECT feature_id AS beta_turn_type_six_b_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_six_b'; --- ************************************************ --- *** relation: beta_turn_type_eight *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of four consecutive peptide resi *** --- *** dues that may contain one H-bond, which, *** --- *** if present, is between the main-chain C *** --- *** O of the first residue and the main-chai *** --- *** n NH of the fourth and is characterized *** --- *** by the dihedral angles: Residue(i+1): ph *** --- *** i ~ -60 degrees, psi ~ -30 degrees. Resi *** --- *** due(i+2): phi ~ -120 degrees, psi ~ 120 *** --- *** degrees. *** --- ************************************************ --- CREATE VIEW beta_turn_type_eight AS SELECT feature_id AS beta_turn_type_eight_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'beta_turn_type_eight'; --- ************************************************ --- *** relation: dre_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -10 and -60 relative to t *** --- *** he TSS. Consensus sequence is WATCGATW. *** --- ************************************************ --- CREATE VIEW dre_motif AS SELECT feature_id AS dre_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DRE_motif'; --- ************************************************ --- *** relation: dmv4_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, located i *** --- *** mmediately upstream of some TATA box ele *** --- *** ments with respect to the TSS (+1). Cons *** --- *** ensus sequence is YGGTCACACTR. Marked sp *** --- *** atial preference within core promoter; t *** --- *** end to occur near the TSS, although not *** --- *** as tightly as INR (SO:0000014). *** --- ************************************************ --- CREATE VIEW dmv4_motif AS SELECT feature_id AS dmv4_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv4_motif'; --- ************************************************ --- *** relation: e_box_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and +1 relative to th *** --- *** e TSS. Consensus sequence is AWCAGCTGWT. *** --- *** Tends to co-occur with DMv2 (SO:0001161 *** --- *** ). Tends to not occur with DPE motif (SO *** --- *** :0000015). *** --- ************************************************ --- CREATE VIEW e_box_motif AS SELECT feature_id AS e_box_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'E_box_motif'; --- ************************************************ --- *** relation: dmv5_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -50 and -10 relative to t *** --- *** he TSS. Consensus sequence is KTYRGTATWT *** --- *** TT. Tends to co-occur with DMv4 (SO:0001 *** --- *** 157) . Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv5_motif AS SELECT feature_id AS dmv5_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv5_motif'; --- ************************************************ --- *** relation: dmv3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -30 and +15 relative to t *** --- *** he TSS. Consensus sequence is KNNCAKCNCT *** --- *** RNY. Tends to co-occur with DMv2 (SO:000 *** --- *** 1161). Tends to not occur with DPE motif *** --- *** (SO:0000015) or MTE (0001162). *** --- ************************************************ --- CREATE VIEW dmv3_motif AS SELECT feature_id AS dmv3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv3_motif'; --- ************************************************ --- *** relation: dmv2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between -60 and -45 relative to t *** --- *** he TSS. Consensus sequence is MKSYGGCARC *** --- *** GSYSS. Tends to co-occur with DMv3 (SO:0 *** --- *** 001160). Tends to not occur with DPE mot *** --- *** if (SO:0000015) or MTE (SO:0001162). *** --- ************************************************ --- CREATE VIEW dmv2_motif AS SELECT feature_id AS dmv2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv2_motif'; --- ************************************************ --- *** relation: mte *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters, usually l *** --- *** ocated between +20 and +30 relative to t *** --- *** he TSS. Consensus sequence is CSARCSSAAC *** --- *** GS. Tends to co-occur with INR motif (SO *** --- *** :0000014). Tends to not occur with DPE m *** --- *** otif (SO:0000015) or DMv5 (SO:0001159). *** --- ************************************************ --- CREATE VIEW mte AS SELECT feature_id AS mte_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'MTE'; --- ************************************************ --- *** relation: inr1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** TCATTCG. *** --- ************************************************ --- CREATE VIEW inr1_motif AS SELECT feature_id AS inr1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR1_motif'; --- ************************************************ --- *** relation: dpe1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CGGACGT. *** --- ************************************************ --- CREATE VIEW dpe1_motif AS SELECT feature_id AS dpe1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DPE1_motif'; --- ************************************************ --- *** relation: dmv1_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter motif with consensus sequence *** --- *** CARCCCT. *** --- ************************************************ --- CREATE VIEW dmv1_motif AS SELECT feature_id AS dmv1_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DMv1_motif'; --- ************************************************ --- *** relation: gaga_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAGAGCG. *** --- ************************************************ --- CREATE VIEW gaga_motif AS SELECT feature_id AS gaga_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GAGA_motif'; --- ************************************************ --- *** relation: ndm2_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus CGMYGYCR. *** --- ************************************************ --- CREATE VIEW ndm2_motif AS SELECT feature_id AS ndm2_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM2_motif'; --- ************************************************ --- *** relation: ndm3_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A non directional promoter motif with co *** --- *** nsensus sequence GAAAGCT. *** --- ************************************************ --- CREATE VIEW ndm3_motif AS SELECT feature_id AS ndm3_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NDM3_motif'; --- ************************************************ --- *** relation: ds_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded RNA. *** --- ************************************************ --- CREATE VIEW ds_rna_viral_sequence AS SELECT feature_id AS ds_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_RNA_viral_sequence'; --- ************************************************ --- *** relation: polinton *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of DNA transposon that populates *** --- *** the genomes of protists, fungi, and anim *** --- *** als, characterized by a unique set of pr *** --- *** oteins necessary for their transposition *** --- *** , including a protein-primed DNA polymer *** --- *** ase B, retroviral integrase, cysteine pr *** --- *** otease, and ATPase. Polintons are charac *** --- *** terized by 6-bp target site duplications *** --- *** , terminal-inverted repeats that are sev *** --- *** eral hundred nucleotides long, and 5'-AG *** --- *** and TC-3' termini. Polintons exist as a *** --- *** utonomous and nonautonomous elements. *** --- ************************************************ --- CREATE VIEW polinton AS SELECT feature_id AS polinton_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polinton'; --- ************************************************ --- *** relation: rrna_21s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it in mitochondrial rRNA. *** --- ************************************************ --- CREATE VIEW rrna_21s AS SELECT feature_id AS rrna_21s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_21S'; --- ************************************************ --- *** relation: trna_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a tRNA. *** --- ************************************************ --- CREATE VIEW trna_region AS SELECT feature_id AS trna_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'tRNA_region'; --- ************************************************ --- *** relation: anticodon_loop *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of seven nucleotide bases in *** --- *** tRNA which contains the anticodon. It ha *** --- *** s the sequence 5'-pyrimidine-purine-anti *** --- *** codon-modified purine-any base-3. *** --- ************************************************ --- CREATE VIEW anticodon_loop AS SELECT feature_id AS anticodon_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon_loop'; --- ************************************************ --- *** relation: anticodon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of three nucleotide bases in *** --- *** tRNA which recognizes a codon in mRNA. *** --- ************************************************ --- CREATE VIEW anticodon AS SELECT feature_id AS anticodon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'anticodon'; --- ************************************************ --- *** relation: cca_tail *** --- *** relation type: VIEW *** --- *** *** --- *** Base sequence at the 3' end of a tRNA. T *** --- *** he 3'-hydroxyl group on the terminal ade *** --- *** nosine is the attachment point for the a *** --- *** mino acid. *** --- ************************************************ --- CREATE VIEW cca_tail AS SELECT feature_id AS cca_tail_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CCA_tail'; --- ************************************************ --- *** relation: dhu_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of nucleotide b *** --- *** ases in tRNA. It contains several dihydr *** --- *** ouracil residues. *** --- ************************************************ --- CREATE VIEW dhu_loop AS SELECT feature_id AS dhu_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DHU_loop'; --- ************************************************ --- *** relation: t_loop *** --- *** relation type: VIEW *** --- *** *** --- *** Non-base-paired sequence of three nucleo *** --- *** tide bases in tRNA. It has sequence T-Ps *** --- *** i-C. *** --- ************************************************ --- CREATE VIEW t_loop AS SELECT feature_id AS t_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_loop'; --- ************************************************ --- *** relation: pyrrolysine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding pyrrolysyl *** --- *** tRNA (SO:0000766). *** --- ************************************************ --- CREATE VIEW pyrrolysine_trna_primary_transcript AS SELECT feature_id AS pyrrolysine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: u3_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** U3 snoRNA is a member of the box C/D cla *** --- *** ss of small nucleolar RNAs. The U3 snoRN *** --- *** A secondary structure is characterised b *** --- *** y a small 5' domain (with boxes A and A' *** --- *** ), and a larger 3' domain (with boxes B, *** --- *** C, C', and D), the two domains being li *** --- *** nked by a single-stranded hinge. Boxes B *** --- *** and C form the B/C motif, which appears *** --- *** to be exclusive to U3 snoRNAs, and boxe *** --- *** s C' and D form the C'/D motif. The latt *** --- *** er is functionally similar to the C/D mo *** --- *** tifs found in other snoRNAs. The 5' doma *** --- *** in and the hinge region act as a pre-rRN *** --- *** A-binding domain. The 3' domain has cons *** --- *** erved protein-binding sites. Both the bo *** --- *** x B/C and box C'/D motifs are sufficient *** --- *** for nuclear retention of U3 snoRNA. The *** --- *** box C'/D motif is also necessary for nu *** --- *** cleolar localization, stability and hype *** --- *** rmethylation of U3 snoRNA. Both box B/C *** --- *** and C'/D motifs are involved in specific *** --- *** protein interactions and are necessary *** --- *** for the rRNA processing functions of U3 *** --- *** snoRNA. *** --- ************************************************ --- CREATE VIEW u3_snorna AS SELECT feature_id AS u3_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U3_snoRNA'; --- ************************************************ --- *** relation: au_rich_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is rich in AUUUA pen *** --- *** tamers. Messenger RNAs bearing multiple *** --- *** AU-rich elements are often unstable. *** --- ************************************************ --- CREATE VIEW au_rich_element AS SELECT feature_id AS au_rich_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'AU_rich_element'; --- ************************************************ --- *** relation: bruno_response_element *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting element found in the 3' UTR *** --- *** of some mRNA which is bound by the Dros *** --- *** ophila Bruno protein and its homologs. *** --- ************************************************ --- CREATE VIEW bruno_response_element AS SELECT feature_id AS bruno_response_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Bruno_response_element'; --- ************************************************ --- *** relation: iron_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory sequence found in the 5' an *** --- *** d 3' UTRs of many mRNAs which encode iro *** --- *** n-binding proteins. It has a hairpin str *** --- *** ucture and is recognized by trans-acting *** --- *** proteins known as iron-regulatory prote *** --- *** ins. *** --- ************************************************ --- CREATE VIEW iron_responsive_element AS SELECT feature_id AS iron_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'iron_responsive_element'; --- ************************************************ --- *** relation: morpholino_backbone *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of nucleobases bound to a morpholino *** --- *** backbone. A morpholino backbone consist *** --- *** s of morpholine (CHEBI:34856) rings conn *** --- *** ected by phosphorodiamidate linkages. *** --- ************************************************ --- CREATE VIEW morpholino_backbone AS SELECT feature_id AS morpholino_backbone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_backbone'; --- ************************************************ --- *** relation: pna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence compo *** --- *** sed of peptide nucleic acid (CHEBI:48021 *** --- *** ), a chemical consisting of nucleobases *** --- *** bound to a backbone composed of repeatin *** --- *** g N-(2-aminoethyl)-glycine units linked *** --- *** by peptide bonds. The purine and pyrimid *** --- *** ine bases are linked to the backbone by *** --- *** methylene carbonyl bonds. *** --- ************************************************ --- CREATE VIEW pna AS SELECT feature_id AS pna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PNA'; --- ************************************************ --- *** relation: enzymatic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** with or without an associated ribonucle *** --- *** oprotein. *** --- ************************************************ --- CREATE VIEW enzymatic AS SELECT feature_id AS enzymatic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic' OR cvterm.name = 'enzymatic'; --- ************************************************ --- *** relation: ribozymic *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the sequence of *** --- *** a transcript that has catalytic activity *** --- *** even without an associated ribonucleopr *** --- *** otein. *** --- ************************************************ --- CREATE VIEW ribozymic AS SELECT feature_id AS ribozymic_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozymic'; --- ************************************************ --- *** relation: pseudouridylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of pseu *** --- *** douridylation in an RNA molecule by base *** --- *** pairing with a short sequence around th *** --- *** e target residue. *** --- ************************************************ --- CREATE VIEW pseudouridylation_guide_snorna AS SELECT feature_id AS pseudouridylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridylation_guide_snoRNA'; --- ************************************************ --- *** relation: lna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of 'locked' deoxyribose r *** --- *** ings connected to a phosphate backbone. *** --- *** The deoxyribose unit's conformation is ' *** --- *** locked' by a 2'-C,4'-C-oxymethylene link *** --- *** . *** --- ************************************************ --- CREATE VIEW lna AS SELECT feature_id AS lna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA'; --- ************************************************ --- *** relation: lna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of LNA residues. *** --- ************************************************ --- CREATE VIEW lna_oligo AS SELECT feature_id AS lna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'LNA_oligo'; --- ************************************************ --- *** relation: tna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of threose rings connecte *** --- *** d to a phosphate backbone. *** --- ************************************************ --- CREATE VIEW tna AS SELECT feature_id AS tna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA'; --- ************************************************ --- *** relation: tna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of TNA residues. *** --- ************************************************ --- CREATE VIEW tna_oligo AS SELECT feature_id AS tna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TNA_oligo'; --- ************************************************ --- *** relation: gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a sequence consi *** --- *** sting of nucleobases attached to a repea *** --- *** ting unit made of an acyclic three-carbo *** --- *** n propylene glycol connected to a phosph *** --- *** ate backbone. It has two enantiomeric fo *** --- *** rms, (R)-GNA and (S)-GNA. *** --- ************************************************ --- CREATE VIEW gna AS SELECT feature_id AS gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA' OR cvterm.name = 'S_GNA' OR cvterm.name = 'GNA'; --- ************************************************ --- *** relation: gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of GNA residues. *** --- ************************************************ --- CREATE VIEW gna_oligo AS SELECT feature_id AS gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'GNA_oligo'; --- ************************************************ --- *** relation: r_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (R)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW r_gna AS SELECT feature_id AS r_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA'; --- ************************************************ --- *** relation: r_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (R)-GNA residues. *** --- ************************************************ --- CREATE VIEW r_gna_oligo AS SELECT feature_id AS r_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'R_GNA_oligo'; --- ************************************************ --- *** relation: s_gna *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a GNA sequence i *** --- *** n the (S)-GNA enantiomer. *** --- ************************************************ --- CREATE VIEW s_gna AS SELECT feature_id AS s_gna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA'; --- ************************************************ --- *** relation: s_gna_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of (S)-GNA residues. *** --- ************************************************ --- CREATE VIEW s_gna_oligo AS SELECT feature_id AS s_gna_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'S_GNA_oligo'; --- ************************************************ --- *** relation: ds_dna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ds_DNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as double stranded DNA. *** --- ************************************************ --- CREATE VIEW ds_dna_viral_sequence AS SELECT feature_id AS ds_dna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ds_DNA_viral_sequence'; --- ************************************************ --- *** relation: ss_rna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ss_RNA_viral_sequence is a viral_seque *** --- *** nce that is the sequence of a virus that *** --- *** exists as single stranded RNA. *** --- ************************************************ --- CREATE VIEW ss_rna_viral_sequence AS SELECT feature_id AS ss_rna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence'; --- ************************************************ --- *** relation: negative_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A negative_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** is complementary to mRNA and must be con *** --- *** verted to positive sense RNA by RNA poly *** --- *** merase before translation. *** --- ************************************************ --- CREATE VIEW negative_sense_ssrna_viral_sequence AS SELECT feature_id AS negative_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'negative_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: positive_sense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A positive_sense_RNA_viral_sequence is a *** --- *** ss_RNA_viral_sequence that is the seque *** --- *** nce of a single stranded RNA virus that *** --- *** can be immediately translated by the hos *** --- *** t. *** --- ************************************************ --- CREATE VIEW positive_sense_ssrna_viral_sequence AS SELECT feature_id AS positive_sense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'positive_sense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: ambisense_ssrna_viral_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A ambisense_RNA_virus is a ss_RNA_viral_ *** --- *** sequence that is the sequence of a singl *** --- *** e stranded RNA virus with both messenger *** --- *** and anti messenger polarity. *** --- ************************************************ --- CREATE VIEW ambisense_ssrna_viral_sequence AS SELECT feature_id AS ambisense_ssrna_viral_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ambisense_ssRNA_viral_sequence'; --- ************************************************ --- *** relation: rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which RNA polymerase b *** --- *** inds, to begin transcription. *** --- ************************************************ --- CREATE VIEW rna_polymerase_promoter AS SELECT feature_id AS rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'RNA_polymerase_promoter'; --- ************************************************ --- *** relation: phage_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which Bacteriophage RN *** --- *** A polymerase binds, to begin transcripti *** --- *** on. *** --- ************************************************ --- CREATE VIEW phage_rna_polymerase_promoter AS SELECT feature_id AS phage_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: sp6_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the SP6 RNA poly *** --- *** merase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW sp6_rna_polymerase_promoter AS SELECT feature_id AS sp6_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SP6_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t3_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence to which the T3 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t3_rna_polymerase_promoter AS SELECT feature_id AS t3_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T3_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: t7_rna_polymerase_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** A region (DNA) to which the T7 RNA polym *** --- *** erase binds, to begin transcription. *** --- ************************************************ --- CREATE VIEW t7_rna_polymerase_promoter AS SELECT feature_id AS t7_rna_polymerase_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T7_RNA_Polymerase_Promoter'; --- ************************************************ --- *** relation: five_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 5' end of a transcr *** --- *** ipt that usually codes for a protein. Th *** --- *** ese regions tend to be conserved across *** --- *** species and do not change much within a *** --- *** gene family. *** --- ************************************************ --- CREATE VIEW five_prime_est AS SELECT feature_id AS five_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_EST'; --- ************************************************ --- *** relation: three_prime_est *** --- *** relation type: VIEW *** --- *** *** --- *** An EST read from the 3' end of a transcr *** --- *** ipt. They are more likely to fall within *** --- *** non-coding, or untranslated regions(UTR *** --- *** s). *** --- ************************************************ --- CREATE VIEW three_prime_est AS SELECT feature_id AS three_prime_est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_EST'; --- ************************************************ --- *** relation: translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA (not divisible by 3 b *** --- *** ases) that is skipped during the process *** --- *** of translational frameshifting (GO:0006 *** --- *** 452), causing the reading frame to be di *** --- *** fferent. *** --- ************************************************ --- CREATE VIEW translational_frameshift AS SELECT feature_id AS translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'translational_frameshift'; --- ************************************************ --- *** relation: plus_1_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 1 base long that is s *** --- *** kipped during the process of translation *** --- *** al frameshifting (GO:0006452), causing t *** --- *** he reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_1_translational_frameshift AS SELECT feature_id AS plus_1_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translational_frameshift'; --- ************************************************ --- *** relation: plus_2_translational_frameshift *** --- *** relation type: VIEW *** --- *** *** --- *** The region of mRNA 2 bases long that is *** --- *** skipped during the process of translatio *** --- *** nal frameshifting (GO:0006452), causing *** --- *** the reading frame to be different. *** --- ************************************************ --- CREATE VIEW plus_2_translational_frameshift AS SELECT feature_id AS plus_2_translational_frameshift_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_translational_frameshift'; --- ************************************************ --- *** relation: group_iii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group III introns are introns found in t *** --- *** he mRNA of the plastids of euglenoid pro *** --- *** tists. They are spliced by a two step tr *** --- *** ansesterification with bulged adenosine *** --- *** as initiating nucleophile. *** --- ************************************************ --- CREATE VIEW group_iii_intron AS SELECT feature_id AS group_iii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_III_intron'; --- ************************************************ --- *** relation: noncoding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The maximal intersection of exon and UTR *** --- *** . *** --- ************************************************ --- CREATE VIEW noncoding_region_of_exon AS SELECT feature_id AS noncoding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'noncoding_region_of_exon'; --- ************************************************ --- *** relation: coding_region_of_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The region of an exon that encodes for p *** --- *** rotein sequence. *** --- ************************************************ --- CREATE VIEW coding_region_of_exon AS SELECT feature_id AS coding_region_of_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'coding_region_of_exon'; --- ************************************************ --- *** relation: endonuclease_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron that spliced via endonucleolyt *** --- *** ic cleavage and ligation rather than tra *** --- *** nsesterification. *** --- ************************************************ --- CREATE VIEW endonuclease_spliced_intron AS SELECT feature_id AS endonuclease_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'endonuclease_spliced_intron'; --- ************************************************ --- *** relation: protein_coding_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW protein_coding_gene AS SELECT feature_id AS protein_coding_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'protein_coding_gene'; --- ************************************************ --- *** relation: transgenic_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** An insertion that derives from another o *** --- *** rganism, via the use of recombinant DNA *** --- *** technology. *** --- ************************************************ --- CREATE VIEW transgenic_insertion AS SELECT feature_id AS transgenic_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transgenic_insertion'; --- ************************************************ --- *** relation: retrogene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW retrogene AS SELECT feature_id AS retrogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retrogene'; --- ************************************************ --- *** relation: silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by RNA *** --- *** interference. *** --- ************************************************ --- CREATE VIEW silenced_by_rna_interference AS SELECT feature_id AS silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_RNA_interference'; --- ************************************************ --- *** relation: silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone modification. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_modification AS SELECT feature_id AS silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation' OR cvterm.name = 'silenced_by_histone_deacetylation' OR cvterm.name = 'silenced_by_histone_modification'; --- ************************************************ --- *** relation: silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone methylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_methylation AS SELECT feature_id AS silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_methylation'; --- ************************************************ --- *** relation: silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing an epigenetic pr *** --- *** ocess where a gene is inactivated by his *** --- *** tone deacetylation. *** --- ************************************************ --- CREATE VIEW silenced_by_histone_deacetylation AS SELECT feature_id AS silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: gene_silenced_by_rna_interference *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by RNA interfere *** --- *** nce. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_rna_interference AS SELECT feature_id AS gene_silenced_by_rna_interference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_RNA_interference'; --- ************************************************ --- *** relation: gene_silenced_by_histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone modif *** --- *** ication. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_modification AS SELECT feature_id AS gene_silenced_by_histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'gene_silenced_by_histone_modification'; --- ************************************************ --- *** relation: gene_silenced_by_histone_methylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone methy *** --- *** lation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_methylation AS SELECT feature_id AS gene_silenced_by_histone_methylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_methylation'; --- ************************************************ --- *** relation: gene_silenced_by_histone_deacetylation *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is silenced by histone deace *** --- *** tylation. *** --- ************************************************ --- CREATE VIEW gene_silenced_by_histone_deacetylation AS SELECT feature_id AS gene_silenced_by_histone_deacetylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_silenced_by_histone_deacetylation'; --- ************************************************ --- *** relation: dihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5,6-dih *** --- *** ydrouracil is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW dihydrouridine AS SELECT feature_id AS dihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine'; --- ************************************************ --- *** relation: pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which the 5- posi *** --- *** tion of the uracil is bound to the ribos *** --- *** e ring instead of the 4- position. *** --- ************************************************ --- CREATE VIEW pseudouridine AS SELECT feature_id AS pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudouridine'; --- ************************************************ --- *** relation: inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which hypoxanthin *** --- *** e is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW inosine AS SELECT feature_id AS inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'inosine'; --- ************************************************ --- *** relation: seven_methylguanine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which guanine is *** --- *** methylated at the 7- position. *** --- ************************************************ --- CREATE VIEW seven_methylguanine AS SELECT feature_id AS seven_methylguanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanine'; --- ************************************************ --- *** relation: ribothymidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which thymine is *** --- *** bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW ribothymidine AS SELECT feature_id AS ribothymidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribothymidine'; --- ************************************************ --- *** relation: methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified RNA base in which methylhypox *** --- *** anthine is bound to the ribose ring. *** --- ************************************************ --- CREATE VIEW methylinosine AS SELECT feature_id AS methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine'; --- ************************************************ --- *** relation: mobile *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a feature that h *** --- *** as either intra-genome or intracellular *** --- *** mobility. *** --- ************************************************ --- CREATE VIEW mobile AS SELECT feature_id AS mobile_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mobile'; --- ************************************************ --- *** relation: replicon *** --- *** relation type: VIEW *** --- *** *** --- *** A region containing at least one unique *** --- *** origin of replication and a unique termi *** --- *** nation site. *** --- ************************************************ --- CREATE VIEW replicon AS SELECT feature_id AS replicon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'replicon'; --- ************************************************ --- *** relation: base *** --- *** relation type: VIEW *** --- *** *** --- *** A base is a sequence feature that corres *** --- *** ponds to a single unit of a nucleotide p *** --- *** olymer. *** --- ************************************************ --- CREATE VIEW base AS SELECT feature_id AS base_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'base'; --- ************************************************ --- *** relation: amino_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence feature that corresponds to a *** --- *** single amino acid residue in a polypept *** --- *** ide. *** --- ************************************************ --- CREATE VIEW amino_acid AS SELECT feature_id AS amino_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'amino_acid'; --- ************************************************ --- *** relation: major_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW major_tss AS SELECT feature_id AS major_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'major_TSS'; --- ************************************************ --- *** relation: minor_tss *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minor_tss AS SELECT feature_id AS minor_tss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minor_TSS'; --- ************************************************ --- *** relation: tss_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region of a gene from the 5' most TS *** --- *** S to the 3' TSS. *** --- ************************************************ --- CREATE VIEW tss_region AS SELECT feature_id AS tss_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TSS_region'; --- ************************************************ --- *** relation: encodes_alternate_transcription_start_sites *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW encodes_alternate_transcription_start_sites AS SELECT feature_id AS encodes_alternate_transcription_start_sites_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_alternate_transcription_start_sites'; --- ************************************************ --- *** relation: mirna_primary_transcript_region *** --- *** relation type: VIEW *** --- *** *** --- *** A part of an miRNA primary_transcript. *** --- ************************************************ --- CREATE VIEW mirna_primary_transcript_region AS SELECT feature_id AS mirna_primary_transcript_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'miRNA_primary_transcript_region'; --- ************************************************ --- *** relation: pre_mirna *** --- *** relation type: VIEW *** --- *** *** --- *** The 60-70 nucleotide region remain after *** --- *** Drosha processing of the primary transc *** --- *** ript, that folds back upon itself to for *** --- *** m a hairpin sructure. *** --- ************************************************ --- CREATE VIEW pre_mirna AS SELECT feature_id AS pre_mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pre_miRNA'; --- ************************************************ --- *** relation: mirna_stem *** --- *** relation type: VIEW *** --- *** *** --- *** The stem of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_stem AS SELECT feature_id AS mirna_stem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_stem'; --- ************************************************ --- *** relation: mirna_loop *** --- *** relation type: VIEW *** --- *** *** --- *** The loop of the hairpin loop formed by f *** --- *** olding of the pre-miRNA. *** --- ************************************************ --- CREATE VIEW mirna_loop AS SELECT feature_id AS mirna_loop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_loop'; --- ************************************************ --- *** relation: synthetic_oligo *** --- *** relation type: VIEW *** --- *** *** --- *** An oligo composed of synthetic nucleotid *** --- *** es. *** --- ************************************************ --- CREATE VIEW synthetic_oligo AS SELECT feature_id AS synthetic_oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'synthetic_oligo'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome of known length t *** --- *** hat is composed by ordering and aligning *** --- *** two or more different regions. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'assembly'; --- ************************************************ --- *** relation: fragment_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A fragment assembly is a genome assembly *** --- *** that orders overlapping fragments of th *** --- *** e genome based on landmark sequences. Th *** --- *** e base pair distance between the landmar *** --- *** ks is known allowing additivity of lengt *** --- *** hs. *** --- ************************************************ --- CREATE VIEW fragment_assembly AS SELECT feature_id AS fragment_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'fragment_assembly'; --- ************************************************ --- *** relation: fingerprint_map *** --- *** relation type: VIEW *** --- *** *** --- *** A fingerprint_map is a physical map comp *** --- *** osed of restriction fragments. *** --- ************************************************ --- CREATE VIEW fingerprint_map AS SELECT feature_id AS fingerprint_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fingerprint_map'; --- ************************************************ --- *** relation: sts_map *** --- *** relation type: VIEW *** --- *** *** --- *** An STS map is a physical map organized b *** --- *** y the unique STS landmarks. *** --- ************************************************ --- CREATE VIEW sts_map AS SELECT feature_id AS sts_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS_map'; --- ************************************************ --- *** relation: rh_map *** --- *** relation type: VIEW *** --- *** *** --- *** A radiation hybrid map is a physical map *** --- *** . *** --- ************************************************ --- CREATE VIEW rh_map AS SELECT feature_id AS rh_map_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RH_map'; --- ************************************************ --- *** relation: sonicate_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA fragment generated by sonication. *** --- *** Sonication is a technique used to sheer *** --- *** DNA into smaller fragments. *** --- ************************************************ --- CREATE VIEW sonicate_fragment AS SELECT feature_id AS sonicate_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sonicate_fragment'; --- ************************************************ --- *** relation: polyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is an exact multi *** --- *** ple of the haploid number and is greater *** --- *** than the diploid number. *** --- ************************************************ --- CREATE VIEW polyploid AS SELECT feature_id AS polyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'polyploid'; --- ************************************************ --- *** relation: autopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from the same organism *** --- *** . *** --- ************************************************ --- CREATE VIEW autopolyploid AS SELECT feature_id AS autopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autopolyploid'; --- ************************************************ --- *** relation: allopolyploid *** --- *** relation type: VIEW *** --- *** *** --- *** A polyploid where the multiple chromosom *** --- *** e set was derived from a different organ *** --- *** ism. *** --- ************************************************ --- CREATE VIEW allopolyploid AS SELECT feature_id AS allopolyploid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'allopolyploid'; --- ************************************************ --- *** relation: homing_endonuclease_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The binding site (recognition site) of a *** --- *** homing endonuclease. The binding site i *** --- *** s typically large. *** --- ************************************************ --- CREATE VIEW homing_endonuclease_binding_site AS SELECT feature_id AS homing_endonuclease_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homing_endonuclease_binding_site'; --- ************************************************ --- *** relation: octamer_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence element characteristic of som *** --- *** e RNA polymerase II promoters with seque *** --- *** nce ATTGCAT that binds Pou-domain transc *** --- *** ription factors. *** --- ************************************************ --- CREATE VIEW octamer_motif AS SELECT feature_id AS octamer_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'octamer_motif'; --- ************************************************ --- *** relation: apicoplast_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome originating in an apicoplas *** --- *** t. *** --- ************************************************ --- CREATE VIEW apicoplast_chromosome AS SELECT feature_id AS apicoplast_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'apicoplast_chromosome'; --- ************************************************ --- *** relation: sequence_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of discontinuous sequences. *** --- ************************************************ --- CREATE VIEW sequence_collection AS SELECT feature_id AS sequence_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kinetoplast' OR cvterm.name = 'genome' OR cvterm.name = 'contig_collection' OR cvterm.name = 'peptide_collection' OR cvterm.name = 'variant_collection' OR cvterm.name = 'kinetoplast' OR cvterm.name = 'reference_genome' OR cvterm.name = 'variant_genome' OR cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'sequence_collection'; --- ************************************************ --- *** relation: overlapping_feature_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous region of sequence composed *** --- *** of the overlapping of multiple sequence *** --- *** _features, which ultimately provides evi *** --- *** dence for another sequence_feature. *** --- ************************************************ --- CREATE VIEW overlapping_feature_set AS SELECT feature_id AS overlapping_feature_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'overlapping_feature_set'; --- ************************************************ --- *** relation: overlapping_est_set *** --- *** relation type: VIEW *** --- *** *** --- *** A continous experimental result region e *** --- *** xtending the length of multiple overlapp *** --- *** ing EST's. *** --- ************************************************ --- CREATE VIEW overlapping_est_set AS SELECT feature_id AS overlapping_est_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'overlapping_EST_set'; --- ************************************************ --- *** relation: ncrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW ncrna_gene AS SELECT feature_id AS ncrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'ncRNA_gene'; --- ************************************************ --- *** relation: grna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW grna_gene AS SELECT feature_id AS grna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gRNA_gene'; --- ************************************************ --- *** relation: mirna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW mirna_gene AS SELECT feature_id AS mirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_gene'; --- ************************************************ --- *** relation: scrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW scrna_gene AS SELECT feature_id AS scrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA_gene'; --- ************************************************ --- *** relation: snorna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snorna_gene AS SELECT feature_id AS snorna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA_gene'; --- ************************************************ --- *** relation: snrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW snrna_gene AS SELECT feature_id AS snrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA_gene'; --- ************************************************ --- *** relation: srp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW srp_rna_gene AS SELECT feature_id AS srp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA_gene'; --- ************************************************ --- *** relation: strna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW strna_gene AS SELECT feature_id AS strna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA_gene'; --- ************************************************ --- *** relation: tmrna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tmrna_gene AS SELECT feature_id AS tmrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tmRNA_gene'; --- ************************************************ --- *** relation: trna_gene *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW trna_gene AS SELECT feature_id AS trna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_gene'; --- ************************************************ --- *** relation: modified_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified adenine is an adenine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_adenosine AS SELECT feature_id AS modified_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'modified_adenosine'; --- ************************************************ --- *** relation: modified_inosine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified inosine is an inosine base fe *** --- *** ature that has been altered. *** --- ************************************************ --- CREATE VIEW modified_inosine AS SELECT feature_id AS modified_inosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'modified_inosine'; --- ************************************************ --- *** relation: modified_cytidine *** --- *** relation type: VIEW *** --- *** *** --- *** A modified cytidine is a cytidine base f *** --- *** eature which has been altered. *** --- ************************************************ --- CREATE VIEW modified_cytidine AS SELECT feature_id AS modified_cytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'modified_cytidine'; --- ************************************************ --- *** relation: modified_guanosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_guanosine AS SELECT feature_id AS modified_guanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'modified_guanosine'; --- ************************************************ --- *** relation: modified_uridine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_uridine AS SELECT feature_id AS modified_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'modified_uridine'; --- ************************************************ --- *** relation: one_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1-methylinosine is a modified insosine. *** --- ************************************************ --- CREATE VIEW one_methylinosine AS SELECT feature_id AS one_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylinosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethylinosine is a modified ino *** --- *** sine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylinosine AS SELECT feature_id AS one_two_prime_o_dimethylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylinosine'; --- ************************************************ --- *** relation: two_prime_o_methylinosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylinosine is a modified inosine *** --- *** . *** --- ************************************************ --- CREATE VIEW two_prime_o_methylinosine AS SELECT feature_id AS two_prime_o_methylinosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylinosine'; --- ************************************************ --- *** relation: three_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 3-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW three_methylcytidine AS SELECT feature_id AS three_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylcytidine'; --- ************************************************ --- *** relation: five_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-methylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_methylcytidine AS SELECT feature_id AS five_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylcytidine'; --- ************************************************ --- *** relation: two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2'-O-methylcytidine is a modified cytidi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylcytidine AS SELECT feature_id AS two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: two_thiocytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 2-thiocytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW two_thiocytidine AS SELECT feature_id AS two_thiocytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiocytidine'; --- ************************************************ --- *** relation: n4_acetylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_acetylcytidine AS SELECT feature_id AS n4_acetylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetylcytidine'; --- ************************************************ --- *** relation: five_formylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formylcytidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW five_formylcytidine AS SELECT feature_id AS five_formylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formylcytidine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5,2'-O-dimethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethylcytidine AS SELECT feature_id AS five_two_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: n4_acetyl_2_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-acetyl-2'-O-methylcytidine is a modif *** --- *** ied cytidine. *** --- ************************************************ --- CREATE VIEW n4_acetyl_2_prime_o_methylcytidine AS SELECT feature_id AS n4_acetyl_2_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine'; --- ************************************************ --- *** relation: lysidine *** --- *** relation type: VIEW *** --- *** *** --- *** Lysidine is a modified cytidine. *** --- ************************************************ --- CREATE VIEW lysidine AS SELECT feature_id AS lysidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysidine'; --- ************************************************ --- *** relation: n4_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4-methylcytidine is a modified cytidine *** --- *** . *** --- ************************************************ --- CREATE VIEW n4_methylcytidine AS SELECT feature_id AS n4_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_methylcytidine'; --- ************************************************ --- *** relation: n4_2_prime_o_dimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4,2'-O-dimethylcytidine is a modified c *** --- *** ytidine. *** --- ************************************************ --- CREATE VIEW n4_2_prime_o_dimethylcytidine AS SELECT feature_id AS n4_2_prime_o_dimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_2_prime_O_dimethylcytidine'; --- ************************************************ --- *** relation: five_hydroxymethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-hydroxymethylcytidine is a modified cy *** --- *** tidine. *** --- ************************************************ --- CREATE VIEW five_hydroxymethylcytidine AS SELECT feature_id AS five_hydroxymethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxymethylcytidine'; --- ************************************************ --- *** relation: five_formyl_two_prime_o_methylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** 5-formyl-2'-O-methylcytidine is a modifi *** --- *** ed cytidine. *** --- ************************************************ --- CREATE VIEW five_formyl_two_prime_o_methylcytidine AS SELECT feature_id AS five_formyl_two_prime_o_methylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_formyl_two_prime_O_methylcytidine'; --- ************************************************ --- *** relation: n4_n4_2_prime_o_trimethylcytidine *** --- *** relation type: VIEW *** --- *** *** --- *** N4_N4_2_prime_O_trimethylcytidine is a m *** --- *** odified cytidine. *** --- ************************************************ --- CREATE VIEW n4_n4_2_prime_o_trimethylcytidine AS SELECT feature_id AS n4_n4_2_prime_o_trimethylcytidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine'; --- ************************************************ --- *** relation: one_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW one_methyladenosine AS SELECT feature_id AS one_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyladenosine'; --- ************************************************ --- *** relation: two_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methyladenosine is a modified adenosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW two_methyladenosine AS SELECT feature_id AS two_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methyladenosine'; --- ************************************************ --- *** relation: n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_methyladenosine AS SELECT feature_id AS n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyladenosine'; --- ************************************************ --- *** relation: two_prime_o_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyladenosine AS SELECT feature_id AS two_prime_o_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_methyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_methyladenosine is a mod *** --- *** ified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_methyladenosine AS SELECT feature_id AS two_methylthio_n6_methyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_methyladenosine'; --- ************************************************ --- *** relation: n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_isopentenyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_isopentenyladenosine AS SELECT feature_id AS n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_isopentenyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_isopentenyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_isopentenyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_isopentenyladenosine AS SELECT feature_id AS two_methylthio_n6_isopentenyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_isopentenyladenosine'; --- ************************************************ --- *** relation: n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_cis_hydroxyisopentenyl_adenosine is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_cis_hydroxyisopentenyl_adenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_cis_hydroxyisopentenyl_a *** --- *** denosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_cis_hydroxyisopentenyl_adenosine AS SELECT feature_id AS two_methylthio_n6_cis_hydroxyisopentenyl_adenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine'; --- ************************************************ --- *** relation: n6_glycinylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_glycinylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_glycinylcarbamoyladenosine AS SELECT feature_id AS n6_glycinylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_glycinylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_threonylcarbamoyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_threonyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_threonyl_carbamoyladenos *** --- *** ine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_threonyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_threonyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine'; --- ************************************************ --- *** relation: n6_methyl_n6_threonylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_methyl_N6_threonylcarbamoyladenosine *** --- *** is a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_methyl_n6_threonylcarbamoyladenosine AS SELECT feature_id AS n6_methyl_n6_threonylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine'; --- ************************************************ --- *** relation: n6_hydroxynorvalylcarbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_hydroxynorvalylcarbamoyladenosine is *** --- *** a modified adenosine. *** --- ************************************************ --- CREATE VIEW n6_hydroxynorvalylcarbamoyladenosine AS SELECT feature_id AS n6_hydroxynorvalylcarbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine'; --- ************************************************ --- *** relation: two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_methylthio_N6_hydroxynorvalyl_carbamoy *** --- *** ladenosine is a modified adenosine. *** --- ************************************************ --- CREATE VIEW two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine AS SELECT feature_id AS two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine'; --- ************************************************ --- *** relation: two_prime_o_riboA_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosyladenosine_phosphate is a *** --- *** modified adenosine. *** --- ************************************************ --- CREATE VIEW two_prime_o_riboA_phosphate AS SELECT feature_id AS two_prime_o_riboA_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosyladenosine_phosphate'; --- ************************************************ --- *** relation: n6_n6_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_dimethyladenosine is a modified ad *** --- *** enosine. *** --- ************************************************ --- CREATE VIEW n6_n6_dimethyladenosine AS SELECT feature_id AS n6_n6_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_dimethyladenosine'; --- ************************************************ --- *** relation: n6_2_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_2prime_O_dimethyladenosine is a modif *** --- *** ied adenosine. *** --- ************************************************ --- CREATE VIEW n6_2_prime_o_dimethyladenosine AS SELECT feature_id AS n6_2_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_2_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_n6_2_prime_o_trimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_N6_2prime_O_trimethyladenosine is a m *** --- *** odified adenosine. *** --- ************************************************ --- CREATE VIEW n6_n6_2_prime_o_trimethyladenosine AS SELECT feature_id AS n6_n6_2_prime_o_trimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1,2'-O-dimethyladenosine is a modified a *** --- *** denosine. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethyladenosine AS SELECT feature_id AS one_two_prime_o_dimethyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethyladenosine'; --- ************************************************ --- *** relation: n6_acetyladenosine *** --- *** relation type: VIEW *** --- *** *** --- *** N6_acetyladenosine is a modified adenosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW n6_acetyladenosine AS SELECT feature_id AS n6_acetyladenosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N6_acetyladenosine'; --- ************************************************ --- *** relation: seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7-deazaguanosine is a moddified guanosin *** --- *** e. *** --- ************************************************ --- CREATE VIEW seven_deazaguanosine AS SELECT feature_id AS seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'seven_deazaguanosine'; --- ************************************************ --- *** relation: queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Queuosine is a modified 7-deazoguanosine *** --- *** . *** --- ************************************************ --- CREATE VIEW queuosine AS SELECT feature_id AS queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'queuosine'; --- ************************************************ --- *** relation: epoxyqueuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Epoxyqueuosine is a modified 7-deazoguan *** --- *** osine. *** --- ************************************************ --- CREATE VIEW epoxyqueuosine AS SELECT feature_id AS epoxyqueuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'epoxyqueuosine'; --- ************************************************ --- *** relation: galactosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Galactosyl_queuosine is a modified 7-dea *** --- *** zoguanosine. *** --- ************************************************ --- CREATE VIEW galactosyl_queuosine AS SELECT feature_id AS galactosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'galactosyl_queuosine'; --- ************************************************ --- *** relation: mannosyl_queuosine *** --- *** relation type: VIEW *** --- *** *** --- *** Mannosyl_queuosine is a modified 7-deazo *** --- *** guanosine. *** --- ************************************************ --- CREATE VIEW mannosyl_queuosine AS SELECT feature_id AS mannosyl_queuosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mannosyl_queuosine'; --- ************************************************ --- *** relation: seven_cyano_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_cyano_7_deazaguanosine is a modified 7 *** --- *** -deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_cyano_seven_deazaguanosine AS SELECT feature_id AS seven_cyano_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_cyano_seven_deazaguanosine'; --- ************************************************ --- *** relation: seven_aminomethyl_seven_deazaguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_aminomethyl_7_deazaguanosine is a modi *** --- *** fied 7-deazoguanosine. *** --- ************************************************ --- CREATE VIEW seven_aminomethyl_seven_deazaguanosine AS SELECT feature_id AS seven_aminomethyl_seven_deazaguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_aminomethyl_seven_deazaguanosine'; --- ************************************************ --- *** relation: archaeosine *** --- *** relation type: VIEW *** --- *** *** --- *** Archaeosine is a modified 7-deazoguanosi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW archaeosine AS SELECT feature_id AS archaeosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeosine'; --- ************************************************ --- *** relation: one_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW one_methylguanosine AS SELECT feature_id AS one_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylguanosine'; --- ************************************************ --- *** relation: n2_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_methylguanosine is a modified guanosi *** --- *** ne base feature. *** --- ************************************************ --- CREATE VIEW n2_methylguanosine AS SELECT feature_id AS n2_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_methylguanosine'; --- ************************************************ --- *** relation: seven_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 7_methylguanosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW seven_methylguanosine AS SELECT feature_id AS seven_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'seven_methylguanosine'; --- ************************************************ --- *** relation: two_prime_o_methylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylguanosine is a modified g *** --- *** uanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylguanosine AS SELECT feature_id AS two_prime_o_methylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylguanosine'; --- ************************************************ --- *** relation: n2_n2_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_dimethylguanosine is a modified gu *** --- *** anosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_dimethylguanosine AS SELECT feature_id AS n2_n2_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_dimethylguanosine'; --- ************************************************ --- *** relation: n2_2_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_2prime_O_dimethylguanosine is a modif *** --- *** ied guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_2_prime_o_dimethylguanosine AS SELECT feature_id AS n2_2_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_2_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_2_prime_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_2prime_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_2_prime_o_trimethylguanosine AS SELECT feature_id AS n2_n2_2_prime_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine'; --- ************************************************ --- *** relation: two_prime_o_ribosylguanosine_phosphate *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_ribosylguanosine_phosphate is a *** --- *** modified guanosine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_ribosylguanosine_phosphate AS SELECT feature_id AS two_prime_o_ribosylguanosine_phosphate_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_ribosylguanosine_phosphate'; --- ************************************************ --- *** relation: wybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wybutosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW wybutosine AS SELECT feature_id AS wybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wybutosine'; --- ************************************************ --- *** relation: peroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Peroxywybutosine is a modified guanosine *** --- *** base feature. *** --- ************************************************ --- CREATE VIEW peroxywybutosine AS SELECT feature_id AS peroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peroxywybutosine'; --- ************************************************ --- *** relation: hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Hydroxywybutosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW hydroxywybutosine AS SELECT feature_id AS hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydroxywybutosine'; --- ************************************************ --- *** relation: undermodified_hydroxywybutosine *** --- *** relation type: VIEW *** --- *** *** --- *** Undermodified_hydroxywybutosine is a mod *** --- *** ified guanosine base feature. *** --- ************************************************ --- CREATE VIEW undermodified_hydroxywybutosine AS SELECT feature_id AS undermodified_hydroxywybutosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'undermodified_hydroxywybutosine'; --- ************************************************ --- *** relation: wyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Wyosine is a modified guanosine base fea *** --- *** ture. *** --- ************************************************ --- CREATE VIEW wyosine AS SELECT feature_id AS wyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'wyosine'; --- ************************************************ --- *** relation: methylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Methylwyosine is a modified guanosine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW methylwyosine AS SELECT feature_id AS methylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylwyosine'; --- ************************************************ --- *** relation: n2_7_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_dimethylguanosine is a modified gua *** --- *** nosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_dimethylguanosine AS SELECT feature_id AS n2_7_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_dimethylguanosine'; --- ************************************************ --- *** relation: n2_n2_7_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_N2_7_trimethylguanosine is a modified *** --- *** guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_n2_7_trimethylguanosine AS SELECT feature_id AS n2_n2_7_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_N2_7_trimethylguanosine'; --- ************************************************ --- *** relation: one_two_prime_o_dimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_2prime_O_dimethylguanosine is a modifi *** --- *** ed guanosine base feature. *** --- ************************************************ --- CREATE VIEW one_two_prime_o_dimethylguanosine AS SELECT feature_id AS one_two_prime_o_dimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_two_prime_O_dimethylguanosine'; --- ************************************************ --- *** relation: four_demethylwyosine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_demethylwyosine is a modified guanosin *** --- *** e base feature. *** --- ************************************************ --- CREATE VIEW four_demethylwyosine AS SELECT feature_id AS four_demethylwyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_demethylwyosine'; --- ************************************************ --- *** relation: isowyosine *** --- *** relation type: VIEW *** --- *** *** --- *** Isowyosine is a modified guanosine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW isowyosine AS SELECT feature_id AS isowyosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isowyosine'; --- ************************************************ --- *** relation: n2_7_2prirme_o_trimethylguanosine *** --- *** relation type: VIEW *** --- *** *** --- *** N2_7_2prirme_O_trimethylguanosine is a m *** --- *** odified guanosine base feature. *** --- ************************************************ --- CREATE VIEW n2_7_2prirme_o_trimethylguanosine AS SELECT feature_id AS n2_7_2prirme_o_trimethylguanosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'N2_7_2prirme_O_trimethylguanosine'; --- ************************************************ --- *** relation: five_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW five_methyluridine AS SELECT feature_id AS five_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyluridine'; --- ************************************************ --- *** relation: two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methyluridine AS SELECT feature_id AS two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_2_prime_O_dimethyluridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_two_prime_o_dimethyluridine AS SELECT feature_id AS five_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: one_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW one_methylpseudouridine AS SELECT feature_id AS one_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methylpseudouridine'; --- ************************************************ --- *** relation: two_prime_o_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2prime_O_methylpseudouridine is a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW two_prime_o_methylpseudouridine AS SELECT feature_id AS two_prime_o_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_prime_O_methylpseudouridine'; --- ************************************************ --- *** relation: two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW two_thiouridine AS SELECT feature_id AS two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thiouridine'; --- ************************************************ --- *** relation: four_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 4_thiouridine is a modified uridine base *** --- *** feature. *** --- ************************************************ --- CREATE VIEW four_thiouridine AS SELECT feature_id AS four_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_thiouridine'; --- ************************************************ --- *** relation: five_methyl_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyl_2_thiouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyl_2_thiouridine AS SELECT feature_id AS five_methyl_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyl_2_thiouridine'; --- ************************************************ --- *** relation: two_thio_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 2_thio_2prime_O_methyluridine is a modif *** --- *** ied uridine base feature. *** --- ************************************************ --- CREATE VIEW two_thio_two_prime_o_methyluridine AS SELECT feature_id AS two_thio_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'two_thio_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: three_three_amino_three_carboxypropyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_3_amino_3_carboxypropyl_uridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW three_three_amino_three_carboxypropyl_uridine AS SELECT feature_id AS three_three_amino_three_carboxypropyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_three_amino_three_carboxypropyl_uridine'; --- ************************************************ --- *** relation: five_hydroxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_hydroxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_hydroxyuridine AS SELECT feature_id AS five_hydroxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_hydroxyuridine'; --- ************************************************ --- *** relation: five_methoxyuridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxyuridine is a modified uridine b *** --- *** ase feature. *** --- ************************************************ --- CREATE VIEW five_methoxyuridine AS SELECT feature_id AS five_methoxyuridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxyuridine'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid AS SELECT feature_id AS uridine_five_oxyacetic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid'; --- ************************************************ --- *** relation: uridine_five_oxyacetic_acid_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** Uridine_5_oxyacetic_acid_methyl_ester is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW uridine_five_oxyacetic_acid_methyl_ester AS SELECT feature_id AS uridine_five_oxyacetic_acid_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine is a modi *** --- *** fied uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine'; --- ************************************************ --- *** relation: five_carboxyhydroxymethyl_uridine_methyl_ester *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxyhydroxymethyl_uridine_methyl_es *** --- *** ter is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxyhydroxymethyl_uridine_methyl_ester AS SELECT feature_id AS five_carboxyhydroxymethyl_uridine_methyl_ester_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyluridine AS SELECT feature_id AS five_methoxycarbonylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyluridine'; --- ************************************************ --- *** relation: five_methoxycarbonylmethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** Five_methoxycarbonylmethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_methoxycarbonylmethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_methoxycarbonylmethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_mcm_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methoxycarbonylmethyl_2_thiouridine is *** --- *** a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mcm_2_thiouridine AS SELECT feature_id AS five_mcm_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_aminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_aminomethyl_2_thiouridine is a modifie *** --- *** d uridine base feature. *** --- ************************************************ --- CREATE VIEW five_aminomethyl_two_thiouridine AS SELECT feature_id AS five_aminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_aminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyluridine AS SELECT feature_id AS five_methylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyluridine'; --- ************************************************ --- *** relation: five_mam_2_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_thiouridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_mam_2_thiouridine AS SELECT feature_id AS five_mam_2_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_methylaminomethyl_two_selenouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methylaminomethyl_2_selenouridine is a *** --- *** modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_methylaminomethyl_two_selenouridine AS SELECT feature_id AS five_methylaminomethyl_two_selenouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methylaminomethyl_two_selenouridine'; --- ************************************************ --- *** relation: five_carbamoylmethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyluridine is a modified u *** --- *** ridine base feature. *** --- ************************************************ --- CREATE VIEW five_carbamoylmethyluridine AS SELECT feature_id AS five_carbamoylmethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyluridine'; --- ************************************************ --- *** relation: five_cm_2_prime_o_methU *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carbamoylmethyl_2_prime_O_methyluridin *** --- *** e is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_cm_2_prime_o_methU AS SELECT feature_id AS five_cm_2_prime_o_methU_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyluridine is a m *** --- *** odified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyluridine AS SELECT feature_id AS five_carboxymethylaminomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_prime_O_met *** --- *** hyluridine is a modified uridine base fe *** --- *** ature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: five_carboxymethylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethylaminomethyl_2_thiouridine *** --- *** is a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethylaminomethyl_two_thiouridine AS SELECT feature_id AS five_carboxymethylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: three_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methyluridine is a modified uridine ba *** --- *** se feature. *** --- ************************************************ --- CREATE VIEW three_methyluridine AS SELECT feature_id AS three_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methyluridine'; --- ************************************************ --- *** relation: one_methyl_3_3_amino_three_carboxypropyl_pseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 1_methyl_3_3_amino_3_carboxypropyl_pseud *** --- *** ouridine is a modified uridine base feat *** --- *** ure. *** --- ************************************************ --- CREATE VIEW one_methyl_3_3_amino_three_carboxypropyl_pseudouridine AS SELECT feature_id AS one_methyl_3_3_amino_three_carboxypropyl_pseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine'; --- ************************************************ --- *** relation: five_carboxymethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_carboxymethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_carboxymethyluridine AS SELECT feature_id AS five_carboxymethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_carboxymethyluridine'; --- ************************************************ --- *** relation: three_two_prime_o_dimethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_2prime_O_dimethyluridine is a modified *** --- *** uridine base feature. *** --- ************************************************ --- CREATE VIEW three_two_prime_o_dimethyluridine AS SELECT feature_id AS three_two_prime_o_dimethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_two_prime_O_dimethyluridine'; --- ************************************************ --- *** relation: five_methyldihydrouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_methyldihydrouridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_methyldihydrouridine AS SELECT feature_id AS five_methyldihydrouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_methyldihydrouridine'; --- ************************************************ --- *** relation: three_methylpseudouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 3_methylpseudouridine is a modified urid *** --- *** ine base feature. *** --- ************************************************ --- CREATE VIEW three_methylpseudouridine AS SELECT feature_id AS three_methylpseudouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_methylpseudouridine'; --- ************************************************ --- *** relation: five_taurinomethyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyluridine is a modified uri *** --- *** dine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyluridine AS SELECT feature_id AS five_taurinomethyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyluridine'; --- ************************************************ --- *** relation: five_taurinomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_taurinomethyl_2_thiouridineis a modifi *** --- *** ed uridine base feature. *** --- ************************************************ --- CREATE VIEW five_taurinomethyl_two_thiouridine AS SELECT feature_id AS five_taurinomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_taurinomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_uridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_uridine is a mo *** --- *** dified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_uridine AS SELECT feature_id AS five_isopentenylaminomethyl_uridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_uridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_thiouridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2_thiouridine i *** --- *** s a modified uridine base feature. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_thiouridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_thiouridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine'; --- ************************************************ --- *** relation: five_isopentenylaminomethyl_two_prime_o_methyluridine *** --- *** relation type: VIEW *** --- *** *** --- *** 5_isopentenylaminomethyl_2prime_O_methyl *** --- *** uridine is a modified uridine base featu *** --- *** re. *** --- ************************************************ --- CREATE VIEW five_isopentenylaminomethyl_two_prime_o_methyluridine AS SELECT feature_id AS five_isopentenylaminomethyl_two_prime_o_methyluridine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine'; --- ************************************************ --- *** relation: histone_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues of a *** --- *** histone. *** --- ************************************************ --- CREATE VIEW histone_binding_site AS SELECT feature_id AS histone_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_binding_site'; --- ************************************************ --- *** relation: cds_fragment *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cds_fragment AS SELECT feature_id AS cds_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_fragment'; --- ************************************************ --- *** relation: modified_amino_acid_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified amino ac *** --- *** id feature. *** --- ************************************************ --- CREATE VIEW modified_amino_acid_feature AS SELECT feature_id AS modified_amino_acid_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'modified_amino_acid_feature'; --- ************************************************ --- *** relation: modified_glycine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glycine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_glycine AS SELECT feature_id AS modified_glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_glycine'; --- ************************************************ --- *** relation: modified_l_alanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified alanine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_alanine AS SELECT feature_id AS modified_l_alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_alanine'; --- ************************************************ --- *** relation: modified_l_asparagine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified asparagi *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_asparagine AS SELECT feature_id AS modified_l_asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_asparagine'; --- ************************************************ --- *** relation: modified_l_aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified aspartic *** --- *** acid amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_aspartic_acid AS SELECT feature_id AS modified_l_aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_aspartic_acid'; --- ************************************************ --- *** relation: modified_l_cysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified cysteine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_cysteine AS SELECT feature_id AS modified_l_cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_cysteine'; --- ************************************************ --- *** relation: modified_l_glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW modified_l_glutamic_acid AS SELECT feature_id AS modified_l_glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamic_acid'; --- ************************************************ --- *** relation: modified_l_threonine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified threonin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_threonine AS SELECT feature_id AS modified_l_threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_threonine'; --- ************************************************ --- *** relation: modified_l_tryptophan *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tryptoph *** --- *** an amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tryptophan AS SELECT feature_id AS modified_l_tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tryptophan'; --- ************************************************ --- *** relation: modified_l_glutamine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified glutamin *** --- *** e amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_glutamine AS SELECT feature_id AS modified_l_glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_glutamine'; --- ************************************************ --- *** relation: modified_l_methionine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified methioni *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_methionine AS SELECT feature_id AS modified_l_methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_methionine'; --- ************************************************ --- *** relation: modified_l_isoleucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified isoleuci *** --- *** ne amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_isoleucine AS SELECT feature_id AS modified_l_isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_isoleucine'; --- ************************************************ --- *** relation: modified_l_phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified phenylal *** --- *** anine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_phenylalanine AS SELECT feature_id AS modified_l_phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_phenylalanine'; --- ************************************************ --- *** relation: modified_l_histidine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified histidie *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_histidine AS SELECT feature_id AS modified_l_histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_histidine'; --- ************************************************ --- *** relation: modified_l_serine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified serine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_serine AS SELECT feature_id AS modified_l_serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_serine'; --- ************************************************ --- *** relation: modified_l_lysine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified lysine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_lysine AS SELECT feature_id AS modified_l_lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_lysine'; --- ************************************************ --- *** relation: modified_l_leucine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified leucine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_leucine AS SELECT feature_id AS modified_l_leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_leucine'; --- ************************************************ --- *** relation: modified_l_selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified selenocy *** --- *** steine amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_selenocysteine AS SELECT feature_id AS modified_l_selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_selenocysteine'; --- ************************************************ --- *** relation: modified_l_valine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified valine a *** --- *** mino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_valine AS SELECT feature_id AS modified_l_valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_valine'; --- ************************************************ --- *** relation: modified_l_proline *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified proline *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_proline AS SELECT feature_id AS modified_l_proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_proline'; --- ************************************************ --- *** relation: modified_l_tyrosine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified tyrosine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_tyrosine AS SELECT feature_id AS modified_l_tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_tyrosine'; --- ************************************************ --- *** relation: modified_l_arginine *** --- *** relation type: VIEW *** --- *** *** --- *** A post translationally modified arginine *** --- *** amino acid feature. *** --- ************************************************ --- CREATE VIEW modified_l_arginine AS SELECT feature_id AS modified_l_arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_L_arginine'; --- ************************************************ --- *** relation: peptidyl *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing the nature of a *** --- *** proteinaceous polymer, where by the amin *** --- *** o acid units are joined by peptide bonds *** --- *** . *** --- ************************************************ --- CREATE VIEW peptidyl AS SELECT feature_id AS peptidyl_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptidyl'; --- ************************************************ --- *** relation: cleaved_for_gpi_anchor_region *** --- *** relation type: VIEW *** --- *** *** --- *** The C-terminal residues of a polypeptide *** --- *** which are exchanged for a GPI-anchor. *** --- ************************************************ --- CREATE VIEW cleaved_for_gpi_anchor_region AS SELECT feature_id AS cleaved_for_gpi_anchor_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_for_gpi_anchor_region'; --- ************************************************ --- *** relation: biomaterial_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is intended for use in an *** --- *** experiment. *** --- ************************************************ --- CREATE VIEW biomaterial_region AS SELECT feature_id AS biomaterial_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'biomaterial_region'; --- ************************************************ --- *** relation: experimental_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A region which is the result of some arb *** --- *** itrary experimental procedure. The proce *** --- *** dure may be carried out with biological *** --- *** material or inside a computer. *** --- ************************************************ --- CREATE VIEW experimental_feature AS SELECT feature_id AS experimental_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimental_feature'; --- ************************************************ --- *** relation: biological_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by its disposition to b *** --- *** e involved in a biological process. *** --- ************************************************ --- CREATE VIEW biological_region AS SELECT feature_id AS biological_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'biological_region'; --- ************************************************ --- *** relation: topologically_defined_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is defined according to it *** --- *** s relations with other regions within th *** --- *** e same sequence. *** --- ************************************************ --- CREATE VIEW topologically_defined_region AS SELECT feature_id AS topologically_defined_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'topologically_defined_region'; --- ************************************************ --- *** relation: translocation_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a tr *** --- *** anslocation begins or ends. *** --- ************************************************ --- CREATE VIEW translocation_breakpoint AS SELECT feature_id AS translocation_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_breakpoint'; --- ************************************************ --- *** relation: insertion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a in *** --- *** sertion begins or ends. *** --- ************************************************ --- CREATE VIEW insertion_breakpoint AS SELECT feature_id AS insertion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_breakpoint'; --- ************************************************ --- *** relation: deletion_breakpoint *** --- *** relation type: VIEW *** --- *** *** --- *** The point within a chromosome where a de *** --- *** letion begins or ends. *** --- ************************************************ --- CREATE VIEW deletion_breakpoint AS SELECT feature_id AS deletion_breakpoint_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_breakpoint'; --- ************************************************ --- *** relation: five_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located five prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW five_prime_flanking_region AS SELECT feature_id AS five_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_flanking_region'; --- ************************************************ --- *** relation: three_prime_flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** A flanking region located three prime of *** --- *** a specific region. *** --- ************************************************ --- CREATE VIEW three_prime_flanking_region AS SELECT feature_id AS three_prime_flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_flanking_region'; --- ************************************************ --- *** relation: transcribed_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region, defined by a til *** --- *** ing array experiment to be transcribed a *** --- *** t some level. *** --- ************************************************ --- CREATE VIEW transcribed_fragment AS SELECT feature_id AS transcribed_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcribed_fragment'; --- ************************************************ --- *** relation: cis_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Intronic 2 bp region bordering exon. A s *** --- *** plice_site that adjacent_to exon and ove *** --- *** rlaps intron. *** --- ************************************************ --- CREATE VIEW cis_splice_site AS SELECT feature_id AS cis_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'cis_splice_site'; --- ************************************************ --- *** relation: trans_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** Primary transcript region bordering tran *** --- *** s-splice junction. *** --- ************************************************ --- CREATE VIEW trans_splice_site AS SELECT feature_id AS trans_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'trans_splice_site'; --- ************************************************ --- *** relation: splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between an intron and an ex *** --- *** on. *** --- ************************************************ --- CREATE VIEW splice_junction AS SELECT feature_id AS splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_junction'; --- ************************************************ --- *** relation: conformational_switch *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a polypeptide, involved in t *** --- *** he transition from one conformational st *** --- *** ate to another. *** --- ************************************************ --- CREATE VIEW conformational_switch AS SELECT feature_id AS conformational_switch_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_switch'; --- ************************************************ --- *** relation: dye_terminator_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the dye terminator me *** --- *** thod of sequencing. *** --- ************************************************ --- CREATE VIEW dye_terminator_read AS SELECT feature_id AS dye_terminator_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dye_terminator_read'; --- ************************************************ --- *** relation: pyrosequenced_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by pyrosequencing techno *** --- *** logy. *** --- ************************************************ --- CREATE VIEW pyrosequenced_read AS SELECT feature_id AS pyrosequenced_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrosequenced_read'; --- ************************************************ --- *** relation: ligation_based_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by ligation based sequen *** --- *** cing technologies. *** --- ************************************************ --- CREATE VIEW ligation_based_read AS SELECT feature_id AS ligation_based_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ligation_based_read'; --- ************************************************ --- *** relation: polymerase_synthesis_read *** --- *** relation type: VIEW *** --- *** *** --- *** A read produced by the polymerase based *** --- *** sequence by synthesis method. *** --- ************************************************ --- CREATE VIEW polymerase_synthesis_read AS SELECT feature_id AS polymerase_synthesis_read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymerase_synthesis_read'; --- ************************************************ --- *** relation: cis_regulatory_frameshift_element *** --- *** relation type: VIEW *** --- *** *** --- *** A structural region in an RNA molecule w *** --- *** hich promotes ribosomal frameshifting of *** --- *** cis coding sequence. *** --- ************************************************ --- CREATE VIEW cis_regulatory_frameshift_element AS SELECT feature_id AS cis_regulatory_frameshift_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cis_regulatory_frameshift_element'; --- ************************************************ --- *** relation: expressed_sequence_assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence assembly derived from express *** --- *** ed sequences. *** --- ************************************************ --- CREATE VIEW expressed_sequence_assembly AS SELECT feature_id AS expressed_sequence_assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_assembly'; --- ************************************************ --- *** relation: dna_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith DNA. *** --- ************************************************ --- CREATE VIEW dna_binding_site AS SELECT feature_id AS dna_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'DNA_binding_site'; --- ************************************************ --- *** relation: cryptic_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is not transcribed under nor *** --- *** mal conditions and is not critical to no *** --- *** rmal cellular functioning. *** --- ************************************************ --- CREATE VIEW cryptic_gene AS SELECT feature_id AS cryptic_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene' OR cvterm.name = 'cryptic_gene'; --- ************************************************ --- *** relation: three_prime_race_clone *** --- *** relation type: VIEW *** --- *** *** --- *** A three prime RACE (Rapid Amplification *** --- *** of cDNA Ends) clone is a cDNA clone copi *** --- *** ed from the 3' end of an mRNA (using a p *** --- *** oly-dT primer to capture the polyA tail *** --- *** and a gene-specific or randomly primed 5 *** --- *** ' primer), and spliced into a vector for *** --- *** propagation in a suitable host. *** --- ************************************************ --- CREATE VIEW three_prime_race_clone AS SELECT feature_id AS three_prime_race_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RACE_clone'; --- ************************************************ --- *** relation: cassette_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A cassette pseudogene is a kind of gene *** --- *** in an inactive form which may recombine *** --- *** at a telomeric locus to form a functiona *** --- *** l copy. *** --- ************************************************ --- CREATE VIEW cassette_pseudogene AS SELECT feature_id AS cassette_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_pseudogene'; --- ************************************************ --- *** relation: alanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alanine AS SELECT feature_id AS alanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alanine'; --- ************************************************ --- *** relation: valine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW valine AS SELECT feature_id AS valine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'valine'; --- ************************************************ --- *** relation: leucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW leucine AS SELECT feature_id AS leucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'leucine'; --- ************************************************ --- *** relation: isoleucine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW isoleucine AS SELECT feature_id AS isoleucine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'isoleucine'; --- ************************************************ --- *** relation: proline *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proline AS SELECT feature_id AS proline_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proline'; --- ************************************************ --- *** relation: tryptophan *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tryptophan AS SELECT feature_id AS tryptophan_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tryptophan'; --- ************************************************ --- *** relation: phenylalanine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW phenylalanine AS SELECT feature_id AS phenylalanine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'phenylalanine'; --- ************************************************ --- *** relation: methionine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW methionine AS SELECT feature_id AS methionine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methionine'; --- ************************************************ --- *** relation: glycine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glycine AS SELECT feature_id AS glycine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glycine'; --- ************************************************ --- *** relation: serine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW serine AS SELECT feature_id AS serine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'serine'; --- ************************************************ --- *** relation: threonine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW threonine AS SELECT feature_id AS threonine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'threonine'; --- ************************************************ --- *** relation: tyrosine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tyrosine AS SELECT feature_id AS tyrosine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tyrosine'; --- ************************************************ --- *** relation: cysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cysteine AS SELECT feature_id AS cysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cysteine'; --- ************************************************ --- *** relation: glutamine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamine AS SELECT feature_id AS glutamine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamine'; --- ************************************************ --- *** relation: asparagine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW asparagine AS SELECT feature_id AS asparagine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'asparagine'; --- ************************************************ --- *** relation: lysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lysine AS SELECT feature_id AS lysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysine'; --- ************************************************ --- *** relation: arginine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW arginine AS SELECT feature_id AS arginine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'arginine'; --- ************************************************ --- *** relation: histidine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW histidine AS SELECT feature_id AS histidine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histidine'; --- ************************************************ --- *** relation: aspartic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW aspartic_acid AS SELECT feature_id AS aspartic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aspartic_acid'; --- ************************************************ --- *** relation: glutamic_acid *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW glutamic_acid AS SELECT feature_id AS glutamic_acid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'glutamic_acid'; --- ************************************************ --- *** relation: selenocysteine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW selenocysteine AS SELECT feature_id AS selenocysteine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine'; --- ************************************************ --- *** relation: pyrrolysine *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pyrrolysine AS SELECT feature_id AS pyrrolysine_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrrolysine'; --- ************************************************ --- *** relation: transcribed_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A region defined by a set of transcribed *** --- *** sequences from the same gene or express *** --- *** ed pseudogene. *** --- ************************************************ --- CREATE VIEW transcribed_cluster AS SELECT feature_id AS transcribed_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster' OR cvterm.name = 'transcribed_cluster'; --- ************************************************ --- *** relation: unigene_cluster *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of transcribed_cluster defined by *** --- *** a set of transcribed sequences from the *** --- *** a unique gene. *** --- ************************************************ --- CREATE VIEW unigene_cluster AS SELECT feature_id AS unigene_cluster_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unigene_cluster'; --- ************************************************ --- *** relation: crispr *** --- *** relation type: VIEW *** --- *** *** --- *** Clustered Palindromic Repeats interspers *** --- *** ed with bacteriophage derived spacer seq *** --- *** uences. *** --- ************************************************ --- CREATE VIEW crispr AS SELECT feature_id AS crispr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CRISPR'; --- ************************************************ --- *** relation: insulator_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in an insulator reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW insulator_binding_site AS SELECT feature_id AS insulator_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator_binding_site'; --- ************************************************ --- *** relation: enhancer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the enhancer reg *** --- *** ion of a nucleotide molecule, interacts *** --- *** selectively and non-covalently with poly *** --- *** peptide residues. *** --- ************************************************ --- CREATE VIEW enhancer_binding_site AS SELECT feature_id AS enhancer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_binding_site'; --- ************************************************ --- *** relation: contig_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of contigs. *** --- ************************************************ --- CREATE VIEW contig_collection AS SELECT feature_id AS contig_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig_collection'; --- ************************************************ --- *** relation: lincrna *** --- *** relation type: VIEW *** --- *** *** --- *** A multiexonic non-coding RNA transcribed *** --- *** by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW lincrna AS SELECT feature_id AS lincrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA'; --- ************************************************ --- *** relation: ust *** --- *** relation type: VIEW *** --- *** *** --- *** An EST spanning part or all of the untra *** --- *** nslated regions of a protein-coding tran *** --- *** script. *** --- ************************************************ --- CREATE VIEW ust AS SELECT feature_id AS ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'UST'; --- ************************************************ --- *** relation: three_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** A UST located in the 3'UTR of a protein- *** --- *** coding transcript. *** --- ************************************************ --- CREATE VIEW three_prime_ust AS SELECT feature_id AS three_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UST'; --- ************************************************ --- *** relation: five_prime_ust *** --- *** relation type: VIEW *** --- *** *** --- *** An UST located in the 5'UTR of a protein *** --- *** -coding transcript. *** --- ************************************************ --- CREATE VIEW five_prime_ust AS SELECT feature_id AS five_prime_ust_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UST'; --- ************************************************ --- *** relation: rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a RACE product; typically a fe *** --- *** w hundred base pairs long. *** --- ************************************************ --- CREATE VIEW rst AS SELECT feature_id AS rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'RST'; --- ************************************************ --- *** relation: three_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 3'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW three_prime_rst AS SELECT feature_id AS three_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_RST'; --- ************************************************ --- *** relation: five_prime_rst *** --- *** relation type: VIEW *** --- *** *** --- *** A tag produced from a single sequencing *** --- *** read from a 5'-RACE product; typically a *** --- *** few hundred base pairs long. *** --- ************************************************ --- CREATE VIEW five_prime_rst AS SELECT feature_id AS five_prime_rst_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_RST'; --- ************************************************ --- *** relation: ust_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an UST sequence. *** --- ************************************************ --- CREATE VIEW ust_match AS SELECT feature_id AS ust_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UST_match'; --- ************************************************ --- *** relation: rst_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an RST sequence. *** --- ************************************************ --- CREATE VIEW rst_match AS SELECT feature_id AS rst_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RST_match'; --- ************************************************ --- *** relation: primer_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match to a primer sequence. *** --- ************************************************ --- CREATE VIEW primer_match AS SELECT feature_id AS primer_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_match'; --- ************************************************ --- *** relation: mirna_antiguide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the pri miRNA that basepairs *** --- *** with the guide to form the hairpin. *** --- ************************************************ --- CREATE VIEW mirna_antiguide AS SELECT feature_id AS mirna_antiguide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_antiguide'; --- ************************************************ --- *** relation: trans_splice_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between the spliced leader *** --- *** and the first exon of the mRNA. *** --- ************************************************ --- CREATE VIEW trans_splice_junction AS SELECT feature_id AS trans_splice_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_junction'; --- ************************************************ --- *** relation: outron *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a primary transcript, that i *** --- *** s removed via trans splicing. *** --- ************************************************ --- CREATE VIEW outron AS SELECT feature_id AS outron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'outron'; --- ************************************************ --- *** relation: natural_plasmid *** --- *** relation type: VIEW *** --- *** *** --- *** A plasmid that occurs naturally. *** --- ************************************************ --- CREATE VIEW natural_plasmid AS SELECT feature_id AS natural_plasmid_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'natural_plasmid'; --- ************************************************ --- *** relation: gene_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A gene trap construct is a type of engin *** --- *** eered plasmid which is designed to integ *** --- *** rate into a genome and produce a fusion *** --- *** transcript between exons of the gene int *** --- *** o which it inserts and a reporter elemen *** --- *** t in the construct. Gene traps contain a *** --- *** splice acceptor, do not contain promote *** --- *** r elements for the reporter, and are mut *** --- *** agenic. Gene traps may be bicistronic wi *** --- *** th the second cassette containing a prom *** --- *** oter driving an a selectable marker. *** --- ************************************************ --- CREATE VIEW gene_trap_construct AS SELECT feature_id AS gene_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_trap_construct'; --- ************************************************ --- *** relation: promoter_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter trap construct is a type of e *** --- *** ngineered plasmid which is designed to i *** --- *** ntegrate into a genome and express a rep *** --- *** orter when inserted in close proximity t *** --- *** o a promoter element. Promoter traps typ *** --- *** ically do not contain promoter elements *** --- *** and are mutagenic. *** --- ************************************************ --- CREATE VIEW promoter_trap_construct AS SELECT feature_id AS promoter_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter_trap_construct'; --- ************************************************ --- *** relation: enhancer_trap_construct *** --- *** relation type: VIEW *** --- *** *** --- *** An enhancer trap construct is a type of *** --- *** engineered plasmid which is designed to *** --- *** integrate into a genome and express a re *** --- *** porter when the expression from a basic *** --- *** minimal promoter is enhanced by genomic *** --- *** enhancer elements. Enhancer traps contai *** --- *** n promoter elements and are not usually *** --- *** mutagenic. *** --- ************************************************ --- CREATE VIEW enhancer_trap_construct AS SELECT feature_id AS enhancer_trap_construct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer_trap_construct'; --- ************************************************ --- *** relation: pac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a P *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW pac_end AS SELECT feature_id AS pac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PAC_end'; --- ************************************************ --- *** relation: rapd *** --- *** relation type: VIEW *** --- *** *** --- *** RAPD is a 'PCR product' where a sequence *** --- *** variant is identified through the use o *** --- *** f PCR with random primers. *** --- ************************************************ --- CREATE VIEW rapd AS SELECT feature_id AS rapd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RAPD'; --- ************************************************ --- *** relation: shadow_enhancer *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW shadow_enhancer AS SELECT feature_id AS shadow_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'shadow_enhancer'; --- ************************************************ --- *** relation: snv *** --- *** relation type: VIEW *** --- *** *** --- *** SNVs are single nucleotide positions in *** --- *** genomic DNA at which different sequence *** --- *** alternatives exist. *** --- ************************************************ --- CREATE VIEW snv AS SELECT feature_id AS snv_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'SNV'; --- ************************************************ --- *** relation: x_element_combinatorial_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An X element combinatorial repeat is a r *** --- *** epeat region located between the X eleme *** --- *** nt and the telomere or adjacent Y' eleme *** --- *** nt. *** --- ************************************************ --- CREATE VIEW x_element_combinatorial_repeat AS SELECT feature_id AS x_element_combinatorial_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element_combinatorial_repeat'; --- ************************************************ --- *** relation: y_prime_element *** --- *** relation type: VIEW *** --- *** *** --- *** A Y' element is a repeat region (SO:0000 *** --- *** 657) located adjacent to telomeric repea *** --- *** ts or X element combinatorial repeats, e *** --- *** ither as a single copy or tandem repeat *** --- *** of two to four copies. *** --- ************************************************ --- CREATE VIEW y_prime_element AS SELECT feature_id AS y_prime_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_prime_element'; --- ************************************************ --- *** relation: standard_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the data is minimally filtered or u *** --- *** n-filtered, from any number of sequencin *** --- *** g platforms, and is assembled into conti *** --- *** gs. Genome sequence of this quality may *** --- *** harbour regions of poor quality and can *** --- *** be relatively incomplete. *** --- ************************************************ --- CREATE VIEW standard_draft AS SELECT feature_id AS standard_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft'; --- ************************************************ --- *** relation: high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here overall coverage represents at leas *** --- *** t 90 percent of the genome. *** --- ************************************************ --- CREATE VIEW high_quality_draft AS SELECT feature_id AS high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_quality_draft'; --- ************************************************ --- *** relation: improved_high_quality_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here additional work has been performed, *** --- *** using either manual or automated method *** --- *** s, such as gap resolution. *** --- ************************************************ --- CREATE VIEW improved_high_quality_draft AS SELECT feature_id AS improved_high_quality_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'improved_high_quality_draft'; --- ************************************************ --- *** relation: annotation_directed_improved_draft *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence,wh *** --- *** ere annotation, and verification of codi *** --- *** ng regions has occurred. *** --- ************************************************ --- CREATE VIEW annotation_directed_improved_draft AS SELECT feature_id AS annotation_directed_improved_draft_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'annotation_directed_improved_draft'; --- ************************************************ --- *** relation: noncontiguous_finished *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** here the assembly is high quality, closu *** --- *** re approaches have been successful for m *** --- *** ost gaps, misassemblies and low quality *** --- *** regions. *** --- ************************************************ --- CREATE VIEW noncontiguous_finished AS SELECT feature_id AS noncontiguous_finished_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'noncontiguous_finished'; --- ************************************************ --- *** relation: finished_genome *** --- *** relation type: VIEW *** --- *** *** --- *** The status of a whole genome sequence, w *** --- *** ith less than 1 error per 100,000 base p *** --- *** airs. *** --- ************************************************ --- CREATE VIEW finished_genome AS SELECT feature_id AS finished_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'finished_genome'; --- ************************************************ --- *** relation: intronic_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is part of an i *** --- *** ntron. *** --- ************************************************ --- CREATE VIEW intronic_regulatory_region AS SELECT feature_id AS intronic_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intronic_regulatory_region'; --- ************************************************ --- *** relation: centromere_dna_element_i *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region compos *** --- *** ed of 8-11bp which enables binding by th *** --- *** e centromere binding factor 1(Cbf1p). *** --- ************************************************ --- CREATE VIEW centromere_dna_element_i AS SELECT feature_id AS centromere_dna_element_i_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_I'; --- ************************************************ --- *** relation: centromere_dna_element_ii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element II (CDEII) is p *** --- *** art a conserved region of the centromere *** --- *** , consisting of a consensus region that *** --- *** is AT-rich and ~ 75-100 bp in length. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_ii AS SELECT feature_id AS centromere_dna_element_ii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_II'; --- ************************************************ --- *** relation: centromere_dna_element_iii *** --- *** relation type: VIEW *** --- *** *** --- *** A centromere DNA Element I (CDEI) is a c *** --- *** onserved region, part of the centromere, *** --- *** consisting of a consensus region that c *** --- *** onsists of a 25-bp which enables binding *** --- *** by the centromere DNA binding factor 3 *** --- *** (CBF3) complex. *** --- ************************************************ --- CREATE VIEW centromere_dna_element_iii AS SELECT feature_id AS centromere_dna_element_iii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere_DNA_Element_III'; --- ************************************************ --- *** relation: telomeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The telomeric repeat is a repeat region, *** --- *** part of the chromosome, which in yeast, *** --- *** is a G-rich terminal sequence of the fo *** --- *** rm (TG(1-3))n or more precisely ((TG)(1- *** --- *** 6)TG(2-3))n. *** --- ************************************************ --- CREATE VIEW telomeric_repeat AS SELECT feature_id AS telomeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomeric_repeat'; --- ************************************************ --- *** relation: x_element *** --- *** relation type: VIEW *** --- *** *** --- *** The X element is a conserved region, of *** --- *** the telomere, of ~475 bp that contains a *** --- *** n ARS sequence and in most cases an Abf1 *** --- *** p binding site. *** --- ************************************************ --- CREATE VIEW x_element AS SELECT feature_id AS x_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'X_element'; --- ************************************************ --- *** relation: yac_end *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence from the end of a Y *** --- *** AC clone that may provide a highly speci *** --- *** fic marker. *** --- ************************************************ --- CREATE VIEW yac_end AS SELECT feature_id AS yac_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'YAC_end'; --- ************************************************ --- *** relation: whole_genome_sequence_status *** --- *** relation type: VIEW *** --- *** *** --- *** The status of whole genome sequence. *** --- ************************************************ --- CREATE VIEW whole_genome_sequence_status AS SELECT feature_id AS whole_genome_sequence_status_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'standard_draft' OR cvterm.name = 'high_quality_draft' OR cvterm.name = 'improved_high_quality_draft' OR cvterm.name = 'annotation_directed_improved_draft' OR cvterm.name = 'noncontiguous_finished' OR cvterm.name = 'finished_genome' OR cvterm.name = 'whole_genome_sequence_status'; --- ************************************************ --- *** relation: heritable_phenotypic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A biological_region characterized as a s *** --- *** ingle heritable trait in a phenotype scr *** --- *** een. The heritable phenotype may be mapp *** --- *** ed to a chromosome but generally has not *** --- *** been characterized to a specific gene l *** --- *** ocus. *** --- ************************************************ --- CREATE VIEW heritable_phenotypic_marker AS SELECT feature_id AS heritable_phenotypic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker'; --- ************************************************ --- *** relation: peptide_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of peptide sequences. *** --- ************************************************ --- CREATE VIEW peptide_collection AS SELECT feature_id AS peptide_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_collection'; --- ************************************************ --- *** relation: high_identity_region *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature with high sequen *** --- *** ce identity to another sequence. *** --- ************************************************ --- CREATE VIEW high_identity_region AS SELECT feature_id AS high_identity_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'high_identity_region'; --- ************************************************ --- *** relation: processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript for which no open reading f *** --- *** rame has been identified and for which n *** --- *** o other function has been determined. *** --- ************************************************ --- CREATE VIEW processed_transcript AS SELECT feature_id AS processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_transcript'; --- ************************************************ --- *** relation: assortment_derived_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome variation derived from an e *** --- *** vent during meiosis. *** --- ************************************************ --- CREATE VIEW assortment_derived_variation AS SELECT feature_id AS assortment_derived_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'assortment_derived_variation'; --- ************************************************ --- *** relation: reference_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) taken as the standard for a given *** --- *** organism and genome assembly. *** --- ************************************************ --- CREATE VIEW reference_genome AS SELECT feature_id AS reference_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reference_genome'; --- ************************************************ --- *** relation: variant_genome *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of sequences (often chromos *** --- *** omes) of an individual. *** --- ************************************************ --- CREATE VIEW variant_genome AS SELECT feature_id AS variant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome' OR cvterm.name = 'variant_genome'; --- ************************************************ --- *** relation: variant_collection *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of one or more sequences of *** --- *** an individual. *** --- ************************************************ --- CREATE VIEW variant_collection AS SELECT feature_id AS variant_collection_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_variation' OR cvterm.name = 'allele' OR cvterm.name = 'haplotype' OR cvterm.name = 'genotype' OR cvterm.name = 'diplotype' OR cvterm.name = 'assortment_derived_variation' OR cvterm.name = 'chromosome_number_variation' OR cvterm.name = 'chromosome_structure_variation' OR cvterm.name = 'assortment_derived_duplication' OR cvterm.name = 'assortment_derived_deficiency_plus_duplication' OR cvterm.name = 'assortment_derived_deficiency' OR cvterm.name = 'assortment_derived_aneuploid' OR cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'variant_collection'; --- ************************************************ --- *** relation: alteration_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW alteration_attribute AS SELECT feature_id AS alteration_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_variation_attribute' OR cvterm.name = 'insertion_attribute' OR cvterm.name = 'inversion_attribute' OR cvterm.name = 'translocaton_attribute' OR cvterm.name = 'duplication_attribute' OR cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'free' OR cvterm.name = 'alteration_attribute'; --- ************************************************ --- *** relation: chromosomal_variation_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomal_variation_attribute AS SELECT feature_id AS chromosomal_variation_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal' OR cvterm.name = 'interchromosomal' OR cvterm.name = 'chromosomal_variation_attribute'; --- ************************************************ --- *** relation: intrachromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW intrachromosomal AS SELECT feature_id AS intrachromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrachromosomal'; --- ************************************************ --- *** relation: interchromosomal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW interchromosomal AS SELECT feature_id AS interchromosomal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal'; --- ************************************************ --- *** relation: insertion_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of a chromosomal insertion,. *** --- ************************************************ --- CREATE VIEW insertion_attribute AS SELECT feature_id AS insertion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem' OR cvterm.name = 'direct' OR cvterm.name = 'inverted' OR cvterm.name = 'insertion_attribute'; --- ************************************************ --- *** relation: tandem *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW tandem AS SELECT feature_id AS tandem_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem'; --- ************************************************ --- *** relation: direct *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is not in a cytologically inverted or *** --- *** ientation. *** --- ************************************************ --- CREATE VIEW direct AS SELECT feature_id AS direct_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct'; --- ************************************************ --- *** relation: inverted *** --- *** relation type: VIEW *** --- *** *** --- *** A quality of an insertion where the inse *** --- *** rt is in a cytologically inverted orient *** --- *** ation. *** --- ************************************************ --- CREATE VIEW inverted AS SELECT feature_id AS inverted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted'; --- ************************************************ --- *** relation: free *** --- *** relation type: VIEW *** --- *** *** --- *** The quality of a duplication where the n *** --- *** ew region exists independently of the or *** --- *** iginal. *** --- ************************************************ --- CREATE VIEW free AS SELECT feature_id AS free_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free'; --- ************************************************ --- *** relation: inversion_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW inversion_attribute AS SELECT feature_id AS inversion_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric' OR cvterm.name = 'paracentric' OR cvterm.name = 'inversion_attribute'; --- ************************************************ --- *** relation: pericentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pericentric AS SELECT feature_id AS pericentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric'; --- ************************************************ --- *** relation: paracentric *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paracentric AS SELECT feature_id AS paracentric_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric'; --- ************************************************ --- *** relation: translocaton_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW translocaton_attribute AS SELECT feature_id AS translocaton_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal' OR cvterm.name = 'insertional' OR cvterm.name = 'translocaton_attribute'; --- ************************************************ --- *** relation: reciprocal *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW reciprocal AS SELECT feature_id AS reciprocal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal'; --- ************************************************ --- *** relation: insertional *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW insertional AS SELECT feature_id AS insertional_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertional'; --- ************************************************ --- *** relation: duplication_attribute *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW duplication_attribute AS SELECT feature_id AS duplication_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free' OR cvterm.name = 'duplication_attribute'; --- ************************************************ --- *** relation: chromosomally_aberrant_genome *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosomally_aberrant_genome AS SELECT feature_id AS chromosomally_aberrant_genome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomally_aberrant_genome'; --- ************************************************ --- *** relation: assembly_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment differs from the orig *** --- *** inal assembly due to an improvement that *** --- *** replaces a mistake. *** --- ************************************************ --- CREATE VIEW assembly_error_correction AS SELECT feature_id AS assembly_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assembly_error_correction'; --- ************************************************ --- *** relation: base_call_error_correction *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the final nuc *** --- *** leotide assignment is different from tha *** --- *** t given by the base caller due to an imp *** --- *** rovement that replaces a mistake. *** --- ************************************************ --- CREATE VIEW base_call_error_correction AS SELECT feature_id AS base_call_error_correction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'base_call_error_correction'; --- ************************************************ --- *** relation: peptide_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A region of peptide sequence used to tar *** --- *** get the polypeptide molecule to a specif *** --- *** ic organelle. *** --- ************************************************ --- CREATE VIEW peptide_localization_signal AS SELECT feature_id AS peptide_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'peptide_localization_signal'; --- ************************************************ --- *** relation: nuclear_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nucleus. *** --- ************************************************ --- CREATE VIEW nuclear_localization_signal AS SELECT feature_id AS nuclear_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_localization_signal'; --- ************************************************ --- *** relation: endosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the endosome. *** --- ************************************************ --- CREATE VIEW endosomal_localization_signal AS SELECT feature_id AS endosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'endosomal_localization_signal'; --- ************************************************ --- *** relation: lysosomal_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the lysosome. *** --- ************************************************ --- CREATE VIEW lysosomal_localization_signal AS SELECT feature_id AS lysosomal_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lysosomal_localization_signal'; --- ************************************************ --- *** relation: nuclear_export_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to he cytoplasm. *** --- ************************************************ --- CREATE VIEW nuclear_export_signal AS SELECT feature_id AS nuclear_export_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_export_signal'; --- ************************************************ --- *** relation: recombination_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A region recognized by a recombinase. *** --- ************************************************ --- CREATE VIEW recombination_signal_sequence AS SELECT feature_id AS recombination_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_signal_sequence'; --- ************************************************ --- *** relation: cryptic_splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** A splice site that is in part of the tra *** --- *** nscript not normally spliced. They occur *** --- *** via mutation or transcriptional error. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site AS SELECT feature_id AS cryptic_splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site'; --- ************************************************ --- *** relation: nuclear_rim_localization_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide region that targets a poly *** --- *** peptide to the nuclear rim. *** --- ************************************************ --- CREATE VIEW nuclear_rim_localization_signal AS SELECT feature_id AS nuclear_rim_localization_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclear_rim_localization_signal'; --- ************************************************ --- *** relation: p_element *** --- *** relation type: VIEW *** --- *** *** --- *** A P_element is a DNA transposon responsi *** --- *** ble for hybrid dysgenesis. *** --- ************************************************ --- CREATE VIEW p_element AS SELECT feature_id AS p_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'p_element'; --- ************************************************ --- *** relation: functional_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which the function *** --- *** of a gene product is altered with respe *** --- *** ct to a reference. *** --- ************************************************ --- CREATE VIEW functional_variant AS SELECT feature_id AS functional_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript_function_variant' OR cvterm.name = 'translational_product_function_variant' OR cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'functional_variant'; --- ************************************************ --- *** relation: structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes one or m *** --- *** ore sequence features. *** --- ************************************************ --- CREATE VIEW structural_variant AS SELECT feature_id AS structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silent_mutation' OR cvterm.name = 'copy_number_change' OR cvterm.name = 'gene_variant' OR cvterm.name = 'regulatory_region_variant' OR cvterm.name = 'intergenic_variant' OR cvterm.name = 'upstream_gene_variant' OR cvterm.name = 'downstream_gene_variant' OR cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'TF_binding_site_variant' OR cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'structural_variant'; --- ************************************************ --- *** relation: transcript_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the func *** --- *** tioning of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcript_function_variant AS SELECT feature_id AS transcript_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'level_of_transcript_variant' OR cvterm.name = 'transcript_processing_variant' OR cvterm.name = 'transcript_stability_variant' OR cvterm.name = 'transcription_variant' OR cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcript_function_variant'; --- ************************************************ --- *** relation: translational_product_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the func *** --- *** tioning of a translational product with *** --- *** respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_function_variant AS SELECT feature_id AS translational_product_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translational_product_level_variant' OR cvterm.name = 'polypeptide_function_variant' OR cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'translational_product_function_variant'; --- ************************************************ --- *** relation: level_of_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which alters the leve *** --- *** l of a transcript. *** --- ************************************************ --- CREATE VIEW level_of_transcript_variant AS SELECT feature_id AS level_of_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant' OR cvterm.name = 'increased_transcript_level_variant' OR cvterm.name = 'level_of_transcript_variant'; --- ************************************************ --- *** relation: decreased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_level_variant AS SELECT feature_id AS decreased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_level_variant'; --- ************************************************ --- *** relation: increased_transcript_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the le *** --- *** vel of mature, spliced and processed RNA *** --- *** with respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_level_variant AS SELECT feature_id AS increased_transcript_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_level_variant'; --- ************************************************ --- *** relation: transcript_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that affects the post *** --- *** transcriptional processing of a transcr *** --- *** ipt with respect to a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW transcript_processing_variant AS SELECT feature_id AS transcript_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant' OR cvterm.name = 'polyadenylation_variant' OR cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'transcript_processing_variant'; --- ************************************************ --- *** relation: editing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** the process of editing is disrupted with *** --- *** respect to the reference. *** --- ************************************************ --- CREATE VIEW editing_variant AS SELECT feature_id AS editing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'editing_variant'; --- ************************************************ --- *** relation: polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes polyaden *** --- *** ylation with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polyadenylation_variant AS SELECT feature_id AS polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'polyadenylation_variant'; --- ************************************************ --- *** relation: transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes the stability of *** --- *** a transcript with respect to a reference *** --- *** sequence. *** --- ************************************************ --- CREATE VIEW transcript_stability_variant AS SELECT feature_id AS transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'transcript_stability_variant'; --- ************************************************ --- *** relation: decreased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcript_stability_variant AS SELECT feature_id AS decreased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcript_stability_variant'; --- ************************************************ --- *** relation: increased_transcript_stability_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases transc *** --- *** ript stability with respect to a referen *** --- *** ce sequence. *** --- ************************************************ --- CREATE VIEW increased_transcript_stability_variant AS SELECT feature_id AS increased_transcript_stability_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcript_stability_variant'; --- ************************************************ --- *** relation: transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant that changes alters the transc *** --- *** ription of a transcript with respect to *** --- *** a reference sequence. *** --- ************************************************ --- CREATE VIEW transcription_variant AS SELECT feature_id AS transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcription_variant'; --- ************************************************ --- *** relation: rate_of_transcription_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the rate *** --- *** of transcription with respect to a refe *** --- *** rence sequence. *** --- ************************************************ --- CREATE VIEW rate_of_transcription_variant AS SELECT feature_id AS rate_of_transcription_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'rate_of_transcription_variant'; --- ************************************************ --- *** relation: increased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that increases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW increased_transcription_rate_variant AS SELECT feature_id AS increased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_transcription_rate_variant'; --- ************************************************ --- *** relation: decreased_transcription_rate_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that decreases the ra *** --- *** te of transcription with respect to a re *** --- *** ference sequence. *** --- ************************************************ --- CREATE VIEW decreased_transcription_rate_variant AS SELECT feature_id AS decreased_transcription_rate_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_transcription_rate_variant'; --- ************************************************ --- *** relation: translational_product_level_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A functional variant that changes the tr *** --- *** anslational product level with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW translational_product_level_variant AS SELECT feature_id AS translational_product_level_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'translational_product_level_variant'; --- ************************************************ --- *** relation: polypeptide_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes polypep *** --- *** tide functioning with respect to a refer *** --- *** ence sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_function_variant AS SELECT feature_id AS polypeptide_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_function_variant'; --- ************************************************ --- *** relation: decreased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which decreases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW decreased_translational_product_level AS SELECT feature_id AS decreased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_translational_product_level'; --- ************************************************ --- *** relation: increased_translational_product_level *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which increases the t *** --- *** ranslational product level with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW increased_translational_product_level AS SELECT feature_id AS increased_translational_product_level_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_translational_product_level'; --- ************************************************ --- *** relation: polypeptide_gain_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes gain of *** --- *** polypeptide function with respect to a r *** --- *** eference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_gain_of_function_variant AS SELECT feature_id AS polypeptide_gain_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_gain_of_function_variant'; --- ************************************************ --- *** relation: polypeptide_localization_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which changes the loc *** --- *** alization of a polypeptide with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_localization_variant AS SELECT feature_id AS polypeptide_localization_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_localization_variant'; --- ************************************************ --- *** relation: polypeptide_loss_of_function_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the loss *** --- *** of a polypeptide function with respect t *** --- *** o a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_loss_of_function_variant AS SELECT feature_id AS polypeptide_loss_of_function_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_loss_of_function_variant'; --- ************************************************ --- *** relation: inactive_ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a ligand binding site with re *** --- *** spect to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_ligand_binding_site AS SELECT feature_id AS inactive_ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'inactive_ligand_binding_site'; --- ************************************************ --- *** relation: polypeptide_partial_loss_of_function *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes some but *** --- *** not all loss of polypeptide function wit *** --- *** h respect to a reference sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_partial_loss_of_function AS SELECT feature_id AS polypeptide_partial_loss_of_function_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_partial_loss_of_function'; --- ************************************************ --- *** relation: polypeptide_post_translational_processing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** in post translational processing of the *** --- *** peptide with respect to a reference sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW polypeptide_post_translational_processing_variant AS SELECT feature_id AS polypeptide_post_translational_processing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_post_translational_processing_variant'; --- ************************************************ --- *** relation: copy_number_change *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where copies of a fea *** --- *** ture (CNV) are either increased or decre *** --- *** ased. *** --- ************************************************ --- CREATE VIEW copy_number_change AS SELECT feature_id AS copy_number_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_change'; --- ************************************************ --- *** relation: gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where the structure o *** --- *** f the gene is changed. *** --- ************************************************ --- CREATE VIEW gene_variant AS SELECT feature_id AS gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'gene_variant'; --- ************************************************ --- *** relation: gene_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a two genes h *** --- *** ave become joined. *** --- ************************************************ --- CREATE VIEW gene_fusion AS SELECT feature_id AS gene_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_fusion'; --- ************************************************ --- *** relation: regulatory_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a regu *** --- *** latory region. *** --- ************************************************ --- CREATE VIEW regulatory_region_variant AS SELECT feature_id AS regulatory_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant' OR cvterm.name = 'regulatory_region_variant'; --- ************************************************ --- *** relation: stop_retained_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se in the terminator codon is changed, b *** --- *** ut the terminator remains. *** --- ************************************************ --- CREATE VIEW stop_retained_variant AS SELECT feature_id AS stop_retained_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant'; --- ************************************************ --- *** relation: splicing_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the proc *** --- *** ess of splicing. *** --- ************************************************ --- CREATE VIEW splicing_variant AS SELECT feature_id AS splicing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'splicing_variant'; --- ************************************************ --- *** relation: cryptic_splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant causing a new (functi *** --- *** onal) splice site. *** --- ************************************************ --- CREATE VIEW cryptic_splice_site_variant AS SELECT feature_id AS cryptic_splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'cryptic_splice_site_variant'; --- ************************************************ --- *** relation: cryptic_splice_acceptor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new acceptor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_acceptor AS SELECT feature_id AS cryptic_splice_acceptor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_acceptor'; --- ************************************************ --- *** relation: cryptic_splice_donor *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a new splice *** --- *** site is created due to the activation of *** --- *** a new donor. *** --- ************************************************ --- CREATE VIEW cryptic_splice_donor AS SELECT feature_id AS cryptic_splice_donor_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptic_splice_donor'; --- ************************************************ --- *** relation: exon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an exon is lo *** --- *** st from the transcript. *** --- ************************************************ --- CREATE VIEW exon_loss AS SELECT feature_id AS exon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_loss'; --- ************************************************ --- *** relation: intron_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby an intron is *** --- *** gained by the processed transcript; usua *** --- *** lly a result of an alteration of the don *** --- *** or or acceptor. *** --- ************************************************ --- CREATE VIEW intron_gain AS SELECT feature_id AS intron_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intron_gain'; --- ************************************************ --- *** relation: splice_acceptor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the 2 base *** --- *** region at the 3' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_acceptor_variant AS SELECT feature_id AS splice_acceptor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant'; --- ************************************************ --- *** relation: splice_donor_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A splice variant that changes the2 base *** --- *** region at the 5' end of an intron. *** --- ************************************************ --- CREATE VIEW splice_donor_variant AS SELECT feature_id AS splice_donor_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_variant'; --- ************************************************ --- *** relation: transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the stru *** --- *** cture of the transcript. *** --- ************************************************ --- CREATE VIEW transcript_variant AS SELECT feature_id AS transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'transcript_variant'; --- ************************************************ --- *** relation: complex_change_in_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant with a complex INDE *** --- *** L- Insertion or deletion that spans an e *** --- *** xon/intron border or a coding sequence/U *** --- *** TR border. *** --- ************************************************ --- CREATE VIEW complex_change_in_transcript AS SELECT feature_id AS complex_change_in_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_in_transcript'; --- ************************************************ --- *** relation: stop_lost *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the terminator codon (stop) is cha *** --- *** nged, resulting in an elongated transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW stop_lost AS SELECT feature_id AS stop_lost_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_lost'; --- ************************************************ --- *** relation: coding_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the codi *** --- *** ng sequence. *** --- ************************************************ --- CREATE VIEW coding_sequence_variant AS SELECT feature_id AS coding_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'coding_sequence_variant'; --- ************************************************ --- *** relation: codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes at least *** --- *** one base in a codon. *** --- ************************************************ --- CREATE VIEW codon_variant AS SELECT feature_id AS codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'codon_variant'; --- ************************************************ --- *** relation: initiator_codon_change *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the first codon of a transcrip *** --- *** t. *** --- ************************************************ --- CREATE VIEW initiator_codon_change AS SELECT feature_id AS initiator_codon_change_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'initiator_codon_change'; --- ************************************************ --- *** relation: non_synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid or stop codon. *** --- ************************************************ --- CREATE VIEW non_synonymous_codon AS SELECT feature_id AS non_synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'non_synonymous_codon'; --- ************************************************ --- *** relation: conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different but *** --- *** similar amino acid. These variants may *** --- *** or may not be deleterious. *** --- ************************************************ --- CREATE VIEW conservative_missense_codon AS SELECT feature_id AS conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon'; --- ************************************************ --- *** relation: non_conservative_missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for an amino acid w *** --- *** ith different biochemical properties. *** --- ************************************************ --- CREATE VIEW non_conservative_missense_codon AS SELECT feature_id AS non_conservative_missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_missense_codon'; --- ************************************************ --- *** relation: stop_gained *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed, resulting in *** --- *** a premature stop codon, leading to a sh *** --- *** ortened transcript. *** --- ************************************************ --- CREATE VIEW stop_gained AS SELECT feature_id AS stop_gained_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_gained'; --- ************************************************ --- *** relation: synonymous_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby a base of a c *** --- *** odon is changed, but there is no resulti *** --- *** ng change to the encoded amino acid. *** --- ************************************************ --- CREATE VIEW synonymous_codon AS SELECT feature_id AS synonymous_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'synonymous_codon'; --- ************************************************ --- *** relation: frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** because the number of nucleotides inser *** --- *** ted or deleted is not a multiple of thre *** --- *** e. *** --- ************************************************ --- CREATE VIEW frameshift_variant AS SELECT feature_id AS frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'frameshift_variant'; --- ************************************************ --- *** relation: terminator_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** of the bases in the terminator codon is *** --- *** changed. *** --- ************************************************ --- CREATE VIEW terminator_codon_variant AS SELECT feature_id AS terminator_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminator_codon_variant'; --- ************************************************ --- *** relation: frame_restoring_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that reverts the sequ *** --- *** ence of a previous frameshift mutation b *** --- *** ack to the initial frame. *** --- ************************************************ --- CREATE VIEW frame_restoring_variant AS SELECT feature_id AS frame_restoring_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'frame_restoring_variant'; --- ************************************************ --- *** relation: minus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base ahead. *** --- ************************************************ --- CREATE VIEW minus_1_frameshift_variant AS SELECT feature_id AS minus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_frameshift_variant'; --- ************************************************ --- *** relation: minus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW minus_2_frameshift_variant AS SELECT feature_id AS minus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_2_frameshift_variant'; --- ************************************************ --- *** relation: plus_1_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which causes a disrup *** --- *** tion of the translational reading frame, *** --- *** by shifting one base backward. *** --- ************************************************ --- CREATE VIEW plus_1_frameshift_variant AS SELECT feature_id AS plus_1_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_frameshift_variant'; --- ************************************************ --- *** relation: plus_2_frameshift_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW plus_2_frameshift_variant AS SELECT feature_id AS plus_2_frameshift_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_2_frameshift variant'; --- ************************************************ --- *** relation: transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a transcript t *** --- *** hat changes the secondary structure of t *** --- *** he RNA product. *** --- ************************************************ --- CREATE VIEW transcript_secondary_structure_variant AS SELECT feature_id AS transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: compensatory_transcript_secondary_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A secondary structure variant that compe *** --- *** nsate for the change made by a previous *** --- *** variant. *** --- ************************************************ --- CREATE VIEW compensatory_transcript_secondary_structure_variant AS SELECT feature_id AS compensatory_transcript_secondary_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant'; --- ************************************************ --- *** relation: translational_product_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within the transcript *** --- *** that changes the structure of the trans *** --- *** lational product. *** --- ************************************************ --- CREATE VIEW translational_product_structure_variant AS SELECT feature_id AS translational_product_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'translational_product_structure_variant'; --- ************************************************ --- *** relation: threed_polypeptide_structure_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW threed_polypeptide_structure_variant AS SELECT feature_id AS threed_polypeptide_structure_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = '3D_polypeptide_structure_variant'; --- ************************************************ --- *** relation: complex_3d_structural_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the resu *** --- *** lting polypeptide structure. *** --- ************************************************ --- CREATE VIEW complex_3d_structural_variant AS SELECT feature_id AS complex_3d_structural_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_3D_structural_variant'; --- ************************************************ --- *** relation: conformational_change_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in the CDS region tha *** --- *** t causes a conformational change in the *** --- *** resulting polypeptide sequence. *** --- ************************************************ --- CREATE VIEW conformational_change_variant AS SELECT feature_id AS conformational_change_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conformational_change_variant'; --- ************************************************ --- *** relation: complex_change_of_translational_product_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW complex_change_of_translational_product_variant AS SELECT feature_id AS complex_change_of_translational_product_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_change_of_translational_product_variant'; --- ************************************************ --- *** relation: polypeptide_sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes a change in the resulting polypep *** --- *** tide sequence. *** --- ************************************************ --- CREATE VIEW polypeptide_sequence_variant AS SELECT feature_id AS polypeptide_sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'polypeptide_sequence_variant'; --- ************************************************ --- *** relation: amino_acid_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the loss of an amino acid from the *** --- *** resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_deletion AS SELECT feature_id AS amino_acid_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_deletion'; --- ************************************************ --- *** relation: amino_acid_insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant within a CDS resultin *** --- *** g in the gain of an amino acid to the re *** --- *** sulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_insertion AS SELECT feature_id AS amino_acid_insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'amino_acid_insertion'; --- ************************************************ --- *** relation: amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon resulting *** --- *** in the substitution of one amino acid fo *** --- *** r another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW amino_acid_substitution AS SELECT feature_id AS amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'amino_acid_substitution'; --- ************************************************ --- *** relation: conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a similar amino acid f *** --- *** or another in the resulting polypeptide. *** --- ************************************************ --- CREATE VIEW conservative_amino_acid_substitution AS SELECT feature_id AS conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: non_conservative_amino_acid_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of a codon causing th *** --- *** e substitution of a non conservative ami *** --- *** no acid for another in the resulting pol *** --- *** ypeptide. *** --- ************************************************ --- CREATE VIEW non_conservative_amino_acid_substitution AS SELECT feature_id AS non_conservative_amino_acid_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_conservative_amino_acid_substitution'; --- ************************************************ --- *** relation: elongated_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide AS SELECT feature_id AS elongated_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide'; --- ************************************************ --- *** relation: elongated_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the C terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_c_terminal AS SELECT feature_id AS elongated_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes elongation of the resulting polyp *** --- *** eptide sequence at the N terminus. *** --- ************************************************ --- CREATE VIEW elongated_polypeptide_n_terminal AS SELECT feature_id AS elongated_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the C termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_in_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_c_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the C te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_c_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_c_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal'; --- ************************************************ --- *** relation: elongated_in_frame_polypeptide_n_terminal_elongation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes in frame elongation of the result *** --- *** ing polypeptide sequence at the N termin *** --- *** us. *** --- ************************************************ --- CREATE VIEW elongated_in_frame_polypeptide_n_terminal_elongation AS SELECT feature_id AS elongated_in_frame_polypeptide_n_terminal_elongation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation'; --- ************************************************ --- *** relation: elongated_out_of_frame_polypeptide_n_terminal *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant with in the CDS that *** --- *** causes out of frame elongation of the re *** --- *** sulting polypeptide sequence at the N te *** --- *** rminus. *** --- ************************************************ --- CREATE VIEW elongated_out_of_frame_polypeptide_n_terminal AS SELECT feature_id AS elongated_out_of_frame_polypeptide_n_terminal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal'; --- ************************************************ --- *** relation: polypeptide_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a fusion *** --- *** of two polypeptide sequences. *** --- ************************************************ --- CREATE VIEW polypeptide_fusion AS SELECT feature_id AS polypeptide_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_fusion'; --- ************************************************ --- *** relation: polypeptide_truncation *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant of the CD that causes *** --- *** a truncation of the resulting polypepti *** --- *** de. *** --- ************************************************ --- CREATE VIEW polypeptide_truncation AS SELECT feature_id AS polypeptide_truncation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_truncation'; --- ************************************************ --- *** relation: inactive_catalytic_site *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes the inact *** --- *** ivation of a catalytic site with respect *** --- *** to a reference sequence. *** --- ************************************************ --- CREATE VIEW inactive_catalytic_site AS SELECT feature_id AS inactive_catalytic_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inactive_catalytic_site'; --- ************************************************ --- *** relation: nc_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant of a non coding RNA *** --- *** gene. *** --- ************************************************ --- CREATE VIEW nc_transcript_variant AS SELECT feature_id AS nc_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant' OR cvterm.name = 'nc_transcript_variant'; --- ************************************************ --- *** relation: mature_mirna_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant located with the se *** --- *** quence of the mature miRNA. *** --- ************************************************ --- CREATE VIEW mature_mirna_variant AS SELECT feature_id AS mature_mirna_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_miRNA_variant'; --- ************************************************ --- *** relation: nmd_transcript_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A variant in a transcript that is the ta *** --- *** rget of NMD. *** --- ************************************************ --- CREATE VIEW nmd_transcript_variant AS SELECT feature_id AS nmd_transcript_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'NMD_transcript_variant'; --- ************************************************ --- *** relation: utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant that is located wit *** --- *** hin the UTR. *** --- ************************************************ --- CREATE VIEW utr_variant AS SELECT feature_id AS utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'UTR_variant'; --- ************************************************ --- *** relation: five_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 5' UTR. *** --- ************************************************ --- CREATE VIEW five_prime_utr_variant AS SELECT feature_id AS five_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5_prime_UTR_variant'; --- ************************************************ --- *** relation: three_prime_utr_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A UTR variant of the 3' UTR. *** --- ************************************************ --- CREATE VIEW three_prime_utr_variant AS SELECT feature_id AS three_prime_utr_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '3_prime_UTR_variant'; --- ************************************************ --- *** relation: terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A codon variant that changes at least on *** --- *** e base of the last codon of the transcri *** --- *** pt. *** --- ************************************************ --- CREATE VIEW terminal_codon_variant AS SELECT feature_id AS terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminal_codon_variant'; --- ************************************************ --- *** relation: incomplete_terminal_codon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant where at least one ba *** --- *** se of the final codon of an incompletely *** --- *** annotated transcript is changed. *** --- ************************************************ --- CREATE VIEW incomplete_terminal_codon_variant AS SELECT feature_id AS incomplete_terminal_codon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'incomplete_terminal_codon_variant'; --- ************************************************ --- *** relation: intron_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript variant occurring within an *** --- *** intron. *** --- ************************************************ --- CREATE VIEW intron_variant AS SELECT feature_id AS intron_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'intron_variant'; --- ************************************************ --- *** relation: intergenic_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located in the interg *** --- *** enic region, between genes. *** --- ************************************************ --- CREATE VIEW intergenic_variant AS SELECT feature_id AS intergenic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_variant'; --- ************************************************ --- *** relation: splice_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes the firs *** --- *** t two or last two bases of an intron, or *** --- *** the 5th base from the start of the intr *** --- *** on in the orientation of the transcript. *** --- ************************************************ --- CREATE VIEW splice_site_variant AS SELECT feature_id AS splice_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR cvterm.name = 'splice_site_variant'; --- ************************************************ --- *** relation: splice_region_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant in which a change has *** --- *** occurred within the region of the splic *** --- *** e site, either within 1-3 bases of the e *** --- *** xon or 3-8 bases of the intron. *** --- ************************************************ --- CREATE VIEW splice_region_variant AS SELECT feature_id AS splice_region_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_region_variant'; --- ************************************************ --- *** relation: upstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 5' of a gene. *** --- ************************************************ --- CREATE VIEW upstream_gene_variant AS SELECT feature_id AS upstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_upstream_variant' OR cvterm.name = '2KB_upstream_variant' OR cvterm.name = 'upstream_gene_variant'; --- ************************************************ --- *** relation: downstream_gene_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located 3' of a gene. *** --- ************************************************ --- CREATE VIEW downstream_gene_variant AS SELECT feature_id AS downstream_gene_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '5KB_downstream_variant' OR cvterm.name = '500B_downstream_variant' OR cvterm.name = 'downstream_gene_variant'; --- ************************************************ --- *** relation: fivekb_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5 KB o *** --- *** f the end of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_downstream_variant AS SELECT feature_id AS fivekb_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant' OR cvterm.name = '5KB_downstream_variant'; --- ************************************************ --- *** relation: fivehundred_b_downstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a half *** --- *** KB of the end of a gene. *** --- ************************************************ --- CREATE VIEW fivehundred_b_downstream_variant AS SELECT feature_id AS fivehundred_b_downstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '500B_downstream_variant'; --- ************************************************ --- *** relation: fivekb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 5KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW fivekb_upstream_variant AS SELECT feature_id AS fivekb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant' OR cvterm.name = '5KB_upstream_variant'; --- ************************************************ --- *** relation: twokb_upstream_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within 2KB 5' *** --- *** of a gene. *** --- ************************************************ --- CREATE VIEW twokb_upstream_variant AS SELECT feature_id AS twokb_upstream_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = '2KB_upstream_variant'; --- ************************************************ --- *** relation: rrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for ribosomal RNA. *** --- ************************************************ --- CREATE VIEW rrna_gene AS SELECT feature_id AS rrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_gene'; --- ************************************************ --- *** relation: pirna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes for an piwi associat *** --- *** ed RNA. *** --- ************************************************ --- CREATE VIEW pirna_gene AS SELECT feature_id AS pirna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'piRNA_gene'; --- ************************************************ --- *** relation: rnase_p_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes an RNase P RNA. *** --- ************************************************ --- CREATE VIEW rnase_p_rna_gene AS SELECT feature_id AS rnase_p_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA_gene'; --- ************************************************ --- *** relation: rnase_mrp_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes a RNase_MRP_RNA. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna_gene AS SELECT feature_id AS rnase_mrp_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA_gene'; --- ************************************************ --- *** relation: lincrna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that encodes large intervening no *** --- *** n-coding RNA. *** --- ************************************************ --- CREATE VIEW lincrna_gene AS SELECT feature_id AS lincrna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lincRNA_gene'; --- ************************************************ --- *** relation: mathematically_defined_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A mathematically defined repeat (MDR) is *** --- *** a experimental feature that is determin *** --- *** ed by querying overlapping oligomers of *** --- *** length k against a database of shotgun s *** --- *** equence data and identifying regions in *** --- *** the query sequence that exceed a statist *** --- *** ically determined threshold of repetitiv *** --- *** eness. *** --- ************************************************ --- CREATE VIEW mathematically_defined_repeat AS SELECT feature_id AS mathematically_defined_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mathematically_defined_repeat'; --- ************************************************ --- *** relation: telomerase_rna_gene *** --- *** relation type: VIEW *** --- *** *** --- *** A telomerase RNA gene is a non coding RN *** --- *** A gene the RNA product of which is a com *** --- *** ponent of telomerase. *** --- ************************************************ --- CREATE VIEW telomerase_rna_gene AS SELECT feature_id AS telomerase_rna_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA_gene'; --- ************************************************ --- *** relation: targeting_vector *** --- *** relation type: VIEW *** --- *** *** --- *** An engineered vector that is able to tak *** --- *** e part in homologous recombination in a *** --- *** host with the intent of introducing site *** --- *** specific genomic modifications. *** --- ************************************************ --- CREATE VIEW targeting_vector AS SELECT feature_id AS targeting_vector_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'targeting_vector'; --- ************************************************ --- *** relation: genetic_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A measurable sequence feature that varie *** --- *** s within a population. *** --- ************************************************ --- CREATE VIEW genetic_marker AS SELECT feature_id AS genetic_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'genetic_marker'; --- ************************************************ --- *** relation: dart_marker *** --- *** relation type: VIEW *** --- *** *** --- *** A genetic marker, discovered using Diver *** --- *** sity Arrays Technology (DArT) technology *** --- *** . *** --- ************************************************ --- CREATE VIEW dart_marker AS SELECT feature_id AS dart_marker_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DArT_marker'; --- ************************************************ --- *** relation: kozak_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of ribosome entry site, specific *** --- *** to Eukaryotic organisms that overlaps pa *** --- *** rt of both 5' UTR and CDS sequence. *** --- ************************************************ --- CREATE VIEW kozak_sequence AS SELECT feature_id AS kozak_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'kozak_sequence'; --- ************************************************ --- *** relation: nested_transposon *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon that is disrupted by the in *** --- *** sertion of another element. *** --- ************************************************ --- CREATE VIEW nested_transposon AS SELECT feature_id AS nested_transposon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_transposon'; --- ************************************************ --- *** relation: nested_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is disrupted by the insert *** --- *** ion of another element. *** --- ************************************************ --- CREATE VIEW nested_repeat AS SELECT feature_id AS nested_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'nested_repeat'; --- ************************************************ --- *** relation: inframe_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which does not cause *** --- *** a disruption of the translational readin *** --- *** g frame. *** --- ************************************************ --- CREATE VIEW inframe_variant AS SELECT feature_id AS inframe_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'inframe_variant'; --- ************************************************ --- *** relation: inframe_codon_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which gains a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_gain AS SELECT feature_id AS inframe_codon_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_gain'; --- ************************************************ --- *** relation: inframe_codon_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant which loses a codon, *** --- *** and does not cause a disruption of the t *** --- *** ranslational reading frame. *** --- ************************************************ --- CREATE VIEW inframe_codon_loss AS SELECT feature_id AS inframe_codon_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inframe_codon_loss'; --- ************************************************ --- *** relation: retinoic_acid_responsive_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transcription factor binding site of v *** --- *** ariable direct repeats of the sequence P *** --- *** uGGTCA spaced by five nucleotides (DR5) *** --- *** found in the promoters of retinoic acid- *** --- *** responsive genes, to which retinoic acid *** --- *** receptors bind. *** --- ************************************************ --- CREATE VIEW retinoic_acid_responsive_element AS SELECT feature_id AS retinoic_acid_responsive_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retinoic_acid_responsive_element'; --- ************************************************ --- *** relation: nucleotide_to_protein_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the nucleotide m *** --- *** olecule, interacts selectively and non-c *** --- *** ovalently with polypeptide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_to_protein_binding_site AS SELECT feature_id AS nucleotide_to_protein_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'nucleotide_to_protein_binding_site'; --- ************************************************ --- *** relation: nucleotide_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith nucleotide residues. *** --- ************************************************ --- CREATE VIEW nucleotide_binding_site AS SELECT feature_id AS nucleotide_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'nucleotide_binding_site'; --- ************************************************ --- *** relation: metal_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith metal ions. *** --- ************************************************ --- CREATE VIEW metal_binding_site AS SELECT feature_id AS metal_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'metal_binding_site'; --- ************************************************ --- *** relation: ligand_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the molecule, in *** --- *** teracts selectively and non-covalently w *** --- *** ith a small molecule such as a drug, or *** --- *** hormone. *** --- ************************************************ --- CREATE VIEW ligand_binding_site AS SELECT feature_id AS ligand_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'ligand_binding_site'; --- ************************************************ --- *** relation: nested_tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** An NTR is a nested repeat of two distinc *** --- *** t tandem motifs interspersed with each o *** --- *** ther. *** --- ************************************************ --- CREATE VIEW nested_tandem_repeat AS SELECT feature_id AS nested_tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nested_tandem_repeat'; --- ************************************************ --- *** relation: promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW promoter_element AS SELECT feature_id AS promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'promoter_element'; --- ************************************************ --- *** relation: core_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW core_promoter_element AS SELECT feature_id AS core_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'core_promoter_element'; --- ************************************************ --- *** relation: rna_polymerase_ii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase II. *** --- ************************************************ --- CREATE VIEW rna_polymerase_ii_tata_box AS SELECT feature_id AS rna_polymerase_ii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_II_TATA_box'; --- ************************************************ --- *** relation: rna_polymerase_iii_tata_box *** --- *** relation type: VIEW *** --- *** *** --- *** A TATA box core promoter of a gene trans *** --- *** cribed by RNA polymerase III. *** --- ************************************************ --- CREATE VIEW rna_polymerase_iii_tata_box AS SELECT feature_id AS rna_polymerase_iii_tata_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNA_polymerase_III_TATA_box'; --- ************************************************ --- *** relation: bred_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A core TRNA polymerase II promoter eleme *** --- *** nt with consensus (G/A)T(T/G/A)(T/A)(G/T *** --- *** )(T/G)(T/G). *** --- ************************************************ --- CREATE VIEW bred_motif AS SELECT feature_id AS bred_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BREd_motif'; --- ************************************************ --- *** relation: dce *** --- *** relation type: VIEW *** --- *** *** --- *** A discontinuous core element of RNA poly *** --- *** merase II transcribed genes, situated do *** --- *** wnstream of the TSS. It is composed of t *** --- *** hree sub elements: SI, SII and SIII. *** --- ************************************************ --- CREATE VIEW dce AS SELECT feature_id AS dce_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE'; --- ************************************************ --- *** relation: dce_si *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement, with consensus sequence CTTC. *** --- ************************************************ --- CREATE VIEW dce_si AS SELECT feature_id AS dce_si_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SI'; --- ************************************************ --- *** relation: dce_sii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence CTGT. *** --- ************************************************ --- CREATE VIEW dce_sii AS SELECT feature_id AS dce_sii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SII'; --- ************************************************ --- *** relation: dce_siii *** --- *** relation type: VIEW *** --- *** *** --- *** A sub element of the DCE core promoter e *** --- *** lement with consensus sequence AGC. *** --- ************************************************ --- CREATE VIEW dce_siii AS SELECT feature_id AS dce_siii_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'DCE_SIII'; --- ************************************************ --- *** relation: proximal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW proximal_promoter_element AS SELECT feature_id AS proximal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element'; --- ************************************************ --- *** relation: rnapol_ii_core_promoter *** --- *** relation type: VIEW *** --- *** *** --- *** The minimal portion of the promoter requ *** --- *** ired to properly initiate transcription *** --- *** in RNA polymerase II transcribed genes. *** --- ************************************************ --- CREATE VIEW rnapol_ii_core_promoter AS SELECT feature_id AS rnapol_ii_core_promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNApol_II_core_promoter'; --- ************************************************ --- *** relation: distal_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW distal_promoter_element AS SELECT feature_id AS distal_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distal_promoter_element'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma_70 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma_70 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma_70_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma_70'; --- ************************************************ --- *** relation: bacterial_rnapol_promoter_sigma54 *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW bacterial_rnapol_promoter_sigma54 AS SELECT feature_id AS bacterial_rnapol_promoter_sigma54_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bacterial_RNApol_promoter_sigma54'; --- ************************************************ --- *** relation: minus_12_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_12_signal AS SELECT feature_id AS minus_12_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_12_signal'; --- ************************************************ --- *** relation: minus_24_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region about 12-bp upstream *** --- *** of the start point of bacterial transcri *** --- *** ption units, involved with sigma factor *** --- *** 54. *** --- ************************************************ --- CREATE VIEW minus_24_signal AS SELECT feature_id AS minus_24_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_24_signal'; --- ************************************************ --- *** relation: a_box_type_1 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 1 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_1 AS SELECT feature_id AS a_box_type_1_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_1'; --- ************************************************ --- *** relation: a_box_type_2 *** --- *** relation type: VIEW *** --- *** *** --- *** An A box within an RNA polymerase III ty *** --- *** pe 2 promoter. *** --- ************************************************ --- CREATE VIEW a_box_type_2 AS SELECT feature_id AS a_box_type_2_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_box_type_2'; --- ************************************************ --- *** relation: intermediate_element *** --- *** relation type: VIEW *** --- *** *** --- *** A core promoter region of RNA polymerase *** --- *** III type 1 promoters. *** --- ************************************************ --- CREATE VIEW intermediate_element AS SELECT feature_id AS intermediate_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intermediate_element'; --- ************************************************ --- *** relation: regulatory_promoter_element *** --- *** relation type: VIEW *** --- *** *** --- *** A promoter element that is not part of t *** --- *** he core promoter, but provides the promo *** --- *** ter with a specific regulatory region. *** --- ************************************************ --- CREATE VIEW regulatory_promoter_element AS SELECT feature_id AS regulatory_promoter_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'regulatory_promoter_element'; --- ************************************************ --- *** relation: transcription_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of transcript *** --- *** ion. *** --- ************************************************ --- CREATE VIEW transcription_regulatory_region AS SELECT feature_id AS transcription_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'transcription_regulatory_region'; --- ************************************************ --- *** relation: translation_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of translatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW translation_regulatory_region AS SELECT feature_id AS translation_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator' OR cvterm.name = 'translation_regulatory_region'; --- ************************************************ --- *** relation: recombination_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of recombinat *** --- *** ion. *** --- ************************************************ --- CREATE VIEW recombination_regulatory_region AS SELECT feature_id AS recombination_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'recombination_regulatory_region'; --- ************************************************ --- *** relation: replication_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory region that is involved in *** --- *** the control of the process of nucleotide *** --- *** replication. *** --- ************************************************ --- CREATE VIEW replication_regulatory_region AS SELECT feature_id AS replication_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'replication_regulatory_region'; --- ************************************************ --- *** relation: sequence_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence motif is a nucleotide or amin *** --- *** o-acid sequence pattern that may have bi *** --- *** ological significance. *** --- ************************************************ --- CREATE VIEW sequence_motif AS SELECT feature_id AS sequence_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'sequence_motif'; --- ************************************************ --- *** relation: experimental_feature_attribute *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute of an experimentally derive *** --- *** d feature. *** --- ************************************************ --- CREATE VIEW experimental_feature_attribute AS SELECT feature_id AS experimental_feature_attribute_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score' OR cvterm.name = 'quality_value' OR cvterm.name = 'experimental_feature_attribute'; --- ************************************************ --- *** relation: score *** --- *** relation type: VIEW *** --- *** *** --- *** The score of an experimentally derived f *** --- *** eature such as a p-value. *** --- ************************************************ --- CREATE VIEW score AS SELECT feature_id AS score_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'score'; --- ************************************************ --- *** relation: quality_value *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental feature attribute that d *** --- *** efines the quality of the feature in a q *** --- *** uantitative way, such as a phred quality *** --- *** score. *** --- ************************************************ --- CREATE VIEW quality_value AS SELECT feature_id AS quality_value_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quality_value'; --- ************************************************ --- *** relation: restriction_enzyme_recognition_site *** --- *** relation type: VIEW *** --- *** *** --- *** The nucleotide region (usually a palindr *** --- *** ome) that is recognized by a restriction *** --- *** enzyme. This may or may not be equal to *** --- *** the restriction enzyme binding site. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_recognition_site AS SELECT feature_id AS restriction_enzyme_recognition_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'restriction_enzyme_recognition_site'; --- ************************************************ --- *** relation: restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary at which a restriction enzy *** --- *** me breaks the nucleotide sequence. *** --- ************************************************ --- CREATE VIEW restriction_enzyme_cleavage_junction AS SELECT feature_id AS restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site' OR cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: five_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The restriction enzyme cleavage junction *** --- *** on the 5' strand of the nucleotide sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW five_prime_restriction_enzyme_junction AS SELECT feature_id AS five_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: three_prime_restriction_enzyme_junction *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW three_prime_restriction_enzyme_junction AS SELECT feature_id AS three_prime_restriction_enzyme_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_restriction_enzyme_junction'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: sticky_end_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sticky_end_restriction_enzyme_cleavage_site AS SELECT feature_id AS sticky_end_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: blunt_end_restriction_enzyme_cleavage_junction *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** both strands are cut at the same positi *** --- *** on. *** --- ************************************************ --- CREATE VIEW blunt_end_restriction_enzyme_cleavage_junction AS SELECT feature_id AS blunt_end_restriction_enzyme_cleavage_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'blunt_end_restriction_enzyme_cleavage_junction'; --- ************************************************ --- *** relation: single_strand_restriction_enzyme_cleavage_site *** --- *** relation type: VIEW *** --- *** *** --- *** A restriction enzyme cleavage site where *** --- *** by only one strand is cut. *** --- ************************************************ --- CREATE VIEW single_strand_restriction_enzyme_cleavage_site AS SELECT feature_id AS single_strand_restriction_enzyme_cleavage_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_restriction_enzyme_junction' OR cvterm.name = 'three_prime_restriction_enzyme_junction' OR cvterm.name = 'single_strand_restriction_enzyme_cleavage_site'; --- ************************************************ --- *** relation: restriction_enzyme_single_strand_overhang *** --- *** relation type: VIEW *** --- *** *** --- *** A terminal region of DNA sequence where *** --- *** the end of the region is not blunt ended *** --- *** . *** --- ************************************************ --- CREATE VIEW restriction_enzyme_single_strand_overhang AS SELECT feature_id AS restriction_enzyme_single_strand_overhang_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_enzyme_single_strand_overhang'; --- ************************************************ --- *** relation: experimentally_defined_binding_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that has been implicated in bin *** --- *** ding although the exact coordinates of b *** --- *** inding may be unknown. *** --- ************************************************ --- CREATE VIEW experimentally_defined_binding_region AS SELECT feature_id AS experimentally_defined_binding_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'experimentally_defined_binding_region'; --- ************************************************ --- *** relation: chip_seq_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence identified by CHiP *** --- *** seq technology to contain a protein bind *** --- *** ing site. *** --- ************************************************ --- CREATE VIEW chip_seq_region AS SELECT feature_id AS chip_seq_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CHiP_seq_region'; --- ************************************************ --- *** relation: aspe_primer *** --- *** relation type: VIEW *** --- *** *** --- *** "A primer containing an SNV at the 3' en *** --- *** d for accurate genotyping. *** --- ************************************************ --- CREATE VIEW aspe_primer AS SELECT feature_id AS aspe_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ASPE_primer'; --- ************************************************ --- *** relation: dcaps_primer *** --- *** relation type: VIEW *** --- *** *** --- *** A primer with one or more mis-matches to *** --- *** the DNA template corresponding to a pos *** --- *** ition within a restriction enzyme recogn *** --- *** ition site. *** --- ************************************************ --- CREATE VIEW dcaps_primer AS SELECT feature_id AS dcaps_primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dCAPS_primer'; --- ************************************************ --- *** relation: histone_modification *** --- *** relation type: VIEW *** --- *** *** --- *** Histone modification is a post translati *** --- *** onally modified region whereby residues *** --- *** of the histone protein are modified by m *** --- *** ethylation, acetylation, phosphorylation *** --- *** , ubiquitination, sumoylation, citrullin *** --- *** ation, or ADP-ribosylation. *** --- ************************************************ --- CREATE VIEW histone_modification AS SELECT feature_id AS histone_modification_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_modification'; --- ************************************************ --- *** relation: histone_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where the mo *** --- *** dification is the methylation of the res *** --- *** idue. *** --- ************************************************ --- CREATE VIEW histone_methylation_site AS SELECT feature_id AS histone_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'histone_methylation_site'; --- ************************************************ --- *** relation: histone_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification where the modific *** --- *** ation is the acylation of the residue. *** --- ************************************************ --- CREATE VIEW histone_acetylation_site AS SELECT feature_id AS histone_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'histone_acetylation_site'; --- ************************************************ --- *** relation: h3k9_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h3k9_acetylation_site AS SELECT feature_id AS h3k9_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_acetylation_site'; --- ************************************************ --- *** relation: h3k14_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k14_acetylation_site AS SELECT feature_id AS h3k14_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K14_acetylation_site'; --- ************************************************ --- *** relation: h3k4_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is mono-methylated. *** --- ************************************************ --- CREATE VIEW h3k4_monomethylation_site AS SELECT feature_id AS h3k4_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site'; --- ************************************************ --- *** relation: h3k4_trimethylation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 protein is tri-methyla *** --- *** ted. *** --- ************************************************ --- CREATE VIEW h3k4_trimethylation AS SELECT feature_id AS h3k4_trimethylation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_trimethylation'; --- ************************************************ --- *** relation: h3k9_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is tri *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k9_trimethylation_site AS SELECT feature_id AS h3k9_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site'; --- ************************************************ --- *** relation: h3k27_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_monomethylation_site AS SELECT feature_id AS h3k27_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site'; --- ************************************************ --- *** relation: h3k27_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k27_trimethylation_site AS SELECT feature_id AS h3k27_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_trimethylation_site'; --- ************************************************ --- *** relation: h3k79_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no- methylated. *** --- ************************************************ --- CREATE VIEW h3k79_monomethylation_site AS SELECT feature_id AS h3k79_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site'; --- ************************************************ --- *** relation: h3k79_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k79_dimethylation_site AS SELECT feature_id AS h3k79_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_dimethylation_site'; --- ************************************************ --- *** relation: h3k79_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k79_trimethylation_site AS SELECT feature_id AS h3k79_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_trimethylation_site'; --- ************************************************ --- *** relation: h4k20_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 20th residue (a lysine), from t *** --- *** he start of the H34histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h4k20_monomethylation_site AS SELECT feature_id AS h4k20_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K20_monomethylation_site'; --- ************************************************ --- *** relation: h2bk5_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H2B protein is methylated *** --- *** . *** --- ************************************************ --- CREATE VIEW h2bk5_monomethylation_site AS SELECT feature_id AS h2bk5_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2BK5_monomethylation_site'; --- ************************************************ --- *** relation: isre *** --- *** relation type: VIEW *** --- *** *** --- *** An ISRE is a transcriptional cis regulat *** --- *** ory region, containing the consensus reg *** --- *** ion: YAGTTTC(A/T)YTTTYCC, responsible fo *** --- *** r increased transcription via interferon *** --- *** binding. *** --- ************************************************ --- CREATE VIEW isre AS SELECT feature_id AS isre_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ISRE'; --- ************************************************ --- *** relation: histone_ubiqitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site where ubiqui *** --- *** tin may be added. *** --- ************************************************ --- CREATE VIEW histone_ubiqitination_site AS SELECT feature_id AS histone_ubiqitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'histone_ubiqitination_site'; --- ************************************************ --- *** relation: h2b_ubiquitination_site *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification site on H2B where *** --- *** ubiquitin may be added. *** --- ************************************************ --- CREATE VIEW h2b_ubiquitination_site AS SELECT feature_id AS h2b_ubiquitination_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H2B_ubiquitination_site'; --- ************************************************ --- *** relation: h3k18_acetylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 14th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k18_acetylation_site AS SELECT feature_id AS h3k18_acetylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K18_acetylation_site'; --- ************************************************ --- *** relation: h3k23_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 23rd residue (a lysine), from the st *** --- *** art of the H3 histone protein is acylate *** --- *** d. *** --- ************************************************ --- CREATE VIEW h3k23_acylation_site AS SELECT feature_id AS h3k23_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K23_acylation site'; --- ************************************************ --- *** relation: epigenetically_modified_region *** --- *** relation type: VIEW *** --- *** *** --- *** A biological region implicated in inheri *** --- *** ted changes caused by mechanisms other t *** --- *** han changes in the underlying DNA sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW epigenetically_modified_region AS SELECT feature_id AS epigenetically_modified_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'epigenetically_modified_region'; --- ************************************************ --- *** relation: h3k27_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h3k27_acylation_site AS SELECT feature_id AS h3k27_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_acylation_site'; --- ************************************************ --- *** relation: h3k36_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is mo *** --- *** no-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_monomethylation_site AS SELECT feature_id AS h3k36_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site'; --- ************************************************ --- *** relation: h3k36_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k36_dimethylation_site AS SELECT feature_id AS h3k36_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_dimethylation_site'; --- ************************************************ --- *** relation: h3k36_trimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is tr *** --- *** i-methylated. *** --- ************************************************ --- CREATE VIEW h3k36_trimethylation_site AS SELECT feature_id AS h3k36_trimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_trimethylation_site'; --- ************************************************ --- *** relation: h3k4_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 4th residue (a lysine), from th *** --- *** e start of the H3 histone protein is di- *** --- *** methylated. *** --- ************************************************ --- CREATE VIEW h3k4_dimethylation_site AS SELECT feature_id AS h3k4_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_dimethylation_site'; --- ************************************************ --- *** relation: h3k27_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is di *** --- *** -methylated. *** --- ************************************************ --- CREATE VIEW h3k27_dimethylation_site AS SELECT feature_id AS h3k27_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_dimethylation_site'; --- ************************************************ --- *** relation: h3k9_monomethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is mon *** --- *** o-methylated. *** --- ************************************************ --- CREATE VIEW h3k9_monomethylation_site AS SELECT feature_id AS h3k9_monomethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_monomethylation_site'; --- ************************************************ --- *** relation: h3k9_dimethylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein may be *** --- *** dimethylated. *** --- ************************************************ --- CREATE VIEW h3k9_dimethylation_site AS SELECT feature_id AS h3k9_dimethylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_dimethylation_site'; --- ************************************************ --- *** relation: h4k16_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 16th residue (a lysine), from t *** --- *** he start of the H4 histone protein is ac *** --- *** ylated. *** --- ************************************************ --- CREATE VIEW h4k16_acylation_site AS SELECT feature_id AS h4k16_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K16_acylation_site'; --- ************************************************ --- *** relation: h4k5_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 5th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k5_acylation_site AS SELECT feature_id AS h4k5_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K5_acylation_site'; --- ************************************************ --- *** relation: h4k8_acylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 8th residue (a lysine), from th *** --- *** e start of the H4 histone protein is acy *** --- *** lated. *** --- ************************************************ --- CREATE VIEW h4k8_acylation_site AS SELECT feature_id AS h4k8_acylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K8_acylation site'; --- ************************************************ --- *** relation: h3k27_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 27th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k27_methylation_site AS SELECT feature_id AS h3k27_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K27_methylation_site'; --- ************************************************ --- *** relation: h3k36_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 36th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k36_methylation_site AS SELECT feature_id AS h3k36_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K36_methylation_site'; --- ************************************************ --- *** relation: h3k4_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification, whereby *** --- *** the 4th residue (a lysine), from the sta *** --- *** rt of the H3 protein is methylated. *** --- ************************************************ --- CREATE VIEW h3k4_methylation_site AS SELECT feature_id AS h3k4_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K4_methylation_site'; --- ************************************************ --- *** relation: h3k79_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 79th residue (a lysine), from t *** --- *** he start of the H3 histone protein is me *** --- *** thylated. *** --- ************************************************ --- CREATE VIEW h3k79_methylation_site AS SELECT feature_id AS h3k79_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K79_methylation_site'; --- ************************************************ --- *** relation: h3k9_methylation_site *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of histone modification site, whe *** --- *** reby the 9th residue (a lysine), from th *** --- *** e start of the H3 histone protein is met *** --- *** hylated. *** --- ************************************************ --- CREATE VIEW h3k9_methylation_site AS SELECT feature_id AS h3k9_methylation_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_methylation_site'; --- ************************************************ --- *** relation: histone_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A histone modification, whereby the hist *** --- *** one protein is acylated at multiple site *** --- *** s in a region. *** --- ************************************************ --- CREATE VIEW histone_acylation_region AS SELECT feature_id AS histone_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'histone_acylation_region'; --- ************************************************ --- *** relation: h4k_acylation_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the H4 histone whereby multi *** --- *** ple lysines are acylated. *** --- ************************************************ --- CREATE VIEW h4k_acylation_region AS SELECT feature_id AS h4k_acylation_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'H4K_acylation_region'; --- ************************************************ --- *** relation: gene_with_non_canonical_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a start codon other than AUG *** --- *** . *** --- ************************************************ --- CREATE VIEW gene_with_non_canonical_start_codon AS SELECT feature_id AS gene_with_non_canonical_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'gene_with_non_canonical_start_codon'; --- ************************************************ --- *** relation: gene_with_start_codon_cug *** --- *** relation type: VIEW *** --- *** *** --- *** A gene with a translational start codon *** --- *** of CUG. *** --- ************************************************ --- CREATE VIEW gene_with_start_codon_cug AS SELECT feature_id AS gene_with_start_codon_cug_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_with_start_codon_CUG'; --- ************************************************ --- *** relation: pseudogenic_gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene segment which when incorporated b *** --- *** y somatic recombination in the final gen *** --- *** e transcript results in a nonfunctional *** --- *** product. *** --- ************************************************ --- CREATE VIEW pseudogenic_gene_segment AS SELECT feature_id AS pseudogenic_gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment'; --- ************************************************ --- *** relation: copy_number_gain *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given regions is greater than *** --- *** the reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_gain AS SELECT feature_id AS copy_number_gain_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_gain'; --- ************************************************ --- *** relation: copy_number_loss *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration whereby the copy n *** --- *** umber of a given region is less than the *** --- *** reference sequence. *** --- ************************************************ --- CREATE VIEW copy_number_loss AS SELECT feature_id AS copy_number_loss_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'copy_number_loss'; --- ************************************************ --- *** relation: upd *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from one parent and no copies of the *** --- *** same chromosome or region from the other *** --- *** parent. *** --- ************************************************ --- CREATE VIEW upd AS SELECT feature_id AS upd_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy' OR cvterm.name = 'paternal_uniparental_disomy' OR cvterm.name = 'UPD'; --- ************************************************ --- *** relation: maternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the mother and no copies of the *** --- *** same chromosome or region from the fathe *** --- *** r. *** --- ************************************************ --- CREATE VIEW maternal_uniparental_disomy AS SELECT feature_id AS maternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_uniparental_disomy'; --- ************************************************ --- *** relation: paternal_uniparental_disomy *** --- *** relation type: VIEW *** --- *** *** --- *** Uniparental disomy is a sequence_alterat *** --- *** ion where a diploid individual receives *** --- *** two copies for all or part of a chromoso *** --- *** me from the father and no copies of the *** --- *** same chromosome or region from the mothe *** --- *** r. *** --- ************************************************ --- CREATE VIEW paternal_uniparental_disomy AS SELECT feature_id AS paternal_uniparental_disomy_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_uniparental_disomy'; --- ************************************************ --- *** relation: open_chromatin_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that in the normal state *** --- *** of the chromosome corresponds to an unfo *** --- *** lded, un-complexed stretch of double-str *** --- *** anded DNA. *** --- ************************************************ --- CREATE VIEW open_chromatin_region AS SELECT feature_id AS open_chromatin_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'open_chromatin_region'; --- ************************************************ --- *** relation: sl3_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 3 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL3 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl3_acceptor_site AS SELECT feature_id AS sl3_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL3_acceptor_site'; --- ************************************************ --- *** relation: sl4_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 4 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL4 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl4_acceptor_site AS SELECT feature_id AS sl4_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL4_acceptor_site'; --- ************************************************ --- *** relation: sl5_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 5 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL5 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl5_acceptor_site AS SELECT feature_id AS sl5_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL5_acceptor_site'; --- ************************************************ --- *** relation: sl6_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 6 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL6 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl6_acceptor_site AS SELECT feature_id AS sl6_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL6_acceptor_site'; --- ************************************************ --- *** relation: sl7_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 7 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL7 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl7_acceptor_site AS SELECT feature_id AS sl7_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL7_acceptor_site'; --- ************************************************ --- *** relation: sl8_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 8 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL8 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl8_acceptor_site AS SELECT feature_id AS sl8_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL8_acceptor_site'; --- ************************************************ --- *** relation: sl9_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 9 RNA leader sequence to the 5' end of a *** --- *** n mRNA. SL9 acceptor sites occur in gene *** --- *** s in internal segments of polycistronic *** --- *** transcripts. *** --- ************************************************ --- CREATE VIEW sl9_acceptor_site AS SELECT feature_id AS sl9_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL9_acceptor_site'; --- ************************************************ --- *** relation: sl10_accceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 10 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL10 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl10_accceptor_site AS SELECT feature_id AS sl10_accceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL10_accceptor_site'; --- ************************************************ --- *** relation: sl11_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 11 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL11 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl11_acceptor_site AS SELECT feature_id AS sl11_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL11_acceptor_site'; --- ************************************************ --- *** relation: sl12_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** A SL2_acceptor_site which appends the SL *** --- *** 12 RNA leader sequence to the 5' end of *** --- *** an mRNA. SL12 acceptor sites occur in ge *** --- *** nes in internal segments of polycistroni *** --- *** c transcripts. *** --- ************************************************ --- CREATE VIEW sl12_acceptor_site AS SELECT feature_id AS sl12_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SL12_acceptor_site'; --- ************************************************ --- *** relation: duplicated_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose via gene duplica *** --- *** tion. Generally duplicated pseudogenes h *** --- *** ave the same structure as the original g *** --- *** ene, including intron-exon structure and *** --- *** some regulatory sequence. *** --- ************************************************ --- CREATE VIEW duplicated_pseudogene AS SELECT feature_id AS duplicated_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'duplicated_pseudogene'; --- ************************************************ --- *** relation: unitary_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene, deactivated from original *** --- *** state by mutation, fixed in a population *** --- *** . *** --- ************************************************ --- CREATE VIEW unitary_pseudogene AS SELECT feature_id AS unitary_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unitary_pseudogene'; --- ************************************************ --- *** relation: non_processed_pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A pseudogene that arose from a means oth *** --- *** er than retrotransposition. *** --- ************************************************ --- CREATE VIEW non_processed_pseudogene AS SELECT feature_id AS non_processed_pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'non_processed_pseudogene'; --- ************************************************ --- *** relation: variant_quality *** --- *** relation type: VIEW *** --- *** *** --- *** A dependent entity that inheres in a bea *** --- *** rer, a sequence variant. *** --- ************************************************ --- CREATE VIEW variant_quality AS SELECT feature_id AS variant_quality_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'variant_origin' OR cvterm.name = 'variant_frequency' OR cvterm.name = 'variant_phenotype' OR cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_quality'; --- ************************************************ --- *** relation: variant_origin *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its origin. *** --- ************************************************ --- CREATE VIEW variant_origin AS SELECT feature_id AS variant_origin_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant' OR cvterm.name = 'paternal_variant' OR cvterm.name = 'somatic_variant' OR cvterm.name = 'germline_variant' OR cvterm.name = 'pedigree_specific_variant' OR cvterm.name = 'population_specific_variant' OR cvterm.name = 'de_novo_variant' OR cvterm.name = 'variant_origin'; --- ************************************************ --- *** relation: variant_frequency *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW variant_frequency AS SELECT feature_id AS variant_frequency_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant' OR cvterm.name = 'rare_variant' OR cvterm.name = 'polymorphic_variant' OR cvterm.name = 'common_variant' OR cvterm.name = 'fixed_variant' OR cvterm.name = 'variant_frequency'; --- ************************************************ --- *** relation: unique_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A physical quality which inheres to the *** --- *** variant by virtue of the number instance *** --- *** s of the variant within a population. *** --- ************************************************ --- CREATE VIEW unique_variant AS SELECT feature_id AS unique_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unique_variant'; --- ************************************************ --- *** relation: rare_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW rare_variant AS SELECT feature_id AS rare_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rare_variant'; --- ************************************************ --- *** relation: polymorphic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW polymorphic_variant AS SELECT feature_id AS polymorphic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polymorphic_variant'; --- ************************************************ --- *** relation: common_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW common_variant AS SELECT feature_id AS common_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'common_variant'; --- ************************************************ --- *** relation: fixed_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW fixed_variant AS SELECT feature_id AS fixed_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'fixed_variant'; --- ************************************************ --- *** relation: variant_phenotype *** --- *** relation type: VIEW *** --- *** *** --- *** A quality inhering in a variant by virtu *** --- *** e of its phenotype. *** --- ************************************************ --- CREATE VIEW variant_phenotype AS SELECT feature_id AS variant_phenotype_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant' OR cvterm.name = 'disease_associated_variant' OR cvterm.name = 'disease_causing_variant' OR cvterm.name = 'lethal_variant' OR cvterm.name = 'quantitative_variant' OR cvterm.name = 'variant_phenotype'; --- ************************************************ --- *** relation: benign_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW benign_variant AS SELECT feature_id AS benign_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'benign_variant'; --- ************************************************ --- *** relation: disease_associated_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_associated_variant AS SELECT feature_id AS disease_associated_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_associated_variant'; --- ************************************************ --- *** relation: disease_causing_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW disease_causing_variant AS SELECT feature_id AS disease_causing_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'disease_causing_variant'; --- ************************************************ --- *** relation: lethal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW lethal_variant AS SELECT feature_id AS lethal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lethal_variant'; --- ************************************************ --- *** relation: quantitative_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW quantitative_variant AS SELECT feature_id AS quantitative_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'quantitative_variant'; --- ************************************************ --- *** relation: maternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW maternal_variant AS SELECT feature_id AS maternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'maternal_variant'; --- ************************************************ --- *** relation: paternal_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW paternal_variant AS SELECT feature_id AS paternal_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paternal_variant'; --- ************************************************ --- *** relation: somatic_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW somatic_variant AS SELECT feature_id AS somatic_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'somatic_variant'; --- ************************************************ --- *** relation: germline_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW germline_variant AS SELECT feature_id AS germline_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'germline_variant'; --- ************************************************ --- *** relation: pedigree_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW pedigree_specific_variant AS SELECT feature_id AS pedigree_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pedigree_specific_variant'; --- ************************************************ --- *** relation: population_specific_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW population_specific_variant AS SELECT feature_id AS population_specific_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'population_specific_variant'; --- ************************************************ --- *** relation: de_novo_variant *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW de_novo_variant AS SELECT feature_id AS de_novo_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'de_novo_variant'; --- ************************************************ --- *** relation: tf_binding_site_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant located within a tran *** --- *** scription factor binding site. *** --- ************************************************ --- CREATE VIEW tf_binding_site_variant AS SELECT feature_id AS tf_binding_site_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site_variant'; --- ************************************************ --- *** relation: missense_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant whereby at least one *** --- *** base of a codon is changed resulting in *** --- *** a codon that encodes for a different ami *** --- *** no acid. *** --- ************************************************ --- CREATE VIEW missense_codon AS SELECT feature_id AS missense_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'missense_codon'; --- ************************************************ --- *** relation: complex_structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- *** A structural sequence alteration where t *** --- *** here are multiple equally plausible expl *** --- *** anations for the change. *** --- ************************************************ --- CREATE VIEW complex_structural_alteration AS SELECT feature_id AS complex_structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration'; --- ************************************************ --- *** relation: structural_alteration *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW structural_alteration AS SELECT feature_id AS structural_alteration_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'structural_alteration'; --- ************************************************ --- *** relation: loss_of_heterozygosity *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW loss_of_heterozygosity AS SELECT feature_id AS loss_of_heterozygosity_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'loss_of_heterozygosity'; --- ************************************************ --- *** relation: splice_donor_5th_base_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that causes a change *** --- *** at the 5th base pair after the start of *** --- *** the intron in the orientation of the tra *** --- *** nscript. *** --- ************************************************ --- CREATE VIEW splice_donor_5th_base_variant AS SELECT feature_id AS splice_donor_5th_base_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_5th_base_variant'; --- ************************************************ --- *** relation: u_box *** --- *** relation type: VIEW *** --- *** *** --- *** An U-box is a conserved T-rich region up *** --- *** stream of a retroviral polypurine tract *** --- *** that is involved in PPT primer creation *** --- *** during reverse transcription. *** --- ************************************************ --- CREATE VIEW u_box AS SELECT feature_id AS u_box_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U_box'; --- ************************************************ --- *** relation: mating_type_region *** --- *** relation type: VIEW *** --- *** *** --- *** A specialized region in the genomes of s *** --- *** ome yeast and fungi, the genes of which *** --- *** regulate mating type. *** --- ************************************************ --- CREATE VIEW mating_type_region AS SELECT feature_id AS mating_type_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mating_type_region'; --- ************************************************ --- *** relation: paired_end_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** An assembly region that has been sequenc *** --- *** ed from both ends resulting in a read_pa *** --- *** ir (mate_pair). *** --- ************************************************ --- CREATE VIEW paired_end_fragment AS SELECT feature_id AS paired_end_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paired_end_fragment'; --- ************************************************ --- *** relation: exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes exon seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW exon_variant AS SELECT feature_id AS exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'exon_variant'; --- ************************************************ --- *** relation: non_coding_exon_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence variant that changes non-codi *** --- *** ng exon sequence. *** --- ************************************************ --- CREATE VIEW non_coding_exon_variant AS SELECT feature_id AS non_coding_exon_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_coding_exon_variant'; --- ************************************************ --- *** relation: clone_end *** --- *** relation type: VIEW *** --- *** *** --- *** A read from an end of the clone sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW clone_end AS SELECT feature_id AS clone_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_end'; --- ************************************************ --- *** relation: point_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A point centromere is a relatively small *** --- *** centromere (about 125 bp DNA) in discre *** --- *** te sequence, found in some yeast includi *** --- *** ng S. cerevisiae. *** --- ************************************************ --- CREATE VIEW point_centromere AS SELECT feature_id AS point_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_centromere'; --- ************************************************ --- *** relation: regional_centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A regional centromere is a large modular *** --- *** centromere found in fission yeast and h *** --- *** igher eukaryotes. It consist of a centra *** --- *** l core region flanked by inverted inner *** --- *** and outer repeat regions. *** --- ************************************************ --- CREATE VIEW regional_centromere AS SELECT feature_id AS regional_centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere'; --- ************************************************ --- *** relation: regional_centromere_central_core *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved region within the central re *** --- *** gion of a modular centromere, where the *** --- *** kinetochore is formed. *** --- ************************************************ --- CREATE VIEW regional_centromere_central_core AS SELECT feature_id AS regional_centromere_central_core_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_central_core'; --- ************************************************ --- *** relation: centromeric_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat region found within the modular *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW centromeric_repeat AS SELECT feature_id AS centromeric_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'centromeric_repeat'; --- ************************************************ --- *** relation: regional_centromere_inner_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The inner repeat region of a modular cen *** --- *** tromere. This region is adjacent to the *** --- *** central core, on each chromosome arm. *** --- ************************************************ --- CREATE VIEW regional_centromere_inner_repeat_region AS SELECT feature_id AS regional_centromere_inner_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_inner_repeat_region'; --- ************************************************ --- *** relation: regional_centromere_outer_repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** The heterochromatic outer repeat region *** --- *** of a modular centromere. These repeats e *** --- *** xist in tandem arrays on both chromosome *** --- *** arms. *** --- ************************************************ --- CREATE VIEW regional_centromere_outer_repeat_region AS SELECT feature_id AS regional_centromere_outer_repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regional_centromere_outer_repeat_region'; --- ************************************************ --- *** relation: tasirna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a 21 nucleotide double s *** --- *** tranded, polyadenylated non coding RNA, *** --- *** transcribed from the TAS gene. *** --- ************************************************ --- CREATE VIEW tasirna AS SELECT feature_id AS tasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA'; --- ************************************************ --- *** relation: tasirna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding a tasiRNA. *** --- ************************************************ --- CREATE VIEW tasirna_primary_transcript AS SELECT feature_id AS tasirna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tasiRNA_primary_transcript'; --- ************************************************ --- *** relation: increased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is increased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW increased_polyadenylation_variant AS SELECT feature_id AS increased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'increased_polyadenylation_variant'; --- ************************************************ --- *** relation: decreased_polyadenylation_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript processing variant whereby *** --- *** polyadenylation of the encoded transcrip *** --- *** t is decreased with respect to the refer *** --- *** ence. *** --- ************************************************ --- CREATE VIEW decreased_polyadenylation_variant AS SELECT feature_id AS decreased_polyadenylation_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decreased_polyadenylation_variant'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence that is involved in *** --- *** the control of a biological process. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: u14_snorna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary transcript of an evolutionar *** --- *** ily conserved eukaryotic low molecular w *** --- *** eight RNA capable of intermolecular hybr *** --- *** idization with both homologous and heter *** --- *** ologous 18S rRNA. *** --- ************************************************ --- CREATE VIEW u14_snorna_primary_transcript AS SELECT feature_id AS u14_snorna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snoRNA_primary_transcript'; --- ************************************************ --- *** relation: methylation_guide_snorna *** --- *** relation type: VIEW *** --- *** *** --- *** A snoRNA that specifies the site of 2'-O *** --- *** -ribose methylation in an RNA molecule b *** --- *** y base pairing with a short sequence aro *** --- *** und the target residue. *** --- ************************************************ --- CREATE VIEW methylation_guide_snorna AS SELECT feature_id AS methylation_guide_snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylation_guide_snoRNA'; --- ************************************************ --- *** relation: rrna_cleavage_rna *** --- *** relation type: VIEW *** --- *** *** --- *** An ncRNA that is part of a ribonucleopro *** --- *** tein that cleaves the primary pre-rRNA t *** --- *** ranscript in the process of producing ma *** --- *** ture rRNA molecules. *** --- ************************************************ --- CREATE VIEW rrna_cleavage_rna AS SELECT feature_id AS rrna_cleavage_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_cleavage_RNA'; --- ************************************************ --- *** relation: exon_of_single_exon_gene *** --- *** relation type: VIEW *** --- *** *** --- *** An exon that is the only exon in a gene. *** --- ************************************************ --- CREATE VIEW exon_of_single_exon_gene AS SELECT feature_id AS exon_of_single_exon_gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_of_single_exon_gene'; --- ************************************************ --- *** relation: cassette_array_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW cassette_array_member AS SELECT feature_id AS cassette_array_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member'; --- ************************************************ --- *** relation: gene_cassette_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_cassette_member AS SELECT feature_id AS gene_cassette_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member'; --- ************************************************ --- *** relation: gene_subarray_member *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW gene_subarray_member AS SELECT feature_id AS gene_subarray_member_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray_member'; --- ************************************************ --- *** relation: primer_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** Non-covalent primer binding site for ini *** --- *** tiation of replication, transcription, o *** --- *** r reverse transcription. *** --- ************************************************ --- CREATE VIEW primer_binding_site AS SELECT feature_id AS primer_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer_binding_site'; --- ************************************************ --- *** relation: gene_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array includes two or more genes, or *** --- *** two or more gene subarrays, contiguously *** --- *** arranged where the individual genes, or *** --- *** subarrays, are either identical in sequ *** --- *** ence, or essentially so. *** --- ************************************************ --- CREATE VIEW gene_array AS SELECT feature_id AS gene_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_array'; --- ************************************************ --- *** relation: gene_subarray *** --- *** relation type: VIEW *** --- *** *** --- *** A subarray is, by defintition, a member *** --- *** of a gene array (SO:0005851); the member *** --- *** s of a subarray may differ substantially *** --- *** in sequence, but are closely related in *** --- *** function. *** --- ************************************************ --- CREATE VIEW gene_subarray AS SELECT feature_id AS gene_subarray_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_subarray'; --- ************************************************ --- *** relation: gene_cassette *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that can be substituted for a rel *** --- *** ated gene at a different site in the gen *** --- *** ome. *** --- ************************************************ --- CREATE VIEW gene_cassette AS SELECT feature_id AS gene_cassette_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette'; --- ************************************************ --- *** relation: gene_cassette_array *** --- *** relation type: VIEW *** --- *** *** --- *** An array of non-functional genes whose m *** --- *** embers, when captured by recombination f *** --- *** orm functional genes. *** --- ************************************************ --- CREATE VIEW gene_cassette_array AS SELECT feature_id AS gene_cassette_array_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_cassette_array'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: selenocysteine_trna_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript encoding seryl tRNA *** --- *** (SO:000269). *** --- ************************************************ --- CREATE VIEW selenocysteine_trna_primary_transcript AS SELECT feature_id AS selenocysteine_trna_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript'; --- ************************************************ --- *** relation: selenocysteinyl_trna *** --- *** relation type: VIEW *** --- *** *** --- *** A tRNA sequence that has a selenocystein *** --- *** e anticodon, and a 3' selenocysteine bin *** --- *** ding region. *** --- ************************************************ --- CREATE VIEW selenocysteinyl_trna AS SELECT feature_id AS selenocysteinyl_trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'selenocysteinyl_tRNA'; --- ************************************************ --- *** relation: syntenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region in which two or more pairs of h *** --- *** omologous markers occur on the same chro *** --- *** mosome in two or more species. *** --- ************************************************ --- CREATE VIEW syntenic_region AS SELECT feature_id AS syntenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'syntenic_region'; --- ************************************************ --- *** relation: biochemical_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a peptide that is involved i *** --- *** n a biochemical function. *** --- ************************************************ --- CREATE VIEW biochemical_region_of_peptide AS SELECT feature_id AS biochemical_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide'; --- ************************************************ --- *** relation: molecular_contact_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region that is involved a contact with *** --- *** another molecule. *** --- ************************************************ --- CREATE VIEW molecular_contact_region AS SELECT feature_id AS molecular_contact_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region'; --- ************************************************ --- *** relation: intrinsically_unstructured_polypeptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of polypeptide chain with high *** --- *** conformational flexibility. *** --- ************************************************ --- CREATE VIEW intrinsically_unstructured_polypeptide_region AS SELECT feature_id AS intrinsically_unstructured_polypeptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region'; --- ************************************************ --- *** relation: catmat_left_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_three AS SELECT feature_id AS catmat_left_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_three'; --- ************************************************ --- *** relation: catmat_left_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i psi -10 boun *** --- *** ds -50 to 30, res i+1: phi -90 bounds -1 *** --- *** 20 to -60, res i+1: psi -10 bounds -50 t *** --- *** o 30, res i+2: phi -75 bounds -100 to -5 *** --- *** 0, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_left_handed_four AS SELECT feature_id AS catmat_left_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_left_handed_four'; --- ************************************************ --- *** relation: catmat_right_handed_three *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 3 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -75 bounds - *** --- *** 100 to -50, res i+1: psi 140 bounds 110 *** --- *** to 170. An extra restriction of the leng *** --- *** th of the O to O distance would be usefu *** --- *** l, that it be less than 5 Angstrom. More *** --- *** precisely these two oxygens are the mai *** --- *** n chain carbonyl oxygen atoms of residue *** --- *** s i-1 and i+1. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_three AS SELECT feature_id AS catmat_right_handed_three_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_three'; --- ************************************************ --- *** relation: catmat_right_handed_four *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of 4 consecutive residues with d *** --- *** ihedral angles as follows: res i: phi -9 *** --- *** 0 bounds -120 to -60, res i: psi -10 bou *** --- *** nds -50 to 30, res i+1: phi -90 bounds - *** --- *** 120 to -60, res i+1: psi -10 bounds -50 *** --- *** to 30, res i+2: phi -75 bounds -100 to - *** --- *** 50, res i+2: psi 140 bounds 110 to 170. *** --- *** The extra restriction of the length of t *** --- *** he O to O distance is similar, that it b *** --- *** e less than 5 Angstrom. In this case the *** --- *** se two Oxygen atoms are the main chain c *** --- *** arbonyl oxygen atoms of residues i-1 and *** --- *** i+2. *** --- ************************************************ --- CREATE VIEW catmat_right_handed_four AS SELECT feature_id AS catmat_right_handed_four_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'catmat_right_handed_four'; --- ************************************************ --- *** relation: alpha_beta_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A motif of five consecutive residues and *** --- *** two H-bonds in which: H-bond between CO *** --- *** of residue(i) and NH of residue(i+4), H *** --- *** -bond between CO of residue(i) and NH of *** --- *** residue(i+3),Phi angles of residues(i+1 *** --- *** ), (i+2) and (i+3) are negative. *** --- ************************************************ --- CREATE VIEW alpha_beta_motif AS SELECT feature_id AS alpha_beta_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alpha_beta_motif'; --- ************************************************ --- *** relation: lipoprotein_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** A peptide that acts as a signal for both *** --- *** membrane translocation and lipid attach *** --- *** ment in prokaryotes. *** --- ************************************************ --- CREATE VIEW lipoprotein_signal_peptide AS SELECT feature_id AS lipoprotein_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'lipoprotein_signal_peptide'; --- ************************************************ --- *** relation: no_output *** --- *** relation type: VIEW *** --- *** *** --- *** An experimental region wherean analysis *** --- *** has been run and not produced any annota *** --- *** tion. *** --- ************************************************ --- CREATE VIEW no_output AS SELECT feature_id AS no_output_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'no_output'; --- ************************************************ --- *** relation: cleaved_peptide_region *** --- *** relation type: VIEW *** --- *** *** --- *** The cleaved_peptide_regon is the a regio *** --- *** n of peptide sequence that is cleaved du *** --- *** ring maturation. *** --- ************************************************ --- CREATE VIEW cleaved_peptide_region AS SELECT feature_id AS cleaved_peptide_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'cleaved_peptide_region'; --- ************************************************ --- *** relation: peptide_coil *** --- *** relation type: VIEW *** --- *** *** --- *** Irregular, unstructured regions of a pro *** --- *** tein's backbone, as distinct from the re *** --- *** gular region (namely alpha helix and bet *** --- *** a strand - characterised by specific pat *** --- *** terns of main-chain hydrogen bonds). *** --- ************************************************ --- CREATE VIEW peptide_coil AS SELECT feature_id AS peptide_coil_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'peptide_coil'; --- ************************************************ --- *** relation: hydrophobic_region_of_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** Hydrophobic regions are regions with a l *** --- *** ow affinity for water. *** --- ************************************************ --- CREATE VIEW hydrophobic_region_of_peptide AS SELECT feature_id AS hydrophobic_region_of_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hydrophobic_region_of_peptide'; --- ************************************************ --- *** relation: n_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The amino-terminal positively-charged re *** --- *** gion of a signal peptide (approx 1-5 aa) *** --- *** . *** --- ************************************************ --- CREATE VIEW n_terminal_region AS SELECT feature_id AS n_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'n_terminal_region'; --- ************************************************ --- *** relation: c_terminal_region *** --- *** relation type: VIEW *** --- *** *** --- *** The more polar, carboxy-terminal region *** --- *** of the signal peptide (approx 3-7 aa). *** --- ************************************************ --- CREATE VIEW c_terminal_region AS SELECT feature_id AS c_terminal_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'c_terminal_region'; --- ************************************************ --- *** relation: central_hydrophobic_region_of_signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The central, hydrophobic region of the s *** --- *** ignal peptide (approx 7-15 aa). *** --- ************************************************ --- CREATE VIEW central_hydrophobic_region_of_signal_peptide AS SELECT feature_id AS central_hydrophobic_region_of_signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'central_hydrophobic_region_of_signal_peptide'; --- ************************************************ --- *** relation: polypeptide_conserved_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A conserved motif is a short (up to 20 a *** --- *** mino acids) region of biological interes *** --- *** t that is conserved in different protein *** --- *** s. They may or may not have functional o *** --- *** r structural significance within the pro *** --- *** teins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_motif AS SELECT feature_id AS polypeptide_conserved_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_conserved_motif'; --- ************************************************ --- *** relation: polypeptide_binding_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide binding motif is a short ( *** --- *** up to 20 amino acids) polypeptide region *** --- *** of biological interest that contains on *** --- *** e or more amino acids experimentally sho *** --- *** wn to bind to a ligand. *** --- ************************************************ --- CREATE VIEW polypeptide_binding_motif AS SELECT feature_id AS polypeptide_binding_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_binding_motif'; --- ************************************************ --- *** relation: polypeptide_catalytic_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A polypeptide catalytic motif is a short *** --- *** (up to 20 amino acids) polypeptide regi *** --- *** on that contains one or more active site *** --- *** residues. *** --- ************************************************ --- CREATE VIEW polypeptide_catalytic_motif AS SELECT feature_id AS polypeptide_catalytic_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_catalytic_motif'; --- ************************************************ --- *** relation: polypeptide_dna_contact *** --- *** relation type: VIEW *** --- *** *** --- *** A binding site that, in the polypeptide *** --- *** molecule, interacts selectively and non- *** --- *** covalently with DNA. *** --- ************************************************ --- CREATE VIEW polypeptide_dna_contact AS SELECT feature_id AS polypeptide_dna_contact_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_DNA_contact'; --- ************************************************ --- *** relation: polypeptide_conserved_region *** --- *** relation type: VIEW *** --- *** *** --- *** A subsection of sequence with biological *** --- *** interest that is conserved in different *** --- *** proteins. They may or may not have func *** --- *** tional or structural significance within *** --- *** the proteins in which they are found. *** --- ************************************************ --- CREATE VIEW polypeptide_conserved_region AS SELECT feature_id AS polypeptide_conserved_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'polypeptide_conserved_region'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration where the length o *** --- *** f the change in the variant is the same *** --- *** as that of the reference. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'substitution'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A single nucleotide change which has occ *** --- *** urred at the same position of a correspo *** --- *** nding nucleotide in a reference sequence *** --- *** . *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: transition *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into an other pyrimidine nucleotide, *** --- *** or change of a purine nucleotide, A or G *** --- *** , into an other purine nucleotide. *** --- ************************************************ --- CREATE VIEW transition AS SELECT feature_id AS transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'transition'; --- ************************************************ --- *** relation: pyrimidine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a pyrimidine, C or T, *** --- *** for another pyrimidine. *** --- ************************************************ --- CREATE VIEW pyrimidine_transition AS SELECT feature_id AS pyrimidine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'pyrimidine_transition'; --- ************************************************ --- *** relation: c_to_t_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a cytidine to a thymine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition AS SELECT feature_id AS c_to_t_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'C_to_T_transition'; --- ************************************************ --- *** relation: c_to_t_transition_at_pcpg_site *** --- *** relation type: VIEW *** --- *** *** --- *** The transition of cytidine to thymine oc *** --- *** curring at a pCpG site as a consequence *** --- *** of the spontaneous deamination of 5'-met *** --- *** hylcytidine. *** --- ************************************************ --- CREATE VIEW c_to_t_transition_at_pcpg_site AS SELECT feature_id AS c_to_t_transition_at_pcpg_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_T_transition_at_pCpG_site'; --- ************************************************ --- *** relation: t_to_c_transition *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW t_to_c_transition AS SELECT feature_id AS t_to_c_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_C_transition'; --- ************************************************ --- *** relation: purine_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A substitution of a purine, A or G, for *** --- *** another purine. *** --- ************************************************ --- CREATE VIEW purine_transition AS SELECT feature_id AS purine_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'purine_transition'; --- ************************************************ --- *** relation: a_to_g_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of an adenine to a guanine. *** --- ************************************************ --- CREATE VIEW a_to_g_transition AS SELECT feature_id AS a_to_g_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_G_transition'; --- ************************************************ --- *** relation: g_to_a_transition *** --- *** relation type: VIEW *** --- *** *** --- *** A transition of a guanine to an adenine. *** --- ************************************************ --- CREATE VIEW g_to_a_transition AS SELECT feature_id AS g_to_a_transition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_A_transition'; --- ************************************************ --- *** relation: transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G, or *** --- *** vice versa. *** --- ************************************************ --- CREATE VIEW transversion AS SELECT feature_id AS transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'transversion'; --- ************************************************ --- *** relation: pyrimidine_to_purine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a pyrimidine nucleotide, C or *** --- *** T, into a purine nucleotide, A or G. *** --- ************************************************ --- CREATE VIEW pyrimidine_to_purine_transversion AS SELECT feature_id AS pyrimidine_to_purine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'pyrimidine_to_purine_transversion'; --- ************************************************ --- *** relation: c_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from cytidine to adenine. *** --- ************************************************ --- CREATE VIEW c_to_a_transversion AS SELECT feature_id AS c_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_A_transversion'; --- ************************************************ --- *** relation: c_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW c_to_g_transversion AS SELECT feature_id AS c_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'C_to_G_transversion'; --- ************************************************ --- *** relation: t_to_a_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to A. *** --- ************************************************ --- CREATE VIEW t_to_a_transversion AS SELECT feature_id AS t_to_a_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_A_transversion'; --- ************************************************ --- *** relation: t_to_g_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from T to G. *** --- ************************************************ --- CREATE VIEW t_to_g_transversion AS SELECT feature_id AS t_to_g_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'T_to_G_transversion'; --- ************************************************ --- *** relation: purine_to_pyrimidine_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** Change of a purine nucleotide, A or G , *** --- *** into a pyrimidine nucleotide C or T. *** --- ************************************************ --- CREATE VIEW purine_to_pyrimidine_transversion AS SELECT feature_id AS purine_to_pyrimidine_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion'; --- ************************************************ --- *** relation: a_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to cytidine. *** --- ************************************************ --- CREATE VIEW a_to_c_transversion AS SELECT feature_id AS a_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_C_transversion'; --- ************************************************ --- *** relation: a_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from adenine to thymine. *** --- ************************************************ --- CREATE VIEW a_to_t_transversion AS SELECT feature_id AS a_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'A_to_T_transversion'; --- ************************************************ --- *** relation: g_to_c_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to cytidine. *** --- ************************************************ --- CREATE VIEW g_to_c_transversion AS SELECT feature_id AS g_to_c_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_C_transversion'; --- ************************************************ --- *** relation: g_to_t_transversion *** --- *** relation type: VIEW *** --- *** *** --- *** A transversion from guanine to thymine. *** --- ************************************************ --- CREATE VIEW g_to_t_transversion AS SELECT feature_id AS g_to_t_transversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'G_to_T_transversion'; --- ************************************************ --- *** relation: intrachromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation within *** --- *** a single chromosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_mutation AS SELECT feature_id AS intrachromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'intrachromosomal_mutation'; --- ************************************************ --- *** relation: chromosomal_deletion *** --- *** relation type: VIEW *** --- *** *** --- *** An incomplete chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_deletion AS SELECT feature_id AS chromosomal_deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'chromosomal_deletion'; --- ************************************************ --- *** relation: chromosomal_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation where a reg *** --- *** ion of the chromosome is inverted with r *** --- *** espect to wild type. *** --- ************************************************ --- CREATE VIEW chromosomal_inversion AS SELECT feature_id AS chromosomal_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_inversion'; --- ************************************************ --- *** relation: interchromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal structure variation whereb *** --- *** y more than one chromosome is involved. *** --- ************************************************ --- CREATE VIEW interchromosomal_mutation AS SELECT feature_id AS interchromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_mutation'; --- ************************************************ --- *** relation: indel *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence alteration which included an *** --- *** insertion and a deletion, affecting 2 or *** --- *** more bases. *** --- ************************************************ --- CREATE VIEW indel AS SELECT feature_id AS indel_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'indel'; --- ************************************************ --- *** relation: duplication *** --- *** relation type: VIEW *** --- *** *** --- *** One or more nucleotides are added betwee *** --- *** n two adjacent nucleotides in the sequen *** --- *** ce; the inserted sequence derives from, *** --- *** or is identical in sequence to, nucleoti *** --- *** des adjacent to insertion point. *** --- ************************************************ --- CREATE VIEW duplication AS SELECT feature_id AS duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'duplication'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: chromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An extra chromosome. *** --- ************************************************ --- CREATE VIEW chromosomal_duplication AS SELECT feature_id AS chromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'chromosomal_duplication'; --- ************************************************ --- *** relation: intrachromosomal_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication that occurred within a chr *** --- *** omosome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_duplication AS SELECT feature_id AS intrachromosomal_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_duplication'; --- ************************************************ --- *** relation: direct_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are in the same orientation. *** --- ************************************************ --- CREATE VIEW direct_tandem_duplication AS SELECT feature_id AS direct_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication'; --- ************************************************ --- *** relation: inverted_tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A tandem duplication where the individua *** --- *** l regions are not in the same orientatio *** --- *** n. *** --- ************************************************ --- CREATE VIEW inverted_tandem_duplication AS SELECT feature_id AS inverted_tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_tandem_duplication'; --- ************************************************ --- *** relation: intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred within a chrom *** --- *** osome. *** --- ************************************************ --- CREATE VIEW intrachromosomal_transposition AS SELECT feature_id AS intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'intrachromosomal_transposition'; --- ************************************************ --- *** relation: compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant where a m *** --- *** onocentric element is caused by the fusi *** --- *** on of two chromosome arms. *** --- ************************************************ --- CREATE VIEW compound_chromosome AS SELECT feature_id AS compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'compound_chromosome'; --- ************************************************ --- *** relation: robertsonian_fusion *** --- *** relation type: VIEW *** --- *** *** --- *** A non reciprocal translocation whereby t *** --- *** he participating chromosomes break at th *** --- *** eir centromeres and the long arms fuse t *** --- *** o form a single chromosome with a single *** --- *** centromere. *** --- ************************************************ --- CREATE VIEW robertsonian_fusion AS SELECT feature_id AS robertsonian_fusion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Robertsonian_fusion'; --- ************************************************ --- *** relation: chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation. Rearrangem *** --- *** ents that alter the pairing of telomeres *** --- *** are classified as translocations. *** --- ************************************************ --- CREATE VIEW chromosomal_translocation AS SELECT feature_id AS chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'chromosomal_translocation'; --- ************************************************ --- *** relation: ring_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome is a chromosome whose *** --- *** arms have fused together to form a ring, *** --- *** often with the loss of the ends of the *** --- *** chromosome. *** --- ************************************************ --- CREATE VIEW ring_chromosome AS SELECT feature_id AS ring_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'ring_chromosome'; --- ************************************************ --- *** relation: pericentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that includes th *** --- *** e centromere. *** --- ************************************************ --- CREATE VIEW pericentric_inversion AS SELECT feature_id AS pericentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pericentric_inversion'; --- ************************************************ --- *** relation: paracentric_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion that does not in *** --- *** clude the centromere. *** --- ************************************************ --- CREATE VIEW paracentric_inversion AS SELECT feature_id AS paracentric_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'paracentric_inversion'; --- ************************************************ --- *** relation: reciprocal_chromosomal_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation with two bre *** --- *** aks; two chromosome segments have simply *** --- *** been exchanged. *** --- ************************************************ --- CREATE VIEW reciprocal_chromosomal_translocation AS SELECT feature_id AS reciprocal_chromosomal_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reciprocal_chromosomal_translocation'; --- ************************************************ --- *** relation: autosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome is the aneupl *** --- *** oid product of recombination between a p *** --- *** ericentric inversion and a cytologically *** --- *** wild-type chromosome. *** --- ************************************************ --- CREATE VIEW autosynaptic_chromosome AS SELECT feature_id AS autosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'autosynaptic_chromosome'; --- ************************************************ --- *** relation: homo_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two copies *** --- *** of the same chromosomal arm attached to *** --- *** a common centromere. The chromosome is *** --- *** diploid for the arm involved. *** --- ************************************************ --- CREATE VIEW homo_compound_chromosome AS SELECT feature_id AS homo_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'homo_compound_chromosome'; --- ************************************************ --- *** relation: hetero_compound_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** A compound chromosome whereby two arms f *** --- *** rom different chromosomes are connected *** --- *** through the centromere of one of them. *** --- ************************************************ --- CREATE VIEW hetero_compound_chromosome AS SELECT feature_id AS hetero_compound_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hetero_compound_chromosome'; --- ************************************************ --- *** relation: chromosome_fission *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome that occurred by the divisi *** --- *** on of a larger chromosome. *** --- ************************************************ --- CREATE VIEW chromosome_fission AS SELECT feature_id AS chromosome_fission_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_fission'; --- ************************************************ --- *** relation: dexstrosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** An autosynaptic chromosome carrying the *** --- *** two right (D = dextro) telomeres. *** --- ************************************************ --- CREATE VIEW dexstrosynaptic_chromosome AS SELECT feature_id AS dexstrosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dexstrosynaptic_chromosome'; --- ************************************************ --- *** relation: laevosynaptic_chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** LS is an autosynaptic chromosome carryin *** --- *** g the two left (L = levo) telomeres. *** --- ************************************************ --- CREATE VIEW laevosynaptic_chromosome AS SELECT feature_id AS laevosynaptic_chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'laevosynaptic_chromosome'; --- ************************************************ --- *** relation: free_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** the duplicated sequences are carried as *** --- *** a free centric element. *** --- ************************************************ --- CREATE VIEW free_duplication AS SELECT feature_id AS free_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication' OR cvterm.name = 'free_duplication'; --- ************************************************ --- *** relation: free_ring_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A ring chromosome which is a copy of ano *** --- *** ther chromosome. *** --- ************************************************ --- CREATE VIEW free_ring_duplication AS SELECT feature_id AS free_ring_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_ring_duplication'; --- ************************************************ --- *** relation: complex_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variant with 4 or *** --- *** more breakpoints. *** --- ************************************************ --- CREATE VIEW complex_chromosomal_mutation AS SELECT feature_id AS complex_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby a translo *** --- *** cation occurs in which one of the four b *** --- *** roken ends loses a segment before re-joi *** --- *** ning. *** --- ************************************************ --- CREATE VIEW deficient_translocation AS SELECT feature_id AS deficient_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_translocation'; --- ************************************************ --- *** relation: inversion_cum_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby the *** --- *** first two breaks are in the same chromos *** --- *** ome, and the region between them is rejo *** --- *** ined in inverted order to the other side *** --- *** of the first break, such that both side *** --- *** s of break one are present on the same c *** --- *** hromosome. The remaining free ends are j *** --- *** oined as a translocation with those resu *** --- *** lting from the third break. *** --- ************************************************ --- CREATE VIEW inversion_cum_translocation AS SELECT feature_id AS inversion_cum_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_cum_translocation'; --- ************************************************ --- *** relation: bipartite_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal mutation whereby the *** --- *** (large) region between the first two br *** --- *** eaks listed is lost, and the two flankin *** --- *** g segments (one of them centric) are joi *** --- *** ned as a translocation to the free ends *** --- *** resulting from the third break. *** --- ************************************************ --- CREATE VIEW bipartite_duplication AS SELECT feature_id AS bipartite_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_duplication'; --- ************************************************ --- *** relation: cyclic_translocation *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal translocation whereby thre *** --- *** e breaks occurred in three different chr *** --- *** omosomes. The centric segment resulting *** --- *** from the first break listed is joined to *** --- *** the acentric segment resulting from the *** --- *** second, rather than the third. *** --- ************************************************ --- CREATE VIEW cyclic_translocation AS SELECT feature_id AS cyclic_translocation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cyclic_translocation'; --- ************************************************ --- *** relation: bipartite_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal inversion caused by three *** --- *** breaks in the same chromosome; both cent *** --- *** ral segments are inverted in place (i.e. *** --- *** , they are not transposed). *** --- ************************************************ --- CREATE VIEW bipartite_inversion AS SELECT feature_id AS bipartite_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'bipartite_inversion'; --- ************************************************ --- *** relation: uninvert_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically the *** --- *** same orientation as its flanking segmen *** --- *** ts. *** --- ************************************************ --- CREATE VIEW uninvert_insert_dup AS SELECT feature_id AS uninvert_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication'; --- ************************************************ --- *** relation: inverted_insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the insertion is in cytologically inv *** --- *** erted orientation with respect to its fl *** --- *** anking segments. *** --- ************************************************ --- CREATE VIEW inverted_insertional_duplication AS SELECT feature_id AS inverted_insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_insertional_duplication'; --- ************************************************ --- *** relation: insertional_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome duplication involving the i *** --- *** nsertion of a duplicated region (as oppo *** --- *** sed to a free duplication). *** --- ************************************************ --- CREATE VIEW insertional_duplication AS SELECT feature_id AS insertional_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'insertional_duplication'; --- ************************************************ --- *** relation: interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosome structure variation whereby *** --- *** a transposition occurred between chromo *** --- *** somes. *** --- ************************************************ --- CREATE VIEW interchromosomal_transposition AS SELECT feature_id AS interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the insertion is in cytologi *** --- *** cally inverted orientation with respect *** --- *** to its flanking segment. *** --- ************************************************ --- CREATE VIEW invert_inter_transposition AS SELECT feature_id AS invert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_inter_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transition where the *** --- *** segment between the first two breaks li *** --- *** sted is removed and inserted at the thir *** --- *** d break; the insertion is in cytological *** --- *** ly the same orientation as its flanking *** --- *** segments. *** --- ************************************************ --- CREATE VIEW uninvert_inter_transposition AS SELECT feature_id AS uninvert_inter_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_interchromosomal_transposition'; --- ************************************************ --- *** relation: invert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically inverted orientation with respec *** --- *** t to its flanking segments. *** --- ************************************************ --- CREATE VIEW invert_intra_transposition AS SELECT feature_id AS invert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uninvert_intra_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the insertion is in cytolo *** --- *** gically the same orientation as its flan *** --- *** king segments. *** --- ************************************************ --- CREATE VIEW uninvert_intra_transposition AS SELECT feature_id AS uninvert_intra_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'uninverted_intrachromosomal_transposition'; --- ************************************************ --- *** relation: unorient_insert_dup *** --- *** relation type: VIEW *** --- *** *** --- *** An insertional duplication where a copy *** --- *** of the segment between the first two bre *** --- *** aks listed is inserted at the third brea *** --- *** k; the orientation of the insertion with *** --- *** respect to its flanking segments is not *** --- *** recorded. *** --- ************************************************ --- CREATE VIEW unorient_insert_dup AS SELECT feature_id AS unorient_insert_dup_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_insertional_duplication'; --- ************************************************ --- *** relation: unoriented_interchromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An interchromosomal transposition whereb *** --- *** y a copy of the segment between the firs *** --- *** t two breaks listed is inserted at the t *** --- *** hird break; the orientation of the inser *** --- *** tion with respect to its flanking segmen *** --- *** ts is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_interchromosomal_transposition AS SELECT feature_id AS unoriented_interchromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_interchromosomal_transposition'; --- ************************************************ --- *** relation: unoriented_intrachromosomal_transposition *** --- *** relation type: VIEW *** --- *** *** --- *** An intrachromosomal transposition whereb *** --- *** y the segment between the first two brea *** --- *** ks listed is removed and inserted at the *** --- *** third break; the orientation of the ins *** --- *** ertion with respect to its flanking segm *** --- *** ents is not recorded. *** --- ************************************************ --- CREATE VIEW unoriented_intrachromosomal_transposition AS SELECT feature_id AS unoriented_intrachromosomal_transposition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'unoriented_intrachromosomal_transposition'; --- ************************************************ --- *** relation: uncharacterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW uncharacterised_chromosomal_mutation AS SELECT feature_id AS uncharacterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation'; --- ************************************************ --- *** relation: deficient_inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A chromosomal deletion whereby three bre *** --- *** aks occur in the same chromosome; one ce *** --- *** ntral region is lost, and the other is i *** --- *** nverted. *** --- ************************************************ --- CREATE VIEW deficient_inversion AS SELECT feature_id AS deficient_inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deficient_inversion'; --- ************************************************ --- *** relation: tandem_duplication *** --- *** relation type: VIEW *** --- *** *** --- *** A duplication consisting of 2 identical *** --- *** adjacent regions. *** --- ************************************************ --- CREATE VIEW tandem_duplication AS SELECT feature_id AS tandem_duplication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'tandem_duplication'; --- ************************************************ --- *** relation: partially_characterised_chromosomal_mutation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW partially_characterised_chromosomal_mutation AS SELECT feature_id AS partially_characterised_chromosomal_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'partially_characterised_chromosomal_mutation'; --- ************************************************ --- *** relation: chromosome_number_variation *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of chromosome variation where the *** --- *** chromosome complement is not an exact m *** --- *** ultiple of the haploid number. *** --- ************************************************ --- CREATE VIEW chromosome_number_variation AS SELECT feature_id AS chromosome_number_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'aneuploid' OR cvterm.name = 'polyploid' OR cvterm.name = 'hyperploid' OR cvterm.name = 'hypoploid' OR cvterm.name = 'autopolyploid' OR cvterm.name = 'allopolyploid' OR cvterm.name = 'chromosome_number_variation'; --- ************************************************ --- *** relation: chromosome_structure_variation *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW chromosome_structure_variation AS SELECT feature_id AS chromosome_structure_variation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'free_chromosome_arm' OR cvterm.name = 'chromosomal_transposition' OR cvterm.name = 'aneuploid_chromosome' OR cvterm.name = 'intrachromosomal_mutation' OR cvterm.name = 'interchromosomal_mutation' OR cvterm.name = 'chromosomal_duplication' OR cvterm.name = 'compound_chromosome' OR cvterm.name = 'autosynaptic_chromosome' OR cvterm.name = 'complex_chromosomal_mutation' OR cvterm.name = 'uncharacterised_chromosomal_mutation' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'inversion_derived_aneuploid_chromosome' OR cvterm.name = 'chromosomal_deletion' OR cvterm.name = 'chromosomal_inversion' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'ring_chromosome' OR cvterm.name = 'chromosome_fission' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_bipartite_deficiency' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_aneuploid' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'pericentric_inversion' OR cvterm.name = 'paracentric_inversion' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'bipartite_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_inversion' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'inverted_ring_chromosome' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'chromosomal_translocation' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'interchromosomal_transposition' OR cvterm.name = 'translocation_element' OR cvterm.name = 'Robertsonian_fusion' OR cvterm.name = 'reciprocal_chromosomal_translocation' OR cvterm.name = 'deficient_translocation' OR cvterm.name = 'inversion_cum_translocation' OR cvterm.name = 'cyclic_translocation' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'deficient_interchromosomal_transposition' OR cvterm.name = 'inverted_interchromosomal_transposition' OR cvterm.name = 'uninverted_interchromosomal_transposition' OR cvterm.name = 'unoriented_interchromosomal_transposition' OR cvterm.name = 'interchromosomal_duplication' OR cvterm.name = 'intrachromosomal_duplication' OR cvterm.name = 'free_duplication' OR cvterm.name = 'insertional_duplication' OR cvterm.name = 'inversion_derived_deficiency_plus_duplication' OR cvterm.name = 'inversion_derived_bipartite_duplication' OR cvterm.name = 'inversion_derived_duplication_plus_aneuploid' OR cvterm.name = 'intrachromosomal_transposition' OR cvterm.name = 'bipartite_duplication' OR cvterm.name = 'deficient_intrachromosomal_transposition' OR cvterm.name = 'inverted_intrachromosomal_transposition' OR cvterm.name = 'uninverted_intrachromosomal_transposition' OR cvterm.name = 'unoriented_intrachromosomal_transposition' OR cvterm.name = 'free_ring_duplication' OR cvterm.name = 'uninverted_insertional_duplication' OR cvterm.name = 'inverted_insertional_duplication' OR cvterm.name = 'unoriented_insertional_duplication' OR cvterm.name = 'compound_chromosome_arm' OR cvterm.name = 'homo_compound_chromosome' OR cvterm.name = 'hetero_compound_chromosome' OR cvterm.name = 'dexstrosynaptic_chromosome' OR cvterm.name = 'laevosynaptic_chromosome' OR cvterm.name = 'partially_characterised_chromosomal_mutation' OR cvterm.name = 'chromosome_structure_variation'; --- ************************************************ --- *** relation: alternatively_spliced_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript that is alternatively splic *** --- *** ed. *** --- ************************************************ --- CREATE VIEW alternatively_spliced_transcript AS SELECT feature_id AS alternatively_spliced_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'alternatively_spliced_transcript'; --- ************************************************ --- *** relation: encodes_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, but *** --- *** encodes only one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_1_polypeptide AS SELECT feature_id AS encodes_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_1_polypeptide'; --- ************************************************ --- *** relation: encodes_greater_than_1_polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide. *** --- ************************************************ --- CREATE VIEW encodes_greater_than_1_polypeptide AS SELECT feature_id AS encodes_greater_than_1_polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides' OR cvterm.name = 'encodes_overlapping_peptides' OR cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_greater_than_1_polypeptide'; --- ************************************************ --- *** relation: encodes_different_polypeptides_different_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different stop codons. *** --- ************************************************ --- CREATE VIEW encodes_different_polypeptides_different_stop AS SELECT feature_id AS encodes_different_polypeptides_different_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides_different_start *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides_different_start AS SELECT feature_id AS encodes_overlapping_peptides_different_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_peptides_different_start'; --- ************************************************ --- *** relation: encodes_disjoint_polypeptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** do not have overlapping peptide sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW encodes_disjoint_polypeptides AS SELECT feature_id AS encodes_disjoint_polypeptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_disjoint_polypeptides'; --- ************************************************ --- *** relation: encodes_overlapping_polypeptides_different_start_and_stop *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences, but *** --- *** use different start and stop codons. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_polypeptides_different_start_and_stop AS SELECT feature_id AS encodes_overlapping_polypeptides_different_start_and_stop_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop'; --- ************************************************ --- *** relation: encodes_overlapping_peptides *** --- *** relation type: VIEW *** --- *** *** --- *** A gene that is alternately spliced, and *** --- *** encodes more than one polypeptide, that *** --- *** have overlapping peptide sequences. *** --- ************************************************ --- CREATE VIEW encodes_overlapping_peptides AS SELECT feature_id AS encodes_overlapping_peptides_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'encodes_different_polypeptides_different_stop' OR cvterm.name = 'encodes_overlapping_peptides_different_start' OR cvterm.name = 'encodes_overlapping_polypeptides_different_start_and_stop' OR cvterm.name = 'encodes_overlapping_peptides'; --- ************************************************ --- *** relation: cryptogene *** --- *** relation type: VIEW *** --- *** *** --- *** A maxicircle gene so extensively edited *** --- *** that it cannot be matched to its edited *** --- *** mRNA sequence. *** --- ************************************************ --- CREATE VIEW cryptogene AS SELECT feature_id AS cryptogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cryptogene'; --- ************************************************ --- *** relation: dicistronic_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that has the qualit *** --- *** y dicistronic. *** --- ************************************************ --- CREATE VIEW dicistronic_primary_transcript AS SELECT feature_id AS dicistronic_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dicistronic_primary_transcript'; --- ************************************************ --- *** relation: member_of_regulon *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW member_of_regulon AS SELECT feature_id AS member_of_regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'member_of_regulon'; --- ************************************************ --- *** relation: cds_independently_known *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS with the evidence status of being *** --- *** independently known. *** --- ************************************************ --- CREATE VIEW cds_independently_known AS SELECT feature_id AS cds_independently_known_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_independently_known'; --- ************************************************ --- *** relation: orphan_cds *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS whose predicted amino acid sequenc *** --- *** e is unsupported by any experimental evi *** --- *** dence or by any match with any other kno *** --- *** wn sequence. *** --- ************************************************ --- CREATE VIEW orphan_cds AS SELECT feature_id AS orphan_cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS'; --- ************************************************ --- *** relation: cds_supported_by_domain_match_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by domain simila *** --- *** rity. *** --- ************************************************ --- CREATE VIEW cds_supported_by_domain_match_data AS SELECT feature_id AS cds_supported_by_domain_match_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data'; --- ************************************************ --- *** relation: cds_supported_by_sequence_similarity_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by sequence simi *** --- *** larity data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_sequence_similarity_data AS SELECT feature_id AS cds_supported_by_sequence_similarity_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data'; --- ************************************************ --- *** relation: cds_predicted *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is predicted. *** --- ************************************************ --- CREATE VIEW cds_predicted AS SELECT feature_id AS cds_predicted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'CDS_predicted'; --- ************************************************ --- *** relation: cds_supported_by_est_or_cdna_data *** --- *** relation type: VIEW *** --- *** *** --- *** A CDS that is supported by similarity to *** --- *** EST or cDNA data. *** --- ************************************************ --- CREATE VIEW cds_supported_by_est_or_cdna_data AS SELECT feature_id AS cds_supported_by_est_or_cdna_data_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS_supported_by_EST_or_cDNA_data'; --- ************************************************ --- *** relation: internal_shine_dalgarno_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A Shine-Dalgarno sequence that stimulate *** --- *** s recoding through interactions with the *** --- *** anti-Shine-Dalgarno in the RNA of small *** --- *** ribosomal subunits of translating ribos *** --- *** omes. The signal is only operative in Ba *** --- *** cteria. *** --- ************************************************ --- CREATE VIEW internal_shine_dalgarno_sequence AS SELECT feature_id AS internal_shine_dalgarno_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence'; --- ************************************************ --- *** relation: recoded_mrna *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of a mature mRNA transcript *** --- *** , modified before translation or during *** --- *** translation, usually by special cis-acti *** --- *** ng signals. *** --- ************************************************ --- CREATE VIEW recoded_mrna AS SELECT feature_id AS recoded_mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'recoded_mRNA'; --- ************************************************ --- *** relation: minus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of -1. *** --- ************************************************ --- CREATE VIEW minus_1_translationally_frameshifted AS SELECT feature_id AS minus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: plus_1_translationally_frameshifted *** --- *** relation type: VIEW *** --- *** *** --- *** An attribute describing a translational *** --- *** frameshift of +1. *** --- ************************************************ --- CREATE VIEW plus_1_translationally_frameshifted AS SELECT feature_id AS plus_1_translationally_frameshifted_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'plus_1_translationally_frameshifted'; --- ************************************************ --- *** relation: mrna_recoded_by_translational_bypass *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA where translation was sus *** --- *** pended at a particular codon and resumed *** --- *** at a particular non-overlapping downstr *** --- *** eam codon. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_translational_bypass AS SELECT feature_id AS mrna_recoded_by_translational_bypass_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_translational_bypass'; --- ************************************************ --- *** relation: mrna_recoded_by_codon_redefinition *** --- *** relation type: VIEW *** --- *** *** --- *** A recoded_mRNA that was modified by an a *** --- *** lteration of codon meaning. *** --- ************************************************ --- CREATE VIEW mrna_recoded_by_codon_redefinition AS SELECT feature_id AS mrna_recoded_by_codon_redefinition_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA_recoded_by_codon_redefinition'; --- ************************************************ --- *** relation: recoding_stimulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A site in an mRNA sequence that stimulat *** --- *** es the recoding of a region in the same *** --- *** mRNA. *** --- ************************************************ --- CREATE VIEW recoding_stimulatory_region AS SELECT feature_id AS recoding_stimulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'recoding_stimulatory_region'; --- ************************************************ --- *** relation: four_bp_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon with 4 base *** --- *** pairs. *** --- ************************************************ --- CREATE VIEW four_bp_start_codon AS SELECT feature_id AS four_bp_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'four_bp_start_codon'; --- ************************************************ --- *** relation: archaeal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron characteristic of Archaeal tRN *** --- *** A and rRNA genes, where intron transcrip *** --- *** t generates a bulge-helix-bulge motif th *** --- *** at is recognised by a splicing endoribon *** --- *** uclease. *** --- ************************************************ --- CREATE VIEW archaeal_intron AS SELECT feature_id AS archaeal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'archaeal_intron'; --- ************************************************ --- *** relation: trna_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron found in tRNA that is spliced *** --- *** via endonucleolytic cleavage and ligatio *** --- *** n rather than transesterification. *** --- ************************************************ --- CREATE VIEW trna_intron AS SELECT feature_id AS trna_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA_intron'; --- ************************************************ --- *** relation: ctg_start_codon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-canonical start codon of sequence *** --- *** CTG. *** --- ************************************************ --- CREATE VIEW ctg_start_codon AS SELECT feature_id AS ctg_start_codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CTG_start_codon'; --- ************************************************ --- *** relation: secis_element *** --- *** relation type: VIEW *** --- *** *** --- *** The incorporation of selenocysteine into *** --- *** a protein sequence is directed by an in *** --- *** -frame UGA codon (usually a stop codon) *** --- *** within the coding region of the mRNA. Se *** --- *** lenoprotein mRNAs contain a conserved se *** --- *** condary structure in the 3' UTR that is *** --- *** required for the distinction of UGA stop *** --- *** from UGA selenocysteine. The selenocyst *** --- *** eine insertion sequence (SECIS) is aroun *** --- *** d 60 nt in length and adopts a hairpin s *** --- *** tructure which is sufficiently well-defi *** --- *** ned and conserved to act as a computatio *** --- *** nal screen for selenoprotein genes. *** --- ************************************************ --- CREATE VIEW secis_element AS SELECT feature_id AS secis_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SECIS_element'; --- ************************************************ --- *** relation: retron *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence coding for a short, single-stra *** --- *** nded, DNA sequence via a retrotransposed *** --- *** RNA intermediate; characteristic of som *** --- *** e microbial genomes. *** --- ************************************************ --- CREATE VIEW retron AS SELECT feature_id AS retron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'retron'; --- ************************************************ --- *** relation: three_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** downstream of the recoding site. *** --- ************************************************ --- CREATE VIEW three_prime_recoding_site AS SELECT feature_id AS three_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'three_prime_recoding_site'; --- ************************************************ --- *** relation: three_prime_stem_loop_structure *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory region, the stem- *** --- *** loop secondary structural element is dow *** --- *** nstream of the redefined region. *** --- ************************************************ --- CREATE VIEW three_prime_stem_loop_structure AS SELECT feature_id AS three_prime_stem_loop_structure_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_stem_loop_structure'; --- ************************************************ --- *** relation: five_prime_recoding_site *** --- *** relation type: VIEW *** --- *** *** --- *** The recoding stimulatory signal located *** --- *** upstream of the recoding site. *** --- ************************************************ --- CREATE VIEW five_prime_recoding_site AS SELECT feature_id AS five_prime_recoding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_recoding_site'; --- ************************************************ --- *** relation: flanking_three_prime_quadruplet_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** Four base pair sequence immediately down *** --- *** stream of the redefined region. The rede *** --- *** fined region is a frameshift site. The q *** --- *** uadruplet is 2 overlapping codons. *** --- ************************************************ --- CREATE VIEW flanking_three_prime_quadruplet_recoding_signal AS SELECT feature_id AS flanking_three_prime_quadruplet_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal'; --- ************************************************ --- *** relation: uag_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAG stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uag_stop_codon_signal AS SELECT feature_id AS uag_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal'; --- ************************************************ --- *** relation: uaa_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UAA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uaa_stop_codon_signal AS SELECT feature_id AS uaa_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAA_stop_codon_signal'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: uga_stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A stop codon signal for a UGA stop codon *** --- *** redefinition. *** --- ************************************************ --- CREATE VIEW uga_stop_codon_signal AS SELECT feature_id AS uga_stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UGA_stop_codon_signal'; --- ************************************************ --- *** relation: three_prime_repeat_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal, downstrea *** --- *** m sequence important for recoding that c *** --- *** ontains repetitive elements. *** --- ************************************************ --- CREATE VIEW three_prime_repeat_recoding_signal AS SELECT feature_id AS three_prime_repeat_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_repeat_recoding_signal'; --- ************************************************ --- *** relation: distant_three_prime_recoding_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding signal that is found many hun *** --- *** dreds of nucleotides 3' of a redefined s *** --- *** top codon. *** --- ************************************************ --- CREATE VIEW distant_three_prime_recoding_signal AS SELECT feature_id AS distant_three_prime_recoding_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'distant_three_prime_recoding_signal'; --- ************************************************ --- *** relation: stop_codon_signal *** --- *** relation type: VIEW *** --- *** *** --- *** A recoding stimulatory signal that is a *** --- *** stop codon and has effect on efficiency *** --- *** of recoding. *** --- ************************************************ --- CREATE VIEW stop_codon_signal AS SELECT feature_id AS stop_codon_signal_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'stop_codon_signal'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gene_segment *** --- *** relation type: VIEW *** --- *** *** --- *** A gene component region which acts as a *** --- *** recombinational unit of a gene whose fun *** --- *** ctional form is generated through somati *** --- *** c recombination. *** --- ************************************************ --- CREATE VIEW gene_segment AS SELECT feature_id AS gene_segment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'gene_segment'; CREATE TABLE sequence_cv_lookup_table (sequence_cv_lookup_table_id serial not null, primary key(sequence_cv_lookup_table_id), original_cvterm_name varchar(1024), relation_name varchar(128)); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_variant','transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helitron','helitron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_initiator_methionine','cleaved_initiator_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epoxyqueuosine','epoxyqueuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4atac_snrna','u4atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast','kinetoplast'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_n_terminal','elongated_out_of_frame_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shadow_enhancer','shadow_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered','engineered'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_ii_tata_box','rna_polymerase_ii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_aminomethyl_seven_deazaguanosine','seven_aminomethyl_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_motif','sequence_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity','low_complexity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est_match','est_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_nonamer','v_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_c_cluster','d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_21s','rrna_21s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_factor','bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethyluridine','five_carboxymethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dinucleotide_repeat_microsatellite_feature','dinucleotide_repeat_microsatellite_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_methyladenosine','two_methylthio_n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_mrna','trans_spliced_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_c_transversion','g_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heptamer_of_recombination_feature_of_vertebrate_immune_system_gene','heptamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genotype','so_genotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_region','cloned_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_coding_piece','tmrna_coding_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_6s','rna_6s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element','x_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle','minicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_encoding','grna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endonuclease_spliced_intron','endonuclease_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional_duplication','insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('databank_entry','databank_entry'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine','glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_phenotype','variant_phenotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_cluster','v_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl12_acceptor_site','sl12_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nickel_ion_contact_site','polypeptide_nickel_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_rna_chromosome','circular_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wc_base_pair','wc_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pcr_product','pcr_product'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3_prime_utr_variant','three_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_three_amino_three_carboxypropyl_uridine','three_three_amino_three_carboxypropyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('site_specific_recombination_target_region','site_specific_recombination_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polycistronic_transcript','gene_with_polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue','rescue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_hypersensitive_site','nuclease_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_gene_variant','upstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_loop','mirna_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_cdna','double_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_post_translational_processing_variant','polypeptide_post_translational_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('2kb_upstream_variant','twokb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_domain_match','supported_by_domain_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylpseudouridine','one_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n_terminal_region','n_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_site','blunt_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_result_region','experimental_result_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine_trna_primary_transcript','methionine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr','utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_terminal_residue','non_terminal_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('member_of_regulon','member_of_regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine_trna_primary_transcript','thr_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_sequence_similarity_data','cds_supported_by_sequence_similarity_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_region','polypeptide_structural_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_gene','trna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_tungsten_ion_contact_site','polypeptide_tungsten_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_six','beta_bulge_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_c_cluster','d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_location','sequence_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_right_left_motif','polypeptide_nest_right_left_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_polypeptides_different_start_and_stop','encodes_overlapping_polypeptides_different_start_and_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_gene','leucoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_rna','y_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced_transcript','trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted','inverted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_regulatory_region','splicing_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('branch_site','branch_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop_five','beta_bulge_loop_five'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakpoint','chromosome_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_uncertainty','sequence_uncertainty'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyl_n6_threonylcarbamoyladenosine','n6_methyl_n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_with_frameshift','gene_with_mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compositionally_biased_region_of_peptide','compositionally_biased_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_c_cluster','vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna','pirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_hoogsteen_base_pair','reverse_hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophanyl_trna','tryptophanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_primed_cdna_clone','polya_primed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_chromosome','leucoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('status','status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_retrotransposon','ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna','rnase_p_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conjugative_transposon','conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('improved_high_quality_draft','improved_high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_gain','copy_number_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linkage_group','linkage_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_trans_spliced_transcript','gene_with_trans_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl8_acceptor_site','sl8_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_coil','peptide_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine_trna_primary_transcript','pyrrolysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_c_cluster','v_vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_sequence','phage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_methylation_site','h3k79_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded','recoded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposon_fragment','transposon_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_c_cluster','vj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_domain','editing_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyluridine','five_methylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_ii','centromere_dna_element_ii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alteration_attribute','alteration_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon_polymeric_tract','non_ltr_retrotransposon_polymeric_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transversion','transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan','tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recursive_splice_site','recursive_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_fusion','polypeptide_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator_binding_site','insulator_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_polyadenylation_variant','increased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline_trna_primary_transcript','proline_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_fragment','repeat_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blocked_reading_frame','blocked_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_snorna_primary_transcript','rrna_cleavage_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_isopentenyladenosine','n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_arginine','modified_l_arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_motif','polypeptide_conserved_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric','paracentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t3_rna_polymerase_promoter','t3_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_duplication','inversion_derived_bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_acceptor_site','trans_splice_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_2','a_box_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rre_rna','rre_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosyladenosine_phosphate','two_prime_o_riboA_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac_end','pac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extramembrane_polypeptide_region','extramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_change','copy_number_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein','intein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endosomal_localization_signal','endosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('twintron','twintron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_primary_transcript','scrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_prime_o_methyluridine','five_carboxymethylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('somatic_variant','somatic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication','duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_encoding','tmrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_cobalt_ion_contact_site','polypeptide_cobalt_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanked','flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion','inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ctg_start_codon','ctg_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine_trna_primary_transcript','tyrosine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('eukaryotic_terminator','eukaryotic_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_flanked','frt_flanked'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron_region','spliceosomal_intron_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_region_of_exon','coding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_cdna_insert','cloned_cdna_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcription_rate_variant','decreased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_c_cluster','v_vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_p_rna_gene','rnase_p_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated','translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidyl_trna','histidyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sonicate_fragment','sonicate_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_recoded_mrna','gene_with_recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyluridine','two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cosmid','cosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_rna_interference','silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_missense_codon','non_conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna','snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript','mature_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridylation_guide_snorna','pseudouridylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_gene','c_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_transcript','processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed_gene','floxed_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spot_42_rna','spot_42_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_clone','cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site','cryptic_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_gene_segment','pseudogenic_gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr','three_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_ii_intron','group_ii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna_gene','rnase_mrp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_alteration','structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna_oligo','pna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_sequence','insertion_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('junction','junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous','paralogous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna','tna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_thiouridine','five_isopentenylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_tandem_repeat','nested_tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift','minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_three_prime_splice_site','non_canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_non_canonical_start_codon','gene_with_non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_rrna','pseudogenic_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_turn','serine_threonine_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene','j_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_trimethylation_site','h3k27_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_primary_transcript','strna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_eliminated_sequence','internal_eliminated_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded_gene','allelically_excluded_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('qtl','qtl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_est','three_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bred_motif','bred_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse','reverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_encoding','mirna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_2_prime_o_trimethylguanosine','n2_n2_2_prime_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_function_variant','translational_product_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternate_transcription_start_sites','encodes_alternate_transcription_start_sites'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array','gene_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetranucleotide_repeat_microsatellite_feature','tetranuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_aminomethyl_two_thiouridine','five_aminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_primary_transcript','monocistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snv','snv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct','direct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_genetic_element','mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_ligand_contact','polypeptide_ligand_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biomaterial_region','biomaterial_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_flanking_region','transposable_element_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symmetric_rna_internal_loop','symmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_1_frameshift','mrna_with_plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_regulated','transcriptionally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_intron','five_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_feature','vertebrate_immune_system_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine_methyl_ester','five_carboxyhydroxymethyl_uridine_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_transposition','chromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_gene','proplastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_trna_primary_transcript','serine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attp_site','attp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense','antisense'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat_element','terminal_inverted_repeat_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coiled_coil','coiled_coil'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_cluster','v_vdj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_by_a_to_i_substitution','edited_transcript_by_a_to_i_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_primary_transcript','protein_coding_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mite','mite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_site_variant','cryptic_splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion','insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('secis_element','secis_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle','maxicircle'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss','tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pedigree_specific_variant','pedigree_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine','cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribothymidine','ribothymidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_adjacent_residues','non_adjacent_residues'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_modification','histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_ribosome_entry_site','internal_ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('outron','outron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_repeat','polypeptide_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_start','clone_insert_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attr_site','attr_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv3_motif','dmv3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_mrna','capped_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_rearrangement_feature','sequence_rearrangement_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_chromosome','apicoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_two','beta_turn_type_six_a_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated','invalidated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine','valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_regulated_gene','translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_insertion','amino_acid_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_targeting_sequence','promoter_targeting_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polinton','polinton'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_tag','engineered_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_coding_exon_variant','non_coding_exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylcytidine','five_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl5_acceptor_site','sl5_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated','positively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudouridine','pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amplification_origin','amplification_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_insertional_duplication','unorient_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_constitutive','transcriptionally_constitutive'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('extrachromosomal_mobile_genetic_element','extrachromosomal_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_origin','variant_origin'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_region','utr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna','mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosine','tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr1_motif','inr1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2b_ubiquitination_site','h2b_ubiquitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_acetyladenosine','n6_acetyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_splice_site','cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('floxed','floxed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_two','beta_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_variant','utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_terminal_region','c_terminal_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_regulatory_region','transcription_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_leucine','modified_l_leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr_component','five_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acylation_region','histone_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_c_cluster','vdj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_part','chromosome_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptional_cis_regulatory_region','transcriptional_cis_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanyl_trna','phenylalanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_site','insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gc_rich_promoter_region','gc_rich_promoter_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_est_set','overlapping_est_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_two','asx_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon_loop','anticodon_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv5_motif','dmv5_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl1_acceptor_site','sl1_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_region','cds_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region_variant','regulatory_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_dimethylation_site','h3k9_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_gained','stop_gained'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna_gene','telomerase_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_c_cluster','v_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_insert','engineered_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_inverted_gene','recombinationally_inverted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microarray_oligo','microarray_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_array_member','cassette_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift_variant','plus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_snrna','u12_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_est_or_cdna','supported_by_est_or_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_10_signal','minus_10_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert_end','clone_insert_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inr_motif','inr_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_stem_loop_structure','three_prime_stem_loop_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rflp_fragment','rflp_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phage_rna_polymerase_promoter','phage_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_transition','pyrimidine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrinsically_unstructured_polypeptide_region','intrinsically_unstructured_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_2_prime_o_dimethylguanosine','n2_2_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_loss','exon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeal_intron','archaeal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna','lna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_junction','exon_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t7_rna_polymerase_promoter','t7_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_interchromosomal_transposition','invert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('episome','episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_insertional_duplication','uninvert_insert_dup'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free','free'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_difference','sequence_difference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k5_acylation_site','h4k5_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_c_cluster','v_d_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_conflict','sequence_conflict'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nmd_transcript_variant','nmd_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_clone','tiling_path_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iii_intron','group_iii_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_glycine','modified_glycine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_alteration','sequence_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyploid','polyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mathematically_defined_repeat','mathematically_defined_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_modification','gene_silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_cluster','v_vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine_trna_primary_transcript','isoleucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_small_subunit_primary_transcript','rrna_small_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ltr_component','ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_framshift','plus_2_framshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_structure_variant','translational_product_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid_trna_primary_transcript','glutamic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_rearranged_at_dna_level','gene_rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript','edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_partial_processing','invalidated_by_partial_processing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_stability_variant','increased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequencing_primer','sequencing_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_for_gpi_anchor_region','cleaved_for_gpi_anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_cysteine','modified_l_cysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr','five_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_recognition_site','restriction_enzyme_recognition_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frt_site','frt_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_inverted_repeat','terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_i','centromere_dna_element_i'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transition','transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_junction','deletion_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_right_handed_type_one','beta_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_ribosylguanosine_phosphate','two_prime_o_ribosylguanosine_phosphate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyl_two_prime_o_methyluridine','five_cm_2_prime_o_methU'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_transcribed_spacer_region','internal_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic','dicistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supported_by_sequence_similarity','supported_by_sequence_similarity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reverse_primer','reverse_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_three_prime_ltr_region','u3_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine_trna_primary_transcript','glutamine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_promoter','rnapol_ii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping','overlapping'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_beta_motif','alpha_beta_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_transposable_element','engineered_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward_primer','forward_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attctn_site','attctn_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_recombination_signal_sequence','five_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6_snrna','u6_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_gene','recombinationally_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_threonylcarbamoyladenosine','n6_threonylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carbamoylmethyluridine','five_carbamoylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_fragment','cds_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genome','genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_translational_product_level','increased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_product_level_variant','translational_product_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter','promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding_gene','protein_coding_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_snrna','u5_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wybutosine','wybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylwyosine','methylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('large_subunit_rrna','large_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomally_aberrant_genome','chromosomally_aberrant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_2_prime_o_dimethylcytidine','n4_2_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition','c_to_t_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bidirectional_promoter','bidirectional_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated_cdna_clone','validated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('k_turn_rna_motif','k_turn_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_fragment','transcribed_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ust','five_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr_intron','three_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrogene','retrogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrimidine_to_purine_transversion','pyrimidine_to_purine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sine_element','sine_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_rst','five_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('utr_intron','utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_transposition','interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_sequence_secondary_structure','rna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_in_transcript','complex_change_in_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element','engineered_foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_rna_viral_sequence','ds_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fosmid','fosmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_substitution','complex_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('validated','validated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_snrna','u2_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplication_attribute','duplication_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('caat_signal','caat_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_cluster','c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_region','consensus_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_spacer','vertebrate_immune_system_gene_recombination_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_restriction_enzyme_junction','three_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_trap_construct','gene_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_aptamer','rna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_induced','transcriptionally_induced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal','intrachromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_localization_signal','nuclear_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_region','rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site_part','inversion_site_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_frameshift variant','plus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('origin_of_replication','origin_of_replication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('standard_draft','standard_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_dimethylation_site','h3k79_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_internal_loop','rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ultracontig','ultracontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptidyl','peptidyl'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_region','polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_region','epigenetically_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_insertion','transgenic_insertion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_antiguide','mirna_antiguide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rearranged_at_dna_level','rearranged_at_dna_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_variant','intergenic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_spacer','v_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strand_attribute','strand_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_lost','stop_lost'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced','alternatively_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formyl_two_prime_o_methylcytidine','five_formyl_two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_location','plasmid_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_bp_start_codon','four_bp_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcription_rate_variant','increased_transcription_rate_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged','recombinationally_rearranged'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_3d_structural_variant','complex_3d_structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chimeric_cdna_clone','chimeric_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna_primary_transcript','tasirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_transcript','gene_with_dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ltr_component','three_prime_ltr_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retron','retron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autopolyploid','autopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine','phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translation_regulatory_region','translation_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transit_peptide','transit_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_deletion','amino_acid_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_28s','rrna_28s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylinosine','one_two_prime_o_dimethylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonine','threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_minor_rna_motif','a_minor_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_cluster','j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce','dce'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quantitative_variant','quantitative_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysosomal_localization_signal','lysosomal_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_cluster','d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_arm','chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kinetoplast_gene','kinetoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('line_element','line_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('solo_ltr','solo_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('external_transcribed_spacer_region','external_transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_transcribed_region','non_transcribed_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_stem','mirna_stem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_c_cluster','dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hyperploid','hyperploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic','cryptic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_acetylation_site','h3k9_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alpha_helix','alpha_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion','fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_cluster','vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isowyosine','isowyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paracentric_inversion','paracentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homing_endonuclease_binding_site','homing_endonuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tna_oligo','tna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_gene','mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_fragment','restriction_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_pair','base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_antiparallel','inside_intron_antiparallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_binding_site','dna_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_cytidine','modified_cytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydrophobic_region_of_peptide','hydrophobic_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_primary_transcript','polycistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_proline','modified_l_proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('overlapping_feature_set','overlapping_feature_set'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_two','asx_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_duplication','interchromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_loss','inframe_codon_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('substitution','substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucine','isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('functional_variant','functional_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_recoding_site','three_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_stability_variant','transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_upstream_variant','fivekb_upstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_of_type_2_rnapol_iii_promoter','terminator_of_type_2_rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycine_trna_primary_transcript','glycine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_variant','intron_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_outer_repeat_region','regional_centromere_outer_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replication_regulatory_region','replication_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mating_type_region','mating_type_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_heptamer','v_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dispersed_repeat','dispersed_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer','primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_domain','polypeptide_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type','wild_type'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fusion_gene','fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_function_variant','transcript_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_member_region','gene_member_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginyl_trna','arginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compensatory_transcript_secondary_structure_variant','compensatory_transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_base_feature','methylated_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_intrachromosomal_transposition','uninvert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_gene','scrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_18s','rrna_18s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_1','rnapol_iii_promoter_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_mutation','point_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudoknot','pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_quartet','g_quartet'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop','schellmann_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_selenocysteine','modified_l_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pna','pna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon','three_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_gene','endogenous_retroviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_segment','vertebrate_immunoglobulin_t_cell_receptor_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_translational_bypass','mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_region','engineered_foreign_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_encoding','snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_est','five_prime_est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foldback_element','foldback_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_encoding','srp_rna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_c_cluster','d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_c_cluster','dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_ubiqitination_site','histone_ubiqitination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_structural_alteration','complex_structural_alteration'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_encoding','rrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_recoded_by_codon_redefinition','mrna_recoded_by_codon_redefinition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyluridine','five_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_sequence','polya_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metabolic_island','metabolic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous','homologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('immature_peptide_region','immature_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h2bk5_monomethylation_site','h2bk5_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_attribute','sequence_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sirna','sirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dart_marker','dart_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_motif','nucleotide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translationally_frameshifted','plus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_intron','trna_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_noncoding_exon','five_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_motif','dna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_strand','beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_oligo','ds_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyladenosine','one_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oxys_rna','oxys_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_motif','asx_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxyuridine','five_hydroxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_exon','coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_translational_frameshift','plus_1_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_formylcytidine','five_formylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_dimethylation_site','h3k27_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliced_leader_rna','spliced_leader_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_chromosome','mitochondrial_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fragment','gene_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_2prirme_o_trimethylguanosine','n2_7_2prirme_o_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift','frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide_cleavage_site','propeptide_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyldihydrouridine','five_methyldihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid','amino_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_breakpoint','translocation_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5_8s','rrna_5_8s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('helix_turn_helix','helix_turn_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('simple_sequence_length_variation','simple_sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionine','methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_loss_of_function_variant','polypeptide_loss_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_gene','transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('whole_genome_sequence_status','whole_genome_sequence_status'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_island','genomic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_segment','gene_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_gene','snrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_region','engineered_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('common_variant','common_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptogene','cryptogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_noncoding_region','three_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_rna_interference','gene_silenced_by_rna_interference'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_interchromosomal_transposition','d_interchr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_variant_site','natural_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly','assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('major_tss','major_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna','trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides','encodes_overlapping_peptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_conserved_region','nc_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('locus_control_region','locus_control_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna_oligo','s_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_chromosome','dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_b','beta_turn_type_six_b'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loss_of_heterozygosity','loss_of_heterozygosity'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_gene','engineered_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wobble_base_pair','wobble_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_amino_acid_feature','modified_amino_acid_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_c_transition','t_to_c_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocaton_attribute','translocaton_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_sequence','apicoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminal_codon_variant','terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irlinv_site','irlinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_sequence','synthetic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_1_polypeptide','encodes_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iia_intron','group_iia_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomere','telomere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_intron','interior_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_mrna','edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_three','catmat_right_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_duplication','tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_gene','tmrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_region','pre_edited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_hydroxynorvalylcarbamoyladenosine','n6_hydroxynorvalylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_chromosome','nucleomorphic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragmentary','fragmentary'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single','single'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('binding_site','binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanine','seven_methylguanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('target_site_duplication','target_site_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_gene','vdj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_nucleic_acid','bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_localization_signal','peptide_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_right_handed_four','catmat_right_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_acylation_site','h3k27_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome','compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_end','coding_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gap','gap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligand_binding_site','ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upstream_aug_codon','upstream_aug_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_transcript','pseudogenic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('satellite_dna','satellite_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency_plus_duplication','assortment_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element','transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('endogenous_retroviral_sequence','endogenous_retroviral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('microsatellite','microsatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_different_polypeptides_different_stop','encodes_different_polypeptides_different_stop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript','primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus_mrna','consensus_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_peptide_loop','membrane_peptide_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign','so_foreign'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_independent_bacterial_terminator','rho_independent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u_box','u_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_deacetylation','gene_silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vdj_j_c_cluster','vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cpg_island','cpg_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype','haplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylinosine','two_prime_o_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna','dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_rna_chromosome','circular_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_protein_region','mature_protein_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('b_box','b_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_zinc_ion_contact_site','polypeptide_zinc_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray_member','gene_subarray_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette','gene_cassette'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oric','oric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion_breakpoint','deletion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_attribute','insertion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_plus_2_frameshift','mrna_with_plus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chip_seq_region','chip_seq_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_right_handed_type_one','asx_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_cluster','transcribed_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tyrosyl_trna','tyrosyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous','orthologous'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('s_gna','s_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_three_prime_splice_site','canonical_three_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_exon','noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lethal_variant','lethal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minor_tss','minor_tss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethylcytidine','five_two_prime_o_dimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_trimethylation_site','h3k36_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_chromosome','macronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_translocation','deficient_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read_pair','read_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_with_translational_frameshift','transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('finished_genome','finished_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_3','rnapol_iii_promoter_type_3'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_transposon','dna_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orf','orf'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('right_handed_peptide_helix','right_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_left_right_motif','polypeptide_nest_left_right_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topology_attribute','topology_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirtron','mirtron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_motif','polypeptide_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl9_acceptor_site','sl9_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proplastid_sequence','proplastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated_gene','negatively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retinoic_acid_responsive_element','retinoic_acid_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_encoding','c_d_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_assembly','sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_gene','chromoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dcaps_primer','dcaps_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_clip','five_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path','golden_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_acceptor_variant','splice_acceptor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine','alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cleaved_peptide_region','cleaved_peptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_j_cluster','v_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_region','pseudogenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator_codon_variant','terminator_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna','methylation_guide_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_j_c_cluster','v_vj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_start_codon','non_canonical_start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_mrna_recoded_by_translational_bypass','gene_with_mrna_recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_turn_motif','polypeptide_turn_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autocatalytically_spliced_intron','autocatalytically_spliced_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile','mobile'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem','tandem'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron','intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clip','clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dye_terminator_read','dye_terminator_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv4_motif','dmv4_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('au_rich_element','au_rich_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_breakpoint','inversion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_siii','dce_siii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_recoding_site','five_prime_recoding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_protein_coding','non_protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mobile_intron','mobile_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment','vertebrate_immunoglobulin_t_cell_receptor_rearranged_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_one','st_turn_right_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna','rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron_parallel','inside_intron_parallel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('spliceosomal_intron','spliceosomal_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phagemid','phagemid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_block','editing_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fragment_assembly','fragment_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_acceptor_piece','tmrna_acceptor_piece'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six','beta_turn_type_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_rst','three_prime_rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteine_trna_primary_transcript','cysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_gene','post_translationally_regulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcriptionally_repressed','transcriptionally_repressed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crm','crm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cointegrated_plasmid','cointegrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequencing_information','polypeptide_sequencing_information'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_spacer','three_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path_fragment','tiling_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural','so_natural'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pi_helix','pi_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_base_call_error','possible_base_call_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_truncation','polypeptide_truncation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k14_acetylation_site','h3k14_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('adaptive_island','adaptive_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid','uridine_five_oxyacetic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl7_acceptor_site','sl7_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_2_translational_frameshift','plus_2_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_retained_variant','stop_retained_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homologous_region','homologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('500b_downstream_variant','fivehundred_b_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_utr','internal_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_cytoplasmic_polypeptide_region','non_cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature','experimental_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_chromosome','nuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar','exemplar'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_ii_core_promoter','rnapol_ii_core_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_methylation_site','h3k9_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanine_trna_primary_transcript','alanine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_variation','assortment_derived_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_dimethylguanosine','n2_n2_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_hook_turn','rna_hook_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcribed_spacer_region','transcribed_spacer_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_gene','plasmid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna','u14_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('galactosyl_queuosine','galactosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_gene','cyanelle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wild_type_rescue_gene','wild_type_rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u12_intron','u12_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aptamer','aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_mrna','recoded_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_transposon','nested_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site_variant','tf_binding_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronuclear_sequence','macronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust','ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine','selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_out_of_frame_polypeptide_c_terminal','elongated_out_of_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_mrna','gene_with_dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match_part','match_part'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorphic_sequence','nucleomorphic_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('apicoplast_gene','apicoplast_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulon','regulon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid_vector','plasmid_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tryptophan','modified_l_tryptophan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_chromosome_arm','free_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_primary_transcript','srp_rna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn','asx_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_binding_site','anchor_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript','rrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reading_frame','reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k23_acylation site','h3k23_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_variant','maternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dhu_loop','dhu_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetylcytidine','n4_acetylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimental_feature_attribute','experimental_feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_gene','silenced_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cloned_genomic_insert','cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_gain','intron_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_sequence_secondary_structure','dna_sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna_match','cdna_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_flanking_region','five_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysyl_trna','pyrrolysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_cis_hydroxyisopentenyl_adenosine','two_methylthio_n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_component','repeat_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methyl_three_three_amino_three_carboxypropyl_pseudouridine','one_methyl_3_3_amino_three_carboxypropyl_pseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rpra_rna','rpra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_sensitive_site','nuclease_sensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_amino_acid_substitution','conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_noncoding_region','five_prime_coding_exon_noncoding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter','rnapol_iii_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tryptophan_trna_primary_transcript','try_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncontiguous_finished','noncontiguous_finished'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('region','region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tf_binding_site','tf_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attl_site','attl_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_plasmid','natural_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('upd','upd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conservative_missense_codon','conservative_missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_dimethyladenosine','n6_n6_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('laevosynaptic_chromosome','laevosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_structural_element','chromosomal_structural_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_array','gene_cassette_array'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_gene_cluster','vertebrate_immunoglobulin_t_cell_receptor_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('canonical_five_prime_splice_site','canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bound_by_protein','bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts_map','sts_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnazyme','dnazyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silent_mutation','silent_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_cluster','v_d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distal_promoter_element','distal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_duplication','bipartite_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hydroxywybutosine','hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dihydrouridine','dihydrouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon_coding_region','five_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_one','beta_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_trimethylation','h3k4_trimethylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_codon','recoded_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted','predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('resolution_site','resolution_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_cyano_seven_deazaguanosine','seven_cyano_seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_associated_variant','disease_associated_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_switch','conformational_switch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulated','regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_repeat','inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_a_transversion','t_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attc_site','attc_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methyladenosine','two_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cross_genome_match','cross_genome_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tandem_repeat','tandem_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_loss','copy_number_loss'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_primary_transcript','antisense_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_collection','sequence_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_polyadenylated_mrna','gene_with_polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_i_promoter','rnapol_i_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methyluridine','three_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('start_codon','start_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposon','retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_c_terminal','elongated_in_frame_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene','v_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_dna','chloroplast_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negative_sense_ssrna_viral_sequence','negative_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_binding_site','primer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_box','c_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plasmid','plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biological_region','biological_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_a_transition','g_to_a_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_canonical_five_prime_splice_site','non_canonical_five_prime_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna_primary_transcript','c_d_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_region','trna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_cis_hydroxyisopentenyl_adenosine','n6_cis_hydroxyisopentenyl_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_sequence','chloroplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_frequency','variant_frequency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_region','exon_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_five_prime_ltr_region','r_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_c_cluster','v_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_three_prime_ltr_region','r_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna','snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylinosine','one_methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_codon_gain','inframe_codon_gain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_gene_recombination_feature','j_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_structural_motif','polypeptide_structural_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved_region','conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl3_acceptor_site','sl3_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('remark','remark'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fixed_variant','fixed_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_dna_contact','polypeptide_dna_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon','codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_23s','rrna_23s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_gain_of_function_variant','polypeptide_gain_of_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna','mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glycyl_trna','glycyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_sequence','cyanelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_independently_known','cds_independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insulator','insulator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positive_sense_ssrna_viral_sequence','positive_sense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sticky_end_restriction_enzyme_cleavage_site','sticky_end_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_match','expressed_sequence_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('possible_assembly_error','possible_assembly_error'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_snorna','u3_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_manganese_ion_contact_site','polypeptide_manganese_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k16_acylation_site','h4k16_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('g_to_t_transversion','g_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature_of_rearranged_gene','recombination_feature_of_rearranged_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_coding_exon_coding_region','three_prime_coding_exon_coding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_primary_transcript','tmrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_cdna','single_stranded_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_determined','experimentally_determined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_exon','pseudogenic_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u2_intron','u2_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome','chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_alternately_spliced_transcripts','encodes_alternately_spliced_transcripts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aberrant_processed_transcript','aberrant_processed_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_change_of_translational_product_variant','complex_change_of_translational_product_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna','gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dsra_rna','dsra_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intron_domain','intron_domain'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_predicted','cds_predicted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_asparagine','modified_l_asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inframe_variant','inframe_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_nonamer','five_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl2_acceptor_site','sl2_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_localization_variant','polypeptide_localization_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_si','dce_si'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_primary_transcript','snrna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation','translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_methylation_site','h3k27_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_phenylalanine','modified_l_phenylalanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna','lincrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_valine','modified_l_valine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac','yac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('signal_peptide','signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_ltr_region','r_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna_gene','srp_rna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_n_terminal','elongated_polypeptide_n_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_hotspot','recombination_hotspot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_c_cluster','v_dj_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('viral_sequence','viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_terminal_inverted_repeat','five_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_thiouridine','five_mcm_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited','edited'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('breu_motif','breu_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_start','coding_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_monomethylation_site','h3k9_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_utr','three_prime_utr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe1_motif','dpe1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_tyrosine','modified_l_tyrosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_j_c_cluster','v_d_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_methylation','silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_inversion','deficient_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_level_variant','decreased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiouridine','two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylation_variant','polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_iii_tata_box','rna_polymerase_iii_tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thio_two_prime_o_methyluridine','two_thio_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k18_acetylation_site','h3k18_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucoplast_sequence','leucoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds','cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_signal_sequence','polya_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_sequence','micronuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamyl_trna','glutamyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k27_monomethylation_site','h3k27_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift_variant','minus_2_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_gene','strna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted_gene','paternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_chromosome','rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm3_motif','ndm3_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u1_snrna','u1_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_hydroxymethylcytidine','five_hydroxymethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_feature','recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_disjoint_polypeptides','encodes_disjoint_polypeptides'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated','post_translationally_regulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_fusion_gene','engineered_fusion_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_recombination_signal_sequence','three_prime_d_recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate','intermediate'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_calcium_ion_contact_site','polypeptide_calcium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic_region','syntenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_collection','variant_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_donor','cryptic_splice_donor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_error_correction','assembly_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sugar_edge_base_pair','sugar_edge_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_gene','engineered_foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_monomethylation_site','h3k4_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_acetyl_2_prime_o_methylcytidine','n4_acetyl_2_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_by_ab_initio_computation','predicted_by_ab_initio_computation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_secondary_structure','polypeptide_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna_gene','ncrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_junction_loop','rna_junction_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('haplotype_block','haplotype_block'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oriv','oriv'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_collection','peptide_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ambisense_ssrna_viral_sequence','ambisense_ssrna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_oligo','morpholino_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere','centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified_gene','epigenetically_modified_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_inversion','chromosomal_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_35_signal','minus_35_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_two_prime_o_dimethyluridine','three_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_thiouridine','four_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcription_end_site','transcription_end_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pirna_gene','pirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_mirna','pre_mirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cysteinyl_trna','cysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_three','catmat_left_handed_three'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_splice_acceptor','cryptic_splice_acceptor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_seven','schellmann_loop_seven'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_c_cluster','v_vdj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transposable_element_insertion_site','transposable_element_insertion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translocation_element','translocation_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript_region','mirna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan_cds','orphan_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_mrna','monocistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('natural_transposable_element','natural_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('golden_path_fragment','golden_path_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lipoprotein_signal_peptide','lipoprotein_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine','arginine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_rna_chromosome','linear_double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k8_acylation site','h4k8_acylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_large_subunit_primary_transcript','rrna_large_subunit_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('irrinv_site','irrinv_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_sequence','plastid_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base_call_error_correction','base_call_error_correction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_plasmid','integrated_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_methionine','modified_l_methionine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_rna_chromosome','linear_single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_sequence','chromoplast_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proximal_promoter_element','proximal_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_read','contig_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_trap_construct','promoter_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_selenocysteine','stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_methylguanosine','seven_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn','gamma_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna','tmrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methionyl_trna','methionyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synonymous_codon','synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cdna','cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl4_acceptor_site','sl4_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclease_binding_site','nuclease_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uridine_five_oxyacetic_acid_methyl_ester','uridine_five_oxyacetic_acid_methyl_ester'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_race_clone','three_prime_race_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_double_stranded_dna_chromosome','circular_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('consensus','consensus'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('positively_autoregulated_gene','positively_autoregulated_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tss_region','tss_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_histidine','modified_l_histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unitary_pseudogene','unitary_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_metal_contact','polypeptide_metal_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integron','integron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_loop','d_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decayed_exon','decayed_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_signal_sequence','recombination_signal_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_inosine','modified_inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_three_prime_overlap','three_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_j_cluster','v_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_five_prime_overlap','three_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombination_regulatory_region','recombination_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge_loop','beta_bulge_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_cleavage_junction','restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('blunt_end_restriction_enzyme_cleavage_junction','blunt_end_restriction_enzyme_cleavage_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intergenic_region','intergenic_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv2_motif','dmv2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_mutation','intrachromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antisense_rna','antisense_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_feature','sequence_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_glycinylcarbamoyladenosine','n6_glycinylcarbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_classic','gamma_turn_classic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_cis_splice_site','three_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rapd','rapd'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_ring_chromosome','inverted_ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cca_tail','cca_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_double_stranded_dna_chromosome','linear_double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_five_prime_ltr_region','u5_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bruno_response_element','bruno_response_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_to_g_transversion','t_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_a_transversion','c_to_a_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('macronucleus_destined_segment','macronucleus_destined_segment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('distant_three_prime_recoding_signal','distant_three_prime_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pre_edited_mrna','pre_edited_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('p_element','p_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pac','pac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_fusion','gene_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('base','base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_redefined','codon_redefined'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_mrna','polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('codon_variant','codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyl_two_prime_o_methyluridine','five_methoxycarbonylmethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('match','match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_read_through','gene_with_stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparaginyl_trna','asparaginyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('threonyl_trna','threonyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_five_prime_ltr_region','u3_five_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_ltr','five_prime_ltr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_gene','vj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rho_dependent_bacterial_terminator','rho_dependent_bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_methylguanosine','n2_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_flanking_region','three_prime_flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomically_contaminated_cdna_clone','genomically_contaminated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_guide_sequence','internal_guide_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_target_site','mirna_target_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_three_prime_ltr_region','u5_three_prime_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('undermodified_hydroxywybutosine','undermodified_hydroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('introgressed_chromosome_region','introgressed_chromosome_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translationally_frameshifted','translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_spliced','trans_spliced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylation_guide_snorna_primary_transcript','methylation_guide_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine','leucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_deletion','chromosomal_deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_uridine','five_isopentenylaminomethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon','stop_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_threonyl_carbamoyladenosine','two_methylthio_n6_threonyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_polyadenylation_variant','decreased_polyadenylation_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('biochemical_region_of_peptide','biochemical_region_of_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interband','interband'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_constraint_sequence','dna_constraint_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_insert','clone_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snp','snp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromoplast_chromosome','chromoplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_25s','rrna_25s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tata_box','tata_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plastid_gene','plastid_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asx_turn_left_handed_type_one','asx_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_uridine','modified_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dce_sii','dce_sii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intramembrane_polypeptide_region','intramembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysyl_trna','lysyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rr_tract','rr_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_primary_transcript_region','rrna_primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k20_monomethylation_site','h4k20_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ds_dna_viral_sequence','ds_dna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternatively_spliced_transcript','alternatively_spliced_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_copper_ion_contact_site','polypeptide_copper_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna_encoding','scrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_duplication','chromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone','clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_isoleucine','modified_l_isoleucine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_subarray','gene_subarray'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hetero_compound_chromosome','hetero_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_transcript','dicistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_ligand_binding_site','inactive_ligand_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_methylation','silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl6_acceptor_site','sl6_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('t_loop','t_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('targeting_vector','targeting_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_thiocytidine','two_thiocytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_serine','modified_l_serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('srp_rna','srp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_repeat_recoding_signal','three_prime_repeat_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rate_of_transcription_variant','rate_of_transcription_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylguanosine','two_prime_o_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_binding_motif','polypeptide_binding_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recombinationally_rearranged_vertebrate_immune_system_gene','recombinationally_rearranged_vertebrate_immune_system_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box','a_box'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splicing_variant','splicing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_methylguanosine','one_methylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamine','modified_l_glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_variant','sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_length_variation','sequence_length_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna_encoding','strna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('plus_1_frameshift','plus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('topologically_defined_region','topologically_defined_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_cds','edited_cds'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_modification','gene_silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('e_box_motif','e_box_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_uniparental_disomy','paternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_subunit_rrna','small_subunit_rrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dnasei_hypersensitive_site','dnasei_hypersensitive_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_c_cluster','v_d_dj_j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('compound_chromosome_arm','compound_chromosome_arm'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('score','score'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('feature_attribute','feature_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_match','protein_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('downstream_gene_variant','downstream_gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl10_accceptor_site','sl10_accceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_variation','chromosome_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_motif','serine_threonine_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_box_type_1','a_box_type_1'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allelically_excluded','allelically_excluded'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_aneuploid','assortment_derived_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rare_variant','rare_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_isopentenylaminomethyl_two_prime_o_methyluridine','five_isopentenylaminomethyl_two_prime_o_methyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_central_core','regional_centromere_central_core'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gna_oligo','gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_transcript_variant','nc_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('copy_number_variation','copy_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced','silenced'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylcytidine','three_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dexstrosynaptic_chromosome','dexstrosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_insertional_duplication','inverted_insertional_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_mini_gene','rescue_mini_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catmat_left_handed_four','catmat_left_handed_four'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alternate_sequence_site','alternate_sequence_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_iron_ion_contact_site','polypeptide_iron_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_t_transition_at_pcpg_site','c_to_t_transition_at_pcpg_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_molybdenum_ion_contact_site','polypeptide_molybdenum_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('phenylalanine_trna_primary_transcript','phe_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_translational_product_level','decreased_translational_product_level'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_primary_transcript','h_aca_box_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna','r_gna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_sequence_variant','coding_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_partial_loss_of_function','polypeptide_partial_loss_of_function'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_restriction_enzyme_junction','five_prime_restriction_enzyme_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_transposition','intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_a','methylated_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_16s','rrna_16s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('disease_causing_variant','disease_causing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_methylcytidine','n4_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('riboswitch','riboswitch'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('duplicated_pseudogene','duplicated_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_duplication','assortment_derived_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_regulatory_element','chromosomal_regulatory_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_five_prime_overlap','five_prime_five_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_function_variant','polypeptide_function_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozymic','ribozymic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_bipartite_deficiency','inversion_derived_bipartite_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_contamination','invalidated_by_genomic_contamination'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_genome','variant_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vj_j_cluster','vj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_number_variation','chromosome_number_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_attribute','gene_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uag_stop_codon_signal','uag_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_match','nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_mirna_variant','mature_mirna_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_two','st_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epigenetically_modified','epigenetically_modified'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_duplication','inversion_derived_deficiency_plus_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_selenouridine','five_methylaminomethyl_two_selenouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid_trna_primary_transcript','aspartic_acid_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_mt_pseudogene','nuclear_mt_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exonic_splice_enhancer','exonic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u4_snrna','u4_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('csrb_rsmb_rna','csrb_rsmb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_1_intron_homing_endonuclease_target_region','group_1_intron_homing_endonuclease_target_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('crispr','crispr'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_gene','snorna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_junction','trans_splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_three_prime_quadruplet_recoding_signal','flanking_three_prime_quadruplet_recoding_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vdj_j_cluster','v_vdj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cassette_pseudogene','cassette_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('incomplete_terminal_codon_variant','incomplete_terminal_codon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_modification','silenced_by_histone_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_gene','proviral_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxyhydroxymethyl_uridine','five_carboxyhydroxymethyl_uridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mt_gene','mt_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_rna_chromosome','single_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_stimulatory_region','recoding_stimulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyluridine','five_taurinomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_threonine','modified_l_threonine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_cluster','v_d_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('synthetic_oligo','synthetic_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_to_pyrimidine_transversion','purine_to_pyrimidine_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('editing_variant','editing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('antiparallel_beta_strand','antiparallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('central_hydrophobic_region_of_signal_peptide','central_hydrophobic_region_of_signal_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integrated_mobile_genetic_element','integrated_mobile_genetic_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('parallel_beta_strand','parallel_beta_strand'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_dj_cluster','v_dj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dre_motif','dre_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_ltr_retrotransposon','non_ltr_retrotransposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('r_gna_oligo','r_gna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autoregulated','autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_lysine','modified_l_lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_end','bac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrrolysine','pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_quality_draft','high_quality_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine','lysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide','elongated_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unique_variant','unique_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_protein_contact','protein_protein_contact'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_attribute','inversion_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_binding_site','nucleotide_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site','splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_synonymous_codon','non_synonymous_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5kb_downstream_variant','fivekb_downstream_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_translocation','chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('epitope','epitope'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allele','allele'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n4_n4_2_prime_o_trimethylcytidine','n4_n4_2_prime_o_trimethylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u5_ltr_region','u5_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paired_end_fragment','paired_end_fragment'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rescue_gene','rescue_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic_transposable_element','transgenic_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_conserved_region','polypeptide_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sts','sts'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_c_transversion','a_to_c_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_ii_rna','class_ii_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nonamer_of_recombination_feature_of_vertebrate_immune_system_gene','nonamer_of_recombination_feature_of_vertebrate_im_sys_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unedited_region','unedited_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lambda_vector','lambda_vector'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene','gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('alanyl_trna','alanyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('amino_acid_substitution','amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('virtual_sequence','virtual_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_iib_intron','group_iib_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('retrotransposed','retrotransposed'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_2_frameshift','mrna_with_minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymer_attribute','polymer_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('autosynaptic_chromosome','autosynaptic_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peptide_helix','peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_processed_cdna_clone','partially_processed_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst_match','rst_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternally_imprinted','paternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('predicted_gene','predicted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('x_element_combinatorial_repeat','x_element_combinatorial_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('robertsonian_fusion','robertsonian_fusion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylpseudouridine','two_prime_o_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric_inversion','pericentric_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartyl_trna','aspartyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('strna','strna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_intron','three_prime_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear','linear'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_nonamer','j_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_t_transversion','a_to_t_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('idna','idna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_n2_7_trimethylguanosine','n2_n2_7_trimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('complex_chromosomal_mutation','complex_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_deficiency_plus_aneuploid','inversion_derived_deficiency_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_methylation_site','h3k4_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asymmetric_rna_internal_loop','asymmetric_rna_internal_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deletion','deletion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_monomethylation_site','h3k79_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyclic_translocation','cyclic_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ars','ars'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutaminyl_trna','glutaminyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('allopolyploid','allopolyploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('replicon','replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methylcytidine','two_prime_o_methylcytidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere','regional_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_left_handed_type_one','st_turn_left_handed_type_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paralogous_region','paralogous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mature_transcript_region','mature_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_frameshift','mrna_with_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reference_genome','reference_genome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_interchromosomal_transposition','unoriented_interchromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_dj_j_cluster','d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maxicircle_gene','maxicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('st_turn_right_handed_type_two','st_turn_right_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snrna_encoding','snrna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('annotation_directed_improved_draft','annotation_directed_improved_draft'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_spacer','five_prime_d_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('read','read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('arginine_trna_primary_transcript','arg_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo_u_tail','oligo_u_tail'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoding_pseudoknot','recoding_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methylaminomethyl_two_thiouridine','five_mam_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic','monocistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('3d_polypeptide_structure_variant','threed_polypeptide_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transmembrane_polypeptide_region','transmembrane_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_processing_variant','transcript_processing_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vector_replicon','vector_replicon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternal_uniparental_disomy','maternal_uniparental_disomy'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pyrosequenced_read','pyrosequenced_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_site_variant','splice_site_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_magnesium_ion_contact_site','polypeptide_magnesium_ion_contact_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic_transcript','polycistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polya_site','polya_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosomal_variation_attribute','chromosomal_variation_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_duplication','free_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_structure_variation','chromosome_structure_variation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_rna_base_feature','modified_rna_base_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mutated_variant_site','mutated_variant_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gaga_motif','gaga_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromeric_repeat','centromeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_gene','rrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal_mutation','interchromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prophage','prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('syntenic','syntenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_repetitive_element','engineered_foreign_repetitive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translated_nucleotide_match','translated_nucleotide_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_variant','exon_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna','h_aca_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vault_rna','vault_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orphan','orphan'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('linear_single_stranded_dna_chromosome','linear_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomeric_repeat','telomeric_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_greater_than_1_polypeptide','encodes_greater_than_1_polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('atti_site','atti_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_start_codon_cug','gene_with_start_codon_cug'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_histone_deacetylation','silenced_by_histone_deacetylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reagent','reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_fission','chromosome_fission'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ct_gene','ct_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped_primary_transcript','capped_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylinosine','methylinosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_spacer','j_spacer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamine','glutamine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_guanosine','modified_guanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n2_7_dimethylguanosine','n2_7_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k79_trimethylation_site','h3k79_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_heptamer','three_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_cdna_clone','invalidated_cdna_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('terminator','terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stem_loop','stem_loop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_utr_intron','five_prime_utr_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unoriented_intrachromosomal_transposition','unoriented_intrachromosomal_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_band','chromosome_band'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mini_exon_donor_rna','mini_exon_donor_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid','aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methyl_2_thiouridine','five_methyl_2_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_dna_methylation','gene_silenced_by_dna_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_foreign_transposable_element_gene','engineered_foreign_transposable_element_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('processed_pseudogene','processed_pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('supercontig','supercontig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_encoding','trna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal_chromosomal_translocation','reciprocal_chromosomal_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tasirna','tasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hoogsteen_base_pair','hoogsteen_base_pair'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regional_centromere_inner_repeat_region','regional_centromere_inner_repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('yac_end','yac_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('purine_transition','purine_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_d_box_snorna','c_d_box_snorna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('snorna_primary_transcript','snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_vj_cluster','v_vj_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_regulatory_region','intronic_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u3_ltr_region','u3_ltr_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attenuator','attenuator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_noncoding_exon','three_prime_noncoding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u14_snorna_primary_transcript','u14_snorna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene_recombination_feature','d_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mte','mte'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gcvb_rna','gcvb_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rst','rst'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operator','operator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ring_chromosome','ring_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ndm2_motif','ndm2_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k4_dimethylation_site','h3k4_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteine_trna_primary_transcript','selenocysteine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('edited_transcript_feature','edited_transcript_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_redefined_as_pyrrolysine','stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('homo_compound_chromosome','homo_compound_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_gene','foreign_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('four_demethylwyosine','four_demethylwyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna','guide_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_methylpseudouridine','three_methylpseudouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_aneuploid_chromosome','inversion_derived_aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('decreased_transcript_stability_variant','decreased_transcript_stability_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lincrna_gene','lincrna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('specific_recombination_site','specific_recombination_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inosine','inosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('foreign_transposable_element','foreign_transposable_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_gene','d_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bipartite_inversion','bipartite_inversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_plasmid','engineered_plasmid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group_regulatory_region','gene_group_regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vd_gene','vd_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_region','regulatory_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sl11_acceptor_site','sl11_acceptor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('guide_rna_region','guide_rna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_base','modified_base'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_polypeptide_c_terminal','elongated_polypeptide_c_terminal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_ten_helix','three_ten_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('elongated_in_frame_polypeptide_n_terminal_elongation','elongated_in_frame_polypeptide_n_terminal_elongation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sarcin_like_rna_motif','sarcin_like_rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_translationally_frameshifted','minus_1_translationally_frameshifted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_alanine','modified_l_alanine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_cum_translocation','inversion_cum_translocation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tag','tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uninverted_interchromosomal_transposition','uninvert_inter_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_gene','cryptic_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pericentric','pericentric'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgenic','transgenic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_clone','genomic_clone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chromosome_breakage_sequence','chromosome_breakage_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_j_cluster','d_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a_one','beta_turn_type_six_a_one'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribosome_entry_site','ribosome_entry_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('left_handed_peptide_helix','left_handed_peptide_helix'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dna_aptamer','dna_aptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('i_motif','i_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('deficient_intrachromosomal_transposition','d_intrachr_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_stranded_dna_chromosome','single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('methylated_c','methylated_c'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('clone_end','clone_end'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ligation_based_read','ligation_based_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('expressed_sequence_assembly','expressed_sequence_assembly'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_two_prime_o_dimethyluridine','five_two_prime_o_dimethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine_trna_primary_transcript','histidine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orthologous_region','orthologous_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valine_trna_primary_transcript','valine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon_member','operon_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('missense_codon','missense_codon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma54','bacterial_rnapol_promoter_sigma54'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_group','gene_group'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('small_regulatory_ncrna','small_regulatory_ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intrachromosomal_duplication','intrachromosomal_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_conservative_amino_acid_substitution','non_conservative_amino_acid_substitution'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uaa_stop_codon_signal','uaa_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_methylation_site','h3k36_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_variant','transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_2_frameshift','minus_2_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('organelle_sequence','organelle_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('initiator_codon_change','initiator_codon_change'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cryptic_prophage','cryptic_prophage'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micf_rna','micf_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_tandem_duplication','direct_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conserved','conserved'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('telomerase_rna','telomerase_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u6atac_snrna','u6atac_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('attb_site','attb_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_array_member','gene_array_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated_mrna','polyadenylated_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('symbiosis_island','symbiosis_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_variant','polymorphic_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_junction','splice_junction'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('fingerprint_map','fingerprint_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('single_strand_restriction_enzyme_cleavage_site','single_strand_restriction_enzyme_cleavage_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('wyosine','wyosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uga_stop_codon_signal','uga_stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_24_signal','minus_24_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cytoplasmic_polypeptide_region','cytoplasmic_polypeptide_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h4k_acylation_region','h4k_acylation_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethylguanosine','one_two_prime_o_dimethylguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rh_map','rh_map'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silenced_by_dna_modification','silenced_by_dna_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inactive_catalytic_site','inactive_catalytic_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anticodon','anticodon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seven_deazaguanosine','seven_deazaguanosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine','asparagine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('probe','probe'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('defective_conjugative_transposon','defective_conjugative_transposon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('archaeosine','archaeosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('molecular_contact_region','molecular_contact_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nested_repeat','nested_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('membrane_structure','membrane_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig_collection','contig_collection'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tetraloop','tetraloop'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('coding_conserved_region','coding_conserved_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('long_terminal_repeat','long_terminal_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immune_system_gene_recombination_signal_feature','vertebrate_immune_system_gene_recombination_signal_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('untranslated_region_polycistronic_mrna','untranslated_region_polycistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucine_trna_primary_transcript','leucine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('high_identity_region','high_identity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular_single_stranded_dna_chromosome','circular_single_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_rim_localization_signal','nuclear_rim_localization_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isoleucyl_trna','isoleucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertion_breakpoint','insertion_breakpoint'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('5_prime_utr_variant','five_prime_utr_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transgene','transgene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_region','mrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_attribute','transcript_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine_threonine_staple_motif','serine_threonine_staple_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_coding','protein_coding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_bound_by_factor','enhancer_bound_by_factor'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('recoded_by_translational_bypass','recoded_by_translational_bypass'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('operon','operon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('monocistronic_transcript','monocistronic_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('reciprocal','reciprocal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polyadenylated','polyadenylated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('unigene_cluster','unigene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('vertebrate_immunoglobulin_t_cell_receptor_rearranged_gene_cluster','vertebrate_ig_t_cell_receptor_rearranged_gene_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_cassette_member','gene_cassette_member'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_read_through','stop_codon_read_through'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_transcript_with_translational_frameshift','gene_with_transcript_with_translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('variant_quality','variant_quality'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mnp','mnp'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('glutamic_acid','glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('y_prime_element','y_prime_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn','beta_turn'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pathogenic_island','pathogenic_island'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ust_match','ust_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_protein','transcript_bound_by_protein'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_methyladenosine','n6_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cyanelle_chromosome','cyanelle_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('orit','orit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted','maternally_imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('chloroplast_chromosome','chloroplast_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minicircle_gene','minicircle_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_catalytic_motif','polypeptide_catalytic_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnapol_iii_promoter_type_2','rnapol_iii_promoter_type_2'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('no_output','no_output'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_coding_exon','interior_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_taurinomethyl_two_thiouridine','five_taurinomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k9_trimethylation_site','h3k9_trimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_secondary_structure_variant','transcript_secondary_structure_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide','polypeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_5th_base_variant','splice_donor_5th_base_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymerase_synthesis_read','polymerase_synthesis_read'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_binding_site','enhancer_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleotide_to_protein_binding_site','nucleotide_to_protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_left_handed_type_two','beta_turn_left_handed_type_two'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_genomic_polya_primed_cdna','invalidated_by_genomic_polya_primed_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_edited_transcript','gene_with_edited_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dmv1_motif','dmv1_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_12_signal','minus_12_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_modified_region','post_translationally_modified_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proline','proline'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('flanking_region','flanking_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_isopentenyladenosine','two_methylthio_n6_isopentenyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypyrimidine_tract','polypyrimidine_tract'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxyuridine','five_methoxyuridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_to_gene_feature','gene_to_gene_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac_cloned_genomic_insert','bac_cloned_genomic_insert'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_heptamer','j_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_ust','three_prime_ust'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_2_prime_o_dimethyladenosine','n6_2_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_site','trans_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('de_novo_variant','de_novo_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_rescue_region','engineered_rescue_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleomorph_gene','nucleomorph_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_attribute','mrna_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_three_prime_overlap','five_prime_three_prime_overlap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('group_i_intron','group_i_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('d_cluster','d_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('open_chromatin_region','open_chromatin_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genomic_dna','genomic_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inside_intron','inside_intron'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hammerhead_ribozyme','hammerhead_ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_d_heptamer','five_prime_d_heptamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intronic_splice_enhancer','intronic_splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_adenosine','modified_adenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyluridine','five_carboxymethylaminomethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_region','repeat_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('repeat_unit','repeat_unit'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_dna_chromosome','double_stranded_dna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('heritable_phenotypic_marker','heritable_phenotypic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('template_region','template_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primary_transcript_region','primary_transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_dna','mitochondrial_dna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_region','transcript_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_acetylation_site','histone_acetylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ribozyme','ribozyme'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('matrix_attachment_site','matrix_attachment_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('imprinted','imprinted'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_sequence_variant','polypeptide_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('est','est'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_motif','rna_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_variation_site','polypeptide_variation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('class_i_rna','class_i_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('oligo','oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('stop_codon_signal','stop_codon_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('hypoploid','hypoploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exemplar_mrna','exemplar_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('experimentally_defined_binding_region','experimentally_defined_binding_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('c_to_g_transversion','c_to_g_transversion'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('active_peptide','active_peptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mannosyl_queuosine','mannosyl_queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_pyrrolysine','gene_with_stop_codon_redefined_as_pyrrolysine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('queuosine','queuosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lna_oligo','lna_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('independently_known','independently_known'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_region','proviral_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('capped','capped'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minus_1_frameshift_variant','minus_1_frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direction_attribute','direction_attribute'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('micronuclear_chromosome','micronuclear_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene_by_unequal_crossing_over','pseudogene_by_unequal_crossing_over'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('one_two_prime_o_dimethyladenosine','one_two_prime_o_dimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dpe_motif','dpe_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frame_restoring_variant','frame_restoring_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('seryl_trna','seryl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('structural_variant','structural_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('regulatory_promoter_element','regulatory_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('integration_excision_site','integration_excision_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('noncoding_region_of_exon','noncoding_region_of_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnase_mrp_rna','rnase_mrp_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_export_signal','nuclear_export_signal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_methoxycarbonylmethyluridine','five_methoxycarbonylmethyluridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon_of_single_exon_gene','exon_of_single_exon_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_dicistronic_primary_transcript','gene_with_dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sequence_secondary_structure','sequence_secondary_structure'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter_sigma_70','bacterial_rnapol_promoter_sigma_70'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tiling_path','tiling_path'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_sequence','nuclear_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('contig','contig'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('quality_value','quality_value'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('kozak_sequence','kozak_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('population_specific_variant','population_specific_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('catalytic_residue','catalytic_residue'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_site','inversion_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspartic_acid','aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dif_site','dif_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_gene','mirna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('valyl_trna','valyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_tandem_duplication','inverted_tandem_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cis_regulatory_frameshift_element','cis_regulatory_frameshift_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('minisatellite','minisatellite'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assembly_component','assembly_component'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('low_complexity_region','low_complexity_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('morpholino_backbone','morpholino_backbone'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('designed_sequence','designed_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('n6_n6_2_prime_o_trimethyladenosine','n6_n6_2_prime_o_trimethyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna_polymerase_promoter','rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_gene_recombination_feature','v_gene_recombination_feature'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_carboxymethylaminomethyl_two_thiouridine','five_carboxymethylaminomethyl_two_thiouridine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('free_ring_duplication','free_ring_duplication'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('point_centromere','point_centromere'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_mrna','dicistronic_mrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interchromosomal','interchromosomal'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('uncharacterised_chromosomal_mutation','uncharacterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_cis_splice_site','five_prime_cis_splice_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('octamer_motif','octamer_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('encodes_overlapping_peptides_different_start','encodes_overlapping_peptides_different_start'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_rna_viral_sequence','ss_rna_viral_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('indel','indel'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dicistronic_primary_transcript','dicistronic_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('protein_binding_site','protein_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polycistronic','polycistronic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('asparagine_trna_primary_transcript','asparagine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_enhancer','splice_enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aneuploid_chromosome','aneuploid_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('peroxywybutosine','peroxywybutosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_aspartic_acid','modified_l_aspartic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('engineered_episome','engineered_episome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rnai_reagent','rnai_reagent'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rasirna','rasirna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('tmrna_region','tmrna_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('increased_transcript_level_variant','increased_transcript_level_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_rnapol_promoter','bacterial_rnapol_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mitochondrial_sequence','mitochondrial_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trinucleotide_repeat_microsatellite_feature','trinuc_repeat_microsat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_stability','post_translationally_regulated_by_protein_stability'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nc_primary_transcript','nc_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('iron_responsive_element','iron_responsive_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('v_d_dj_j_cluster','v_d_dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('forward','forward'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('proviral_location','proviral_location'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_binding_site','histone_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('promoter_element','promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pse_motif','pse_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_eight','beta_turn_type_eight'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double','double'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_est_or_cdna_data','cds_supported_by_est_or_cdna_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('double_stranded_rna_chromosome','double_stranded_rna_chromosome'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('modified_l_glutamic_acid','modified_l_glutamic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polypeptide_nest_motif','polypeptide_nest_motif'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('translational_frameshift','translational_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_terminal_inverted_repeat','three_prime_terminal_inverted_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogenic_trna','pseudogenic_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cap','cap'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_coding_exon','five_prime_coding_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic','enzymatic'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('interior_exon','interior_exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('genetic_marker','genetic_marker'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('a_to_g_transition','a_to_g_transition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine','two_methylthio_n6_hydroxynorvalyl_carbamoyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('isre','isre'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('maternally_imprinted_gene','maternally_imprinted_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('circular','circular'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_pseudoknot','h_pseudoknot'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intermediate_element','intermediate_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript','transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('pseudogene','pseudogene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('direct_repeat','direct_repeat'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bacterial_terminator','bacterial_terminator'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('diplotype','diplotype'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('metal_binding_site','metal_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_gene','dj_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('two_prime_o_methyladenosine','two_prime_o_methyladenosine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_region_variant','splice_region_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('aspe_primer','aspe_primer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_binding_site','restriction_enzyme_binding_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('bac','bac'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('dj_j_cluster','dj_j_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_dimethylation_site','h3k36_dimethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trans_splice_donor_site','trans_splice_donor_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_variant','gene_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('conformational_change_variant','conformational_change_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h3k36_monomethylation_site','h3k36_monomethylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nucleic_acid','nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('invalidated_by_chimeric_cdna','invalidated_by_chimeric_cdna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histidine','histidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_component_region','gene_component_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('primer_match','primer_match'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('trna_primary_transcript','trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('loxp_site','loxp_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('serine','serine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('propeptide','propeptide'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('five_prime_open_reading_frame','five_prime_open_reading_frame'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('schellmann_loop_six','schellmann_loop_six'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('shine_dalgarno_sequence','shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sp6_rna_polymerase_promoter','sp6_rna_polymerase_promoter'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('centromere_dna_element_iii','centromere_dna_element_iii'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysine_trna_primary_transcript','lysine_trna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('j_c_cluster','j_c_cluster'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('assortment_derived_deficiency','assortment_derived_deficiency'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mirna_primary_transcript','mirna_primary_transcript'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_5s','rrna_5s'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('leucyl_trna','leucyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inverted_intrachromosomal_transposition','invert_intra_transposition'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enzymatic_rna','enzymatic_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('germline_variant','germline_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('negatively_autoregulated','negatively_autoregulated'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('benign_variant','benign_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('anchor_region','anchor_region'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('exon','exon'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_turn_type_six_a','beta_turn_type_six_a'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('random_sequence','random_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('partially_characterised_chromosomal_mutation','partially_characterised_chromosomal_mutation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rna','rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('core_promoter_element','core_promoter_element'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('restriction_enzyme_single_strand_overhang','restriction_enzyme_single_strand_overhang'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ss_oligo','ss_oligo'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('histone_methylation_site','histone_methylation_site'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('inversion_derived_duplication_plus_aneuploid','inversion_derived_duplication_plus_aneuploid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('transcript_bound_by_nucleic_acid','transcript_bound_by_nucleic_acid'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('intein_containing','intein_containing'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('h_aca_box_snorna_encoding','h_aca_box_snorna_encoding'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('rrna_cleavage_rna','rrna_cleavage_rna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer_trap_construct','enhancer_trap_construct'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gamma_turn_inverse','gamma_turn_inverse'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_d_nonamer','three_prime_d_nonamer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('paternal_variant','paternal_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('level_of_transcript_variant','level_of_transcript_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('selenocysteinyl_trna','selenocysteinyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_silenced_by_histone_methylation','gene_silenced_by_histone_methylation'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('u11_snrna','u11_snrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('scrna','scrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('gene_with_stop_codon_redefined_as_selenocysteine','gene_with_stop_codon_redefined_as_selenocysteine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('silencer','silencer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('sage_tag','sage_tag'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('mrna_with_minus_1_frameshift','mrna_with_minus_1_frameshift'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('nuclear_gene','nuclear_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('cds_supported_by_domain_match_data','cds_supported_by_domain_match_data'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('internal_shine_dalgarno_sequence','internal_shine_dalgarno_sequence'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('prolyl_trna','prolyl_trna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('lysidine','lysidine'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('beta_bulge','beta_bulge'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('post_translationally_regulated_by_protein_modification','post_translationally_regulated_by_protein_modification'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('splice_donor_variant','splice_donor_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('ncrna','ncrna'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('grna_gene','grna_gene'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('enhancer','enhancer'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('polymorphic_sequence_variant','polymorphic_sequence_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('three_prime_clip','three_prime_clip'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('frameshift_variant','frameshift_variant'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('insertional','insertional'); INSERT INTO sequence_cv_lookup_table (original_cvterm_name,relation_name) VALUES ('non_processed_pseudogene','non_processed_pseudogene'); CREATE INDEX sequence_cv_lookup_table_idx ON sequence_cv_lookup_table (original_cvterm_name); SET search_path=public,pg_catalog; chado-1.23/modules/sequence/bridges/sofa-bridge.sql000644 000765 000024 00000363421 11256710112 022401 0ustar00cainstaff000000 000000 CREATE SCHEMA sofa; --- ************************************************ --- *** relation: transcription_end_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site where transcription ends. *** --- ************************************************ --- CREATE VIEW transcription_end_site AS SELECT feature_id AS transcription_end_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_end_site'; --- ************************************************ --- *** relation: repeat_family *** --- *** relation type: VIEW *** --- *** *** --- *** A group of characterized repeat sequence *** --- *** s. *** --- ************************************************ --- CREATE VIEW repeat_family AS SELECT feature_id AS repeat_family_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_family'; --- ************************************************ --- *** relation: intron *** --- *** relation type: VIEW *** --- *** *** --- *** A segment of DNA that is transcribed, bu *** --- *** t removed from within the transcript by *** --- *** splicing together the sequences (exons) *** --- *** on either side of it. *** --- ************************************************ --- CREATE VIEW intron AS SELECT feature_id AS intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intron'; --- ************************************************ --- *** relation: tiling_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of regions which overlap with mini *** --- *** mal polymorphism to form a linear sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW tiling_path AS SELECT feature_id AS tiling_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path'; --- ************************************************ --- *** relation: tiling_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of sequence that makes up a tili *** --- *** ng_path.SO:0000472. *** --- ************************************************ --- CREATE VIEW tiling_path_fragment AS SELECT feature_id AS tiling_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tiling_path_fragment'; --- ************************************************ --- *** relation: located_sequence_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A biological feature that can be attribu *** --- *** ted to a region of biological sequence. *** --- ************************************************ --- CREATE VIEW located_sequence_feature AS SELECT feature_id AS located_sequence_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'located_sequence_feature'; --- ************************************************ --- *** relation: primer *** --- *** relation type: VIEW *** --- *** *** --- *** A short preexisting polynucleotide chain *** --- *** to which new deoxyribonucleotides can b *** --- *** e added by DNA polymerase. *** --- ************************************************ --- CREATE VIEW primer AS SELECT feature_id AS primer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primer'; --- ************************************************ --- *** relation: snp *** --- *** relation type: VIEW *** --- *** *** --- *** SNPs are single base pair positions in g *** --- *** enomic DNA at which different sequence a *** --- *** lternatives (alleles) exist in normal in *** --- *** dividuals in some population(s), wherein *** --- *** the least frequent allele has an abunda *** --- *** nce of 10r greater. *** --- ************************************************ --- CREATE VIEW snp AS SELECT feature_id AS snp_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SNP'; --- ************************************************ --- *** relation: integrated_virus *** --- *** relation type: VIEW *** --- *** *** --- *** A viral sequence which has integrated in *** --- *** to the host genome. *** --- ************************************************ --- CREATE VIEW integrated_virus AS SELECT feature_id AS integrated_virus_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'integrated_virus'; --- ************************************************ --- *** relation: methylated_c *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated deoxy-cytosine. *** --- ************************************************ --- CREATE VIEW methylated_c AS SELECT feature_id AS methylated_c_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_C'; --- ************************************************ --- *** relation: reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence used in experiment. *** --- ************************************************ --- CREATE VIEW reagent AS SELECT feature_id AS reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reagent'; --- ************************************************ --- *** relation: oligo *** --- *** relation type: VIEW *** --- *** *** --- *** A short oligonucleotide sequence, of len *** --- *** gth on the order of 10's of bases; eithe *** --- *** r single or double stranded. *** --- ************************************************ --- CREATE VIEW oligo AS SELECT feature_id AS oligo_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligo'; --- ************************************************ --- *** relation: junction *** --- *** relation type: VIEW *** --- *** *** --- *** A junction refers to an interbase locati *** --- *** on of zero in a sequence. *** --- ************************************************ --- CREATE VIEW junction AS SELECT feature_id AS junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'junction'; --- ************************************************ --- *** relation: u14_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U14 small nucleolar RNA (U14 snoRNA) is *** --- *** required for early cleavages of eukaryot *** --- *** ic precursor rRNAs. In yeasts, this mole *** --- *** cule possess a stem-loop region (known a *** --- *** s the Y-domain) which is essential for f *** --- *** unction. A similar structure, but with a *** --- *** different consensus sequence, is found *** --- *** in plants, but is absent in vertebrates. *** --- ************************************************ --- CREATE VIEW u14_snrna AS SELECT feature_id AS u14_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U14_snRNA'; --- ************************************************ --- *** relation: vault_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A family of RNAs are found as part of th *** --- *** e enigmatic vault ribonuceoprotein compl *** --- *** ex. The complex consists of a major vaul *** --- *** t protein (MVP), two minor vault protein *** --- *** s (VPARP and TEP1), and several small un *** --- *** translated RNA molecules. It has been su *** --- *** ggested that the vault complex is involv *** --- *** ed in drug resistance. *** --- ************************************************ --- CREATE VIEW vault_rna AS SELECT feature_id AS vault_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'vault_RNA'; --- ************************************************ --- *** relation: sts *** --- *** relation type: VIEW *** --- *** *** --- *** Short (typically a few hundred base pair *** --- *** s) DNA sequence that has a single occurr *** --- *** ence in a genome and whose location and *** --- *** base sequence are known. *** --- ************************************************ --- CREATE VIEW sts AS SELECT feature_id AS sts_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'STS'; --- ************************************************ --- *** relation: y_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Y RNAs are components of the Ro ribonucl *** --- *** eoprotein particle (Ro RNP), in associat *** --- *** ion with Ro60 and La proteins. The Y RNA *** --- *** s and Ro60 and La proteins are well cons *** --- *** erved, but the function of the Ro RNP is *** --- *** not known. In humans the RNA component *** --- *** can be one of four small RNAs: hY1, hY3, *** --- *** hY4 and hY5. These small RNAs are predi *** --- *** cted to fold into a conserved secondary *** --- *** structure containing three stem structur *** --- *** es. The largest of the four, hY1, contai *** --- *** ns an additional hairpin. *** --- ************************************************ --- CREATE VIEW y_rna AS SELECT feature_id AS y_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Y_RNA'; --- ************************************************ --- *** relation: exon_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The boundary between two exons in a proc *** --- *** essed transcript. *** --- ************************************************ --- CREATE VIEW exon_junction AS SELECT feature_id AS exon_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon_junction'; --- ************************************************ --- *** relation: rrna_18s *** --- *** relation type: VIEW *** --- *** *** --- *** 18S_rRNA -A large polynucleotide which f *** --- *** unctions as a part of the small subunit *** --- *** of the ribosome *** --- ************************************************ --- CREATE VIEW rrna_18s AS SELECT feature_id AS rrna_18s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_18S'; --- ************************************************ --- *** relation: binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region on the surface of a molecule th *** --- *** at may interact with another molecule. *** --- ************************************************ --- CREATE VIEW binding_site AS SELECT feature_id AS binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'binding_site'; --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that closely resembles a know *** --- *** n functional gene, at another locus with *** --- *** in a genome, that is non-functional as a *** --- *** consequence of (usually several) mutati *** --- *** ons that prevent either its transcriptio *** --- *** n or translation (or both). In general, *** --- *** pseudogenes result from either reverse t *** --- *** ranscription of a transcript of their "n *** --- *** ormal" paralog (SO:0000043) (in which ca *** --- *** se the pseudogene typically lacks intron *** --- *** s and includes a poly(A) tail) or from r *** --- *** ecombination (SO:0000044) (in which case *** --- *** the pseudogene is typically a tandem du *** --- *** plication of its "normal" paralog). *** --- ************************************************ --- CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: rnai_reagent *** --- *** relation type: VIEW *** --- *** *** --- *** A double stranded RNA duplex, at least 2 *** --- *** 0bp long, used experimentally to inhibit *** --- *** gene function by RNA interference. *** --- ************************************************ --- CREATE VIEW rnai_reagent AS SELECT feature_id AS rnai_reagent_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNAi_reagent'; --- ************************************************ --- *** relation: rflp_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** A polymorphism detectable by the size di *** --- *** fferences in DNA fragments generated by *** --- *** a restriction enzyme. *** --- ************************************************ --- CREATE VIEW rflp_fragment AS SELECT feature_id AS rflp_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RFLP_fragment'; --- ************************************************ --- *** relation: telomere *** --- *** relation type: VIEW *** --- *** *** --- *** A specific structure at the end of a lin *** --- *** ear chromosome, required for the integri *** --- *** ty and maintenence of the end, *** --- ************************************************ --- CREATE VIEW telomere AS SELECT feature_id AS telomere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomere'; --- ************************************************ --- *** relation: polya_signal_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** The recognition sequence necessary for e *** --- *** ndonuclease cleavage of an RNA transcrip *** --- *** t that is followed by polyadenylation; c *** --- *** onsensus=AATAAA. *** --- ************************************************ --- CREATE VIEW polya_signal_sequence AS SELECT feature_id AS polya_signal_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_signal_sequence'; --- ************************************************ --- *** relation: silencer *** --- *** relation type: VIEW *** --- *** *** --- *** Combination of short DNA sequence elemen *** --- *** ts which suppress the transcription of a *** --- *** n adjacent gene or genes. *** --- ************************************************ --- CREATE VIEW silencer AS SELECT feature_id AS silencer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'silencer'; --- ************************************************ --- *** relation: gene_group *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of related genes. *** --- ************************************************ --- CREATE VIEW gene_group AS SELECT feature_id AS gene_group_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_group'; --- ************************************************ --- *** relation: polya_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site on an RNA transcript to which w *** --- *** ill be added adenine residues by post-tr *** --- *** anscriptional polyadenylation. *** --- ************************************************ --- CREATE VIEW polya_site AS SELECT feature_id AS polya_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_site'; --- ************************************************ --- *** relation: insulator *** --- *** relation type: VIEW *** --- *** *** --- *** Nucleic acid regulatory sequences that l *** --- *** imit or oppose the action of ENHANCER EL *** --- *** EMENTS and define the boundary between d *** --- *** ifferentially regulated gene loci. *** --- ************************************************ --- CREATE VIEW insulator AS SELECT feature_id AS insulator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insulator'; --- ************************************************ --- *** relation: chromosomal_structural_element *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a chromosome that has structur *** --- *** al function. *** --- ************************************************ --- CREATE VIEW chromosomal_structural_element AS SELECT feature_id AS chromosomal_structural_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosomal_structural_element'; --- ************************************************ --- *** relation: nc_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that is never trans *** --- *** lated into a protein. *** --- ************************************************ --- CREATE VIEW nc_primary_transcript AS SELECT feature_id AS nc_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nc_primary_transcript'; --- ************************************************ --- *** relation: p_coding_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A primary transcript that, at least in p *** --- *** art, encodes one or more proteins. *** --- ************************************************ --- CREATE VIEW p_coding_primary_transcript AS SELECT feature_id AS p_coding_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_coding_primary_transcript'; --- ************************************************ --- *** relation: substitution *** --- *** relation type: VIEW *** --- *** *** --- *** Any change in genomic DNA caused by a si *** --- *** ngle event. *** --- ************************************************ --- CREATE VIEW substitution AS SELECT feature_id AS substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'substitution'; --- ************************************************ --- *** relation: complex_substitution *** --- *** relation type: VIEW *** --- *** *** --- *** When no simple or well defined DNA mutat *** --- *** ion event describes the observed DNA cha *** --- *** nge, the keyword "complex" should be use *** --- *** d. Usually there are multiple equally pl *** --- *** ausible explanations for the change. *** --- ************************************************ --- CREATE VIEW complex_substitution AS SELECT feature_id AS complex_substitution_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'complex_substitution'; --- ************************************************ --- *** relation: point_mutation *** --- *** relation type: VIEW *** --- *** *** --- *** A mutation event where a single DNA nucl *** --- *** eotide changes into another nucleotide. *** --- ************************************************ --- CREATE VIEW point_mutation AS SELECT feature_id AS point_mutation_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'point_mutation'; --- ************************************************ --- *** relation: restriction_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** Any of the individual polynucleotide seq *** --- *** uences produced by digestion of DNA with *** --- *** a restriction endonuclease. *** --- ************************************************ --- CREATE VIEW restriction_fragment AS SELECT feature_id AS restriction_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'restriction_fragment'; --- ************************************************ --- *** relation: sequence_difference *** --- *** relation type: VIEW *** --- *** *** --- *** A region where the sequences differs fro *** --- *** m that of a specified sequence. *** --- ************************************************ --- CREATE VIEW sequence_difference AS SELECT feature_id AS sequence_difference_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_difference'; --- ************************************************ --- *** relation: chromosome *** --- *** relation type: VIEW *** --- *** *** --- *** Structural unit composed of long DNA mol *** --- *** ecule. *** --- ************************************************ --- CREATE VIEW chromosome AS SELECT feature_id AS chromosome_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome'; --- ************************************************ --- *** relation: operator *** --- *** relation type: VIEW *** --- *** *** --- *** A regulatory element of an operon to whi *** --- *** ch activators or repressors bind hereby *** --- *** effecting translation of genes in that o *** --- *** peron. *** --- ************************************************ --- CREATE VIEW operator AS SELECT feature_id AS operator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operator'; --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence, aligned to another *** --- *** sequence with some statistical signific *** --- *** ance, using an algorithm such as BLAST o *** --- *** r SIM4. *** --- ************************************************ --- CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match'; --- ************************************************ --- *** relation: remark *** --- *** relation type: VIEW *** --- *** *** --- *** A comment about the sequence. *** --- ************************************************ --- CREATE VIEW remark AS SELECT feature_id AS remark_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'remark'; --- ************************************************ --- *** relation: splice_enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** Region of a transcript that regulates sp *** --- *** licing. *** --- ************************************************ --- CREATE VIEW splice_enhancer AS SELECT feature_id AS splice_enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_enhancer'; --- ************************************************ --- *** relation: possible_base_call_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where the validity *** --- *** of the base calling is questionable. *** --- ************************************************ --- CREATE VIEW possible_base_call_error AS SELECT feature_id AS possible_base_call_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_base_call_error'; --- ************************************************ --- *** relation: signal_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence for an N-terminal domain of *** --- *** a secreted protein; this domain is invo *** --- *** lved in attaching nascent polypeptide to *** --- *** the membrane leader sequence. *** --- ************************************************ --- CREATE VIEW signal_peptide AS SELECT feature_id AS signal_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'signal_peptide'; --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** Expressed Sequence Tag: The sequence of *** --- *** a single sequencing read from a cDNA clo *** --- *** ne or PCR product; typically a few hundr *** --- *** ed base pairs long. *** --- ************************************************ --- CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST'; --- ************************************************ --- *** relation: possible_assembly_error *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where there may hav *** --- *** e been an error in the assembly. *** --- ************************************************ --- CREATE VIEW possible_assembly_error AS SELECT feature_id AS possible_assembly_error_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'possible_assembly_error'; --- ************************************************ --- *** relation: mature_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The coding sequence for the mature or fi *** --- *** nal peptide or protein product following *** --- *** post-translational modification. *** --- ************************************************ --- CREATE VIEW mature_peptide AS SELECT feature_id AS mature_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mature_peptide'; --- ************************************************ --- *** relation: experimental_result_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence implicated in an ex *** --- *** perimental result. *** --- ************************************************ --- CREATE VIEW experimental_result_region AS SELECT feature_id AS experimental_result_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'experimental_result_region'; --- ************************************************ --- *** relation: nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a nucleotide sequence. *** --- ************************************************ --- CREATE VIEW nucleotide_match AS SELECT feature_id AS nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_match'; --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** Small non-coding RNA in the nucleoplasm. *** --- *** A small nuclear RNA molecule involved i *** --- *** n pre-mRNA splicing and processing *** --- ************************************************ --- CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** A locatable region of genomic sequence, *** --- *** corresponding to a unit of inheritance, *** --- *** which is associated with regulatory regi *** --- *** ons, transcribed regions and/or other fu *** --- *** nctional sequence regions *** --- ************************************************ --- CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene'; --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Small nucleolar RNAs (snoRNAs) are invol *** --- *** ved in the processing and modification o *** --- *** f rRNA in the nucleolus. There are two m *** --- *** ain classes of snoRNAs: the box C/D clas *** --- *** s, and the box H/ACA class. U3 snoRNA is *** --- *** a member of the box C/D class. Indeed, *** --- *** the box C/D element is a subset of the s *** --- *** ix short sequence elements found in all *** --- *** U3 snoRNAs, namely boxes A, A', B, C, C' *** --- *** , and D. The U3 snoRNA secondary structu *** --- *** re is characterised by a small 5' domain *** --- *** (with boxes A and A'), and a larger 3' *** --- *** domain (with boxes B, C, C', and D), the *** --- *** two domains being linked by a single-st *** --- *** randed hinge. Boxes B and C form the B/C *** --- *** motif, which appears to be exclusive to *** --- *** U3 snoRNAs, and boxes C' and D form the *** --- *** C'/D motif. The latter is functionally *** --- *** similar to the C/D motifs found in other *** --- *** snoRNAs. The 5' domain and the hinge re *** --- *** gion act as a pre-rRNA-binding domain. T *** --- *** he 3' domain has conserved protein-bindi *** --- *** ng sites. Both the box B/C and box C'/D *** --- *** motifs are sufficient for nuclear retent *** --- *** ion of U3 snoRNA. The box C'/D motif is *** --- *** also necessary for nucleolar localizatio *** --- *** n, stability and hypermethylation of U3 *** --- *** snoRNA. Both box B/C and C'/D motifs are *** --- *** involved in specific protein interactio *** --- *** ns and are necessary for the rRNA proces *** --- *** sing functions of U3 snoRNA. *** --- ************************************************ --- CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: tandem_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** Two or more adjacent copies of a DNA seq *** --- *** uence. *** --- ************************************************ --- CREATE VIEW tandem_repeat AS SELECT feature_id AS tandem_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tandem_repeat'; --- ************************************************ --- *** relation: p_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a protein sequence. *** --- ************************************************ --- CREATE VIEW p_match AS SELECT feature_id AS p_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein_match'; --- ************************************************ --- *** relation: mirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small, ~22-nt, RNA molecule that is the *** --- *** endogenous transcript of a miRNA gene. m *** --- *** iRNAs are produced from precursor molecu *** --- *** les (SO:0000647) that can form local hai *** --- *** rpin strcutures, which ordinarily are pr *** --- *** ocessed (via the Dicer pathway) such tha *** --- *** t a single miRNA molecule accumulates fr *** --- *** om one arm of a hairpinprecursor molecul *** --- *** e. miRNAs may trigger the cleavage of th *** --- *** eir target molecules oract as translatio *** --- *** nal repressors. *** --- ************************************************ --- CREATE VIEW mirna AS SELECT feature_id AS mirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'miRNA'; --- ************************************************ --- *** relation: trans_splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The process that produces mature transcr *** --- *** ipts by combining exons of independent p *** --- *** re-mRNA molecules. The acceptor site lie *** --- *** s on the 3' of these molecules. *** --- ************************************************ --- CREATE VIEW trans_splice_acceptor_site AS SELECT feature_id AS trans_splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'trans_splice_acceptor_site'; --- ************************************************ --- *** relation: virtual_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** A continous piece of sequence similar to *** --- *** the 'virtual contig' concept of ensembl *** --- *** . *** --- ************************************************ --- CREATE VIEW virtual_sequence AS SELECT feature_id AS virtual_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'virtual_sequence'; --- ************************************************ --- *** relation: utr *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA sequences that are untrans *** --- *** lated and lie five prime and three prime *** --- *** to sequences which are translated. *** --- ************************************************ --- CREATE VIEW utr AS SELECT feature_id AS utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'UTR'; --- ************************************************ --- *** relation: five_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 5' end of a mature trans *** --- *** cript (preceding the initiation codon) t *** --- *** hat is not translated into a protein. *** --- ************************************************ --- CREATE VIEW five_prime_utr AS SELECT feature_id AS five_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'five_prime_UTR'; --- ************************************************ --- *** relation: three_prime_utr *** --- *** relation type: VIEW *** --- *** *** --- *** A region at the 3' end of a mature trans *** --- *** cript (following the stop codon) that is *** --- *** not translated into a protein. *** --- ************************************************ --- CREATE VIEW three_prime_utr AS SELECT feature_id AS three_prime_utr_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'three_prime_UTR'; --- ************************************************ --- *** relation: ribosome_entry_site *** --- *** relation type: VIEW *** --- *** *** --- *** Region in mRNA where ribosome assembles. *** --- ************************************************ --- CREATE VIEW ribosome_entry_site AS SELECT feature_id AS ribosome_entry_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribosome_entry_site'; --- ************************************************ --- *** relation: assembly *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of nucleotides that has been *** --- *** algorithmically derived from an alignmen *** --- *** t of two or more different sequences. *** --- ************************************************ --- CREATE VIEW assembly AS SELECT feature_id AS assembly_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assembly'; --- ************************************************ --- *** relation: nucleotide_motif *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence correspo *** --- *** nding to a known motif. *** --- ************************************************ --- CREATE VIEW nucleotide_motif AS SELECT feature_id AS nucleotide_motif_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nucleotide_motif'; --- ************************************************ --- *** relation: minisatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A repetitive sequence spanning 500 to 20 *** --- *** ,000 base pairs (a repeat unit is 5 - 30 *** --- *** base pairs). *** --- ************************************************ --- CREATE VIEW minisatellite AS SELECT feature_id AS minisatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'minisatellite'; --- ************************************************ --- *** relation: reading_frame *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleic acid sequence that when read a *** --- *** s sequential triplets, has the potential *** --- *** of encoding a sequential string of amin *** --- *** o acids. It does not contain the start o *** --- *** r stop codon. *** --- ************************************************ --- CREATE VIEW reading_frame AS SELECT feature_id AS reading_frame_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'reading_frame'; --- ************************************************ --- *** relation: antisense_rna *** --- *** relation type: VIEW *** --- *** *** --- *** Antisense RNA is RNA that is transcribed *** --- *** from the coding, rather than the templa *** --- *** te, strand of DNA. It is therefore compl *** --- *** ementary to mRNA. *** --- ************************************************ --- CREATE VIEW antisense_rna AS SELECT feature_id AS antisense_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_RNA'; --- ************************************************ --- *** relation: antisense_primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The reverse complement of the primary tr *** --- *** anscript. *** --- ************************************************ --- CREATE VIEW antisense_primary_transcript AS SELECT feature_id AS antisense_primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'antisense_primary_transcript'; --- ************************************************ --- *** relation: microsatellite *** --- *** relation type: VIEW *** --- *** *** --- *** A very short unit sequence of DNA (2 to *** --- *** 4 bp) that is repeated multiple times in *** --- *** tandem. *** --- ************************************************ --- CREATE VIEW microsatellite AS SELECT feature_id AS microsatellite_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'microsatellite'; --- ************************************************ --- *** relation: ultracontig *** --- *** relation type: VIEW *** --- *** *** --- *** An ordered and oriented set of scaffolds *** --- *** based on somewhat weaker sets of infere *** --- *** ntial evidence such as one set of mate p *** --- *** air reads together with supporting evide *** --- *** nce from ESTs or location of markers fro *** --- *** m SNP or microsatellite maps, or cytogen *** --- *** etic localization of contained markers. *** --- ************************************************ --- CREATE VIEW ultracontig AS SELECT feature_id AS ultracontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ultracontig'; --- ************************************************ --- *** relation: sirna *** --- *** relation type: VIEW *** --- *** *** --- *** Small RNA molecule that is the product o *** --- *** f a longerexogenous or endogenous dsRNA, *** --- *** which is either a bimolecular duplexe o *** --- *** r very longhairpin, processed (via the D *** --- *** icer pathway) such that numerous siRNAs *** --- *** accumulatefrom both strands of the dsRNA *** --- *** . sRNAs trigger the cleavage of their ta *** --- *** rget molecules. *** --- ************************************************ --- CREATE VIEW sirna AS SELECT feature_id AS sirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'siRNA'; --- ************************************************ --- *** relation: strna *** --- *** relation type: VIEW *** --- *** *** --- *** Non-coding RNAs of about 21 nucleotides *** --- *** in length that regulate temporal develop *** --- *** ment; first discovered in C. elegans. *** --- ************************************************ --- CREATE VIEW strna AS SELECT feature_id AS strna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'stRNA'; --- ************************************************ --- *** relation: centromere *** --- *** relation type: VIEW *** --- *** *** --- *** A region of chromosome where the spindle *** --- *** fibers attach during mitosis and meiosi *** --- *** s. *** --- ************************************************ --- CREATE VIEW centromere AS SELECT feature_id AS centromere_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'centromere'; --- ************************************************ --- *** relation: attenuator *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence segment located between the p *** --- *** romoter and a structural gene that cause *** --- *** s partial termination of transcription. *** --- ************************************************ --- CREATE VIEW attenuator AS SELECT feature_id AS attenuator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'attenuator'; --- ************************************************ --- *** relation: terminator *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence of DNA located either at th *** --- *** e end of the transcript that causes RNA *** --- *** polymerase to terminate transcription. *** --- ************************************************ --- CREATE VIEW terminator AS SELECT feature_id AS terminator_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'terminator'; --- ************************************************ --- *** relation: assembly_component *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence which may be used t *** --- *** o manufacture a longer assembled, sequen *** --- *** ce. *** --- ************************************************ --- CREATE VIEW assembly_component AS SELECT feature_id AS assembly_component_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'assembly_component'; --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the genome that codes for po *** --- *** rtion of spliced messenger RNA (SO:00002 *** --- *** 34); may contain 5'-untranslated region *** --- *** (SO:0000204), all open reading frames (S *** --- *** O:0000236) and 3'-untranslated region (S *** --- *** O:0000205). *** --- ************************************************ --- CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon'; --- ************************************************ --- *** relation: supercontig *** --- *** relation type: VIEW *** --- *** *** --- *** One or more contigs that have been order *** --- *** ed and oriented using end-read informati *** --- *** on. Contains gaps that are filled with N *** --- *** 's. *** --- ************************************************ --- CREATE VIEW supercontig AS SELECT feature_id AS supercontig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'supercontig'; --- ************************************************ --- *** relation: contig *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence derived from seque *** --- *** nce assembly. Has no gaps, but may conta *** --- *** in N's from unvailable bases. *** --- ************************************************ --- CREATE VIEW contig AS SELECT feature_id AS contig_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'contig'; --- ************************************************ --- *** relation: codon *** --- *** relation type: VIEW *** --- *** *** --- *** A set of (usually) three nucleotide base *** --- *** s in a DNA or RNA sequence, which togeth *** --- *** er signify a unique amino acid or the te *** --- *** rmination of translation. *** --- ************************************************ --- CREATE VIEW codon AS SELECT feature_id AS codon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'codon'; --- ************************************************ --- *** relation: pseudogenic_exon *** --- *** relation type: VIEW *** --- *** *** --- *** The exon of a pseudogene. *** --- ************************************************ --- CREATE VIEW pseudogenic_exon AS SELECT feature_id AS pseudogenic_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_exon'; --- ************************************************ --- *** relation: ars *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence that can autonomously replica *** --- *** te, as a plasmid, when transformed into *** --- *** a bacterial host. *** --- ************************************************ --- CREATE VIEW ars AS SELECT feature_id AS ars_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ARS'; --- ************************************************ --- *** relation: insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction where an insertion occurred *** --- *** . *** --- ************************************************ --- CREATE VIEW insertion_site AS SELECT feature_id AS insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion_site'; --- ************************************************ --- *** relation: inverted_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence is complementarily repeated *** --- *** on the opposite strand. Example: GCTGA- *** --- *** ----TCAGC. *** --- ************************************************ --- CREATE VIEW inverted_repeat AS SELECT feature_id AS inverted_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inverted_repeat'; --- ************************************************ --- *** relation: origin_of_transfer *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a DNA molecule whre transfer *** --- *** is initiated during the process of conj *** --- *** ugation or mobilization. *** --- ************************************************ --- CREATE VIEW origin_of_transfer AS SELECT feature_id AS origin_of_transfer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'origin_of_transfer'; --- ************************************************ --- *** relation: t_element_insertion_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction in a genome where a transpo *** --- *** sable_element has inserted. *** --- ************************************************ --- CREATE VIEW t_element_insertion_site AS SELECT feature_id AS t_element_insertion_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: transit_peptide *** --- *** relation type: VIEW *** --- *** *** --- *** The coding sequence for an N-terminal do *** --- *** main of a nuclear-encoded organellar pro *** --- *** tein: this domain is involved in post tr *** --- *** anslational import of the protein into t *** --- *** he organelle. *** --- ************************************************ --- CREATE VIEW transit_peptide AS SELECT feature_id AS transit_peptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transit_peptide'; --- ************************************************ --- *** relation: rrna_5s *** --- *** relation type: VIEW *** --- *** *** --- *** 5S ribosomal RNA (5S rRNA) is a componen *** --- *** t of the large ribosomal subunit in both *** --- *** prokaryotes and eukaryotes. In eukaryot *** --- *** es, it is synthesised by RNA polymerase *** --- *** III (the other eukaryotic rRNAs are clea *** --- *** ved from a 45S precursor synthesised by *** --- *** RNA polymerase I). In Xenopus oocytes, i *** --- *** t has been shown that fingers 4-7 of the *** --- *** nine-zinc finger transcription factor T *** --- *** FIIIA can bind to the central region of *** --- *** 5S RNA. Thus, in addition to positively *** --- *** regulating 5S rRNA transcription, TFIIIA *** --- *** also stabilises 5S rRNA until it is req *** --- *** uired for transcription. *** --- ************************************************ --- CREATE VIEW rrna_5s AS SELECT feature_id AS rrna_5s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5S'; --- ************************************************ --- *** relation: origin_of_replication *** --- *** relation type: VIEW *** --- *** *** --- *** The origin of replication; starting site *** --- *** for duplication of a nucleic acid molec *** --- *** ule to give two identical copies. *** --- ************************************************ --- CREATE VIEW origin_of_replication AS SELECT feature_id AS origin_of_replication_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'origin_of_replication'; --- ************************************************ --- *** relation: rrna_28s *** --- *** relation type: VIEW *** --- *** *** --- *** A component of the large ribosomal subun *** --- *** it. *** --- ************************************************ --- CREATE VIEW rrna_28s AS SELECT feature_id AS rrna_28s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_28S'; --- ************************************************ --- *** relation: sequence_ontology *** --- *** relation type: VIEW *** --- *** *** --- ************************************************ --- CREATE VIEW sequence_ontology AS SELECT feature_id AS sequence_ontology_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'Sequence_Ontology'; --- ************************************************ --- *** relation: cap *** --- *** relation type: VIEW *** --- *** *** --- *** A structure consisting of a 7-methylguan *** --- *** osine in 5'-5' triphosphate linkage with *** --- *** the first nucleotide of an mRNA. It is *** --- *** added post-transcriptionally, and is not *** --- *** encoded in the DNA. *** --- ************************************************ --- CREATE VIEW cap AS SELECT feature_id AS cap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cap'; --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** An mRNA sequence that does not encode fo *** --- *** r a protein rather the RNA molecule is t *** --- *** he gene product. *** --- ************************************************ --- CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: region *** --- *** relation type: VIEW *** --- *** *** --- *** Continuous sequence. *** --- ************************************************ --- CREATE VIEW region AS SELECT feature_id AS region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'region'; --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence containing one or m *** --- *** ore repeat units. *** --- ************************************************ --- CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: dispersed_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat that is located at dispersed si *** --- *** tes in the genome. *** --- ************************************************ --- CREATE VIEW dispersed_repeat AS SELECT feature_id AS dispersed_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'dispersed_repeat'; --- ************************************************ --- *** relation: pcr_product *** --- *** relation type: VIEW *** --- *** *** --- *** A region amplified by a PCR reaction. *** --- ************************************************ --- CREATE VIEW pcr_product AS SELECT feature_id AS pcr_product_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'PCR_product'; --- ************************************************ --- *** relation: read_pair *** --- *** relation type: VIEW *** --- *** *** --- *** A pair of sequencing reads in which the *** --- *** two members of the pair are related by o *** --- *** riginating at either end of a clone inse *** --- *** rt. *** --- ************************************************ --- CREATE VIEW read_pair AS SELECT feature_id AS read_pair_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read_pair'; --- ************************************************ --- *** relation: group_i_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group I catalytic introns are large self *** --- *** -splicing ribozymes. They catalyse their *** --- *** own excision from mRNA, tRNA and rRNA p *** --- *** recursors in a wide range of organisms. *** --- *** The core secondary structure consists of *** --- *** 9 paired regions (P1-P9). These fold to *** --- *** essentially two domains, the P4-P6 doma *** --- *** in (formed from the stacking of P5, P4, *** --- *** P6 and P6a helices) and the P3-P9 domain *** --- *** (formed from the P8, P3, P7 and P9 heli *** --- *** ces). Group I catalytic introns often ha *** --- *** ve long ORFs inserted in loop regions. *** --- ************************************************ --- CREATE VIEW group_i_intron AS SELECT feature_id AS group_i_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_I_intron'; --- ************************************************ --- *** relation: a_spliced_intron *** --- *** relation type: VIEW *** --- *** *** --- *** A self spliced intron. *** --- ************************************************ --- CREATE VIEW a_spliced_intron AS SELECT feature_id AS a_spliced_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'autocatalytically_spliced_intron'; --- ************************************************ --- *** relation: read *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence obtained from a single sequen *** --- *** cing experiment. Typically a read is pro *** --- *** duced when a base calling program interp *** --- *** rets information from a chromatogram tra *** --- *** ce file produced from a sequencing machi *** --- *** ne. *** --- ************************************************ --- CREATE VIEW read AS SELECT feature_id AS read_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'read'; --- ************************************************ --- *** relation: clone *** --- *** relation type: VIEW *** --- *** *** --- *** A piece of DNA that has been inserted in *** --- *** a vector so that it can be propagated i *** --- *** n E. coli or some other organism. *** --- ************************************************ --- CREATE VIEW clone AS SELECT feature_id AS clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone'; --- ************************************************ --- *** relation: inversion *** --- *** relation type: VIEW *** --- *** *** --- *** A continuous nucleotide sequence is inve *** --- *** rted in the same position. *** --- ************************************************ --- CREATE VIEW inversion AS SELECT feature_id AS inversion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'inversion'; --- ************************************************ --- *** relation: deletion *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence that is deleted. *** --- ************************************************ --- CREATE VIEW deletion AS SELECT feature_id AS deletion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion'; --- ************************************************ --- *** relation: small_regulatory_ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW small_regulatory_ncrna AS SELECT feature_id AS small_regulatory_ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'small_regulatory_ncRNA'; --- ************************************************ --- *** relation: pseudogenic_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript of a pseudogene *** --- ************************************************ --- CREATE VIEW pseudogenic_transcript AS SELECT feature_id AS pseudogenic_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_transcript'; --- ************************************************ --- *** relation: enzymatic_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A non-coding RNA, usually with a specifi *** --- *** c secondary structure, that acts to regu *** --- *** late gene expression. *** --- ************************************************ --- CREATE VIEW enzymatic_rna AS SELECT feature_id AS enzymatic_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enzymatic_RNA'; --- ************************************************ --- *** relation: databank_entry *** --- *** relation type: VIEW *** --- *** *** --- *** The sequence referred to by an entry in *** --- *** a databank such as Genbank or SwissProt. *** --- ************************************************ --- CREATE VIEW databank_entry AS SELECT feature_id AS databank_entry_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'databank_entry'; --- ************************************************ --- *** relation: gap *** --- *** relation type: VIEW *** --- *** *** --- *** A gap in the sequence of known length. T *** --- *** He unkown bases are filled in with N's. *** --- ************************************************ --- CREATE VIEW gap AS SELECT feature_id AS gap_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gap'; --- ************************************************ --- *** relation: ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA with catalytic activity. *** --- ************************************************ --- CREATE VIEW ribozyme AS SELECT feature_id AS ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ribozyme'; --- ************************************************ --- *** relation: rrna_5_8s *** --- *** relation type: VIEW *** --- *** *** --- *** 5.8S ribosomal RNA (5.8S rRNA) is a comp *** --- *** onent of the large subunit of the eukary *** --- *** otic ribosome. It is transcribed by RNA *** --- *** polymerase I as part of the 45S precurso *** --- *** r that also contains 18S and 28S rRNA. F *** --- *** unctionally, it is thought that 5.8S rRN *** --- *** A may be involved in ribosome translocat *** --- *** ion. It is also known to form covalent l *** --- *** inkage to the p53 tumour suppressor prot *** --- *** ein. 5.8S rRNA is also found in archaea. *** --- ************************************************ --- CREATE VIEW rrna_5_8s AS SELECT feature_id AS rrna_5_8s_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA_5.8S'; --- ************************************************ --- *** relation: spliceosomal_intron *** --- *** relation type: VIEW *** --- *** *** --- *** An intron which is spliced by the splice *** --- *** osome. *** --- ************************************************ --- CREATE VIEW spliceosomal_intron AS SELECT feature_id AS spliceosomal_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'spliceosomal_intron'; --- ************************************************ --- *** relation: srp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The signal recognition particle (SRP) is *** --- *** a universally conserved ribonucleoprote *** --- *** in. It is involved in the co-translation *** --- *** al targeting of proteins to membranes. T *** --- *** he eukaryotic SRP consists of a 300-nucl *** --- *** eotide 7S RNA and six proteins: SRPs 72, *** --- *** 68, 54, 19, 14, and 9. Archaeal SRP con *** --- *** sists of a 7S RNA and homologues of the *** --- *** eukaryotic SRP19 and SRP54 proteins. In *** --- *** most eubacteria, the SRP consists of a 4 *** --- *** .5S RNA and the Ffh protein (a homologue *** --- *** of the eukaryotic SRP54 protein). Eukar *** --- *** yotic and archaeal 7S RNAs have very sim *** --- *** ilar secondary structures, with eight he *** --- *** lical elements. These fold into the Alu *** --- *** and S domains, separated by a long linke *** --- *** r region. Eubacterial SRP is generally a *** --- *** simpler structure, with the M domain of *** --- *** Ffh bound to a region of the 4.5S RNA t *** --- *** hat corresponds to helix 8 of the eukary *** --- *** otic and archaeal SRP S domain. Some Gra *** --- *** m-positive bacteria (e.g. Bacillus subti *** --- *** lis), however, have a larger SRP RNA tha *** --- *** t also has an Alu domain. The Alu domain *** --- *** is thought to mediate the peptide chain *** --- *** elongation retardation function of the *** --- *** SRP. The universally conserved helix whi *** --- *** ch interacts with the SRP54/Ffh M domain *** --- *** mediates signal sequence recognition. I *** --- *** n eukaryotes and archaea, the SRP19-heli *** --- *** x 6 complex is thought to be involved in *** --- *** SRP assembly and stabilizes helix 8 for *** --- *** SRP54 binding. *** --- ************************************************ --- CREATE VIEW srp_rna AS SELECT feature_id AS srp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SRP_RNA'; --- ************************************************ --- *** relation: insertion *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence identified as havin *** --- *** g been inserted. *** --- ************************************************ --- CREATE VIEW insertion AS SELECT feature_id AS insertion_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'insertion'; --- ************************************************ --- *** relation: scrna *** --- *** relation type: VIEW *** --- *** *** --- *** Any one of several small cytoplasmic RNA *** --- *** moleculespresent in the cytoplasm and s *** --- *** ometimes nucleus of a eukaryote. *** --- ************************************************ --- CREATE VIEW scrna AS SELECT feature_id AS scrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'scRNA'; --- ************************************************ --- *** relation: est_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against an EST sequence. *** --- ************************************************ --- CREATE VIEW est_match AS SELECT feature_id AS est_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST_match'; --- ************************************************ --- *** relation: clip *** --- *** relation type: VIEW *** --- *** *** --- *** Part of the primary transcript that is c *** --- *** lipped off during processing. *** --- ************************************************ --- CREATE VIEW clip AS SELECT feature_id AS clip_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clip'; --- ************************************************ --- *** relation: modified_base_site *** --- *** relation type: VIEW *** --- *** *** --- *** A modified nucleotide, i.e. a nucleotide *** --- *** other than A, T, C. G or (in RNA) U. *** --- ************************************************ --- CREATE VIEW modified_base_site AS SELECT feature_id AS modified_base_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'modified_base_site'; --- ************************************************ --- *** relation: processed_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** A transcript which has undergone process *** --- *** ing to remove parts such as introns and *** --- *** transcribed_spacer_regions. *** --- ************************************************ --- CREATE VIEW processed_transcript AS SELECT feature_id AS processed_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_transcript'; --- ************************************************ --- *** relation: methylated_base_feature *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide modified by methylation. *** --- ************************************************ --- CREATE VIEW methylated_base_feature AS SELECT feature_id AS methylated_base_feature_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_base_feature'; --- ************************************************ --- *** relation: methylated_a *** --- *** relation type: VIEW *** --- *** *** --- *** A methylated adenine. *** --- ************************************************ --- CREATE VIEW methylated_a AS SELECT feature_id AS methylated_a_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'methylated_A'; --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Messenger RNA is the intermediate molecu *** --- *** le between DNA and protein. It includes *** --- *** UTR and coding sequences. It does not c *** --- *** ontain introns. *** --- ************************************************ --- CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: cpg_island *** --- *** relation type: VIEW *** --- *** *** --- *** Regions of a few hundred to a few thousa *** --- *** nd bases in vertebrate genomes that are *** --- *** relatively GC and CpG rich; they are typ *** --- *** ically unmethylated and often found near *** --- *** the 5' ends of genes. *** --- ************************************************ --- CREATE VIEW cpg_island AS SELECT feature_id AS cpg_island_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CpG_island'; --- ************************************************ --- *** relation: splice_site *** --- *** relation type: VIEW *** --- *** *** --- *** The position where intron is excised. *** --- ************************************************ --- CREATE VIEW splice_site AS SELECT feature_id AS splice_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_site'; --- ************************************************ --- *** relation: tf_binding_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of a molecule that binds to a t *** --- *** ranscription factor. *** --- ************************************************ --- CREATE VIEW tf_binding_site AS SELECT feature_id AS tf_binding_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'TF_binding_site'; --- ************************************************ --- *** relation: splice_donor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction between the 3 prime end of *** --- *** an exon and the following intron. *** --- ************************************************ --- CREATE VIEW splice_donor_site AS SELECT feature_id AS splice_donor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_donor_site'; --- ************************************************ --- *** relation: orf *** --- *** relation type: VIEW *** --- *** *** --- *** The inframe interval between the stop co *** --- *** dons of a reading frame which when read *** --- *** as sequential triplets, has the potentia *** --- *** l of encoding a sequential string of ami *** --- *** no acids. TER(NNN)nTER *** --- ************************************************ --- CREATE VIEW orf AS SELECT feature_id AS orf_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ORF'; --- ************************************************ --- *** relation: splice_acceptor_site *** --- *** relation type: VIEW *** --- *** *** --- *** The junction between the 3 prime end of *** --- *** an intron and the following exon. *** --- ************************************************ --- CREATE VIEW splice_acceptor_site AS SELECT feature_id AS splice_acceptor_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'splice_acceptor_site'; --- ************************************************ --- *** relation: enhancer *** --- *** relation type: VIEW *** --- *** *** --- *** A cis-acting sequence that increases the *** --- *** utilization of (some) eukaryotic promot *** --- *** ers, and can function in either orientat *** --- *** ion and in any location (upstream or dow *** --- *** nstream) relative to the promoter. *** --- ************************************************ --- CREATE VIEW enhancer AS SELECT feature_id AS enhancer_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'enhancer'; --- ************************************************ --- *** relation: flanking_region *** --- *** relation type: VIEW *** --- *** *** --- *** The DNA sequences extending on either si *** --- *** de of a specific locus. *** --- ************************************************ --- CREATE VIEW flanking_region AS SELECT feature_id AS flanking_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'flanking_region'; --- ************************************************ --- *** relation: promoter *** --- *** relation type: VIEW *** --- *** *** --- *** The region on a DNA molecule involved in *** --- *** RNA polymerase binding to initiate tran *** --- *** scription. *** --- ************************************************ --- CREATE VIEW promoter AS SELECT feature_id AS promoter_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'promoter'; --- ************************************************ --- *** relation: hammerhead_ribozyme *** --- *** relation type: VIEW *** --- *** *** --- *** A small catalytic RNA motif that catalyz *** --- *** es self-cleavage reaction. Its name come *** --- *** s from its secondary structure which res *** --- *** embles a carpenter's hammer. The hammerh *** --- *** ead ribozyme is involved in the replicat *** --- *** ion of some viroid and some satellite RN *** --- *** As. *** --- ************************************************ --- CREATE VIEW hammerhead_ribozyme AS SELECT feature_id AS hammerhead_ribozyme_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'hammerhead_ribozyme'; --- ************************************************ --- *** relation: rasirna *** --- *** relation type: VIEW *** --- *** *** --- *** A small, 17-28-nt, small interfering RNA *** --- *** derived from transcripts ofrepetitive e *** --- *** lements. *** --- ************************************************ --- CREATE VIEW rasirna AS SELECT feature_id AS rasirna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rasiRNA'; --- ************************************************ --- *** relation: rnase_mrp_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA molecule essential for the catal *** --- *** ytic activity of RNase MRP, an enzymatic *** --- *** ally active ribonucleoprotein with two d *** --- *** istinct roles in eukaryotes. In mitochon *** --- *** dria it plays a direct role in the initi *** --- *** ation of mitochondrial DNA replication. *** --- *** In the nucleus it is involved in precurs *** --- *** or rRNA processing, where it cleaves the *** --- *** internal transcribed spacer 1 between 1 *** --- *** 8S and 5.8S rRNAs. *** --- ************************************************ --- CREATE VIEW rnase_mrp_rna AS SELECT feature_id AS rnase_mrp_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_MRP_RNA'; --- ************************************************ --- *** relation: rnase_p_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of Ribonuclease P (RNa *** --- *** se P), a ubiquitous endoribonuclease, fo *** --- *** und in archaea, bacteria and eukarya as *** --- *** well as chloroplasts and mitochondria. I *** --- *** ts best characterised activity is the ge *** --- *** neration of mature 5 prime ends of tRNAs *** --- *** by cleaving the 5 prime leader elements *** --- *** of precursor-tRNAs. Cellular RNase Ps a *** --- *** re ribonucleoproteins. RNA from bacteria *** --- *** l RNase Ps retains its catalytic activit *** --- *** y in the absence of the protein subunit, *** --- *** i.e. it is a ribozyme. Isolated eukaryo *** --- *** tic and archaeal RNase P RNA has not bee *** --- *** n shown to retain its catalytic function *** --- *** , but is still essential for the catalyt *** --- *** ic activity of the holoenzyme. Although *** --- *** the archaeal and eukaryotic holoenzymes *** --- *** have a much greater protein content than *** --- *** the bacterial ones, the RNA cores from *** --- *** all the three lineages are homologous. H *** --- *** elices corresponding to P1, P2, P3, P4, *** --- *** and P10/11 are common to all cellular RN *** --- *** ase P RNAs. Yet, there is considerable s *** --- *** equence variation, particularly among th *** --- *** e eukaryotic RNAs. *** --- ************************************************ --- CREATE VIEW rnase_p_rna AS SELECT feature_id AS rnase_p_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'RNase_P_RNA'; --- ************************************************ --- *** relation: transcript *** --- *** relation type: VIEW *** --- *** *** --- *** An RNA synthesized on a DNA or RNA templ *** --- *** ate by an RNA polymerase. *** --- ************************************************ --- CREATE VIEW transcript AS SELECT feature_id AS transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcript'; --- ************************************************ --- *** relation: regulon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of genes, whether linked as a cl *** --- *** uster or not, that respond to a common r *** --- *** egulatory signal. *** --- ************************************************ --- CREATE VIEW regulon AS SELECT feature_id AS regulon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulon'; --- ************************************************ --- *** relation: direct_repeat *** --- *** relation type: VIEW *** --- *** *** --- *** A repeat where the same sequence is repe *** --- *** ated in the same direction. Example: GCT *** --- *** GA-----GCTGA. *** --- ************************************************ --- CREATE VIEW direct_repeat AS SELECT feature_id AS direct_repeat_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'direct_repeat'; --- ************************************************ --- *** relation: transcription_start_site *** --- *** relation type: VIEW *** --- *** *** --- *** The site where transcription begins. *** --- ************************************************ --- CREATE VIEW transcription_start_site AS SELECT feature_id AS transcription_start_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_start_site'; --- ************************************************ --- *** relation: cds *** --- *** relation type: VIEW *** --- *** *** --- *** A contiguous sequence which begins with, *** --- *** and includes, a start codon and ends wi *** --- *** th, and includes, a stop codon. *** --- ************************************************ --- CREATE VIEW cds AS SELECT feature_id AS cds_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'CDS'; --- ************************************************ --- *** relation: guide_rna *** --- *** relation type: VIEW *** --- *** *** --- *** A short 3'-uridylated RNA that can form *** --- *** a perfect duplex (except for the oligoU *** --- *** tail (SO:0000609)) with a stretch of mat *** --- *** ure edited mRNA. *** --- ************************************************ --- CREATE VIEW guide_rna AS SELECT feature_id AS guide_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'guide_RNA'; --- ************************************************ --- *** relation: group_ii_intron *** --- *** relation type: VIEW *** --- *** *** --- *** Group II introns are found in rRNA, tRNA *** --- *** and mRNA of organelles in fungi, plants *** --- *** and protists, and also in mRNA in bacte *** --- *** ria. They are large self-splicing ribozy *** --- *** mes and have 6 structural domains (usual *** --- *** ly designated dI to dVI). A subset of gr *** --- *** oup II introns also encode essential spl *** --- *** icing proteins in intronic ORFs. The len *** --- *** gth of these introns can therefore be up *** --- *** to 3kb. Splicing occurs in almost ident *** --- *** ical fashion to nuclear pre-mRNA splicin *** --- *** g with two transesterification steps. Th *** --- *** e 2' hydroxyl of a bulged adenosine in d *** --- *** omain VI attacks the 5' splice site, fol *** --- *** lowed by nucleophilic attack on the 3' s *** --- *** plice site by the 3' OH of the upstream *** --- *** exon. Protein machinery is required for *** --- *** splicing in vivo, and long range intron- *** --- *** intron and intron-exon interactions are *** --- *** important for splice site positioning. G *** --- *** roup II introns are further sub-classifi *** --- *** ed into groups IIA and IIB which differ *** --- *** in splice site consensus, distance of bu *** --- *** lged A from 3' splice site, some tertiar *** --- *** y interactions, and intronic ORF phyloge *** --- *** ny. *** --- ************************************************ --- CREATE VIEW group_ii_intron AS SELECT feature_id AS group_ii_intron_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'group_II_intron'; --- ************************************************ --- *** relation: intergenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** The region between two known genes. *** --- ************************************************ --- CREATE VIEW intergenic_region AS SELECT feature_id AS intergenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'intergenic_region'; --- ************************************************ --- *** relation: cross_genome_match *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide match against a sequence fr *** --- *** om another organism. *** --- ************************************************ --- CREATE VIEW cross_genome_match AS SELECT feature_id AS cross_genome_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cross_genome_match'; --- ************************************************ --- *** relation: regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A DNA sequence that controls the express *** --- *** ion of a gene. *** --- ************************************************ --- CREATE VIEW regulatory_region AS SELECT feature_id AS regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'regulatory_region'; --- ************************************************ --- *** relation: operon *** --- *** relation type: VIEW *** --- *** *** --- *** A group of contiguous genes transcribed *** --- *** as a single (polycistronic) mRNA from a *** --- *** single regulatory region. *** --- ************************************************ --- CREATE VIEW operon AS SELECT feature_id AS operon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'operon'; --- ************************************************ --- *** relation: clone_start *** --- *** relation type: VIEW *** --- *** *** --- *** The start of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_start AS SELECT feature_id AS clone_start_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_start'; --- ************************************************ --- *** relation: pseudogenic_region *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of a functio *** --- *** nal entitity. *** --- ************************************************ --- CREATE VIEW pseudogenic_region AS SELECT feature_id AS pseudogenic_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogenic_region'; --- ************************************************ --- *** relation: telomerase_rna *** --- *** relation type: VIEW *** --- *** *** --- *** The RNA component of telomerase, a rever *** --- *** se transcriptase that synthesises telome *** --- *** ric DNA. *** --- ************************************************ --- CREATE VIEW telomerase_rna AS SELECT feature_id AS telomerase_rna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'telomerase_RNA'; --- ************************************************ --- *** relation: u1_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U1 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Its 5' end forms complem *** --- *** entary base pairs with the 5' splice jun *** --- *** ction, thus defining the 5' donor site o *** --- *** f an intron. There are significant diffe *** --- *** rences in sequence and secondary structu *** --- *** re between metazoan and yeast U1 snRNAs, *** --- *** the latter being much longer (568 nucle *** --- *** otides as compared to 164 nucleotides in *** --- *** human). Nevertheless, secondary structu *** --- *** re predictions suggest that all U1 snRNA *** --- *** s share a 'common core' consisting of he *** --- *** lices I, II, the proximal region of III, *** --- *** and IV. *** --- ************************************************ --- CREATE VIEW u1_snrna AS SELECT feature_id AS u1_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U1_snRNA'; --- ************************************************ --- *** relation: decayed_exon *** --- *** relation type: VIEW *** --- *** *** --- *** A non-functional descendent of an exon. *** --- ************************************************ --- CREATE VIEW decayed_exon AS SELECT feature_id AS decayed_exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'decayed_exon'; --- ************************************************ --- *** relation: u2_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U2 is a small nuclear RNA (snRNA) compon *** --- *** ent of the spliceosome (involved in pre- *** --- *** mRNA splicing). Complementary binding be *** --- *** tween U2 snRNA (in an area lying towards *** --- *** the 5' end but 3' to hairpin I) and the *** --- *** branchpoint sequence (BPS) of the intro *** --- *** n results in the bulging out of an unpai *** --- *** red adenine, on the BPS, which initiates *** --- *** a nucleophilic attack at the intronic 5 *** --- *** ' splice site, thus starting the first o *** --- *** f two transesterification reactions that *** --- *** mediate splicing. *** --- ************************************************ --- CREATE VIEW u2_snrna AS SELECT feature_id AS u2_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U2_snRNA'; --- ************************************************ --- *** relation: u4_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U4 small nuclear RNA (U4 snRNA) is a com *** --- *** ponent of the major U2-dependent spliceo *** --- *** some. It forms a duplex with U6, and wit *** --- *** h each splicing round, it is displaced f *** --- *** rom U6 (and the spliceosome) in an ATP-d *** --- *** ependent manner, allowing U6 to refold a *** --- *** nd create the active site for splicing c *** --- *** atalysis. A recycling process involving *** --- *** protein Prp24 re-anneals U4 and U6. *** --- ************************************************ --- CREATE VIEW u4_snrna AS SELECT feature_id AS u4_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4_snRNA'; --- ************************************************ --- *** relation: u4atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** An snRNA required for the splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns. It forms a base paire *** --- *** d complex with U6atac_snRNA (SO:0000397) *** --- *** . *** --- ************************************************ --- CREATE VIEW u4atac_snrna AS SELECT feature_id AS u4atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U4atac_snRNA'; --- ************************************************ --- *** relation: u5_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U5 RNA is a component of both types of k *** --- *** nown spliceosome. The precise function o *** --- *** f this molecule is unknown, though it is *** --- *** known that the 5' loop is required for *** --- *** splice site selection and p220 binding, *** --- *** and that both the 3' stem-loop and the S *** --- *** m site are important for Sm protein bind *** --- *** ing and cap methylation. *** --- ************************************************ --- CREATE VIEW u5_snrna AS SELECT feature_id AS u5_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U5_snRNA'; --- ************************************************ --- *** relation: golden_path_fragment *** --- *** relation type: VIEW *** --- *** *** --- *** One of the pieces of sequence that make *** --- *** up a golden path. *** --- ************************************************ --- CREATE VIEW golden_path_fragment AS SELECT feature_id AS golden_path_fragment_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_fragment'; --- ************************************************ --- *** relation: gene_group_regulatory_region *** --- *** relation type: VIEW *** --- *** *** --- *** A kind of regulatory region that regulat *** --- *** es a gene_group such as an operon, rathe *** --- *** r than an individual gene. *** --- ************************************************ --- CREATE VIEW gene_group_regulatory_region AS SELECT feature_id AS gene_group_regulatory_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene_group_regulatory_region'; --- ************************************************ --- *** relation: u6_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6 snRNA is a component of the spliceoso *** --- *** me which is involved in splicing pre-mRN *** --- *** A. The putative secondary structure cons *** --- *** ensus base pairing is confined to a shor *** --- *** t 5' stem loop, but U6 snRNA is thought *** --- *** to form extensive base-pair interactions *** --- *** with U4 snRNA. *** --- ************************************************ --- CREATE VIEW u6_snrna AS SELECT feature_id AS u6_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6_snRNA'; --- ************************************************ --- *** relation: u6atac_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U6atac_snRNA -An snRNA required for the *** --- *** splicing of the minor U12-dependent clas *** --- *** s of eukaryotic nuclear introns. It form *** --- *** s a base paired complex with U4atac_snRN *** --- *** A (SO:0000394). *** --- ************************************************ --- CREATE VIEW u6atac_snrna AS SELECT feature_id AS u6atac_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U6atac_snRNA'; --- ************************************************ --- *** relation: t_element *** --- *** relation type: VIEW *** --- *** *** --- *** A transposon or insertion sequence. An e *** --- *** lement that can insert in a variety of D *** --- *** NA sequences. *** --- ************************************************ --- CREATE VIEW t_element AS SELECT feature_id AS t_element_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: u11_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** U11 snRNA plays a role in splicing of th *** --- *** e minor U12-dependent class of eukaryoti *** --- *** c nuclear introns, similar to U1 snRNA i *** --- *** n the major class spliceosome it base pa *** --- *** irs to the conserved 5' splice site sequ *** --- *** ence. *** --- ************************************************ --- CREATE VIEW u11_snrna AS SELECT feature_id AS u11_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U11_snRNA'; --- ************************************************ --- *** relation: expressed_sequence_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match to an EST or cDNA sequence. *** --- ************************************************ --- CREATE VIEW expressed_sequence_match AS SELECT feature_id AS expressed_sequence_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'expressed_sequence_match'; --- ************************************************ --- *** relation: u12_snrna *** --- *** relation type: VIEW *** --- *** *** --- *** The U12 small nuclear (snRNA), together *** --- *** with U4atac/U6atac, U5, and U11 snRNAs a *** --- *** nd associated proteins, forms a spliceos *** --- *** ome that cleaves a divergent class of lo *** --- *** w-abundance pre-mRNA introns. *** --- ************************************************ --- CREATE VIEW u12_snrna AS SELECT feature_id AS u12_snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'U12_snRNA'; --- ************************************************ --- *** relation: nuclease_sensitive_site *** --- *** relation type: VIEW *** --- *** *** --- *** A region of nucleotide sequence targetin *** --- *** g by a nuclease enzyme. *** --- ************************************************ --- CREATE VIEW nuclease_sensitive_site AS SELECT feature_id AS nuclease_sensitive_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'nuclease_sensitive_site'; --- ************************************************ --- *** relation: clone_end *** --- *** relation type: VIEW *** --- *** *** --- *** The end of the clone insert. *** --- ************************************************ --- CREATE VIEW clone_end AS SELECT feature_id AS clone_end_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'clone_end'; --- ************************************************ --- *** relation: polypeptide *** --- *** relation type: VIEW *** --- *** *** --- *** A sequence of amino acids linked by pept *** --- *** ide bonds which may lack appreciable ter *** --- *** tiary structure and may not be liable to *** --- *** irreversable denaturation. *** --- ************************************************ --- CREATE VIEW polypeptide AS SELECT feature_id AS polypeptide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypeptide'; --- ************************************************ --- *** relation: deletion_junction *** --- *** relation type: VIEW *** --- *** *** --- *** The space between two bases in a sequenc *** --- *** e which marks the position where a delet *** --- *** ion has occured. *** --- ************************************************ --- CREATE VIEW deletion_junction AS SELECT feature_id AS deletion_junction_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'deletion_junction'; --- ************************************************ --- *** relation: golden_path *** --- *** relation type: VIEW *** --- *** *** --- *** A set of subregions selected from sequen *** --- *** ce contigs which when concatenated form *** --- *** a nonredundant linear sequence. *** --- ************************************************ --- CREATE VIEW golden_path AS SELECT feature_id AS golden_path_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path'; --- ************************************************ --- *** relation: cdna_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against cDNA sequence. *** --- ************************************************ --- CREATE VIEW cdna_match AS SELECT feature_id AS cdna_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_match'; --- ************************************************ --- *** relation: sequence_variant *** --- *** relation type: VIEW *** --- *** *** --- *** A region of sequence where variation has *** --- *** been observed. *** --- ************************************************ --- CREATE VIEW sequence_variant AS SELECT feature_id AS sequence_variant_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'sequence_variant'; --- ************************************************ --- *** relation: match_set *** --- *** relation type: VIEW *** --- *** *** --- *** A collection of match parts *** --- ************************************************ --- CREATE VIEW match_set AS SELECT feature_id AS match_set_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_set'; --- ************************************************ --- *** relation: match_part *** --- *** relation type: VIEW *** --- *** *** --- *** A part of a match, for example an hsp fr *** --- *** om blast isa match_part. *** --- ************************************************ --- CREATE VIEW match_part AS SELECT feature_id AS match_part_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match_part'; --- ************************************************ --- *** relation: tag *** --- *** relation type: VIEW *** --- *** *** --- *** A nucleotide sequence that may be used t *** --- *** o identify a larger sequence. *** --- ************************************************ --- CREATE VIEW tag AS SELECT feature_id AS tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tag'; --- ************************************************ --- *** relation: rrna *** --- *** relation type: VIEW *** --- *** *** --- *** RNA that comprises part of a ribosome, a *** --- *** nd that can provide both structural scaf *** --- *** folding and catalytic activity. *** --- ************************************************ --- CREATE VIEW rrna AS SELECT feature_id AS rrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'rRNA'; --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Transfer RNA (tRNA) molecules are approx *** --- *** imately 80 nucleotides in length. Their *** --- *** secondary structure includes four short *** --- *** double-helical elements and three loops *** --- *** (D, anti-codon, and T loops). Further hy *** --- *** drogen bonds mediate the characteristic *** --- *** L-shaped molecular structure. tRNAs have *** --- *** two regions of fundamental functional i *** --- *** mportance: the anti-codon, which is resp *** --- *** onsible for specific mRNA codon recognit *** --- *** ion, and the 3' end, to which the tRNA's *** --- *** corresponding amino acid is attached (b *** --- *** y aminoacyl-tRNA synthetases). tRNAs cop *** --- *** e with the degeneracy of the genetic cod *** --- *** e in two manners: having more than one t *** --- *** RNA (with a specific anti-codon) for a p *** --- *** articular amino acid; and 'wobble' base- *** --- *** pairing, i.e. permitting non-standard ba *** --- *** se-pairing at the 3rd anti-codon positio *** --- *** n. *** --- ************************************************ --- CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: sage_tag *** --- *** relation type: VIEW *** --- *** *** --- *** A short diagnostic sequence tag, serial *** --- *** analysis of gene expression (SAGE), that *** --- *** allows the quantitative and simultaneou *** --- *** s analysis of a large number of transcri *** --- *** pts. *** --- ************************************************ --- CREATE VIEW sage_tag AS SELECT feature_id AS sage_tag_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'SAGE_tag'; --- ************************************************ --- *** relation: polya_sequence *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence of about 100 nucleotides of A a *** --- *** dded to the 3' end of most eukaryotic mR *** --- *** NAs. *** --- ************************************************ --- CREATE VIEW polya_sequence AS SELECT feature_id AS polya_sequence_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polyA_sequence'; --- ************************************************ --- *** relation: translated_nucleotide_match *** --- *** relation type: VIEW *** --- *** *** --- *** A match against a translated sequence. *** --- ************************************************ --- CREATE VIEW translated_nucleotide_match AS SELECT feature_id AS translated_nucleotide_match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'translated_nucleotide_match'; --- ************************************************ --- *** relation: branch_site *** --- *** relation type: VIEW *** --- *** *** --- *** A pyrimidine rich sequence near the 3' e *** --- *** nd of an intron to which the 5'end becom *** --- *** es covalently bound during nuclear splic *** --- *** ing. The resulting structure resembles a *** --- *** lariat. *** --- ************************************************ --- CREATE VIEW branch_site AS SELECT feature_id AS branch_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'branch_site'; --- ************************************************ --- *** relation: polypyrimidine_tract *** --- *** relation type: VIEW *** --- *** *** --- *** The polypyrimidine tract is one of the c *** --- *** is-acting sequence elements directing in *** --- *** tron removal in pre-mRNA splicing. *** --- ************************************************ --- CREATE VIEW polypyrimidine_tract AS SELECT feature_id AS polypyrimidine_tract_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'polypyrimidine_tract'; --- ************************************************ --- *** relation: non_transcribed_region *** --- *** relation type: VIEW *** --- *** *** --- *** A region of the gene which is not transc *** --- *** ribed. *** --- ************************************************ --- CREATE VIEW non_transcribed_region AS SELECT feature_id AS non_transcribed_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'non_transcribed_region'; --- ************************************************ --- *** relation: primary_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** The primary (initial, unprocessed) trans *** --- *** cript; includes five_prime_clip (SO:0000 *** --- *** 555), five_prime_untranslated_region (SO *** --- *** :0000204), open reading frames (SO:00002 *** --- *** 36), introns (SO:0000188) and three_prim *** --- *** e_ untranslated_region (three_prime_UTR) *** --- *** , and three_prime_clip (SO:0000557). *** --- ************************************************ --- CREATE VIEW primary_transcript AS SELECT feature_id AS primary_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'primary_transcript'; chado-1.23/modules/sequence/bridges/bin/create-sofa-bridge.pl000755 000765 000024 00000033374 11723234555 024245 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Carp; use DBI; use Getopt::Long; use Time::HiRes qw( time ); use GO::Parser; use Data::Dumper; # POD DOCS AT END use constant MAX_RELATION_NAME_LEN => 31; my $debug; my $help; my $db; my $file; my $user; my $pass; my $id_based; my $PROPTYPE_ID = 'type_id'; my $drop; my $counts; my $RTYPE = 'VIEW'; my $schema = 'sofa'; my $verbose; my $do_closure=1; GetOptions( "help|h"=>\$help, "db|d=s"=>\$db, "file|f=s"=>\$file, "user|u=s"=>\$user, "pass|p=s"=>\$pass, "id_based|i"=>\$id_based, "count|c"=>\$counts, "drop"=>\$drop, "ptype_id=s"=>\$PROPTYPE_ID, "rtype|r=s"=>\$RTYPE, "verbose|v"=>\$verbose, ); if ($help) { system("perldoc $0"); exit 0; } if ($RTYPE ne 'VIEW' && $RTYPE ne 'TABLE') { die "RTYPE: $RTYPE is not VIEW or TABLE"; } my $dbh; my $DBI = 'DBIx::DBStag'; if ($db) { eval { require "DBIx/DBStag.pm"; msg("Connecting via DBStag"); my $sdbh = DBIx::DBStag->connect($db, $user, $pass); $dbh = $sdbh->dbh; }; if ($@) { # stag not installed - use DBI msg("Connecting via DBI"); $dbh = DBI->connect($db, $user, $pass); } msg("Connected"); $dbh->{RaiseError} = 1; } # ============================================================== # PARSE SOFA # ============================================================== my $p = GO::Parser->new({handler=>'obj'}); my $f = shift || die "must pass SO or SOFA file"; $p->parse($f); my $graph = $p->handler->graph; # ============================================================== # GET FEATURE TYPES # ============================================================== # this is only the feature types for which a feature exists within # the particular chado implementation my @terms = grep {!$_->is_relationship_type} @{$graph->get_all_terms}; # ============================================================== # GET CVTERM IDS # ============================================================== my $trows = []; my $used_type_ids; if ($dbh) { msg("getting type to prop mappings"); $trows = $dbh->selectall_arrayref("SELECT DISTINCT cvterm_id, cvterm.name FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='sequence'"); die "could not find terms" unless @$trows; $used_type_ids = $dbh->selectcol_arrayref("SELECT DISTINCT type_id FROM feature"); } my %used_type_idh = map { $_=>1 } @$used_type_ids; my %n2id = map { $_->[1] => $_->[0] } @$trows; my %id2n = reverse %n2id; my %namemap = (); my %abbrev = (); # make them database-safe (remove certain characters) if ($schema) { print "CREATE SCHEMA $schema;\n\n"; } msg("generating SO layer...."); foreach my $term (@terms) { my $tname = $term->name; my $def = $term->definition || ''; my $vname = safename($tname); my (@cols, @selcols, $sel); my @fcols = qw( feature_id dbxref_id organism_id name uniquename residues seqlen md5checksum type_id is_analysis timeaccessioned timelastmodified ); my @ifcols = qw( feature_id dbxref_id organism_id name uniquename ); my $vfmt = join("\n", "CREATE $RTYPE $vname AS", " SELECT", " feature_id AS $vname"."_id,", " feature.*", " FROM", " feature %s", " WHERE %s", ); my $from = "INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)"; my $where = "cvterm.name = '$tname'"; if ($id_based) { my $id = $n2id{$tname}; $where = "feature.type_id = $id"; } if ($do_closure) { my $cterms = $graph->get_recursive_child_terms_by_type($term->acc); my @pnames = map {$_->name} @$cterms; if (%used_type_idh) { @pnames = grep { $used_type_idh{$n2id{$_}} } @pnames; } @pnames = map {safename($_)} @pnames; if ($id_based) { $where = join(' OR ', map {"cvterm.name = '$_'"} map {$n2id{$_}} @pnames); } else { $where = join(' OR ', map {"cvterm.name = '$_'"} @pnames); } } my $cmnt = ""; if ($id_based) { my $id = $n2id{$tname}; if (!$id) { print STDERR "no id for $tname\n" unless $id; next; } $from = ""; $cmnt = "--- This view is derived from the cvterm database ID.\n". "--- This will be more efficient, but the views MUST be regenerated\n". "--- when the Sequence Ontology in the database changes\n"; } my $vsql = sprintf($vfmt, $from, $where); if ($drop) { print"DROP $RTYPE $vname CASCADE;\n"; } my $defcmt = ''; if ($def) { my $S = 40; while ($def) { $defcmt .= sprintf("--- *** %-40s ***\n",substr($def,0,$S,'')); } } printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". $defcmt. "--- ************************************************\n". "---\n". "\n". "$vsql;\n\n", $vname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@cols) { print "CREATE INDEX $vname"."_idx_$col ON $vname ($col);\n"; } } } $dbh->disconnect if $dbh; print STDERR "Done!\n"; exit 0; sub msg { return unless $verbose; print STDERR "@_\n"; } # ============================================================== # safename(string): returns string # ============================================================== # makes a name db-safe; also adds the mapping # from the original name to safe name in the global lookup %namemap sub safename { my $orig = shift; my $n = lc($orig); $n =~ s/\./_/; my @parts = (); @parts = split(/_/, $n); @parts = map {$abbrev{$_} || $_} @parts; if (length("@parts") > MAX_RELATION_NAME_LEN) { @parts = split(/_/, $n); my $part_i = 0; while (length("@parts") > MAX_RELATION_NAME_LEN) { if ($part_i > @parts) { die "cannot shorten $orig [got $n]"; } my $part = $parts[$part_i]; my $ab = substr($part, 0, 1); $abbrev{$part} = $ab; $parts[$part_i] = $ab; # print " FROM: $part => $ab\n"; $part_i++; } } $n = ''; while (my $part = shift @parts) { $n .= $part; if (@parts && (length($part) > 1 || length($parts[0]) > 1)) { $n.= '_'; } } # print "NAMEMAP: $orig -> $n\n"; $namemap{lc($orig)} = $n; } __END__ =head1 NAME create-sofa-bridge.pl =head1 SYNPOSIS create-sofa-bridge.pl -d 'dbi:Pg:dbname=chado' sofa.obo =head1 ARGUMENTS =over =item -d DBI-LOCATOR Database to use as source (does not actually write to database) =item -i use internal surrogate database IDs (layer will be NON-PORTABLE) =item -r|rtype RELATION-TYPE RELATION-TYPE must be either TABLE or VIEW; the default is VIEW This determines whether the layer consists of materialized views (ie TABLEs), or views =item -d|drop If this is specified, then DROP VIEW/TABLE statements will be created this is useful if you wish to REPLACE an existing SO layer =back =head1 DESCRIPTION Generates views for every term in SO or SOFA Chado is a modular database for bioinformatics. The chado sequence module is generic and has no built-in type system for sequence feature data. Instead it relies on an external ontology to provide semantics for feature types. The canonical ontology for sequence features in the Sequence Ontology (ref). Chado has a module specifically for housing ontologies. The combination of SO plus Chado gives a rigorous yet flexible hybrid relational-ontology model for storing and querying genomic and proteomic data. One negative impact of this hybrid model is that apparently simple queries are hard to express, and may be inefficient. For example, an SQL select to get the gene count in the database requires joining two relations (ie tables), instead of one relation (as expected in a database in which types are encoded relationally, such as ensembl). To fetch mRNAs with exons attached requires a 5 relation join. Even more joins must be introduced if we wish to perform the transitive closure over types (for example, a query for transcripts should return features directly typed to transcript, as well as to subtypes, such as mRNA, tRNA, etc). One solution is to deal with typing issues in the middleware; however, a solution which allows a user to make ad-hoc queries regarding typed features in the databae is still required. We propose a solution to this problem - a chado Sequence Ontology extension layer. This layer provides relations for all commonly used sequence ontology types (for example, gene, exon, transposable_element, intron, ...). These relations can be queried as if they are any other relation in the database; for example: SELECT count(*) FROM gene; SELECT * FROM mrna WHERE name like 'CR400%'; IMPLEMENTATION ============== LAYER TYPE ---------- The SO layer is generated directly from a chado database instance. Perl scripts query the database and the SO OBO file. The implementations are possible: 1. Portable SO View layer These views are portable and can be applied to any instance of chado. They work by joining on the name of the SO type; if SO names change, then this layer will have to be rebuilt. The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature INNER JOIN cvterm ON (feature.type_id=cvterm.cvterm_id) WHERE cvterm.name = 'foo'; [this is for basic features only] 2. Non-portable SO View layer These views are constructed from the surrogate primary key of the sequence ontology term in chado (cvterm.cvterm_id). Surrogate primary keys are not portable between database instantiations; surrogate keys should never be exposed outside the database. This layer becomes obsolete if the sequence ontology is ever reloaded (because the surrogate keys are not guaranteed to be preserved between loads). We provide triggers that removes a SO view if the underlying ontology term in the database is updated or deleted [TODO]. This layer is faster and more efficient than the non-portable layer (because it is not actually necessary to join to the cvterm table) The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (where 1234 is the surrogate primary key of type 'foo' in the cvterm relation) The extra speed of this layer comes at the price of less update flexibility 3. Materialized View (Table) layer This is the fastest yet most update-restrictive way to construct the layer. Each SO type gets a table rather than a view. This is the fastest; for example, when fetching genes, the database engine knows to only look in one single (smaller) table rather than filtering out the gene type from the (possibly enormous) feature table. The table is constructed like this: CREATE TABLE foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (plus indexing SQL statements) This layer is only practical if chado is used in "data-warehouse" mode; modification of the underlying feature data renders the materialized views stale. One possibility is automatically rebuilding the materialized view when the underlying feature table changes; however, this could lead to extremely slow updates IMPLICIT TYPES -------------- Not all types are instantiated within a chado database; for example, there are no intron or UTR features as these are derivable from other features. Nevertheless it can be useful to perform queries on derivable types as if they were actually present. [this is all TODO] These types are derived using type-specific rules. For example, an intron rules can be stated in SQL as derived from exon sibling pairs (cv above) [[EXAMPLE SQL]] [[SKOLEM FUNCTIONS]] Again, implicit types can be implemented as portable or non-portable views, or as materialized views (tables). Implicit types intron utr3 utr5 splice_site dicistronic_gene protein_coding_gene [currently implicit in chado via transcript type] exon5prime exon3prime coding_exon partially_coding_exon intergenic_region [HARD] discuss - expressing these rules in SQL vs expressing in some other delcarative language (first order predicate logic; KIF; Prolog/horn clauses) then translating automatically to SQL. ========== DISCUSSION ========== Selection of which of the 3 implementation strategies to use is purely a DB admin decision. The person constructing the SQL queries need not know or care (other than perhaps to be aware for efficiency reasons) how the layer is implemented - as far as they are concerned they have relations such as gene, transcript, variation etc that act just like normal tables when queried (but not updated - discuss updates on views) The view layer is not necessarily limited to chado databases - any relational database implemented with a DBMS that allows views (currently any DBMS other than mysql) is fair game. For example, one could take a postgres or oracle instantiation of ensembl and write a SO layer generator. Note that ensembl already has a relationally-expressed notion of entities such as gene, exon etc. One way round that is to keep the SO layer seperate in the db; eg through postgresql SCHEMAs. This points the way forward to a unified standard for querying genomic databases; whilst adoption of standards for genomic relational databases is a fraught issue at best (different groups and projects prefer their own schemas for good reasons), we can see the need for there being a common user-query layer, based on a standard of feature types (ie SO). [discussion of difficulties with doing apparently simple (and complex) queries on existing relational databases] =cut chado-1.23/modules/sequence/bdgp/bdgp-indexes.sql000644 000765 000024 00000000732 11256710141 022060 0ustar00cainstaff000000 000000 ---********************************************************** --- depends on featureloc_idx3 index --- make query by range faster ---********************************************************** CLUSTER featureloc_idx3 on featureloc; ---unique index/constraint(?) (subject_id, object_id) is not adequate ALTER TABLE cvtermpath DROP CONSTRAINT cvtermpath_subject_id_key; CREATE UNIQUE INDEX cvtermpath_subject_id_key ON cvtermpath(subject_id, object_id, cv_id, pathdistance); chado-1.23/modules/sequence/bdgp/bdgp-views.sql000644 000765 000024 00000013553 11256710141 021563 0ustar00cainstaff000000 000000 -- bdgp-views.sql -- -- Chris Mungall, BDGP -- -- these are a set of handy views used over chado within BDGP -- typically they provide a flatter/denormalised view over chado -- which is useful for simplifying queries -- ================================================ -- featurepropd = featureprop * cvterm -- ================================================ -- Adds property type name to featureprop CREATE OR REPLACE VIEW featurepropd AS SELECT featureprop.*, cvterm.name AS type FROM featureprop INNER JOIN cvterm ON (featureprop.type_id=cvterm.cvterm_id); -- ================================================ -- dbxrefd = dbxref * db -- ================================================ -- Adds dbname to dbxref CREATE OR REPLACE VIEW dbxrefd AS SELECT dbxref.*, db.name AS dbname, db.name || ':' || dbxref.accession AS dbxrefstr FROM dbxref INNER JOIN db USING (db_id); -- ================================================ -- xcvterm = cvterm * dbxref -- ================================================ -- Adds dbxref to cvterm CREATE OR REPLACE VIEW xcvterm AS SELECT cvterm.*, dbxrefd.dbname, dbxrefd.accession, dbxrefd.version, cv.name AS cvname FROM cvterm INNER JOIN dbxrefd USING (dbxref_id) INNER JOIN cv USING (cv_id); -- ================================================ -- tfeature = feature * cvterm -- ================================================ -- Adds feature type name to feature CREATE OR REPLACE VIEW tfeature AS SELECT feature.*, cvterm.name AS type FROM feature INNER JOIN cvterm ON (feature.type_id=cvterm.cvterm_id); -- ================================================ -- xfeature = feature * dbxref -- ================================================ -- Adds dbxref to feature CREATE OR REPLACE VIEW xfeature AS SELECT feature.*, dbxrefd.dbname, dbxrefd.accession, dbxrefd.version FROM feature INNER JOIN dbxrefd USING (dbxref_id); -- ================================================ -- featurex = feature * feature_dbxref * dbxref -- ================================================ -- Adds dbxref to feature CREATE OR REPLACE VIEW featurex AS SELECT feature.*, dbxrefd.dbname, dbxrefd.accession, dbxrefd.version FROM feature INNER JOIN feature_dbxref USING (feature_id) INNER JOIN dbxrefd USING (dbxref_id); -- ================================================ -- txfeature = xfeature * cvterm -- ================================================ -- cross product of tfeature and xfeature CREATE OR REPLACE VIEW txfeature AS SELECT xfeature.*, cvterm.name AS type FROM xfeature INNER JOIN cvterm ON (xfeature.type_id=cvterm.cvterm_id); -- ================================================ -- featurelocf = featureloc * (src)feature -- ================================================ -- Adds srcfeature name to featureloc CREATE OR REPLACE VIEW featurelocf AS SELECT featureloc.*, feature.name AS srcname, feature.uniquename AS srcuniquename FROM featureloc INNER JOIN feature ON (featureloc.srcfeature_id=feature.feature_id); -- ================================================ -- featurefl = feature * featureloc (rank=0) (locgroup 0) -- ================================================ -- adds main location to feature CREATE OR REPLACE VIEW featurefl AS SELECT feature.*, featureloc.featureloc_id, featureloc.srcfeature_id, featureloc.fmin, featureloc.fmax, featureloc.strand, featureloc.is_fmin_partial, featureloc.is_fmax_partial, featureloc.strand, featureloc.phase, featureloc.residue_info, featureloc.locgroup, featureloc.rank FROM feature INNER JOIN featureloc USING (feature_id) WHERE rank=0 AND locgroup=0; -- ================================================ -- featureflf = feature * featureloc * srcfeature (rank=0) (locgroup 0) -- ================================================ -- as featurefl, but also adds the uniquename of the srcfeature CREATE OR REPLACE VIEW featureflf AS SELECT feature.*, featureloc.featureloc_id, featureloc.srcfeature_id, featureloc.fmin, featureloc.fmax, featureloc.strand, featureloc.is_fmin_partial, featureloc.is_fmax_partial, featureloc.strand, featureloc.phase, featureloc.residue_info, featureloc.locgroup, featureloc.rank, srcfeature.name AS srcname, srcfeature.uniquename AS srcuniquename FROM feature INNER JOIN featureloc ON (feature.feature_id = featureloc.feature_id) INNER JOIN feature AS srcfeature ON (featureloc.srcfeature_id = srcfeature.feature_id) WHERE rank=0 AND locgroup=0; -- ================================================ -- featurepair = feature * featureloc^2 (locgroup 0) -- ================================================ -- features with two locations CREATE OR REPLACE VIEW featurepair AS SELECT feature.*, fl1.srcfeature_id, fl1.fmin, fl1.fmax, fl1.strand, fl1.phase, fl2.srcfeature_id AS tsrcfeature_id, fl2.fmin AS tfmin, fl2.fmax AS tfmax, fl2.strand AS tstrand, fl2.phase AS tphase FROM feature INNER JOIN featureloc AS fl1 USING (feature_id) INNER JOIN featureloc AS fl2 USING (feature_id) WHERE fl1.rank=0 AND fl2.rank=0 AND fl1.locgroup=0 AND fl2.locgroup=0; -- ================================================ -- featuresyn = feature * feature_synonym * synonym -- ================================================ CREATE OR REPLACE VIEW featuresyn AS SELECT feature.*, pub_id, is_current, is_internal, synonym.synonym_id, synonym.type_id AS synonym_type_id, synonym.name AS synonym_name, synonym.synonym_sgml FROM feature INNER JOIN feature_synonym USING (feature_id) INNER JOIN synonym USING (synonym_id); chado-1.23/modules/sequence/bdgp/bin/000755 000765 000024 00000000000 12061672375 017547 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/bdgp/doc/000755 000765 000024 00000000000 12061672375 017544 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/bdgp/populate-match-floc.sql000644 000765 000024 00000002766 11256710141 023364 0ustar00cainstaff000000 000000 -- -- the location of a parent match feature is the maximal extent -- of the featurelocs of the child, on a per-rank basis -- CREATE TEMPORARY TABLE floc_tmp AS SELECT feature_relationship.object_id AS feature_id, featureloc.rank AS rank, min(featureloc.fmin) AS fmin, max(featureloc.fmax) AS fmax, min(featureloc.strand) AS strandmin, max(featureloc.strand) AS strandmax FROM feature INNER JOIN featureloc USING (feature_id) INNER JOIN feature_relationship ON (featureloc.feature_id=subject_id) WHERE feature.type_id IN (SELECT cvterm_id FROM cvterm WHERE name='match') AND locgroup = 0 GROUP BY feature_relationship.object_id, featureloc.rank; -- -- how do we treat child features on varying strands? -- we can either insert consistent-only or insert all -- OPTION 1 INSERT INTO featureloc (feature_id,rank,fmin,fmax,strand) SELECT feature_id,rank,fmin,fmax,strandmin FROM floc_tmp WHERE strandmin = strandmax ORDER BY feature_id,rank; -- OPTION 2 -- just choose strand 1; or should it be strand 0? INSERT INTO featureloc (feature_id,rank,fmin,fmax,strand) SELECT feature_id,rank,fmin,fmax,1 FROM floc_tmp ORDER BY feature_id,rank; -- report inconsistent; -- perhaps we actually want to include these, with arbitrary strand? SELECT count(feature_id) FROM floc_tmp WHERE strandmin != strandmax; SELECT feature_id FROM floc_tmp WHERE strandmin != strandmax; chado-1.23/modules/sequence/bdgp/README000644 000765 000024 00000000607 11256710141 017647 0ustar00cainstaff000000 000000 This directory is for BDGP extensions to Chado Feel free to use any of these extensions - however, be aware that they are experimental and may be liable to change. Currently these extensions are not a supported part of chado. The BDGP extensions currently comprise of * BDGP Views bdgp-views.sql * Sequence Ontology Layer so-views.sql -- portable SO view layer chado-1.23/modules/sequence/bdgp/so-views.sql000755 000765 000024 00000324405 11256710141 021274 0ustar00cainstaff000000 000000 --- ************************************************ --- *** relation: so *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "so" CREATE VIEW so AS SELECT feature_id AS so_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'so'; --- ************************************************ --- *** relation: so_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "so" CREATE VIEW so_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, so1.feature_id AS feature_id1, so1.dbxref_id AS dbxref_id1, so1.organism_id AS organism_id1, so1.name AS name1, so1.uniquename AS uniquename1, so1.residues AS residues1, so1.seqlen AS seqlen1, so1.md5checksum AS md5checksum1, so1.type_id AS type_id1, so1.is_analysis AS is_analysis1, so1.timeaccessioned AS timeaccessioned1, so1.timelastmodified AS timelastmodified1, so2.feature_id AS feature_id2, so2.dbxref_id AS dbxref_id2, so2.organism_id AS organism_id2, so2.name AS name2, so2.uniquename AS uniquename2, so2.residues AS residues2, so2.seqlen AS seqlen2, so2.md5checksum AS md5checksum2, so2.type_id AS type_id2, so2.is_analysis AS is_analysis2, so2.timeaccessioned AS timeaccessioned2, so2.timelastmodified AS timelastmodified2 FROM so AS so1 INNER JOIN feature_relationship AS fr1 ON (so1.so_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN so AS so2 ON (so1.so_id = fr2.subject_id); --- ************************************************ --- *** relation: so_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "so" CREATE VIEW so_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, so1.feature_id AS feature_id1, so1.dbxref_id AS dbxref_id1, so1.organism_id AS organism_id1, so1.name AS name1, so1.uniquename AS uniquename1, so1.residues AS residues1, so1.seqlen AS seqlen1, so1.md5checksum AS md5checksum1, so1.type_id AS type_id1, so1.is_analysis AS is_analysis1, so1.timeaccessioned AS timeaccessioned1, so1.timelastmodified AS timelastmodified1, so2.feature_id AS feature_id2, so2.dbxref_id AS dbxref_id2, so2.organism_id AS organism_id2, so2.name AS name2, so2.uniquename AS uniquename2, so2.residues AS residues2, so2.seqlen AS seqlen2, so2.md5checksum AS md5checksum2, so2.type_id AS type_id2, so2.is_analysis AS is_analysis2, so2.timeaccessioned AS timeaccessioned2, so2.timelastmodified AS timelastmodified2 FROM so AS so1 INNER JOIN feature_relationship AS fr1 ON (so1.so_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN so AS so2 ON (so1.so_id = fr2.object_id); --- ************************************************ --- *** relation: te *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "transposable_element" CREATE VIEW te AS SELECT feature_id AS te_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element'; --- ************************************************ --- *** relation: te_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "transposable_element" CREATE VIEW te_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, te1.feature_id AS feature_id1, te1.dbxref_id AS dbxref_id1, te1.organism_id AS organism_id1, te1.name AS name1, te1.uniquename AS uniquename1, te1.residues AS residues1, te1.seqlen AS seqlen1, te1.md5checksum AS md5checksum1, te1.type_id AS type_id1, te1.is_analysis AS is_analysis1, te1.timeaccessioned AS timeaccessioned1, te1.timelastmodified AS timelastmodified1, te2.feature_id AS feature_id2, te2.dbxref_id AS dbxref_id2, te2.organism_id AS organism_id2, te2.name AS name2, te2.uniquename AS uniquename2, te2.residues AS residues2, te2.seqlen AS seqlen2, te2.md5checksum AS md5checksum2, te2.type_id AS type_id2, te2.is_analysis AS is_analysis2, te2.timeaccessioned AS timeaccessioned2, te2.timelastmodified AS timelastmodified2 FROM te AS te1 INNER JOIN feature_relationship AS fr1 ON (te1.te_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN te AS te2 ON (te1.te_id = fr2.subject_id); --- ************************************************ --- *** relation: te_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "transposable_element" CREATE VIEW te_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, te1.feature_id AS feature_id1, te1.dbxref_id AS dbxref_id1, te1.organism_id AS organism_id1, te1.name AS name1, te1.uniquename AS uniquename1, te1.residues AS residues1, te1.seqlen AS seqlen1, te1.md5checksum AS md5checksum1, te1.type_id AS type_id1, te1.is_analysis AS is_analysis1, te1.timeaccessioned AS timeaccessioned1, te1.timelastmodified AS timelastmodified1, te2.feature_id AS feature_id2, te2.dbxref_id AS dbxref_id2, te2.organism_id AS organism_id2, te2.name AS name2, te2.uniquename AS uniquename2, te2.residues AS residues2, te2.seqlen AS seqlen2, te2.md5checksum AS md5checksum2, te2.type_id AS type_id2, te2.is_analysis AS is_analysis2, te2.timeaccessioned AS timeaccessioned2, te2.timelastmodified AS timelastmodified2 FROM te AS te1 INNER JOIN feature_relationship AS fr1 ON (te1.te_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN te AS te2 ON (te1.te_id = fr2.object_id); --- ************************************************ --- *** relation: chromosome_arm *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "chromosome_arm" CREATE VIEW chromosome_arm AS SELECT feature_id AS chromosome_arm_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_arm'; --- ************************************************ --- *** relation: chromosome_arm_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "chromosome_arm" CREATE VIEW chromosome_arm_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, chromosome_arm1.feature_id AS feature_id1, chromosome_arm1.dbxref_id AS dbxref_id1, chromosome_arm1.organism_id AS organism_id1, chromosome_arm1.name AS name1, chromosome_arm1.uniquename AS uniquename1, chromosome_arm1.residues AS residues1, chromosome_arm1.seqlen AS seqlen1, chromosome_arm1.md5checksum AS md5checksum1, chromosome_arm1.type_id AS type_id1, chromosome_arm1.is_analysis AS is_analysis1, chromosome_arm1.timeaccessioned AS timeaccessioned1, chromosome_arm1.timelastmodified AS timelastmodified1, chromosome_arm2.feature_id AS feature_id2, chromosome_arm2.dbxref_id AS dbxref_id2, chromosome_arm2.organism_id AS organism_id2, chromosome_arm2.name AS name2, chromosome_arm2.uniquename AS uniquename2, chromosome_arm2.residues AS residues2, chromosome_arm2.seqlen AS seqlen2, chromosome_arm2.md5checksum AS md5checksum2, chromosome_arm2.type_id AS type_id2, chromosome_arm2.is_analysis AS is_analysis2, chromosome_arm2.timeaccessioned AS timeaccessioned2, chromosome_arm2.timelastmodified AS timelastmodified2 FROM chromosome_arm AS chromosome_arm1 INNER JOIN feature_relationship AS fr1 ON (chromosome_arm1.chromosome_arm_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN chromosome_arm AS chromosome_arm2 ON (chromosome_arm1.chromosome_arm_id = fr2.subject_id); --- ************************************************ --- *** relation: chromosome_arm_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "chromosome_arm" CREATE VIEW chromosome_arm_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, chromosome_arm1.feature_id AS feature_id1, chromosome_arm1.dbxref_id AS dbxref_id1, chromosome_arm1.organism_id AS organism_id1, chromosome_arm1.name AS name1, chromosome_arm1.uniquename AS uniquename1, chromosome_arm1.residues AS residues1, chromosome_arm1.seqlen AS seqlen1, chromosome_arm1.md5checksum AS md5checksum1, chromosome_arm1.type_id AS type_id1, chromosome_arm1.is_analysis AS is_analysis1, chromosome_arm1.timeaccessioned AS timeaccessioned1, chromosome_arm1.timelastmodified AS timelastmodified1, chromosome_arm2.feature_id AS feature_id2, chromosome_arm2.dbxref_id AS dbxref_id2, chromosome_arm2.organism_id AS organism_id2, chromosome_arm2.name AS name2, chromosome_arm2.uniquename AS uniquename2, chromosome_arm2.residues AS residues2, chromosome_arm2.seqlen AS seqlen2, chromosome_arm2.md5checksum AS md5checksum2, chromosome_arm2.type_id AS type_id2, chromosome_arm2.is_analysis AS is_analysis2, chromosome_arm2.timeaccessioned AS timeaccessioned2, chromosome_arm2.timelastmodified AS timelastmodified2 FROM chromosome_arm AS chromosome_arm1 INNER JOIN feature_relationship AS fr1 ON (chromosome_arm1.chromosome_arm_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN chromosome_arm AS chromosome_arm2 ON (chromosome_arm1.chromosome_arm_id = fr2.object_id); --- ************************************************ --- *** relation: chromosome_band *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "chromosome_band" CREATE VIEW chromosome_band AS SELECT feature_id AS chromosome_band_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'chromosome_band'; --- ************************************************ --- *** relation: chromosome_band_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "chromosome_band" CREATE VIEW chromosome_band_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, chromosome_band1.feature_id AS feature_id1, chromosome_band1.dbxref_id AS dbxref_id1, chromosome_band1.organism_id AS organism_id1, chromosome_band1.name AS name1, chromosome_band1.uniquename AS uniquename1, chromosome_band1.residues AS residues1, chromosome_band1.seqlen AS seqlen1, chromosome_band1.md5checksum AS md5checksum1, chromosome_band1.type_id AS type_id1, chromosome_band1.is_analysis AS is_analysis1, chromosome_band1.timeaccessioned AS timeaccessioned1, chromosome_band1.timelastmodified AS timelastmodified1, chromosome_band2.feature_id AS feature_id2, chromosome_band2.dbxref_id AS dbxref_id2, chromosome_band2.organism_id AS organism_id2, chromosome_band2.name AS name2, chromosome_band2.uniquename AS uniquename2, chromosome_band2.residues AS residues2, chromosome_band2.seqlen AS seqlen2, chromosome_band2.md5checksum AS md5checksum2, chromosome_band2.type_id AS type_id2, chromosome_band2.is_analysis AS is_analysis2, chromosome_band2.timeaccessioned AS timeaccessioned2, chromosome_band2.timelastmodified AS timelastmodified2 FROM chromosome_band AS chromosome_band1 INNER JOIN feature_relationship AS fr1 ON (chromosome_band1.chromosome_band_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN chromosome_band AS chromosome_band2 ON (chromosome_band1.chromosome_band_id = fr2.subject_id); --- ************************************************ --- *** relation: chromosome_band_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "chromosome_band" CREATE VIEW chromosome_band_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, chromosome_band1.feature_id AS feature_id1, chromosome_band1.dbxref_id AS dbxref_id1, chromosome_band1.organism_id AS organism_id1, chromosome_band1.name AS name1, chromosome_band1.uniquename AS uniquename1, chromosome_band1.residues AS residues1, chromosome_band1.seqlen AS seqlen1, chromosome_band1.md5checksum AS md5checksum1, chromosome_band1.type_id AS type_id1, chromosome_band1.is_analysis AS is_analysis1, chromosome_band1.timeaccessioned AS timeaccessioned1, chromosome_band1.timelastmodified AS timelastmodified1, chromosome_band2.feature_id AS feature_id2, chromosome_band2.dbxref_id AS dbxref_id2, chromosome_band2.organism_id AS organism_id2, chromosome_band2.name AS name2, chromosome_band2.uniquename AS uniquename2, chromosome_band2.residues AS residues2, chromosome_band2.seqlen AS seqlen2, chromosome_band2.md5checksum AS md5checksum2, chromosome_band2.type_id AS type_id2, chromosome_band2.is_analysis AS is_analysis2, chromosome_band2.timeaccessioned AS timeaccessioned2, chromosome_band2.timelastmodified AS timelastmodified2 FROM chromosome_band AS chromosome_band1 INNER JOIN feature_relationship AS fr1 ON (chromosome_band1.chromosome_band_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN chromosome_band AS chromosome_band2 ON (chromosome_band1.chromosome_band_id = fr2.object_id); --- ************************************************ --- *** relation: gene *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "gene" CREATE VIEW gene AS SELECT feature_id AS gene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'gene'; --- ************************************************ --- *** relation: gene_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "gene" CREATE VIEW gene_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, gene1.feature_id AS feature_id1, gene1.dbxref_id AS dbxref_id1, gene1.organism_id AS organism_id1, gene1.name AS name1, gene1.uniquename AS uniquename1, gene1.residues AS residues1, gene1.seqlen AS seqlen1, gene1.md5checksum AS md5checksum1, gene1.type_id AS type_id1, gene1.is_analysis AS is_analysis1, gene1.timeaccessioned AS timeaccessioned1, gene1.timelastmodified AS timelastmodified1, gene2.feature_id AS feature_id2, gene2.dbxref_id AS dbxref_id2, gene2.organism_id AS organism_id2, gene2.name AS name2, gene2.uniquename AS uniquename2, gene2.residues AS residues2, gene2.seqlen AS seqlen2, gene2.md5checksum AS md5checksum2, gene2.type_id AS type_id2, gene2.is_analysis AS is_analysis2, gene2.timeaccessioned AS timeaccessioned2, gene2.timelastmodified AS timelastmodified2 FROM gene AS gene1 INNER JOIN feature_relationship AS fr1 ON (gene1.gene_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN gene AS gene2 ON (gene1.gene_id = fr2.subject_id); --- ************************************************ --- *** relation: gene_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "gene" CREATE VIEW gene_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, gene1.feature_id AS feature_id1, gene1.dbxref_id AS dbxref_id1, gene1.organism_id AS organism_id1, gene1.name AS name1, gene1.uniquename AS uniquename1, gene1.residues AS residues1, gene1.seqlen AS seqlen1, gene1.md5checksum AS md5checksum1, gene1.type_id AS type_id1, gene1.is_analysis AS is_analysis1, gene1.timeaccessioned AS timeaccessioned1, gene1.timelastmodified AS timelastmodified1, gene2.feature_id AS feature_id2, gene2.dbxref_id AS dbxref_id2, gene2.organism_id AS organism_id2, gene2.name AS name2, gene2.uniquename AS uniquename2, gene2.residues AS residues2, gene2.seqlen AS seqlen2, gene2.md5checksum AS md5checksum2, gene2.type_id AS type_id2, gene2.is_analysis AS is_analysis2, gene2.timeaccessioned AS timeaccessioned2, gene2.timelastmodified AS timelastmodified2 FROM gene AS gene1 INNER JOIN feature_relationship AS fr1 ON (gene1.gene_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN gene AS gene2 ON (gene1.gene_id = fr2.object_id); --- ************************************************ --- *** relation: est *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "EST" CREATE VIEW est AS SELECT feature_id AS est_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'EST'; --- ************************************************ --- *** relation: est_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "EST" CREATE VIEW est_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, est1.feature_id AS feature_id1, est1.dbxref_id AS dbxref_id1, est1.organism_id AS organism_id1, est1.name AS name1, est1.uniquename AS uniquename1, est1.residues AS residues1, est1.seqlen AS seqlen1, est1.md5checksum AS md5checksum1, est1.type_id AS type_id1, est1.is_analysis AS is_analysis1, est1.timeaccessioned AS timeaccessioned1, est1.timelastmodified AS timelastmodified1, est2.feature_id AS feature_id2, est2.dbxref_id AS dbxref_id2, est2.organism_id AS organism_id2, est2.name AS name2, est2.uniquename AS uniquename2, est2.residues AS residues2, est2.seqlen AS seqlen2, est2.md5checksum AS md5checksum2, est2.type_id AS type_id2, est2.is_analysis AS is_analysis2, est2.timeaccessioned AS timeaccessioned2, est2.timelastmodified AS timelastmodified2 FROM est AS est1 INNER JOIN feature_relationship AS fr1 ON (est1.est_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN est AS est2 ON (est1.est_id = fr2.subject_id); --- ************************************************ --- *** relation: est_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "EST" CREATE VIEW est_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, est1.feature_id AS feature_id1, est1.dbxref_id AS dbxref_id1, est1.organism_id AS organism_id1, est1.name AS name1, est1.uniquename AS uniquename1, est1.residues AS residues1, est1.seqlen AS seqlen1, est1.md5checksum AS md5checksum1, est1.type_id AS type_id1, est1.is_analysis AS is_analysis1, est1.timeaccessioned AS timeaccessioned1, est1.timelastmodified AS timelastmodified1, est2.feature_id AS feature_id2, est2.dbxref_id AS dbxref_id2, est2.organism_id AS organism_id2, est2.name AS name2, est2.uniquename AS uniquename2, est2.residues AS residues2, est2.seqlen AS seqlen2, est2.md5checksum AS md5checksum2, est2.type_id AS type_id2, est2.is_analysis AS is_analysis2, est2.timeaccessioned AS timeaccessioned2, est2.timelastmodified AS timelastmodified2 FROM est AS est1 INNER JOIN feature_relationship AS fr1 ON (est1.est_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN est AS est2 ON (est1.est_id = fr2.object_id); --- ************************************************ --- *** relation: exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "exon" CREATE VIEW exon AS SELECT feature_id AS exon_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'exon'; --- ************************************************ --- *** relation: exon_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "exon" CREATE VIEW exon_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, exon1.feature_id AS feature_id1, exon1.dbxref_id AS dbxref_id1, exon1.organism_id AS organism_id1, exon1.name AS name1, exon1.uniquename AS uniquename1, exon1.residues AS residues1, exon1.seqlen AS seqlen1, exon1.md5checksum AS md5checksum1, exon1.type_id AS type_id1, exon1.is_analysis AS is_analysis1, exon1.timeaccessioned AS timeaccessioned1, exon1.timelastmodified AS timelastmodified1, exon2.feature_id AS feature_id2, exon2.dbxref_id AS dbxref_id2, exon2.organism_id AS organism_id2, exon2.name AS name2, exon2.uniquename AS uniquename2, exon2.residues AS residues2, exon2.seqlen AS seqlen2, exon2.md5checksum AS md5checksum2, exon2.type_id AS type_id2, exon2.is_analysis AS is_analysis2, exon2.timeaccessioned AS timeaccessioned2, exon2.timelastmodified AS timelastmodified2 FROM exon AS exon1 INNER JOIN feature_relationship AS fr1 ON (exon1.exon_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN exon AS exon2 ON (exon1.exon_id = fr2.subject_id); --- ************************************************ --- *** relation: exon_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "exon" CREATE VIEW exon_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, exon1.feature_id AS feature_id1, exon1.dbxref_id AS dbxref_id1, exon1.organism_id AS organism_id1, exon1.name AS name1, exon1.uniquename AS uniquename1, exon1.residues AS residues1, exon1.seqlen AS seqlen1, exon1.md5checksum AS md5checksum1, exon1.type_id AS type_id1, exon1.is_analysis AS is_analysis1, exon1.timeaccessioned AS timeaccessioned1, exon1.timelastmodified AS timelastmodified1, exon2.feature_id AS feature_id2, exon2.dbxref_id AS dbxref_id2, exon2.organism_id AS organism_id2, exon2.name AS name2, exon2.uniquename AS uniquename2, exon2.residues AS residues2, exon2.seqlen AS seqlen2, exon2.md5checksum AS md5checksum2, exon2.type_id AS type_id2, exon2.is_analysis AS is_analysis2, exon2.timeaccessioned AS timeaccessioned2, exon2.timelastmodified AS timelastmodified2 FROM exon AS exon1 INNER JOIN feature_relationship AS fr1 ON (exon1.exon_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN exon AS exon2 ON (exon1.exon_id = fr2.object_id); --- ************************************************ --- *** relation: t_start_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "transcription_start_site" CREATE VIEW t_start_site AS SELECT feature_id AS t_start_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transcription_start_site'; --- ************************************************ --- *** relation: t_start_site_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "transcription_start_site" CREATE VIEW t_start_site_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, t_start_site1.feature_id AS feature_id1, t_start_site1.dbxref_id AS dbxref_id1, t_start_site1.organism_id AS organism_id1, t_start_site1.name AS name1, t_start_site1.uniquename AS uniquename1, t_start_site1.residues AS residues1, t_start_site1.seqlen AS seqlen1, t_start_site1.md5checksum AS md5checksum1, t_start_site1.type_id AS type_id1, t_start_site1.is_analysis AS is_analysis1, t_start_site1.timeaccessioned AS timeaccessioned1, t_start_site1.timelastmodified AS timelastmodified1, t_start_site2.feature_id AS feature_id2, t_start_site2.dbxref_id AS dbxref_id2, t_start_site2.organism_id AS organism_id2, t_start_site2.name AS name2, t_start_site2.uniquename AS uniquename2, t_start_site2.residues AS residues2, t_start_site2.seqlen AS seqlen2, t_start_site2.md5checksum AS md5checksum2, t_start_site2.type_id AS type_id2, t_start_site2.is_analysis AS is_analysis2, t_start_site2.timeaccessioned AS timeaccessioned2, t_start_site2.timelastmodified AS timelastmodified2 FROM t_start_site AS t_start_site1 INNER JOIN feature_relationship AS fr1 ON (t_start_site1.t_start_site_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN t_start_site AS t_start_site2 ON (t_start_site1.t_start_site_id = fr2.subject_id); --- ************************************************ --- *** relation: t_start_site_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "transcription_start_site" CREATE VIEW t_start_site_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, t_start_site1.feature_id AS feature_id1, t_start_site1.dbxref_id AS dbxref_id1, t_start_site1.organism_id AS organism_id1, t_start_site1.name AS name1, t_start_site1.uniquename AS uniquename1, t_start_site1.residues AS residues1, t_start_site1.seqlen AS seqlen1, t_start_site1.md5checksum AS md5checksum1, t_start_site1.type_id AS type_id1, t_start_site1.is_analysis AS is_analysis1, t_start_site1.timeaccessioned AS timeaccessioned1, t_start_site1.timelastmodified AS timelastmodified1, t_start_site2.feature_id AS feature_id2, t_start_site2.dbxref_id AS dbxref_id2, t_start_site2.organism_id AS organism_id2, t_start_site2.name AS name2, t_start_site2.uniquename AS uniquename2, t_start_site2.residues AS residues2, t_start_site2.seqlen AS seqlen2, t_start_site2.md5checksum AS md5checksum2, t_start_site2.type_id AS type_id2, t_start_site2.is_analysis AS is_analysis2, t_start_site2.timeaccessioned AS timeaccessioned2, t_start_site2.timelastmodified AS timelastmodified2 FROM t_start_site AS t_start_site1 INNER JOIN feature_relationship AS fr1 ON (t_start_site1.t_start_site_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN t_start_site AS t_start_site2 ON (t_start_site1.t_start_site_id = fr2.object_id); --- ************************************************ --- *** relation: p_transcript *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "processed_transcript" CREATE VIEW p_transcript AS SELECT feature_id AS p_transcript_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'processed_transcript'; --- ************************************************ --- *** relation: p_transcript_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "processed_transcript" CREATE VIEW p_transcript_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, p_transcript1.feature_id AS feature_id1, p_transcript1.dbxref_id AS dbxref_id1, p_transcript1.organism_id AS organism_id1, p_transcript1.name AS name1, p_transcript1.uniquename AS uniquename1, p_transcript1.residues AS residues1, p_transcript1.seqlen AS seqlen1, p_transcript1.md5checksum AS md5checksum1, p_transcript1.type_id AS type_id1, p_transcript1.is_analysis AS is_analysis1, p_transcript1.timeaccessioned AS timeaccessioned1, p_transcript1.timelastmodified AS timelastmodified1, p_transcript2.feature_id AS feature_id2, p_transcript2.dbxref_id AS dbxref_id2, p_transcript2.organism_id AS organism_id2, p_transcript2.name AS name2, p_transcript2.uniquename AS uniquename2, p_transcript2.residues AS residues2, p_transcript2.seqlen AS seqlen2, p_transcript2.md5checksum AS md5checksum2, p_transcript2.type_id AS type_id2, p_transcript2.is_analysis AS is_analysis2, p_transcript2.timeaccessioned AS timeaccessioned2, p_transcript2.timelastmodified AS timelastmodified2 FROM p_transcript AS p_transcript1 INNER JOIN feature_relationship AS fr1 ON (p_transcript1.p_transcript_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN p_transcript AS p_transcript2 ON (p_transcript1.p_transcript_id = fr2.subject_id); --- ************************************************ --- *** relation: p_transcript_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "processed_transcript" CREATE VIEW p_transcript_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, p_transcript1.feature_id AS feature_id1, p_transcript1.dbxref_id AS dbxref_id1, p_transcript1.organism_id AS organism_id1, p_transcript1.name AS name1, p_transcript1.uniquename AS uniquename1, p_transcript1.residues AS residues1, p_transcript1.seqlen AS seqlen1, p_transcript1.md5checksum AS md5checksum1, p_transcript1.type_id AS type_id1, p_transcript1.is_analysis AS is_analysis1, p_transcript1.timeaccessioned AS timeaccessioned1, p_transcript1.timelastmodified AS timelastmodified1, p_transcript2.feature_id AS feature_id2, p_transcript2.dbxref_id AS dbxref_id2, p_transcript2.organism_id AS organism_id2, p_transcript2.name AS name2, p_transcript2.uniquename AS uniquename2, p_transcript2.residues AS residues2, p_transcript2.seqlen AS seqlen2, p_transcript2.md5checksum AS md5checksum2, p_transcript2.type_id AS type_id2, p_transcript2.is_analysis AS is_analysis2, p_transcript2.timeaccessioned AS timeaccessioned2, p_transcript2.timelastmodified AS timelastmodified2 FROM p_transcript AS p_transcript1 INNER JOIN feature_relationship AS fr1 ON (p_transcript1.p_transcript_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN p_transcript AS p_transcript2 ON (p_transcript1.p_transcript_id = fr2.object_id); --- ************************************************ --- *** relation: mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "mRNA" CREATE VIEW mrna AS SELECT feature_id AS mrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'mRNA'; --- ************************************************ --- *** relation: mrna_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "mRNA" CREATE VIEW mrna_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, mrna1.feature_id AS feature_id1, mrna1.dbxref_id AS dbxref_id1, mrna1.organism_id AS organism_id1, mrna1.name AS name1, mrna1.uniquename AS uniquename1, mrna1.residues AS residues1, mrna1.seqlen AS seqlen1, mrna1.md5checksum AS md5checksum1, mrna1.type_id AS type_id1, mrna1.is_analysis AS is_analysis1, mrna1.timeaccessioned AS timeaccessioned1, mrna1.timelastmodified AS timelastmodified1, mrna2.feature_id AS feature_id2, mrna2.dbxref_id AS dbxref_id2, mrna2.organism_id AS organism_id2, mrna2.name AS name2, mrna2.uniquename AS uniquename2, mrna2.residues AS residues2, mrna2.seqlen AS seqlen2, mrna2.md5checksum AS md5checksum2, mrna2.type_id AS type_id2, mrna2.is_analysis AS is_analysis2, mrna2.timeaccessioned AS timeaccessioned2, mrna2.timelastmodified AS timelastmodified2 FROM mrna AS mrna1 INNER JOIN feature_relationship AS fr1 ON (mrna1.mrna_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN mrna AS mrna2 ON (mrna1.mrna_id = fr2.subject_id); --- ************************************************ --- *** relation: mrna_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "mRNA" CREATE VIEW mrna_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, mrna1.feature_id AS feature_id1, mrna1.dbxref_id AS dbxref_id1, mrna1.organism_id AS organism_id1, mrna1.name AS name1, mrna1.uniquename AS uniquename1, mrna1.residues AS residues1, mrna1.seqlen AS seqlen1, mrna1.md5checksum AS md5checksum1, mrna1.type_id AS type_id1, mrna1.is_analysis AS is_analysis1, mrna1.timeaccessioned AS timeaccessioned1, mrna1.timelastmodified AS timelastmodified1, mrna2.feature_id AS feature_id2, mrna2.dbxref_id AS dbxref_id2, mrna2.organism_id AS organism_id2, mrna2.name AS name2, mrna2.uniquename AS uniquename2, mrna2.residues AS residues2, mrna2.seqlen AS seqlen2, mrna2.md5checksum AS md5checksum2, mrna2.type_id AS type_id2, mrna2.is_analysis AS is_analysis2, mrna2.timeaccessioned AS timeaccessioned2, mrna2.timelastmodified AS timelastmodified2 FROM mrna AS mrna1 INNER JOIN feature_relationship AS fr1 ON (mrna1.mrna_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN mrna AS mrna2 ON (mrna1.mrna_id = fr2.object_id); --- ************************************************ --- *** relation: ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "ncRNA" CREATE VIEW ncrna AS SELECT feature_id AS ncrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'ncRNA'; --- ************************************************ --- *** relation: ncrna_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "ncRNA" CREATE VIEW ncrna_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, ncrna1.feature_id AS feature_id1, ncrna1.dbxref_id AS dbxref_id1, ncrna1.organism_id AS organism_id1, ncrna1.name AS name1, ncrna1.uniquename AS uniquename1, ncrna1.residues AS residues1, ncrna1.seqlen AS seqlen1, ncrna1.md5checksum AS md5checksum1, ncrna1.type_id AS type_id1, ncrna1.is_analysis AS is_analysis1, ncrna1.timeaccessioned AS timeaccessioned1, ncrna1.timelastmodified AS timelastmodified1, ncrna2.feature_id AS feature_id2, ncrna2.dbxref_id AS dbxref_id2, ncrna2.organism_id AS organism_id2, ncrna2.name AS name2, ncrna2.uniquename AS uniquename2, ncrna2.residues AS residues2, ncrna2.seqlen AS seqlen2, ncrna2.md5checksum AS md5checksum2, ncrna2.type_id AS type_id2, ncrna2.is_analysis AS is_analysis2, ncrna2.timeaccessioned AS timeaccessioned2, ncrna2.timelastmodified AS timelastmodified2 FROM ncrna AS ncrna1 INNER JOIN feature_relationship AS fr1 ON (ncrna1.ncrna_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN ncrna AS ncrna2 ON (ncrna1.ncrna_id = fr2.subject_id); --- ************************************************ --- *** relation: ncrna_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "ncRNA" CREATE VIEW ncrna_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, ncrna1.feature_id AS feature_id1, ncrna1.dbxref_id AS dbxref_id1, ncrna1.organism_id AS organism_id1, ncrna1.name AS name1, ncrna1.uniquename AS uniquename1, ncrna1.residues AS residues1, ncrna1.seqlen AS seqlen1, ncrna1.md5checksum AS md5checksum1, ncrna1.type_id AS type_id1, ncrna1.is_analysis AS is_analysis1, ncrna1.timeaccessioned AS timeaccessioned1, ncrna1.timelastmodified AS timelastmodified1, ncrna2.feature_id AS feature_id2, ncrna2.dbxref_id AS dbxref_id2, ncrna2.organism_id AS organism_id2, ncrna2.name AS name2, ncrna2.uniquename AS uniquename2, ncrna2.residues AS residues2, ncrna2.seqlen AS seqlen2, ncrna2.md5checksum AS md5checksum2, ncrna2.type_id AS type_id2, ncrna2.is_analysis AS is_analysis2, ncrna2.timeaccessioned AS timeaccessioned2, ncrna2.timelastmodified AS timelastmodified2 FROM ncrna AS ncrna1 INNER JOIN feature_relationship AS fr1 ON (ncrna1.ncrna_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN ncrna AS ncrna2 ON (ncrna1.ncrna_id = fr2.object_id); --- ************************************************ --- *** relation: snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "snoRNA" CREATE VIEW snorna AS SELECT feature_id AS snorna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snoRNA'; --- ************************************************ --- *** relation: snorna_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "snoRNA" CREATE VIEW snorna_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, snorna1.feature_id AS feature_id1, snorna1.dbxref_id AS dbxref_id1, snorna1.organism_id AS organism_id1, snorna1.name AS name1, snorna1.uniquename AS uniquename1, snorna1.residues AS residues1, snorna1.seqlen AS seqlen1, snorna1.md5checksum AS md5checksum1, snorna1.type_id AS type_id1, snorna1.is_analysis AS is_analysis1, snorna1.timeaccessioned AS timeaccessioned1, snorna1.timelastmodified AS timelastmodified1, snorna2.feature_id AS feature_id2, snorna2.dbxref_id AS dbxref_id2, snorna2.organism_id AS organism_id2, snorna2.name AS name2, snorna2.uniquename AS uniquename2, snorna2.residues AS residues2, snorna2.seqlen AS seqlen2, snorna2.md5checksum AS md5checksum2, snorna2.type_id AS type_id2, snorna2.is_analysis AS is_analysis2, snorna2.timeaccessioned AS timeaccessioned2, snorna2.timelastmodified AS timelastmodified2 FROM snorna AS snorna1 INNER JOIN feature_relationship AS fr1 ON (snorna1.snorna_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN snorna AS snorna2 ON (snorna1.snorna_id = fr2.subject_id); --- ************************************************ --- *** relation: snorna_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "snoRNA" CREATE VIEW snorna_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, snorna1.feature_id AS feature_id1, snorna1.dbxref_id AS dbxref_id1, snorna1.organism_id AS organism_id1, snorna1.name AS name1, snorna1.uniquename AS uniquename1, snorna1.residues AS residues1, snorna1.seqlen AS seqlen1, snorna1.md5checksum AS md5checksum1, snorna1.type_id AS type_id1, snorna1.is_analysis AS is_analysis1, snorna1.timeaccessioned AS timeaccessioned1, snorna1.timelastmodified AS timelastmodified1, snorna2.feature_id AS feature_id2, snorna2.dbxref_id AS dbxref_id2, snorna2.organism_id AS organism_id2, snorna2.name AS name2, snorna2.uniquename AS uniquename2, snorna2.residues AS residues2, snorna2.seqlen AS seqlen2, snorna2.md5checksum AS md5checksum2, snorna2.type_id AS type_id2, snorna2.is_analysis AS is_analysis2, snorna2.timeaccessioned AS timeaccessioned2, snorna2.timelastmodified AS timelastmodified2 FROM snorna AS snorna1 INNER JOIN feature_relationship AS fr1 ON (snorna1.snorna_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN snorna AS snorna2 ON (snorna1.snorna_id = fr2.object_id); --- ************************************************ --- *** relation: snrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "snRNA" CREATE VIEW snrna AS SELECT feature_id AS snrna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'snRNA'; --- ************************************************ --- *** relation: snrna_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "snRNA" CREATE VIEW snrna_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, snrna1.feature_id AS feature_id1, snrna1.dbxref_id AS dbxref_id1, snrna1.organism_id AS organism_id1, snrna1.name AS name1, snrna1.uniquename AS uniquename1, snrna1.residues AS residues1, snrna1.seqlen AS seqlen1, snrna1.md5checksum AS md5checksum1, snrna1.type_id AS type_id1, snrna1.is_analysis AS is_analysis1, snrna1.timeaccessioned AS timeaccessioned1, snrna1.timelastmodified AS timelastmodified1, snrna2.feature_id AS feature_id2, snrna2.dbxref_id AS dbxref_id2, snrna2.organism_id AS organism_id2, snrna2.name AS name2, snrna2.uniquename AS uniquename2, snrna2.residues AS residues2, snrna2.seqlen AS seqlen2, snrna2.md5checksum AS md5checksum2, snrna2.type_id AS type_id2, snrna2.is_analysis AS is_analysis2, snrna2.timeaccessioned AS timeaccessioned2, snrna2.timelastmodified AS timelastmodified2 FROM snrna AS snrna1 INNER JOIN feature_relationship AS fr1 ON (snrna1.snrna_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN snrna AS snrna2 ON (snrna1.snrna_id = fr2.subject_id); --- ************************************************ --- *** relation: snrna_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "snRNA" CREATE VIEW snrna_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, snrna1.feature_id AS feature_id1, snrna1.dbxref_id AS dbxref_id1, snrna1.organism_id AS organism_id1, snrna1.name AS name1, snrna1.uniquename AS uniquename1, snrna1.residues AS residues1, snrna1.seqlen AS seqlen1, snrna1.md5checksum AS md5checksum1, snrna1.type_id AS type_id1, snrna1.is_analysis AS is_analysis1, snrna1.timeaccessioned AS timeaccessioned1, snrna1.timelastmodified AS timelastmodified1, snrna2.feature_id AS feature_id2, snrna2.dbxref_id AS dbxref_id2, snrna2.organism_id AS organism_id2, snrna2.name AS name2, snrna2.uniquename AS uniquename2, snrna2.residues AS residues2, snrna2.seqlen AS seqlen2, snrna2.md5checksum AS md5checksum2, snrna2.type_id AS type_id2, snrna2.is_analysis AS is_analysis2, snrna2.timeaccessioned AS timeaccessioned2, snrna2.timelastmodified AS timelastmodified2 FROM snrna AS snrna1 INNER JOIN feature_relationship AS fr1 ON (snrna1.snrna_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN snrna AS snrna2 ON (snrna1.snrna_id = fr2.object_id); --- ************************************************ --- *** relation: trna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "tRNA" CREATE VIEW trna AS SELECT feature_id AS trna_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'tRNA'; --- ************************************************ --- *** relation: trna_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "tRNA" CREATE VIEW trna_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, trna1.feature_id AS feature_id1, trna1.dbxref_id AS dbxref_id1, trna1.organism_id AS organism_id1, trna1.name AS name1, trna1.uniquename AS uniquename1, trna1.residues AS residues1, trna1.seqlen AS seqlen1, trna1.md5checksum AS md5checksum1, trna1.type_id AS type_id1, trna1.is_analysis AS is_analysis1, trna1.timeaccessioned AS timeaccessioned1, trna1.timelastmodified AS timelastmodified1, trna2.feature_id AS feature_id2, trna2.dbxref_id AS dbxref_id2, trna2.organism_id AS organism_id2, trna2.name AS name2, trna2.uniquename AS uniquename2, trna2.residues AS residues2, trna2.seqlen AS seqlen2, trna2.md5checksum AS md5checksum2, trna2.type_id AS type_id2, trna2.is_analysis AS is_analysis2, trna2.timeaccessioned AS timeaccessioned2, trna2.timelastmodified AS timelastmodified2 FROM trna AS trna1 INNER JOIN feature_relationship AS fr1 ON (trna1.trna_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN trna AS trna2 ON (trna1.trna_id = fr2.subject_id); --- ************************************************ --- *** relation: trna_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "tRNA" CREATE VIEW trna_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, trna1.feature_id AS feature_id1, trna1.dbxref_id AS dbxref_id1, trna1.organism_id AS organism_id1, trna1.name AS name1, trna1.uniquename AS uniquename1, trna1.residues AS residues1, trna1.seqlen AS seqlen1, trna1.md5checksum AS md5checksum1, trna1.type_id AS type_id1, trna1.is_analysis AS is_analysis1, trna1.timeaccessioned AS timeaccessioned1, trna1.timelastmodified AS timelastmodified1, trna2.feature_id AS feature_id2, trna2.dbxref_id AS dbxref_id2, trna2.organism_id AS organism_id2, trna2.name AS name2, trna2.uniquename AS uniquename2, trna2.residues AS residues2, trna2.seqlen AS seqlen2, trna2.md5checksum AS md5checksum2, trna2.type_id AS type_id2, trna2.is_analysis AS is_analysis2, trna2.timeaccessioned AS timeaccessioned2, trna2.timelastmodified AS timelastmodified2 FROM trna AS trna1 INNER JOIN feature_relationship AS fr1 ON (trna1.trna_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN trna AS trna2 ON (trna1.trna_id = fr2.object_id); --- ************************************************ --- *** relation: match *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "match" CREATE VIEW match AS SELECT feature_id AS match_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'match'; --- ************************************************ --- *** relation: match_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "match" CREATE VIEW match_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, match1.feature_id AS feature_id1, match1.dbxref_id AS dbxref_id1, match1.organism_id AS organism_id1, match1.name AS name1, match1.uniquename AS uniquename1, match1.residues AS residues1, match1.seqlen AS seqlen1, match1.md5checksum AS md5checksum1, match1.type_id AS type_id1, match1.is_analysis AS is_analysis1, match1.timeaccessioned AS timeaccessioned1, match1.timelastmodified AS timelastmodified1, match2.feature_id AS feature_id2, match2.dbxref_id AS dbxref_id2, match2.organism_id AS organism_id2, match2.name AS name2, match2.uniquename AS uniquename2, match2.residues AS residues2, match2.seqlen AS seqlen2, match2.md5checksum AS md5checksum2, match2.type_id AS type_id2, match2.is_analysis AS is_analysis2, match2.timeaccessioned AS timeaccessioned2, match2.timelastmodified AS timelastmodified2 FROM match AS match1 INNER JOIN feature_relationship AS fr1 ON (match1.match_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN match AS match2 ON (match1.match_id = fr2.subject_id); --- ************************************************ --- *** relation: match_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "match" CREATE VIEW match_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, match1.feature_id AS feature_id1, match1.dbxref_id AS dbxref_id1, match1.organism_id AS organism_id1, match1.name AS name1, match1.uniquename AS uniquename1, match1.residues AS residues1, match1.seqlen AS seqlen1, match1.md5checksum AS md5checksum1, match1.type_id AS type_id1, match1.is_analysis AS is_analysis1, match1.timeaccessioned AS timeaccessioned1, match1.timelastmodified AS timelastmodified1, match2.feature_id AS feature_id2, match2.dbxref_id AS dbxref_id2, match2.organism_id AS organism_id2, match2.name AS name2, match2.uniquename AS uniquename2, match2.residues AS residues2, match2.seqlen AS seqlen2, match2.md5checksum AS md5checksum2, match2.type_id AS type_id2, match2.is_analysis AS is_analysis2, match2.timeaccessioned AS timeaccessioned2, match2.timelastmodified AS timelastmodified2 FROM match AS match1 INNER JOIN feature_relationship AS fr1 ON (match1.match_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN match AS match2 ON (match1.match_id = fr2.object_id); --- ************************************************ --- *** relation: g_path_region *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "golden_path_region" CREATE VIEW g_path_region AS SELECT feature_id AS g_path_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'golden_path_region'; --- ************************************************ --- *** relation: g_path_region_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "golden_path_region" CREATE VIEW g_path_region_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, g_path_region1.feature_id AS feature_id1, g_path_region1.dbxref_id AS dbxref_id1, g_path_region1.organism_id AS organism_id1, g_path_region1.name AS name1, g_path_region1.uniquename AS uniquename1, g_path_region1.residues AS residues1, g_path_region1.seqlen AS seqlen1, g_path_region1.md5checksum AS md5checksum1, g_path_region1.type_id AS type_id1, g_path_region1.is_analysis AS is_analysis1, g_path_region1.timeaccessioned AS timeaccessioned1, g_path_region1.timelastmodified AS timelastmodified1, g_path_region2.feature_id AS feature_id2, g_path_region2.dbxref_id AS dbxref_id2, g_path_region2.organism_id AS organism_id2, g_path_region2.name AS name2, g_path_region2.uniquename AS uniquename2, g_path_region2.residues AS residues2, g_path_region2.seqlen AS seqlen2, g_path_region2.md5checksum AS md5checksum2, g_path_region2.type_id AS type_id2, g_path_region2.is_analysis AS is_analysis2, g_path_region2.timeaccessioned AS timeaccessioned2, g_path_region2.timelastmodified AS timelastmodified2 FROM g_path_region AS g_path_region1 INNER JOIN feature_relationship AS fr1 ON (g_path_region1.g_path_region_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN g_path_region AS g_path_region2 ON (g_path_region1.g_path_region_id = fr2.subject_id); --- ************************************************ --- *** relation: g_path_region_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "golden_path_region" CREATE VIEW g_path_region_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, g_path_region1.feature_id AS feature_id1, g_path_region1.dbxref_id AS dbxref_id1, g_path_region1.organism_id AS organism_id1, g_path_region1.name AS name1, g_path_region1.uniquename AS uniquename1, g_path_region1.residues AS residues1, g_path_region1.seqlen AS seqlen1, g_path_region1.md5checksum AS md5checksum1, g_path_region1.type_id AS type_id1, g_path_region1.is_analysis AS is_analysis1, g_path_region1.timeaccessioned AS timeaccessioned1, g_path_region1.timelastmodified AS timelastmodified1, g_path_region2.feature_id AS feature_id2, g_path_region2.dbxref_id AS dbxref_id2, g_path_region2.organism_id AS organism_id2, g_path_region2.name AS name2, g_path_region2.uniquename AS uniquename2, g_path_region2.residues AS residues2, g_path_region2.seqlen AS seqlen2, g_path_region2.md5checksum AS md5checksum2, g_path_region2.type_id AS type_id2, g_path_region2.is_analysis AS is_analysis2, g_path_region2.timeaccessioned AS timeaccessioned2, g_path_region2.timelastmodified AS timelastmodified2 FROM g_path_region AS g_path_region1 INNER JOIN feature_relationship AS fr1 ON (g_path_region1.g_path_region_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN g_path_region AS g_path_region2 ON (g_path_region1.g_path_region_id = fr2.object_id); --- ************************************************ --- *** relation: bac *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "BAC" CREATE VIEW bac AS SELECT feature_id AS bac_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'BAC'; --- ************************************************ --- *** relation: bac_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "BAC" CREATE VIEW bac_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, bac1.feature_id AS feature_id1, bac1.dbxref_id AS dbxref_id1, bac1.organism_id AS organism_id1, bac1.name AS name1, bac1.uniquename AS uniquename1, bac1.residues AS residues1, bac1.seqlen AS seqlen1, bac1.md5checksum AS md5checksum1, bac1.type_id AS type_id1, bac1.is_analysis AS is_analysis1, bac1.timeaccessioned AS timeaccessioned1, bac1.timelastmodified AS timelastmodified1, bac2.feature_id AS feature_id2, bac2.dbxref_id AS dbxref_id2, bac2.organism_id AS organism_id2, bac2.name AS name2, bac2.uniquename AS uniquename2, bac2.residues AS residues2, bac2.seqlen AS seqlen2, bac2.md5checksum AS md5checksum2, bac2.type_id AS type_id2, bac2.is_analysis AS is_analysis2, bac2.timeaccessioned AS timeaccessioned2, bac2.timelastmodified AS timelastmodified2 FROM bac AS bac1 INNER JOIN feature_relationship AS fr1 ON (bac1.bac_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN bac AS bac2 ON (bac1.bac_id = fr2.subject_id); --- ************************************************ --- *** relation: bac_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "BAC" CREATE VIEW bac_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, bac1.feature_id AS feature_id1, bac1.dbxref_id AS dbxref_id1, bac1.organism_id AS organism_id1, bac1.name AS name1, bac1.uniquename AS uniquename1, bac1.residues AS residues1, bac1.seqlen AS seqlen1, bac1.md5checksum AS md5checksum1, bac1.type_id AS type_id1, bac1.is_analysis AS is_analysis1, bac1.timeaccessioned AS timeaccessioned1, bac1.timelastmodified AS timelastmodified1, bac2.feature_id AS feature_id2, bac2.dbxref_id AS dbxref_id2, bac2.organism_id AS organism_id2, bac2.name AS name2, bac2.uniquename AS uniquename2, bac2.residues AS residues2, bac2.seqlen AS seqlen2, bac2.md5checksum AS md5checksum2, bac2.type_id AS type_id2, bac2.is_analysis AS is_analysis2, bac2.timeaccessioned AS timeaccessioned2, bac2.timelastmodified AS timelastmodified2 FROM bac AS bac1 INNER JOIN feature_relationship AS fr1 ON (bac1.bac_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN bac AS bac2 ON (bac1.bac_id = fr2.object_id); --- ************************************************ --- *** relation: cdna_clone *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "cDNA_clone" CREATE VIEW cdna_clone AS SELECT feature_id AS cdna_clone_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'cDNA_clone'; --- ************************************************ --- *** relation: cdna_clone_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "cDNA_clone" CREATE VIEW cdna_clone_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, cdna_clone1.feature_id AS feature_id1, cdna_clone1.dbxref_id AS dbxref_id1, cdna_clone1.organism_id AS organism_id1, cdna_clone1.name AS name1, cdna_clone1.uniquename AS uniquename1, cdna_clone1.residues AS residues1, cdna_clone1.seqlen AS seqlen1, cdna_clone1.md5checksum AS md5checksum1, cdna_clone1.type_id AS type_id1, cdna_clone1.is_analysis AS is_analysis1, cdna_clone1.timeaccessioned AS timeaccessioned1, cdna_clone1.timelastmodified AS timelastmodified1, cdna_clone2.feature_id AS feature_id2, cdna_clone2.dbxref_id AS dbxref_id2, cdna_clone2.organism_id AS organism_id2, cdna_clone2.name AS name2, cdna_clone2.uniquename AS uniquename2, cdna_clone2.residues AS residues2, cdna_clone2.seqlen AS seqlen2, cdna_clone2.md5checksum AS md5checksum2, cdna_clone2.type_id AS type_id2, cdna_clone2.is_analysis AS is_analysis2, cdna_clone2.timeaccessioned AS timeaccessioned2, cdna_clone2.timelastmodified AS timelastmodified2 FROM cdna_clone AS cdna_clone1 INNER JOIN feature_relationship AS fr1 ON (cdna_clone1.cdna_clone_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN cdna_clone AS cdna_clone2 ON (cdna_clone1.cdna_clone_id = fr2.subject_id); --- ************************************************ --- *** relation: cdna_clone_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "cDNA_clone" CREATE VIEW cdna_clone_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, cdna_clone1.feature_id AS feature_id1, cdna_clone1.dbxref_id AS dbxref_id1, cdna_clone1.organism_id AS organism_id1, cdna_clone1.name AS name1, cdna_clone1.uniquename AS uniquename1, cdna_clone1.residues AS residues1, cdna_clone1.seqlen AS seqlen1, cdna_clone1.md5checksum AS md5checksum1, cdna_clone1.type_id AS type_id1, cdna_clone1.is_analysis AS is_analysis1, cdna_clone1.timeaccessioned AS timeaccessioned1, cdna_clone1.timelastmodified AS timelastmodified1, cdna_clone2.feature_id AS feature_id2, cdna_clone2.dbxref_id AS dbxref_id2, cdna_clone2.organism_id AS organism_id2, cdna_clone2.name AS name2, cdna_clone2.uniquename AS uniquename2, cdna_clone2.residues AS residues2, cdna_clone2.seqlen AS seqlen2, cdna_clone2.md5checksum AS md5checksum2, cdna_clone2.type_id AS type_id2, cdna_clone2.is_analysis AS is_analysis2, cdna_clone2.timeaccessioned AS timeaccessioned2, cdna_clone2.timelastmodified AS timelastmodified2 FROM cdna_clone AS cdna_clone1 INNER JOIN feature_relationship AS fr1 ON (cdna_clone1.cdna_clone_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN cdna_clone AS cdna_clone2 ON (cdna_clone1.cdna_clone_id = fr2.object_id); --- ************************************************ --- *** relation: oligonucleotide *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "oligonucleotide" CREATE VIEW oligonucleotide AS SELECT feature_id AS oligonucleotide_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'oligonucleotide'; --- ************************************************ --- *** relation: oligonucleotide_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "oligonucleotide" CREATE VIEW oligonucleotide_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, oligonucleotide1.feature_id AS feature_id1, oligonucleotide1.dbxref_id AS dbxref_id1, oligonucleotide1.organism_id AS organism_id1, oligonucleotide1.name AS name1, oligonucleotide1.uniquename AS uniquename1, oligonucleotide1.residues AS residues1, oligonucleotide1.seqlen AS seqlen1, oligonucleotide1.md5checksum AS md5checksum1, oligonucleotide1.type_id AS type_id1, oligonucleotide1.is_analysis AS is_analysis1, oligonucleotide1.timeaccessioned AS timeaccessioned1, oligonucleotide1.timelastmodified AS timelastmodified1, oligonucleotide2.feature_id AS feature_id2, oligonucleotide2.dbxref_id AS dbxref_id2, oligonucleotide2.organism_id AS organism_id2, oligonucleotide2.name AS name2, oligonucleotide2.uniquename AS uniquename2, oligonucleotide2.residues AS residues2, oligonucleotide2.seqlen AS seqlen2, oligonucleotide2.md5checksum AS md5checksum2, oligonucleotide2.type_id AS type_id2, oligonucleotide2.is_analysis AS is_analysis2, oligonucleotide2.timeaccessioned AS timeaccessioned2, oligonucleotide2.timelastmodified AS timelastmodified2 FROM oligonucleotide AS oligonucleotide1 INNER JOIN feature_relationship AS fr1 ON (oligonucleotide1.oligonucleotide_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN oligonucleotide AS oligonucleotide2 ON (oligonucleotide1.oligonucleotide_id = fr2.subject_id); --- ************************************************ --- *** relation: oligonucleotide_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "oligonucleotide" CREATE VIEW oligonucleotide_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, oligonucleotide1.feature_id AS feature_id1, oligonucleotide1.dbxref_id AS dbxref_id1, oligonucleotide1.organism_id AS organism_id1, oligonucleotide1.name AS name1, oligonucleotide1.uniquename AS uniquename1, oligonucleotide1.residues AS residues1, oligonucleotide1.seqlen AS seqlen1, oligonucleotide1.md5checksum AS md5checksum1, oligonucleotide1.type_id AS type_id1, oligonucleotide1.is_analysis AS is_analysis1, oligonucleotide1.timeaccessioned AS timeaccessioned1, oligonucleotide1.timelastmodified AS timelastmodified1, oligonucleotide2.feature_id AS feature_id2, oligonucleotide2.dbxref_id AS dbxref_id2, oligonucleotide2.organism_id AS organism_id2, oligonucleotide2.name AS name2, oligonucleotide2.uniquename AS uniquename2, oligonucleotide2.residues AS residues2, oligonucleotide2.seqlen AS seqlen2, oligonucleotide2.md5checksum AS md5checksum2, oligonucleotide2.type_id AS type_id2, oligonucleotide2.is_analysis AS is_analysis2, oligonucleotide2.timeaccessioned AS timeaccessioned2, oligonucleotide2.timelastmodified AS timelastmodified2 FROM oligonucleotide AS oligonucleotide1 INNER JOIN feature_relationship AS fr1 ON (oligonucleotide1.oligonucleotide_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN oligonucleotide AS oligonucleotide2 ON (oligonucleotide1.oligonucleotide_id = fr2.object_id); --- ************************************************ --- *** relation: repeat_region *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "repeat_region" CREATE VIEW repeat_region AS SELECT feature_id AS repeat_region_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'repeat_region'; --- ************************************************ --- *** relation: repeat_region_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "repeat_region" CREATE VIEW repeat_region_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, repeat_region1.feature_id AS feature_id1, repeat_region1.dbxref_id AS dbxref_id1, repeat_region1.organism_id AS organism_id1, repeat_region1.name AS name1, repeat_region1.uniquename AS uniquename1, repeat_region1.residues AS residues1, repeat_region1.seqlen AS seqlen1, repeat_region1.md5checksum AS md5checksum1, repeat_region1.type_id AS type_id1, repeat_region1.is_analysis AS is_analysis1, repeat_region1.timeaccessioned AS timeaccessioned1, repeat_region1.timelastmodified AS timelastmodified1, repeat_region2.feature_id AS feature_id2, repeat_region2.dbxref_id AS dbxref_id2, repeat_region2.organism_id AS organism_id2, repeat_region2.name AS name2, repeat_region2.uniquename AS uniquename2, repeat_region2.residues AS residues2, repeat_region2.seqlen AS seqlen2, repeat_region2.md5checksum AS md5checksum2, repeat_region2.type_id AS type_id2, repeat_region2.is_analysis AS is_analysis2, repeat_region2.timeaccessioned AS timeaccessioned2, repeat_region2.timelastmodified AS timelastmodified2 FROM repeat_region AS repeat_region1 INNER JOIN feature_relationship AS fr1 ON (repeat_region1.repeat_region_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN repeat_region AS repeat_region2 ON (repeat_region1.repeat_region_id = fr2.subject_id); --- ************************************************ --- *** relation: repeat_region_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "repeat_region" CREATE VIEW repeat_region_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, repeat_region1.feature_id AS feature_id1, repeat_region1.dbxref_id AS dbxref_id1, repeat_region1.organism_id AS organism_id1, repeat_region1.name AS name1, repeat_region1.uniquename AS uniquename1, repeat_region1.residues AS residues1, repeat_region1.seqlen AS seqlen1, repeat_region1.md5checksum AS md5checksum1, repeat_region1.type_id AS type_id1, repeat_region1.is_analysis AS is_analysis1, repeat_region1.timeaccessioned AS timeaccessioned1, repeat_region1.timelastmodified AS timelastmodified1, repeat_region2.feature_id AS feature_id2, repeat_region2.dbxref_id AS dbxref_id2, repeat_region2.organism_id AS organism_id2, repeat_region2.name AS name2, repeat_region2.uniquename AS uniquename2, repeat_region2.residues AS residues2, repeat_region2.seqlen AS seqlen2, repeat_region2.md5checksum AS md5checksum2, repeat_region2.type_id AS type_id2, repeat_region2.is_analysis AS is_analysis2, repeat_region2.timeaccessioned AS timeaccessioned2, repeat_region2.timelastmodified AS timelastmodified2 FROM repeat_region AS repeat_region1 INNER JOIN feature_relationship AS fr1 ON (repeat_region1.repeat_region_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN repeat_region AS repeat_region2 ON (repeat_region1.repeat_region_id = fr2.object_id); --- ************************************************ --- *** relation: tei_site *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "transposable_element_insertion_site" CREATE VIEW tei_site AS SELECT feature_id AS tei_site_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'transposable_element_insertion_site'; --- ************************************************ --- *** relation: tei_site_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "transposable_element_insertion_site" CREATE VIEW tei_site_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, tei_site1.feature_id AS feature_id1, tei_site1.dbxref_id AS dbxref_id1, tei_site1.organism_id AS organism_id1, tei_site1.name AS name1, tei_site1.uniquename AS uniquename1, tei_site1.residues AS residues1, tei_site1.seqlen AS seqlen1, tei_site1.md5checksum AS md5checksum1, tei_site1.type_id AS type_id1, tei_site1.is_analysis AS is_analysis1, tei_site1.timeaccessioned AS timeaccessioned1, tei_site1.timelastmodified AS timelastmodified1, tei_site2.feature_id AS feature_id2, tei_site2.dbxref_id AS dbxref_id2, tei_site2.organism_id AS organism_id2, tei_site2.name AS name2, tei_site2.uniquename AS uniquename2, tei_site2.residues AS residues2, tei_site2.seqlen AS seqlen2, tei_site2.md5checksum AS md5checksum2, tei_site2.type_id AS type_id2, tei_site2.is_analysis AS is_analysis2, tei_site2.timeaccessioned AS timeaccessioned2, tei_site2.timelastmodified AS timelastmodified2 FROM tei_site AS tei_site1 INNER JOIN feature_relationship AS fr1 ON (tei_site1.tei_site_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN tei_site AS tei_site2 ON (tei_site1.tei_site_id = fr2.subject_id); --- ************************************************ --- *** relation: tei_site_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "transposable_element_insertion_site" CREATE VIEW tei_site_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, tei_site1.feature_id AS feature_id1, tei_site1.dbxref_id AS dbxref_id1, tei_site1.organism_id AS organism_id1, tei_site1.name AS name1, tei_site1.uniquename AS uniquename1, tei_site1.residues AS residues1, tei_site1.seqlen AS seqlen1, tei_site1.md5checksum AS md5checksum1, tei_site1.type_id AS type_id1, tei_site1.is_analysis AS is_analysis1, tei_site1.timeaccessioned AS timeaccessioned1, tei_site1.timelastmodified AS timelastmodified1, tei_site2.feature_id AS feature_id2, tei_site2.dbxref_id AS dbxref_id2, tei_site2.organism_id AS organism_id2, tei_site2.name AS name2, tei_site2.uniquename AS uniquename2, tei_site2.residues AS residues2, tei_site2.seqlen AS seqlen2, tei_site2.md5checksum AS md5checksum2, tei_site2.type_id AS type_id2, tei_site2.is_analysis AS is_analysis2, tei_site2.timeaccessioned AS timeaccessioned2, tei_site2.timelastmodified AS timelastmodified2 FROM tei_site AS tei_site1 INNER JOIN feature_relationship AS fr1 ON (tei_site1.tei_site_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN tei_site AS tei_site2 ON (tei_site1.tei_site_id = fr2.object_id); --- ************************************************ --- *** relation: pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "pseudogene" CREATE VIEW pseudogene AS SELECT feature_id AS pseudogene_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'pseudogene'; --- ************************************************ --- *** relation: pseudogene_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "pseudogene" CREATE VIEW pseudogene_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, pseudogene1.feature_id AS feature_id1, pseudogene1.dbxref_id AS dbxref_id1, pseudogene1.organism_id AS organism_id1, pseudogene1.name AS name1, pseudogene1.uniquename AS uniquename1, pseudogene1.residues AS residues1, pseudogene1.seqlen AS seqlen1, pseudogene1.md5checksum AS md5checksum1, pseudogene1.type_id AS type_id1, pseudogene1.is_analysis AS is_analysis1, pseudogene1.timeaccessioned AS timeaccessioned1, pseudogene1.timelastmodified AS timelastmodified1, pseudogene2.feature_id AS feature_id2, pseudogene2.dbxref_id AS dbxref_id2, pseudogene2.organism_id AS organism_id2, pseudogene2.name AS name2, pseudogene2.uniquename AS uniquename2, pseudogene2.residues AS residues2, pseudogene2.seqlen AS seqlen2, pseudogene2.md5checksum AS md5checksum2, pseudogene2.type_id AS type_id2, pseudogene2.is_analysis AS is_analysis2, pseudogene2.timeaccessioned AS timeaccessioned2, pseudogene2.timelastmodified AS timelastmodified2 FROM pseudogene AS pseudogene1 INNER JOIN feature_relationship AS fr1 ON (pseudogene1.pseudogene_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN pseudogene AS pseudogene2 ON (pseudogene1.pseudogene_id = fr2.subject_id); --- ************************************************ --- *** relation: pseudogene_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "pseudogene" CREATE VIEW pseudogene_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, pseudogene1.feature_id AS feature_id1, pseudogene1.dbxref_id AS dbxref_id1, pseudogene1.organism_id AS organism_id1, pseudogene1.name AS name1, pseudogene1.uniquename AS uniquename1, pseudogene1.residues AS residues1, pseudogene1.seqlen AS seqlen1, pseudogene1.md5checksum AS md5checksum1, pseudogene1.type_id AS type_id1, pseudogene1.is_analysis AS is_analysis1, pseudogene1.timeaccessioned AS timeaccessioned1, pseudogene1.timelastmodified AS timelastmodified1, pseudogene2.feature_id AS feature_id2, pseudogene2.dbxref_id AS dbxref_id2, pseudogene2.organism_id AS organism_id2, pseudogene2.name AS name2, pseudogene2.uniquename AS uniquename2, pseudogene2.residues AS residues2, pseudogene2.seqlen AS seqlen2, pseudogene2.md5checksum AS md5checksum2, pseudogene2.type_id AS type_id2, pseudogene2.is_analysis AS is_analysis2, pseudogene2.timeaccessioned AS timeaccessioned2, pseudogene2.timelastmodified AS timelastmodified2 FROM pseudogene AS pseudogene1 INNER JOIN feature_relationship AS fr1 ON (pseudogene1.pseudogene_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN pseudogene AS pseudogene2 ON (pseudogene1.pseudogene_id = fr2.object_id); --- ************************************************ --- *** relation: protein *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology 'Typed Feature' View *** --- *** *** --- ************************************************ --- --- SO Term: --- "protein" CREATE VIEW protein AS SELECT feature_id AS protein_id, feature.* FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id) WHERE cvterm.name = 'protein'; --- ************************************************ --- *** relation: protein_pair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Pair View *** --- *** features linked by common container *** --- ************************************************ --- --- SO Term: --- "protein" CREATE VIEW protein_pair AS SELECT fr1.object_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, protein1.feature_id AS feature_id1, protein1.dbxref_id AS dbxref_id1, protein1.organism_id AS organism_id1, protein1.name AS name1, protein1.uniquename AS uniquename1, protein1.residues AS residues1, protein1.seqlen AS seqlen1, protein1.md5checksum AS md5checksum1, protein1.type_id AS type_id1, protein1.is_analysis AS is_analysis1, protein1.timeaccessioned AS timeaccessioned1, protein1.timelastmodified AS timelastmodified1, protein2.feature_id AS feature_id2, protein2.dbxref_id AS dbxref_id2, protein2.organism_id AS organism_id2, protein2.name AS name2, protein2.uniquename AS uniquename2, protein2.residues AS residues2, protein2.seqlen AS seqlen2, protein2.md5checksum AS md5checksum2, protein2.type_id AS type_id2, protein2.is_analysis AS is_analysis2, protein2.timeaccessioned AS timeaccessioned2, protein2.timelastmodified AS timelastmodified2 FROM protein AS protein1 INNER JOIN feature_relationship AS fr1 ON (protein1.protein_id = fr1.subject_id) INNER JOIN feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id) INNER JOIN protein AS protein2 ON (protein1.protein_id = fr2.subject_id); --- ************************************************ --- *** relation: protein_invpair *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology Feature Inverse Pair *** --- *** features linked by common contained *** --- *** child feature *** --- ************************************************ --- --- SO Term: --- "protein" CREATE VIEW protein_invpair AS SELECT fr1.subject_id, fr1.rank AS rank1, fr2.rank AS rank2, fr2.rank - fr1.rank AS rankdiff, protein1.feature_id AS feature_id1, protein1.dbxref_id AS dbxref_id1, protein1.organism_id AS organism_id1, protein1.name AS name1, protein1.uniquename AS uniquename1, protein1.residues AS residues1, protein1.seqlen AS seqlen1, protein1.md5checksum AS md5checksum1, protein1.type_id AS type_id1, protein1.is_analysis AS is_analysis1, protein1.timeaccessioned AS timeaccessioned1, protein1.timelastmodified AS timelastmodified1, protein2.feature_id AS feature_id2, protein2.dbxref_id AS dbxref_id2, protein2.organism_id AS organism_id2, protein2.name AS name2, protein2.uniquename AS uniquename2, protein2.residues AS residues2, protein2.seqlen AS seqlen2, protein2.md5checksum AS md5checksum2, protein2.type_id AS type_id2, protein2.is_analysis AS is_analysis2, protein2.timeaccessioned AS timeaccessioned2, protein2.timelastmodified AS timelastmodified2 FROM protein AS protein1 INNER JOIN feature_relationship AS fr1 ON (protein1.protein_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id) INNER JOIN protein AS protein2 ON (protein1.protein_id = fr2.object_id); --- ************************************************ --- *** relation: mrna2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: mrna --- Predicate: PART-OF CREATE VIEW mrna2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS mrna_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN mrna ON (mrna.feature_id = object_id); --- ************************************************ --- *** relation: ncrna2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: ncrna --- Predicate: PART-OF CREATE VIEW ncrna2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS ncrna_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN ncrna ON (ncrna.feature_id = object_id); --- ************************************************ --- *** relation: snorna2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: snorna --- Predicate: PART-OF CREATE VIEW snorna2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS snorna_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN snorna ON (snorna.feature_id = object_id); --- ************************************************ --- *** relation: snrna2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: snrna --- Predicate: PART-OF CREATE VIEW snrna2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS snrna_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN snrna ON (snrna.feature_id = object_id); --- ************************************************ --- *** relation: trna2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: trna --- Predicate: PART-OF CREATE VIEW trna2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS trna_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN trna ON (trna.feature_id = object_id); --- ************************************************ --- *** relation: pseudogene2exon *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: exon --- Object Type: pseudogene --- Predicate: PART-OF CREATE VIEW pseudogene2exon AS SELECT feature_relationship_id, subject_id AS exon_id, object_id AS pseudogene_id, subject_id, object_id, feature_relationship.type_id FROM exon INNER JOIN feature_relationship ON (exon.feature_id = subject_id) INNER JOIN pseudogene ON (pseudogene.feature_id = object_id); --- ************************************************ --- *** relation: gene2mrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: mrna --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2mrna AS SELECT feature_relationship_id, subject_id AS mrna_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM mrna INNER JOIN feature_relationship ON (mrna.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: gene2ncrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: ncrna --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2ncrna AS SELECT feature_relationship_id, subject_id AS ncrna_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM ncrna INNER JOIN feature_relationship ON (ncrna.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: gene2snorna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: snorna --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2snorna AS SELECT feature_relationship_id, subject_id AS snorna_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM snorna INNER JOIN feature_relationship ON (snorna.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: gene2snrna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: snrna --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2snrna AS SELECT feature_relationship_id, subject_id AS snrna_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM snrna INNER JOIN feature_relationship ON (snrna.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: gene2trna *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: trna --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2trna AS SELECT feature_relationship_id, subject_id AS trna_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM trna INNER JOIN feature_relationship ON (trna.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: match2match *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: match --- Object Type: match --- Predicate: PART-OF CREATE VIEW match2match AS SELECT feature_relationship_id, subject_id AS match_id, object_id AS match_id, subject_id, object_id, feature_relationship.type_id FROM match INNER JOIN feature_relationship ON (match.feature_id = subject_id) INNER JOIN match ON (match.feature_id = object_id); --- ************************************************ --- *** relation: chromosome_arm2g_path_region *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: g_path_region --- Object Type: chromosome_arm --- Predicate: PART-OF CREATE VIEW chromosome_arm2g_path_region AS SELECT feature_relationship_id, subject_id AS g_path_region_id, object_id AS chromosome_arm_id, subject_id, object_id, feature_relationship.type_id FROM g_path_region INNER JOIN feature_relationship ON (g_path_region.feature_id = subject_id) INNER JOIN chromosome_arm ON (chromosome_arm.feature_id = object_id); --- ************************************************ --- *** relation: gene2pseudogene *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: pseudogene --- Object Type: gene --- Predicate: PART-OF CREATE VIEW gene2pseudogene AS SELECT feature_relationship_id, subject_id AS pseudogene_id, object_id AS gene_id, subject_id, object_id, feature_relationship.type_id FROM pseudogene INNER JOIN feature_relationship ON (pseudogene.feature_id = subject_id) INNER JOIN gene ON (gene.feature_id = object_id); --- ************************************************ --- *** relation: mrna2protein *** --- *** relation type: VIEW *** --- *** *** --- *** Sequence Ontology PART-OF view *** --- ************************************************ --- --- Subject Type: protein --- Object Type: mrna --- Predicate: PART-OF CREATE VIEW mrna2protein AS SELECT feature_relationship_id, subject_id AS protein_id, object_id AS mrna_id, subject_id, object_id, feature_relationship.type_id FROM protein INNER JOIN feature_relationship ON (protein.feature_id = subject_id) INNER JOIN mrna ON (mrna.feature_id = object_id); chado-1.23/modules/sequence/bdgp/doc/chado-sequence-ontology-layer.sxi000644 000765 000024 00000124437 11256710136 026143 0ustar00cainstaff000000 000000 PK§00ÿe´Ð$*$*-Pictures/100000000000011E000002E146F44112.gifGIF87aáw,ᇀ€€€€€€€€ÀÀÀÀÜÀ¦Êð333333""")))UUUMMMBBB999ÿ|€ÿPPÖ“ÌìÿïÖÆççÖ­©3ÿf™Ì333f3™3Ì3ÿ3f3fff™fÌfÿf™3™f™™™Ì™ÿ™Ì3ÌfÌ™ÌÌÌÿÌfÿ™ÿÌÿÿ33ÿf3™3Ì3ÿ33ÿ333f33™33Ì33ÿ33f33f3ff3™f3Ìf3ÿf3™33™3f™3™™3Ì™3ÿ™3Ì33Ì3fÌ3™Ì3ÌÌ3ÿÌ33ÿ3fÿ3™ÿ3Ìÿ3ÿÿ3f3fff™fÌfÿf3f33ff3f™3fÌ3fÿ3fff3fffff™ffÌff™f3™ff™f™™fÌ™fÿ™fÌf3Ìf™ÌfÌÌfÿÌfÿf3ÿf™ÿfÌÿfÿÌÌÿ™™™3™™™Ì™™33™f™Ì3™ÿ™f™3f™f3™™f™Ìf™ÿ3™3™™f™™™™™Ì™™ÿ™™Ì™3Ì™fÌf™Ì™ÌÌ™ÿÌ™ÿ™3ÿ™fÌ™™ÿ™Ìÿ™ÿÿ™Ì3™fÌ™ÌÌÌ3™33Ìf3Ì™3ÌÌ3Ìÿ3ÌfÌ3fÌff™™fÌÌfÌÿf™™Ì3™Ìf™Ì™™ÌÌ™Ìÿ™ÌÌÌ3ÌÌfÌÌ™ÌÌÌÌÌÿÌÌÿÌ3ÿÌfÿ™™ÿÌÌÿÌÿÿÌ3Ìfÿ™ÿ3Ì33ÿf3ÿ™3ÿÌ3ÿÿ3ÿfÿ3fÿffÌ™fÿÌfÿÿfÌ™ÿ3™ÿf™ÿ™™ÿÌ™ÿÿ™ÿÌÿ3ÌÿfÌÿ™ÌÿÌÌÿÿÌÿ3ÿÿfÿÌ™ÿÿÌÿÿÿfffÿfÿÿfffÿÿfÿfÿÿ¥!___www†††–––ËË˲²²×××ÝÝÝãããêêêñññøøøÿûð  ¤€€€ÿÿÿÿÿÿÿÿÿÿÿÿþÿ H° Áƒ*\È°¡Ã‡#JœH±¢Å‹3jÜȱ£Ç CŠI²¤É“(QXÉ’%Ã-¤„ØÍ6æt˜s§Ážy±ä¥ÐgA£3Dú3žÀxL“.¥ubÕ©:^…(Ô)T¢«nMÉt¬Ïœ0WÊü—V¨ÀhY® ÀÚ¶ÓÚMˆTïÚº{]Â} •­\¾oëÞúÏ%๊¯l,ð±d›qÕ&ÖÖéÓž‘]ú}›÷°aº˜Ž¥Šµ¨g‚¼öŒW—´íØÿ Kæ¥;voÙˆo<èmºÄs‹}K÷·òÛÅ›Ÿýœ²uܽ¥WÍœ÷ôâ„«þÇ®ÜíGÌ-w[Ï~=A½{­_ç.ßøüÛJm/u©étúƒé÷SáÁ6`}øå÷_‚òàƒÞ'¡Mn!w^k eÇ_€¦¡Q5m§š‡ð1h_ˆaxZ|™Mö¡m%ÞÇ!}Nhâ/®Æšƒ"ÚG㉪bCþ5•àŒA¦á@½¤Œž-ˆdƒÂ1ùä•BøŽŽVÕ¸”gÎýVqcbwel Aø|p-‰Jk®—ünÀo\ı '¡â™,s¿("í±çqËW©²3mnÍ4ªLÐÎ÷üž´ í4¸DçÊTÇùòì È5ÉàÓ\_5Ÿ`Ï£4Ï¿œ&É]§ 0M#T°Ç®$üO©®6«öÝ}-Ñþ½ï‹÷ßðê øà] NøáAN‘âˆ7.ãAîøäI‘å”gž±IDó­oÙš‡ùI5¿í±Ü5­5÷´«s*úà˜;„²Ø=S 1±víä'T¯½~wìì2D5ÜX=\¯ë»ÚÀ3„²Ë.ë§[…•.xóôæ¬}7HGÙJì$¶:ÚÖN:CÝ-=«–O8ö ¡<¼ÕÅ H!\Dáö™ûißÐìêËèäS˜i¹ewúãßÓü‡ÒÁ-n;ÌZÇ: éÕüfAbÐ ìàäB(/šðrç;¡ ƹº°)|¡ BÂh°oœ¡ãjHƘî`þr‹ ë¨¤» .Än:ÔV B»ªÙ®(VT|ê%Q*<ü‡ü¨¯¹Î'¿ e®r©A†3®º"F²ø¼±yÏ7@ŠþrB=¾ é;âÑNr”§ÆŠ°q{9K_ÕŒFDÒê:D1O°„£>n®$mTÚSvŸ>ËE‹ÌÒqåÈÅ-!óKÚÕ( ÆF‘F #%ÔÉ‹°‘!M<š+ÇõUï4A”"…£5A}(N­] òCƒÉ­Œ-‘•R&h2ÚªV0bL0'òʆxîj9œfÿ>‰-fiXÕü¦ûÂ)N둳œ¾;':E§N„\“ƒëä F°‘’ñþŒ×<½ô&ºB”³¶OM dx«ß©6âÂÔM1‘¦žÉÐD4)Ul0QΈ° øè@ÞxÇîd'ÑáE]¼ž³í‘U*}”K¿”ÇüÑe¥|ô ¯¾‡™í òŸ„œ’P›FŸ©ÈFZ9ª;RBZm“4ê’ž„Ôº5Uœôbû”z¦m ¡ì)¯ÚHªîïEšÕ¢P¸Î…®séZ&:§M)ÍéˆXz×ëèq?(%Ô_ózßòB’š€lÏsÓ›^1r¨¯‚X‘Ú¯Ò·4s-F ; 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"file|f=s"=>\$file, "user|u=s"=>\$user, "pass|p=s"=>\$pass, "id_based|i"=>\$id_based, "count|c"=>\$counts, "drop"=>\$drop, "ptype_id=s"=>\$PROPTYPE_ID, "rtype|r=s"=>\$RTYPE, "verbose|v"=>\$verbose, ); if ($help) { system("perldoc $0"); exit 0; } if ($RTYPE ne 'VIEW' && $RTYPE ne 'TABLE') { die "RTYPE: $RTYPE is not VIEW or TABLE"; } my $dbh; my $DBI = 'DBIx::DBStag'; eval { require "DBIx/DBStag.pm"; msg("Connecting via DBStag"); my $sdbh = DBIx::DBStag->connect($db, $user, $pass); $dbh = $sdbh->dbh; }; if ($@) { # stag not installed - use DBI msg("Connecting via DBI"); $dbh = DBI->connect($db, $user, $pass); } msg("Connected"); $dbh->{RaiseError} = 1; # ============================================================== # GET FEATURE TYPES # ============================================================== # this is only the feature types for which a feature exists within # the particular chado implementation msg("getting ftypes"); my $ftypes = $dbh->selectall_arrayref(q[SELECT DISTINCT cvterm.cvterm_id, cvterm.name FROM feature INNER JOIN cvterm ON (cvterm_id=type_id) ]); # ============================================================== # GET FEATURE PROPERTY TAG NAMES # ============================================================== # featureprops are tag=value pairs; the tags are cvterms msg("getting prop types"); my $ptypes = $dbh->selectall_arrayref("SELECT DISTINCT cvterm.cvterm_id, cvterm.name FROM featureprop INNER JOIN cvterm ON (cvterm_id=$PROPTYPE_ID)"); # ============================================================== # GET FEATURE TYPE TO PROPERTY MAPPING # ============================================================== # some feature types only have some kind of property; # for example, the cvterm 'Ka/Ks' may only apply to exon features # this produces a mapping of feature type => property type # based on internal database surrogate ids msg("getting type to prop mappings"); my $ft2ps = $dbh->selectall_arrayref("SELECT DISTINCT feature.type_id, featureprop.type_id FROM featureprop INNER JOIN feature USING (feature_id)"); # ============================================================== # GET FEATURE RELATIONSHIPS # ============================================================== # by type - for example, (mRNA, gene) (exon, mRNA) msg("getting feature rels"); my $featurerels = $dbh->selectall_arrayref(q[SELECT DISTINCT subjf.type_id, objf.type_id FROM feature_relationship INNER JOIN feature AS subjf ON (subjf.feature_id =subject_id) INNER JOIN feature AS objf ON (objf.feature_id = object_id) ]); # ============================================================== # GET FEATURE TRIPLE RELATIONSHIPS # ============================================================== # for example (exon,mRNA,gene) msg("getting feature triple-rels"); my $featurereltriples = $dbh->selectall_arrayref(q[SELECT DISTINCT f1.type_id, f2.type_id, f3.type_id FROM feature_relationship AS fr1 INNER JOIN feature AS f1 ON (f1.feature_id = fr1.subject_id) INNER JOIN feature AS f2 ON (f2.feature_id = fr1.object_id) INNER JOIN feature_relationship AS fr2 ON (f2.feature_id = fr2.subject_id) INNER JOIN feature AS f3 ON (f3.feature_id = fr2.object_id) ]); # ftypes and ptypes are two columns; id and name # create a lookup table my %typemap = map {$_->[0] => $_->[1]} (@$ftypes, @$ptypes); my %namemap = (); my %abbrev = (); # get all the feature type names and property names my @names = map {$_->[1]} (@$ftypes, @$ptypes); # make them database-safe (remove certain characters) my @safenames = map {safename($_)} @names; my @so_relations = (); msg("generating SO layer...."); print "CREATE SCHEMA so;\n"; print "SET search_path=so,public,pg_catalog;\n\n"; foreach my $type (@$ftypes) { my $tname = $type->[1]; my $vname = $namemap{lc($tname)} || die("nothing for @$type"); my (@cols, @selcols, $sel); my @fcols = qw( feature_id dbxref_id organism_id name uniquename residues seqlen md5checksum type_id is_analysis timeaccessioned timelastmodified ); my @ifcols = qw( feature_id dbxref_id organism_id name uniquename ); my $vfmt = join("\n", "CREATE $RTYPE $vname AS", " SELECT", " feature_id AS $vname"."_id,", # " CAST($vname' AS VARCHAR(64)) AS typestr,", " feature.*", " FROM", " feature %s", " WHERE %s", ); my $from = "INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)"; my $where = "cvterm.name = '$tname'"; my $cmnt = ""; if ($id_based) { $from = ""; $where = "feature.type_id = $type->[0]"; $cmnt = "--- This view is derived from the cvterm database ID.\n". "--- This will be more efficient, but the views MUST be regenerated\n". "--- when the Sequence Ontology in the database changes\n"; } my $vsql = sprintf($vfmt, $from, $where); if ($drop) { print"DROP $RTYPE $vname CASCADE;\n"; } printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". "--- *** Sequence Ontology 'Typed Feature' View ***\n". "--- *** ***\n". "--- ************************************************\n". "---\n". "--- SO Term:\n". "--- \"$tname\"\n". $cmnt. "\n". "$vsql;\n\n", $vname); push(@so_relations, $vname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@ifcols, $vname.'_id') { print "CREATE INDEX $vname"."_idx_$col ON $vname ($col);\n"; } } # PAIRS foreach my $is_consecutive (0, 1) { my $prefix = $is_consecutive ? 'c':''; my $pvname = $prefix.'sib_'.$vname; my $where = $is_consecutive ? " WHERE fr2.rank - fr1.rank = 1\n" : ""; if ($drop) { print"DROP $RTYPE $pvname CASCADE;\n"; } @cols = (); @selcols = map { my $n = $_; map { my $alias = "$_$n"; # if (/(.*)_id/) { # $alias = "$1$n"."_id"; # } push(@cols, $alias); " $vname$n.$_ AS $alias" } @fcols } qw(1 2); $sel = join(",\n", @selcols); my $vname1 = $vname . '1'; my $vname2 = $vname . '2'; printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". "--- *** Sequence Ontology Feature Sibling View ***\n". "--- *** features linked by common container ***\n". "--- ************************************************\n". "---\n". "--- SO Term:\n". "--- \"$tname\"\n". "CREATE $RTYPE $pvname AS\n". " SELECT\n". " fr1.object_id,\n". " fr1.rank AS rank1,\n". " fr2.rank AS rank2,\n". " fr2.rank - fr1.rank AS rankdiff,\n". "$sel\n". " FROM\n". " $vname AS $vname1 INNER JOIN\n". " feature_relationship AS fr1 ON ($vname1.$vname"."_id = fr1.subject_id)\n". " INNER JOIN\n". " feature_relationship AS fr2 ON (fr2.object_id = fr1.object_id)\n". " INNER JOIN\n". " $vname AS $vname2 ON ($vname1.$vname"."_id = fr2.subject_id)\n". $where. ";\n\n", $pvname); push(@so_relations, $pvname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@cols, 'rankdiff') { print "CREATE INDEX $pvname"."_idx_$col ON $pvname ($col);\n"; } } # INVERSE PAIRS $pvname = $prefix . $vname . '_invsib'; if ($drop) { print"DROP $RTYPE $pvname CASCADE;\n"; } @cols = (); @selcols = map { my $n = $_; map { my $alias = "$_$n"; # if (/(.*)_id/) { # $alias = "$1$n"."_id"; # } push(@cols, $alias); " $vname$n.$_ AS $alias" } @fcols } qw(1 2); $sel = join(",\n", @selcols); $vname1 = $vname . '1'; $vname2 = $vname . '2'; printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". "--- *** Sequence Ontology Feature Inverse Pair ***\n". "--- *** features linked by common contained ***\n". "--- *** child feature ***\n". "--- ************************************************\n". "---\n". "--- SO Term:\n". "--- \"$tname\"\n". "CREATE $RTYPE $pvname AS\n". " SELECT\n". " fr1.subject_id,\n". " fr1.rank AS rank1,\n". " fr2.rank AS rank2,\n". " fr2.rank - fr1.rank AS rankdiff,\n". "$sel\n". " FROM\n". " $vname AS $vname1 INNER JOIN\n". " feature_relationship AS fr1 ON ($vname1.$vname"."_id = fr1.object_id)\n". " INNER JOIN\n". " feature_relationship AS fr2 ON (fr2.subject_id = fr1.subject_id)\n". " INNER JOIN\n". " $vname AS $vname2 ON ($vname1.$vname"."_id = fr2.object_id);\n". "\n\n", $pvname); push(@so_relations, $pvname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@cols) { print "CREATE INDEX $pvname"."_idx_$col ON $pvname ($col);\n"; } } } } msg("generating feature rels"); # FEATURE RELATIONSHIPS foreach my $fr (@$featurerels) { my ($stid, $otid) = @$fr; msg("SubObj type_ids: $stid $otid"); my $st1 = $typemap{$stid} || die "no type for $stid"; my $ot1 = $typemap{$otid} || die "no type for $otid"; my $st = $namemap{lc($st1)} || die "no namemap for $st1"; my $ot = $namemap{lc($ot1)} || die "no namemap for $ot1"; my $vname = $ot."2".$st; my @cols = ( 'feature_relationship_id', $st.'_id', $ot.'_id', 'subject_id', 'object_id' ); my $vsql = join("\n", "CREATE $RTYPE $vname AS", " SELECT", " feature_relationship_id,", " subject_id AS $st"."_id,", " object_id AS $ot"."_id,", " subject_id,", " object_id,", " feature_relationship.type_id", " FROM", " $st INNER JOIN feature_relationship ON ($st.feature_id = subject_id)", " INNER JOIN $ot ON ($ot.feature_id = object_id)", ); if ($drop) { print"DROP $RTYPE $vname CASCADE;\n"; } printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". "--- *** Sequence Ontology PART-OF view ***\n". "--- ************************************************\n". "---\n". "--- Subject Type: $st\n". "--- Object Type: $ot\n". "--- Predicate: PART-OF\n". "\n". "$vsql;\n\n", $vname); push(@so_relations, $vname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@cols) { print "CREATE INDEX $vname"."_idx_$col ON $vname ($col);\n"; } } } # FEATURE RELATIONSHIP TRIPLES foreach my $fr (@$featurereltriples) { my ($tid1, $tid2, $tid3) = @$fr; my $t1x = $typemap{$tid1} || die "no type for $tid1"; my $t2x = $typemap{$tid2} || die "no type for $tid2"; my $t3x = $typemap{$tid3} || die "no type for $tid3"; my $t1 = $namemap{lc($t1x)} || die "no namemap for $t1x"; my $t2 = $namemap{lc($t2x)} || die "no namemap for $t2x"; my $t3 = $namemap{lc($t3x)} || die "no namemap for $t3x"; my $vname = $t3."2".$t2."2".$t1; my @cols = ( $t1.'_id', $t2.'_id', $t3.'_id', ); my $vsql = join("\n", "CREATE $RTYPE $vname AS", " SELECT", " $t1.feature_id AS $t1"."_id,", " $t2.feature_id AS $t2"."_id,", " $t3.feature_id AS $t3"."_id,", " fr1.type_id AS fr1_type_id,", " fr2.type_id AS fr2_type_id", " FROM", " $t1 INNER JOIN feature_relationship AS fr1 ON ($t1.feature_id = fr1.subject_id)", " INNER JOIN $t2 ON ($t2.feature_id = fr1.object_id)", " INNER JOIN feature_relationship AS fr2 ON ($t2.feature_id = fr2.subject_id)", " INNER JOIN $t3 ON ($t3.feature_id = fr2.object_id)", ); if ($drop) { print"DROP $RTYPE $vname CASCADE;\n"; } printf("--- ************************************************\n". "--- *** relation: %-31s***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". "--- *** Sequence Ontology TRIPLE-REL view ***\n". "--- ************************************************\n". "---\n". "\n". "$vsql;\n\n", $vname); push(@so_relations, $vname); if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@cols) { print "CREATE INDEX $vname"."_idx_$col ON $vname ($col);\n"; } } } $dbh->disconnect; print "\n\nSET search_path = public,pg_catalog;\n"; print STDERR "Done!\n"; exit 0; sub msg { return unless $verbose; print STDERR "@_\n"; } # ============================================================== # safename(string): returns string # ============================================================== # makes a name db-safe; also adds the mapping # from the original name to safe name in the global lookup %namemap sub safename { my $orig = shift; my $n = lc($orig); my @parts = (); @parts = split(/_/, $n); @parts = map {$abbrev{$_} || $_} @parts; if (length("@parts") > MAX_RELATION_NAME_LEN) { @parts = split(/_/, $n); my $part_i = 0; while (length("@parts") > MAX_RELATION_NAME_LEN) { if ($part_i > @parts) { die "cannot shorten $orig [got $n]"; } my $part = $parts[$part_i]; my $ab = substr($part, 0, 1); $abbrev{$part} = $ab; $parts[$part_i] = $ab; # print " FROM: $part => $ab\n"; $part_i++; } } $n = ''; while (my $part = shift @parts) { $n .= $part; if (@parts && (length($part) > 1 || length($parts[0]) > 1)) { $n.= '_'; } } # print "NAMEMAP: $orig -> $n\n"; $namemap{lc($orig)} = $n; } __END__ =head1 NAME create-so-layer.pl =head1 SYNPOSIS create-so-layer.pl -d 'dbi:Pg:dbname=chado;hostname=mypghost.foo.org' =head1 ARGUMENTS =over =item -d DBI-LOCATOR Database to use as source (does not actually write to database) =item -i use internal surrogate database IDs (layer will be NON-PORTABLE) =item -r|rtype RELATION-TYPE RELATION-TYPE must be either TABLE or VIEW; the default is VIEW This determines whether the layer consists of materialized views (ie TABLEs), or views =item -d|drop If this is specified, then DROP VIEW/TABLE statements will be created this is useful if you wish to REPLACE an existing SO layer =back =head1 DESCRIPTION Chado is a modular database for bioinformatics. The chado sequence module is generic and has no built-in type system for sequence feature data. Instead it relies on an external ontology to provide semantics for feature types. The canonical ontology for sequence features in the Sequence Ontology (ref). Chado has a module specifically for housing ontologies. The combination of SO plus Chado gives a rigorous yet flexible hybrid relational-ontology model for storing and querying genomic and proteomic data. One negative impact of this hybrid model is that apparently simple queries are hard to express, and may be inefficient. For example, an SQL select to get the gene count in the database requires joining two relations (ie tables), instead of one relation (as expected in a database in which types are encoded relationally, such as ensembl). To fetch mRNAs with exons attached requires a 5 relation join. Even more joins must be introduced if we wish to perform the transitive closure over types (for example, a query for transcripts should return features directly typed to transcript, as well as to subtypes, such as mRNA, tRNA, etc). One solution is to deal with typing issues in the middleware; however, a solution which allows a user to make ad-hoc queries regarding typed features in the databae is still required. We propose a solution to this problem - a chado Sequence Ontology extension layer. This layer provides relations for all commonly used sequence ontology types (for example, gene, exon, transposable_element, intron, ...). These relations can be queried as if they are any other relation in the database; for example: SELECT count(*) FROM gene; SELECT * FROM mrna WHERE name like 'CR400%'; Other relations are also provided which represent instantiation Sequence Ontology part_of and develops_from relationships. For example, SO contains the relationship "transcript part_of gene", so we would expect to find instantiations of this relationship in a chado database. We create "virtual linking relations" for all these, for example: gene2transcript -- gene to *any* transcript feature gene2mrna -- gene to mRNA feature specifically mrna2exon trna2exon mrna2protein [polypeptide??] gene2mrna2exon This allows a more natural way of expressing queries, for example over gene models; compare: SELECT * FROM gene2mrna NATURAL JOIN mrna2exon NATURAL JOIN mrna2protein NATURALJOIN gene NATURAL JOIN mrna NATURAL JOIN exon NATURAL JOIN protein with: [equivalent direct chado SQL query without SO layer] In addition, we provide relations for other more complex and transitive relationship types in SO Transitive relationship types: [TODO] All relationship types in SO are transitive; for example, transcript is proper part of gene, exon is proper part of transcripts; therefore exon is transitively part of gene. Again, virtual linking tables can be generated from a chado instance; so far we generate gene2exon gene2protein Currently these are the only transitive non-isa chains in SO (TODO - karen check..) We also provide transitive linking tables that explicitly include the full path: gene2transcript2exon gene2mrna2exon gene2trna2exon gene2ncrna2exon Other relationship chains: [THE FOLLOWING TWO FORMS ARE JUST SQLization OF KAREN'S IDEAS ON MEREONOMY WITH SO; check with karen re the names "sibling pairs" "parent pairs"] Sibling pairs Sibling pairs are features of any type related by a common parent; for example, exons that share the same transcript container. We create virtual linking tables for these; for example exon_pair transcript_pair protein_pair Consecutive Sibling pairs [TODO] These are sibling pairs when the siblings are explicitly consecutive; this is provided by the feature_relationship.rank table in chado Parent pairs: An parent pair is two features with a child/contained feature in common. For example, two mRNAs that produce the same protein; two transcripts that contain the same exon (note that this is almost always when the transcripts are siblings-by-parent-genes; but a parent pair allows the user to see by which exons the transcripts are related) transcript_invpair protein_invpair PROPERTIES [TODO] features can have any number of property name=value pairs attached to them in chado. The name of the property comes from a controlled vocabulary of sequence feature properties. Eventually the canonical list of properties will be regulated by SO, for now they live in chado as an external ontology. Again, because the featureprop table has a foreign key to the primary surrogate key in the cvterm table, some queries can be awkward to express and involve many joins. To get round this, the SO layer also provides views for common properties; here we have a cross-product between relations, but not all relations have all properties; for example, only exons and predicted exons have the property KaKs feature_foo gene_foo feature_kaks exon_kaks IMPLEMENTATION ============== LAYER TYPE ---------- The SO layer is generated directly from a chado database instance. Perl scripts query the database and the SO OBO file. The implementations are possible: 1. Portable SO View layer These views are portable and can be applied to any instance of chado. They work by joining on the name of the SO type; if SO names change, then this layer will have to be rebuilt. The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature INNER JOIN cvterm ON (feature.type_id=cvterm.cvterm_id) WHERE cvterm.name = 'foo'; [this is for basic features only] 2. Non-portable SO View layer These views are constructed from the surrogate primary key of the sequence ontology term in chado (cvterm.cvterm_id). Surrogate primary keys are not portable between database instantiations; surrogate keys should never be exposed outside the database. This layer becomes obsolete if the sequence ontology is ever reloaded (because the surrogate keys are not guaranteed to be preserved between loads). We provide triggers that removes a SO view if the underlying ontology term in the database is updated or deleted [TODO]. This layer is faster and more efficient than the non-portable layer (because it is not actually necessary to join to the cvterm table) The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (where 1234 is the surrogate primary key of type 'foo' in the cvterm relation) The extra speed of this layer comes at the price of less update flexibility 3. Materialized View (Table) layer This is the fastest yet most update-restrictive way to construct the layer. Each SO type gets a table rather than a view. This is the fastest; for example, when fetching genes, the database engine knows to only look in one single (smaller) table rather than filtering out the gene type from the (possibly enormous) feature table. The table is constructed like this: CREATE TABLE foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (plus indexing SQL statements) This layer is only practical if chado is used in "data-warehouse" mode; modification of the underlying feature data renders the materialized views stale. One possibility is automatically rebuilding the materialized view when the underlying feature table changes; however, this could lead to extremely slow updates IMPLICIT TYPES -------------- Not all types are instantiated within a chado database; for example, there are no intron or UTR features as these are derivable from other features. Nevertheless it can be useful to perform queries on derivable types as if they were actually present. [this is all TODO] These types are derived using type-specific rules. For example, an intron rules can be stated in SQL as derived from exon sibling pairs (cv above) [[EXAMPLE SQL]] [[SKOLEM FUNCTIONS]] Again, implicit types can be implemented as portable or non-portable views, or as materialized views (tables). Implicit types intron utr3 utr5 splice_site dicistronic_gene protein_coding_gene [currently implicit in chado via transcript type] exon5prime exon3prime coding_exon partially_coding_exon intergenic_region [HARD] discuss - expressing these rules in SQL vs expressing in some other delcarative language (first order predicate logic; KIF; Prolog/horn clauses) then translating automatically to SQL. ========== DISCUSSION ========== Selection of which of the 3 implementation strategies to use is purely a DB admin decision. The person constructing the SQL queries need not know or care (other than perhaps to be aware for efficiency reasons) how the layer is implemented - as far as they are concerned they have relations such as gene, transcript, variation etc that act just like normal tables when queried (but not updated - discuss updates on views) The view layer is not necessarily limited to chado databases - any relational database implemented with a DBMS that allows views (currently any DBMS other than mysql) is fair game. For example, one could take a postgres or oracle instantiation of ensembl and write a SO layer generator. Note that ensembl already has a relationally-expressed notion of entities such as gene, exon etc. One way round that is to keep the SO layer seperate in the db; eg through postgresql SCHEMAs. This points the way forward to a unified standard for querying genomic databases; whilst adoption of standards for genomic relational databases is a fraught issue at best (different groups and projects prefer their own schemas for good reasons), we can see the need for there being a common user-query layer, based on a standard of feature types (ie SO). [discussion of difficulties with doing apparently simple (and complex) queries on existing relational databases] =cut chado-1.23/modules/sequence/apollo-bridge/ad_hoc_cv000644 000765 000024 00000001467 11256710122 022427 0ustar00cainstaff000000 000000 [pub type] computer file curator publication Book DNA/RNA sequence record abstract archive automatic genome annotation bibliographic list biography book book review booklet conference report curated genome annotation demonstration editorial erratum film interview jigsaw puzzle letter meeting report microfiche microscope slides news article note obituary other patent personal communication poem press release protein sequence record recording retraction review slides spoof stock list supplementary material tactile diagram teaching note thesis unpublished video paper journal null pub submitted [pub relationship type] also_in corrects makes_obsolete published_in [pubprop type] abbreviation abstract abstract_languages cam_offprint comment errata erratum internalnotes languages series_abbrev [apollo] suffix prefix chado-1.23/modules/sequence/apollo-bridge/apollo-triggers.plpgsql000644 000765 000024 00000141114 11256710122 025307 0ustar00cainstaff000000 000000 -- these are nearly identical to the triggers that flybase uses, but will -- serve as the foundation of general triggers for GMOD. Things that need to -- be done: -- --* indentify the items that have to be dynamically (at make time) extrapolated. --* allow a more flexible naming scheme --* remove the portion creating a flybase dbxref. --* probably 20 more things I haven't thought of yet. --gets the next available uniquename; note that it is --destructive because it calls nextval on a sequence CREATE OR REPLACE FUNCTION next_uniquename() RETURNS varchar AS ' DECLARE prename varchar; f_uniquename varchar; prefix varchar; suffix varchar; id varchar; maxid int; BEGIN SELECT INTO prefix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''prefix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO suffix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''suffix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO maxid nextval(''uniquename_id_generator''); RAISE NOTICE ''maxid is:%'', maxid; id:=lpad(maxid, 6, ''000000''); f_uniquename:=CAST(prefix||id||suffix as VARCHAR); RETURN f_uniquename; END; 'LANGUAGE plpgsql; DROP TRIGGER tr_feature_del ON feature; CREATE OR REPLACE function fn_feature_del() RETURNS TRIGGER AS ' DECLARE f_type cvterm.name%TYPE; f_id_gene feature.feature_id%TYPE; f_id_transcript feature.feature_id%TYPE; f_id_exon feature.feature_id%TYPE; f_id_exon_temp feature.feature_id%TYPE; f_id_protein feature.feature_id%TYPE; f_id_allele feature.feature_id%TYPE; fr_object_id feature.feature_id%TYPE; f_type_gene CONSTANT varchar :=''gene''; f_type_exon CONSTANT varchar :=''exon''; f_type_transcript CONSTANT varchar :=''mRNA''; f_type_snoRNA CONSTANT varchar :=''snoRNA''; f_type_ncRNA CONSTANT varchar :=''ncRNA''; f_type_snRNA CONSTANT varchar :=''snRNA''; f_type_tRNA CONSTANT varchar :=''tRNA''; f_type_rRNA CONSTANT varchar :=''rRNA''; f_type_promoter CONSTANT varchar :=''promoter''; f_type_repeat_region CONSTANT varchar :=''repeat_region''; f_type_miRNA CONSTANT varchar :=''miRNA''; f_type_transposable_element CONSTANT varchar :=''transposable_element''; f_type_pseudo CONSTANT varchar :=''pseudogene''; f_type_protein CONSTANT varchar :=''polypeptide''; f_type_allele CONSTANT varchar :=''alleleof''; f_return feature.feature_id%TYPE; f_row feature%ROWTYPE; fr_row_transcript feature_relationship%ROWTYPE; fr_row_exon feature_relationship%ROWTYPE; fr_row_protein feature_relationship%ROWTYPE; message varchar(255); BEGIN RAISE NOTICE ''enter f_d, feature uniquename:%, type_id:%'',OLD.uniquename, OLD.type_id; f_return:=OLD.feature_id; SELECT INTO f_type c.name from feature f, cvterm c where f.feature_id=OLD.feature_id and f.type_id=c.cvterm_id; IF f_type=f_type_gene THEN SELECT INTO f_id_allele fr.subject_id from feature_relationship fr, cvterm c where (fr.object_id=OLD.feature_id or fr.subject_id=OLD.feature_id) and fr.type_id=c.cvterm_id and c.name=f_type_allele; IF NOT FOUND THEN FOR fr_row_transcript IN SELECT * from feature_relationship fr where fr.object_id=OLD.feature_id LOOP SELECT INTO f_id_transcript f.feature_id from feature f, cvterm c where f.feature_id=fr_row_transcript.subject_id and f.type_id=c.cvterm_id and (c.name=f_type_transcript or c.name=f_type_ncRNA or c.name=f_type_snoRNA or c.name=f_type_snRNA or c.name=f_type_tRNA or c.name=f_type_rRNA or c.name=f_type_pseudo or c.name=f_type_miRNA or c.name=f_type_transposable_element or c.name=f_type_promoter or c.name=f_type_repeat_region); SELECT INTO f_id_gene f.feature_id from feature f, feature_relationship fr, cvterm c where f.feature_id=fr.object_id and fr.subject_id=f_id_transcript and f.type_id=c.cvterm_id and c.name=f_type_gene and f.feature_id !=OLD.feature_id; IF f_id_gene IS NULL and f_id_transcript IS NOT NULL THEN RAISE NOTICE ''delete lonely transcript:%'', f_id_transcript; message:=CAST(''delete lonely transcript''||f_id_transcript AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', f_id_transcript); delete from feature where feature_id=f_id_transcript; ELSIF f_id_gene IS NOT NULL AND F_id_transcript IS NOT NULL THEN RAISE NOTICE ''There is another gene:% associated with this transcript:%, so this transcript will be kept'',f_id_gene, f_id_transcript; message:=CAST(''There is another gene:''||f_id_gene||'' associated with this transcript:''||f_id_transcript AS TEXT); END IF; END LOOP; message:=CAST(''delete gene:''||OLD.feature_id AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', OLD.feature_id); ELSE RAISE NOTICE ''there is other allele associated with this gene:%'', f_id_allele; message:=CAST(''There is other allele associated with this gene:''||f_id_allele AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', f_id_transcript); return NULL; END IF; ELSIF (f_type=f_type_transcript or f_type=f_type_ncRNA or f_type=f_type_snoRNA or f_type=f_type_snRNA or f_type=f_type_tRNA or f_type=f_type_rRNA or f_type=f_type_pseudo or f_type=f_type_miRNA or f_type=f_type_transposable_element or f_type=f_type_promoter or f_type=f_type_repeat_region) THEN FOR fr_row_exon IN SELECT * from feature_relationship fr where fr.object_id=OLD.feature_id LOOP select INTO f_id_exon f.feature_id from feature f, cvterm c where f.feature_id=fr_row_exon.subject_id and f.type_id=c.cvterm_id and c.name=f_type_exon; SELECT INTO f_id_transcript f.feature_id from feature f, feature_relationship fr, cvterm c where f.feature_id=fr.object_id and fr.subject_id=f_id_exon and f.type_id=c.cvterm_id and (c.name=f_type_transcript or c.name=f_type_ncRNA or c.name=f_type_snoRNA or c.name=f_type_snRNA or c.name=f_type_tRNA or c.name=f_type_rRNA or c.name=f_type_pseudo or c.name=f_type_miRNA or c.name=f_type_transposable_element or c.name=f_type_promoter or c.name=f_type_repeat_region) and f.feature_id!=OLD.feature_id; IF f_id_transcript IS NULL and f_id_exon IS NOT NULL THEN RAISE NOTICE ''delete lonely exon:%'', f_id_exon; delete from feature where feature_id=f_id_exon; message:=CAST(''delete lonely exon:''||f_id_exon AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', f_id_exon); ELSIF f_id_transcript IS NOT NULL and f_id_exon IS NOT NULL THEN RAISE NOTICE ''There is another transcript:% associated with this exon:%, so this exon will be kept'', f_id_transcript, f_id_exon; message:=CAST(''There is another transcript:''||f_id_transcript||'' associated with this exon:''||f_id_exon AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', f_id_exon); END IF; END LOOP; FOR fr_row_protein IN SELECT * from feature_relationship fr where fr.object_id=OLD.feature_id LOOP SELECT INTO f_id_protein f.feature_id from feature f, cvterm c where f.feature_id=fr_row_protein.subject_id and f.type_id=c.cvterm_id and c.name=f_type_protein; SELECT INTO f_id_transcript f.feature_id from feature f, feature_relationship fr, cvterm c where f.feature_id=fr.object_id and fr.subject_id=f_id_protein and f.type_id=c.cvterm_id and (c.name=f_type_transcript or c.name=f_type_ncRNA or c.name=f_type_snoRNA or c.name=f_type_snRNA or c.name=f_type_tRNA or c.name=f_type_rRNA or c.name=f_type_pseudo or c.name=f_type_miRNA or c.name=f_type_transposable_element or c.name=f_type_promoter or c.name=f_type_repeat_region) and f.feature_id !=OLD.feature_id; IF f_id_transcript IS NULL and f_id_protein IS NOT NULL THEN RAISE NOTICE ''delete lonely polypeptide:%'', f_id_protein; delete from feature where feature_id=f_id_protein; message:=CAST(''delete lonely polypeptide:''||f_id_protein AS TEXT); insert into trigger_log(value, table_name, id) values(message, ''feature'', f_id_protein); ELSIF f_id_transcript IS NOT NULL and f_id_protein IS NOT NULL THEN RAISE NOTICE ''There is another transcript:% associated with this polypeptide:%, so this exon will be kept'', f_id_transcript, f_id_protein; END IF; END LOOP; END IF; RAISE NOTICE ''leave f_d ....''; RETURN OLD; END; 'LANGUAGE 'plpgsql'; GRANT ALL ON FUNCTION fn_feature_del() TO PUBLIC; CREATE TRIGGER tr_feature_del BEFORE DELETE ON feature for EACH ROW EXECUTE PROCEDURE fn_feature_del(); DROP TRIGGER feature_assignname_tr_i ON feature; CREATE OR REPLACE FUNCTION feature_assignname_fn_i() RETURNS TRIGGER AS ' DECLARE maxid int; pos int; id varchar(255); max_id int; is_anal feature.is_analysis%TYPE; prefix cvtermprop.value%TYPE; suffix cvtermprop.value%TYPE; f_row_g feature%ROWTYPE; f_row_e feature%ROWTYPE; f_row_t feature%ROWTYPE; f_row_p feature%ROWTYPE; f_type cvterm.name%TYPE; f_type_id cvterm.cvterm_id%TYPE; letter_t varchar; letter_p varchar; f_uniquename_temp feature.uniquename%TYPE; f_uniquename feature.uniquename%TYPE; f_uniquename_tr feature.uniquename%TYPE; f_uniquename_exon feature.uniquename%TYPE; f_uniquename_protein feature.uniquename%TYPE; f_name feature.name%TYPE; s_type_id synonym.type_id%TYPE; s_id synonym.synonym_id%TYPE; c_cv_id cv.cv_id%TYPE; f_s_id feature_synonym.feature_synonym_id%TYPE; fr_row feature_relationship%ROWTYPE; f_type_gene CONSTANT varchar :=''gene''; f_type_exon CONSTANT varchar :=''exon''; f_type_transcript CONSTANT varchar :=''mRNA''; f_type_snoRNA CONSTANT varchar :=''snoRNA''; f_type_ncRNA CONSTANT varchar :=''ncRNA''; f_type_snRNA CONSTANT varchar :=''snRNA''; f_type_tRNA CONSTANT varchar :=''tRNA''; f_type_rRNA CONSTANT varchar :=''rRNA''; f_type_promoter CONSTANT varchar :=''promoter''; f_type_repeat_region CONSTANT varchar :=''repeat_region''; f_type_miRNA CONSTANT varchar :=''miRNA''; f_type_transposable_element CONSTANT varchar :=''transposable_element''; f_type_pseudo CONSTANT varchar :=''pseudogene''; f_type_protein CONSTANT varchar :=''polypeptide''; f_type_allele CONSTANT varchar :=''alleleof''; f_type_remark CONSTANT varchar :=''remark''; f_dbname_gadfly CONSTANT varchar :=''DB:GR''; f_dbname_FB CONSTANT varchar :=''null''; o_genus CONSTANT varchar :=''Oryza''; o_species CONSTANT varchar:=''sativa''; c_name_synonym CONSTANT varchar:=''synonym''; cv_cvname_synonym CONSTANT varchar:=''null''; p_miniref CONSTANT varchar:=''none''; p_id pub.pub_id%TYPE; BEGIN SELECT INTO is_anal is_analysis FROM feature WHERE uniquename = NEW.uniquename and type_id = NEW.type_id and organism_id = NEW.organism_id; IF (is_anal) THEN RETURN NEW; END IF; SELECT INTO prefix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''prefix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO suffix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''suffix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO f_type c.name from feature f, cvterm c where f.type_id=c.cvterm_id and f.uniquename=NEW.uniquename and f.organism_id =NEW.organism_id; SELECT INTO p_id pub_id from pub where uniquename = p_miniref; SELECT INTO s_type_id cvterm_id from cvterm c1, cv c2 where c1.name=c_name_synonym and c2.name=cv_cvname_synonym and c1.cv_id=c2.cv_id; RAISE NOTICE ''assigning names, prefix:%, suffix:%, type:%, current uniquename:%'',prefix,suffix,f_type,NEW.uniquename; IF (NEW.uniquename like prefix||''%:temp%''||suffix OR NEW.uniquename like prefix||''%-temp%'') THEN SELECT INTO f_type c.name from feature f, cvterm c where f.type_id=c.cvterm_id and f.uniquename=NEW.uniquename and f.organism_id =NEW.organism_id; --SELECT INTO p_id pub_id from pub where uniquename = p_miniref; --SELECT INTO s_type_id cvterm_id from cvterm c1, cv c2 where c1.name=c_name_synonym and c2.name=cv_cvname_synonym and c1.cv_id=c2.cv_id; SELECT INTO f_uniquename * FROM next_uniquename(); SELECT INTO f_row_g * from feature where uniquename=NEW.uniquename and organism_id=NEW.organism_id; IF f_type = f_type_gene THEN IF NEW.name like ''%temp%'' or NEW.name IS NULL THEN f_name = f_uniquename; UPDATE feature set uniquename=f_uniquename, name=f_uniquename where feature_id=f_row_g.feature_id; ELSE f_name = f_row_g.name; UPDATE feature set uniquename=f_uniquename where feature_id=f_row_g.feature_id; END IF; ELSIF (f_type=f_type_transcript or f_type=f_type_ncRNA or f_type=f_type_snoRNA or f_type=f_type_snRNA or f_type=f_type_tRNA or f_type=f_type_rRNA or f_type=f_type_pseudo or f_type=f_type_miRNA or f_type=f_type_protein or f_type=f_type_exon) THEN IF NEW.name like ''%temp%'' or NEW.name IS NULL THEN f_name = null; ELSE f_name = f_row_g.name; END IF; UPDATE feature set uniquename=f_uniquename,name=f_name where feature_id=f_row_g.feature_id; ELSIF ( f_type=f_type_transposable_element or f_type=f_type_promoter or f_type=f_type_repeat_region or f_type=f_type_remark ) THEN IF NEW.name like ''%temp%'' or NEW.name IS NULL THEN f_name := CAST(f_uniquename||''-''||f_type AS TEXT); UPDATE feature set uniquename=f_uniquename, name=f_uniquename where feature_id=f_row_g.feature_id; ELSE f_name = f_row_g.name; UPDATE feature set uniquename=f_uniquename, name=f_name where feature_id=f_row_g.feature_id; END IF; END IF; RAISE NOTICE ''new uniquename of this feature is:%'', f_uniquename; --insert into synonym, feature_synonym SELECT INTO s_id synonym_id from synonym where name=f_uniquename and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(f_uniquename, f_uniquename, s_type_id); SELECT INTO s_id synonym_id from synonym where name=f_uniquename and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row_g.feature_id and synonym_id=s_id and pub_id=p_id; IF f_s_id IS NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row_g.feature_id, s_id, p_id, ''true''); END IF; RAISE NOTICE ''feature_id:%, synonym_id:% for uniquename'', f_row_g.feature_id, s_id; IF f_name IS NOT NULL THEN SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(f_name, f_name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row_g.feature_id and synonym_id=s_id and pub_id=p_id; IF f_s_id IS NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row_g.feature_id, s_id, p_id, ''true''); END IF; RAISE NOTICE ''feature_id:%, synonym_id:% for name'', f_row_g.feature_id, s_id; END IF; END IF; --ends if uniquename like temp return NEW; END; 'LANGUAGE plpgsql; GRANT ALL ON FUNCTION feature_assignname_fn_i() TO PUBLIC; CREATE TRIGGER feature_assignname_tr_i AFTER INSERT ON feature for EACH ROW EXECUTE PROCEDURE feature_assignname_fn_i(); DROP TRIGGER feature_relationship_tr_d ON feature_relationship; CREATE OR REPLACE FUNCTION feature_relationship_fn_d() RETURNS TRIGGER AS ' DECLARE maxid int; id varchar(255); loginfo varchar(255); len int; f_row_g feature%ROWTYPE; f_row_e feature%ROWTYPE; f_row_t feature%ROWTYPE; f_row_p feature%ROWTYPE; f_type cvterm.name%TYPE; f_type_temp cvterm.name%TYPE; letter_e varchar(100); letter_t varchar(100); letter_p varchar(100); f_uniquename_gene feature.uniquename%TYPE; f_uniquename_transcript feature.uniquename%TYPE; f_uniquename_exon feature.uniquename%TYPE; f_uniquename_protein feature.uniquename%TYPE; f_d_id feature_dbxref.feature_dbxref_id%TYPE; d_id dbxref.dbxref_id%TYPE; s_type_id synonym.type_id%TYPE; s_id synonym.synonym_id%TYPE; p_id pub.pub_id%TYPE; fr_row feature_relationship%ROWTYPE; f_accession_temp varchar(255); f_accession varchar(255); f_type_gene CONSTANT varchar :=''gene''; f_type_exon CONSTANT varchar :=''exon''; f_type_transcript CONSTANT varchar :=''mRNA''; f_type_snoRNA CONSTANT varchar :=''snoRNA''; f_type_ncRNA CONSTANT varchar :=''ncRNA''; f_type_snRNA CONSTANT varchar :=''snRNA''; f_type_tRNA CONSTANT varchar :=''tRNA''; f_type_rRNA CONSTANT varchar :=''rRNA''; f_type_promoter CONSTANT varchar :=''promoter''; f_type_repeat_region CONSTANT varchar :=''repeat_region''; f_type_miRNA CONSTANT varchar :=''miRNA''; f_type_transposable_element CONSTANT varchar :=''transposable_element''; f_type_pseudo CONSTANT varchar :=''pseudogene''; f_type_protein CONSTANT varchar :=''polypeptide''; f_type_allele CONSTANT varchar :=''alleleof''; f_dbname_gadfly CONSTANT varchar :=''Gadfly''; f_dbname_FB CONSTANT varchar :=''FlyBase''; c_name_synonym CONSTANT varchar:=''synonym''; cv_cvname_synonym CONSTANT varchar:=''synonym type''; p_miniref CONSTANT varchar:=''none''; BEGIN RAISE NOTICE ''enter fr_d, fr.object_id:%, fr.subject_id:%'', OLD.object_id, OLD.subject_id; SELECT INTO f_type name from cvterm where cvterm_id=OLD.type_id; IF f_type=f_type_allele THEN RAISE NOTICE ''delete relationship beteen gene:% and allele:%'', OLD.object_id, OLD.subject_id; ELSE SELECT INTO f_type c.name from feature f, cvterm c where f.type_id=c.cvterm_id and f.feature_id=OLD.object_id; IF f_type=f_type_gene THEN SELECT INTO f_type_temp c.name from feature f, cvterm c where f.feature_id=OLD.subject_id and f.type_id=c.cvterm_id; IF (f_type_temp=f_type_transcript or f_type_temp=f_type_ncRNA or f_type_temp=f_type_snoRNA or f_type_temp=f_type_snRNA or f_type_temp=f_type_tRNA or f_type_temp=f_type_rRNA or f_type_temp=f_type_miRNA or f_type_temp=f_type_pseudo or f_type_temp=f_type_transposable_element or f_type_temp=f_type_promoter or f_type_temp=f_type_repeat_region ) THEN SELECT INTO fr_row * from feature_relationship where object_id<>OLD.object_id and subject_id=OLD.subject_id; IF fr_row.object_id IS NULL THEN RAISE NOTICE ''delete this lonely transcript:%'', OLD.subject_id; delete from feature where feature_id=OLD.subject_id; END IF; ELSE RAISE NOTICE ''wrong feature_relationship: gene->NO_transcript:object_id:%, subject_id:%'', OLD.object_id, OLD.subject_id; END IF; ELSIF (f_type=f_type_transcript or f_type=f_type_snoRNA or f_type=f_type_ncRNA or f_type=f_type_snRNA or f_type=f_type_tRNA or f_type=f_type_miRNA or f_type=f_type_rRNA or f_type=f_type_pseudo or f_type=f_type_transposable_element or f_type=f_type_promoter or f_type=f_type_repeat_region) THEN SELECT INTO f_type_temp c.name from feature f, cvterm c where f.feature_id=OLD.subject_id and f.type_id=c.cvterm_id; IF f_type_temp=f_type_protein or f_type_temp=f_type_exon THEN SELECT INTO fr_row * from feature_relationship where subject_id=OLD.subject_id and object_id<>OLD.object_id; IF fr_row.object_id IS NULL THEN RAISE NOTICE ''delete this lonely exon/polypeptide:%'', OLD.subject_id; delete from feature where feature_id=OLD.subject_id; END IF; ELSE RAISE NOTICE ''wrong relationship: transcript->NO_polypeptide/exon: objfeature:%, subjfeature:%'',OLD.object_id, OLD.subject_id; END IF; END IF; END IF; RAISE NOTICE ''leave fr_d ....''; RETURN OLD; END; 'LANGUAGE plpgsql; GRANT ALL ON FUNCTION feature_relationship_fn_d() TO PUBLIC; CREATE TRIGGER feature_relationship_tr_d BEFORE DELETE ON feature_relationship for EACH ROW EXECUTE PROCEDURE feature_relationship_fn_d(); DROP TABLE trigger_log; CREATE TABLE trigger_log( value varchar(255) not null, timeaccessioned timestamp not null default current_timestamp, table_name varchar(50), id int ); GRANT ALL ON TABLE trigger_log TO PUBLIC; DROP TRIGGER feature_relationship_propagatename_tr_i ON feature_relationship; CREATE OR REPLACE FUNCTION feature_relationship_propagatename_fn_i() RETURNS TRIGGER AS ' DECLARE maxid int; exon_id int; id varchar(255); maxid_fb int; id_fb varchar(255); loginfo varchar(255); len int; prefix varchar; suffix varchar; f_row_g feature%ROWTYPE; f_row_e feature%ROWTYPE; f_row_t feature%ROWTYPE; f_row_p feature%ROWTYPE; fl_row_e featureloc%ROWTYPE; f_type cvterm.name%TYPE; f_type_temp cvterm.name%TYPE; letter_t varchar(100); letter_p varchar(100); f_dbxref_id feature.dbxref_id%TYPE; fb_accession dbxref.accession%TYPE; d_accession dbxref.accession%TYPE; f_name_gene feature.name%TYPE; f_name feature.name%TYPE; f_d_id feature_dbxref.feature_dbxref_id%TYPE; dx_id dbxref.dbxref_id%TYPE; d_id db.db_id%TYPE; s_type_id synonym.type_id%TYPE; s_id synonym.synonym_id%TYPE; p_id pub.pub_id%TYPE; p_type_id cvterm.cvterm_id%TYPE; c_cv_id cv.cv_id%TYPE; f_s_id feature_synonym.feature_synonym_id%TYPE; fr_row feature_relationship%ROWTYPE; f_accession_temp varchar(255); f_accession varchar(255); f_type_gene CONSTANT varchar :=''gene''; f_type_exon CONSTANT varchar :=''exon''; f_type_transcript CONSTANT varchar :=''mRNA''; f_type_snoRNA CONSTANT varchar :=''snoRNA''; f_type_ncRNA CONSTANT varchar :=''ncRNA''; f_type_snRNA CONSTANT varchar :=''snRNA''; f_type_tRNA CONSTANT varchar :=''tRNA''; f_type_promoter CONSTANT varchar :=''promoter''; f_type_repeat_region CONSTANT varchar :=''repeat_region''; f_type_miRNA CONSTANT varchar :=''miRNA''; f_type_transposable_element CONSTANT varchar :=''transposable_element''; f_type_rRNA CONSTANT varchar :=''rRNA''; f_type_pseudo CONSTANT varchar :=''pseudogene''; f_type_protein CONSTANT varchar :=''polypeptide''; f_type_allele CONSTANT varchar :=''alleleof''; f_dbname_gadfly CONSTANT varchar :=''DB:GR''; f_dbname_FB CONSTANT varchar :=''null''; c_name_synonym CONSTANT varchar:=''synonym''; cv_cvname_synonym CONSTANT varchar:=''null''; p_miniref CONSTANT varchar:=''none''; p_cvterm_name CONSTANT varchar:=''computer file''; p_cv_name CONSTANT varchar:=''pub type''; fng_type_id cvterm.cvterm_id%TYPE; BEGIN SELECT INTO prefix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''prefix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO suffix cp.value FROM cvtermprop cp, cvterm, cv WHERE cvterm.name = ''suffix'' and cp.cvterm_id = cvterm.cvterm_id and cvterm.cv_id = cv.cv_id and cv.name = ''apollo''; SELECT INTO p_id pub_id from pub where uniquename = p_miniref; SELECT INTO s_type_id cvterm_id from cvterm c1, cv c2 where c1.name=c_name_synonym and c2.name=cv_cvname_synonym and c1.cv_id=c2.cv_id; RAISE NOTICE ''propagating names, prefix:%, suffix:%'',prefix,suffix; RAISE NOTICE ''enter fr_i, fr.object_id:%, fr.subject_id:%'', NEW.object_id, NEW.subject_id; SELECT INTO f_type c.name from feature f, cvterm c where f.type_id=c.cvterm_id and f.feature_id=NEW.object_id; SELECT INTO f_name name from feature where feature_id = NEW.subject_id; -- OK, the thing having a child added is a gene IF ((f_name IS NULL OR f_name like prefix||''%temp%'') and f_type=f_type_gene) THEN SELECT INTO f_type_temp c.name from feature f, cvterm c where f.feature_id=NEW.subject_id and f.type_id=c.cvterm_id; IF (f_type_temp=f_type_transcript or f_type_temp=f_type_snoRNA or f_type_temp=f_type_ncRNA or f_type_temp=f_type_snRNA or f_type_temp=f_type_tRNA or f_type_temp=f_type_rRNA or f_type_temp=f_type_miRNA or f_type_temp=f_type_pseudo or f_type_temp=f_type_transposable_element or f_type_temp=f_type_promoter or f_type_temp=f_type_repeat_region) THEN --generate a new name based on the gene name --the name is like: genename-transcript# SELECT INTO f_name_gene name from feature where feature_id=NEW.object_id; -- SELECT INTO maxid to_number(max(substring(name from (length(f_name_gene)+1+10))), ''99999'') FROM feature where name like f_name_gene||''-transcript%''; SELECT INTO c_cv_id cv_id FROM cv WHERE name = ''Sequence Ontology Feature Annotation''; SELECT INTO fng_type_id cvterm_id FROM cvterm WHERE name = ''transcript'' AND cv_id = c_cv_id; SELECT INTO maxid count FROM feature_namegenerator WHERE name = f_name_gene AND type_id = fng_type_id; IF maxid IS NULL THEN maxid = 1; ELSE maxid = maxid + 1; END IF; f_name:=CAST(f_name_gene||''-transcript''||maxid AS TEXT); RAISE NOTICE ''start to update feature, gene name:%, new feature name:%'', f_name_gene, f_name; UPDATE feature set name=f_name where feature_id=NEW.subject_id; DELETE FROM feature_namegenerator WHERE name = f_name_gene AND type_id = fng_type_id; INSERT INTO feature_namegenerator (name,type_id,count) VALUES (f_name_gene, fng_type_id, maxid); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(f_name, f_name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; END IF; RAISE NOTICE ''start to insert feature_synonym:synonym_id:%,feature_id:%, pub_id:%'', s_id, NEW.subject_id, p_id; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=NEW.subject_id and synonym_id=s_id and pub_id=p_id; IF f_s_id IS NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (NEW.subject_id, s_id, p_id, ''true''); END IF; END IF; -- here the thing having a child added is a second level thing (eg, a transcript is getting an exon or protein) ELSIF ((f_name IS NULL OR f_name like prefix||''%temp%'') and (f_type=f_type_transcript or f_type=f_type_ncRNA or f_type=f_type_snoRNA or f_type=f_type_snRNA or f_type=f_type_tRNA or f_type=f_type_rRNA or f_type=f_type_miRNA or f_type=f_type_pseudo or f_type=f_type_transposable_element or f_type=f_type_promoter or f_type=f_type_repeat_region) ) THEN SELECT INTO f_name_gene f.name from feature f, feature_relationship fr, cvterm c where f.feature_id=fr.object_id and fr.subject_id=NEW.object_id and f.type_id=c.cvterm_id and c.name=f_type_gene; SELECT INTO f_type_temp c.name from feature f, cvterm c where f.feature_id=NEW.subject_id and f.type_id=c.cvterm_id; --adding a protein to a transcript IF f_type_temp=f_type_protein THEN IF f_name_gene IS NOT NULL THEN SELECT INTO f_row_p * from feature where feature_id=NEW.subject_id; --create a new name for this protein (again repeating code in assign_names) --SELECT INTO maxid to_number(max(substring(name from (length(f_name_gene)+1+12))), ''99999'') FROM feature where name like f_name_gene||''-polypeptide%''; SELECT INTO c_cv_id cv_id FROM cv WHERE name = ''Sequence Ontology''; SELECT INTO fng_type_id cvterm_id FROM cvterm WHERE name = f_type_protein AND cv_id = c_cv_id; SELECT INTO maxid count FROM feature_namegenerator WHERE name = f_name_gene AND type_id = fng_type_id; IF maxid IS NULL THEN maxid = 1; ELSE maxid = maxid + 1; END IF; f_name:=CAST(f_name_gene||''-''||f_type_protein||maxid AS TEXT); RAISE NOTICE ''update name of polypeptide:% to new name:%'',f_row_p.name, f_name; UPDATE feature set name=f_name where feature_id=NEW.subject_id; DELETE FROM feature_namegenerator WHERE name = f_name_gene AND type_id = fng_type_id; INSERT INTO feature_namegenerator (name,type_id,count) VALUES (f_name_gene, fng_type_id, maxid); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(f_name, f_name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row_p.feature_id and synonym_id=s_id; IF f_s_id is NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row_p.feature_id, s_id, p_id, ''true''); END IF; ELSE RAISE NOTICE ''Couldnt find a gene to add this polypeptide to (feature_id:%)'', NEW.subject_id ; END IF; --adding an exon to a transcript ELSIF f_type_temp=f_type_exon THEN IF f_name_gene IS NOT NULL THEN SELECT INTO f_row_e * from feature where feature_id=NEW.subject_id; SELECT INTO fl_row_e * from featureloc where feature_id = NEW.subject_id and rank=0; IF fl_row_e.fmin IS NULL OR fl_row_e.fmax IS NULL THEN RAISE NOTICE ''cant create exon name for feature_id % since there is no featureloc entry'', NEW.subject_id; RETURN NEW; ELSE f_name:=CAST(f_name_gene||'':''||fl_row_e.fmin||''-''||fl_row_e.fmax AS TEXT); END IF; RAISE NOTICE ''exon new name:%'', f_name; UPDATE feature set name=f_name where feature_id=NEW.subject_id; SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(f_name, f_name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=f_name and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row_e.feature_id and synonym_id=s_id; IF f_s_id is NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row_e.feature_id, s_id, p_id, ''true''); END IF; ELSE RAISE NOTICE ''Couldnt find a gene to add this exon to (feature_id:%)'',NEW.subject_id; END IF; END IF; ELSE --nothing to do, the name is not null or containing temp -- RAISE NOTICE ''no link to gene for this transcript or wrong feature_relationship: transcript->polypeptide/exon:object_id:%, subject_id:%'', NEW.object_id, NEW.subject_id; END IF; RAISE NOTICE ''leave fr_i ....''; RETURN NEW; END; 'LANGUAGE plpgsql; GRANT ALL ON FUNCTION feature_relationship_propagatename_fn_i() TO PUBLIC; CREATE TRIGGER feature_relationship_propagatename_tr_i AFTER INSERT ON feature_relationship FOR EACH ROW EXECUTE PROCEDURE feature_relationship_propagatename_fn_i(); DROP TRIGGER feature_update_name_tr_u ON feature; CREATE OR REPLACE FUNCTION feature_fn_u() RETURNS TRIGGER AS ' DECLARE f_type cvterm.name%TYPE; f_type_gene CONSTANT varchar :=''gene''; f_row feature%ROWTYPE; s_type_id synonym.type_id%TYPE; s_id synonym.synonym_id%TYPE; f_s_id feature_synonym.feature_synonym_id%TYPE; p_id pub.pub_id%TYPE; p_miniref CONSTANT varchar:=''none''; c_name_synonym CONSTANT varchar:=''synonym''; cv_cvname_synonym CONSTANT varchar:=''null''; name_suffix varchar; child_name varchar; BEGIN IF OLD.uniquename <> NEW.uniquename AND OLD.uniquename NOT LIKE ''%temp%'' THEN RAISE NOTICE ''You may not change the uniquename of a feature''; RAISE NOTICE ''if you feel you must, contact your database admin''; RETURN OLD; END IF; IF OLD.name = NEW.name THEN --not updating name, so go ahead RETURN NEW; END IF; --fetch a few useful things SELECT INTO s_type_id cvterm_id from cvterm c1, cv c2 where c1.name=c_name_synonym and c2.name=cv_cvname_synonym and c1.cv_id=c2.cv_id; SELECT INTO f_type cv.name FROM feature f, cvterm cv WHERE f.feature_id = OLD.feature_id and f.type_id = cv.cvterm_id; SELECT INTO p_id pub_id from pub where uniquename = p_miniref; -- IF f_type <> f_type_gene THEN -- --its not a gene, so go ahead -- --but insert the new name into the synonym table --On gene name update, we also update the gene inner synonym (ie himself) --so for all features, the inner synonym gets updated IF NEW.name IS NOT NULL THEN SELECT INTO s_id synonym_id from synonym where name=NEW.name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(NEW.name, NEW.name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=NEW.name and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=NEW.feature_id and synonym_id=s_id and pub_id=p_id; IF f_s_id IS NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (NEW.feature_id, s_id, p_id, ''true''); END IF; END IF; IF f_type <> f_type_gene THEN --its not a gene, so go ahead RETURN NEW; END IF; --OK, so its a gene, and were changing the name... --For corectly handling alternate transcript of a gene, we must add a distinct in order not to process the same exon multiple times (exons are shared in chado) FOR f_row IN SELECT DISTINCT f.* FROM feature f, get_sub_feature_ids(OLD.feature_id) ch WHERE f.feature_id = ch.feature_id LOOP --This one process the transcripts and the proteins -- IF f_row.name LIKE OLD.name||''-%'' THEN -- SELECT INTO name_suffix substring(name from OLD.name||''(-.+)'') FROM feature where feature_id = f_row.feature_id; -- child_name = NEW.name||name_suffix; -- UPDATE feature SET name = child_name WHERE feature_id = f_row.feature_id; -- SELECT INTO s_id synonym_id from synonym where name=child_name and type_id=s_type_id; -- IF s_id IS NULL THEN -- INSERT INTO synonym(name, synonym_sgml, type_id) values(child_name, child_name, s_type_id); -- SELECT INTO s_id synonym_id from synonym where name=child_name and type_id=s_type_id; -- END IF; -- SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row.feature_id and synonym_id=s_id and pub_id=p_id; -- IF f_s_id IS NULL THEN -- INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row.feature_id, s_id, p_id, ''true''); -- END IF; -- END IF; --And this one process the exons (of form gene_name:something) --Be careful, this could lead to problems with some autogenerated split names which for flybase are also of the form gene_name:#) TODO : move this regexp to something like /gene_name:\d-\d/ IF f_row.name LIKE OLD.name||'':%'' THEN SELECT INTO name_suffix substring(name from OLD.name||''(:.+)'') FROM feature where feature_id = f_row.feature_id; child_name = NEW.name||name_suffix; RAISE NOTICE ''feature_id:%, name:% , new name : %, namesuffix:%, geneName:%'', f_row.feature_id, f_row.name, child_name,name_suffix, NEW.name ; UPDATE feature SET name = child_name WHERE feature_id = f_row.feature_id; SELECT INTO s_id synonym_id from synonym where name=child_name and type_id=s_type_id; IF s_id IS NULL THEN INSERT INTO synonym(name, synonym_sgml, type_id) values(child_name, child_name, s_type_id); SELECT INTO s_id synonym_id from synonym where name=child_name and type_id=s_type_id; END IF; SELECT INTO f_s_id feature_synonym_id from feature_synonym where feature_id=f_row.feature_id and synonym_id=s_id and pub_id=p_id; IF f_s_id IS NULL THEN INSERT INTO feature_synonym(feature_id, synonym_id, pub_id, is_current) values (f_row.feature_id, s_id, p_id, ''true''); END IF; END IF; END LOOP; RETURN NEW; END; 'LANGUAGE plpgsql; CREATE TRIGGER feature_update_name_tr_u BEFORE UPDATE ON feature FOR EACH ROW EXECUTE PROCEDURE feature_fn_u(); -- function to fascilitate gene merges -- returns the uniquename of the merged gene --WARNING: COMPLETELY UNTESTED CREATE OR REPLACE FUNCTION apollo_merge(varchar, varchar) RETURNS varchar AS ' DECLARE f1_uniquename ALIAS FOR $1; f2_uniquename ALIAS FOR $2; f_uniquename feature.uniquename%TYPE; f1_fid feature.feature_id%TYPE; f2_fid feature.feature_id%TYPE; f_id feature.feature_id%TYPE; f1_type cvterm.name%TYPE; f2_type cvterm.name%TYPE; f1_organism_id feature.organism_id%TYPE; f2_organism_id feature.organism_id%TYPE; f_type_gene CONSTANT varchar :=''gene''; c_cvterm_id cvterm.cvterm_id%TYPE; s_id synonym.synonym_id%TYPE; dbxref_id dbxref.dbxref_id%TYPE; fd_row feature_dbxref%ROWTYPE; p_id pub.pub_id%TYPE; fpub_row feature_pub%ROWTYPE; fp_row featureprop%ROWTYPE; fc_row feature_cvterm%ROWTYPE; fs_row feature_synonym%ROWTYPE; BEGIN --check that they are both genes SELECT INTO f1_type c.name FROM feature f, cvterm c WHERE f.uniquename = f1_uniquename AND f.type_id = c.cvterm_id; SELECT INTO f2_type c.name FROM feature f, cvterm c WHERE f.uniquename = f1_uniquename AND f.type_id = c.cvterm_id; IF f1_type <> f_type_gene OR f2_type <> f_type_gene THEN RAISE NOTICE ''The uniquenames for the features provided must be those of genes''; RETURN OLD; END IF; --check that they come from the same organism SELECT INTO f1_organism_id FROM feature WHERE uniquename=f1_uniquename; SELECT INTO f2_organism_id FROM feature WHERE uniquename=f2_uniquename; IF f1_organism_id <> f2_organism_id THEN RAISE NOTICE ''The merged genes must come from the same organism''; RETURN OLD; END IF; SELECT INTO c_cvterm_id type_id FROM feature WHERE uniquename = f1_uniquename; SELECT INTO f_uniquename next_uniquename(); --create the new gene INSERT INTO feature (organism_id, uniquename, type_id) VALUES (f1_organism_id, f_uniquename, c_cvterm_id); SELECT INTO f_id feature_id FROM feature WHERE uniquename = f_uniquename AND organism_id = f_organism_id AND type_id = c_cvterm_id; SELECT INTO f1_id feature_id FROM feature WHERE uniquename = f1_uniquename AND organism_id = f1_organism_id AND type_id = c_cvterm_id; SELECT INTO f2_id feature_id FROM feature WHERE uniquename = f2_uniquename AND organism_id = f2_organism_id AND type_id = c_cvterm_id; --add synonyms to new feature for all of the synonyms of the old feature FOR fs_row IN SELECT * FROM feature_synonym WHERE feature_id = f1_id OR feature_id = f2_id LOOP INSERT INTO feature_synonym (feature_id, synonym_id) VALUES (f_id, fs_row.synonym_id); END LOOP; --copy dbxref, featureprop, cvterms, pubs to the new gene FOR fd_row IN SELECT * FROM feature_dbxref WHERE feature_id = f1_id OR feature_id = f2_id LOOP INSERT INTO feature_dbxref (feature_id,dbxref_id,is_current) VALUES (f_id, fd_row.dbxref_id, 0); END LOOP; FOR fp_row IN SELECT * FROM featureprop WHERE feature_id = f1_id OR feature_id = f2_id LOOP INSERT INTO featureprop (feature_id,type_id,value,rank) VALUES (f_id,fp_row.type_id,fp_row.value,fp_row.rank); END LOOP; FOR fc_row IN SELECT * FROM feature_cvterm WHERE feature_id = f1_id OR feature_id = f2_id LOOP INSERT INTO feature_cvterm (feature_id,cvterm_id,pub_id,is_not) VALUES (f_id,fc_row.cvterm_id,fc_row.pub_id,fc_row.is_not); END LOOP; FOR fpub_row IN SELECT * FROM feature_pub WHERE feature_id = f1_id OR feature_id = f2_id LOOP INSERT INTO feature_pub (feature_id,pub_id) VALUES (f_id,fpub_row.pub_id); END LOOP; --delete featureloc entries for old genes DELETE FROM featureloc WHERE feature_id=f1_id; DELETE FROM featureloc WHERE feature_id=f2_id; --mark old gene features as obsolete UPDATE feature SET is_obsolete=true WHERE feature_id=f1_id; UPDATE feature SET is_obsolete=true WHERE feature_id=f2_id; --note in either feature_relationship or featureprop the origin of this gene RETURN f_uniquename; END; 'LANGUAGE plpgsql; -- function to fascilitate gene splits -- Takes three arguments: -- -the feature_id of the old gene that was split -- -the feature_id of the new genes --WARNING: COMPLETELY UNTESTED CREATE OR REPLACE FUNCTION apollo_split(int,int,int) RETURNS int AS ' DECLARE f_id ALIAS FOR $1; f1_id ALIAS FOR $2; f2_id ALIAS FOR $3; f_type cvterm.name%TYPE; f_organism_id feature.organism_id%TYPE; f1_organism_id feature.organism_id%TYPE; f2_organism_id feature.organism_id%TYPE; f_type_gene CONSTANT varchar :=''gene''; c_cvterm_id cvterm.cvterm_id%TYPE; fs_row feature_synonym%ROWTYPE; fd_row feature_dbxref%ROWTYPE; fpub_row pub%ROWTYPE; fp_row featureprop%ROWTYPE; fc_row feature_cvterm%ROWTYPE; BEGIN --do some error checking; first, make sure they are all genes SELECT INTO f_type c.name FROM feature f, cvterm c WHERE f.feature_id = f_id AND f.type_id = c.cvterm_id; IF f_type <> f_type_gene THEN RAISE NOTICE ''The uniquename for the feature provided must be that of a gene''; RETURN OLD; END IF; SELECT INTO f_type c.name FROM feature f, cvterm c WHERE f.feature_id = f1_id AND f.type_id = c.cvterm_id; IF f_type <> f_type_gene THEN RAISE NOTICE ''The uniquename for the feature provided must be that of a gene''; RETURN OLD; END IF; SELECT INTO f_type c.name FROM feature f, cvterm c WHERE f.feature_id = f2_id AND f.type_id = c.cvterm_id; IF f_type <> f_type_gene THEN RAISE NOTICE ''The uniquename for the feature provided must be that of a gene''; RETURN OLD; END IF; --more error checking: are they all from the same organism? SELECT INTO f_organism_id organism_id FROM feature WHERE feature_id = f_id; SELECT INTO f1_organism_id organism_id FROM feature WHERE feature_id = f1_id; SELECT INTO f2_organism_id organism_id FROM feature WHERE feature_id = f2_id; IF f_organism_id <> f1_organism_id OR f_organism_id <> f2_organism_id THEN RAISE NOTICE ''The new gene and the old genes need to come from the same organism''; RETURN OLD; END IF; SELECT INTO c_cvterm_id type_id FROM feature WHERE feature_id = f_id; --add synonyms to new feature for all of the synonyms of the old feature FOR fs_row IN SELECT * FROM feature_synonym WHERE feature_id = f_id LOOP INSERT INTO feature_synonym (feature_id, synonym_id, pub_id) VALUES (f1_id, fs_row.synonym_id, fs_row.pub_id); INSERT INTO feature_synonym (feature_id, synonym_id, pub_id) VALUES (f2_id, fs_row.synonym_id, fs_row.pub_id); END LOOP; --copy dbxref, featureprop, cvterms, pubs to the new gene FOR fd_row IN SELECT * FROM feature_dbxref WHERE feature_id = f_id LOOP INSERT INTO feature_dbxref (feature_id,dbxref_id,is_current) VALUES (f1_id, fd_row.dbxref_id, 0); INSERT INTO feature_dbxref (feature_id,dbxref_id,is_current) VALUES (f2_id, fd_row.dbxref_id, 0); END LOOP; FOR fp_row IN SELECT * FROM featureprop WHERE feature_id = f_id LOOP INSERT INTO featureprop (feature_id,type_id,value,rank) VALUES (f1_id,fp_row.type_id,fp_row.value,fp_row.rank); INSERT INTO featureprop (feature_id,type_id,value,rank) VALUES (f2_id,fp_row.type_id,fp_row.value,fp_row.rank); END LOOP; FOR fc_row IN SELECT * FROM feature_cvterm WHERE feature_id = f_id LOOP INSERT INTO feature_cvterm (feature_id,cvterm_id,pub_id,is_not) VALUES (f1_id,fc_row.cvterm_id,fc_row.pub_id,fc_row.is_not); INSERT INTO feature_cvterm (feature_id,cvterm_id,pub_id,is_not) VALUES (f2_id,fc_row.cvterm_id,fc_row.pub_id,fc_row.is_not); END LOOP; FOR fpub_row IN SELECT * FROM feature_pub WHERE feature_id = f_id LOOP INSERT INTO feature_pub (feature_id,pub_id) VALUES (f1_id,p_row.pub_id); INSERT INTO feature_pub (feature_id,pub_id) VALUES (f2_id,p_row.pub_id); END LOOP; --delete featureloc entries for old genes DELETE FROM featureloc WHERE feature_id=f_id; --mark old gene features as obsolete UPDATE feature SET is_obsolete=true WHERE feature_id=f_id; --note in either feature_relationship or featureprop the origin of this gene RETURN 1; END; 'LANGUAGE plpgsql; chado-1.23/modules/sequence/apollo-bridge/apollo.inserts000644 000765 000024 00000045724 11256710122 023502 0ustar00cainstaff000000 000000 --creates several items that Apollo expects to be in the database: -- a property type cv and terms -- a pub type cv and terms -- a pubrelationship type cv and terms -- a pubprop type cv and terms --Rice EST_match --Rice cDNA_match --Maize EST_match --Maize cross_genome_match --Rice protein_match --FgenesH:Monocot insert into analysis (name,program,programversion,sourcename) values ('Rice_EST_match','blat','1','Rice_EST'); insert into analysis (name,program,programversion,sourcename) values ('Rice_cDNA_match','blat','1','Rice_cDNA'); insert into analysis (name,program,programversion,sourcename) values ('Maize_EST_match','blat','1','Maize_EST'); insert into analysis (name,program,programversion,sourcename) values ('Rice_protein_match','blat','1','Rice_protein'); insert into analysis (name,program,programversion,sourcename) values ('Maize_cross_genome_match','blat','1','Maize_genome'); insert into analysis (name,program,programversion,sourcename) values ('FgenesH_Monocot','FgenesH','1','na'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_EST_match','blat','1','Sourghum_EST'); insert into analysis (name,program,programversion,sourcename) values ('Barley_EST_match','blat','1','Barley_EST'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_EST_match','blat','1','Wheat_EST'); insert into analysis (name,program,programversion,sourcename) values ('Rice_cross_genome_match','blat','1','Rice_genome'); insert into analysis (name,program,programversion,sourcename) values ('Millet_EST_match','blat','1','Millet_EST'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Japonica_BACend_nucleotide_match','blat','1','Rice_Japonica_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceSativa_bacends_omap_nucleotide_match','blat','1','riceSativa_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Australiensis_BACend_nucleotide_match','blat','1','Rice_Australiensis_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceAustraliensis_bacends_omap_nucleotide_match','blat','1','riceAustraliensis_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Punctata_BACend_nucleotide_match','blat','1','Rice_Punctata_BACend'); insert into analysis (name,program,programversion,sourcename) values ('ricePunctata_bacends_omap_nucleotide_match','blat','1','ricePunctata_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Maize_MAGI_ISU_cross_genome_match','blat','1','Maize_MAGI_ISU'); insert into analysis (name,program,programversion,sourcename) values ('Maize_hi_cot_Bennetzen_cross_genome_match','blat','1','Maize_hi_cot_Bennetzen'); insert into analysis (name,program,programversion,sourcename) values ('Maize_meth_filt_hi_cot_cluster_cross_genome_match','blat','1','Maize_meth_filt_hi_cot_cluster'); insert into analysis (name,program,programversion,sourcename) values ('Maize_hi_cot_TIGR_cross_genome_match','blat','1','Maize_hi_cot_TIGR'); insert into analysis (name,program,programversion,sourcename) values ('Maize_BACend_cross_genome_match','blat','1','Maize_BACend'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Nivara_BACend_nucleotide_match','blat','1','Rice_Nivara_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceNivara_bacends_omap_nucleotide_match','blat','1','riceNivara_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Rufipogon_BACend_nucleotide_match','blat','1','Rice_Rufipogon_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceRufipogon_bacends_omap_nucleotide_match','blat','1','riceRufipogon_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_orion_cross_genome_match','blat','1','Sorghum_orion'); insert into analysis (name,program,programversion,sourcename) values ('Maize_meth_filt_CSHL_Mccombie_cross_genome_match','blat','1','Maize_meth_filt_CSHL_Mccombie'); insert into analysis (name,program,programversion,sourcename) values ('Maize_meth_filt_TIGR_cross_genome_match','blat','1','Maize_meth_filt_TIGR'); insert into analysis (name,program,programversion,sourcename) values ('Ryegrass_Sequence_cross_genome_match','blat','1','Ryegrass_Sequence'); insert into analysis (name,program,programversion,sourcename) values ('Ryegrass_Assembly_cross_genome_match','blat','1','Ryegrass_Assembly'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Glaberrima_BACend_nucleotide_match','blat','1','Rice_Glaberrima_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceGlaberrima_bacends_omap_nucleotide_match','blat','1','riceGlaberrima_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Rice_unmapped_BAC_back_nucleotide_match','blat','1','Rice_unmapped_BAC_back'); insert into analysis (name,program,programversion,sourcename) values ('Rice_ArrayTarget_Affy57K_cDNA_match','blat','1','Rice_ArrayTarget_Affy57K'); insert into analysis (name,program,programversion,sourcename) values ('Rice_GI_EST_match','blat','1','Rice_GI'); insert into analysis (name,program,programversion,sourcename) values ('Rice_jap_cDNA_KOME_cDNA_match','blat','1','Rice_jap_cDNA_KOME'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Brachyantha_BACend_nucleotide_match','blat','1','Rice_Brachyantha_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceBrachyantha_bacends_omap_nucleotide_match','blat','1','riceBrachyantha_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Osativa_TUG_PlantGDB_EST_match','blat','1','Osativa_TUG_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Rice_tug_EST_match','blat','1','Rice_tug'); insert into analysis (name,program,programversion,sourcename) values ('Rice_Alta_BACend_nucleotide_match','blat','1','Rice_Alta_BACend'); insert into analysis (name,program,programversion,sourcename) values ('riceAlta_bacends_omap_nucleotide_match','blat','1','riceAlta_bacends_omap'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_cluster_Pratt_EST_match','blat','1','Sorghum_cluster_Pratt'); insert into analysis (name,program,programversion,sourcename) values ('Maize_est_EST_match','blat','1','Maize_est'); insert into analysis (name,program,programversion,sourcename) values ('Maize_GI_EST_match','blat','1','Maize_GI'); insert into analysis (name,program,programversion,sourcename) values ('Maize_ArrayTarget_NSF58K_cDNA_match','blat','1','Maize_ArrayTarget_NSF58K'); insert into analysis (name,program,programversion,sourcename) values ('Zmays_TUG_PlantGDB_EST_match','blat','1','Zmays_TUG_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_est_EST_match','blat','1','Wheat_est'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_GI_EST_match','blat','1','Wheat_GI'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_tug_EST_match','blat','1','Wheat_tug'); insert into analysis (name,program,programversion,sourcename) values ('Taestivum_TUG_PlantGDB_EST_match','blat','1','Taestivum_TUG_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_ArrayTarget_Affy61K_cDNA_match','blat','1','Wheat_ArrayTarget_Affy61K'); insert into analysis (name,program,programversion,sourcename) values ('Barley_est_EST_match','blat','1','Barley_est'); insert into analysis (name,program,programversion,sourcename) values ('Barley_GI_EST_match','blat','1','Barley_GI'); insert into analysis (name,program,programversion,sourcename) values ('Barley_ArrayTarget_Affy22K_cDNA_match','blat','1','Barley_ArrayTarget_Affy22K'); insert into analysis (name,program,programversion,sourcename) values ('Hvulgare_TUG_PlantGDB_EST_match','blat','1','Hvulgare_TUG_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Sugarcane_est_EST_match','blat','1','Sugarcane_est'); insert into analysis (name,program,programversion,sourcename) values ('Barley_tug_EST_match','blat','1','Barley_tug'); insert into analysis (name,program,programversion,sourcename) values ('Maize_markers_cross_genome_match','blat','1','Maize_markers'); insert into analysis (name,program,programversion,sourcename) values ('Rice_ind_est_EST_match','blat','1','Rice_ind_est'); insert into analysis (name,program,programversion,sourcename) values ('Rice_ind_cluster_EST_match','blat','1','Rice_ind_cluster'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_GI_EST_match','blat','1','Sorghum_GI'); insert into analysis (name,program,programversion,sourcename) values ('Rice_est_EST_match','blat','1','Rice_est'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_CDNA_cDNA_match','blat','1','Sorghum_CDNA'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_est_EST_match','blat','1','Sorghum_est'); insert into analysis (name,program,programversion,sourcename) values ('Sbicolor_TUG_PlantGDB_EST_match','blat','1','Sbicolor_TUG_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Maize_tug_EST_match','blat','1','Maize_tug'); insert into analysis (name,program,programversion,sourcename) values ('Maize_ArrayTarget_Affy18K_cDNA_match','blat','1','Maize_ArrayTarget_Affy18K'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_tug_EST_match','blat','1','Sorghum_tug'); insert into analysis (name,program,programversion,sourcename) values ('Maize_cornsensus_cDNA_match','blat','1','Maize_cornsensus'); insert into analysis (name,program,programversion,sourcename) values ('Millet_est_EST_match','blat','1','Millet_est'); insert into analysis (name,program,programversion,sourcename) values ('Maize_CDs_cDNA_match','blat','1','Maize_CDs'); insert into analysis (name,program,programversion,sourcename) values ('Maize_Unigene_Panzea_EST_match','blat','1','Maize_Unigene_Panzea'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_markers_cross_genome_match','blat','1','Wheat_markers'); insert into analysis (name,program,programversion,sourcename) values ('Rice_BAC_nucleotide_match','blat','1','Rice_BAC'); insert into analysis (name,program,programversion,sourcename) values ('Rice_unmapped_BAC_front_nucleotide_match','blat','1','Rice_unmapped_BAC_front'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_Markers_cross_genome_match','blat','1','Sorghum_Markers'); insert into analysis (name,program,programversion,sourcename) values ('Rice_CDS_cDNA_match','blat','1','Rice_CDS'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_gss-read_Klein_cross_genome_match','blat','1','Sorghum_gss-read_Klein'); insert into analysis (name,program,programversion,sourcename) values ('RiceAlta_BACend_OMAP_nucleotide_match','blat','1','RiceAlta_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceBrachyantha_BACend_OMAP_nucleotide_match','blat','1','RiceBrachyantha_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceJaponica_BACend_OMAP_nucleotide_match','blat','1','RiceJaponica_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceAustraliensis_BACend_OMAP_nucleotide_match','blat','1','RiceAustraliensis_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceCoarctata_BACend_OMAP_nucleotide_match','blat','1','RiceCoarctata_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RicePunctata_BACend_OMAP_nucleotide_match','blat','1','RicePunctata_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceGlaberrima_BACend_OMAP_nucleotide_match','blat','1','RiceGlaberrima_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceNivara_BACend_OMAP_nucleotide_match','blat','1','RiceNivara_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('Rice_ESTCluster_PlantGDB_EST_match','blat','1','Rice_ESTCluster_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Barley_ESTCluster_PlantGDB_EST_match','blat','1','Barley_ESTCluster_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Wheat_ESTCluster_PlantGDB_EST_match','blat','1','Wheat_ESTCluster_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_ESTCluster3P_LGBPratt_EST_match','blat','1','Sorghum_ESTCluster3P_LGBPratt'); insert into analysis (name,program,programversion,sourcename) values ('Sorghum_ESTCluster_PlantGDB_EST_match','blat','1','Sorghum_ESTCluster_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('Maize_ESTCluster_PlantGDB_EST_match','blat','1','Maize_ESTCluster_PlantGDB'); insert into analysis (name,program,programversion,sourcename) values ('RiceRufipogon_BACend_OMAP_nucleotide_match','blat','1','RiceRufipogon_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('Maize_Seq_Panzea_EST_match','blat','1','Maize_Seq_Panzea'); insert into analysis (name,program,programversion,sourcename) values ('RiceMinuta_BACend_OMAP_nucleotide_match','blat','1','RiceMinuta_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceGranulata_BACend_OMAP_nucleotide_match','blat','1','RiceGranulata_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceRidleyi_BACend_OMAP_nucleotide_match','blat','1','RiceRidleyi_BACend_OMAP'); insert into analysis (name,program,programversion,sourcename) values ('RiceOfficinalis_BACend_OMAP_nucleotide_match','blat','1','RiceOfficinalis_BACend_OMAP'); insert into db (name) values ('DB:TIGR_EGAD'); insert into db (name) values ('DB:Maize_Seq_Panzea'); insert into db (name) values ('DB:RiceRufipogon_BACend_OMAP'); insert into db (name) values ('DB:Maize_ESTCluster_PlantGDB'); insert into db (name) values ('DB:Sorghum_ESTCluster_PlantGDB'); insert into db (name) values ('DB:Sorghum_ESTCluster3P_LGBPratt'); insert into db (name) values ('DB:Wheat_ESTCluster_PlantGDB'); insert into db (name) values ('DB:Barley_ESTCluster_PlantGDB'); insert into db (name) values ('DB:Rice_ESTCluster_PlantGDB'); insert into db (name) values ('DB:RiceNivara_BACend_OMAP'); insert into db (name) values ('DB:RiceGlaberrima_BACend_OMAP'); insert into db (name) values ('DB:RicePunctata_BACend_OMAP'); insert into db (name) values ('DB:RiceCoarctata_BACend_OMAP'); insert into db (name) values ('DB:RiceJaponica_BACend_OMAP'); insert into db (name) values ('DB:RiceBrachyantha_BACend_OMAP'); insert into db (name) values ('DB:RiceAlta_BACend_OMAP'); insert into db (name) values ('DB:Sorghum_gss-read_Klein'); insert into db (name) values ('DB:Rice_CDS'); insert into db (name) values ('DB:Sorghum_Markers'); insert into db (name) values ('DB:Rice_BAC'); insert into db (name) values ('DB:Wheat_Markers'); insert into db (name) values ('DB:Maize_cornsensus'); insert into db (name) values ('DB:Sorghum_tug'); insert into db (name) values ('DB:Maize_tug'); insert into db (name) values ('DB:Sorghum_CDNA'); insert into db (name) values ('DB:Sorghum_GI'); insert into db (name) values ('DB:Rice_ind_cluster'); insert into db (name) values ('DB:Rice_ind_est'); insert into db (name) values ('DB:Maize_markers'); insert into db (name) values ('DB:Barley_tug'); insert into db (name) values ('DB:Sugarcane_est'); insert into db (name) values ('DB:Barley_GI'); insert into db (name) values ('DB:Wheat_tug'); insert into db (name) values ('DB:Wheat_GI'); insert into db (name) values ('DB:Wheat_est'); insert into db (name) values ('DB:Maize_GI'); insert into db (name) values ('DB:Sorghum_cluster_Pratt'); insert into db (name) values ('DB:EST_match'); insert into db (name) values ('DB:Rice_tug'); insert into db (name) values ('DB:cDNA_match'); insert into db (name) values ('DB:Rice_GI'); insert into db (name) values ('DB:TIGR_Maize'); insert into db (name) values ('DB:TIGR_Osa'); insert into db (name) values ('DB:nucleotide_match'); insert into db (name) values ('DB:Sorghum_Orion'); insert into db (name) values ('DB:cross_genome_match'); insert into db (name) values ('DB:Maize_hi_cot_TIGR'); insert into db (name) values ('DB:Maize_meth_filt_TIGR'); insert into pub (uniquename, title, type_id) values ('none', 'none', (select cvterm_id from cvterm where name = 'null pub' and cv_id in (select cv_id from cv where name='pub type') ) ); --for the new triggers create sequence uniquename_id_generator; insert into cvtermprop (cvterm_id,type_id,value) values ((select cvterm_id from cvterm where name='prefix' and cv_id in (select cv_id from cv where name='apollo')),(select cvterm_id from cvterm where name='is_a' and cv_id in (select cv_id from cv where name='relationship')),'RICE'); insert into cvtermprop (cvterm_id,type_id,value) values ((select cvterm_id from cvterm where name='suffix' and cv_id in (select cv_id from cv where name='apollo')),(select cvterm_id from cvterm where name='is_a' and cv_id in (select cv_id from cv where name='relationship')),''); insert into dbxref (db_id, accession) values ((select db_id from db where name='null'),'Relationship Ontology:producedby'); insert into cvterm (name, cv_id, dbxref_id, is_relationshiptype) values ('producedby',(select cv_id from cv where name='Relationship Ontology'),(select dbxref_id from dbxref where accession = 'Relationship Ontology:producedby'),1); CREATE TABLE feature_namegenerator ( feature_namegenerator_id serial not null, primary key (feature_namegenerator_id), name varchar(255), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, count int -- constraint feature_namegenerator_c1 unique (name,type_id) ); INSERT INTO feature_namegenerator (name,type_id,count) SELECT substr(name, 0 , (position('-' in name))), (select cvterm_id from cvterm where cv_id=7 and name='transcript'), to_number(max(substring(name from 21)), '99999') FROM feature WHERE name like 'RICE%-transcript%' group by name; INSERT INTO feature_namegenerator (name,type_id,count) SELECT substr(name, 0 , (position('-' in name))), (select cvterm_id from cvterm where cv_id=14 and name='protein'), to_number(max(substring(name from 19)), '99999') FROM feature WHERE name like 'RICE%-protein%' group by name; delete from feature_namegenerator where feature_namegenerator_id not in (select feature_namegenerator_id from feature_namegenerator where count = max(count) group by name,type_id); alter table feature_namegenerator add constraint feature_namegenerator_c1 unique (name,type_id); chado-1.23/modules/sequence/apollo-bridge/cv_inserts.sql000644 000765 000024 00000046370 11256710122 023501 0ustar00cainstaff000000 000000 INSERT INTO cv (name) VALUES ('pub type'); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:computer file'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'computer file',(select dbxref_id from dbxref where accession='pub type:computer file')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:curator'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'curator',(select dbxref_id from dbxref where accession='pub type:curator')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:publication'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'publication',(select dbxref_id from dbxref where accession='pub type:publication')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:Book'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'Book',(select dbxref_id from dbxref where accession='pub type:Book')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:DNA/RNA sequence record'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'DNA/RNA sequence record',(select dbxref_id from dbxref where accession='pub type:DNA/RNA sequence record')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:abstract'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'abstract',(select dbxref_id from dbxref where accession='pub type:abstract')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:archive'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'archive',(select dbxref_id from dbxref where accession='pub type:archive')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:automatic genome annotation'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'automatic genome annotation',(select dbxref_id from dbxref where accession='pub type:automatic genome annotation')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:bibliographic list'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'bibliographic list',(select dbxref_id from dbxref where accession='pub type:bibliographic list')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:biography'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'biography',(select dbxref_id from dbxref where accession='pub type:biography')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:book'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'book',(select dbxref_id from dbxref where accession='pub type:book')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:book review'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'book review',(select dbxref_id from dbxref where accession='pub type:book review')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:booklet'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'booklet',(select dbxref_id from dbxref where accession='pub type:booklet')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:conference report'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'conference report',(select dbxref_id from dbxref where accession='pub type:conference report')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:curated genome annotation'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'curated genome annotation',(select dbxref_id from dbxref where accession='pub type:curated genome annotation')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:demonstration'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'demonstration',(select dbxref_id from dbxref where accession='pub type:demonstration')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:editorial'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'editorial',(select dbxref_id from dbxref where accession='pub type:editorial')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:erratum'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'erratum',(select dbxref_id from dbxref where accession='pub type:erratum')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:film'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'film',(select dbxref_id from dbxref where accession='pub type:film')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:interview'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'interview',(select dbxref_id from dbxref where accession='pub type:interview')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:jigsaw puzzle'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'jigsaw puzzle',(select dbxref_id from dbxref where accession='pub type:jigsaw puzzle')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:letter'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'letter',(select dbxref_id from dbxref where accession='pub type:letter')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:meeting report'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'meeting report',(select dbxref_id from dbxref where accession='pub type:meeting report')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:microfiche'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'microfiche',(select dbxref_id from dbxref where accession='pub type:microfiche')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:microscope slides'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'microscope slides',(select dbxref_id from dbxref where accession='pub type:microscope slides')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:news article'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'news article',(select dbxref_id from dbxref where accession='pub type:news article')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:note'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'note',(select dbxref_id from dbxref where accession='pub type:note')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:obituary'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'obituary',(select dbxref_id from dbxref where accession='pub type:obituary')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:other'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'other',(select dbxref_id from dbxref where accession='pub type:other')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:patent'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'patent',(select dbxref_id from dbxref where accession='pub type:patent')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:personal communication'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'personal communication',(select dbxref_id from dbxref where accession='pub type:personal communication')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:poem'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'poem',(select dbxref_id from dbxref where accession='pub type:poem')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:press release'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'press release',(select dbxref_id from dbxref where accession='pub type:press release')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:protein sequence record'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'protein sequence record',(select dbxref_id from dbxref where accession='pub type:protein sequence record')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:recording'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'recording',(select dbxref_id from dbxref where accession='pub type:recording')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:retraction'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'retraction',(select dbxref_id from dbxref where accession='pub type:retraction')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:review'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'review',(select dbxref_id from dbxref where accession='pub type:review')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:slides'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'slides',(select dbxref_id from dbxref where accession='pub type:slides')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:spoof'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'spoof',(select dbxref_id from dbxref where accession='pub type:spoof')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:stock list'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'stock list',(select dbxref_id from dbxref where accession='pub type:stock list')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:supplementary material'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'supplementary material',(select dbxref_id from dbxref where accession='pub type:supplementary material')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:tactile diagram'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'tactile diagram',(select dbxref_id from dbxref where accession='pub type:tactile diagram')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:teaching note'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'teaching note',(select dbxref_id from dbxref where accession='pub type:teaching note')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:thesis'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'thesis',(select dbxref_id from dbxref where accession='pub type:thesis')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:unpublished'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'unpublished',(select dbxref_id from dbxref where accession='pub type:unpublished')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:video'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'video',(select dbxref_id from dbxref where accession='pub type:video')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:paper'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'paper',(select dbxref_id from dbxref where accession='pub type:paper')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:journal'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'journal',(select dbxref_id from dbxref where accession='pub type:journal')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:null pub'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'null pub',(select dbxref_id from dbxref where accession='pub type:null pub')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub type:submitted'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub type'),'submitted',(select dbxref_id from dbxref where accession='pub type:submitted')); INSERT INTO cv (name) VALUES ('pub relationship type'); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub relationship type:also_in'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub relationship type'),'also_in',(select dbxref_id from dbxref where accession='pub relationship type:also_in')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub relationship type:corrects'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub relationship type'),'corrects',(select dbxref_id from dbxref where accession='pub relationship type:corrects')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub relationship type:makes_obsolete'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub relationship type'),'makes_obsolete',(select dbxref_id from dbxref where accession='pub relationship type:makes_obsolete')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pub relationship type:published_in'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pub relationship type'),'published_in',(select dbxref_id from dbxref where accession='pub relationship type:published_in')); INSERT INTO cv (name) VALUES ('pubprop type'); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:abbreviation'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'abbreviation',(select dbxref_id from dbxref where accession='pubprop type:abbreviation')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:abstract'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'abstract',(select dbxref_id from dbxref where accession='pubprop type:abstract')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:abstract_languages'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'abstract_languages',(select dbxref_id from dbxref where accession='pubprop type:abstract_languages')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:cam_offprint'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'cam_offprint',(select dbxref_id from dbxref where accession='pubprop type:cam_offprint')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:comment'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'comment',(select dbxref_id from dbxref where accession='pubprop type:comment')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:errata'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'errata',(select dbxref_id from dbxref where accession='pubprop type:errata')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:erratum'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'erratum',(select dbxref_id from dbxref where accession='pubprop type:erratum')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:internalnotes'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'internalnotes',(select dbxref_id from dbxref where accession='pubprop type:internalnotes')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:languages'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'languages',(select dbxref_id from dbxref where accession='pubprop type:languages')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'pubprop type:series_abbrev'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='pubprop type'),'series_abbrev',(select dbxref_id from dbxref where accession='pubprop type:series_abbrev')); INSERT INTO cv (name) VALUES ('apollo'); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'apollo:suffix'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='apollo'),'suffix',(select dbxref_id from dbxref where accession='apollo:suffix')); INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), 'apollo:prefix'); INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='apollo'),'prefix',(select dbxref_id from dbxref where accession='apollo:prefix')); chado-1.23/modules/sequence/apollo-bridge/insert_ad_doc_cv.pl000755 000765 000024 00000002356 11723234477 024437 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; open ONTO, "ad_hoc_cv" or die "couldn't open ad_hoc_cv:$!\n"; open INSERTS, ">cv_inserts.sql" or die "couldn't open cv_inserts.sql: $!\n"; my $cv; while () { if (/^#/) { print INSERTS "\n"; } elsif (/^\[(.+)\]/) { $cv = $1; print INSERTS "INSERT INTO cv (name) VALUES ('$cv');\n"; } elsif (/^(.+)$/) { my $term=$1; if ($term =~ /(.+)\s+\[REL\]/) { my $cvterm = $1; print INSERTS "INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), '$cv:$cvterm');\n"; print INSERTS "INSERT INTO cvterm (cv_id,name,dbxref_id,is_relationshiptype) VALUES ((select cv_id from cv where name='$cv'),'$cvterm',(select dbxref_id from dbxref where accession='$cv:$cvterm'),1);\n"; } else { my $cvterm = $term; print INSERTS "INSERT INTO dbxref (db_id,accession) VALUES ((select db_id from db where name='null'), '$cv:$cvterm');\n"; print INSERTS "INSERT INTO cvterm (cv_id,name,dbxref_id) VALUES ((select cv_id from cv where name='$cv'),'$cvterm',(select dbxref_id from dbxref where accession='$cv:$cvterm'));\n"; } } } close ONTO; close INSERTS; chado-1.23/modules/sequence/apollo-bridge/naming_rules.txt000644 000765 000024 00000003572 11256710122 024022 0ustar00cainstaff000000 000000 The triggers contained in the apollo-triggers.plpgsql file assign names according to the following rules: 1. If the feature has 'prefix:temp' in the uniquename, it gets renamed using a db sequence for generating uniquenames. Note that 'prefix' is a MOD specific string set at the time the chado database is created. a. If the feature is a gene and the name has 'prefix:temp' in it, it is set equal to the uniquename, otherwise it is left as is. b. Otherwise if the feature is not a gene and the feature name has 'prefix:temp' in it, it is set to null so that it can be renamed later. 2. When features are given parents via a part_of or producedby relationship (via an insert into feature_relationship), the child feature's name is created based on the gene's uniquename. The rules are these: a. If it is a transcript type (ie, mRNA, tRNA, miRNA) or a polypeptide, the name is of the form "gene_uniquename-type_nameNN" where NN is the next available number for that feature type associated with that gene (see the examples below). b. If the feature is an exon, it is given a name based on the gene's uniquename and fmin and fmax for the exon. EXAMPLE CASE feature tmp name tmp uname final name final uname gene null RICE:temp3 RICE0001 RICE0001 gene RICE:temp4 RICE:temp4 RICE0002 RICE0002 gene Adh RICE:temp5 Adh RICE0003 mRNA null RICE:temp1 RICE0003-mRNA1 RICE0004 mRNA Adh cononical RICE:temp33 Adh cononical RICE0005 mRNA RICE:temp2 RICE:temp2 RICE0003-mRNA2 RICE0006 exon null RICE:temp38 RICE0003:33-76 RICE0007 exon RICE:temp1 RICE:temp1 RICE0003:2-25 RICE0008 protein null RICE:temp34 RICE0003-protein1 RICE0009 protein cftr-delF508 RICE:temp44 cftr-delF508 RICE0010 miRNA null RICE:temp22 RICE0001-miRNA1 RICE0011 mRNA Adh-mRNA1 RICE:temp9 Adh-mRNA1 RICE0012 protein Adh-protein1 RICE:temp8 Adh-protein1 RICE0013 chado-1.23/modules/sequence/apollo-bridge/sample_db/000755 000765 000024 00000000000 12061672375 022531 5ustar00cainstaff000000 000000 chado-1.23/modules/sequence/apollo-bridge/sample_db/README000644 000765 000024 00000000250 11256710121 023371 0ustar00cainstaff000000 000000 The sample database that used to be in this directory has been moved to its own cvs repository in the gmod cvs, in a repository called 'sample_dbs'. Scott Cain 1/9/07 chado-1.23/modules/pub/pub.html000644 000765 000024 00000052225 11256710057 016516 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

pub
pub_relationship
pub_dbxref
pubauthor
pubprop

pub

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Comments:

$Id: pub.html,v 1.3 2007-03-16 01:28:38 briano Exp $
==========================================
Chado pub module
=================================================================
Dependencies:
:import cvterm from cv
:import dbxref from general
=================================================================
================================================
TABLE: pub
================================================
A documented provenance artefact - publications, documents, personal communication.
Field Name Data Type Size Default Value Other Foreign Key
pub_id integer 11 PRIMARY KEY, NOT NULL
title text 64000 Descriptive general heading.
volumetitle text 64000 Title of part if one of a series.
volume varchar 255
series_name varchar 255 Full name of (journal) series.
issue varchar 255
pyear varchar 255
pages varchar 255 Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 10 NOT NULL, The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. cvterm.cvterm_id
is_obsolete boolean 0 false
publisher varchar 255
pubplace varchar 255

Indices

Name Fields
pub_idx1 type_id

Constraints

Type Fields
NOT NULL pub_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE uniquename

pub_relationship

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Comments:

================================================
TABLE: pub_relationship
================================================
Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.
Field Name Data Type Size Default Value Other Foreign Key
pub_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL pub.pub_id
object_id integer 10 UNIQUE, NOT NULL pub.pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
pub_relationship_idx1 subject_id
pub_relationship_idx2 object_id
pub_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL pub_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_id, object_id, type_id

pub_dbxref

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Comments:

================================================
TABLE: pub_dbxref
================================================
Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...
Field Name Data Type Size Default Value Other Foreign Key
pub_dbxref_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
pub_dbxref_idx1 pub_id
pub_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL pub_dbxref_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE pub_id, dbxref_id

pubauthor

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Comments:

================================================
TABLE: pubauthor
================================================
An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.
Field Name Data Type Size Default Value Other Foreign Key
pubauthor_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
rank integer 10 UNIQUE, NOT NULL, Order of author in author list for this pub - order is important.
editor boolean 0 false Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.
surname varchar 100 NOT NULL
givennames varchar 100 First name, initials
suffix varchar 100 Jr., Sr., etc

Indices

Name Fields
pubauthor_idx2 pub_id

Constraints

Type Fields
NOT NULL pubauthor_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
NOT NULL surname
UNIQUE pub_id, rank

pubprop

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Comments:

================================================
TABLE: pubprop
================================================
Property-value pairs for a pub. Follows standard chado pattern.
Field Name Data Type Size Default Value Other Foreign Key
pubprop_id integer 11 PRIMARY KEY, NOT NULL
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 UNIQUE

Indices

Name Fields
pubprop_idx1 pub_id
pubprop_idx2 type_id

Constraints

Type Fields
NOT NULL pubprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
UNIQUE pub_id, type_id, rank
Created by SQL::Translator 0.08 chado-1.23/modules/pub/pub.sql000644 000765 000024 00000012540 11256710057 016345 0ustar00cainstaff000000 000000 -- $Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $ -- ========================================== -- Chado pub module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: pub -- ================================================ create table pub ( pub_id serial not null, primary key (pub_id), title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, is_obsolete boolean default 'false', publisher varchar(255), pubplace varchar(255), constraint pub_c1 unique (uniquename) ); CREATE INDEX pub_idx1 ON pub (type_id); COMMENT ON TABLE pub IS 'A documented provenance artefact - publications, documents, personal communication.'; COMMENT ON COLUMN pub.title IS 'Descriptive general heading.'; COMMENT ON COLUMN pub.volumetitle IS 'Title of part if one of a series.'; COMMENT ON COLUMN pub.series_name IS 'Full name of (journal) series.'; COMMENT ON COLUMN pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'; COMMENT ON COLUMN pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.'; -- ================================================ -- TABLE: pub_relationship -- ================================================ create table pub_relationship ( pub_relationship_id serial not null, primary key (pub_relationship_id), subject_id int not null, foreign key (subject_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint pub_relationship_c1 unique (subject_id,object_id,type_id) ); create index pub_relationship_idx1 on pub_relationship (subject_id); create index pub_relationship_idx2 on pub_relationship (object_id); create index pub_relationship_idx3 on pub_relationship (type_id); COMMENT ON TABLE pub_relationship IS 'Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.'; -- ================================================ -- TABLE: pub_dbxref -- ================================================ create table pub_dbxref ( pub_dbxref_id serial not null, primary key (pub_dbxref_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint pub_dbxref_c1 unique (pub_id,dbxref_id) ); create index pub_dbxref_idx1 on pub_dbxref (pub_id); create index pub_dbxref_idx2 on pub_dbxref (dbxref_id); COMMENT ON TABLE pub_dbxref IS 'Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...'; -- ================================================ -- TABLE: pubauthor -- ================================================ create table pubauthor ( pubauthor_id serial not null, primary key (pubauthor_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null, editor boolean default 'false', surname varchar(100) not null, givennames varchar(100), suffix varchar(100), constraint pubauthor_c1 unique (pub_id, rank) ); create index pubauthor_idx2 on pubauthor (pub_id); COMMENT ON TABLE pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.'; COMMENT ON COLUMN pubauthor.givennames IS 'First name, initials'; COMMENT ON COLUMN pubauthor.suffix IS 'Jr., Sr., etc'; COMMENT ON COLUMN pubauthor.rank IS 'Order of author in author list for this pub - order is important.'; COMMENT ON COLUMN pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.'; -- ================================================ -- TABLE: pubprop -- ================================================ create table pubprop ( pubprop_id serial not null, primary key (pubprop_id), pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text not null, rank integer, constraint pubprop_c1 unique (pub_id,type_id,rank) ); create index pubprop_idx1 on pubprop (pub_id); create index pubprop_idx2 on pubprop (type_id); COMMENT ON TABLE pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.'; chado-1.23/modules/project/project.html000644 000765 000024 00000036342 11460104607 020253 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

project
projectprop
project_relationship
project_pub
project_contact

project

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Comments:

=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import contact from contact
=================================================================
================================================
TABLE: project
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
project_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NOT NULL

Constraints

Type Fields
NOT NULL project_id
NOT NULL name
NOT NULL description
UNIQUE name

projectprop

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Comments:

================================================
TABLE: projectprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
projectprop_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL projectprop_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE project_id, type_id, rank

project_relationship

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Comments:

================================================
TABLE: project_relationship
================================================
A project can be composed of several smaller scale projects
Field Name Data Type Size Default Value Other Foreign Key
project_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_project_id integer 10 UNIQUE, NOT NULL project.project_id
object_project_id integer 10 UNIQUE, NOT NULL project.project_id
type_id integer 10 UNIQUE, NOT NULL, The type of relationship being stated, such as "is part of". cvterm.cvterm_id

Constraints

Type Fields
NOT NULL project_relationship_id
NOT NULL subject_project_id
FOREIGN KEY subject_project_id
NOT NULL object_project_id
FOREIGN KEY object_project_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_project_id, object_project_id, type_id

project_pub

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Comments:

Linking project(s) to publication(s)
Field Name Data Type Size Default Value Other Foreign Key
project_pub_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
project_pub_idx1 project_id
project_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL project_pub_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE project_id, pub_id

project_contact

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Comments:

Linking project(s) to contact(s)
Field Name Data Type Size Default Value Other Foreign Key
project_contact_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 UNIQUE, NOT NULL project.project_id
contact_id integer 10 UNIQUE, NOT NULL contact.contact_id

Indices

Name Fields
project_contact_idx1 project_id
project_contact_idx2 contact_id

Constraints

Type Fields
NOT NULL project_contact_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL contact_id
FOREIGN KEY contact_id
UNIQUE project_id, contact_id
Created by SQL::Translator 0.11003 chado-1.23/modules/project/project.sql000644 000765 000024 00000007557 11770647731 020132 0ustar00cainstaff000000 000000 -- ========================================== -- Chado project module. Used primarily by other Chado modules to -- group experiments, stocks, and so forth that are associated with -- eachother administratively or organizationally. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import pub from pub -- :import contact from contact -- ================================================================= -- ================================================ -- TABLE: project -- ================================================ create table project ( project_id serial not null, primary key (project_id), name varchar(255) not null, description varchar(255) not null, constraint project_c1 unique (name) ); COMMENT ON TABLE project IS 'A project is some kind of planned endeavor. Used primarily by other Chado modules to group experiments, stocks, and so forth that are associated with eachother administratively or organizationally.'; -- ================================================ -- TABLE: projectprop -- ================================================ CREATE TABLE projectprop ( projectprop_id serial NOT NULL, PRIMARY KEY (projectprop_id), project_id integer NOT NULL, FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, value text, rank integer not null default 0, CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank) ); COMMENT ON TABLE project IS 'Standard Chado flexible property table for projects.'; -- ================================================ -- TABLE: project_relationship -- ================================================ CREATE TABLE project_relationship ( project_relationship_id serial NOT NULL, PRIMARY KEY (project_relationship_id), subject_project_id integer NOT NULL, FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE, object_project_id integer NOT NULL, FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE, type_id integer NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT, CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id) ); COMMENT ON TABLE project_relationship IS 'Linking table for relating projects to each other. For example, a given project could be composed of several smaller subprojects'; COMMENT ON COLUMN project_relationship.type_id IS 'The cvterm type of the relationship being stated, such as "part of".'; create table project_pub ( project_pub_id serial not null, primary key (project_pub_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint project_pub_c1 unique (project_id,pub_id) ); create index project_pub_idx1 on project_pub (project_id); create index project_pub_idx2 on project_pub (pub_id); COMMENT ON TABLE project_pub IS 'Linking table for associating projects and publications.'; create table project_contact ( project_contact_id serial not null, primary key (project_contact_id), project_id int not null, foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED, contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint project_contact_c1 unique (project_id,contact_id) ); create index project_contact_idx1 on project_contact (project_id); create index project_contact_idx2 on project_contact (contact_id); COMMENT ON TABLE project_contact IS 'Linking table for associating projects and contacts.'; chado-1.23/modules/phylogeny/Changes000644 000765 000024 00000000553 11256710154 017560 0ustar00cainstaff000000 000000 2005-07-25 [cjm] - removed phylonode.phylonode_idx - not required - added examples - removed NOT NULL from phylonode.type_id - removed NOT NULL from phylonode.feature_id - removed NOT NULL from phylotree.type_id - added functions chado-1.23/modules/phylogeny/examples/000755 000765 000024 00000000000 12061672376 020110 5ustar00cainstaff000000 000000 chado-1.23/modules/phylogeny/functions/000755 000765 000024 00000000000 12061672375 020301 5ustar00cainstaff000000 000000 chado-1.23/modules/phylogeny/phylogeny.html000644 000765 000024 00000075542 11375313661 021207 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

phylotree
phylotree_pub
phylonode
phylonode_dbxref
phylonode_pub
phylonode_organism
phylonodeprop
phylonode_relationship

phylotree

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Comments:

$Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $
==========================================
Chado phylogenetics module
Richard Bruskiewich
Chris Mungall
Initial design: 2004-05-27
============
DEPENDENCIES
============
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from general
:import analysis from companalysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: phylotree
================================================
Global anchor for phylogenetic tree.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_id integer 11 PRIMARY KEY, UNIQUE, NOT NULL
dbxref_id integer 10 NOT NULL dbxref.dbxref_id
name varchar 255 NULL
type_id integer 10 Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". cvterm.cvterm_id
analysis_id integer 10 NULL analysis.analysis_id
comment text 64000 NULL

Indices

Name Fields
phylotree_idx1 phylotree_id

Constraints

Type Fields
NOT NULL phylotree_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY type_id
FOREIGN KEY analysis_id
UNIQUE phylotree_id

phylotree_pub

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Comments:

================================================
TABLE: phylotree_pub
================================================
Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_pub_id integer 11 PRIMARY KEY, NOT NULL
phylotree_id integer 10 UNIQUE, NOT NULL phylotree.phylotree_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylotree_pub_idx1 phylotree_id
phylotree_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL phylotree_pub_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE phylotree_id, pub_id

phylonode

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Comments:

================================================
TABLE: phylonode
================================================
Bootstrap float null.
This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_id integer 11 PRIMARY KEY, NOT NULL
phylotree_id integer 10 UNIQUE, NOT NULL phylotree.phylotree_id
parent_phylonode_id integer 10 NULL Root phylonode can have null parent_phylonode_id value. phylonode.phylonode_id
left_idx integer 10 UNIQUE, NOT NULL
right_idx integer 10 UNIQUE, NOT NULL
type_id integer 10 Type: e.g. root, interior, leaf. cvterm.cvterm_id
feature_id integer 10 Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it. feature.feature_id
label varchar 255 NULL
distance float 20 NULL

Constraints

Type Fields
NOT NULL phylonode_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
FOREIGN KEY parent_phylonode_id
NOT NULL left_idx
NOT NULL right_idx
FOREIGN KEY type_id
FOREIGN KEY feature_id
UNIQUE phylotree_id, left_idx
UNIQUE phylotree_id, right_idx

phylonode_dbxref

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Comments:

================================================
TABLE: phylonode_dbxref
================================================
For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_dbxref_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
phylonode_dbxref_idx1 phylonode_id
phylonode_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL phylonode_dbxref_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE phylonode_id, dbxref_id

phylonode_pub

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Comments:

================================================
TABLE: phylonode_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonode_pub_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylonode_pub_idx1 phylonode_id
phylonode_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL phylonode_pub_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE phylonode_id, pub_id

phylonode_organism

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Comments:

================================================
TABLE: phylonode_organism
================================================
This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).
Field Name Data Type Size Default Value Other Foreign Key
phylonode_organism_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL, One phylonode cannot refer to >1 organism. phylonode.phylonode_id
organism_id integer 10 NOT NULL organism.organism_id

Indices

Name Fields
phylonode_organism_idx1 phylonode_id
phylonode_organism_idx2 organism_id

Constraints

Type Fields
NOT NULL phylonode_organism_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL organism_id
FOREIGN KEY organism_id
UNIQUE phylonode_id

phylonodeprop

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Comments:

================================================
TABLE: phylonodeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonodeprop_id integer 11 PRIMARY KEY, NOT NULL
phylonode_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 10 UNIQUE, NOT NULL, type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL
rank integer 10 0 UNIQUE, NOT NULL, It is not clear how useful the rank concept is here, leave it in for now.

Indices

Name Fields
phylonodeprop_idx1 phylonode_id
phylonodeprop_idx2 type_id

Constraints

Type Fields
NOT NULL phylonodeprop_id
NOT NULL phylonode_id
FOREIGN KEY phylonode_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE phylonode_id, type_id, value, rank

phylonode_relationship

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Comments:

================================================
TABLE: phylonode_relationship
================================================
This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
object_id integer 10 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10
phylotree_id integer 10 NOT NULL phylotree.phylotree_id

Indices

Name Fields
phylonode_relationship_idx1 subject_id
phylonode_relationship_idx2 object_id
phylonode_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL phylonode_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL phylotree_id
FOREIGN KEY phylotree_id
UNIQUE subject_id, object_id, type_id
Created by SQL::Translator 0.11005 chado-1.23/modules/phylogeny/phylogeny.sql000644 000765 000024 00000021174 11256710154 021026 0ustar00cainstaff000000 000000 -- $Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $ -- ========================================== -- Chado phylogenetics module -- -- Richard Bruskiewich -- Chris Mungall -- -- Initial design: 2004-05-27 -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import dbxref from general -- :import analysis from companalysis -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: phylotree -- ================================================ create table phylotree ( phylotree_id serial not null, primary key (phylotree_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, name varchar(255) null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, analysis_id int null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade, comment text null, unique(phylotree_id) ); create index phylotree_idx1 on phylotree (phylotree_id); COMMENT ON TABLE phylotree IS 'Global anchor for phylogenetic tree.'; COMMENT ON COLUMN phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".'; -- ================================================ -- TABLE: phylotree_pub -- ================================================ create table phylotree_pub ( phylotree_pub_id serial not null, primary key (phylotree_pub_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylotree_id, pub_id) ); create index phylotree_pub_idx1 on phylotree_pub (phylotree_id); create index phylotree_pub_idx2 on phylotree_pub (pub_id); COMMENT ON TABLE phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.'; -- ================================================ -- TABLE: phylonode -- ================================================ create table phylonode ( phylonode_id serial not null, primary key (phylonode_id), phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, parent_phylonode_id int null, foreign key (parent_phylonode_id) references phylonode (phylonode_id) on delete cascade, left_idx int not null, right_idx int not null, type_id int, foreign key(type_id) references cvterm (cvterm_id) on delete cascade, feature_id int, foreign key (feature_id) references feature (feature_id) on delete cascade, label varchar(255) null, distance float null, -- Bootstrap float null. unique(phylotree_id, left_idx), unique(phylotree_id, right_idx) ); COMMENT ON TABLE phylonode IS 'This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.'; COMMENT ON COLUMN phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.'; COMMENT ON COLUMN phylonode.type_id IS 'Type: e.g. root, interior, leaf.'; COMMENT ON COLUMN phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.'; -- ================================================ -- TABLE: phylonode_dbxref -- ================================================ create table phylonode_dbxref ( phylonode_dbxref_id serial not null, primary key (phylonode_dbxref_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade, unique(phylonode_id,dbxref_id) ); create index phylonode_dbxref_idx1 on phylonode_dbxref (phylonode_id); create index phylonode_dbxref_idx2 on phylonode_dbxref (dbxref_id); COMMENT ON TABLE phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.'; -- ================================================ -- TABLE: phylonode_pub -- ================================================ create table phylonode_pub ( phylonode_pub_id serial not null, primary key (phylonode_pub_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade, unique(phylonode_id, pub_id) ); create index phylonode_pub_idx1 on phylonode_pub (phylonode_id); create index phylonode_pub_idx2 on phylonode_pub (pub_id); -- ================================================ -- TABLE: phylonode_organism -- ================================================ create table phylonode_organism ( phylonode_organism_id serial not null, primary key (phylonode_organism_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade, unique(phylonode_id) ); create index phylonode_organism_idx1 on phylonode_organism (phylonode_id); create index phylonode_organism_idx2 on phylonode_organism (organism_id); COMMENT ON TABLE phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).'; COMMENT ON COLUMN phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.'; -- ================================================ -- TABLE: phylonodeprop -- ================================================ create table phylonodeprop ( phylonodeprop_id serial not null, primary key (phylonodeprop_id), phylonode_id int not null, foreign key (phylonode_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', -- It is not clear how useful the rank concept is here, leave it in for now. rank int not null default 0, unique(phylonode_id, type_id, value, rank) ); create index phylonodeprop_idx1 on phylonodeprop (phylonode_id); create index phylonodeprop_idx2 on phylonodeprop (type_id); COMMENT ON COLUMN phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.'; -- ================================================ -- TABLE: phylonode_relationship -- ================================================ create table phylonode_relationship ( phylonode_relationship_id serial not null, primary key (phylonode_relationship_id), subject_id int not null, foreign key (subject_id) references phylonode (phylonode_id) on delete cascade, object_id int not null, foreign key (object_id) references phylonode (phylonode_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, rank int, phylotree_id int not null, foreign key (phylotree_id) references phylotree (phylotree_id) on delete cascade, unique(subject_id, object_id, type_id) ); create index phylonode_relationship_idx1 on phylonode_relationship (subject_id); create index phylonode_relationship_idx2 on phylonode_relationship (object_id); create index phylonode_relationship_idx3 on phylonode_relationship (type_id); COMMENT ON TABLE phylonode_relationship IS 'This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.'; chado-1.23/modules/phylogeny/functions/phylo.plpgsql000644 000765 000024 00000001247 11256710154 023035 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION phylonode_depth(INT) RETURNS FLOAT AS 'DECLARE id ALIAS FOR $1; DECLARE depth FLOAT := 0; DECLARE curr_node phylonode%ROWTYPE; BEGIN SELECT INTO curr_node * FROM phylonode WHERE phylonode_id=id; depth = depth + curr_node.distance; IF curr_node.parent_phylonode_id IS NULL THEN RETURN depth; ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id); END IF; END ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION phylonode_height(INT) RETURNS FLOAT AS ' SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0) FROM phylonode WHERE parent_phylonode_id = $1 ' LANGUAGE 'sql'; chado-1.23/modules/phylogeny/functions/phylo.sqlapi000644 000765 000024 00000000605 11256710154 022641 0ustar00cainstaff000000 000000 COMMENT ON FUNCTION phylonode_depth(INT) IS 'returns as a FLOAT the depth of the node with a particular phylonode_id - depth is defined as the sum of distances from the node to the root'; COMMENT ON FUNCTION phylonode_height(INT) IS 'returns as a FLOAT the height of the node with a particular phylonode_id - height is defined as the maximum total distance from the node to the leaves'; chado-1.23/modules/phylogeny/examples/org.chado-xml000644 000765 000024 00000001530 11256710154 022464 0ustar00cainstaff000000 000000 Fungi Fungi Metazoa Metazoa Primates Primates human Homo sapiens nematode Nematoda yeast Saccharomyces cerevisiae chado-1.23/modules/phylogeny/examples/README000644 000765 000024 00000000303 11256710154 020754 0ustar00cainstaff000000 000000 Example data for phylogeny module in chado-xml Use a generic loader to put this in db; either XML::XORT or DBIx::DBStag If your test db does not have organisms loaded, first load org.chado-xml chado-1.23/modules/phylogeny/examples/sample-phylo.chado-xml000644 000765 000024 00000017526 11256710154 024323 0ustar00cainstaff000000 000000 Fungi Fungi Metazoa Metazoa Primates Primates human Homo sapiens nematode Nematoda yeast Saccharomyces cerevisiae phylogenetic_property phylogenetic_property B phylogenetic_property D phylogenetic_property E phylogenetic_property S 1 test 0 1 24 D N E 1.1.1.1 0.1 node1 14 23 S Fungi NCBITaxon:4751 0.11 node8 19 20 E 1.1.1.1 S yeast NCBITaxon:4932 0.12 node8 17 18 E 1.1.1.1 S yeast NCBITaxon:4932 0.13 node8 15 16 E 1.1.1.1 S yeast NCBITaxon:4932 0.09 node8 21 22 E 1.1.1.1 S yeast NCBITaxon:4932 0.1 node1 2 13 D N E 1.1.1.1 S Metazoa NCBITaxon:33208 0.12 node2 11 12 E 1.1.1.1 S insect 0.1 node2 9 10 E 1.1.1.1 S nematode NCBITaxon:6231 0.05 node2 3 8 B 100 D Y E 1.1.1.1 S Primates NCBITaxon:9443 0.11 node3 6 7 E 1.1.1.1 S human NCBITaxon:9606 0.1 node3 4 5 E 1.1.1.1 S human NCBITaxon:9606 chado-1.23/modules/phylogeny/examples/sample-phylo.nhx000644 000765 000024 00000000631 11256710154 023231 0ustar00cainstaff000000 000000 (((ADH2:0.1[&&NHX:S=human:E=1.1.1.1],ADH1:0.11[&&NHX:S=human:E=1.1.1.1]):0.05[&&NHX:S=Primates:E=1.1.1.1:D=Y:B=100],ADHY:0.1[&&NHX:S=nematode:E=1.1.1.1],ADHX:0.12[&&NHX:S=insect:E=1.1.1.1]):0.1[&&NHX:S=Metazoa:E=1.1.1.1:D=N],(ADH4:0.09[&&NHX:S=yeast:E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast:E=1.1.1.1],ADH2:0.12[&&NHX:S=yeast:E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast:E=1.1.1.1]):0.1[&&NHX:S=Fungi])[&&NHX:E=1.1.1.1:D=N]; chado-1.23/modules/phenotype/phenotype.html000644 000765 000024 00000030412 11610541007 021151 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

phenotype
phenotype_cvterm
feature_phenotype

phenotype

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Comments:

$Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $
==========================================
Chado phenotype module
05-31-2011
added 'name' column to phenotype. non-unique human readable field.
=================================================================
Dependencies:
:import cvterm from cv
:import feature from sequence
=================================================================
================================================
TABLE: phenotype
================================================
A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
name text 64000 null
observable_id integer 10 The entity: e.g. anatomy_part, biological_process. cvterm.cvterm_id
attr_id integer 10 Phenotypic attribute (quality, property, attribute, character) - drawn from PATO. cvterm.cvterm_id
value text 64000 Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
cvalue_id integer 10 Phenotype attribute value (state). cvterm.cvterm_id
assay_id integer 10 Evidence type. cvterm.cvterm_id

Indices

Name Fields
phenotype_idx1 cvalue_id
phenotype_idx2 observable_id
phenotype_idx3 attr_id

Constraints

Type Fields
NOT NULL phenotype_id
NOT NULL uniquename
FOREIGN KEY observable_id
FOREIGN KEY attr_id
FOREIGN KEY cvalue_id
FOREIGN KEY assay_id
UNIQUE uniquename

phenotype_cvterm

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Comments:

================================================
TABLE: phenotype_cvterm
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
phenotype_cvterm_id integer 11 PRIMARY KEY, NOT NULL
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
phenotype_cvterm_idx1 phenotype_id
phenotype_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL phenotype_cvterm_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL rank
UNIQUE phenotype_id, cvterm_id, rank

feature_phenotype

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Comments:

================================================
TABLE: feature_phenotype
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
feature_phenotype_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id

Indices

Name Fields
feature_phenotype_idx1 feature_id
feature_phenotype_idx2 phenotype_id

Constraints

Type Fields
NOT NULL feature_phenotype_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
UNIQUE feature_id, phenotype_id
Created by SQL::Translator 0.11003 chado-1.23/modules/phenotype/phenotype.sql000644 000765 000024 00000010751 11660267217 021025 0ustar00cainstaff000000 000000 -- $Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $ -- ========================================== -- Chado phenotype module -- -- 05-31-2011 -- added 'name' column to phenotype. non-unique human readable field. -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- :import feature from sequence -- ================================================================= -- ================================================ -- TABLE: phenotype -- ================================================ CREATE TABLE phenotype ( phenotype_id SERIAL NOT NULL, primary key (phenotype_id), uniquename TEXT NOT NULL, name TEXT default null, observable_id INT, FOREIGN KEY (observable_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, attr_id INT, FOREIGN KEY (attr_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, value TEXT, cvalue_id INT, FOREIGN KEY (cvalue_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, assay_id INT, FOREIGN KEY (assay_id) REFERENCES cvterm (cvterm_id) ON DELETE SET NULL, CONSTRAINT phenotype_c1 UNIQUE (uniquename) ); CREATE INDEX phenotype_idx1 ON phenotype (cvalue_id); CREATE INDEX phenotype_idx2 ON phenotype (observable_id); CREATE INDEX phenotype_idx3 ON phenotype (attr_id); COMMENT ON TABLE phenotype IS 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.'; COMMENT ON COLUMN phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.'; COMMENT ON COLUMN phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.'; COMMENT ON COLUMN phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.'; COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).'; COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.'; -- ================================================ -- TABLE: phenotype_cvterm -- ================================================ CREATE TABLE phenotype_cvterm ( phenotype_cvterm_id SERIAL NOT NULL, primary key (phenotype_cvterm_id), phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, cvterm_id INT NOT NULL, FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, rank int not null default 0, CONSTRAINT phenotype_cvterm_c1 UNIQUE (phenotype_id, cvterm_id, rank) ); CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id); CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id); COMMENT ON TABLE phenotype_cvterm IS NULL; -- ================================================ -- TABLE: feature_phenotype -- ================================================ CREATE TABLE feature_phenotype ( feature_phenotype_id SERIAL NOT NULL, primary key (feature_phenotype_id), feature_id INT NOT NULL, FOREIGN KEY (feature_id) REFERENCES feature (feature_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, CONSTRAINT feature_phenotype_c1 UNIQUE (feature_id,phenotype_id) ); CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id); CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id); COMMENT ON TABLE feature_phenotype IS NULL; create table phenotypeprop ( phenotypeprop_id serial not null, primary key (phenotypeprop_id), phenotype_id int not null, foreign key (phenotype_id) references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint phenotypeprop_c1 unique (phenotype_id,type_id,rank) ); create index phenotypeprop_idx1 on phenotypeprop (phenotype_id); create index phenotypeprop_idx2 on phenotypeprop (type_id); COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, phenotypeprop_c1, for the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.'; chado-1.23/modules/organism/examples/000755 000765 000024 00000000000 12061672375 017710 5ustar00cainstaff000000 000000 chado-1.23/modules/organism/functions/000755 000765 000024 00000000000 12061672376 020103 5ustar00cainstaff000000 000000 chado-1.23/modules/organism/organism.html000644 000765 000024 00000026216 11256710057 020601 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

organism
organism_dbxref
organismprop

organism

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Comments:

$Id: organism.html,v 1.5 2007-04-16 16:24:12 scottcain Exp $
==========================================
Chado organism module
============
DEPENDENCIES
============
:import cvterm from cv
:import dbxref from general
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: organism
================================================
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
Field Name Data Type Size Default Value Other Foreign Key
organism_id integer 11 PRIMARY KEY, NOT NULL
abbreviation varchar 255 NULL
genus varchar 255 UNIQUE, NOT NULL
species varchar 255 UNIQUE, NOT NULL, A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.
common_name varchar 255 NULL
comment text 64000 NULL

Constraints

Type Fields
NOT NULL organism_id
NOT NULL genus
NOT NULL species
UNIQUE genus, species

organism_dbxref

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Comments:

================================================
TABLE: organism_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
organism_dbxref_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
organism_dbxref_idx1 organism_id
organism_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL organism_dbxref_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE organism_id, dbxref_id

organismprop

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Comments:

================================================
TABLE: organismprop
================================================
Tag-value properties - follows standard chado model.
Field Name Data Type Size Default Value Other Foreign Key
organismprop_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
organismprop_idx1 organism_id
organismprop_idx2 type_id

Constraints

Type Fields
NOT NULL organismprop_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE organism_id, type_id, rank
Created by SQL::Translator 0.08_01 chado-1.23/modules/organism/organism.sql000644 000765 000024 00000005501 11256710057 020426 0ustar00cainstaff000000 000000 -- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $ -- ========================================== -- Chado organism module -- -- ============ -- DEPENDENCIES -- ============ -- :import cvterm from cv -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: organism -- ================================================ create table organism ( organism_id serial not null, primary key (organism_id), abbreviation varchar(255) null, genus varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, constraint organism_c1 unique (genus,species) ); COMMENT ON TABLE organism IS 'The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.'; COMMENT ON COLUMN organism.species IS 'A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.'; -- ================================================ -- TABLE: organism_dbxref -- ================================================ create table organism_dbxref ( organism_dbxref_id serial not null, primary key (organism_dbxref_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint organism_dbxref_c1 unique (organism_id,dbxref_id) ); create index organism_dbxref_idx1 on organism_dbxref (organism_id); create index organism_dbxref_idx2 on organism_dbxref (dbxref_id); -- ================================================ -- TABLE: organismprop -- ================================================ create table organismprop ( organismprop_id serial not null, primary key (organismprop_id), organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint organismprop_c1 unique (organism_id,type_id,rank) ); create index organismprop_idx1 on organismprop (organism_id); create index organismprop_idx2 on organismprop (type_id); COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.'; chado-1.23/modules/organism/functions/organism-loading.plpgsql000644 000765 000024 00000001362 11256710057 024735 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_genus ALIAS FOR $1; v_species ALIAS FOR $2; v_common_name ALIAS FOR $3; v_organism_id INTEGER; BEGIN SELECT INTO v_organism_id organism_id FROM organism WHERE genus=v_genus AND species=v_species; IF NOT FOUND THEN INSERT INTO organism (genus,species,common_name) VALUES (v_genus,v_species,v_common_name); RETURN currval(''organism_organism_id_seq''); ELSE UPDATE organism SET common_name=v_common_name WHERE organism_id = v_organism_id; END IF; RETURN v_organism_id; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/organism/functions/organism.plpgsql000644 000765 000024 00000001174 11256710057 023323 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=$1 AND species=$2 ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE genus=substring($1,1,position('' '' IN $1)-1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT AS ' SELECT organism_id FROM organism WHERE substr(genus,1,1)=substring($1,1,1) AND species=substring($1,position('' '' IN $1)+1) ' LANGUAGE 'sql'; chado-1.23/modules/organism/functions/organism.sqlapi000644 000765 000024 00000001452 11256710057 023131 0ustar00cainstaff000000 000000 DECLARE FUNCTION get_organism_id(genus VARCHAR, species VARCHAR) RETURN INT; COMMENT ON FUNCTION get_organism_id(VARCHAR, VARCHAR) IS 'returns an organism based on its binomial genus species unique key'; DECLARE FUNCTION get_organism_id(binomial VARCHAR) RETURN INT; COMMENT ON FUNCTION get_organism_id(VARCHAR) IS 'returns an organism based on its binomial unique key. The binomial is passed as a single string. The string will split on the FIRST space - before the space is the genus, after the species. For example "Drosophila Melanogaster'; DECLARE FUNCTION get_organism_id_abbrev(binomial VARCHAR) RETURNS INT; COMMENT ON FUNCTION get_organism_id_abbrev(VARCHAR) IS 'as get_organism_id(binomial), except only the first letter of the genus is used. In theory this should still result in a unique key'; chado-1.23/modules/organism/examples/examples-orgs.chado-xml000644 000765 000024 00000001530 11256710057 024266 0ustar00cainstaff000000 000000 Fungi Fungi Metazoa Metazoa Primates Primates human Homo sapiens nematode Nematoda yeast Saccharomyces cerevisiae chado-1.23/modules/natural_diversity/natural_diversity.html000644 000765 000024 00000176774 11610541017 024472 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

nd_geolocation
nd_experiment
nd_experiment_project
nd_experimentprop
nd_experiment_pub
nd_geolocationprop
nd_protocol
nd_reagent
nd_protocol_reagent
nd_protocolprop
nd_experiment_stock
nd_experiment_protocol
nd_experiment_phenotype
nd_experiment_genotype
nd_reagent_relationship
nd_reagentprop
nd_experiment_stockprop
nd_experiment_stock_dbxref
nd_experiment_dbxref
nd_experiment_contact

nd_geolocation

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Comments:

=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import phenotype from phenotype
:import organism from organism
:import genotype from genetic
:import contact from contact
:import project from project
:import stock from stock
:import synonym
=================================================================
this probably needs some work, depending on how cross-database we
want to be. In Postgres, at least, there are much better ways to
represent geo information.
The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocation_id integer 11 PRIMARY KEY, NOT NULL
description varchar 255 A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.
latitude real 10 The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.
longitude real 10 The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.
geodetic_datum varchar 32 The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.
altitude real 10 The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.

Constraints

Type Fields
NOT NULL nd_geolocation_id

nd_experiment

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Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_id integer 11 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 10 NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_experiment_id
NOT NULL nd_geolocation_id
FOREIGN KEY nd_geolocation_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_geolocation_id
FOREIGN KEY type_id

nd_experiment_project

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Comments:

used to be nd_diversityexperiment_project
then was nd_assay_project
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_project_id integer 11 PRIMARY KEY, NOT NULL
project_id integer 10 NOT NULL project.project_id
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id

Constraints

Type Fields
NOT NULL nd_experiment_project_id
NOT NULL project_id
FOREIGN KEY project_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY project_id
FOREIGN KEY nd_experiment_id

nd_experimentprop

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Field Name Data Type Size Default Value Other Foreign Key
nd_experimentprop_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL nd_experimentprop_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_experiment_id, type_id, rank
FOREIGN KEY nd_experiment_id
FOREIGN KEY type_id

nd_experiment_pub

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Comments:

Linking nd_experiment(s) to publication(s)
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_pub_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
nd_experiment_pub_idx1 nd_experiment_id
nd_experiment_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL nd_experiment_pub_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE nd_experiment_id, pub_id

nd_geolocationprop

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Comments:

Property/value associations for geolocations. This table can store the properties such as location and environment
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocationprop_id integer 11 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 10 UNIQUE, NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_geolocationprop_id
NOT NULL nd_geolocation_id
FOREIGN KEY nd_geolocation_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_geolocation_id, type_id, rank
FOREIGN KEY nd_geolocation_id
FOREIGN KEY type_id

nd_protocol

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Comments:

A protocol can be anything that is done as part of the experiment.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The protocol name.
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_protocol_id
NOT NULL name
UNIQUE name
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY type_id

nd_reagent

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Comments:

A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_id integer 11 PRIMARY KEY, NOT NULL
name varchar 80 NOT NULL, The name of the reagent. The name should be unique for a given type.
type_id integer 10 NOT NULL, The type of the reagent, for example linker oligomer, or forward primer. cvterm.cvterm_id
feature_id integer 10 If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.

Constraints

Type Fields
NOT NULL nd_reagent_id
NOT NULL name
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY type_id

nd_protocol_reagent

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Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_reagent_id integer 11 PRIMARY KEY, NOT NULL
nd_protocol_id integer 10 NOT NULL nd_protocol.nd_protocol_id
reagent_id integer 10 NOT NULL nd_reagent.nd_reagent_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_protocol_reagent_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
NOT NULL reagent_id
FOREIGN KEY reagent_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_protocol_id
FOREIGN KEY reagent_id
FOREIGN KEY type_id

nd_protocolprop

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Comments:

Property/value associations for protocol.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocolprop_id integer 11 PRIMARY KEY, NOT NULL
nd_protocol_id integer 10 UNIQUE, NOT NULL, The protocol to which the property applies. nd_protocol.nd_protocol_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_protocolprop_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_protocol_id, type_id, rank
FOREIGN KEY nd_protocol_id
FOREIGN KEY type_id

nd_experiment_stock

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Comments:

Part of a stock or a clone of a stock that is used in an experiment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
stock_id integer 10 NOT NULL, stock used in the extraction or the corresponding stock for the clone stock.stock_id
type_id integer 10 NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_experiment_stock_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL stock_id
FOREIGN KEY stock_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY stock_id
FOREIGN KEY type_id

nd_experiment_protocol

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Comments:

Linking table: experiments to the protocols they involve.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_protocol_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
nd_protocol_id integer 10 NOT NULL nd_protocol.nd_protocol_id

Constraints

Type Fields
NOT NULL nd_experiment_protocol_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL nd_protocol_id
FOREIGN KEY nd_protocol_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY nd_protocol_id

nd_experiment_phenotype

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Comments:

Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_phenotype_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id

Constraints

Type Fields
NOT NULL nd_experiment_phenotype_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
UNIQUE nd_experiment_id, phenotype_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY phenotype_id

nd_experiment_genotype

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Comments:

Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_genotype_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id

Constraints

Type Fields
NOT NULL nd_experiment_genotype_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
UNIQUE nd_experiment_id, genotype_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY genotype_id

nd_reagent_relationship

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Comments:

Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_reagent_id integer 10 NOT NULL, The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. nd_reagent.nd_reagent_id
object_reagent_id integer 10 NOT NULL, The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. nd_reagent.nd_reagent_id
type_id integer 10 NOT NULL, The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. cvterm.cvterm_id

Constraints

Type Fields
NOT NULL nd_reagent_relationship_id
NOT NULL subject_reagent_id
FOREIGN KEY subject_reagent_id
NOT NULL object_reagent_id
FOREIGN KEY object_reagent_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY subject_reagent_id
FOREIGN KEY object_reagent_id
FOREIGN KEY type_id

nd_reagentprop

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Field Name Data Type Size Default Value Other Foreign Key
nd_reagentprop_id integer 11 PRIMARY KEY, NOT NULL
nd_reagent_id integer 10 UNIQUE, NOT NULL nd_reagent.nd_reagent_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL nd_reagentprop_id
NOT NULL nd_reagent_id
FOREIGN KEY nd_reagent_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_reagent_id, type_id, rank
FOREIGN KEY nd_reagent_id
FOREIGN KEY type_id

nd_experiment_stockprop

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Comments:

Property/value associations for experiment_stocks. This table can store the properties such as treatment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stockprop_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 10 UNIQUE, NOT NULL, The experiment_stock to which the property applies. nd_experiment_stock.nd_experiment_stock_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Constraints

Type Fields
NOT NULL nd_experiment_stockprop_id
NOT NULL nd_experiment_stock_id
FOREIGN KEY nd_experiment_stock_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE nd_experiment_stock_id, type_id, rank
FOREIGN KEY nd_experiment_stock_id
FOREIGN KEY type_id

nd_experiment_stock_dbxref

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Comments:

Cross-reference experiment_stock to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_dbxref_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 10 NOT NULL nd_experiment_stock.nd_experiment_stock_id
dbxref_id integer 10 NOT NULL dbxref.dbxref_id

Constraints

Type Fields
NOT NULL nd_experiment_stock_dbxref_id
NOT NULL nd_experiment_stock_id
FOREIGN KEY nd_experiment_stock_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY nd_experiment_stock_id
FOREIGN KEY dbxref_id

nd_experiment_dbxref

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Comments:

Cross-reference experiment to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_dbxref_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
dbxref_id integer 10 NOT NULL dbxref.dbxref_id

Constraints

Type Fields
NOT NULL nd_experiment_dbxref_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY dbxref_id

nd_experiment_contact

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Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_contact_id integer 11 PRIMARY KEY, NOT NULL
nd_experiment_id integer 10 NOT NULL nd_experiment.nd_experiment_id
contact_id integer 10 NOT NULL contact.contact_id

Constraints

Type Fields
NOT NULL nd_experiment_contact_id
NOT NULL nd_experiment_id
FOREIGN KEY nd_experiment_id
NOT NULL contact_id
FOREIGN KEY contact_id
FOREIGN KEY nd_experiment_id
FOREIGN KEY contact_id
Created by SQL::Translator 0.11003 chado-1.23/modules/natural_diversity/natural_diversity.sql000644 000765 000024 00000033432 11600145520 024302 0ustar00cainstaff000000 000000 -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import phenotype from phenotype -- :import organism from organism -- :import genotype from genetic -- :import contact from contact -- :import project from project -- :import stock from stock -- :import synonym -- ================================================================= -- this probably needs some work, depending on how cross-database we -- want to be. In Postgres, at least, there are much better ways to -- represent geo information. CREATE TABLE nd_geolocation ( nd_geolocation_id serial PRIMARY KEY NOT NULL, description character varying(255), latitude real, longitude real, geodetic_datum character varying(32), altitude real ); COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.'; COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.'; COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.'; COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.'; COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.'; COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.'; CREATE TABLE nd_experiment ( nd_experiment_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); -- --used to be nd_diversityexperiment_project --then was nd_assay_project CREATE TABLE nd_experiment_project ( nd_experiment_project_id serial PRIMARY KEY NOT NULL, project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_experimentprop ( nd_experimentprop_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED , value text null, rank integer NOT NULL default 0, constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank) ); CREATE TABLE nd_experiment_pub ( nd_experiment_pub_id serial PRIMARY KEY not null, nd_experiment_id int not null, foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id) ); create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id); create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id); COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)'; CREATE TABLE nd_geolocationprop ( nd_geolocationprop_id serial PRIMARY KEY NOT NULL, nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer NOT NULL DEFAULT 0, constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank) ); COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment'; COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_protocol ( nd_protocol_id serial PRIMARY KEY NOT NULL, name character varying(255) NOT NULL unique, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.'; COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.'; CREATE TABLE nd_reagent ( nd_reagent_id serial PRIMARY KEY NOT NULL, name character varying(80) NOT NULL, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, feature_id integer ); COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.'; COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.'; COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.'; COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.'; CREATE TABLE nd_protocol_reagent ( nd_protocol_reagent_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); CREATE TABLE nd_protocolprop ( nd_protocolprop_id serial PRIMARY KEY NOT NULL, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank) ); COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.'; COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.'; COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock ( nd_experiment_stock_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment'; COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone'; CREATE TABLE nd_experiment_protocol ( nd_experiment_protocol_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.'; CREATE TABLE nd_experiment_phenotype ( nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED, constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id) ); COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.'; CREATE TABLE nd_experiment_genotype ( nd_experiment_genotype_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED , constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id) ); COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.'; CREATE TABLE nd_reagent_relationship ( nd_reagent_relationship_id serial PRIMARY KEY NOT NULL, subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.'; COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.'; CREATE TABLE nd_reagentprop ( nd_reagentprop_id serial PRIMARY KEY NOT NULL, nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank) ); CREATE TABLE nd_experiment_stockprop ( nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank integer DEFAULT 0 NOT NULL, constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank) ); COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment'; COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.'; COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.'; COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.'; COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.'; CREATE TABLE nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc'; CREATE TABLE nd_experiment_dbxref ( nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED ); COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc'; CREATE TABLE nd_experiment_contact ( nd_experiment_contact_id serial PRIMARY KEY NOT NULL, nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED, contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED ); chado-1.23/modules/map/map.html000644 000765 000024 00000037174 11256710150 016474 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

featuremap
featurerange
featurepos
featuremap_pub

featuremap

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Comments:

$Id: map.html,v 1.3 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado map module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
=================================================================
================================================
TABLE: featuremap
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE
description text 64000
unittype_id integer 10 NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL featuremap_id
FOREIGN KEY unittype_id
UNIQUE name

featurerange

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Comments:

================================================
TABLE: featurerange
================================================
In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.
Field Name Data Type Size Default Value Other Foreign Key
featurerange_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 10 NOT NULL, featuremap_id is the id of the feature being mapped. featuremap.featuremap_id
feature_id integer 10 NOT NULL feature.feature_id
leftstartf_id integer 10 NOT NULL feature.feature_id
leftendf_id integer 10 feature.feature_id
rightstartf_id integer 10 feature.feature_id
rightendf_id integer 10 NOT NULL feature.feature_id
rangestr varchar 255

Indices

Name Fields
featurerange_idx1 featuremap_id
featurerange_idx2 feature_id
featurerange_idx3 leftstartf_id
featurerange_idx4 leftendf_id
featurerange_idx5 rightstartf_id
featurerange_idx6 rightendf_id

Constraints

Type Fields
NOT NULL featurerange_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL leftstartf_id
FOREIGN KEY leftstartf_id
FOREIGN KEY leftendf_id
FOREIGN KEY rightstartf_id
NOT NULL rightendf_id
FOREIGN KEY rightendf_id

featurepos

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Comments:

================================================
TABLE: featurepos
================================================
Field Name Data Type Size Default Value Other Foreign Key
featurepos_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 11 NOT NULL featuremap.featuremap_id
feature_id integer 10 NOT NULL feature.feature_id
map_feature_id integer 10 NOT NULL, map_feature_id links to the feature (map) upon which the feature is being localized. feature.feature_id
mappos float 20 NOT NULL

Indices

Name Fields
featurepos_idx1 featuremap_id
featurepos_idx2 feature_id
featurepos_idx3 map_feature_id

Constraints

Type Fields
NOT NULL featurepos_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL map_feature_id
FOREIGN KEY map_feature_id
NOT NULL mappos

featuremap_pub

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Comments:

================================================
TABLE: featuremap_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_pub_id integer 11 PRIMARY KEY, NOT NULL
featuremap_id integer 10 NOT NULL featuremap.featuremap_id
pub_id integer 10 NOT NULL pub.pub_id

Indices

Name Fields
featuremap_pub_idx1 featuremap_id
featuremap_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL featuremap_pub_id
NOT NULL featuremap_id
FOREIGN KEY featuremap_id
NOT NULL pub_id
FOREIGN KEY pub_id
Created by SQL::Translator 0.08_01 chado-1.23/modules/map/map.sql000644 000765 000024 00000010206 11256710150 016312 0ustar00cainstaff000000 000000 -- $Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado map module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: featuremap -- ================================================ create table featuremap ( featuremap_id serial not null, primary key (featuremap_id), name varchar(255), description text, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, constraint featuremap_c1 unique (name) ); -- ================================================ -- TABLE: featurerange -- ================================================ create table featurerange ( featurerange_id serial not null, primary key (featurerange_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftstartf_id int not null, foreign key (leftstartf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, leftendf_id int, foreign key (leftendf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightstartf_id int, foreign key (rightstartf_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, rightendf_id int not null, foreign key (rightendf_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, rangestr varchar(255) ); create index featurerange_idx1 on featurerange (featuremap_id); create index featurerange_idx2 on featurerange (feature_id); create index featurerange_idx3 on featurerange (leftstartf_id); create index featurerange_idx4 on featurerange (leftendf_id); create index featurerange_idx5 on featurerange (rightstartf_id); create index featurerange_idx6 on featurerange (rightendf_id); COMMENT ON TABLE featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.'; COMMENT ON COLUMN featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.'; -- ================================================ -- TABLE: featurepos -- ================================================ create table featurepos ( featurepos_id serial not null, primary key (featurepos_id), featuremap_id serial not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, map_feature_id int not null, foreign key (map_feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, mappos float not null ); create index featurepos_idx1 on featurepos (featuremap_id); create index featurepos_idx2 on featurepos (feature_id); create index featurepos_idx3 on featurepos (map_feature_id); COMMENT ON COLUMN featurepos.map_feature_id IS 'map_feature_id links to the feature (map) upon which the feature is being localized.'; -- ================================================ -- TABLE: featuremap_pub -- ================================================ create table featuremap_pub ( featuremap_pub_id serial not null, primary key (featuremap_pub_id), featuremap_id int not null, foreign key (featuremap_id) references featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED ); create index featuremap_pub_idx1 on featuremap_pub (featuremap_id); create index featuremap_pub_idx2 on featuremap_pub (pub_id); chado-1.23/modules/mage/mage.html000644 000765 000024 00000432370 11435270312 016761 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

mageml
magedocumentation
protocol
protocolparam
channel
arraydesign
arraydesignprop
assay
assayprop
assay_project
biomaterial
biomaterial_relationship
biomaterialprop
biomaterial_dbxref
treatment
biomaterial_treatment
assay_biomaterial
acquisition
acquisitionprop
acquisition_relationship
quantification
quantificationprop
quantification_relationship
control
element
elementresult
element_relationship
elementresult_relationship
study
study_assay
studydesign
studydesignprop
studyfactor
studyfactorvalue
studyprop
studyprop_feature

mageml

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Comments:

$Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $
==========================================
Chado mage module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import contact from contact
:import dbxref from general
:import tableinfo from general
:import project from project
:import analysis from companalysis
=================================================================
================================================
TABLE: mageml
================================================
This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.
Field Name Data Type Size Default Value Other Foreign Key
mageml_id integer 11 PRIMARY KEY, NOT NULL
mage_package text 64000 NOT NULL
mage_ml text 64000 NOT NULL

Constraints

Type Fields
NOT NULL mageml_id
NOT NULL mage_package
NOT NULL mage_ml

magedocumentation

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Comments:

================================================
TABLE: magedocumentation
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
magedocumentation_id integer 11 PRIMARY KEY, NOT NULL
mageml_id integer 10 NOT NULL mageml.mageml_id
tableinfo_id integer 10 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
mageidentifier text 64000 NOT NULL

Indices

Name Fields
magedocumentation_idx1 mageml_id
magedocumentation_idx2 tableinfo_id
magedocumentation_idx3 row_id

Constraints

Type Fields
NOT NULL magedocumentation_id
NOT NULL mageml_id
FOREIGN KEY mageml_id
NOT NULL tableinfo_id
FOREIGN KEY tableinfo_id
NOT NULL row_id
NOT NULL mageidentifier

protocol

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Comments:

================================================
TABLE: protocol
================================================
Procedural notes on how data was prepared and processed.
Field Name Data Type Size Default Value Other Foreign Key
protocol_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NOT NULL cvterm.cvterm_id
pub_id integer 10 NULL pub.pub_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
uri text 64000 NULL
protocoldescription text 64000 NULL
hardwaredescription text 64000 NULL
softwaredescription text 64000 NULL

Indices

Name Fields
protocol_idx1 type_id
protocol_idx2 pub_id
protocol_idx3 dbxref_id

Constraints

Type Fields
NOT NULL protocol_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY pub_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

protocolparam

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Comments:

================================================
TABLE: protocolparam
================================================
Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.
Field Name Data Type Size Default Value Other Foreign Key
protocolparam_id integer 11 PRIMARY KEY, NOT NULL
protocol_id integer 10 NOT NULL protocol.protocol_id
name text 64000 NOT NULL
datatype_id integer 10 NULL cvterm.cvterm_id
unittype_id integer 10 NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
protocolparam_idx1 protocol_id
protocolparam_idx2 datatype_id
protocolparam_idx3 unittype_id

Constraints

Type Fields
NOT NULL protocolparam_id
NOT NULL protocol_id
FOREIGN KEY protocol_id
NOT NULL name
FOREIGN KEY datatype_id
FOREIGN KEY unittype_id
NOT NULL rank

channel

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Comments:

================================================
TABLE: channel
================================================
Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).
Field Name Data Type Size Default Value Other Foreign Key
channel_id integer 11 PRIMARY KEY, NOT NULL
name text 64000 UNIQUE, NOT NULL
definition text 64000 NOT NULL

Constraints

Type Fields
NOT NULL channel_id
NOT NULL name
NOT NULL definition
UNIQUE name

arraydesign

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Comments:

================================================
TABLE: arraydesign
================================================
General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).
Field Name Data Type Size Default Value Other Foreign Key
arraydesign_id integer 11 PRIMARY KEY, NOT NULL
manufacturer_id integer 10 NOT NULL contact.contact_id
platformtype_id integer 10 NOT NULL cvterm.cvterm_id
substratetype_id integer 10 NULL cvterm.cvterm_id
protocol_id integer 10 NULL protocol.protocol_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
version text 64000 NULL
description text 64000 NULL
array_dimensions text 64000 NULL
element_dimensions text 64000 NULL
num_of_elements integer 10 NULL
num_array_columns integer 10 NULL
num_array_rows integer 10 NULL
num_grid_columns integer 10 NULL
num_grid_rows integer 10 NULL
num_sub_columns integer 10 NULL
num_sub_rows integer 10 NULL

Indices

Name Fields
arraydesign_idx1 manufacturer_id
arraydesign_idx2 platformtype_id
arraydesign_idx3 substratetype_id
arraydesign_idx4 protocol_id
arraydesign_idx5 dbxref_id

Constraints

Type Fields
NOT NULL arraydesign_id
NOT NULL manufacturer_id
FOREIGN KEY manufacturer_id
NOT NULL platformtype_id
FOREIGN KEY platformtype_id
FOREIGN KEY substratetype_id
FOREIGN KEY protocol_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

arraydesignprop

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Comments:

================================================
TABLE: arraydesignprop
================================================
Extra array design properties that are not accounted for in arraydesign.
Field Name Data Type Size Default Value Other Foreign Key
arraydesignprop_id integer 11 PRIMARY KEY, NOT NULL
arraydesign_id integer 10 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
arraydesignprop_idx1 arraydesign_id
arraydesignprop_idx2 type_id

Constraints

Type Fields
NOT NULL arraydesignprop_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE arraydesign_id, type_id, rank

assay

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Comments:

================================================
TABLE: assay
================================================
An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.
Field Name Data Type Size Default Value Other Foreign Key
assay_id integer 11 PRIMARY KEY, NOT NULL
arraydesign_id integer 10 NOT NULL arraydesign.arraydesign_id
protocol_id integer 10 NULL protocol.protocol_id
assaydate timestamp 0 current_timestamp
arrayidentifier text 64000 NULL
arraybatchidentifier text 64000 NULL
operator_id integer 10 NOT NULL contact.contact_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
assay_idx1 arraydesign_id
assay_idx2 protocol_id
assay_idx3 operator_id
assay_idx4 dbxref_id

Constraints

Type Fields
NOT NULL assay_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
FOREIGN KEY protocol_id
NOT NULL operator_id
FOREIGN KEY operator_id
FOREIGN KEY dbxref_id
UNIQUE name

assayprop

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Comments:

================================================
TABLE: assayprop
================================================
Extra assay properties that are not accounted for in assay.
Field Name Data Type Size Default Value Other Foreign Key
assayprop_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assayprop_idx1 assay_id
assayprop_idx2 type_id

Constraints

Type Fields
NOT NULL assayprop_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE assay_id, type_id, rank

assay_project

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Comments:

================================================
TABLE: assay_project
================================================
Link assays to projects.
Field Name Data Type Size Default Value Other Foreign Key
assay_project_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
project_id integer 10 UNIQUE, NOT NULL project.project_id

Indices

Name Fields
assay_project_idx1 assay_id
assay_project_idx2 project_id

Constraints

Type Fields
NOT NULL assay_project_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL project_id
FOREIGN KEY project_id
UNIQUE assay_id, project_id

biomaterial

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Comments:

================================================
TABLE: biomaterial
================================================
A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_id integer 11 PRIMARY KEY, NOT NULL
taxon_id integer 10 NULL organism.organism_id
biosourceprovider_id integer 10 NULL contact.contact_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
biomaterial_idx1 taxon_id
biomaterial_idx2 biosourceprovider_id
biomaterial_idx3 dbxref_id

Constraints

Type Fields
NOT NULL biomaterial_id
FOREIGN KEY taxon_id
FOREIGN KEY biosourceprovider_id
FOREIGN KEY dbxref_id
UNIQUE name

biomaterial_relationship

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Comments:

================================================
TABLE: biomaterial_relationship
================================================
Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id

Indices

Name Fields
biomaterial_relationship_idx1 subject_id
biomaterial_relationship_idx2 object_id
biomaterial_relationship_idx3 type_id

Constraints

Type Fields
NOT NULL biomaterial_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

biomaterialprop

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Comments:

================================================
TABLE: biomaterialprop
================================================
Extra biomaterial properties that are not accounted for in biomaterial.
Field Name Data Type Size Default Value Other Foreign Key
biomaterialprop_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
biomaterialprop_idx1 biomaterial_id
biomaterialprop_idx2 type_id

Constraints

Type Fields
NOT NULL biomaterialprop_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE biomaterial_id, type_id, rank

biomaterial_dbxref

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Comments:

================================================
TABLE: biomaterial_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_dbxref_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
biomaterial_dbxref_idx1 biomaterial_id
biomaterial_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL biomaterial_dbxref_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
UNIQUE biomaterial_id, dbxref_id

treatment

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Comments:

================================================
TABLE: treatment
================================================
A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.
Field Name Data Type Size Default Value Other Foreign Key
treatment_id integer 11 PRIMARY KEY, NOT NULL
rank integer 10 0 NOT NULL
biomaterial_id integer 10 NOT NULL biomaterial.biomaterial_id
type_id integer 10 NOT NULL cvterm.cvterm_id
protocol_id integer 10 NULL protocol.protocol_id
name text 64000 NULL

Indices

Name Fields
treatment_idx1 biomaterial_id
treatment_idx2 type_id
treatment_idx3 protocol_id

Constraints

Type Fields
NOT NULL treatment_id
NOT NULL rank
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL type_id
FOREIGN KEY type_id
FOREIGN KEY protocol_id

biomaterial_treatment

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================================================
TABLE: biomaterial_treatment
================================================
Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_treatment_id integer 11 PRIMARY KEY, NOT NULL
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
treatment_id integer 10 UNIQUE, NOT NULL treatment.treatment_id
unittype_id integer 10 NULL cvterm.cvterm_id
value float 15 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
biomaterial_treatment_idx1 biomaterial_id
biomaterial_treatment_idx2 treatment_id
biomaterial_treatment_idx3 unittype_id

Constraints

Type Fields
NOT NULL biomaterial_treatment_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
NOT NULL treatment_id
FOREIGN KEY treatment_id
FOREIGN KEY unittype_id
NOT NULL rank
UNIQUE biomaterial_id, treatment_id

assay_biomaterial

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Comments:

================================================
TABLE: assay_biomaterial
================================================
A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).
Field Name Data Type Size Default Value Other Foreign Key
assay_biomaterial_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id
biomaterial_id integer 10 UNIQUE, NOT NULL biomaterial.biomaterial_id
channel_id integer 10 NULL UNIQUE channel.channel_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assay_biomaterial_idx1 assay_id
assay_biomaterial_idx2 biomaterial_id
assay_biomaterial_idx3 channel_id

Constraints

Type Fields
NOT NULL assay_biomaterial_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL biomaterial_id
FOREIGN KEY biomaterial_id
FOREIGN KEY channel_id
NOT NULL rank
UNIQUE assay_id, biomaterial_id, channel_id, rank

acquisition

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Comments:

================================================
TABLE: acquisition
================================================
This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_id integer 11 PRIMARY KEY, NOT NULL
assay_id integer 10 NOT NULL assay.assay_id
protocol_id integer 10 NULL protocol.protocol_id
channel_id integer 10 NULL channel.channel_id
acquisitiondate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
acquisition_idx1 assay_id
acquisition_idx2 protocol_id
acquisition_idx3 channel_id

Constraints

Type Fields
NOT NULL acquisition_id
NOT NULL assay_id
FOREIGN KEY assay_id
FOREIGN KEY protocol_id
FOREIGN KEY channel_id
UNIQUE name

acquisitionprop

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================================================
TABLE: acquisitionprop
================================================
Parameters associated with image acquisition.
Field Name Data Type Size Default Value Other Foreign Key
acquisitionprop_id integer 11 PRIMARY KEY, NOT NULL
acquisition_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisitionprop_idx1 acquisition_id
acquisitionprop_idx2 type_id

Constraints

Type Fields
NOT NULL acquisitionprop_id
NOT NULL acquisition_id
FOREIGN KEY acquisition_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE acquisition_id, type_id, rank

acquisition_relationship

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Comments:

================================================
TABLE: acquisition_relationship
================================================
Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL acquisition.acquisition_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisition_relationship_idx1 subject_id
acquisition_relationship_idx2 type_id
acquisition_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL acquisition_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

quantification

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Comments:

================================================
TABLE: quantification
================================================
Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.
Field Name Data Type Size Default Value Other Foreign Key
quantification_id integer 11 PRIMARY KEY, NOT NULL
acquisition_id integer 10 NOT NULL acquisition.acquisition_id
operator_id integer 10 NULL contact.contact_id
protocol_id integer 10 NULL protocol.protocol_id
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
quantificationdate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
quantification_idx1 acquisition_id
quantification_idx2 operator_id
quantification_idx3 protocol_id
quantification_idx4 analysis_id

Constraints

Type Fields
NOT NULL quantification_id
NOT NULL acquisition_id
FOREIGN KEY acquisition_id
FOREIGN KEY operator_id
FOREIGN KEY protocol_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
UNIQUE name, analysis_id

quantificationprop

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Comments:

================================================
TABLE: quantificationprop
================================================
Extra quantification properties that are not accounted for in quantification.
Field Name Data Type Size Default Value Other Foreign Key
quantificationprop_id integer 11 PRIMARY KEY, NOT NULL
quantification_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
quantificationprop_idx1 quantification_id
quantificationprop_idx2 type_id

Constraints

Type Fields
NOT NULL quantificationprop_id
NOT NULL quantification_id
FOREIGN KEY quantification_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE quantification_id, type_id, rank

quantification_relationship

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Comments:

================================================
TABLE: quantification_relationship
================================================
There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.
Field Name Data Type Size Default Value Other Foreign Key
quantification_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL quantification.quantification_id

Indices

Name Fields
quantification_relationship_idx1 subject_id
quantification_relationship_idx2 type_id
quantification_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL quantification_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

control

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Comments:

================================================
TABLE: control
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
control_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NOT NULL cvterm.cvterm_id
assay_id integer 10 NOT NULL assay.assay_id
tableinfo_id integer 10 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
name text 64000 NULL
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
control_idx1 type_id
control_idx2 assay_id
control_idx3 tableinfo_id
control_idx4 row_id

Constraints

Type Fields
NOT NULL control_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL tableinfo_id
FOREIGN KEY tableinfo_id
NOT NULL row_id
NOT NULL rank

element

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Comments:

================================================
TABLE: element
================================================
Represents a feature of the array. This is typically a region of the array coated or bound to DNA.
Field Name Data Type Size Default Value Other Foreign Key
element_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 NULL UNIQUE feature.feature_id
arraydesign_id integer 10 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 10 NULL cvterm.cvterm_id
dbxref_id integer 10 NULL dbxref.dbxref_id

Indices

Name Fields
element_idx1 feature_id
element_idx2 arraydesign_id
element_idx3 type_id
element_idx4 dbxref_id

Constraints

Type Fields
NOT NULL element_id
FOREIGN KEY feature_id
NOT NULL arraydesign_id
FOREIGN KEY arraydesign_id
FOREIGN KEY type_id
FOREIGN KEY dbxref_id
UNIQUE feature_id, arraydesign_id

elementresult

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Comments:

================================================
TABLE: element_result
================================================
An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_id integer 11 PRIMARY KEY, NOT NULL
element_id integer 10 UNIQUE, NOT NULL element.element_id
quantification_id integer 10 UNIQUE, NOT NULL quantification.quantification_id
signal float 20 NOT NULL

Indices

Name Fields
elementresult_idx1 element_id
elementresult_idx2 quantification_id
elementresult_idx3 signal

Constraints

Type Fields
NOT NULL elementresult_id
NOT NULL element_id
FOREIGN KEY element_id
NOT NULL quantification_id
FOREIGN KEY quantification_id
NOT NULL signal
UNIQUE element_id, quantification_id

element_relationship

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Comments:

================================================
TABLE: element_relationship
================================================
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Field Name Data Type Size Default Value Other Foreign Key
element_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL element.element_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL element.element_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
element_relationship_idx1 subject_id
element_relationship_idx2 type_id
element_relationship_idx3 object_id
element_relationship_idx4 value

Constraints

Type Fields
NOT NULL element_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

elementresult_relationship

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Comments:

================================================
TABLE: elementresult_relationship
================================================
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL elementresult.elementresult_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL elementresult.elementresult_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
elementresult_relationship_idx1 subject_id
elementresult_relationship_idx2 type_id
elementresult_relationship_idx3 object_id
elementresult_relationship_idx4 value

Constraints

Type Fields
NOT NULL elementresult_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL rank
UNIQUE subject_id, object_id, type_id, rank

study

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Comments:

================================================
TABLE: study
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_id integer 11 PRIMARY KEY, NOT NULL
contact_id integer 10 NOT NULL contact.contact_id
pub_id integer 10 NULL pub.pub_id
dbxref_id integer 10 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
description text 64000 NULL

Indices

Name Fields
study_idx1 contact_id
study_idx2 pub_id
study_idx3 dbxref_id

Constraints

Type Fields
NOT NULL study_id
NOT NULL contact_id
FOREIGN KEY contact_id
FOREIGN KEY pub_id
FOREIGN KEY dbxref_id
NOT NULL name
UNIQUE name

study_assay

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Comments:

================================================
TABLE: study_assay
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_assay_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 UNIQUE, NOT NULL study.study_id
assay_id integer 10 UNIQUE, NOT NULL assay.assay_id

Indices

Name Fields
study_assay_idx1 study_id
study_assay_idx2 assay_id

Constraints

Type Fields
NOT NULL study_assay_id
NOT NULL study_id
FOREIGN KEY study_id
NOT NULL assay_id
FOREIGN KEY assay_id
UNIQUE study_id, assay_id

studydesign

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Comments:

================================================
TABLE: studydesign
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesign_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 NOT NULL study.study_id
description text 64000 NULL

Indices

Name Fields
studydesign_idx1 study_id

Constraints

Type Fields
NOT NULL studydesign_id
NOT NULL study_id
FOREIGN KEY study_id

studydesignprop

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Comments:

================================================
TABLE: studydesignprop
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesignprop_id integer 11 PRIMARY KEY, NOT NULL
studydesign_id integer 10 UNIQUE, NOT NULL studydesign.studydesign_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studydesignprop_idx1 studydesign_id
studydesignprop_idx2 type_id

Constraints

Type Fields
NOT NULL studydesignprop_id
NOT NULL studydesign_id
FOREIGN KEY studydesign_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE studydesign_id, type_id, rank

studyfactor

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Comments:

================================================
TABLE: studyfactor
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactor_id integer 11 PRIMARY KEY, NOT NULL
studydesign_id integer 10 NOT NULL studydesign.studydesign_id
type_id integer 10 NULL cvterm.cvterm_id
name text 64000 NOT NULL
description text 64000 NULL

Indices

Name Fields
studyfactor_idx1 studydesign_id
studyfactor_idx2 type_id

Constraints

Type Fields
NOT NULL studyfactor_id
NOT NULL studydesign_id
FOREIGN KEY studydesign_id
FOREIGN KEY type_id
NOT NULL name

studyfactorvalue

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Comments:

================================================
TABLE: studyfactorvalue
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactorvalue_id integer 11 PRIMARY KEY, NOT NULL
studyfactor_id integer 10 NOT NULL studyfactor.studyfactor_id
assay_id integer 10 NOT NULL assay.assay_id
factorvalue text 64000 NULL
name text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
studyfactorvalue_idx1 studyfactor_id
studyfactorvalue_idx2 assay_id

Constraints

Type Fields
NOT NULL studyfactorvalue_id
NOT NULL studyfactor_id
FOREIGN KEY studyfactor_id
NOT NULL assay_id
FOREIGN KEY assay_id
NOT NULL rank

studyprop

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Comments:

studyprop and studyprop_feature added for Kara Dolinski's group
Here is her description of it:
Both of the tables are used for our YFGdb project
(http://yfgdb.princeton.edu/), which uses chado.
Here is how we use those tables, using the following example:
http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969
The above data set is represented as a row in the STUDY table. We have
lots of attributes that we want to store about each STUDY (status, etc)
and in the official schema, the only prop table we could use was the
STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN
table when we often have no real data to store in that table (small
percent of our collection use MAGE-ML unfortunately, and even fewer
provide all the data in the MAGE model, of which STUDYDESIGN is a vestige).
So, we created a STUDYPROP table. I'd think this table would be
generally useful to people storing various types of data sets via the
STUDY table.
The other new table is STUDYPROP_FEATURE. This basically allows us to
group features together per study. For example, we can store microarray
clustering results by saying that the STUDYPROP type is 'cluster' (via
type_id -> CVTERM of course), the value is 'cluster id 123', and then
that cluster would be associated with all the features that are in that
cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is
fine by us!
studyprop
Field Name Data Type Size Default Value Other Foreign Key
studyprop_id integer 11 PRIMARY KEY, NOT NULL
study_id integer 10 UNIQUE, NOT NULL study.study_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studyprop_idx1 study_id
studyprop_idx2 type_id

Constraints

Type Fields
NOT NULL studyprop_id
NOT NULL study_id
FOREIGN KEY study_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE study_id, type_id, rank

studyprop_feature

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Comments:

studyprop_feature
Field Name Data Type Size Default Value Other Foreign Key
studyprop_feature_id integer 11 PRIMARY KEY, NOT NULL
studyprop_id integer 10 UNIQUE, NOT NULL studyprop.studyprop_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
type_id integer 10 cvterm.cvterm_id

Indices

Name Fields
studyprop_feature_idx1 studyprop_id
studyprop_feature_idx2 feature_id

Constraints

Type Fields
NOT NULL studyprop_feature_id
NOT NULL studyprop_id
FOREIGN KEY studyprop_id
NOT NULL feature_id
FOREIGN KEY feature_id
FOREIGN KEY type_id
UNIQUE studyprop_id, feature_id
Created by SQL::Translator 0.11003 chado-1.23/modules/mage/mage.sql000644 000765 000024 00000107247 11435270312 016616 0ustar00cainstaff000000 000000 -- $Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $ -- ========================================== -- Chado mage module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- :import contact from contact -- :import dbxref from general -- :import tableinfo from general -- :import project from project -- :import analysis from companalysis -- ================================================================= -- ================================================ -- TABLE: mageml -- ================================================ create table mageml ( mageml_id serial not null, primary key (mageml_id), mage_package text not null, mage_ml text not null ); COMMENT ON TABLE mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.'; -- ================================================ -- TABLE: magedocumentation -- ================================================ create table magedocumentation ( magedocumentation_id serial not null, primary key (magedocumentation_id), mageml_id int not null, foreign key (mageml_id) references mageml (mageml_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, mageidentifier text not null ); create index magedocumentation_idx1 on magedocumentation (mageml_id); create index magedocumentation_idx2 on magedocumentation (tableinfo_id); create index magedocumentation_idx3 on magedocumentation (row_id); COMMENT ON TABLE magedocumentation IS NULL; -- ================================================ -- TABLE: protocol -- ================================================ create table protocol ( protocol_id serial not null, primary key (protocol_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, uri text null, protocoldescription text null, hardwaredescription text null, softwaredescription text null, constraint protocol_c1 unique (name) ); create index protocol_idx1 on protocol (type_id); create index protocol_idx2 on protocol (pub_id); create index protocol_idx3 on protocol (dbxref_id); COMMENT ON TABLE protocol IS 'Procedural notes on how data was prepared and processed.'; -- ================================================ -- TABLE: protocolparam -- ================================================ create table protocolparam ( protocolparam_id serial not null, primary key (protocolparam_id), protocol_id int not null, foreign key (protocol_id) references protocol (protocol_id) on delete cascade INITIALLY DEFERRED, name text not null, datatype_id int null, foreign key (datatype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value text null, rank int not null default 0 ); create index protocolparam_idx1 on protocolparam (protocol_id); create index protocolparam_idx2 on protocolparam (datatype_id); create index protocolparam_idx3 on protocolparam (unittype_id); COMMENT ON TABLE protocolparam IS 'Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.'; -- ================================================ -- TABLE: channel -- ================================================ create table channel ( channel_id serial not null, primary key (channel_id), name text not null, definition text not null, constraint channel_c1 unique (name) ); COMMENT ON TABLE channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).'; -- ================================================ -- TABLE: arraydesign -- ================================================ create table arraydesign ( arraydesign_id serial not null, primary key (arraydesign_id), manufacturer_id int not null, foreign key (manufacturer_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, platformtype_id int not null, foreign key (platformtype_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, substratetype_id int null, foreign key (substratetype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, version text null, description text null, array_dimensions text null, element_dimensions text null, num_of_elements int null, num_array_columns int null, num_array_rows int null, num_grid_columns int null, num_grid_rows int null, num_sub_columns int null, num_sub_rows int null, constraint arraydesign_c1 unique (name) ); create index arraydesign_idx1 on arraydesign (manufacturer_id); create index arraydesign_idx2 on arraydesign (platformtype_id); create index arraydesign_idx3 on arraydesign (substratetype_id); create index arraydesign_idx4 on arraydesign (protocol_id); create index arraydesign_idx5 on arraydesign (dbxref_id); COMMENT ON TABLE arraydesign IS 'General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).'; -- ================================================ -- TABLE: arraydesignprop -- ================================================ create table arraydesignprop ( arraydesignprop_id serial not null, primary key (arraydesignprop_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint arraydesignprop_c1 unique (arraydesign_id,type_id,rank) ); create index arraydesignprop_idx1 on arraydesignprop (arraydesign_id); create index arraydesignprop_idx2 on arraydesignprop (type_id); COMMENT ON TABLE arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.'; -- ================================================ -- TABLE: assay -- ================================================ create table assay ( assay_id serial not null, primary key (assay_id), arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, assaydate timestamp null default current_timestamp, arrayidentifier text null, arraybatchidentifier text null, operator_id int not null, foreign key (operator_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint assay_c1 unique (name) ); create index assay_idx1 on assay (arraydesign_id); create index assay_idx2 on assay (protocol_id); create index assay_idx3 on assay (operator_id); create index assay_idx4 on assay (dbxref_id); COMMENT ON TABLE assay IS 'An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.'; -- ================================================ -- TABLE: assayprop -- ================================================ create table assayprop ( assayprop_id serial not null, primary key (assayprop_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint assayprop_c1 unique (assay_id,type_id,rank) ); create index assayprop_idx1 on assayprop (assay_id); create index assayprop_idx2 on assayprop (type_id); COMMENT ON TABLE assayprop IS 'Extra assay properties that are not accounted for in assay.'; -- ================================================ -- TABLE: assay_project -- ================================================ create table assay_project ( assay_project_id serial not null, primary key (assay_project_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) INITIALLY DEFERRED, project_id int not null, foreign key (project_id) references project (project_id) INITIALLY DEFERRED, constraint assay_project_c1 unique (assay_id,project_id) ); create index assay_project_idx1 on assay_project (assay_id); create index assay_project_idx2 on assay_project (project_id); COMMENT ON TABLE assay_project IS 'Link assays to projects.'; -- ================================================ -- TABLE: biomaterial -- ================================================ create table biomaterial ( biomaterial_id serial not null, primary key (biomaterial_id), taxon_id int null, foreign key (taxon_id) references organism (organism_id) on delete set null INITIALLY DEFERRED, biosourceprovider_id int null, foreign key (biosourceprovider_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text null, description text null, constraint biomaterial_c1 unique (name) ); create index biomaterial_idx1 on biomaterial (taxon_id); create index biomaterial_idx2 on biomaterial (biosourceprovider_id); create index biomaterial_idx3 on biomaterial (dbxref_id); COMMENT ON TABLE biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.'; -- ================================================ -- TABLE: biomaterial_relationship -- ================================================ create table biomaterial_relationship ( biomaterial_relationship_id serial not null, primary key (biomaterial_relationship_id), subject_id int not null, foreign key (subject_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references biomaterial (biomaterial_id) INITIALLY DEFERRED, constraint biomaterial_relationship_c1 unique (subject_id,object_id,type_id) ); create index biomaterial_relationship_idx1 on biomaterial_relationship (subject_id); create index biomaterial_relationship_idx2 on biomaterial_relationship (object_id); create index biomaterial_relationship_idx3 on biomaterial_relationship (type_id); COMMENT ON TABLE biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.'; -- ================================================ -- TABLE: biomaterialprop -- ================================================ create table biomaterialprop ( biomaterialprop_id serial not null, primary key (biomaterialprop_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint biomaterialprop_c1 unique (biomaterial_id,type_id,rank) ); create index biomaterialprop_idx1 on biomaterialprop (biomaterial_id); create index biomaterialprop_idx2 on biomaterialprop (type_id); COMMENT ON TABLE biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.'; -- ================================================ -- TABLE: biomaterial_dbxref -- ================================================ create table biomaterial_dbxref ( biomaterial_dbxref_id serial not null, primary key (biomaterial_dbxref_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, constraint biomaterial_dbxref_c1 unique (biomaterial_id,dbxref_id) ); create index biomaterial_dbxref_idx1 on biomaterial_dbxref (biomaterial_id); create index biomaterial_dbxref_idx2 on biomaterial_dbxref (dbxref_id); -- ================================================ -- TABLE: treatment -- ================================================ create table treatment ( treatment_id serial not null, primary key (treatment_id), rank int not null default 0, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, name text null ); create index treatment_idx1 on treatment (biomaterial_id); create index treatment_idx2 on treatment (type_id); create index treatment_idx3 on treatment (protocol_id); COMMENT ON TABLE treatment IS 'A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.'; -- ================================================ -- TABLE: biomaterial_treatment -- ================================================ create table biomaterial_treatment ( biomaterial_treatment_id serial not null, primary key (biomaterial_treatment_id), biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, treatment_id int not null, foreign key (treatment_id) references treatment (treatment_id) on delete cascade INITIALLY DEFERRED, unittype_id int null, foreign key (unittype_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, value float(15) null, rank int not null default 0, constraint biomaterial_treatment_c1 unique (biomaterial_id,treatment_id) ); create index biomaterial_treatment_idx1 on biomaterial_treatment (biomaterial_id); create index biomaterial_treatment_idx2 on biomaterial_treatment (treatment_id); create index biomaterial_treatment_idx3 on biomaterial_treatment (unittype_id); COMMENT ON TABLE biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).'; -- ================================================ -- TABLE: assay_biomaterial -- ================================================ create table assay_biomaterial ( assay_biomaterial_id serial not null, primary key (assay_biomaterial_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, biomaterial_id int not null, foreign key (biomaterial_id) references biomaterial (biomaterial_id) on delete cascade INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, rank int not null default 0, constraint assay_biomaterial_c1 unique (assay_id,biomaterial_id,channel_id,rank) ); create index assay_biomaterial_idx1 on assay_biomaterial (assay_id); create index assay_biomaterial_idx2 on assay_biomaterial (biomaterial_id); create index assay_biomaterial_idx3 on assay_biomaterial (channel_id); COMMENT ON TABLE assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).'; -- ================================================ -- TABLE: acquisition -- ================================================ create table acquisition ( acquisition_id serial not null, primary key (acquisition_id), assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, channel_id int null, foreign key (channel_id) references channel (channel_id) on delete set null INITIALLY DEFERRED, acquisitiondate timestamp null default current_timestamp, name text null, uri text null, constraint acquisition_c1 unique (name) ); create index acquisition_idx1 on acquisition (assay_id); create index acquisition_idx2 on acquisition (protocol_id); create index acquisition_idx3 on acquisition (channel_id); COMMENT ON TABLE acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.'; -- ================================================ -- TABLE: acquisitionprop -- ================================================ create table acquisitionprop ( acquisitionprop_id serial not null, primary key (acquisitionprop_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisitionprop_c1 unique (acquisition_id,type_id,rank) ); create index acquisitionprop_idx1 on acquisitionprop (acquisition_id); create index acquisitionprop_idx2 on acquisitionprop (type_id); COMMENT ON TABLE acquisitionprop IS 'Parameters associated with image acquisition.'; -- ================================================ -- TABLE: acquisition_relationship -- ================================================ create table acquisition_relationship ( acquisition_relationship_id serial not null, primary key (acquisition_relationship_id), subject_id int not null, foreign key (subject_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint acquisition_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index acquisition_relationship_idx1 on acquisition_relationship (subject_id); create index acquisition_relationship_idx2 on acquisition_relationship (type_id); create index acquisition_relationship_idx3 on acquisition_relationship (object_id); COMMENT ON TABLE acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.'; -- ================================================ -- TABLE: quantification -- ================================================ create table quantification ( quantification_id serial not null, primary key (quantification_id), acquisition_id int not null, foreign key (acquisition_id) references acquisition (acquisition_id) on delete cascade INITIALLY DEFERRED, operator_id int null, foreign key (operator_id) references contact (contact_id) on delete set null INITIALLY DEFERRED, protocol_id int null, foreign key (protocol_id) references protocol (protocol_id) on delete set null INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, quantificationdate timestamp null default current_timestamp, name text null, uri text null, constraint quantification_c1 unique (name,analysis_id) ); create index quantification_idx1 on quantification (acquisition_id); create index quantification_idx2 on quantification (operator_id); create index quantification_idx3 on quantification (protocol_id); create index quantification_idx4 on quantification (analysis_id); COMMENT ON TABLE quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.'; -- ================================================ -- TABLE: quantificationprop -- ================================================ create table quantificationprop ( quantificationprop_id serial not null, primary key (quantificationprop_id), quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint quantificationprop_c1 unique (quantification_id,type_id,rank) ); create index quantificationprop_idx1 on quantificationprop (quantification_id); create index quantificationprop_idx2 on quantificationprop (type_id); COMMENT ON TABLE quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.'; -- ================================================ -- TABLE: quantification_relationship -- ================================================ create table quantification_relationship ( quantification_relationship_id serial not null, primary key (quantification_relationship_id), subject_id int not null, foreign key (subject_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, constraint quantification_relationship_c1 unique (subject_id,object_id,type_id) ); create index quantification_relationship_idx1 on quantification_relationship (subject_id); create index quantification_relationship_idx2 on quantification_relationship (type_id); create index quantification_relationship_idx3 on quantification_relationship (object_id); COMMENT ON TABLE quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.'; -- ================================================ -- TABLE: control -- ================================================ create table control ( control_id serial not null, primary key (control_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, tableinfo_id int not null, foreign key (tableinfo_id) references tableinfo (tableinfo_id) on delete cascade INITIALLY DEFERRED, row_id int not null, name text null, value text null, rank int not null default 0 ); create index control_idx1 on control (type_id); create index control_idx2 on control (assay_id); create index control_idx3 on control (tableinfo_id); create index control_idx4 on control (row_id); COMMENT ON TABLE control IS NULL; -- ================================================ -- TABLE: element -- ================================================ create table element ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, constraint element_c1 unique (feature_id,arraydesign_id) ); create index element_idx1 on element (feature_id); create index element_idx2 on element (arraydesign_id); create index element_idx3 on element (type_id); create index element_idx4 on element (dbxref_id); COMMENT ON TABLE element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.'; -- ================================================ -- TABLE: element_result -- ================================================ create table elementresult ( elementresult_id serial not null, primary key (elementresult_id), element_id int not null, foreign key (element_id) references element (element_id) on delete cascade INITIALLY DEFERRED, quantification_id int not null, foreign key (quantification_id) references quantification (quantification_id) on delete cascade INITIALLY DEFERRED, signal float not null, constraint elementresult_c1 unique (element_id,quantification_id) ); create index elementresult_idx1 on elementresult (element_id); create index elementresult_idx2 on elementresult (quantification_id); create index elementresult_idx3 on elementresult (signal); COMMENT ON TABLE elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.'; -- ================================================ -- TABLE: element_relationship -- ================================================ create table element_relationship ( element_relationship_id serial not null, primary key (element_relationship_id), subject_id int not null, foreign key (subject_id) references element (element_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references element (element_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint element_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index element_relationship_idx1 on element_relationship (subject_id); create index element_relationship_idx2 on element_relationship (type_id); create index element_relationship_idx3 on element_relationship (object_id); create index element_relationship_idx4 on element_relationship (value); COMMENT ON TABLE element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: elementresult_relationship -- ================================================ create table elementresult_relationship ( elementresult_relationship_id serial not null, primary key (elementresult_relationship_id), subject_id int not null, foreign key (subject_id) references elementresult (elementresult_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references elementresult (elementresult_id) INITIALLY DEFERRED, value text null, rank int not null default 0, constraint elementresult_relationship_c1 unique (subject_id,object_id,type_id,rank) ); create index elementresult_relationship_idx1 on elementresult_relationship (subject_id); create index elementresult_relationship_idx2 on elementresult_relationship (type_id); create index elementresult_relationship_idx3 on elementresult_relationship (object_id); create index elementresult_relationship_idx4 on elementresult_relationship (value); COMMENT ON TABLE elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.'; -- ================================================ -- TABLE: study -- ================================================ create table study ( study_id serial not null, primary key (study_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, pub_id int null, foreign key (pub_id) references pub (pub_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name text not null, description text null, constraint study_c1 unique (name) ); create index study_idx1 on study (contact_id); create index study_idx2 on study (pub_id); create index study_idx3 on study (dbxref_id); COMMENT ON TABLE study IS NULL; -- ================================================ -- TABLE: study_assay -- ================================================ create table study_assay ( study_assay_id serial not null, primary key (study_assay_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, constraint study_assay_c1 unique (study_id,assay_id) ); create index study_assay_idx1 on study_assay (study_id); create index study_assay_idx2 on study_assay (assay_id); COMMENT ON TABLE study_assay IS NULL; -- ================================================ -- TABLE: studydesign -- ================================================ create table studydesign ( studydesign_id serial not null, primary key (studydesign_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade INITIALLY DEFERRED, description text null ); create index studydesign_idx1 on studydesign (study_id); COMMENT ON TABLE studydesign IS NULL; -- ================================================ -- TABLE: studydesignprop -- ================================================ create table studydesignprop ( studydesignprop_id serial not null, primary key (studydesignprop_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint studydesignprop_c1 unique (studydesign_id,type_id,rank) ); create index studydesignprop_idx1 on studydesignprop (studydesign_id); create index studydesignprop_idx2 on studydesignprop (type_id); COMMENT ON TABLE studydesignprop IS NULL; -- ================================================ -- TABLE: studyfactor -- ================================================ create table studyfactor ( studyfactor_id serial not null, primary key (studyfactor_id), studydesign_id int not null, foreign key (studydesign_id) references studydesign (studydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, name text not null, description text null ); create index studyfactor_idx1 on studyfactor (studydesign_id); create index studyfactor_idx2 on studyfactor (type_id); COMMENT ON TABLE studyfactor IS NULL; -- ================================================ -- TABLE: studyfactorvalue -- ================================================ create table studyfactorvalue ( studyfactorvalue_id serial not null, primary key (studyfactorvalue_id), studyfactor_id int not null, foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED, assay_id int not null, foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED, factorvalue text null, name text null, rank int not null default 0 ); create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id); create index studyfactorvalue_idx2 on studyfactorvalue (assay_id); COMMENT ON TABLE studyfactorvalue IS NULL; -- -- studyprop and studyprop_feature added for Kara Dolinski's group -- -- Here is her description of it: --Both of the tables are used for our YFGdb project --(http://yfgdb.princeton.edu/), which uses chado. -- --Here is how we use those tables, using the following example: -- --http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969 -- --The above data set is represented as a row in the STUDY table. We have --lots of attributes that we want to store about each STUDY (status, etc) --and in the official schema, the only prop table we could use was the --STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN --table when we often have no real data to store in that table (small --percent of our collection use MAGE-ML unfortunately, and even fewer --provide all the data in the MAGE model, of which STUDYDESIGN is a vestige). --So, we created a STUDYPROP table. I'd think this table would be --generally useful to people storing various types of data sets via the --STUDY table. -- --The other new table is STUDYPROP_FEATURE. This basically allows us to --group features together per study. For example, we can store microarray --clustering results by saying that the STUDYPROP type is 'cluster' (via --type_id -> CVTERM of course), the value is 'cluster id 123', and then --that cluster would be associated with all the features that are in that --cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is -- fine by us! -- --studyprop create table studyprop ( studyprop_id serial not null, primary key (studyprop_id), study_id int not null, foreign key (study_id) references study (study_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text null, rank int not null default 0, unique (study_id,type_id,rank) ); create index studyprop_idx1 on studyprop (study_id); create index studyprop_idx2 on studyprop (type_id); --studyprop_feature CREATE TABLE studyprop_feature ( studyprop_feature_id serial NOT NULL, primary key (studyprop_feature_id), studyprop_id integer NOT NULL, foreign key (studyprop_id) references studyprop(studyprop_id) on delete cascade, feature_id integer NOT NULL, foreign key (feature_id) references feature (feature_id) on delete cascade, type_id integer, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, unique (studyprop_id, feature_id) ); create index studyprop_feature_idx1 on studyprop_feature (studyprop_id); create index studyprop_feature_idx2 on studyprop_feature (feature_id); chado-1.23/modules/mage/mage.views000644 000765 000024 00000032364 11256710150 017151 0ustar00cainstaff000000 000000 -- This file is contributed by Allen Day and is specific to his own work. -- It is included for illustrative purposes, these tables and views -- are not part of the mage module. It gives an example of how the -- generic element and elementresult tables in the mage module can be -- used to represent different types of data. Another way to do this is -- with PostgreSQL table subclasses. There is a performance gain for -- typical usage in splitting data into subclass tables rather than -- using views to filter. CREATE TABLE affymetrixprobeset ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name varchar(255) NULL ); --ALTER TABLE affymetrixprobeset ADD CONSTRAINT affymetrixprobeset_c2 FOREIGN KEY (dbxref_id) REFERENCES dbxref (dbxref_id); --ALTER TABLE affymetrixprobeset ADD CONSTRAINT affymetrixprobeset_c3 FOREIGN KEY (arraydesign_id) REFERENCES arraydesign (arraydesign_id); --ALTER TABLE affymetrixprobeset ADD CONSTRAINT affymetrixprobeset_c4 FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id); --ALTER TABLE affymetrixprobeset ADD CONSTRAINT affymetrixprobeset_c5 FOREIGN KEY (feature_id) REFERENCES feature (feature_id); CREATE INDEX affymetrixprobeset_idx1 ON affymetrixprobeset (name); CREATE INDEX affymetrixprobeset_idx2 ON affymetrixprobeset (feature_id); CREATE INDEX affymetrixprobeset_idx3 ON affymetrixprobeset (dbxref_id); CREATE INDEX affymetrixprobeset_idx4 ON affymetrixprobeset (arraydesign_id); CREATE INDEX affymetrixprobeset_idx5 ON affymetrixprobeset (type_id); CREATE UNIQUE INDEX affymetrixprobeset_idx6 ON affymetrixprobeset (name,arraydesign_id); CREATE UNIQUE INDEX affymetrixprobeset_idx7 ON affymetrixprobeset (feature_id,arraydesign_id); CREATE TABLE affymetrixprobe ( element_id serial not null, primary key (element_id), feature_id int null, foreign key (feature_id) references feature (feature_id) on delete set null INITIALLY DEFERRED, arraydesign_id int not null, foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade INITIALLY DEFERRED, type_id int null, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, dbxref_id int null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, name varchar(255) NULL, affymetrixprobeset_id int NULL, row int NOT NULL, col int NOT NULL ); --ALTER TABLE affymetrixprobe ADD CONSTRAINT affymetrixprobe_c1 FOREIGN KEY (feature_id) REFERENCES feature (feature_id); --ALTER TABLE affymetrixprobe ADD CONSTRAINT affymetrixprobe_c2 FOREIGN KEY (dbxref_id) REFERENCES dbxref (dbxref_id); --ALTER TABLE affymetrixprobe ADD CONSTRAINT affymetrixprobe_c3 FOREIGN KEY (arraydesign_id) REFERENCES arraydesign (arraydesign_id); --ALTER TABLE affymetrixprobe ADD CONSTRAINT affymetrixprobe_c4 FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id); ALTER TABLE affymetrixprobe ADD CONSTRAINT affymetrixprobe_c5 FOREIGN KEY (affymetrixprobeset_id) REFERENCES affymetrixprobeset (element_id); CREATE INDEX affymetrixprobe_idx1 ON affymetrixprobe (affymetrixprobeset_id); CREATE INDEX affymetrixprobe_idx2 ON affymetrixprobe (name); CREATE INDEX affymetrixprobe_idx3 ON affymetrixprobe (feature_id); CREATE INDEX affymetrixprobe_idx4 ON affymetrixprobe (dbxref_id); CREATE INDEX affymetrixprobe_idx5 ON affymetrixprobe (arraydesign_id); CREATE INDEX affymetrixprobe_idx6 ON affymetrixprobe (type_id); CREATE TABLE affymetrixcel ( mean float NOT NULL, sd float NOT NULL, pixels int NOT NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixcel ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixcel ADD CONSTRAINT affymetrixcel_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobe (element_id); ALTER TABLE affymetrixcel ADD CONSTRAINT affymetrixcel_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixcel_idx1 ON affymetrixcel (mean); CREATE INDEX affymetrixcel_idx2 ON affymetrixcel (sd); CREATE INDEX affymetrixcel_idx3 ON affymetrixcel (pixels); CREATE INDEX affymetrixcel_idx4 ON affymetrixcel (element_id); CREATE INDEX affymetrixcel_idx5 ON affymetrixcel (quantification_id); CREATE TABLE affymetrixsnp ( call smallint NULL, call_p float NULL, _signal _float4 NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixsnp ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixsnp ADD CONSTRAINT affymetrixsnp_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixsnp ADD CONSTRAINT affymetrixsnp_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixsnp_idx1 ON affymetrixsnp (call); CREATE INDEX affymetrixsnp_idx2 ON affymetrixsnp (signal); CREATE INDEX affymetrixsnp_idx4 ON affymetrixsnp (element_id); CREATE INDEX affymetrixsnp_idx5 ON affymetrixsnp (quantification_id); CREATE INDEX affymetrixsnp_idx6 ON affymetrixsnp (call_p); CREATE TABLE affymetrixpsi ( q1pas INT NULL, q1pbs INT NULL, q1mas INT NULL, q1mbs INT NULL, q1paa INT NULL, q1pba INT NULL, q1maa INT NULL, q1mba INT NULL, q2pas INT NULL, q2pbs INT NULL, q2mas INT NULL, q2mbs INT NULL, q2paa INT NULL, q2pba INT NULL, q2maa INT NULL, q2mba INT NULL, q3pas INT NULL, q3pbs INT NULL, q3mas INT NULL, q3mbs INT NULL, q3paa INT NULL, q3pba INT NULL, q3maa INT NULL, q3mba INT NULL, q4pas INT NULL, q4pbs INT NULL, q4mas INT NULL, q4mbs INT NULL, q4paa INT NULL, q4pba INT NULL, q4maa INT NULL, q4mba INT NULL, q5pas INT NULL, q5pbs INT NULL, q5mas INT NULL, q5mbs INT NULL, q5paa INT NULL, q5pba INT NULL, q5maa INT NULL, q5mba INT NULL, q6pas INT NULL, q6pbs INT NULL, q6mas INT NULL, q6mbs INT NULL, q6paa INT NULL, q6pba INT NULL, q6maa INT NULL, q6mba INT NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixpsi ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixpsi ADD CONSTRAINT affymetrixpsi_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixpsi ADD CONSTRAINT affymetrixpsi_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixpsi_idx4 ON affymetrixpsi (element_id); CREATE INDEX affymetrixpsi_idx5 ON affymetrixpsi (quantification_id); CREATE TABLE affymetrixmas5 ( call char(1) NOT NULL, call_p float NOT NULL, statpairs int NOT NULL, statpairsused int NOT NULL, z float NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixmas5 ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixmas5 ADD CONSTRAINT affymetrixmas5_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixmas5 ADD CONSTRAINT affymetrixmas5_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixmas5_idx1 ON affymetrixmas5 (signal); CREATE INDEX affymetrixmas5_idx2 ON affymetrixmas5 (call); CREATE INDEX affymetrixmas5_idx3 ON affymetrixmas5 (call_p); CREATE INDEX affymetrixmas5_idx4 ON affymetrixmas5 (element_id); CREATE INDEX affymetrixmas5_idx5 ON affymetrixmas5 (quantification_id); CREATE INDEX affymetrixmas5_idx6 ON affymetrixmas5 (z); CREATE TABLE affymetrixdchip ( z float NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixdchip ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixdchip ADD CONSTRAINT affymetrixdchip_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixdchip ADD CONSTRAINT affymetrixdchip_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixdchip_idx1 ON affymetrixdchip (element_id); CREATE INDEX affymetrixdchip_idx2 ON affymetrixdchip (quantification_id); CREATE INDEX affymetrixdchip_idx3 ON affymetrixdchip (signal); CREATE INDEX affymetrixdchip_idx6 ON affymetrixdchip (z); CREATE TABLE affymetrixvsn ( z float NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixvsn ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixvsn ADD CONSTRAINT affymetrixvsn_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixvsn ADD CONSTRAINT affymetrixvsn_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixvsn_idx1 ON affymetrixvsn (element_id); CREATE INDEX affymetrixvsn_idx2 ON affymetrixvsn (quantification_id); CREATE INDEX affymetrixvsn_idx3 ON affymetrixvsn (signal); CREATE INDEX affymetrixvsn_idx6 ON affymetrixvsn (z); CREATE TABLE affymetrixsea ( ) INHERITS ( elementresult ); ALTER TABLE affymetrixsea ADD PRIMARY KEY (elementresult_id); --ALTER TABLE affymetrixsea ADD CONSTRAINT affymetrixsea_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixsea ADD CONSTRAINT affymetrixsea_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixsea_idx1 ON affymetrixsea (element_id); CREATE INDEX affymetrixsea_idx2 ON affymetrixsea (quantification_id); CREATE INDEX affymetrixsea_idx3 ON affymetrixsea (signal); CREATE TABLE affymetrixplier ( ) INHERITS ( elementresult ); ALTER TABLE affymetrixplier ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixplier ADD CONSTRAINT affymetrixplier_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixplier ADD CONSTRAINT affymetrixplier_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixplier_idx1 ON affymetrixplier (element_id); CREATE INDEX affymetrixplier_idx2 ON affymetrixplier (quantification_id); CREATE INDEX affymetrixplier_idx3 ON affymetrixplier (signal); CREATE TABLE affymetrixdabg ( call_p float NOT NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixdabg ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixdabg ADD CONSTRAINT affymetrixdabg_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixdabg ADD CONSTRAINT affymetrixdabg_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixdabg_idx1 ON affymetrixdabg (element_id); CREATE INDEX affymetrixdabg_idx2 ON affymetrixdabg (quantification_id); CREATE INDEX affymetrixdabg_idx3 ON affymetrixdabg (call_p); CREATE TABLE affymetrixrma ( z float NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixrma ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixrma ADD CONSTRAINT affymetrixrma_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixrma ADD CONSTRAINT affymetrixrma_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixrma_idx1 ON affymetrixrma (element_id); CREATE INDEX affymetrixrma_idx2 ON affymetrixrma (quantification_id); CREATE INDEX affymetrixrma_idx3 ON affymetrixrma (signal); CREATE INDEX affymetrixrma_idx6 ON affymetrixrma (z); CREATE TABLE affymetrixgcrma ( z float NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixgcrma ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixgcrma ADD CONSTRAINT affymetrixgcrma_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixgcrma ADD CONSTRAINT affymetrixgcrma_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixgcrma_idx1 ON affymetrixgcrma (element_id); CREATE INDEX affymetrixgcrma_idx2 ON affymetrixgcrma (quantification_id); CREATE INDEX affymetrixgcrma_idx3 ON affymetrixgcrma (signal); CREATE INDEX affymetrixgcrma_idx6 ON affymetrixgcrma (z); CREATE TABLE affymetrixprobesetstat ( mean float NOT NULL, median float NOT NULL, quartile1 float NOT NULL, quartile3 float NOT NULL, sd float NOT NULL, n int NOT NULL ) INHERITS ( elementresult ); ALTER TABLE affymetrixprobesetstat ADD PRIMARY KEY (elementresult_id); ALTER TABLE affymetrixprobesetstat ADD CONSTRAINT affymetrixprobesetstat_c1 FOREIGN KEY (element_id) REFERENCES affymetrixprobeset (element_id); ALTER TABLE affymetrixprobesetstat ADD CONSTRAINT affymetrixprobesetstat_c2 FOREIGN KEY (quantification_id) REFERENCES quantification (quantification_id); CREATE INDEX affymetrixprobesetstat_idx1 ON affymetrixprobesetstat (element_id); CREATE INDEX affymetrixprobesetstat_idx2 ON affymetrixprobesetstat (quantification_id); CREATE INDEX affymetrixprobesetstat_idx3 ON affymetrixprobesetstat (mean); CREATE INDEX affymetrixprobesetstat_idx4 ON affymetrixprobesetstat (median); CREATE INDEX affymetrixprobesetstat_idx5 ON affymetrixprobesetstat (quartile1); CREATE INDEX affymetrixprobesetstat_idx6 ON affymetrixprobesetstat (quartile3); CREATE INDEX affymetrixprobesetstat_idx7 ON affymetrixprobesetstat (sd); CREATE INDEX affymetrixprobesetstat_idx8 ON affymetrixprobesetstat (n); chado-1.23/modules/library/library.html000644 000765 000024 00000073450 11256710103 020245 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

library
library_synonym
library_pub
libraryprop
libraryprop_pub
library_cvterm
library_feature
library_dbxref

library

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Comments:

$Id: library.html,v 1.4 2008-03-28 16:05:30 scottcain Exp $
=================================================================
Dependencies:
:import feature from sequence
:import synonym from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
=================================================================
================================================
TABLE: library
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_id integer 11 PRIMARY KEY, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
name varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" cvterm.cvterm_id
is_obsolete integer 10 0 NOT NULL
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Indices

Name Fields
library_name_ind1 name
library_idx1 organism_id
library_idx2 type_id
library_idx3 uniquename

Constraints

Type Fields
NOT NULL library_id
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL is_obsolete
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE organism_id, uniquename, type_id

library_synonym

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Comments:

================================================
TABLE: library_synonym
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_synonym_id integer 11 PRIMARY KEY, NOT NULL
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 true NOT NULL, The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
library_synonym_idx1 synonym_id
library_synonym_idx2 library_id
library_synonym_idx3 pub_id

Constraints

Type Fields
NOT NULL library_synonym_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, library_id, pub_id

library_pub

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Comments:

================================================
TABLE: library_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_pub_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_pub_idx1 library_id
library_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL library_pub_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, pub_id

libraryprop

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Comments:

================================================
TABLE: libraryprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
libraryprop_idx1 library_id
libraryprop_idx2 type_id

Constraints

Type Fields
NOT NULL libraryprop_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE library_id, type_id, rank

libraryprop_pub

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Comments:

================================================
TABLE: libraryprop_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_pub_id integer 11 PRIMARY KEY, NOT NULL
libraryprop_id integer 10 UNIQUE, NOT NULL libraryprop.libraryprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
libraryprop_pub_idx1 libraryprop_id
libraryprop_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL libraryprop_pub_id
NOT NULL libraryprop_id
FOREIGN KEY libraryprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE libraryprop_id, pub_id

library_cvterm

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Comments:

================================================
TABLE: library_cvterm
================================================
The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
Field Name Data Type Size Default Value Other Foreign Key
library_cvterm_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_cvterm_idx1 library_id
library_cvterm_idx2 cvterm_id
library_cvterm_idx3 pub_id

Constraints

Type Fields
NOT NULL library_cvterm_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE library_id, cvterm_id, pub_id

library_feature

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Comments:

================================================
TABLE: library_feature
================================================
library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
Field Name Data Type Size Default Value Other Foreign Key
library_feature_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id

Indices

Name Fields
library_feature_idx1 library_id
library_feature_idx2 feature_id

Constraints

Type Fields
NOT NULL library_feature_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL feature_id
FOREIGN KEY feature_id
UNIQUE library_id, feature_id

library_dbxref

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Comments:

================================================
TABLE: library_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_dbxref_id integer 11 PRIMARY KEY, NOT NULL
library_id integer 10 UNIQUE, NOT NULL library.library_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
library_dbxref_idx1 library_id
library_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL library_dbxref_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE library_id, dbxref_id
Created by SQL::Translator 0.08001 chado-1.23/modules/library/library.sql000644 000765 000024 00000017474 11256710103 020104 0ustar00cainstaff000000 000000 -- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $ -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import synonym from sequence -- :import cvterm from cv -- :import pub from pub -- :import organism from organism -- ================================================================= -- ================================================ -- TABLE: library -- ================================================ create table library ( library_id serial not null, primary key (library_id), organism_id int not null, foreign key (organism_id) references organism (organism_id), name varchar(255), uniquename text not null, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), is_obsolete int not null default 0, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint library_c1 unique (organism_id,uniquename,type_id) ); create index library_name_ind1 on library(name); create index library_idx1 on library (organism_id); create index library_idx2 on library (type_id); create index library_idx3 on library (uniquename); COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"'; -- ================================================ -- TABLE: library_synonym -- ================================================ create table library_synonym ( library_synonym_id serial not null, primary key (library_synonym_id), synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', is_internal boolean not null default 'false', constraint library_synonym_c1 unique (synonym_id,library_id,pub_id) ); create index library_synonym_idx1 on library_synonym (synonym_id); create index library_synonym_idx2 on library_synonym (library_id); create index library_synonym_idx3 on library_synonym (pub_id); COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.'; COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.'; COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.'; -- ================================================ -- TABLE: library_pub -- ================================================ create table library_pub ( library_pub_id serial not null, primary key (library_pub_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint library_pub_c1 unique (library_id,pub_id) ); create index library_pub_idx1 on library_pub (library_id); create index library_pub_idx2 on library_pub (pub_id); -- ================================================ -- TABLE: libraryprop -- ================================================ create table libraryprop ( libraryprop_id serial not null, primary key (libraryprop_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id), value text null, rank int not null default 0, constraint libraryprop_c1 unique (library_id,type_id,rank) ); create index libraryprop_idx1 on libraryprop (library_id); create index libraryprop_idx2 on libraryprop (type_id); -- ================================================ -- TABLE: libraryprop_pub -- ================================================ create table libraryprop_pub ( libraryprop_pub_id serial not null, primary key (libraryprop_pub_id), libraryprop_id int not null, foreign key (libraryprop_id) references libraryprop (libraryprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint libraryprop_pub_c1 unique (libraryprop_id,pub_id) ); create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id); create index libraryprop_pub_idx2 on libraryprop_pub (pub_id); -- ================================================ -- TABLE: library_cvterm -- ================================================ create table library_cvterm ( library_cvterm_id serial not null, primary key (library_cvterm_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id), pub_id int not null, foreign key (pub_id) references pub (pub_id), constraint library_cvterm_c1 unique (library_id,cvterm_id,pub_id) ); create index library_cvterm_idx1 on library_cvterm (library_id); create index library_cvterm_idx2 on library_cvterm (cvterm_id); create index library_cvterm_idx3 on library_cvterm (pub_id); COMMENT ON TABLE library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.'; -- ================================================ -- TABLE: library_feature -- ================================================ create table library_feature ( library_feature_id serial not null, primary key (library_feature_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, constraint library_feature_c1 unique (library_id,feature_id) ); create index library_feature_idx1 on library_feature (library_id); create index library_feature_idx2 on library_feature (feature_id); COMMENT ON TABLE library_feature IS 'library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".'; -- ================================================ -- TABLE: library_dbxref -- ================================================ create table library_dbxref ( library_dbxref_id serial not null, primary key (library_dbxref_id), library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint library_dbxref_c1 unique (library_id,dbxref_id) ); create index library_dbxref_idx1 on library_dbxref (library_id); create index library_dbxref_idx2 on library_dbxref (dbxref_id); chado-1.23/modules/genetic/genetic.html000644 000765 000024 00000114552 11610541003 020163 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

genotype
feature_genotype
environment
environment_cvterm
phenstatement
phendesc
phenotype_comparison
phenotype_comparison_cvterm
genotypeprop

genotype

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Comments:

$Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $
==========================================
Chado genetics module
changes 2011-05-31
added type_id to genotype (can be null for backward compatibility)
added genotypeprop table
2006-04-11
split out phenotype tables into phenotype module
redesigned 2003-10-28
changes 2003-11-10:
incorporating suggestions to make everything a gcontext; use
gcontext_relationship to make some gcontexts derivable from others. we
would incorporate environment this way - just add the environment
descriptors as properties of the child gcontext
changes 2004-06 (Documented by DE: 10-MAR-2005):
Many, including rename of gcontext to genotype, split
phenstatement into phenstatement & phenotype, created environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
============
DEPENDENCIES
============
:import feature from sequence
:import phenotype from phenotype
:import cvterm from cv
:import pub from pub
:import dbxref from general
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: genotype
================================================
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
Field Name Data Type Size Default Value Other Foreign Key
genotype_id integer 11 PRIMARY KEY, NOT NULL
name text 64000 Optional alternative name for a genotype, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a genotype; typically derived from the features making up the genotype.
description varchar 255
type_id integer 10 NOT NULL cvterm.cvterm_id

Indices

Name Fields
genotype_idx1 uniquename
genotype_idx2 name

Constraints

Type Fields
NOT NULL genotype_id
NOT NULL uniquename
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE uniquename

feature_genotype

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Comments:

===============================================
TABLE: feature_genotype
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
feature_genotype_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
chromosome_id integer 10 UNIQUE, A feature of SO type "chromosome". feature.feature_id
rank integer 10 UNIQUE, NOT NULL, rank can be used for n-ploid organisms or to preserve order.
cgroup integer 10 UNIQUE, NOT NULL, Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
feature_genotype_idx1 feature_id
feature_genotype_idx2 genotype_id

Constraints

Type Fields
NOT NULL feature_genotype_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
FOREIGN KEY chromosome_id
NOT NULL rank
NOT NULL cgroup
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
UNIQUE feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup

environment

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Comments:

================================================
TABLE: environment
================================================
The environmental component of a phenotype description.
Field Name Data Type Size Default Value Other Foreign Key
environment_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
environment_idx1 uniquename

Constraints

Type Fields
NOT NULL environment_id
NOT NULL uniquename
UNIQUE uniquename

environment_cvterm

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Comments:

================================================
TABLE: environment_cvterm
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
environment_cvterm_id integer 11 PRIMARY KEY, NOT NULL
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
environment_cvterm_idx1 environment_id
environment_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL environment_cvterm_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
UNIQUE environment_id, cvterm_id

phenstatement

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Comments:

================================================
TABLE: phenstatement
================================================
Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.
Field Name Data Type Size Default Value Other Foreign Key
phenstatement_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
phenotype_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phenstatement_idx1 genotype_id
phenstatement_idx2 phenotype_id

Constraints

Type Fields
NOT NULL phenstatement_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL phenotype_id
FOREIGN KEY phenotype_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE genotype_id, phenotype_id, environment_id, type_id, pub_id

phendesc

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Comments:

================================================
TABLE: phendesc
================================================
A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
Field Name Data Type Size Default Value Other Foreign Key
phendesc_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 10 UNIQUE, NOT NULL environment.environment_id
description text 64000 NOT NULL
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phendesc_idx1 genotype_id
phendesc_idx2 environment_id
phendesc_idx3 pub_id

Constraints

Type Fields
NOT NULL phendesc_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL environment_id
FOREIGN KEY environment_id
NOT NULL description
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE genotype_id, environment_id, type_id, pub_id

phenotype_comparison

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Comments:

================================================
TABLE: phenotype_comparison
================================================
Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_id integer 11 PRIMARY KEY, NOT NULL
genotype1_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment1_id integer 10 UNIQUE, NOT NULL environment.environment_id
genotype2_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
environment2_id integer 10 UNIQUE, NOT NULL environment.environment_id
phenotype1_id integer 10 UNIQUE, NOT NULL phenotype.phenotype_id
phenotype2_id integer 10 phenotype.phenotype_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
organism_id integer 10 NOT NULL organism.organism_id

Indices

Name Fields
phenotype_comparison_idx1 genotype1_id
phenotype_comparison_idx2 genotype2_id
phenotype_comparison_idx4 pub_id

Constraints

Type Fields
NOT NULL phenotype_comparison_id
NOT NULL genotype1_id
FOREIGN KEY genotype1_id
NOT NULL environment1_id
FOREIGN KEY environment1_id
NOT NULL genotype2_id
FOREIGN KEY genotype2_id
NOT NULL environment2_id
FOREIGN KEY environment2_id
NOT NULL phenotype1_id
FOREIGN KEY phenotype1_id
FOREIGN KEY phenotype2_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL organism_id
FOREIGN KEY organism_id
UNIQUE genotype1_id, environment1_id, genotype2_id, environment2_id, phenotype1_id, pub_id

phenotype_comparison_cvterm

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Comments:

================================================
TABLE: phenotype_comparison_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_cvterm_id integer 11 PRIMARY KEY, NOT NULL
phenotype_comparison_id integer 10 UNIQUE, NOT NULL phenotype_comparison.phenotype_comparison_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 NOT NULL pub.pub_id
rank integer 10 0 NOT NULL

Indices

Name Fields
phenotype_comparison_cvterm_idx1 phenotype_comparison_id
phenotype_comparison_cvterm_idx2 cvterm_id

Constraints

Type Fields
NOT NULL phenotype_comparison_cvterm_id
NOT NULL phenotype_comparison_id
FOREIGN KEY phenotype_comparison_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
UNIQUE phenotype_comparison_id, cvterm_id

genotypeprop

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Comments:

================================================
TABLE: genotypeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
genotypeprop_id integer 11 PRIMARY KEY, NOT NULL
genotype_id integer 10 UNIQUE, NOT NULL genotype.genotype_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
genotypeprop_idx1 genotype_id
genotypeprop_idx2 type_id

Constraints

Type Fields
NOT NULL genotypeprop_id
NOT NULL genotype_id
FOREIGN KEY genotype_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE genotype_id, type_id, rank
Created by SQL::Translator 0.11003 chado-1.23/modules/genetic/genetic.sql000644 000765 000024 00000024605 11571467743 020045 0ustar00cainstaff000000 000000 -- $Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $ -- ========================================== -- Chado genetics module -- -- changes 2011-05-31 -- added type_id to genotype (can be null for backward compatibility) -- added genotypeprop table -- 2006-04-11 -- split out phenotype tables into phenotype module -- -- redesigned 2003-10-28 -- -- changes 2003-11-10: -- incorporating suggestions to make everything a gcontext; use -- gcontext_relationship to make some gcontexts derivable from others. we -- would incorporate environment this way - just add the environment -- descriptors as properties of the child gcontext -- -- changes 2004-06 (Documented by DE: 10-MAR-2005): -- Many, including rename of gcontext to genotype, split -- phenstatement into phenstatement & phenotype, created environment -- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import phenotype from phenotype -- :import cvterm from cv -- :import pub from pub -- :import dbxref from general -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: genotype -- ================================================ create table genotype ( genotype_id serial not null, primary key (genotype_id), name text, uniquename text not null, description varchar(255), type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, constraint genotype_c1 unique (uniquename) ); create index genotype_idx1 on genotype(uniquename); create index genotype_idx2 on genotype(name); COMMENT ON TABLE genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.'; COMMENT ON COLUMN genotype.uniquename IS 'The unique name for a genotype; typically derived from the features making up the genotype.'; COMMENT ON COLUMN genotype.name IS 'Optional alternative name for a genotype, for display purposes.'; -- =============================================== -- TABLE: feature_genotype -- ================================================ create table feature_genotype ( feature_genotype_id serial not null, primary key (feature_genotype_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade, genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade, chromosome_id int, foreign key (chromosome_id) references feature (feature_id) on delete set null, rank int not null, cgroup int not null, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint feature_genotype_c1 unique (feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup) ); create index feature_genotype_idx1 on feature_genotype (feature_id); create index feature_genotype_idx2 on feature_genotype (genotype_id); COMMENT ON TABLE feature_genotype IS NULL; COMMENT ON COLUMN feature_genotype.rank IS 'rank can be used for n-ploid organisms or to preserve order.'; COMMENT ON COLUMN feature_genotype.cgroup IS 'Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).'; COMMENT ON COLUMN feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".'; -- ================================================ -- TABLE: environment -- ================================================ create table environment ( environment_id serial not NULL, primary key (environment_id), uniquename text not null, description text, constraint environment_c1 unique (uniquename) ); create index environment_idx1 on environment(uniquename); COMMENT ON TABLE environment IS 'The environmental component of a phenotype description.'; -- ================================================ -- TABLE: environment_cvterm -- ================================================ create table environment_cvterm ( environment_cvterm_id serial not null, primary key (environment_cvterm_id), environment_id int not null, foreign key (environment_id) references environment (environment_id) on delete cascade, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, constraint environment_cvterm_c1 unique (environment_id, cvterm_id) ); create index environment_cvterm_idx1 on environment_cvterm (environment_id); create index environment_cvterm_idx2 on environment_cvterm (cvterm_id); COMMENT ON TABLE environment_cvterm IS NULL; -- ================================================ -- TABLE: phenstatement -- ================================================ CREATE TABLE phenstatement ( phenstatement_id SERIAL NOT NULL, primary key (phenstatement_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype_id INT NOT NULL, FOREIGN KEY (phenotype_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phenstatement_c1 UNIQUE (genotype_id,phenotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phenstatement_idx1 ON phenstatement (genotype_id); CREATE INDEX phenstatement_idx2 ON phenstatement (phenotype_id); COMMENT ON TABLE phenstatement IS 'Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.'; -- ================================================ -- TABLE: phendesc -- ================================================ CREATE TABLE phendesc ( phendesc_id SERIAL NOT NULL, primary key (phendesc_id), genotype_id INT NOT NULL, FOREIGN KEY (genotype_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment_id INT NOT NULL, FOREIGN KEY (environment_id) REFERENCES environment ( environment_id) ON DELETE CASCADE, description TEXT NOT NULL, type_id INT NOT NULL, FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, CONSTRAINT phendesc_c1 UNIQUE (genotype_id,environment_id,type_id,pub_id) ); CREATE INDEX phendesc_idx1 ON phendesc (genotype_id); CREATE INDEX phendesc_idx2 ON phendesc (environment_id); CREATE INDEX phendesc_idx3 ON phendesc (pub_id); COMMENT ON TABLE phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.'; -- ================================================ -- TABLE: phenotype_comparison -- ================================================ CREATE TABLE phenotype_comparison ( phenotype_comparison_id SERIAL NOT NULL, primary key (phenotype_comparison_id), genotype1_id INT NOT NULL, FOREIGN KEY (genotype1_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment1_id INT NOT NULL, FOREIGN KEY (environment1_id) REFERENCES environment (environment_id) ON DELETE CASCADE, genotype2_id INT NOT NULL, FOREIGN KEY (genotype2_id) REFERENCES genotype (genotype_id) ON DELETE CASCADE, environment2_id INT NOT NULL, FOREIGN KEY (environment2_id) REFERENCES environment (environment_id) ON DELETE CASCADE, phenotype1_id INT NOT NULL, FOREIGN KEY (phenotype1_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, phenotype2_id INT, FOREIGN KEY (phenotype2_id) REFERENCES phenotype (phenotype_id) ON DELETE CASCADE, pub_id INT NOT NULL, FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE CASCADE, organism_id INT NOT NULL, FOREIGN KEY (organism_id) REFERENCES organism (organism_id) ON DELETE CASCADE, CONSTRAINT phenotype_comparison_c1 UNIQUE (genotype1_id,environment1_id,genotype2_id,environment2_id,phenotype1_id,pub_id) ); CREATE INDEX phenotype_comparison_idx1 on phenotype_comparison (genotype1_id); CREATE INDEX phenotype_comparison_idx2 on phenotype_comparison (genotype2_id); CREATE INDEX phenotype_comparison_idx4 on phenotype_comparison (pub_id); COMMENT ON TABLE phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.'; -- ================================================ -- TABLE: phenotype_comparison_cvterm -- ================================================ CREATE TABLE phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id serial not null, primary key (phenotype_comparison_cvterm_id), phenotype_comparison_id int not null, FOREIGN KEY (phenotype_comparison_id) references phenotype_comparison (phenotype_comparison_id) on delete cascade, cvterm_id int not null, FOREIGN KEY (cvterm_id) references cvterm (cvterm_id) on delete cascade, pub_id INT not null, FOREIGN KEY (pub_id) references pub (pub_id) on delete cascade, rank int not null default 0, CONSTRAINT phenotype_comparison_cvterm_c1 unique (phenotype_comparison_id, cvterm_id) ); CREATE INDEX phenotype_comparison_cvterm_idx1 on phenotype_comparison_cvterm (phenotype_comparison_id); CREATE INDEX phenotype_comparison_cvterm_idx2 on phenotype_comparison_cvterm (cvterm_id); -- ================================================ -- TABLE: genotypeprop -- ================================================ create table genotypeprop ( genotypeprop_id serial not null, primary key (genotypeprop_id), genotype_id int not null, foreign key (genotype_id) references genotype (genotype_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint genotypeprop_c1 unique (genotype_id,type_id,rank) ); create index genotypeprop_idx1 on genotypeprop (genotype_id); create index genotypeprop_idx2 on genotypeprop (type_id); chado-1.23/modules/general/functions/000755 000765 000024 00000000000 12061672375 017700 5ustar00cainstaff000000 000000 chado-1.23/modules/general/general.html000644 000765 000024 00000026776 11435270312 020202 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

tableinfo
db
dbxref

tableinfo

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Comments:

$Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $
==========================================
Chado general module
================================================
TABLE: tableinfo
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
tableinfo_id integer 11 PRIMARY KEY, NOT NULL
name varchar 30 UNIQUE, NOT NULL
primary_key_column varchar 30 NULL
is_view integer 10 0 NOT NULL
view_on_table_id integer 10 NULL
superclass_table_id integer 10 NULL
is_updateable integer 10 1 NOT NULL
modification_date date 0 now() NOT NULL

Constraints

Type Fields
NOT NULL tableinfo_id
NOT NULL name
NOT NULL is_view
NOT NULL is_updateable
NOT NULL modification_date
UNIQUE name

db

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Comments:

================================================
TABLE: db
================================================
A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.
Field Name Data Type Size Default Value Other Foreign Key
db_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL contact_id int,
urlprefix varchar 255 NULL
url varchar 255 NULL

Constraints

Type Fields
NOT NULL db_id
NOT NULL name
UNIQUE name

dbxref

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Comments:

================================================
TABLE: dbxref
================================================
A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.
Field Name Data Type Size Default Value Other Foreign Key
dbxref_id integer 11 PRIMARY KEY, NOT NULL
db_id integer 10 UNIQUE, NOT NULL db.db_id
accession varchar 255 UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version varchar 255 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
dbxref_idx1 db_id
dbxref_idx2 accession
dbxref_idx3 version

Constraints

Type Fields
NOT NULL dbxref_id
NOT NULL db_id
FOREIGN KEY db_id
NOT NULL accession
NOT NULL version
UNIQUE db_id, accession, version
Created by SQL::Translator 0.11003 chado-1.23/modules/general/general.sql000644 000765 000024 00000005355 11435270312 020023 0ustar00cainstaff000000 000000 -- $Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $ -- ========================================== -- Chado general module -- -- ================================================ -- TABLE: tableinfo -- ================================================ create table tableinfo ( tableinfo_id serial not null, primary key (tableinfo_id), name varchar(30) not null, primary_key_column varchar(30) null, is_view int not null default 0, view_on_table_id int null, superclass_table_id int null, is_updateable int not null default 1, modification_date date not null default now(), constraint tableinfo_c1 unique (name) ); COMMENT ON TABLE tableinfo IS NULL; -- ================================================ -- TABLE: db -- ================================================ create table db ( db_id serial not null, primary key (db_id), name varchar(255) not null, -- contact_id int, -- foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, description varchar(255) null, urlprefix varchar(255) null, url varchar(255) null, constraint db_c1 unique (name) ); COMMENT ON TABLE db IS 'A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.'; -- ================================================ -- TABLE: dbxref -- ================================================ create table dbxref ( dbxref_id serial not null, primary key (dbxref_id), db_id int not null, foreign key (db_id) references db (db_id) on delete cascade INITIALLY DEFERRED, accession varchar(255) not null, version varchar(255) not null default '', description text, constraint dbxref_c1 unique (db_id,accession,version) ); create index dbxref_idx1 on dbxref (db_id); create index dbxref_idx2 on dbxref (accession); create index dbxref_idx3 on dbxref (version); COMMENT ON TABLE dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.'; COMMENT ON COLUMN dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.'; chado-1.23/modules/general/views/000755 000765 000024 00000000000 12061672375 017025 5ustar00cainstaff000000 000000 chado-1.23/modules/general/views/general-report.sql000644 000765 000024 00000000275 11256710150 022465 0ustar00cainstaff000000 000000 CREATE VIEW db_dbxref_count AS SELECT db.name,count(*) AS num_dbxrefs FROM db INNER JOIN dbxref USING (db_id) GROUP BY db.name; COMMENT ON VIEW db_dbxref_count IS 'per-db dbxref counts'; chado-1.23/modules/general/functions/general-loading.plpgsql000644 000765 000024 00000002060 11635706552 024333 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION store_db (VARCHAR) RETURNS INT AS 'DECLARE v_name ALIAS FOR $1; v_db_id INTEGER; BEGIN SELECT INTO v_db_id db_id FROM db WHERE name=v_name; IF NOT FOUND THEN INSERT INTO db (name) VALUES (v_name); RETURN currval(''db_db_id_seq''); END IF; RETURN v_db_id; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION store_dbxref (VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_dbname ALIAS FOR $1; v_accession ALIAS FOR $2; v_db_id INTEGER; v_dbxref_id INTEGER; BEGIN SELECT INTO v_db_id store_db(v_dbname); SELECT INTO v_dbxref_id dbxref_id FROM dbxref WHERE db_id=v_db_id AND accession=v_accession; IF NOT FOUND THEN INSERT INTO dbxref (db_id,accession) VALUES (v_db_id,v_accession); RETURN currval(''dbxref_dbxref_id_seq''); END IF; RETURN v_dbxref_id; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/general/functions/general-loading.sqlapi000644 000765 000024 00000000264 11256710150 024132 0ustar00cainstaff000000 000000 COMMENT ON FUNCTION store_db (VARCHAR) IS 'stores a db and retrieves its id'; COMMENT ON FUNCTION store_dbxref (VARCHAR,VARCHAR) IS 'stores a dbxref by db.name and accession'; chado-1.23/modules/expression/expression.html000644 000765 000024 00000076136 11256710071 021543 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

expression
expression_cvterm
expression_cvtermprop
expressionprop
expression_pub
feature_expression
feature_expressionprop
eimage
expression_image

expression

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Comments:

$Id: expression.html,v 1.3 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado expression module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
=================================================================
================================================
TABLE: expression
================================================
The expression table is essentially a bridge table.
Field Name Data Type Size Default Value Other Foreign Key
expression_id integer 11 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
md5checksum char 32
description text 64000

Constraints

Type Fields
NOT NULL expression_id
NOT NULL uniquename
UNIQUE uniquename

expression_cvterm

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Comments:

================================================
TABLE: expression_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_cvterm_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 NOT NULL
cvterm_type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
expression_cvterm_idx1 expression_id
expression_cvterm_idx2 cvterm_id
expression_cvterm_idx3 cvterm_type_id

Constraints

Type Fields
NOT NULL expression_cvterm_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL rank
NOT NULL cvterm_type_id
FOREIGN KEY cvterm_type_id
UNIQUE expression_id, cvterm_id, cvterm_type_id

expression_cvtermprop

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================================================
TABLE: expression_cvtermprop
================================================
Extensible properties for expression to cvterm associations. Examples: qualifiers.
Field Name Data Type Size Default Value Other Foreign Key
expression_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
expression_cvterm_id integer 10 UNIQUE, NOT NULL expression_cvterm.expression_cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv. cvterm.cvterm_id
value text 64000 NULL The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
expression_cvtermprop_idx1 expression_cvterm_id
expression_cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL expression_cvtermprop_id
NOT NULL expression_cvterm_id
FOREIGN KEY expression_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE expression_cvterm_id, type_id, rank

expressionprop

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Comments:

================================================
TABLE: expressionprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
expressionprop_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
expressionprop_idx1 expression_id
expressionprop_idx2 type_id

Constraints

Type Fields
NOT NULL expressionprop_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE expression_id, type_id, rank

expression_pub

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Comments:

================================================
TABLE: expression_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_pub_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
expression_pub_idx1 expression_id
expression_pub_idx2 pub_id

Constraints

Type Fields
NOT NULL expression_pub_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE expression_id, pub_id

feature_expression

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Comments:

================================================
TABLE: feature_expression
================================================
Field Name Data Type Size Default Value Other Foreign Key
feature_expression_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_expression_idx1 expression_id
feature_expression_idx2 feature_id
feature_expression_idx3 pub_id

Constraints

Type Fields
NOT NULL feature_expression_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE expression_id, feature_id, pub_id

feature_expressionprop

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================================================
TABLE: feature_expressionprop
================================================
Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_expressionprop_id integer 11 PRIMARY KEY, NOT NULL
feature_expression_id integer 10 UNIQUE, NOT NULL feature_expression.feature_expression_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_expressionprop_idx1 feature_expression_id
feature_expressionprop_idx2 type_id

Constraints

Type Fields
NOT NULL feature_expressionprop_id
NOT NULL feature_expression_id
FOREIGN KEY feature_expression_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE feature_expression_id, type_id, rank

eimage

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Comments:

================================================
TABLE: eimage
================================================
Field Name Data Type Size Default Value Other Foreign Key
eimage_id integer 11 PRIMARY KEY, NOT NULL
eimage_data text 64000 We expect images in eimage_data (e.g. JPEGs) to be uuencoded.
eimage_type varchar 255 NOT NULL, Describes the type of data in eimage_data.
image_uri varchar 255

Constraints

Type Fields
NOT NULL eimage_id
NOT NULL eimage_type

expression_image

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Comments:

================================================
TABLE: expression_image
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_image_id integer 11 PRIMARY KEY, NOT NULL
expression_id integer 10 UNIQUE, NOT NULL expression.expression_id
eimage_id integer 10 UNIQUE, NOT NULL eimage.eimage_id

Indices

Name Fields
expression_image_idx1 expression_id
expression_image_idx2 eimage_id

Constraints

Type Fields
NOT NULL expression_image_id
NOT NULL expression_id
FOREIGN KEY expression_id
NOT NULL eimage_id
FOREIGN KEY eimage_id
UNIQUE expression_id, eimage_id
Created by SQL::Translator 0.08_01 chado-1.23/modules/expression/expression.sql000644 000765 000024 00000020232 11256710071 021360 0ustar00cainstaff000000 000000 -- $Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado expression module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- :import pub from pub -- ================================================================= -- ================================================ -- TABLE: expression -- ================================================ create table expression ( expression_id serial not null, primary key (expression_id), uniquename text not null, md5checksum character(32), description text, constraint expression_c1 unique(uniquename) ); COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.'; -- ================================================ -- TABLE: expression_cvterm -- ================================================ create table expression_cvterm ( expression_cvterm_id serial not null, primary key (expression_cvterm_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, cvterm_type_id int not null, foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id) ); create index expression_cvterm_idx1 on expression_cvterm (expression_id); create index expression_cvterm_idx2 on expression_cvterm (cvterm_id); create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id); --================================================ -- TABLE: expression_cvtermprop -- ================================================ create table expression_cvtermprop ( expression_cvtermprop_id serial not null, primary key (expression_cvtermprop_id), expression_cvterm_id int not null, foreign key (expression_cvterm_id) references expression_cvterm (expression_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expression_cvtermprop_c1 unique (expression_cvterm_id,type_id,rank) ); create index expression_cvtermprop_idx1 on expression_cvtermprop (expression_cvterm_id); create index expression_cvtermprop_idx2 on expression_cvtermprop (type_id); COMMENT ON TABLE expression_cvtermprop IS 'Extensible properties for expression to cvterm associations. Examples: qualifiers.'; COMMENT ON COLUMN expression_cvtermprop.type_id IS 'The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.'; COMMENT ON COLUMN expression_cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.'; COMMENT ON COLUMN expression_cvtermprop.rank IS 'Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: expressionprop -- ================================================ create table expressionprop ( expressionprop_id serial not null, primary key (expressionprop_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint expressionprop_c1 unique (expression_id,type_id,rank) ); create index expressionprop_idx1 on expressionprop (expression_id); create index expressionprop_idx2 on expressionprop (type_id); -- ================================================ -- TABLE: expression_pub -- ================================================ create table expression_pub ( expression_pub_id serial not null, primary key (expression_pub_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint expression_pub_c1 unique(expression_id,pub_id) ); create index expression_pub_idx1 on expression_pub (expression_id); create index expression_pub_idx2 on expression_pub (pub_id); -- ================================================ -- TABLE: feature_expression -- ================================================ create table feature_expression ( feature_expression_id serial not null, primary key (feature_expression_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint feature_expression_c1 unique(expression_id,feature_id,pub_id) ); create index feature_expression_idx1 on feature_expression (expression_id); create index feature_expression_idx2 on feature_expression (feature_id); create index feature_expression_idx3 on feature_expression (pub_id); -- ================================================ -- TABLE: feature_expressionprop -- ================================================ create table feature_expressionprop ( feature_expressionprop_id serial not null, primary key (feature_expressionprop_id), feature_expression_id int not null, foreign key (feature_expression_id) references feature_expression (feature_expression_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint feature_expressionprop_c1 unique (feature_expression_id,type_id,rank) ); create index feature_expressionprop_idx1 on feature_expressionprop (feature_expression_id); create index feature_expressionprop_idx2 on feature_expressionprop (type_id); COMMENT ON TABLE feature_expressionprop IS 'Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.'; -- ================================================ -- TABLE: eimage -- ================================================ create table eimage ( eimage_id serial not null, primary key (eimage_id), eimage_data text, eimage_type varchar(255) not null, image_uri varchar(255) ); COMMENT ON COLUMN eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.'; COMMENT ON COLUMN eimage.eimage_type IS 'Describes the type of data in eimage_data.'; -- ================================================ -- TABLE: expression_image -- ================================================ create table expression_image ( expression_image_id serial not null, primary key (expression_image_id), expression_id int not null, foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED, eimage_id int not null, foreign key (eimage_id) references eimage (eimage_id) on delete cascade INITIALLY DEFERRED, constraint expression_image_c1 unique(expression_id,eimage_id) ); create index expression_image_idx1 on expression_image (expression_id); create index expression_image_idx2 on expression_image (eimage_id); chado-1.23/modules/cv/bridges/000755 000765 000024 00000000000 12061672375 016302 5ustar00cainstaff000000 000000 chado-1.23/modules/cv/cv-dbapi.sqli000644 000765 000024 00000017005 11256710112 017230 0ustar00cainstaff000000 000000 -- $Id: cv-dbapi.sqli,v 1.2 2005-04-25 20:59:24 sshu Exp $ -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- cv-dbapi.sqli -- -- STATUS: alpha -- -- this interface describes the functions implemented by -- a chado database over the cv module -- -- -- the interface is specified in pseudo-SQL function syntax -- it is intended as formal documentation for DB Admins and -- application programmers. It is not intended to be used -- directly by the DB. The DB should implement these functions -- using a language pertinent to the DBMS implementing policies -- pertinent to the policy chosen by the MOD and DB Admin. -- -- a default postgresql implementation will be provided, in -- the functions/ directory. hopefully it should not be difficult -- to port these to other DBMS systems -- -- the DB API contains granual 'atomic' functions; that is, -- functions that neither accept not return complex datatypes -- such as objects, XML or other data structures. -- The API accepts/returns primitive values and relations. -- As such, the DB API is perhaps mostly useful for applications that -- modify the database. The API is intended to be complementary -- to APIs that accept or return complex datatypes, such as ChadoXML -- -- CONVENTIONS: -- functions are generally named _ -- the noun phrase typically refers to a chado table name, -- a type in some ontology such as SO, or an emergent -- table/type, such as "gene model" -- -- TODO: Document possible exceptions raised -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- ************************************************************ -- ** Data Modification Functions ** -- ** ** -- ** Calling any of these functions can result in data ** -- ** being modified ** -- ** ** -- ** Each function should note in the comments which ** -- ** tables are affected ** -- ** [d] - may result in deletion ** -- ** [u] - may result in update ** -- ** [i] - may result in insertion ** -- ** Cascading deletes are not explicitly noted; ** -- ** (ie if table 'feature' can be deleted then ** -- ** 'featureloc' may be deleted as a consequence) ** -- ************************************************************ -- ============================================================ -- FUNCTION: fill_cvtermpath -- ============================================================ -- rebuild cvtermpath for the ontology (cv.id or cv.name as arg) -- impl: see functions/fill_cvtermpath.plpgsql -- TABLES AFFECTED: cvtermpath[d, i] DECLARE FUNCTION fill_cvtermpath(cv_id integer not null); DECLARE FUNCTION fill_cvtermpath(cv_name varchar not null); -- ************************************************************ -- ** Non-modifying Functions ** -- ************************************************************ -- The functions below have no side-effects (ie they never -- result in update/delete/insert of any data) -- ============================================================ -- FUNCTION: get_all_subject_ids -- ============================================================ -- return cvterm child cvterm_id and their child cvterm_id -- all way down to leaf nodes of the onotlogy -- + root_cvterm_id - root of the cvterm graph -- NOTE: be aware of duplicate object_id in the return set -- impl: see functions/get_subj_obj_ids.plpgsql DECLARE FUNCTION get_all_subject_ids(root_cvterm_id integer not null) RETURNS setof subject_id; -- ============================================================ -- FUNCTION: get_graph_below -- ============================================================ -- return cvterm graph whose root (object_id) is root_cvterm_id -- + root_feature_id - root of the cvterm graph -- impl: see functions/get_subj_obj_ids.plpgsql DECLARE FUNCTION get_graph_below(root_cvterm_id integer not null) RETURNS setof subject_id, object_id, type_id; -- ============================================================ -- FUNCTION: get_graph_above -- ============================================================ -- return cvterm graph whose leaf (subject_id) is leaf_cvterm_id -- + leaf_feature_id - leaf of the cvterm graph -- impl: see functions/get_subj_obj_ids.plpgsql DECLARE FUNCTION get_graph_above(leaf_cvterm_id integer not null) RETURNS setof subject_id, object_id, type_id; -- ============================================================ -- FUNCTION: get_all_object_ids -- ============================================================ -- return cvterm parent cvterm_id and their parent cvterm_id -- all way up to root of the ontology -- + leaf_cvterm_id - leaf of the cvterm graph -- NOTE: be aware of duplicate subject_id in the return set -- impl: see functions/get_subj_obj_ids.plpgsql DECLARE FUNCTION get_all_object_ids(root_cvterm_id integer not null) RETURNS setof object_id; -- ============================================================ -- FUNCTION: get_it_sub_cvterm_ids -- ============================================================ -- return all cvterms that are specified by the sql or child terms -- of the terms specified by sql or their child terms -- + sql -- must be like 'select distinct subject_id from ...' -- impl: see functions/get_subj_obj_ids.plpgsql DECLARE FUNCTION get_it_sub_cvterm_ids(sql text not null) RETURNS setof subject_id; -- ============================================================ -- FUNCTION: get_cycle_cvterm_ids -- ============================================================ -- return all cvterms that are on cycle paths -- + sql -- must be like 'select distinct * from get_cycle_cvterm_ids(cvid)' -- as a term may appear multiple times in the return set if there is multiple-path to it from root -- impl: see functions/detect_cycle.plpgsql DECLARE FUNCTION get_cycle_cvterm_ids(cvid integer not null) RETURNS setof integer; -- ============================================================ -- FUNCTION: get_cycle_cvterm_id -- ============================================================ -- return cvterm id that is on cycle paths, -- the first term on cycle path found starting from ontology root -- impl: see functions/detect_cycle.plpgsql DECLARE FUNCTION get_cycle_cvterm_id(ontology_name varchar not null) RETURNS integer; -- ============================================================ -- FUNCTION: get_cycle_cvterm_id -- ============================================================ -- return cvterm id that is on cycle path, -- the first term on cycle path found starting from ontology root -- impl: see functions/detect_cycle.plpgsql DECLARE FUNCTION get_cycle_cvterm_id(cvid integer not null) RETURNS integer; -- ============================================================ -- FUNCTION: get_cycle_cvterm_id -- ============================================================ -- return cvterm id that is on cycle path, -- the first term on cycle path found starting from root term passed in -- impl: see functions/detect_cycle.plpgsql DECLARE FUNCTION get_cycle_cvterm_id(cvid integer not null, rootid integer not null) RETURNS integer; chado-1.23/modules/cv/cv.html000644 000765 000024 00000121464 11610540777 016170 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

cv
cvterm
cvterm_relationship
cvtermpath
cvtermsynonym
cvterm_dbxref
cvtermprop
dbxrefprop
cvprop
chadoprop

cv

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Comments:

$Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $
==========================================
Chado cv module
=================================================================
Dependencies:
:import dbxref from general
=================================================================
================================================
TABLE: cv
================================================
A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.
Field Name Data Type Size Default Value Other Foreign Key
cv_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.
definition text 64000 A text description of the criteria for membership of this ontology.

Constraints

Type Fields
NOT NULL cv_id
NOT NULL name
UNIQUE name

cvterm

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Comments:

================================================
TABLE: cvterm
================================================
A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_id integer 11 PRIMARY KEY, NOT NULL
cv_id integer 10 UNIQUE, NOT NULL, The cv or ontology or namespace to which this cvterm belongs. cv.cv_id
name varchar 1024 UNIQUE, NOT NULL, A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.
definition text 64000 A human-readable text definition.
dbxref_id integer 10 UNIQUE, NOT NULL, Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref. dbxref.dbxref_id
is_obsolete integer 10 0 UNIQUE, NOT NULL, Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.
is_relationshiptype integer 10 0 NOT NULL, Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.

Indices

Name Fields
cvterm_idx1 cv_id
cvterm_idx2 name
cvterm_idx3 dbxref_id

Constraints

Type Fields
NOT NULL cvterm_id
NOT NULL cv_id
FOREIGN KEY cv_id
NOT NULL name
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_obsolete
NOT NULL is_relationshiptype
UNIQUE name, cv_id, is_obsolete
UNIQUE dbxref_id

cvterm_relationship

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Comments:

A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.
The OBO identifier is globally unique.
================================================
TABLE: cvterm_relationship
================================================
A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".
Field Name Data Type Size Default Value Other Foreign Key
cvterm_relationship_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node. cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node. cvterm.cvterm_id

Indices

Name Fields
cvterm_relationship_idx1 type_id
cvterm_relationship_idx2 subject_id
cvterm_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL cvterm_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id

cvtermpath

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TABLE: cvtermpath
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The reflexive transitive closure of the cvterm_relationship relation.
Field Name Data Type Size Default Value Other Foreign Key
cvtermpath_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
cv_id integer 10 NOT NULL, Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm. cv.cv_id
pathdistance integer 10 UNIQUE, The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).

Indices

Name Fields
cvtermpath_idx1 type_id
cvtermpath_idx2 subject_id
cvtermpath_idx3 object_id
cvtermpath_idx4 cv_id

Constraints

Type Fields
NOT NULL cvtermpath_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL cv_id
FOREIGN KEY cv_id
UNIQUE subject_id, object_id, type_id, pathdistance

cvtermsynonym

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TABLE: cvtermsynonym
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A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".
Field Name Data Type Size Default Value Other Foreign Key
cvtermsynonym_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
synonym varchar 1024 UNIQUE, NOT NULL
type_id integer 10 A synonym can be exact, narrower, or broader than. cvterm.cvterm_id

Indices

Name Fields
cvtermsynonym_idx1 cvterm_id

Constraints

Type Fields
NOT NULL cvtermsynonym_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL synonym
FOREIGN KEY type_id
UNIQUE cvterm_id, synonym

cvterm_dbxref

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TABLE: cvterm_dbxref
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In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_dbxref_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_for_definition integer 10 0 NOT NULL, A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.

Indices

Name Fields
cvterm_dbxref_idx1 cvterm_id
cvterm_dbxref_idx2 dbxref_id

Constraints

Type Fields
NOT NULL cvterm_dbxref_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_for_definition
UNIQUE cvterm_id, dbxref_id

cvtermprop

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TABLE: cvtermprop
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Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
Field Name Data Type Size Default Value Other Foreign Key
cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL, The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
cvtermprop_idx1 cvterm_id
cvtermprop_idx2 type_id

Constraints

Type Fields
NOT NULL cvtermprop_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE cvterm_id, type_id, value, rank

dbxrefprop

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TABLE: dbxrefprop
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Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.
Field Name Data Type Size Default Value Other Foreign Key
dbxrefprop_id integer 11 PRIMARY KEY, NOT NULL
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
dbxrefprop_idx1 dbxref_id
dbxrefprop_idx2 type_id

Constraints

Type Fields
NOT NULL dbxrefprop_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL value
NOT NULL rank
UNIQUE dbxref_id, type_id, rank

cvprop

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TABLE: cvprop
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Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version
Field Name Data Type Size Default Value Other Foreign Key
cvprop_id integer 11 PRIMARY KEY, NOT NULL
cv_id integer 10 UNIQUE, NOT NULL cv.cv_id
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULL cvprop_id
NOT NULL cv_id
FOREIGN KEY cv_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cv_id, type_id, rank

chadoprop

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TABLE: chadoprop
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This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version
Field Name Data Type Size Default Value Other Foreign Key
chadoprop_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULL chadoprop_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE type_id, rank
Created by SQL::Translator 0.11003 chado-1.23/modules/cv/cv.sql000644 000765 000024 00000036342 11610540640 016010 0ustar00cainstaff000000 000000 -- $Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $ -- ========================================== -- Chado cv module -- -- ================================================================= -- Dependencies: -- -- :import dbxref from general -- ================================================================= -- ================================================ -- TABLE: cv -- ================================================ create table cv ( cv_id serial not null, primary key (cv_id), name varchar(255) not null, definition text, constraint cv_c1 unique (name) ); COMMENT ON TABLE cv IS 'A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.'; COMMENT ON COLUMN cv.name IS 'The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.'; COMMENT ON COLUMN cv.definition IS 'A text description of the criteria for membership of this ontology.'; -- ================================================ -- TABLE: cvterm -- ================================================ create table cvterm ( cvterm_id serial not null, primary key (cvterm_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, name varchar(1024) not null, definition text, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED, is_obsolete int not null default 0, is_relationshiptype int not null default 0, constraint cvterm_c1 unique (name,cv_id,is_obsolete), constraint cvterm_c2 unique (dbxref_id) ); create index cvterm_idx1 on cvterm (cv_id); create index cvterm_idx2 on cvterm (name); create index cvterm_idx3 on cvterm (dbxref_id); COMMENT ON TABLE cvterm IS 'A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.'; COMMENT ON COLUMN cvterm.cv_id IS 'The cv or ontology or namespace to which this cvterm belongs.'; COMMENT ON COLUMN cvterm.name IS 'A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.'; COMMENT ON COLUMN cvterm.definition IS 'A human-readable text definition.'; COMMENT ON COLUMN cvterm.dbxref_id IS 'Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.'; COMMENT ON COLUMN cvterm.is_obsolete IS 'Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.'; COMMENT ON COLUMN cvterm.is_relationshiptype IS 'Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.'; COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.'; COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.'; -- ================================================ -- TABLE: cvterm_relationship -- ================================================ create table cvterm_relationship ( cvterm_relationship_id serial not null, primary key (cvterm_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvterm_relationship_c1 unique (subject_id,object_id,type_id) ); create index cvterm_relationship_idx1 on cvterm_relationship (type_id); create index cvterm_relationship_idx2 on cvterm_relationship (subject_id); create index cvterm_relationship_idx3 on cvterm_relationship (object_id); COMMENT ON TABLE cvterm_relationship IS 'A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".'; COMMENT ON COLUMN cvterm_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.'; COMMENT ON COLUMN cvterm_relationship.object_id IS 'The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.'; COMMENT ON COLUMN cvterm_relationship.type_id IS 'The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.'; -- ================================================ -- TABLE: cvtermpath -- ================================================ create table cvtermpath ( cvtermpath_id serial not null, primary key (cvtermpath_id), type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete set null INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, cv_id int not null, foreign key (cv_id) references cv (cv_id) on delete cascade INITIALLY DEFERRED, pathdistance int, constraint cvtermpath_c1 unique (subject_id,object_id,type_id,pathdistance) ); create index cvtermpath_idx1 on cvtermpath (type_id); create index cvtermpath_idx2 on cvtermpath (subject_id); create index cvtermpath_idx3 on cvtermpath (object_id); create index cvtermpath_idx4 on cvtermpath (cv_id); COMMENT ON TABLE cvtermpath IS 'The reflexive transitive closure of the cvterm_relationship relation.'; COMMENT ON COLUMN cvtermpath.type_id IS 'The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.'; COMMENT ON COLUMN cvtermpath.cv_id IS 'Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.'; COMMENT ON COLUMN cvtermpath.pathdistance IS 'The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).'; -- ================================================ -- TABLE: cvtermsynonym -- ================================================ create table cvtermsynonym ( cvtermsynonym_id serial not null, primary key (cvtermsynonym_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, synonym varchar(1024) not null, type_id int, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cvtermsynonym_c1 unique (cvterm_id,synonym) ); create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id); COMMENT ON TABLE cvtermsynonym IS 'A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".'; COMMENT ON COLUMN cvtermsynonym.type_id IS 'A synonym can be exact, narrower, or broader than.'; -- ================================================ -- TABLE: cvterm_dbxref -- ================================================ create table cvterm_dbxref ( cvterm_dbxref_id serial not null, primary key (cvterm_dbxref_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_for_definition int not null default 0, constraint cvterm_dbxref_c1 unique (cvterm_id,dbxref_id) ); create index cvterm_dbxref_idx1 on cvterm_dbxref (cvterm_id); create index cvterm_dbxref_idx2 on cvterm_dbxref (dbxref_id); COMMENT ON TABLE cvterm_dbxref IS 'In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.'; COMMENT ON COLUMN cvterm_dbxref.is_for_definition IS 'A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.'; -- ================================================ -- TABLE: cvtermprop -- ================================================ create table cvtermprop ( cvtermprop_id serial not null, primary key (cvtermprop_id), cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text not null default '', rank int not null default 0, unique(cvterm_id, type_id, value, rank) ); create index cvtermprop_idx1 on cvtermprop (cvterm_id); create index cvtermprop_idx2 on cvtermprop (type_id); COMMENT ON TABLE cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.'; COMMENT ON COLUMN cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvtermprop.rank IS 'Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: dbxrefprop -- ================================================ create table dbxrefprop ( dbxrefprop_id serial not null, primary key (dbxrefprop_id), dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text not null default '', rank int not null default 0, constraint dbxrefprop_c1 unique (dbxref_id,type_id,rank) ); create index dbxrefprop_idx1 on dbxrefprop (dbxref_id); create index dbxrefprop_idx2 on dbxrefprop (type_id); COMMENT ON TABLE dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.'; -- ================================================ -- TABLE: cvprop -- ================================================ create table cvprop ( cvprop_id serial not null, primary key (cvprop_id), cv_id int not null, foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint cvprop_c1 unique (cv_id,type_id,rank) ); COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version'; COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; -- ================================================ -- TABLE: chadoprop -- ================================================ create table chadoprop ( chadoprop_id serial not null, primary key (chadoprop_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED, value text, rank int not null default 0, constraint chadoprop_c1 unique (type_id,rank) ); COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version'; COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.'; COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.'; COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.'; chado-1.23/modules/cv/functions/000755 000765 000024 00000000000 12061672376 016674 5ustar00cainstaff000000 000000 chado-1.23/modules/cv/views/000755 000765 000024 00000000000 12061672376 016021 5ustar00cainstaff000000 000000 chado-1.23/modules/cv/views/cv-convenience-views.sql000644 000765 000024 00000000711 11256710112 022560 0ustar00cainstaff000000 000000 CREATE VIEW cvterm_relationship_with_typename AS SELECT cvterm_relationship.*, typeterm.name AS typename, typeterm.cv_id AS typeterm_cv_id FROM cvterm_relationship INNER JOIN cvterm AS typeterm ON (type_id=typeterm.cvterm_id); CREATE VIEW cvtermprop_with_propname AS SELECT cvtermprop.*, propterm.name AS propname, propterm.cv_id AS propterm_cv_id FROM cvtermprop INNER JOIN cvterm AS propterm ON (type_id=propterm.cvterm_id); chado-1.23/modules/cv/views/cv-logical-definitions-views.sql000644 000765 000024 00000003551 11256710112 024214 0ustar00cainstaff000000 000000 -- Cross-products, logical definitions -- These views are for advanced use - you will only need them if -- you are loading ontologies that use either advanced obo format 1.2 -- features or OWL DL ontologies. Please read the relevant documentation -- first -- keywords: defined classes, OWL, Aristotelian definitions CREATE OR REPLACE VIEW is_anonymous_cvterm AS SELECT cvterm_id FROM cvtermprop_with_propname WHERE propname='is_anonymous' AND value='1'; CREATE OR REPLACE VIEW cvterm_ldef_intersection AS SELECT * FROM cvterm_relationship_with_typename WHERE typename='intersection_of'; COMMENT ON VIEW cvterm_ldef_intersection IS 'for advanced OWL/Description Logic style definitions, chado allows the specification of an equivalentClass using intersection_of links between the defined term and the cross-product'; CREATE OR REPLACE VIEW cvterm_genus AS SELECT i.subject_id AS cvterm_id, i.object_id AS genus_id FROM cvterm_ldef_intersection AS i WHERE i.object_id NOT IN (SELECT cvterm_id FROM is_anonymous_cvterm); COMMENT ON VIEW cvterm_genus IS 'In a logical (cross-product) definition, there is a generic term (genus) and discriminating characteristics. E.g. a biosynthesis (genus) which outputs cysteine (differentia). The genus is the -true- is_a parent'; CREATE OR REPLACE VIEW cvterm_differentium AS SELECT i.subject_id AS cvterm_id, diff.* FROM cvterm_ldef_intersection AS i INNER JOIN cvterm_relationship AS diff ON (i.object_id=diff.subject_id) INNER JOIN is_anonymous_cvterm AS anon ON (anon.cvterm_id=i.object_id); COMMENT ON VIEW cvterm_differentium IS 'In a logical (cross-product) definition, there is a generic term (genus) and discriminating characteristics. E.g. a biosynthesis (genus) which outputs cysteine (differentia). Each differentium is a link via a relation to another cvterm which discriminates the defined term from other is_a siblings'; chado-1.23/modules/cv/views/cv-report.sql000644 000765 000024 00000003610 11256710112 020445 0ustar00cainstaff000000 000000 CREATE VIEW cv_cvterm_count AS SELECT cv.name,count(*) AS num_terms_excl_obs FROM cv INNER JOIN cvterm USING (cv_id) WHERE is_obsolete=0 GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)'; CREATE VIEW cv_cvterm_count_with_obs AS SELECT cv.name,count(*) AS num_terms_incl_obs FROM cv INNER JOIN cvterm USING (cv_id) GROUP BY cv.name; COMMENT ON VIEW cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)'; CREATE VIEW cv_link_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_links FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvterm_relationship ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_link_count IS 'per-cv summary of number of links (cvterm_relationships) broken down by relationship_type. num_links is the total # of links of the specified type in which the subject_id of the link is in the named cv'; CREATE VIEW cv_path_count AS SELECT cv.name AS cv_name, relation.name AS relation_name, relation_cv.name AS relation_cv_name, count(*) AS num_paths FROM cv INNER JOIN cvterm ON (cvterm.cv_id=cv.cv_id) INNER JOIN cvtermpath ON (cvterm.cvterm_id=subject_id) INNER JOIN cvterm AS relation ON (type_id=relation.cvterm_id) INNER JOIN cv AS relation_cv ON (relation.cv_id=relation_cv.cv_id) GROUP BY cv.name,relation.name,relation_cv.name; COMMENT ON VIEW cv_path_count IS 'per-cv summary of number of paths (cvtermpaths) broken down by relationship_type. num_paths is the total # of paths of the specified type in which the subject_id of the path is in the named cv. See also: cv_distinct_relations'; chado-1.23/modules/cv/views/cv-stats.sql000644 000765 000024 00000000064 11256710112 020270 0ustar00cainstaff000000 000000 CREATE VIEW avg_number_of_paths_to_root AS SELECT chado-1.23/modules/cv/views/cv-views.sql000644 000765 000024 00000005400 11256710112 020266 0ustar00cainstaff000000 000000 CREATE OR REPLACE VIEW cv_root AS SELECT cv_id, cvterm_id AS root_cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT subject_id FROM cvterm_relationship) AND is_obsolete=0; COMMENT ON VIEW cv_root IS 'the roots of a cv are the set of terms which have no parents (terms that are not the subject of a relation). Most cvs will have a single root, some may have >1. All will have at least 1'; CREATE OR REPLACE VIEW cv_leaf AS SELECT cv_id, cvterm_id FROM cvterm WHERE cvterm_id NOT IN ( SELECT object_id FROM cvterm_relationship); COMMENT ON VIEW cv_leaf IS 'the leaves of a cv are the set of terms which have no children (terms that are not the object of a relation). All cvs will have at least 1 leaf'; CREATE OR REPLACE VIEW common_ancestor_cvterm AS SELECT p1.subject_id AS cvterm1_id, p2.subject_id AS cvterm2_id, p1.object_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.object_id = p2.object_id; COMMENT ON VIEW common_ancestor_cvterm IS 'The common ancestor of any two terms is the intersection of both terms ancestors. Two terms can have multiple common ancestors. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW common_descendant_cvterm AS SELECT p1.object_id AS cvterm1_id, p2.object_id AS cvterm2_id, p1.subject_id AS ancestor_cvterm_id, p1.pathdistance AS pathdistance1, p2.pathdistance AS pathdistance2, p1.pathdistance + p2.pathdistance AS total_pathdistance FROM cvtermpath AS p1, cvtermpath AS p2 WHERE p1.subject_id = p2.subject_id; COMMENT ON VIEW common_descendant_cvterm IS 'The common descendant of any two terms is the intersection of both terms descendants. Two terms can have multiple common descendants. Use total_pathdistance to get the least common ancestor'; CREATE OR REPLACE VIEW stats_paths_to_root AS SELECT subject_id AS cvterm_id, count(DISTINCT cvtermpath_id) AS total_paths, avg(pathdistance) AS avg_distance, min(pathdistance) AS min_distance, max(pathdistance) AS max_distance FROM cvtermpath INNER JOIN cv_root ON (object_id=root_cvterm_id) GROUP BY cvterm_id; COMMENT ON VIEW stats_paths_to_root IS 'per-cvterm statistics on its placement in the DAG relative to the root. There may be multiple paths from any term to the root. This gives the total number of paths, and the average minimum and maximum distances. Here distance is defined by cvtermpath.pathdistance'; chado-1.23/modules/cv/functions/cv-helper.plpgsql000644 000765 000024 00000000463 11256710107 022156 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION get_cv_id_for_relation() RETURNS INT AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql'; CREATE OR REPLACE FUNCTION get_cvterm_id_for_is_a() RETURNS INT AS 'SELECT cvterm_id FROM cvterm WHERE name=''is_a'' AND cv_id=get_cv_id_for_relation()' LANGUAGE 'sql'; chado-1.23/modules/cv/functions/cv-helper.sqlapi000644 000765 000024 00000000355 11256710107 021765 0ustar00cainstaff000000 000000 COMMENT ON FUNCTION get_cv_id_for_relation() IS 'returns the cv.cv_id for the foundational relation ontology (OBO_REL)'; COMMENT ON FUNCTION get_cvterm_id_for_is_a() IS 'returns the cvterm.cvterm_id for the foundational is_a relation'; chado-1.23/modules/cv/functions/deductive_closure.plpgsql000644 000765 000024 00000020325 11256710107 024000 0ustar00cainstaff000000 000000 CREATE TYPE closure_result AS (cvterm_id INTEGER, pathdistance INTEGER); -- results may not be distinct CREATE OR REPLACE FUNCTION _closure_over_IS_A(INTEGER, INTEGER) RETURNS SETOF INTEGER AS $$ DECLARE term ALIAS FOR $1; is_a_id ALIAS FOR $2; inner_row RECORD; outer_row RECORD; BEGIN -- get direct is_a parents FOR inner_row IN SELECT object_id AS cvterm_id FROM cvterm_relationship WHERE subject_id = term AND type_id=is_a_id LOOP -- return direct is_a parents RETURN NEXT inner_row.cvterm_id; -- recursive, self-call FOR outer_row IN SELECT * FROM _closure_over_IS_A(inner_row.cvterm_id, is_a_id) LOOP RETURN NEXT outer_row._closure_over_IS_A; END LOOP; END LOOP; RETURN; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION closure_over_IS_A(INTEGER) RETURNS SETOF INTEGER AS $$ DECLARE is_a_id INTEGER; r RECORD; BEGIN SELECT INTO is_a_id get_cvterm_id_for_is_a(); FOR r IN SELECT * FROM _closure_over_IS_A($1, is_a_id) LOOP RETURN NEXT r._closure_over_IS_A; END LOOP; RETURN; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION closure_over_reflexive_IS_A(INTEGER) RETURNS SETOF INTEGER AS $$ DECLARE is_a_id INTEGER; r RECORD; BEGIN SELECT INTO is_a_id get_cvterm_id_for_is_a(); FOR r IN SELECT * FROM _closure_over_IS_A($1, is_a_id) UNION SELECT $1 LOOP RETURN NEXT r._closure_over_IS_A; END LOOP; RETURN; END; $$ LANGUAGE 'plpgsql'; -- implements: -- X R Z <= X is_a* Y, Y R Z -- but not: -- X R Z <= X R Y, Y is_a+ Z CREATE OR REPLACE FUNCTION _closure_over_relation_with_dist_partial(INTEGER,INTEGER,INTEGER,INTEGER) RETURNS SETOF closure_result AS $$ DECLARE term ALIAS FOR $1; relation_id ALIAS FOR $2; is_a_id ALIAS FOR $3; depth ALIAS FOR $4; depth2 INTEGER; isa_plus_r RECORD; direct_link_r closure_result%ROWTYPE; trans_link_r closure_result%ROWTYPE; BEGIN depth2 := depth+1; -- get ALL is_a* parents FOR isa_plus_r IN SELECT * FROM _closure_over_is_a(term,is_a_id) AS cvterm_id UNION SELECT term AS cvterm_id LOOP RAISE NOTICE ''is_a %'', isa_plus_r.cvterm_id; FOR direct_link_r IN SELECT object_id AS cvterm_id, depth2 AS pathdistance FROM cvterm_relationship WHERE subject_id = isa_plus_r.cvterm_id AND type_id=relation_id LOOP RAISE NOTICE ''obj % dist % / % '', direct_link_r.cvterm_id, depth2, direct_link_r.pathdistance; -- return direct R parents RETURN NEXT direct_link_r; -- recursive, self-call FOR trans_link_r IN SELECT * FROM _closure_over_relation_with_dist_partial(direct_link_r.cvterm_id, relation_id, is_a_id, depth2) LOOP RETURN NEXT trans_link_r; END LOOP; END LOOP; END LOOP; RETURN; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION closure_over_relation_with_dist(INTEGER,INTEGER) RETURNS SETOF closure_result AS $$ DECLARE is_a_id INTEGER; r closure_result%ROWTYPE; r_plus_is_a closure_result%ROWTYPE; BEGIN SELECT INTO is_a_id get_cvterm_id_for_is_a(); FOR r IN SELECT * FROM _closure_over_relation_with_dist_partial($1,$2,is_a_id,0) AS cvterm_id LOOP FOR r_plus_is_a IN SELECT cvterm_id, r.pathdistance FROM _closure_over_is_a(r.cvterm_id,is_a_id) AS cvterm_id UNION SELECT r.* LOOP RETURN NEXT r_plus_is_a; END LOOP; END LOOP; RETURN; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION forward_chain() RETURNS INT AS $$ DECLARE num_assertions INTEGER; total_assertions INTEGER; BEGIN total_assertions := 0; PERFORM seed_cvtermpath(); -- keep adding new facts until exhausted LOOP SELECT INTO num_assertions forward_chain_iteration(); total_assertions := total_assertions + num_assertions; RAISE LOG 'Asserted % new facts; current_total=%', num_assertions, total_assertions; EXIT WHEN num_assertions > 0; END LOOP; RETURN total_assertions; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION seed_cvtermpath() RETURNS INT AS $$ DECLARE num_assertions INTEGER; is_a_id INTEGER; BEGIN RAISE LOG 'Seeding cvtermpath'; -- seed cvtermpath with direct asserted links INSERT INTO cvtermpath (subject_id,type_id,object_id,pathdistance) SELECT DISTINCT link.subject_id, link.type_id, link.object_id, 1 FROM cvterm_relationship AS link LEFT JOIN cvtermpath AS p1 USING (subject_id,type_id,object_id) -- exclude pre-populated links WHERE p1.cvtermpath_id IS NULL; -- this is how we do a SELECT MINUS GET DIAGNOSTICS num_assertions = ROW_COUNT; RAISE LOG 'Seeded cvtermpath with % links', num_assertions; SELECT INTO is_a_id get_cvterm_id_for_is_a(); -- seed cvtermpath with reflexive is_a INSERT INTO cvtermpath (subject_id,type_id,object_id,pathdistance) SELECT DISTINCT t.cvterm_id, is_a_id, t.cvterm_id, 0 FROM cvterm AS t LEFT JOIN cvtermpath AS p1 ON (p1.subject_id=t.cvterm_id,p1.type_id=t.is_a_id,p1.object_id=t.cvterm_id) -- exclude pre-populated links WHERE p1.cvtermpath_id IS NULL; -- this is how we do a SELECT MINUS GET DIAGNOSTICS num_assertions = ROW_COUNT; RAISE LOG 'Seeded cvtermpath with % links', num_assertions; RETURN num_assertions; END; $$ LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION forward_chain_iteration() RETURNS INT AS $$ DECLARE num_assertions INTEGER; total_assertions INTEGER; BEGIN total_assertions := 0; -- add your own rules here: SELECT INTO num_assertions forward_chain_iteration_rule_is_a(); total_assertions := total_assertions + num_assertions; -- end of rules section RETURN total_assertions; END; $$ LANGUAGE 'plpgsql'; -- IS_A rule -- X is_a Y, Y is_a Z => X is_a Z CREATE OR REPLACE FUNCTION forward_chain_iteration_rule_is_a() RETURNS INT AS $$ DECLARE is_a_id INTEGER; num_assertions INTEGER; BEGIN RAISE LOG 'Applying rule: IS_A'; SELECT INTO is_a_id get_cvterm_id_for_is_a(); INSERT INTO cvtermpath (subject_id,type_id,object_id,pathdistance) SELECT DISTINCT p.subject_id, is_a_id, link.object_id, p.pathdistance+1 FROM cvtermpath AS p -- extend this INNER JOIN cvterm_relationship AS link ON (p.object_id = link.subject_id) -- using this LEFT JOIN cvtermpath AS p1 ON (p1.subject_id=p.subject_id AND p1.object_id=link.object_id AND p1.type_id=is_a_id) -- excluding this [pathdist??] WHERE link.type_id=is_a_id AND p.type_id=is_a_id AND p1.cvtermpath_id IS NULL; -- exclude existing paths GET DIAGNOSTICS num_assertions = ROW_COUNT; RAISE LOG 'RULE:IS_A iteration produced % links', num_assertions; RETURN num_assertions; END; $$ LANGUAGE 'plpgsql'; -- TRANSITIVE-OVER-IS_A rule -- X is_a+ Y, Y R Z => X R Z CREATE OR REPLACE FUNCTION forward_chain_iteration_rule_trans_over_is_a() RETURNS INT AS $$ DECLARE is_a_id INTEGER; num_assertions INTEGER; BEGIN RAISE LOG 'Applying rule: TRANS_OVER_IS_A'; SELECT INTO is_a_id get_cvterm_id_for_is_a(); INSERT INTO cvtermpath (subject_id,type_id,object_id,pathdistance) SELECT DISTINCT p_is_a.subject_id, p_rel.type_id p_rel.object_id, p_rel.pathdistance+1 FROM cvtermpath AS p_is_a -- extend this INNER JOIN cvtermpath AS p_rel ON (p_is_a.object_id = p_rel.subject_id) -- using this LEFT JOIN cvtermpath AS p1 ON (p1.subject_id=p_is_a.subject_id AND p1.object_id=p_rel.object_id AND p1.type_id=p_rel.type_id) -- excluding this [pathdist??] WHERE p_is_a.type_id=is_a_id AND p1.cvtermpath_id IS NULL; -- exclude existing paths GET DIAGNOSTICS num_assertions = ROW_COUNT; RAISE LOG 'Applied rule:TRANS_OVER_IS_A iteration produced % links', num_assertions; RETURN num_assertions; END; $$ LANGUAGE 'plpgsql'; chado-1.23/modules/cv/functions/deductive_closure.sqlapi000644 000765 000024 00000003613 11256710107 023610 0ustar00cainstaff000000 000000 CREATE TYPE closure_result AS (cvterm_id INTEGER, pathdistance INTEGER); DECLARE FUNCTION closure_over_is_a(cvterm_id INTEGER) RETURNS SETOF INTEGER; COMMENT ON FUNCTION closure_over_is_a(INTEGER) IS 'Performs the deductive closure over the is_a relation. Returns every cvterm_id which is a direct or indirect is_a parent of the input term. Implements the rule: X is_a Z <= X is_a Y, Y is_a Z [transitive] '; DECLARE FUNCTION closure_over_reflexive_is_a(cvterm_id INTEGER) RETURNS SETOF INTEGER; COMMENT ON FUNCTION closure_over_reflexive_is_a(INTEGER) IS 'Performs the deductive closure over the is_a relation, treating the is_a relation as reflexive. i.e. X is_a X [reflexive] '; DECLARE FUNCTION closure_over_relation(cvterm_id INTEGER, relation_cvterm_id INTEGER) RETURNS SETOF INTEGER; DECLARE FUNCTION closure_over_relation_with_dist(cvterm_id INTEGER, relation_cvterm_id INTEGER) RETURNS SETOF closure_result; COMMENT ON FUNCTION closure_over_relation_with_dist(INTEGER,INTEGER) IS 'Performs the deductive closure over non-is_a transitive relation (eg part_of). Returns every cvterm_id which is a direct or indirect is_a parent of the input term. Implements the rules: X R Z <= X R Y, Y R Z [transitive] X R Z <= X is_a[transitive] Y, Y R Z X R Z <= X R Y, Y is_a[transitive] Z For example, if we have A is_a B, B is_a C, C part_of D, D part_of E, E is_a F, F part_of G, G is_a H Then A is part_of D, E, F, G, H In addition, the distance is returned; this is the number of connecting links of type R (links of type is_a are not counted here) Note: this function returns a set, so it should be called like this: SELECT * FROM closure_over_relation_with_dist( , ); Note: this will not check to see if the relation has been explicitly declared transitive '; chado-1.23/modules/cv/functions/detect_cycle.plpgsql000644 000765 000024 00000013151 11256710107 022716 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION _fill_cvtermpath4node2detect_cycle(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; ccount int; ecount int; rtn int; BEGIN EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = ''|| origin || '' AND p2.subject_id = '' || child_id || ''AND '' || depth || ''> 0''; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE EXCEPTION ''FOUND CYCLE: node % on cycle path'',origin; RETURN origin; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND '' || origin || ''<>'' || child_id; GET DIAGNOSTICS ecount = ROW_COUNT; IF (ecount > 0) THEN --RAISE NOTICE ''FOUND TWICE (node), will check root obj % subj %'',origin, child_id; SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; EXECUTE ''SELECT * FROM tmpcvtermpath WHERE cv_id = '' || cvid || '' AND object_id = '' || origin || '' AND subject_id = '' || child_id || '' AND pathdistance = '' || depth; GET DIAGNOSTICS exist_c = ROW_COUNT; IF (exist_c = 0) THEN EXECUTE ''INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES('' || origin || '', '' || child_id || '', '' || cvid || '', '' || typeid || '', '' || depth || '')''; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP --RAISE NOTICE ''DOING for node, % %'', origin, cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); IF (rtn > 0) THEN RETURN rtn; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root2detect_cycle(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; ccount int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; rtn int; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP EXECUTE ''SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id='' || rootid || '' AND p1.subject_id='' || cterm.subject_id; GET DIAGNOSTICS ccount = ROW_COUNT; IF (ccount > 0) THEN --RAISE NOTICE ''FOUND TWICE (root), will check root obj % subj %'',rootid,cterm.subject_id; SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0); IF (rtn > 0) THEN RETURN rtn; END IF; ELSE SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid); IF (rtn > 0) THEN RETURN rtn; END IF; END IF; END LOOP; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; rootid alias for $2; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_ids(INTEGER) RETURNS SETOF INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id); IF (rtn > 0) THEN RETURN NEXT rtn; END IF; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; rtn int; BEGIN CREATE TEMP TABLE tmpcvtermpath(object_id int, subject_id int, cv_id int, type_id int, pathdistance int); CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id); FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id); IF (rtn > 0) THEN DROP TABLE tmpcvtermpath; RETURN rtn; END IF; END LOOP; DROP TABLE tmpcvtermpath; RETURN 0; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_cycle_cvterm_id(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn get_cycle_cvterm_id(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/cv/functions/fill_cvtermpath.plpgsql000644 000765 000024 00000005162 11256710107 023455 0ustar00cainstaff000000 000000 --- example: select * from fill_cvtermpath(7); where 7 is cv_id for an ontology --- fill path from the node to its children and their children CREATE OR REPLACE FUNCTION _fill_cvtermpath4node(INTEGER, INTEGER, INTEGER, INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE origin alias for $1; child_id alias for $2; cvid alias for $3; typeid alias for $4; depth alias for $5; cterm cvterm_relationship%ROWTYPE; exist_c int; BEGIN --- RAISE NOTICE ''depth=% root=%'', depth,child_id; --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1 SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth; IF (exist_c = 0) THEN INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth); END IF; FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _fill_cvtermpath4root(INTEGER, INTEGER) RETURNS INTEGER AS ' DECLARE rootid alias for $1; cvid alias for $2; ttype int; cterm cvterm_relationship%ROWTYPE; child cvterm_relationship%ROWTYPE; BEGIN SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a''); PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0); FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid); -- RAISE NOTICE ''DONE for term, %'', cterm.subject_id; END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(INTEGER) RETURNS INTEGER AS ' DECLARE cvid alias for $1; root cvterm%ROWTYPE; BEGIN DELETE FROM cvtermpath WHERE cv_id = cvid; FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id); END LOOP; RETURN 1; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION fill_cvtermpath(cv.name%TYPE) RETURNS INTEGER AS ' DECLARE cvname alias for $1; cv_id int; rtn int; BEGIN SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname; SELECT INTO rtn fill_cvtermpath(cv_id); RETURN rtn; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/cv/functions/get_subj_obj_ids.plpgsql000644 000765 000024 00000007602 11256710107 023566 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION _get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: parent term id ---return: all children term id and their parent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_subject_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_below(integer) RETURNS SETOF cvtermpath AS ' DECLARE root alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION get_graph_above(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; CREATE OR REPLACE FUNCTION _get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; cterm2 cvtermpath%ROWTYPE; BEGIN FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: child term id ---return: all parent term id and their childrent term id with relationship type id CREATE OR REPLACE FUNCTION get_all_object_ids(integer) RETURNS SETOF cvtermpath AS ' DECLARE leaf alias for $1; cterm cvtermpath%ROWTYPE; exist_c int; BEGIN SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0; IF (exist_c > 0) THEN FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP RETURN NEXT cterm; END LOOP; ELSE FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP RETURN NEXT cterm; END LOOP; END IF; RETURN; END; ' LANGUAGE 'plpgsql'; ---arg: sql statement which must be in the form of select cvterm_id from ... ---return: a set of cvterm ids that includes what is in sql statement and their children (subject ids) CREATE OR REPLACE FUNCTION get_it_sub_cvterm_ids(text) RETURNS SETOF cvterm AS ' DECLARE query alias for $1; cterm cvterm%ROWTYPE; cterm2 cvterm%ROWTYPE; BEGIN FOR cterm IN EXECUTE query LOOP RETURN NEXT cterm; FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP RETURN NEXT cterm2; END LOOP; END LOOP; RETURN; END; ' LANGUAGE 'plpgsql'; chado-1.23/modules/cv/bridges/bin/000755 000765 000024 00000000000 12061672375 017052 5ustar00cainstaff000000 000000 chado-1.23/modules/cv/bridges/godb-bridge.plpgsql000644 000765 000024 00000031257 11256710107 022052 0ustar00cainstaff000000 000000 CREATE SCHEMA godb; --Activate this to make this bridge take precedence --SET SEARCH PATH TO godb,public; -- (note that placing godb first in the search path means -- that godb.dbxref takes precedence over public.dbxref) CREATE TABLE godb.instance_data ( release_name varchar(255), release_type varchar(255), release_notes text ); --- helper views --view CREATE VIEW godb.v_go_acc AS SELECT dbxref_id AS dbxref_id, db.name || ':' || dbxref.accession AS acc FROM public.dbxref INNER JOIN public.db USING (db_id); --materialized view CREATE TABLE godb.go_acc ( dbxref_id int, acc text ); CREATE INDEX go_acc_idx1 ON godb.go_acc (dbxref_id); CREATE INDEX go_acc_idx2 ON godb.go_acc (acc); --load INSERT INTO godb.go_acc SELECT * FROM godb.v_go_acc; --- dbxref [clash] --view CREATE VIEW godb.v_dbxref AS SELECT dbxref_id AS id, db.name AS xref_dbname, dbxref.accession AS xref_key, CAST(NULL AS VARCHAR) AS xref_keytype, dbxref.description AS xref_desc FROM public.dbxref INNER JOIN public.db USING (db_id); --materialized view CREATE TABLE godb.dbxref ( id int, xref_dbname varchar(255), xref_key varchar(255), xref_keytype varchar(255), xref_desc text ); CREATE INDEX dbxref_idx1 ON godb.dbxref (id); CREATE INDEX dbxref_idx2 ON godb.dbxref (xref_dbname); CREATE INDEX dbxref_idx3 ON godb.dbxref (xref_key); CREATE INDEX dbxref_idx4 ON godb.dbxref (xref_keytype); CREATE INDEX dbxref_idx5 ON godb.dbxref (xref_desc); --load INSERT INTO godb.dbxref SELECT * FROM godb.v_dbxref; -- --/allen -- -- db [clash] (note in godb, db is only refered to from association table) --view CREATE VIEW godb.v_db AS SELECT db_id AS id, name AS name, name AS fullname, CAST(NULL AS VARCHAR) AS datatype, CAST(NULL AS VARCHAR) AS url_syntax FROM public.db; --materialized view CREATE TABLE godb.db ( id int, name varchar(255), fullname varchar(255), datatype varchar(255), url_syntax varchar(255) ); CREATE INDEX db_idx1 ON godb.db (id); CREATE INDEX db_idx2 ON godb.db (name); CREATE INDEX db_idx3 ON godb.db (fullname); CREATE INDEX db_idx4 ON godb.db (datatype); CREATE INDEX db_idx5 ON godb.db (url_syntax); --load INSERT INTO godb.db SELECT * FROM godb.v_db; --- term --view CREATE VIEW godb.v_term AS SELECT cvterm_id AS id, godb.go_acc.acc AS acc, name AS name, is_obsolete AS is_obsolete, 0 AS is_root FROM public.cvterm INNER JOIN godb.go_acc USING (dbxref_id); --materialized_view CREATE TABLE godb.term ( id int, acc text, name varchar(1024), is_obsolete int, is_root int ); CREATE INDEX term_idx1 ON godb.term (id); CREATE INDEX term_idx2 ON godb.term (acc); CREATE INDEX term_idx3 ON godb.term (name); CREATE INDEX term_idx4 ON godb.term (is_obsolete); CREATE INDEX term_idx5 ON godb.term (is_root); --load INSERT INTO godb.term SELECT * FROM godb.v_term; UPDATE godb.term SET is_root = 1 WHERE id IN (SELECT cvterm_id FROM public.cvterm WHERE cvterm_id NOT IN (SELECT DISTINCT subject_id FROM public.cvterm_relationship) AND is_obsolete = 0 AND is_relationshiptype = 0); --- term_definition --view CREATE VIEW godb.term_definition AS SELECT cvterm_id AS term_id, definition AS term_definition FROM public.cvterm WHERE definition IS NOT NULL; --- term_dbxref --view CREATE VIEW godb.term_dbxref AS SELECT cvterm_id AS term_id, dbxref_id AS dbxref_id, 0 AS is_for_definition FROM public.cvterm_dbxref; --- term_synonym --view CREATE VIEW godb.term_synonym AS SELECT cvterm_id AS term_id, synonym AS term_synonym, type_id AS synonym_type_id FROM public.cvtermsynonym; --- term2term --view CREATE VIEW godb.v_term2term AS SELECT cvterm_relationship_id AS id, type_id AS relationship_type_id, object_id AS term1_id, subject_id AS term2_id FROM public.cvterm_relationship; --materialized view CREATE TABLE godb.term2term ( id int, relationship_type_id int, term1_id int, term2_id int ); CREATE INDEX term2term_idx1 ON godb.term2term (id); CREATE INDEX term2term_idx2 ON godb.term2term (relationship_type_id); CREATE INDEX term2term_idx3 ON godb.term2term (term1_id); CREATE INDEX term2term_idx4 ON godb.term2term (term2_id); --load INSERT INTO godb.term2term SELECT * FROM godb.v_term2term; --- graph_path --view CREATE VIEW godb.v_graph_path AS SELECT cvtermpath_id AS id, object_id AS term1_id, subject_id AS term2_id, pathdistance AS distance FROM public.cvtermpath; --materialized view CREATE TABLE godb.graph_path ( id int, term1_id int, term2_id int, distance int ); CREATE INDEX graph_path_idx1 ON godb.graph_path (id); CREATE INDEX graph_path_idx2 ON godb.graph_path (term1_id); CREATE INDEX graph_path_idx3 ON godb.graph_path (term2_id); CREATE INDEX graph_path_idx4 ON godb.graph_path (distance); --load INSERT INTO godb.graph_path SELECT * FROM godb.v_graph_path; --Activate this to make this bridge take precedence --SET SEARCH PATH TO godb,public; -- species --view CREATE VIEW godb.species AS SELECT organism_id AS id, --FIXME this cast does not work -- CAST(accession AS INT) AS ncbi_taxa_id, accession AS ncbi_taxa_id, common_name, CAST(NULL AS VARCHAR) AS lineage_string, genus, species FROM public.organism INNER JOIN public.organism_dbxref USING (organism_id) INNER JOIN public.dbxref USING (dbxref_id) --schema correct? INNER JOIN public.db USING (db_id) --schema correct? WHERE db.name='NCBITaxon'; -- gene_product -- note: secondary_species_id; eg for host species with parasite -- this will be handled by a feature_relationship in chado --view CREATE VIEW godb.gene_product AS SELECT feature_id AS id, name AS symbol, dbxref_id AS dbxref_id, organism_id AS species_id, CAST(NULL AS INT) AS secondary_species_id, type_id, -- todo: make this a left outer join on a featureprop name AS fullname FROM public.feature; -- gene_product_synonym --view CREATE VIEW godb.gene_product_synonym AS SELECT feature_id AS gene_product_id, synonym.name AS product_synonym FROM public.feature_synonym INNER JOIN public.synonym USING (synonym_id); -- gene_product_property --view CREATE VIEW godb.gene_product_property AS SELECT feature_id AS gene_product_id, prop.name AS property_key, value AS property_value FROM public.featureprop INNER JOIN public.cvterm AS prop ON (type_id=cvterm_id); -- association --view CREATE VIEW godb.association AS SELECT feature_cvterm_id AS id, cvterm_id AS term_id, feature_id AS gene_product_id, is_not AS is_not, -- not used in godb; maybe never will be 0 AS role_group, -- lets be lazy for now; these are actually feature_cvtermprops 0 AS assocdate, 0 AS source_db_id FROM public.feature_cvterm; -- association_qualifier --view CREATE VIEW godb.association_qualifier AS SELECT feature_cvtermprop_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop; -- evidence -- TODO!! --view CREATE VIEW godb.evidence AS SELECT feature_cvtermprop_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop INNER JOIN public.feature_cvterm_dbxref USING (feature_cvterm_id); -- evidence_dbxref -- TODO --view CREATE VIEW godb.evidence_dbxref AS SELECT feature_cvterm_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop INNER JOIN public.feature_cvterm_dbxref USING (feature_cvterm_id); -- seq --view CREATE VIEW godb.seq AS SELECT feature_id AS id, feature.name AS display_id, feature.name AS description, residues AS seq, seqlen AS seq_len, md5checksum, type.name AS moltype, -- this is never used 0 AS timestamp FROM public.feature INNER JOIN public.cvterm AS type ON (type_id=cvterm_id); -- seq_property [not used?] --view CREATE VIEW godb.seq_property AS SELECT * FROM public.feature WHERE NULL; -- seq_dbxref -- [in GO this typically has interpro ids, etc; diff semantics here] --view CREATE VIEW godb.seq_dbxref AS SELECT feature_id AS seq_id, dbxref_id FROM public.feature_dbxref; -- gene_product_seq -- 1:{0,1} relationship between features and seqs in chado --view CREATE VIEW godb.gene_product_seq AS SELECT feature_id AS gene_product_id, feature_id AS seq_id FROM public.feature WHERE feature.residues IS NOT NULL; -- gene_product_count -- this is an OPTIONAL godb optimization -- simulate a rowless table for now --view CREATE VIEW godb.gene_product_count AS SELECT * FROM public.feature WHERE NULL; -- ************************************************************ -- UPDATE RULES -- ************************************************************ -- NOT COMPLETE -- we don't really need these as loading is easy enough -- to do with xslts CREATE RULE "_RuleI_term_definition" AS ON INSERT TO godb.term_definition DO INSTEAD UPDATE public.cvterm SET definition = NEW.term_definition WHERE cvterm_id = NEW.term_id; CREATE RULE "_RuleU_term_definition" AS ON UPDATE TO godb.term_definition DO INSTEAD UPDATE public.cvterm SET definition = NEW.term_definition WHERE cvterm_id = OLD.term_id; CREATE RULE "_RuleD_term_definition" AS ON DELETE TO godb.term_definition DO INSTEAD UPDATE public.cvterm SET definition = NULL WHERE cvterm_id = OLD.term_id; CREATE RULE "_RuleI_term2term" AS ON INSERT TO godb.term2term DO INSTEAD INSERT INTO public.cvterm_relationship ( type_id, object_id, subject_id) VALUES ( NEW.relationship_type_id, NEW.term1_id, NEW.term2_id ); CREATE RULE "_RuleU_term2term" AS ON UPDATE TO godb.term2term DO INSTEAD UPDATE public.cvterm_relationship SET type_id = NEW.relationship_type_id, object_id = NEW.term1_id, subject_id = NEW.term2_id WHERE cvterm_relationship_id = OLD.id; CREATE RULE "_RuleD_term2term" AS ON DELETE TO godb.term2term DO INSTEAD DELETE FROM public.cvterm_relationship WHERE cvterm_relationship_id = OLD.id; CREATE RULE "_RuleI_graph_path" AS ON INSERT TO godb.graph_path DO INSTEAD INSERT INTO public.cvtermpath ( type_id, object_id, subject_id, pathdistance) VALUES ( NULL, NEW.term1_id, NEW.term2_id, NEW.distance ); CREATE RULE "_RuleU_graph_path" AS ON UPDATE TO godb.graph_path DO INSTEAD UPDATE public.cvtermpath SET type_id = NULL, object_id = NEW.term1_id, subject_id = NEW.term2_id, pathdistance = NEW.distance WHERE cvtermpath_id = OLD.id; CREATE RULE "_RuleD_graph_path" AS ON DELETE TO godb.graph_path DO INSTEAD DELETE FROM public.cvtermpath WHERE cvtermpath_id = OLD.id; CREATE RULE "_RuleI_term_synonym" AS ON INSERT TO godb.term_synonym DO INSTEAD INSERT INTO public.cvtermsynonym (cvterm_id, synonym) VALUES (NEW.term_id, NEW.term_synonym); CREATE RULE "_RuleU_term_synonym" AS ON UPDATE TO godb.term_synonym DO INSTEAD UPDATE public.cvtermsynonym SET cvterm_id = NEW.term_id, synonym = NEW.term_synonym WHERE cvterm_id = OLD.term_id AND synonym = OLD.term_synonym; CREATE RULE "_RuleD_term_synonym" AS ON DELETE TO godb.term_synonym DO INSTEAD DELETE FROM public.cvtermsynonym WHERE cvterm_id = OLD.term_id AND synonym = OLD.term_synonym; CREATE RULE "_RuleI_term_dbxref" AS ON INSERT TO godb.term_dbxref DO INSTEAD INSERT INTO public.cvterm_dbxref (cvterm_id, dbxref_id) VALUES (NEW.term_id, NEW.dbxref_id); CREATE RULE "_RuleU_term_dbxref" AS ON UPDATE TO godb.term_dbxref DO INSTEAD UPDATE public.cvterm_dbxref SET cvterm_id = NEW.term_id, dbxref_id = NEW.dbxref_id WHERE cvterm_id = OLD.term_id AND dbxref_id = OLD.dbxref_id; CREATE RULE "_RuleD_term_dbxref" AS ON DELETE TO godb.term_dbxref DO INSTEAD DELETE FROM public.cvterm_dbxref WHERE cvterm_id = OLD.term_id AND dbxref_id = OLD.dbxref_id; chado-1.23/modules/cv/bridges/godb-bridge.sql.xml000644 000765 000024 00000030362 11256710107 021762 0ustar00cainstaff000000 000000 Bridge layer for GO Database schema - allows chado to "masquerade" as a GO-DB Schema, which means we can use go-db software; eg AmiGO. Currently read-only Activate this to make this bridge take precedence SET SEARCH_PATH TO godb,public; (note that placing godb first in the search path means that godb.dbxref takes precedence over public.dbxref) SELECT '' AS release_name, '' AS release_type, '' AS release_notes; helper table - doesn't actually represent a godb table table name clash - be sure to prefix with schema name SELECT dbxref_id AS dbxref_id, db.name || ':' || dbxref.accession AS acc FROM public.dbxref INNER JOIN public.db USING (db_id); CREATE INDEX go_acc_idx1 ON godb.go_acc (dbxref_id); CREATE INDEX go_acc_idx2 ON godb.go_acc (acc); table name clash - be sure to prefix with schema name SELECT dbxref_id AS id, db.name AS xref_dbname, dbxref.accession AS xref_key, CAST(NULL AS VARCHAR) AS xref_keytype, dbxref.description AS xref_desc FROM public.dbxref INNER JOIN public.db USING (db_id); CREATE INDEX dbxref_idx1 ON godb.dbxref (id); CREATE INDEX dbxref_idx2 ON godb.dbxref (xref_dbname); CREATE INDEX dbxref_idx3 ON godb.dbxref (xref_key); CREATE INDEX dbxref_idx4 ON godb.dbxref (xref_keytype); CREATE INDEX dbxref_idx5 ON godb.dbxref (xref_desc); table name clash - be sure to prefix with schema name. (note in godb, db is only refered to from association table) This table is not used much by the go db code, no need to materialize SELECT db_id AS id, name AS name, name AS fullname, CAST(NULL AS VARCHAR) AS datatype, CAST(NULL AS VARCHAR) AS url_syntax FROM public.db; SELECT cvterm_id AS id, godb.go_acc.acc AS acc, name AS name, is_obsolete AS is_obsolete, 0 AS is_root FROM public.cvterm INNER JOIN godb.go_acc USING (dbxref_id); CREATE INDEX term_idx1 ON godb.term (id); CREATE INDEX term_idx2 ON godb.term (acc); CREATE INDEX term_idx3 ON godb.term (name); CREATE INDEX term_idx4 ON godb.term (is_obsolete); CREATE INDEX term_idx5 ON godb.term (is_root); UPDATE term SET is_root = 1 WHERE id IN (SELECT cvterm_id FROM cvterm WHERE NOT EXISTS ( SELECT subject_id FROM cvterm_relationship WHERE subject_id=cvterm_id) AND is_obsolete = 0 AND is_relationshiptype = 0); SELECT cvterm_id AS term_id, definition AS term_definition, CAST('' AS VARCHAR) AS term_comment FROM public.cvterm WHERE definition IS NOT NULL; SELECT cvterm_id AS term_id, dbxref_id AS dbxref_id, is_for_definition FROM public.cvterm_dbxref; SELECT cvterm_id AS term_id, synonym AS term_synonym, type_id AS synonym_type_id FROM public.cvtermsynonym; SELECT cvterm_relationship_id AS id, type_id AS relationship_type_id, object_id AS term1_id, subject_id AS term2_id FROM public.cvterm_relationship; CREATE INDEX term2term_idx1 ON godb.term2term (id); CREATE INDEX term2term_idx2 ON godb.term2term (relationship_type_id); CREATE INDEX term2term_idx3 ON godb.term2term (term1_id); CREATE INDEX term2term_idx4 ON godb.term2term (term2_id); SELECT cvtermpath_id AS id, object_id AS term1_id, subject_id AS term2_id, pathdistance AS distance FROM public.cvtermpath; CREATE INDEX graph_path_idx1 ON godb.graph_path (id); CREATE INDEX graph_path_idx2 ON godb.graph_path (term1_id); CREATE INDEX graph_path_idx3 ON godb.graph_path (term2_id); CREATE INDEX graph_path_idx4 ON godb.graph_path (distance); SELECT organism_id AS id, -- CAST(accession AS INT) AS ncbi_taxa_id, accession AS ncbi_taxa_id, common_name, CAST(NULL AS VARCHAR) AS lineage_string, genus, species FROM organism INNER JOIN public.organism_dbxref USING (organism_id) INNER JOIN public.dbxref USING (dbxref_id) INNER JOIN public.db USING (db_id) WHERE db.name='NCBITaxon'; -- note: secondary_species_id; eg for host species with parasite -- this will be handled by a feature_relationship in chado SELECT feature_id AS id, name AS symbol, dbxref_id AS dbxref_id, organism_id AS species_id, CAST(NULL AS INT) AS secondary_species_id, type_id, -- todo: make this a left outer join on a featureprop name AS fullname FROM public.feature; SELECT feature_id AS gene_product_id, synonym.name AS product_synonym FROM feature_synonym INNER JOIN public.synonym USING (synonym_id); SELECT feature_id AS gene_product_id, prop.name AS property_key, value AS property_value FROM featureprop INNER JOIN public.cvterm AS prop ON (type_id=cvterm_id); SELECT feature_cvterm_id AS id, cvterm_id AS term_id, feature_id AS gene_product_id, is_not, -- not used in godb; maybe never will be 0 AS role_group, -- lets be lazy for now; these are actually feature_cvtermprops 0 AS assocdate, 0 AS source_db_id FROM public.feature_cvterm; SELECT feature_cvtermprop_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop; TODO SELECT feature_cvtermprop_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop INNER JOIN public.feature_cvterm_dbxref USING (feature_cvterm_id); TODO SELECT feature_cvterm_id AS id, feature_cvterm_id AS association_id, type_id AS term_id, value AS value FROM public.feature_cvtermprop INNER JOIN public.feature_cvterm_dbxref USING (feature_cvterm_id); SELECT feature_id AS id, feature.name AS display_id, feature.name AS description, residues AS seq, seqlen AS seq_len, md5checksum, type.name AS moltype, -- this is never used 0 AS timestamp FROM public.feature INNER JOIN public.cvterm AS type ON (type_id=cvterm_id); SELECT * FROM public.feature WHERE NULL; -- [in GO this typically has interpro ids, etc; diff semantics here] SELECT feature_id AS seq_id, dbxref_id FROM public.feature_dbxref; -- 1:{0,1} relationship between features and seqs in chado SELECT feature_id AS gene_product_id, feature_id AS seq_id FROM public.feature WHERE feature.residues IS NOT NULL; -- this is an OPTIONAL godb optimization -- simulate a rowless table for now SELECT * FROM public.feature WHERE NULL; -- ************************************************************ -- UPDATE RULES -- ************************************************************ -- NOT COMPLETE -- we don't really need these as loading is easy enough -- to do with xslts CREATE RULE "_RuleI_term_definition" AS ON INSERT TO term_definition DO INSTEAD UPDATE cvterm SET definition = NEW.term_definition WHERE cvterm_id = NEW.term_id; CREATE RULE "_RuleU_term_definition" AS ON UPDATE TO term_definition DO INSTEAD UPDATE cvterm SET definition = NEW.term_definition WHERE cvterm_id = OLD.term_id; CREATE RULE "_RuleD_term_definition" AS ON DELETE TO term_definition DO INSTEAD UPDATE cvterm SET definition = NULL WHERE cvterm_id = OLD.term_id; CREATE RULE "_RuleI_term2term" AS ON INSERT TO term2term DO INSTEAD INSERT INTO cvterm_relationship ( type_id, object_id, subject_id) VALUES ( NEW.relationship_type_id, NEW.term1_id, NEW.term2_id ); CREATE RULE "_RuleU_term2term" AS ON UPDATE TO term2term DO INSTEAD UPDATE cvterm_relationship SET type_id = NEW.relationship_type_id, object_id = NEW.term1_id, subject_id = NEW.term2_id WHERE cvterm_relationship_id = OLD.id; CREATE RULE "_RuleD_term2term" AS ON DELETE TO term2term DO INSTEAD DELETE FROM cvterm_relationship WHERE cvterm_relationship_id = OLD.id; CREATE RULE "_RuleI_graph_path" AS ON INSERT TO graph_path DO INSTEAD INSERT INTO cvtermpath ( type_id, object_id, subject_id, pathdistance) VALUES ( NULL, NEW.term1_id, NEW.term2_id, NEW.distance ); CREATE RULE "_RuleU_graph_path" AS ON UPDATE TO graph_path DO INSTEAD UPDATE cvtermpath SET type_id = NULL, object_id = NEW.term1_id, subject_id = NEW.term2_id, pathdistance = NEW.distance WHERE cvtermpath_id = OLD.id; CREATE RULE "_RuleD_graph_path" AS ON DELETE TO graph_path DO INSTEAD DELETE FROM cvtermpath WHERE cvtermpath_id = OLD.id; CREATE RULE "_RuleI_term_synonym" AS ON INSERT TO term_synonym DO INSTEAD INSERT INTO cvtermsynonym (cvterm_id, synonym) VALUES (NEW.term_id, NEW.term_synonym); CREATE RULE "_RuleU_term_synonym" AS ON UPDATE TO term_synonym DO INSTEAD UPDATE cvtermsynonym SET cvterm_id = NEW.term_id, synonym = NEW.term_synonym WHERE cvterm_id = OLD.term_id AND synonym = OLD.term_synonym; CREATE RULE "_RuleD_term_synonym" AS ON DELETE TO term_synonym DO INSTEAD DELETE FROM cvtermsynonym WHERE cvterm_id = OLD.term_id AND synonym = OLD.term_synonym; CREATE RULE "_RuleI_term_dbxref" AS ON INSERT TO term_dbxref DO INSTEAD INSERT INTO cvterm_dbxref (cvterm_id, dbxref_id) VALUES (NEW.term_id, NEW.dbxref_id); CREATE RULE "_RuleU_term_dbxref" AS ON UPDATE TO term_dbxref DO INSTEAD UPDATE cvterm_dbxref SET cvterm_id = NEW.term_id, dbxref_id = NEW.dbxref_id WHERE cvterm_id = OLD.term_id AND dbxref_id = OLD.dbxref_id; CREATE RULE "_RuleD_term_dbxref" AS ON DELETE TO term_dbxref DO INSTEAD DELETE FROM cvterm_dbxref WHERE cvterm_id = OLD.term_id AND dbxref_id = OLD.dbxref_id; chado-1.23/modules/cv/bridges/bin/create-bridge-sql.pl000755 000765 000024 00000004266 11723234437 022711 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Data::Stag; my %relation_type_h = (); while (@ARGV && $ARGV[0] =~ /^(\-.+)/) { my $switch = shift @ARGV; if ($switch eq '-t' || $switch eq '--table') { while (@ARGV > 1 && $ARGV[0] !~ /^\-/) { $relation_type_h{shift @ARGV} = 'table'; } } elsif ($switch eq '-v' || $switch eq '--view') { while (@ARGV > 1 && $ARGV[0] !~ /^\-/) { $relation_type_h{shift @ARGV} = 'view'; } } elsif ($switch eq '-h' || $switch eq '--help') { print usage(); exit 0; } else { die "unknown option: $switch"; } } my $f = shift @ARGV; my $bridge = Data::Stag->parse($f); my $schema = $bridge->sget('@/schema'); print "CREATE SCHEMA $schema;\n\n"; foreach my $relation ($bridge->get_relation) { my $id = $relation->sget('@/id'); my @indexes = $relation->get_index; my $relation_type; # anything with indexes is by default a table if (@indexes) { $relation_type = "table"; } # command line override if ($relation_type_h{'ALL'}) { $relation_type = $relation_type_h{'ALL'}; } if ($relation_type_h{$id}) { $relation_type = $relation_type_h{$id}; } my $sql = $relation->sget_sql; $sql =~ s/^\s+//; $sql =~ s/\;\s*//; printf("CREATE %s %s.%s AS\n%s;\n", uc($relation_type), $schema, $id, $sql); print "$_\n" foreach @indexes; print "\n\n"; } exit 0; # -- sub usage { return < bridge.sql Options: -t --table : list of relations to be materialized -v --view : list of relations to be unmaterialized ALL can be used to specify a default Examples: create-bridge-sql.pl -v term term2term godb-bridge.sql.xml > godb-bridge.sql create-bridge-sql.pl -v ALL -t term godb-bridge.sql.xml > godb-bridge.sql TODO: Currently the autogenerated bridge can only be applied once. It would be nice (and easy) to have code to arbitrarily switch between tables and views at any points in the database lifecycle Also - finer grained control over indexes EOM ; } chado-1.23/modules/contact/contact.html000644 000765 000024 00000016577 11256710070 020235 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

contact
contact_relationship

contact

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Comments:

$Id: contact.html,v 1.2 2007-03-16 01:28:37 briano Exp $
================================================
TABLE: contact
================================================
Model persons, institutes, groups, organizations, etc.
Field Name Data Type Size Default Value Other Foreign Key
contact_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 NULL What type of contact is this? e.g. "person", "lab", etc. cvterm.cvterm_id
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL

Constraints

Type Fields
NOT NULL contact_id
FOREIGN KEY type_id
NOT NULL name
UNIQUE name

contact_relationship

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Comments:

================================================
TABLE: contact_relationship
================================================
Model relationships between contacts
Field Name Data Type Size Default Value Other Foreign Key
contact_relationship_id integer 11 PRIMARY KEY, NOT NULL
type_id integer 10 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 10 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node. contact.contact_id
object_id integer 10 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node. contact.contact_id

Indices

Name Fields
contact_relationship_idx1 type_id
contact_relationship_idx2 subject_id
contact_relationship_idx3 object_id

Constraints

Type Fields
NOT NULL contact_relationship_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
UNIQUE subject_id, object_id, type_id
Created by SQL::Translator 0.08 chado-1.23/modules/contact/contact.sql000644 000765 000024 00000004573 11256710070 020061 0ustar00cainstaff000000 000000 -- $Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $ -- ========================================== -- Chado contact module -- -- ================================================================= -- Dependencies: -- -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: contact -- ================================================ create table contact ( contact_id serial not null, primary key (contact_id), type_id int null, foreign key (type_id) references cvterm (cvterm_id), name varchar(255) not null, description varchar(255) null, constraint contact_c1 unique (name) ); COMMENT ON TABLE contact IS 'Model persons, institutes, groups, organizations, etc.'; COMMENT ON COLUMN contact.type_id IS 'What type of contact is this? E.g. "person", "lab".'; -- ================================================ -- TABLE: contact_relationship -- ================================================ create table contact_relationship ( contact_relationship_id serial not null, primary key (contact_relationship_id), type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, subject_id int not null, foreign key (subject_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED, constraint contact_relationship_c1 unique (subject_id,object_id,type_id) ); create index contact_relationship_idx1 on contact_relationship (type_id); create index contact_relationship_idx2 on contact_relationship (subject_id); create index contact_relationship_idx3 on contact_relationship (object_id); COMMENT ON TABLE contact_relationship IS 'Model relationships between contacts'; COMMENT ON COLUMN contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.'; COMMENT ON COLUMN contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.'; COMMENT ON COLUMN contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.'; chado-1.23/modules/contact/contactprop.sql000644 000765 000024 00000001351 11256710070 020751 0ustar00cainstaff000000 000000 -- ================================================ -- TABLE: contactprop -- ================================================ -- contactprop models person/lab properties, such as email, phone, etc. -- the cvterms come from FOAF project, see the spec at http://xmlns.com/foaf/spec/ create table contactprop ( contactprop_id serial not null, primary key (contactprop_id), contact_id int not null, foreign key (contact_id) references contact (contact_id) on delete cascade, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade, value text, unique (contact_id, type_id, value) ); create index contactprop_idx1 on contactprop (contactprop_id); create index contactprop_idx2 on contactprop (type_id); chado-1.23/modules/companalysis/companalysis.html000644 000765 000024 00000045603 11316304134 022340 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

analysis
analysisprop
analysisfeature
analysisfeatureprop

analysis

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Comments:

$Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado companalysis module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
=================================================================
================================================
TABLE: analysis
================================================
An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.
Field Name Data Type Size Default Value Other Foreign Key
analysis_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.
description text 64000
program varchar 255 UNIQUE, NOT NULL, Program name, e.g. blastx, blastp, sim4, genscan.
programversion varchar 255 UNIQUE, NOT NULL, Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].
algorithm varchar 255 Algorithm name, e.g. blast.
sourcename varchar 255 UNIQUE, Source name, e.g. cDNA, SwissProt.
sourceversion varchar 255
sourceuri text 64000 This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).
timeexecuted timestamp 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULL analysis_id
NOT NULL program
NOT NULL programversion
NOT NULL timeexecuted
UNIQUE program, programversion, sourcename

analysisprop

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Comments:

================================================
TABLE: analysisprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
analysisprop_id integer 11 PRIMARY KEY, NOT NULL
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
analysisprop_idx1 analysis_id
analysisprop_idx2 type_id

Constraints

Type Fields
NOT NULL analysisprop_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE analysis_id, type_id, rank

analysisfeature

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Comments:

================================================
TABLE: analysisfeature
================================================
Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject
Field Name Data Type Size Default Value Other Foreign Key
analysisfeature_id integer 11 PRIMARY KEY, NOT NULL
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
analysis_id integer 10 UNIQUE, NOT NULL analysis.analysis_id
rawscore float 20 This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.
normscore float 20 This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.
significance float 20 This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.
identity float 20 Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.

Indices

Name Fields
analysisfeature_idx1 feature_id
analysisfeature_idx2 analysis_id

Constraints

Type Fields
NOT NULL analysisfeature_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL analysis_id
FOREIGN KEY analysis_id
UNIQUE feature_id, analysis_id

analysisfeatureprop

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Field Name Data Type Size Default Value Other Foreign Key
analysisfeatureprop_id integer 11 PRIMARY KEY, NOT NULL
analysisfeature_id integer 10 UNIQUE, NOT NULL analysisfeature.analysisfeature_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL analysisfeature_id
FOREIGN KEY analysisfeature_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE analysisfeature_id, type_id, rank
FOREIGN KEY analysisfeature_id
FOREIGN KEY type_id
Created by SQL::Translator 0.11003 chado-1.23/modules/companalysis/companalysis.sql000644 000765 000024 00000014216 11310234502 022162 0ustar00cainstaff000000 000000 -- $Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $ -- ========================================== -- Chado companalysis module -- -- ================================================================= -- Dependencies: -- -- :import feature from sequence -- :import cvterm from cv -- ================================================================= -- ================================================ -- TABLE: analysis -- ================================================ create table analysis ( analysis_id serial not null, primary key (analysis_id), name varchar(255), description text, program varchar(255) not null, programversion varchar(255) not null, algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp not null default current_timestamp, constraint analysis_c1 unique (program,programversion,sourcename) ); COMMENT ON TABLE analysis IS 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.'; COMMENT ON COLUMN analysis.name IS 'A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.'; COMMENT ON COLUMN analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.'; COMMENT ON COLUMN analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'; COMMENT ON COLUMN analysis.algorithm IS 'Algorithm name, e.g. blast.'; COMMENT ON COLUMN analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.'; COMMENT ON COLUMN analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).'; -- ================================================ -- TABLE: analysisprop -- ================================================ create table analysisprop ( analysisprop_id serial not null, primary key (analysisprop_id), analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text, rank int not null default 0, constraint analysisprop_c1 unique (analysis_id,type_id,rank) ); create index analysisprop_idx1 on analysisprop (analysis_id); create index analysisprop_idx2 on analysisprop (type_id); -- ================================================ -- TABLE: analysisfeature -- ================================================ create table analysisfeature ( analysisfeature_id serial not null, primary key (analysisfeature_id), feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, analysis_id int not null, foreign key (analysis_id) references analysis (analysis_id) on delete cascade INITIALLY DEFERRED, rawscore double precision, normscore double precision, significance double precision, identity double precision, constraint analysisfeature_c1 unique (feature_id,analysis_id) ); create index analysisfeature_idx1 on analysisfeature (feature_id); create index analysisfeature_idx2 on analysisfeature (analysis_id); COMMENT ON TABLE analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject'; COMMENT ON COLUMN analysisfeature.identity IS 'Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.'; COMMENT ON COLUMN analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.'; COMMENT ON COLUMN analysisfeature.normscore IS 'This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.'; COMMENT ON COLUMN analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.'; CREATE TABLE analysisfeatureprop ( analysisfeatureprop_id SERIAL PRIMARY KEY, analysisfeature_id INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, type_id INTEGER NOT NULL REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, value TEXT, rank INTEGER NOT NULL, CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank) ); chado-1.23/modules/companalysis/functions/000755 000765 000024 00000000000 12061672376 020766 5ustar00cainstaff000000 000000 chado-1.23/modules/companalysis/functions/companalysis-loading.plpgsql000644 000765 000024 00000001465 11256710072 026504 0ustar00cainstaff000000 000000 CREATE OR REPLACE FUNCTION store_analysis (VARCHAR,VARCHAR,VARCHAR) RETURNS INT AS 'DECLARE v_program ALIAS FOR $1; v_programversion ALIAS FOR $2; v_sourcename ALIAS FOR $3; pkval INTEGER; BEGIN SELECT INTO pkval analysis_id FROM analysis WHERE program=v_program AND programversion=v_programversion AND sourcename=v_sourcename; IF NOT FOUND THEN INSERT INTO analysis (program,programversion,sourcename) VALUES (v_program,v_programversion,v_sourcename); RETURN currval(''analysis_analysis_id_seq''); END IF; RETURN pkval; END; ' LANGUAGE 'plpgsql'; --CREATE OR REPLACE FUNCTION store_analysisfeature --() --RETURNS INT AS --'DECLARE -- v_srcfeature_id ALIAS FOR $1; chado-1.23/modules/companalysis/functions/companalysis-loading.sqlapi000644 000765 000024 00000000422 11256710072 026303 0ustar00cainstaff000000 000000 DECLARE FUNCTION store_analysis (program VARCHAR, programversion VARCHAR, sourcename VARCHAR) RETURNS INT; COMMENT ON FUNCTION store_analysis(VARCHAR,VARCHAR,VARCHAR) IS 'Updates or inserts an analysis'; chado-1.23/modules/cell_line/cell_line.html000644 000765 000024 00000110356 11316304140 021003 0ustar00cainstaff000000 000000 Description of Schema

Description of Schema

Tables

cell_line
cell_line_relationship
cell_line_synonym
cell_line_cvterm
cell_line_dbxref
cell_lineprop
cell_lineprop_pub
cell_line_feature
cell_line_cvtermprop
cell_line_pub
cell_line_library

cell_line

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Comments:

==========================================
Chado cell line module
============
DEPENDENCIES
============
:import feature from sequence
:import synonym from sequence
:import library from library
:import cvterm from cv
:import dbxref from general
:import pub from pub
:import organism from organism
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: cell_line
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_id integer 11 PRIMARY KEY, NOT NULL
name varchar 255 NULL
uniquename varchar 255 UNIQUE, NOT NULL
organism_id integer 10 UNIQUE, NOT NULL organism.organism_id
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULL cell_line_id
NOT NULL uniquename
NOT NULL organism_id
FOREIGN KEY organism_id
NOT NULL timeaccessioned
NOT NULL timelastmodified
UNIQUE uniquename, organism_id

cell_line_relationship

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Comments:

================================================
TABLE: cell_line_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_relationship_id integer 11 PRIMARY KEY, NOT NULL
subject_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
object_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULL cell_line_relationship_id
NOT NULL subject_id
FOREIGN KEY subject_id
NOT NULL object_id
FOREIGN KEY object_id
NOT NULL type_id
FOREIGN KEY type_id
UNIQUE subject_id, object_id, type_id

cell_line_synonym

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Comments:

================================================
TABLE: cell_line_synonym
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_synonym_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
is_current boolean 0 false NOT NULL
is_internal boolean 0 false NOT NULL

Constraints

Type Fields
NOT NULL cell_line_synonym_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL synonym_id
FOREIGN KEY synonym_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL is_current
NOT NULL is_internal
UNIQUE synonym_id, cell_line_id, pub_id

cell_line_cvterm

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Comments:

================================================
TABLE: cell_line_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvterm_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_line_cvterm_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL cvterm_id
FOREIGN KEY cvterm_id
NOT NULL pub_id
FOREIGN KEY pub_id
NOT NULL rank
UNIQUE cell_line_id, cvterm_id, pub_id, rank

cell_line_dbxref

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Comments:

================================================
TABLE: cell_line_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_dbxref_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
dbxref_id integer 10 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Constraints

Type Fields
NOT NULL cell_line_dbxref_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL dbxref_id
FOREIGN KEY dbxref_id
NOT NULL is_current
UNIQUE cell_line_id, dbxref_id

cell_lineprop

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Comments:

================================================
TABLE: cell_lineprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_lineprop_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cell_line_id, type_id, rank

cell_lineprop_pub

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Comments:

================================================
TABLE: cell_lineprop_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_pub_id integer 11 PRIMARY KEY, NOT NULL
cell_lineprop_id integer 10 UNIQUE, NOT NULL cell_lineprop.cell_lineprop_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_lineprop_pub_id
NOT NULL cell_lineprop_id
FOREIGN KEY cell_lineprop_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_lineprop_id, pub_id

cell_line_feature

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Comments:

================================================
TABLE: cell_line_feature
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_feature_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_feature_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL feature_id
FOREIGN KEY feature_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, feature_id, pub_id

cell_line_cvtermprop

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Comments:

================================================
TABLE: cell_line_cvtermprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvtermprop_id integer 11 PRIMARY KEY, NOT NULL
cell_line_cvterm_id integer 10 UNIQUE, NOT NULL cell_line_cvterm.cell_line_cvterm_id
type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULL cell_line_cvtermprop_id
NOT NULL cell_line_cvterm_id
FOREIGN KEY cell_line_cvterm_id
NOT NULL type_id
FOREIGN KEY type_id
NOT NULL rank
UNIQUE cell_line_cvterm_id, type_id, rank

cell_line_pub

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Comments:

================================================
TABLE: cell_line_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_pub_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_pub_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, pub_id

cell_line_library

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Comments:

================================================
TABLE: cell_line_library
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_library_id integer 11 PRIMARY KEY, NOT NULL
cell_line_id integer 10 UNIQUE, NOT NULL cell_line.cell_line_id
library_id integer 10 UNIQUE, NOT NULL library.library_id
pub_id integer 10 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULL cell_line_library_id
NOT NULL cell_line_id
FOREIGN KEY cell_line_id
NOT NULL library_id
FOREIGN KEY library_id
NOT NULL pub_id
FOREIGN KEY pub_id
UNIQUE cell_line_id, library_id, pub_id
Created by SQL::Translator 0.11003 chado-1.23/modules/cell_line/cell_line.sql000644 000765 000024 00000017453 11256710057 020655 0ustar00cainstaff000000 000000 -- ========================================== -- Chado cell line module -- -- ============ -- DEPENDENCIES -- ============ -- :import feature from sequence -- :import synonym from sequence -- :import library from library -- :import cvterm from cv -- :import dbxref from general -- :import pub from pub -- :import organism from organism -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ================================================ -- TABLE: cell_line -- ================================================ create table cell_line ( cell_line_id serial not null, primary key (cell_line_id), name varchar(255) null, uniquename varchar(255) not null, organism_id int not null, foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED, timeaccessioned timestamp not null default current_timestamp, timelastmodified timestamp not null default current_timestamp, constraint cell_line_c1 unique (uniquename, organism_id) ); grant all on cell_line to PUBLIC; -- ================================================ -- TABLE: cell_line_relationship -- ================================================ create table cell_line_relationship ( cell_line_relationship_id serial not null, primary key (cell_line_relationship_id), subject_id int not null, foreign key (subject_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, object_id int not null, foreign key (object_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_relationship_c1 unique (subject_id, object_id, type_id) ); grant all on cell_line_relationship to PUBLIC; -- ================================================ -- TABLE: cell_line_synonym -- ================================================ create table cell_line_synonym ( cell_line_synonym_id serial not null, primary key (cell_line_synonym_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, synonym_id int not null, foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'false', is_internal boolean not null default 'false', constraint cell_line_synonym_c1 unique (synonym_id,cell_line_id,pub_id) ); grant all on cell_line_synonym to PUBLIC; -- ================================================ -- TABLE: cell_line_cvterm -- ================================================ create table cell_line_cvterm ( cell_line_cvterm_id serial not null, primary key (cell_line_cvterm_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, cvterm_id int not null, foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, rank int not null default 0, constraint cell_line_cvterm_c1 unique (cell_line_id,cvterm_id,pub_id,rank) ); grant all on cell_line_cvterm to PUBLIC; -- ================================================ -- TABLE: cell_line_dbxref -- ================================================ create table cell_line_dbxref ( cell_line_dbxref_id serial not null, primary key (cell_line_dbxref_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, dbxref_id int not null, foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED, is_current boolean not null default 'true', constraint cell_line_dbxref_c1 unique (cell_line_id,dbxref_id) ); grant all on cell_line_dbxref to PUBLIC; -- ================================================ -- TABLE: cell_lineprop -- ================================================ create table cell_lineprop ( cell_lineprop_id serial not null, primary key (cell_lineprop_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_lineprop_c1 unique (cell_line_id,type_id,rank) ); grant all on cell_lineprop to PUBLIC; -- ================================================ -- TABLE: cell_lineprop_pub -- ================================================ create table cell_lineprop_pub ( cell_lineprop_pub_id serial not null, primary key (cell_lineprop_pub_id), cell_lineprop_id int not null, foreign key (cell_lineprop_id) references cell_lineprop (cell_lineprop_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_lineprop_pub_c1 unique (cell_lineprop_id,pub_id) ); grant all on cell_lineprop_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_feature -- ================================================ create table cell_line_feature ( cell_line_feature_id serial not null, primary key (cell_line_feature_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, feature_id int not null, foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_feature_c1 unique (cell_line_id, feature_id, pub_id) ); grant all on cell_line_feature to PUBLIC; -- ================================================ -- TABLE: cell_line_cvtermprop -- ================================================ create table cell_line_cvtermprop ( cell_line_cvtermprop_id serial not null, primary key (cell_line_cvtermprop_id), cell_line_cvterm_id int not null, foreign key (cell_line_cvterm_id) references cell_line_cvterm (cell_line_cvterm_id) on delete cascade INITIALLY DEFERRED, type_id int not null, foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED, value text null, rank int not null default 0, constraint cell_line_cvtermprop_c1 unique (cell_line_cvterm_id, type_id, rank) ); grant all on cell_line_cvtermprop to PUBLIC; -- ================================================ -- TABLE: cell_line_pub -- ================================================ create table cell_line_pub ( cell_line_pub_id serial not null, primary key (cell_line_pub_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_pub_c1 unique (cell_line_id, pub_id) ); grant all on cell_line_pub to PUBLIC; -- ================================================ -- TABLE: cell_line_library -- ================================================ create table cell_line_library ( cell_line_library_id serial not null, primary key (cell_line_library_id), cell_line_id int not null, foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED, library_id int not null, foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED, pub_id int not null, foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED, constraint cell_line_library_c1 unique (cell_line_id, library_id, pub_id) ); grant all on cell_line_library to PUBLIC; chado-1.23/modules/bin/makedep.pl000644 000765 000024 00000010011 11723234377 016757 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # # (c) Hilmar Lapp, hlapp at gmx.net, 2007. # # You may use, modify, and distribute this script under the same terms # as Perl itself. Consult the Perl Artistic License. use strict; use warnings; use Getopt::Long; ################################################################# # global variables ################################################################# my $mod_names; my $help; ################################################################# # main ################################################################# my $ok = GetOptions("modules=s",\$mod_names, "h|help", \$help); if ($help) { usage(); exit(0); } my @modules = (); if ($mod_names) { @modules = split(/[, ]+/,$mod_names); } else { @modules = @ARGV; } die "No module(s) provided on the command line\n" unless @modules; my $module_name_map = {}; foreach my $mod_name (@modules) { my $module = get_dep_tree($mod_name,$module_name_map); $module_name_map->{$mod_name} = $module; } @modules = values(%$module_name_map); foreach my $module (@modules) { print_schema($module); } ################################################################# # functions ################################################################# sub get_dep_tree { my $mod_name = shift; my $module_name_map = shift || {}; my @deps = (); my @new_mods = (); my $modf; my $mod_file = get_module_sqlfile($mod_name); print STDERR "checking module $mod_name for dependencies ...\n"; open($modf, "<$mod_file") or die "cannot open $mod_file for reading: $!\n"; while (<$modf>) { if (/^--\s*:import\s+\S+\s+from\s+(\S+)/i) { my $dep = $1; chomp($dep); push(@deps, $dep); } } close($modf); my @dep_mods = (); foreach my $dep (@deps) { my $dep_mod = $module_name_map->{$dep}; if (!$dep_mod) { $dep_mod = get_dep_tree($dep, $module_name_map); $module_name_map->{$dep} = $dep_mod; } push(@dep_mods, $dep_mod); } return {'-name'=>$mod_name, '-deps'=>\@dep_mods}; } sub print_schema { my $module = shift; return 1 if $module->{-is_printed}; # need to print dependencies first that have not been printed yet foreach my $dep (@{$module->{-deps}}) { print_schema($dep) unless $dep->{-is_printed}; } my $mod_name = $module->{-name}; print STDERR "printing schema for module $mod_name ...\n"; print "-- ######################################################\n"; print "-- module $mod_name\n"; print "-- ######################################################\n"; my $modf; my $mod_file = get_module_sqlfile($mod_name); open $modf, "<$mod_file" or die "unable to open $mod_file for reading: $!\n"; while (<$modf>) { next if /^--/; print $_; } close($modf); $module->{-is_printed} = 1; return 1; } sub get_module_sqlfile { my $mod_name = shift; return $mod_name if (-e $mod_name) && (! -d $mod_name); return $mod_name."/".$mod_name.".sql"; } sub usage { print <<_USAGE; Usage: makedep.pl [ ...] > chado.ddl Example: makedep.pl --modules companalysis,contact,cv,expression,general,genetic,library,map,organism,phenotype,phylogeny,pub,sequence,www,stock > chado.ddl Options: -h|--help prints this message and exits --modules a string of comma or space-delimited module names Accepts a series of one or more Chado modules, either by name (such as cv) or as actual SQL file names (for example, when using custom written modules), and extracts from each one the dependencies (currently by using the :import comments) in a recursive manner. It then prints to stdout the schema DDL scripts of the desired modules and all their dependencies in the proper order, such that all dependencies have been created when a particular module is instantiated. The desired module(s) may be given using the --modules parameter, or simply by enumerating them on the command line. _USAGE } chado-1.23/modules/bin/mk.pl000755 000765 000024 00000000240 11723234407 015760 0ustar00cainstaff000000 000000 #!/usr/bin/env perl foreach $f (@ARGV) { open(F,$f) || die("no $f"); while() { next if /^\#/; print `cat $_`; } close(F); } chado-1.23/modules/audit/add-audits.tmpl000644 000765 000024 00000003776 11256710103 020276 0ustar00cainstaff000000 000000 --audit tables generated from -- % sqlt -f PostgreSQL -t TTSchema --template add-audits.tmpl nofuncs.sql>audit_tables.sql [% FOREACH table IN schema.get_tables %] DROP TABLE audit_[% table.name %]; CREATE TABLE audit_[% table.name %] ( [% FOREACH field IN table.get_fields %] [% field.name %] [% IF field.data_type == 'serial'; 'int'; ELSE; field.data_type; END %][% IF field.size AND (field.data_type == 'char' OR field.data_type == 'varchar') %]([% field.size.join(', ') %])[% END %], [% END %] transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_[% table.name %] to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_[% table.name %]() RETURNS trigger AS ' DECLARE [% FOREACH field IN table.get_fields %][% field.name %]_var [% IF field.data_type == 'serial'; 'int'; ELSE; field.data_type; END %][% IF field.size AND (field.data_type == 'char' OR field.data_type == 'varchar') %]([% field.size.join(', ') %])[% END %]; [% END %] transaction_type_var char; BEGIN [% FOREACH field IN table.get_fields %][% field.name %]_var = OLD.[% field.name %]; [% END %] IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_[% table.name %] ( [% FOREACH field IN table.get_fields %] [% field.name %], [% END %] transaction_type ) VALUES ( [% FOREACH field IN table.get_fields %] [% field.name %]_var, [% END %] transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER [% table.name %]_audit_ud ON [% table.name %]; CREATE TRIGGER [% table.name %]_audit_ud BEFORE UPDATE OR DELETE ON [% table.name %] FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_[% table.name %] (); [% END %] chado-1.23/modules/audit/audit_tables.sql000644 000765 000024 00001166667 11634146362 020566 0ustar00cainstaff000000 000000 --audit tables generated from -- % sqlt -f PostgreSQL -t TTSchema --template add-audits.tmpl nofuncs.sql>audit_tables.sql DROP TABLE audit_tableinfo; CREATE TABLE audit_tableinfo ( tableinfo_id integer, name varchar(30), primary_key_column varchar(30), is_view integer, view_on_table_id integer, superclass_table_id integer, is_updateable integer, modification_date date, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_tableinfo to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_tableinfo() RETURNS trigger AS ' DECLARE tableinfo_id_var integer; name_var varchar(30); primary_key_column_var varchar(30); is_view_var integer; view_on_table_id_var integer; superclass_table_id_var integer; is_updateable_var integer; modification_date_var date; transaction_type_var char; BEGIN tableinfo_id_var = OLD.tableinfo_id; name_var = OLD.name; primary_key_column_var = OLD.primary_key_column; is_view_var = OLD.is_view; view_on_table_id_var = OLD.view_on_table_id; superclass_table_id_var = OLD.superclass_table_id; is_updateable_var = OLD.is_updateable; modification_date_var = OLD.modification_date; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_tableinfo ( tableinfo_id, name, primary_key_column, is_view, view_on_table_id, superclass_table_id, is_updateable, modification_date, transaction_type ) VALUES ( tableinfo_id_var, name_var, primary_key_column_var, is_view_var, view_on_table_id_var, superclass_table_id_var, is_updateable_var, modification_date_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER tableinfo_audit_ud ON tableinfo; CREATE TRIGGER tableinfo_audit_ud BEFORE UPDATE OR DELETE ON tableinfo FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_tableinfo (); DROP TABLE audit_db; CREATE TABLE audit_db ( db_id integer, name varchar(255), description varchar(255), urlprefix varchar(255), url varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_db to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_db() RETURNS trigger AS ' DECLARE db_id_var integer; name_var varchar(255); description_var varchar(255); urlprefix_var varchar(255); url_var varchar(255); transaction_type_var char; BEGIN db_id_var = OLD.db_id; name_var = OLD.name; description_var = OLD.description; urlprefix_var = OLD.urlprefix; url_var = OLD.url; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_db ( db_id, name, description, urlprefix, url, transaction_type ) VALUES ( db_id_var, name_var, description_var, urlprefix_var, url_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER db_audit_ud ON db; CREATE TRIGGER db_audit_ud BEFORE UPDATE OR DELETE ON db FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_db (); DROP TABLE audit_dbxref; CREATE TABLE audit_dbxref ( dbxref_id integer, db_id integer, accession varchar(255), version varchar(255), description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_dbxref() RETURNS trigger AS ' DECLARE dbxref_id_var integer; db_id_var integer; accession_var varchar(255); version_var varchar(255); description_var text; transaction_type_var char; BEGIN dbxref_id_var = OLD.dbxref_id; db_id_var = OLD.db_id; accession_var = OLD.accession; version_var = OLD.version; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_dbxref ( dbxref_id, db_id, accession, version, description, transaction_type ) VALUES ( dbxref_id_var, db_id_var, accession_var, version_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER dbxref_audit_ud ON dbxref; CREATE TRIGGER dbxref_audit_ud BEFORE UPDATE OR DELETE ON dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_dbxref (); DROP TABLE audit_cv; CREATE TABLE audit_cv ( cv_id integer, name varchar(255), definition text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cv to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cv() RETURNS trigger AS ' DECLARE cv_id_var integer; name_var varchar(255); definition_var text; transaction_type_var char; BEGIN cv_id_var = OLD.cv_id; name_var = OLD.name; definition_var = OLD.definition; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cv ( cv_id, name, definition, transaction_type ) VALUES ( cv_id_var, name_var, definition_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cv_audit_ud ON cv; CREATE TRIGGER cv_audit_ud BEFORE UPDATE OR DELETE ON cv FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cv (); DROP TABLE audit_cvterm; CREATE TABLE audit_cvterm ( cvterm_id integer, cv_id integer, name varchar(1024), definition text, dbxref_id integer, is_obsolete integer, is_relationshiptype integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvterm() RETURNS trigger AS ' DECLARE cvterm_id_var integer; cv_id_var integer; name_var varchar(1024); definition_var text; dbxref_id_var integer; is_obsolete_var integer; is_relationshiptype_var integer; transaction_type_var char; BEGIN cvterm_id_var = OLD.cvterm_id; cv_id_var = OLD.cv_id; name_var = OLD.name; definition_var = OLD.definition; dbxref_id_var = OLD.dbxref_id; is_obsolete_var = OLD.is_obsolete; is_relationshiptype_var = OLD.is_relationshiptype; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvterm ( cvterm_id, cv_id, name, definition, dbxref_id, is_obsolete, is_relationshiptype, transaction_type ) VALUES ( cvterm_id_var, cv_id_var, name_var, definition_var, dbxref_id_var, is_obsolete_var, is_relationshiptype_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvterm_audit_ud ON cvterm; CREATE TRIGGER cvterm_audit_ud BEFORE UPDATE OR DELETE ON cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvterm (); DROP TABLE audit_cvterm_relationship; CREATE TABLE audit_cvterm_relationship ( cvterm_relationship_id integer, type_id integer, subject_id integer, object_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvterm_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvterm_relationship() RETURNS trigger AS ' DECLARE cvterm_relationship_id_var integer; type_id_var integer; subject_id_var integer; object_id_var integer; transaction_type_var char; BEGIN cvterm_relationship_id_var = OLD.cvterm_relationship_id; type_id_var = OLD.type_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvterm_relationship ( cvterm_relationship_id, type_id, subject_id, object_id, transaction_type ) VALUES ( cvterm_relationship_id_var, type_id_var, subject_id_var, object_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvterm_relationship_audit_ud ON cvterm_relationship; CREATE TRIGGER cvterm_relationship_audit_ud BEFORE UPDATE OR DELETE ON cvterm_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvterm_relationship (); DROP TABLE audit_cvtermpath; CREATE TABLE audit_cvtermpath ( cvtermpath_id integer, type_id integer, subject_id integer, object_id integer, cv_id integer, pathdistance integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvtermpath to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvtermpath() RETURNS trigger AS ' DECLARE cvtermpath_id_var integer; type_id_var integer; subject_id_var integer; object_id_var integer; cv_id_var integer; pathdistance_var integer; transaction_type_var char; BEGIN cvtermpath_id_var = OLD.cvtermpath_id; type_id_var = OLD.type_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; cv_id_var = OLD.cv_id; pathdistance_var = OLD.pathdistance; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvtermpath ( cvtermpath_id, type_id, subject_id, object_id, cv_id, pathdistance, transaction_type ) VALUES ( cvtermpath_id_var, type_id_var, subject_id_var, object_id_var, cv_id_var, pathdistance_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvtermpath_audit_ud ON cvtermpath; CREATE TRIGGER cvtermpath_audit_ud BEFORE UPDATE OR DELETE ON cvtermpath FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvtermpath (); DROP TABLE audit_cvtermsynonym; CREATE TABLE audit_cvtermsynonym ( cvtermsynonym_id integer, cvterm_id integer, synonym varchar(1024), type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvtermsynonym to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvtermsynonym() RETURNS trigger AS ' DECLARE cvtermsynonym_id_var integer; cvterm_id_var integer; synonym_var varchar(1024); type_id_var integer; transaction_type_var char; BEGIN cvtermsynonym_id_var = OLD.cvtermsynonym_id; cvterm_id_var = OLD.cvterm_id; synonym_var = OLD.synonym; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvtermsynonym ( cvtermsynonym_id, cvterm_id, synonym, type_id, transaction_type ) VALUES ( cvtermsynonym_id_var, cvterm_id_var, synonym_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvtermsynonym_audit_ud ON cvtermsynonym; CREATE TRIGGER cvtermsynonym_audit_ud BEFORE UPDATE OR DELETE ON cvtermsynonym FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvtermsynonym (); DROP TABLE audit_cvterm_dbxref; CREATE TABLE audit_cvterm_dbxref ( cvterm_dbxref_id integer, cvterm_id integer, dbxref_id integer, is_for_definition integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvterm_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvterm_dbxref() RETURNS trigger AS ' DECLARE cvterm_dbxref_id_var integer; cvterm_id_var integer; dbxref_id_var integer; is_for_definition_var integer; transaction_type_var char; BEGIN cvterm_dbxref_id_var = OLD.cvterm_dbxref_id; cvterm_id_var = OLD.cvterm_id; dbxref_id_var = OLD.dbxref_id; is_for_definition_var = OLD.is_for_definition; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvterm_dbxref ( cvterm_dbxref_id, cvterm_id, dbxref_id, is_for_definition, transaction_type ) VALUES ( cvterm_dbxref_id_var, cvterm_id_var, dbxref_id_var, is_for_definition_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvterm_dbxref_audit_ud ON cvterm_dbxref; CREATE TRIGGER cvterm_dbxref_audit_ud BEFORE UPDATE OR DELETE ON cvterm_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvterm_dbxref (); DROP TABLE audit_cvtermprop; CREATE TABLE audit_cvtermprop ( cvtermprop_id integer, cvterm_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvtermprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvtermprop() RETURNS trigger AS ' DECLARE cvtermprop_id_var integer; cvterm_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN cvtermprop_id_var = OLD.cvtermprop_id; cvterm_id_var = OLD.cvterm_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvtermprop ( cvtermprop_id, cvterm_id, type_id, value, rank, transaction_type ) VALUES ( cvtermprop_id_var, cvterm_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvtermprop_audit_ud ON cvtermprop; CREATE TRIGGER cvtermprop_audit_ud BEFORE UPDATE OR DELETE ON cvtermprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvtermprop (); DROP TABLE audit_dbxrefprop; CREATE TABLE audit_dbxrefprop ( dbxrefprop_id integer, dbxref_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_dbxrefprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_dbxrefprop() RETURNS trigger AS ' DECLARE dbxrefprop_id_var integer; dbxref_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN dbxrefprop_id_var = OLD.dbxrefprop_id; dbxref_id_var = OLD.dbxref_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_dbxrefprop ( dbxrefprop_id, dbxref_id, type_id, value, rank, transaction_type ) VALUES ( dbxrefprop_id_var, dbxref_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER dbxrefprop_audit_ud ON dbxrefprop; CREATE TRIGGER dbxrefprop_audit_ud BEFORE UPDATE OR DELETE ON dbxrefprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_dbxrefprop (); DROP TABLE audit_cvprop; CREATE TABLE audit_cvprop ( cvprop_id integer, cv_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cvprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cvprop() RETURNS trigger AS ' DECLARE cvprop_id_var integer; cv_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN cvprop_id_var = OLD.cvprop_id; cv_id_var = OLD.cv_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cvprop ( cvprop_id, cv_id, type_id, value, rank, transaction_type ) VALUES ( cvprop_id_var, cv_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cvprop_audit_ud ON cvprop; CREATE TRIGGER cvprop_audit_ud BEFORE UPDATE OR DELETE ON cvprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cvprop (); DROP TABLE audit_chadoprop; CREATE TABLE audit_chadoprop ( chadoprop_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_chadoprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_chadoprop() RETURNS trigger AS ' DECLARE chadoprop_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN chadoprop_id_var = OLD.chadoprop_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_chadoprop ( chadoprop_id, type_id, value, rank, transaction_type ) VALUES ( chadoprop_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER chadoprop_audit_ud ON chadoprop; CREATE TRIGGER chadoprop_audit_ud BEFORE UPDATE OR DELETE ON chadoprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_chadoprop (); DROP TABLE audit_pub; CREATE TABLE audit_pub ( pub_id integer, title text, volumetitle text, volume varchar(255), series_name varchar(255), issue varchar(255), pyear varchar(255), pages varchar(255), miniref varchar(255), uniquename text, type_id integer, is_obsolete boolean, publisher varchar(255), pubplace varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_pub() RETURNS trigger AS ' DECLARE pub_id_var integer; title_var text; volumetitle_var text; volume_var varchar(255); series_name_var varchar(255); issue_var varchar(255); pyear_var varchar(255); pages_var varchar(255); miniref_var varchar(255); uniquename_var text; type_id_var integer; is_obsolete_var boolean; publisher_var varchar(255); pubplace_var varchar(255); transaction_type_var char; BEGIN pub_id_var = OLD.pub_id; title_var = OLD.title; volumetitle_var = OLD.volumetitle; volume_var = OLD.volume; series_name_var = OLD.series_name; issue_var = OLD.issue; pyear_var = OLD.pyear; pages_var = OLD.pages; miniref_var = OLD.miniref; uniquename_var = OLD.uniquename; type_id_var = OLD.type_id; is_obsolete_var = OLD.is_obsolete; publisher_var = OLD.publisher; pubplace_var = OLD.pubplace; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_pub ( pub_id, title, volumetitle, volume, series_name, issue, pyear, pages, miniref, uniquename, type_id, is_obsolete, publisher, pubplace, transaction_type ) VALUES ( pub_id_var, title_var, volumetitle_var, volume_var, series_name_var, issue_var, pyear_var, pages_var, miniref_var, uniquename_var, type_id_var, is_obsolete_var, publisher_var, pubplace_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER pub_audit_ud ON pub; CREATE TRIGGER pub_audit_ud BEFORE UPDATE OR DELETE ON pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_pub (); DROP TABLE audit_pub_relationship; CREATE TABLE audit_pub_relationship ( pub_relationship_id integer, subject_id integer, object_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_pub_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_pub_relationship() RETURNS trigger AS ' DECLARE pub_relationship_id_var integer; subject_id_var integer; object_id_var integer; type_id_var integer; transaction_type_var char; BEGIN pub_relationship_id_var = OLD.pub_relationship_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_pub_relationship ( pub_relationship_id, subject_id, object_id, type_id, transaction_type ) VALUES ( pub_relationship_id_var, subject_id_var, object_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER pub_relationship_audit_ud ON pub_relationship; CREATE TRIGGER pub_relationship_audit_ud BEFORE UPDATE OR DELETE ON pub_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_pub_relationship (); DROP TABLE audit_pub_dbxref; CREATE TABLE audit_pub_dbxref ( pub_dbxref_id integer, pub_id integer, dbxref_id integer, is_current boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_pub_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_pub_dbxref() RETURNS trigger AS ' DECLARE pub_dbxref_id_var integer; pub_id_var integer; dbxref_id_var integer; is_current_var boolean; transaction_type_var char; BEGIN pub_dbxref_id_var = OLD.pub_dbxref_id; pub_id_var = OLD.pub_id; dbxref_id_var = OLD.dbxref_id; is_current_var = OLD.is_current; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_pub_dbxref ( pub_dbxref_id, pub_id, dbxref_id, is_current, transaction_type ) VALUES ( pub_dbxref_id_var, pub_id_var, dbxref_id_var, is_current_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER pub_dbxref_audit_ud ON pub_dbxref; CREATE TRIGGER pub_dbxref_audit_ud BEFORE UPDATE OR DELETE ON pub_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_pub_dbxref (); DROP TABLE audit_pubauthor; CREATE TABLE audit_pubauthor ( pubauthor_id integer, pub_id integer, rank integer, editor boolean, surname varchar(100), givennames varchar(100), suffix varchar(100), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_pubauthor to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_pubauthor() RETURNS trigger AS ' DECLARE pubauthor_id_var integer; pub_id_var integer; rank_var integer; editor_var boolean; surname_var varchar(100); givennames_var varchar(100); suffix_var varchar(100); transaction_type_var char; BEGIN pubauthor_id_var = OLD.pubauthor_id; pub_id_var = OLD.pub_id; rank_var = OLD.rank; editor_var = OLD.editor; surname_var = OLD.surname; givennames_var = OLD.givennames; suffix_var = OLD.suffix; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_pubauthor ( pubauthor_id, pub_id, rank, editor, surname, givennames, suffix, transaction_type ) VALUES ( pubauthor_id_var, pub_id_var, rank_var, editor_var, surname_var, givennames_var, suffix_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER pubauthor_audit_ud ON pubauthor; CREATE TRIGGER pubauthor_audit_ud BEFORE UPDATE OR DELETE ON pubauthor FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_pubauthor (); DROP TABLE audit_pubprop; CREATE TABLE audit_pubprop ( pubprop_id integer, pub_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_pubprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_pubprop() RETURNS trigger AS ' DECLARE pubprop_id_var integer; pub_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN pubprop_id_var = OLD.pubprop_id; pub_id_var = OLD.pub_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_pubprop ( pubprop_id, pub_id, type_id, value, rank, transaction_type ) VALUES ( pubprop_id_var, pub_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER pubprop_audit_ud ON pubprop; CREATE TRIGGER pubprop_audit_ud BEFORE UPDATE OR DELETE ON pubprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_pubprop (); DROP TABLE audit_organism; CREATE TABLE audit_organism ( organism_id integer, abbreviation varchar(255), genus varchar(255), species varchar(255), common_name varchar(255), comment text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_organism to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_organism() RETURNS trigger AS ' DECLARE organism_id_var integer; abbreviation_var varchar(255); genus_var varchar(255); species_var varchar(255); common_name_var varchar(255); comment_var text; transaction_type_var char; BEGIN organism_id_var = OLD.organism_id; abbreviation_var = OLD.abbreviation; genus_var = OLD.genus; species_var = OLD.species; common_name_var = OLD.common_name; comment_var = OLD.comment; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_organism ( organism_id, abbreviation, genus, species, common_name, comment, transaction_type ) VALUES ( organism_id_var, abbreviation_var, genus_var, species_var, common_name_var, comment_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER organism_audit_ud ON organism; CREATE TRIGGER organism_audit_ud BEFORE UPDATE OR DELETE ON organism FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_organism (); DROP TABLE audit_organism_dbxref; CREATE TABLE audit_organism_dbxref ( organism_dbxref_id integer, organism_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_organism_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_organism_dbxref() RETURNS trigger AS ' DECLARE organism_dbxref_id_var integer; organism_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN organism_dbxref_id_var = OLD.organism_dbxref_id; organism_id_var = OLD.organism_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_organism_dbxref ( organism_dbxref_id, organism_id, dbxref_id, transaction_type ) VALUES ( organism_dbxref_id_var, organism_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER organism_dbxref_audit_ud ON organism_dbxref; CREATE TRIGGER organism_dbxref_audit_ud BEFORE UPDATE OR DELETE ON organism_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_organism_dbxref (); DROP TABLE audit_organismprop; CREATE TABLE audit_organismprop ( organismprop_id integer, organism_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_organismprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_organismprop() RETURNS trigger AS ' DECLARE organismprop_id_var integer; organism_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN organismprop_id_var = OLD.organismprop_id; organism_id_var = OLD.organism_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_organismprop ( organismprop_id, organism_id, type_id, value, rank, transaction_type ) VALUES ( organismprop_id_var, organism_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER organismprop_audit_ud ON organismprop; CREATE TRIGGER organismprop_audit_ud BEFORE UPDATE OR DELETE ON organismprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_organismprop (); DROP TABLE audit_feature; CREATE TABLE audit_feature ( feature_id integer, dbxref_id integer, organism_id integer, name varchar(255), uniquename text, residues text, seqlen integer, md5checksum char(32), type_id integer, is_analysis boolean, is_obsolete boolean, timeaccessioned timestamp, timelastmodified timestamp, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature() RETURNS trigger AS ' DECLARE feature_id_var integer; dbxref_id_var integer; organism_id_var integer; name_var varchar(255); uniquename_var text; residues_var text; seqlen_var integer; md5checksum_var char(32); type_id_var integer; is_analysis_var boolean; is_obsolete_var boolean; timeaccessioned_var timestamp; timelastmodified_var timestamp; transaction_type_var char; BEGIN feature_id_var = OLD.feature_id; dbxref_id_var = OLD.dbxref_id; organism_id_var = OLD.organism_id; name_var = OLD.name; uniquename_var = OLD.uniquename; residues_var = OLD.residues; seqlen_var = OLD.seqlen; md5checksum_var = OLD.md5checksum; type_id_var = OLD.type_id; is_analysis_var = OLD.is_analysis; is_obsolete_var = OLD.is_obsolete; timeaccessioned_var = OLD.timeaccessioned; timelastmodified_var = OLD.timelastmodified; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature ( feature_id, dbxref_id, organism_id, name, uniquename, residues, seqlen, md5checksum, type_id, is_analysis, is_obsolete, timeaccessioned, timelastmodified, transaction_type ) VALUES ( feature_id_var, dbxref_id_var, organism_id_var, name_var, uniquename_var, residues_var, seqlen_var, md5checksum_var, type_id_var, is_analysis_var, is_obsolete_var, timeaccessioned_var, timelastmodified_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_audit_ud ON feature; CREATE TRIGGER feature_audit_ud BEFORE UPDATE OR DELETE ON feature FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature (); DROP TABLE audit_featureloc; CREATE TABLE audit_featureloc ( featureloc_id integer, feature_id integer, srcfeature_id integer, fmin integer, is_fmin_partial boolean, fmax integer, is_fmax_partial boolean, strand integer, phase integer, residue_info text, locgroup integer, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featureloc to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featureloc() RETURNS trigger AS ' DECLARE featureloc_id_var integer; feature_id_var integer; srcfeature_id_var integer; fmin_var integer; is_fmin_partial_var boolean; fmax_var integer; is_fmax_partial_var boolean; strand_var integer; phase_var integer; residue_info_var text; locgroup_var integer; rank_var integer; transaction_type_var char; BEGIN featureloc_id_var = OLD.featureloc_id; feature_id_var = OLD.feature_id; srcfeature_id_var = OLD.srcfeature_id; fmin_var = OLD.fmin; is_fmin_partial_var = OLD.is_fmin_partial; fmax_var = OLD.fmax; is_fmax_partial_var = OLD.is_fmax_partial; strand_var = OLD.strand; phase_var = OLD.phase; residue_info_var = OLD.residue_info; locgroup_var = OLD.locgroup; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featureloc ( featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank, transaction_type ) VALUES ( featureloc_id_var, feature_id_var, srcfeature_id_var, fmin_var, is_fmin_partial_var, fmax_var, is_fmax_partial_var, strand_var, phase_var, residue_info_var, locgroup_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featureloc_audit_ud ON featureloc; CREATE TRIGGER featureloc_audit_ud BEFORE UPDATE OR DELETE ON featureloc FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featureloc (); DROP TABLE audit_featureloc_pub; CREATE TABLE audit_featureloc_pub ( featureloc_pub_id integer, featureloc_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featureloc_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featureloc_pub() RETURNS trigger AS ' DECLARE featureloc_pub_id_var integer; featureloc_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN featureloc_pub_id_var = OLD.featureloc_pub_id; featureloc_id_var = OLD.featureloc_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featureloc_pub ( featureloc_pub_id, featureloc_id, pub_id, transaction_type ) VALUES ( featureloc_pub_id_var, featureloc_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featureloc_pub_audit_ud ON featureloc_pub; CREATE TRIGGER featureloc_pub_audit_ud BEFORE UPDATE OR DELETE ON featureloc_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featureloc_pub (); DROP TABLE audit_feature_pub; CREATE TABLE audit_feature_pub ( feature_pub_id integer, feature_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_pub() RETURNS trigger AS ' DECLARE feature_pub_id_var integer; feature_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN feature_pub_id_var = OLD.feature_pub_id; feature_id_var = OLD.feature_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_pub ( feature_pub_id, feature_id, pub_id, transaction_type ) VALUES ( feature_pub_id_var, feature_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_pub_audit_ud ON feature_pub; CREATE TRIGGER feature_pub_audit_ud BEFORE UPDATE OR DELETE ON feature_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_pub (); DROP TABLE audit_feature_pubprop; CREATE TABLE audit_feature_pubprop ( feature_pubprop_id integer, feature_pub_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_pubprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_pubprop() RETURNS trigger AS ' DECLARE feature_pubprop_id_var integer; feature_pub_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN feature_pubprop_id_var = OLD.feature_pubprop_id; feature_pub_id_var = OLD.feature_pub_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_pubprop ( feature_pubprop_id, feature_pub_id, type_id, value, rank, transaction_type ) VALUES ( feature_pubprop_id_var, feature_pub_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_pubprop_audit_ud ON feature_pubprop; CREATE TRIGGER feature_pubprop_audit_ud BEFORE UPDATE OR DELETE ON feature_pubprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_pubprop (); DROP TABLE audit_featureprop; CREATE TABLE audit_featureprop ( featureprop_id integer, feature_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featureprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featureprop() RETURNS trigger AS ' DECLARE featureprop_id_var integer; feature_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN featureprop_id_var = OLD.featureprop_id; feature_id_var = OLD.feature_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featureprop ( featureprop_id, feature_id, type_id, value, rank, transaction_type ) VALUES ( featureprop_id_var, feature_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featureprop_audit_ud ON featureprop; CREATE TRIGGER featureprop_audit_ud BEFORE UPDATE OR DELETE ON featureprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featureprop (); DROP TABLE audit_featureprop_pub; CREATE TABLE audit_featureprop_pub ( featureprop_pub_id integer, featureprop_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featureprop_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featureprop_pub() RETURNS trigger AS ' DECLARE featureprop_pub_id_var integer; featureprop_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN featureprop_pub_id_var = OLD.featureprop_pub_id; featureprop_id_var = OLD.featureprop_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featureprop_pub ( featureprop_pub_id, featureprop_id, pub_id, transaction_type ) VALUES ( featureprop_pub_id_var, featureprop_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featureprop_pub_audit_ud ON featureprop_pub; CREATE TRIGGER featureprop_pub_audit_ud BEFORE UPDATE OR DELETE ON featureprop_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featureprop_pub (); DROP TABLE audit_feature_dbxref; CREATE TABLE audit_feature_dbxref ( feature_dbxref_id integer, feature_id integer, dbxref_id integer, is_current boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_dbxref() RETURNS trigger AS ' DECLARE feature_dbxref_id_var integer; feature_id_var integer; dbxref_id_var integer; is_current_var boolean; transaction_type_var char; BEGIN feature_dbxref_id_var = OLD.feature_dbxref_id; feature_id_var = OLD.feature_id; dbxref_id_var = OLD.dbxref_id; is_current_var = OLD.is_current; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_dbxref ( feature_dbxref_id, feature_id, dbxref_id, is_current, transaction_type ) VALUES ( feature_dbxref_id_var, feature_id_var, dbxref_id_var, is_current_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_dbxref_audit_ud ON feature_dbxref; CREATE TRIGGER feature_dbxref_audit_ud BEFORE UPDATE OR DELETE ON feature_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_dbxref (); DROP TABLE audit_feature_relationship; CREATE TABLE audit_feature_relationship ( feature_relationship_id integer, subject_id integer, object_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_relationship() RETURNS trigger AS ' DECLARE feature_relationship_id_var integer; subject_id_var integer; object_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN feature_relationship_id_var = OLD.feature_relationship_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_relationship ( feature_relationship_id, subject_id, object_id, type_id, value, rank, transaction_type ) VALUES ( feature_relationship_id_var, subject_id_var, object_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_relationship_audit_ud ON feature_relationship; CREATE TRIGGER feature_relationship_audit_ud BEFORE UPDATE OR DELETE ON feature_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_relationship (); DROP TABLE audit_feature_relationship_pub; CREATE TABLE audit_feature_relationship_pub ( feature_relationship_pub_id integer, feature_relationship_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_relationship_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_relationship_pub() RETURNS trigger AS ' DECLARE feature_relationship_pub_id_var integer; feature_relationship_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN feature_relationship_pub_id_var = OLD.feature_relationship_pub_id; feature_relationship_id_var = OLD.feature_relationship_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_relationship_pub ( feature_relationship_pub_id, feature_relationship_id, pub_id, transaction_type ) VALUES ( feature_relationship_pub_id_var, feature_relationship_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_relationship_pub_audit_ud ON feature_relationship_pub; CREATE TRIGGER feature_relationship_pub_audit_ud BEFORE UPDATE OR DELETE ON feature_relationship_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_relationship_pub (); DROP TABLE audit_feature_relationshipprop; CREATE TABLE audit_feature_relationshipprop ( feature_relationshipprop_id integer, feature_relationship_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_relationshipprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_relationshipprop() RETURNS trigger AS ' DECLARE feature_relationshipprop_id_var integer; feature_relationship_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN feature_relationshipprop_id_var = OLD.feature_relationshipprop_id; feature_relationship_id_var = OLD.feature_relationship_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_relationshipprop ( feature_relationshipprop_id, feature_relationship_id, type_id, value, rank, transaction_type ) VALUES ( feature_relationshipprop_id_var, feature_relationship_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_relationshipprop_audit_ud ON feature_relationshipprop; CREATE TRIGGER feature_relationshipprop_audit_ud BEFORE UPDATE OR DELETE ON feature_relationshipprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_relationshipprop (); DROP TABLE audit_feature_relationshipprop_pub; CREATE TABLE audit_feature_relationshipprop_pub ( feature_relationshipprop_pub_id integer, feature_relationshipprop_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_relationshipprop_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_relationshipprop_pub() RETURNS trigger AS ' DECLARE feature_relationshipprop_pub_id_var integer; feature_relationshipprop_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN feature_relationshipprop_pub_id_var = OLD.feature_relationshipprop_pub_id; feature_relationshipprop_id_var = OLD.feature_relationshipprop_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_relationshipprop_pub ( feature_relationshipprop_pub_id, feature_relationshipprop_id, pub_id, transaction_type ) VALUES ( feature_relationshipprop_pub_id_var, feature_relationshipprop_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_relationshipprop_pub_audit_ud ON feature_relationshipprop_pub; CREATE TRIGGER feature_relationshipprop_pub_audit_ud BEFORE UPDATE OR DELETE ON feature_relationshipprop_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_relationshipprop_pub (); DROP TABLE audit_feature_cvterm; CREATE TABLE audit_feature_cvterm ( feature_cvterm_id integer, feature_id integer, cvterm_id integer, pub_id integer, is_not boolean, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_cvterm() RETURNS trigger AS ' DECLARE feature_cvterm_id_var integer; feature_id_var integer; cvterm_id_var integer; pub_id_var integer; is_not_var boolean; rank_var integer; transaction_type_var char; BEGIN feature_cvterm_id_var = OLD.feature_cvterm_id; feature_id_var = OLD.feature_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; is_not_var = OLD.is_not; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_cvterm ( feature_cvterm_id, feature_id, cvterm_id, pub_id, is_not, rank, transaction_type ) VALUES ( feature_cvterm_id_var, feature_id_var, cvterm_id_var, pub_id_var, is_not_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_cvterm_audit_ud ON feature_cvterm; CREATE TRIGGER feature_cvterm_audit_ud BEFORE UPDATE OR DELETE ON feature_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_cvterm (); DROP TABLE audit_feature_cvtermprop; CREATE TABLE audit_feature_cvtermprop ( feature_cvtermprop_id integer, feature_cvterm_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_cvtermprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_cvtermprop() RETURNS trigger AS ' DECLARE feature_cvtermprop_id_var integer; feature_cvterm_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN feature_cvtermprop_id_var = OLD.feature_cvtermprop_id; feature_cvterm_id_var = OLD.feature_cvterm_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_cvtermprop ( feature_cvtermprop_id, feature_cvterm_id, type_id, value, rank, transaction_type ) VALUES ( feature_cvtermprop_id_var, feature_cvterm_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_cvtermprop_audit_ud ON feature_cvtermprop; CREATE TRIGGER feature_cvtermprop_audit_ud BEFORE UPDATE OR DELETE ON feature_cvtermprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_cvtermprop (); DROP TABLE audit_feature_cvterm_dbxref; CREATE TABLE audit_feature_cvterm_dbxref ( feature_cvterm_dbxref_id integer, feature_cvterm_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_cvterm_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_cvterm_dbxref() RETURNS trigger AS ' DECLARE feature_cvterm_dbxref_id_var integer; feature_cvterm_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN feature_cvterm_dbxref_id_var = OLD.feature_cvterm_dbxref_id; feature_cvterm_id_var = OLD.feature_cvterm_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_cvterm_dbxref ( feature_cvterm_dbxref_id, feature_cvterm_id, dbxref_id, transaction_type ) VALUES ( feature_cvterm_dbxref_id_var, feature_cvterm_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_cvterm_dbxref_audit_ud ON feature_cvterm_dbxref; CREATE TRIGGER feature_cvterm_dbxref_audit_ud BEFORE UPDATE OR DELETE ON feature_cvterm_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_cvterm_dbxref (); DROP TABLE audit_feature_cvterm_pub; CREATE TABLE audit_feature_cvterm_pub ( feature_cvterm_pub_id integer, feature_cvterm_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_cvterm_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_cvterm_pub() RETURNS trigger AS ' DECLARE feature_cvterm_pub_id_var integer; feature_cvterm_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN feature_cvterm_pub_id_var = OLD.feature_cvterm_pub_id; feature_cvterm_id_var = OLD.feature_cvterm_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_cvterm_pub ( feature_cvterm_pub_id, feature_cvterm_id, pub_id, transaction_type ) VALUES ( feature_cvterm_pub_id_var, feature_cvterm_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_cvterm_pub_audit_ud ON feature_cvterm_pub; CREATE TRIGGER feature_cvterm_pub_audit_ud BEFORE UPDATE OR DELETE ON feature_cvterm_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_cvterm_pub (); DROP TABLE audit_synonym; CREATE TABLE audit_synonym ( synonym_id integer, name varchar(255), type_id integer, synonym_sgml varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_synonym to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_synonym() RETURNS trigger AS ' DECLARE synonym_id_var integer; name_var varchar(255); type_id_var integer; synonym_sgml_var varchar(255); transaction_type_var char; BEGIN synonym_id_var = OLD.synonym_id; name_var = OLD.name; type_id_var = OLD.type_id; synonym_sgml_var = OLD.synonym_sgml; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_synonym ( synonym_id, name, type_id, synonym_sgml, transaction_type ) VALUES ( synonym_id_var, name_var, type_id_var, synonym_sgml_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER synonym_audit_ud ON synonym; CREATE TRIGGER synonym_audit_ud BEFORE UPDATE OR DELETE ON synonym FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_synonym (); DROP TABLE audit_feature_synonym; CREATE TABLE audit_feature_synonym ( feature_synonym_id integer, synonym_id integer, feature_id integer, pub_id integer, is_current boolean, is_internal boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_synonym to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_synonym() RETURNS trigger AS ' DECLARE feature_synonym_id_var integer; synonym_id_var integer; feature_id_var integer; pub_id_var integer; is_current_var boolean; is_internal_var boolean; transaction_type_var char; BEGIN feature_synonym_id_var = OLD.feature_synonym_id; synonym_id_var = OLD.synonym_id; feature_id_var = OLD.feature_id; pub_id_var = OLD.pub_id; is_current_var = OLD.is_current; is_internal_var = OLD.is_internal; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_synonym ( feature_synonym_id, synonym_id, feature_id, pub_id, is_current, is_internal, transaction_type ) VALUES ( feature_synonym_id_var, synonym_id_var, feature_id_var, pub_id_var, is_current_var, is_internal_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_synonym_audit_ud ON feature_synonym; CREATE TRIGGER feature_synonym_audit_ud BEFORE UPDATE OR DELETE ON feature_synonym FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_synonym (); DROP TABLE audit_gencode; CREATE TABLE audit_gencode ( gencode_id integer, organismstr VARCHAR, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_gencode to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_gencode() RETURNS trigger AS ' DECLARE gencode_id_var integer; organismstr_var VARCHAR; transaction_type_var char; BEGIN gencode_id_var = OLD.gencode_id; organismstr_var = OLD.organismstr; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_gencode ( gencode_id, organismstr, transaction_type ) VALUES ( gencode_id_var, organismstr_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER gencode_audit_ud ON gencode; CREATE TRIGGER gencode_audit_ud BEFORE UPDATE OR DELETE ON gencode FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_gencode (); DROP TABLE audit_gencode_codon_aa; CREATE TABLE audit_gencode_codon_aa ( gencode_id integer, codon char(3), aa char(1), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_gencode_codon_aa to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_gencode_codon_aa() RETURNS trigger AS ' DECLARE gencode_id_var integer; codon_var char(3); aa_var char(1); transaction_type_var char; BEGIN gencode_id_var = OLD.gencode_id; codon_var = OLD.codon; aa_var = OLD.aa; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_gencode_codon_aa ( gencode_id, codon, aa, transaction_type ) VALUES ( gencode_id_var, codon_var, aa_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER gencode_codon_aa_audit_ud ON gencode_codon_aa; CREATE TRIGGER gencode_codon_aa_audit_ud BEFORE UPDATE OR DELETE ON gencode_codon_aa FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_gencode_codon_aa (); DROP TABLE audit_gencode_startcodon; CREATE TABLE audit_gencode_startcodon ( gencode_id integer, codon char(3), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_gencode_startcodon to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_gencode_startcodon() RETURNS trigger AS ' DECLARE gencode_id_var integer; codon_var char(3); transaction_type_var char; BEGIN gencode_id_var = OLD.gencode_id; codon_var = OLD.codon; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_gencode_startcodon ( gencode_id, codon, transaction_type ) VALUES ( gencode_id_var, codon_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER gencode_startcodon_audit_ud ON gencode_startcodon; CREATE TRIGGER gencode_startcodon_audit_ud BEFORE UPDATE OR DELETE ON gencode_startcodon FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_gencode_startcodon (); DROP TABLE audit_analysis; CREATE TABLE audit_analysis ( analysis_id integer, name varchar(255), description text, program varchar(255), programversion varchar(255), algorithm varchar(255), sourcename varchar(255), sourceversion varchar(255), sourceuri text, timeexecuted timestamp, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_analysis to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_analysis() RETURNS trigger AS ' DECLARE analysis_id_var integer; name_var varchar(255); description_var text; program_var varchar(255); programversion_var varchar(255); algorithm_var varchar(255); sourcename_var varchar(255); sourceversion_var varchar(255); sourceuri_var text; timeexecuted_var timestamp; transaction_type_var char; BEGIN analysis_id_var = OLD.analysis_id; name_var = OLD.name; description_var = OLD.description; program_var = OLD.program; programversion_var = OLD.programversion; algorithm_var = OLD.algorithm; sourcename_var = OLD.sourcename; sourceversion_var = OLD.sourceversion; sourceuri_var = OLD.sourceuri; timeexecuted_var = OLD.timeexecuted; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_analysis ( analysis_id, name, description, program, programversion, algorithm, sourcename, sourceversion, sourceuri, timeexecuted, transaction_type ) VALUES ( analysis_id_var, name_var, description_var, program_var, programversion_var, algorithm_var, sourcename_var, sourceversion_var, sourceuri_var, timeexecuted_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER analysis_audit_ud ON analysis; CREATE TRIGGER analysis_audit_ud BEFORE UPDATE OR DELETE ON analysis FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_analysis (); DROP TABLE audit_analysisprop; CREATE TABLE audit_analysisprop ( analysisprop_id integer, analysis_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_analysisprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_analysisprop() RETURNS trigger AS ' DECLARE analysisprop_id_var integer; analysis_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN analysisprop_id_var = OLD.analysisprop_id; analysis_id_var = OLD.analysis_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_analysisprop ( analysisprop_id, analysis_id, type_id, value, rank, transaction_type ) VALUES ( analysisprop_id_var, analysis_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER analysisprop_audit_ud ON analysisprop; CREATE TRIGGER analysisprop_audit_ud BEFORE UPDATE OR DELETE ON analysisprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_analysisprop (); DROP TABLE audit_analysisfeature; CREATE TABLE audit_analysisfeature ( analysisfeature_id integer, feature_id integer, analysis_id integer, rawscore float, normscore float, significance float, identity float, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_analysisfeature to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_analysisfeature() RETURNS trigger AS ' DECLARE analysisfeature_id_var integer; feature_id_var integer; analysis_id_var integer; rawscore_var float; normscore_var float; significance_var float; identity_var float; transaction_type_var char; BEGIN analysisfeature_id_var = OLD.analysisfeature_id; feature_id_var = OLD.feature_id; analysis_id_var = OLD.analysis_id; rawscore_var = OLD.rawscore; normscore_var = OLD.normscore; significance_var = OLD.significance; identity_var = OLD.identity; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_analysisfeature ( analysisfeature_id, feature_id, analysis_id, rawscore, normscore, significance, identity, transaction_type ) VALUES ( analysisfeature_id_var, feature_id_var, analysis_id_var, rawscore_var, normscore_var, significance_var, identity_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER analysisfeature_audit_ud ON analysisfeature; CREATE TRIGGER analysisfeature_audit_ud BEFORE UPDATE OR DELETE ON analysisfeature FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_analysisfeature (); DROP TABLE audit_analysisfeatureprop; CREATE TABLE audit_analysisfeatureprop ( analysisfeatureprop_id integer, analysisfeature_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_analysisfeatureprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_analysisfeatureprop() RETURNS trigger AS ' DECLARE analysisfeatureprop_id_var integer; analysisfeature_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN analysisfeatureprop_id_var = OLD.analysisfeatureprop_id; analysisfeature_id_var = OLD.analysisfeature_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_analysisfeatureprop ( analysisfeatureprop_id, analysisfeature_id, type_id, value, rank, transaction_type ) VALUES ( analysisfeatureprop_id_var, analysisfeature_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER analysisfeatureprop_audit_ud ON analysisfeatureprop; CREATE TRIGGER analysisfeatureprop_audit_ud BEFORE UPDATE OR DELETE ON analysisfeatureprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_analysisfeatureprop (); DROP TABLE audit_phenotype; CREATE TABLE audit_phenotype ( phenotype_id integer, uniquename text, name text, observable_id integer, attr_id integer, value text, cvalue_id integer, assay_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phenotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phenotype() RETURNS trigger AS ' DECLARE phenotype_id_var integer; uniquename_var text; name_var text; observable_id_var integer; attr_id_var integer; value_var text; cvalue_id_var integer; assay_id_var integer; transaction_type_var char; BEGIN phenotype_id_var = OLD.phenotype_id; uniquename_var = OLD.uniquename; name_var = OLD.name; observable_id_var = OLD.observable_id; attr_id_var = OLD.attr_id; value_var = OLD.value; cvalue_id_var = OLD.cvalue_id; assay_id_var = OLD.assay_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phenotype ( phenotype_id, uniquename, name, observable_id, attr_id, value, cvalue_id, assay_id, transaction_type ) VALUES ( phenotype_id_var, uniquename_var, name_var, observable_id_var, attr_id_var, value_var, cvalue_id_var, assay_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phenotype_audit_ud ON phenotype; CREATE TRIGGER phenotype_audit_ud BEFORE UPDATE OR DELETE ON phenotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phenotype (); DROP TABLE audit_phenotype_cvterm; CREATE TABLE audit_phenotype_cvterm ( phenotype_cvterm_id integer, phenotype_id integer, cvterm_id integer, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phenotype_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phenotype_cvterm() RETURNS trigger AS ' DECLARE phenotype_cvterm_id_var integer; phenotype_id_var integer; cvterm_id_var integer; rank_var integer; transaction_type_var char; BEGIN phenotype_cvterm_id_var = OLD.phenotype_cvterm_id; phenotype_id_var = OLD.phenotype_id; cvterm_id_var = OLD.cvterm_id; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phenotype_cvterm ( phenotype_cvterm_id, phenotype_id, cvterm_id, rank, transaction_type ) VALUES ( phenotype_cvterm_id_var, phenotype_id_var, cvterm_id_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phenotype_cvterm_audit_ud ON phenotype_cvterm; CREATE TRIGGER phenotype_cvterm_audit_ud BEFORE UPDATE OR DELETE ON phenotype_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phenotype_cvterm (); DROP TABLE audit_feature_phenotype; CREATE TABLE audit_feature_phenotype ( feature_phenotype_id integer, feature_id integer, phenotype_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_phenotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_phenotype() RETURNS trigger AS ' DECLARE feature_phenotype_id_var integer; feature_id_var integer; phenotype_id_var integer; transaction_type_var char; BEGIN feature_phenotype_id_var = OLD.feature_phenotype_id; feature_id_var = OLD.feature_id; phenotype_id_var = OLD.phenotype_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_phenotype ( feature_phenotype_id, feature_id, phenotype_id, transaction_type ) VALUES ( feature_phenotype_id_var, feature_id_var, phenotype_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_phenotype_audit_ud ON feature_phenotype; CREATE TRIGGER feature_phenotype_audit_ud BEFORE UPDATE OR DELETE ON feature_phenotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_phenotype (); DROP TABLE audit_genotype; CREATE TABLE audit_genotype ( genotype_id integer, name text, uniquename text, description varchar(255), type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_genotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_genotype() RETURNS trigger AS ' DECLARE genotype_id_var integer; name_var text; uniquename_var text; description_var varchar(255); type_id_var integer; transaction_type_var char; BEGIN genotype_id_var = OLD.genotype_id; name_var = OLD.name; uniquename_var = OLD.uniquename; description_var = OLD.description; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_genotype ( genotype_id, name, uniquename, description, type_id, transaction_type ) VALUES ( genotype_id_var, name_var, uniquename_var, description_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER genotype_audit_ud ON genotype; CREATE TRIGGER genotype_audit_ud BEFORE UPDATE OR DELETE ON genotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_genotype (); DROP TABLE audit_feature_genotype; CREATE TABLE audit_feature_genotype ( feature_genotype_id integer, feature_id integer, genotype_id integer, chromosome_id integer, rank integer, cgroup integer, cvterm_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_genotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_genotype() RETURNS trigger AS ' DECLARE feature_genotype_id_var integer; feature_id_var integer; genotype_id_var integer; chromosome_id_var integer; rank_var integer; cgroup_var integer; cvterm_id_var integer; transaction_type_var char; BEGIN feature_genotype_id_var = OLD.feature_genotype_id; feature_id_var = OLD.feature_id; genotype_id_var = OLD.genotype_id; chromosome_id_var = OLD.chromosome_id; rank_var = OLD.rank; cgroup_var = OLD.cgroup; cvterm_id_var = OLD.cvterm_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_genotype ( feature_genotype_id, feature_id, genotype_id, chromosome_id, rank, cgroup, cvterm_id, transaction_type ) VALUES ( feature_genotype_id_var, feature_id_var, genotype_id_var, chromosome_id_var, rank_var, cgroup_var, cvterm_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_genotype_audit_ud ON feature_genotype; CREATE TRIGGER feature_genotype_audit_ud BEFORE UPDATE OR DELETE ON feature_genotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_genotype (); DROP TABLE audit_environment; CREATE TABLE audit_environment ( environment_id integer, uniquename text, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_environment to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_environment() RETURNS trigger AS ' DECLARE environment_id_var integer; uniquename_var text; description_var text; transaction_type_var char; BEGIN environment_id_var = OLD.environment_id; uniquename_var = OLD.uniquename; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_environment ( environment_id, uniquename, description, transaction_type ) VALUES ( environment_id_var, uniquename_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER environment_audit_ud ON environment; CREATE TRIGGER environment_audit_ud BEFORE UPDATE OR DELETE ON environment FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_environment (); DROP TABLE audit_environment_cvterm; CREATE TABLE audit_environment_cvterm ( environment_cvterm_id integer, environment_id integer, cvterm_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_environment_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_environment_cvterm() RETURNS trigger AS ' DECLARE environment_cvterm_id_var integer; environment_id_var integer; cvterm_id_var integer; transaction_type_var char; BEGIN environment_cvterm_id_var = OLD.environment_cvterm_id; environment_id_var = OLD.environment_id; cvterm_id_var = OLD.cvterm_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_environment_cvterm ( environment_cvterm_id, environment_id, cvterm_id, transaction_type ) VALUES ( environment_cvterm_id_var, environment_id_var, cvterm_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER environment_cvterm_audit_ud ON environment_cvterm; CREATE TRIGGER environment_cvterm_audit_ud BEFORE UPDATE OR DELETE ON environment_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_environment_cvterm (); DROP TABLE audit_phenstatement; CREATE TABLE audit_phenstatement ( phenstatement_id integer, genotype_id integer, environment_id integer, phenotype_id integer, type_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phenstatement to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phenstatement() RETURNS trigger AS ' DECLARE phenstatement_id_var integer; genotype_id_var integer; environment_id_var integer; phenotype_id_var integer; type_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN phenstatement_id_var = OLD.phenstatement_id; genotype_id_var = OLD.genotype_id; environment_id_var = OLD.environment_id; phenotype_id_var = OLD.phenotype_id; type_id_var = OLD.type_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phenstatement ( phenstatement_id, genotype_id, environment_id, phenotype_id, type_id, pub_id, transaction_type ) VALUES ( phenstatement_id_var, genotype_id_var, environment_id_var, phenotype_id_var, type_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phenstatement_audit_ud ON phenstatement; CREATE TRIGGER phenstatement_audit_ud BEFORE UPDATE OR DELETE ON phenstatement FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phenstatement (); DROP TABLE audit_phendesc; CREATE TABLE audit_phendesc ( phendesc_id integer, genotype_id integer, environment_id integer, description text, type_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phendesc to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phendesc() RETURNS trigger AS ' DECLARE phendesc_id_var integer; genotype_id_var integer; environment_id_var integer; description_var text; type_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN phendesc_id_var = OLD.phendesc_id; genotype_id_var = OLD.genotype_id; environment_id_var = OLD.environment_id; description_var = OLD.description; type_id_var = OLD.type_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phendesc ( phendesc_id, genotype_id, environment_id, description, type_id, pub_id, transaction_type ) VALUES ( phendesc_id_var, genotype_id_var, environment_id_var, description_var, type_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phendesc_audit_ud ON phendesc; CREATE TRIGGER phendesc_audit_ud BEFORE UPDATE OR DELETE ON phendesc FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phendesc (); DROP TABLE audit_phenotype_comparison; CREATE TABLE audit_phenotype_comparison ( phenotype_comparison_id integer, genotype1_id integer, environment1_id integer, genotype2_id integer, environment2_id integer, phenotype1_id integer, phenotype2_id integer, pub_id integer, organism_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phenotype_comparison to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phenotype_comparison() RETURNS trigger AS ' DECLARE phenotype_comparison_id_var integer; genotype1_id_var integer; environment1_id_var integer; genotype2_id_var integer; environment2_id_var integer; phenotype1_id_var integer; phenotype2_id_var integer; pub_id_var integer; organism_id_var integer; transaction_type_var char; BEGIN phenotype_comparison_id_var = OLD.phenotype_comparison_id; genotype1_id_var = OLD.genotype1_id; environment1_id_var = OLD.environment1_id; genotype2_id_var = OLD.genotype2_id; environment2_id_var = OLD.environment2_id; phenotype1_id_var = OLD.phenotype1_id; phenotype2_id_var = OLD.phenotype2_id; pub_id_var = OLD.pub_id; organism_id_var = OLD.organism_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phenotype_comparison ( phenotype_comparison_id, genotype1_id, environment1_id, genotype2_id, environment2_id, phenotype1_id, phenotype2_id, pub_id, organism_id, transaction_type ) VALUES ( phenotype_comparison_id_var, genotype1_id_var, environment1_id_var, genotype2_id_var, environment2_id_var, phenotype1_id_var, phenotype2_id_var, pub_id_var, organism_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phenotype_comparison_audit_ud ON phenotype_comparison; CREATE TRIGGER phenotype_comparison_audit_ud BEFORE UPDATE OR DELETE ON phenotype_comparison FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phenotype_comparison (); DROP TABLE audit_phenotype_comparison_cvterm; CREATE TABLE audit_phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id integer, phenotype_comparison_id integer, cvterm_id integer, pub_id integer, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phenotype_comparison_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phenotype_comparison_cvterm() RETURNS trigger AS ' DECLARE phenotype_comparison_cvterm_id_var integer; phenotype_comparison_id_var integer; cvterm_id_var integer; pub_id_var integer; rank_var integer; transaction_type_var char; BEGIN phenotype_comparison_cvterm_id_var = OLD.phenotype_comparison_cvterm_id; phenotype_comparison_id_var = OLD.phenotype_comparison_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phenotype_comparison_cvterm ( phenotype_comparison_cvterm_id, phenotype_comparison_id, cvterm_id, pub_id, rank, transaction_type ) VALUES ( phenotype_comparison_cvterm_id_var, phenotype_comparison_id_var, cvterm_id_var, pub_id_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phenotype_comparison_cvterm_audit_ud ON phenotype_comparison_cvterm; CREATE TRIGGER phenotype_comparison_cvterm_audit_ud BEFORE UPDATE OR DELETE ON phenotype_comparison_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phenotype_comparison_cvterm (); DROP TABLE audit_genotypeprop; CREATE TABLE audit_genotypeprop ( genotypeprop_id integer, genotype_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_genotypeprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_genotypeprop() RETURNS trigger AS ' DECLARE genotypeprop_id_var integer; genotype_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN genotypeprop_id_var = OLD.genotypeprop_id; genotype_id_var = OLD.genotype_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_genotypeprop ( genotypeprop_id, genotype_id, type_id, value, rank, transaction_type ) VALUES ( genotypeprop_id_var, genotype_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER genotypeprop_audit_ud ON genotypeprop; CREATE TRIGGER genotypeprop_audit_ud BEFORE UPDATE OR DELETE ON genotypeprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_genotypeprop (); DROP TABLE audit_featuremap; CREATE TABLE audit_featuremap ( featuremap_id integer, name varchar(255), description text, unittype_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featuremap to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featuremap() RETURNS trigger AS ' DECLARE featuremap_id_var integer; name_var varchar(255); description_var text; unittype_id_var integer; transaction_type_var char; BEGIN featuremap_id_var = OLD.featuremap_id; name_var = OLD.name; description_var = OLD.description; unittype_id_var = OLD.unittype_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featuremap ( featuremap_id, name, description, unittype_id, transaction_type ) VALUES ( featuremap_id_var, name_var, description_var, unittype_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featuremap_audit_ud ON featuremap; CREATE TRIGGER featuremap_audit_ud BEFORE UPDATE OR DELETE ON featuremap FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featuremap (); DROP TABLE audit_featurerange; CREATE TABLE audit_featurerange ( featurerange_id integer, featuremap_id integer, feature_id integer, leftstartf_id integer, leftendf_id integer, rightstartf_id integer, rightendf_id integer, rangestr varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featurerange to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featurerange() RETURNS trigger AS ' DECLARE featurerange_id_var integer; featuremap_id_var integer; feature_id_var integer; leftstartf_id_var integer; leftendf_id_var integer; rightstartf_id_var integer; rightendf_id_var integer; rangestr_var varchar(255); transaction_type_var char; BEGIN featurerange_id_var = OLD.featurerange_id; featuremap_id_var = OLD.featuremap_id; feature_id_var = OLD.feature_id; leftstartf_id_var = OLD.leftstartf_id; leftendf_id_var = OLD.leftendf_id; rightstartf_id_var = OLD.rightstartf_id; rightendf_id_var = OLD.rightendf_id; rangestr_var = OLD.rangestr; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featurerange ( featurerange_id, featuremap_id, feature_id, leftstartf_id, leftendf_id, rightstartf_id, rightendf_id, rangestr, transaction_type ) VALUES ( featurerange_id_var, featuremap_id_var, feature_id_var, leftstartf_id_var, leftendf_id_var, rightstartf_id_var, rightendf_id_var, rangestr_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featurerange_audit_ud ON featurerange; CREATE TRIGGER featurerange_audit_ud BEFORE UPDATE OR DELETE ON featurerange FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featurerange (); DROP TABLE audit_featurepos; CREATE TABLE audit_featurepos ( featurepos_id integer, featuremap_id integer, feature_id integer, map_feature_id integer, mappos float, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featurepos to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featurepos() RETURNS trigger AS ' DECLARE featurepos_id_var integer; featuremap_id_var integer; feature_id_var integer; map_feature_id_var integer; mappos_var float; transaction_type_var char; BEGIN featurepos_id_var = OLD.featurepos_id; featuremap_id_var = OLD.featuremap_id; feature_id_var = OLD.feature_id; map_feature_id_var = OLD.map_feature_id; mappos_var = OLD.mappos; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featurepos ( featurepos_id, featuremap_id, feature_id, map_feature_id, mappos, transaction_type ) VALUES ( featurepos_id_var, featuremap_id_var, feature_id_var, map_feature_id_var, mappos_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featurepos_audit_ud ON featurepos; CREATE TRIGGER featurepos_audit_ud BEFORE UPDATE OR DELETE ON featurepos FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featurepos (); DROP TABLE audit_featuremap_pub; CREATE TABLE audit_featuremap_pub ( featuremap_pub_id integer, featuremap_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_featuremap_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_featuremap_pub() RETURNS trigger AS ' DECLARE featuremap_pub_id_var integer; featuremap_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN featuremap_pub_id_var = OLD.featuremap_pub_id; featuremap_id_var = OLD.featuremap_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_featuremap_pub ( featuremap_pub_id, featuremap_id, pub_id, transaction_type ) VALUES ( featuremap_pub_id_var, featuremap_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER featuremap_pub_audit_ud ON featuremap_pub; CREATE TRIGGER featuremap_pub_audit_ud BEFORE UPDATE OR DELETE ON featuremap_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_featuremap_pub (); DROP TABLE audit_phylotree; CREATE TABLE audit_phylotree ( phylotree_id integer, dbxref_id integer, name varchar(255), type_id integer, analysis_id integer, comment text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylotree to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylotree() RETURNS trigger AS ' DECLARE phylotree_id_var integer; dbxref_id_var integer; name_var varchar(255); type_id_var integer; analysis_id_var integer; comment_var text; transaction_type_var char; BEGIN phylotree_id_var = OLD.phylotree_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; type_id_var = OLD.type_id; analysis_id_var = OLD.analysis_id; comment_var = OLD.comment; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylotree ( phylotree_id, dbxref_id, name, type_id, analysis_id, comment, transaction_type ) VALUES ( phylotree_id_var, dbxref_id_var, name_var, type_id_var, analysis_id_var, comment_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylotree_audit_ud ON phylotree; CREATE TRIGGER phylotree_audit_ud BEFORE UPDATE OR DELETE ON phylotree FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylotree (); DROP TABLE audit_phylotree_pub; CREATE TABLE audit_phylotree_pub ( phylotree_pub_id integer, phylotree_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylotree_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylotree_pub() RETURNS trigger AS ' DECLARE phylotree_pub_id_var integer; phylotree_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN phylotree_pub_id_var = OLD.phylotree_pub_id; phylotree_id_var = OLD.phylotree_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylotree_pub ( phylotree_pub_id, phylotree_id, pub_id, transaction_type ) VALUES ( phylotree_pub_id_var, phylotree_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylotree_pub_audit_ud ON phylotree_pub; CREATE TRIGGER phylotree_pub_audit_ud BEFORE UPDATE OR DELETE ON phylotree_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylotree_pub (); DROP TABLE audit_phylonode; CREATE TABLE audit_phylonode ( phylonode_id integer, phylotree_id integer, parent_phylonode_id integer, left_idx integer, right_idx integer, type_id integer, feature_id integer, label varchar(255), distance float, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonode to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonode() RETURNS trigger AS ' DECLARE phylonode_id_var integer; phylotree_id_var integer; parent_phylonode_id_var integer; left_idx_var integer; right_idx_var integer; type_id_var integer; feature_id_var integer; label_var varchar(255); distance_var float; transaction_type_var char; BEGIN phylonode_id_var = OLD.phylonode_id; phylotree_id_var = OLD.phylotree_id; parent_phylonode_id_var = OLD.parent_phylonode_id; left_idx_var = OLD.left_idx; right_idx_var = OLD.right_idx; type_id_var = OLD.type_id; feature_id_var = OLD.feature_id; label_var = OLD.label; distance_var = OLD.distance; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonode ( phylonode_id, phylotree_id, parent_phylonode_id, left_idx, right_idx, type_id, feature_id, label, distance, transaction_type ) VALUES ( phylonode_id_var, phylotree_id_var, parent_phylonode_id_var, left_idx_var, right_idx_var, type_id_var, feature_id_var, label_var, distance_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonode_audit_ud ON phylonode; CREATE TRIGGER phylonode_audit_ud BEFORE UPDATE OR DELETE ON phylonode FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonode (); DROP TABLE audit_phylonode_dbxref; CREATE TABLE audit_phylonode_dbxref ( phylonode_dbxref_id integer, phylonode_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonode_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonode_dbxref() RETURNS trigger AS ' DECLARE phylonode_dbxref_id_var integer; phylonode_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN phylonode_dbxref_id_var = OLD.phylonode_dbxref_id; phylonode_id_var = OLD.phylonode_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonode_dbxref ( phylonode_dbxref_id, phylonode_id, dbxref_id, transaction_type ) VALUES ( phylonode_dbxref_id_var, phylonode_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonode_dbxref_audit_ud ON phylonode_dbxref; CREATE TRIGGER phylonode_dbxref_audit_ud BEFORE UPDATE OR DELETE ON phylonode_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonode_dbxref (); DROP TABLE audit_phylonode_pub; CREATE TABLE audit_phylonode_pub ( phylonode_pub_id integer, phylonode_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonode_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonode_pub() RETURNS trigger AS ' DECLARE phylonode_pub_id_var integer; phylonode_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN phylonode_pub_id_var = OLD.phylonode_pub_id; phylonode_id_var = OLD.phylonode_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonode_pub ( phylonode_pub_id, phylonode_id, pub_id, transaction_type ) VALUES ( phylonode_pub_id_var, phylonode_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonode_pub_audit_ud ON phylonode_pub; CREATE TRIGGER phylonode_pub_audit_ud BEFORE UPDATE OR DELETE ON phylonode_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonode_pub (); DROP TABLE audit_phylonode_organism; CREATE TABLE audit_phylonode_organism ( phylonode_organism_id integer, phylonode_id integer, organism_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonode_organism to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonode_organism() RETURNS trigger AS ' DECLARE phylonode_organism_id_var integer; phylonode_id_var integer; organism_id_var integer; transaction_type_var char; BEGIN phylonode_organism_id_var = OLD.phylonode_organism_id; phylonode_id_var = OLD.phylonode_id; organism_id_var = OLD.organism_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonode_organism ( phylonode_organism_id, phylonode_id, organism_id, transaction_type ) VALUES ( phylonode_organism_id_var, phylonode_id_var, organism_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonode_organism_audit_ud ON phylonode_organism; CREATE TRIGGER phylonode_organism_audit_ud BEFORE UPDATE OR DELETE ON phylonode_organism FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonode_organism (); DROP TABLE audit_phylonodeprop; CREATE TABLE audit_phylonodeprop ( phylonodeprop_id integer, phylonode_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonodeprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonodeprop() RETURNS trigger AS ' DECLARE phylonodeprop_id_var integer; phylonode_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN phylonodeprop_id_var = OLD.phylonodeprop_id; phylonode_id_var = OLD.phylonode_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonodeprop ( phylonodeprop_id, phylonode_id, type_id, value, rank, transaction_type ) VALUES ( phylonodeprop_id_var, phylonode_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonodeprop_audit_ud ON phylonodeprop; CREATE TRIGGER phylonodeprop_audit_ud BEFORE UPDATE OR DELETE ON phylonodeprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonodeprop (); DROP TABLE audit_phylonode_relationship; CREATE TABLE audit_phylonode_relationship ( phylonode_relationship_id integer, subject_id integer, object_id integer, type_id integer, rank integer, phylotree_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_phylonode_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_phylonode_relationship() RETURNS trigger AS ' DECLARE phylonode_relationship_id_var integer; subject_id_var integer; object_id_var integer; type_id_var integer; rank_var integer; phylotree_id_var integer; transaction_type_var char; BEGIN phylonode_relationship_id_var = OLD.phylonode_relationship_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; type_id_var = OLD.type_id; rank_var = OLD.rank; phylotree_id_var = OLD.phylotree_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_phylonode_relationship ( phylonode_relationship_id, subject_id, object_id, type_id, rank, phylotree_id, transaction_type ) VALUES ( phylonode_relationship_id_var, subject_id_var, object_id_var, type_id_var, rank_var, phylotree_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER phylonode_relationship_audit_ud ON phylonode_relationship; CREATE TRIGGER phylonode_relationship_audit_ud BEFORE UPDATE OR DELETE ON phylonode_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_phylonode_relationship (); DROP TABLE audit_contact; CREATE TABLE audit_contact ( contact_id integer, type_id integer, name varchar(255), description varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_contact to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_contact() RETURNS trigger AS ' DECLARE contact_id_var integer; type_id_var integer; name_var varchar(255); description_var varchar(255); transaction_type_var char; BEGIN contact_id_var = OLD.contact_id; type_id_var = OLD.type_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_contact ( contact_id, type_id, name, description, transaction_type ) VALUES ( contact_id_var, type_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER contact_audit_ud ON contact; CREATE TRIGGER contact_audit_ud BEFORE UPDATE OR DELETE ON contact FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_contact (); DROP TABLE audit_contact_relationship; CREATE TABLE audit_contact_relationship ( contact_relationship_id integer, type_id integer, subject_id integer, object_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_contact_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_contact_relationship() RETURNS trigger AS ' DECLARE contact_relationship_id_var integer; type_id_var integer; subject_id_var integer; object_id_var integer; transaction_type_var char; BEGIN contact_relationship_id_var = OLD.contact_relationship_id; type_id_var = OLD.type_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_contact_relationship ( contact_relationship_id, type_id, subject_id, object_id, transaction_type ) VALUES ( contact_relationship_id_var, type_id_var, subject_id_var, object_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER contact_relationship_audit_ud ON contact_relationship; CREATE TRIGGER contact_relationship_audit_ud BEFORE UPDATE OR DELETE ON contact_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_contact_relationship (); DROP TABLE audit_expression; CREATE TABLE audit_expression ( expression_id integer, uniquename text, md5checksum char(32), description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expression to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expression() RETURNS trigger AS ' DECLARE expression_id_var integer; uniquename_var text; md5checksum_var char(32); description_var text; transaction_type_var char; BEGIN expression_id_var = OLD.expression_id; uniquename_var = OLD.uniquename; md5checksum_var = OLD.md5checksum; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expression ( expression_id, uniquename, md5checksum, description, transaction_type ) VALUES ( expression_id_var, uniquename_var, md5checksum_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expression_audit_ud ON expression; CREATE TRIGGER expression_audit_ud BEFORE UPDATE OR DELETE ON expression FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expression (); DROP TABLE audit_expression_cvterm; CREATE TABLE audit_expression_cvterm ( expression_cvterm_id integer, expression_id integer, cvterm_id integer, rank integer, cvterm_type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expression_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expression_cvterm() RETURNS trigger AS ' DECLARE expression_cvterm_id_var integer; expression_id_var integer; cvterm_id_var integer; rank_var integer; cvterm_type_id_var integer; transaction_type_var char; BEGIN expression_cvterm_id_var = OLD.expression_cvterm_id; expression_id_var = OLD.expression_id; cvterm_id_var = OLD.cvterm_id; rank_var = OLD.rank; cvterm_type_id_var = OLD.cvterm_type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expression_cvterm ( expression_cvterm_id, expression_id, cvterm_id, rank, cvterm_type_id, transaction_type ) VALUES ( expression_cvterm_id_var, expression_id_var, cvterm_id_var, rank_var, cvterm_type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expression_cvterm_audit_ud ON expression_cvterm; CREATE TRIGGER expression_cvterm_audit_ud BEFORE UPDATE OR DELETE ON expression_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expression_cvterm (); DROP TABLE audit_expression_cvtermprop; CREATE TABLE audit_expression_cvtermprop ( expression_cvtermprop_id integer, expression_cvterm_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expression_cvtermprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expression_cvtermprop() RETURNS trigger AS ' DECLARE expression_cvtermprop_id_var integer; expression_cvterm_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN expression_cvtermprop_id_var = OLD.expression_cvtermprop_id; expression_cvterm_id_var = OLD.expression_cvterm_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expression_cvtermprop ( expression_cvtermprop_id, expression_cvterm_id, type_id, value, rank, transaction_type ) VALUES ( expression_cvtermprop_id_var, expression_cvterm_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expression_cvtermprop_audit_ud ON expression_cvtermprop; CREATE TRIGGER expression_cvtermprop_audit_ud BEFORE UPDATE OR DELETE ON expression_cvtermprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expression_cvtermprop (); DROP TABLE audit_expressionprop; CREATE TABLE audit_expressionprop ( expressionprop_id integer, expression_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expressionprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expressionprop() RETURNS trigger AS ' DECLARE expressionprop_id_var integer; expression_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN expressionprop_id_var = OLD.expressionprop_id; expression_id_var = OLD.expression_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expressionprop ( expressionprop_id, expression_id, type_id, value, rank, transaction_type ) VALUES ( expressionprop_id_var, expression_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expressionprop_audit_ud ON expressionprop; CREATE TRIGGER expressionprop_audit_ud BEFORE UPDATE OR DELETE ON expressionprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expressionprop (); DROP TABLE audit_expression_pub; CREATE TABLE audit_expression_pub ( expression_pub_id integer, expression_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expression_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expression_pub() RETURNS trigger AS ' DECLARE expression_pub_id_var integer; expression_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN expression_pub_id_var = OLD.expression_pub_id; expression_id_var = OLD.expression_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expression_pub ( expression_pub_id, expression_id, pub_id, transaction_type ) VALUES ( expression_pub_id_var, expression_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expression_pub_audit_ud ON expression_pub; CREATE TRIGGER expression_pub_audit_ud BEFORE UPDATE OR DELETE ON expression_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expression_pub (); DROP TABLE audit_feature_expression; CREATE TABLE audit_feature_expression ( feature_expression_id integer, expression_id integer, feature_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_expression to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_expression() RETURNS trigger AS ' DECLARE feature_expression_id_var integer; expression_id_var integer; feature_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN feature_expression_id_var = OLD.feature_expression_id; expression_id_var = OLD.expression_id; feature_id_var = OLD.feature_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_expression ( feature_expression_id, expression_id, feature_id, pub_id, transaction_type ) VALUES ( feature_expression_id_var, expression_id_var, feature_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_expression_audit_ud ON feature_expression; CREATE TRIGGER feature_expression_audit_ud BEFORE UPDATE OR DELETE ON feature_expression FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_expression (); DROP TABLE audit_feature_expressionprop; CREATE TABLE audit_feature_expressionprop ( feature_expressionprop_id integer, feature_expression_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_feature_expressionprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_feature_expressionprop() RETURNS trigger AS ' DECLARE feature_expressionprop_id_var integer; feature_expression_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN feature_expressionprop_id_var = OLD.feature_expressionprop_id; feature_expression_id_var = OLD.feature_expression_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_feature_expressionprop ( feature_expressionprop_id, feature_expression_id, type_id, value, rank, transaction_type ) VALUES ( feature_expressionprop_id_var, feature_expression_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER feature_expressionprop_audit_ud ON feature_expressionprop; CREATE TRIGGER feature_expressionprop_audit_ud BEFORE UPDATE OR DELETE ON feature_expressionprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_feature_expressionprop (); DROP TABLE audit_eimage; CREATE TABLE audit_eimage ( eimage_id integer, eimage_data text, eimage_type varchar(255), image_uri varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_eimage to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_eimage() RETURNS trigger AS ' DECLARE eimage_id_var integer; eimage_data_var text; eimage_type_var varchar(255); image_uri_var varchar(255); transaction_type_var char; BEGIN eimage_id_var = OLD.eimage_id; eimage_data_var = OLD.eimage_data; eimage_type_var = OLD.eimage_type; image_uri_var = OLD.image_uri; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_eimage ( eimage_id, eimage_data, eimage_type, image_uri, transaction_type ) VALUES ( eimage_id_var, eimage_data_var, eimage_type_var, image_uri_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER eimage_audit_ud ON eimage; CREATE TRIGGER eimage_audit_ud BEFORE UPDATE OR DELETE ON eimage FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_eimage (); DROP TABLE audit_expression_image; CREATE TABLE audit_expression_image ( expression_image_id integer, expression_id integer, eimage_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_expression_image to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_expression_image() RETURNS trigger AS ' DECLARE expression_image_id_var integer; expression_id_var integer; eimage_id_var integer; transaction_type_var char; BEGIN expression_image_id_var = OLD.expression_image_id; expression_id_var = OLD.expression_id; eimage_id_var = OLD.eimage_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_expression_image ( expression_image_id, expression_id, eimage_id, transaction_type ) VALUES ( expression_image_id_var, expression_id_var, eimage_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER expression_image_audit_ud ON expression_image; CREATE TRIGGER expression_image_audit_ud BEFORE UPDATE OR DELETE ON expression_image FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_expression_image (); DROP TABLE audit_project; CREATE TABLE audit_project ( project_id integer, name varchar(255), description varchar(255), transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_project to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_project() RETURNS trigger AS ' DECLARE project_id_var integer; name_var varchar(255); description_var varchar(255); transaction_type_var char; BEGIN project_id_var = OLD.project_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_project ( project_id, name, description, transaction_type ) VALUES ( project_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER project_audit_ud ON project; CREATE TRIGGER project_audit_ud BEFORE UPDATE OR DELETE ON project FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_project (); DROP TABLE audit_projectprop; CREATE TABLE audit_projectprop ( projectprop_id integer, project_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_projectprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_projectprop() RETURNS trigger AS ' DECLARE projectprop_id_var integer; project_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN projectprop_id_var = OLD.projectprop_id; project_id_var = OLD.project_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_projectprop ( projectprop_id, project_id, type_id, value, rank, transaction_type ) VALUES ( projectprop_id_var, project_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER projectprop_audit_ud ON projectprop; CREATE TRIGGER projectprop_audit_ud BEFORE UPDATE OR DELETE ON projectprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_projectprop (); DROP TABLE audit_project_relationship; CREATE TABLE audit_project_relationship ( project_relationship_id integer, subject_project_id integer, object_project_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_project_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_project_relationship() RETURNS trigger AS ' DECLARE project_relationship_id_var integer; subject_project_id_var integer; object_project_id_var integer; type_id_var integer; transaction_type_var char; BEGIN project_relationship_id_var = OLD.project_relationship_id; subject_project_id_var = OLD.subject_project_id; object_project_id_var = OLD.object_project_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_project_relationship ( project_relationship_id, subject_project_id, object_project_id, type_id, transaction_type ) VALUES ( project_relationship_id_var, subject_project_id_var, object_project_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER project_relationship_audit_ud ON project_relationship; CREATE TRIGGER project_relationship_audit_ud BEFORE UPDATE OR DELETE ON project_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_project_relationship (); DROP TABLE audit_project_pub; CREATE TABLE audit_project_pub ( project_pub_id integer, project_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_project_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_project_pub() RETURNS trigger AS ' DECLARE project_pub_id_var integer; project_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN project_pub_id_var = OLD.project_pub_id; project_id_var = OLD.project_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_project_pub ( project_pub_id, project_id, pub_id, transaction_type ) VALUES ( project_pub_id_var, project_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER project_pub_audit_ud ON project_pub; CREATE TRIGGER project_pub_audit_ud BEFORE UPDATE OR DELETE ON project_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_project_pub (); DROP TABLE audit_project_contact; CREATE TABLE audit_project_contact ( project_contact_id integer, project_id integer, contact_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_project_contact to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_project_contact() RETURNS trigger AS ' DECLARE project_contact_id_var integer; project_id_var integer; contact_id_var integer; transaction_type_var char; BEGIN project_contact_id_var = OLD.project_contact_id; project_id_var = OLD.project_id; contact_id_var = OLD.contact_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_project_contact ( project_contact_id, project_id, contact_id, transaction_type ) VALUES ( project_contact_id_var, project_id_var, contact_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER project_contact_audit_ud ON project_contact; CREATE TRIGGER project_contact_audit_ud BEFORE UPDATE OR DELETE ON project_contact FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_project_contact (); DROP TABLE audit_mageml; CREATE TABLE audit_mageml ( mageml_id integer, mage_package text, mage_ml text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_mageml to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_mageml() RETURNS trigger AS ' DECLARE mageml_id_var integer; mage_package_var text; mage_ml_var text; transaction_type_var char; BEGIN mageml_id_var = OLD.mageml_id; mage_package_var = OLD.mage_package; mage_ml_var = OLD.mage_ml; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_mageml ( mageml_id, mage_package, mage_ml, transaction_type ) VALUES ( mageml_id_var, mage_package_var, mage_ml_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER mageml_audit_ud ON mageml; CREATE TRIGGER mageml_audit_ud BEFORE UPDATE OR DELETE ON mageml FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_mageml (); DROP TABLE audit_magedocumentation; CREATE TABLE audit_magedocumentation ( magedocumentation_id integer, mageml_id integer, tableinfo_id integer, row_id integer, mageidentifier text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_magedocumentation to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_magedocumentation() RETURNS trigger AS ' DECLARE magedocumentation_id_var integer; mageml_id_var integer; tableinfo_id_var integer; row_id_var integer; mageidentifier_var text; transaction_type_var char; BEGIN magedocumentation_id_var = OLD.magedocumentation_id; mageml_id_var = OLD.mageml_id; tableinfo_id_var = OLD.tableinfo_id; row_id_var = OLD.row_id; mageidentifier_var = OLD.mageidentifier; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_magedocumentation ( magedocumentation_id, mageml_id, tableinfo_id, row_id, mageidentifier, transaction_type ) VALUES ( magedocumentation_id_var, mageml_id_var, tableinfo_id_var, row_id_var, mageidentifier_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER magedocumentation_audit_ud ON magedocumentation; CREATE TRIGGER magedocumentation_audit_ud BEFORE UPDATE OR DELETE ON magedocumentation FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_magedocumentation (); DROP TABLE audit_protocol; CREATE TABLE audit_protocol ( protocol_id integer, type_id integer, pub_id integer, dbxref_id integer, name text, uri text, protocoldescription text, hardwaredescription text, softwaredescription text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_protocol to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_protocol() RETURNS trigger AS ' DECLARE protocol_id_var integer; type_id_var integer; pub_id_var integer; dbxref_id_var integer; name_var text; uri_var text; protocoldescription_var text; hardwaredescription_var text; softwaredescription_var text; transaction_type_var char; BEGIN protocol_id_var = OLD.protocol_id; type_id_var = OLD.type_id; pub_id_var = OLD.pub_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; uri_var = OLD.uri; protocoldescription_var = OLD.protocoldescription; hardwaredescription_var = OLD.hardwaredescription; softwaredescription_var = OLD.softwaredescription; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_protocol ( protocol_id, type_id, pub_id, dbxref_id, name, uri, protocoldescription, hardwaredescription, softwaredescription, transaction_type ) VALUES ( protocol_id_var, type_id_var, pub_id_var, dbxref_id_var, name_var, uri_var, protocoldescription_var, hardwaredescription_var, softwaredescription_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER protocol_audit_ud ON protocol; CREATE TRIGGER protocol_audit_ud BEFORE UPDATE OR DELETE ON protocol FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_protocol (); DROP TABLE audit_protocolparam; CREATE TABLE audit_protocolparam ( protocolparam_id integer, protocol_id integer, name text, datatype_id integer, unittype_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_protocolparam to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_protocolparam() RETURNS trigger AS ' DECLARE protocolparam_id_var integer; protocol_id_var integer; name_var text; datatype_id_var integer; unittype_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN protocolparam_id_var = OLD.protocolparam_id; protocol_id_var = OLD.protocol_id; name_var = OLD.name; datatype_id_var = OLD.datatype_id; unittype_id_var = OLD.unittype_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_protocolparam ( protocolparam_id, protocol_id, name, datatype_id, unittype_id, value, rank, transaction_type ) VALUES ( protocolparam_id_var, protocol_id_var, name_var, datatype_id_var, unittype_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER protocolparam_audit_ud ON protocolparam; CREATE TRIGGER protocolparam_audit_ud BEFORE UPDATE OR DELETE ON protocolparam FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_protocolparam (); DROP TABLE audit_channel; CREATE TABLE audit_channel ( channel_id integer, name text, definition text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_channel to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_channel() RETURNS trigger AS ' DECLARE channel_id_var integer; name_var text; definition_var text; transaction_type_var char; BEGIN channel_id_var = OLD.channel_id; name_var = OLD.name; definition_var = OLD.definition; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_channel ( channel_id, name, definition, transaction_type ) VALUES ( channel_id_var, name_var, definition_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER channel_audit_ud ON channel; CREATE TRIGGER channel_audit_ud BEFORE UPDATE OR DELETE ON channel FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_channel (); DROP TABLE audit_arraydesign; CREATE TABLE audit_arraydesign ( arraydesign_id integer, manufacturer_id integer, platformtype_id integer, substratetype_id integer, protocol_id integer, dbxref_id integer, name text, version text, description text, array_dimensions text, element_dimensions text, num_of_elements integer, num_array_columns integer, num_array_rows integer, num_grid_columns integer, num_grid_rows integer, num_sub_columns integer, num_sub_rows integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_arraydesign to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_arraydesign() RETURNS trigger AS ' DECLARE arraydesign_id_var integer; manufacturer_id_var integer; platformtype_id_var integer; substratetype_id_var integer; protocol_id_var integer; dbxref_id_var integer; name_var text; version_var text; description_var text; array_dimensions_var text; element_dimensions_var text; num_of_elements_var integer; num_array_columns_var integer; num_array_rows_var integer; num_grid_columns_var integer; num_grid_rows_var integer; num_sub_columns_var integer; num_sub_rows_var integer; transaction_type_var char; BEGIN arraydesign_id_var = OLD.arraydesign_id; manufacturer_id_var = OLD.manufacturer_id; platformtype_id_var = OLD.platformtype_id; substratetype_id_var = OLD.substratetype_id; protocol_id_var = OLD.protocol_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; version_var = OLD.version; description_var = OLD.description; array_dimensions_var = OLD.array_dimensions; element_dimensions_var = OLD.element_dimensions; num_of_elements_var = OLD.num_of_elements; num_array_columns_var = OLD.num_array_columns; num_array_rows_var = OLD.num_array_rows; num_grid_columns_var = OLD.num_grid_columns; num_grid_rows_var = OLD.num_grid_rows; num_sub_columns_var = OLD.num_sub_columns; num_sub_rows_var = OLD.num_sub_rows; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_arraydesign ( arraydesign_id, manufacturer_id, platformtype_id, substratetype_id, protocol_id, dbxref_id, name, version, description, array_dimensions, element_dimensions, num_of_elements, num_array_columns, num_array_rows, num_grid_columns, num_grid_rows, num_sub_columns, num_sub_rows, transaction_type ) VALUES ( arraydesign_id_var, manufacturer_id_var, platformtype_id_var, substratetype_id_var, protocol_id_var, dbxref_id_var, name_var, version_var, description_var, array_dimensions_var, element_dimensions_var, num_of_elements_var, num_array_columns_var, num_array_rows_var, num_grid_columns_var, num_grid_rows_var, num_sub_columns_var, num_sub_rows_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER arraydesign_audit_ud ON arraydesign; CREATE TRIGGER arraydesign_audit_ud BEFORE UPDATE OR DELETE ON arraydesign FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_arraydesign (); DROP TABLE audit_arraydesignprop; CREATE TABLE audit_arraydesignprop ( arraydesignprop_id integer, arraydesign_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_arraydesignprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_arraydesignprop() RETURNS trigger AS ' DECLARE arraydesignprop_id_var integer; arraydesign_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN arraydesignprop_id_var = OLD.arraydesignprop_id; arraydesign_id_var = OLD.arraydesign_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_arraydesignprop ( arraydesignprop_id, arraydesign_id, type_id, value, rank, transaction_type ) VALUES ( arraydesignprop_id_var, arraydesign_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER arraydesignprop_audit_ud ON arraydesignprop; CREATE TRIGGER arraydesignprop_audit_ud BEFORE UPDATE OR DELETE ON arraydesignprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_arraydesignprop (); DROP TABLE audit_assay; CREATE TABLE audit_assay ( assay_id integer, arraydesign_id integer, protocol_id integer, assaydate timestamp, arrayidentifier text, arraybatchidentifier text, operator_id integer, dbxref_id integer, name text, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_assay to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_assay() RETURNS trigger AS ' DECLARE assay_id_var integer; arraydesign_id_var integer; protocol_id_var integer; assaydate_var timestamp; arrayidentifier_var text; arraybatchidentifier_var text; operator_id_var integer; dbxref_id_var integer; name_var text; description_var text; transaction_type_var char; BEGIN assay_id_var = OLD.assay_id; arraydesign_id_var = OLD.arraydesign_id; protocol_id_var = OLD.protocol_id; assaydate_var = OLD.assaydate; arrayidentifier_var = OLD.arrayidentifier; arraybatchidentifier_var = OLD.arraybatchidentifier; operator_id_var = OLD.operator_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_assay ( assay_id, arraydesign_id, protocol_id, assaydate, arrayidentifier, arraybatchidentifier, operator_id, dbxref_id, name, description, transaction_type ) VALUES ( assay_id_var, arraydesign_id_var, protocol_id_var, assaydate_var, arrayidentifier_var, arraybatchidentifier_var, operator_id_var, dbxref_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER assay_audit_ud ON assay; CREATE TRIGGER assay_audit_ud BEFORE UPDATE OR DELETE ON assay FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_assay (); DROP TABLE audit_assayprop; CREATE TABLE audit_assayprop ( assayprop_id integer, assay_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_assayprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_assayprop() RETURNS trigger AS ' DECLARE assayprop_id_var integer; assay_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN assayprop_id_var = OLD.assayprop_id; assay_id_var = OLD.assay_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_assayprop ( assayprop_id, assay_id, type_id, value, rank, transaction_type ) VALUES ( assayprop_id_var, assay_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER assayprop_audit_ud ON assayprop; CREATE TRIGGER assayprop_audit_ud BEFORE UPDATE OR DELETE ON assayprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_assayprop (); DROP TABLE audit_assay_project; CREATE TABLE audit_assay_project ( assay_project_id integer, assay_id integer, project_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_assay_project to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_assay_project() RETURNS trigger AS ' DECLARE assay_project_id_var integer; assay_id_var integer; project_id_var integer; transaction_type_var char; BEGIN assay_project_id_var = OLD.assay_project_id; assay_id_var = OLD.assay_id; project_id_var = OLD.project_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_assay_project ( assay_project_id, assay_id, project_id, transaction_type ) VALUES ( assay_project_id_var, assay_id_var, project_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER assay_project_audit_ud ON assay_project; CREATE TRIGGER assay_project_audit_ud BEFORE UPDATE OR DELETE ON assay_project FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_assay_project (); DROP TABLE audit_biomaterial; CREATE TABLE audit_biomaterial ( biomaterial_id integer, taxon_id integer, biosourceprovider_id integer, dbxref_id integer, name text, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_biomaterial to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_biomaterial() RETURNS trigger AS ' DECLARE biomaterial_id_var integer; taxon_id_var integer; biosourceprovider_id_var integer; dbxref_id_var integer; name_var text; description_var text; transaction_type_var char; BEGIN biomaterial_id_var = OLD.biomaterial_id; taxon_id_var = OLD.taxon_id; biosourceprovider_id_var = OLD.biosourceprovider_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_biomaterial ( biomaterial_id, taxon_id, biosourceprovider_id, dbxref_id, name, description, transaction_type ) VALUES ( biomaterial_id_var, taxon_id_var, biosourceprovider_id_var, dbxref_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER biomaterial_audit_ud ON biomaterial; CREATE TRIGGER biomaterial_audit_ud BEFORE UPDATE OR DELETE ON biomaterial FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_biomaterial (); DROP TABLE audit_biomaterial_relationship; CREATE TABLE audit_biomaterial_relationship ( biomaterial_relationship_id integer, subject_id integer, type_id integer, object_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_biomaterial_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_biomaterial_relationship() RETURNS trigger AS ' DECLARE biomaterial_relationship_id_var integer; subject_id_var integer; type_id_var integer; object_id_var integer; transaction_type_var char; BEGIN biomaterial_relationship_id_var = OLD.biomaterial_relationship_id; subject_id_var = OLD.subject_id; type_id_var = OLD.type_id; object_id_var = OLD.object_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_biomaterial_relationship ( biomaterial_relationship_id, subject_id, type_id, object_id, transaction_type ) VALUES ( biomaterial_relationship_id_var, subject_id_var, type_id_var, object_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER biomaterial_relationship_audit_ud ON biomaterial_relationship; CREATE TRIGGER biomaterial_relationship_audit_ud BEFORE UPDATE OR DELETE ON biomaterial_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_biomaterial_relationship (); DROP TABLE audit_biomaterialprop; CREATE TABLE audit_biomaterialprop ( biomaterialprop_id integer, biomaterial_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_biomaterialprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_biomaterialprop() RETURNS trigger AS ' DECLARE biomaterialprop_id_var integer; biomaterial_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN biomaterialprop_id_var = OLD.biomaterialprop_id; biomaterial_id_var = OLD.biomaterial_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_biomaterialprop ( biomaterialprop_id, biomaterial_id, type_id, value, rank, transaction_type ) VALUES ( biomaterialprop_id_var, biomaterial_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER biomaterialprop_audit_ud ON biomaterialprop; CREATE TRIGGER biomaterialprop_audit_ud BEFORE UPDATE OR DELETE ON biomaterialprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_biomaterialprop (); DROP TABLE audit_biomaterial_dbxref; CREATE TABLE audit_biomaterial_dbxref ( biomaterial_dbxref_id integer, biomaterial_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_biomaterial_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_biomaterial_dbxref() RETURNS trigger AS ' DECLARE biomaterial_dbxref_id_var integer; biomaterial_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN biomaterial_dbxref_id_var = OLD.biomaterial_dbxref_id; biomaterial_id_var = OLD.biomaterial_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_biomaterial_dbxref ( biomaterial_dbxref_id, biomaterial_id, dbxref_id, transaction_type ) VALUES ( biomaterial_dbxref_id_var, biomaterial_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER biomaterial_dbxref_audit_ud ON biomaterial_dbxref; CREATE TRIGGER biomaterial_dbxref_audit_ud BEFORE UPDATE OR DELETE ON biomaterial_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_biomaterial_dbxref (); DROP TABLE audit_treatment; CREATE TABLE audit_treatment ( treatment_id integer, rank integer, biomaterial_id integer, type_id integer, protocol_id integer, name text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_treatment to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_treatment() RETURNS trigger AS ' DECLARE treatment_id_var integer; rank_var integer; biomaterial_id_var integer; type_id_var integer; protocol_id_var integer; name_var text; transaction_type_var char; BEGIN treatment_id_var = OLD.treatment_id; rank_var = OLD.rank; biomaterial_id_var = OLD.biomaterial_id; type_id_var = OLD.type_id; protocol_id_var = OLD.protocol_id; name_var = OLD.name; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_treatment ( treatment_id, rank, biomaterial_id, type_id, protocol_id, name, transaction_type ) VALUES ( treatment_id_var, rank_var, biomaterial_id_var, type_id_var, protocol_id_var, name_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER treatment_audit_ud ON treatment; CREATE TRIGGER treatment_audit_ud BEFORE UPDATE OR DELETE ON treatment FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_treatment (); DROP TABLE audit_biomaterial_treatment; CREATE TABLE audit_biomaterial_treatment ( biomaterial_treatment_id integer, biomaterial_id integer, treatment_id integer, unittype_id integer, value float, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_biomaterial_treatment to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_biomaterial_treatment() RETURNS trigger AS ' DECLARE biomaterial_treatment_id_var integer; biomaterial_id_var integer; treatment_id_var integer; unittype_id_var integer; value_var float; rank_var integer; transaction_type_var char; BEGIN biomaterial_treatment_id_var = OLD.biomaterial_treatment_id; biomaterial_id_var = OLD.biomaterial_id; treatment_id_var = OLD.treatment_id; unittype_id_var = OLD.unittype_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_biomaterial_treatment ( biomaterial_treatment_id, biomaterial_id, treatment_id, unittype_id, value, rank, transaction_type ) VALUES ( biomaterial_treatment_id_var, biomaterial_id_var, treatment_id_var, unittype_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER biomaterial_treatment_audit_ud ON biomaterial_treatment; CREATE TRIGGER biomaterial_treatment_audit_ud BEFORE UPDATE OR DELETE ON biomaterial_treatment FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_biomaterial_treatment (); DROP TABLE audit_assay_biomaterial; CREATE TABLE audit_assay_biomaterial ( assay_biomaterial_id integer, assay_id integer, biomaterial_id integer, channel_id integer, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_assay_biomaterial to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_assay_biomaterial() RETURNS trigger AS ' DECLARE assay_biomaterial_id_var integer; assay_id_var integer; biomaterial_id_var integer; channel_id_var integer; rank_var integer; transaction_type_var char; BEGIN assay_biomaterial_id_var = OLD.assay_biomaterial_id; assay_id_var = OLD.assay_id; biomaterial_id_var = OLD.biomaterial_id; channel_id_var = OLD.channel_id; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_assay_biomaterial ( assay_biomaterial_id, assay_id, biomaterial_id, channel_id, rank, transaction_type ) VALUES ( assay_biomaterial_id_var, assay_id_var, biomaterial_id_var, channel_id_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER assay_biomaterial_audit_ud ON assay_biomaterial; CREATE TRIGGER assay_biomaterial_audit_ud BEFORE UPDATE OR DELETE ON assay_biomaterial FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_assay_biomaterial (); DROP TABLE audit_acquisition; CREATE TABLE audit_acquisition ( acquisition_id integer, assay_id integer, protocol_id integer, channel_id integer, acquisitiondate timestamp, name text, uri text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_acquisition to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_acquisition() RETURNS trigger AS ' DECLARE acquisition_id_var integer; assay_id_var integer; protocol_id_var integer; channel_id_var integer; acquisitiondate_var timestamp; name_var text; uri_var text; transaction_type_var char; BEGIN acquisition_id_var = OLD.acquisition_id; assay_id_var = OLD.assay_id; protocol_id_var = OLD.protocol_id; channel_id_var = OLD.channel_id; acquisitiondate_var = OLD.acquisitiondate; name_var = OLD.name; uri_var = OLD.uri; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_acquisition ( acquisition_id, assay_id, protocol_id, channel_id, acquisitiondate, name, uri, transaction_type ) VALUES ( acquisition_id_var, assay_id_var, protocol_id_var, channel_id_var, acquisitiondate_var, name_var, uri_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER acquisition_audit_ud ON acquisition; CREATE TRIGGER acquisition_audit_ud BEFORE UPDATE OR DELETE ON acquisition FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_acquisition (); DROP TABLE audit_acquisitionprop; CREATE TABLE audit_acquisitionprop ( acquisitionprop_id integer, acquisition_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_acquisitionprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_acquisitionprop() RETURNS trigger AS ' DECLARE acquisitionprop_id_var integer; acquisition_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN acquisitionprop_id_var = OLD.acquisitionprop_id; acquisition_id_var = OLD.acquisition_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_acquisitionprop ( acquisitionprop_id, acquisition_id, type_id, value, rank, transaction_type ) VALUES ( acquisitionprop_id_var, acquisition_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER acquisitionprop_audit_ud ON acquisitionprop; CREATE TRIGGER acquisitionprop_audit_ud BEFORE UPDATE OR DELETE ON acquisitionprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_acquisitionprop (); DROP TABLE audit_acquisition_relationship; CREATE TABLE audit_acquisition_relationship ( acquisition_relationship_id integer, subject_id integer, type_id integer, object_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_acquisition_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_acquisition_relationship() RETURNS trigger AS ' DECLARE acquisition_relationship_id_var integer; subject_id_var integer; type_id_var integer; object_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN acquisition_relationship_id_var = OLD.acquisition_relationship_id; subject_id_var = OLD.subject_id; type_id_var = OLD.type_id; object_id_var = OLD.object_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_acquisition_relationship ( acquisition_relationship_id, subject_id, type_id, object_id, value, rank, transaction_type ) VALUES ( acquisition_relationship_id_var, subject_id_var, type_id_var, object_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER acquisition_relationship_audit_ud ON acquisition_relationship; CREATE TRIGGER acquisition_relationship_audit_ud BEFORE UPDATE OR DELETE ON acquisition_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_acquisition_relationship (); DROP TABLE audit_quantification; CREATE TABLE audit_quantification ( quantification_id integer, acquisition_id integer, operator_id integer, protocol_id integer, analysis_id integer, quantificationdate timestamp, name text, uri text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_quantification to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_quantification() RETURNS trigger AS ' DECLARE quantification_id_var integer; acquisition_id_var integer; operator_id_var integer; protocol_id_var integer; analysis_id_var integer; quantificationdate_var timestamp; name_var text; uri_var text; transaction_type_var char; BEGIN quantification_id_var = OLD.quantification_id; acquisition_id_var = OLD.acquisition_id; operator_id_var = OLD.operator_id; protocol_id_var = OLD.protocol_id; analysis_id_var = OLD.analysis_id; quantificationdate_var = OLD.quantificationdate; name_var = OLD.name; uri_var = OLD.uri; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_quantification ( quantification_id, acquisition_id, operator_id, protocol_id, analysis_id, quantificationdate, name, uri, transaction_type ) VALUES ( quantification_id_var, acquisition_id_var, operator_id_var, protocol_id_var, analysis_id_var, quantificationdate_var, name_var, uri_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER quantification_audit_ud ON quantification; CREATE TRIGGER quantification_audit_ud BEFORE UPDATE OR DELETE ON quantification FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_quantification (); DROP TABLE audit_quantificationprop; CREATE TABLE audit_quantificationprop ( quantificationprop_id integer, quantification_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_quantificationprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_quantificationprop() RETURNS trigger AS ' DECLARE quantificationprop_id_var integer; quantification_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN quantificationprop_id_var = OLD.quantificationprop_id; quantification_id_var = OLD.quantification_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_quantificationprop ( quantificationprop_id, quantification_id, type_id, value, rank, transaction_type ) VALUES ( quantificationprop_id_var, quantification_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER quantificationprop_audit_ud ON quantificationprop; CREATE TRIGGER quantificationprop_audit_ud BEFORE UPDATE OR DELETE ON quantificationprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_quantificationprop (); DROP TABLE audit_quantification_relationship; CREATE TABLE audit_quantification_relationship ( quantification_relationship_id integer, subject_id integer, type_id integer, object_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_quantification_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_quantification_relationship() RETURNS trigger AS ' DECLARE quantification_relationship_id_var integer; subject_id_var integer; type_id_var integer; object_id_var integer; transaction_type_var char; BEGIN quantification_relationship_id_var = OLD.quantification_relationship_id; subject_id_var = OLD.subject_id; type_id_var = OLD.type_id; object_id_var = OLD.object_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_quantification_relationship ( quantification_relationship_id, subject_id, type_id, object_id, transaction_type ) VALUES ( quantification_relationship_id_var, subject_id_var, type_id_var, object_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER quantification_relationship_audit_ud ON quantification_relationship; CREATE TRIGGER quantification_relationship_audit_ud BEFORE UPDATE OR DELETE ON quantification_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_quantification_relationship (); DROP TABLE audit_control; CREATE TABLE audit_control ( control_id integer, type_id integer, assay_id integer, tableinfo_id integer, row_id integer, name text, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_control to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_control() RETURNS trigger AS ' DECLARE control_id_var integer; type_id_var integer; assay_id_var integer; tableinfo_id_var integer; row_id_var integer; name_var text; value_var text; rank_var integer; transaction_type_var char; BEGIN control_id_var = OLD.control_id; type_id_var = OLD.type_id; assay_id_var = OLD.assay_id; tableinfo_id_var = OLD.tableinfo_id; row_id_var = OLD.row_id; name_var = OLD.name; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_control ( control_id, type_id, assay_id, tableinfo_id, row_id, name, value, rank, transaction_type ) VALUES ( control_id_var, type_id_var, assay_id_var, tableinfo_id_var, row_id_var, name_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER control_audit_ud ON control; CREATE TRIGGER control_audit_ud BEFORE UPDATE OR DELETE ON control FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_control (); DROP TABLE audit_element; CREATE TABLE audit_element ( element_id integer, feature_id integer, arraydesign_id integer, type_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_element to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_element() RETURNS trigger AS ' DECLARE element_id_var integer; feature_id_var integer; arraydesign_id_var integer; type_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN element_id_var = OLD.element_id; feature_id_var = OLD.feature_id; arraydesign_id_var = OLD.arraydesign_id; type_id_var = OLD.type_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_element ( element_id, feature_id, arraydesign_id, type_id, dbxref_id, transaction_type ) VALUES ( element_id_var, feature_id_var, arraydesign_id_var, type_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER element_audit_ud ON element; CREATE TRIGGER element_audit_ud BEFORE UPDATE OR DELETE ON element FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_element (); DROP TABLE audit_elementresult; CREATE TABLE audit_elementresult ( elementresult_id integer, element_id integer, quantification_id integer, signal float, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_elementresult to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_elementresult() RETURNS trigger AS ' DECLARE elementresult_id_var integer; element_id_var integer; quantification_id_var integer; signal_var float; transaction_type_var char; BEGIN elementresult_id_var = OLD.elementresult_id; element_id_var = OLD.element_id; quantification_id_var = OLD.quantification_id; signal_var = OLD.signal; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_elementresult ( elementresult_id, element_id, quantification_id, signal, transaction_type ) VALUES ( elementresult_id_var, element_id_var, quantification_id_var, signal_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER elementresult_audit_ud ON elementresult; CREATE TRIGGER elementresult_audit_ud BEFORE UPDATE OR DELETE ON elementresult FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_elementresult (); DROP TABLE audit_element_relationship; CREATE TABLE audit_element_relationship ( element_relationship_id integer, subject_id integer, type_id integer, object_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_element_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_element_relationship() RETURNS trigger AS ' DECLARE element_relationship_id_var integer; subject_id_var integer; type_id_var integer; object_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN element_relationship_id_var = OLD.element_relationship_id; subject_id_var = OLD.subject_id; type_id_var = OLD.type_id; object_id_var = OLD.object_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_element_relationship ( element_relationship_id, subject_id, type_id, object_id, value, rank, transaction_type ) VALUES ( element_relationship_id_var, subject_id_var, type_id_var, object_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER element_relationship_audit_ud ON element_relationship; CREATE TRIGGER element_relationship_audit_ud BEFORE UPDATE OR DELETE ON element_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_element_relationship (); DROP TABLE audit_elementresult_relationship; CREATE TABLE audit_elementresult_relationship ( elementresult_relationship_id integer, subject_id integer, type_id integer, object_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_elementresult_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_elementresult_relationship() RETURNS trigger AS ' DECLARE elementresult_relationship_id_var integer; subject_id_var integer; type_id_var integer; object_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN elementresult_relationship_id_var = OLD.elementresult_relationship_id; subject_id_var = OLD.subject_id; type_id_var = OLD.type_id; object_id_var = OLD.object_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_elementresult_relationship ( elementresult_relationship_id, subject_id, type_id, object_id, value, rank, transaction_type ) VALUES ( elementresult_relationship_id_var, subject_id_var, type_id_var, object_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER elementresult_relationship_audit_ud ON elementresult_relationship; CREATE TRIGGER elementresult_relationship_audit_ud BEFORE UPDATE OR DELETE ON elementresult_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_elementresult_relationship (); DROP TABLE audit_study; CREATE TABLE audit_study ( study_id integer, contact_id integer, pub_id integer, dbxref_id integer, name text, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_study to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_study() RETURNS trigger AS ' DECLARE study_id_var integer; contact_id_var integer; pub_id_var integer; dbxref_id_var integer; name_var text; description_var text; transaction_type_var char; BEGIN study_id_var = OLD.study_id; contact_id_var = OLD.contact_id; pub_id_var = OLD.pub_id; dbxref_id_var = OLD.dbxref_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_study ( study_id, contact_id, pub_id, dbxref_id, name, description, transaction_type ) VALUES ( study_id_var, contact_id_var, pub_id_var, dbxref_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER study_audit_ud ON study; CREATE TRIGGER study_audit_ud BEFORE UPDATE OR DELETE ON study FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_study (); DROP TABLE audit_study_assay; CREATE TABLE audit_study_assay ( study_assay_id integer, study_id integer, assay_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_study_assay to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_study_assay() RETURNS trigger AS ' DECLARE study_assay_id_var integer; study_id_var integer; assay_id_var integer; transaction_type_var char; BEGIN study_assay_id_var = OLD.study_assay_id; study_id_var = OLD.study_id; assay_id_var = OLD.assay_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_study_assay ( study_assay_id, study_id, assay_id, transaction_type ) VALUES ( study_assay_id_var, study_id_var, assay_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER study_assay_audit_ud ON study_assay; CREATE TRIGGER study_assay_audit_ud BEFORE UPDATE OR DELETE ON study_assay FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_study_assay (); DROP TABLE audit_studydesign; CREATE TABLE audit_studydesign ( studydesign_id integer, study_id integer, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studydesign to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studydesign() RETURNS trigger AS ' DECLARE studydesign_id_var integer; study_id_var integer; description_var text; transaction_type_var char; BEGIN studydesign_id_var = OLD.studydesign_id; study_id_var = OLD.study_id; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studydesign ( studydesign_id, study_id, description, transaction_type ) VALUES ( studydesign_id_var, study_id_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studydesign_audit_ud ON studydesign; CREATE TRIGGER studydesign_audit_ud BEFORE UPDATE OR DELETE ON studydesign FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studydesign (); DROP TABLE audit_studydesignprop; CREATE TABLE audit_studydesignprop ( studydesignprop_id integer, studydesign_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studydesignprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studydesignprop() RETURNS trigger AS ' DECLARE studydesignprop_id_var integer; studydesign_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN studydesignprop_id_var = OLD.studydesignprop_id; studydesign_id_var = OLD.studydesign_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studydesignprop ( studydesignprop_id, studydesign_id, type_id, value, rank, transaction_type ) VALUES ( studydesignprop_id_var, studydesign_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studydesignprop_audit_ud ON studydesignprop; CREATE TRIGGER studydesignprop_audit_ud BEFORE UPDATE OR DELETE ON studydesignprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studydesignprop (); DROP TABLE audit_studyfactor; CREATE TABLE audit_studyfactor ( studyfactor_id integer, studydesign_id integer, type_id integer, name text, description text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studyfactor to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studyfactor() RETURNS trigger AS ' DECLARE studyfactor_id_var integer; studydesign_id_var integer; type_id_var integer; name_var text; description_var text; transaction_type_var char; BEGIN studyfactor_id_var = OLD.studyfactor_id; studydesign_id_var = OLD.studydesign_id; type_id_var = OLD.type_id; name_var = OLD.name; description_var = OLD.description; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studyfactor ( studyfactor_id, studydesign_id, type_id, name, description, transaction_type ) VALUES ( studyfactor_id_var, studydesign_id_var, type_id_var, name_var, description_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studyfactor_audit_ud ON studyfactor; CREATE TRIGGER studyfactor_audit_ud BEFORE UPDATE OR DELETE ON studyfactor FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studyfactor (); DROP TABLE audit_studyfactorvalue; CREATE TABLE audit_studyfactorvalue ( studyfactorvalue_id integer, studyfactor_id integer, assay_id integer, factorvalue text, name text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studyfactorvalue to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studyfactorvalue() RETURNS trigger AS ' DECLARE studyfactorvalue_id_var integer; studyfactor_id_var integer; assay_id_var integer; factorvalue_var text; name_var text; rank_var integer; transaction_type_var char; BEGIN studyfactorvalue_id_var = OLD.studyfactorvalue_id; studyfactor_id_var = OLD.studyfactor_id; assay_id_var = OLD.assay_id; factorvalue_var = OLD.factorvalue; name_var = OLD.name; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studyfactorvalue ( studyfactorvalue_id, studyfactor_id, assay_id, factorvalue, name, rank, transaction_type ) VALUES ( studyfactorvalue_id_var, studyfactor_id_var, assay_id_var, factorvalue_var, name_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studyfactorvalue_audit_ud ON studyfactorvalue; CREATE TRIGGER studyfactorvalue_audit_ud BEFORE UPDATE OR DELETE ON studyfactorvalue FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studyfactorvalue (); DROP TABLE audit_studyprop; CREATE TABLE audit_studyprop ( studyprop_id integer, study_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studyprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studyprop() RETURNS trigger AS ' DECLARE studyprop_id_var integer; study_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN studyprop_id_var = OLD.studyprop_id; study_id_var = OLD.study_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studyprop ( studyprop_id, study_id, type_id, value, rank, transaction_type ) VALUES ( studyprop_id_var, study_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studyprop_audit_ud ON studyprop; CREATE TRIGGER studyprop_audit_ud BEFORE UPDATE OR DELETE ON studyprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studyprop (); DROP TABLE audit_studyprop_feature; CREATE TABLE audit_studyprop_feature ( studyprop_feature_id integer, studyprop_id integer, feature_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_studyprop_feature to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_studyprop_feature() RETURNS trigger AS ' DECLARE studyprop_feature_id_var integer; studyprop_id_var integer; feature_id_var integer; type_id_var integer; transaction_type_var char; BEGIN studyprop_feature_id_var = OLD.studyprop_feature_id; studyprop_id_var = OLD.studyprop_id; feature_id_var = OLD.feature_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_studyprop_feature ( studyprop_feature_id, studyprop_id, feature_id, type_id, transaction_type ) VALUES ( studyprop_feature_id_var, studyprop_id_var, feature_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER studyprop_feature_audit_ud ON studyprop_feature; CREATE TRIGGER studyprop_feature_audit_ud BEFORE UPDATE OR DELETE ON studyprop_feature FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_studyprop_feature (); DROP TABLE audit_stock; CREATE TABLE audit_stock ( stock_id integer, dbxref_id integer, organism_id integer, name varchar(255), uniquename text, description text, type_id integer, is_obsolete boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock() RETURNS trigger AS ' DECLARE stock_id_var integer; dbxref_id_var integer; organism_id_var integer; name_var varchar(255); uniquename_var text; description_var text; type_id_var integer; is_obsolete_var boolean; transaction_type_var char; BEGIN stock_id_var = OLD.stock_id; dbxref_id_var = OLD.dbxref_id; organism_id_var = OLD.organism_id; name_var = OLD.name; uniquename_var = OLD.uniquename; description_var = OLD.description; type_id_var = OLD.type_id; is_obsolete_var = OLD.is_obsolete; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock ( stock_id, dbxref_id, organism_id, name, uniquename, description, type_id, is_obsolete, transaction_type ) VALUES ( stock_id_var, dbxref_id_var, organism_id_var, name_var, uniquename_var, description_var, type_id_var, is_obsolete_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_audit_ud ON stock; CREATE TRIGGER stock_audit_ud BEFORE UPDATE OR DELETE ON stock FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock (); DROP TABLE audit_stock_pub; CREATE TABLE audit_stock_pub ( stock_pub_id integer, stock_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_pub() RETURNS trigger AS ' DECLARE stock_pub_id_var integer; stock_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN stock_pub_id_var = OLD.stock_pub_id; stock_id_var = OLD.stock_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_pub ( stock_pub_id, stock_id, pub_id, transaction_type ) VALUES ( stock_pub_id_var, stock_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_pub_audit_ud ON stock_pub; CREATE TRIGGER stock_pub_audit_ud BEFORE UPDATE OR DELETE ON stock_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_pub (); DROP TABLE audit_stockprop; CREATE TABLE audit_stockprop ( stockprop_id integer, stock_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stockprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stockprop() RETURNS trigger AS ' DECLARE stockprop_id_var integer; stock_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN stockprop_id_var = OLD.stockprop_id; stock_id_var = OLD.stock_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stockprop ( stockprop_id, stock_id, type_id, value, rank, transaction_type ) VALUES ( stockprop_id_var, stock_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stockprop_audit_ud ON stockprop; CREATE TRIGGER stockprop_audit_ud BEFORE UPDATE OR DELETE ON stockprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stockprop (); DROP TABLE audit_stockprop_pub; CREATE TABLE audit_stockprop_pub ( stockprop_pub_id integer, stockprop_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stockprop_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stockprop_pub() RETURNS trigger AS ' DECLARE stockprop_pub_id_var integer; stockprop_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN stockprop_pub_id_var = OLD.stockprop_pub_id; stockprop_id_var = OLD.stockprop_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stockprop_pub ( stockprop_pub_id, stockprop_id, pub_id, transaction_type ) VALUES ( stockprop_pub_id_var, stockprop_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stockprop_pub_audit_ud ON stockprop_pub; CREATE TRIGGER stockprop_pub_audit_ud BEFORE UPDATE OR DELETE ON stockprop_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stockprop_pub (); DROP TABLE audit_stock_relationship; CREATE TABLE audit_stock_relationship ( stock_relationship_id integer, subject_id integer, object_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_relationship() RETURNS trigger AS ' DECLARE stock_relationship_id_var integer; subject_id_var integer; object_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN stock_relationship_id_var = OLD.stock_relationship_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_relationship ( stock_relationship_id, subject_id, object_id, type_id, value, rank, transaction_type ) VALUES ( stock_relationship_id_var, subject_id_var, object_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_relationship_audit_ud ON stock_relationship; CREATE TRIGGER stock_relationship_audit_ud BEFORE UPDATE OR DELETE ON stock_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_relationship (); DROP TABLE audit_stock_relationship_cvterm; CREATE TABLE audit_stock_relationship_cvterm ( stock_relationship_cvterm_id integer, stock_relationship_id integer, cvterm_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_relationship_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_relationship_cvterm() RETURNS trigger AS ' DECLARE stock_relationship_cvterm_id_var integer; stock_relationship_id_var integer; cvterm_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN stock_relationship_cvterm_id_var = OLD.stock_relationship_cvterm_id; stock_relationship_id_var = OLD.stock_relationship_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_relationship_cvterm ( stock_relationship_cvterm_id, stock_relationship_id, cvterm_id, pub_id, transaction_type ) VALUES ( stock_relationship_cvterm_id_var, stock_relationship_id_var, cvterm_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_relationship_cvterm_audit_ud ON stock_relationship_cvterm; CREATE TRIGGER stock_relationship_cvterm_audit_ud BEFORE UPDATE OR DELETE ON stock_relationship_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_relationship_cvterm (); DROP TABLE audit_stock_relationship_pub; CREATE TABLE audit_stock_relationship_pub ( stock_relationship_pub_id integer, stock_relationship_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_relationship_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_relationship_pub() RETURNS trigger AS ' DECLARE stock_relationship_pub_id_var integer; stock_relationship_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN stock_relationship_pub_id_var = OLD.stock_relationship_pub_id; stock_relationship_id_var = OLD.stock_relationship_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_relationship_pub ( stock_relationship_pub_id, stock_relationship_id, pub_id, transaction_type ) VALUES ( stock_relationship_pub_id_var, stock_relationship_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_relationship_pub_audit_ud ON stock_relationship_pub; CREATE TRIGGER stock_relationship_pub_audit_ud BEFORE UPDATE OR DELETE ON stock_relationship_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_relationship_pub (); DROP TABLE audit_stock_dbxref; CREATE TABLE audit_stock_dbxref ( stock_dbxref_id integer, stock_id integer, dbxref_id integer, is_current boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_dbxref() RETURNS trigger AS ' DECLARE stock_dbxref_id_var integer; stock_id_var integer; dbxref_id_var integer; is_current_var boolean; transaction_type_var char; BEGIN stock_dbxref_id_var = OLD.stock_dbxref_id; stock_id_var = OLD.stock_id; dbxref_id_var = OLD.dbxref_id; is_current_var = OLD.is_current; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_dbxref ( stock_dbxref_id, stock_id, dbxref_id, is_current, transaction_type ) VALUES ( stock_dbxref_id_var, stock_id_var, dbxref_id_var, is_current_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_dbxref_audit_ud ON stock_dbxref; CREATE TRIGGER stock_dbxref_audit_ud BEFORE UPDATE OR DELETE ON stock_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_dbxref (); DROP TABLE audit_stock_cvterm; CREATE TABLE audit_stock_cvterm ( stock_cvterm_id integer, stock_id integer, cvterm_id integer, pub_id integer, is_not boolean, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_cvterm() RETURNS trigger AS ' DECLARE stock_cvterm_id_var integer; stock_id_var integer; cvterm_id_var integer; pub_id_var integer; is_not_var boolean; rank_var integer; transaction_type_var char; BEGIN stock_cvterm_id_var = OLD.stock_cvterm_id; stock_id_var = OLD.stock_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; is_not_var = OLD.is_not; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_cvterm ( stock_cvterm_id, stock_id, cvterm_id, pub_id, is_not, rank, transaction_type ) VALUES ( stock_cvterm_id_var, stock_id_var, cvterm_id_var, pub_id_var, is_not_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_cvterm_audit_ud ON stock_cvterm; CREATE TRIGGER stock_cvterm_audit_ud BEFORE UPDATE OR DELETE ON stock_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_cvterm (); DROP TABLE audit_stock_cvtermprop; CREATE TABLE audit_stock_cvtermprop ( stock_cvtermprop_id integer, stock_cvterm_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_cvtermprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_cvtermprop() RETURNS trigger AS ' DECLARE stock_cvtermprop_id_var integer; stock_cvterm_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN stock_cvtermprop_id_var = OLD.stock_cvtermprop_id; stock_cvterm_id_var = OLD.stock_cvterm_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_cvtermprop ( stock_cvtermprop_id, stock_cvterm_id, type_id, value, rank, transaction_type ) VALUES ( stock_cvtermprop_id_var, stock_cvterm_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_cvtermprop_audit_ud ON stock_cvtermprop; CREATE TRIGGER stock_cvtermprop_audit_ud BEFORE UPDATE OR DELETE ON stock_cvtermprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_cvtermprop (); DROP TABLE audit_stock_genotype; CREATE TABLE audit_stock_genotype ( stock_genotype_id integer, stock_id integer, genotype_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_genotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_genotype() RETURNS trigger AS ' DECLARE stock_genotype_id_var integer; stock_id_var integer; genotype_id_var integer; transaction_type_var char; BEGIN stock_genotype_id_var = OLD.stock_genotype_id; stock_id_var = OLD.stock_id; genotype_id_var = OLD.genotype_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_genotype ( stock_genotype_id, stock_id, genotype_id, transaction_type ) VALUES ( stock_genotype_id_var, stock_id_var, genotype_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_genotype_audit_ud ON stock_genotype; CREATE TRIGGER stock_genotype_audit_ud BEFORE UPDATE OR DELETE ON stock_genotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_genotype (); DROP TABLE audit_stockcollection; CREATE TABLE audit_stockcollection ( stockcollection_id integer, type_id integer, contact_id integer, name varchar(255), uniquename text, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stockcollection to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stockcollection() RETURNS trigger AS ' DECLARE stockcollection_id_var integer; type_id_var integer; contact_id_var integer; name_var varchar(255); uniquename_var text; transaction_type_var char; BEGIN stockcollection_id_var = OLD.stockcollection_id; type_id_var = OLD.type_id; contact_id_var = OLD.contact_id; name_var = OLD.name; uniquename_var = OLD.uniquename; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stockcollection ( stockcollection_id, type_id, contact_id, name, uniquename, transaction_type ) VALUES ( stockcollection_id_var, type_id_var, contact_id_var, name_var, uniquename_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stockcollection_audit_ud ON stockcollection; CREATE TRIGGER stockcollection_audit_ud BEFORE UPDATE OR DELETE ON stockcollection FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stockcollection (); DROP TABLE audit_stockcollectionprop; CREATE TABLE audit_stockcollectionprop ( stockcollectionprop_id integer, stockcollection_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stockcollectionprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stockcollectionprop() RETURNS trigger AS ' DECLARE stockcollectionprop_id_var integer; stockcollection_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN stockcollectionprop_id_var = OLD.stockcollectionprop_id; stockcollection_id_var = OLD.stockcollection_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stockcollectionprop ( stockcollectionprop_id, stockcollection_id, type_id, value, rank, transaction_type ) VALUES ( stockcollectionprop_id_var, stockcollection_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stockcollectionprop_audit_ud ON stockcollectionprop; CREATE TRIGGER stockcollectionprop_audit_ud BEFORE UPDATE OR DELETE ON stockcollectionprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stockcollectionprop (); DROP TABLE audit_stockcollection_stock; CREATE TABLE audit_stockcollection_stock ( stockcollection_stock_id integer, stockcollection_id integer, stock_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stockcollection_stock to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stockcollection_stock() RETURNS trigger AS ' DECLARE stockcollection_stock_id_var integer; stockcollection_id_var integer; stock_id_var integer; transaction_type_var char; BEGIN stockcollection_stock_id_var = OLD.stockcollection_stock_id; stockcollection_id_var = OLD.stockcollection_id; stock_id_var = OLD.stock_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stockcollection_stock ( stockcollection_stock_id, stockcollection_id, stock_id, transaction_type ) VALUES ( stockcollection_stock_id_var, stockcollection_id_var, stock_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stockcollection_stock_audit_ud ON stockcollection_stock; CREATE TRIGGER stockcollection_stock_audit_ud BEFORE UPDATE OR DELETE ON stockcollection_stock FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stockcollection_stock (); DROP TABLE audit_stock_dbxrefprop; CREATE TABLE audit_stock_dbxrefprop ( stock_dbxrefprop_id integer, stock_dbxref_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_stock_dbxrefprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_stock_dbxrefprop() RETURNS trigger AS ' DECLARE stock_dbxrefprop_id_var integer; stock_dbxref_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN stock_dbxrefprop_id_var = OLD.stock_dbxrefprop_id; stock_dbxref_id_var = OLD.stock_dbxref_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_stock_dbxrefprop ( stock_dbxrefprop_id, stock_dbxref_id, type_id, value, rank, transaction_type ) VALUES ( stock_dbxrefprop_id_var, stock_dbxref_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER stock_dbxrefprop_audit_ud ON stock_dbxrefprop; CREATE TRIGGER stock_dbxrefprop_audit_ud BEFORE UPDATE OR DELETE ON stock_dbxrefprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_stock_dbxrefprop (); DROP TABLE audit_library; CREATE TABLE audit_library ( library_id integer, organism_id integer, name varchar(255), uniquename text, type_id integer, is_obsolete integer, timeaccessioned timestamp, timelastmodified timestamp, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library() RETURNS trigger AS ' DECLARE library_id_var integer; organism_id_var integer; name_var varchar(255); uniquename_var text; type_id_var integer; is_obsolete_var integer; timeaccessioned_var timestamp; timelastmodified_var timestamp; transaction_type_var char; BEGIN library_id_var = OLD.library_id; organism_id_var = OLD.organism_id; name_var = OLD.name; uniquename_var = OLD.uniquename; type_id_var = OLD.type_id; is_obsolete_var = OLD.is_obsolete; timeaccessioned_var = OLD.timeaccessioned; timelastmodified_var = OLD.timelastmodified; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library ( library_id, organism_id, name, uniquename, type_id, is_obsolete, timeaccessioned, timelastmodified, transaction_type ) VALUES ( library_id_var, organism_id_var, name_var, uniquename_var, type_id_var, is_obsolete_var, timeaccessioned_var, timelastmodified_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_audit_ud ON library; CREATE TRIGGER library_audit_ud BEFORE UPDATE OR DELETE ON library FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library (); DROP TABLE audit_library_synonym; CREATE TABLE audit_library_synonym ( library_synonym_id integer, synonym_id integer, library_id integer, pub_id integer, is_current boolean, is_internal boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library_synonym to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library_synonym() RETURNS trigger AS ' DECLARE library_synonym_id_var integer; synonym_id_var integer; library_id_var integer; pub_id_var integer; is_current_var boolean; is_internal_var boolean; transaction_type_var char; BEGIN library_synonym_id_var = OLD.library_synonym_id; synonym_id_var = OLD.synonym_id; library_id_var = OLD.library_id; pub_id_var = OLD.pub_id; is_current_var = OLD.is_current; is_internal_var = OLD.is_internal; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library_synonym ( library_synonym_id, synonym_id, library_id, pub_id, is_current, is_internal, transaction_type ) VALUES ( library_synonym_id_var, synonym_id_var, library_id_var, pub_id_var, is_current_var, is_internal_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_synonym_audit_ud ON library_synonym; CREATE TRIGGER library_synonym_audit_ud BEFORE UPDATE OR DELETE ON library_synonym FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library_synonym (); DROP TABLE audit_library_pub; CREATE TABLE audit_library_pub ( library_pub_id integer, library_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library_pub() RETURNS trigger AS ' DECLARE library_pub_id_var integer; library_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN library_pub_id_var = OLD.library_pub_id; library_id_var = OLD.library_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library_pub ( library_pub_id, library_id, pub_id, transaction_type ) VALUES ( library_pub_id_var, library_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_pub_audit_ud ON library_pub; CREATE TRIGGER library_pub_audit_ud BEFORE UPDATE OR DELETE ON library_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library_pub (); DROP TABLE audit_libraryprop; CREATE TABLE audit_libraryprop ( libraryprop_id integer, library_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_libraryprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_libraryprop() RETURNS trigger AS ' DECLARE libraryprop_id_var integer; library_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN libraryprop_id_var = OLD.libraryprop_id; library_id_var = OLD.library_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_libraryprop ( libraryprop_id, library_id, type_id, value, rank, transaction_type ) VALUES ( libraryprop_id_var, library_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER libraryprop_audit_ud ON libraryprop; CREATE TRIGGER libraryprop_audit_ud BEFORE UPDATE OR DELETE ON libraryprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_libraryprop (); DROP TABLE audit_libraryprop_pub; CREATE TABLE audit_libraryprop_pub ( libraryprop_pub_id integer, libraryprop_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_libraryprop_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_libraryprop_pub() RETURNS trigger AS ' DECLARE libraryprop_pub_id_var integer; libraryprop_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN libraryprop_pub_id_var = OLD.libraryprop_pub_id; libraryprop_id_var = OLD.libraryprop_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_libraryprop_pub ( libraryprop_pub_id, libraryprop_id, pub_id, transaction_type ) VALUES ( libraryprop_pub_id_var, libraryprop_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER libraryprop_pub_audit_ud ON libraryprop_pub; CREATE TRIGGER libraryprop_pub_audit_ud BEFORE UPDATE OR DELETE ON libraryprop_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_libraryprop_pub (); DROP TABLE audit_library_cvterm; CREATE TABLE audit_library_cvterm ( library_cvterm_id integer, library_id integer, cvterm_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library_cvterm() RETURNS trigger AS ' DECLARE library_cvterm_id_var integer; library_id_var integer; cvterm_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN library_cvterm_id_var = OLD.library_cvterm_id; library_id_var = OLD.library_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library_cvterm ( library_cvterm_id, library_id, cvterm_id, pub_id, transaction_type ) VALUES ( library_cvterm_id_var, library_id_var, cvterm_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_cvterm_audit_ud ON library_cvterm; CREATE TRIGGER library_cvterm_audit_ud BEFORE UPDATE OR DELETE ON library_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library_cvterm (); DROP TABLE audit_library_feature; CREATE TABLE audit_library_feature ( library_feature_id integer, library_id integer, feature_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library_feature to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library_feature() RETURNS trigger AS ' DECLARE library_feature_id_var integer; library_id_var integer; feature_id_var integer; transaction_type_var char; BEGIN library_feature_id_var = OLD.library_feature_id; library_id_var = OLD.library_id; feature_id_var = OLD.feature_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library_feature ( library_feature_id, library_id, feature_id, transaction_type ) VALUES ( library_feature_id_var, library_id_var, feature_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_feature_audit_ud ON library_feature; CREATE TRIGGER library_feature_audit_ud BEFORE UPDATE OR DELETE ON library_feature FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library_feature (); DROP TABLE audit_library_dbxref; CREATE TABLE audit_library_dbxref ( library_dbxref_id integer, library_id integer, dbxref_id integer, is_current boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_library_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_library_dbxref() RETURNS trigger AS ' DECLARE library_dbxref_id_var integer; library_id_var integer; dbxref_id_var integer; is_current_var boolean; transaction_type_var char; BEGIN library_dbxref_id_var = OLD.library_dbxref_id; library_id_var = OLD.library_id; dbxref_id_var = OLD.dbxref_id; is_current_var = OLD.is_current; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_library_dbxref ( library_dbxref_id, library_id, dbxref_id, is_current, transaction_type ) VALUES ( library_dbxref_id_var, library_id_var, dbxref_id_var, is_current_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER library_dbxref_audit_ud ON library_dbxref; CREATE TRIGGER library_dbxref_audit_ud BEFORE UPDATE OR DELETE ON library_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_library_dbxref (); DROP TABLE audit_cell_line; CREATE TABLE audit_cell_line ( cell_line_id integer, name varchar(255), uniquename varchar(255), organism_id integer, timeaccessioned timestamp, timelastmodified timestamp, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line() RETURNS trigger AS ' DECLARE cell_line_id_var integer; name_var varchar(255); uniquename_var varchar(255); organism_id_var integer; timeaccessioned_var timestamp; timelastmodified_var timestamp; transaction_type_var char; BEGIN cell_line_id_var = OLD.cell_line_id; name_var = OLD.name; uniquename_var = OLD.uniquename; organism_id_var = OLD.organism_id; timeaccessioned_var = OLD.timeaccessioned; timelastmodified_var = OLD.timelastmodified; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line ( cell_line_id, name, uniquename, organism_id, timeaccessioned, timelastmodified, transaction_type ) VALUES ( cell_line_id_var, name_var, uniquename_var, organism_id_var, timeaccessioned_var, timelastmodified_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_audit_ud ON cell_line; CREATE TRIGGER cell_line_audit_ud BEFORE UPDATE OR DELETE ON cell_line FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line (); DROP TABLE audit_cell_line_relationship; CREATE TABLE audit_cell_line_relationship ( cell_line_relationship_id integer, subject_id integer, object_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_relationship() RETURNS trigger AS ' DECLARE cell_line_relationship_id_var integer; subject_id_var integer; object_id_var integer; type_id_var integer; transaction_type_var char; BEGIN cell_line_relationship_id_var = OLD.cell_line_relationship_id; subject_id_var = OLD.subject_id; object_id_var = OLD.object_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_relationship ( cell_line_relationship_id, subject_id, object_id, type_id, transaction_type ) VALUES ( cell_line_relationship_id_var, subject_id_var, object_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_relationship_audit_ud ON cell_line_relationship; CREATE TRIGGER cell_line_relationship_audit_ud BEFORE UPDATE OR DELETE ON cell_line_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_relationship (); DROP TABLE audit_cell_line_synonym; CREATE TABLE audit_cell_line_synonym ( cell_line_synonym_id integer, cell_line_id integer, synonym_id integer, pub_id integer, is_current boolean, is_internal boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_synonym to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_synonym() RETURNS trigger AS ' DECLARE cell_line_synonym_id_var integer; cell_line_id_var integer; synonym_id_var integer; pub_id_var integer; is_current_var boolean; is_internal_var boolean; transaction_type_var char; BEGIN cell_line_synonym_id_var = OLD.cell_line_synonym_id; cell_line_id_var = OLD.cell_line_id; synonym_id_var = OLD.synonym_id; pub_id_var = OLD.pub_id; is_current_var = OLD.is_current; is_internal_var = OLD.is_internal; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_synonym ( cell_line_synonym_id, cell_line_id, synonym_id, pub_id, is_current, is_internal, transaction_type ) VALUES ( cell_line_synonym_id_var, cell_line_id_var, synonym_id_var, pub_id_var, is_current_var, is_internal_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_synonym_audit_ud ON cell_line_synonym; CREATE TRIGGER cell_line_synonym_audit_ud BEFORE UPDATE OR DELETE ON cell_line_synonym FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_synonym (); DROP TABLE audit_cell_line_cvterm; CREATE TABLE audit_cell_line_cvterm ( cell_line_cvterm_id integer, cell_line_id integer, cvterm_id integer, pub_id integer, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_cvterm to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_cvterm() RETURNS trigger AS ' DECLARE cell_line_cvterm_id_var integer; cell_line_id_var integer; cvterm_id_var integer; pub_id_var integer; rank_var integer; transaction_type_var char; BEGIN cell_line_cvterm_id_var = OLD.cell_line_cvterm_id; cell_line_id_var = OLD.cell_line_id; cvterm_id_var = OLD.cvterm_id; pub_id_var = OLD.pub_id; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_cvterm ( cell_line_cvterm_id, cell_line_id, cvterm_id, pub_id, rank, transaction_type ) VALUES ( cell_line_cvterm_id_var, cell_line_id_var, cvterm_id_var, pub_id_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_cvterm_audit_ud ON cell_line_cvterm; CREATE TRIGGER cell_line_cvterm_audit_ud BEFORE UPDATE OR DELETE ON cell_line_cvterm FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_cvterm (); DROP TABLE audit_cell_line_dbxref; CREATE TABLE audit_cell_line_dbxref ( cell_line_dbxref_id integer, cell_line_id integer, dbxref_id integer, is_current boolean, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_dbxref() RETURNS trigger AS ' DECLARE cell_line_dbxref_id_var integer; cell_line_id_var integer; dbxref_id_var integer; is_current_var boolean; transaction_type_var char; BEGIN cell_line_dbxref_id_var = OLD.cell_line_dbxref_id; cell_line_id_var = OLD.cell_line_id; dbxref_id_var = OLD.dbxref_id; is_current_var = OLD.is_current; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_dbxref ( cell_line_dbxref_id, cell_line_id, dbxref_id, is_current, transaction_type ) VALUES ( cell_line_dbxref_id_var, cell_line_id_var, dbxref_id_var, is_current_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_dbxref_audit_ud ON cell_line_dbxref; CREATE TRIGGER cell_line_dbxref_audit_ud BEFORE UPDATE OR DELETE ON cell_line_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_dbxref (); DROP TABLE audit_cell_lineprop; CREATE TABLE audit_cell_lineprop ( cell_lineprop_id integer, cell_line_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_lineprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_lineprop() RETURNS trigger AS ' DECLARE cell_lineprop_id_var integer; cell_line_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN cell_lineprop_id_var = OLD.cell_lineprop_id; cell_line_id_var = OLD.cell_line_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_lineprop ( cell_lineprop_id, cell_line_id, type_id, value, rank, transaction_type ) VALUES ( cell_lineprop_id_var, cell_line_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_lineprop_audit_ud ON cell_lineprop; CREATE TRIGGER cell_lineprop_audit_ud BEFORE UPDATE OR DELETE ON cell_lineprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_lineprop (); DROP TABLE audit_cell_lineprop_pub; CREATE TABLE audit_cell_lineprop_pub ( cell_lineprop_pub_id integer, cell_lineprop_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_lineprop_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_lineprop_pub() RETURNS trigger AS ' DECLARE cell_lineprop_pub_id_var integer; cell_lineprop_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN cell_lineprop_pub_id_var = OLD.cell_lineprop_pub_id; cell_lineprop_id_var = OLD.cell_lineprop_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_lineprop_pub ( cell_lineprop_pub_id, cell_lineprop_id, pub_id, transaction_type ) VALUES ( cell_lineprop_pub_id_var, cell_lineprop_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_lineprop_pub_audit_ud ON cell_lineprop_pub; CREATE TRIGGER cell_lineprop_pub_audit_ud BEFORE UPDATE OR DELETE ON cell_lineprop_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_lineprop_pub (); DROP TABLE audit_cell_line_feature; CREATE TABLE audit_cell_line_feature ( cell_line_feature_id integer, cell_line_id integer, feature_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_feature to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_feature() RETURNS trigger AS ' DECLARE cell_line_feature_id_var integer; cell_line_id_var integer; feature_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN cell_line_feature_id_var = OLD.cell_line_feature_id; cell_line_id_var = OLD.cell_line_id; feature_id_var = OLD.feature_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_feature ( cell_line_feature_id, cell_line_id, feature_id, pub_id, transaction_type ) VALUES ( cell_line_feature_id_var, cell_line_id_var, feature_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_feature_audit_ud ON cell_line_feature; CREATE TRIGGER cell_line_feature_audit_ud BEFORE UPDATE OR DELETE ON cell_line_feature FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_feature (); DROP TABLE audit_cell_line_cvtermprop; CREATE TABLE audit_cell_line_cvtermprop ( cell_line_cvtermprop_id integer, cell_line_cvterm_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_cvtermprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_cvtermprop() RETURNS trigger AS ' DECLARE cell_line_cvtermprop_id_var integer; cell_line_cvterm_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN cell_line_cvtermprop_id_var = OLD.cell_line_cvtermprop_id; cell_line_cvterm_id_var = OLD.cell_line_cvterm_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_cvtermprop ( cell_line_cvtermprop_id, cell_line_cvterm_id, type_id, value, rank, transaction_type ) VALUES ( cell_line_cvtermprop_id_var, cell_line_cvterm_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_cvtermprop_audit_ud ON cell_line_cvtermprop; CREATE TRIGGER cell_line_cvtermprop_audit_ud BEFORE UPDATE OR DELETE ON cell_line_cvtermprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_cvtermprop (); DROP TABLE audit_cell_line_pub; CREATE TABLE audit_cell_line_pub ( cell_line_pub_id integer, cell_line_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_pub() RETURNS trigger AS ' DECLARE cell_line_pub_id_var integer; cell_line_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN cell_line_pub_id_var = OLD.cell_line_pub_id; cell_line_id_var = OLD.cell_line_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_pub ( cell_line_pub_id, cell_line_id, pub_id, transaction_type ) VALUES ( cell_line_pub_id_var, cell_line_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_pub_audit_ud ON cell_line_pub; CREATE TRIGGER cell_line_pub_audit_ud BEFORE UPDATE OR DELETE ON cell_line_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_pub (); DROP TABLE audit_cell_line_library; CREATE TABLE audit_cell_line_library ( cell_line_library_id integer, cell_line_id integer, library_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_cell_line_library to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_cell_line_library() RETURNS trigger AS ' DECLARE cell_line_library_id_var integer; cell_line_id_var integer; library_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN cell_line_library_id_var = OLD.cell_line_library_id; cell_line_id_var = OLD.cell_line_id; library_id_var = OLD.library_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_cell_line_library ( cell_line_library_id, cell_line_id, library_id, pub_id, transaction_type ) VALUES ( cell_line_library_id_var, cell_line_id_var, library_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER cell_line_library_audit_ud ON cell_line_library; CREATE TRIGGER cell_line_library_audit_ud BEFORE UPDATE OR DELETE ON cell_line_library FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_cell_line_library (); DROP TABLE audit_nd_geolocation; CREATE TABLE audit_nd_geolocation ( nd_geolocation_id integer, description varchar(255), latitude real, longitude real, geodetic_datum varchar(32), altitude real, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_geolocation to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_geolocation() RETURNS trigger AS ' DECLARE nd_geolocation_id_var integer; description_var varchar(255); latitude_var real; longitude_var real; geodetic_datum_var varchar(32); altitude_var real; transaction_type_var char; BEGIN nd_geolocation_id_var = OLD.nd_geolocation_id; description_var = OLD.description; latitude_var = OLD.latitude; longitude_var = OLD.longitude; geodetic_datum_var = OLD.geodetic_datum; altitude_var = OLD.altitude; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_geolocation ( nd_geolocation_id, description, latitude, longitude, geodetic_datum, altitude, transaction_type ) VALUES ( nd_geolocation_id_var, description_var, latitude_var, longitude_var, geodetic_datum_var, altitude_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_geolocation_audit_ud ON nd_geolocation; CREATE TRIGGER nd_geolocation_audit_ud BEFORE UPDATE OR DELETE ON nd_geolocation FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_geolocation (); DROP TABLE audit_nd_experiment; CREATE TABLE audit_nd_experiment ( nd_experiment_id integer, nd_geolocation_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment() RETURNS trigger AS ' DECLARE nd_experiment_id_var integer; nd_geolocation_id_var integer; type_id_var integer; transaction_type_var char; BEGIN nd_experiment_id_var = OLD.nd_experiment_id; nd_geolocation_id_var = OLD.nd_geolocation_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment ( nd_experiment_id, nd_geolocation_id, type_id, transaction_type ) VALUES ( nd_experiment_id_var, nd_geolocation_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_audit_ud ON nd_experiment; CREATE TRIGGER nd_experiment_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment (); DROP TABLE audit_nd_experiment_project; CREATE TABLE audit_nd_experiment_project ( nd_experiment_project_id integer, project_id integer, nd_experiment_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_project to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_project() RETURNS trigger AS ' DECLARE nd_experiment_project_id_var integer; project_id_var integer; nd_experiment_id_var integer; transaction_type_var char; BEGIN nd_experiment_project_id_var = OLD.nd_experiment_project_id; project_id_var = OLD.project_id; nd_experiment_id_var = OLD.nd_experiment_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_project ( nd_experiment_project_id, project_id, nd_experiment_id, transaction_type ) VALUES ( nd_experiment_project_id_var, project_id_var, nd_experiment_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_project_audit_ud ON nd_experiment_project; CREATE TRIGGER nd_experiment_project_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_project FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_project (); DROP TABLE audit_nd_experimentprop; CREATE TABLE audit_nd_experimentprop ( nd_experimentprop_id integer, nd_experiment_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experimentprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experimentprop() RETURNS trigger AS ' DECLARE nd_experimentprop_id_var integer; nd_experiment_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN nd_experimentprop_id_var = OLD.nd_experimentprop_id; nd_experiment_id_var = OLD.nd_experiment_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experimentprop ( nd_experimentprop_id, nd_experiment_id, type_id, value, rank, transaction_type ) VALUES ( nd_experimentprop_id_var, nd_experiment_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experimentprop_audit_ud ON nd_experimentprop; CREATE TRIGGER nd_experimentprop_audit_ud BEFORE UPDATE OR DELETE ON nd_experimentprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experimentprop (); DROP TABLE audit_nd_experiment_pub; CREATE TABLE audit_nd_experiment_pub ( nd_experiment_pub_id integer, nd_experiment_id integer, pub_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_pub to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_pub() RETURNS trigger AS ' DECLARE nd_experiment_pub_id_var integer; nd_experiment_id_var integer; pub_id_var integer; transaction_type_var char; BEGIN nd_experiment_pub_id_var = OLD.nd_experiment_pub_id; nd_experiment_id_var = OLD.nd_experiment_id; pub_id_var = OLD.pub_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_pub ( nd_experiment_pub_id, nd_experiment_id, pub_id, transaction_type ) VALUES ( nd_experiment_pub_id_var, nd_experiment_id_var, pub_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_pub_audit_ud ON nd_experiment_pub; CREATE TRIGGER nd_experiment_pub_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_pub FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_pub (); DROP TABLE audit_nd_geolocationprop; CREATE TABLE audit_nd_geolocationprop ( nd_geolocationprop_id integer, nd_geolocation_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_geolocationprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_geolocationprop() RETURNS trigger AS ' DECLARE nd_geolocationprop_id_var integer; nd_geolocation_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN nd_geolocationprop_id_var = OLD.nd_geolocationprop_id; nd_geolocation_id_var = OLD.nd_geolocation_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_geolocationprop ( nd_geolocationprop_id, nd_geolocation_id, type_id, value, rank, transaction_type ) VALUES ( nd_geolocationprop_id_var, nd_geolocation_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_geolocationprop_audit_ud ON nd_geolocationprop; CREATE TRIGGER nd_geolocationprop_audit_ud BEFORE UPDATE OR DELETE ON nd_geolocationprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_geolocationprop (); DROP TABLE audit_nd_protocol; CREATE TABLE audit_nd_protocol ( nd_protocol_id integer, name varchar(255), type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_protocol to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_protocol() RETURNS trigger AS ' DECLARE nd_protocol_id_var integer; name_var varchar(255); type_id_var integer; transaction_type_var char; BEGIN nd_protocol_id_var = OLD.nd_protocol_id; name_var = OLD.name; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_protocol ( nd_protocol_id, name, type_id, transaction_type ) VALUES ( nd_protocol_id_var, name_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_protocol_audit_ud ON nd_protocol; CREATE TRIGGER nd_protocol_audit_ud BEFORE UPDATE OR DELETE ON nd_protocol FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_protocol (); DROP TABLE audit_nd_reagent; CREATE TABLE audit_nd_reagent ( nd_reagent_id integer, name varchar(80), type_id integer, feature_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_reagent to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_reagent() RETURNS trigger AS ' DECLARE nd_reagent_id_var integer; name_var varchar(80); type_id_var integer; feature_id_var integer; transaction_type_var char; BEGIN nd_reagent_id_var = OLD.nd_reagent_id; name_var = OLD.name; type_id_var = OLD.type_id; feature_id_var = OLD.feature_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_reagent ( nd_reagent_id, name, type_id, feature_id, transaction_type ) VALUES ( nd_reagent_id_var, name_var, type_id_var, feature_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_reagent_audit_ud ON nd_reagent; CREATE TRIGGER nd_reagent_audit_ud BEFORE UPDATE OR DELETE ON nd_reagent FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_reagent (); DROP TABLE audit_nd_protocol_reagent; CREATE TABLE audit_nd_protocol_reagent ( nd_protocol_reagent_id integer, nd_protocol_id integer, reagent_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_protocol_reagent to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_protocol_reagent() RETURNS trigger AS ' DECLARE nd_protocol_reagent_id_var integer; nd_protocol_id_var integer; reagent_id_var integer; type_id_var integer; transaction_type_var char; BEGIN nd_protocol_reagent_id_var = OLD.nd_protocol_reagent_id; nd_protocol_id_var = OLD.nd_protocol_id; reagent_id_var = OLD.reagent_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_protocol_reagent ( nd_protocol_reagent_id, nd_protocol_id, reagent_id, type_id, transaction_type ) VALUES ( nd_protocol_reagent_id_var, nd_protocol_id_var, reagent_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_protocol_reagent_audit_ud ON nd_protocol_reagent; CREATE TRIGGER nd_protocol_reagent_audit_ud BEFORE UPDATE OR DELETE ON nd_protocol_reagent FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_protocol_reagent (); DROP TABLE audit_nd_protocolprop; CREATE TABLE audit_nd_protocolprop ( nd_protocolprop_id integer, nd_protocol_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_protocolprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_protocolprop() RETURNS trigger AS ' DECLARE nd_protocolprop_id_var integer; nd_protocol_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN nd_protocolprop_id_var = OLD.nd_protocolprop_id; nd_protocol_id_var = OLD.nd_protocol_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_protocolprop ( nd_protocolprop_id, nd_protocol_id, type_id, value, rank, transaction_type ) VALUES ( nd_protocolprop_id_var, nd_protocol_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_protocolprop_audit_ud ON nd_protocolprop; CREATE TRIGGER nd_protocolprop_audit_ud BEFORE UPDATE OR DELETE ON nd_protocolprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_protocolprop (); DROP TABLE audit_nd_experiment_stock; CREATE TABLE audit_nd_experiment_stock ( nd_experiment_stock_id integer, nd_experiment_id integer, stock_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_stock to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_stock() RETURNS trigger AS ' DECLARE nd_experiment_stock_id_var integer; nd_experiment_id_var integer; stock_id_var integer; type_id_var integer; transaction_type_var char; BEGIN nd_experiment_stock_id_var = OLD.nd_experiment_stock_id; nd_experiment_id_var = OLD.nd_experiment_id; stock_id_var = OLD.stock_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_stock ( nd_experiment_stock_id, nd_experiment_id, stock_id, type_id, transaction_type ) VALUES ( nd_experiment_stock_id_var, nd_experiment_id_var, stock_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_stock_audit_ud ON nd_experiment_stock; CREATE TRIGGER nd_experiment_stock_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_stock FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_stock (); DROP TABLE audit_nd_experiment_protocol; CREATE TABLE audit_nd_experiment_protocol ( nd_experiment_protocol_id integer, nd_experiment_id integer, nd_protocol_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_protocol to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_protocol() RETURNS trigger AS ' DECLARE nd_experiment_protocol_id_var integer; nd_experiment_id_var integer; nd_protocol_id_var integer; transaction_type_var char; BEGIN nd_experiment_protocol_id_var = OLD.nd_experiment_protocol_id; nd_experiment_id_var = OLD.nd_experiment_id; nd_protocol_id_var = OLD.nd_protocol_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_protocol ( nd_experiment_protocol_id, nd_experiment_id, nd_protocol_id, transaction_type ) VALUES ( nd_experiment_protocol_id_var, nd_experiment_id_var, nd_protocol_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_protocol_audit_ud ON nd_experiment_protocol; CREATE TRIGGER nd_experiment_protocol_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_protocol FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_protocol (); DROP TABLE audit_nd_experiment_phenotype; CREATE TABLE audit_nd_experiment_phenotype ( nd_experiment_phenotype_id integer, nd_experiment_id integer, phenotype_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_phenotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_phenotype() RETURNS trigger AS ' DECLARE nd_experiment_phenotype_id_var integer; nd_experiment_id_var integer; phenotype_id_var integer; transaction_type_var char; BEGIN nd_experiment_phenotype_id_var = OLD.nd_experiment_phenotype_id; nd_experiment_id_var = OLD.nd_experiment_id; phenotype_id_var = OLD.phenotype_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_phenotype ( nd_experiment_phenotype_id, nd_experiment_id, phenotype_id, transaction_type ) VALUES ( nd_experiment_phenotype_id_var, nd_experiment_id_var, phenotype_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_phenotype_audit_ud ON nd_experiment_phenotype; CREATE TRIGGER nd_experiment_phenotype_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_phenotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_phenotype (); DROP TABLE audit_nd_experiment_genotype; CREATE TABLE audit_nd_experiment_genotype ( nd_experiment_genotype_id integer, nd_experiment_id integer, genotype_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_genotype to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_genotype() RETURNS trigger AS ' DECLARE nd_experiment_genotype_id_var integer; nd_experiment_id_var integer; genotype_id_var integer; transaction_type_var char; BEGIN nd_experiment_genotype_id_var = OLD.nd_experiment_genotype_id; nd_experiment_id_var = OLD.nd_experiment_id; genotype_id_var = OLD.genotype_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_genotype ( nd_experiment_genotype_id, nd_experiment_id, genotype_id, transaction_type ) VALUES ( nd_experiment_genotype_id_var, nd_experiment_id_var, genotype_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_genotype_audit_ud ON nd_experiment_genotype; CREATE TRIGGER nd_experiment_genotype_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_genotype FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_genotype (); DROP TABLE audit_nd_reagent_relationship; CREATE TABLE audit_nd_reagent_relationship ( nd_reagent_relationship_id integer, subject_reagent_id integer, object_reagent_id integer, type_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_reagent_relationship to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_reagent_relationship() RETURNS trigger AS ' DECLARE nd_reagent_relationship_id_var integer; subject_reagent_id_var integer; object_reagent_id_var integer; type_id_var integer; transaction_type_var char; BEGIN nd_reagent_relationship_id_var = OLD.nd_reagent_relationship_id; subject_reagent_id_var = OLD.subject_reagent_id; object_reagent_id_var = OLD.object_reagent_id; type_id_var = OLD.type_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_reagent_relationship ( nd_reagent_relationship_id, subject_reagent_id, object_reagent_id, type_id, transaction_type ) VALUES ( nd_reagent_relationship_id_var, subject_reagent_id_var, object_reagent_id_var, type_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_reagent_relationship_audit_ud ON nd_reagent_relationship; CREATE TRIGGER nd_reagent_relationship_audit_ud BEFORE UPDATE OR DELETE ON nd_reagent_relationship FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_reagent_relationship (); DROP TABLE audit_nd_reagentprop; CREATE TABLE audit_nd_reagentprop ( nd_reagentprop_id integer, nd_reagent_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_reagentprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_reagentprop() RETURNS trigger AS ' DECLARE nd_reagentprop_id_var integer; nd_reagent_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN nd_reagentprop_id_var = OLD.nd_reagentprop_id; nd_reagent_id_var = OLD.nd_reagent_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_reagentprop ( nd_reagentprop_id, nd_reagent_id, type_id, value, rank, transaction_type ) VALUES ( nd_reagentprop_id_var, nd_reagent_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_reagentprop_audit_ud ON nd_reagentprop; CREATE TRIGGER nd_reagentprop_audit_ud BEFORE UPDATE OR DELETE ON nd_reagentprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_reagentprop (); DROP TABLE audit_nd_experiment_stockprop; CREATE TABLE audit_nd_experiment_stockprop ( nd_experiment_stockprop_id integer, nd_experiment_stock_id integer, type_id integer, value text, rank integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_stockprop to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_stockprop() RETURNS trigger AS ' DECLARE nd_experiment_stockprop_id_var integer; nd_experiment_stock_id_var integer; type_id_var integer; value_var text; rank_var integer; transaction_type_var char; BEGIN nd_experiment_stockprop_id_var = OLD.nd_experiment_stockprop_id; nd_experiment_stock_id_var = OLD.nd_experiment_stock_id; type_id_var = OLD.type_id; value_var = OLD.value; rank_var = OLD.rank; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_stockprop ( nd_experiment_stockprop_id, nd_experiment_stock_id, type_id, value, rank, transaction_type ) VALUES ( nd_experiment_stockprop_id_var, nd_experiment_stock_id_var, type_id_var, value_var, rank_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_stockprop_audit_ud ON nd_experiment_stockprop; CREATE TRIGGER nd_experiment_stockprop_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_stockprop FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_stockprop (); DROP TABLE audit_nd_experiment_stock_dbxref; CREATE TABLE audit_nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id integer, nd_experiment_stock_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_stock_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_stock_dbxref() RETURNS trigger AS ' DECLARE nd_experiment_stock_dbxref_id_var integer; nd_experiment_stock_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN nd_experiment_stock_dbxref_id_var = OLD.nd_experiment_stock_dbxref_id; nd_experiment_stock_id_var = OLD.nd_experiment_stock_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_stock_dbxref ( nd_experiment_stock_dbxref_id, nd_experiment_stock_id, dbxref_id, transaction_type ) VALUES ( nd_experiment_stock_dbxref_id_var, nd_experiment_stock_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_stock_dbxref_audit_ud ON nd_experiment_stock_dbxref; CREATE TRIGGER nd_experiment_stock_dbxref_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_stock_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_stock_dbxref (); DROP TABLE audit_nd_experiment_dbxref; CREATE TABLE audit_nd_experiment_dbxref ( nd_experiment_dbxref_id integer, nd_experiment_id integer, dbxref_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_dbxref to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_dbxref() RETURNS trigger AS ' DECLARE nd_experiment_dbxref_id_var integer; nd_experiment_id_var integer; dbxref_id_var integer; transaction_type_var char; BEGIN nd_experiment_dbxref_id_var = OLD.nd_experiment_dbxref_id; nd_experiment_id_var = OLD.nd_experiment_id; dbxref_id_var = OLD.dbxref_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_dbxref ( nd_experiment_dbxref_id, nd_experiment_id, dbxref_id, transaction_type ) VALUES ( nd_experiment_dbxref_id_var, nd_experiment_id_var, dbxref_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_dbxref_audit_ud ON nd_experiment_dbxref; CREATE TRIGGER nd_experiment_dbxref_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_dbxref FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_dbxref (); DROP TABLE audit_nd_experiment_contact; CREATE TABLE audit_nd_experiment_contact ( nd_experiment_contact_id integer, nd_experiment_id integer, contact_id integer, transaction_date timestamp not null default now(), transaction_type char(1) not null ); GRANT ALL on audit_nd_experiment_contact to PUBLIC; CREATE OR REPLACE FUNCTION audit_update_delete_nd_experiment_contact() RETURNS trigger AS ' DECLARE nd_experiment_contact_id_var integer; nd_experiment_id_var integer; contact_id_var integer; transaction_type_var char; BEGIN nd_experiment_contact_id_var = OLD.nd_experiment_contact_id; nd_experiment_id_var = OLD.nd_experiment_id; contact_id_var = OLD.contact_id; IF TG_OP = ''DELETE'' THEN transaction_type_var = ''D''; ELSE transaction_type_var = ''U''; END IF; INSERT INTO audit_nd_experiment_contact ( nd_experiment_contact_id, nd_experiment_id, contact_id, transaction_type ) VALUES ( nd_experiment_contact_id_var, nd_experiment_id_var, contact_id_var, transaction_type_var ); IF TG_OP = ''DELETE'' THEN return OLD; ELSE return NEW; END IF; END ' LANGUAGE plpgsql; DROP TRIGGER nd_experiment_contact_audit_ud ON nd_experiment_contact; CREATE TRIGGER nd_experiment_contact_audit_ud BEFORE UPDATE OR DELETE ON nd_experiment_contact FOR EACH ROW EXECUTE PROCEDURE audit_update_delete_nd_experiment_contact (); chado-1.23/modules/audit/make_audit_ddl000755 000765 000024 00000004442 11723234350 020230 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # # make_audit_ddl # # Perl script reads idb ddl from cvs module directories and # for each table produces the corresponding audit table named # tablename_audit. # # columns of type 'serial' are changed to 'int' # primary key declarations are removed # foreign key declarations are removed # unique column declarations are removed # additional columns added to each table: # transaction_date timestamp not null # transaction_type char not null # all priveleges granted to public # # #---------------------------------------------------------------------------# #---------------------------------------------------------------------------# # ## General setup # $cvsdir = "/Users/emmert/cvs/scratch/idb/flydb/"; #$cvsdir = "../"; ## open the master module list $modlist = $cvsdir . "idb-full.modules"; open(mlist,$modlist); while () { chop($_) if $_ =~ /\n$/; ## now for each module open the .sql file for parsing $sqlfile = $cvsdir . $_; # print "\nopening $sqlfile...\n"; open(sfile,$sqlfile); ## for each table we add _audit to the table name, get rid of foreign ## keys, and set up grant statement. ## ## printing here is a little fiddly to handle correct placement of commas ## in create table statements... while () { if ( ($_ !~ /^#/) && ($_ !~ /^\s*$/) && ($_ !~ /foreign key/) && ($_ !~ /unique/) && ($_ !~ /primary key/) ) { chop($_) if $_ =~ /\n$/; chop($_) if $_ =~ /\,$/; $_ =~ s/serial/int/; if ($_ =~ /(^.*create table) (.*) \(/) { $tabst = 0; $_ = $1 . " " . $2 . "_audit ("; $tname = $2 . "_audit"; print "$_"; } elsif ($_ =~ /\)\;/) { print ",\n\ttransaction_date timestamp not null,"; print "\n\ttransaction_type char not null"; print "\n$_\n"; print "GRANT ALL on $tname to PUBLIC;\n\n"; } elsif ($tabst == 0) { print "\n$_"; $tabst++; } ## when create view statements appear we can assume that the create table ## statements are all handled... elsif ($_ =~ /create view/) { close(sfile); } else { if ($_ =~ /timeentered|timelastmod/) { $_ =~ s/ default current_timestamp//; } print ",\n$_"; $tabst++; } } } } chado-1.23/load/bin/000755 000765 000024 00000000000 12061672376 014273 5ustar00cainstaff000000 000000 chado-1.23/load/Build.PL000644 000765 000024 00000001127 11665754132 015020 0ustar00cainstaff000000 000000 use strict; use lib 'lib'; use Bio::Chado::Builder; use Data::Dumper; my $VERSION = 1.23; my $conf = shift; my $m = Bio::Chado::Builder->new( dist_name => 'Chado', dist_author => 'Allen Day', dist_abstract => 'Supplemental Build script for Chado--not stand alone', dist_version => $VERSION, load_conf => $conf, module_name => 'BioChado_supplemental', ); print "initializing load scripts...\n"; # populates tt2 templates specified in load.conf $m->dispatch('tokenize'); # can test by issuing a dispatch... #$m->dispatch('refseq'); $m->create_build_script; chado-1.23/load/etc/000755 000765 000024 00000000000 12061672376 014276 5ustar00cainstaff000000 000000 chado-1.23/load/tt2/000755 000765 000024 00000000000 12061672375 014233 5ustar00cainstaff000000 000000 chado-1.23/load/tt2/load.conf.tt2000644 000765 000024 00000011547 11636251222 016530 0ustar00cainstaff000000 000000 [% db_driver %] [% db_name %] [% db_username %] [% db_password %] [% db_host %] [% db_port %] [% db_organism %] [% working_dir %] [% external_ddl %] [% db_name %] [% FOREACH f=sql_files %][% f %] [% END %] chado-1.23/load/etc/chap.obo000644 000765 000024 00000041221 11256707606 015712 0ustar00cainstaff000000 000000 format-version: 1.2 date: 15:08:2007 20:40 saved-by: cjm auto-generated-by: OBO-Edit 2.000-beta11 subsetdef: camcur "camcur" default-namespace: pub remark: Chado provenance ontology. Derived from 'descriptor' branch of FBcv. DRAFT!! [Term] id: CHAP:0000001 name: death certificate namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000001 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000013 name: information entity namespace: FlyBase miscellaneous CV xref: FBcv:0000013 [Term] id: CHAP:0000015 name: postage stamp namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000015 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000140 name: FlyBase analysis namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000140 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000149 name: species list namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000149 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000151 name: archive namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000151 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000188 name: publication descriptor namespace: FlyBase miscellaneous CV xref: FBcv:0000188 is_obsolete: true [Term] id: CHAP:0000189 name: provenance namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000189 is_a: CHAP:0000013 ! information entity [Term] id: CHAP:0000190 name: abstract namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000190 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000191 name: advertisement namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000191 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000192 name: autobiography namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000192 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000193 name: bibliographic list namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000193 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000194 name: biography namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000194 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000195 name: book namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000195 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000196 name: booklet namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000196 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000197 name: book review namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000197 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000198 name: computer file namespace: pub comment: Proforma field: P1. subset: camcur synonym: "CD-ROM" RELATED [] xref: FBcv:0000198 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000199 name: conference report namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000199 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000200 name: demonstration namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000200 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000201 name: DNA/RNA sequence record namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000201 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000202 name: protein sequence record namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000202 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000203 name: erratum namespace: pub comment: Proforma field: P1. subset: camcur synonym: "correction" RELATED [] xref: FBcv:0000203 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000204 name: film namespace: pub comment: Proforma field: P1. subset: camcur synonym: "video" RELATED [] xref: FBcv:0000204 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000205 name: interview namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000205 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000206 name: jigsaw puzzle namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000206 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000207 name: letter namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000207 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000208 name: microscope slides namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000208 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000209 name: news article namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000209 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000210 name: note namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000210 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000211 name: obituary namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000211 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000212 name: paper namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000212 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000213 name: patent namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000213 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000214 name: personal communication to FlyBase namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000214 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000215 name: poem namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000215 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000216 name: poster namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000216 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000217 name: press release namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000217 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000218 name: recording namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000218 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000219 name: retraction namespace: pub comment: Proforma field: P1. subset: camcur synonym: "erratum" RELATED [] xref: FBcv:0000219 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000220 name: review namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000220 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000221 name: slides namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000221 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000222 name: spoof namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000222 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000223 name: stock list namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000223 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000224 name: supplementary material namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000224 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000225 name: T-shirt namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000225 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000226 name: tactile diagram namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000226 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000227 name: teaching note namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000227 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000228 name: thesis namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000228 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000229 name: curated genome annotation namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000229 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000230 name: automatic genome annotation namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000230 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000231 name: white paper namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000231 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000233 name: unpublished namespace: pub comment: Proforma field: P1. subset: camcur synonym: "privately distributed report" RELATED [] xref: FBcv:0000233 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000234 name: language namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000234 is_a: CHAP:0000013 ! information entity [Term] id: CHAP:0000235 name: Afrikaans namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000235 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000236 name: Arabic namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000236 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000237 name: Armenian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000237 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000238 name: Belarussian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur synonym: "Belarusian" RELATED [] xref: FBcv:0000238 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000239 name: Bulgarian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000239 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000240 name: Catalan namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000240 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000241 name: Chinese namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000241 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000242 name: Cumbrian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000242 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000243 name: Czech namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000243 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000244 name: Danish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000244 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000245 name: Dutch namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000245 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000246 name: English namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000246 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000247 name: Estonian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000247 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000248 name: Faroese namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000248 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000249 name: Farsi namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000249 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000250 name: Finnish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000250 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000251 name: Flemish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000251 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000252 name: French namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000252 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000253 name: German namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000253 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000254 name: Greek namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000254 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000255 name: Hebrew namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000255 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000256 name: Hungarian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000256 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000257 name: Icelandic namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000257 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000258 name: Indonesian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000258 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000259 name: Italian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000259 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000260 name: Japanese namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000260 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000261 name: Jugoslavian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000261 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000262 name: Korean namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000262 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000263 name: Latin namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000263 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000264 name: Latvian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000264 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000265 name: Lithuanian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000265 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000266 name: Malay namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000266 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000267 name: Malayalam namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000267 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000268 name: Norwegian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000268 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000269 name: Polish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000269 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000270 name: Portuguese namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000270 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000271 name: Serbo-Croat(Roman) namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000271 is_a: CHAP:0000274 ! Serbo-Croat [Term] id: CHAP:0000272 name: Romanian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000272 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000273 name: Russian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000273 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000274 name: Serbo-Croat namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000274 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000275 name: Slovak namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000275 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000276 name: Slovenian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000276 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000277 name: Spanish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000277 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000278 name: Swedish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000278 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000279 name: Turkish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000279 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000280 name: Ukrainian namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000280 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000281 name: Yiddish namespace: language comment: Proforma field: P13. Proforma field: P14. subset: camcur xref: FBcv:0000281 is_a: CHAP:0000234 ! language [Term] id: CHAP:0000650 name: editorial namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000650 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000651 name: meeting report namespace: pub comment: Proforma field: P1. subset: camcur xref: FBcv:0000651 is_a: CHAP:0000189 ! provenance [Term] id: CHAP:0000652 name: compendium namespace: pub subset: camcur xref: FBcv:0000652 is_a: CHAP:0000189 ! provenance chado-1.23/load/etc/extra.sql000644 000765 000024 00000002034 11256707606 016141 0ustar00cainstaff000000 000000 /* we need to have the ontologies loaded before we can do this. "make prepdb" now needs to come after "make ontologies" */ insert into cvterm_relationship (subject_id,object_id,type_id) values ( (select cvterm_id from cvterm where name = 'blood_cell' and cv_id = (select cv_id from cv where name = 'Cell Ontology')), (select cvterm_id from cvterm where name = 'blood' and cv_id = (select cv_id from cv where name = 'Mouse Adult Anatomy Ontology')), (select cvterm_id from cvterm where name = 'part_of' and cv_id = (select cv_id from cv where name = 'Relationship Ontology')) ); insert into cvterm_relationship (subject_id,object_id,type_id) values ( (select cvterm_id from cvterm where name = 'chondrocyte' and cv_id = (select cv_id from cv where name = 'Cell Ontology')), (select cvterm_id from cvterm where name = 'cartilage' and cv_id = (select cv_id from cv where name = 'Mouse Adult Anatomy Ontology')), (select cvterm_id from cvterm where name = 'part_of' and cv_id = (select cv_id from cv where name = 'Relationship Ontology')) ); chado-1.23/load/etc/feature_property.obo000644 000765 000024 00000027157 11256707606 020412 0ustar00cainstaff000000 000000 format-version: 1.2 date: 10:06:2005 15:07 saved-by: cjm default-namespace: unknown autogenerated-by: /Users/cjm/cvs/go-dev/go-perl/scripts/go2fmt.pl default-namespace: feature_property remark: Initially generated by Chris Mungall, sourced from FB and Rice chado. TODO: TIGR Chado; TODO: GFF3 subsetdef: fpo_sgd "SGD and related dbs subset" subsetdef: fpo_gff "GFF3 specific tags" subsetdef: fpo_apollo "properties with fixed semantics in apollo" [Typedef] id: SOFP:feature_property name: feature_property namespace: feature_property def: "A general purpose relation between a biological feature and some value" [so:cjm] [Typedef] id: SOFP:aminoacid name: aminoacid namespace: feature_property def: "amino acid coded for by a tRNA transcript feature" [so:cjm] is_a: SOFP:feature_property domain: SO:0000253 range: CHEBI:22477 [Typedef] id: SOFP:anticodon name: anticodon namespace: feature_property def: "anticodon coded for by a tRNA transcript feature" [so:cjm] is_a: SOFP:feature_property domain: SO:0000253 range: xsd:string range_def: "A 3 character string representing the anticodon using the IUPAC DNA Sequence alphabet; for example ATG. RNA seqs MUST be converted to DNA seqs" [] comments: Note the difference between GENBANK_SOFP:anticodon and SOFP:anticodon; the former includes the base range [Typedef] id: SOFP:citation name: citation namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 [Typedef] id: SOFP:comment name: comment namespace: feature_property def: "Annotation comments, from a human curator" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:cyto_range name: cyto_range namespace: feature_property def: "The cytological range covered by a feature. May be auto-generated from sequence coordinates, or determined by experimental methods" [so:cjm] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "Must conform to naming standard for that species; typically fly-style (eg 41A2-B3) or normal (eg 14p28.1-q32.2)" [so:cjm] comments: If auto-derived, may be redundant with feature location [Typedef] id: SOFP:description name: description namespace: feature_property def: "Free-text description of feature" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comments: Often sourced from fasta header, in which case it includes everything after the > symbol [Typedef] id: SOFP:dicistronic name: dicistronic namespace: feature_property def: "true if transcript codes for >1 non-overlapping CDSs" [] is_a: SOFP:feature_property domain: SO:0000115 ! transcript_feature range: xsd:boolean comments: redundant with secondary classification term SO:0000079 [Typedef] id: SOFP:element name: element namespace: feature_property def: "name of transposable element class" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: in chado or gff, this may also be indicated by a reference to a class in an ontology of TE classes [Typedef] id: SOFP:encoded_symbol name: encoded_symbol namespace: feature_property def: "dicistronic CDS/proteins are attached to a single gene feature representing the whole cassette - in which case the symbol refers to the cassette. encoded_symbol refers to a gene in the sense of non-overlapping CDS set. cf Adh and Adhr in dmel" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:evidenceGB name: evidenceGB namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "'experimental'" comment: same as GENBANK_SOFP:experimental?? [Typedef] id: SOFP:linked_to name: linked_to namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: someone please define.. to do with restriction fragments? [Typedef] id: SOFP:missing_start_codon name: missing_start_codon namespace: feature_property def: "true if start of CDS is unknown" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:boolean comment: in chado, redundant with featureloc.is_{fmin,fmax}_partial [Typedef] id: SOFP:missing_stop_codon name: missing_stop_codon namespace: feature_property def: "true if end of CDS is unknown" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:boolean comment: in chado, redundant with featureloc.is_{fmin,fmax}_partial [Typedef] id: SOFP:na_change name: na_change namespace: feature_property def: "A nucleic acid modification in some variant feature relative to the reference sequence" [] is_a: SOFP:feature_property domain: SO:0000109 ! sequence_variant range: xsd:string range_def: "" comment: in chado, this is redundant with featureloc.residue_info[rank=0,1] [Typedef] id: SOFP:non_canonical_start_codon name: non_canonical_start_codon namespace: feature_property def: "The sequence of the biological start codon" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "3-character DNA sequence, must be different from ATG" [] [Typedef] id: SOFP:owner name: owner namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:pr_change name: pr_change namespace: feature_property def: "An amino acid modification in some variant feature relative to the reference sequence" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: ". @ represents stop codon" comment: see also: na_change; in chado, this is redundant with featureloc.residue_info[rank=0,1] [Typedef] id: SOFP:problem name: problem namespace: feature_property def: "True if the annotation for this feature is problematic in some way; more details can be found in the comments property" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:boolean [Typedef] id: SOFP:readthrough_stop_codon name: readthrough_stop_codon namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:boolean [Typedef] id: SOFP:reported_na_change name: reported_na_change namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "As for na_change, suffixed with |" [] [Typedef] id: SOFP:reported_pr_change name: reported_pr_change namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "As for pr_change, suffixed with |" [] [Typedef] id: SOFP:sp_comment name: sp_comment namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: is this deprecated? originally sourced from gadfly pep validation pipeline - of little interest to others than flybase [Typedef] id: SOFP:sp_status name: sp_status namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: is this deprecated? originally sourced from gadfly pep validation pipeline - of little interest to others than flybase [Typedef] id: SOFP:status name: status namespace: feature_property def: "Annotation workflow status" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "'not done'" [Typedef] id: SOFP:source name: source namespace: feature_property def: "Source from which feature originates - may be a computer program or analysis, or a group. Corresponds to GFF column 2" [] subset: fpo_gff is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:symbol name: symbol namespace: feature_property def: "Community symbol" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:validation_flag name: validation_flag namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "TODO: define the list of allowed values in an ontology" [] [Typedef] id: SOFP:synonym name: synonym exact_synonym: "Alias" [] namespace: feature_property def: "Historic community symbol, may have originally been symbol" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: In chado, this is redundant with the synonym table. GFF3 uses the tag "Alias" [Typedef] id: SOFP:date name: date namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:date comment: date of what?? Annotation?? [Typedef] id: SOFP:internal_synonym name: internal_synonym namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: FB specific? [Typedef] id: SOFP:qseq_type name: qseq_type namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: deprecated? [Typedef] id: SOFP:unixdate name: unixdate namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:integer range_def: "No of seconds since unix time zero, 1 Jan 1970" [] comment: date of what?? Annotation?? [Typedef] id: SOFP:gbunit name: gbunit namespace: feature_property def: "Name of genbank scaffold sequence intersected by the feature" [] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: " - taken from NCBI/EMBL/DDBJ" [] [Typedef] id: SOFP:keywords name: keywords namespace: feature_property is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:orf_classification name: orf_classification namespace: feature_property def: "gene call confidence flag" subset: fpo_sgd is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: "'Dubious'|'Uncharacterized'|'Verified'" [] comment: Currently only used by SGD [Typedef] id: SOFP:ontology_term name: ontology_term namespace: feature_property def: "A term from some ontology classifying the feature" [] subset: fpo_gff is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string range_def: " of a term in some ontology" [] comment: In chado, this is redundant with the feature_cvterm table [Typedef] id: SOFP:protein_id name: protein_id namespace: feature_property def: "A protein sequence identifier" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: Should really be a dbxref [so:sjc] [Typedef] id: SOFP:organism name: organism namespace: feature_property def: "The name of the organism" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: In chado, this is redundant with the organism table [so:sjc] [Typedef] id: SOFP:mol_type name: mol_type namespace: feature_property def: "The type of molecule" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: Presumably, this could be inferred from the SO type [so:sjc] [Typedef] id: SOFP:dev_stage name: dev_stage namespace: feature_property def: "Stage of development" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:chromosome name: chromosome namespace: feature_property def: "Name of chromosome the feature occurs on(?)" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string comment: What is this for? [so:sjc] [Typedef] id: SOFP:map name: map namespace: feature_property def: "A map location" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:finished name: finished namespace: feature_property def: "If the annotation of the feature is complete" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:boolean [Typedef] id: SOFP:Note name: Note namespace: feature_property def: "A GFF3 Note attribute" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:Gap name: Gap namespace: feature_property def: "A GFF3 Gap cigar string" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string [Typedef] id: SOFP:score name: score namespace: feature_property def: "A GFF3 score" [so:sjc] is_a: SOFP:feature_property domain: SO:0000110 range: xsd:string chado-1.23/load/etc/genbank_feature_property.obo000644 000765 000024 00000077740 11256707606 022102 0ustar00cainstaff000000 000000 format-version: 1.2 date: 24:05:2005 17:23 saved-by: cjm auto-generated-by: DAG-Edit 1.419 rev 3 default-namespace: feature_property remark: cvs version: $Revision: 1.1 $ remark: converted by Chris Mungall; source: http://www.ncbi.nlm.nih.gov/collab/FT [Typedef] id: GENBANK_SOFP:allele name: allele is_a: SOFP:feature_property domain: SO:000110 def: "name of the allele for the given gene " [] range: xsd:string comment: all gene-related features (exon, CDS etc) for a given gene should share the same /allele qualifier value; the /allele qualifier value must, by definition, be different from the /gene qualifier value; when used with the variation feature key, the allele qualifier value should be that of the variant. [Typedef] id: GENBANK_SOFP:anticodon name: genbank:anticodon is_a: SOFP:feature_property domain: SO:000110 def: "location of the anticodon of tRNA and the amino acid for which it codes" [] range: xsd:string range_def: "(pos:,aa:) where base_range is the position of the anticodon and amino_acid is the abbreviation for the amino acid encoded" [] comments: Note the difference between GENBANK_SOFP:anticodon and SOFP:anticodon; the former includes the base range [Typedef] id: GENBANK_SOFP:bound_moiety name: bound_moiety is_a: SOFP:feature_property domain: SO:000110 def: "name of the molecule/complex that may bind to the given feature " [] range: xsd:string comment: Multiple /bound_moiety qualifiers are legal on 'promoter' and 'enhancer' features. A single /bound_moiety qualifier is legal on the 'misc_binding', 'oriT' and 'protein_bind' features. [Typedef] id: GENBANK_SOFP:cell_line name: cell_line is_a: SOFP:feature_property domain: SO:000110 def: "cell line from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:cell_type name: cell_type is_a: SOFP:feature_property domain: SO:000110 def: "cell type from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:chromosome name: chromosome is_a: SOFP:feature_property domain: SO:000110 def: "chromosome (e.g. Chromosome number) from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:citation name: citation is_a: SOFP:feature_property domain: SO:000110 def: "reference to a citation listed in the entry reference field" [] range: xsd:integer range_def: "[integer-number] where integer-number is the number of the reference as enumerated in the reference field" [] comment: used to indicate the citation providing the claim of and/or evidence for a feature; brackets are used for conformity. [Typedef] id: GENBANK_SOFP:clone name: clone is_a: SOFP:feature_property domain: SO:000110 def: "clone from which the sequence was obtained" [] range: xsd:string comment: not more than one clone should be specified for a given source feature; to indicate that the sequence was obtained from multiple clones, multiple source features should be given. [Typedef] id: GENBANK_SOFP:clone_lib name: clone_lib is_a: SOFP:feature_property domain: SO:000110 def: "clone library from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:codon name: codon is_a: SOFP:feature_property domain: SO:000110 def: "specifies a codon which is different from any found in the reference genetic code" [] range: xsd:string range_def: "(seq:'codon-sequence',aa:) where 'codon-sequence' contains the bases of the codon and is the abbreviation for the translated amino acid, the abbreviation for a modified unusual amino_acids from section 7.5, or the word OTHER" [] comment: used to specify unusual genetic codes, organellar codes, etc, that are different from the 'normal' code for the organism; the codon specified by 'seq' codes for the amino acid or stop codon specified by 'aa'; the codon that is specified is used throughout the CDS; amino acids that are not on the controlled vocabulary list can be annotated by using 'aa:OTHER' as the amino acid designation, and by giving the name of the residue in a /note qualifier; only nucleotides a, g, c or t can be used in 'codon-sequence'; multiple /codon qualifiers should be used to describe ambiguous nucleotides. [Typedef] id: GENBANK_SOFP:codon_start name: codon_start is_a: SOFP:feature_property domain: SO:000110 def: "indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature." [] range: xsd:integer range_def: "1 or 2 or 3" [] [Typedef] id: GENBANK_SOFP:compare name: compare is_a: SOFP:feature_property domain: SO:000110 def: "Reference details of an existing public INSD entry to which a comparison is made" [] range: xsd:string comment: This qualifier may be used on the following features: misc_difference, conflict, unsure, old_sequence and variation. The features 'old_sequence' and 'conflict' must have either a /citation or a /compare qualifier. Multiple /compare qualifiers with different contents are allowed within a single feature. This qualifier is not intended for large-scale annotation of variations, such as SNPs. [Typedef] id: GENBANK_SOFP:cons_splice name: cons_splice is_a: SOFP:feature_property domain: SO:000110 def: "differentiates between intron splice sites that conform to the 5'-GT ... AG-3' splice site consensus" [] range: xsd:string range_def: "(5'site:, 3'site:), where can be 'YES', 'NO' or 'ABSENT'" [] /cons_splice=(5'site:ABSENT, 3'site:NO) comment: since the vast majority of splice sites conform to the consensus, this qualifier should be used only when one does not and the sequence has been checked; 'ABSENT' can be used when one of the termini is not part of the sequence and information on splice site is not available. [Typedef] id: GENBANK_SOFP:country name: country is_a: SOFP:feature_property domain: SO:000110 def: "Geographical origin of sequenced sample, intended for epidemiological or population studies." [] range: xsd:string range_def: "'[:][, ]' where country_value is any value from the controlled vocabulary at URL:http://www.ncbi.nlm.nih.gov/projects/collab/country.html " [] /country='France:Cote d'Azur, Antibes' /country='Atlantic Ocean:Charlie Gibbs Fracture Zone' comment: Intended to provide a reference to the site where the source organism was isolated or sampled. Regions and localities should be indicated where possible. Note that the physical geography of the isolation or sampling site should be represented in /isolation_source. [Typedef] id: GENBANK_SOFP:cultivar name: cultivar is_a: SOFP:feature_property domain: SO:000110 def: "cultivar (cultivated variety) of plant from which sequence was obtained. " [] range: xsd:string /cultivar='Tenuifolius' /cultivar='Candy Cane' /cultivar='IR36' comment: 'cultivar' is applied solely to products of artificial selection; use the variety qualifier for natural, named plant and fungal varieties; [Typedef] id: GENBANK_SOFP:db_xref name: db_xref is_a: SOFP:feature_property domain: SO:000110 def: "database cross-reference: pointer to related information in another database." [] range: xsd:string range_def: "':' where database is the name of the database containing related information, and identifier is the internal identifier of the related information according to the naming conventions of the cross-referenced database." [] comment: the complete list of allowed database types is kept on NCBI's public WWW server, at URL: http://www.ncbi.nlm.nih.gov/projects/collab/ [Typedef] id: GENBANK_SOFP:dev_stage name: dev_stage is_a: SOFP:feature_property domain: SO:000110 def: "if the sequence was obtained from an organism in a specific developmental stage, it is specified with this qualifier" [] range: xsd:string [Typedef] id: GENBANK_SOFP:direction name: direction is_a: SOFP:feature_property domain: SO:000110 def: "direction of DNA replication" [] range: xsd:string range_def: "left, right, or both where left indicates toward the 5' end of the entry sequence (as presented) and right indicates toward the 3' end" [] [Typedef] id: GENBANK_SOFP:EC_number name: EC_number is_a: SOFP:feature_property domain: SO:000110 def: "Enzyme Commission number for enzyme product of sequence" [] range: xsd:string comment: valid values for EC numbers are defined in the list prepared by the IUPAC-IUB Commission on Biochemical Enzyme Nomenclature (published in Enzyme Nomenclature 1984 New York: Academic Press (1984) or a more recent revision thereof). [Typedef] id: GENBANK_SOFP:ecotype name: ecotype is_a: SOFP:feature_property domain: SO:000110 def: "a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat." [] comment: an example of such a population is one that has adapted hairier than normal leaves as a response to an especially sunny habitat. 'Ecotype' is often applied to standard genetic stocks of Arabidopsis thaliana, but it can be applied to any sessile organism. [Typedef] id: GENBANK_SOFP:environmental_sample name: environmental_sample is_a: SOFP:feature_property domain: SO:000110 def: "identifies sequences derived by direct molecular isolation (PCR, DGGE, or other anonymous methods) from an environmental sample with no reliable identification of the source organism" [] range: xsd:boolean comment: used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. [Typedef] id: GENBANK_SOFP:estimated_length name: estimated_length is_a: SOFP:feature_property domain: SO:000110 def: "estimated length of the gap in the sequence" [] range: xsd:string range_def: "unknown or " [] /estimated_length=342 [Typedef] id: GENBANK_SOFP:evidence name: evidence is_a: SOFP:feature_property domain: SO:000110 def: "value indicating the nature of supporting evidence, distinguishing between experimentally determined and theoretically derived data" [] range: xsd:string range_def: "experimental, not_experimental" [] comment: experimental indicates that the feature identification or assignment is supported by direct experimental evidence; not_experimental indicates that the data for the feature are derived (eg promotor as identified by consensus match). [Typedef] id: GENBANK_SOFP:exception name: exception is_a: SOFP:feature_property domain: SO:000110 def: "indicates that the amino acid or RNA sequence will not translate or agree with the DNA sequence according to standard biological rules." [] range: xsd:string /exception='reasons given in citation' comment: only to be used to describe biological mechanisms such as RNA editing; where the exception cannot easily be described a published citation must be referred to; protein translation of /exception CDS will be different from the according conceptual translation; - must not be used where transl_except would be adequate, e.g. in case of stop codon completion use: /transl_except=(pos:6883,aa:TERM) /note='TAA stop codon is completed by addition of 3' A residues to mRNA'. - must not be used for ribosomal slippage, instead use join operator, e.g.: CDS join(486..1784,1787..4810) /note='ribosomal slip on tttt sequence at 1784..1787' [Typedef] id: GENBANK_SOFP:focus name: focus is_a: SOFP:feature_property domain: SO:000110 def: "defines the source feature of primary biological interest for records that have multiple source features originating from different organisms " [] range: xsd:boolean comment: the /focus qualifier identifies the organism which is displayed in the organism line and determines the DDBJ/EMBL/GenBank taxonomic division the entry will appear in; if no translation table is specified, the organism with /focus will define the translation table; within an entry with several source features, only one will exist with /focus on it; multi-source entries with a /transgenic source feature do not require a /focus qualifier. [Typedef] id: GENBANK_SOFP:frequency name: frequency is_a: SOFP:feature_property domain: SO:000110 def: "frequency of the occurrence of a feature" [] range: xsd:string range_def: "text representing the fraction of population carrying the variation expressed as a decimal fraction" [] [Typedef] id: GENBANK_SOFP:function name: function is_a: SOFP:feature_property domain: SO:000110 def: "function attributed to a sequence" [] range: xsd:string comment: /function is used when the gene name and/or product name do not convey the function attributable to a sequence. [Typedef] id: GENBANK_SOFP:gene name: gene is_a: SOFP:feature_property domain: SO:000110 def: "symbol of the gene corresponding to a sequence region" [] range: xsd:string [Typedef] id: GENBANK_SOFP:germline name: germline is_a: SOFP:feature_property domain: SO:000110 def: "if the sequence shown is DNA and a member of the immunoglobulin family, this qualifier is used to denote that the sequence is from unrearranged DNA. " [] range: xsd:boolean comment: /germline cannot be used in the same entry/record as /rearranged [Typedef] id: GENBANK_SOFP:haplotype name: haplotype is_a: SOFP:feature_property domain: SO:000110 def: "haplotype of organism from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:insertion_seq name: insertion_seq is_a: SOFP:feature_property domain: SO:000110 def: "insertion sequence element from which the sequence was obtained" [] range: xsd:string comment: /insertion_seq is legal on repeat_region feature key; [Typedef] id: GENBANK_SOFP:isolate name: isolate is_a: SOFP:feature_property domain: SO:000110 def: "individual isolate from which the sequence was obtained" [] range: xsd:string /isolate='DGGE band PSBAC-13' [Typedef] id: GENBANK_SOFP:isolation_source name: isolation_source is_a: SOFP:feature_property domain: SO:000110 def: "describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived" [] range: xsd:string Pelleted ration-fed steer #67' /isolation_source='permanent Antarctic sea ice' /isolation_source='denitrifying activated sludge from carbon_limited continuous reactor' comment: used only with the source feature key; source feature keys containing an /environmental_sample qualifier should also contain an /isolation_source qualifier; the /country qualifier should be used to describe the country and major geographical sub-region. [Typedef] id: GENBANK_SOFP:label name: label is_a: SOFP:feature_property domain: SO:000110 def: "a label used to permanently tag a feature" [] range: xsd:string range_def: "feature_label " [] comment: feature labels follow the naming conventions for all feature table objects (see Sections 3.1 and 3.4) [Typedef] id: GENBANK_SOFP:lab_host name: lab_host is_a: SOFP:feature_property domain: SO:000110 def: "laboratory host used to propagate the organism from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:locus_tag name: locus_tag is_a: SOFP:feature_property domain: SO:000110 def: "feature tag assigned for tracking purposes " [] but not '<1-5 letters><5-9 digit integer>[.]' /locus_tag='YPO0002' comment: /locus_tag can be used with any feature where /gene is valid; identical /locus_tag values may be used within an entry/record, but only if the identical /locus_tag values are associated with the same gene; in all other circumstances the /locus_tag value must be unique within that entry/record. Multiple /locus_tag values are not allowed within one feature for entries created after 15-OCT-2004. If a /locus_tag needs to be re-assigned the /old_locus_tag qualifier should be used to store the old value. Existing records where multiple /locus_tag qualifiers are present will be retrofitted by January 2005. The /locus_tag value should not be in a format which resembles INSD accession numbers, accession.version, or /proteid_id identifiers. [Typedef] id: GENBANK_SOFP:map name: map is_a: SOFP:feature_property domain: SO:000110 def: "genomic map position of feature" [] range: xsd:string [Typedef] id: GENBANK_SOFP:macronuclear name: macronuclear is_a: SOFP:feature_property domain: SO:000110 def: "if the sequence shown is DNA and from an organism which undergoes chromosomal differentiation between macronuclear and micronuclear stages, this qualifier is used to denote that the sequence is from macronuclear DNA. " [] range: xsd:boolean [Typedef] id: GENBANK_SOFP:mod_base name: mod_base is_a: SOFP:feature_property domain: SO:000110 def: "abbreviation for a modified nucleotide base" [] range: xsd:string comment: modified nucleotides not found in the restricted vocabulary list can be annotated by entering '/mod_base=OTHER' with '/note='name of modified base'' [Typedef] id: GENBANK_SOFP:mol_type name: mol_type is_a: SOFP:feature_property domain: SO:000110 def: "in vivo molecule type of sequence " [] range: xsd:string range_def: "'genomic DNA', 'genomic RNA', 'mRNA', 'tRNA', 'rRNA', 'snoRNA', 'snRNA', 'scRNA', 'pre-RNA', 'other RNA', 'other DNA', 'unassigned DNA', 'unassigned RNA'" [] comment: these text values describe the in vivo molecule that has been sequenced and not the sequencing technique that has been used (e.g. mRNA is a valid value, cDNA is not); the value 'genomic DNA' does not imply that the molecule is nuclear (e.g. organelle and plasmid DNA should be described using 'genomic DNA'); ribosomal RNA genes should be described using 'genomic DNA'; 'rRNA' should only be used if the ribosomal RNA molecule itself has been sequenced; /mol_type is mandatory on every source feature key; all /mol_type values within one entry/record must be the same; values 'other RNA' and 'other DNA' should be applied to synthetic molecules, values 'unassigned DNA', 'unassigned RNA' should be applied were in vivo molecule is unknown; [Typedef] id: GENBANK_SOFP:note name: note is_a: SOFP:feature_property domain: SO:000110 def: "any comment or additional information" [] range: xsd:string [Typedef] id: GENBANK_SOFP:number name: number is_a: SOFP:feature_property domain: SO:000110 def: "a number to indicate the order of genetic elements (e.g., exons or introns) in the 5' to 3' direction" [] range: xsd:string range_def: "unquoted text (single token) " [] /number=6B comment: text limited to integers, letters or combination of integers and/or letters represented as an unquoted single token (e.g. 5a, XIIb); any additional terms should be included in /standard_name. Example: /number=2A /standard_name='long' [Typedef] id: GENBANK_SOFP:old_locus_tag name: old_locus_tag is_a: SOFP:feature_property domain: SO:000110 def: "feature tag assigned for tracking purposes " [] /locus_tag='YPO0002' comment: /old_locus_tag can be used with any feature where /gene is valid and where a /locus_tag qualifier is present. Identical /old_locus_tag values may be used within an entry/record, but only if the identical /old_locus_tag values are associated with the same gene; in all other circumstances the /old_locus_tag value must be unique within that entry/record. Multiple/old_locus_tag qualifiers with distinct values are allowed within a single feature; /old_locus_tag and /locus_tag values must not be identical within a single feature. [Typedef] id: GENBANK_SOFP:operon name: operon is_a: SOFP:feature_property domain: SO:000110 def: "name of the operon the feature belongs to" [] range: xsd:string comment: currently valid only on Prokaryota-specific features [Typedef] id: GENBANK_SOFP:organelle name: organelle is_a: SOFP:feature_property domain: SO:000110 def: "type of membrane-bound intracellular structure from which the sequence was obtained" [] range: xsd:string range_def: "mitochondrion, nucleomorph, plastid, mitochondrion:kinetoplast, plastid:chloroplast, plastid:apicoplast, plastid:chromoplast, plastid:cyanelle, plastid:leucoplast, plastid:proplastid," [] /organelle='nucleomorph' /organelle='plastid' /organelle='mitochondrion:kinetoplast' /organelle='plastid:chloroplast' /organelle='plastid:apicoplast' /organelle='plastid:chromoplast' /organelle='plastid:cyanelle' /organelle='plastid:leucoplast' /organelle='plastid:proplastid' [Typedef] id: GENBANK_SOFP:organism name: organism is_a: SOFP:feature_property domain: SO:000110 def: "scientific name of the organism that provided the sequenced genetic material. " [] range: xsd:string comment: the organism name which appears on the OS or ORGANISM line will match the value of the /organism qualifier of the source key in the simplest case of a one-source sequence. NOTE: in chado, this is redundant with the organism table [Typedef] id: GENBANK_SOFP:partial name: partial is_a: SOFP:feature_property domain: SO:000110 def: "differentiates between complete regions and partial ones" [] range: xsd:boolean comment: not to be used for new entries from 15-DEC-2001; use '<' and '>' signs in the location descriptors to indicate that the sequence is partial. [Typedef] id: GENBANK_SOFP:PCR_conditions name: PCR_conditions is_a: SOFP:feature_property domain: SO:000110 def: "description of reaction conditions and components for PCR " [] range: xsd:string range_def: "'text' " [] comment: used with primer_bind key [Typedef] id: GENBANK_SOFP:phenotype name: phenotype is_a: SOFP:feature_property domain: SO:000110 def: "phenotype conferred by the feature" [] range: xsd:string [Typedef] id: GENBANK_SOFP:pop_variant name: pop_variant is_a: SOFP:feature_property domain: SO:000110 def: "population variant from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:plasmid name: plasmid is_a: SOFP:feature_property domain: SO:000110 def: "name of plasmid from which sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:product name: product is_a: SOFP:feature_property domain: SO:000110 def: "name of a product encoded by a sequence" [] range: xsd:string [Typedef] id: GENBANK_SOFP:protein_id name: protein_id is_a: SOFP:feature_property domain: SO:000110 def: "protein identifier, issued by International collaborators. this qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point." [] range: xsd:string comment: when the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. [Typedef] id: GENBANK_SOFP:proviral name: proviral is_a: SOFP:feature_property domain: SO:000110 def: "if the sequence shown is viral and integrated into another organism's genome, this qualifier is used to denote that " [] range: xsd:boolean comment: /proviral cannot be used in the same entry/record as /virion [Typedef] id: GENBANK_SOFP:pseudo name: pseudo is_a: SOFP:feature_property domain: SO:000110 def: "indicates that this feature is a non-functional version of the element named by the feature key" [] range: xsd:boolean [Typedef] id: GENBANK_SOFP:rearranged name: rearranged is_a: SOFP:feature_property domain: SO:000110 def: "if the sequence shown is DNA and a member of the immunoglobulin family, this qualifier is used to denote that the sequence is from rearranged DNA. " [] range: xsd:boolean comment: /rearranged cannot be used in the same entry/record as /germline [Typedef] id: GENBANK_SOFP:replace name: replace is_a: SOFP:feature_property domain: SO:000110 def: "indicates that the sequence identified a feature's intervals is replaced by the sequence shown in 'text'; if no sequence is contained within the qualifier, this indicates a deletion." [] range: xsd:string /replace='' [Typedef] id: GENBANK_SOFP:rpt_family name: rpt_family is_a: SOFP:feature_property domain: SO:000110 def: "type of repeated sequence; 'Alu' or 'Kpn', for example" [] range: xsd:string comment: preferred usage is to qualify the repeat_region instead of any of the constituent repeat_units [Typedef] id: GENBANK_SOFP:rpt_type name: rpt_type is_a: SOFP:feature_property domain: SO:000110 def: "organization of repeated sequence" [] range: xsd:string range_def: "tandem, inverted, flanking, terminal, direct, dispersed, and other" [] comment: preferred usage is to qualify the repeat_region instead of any of the constituent repeat_units. definitions of these values will be added in a future release of this document. see Singer, M. Int Rev Cytol 76, 67-112 (1982); Cell 26, 293-95 (1981); Hardman, N. Biochem J 234, 1-11 (1986). [Typedef] id: GENBANK_SOFP:rpt_unit name: rpt_unit is_a: SOFP:feature_property domain: SO:000110 def: "identity of repeat unit" [] range: xsd:string range_def: "'text' or " [] /rpt_unit=202..245 comment: used to indicate the literal sequence, or the base range of the sequence that constitutes a repeat_region or a single repeat_unit; the repeat family name should not be entered in /rpt_unit='text'; /rpt_family should be used instead. [Typedef] id: GENBANK_SOFP:segment name: segment is_a: SOFP:feature_property domain: SO:000110 def: "name of viral or phage segment sequenced" [] range: xsd:string [Typedef] id: GENBANK_SOFP:serotype name: serotype is_a: SOFP:feature_property domain: SO:000110 def: "serological variety of a species characterized by its antigenic properties" [] range: xsd:string comment: used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for the prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B 'Infraspecific Terms'. [Typedef] id: GENBANK_SOFP:serovar name: serovar is_a: SOFP:feature_property domain: SO:000110 def: "serological variety of a species (usually a prokaryote) characterized by its antigenic properties" [] range: xsd:string comment: used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B 'Infraspecific Terms'. [Typedef] id: GENBANK_SOFP:sex name: sex is_a: SOFP:feature_property domain: SO:000110 def: "sex of the organism from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:specific_host name: specific_host is_a: SOFP:feature_property domain: SO:000110 def: "natural host from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:specimen_voucher name: specimen_voucher is_a: SOFP:feature_property domain: SO:000110 def: "an identifier of the individual or collection of the source organism and the place where it is currently stored, usually an institution." [] range: xsd:string Herbarium)' [Typedef] id: GENBANK_SOFP:standard_name name: standard_name is_a: SOFP:feature_property domain: SO:000110 def: "accepted standard name for this feature" [] range: xsd:string comment: use /standard_name to give full gene name, but use /gene to give gene symbol (in the above example /gene='Dt'). [Typedef] id: GENBANK_SOFP:strain name: strain is_a: SOFP:feature_property domain: SO:000110 def: "strain from which sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:sub_clone name: sub_clone is_a: SOFP:feature_property domain: SO:000110 def: "sub-clone from which sequence was obtained" [] range: xsd:string comment: the comments on /clone apply to /sub_clone [Typedef] id: GENBANK_SOFP:sub_species name: sub_species is_a: SOFP:feature_property domain: SO:000110 def: "name of sub-species of organism from which sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:sub_strain name: sub_strain is_a: SOFP:feature_property domain: SO:000110 def: "sub_strain from which sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:tissue_lib name: tissue_lib is_a: SOFP:feature_property domain: SO:000110 def: "tissue library from which sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:tissue_type name: tissue_type is_a: SOFP:feature_property domain: SO:000110 def: "tissue type from which the sequence was obtained" [] range: xsd:string [Typedef] id: GENBANK_SOFP:transgenic name: transgenic is_a: SOFP:feature_property domain: SO:000110 def: "identifies the source feature of the organism which was the recipient of transgenic DNA" [] range: xsd:boolean comment: transgenic sequences must at least have two source feature keys; the source feature key describing the organism of the recipient DNA must span the whole sequence; the /transgenic qualifier identifies the organism which is displayed in the organism line and determines that the entry will appear in the DDBJ/EMBL/GenBank Synthetic Construct division; multi-source entries including a /transgenic source feature should not have a /focus qualifier. [Typedef] id: GENBANK_SOFP:translation name: translation is_a: SOFP:feature_property domain: SO:000110 def: "automatically generated one-letter abbreviated amino acid sequence derived from either the universal genetic code or the table as specified in /transl_table and as determined by exceptions in the /transl_except and /codon qualifiers" [] range: xsd:string range_def: "IUPAC one-letter amino acid abbreviation, 'X' is to be used for AA exceptions." [] comment: to be used with CDS feature only; this is a mandatory qualifier to the CDS feature key except for /pseudo CDSs; see /transl_table for definition and location of genetic code Tables. [Typedef] id: GENBANK_SOFP:transl_except name: transl_except is_a: SOFP:feature_property domain: SO:000110 def: "translational exception: single codon the translation of which does not conform to genetic code defined by Organism and /codon=" [] range: xsd:string range_def: "(pos:location,aa:) where amino_acid is the amino acid coded by the codon at the base_range position" [] /transl_except=(pos:1017,aa:TERM) /transl_except=(pos:2000..2001,aa:TERM) /transl_except=(pos:X22222:15..17,aa:Ala) comment: if the amino acid is not on the restricted vocabulary list use e.g., '/transl_except=(pos:213..215,aa:OTHER)' with '/note='name of unusual amino acid''; for modified amino-acid selenocysteine use three letter code 'Sec' (one letter code 'U' in amino-acid sequence) /transl_except=(pos:1002..1004,aa:Sec); for partial termination codons where TAA stop codon is completed by the addition of 3' A residues to the mRNA either a single base_position or a base_range is used, e.g. if partial stop codon is a single base: /transl_except=(pos:1017,aa:TERM) if partial stop codon consists of two bases: /transl_except=(pos:2000..2001,aa:TERM) with '/note='stop codon completed by the addition of 3' A residues to the mRNA'. [Typedef] id: GENBANK_SOFP:transl_table name: transl_table is_a: SOFP:feature_property domain: SO:000110 def: "definition of genetic code table used if other than universal genetic code table. Tables used are described in appendix V, section 7.5.5." [] range: xsd:integer range_def: ") { next if /^\#/; chomp; $OPTIONS{$1} = $2 if /^(\w+)\s*=\s*(.+)/; } close F; } open OUT,">$file" or die "Can't create $file: $!"; print OUT "$Config{startperl}\n"; if ($OPTIONS{LIB}) { print OUT "use lib '$OPTIONS{LIB}';\n"; } if ($OPTIONS{PREFIX}) { print OUT "use lib '$OPTIONS{PREFIX}/lib';\n"; } print OUT <<'!NO!SUBS!'; use strict; use warnings; #use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; use Bio::FeatureIO; use Bio::SeqIO; use Getopt::Long; use Data::Dumper; use Pod::Usage; use URI::Escape; use Carp; use Bio::GMOD::DB::Adapter; use ExtUtils::MakeMaker; #to get prompt use Module::Load; =head1 NAME $0 - Bulk loads gff3 files into a chado database. =head1 SYNOPSIS % $0 [options] % cat | $0 [options] =head1 OPTIONS --gfffile The file containing GFF3 (optional, can read from stdin) --fastafile Fasta file to load sequence from --organism The organism for the data (use the value 'fromdata' to read from GFF organism=xxx) --dbprofile Database config profile name --dbname Database name --dbuser Database user name --dbpass Database password --dbhost Database host --dbport Database port --analysis The GFF data is from computational analysis --noload Create bulk load files, but don't actually load them. --nosequence Don't load sequence even if it is in the file --notransact Don't use a single transaction to load the database --drop_indexes Drop indexes of affected tables before starting load and recreate after load is finished; generally does not help performance. --validate Validate SOFA terms before attempting insert (can cause script startup to be slow, off by default) --ontology Give directions for handling misc Ontology_terms --skip_vacuum Skip vacuuming the tables after the inserts (default) --no_skip_vaccum Don't skip vacuuming the tables --inserts Print INSERT statements instead of COPY FROM STDIN --noexon Don't convert CDS features to exons (but still create polypeptide features) --recreate_cache Causes the uniquename cache to be recreated --remove_lock Remove the lock to allow a new process to run --save_tmpfiles Save the temp files used for loading the database --random_tmp_dir Use a randomly generated tmp dir (the default is to use the current directory) --no_target_syn By default, the loader adds the targetId in the synonyms list of the feature. This flag desactivate this. --unique_target Trust the unicity of the target IDs. IDs are case sensitive. By default, the uniquename of a new target will be 'TargetId_PrimaryKey'. With this flag, it will be 'TargetId'. Furthermore, the Name of the created target will be its TargetId, instead of the feature's Name. --dbxref Use either the first Dbxref annotation as the primary dbxref (that goes into feature.dbxref_id), or if an optional argument is supplied, the first dbxref that has a database part (ie, before the ':') that matches the supplied pattern is used. --delete Instead of inserting features into the database, use the GFF lines to delete features as though the CRUD=delete-all option were set on all lines (see 'Deletes and updates via GFF below'). The loader will ask for confirmation before continuing. --delete_i_really_mean_it Works like --delete except that it does not ask for confirmation. --fp_cv Name of the feature property controlled vocabulary (defaults to 'feature_property'). --noaddfpcv By default, the loader adds GFF attribute types as new feature_property cv terms when missing. This flag deactivates it. ** dgg note: should rename this flag: --[no]autoupdate for Chado tables cvterm, cv, db, organism, analysis ... --manual Detailed manual pages --custom_adapter Use a custom subclass adaptor for Bio::GMOD::DB::Adapter Provide the path to the adapter as an argument --private_schema Load the data into a non-public schema. --use_public_cv When loading into a non-public schema, load any cv and cvterm data into the public schema --end_sql SQL code to execute after the data load is complete --allow_external_parent Allow Parent tags to refer to IDs outside the current GFF file Note that all of the arguments that begin 'db' as well as organism can be provided by default by Bio::GMOD::Config, which was installed when 'make install' was run. Also note the the option dbprofile and all other db* options are mutually exclusive--if you supply dbprofile, do not supply any other db* options, as they will not be used. =head1 DESCRIPTION The GFF in the datafile must be version 3 due to its tighter control of the specification and use of controlled vocabulary. Accordingly, the names of feature types must be exactly those in the Sequence Ontology Feature Annotation (SOFA), not the synonyms and not the accession numbers (SO accession numbers may be supported in future versions of this script). Note that the ##sequence-region directive is not supported as a way of declaring a reference sequence for a GFF3 file. The ##sequence-region directive is not expressive enough to define what type of thing the sequence is (ie, is it a chromosome, a contig, an arm, etc?). If your GFF file uses a ##sequence-region directive in this way, you must convert it to a full GFF3 line. For example, if you have this line: ##sequence-region chrI 1 9999999 Then is should be converted to a GFF3 line like this: chrI . chromosome 1 9999999 . . . ID=chrI =head2 How GFF3 is stored in chado Here is summary of how GFF3 data is stored in chado: =over =item Column 1 (reference sequence) The reference sequence for the feature becomes the srcfeature_id of the feature in the featureloc table for that feature. That featureloc generally assigned a rank of zero if there are other locations associated with this feature (for instance, for a match feature), the other locations will be assigned featureloc.rank values greater than zero. =item Column 2 (source) The source is stored as a dbxref. The chado instance must of an entry in the db table named 'GFF_source'. The script will then create a dbxref entry for the feature's source and associate it to the feature via the feature_dbxref table. =item Column 3 (type) The cvterm.cvterm_id of the SOFA type is stored in feature.type_id. =item Column 4 (start) The value of start minus 1 is stored in featureloc.fmin (one is subtracted because chado uses interbase coordinates, whereas GFF uses base coordinates). =item Column 5 (end) The value of end is stored in featureloc.fmax. =item Column 6 (score) The score is stored in one of the score columns in the analysisfeature table. The default is analysisfeature.significance. See the section below on analysis results for more information. =item Column 7 (strand) The strand is stored in featureloc.strand. =item Column 8 (phase) The phase is stored in featureloc.phase. Note that there is currently a problem with the chado schema for the case of single exons having different phases in different transcripts. If your data has just such a case, complain to gmod-schema@lists.sourceforge.net to find ways to address this problem. =item Column 9 (group) Here is where the magic happens. =over =item Assigning feature.name, feature.uniquename The values of feature.name and feature.uniquename are assigned according to these simple rules: =over =item If there is an ID tag, that is used as feature.uniquename otherwise, it is assigned a uniquename that is equal to 'auto' concatenated with the feature_id. =item If there is a Name tag, it's value is set to feature.name; otherwise it is null. Note that these rules are much more simple than that those that Bio::DB::GFF uses, and may need to be revisited. =back =item Assigning feature_relationship entries All Parent tagged features are assigned feature_relationship entries of 'part_of' to their parent features. Derived_from tags are assigned 'derived_from' relationships. Note that parent features must appear in the file before any features use a Parent or Derived_from tags referring to that feature. =item Alias tags Alias values are stored in the synonym table, under both synonym.name and synonym.synonym_sgml, and are linked to the feature via the feature_synonym table. =item Dbxref tags Dbxref values must be of the form 'db_name:accession', where db_name must have an entry in the db table, with a value of db.name equal to 'DB:db_name'; several database names were preinstalled with the database when 'make prepdb' was run. Execute 'SELECT name FROM db' to find out what databases are already availble. New dbxref entries are created in the dbxref table, and dbxrefs are linked to features via the feature_dbxref table. =item Gap tags Currently is mostly ignored--the value is stored as a featureprop, but otherwise is not used yet. =item Note tags The values are stored as featureprop entries for the feature. =item Any custom (ie, lowercase-first) tags Custom tags are supported. If the tag doesn't already exist in the cvterm table, it will be created. The value will stored with its associated cvterm in the featureprop table. =item Ontology_term When the Ontology_term tags are used, items from the Gene Ontology and Sequence Ontology will be processed automatically when the standard DB:accession format is used (e.g. GO:0001234). To use other ontology terms, you must specify that mapping of the DB indentifiers in the GFF file and the name of the ontologies in the cv table as a comma separated tag=value pairs. For example, to use plant and cell ontology terms, you would supply on the command line: --ontology 'PO=plant ontology,CL=cell ontology' where 'plant ontology' and 'cell ontology' are the names in the cv table exactly as they appear. =item Target tags Proper processing of Target tags requires that there be two source features already available in the database, the 'primary' source feature (the chromosome or contig) and the 'subject' from the similarity analysis, like an EST, cDNA or syntenic chromosome. If the subject feature is not present, the loader will attempt to create a placeholder feature object in its place. If you have a fasta file the contains the subject, you can use the perl script, L, that comes with this distribution to make a GFF3 file suitable for loading into chado before loading your analysis results. =item CDS and UTR features The way CDS features are represented in Chado is as an intersection of a transcript's exons and the transcripts polypeptide feature. To allow proper translation of a GFF3 file's CDS features, this loader will convert CDS and UTR feature lines to corresponding exon features (and add a featureprop note that the exon was inferred from a GFF3 CDS and/or UTR line), and create a polypeptide feature that spans the genomic region from the start of translation to the stop. If your GFF3 file contains both exon and CDS/UTR features, then you will want to suppress the creation of the exon features and instead will only want a polypeptide feature to be created. To do this, use the --noexon option. In this case, the CDS and UTR features will still be converted to exon features as described above. Note that in the case where your GFF file contains CDS and/or UTR features that do not belong to 'central dogma' genes (that is, that have a gene, transcript and CDS/exon features), none of the above will happen and the features will be stored as is. =back =back =head2 NOTES =over =item Loading fasta file When the --fastafile is provided with an argument that is the path to a file containing fasta sequence, the loader will attempt to update the feature table with the sequence provided. Note that the ID provided in the fasta description line must exactly match what is in the feature table uniquename field. Be careful if it is possible that the uniquename of the feature was changed to ensure uniqueness when it was loaded from the original GFF. Also note that when loading sequence from a fasta file, loading GFF from standard in is disabled. Sorry for any inconvenience. =item ##sequence-region This script does not use sequence-region directives for anything. If it represents a feature that needs to be inserted into the database, it should be represented with a full GFF line. This includes the reference sequence for the features if it is not already in the database, like a chromosome. For example, this: ##sequence-region chr1 1 213456789 should change to this: chr1 UCSC chromosome 1 213456789 . . . ID=chr1 =item Transactions This application will, by default, try to load all of the data at once as a single transcation. This is safer from the database's point of view, since if anything bad happens during the load, the transaction will be rolled back and the database will be untouched. The problem occurs if there are many (say, greater than a 2-300,000) rows in the GFF file. When that is the case, doing the load as a single transcation can result in the machine running out of memory and killing processes. If --notranscat is provided on the commandline, each table will be loaded as a separate transaction. =item SQL INSERTs versus COPY FROM This bulk loader was originally designed to use the PostgreSQL COPY FROM syntax for bulk loading of data. However, as mentioned in the 'Transactions' section, memory issues can sometimes interfere with such bulk loads. In another effort to circumvent this issue, the bulk loader has been modified to optionally create INSERT statements instead of the COPY FROM statements. INSERT statements will load much more slowly than COPY FROM statements, but as they load and commit individually, they are more more likely to complete successfully. As an indication of the speed differences involved, loading yeast GFF3 annotations (about 16K rows), it takes about 5 times longer using INSERTs versus COPY on my laptop. =item Deletes and updates via GFF There is rudimentary support for modifying the features in an existing database via GFF. Currently, there is only support for deleting. In order to delete, the GFF line must have a custom tag in the ninth column, 'CRUD' (for Create, Replace, Update and Delete) and have a recognized value. Currently the two recognized values are CRUD=delete and CRUD=delete-all. IMPORTANT NOTE: Using the delete operations have the potential of creating orphan features (eg, exons whose gene has been deleted). You should be careful to make sure that doesn't happen. Included in this distribution is a PostgreSQL trigger (written in plpgsql) that will delete all orphan children recursively, so if a gene is deleted, all transcripts, exons and polypeptides that belong to that gene will be deleted too. See the file modules/sequence/functions/delete-trigger.plpgsql for more information. =over =item delete The delete option will delete one and only one feature for which the name, type and organism match what is in the GFF line with what is in the database. Note that feature.uniquename are not considered, nor are the coordinates presented in the GFF file. This is so that updates via GFF can be done on the coordinants. If there is more than one feature for which the name, type and organism match, the loader will print an error message and stop. If there are no features that match the name, type and organism, the loader will print a warning message and continue. =item delete-all The delete-all option works similarly to the delete option, except that it will delete all features that match the name, type and organism in the GFF line (as opposed to allowing only one feature to be deleted). If there are no features that match, the loader will print a warning message and continue. =back =item The run lock The bulk loader is not a multiuser application. If two separate bulk load processes try to load data into the database at the same time, at least one and possibly all loads will fail. To keep this from happening, the bulk loader places a lock in the database to prevent other gmod_bulk_load_gff3.pl processes from running at the same time. When the application exits normally, this lock will be removed, but if it crashes for some reason, the lock will not be removed. To remove the lock from the command line, provide the flag --remove_lock. Note that if the loader crashed necessitating the removal of the lock, you also may need to rebuild the uniquename cache (see the next section). =item The uniquename cache The loader uses the chado database to create a table that caches feature_ids, uniquenames, type_ids, and organism_ids of the features that exist in the database at the time the load starts and the features that will be added when the load is complete. If it is possilbe that new features have been added via some method that is not this loader (eg, Apollo edits or loads with XORT) or if a previous load using this loader was aborted, then you should supply the --recreate_cache option to make sure the cache is fresh. =item Sequence By default, if there is sequence in the GFF file, it will be loaded into the residues column in the feature table row that corresponds to that feature. By supplying the --nosequence option, the sequence will be skipped. You might want to do this if you have very large sequences, which can be difficult to load. In this context, "very large" means more than 200MB. Also note that for sequences to load properly, the GFF file must have the ##FASTA directive (it is required for proper parsing by Bio::FeatureIO), and the ID of the feature must be exactly the same as the name of the sequence following the > in the fasta section. =item The ORGANISM table This script assumes that the organism table is populated with information about your organism. If you are unsure if that is the case, you can execute this command from the psql command-line: select * from organism; If you do not see your organism listed, execute this command to insert it: insert into organism (abbreviation, genus, species, common_name) values ('H.sapiens', 'Homo','sapiens','Human'); substituting in the appropriate values for your organism. =item Parents/children order Parents must come before children in the GFF file. =item Analysis If you are loading analysis results (ie, blat results, gene predictions), you should specify the -a flag. If no arguments are supplied with the -a, then the loader will assume that the results belong to an analysis set with a name that is the concatenation of the source (column 2) and the method (column 3) with an underscore in between. Otherwise, the argument provided with -a will be taken as the name of the analysis set. Either way, the analysis set must already be in the analysis table. The easist way to do this is to insert it directly in the psql shell: INSERT INTO analysis (name, program, programversion) VALUES ('genscan 2005-2-28','genscan','5.4'); There are other columns in the analysis table that are optional; see the schema documentation and '\d analysis' in psql for more information. Chado has four possible columns for storing the score in the GFF score column; please use whichever is most appropriate and identifiy it with --score_col flag (significance is the default). Note that the name of the column can be shortened to one letter. If you have more than one score associated with each feature, you can put the other scores in the ninth column as a tag=value pair, like 'identity=99', and the bulk loader will put it in the featureprop table (provided there is a cvterm for identity; see the section above concerning custom tags). Available options are: =over =item significance (default) =item identity =item normscore =item rawscore =back A planned addtion to the functionality of handling analysis results is to allow "mixed" GFF files, where some lines are analysis results and some are not. Additionally, one will be able to supply lists of types (optionally with sources) and their associated entry in the analysis table. The format will probably be tag value pairs: --analysis match:Rice_est=rice_est_blast, \ match:Maize_cDNA=maize_cdna_blast, \ mRNA=genscan_prediction,exon=genscan_prediction =item Grouping features by ID The GFF3 specification allows features like CDSes and match_parts to be grouped together by sharing the same ID. This loader does not support this method of grouping. Instead the parent feature must be explicitly created before the parts and the parts must refer to the parent with the Parent tag. =item External Parent IDs The GFF3 specification states that IDs are only valid within a single GFF file, so you can't have Parent tags that refer to IDs in another file. By specificifying the "allow_external_parent" flag, you can relax this restriction. A word of warning however: if the parent feature's uniquename/ID was modified during loading (to make it unique), this functionality won't work, as it won't beable to find the original feature correctly. Actually, it may be worse than not working, it may attach child features to the wrong parent. This is why it is a bad idea to use this functionality! Please use with caution. =back =head1 AUTHORS Allen Day Eallenday@ucla.eduE, Scott Cain Escain@cpan.orgE Copyright (c) 2011 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ($ORGANISM, $GFFFILE,$FASTAFILE,$DBPROFILE, $DBNAME, $DBUSER, $DBPASS,$DBHOST, $DBPORT, $ANALYSIS, $ANALYSIS_GROUP, $GLOBAL_ANALYSIS, $NOLOAD, $VALIDATE, $INSERTS, $NOTRANSACT, $NOSEQUENCE, $SCORE_COL, $ONTOLOGY, $SKIP_VACUUM, $DROP_INDEX, $NOEXON, $NOUNIQUECACHE, $RECREATE_CACHE, $SAVE_TMPFILES,$RANDOM_TMP_DIR, $NO_TARGET_SYN, $UNIQUE_TARGET, $DBXREF, $FP_CV, $NO_ADDFP_CV, $MANPAGE, $DEBUG, $DELETE, $DELETE_CONFIRM, $CUSTOM_ADAPTER, $PRIVATE_SCHEMA, $USE_PUBLIC_CV, $NO_SKIP_VACUUM, $END_SQL, $REMOVE_LOCK, $ALLOW_EXTERNAL_PARENT, ); GetOptions( 'organism=s' => \$ORGANISM, 'gfffile=s' => \$GFFFILE, 'fastafile=s'=> \$FASTAFILE, 'dbprofile=s'=> \$DBPROFILE, 'dbname=s' => \$DBNAME, 'dbuser=s' => \$DBUSER, 'dbpass=s' => \$DBPASS, 'dbhost=s' => \$DBHOST, 'dbport=s' => \$DBPORT, 'analysis:s' => \$ANALYSIS, # = means it is required, : means optional 'noload' => \$NOLOAD, 'validate' => \$VALIDATE, 'notransact' => \$NOTRANSACT, 'nosequence' => \$NOSEQUENCE, 'score_col=s'=> \$SCORE_COL, 'ontology=s' => \$ONTOLOGY, 'skip_vacuum'=> \$SKIP_VACUUM, 'no_skip_vacuum' => \$NO_SKIP_VACUUM, 'drop_indexes'=>\$DROP_INDEX, 'inserts' => \$INSERTS, 'noexon' => \$NOEXON, 'nouniquecache'=> \$NOUNIQUECACHE, 'recreate_cache'=> \$RECREATE_CACHE, 'remove_lock' => \$REMOVE_LOCK, 'save_tmpfiles'=>\$SAVE_TMPFILES, 'random_tmp_dir'=>\$RANDOM_TMP_DIR, 'no_target_syn'=> \$NO_TARGET_SYN, 'unique_target' => \$UNIQUE_TARGET, 'dbxref:s' => \$DBXREF, 'fp_cv:s' => \$FP_CV, 'noaddfpcv' => \$NO_ADDFP_CV, 'manual' => \$MANPAGE, 'debug' => \$DEBUG, 'delete' => \$DELETE, 'delete_i_really_mean_it' => \$DELETE_CONFIRM, 'custom_adapter=s' => \$CUSTOM_ADAPTER, 'private_schema=s' => \$PRIVATE_SCHEMA, 'use_public_cv' => \$USE_PUBLIC_CV, 'end_sql:s' => \$END_SQL, 'allow_external_parent' => \$ALLOW_EXTERNAL_PARENT, ) # or ( system( 'pod2text', $0 ), exit -1 ); or pod2usage(-verbose => 1, -exitval => 1); pod2usage(-verbose => 2, -exitval => 1) if $MANPAGE; $SIG{__DIE__} = $SIG{INT} = 'cleanup_handler'; my $ORGANISM_FROM_CMDLINE = $ORGANISM; unless ($DBNAME) { if (eval {require Bio::GMOD::Config; Bio::GMOD::Config->import(); require Bio::GMOD::DB::Config; Bio::GMOD::DB::Config->import(); 1; } ) { my $gmod_conf = $ENV{'GMOD_ROOT'} || "/var/lib/gmod" ? Bio::GMOD::Config->new($ENV{'GMOD_ROOT'} || "/var/lib/gmod") : Bio::GMOD::Config->new(); my $profile = $DBPROFILE || 'default'; my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,$profile); $DBNAME = $db_conf->name(); $DBUSER = $db_conf->user(); $DBPASS = $db_conf->password(); $DBHOST = $db_conf->host(); $DBPORT = $db_conf->port(); $ORGANISM ||= $db_conf->organism(); } } $GFFFILE ||='stdin'; #nobody better name their file 'stdin' #$DBNAME ||='chado'; $DBPASS ||=''; $DBHOST ||='localhost'; $DBPORT ||='5432'; $VALIDATE ||=0; $NOTRANSACT ||=0; $NOSEQUENCE ||=0; $INSERTS ||=0; $SCORE_COL ||='significance'; $FP_CV ||='feature_property'; $NO_ADDFP_CV ||=0; die "You must supply a database name" unless $DBNAME; #die "You must supply an organism" unless $ORGANISM; $GLOBAL_ANALYSIS=0; if ((defined $ANALYSIS) and ($ANALYSIS eq '')) { $ANALYSIS = 1; #ie, it was specified on the command line with no arg } elsif ($ANALYSIS) { $GLOBAL_ANALYSIS = 1; $ANALYSIS_GROUP = $ANALYSIS; # analysis group specified on the command line $ANALYSIS = 1; } else { $ANALYSIS = 0; } if ((defined $DBXREF) and ($DBXREF eq '')) { $DBXREF=1; #ie, it was on the command line with no arg } $SKIP_VACUUM = $NO_SKIP_VACUUM ? 0 : 1; my %argv; $argv{organism} = $ORGANISM; $argv{gfffile} = $GFFFILE; $argv{fastafile} = $FASTAFILE; $argv{dbprofile} = $DBPROFILE; $argv{dbname} = $DBNAME; $argv{dbuser} = $DBUSER; $argv{dbpass} = $DBPASS; $argv{dbhost} = $DBHOST; $argv{dbport} = $DBPORT; $argv{is_analysis} = $ANALYSIS; $argv{noload} = $NOLOAD; $argv{validate} = $VALIDATE; $argv{notransact} = $NOTRANSACT; $argv{nosequence} = $NOSEQUENCE; $argv{score_col} = $SCORE_COL; $argv{ontology} = $ONTOLOGY; $argv{skip_vacuum} = $SKIP_VACUUM; $argv{drop_indexes} = $DROP_INDEX; $argv{inserts} = $INSERTS; $argv{global_analysis}=$GLOBAL_ANALYSIS; $argv{analysis_group}=$ANALYSIS_GROUP; $argv{noexon} = $NOEXON; $argv{nouniquecache}= $NOUNIQUECACHE; $argv{recreate_cache}=$RECREATE_CACHE; $argv{save_tmpfiles}= $SAVE_TMPFILES; $argv{random_tmp_dir}=$RANDOM_TMP_DIR; $argv{no_target_syn}= $NO_TARGET_SYN; $argv{unique_target}= $UNIQUE_TARGET; $argv{dbxref} = $DBXREF; $argv{fp_cv} = $FP_CV; $argv{addpropertycv}= ! $NO_ADDFP_CV; #dgg $argv{private_schema} = $PRIVATE_SCHEMA; $argv{use_public_cv}= $USE_PUBLIC_CV; $argv{allow_external_parent} = $ALLOW_EXTERNAL_PARENT; #allow a feature_id to be referenced by multiple featureloc.feature_id's my %locgroup = (); ######################## my $adapter = 'Bio::GMOD::DB::Adapter'; if ($CUSTOM_ADAPTER) { $adapter = "$adapter\:\:$CUSTOM_ADAPTER"; unless (eval {load $adapter; 1; } ) { warn "\n\nWhile attempting to load Bio::GMOD::DB::Adapter::$CUSTOM_ADAPTER\n"; warn "an error was encountered. Please check that this is a valid perl module\n"; warn "and that it is in perl's search path.\n"; warn "\nError was: $@\n"; warn "Exiting...\n\n"; exit(-1); } } my $chado = $adapter->new(%argv); $chado->remove_lock(force => 1) if $REMOVE_LOCK; $chado->place_lock(); my $lock = 1; #if we need custom ontology mapping, cache them here if ($ONTOLOGY) { my @pairs = split /\,/, $ONTOLOGY; foreach (@pairs) { my ($tag, $value) = split/\=/; $chado->cache('ontology',$tag, $value); } } $chado->file_handles(); my $gffio; if ($GFFFILE eq 'stdin' and !$FASTAFILE) { $gffio = Bio::FeatureIO->new(-fh => \*STDIN , -format => 'gff', -ignore_seq_region => 1, -validate_terms => $VALIDATE); } elsif ($GFFFILE and $GFFFILE ne 'stdin') { $gffio = Bio::FeatureIO->new(-file => $GFFFILE, -format => 'gff', -ignore_seq_region => 1, -validate_terms => $VALIDATE); } warn "Preparing data for inserting into the $DBNAME database\n"; warn "(This may take a while ...)\n"; my $seen_cds = my $seen_exon = my $seen_bad_cds = 0; my $ORGANISM_FROMDATA= ($ORGANISM =~ /fromdata/); if($ORGANISM_FROMDATA) { $ORGANISM= "null"; # is this useful? } elsif ($ORGANISM_FROM_CMDLINE) { $ORGANISM = $ORGANISM_FROM_CMDLINE; $chado->organism($ORGANISM); $chado->organism_id($ORGANISM) or die "$ORGANISM organism not found in the database"; } elsif (defined $gffio && $gffio->organism) { $ORGANISM = $gffio->organism; $chado->organism($ORGANISM); $chado->organism_id($ORGANISM) or die "$ORGANISM organism not found in the database"; } else { $chado->organism($ORGANISM); $chado->organism_id($ORGANISM) or die "$ORGANISM organism not found in the database"; } if ($DELETE && !$DELETE_CONFIRM) { my $really_delete = prompt("Do you really want me to delete features using this GFF file",'N'); if (lc $really_delete eq 'y') { $DELETE_CONFIRM = $DELETE; } else { warn "OK, I'm stopping instead.\n\n"; $chado->remove_lock(); exit(0); } } my ($analysis_err_str,$cds_err_str); my $processing_CDS = 0; my $feature_iterator; my $itern=0; my %seen_organism; FEATURE: while(my $feature = (defined $feature_iterator && $feature_iterator->next_feature) || (defined $gffio && $gffio->next_feature)){ $chado->primary_dbxref(''); my $featuretype = $feature->type->name; # dgg: pull organism from 1st feature?? # * may be many per gff-file; e.g. uniprot input if($ORGANISM_FROMDATA) { my($gff_organism) = defined($feature->annotation->get_Annotations('organism')) ? ($feature->annotation->get_Annotations('organism'))[0] : ''; if($gff_organism && $gff_organism ne $chado->organism()) { $ORGANISM = "$gff_organism";# is it pesky bperl object? warn "Organism $ORGANISM from data\n" unless($seen_organism{$ORGANISM}++); $chado->organism($ORGANISM); $chado->organism_id($ORGANISM) #? dont die if many orgs? auto-add * or die "$ORGANISM organism not found in the database"; } } if($feature->annotation->get_Annotations('CRUD')||$DELETE_CONFIRM ) { my $continue = $chado->handle_crud($feature, $DELETE_CONFIRM); next if ($continue == 1 || $DELETE_CONFIRM); #that is, this was a delete or update operation #and it is done } $itern++; warn(join(",","f".$itern,$featuretype,$feature->seq_id),"\n") if $DEBUG; $seen_exon= 1 if $featuretype =~ /exon$/ and !$processing_CDS; if ($featuretype =~ /(CDS|UTR)/) { my $continue_on = $chado->handle_CDS($feature); $seen_cds = 1 if !$seen_cds && $featuretype =~ /CDS/; next FEATURE unless ($continue_on == 0); if (!$seen_bad_cds ) { warn <nextfeature(); my $nextfeatureloc = $chado->nextfeatureloc(); my $type = $chado->get_type($featuretype); my ($src, $seqlen) = $chado->get_src_seqlen($feature); if(!$src){ $src = $chado->src_second_chance($feature); } die "no feature for ".$feature->seq_id unless $src; if($feature->annotation->get_Annotations('Parent')){ $chado->handle_parent($feature); } if($feature->annotation->get_Annotations('Derives_from')){ $chado->handle_derives_from($feature); } my $source = defined ($feature->source) ? $feature->source->value : '.'; my($uniquename) = defined(($feature->annotation->get_Annotations('ID'))[0]) ? ($feature->annotation->get_Annotations('ID'))[0]->value : "auto".$nextfeature; $uniquename = $uniquename->value if ref($uniquename); $uniquename = $chado->uniquename_validation( $uniquename, $type, $chado->organism_id, $nextfeature); if (defined(($feature->annotation->get_Annotations('ID'))[0]) && ($feature->annotation->get_Annotations('ID'))[0]->value ne $uniquename) { #need to keep a temporary map of modified uniquenames $chado->modified_uniquename( orig_id => ($feature->annotation->get_Annotations('ID'))[0]->value, modified_id => $uniquename, organism_id=>$chado->organism_id); } my($name) = defined(($feature->annotation->get_Annotations('Name'))[0]) ? ($feature->annotation->get_Annotations('Name'))[0]->value : defined(($feature->annotation->get_Annotations('ID'))[0]) ? ($feature->annotation->get_Annotations('ID'))[0]->value : "$featuretype-$uniquename"; $name = $name->value if ref($name); if ($uniquename eq $feature->seq_id or (defined( $chado->modified_uniquename(modified_id => $uniquename, organism_id => $chado->organism_id)) and $chado->modified_uniquename(modified_id => $uniquename, organism_id => $chado->organism_id) eq $feature->seq_id)) { $chado->reftype_property($featuretype,$type); # a reference sequence?? yes } my $current_feature_id=0; if($chado->cache('feature',$uniquename)){ #seen this feature before $locgroup{$uniquename}++; } else { $chado->cache('feature',$uniquename,$nextfeature); $locgroup{$uniquename} = 0; $current_feature_id=$nextfeature; } #if there are Targets, match types or scores and this is not ANALYSIS, #there is a problem. # if (!$analysis_err_str && !$ANALYSIS && ( ((scalar($feature->annotation->get_Annotations('Target'))>0) and ((($feature->annotation->get_Annotations('Target'))[0]->can('value') && ($feature->annotation->get_Annotations('Target'))[0]->value) or (($feature->annotation->get_Annotations('Target'))[0]->can('display_text') && ($feature->annotation->get_Annotations('Target'))[0]->display_text))) or (defined($feature->score) and $feature->score ne '.') or $featuretype =~ /match/ ) ) { my @errs; push @errs, '* Has Target attributes' if (scalar($feature->annotation->get_Annotations('Target'))>0 and ($feature->annotation->get_Annotations('Target'))[0]->as_text); push @errs, '* Has scores' if (defined($feature->score) and $feature->score ne '.'); push @errs, '* Has a match feature type' if ($featuretype =~ /match/); $analysis_err_str = join("\n", @errs); warn "\nThis file was not declared as analysis results (with the --analysis flag,\nbut this file contains attributes that imply that it is:\n$analysis_err_str\nYou can safely ignore this message if you don't need to access scores\nassociated with these features.\n\n"; } if ($ANALYSIS && $featuretype =~ /match/ && !defined($feature->annotation->get_Annotations('Target'))) { if (($feature->annotation->get_Annotations('ID'))[0]->can('value')) { $chado->cache('feature', ($feature->annotation->get_Annotations('ID'))[0]->value, $nextfeature); } elsif (($feature->annotation->get_Annotations('ID'))[0]->can('display_text')) { $chado->cache('feature', ($feature->annotation->get_Annotations('ID'))[0]->display_text, $nextfeature); } } #don't write a featureloc entry for srcfeatures unless ($src eq '\N' or $src == $nextfeature) { #need to convert from base to interbase coords my $start = $feature->start eq '.' ? '\N' : ($feature->start - 1); my $end = $feature->end eq '.' ? '\N' : defined($feature->end) ? $feature->end : '\N'; my $phase = ($feature->phase eq '.' or $feature->phase eq '') ? '\N' : $feature->phase; $chado->print_floc($nextfeatureloc, $chado->cache('feature',$uniquename), $src, $start, $end, $feature->strand, $phase,'0',$locgroup{$uniquename}); } if ($feature->annotation->get_Annotations('Gap')) { $chado->handle_gap($feature,$uniquename); } if ($feature->annotation->get_Annotations('Note')) { $chado->handle_note($feature,$uniquename); } #try to put unreserved tags in featureprop #this requires that the terms exist in cvterm (and therefore that they #have a dbxref) my @unreserved_tags = grep {/^[a-z]/} $feature->annotation->get_all_annotation_keys(); if ( @unreserved_tags > 0 ) { $chado->handle_unreserved_tags($feature,$uniquename,@unreserved_tags); } if ( $chado->{const}{source_success} && $source && $source ne '.') { $chado->handle_source($feature,$uniquename,$source); } if ($feature->annotation->get_Annotations('Ontology_term')) { $chado->handle_ontology_term($feature,$uniquename); } if ($feature->annotation->get_Annotations('Dbxref') or $feature->annotation->get_Annotations('dbxref')) { $chado->handle_dbxref($feature,$uniquename); } my @aliases; if ($feature->annotation->get_Annotations('Alias')) { @aliases = map {$_->value} $feature->annotation->get_Annotations('Alias'); } #if the uniquename was modified, put the orig ID in the alias list push @aliases, $chado->modified_uniquename(modified_id=>$uniquename,organism_id=>$chado->organism_id) if $chado->modified_uniquename(modified_id=>$uniquename,organism_id=>$chado->organism_id); #Un-denormalizing the synonym table #if ($name ne '\N') { # push @aliases, $name; #} #push @aliases, $uniquename; #need to unique-ify the list my %count; my @ualiases = grep {++$count{$_} < 2} @aliases; foreach my $alias (@ualiases) { $chado->synonyms($alias,$chado->cache('feature',$uniquename)); } if($current_feature_id or $chado->cache('srcfeature',$nextfeature)) { $chado->print_f($nextfeature,$chado->organism_id,$name,$uniquename,$type,$seqlen,$chado->primary_dbxref); } if ($ANALYSIS && !defined(($feature->annotation->get_Annotations('Target'))[0])) { $chado->handle_nontarget_analysis($feature,$uniquename); } $chado->nextfeatureloc('++'); #now deal with creating another feature for targets if (!$ANALYSIS && defined(($feature->annotation->get_Annotations('Target'))[0])) { die "Features in this GFF file have Target tags, but you did not indicate\n" ."--analysis on the command line"; } elsif (defined(($feature->annotation->get_Annotations('Target'))[0])) { $chado->handle_target($feature, $uniquename,$name,$featuretype,$type); } $chado->nextfeature('++'); } if ($feature_iterator = $chado->process_CDS() ) { $processing_CDS=1; goto FEATURE; } $chado->end_files(); #$search_uniquename->finish; #$validate_uniquename->finish; #deal with sequence unless ($NOSEQUENCE or !defined $gffio) { #ugh--reversed unless logic while (my $seq = $gffio->next_seq) { my $string = $seq->seq(); my $name = $seq->display_id(); $chado->print_seq($name,$string); } } if ($FASTAFILE) { #use SeqIO to parse the fasta file my $in = Bio::SeqIO->new(-file => $FASTAFILE, -format => 'fasta'); while (my $seq = $in->next_seq) { $chado->print_fasta($seq->display_id,$seq->seq); } } $chado->flush_caches(); $chado->load_data() unless $NOLOAD; if ($END_SQL) { $chado->dbh->do($END_SQL); } $chado->remove_lock(); exit(0); sub cleanup_handler { warn "@_\nAbnormal termination, trying to clean up...\n\n" if @_; #gets the message that the die signal sent if there is one if ($chado && $chado->dbh->ping) { #$chado->dbh->{AutoCommit} = 1; $chado->cleanup_tmp_table; if ($lock) { warn "Trying to remove the run lock (so that --remove_lock won't be needed)...\n"; $chado->remove_lock; #remove the lock only if we've set it } #$chado->dbh->rollback; print STDERR "Exiting...\n"; } exit(1); } !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; chdir $origdir; chado-1.23/load/bin/load_gff3.PLS000755 000765 000024 00000134553 11660526631 016511 0ustar00cainstaff000000 000000 #!perl -w use Config; use File::Basename qw(&basename &dirname); use FindBin '$Bin'; use Cwd; $origdir = cwd; chdir dirname($0); $file = basename($0, '.PL','.PLS'); $file = "gmod_$file.pl"; my %OPTIONS; if (open F,"$Bin/../../build.conf") { while () { next if /^\#/; chomp; $OPTIONS{$1} = $2 if /^(\w+)\s*=\s*(.+)/; } close F; } open OUT,">$file" or die "Can't create $file: $!"; print OUT "$Config{startperl}\n"; if ($OPTIONS{LIB}) { print OUT "use lib '$OPTIONS{LIB}';\n"; } if ($OPTIONS{PREFIX}) { print OUT "use lib '$OPTIONS{PREFIX}/lib'i\n"; } print OUT <<'!NO!SUBS!'; use strict; use warnings; #use lib '/Users/cain/cvs_stuff/schema/trunk/chado/lib'; use Bio::Tools::GFF; use Bio::SeqIO; use Bio::Chado::AutoDBI; use Bio::Chado::LoadDBI; use Data::Dumper; use Getopt::Long; use Term::ProgressBar; use File::Temp qw(tempfile); use constant DEBUG => 0; $| = 1; =head1 NAME gmod_load_gff3.pl - Load gff3 files into a chado database. =head1 SYNOPSIS % gmod_load_gff3.pl --organism Human --srcdb 'DB:refseq' --gfffile refseq.gff =head1 COMMAND-LINE OPTIONS The following command line options are available. Note that they can be abbreviated to one letter. --cache (optional, defaults to 1000) The number of features to cache before committing to the database --force (optional, defaults to false) Force the file to load, even if it has already been loaded before --gfffile (required) The name of the GFF3 file --organism (optional, default from --dbprofile) Common name of the organism --srcdb (optional) The name of the source database --uniquename (optional) The tag to use to provide feature.uniquename ? --ontology (optional) Ontology to use instead ? of the default. Note that ? this should be detected ? automatically, but isn't ? yet. --dbprofile (optional, defaults to 'default') Name of the database profile used by Bio::GMOD::Config to get the organism. --fp_cv (optional, defaults to 'feature_property') Name of the feature property cv =head1 DESCRIPTION WARNING: this loader doesn't handle cds and exon features the same way as the bulk loader (yet!). ANOTHER WARNING: This script is incompatible with the Sequence Ontology views that are created automatically for Chado and reside in the 'so' schema. Specifically, the view "so.genotype" will cause the initialization of this script to fail. To fix this problem and use this script, you need to remove the genotype view: DROP VIEW so.genotype; The most important thing to know about this loader is that it is SLOW! The bulk loader (gmod_bulk_load_gff3.pl, also in this distribution) is many times faster (perhaps 100 times faster). The only real advantage is the this loader is easier to port to other database systems because it runs on Class::DBI middleware. The gmod_load_gff3.pl script takes genomic annotations in the GFF3 format and loads them into several tables in chado. (see L for a description of the format). There are two types of data tags in GFF3: those that are part of the specification, and those that aren't. There is a short list of those that are part of the spec (ie, reserved) They include ID, Parent, Name, Alias, Target, and Gap. Tags that are part of the spec are first letter capitalized and all other tags are all lower case. All tags that are part of the spec are handled as special cases during the insert, as well as some non-spec tags. These include 'description', tags beginning with 'db:' or 'DB:', and tags beginning with 'cvterm:'. All other tags are inserted into the same table (featureprop). If that is not the desired behavior for a given tag, you may look at modifying the load_custom_tags subroutine. If you have a modification that you feel might be particularly useful, please email your suggestion to the authors. (Note that this behavior might better be module-ized, so that we could provide an empty 'custom tag processing' module, that if installed, would provide addtional processing of custom tags. Add it to the todo list.) =head2 NOTES =over =item The ORGANISM table This script assumes that the organism table is populated with information about your organism. If you are unsure if that is the case, you can execute this command from the psql command-line: select * from organism; If you do not see your organism listed, execute this command to insert it: insert into organism (abbreviation, genus, species, common_name) values ('H.sapiens', 'Homo','sapiens','Human'); substituting in the appropriate values for your organism. =item The DB table This script assumes that the db table is populated with a row describing the database that is the source of these annotations. If you are unsure, execute this command: select * from db; If you do not see your database listed, execute this command: insert into db (name) values ('DB:refseq'); Substituting for the name of your database. A more complete insert command may be appropriate in your case, but this should work in a pinch. =item GFF3 The GFF in the datafile must be version 3 due to its tighter control of the specification and use of controlled vocabulary. Accordingly, the names of feature types must be exactly those in the Sequence Ontology, not the synonyms and not the accession numbers (SO accession numbers may be supported in future versions of this script). Also, in order for the load to be successful, the reference sequences (eg, chromosomes or contigs) must be defined in the GFF file before any features on them are listed. This can be done either by the reference-sequence meta data specification, which would be lines that look like this: ##sequence-region chr1 1 246127941 or with a standard GFF line: chr1 NCBI chromosome 1 246127941 . . . ID=chr1 Do not use both. Note that if the '##sequence-region' notation is used, this script will not be able to determine the type of sequence and therefore will assign it the 'region' type which is very general. If that is not what you want, use the standard GFF line to specify the reference sequence. =item Uniquename By providing the command line flag --uniquename, the user indicates what GFF tag to uses as the feature.uniquename when inserting into the feature table. Note that this name must be unique among all features in the feature table; if it is not, the load of that feature will probably fail. =item Analysis Results Currently, this loader doesn't capture analysis results. That is, it doesn't populate the analysis or analysisfeature tables and ignores the score column in the GFF3. =back =head1 AUTHORS Allen Day Eallenday@ucla.eduE, Scott Cain Ecain@cshl.orgE Copyright (c) 2003-2004 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ( undef, $TMPFASTA ) = tempfile( "XXXXXX", ".fa", SUFFIX => '.fa' ); my ( undef, $TMPGFF ) = tempfile( "XXXXXX", ".gff", SUFFIX => '.gff' ); warn $TMPFASTA if DEBUG; warn $TMPGFF if DEBUG; my ( $ORGANISM,$GFFFILE,$UNIQUENAME,$CACHE_SIZE,$FORCE_LOAD, $ONTOLOGY,$DBPROFILE, $FP_CV, $SRC_DB ); my ( $progress, $next_update, $linecount ) = ( undef, undef, undef ); #progressbar; my ( $chado_db, $chado_organism, $nullpub ) = ( undef, undef, undef ); my $feature_count = 0; #for cache/flush my ($auto_cv, $fp_cv); my $null_db_id; my %srcfeature = (); my %feature = (); my %featureloc_locgroup = (); my %dbxref = (); my %cvterm = (); my $so; my $gff_source_db; my %gff_source; initialize(); my $mtime = ( stat($GFFFILE) )[9]; my ($pub) = Bio::Chado::CDBI::Pub->search( title => $GFFFILE . " " . $mtime ); if ( $pub and !$FORCE_LOAD ) { print "\nIt appears that you have already loaded this exact file\n"; print "Do you want to continue [no]? "; chomp( my $response = ); unless ( $response =~ /^[Yy]/ ) { print "OK--bye.\n"; exit 0; } } else { $pub = Bio::Chado::CDBI::Pub->find_or_create( { title => $GFFFILE . " " . $mtime, miniref => $GFFFILE . " " . $mtime, uniquename => $GFFFILE . " " . $mtime, type_id => $cvterm{gff_file}->id } ); } die "unable to find or create a pub entry in the pub table" unless $pub; #iterate over each feature in the gff, caching objects up to #CACHE_SIZE, then flushing. this is a way to break our large #load transaction into multiple cache/flush mini-transactions my @transaction; my $gffio = Bio::Tools::GFF->new( -file => $TMPGFF, -gff_version => 3 ); #my $gffio = Bio::Tools::GFF->new(-file => $GFFFILE, -gff_version => 3); $feature_count += load_segments($gffio); while ( my $gff_feature = $gffio->next_feature() ) { cache_cvterm( $gff_feature->primary_tag, $so->id ); my ($chado_type) = $cvterm{ $gff_feature->primary_tag }; die $gff_feature->primary_tag . " could not be found in your cvterm table.\n" . "Either the Sequence Ontology was incorrectly loaded,\n" . "or this file doesn't contain GFF3" unless $chado_type; if ($gff_feature->primary_tag eq "CDS") { warn "This GFF file contains CDS features, but this loader has not\n" . "yet been modified to handle CDS features in the standard GMOD/Chado\n" . "way. It is suggested that you use gmod_bulk_load_gff3.pl instead\n\n"; } my ($id) = $gff_feature->has_tag('ID') ? $gff_feature->get_tag_values('ID') : ''; my ($parent) = $gff_feature->has_tag('Parent') ? $gff_feature->get_tag_values('Parent') : ''; # look up the feature # problem here: two places that the reference sequence/srcfeature # might be found: either in the GFF file (in which case, look # for it in a hash here) or in the database already. If it is # in the database already, it might be very difficult to look up # via seq_id. I'll solve the first problem and think about the # second sjc 3/23/04 if ( ($id ne $gff_feature->seq_id) && ($gff_feature->seq_id ne '.') ) { ( $srcfeature{$gff_feature->seq_id} ) = Bio::Chado::CDBI::Feature->search( name => $gff_feature->seq_id ) unless $srcfeature{$gff_feature->seq_id}; unless ( $srcfeature{$gff_feature->seq_id} ) { warn "\n" . "*" x 72 . "\n"; warn "Unable to find a source feature id for the reference sequence in this line:\n"; warn $gff_feature->gff_string . "\n\n"; warn "That is, " . $gff_feature->seq_id . " should either have a entry in the \n"; warn "feature table or earlier in this GFF file and it doesn't.\n\n"; warn "*" x 72 . "\n"; exit 1; } } #is this general, or what should really be done here? #parse the dbxref and get the appropriate db_id #or take commandline arg mapping them out if ( $id && !$dbxref{$id} ) { my ($chado_dbxref) = Bio::Chado::CDBI::Dbxref->find_or_create( { db_id => $chado_db->id, accession => $id, } ); $dbxref{$id} = $chado_dbxref; } my $chado_feature = load_feature_locations( $gff_feature, $chado_type, $id ); $feature_count++; $feature{$id} = $chado_feature if $gff_feature->has_tag('ID'); my @tags = $gff_feature->all_tags; foreach my $tag (@tags) { if ( $tag eq 'ID' ) { #this currently doesn't do anything. ID is used elsewhere though } elsif ( $tag eq 'Parent' ) { load_Parent_tag( $gff_feature, $chado_feature ); } elsif ( $tag eq 'Alias' ) { load_Alias_tag( $gff_feature, $chado_feature ); } elsif ( $tag eq 'Name' ) { load_Name_tag( $gff_feature, $chado_feature ); } elsif ( $tag eq 'Target' ) { load_Target_tag( $gff_feature, $chado_feature ); } elsif ( $tag eq 'Note' ) { load_Note_tag( $gff_feature, $chado_feature ); } elsif ( $tag eq 'Ontology_term' || $tag =~ /^cvterm/) { load_Ontology_term( $gff_feature, $chado_feature, $tag ); } elsif ( $tag eq 'Dbxref' || $tag =~ /^dbxref/) { load_Dbxref_term( $gff_feature, $chado_feature, $tag ); } elsif ( $tag =~ /^[A-Z]/ ) { die "$0 doesn't handle '$tag' tags yet. are you sure it's allowed by the GFF3 spec?"; } elsif ( defined $UNIQUENAME && $tag eq $UNIQUENAME ) { # do nothing--we already used this information to create the feature } elsif ( $tag =~ /^[a-z]/ ) { load_custom_tags( $gff_feature, $chado_feature, $tag ); } } if ( $feature_count % $CACHE_SIZE == 0 ) { $_->dbi_commit foreach @transaction; @transaction = (); } $next_update = $progress->update($feature_count) if ( $feature_count > $next_update ); $progress->update($feature_count) if ( $feature_count >= $next_update ); $progress->update($linecount) if ( $next_update >= $linecount ); } $_->dbi_commit foreach @transaction; $gffio->close(); print "\n$feature_count features added\n"; my $seqs_loaded = load_sequences(); print "\n$seqs_loaded sequences added\n"; print "Done\n"; exit 0; =pod =head1 load_custom_tags Handles inserting non-reserved tags into chado. Determines if the tag falls into a short list of tags for custom handling and deals with them appropriately. If the tag is not on the list, the information is placed in the featureprop table. =cut sub load_custom_tags { my $gff_feature = shift; my $chado_feature = shift; my $tag = shift; my @d = $gff_feature->get_tag_values($tag); if (0) { } elsif ( $tag eq 'description' ) { foreach my $d (@d) { next if $d eq ''; my ($featureprop) = Bio::Chado::CDBI::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $cvterm{description}->id, value => $d, } ); push @transaction, ($featureprop); } } elsif ( $tag =~ /^db:/ ) { $tag =~ s/^db:/DB:/; my $add_db = 0; my ($db) = Bio::Chado::CDBI::Db->search( name => $tag ); if ( !$db ) { $add_db = 1; $db = Bio::Chado::CDBI::Db->find_or_create( { name => $tag, } ); } die "couldn't create db $db" unless $db; push @transaction, $db if $add_db; foreach my $d (@d) { next if $d eq ''; my ($dbxref) = Bio::Chado::CDBI::Dbxref->find_or_create( { db_id => $db->id, accession => $d } ); my ($feature_dbxref) = Bio::Chado::CDBI::Feature_Dbxref->find_or_create( { feature_id => $chado_feature->id, dbxref_id => $dbxref->id, } ); push @transaction, ( $dbxref, $feature_dbxref ); } } elsif ( $tag eq 'dbxref') { load_Dbxref_term($gff_feature,$chado_feature,$tag); } else { unless ( defined $cvterm{$tag} ) { cache_cvterm($tag, $fp_cv ? $fp_cv->id : 0); $progress->message("Data with the $tag tag are being placed in the featureprop table"); } my $rank = 0; foreach my $d (@d) { next if $d eq ''; my ($featureprop) = Bio::Chado::CDBI::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $cvterm{$tag}->id, value => $d, rank => $rank, } ); $rank++; push @transaction, $featureprop; } } } =pod =head1 load_Dbxref_term Loads dbxrefs. =cut sub load_Dbxref_term { my $gff_feature = shift; my $chado_feature = shift; my $tag = shift; my @d = $gff_feature->get_tag_values($tag); foreach my $d (@d) { next if $d eq ''; if ($d =~ /(.+):(.+)/) { $tag = "DB:$1"; $d = $2; } else { die "unable to determine database for dbxref: $d\n"; } my $add_db = 0; my ($db) = Bio::Chado::CDBI::Db->search( name => $tag ); if ( !$db ) { $add_db = 1; $db = Bio::Chado::CDBI::Db->find_or_create( { name => $tag, } ); } die "couldn't create db $db" unless $db; push @transaction, $db if $add_db; my ($dbxref) = Bio::Chado::CDBI::Dbxref->find_or_create( { db_id => $db->id, accession => $d } ); my ($feature_dbxref) = Bio::Chado::CDBI::Feature_Dbxref->find_or_create( { feature_id => $chado_feature->id, dbxref_id => $dbxref->id, } ); push @transaction, ( $dbxref, $feature_dbxref ); } } =head1 load_Ontology_term Loads ontology terms to feature_cvterm. =cut sub load_Ontology_term { my $gff_feature = shift; my $chado_feature = shift; my $tag = shift; my @d = $gff_feature->get_tag_values($tag); foreach my $d (@d) { next if $d eq ''; my $db; if ($d =~ /([^:]+)\:([^:]+)/ ) { $db = $1; $d = $2; } my $dbxref; my $db_obj_iterator; if ($db) { if ($db eq 'GO' or $db eq 'SO') { $db_obj_iterator = Bio::Chado::CDBI::Db->search( name => $db ); } else { $progress->message( "I don't know how to deal with OntologyTerms like $db:$d\n") and next; } while (!$dbxref and my $db_obj = $db_obj_iterator->next) { ($dbxref) = Bio::Chado::CDBI::Dbxref->search( accession => $d , db_id => $db_obj->id ); } } else { ($dbxref) = Bio::Chado::CDBI::Dbxref->search( accession => $d ); } $progress->message("couldn't find cvterm in dbxref: $d") and next unless $dbxref; my ($cvterm) = Bio::Chado::CDBI::Cvterm->search( dbxref_id => $dbxref->id ); next unless $cvterm; my ($feature_cvterm) = Bio::Chado::CDBI::Feature_Cvterm->find_or_create( { feature_id => $chado_feature->id, cvterm_id => $cvterm->id, pub_id => $nullpub->id, } ); push @transaction, $feature_cvterm; } } =pod =head1 load_Note_tag Loads Note tag values to the featureprop table. =cut sub load_Note_tag { my $gff_feature = shift; my $chado_feature = shift; cache_cvterm('Note') unless ( defined $cvterm{'Note'} ); my @d = $gff_feature->get_tag_values('Note'); my $rank = 0; foreach my $d (@d) { next if $d eq ''; my ($featureprop) = Bio::Chado::CDBI::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $cvterm{'Note'}->id, value => $d, rank => $rank, } ); push @transaction, $featureprop; $rank++; } } =pod =head1 load_Target_tag Loads Target values. These are used for alignment information. =cut sub load_Target_tag { my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Target') ) { my @targets = $gff_feature->get_tag_values('Target'); foreach my $target (@targets) { my ( $tstart, $tend ); if ( $target =~ /^(\S+?)\+(\d+)\+(\d+)$/ ) { ( $target, $tstart, $tend ) = ( $1, $2, $3 ); } else { die "your Target attribute seems to be improperly formated"; } my ($chado_synonym1) = Bio::Chado::CDBI::Synonym->find_or_create( { name => $target, synonym_sgml => $target, type_id => $cvterm{synonym}->id } ); my ($chado_synonym2) = Bio::Chado::CDBI::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $pub->id, } ); my ($chado_featureloc) = Bio::Chado::CDBI::Featureloc->find_or_create( { feature_id => $chado_feature->id, srcfeature_id => $chado_feature->id, fmin => $tstart, fmax => $tend, rank => 1 #potential bug here -allenday } ); my ($chado_featureprop) = Bio::Chado::CDBI::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $cvterm{score}->id, value => $gff_feature->score } ); push @transaction, $chado_synonym1; push @transaction, $chado_synonym2; push @transaction, $chado_featureloc; push @transaction, $chado_featureprop; } } } =pod =head1 load_Parent_tag Loads Parent tag values. These are used to denote a parent feature of the given feature. =cut sub load_Parent_tag { my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Parent') ) { my @parents = $gff_feature->get_tag_values('Parent'); foreach my $parent (@parents) { next if $parent eq ''; my $reltype = ( $gff_feature->primary_tag eq 'protein' || $gff_feature->primary_tag eq 'polypeptide' ) ? $cvterm{develops_from} : $cvterm{part_of}; #unhandled exception: what if $feature{$parent} hasn't been seen yet? ( $feature{$parent} ) = Bio::Chado::CDBI::Feature->search( name => $parent ) unless $feature{$parent}; my $chado_feature_relationship = Bio::Chado::CDBI::Feature_Relationship->find_or_create( { subject_id => $chado_feature->id, object_id => $feature{$parent}->id, type_id => $reltype, } ); push @transaction, $chado_feature_relationship; } } } =pod =head1 load_Alias_tag Loads Alias tag values. These are used for synonyms. =cut sub load_Alias_tag { my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Alias') ) { my @aliases; if ( $gff_feature->has_tag('Alias') ) { push @aliases, $gff_feature->get_tag_values('Alias'); } foreach my $alias (@aliases) { next if $alias eq ''; #create the synonym my ($chado_synonym1) = Bio::Chado::CDBI::Synonym->find_or_create( { name => $alias, synonym_sgml => $alias, type_id => $cvterm{synonym}->id } ); #and link it to the feature via feature_synonym my ($chado_synonym2) = Bio::Chado::CDBI::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $pub->id, } ); push @transaction, $chado_synonym1; push @transaction, $chado_synonym2; } } } =pod =head1 load_Name_tag Loads Name tag values. =cut sub load_Name_tag { my $gff_feature = shift; my $chado_feature = shift; my @names; if ( $gff_feature->has_tag('Name') ) { @names = $gff_feature->get_tag_values('Name'); } elsif ($gff_feature->has_tag('ID') ) { @names = $gff_feature->get_tag_values('ID'); } else { return; } foreach my $name (@names) { next if $name eq ''; my ($chado_synonym1) = Bio::Chado::CDBI::Synonym->find_or_create( { name => $name, synonym_sgml => $name, type_id => $cvterm{synonym}->id } ); my ($chado_synonym2) = Bio::Chado::CDBI::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $pub->id, } ); push @transaction, $chado_synonym1; push @transaction, $chado_synonym2; } } sub initialize { GetOptions( 'organism:s' => \$ORGANISM, 'srcdb:s' => \$SRC_DB, 'gfffile:s' => \$GFFFILE, 'uniquename:s'=>\$UNIQUENAME, 'cache:s' => \$CACHE_SIZE, 'force' => \$FORCE_LOAD, 'ontology:s' => \$ONTOLOGY, 'dbprofile:s'=> \$DBPROFILE, 'fp_cv:s' => \$FP_CV, ) or ( system( 'pod2text', $0 ), exit -1 ); unless($ORGANISM) { if (eval {require Bio::GMOD::Config; Bio::GMOD::Config->import(); require Bio::GMOD::DB::Config; Bio::GMOD::DB::Config->import(); 1; } ) { my $gmod_conf = $ENV{'GMOD_ROOT'} || "/var/lib/gmod" ? Bio::GMOD::Config->new($ENV{'GMOD_ROOT'} || "/var/lib/gmod") : Bio::GMOD::Config->new(); my $profile = $DBPROFILE || 'default'; my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,$profile); $ORGANISM = $db_conf->organism(); } } $SRC_DB ||= 'DB:refseq'; $CACHE_SIZE ||= 1000; $ONTOLOGY ||= 'sequence'; $FP_CV ||= 'feature_property'; die "\nYou must specify a GFF file\n" unless $GFFFILE; #deal with GFF3 files that contain sequence # this is ugly, ugly, ugly, but in addtion to dealing with # sequence, it also fixes Allen's method of tracking progress die "$GFFFILE does not exist" unless ( -e $GFFFILE ); my $linenumber = `grep -n "^>" $GFFFILE`; if ( $linenumber =~ /^(\d+)/ ) { $linenumber = $1; system("tail -n +$linenumber $GFFFILE > $TMPFASTA"); $linenumber -= 1; system("head -n $linenumber $GFFFILE > $TMPGFF"); #we don't want to do this, as the filename is used in a pub record #$GFFFILE = $TMPGFF; } else { $TMPGFF = $GFFFILE; } #count the file lines. we need this to track load progress open( WC, "grep -c -v '^#' $TMPGFF |" ); # open(WC,"grep -c -v '^#' $GFFFILE |"); $linecount = ; chomp $linecount; close(WC); ($linecount) = $linecount =~ /^\s*?(\d+)/; $progress = Term::ProgressBar->new( { name => "Approx $linecount features", count => $linecount, ETA => 'linear', } ); $progress->max_update_rate(1); $next_update = 0; Bio::Chado::LoadDBI->init(); ($auto_cv) = Bio::Chado::CDBI::Cv->search( { name => 'autocreated', } ); ($fp_cv) = Bio::Chado::CDBI::Cv->search( { name => $FP_CV, } ); die "Unable to find a 'autocreated' cv in the cv table; please add one" unless $auto_cv; warn "No feature property cv found; unknown tags will be put in 'autocreated'" unless $fp_cv; ($so) = Bio::Chado::CDBI::Cv->search( { name => $ONTOLOGY } ); die "Unable to find $ONTOLOGY in cv table; that is a pretty big problem" unless $so; # find needed cvterm and other pieces of information my @needed_cvterms = qw(description synonym note develops_from part_of gff_file score protein); foreach my $n (@needed_cvterms) { cache_cvterm($n, $fp_cv ? $fp_cv->id : 0); } cache_cvterm('region',$so->id); #make sure to get the SO region term my @chado_organisms = Bio::Chado::CDBI::Organism->search( common_name => lc($ORGANISM)); if (scalar @chado_organisms > 1) { die "More than one organism has the common name $ORGANISM. Please\n" . "rerun the loader, specifying the the abbreviation or the genus\n" . "and species enclosed in quotes\n\n"; } elsif (scalar @chado_organisms == 1) { $chado_organism = $chado_organisms[0]; } @chado_organisms = Bio::Chado::CDBI::Organism->search( abbreviation => ucfirst($ORGANISM)) unless($chado_organism); if (scalar @chado_organisms > 1) { die "More than one organism has the abbreviation $ORGANISM. Please\n" . "rerun the loader, specifying the the genus and species enclosed in quotes\n\n"; } elsif (scalar @chado_organisms == 1) { $chado_organism = $chado_organisms[0]; } else { my ($genus, $species) = split /\s+/, $ORGANISM; ($chado_organism) = Bio::Chado::CDBI::Organism->search( genus => $genus, species => $species ); } ($chado_db) = Bio::Chado::CDBI::Db->search( name => $SRC_DB ) if $SRC_DB; ($nullpub) = Bio::Chado::CDBI::Pub->search(miniref => 'null' ); unless ($chado_organism) { warn "\n\nCouldn't find or create organism $ORGANISM.\n"; warn "The current contents of the organism table is:\n\n"; my @all_columns = Bio::Chado::CDBI::Organism->columns; printf "%15s %8s %11s %11s %12s %15s\n\n", sort @all_columns; my $organism_iterator = Bio::Chado::CDBI::Organism->retrieve_all(); while(my $organism = $organism_iterator->next){ my @cols = map { $organism->$_ } sort $organism->columns; printf "%15s %8s %11s %11s %12s %15s\n", @cols; } print "\nPlease see \`perldoc gmod_load_gff3.pl\` for more information\n"; exit 1; } unless ($chado_db) { warn "\n\nCouldn't find or create database $SRC_DB.\n"; warn "The current contents of the database table is:\n\n"; my @all_columns = Bio::Chado::CDBI::Db->columns; printf "%10s %6s %13s %25s %5s %10s\n\n", sort @all_columns; my $db_iterator = Bio::Chado::CDBI::Db->retrieve_all(); while(my $db = $db_iterator->next){ my @cols = map { $db->$_ } sort $db->columns; printf "%10s %6s %13s %25s %5s %10s\n", @cols; } print "\nPlease see \`perldoc gmod_load_gff3.pl\` for more information\n"; exit 1; } } sub load_segments { my $gffio = shift; my $i = 0; # creates the features for each gff segment while ( my $gff_segment = $gffio->next_segment() ) { my ($segment) = Bio::Chado::CDBI::Feature->search( { name => $gff_segment->display_id , organism_id => $chado_organism } ); if ( !$segment ) { # about uniquenames here: since these are coming from ##sequence_region # meta stuff in the header, there will be no uniquename attribute, so the # only thing to do is to generate one. my $f = Bio::Chado::CDBI::Feature->create( { organism_id => $chado_organism, name => $gff_segment->display_id, uniquename => $gff_segment->display_id . '_region', type_id => $cvterm{'region'}, seqlen => $gff_segment->end } ); $i++; $f->dbi_commit; $srcfeature{ $f->name } = $f; } else { $srcfeature{ $segment->name } = $segment; } } return $i; } sub load_sequences { my $seqs_loaded = 0; if ( -e $TMPFASTA ) { Bio::Chado::CDBI::Feature->set_sql( update_residues => qq{UPDATE feature SET residues = residues || ? WHERE feature_id = ?} ); my $sth = Bio::Chado::CDBI::Feature->sql_update_residues; print STDERR "loading sequence data...\n"; #count the file lines. we need this to track load progress open( WC, "grep -c '^>' $TMPFASTA |" ); $linecount = ; chomp $linecount; close(WC); ($linecount) = $linecount =~ /^\s*?(\d+)/; $progress = Term::ProgressBar->new( { name => "Approx $linecount sequences", count => $linecount, ETA => 'linear', } ); $progress->max_update_rate(1); $next_update = 0; my $in = Bio::SeqIO->new( -file => $TMPFASTA, '-format' => 'Fasta' ); while ( my $seq = $in->next_seq() ) { my $name = $seq->id; my @chado_feature = Bio::Chado::CDBI::Feature->search( { 'name' => $name , organism_id => $chado_organism} ); unless (@chado_feature) { #check synonym and dbxref my ($dbh) = Bio::Chado::CDBI::DBI->db_handles(); my $sth = $dbh->prepare( "SELECT feature_id FROM feature_dbxref fd join dbxref d using (dbxref_id) WHERE d.accession = ?" ); $sth->execute($name) or die $sth->errstr; my $rows = $sth->rows; if ($rows < 1) { $sth = $dbh->prepare( "SELECT feature_id FROM feature_synonym fs join synonym s using (synonym_id) WHERE s.name = ?" ); $sth->execute($name) or die $sth->errstr; } while (my $hashref = $sth->fetchrow_hashref) { my @temp_feat = Bio::Chado::CDBI::Feature->search( {'feature_id' => $$hashref{'feature_id'} } ); push @chado_feature, @temp_feat; } } #no, let's just load the sequence into all of them #die "couldn't uniquely identify the sequence identified by $name" # unless (scalar @chado_feature == 1); $progress->message("no feature for sequence $name") unless scalar(@chado_feature); $progress->message("multiple features for sequence $name\n") if scalar(@chado_feature) > 1; my $dna = $seq->seq; undef $seq; #get this thing out of here ASAP, it's using memory foreach my $f (@chado_feature) { $f->residues(''); $f->update; $f->dbi_commit; $progress->message("copying Bio::Seq sequence to simple scalar variable") if DEBUG; $progress->message("copied. Bio::Seq object purged to conserve memory") if DEBUG; my $shredsize = 100_000_000; #don't increase this... my $offset = 0; my $dnalen = length($dna); while ( $offset < $dnalen ) { $progress->message("loading shred. offset: $offset bp") if DEBUG; my $shred = substr( $dna, $offset, $shredsize ); $progress->message("${offset}bp loaded") if $offset > 0 and DEBUG; $sth->execute( $shred, $f->id ); $progress->message("loaded shred") if DEBUG; $offset += $shredsize; } $progress->message("${dnalen}bp loaded") if DEBUG; $f->update; $progress->message("pre dbi_commit") if DEBUG; $f->dbi_commit; $progress->message("post dbi_commit") if DEBUG; } $seqs_loaded++; $next_update = $progress->update($seqs_loaded) if ( $seqs_loaded > $next_update ); $progress->update($seqs_loaded) if ( $seqs_loaded >= $next_update ); $progress->update($linecount) if ( $next_update >= $linecount ); } unlink $TMPFASTA unless $TMPFASTA eq $GFFFILE; unlink $TMPGFF unless $TMPGFF eq $GFFFILE; } return $seqs_loaded; } sub load_feature_locations { my $gff_feature = shift; my $chado_type = shift; my $id = shift; ## GFF features are base-oriented, so we must add 1 to the diff ## between the end base and the start base, to get the number of ## intervening bases between the start and end intervals my $seqlen = ( $gff_feature->end - $gff_feature->start ) + 1; ## we must convert between base-oriented coordinates (GFF3) and ## interbase coordinates (chado) ## ## interbase counts *between* bases (starting from 0) ## GFF3 (and blast, bioperl, etc) count the actual bases (origin 1) ## ## ## 0 1 2 3 4 5 6 7 8 : INTERBASE ## A T G C G T A T ## 1 2 3 4 5 6 7 8 : BIOPERL/GFF ## ## from the above we can see that we need to add/subtract 1 from fmin ## we don't touch fmax my $fmin = $gff_feature->start - 1; # GFF -> InterBase my $fmax = $gff_feature->end; my $frame = $gff_feature->frame eq '.' ? 0 : $gff_feature->frame; # logic for creating feature.uniquename and feature.name (040414 allenday): # # if you decide to change the logic, please email the gmod-schema list before committing. # many people depend on the convention outlined here. # # UNIQUENAME # # 1. if --uniquename tag given, use data from that tag, or die if non-existant # 2. else, if ID tag available, use its value # 3. else, use a combination of GFF objects primary tag, seq_id, and, if available, # positional information. # 4. die, not enough information to generate a uniquename # # NAME # # 1. use Name tag if available # 2. else, use ID tag if available # 3. else, feature has no name # my $uniquename = ''; my $name = ''; if( defined($UNIQUENAME) and $gff_feature->has_tag($UNIQUENAME) ) { ($uniquename) = $gff_feature->get_tag_values($UNIQUENAME); } elsif( defined($UNIQUENAME) ) { die("The --uniquename tag was specified as '$UNIQUENAME, but a feature was found without this tag"); } elsif( $gff_feature->has_tag('ID') ) { ($uniquename) = $gff_feature->get_tag_values('ID'); } elsif( $gff_feature->primary_tag and $gff_feature->seq_id ) { my $position = $fmax eq '.' ? '' : ":$fmin..$fmax"; my($parentname) = $gff_feature->has_tag('Parent') ? $gff_feature->get_tag_values('Parent') : ''; $uniquename = sprintf("_%s_%s_%s%s", $parentname, $gff_feature->primary_tag, $gff_feature->seq_id, $position ); } else { die("not enough information available to make a uniquename for $gff_feature"); } my %feature_attributes = ( organism_id => $chado_organism->id, type_id => $chado_type->id, uniquename => $uniquename, ); my $used_ID_for_Name = 0; if ( $gff_feature->has_tag('Name') ) { ($name) = $gff_feature->get_tag_values('Name'); $feature_attributes{name} = $name; } elsif ( $gff_feature->has_tag('ID') ) { ($name) = $gff_feature->get_tag_values('ID'); $feature_attributes{name} = $name; $used_ID_for_Name = 1; } my $chado_feature; if ( $gff_feature->has_tag('Name') ) { ($name) = $gff_feature->get_tag_values('Name'); } elsif ( $gff_feature->has_tag('ID') ){ ($name) = $gff_feature->get_tag_values('ID'); } ($chado_feature) = Bio::Chado::CDBI::Feature->find_or_create(\%feature_attributes); if(!defined($chado_feature->seqlen)){ $chado_feature->seqlen($seqlen); $chado_feature->update; $chado_feature->dbi_commit; } push @transaction, $chado_feature; if ($used_ID_for_Name) { load_Name_tag ($gff_feature, $chado_feature); } my $source = $gff_feature->source_tag(); if ( $source && $source ne '.') { #make source a feature prop unless ($gff_source_db) {#create a new db for keeping GFF sources $gff_source_db = Bio::Chado::CDBI::Db->find_or_create( { name => 'GFF_source', description => 'A collection of sources (ie, column 2) from GFF files', } ); push @transaction, $gff_source_db; } unless ($gff_source{$source}) { #now make a dbxref for the source $gff_source{$source} = Bio::Chado::CDBI::Dbxref->find_or_create( { db_id => $gff_source_db->id, accession => $source, } ); push @transaction, $gff_source{$source}; } #now tie feature and source together in feature_dbxref my $feature_dbxref = Bio::Chado::CDBI::Feature_Dbxref->find_or_create( { feature_id => $chado_feature->id, dbxref_id => $gff_source{$source}->id }); push @transaction, $feature_dbxref; } $chado_feature->dbxref_id( $dbxref{$id} ) if $gff_feature->has_tag('ID'); # is this the right thing to do here? $chado_feature->update; # flush updates to this feature object if ( $id eq $gff_feature->seq_id or $gff_feature->seq_id eq '.' ) { #ie, this is a srcfeature (ie, fref) so only create the feature $srcfeature{$gff_feature->seq_id} = $chado_feature; return ($chado_feature); } # find pre-existing feature locations that were loaded prior # to this GFF3 file. if(!$featureloc_locgroup{ $chado_feature->id }){ my $max_locgroup = undef; foreach my $previous_featureloc (Bio::Chado::CDBI::Featureloc->search( feature_id => $chado_feature->id, )){ if($fmin == $previous_featureloc->fmin and $fmax == $previous_featureloc->fmax and $previous_featureloc->srcfeature_id == $srcfeature{$gff_feature->seq_id}->id ){ return $chado_feature; } $max_locgroup = $max_locgroup > $previous_featureloc->locgroup ? $max_locgroup : $previous_featureloc->locgroup; } if(defined($max_locgroup)){ $featureloc_locgroup{ $chado_feature->id } = $max_locgroup; } } # add feature location $featureloc_locgroup{ $chado_feature->id }++; my $locgroup = $featureloc_locgroup{ $chado_feature->id }; my($parent) = $gff_feature->has_tag('Parent') ? $gff_feature->get_tag_values('Parent') : (); if($parent && $featureloc_locgroup{ $feature{$parent} }){ $locgroup = $featureloc_locgroup{ $feature{$parent} }; } $locgroup ||= 0; if (DEBUG) { $progress->message("adding featureloc for gff string:"); $progress->message("\t".$gff_feature->gff_string); # print STDERR $chado_feature->id , "\t" , $locgroup , "\n"; if($parent){ $progress->message("srcfeature_id: " . Dumper($feature{$parent})); } } my $chado_featureloc = Bio::Chado::CDBI::Featureloc->find_or_create( { feature_id => $chado_feature->id, fmin => $fmin, fmax => $fmax, strand => $gff_feature->strand, phase => $frame, locgroup => $locgroup, srcfeature_id => $srcfeature{$gff_feature->seq_id}->id, } ); push @transaction, $chado_featureloc; return ($chado_feature); } sub cache_cvterm { my $name = shift; my $soid = shift; #we need an ontology source check here. GO has an obsolete term for 'protein', but we want the #one from SO. if ($soid && !$cvterm{$name} ) { ( $cvterm{$name} ) = Bio::Chado::CDBI::Cvterm->search( { name => $name, cv_id=> $soid } ) || Bio::Chado::CDBI::Cvterm->search( { name => ucfirst($name), cv_id=> $soid } ); } if (!$cvterm{$name} and !$soid) { ( $cvterm{$name} )=Bio::Chado::CDBI::Cvterm->search( { name => $name } ) ||Bio::Chado::CDBI::Cvterm->search( { name => ucfirst($name) } ); } $cvterm{$name} = $cvterm{$name}->next() if defined( $cvterm{$name} ) and $cvterm{$name}->isa('Class::DBI::Iterator'); if ( !$cvterm{$name} && $soid != $so->id ) { unless ($null_db_id) { my ($null_db) = Bio::Chado::CDBI::Db->search( { name => 'null' } ); $null_db_id = $null_db->id; } my ($dbxref) = Bio::Chado::CDBI::Dbxref->find_or_create( { db_id => $null_db_id, accession => $auto_cv->name.":".$name, } ); ( $cvterm{$name} ) = Bio::Chado::CDBI::Cvterm->find_or_create( { name => $name, cv_id => $auto_cv->id, definition => 'autocreated by gmod_load_gff3.pl', dbxref_id => $dbxref->id, } ); } die "unable to create a '$name' entry in the cvterm table" if (!$cvterm{$name} && !$soid ); } !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; chdir $origdir; chado-1.23/lib/Bio/000755 000765 000024 00000000000 12061672375 014062 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/Chado/000755 000765 000024 00000000000 12061672375 015100 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/FeatureIO/000755 000765 000024 00000000000 12061672375 015705 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/000755 000765 000024 00000000000 12061672376 014611 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/Bulkfiles/000755 000765 000024 00000000000 12061672376 016531 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/Bulkfiles.pm000644 000765 000024 00000276233 11256707534 017104 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles; use strict; =head1 NAME Bio::GMOD::Bulkfiles -- produce bulk sequence and feature files from Chado genome database for public distribution . =head1 ABOUT Bulkfiles This generates Fasta, GFF, DNA and other bulk genome annotation files at ftp://flybase.net/genomes/Drosophila_melanogaster/current/ .. (and other species) It works with several FlyBase chado dbs, and with SGDLite chado db Bulkfiles is mostly self-contained, but uses a few BioPerl parts plus XML::Simple for configuration files. All of the organism/database-specific logic should be in these configuration files (see GMODTools/conf/bulkfiles/) fbbulk-r4.xml, sgdbulk1.xml .. -- organism/database/release specific options chadofeatsql.xml -- chado db sql calls to dump features chadofeatconv.xml -- feature conversion options =head1 INPUTS Chado genome databases available (aug 2004) are ftp://flybase.net/genomes/Drosophila_melanogaster/current/pgsql/chado_r3_2_26_s.gz http://sgdlite.princeton.edu/download/sgdlite/2004_05_19_sgdlite.sql.gz Given a postgres db installation, load dump file with createdb sgdlite_20040519 (zcat 2004_05_19_sgdlite.sql.gz | psql -d sgdlite_20040519 -f - ) >& log.load & =head1 OUTPUTS DNA files (full chromosomes) in raw and fasta formats GFF (v3) feature files FFF (v1) feature files (used in FlyBase, each complex feature one line using GenBank/EMBL locations) Fasta sequence for each selected feature set, with headers from feature files BLAST Index files (NCBI) Chado database overview tables. A standard genome webpage for access to bulk data. =head1 REQUIREMENTS and INSTALLATION Uses a few GMOD, BioPerl, other Perl5 modules, including Bio::GMOD::Config.pm (and included Config2.pm) XML::Simple Program looks for conf/ folder with .xml files. You likely only need to edit fbbulk-r4.xml equivalent. =head1 USAGE # see bin/bulkfiles.pl use Bio::GMOD::Bulkfiles; my $bulkfiles= Bio::GMOD::Bulkfiles->new( configfile => 'fbbulk-r4', # data-release config file, required param debug => 1, showconfig => 0, failonerror => 1, ); $bulkfiles->dumpFeatures(); # extract feature tables from chado sql db $bulkfiles->sortNSplitByChromosome(); # collate and separate by chromosome $bulkfiles->dumpChromosomeBases(); # extract chromosome dna files # produce various output format bulk files from above my $result= $bulkfiles->makeFiles( formats => [qw(fff gff fasta blast gnomap)], chromosomes => [qw(all)] ); print STDERR "Bulkfiles done. result=",$result,"\n"; =head1 WHY Bulkfiles? (rather than using other middleware layers to chado db - chadoxml, chadodbi, bioperl, ...) The general logic is 1. dump all chado db features using simple (and quick) sql, to common intermediate table files, and chromosome dna to raw files. The feature info is simple: type, location, name/id, and a few attributes (db_xrefs,..) 2. postprocess these table files to create the various public use formats (the time-consuming and configurable part), organized into per-chromosome files. Here are some reasons we take this approach: a. using simple sql to dump all db features to intermediate table allows easy checks that all features get to bulk files b. simple sql dump is fast (30 - 60 min for full fly genome), reliable in getting all mapped features by keeping logic simple c. process table output in stages - better debugging of steps in process, and can split processing among computers c1. the stages are loosely coupled - one can go back, tweek configurations and get a new output w/o redoing the complete extraction process. d. convert one common feature table + dna to several output formats in one step, or repeatedly as needed. e. combine features from several chado dbs (flybase now has 3 chado dbs for d.mel genome features), and add other sources like flybase cytology features. f. need fairly complex and data specific configurations - moving that to config files keeps code reusable. g. each genome chado database has different policy and choices with respect to feature, vocabulary and other data. A highly configurable tool, with data extraction and correction methods that are separate and tunable is needed to adapt to such variation in genome databases. =head1 CONFIGURATION These are essential parts to change for a specific database release. See e.g., conf/sgdbulk1.xml. -- include config files allow many of these options can be packaged separately for reuse among main release configs. E.g. conf/bulkfiles/fbreleases.xml contains release name, date, databse access and identified by relid value SGD Chado DB Lite r1 -- your release title -- various releases and their chado db name -- database connection information (release.db overrides this db.name) -- organism info scer Saccharomyces cerevisiae -- configure chado feature sql dump information chromosomes -- which sql elements to use features matches analysis -- configure chado dna/residue sql dump information -- config. for output files; see conf/bulkfiles/filesets.xml -- feature sets to make fasta bulk files -- see conf/bulkfiles/featuresets.xml gene mRNA -- more fasta dump information MORE CONFIG FILES: chadofeatsql.xml -- chado db sql calls to dump features sql for various feature classes, including chromosomes, gene model, matches, analysis, synteny, with some helper sql views and postprocessing scripts. chadofeatconv.xml -- feature conversion options this is mostly about how to process specific features (all SO terms). Tied into Bulkfiles::FeatureWriter code. =head1 NOTES genomic sequence file utilities, part2; parts converted from flybase/work.local/chado_r3_2_26/soft/chado2flat2.pl flybase/work.local/chado_r3_2_26/soft/chadosql2flatfeat.pl Find source here set cvsd=':pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod' cvs -d $cvsd login cvs -d $cvsd co schema/GMODTools Backup CVS: set cvsd=':pserver:anonymous@eugenes.org:/bio/cvs' cvs -d $cvsd co -d GMODTools gmod/schema/GMODTools =head1 QUICK TEST (Postgres active): # get soft cvs -d $cvsd co -d GMODTools schema/GMODTools # load a genome chado db to Postgres wget http://http://sgdlite.princeton.edu/download/sgdlite/2004_05_19_sgdlite.sql.gz createdb sgdlite_20040519 (zcat *sgdlite.sql.gz | psql -d sgdlite_20040519 -f - ) >& log.load # set GMOD_ROOT to here and run default config cd GMODTools env GMOD_ROOT=$PWD perl -I./lib/ bin/bulkfiles.pl sgdbulk1 =head1 UPDATES 2007-Oct, version 1.1 - No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default). - Gene Ontology association file output, see go_association tags in configurations formatted as per http://geneontology.org/GO.format.annotation.shtml - Validate main variables in chado database: ${golden_path}, ${seq_ontology} This step, on now by default, checks that database contains values set in configuration for chromosome type, sequence ontology CV name, and any other critical variables. If failed, db is inspected for real values. - miscellany bugs cured and configuration updates. tables/overview now again active. =head2 no_csomesplit update this change is needed to handle partially assembled genomes (the common first draft) with many scaffolds (10,000s of < 1MB to 100,000s of < 100Kb segments) The old state assumes a handful of full or nearly full chromosomes implicitly by producing 1 file/golden_path segment, at least as temporary working files. This is a problem for any file system, where > 1,000 files/folder is problematic and > 100,000 can be serious. THis isnt needful design, just how the program grew (for drosophila genome data with 5 golden_path segments). First try: use "sum" as special chromosome name, "all" is already used specially for final output of public files with all csomes in one file. Main changes are to these subs here: See filesets.xml configuration with flags no_csomesplit, perchr and makeall Features: sortNSplitByChromosome : produce temporary per-csome feature files (tmp/chadofeat-org-csome) getFeatTableFiles : collect temp per-csome feat. files for further processing -- this hands data to downstream BulkWriter packages for final file (GFF,..) creation. Then the filesets perchr and makeall flags control final file set. >> need to revise downstream packs (FeatureWriter, ...) to not split into per-csome files (done before 'makeall' option) Dna: -- possibly revise here to use chado sql calls instead of temp dna files? dumpChromosomeBases: create dna string files from chado feature.residues see ## for making Unknown 'bag' chromosomes from parts ## $csomeset->{$chr}->{parts} getBasesFromFiles: return data from dna string files Note use of Bio::GMOD::Bulkfiles::MyLargePrimarySeq for dna files. >> first try using only chadodb get residues failed to create chromosome.fasta (no dna/ files). other fasta looked ok. See FastaWriter:processFasta : has special raw2Fasta for csomes., =head2 Gene Ontology association table * this is in essense done. See filesets.xml: go_association, and SQL code in chadofeatsqll.xml, to use, add to site_defaults, go_association - this should be a relatively simple subclass for producing GO association files. Need (1) Chado SQL to produce basic table, per gene feature, of linked GO terms via what link table(s)? -- curated GO terms via feature_cvterm : 52929 in _dmel_r4_3_16? -- also find IEA GO terms via analysisfeature to alt-species proteins select fc.cvterm_id, count(distinct fc.feature_id) as n_feature, (select name from cvterm where cvterm_id = fc.cvterm_id) as term from feature_cvterm fc group by fc.cvterm_id; -- add restriction to GO CV tables ... * something weird here, parameciumDB queries slower than _dmel_r4_3_16, a larger chado db; maybe we loaded it wrong, with char encoding (UTF-8) instead of SQL_ASCII (2) perl code to reformat to GO spec. =head1 TODO =head2 Gene Pages XML - see wfleabase.org/search/ with resultant gene page reports using simple GeneSummary XML - output from chado using genepage SQL for all properties/gene feature =head2 New project configurations - should add user interface software to prompt for the few basic required variables (chado db name, golden_path, choices for output, ...) and create project configuration.xml from template.xml =head2 Other useful output files? - BulkWriter.pm now does basic SQL query to table file, add some other useful table file outputs? gene IDs x synonyms? =head2 Remove FFF intermediate for GFF only - drop the now awkward FFF format for GFF as primary feature format, use to create Fasta from it. =head1 SEE ALSO GMOD::Chado::SeqUtils -- older sequence in/out/check methods for Chado DB =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- #debug# #use lib("/bio/argos/common/perl/lib", "/bio/argos/common/system-local/perl/lib"); #use lib("/Users/gilbertd/bio/dev/gmod/schema/GMODTools/lib/"); use POSIX; use FileHandle; use File::Basename; use File::Spec::Functions qw/ catdir catfile /; use File::Path; ## mkpath use File::Temp qw/ tempfile tempdir /; use FindBin qw( $RealBin); #? eval use DBI; use Bio::Location::Simple; use Bio::PrimarySeq; # see MyLargePrimarySeq use use Bio::GMOD::Bulkfiles::BulkWriter; # see getWriter() - base class BulkWriter, loads any other subclasses use Bio::GMOD::Bulkfiles::MyLargePrimarySeq; use Bio::GMOD::Bulkfiles::MySplitLocation; # see below require Bio::GMOD::Config2; dont use our $DEBUG = 0; my $VERSION = "1.1"; # no_csomesplit update use vars qw/ @ENV_KEYS @featset @allfeats %mapchr_pattern $fndel /; # special config keys to put in ENV for Config2 reader # 0710: add more: ENV_default set : golden_path seq_ontology # too many rel.variables: relid , release_id == rel ?? BEGIN{@ENV_KEYS= qw( species org date title datadir rel relfull relid release_url release_id release_date GFF_source taxon ftp_url golden_path seq_ontology );} my $defaultconfigfile="bulkfiles"; # was 'sequtil' my %dnaseqs=(); #? package global - read only BioseqFile my @defaultformats= qw(overview fff gff fasta tables blast ); # gnomap sub new { my $that= shift; my $class= ref($that) || $that; my %fields = @_; my $self = \%fields; # config should be one bless $self, $class; $self->init(); return $self; } sub closeit { my ($self)= @_; my $dbh= delete $self->{dbh}; if ($dbh) { $dbh->disconnect(); } } sub DESTROY { my $self = shift; $self->closeit(); } sub init { my $self= shift; # $self->{tag}= 'Bulkfiles' unless (exists $self->{tag} ); ## $self->{outh}= *STDOUT unless ( exists $self->{outh} ); ## DROP THIS ?? $DEBUG= $self->{debug} if defined $self->{debug}; my $cdate= POSIX::strftime("%F %T", localtime( $^T )); $cdate =~ s/[^\w-]/_/g; ## make sure no space in date ! $self->{date}= $cdate; $self->{failonerror}= 0 unless defined $self->{failonerror}; $self->{skiponerror}= 1 unless defined $self->{skiponerror}; $self->{ignoredbresidues}= 0 unless defined $self->{ignoredbresidues}; $self->{addids}= 0 unless defined $self->{addids}; $self->{config}={} unless defined $self->{config}; $self->{configfile}= $defaultconfigfile unless defined $self->{configfile}; $self->{verbose}=0 unless defined $self->{verbose}; # no_csomesplit is now a call option, but respect only if >0, replacing config value $self->readConfig($self->{configfile}); # calls initData() } =item readConfig($configfile) read a configuration file - adds to any loaded configs -- changed location to conf/bulkfiles/ -- read all of these (no) but need to locate subdir =cut sub readConfig { my $self= shift; $self->{config}= $self->callReadConfig(@_); $self->initData(); } # dont dupl this elsewhere e.g. BulkWriter.pm subs sub callReadConfig { my $self= shift; my ($configfile)= @_; my $returnConfig= {}; my $replacevariables= $DEBUG; #?? make default, then drop rereadConfig eval { my $config2= $self->{config2}; # Config2 object, not hash unless(ref $config2) { require Bio::GMOD::Config2; $self->{config2}= $config2= Bio::GMOD::Config2->new( { searchpath => [ 'GMODTools/conf/bulkfiles', 'conf/bulkfiles', 'conf', ], debug => $DEBUG, read_includes => 1, # process include = 'conf.file' } ); } my @showtags= ($self->{verbose}) ? qw(name title date about) : qw(title date); $config2->setargs( showtags => \@showtags ); # $self->{config}= $returnConfig= $config2->readConfig( $configfile, {}, {}); ## need empty hashrefs! ## added processing of include="include.conf" unless ($config2->readConfigOk()) { warn "** Error with configuration files\n"; die if($self->{failonerror} || $self->{automake}); } if($replacevariables) { # 0710 update my @keys= @ENV_KEYS; # also inspect config for simple keys foreach my $k (keys %$returnConfig) { my $v= $$returnConfig{$k}; push(@keys, $k) unless(ref($v)); } foreach my $k (@keys) { my $v= $$returnConfig{$k}; $ENV{$k}= $v if(defined $v and not defined $ENV{$k}); } print STDERR "readConfig:pass2 for variables=@keys\n" if $DEBUG; # readConfig replace=>1 is bad, replaces 1st/primary values with backup values :( # new updateVariables will touch only ${variable} set # recurses thru all of config hash to find '${variable}' matching %ENV keys $returnConfig= $self->{config2}->updateVariables( $returnConfig, { Variables => \%ENV, replace =>1 }, ); } print STDERR $config2->showConfig( $returnConfig, { debug => $DEBUG }) if ($self->{showconfig}); }; if ($@) { my $cf= $self->{config2}->{filename}; warn "Config2: file=$cf; err: $@"; die if ($self->{failonerror} || $self->{automake}); } return $returnConfig; } sub rereadConfig { my $self= shift; print STDERR "rereadConfig\n" if $DEBUG; my $config= $self->config; foreach my $k (@ENV_KEYS) { defined $$config{$k} and $ENV{$k}= $$config{$k}; } my $newconfig= {}; eval { ## need to replace ${variables} with config values ## so need to change $self->{config} hash, not newconfig ## still need rereadConfig after above updateVariables, as init() changes config ## but could use a 2nd updateVariables here instead ?? $self->{config2}->updateVariables( $config, { Variables => \%ENV, replace =>1 }, ); # $newconfig= $self->{config2}->readConfig( $self->{configfile}, # { Variables => \%ENV }, $newconfig, ); # $self->config->{doc} = $newconfig->{doc} if $newconfig->{doc}; }; if ($@) { my $cf= $self->{config2}->{filename}; warn "Config2: file=$cf; err: $@"; } # print STDERR "new.doc.content=",$newconfig->{doc}->{content},"\n" if $DEBUG; } sub updateConfigVars { my $self= shift; my $config= $self->config; foreach my $k (@ENV_KEYS) { defined $$config{$k} and $ENV{$k}= $$config{$k}; } eval { $self->{config2}->updateVariables( $config, { Variables => \%ENV, replace =>1 }, ); }; if ($@) { warn "Config2: file=",$self->{config2}->{filename},"; err: $@"; } } sub config { return shift->{config}; } sub getconfig { my $self= shift; my $cf= $self->{config2}; if ($cf && @_) { return $cf->get(@_); } } =item get_filename $fname= get_filename($org, $chr, $featn, $rel, $format) make standard output file name "${org}_${chr}_${featn}_${rel}.${format}" See split_filename; need to parse above out of file name, but chr, featn, rel can have '_'. Use '-' instead and disallow in parts? Use '.'? =cut sub get_filename { my $self= shift; my( $org, $chr, $featn, $rel, $format)= @_; unless ( $org ) { $org="noname"; } if ( $chr ) { $chr="$fndel${chr}"; } else { $chr=''; } if ( $featn ) { $featn="$fndel${featn}"; } else { $featn=''; } if ( $rel ) { $rel="$fndel${rel}"; } else { $rel=''; } unless ( $format ) { $format="txt"; } my $filename="${org}${chr}${featn}${rel}.${format}"; return $filename; } =item split_filename ( $org, $chr, $featn, $rel, $format)= split_filename($filename) parse standard output file name "${org}-${chr}-${featn}-${rel}.${format}" THIS IS problematic - both featn and rel can have _, need other split method now chr can have _: dpse_4_group2_transposable_element_rel_2_1.. BAD NEWS: dpse 4_group5; XR_group3; ... underscore wont do it $fndel="."; dpse.4_group2.transposable_element.rel_2.1.fasta $fndel="-"; dpse-4_group2-transposable_element-rel_2.1.fasta $fndel="="; dpse=4_group2=transposable_element=rel_2.1.fasta $fndel="--"; dpse--4_group2--transposable_element--rel_2.1.fasta $fndel="#"; dpse#4_group2#transposable_element#rel_2.1.fasta =cut sub split_filename { my $self= shift; my ($fname,$no_orgchr)= @_; my( $org, $chr, $featn, $rel, $format, $path, $featORrel, $gz, $xtra); if ($fname =~ s/(\.gz)$//) { $gz=$1; } ($fname, $path, $format) = File::Basename::fileparse($fname, '\.[^\.]+'); $format .= $gz if $gz; #?? if($no_orgchr) { # only fname, format valid ... ($org,$chr,$featn,$rel)= ('')x4; $featn= $fname; #??? $chr="all"; } else { #my $nu= ($fname =~ tr/$fndel/$fndel/);## bad my @v= split(/$fndel/, $fname, 4); #! rel can have _; !! chr can have _; feat might have _ my $nu= scalar(@v); if (@v == 4) { ($org,$chr,$featn,$rel)= @v; $nu++ if (index($rel,$fndel)>=0); } elsif (@v == 3) { ($org,$chr,$featORrel)= @v; # might also be $feat,$chr,$xxx if ($featORrel =~ /\d/) { $rel= $featORrel; $featn=''; } else { $featn= $featORrel; $rel=''; } } elsif (@v == 2) { ($org,$chr)= @v; $featn= $rel='';} ## might also be ($featn,$chr) if ($nu > 4 || $nu<3) { warn "split_filename : ambiguous parts $org,$chr,$featn,$rel from '$fname'\n"; } } return ( $org, $chr, $featn, $rel, $format); } =item dnafile($chr) locate file of raw chromosome dna bases ?? change naming of dnafile() to same as others using get_filename now: dna-chrIX.fasta,raw to : scer_chrIII_dna_sgdr1.fasta,raw =cut sub dnafile { my ($self, $chrOrFile)= @_; #? search for it .. if ($self->config->{dnafiles}->{path}); if ($chrOrFile) { my $dnafile=""; if (-e $chrOrFile) { $dnafile= $chrOrFile; } else { my $org= $self->config->{org}; my $rel= $self->config->{rel}; my $fn= $self->get_filename($org,$chrOrFile,'dna',$rel,'raw'); # my $fn= "dna-$chrOrFile.raw"; $dnafile = catfile( $self->{dnadir}, $fn); } $self->{dnafile}= $dnafile; } return $self->{dnafile}; } =item remapArm -- unordered contigs -- singles (? no feats) and doubles - put into common out files? -- if so, need to offset start/end to fit into unorderd 'chromosome' See also FeatureWriter remapName, remapArm ... =cut sub remapArm { my ($self,$arm,$fmin,$fmax,$strand,$csomeset)= @_; my $savearm= $arm; $csomeset= {} unless($csomeset); if ($csomeset->{'_part2chr'}->{$arm}) { $arm= $csomeset->{'_part2chr'}->{$arm}; } else { foreach my $mp (sort keys %mapchr_pattern) { next if ($mp eq 'null'); # dummy? my $from= $mapchr_pattern{$mp}->{from}; next unless($from); my $to = $mapchr_pattern{$mp}->{to}; #$arm =~ s/$from/$to/g; if ($to =~ /\$/) { $arm =~ s/$from/eval($to)/e; } else { $arm =~ s/$from/$to/g; } } } ## drop arm if $arm is mapped to "" ## need to trap $arm not in $csomeset -- errors like Contig_Contig below ## which either need to be remapped or otherwise handled. ## if (!$csomeset->{$arm}) { } elsif ($csomeset->{$arm} && ref($csomeset->{$arm}->{parts})) { my $parts= $csomeset->{$arm}->{parts}; MATCHPART: foreach my $p (@$parts) { my $nm = $p->{name}; #? or id ? if ($nm eq $savearm) { #?? is this ok my $b = $p->{start}; my $e = $p->{length} + $b; my $st= $p->{strand}; if ($st < 0) { #($st eq '-')?? do we need to flip all - min,max relative to arm.e ? $strand= -$strand; ($fmax,$fmin) = ($e - $fmin-1, $e - $fmax-1); } else { $fmin += $b - 1; $fmax += $b - 1; } last MATCHPART; } } } return($arm,$fmin,$fmax,$strand,$savearm); } =item dumpChromosomeBases $sequtil->dumpChromosomeBases( \@chromosomes or $config->chromosomes) foreach chr @chromosomes write dnafile() getBasesFromDb($chrID) >> moved out >>$sequtil->raw2Fasta() if $config->{dofasta}; -- write from db to files oct04 -- add option to create 'chr-U' from bag of Unknown_* golden_path entries in getChromosomeTable. ** See FeatureWriter remapArm and precursor work w/ Dpse; need to create ordered Uknown chr, joining contigs end-to-end. oct07 -- need no_csomesplit / no dna files option (for 100,000s of scaffolds cases) =cut sub dumpChromosomeBases { my ($self, $chromosomes)= @_; #? or chromosome->{} my @files=(); my $csomeset= $self->getChromosomeTable(); $chromosomes= $self->getChromosomes() unless (ref $chromosomes); my $no_csomesplit= $self->config->{no_csomesplit} || 0; # FIXME: 0710 #? $chromosomes=["sum"] if($no_csomesplit); # 2007oct; not "all", other special csome name ! # ^^ can we use one dna.raw file with simple csome byte index instead of many files? # or chado db feature.residues fetch as csome 'file' if($no_csomesplit) { my $chr="sum"; #? "sum" or "all" my $dnafile= $self->dnafile($chr); #? add $org option return [ { path => $dnafile, type => 'dna/raw', name => $chr, chr => $chr, } ]; } ##? change naming of dnafile() to same as other files? ## using get_filename my $saveorg= $self->config->{org}; foreach my $chr (@$chromosomes) { next if $chr eq 'all'; my $spp= $csomeset->{$chr}->{species}; ## FIX $dnafile name for this ! my $org= $self->speciesAbbrev($spp); ## next if($org && $org ne $self->config->{org}); ## skip if $spp ne $self->config->{species} ? or Rename ; but need spp abbrev $self->config->{org}= $org if $org; my $dnafile= $self->dnafile($chr); #? add $org option $self->config->{org}= $saveorg; print STDERR "dumpChromosomeBases $dnafile\n" if $DEBUG; if (-e $dnafile) { warn "dumpChromosomeBases: wont overwrite $dnafile"; # die if failonerror ?? optionally clean/rewrite ? } ## for making Unknown 'bag' chromosomes from parts elsif (ref($csomeset->{$chr}->{parts})) { my $parts= $csomeset->{$chr}->{parts}; my $len= 0; my $np= 0; open(DNA,">$dnafile"); foreach my $p (@$parts) { my $id= $p->{id}; my $bases= ($id) ? $self->getBasesFromDb($id,1) : ''; print DNA $bases if ($bases); $len += length($bases); $np++; } close(DNA); print STDERR " dumped $chr parts=$np, total_length=",$len,"\n" if $DEBUG; push(@files, { path => $dnafile, type => 'dna/raw', name => $chr, chr => $chr, }); } else { my $id= $csomeset->{$chr}->{id} || $chr; my $bases= $self->getBasesFromDb($id,1); if ($bases) { open(DNA,">$dnafile"); print DNA $bases; close(DNA); print STDERR " dumped length=",length($bases),"\n" if $DEBUG; push(@files, { path => $dnafile, type => 'dna/raw', name => $chr, chr => $chr, }); } else { warn "dumpChromosomeBases: no bases for $dnafile\n"; die if $self->{failonerror}; } } } return \@files; } =item getChromosomeFiles() return fileset of dna/raw chromosomes =cut sub getChromosomeFiles { my ($self, $chromosomes)= @_; $chromosomes= $self->getChromosomes() unless (ref $chromosomes); my @files=(); ## FIXME: no_csomesplit my $no_csomesplit= $self->config->{no_csomesplit} || 0; # FIXME: 0710 foreach my $chr (@$chromosomes) { next if $chr eq 'all'; my $dnafile= $self->dnafile($chr); if (-e $dnafile) { push(@files, { path => $dnafile, type => 'dna/raw', name => $chr, chr => $chr }); } } return \@files; } =item getDumpFiles($targets) return list of feature dump files =cut sub getDumpFiles { my ($self, $targets, $fdump)= @_; $fdump= $self->config->{featdump} unless($fdump); my @files=(); my @missing=(); my $seqsql = $self->getSeqSql($fdump->{config},$fdump->{ENV}); my $outpath= $self->getReleaseSubdir( $fdump->{'path'} || catdir( $self->config->{TMP}, "featdump") ); $fdump->{'path'}= $outpath; # save for reuse my $sqltag = $fdump->{tag} || "feature_sql"; my $sqltype = $fdump->{type}; unless($targets) { $targets = $fdump->{target}; } # should be array ? unless($targets) { my @tg= sort keys %{$seqsql->{$sqltag}}; $targets= \@tg; } unless(ref $targets) { $targets= [ $targets ]; } foreach my $tgname (@$targets) { my $fs= $seqsql->{$sqltag}->{$tgname}; unless($fs) { next; } my $type= $fs->{type}; my $sql = $fs->{sql}; my $outn= $fs->{output} || $tgname.".tsv"; unless($sql && (!$sqltype || $type =~ m/\b$sqltype\b/)) { warn "getDumpFiles skip: $tgname/$type<>$sqltype\n"; next; } #?? my $outf= catfile($outpath,$outn); if(! -e $outf && -e "$outf.gz") { $outf .=".gz";} # changed keys: name => to target => ; file => to name => if (-e $outf) { push(@files, { path => $outf, type => $type, target => $tgname, name => $outn, }); } else { push(@missing, { path => $outf, type => $type, target => $tgname, name => $outn, }); } } return (wantarray) ? (\@files,\@missing) : \@files; } =item getFastaFiles() return fileset of available features/fasta =cut sub getFastaFiles { my ($self, $chromosomes)= @_; my @files=(); $chromosomes= $self->getChromosomes() unless (ref $chromosomes); #? drop this; moved fasta out of dnadir .. foreach my $chr (@$chromosomes) { my $dnafile= $self->dnafile($chr); (my $fastafile = $dnafile.".fasta") =~ s/\.raw//; if(! -e $fastafile && -e "$fastafile.gz") { $fastafile .=".gz";} if (-e $fastafile) { push(@files, { path => $fastafile, type => 'chromosome/fasta', name => $chr, chr => $chr}); } } my $fset= $self->getFilesetInfo('fasta'); my $fadir= $self->getReleaseSubdir( $fset->{path} || 'fasta/'); if (opendir(D, $fadir)) { foreach my $fa (grep(/^\w/,readdir(D))) { my ( $org, $chr, $featn, $rel, $format)= $self->split_filename($fa); $featn = 'feature' unless($featn); next unless( grep {$chr eq $_} @$chromosomes ); #? push(@files, { path => "$fadir/$fa", type => "$featn/fasta", name => $fa, chr => $chr }); } closedir(D); } return \@files; } sub getFeatFiles { my ($self, $chromosomes)= @_; my @files=(); my $fset= $self->getFilesetInfo('fff'); my $featdir= $self->getReleaseSubdir( $fset->{path} || 'fff/'); $chromosomes= $self->getChromosomes() unless (ref $chromosomes); if (opendir(D, $featdir)) { foreach my $fa (grep(/^\w/,readdir(D))) { my ( $org, $chr, $featn, $rel, $format)= $self->split_filename($fa); next unless( grep {$chr eq $_} @$chromosomes ); $featn ||= 'feature'; push(@files, { path => "$featdir/$fa", type => "$featn/fff", name => $fa, chr => $chr }); } closedir(D); } return \@files; } sub getFeatTableFiles { my ($self, $chromosomes)= @_; my @files=(); my $fdump= $self->config->{featdump}; my $outpath= $self->getReleaseSubdir( $fdump->{'path'} || "tmp/") ; my $outname= catfile( $outpath, $fdump->{splitname} || "chadofeat"); my $no_csomesplit= $self->config->{no_csomesplit} || 0; # FIXME: 0710 $chromosomes= $self->getChromosomes() unless (ref $chromosomes); ##my $spp= $csomeset->{$chr}->{species}; ## FIX $dnafile name for this ! my $spp= $self->config->{species} || $self->config->{org}; my $orgabbr= $self->speciesAbbrev($spp, "org4"); print STDERR "# feature_table org=$orgabbr species=$spp path=$outpath \n" if $DEBUG; $chromosomes=["sum"] if($no_csomesplit); # 2007oct; not "all", other special csome name ! foreach my $chr (@$chromosomes) { next if $chr eq 'all'; my $fn; #^^ FIXME for species file name: chadofeat-dmel2L.tsv .. chadofeat-dpseXR_group9.tsv # ? add spp to getChromosomes() ? $fn= "$outname-$orgabbr$chr.tsv"; if(! -e $fn && -e "$fn.gz") { $fn .=".gz"; } #$fn= "$outname-$chr.tsv" unless( -e $fn); push(@files, { path => $fn, type => 'feature_table', name => $chr, org => $orgabbr }); } print STDERR "# feature_table files=",join(",",map{ basename($_->{path})}@files),"\n" if $DEBUG; return \@files; } sub getFilesetInfo { my ($self, $type)= @_; ## regularize configs so new format can be added w/o special tag names my $fset; $fset= $self->config->{fileset_override}->{$type}; return $fset if (ref $fset); $fset= $self->config->{fileset}->{$type}; return $fset if (ref $fset); my @oldset= qw( featdump dnafiles featfiles fastafiles blastfiles gnomapfiles gbrowsefiles ); foreach my $ms (@oldset) { my $fset= $self->config->{$ms}; if (ref $fset && $fset->{type} eq $type) { return $fset; } } return {}; } sub getFilesByType { my ($self, $type, $chromosomes)= @_; my @files=(); $chromosomes= $self->getChromosomes() unless (ref $chromosomes); ## $type maybe [] arrayref my @types= (ref $type) ? @$type : ( $type ) ; foreach $type (@types) { my $fset= $self->getFilesetInfo($type); next unless $fset; my $path= $fset->{path} || $type; my $dir = $self->getReleaseSubdir( $path, 'nocreate' ); my $no_orgchr= (defined $fset->{no_orgchr}) ? $fset->{no_orgchr} : 0; if (opendir(D, $dir)) { my $filepattern= '\w'; # ($filepattern, undef) = File::Basename::fileparse($path) if ($path !~ m,/$,); # >> err fileparse(): need a valid pathname if ($path !~ m,/$,){ my $e= rindex($path,'/'); $filepattern= ($e<0) ? $path : substr($path,$e+1); } foreach my $fa (grep(/^$filepattern/,readdir(D))) { my ( $org, $chr, $featn, $rel, $format); ( $org, $chr, $featn, $rel, $format)=$self->split_filename($fa,$no_orgchr); next unless( $no_orgchr || grep {$chr eq $_} @$chromosomes ); $featn ||= 'feature'; push( @files, { path => "$dir/$fa", type => "$featn/$type", name => $fa, format => $format, chr => $chr, rel => $rel, org => $org, no_orgchr => $no_orgchr, }); } closedir(D); } } return \@files; } sub getFiles { my ($self, $type, $chromosomes)= @_; my @filesets=(); ## $type maybe [] arrayref my @types= (ref $type) ? @$type : ( $type ) ; foreach $type (@types) { my $fileset; ## old way CASE: { $type eq 'feature_table' && do { $fileset= $self->getFeatTableFiles($chromosomes); last CASE }; $type eq 'dna' && do { $fileset= $self->getChromosomeFiles($chromosomes); last CASE }; #$type eq 'fff' && do { $fileset= $self->getFeatFiles($chromosomes); last CASE }; #$type eq 'fasta' && do { $fileset= $self->getFastaFiles($chromosomes); last CASE }; # new way: $fileset= $self->getFilesByType($type, $chromosomes); } push(@filesets, @$fileset) if $fileset; } return \@filesets; } sub gzipFiles { my ($self, $formats, $chromosomes)= @_; my @formats= ref $formats ? @$formats : qw( fff gff fasta dna gnomap blast) ; foreach my $type (@formats) { my $finfo= $self->getFilesetInfo($type); if (ref $finfo && $finfo->{dogzip}) { my $fileset= $self->getFiles($type, $chromosomes); print STDERR "gzipping $finfo->{path}\n" if $DEBUG; foreach my $fs (@$fileset) { system("gzip -f ".$fs->{path}) if (-e $fs->{path} && $fs->{path} !~ /\.gz$/); } } } } #============================================= =item sortNSplitByChromosome($fileset) sort chado feature dump fileset by arm, location and split into chromosome file set =cut sub sortNSplitByChromosome { my ($self, $fileset)= @_; my $sorter=`which sort`; chomp($sorter); ## '/bin/sort'; '/usr/bin/sort'; ## WATCH OUT - TAB here in ' ' ; does shell understand '^I' instead ? #DEBUG off#my $sortfeaturescmd= "$sorter -t' ' -k 1,1 -k 2,2n"; #? add -k 3,3rn ; nope end not there my $sortfeaturescmd= "$sorter -t' ' -k 1,1 -k 2,2n -k 3,3rn"; $fileset= $self->getDumpFiles() unless(ref $fileset); # return undef unless(ref $fileset); my $fdump = $self->config->{featdump}; my $outpath= $self->getReleaseSubdir( $fdump->{'path'} || "tmp/") ; my $outname= catfile( $outpath, $fdump->{splitname} || "chadofeat"); my $intype = $fdump->{type}; my $no_csomesplit= $self->config->{no_csomesplit} || 0; # FIXME: 0710 my $tfset = $self->getFilesetInfo('tables'); my $tabdir = $self->getReleaseSubdir( $tfset->{path} || 'tables/'); my $sumfile= catfile( $tabdir, "feature_table-summary.txt"); ## check first existance of outname files, and age ## if newer than input fileset, leave as is, return file names ? my $chromosomes= $self->getChromosomes(); ## $self->config->{chromosomes}; my $chr= $$chromosomes[0]; ##FIXME: my $testout= $outname-$orgabbr.$chr; ## dmel2R, my $orgabbr= $self->config->{org} || $self->speciesAbbrev("","org4"); my $testout= "$outname-$orgabbr$chr.tsv"; if(! -e $testout && -e "$testout.gz") { $testout .=".gz"; } my $uptodate= (-e $testout) ? 1 : 0; my $scmd=""; foreach my $fs (@$fileset) { my $fp= $fs->{path}; next unless($fs->{type} eq $intype); #?? ## if(! -e $fp && -e "$fp.gz") { $fp .=".gz"; } ## fileset will already have .gz if so unless(-e $fp) { warn "missing dumpfile $fp"; next; } # die if $self->{failonerror}; if ($uptodate && _isold($fp, $testout)) { $uptodate= 0 ; } $scmd .= "$fp "; } if($uptodate) { my @files=(); foreach my $chr (@$chromosomes) { my $fn= "$outname-$orgabbr$chr.tsv"; ## dmel2R, push(@files, { path => $fn, type => 'feature_table', name => $chr, chr => $chr, }); } return \@files; } unless($scmd) { warn "sortNSplitByChromosome: no dumpfiles at $outpath"; return undef; } # die if $self->{failonerror}; if($scmd =~ /\.gz /){ $scmd= "gunzip -c $scmd"; } else { $scmd= "cat $scmd"; } $scmd = "$scmd | $sortfeaturescmd |"; print STDERR "sortNSplitByChromosome:\n $scmd\n" if $DEBUG; print STDERR " to csomeSplit($outname)\n" if $DEBUG; open(FS,$scmd) || die $scmd; my $files= $self->csomeSplit(*FS, $outname, $sumfile, $no_csomesplit); close(FS); ## with remapArm, need to resort each output file foreach my $finfo (@$files) { next unless ($finfo->{dosort}); my $path= $finfo->{path}; my $cmd="cat $path | $sortfeaturescmd > $path.new"; if (system($cmd) == 0) { rename("$path.new",$path); $finfo->{dosort}= 0; } else { my $err= $? >> 8; warn "resort $path failed: $err"; } } return $files; } =item csomeSplit($inh, $outname, $sumfile) split sorted input feature_table files into per-chromosome (and now per-organism) feature fileset 2007Oct: add this flag ENV_default: output_by_golden_path=1 instead use: csome_split=1 to separate output by chromosome/scaffold/..., otherwise lump output by feature types, for all csomes. -- how much work to implement this? as all downstream outputs are csome-split now. =cut sub csomeSplit { my($self, $inh, $outname, $sumfile, $no_csomesplit)= @_; $outname ||= "chadofeats"; my @files=(); my $fh= undef; my %fhs=(); my %csomefeats= (); my $lastoid=''; my $csomeset = $self->getChromosomeTable(); ## pass value my $organisms= $self->config->{organism}; my %fhsorts=(); while(<$inh>) { next unless(/^\w/); chomp(); my ($arm,$fmin,$fmax,$strand,$orgid,$type,$name,$id,$oid,$attr_type,$attribute) = split("\t"); my $oldarm; my $oldfmax= $fmax; # bug 0710: getting 's.cerevisiae' instead of 'scer'; from chado db ?? my $orgabbr= $organisms->{$orgid}->{org4} || $organisms->{$orgid}->{abbreviation}; $orgabbr = "org$orgid" unless($orgabbr); #?? skip null orgabbr : not wanted ? ($arm,$fmin,$fmax,$strand,$oldarm)= $self->remapArm($arm,$fmin,$fmax,$strand,$csomeset); # for Unknown.. and other fragments ? need to do before sorter call ## -- BUG: remapArm U isnt sorted; need to check after 1st create files ## -- BUG2: renameArm needs to be called other places, change ChromosomeTable next unless($arm && $arm ne 'skip'); #? if ($attr_type eq 'to_species') { my $toorg= $self->speciesAbbrev($attribute); ## , "org4" ## my $toorg= $organisms->{$attribute}->{abbreviation}; $attribute= $toorg if $toorg; } my $dosort= ($arm ne $oldarm || $fmax ne $oldfmax); my $armfile= ($no_csomesplit) ? "sum" : $arm; my $fhname= $orgabbr.$armfile; ## dmel2R, unless($fhs{$fhname}) { my $fn= "$outname-$fhname.tsv"; $fh= $fhs{$fhname}= new FileHandle(">$fn"); die "Failed to create csome feature file '$fn'" unless($fh); push(@files, { path => $fn, name => $armfile, chr => $arm, org => $orgabbr, type => 'feature_table', # should be $fs->{type} == feature_table dosort => $dosort, }); } $fhsorts{$fhname} += $dosort; $fh= $fhs{$fhname}; ## drop $orgid from this output set print $fh join("\t",$arm,$fmin,$fmax,$strand,$type,$name,$id,$oid,$attr_type,$attribute) ,"\n"; unless($oid eq $lastoid) { $csomefeats{$fhname}{$type}++; $csomefeats{all}{$type}++; } $lastoid= $oid; } foreach my $fhname (keys %fhs) { $fh= $fhs{$fhname}; close($fh) if $fh; } foreach my $f (@files) { my $fhname= $f->{org} . $f->{chr}; $f->{dosort}= 1 if ($fhsorts{$fhname}); } ## these counts are bad; include dup rows/feature (e.g 4x gene count) ## need to use distinct oid . if ( $sumfile ) { $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; my $date = $self->config->{date}; my $org = $self->config->{species} || $self->config->{org}; #^^ use $orgid !?? print $fh "# Database feature summary for $org from $title [$date]\n"; my @fl= grep { 'all' ne $_ } sort keys %csomefeats; foreach my $arm ('all', @fl) { print $fh (($arm eq 'all') ? "\n# ALL chromosomes\n" : "\n# Chromosome $arm\n"); foreach my $t (sort keys %{$csomefeats{$arm}}) { print $fh "$t\t$csomefeats{$arm}{$t}\n"; } print $fh "#","="x50,"\n"; } close($fh); push(@files, { path => $sumfile, type => 'feature/summary', name => 'summary', }); } return \@files; } sub preMake { my $self= shift; my ($what)= @_; my $ok= 0; my ($dumpfiles,$chrfeats,$dnafiles); # parts from bulkfiles.pl not run by default; save user some hassle here if ($what =~ /feature_table/ && !$self->{didmake}{feature_table}) { warn "Automaking feature_table files\n"; $dumpfiles= $self->dumpFeatures(); $chrfeats= $self->sortNSplitByChromosome(); $self->{didmake}{feature_table}=1; $ok= 1 if(@$chrfeats); } if ($what =~ /dna/ && !$self->{didmake}{dna}) { warn "Automaking dna files\n"; $dnafiles= $self->dumpChromosomeBases(); $self->{didmake}{dna}=1; $ok= 1 if(@$dnafiles); } return $ok; } sub missingData { my $self= shift; my ($fileset, $maketype, $what)= @_; if( @$fileset && $self->{automake} ) { my @didmake= keys %{$self->{didmake}}; my $current= grep /$maketype/, @didmake; unless($current) { (my $msg = $what) =~ s/;.*$//; warn "Using pre-existing $msg\n"; warn "Use '/bin/rm -rf ",$self->getReleaseDir(),"' for clean make\n" if($what =~ /chromosomes/); } } unless(@$fileset){ warn "Missing ",$what,"\n"; die if $self->{failonerror}; } } =item makeFiles( %args ) primary method; mostly it calls FeatureWriter() package to handle also prints any config->doc entries arguments: infiles => \@fileset, # required formats => [ 'gff', 'fasta', 'fff', 'blast' ] # optional =cut sub makeFiles { my $self= shift; my %args= @_; my @results=(); print STDERR "makeFiles\n" if $DEBUG; # debug $self->rereadConfig(); # == updateConfigVars; replace doc ${values} $self->writeDocs( $self->config->{doc} ); #? unless already wrote ? move this to Writer module my $automake= $args{automake} || $self->{automake} ; ## dang change in caller bulkfiles.pl; dropped @outformats, now find ## downstream writers look at this input %args for that: should it (a) ignore $args{outformats} ## or (b) should this method add \@outformats to args? my @outformats=(); # check config if ($args{formats}) { my $formats= $args{formats}; @outformats= (ref $formats) ? @$formats : ($formats); } unless(@outformats>0) { @outformats= @{ $self->config->{outformats} || \@defaultformats } ; } # automake, etc, add outformat fff if need be # push(@outformats,"fff") # still a dependency, but intermediate format # if ($automake && !grep(/fff/, @outformats) && grep(/fasta/, @outformats)); # bug^ recreates fff already made; $args{formats}= \@outformats; #??? want this my %outformats= map{ $_,1; } @outformats; print STDERR "makeFiles: outformats= @outformats\n" if $DEBUG; if (delete $outformats{'overview'}) { my $overviewset = $self->getFilesetInfo('overview'); if($overviewset) { ## check for already done overview files .. my ($ovfiles,$ovmissing)= $self->getDumpFiles(['overview'], $overviewset); ## FIXME: bug in above x config? 'overview' files are tagged 'summary' in chadofeatsql ?? if(1 or scalar(@$ovmissing)) { $ovfiles = $self->dumpFeatures($overviewset, undef, "colnames"); } my $ovlist= join(" ",map {$_->{name}} @$ovfiles); push @results, "overviews:$ovlist"; warn "** Please review overview tables for validity **\noverviews:$ovlist\n" if($automake||$DEBUG); # && return ?? $self->getOrganismTable() if($ovlist =~ /organism/); } } ## 0710: insert here optional validateVariables: seq_ontology, golden_path at least ## valid=0 default flag handles this for newuser: $self->config->{newuser} $self->validateVariables() unless( $self->config->{valid} ); ## getChromosomes needs chromosomes.tsv .. essential it exist here my $fileset= $self->getDumpFiles(['chromosomes']); if($automake && ! @$fileset) { $self->preMake('feature_table'); # returns $ok $fileset= $self->getDumpFiles(['chromosomes']); } $self->missingData( $fileset, 'feature_table', "chromosomes.tsv table file; make with -featdump"); my $chromosomes= undef; if (ref $args{chromosomes}) { $chromosomes= $args{chromosomes}; $args{noall}=1; } elsif (ref $args{chr}) { $chromosomes= $args{chr}; $args{noall}=1; } ## dont do 'all' if subset ! unless (ref $chromosomes && @$chromosomes > 0 && $chromosomes->[0] ne 'all') { $chromosomes= [ 'all', @{$self->getChromosomes()} ]; $args{noall}=0; } # FIXME trick - getFeatureWriter loads common config for featmap/featset needed by others my $featwriter= $self->getWriter('fff'); my $featfiles = $self->getFiles('fff', $chromosomes); if ($automake && !@$featfiles && ($outformats{'fasta'} || $outformats{'gnomap'})) { #(grep /fasta|gnomap/, @outformats)) $outformats{'fff'}=1; } ## this one takes a while; split chromosomes among processors if ($outformats{'fff'} || $outformats{'gff'}) { ## grep /fff|gff/, @outformats) delete $outformats{'fff'}; delete $outformats{'gff'}; my $chrfeats = $self->getFiles('feature_table', $chromosomes); if ($automake && !@$chrfeats) { $self->preMake('feature_table'); # returns $ok $chrfeats = $self->getFiles('feature_table', $chromosomes); } if ($DEBUG) { print STDERR "read feature tables= ",join(" ",map {$_->{name}} @$chrfeats),"\n"; } $self->missingData( $chrfeats, 'feature_table', "feature_table files; make with -featdump"); push @results, $featwriter->makeFiles( %args, infiles => $chrfeats, chromosomes => $chromosomes ); } my $featfiles = $self->getFiles('fff', $chromosomes); my $dnafiles = $self->getFiles('dna', $chromosomes); if ($automake && !@$dnafiles && $outformats{'fasta'}) { $self->preMake('dna'); $dnafiles = $self->getFiles('dna', $chromosomes); } # if ($automake && !@$featfiles && ($outformats{'fasta'} || $outformats{'gnomap'})) { #(grep /fasta|gnomap/, @outformats)) # $self->preMake('fff'); # not active? # $featfiles = $self->getFiles('fff', $chromosomes); # } if ($DEBUG) { my @cn= @$chromosomes; # FIXME too long to list for some, no_csomesplit @cn= (@cn[0..20],".. more ..") if(@cn>30); print STDERR "make chromosomes= @cn\n"; my @fn= map {$_->{name}} @$featfiles; print STDERR "with featfiles= @fn\n"; my @dn= map {$_->{name}} @$dnafiles; print STDERR "with dnafiles= @dn\n"; } if (delete $outformats{'fasta'}) { $self->missingData( $featfiles, "fff", "fff files; make with -format fff"); $self->missingData( $dnafiles, "dna", "dna files; make with -dnadump"); my $writer= $self->getWriter('fasta'); push @results, $writer->makeFiles(%args, infiles => $featfiles, chromosomes => $chromosomes); } if (delete $outformats{'blast'}) { my $fafiles = $self->getFiles( 'fasta', $chromosomes); $self->missingData( $fafiles, 'fasta', "fasta files; make with -format fasta"); my $writer = $self->getWriter('blast'); # this works; eval new writer push @results, $writer->makeFiles( %args, infiles => $fafiles, chromosomes => $chromosomes ); } if (delete $outformats{'gnomap'}) { # move to generic handler below $self->missingData( $featfiles, "fff","fff files; make with -format fff"); my $writer= $self->getWriter('gnomap'); push @results, $writer->makeFiles(%args, infiles => [ @$featfiles, @$dnafiles ], chromosomes => $chromosomes); # needs $featfiles } # my @moreformats= grep !/(fff|gff|dna|fasta|blast|gnomap)/,@outformats; my @moreformats= grep { $outformats{$_} } @outformats; # preserve call-order foreach my $fmt (@moreformats) { my $writer= $self->getWriter($fmt); my $fset = $self->getFilesetInfo($fmt); my $infiles; if($fset->{input} =~ /feature_table/) { $infiles = $self->getFiles('feature_table', $chromosomes); $self->missingData( $infiles, 'feature_table', "feature_table files; make with -featdump"); } else { # ($fset->{input} =~ /fff/) $infiles= [ @$featfiles, @$dnafiles ]; #?? always # $self->missingData( $featfiles, "fff", "fff files; make with -format fff"); # $self->missingData( $dnafiles, "dna", "dna files; make with -dnadump"); } if (!$writer) { warn "no writer for $fmt\n"; } else { push @results, $writer->makeFiles( %args, name => $fmt, filesetinfo => $fset, infiles => $infiles, chromosomes => $chromosomes); } } =item more formats using SQL queries -- need a Writer to handle dumpFeatures : see BulkWriter now if (delete $outformats{'go_association'}) { my $fset = $self->getFilesetInfo('go_association'); if($fset) { # my ($ovfiles,$ovmissing)= $self->getDumpFiles(['go_association'], $fset); my $ovfiles = $self->dumpFeatures($fset, undef, "colnames"); my $ovlist= join(" ",map {$_->{name}} @$ovfiles); push @results, "output:$ovlist"; } } =cut $self->gzipFiles( \@outformats, $chromosomes ); my $lok= $self->makeCurrentLink() if (@results && $self->config->{make_current}); #? put most of above in eval{} block so we return error info if failed ?? push(@results,"\nBulkfiles are located at ".$self->getReleaseDir()) if(@results); return join(", ",@results); #what? } =item writeDocs( $docs or $self->config->{doc}) print docs from config file .. move this into own BulkWriter subclass ? need some fix to writeDocs for doc->path at top level or not-releasedir =cut sub writeDocs { my ($self, $docs)= @_; my $ndoc= 0; if (ref $docs) { # check for 1 or many (name keys, darn xmlsimple); is tag 'name' or 'id' ? my $reldir = $self->getReleaseDir(); my $datadir= $self->config->{datadir}; # must exist my $species= $self->speciesFull(); if ($docs->{content}) { my %dd= (); if ($docs->{name}) { %dd= ( $docs->{name} => $docs ); } elsif ($docs->{id}) { %dd= ( $docs->{id} => $docs ); } else { %dd= ( 'untitled' => $docs ); } $docs= \%dd; } foreach my $dname (sort keys %$docs) { next if ($docs->{$dname}->{hidden}); ## == 1 my $data = $docs->{$dname}->{content} || ''; my $dpath= $docs->{$dname}->{path} || $dname; $dpath =~ s/\${datadir}/$datadir/; $dpath =~ s/\${species}/$species/; my $norel=($dpath =~ m/$datadir/ || $dpath =~ m,^/,); my $fn= ($norel) ? $dpath : catfile( $reldir, $dpath); print STDERR "write doc $dname $fn\n" if $DEBUG; if( open(DOC,">$fn") ) { print DOC $data; close(DOC); $ndoc++; } else { warn "ERROR: cant write $fn\n"; } } } print STDERR "writeDocs n=$ndoc\n" if $DEBUG; # debug return $ndoc; } =item getWriter Replaced getXxxWriter with generic getWriter('type') =cut sub getWriter { my ($self, $type)= @_; my $finfo= $self->getFilesetInfo($type); if (ref $finfo && $finfo->{handler}) { my $configfile= $finfo->{config}; my $pkg= $finfo->{handler}; if($pkg eq "Bulkfiles") { return $self; } #?? can we do this; needs BulkWriter methods unless($pkg =~ /\:\:/) { $pkg= "Bio::GMOD::Bulkfiles::".$pkg; } my $eval= "use $pkg; $pkg->new( configfile => \$configfile, fileinfo => \$finfo, handler => \$self, debug => \$DEBUG, showconfig => \$self->{showconfig}, );"; ##print STDERR "getWriter: eval $eval\n" if $DEBUG; my $writer= eval $eval; if ($@) { warn $@; die if($self->{failonerror}); } return $writer if ref $writer; } # print STDERR "getWriter('$type'): eval failed\n" if $DEBUG; # ## old way # CASE: { # $type eq 'fasta' && return $self->getFastaWriter(); # $type eq 'blast' && return $self->getBlastWriter(); # $type eq 'fff' && return $self->getFeatureWriter(); # $type eq 'gff' && return $self->getFeatureWriter(); # $type eq 'gnomap' && return $self->getGnomapWriter(); # } warn "no writer module for $type\n"; } #=================================================== =item getChromosomeTable locate and read feature dump of chromosomes (or equivalent parts) 2L 1 22217931 0 chromosome_arm 2L 2L 1 species Drosophila_melanogaster 2R 1 20302755 0 chromosome_arm 2R 2R 2 species Drosophila_melanogaster 3L 1 23352213 0 chromosome_arm 3L 3L 4 species Drosophila_melanogaster 3R 1 27890790 0 chromosome_arm 3R 3R 3 species Drosophila_melanogaster 4 1 1237870 0 chromosome_arm 4 4 5 species Drosophila_melanogaster U 1 11561901 0 chromosome_arm U U 7 species Drosophila_melanogaster X 1 21780003 0 chromosome_arm X X 6 species Drosophila_melanogaster oct04 -- add option to create 'chr-U' from bag of Unknown_* golden_path entries in getChromosomeTable. Have some 2000+ Unknown_group and Unknown_singleton golden_path/ultra_scaffold entries in Dpse r2.1. need also map contig -> contig_contig -> ultra_scaffold Contig1083_Contig6433 0 11665 1 3 contig Contig1083 3209332 parent_oid 3208389:1 Unknown_group3 0 15476 1 3 golden_path_region Contig1083_Contig6433 Contig1083_Contig6433 3208389 parent_oid 3798908:1 return hash { '3R' => { 'length' => 27890789, 'start' => 1, 'oid' => 3, 'strand' => '0', 'type' => 'chromosome_arm', 'name' => '3R' }, 4 => { 'length' => 1237869, 'start' => 1, 'oid' => 5, 'strand' => '0', 'type' => 'chromosome_arm', 'name' => 4 }, } =cut sub getChromosomeTable { my $self= shift; my $config= $self->config; if (defined $config->{chromosome}) { return $config->{chromosome}; } my $chromosome= {}; my $chrparts = {}; # for dpse map Unknown ultra_scaffold/golden_path_fragment to U my $part2chr = {}; # map golden_path_region name to chr-arm name my $chrpartpattern= $config->{chrpart_pattern}; my %orgset = (); my $nozombiechromosomes= $config->{nozombiechromosomes}; # dpse chado duplicate 0-length chromosome entries ## need remapArm() here, but csomeset is result of this method ... ## BUT featdump tables are not remapped until csomeSplit(); cant use remapped names til after that #? allow only one species per make run ? my $myspp= $config->{species}; $myspp =~ s/ /_/g; my $myorg= $config->{org} || $self->speciesAbbrev($myspp); my $fileset= $self->getDumpFiles(['chromosomes']); my $path= (ref $fileset) ? $fileset->[0]->{path} : undef; if ($path && open(CF,$path)) { while() { next unless(/^\w/); next if(/^arm\tfmin/); # header from sql out -- should be 'chromosome' or 'chr' instead of 'arm' chomp; my $oldarm; my ($arm,$fmin,$fmax,$strand,$orgid,$type,$name,$id,$oid,$attr_type,$attribute) = split("\t"); next unless($id); #? ## sgdlite uses messy chr ID -- use name instead here ? better: $arm is best of both ## fb-dpse has zero-length chromosomes, and duplicates (some zero some not) ## ? skip zero len csomes ? for output at least ## use $strand == rank here -- assume input file is ordered by that. ## need ($arm,$golden_path,...)= mapChr($arm) ## ? need some compound chr{arm} with multiple ids for Unknown bag? ($arm,$fmin,$fmax,$strand,$oldarm)= $self->remapArm($arm,$fmin,$fmax,$strand,undef); next unless($arm && $arm ne 'skip'); #? my $species= ($attr_type eq 'species') ? $attribute : $config->{species}; $species =~ s/ /_/g; my $org= $self->speciesAbbrev($species); $org= $self->speciesAbbrev($orgid) unless($org); $org= "null" unless($org); next unless($myorg eq $org || $myspp eq $species); #?? dec05; for dpse+dmel db next if ($nozombiechromosomes && $fmax <= $fmin); my $org4= $self->speciesAbbrev($orgid, "org4"); my $chrvals= { arm => $arm, oldarm => $oldarm, # rarely differs from arm ... name => $name || $id, id => $id, type => $type, start => $fmin, length => ($fmax - $fmin + 1), strand => $strand, oid => $oid, species => $species, orgid => $orgid, ## NEED THIS, now all feature_table have organism_id org => $org, }; my($genus,$spp)= split(/_/,$species,2); $orgset{$orgid}= { organism_id => $orgid, abbreviation => lc($org), org4 => $org4, genus => $genus, species => $spp, fullspecies => $species, }; if ($chrpartpattern && $type =~ /$chrpartpattern/) { #== golden_path_fragment|golden_path_region, other? unless($chrparts->{$arm}) { $chrparts->{$arm}= []; } push(@{$chrparts->{$arm}}, $chrvals); $part2chr->{$id}= $arm; } else { #? check type =~ ^(chromosome_arm|golden_path|ultra_scaffold)$ $chromosome->{$arm}= $chrvals; } } close(CF); } $chromosome->{'_part2chr'}= $part2chr if( %$part2chr ); foreach my $arm (keys %$chrparts) { unless($chromosome->{$arm}) { ## make pseudochr from parts? $chromosome->{$arm}= { arm => $arm, name => $arm, id => $arm, type => 'golden_path', # fixme start => 1, length => 0, # fixme strand => 0, oid => 0, species => '', org => '', # fixme }; } $chromosome->{$arm}->{parts}= $chrparts->{$arm}; } my $organisms = $self->getOrganismTable(\%orgset); $config->{chromosome}= $chromosome; $self->getChromosomes(); warn "N chromosomes=",scalar(keys %{$chromosome}),"\n" if $DEBUG; return $chromosome; } sub getOrganismTable { my $self= shift; my($orgset)= @_; ## add read from overview tables/organisms-overview.txt ## flds: qw(Organism_id Abbreviation Genus Species Common_name N_features Comment) unless($self->{did_organism}) { my $overviewset = $self->getFilesetInfo('overview'); my $tabdir = $self->getReleaseSubdir( $overviewset->{path} || 'tables/'); my $tabfile= catfile( $tabdir, "organisms-overview.txt"); my @colheads; if( open(DOC,$tabfile) ) { $orgset= {} unless(ref $orgset); $self->{did_organism}++; while(){ chomp; my @col= split "\t"; if(/^Organism_id/i){ @colheads= @col; } elsif(/^\d/ && scalar(@col) > 3) { foreach (@col) { $_='' if($_ eq "\\N"); } my($orgid,$abbreviation,$genus,$species,$common,@xtra)= @col; my $fullspecies= $genus."_".$species; unless($abbreviation) { $abbreviation= $self->speciesAbbrev($fullspecies); } my $org4= $self->species4letter($fullspecies); $orgset->{$orgid}= { organism_id => $orgid, org4 => $org4, abbreviation => lc($abbreviation), genus => $genus, species => $species, fullspecies => $fullspecies, from_db => 1, }; } } close(DOC); } } my $organisms= $self->config->{organism}; $organisms= {} unless(ref $organisms); my $norgs=0; if(ref $orgset) { foreach my $orgid (keys %$orgset) { my $orgref= $orgset->{$orgid}; $organisms->{$orgid}={} unless(ref $organisms->{$orgid}); next if( $organisms->{$orgid}->{from_db} && ! $orgref->{from_db}); $organisms->{$orgid}->{organism_id}= $orgid; my $fullspecies= $orgref->{fullspecies} || $orgref->{genus}."_".$orgref->{species}; $organisms->{$orgid}->{fullspecies}= $fullspecies; $organisms->{$orgid}->{species}= $fullspecies; #?? need this same as fullspecies?? $organisms->{$orgid}->{from_db}= $orgref->{from_db} || 0; $organisms->{$orgid}->{org4}= $self->species4letter($fullspecies); my $abbrev= $orgref->{abbreviation} || $self->speciesAbbrev( $fullspecies ); $organisms->{$orgid}->{abbreviation}= $abbrev; $organisms->{$abbrev}= $organisms->{$orgid}; # copy for orgid lookup $norgs++; } warn "Organisms n_entries=$norgs\n" if $DEBUG; } $self->config->{organism}= $organisms; return $organisms; } sub getChromosomes { my $self= shift; my $config= $self->config; unless(ref $config->{chromosomes}) { my $chromosome= $self->getChromosomeTable(); my @csomes= grep !/^_/, sort keys %$chromosome; $config->{chromosomes}= \@csomes; } return $config->{chromosomes}; } # this needs to be a configuration choice (how many genus,species letters) # and combine with chado table abbreviation, locase or not, ... have too many # abbreviations now, used in file names. Need simpler common abbrev. sub species4letter { my $self= shift; my ($spp)= @_; $spp ||= $self->config->{species} || $self->config->{org}; $spp =~ s/ /_/g; my $spattern= $self->config->{species_short_pattern} || '^(\w)[^_]*_(\w{1,3})'; my( $ga, $sa) = $spp =~ m/$spattern/; return lc($ga.$sa) if($ga and $sa); #? should lc() be a _pattern option? return lc( substr($spp,0,4) ); #?? } sub speciesAbbrev { my $self= shift; my ($spp, $org4letter)= @_; $spp = $spp || $self->config->{species} || $self->config->{org} || ""; $spp =~ s/ /_/g; my $organisms= $self->config->{organism}; if (ref $organisms) { local $^W=0; # kill warnings of undef orgset values foreach my $org (reverse sort keys %{$organisms}) { my $orgset= $organisms->{$org}; if ($spp eq $org || $spp eq $orgset->{fullspecies} || $spp eq $orgset->{species} || $spp eq $orgset->{organism_id} ) { if($org4letter) { my $org4= $orgset->{org4} || $self->species4letter($spp); return $org4; } elsif ($org =~ /\d+/) { # watchout for org == orgid here my $abbr= $orgset->{abbreviation}; return $abbr if $abbr; } else { return $org; } } } } return $self->species4letter($spp); } ## fix this; should always prefer $self->config->{species}; ? ## $organisms->{$orgid}->{fullspecies} second choice? ## problems with ' ',_ in species such as ## genus=Anopheles species='gambiae str. PEST' sub speciesFull { my $self= shift; my ($org)= @_; my $species= ''; $species= $self->config->{species}; $species =~ s/ /_/g; return $species if($species =~ m/_/); # problems $org= $org || $species || $self->config->{org}; $org= $self->speciesAbbrev($org); my $organisms= $self->config->{organism}; if(ref $organisms && $organisms->{$org}->{species}) { $species= $organisms->{$org}->{species}; $self->config->{species}= $species if ($species =~ m/_/); } return $species; } sub speciesFull_OLD { my $self= shift; my ($org)= @_; my $species= ''; unless($org) { $species= $self->config->{species}; $species =~ s/ /_/g; return $species if($species =~ m/_/); } $org= $org || $species || $self->config->{org}; $org= $self->speciesAbbrev($org); my $organisms= $self->config->{organism}; $species= $organisms->{$org}->{species} if ($organisms->{$org}->{species}); $self->config->{species}= $species if ($species =~ m/_/); return $species; } =item splitFFF split flat feature format line to fields ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr) = splitFFF($fffeature, $chr) =cut sub splitFFF { my( $self, $fffeature, $chr)= @_; my($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$bstart); chomp($fffeature); my @v= split "\t", $fffeature; foreach (@v) { $_='' if $_ eq '-'; } my $ffformat = $self->{ffformat} || 0; #? test always unless( $ffformat > 0 ) { if ( @v > 7 || ($v[0] =~ /^\w/ && $v[1] =~ /^\d+$/)) { $ffformat= 2; } else { $ffformat= 1; } } if ($ffformat == 1) { ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes)= @v; } elsif ($ffformat == 2) { ($chr,$bstart,$type,$name,$cytomap,$baseloc,$id,$dbxref,$notes)= @v; } $self->{gotffformat}= $ffformat; return ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr); } =item $interfff= intergeneFromFFF2($chr,$fff1,$fff2) return fff line for region between two features (any feature types ok, intergenic regions most interesting) =cut sub intergeneFromFFF2 { my ($self, $chr, $fff1, $fff2)= @_; my $newfff=''; my ($type,$name1,$cytomap,$baseloc1,$id1,$dbxref,$notes); my ($chr2,$name2,$baseloc2,$id2); my $intergenetype='intergene'; # FIXME ($type,$name1,$cytomap,$baseloc1,$id1,$dbxref,$notes,$chr) = $self->splitFFF( $fff1, $chr); my($start1,$stop1,$strand1)= $self->maxrange($baseloc1); ($type,$name2,$cytomap,$baseloc2,$id2,$dbxref,$notes, $chr2) = $self->splitFFF( $fff2, $chr); my($start2,$stop2,$strand2)= $self->maxrange($baseloc2); if ($chr eq $chr2 && ($stop1 + 2) < $start2) { my $iname= "$name1/$name2"; my $iid= "$id1/$id2"; my $interloc= ($stop1+1)."..".($start2-1); if ($self->{gotffformat} == 2) { $newfff= join("\t", $chr, $stop1, $intergenetype, $iname,'-', $interloc, $iid,$dbxref,$notes); } else { $newfff= join("\t", $intergenetype, $iname,'-', $interloc, $iid,$dbxref,$notes); } } return $newfff; } ## no_csomesplit: replace dna/ files w/ chado db calls for all?? see dumpChromosomeBases sub getDnaSeqFromDb { my($self,$chr)= @_; my $csomeset= $self->getChromosomeTable(); my $id= $csomeset->{$chr}->{id} || $chr; my $bases= $self->getBasesFromDb($id,1); unless ($bases) { warn "getDnaSeqFromDb: no bases for segment:$chr\n"; die if $self->{failonerror}; } return $bases; } sub getDnaSeq { my ($self, $chr)= @_; my $seq= $dnaseqs{$chr}; unless($seq) { my $no_csomesplit= $self->config->{no_csomesplit} || 0; # 2007oct: old default, change for many small scaffolds if($no_csomesplit) { my $dna= $self->getDnaSeqFromDb($chr); $seq= Bio::PrimarySeq->new( -id=>$chr, -seq => $dna); print STDERR "getDnaSeqFromDb $chr, length=",$seq->length(),"\n" if $DEBUG; } else { my $dnafile= $self->dnafile($chr); #"$dnadir/dna-$chr.raw"; $seq= Bio::GMOD::Bulkfiles::MyLargePrimarySeq->new( -id=>$chr, -file => $dnafile); print STDERR "open dnafile $dnafile, length=",$seq->length(),"\n" if $DEBUG; } $dnaseqs{$chr}= $seq; } return $seq; } sub getBases { my($self, $usedb,$type,$chr,$baseloc,$id,$name,$subrange,$makeaa)= @_; my $bases= undef; if($usedb && $id) { $bases= $self->getBasesFromDb($id); use constant FIX_AAMISSING_STOP => 1; if(FIX_AAMISSING_STOP) { if($makeaa && $bases) { $bases .='*' unless($bases =~ /\*$/); # annoying non-standard store if(ref $self->{gotbases}) { $self->{gotbases}->{'md5checksum'}=0; } # no longer valid } } return $bases if($bases || $self->{failonerror}); # >> no; try from files: $self->{skiponerror}); } unless ($bases) { $bases= $self->getBasesFromFiles($type,$chr,$baseloc,$name,$subrange); if($makeaa) { $bases= $self->dna2protein($bases); } } return $bases; } # but see Bio/GMOD/DB/Config.pm sub dbiDSN { my ($self, $dsn)= @_; my $config= $self->config; my ($dbuser,$dbpass)=("",""); if ($dsn && $dsn =~ /^dbi:/) { $self->{dsn}= $dsn; } if (ref $config->{db}) { my $dbname= $config->{db}->{name}; my $relid= $config->{relid}; #? or now use promoted {release_dbname} my $reldb= ($relid && defined $config->{release}->{$relid}) ? $config->{release}->{$relid}->{dbname} :''; $dbname= $reldb if ($reldb); unless($dbname) { warn "missing dbname"; die if $self->{failonerror}; } ## ? handle dbi:mysql:database=dmel_r41_20050207;host=localhost;port=3306;mysql_socket=/tmp/fbmysql.sock if($config->{db}->{dsn}){ $dsn = $config->{db}->{dsn}; } else { $dsn = "dbi:" . $config->{db}->{driver} || "Pg"; $dsn .= ":dbname=" .$dbname; $dsn .= ";host=" .$config->{db}->{host} if $config->{db}->{host}; $dsn .= ";port=" .$config->{db}->{port} if $config->{db}->{port}; #?? $self->{dsn}= $dsn; } $dbuser= $config->{db}->{user} if $config->{db}->{user}; $dbpass= $config->{db}->{password} if $config->{db}->{password}; } ## if ($self->{dsn}) { $dsn= $self->{dsn}; } return (wantarray) ? ($dsn,$dbuser,$dbpass) : $dsn; } sub dbiConnect { my ($self)= @_; my $dbh= $self->{dbh}; unless($dbh) { my $tdsn= $self->dbiDSN(); print STDERR "DBI->connect( $tdsn )\n" if $DEBUG; $dbh = DBI->connect( $self->dbiDSN() ) or die("unable to open db( $tdsn )"); # throw ? $self->{dbh}= $dbh; } return $dbh; } =item getSeqSql($sqlconf) read in config file with feature dump sql scripts =cut sub getSeqSql { my ($self, $sqlconf, $sqlenv)= @_; $sqlconf = 'chadofeatsql' unless($sqlconf); $sqlenv= $self->config unless (ref $sqlenv); # print STDERR "sqlenv.$sqlconf: ",join("\n ", map{ $_."=".$sqlenv->{$_}} keys %$sqlenv ),"\n" # if ($DEBUG>1); my $config2= $self->{config2}; #?? Config2 object, not hash my $seqsql = $self->{$sqlconf} || ''; unless($seqsql) { $seqsql= $config2->readConfig( $sqlconf, {Variables => $sqlenv}, {} ); print STDERR $config2->showConfig($seqsql, { debug => $DEBUG }) if ($self->{showconfig} && $DEBUG>1); } # has undefined Variables? try to define my $sqxml= $config2->showConfig( $seqsql, { debug => 0 }); if ( $sqxml =~ m/\$\{/ ) { eval { $seqsql= $self->{config2}->updateVariables( $seqsql, { Variables => \%ENV, replace =>1 }, ); }; if ($@) { warn "Config2: getSeqSql=$sqlconf; err: $@"; } } if ( $sqxml =~ m/\$\{/ && ref($seqsql->{ENV_default}) ) { my %env= %{$seqsql->{ENV_default}}; foreach my $k (keys %env) { $env{$k}= $sqlenv->{$k} if($sqlenv->{$k}); } $seqsql= $config2->readConfig( $sqlconf, {Variables => \%env}, {} ); } # print STDERR "seqsql.$sqlconf xml: ", $config2->showConfig( $seqsql, { debug => 0 }),"\n" # if ($DEBUG>1); $self->{$sqlconf}= $seqsql; return $seqsql; } =item validateVariables validate config values for seq_ontology, golden_path, species?? to exist in database =cut sub validateVariables { my ($self)= @_; return if $self->{didvalidatevars}; $self->{didvalidatevars}= 1; warn "Validating...\n" if($DEBUG||$self->{automake}); my $note=""; my $doinspect= ($DEBUG or $self->{verbose} or $self->config->{newuser}) ? 1 : 0; ## ? newuser, verbose, DEBUG, ... my $fdump = $self->config->{featdump}; my $seqsql = $self->getSeqSql($fdump->{config},$fdump->{ENV}); my $sqltag = $fdump->{tag} || "feature_sql"; my $sqltype = 'validate'; # other types? my @sqlparam=(); ## tag names here are now seq_ontology_check, golden_path_check my $dbh= $self->dbiConnect(); my @targets= sort keys %{$seqsql->{$sqltag}}; foreach my $tgname (@targets) { my $fs = $seqsql->{$sqltag}->{$tgname}; my $type= $fs->{type}; my $sql = $fs->{sql}; next unless($sql && ( $type =~ m/\b$sqltype\b/) ); $note.= "$tgname = "; print STDERR "$type:$tgname\n" if $DEBUG; # sql=$sql # local $^W=0; # kill warnings of undef values my $nrow= 0; my $err=""; my $sth = $dbh->prepare($sql) or $err= "Failed to prepare $sql"; unless($err) { $sth->execute() or $err= "Failed to execute sql"; } unless($err) { while (my $row = $sth->fetchrow_arrayref) { $nrow++; } } $sth->finish(); my $sql_inspect = $fs->{sql_inspect}; # optionally show this inspect even if no err if($err or $nrow == 0) { $err .= "*** Failed validation check for $tgname\n"; $err .= $fs->{warning}."\n" if($fs->{warning}); $err .= "$tgname sql=$sql\n"; warn $err; $err= "Invalid $tgname\n"; $doinspect= 1; } if($doinspect and $sql_inspect) { ##??? problems with this for chromosome checks (using a join) very long for parameciumDB ## why? is it bug in sql/postgres/database tuning? using some scan instead of index search? ## explain high cost in chado pg is with Sort for Group ## Sort (cost=178872.73..179239.36 rows=146652 width=560); Sort Key: f.type_id, t.name warn "\nInspecting database for $tgname values...\n"; print STDERR ("-") x 60, "\n"; my $result= $self->getFeaturesFromDb( *STDERR, $sql_inspect, undef, "colnames"); print STDERR ("-") x 60, "\n"; } if ($err) { warn $err; die if($self->{failonerror}); #?? ||$self->{automake} $note.="Invalid "; } else { $note.="Ok "; } } warn "Variable checks: $note\n" if($DEBUG||$self->{automake}); } =item updateSqlViews add views to db used by sql feature calls. this may fail if one lacks update permissions; assume user knows about such =cut sub updateSqlViews { my ($self, $seqsql, $sqltag)= @_; return if $self->{didsqlviews}; $self->{didsqlviews}= 1; unless($seqsql) { my $fdump = $self->config->{featdump}; $seqsql = $self->getSeqSql($fdump->{config},$fdump->{ENV}); } $sqltag ||= "feature_sql"; my $sqltype = 'view'; # other types? procedures ? my $dbh= $self->dbiConnect(); my @targets= sort keys %{$seqsql->{$sqltag}}; foreach my $tgname (@targets) { my $fs= $seqsql->{$sqltag}->{$tgname}; my $type= $fs->{type}; my $sql = $fs->{sql}; unless($sql && ( $type =~ m/\b$sqltype\b/) ) { next; } print STDERR "do sql $tgname $type\n" if $DEBUG; my $result = $dbh->do($sql) or warn "unable to do sql $tgname $type"; } } =item dumpFeatures dumpFeatures($fdump, $sqlconf) - extract feature_table s from chado db using feature sql config info -- add other config items for sql dumps - organism_table; lists; .. -- use fileset instead of featdump =cut sub dumpFeatures { my ($self, $fdump, $sqlconf, $dumpflags)= @_; my @files=(); $dumpflags ||=""; ## add colnames for overview.txt; look in $fdump->{dumpflags} ?? $fdump ||= $self->config->{featdump}; $sqlconf ||= $fdump->{config_sql} || $fdump->{config}; my $seqsql = $self->getSeqSql($sqlconf,$fdump->{ENV}); $self->updateSqlViews($seqsql, $fdump->{tag}); my $outpath= $self->getReleaseSubdir( $fdump->{'path'} || catdir( $self->config->{TMP}, "featdump") ); $fdump->{'path'}= $outpath; # save for reuse my $sqltag = $fdump->{tag} || "feature_sql"; my $sqltype = $fdump->{type}; my $targets = $fdump->{target}; # should be array ? unless($targets) { my @tg= sort keys %{$seqsql->{$sqltag}}; $targets= \@tg; } unless(ref $targets) { $targets= [ $targets ]; } foreach my $tgname (@$targets) { my $fs= $seqsql->{$sqltag}->{$tgname}; unless($fs) { warn "no sql dump target $tgname in $sqlconf"; next; } my $type= $fs->{type}; my $sql = $fs->{sql}; my $outn= $fs->{output} || $tgname.".tsv"; unless($sql && (!$sqltype || $type =~ m/\b$sqltype\b/)) { warn "dumpFeatures skip: $tgname/$type<>$sqltype\n"; next; } #?? my $outf= catfile($outpath,$outn); my $outh= new FileHandle(">$outf"); print STDERR "sql dump $tgname $type $outf\n" if $DEBUG; my $nout= $self->getFeaturesFromDb( $outh, $sql, undef, $dumpflags);# \@sqlparam ? print STDERR "sql dump $tgname n rows=$nout\n" if $DEBUG; close($outh); my $fixme = $fs->{script}; # may be array/hash of scripts ? if ($fixme && $fixme->{type} eq 'postprocess') { my $shell= $fixme->{shell} || $fixme->{language}; my $spath= catfile( $self->config->{TMP}, $fixme->{name}); my $fixinput= $outf; print STDERR "postprocess $shell $spath $fixinput\n" if $DEBUG; open(SH,">$spath"); print SH $fixme->{content}; close(SH); my $sresult= `$shell $spath $fixinput`; #?? what of perl params # how do i pipe table into script ?? and out again to replace old # this works: perl -i.old rdump $r/tmp/featdump/analysis.tsv } ## changed keys: name=> target; file=> name push(@files, { path => $outf, type => $type, target => $tgname, name => $outn, }); } return \@files; } =item getFeaturesFromDb $nrows = self->getFeaturesFromDb( $outh, $sql, \@sqlparam, $flags) $table = self->getFeaturesFromDb( undef, $sql, \@sqlparam, $flags) =cut sub getFeaturesFromDb { my ($self, $outh, $sql, $sqlparam, $flags)= @_; my $err=""; my $dbh = $self->dbiConnect(); my $sth = $dbh->prepare($sql) or $err= "failed to prepare $sql"; if (ref $sqlparam) { $sth->execute(@$sqlparam) or $err= "failed to execute sql" ; } else { $sth->execute() or $err= "failed to execute sql"; } if ($err) { warn $err; die if($self->{failonerror}); return -1; } ## analysis sql gets lots of: Use of uninitialized value in join ## OUT OF MEM error here with ParameciumDB during fetchrow to tmp/featdump file ## get same memerr when run psql -f features.sql, so it isn't Bulkfiles problem ! ## *** malloc: vm_allocate(size=67108864) failed (error code=3); could be gffattr_gmodel local $^W=0; # kill warnings of undef values my $result= 0; if($outh) { print $outh join("\t",@{$sth->{NAME}})."\n" if($flags=~/colname/i); while (my $row = $sth->fetchrow_arrayref) { print $outh join("\t",@$row),"\n"; $result++; } } else { $result = join("\t",@{$sth->{NAME}})."\n" if($flags=~/colname/i); # is this ok? while (my $row = $sth->fetchrow_arrayref) { $result .= join("\t",@$row)."\n"; } } $sth->finish(); return $result; } =item $bases= getBasesFromDb( $uniquename) =cut sub getBasesFromDb { my ($self, $uniquename, $iscsome)= @_; my $dbh= $self->dbiConnect(); my $sql=""; $sql= $self->config->{dnadump}->{sql_csome} if ($iscsome); $sql ||= $self->config->{dnadump}->{sql}; $sql ||= "select feature_id, residues, md5checksum, seqlen, name from feature where uniquename = ?"; my $err=""; my $sth = $dbh->prepare($sql) or $err="unable to prepare feature_id"; unless($err) { $sth->execute($uniquename) or $err="failed to execute feature_id"; } if ($err) { warn $err; die if ($self->{failonerror}); return undef; } ## check for >1 row! e.g. flybase dpse has 2+ csome entries, 1 w/o bases, for same ID my($hashref,$feature_id,$bases)=(undef,undef,""); while (my $nextrow = $sth->fetchrow_hashref) { $hashref = $nextrow; $feature_id = $$hashref{'feature_id'}; $bases= $$hashref{'residues'} || ""; last if $bases; } $self->{gotbases}= $hashref; ## return md5checksum, seqlen fields ;stick all other fields into self $sth->finish(); print STDERR "getBasesFromDb $uniquename -> $feature_id ; n bases=",length($bases),"\n" if (!$bases || $DEBUG > 1); return $bases; } sub getLastBasesFeature { my ($self)= @_; return $self->{gotbases}; } sub maxrange { my ($self, $range)= @_; my ($pre, $suf,$start,$stop, $b, $u); $start= -9; $stop= $start; $range =~ s/^([^\d<>-]*)//; $pre= $1; $range =~ s/(\D*)$//; $suf= $1; my $strand= ($pre =~ /^complement/) ? -1 : 1; if ($range =~ m/^([<>]*)([\d\-]+)/) { $u= $1; $start= $2; $start-- if ($u eq '<'); } if ($range =~ m/([<>]*)([\d\-]+)$/) { $u= $1; $stop= $2; $stop++ if ($u eq '>'); } return ($start,$stop,$strand); } sub dna2protein { my($self, $dna)= @_; my $aa= undef; eval { require Bio::Tools::CodonTable; my $codonTable = Bio::Tools::CodonTable->new(); $aa = $codonTable->translate($dna); }; if ($@) { warn "dna2protein: err: $@"; die if ($self->{failonerror} || $self->{automake}); } return $aa; } sub getBasesFromFiles { my($self, $type,$chr,$baseloc,$name,$subrange)= @_; my $bases= undef; my $gotloc= $baseloc; my $dnaseq= $self->getDnaSeq($chr); if ($dnaseq) { my ($start,$stop,$strand)= $self->maxrange($baseloc); my ($subrb,$subre,$rs)=(0,0,0); if ($subrange) { # need some more logic in $subrange to get just upstream or downstream sections # readseq's: start +/- offset1, stop +/- offset2; eg. (start-2000,start); (stop,stop+2000); (start-2000,stop); (start,stop+2000) my $maxseq= $dnaseq->length(); ($subrb,$subre,$rs)= $self->maxrange($subrange); if ($subrb) { $start += $subrb ; $start=1 if $start<=0; } # need dnaseq min/max ! if ($subre) { $stop += $subre ; $stop=$maxseq if $stop> $maxseq; } # need dnaseq min/max ! } my $range= $baseloc; $range =~ s/^[\w]*\(?//; ##s/^([^\d<>-]*)//; $range =~ s/\)?\s*$//; my @locs= split(/,/,$range); =item handle Bioperl version -strand effects 080620: Bioperl versions are unpredictable in how they handle multiexon -strand thru Location::Split and (Large)PrimarySeq use of revcomp for -split locs. Avoid this by feeding in only +strand exons, but for rare cases of mixed strand genes, then do explicit revcom on final CDS-dna when needed. Input baseloc is simple form: complement(x,y,z), NOT messy join(comp(x),comp(y),comp(z)). add_sub_Location(start,stop,exon+strand) will always use exon+strand even when CDS is -topstrand. This still allows per exon -strand, e.g., compl(x,y,compl(z)) => (-x, -y, +z) =cut if (@locs>1) { ## avoid bad strand() handling in Bio::Location::Split(); my $sloc = Bio::GMOD::Bulkfiles::MySplitLocation->new(); my $topstrand= $strand; # $sloc->strand($topstrand); # Bioperl action here was bad; AVOID THIS # if ($topstrand < 0) { @locs = reverse @locs; } # not right now; AVOID THIS foreach my $loc (@locs) { ($start,$stop,$strand)= $self->maxrange($loc); # $strand= -$strand if ($topstrand < 0); # AVOID THIS $sloc->add_sub_Location( new Bio::Location::Simple( -start => $start, -end => $stop, -strand => $strand, )); } $bases= $dnaseq->subseq($sloc); # should always return forward strand dna, but for mixed exons if($topstrand < 0 && $bases) { $bases= _dna_revcomp($bases); } # if($topstrand < 0 && $bases) { warn "DEBUG: need _dna_revcomp(bases) for $name, loc=$baseloc; sloc=",$sloc->to_FTstring(),"\n"; } $sloc->strand($topstrand); # BUT add in strand for to_FTstring .. $gotloc= $sloc->to_FTstring(); # moved down; might mess w/ exon strands ## warn "feat=$name, got featloc=",$gotloc,"\n" if $DEBUG; } else { ## given warnings do we need to swap start,stop for -strand ? my $sloc= new Bio::Location::Simple( -start => $start, -end => $stop, -strand => $strand, ); $bases= $dnaseq->subseq($sloc); $gotloc= $sloc->to_FTstring(); } } print STDERR "dna-file: $name, bases=",length($bases),"\n" if $DEBUG > 1; if (!$subrange && ($gotloc ne $baseloc)) { my $ok= 0; ## check for silly 123..123 => 123 change while ($baseloc =~ m/(\d+)\.\.(\d+)/g) { my($a,$b)= ($1,$2); if ($a eq $b) { $ok=1; last; } } warn "dna-file: WARNING $name, loc-out=$gotloc ne loc-in=$baseloc\n" unless $ok; } return $bases; } sub _dna_revcomp { my($bases)= @_; ## Bioperl: $bases = Bio::PrimarySeq->new(-seq => $bases)->revcom()->seq(); ## simple way: $bases =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; # complement, doesnt do RNA u/U>t/T return CORE::reverse $bases; } sub _isold { my($source,$target) = @_; ## not for symlinks or dirs my $res= 0; my $targtime= -M $target; ## -M is file age in days.hrs before now if (! -f $target) { return 1; } elsif ( -l $source ) { # $source= _getLinkOriginal($source); $res= (-M $source) < $targtime; } elsif ( -f $source ) { $res= (-M $source) < $targtime; } else { $res= 0; } return $res; } sub _getLinkOriginal { my($source) = @_; my $rsource= readlink($source); return $source unless ($rsource); if ($rsource =~ m/^\.\./) { my $at= rindex( $source,'/'); $rsource= substr($source,0,$at) . '/' . $rsource; } return $rsource; } ## option to symlink ReleaseDir to 'current' for genomeweb path sub makeCurrentLink { my ($self)= @_; my $sok= 0; my $reldir = $self->getReleaseDir(); my $subdir = $self->config->{relfull} || $self->config->{rel} || "release"; my $curdir = $reldir; unless($curdir =~ s,$subdir$,current,) { $sok= -1; return $sok; # what? } if( -l $curdir) { my $lsource = _getLinkOriginal($curdir); if ($lsource =~ m/$subdir$/) { $sok= 1; } else { warn "unlink old $curdir -> $lsource\n" if $DEBUG; unlink($curdir); $sok= 1; # unlink err? } } elsif( -d $curdir) { warn "'$curdir' is directory, not symlink\n"; $sok= -1; } unless(-e $curdir) { (my $topdir= $curdir) =~ s,current$,,; my $olddir= $ENV{'PWD'}; #?? not safe? $sok = chdir($topdir); # NOTE: relative link; subdir has no path $sok = symlink($subdir,'current') if $sok; chdir($olddir); } warn "Changed 'current' release symlink to $reldir; ok=$sok\n"; return $sok; } sub makePath { my($self, $dir, $errmsg, $failonerr)= @_; return 0 unless($dir); # ok or not? return 1 if(-d $dir); eval { mkpath($dir,$DEBUG); }; # 0777 permission if ($@) { $failonerr= ($self->{failonerror}||$self->{automake}) unless(defined $failonerr); warn "ERROR: Couldn't create path $dir: $@\n$errmsg\n"; die if ($failonerr); return 0; } else { return 1; } } sub getReleaseDir { my($self)= @_; my $config = $self->config; my $releasedir= $config->{releasedir}; return $releasedir if ($releasedir && -d $releasedir); ## optiona/default: add full species to path, if not there ... my $datadir= $config->{datadir}; # must exist my $species= $self->speciesFull(); my $org= $self->config->{org}; my $subdir = $config->{relfull} || $config->{rel} || "release"; $datadir= catdir($datadir, $species) unless($datadir =~ m/$species|$org/); $releasedir= catdir($datadir, $subdir); $config->{releasedir} = $releasedir; if( ! -d $datadir) { warn " missing data dir $datadir\n"; } else { $self->makePath($releasedir, "Release path $subdir needed"); } return $releasedir; } sub getReleaseSubdir { my($self, $subdir, $flags)= @_; my $config= $self->config; $flags ||= ""; unless(-d $subdir) { my ($filename,$ext); if ($subdir !~ m,/$, && $subdir =~ m,/, && $subdir =~ m,\.,) { ($filename, $subdir, $ext) = File::Basename::fileparse($subdir, '\.[^\.]+'); } my $reldir= $self->getReleaseDir(); $subdir= catdir($reldir,$subdir) unless(-d $subdir); $self->makePath($subdir, "Release subdir $subdir needed") unless(-d $subdir || $flags =~ /nocreate|nomake/); ## mkpath } return $subdir; } # ## promote all to top of config .. # sub promoteRelease { my($self, $config)= @_; my $cdate= $self->{date}; $cdate =~ s/[^\w-]/_/g; ## make sure no space in date ! my $relid= $config->{relid}; unless($relid) { $relid= $config->{relid}= $cdate; } unless( ref $config->{release}->{$relid} ) { $config->{release}->{$relid}= { date => $cdate, }; } if($relid && ref $config->{release}->{$relid}) { my %relh= %{$config->{release}->{$relid}}; foreach my $k (keys %relh) { $config->{'release_'.$k}= $config->{$k}= $relh{$k} ; # double-store: too many 'date' keys in conf files; use '${release_key}' by preference } } unless($config->{rel}) { # used much, relid ~= rel my $org= $config->{org} || "rel"; $config->{rel}= $org.$relid; } $config->{'release_id'}= $config->{rel} unless($config->{'release_id'}); ## alias of config variables ?? $self->updateConfigVars(); # install ${release_} variables } sub initData { my($self, $config, $oroot)= @_; # check $self for params unless(ref $config) { $config= $self->config || {}; } $self->{config}= $config; $self->{verbose}= $self->{verbose} || $config->{verbose}; ## added $self->config->{newuser} ; turn on verbose, valid checks with this $config->{no_csomesplit}= $self->{no_csomesplit} if($self->{no_csomesplit}); if (ref $config->{ENV}) { foreach my $key (%{$config->{ENV}}) { $ENV{$key}= $config->{ENV}->{$key} unless($ENV{$key}); } } $self->promoteRelease($config); unless(defined $oroot && -d $oroot) { if (defined $config->{ROOT}) { $oroot= $config->{ROOT}; } elsif ($ENV{ARGOS_SERVICE_ROOT}) { $oroot= $ENV{ARGOS_SERVICE_ROOT}; } elsif ($ENV{ARGOS_ROOT} && $config->{SERVICE}) { $oroot= $ENV{ARGOS_ROOT}.'/'.$config->{SERVICE}; } elsif ($ENV{GMOD_ROOT}) { $oroot= $ENV{GMOD_ROOT}; } unless(defined $oroot && -d $oroot) { my $bin = "$FindBin::RealBin"; if ( -e "$bin/../common/") { $oroot= "$bin/../"; } elsif ( -e "$bin/../conf/") { $oroot= "$bin/../"; } # ^^ this is putting data into GMODTools/ folder - ok? no? else { $oroot= "./"; } $oroot=`cd "$oroot" && pwd`; chomp($oroot); } } print STDERR "Using rootpath=$oroot\n" if $DEBUG; # is this bad? $self->{rootpath} = $config->{rootpath} = $oroot; # gmod_root ?? my $datadir= $config->{datadir} || "genomes"; $datadir= "$oroot/$datadir" unless(-d $datadir); if (!-d $datadir && -d $oroot) { $self->makePath($datadir, "** Need writeable data dir=$datadir\nChange configuration datadir\n", 1); #mkpath($datadir,$DEBUG); } $config->{datadir} = $datadir; my $tmpdir= $config->{TMP} || $self->getReleaseSubdir( "tmp/"); # will make dirs inside datadir unless( $tmpdir && $self->makePath($tmpdir,"** Need writeable TMP folder\nTrying other..\n",0) ) { $tmpdir = File::Temp::tempdir( "gmodXXXX", TMPDIR => 1, CLEANUP => 1 ); $self->makePath($tmpdir, "** Need writeable TMP=$tmpdir\nChange configuration TMP\n", 1); warn "Using TMP=$tmpdir\n"; } $config->{TMP} = $tmpdir; $self->{idpattern}= $config->{idpattern} || '[A-Za-z]+\d+'; $fndel= $config->{filepart_delimiter} || '-'; my $fset= $self->getFilesetInfo('dna'); my $dnadir= $self->getReleaseSubdir( $fset->{path} || 'dna/'); $self->{dnadir} = $dnadir; # see getChromosomeTable: $chromosome= $config->{chromosome} if (ref $config->{chromosome}); $self->{addids}= $config->{addids} if defined $config->{addids} ; $self->{ignoredbresidues}= $config->{ignoredbresidues} if defined $config->{ignoredbresidues} ; ## FIXME -- tests w/ this allfeats can be bad ... @allfeats= (ref $config->{allfeats}) ? @{$config->{allfeats}} : qw( BAC CDS DNA_motif EST RNA_motif aberration_junction cDNA_clone enhancer five_prime_UTR gene insertion_site intron mRNA mRNA_genscan mRNA_piecegenie mature_peptide ncRNA oligo oligonucleotide point_mutation polyA_site processed_transcript protein protein_binding_site pseudogene rRNA region regulatory_region repeat_region rescue_fragment segment golden_path_fragment scaffold golden_path sequence_variant signal_peptide snRNA snoRNA so source tRNA tRNA_trnascan three_prime_UTR transcription_start_site transposable_element transposable_element_insertion transposable_element_insertion_site transposable_element_pred ); %mapchr_pattern= %{ $config->{'mapchr_pattern'} } if ref $config->{'mapchr_pattern'}; # add all featset? if (ref $config->{featset}) { @featset= @{$config->{featset}}; } elsif ($config->{featset}) { @featset= ($config->{featset}); } # singleton else { @featset= qw(gene mRNA CDS transcript translation tRNA miscRNA transposon pseudogene gene_extended2000 five_prime_UTR three_prime_UTR intron ); } $config->{featset}= \@featset; my @fastafeatok=(); push(@fastafeatok, @featset); # ?? not @allfeats if (ref $config->{featmap}) { my $fm= $config->{featmap}; foreach my $fk (keys %$fm) { push(@fastafeatok, $fk); if (ref $fm->{$fk} && defined $fm->{$fk}->{types}) { my @ft= split(/[\s,;]/, $fm->{$fk}->{types} ); push(@fastafeatok, @ft); } } } $config->{fastafeatok}= \@fastafeatok; ## add these to %ENV before more configs so they get replaced .. foreach my $k (@ENV_KEYS) { defined $$config{$k} and $ENV{$k}= $$config{$k}; } } #----------- =head1 package Bio::GMOD::Bulkfiles::MySplitLocation patch for Bio::Location::Split -- moved to sep. file =head1 package Bio::GMOD::Bulkfiles::MyLargePrimarySeq -- moved to sep. file patch to use Bio::Seq::LargePrimarySeq to read feature locations from dna.raw files. my $dnaseq= Bio::GMOD::Bulkfiles::MyLargePrimarySeq->new( -file => $dnafile); $loc= new Bio::Location::something(...); $bases= $dnaseq->subseq($loc); =cut 1; chado-1.23/lib/Bio/GMOD/Config.pm000644 000765 000024 00000014500 11627502661 016350 0ustar00cainstaff000000 000000 package Bio::GMOD::Config; use strict; =head1 NAME Bio::GMOD::Config -- a GMOD utility package for reading config files =head1 SYNOPSIS $ export GMOD_ROOT=/usr/local/gmod my $conf = Bio::GMOD::Config->new(); my $tmpdir = $conf->tmpdir(); my $confdir = $conf->confdir(); my $version = $conf->version(); my @dbnames = $conf->available_dbs(); =head1 DESCRIPTION Bio::GMOD::Config is a module to allow programmatic access to the configuration files in GMOD_ROOT/conf. Typically, these files will be gmod.conf (containing site-wide parameters), and one each configuration file for each database, named dbname.conf, containing database connection parameters, which are accessed through Bio::GMOD::Config::DB objects. =head1 METHODS =cut use File::Spec::Functions qw/ catdir catfile /; =head2 new Title : new Usage : my $config = Bio::GMOD::Config->new('/path/to/gmod'); Function: create new Bio::GMOD::Config object Returns : new Bio::GMOD::Config Args : optional path to gmod installation Status : Public Takes one optional argument that is the path to the root of the GMOD installation. If that argument is not provided, Bio::GMOD::Config will fall back to the enviroment variable GMOD_ROOT, which should be defined for any GMOD installation. =cut sub new { my $self = shift; my $arg = shift; my $root; if ($arg) { $root = $arg; #can override the environment variable } else { $root = $ENV{'GMOD_ROOT'}; #required } die "Please set the GMOD_ROOT environment variable\n" ."It is required from proper functioning of gmod" unless ($root); my $confdir = catdir($root, 'conf'); #not clear to me what should be in #gmod.conf since db stuff should go in #db.conf (per programmers guide) my @db; opendir CONFDIR, $confdir or die "couldn't open $confdir directory for reading:$!\n"; my $dbname; while (my $dbfile = readdir(CONFDIR) ) { if ($dbfile =~ /^(\w+)\.conf/) { push @db, $1; } else { next; } } closedir CONFDIR; my %conf; my $conffile = catfile($confdir, 'gmod.conf'); open CONF, $conffile or die "Unable to open $conffile: $!\n"; while () { next if /^\#/; if (/(\w+)\s*=\s*(\S.*)$/) { $conf{$1}=$2; } } close CONF; return bless {db => \@db, conf => \%conf, confdir => $confdir, gmod_root=> $root}, $self; } =head2 available_dbs Title : available_dbs Usage : my @dbs = $config->available_dbs(); Function: returns a list of database config files Returns : see above Args : none Status : public This method returns reference to a list of database configuration files available in GMOD_ROOT/conf. =cut sub available_dbs { shift->{'db'}; } =head2 all_tags Title : all_tags Usage : @tags = $config->all_tags(); Function: returns a list of parameters (ie, hash keys) for a given database Returns : see above Args : none Status : public Returns a list of database connection parameters (ie, hash keys) for a given database configuration file. =cut sub all_tags { my $self = shift; my $params = $self->{'conf'}; my @params; foreach (keys %$params) { push @params, $_; } return @params; } =head2 has_tag Title : has_tag Usage : $bool = $conf->has_tag('TMP'); Function: Returns true if the tag is contained in the config file Returns : see above Args : name of tag Status : public =cut sub has_tag{ my $self = shift; my $tag = shift; my $conf = $self->{'conf'}; if (defined $$conf{$tag}) { return 1; } else { return 0; } } =head2 get_tag_value Title : get_tag_value Usage : $value = $conf->get_tag_value($tag); Function: return the value of a config parameter Returns : see above Args : name of a tag Status : Public =cut sub get_tag_value { my $self = shift; my $tag = shift; my $conf = $self->{'conf'}; if (defined $$conf{$tag}) { return $$conf{$tag}; } else { return; } } =head2 confdir Title : confdir Usage : $confdir = $config->confdir(); Function: returns the path to the configuration directory Returns : see above Args : none Status : public =cut sub confdir { shift->{'confdir'}; } =head2 version Title : version Usage : $version = $config->version(); Function: returns the version of the currently installed Chado software Returns : see above Args : none Status : public =cut sub version { shift->get_tag_value('VERSION');; } =head2 tmp Title : tmp Usage : $tmpdir = $config->tmpdir(); Function: returns the path to the GMOD tmp directory Returns : see above Args : none Status : public Returns the path to the GMOD tmp directory. =cut sub tmpdir { shift->get_tag_value('TMP'); } =head2 gmod_root Title : gmod_root Usage : $gmod_root = $config->gmod_root(); Function: returns the path to the GMOD root directory Returns : see above Args : none Status : public Returns the path to the GMOD root directory. =cut sub gmod_root { shift->{'gmod_root'}; } 1; =head1 AUTHOR Scott Cain Escain@cpan.orgE. Copyright (c) 2011 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut chado-1.23/lib/Bio/GMOD/Config2.pm000644 000765 000024 00000042176 11256707534 016450 0ustar00cainstaff000000 000000 package Bio::GMOD::Config2; use strict; =head1 NAME Bio::GMOD::Config2 -- an extended GMOD utility package for reading config files =head1 SYNOPSIS $ export GMOD_ROOT=/usr/local/gmod .. use Bio::GMOD::Config2; my $conf2 = Bio::GMOD::Config2->new(); my $confdir = $conf2->confdir(); $confhash = $conf2->config(); $confhash = $conf2->readConfig($file); # can be XML, Perl-Struct or key=value $confhash = $conf2->readConfDir($dir, '(gmod|\w+db)\.conf'); $dbname = $conf2->get('CHADO_DB_NAME'); $oldname = $conf2->put( CHADO_DB_NAME => 'mydb'); print $conf2->showConfig(); # XML::Simple output =head1 NOTES Check %ENV for GMOD variables (ROOT path, etc.) and reads if needed conf/gmod.conf key value files into ENV Assumes program is in project subfolder bin/ or like, and sibling conf/ folder exists with gmod.conf key=value settings to be loaded in %ENV at run time. merge/extend of Bio::GMOD::Config from Scott Cain and older dgg version =head1 AUTHOR Don Gilbert, Feb..Aug 2004. =head1 METHODS =cut use Config; # system Config ... namespace problems w/ lib use use FindBin qw( $Bin ); ## dang, this uses system Config.pm, name conflict here use Cwd qw(abs_path); use File::Spec::Functions qw/ catdir catfile /; use File::Basename; ### use Bio::GMOD::Config; use vars qw/@ISA $BASE @CONF_SUF $ROOT $INIT $Variables/; our $DEBUG; our $VERSION = "0.5"; BEGIN { ### @ISA = qw/ Bio::GMOD::Config /; ## DO WE NEED THIS base package at all? #? $DEBUG = 0; $ROOT= "GMOD_ROOT"; $INIT= "GMOD_INIT"; $BASE= undef; @CONF_SUF= (".conf", ".cnf", ".xml", "" ); $Variables= \%ENV; #? } =head2 new Title : new Usage : my $config = Bio::GMOD::Config2->new('/path/to/gmod'); Function: create new Bio::GMOD::Config object Returns : new Bio::GMOD::Config2 Args : optional path to gmod installation Status : Public Takes one optional argument that is the path to the root of the GMOD installation. If that argument is not provided, Bio::GMOD::Config will fall back to the enviroment variable GMOD_ROOT, which should be defined for any GMOD installation. =cut sub new { my $self = shift; my $arg = shift; my $root; my %args=(); if (ref($arg) =~ /ARRAY/) { %args= @$arg; $root= $args{'gmod_root'}; } elsif (ref($arg) =~ /HASH/) { %args= %$arg; $root= $args{'gmod_root'}; } elsif ($arg) { $root = $arg; } #can override the environment variable $DEBUG= $args{debug} if defined $args{debug}; unless($root){ if ($BASE) { $root= $BASE->{'gmod_root'}; } else { $root = $ENV{'GMOD_ROOT'}; } #required } my @db= (); # dgg - drop this ? my $confhash= {}; # need options for subdirs inside conf/ at least: bulkfiles/ gbrowse.conf/ ... my @sp= (); if ($args{searchpath}) { foreach my $sp (@ { $args{searchpath} }) { ##print STDERR "Config2: searchpath $sp\n"; #DEBUG if (-d $sp) { push(@sp, $sp); } else { $sp= catdir($root, $sp); push(@sp, $sp) if (-d $sp); } } } my $searchpath= \@sp; my $confdir = $args{confdir} || 'conf'; $confdir= catdir($root, $confdir) unless($confdir =~ m,^/,); #unixism my $confpatt= $args{confpatt} || '(gmod|[\w_\-]+db)\.conf$'; # FIXME - need caller opts my $read_includes= $args{read_includes} || 0; my $showtags= $args{showtags} || []; if (%args) { delete $args{conf}; # can we delete @args{qw( conf confdir ..)} delete $args{confdir}; delete $args{confpatt}; delete $args{read_includes}; delete $args{showtags}; delete $args{gmod_root}; delete $args{searchpath}; my @keys= keys %args; @$confhash{@keys}= @args{@keys} if @keys; } return bless {db => \@db, conf => $confhash, confdir => $confdir, confpatt => $confpatt, showtags => $showtags, read_includes => $read_includes, searchpath => $searchpath, gmod_root=> $root }, $self; } sub setargs { my $self = shift; my %args= @_; # searchpath confdir need handlin.... foreach my $k (qw(confpatt read_includes showtags)) { $self->{$k}= $args{$k} if defined $args{$k}; } } =head2 $confhash= config() =head2 $rootpath= gmod_root() =head2 $configdir= confdir() =head2 get(key) return value of key found in gmod.conf $db= $conf->get('CHADO_DB_NAME'); %keyvals= $conf->get( qw(CHADO_DB_NAME CHADO_DB_USERNAME) ); SEE ALSO get_tag_value =head2 put(key,val) put/set GMOD::Config value, returns any old value $conf->put('CHADO_DB_NAME',$dbname); %oldvals= $conf->put( CHADO_DB_NAME => $dbname, CHADO_DB_USERNAME => 'me', CHADO_DB_PASSWORD => 'guess', ); =cut sub config { return shift->{'conf'}; } # same as Bio::GMOD::Config sub gmod_root { return shift->{gmod_root}; } sub confdir { return shift->{confdir}; } sub get { my $self = shift; my $confhash = $self->{'conf'}; # \%GmodConfig; my @keys= @_; if (@keys>1 || wantarray) { my %vals=(); @vals{@keys} = @{%$confhash}{@keys}; return %vals; } else { return (defined $confhash->{$keys[0]} ? $confhash->{$keys[0]} : undef); } } sub put { my $self = shift; my $confhash = $self->{'conf'}; # \%GmodConfig; my %keyvals= @_; my %oldvals=(); my @keys= keys %keyvals; @oldvals{@keys} = @{%$confhash}{@keys}; @{%$confhash}{@keys} = @keyvals{@keys}; return %oldvals; } sub _cleanval { local $_= shift; s/^\s*//; s/\\?\s*$//; if (s/^(["'])//) { s/$1$//; } if ($Variables) { s/\$\{(\w+)\}/$Variables->{$1}/g; # convert $KEY to $ENV{$KEY} to value } return $_; } sub _find_file { my($file, @search_path) = @_; my($filename, $filedir) = File::Basename::fileparse($file); if(!@search_path || $filename ne $file) { return($file) if(-e $file); } else { foreach my $path (@search_path) { my $fullpath = catfile($path, $file); return($fullpath) if(-e $fullpath); } } return undef; } sub _find_file2 { my($file, $suffix, $search_path) = @_; my($filename, $filedir) = File::Basename::fileparse($file); if(!$search_path || $filename ne $file) { foreach my $sf (@$suffix) { my $fullpath = $file . $sf; ##print STDERR "Config2::_find_file2 look at $fullpath\n" ;#if $DEBUG; return($fullpath) if(-e $fullpath); } } else { foreach my $path (@$search_path) { foreach my $sf (@$suffix) { my $fullpath = catfile($path, $file) . $sf; ##print STDERR "Config2::_find_file2 look at $fullpath\n" ;#if $DEBUG; return($fullpath) if(-e $fullpath); } } } return undef; } =head2 appendHash($tohash, $addhash, $replace) add keys to hash without replacing existing .. prefered behavior ? unless $replace is flagged =cut sub appendHash { my $self = shift; my ($tohash, $addhash, $replace)= @_; # -- need to be careful here, DONT replace existing key ? my @keys= keys %$addhash; if ($replace) { @{$tohash}{@keys}= @{%$addhash}{@keys}; } else { foreach my $k (@keys) { $$tohash{$k}= $$addhash{$k} unless defined $$tohash{$k}; } } } =head2 readKeyValue($confval, $confhash) Read $confval string for key=value lines Return hash-ref options =cut sub readKeyValue { my $self = shift; my ($confval, $confhash, $replace)= @_; $confhash = $self->{'conf'} unless(ref $confhash); $confhash = {} unless(ref $confhash); my ($k,$v,$noappend); foreach (split(/\n/,$confval)) { next if(/^\s*[\#\!]/ || /^\s*$/); # skip comments, etc. if (/^([^\s=:]+)\s*[=:]\s*(.*)$/) { # must have value=(*.) to allow blanks ($k,$v)=($1,$2); $noappend= (defined $confhash->{$k} && !$replace); $confhash->{$k}= _cleanval($v) unless($noappend); } elsif ($k && s/^\s+//) { $confhash->{$k} .= _cleanval($_) unless($noappend); } } return $confhash; } our $readConfigOk; sub readConfigOk { return $readConfigOk; } =head2 readConfigFile($file, $opts) read one file; see readConfig =cut sub readConfigFile { my $self = shift; my($file, $opts, $included)= @_; my $confhash = {}; unless ($file && -e $file) { my($filename, $filedir); $filedir= $self->{confdir}; # full path push(@{$opts->{searchpath}},$filedir) if (-d $filedir); $filedir= "conf/"; push(@{$opts->{searchpath}},$filedir) if (-d $filedir); ($filename, $filedir) = File::Basename::fileparse($0); push(@{$opts->{searchpath}},$filedir) if (-d $filedir); if ($file) { ($filename, $filedir) = File::Basename::fileparse($file); push(@{$opts->{searchpath}},$filedir) if (-d $filedir); } } unless( $file ) { my ($ScriptDir, $Extension); ($file, $ScriptDir, $Extension) = File::Basename::fileparse($0, '\.[^\.]+'); } if ($file && !-e $file) { my @suf= @CONF_SUF; ##(".conf", ".cnf", ".xml", "" ); my $cnf= _find_file2( $file, \@suf, $opts->{searchpath} ); if ($cnf) { $file= $cnf; } } ##print STDERR "Config2::readConfig look at $file\n" if $DEBUG; $self->{filename}= $file unless($included); if (!$file || ($file =~ /\.xml/ && -e $file)) { require XML::Simple; ## will attemp to read $0.xml file if no file given my $xs = new XML::Simple(%$opts); # (NoAttr => 1, KeepRoot => 1);#options $confhash = $xs->XMLin( $file); } elsif (-f $file) { ## handle key-value file OR perl-struct open(F,$file); my $confval= join("",); close(F); if ($confval =~ m/=>/s && $confval =~ m/[\{\}\(\)]/s) { $confhash= eval $confval; if ($@) { warn " error $@"; } } else { #? check for \w+ [:=] lines first ? $confhash= $self->readKeyValue($confval, $confhash); } } if (scalar(%$confhash)) { $readConfigOk= 1; } print STDERR "Config2: read: $file ok=$readConfigOk\n" if $DEBUG; if (ref $self->{showtags} && !$self->{showntags}{$file}) { $self->{showntags}{$file}=1; my $show=''; foreach my $tag (@{$self->{showtags}}) { my $showval=''; my $val= $$confhash{$tag}; if( ref($val) eq 'HASH') { # hash of hash :( my @keys = sort keys %$val; foreach my $k (@keys) { my $vv= $$val{$k}; if(ref($vv) eq 'HASH') { $vv= $vv->{content}; } $showval .= "\n $k = ". $vv; } ##$showval .= join("\n", @{$val}{@keys}); } elsif( ref($val) eq 'ARRAY') { $showval .= join("\n", @{$val}); } elsif($val) { $showval .="$val"; } $show.= "$tag = $showval; " if $showval; } print STDERR "Config: $show from $file\n" if $show; } return $confhash; } =head2 readConfig($file, $opts) Read configurations in these formats XML::Simple OR Perl-struct OR key=value config file Parameters $file = input file; $opts = XML::Simple options hash-ref Return hash-ref options =cut sub readConfig { my $self = shift; my($file, $opts, $confhash)= @_; $readConfigOk= 0; if(ref $opts) { $opts= { %$opts }; $opts->{Variables}= $Variables unless($opts->{Variables}); } else { $opts= { Variables => $Variables }; } $confhash = $self->{'conf'} unless(ref $confhash); # always exists ? $confhash = {} unless(ref $confhash); $DEBUG= delete $opts->{debug} if (defined $opts->{debug}); my $replacekeys= delete $opts->{replace} || 0; ##print STDERR "Config2::readConfig in=$file\n" if $DEBUG; unless ($opts->{searchpath}) { $opts->{searchpath}= [ @{$self->{'searchpath'}} ]; } my $conf1 = $self->readConfigFile($file, $opts, 0); $self->appendHash($confhash, $conf1, $replacekeys) if ($conf1); ## $self->{filename}= $file; if ($self->{read_includes} && $$confhash{include}) { ## $self->{read_includes}= 0; ## MUST NOT RECURSE HERE... ##? but can we do nested includes ?? need to check each conf1 my %didinc=(); my $inc= $$confhash{include}; my @inc= (ref($inc) =~ /ARRAY/) ? @$inc : ($inc); my $saveConfigOk= $readConfigOk; foreach $inc (@inc) { next if ($didinc{$inc}); $didinc{$inc}++; $readConfigOk= 0; $conf1= $self->readConfigFile($inc, $opts, 1); ## need some warning/die if not found warn "Config2: MISSING include=$inc \n" unless $readConfigOk; if ($conf1) { my $inc1= delete $$conf1{include}; if($inc1) { push(@inc, (ref($inc1) =~ /ARRAY/) ? @$inc1 : ($inc1)); } $self->appendHash($confhash, $conf1, $replacekeys); } $saveConfigOk=0 unless($readConfigOk); } $readConfigOk= $saveConfigOk; } return $confhash; } sub updateVariables { my $self = shift; my( $confhash, $opts)= @_; $DEBUG= delete $opts->{debug} if (defined $opts->{debug}); $confhash = $self->{'conf'} unless(ref $confhash); # always exists ? $confhash = {} unless(ref $confhash); my $env= (ref $opts and ref $opts->{Variables}) ? $opts->{Variables} : $Variables; _update1Value( $confhash, $env); return $confhash; } sub _update1Value { my($val,$env)= @_; if( ref($val) eq 'HASH') { foreach my $tag (sort keys %$val) { $$val{$tag} = _update1Value( $$val{$tag}, $env); } } elsif( ref($val) eq 'ARRAY') { foreach (@$val){ $_= _update1Value( $_, $env); } } else { while ( $val =~ m/\$\{(\w+)\}/g) { my $var=$1; my $enval= $env->{$var}; #only if defined, leave otherwise if (defined $enval) { if($enval =~ m/\$\{(\w+)\}/) { $enval= _update1Value( $enval, $env); } print STDERR "UPVAL1: \$\{$var\} => $enval\n" if $DEBUG; $val =~ s/\$\{$var\}/$enval/; } } } return $val; } =head2 showConfig($confhash, $opts) $confhash = options hash-ref $opts = XML::Simple options hash-ref (debug => 1 Data dumper out) return XML::Simple of input =cut sub showConfig { my $self = shift; my($confhash,$opts)= @_; $confhash = $self->{'conf'} unless(ref $confhash); # always exists ? $opts= ($opts) ? { %$opts } : {}; my $debug= delete $$opts{debug}; $debug= $DEBUG unless defined $debug; my $xml =''; if ($debug) { require Data::Dumper; my $dd = Data::Dumper->new([$confhash]); $dd->Terse(1); $xml.= "\n"; } require XML::Simple; my $xs = new XML::Simple( %$opts); #NoAttr => 1, KeepRoot => 1 $xml .= $xs->XMLout( $confhash ); return $xml; } sub _updir { #? my $self = shift; my ($atdir,$todirs)= @_; my $dir= $atdir; my $ok= 0; my $cod; foreach my $td (@$todirs) { $cod= catdir($dir, $td); $ok= (-d $cod); last if $ok; } while (!$ok && length($dir)>2) { $dir= "$dir/.."; ##NOT File::Basename::dirname($dir)."/.."; $dir=`cd "$dir" && pwd`; chomp($dir); ##warn " _updir $dir\n" if $DEBUG; foreach my $td (@$todirs) { $cod= catdir($dir, $td); $ok= (-d $cod); last if $ok; } } return ($ok) ? $dir : $atdir; } =head2 $confhash= readConfDir( $dir, $confpatt, $confhash) Process all config files of confpatt in dir folder. note: this can load in things you may not want (e.g. all the .xml.old files...) =cut our $readConfDirOk; sub readConfDir { my $self = shift; my( $confdir, $confpatt, $confhash)= @_; $confdir = $self->{'confdir'} unless($confdir); $confpatt = $self->{'confpatt'} unless($confpatt); $confhash = $self->{'conf'} unless(ref $confhash); # always exists ? $confhash = {} unless(ref $confhash); $readConfDirOk= 0; if ( opendir( DIR, $confdir ) ) { my @conf = grep ( /$confpatt/, readdir(DIR)); closedir(DIR); foreach my $file (sort @conf) { my $confpath= catfile($confdir,$file); $confhash= $self->readConfig( $confpath, { debug => $DEBUG, Variables => $Variables }, $confhash); $readConfDirOk ||= $readConfigOk; } } warn " readConfDir $confdir ok=$readConfDirOk\n" if $DEBUG; return $confhash; } sub init_conf { my $self= shift; my $myroot = $self->{'gmod_root'}; my $confpatt = $self->{'confpatt'}; my $confhash = $self->readConfDir(); unless($readConfDirOk) { warn " no $confpatt file at $myroot/conf; setenv $ROOT to locate." } else { # if ($SetEnv) $self->appendHash( \%ENV, $confhash, 0); # -- need to be careful here, DONT replace existing key ? # my @keys= keys %$confhash; # foreach my $k (@keys) { $ENV{$k}= $$confhash{$k} unless defined $ENV{$k}; } # @ENV{@keys}= @{%$confhash}{@keys}; } $ENV{$INIT}= 1; my @inc=(); my $libdir= catdir($myroot,"lib"); push(@inc, $libdir) if (-d $libdir); push(@inc, split /:/, $ENV{'PERL5LIB'}) if (defined $ENV{'PERL5LIB'}); foreach my $p (@inc) { unshift(@INC,$p) unless( grep /^$p$/i,@INC ); } } =head2 BEGIN At eval time (use, require), this checks %ENV for GMOD_ROOT and GMOD_INIT. If not found, it looks in folder above calling script for conf/gmod.conf as KEY=value to be loaded into %ENV. $ENV{GMOD_INIT}=1 prevents this loading. =cut BEGIN { $DEBUG = $ENV{'DEBUG'} unless defined $DEBUG; unless($ENV{$INIT}) { my $myroot; if (defined $ENV{$ROOT} && -d $ENV{$ROOT}) { $myroot= $ENV{$ROOT}; } else { $myroot= abs_path("$Bin"); } $myroot= _updir( $myroot, ["conf"] ); # in case we are not in bin/ folder $BASE= __PACKAGE__->new($myroot); #?? my $self= Bio::GMOD::Config2->new($myroot); $BASE->init_conf(); } } 1; chado-1.23/lib/Bio/GMOD/DB/000755 000765 000024 00000000000 12061672376 015076 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/Load/000755 000765 000024 00000000000 12061672375 015467 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/Load.pm000644 000765 000024 00000015323 11256707760 016033 0ustar00cainstaff000000 000000 package Bio::GMOD::Load; use strict; use Chado::AutoDBI; use Chado::LoadDBI; use Bio::GMOD::Util; use Class::DBI::ConceptSearch; use Bio::GMOD::Config; use Bio::Root::Root; use Bio::GMOD::Util; =head2 new =over =item Usage $obj->new() =item Function =item Returns =item Arguments =back =cut sub new { my $proto = shift; my $self = bless {}, ref($proto) || $proto; my $conf = Bio::GMOD::Config->new(); my $cs_config_file = $conf->get_tag_value('CONCEPT_SEARCH_CONFIG'); my $cs_config; open CONF, $cs_config or $self->throw("unable to open ConceptSearch config file: $!"); while () { $cs_config .= $_; } close CONF; my $cs = Class::DBI::ConceptSearch->new(xml => $config); $self->concept_search($cs); return $self; } =head2 concept_search =over =item Usage $obj->concept_search() #get existing value $obj->concept_search($newval) #set new value =item Function =item Returns value of concept_search (a scalar) =item Arguments new value of concept_search (to set) =back =cut sub concept_search { my $self = shift; return $self->{'concept_search'} = shift if defined(@_); return $self->{'concept_search'}; } =head2 search =over =item Usage $obj->search() =item Function =item Returns =item Arguments hash of search terms =back =cut sub search { my ($self, %argv) = @_; return unless %argv; my @object = $self->concept_search()->search( %argv ); return @object; } =head2 find_or_create =over =item Usage $obj->find_or_create() =item Function =item Returns =item Arguments =back =cut sub find_or_create { my ($self, %argv) = @_; } =head2 cache_feature =over =item Usage $obj->cache_feature() =item Function =item Returns =item Arguments =back =cut sub cache_feature { my ($self, %argv) = @_; } =head2 cv =over =item Usage $obj->cv() =item Function =item Returns =item Arguments =back =cut sub cv { my $self = shift; return $self->{'cv'} if $self->{'cv'}; $self->{'cv'} = Chado::Cv->find_or_create( { name => 'autocreated', definition => 'auto created by load_gff3.pl' } ); return $self->{'cv'}; } =head2 so =over =item Usage $obj->so() =item Function =item Returns =item Arguments =back =cut sub so { my $self = shift; return $self->{'so'} if $self->{'so'}; $self->{'so'} = Chado::Cv->search( { name => 'Sequence Ontology' } ); die "Unable to find Sequence Ontology in cv table; that is a pretty big problem" unless $self->{'so'}; return $self->{'so'}; } sub cache_cvterm { my $self = shift; my $name = shift; my $soid = shift; ( $cvterm{$name} ) = Chado::Cvterm->search( { name => $name, cv_id=> $soid } ) || Chado::Cvterm->search( { name => ucfirst($name), cv_id=> $soid } ); $cvterm{$name} = $cvterm{$name}->next() if defined( $cvterm{$name} ) and $cvterm{$name}->isa('Class::DBI::Iterator'); if ( !$cvterm{$name} && !$soid ) { ( $cvterm{$name} ) = Chado::Cvterm->find_or_create( { name => $name, cv_id => $self->cv()->id, definition => 'autocreated by gmod_load_gff3.pl', } ); } die "unable to create a '$name' entry in the cvterm table" if (!$cvterm{$name} && !$soid ); die "$name could not be found in your cvterm table.\n" ."Either the Sequence Ontology was incorrectly loaded,\n" ."or this file doesn't contain GFF3" if (!$cvterm{$name} && $soid); } =head2 srcfeature =over =item Usage $obj->srcfeature() #get existing value $obj->srcfeature($newval) #set new value =item Function =item Returns value of srcfeature (a scalar) =item Arguments new value of srcfeature (to set) =back =cut sub srcfeature { my $self = shift; return unless defined $_[0]; return ${$self->{'srcfeature'}}->$_[0] = $_[1] if defined($_[1]); return ${$self->{'srcfeature'}}->$_[0]; } =head2 featureloc_locgroup =over =item Usage $obj->featureloc_locgroup() #get existing value $obj->featureloc_locgroup($newval) #set new value =item Function =item Returns value of featureloc_locgroup (a scalar) =item Arguments new value of featureloc_locgroup (to set) =back =cut sub featureloc_locgroup { my $self = shift; return unless defined $_[0]; return ${$self->{'featureloc_locgroup'}}->$_[0] = $_[1] if defined($_[1]); return ${$self->{'featureloc_locgroup'}}->$_[0]; } =head2 feature =over =item Usage $obj->feature() #get existing value $obj->feature($newval) #set new value =item Function =item Returns value of feature (a scalar) =item Arguments new value of feature (to set) =back =cut sub feature { my $self = shift; return unless defined $_[0]; return ${$self->{'feature'}}->$_[0] = $_[1] if defined($_[1]); return ${$self->{'feature'}}->$_[0]; } =head2 gff_source =over =item Usage $obj->gff_source() #get existing value $obj->gff_source($newval) #set new value =item Function =item Returns value of gff_source (a scalar) =item Arguments new value of gff_source (to set) =back =cut sub gff_source { my $self = shift; return unless defined $_[0]; return ${$self->{'gff_source'}}->$_[0] = $_[1] if defined($_[1]); return ${$self->{'gff_source'}}->$_[0]; } =head2 dbxref =over =item Usage $obj->dbxref() #get existing value $obj->dbxref($newval) #set new value =item Function =item Returns value of dbxref (a scalar) =item Arguments new value of dbxref (to set) =back =cut sub dbxref { my $self = shift; return unless defined $_[0]; return ${$self->{'dbxref'}}->$_[0] = $_[1] if defined($_[1]); return ${$self->{'dbxref'}}->$_[0]; } =head2 gff_source_db =over =item Usage $obj->gff_source_db() #get existing value $obj->gff_source_db($newval) #set new value =item Function =item Returns value of gff_source_db (a scalar) =item Arguments new value of gff_source_db (to set) =back =cut sub gff_source_db { my $self = shift; return $self->{'gff_source_db'} = shift if defined(@_); return $self->{'gff_source_db'}; } chado-1.23/lib/Bio/GMOD/SeqUtils.pm000644 000765 000024 00000045752 11256707534 016735 0ustar00cainstaff000000 000000 =head1 NAME GMOD::Chado::SeqUtils -- common sequence in/out/check methods for Chado DB =head1 SYNOPSIS =head1 SEE ALSO GMOD Chado sequence scripts for init_db, load_newseq, dump_seq, list_db . gmod_init_db.pl -- initialize a new database, adding organisms, intialize.sql, ontology data sets. gmod_load_newseq.pl -- add miscellaneous organism sequences, cDNA, EST, microsatellites, etc. not located on genome. Optionally generate PublicID for these. gmod_dump_seq.pl -- output sequences selected by organism, publication (input file), seq type. gmod_list_db.pl -- show feature statistics for chado db: # per organism, per seq type, per publication/infile, and checksum test for sequence duplications. =head1 AUTHOR Don Gilbert, Feb 2004. =head1 METHODS =cut package GMOD::Chado::SeqUtils; use strict; # use lib('/bio/biodb/common/perl/lib','/bio/biodb/common/system-local/perl/lib'); # test use GMOD::Chado::LoadDBI; use vars qw( @dbparts %cvterm %org_cache $nullcontact ); our $DEBUG; use constant SequenceOntology => 'Sequence Ontology'; use constant IDCounter => 'PublicID:counter'; # dbIdCounter == # Db->name key BEGIN { $DEBUG= 0 unless defined $DEBUG; @dbparts= qw(NAME HOST PORT USERNAME PASSWORD); #? get from Chado::LoadDBI ? %cvterm = (); %org_cache = (); } sub new { my $that= shift; my $class= ref($that) || $that; my %fields = @_; my $self = \%fields; bless $self, $class; $self->init(); return $self; } sub init { my $self= shift; $self->{readwrite}= 0 unless defined $self->{readwrite}; $self->{verbose}= 0 unless defined $self->{verbose}; $self->{dochecksum}= 0 unless defined $self->{dochecksum}; $self->{defline_species}= 1 unless defined $self->{defline_species}; # $self->{autocv}= 0 unless defined $self->{autocv}; } =item openChadoDB( %params ) basically calls Chado::LoadDBI->init( %$dbvals ) and setReadWrite flag, inits some values from db parameters: verbose => 1/0 readwrite => 1/0, r/w, t/f dbvalues => \%dbvalues from getDatabaseOpenParams =cut sub openChadoDB { my $self = shift; my %opts = @_; $self->{$_}= $opts{$_} foreach (keys %opts); die "openChadoDB: call with dbvalues => \%dbvalues from getDatabaseOpenParams" unless (ref $self->{dbvalues}); GMOD::Chado::LoadDBI->init( %{$self->{dbvalues}} ); # some useful values for readwrite only ? # ($nullpub) = Bio::Chado::CDBI::Pub->search( miniref => 'null' ); ($nullcontact) = Bio::Chado::CDBI::Contact->search( name => 'null' ); $self->initAutoCvTable(); } =item getDatabaseOpenParams() Runtime checks for Bio::Chado::CDBI::LoadDBI values of NAME HOST PORT USERNAME PASSWORD [from getDatabaseParamKeys()] Checks %ENV for $GMOD_SERVICE_key, CHADO_DB_key, e.g. FLYBASE_DB_NAME = flybase-chado1 FLYBASE_DB_PORT = 7404 -- fallback to CHADO if GMOD_SERVICE is not defined CHADO_DB_NAME = chado-test CHADO_DB_PORT = 7302 Returns hash with these values, suitable for call to @ARG GetOptions() my %dbvals= getDatabaseOpenParams(); my $ok= GetOptions( 'dbname:s' => \$dbvals{NAME}, 'name:s' => \$dbvals{NAME}, 'host:s' => \$dbvals{HOST}, 'port:s' => \$dbvals{PORT}, 'username:s' => \$dbvals{USERNAME}, 'password:s' => \$dbvals{PASSWORD}, @otherOpts, ); =cut sub getDatabaseParamKeys { my $self= shift; return @dbparts; } sub getDatabaseOpenParams { my $self= shift; my %dbvals= map { $_ => '' } @dbparts; ## check %ENV - first service_db keys, default to chado_db = flybase, eugenes, daphnia, etc. my @service_db= ('CHADO_DB'); # what service is calling us ? unshift(@service_db, $ENV{'GMOD_SERVICE'}.'_DB') if (defined $ENV{'GMOD_SERVICE'}); unshift(@service_db, $ENV{'ARGOS_SERVICE'}.'_DB') if (defined $ENV{'ARGOS_SERVICE'}); foreach my $service_db (@service_db) { foreach my $part (@dbparts) { next if ($dbvals{$part}); my $v= $ENV{$service_db.'_'.uc($part)}; $dbvals{$part}= $v if ($v); } } return %dbvals; } =item getSeqType($seqtype, $ontology) return Bio::Chado::CDBI::Cvterm matching seqtype from ontology. Supports use of SO seq types =cut sub getSeqType { my ($self, $seqtype, $ontname)= @_; my $type_id= undef; my $sotype = undef; $ontname = SequenceOntology unless($ontname); return $cvterm{$seqtype} if ($cvterm{$seqtype}); my @sotype = Bio::Chado::CDBI::Cvterm->search( name => $seqtype ) || Bio::Chado::CDBI::Cvterm->search_like( name => "%$seqtype%" ); unless(@sotype) { print STDERR "Seq type=$seqtype not found. Please choose a type from $ontname"; return undef; } elsif (@sotype > 1) { print STDERR "These terms from $ontname match '$seqtype'.\n"; print STDERR " ",$_->name,"\n" foreach (@sotype); # allow user choice here.. print STDERR "Choose Sequence type? \n"; #? STDERR? chomp( $seqtype = ); foreach my $sot (@sotype) { if ($sot->name eq $seqtype) { $sotype= $sot; last; } } return undef unless($sotype); } else { $sotype= shift @sotype; } $sotype = $sotype->first() if defined( $sotype ) and $sotype->isa('Class::DBI::Iterator'); my ($socv) = Bio::Chado::CDBI::Cv->search( name => $ontname ); unless ($socv) { print STDERR "Ontology $ontname is not loaded; using $seqtype"; $self->cache_cvterm($seqtype); } elsif( $sotype->cv_id == $socv->id) { print "Using seq type=".$sotype->name." from $ontname\n" if $self->{verbose}; $cvterm{$seqtype}= $sotype; } else { print STDERR "$seqtype is not listed in $ontname"; return undef; } return $cvterm{$seqtype}; } sub initAutoCvTable { my ( $self ) = @_; ($self->{autocv}) = Bio::Chado::CDBI::Cv->search( name => 'autocreated' ); if(!$self->{autocv} && $self->{readwrite}) { ($self->{autocv}) = Bio::Chado::CDBI::Cv->find_or_create( { name => 'autocreated', definition => "auto created by $0", } ); } } =item cache_cvterm( $name [, $cv] ) Look for $name in Bio::Chado::CDBI::Cvterm. If not found and readwrite, add to cvterm table, with cv->id (autocv default) Store in hash for frequent reuse. return Bio::Chado::CDBI::Cvterm =cut sub cache_cvterm { my ( $self, $name, $cv ) = @_; return unless $name; $cv= $self->{autocv} unless($cv); unless (defined $cvterm{$name}) { my ($term) = Bio::Chado::CDBI::Cvterm->search( name => $name ) || Bio::Chado::CDBI::Cvterm->search( name => ucfirst($name) ); if ( $term ) { $term = $term->first() if defined( $term ) and $term->isa('Class::DBI::Iterator'); } elsif ($self->{readwrite} && $cv) { $term = Bio::Chado::CDBI::Cvterm->find_or_create( { name => $name, cv_id => $cv->id, definition => "auto created by $0", } ) ; warn "unable to create a '$name' entry in the cvterm table" unless($term); } $cvterm{$name} = $term; } return $cvterm{$name}; } =item getOrganism( $organism, $quiet) return Bio::Chado::CDBI::Organism matching common name, abbreviation (best) or genus. Prompts for choice if ! $quiet =cut sub getOrganism { my ($self, $organism, $quiet)= @_; return undef unless($organism); my $chadorg= $org_cache{$organism}; return $chadorg if $chadorg; my $iter = Bio::Chado::CDBI::Organism->search( common_name => lc($organism) ) || Bio::Chado::CDBI::Organism->search( abbreviation => ucfirst($organism) ) || Bio::Chado::CDBI::Organism->search( genus => $organism ); if ($iter) { if ( $iter->count == 1 ) { #? || quiet $chadorg = $iter->first(); } elsif (!$quiet) { print STDERR "The organism '$organism' matches these:\n"; for (my $org = $iter->first; ($org) ; $org= $iter->next) { print STDERR " ".$org->genus." ".$org->species."/".$org->abbreviation."/".$org->common_name."\n"; } print STDERR "Select organism? (abbreviation): \n"; chomp( $organism = ); for (my $org = $iter->first; ($org) ; $org= $iter->next) { if ($org->abbreviation() eq $organism) { $chadorg= $org; last; } } } } else { print STDERR "The organism '$organism' could not be found.\n"; unless($quiet) { print STDERR "Available organisms:\n"; $iter = Bio::Chado::CDBI::Organism->retrieve_all; for (my $org = $iter->first; ($org) ; $org= $iter->next) { print STDERR " ".$org->genus." ".$org->species."/".$org->abbreviation."/".$org->common_name."\n"; } print STDERR "Select organism? (abbreviation): \n"; chomp( $organism = ); for (my $org = $iter->first; ($org) ; $org= $iter->next) { if ($org->abbreviation() eq $organism) { $chadorg= $org; last; } } } } if ($chadorg) { $org_cache{$organism}= $chadorg; print "Working with ".$chadorg->genus." ".$chadorg->species.".\n"; } return $chadorg; } =pod =item getSynonyms($chado_feature) fetch synonym values, returns (wantarray) ? list : first =cut sub getSynonyms { my ($self, $chado_feature) = @_; my @ftsyn = Bio::Chado::CDBI::Feature_Synonym->search( feature_id => $chado_feature->id, # pub_id => $pub->id, ); if (wantarray) { my @names= (); push @names, $_->synonym->name() foreach (@ftsyn); return @names; } else { return (@ftsyn) ? $ftsyn[0]->synonym->name() : undef; } } =pod =item getPubFeatures($pub) return features given $pub->id (OUTFILE reference) =cut sub getPubFeatures { my ($self, $pub) = @_; my @allfeats= (); my @fpub = Bio::Chado::CDBI::Feature_Pub->search( pub_id => $pub->id, { order_by=>'feature_id' }, ); # print "getPubFeatures ".$pub->id." n= ".scalar(@fpub)."\n" if $self->{verbose}; push @allfeats, $_->feature_id foreach (@fpub); return @allfeats; } =pod =item getFeaturePubs($feat) return pubs given $feat->feature_id =cut sub getFeaturePubs { my ($self, $ft) = @_; my @items= (); my @fpub = Bio::Chado::CDBI::Feature_Pub->search( feature_id => $ft->id, { order_by=>'pub_id' }, ); push @items, $_->pub_id foreach (@fpub); return @items; } =item getDbxrefs($chado_feature) @dbxrefs is array of DbName:DbAccession =cut sub getDbxrefs { my ($self, $chado_feature) = @_; my @dbxrefs= (); my @feature_dbxref = Bio::Chado::CDBI::Feature_Dbxref->search( feature_id => $chado_feature->id, ); foreach my $d (@feature_dbxref) { next unless $d->dbxref_id; my $acc= $d->dbxref_id->accession; my $db = $d->dbxref_id->db_id->name; ## cache this one push(@dbxrefs, "$db:$acc"); } return @dbxrefs; } =pod =item getProperties($chado_feature) get property values from the featureprop table. %props is hash of property name => value -- need bag, not hash - many vals per name =cut sub getProperties { my ($self, $chado_feature) = @_; my %props= (); my @featureprop = Bio::Chado::CDBI::Featureprop->search( feature_id => $chado_feature->id, ); foreach my $p (@featureprop) { next unless $p->type_id; my $tpid= $p->type_id; my $tpname= $self->{type_id}{$tpid}; unless($tpname) { $self->{type_id}{$tpid}= $tpname= $tpid->name; } #my $tpname= $p->type_id->name; $props{$tpname} .= "," if ($props{$tpname}); $props{$tpname} .= $p->value; } return %props; } =item dumpSequences($outh, @chado_features) Write sequences to $outh from Bio::Chado::CDBI::Features. Includes seq_type, synonyms, feature_properties, feature_dbxrefs on defline Only fasta dump now. E.g. >WFcd0000100 len=567;type=cDNA_clone;synonym=P1-E62000FW40325,WFBid100;contact=JColbo urne;library=CGBvntr;date=Jan2004;taxon=D.pulicaria;clone=P1-E62000FW40325;strain=Mar ieLake,Oregon GCGGGAGNCCGGTATATTGCAGAGTGGCATTATGGCCGNGAAGCAGTNGT ATCAACGCANAGTGGCCATTATGGCCGGGAAGCAGTGGTATCAACGCACG ## this is SLOW for 15K seq-feature database ... .. use iterator, not @feaure array .. .. cache common values .. =cut sub dumpSequences { my ($self, $outh, $chado_features)= @_; my $i = 0; # print "dumpSequences n= ".scalar(@chado_features)."\n" if $self->{verbose}; if (!defined($chado_features)) { warn "Need Bio::Chado::CDBI::Feature param"; return -1; } elsif ($chado_features->isa('Class::DBI::Iterator')) { for (my $ft = $chado_features->first; ($ft) ; $ft= $chado_features->next) { my $res = $ft->residues; my $defline= $self->getFeatureDefline($ft); print $outh $defline,"\n"; $res =~ s/(.{1,50})/$1\n/g; print $outh $res,"\n"; $i++; } return $i; } my @fts=(); if (ref $chado_features =~ /ARRAY/) { @fts= @$chado_features; } elsif ($chado_features->isa('Bio::Chado::CDBI::Feature')) { @fts= ($chado_features); } foreach my $ft (@fts) { my $res = $ft->residues; my $defline= $self->getFeatureDefline($ft); print $outh $defline,"\n"; $res =~ s/(.{1,50})/$1\n/g; print $outh $res,"\n"; $i++; } return $i; } =item getFeatureDefline($chado_feature) return basic >fasta string of chado_feature information =cut sub getFeatureDefline { my ($self, $chado_feature)= @_; #should we bother w/ Bio::Seq construction -> SeqIO::writeseq(seq); ? my $name= $chado_feature->name; my $len = $chado_feature->seqlen; my $defline= ">$name len=$len"; my $tpid= $chado_feature->type_id; my $tpname= $self->{type_id}{$tpid}; unless($tpname) { $self->{type_id}{$tpid}= $tpname= $tpid->name; } $defline .= "; type=" . $tpname; ## $tpid->name $ cache this my @synonyms= $self->getSynonyms($chado_feature); $defline .= "; synonym=".join(",",@synonyms) if @synonyms; my %props= $self->getProperties($chado_feature); if ($self->{defline_species}) { #?? always/sometimes add species=$org->genus." ".$org->species; my $org= $chado_feature->organism_id; # my $ospp= $org->species; # my $species= $org->genus." ".$org->species; my $ospp= $self->{spponly}{$org}; unless($ospp) { $self->{spponly}{$org}= $ospp= $org->species; } my $species= $self->{species}{$org}; unless($species) { $self->{species}{$org}= $species= $org->genus." ".$org->species; } foreach (qw(taxon species organism)) { my $spp= $props{$_}; if ($spp && $spp =~ /$ospp/i) { delete $props{$_}; } #what - do both?; ignore this? } $defline .= "; species=".$species; } $defline .= "; ".join("; ", (map{ "$_=$props{$_}"} sort keys %props)) if %props; my @dbxrefs= $self->getDbxrefs($chado_feature); $defline .= "; dbxref=".join(",",@dbxrefs) if @dbxrefs; if ($self->{dochecksum}) { # only if really want my $check= $chado_feature->md5checksum; ## add if not 0 $defline .= "; checksum=$check" if ($check); } return $defline; } #? *defline = &getFeatureDefline; =item lastPublicId($idtag, [$lastid]) Get [Set] last public id number for given idtag =cut sub lastPublicId { my($self, $idtag, $idclass, $lastid)= @_; my ($iddb) = Bio::Chado::CDBI::Db->search( name => IDCounter ); # $dbIdCounter if (!$iddb && $self->{readwrite}) { ($iddb) = Bio::Chado::CDBI::Db->find_or_create( { name => IDCounter, description => "database id counters created by $0", contact_id => $nullcontact, #?? # urlprefix => $idtag, #? # url => $url, } ) ; $iddb->dbi_commit if $iddb; } #? save idbx my ($idbx) = Bio::Chado::CDBI::Dbxref->search( accession => $idtag , db_id => $iddb->id); $idbx = $idbx->first() if defined($idbx) and $idbx->isa('Class::DBI::Iterator'); if($idbx) { if (defined $lastid && $self->{readwrite}) { $idbx->version($lastid); $idbx->update(); $idbx->dbi_commit(); print "Put last id for $idtag = $lastid\n" if ($self->{verbose}); } else { $lastid= $idbx->version(); print "Get last id for $idtag = $lastid\n" if ($self->{verbose}); } } else { $lastid= 0; if ( $self->{readwrite} ) { $idbx= Bio::Chado::CDBI::Dbxref->find_or_create( { accession => $idtag, version => $lastid, # our data ! db_id => $iddb->id, description => "id counter for $idclass by $0", } ); $idbx->dbi_commit if $idbx; print "New last id for $idtag = $lastid\n" if ($self->{verbose}); } } return $lastid; } =item listPublicIds($outhandle) list public id counters =cut sub listPublicIds { my ($self, $outhandle)= @_; print $outhandle "\nPublic ID counter\n"; print $outhandle join("\t",qw(ID_Tag Last_ID Description)),"\n"; my ($iddb) = Bio::Chado::CDBI::Db->search( name => IDCounter ); if ($iddb) { my $iter = Bio::Chado::CDBI::Dbxref->search( db_id => $iddb->id); for (my $idbx= $iter->first(); ($idbx); $idbx= $iter->next()) { my $idtag = $idbx->accession(); my $lastid= $idbx->version(); my $desc = $idbx->description(); print $outhandle join("\t", $idtag, $lastid, $desc),"\n"; } } print $outhandle "-"x60,"\n\n"; } =item listDupChecksums( $outhandle, [$feature_iterator]) checks thru features md5checksum for duplicates and lists any if feature_iterator is null, checks all Bio::Chado::CDBI::Feature =cut sub listDupChecksums { my ($self, $outhandle, $iter)= @_; print $outhandle "\nDuplicate checksums\n"; print $outhandle join("\t",qw(Name____ Length Seq_type Synonym Feat_id Publication Checksum)),"\n"; my %checks=(); $iter = Bio::Chado::CDBI::Feature->retrieve_all unless($iter); for (my $fit = $iter->first; ($fit) ; $fit= $iter->next) { my $ck= $fit->md5checksum; next unless($ck); $checks{$ck}++; } foreach my $ck (keys %checks) { next unless ($checks{$ck}>1); $iter= Bio::Chado::CDBI::Feature->search( md5checksum => $ck ); for (my $fit = $iter->first; ($fit) ; $fit= $iter->next) { my $syn= $self->getSynonyms($fit); my @pub= $self->getFeaturePubs($fit); my $pub= (@pub ? "'".$pub[0]->title()."'" : ''); print $outhandle join("\t", $fit->name, $fit->seqlen, $fit->type_id->name, $syn, $fit->feature_id, $pub, $ck), "\n"; } } print $outhandle "-"x60,"\n\n"; } 1; chado-1.23/lib/Bio/GMOD/Load/GFF.pm000644 000765 000024 00000076311 11256707755 016445 0ustar00cainstaff000000 000000 package Bio::GMOD::Load::GFF; use strict; use Bio::SeqIO; use lib '../../../lib'; use Chado::AutoDBI; use Chado::LoadDBI; use Data::Dumper; use File::Temp qw(tempfile); =head1 NAME Bio::GMOD::Load::GFF - loads GFF3 data to a chado database =head1 SYNOPSIS my $loader = Bio::GMOD::Load::GFF->new( gfffile => '/usr/local/gmod/src/gff/yeast.gff', organism => 'yeast', src_db => 'DB:SGD' ); =head1 AUTHORS Scott Cain Ecain@cshl.orgE Copyright (c) 2004 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 APPENDIX The rest of the documentation details each of the object methods. =cut use vars qw( @ISA ); @ISA = qw( Bio::GMOD::Load ); use constant DEBUG => 1; sub new { my $proto = shift; my $self = bless {}, ref($proto) || $proto; my %arg = @_; foreach my $key (keys %arg) { warn "B::G::L::GFF args: $key, $arg{$key}\n" if DEBUG; } warn "gfffile: $arg{'gfffile'}" if DEBUG; $self->gfffile($arg{'gfffile'}); $self->organism($arg{'organism'}); $self->src_db($arg{'src_db'}); $self->cache_size($arg{'cache_size'}); $self->force_load($arg{'force'}); my ( undef, $TMPFASTA ) = tempfile( $arg{'pid'}, ".fa", SUFFIX => '.fa' ); my ( undef, $TMPGFF ) = tempfile( $arg{'pid'}, ".gff", SUFFIX => '.gff' ); $self->tmpfasta($TMPFASTA); $self->tmpgff($TMPGFF); $self->transaction(); #initialize transaction queue $self->initialize(); #handles all kinds of stuff return $self; } =head2 force_load =over =item Usage $obj->force_load() #get existing value $obj->force_load($newval) #set new value =item Function =item Returns value of force_load (a scalar) =item Arguments new value of force_load (to set) =back =cut sub force_load { my $self = shift; return $self->{'force_load'} = shift if defined(@_); return $self->{'force_load'}; } =head2 cache_size =over =item Usage $obj->cache_size() #get existing value $obj->cache_size($newval) #set new value =item Function =item Returns value of cache_size (a scalar) =item Arguments new value of cache_size (to set) =back =cut sub cache_size { my $self = shift; return $self->{'cache_size'} = shift if defined(@_); return $self->{'cache_size'}; } =head2 commit_cache =over =item Usage $obj->commit_cache() =item Function =item Returns =item Arguments =back =cut sub commit_cache { my $self = shift; $self->transaction(); return; } =head2 gfffile =over =item Usage $obj->gfffile() #get existing value $obj->gfffile($newval) #set new value =item Function =item Returns value of gfffile (a scalar) =item Arguments new value of gfffile (to set) =back =cut sub gfffile { my $self = shift; warn "in sub gfffile: @_" if DEBUG; return $self->{'gfffile'} = shift if defined(@_); return $self->{'gfffile'}; } =head2 organism =over =item Usage $obj->organism() #get existing value $obj->organism($newval) #set new value =item Function =item Returns value of organism (a scalar) =item Arguments new value of organism (to set) =back =cut sub organism { my $self = shift; return $self->{'organism'} = shift if defined(@_); return $self->{'organism'}; } =head2 src_db =over =item Usage $obj->src_db() #get existing value $obj->src_db($newval) #set new value =item Function =item Returns value of src_db (a scalar) =item Arguments new value of src_db (to set) =back =cut sub src_db { my $self = shift; return $self->{'src_db'} = shift if defined(@_); return $self->{'src_db'}; } =head2 transaction =over =item Usage $obj->transaction() #commits current transactions and #clears transaction queue $obj->transaction($newval) #adds object to transaction queue =item Function Handles the transaction queue. When called with no arguments, it commits any Class::DBI transactions that are currently in the queue and empties the queue. When called with a Class::DBI object, it adds the object to the commit queue. =item Returns Nothing =item Arguments See function above =back =cut sub transaction { my $self = shift; my $arg = shift; if ($arg) { # add it to the queue push @{$self->{'transaction'}}, $arg; } else { # do the commit and flush the queue $_->dbi_commit foreach @{$self->{'transaction'}}; @{$self->{'transaction'}} = (); } return $self->{'transaction'} = shift if defined(@_); return $self->{'transaction'}; } =head2 tmpfasta =over =item Usage $obj->tmpfasta() #get existing value $obj->tmpfasta($newval) #set new value =item Function =item Returns value of tmpfasta (a scalar) =item Arguments new value of tmpfasta (to set) =back =cut sub tmpfasta { my $self = shift; return $self->{'tmpfasta'} = shift if defined(@_); return $self->{'tmpfasta'}; } =head2 tmpgff =over =item Usage $obj->tmpgff() #get existing value $obj->tmpgff($newval) #set new value =item Function =item Returns value of tmpgff (a scalar) =item Arguments new value of tmpgff (to set) =back =cut sub tmpgff { my $self = shift; return $self->{'tmpgff'} = shift if defined(@_); return $self->{'tmpgff'}; } =head1 load_custom_tags Handles inserting non-reserved tags into chado. Determines if the tag falls into a short list of tags for custom handling and deals with them appropriately. If the tag is not on the list, the information is placed in the featureprop table. =cut sub load_custom_tags { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; my $tag = shift; my @d = $gff_feature->get_tag_values($tag); if (0) { } elsif ( $tag eq 'description' ) { foreach my $d (@d) { my ($featureprop) = Chado::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $self->cache_cvterm('description')->id, value => $d, } ); $self->transaction($featureprop); } } elsif ( $tag =~ /^db:/ ) { $tag =~ s/^db:/DB:/; my ($db) = Chado::Db->search( name => $tag ); if ( !$db ) { $db = Chado::Db->find_or_create( { name => $tag, contact_id => $self->nullcontact()->id, } ); } die "couldn't create db $db" unless $db; $self->transaction($db); foreach my $d (@d) { my ($dbxref) = Chado::Dbxref->find_or_create( { db_id => $db->id, accession => $d } ); my ($feature_dbxref) = Chado::Feature_Dbxref->find_or_create( { feature_id => $chado_feature->id, dbxref_id => $dbxref->id, } ); $self->transaction( $dbxref ); $self->transaction( $feature_dbxref ); } } else { foreach my $d (@d) { my ($featureprop) = Chado::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $self->cache_cvterm($tag)->id, value => $d, } ); $self->transaction($featureprop); } } } =pod =head1 load_Ontology_term Loads ontology terms to feature_cvterm. =cut sub load_Ontology_term { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; my $tag = shift; my @d = $gff_feature->get_tag_values($tag); foreach my $d (@d) { my ($dbxref) = Chado::Dbxref->search( accession => $d ); warn "couldn't find cvterm in dbxref: $d" and next unless $dbxref; my ($cvterm) = Chado::Cvterm->search( dbxref_id => $dbxref->id ); next unless $cvterm; my ($feature_cvterm) = Chado::Feature_Cvterm->find_or_create( { feature_id => $chado_feature->id, cvterm_id => $cvterm->id, pub_id => $self->nullpub()->id, } ); $self->transaction($feature_cvterm); } } =pod =head1 load_Note_tag Loads Note tag values to the featureprop table. =cut sub load_Note_tag { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; my @d = $gff_feature->get_tag_values('Note'); foreach my $d (@d) { my ($featureprop) = Chado::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $self->cache_cvterm('Note')->id, value => $d, } ); } } =pod =head1 load_Target_tag Loads Target values. These are used for alignment information. =cut sub load_Target_tag { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Target') ) { my @targets = $gff_feature->get_tag_values('Target'); foreach my $target (@targets) { my ( $tstart, $tend ); if ( $target =~ /^(\S+?)\+(\d+)\+(\d+)$/ ) { ( $target, $tstart, $tend ) = ( $1, $2, $3 ); } else { die "your Target attribute seems to be improperly formated"; } my ($chado_synonym1) = Chado::Synonym->find_or_create( { name => $target, synonym_sgml => $target, type_id => $self->cache_cvterm('synonym')->id } ); my ($chado_synonym2) = Chado::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $self->pub()->id, } ); my ($chado_featureloc) = Chado::Featureloc->find_or_create( { feature_id => $chado_feature->id, srcfeature_id => $chado_feature->id, fmin => $tstart, fmax => $tend, rank => 1 #potential bug here -allenday } ); my ($chado_featureprop) = Chado::Featureprop->find_or_create( { feature_id => $chado_feature->id, type_id => $self->cache_cvterm('score')->id, value => $gff_feature->score } ); $self->transaction( $chado_synonym1 ); $self->transaction( $chado_synonym2 ); $self->transaction( $chado_featureloc ); $self->transaction( $chado_featureprop ); } } } =pod =head1 load_Parent_tag Loads Parent tag values. These are used to denote a parent feature of the given feature. =cut sub load_Parent_tag { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Parent') ) { my @parents = $gff_feature->get_tag_values('Parent'); foreach my $parent (@parents) { my $reltype = ( $gff_feature->primary_tag eq 'protein' || $gff_feature->primary_tag eq 'polypeptide' ) ? $self->cache_cvterm('develops_from') : $self->cache_cvterm('part_of'); #unhandled exception: what if $feature{$parent} hasn't been seen yet? $self->feature($parent, Chado::Feature->search( name => $parent )) unless $self->feature($parent); my $chado_feature_relationship = Chado::Feature_Relationship->find_or_create( { subject_id => $chado_feature->id, object_id => $self->feature($parent)->id, type_id => $reltype, } ); $self->transaction( $chado_feature_relationship ); } } } =pod =head1 load_Alias_tag Loads Alias tag values. These are used for synonyms. =cut sub load_Alias_tag { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; if ( $gff_feature->has_tag('Alias') ) { my @aliases; if ( $gff_feature->has_tag('Alias') ) { push @aliases, $gff_feature->get_tag_values('Alias'); } foreach my $alias (@aliases) { #create the synonym my ($chado_synonym1) = Chado::Synonym->find_or_create( { name => $alias, synonym_sgml => $alias, type_id => $self->cache_cvterm('synonym')->id } ); #and link it to the feature via feature_synonym my ($chado_synonym2) = Chado::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $self->pub()->id, } ); $self->transaction( $chado_synonym1 ); $self->transaction( $chado_synonym2 ); } } } =pod =head1 load_Name_tag Loads Name tag values. =cut sub load_Name_tag { my $self = shift; my $gff_feature = shift; my $chado_feature = shift; my @names; if ( $gff_feature->has_tag('Name') ) { @names = $gff_feature->get_tag_values('Name'); } elsif ($gff_feature->has_tag('ID') ) { @names = $gff_feature->get_tag_values('ID'); } else { return; } foreach my $name (@names) { my ($chado_synonym1) = Chado::Synonym->find_or_create( { name => $name, synonym_sgml => $name, type_id => $self->cache_cvterm('synonym')->id } ); my ($chado_synonym2) = Chado::Feature_Synonym->find_or_create( { synonym_id => $chado_synonym1->id, feature_id => $chado_feature->id, pub_id => $self->pub()->id, } ); $self->transaction( $chado_synonym1 ); $self->transaction( $chado_synonym2 ); } } sub initialize { my $self = shift; my $gfffile = $self->gfffile(); warn "gfffile: $gfffile" if DEBUG; my $linenumber = `grep -n "^>" $gfffile`; if ( $linenumber =~ /^(\d+)/ ) { $linenumber = $1; system("tail +$linenumber $self->gfffile() > ".$self->tmpfasta() ); $linenumber -= 1; system("head -$linenumber $self->gfffile() > ".$self->tmpgff() ); #we don't want to do this, as the filename is used in a pub record #$GFFFILE = $TMPGFF; } #count the file lines. we need this to track load progress Chado::LoadDBI->init(); # find needed cvterm and other pieces of information my @needed_cvterms = qw(description synonym region note develops_from part_of gff_file score protein); foreach my $n (@needed_cvterms) { $self->cache_cvterm($n); } unless ($self->chado_organism()) { warn "\n\nCouldn't find or create organism ".$self->organism().".\n"; warn "The current contents of the organism table is:\n\n"; my @all_columns = Chado::Organism->columns; printf "%15s %8s %11s %11s %12s %15s\n\n", sort @all_columns; my $organism_iterator = Chado::Organism->retrieve_all(); while(my $organism = $organism_iterator->next){ my @cols = map { $organism->$_ } sort $organism->columns; printf "%15s %8s %11s %11s %12s %15s\n", @cols; } print "\nPlease see \`perldoc gmod_load_gff3.pl\` for more information\n"; exit 1; } unless ($self->chado_db() ) { warn "\n\nCouldn't find or create database ".$self->src_DB().".\n"; warn "The current contents of the database table is:\n\n"; my @all_columns = Chado::Db->columns; printf "%10s %6s %13s %25s %5s %10s\n\n", sort @all_columns; my $db_iterator = Chado::Db->retrieve_all(); while(my $db = $db_iterator->next){ my @cols = map { $db->$_ } sort $db->columns; printf "%10s %6s %13s %25s %5s %10s\n", @cols; } print "\nPlease see \`perldoc gmod_load_gff3.pl\` for more information\n"; exit 1; } } =head2 chado_db =over =item Usage $obj->chado_db() =item Function =item Returns The Class::DBI object for the row of the db table corresponding to the current src_db; if it does not exist, it will create it. =item Arguments =back =cut sub chado_db { my $self = shift; return $self->{'chado_db'} if $self->{'chado_db'}; ($self->{'chado_db'}) = Chado::Db->search( name => $self->src_db() ); return $self->{'chado_db'}; } =head2 nullpub =over =item Usage $obj->nullpub() =item Function =item Returns The Class::DBI object for the 'null publication' row of the pub table; if it doesn't exist, it will create it. =item Arguments =back =cut sub nullpub { my $self = shift; return $self->{'nullpub'} if $self->{'nullpub'}; ($self->{'nullpub'}) = Chado::Pub->search( miniref => 'null' ); return $self->{'nullpub'}; } =head2 nullcontact =over =item Usage $obj->nullcontact() =item Function =item Returns The Class::DBI object for the null contact in the --- table; if it does not already exist, it will attempt to create it. =item Arguments =back =cut sub nullcontact { my $self = shift; return $self->{'nullcontact'} if $self->{'nullcontact'}; ($self->{'nullcontact'}) = Chado::Contact->search( name => 'null' ); return $self->{'nullcontact'}; } =head2 chado_organism =over =item Usage $obj->chado_organism() =item Function =item Returns Returns the Class::DBI object for the current organism table row; if it does not exist, it will attempt to create it. =item Arguments None =back =cut sub chado_organism { my $self = shift; return $self->{'chado_organism'} if $self->{'chado_organism'}; ($self->{'chado_organism'}) = Chado::Organism->search( common_name => lc($self->organism() )); ($self->{'chado_organism'}) = Chado::Organism->search( abbreviation => ucfirst($self->organism())) unless($self->{'chado_organism'} ); ($self->{'chado_organism'}) = Chado::Organism->search( genus => $self->organism() ) unless($self->{'chado_organism'} ); return $self->{'chado_organism'}; } sub load_segments { my $self = shift; my $gffio = shift; my $i = 0; # creates the features for each gff segment while ( my $gff_segment = $gffio->next_segment() ) { my ($segment) = Chado::Feature->search( { name => $gff_segment->display_id } ); if ( !$segment ) { # about uniquenames here: since these are coming from ##sequence_region # meta stuff in the header, there will be no uniquename attribute, so the # only thing to do is to generate one. my $f = Chado::Feature->create( { organism_id => $self->chado_organism()->id, name => $gff_segment->display_id, uniquename => $gff_segment->display_id . '_region', type_id => $self->cache_cvterm('region'), seqlen => $gff_segment->end } ); $i++; $f->dbi_commit; $self->srcfeature($f->name, $f); } else { $self->srcfeature($segment->name, $segment); } } return $i; } sub load_sequences { my $self = shift; my $seqs_loaded = 0; if ( -e $self->tmpfasta() ) { Chado::Feature->set_sql( update_residues => qq{UPDATE feature SET residues = residues || ? WHERE feature_id = ?} ); my $sth = Chado::Feature->sql_update_residues; print STDERR "loading sequence data...\n"; my $in = Bio::SeqIO->new( -file => $self->tmpfasta() , '-format' => 'Fasta' ); while ( my $seq = $in->next_seq() ) { my $name = $seq->id; my @chado_feature = Chado::Feature->search( { 'name' => $name } ); #no, let's just load the sequence into all of them #die "couldn't uniquely identify the sequence identified by $name" # unless (scalar @chado_feature == 1); warn "no feature for sequence $name" unless scalar(@chado_feature); warn "multiple features for sequence $name\n" if scalar(@chado_feature) > 1; foreach my $f (@chado_feature) { $f->residues(''); $f->update; $f->dbi_commit; warn "copying Bio::Seq sequence to simple scalar variable" if DEBUG; my $dna = $seq->seq; undef $seq; #get this thing out of here ASAP, it's using memory warn "copied. Bio::Seq object purged to conserve memory" if DEBUG; my $shredsize = 100_000_000; #don't increase this... my $offset = 0; my $dnalen = length($dna); while ( $offset < $dnalen ) { warn "loading shred. offset: $offset bp" if DEBUG; my $shred = substr( $dna, $offset, $shredsize ); warn "${offset}bp loaded" if $offset > 0 and DEBUG; $sth->execute( $shred, $f->id ); warn "loaded shred" if DEBUG; $offset += $shredsize; } warn "${dnalen}bp loaded" if DEBUG; $f->update; warn "pre dbi_commit" if DEBUG; $f->dbi_commit; warn "post dbi_commit" if DEBUG; } $seqs_loaded++; } unlink $self->tmpfasta() unless $self->tmpfasta() eq $self->gfffile(); unlink $self->tmpgff() unless $self->tmpgff() eq $self->gfffile(); } return $seqs_loaded; } sub load_feature_locations { my $self = shift; my $gff_feature = shift; my $chado_type = shift; my $id = shift; ## GFF features are base-oriented, so we must add 1 to the diff ## between the end base and the start base, to get the number of ## intervening bases between the start and end intervals my $seqlen = ( $gff_feature->end - $gff_feature->start ) + 1; ## we must convert between base-oriented coordinates (GFF3) and ## interbase coordinates (chado) ## ## interbase counts *between* bases (starting from 0) ## GFF3 (and blast, bioperl, etc) count the actual bases (origin 1) ## ## ## 0 1 2 3 4 5 6 7 8 : INTERBASE ## A T G C G T A T ## 1 2 3 4 5 6 7 8 : BIOPERL/GFF ## ## from the above we can see that we need to add/subtract 1 from fmin ## we don't touch fmax my $fmin = $gff_feature->start - 1; # GFF -> InterBase my $fmax = $gff_feature->end; my $frame = $gff_feature->frame eq '.' ? 0 : $gff_feature->frame; # logic for creating feature.uniquename and feature.name (040414 allenday): # # if you decide to change the logic, please email the gmod-schema list before committing. # many people depend on the convention outlined here. # # UNIQUENAME # # 1. else, if ID tag available, use its value # 2. else, use a combination of GFF objects primary tag, seq_id, and, if available, # positional information. # 3. die, not enough information to generate a uniquename # # NAME # # 1. use Name tag if available # 2. else, use ID tag if available # 3. else, feature has no name # my $uniquename = ''; my $name = ''; if( $gff_feature->has_tag('ID') ) { ($uniquename) = $gff_feature->get_tag_values('ID'); } elsif( $gff_feature->primary_tag and $gff_feature->seq_id ) { my $position = $fmax eq '.' ? '' : ":$fmin..$fmax"; my($parentname) = $gff_feature->has_tag('Parent') ? $gff_feature->get_tag_values('Parent') : ''; $uniquename = sprintf("_%s_%s_%s%s", $parentname, $gff_feature->primary_tag, $gff_feature->seq_id, $position ); } else { die("not enough information available to make a uniquename for $gff_feature"); } my %feature_attributes = ( organism_id => $self->chado_organism()->id, type_id => $chado_type->id, uniquename => $uniquename, ); my $used_ID_for_Name = 0; if ( $gff_feature->has_tag('Name') ) { ($name) = $gff_feature->get_tag_values('Name'); $feature_attributes{name} = $name; } elsif ( $gff_feature->has_tag('ID') ) { ($name) = $gff_feature->get_tag_values('ID'); $feature_attributes{name} = $name; $used_ID_for_Name = 1; } my $chado_feature; if ( $gff_feature->has_tag('Name') ) { ($name) = $gff_feature->get_tag_values('Name'); } elsif ( $gff_feature->has_tag('ID') ){ ($name) = $gff_feature->get_tag_values('ID'); } ($chado_feature) = Chado::Feature->find_or_create(\%feature_attributes); if(!defined($chado_feature->seqlen)){ $chado_feature->seqlen($seqlen); $chado_feature->update; $chado_feature->dbi_commit; } $self->transaction( $chado_feature ); if ($used_ID_for_Name) { load_Name_tag ($gff_feature, $chado_feature); } my $source = $gff_feature->source_tag(); if ( $source && $source ne '.') { #make source a feature prop unless ($self->gff_source_db() ) {#create a new db for keeping GFF sources $self->gff_source_db( Chado::Db->find_or_create( { name => 'GFF_sources', contact_id => $self->nullcontact()->id, description => 'A collection of sources (ie, column 2) from GFF files', } ) ); $self->transaction( $self->gff_source_db() ); } unless ($self->gff_source($source)) { #now make a dbxref for the source $self->gff_source($source, Chado::Dbxref->find_or_create( { db_id => $self->gff_source_db()->id, accession => $source, } ) ); $self->transaction( $self->gff_source($source) ); } #now tie feature and source together in feature_dbxref my $feature_dbxref = Chado::Feature_Dbxref->find_or_create( { feature_id => $chado_feature->id, dbxref_id => $self->gff_source($source)->id }); $self->transaction( $feature_dbxref ); } if ( $id eq $gff_feature->seq_id or $gff_feature->seq_id eq '.' ) { #ie, this is a srcfeature (ie, fref) so only create the feature $self->srcfeature($gff_feature->seq_id, $chado_feature); return ($chado_feature); } $chado_feature->dbxref_id( $self->dbxref($id) ) if $gff_feature->has_tag('ID'); # is this the right thing to do here? $chado_feature->update; # flush updates to this feature object # find pre-existing feature locations that were loaded prior # to this GFF3 file. if(!$self->featureloc_locgroup( $chado_feature->id ) ){ my $max_locgroup = undef; foreach my $previous_featureloc (Chado::Featureloc->search( feature_id => $chado_feature->id, )){ if($fmin == $previous_featureloc->fmin and $fmax == $previous_featureloc->fmax and $previous_featureloc->srcfeature_id == $self->srcfeature($gff_feature->seq_id)->id ){ return $chado_feature; } $max_locgroup = $max_locgroup > $previous_featureloc->locgroup ? $max_locgroup : $previous_featureloc->locgroup; } if(defined($max_locgroup)){ $self->featureloc_locgroup( $chado_feature->id , $max_locgroup); } } # add feature location $self->featureloc_locgroup($chado_feature->id , $self->featureloc_locgroup($chado_feature->id)+1 ); my $locgroup = $self->featureloc_locgroup( $chado_feature->id ); my($parent) = $gff_feature->has_tag('Parent') ? $gff_feature->get_tag_values('Parent') : (); if($parent && $self->featureloc_locgroup( $self->feature($parent) )){ $locgroup = $self->featureloc_locgroup( $self->feature($parent) ); } $locgroup ||= 0; if (DEBUG) { warn "adding featureloc for gff string:"; warn "\t".$gff_feature->gff_string; # print STDERR $chado_feature->id , "\t" , $locgroup , "\n"; if($parent){ warn "srcfeature_id: " . Dumper($self->feature($parent)); } } my $chado_featureloc = Chado::Featureloc->find_or_create( { feature_id => $chado_feature->id, fmin => $fmin, fmax => $fmax, strand => $gff_feature->strand, phase => $frame, locgroup => $locgroup, srcfeature_id => $self->srcfeature($gff_feature->seq_id)->id, } ); $self->transaction( $chado_featureloc ); return ($chado_feature); } =head2 pub =over =item Usage $obj->pub() #get existing value $obj->pub($newval) #set new value =item Function When called with a 'uniqified' gff file name, creates an entry in the pub table; on subsequent calls with no argument, it returns the Class::DBI object for that table entry. =item Returns value of pub (a scalar) =item Arguments new value of pub (to set) =back =cut sub pub { my $self = shift; if (defined @_) { my $file_uname = shift; my ($pub) = Chado::Pub->search( title => $file_uname ); if ($pub and !($self->force_load())) { print "\nIt appears that you have already loaded this exact file\n"; print "Do you want to continue [no]? "; chomp( my $response = ); unless ( $response =~ /^[Yy]/ ) { print "OK--bye.\n"; exit 0; } } else { $pub = Chado::Pub->find_or_create( { title => $file_uname, miniref => $file_uname, uniquename => $file_uname, type_id => $self->cache_cvterm('gff_file')->id } ); } die "unable to find or create a pub entry in the pub table" unless $pub; } else { return $self->{'pub'}; } return $self->{'pub'} = shift if defined(@_); } chado-1.23/lib/Bio/GMOD/DB/Adapter/000755 000765 000024 00000000000 12061672376 016456 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/DB/Adapter.pm000644 000765 000024 00000420736 11727710242 017021 0ustar00cainstaff000000 000000 package Bio::GMOD::DB::Adapter; use strict; use Carp qw/cluck confess/; use DBI; use File::Temp qw/ tempdir /; use Data::Dumper; use URI::Escape; use Sys::Hostname; use Bio::SeqFeature::Generic; use Bio::GMOD::DB::Adapter::FeatureIterator; use base 'Bio::Root::Root'; ## dgg## use FreezeThaw qw( freeze thaw safeFreeze ); ## see below; Data::Dumper is better #set lots of package-wide variables: # dgg; drop these for $self->{nextoid}{$table} my ( $part_of,$derives_from,$sofa_id); # $nextfeaturerel, # $nextfeatureprop, # $nextfeaturecvterm, # $nextsynonym, # $nextfeaturesynonym, # $nextfeaturedbxref, # $nextdbxref, # $nextanalysisfeature, #------------ START Table Entries ------------------------------ # any new table to populate needs entries here (and a print_tablename) # @tables array sets the order for which things will be inserted into # the database my @tables = ( "organism", #dgg "analysis", #dgg "db", ## dgg "dbxref", "cv", ## dgg "cvterm", ## dgg "feature", "featureloc", "feature_relationship", "featureprop", "feature_cvterm", "synonym", "feature_synonym", "feature_dbxref", "analysisfeature", ); my %use_public_tables = ( db => "public.db", cv => "public.cv", cvterm => "public.cvterm", organism => "public.organism", ); my %sequences = ( feature => "feature_feature_id_seq", featureloc => "featureloc_featureloc_id_seq", feature_relationship => "feature_relationship_feature_relationship_id_seq", featureprop => "featureprop_featureprop_id_seq", feature_cvterm => "feature_cvterm_feature_cvterm_id_seq", synonym => "synonym_synonym_id_seq", feature_synonym => "feature_synonym_feature_synonym_id_seq", dbxref => "dbxref_dbxref_id_seq", feature_dbxref => "feature_dbxref_feature_dbxref_id_seq", analysisfeature => "analysisfeature_analysisfeature_id_seq", cvterm => "cvterm_cvterm_id_seq", # dgg db => "db_db_id_seq", # dgg cv => "cv_cv_id_seq", # dgg analysis => "analysis_analysis_id_seq", # dgg organism => "organism_organism_id_seq", # dgg ); my %copystring = ( feature => "(feature_id,organism_id,name,uniquename,type_id,is_analysis,seqlen,dbxref_id)", featureloc => "(featureloc_id,feature_id,srcfeature_id,fmin,fmax,strand,phase,rank,locgroup)", feature_relationship => "(feature_relationship_id,subject_id,object_id,type_id)", featureprop => "(featureprop_id,feature_id,type_id,value,rank)", feature_cvterm => "(feature_cvterm_id,feature_id,cvterm_id,pub_id)", synonym => "(synonym_id,name,type_id,synonym_sgml)", feature_synonym => "(feature_synonym_id,synonym_id,feature_id,pub_id)", dbxref => "(dbxref_id,db_id,accession,version,description)", feature_dbxref => "(feature_dbxref_id,feature_id,dbxref_id)", analysisfeature => "(analysisfeature_id,feature_id,analysis_id,significance,rawscore,normscore,identity)", cvterm => "(cvterm_id,cv_id,name,dbxref_id,definition)", # is_obsolete, is_relationshiptype ## dgg db => "(db_id,name,description)", # ,urlprefix,url ## dgg cv => "(cv_id,name,definition)", ## dgg analysis => "(analysis_id,name,program,programversion,sourcename)", ## dgg organism => "(organism_id,genus,species,common_name,abbreviation)", ## dgg ); #------------ END Table Entries ------------------------------ ## dgg; see sub file_handles my %files = map { $_ => 'FH'.$_; } @tables,'sequence','delete'; # SEQ special case in feature table # ( # feature => 'F', # featureloc => 'FLOC', # feature_relationship => 'FREL', # featureprop => 'FPROP', # feature_cvterm => 'FCV', # synonym => 'SYN', # feature_synonym => 'FS', # dbxref => 'DBX', # feature_dbxref => 'FDBX', # analysisfeature => 'AF', # sequence => 'SEQ', # cvterm => 'CVTERM', # dgg # db => 'DB', # dgg # cv => 'CV', # dgg # ); use constant SEARCH_NAME => "SELECT feature_id FROM feature WHERE name=?"; use constant COUNT_NAME => "SELECT COUNT(*) FROM feature WHERE name=?"; use constant SEARCH_CVTERM_ID => "SELECT cvterm_id FROM cvterm WHERE name=? AND cv_id=?"; use constant SEARCH_SOURCE_DBXREF => "SELECT dbxref_id FROM dbxref WHERE accession=? AND db_id=?"; use constant SEARCH_DBXREF => "SELECT dbxref_id FROM dbxref WHERE accession=? AND db_id in (SELECT db_id FROM db WHERE name like ? OR name like ?)"; use constant SEARCH_CVTERM_ID_W_DBXREF => "SELECT cvterm_id FROM cvterm WHERE dbxref_id=?"; use constant SEARCH_DB => "SELECT db_id FROM db WHERE name =?"; use constant SEARCH_LONG_DBXREF => "SELECT dbxref_id FROM dbxref WHERE accession =? AND version =? AND db_id =?"; ## dgg patch see note below # use constant SEARCH_ANALYSIS => # "SELECT analysis_id FROM analysis WHERE name=?"; use constant SEARCH_ANALYSIS => "SELECT analysis_id FROM analysis WHERE (name = ?) OR (program=? and (sourcename=? OR sourcename is NULL))"; use constant SEARCH_SYNONYM => "SELECT synonym_id FROM synonym WHERE name=? AND type_id=?"; use constant CREATE_CACHE_TABLE => "CREATE TABLE public.tmp_gff_load_cache ( feature_id int, uniquename varchar(1000), type_id int, organism_id int )"; use constant DROP_CACHE_TABLE => "DROP TABLE public.tmp_gff_load_cache"; use constant VERIFY_TMP_TABLE => "SELECT count(*) FROM pg_class WHERE relname=? and relkind='r'"; use constant POPULATE_CACHE_TABLE => "INSERT INTO public.tmp_gff_load_cache SELECT feature_id,uniquename,type_id,organism_id FROM feature"; use constant CREATE_CACHE_TABLE_INDEX1 => "CREATE INDEX tmp_gff_load_cache_idx1 ON public.tmp_gff_load_cache (feature_id)"; use constant CREATE_CACHE_TABLE_INDEX2 => "CREATE INDEX tmp_gff_load_cache_idx2 ON public.tmp_gff_load_cache (uniquename)"; use constant CREATE_CACHE_TABLE_INDEX3 => "CREATE INDEX tmp_gff_load_cache_idx3 ON public.tmp_gff_load_cache (uniquename,type_id,organism_id)"; use constant VALIDATE_TYPE_ID => "SELECT feature_id FROM public.tmp_gff_load_cache WHERE type_id = ? AND organism_id = ? AND uniquename = ?"; use constant VALIDATE_ORGANISM_ID => "SELECT feature_id FROM public.tmp_gff_load_cache WHERE organism_id = ? AND uniquename = ?"; use constant VALIDATE_UNIQUENAME => "SELECT feature_id FROM public.tmp_gff_load_cache WHERE uniquename=?"; use constant INSERT_CACHE_TYPE_ID => "INSERT INTO public.tmp_gff_load_cache (feature_id,uniquename,type_id,organism_id) VALUES (?,?,?,?)"; use constant INSERT_CACHE_UNIQUENAME => "INSERT INTO public.tmp_gff_load_cache (feature_id,uniquename) VALUES (?,?)"; use constant INSERT_GFF_SORT_TMP => "INSERT INTO gff_sort_tmp (refseq,id,parent,gffline) VALUES (?,?,?,?)"; use constant CREATE_META_TABLE => "CREATE TABLE gff_meta ( name varchar(100), hostname varchar(100), starttime timestamp not null default now() )"; use constant SELECT_FROM_META => "SELECT name,hostname,starttime FROM gff_meta"; use constant INSERT_INTO_META => "INSERT INTO gff_meta (name,hostname) VALUES (?,?)"; use constant DELETE_FROM_META => "DELETE FROM gff_meta WHERE name = ? AND hostname = ?"; use constant TMP_TABLE_CLEANUP => "DELETE FROM tmp_gff_load_cache WHERE feature_id >= ?"; my $ALLOWED_UNIQUENAME_CACHE_KEYS = "feature_id|type_id|organism_id|uniquename|validate"; my $ALLOWED_CACHE_KEYS = "analysis|db|dbxref|feature|parent|source|synonym|type|ontology|property|const|srcfeature"; sub new { my $class = shift; my %arg = @_; my $self = bless {}, ref($class) || $class; my $dbname = $arg{dbname}; my $dbport = $arg{dbport}; my $dbhost = $arg{dbhost}; my $dbuser = $arg{dbuser}; my $dbpass = $arg{dbpass}; my $notrans= $arg{notransact}; my $skipinit=$arg{skipinit}; my $private_schema = $arg{private_schema}; my $dbh = DBI->connect( "dbi:Pg:dbname=$dbname;port=$dbport;host=$dbhost", $dbuser, $dbpass, {AutoCommit => $notrans, TraceLevel => 0} ) or $self->throw("couldn't connect to the database"); if ($private_schema) { $dbh->do("SET search_path=$private_schema,public,pg_catalog"); } $self->dbh($dbh); $self->dbname( $arg{dbname} ); $self->dbport( $arg{dbport} ); $self->dbhost( $arg{dbhost} ); $self->dbuser( $arg{dbuser} ); $self->dbpass( $arg{dbpass} ); $self->notransact( $arg{notransact} ); $self->nosequence( $arg{nosequence} ); $self->inserts( $arg{inserts} ); $self->score_col( $arg{score_col} ); $self->global_analysis( $arg{global_analysis} ); $self->analysis_group( $arg{analysis_group} ); $self->is_analysis( $arg{is_analysis} ); $self->organism( $arg{organism} ); $self->dbprofile( $arg{dbprofile} ); $self->noload( $arg{noload} ); $self->skip_vacuum( $arg{skip_vacuum} ); $self->drop_indexes_flag($arg{drop_indexes_flag}); $self->noexon( $arg{noexon} ); $self->nouniquecache( $arg{nouniquecache} ); $self->recreate_cache( $arg{recreate_cache} ); $self->save_tmpfiles( $arg{save_tmpfiles} ); $self->random_tmp_dir( $arg{random_tmp_dir} ); $self->no_target_syn( $arg{no_target_syn} ); $self->unique_target( $arg{unique_target} ); $self->dbxref( $arg{dbxref} ); $self->fp_cv( $arg{fp_cv} || 'autocreated' ); $self->{'addpropertycv'}= $arg{addpropertycv}; # dgg $self->private_schema( $arg{private_schema} ); $self->use_public_cv( $arg{use_public_cv} ); $self->allow_external_parent($arg{allow_external_parent}); $self->{const}{source_success} = 1; #flag to indicate GFF_source is in db table $self->prepare_queries(); unless ($skipinit) { $self->initialize_ontology(); $self->initialize_sequences(); $self->initialize_uniquename_cache(); } $self->cds_db_exists(0); return $self; } =head2 prepare_queries =over =item Usage $obj->prepare_queries() =item Function Does dbi prepare on several cached queries =item Returns void =item Arguments none =back =cut sub prepare_queries { my $self = shift; my $dbh = $self->dbh(); $self->{'queries'}{'search_name'} = $dbh->prepare(SEARCH_NAME); $self->{'queries'}{'count_name'} = $dbh->prepare(COUNT_NAME); $self->{'queries'}{'search_cvterm_id'} = $dbh->prepare(SEARCH_CVTERM_ID); $self->{'queries'}{'search_source_dbxref'} = $dbh->prepare(SEARCH_SOURCE_DBXREF); $self->{'queries'}{'search_dbxref'} = $dbh->prepare(SEARCH_DBXREF); $self->{'queries'}{'search_cvterm_id_w_dbxref'} = $dbh->prepare(SEARCH_CVTERM_ID_W_DBXREF); $self->{'queries'}{'search_db'} = $dbh->prepare(SEARCH_DB); $self->{'queries'}{'search_long_dbxref'} = $dbh->prepare(SEARCH_LONG_DBXREF); $self->{'queries'}{'search_analysis'} = $dbh->prepare(SEARCH_ANALYSIS); $self->{'queries'}{'search_synonym'} = $dbh->prepare(SEARCH_SYNONYM); $self->{'queries'}{'validate_type_id'} = $dbh->prepare(VALIDATE_TYPE_ID); $self->{'queries'}{'validate_organism_id'} = $dbh->prepare(VALIDATE_ORGANISM_ID); $self->{'queries'}{'validate_uniquename'} = $dbh->prepare(VALIDATE_UNIQUENAME); $self->{'queries'}{'insert_cache_type_id'} = $dbh->prepare(INSERT_CACHE_TYPE_ID); $self->{'queries'}{'insert_cache_uniquename'} = $dbh->prepare(INSERT_CACHE_UNIQUENAME); $self->{'queries'}{'insert_gff_sort_tmp'} = $dbh->prepare(INSERT_GFF_SORT_TMP); return; } =head2 constraint =over =item Usage $obj->constraint() =item Function Manages database constraints =item Returns Updates cache and returns true if the constraint has not be violoated, otherwise returns false. =item Arguments A hash with keys: name constraint name terms a anonymous array with column values The array contains the column values in the 'right' order: feature_synonym_c1: [feature_id, synonym_id] feature_dbxref_c1: [feature_id, dbxref_id] feature_cvterm_c1: [feature_id, cvterm_id] featureprop_c1: [feature_id, cvterm_id, rank] =back =cut sub constraint { my ($self, %argv) = @_; my $constraint = $argv{name}; my @terms = @{ $argv{terms} }; if ($constraint eq 'feature_synonym_c1' || $constraint eq 'feature_dbxref_c1' || $constraint eq 'feature_cvterm_c1') { $self->throw( "wrong number of constraint terms") if (@terms != 2); if ($self->{$constraint}{$terms[0]}{$terms[1]}) { return 0; #this combo is already in the constraint } else { $self->{$constraint}{$terms[0]}{$terms[1]}++; return 1; } } elsif ($constraint eq 'featureprop_c1') { $self->throw("wrong number of constraint terms") if (@terms != 3); if ($self->{$constraint}{$terms[0]}{$terms[1]}{$terms[2]}) { return 0; #this combo is already in the constraint } else { $self->{$constraint}{$terms[0]}{$terms[1]}{$terms[2]}++; return 1; } } else { $self->throw("I don't know how to deal with the constraint $constraint: typo?"); } } =head2 cache =over =item Usage $obj->cache() =item Function Handles generic data cache hash of hashes from bulk_load_gff3 =item Returns The cached value =item Arguments The name of one of several top level cache keys: analysis db #db.db_id cache dbxref feature parent #featureloc.srcfeature_id ; parent feature source #dbxref.dbxref_id ; gff_source synonym type #cvterm.cvterm_id cache ontology srcfeature #feature_id is a srcfeature and a tag and optional value that gets stored in the cache. If no value is passed, it is returned, otherwise void is returned. =back =cut sub cache { my ($self, $top_level, $key, $value) = @_; if ($top_level !~ /($ALLOWED_CACHE_KEYS)/) { confess "I don't know what to do with the key '$top_level'". " in the cache method; it's probably because of a typo"; } return $self->{cache}{$top_level}{$key} unless defined($value); return $self->{cache}{$top_level}{$key} = $value; } =head2 nextoid =over =item Usage $obj->nextoid($table) #get existing value $obj->nextoid($table,$newval) #set new value =item Function =item Returns value of next table id (a scalar) =item Arguments new value of next table id (to set) =back =cut sub nextoid { my $self = shift; my $table= shift; my $arg = shift if defined(@_); if (defined($arg) && $arg eq '++') { return $self->{'nextoid'}{$table}++; } elsif (defined($arg)) { return $self->{'nextoid'}{$table} = $arg; } return $self->{'nextoid'}{$table} if ($table); # return nextvalueHash(); #?? } sub nextvalueHash { my $self= shift; my %nextval=(); for my $t (@tables) { $nextval{$t} = $self->{'nextoid'}{$t}; } return %nextval; } # return ( # "feature" => $self->nextfeature, # "featureloc" => $self->nextfeatureloc, # "feature_relationship" => $nextfeaturerel, # "featureprop" => $nextfeatureprop, # "feature_cvterm" => $nextfeaturecvterm, # "synonym" => $nextsynonym, # "feature_synonym" => $nextfeaturesynonym, # "feature_dbxref" => $nextfeaturedbxref, # "dbxref" => $nextdbxref, # "analysisfeature" => $nextanalysisfeature, # "cvterm" => $nextcvterm, #dgg # "db" => $nextdbname, #dgg # "cv" => $nextcvname, #dgg # ); =head2 nextfeature =over =item Usage $obj->nextfeature() #get existing value $obj->nextfeature($newval) #set new value =item Function =item Returns value of nextfeature (a scalar) =item Arguments new value of nextfeature (to set) =back =cut ## dgg; keep - this is public; sub nextfeature { my $self = shift; my $fid = $self->nextoid('feature',@_); if (!$self->first_feature_id() ) { $self->first_feature_id( $fid ); } return $fid; # my $arg = shift if defined(@_); # if (defined($arg) && $arg eq '++') { # return $self->{'nextfeature'}++; # } # elsif (defined($arg)) { # return $self->{'nextfeature'} = $arg; # } # return $self->{'nextfeature'}; } =head2 nextfeatureloc =over =item Usage $obj->nextfeatureloc() #get existing value $obj->nextfeatureloc($newval) #set new value =item Function =item Returns value of nextfeatureloc (a scalar) =item Arguments new value of nextfeatureloc (to set) =back =cut ## dgg; keep - this is public; sub nextfeatureloc { my $self = shift; return $self->nextoid('featureloc',@_); # # my $arg = shift if defined(@_); # if (defined($arg) && $arg eq '++') { # return $self->{nextfeatureloc}++; # } # elsif (defined($arg)) { # return $self->{nextfeatureloc} = $arg; # } # return $self->{nextfeatureloc}; } # =head2 nextfeaturerel # # =over # # =item Usage # # $obj->nextfeaturerel() #get existing value # $obj->nextfeaturerel($newval) #set new value # # =item Function # # =item Returns # # value of nextfeaturerel (a scalar) # # =item Arguments # # new value of nextfeaturerel (to set) # # =back # # =cut # # sub nextfeaturerel { # my $self = shift; # return $self->nextoid('feature_relationship',@_); # # return $nextfeaturerel = shift if defined(@_); # # return $nextfeaturerel; # } # =head2 nextfeatureprop # # =over # # =item Usage # # $obj->nextfeatureprop() #get existing value # $obj->nextfeatureprop($newval) #set new value # # =item Function # # =item Returns # # value of nextfeatureprop (a scalar) # # =item Arguments # # new value of nextfeatureprop (to set) # # =back # # =cut # # sub nextfeatureprop { # my $self = shift; # return $self->nextoid('featureprop',@_); # # return $nextfeatureprop = shift if defined(@_); # # return $nextfeatureprop; # } # =head2 nextfeaturecvterm # # =over # # =item Usage # # $obj->nextfeaturecvterm() #get existing value # $obj->nextfeaturecvterm($newval) #set new value # # =item Function # # =item Returns # # value of nextfeaturecvterm (a scalar) # # =item Arguments # # new value of nextfeaturecvterm (to set) # # =back # # =cut # # sub nextfeaturecvterm { # my $self = shift; # return $self->nextoid('feature_cvterm',@_); # # return $nextfeaturecvterm = shift if defined(@_); # # return $nextfeaturecvterm; # } # =head2 nextsynonym # # =over # # =item Usage # # $obj->nextsynonym() #get existing value # $obj->nextsynonym($newval) #set new value # # =item Function # # =item Returns # # value of nextsynonym (a scalar) # # =item Arguments # # new value of nextsynonym (to set) # # =back # # =cut # # sub nextsynonym { # my $self = shift; # return $self->nextoid('synonym',@_); # # return $nextsynonym = shift if defined(@_); # # return $nextsynonym; # } # =head2 nextfeaturesynonym # # =over # # =item Usage # # $obj->nextfeaturesynonym() #get existing value # $obj->nextfeaturesynonym($newval) #set new value # # =item Function # # =item Returns # # value of nextfeaturesynonym (a scalar) # # =item Arguments # # new value of nextfeaturesynonym (to set) # # =back # # =cut # # sub nextfeaturesynonym { # my $self = shift; # return $self->nextoid('feature_synonym',@_); # # return $nextfeaturesynonym = shift if defined(@_); # # return $nextfeaturesynonym; # } # =head2 nextfeaturedbxref # # =over # # =item Usage # # $obj->nextfeaturedbxref() #get existing value # $obj->nextfeaturedbxref($newval) #set new value # # =item Function # # =item Returns # # value of nextfeaturedbxref (a scalar) # # =item Arguments # # new value of nextfeaturedbxref (to set) # # =back # # =cut # # sub nextfeaturedbxref { # my $self = shift; # return $self->nextoid('feature_dbxref',@_); # # return $nextfeaturedbxref = shift if defined(@_); # # return $nextfeaturedbxref; # } # =head2 nextdbxref # # =over # # =item Usage # # $obj->nextdbxref() #get existing value # $obj->nextdbxref($newval) #set new value # # =item Function # # =item Returns # # value of nextdbxref (a scalar) # # =item Arguments # # new value of nextdbxref (to set) # # =back # # =cut # # sub nextdbxref { # my $self = shift; # return $self->nextoid('dbxref',@_); # # return $nextdbxref = shift if defined(@_); # # return $nextdbxref; # } # =head2 nextanalysisfeature # # =over # # =item Usage # # $obj->nextanalysisfeature() #get existing value # $obj->nextanalysisfeature($newval) #set new value # # =item Function # # =item Returns # # value of nextanalysisfeature (a scalar) # # =item Arguments # # new value of nextanalysisfeature (to set) # # =back # # =cut # # sub nextanalysisfeature { # my $self = shift; # return $self->nextoid('analysisfeature',@_); # # return $nextanalysisfeature = shift if defined(@_); # # return $nextanalysisfeature; # } =head2 file_handles =over =item Usage $obj->file_handles() =item Function Creates and keeps track of file handles for temp files =item Returns On create, void. With an arguement, returns the requested file handle =item Arguments If the 'short hand' name of a file handle is given, returns the requested file handle. The short hand file names are: ** dgg; revised this so FH = 'FH'.$tablename F feature FLOC featureloc FREL feature_relationship FPROP featureprop FCV feature_cvterm SYN synonym FS feature_synonym FDBX feature_dbxref DBX dbxref AF analysisfeature SEQ sequence =back =cut sub file_handles { my ($self, $argv) = @_; if ($argv && $argv ne 'close') { my $fhhame= ($argv =~ /^FH/) ? $argv : 'FH'.$argv; #dgg return $self->{file_handles}{$fhhame}; } else { my $file_path = "./"; if ($self->random_tmp_dir ) { $file_path = tempdir( CLEANUP => $self->save_tmpfiles() ? 0 : 1 ); } for my $key (keys %files) { $self->{file_handles}{$files{$key}} = new File::Temp( TEMPLATE => "chado-$key-XXXX", #dgg; was $keyXXXX SUFFIX => '.dat', UNLINK => $self->save_tmpfiles() ? 0 : 1, DIR => $file_path, ); } return; } } =head2 end_files =over =item Usage $obj->end_files() =item Function Appends proper bulk load terminators =item Returns void =item Arguments none =back =cut sub end_files { my $self = shift; unless ($self->inserts) { foreach my $file (@tables) { my $fh = $self->file_handles($files{$file}); print $fh "\\.\n\n"; } } } =head2 uniquename_cache =over =item Usage $obj->uniquename_cache() =item Function Maintains a cache of feature.uniquenames present in the database =item Returns See Arguements. =item Arguments uniquename_cache takes a hash. If it has a key 'validate', it returns the feature_id of the feature corresponding to that uniquename if present, 0 if it is not. Otherwise, it uses the values in the hash to update the uniquename_cache Allowed hash keys: feature_id type_id organism_id uniquename validate =back =cut sub uniquename_cache { my ($self, %argv) = @_; my @bogus_keys = grep {!/($ALLOWED_UNIQUENAME_CACHE_KEYS)/} keys %argv; if (@bogus_keys) { for (@bogus_keys) { warn "I don't know what to do with the key ".$_. " in the uniquename_cache method; it's probably because of a typo\n"; } confess; } if ($argv{validate}) { if (defined $argv{type_id}){ #valididate type & org too $self->{'queries'}{'validate_type_id'}->execute( $argv{type_id}, $argv{organism_id}, $argv{uniquename}, ); my ($feature_id) = $self->{'queries'}{'validate_type_id'}->fetchrow_array; return $feature_id; } elsif (defined $argv{organism_id}) { #validate uniquename and organism $self->{'queries'}{'validate_organism_id'}->execute( $argv{organism_id}, $argv{uniquename}, ); my ($feature_id) = $self->{'queries'}{'validate_organism_id'}->fetchrow_array; return $feature_id; } else { #just validate the uniquename $self->{'queries'}{'validate_uniquename'}->execute($argv{uniquename}); my ($feature_id) = $self->{'queries'}{'validate_uniquename'}->fetchrow_array; return $feature_id; } } elsif ($argv{type_id}) { $self->{'queries'}{'insert_cache_type_id'}->execute( $argv{feature_id}, $argv{uniquename}, $argv{type_id}, $argv{organism_id} ); $self->dbh->commit; return; } } =head2 fp_cv =over =item Usage $obj->fp_cv() #get existing value $obj->fp_cv($newval) #set new value =item Function Gets/sets the name of the feature property cv =item Returns value of fp_cv (a scalar) =item Arguments new value of fp_cv (to set) =back =cut sub fp_cv { my $self = shift; my $fp_cv = shift if defined(@_); return $self->{'fp_cv'} = $fp_cv if defined($fp_cv); return $self->{'fp_cv'}; } =head2 allow_external_parent =over =item Usage $obj->allow_external_parent() #get existing value $obj->allow_external_parent($newval) #set new value =item Function Flag to allow the GFF parser to look in the database for a Parent ID, which is not allowed by the GFF3 spec. =item Returns value of allow_external_parent (a scalar) =item Arguments new value of allow_external_parent (to set) =back =cut sub allow_external_parent { my $self = shift; my $allow_external_parent = shift if defined(@_); return $self->{'allow_external_parent'} = $allow_external_parent if defined($allow_external_parent); return $self->{'allow_external_parent'}; } =head2 recreate_cache =over =item Usage $obj->recreate_cache() #get existing value $obj->recreate_cache($newval) #set new value =item Function =item Returns value of recreate_cache (a scalar) =item Arguments new value of recreate_cache (to set) =back =cut sub recreate_cache { my $self = shift; my $recreate_cache = shift if defined(@_); return $self->{'recreate_cache'} = $recreate_cache if defined($recreate_cache); return $self->{'recreate_cache'}; } =head2 organism_id =over =item Usage $obj->organism_id() #get existing value $obj->organism_id($newval) #set new value =item Function With a organism common name as an arg, sets the organism_id value =item Returns value of organism_id (a scalar) =item Arguments With a organism common name as an arg, sets the organism_id value =back =cut sub organism_id { my $self = shift; my $organism_name = shift; return $self->{'organism_id'} unless $organism_name; ## dgg; handle also 'Saccharomyces cerevisiae' ## dgg; now may have new organism on each gff line (e.g. uniprot data) ## start using $self->cache('organism',...); my ($genus,$species)= split(" ",$organism_name,2); my ($sth,$orgid); if($species && $genus =~ /^[A-Z]/) { $sth = $self->dbh->prepare("SELECT organism_id FROM organism WHERE genus = ? AND species = ?"); $sth->execute($genus,$species); } else { # 2nd way $sth = $self->dbh->prepare("SELECT organism_id FROM organism WHERE common_name = ? OR abbreviation = ?"); $sth->execute($organism_name, $organism_name); if ($sth->rows > 1) { die "\n\nMore than one organism with the common name $organism_name,\ntry using the abbreviation or the genus and species in quotes instead\n\n"; } } ($orgid) = $sth->fetchrow_array; unless($orgid) { # try other way if($species && $genus =~ /^[A-Z]/) { $sth = $self->dbh->prepare("SELECT organism_id FROM organism WHERE common_name = ? OR abbreviation = ?"); $sth->execute($organism_name, $organism_name); } elsif($species) { # 2nd way $sth = $self->dbh->prepare("SELECT organism_id FROM organism WHERE genus = ? AND species = ?"); $sth->execute($genus,$species); } ($orgid) = $sth->fetchrow_array; } # auto-add here if(!$orgid && $self->{'addpropertycv'} && $species && $genus =~ /^[A-Z]/) { # create analysis entry $orgid= $self->nextoid('organism'); $self->print_organism( $orgid, $genus, $species); $self->nextoid('organism','++'); ## $self->cache('organism',$organism_name,$orgid); } $self->{'organism_id'}= $orgid; return $self->{'organism_id'}; } =head2 initialize_uniquename_cache =over =item Usage $obj->initialize_uniquename_cache() =item Function Creates the uniquename cache tables in the database =item Returns void =item Arguments none =back =cut sub initialize_uniquename_cache { my $self = shift; #determine if the table already exists my $dbh = $self->dbh; my $sth = $dbh->prepare(VERIFY_TMP_TABLE); $sth->execute('tmp_gff_load_cache'); my ($table_exists) = $sth->fetchrow_array; if (!$table_exists || $self->recreate_cache() ) { print STDERR "(Re)creating the uniquename cache in the database... "; $dbh->do(DROP_CACHE_TABLE) if ($self->recreate_cache() and $table_exists); print STDERR "\nCreating table...\n"; $dbh->do(CREATE_CACHE_TABLE); print STDERR "Populating table...\n"; $dbh->do(POPULATE_CACHE_TABLE); print STDERR "Creating indexes...\n"; $dbh->do(CREATE_CACHE_TABLE_INDEX1); $dbh->do(CREATE_CACHE_TABLE_INDEX2); $dbh->do(CREATE_CACHE_TABLE_INDEX3); $dbh->commit; print STDERR "Adjusting the primary key sequences (if necessary)..."; $self->update_sequences(); print STDERR "Done.\n"; } return; } =head2 place_lock =over =item Usage $obj->place_lock() =item Function To place a row in the gff_meta table (creating that table if necessary) that will prevent other users/processes from doing GFF bulk loads while the current process is running. =item Returns Nothing =item Arguments None =back =cut sub place_lock { my ($self, %argv) = @_; #first determine if the meta table exists my $dbh = $self->dbh; my $sth = $dbh->prepare(VERIFY_TMP_TABLE); $sth->execute('gff_meta'); my ($table_exists) = $sth->fetchrow_array; if (!$table_exists) { print STDERR "Creating gff_meta table...\n"; $dbh->do(CREATE_META_TABLE); } #check for existing lock my $select_query = $dbh->prepare(SELECT_FROM_META); $select_query->execute(); while (my @result = $select_query->fetchrow_array) { my ($name,$host,$time) = @result; my ($progname,$pid) = split /\-/, $name; if ($progname eq 'gmod_bulk_load_gff3.pl') { print STDERR "\n\n\nWARNING: There is another gmod_bulk_load_gff3.pl process\n"; print STDERR "running on $host, with a process id of $pid\n"; print STDERR "which started at $time\n"; print STDERR "\nIf that process is no longer running, you can remove the lock by providing\n"; print STDERR "the --remove_lock flag when running gmod_bulk_load_gff3.pl\n\n"; print STDERR "Note that if the last bulk load process crashed, you may also need the\n"; print STDERR "--recreate_cache option as well\n\n"; exit(-2); } } my $pid = $$; my $name = "gmod_bulk_load_gff3.pl-$pid"; my $hostname = hostname; my $insert_query = $dbh->prepare(INSERT_INTO_META); $insert_query->execute($name,$hostname); return; } =head2 remove_lock =over =item Usage $obj->remove_lock() =item Function To remove the row in the gff_meta table that prevents other gmod_bulk_load_gff3.pl processes from running while the current process is running. =item Returns Nothing =item Arguments None =back =cut sub remove_lock { my ($self, %argv) = @_; my $dbh = $self->dbh; my $select_query = $dbh->prepare(SELECT_FROM_META) or warn "select prepare failed"; $select_query->execute() or warn "select from meta failed"; my $delete_query = $dbh->prepare(DELETE_FROM_META) or warn "delete prepare failed"; while (my @result = $select_query->fetchrow_array) { my ($name,$host,$time) = @result; if ($name =~ /gmod_bulk_load_gff3/) { $delete_query->execute($name,$host) or warn "removing the lock failed!"; $dbh->commit unless $self->dbh->{AutoCommit}; } } return; } =head2 cleanup_tmp_table =over =item Usage $obj->cleanup_tmp_table() =item Function Called when there is an abnormal exit from a loading program. It deletes entries in the tmp_gff_load_cache table that have feature_ids that were used during the current session. =item Returns Nothing =item Arguments None (it needs the first feature_id, but that is stored in the object). =back =cut sub cleanup_tmp_table { my $self = shift; my $dbh = $self->dbh; my $first_feature = $self->first_feature_id(); return unless $first_feature; my $delete_query = $dbh->prepare(TMP_TABLE_CLEANUP); warn "Attempting to clean up the loader temp table (so that --recreate_cache\nwon't be needed)...\n"; $delete_query->execute($first_feature); return; } =head2 first_feature_id =over =item Usage $obj->first_feature_id() #get existing value $obj->first_feature_id($newval) #set new value =item Function =item Returns value of first_feature_id (a scalar), that is, the feature_id of the first feature parsed in the current session. =item Arguments new value of first_feature_id (to set) =back =cut sub first_feature_id { my $self = shift; my $first_feature_id = shift if defined(@_); return $self->{'first_feature_id'} = $first_feature_id if defined($first_feature_id); return $self->{'first_feature_id'}; } =head2 initialize_ontology =over =item Usage $obj->initialize_ontology() =item Function Initializes part_of, derives_from and SO cv_id =item Returns void =item Arguments none =back =cut sub initialize_ontology { my $self = shift; my $sth = $self->dbh->prepare( "select cvterm_id from cvterm where name = 'part_of' and cv_id in ( SELECT cv_id FROM cv WHERE name='relationship' )"); $sth->execute; ($part_of) = $sth->fetchrow_array(); $sth = $self->dbh->prepare( "select cvterm_id from cvterm where name = 'derives_from' and cv_id in ( SELECT cv_id FROM cv WHERE name='relationship' )"); $sth->execute; ($derives_from) = $sth->fetchrow_array(); $sth = $self->dbh->prepare("select cv_id from cv where name = 'sequence'"); $sth->execute; ($sofa_id) = $sth->fetchrow_array(); #backup plan for old chado instances if(!defined($sofa_id)){ $sth = $self->dbh->prepare( "select cv_id from cv where name = 'Sequence Ontology Feature Annotation' or name='sofa.ontology'"); $sth->execute; ($sofa_id) = $sth->fetchrow_array(); } #backup plan for really old chado instances if(!defined($sofa_id)){ $sth = $self->dbh->prepare( "select cv_id from cv where name = 'Sequence Ontology'"); $sth->execute; ($sofa_id) = $sth->fetchrow_array(); } return; } =head2 initialize_sequences =over =item Usage $obj->initialize_sequences() =item Function Initializes sequence counter variables =item Returns void =item Arguments none =back =cut sub initialize_sequences { my $self = shift; foreach my $table (@tables) { my $sth = $self->dbh->prepare("select nextval('$sequences{$table}')"); $sth->execute; my ($nextoid) = $sth->fetchrow_array(); $self->nextoid($table, $nextoid); } return; } =head2 update_sequences =over =item Usage $obj->update_sequences() =item Function Checks the maximum value of the primary key of the sequence's table and modifies the nextval of the sequence if they are out of sync. It then (re)initializes the sequence cache. =item Returns Nothing =item Arguments None =back =cut sub update_sequences { my $self = shift; foreach my $table (@tables) { my $id_name = $table."_id"; my $max_id_query = "SELECT max($id_name) FROM $table"; my $sth = $self->dbh->prepare($max_id_query); $sth->execute; my ($max_id) = $sth->fetchrow_array(); my $curval_query = "SELECT nextval('$sequences{$table}')"; $sth = $self->dbh->prepare($curval_query); $sth->execute; my ($curval) = $sth->fetchrow_array(); if ($max_id > $curval) { my $setval_query = "SELECT setval('$sequences{$table}',$max_id)"; $sth = $self->dbh->prepare($setval_query); $sth->execute; } } $self->initialize_sequences(); return; } =head2 dbh =over =item Usage $obj->dbh() #get existing value $obj->dbh($newval) #set new value =item Function =item Returns value of dbh (a scalar) =item Arguments new value of dbh (to set) =back =cut sub dbh { my $self = shift; my $dbh = shift if defined(@_); return $self->{'dbh'} = $dbh if defined($dbh); return $self->{'dbh'}; } =head2 nouniquecache =over =item Usage $obj->nouniquecache() #get existing value $obj->nouniquecache($newval) #set new value =item Function =item Returns value of nouniquecache (a scalar) =item Arguments new value of nouniquecache (to set) =back =cut sub nouniquecache { my $self = shift; my $nouniquecache = shift if defined(@_); return $self->{'nouniquecache'} = $nouniquecache if defined($nouniquecache); return $self->{'nouniquecache'}; } =head2 noexon =over =item Usage $obj->noexon() #get existing value $obj->noexon($newval) #set new value =item Function =item Returns value of noexon (a scalar) =item Arguments new value of noexon (to set) =back =cut sub noexon { my $self = shift; my $noexon = shift if defined(@_); return $self->{'noexon'} = $noexon if defined($noexon); return $self->{'noexon'}; } =head2 dbname =over =item Usage $obj->dbname() #get existing value $obj->dbname($newval) #set new value =item Function =item Returns value of dbname (a scalar) =item Arguments new value of dbname (to set) =back =cut sub dbname { my $self = shift; my $dbname = shift if defined(@_); return $self->{'dbname'} = $dbname if defined($dbname); return $self->{'dbname'}; } =head2 dbport =over =item Usage $obj->dbport() #get existing value $obj->dbport($newval) #set new value =item Function =item Returns value of dbport (a scalar) =item Arguments new value of dbport (to set) =back =cut sub dbport { my $self = shift; my $dbport = shift; return $self->{'dbport'} = $dbport if defined($dbport); return $self->{'dbport'}; } =head2 dbhost =over =item Usage $obj->dbhost() #get existing value $obj->dbhost($newval) #set new value =item Function =item Returns value of dbhost (a scalar) =item Arguments new value of dbhost (to set) =back =cut sub dbhost { my $self = shift; my $dbhost = shift; return $self->{'dbhost'} = $dbhost if defined($dbhost); return $self->{'dbhost'}; } =head2 dbuser =over =item Usage $obj->dbuser() #get existing value $obj->dbuser($newval) #set new value =item Function =item Returns value of dbuser (a scalar) =item Arguments new value of dbuser (to set) =back =cut sub dbuser { my $self = shift; my $dbuser = shift; return $self->{'dbuser'} = $dbuser if defined($dbuser); return $self->{'dbuser'}; } =head2 dbpass =over =item Usage $obj->dbpass() #get existing value $obj->dbpass($newval) #set new value =item Function =item Returns value of dbpass (a scalar) =item Arguments new value of dbpass (to set) =back =cut sub dbpass { my $self = shift; my $dbpass = shift; return $self->{'dbpass'} = $dbpass if defined($dbpass); return $self->{'dbpass'}; } =head2 notransact =over =item Usage $obj->notransact() #get existing value $obj->notransact($newval) #set new value =item Function =item Returns value of notransact (a scalar) =item Arguments new value of notransact (to set) =back =cut sub notransact { my $self = shift; my $notransact = shift; return $self->{'notransact'} = $notransact if defined($notransact); return $self->{'notransact'}; } =head2 nosequence =over =item Usage $obj->nosequence() #get existing value $obj->nosequence($newval) #set new value =item Function =item Returns value of nosequence (a scalar) =item Arguments new value of nosequence (to set) =back =cut sub nosequence { my $self = shift; my $nosequence = shift; return $self->{'nosequence'} = $nosequence if defined($nosequence); return $self->{'nosequence'}; } =head2 inserts =over =item Usage $obj->inserts() #get existing value $obj->inserts($newval) #set new value =item Function =item Returns value of inserts (a scalar) =item Arguments new value of inserts (to set) =back =cut sub inserts { my $self = shift; my $inserts = shift if defined(@_); return $self->{'inserts'} = $inserts if defined($inserts); return $self->{'inserts'}; } =head2 score_col =over =item Usage $obj->score_col() #get existing value $obj->score_col($newval) #set new value =item Function =item Returns value of score_col (a scalar) =item Arguments new value of score_col (to set) =back =cut sub score_col { my $self = shift; my $col = shift if defined(@_); return $self->{'score_col'} = $col if defined($col); return $self->{'score_col'}; } =head2 analysis_group =over =item Usage $obj->analysis_group() #get existing value $obj->analysis_group($newval) #set new value =item Function =item Returns value of analysis_group (a scalar) =item Arguments new value of analysis_group (to set) =back =cut sub analysis_group { my $self = shift; my $anal = shift if defined(@_); return $self->{'analysis_group'} = $anal if defined($anal); return $self->{'analysis_group'}; } =head2 global_analysis =over =item Usage $obj->global_analysis() #get existing value $obj->global_analysis($newval) #set new value =item Function =item Returns value of global_analysis (a scalar) =item Arguments new value of global_analysis (to set) =back =cut sub global_analysis { my $self = shift; my $anal = shift if defined(@_); return $self->{'global_analysis'} = $anal if defined($anal); return $self->{'global_analysis'}; } =head2 is_analysis =over =item Usage $obj->is_analysis() #get existing value $obj->is_analysis($newval) #set new value dgg: renamed to flag field name to avoid confusion with analysis table =item Function =item Returns value of is_analysis (a scalar) =item Arguments new value of is_analysis (to set) =back =cut sub is_analysis { my $self = shift; my $is_analysis = shift if defined(@_); return $self->{'is_analysis'} = $is_analysis if defined($is_analysis); return $self->{'is_analysis'}; } =head2 organism =over =item Usage $obj->organism() #get existing value $obj->organism($newval) #set new value =item Function =item Returns value of organism (a scalar) =item Arguments new value of organism (to set) =back =cut sub organism { my $self = shift; my $organism = shift; return $self->{'organism'} = $organism if defined($organism); return $self->{'organism'}; } =head2 dbprofile =over =item Usage $obj->dbprofile() #get existing value $obj->dbprofile($newval) #set new value =item Function =item Returns value of dbprofile (a scalar) =item Arguments new value of dbprofile (to set) =back =cut sub dbprofile { my $self = shift; my $dbprofile = shift; return $self->{'dbprofile'} = $dbprofile if defined($dbprofile); return $self->{'dbprofile'}; } =head2 noload =over =item Usage $obj->noload() #get existing value $obj->noload($newval) #set new value =item Function =item Returns value of noload (a scalar) =item Arguments new value of noload (to set) =back =cut sub noload { my $self = shift; my $noload = shift; return $self->{'noload'} = $noload if defined($noload); return $self->{'noload'}; } =head2 skip_vacuum =over =item Usage $obj->skip_vacuum() #get existing value $obj->skip_vacuum($newval) #set new value =item Function =item Returns value of skip_vacuum (a scalar) =item Arguments new value of skip_vacuum (to set) =back =cut sub skip_vacuum { my $self = shift; my $skip_vacuum = shift; return $self->{'skip_vacuum'} = $skip_vacuum if defined($skip_vacuum); return $self->{'skip_vacuum'}; } =head2 drop_indexes_flag =over =item Usage $obj->drop_indexes_flag() #get existing value $obj->drop_indexes_flag($newval) #set new value =item Function =item Returns value of drop_indexes_flag (a scalar) =item Arguments new value of drop_indexes_flag (to set) =back =cut sub drop_indexes_flag { my $self = shift; my $drop_indexes_flag = shift; return $self->{'drop_indexes_flag'} = $drop_indexes_flag if defined($drop_indexes_flag); return $self->{'drop_indexes_flag'}; } =head2 save_tmpfiles =over =item Usage $obj->save_tmpfiles() #get existing value $obj->save_tmpfiles($newval) #set new value =item Function =item Returns value of save_tmpfiles (a scalar) =item Arguments new value of save_tmpfiles (to set) =back =cut sub save_tmpfiles { my $self = shift; my $save_tmpfiles = shift if defined(@_); return $self->{'save_tmpfiles'} = $save_tmpfiles if defined($save_tmpfiles); return $self->{'save_tmpfiles'}; } =head2 random_tmp_dir =over =item Usage $obj->random_tmp_dir() #get existing value $obj->random_tmp_dir($newval) #set new value =item Function =item Returns value of random_tmp_dir (a scalar) =item Arguments new value of random_tmp_dir (to set) =back =cut sub random_tmp_dir { my $self = shift; my $random_tmp_dir = shift if defined(@_); return $self->{'random_tmp_dir'} = $random_tmp_dir if defined($random_tmp_dir); return $self->{'random_tmp_dir'}; } =head2 no_target_syn =over =item Usage $obj->no_target_syn() #get existing value $obj->no_target_syn($newval) #set new value =item Function =item Returns value of no_target_syn() (a scalar) =item Arguments new value of no_target_syn (to set) =back =cut sub no_target_syn { my $self = shift; my $no_target_syn = shift if defined(@_); return $self->{'no_target_syn'} = $no_target_syn if defined($no_target_syn); return $self->{'no_target_syn'}; } =head2 unique_target =over =item Usage $obj->unique_target() #get existing value $obj->unique_target($newval) #set new value =item Function =item Returns value of unique_target() (a scalar) =item Arguments new value of unique_target (to set) =back =cut sub unique_target { my $self = shift; my $unique_target = shift if defined(@_); return $self->{'unique_target'} = $unique_target if defined($unique_target); return $self->{'unique_target'}; } =head2 private_schema =over =item Usage $obj->private_schema() #get existing value $obj->private_schema($newval) #set new value =item Function Sets the value of private_schema, the name of the private schema to insert data into. If not set, the public schema will be used. =item Returns value of private_schema (a scalar) =item Arguments new value of private_schema (to set) =back =cut sub private_schema { my $self = shift; my $private_schema = shift if defined(@_); return $self->{'private_schema'} = $private_schema if defined($private_schema); return $self->{'private_schema'}; } =head2 use_public_cv =over =item Usage $obj->use_public_cv() #get existing value $obj->use_public_cv($newval) #set new value =item Function When private_schema is set, this flag tells the loader to insert new cv and cvterm data into the public schema instead of the private one. =item Returns value of use_public_cv (a scalar) =item Arguments new value of use_public_cv (to set) =back =cut sub use_public_cv { my $self = shift; my $use_public_cv = shift if defined(@_); return $self->{'use_public_cv'} = $use_public_cv if defined($use_public_cv); return $self->{'use_public_cv'}; } =head2 dbxref =over =item Usage $obj->dbxref() #get existing value $obj->dbxref($newval) #set new value =item Function =item Returns value of dbxref (a scalar) =item Arguments new value of dbxref (to set) =back =cut sub dbxref { my $self = shift; my $dbxref = shift if defined(@_); return $self->{'dbxref'} = $dbxref if defined($dbxref); return $self->{'dbxref'}; } =head2 primary_dbxref =over =item Usage $obj->primary_dbxref() #get existing value $obj->primary_dbxref($newval) #set new value =item Function =item Returns value of primary_dbxref (a scalar) =item Arguments new value of primary_dbxref (to set) =back =cut sub primary_dbxref { my $self = shift; my $primary_dbxref = shift if defined(@_); return $self->{'primary_dbxref'} = $primary_dbxref if defined($primary_dbxref); return $self->{'primary_dbxref'}; } ##################################################################### # # Subs moved directly from gmod_bulk_load_gff3.pl # # sub dbxref_error_message { my $tag = shift; warn <private_schema ? $self->private_schema . "._feature" : "feature"; my $fh = $self->file_handles('delete'); print $fh "DELETE FROM $table WHERE feature_id = $feature_id;\n"; return; } sub print_seq { my $self = shift; my ($name,$string) = @_; my $dbh = $self->dbh; my $organism_id = $self->organism_id; my $uniquename = $self->modified_uniquename(orig_id=>$name, organism_id => $organism_id) ? $self->modified_uniquename(orig_id=>$name, organism_id => $organism_id) : $name; my $fid_query = "SELECT feature_id FROM tmp_gff_load_cache WHERE uniquename = ? AND organism_id = ? AND feature_id >= ?"; my $sth = $dbh->prepare($fid_query); $sth->execute($uniquename,$organism_id,$self->first_feature_id); if ($sth->rows == 0) { warn "No feature found for $uniquename, org_id:$organism_id when trying to add sequence"; return; } elsif ($sth->rows > 1) { warn "More than one feature found for $uniquename, org_id:$organism_id when trying to add sequence"; return; } my ($feature_id) = $sth->fetchrow_array; my $fh = $self->file_handles('sequence'); my $len = length($string); print $fh "UPDATE feature set residues='$string', seqlen=$len WHERE feature_id=$feature_id;\n"; return; } sub print_fasta { my $self = shift; my ($uniquename,$string) = @_; my $dbh = $self->dbh; my $organism_id = $self->organism_id; #assume that the fasta ID matches the uniquename (ie, no munging when it went into the database) my $fid_query = "SELECT feature_id FROM feature WHERE uniquename = ? AND organism_id = ?"; my $sth = $dbh->prepare($fid_query); $sth->execute($uniquename,$organism_id); if ($sth->rows == 0) { warn <rows > 1) { warn "More than one feature found for $uniquename, org_id:$organism_id when trying to add sequence, skipping...\n\n"; return; } my ($feature_id) = $sth->fetchrow_array; my $fh = $self->file_handles('sequence'); my $len = length($string); print $fh "UPDATE feature set residues='$string',seqlen=$len WHERE feature_id=$feature_id;\n"; return; } sub print_af { my $self = shift; my ($af_id,$f_id,$a_id,$score) = @_; my $fh = $self->file_handles('analysisfeature'); if ($self->inserts()) { $score =~ s/\\N/NULL/g; my @scores = split "\t", $score; my @q_scores = map { $self->dbh->quote($_) if $_ ne 'NULL' } @scores; my $q_score = join(',', @q_scores); print $fh "INSERT INTO analysisfeature $copystring{'analysisfeature'} VALUES ($af_id,$f_id,$a_id,$q_score);\n"; } else { print $fh join("\t", ($af_id,$f_id,$a_id,$score)), "\n"; } } sub print_dbx { my $self = shift; my ($dbx_id,$db_id,$acc,$vers,$desc) = @_; my $fh = $self->file_handles('dbxref'); if ($self->inserts()) { my $q_acc = $self->dbh->quote($acc); my $q_vers = $self->dbh->quote($vers); my $q_desc = $desc eq '\N' ? 'NULL' : $self->dbh->quote($desc); print $fh "INSERT INTO dbxref $copystring{'dbxref'} VALUES ($dbx_id,$db_id,$q_acc,$q_vers,$q_desc);\n"; } else { print $fh join("\t",($dbx_id,$db_id,$acc,$vers,$desc)),"\n"; } } sub print_analysis { # dgg my $self = shift; my ($an_id,$name,$program,$source) = @_; unless($name) { $name = ($source) ? "$program.$source" : $program; } $source ||= '\N'; my $progvers= 'null'; # not NULL, but no idea here? dup program? or 'null' ? my $fh = $self->file_handles('analysis'); if ($self->inserts()) { my $q_name = $self->dbh->quote($name); my $q_program = $self->dbh->quote($program); my $q_progvers = $self->dbh->quote($progvers); my $q_source = $source eq '\N' ? 'NULL' : $self->dbh->quote($source); print $fh "INSERT INTO analysis $copystring{'analysis'} VALUES ($an_id,$q_name,$q_program,$q_progvers,$q_source);\n"; } else { print $fh join("\t",($an_id,$name,$program,$progvers,$source) ),"\n"; } } sub print_organism { # dgg my $self = shift; my ($orgid,$genus,$species,$common) = @_; my $table = $self->use_public_cv ? 'public.organism' : 'organism'; $common ||= '\N'; my $abbrev= substr($genus,0,1).'.'.$species; my $fh = $self->file_handles('organism'); if ($self->inserts()) { my $q_genus = $self->dbh->quote($genus); my $q_species = $self->dbh->quote($species); my $q_abbrev = $self->dbh->quote($abbrev); my $q_common = $common eq '\N' ? 'NULL' : $self->dbh->quote($common); print $fh "INSERT INTO $table $copystring{'organism'} VALUES ($orgid,$q_genus,$q_species,$q_common,$q_abbrev);\n"; } else { print $fh join("\t",($orgid,$genus,$species,$common,$abbrev) ),"\n"; } } sub print_cvterm { # dgg my $self = shift; my ($cvterm_id,$cv_id,$name,$dbxref_id,$definition) = @_; my $table = $self->use_public_cv ? 'public.cvterm' : 'cvterm'; $definition ||= '\N'; my $fh = $self->file_handles('cvterm'); if ($self->inserts()) { my $q_acc = $self->dbh->quote($name); my $q_desc = $definition eq '\N' ? 'NULL' : $self->dbh->quote($definition); print $fh "INSERT INTO $table $copystring{'cvterm'} VALUES ($cvterm_id,$cv_id,$q_acc,$dbxref_id,$q_desc);\n"; } else { print $fh join("\t",($cvterm_id,$cv_id,$name,$dbxref_id,$definition)),"\n"; } } sub print_cv { # dgg my $self = shift; my ($cv_id,$name,$definition) = @_; my $table = $self->use_public_cv ? 'public.cv' : 'cv'; $definition ||= '\N'; my $fh = $self->file_handles('cv'); if ($self->inserts()) { my $q_acc = $self->dbh->quote($name); my $q_desc = $definition eq '\N' ? 'NULL' : $self->dbh->quote($definition); print $fh "INSERT INTO $table $copystring{'cv'} VALUES ($cv_id,$q_acc,$q_desc);\n"; } else { print $fh join("\t",($cv_id,$name,$definition)),"\n"; } } sub print_dbname { # dgg my $self = shift; my ($db_id,$name,$description) = @_; my $table = $self->use_public_cv ? 'public.db' : 'db'; $description ||= '\N'; my $fh = $self->file_handles('db'); if ($self->inserts()) { my $q_acc = $self->dbh->quote($name); my $q_desc = $description eq '\N' ? 'NULL' : $self->dbh->quote($description); print $fh "INSERT INTO $table $copystring{'db'} VALUES ($db_id,$q_acc,$q_desc);\n"; } else { print $fh join("\t",($db_id,$name,$description)),"\n"; } } sub print_fs { my $self = shift; my ($fs_id,$s_id,$f_id,$p_id) = @_; my $fh = $self->file_handles('feature_synonym'); if ($self->inserts()) { print $fh "INSERT INTO feature_synonym $copystring{'feature_synonym'} VALUES ($fs_id,$s_id,$f_id,$p_id);\n"; } else { print $fh join("\t", ($fs_id,$s_id,$f_id,$p_id)),"\n"; } } sub print_fdbx { my $self = shift; my ($fd_id,$f_id,$dx_id) = @_; my $fh = $self->file_handles('feature_dbxref'); if ($self->inserts()) { print $fh "INSERT INTO feature_dbxref $copystring{'feature_dbxref'} VALUES ($fd_id,$f_id,$dx_id);\n"; } else { print $fh join("\t",($fd_id,$f_id,$dx_id)),"\n"; } } sub print_fcv { my $self = shift; my ($fcv_id,$f_id,$cvterm_id,$p_id) = @_; my $fh = $self->file_handles('feature_cvterm'); if ($self->inserts()) { print $fh "INSERT INTO feature_cvterm $copystring{'feature_cvterm'} VALUES ($fcv_id,$f_id,$cvterm_id,$p_id);\n"; } else { print $fh join("\t",($fcv_id,$f_id,$cvterm_id,$p_id)),"\n"; } } sub print_syn { my $self = shift; my ($s_id,$syn,$type_id) = @_; my $fh = $self->file_handles('synonym'); if ($self->inserts()) { my $q_syn = $self->dbh->quote($syn); print $fh "INSERT INTO synonym $copystring{'synonym'} VALUES ($s_id,$q_syn,$type_id,$q_syn);\n"; } else { print $fh join("\t", ($s_id,$syn,$type_id,$syn)),"\n"; } } sub print_floc { my $self = shift; my ($featureloc_id,$feature_id,$src_id,$start,$end,$strand,$phase,$rank,$locgroup) = @_; my $fh = $self->file_handles('featureloc'); if ($self->inserts()) { my $q_strand= $strand eq '\N'? 'NULL' : $strand; my $q_phase = $phase eq '\N' ? 'NULL' : $phase; print $fh "INSERT INTO featureloc $copystring{'featureloc'} VALUES ($featureloc_id,$feature_id,$src_id,$start,$end,$q_strand,$q_phase,$rank,$locgroup);\n"; } else { print $fh join("\t", ($featureloc_id, $feature_id, $src_id, $start, $end, $strand, $phase,$rank,$locgroup)),"\n"; } } sub print_fprop { my $self = shift; my ($fp_id,$f_id,$cvterm_id,$value,$rank) = @_; my $fh = $self->file_handles('featureprop'); if ($self->inserts()) { my $q_value = $self->dbh->quote($value); print $fh "INSERT INTO featureprop $copystring{'featureprop'} VALUES ($fp_id,$f_id,$cvterm_id,$q_value,$rank);\n"; } else { print $fh join("\t",($fp_id,$f_id,$cvterm_id,$value,$rank)),"\n"; } } sub print_frel { my $self = shift; my ($nextfeaturerel,$nextfeature,$parent,$part_of) = @_; my $fh = $self->file_handles('feature_relationship'); if ($self->inserts()) { print $fh "INSERT INTO feature_relationship $copystring{'feature_relationship'} VALUES ($nextfeaturerel,$nextfeature,$parent,$part_of);\n"; } else { print $fh join("\t", ($nextfeaturerel,$nextfeature,$parent,$part_of)),"\n"; } } sub print_f { my $self = shift; my ($nextfeature,$organism,$name,$uniquename,$type,$seqlen,$dbxref) = @_; my $fh = $self->file_handles('feature'); if ($self->inserts()) { my $q_name = $self->dbh->quote($name); my $q_uniquename = $self->dbh->quote($uniquename); my $q_seqlen = $seqlen eq '\N' ? 'NULL' : $seqlen; my $q_analysis = $self->is_analysis ? "'true'" : "'false'"; $dbxref ||= 'NULL'; print $fh "INSERT INTO feature $copystring{'feature'} VALUES ($nextfeature,$organism,$q_name,$q_uniquename,$type,$q_analysis,$q_seqlen,$dbxref);\n"; } else { $dbxref ||= '\N'; print $fh join("\t", ($self->nextfeature, $organism, $name, $uniquename, $type, $self->is_analysis,$seqlen,$dbxref)),"\n"; } } sub create_indexes { my $self = shift; my $dbh = $self->dbh(); $dbh->do("ALTER TABLE feature ADD CONSTRAINT feature_c1 unique (organism_id,uniquename,type_id)"); $dbh->do("CREATE INDEX feature_name_ind1 ON feature (name)"); $dbh->do("CREATE INDEX feature_idx1 ON feature (dbxref_id)"); $dbh->do("CREATE INDEX feature_idx2 ON feature (organism_id)"); $dbh->do("CREATE INDEX feature_idx3 ON feature (type_id)"); $dbh->do("CREATE INDEX feature_idx4 ON feature (uniquename)"); $dbh->do("CREATE INDEX feature_idx5 ON feature (lower(name))"); $dbh->do("ALTER TABLE featureloc ADD CONSTRAINT featureloc_c1 unique (feature_id,locgroup,rank)"); $dbh->do("CREATE INDEX featureloc_idx1 ON featureloc (feature_id)"); $dbh->do("CREATE INDEX featureloc_idx2 ON featureloc (srcfeature_id)"); $dbh->do("CREATE INDEX featureloc_idx3 ON featureloc (srcfeature_id,fmin,fmax)"); $dbh->do("ALTER TABLE feature_dbxref ADD CONSTRAINT feature_dbxref_c1 unique (feature_id,dbxref_id)"); $dbh->do("CREATE INDEX feature_dbxref_idx1 ON feature_dbxref (feature_id)"); $dbh->do("CREATE INDEX feature_dbxref_idx2 ON feature_dbxref (dbxref_id)"); $dbh->do("ALTER TABLE feature_relationship ADD CONSTRAINT feature_relationship_c1 unique (subject_id,object_id,type_id,rank)"); $dbh->do("CREATE INDEX feature_relationship_idx1 ON feature_relationship (subject_id)"); $dbh->do("CREATE INDEX feature_relationship_idx2 ON feature_relationship (object_id)"); $dbh->do("CREATE INDEX feature_relationship_idx3 ON feature_relationship (type_id)"); $dbh->do("ALTER TABLE feature_cvterm ADD CONSTRAINT feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id)"); $dbh->do("CREATE INDEX feature_cvterm_idx1 ON feature_cvterm (feature_id)"); $dbh->do("CREATE INDEX feature_cvterm_idx2 ON feature_cvterm (cvterm_id)"); $dbh->do("CREATE INDEX feature_cvterm_idx3 ON feature_cvterm (pub_id)"); $dbh->do("ALTER TABLE synonym ADD CONSTRAINT synonym_c1 unique (name,type_id)"); $dbh->do("CREATE INDEX synonym_idx1 ON synonym (type_id)"); $dbh->do("CREATE INDEX synonym_idx2 ON synonym ((lower(synonym_sgml)))"); $dbh->do("ALTER TABLE feature_synonym ADD CONSTRAINT feature_synonym_c1 unique (synonym_id,feature_id,pub_id)"); $dbh->do("CREATE INDEX feature_synonym_idx1 ON feature_synonym (synonym_id)"); $dbh->do("CREATE INDEX feature_synonym_idx2 ON feature_synonym (feature_id)"); $dbh->do("CREATE INDEX feature_synonym_idx3 ON feature_synonym (pub_id)"); $dbh->do("ALTER TABLE analysisfeature ADD CONSTRAINT analysisfeature_c1 unique (feature_id,analysis_id)"); $dbh->do("CREATE INDEX analysisfeature_idx1 ON analysisfeature (feature_id)"); $dbh->do("CREATE INDEX analysisfeature_idx2 ON analysisfeature (analysis_id)"); } sub drop_indexes { my $self = shift; my $dbh = $self->dbh(); $dbh->do("ALTER TABLE feature DROP CONSTRAINT feature_c1") or die "$!"; $dbh->do("DROP INDEX feature_name_ind1") or die "$!"; $dbh->do("DROP INDEX feature_idx1") or die "$!"; $dbh->do("DROP INDEX feature_idx2") or die "$!"; $dbh->do("DROP INDEX feature_idx3") or die "$!"; $dbh->do("DROP INDEX feature_idx4") or die "$!"; $dbh->do("DROP INDEX feature_idx5") or die "$!"; $dbh->do("ALTER TABLE featureloc DROP CONSTRAINT featureloc_c1") or die "$!"; $dbh->do("DROP INDEX featureloc_idx1") or die "$!"; $dbh->do("DROP INDEX featureloc_idx2") or die "$!"; $dbh->do("DROP INDEX featureloc_idx3") or die "$!"; $dbh->do("ALTER TABLE feature_dbxref DROP CONSTRAINT feature_dbxref_c1") or die "$!"; $dbh->do("DROP INDEX feature_dbxref_idx1") or die "$!"; $dbh->do("DROP INDEX feature_dbxref_idx2") or die "$!"; $dbh->do("ALTER TABLE feature_relationship DROP CONSTRAINT feature_relationship_c1") or die "$!"; $dbh->do("DROP INDEX feature_relationship_idx1") or die "$!"; $dbh->do("DROP INDEX feature_relationship_idx2") or die "$!"; $dbh->do("DROP INDEX feature_relationship_idx3") or die "$!"; $dbh->do("ALTER TABLE feature_cvterm DROP CONSTRAINT feature_cvterm_c1") or die "$!"; $dbh->do("DROP INDEX feature_cvterm_idx1") or die "$!"; $dbh->do("DROP INDEX feature_cvterm_idx2") or die "$!"; $dbh->do("DROP INDEX feature_cvterm_idx3") or die "$!"; $dbh->do("ALTER TABLE synonym DROP CONSTRAINT synonym_c1") or die "$!"; $dbh->do("DROP INDEX synonym_idx1") or die "$!"; $dbh->do("DROP INDEX synonym_idx2") or die "$!"; $dbh->do("ALTER TABLE feature_synonym DROP CONSTRAINT feature_synonym_c1") or die "$!"; $dbh->do("DROP INDEX feature_synonym_idx1") or die "$!"; $dbh->do("DROP INDEX feature_synonym_idx2") or die "$!"; $dbh->do("DROP INDEX feature_synonym_idx3") or die "$!"; $dbh->do("ALTER TABLE analysisfeature DROP CONSTRAINT analysisfeature_c1") or die "$!"; $dbh->do("DROP INDEX analysisfeature_idx1") or die "$!"; $dbh->do("DROP INDEX analysisfeature_idx2") or die "$!"; } sub uniquename_validation { my $self = shift; my ($uniquename, $type, $organism, $nextfeature) = @_; if ( $self->uniquename_cache( validate => 1, type_id => $type, organism_id => $organism, uniquename => $uniquename ) ) { #if this returns non-zero, it is already in the cache and not valid $uniquename = "$uniquename-$nextfeature"; return $self->uniquename_validation($uniquename, $type, $organism, $nextfeature); } else { #this uniquename is valid; cache it and return $self->uniquename_cache( type_id => $type, organism_id => $organism, feature_id => $nextfeature, uniquename => $uniquename, ); return $uniquename; } } =head2 modified_uniquename =over =item Usage $obj->modified_uniquename(orig_id => $id, modified_id => $new_id, organism_id => $organism_id) =item Function Keeps track of uniquenames that had to be modifed from their original GFF3 ID so relationships in the GFF3 can be properly represented in Chado. =item Returns When called with all three pairs of args, nothing. When called with one of orig_id or modified_id args, return the value of the other arg. For example, when called with "orig_id => $id", the method would return $new_id. =item Arguments Two possible hash pairs: orig_id for the ID that was present in the GFF file and modified_id for the uniquename that will be in Chado. Additionally, the organism_id hash pair must be supplied. =back =cut sub modified_uniquename { my ($self, %argv) = @_; if (!defined $argv{'organism_id'}) { confess "organism_id must be supplied to the modified_uniquename method"; } if (defined $argv{'orig_id'} && defined $argv{'modified_id'}) { #set #cluck "organism_id is: ",$argv{'organism_id'}; $self->{'modified_uniquename'}-> {$argv{'organism_id'}}-> {'orig2mod'}-> {$argv{'orig_id'}} = $argv{'modified_id'}; $self->{'modified_uniquename'}-> {$argv{'organism_id'}}-> {'mod2orig'}-> {$argv{'modified_id'}} = $argv{'orig_id'}; return; } elsif (defined $argv{'orig_id'}) { return $self->{'modified_uniquename'}->{$argv{'organism_id'}}->{'orig2mod'}->{$argv{'orig_id'}}; } elsif (defined $argv{'modified_id'}) { return $self->{'modified_uniquename'}->{$argv{'organism_id'}}->{'mod2orig'}->{$argv{'modified_id'}}; } else { cluck"this shouldn't happen in modified_uniquename"; return; } } sub dump_ana_contents { my $self = shift; my $anakey = shift; print STDERR "\n\nCouldn't find $anakey in analysis table\n"; print STDERR "The current contents of the analysis table is:\n\n"; #confess; my $sth = $self->dbh->prepare("SELECT analysis_id,name,program,sourcename FROM analysis"); printf STDERR "%10s %25s %10s %10s\n\n", ('analysis_id','name','program','sourcename'); $sth->execute; while (my $array_ref = $sth->fetchrow_arrayref) { printf STDERR "%10s %25s %10s %10s\n", @$array_ref; } print STDERR "\n\nCouldn't find $anakey in analysis table\n"; print STDERR "\nPlease see \`perldoc gmod_bulk_load_gff3.pl\` for more information\n\n"; exit 1; } sub synonyms { my $self = shift; my $alias = shift; my $feature_id = shift; unless ($self->cache('synonym',$alias)) { unless ($self->cache('type','synonym')) { my $cv_table = $self->use_public_cv ? "public.cv" : "cv"; my $cvterm_table = $self->use_public_cv ? "public.cvterm" : "cvterm"; my $sth = $self->dbh->prepare("SELECT cvterm_id FROM $cvterm_table WHERE (name='synonym' and cv_id in (SELECT cv_id FROM $cv_table WHERE name='null' OR name='local')) OR (name='exact' and cv_id in (SELECT cv_id FROM $cv_table WHERE name='synonym_type') ) ORDER BY name"); $sth->execute; my ($syn_type) = $sth->fetchrow_array; # warn "synonym type: $syn_type\n\n\n\n\n\n"; $self->cache('type','synonym',$syn_type); warn "unable to find synonym type in cvterm table" and next unless $syn_type; } # warn Dumper($self); # warn "\n\n\n\n".$self->cache('type','synonym')."\n\n\n\n"; #check for pre-existing synonyms with this name $self->{queries}{search_synonym}->execute($alias,$self->cache('type','synonym')); my ($synonym) = $self->{queries}{search_synonym}->fetchrow_array; if ($synonym) { unless ($self->{const}{pub}) { my $sth=$self->dbh->prepare("SELECT pub_id FROM pub WHERE miniref = 'null'"); $sth->execute; ($self->{const}{pub}) = $sth->fetchrow_array; } if ( $self->constraint( name => 'feature_synonym_c1', terms=> [ $feature_id , $synonym ] ) ) { $self->print_fs($self->nextoid('feature_synonym'),$synonym,$feature_id,$self->{const}{pub}); $self->nextoid('feature_synonym','++'); #$nextfeaturesynonym++; $self->cache('synonym',$alias,$synonym); } } else { $self->print_syn($self->nextoid('synonym'),$alias,$self->cache('type','synonym')); unless ($self->{const}{pub}) { my $sth=$self->dbh->prepare("SELECT pub_id FROM pub WHERE miniref = 'null'"); $sth->execute; my @row_array = $sth->fetchrow_array; $self->{const}{pub} = $row_array[0]; } if( $self->constraint( name => 'feature_synonym_c1', terms => [ $feature_id , $self->nextoid('synonym') ] ) ) { $self->print_fs($self->nextoid('feature_synonym'),$self->nextoid('synonym'),$feature_id,$self->{const}{pub}); $self->nextoid('feature_synonym','++'); #$nextfeaturesynonym++; $self->cache('synonym',$alias,$self->nextoid('synonym')); $self->nextoid('synonym','++'); #$nextsynonym++; } } } else { if ( $self->constraint( name => 'feature_synonym_c1', terms=> [ $feature_id , $self->cache('synonym',$alias) ] ) ) { $self->print_fs($self->nextoid('feature_synonym'),$self->cache('synonym',$alias),$feature_id,$self->{const}{pub}); $self->nextoid('feature_synonym','++'); #$nextfeaturesynonym++; } } } sub load_data { my $self = shift; if ($self->drop_indexes_flag()) { warn "Dropping indexes...\n"; $self->drop_indexes(); } my %nextvalue = $self->nextvalueHash(); # ( # "feature" => $self->nextfeature, # "featureloc" => $self->nextfeatureloc, # "feature_relationship" => $nextfeaturerel, # "featureprop" => $nextfeatureprop, # "feature_cvterm" => $nextfeaturecvterm, # "synonym" => $nextsynonym, # "feature_synonym" => $nextfeaturesynonym, # "feature_dbxref" => $nextfeaturedbxref, # "dbxref" => $nextdbxref, # "analysisfeature" => $nextanalysisfeature, # "cvterm" => $nextcvterm, #dgg # "db" => $nextdbname, #dgg # "cv" => $nextcvname, #dgg # ); $self->file_handles('delete')->autoflush; if (-s $self->file_handles('delete')->filename > 0) { warn "Processing deletes ...\n"; $self->load_deletes(); } foreach my $table (@tables) { $self->file_handles($files{$table})->autoflush; if (-s $self->file_handles($files{$table})->filename <= 4) { warn "Skipping $table table since the load file is empty...\n"; next; } my $l_table = $self->use_public_cv ? $use_public_tables{$table} : $table; $self->copy_from_stdin($l_table, $copystring{$table}, $files{$table}, #file_handle name $sequences{$table}, $nextvalue{$table}); } ($self->dbh->commit() || die "commit failed: ".$self->dbh->errstr()) unless $self->notransact; $self->dbh->{AutoCommit}=1; $self->load_reftype_property(); # dgg #load sequence unless ($self->nosequence) { $self->load_sequence(); } if ($self->drop_indexes_flag()) { warn "Recreating indexes...\n"; $self->create_indexes(); } unless ($self->skip_vacuum) { warn "Optimizing database (this may take a while) ...\n"; print STDERR " "; foreach (@tables) { print STDERR "$_ "; $self->dbh->do("VACUUM ANALYZE $_"); } warn "\nWhile this script has made an effort to optimize the database, you\n" ."should probably also run VACUUM FULL ANALYZE on the database as well.\n"; } print STDERR "\nDone.\n"; } sub copy_from_stdin { my $self = shift; my $table = shift; my $fields = shift; my $file = shift; my $sequence = shift; my $nextval = shift; my $dbh = $self->dbh(); warn "Loading data into $table table ...\n"; my $fh = $self->file_handles($file); seek($fh,0,0); if ($self->inserts()) { # note that if a password is required, the user will have to enter it system("psql -q -f " . $fh->filename . " " . "-h " . $self->dbhost() . " " . "-p " . $self->dbport() . " " . "-U " . $self->dbuser() . " " . "-d " . $self->dbname() ) && $self->throw("FAILED: loading $file failed (error:$!); I can't go on"); } else { my $query = "COPY $table $fields FROM STDIN;"; #warn "\t".$query; $dbh->do($query) or $self->throw("Error when executing: $query: $!"); while (<$fh>) { if ( ! ($dbh->pg_putline($_)) ) { #error, disconecting $dbh->pg_endcopy; $dbh->rollback; $dbh->disconnect; $self->throw("error while copying data's of file $file, line $."); } #putline returns 1 if succesful } $dbh->pg_endcopy or $self->throw("calling endcopy for $table failed: $!"); } #update the sequence so that later inserts will work $dbh->do("SELECT setval('$sequence', $nextval) FROM $table") or $self->throw("Error when executing: setval('$sequence', $nextval) FROM $table: $!"); } sub load_sequence { my $self = shift; my $dbh = $self->dbh(); warn "Loading sequences (if any) ...\n"; my $fh = $self->file_handles('sequence'); # 'SEQ' seek($fh,0,0); while (<$fh>) { chomp; $dbh->do($_); } } sub load_deletes { my $self = shift; my $dbh = $self->dbh(); my $fh = $self->file_handles('delete'); seek($fh,0,0); while (<$fh>) { chomp; $dbh->do($_); } } =item add this to chado db for gbrowse reference class: insert into cvtermprop (cvterm_id,type_id,value) values(ref_cvtermid,ref_cvtermid,'MapReferenceType'); where ref_cvtermid = cvterm_id for reference type (e.g. chromosome,region,contig,...) my $query = "select cvterm_id from cvtermprop where value = ?"; $value= Bio::DB::Das::Chado->MAP_REFERENCE_TYPE(); =cut sub reftype_property { my $self = shift; my $reftype_property = shift; my $reftype_cvtermid = shift; # warn "Adding reftype_property=$reftype_property,$reftype_cvtermid\n" if($reftype_property); $self->{'reftype_property'}= $reftype_property if($reftype_property); $self->{'reftype_cvtermid'}= $reftype_cvtermid if($reftype_cvtermid); return $self->{'reftype_property'}; } sub load_reftype_property { my $self = shift; my $reftype = $self->reftype_property(); return unless($reftype); warn "Adding cvtermprop=MapReferenceType for '$reftype' ...\n"; my $ref_cvtermid = $self->{'reftype_cvtermid'}; $ref_cvtermid = $self->get_type($reftype) unless($ref_cvtermid); return unless($ref_cvtermid); my $maprefkey=""; ##?? eval { "$maprefkey= Bio::DB::Das::Chado::MAP_REFERENCE_TYPE;" }; warn @$ if($@); $maprefkey ||= 'MapReferenceType'; my $dbh = $self->dbh(); my $sth = $dbh->prepare("SELECT value FROM cvtermprop where cvterm_id = ? and type_id = ?"); $sth->execute($ref_cvtermid,$ref_cvtermid); my $data = $sth->fetchrow_hashref(); return if $$data{'value'}; #?? #? check we haven't already added this ... warn "Adding cvtermprop=$maprefkey to $reftype ...\n"; $sth = $dbh->prepare("INSERT INTO cvtermprop (cvterm_id,type_id,value) VALUES (?,?,?)"); $sth->execute($ref_cvtermid,$ref_cvtermid,$maprefkey) or warn "Error when executing: INSERT INTO cvtermprop: $!\n"; } sub handle_target { my $self = shift; my ($feature, $uniquename,$name,$featuretype,$type) = @_; my $organism_id = $self->organism_id; my @targets = $feature->annotation->get_Annotations('Target'); my $rank = 1; foreach my $target (@targets) { my $target_id = $target->target_id; my $tstart = $target->start -1; #convert to interbase my $tend = $target->end; my $tstrand = $target->strand ? $target->strand : '\N'; my $tsource = ref($feature->source) ? $feature->source->value : $feature->source; $self->synonyms($target_id,$self->cache('feature',$uniquename)) if (!$self->no_target_syn); my $created_target_feature = 0; #check for an existing feature with the Target's uniquename my $real_target_id = $self->modified_uniquename(orig_id => $target_id, organism_id => $organism_id) ? $self->modified_uniquename(orig_id => $target_id, organism_id => $organism_id) : $target_id; if ( $self->uniquename_cache(validate=>1,uniquename=>$real_target_id) ) { $self->print_floc( $self->nextfeatureloc, $self->nextfeature, $self->uniquename_cache(validate=>1,uniquename=>$real_target_id), $tstart, $tend, $tstrand, '\N',$rank,'0' ); } else { $self->create_target_feature($name,$featuretype,$uniquename,$real_target_id,$type,$tstart,$tend,$tstrand,$rank); $created_target_feature = 1; } #print Dumper($feature); my $score = defined($feature->score) ? $feature->score : '\N'; $score = '.' eq $score ? '\N' : $score; my $featuretype = $feature->type->name; my $type = $self->cache('type',$featuretype); # my $ankey = $self->global_analysis ? # $self->analysis_group : # $tsource .'_'. $featuretype; # # unless($self->cache('analysis',$ankey)) { # $self->{queries}{search_analysis}->execute($ankey); # my ($ana) = $self->{queries}{search_analysis}->fetchrow_array; # $self->dump_ana_contents($ankey) unless $ana; # $self->cache('analysis',$ankey,$ana); # } my $ankey = $self->find_analysis($tsource,$featuretype); ## dgg patch, see note below $self->dump_ana_contents($ankey) unless $self->cache('analysis',$ankey); my $score_string; if ($self->score_col =~ /^[Ss]/) { $score_string = "$score\t\\N\t\\N\t\\N"; } elsif ($self->score_col =~ /^[Rr]/) { $score_string = "\\N\t$score\t\\N\t\\N"; } elsif ($self->score_col =~ /^[Nn]/) { $score_string = "\\N\t\\N\t$score\t\\N"; } elsif ($self->score_col =~ /^[Ii]/) { $score_string = "\\N\t\\N\t\\N\t$score"; } $self->print_af($self->nextoid('analysisfeature'), $self->nextfeature-$created_target_feature, #takes care of Allen's nextfeature bug--FINALLY! $self->cache('analysis',$ankey), $score_string); $self->nextoid('analysisfeature','++'); #$nextanalysisfeature++; $self->nextfeatureloc('++'); $rank++; } } sub create_target_feature { my $self = shift; my ($name,$featuretype,$uniquename,$target_id,$type,$tstart,$tend,$tstrand,$rank) = @_; $self->nextfeature('++'); $name ||= "$featuretype-$uniquename"; #$self->print_f($self->nextfeature, $self->organism_id(), $name, $target_id.'_'.$self->nextfeature, $type, '\N','\N'); my $tuniquename = $target_id.'_'.$self->nextfeature; # isn't this double call to nextfeature problematic? #It will unecessrally accelerate the growth of feature_id, and possibly lead to problem with very large and old databases. if ($self->unique_target){ $tuniquename = $target_id; $name = $target_id; } $self->print_f($self->nextfeature, $self->organism_id(), $name,$tuniquename , $type, '\N','\N'); $self->print_floc( $self->nextfeatureloc, ($self->nextfeature)-1, $self->nextfeature, $tstart, $tend, $tstrand, '\N', $rank, '0' ); $self->uniquename_cache( feature_id => $self->nextfeature, type_id => $type, organism_id => $self->organism_id(), uniquename => $target_id ); return; } =item analysis comment d.gilbert, 07mar: data sourcename is important also for analysis use, see the table index: (program, programversion, sourcename) The 'name' field is not a unique value; see schema comments: Note only program and programversion are NOT NULL fields. -- TABLE: analysis -- name: can be NULL -- a way of grouping analyses. this should be a handy -- short identifier that can help people find an analysis they -- want. for instance "tRNAscan", "cDNA", "FlyPep", "SwissProt" -- it should not be assumed to be unique. for instance, there may -- be lots of seperate analyses done against a cDNA database. -- -- program: not NULL (and programversion is NOT NULL...) -- e.g. blastx, blastp, sim4, genscan -- -- sourcename: can be NULL -- e.g. cDNA, SwissProt when analysis_group is not given, here are options for finding from GFF source. Using GFF.method is problematic as any analysis can produce several method/type values (gene,CDS,exon; match, match_part, ...) 1. gff.source == an.program[:.-]an.sourcename -- this is flybase example an. usage e.g. gff: chr4, BLASTx.insectEST, est_match, ... chrX, tBLASTn.yeastProtein, protein_match, ... chado.an: program=tBLASTN, sourcename=yeastgenes 2. gff.source == an.program gff: chr2, genscan, gene, ... chr2, genscan, CDS, ... chado.an: program=genscan programversion=2.0 or genscan 2.0, sourcename=NULL Proposed changes: ... original ... use constant SEARCH_ANALYSIS => "SELECT analysis_id FROM analysis WHERE name=?"; my $ankey = $self->global_analysis ? $self->analysis_group : $source .'_'. $featuretype; ## problem unless ($self->cache('analysis',$ankey)) { $self->{queries}{search_analysis}->execute($ankey); ... new , with option to auto-add analysis names to database use constant SEARCH_ANALYSIS => "SELECT analysis_id FROM analysis WHERE (name = ?) OR (program=? AND (sourcename=? OR sourcename is NULL))"; my $ankey = $self->global_analysis ? $self->analysis_group : $source; my ($anprog,$ansource)= split(/[:\.]/,$ankey,2); unless ($self->cache('analysis',$ankey)) { $self->{queries}{search_analysis}->execute($ankey,$anprog,$ansource); =cut sub find_analysis { my $self = shift; my ($source,$featuretype) = @_; my $ankey = $self->global_analysis ? $self->analysis_group : $source; unless ($self->cache('analysis',$ankey)) { my ($anprog,$ansource)= split(/[:\.]/,$ankey,2); # what is best split pattern? '_' is useful as name part ## GBrowse.conf problem using 'feature = type:prog:source'; ## this affects also gff.source > ch.dbxref ## use/expect convention of 'program.dbsource' in gff.source line? $self->{queries}{search_analysis}->execute($ankey,$anprog,$ansource); my ($an_id) = $self->{queries}{search_analysis}->fetchrow_array; if($an_id) { $self->cache('analysis',$ankey,$an_id); } elsif ($self->{'addpropertycv'}) { # create analysis entry $an_id= $self->nextoid('analysis'); $self->print_analysis( $an_id, $ankey, $anprog, $ansource); $self->nextoid('analysis','++'); $self->cache('analysis',$ankey,$an_id); } } return $ankey; } sub handle_nontarget_analysis { my $self = shift; my ($feature,$uniquename) = @_; my $source = ref($feature->source) ? $feature->source->value : $feature->source; my $score = $feature->score ? $feature->score : '\N'; $score = '.' eq $score ? '\N' : $score; my $featuretype = $feature->type->name; # my $ankey = $self->global_analysis ? # $self->analysis_group : # $source .'_'. $featuretype; # # unless ($self->cache('analysis',$ankey)) { # $self->{queries}{search_analysis}->execute($ankey); # my ($ana) = $self->{queries}{search_analysis}->fetchrow_array; # $self->dump_ana_contents($ankey) unless $ana; # $self->cache('analysis',$ankey,$ana); # } my $ankey = $self->find_analysis($source,$featuretype); ## dgg patch, see note $self->dump_ana_contents($ankey) unless $self->cache('analysis',$ankey); my $score_string; if ($self->score_col =~ /^[Ss]/) { $score_string = "$score\t\\N\t\\N\t\\N"; } elsif ($self->score_col =~ /^[Rr]/) { $score_string = "\\N\t$score\t\\N\t\\N"; } elsif ($self->score_col =~ /^[Nn]/) { $score_string = "\\N\t\\N\t$score\t\\N"; } elsif ($self->score_col =~ /^[Ii]/) { $score_string = "\\N\t\\N\t\\N\t$score"; } $self->print_af($self->nextoid('analysisfeature'),$self->cache('feature',$uniquename),$self->cache('analysis',$ankey),$score_string); $self->nextoid('analysisfeature','++'); #$nextanalysisfeature++; } sub handle_dbxref { my $self = shift; my ($feature,$uniquename) = @_; my @dbxrefs = $feature->annotation->get_Annotations('Dbxref'); push @dbxrefs, $feature->annotation->get_Annotations('dbxref'); my ($dbxref_id,$primary_dbxref_id,$primary_pattern); if (defined $self->dbxref and $self->dbxref ne '1') { $primary_pattern = $self->dbxref; } foreach my $dbxref (@dbxrefs) { my $database = $dbxref->database; my $accession = $dbxref->primary_id; my $version; if ($accession =~ /\S+\.(\d+)$/) { $version = $1; } else { $version = 1; } my $desc = '\N'; #FeatureIO::gff doesn't support descriptions yet #enforcing the unique index on dbxref table if(my $dbxref_id=$self->cache('dbxref',"$database|$accession|$version")){ if ($primary_pattern and $database =~/$primary_pattern/) { $primary_dbxref_id ||= $dbxref_id; } elsif ($self->dbxref eq '1') { $primary_dbxref_id ||= $dbxref_id; } if($self->constraint( name => 'feature_dbxref_c1', terms => [ $self->cache('feature',$uniquename) , $dbxref_id] ) ) { $self->print_fdbx($self->nextoid('feature_dbxref'), $self->cache('feature',$uniquename), $dbxref_id); $self->nextoid('feature_dbxref','++'); #$nextfeaturedbxref++; } } else { unless ($self->cache('db',$database)) { $self->{queries}{search_db}->execute("$database"); my($db_id) = $self->{queries}{search_db}->fetchrow_array; unless($db_id) { ## dgg: this 'DB:' prefix on db names in chado is not desired $self->{queries}{search_db}->execute("DB:$database"); ($db_id) = $self->{queries}{search_db}->fetchrow_array; } if(!$db_id && $self->{'addpropertycv'}) { # dgg: use same flag for add db names $db_id= $self->nextoid('db');# $nextdbname++; $self->print_dbname($db_id,$database,"autocreated:$database"); $self->nextoid('db','++'); } warn "couldn't find database '$database' in db table" and next unless $db_id; $self->cache('db',$database,$db_id); } #check for an existing dbxref--this could slow things down a lot! $self->{queries}{search_long_dbxref}->execute($accession, $version,$self->cache('db',$database)); ($dbxref_id) = $self->{queries}{search_long_dbxref}->fetchrow_array; if ($dbxref_id) { if($self->constraint( name => 'feature_dbxref_c1', terms=> [ $self->cache('feature',$uniquename), $dbxref_id ] ) ) { $self->print_fdbx($self->nextoid('feature_dbxref'), $self->cache('feature',$uniquename), $dbxref_id); $self->nextoid('feature_dbxref','++'); #$nextfeaturedbxref++; } $self->cache('dbxref',"$database|$accession|$version",$dbxref_id); } else { $dbxref_id = $self->nextoid('dbxref'); # $nextdbxref; if($self->constraint( name => 'feature_dbxref_c1', terms=> [ $self->cache('feature',$uniquename), $dbxref_id ] ) ){ $self->print_fdbx($self->nextoid('feature_dbxref'), $self->cache('feature',$uniquename), $dbxref_id); $self->nextoid('feature_dbxref','++'); #$nextfeaturedbxref++; } $self->print_dbx($dbxref_id, $self->cache('db',$database), $accession, $version, $desc); $self->cache('dbxref',"$database|$accession|$version",$dbxref_id); $self->nextoid('dbxref','++'); ##$nextdbxref++; } if (defined $primary_pattern and defined $database and $database =~/$primary_pattern/) { $primary_dbxref_id ||= $dbxref_id; } elsif (defined $self->dbxref and $self->dbxref eq '1') { $primary_dbxref_id ||= $dbxref_id; } } } $self->primary_dbxref($primary_dbxref_id) if ($primary_dbxref_id && $self->dbxref); } sub handle_ontology_term { my $self = shift; my ($feature,$uniquename) = @_; my @cvterms = map {$_->identifier} $feature->annotation->get_Annotations('Ontology_term'); my %count; my @ucvterms = grep {++$count{$_} < 2} @cvterms; foreach my $term (@ucvterms) { next unless $term; unless ($self->cache('type',$term)) { ## shouldnt this be cache('ontology',$term) ?? dgg my($d,$a) = $term =~ /^(.+?):(.+?)$/; my $db_name; if ($d eq 'GO') { $self->{queries}{search_dbxref}->execute($a,'%Gene Ontology%' ,'GO'); } elsif ($d eq 'SO') { $self->{queries}{search_dbxref}->execute($a,'Sequence Ontology' ,'SO'); } elsif ($self->cache('ontology',$d)) { $self->{queries}{search_dbxref}->execute($a,$self->cache('ontology',$d), $d ); } my ($dbxref) = $self->{queries}{search_dbxref}->fetchrow_array; warn "couldn't find $term in dbxref for db:". $self->cache('ontology',$d)." ($d)\n" and next unless $dbxref; $self->{queries}{search_cvterm_id_w_dbxref}->execute($dbxref); my ($temp_cvterm) = $self->{queries}{search_cvterm_id_w_dbxref}->fetchrow_array; $self->cache('type',$term, $temp_cvterm); warn "couldn't find $term 's cvterm_id in cvterm table\n" and next unless $temp_cvterm; } unless ($self->{const}{pub}) { my $sth = $self->dbh->prepare("SELECT pub_id FROM pub WHERE miniref = 'null'"); $sth->execute; ($self->{const}{pub}) = $sth->fetchrow_array; } if($self->constraint( name => 'feature_cvterm_c1', terms => [ $self->cache('feature',$uniquename), $self->cache('type',$term) ] ) ){ $self->print_fcv($self->nextoid('feature_cvterm'),$self->cache('feature',$uniquename),$self->cache('type',$term),$self->{const}{pub}); $self->nextoid('feature_cvterm','++'); # $nextfeaturecvterm++; } } } sub handle_source { my $self = shift; my ($feature,$uniquename,$source) = @_; unless ($self->{const}{gff_source_db}) { my $sth = $self->dbh->prepare("SELECT db_id FROM db WHERE name='GFF_source'"); $sth->execute; ($self->{const}{gff_source_db}) = $sth->fetchrow_array; } if ($self->{const}{gff_source_db}) { unless ($self->cache('dbxref',$source)) { #first, check if this source is already in the database $self->{queries}{search_source_dbxref}->execute($source, $self->{const}{gff_source_db}); my ($chado_source) = $self->{queries}{search_source_dbxref}->fetchrow_array; if ($chado_source) { $self->cache('dbxref',$source,$chado_source); } else { $self->cache('dbxref',$source,$self->nextoid('dbxref')); $self->print_dbx($self->nextoid('dbxref'),$self->{const}{gff_source_db},$source,1,'\N'); $self->nextoid('dbxref','++'); #$nextdbxref++; } } my $dbxref_id = $self->cache('dbxref',$source); if($self->constraint( name => 'feature_dbxref_c1', terms=> [ $self->cache('feature',$uniquename), $dbxref_id ] ) ){ $self->print_fdbx($self->nextoid('feature_dbxref'),$self->cache('feature',$uniquename),$dbxref_id); $self->nextoid('feature_dbxref','++'); # $nextfeaturedbxref++; } } else { $self->{const}{source_success} = 0; #geting GFF_source failed, so don't try anymore } } sub handle_unreserved_tags { my $self = shift; my ($feature,$uniquename,@unreserved_tags) = @_; foreach my $tag (@unreserved_tags) { next if $tag eq 'source'; next if $tag eq 'phase'; next if $tag eq 'seq_id'; next if $tag eq 'type'; next if $tag eq 'score'; next if $tag eq 'dbxref'; unless ($self->{const}{fp_cv_id} || $self->{const}{tried_fp_cv}){ $self->fp_cv("autocreated") unless($self->fp_cv()); my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv() ."'"); # dgg: dropped 'autocreated' due to SO/auto conflicts for things like 'gene', 'chromosome' # where SO and autocreated cvs are used primarily for type names in Bio/DB/Das/Chado $sth->execute; ($self->{const}{fp_cv_id}) = $sth->fetchrow_array; if(!$self->{const}{fp_cv_id} && $self->{'addpropertycv'}) { # create cv entry $self->{const}{fp_cv_id}= $self->nextoid('cv'); $self->print_cv( $self->{const}{fp_cv_id}, $self->fp_cv()); $self->nextoid('cv','++'); } $self->{const}{tried_fp_cv} = 1; } # if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) { # my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv ."'"); # $sth->execute; # ($self->{const}{fp_cv_id}) = $sth->fetchrow_array; # $self->{const}{tried_fp_cv} = 1; # } ## problems here with auto-added properties that clash with SO/other cvterms; cache-type? my $property_cvterm_id = $self->cache('property',$tag); # $property_cvterm_id = $self->cache('type',$tag) unless($property_cvterm_id); ## dgg; drop this? unless ( $property_cvterm_id ) { #check fp cv first; ## dgg drop this due to conflicts with SO type: autocreated ## my ($tag_cvterm); # == $property_cvterm_id if ($self->{const}{fp_cv_id}) { $self->{queries}{search_cvterm_id}->execute( $tag, $self->{const}{fp_cv_id}) ; ($property_cvterm_id) = $self->{queries}{search_cvterm_id}->fetchrow_array; } if ($property_cvterm_id) { #good, the term is already there $self->cache('property',$tag,$property_cvterm_id); } else { #bad! the term is not there for now we die with a helpful message ## dgg patch if($self->{'addpropertycv'} && $self->{const}{fp_cv_id}) { $property_cvterm_id= $self->nextoid('cvterm'); # $nextcvterm++; my $dbxid= $self->nextoid('dbxref'); #$nextdbxref++; my $cvid = $self->{const}{fp_cv_id}; my $dbxacc= "autocreated:$tag"; ## bad to use gff_source_db id; use 'null' db unless ($self->{const}{null_db}) { my $sth = $self->dbh->prepare("SELECT db_id FROM db WHERE name='null'"); $sth->execute; ($self->{const}{null_db}) = $sth->fetchrow_array; } $self->print_dbx($dbxid,$self->{const}{null_db},$dbxacc,1,'\N'); $self->nextoid('dbxref','++'); $self->cache('dbxref',$dbxacc,$dbxid); $self->print_cvterm($property_cvterm_id, $cvid, $tag, $dbxid); $self->nextoid('cvterm','++'); $self->cache('property',$tag,$property_cvterm_id); } else { dbxref_error_message($tag) && die; } } } #moving on, add this to the featureprop table my @values = map {$_->value} $feature->annotation->get_Annotations($tag); my $rank=0; foreach my $value (@values) { if ( $self->constraint( name => 'featureprop_c1', terms=> [ $self->cache('feature',$uniquename), $self->cache('property',$tag), $rank ] ) ) { $self->print_fprop($self->nextoid('featureprop'),$self->cache('feature',$uniquename),$property_cvterm_id,$value,$rank); $rank++; $self->nextoid('featureprop','++'); # $nextfeatureprop++; } } } } sub handle_note { my $self = shift; my ($feature,$uniquename) = @_; my @notes = map {$_->value} $feature->annotation->get_Annotations('Note'); my $rank = 0; foreach my $note (@notes) { unless ($self->cache('type','Note')) { my $sth = $self->dbh->prepare( "SELECT cvterm_id FROM cvterm WHERE name='Note' AND cv_id in (SELECT cv_id FROM cv WHERE name='null' OR name='local' OR name='feature_property')"); $sth->execute(); my ($note_type) = $sth->fetchrow_array; if ($note_type) { $self->cache('type','Note',$note_type); } else { $self->throw("I couldn't find the 'Note' cvterm in the database;\nDid you load the feature property controlled vocabulary?"); } } if ( $self->constraint( name => 'featureprop_c1', terms=> [ $self->cache('feature',$uniquename), $self->cache('type','Note'), $rank ] ) ) { $self->print_fprop($self->nextoid('featureprop'),$self->cache('feature',$uniquename),$self->cache('type','Note'),uri_unescape($note),$rank); $rank++; $self->nextoid('featureprop','++'); #$nextfeatureprop++; } } } sub handle_gap { my $self = shift; my ($feature,$uniquename) = @_; my @notes = map {$_->value} $feature->annotation->get_Annotations('Gap'); my $rank = 0; foreach my $note (@notes) { unless ($self->cache('type','Gap')) { my $sth = $self->dbh->prepare( "SELECT cvterm_id FROM cvterm WHERE name='Gap' AND cv_id in (SELECT cv_id FROM cv WHERE name='null' OR name='local' OR name='feature_property')"); $sth->execute(); my ($gap_type) = $sth->fetchrow_array; $self->cache('type','Gap',$gap_type); } if ( $self->constraint( name => 'featureprop_c1', terms=> [ $self->cache('feature',$uniquename), $self->cache('type','Gap'), $rank ] ) ) { $self->print_fprop($self->nextoid('featureprop'),$self->cache('feature',$uniquename),$self->cache('type','Gap') ,uri_unescape($note),$rank); $rank++; $self->nextoid('featureprop','++'); #$nextfeatureprop++; } } } =head2 handle_CDS =over =item Usage $obj->handle_CDS($feature_obj) =item Function This function stores CDS and UTR features in a temporary database table for processing after the entire GFF3 file has be seen. If the feature's parents do not correspond to the central dogma (that is, gene -> transcript -> cds), then the method will return false and the CDS or UTR feature will be inserted as is into the database. =item Returns False if the feature doesn't belong to a central dogma gene, otherwise nothing. =item Arguments A Bio::FeatureIO CDS or UTR object =back =cut sub handle_CDS { my $self = shift; my $feat = shift; my $dbh = $self->dbh; my $organism_id = $self->organism_id; # warn Dumper($feat); my $feat_id = ($feat->annotation->get_Annotations('ID'))[0]->value if ($feat && defined(($feat->annotation->get_Annotations('ID'))[0])); my @feat_parents= map {$_->value} $feat->annotation->get_Annotations('Parent') if ($feat && defined(($feat->annotation->get_Annotations('Parent'))[0])); #assume that an exon can have at most one grandparent (gene, operon) my $first_parent = $feat_parents[0]; my $f_parent_uniquename = $self->modified_uniquename(orig_id=>$first_parent, organism_id => $organism_id) ? $self->modified_uniquename(orig_id=>$first_parent, organism_id => $organism_id) : $first_parent; my $parent_id = $self->cache('feature',$f_parent_uniquename) if $f_parent_uniquename; unless ($parent_id) { warn "\n\nThere is a ".$feat->type->name ." feature with no parent (ID:$feat_id) I think that is wrong!\n\n"; } my $feat_grandparent = $self->cache('parent',$parent_id); return 0 unless $feat_grandparent; unless ($self->cds_db_exists()) { $self->create_cds_db; } my $fmin = $feat->start; #check that this is interbase my $fmax = $feat->end; # my $object = safeFreeze $feat; ## original; dgg; was bad for argos perl lib; had real old FreezeThaw ## dgg this works, and doesnt need a new 3rd party perl module: my $dumper = Data::Dumper->new ([[$feat]]); $dumper->Indent(0)->Terse(1)->Purity(1); my $object = $dumper->Dump; my $feat_type = $feat->type->name; ##$feat_type= $feat_type->value if(ref $feat_type); my $seq_id = $feat->seq_id; ## this is a ref->value !! my $insert = qq/ INSERT INTO tmp_cds_handler (gff_id,seq_id,type,fmin,fmax,object) VALUES (?,?,?,?,?,?) /; my $sth = $dbh->prepare($insert); $sth->execute($feat_id,$seq_id,$feat_type,$fmin,$fmax,$object); #get the value of the row just inserted $sth = $dbh->prepare("SELECT currval('tmp_cds_handler_cds_row_id_seq')"); $sth->execute; my ($cds_row_id) = $sth->fetchrow_array; $sth = $dbh->prepare("INSERT INTO tmp_cds_handler_relationship (cds_row_id,parent_id,grandparent_id) VALUES (?,?,?)"); for my $parent (@feat_parents) { $sth->execute($cds_row_id,$parent,$feat_grandparent); } return 1; } =head2 process_CDS =over =item Usage my $feature_iterator = $obj->process_CDS() =item Function Retrieves CDS and UTR objects from a temporary database table and does necessary conversion to exon and polypeptide features and returns a feature iterator to let the bulk loader process them =item Returns A Bio::GMOD::Adaptor::FeatureIterator object =item Arguments None. =back =cut sub process_CDS { my $self = shift; # $self->dbh->commit && die; return unless $self->cds_db_exists; my $dbh = $self->dbh; #get one of the features from the database(!) # print Dumper($self); # die; my $min_feat_query = "SELECT min(fmax) FROM tmp_cds_handler"; my $sth = $dbh->prepare($min_feat_query); $sth->execute; my ($min_feat) = $sth->fetchrow_array; my $cds_utr_query = qq/ SELECT distinct cds.gff_id,cds.object,cds.type,cds.fmin,cds.fmax, rel.grandparent_id FROM tmp_cds_handler cds, tmp_cds_handler_relationship rel WHERE rel.cds_row_id = cds.cds_row_id AND rel.grandparent_id IN (SELECT grandparent_id FROM tmp_cds_handler_relationship WHERE cds_row_id IN (SELECT cds_row_id FROM tmp_cds_handler WHERE fmax = ?)) ORDER BY cds.fmin,cds.gff_id /; $sth = $dbh->prepare($cds_utr_query); $sth->execute($min_feat); my %polypeptide; my @feature_list; my $grandparent; #do stuff, create a list of features while (my $feat_row = $sth->fetchrow_hashref) { $grandparent = $$feat_row{ grandparent_id }; ## dgg: Data::Dumper works and is easier on user (Data::Dumper part of sys perl lib) ## ##my ($feat_obj)= thaw $$feat_row{ object }; # original my $objs = eval $$feat_row{ object }; if($@) { warn @$; } my $feat_obj = $$objs[0]; my $type = $$feat_row{ type }; my $fmin = $$feat_row{ fmin }; my $fmax = $$feat_row{ fmax }; my @parents = map {$_->value} $feat_obj->annotation->get_Annotations('Parent'); for my $parent_id (@parents) { if ($type =~ /CDS/) { #check for a polypeptide with for this parent if ($polypeptide{ $parent_id }) { #add to it if it exists if ( $polypeptide{ $parent_id }->start > $fmin ) { $polypeptide{ $parent_id }->start($fmin); } if ( $polypeptide{ $parent_id }->end < $fmax ) { $polypeptide{ $parent_id }->end($fmax); } } else { #create it if it doesn't my $polyp = Bio::SeqFeature::Annotated->new(); $polyp->start( $fmin ); $polyp->end( $fmax ); $polyp->strand( $feat_obj->strand ); $polyp->name( $parent_id.' polypeptide'); my $srcval= Bio::Annotation::SimpleValue->new( ref($feat_obj->source) ? $feat_obj->source->value : $feat_obj->source); $polyp->source( $srcval ); my $polyp_ac = Bio::Annotation::Collection->new(); $polyp_ac->add_Annotation( 'source', $srcval); $polyp_ac->add_Annotation( 'Note',Bio::Annotation::SimpleValue->new( 'polypeptide feature inferred from GFF3 feature')); $polyp_ac->add_Annotation( 'Derives_from',Bio::Annotation::SimpleValue->new( $parent_id)); $polyp_ac->add_Annotation( 'type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'polypeptide'))); $polyp_ac->add_Annotation( 'seq_id',Bio::Annotation::SimpleValue->new( $feat_obj->seq_id)); $polyp_ac->add_Annotation( 'phase',Bio::Annotation::SimpleValue->new('.')); $polyp->annotation($polyp_ac); $polypeptide{ $parent_id } = $polyp; } } } #create an exon feature (or add to an existing one) my $merged_exon = 0; for my $exon ( @feature_list ) { next unless ($exon->type->name eq 'exon'); if ($exon->start == $fmax - 1 ) { #this feature imideately precedes an existing exon, glue them together $exon->start($fmin); $exon = $self->_merge_annotations($exon, $feat_obj); $merged_exon = 1; } if ($exon->end == $fmin -1 ) { #this feature come right after an existing exon, glue them together $exon->end($fmax); $exon = $self->_merge_annotations($exon, $feat_obj); $merged_exon = 1; } } # if ($merged_exon) { # print Dumper($_) for @feature_list; # } unless ($merged_exon) { #convert the existing feature to an exon my $ac = $feat_obj->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'exon'))); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon inferred from GFF3 ' . $feat_obj->type->name . ' feature line')); $feat_obj->annotation($ac); push @feature_list, $feat_obj; } } #add the polypeptides to the list if ($self->noexon) { #only return the polpeptides if noexon is set @feature_list = values %polypeptide; } else { push @feature_list, values %polypeptide; } #delete the features from the temp tables: my $delete_query = qq/DELETE FROM tmp_cds_handler WHERE cds_row_id IN (SELECT cds_row_id FROM tmp_cds_handler_relationship WHERE grandparent_id =?) /; $sth = $dbh->prepare($delete_query); $sth->execute($grandparent); $dbh->commit; #return an iterator if (@feature_list > 0) { return Bio::GMOD::DB::Adapter::FeatureIterator->new(\@feature_list); } else { return 0; } } =head2 _merge_annotations =over =item Usage $obj->_merge_annotations() =item Function Take two adjecent feature objects and merge their annotations =item Returns The merged feature object (which will be an exon feature) =item Arguments Two feature objects, with the existing exon first =back =cut sub _merge_annotations { my ($self, $exon, $obj2) = @_; my $exon_ac = $exon->annotation; my $obj2_ac = $obj2->annotation; for my $key ( $obj2_ac->get_all_annotation_keys() ) { my @values = $obj2_ac->get_Annotations($key); if ($key eq 'type') { $exon_ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'exon feature the result of two merged features in GFF3, one '. 'of which was a '.$obj2->type->name.' feature')); } elsif ( $key eq 'source' or $key eq 'Parent' or $key eq 'seq_id' or $key eq 'phase' or $key eq 'score' ) { next; } else { for my $value ( @values ) { $exon_ac->add_Annotation($key,$value); } } } $exon->annotation($exon_ac); return $exon; } =pod my $iterator; #so its time to process the most recent set of features and return an iterator if (($feat_id && $self->{cdscache}{id} && $feat_id ne $self->{cdscache}{id}) or ($feat_parent && $self->{cdscache}{parent} && $feat_parent ne $self->{cdscache}{parent}) or (!$self->{cdscache}{id} && !$self->{cdscache}{parent}) ) { #this is a new cds feature so package up the old one to give back if ($self->noexon) { $iterator = Bio::GMOD::DB::Adapter::FeatureIterator->new( $self->{cdscache}{polypeptide_obj} ); } elsif ($self->{cdscache}{polypeptide_obj}) { push @{ $self->{cdscache}{feature_array} }, $self->{cdscache}{polypeptide_obj}; $iterator = Bio::GMOD::DB::Adapter::FeatureIterator->new( \@{ $self->{cdscache}{feature_array} } ); } #now empty the caches and set parent/id $self->{cdscache}{feature_array} = (); $self->{cdscache}{polypeptide_obj} = ''; $self->{cdscache}{id} = $feat_id; $self->{cdscache}{parent} = $feat_parent; } #get the current AnnotationCollection and change # that is, convert CDS features to exon features if ($feat && !$self->noexon) { #check for existing created exons that but up against this feature my $start = $feat->start; my $stop = $feat->end; my $appended_feature_flag = 0; for my $cached_feat ( @{ $self->{cdscache}{feature_array} } ) { if ($stop + 1 == $cached_feat->start) { my $cached_ac = $cached_feat->annotation(); my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon added to from an adjacent feature in GFF3')); my @annot_list = $ac->get_Annotations; for my $annot (@annot_list) { $cached_ac->add_Annotation($annot); } $cached_feat->start($start); $appended_feature_flag = 1; } elsif ( $start == $cached_feat->end + 1 ) { my $cached_ac = $cached_feat->annotation(); my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon added to from an adjacent feature in GFF3')); my @annot_list = $ac->get_Annotations; for my $annot (@annot_list) { $cached_ac->add_Annotation($annot); } $cached_feat->end($stop); $appended_feature_flag = 1; } } unless ( $appended_feature_flag ) { my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'exon'))); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon inferred from GFF3 ' . $feat->type->name . ' feature line')); $feat->annotation($ac); } } if ($feat && !$self->{cdscache}{polypeptide_obj}) { #polypeptide doesn't exist yet, so create it my $polyp = Bio::SeqFeature::Annotated->new(); $polyp->start( $feat->start ); $polyp->end( $feat->end ); $polyp->strand( $feat->strand ); $polyp->name( $feat_parent.' polypeptide'); my $polyp_ac = Bio::Annotation::Collection->new(); $polyp_ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'polypeptide feature inferred from GFF3 CDS feature')); $polyp_ac->add_Annotation('Derives_from',Bio::Annotation::SimpleValue->new( $feat_parent)); $polyp_ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'polypeptide'))); $polyp_ac->add_Annotation('seq_id',Bio::Annotation::SimpleValue->new( $feat->seq_id)); $polyp->annotation($polyp_ac); $self->{cdscache}{polypeptide_obj} = $polyp; } #check for bounds change on the existing polypeptide elsif ( $feat && $self->{cdscache}{polypeptide_obj}->start > $feat->start && $feat->type->name =~ /CDS/ ) { $self->{cdscache}{polypeptide_obj}->start($feat->start); } elsif ( $feat && $self->{cdscache}{polypeptide_obj}->end < $feat->end && $feat->type->name =~ /CDS/ ) { $self->{cdscache}{polypeptide_obj}->end($feat->end); } push @{ $self->{cdscache}{feature_array} }, $feat if $feat; return $iterator; } =cut sub handle_parent { my $self = shift; my ($feature) = @_; my $organism_id = $self->organism_id; for my $p_anot ( $feature->annotation->get_Annotations('Parent') ) { my $orig_pname = $p_anot->value; my $pname = $self->modified_uniquename(orig_id => $orig_pname, organism_id => $organism_id) ? $self->modified_uniquename(orig_id => $orig_pname, organism_id => $organism_id) : $orig_pname; my $parent = $self->cache('feature',$pname); if (!$parent and $self->allow_external_parent() ) { #the uniquename_cache method returns the feature_id when called with "validate" $parent = $self->uniquename_cache( validate => 1, organism_id => $organism_id, uniquename => $pname); } confess "\nno parent $orig_pname ($pname);\nyou probably need to rerun the loader with the --recreate_cache option\n\n" unless $parent; $self->cache('parent',$self->nextfeature,$parent); $self->print_frel($self->nextoid('feature_relationship'),$self->nextfeature,$parent,$part_of); $self->nextoid('feature_relationship','++'); # $nextfeaturerel++; } } sub handle_derives_from { my $self = shift; my ($feature) = @_; my $organism_id = $self->organism_id; for my $p_anot ( $feature->annotation->get_Annotations('Derives_from') ) { my $orig_pname = $p_anot->value; my $pname = $self->modified_uniquename(orig_id => $orig_pname, organism_id => $organism_id) ? $self->modified_uniquename(orig_id => $orig_pname, organism_id => $organism_id) : $orig_pname; my $parent = $self->cache('feature',$pname); confess "no parent ".$orig_pname unless $parent; $self->cache('parent',$self->nextfeature,$parent); $self->print_frel($self->nextoid('feature_relationship'),$self->nextfeature,$parent,$derives_from); $self->nextoid('feature_relationship','++'); #$nextfeaturerel++; } } sub handle_crud { my $self = shift; my $feature = shift; my $force_delete = shift; my ($op) = $feature->annotation->get_Annotations('CRUD'); $op = $op->value if defined($op); if ($force_delete) { $op = 'delete-all'; } my ($name) = $feature->annotation->get_Annotations('Name'); if (!defined($name)) { #try to get the name from the ID ($name) = $feature->annotation->get_Annotations('ID'); if (!defined($name)) { #if it doesn't have a name, don't do anything return 1; } } $name = $name->value if ref($name); my $type = ref($feature->type) ? $feature->type->name : $feature->type; if ($op =~ /delete/) { #determine if a single feature corresponds to what is in the gff line #it is considered to be the same if the type, name (or synonym) #and organism are the same #this sql should be moved to the prepared sql hash after debugging is done my $sql = "SELECT feature_id FROM feature WHERE name = ? and type_id = ? and organism_id = ?"; my $delete_query_handle = $self->dbh->prepare($sql); $delete_query_handle->execute($name, $self->get_type($type), $self->organism_id); my $feature_id_arrayref = $delete_query_handle->fetchall_arrayref; my $feature_id; if (scalar @{$feature_id_arrayref} > 1 and $op ne 'delete-all') { $self->throw("I can't figure out which feature to delete that corresponds to a feature with a name of $name, a type of $type and organism of ".$self->organism.". More than one feature match these criteria"); } elsif (scalar @{$feature_id_arrayref} > 1) { warn "Deleting all features with name $name, type $type and organism ".$self->organism."\n"; for my $id_row (@{$feature_id_arrayref}) { my $feature_id = $$id_row[0]; $self->print_delete($$id_row[0]) if $feature_id; } return 1; } elsif (scalar @{$feature_id_arrayref} == 0) { warn "Couldn't fined a matching feature with name $name, type $type and organism ".$self->organism."\n"; return 1; # warn("Searching for a feature with the name $name to delete yielded nothing; checking synonyms..."); # $sql = "SELECT f.feature_id # FROM feature f, feature_synonym fs, synonym s # WHERE s.name = ? and # s.synonym_id = fs.synonym_id and # fs.feature_id = f.feature_id and # f.type_id = ? and f.organism_id = ?"; # my $delete_by_syn_query_handle = $self->dbh->prepare($sql); # $delete_by_syn_query_handle->execute($name, # $self->get_type($type), # $self->organism_id); # $feature_id_arrayref = $delete_by_syn_query_handle->fetchall_arrayref; # if (scalar @{$feature_id_arrayref} > 1) { # $self->throw("I couldn't figure out which feature to delete when searching by synonym $name; I found more than one matching feature"); # } # elsif (scalar @{$feature_id_arrayref} == 0) { # $self->throw("I couldn't find a matching feature using either feature.name or synonym.name of $name and a type of $type and organism of ".$self->organism.". I can't go on... Bye."); # } # else { # ($feature_id) = $$feature_id_arrayref[0]; # } } else { $feature_id = $$feature_id_arrayref[0][0]; } $self->print_delete($feature_id); return 1; } elsif ($op eq 'replace' or $op eq 'update') { $self->throw("The CRUD operation $op is not supported yet"); } elsif ($op eq 'create') { return 0; #nothing to do--create is the default } else { $self->throw("I don't know what to do for the CRUD operation $op"); } } sub src_second_chance { my $self = shift; my ($feature) = @_; my $organism_id = $self->organism_id; my $src; if($feature->seq_id eq '.'){ $src = '\N'; } else { #check to see if the uniquename had to be changed my $src_uniquename = $self->modified_uniquename(orig_id => $feature->seq_id, organism_id => $organism_id) ? $self->modified_uniquename(orig_id => $feature->seq_id, organism_id => $organism_id) : $feature->seq_id; my ($temp_f_id)= $self->uniquename_cache( validate => 1, uniquename => $src_uniquename ); $self->cache('feature',$src_uniquename,$temp_f_id); unless ($temp_f_id) { $self->{queries}{count_name}->execute($src_uniquename); my ($n_rows) = $self->{queries}{count_name}->fetchrow_array; if (1 < $n_rows) { $self->throw( "more that one source for ".$src_uniquename ); } elsif ( 1==$n_rows) { $self->{queries}{search_name}->execute($src_uniquename); my ($tmp_source) = $self->{queries}{search_name}->fetchrow_array; $self->cache('feature',$src_uniquename,$tmp_source); } else { confess "Unable to find srcfeature " .$feature->seq_id ." in the database.\nPerhaps you need to rerun your data load with the '--recreate_cache' option."; } } $src = $self->cache('feature',$src_uniquename); } return $src; } sub get_type { my $self = shift; my ($featuretype) = @_; return $self->cache('type',$featuretype) if defined $self->cache('type',$featuretype); $self->{queries}{search_cvterm_id}->execute($featuretype, $sofa_id); my ($tmp_type) = $self->{queries}{search_cvterm_id}->fetchrow_array; $self->cache('type',$featuretype,$tmp_type); return $tmp_type if defined $tmp_type; $self->throw( "no cvterm for ".$featuretype ); } sub get_src_seqlen { my $self = shift; my ($feature) = @_; my $organism_id = $self->organism_id; my ($src,$seqlen); if ( defined(($feature->annotation->get_Annotations('ID'))[0]) && $feature->seq_id eq ($feature->annotation->get_Annotations('ID'))[0]->value ) { #this is a srcfeature (ie, a reference sequence) $src = $self->nextfeature; $seqlen = $feature->end - $feature->start +1; $self->cache('feature',$feature->seq_id,$src); $self->cache('srcfeature',$src,1); } else { # normal case my $src_uniquename = $self->modified_uniquename(orig_id=>$feature->seq_id, organism_id => $organism_id) ? $self->modified_uniquename(orig_id=>$feature->seq_id, organism_id => $organism_id) : $feature->seq_id; $src = $self->uniquename_cache( validate => 1, organism_id => $organism_id, uniquename => $src_uniquename ); # $src = $self->cache('feature',$feature->seq_id); $seqlen = '\N'; } return ($src,$seqlen); } sub flush_caches { my $self = shift; $self->{cache} = ''; $self->{uniquename_cache} = ''; return; } ######################################################################### # # Methods that are to be used with the GFF3 preprocessor. It makes # use of the chado database to make a temp table that it uses to sort # content of the GFF file # sub sorter_create_table { my $self = shift; my $dbh = $self->dbh; #determine if the table already exists my $sth = $dbh->prepare("SELECT count(*) FROM pg_tables WHERE tablename='gff_sort_tmp'"); $sth->execute; my ($table_exists) = $sth->fetchrow_array; return if $table_exists; $dbh->do("CREATE TABLE gff_sort_tmp ( refseq varchar(4000), id varchar(4000), parent varchar(4000), gffline varchar(8000), row_id serial not null, primary key(row_id) ) "); $dbh->do("CREATE INDEX gff_sort_tmp_idx1 ON gff_sort_tmp (refseq)"); $dbh->do("CREATE INDEX gff_sort_tmp_idx2 ON gff_sort_tmp (id)"); $dbh->do("CREATE INDEX gff_sort_tmp_idx3 ON gff_sort_tmp (parent)"); return; } sub sorter_vacuum_table { my $self = shift; my $dbh = $self->dbh; $dbh->do("vacuum gff_sort_tmp"); return; } sub sorter_delete_from_table { my $self = shift; my $dbh = $self->dbh; $dbh->do("DELETE FROM gff_sort_tmp"); return; } sub sorter_insert_line { my $self = shift; my ($refseq, $id, $parent, $line) = @_; $self->{'queries'}{'insert_gff_sort_tmp'}->execute( $refseq, $id, $parent, $line) or die "Inserting into the sort table failed:$!,\nProbably due to this line: $line\n"; return; } sub sorter_get_refseqs { my $self = shift; my $dbh = $self->dbh; my $sth = $dbh->prepare("SELECT distinct gffline FROM gff_sort_tmp WHERE refseq = id") or $self->throw(); $sth->execute or $self->throw(); my $result = $sth->fetchall_arrayref or $self->throw(); my @to_return = map { $$_[0] } @$result; return @to_return; } sub sorter_get_no_parents { my $self = shift; my $dbh = $self->dbh; my $sth = $dbh->prepare("SELECT distinct gffline FROM gff_sort_tmp WHERE id is null and parent is null") or $self->throw(); $sth->execute or $self->throw(); my $result = $sth->fetchall_arrayref or $self->throw(); my @to_return = map { $$_[0] } @$result; $sth = $dbh->prepare("SELECT distinct gffline,id FROM gff_sort_tmp WHERE parent is null and refseq != id order by id") or $self->throw(); $sth->execute or $self->throw(); $result = $sth->fetchall_arrayref or $self->throw(); push @to_return, map { $$_[0] } @$result; my %seen = (); my @uniq; for my $item (@to_return) { push(@uniq, $item) unless $seen{$item}++; } return @uniq; } sub sorter_get_second_tier { my $self = shift; my $dbh = $self->dbh; #ARGH! need to deal with multiple parents! my $sth = $dbh->prepare("SELECT distinct gffline,parent,id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent is null) order by parent,id") or $self->throw(); $sth->execute or $self->throw(); my $result = $sth->fetchall_arrayref or $self->throw(); my %seen; my @to_return = grep { ! $seen{$_}++ } map { $$_[0] } @$result; %seen = (); my @uniq; for my $item (@to_return) { push(@uniq, $item) unless $seen{$item}++; } return @uniq; } sub sorter_get_third_tier { my $self = shift; my $dbh = $self->dbh; #ARGH! need to deal with multiple parents! my $sth = $dbh->prepare("SELECT distinct gffline,parent,id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent is null)) order by parent,id ") or $self->throw(); $sth->execute or $self->throw(); my $result = $sth->fetchall_arrayref or $self->throw(); my %seen; my @to_return = grep { ! $seen{$_}++ } map { $$_[0] } @$result; %seen = (); my @uniq; for my $item (@to_return) { push(@uniq, $item) unless $seen{$item}++; } return @uniq; } sub sorter_get_fourth_tier { my $self = shift; my $dbh = $self->dbh; #ARGH! need to deal with multiple parents! my $sth = $dbh->prepare("SELECT distinct gffline,parent,id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent in (SELECT id FROM gff_sort_tmp WHERE parent is null))) order by parent,id ") or $self->throw(); $sth->execute or $self->throw(); my $result = $sth->fetchall_arrayref or $self->throw(); my %seen; my @to_return = grep { ! $seen{$_}++ } map { $$_[0] } @$result; %seen = (); my @uniq; for my $item (@to_return) { push(@uniq, $item) unless $seen{$item}++; } return @uniq; } =head2 cds_db_exists =over =item Usage $obj->cds_db_exists() #get existing value $obj->cds_db_exists($newval) #set new value =item Function Flag for determining if the cds temp database exists =item Returns value of cds_db_exists (a scalar) =item Arguments new value of cds_db_exists (to set) =back =cut sub cds_db_exists { my $self = shift; my $cds_db_exists = shift if defined(@_); return $self->{'cds_db_exists'} = $cds_db_exists if defined($cds_db_exists); return $self->{'cds_db_exists'}; } =head2 create_cds_db =over =item Usage $obj->create_cds_db() =item Function Create the temp database table for dealing with CDS and UTR features =item Returns Nothing =item Arguments None =back =cut sub create_cds_db { my $self = shift; my $dbh = $self->dbh; #determine if the table exists and drop if it does my $exists_query = "SELECT tablename FROM pg_tables WHERE tablename = 'tmp_cds_handler'"; my $sth = $dbh->prepare($exists_query); $sth->execute(); my ($exists) = $sth->fetchrow_array; if ($exists) { warn "Dropping cds temp tables...\n"; $dbh->do("DROP INDEX tmp_cds_handler_seq_id"); $dbh->do("DROP INDEX tmp_cds_handler_fmax"); $dbh->do("DROP INDEX tmp_cds_handler_relationship_grandparent"); $dbh->do("DROP TABLE tmp_cds_handler_relationship"); $dbh->do("DROP TABLE tmp_cds_handler"); $dbh->commit(); } #create the table warn "Creating cds temp tables...\n"; my $table_create = qq/ CREATE TABLE tmp_cds_handler ( cds_row_id serial not null, seq_id varchar(1024), gff_id varchar(1024), type varchar(1024) not null, fmin int not null, fmax int not null, object text not null, primary key(cds_row_id) ) /; $dbh->do($table_create); $dbh->do("CREATE INDEX tmp_cds_handler_seq_id ON tmp_cds_handler (seq_id)"); $dbh->do("CREATE INDEX tmp_cds_handler_fmax ON tmp_cds_handler (fmax)"); $dbh->commit; $table_create = qq/ CREATE TABLE tmp_cds_handler_relationship ( rel_row_id serial not null, cds_row_id int, foreign key (cds_row_id) references tmp_cds_handler (cds_row_id) on delete cascade, parent_id varchar(1024), grandparent_id varchar(1024), primary key(rel_row_id) ) /; $dbh->do($table_create); $dbh->do("CREATE INDEX tmp_cds_handler_relationship_grandparent ON tmp_cds_handler_relationship(grandparent_id)"); $dbh->commit; $self->cds_db_exists(1); return; } 1; chado-1.23/lib/Bio/GMOD/DB/Config.pm000644 000765 000024 00000016466 11665754065 016663 0ustar00cainstaff000000 000000 package Bio::GMOD::DB::Config; use strict; =head1 NAME Bio::GMOD::Config::DB -- a GMOD utility package for reading db config files =head1 SYNOPSIS $ export GMOD_ROOT=/usr/local/gmod my $conf = Bio::GMOD::Config->new(); my $tmpdir = $conf->tmp(); my $confdir = $conf->conf(); #assume there is a file 'chado.conf' with database connetion info my $dbconf = Bio::GMOD::DB::Config->new($conf, 'chado'); my $dbusername = $dbconf->user(); my $dbhostname = $dbconf->port(); # ...etc... =head1 DESCRIPTION Bio::GMOD::DB::Config is a module to allow programmatic access to the database configuration files in GMOD_ROOT/conf. =head1 METHODS =cut use DBI; use File::Spec::Functions qw/ catdir catfile /; use vars '@ISA'; use base qw/ Bio::GMOD::Config /; my $VERSION = 1.23; =head2 new Title : new Usage : my $config = Bio::GMOD::DB::Config->new($conf, 'dbname'); Function: create new Bio::GMOD::DB::Config object Returns : new Bio::GMOD::DB::Config Args : Bio::GMOD::Config object, db config name Status : Public Returns a Bio::GMOD::DB::Config object. If no db config name argument is specified, the configuration file called 'default.conf' will be used. =cut sub new { my $self = shift; my $conf = shift; my $dbname = shift; $dbname ||= 'default'; my $confdir = $conf->confdir; #get from Bio::GMOD::Config my $conffile= catfile($confdir, "$dbname.conf"); my %dbconf; open CONF, $conffile or die "Couldn't open $conffile: $!"; while () { next if /^\#/; if (/(\w+)\s*=\s*(\S.*)/) { $dbconf{$1}=$2; } } close CONF; return bless {conf => \%dbconf}, $self; } =head2 user Title : user Usage : $username = $dbconf->user(); Function: return the value the database username Returns : see above Args : none Status : Public =cut sub user { shift->get_tag_value('DBUSER'); } =head2 password Title : password Usage : $password = $dbconf->password(); Function: return the value the database password Returns : see above Args : none Status : Public =cut sub password { shift->get_tag_value('DBPASS'); } =head2 host Title : host Usage : $host = $dbconf->host(); Function: return the value the database host name Returns : see above Args : none Status : Public =cut sub host { shift->get_tag_value('DBHOST'); } =head2 port Title : port Usage : $port = $dbconf->port(); Function: return the value the database port Returns : see above Args : none Status : Public =cut sub port { shift->get_tag_value('DBPORT'); } =head2 driver Title : driver Usage : $driver = $dbconf->driver(); Function: return the value the database driver Returns : see above Args : none Status : Public =cut sub driver { shift->get_tag_value('DBDRIVER'); } =head2 name Title : name Usage : $dbname = $dbconf->name(); Function: return the value the database name Returns : see above Args : none Status : Public =cut sub name { shift->get_tag_value('DBNAME'); } =head2 sqlfile Title : sqlfile Usage : $sqlfile = $dbconf->sqlfile(); Function: returns the path of the sqlfile (ie, ddl file) the defines the schema Returns : see above Args : none Status : Public =cut sub sqlfile { shift->get_tag_value('SQLFILE'); } =head2 schema Title : schema Usage : $schema = $dbconf->schema(); Function: Returns the schema chado resides in (usually public) Returns : see above Args : none Status : Public =cut sub schema { shift->get_tag_value('SCHEMA'); } =head2 organism Title : organism Usage : $organism = $dbconf->organism(); Function: Returns the common name of the "default" organism of the database, if there is one Returns : A species common name, or undef Args : none Status : Public =cut sub organism { my $self = shift; my $org = $self->get_tag_value('DBORGANISM'); return $org if $org; return undef; } =head2 dbh Title : dbh Usage : $dbh = $dbconf->dbh(); Function: return a database handle Returns : see above Args : none Status : Public =cut sub dbh { my $self = shift; my $dsn = $self->dsn; my $dbh = DBI->connect( $dsn, $self->user(), $self->password() ) or die "couldn't create db connection:$!"; #this should throw--maybe I should inherit from Bio::Root return $dbh; } =head2 dsn Title : dsn Usage : $dsn = $dbconf->dsn(); Function: return a database connection string Returns : see above Args : none Status : Public =cut sub dsn { my $self = shift; my $dsn = "dbi:Pg:dbname=".$self->name(); $dsn .= ";host=".$self->host() if $self->host(); $dsn .= ";port=".$self->port() if $self->port(); return $dsn; } 1; =head1 AUTHOR Scott Cain Ecain@cshl.orgE. Copyright (c) 2004 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut chado-1.23/lib/Bio/GMOD/DB/Tools/000755 000765 000024 00000000000 12061672375 016175 5ustar00cainstaff000000 000000 chado-1.23/lib/Bio/GMOD/DB/Tools/ETA.pm000644 000765 000024 00000004354 11256707757 017162 0ustar00cainstaff000000 000000 package Bio::GMOD::DB::Tools::ETA; $|=1; #does this help? =head1 Bio::GMOD::DB::Tools::ETA A nice little package for displaying the ETA for a process in a terminal =head1 USAGE my $eta = Bio::GMOD::DB::Tools::ETA->new(); $eta->interval(1.2) #only allow updates 1.2 seconds after the last update my $i=0; $eta->begin(); #sets start time $eta->target(3000); #total # of iterations expected while($row = ...){ #doing stuff #whoop-de-do $i++; $eta->update_and_print($i); } #Prints something like: #ETA: 01:33:34 Don't print any newlines if you want the ETA to be displayed in-place! =cut sub new { my $class = shift; my $self = bless {}, $class; $self->{increment} = 1; $self->{begin} = time(); $self->{last_update} = time(); $self->{current} = 0; $self->{interval} = 0; return $self; } sub begin { my $self = shift; $self->{begin} = time(); } sub target { my $self = shift; my $target = shift; $self->{target} = $target if $target; return $self->{target}; } sub interval { my $self = shift; my $interval = shift; $self->{interval} = $interval if $interval; return $self->{interval}; } sub update { my $self = shift; my $current = shift; if($self->{interval} > 0){ $diff = time() - $self->{last_update}; return if $diff < $self->{interval}; } $self->{current} = $current; $self->{elapsed} = time() - $self->{begin}; $self->{elapsed} ||= 1; #round up to 1 second, at least $self->{remaining} = $self->{target} - $self->{current}; $self->{rate} = ($self->{current})/$self->{elapsed}; $self->{eta} = $self->{remaining}/$self->{rate}; $self->{last_update} = time(); } sub update_and_print { my $self = shift; if($self->{interval} > 0) { $diff = time() - $self->{last_update}; return if $diff < $self->{interval}; } $self->update( shift ); $self->print(); } sub print { my $self = shift; print ( " " x 80 . "\r" x 200 ); print "ETA: " . $self->format_secs($self->{eta}); } sub format_secs { my $self = shift; my $sec = int( shift ); my $hour = 0; my $min = 0; if($sec > 60){ $min = int($sec / 60); $sec = $sec - $min*60; if($min > 60){ $hour = int($min / 60); $min = $min - $hour*60; } } foreach($sec, $hour, $min){ next unless $_<10; $_ = "0" . $_; } return "$hour:$min:$sec"; } 1; chado-1.23/lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm000644 000765 000024 00000001727 11256707757 022137 0ustar00cainstaff000000 000000 package Bio::GMOD::DB::Adapter::FeatureIterator; =pod =head1 NAME Bio::GMOD::DB::Adaptor::FeatureIterator =head1 SYNOPSYS my $iterator = Bio::GMOD::DB::Adaptor::FeatureIterator->new(\@features); while (my $feat = $iterator->next_feature() ) { #do stuff with the feature } =head1 DESCRIPTION This is a very simple feature iterator with only two methods: new and next_feature. To use it, you pass in a reference to an array of Bio::SeqFeatureI compliant feature objects, and subsequent invocations of next_feature on the iterator object will give back one feature object until there are no feature objects, when it will return nothing. =head1 AUTHOR =head1 AUTHOR - Scott Cain Email cain@cshl.org =cut sub new { my $package = shift; my $features = ref $_[0] eq 'ARRAY' ? shift : [@_]; return bless $features,$package; } sub next_feature { my $self = shift; return unless @$self; my $next_feature = shift @$self; return $next_feature; } 1; chado-1.23/lib/Bio/GMOD/DB/Adapter/Wormbase.pm000644 000765 000024 00000061272 11256707757 020612 0ustar00cainstaff000000 000000 package Bio::GMOD::DB::Adapter::Wormbase; use base 'Bio::GMOD::DB::Adapter'; sub new { my $class = shift; my %arg = @_; my $self = $class->SUPER::new(%arg); return $self; } sub handle_unreserved_tags { my $self = shift; my ($feature,$uniquename,@unreserved_tags) = @_; foreach my $tag (@unreserved_tags) { next if $tag eq 'source'; next if $tag eq 'phase'; next if $tag eq 'seq_id'; next if $tag eq 'type'; next if $tag eq 'score'; next if $tag eq 'dbxref'; unless ($self->{const}{fp_cv_id} || $self->{const}{tried_fp_cv}){ $self->fp_cv("autocreated") unless($self->fp_cv()); my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv() ."'"); # dgg: dropped 'autocreated' due to SO/auto conflicts for things like 'gene', 'chromosome' # where SO and autocreated cvs are used primarily for type names in Bio/DB/Das/Chado $sth->execute; ($self->{const}{fp_cv_id}) = $sth->fetchrow_array; if(!$self->{const}{fp_cv_id} && $self->{'addpropertycv'}) { # create cv entry $self->{const}{fp_cv_id}= $self->nextoid('cv'); $self->print_cv( $self->{const}{fp_cv_id}, $self->fp_cv()); $self->nextoid('cv','++'); } $self->{const}{tried_fp_cv} = 1; } # if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) { # my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv ."'"); # $sth->execute; # ($self->{const}{fp_cv_id}) = $sth->fetchrow_array; # $self->{const}{tried_fp_cv} = 1; # } ## problems here with auto-added properties that clash with SO/other cvterms; cache-type? my $property_cvterm_id = $self->cache('property',$tag); # $property_cvterm_id = $self->cache('type',$tag) unless($property_cvterm_id); ## dgg; drop this? unless ( $property_cvterm_id ) { #check fp cv first; ## dgg drop this due to conflicts with SO type: autocreated ## my ($tag_cvterm); # == $property_cvterm_id if ($self->{const}{fp_cv_id}) { $self->{queries}{search_cvterm_id}->execute( $tag, $self->{const}{fp_cv_id}) ; ($property_cvterm_id) = $self->{queries}{search_cvterm_id}->fetchrow_array; } if ($property_cvterm_id) { #good, the term is already there $self->cache('property',$tag,$property_cvterm_id); } else { #bad! the term is not there for now we die with a helpful message ## dgg patch if($self->{'addpropertycv'} && $self->{const}{fp_cv_id}) { $property_cvterm_id= $self->nextoid('cvterm'); # $nextcvterm++; my $dbxid= $self->nextoid('dbxref'); #$nextdbxref++; my $cvid = $self->{const}{fp_cv_id}; my $dbxacc= "autocreated:$tag"; ## bad to use gff_source_db id; use 'null' db unless ($self->{const}{null_db}) { my $sth = $self->dbh->prepare("SELECT db_id FROM db WHERE name='null'"); $sth->execute; ($self->{const}{null_db}) = $sth->fetchrow_array; } $self->print_dbx($dbxid,$self->{const}{null_db},$dbxacc,1,'\N'); $self->nextoid('dbxref','++'); $self->cache('dbxref',$dbxacc,$dbxid); $self->print_cvterm($property_cvterm_id, $cvid, $tag, $dbxid); $self->nextoid('cvterm','++'); $self->cache('property',$tag,$property_cvterm_id); } else { dbxref_error_message($tag) && die; } } } #moving on, add this to the featureprop table my @values = map {$_->value} $feature->annotation->get_Annotations($tag); my $rank=0; foreach my $value (@values) { if ( $self->constraint( name => 'featureprop_c1', terms=> [ $self->cache('feature',$uniquename), $self->cache('property',$tag), $rank ] ) ) { $self->print_fprop($self->nextoid('featureprop'),$self->cache('feature',$uniquename),$property_cvterm_id,$value,$rank); $rank++; $self->nextoid('featureprop','++'); # $nextfeatureprop++; } } } } =head2 handle_CDS =over =item Usage $obj->handle_CDS($feature_obj) =item Function This function stores CDS and UTR features in a temporary database table for processing after the entire GFF3 file has be seen. If the feature's parents do not correspond to the central dogma (that is, gene -> transcript -> cds), then the method will return false and the CDS or UTR feature will be inserted as is into the database. =item Returns False if the feature doesn't belong to a central dogma gene, otherwise nothing. =item Arguments A Bio::FeatureIO CDS or UTR object =back =cut sub handle_CDS { my $self = shift; my $feat = shift; my $dbh = $self->dbh; # warn Dumper($feat); my $feat_id = ($feat->annotation->get_Annotations('ID'))[0]->value if ($feat && defined(($feat->annotation->get_Annotations('ID'))[0])); my @feat_parents= map {$_->value} $feat->annotation->get_Annotations('Parent') if ($feat && defined(($feat->annotation->get_Annotations('Parent'))[0])); #assume that an exon can have at most one grandparent (gene, operon) my $parent_id = $self->cache('feature',$feat_parents[0]) if $feat_parents[0]; unless ($parent_id) { warn "\n\nThere is a ".$feat->type->name." feature with no parent (ID:$feat_id) I think that is wrong!\n\n"; } my $feat_grandparent = $self->cache('parent',$parent_id); return 0 unless $feat_grandparent; unless ($self->cds_db_exists()) { $self->create_cds_db; } my $fmin = $feat->start; #check that this is interbase my $fmax = $feat->end; # my $object = safeFreeze $feat; ## original; dgg; was bad for argos perl lib; had real old FreezeThaw ## dgg this works, and doesnt need a new 3rd party perl module: my $dumper = Data::Dumper->new ([[$feat]]); $dumper->Indent(0)->Terse(1)->Purity(1); my $object = $dumper->Dump; my $feat_type = $feat->type->name; ##$feat_type= $feat_type->value if(ref $feat_type); my $seq_id = $feat->seq_id; ## this is a ref->value !! my $insert = qq/ INSERT INTO tmp_cds_handler (gff_id,seq_id,type,fmin,fmax,object) VALUES (?,?,?,?,?,?) /; my $sth = $dbh->prepare($insert); $sth->execute($feat_id,$seq_id,$feat_type,$fmin,$fmax,$object); #get the value of the row just inserted $sth = $dbh->prepare("SELECT currval('tmp_cds_handler_cds_row_id_seq')"); $sth->execute; my ($cds_row_id) = $sth->fetchrow_array; $sth = $dbh->prepare("INSERT INTO tmp_cds_handler_relationship (cds_row_id,parent_id,grandparent_id) VALUES (?,?,?)"); for my $parent (@feat_parents) { $sth->execute($cds_row_id,$parent,$feat_grandparent); } return 1; } =head2 process_CDS =over =item Usage my $feature_iterator = $obj->process_CDS() =item Function Retrieves CDS and UTR objects from a temporary database table and does necessary conversion to exon and polypeptide features and returns a feature iterator to let the bulk loader process them =item Returns A Bio::GMOD::Adaptor::FeatureIterator object =item Arguments None. =back =cut sub process_CDS { my $self = shift; # $self->dbh->commit && die; return unless $self->cds_db_exists; my $dbh = $self->dbh; #get one of the features from the database(!) # print Dumper($self); # die; my $min_feat_query = "SELECT min(fmax) FROM tmp_cds_handler"; my $sth = $dbh->prepare($min_feat_query); $sth->execute; my ($min_feat) = $sth->fetchrow_array; my $cds_utr_query = qq/ SELECT distinct cds.gff_id,cds.object,cds.type,cds.fmin,cds.fmax, rel.grandparent_id FROM tmp_cds_handler cds, tmp_cds_handler_relationship rel WHERE rel.cds_row_id = cds.cds_row_id AND rel.grandparent_id IN (SELECT grandparent_id FROM tmp_cds_handler_relationship WHERE cds_row_id IN (SELECT cds_row_id FROM tmp_cds_handler WHERE fmax = ?)) ORDER BY cds.fmin,cds.gff_id /; $sth = $dbh->prepare($cds_utr_query); $sth->execute($min_feat); my %polypeptide; my @feature_list; my $grandparent; #do stuff, create a list of features while (my $feat_row = $sth->fetchrow_hashref) { $grandparent = $$feat_row{ grandparent_id }; ## dgg: Data::Dumper works and is easier on user (Data::Dumper part of sys perl lib) ## ##my ($feat_obj)= thaw $$feat_row{ object }; # original my $objs = eval $$feat_row{ object }; if($@) { warn @$; } my $feat_obj = $$objs[0]; my $type = $$feat_row{ type }; my $fmin = $$feat_row{ fmin }; my $fmax = $$feat_row{ fmax }; my @parents = map {$_->value} $feat_obj->annotation->get_Annotations('Parent'); for my $parent_id (@parents) { if ($type =~ /CDS/) { #check for a polypeptide with for this parent if ($polypeptide{ $parent_id }) { #add to it if it exists if ( $polypeptide{ $parent_id }->start > $fmin ) { $polypeptide{ $parent_id }->start($fmin); } if ( $polypeptide{ $parent_id }->end < $fmax ) { $polypeptide{ $parent_id }->end($fmax); } } else { #create it if it doesn't my $polyp = Bio::SeqFeature::Annotated->new(); $polyp->start( $fmin ); $polyp->end( $fmax ); $polyp->strand( $feat_obj->strand ); $polyp->name( $parent_id.' polypeptide'); my $srcval= Bio::Annotation::SimpleValue->new( ref($feat_obj->source) ? $feat_obj->source->value : $feat_obj->source); $polyp->source( $srcval ); my $polyp_ac = Bio::Annotation::Collection->new(); $polyp_ac->add_Annotation( 'source', $srcval); $polyp_ac->add_Annotation( 'Note',Bio::Annotation::SimpleValue->new( 'polypeptide feature inferred from GFF3 CDS feature')); $polyp_ac->add_Annotation( 'Derives_from',Bio::Annotation::SimpleValue->new( $parent_id)); $polyp_ac->add_Annotation( 'type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'polypeptide'))); $polyp_ac->add_Annotation( 'seq_id',Bio::Annotation::SimpleValue->new( $feat_obj->seq_id)); $polyp_ac->add_Annotation( 'phase',Bio::Annotation::SimpleValue->new('.')); $polyp->annotation($polyp_ac); $polypeptide{ $parent_id } = $polyp; } } } #create an exon feature (or add to an existing one) my $merged_exon = 0; for my $exon ( @feature_list ) { next unless ($exon->type->name eq 'exon'); if ($exon->start == $fmax - 1 ) { #this feature imideately precedes an existing exon, glue them together $exon->start($fmin); $exon = $self->_merge_annotations($exon, $feat_obj); $merged_exon = 1; } if ($exon->end == $fmin -1 ) { #this feature come right after an existing exon, glue them together $exon->end($fmax); $exon = $self->_merge_annotations($exon, $feat_obj); $merged_exon = 1; } } # if ($merged_exon) { # print Dumper($_) for @feature_list; # } unless ($merged_exon) { #convert the existing feature to an exon my $ac = $feat_obj->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'exon'))); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon inferred from GFF3 ' . $feat_obj->type->name . ' feature line')); $feat_obj->annotation($ac); push @feature_list, $feat_obj; } } #add the polypeptides to the list if ($self->noexon) { #only return the polpeptides if noexon is set @feature_list = values %polypeptide; } else { push @feature_list, values %polypeptide; } #delete the features from the temp tables: my $delete_query = qq/DELETE FROM tmp_cds_handler WHERE cds_row_id IN (SELECT cds_row_id FROM tmp_cds_handler_relationship WHERE grandparent_id =?) /; $sth = $dbh->prepare($delete_query); $sth->execute($grandparent); $dbh->commit; #return an iterator if (@feature_list > 0) { return Bio::GMOD::DB::Adapter::FeatureIterator->new(\@feature_list); } else { return 0; } } =head2 _merge_annotations =over =item Usage $obj->_merge_annotations() =item Function Take two adjecent feature objects and merge their annotations =item Returns The merged feature object (which will be an exon feature) =item Arguments Two feature objects, with the existing exon first =back =cut sub _merge_annotations { my ($self, $exon, $obj2) = @_; my $exon_ac = $exon->annotation; my $obj2_ac = $obj2->annotation; for my $key ( $obj2_ac->get_all_annotation_keys() ) { my @values = $obj2_ac->get_Annotations($key); if ($key eq 'type') { $exon_ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'exon feature the result of two merged features in GFF3, one '. 'of which was a '.$obj2->type->name.' feature')); } elsif ( $key eq 'source' or $key eq 'Parent' or $key eq 'seq_id' or $key eq 'phase' or $key eq 'score' ) { next; } else { for my $value ( @values ) { $exon_ac->add_Annotation($key,$value); } } } $exon->annotation($exon_ac); return $exon; } =pod my $iterator; #so its time to process the most recent set of features and return an iterator if (($feat_id && $self->{cdscache}{id} && $feat_id ne $self->{cdscache}{id}) or ($feat_parent && $self->{cdscache}{parent} && $feat_parent ne $self->{cdscache}{parent}) or (!$self->{cdscache}{id} && !$self->{cdscache}{parent}) ) { #this is a new cds feature so package up the old one to give back if ($self->noexon) { $iterator = Bio::GMOD::DB::Adapter::FeatureIterator->new( $self->{cdscache}{polypeptide_obj} ); } elsif ($self->{cdscache}{polypeptide_obj}) { push @{ $self->{cdscache}{feature_array} }, $self->{cdscache}{polypeptide_obj}; $iterator = Bio::GMOD::DB::Adapter::FeatureIterator->new( \@{ $self->{cdscache}{feature_array} } ); } #now empty the caches and set parent/id $self->{cdscache}{feature_array} = (); $self->{cdscache}{polypeptide_obj} = ''; $self->{cdscache}{id} = $feat_id; $self->{cdscache}{parent} = $feat_parent; } #get the current AnnotationCollection and change # that is, convert CDS features to exon features if ($feat && !$self->noexon) { #check for existing created exons that but up against this feature my $start = $feat->start; my $stop = $feat->end; my $appended_feature_flag = 0; for my $cached_feat ( @{ $self->{cdscache}{feature_array} } ) { if ($stop + 1 == $cached_feat->start) { my $cached_ac = $cached_feat->annotation(); my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon added to from an adjacent feature in GFF3')); my @annot_list = $ac->get_Annotations; for my $annot (@annot_list) { $cached_ac->add_Annotation($annot); } $cached_feat->start($start); $appended_feature_flag = 1; } elsif ( $start == $cached_feat->end + 1 ) { my $cached_ac = $cached_feat->annotation(); my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon added to from an adjacent feature in GFF3')); my @annot_list = $ac->get_Annotations; for my $annot (@annot_list) { $cached_ac->add_Annotation($annot); } $cached_feat->end($stop); $appended_feature_flag = 1; } } unless ( $appended_feature_flag ) { my $ac = $feat->annotation(); $ac->remove_Annotations('type'); $ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'exon'))); $ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'Exon inferred from GFF3 ' . $feat->type->name . ' feature line')); $feat->annotation($ac); } } if ($feat && !$self->{cdscache}{polypeptide_obj}) { #polypeptide doesn't exist yet, so create it my $polyp = Bio::SeqFeature::Annotated->new(); $polyp->start( $feat->start ); $polyp->end( $feat->end ); $polyp->strand( $feat->strand ); $polyp->name( $feat_parent.' polypeptide'); my $polyp_ac = Bio::Annotation::Collection->new(); $polyp_ac->add_Annotation('Note',Bio::Annotation::SimpleValue->new( 'polypeptide feature inferred from GFF3 CDS feature')); $polyp_ac->add_Annotation('Derives_from',Bio::Annotation::SimpleValue->new( $feat_parent)); $polyp_ac->add_Annotation('type',Bio::Annotation::OntologyTerm->new( -term => Bio::Ontology::Term->new(-name=>'polypeptide'))); $polyp_ac->add_Annotation('seq_id',Bio::Annotation::SimpleValue->new( $feat->seq_id)); $polyp->annotation($polyp_ac); $self->{cdscache}{polypeptide_obj} = $polyp; } #check for bounds change on the existing polypeptide elsif ( $feat && $self->{cdscache}{polypeptide_obj}->start > $feat->start && $feat->type->name =~ /CDS/ ) { $self->{cdscache}{polypeptide_obj}->start($feat->start); } elsif ( $feat && $self->{cdscache}{polypeptide_obj}->end < $feat->end && $feat->type->name =~ /CDS/ ) { $self->{cdscache}{polypeptide_obj}->end($feat->end); } push @{ $self->{cdscache}{feature_array} }, $feat if $feat; return $iterator; } =cut sub handle_parent { my $self = shift; my ($feature) = @_; for my $p_anot ( $feature->annotation->get_Annotations('Parent') ) { my $pname = $p_anot->value; my $parent = $self->cache('feature',$pname); die "\nno parent $pname;\nyou probably need to rerun the loader with the --recreate_cache option\n\n" unless $parent; $self->cache('parent',$self->nextfeature,$parent); $self->print_frel($self->nextoid('feature_relationship'),$self->nextfeature,$parent,$part_of); $self->nextoid('feature_relationship','++'); # $nextfeaturerel++; } } sub handle_derives_from { my $self = shift; my ($feature) = @_; for my $p_anot ( $feature->annotation->get_Annotations('Derives_from') ) { my $pname = $p_anot->value; my $parent = $self->cache('feature',$pname); die "no parent ".$pname unless $parent; $self->cache('parent',$self->nextfeature,$parent); $self->print_frel($self->nextoid('feature_relationship'),$self->nextfeature,$parent,$derives_from); $self->nextoid('feature_relationship','++'); #$nextfeaturerel++; } } sub handle_crud { my $self = shift; my $feature = shift; my $force_delete = shift; my ($op) = $feature->annotation->get_Annotations('CRUD'); $op = $op->value if defined($op); if ($force_delete) { $op = 'delete-all'; } my ($name) = $feature->annotation->get_Annotations('Name'); if (!defined($name)) { #try to get the name from the ID ($name) = $feature->annotation->get_Annotations('ID'); if (!defined($name)) { #if it doesn't have a name, don't do anything return 1; } } $name = $name->value if ref($name); my $type = ref($feature->type) ? $feature->type->name : $feature->type; if ($op =~ /delete/) { #determine if a single feature corresponds to what is in the gff line #it is considered to be the same if the type, name (or synonym) #and organism are the same #this sql should be moved to the prepared sql hash after debugging is done my $sql = "SELECT feature_id FROM feature WHERE name = ? and type_id = ? and organism_id = ?"; my $delete_query_handle = $self->dbh->prepare($sql); $delete_query_handle->execute($name, $self->get_type($type), $self->organism_id); my $feature_id_arrayref = $delete_query_handle->fetchall_arrayref; my $feature_id; if (scalar @{$feature_id_arrayref} > 1 and $op ne 'delete-all') { $self->throw("I can't figure out which feature to delete that corresponds to a feature with a name of $name, a type of $type and organism of ".$self->organism.". More than one feature match these criteria"); } elsif (scalar @{$feature_id_arrayref} > 1) { warn "Deleting all features with name $name, type $type and organism ".$self->organism."\n"; for my $id_row (@{$feature_id_arrayref}) { my $feature_id = $$id_row[0]; $self->print_delete($$id_row[0]) if $feature_id; } return 1; } elsif (scalar @{$feature_id_arrayref} == 0) { warn "Couldn't fined a matching feature with name $name, type $type and organism ".$self->organism."\n"; return 1; # warn("Searching for a feature with the name $name to delete yielded nothing; checking synonyms..."); # $sql = "SELECT f.feature_id # FROM feature f, feature_synonym fs, synonym s # WHERE s.name = ? and # s.synonym_id = fs.synonym_id and # fs.feature_id = f.feature_id and # f.type_id = ? and f.organism_id = ?"; # my $delete_by_syn_query_handle = $self->dbh->prepare($sql); # $delete_by_syn_query_handle->execute($name, # $self->get_type($type), # $self->organism_id); # $feature_id_arrayref = $delete_by_syn_query_handle->fetchall_arrayref; # if (scalar @{$feature_id_arrayref} > 1) { # $self->throw("I couldn't figure out which feature to delete when searching by synonym $name; I found more than one matching feature"); # } # elsif (scalar @{$feature_id_arrayref} == 0) { # $self->throw("I couldn't find a matching feature using either feature.name or synonym.name of $name and a type of $type and organism of ".$self->organism.". I can't go on... Bye."); # } # else { # ($feature_id) = $$feature_id_arrayref[0]; # } } else { $feature_id = $$feature_id_arrayref[0][0]; } $self->print_delete($feature_id); return 1; } elsif ($op eq 'replace' or $op eq 'update') { $self->throw("The CRUD operation $op is not supported yet"); } elsif ($op eq 'create') { return 0; #nothing to do--create is the default } else { $self->throw("I don't know what to do for the CRUD operation $op"); } } 1; chado-1.23/lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm000644 000765 000024 00000052234 11256707527 021307 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::AcodeWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::AcodeWriter =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $sequtil= Bio::GMOD::Bulkfiles->new( configfile => 'seqdump-r4', ); my $fwriter= $sequtil->getWriter('acode'); my $result = $fwriter->makeFiles( ); =head1 NOTES genomic sequence file utilities, part3; parts from flybase/work.local/chado_r3_2_26/soft/chado2flat2.pl =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug #use lib("/bio/biodb/common/perl/lib", "/bio/biodb/common/system-local/perl/lib"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::BulkWriter); our $DEBUG = 0; my $VERSION = "1.1"; #my $configfile= "toacode"; #? BulkFiles/AcodeWriter.xml use constant BULK_TYPE => 'acode'; use constant CONFIG_FILE => 'toacode'; use vars qw/ $noIDmap $nameIsId $nameIsSpeciesId $cutdbpattern $indexidtype $gnidpattern $anidpattern /; sub init { my $self= shift; $self->SUPER::init(); $DEBUG= $self->{debug} if defined $self->{debug}; ## superclass does these?? # $self->{bulktype} = $self->BULK_TYPE; # dont need hash val? # $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); # my $config = $self->{config}; # my $sconfig= $self->handler()->{config}; # my $finfo= $self->{fileinfo} || $self->handler()->getFilesetInfo($self->BULK_TYPE); # my $outdir= $self->handler()->getReleaseSubdir( $self->getconfig('path') || $self->BULK_TYPE); # $self->{outdir} = $outdir; ## see instead super.. promoteconfigs # $self->{addids} = $self->getconfig('addids'); # $self->{dropnotes} = $self->getconfig('dropnotes'); # $self->{allowanyfeat} = $self->getconfig('allowanyfeat'); $noIDmap = $self->getconfig('noidmap'); unless($noIDmap) { $noIDmap= join '|', qw(cytowalk misc chromosome match motif sim4 oligo processed protein _peptide repeat regulatory_region repeat_region transposable_element_pred ); } ## mRNA CDS _UTR intron EST cDNA enhancer # _fragment # _junction # _mutation # _site # _variant # $noIDmap =~ s/\s+/|/g; $noIDmap .= '|\bregion'; $nameIsId= $self->getconfig('nameisid') || '^(BAC)'; $nameIsSpeciesId= $self->getconfig('nameisorgid') || '^(gene)$'; # others? rnas? $cutdbpattern= $self->getconfig('idcutdb') || '^(FlyBase|GadFly|GB_protein|GO):'; $indexidtype= $self->getconfig('indexidtype') || '^(gene|pseudogene|\w+RNA)'; $gnidpattern= $self->getconfig('gnidpattern') || '[A-Z]{2}gn\d+'; $anidpattern= $self->getconfig('anidpattern') || '[A-Z]{2}an\d+'; } #-------------- subs ------------- =item makeFiles( %args ) primary method arguments: infiles => \@fileset of fff features and dna sequences, # required =cut sub makeFiles { my $self= shift; my %args= @_; print STDERR "AcodeWriter::makeFiles\n" if $DEBUG; # debug # more sensible that writer should ask handler for kind of files it wants my $intype= $self->config->{informat} || 'fff'; #? maybe array my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; unless(@$fileset) { $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "AcodeWriter: no input '$intype' files found\n"; return $self->status(-1); } } my $featset= $self->handler->{config}->{featset} || []; #? or default set ? my $addids = defined $args{addids} ? $args{addids} : $self->config->{addids}; my $status= 0; my $ok= 1; for (my $ipart= 0; $ok; $ipart++) { $ok= 0; my $infile= $self->openInput( $fileset, $ipart, $intype); if ($infile && $infile->{inh}) { my $inh= $infile->{inh}; my $chr= $infile->{chr}; # if ($addids) { # my $idlist= $self->readIdsFromFFF( $inh, $chr, $self->handler()->{config}); # for featmap ? # $self->{idlist}= $idlist; # $inh= $self->resetInput($infile); #seek($inh,0,0); ## cant do on STDIN ! cant do on PIPE ! # } ## need to know $chr here .. from $fileset infile my $res= $self->process( $inh, $chr, $featset); close($inh); delete $infile->{inh}; $status += $res; $ok= 1; } } print STDERR "AcodeWriter::makeFiles: done\n" if $DEBUG; return $self->status($status); } =item openInput( $fileset ) handle input files .. copied to base class =cut sub openInput { my $self= shift; my( $fileset, $ipart, $intype )= @_; # do per-csome/name $intype ||= $self->config->{informat} || 'fff'; #? maybe array my $atpart= 0; print STDERR "openInput: type=$intype part=$ipart \n" if $DEBUG; foreach my $fs (@$fileset) { my $fp = $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; next unless( $fs->{type} =~ /$intype/); # could it be 'dna/fasta', 'amino/fasta' ? unless(-e $fp) { warn "missing infile $fp"; next; } $atpart++; next unless($atpart > $ipart); print STDERR "openInput: name=$name, type=$type, $fp\n" if $DEBUG; my ( $org, $chr1, $featn, $rel, $format )= $self->split_filename($fp); $fs->{org}= $org; $fs->{chr}= $chr1 unless($fs->{chr}); $fs->{featn}= $featn; $fs->{rel}= $rel; $fs->{format}= $format; if ($fp =~ m/\.(gz|Z)$/) { open(INF,"gunzip -c $fp|"); $fs->{pipe}=1; } else { open(INF, $fp); } my $inh= *INF; $fs->{inh}= $inh; return $fs; } print STDERR "openInput: nothing matches part=$ipart\n" if $DEBUG; return undef; } sub resetInput { my $self= shift; my( $infile )= @_; my $inh= $infile->{inh}; my $fp = $infile->{path}; if ($infile->{pipe} || $fp =~ m/\.(gz|Z)$/) { close($inh) if $inh; open(INF,"gunzip -c $fp|"); $inh= *INF; $infile->{pipe}=1; } elsif (!$inh) { open(INF,$fp); $inh= *INF; } else { seek($inh,0,0); } $infile->{inh}= $inh; return $inh; } =item process =cut sub process { my $self= shift; my( $inh, $chr, $featset )= @_; my $ndone= 0; my $outh= {}; my $outdir= $self->outputpath(); my @features= @$featset; my @fffeatures= grep !/^chromosome/, @features; my $fn= $self->get_filename ( $self->{org}, $chr, 'all', $self->{rel}, $self->BULK_TYPE); $fn= catfile( $outdir, $fn); $outh->{all}= new FileHandle(">$fn"); $self->{outh}= $outh->{all}; $ndone += $self->fromFFFloop( $inh, $outh, $chr, \@fffeatures); foreach my $featn (keys %$outh) { my $fh= $outh->{$featn}; close($fh); #? check size and delete if zero ? } print STDERR "process ndone = $ndone\n" if $DEBUG; return $ndone; } =item acodeHeader my $fah= main->acodeHeader( ID => 'CG123', name => 'MyGene', chr => '2L', loc => '1234..5678', type => 'pseudogene', db_xref => 'FlyBase:FBgn0000123', note => 'BOGUS', ); expected keys: type chr/chromosome loc/location ID name db_xref =cut =item example fff for gene stuff 2L 6338772 gene Cpr 26C3-26C3 6338772..6346282 CG11567 FlyBase:FB an0011567;FlyBase:FBgn0015623;GB:CG11567; gbunit=AE003613;synonym=Cpr;synonym_2nd=CP R;synonym_2nd=NADPH-cytochrome P450 oxidoreductase;synonym_2nd=NCPR;synonym_2nd=P450;synon ym_2nd=P450 reductase;synonym_2nd=cpr; 2L 6338772 mRNA Cpr-RA - join(6338772..6339125,6342158..6342349,6342727..63 43069,6344159..6344283,6344344..6344945,6345031..6345679,6345743..6346282) CG11567-RA FlyBase:FBtr0079250;FlyBase:FBgn0015623;Gadfly:CG11567-RA; synonym=CG11567-RA ; 2L 6342174 CDS Cpr-PA - join(6342174..6342349,6342727..6343069,6344159..63 44283,6344344..6344945,6345031..6345679,6345743..6345884) CG11567-PA FlyBase:FB pp0078880;GB_protein:AAF52367.1;FlyBase:FBgn0015623;Gadfly:CG11567-PA; synonym=CG11567-PA ; 2L 6338772 five_prime_UTR Cpr-RA-u5 - join(6338772..6339125,6342158..634 2173) CG11567-RA-u5 FlyBase:FBgn0015623; 2L 6345888 three_prime_UTR Cpr-RA-u3 - 6345888..6346282 CG11567-RA -u3 FlyBase:FBgn0015623; 2L 6339126 intron Cpr-RA-in - join(6339126..6342157,6342350..6342726,634 3070..6344158,6344284..6344343,6344946..6345030,6345680..6345742) - FlyBase:FB gn0015623; =cut sub acodeHeader { my($self,%vals)= @_; my $type= delete $vals{type}; my $arm = delete $vals{chr} || delete $vals{chromosome}; my $loc = delete $vals{loc} || delete $vals{location}; #$loc= "$arm:$loc" if ($arm && $loc !~ /:/); my $mrna= delete $vals{mrna}; my $ID = delete $vals{ID} || delete $vals{id} || delete $vals{uniquename}; my $name= delete $vals{name}; my $db_xref= delete $vals{db_xref} || delete $vals{dbxref}; if ($db_xref) { $db_xref =~ s/\s*;\s*$//; $db_xref =~ s/;/,/g; $db_xref =~ s/,,/,/g;} my @ids= map { s/$cutdbpattern//i; $_; } split(/,/, $ID.",".$db_xref); my ($anid)= grep /$anidpattern/, @ids; my ($gid) = grep /$gnidpattern/, @ids; my $gsym= $name; my $cgsym= $ID; my $cloc= delete $vals{cytomap}; my $scaf= delete $vals{gbunit}; my $syn = delete $vals{synonym_2nd}; my $isTE=($type =~ /transposable_element/ || $gid =~ /FBti/); # an = TE\d+ ; gn = FBti\d+ my @re=(); push(@re,"ID 1 $anid"); push(@re,"GID 1 $gid"); push(@re,"GSYM 1 $gsym"); push(@re,"CGSYM 1 $cgsym"); push(@re,"ARM 1 $arm"); push(@re,"CLA 1 $type") if $type; push(@re,"CLOC 1 $cloc") if $cloc; push(@re,"SCAF 1 $scaf") if $scaf; my @trns= (); @trns= @{$mrna} if(ref $mrna); my @aa=(); my @bl=(); my $ntr= 0; foreach my $trn (@trns) { my($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr)= @$trn; #push(@aa, $name) if ($type eq 'CDS'); # want aa len here ! push(@bl, $name) if ($type eq 'mRNA'); $ntr++ if ($type eq 'mRNA'); } push(@re,"TRREC ".$ntr) if $ntr; push(@re,"AALEN ".scalar(@aa)." ".$aa[0]) if @aa; my $re= join("\t",@re); my $gadr= "GADR\n{\n"; $gadr .= "RETE|$re\n"; $gadr .= "ID|$anid\n"; $gadr .= "SYM|$cgsym\n"; if ($isTE) { $gadr .= "INSR\n{\n"; ## need INSR variant, FBti/TE $gadr .= "SYM|$gsym\n"; $gadr .= "ID|$gid\n}\n"; } else { $gadr .= "GENSR\n{\n"; ## need INSR variant, FBti/TE $gadr .= "GSYM|$gsym\n"; $gadr .= "ID|$gid\n}\n"; } $gadr.= "CLA|$type\n" if $type; $gadr.= "ARM|$arm\n" if $arm; $gadr.= "SCAF|$scaf\n" if $scaf; $gadr.= "BLOC|$loc\n" if $loc; $gadr.= "CLOCC|$cloc\n" if $cloc; # $gadr.= "SQLEN|$sqlen\n" if $sqlen; $gadr.= "SYN|".join("\n|",split(/[;,]/,$syn))."\n" if $syn; # $gadr.= "GO|$go\n" if $go; my @id2= map { s/$cutdbpattern//i; $_; } grep !/$gid|$anid/, split(/,/,$db_xref); $gadr.= "ID2|".join("\n|",@id2)."\n" if @id2; # $gadr.= "CDNA|".join("\n|",split(/$RECSEP/,$h{CDNA}))."\n" if $h{CDNA}; # $gadr.= "EST|".join("\n|",split(/$RECSEP/,$h{EST}))."\n" if $h{EST}; # $gadr.= "AFFY|".join("\n|",split(/$RECSEP/,$h{AFFY}))."\n" if $h{AFFY}; # my $gcm = join("\n|", split(/$RECSEP/,$h{CMT})); # $gcm =~ s/^\s*//; # $gcm = wrapLong($gcm); # $gadr.= "CMT|$gcm\n" if ($gcm); # $gadr.= "DT|$dt\n" if $dt; foreach my $trn (@trns) { my($type,$nm,$cytomap,$bl,$id,$dbxref,$notes,$chr)= @$trn; # my $nm= $trn->{CTSYM}; # my $aa= $trn->{AALEN}; # my $aan= $trn->{AANAM}; # my $sl= $trn->{SQLEN}; # my $bl= $trn->{mRNA}; # my $cds= $trn->{CDS}; # my $dt= $trn->{DT}; # my $cm= $trn->{PEPCMT}; # my $subr= $trn->{SUBREC}; # $sl .= ' (-)' if ($sl && $bl =~ /complement/); $bl = $self->wrapLong($bl); #$cds= $self->wrapLong($cds); #? store only translation offset? # $cm= join("\n|",split(/$RECSEP/,$cm)); # $cm =~ s/^\s*//; $cm = wrapLong($cm); # my $type= $trn->{TYPE}; # if ($type eq 'CLNSR') { # # note: CLNSR = flybase.clone.Clone subrecord, not used, mar04 # $gadr.= "CLNSR\n{\n"; # $gadr.= "CLA|$ttype\n" if $ttype; # FIXME # $gadr.= "NAM|$nm\n" if $nm; # $gadr.= "SYN|".join("\n|",split(/$RECSEP/,$trn->{SYN}))."\n" if $trn->{SYN}; # $gadr.= "SQLEN|$sl\n" if $sl; # none of these ? # $gadr.= "BLOC|$bl\n" if $bl; # $gadr.= "CMT|$cm\n" if $cm; # $gadr.= "DT|$dt\n" if $dt; #? could get, not # $gadr.= "}\n"; # } elsif if ($type eq 'mRNA') { # note TRREC = flybase.egad.Transcript subrecord $gadr.= "TRREC\n{\n"; $gadr.= "NAM|$nm\n" if $nm; #$gadr.= "SYN|".join("\n|",split(/$RECSEP/,$trn->{SYN}))."\n" if $trn->{SYN}; #$gadr.= "AANAM|$aan\n" if $aan; #$gadr.= "SQLEN|$sl\n" if $sl; #$gadr.= "AALEN|$aa\n" if $aa; $gadr.= "BLOC|$bl\n" if $bl; #$gadr.= "CDS|$cds\n" if $cds; #$gadr.= "CMT|$cm\n" if $cm; #$gadr.= $subr if $subr; #$gadr.= "DT|$dt\n" if $dt; $gadr.= "}\n"; } } $gadr .= "VERS|". $self->{rel}."\n"; $gadr .= "}\n\# EOR\n\n"; return $gadr; } sub putrec { my $self= shift; my ( $outh, $gmain, $gmsub )= @_; my $org= $self->{org} || $self->handler()->{config}->{org}; my($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr)= @$gmain; my @notes= $self->cleanNotes($notes); if ($self->{idlist}) { ## && $types_info->{add_id} addids $dbxref= $self->addIdsToDbxref( ($id ? $id : $name), $dbxref ); } my $fah= $outh->{all}; # $type= $retype->{$type}||$type; my $header= $self->acodeHeader( type => $type, name => $name, chr => $chr, location => $baseloc, ID => $id, db_xref => $dbxref, cytomap => $cytomap, $org ? (species => $org) : (), mrna => $gmsub, @notes ); print $fah $header; } sub wrapLong { my $self= shift; # wrap long lines for acode # FIXME - check for "\n" already in $rng my $rng= shift; my $nl = shift || "\n|"; my $nlen= length($nl); my $al; if (length($rng)>80) { my ($at0, $at, $r2)= (0,0,''); while ($at0>=0) { $at= index($rng,$nl,$at0); $al= $at - $at0; if ($at>=0 && $al<=80) { $at += $nlen; $r2 .= substr($rng,$at0,$at-$at0); $at0= $at; } else { $at= index($rng,"\n",$at0); $al= $at - $at0; if ($at>=0 && $al<=80) { $r2 .= substr($rng,$at0,$at-$at0) . $nl; $at++; $at0= $at; } else { $at= index($rng,",",$at0+60); if ($at<=0) { $at= index($rng,";",$at0+60); } if ($at<=0) { $at= index($rng," ",$at0+60); } if ($at>0) { $at++; $r2 .= substr($rng,$at0,$at-$at0) . $nl; $at0= $at; } else { $r2 .= substr($rng,$at0); $at0= -1; } } } } $rng= $r2; } return $rng; } sub fromFFFloop { my $self= shift; my ( $fffin, $outh, $chrIn, $featset )= @_; my $nout= 0; my $sconfig= $self->handler->{config}; $self->{ffformat}= 0; my %lastfff= (); my $org= $self->{org} || $self->handler()->{config}->{org}; my $allowanyfeat= 1; # (!$featset || $featset =~ /^(any|all)/i) ? 1 # : (defined $self->config->{allowanyfeat}) ? $self->config->{allowanyfeat} # : 0; my @gmsub; my $gmain; my ($gnid,$cgid); my %gmodl; while(<$fffin>) { next unless(/^\w/); chomp; my $fff= $_; my @fvals = $self->handler()->splitFFF($fff, $chrIn); $self->{ffformat}= $self->{gotffformat}; # set by splitFFF my($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr)= @fvals; ## need to collect gene model features together, then make acode # my($types_ok,$retype,$usedb,$subrange,$types_info) # = $self->get_feature_set( $type, $sconfig, $allowanyfeat); #next unless( ($types_ok && $types_ok->{$type}) || ($allowanyfeat && !$didfeat) ); next if ($type =~ /$noIDmap/); ## these should go to evidence ... my @ids= map { s/$cutdbpattern//i; $_; } split(/,/, $id.",".$dbxref); # my ($gid) = grep /FBgn/, @ids; my ($gid) = ($dbxref =~ m/(FBgn\d+)/); my ($cid) = ($id =~ m/(C[GR]\d+)/); # add FBti/TE support if ($type =~ /^(mRNA|CDS)/) { # intron|UTR ??? ## subfeature for acode ## need to check dbxref IDs for same FBgn as for $gmain ! ## instead use hash by $gid/gnid if ($cid) { $gmodl{$cid}= [] unless($gmodl{$cid}); push( @{$gmodl{$cid}}, \@fvals); } next; } elsif ($type =~ /$indexidtype/) { # ^(gene|pseudogene|tRNA) # main feature if ($gmain) { $self->putrec( $outh, $gmain, $gmodl{$cgid}); $nout++; @gmsub=(); $gmain=undef; delete $gmodl{$cgid}; } $gmain= \@fvals; #push(@gmsub,\@fvals); $gnid= $gid; $cgid= $cid; next; } else { next; } } # if ($gmain) { # $self->putrec( $outh, $gmain, \@gmsub); $nout++; @gmsub=(); $gmain=undef; # } if ($gmain) { $self->putrec( $outh, $gmain, $gmodl{$cgid}); $nout++; @gmsub=(); $gmain=undef; delete $gmodl{$cgid}; } return $nout; } ## patch for adding gene IDs to gene model features missing them sub addIdsToDbxref { my $self = shift; my ( $pid, $dbxref )= @_; # my $pid= ($id ? $id : $name); $pid =~ s/[_-].*$//; # try for parent id - db prefix: ? my $idlist= $self->{idlist}; # from readids ... my $idpattern= $self->handler()->{idpattern}; if ($idlist->{$pid}) { my %dtype=(); foreach my $x ( $pid, split(/[,;\s]/,$idlist->{$pid})) { if ( $x =~ m/$idpattern/) { ## /(FBgn|FBti|FBan|CG|CR)\d+/ my $dtype= $1; unless( $dtype{$dtype} || ($dbxref && $dbxref =~ m/$x/) ) { $dbxref .= "," if ($dbxref); $dbxref .= $x; } $dtype{$dtype}++; } } } return ($dbxref); #?? } ##? check notes for synonyms=, other fields? sub cleanNotes { my ($self, $notes)= @_; my @notes= (); if ($notes) { my $dropnotes= $self->config->{dropnotes} || 'xxx'; my %notes=(); foreach my $n (split(/[;]/,$notes)) { if ($n =~ /^(\w+)=(.+)/) { my($k,$v)= ($1,$2); if ($dropnotes !~ m/\b$k\b/) { $notes{$k} .= "$v,"; } } } foreach my $n (sort keys %notes) { $notes{$n} =~ s/,$//; push(@notes, $n, $notes{$n}); } } return @notes; } =item @info= get_feature_set($featset, $config, $allowanyfeat) given feature type or type-class, return info to screen, remap individual features. See config and associated info. args: featset = single feature or feature set class name (given in configs) config = configuration hash allowanyfeat = featset as basic type should be allowed (types_ok) return ($types_ok,$retype,$usedb,$subrange,$types_info) types_ok = hash of which basic types are allowed in featset retype = rename basic types to these for output header usedb = pull residues from database rather than chromosome dna (curated bases) subrange = expansion range (e.g for gene_expanded2000, etc.) types_info = all of featmap information =cut sub get_feature_set { my( $self, $featset, $config, $allowanyfeat)= @_; #return $self->handler()->get_feature_set($featset,$config,$allowanyfeat); my($fromdb,$subrange) = (0,''); my @ft=(); my @retype= (); my $type_info= {}; $config = $self->handler->{config} unless($config); if(!$config->{featmap}->{$featset} && $featset =~ /^(\w+)_extended(\d+)$/) { my ($t,$r)= ($1,$2); $featset= $t; $subrange= "-$r..$r"; } if (defined $config->{featmap}->{$featset}) { my $fm= $config->{featmap}->{$featset}; @ft= split(/[\s,;]/, $fm->{types} || $featset ); #? @{$fm->{types}}; @retype= split(/[\s,;]/, $fm->{typelabel}) if ($fm->{typelabel}); $fromdb= $fm->{fromdb} || 0; $subrange= $fm->{subrange} || $subrange; if ($fm->{method} eq 'between') { $fm->{proc}= '&intergeneFromFFF2'; ## FIXME } $type_info= $fm; # just save all ? } else { CASE: { $featset =~ /^(gene|pseudogene)$/ && do { @ft=($featset); $type_info->{get_id}=1; last CASE; }; $featset =~ /^(CDS|mRNA)$/ && do { @ft=($featset); last CASE; }; $featset =~ /^(five_prime_UTR|three_prime_UTR|intron)$/ && do { @ft=($featset); $type_info->{add_id}= 'gene'; last CASE; }; $featset =~ /^(tRNA|ncRNA|snRNA|snoRNA|rRNA)$/ && do { @ft=($featset); $type_info->{get_id}=1; last CASE; }; $featset =~ /^(miscRNA)$/ && do { @ft=qw(ncRNA snRNA snoRNA rRNA); last CASE; }; $featset =~ /^(transposable_element|transposon)$/ && do { @ft=('transposable_element'); last CASE; }; $featset =~ /^gene_extended(\d+)$/ && do { @ft=('gene'); $subrange="-$1..$1"; @retype=("gene_ex$1"); last CASE; }; $featset =~ /^(transcript)$/ && do { @ft=('mRNA'); $fromdb=1; @retype=('transcript'); last CASE; }; $featset =~ /^(CDS_translation|translation)$/ && do { @ft=('CDS'); $fromdb=1; @retype=('translation'); last CASE; }; default: { if ($allowanyfeat) { @ft=($featset); } elsif (grep {$featset eq $_} @{$config->{fastafeatok}}) { @ft=($featset); } else { return undef; } ## warn "Unknown feature option: $@"; }; } } $fromdb= 0 if $self->handler()->{ignoredbresidues}; my %types_ok= map { $_,1; } @ft; my %retype = map { my $f= shift @ft; $f => $_; } @retype; return (\%types_ok, \%retype, $fromdb, $subrange, $type_info); } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/BlastWriter.pm000644 000765 000024 00000032733 11256707527 021343 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::BlastWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::BlastWriter =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $sequtil= Bio::GMOD::Bulkfiles->new( # was SeqUtil2 configfile => 'seqdump-r4', ); my $fwriter= $sequtil->getBlastWriter(); my $result= $fwriter->makeFiles( infiles => [ @$fastafiles ], # required ); =head1 NOTES genomic sequence file utilities, part3; parts from flybase/work.local/chado_r3_2_26/soft/blastdbupdate.pl =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug #use lib("/bio/biodb/common/perl/lib", "/bio/biodb/common/system-local/perl/lib"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::BulkWriter); our $DEBUG = 0; my $VERSION = "1.1"; #my $configfile= "blastfiles"; #? BulkFiles/BlastWriter.xml use constant BULK_TYPE => 'blast'; use constant CONFIG_FILE => 'blastfiles'; use vars qw/ $formatdb /; sub init { my $self= shift; $self->SUPER::init(); $DEBUG= $self->{debug} if defined $self->{debug}; # $self->{bulktype} = $self->BULK_TYPE; # dont need hash val? # $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; # $self->{failonerror}= 0 unless defined $self->{failonerror}; } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); my $config = $self->{config}; # my $blastdir= $self->handler()->getReleaseSubdir( $self->{finfo}->{path} || 'blast/'); # $self->{blastdir} = $blastdir; $config->{isprot_patt} ||= '(translation|aa_)'; my $blasthome= $config->{blasthome} ; #|| "$oroot/common/servers/blast/Bin"; $formatdb= $config->{formatdb} || "$blasthome/formatdb"; unless(-e $formatdb) { #? check ENV{NCBI} ? sys path ? BioPerl.. ? #formatdbpath = $self->findExecs('formatdb','blastall'); warn "Missing formatdb: $formatdb"; # fail *Module* $self->status(-1,"missing formatdb"); } my $formatdbopts= $config->{formatdbopts} || '-o F '; # T - True: Parse SeqId and create indexes. # -t Title $config->{formatdbopts}= $formatdbopts; } #-------------- subs ------------- =item makeFiles( %args ) primary method makes blast indices. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required =cut sub makeFiles { my $self= shift; my %args= @_; print STDERR "BlastWriter::makeFiles\n" if $DEBUG; # debug my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; unless(@$fileset) { my $intype= $self->getconfig('informat') || 'fasta'; #? maybe array $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "BlastWriter: no input '$intype' files found\n"; return $self->status(-1); } } my @seqfiles= $self->openInput( $fileset ); my $res= $self->processBlastInput( \@seqfiles); print STDERR "BlastWriter::makeFiles: done\n" if $DEBUG; return $self->status($res); #what? } =item openInput( $fileset ) handle input files =cut sub openInput { my $self= shift; my( $fileset )= @_; # do per-csome/name my @files= (); my $inh= undef; return undef unless(ref $fileset); my $intype = $self->getconfig('informat') || 'fasta'; #? maybe array my $featset= $self->getconfig('blastset') || []; my @featset= @$featset; print STDERR "openInput: type=$intype blastset=",join(",",@featset),"\n" if $DEBUG; foreach my $fs (@$fileset) { my $fp= $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; my ($featn,$format)= split /[\/]/, $type; next if( @featset && ! grep({$_ eq $featn} @featset) ); my $ok= ( $type =~ /$intype/ && -s $fp) ; # -e $fp ## need -s $fp here : files must have data (should delete 0 fasta) print STDERR "openInput: name=$name $featn, type=$type, ok=$ok\n" if $DEBUG; next unless $ok; push(@files, $fp); # return full $fs struct w/ $featn ? } return @files; } =item get_filename( $org, $chr, $featn, $rel, $format) make standard output file name "${org}_${chr}_${featn}_${rel}.${format}" =cut sub get_filename { return shift->blastname(@_); ## {sequtil}->get_filename( @_); } sub split_filename { my $self= shift; my ($fname)= @_; my $fndel= $self->getconfig('filepart_delimiter') || '-'; my @v= split(/$fndel/, $fname, 4); if (@v == 2) { splice(@v, 1, 0, 'all'); $fname= join($fndel,@v); } #OR# return ( $v[0], "all", $v[1], "", ""); ## created name w/o -all- chr; fails split ## my $blname= $self->handler->get_filename($org,'',$featn,'',$format); return $self->handler()->split_filename( $fname ); } sub blastname { my $self= shift; my($dbname)= @_; if ($dbname =~ s/(\d[\d\.]*\.\d)/ZYX/) { my $r=$1; $r=~s/\.//g; $dbname =~ s/ZYX/$r/; } # squeeze r3.2.1 to r321 $dbname =~ s/\..*$//; # drop .fasta.gz etc. return $dbname; } =item processBlastInput =cut sub processBlastInput { my $self= shift; my( $rseqfiles )= @_; my $blastdir= $self->outputpath(); my ($doformat, $doconfig)= (1,1); my $ndone= 0; # format only if changed... $self->updateformat( $blastdir, $rseqfiles) if ($doformat); my @blastfiles=(); opendir(D, $blastdir); @blastfiles= grep(/^\w/,readdir(D)); closedir(D); if ($doconfig) { my %dbinfo= $self->getDbDirInfoByTitle( $blastdir, \@blastfiles); $self->update_blastrc( $blastdir, \@blastfiles); $self->update_dbselect( \%dbinfo); $self->update_dbhtml( \%dbinfo); } $ndone= scalar( @blastfiles); print STDERR "processBlastInput ndone = $ndone\n" if $DEBUG; return $ndone; } #------------- # parts from flybase/work.local/chado_r3_2_26/soft/blastdbupdate.pl #------------- sub update_blastrc { my $self= shift; my($path, $rdir)= @_; my $rcdoc= $self->config->{'doc'}->{dbrc}; my @dir= @$rdir; warn "update_blastrc()\n" if $DEBUG; my $nalist= join " ", map{ $self->blastname($_) } grep(/\.(nhr|nal)$/,@dir); my $aalist= join " ", map{ $self->blastname($_) } grep(/\.(phr|pal)$/,@dir); my @rc= split "\n",$rcdoc->{content}; push(@rc, qw/blastn blastp blastx tblastn tblastx/) unless(@rc); foreach (@rc) { s/^blastn.*$/blastn $nalist/; s/^tblastn.*$/tblastn $nalist/; s/^tblastx.*$/tblastx $nalist/; s/^blastp.*$/blastp $aalist/; s/^blastx.*$/blastx $aalist/; } $rcdoc->{content}= join("\n", @rc); $rcdoc->{id}= 'dbrc'; $self->handler()->writeDocs( $rcdoc ); } sub getDbInfo { my $self= shift; my ( $dbhash, $path, $blastfile)= @_; my $blname = $self->blastname($blastfile); ## >> creates name w/o -all- chr; fails split ## my $blname= $self->handler->get_filename($org,'',$featn,'',$format); my ( $org, $chr, $featn, $rel, $format)= $self->split_filename($blname); my $db= $dbhash->{$featn}; # probably this unless($db) { $db= $dbhash->{$blname}; } unless($db) { (my $bl2= $blname) =~s/_r\d+.*//; $db= $dbhash->{$bl2}; } # w/o version unless($db) { my $isprot_patt = $self->config->{isprot_patt}; my $doprot= ($blname =~ m/$isprot_patt/) ? 1 : 0; my $tt= (($chr eq 'all') ? "All" : $chr) . " $org $featn " . (($doprot) ? "(AA)" : "(NT)"); $db= { name => $blname, title => $tt, content => "", }; } my $ftime= -M $blastfile || 0; $ftime= $^T - 24*60*60*$ftime; $db->{date}= POSIX::strftime("%d-%b-%Y", localtime( $ftime )); $db->{blname}= $blname; $db->{files} = $blname; my ($files); ## FIXME need to write .nal, .pal from config? if (-r "$path/$blname.nal") { open(BL,"$blname.nal"); ($files)=grep(/DBLIST/,); close(BL);} elsif (-r "$path/$blname.pal") { open(BL,"$blname.pal"); ($files)=grep(/DBLIST/,); close(BL);} if ($files) { $files =~ s/\s*DBLIST\s*//; $db->{files}= $files; } return $db; } sub getDbDirInfoByTitle { my $self= shift; my($path, $dirlist)= @_; my $dbhash= $self->config->{blastdb}; my @blf= grep(/\.(nhr|phr|nal|pal)$/, @$dirlist); my %dbh=(); foreach my $blf (@blf) { my $db= $self->getDbInfo($dbhash, $path, $blf); next if ($db->{skip}); my $title= $db->{title}; $dbh{$title}= $db; } return %dbh; } sub update_dbhtml { my $self= shift; my($dbh)= @_; warn "update_dbhtml\n" if $DEBUG; my $dbtable= $self->config->{doc}->{dbtable}; my $content= $dbtable->{header}->{content} || ' '; $content .= $dbtable->{tableheader}->{content} || "\n"; foreach my $title (sort keys %$dbh) { my $db = $dbh->{$title}; $content .= "\n"; } $content .= $dbtable->{footer}->{content} || '
Pull-down Menu Database file Update Description
$title $db->{files} $db->{date} $db->{content}
'; $dbtable->{content}= $content; $dbtable->{dbtable}= 'dbrc'; $self->handler()->writeDocs( $dbtable ); } sub update_dbselect { my $self= shift; my($dbh)= @_; warn "update_dbselect \n" if $DEBUG; my $dbselect= $self->config->{doc}->{dbselect}; my $content= $dbselect->{header}->{content} || ''; $content .= "\n"; $content .= $dbselect->{footer}->{content} || ''; $dbselect->{id}= 'dbselect'; $dbselect->{content}= $content; $self->handler()->writeDocs( $dbselect ); } sub updateformat { my $self= shift; # my($path, $rdir)= @_; my ( $blastdir, $datafiles)= @_; my $isprot_patt = $self->config->{isprot_patt}; my @fastafiles= @$datafiles; ##grep(/\.(gz|Z|fa|fasta)$/, @$datafiles); #? or assume all @files are fasta? my %dbset= (); warn "update formatdb \n" if $DEBUG; ## FIXME: input fasta == $org_$chr_$feature_$release ## >> cat all $org_{1..n}_feature into one blastdb my %alldata=(); foreach my $fa (@fastafiles) { my ( $org, $chr, $featn, $rel, $format)= $self->split_filename($fa); ## keep release in blast db name -- ??? ## check here if have 'all' $chr input, if so skip any other $chr in same set ## nov04 - drop release to avoid hassles w/ updates needed all blast config ## to be regenerated -- also leave out 'all' ##my $blrel=''; #= $rel; ##my $blname= $self->handler->get_filename($org,'all',$featn,$blrel,$format); my $blname= $self->handler->get_filename($org,'',$featn,'',$format); $blname= $self->blastname($blname); $alldata{$blname}= $fa if ($chr eq 'all'); ##my ($sfile, $spath, $ext) = File::Basename::fileparse($fa, '\.[^\.]+'); ##my $blname = $self->blastname($sfile); my $blf = $blname . '.nhr'; unless (-e "$blastdir/$blf") { $blf= $blname . '.phr'; } # $_='' unless ($self->isold( $_, "$blastdir/$blf")); # skip current indices if ($self->isold( $fa, "$blastdir/$blf")) { unless($dbset{$blname}) { $dbset{$blname}= []; } push( @{$dbset{$blname}}, $fa); } } warn "BlastWriter: Missing $formatdb" and return -1 unless(-e $formatdb); foreach my $blname (keys %dbset) { my $doprot= ($blname =~ m/$isprot_patt/) ? 1 : 0; my $seqlist= $dbset{$blname}; if ($alldata{$blname}) { $seqlist= [ $alldata{$blname} ]; } $self->formatdb_list( $seqlist, $blastdir, $blname, $doprot); # may chdir } # foreach my $db (@dbs) { # next unless($db && -e $db); # my $doprot= ($db =~ m/$isprot_patt/) ? 1 : 0; # $self->formatdb($db, $blastdir, $doprot); # may chdir # } } sub formatdb_list { my $self= shift; my( $seqlist, $blastdir, $blastname, $doprot)= @_; warn "formatdb( $blastname )\n" if $DEBUG; my $opts= $self->getconfig('formatdbopts'); ##$formatdbopts; if ($doprot) { $opts .= ' -p T ';} else { $opts .= ' -p F '; } warn("#$blastname: cat ",join(" ",@$seqlist)," | $formatdb $opts -i stdin \n") if $DEBUG; my $olddir= $ENV{'PWD'}; #?? not safe? chdir($blastdir); # need for formatdb - no good -out option foreach (@$seqlist) { $_ = catfile($olddir,$_) unless($_ =~ m,^/,); } my $seqlib = join(" ",@$seqlist); my $cat= ($seqlib =~ /\.(gz|Z)/) ? 'gunzip -c' : 'cat'; system("$cat $seqlib | $formatdb $opts -i stdin "); opendir(D,"."); my @f= grep(/stdin/,readdir(D)); closedir(D); foreach my $f (@f) { (my $t= $f) =~ s/stdin/$blastname/; rename($f,$t); } chdir($olddir); } sub formatdb { my $self= shift; my($seqlib, $blastdir, $doprot)= @_; warn "formatdb($seqlib)\n" if $DEBUG; warn "BlastWriter: Missing $formatdb" and return -1 unless(-e $formatdb); my $opts= $self->getconfig('formatdbopts'); ##$formatdbopts; if ($doprot) { $opts .= ' -p T ';} else { $opts .= ' -p F '; } my ($sfile, $spath, $ext) = File::Basename::fileparse($seqlib, '\.[^\.]+'); my $blastname = $self->blastname($sfile); my $olddir= $ENV{'PWD'}; #??? chdir($blastdir); # need for formatdb - no good -out option my $cat= ($seqlib =~ /\.(gz|Z)$/) ? 'gunzip -c' : 'cat'; $seqlib = catfile($olddir,$seqlib) unless($seqlib =~ m,^/,); warn("$cat $seqlib | $formatdb $opts -i stdin \n") if $DEBUG; system("$cat $seqlib | $formatdb $opts -i stdin "); opendir(D,"."); my @f= grep(/stdin/,readdir(D)); closedir(D); foreach my $f (@f) { (my $t= $f) =~ s/stdin/$blastname/; rename($f,$t); } chdir($olddir); } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/BulkWriter.pm000644 000765 000024 00000037545 11310002762 021155 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::BulkWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::BulkWriter >>> use ToFormat/ToFasta/ToGFF/.. instead ? =head1 SYNOPSIS base class for other Bulkfiles writers New output formats are added by subclassing the Bio::GMOD::Bulkfiles::BulkWriter module, which basically takes tabular inputs from the intermediary SQL output and does something with it. Primary methods to subclass: 'makefiles' and 'readInput' =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; our $DEBUG = 0; sub DEBUG { return $DEBUG; } #use constant DEBUG => 1; my $VERSION = "1.1"; #my $configfile= "bulkwriter"; use constant BULK_TYPE => 'other'; use constant CONFIG_FILE => 'bulkwriter'; sub new { my $that= shift; my $class= ref($that) || $that; my %fields = @_; my $self = \%fields; # config should be one bless $self, $class; $self->_init_base(); return $self; } sub DESTROY { my $self = shift; } sub _init_base { my $self= shift; $DEBUG= $self->{debug}; $self->{bulktype} = $self->BULK_TYPE; #"other"; # dont need this hash val? $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; $self->{status}=0; $self->{error}= undef; # new common caller arg: fileinfo is the fileset data # unless(ref $self->{handler}) { if(ref $self->{sequtil}) { $self->{handler}= $self->{sequtil}; } elsif(ref $self->{bulkfiles}) { $self->{handler}= $self->{bulkfiles}; } else { die "Should make ->new(handler => Bio::GMOD::Bulkfiles object)"; } } ## add these to %ENV before reading blastfiles.xml so ${vars} get replaced .. my $sconfig= $self->handler_config; my @keys = qw( species org date title rel relfull relid release_url ); #@ENV{@keys} = @{%$sconfig}{@keys}; foreach my $next_key (@keys) { # printf STDERR "(%s) %s\n", ($next_key, $sconfig->{$next_key}); $ENV{$next_key} = $sconfig->{$next_key}; } $self->init(); # preconfig inits $self->readConfig($self->{configfile}); # == $self->{config}= $self->handler()->callReadConfig($self->{configfile}); $self->initData(); } =item init() Subclass: initialize at new() object, once only =cut sub init { my $self= shift; # for subclasses } sub handler { return shift->{handler}; } # sub sequtil { return shift->{handler}; } # old method; drop # sub bulkfiles { return shift->{handler}; } # old method; drop sub config { return shift->{config}; } sub handler_config { return shift->{handler}->{config}; } sub outputpath { my $self = shift; unless($self->{outputpath}) { my $outputpath= $self->handler()->getReleaseSubdir( $self->getconfig('path') || $self->BULK_TYPE); $self->{outputpath} = $outputpath; } return $self->{outputpath}; } sub status { my $self= shift; if(@_) { ## if status/error already set? $self->{status}= shift; # unless ($self->{status}); $self->{error}= join(",",@_) if (@_); } my $stat= $self->{status}; # check {error} ?? $self->handler()->{didmake}{ $self->BULK_TYPE }= $stat; if ($stat < 0) { $stat="error ".$stat; } elsif ($stat == 1) { $stat='ok'; } return $self->BULK_TYPE."=".$stat; #what? } =item readConfig($configfile) read a configuration file - adds to any loaded configs =cut sub readConfig { my $self= shift; # my ($configfile)= @_; # ?? dont dupl this elsewhere: BulkWriter.pm subs $self->{config}= $self->handler()->callReadConfig(@_); } =item initData Subclass: initialize config & other data after each readConfig =cut sub initData { my($self)= @_; my $config = $self->{config}; my $sconfig= $self->handler_config(); my $oroot= $sconfig->{rootpath}; $self->{failonerror}= $sconfig->{failonerror}||0 unless defined $self->{failonerror}; $self->{skiponerror}= $sconfig->{skiponerror}||1 unless defined $self->{skiponerror}; ## use instead $self->getconfig('key') $self->{org}= $sconfig->{org} || $config->{org} || 'noname'; $self->{rel}= $sconfig->{rel} || $config->{rel} || 'noname'; $self->{sourcetitle}= $sconfig->{title} || $config->{title} || 'untitled'; $self->{sourcefile} = $config->{input} || ''; $self->{date}= $sconfig->{date} || $config->{date} || POSIX::strftime("%d-%B-%Y", localtime( $^T )); # copy any filesets to handler for those functions foreach my $type ( keys %{$config->{fileset}} ) { $sconfig->{fileset}->{$type}= $config->{fileset}->{$type} unless(defined $sconfig->{fileset}->{$type}); } $self->{fileinfo} = $self->handler()->getFilesetInfo($self->BULK_TYPE) unless($self->{fileinfo}); $self->promoteconfigs(); # uses above configs } =item promoteconfigs() copy fileinfo (1) and main config (2nd) values to self->config =cut sub promoteconfigs { my $self = shift; my @mykeys= @_; my $config= $self->{config}; ## $self->{config}= {}; # dont re-getconfig same my %nopromo= map { $_,1; } qw( id doc title about name date ); unless(@mykeys) { @mykeys= grep !$nopromo{$_}, sort keys %{$config}; } my $fileinfo = $self->{fileinfo} || {}; my $mainconf = $self->handler_config() || {}; # copy any release-specific additions/changes to config from mainconf foreach my $key ( @mykeys ) { my $sc= $mainconf->{$key}; $config->{$key}= _mergevars($config->{$key},$sc) if ($sc); } # foreach my $k (@mykeys) { # only main if not fileinfo # $config->{$k}= $mainconf->{$k} # if(defined $mainconf->{$k} && !defined $fileinfo->{$k}); # } # use all of fileinfo foreach my $k (keys %$fileinfo) { $config->{$k}= $fileinfo->{$k}; } $self->{config}= $config; } sub _mergevars { my($v,$add)= @_; if (!$add) { return $v; } elsif (!$v) { return $add; } elsif (!ref($v) && !ref($add)) { return $add; } # new? elsif (ref($v) =~ /HASH/ && ref($add) =~ /HASH/) { foreach my $k (keys %$add) { $v->{$k}= $add->{$k}; } } =item not this ?? duplicates data ; check for new ? elsif (ref($v) =~ /ARRAY/) { if (ref($add) =~ /ARRAY/) { push(@$v, @$add); } else { push(@$v, $add); } } =cut return $v; } =item getconfig(@keys) return config value(s) for key(s); look for key(s) in (1) fileset info; (2) handler.config ?? should this preceed default? (3) default package config =cut sub getconfig { my $self = shift; my @keys= @_; ## need option to choose among fileinfo, handler, default my $fileinfo = $self->{fileinfo} || {}; # 1st priority or drop??? my $mainconf = $self->handler_config() || {}; # 2nd priority; e.g. main release config my $deconfig = $self->{config} || {}; # 3rd priority; default settings if (wantarray) { my %vals=(); foreach my $key (@keys) { $vals{$key}= (defined $fileinfo->{$key}) ? $fileinfo->{$key} : (defined $mainconf->{$key}) ? $mainconf->{$key} : (defined $deconfig->{$key}) ? $deconfig->{$key} : undef; } return %vals; } else { my $key= $keys[0]; return(defined $fileinfo->{$key}) ? $fileinfo->{$key} : (defined $mainconf->{$key}) ? $mainconf->{$key} : (defined $deconfig->{$key}) ? $deconfig->{$key} : undef; } return undef; } #-------------- subs ------------- =item makeFiles( %args ) primary method makes blast indices. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required =cut sub makeFiles { my $self= shift; my %args= @_; print STDERR "makeFiles\n" if $DEBUG; # debug my $status= 0; my $name = $args{name} || $self->{bulktype}; my $filesetinfo = $args{filesetinfo}; # hash of configs my $infiles = $args{infiles}; # array ref of file specs unless(ref $filesetinfo or ref $infiles) { warn "makeFiles $name: needs infiles => \@infiles "; return; } # my @seqfiles= $self->openInput( $infiles ); # my $res= $self->processBlastInput( \@seqfiles); ## no input files here, input from sql query; should be new module, SQLWriter ?? my $dumpfiles= undef; if( $filesetinfo->{input} eq "sql_query" ) { #?? $filesetinfo->{ENV}= \%ENV; # dang, need this for ${variable} replacement in sql? $dumpfiles = $self->handler->dumpFeatures($filesetinfo, undef, "colnames"); $status= scalar(@$dumpfiles); # print STDERR "$name: sql_query status = $status\n" if $DEBUG; } if ($self->config->{makeall} && $status > 0) { my $chromosomes= ""; my $feature= ""; $self->makeall( $chromosomes, $feature, $self->BULK_TYPE); } return $self->status($status); #?? check files made } sub makeall { my $self= shift; my( $chromosomes, $feature, $format )= @_; my $outdir= $self->outputpath(); $chromosomes= $self->handler()->getChromosomes() unless (ref $chromosomes); ## this loop can be common to other writers: makeall( $chromosomes, $feature, $format) ... my $allfn= $self->get_filename ( $self->{org}, 'all', $feature, $self->{rel}, $format); $allfn= catfile( $outdir, $allfn); my @parts=(); foreach my $chr (@$chromosomes) { next if ('all' eq $chr); my $fn= $self->get_filename ( $self->{org}, $chr, $feature, $self->{rel}, $format); $fn= catfile( $outdir, $fn); next unless (-e $fn); push(@parts, $fn); } if (@parts) { unlink $allfn if -e $allfn; # dont append existing my $allfh= new FileHandle(">$allfn"); ## DONT open-append foreach my $fn (@parts) { my $fh= new FileHandle("$fn"); while (<$fh>) { print $allfh $_; } close($fh); unlink $fn if (defined $self->config->{perchr} && $self->config->{perchr} == 0); } close($allfh); } } =item openInput( $fileset ) handle input files =cut =item openInput( $fileset ) handle input files =cut sub openInput { my $self= shift; my( $fileset, $ipart, $intype )= @_; # do per-csome/name ## $intype ||= $self->getconfig('informat') $intype= $self->config->{informat} unless ($intype); #? maybe array print STDERR "openInput: type=$intype part=$ipart \n" if $DEBUG; my $atpart= 0; foreach my $fs (@$fileset) { my $fp = $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; next unless(!$intype || $fs->{type} =~ /$intype/); unless(-e $fp) { warn "missing infile $fp"; next; } $atpart++; next unless($atpart > $ipart); print STDERR "openInput: name=$name, type=$type, $fp\n" if $DEBUG; ## note: fileset maker probably already set these. my ( $org, $chr1, $featn, $rel, $format )= $self->split_filename($fp); $fs->{org}= $org; $fs->{chr}= $chr1 unless($fs->{chr}); $fs->{featn}= $featn; $fs->{rel}= $rel; $fs->{format}= $format; if ($fp =~ m/\.(gz|Z)$/) { open(INF,"gunzip -c $fp|"); $fs->{pipe}=1; } else { open(INF, $fp); } my $inh= *INF; $fs->{inh}= $inh; return $fs; } print STDERR "openInput: nothing matches part=$ipart\n" if $DEBUG; return undef; } sub resetInput { my $self= shift; my( $infile )= @_; my $inh= $infile->{inh}; my $fp = $infile->{path}; if ($infile->{pipe} || $fp =~ m/\.(gz|Z)$/) { close($inh) if $inh; open(INF,"gunzip -c $fp|"); $inh= *INF; $infile->{pipe}=1; } elsif (!$inh) { open(INF,$fp); $inh= *INF; } else { seek($inh,0,0); } $infile->{inh}= $inh; return $inh; } # for base class ... =item makeSymlinks( $fileset, $intype, $toname_patt, $fromdir, $todir ) make file symlinks; input parameters: $fileset, $intype, $toname_patt, $fromdir, $todir $toname_patt = pattern for todir/name with substitutions from fileset-> $name, $type, $chr, $format, $rel, $org e.g., toname_patt = 'dna-$chr.raw' or "\$org-\$chr-\$type-\$rel.\$format" =cut sub makeSymlinks { my $self= shift; my( $fileset, $intype, $toname_patt, $fromdir, $todir )= @_; # do per-csome/name foreach my $fs (@$fileset) { # my $fp= $fs->{path}; # my $name= $fs->{name}; # my $type= $fs->{type}; # my $chr= $fs->{chr}; my($fp,$name,$type,$chr,$format,$rel,$org)= ($fs->{path},$fs->{name},$fs->{type},$fs->{chr}, $fs->{format},$fs->{rel},$fs->{org} ); # can we do () = $fs->{qw(path name ... org)} ? next unless(!$intype || $fs->{type} =~ /$intype/); ## unless(-e $fp) { warn "missing intype file $fp"; next; } my($filename, $dir) = File::Basename::fileparse($fp); my $toname = $toname_patt; # 'dna-$chr.raw' $toname =~ s/\$name/$name/; $toname =~ s/\$type/$type/; $toname =~ s/\$chr/$chr/; $toname =~ s/\$format/$format/; $toname =~ s/\$rel/$rel/; $toname =~ s/\$org/$org/; my $relpath= catfile($fromdir, $filename); my $symname= catfile($todir, $toname); symlink( $relpath, $symname); print STDERR "symlink $toname -> $relpath\n" if $DEBUG; } #return error/ok ? } =item copyFiles( $fileset, $intype, $toname_patt, $todir ) copy files; input parameters: $fileset, $intype, $toname_patt, $todir $toname_patt = pattern for todir/name with substitutions from fileset-> $name, $type, $chr, $format, $rel, $org e.g., toname_patt = 'dna-$chr.raw' or "\$org-\$chr-\$type-\$rel.\$format" =cut sub copyFiles { my $self= shift; my( $fileset, $intype, $toname_patt, $todir )= @_; # do per-csome/name foreach my $fs (@$fileset) { my($fp,$name,$type,$chr,$format,$rel,$org)= ($fs->{path},$fs->{name},$fs->{type},$fs->{chr}, $fs->{format},$fs->{rel},$fs->{org} ); # can we do () = $fs->{qw(path name ... org)} ? next unless( !$intype || $fs->{type} =~ m/$intype/); ## unless(-e $fp) { warn "missing intype file $fp"; next; } ## my($filename, $dir) = File::Basename::fileparse($fp); my $toname = $toname_patt || $name; $toname =~ s/\$name/$name/; $toname =~ s/\$type/$type/; $toname =~ s/\$chr/$chr/; $toname =~ s/\$format/$format/; $toname =~ s/\$rel/$rel/; $toname =~ s/\$org/$org/; my $frompath= $fp; ##catfile($fromdir, $filename); my $topath = catfile($todir, $toname); system('/bin/cp', '-p', $frompath, $topath); print STDERR "copy $frompath to $toname\n" if $DEBUG; } #return error/ok ? } =item readIdsFromFFF pre-read ids from fff input for selected features for others to add_id or filter by id moved to base class for reuse =cut sub readIdsFromFFF { my $self= shift; my ($fffin,$chr,$config)= @_; my $idlist= {}; my $types_info= $config->{featmap}; my $nid=0; while(<$fffin>) { next unless(/^\w/); chomp; my ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr1) = $self->handler()->splitFFF($_, $chr); if ($types_info->{$type}->{get_id}) { $idlist->{$id}= $dbxref; $nid++; } } print STDERR "read ids n=$nid\n" if $DEBUG; return $idlist; } =item get_filename $fname= get_filename( $org, $chr, $featn, $rel, $format) make standard output file name "${org}_${chr}_${featn}_${rel}.${format}" =cut sub get_filename { return shift->handler()->get_filename( @_); } =item split_filename ( $org, $chr, $featn, $rel, $format)= split_filename( $fname) return parts of standard output file name "${org}_${chr}_${featn}_${rel}.${format}" =cut sub split_filename { return shift->handler()->split_filename( @_); } =item isold($source,$target) is source file older than target? ## not for symlinks or dirs =cut sub isold { my $self= shift; my($source,$target) = @_; if (! -e $target) { return 1; } my $res= 0; my $targtime= -M $target; ## -M is file age in days.hrs before now if ( -l $source ) { # $source= getOriginal($source); $res= (-M $source) < $targtime; } elsif ( -e $source ) { $res= (-M $source) < $targtime; } else { $res= 0; } return $res; } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/FastaWriter.pm000644 000765 000024 00000074772 11256707527 021345 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::FastaWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::FastaWriter =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $sequtil= Bio::GMOD::Bulkfiles->new( configfile => 'seqdump-r4', ); my $fwriter= $sequtil->getFastaWriter(); my $result = $fwriter->makeFiles( ); =head1 NOTES genomic sequence file utilities, part3; parts from flybase/work.local/chado_r3_2_26/soft/chado2flat2.pl =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug# #use lib("/bio/argos/common/perl/lib", "/bio/argos/common/system-local/perl/lib"); #use lib("/Users/gilbertd/bio/dev/gmod/schema/GMODTools/lib/"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; # use Bio::GMOD::Bulkfiles::SWISS_CRC64; # see below require use base qw(Bio::GMOD::Bulkfiles::BulkWriter); #use vars qw(@ISA); @ISA= (qw/Bio::GMOD::Bulkfiles::BulkWriter/); our $DEBUG = 0; my $VERSION = "1.1"; #? how do constants overload in perl object inheritance ?? # perldoc constant: Subclasses may .. override those in their base class. # BUT need to do $obj->CONSTANT not CONSTANT use constant BULK_TYPE => 'fasta'; use constant CONFIG_FILE => 'fastawriter'; sub init { my $self= shift; $self->SUPER::init(); $DEBUG= $self->{debug} if defined $self->{debug}; } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); } #-------------- subs ------------- =item makeFiles( %args ) primary method arguments: infiles => \@fileset of fff features and dna sequences, # required =cut sub makeFiles { my $self= shift; my %args= @_; print STDERR "FastaWriter::makeFiles\n" if $DEBUG; # debug # 0710: no_csomesplit : no perchr files, only makeall my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 my $makeall= !$no_csomesplit && !$args{noall} && $self->config->{makeall}; # more sensible that writer should ask handler for kind of files it wants my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; unless(@$fileset) { my $intype= $self->{config}->{informat} || 'fff'; #? maybe array $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "FastaWriter: no input '$intype' files found\n"; return $self->status(-1); } } my $featset= $self->handler_config->{featset} || []; #? or default set ? my $addids = defined $args{addids} ? $args{addids} : $self->getconfig('addids'); my %chrset=(); my $status= 0; my $ok= 1; for (my $ipart= 0; $ok; $ipart++) { $ok= 0; my $infile= $self->openInput( $fileset, $ipart); if ($infile && $infile->{inh}) { my $inh= $infile->{inh}; my $chr= $infile->{chr}; $chrset{$chr}++; if ($addids) { my $idlist= $self->readIdsFromFFF( $inh, $chr, $self->handler_config()); $self->{idlist}= $idlist; $inh= $self->resetInput($infile); #seek($inh,0,0); ## cant do on STDIN ! cant do on PIPE ! } ## need to know $chr here .. from $fileset infile my $res= $self->processFasta( $inh, $chr, $featset); close($inh); delete $infile->{inh}; $status += $res; $ok= 1; } } #? use found $chromosomes= [sort keys %chrset] ; want to keep original sort order $self->makeall( $chromosomes, $featset) if ($makeall && $status > 0) ; print STDERR "FastaWriter::makeFiles: done n=$status\n" if $DEBUG; return $self->status($status); } sub makeall { my $self= shift; my( $chromosomes, $featset )= @_; my $outdir= $self->outputpath(); my @features= @$featset; $chromosomes= $self->handler()->getChromosomes() unless (ref $chromosomes); my $perchr= (defined $self->config->{perchr} && $self->config->{perchr} == 0); # fixme: no_csomesplit foreach my $featn (@features) { ## this loop can be common to other writers: makeall( $chromosomes, $feature, $format) ... # $self->SUPER::makeall($chromosomes, $featn, $self->BULK_TYPE); my $allfn= $self->get_filename ( $self->{org}, 'all', $featn, $self->{rel}, $self->BULK_TYPE); $allfn= catfile( $outdir, $allfn); my @parts=(); foreach my $chr (@$chromosomes) { next if ('all' eq $chr); my $fn= $self->get_filename ( $self->{org}, $chr, $featn, $self->{rel}, $self->BULK_TYPE); $fn= catfile( $outdir, $fn); next unless (-e $fn); push(@parts, $fn); } if (@parts) { unlink $allfn if -e $allfn; # dont append existing my $allfh= new FileHandle(">$allfn"); ## DONT open-append foreach my $fn (@parts) { my $fh= new FileHandle("$fn"); while (<$fh>) { print $allfh $_; } close($fh); unlink $fn if ($perchr); } close($allfh); } } } =item openInput( $fileset ) handle input files .. copied to base class =cut sub openInput { my $self= shift; my( $fileset, $ipart )= @_; # do per-csome/name my $intype= $self->config->{informat} || 'fff'; #? maybe array my $atpart= 0; # print STDERR "openInput: type=$intype part=$ipart \n" if $DEBUG; foreach my $fs (@$fileset) { my $fp = $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; next unless( $fs->{type} =~ /$intype/); # could it be 'dna/fasta', 'amino/fasta' ? unless(-e $fp) { warn "missing infile $fp"; next; } $atpart++; next unless($atpart > $ipart); print STDERR "openInput[$ipart]: name=$name, type=$type, $fp\n" if $DEBUG; my ( $org, $chr1, $featn, $rel, $format )= $self->split_filename($fp); $fs->{org}= $org; $fs->{chr}= $chr1 unless($fs->{chr}); $fs->{featn}= $featn; $fs->{rel}= $rel; $fs->{format}= $format; if ($fp =~ m/\.(gz|Z)$/) { open(INF,"gunzip -c $fp|"); $fs->{pipe}=1; } else { open(INF, $fp); } my $inh= *INF; $fs->{inh}= $inh; return $fs; } print STDERR "openInput: nothing matches part=$ipart, type=$intype\n" if $DEBUG; return undef; } sub resetInput { my $self= shift; my( $infile )= @_; my $inh= $infile->{inh}; my $fp = $infile->{path}; if ($infile->{pipe} || $fp =~ m/\.(gz|Z)$/) { close($inh) if $inh; open(INF,"gunzip -c $fp|"); $inh= *INF; $infile->{pipe}=1; } elsif (!$inh) { open(INF,$fp); $inh= *INF; } else { seek($inh,0,0); } $infile->{inh}= $inh; return $inh; } =item processFasta =cut sub processFasta { my $self= shift; my( $inh, $chr, $featset )= @_; my $ndone= 0; my $outh= {}; my $outdir= $self->outputpath(); ## my @features= @$featset; my @fffeatures= @$featset; print STDERR "processFasta featset=",join(",",@fffeatures),"\n" if $DEBUG; $self->{diddbfa}= {} unless($self->{diddbfa}); my $featmap = $self->handler_config->{featmap}; # NOT local config ; for main config's featmap # add something like this, but dump direct from db, for EST, reagent seqs w/o csome loc # 200710: no_csomesplit update: no dna/ files, draw all seq from chadodb my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 my $write = ($no_csomesplit) ? ">>" : ">"; my $chrout= ($no_csomesplit) ? "all" : $chr; my @dbfeatures= (); my @ffflist= @fffeatures; foreach my $featn (@ffflist) { my $fn= $self->get_filename ( $self->{org}, $chrout, $featn, $self->{rel}, $self->BULK_TYPE); $fn= catfile( $outdir, $fn); print STDERR "processFasta $featn outh=$fn\n" if $DEBUG; ## special case for feat == chromosome/dna -> raw2Fasta if(!$no_csomesplit and $featn eq "chromosome") { $self->raw2Fasta( chr => $chr, fastafile => $fn) unless($self->{diddbfa}->{$featn}); $self->{diddbfa}->{$featn}++; $ndone++; @fffeatures= grep !/^$featn$/, @fffeatures; next; } $outh->{$featn}= new FileHandle("$write$fn"); # no_csomesplit: append dont create here ## check featmap for db vs fff features !? my $fm= $featmap->{$featn}; if($fm && $fm->{onlydb}) { push(@dbfeatures, $featn) unless($self->{diddbfa}->{$featn}); $self->{diddbfa}->{$featn}++; @fffeatures= grep !/^$featn$/, @fffeatures; } } ## dang do this only once; this method called inside chromosome loop; $ndone += $self->fastaFromDb( $outh, \@dbfeatures) if (@dbfeatures); $ndone += $self->fastaFromFFFloop( $inh, $outh, $chr, \@fffeatures) if (@fffeatures); ## ## dang do this only once; this method called inside chromosome loop; ## $ndone += $self->fastaFromDb( $outh, \@dbfeatures) if (@dbfeatures); foreach my $featn (keys %$outh) { my $fh= $outh->{$featn}; close($fh); #? check size and delete if zero or leave for check ? } #print STDERR "process ndone = $ndone\n" if $DEBUG; return $ndone; } sub writeheader { my $self= shift; my($seqid,$start,$stop)= @_; } sub get { my $self= shift; my($fob)= @_; return undef; } sub writeendobj { my $self= shift; #my $fh= $self->{outh}; #print $fh "###\n"; } sub writeobj { my $self= shift; my( $fob )= @_; my $fh= $self->{outh}; my $line= $self->get($fob); print $fh $line if $line; } =item fastaHeader my $fah= main->fastaHeader( ID => 'CG123', name => 'MyGene', chr => '2L', loc => '1234..5678', type => 'pseudogene', db_xref => 'FlyBase:FBgn0000123', note => 'BOGUS', ); expected keys: type chr/chromosome loc/location ID name db_xref =cut sub fastaHeader { my($self,%vals)= @_; my $type= delete $vals{type}; my $chr= delete $vals{chr} || delete $vals{chromosome}; my $loc= delete $vals{loc} || delete $vals{location}; $loc= "$chr:$loc" if ($chr && $loc !~ /:/); my $ID = delete $vals{ID} || delete $vals{id} || delete $vals{uniquename}; my $name= delete $vals{name}; my $db_xref= delete $vals{db_xref} || delete $vals{dbxref}; if ($db_xref) { $db_xref =~ s/\s*;\s*$//; $db_xref =~ s/;/,/g; $db_xref =~ s/,,/,/g;} my %primvals=(); @primvals{qw(type loc ID name db_xref)}= ($type,$loc,$ID,$name,$db_xref); my @d=(); foreach my $hk (qw(type loc ID name db_xref), sort keys %vals) { my $v= $primvals{$hk} || $vals{$hk}; next unless($v); my $key= $hk; if($self->config->{recodekey}->{$hk}) { $key= $self->config->{recodekey}->{$hk}->{content}; } push(@d, "$key=$v"); } my $desc= join("; ", @d); my $fid= ($ID) ? $ID : $name; unless($fid) { $fid= "${type}_${loc}"; $fid =~ tr/a-zA-Z0-9/_/cs; } return "$fid $desc"; } sub fastaFromFFFloop { my $self= shift; my ( $fffin, $outh, $chrIn, $featset )= @_; my $lastchr=""; my $nout= 0; my $sconfig= $self->handler_config; $self->{ffformat}= 0; my %lastfff= (); my $org= $self->{org}; # || $self->handler()->{config}->{org}; my $rel= $self->{rel}; # || $self->handler()->{config}->{rel}; my $allowanyfeat= (!$featset || $featset =~ /^(any|all)/i) ? 1 : (defined $self->config->{allowanyfeat}) ? $self->config->{allowanyfeat} : 0; print STDERR "fastaFromFFFloop: ft=".join(",",@$featset),"\n" if $DEBUG; my $ndebug=0; while(<$fffin>) { next unless(/^\w/); chomp; my $fff= $_; ## my $faline= $self->fastaFromFFF( $_, $chrIn, $featset); ## print $fah $faline if $faline; #? loop here over @$featset ??? # one input line can produce > 1 output fasta, e.g. gene & gene_extended, & intergene? ## add option to handle intergene type feature sets -> subrange? my @fvals = $self->handler()->splitFFF($fff, $chrIn); $self->{ffformat}= $self->{gotffformat}; # set by splitFFF my($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr)= @fvals; my @notes= $self->cleanNotes($notes); my @features= (ref $featset) ? @$featset : ($type); my $didfeat= 0; foreach my $featn (@features) { ## this loop is tricky - print each input fff only once ## UNLESS special case of showing in other types_ok ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr)= @fvals; my($types_ok,$retype,$usedb,$subrange,$types_info) = $self->get_feature_set( $featn, $sconfig, $allowanyfeat); my $fah= $outh->{$featn}; my $hasout = ($fah) ? 1 : 0; my $goodfeat= ( ($types_ok && $types_ok->{$type}) || ($allowanyfeat && !$didfeat) ); # ## why cant we get gene featset now ?? # if($featn =~ /^gene/){ # print STDERR "# fffa loop: $featn>$type ok=$goodfeat did=$didfeat out=$hasout\n" if $DEBUG and 100>$ndebug++; # } next unless($goodfeat and $hasout); $self->{use_dbmd5}= $usedb; #? want sep. flag in featmap.xml ? if ($types_info->{method} eq 'between') { my $lastf= $lastfff{$type}; $lastfff{$type}= $fff; # problems below.. save now if($lastchr eq $chr && $lastf) { ## arg - $lastfff only for same type as this fff ! my $ffftween= $self->handler()->intergeneFromFFF2( $chr, $lastf, $fff); print STDERR "intergene: $ffftween\n" if $DEBUG > 1; next unless($ffftween); ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr) = $self->handler()->splitFFF( $ffftween, $chr); } else { next; } $self->{use_dbmd5}= 0; } if ($self->{idlist} && $types_info->{add_id}) { ## addids $dbxref= $self->addIdsToDbxref( ($id ? $id : $name), $dbxref ); } my ($start,$stop,$strand)= $self->handler()->maxrange($baseloc); my $shortloc= ($stop<0) ? $baseloc : ($strand<0) ? "complement($start..$stop)" : "$start..$stop"; # option for full/short loc in header? my @fnotes= @notes; print STDERR "getBases id=$id type=$type chr=$chr loc=$baseloc\n" if $DEBUG>2; my $bases= $self->handler()->getBases( $usedb, $type, $chr, $baseloc, $id, $name, $subrange, $types_info->{dotranslate}); my $seqlen= $bases ? length($bases) : 0; ## add optional md5checksum, SwissProt CRC64 calcs; ## check if last getBases returned md5checksum my @crcs= $self->getCRCs( $id, \$bases, \@fnotes); my $defline= $self->fastaHeader( type => $retype->{$type}||$type, name => $name, chr => $chr, location => $shortloc, ID => $id, db_xref => $dbxref, $org ? (species => $org) : (), $rel ? (release => $rel) : (), len => $seqlen, @fnotes, @crcs, ); if ($bases) { # my $slen= length($bases); $bases =~ s/(.{1,50})/$1\n/g; print $fah ">$defline\n"; # ; len=$slen print $fah $bases; $nout++; } else { warn "ERROR: missing bases for $defline\n"; if ($self->handler()->{failonerror}) { warn "FAILING: $chrIn $featset \n"; return undef; } # write at least one dummy base so user soft wont screw up print $fah ">$defline; ERROR missing data\nN\n" if($self->config->{writeemptyrecords}); #? write to file or not } $didfeat++; } ($lastchr)=($chr); # $lastfff{$type}= $fff; #? problem } return $nout; } sub getCRCs { my($self, $id, $basesref, $notesref)= @_; ## add optional md5checksum, SwissProt CRC64 calcs; ## check if last getBases returned md5checksum my @retcrcs=(); my($addmd5sum,$addcrc64)= ($self->config->{addmd5sum},$self->config->{addcrc64}); my $use_dbmd5= $self->{use_dbmd5}; if ($addmd5sum) { my $md5=''; my $baseft= ($use_dbmd5) ? $self->handler()->getLastBasesFeature() : undef; if ($baseft && ref($baseft) =~ /HASH/ && $$baseft{'uniquename'} eq $id) { $md5= $$baseft{'md5checksum'}; } if ($md5) { # maybe calc and compare if want to verify ? } elsif(ref($basesref)) { require Digest::MD5; #? problem my $md5sum= Digest::MD5->new; if($md5sum) { $md5sum->add($$basesref); $md5= $md5sum->hexdigest(); } } # warn "CRC id=$id md5=$md5\n" if $DEBUG > 1; push(@retcrcs, "MD5",$md5) if ($md5); } if ($addcrc64 and ref($basesref)) { require Bio::GMOD::Bulkfiles::SWISS_CRC64; my $crc64sum= SWISS_CRC64->new; if($crc64sum) { $crc64sum->add($$basesref); my $crc= $crc64sum->hexsum(); push(@retcrcs, "CRC64",$crc) if ($crc); } } return @retcrcs; } =item fastaFromFFF $fa= $handler->fastaFromFFF( $fffeature,$chr,$featset) return fasta for one input feature line $fffeature = flat-file-feature input line chr = chromosome featset = key for feature type or type-set The flat-file-feature input line looks like @v= split "\t", $fffeature; if ($ffformat == 1) { ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes)= @v; } elsif ($ffformat == 2) { ($chr,$bstart,$type,$name,$cytomap,$baseloc,$id,$dbxref,$notes)= @v; } # format 2 just has leading chromosome, start-position fields for sorting where baseloc == Genbank/EMBL/DDBJ location string == BioPerl FTstring =cut sub fastaFromFFF { my($self, $fffeature, $chrIn, $featset)= @_; my $allowanyfeat= (!$featset || $featset =~ /^(any|all)/i) ? 1 : (defined $self->config->{allowanyfeat}) ? $self->config->{allowanyfeat} : 0; # print STDERR "fastaFromFFF: 1\n" if $DEBUG>1; my $org= $self->{org}; # || $self->handler()->{config}->{org}; my $rel= $self->{rel}; # || $self->handler()->{config}->{rel}; my($types_ok,$retype,$usedb,$subrange,$types_info) = $self->get_feature_set( $featset, undef, $allowanyfeat); return "" unless( ref $types_ok ); my ($type,$name,$cytomap,$baseloc,$id,$dbxref,$notes,$chr) = $self->handler()->splitFFF($fffeature, $chrIn); return "" unless( $allowanyfeat || $types_ok->{$type} ); # print STDERR "fastaFromFFF: 2\n" if $DEBUG>1; $self->{use_dbmd5}= $usedb; #? want sep. flag in featmap.xml ? if ($self->{idlist} && $types_info->{add_id}) { $dbxref= $self->addIdsToDbxref( ($id ? $id : $name), $dbxref ); } my @notes= $self->cleanNotes($notes); my ($start,$stop,$strand)= $self->handler()->maxrange($baseloc); my $shortloc= ($stop<0) ? $baseloc : ($strand<0) ? "complement($start..$stop)" : "$start..$stop"; # option for full/short loc in header? my $bases= $self->handler()->getBases( $usedb, $type, $chr, $baseloc, $id, $name, $subrange, $types_info->{dotranslate}); my $seqlen= $bases ? length($bases) : 0; ## add optional md5checksum, SwissProt CRC64 calcs; my @crcs= $self->getCRCs( $id, \$bases, \@notes); my $defline= $self->fastaHeader( type => $retype->{$type}||$type, name => $name, chr => $chr, location => $shortloc, ID => $id, db_xref => $dbxref, $org ? (species => $org) : (), $rel ? (release => $rel) : (), len => $seqlen, @notes, @crcs, ); if ($bases) { #my $slen= length($bases); $bases =~ s/(.{1,50})/$1\n/g; return ">$defline\n".$bases; # ; len=$slen } else { warn "ERROR: missing bases for $defline\n"; if ($self->handler()->{failonerror}) { warn "FAILING: $featset \n"; return undef; } # write at least one dummy base so user soft wont screw up return ">$defline; ERROR missing data\nN\n" if($self->config->{writeemptyrecords}); #? write to file or not } } =item fastaFromDb For sequences not part of golden_path; not in genome feature table files E.g. reagent sequences (EST, cDNA, misc ..) See =cut sub fastaFromDb { my($self, $outh, $featset)= @_; my @features= (ref $featset) ? @$featset : ($featset); my $org= $self->{org}; my $rel= $self->{rel}; my($species,$genus) = ($self->handler->speciesFull($org),''); ($genus,$species)= split(/[_ ]/,$species,2); ## fixme for genus=Anopheles species='gambiae str. PEST' $species =~ s/_/ /g; # is this always right? my $dbh= $self->handler->dbiConnect(); my $nout= 0; unless($genus and $species) { # this is bug area, from above my $err= "ERROR: fastaFromDb: missing genus:$genus, species:$species for org=$org\n"; if ($err) { ($self->{failonerror}) ? die $err : warn $err; return undef; } } foreach my $featn (@features) { print STDERR "fastaFromDb featn=$featn ?\n" if $DEBUG; my $allowanyfeat= 1; # ???? # (!$featn || $featn =~ /^(any|all)/i) ? 1 # : (defined $self->config->{allowanyfeat}) ? $self->config->{allowanyfeat} # : 0; my($types_ok,$retype,$usedb,$subrange,$types_info) = $self->get_feature_set( $featn, undef, $allowanyfeat); next unless($DEBUG || ref $types_ok ); my $onlydb= $types_info->{onlydb} || 0; ## is this right featmap flag ?? next unless($DEBUG || $onlydb); #?? $usedb= 1; my ($chr,$cytomap)= (undef,undef); my ($baseloc)= (undef); # no location or dummy ?? my $outhandle= $outh->{$featn}; next unless($DEBUG || $outhandle); #?? my $err=""; my $sql=""; my $ftypes= "'" . join("','", sort keys %$types_ok) ."'" ; ### FIXME ... look in chadofeatsql ... ## $sql = $self->config->{feature2fastasql}; $sql = " select f.feature_id, t.name as type, f.residues, f.md5checksum, f.seqlen, f.name, f.uniquename from feature f, organism o, cvterm t where t.name in ($ftypes) and t.cvterm_id = f.type_id and o.genus = '$genus' and o.species = '$species' and o.organism_id = f.organism_id " unless($sql); print STDERR "fastaFromDb sql=$sql\n" if ($DEBUG ); my $sth = $dbh->prepare($sql) or $err="unable to prepare feature_id"; #$sth->execute($ftypes,$genus,$species) or $err="failed to execute feature_id"; $sth->execute() or $err="failed to execute feature_id"; if ($err) { ($self->{failonerror}) ? die $err : warn $err; return undef; } while (my $nextrow = $sth->fetchrow_hashref) { my $type= $$nextrow{'type'}; my $name= $$nextrow{'name'}; my $id = $$nextrow{'uniquename'}; my $feature_id = $$nextrow{'feature_id'}; my $bases= $$nextrow{'residues'}; my $seqlen= length($bases) || 0; ## $$nextrow{'seqlen'}; # my ($start,$stop,$strand)= (1,$seqlen,0); # my $shortloc= "$start..$stop"; my @notes= (); #what: featureprop, featuresynonym; others? $self->cleanNotes($notes); my $dbxref= ''; ##FIXME: $$nextrow{'dbxref'}; if ($self->{idlist} && $types_info->{add_id}) { $dbxref= $self->addIdsToDbxref( ($id ? $id : $name), $dbxref ); } my @crcs= (); ## $self->{use_dbmd5}= $usedb; ## $self->getCRCs( $id, \$bases, \@notes); if ($self->config->{addmd5sum}) { my $md5= $$nextrow{'md5checksum'}; push(@crcs, "MD5",$md5) if ($md5); } my $defline= $self->fastaHeader( type => $retype->{$type}||$type, name => $name, ID => $id, db_xref => $dbxref, # location => $shortloc, # chr => $chr, $org ? (species => $org) : (), $rel ? (release => $rel) : (), len => $seqlen, @notes, @crcs, ); print STDERR "fastaFromDb[$nout]=$defline\n" if ($DEBUG && $nout<4); if ($bases) { $bases =~ s/(.{1,50})/$1\n/g; print $outhandle ">$defline\n"; # ; len=$seqlen print $outhandle $bases; } else { warn "ERROR: missing bases for $defline\n"; if ($self->handler()->{failonerror}) { warn "FAILING: $featset \n"; return -1; } # write at least one dummy base so user soft wont screw up print $outhandle ">$defline; ERROR missing data\nN\n" if($self->config->{writeemptyrecords}); #? write to file or not } $nout++; } # db row $sth->finish(); } return $nout; } ## patch for adding gene IDs to gene model features missing them sub addIdsToDbxref { my $self = shift; my ( $pid, $dbxref )= @_; # my $pid= ($id ? $id : $name); $pid =~ s/[_-].*$//; # try for parent id - db prefix: ? my $idlist= $self->{idlist}; # from readids ... my $idpattern= $self->handler()->{idpattern}; if ($idlist->{$pid}) { my %dtype=(); foreach my $x ( $pid, split(/[,;\s]/,$idlist->{$pid})) { if ( $x =~ m/$idpattern/) { ## /(FBgn|FBti|FBan|CG|CR)\d+/ my $dtype= $1; unless( $dtype{$dtype} || ($dbxref && $dbxref =~ m/$x/) ) { $dbxref .= "," if ($dbxref); $dbxref .= $x; } $dtype{$dtype}++; } } } return ($dbxref); #?? } ##? check notes for synonyms=, other fields? sub cleanNotes { my ($self, $notes)= @_; my @notes= (); if ($notes) { my $dropnotes= $self->config->{dropnotes} || 'xxx'; my %notes=(); foreach my $n (split(/[;]/,$notes)) { if ($n =~ /^(\w+)=(.+)/) { my($k,$v)= ($1,$2); $v=~s/\s+$//; if ($v && $dropnotes !~ m/\b$k\b/) { $notes{$k} .= "$v,"; } } } foreach my $n (sort keys %notes) { $notes{$n} =~ s/,$//; push(@notes, $n, $notes{$n}) if($notes{$n}); } } return @notes; } =item raw2Fasta( %args ) args: fastafile => $file # opt append => 1 # opt, append existing file chr => 'X' # required start => 1 #opt end => 100000 # opt type => 'chromosome' # opt defline => 'fasta defline' # opt print fasta from dna-$chr.raw files, given $chr and optional $start,$end =cut sub raw2Fasta { my $self= shift; my %args= @_; my $chr= $args{chr}; my $fastafile= $args{fastafile}; my $start= $args{start}; my $end= $args{end}; my $defline= $args{defline}; my $type= $args{type} || 'chromosome'; my $append= $args{append}; my $dnafile= $self->handler()->dnafile($chr); unless($fastafile) { ($fastafile = $dnafile.".fasta") =~ s/\.raw//; } if (!$append && -e $fastafile) { warn "raw2Fasta: wont overwrite $fastafile"; return $fastafile; } my $write= ($append) ? ">>" : ">"; my $outh= new FileHandle("$write$fastafile"); my $org= $self->handler()->{config}->{org}; my $rel= $self->handler()->{config}->{rel}; my $fullchr= 0; $start= 1 unless(defined $start && $start>=1); if (-f $dnafile) { my $fh= new FileHandle($dnafile); unless(defined $end) { $fh->seek(0,2); $end= $fh->tell(); $fh->seek(0,0); $fullchr= ($start <= 1); } unless ($end>=$start) { $end= $start; } # what ? my $id= ($fullchr) ? $chr : "$chr:$start..$end"; my $seqlen= 1 + $end - $start; #?? add: $self->getCRCs( $id, \$bases, \@notes); ## but need to read dna 1st; revise crc to do add-lines $defline= $self->fastaHeader( ID => $id, ##"$chr:$start..$end", type => $type, chr => $chr, location => "$start..$end", $org ? (species => $org) : (), $rel ? (release => $rel) : (), len => $seqlen, ) unless $defline; print $outh ">$defline\n"; $fh->seek($start-1,0); my $len= ($end-$start+1); my ($buf,$sz)=('',50); for (my $i=0; $i<$len; $i+=50) { if ($sz+$i>=$len) { $sz= $len-$i; } $fh->read($buf,$sz); print $outh $buf,"\n"; } close($fh); } else { unless ($end>=$start) { $end= $start; } # what ? $defline= $self->fastaHeader( ID => "$chr:$start..$end", type => $type, chr => $chr, location => "$start..$end", $org ? (species => $org) : (), $rel ? (release => $rel) : (), len => 0, ) unless $defline; print $outh ">$defline\nN\n"; # one N base for empties } print $outh "\n"; close $outh; print STDERR "raw2Fasta $fastafile, $defline\n" if $DEBUG; return $fastafile; } =item @info= get_feature_set($featset, $config, $allowanyfeat) given feature type or type-class, return info to screen, remap individual features. See config and associated info. args: featset = single feature or feature set class name (given in configs) config = configuration hash allowanyfeat = featset as basic type should be allowed (types_ok) return ($types_ok,$retype,$usedb,$subrange,$types_info) types_ok = hash of which basic types are allowed in featset retype = rename basic types to these for output header usedb = pull residues from database rather than chromosome dna (curated bases) subrange = expansion range (e.g for gene_expanded2000, etc.) types_info = all of featmap information =cut sub get_feature_set { my( $self, $featset, $config, $allowanyfeat)= @_; #return $self->handler()->get_feature_set($featset,$config,$allowanyfeat); my($fromdb,$subrange) = (0,''); my @ft=(); my @retype= (); my $type_info= {}; $config = $self->handler_config unless($config); if(!$config->{featmap}->{$featset} && $featset =~ /^(\w+)_extended(\d+)$/) { my ($t,$r)= ($1,$2); $featset= $t; $subrange= "-$r..$r"; } if (defined $config->{featmap}->{$featset}) { my $fm= $config->{featmap}->{$featset}; @ft= split(/[\s,;]/, $fm->{types} || $featset ); @retype= split(/[\s,;]/, $fm->{typelabel}) if ($fm->{typelabel}); $fromdb= $fm->{fromdb} || 0; $subrange= $fm->{subrange} || $subrange; $fm->{method} ||= ""; if ($fm->{method} eq 'between') { $fm->{proc}= '&intergeneFromFFF2'; ## FIXME } $type_info= $fm; # just save all ? } else { $type_info->{method} ||= ""; CASE: { $featset =~ /^(gene|pseudogene)$/ && do { @ft=($featset); $type_info->{get_id}=1; last CASE; }; $featset =~ /^(CDS|mRNA)$/ && do { @ft=($featset); last CASE; }; $featset =~ /^(five_prime_UTR|three_prime_UTR|intron)$/ && do { @ft=($featset); $type_info->{add_id}= 'gene'; last CASE; }; $featset =~ /^(tRNA|ncRNA|snRNA|snoRNA|rRNA)$/ && do { @ft=($featset); $type_info->{get_id}=1; last CASE; }; $featset =~ /^(miscRNA)$/ && do { @ft=qw(ncRNA snRNA snoRNA rRNA); last CASE; }; $featset =~ /^(transposable_element|transposon)$/ && do { @ft=('transposable_element'); last CASE; }; $featset =~ /^gene_extended(\d+)$/ && do { @ft=('gene'); $subrange="-$1..$1"; @retype=("gene_ex$1"); last CASE; }; $featset =~ /^(transcript)$/ && do { @ft=('mRNA'); $fromdb=1; @retype=('transcript'); last CASE; }; $featset =~ /^(CDS_translation|translation)$/ && do { @ft=('CDS'); $fromdb=1; @retype=('translation'); last CASE; }; default: { if ($allowanyfeat) { @ft=($featset); } elsif (grep {$featset eq $_} @{$config->{fastafeatok}}) { @ft=($featset); } else { return undef; } ## warn "Unknown feature option: $@"; }; } } foreach (@ft) { if(s/^(["'])//){s/$1$//} } $fromdb= 0 if $self->handler()->{ignoredbresidues}; my %types_ok= map { $_,1; } @ft; my %retype = map { my $f= shift @ft; $f => $_; } @retype; return (\%types_ok, \%retype, $fromdb, $subrange, $type_info); } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm000644 000765 000024 00000274335 11256707527 021677 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::FeatureWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::FeatureWriter ; was ChadoFeatDump =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $sequtil= Bio::GMOD::Bulkfiles->new( # was SeqUtil2 configfile => 'seqdump-r4', ); my $fwriter= $sequtil->getFeatureWriter(); ## was Bio::GMOD::ChadoFeatDump->new( configfile => 'chadofeatdump', sequtil => $sequtil ); my $result= $fwriter->makeFiles( infiles => [ @$seqfiles, @$chrfeats ], # required formats => [ qw(fff gff fasta)] , # optional ); =head1 NOTES genomic sequence file utilities, part3; parts from flybase/work.local/chado_r3_2_26/soft/chadosql2flatfeat.pl =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug #use lib("/bio/biodb/common/perl/lib", "/bio/biodb/common/system-local/perl/lib"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::BulkWriter); our $DEBUG = 0; my $VERSION = "1.1"; use constant BULK_TYPE => 'fff+gff';#?? use constant CONFIG_FILE => 'chadofeatdump'; ## !! change these from our to use vars() for package scope our $maxout = 0; our $ntotalout= 0; our $chromosome= {}; ## read info from chado dump chromosomes.tsv our $fff_mergecols=1; # $self->{fff_mergecols} add chr,start cols for merge our $gff_keepoids= 0; # $self->{gff_keepoids} our @outformats= (); our @defaultformats= qw(fff gff); # cmap ?? fasta - no our %formatOk= ( fff => 1, gff => 1 ); # only these handled here ? our @fclone_fields = qw(chr type fulltype name id oid fmin fmax offloc attr writefff writegff); our $outfile= undef; # "chadofeat"; ## replace w/ get_filename ! our $append=0; # $self->{append} #?? is this used? our %gffForwards=(); our @gffForwards=(); use constant TOP_SORT => -9999999; use constant MAX_FORWARD_RANGE => 990000; # at 500000 lost a handful of oidobs refs; maximum base length allowed for collecting forward refs use constant MIN_FORWARD_RANGE => 20000; # minimum base length for collecting forward refs ## our == global scope; use vars == package scope use vars qw/ %maptype %maptype_pattern %mapname_pattern %mapattr_pattern %maptype_gff %segmentfeats %simplefeat %skipaskid %dropfeat_fff %dropfeat_gff %oidisid_gff %dropid %nameisid %dropname %mergematch %hasdups %keepstrand $rename_child_type $name2type_pattern @GModelParts %GModelParents $CDS_spanType $CDS_exonType /; ## $duptype_pattern sub init { my $self= shift; $self->SUPER::init(); $self->{outh} = {}; ## superclass does these?? $DEBUG= $self->{debug} if defined $self->{debug}; # $self->{bulktype} = $self->BULK_TYPE; # dont need hash val? # $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; $self->setDefaultValues(); #?? use or not? hold-over from pre-config work } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); my $config = $self->{config}; my $sconfig= $self->handler_config; ## SUPER does now #$config->{idpattern} = $self->getconfig('idpattern') || ''; #$config->{intronpatch} = $self->getconfig('intronpatch') || ''; #$config->{utrpatch} = $self->getconfig('utrpatch') || ''; #$config->{gmodel_parts_rename} = $self->getconfig('gmodel_parts_rename') || ''; #$config->{ignore_missingparent} = $self->getconfig('maptype_ignore_missingparent') || ''; ## should get this from $sconfig->{fileset}->{gff}->{noforwards} my $gffinfo= $self->handler()->getFilesetInfo('gff'); $gffinfo->{GFF_source} = $sconfig->{GFF_source} if( $sconfig->{GFF_source}); $self->{gff_config}= $gffinfo; $config->{noforwards} = ($gffinfo && defined $gffinfo->{noforwards}) ? $gffinfo->{noforwards} : $config->{noforwards_gff}; @outformats= @{ $config->{outformats} || \@defaultformats } ; $self->{outputlist}= []; $fff_mergecols= (defined $config->{fff_mergecols} && $config->{fff_mergecols}) || 1; ## add chr,start cols for merge $gff_keepoids = (defined $config->{gff_keepoids} && $config->{gff_keepoids}) || 0; # @csomes= @{ $config->{chromosomes} } if (ref $config->{chromosomes}); if (ref $config->{chromosome}) { $chromosome= $config->{chromosome}; } else { $chromosome= $self->handler()->getChromosomeTable(); $config->{chromosome}= $chromosome; } $rename_child_type= $config->{rename_child_type} if ($config->{rename_child_type}); $name2type_pattern= $config->{name2type_pattern}; ## $duptype_pattern = $config->{duptype_pattern}; %maptype = %{ $config->{'maptype'} } if ref $config->{'maptype'}; %maptype_pattern= %{ $config->{'maptype_pattern'} } if ref $config->{'maptype_pattern'}; %mapname_pattern= %{ $config->{'mapname_pattern'} } if ref $config->{'mapname_pattern'}; %mapattr_pattern= %{ $config->{'mapattr_pattern'} } if ref $config->{'mapattr_pattern'}; %maptype_gff = %{ $config->{'maptype_gff'} } if ref $config->{'maptype_gff'}; %segmentfeats = %{ $config->{'segmentfeats'} } if ref $config->{'segmentfeats'}; %simplefeat = %{ $config->{'simplefeat'} } if ref $config->{'simplefeat'}; %skipaskid = %{ $config->{'skipaskid'} } if ref $config->{'skipaskid'}; %dropfeat_fff = %{ $config->{'dropfeat_fff'} } if ref $config->{'dropfeat_fff'}; %dropfeat_gff = %{ $config->{'dropfeat_gff'} } if ref $config->{'dropfeat_gff'}; %dropid = %{ $config->{'dropid'} } if ref $config->{'dropid'}; %nameisid = %{ $config->{'nameisid'} } if ref $config->{'nameisid'}; %dropname = %{ $config->{'dropname'} } if ref $config->{'dropname'}; %mergematch = %{ $config->{'mergematch'} } if ref $config->{'mergematch'}; %hasdups = %{ $config->{'hasdups'} } if ref $config->{'hasdups'}; %keepstrand = %{ $config->{'keepstrand'} } if ref $config->{'keepstrand'}; %oidisid_gff = %{ $config->{'oidisid_gff'} } if ref $config->{'oidisid_gff'}; my $gmp= $config->{'GModelParts'} || 'CDS five_prime_UTR three_prime_UTR intron'; @GModelParts= (ref $gmp) ? @$gmp : split(/[,\s]+/,$gmp); #@GModelParts = qw( CDS five_prime_UTR three_prime_UTR intron ); #@GModelParts = @{ $config->{'GModelParts'} } if ref $config->{'GModelParts'}; ## jan06: replace CDS/CDS_exon with protein/CDS ... per GFFv3 usage ## fly chado uses 'protein' for mRNA equivalent feature (start,stop) of cds ## and same exons for mRNA and protein $gmp= $config->{'GModelParents'} || 'mRNA'; %GModelParents = map { $_, 1; } ((ref $gmp) ? @$gmp : split(/[,\s]+/,$gmp)); $CDS_spanType= $config->{'CDS_spanType'} || 'CDS'; # change to 'protein' or other ... $CDS_exonType= $config->{'CDS_exonType'} || 'CDS_exon';# change back to CDS push(@GModelParts,$CDS_spanType) unless(grep(/$CDS_spanType/,@GModelParts)); #? require segmentfeats be simplefeat ? map { $simplefeat{$_}=1; } keys %segmentfeats; delete $simplefeat{'gene'}; # dont make this mistake delete $simplefeat{'mRNA'}; # ## merge config from this INTO handler config ? ## that is best place to keep common and ## ? move this out of here; use separate featmap/featset include file? my $fset= $config->{featset}; if (ref $fset && !$sconfig->{featset}) { $sconfig->{featset}= $fset; } my $fmap= $config->{featmap}; if (ref $fmap) { my $smap= $sconfig->{featmap}; unless(ref $smap) { $sconfig->{featmap}= $smap= {}; } my @keys= keys %$fmap; foreach my $k (@keys) { $smap->{$k}= $fmap->{$k} unless defined $smap->{$k}; } } # $fff_mergecols=1; # add chr,start cols for merge # $gff_keepoids= 0; #$DEBUG; #? } #-------------- subs ------------- =item makeFiles( %args ) primary method makes bulk genome sequence files in standard formats. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required formats => [ 'gff', 'fff' ] # optional =cut sub makeFiles { my $self= shift; my %args= @_; my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; my $intype= $self->config->{informat} || 'feature_table'; #? maybe array # 0710: no_csomesplit : no perchr files, only makeall my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 my $makeall= !$no_csomesplit && !$args{noall} && ($self->config->{makeall} || $self->{gff_config}->{makeall}); $self->{append}=1 if($no_csomesplit); #?????? TEST ME unless(@$fileset) { $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "FeatureWriter: no input '$intype' files found\n"; return $self->status(-1); } } my @saveformats= @outformats; ## this may be a mistake: config formats are what we need to make(?) ## args{formats} are what caller/customer wants as result if ($args{formats}) { my $formats= $args{formats}; if(ref $formats) { @outformats= @$formats; } else { @outformats=($formats); } } @outformats= grep { $formatOk{$_}; } @outformats; print STDERR "FeatureWriter::makeFiles outformats= @outformats\n" if $DEBUG; my $status= 0; my $ok= 1; for (my $ipart= 0; $ok; $ipart++) { $ok= 0; my $inh= $self->openInput($fileset, $ipart); if ($inh) { my $res= $self->processChadoTable( $inh); close($inh); $status += $res; $ok= 1; } } if ($makeall && $status > 0) { foreach my $fmt (@outformats) { $self->makeall( $chromosomes, "", $fmt) unless ($fmt eq 'fff'); } } @outformats = @saveformats; print STDERR "FeatureWriter::makeFiles: done n=$status\n" if $DEBUG; return $self->status($status); #?? check files made } ## just now can do only for gff; leave fff split by chr sub makeall { my $self= shift; my( $chromosomes, $feature, $format )= @_; return if ($format eq 'fff'); $feature= ""; $self->{curformat}= $format; $self->config->{path}= $format; #???? # setconfig ?? print STDERR "makeall: $format\n" if $DEBUG; $self->SUPER::makeall($chromosomes, $feature, $format); #?? not seen $self->{curformat}= ''; $self->config->{path}= ''; #???? # setconfig ?? # my $outdir= $self->outputpath(); # $chromosomes= $self->handler()->getChromosomes() unless (ref $chromosomes); # # ## this loop can be common to other writers: makeall( $chromosomes, $feature, $format) ... # my $allfn= $self->get_filename ( $self->{org}, 'all', $feature, $self->{rel}, $format); # $allfn= catfile( $outdir, $allfn); # # my @parts=(); # foreach my $chr (@$chromosomes) { # next if ('all' eq $chr); # my $fn= $self->get_filename ( $self->{org}, $chr, $feature, $self->{rel}, $format); # $fn= catfile( $outdir, $fn); # next unless (-e $fn); # push(@parts, $fn); # } # # if (@parts) { # unlink $allfn if -e $allfn; # dont append existing # my $allfh= new FileHandle(">$allfn"); ## DONT open-append # foreach my $fn (@parts) { # my $fh= new FileHandle("$fn"); # while (<$fh>) { print $allfh $_; } # close($fh); # unlink $fn if (defined $self->config->{perchr} && $self->config->{perchr} == 0); # } # close($allfh); # } } =item openInput( $fileset, $ipart ) handle input files =cut sub openInput { my $self= shift; my( $fileset, $ipart )= @_; # do per-csome/name my $inh= undef; return undef unless(ref $fileset); my $intype= $self->config->{informat} || 'feature_table'; #? maybe array my $atpart= 0; # print STDERR "openInput: type=$intype part=$ipart \n" if $DEBUG; foreach my $fs (@$fileset) { my $fp= $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; next unless($fs->{type} eq $intype); unless(-e $fp) { warn "missing dumpfile $fp"; next; } $atpart++; next unless($atpart > $ipart); print STDERR "openInput[$ipart]: name=$name, type=$type, $fp\n" if $DEBUG; if ($fp =~ m/\.(gz|Z)$/) { open(INF,"gunzip -c $fp|"); } else { open(INF,"$fp"); } $inh= *INF; ## want option to ignore file date, use config date ?? ##my $ftime= $^T - 24*60*60*(-M $fp); ## $self->{date}= POSIX::strftime("%d-%B-%Y", localtime( $ftime )); my ($sfile, undef) = File::Basename::fileparse($fp); $self->{sourcefile}= $sfile; return $inh; # only 1 at a time FIXME ... } print STDERR "openInput: nothing matches part=$ipart, type=$intype\n" if $DEBUG; return undef; } =item openCloseOutput($outh,$chr,$flags) handle output files =cut sub openCloseOutput { my $self= shift; my($outh,$chr,$flags)= @_; my $chrfile= $chr; my $app= defined $self->{append} ? $self->{append} : $append; # 0710: no_csomesplit : no perchr files, only makeall my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 if( $no_csomesplit ) { $app= 1; $chrfile="all"; # or "sum" ?? } if ($outh && $flags =~ /open|close/) { foreach my $fmt (@outformats) { close($outh->{$fmt}) if ($outh->{$fmt}); } } $outh= {}; if ($flags =~ /open/) { $chrfile='undef' unless($chrfile); #?? for unsorted input need to change $append to true after first open? foreach my $fmt (@outformats) { next if ($fmt eq "dummy"); # dang bug w/ config xml my $suffix= $fmt; my $subdir= $fmt; my $outset= $self->{fileset}{$fmt}; #= $self->handler->getFilesetInfo($fmt); if($outset) { $subdir= $outset->{path} || $subdir; $suffix= $outset->{suffix} || $suffix; } ## need option to append or create !? my $ap=($app) ? ">>" : ">"; my $fn; if ($outfile) { $fn="$outfile-$chrfile.$suffix"; } else { $fn= $self->get_filename( $self->{org}, $chrfile, '', $self->{rel}, $suffix); } my $featdir= $self->handler()->getReleaseSubdir( $subdir); my $fpath = catfile( $featdir, $fn); push( @{$self->{outputlist}}, $fpath); #? or save as hash w/ $fmt;... my $exists= ($app && -e $fpath) ? 1 : 0; print STDERR "# output $fpath (append=$exists)\n" if $DEBUG; $outh->{$fmt}= new FileHandle("$ap$fpath"); $self->writeHeader($outh,$fmt,$chr,$exists); } } return $outh; } =item remapXXX processChadoTable handlers to fix various table inputs, according to config mappings =cut sub remapId { my $self= shift; my ($type,$id,$name)= @_; my $save= $id; if (($nameisid{$type}) && $name) { $id= $name; } ## ? not for gff elsif ($dropid{$type} || $id =~ /^NULL:/ || $id =~ /^:\d+/) { $id= undef; } #?? or not# elsif (!$id) { $id= $name; } return ($id,$save); } sub remapName { my $self= shift; my ($type,$name,$id,$fulltype)= @_; my $save= $name; if ( $dropname{$type} ) { $name= ''; } ## handle stupid match name = all the match type + ... #elsif ($type eq 'transposable_element_pred') { $name =~ s/JOSHTRANSPOSON-//; } ## clean unwieldy predictor names: contig...contig... elsif ($type =~ /^(gene|mRNA)/ && $name =~ s/Contig[_\d]+//g) { ##if ($name =~ m/^(twinscan|genewise|genscan)/i) { $name= "${id}_${name}"; } if ($name =~ m/^(twinscan|genewise|genscan|piecegenie)/i) { $name= "${id}_$1"; } } elsif (!$name) { $name= $id unless ($id =~ /^NULL:/i || $id =~ /^:\d+/); } ## dmelr4.1 ; must apply below name patches to id (no name) ## this one could be time sink .. use evaled sub {} ? foreach my $mp (sort keys %mapname_pattern) { next if ($mp eq 'null'); # dummy? my $mtype= $mapname_pattern{$mp}->{type}; next if ($mtype && $type !~ m/$mtype/); if ($mapname_pattern{$mp}->{cuttype}) { my @tparts= split(/[_:.-]/, $type); push(@tparts, split(/[_:.-]/, $fulltype) ); #?? foreach my $t (@tparts) { $name =~ s/\W?$t\W?//; } next; } my $from= $mapname_pattern{$mp}->{from}; next unless($from); my $to = $mapname_pattern{$mp}->{to}; if ($to =~ /\$/) { $name =~ s/$from/eval($to)/e; } else { $name =~ s/$from/$to/g; } } return ($name,$save); } =item remapArm 2 3 segment Contig3266_Contig6542 - complement(3..1555441) Contig3266_Contig654 2 2 1555569 segment Contig143_Contig447 - complement(1555569..2614209) Contig143_Contig447 -- unordered contigs -- singles (? no feats) and doubles - put into common out files? -- if so, need to offset start/end to fit into unorderd 'chromosome' Contig1090 1 contig - - 1..211 Contig1090 GB:AADE01008166; Contig2258_Contig2260 1 contig - - 1..3082 Contig2258 GB:AADE01005006; # Double Dang - need to use segment offset/strand to map segment features =cut sub remapArm { my $self= shift; my ($arm,$fmin,$fmax,$strand)= @_; my $save= $arm; my $armfile= $arm; # my $rf= $armContigs{$arm}; # if ($rf) { # my($armr,$b,$e,$st,$contig)= @$rf; # $arm= $armr; # if ($st eq '-') { #?? do we need to flip all - min,max relative to arm.e ? # $strand= -$strand; # ($fmax,$fmin) = ($e - $fmin-1, $e - $fmax-1); # } # else { # $fmin += $b - 1; # $fmax += $b - 1; # } # } # $armfile=$arm; # # ## need to fix dmel synteny.dump to not put gene name => arm for ortho:nnn # if ($arm eq $save) { # if (lc($org) eq 'dmel' && $arm =~ m/\-/) { # -PA .. others -xxx ? # $armfile= 'genes'; # } # elsif ($arm =~ m/^Contig[^_]+_Contig/) { # $armfile= 'unordered2'; # } # elsif ($arm =~ m/^Contig\w+/) { # $armfile= 'unordered1'; # } # } return($arm,$fmin,$fmax,$strand,$armfile,$save) } sub readArmContigs { my $self= shift; my ($gffh)= @_; # unless($gffh) { warn "cant read arm contigs"; return; } # while(<$gffh>){ # next unless(/^\w/); # my($arm,$x0,$type,$b,$e,$x1,$st,$x2,$attr)= split; # if($type eq 'segment' || $type eq 'golden_path' ||$type eq 'golden_path_region') { # golden_path_region in sql dump # my $contig = ($attr=~m/(Name|dbID)=(\w+)/) ? $2 : ''; # $armContigs{$contig}= [$arm,$b,$e,$st,$contig]; # } # } } =item remapType Types from name ... only when needed Dpse uses gene name_(genscan|genewise|twinscan) ... Dmel uses mRNA name-(genscan|piecegenie) ... ?? anything with '-dummy-' in name is computed type? for Dpse which has gene ..., need to reType mRNA kids also mRNA 13903,12560-AE003590.Sept-dummy-piecegenie mRNA 15793,12560-AE003590.Sept-dummy-genscan transposable_element Name=JOSHTRANSPOSON-jockey{}277-pred transposable_element DBID=TE19092;Name=jockey{}277;cyto_range=21A3-21A3;Dbxref="FlyBase:FBti0019092";Dbxref="Gadfly:TE19092";gbunit=AE003590 Handle more complex types change this to allow complex type:subtype:.. for analysis, other features with pseudo-type like 'match:program:source' want final gff-type/source 'match',fgenesh{_source} or fgenesh:source want final fff-type match_fgenesh{_source} or match:fgenesh{_source} ? check how both gbrowse_fb and gnomap read/handle types gnomap/annomap -- underscores generally used but '.' also ## remap FBan.acode PRG:DB choices blastx_masked_aa_SPTR.worm=blastx_otherspp blastx_masked_aa_SP.hyp.dros=blastx_dros sim4_na_EST.all_nr.dros=EST genscan_dummy=genscan =cut sub remapType { my $self= shift; my ($type,$name)= @_; my $save= $type; $type =~ s/\s/_/g; # must change? ## this one could be time sink .. use evaled sub {} ? foreach my $mp (keys %maptype_pattern) { next if ($mp eq 'null'); my $mname= $maptype_pattern{$mp}->{typename}; next if ($mname && $name !~ m/$mname/); my $from= $maptype_pattern{$mp}->{from}; my $to = $maptype_pattern{$mp}->{to}; $type =~ s/$from/$to/; } my $nutype = $type; # this should be config pattern: ..genscan.. ##if (defined $name && $name =~ m/[-_](genscan|piecegenie|twinscan|genewise|pred|trnascan)/i) { if ($name2type_pattern && defined $name && $name =~ m/$name2type_pattern/i) { $nutype .= "_".lc($1); } $nutype =~ s/[:\.]/_/g; #? $type = $maptype{$nutype} || $type; my $fulltype = $type; #?? here or what. $type =~ s/[:\.]/_/g; #? return ($type,$fulltype,$save); } =item processChadoTable Read input feature table, write bulk output formats FFF and GFF (other formats are derived from these) This step takes longest, e.g. ~ 20 hr on single cpu for D. melangaster. Split by chromosome data among processors to speed up. Joins table lines/feature; builds compound features; checks feature names/types, etc. Input chado feature table dump format (see sql) arm fmin fmax strand type name id oid attr_type attribute 2L 0 305900 1 golden_path AE003590 AE003590 1273141 various_key value Outputs: FFF (also used for fasta, gnomap), GFF FIXME: something here gets very memory piggy, slow, with input feature tables full of match: analysis types (messy names, types, etc.) -- no feats written to fff in many hours !? - due to holding BAC and cytoband features -- try dropping gffForwards; maybe better (gff written) but still memuse balloons -- added clearFinishedObs() - no apparent help; dont see what else is holding objects here -- ok now, added min base loc to keep in oidobs, delete all before runs fast - chr 3L in 10 min. instead of >2hr. =cut use constant LINEBUF_SIZE => 2000; # for forward refs sub getline { my $self= shift; my($fh)= @_; my $n= scalar( @{$self->{linebuf}} ); while (<$fh>) { next unless(/^\w/); next if(/^arm\tfmin/); # header from sql out chomp; push @{$self->{linebuf}}, $_; $n++; last if ($n >= LINEBUF_SIZE); } my $fin= shift @{$self->{linebuf}}; return $fin; } sub popline { my $self= shift; my $fin = shift @{$self->{linebuf}}; return $fin; } sub peekline { my $self= shift; my($n)= @_; $n= 0 unless($n); my $fin= ${$self->{linebuf}}[$n]; return $fin; } sub grepline { my $self= shift; my($patt)= @_; my $grep= grep /$patt/, @{$self->{linebuf}}; return $grep; } sub hasObForwards { my $self= shift; my($fobs,$oidobs)= @_; foreach my $fob (@$fobs) { my $oid= $fob->{oid}; my $paroid= $fob->{paroid}; # may be one of many ! need $oidobs->{parent} my $ftype= $fob->{type}; # my $issimple= $simplefeat{$ftype}; next unless($paroid || $ftype =~ m/^(mRNA|gene)$/); # add CDS ? or do any types w/ paroid? #my $hasfor= grepline("\b$oid\b"); # mainly looking for attrib: parent_oid\t$oid my $hasfor= $self->grepline("parent_oid\t".$oid); my $isfor= 0; # if ($DEBUG && $hasfor) { # # my @val= grep /parent_oid\t$oid/, @{$self->{linebuf}}; # print STDERR "hasForward: $ftype, ",$fob->{name},", $oid\n>","\n"; #join("\n>",@val),"\n"; # } ## ? need reverse: if fob has parent_oid, grep for its object_oid ? unless($hasfor) { $isfor= ($paroid && $self->grepline("\b$paroid\b")); # if ($DEBUG && $isfor) { # # my @val= grep /\b$paroid\b/, @{$self->{linebuf}}; # print STDERR "isForward: $ftype, ",$fob->{name},", par=$paroid\n>", "\n"; # ,join("\n>",@val),"\n"; # } } return 1 if ($hasfor || $isfor); } return 0; } sub newParentOid { my $self= shift; my($fob,$attr_type,$attribute,$oidobs)= @_; ## my $paroid= $fob->{paroid}; ##BAD-exon has many parents## return if($paroid); # my $type= $fob->{type}; return if ($simplefeat{$type}); ## TEST before call my $oid = $fob->{oid}; # do part of this when fob is created: # >> add paroid->child and oid->{parent} refs # defer any requirement for parent/child ob till putLink() ##my($attr_type,$attribute)= split "\t",$addattr; if ($attribute && $attr_type eq 'parent_oid' ) { my($paroid,$rank)= ($attribute, 0); if ($paroid =~ s/:(.*)$//) { $rank=$1; } # dont need rank, but must drop from paroid $fob->{paroid}= $paroid; ## replace OLD ok ?? ## push( @{$fob->{attr}}, "rank\t$attribute"); # ? need this for exon, utr - but tied to parent_oid ## ? got dupl parent_oid for dpse genscan/twinscan genes only ?? screen here? -- gff output only? ## >> problem looks like oids are duplicated among gene/mRNA/CDS and the related genscan/genewise/twinscan/... objects $oidobs->{$paroid}->{child}= [] unless (ref $oidobs->{$paroid}->{child}); push( @{$oidobs->{$paroid}->{child}}, $fob); ##? use $rank to position in {child} array ?? $oidobs->{$oid}->{parent}= [] unless (ref $oidobs->{$oid}->{parent}); push( @{$oidobs->{$oid}->{parent}}, $paroid); } } ## ???? for sgd gene->cds model; insert gene->mrna->cds/exon sub add_mRNA { my $self= shift; my($geneob,$oidobs)= @_; my $geneoid = $geneob->{oid}; my $type= $geneob->{type}; my $make_mrna; $make_mrna= $self->config->{feat_model}->{$type}->{make_mrna}; if ($make_mrna) { # my $mrnaob= { %$geneob }; # shallow clone ! my $mrnaob= $self->cloneBase($geneob); # need locs $mrnaob->{type}= 'mRNA'; # need new $oid; insert in $oidobs->{$oid}->{parent}; .. $self->newParentOid( $mrnaob, 'parent_oid', $geneoid, $oidobs); ## and move kidobs from geneob to mrnaob ... # $mrnaob->{paroid}= $geneoid; # my @kids= @{$oidobs->{$geneoid}->{child}}; # push( @{$oidobs->{$geneoid}->{child}}, $mrnaob); # push( @{$oidobs->{$oid}->{parent}}, $geneoid); } } sub updateParentKidLinks { my $self= shift; my($fobs,$oidobs)= @_; foreach my $fob (@$fobs) { $self->update1ParentKidLinks($fob,$oidobs); } } sub update1ParentKidLinks { my $self= shift; my($fob,$oidobs)= @_; ## my $paroid= $fob->{paroid}; ## FIXME: exons have many parent return unless( $fob->{paroid} ); my $oid = $fob->{oid}; my $type= $fob->{type}; my $ignore_missingparent= $self->config->{maptype_ignore_missingparent} || '^xxxx'; foreach my $paroid ( @{$oidobs->{$oid}->{parent}} ) { my $parob= $oidobs->{$paroid}->{fob}; unless($parob) { warn "MISSING parent ob $paroid for $type:$oid\n" unless ($type =~ /$ignore_missingparent/); # || $id =~ /GA\d/ # these match parts miss parent often: 'repeat|blast|genscan|sim4' next; # return; } ## another fixup for CDS/protein-of-mRNA feature set ## was bad - simplefeat included gene, pseudogene ## dang; now gene children: # insertion, aberration_junction,regulatory_region, # sequence_variant,rescue_fragment, enhancer, etc are missing # -> only gone from fff, not gff ## pseudogene|\w+RNA ## sgdlite has this stuff : ## tRNA contain ncRNA; pseudogene contains CDS (sic!); no mRNA if ($rename_child_type && $fob->{type} ne 'mRNA' && $fob->{type} =~ m/^($rename_child_type)/) { # this is bad for real gene subfeatures like point_mutation my $ptype= $fob->{type}; ## feb05: ## this is causing problems for featuretype purists ; should leave 'gene' and subtype \w+RNA ## as is ?? but fix software to process right; use fulltype == orig; type = recoding ? if ($parob && ( $parob->{type} eq 'gene' || $parob->{type} eq $ptype) ) { ##$parob->{fulltype}= $parob->{type}= $ptype; ##$fob->{fulltype}= $fob->{type}= 'mRNA'; $parob->{type}= $ptype; $fob->{type}= 'mRNA'; } # warn ">pse2: $arm,$fmin,".$parob->{type}."/".$fob->{type}.",$name,$oid,$l_oid\n" if $DEBUG; } if ($fob->{type} =~ m/^(mRNA|CDS)$/) { ## for genscan/twinscan etc mrna's - retype as parent gene_pred type if ($parob->{type} =~ m/^gene([_:.-]\w+)/ ) { $fob->{type} .= $1; if ($parob->{fulltype} =~ m/^gene([_:.-]\w+)/ ) { $fob->{fulltype} .= $1; } } # copy gene id dbxref attr # got gene ids to all mRNA; missing some in CDS; need to do CDS after mRNA my $idpattern= $self->config->{idpattern}; foreach my $pidattr (@{$parob->{attr}}) { next if ($pidattr =~ m/2nd/); #? dbxref_2nd: if (!$idpattern || $pidattr =~ m/$idpattern/) { ## (FBgn|FBti)\d+ push( @{$fob->{attr}}, $pidattr) unless( grep {$pidattr eq $_} @{$fob->{attr}}); last; # add only 1st/primary } } } } } sub handleAttrib { my $self= shift; my($addattr, $attr_type, $attribute, $fobadd)= @_; # nasty fix for _Escape ; to_name=Aaa,CGid should probably be two table lines if ($attr_type eq 'to_name' && $attribute =~ /,/) { my $attr1; ($attr1,$attribute)= split(/,/,$attribute,2); push( @$addattr, "$attr_type\t$attr1"); } # chado-gff loader does odd thing like adding unwanted 'DB:' prefix; # and dbxref=GFF_source:SGD # elsif ($attr_type eq 'dbxref' && $attribute =~ /^DB:\w+:\w+/) { # $attribute =~ s/^DB://; # } # elsif ($attr_type =~ /^dbxref/ && $attribute =~ /^FlyBase Annotation IDs/) { # $attribute =~ s/FlyBase Annotation IDs/FBannot/; # } # elsif ($attr_type eq 'dbxref' && $attribute =~ /^GFF_source:(\S+)/) { # if($fobadd) { $fobadd->{gffsource} = $1; } # $attribute=''; # } foreach my $mp (sort keys %mapattr_pattern) { next if ($mp eq 'null'); # dummy my $mtype= $mapattr_pattern{$mp}->{type}; next if ($mtype && $attr_type !~ m/$mtype/); my $from= $mapattr_pattern{$mp}->{from}; next unless($from); my $to = $mapattr_pattern{$mp}->{to}; if ($to =~ /\$/) { $attribute =~ s/$from/eval($to)/e; } else { $attribute =~ s/$from/$to/g; } } if ($attr_type eq 'dbxref' && $attribute =~ /^GFF_source:(\S+)/) { if($fobadd) { $fobadd->{gffsource} = $1; } $attribute=''; } push( @$addattr, "$attr_type\t$attribute") if $attribute; } sub processChadoTable { my $self= shift; my($fh, $outh)= @_; $outh= $self->{outh} unless(ref $outh); my %origin_one= %{ $self->config->{origin_one} || {} }; my $utrpatch= $self->config->{utrpatch} ; my $intronpatch= $self->config->{intronpatch} ; # patch for intron type; oct04: fmin - no+1,fmax, add+1 my $nozombiechromosomes= $self->config->{nozombiechromosomes}; # dpse chado duplicate 0-length chromosome entries my $tab= "\t"; # '[\|]'; ##"\t"; < '|' is bad sep cause some names have it ! my @fobs=(); my %oidobs=(); # this hash will grow big; can we delete before next chr ? my $fob= undef; my $max_max=0; my $min_max= 0; my $armlen=0; my $ndone= 0; my ($l_arm,$l_oid,$l_fmin,$l_fmax,$l_type)= (0,0,0); my ($arm,$fmin,$fmax,$strand,$type,$name,$id,$oid,$attr_type,$attribute) ; my($s_type, $fulltype, $s_arm, $armfile, $s_name, $s_id); my ($fin,$fhpeek); my %addfob=(); #? use line buffer @fhpeek to grep for missing forward refs ? eg. PA for mRNA ? $self->{linebuf}= []; # while(<$fh>) { # next unless(/^\w/); # next if(/^arm\tfmin/); # header from sql out # chomp; # $fin=$_; } while( $fin= $self->getline($fh) ) { $_= $fin; $ndone++; my @addattr=(); ## loop here over <$fh> while $oid == $l_oid ## only part changing is $attr_type/$attribute my $sameoid= 0; do { ($arm,$fmin,$fmax,$strand,$type,$name,$id,$oid,$attr_type,$attribute) = split("\t",$fin); $self->handleAttrib(\@addattr,$attr_type,$attribute,\%addfob) if ($attribute); ## inner read loop problem? need to process parent_oid attrib only once below my $nextin= $self->peekline(0) || ""; my $joid= index($nextin,"$id\t$oid\t"); $sameoid= ($joid>0); if ($sameoid) { my $ioid= index($fin,"$id\t$oid\t"); $sameoid= ($ioid==$joid && substr($nextin,0,$ioid) eq substr($fin,0,$ioid) ); if ($sameoid) { $fin= $self->popline(); } } } while ($sameoid); #my $tss= ($DEBUG && $type eq 'transcription_start_site'); #warn ">tss1: $arm,$fmin,$type,$name,$oid,$l_oid\n" if $tss; ## data fixes ## dpse chado has chromosomes of fmin=1; fmax = NULL ! no length; drop these (dupl) if ($nozombiechromosomes && $segmentfeats{$type} && $fmax <= $fmin) { ($l_oid,$l_fmin)= (-1,$fmin); next; } if( !defined $fmax ) { $fmax=0; } if( !defined $fmin ) { $fmin=0; } elsif ($intronpatch && $type eq 'intron') { $fmax += 1; } elsif ($utrpatch && $type =~ /_prime_untranslated_region|_prime_UTR/) { $fmin= $fmax if ($fmax == $fmin-1); } elsif( ! ($origin_one{$type} || $fmin == $fmax) ) { $fmin += 1; } # dang -1 chado start if( !defined $strand ) { $strand=0; } # feb05: the zero-base insertion sites ( fmin==fmax ) should not have fmin+1 adjustment # 2L 131986 131986 1 1 transposable_element_insertion_site ## this check only for intron,UTR chado-computed locs ?? ## also looks like computed UTR's can be off by 1 out of gene bounds, if UTR == 0 ## CG2657 = 2L:21918..23888 ; exon1 = 22983..23888 ; exon2 = 21918..22687 ## dmel_chado says -u3 = 21918..2191723889..23888 ; -intron = no+1>22688..22982 if ($fmax < $fmin) { ($fmin,$fmax)= ($fmax,$fmin); $strand= ($strand==0) ? -1 : -$strand; } # ($arm,$fmin,$fmax,$strand,$armfile,$s_arm) # = $self->remapArm($arm,$fmin,$fmax,$strand); # for dpse joined contigs ($type,$fulltype,$s_type)= $self->remapType($type,$name); if (!$type && $DEBUG && !/NULL|repeatmask/) { print STDERR "missing type: $_\n"; } ##<< repeatmasker kid objs if ($type eq 'skip' || !$type) { # or what? undef? got some bad feats w/ no type?? ## dont keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin); ##dont save arm for skip !? if changed here, cant miss below openout.. ($l_oid,$l_fmin)= (-1,$fmin); next; } # ($id,$s_id)= $self->remapId($type,$id,$name); ($name,$s_name)= $self->remapName($type,$name,$id,$fulltype); ## dmelr4.1 patch; cant do this for all dropid - gff needs real ids for exons for instance #if (($dropid{$type} || $nameisid{$type}) && $name) { $id= $name; } ## ## do this in remapId .. ## if (($nameisid{$type}) && $name) { $id= $name; } ## ? not for gff my $loc="$fmin\t$fmax\t$strand"; # dmelr4.1 - need add band attrib even if attrib == parent_oid if ($type eq 'chromosome_band') { ## && !$attribute my $battr_type = 'cyto_range'; my $battribute = $s_name; $battribute =~ s/(cyto|band|\-)//g; push( @addattr, "$battr_type\t$battribute"); $name =~ s/\-cyto//; } ## find quicker way to screen out many match_ dup things ; same simple loc, no id... ## # hasdups -- need to check id == l_id, name = l_name .. ## match_blastn_na_dbEST_dpse="1" ## match_sim4_na_dbEST_same_dmel="1" ## ? do something like this also for EST, protein which differ only by dbxref id ## i.e. feature is location w/ several items matching ## need to turn name/id into dbxref attrib ## feats: processed_transcript , EST, protein ## some chado exons, introns are dupl of same data... diff uniquename for no useful reason ## also check for $oidobs{$oid}->{fob}; if ($oid ne $l_oid && ! $simplefeat{$type} && exists $oidobs{$oid}->{fob}) { my $ok=0; foreach my $dob (@fobs) { if ($dob->{oid} eq $oid) { $ok=1; last; } } if ($ok) { $fob= $oidobs{$oid}->{fob}; $oid= $l_oid= $fob->{oid}; } else { ## FIXME - bad if fob not in @fobs ## .. e.g. repeat region - many locs over arm, few oid's ## most of these we dont want to join - too far apart; need max_max setting below to keep small ranges together? # print STDERR "missed join to last $type,$name,$oid\n" if $DEBUG; } } if ($oid ne $l_oid && $hasdups{$type}) { foreach my $dob (@fobs) { next unless($dob->{type} eq $type); my $dloc= $dob->{loc}->[0]; my($dmin,$dmax,$dstrand)= split("\t",$dloc); if ( $dmin eq $fmin && $dmax eq $fmax && $dstrand eq $strand ) { $fob= $dob; $oid= $l_oid= $fob->{oid}; last; } } } #warn ">tss2d: new $arm,$fmin,$oid,$l_oid\n" if $tss; ## all TSS has same oid now !???? -- odd bug $l_oid == $oid if ( $oid eq $l_oid ) { # same object - cat attributes into one set push( @{$fob->{loc}}, $loc) unless(grep /$loc/,@{$fob->{loc}}); #warn ">tss2S: new $arm,$fmin,$oid,$l_oid\n" if $tss; foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=(); } else { ## new feature object here .. if ($arm ne $l_arm) { $self->putFeats($outh,\@fobs,\%oidobs,'final'); undef @fobs; @fobs=(); undef %oidobs; %oidobs=(); undef %gffForwards; %gffForwards=(); $max_max=0; $min_max= 0; $outh= $self->openCloseOutput($outh, $arm, 'open'); } #? do we need to set a max @fbobs ? ## is this where we lose PA/CDS associated with mRNA/gene ? havent got to yet before putFeats? my $flushok= ($fmin >= $max_max && $fmin > $min_max && scalar(@fobs)>5); if ($flushok) { if ($self->hasObForwards(\@fobs, \%oidobs)) { $flushok = 0; $min_max= $fmin + 2000; ##smaller step so we dont miss chance to flush } warn "hasObForwards no=$flushok at $fmin $type:$name $oid\n" if ($DEBUG>1); } if ($flushok) { ##warn "flushobs at $fmin $type:$name $oid\n" if $DEBUG; my ($nstart, $nleft, $nobs)=(0,0,0); if ($DEBUG>1) { $nobs= scalar(@fobs); } $self->putFeats( $outh, \@fobs, \%oidobs, ''); undef @fobs; @fobs=(); $min_max= $fmin + MIN_FORWARD_RANGE; #?? will this help join parts ## %oidobs will grow big; ## can we clear out other obs yet: %oidobs=(); %gffForwards=(); if no forwards ? if ($DEBUG>1) { while( each %oidobs ){ $nstart++; }} my $clearflag= ($outh->{fff} || !$outh->{gff}) ? 'writefff' : 'writegff'; my $nclear= $self->clearFinishedObs( $clearflag, \%oidobs, $fmin - MAX_FORWARD_RANGE); if ($DEBUG>1) { while( each %oidobs ){ $nleft++; } print STDERR " printed n=$nobs; oidobs: pre-clear=$nstart, cleared=$nclear, left=$nleft\n"; print STDERR " fmin=$fmin, fmax=$fmax, l_fmin=$l_fmin, min_max=$min_max, max_max=$max_max\n"; } } my $newob= {}; push(@fobs,$newob); $fob= $newob; foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=(); #?? dont add here if it is simple feature; wait till know if it is parent or kid? # this is bad for 'gene' NOT? simple feat unless( $simplefeat{$type} ) { $oidobs{$oid}->{fob}= $newob; } # my @fclone_fields = qw(chr type fulltype name id oid fmin fmax offloc attr writefff writegff); $fob->{chr} = $arm; $fob->{type}= $type; $fob->{fulltype}= $fulltype; # colon-delimited complex type 'match:program:source' $fob->{name}= $name; $fob->{id} = $id; $fob->{oid} = $oid; $fob->{fmin}= $fmin; $fob->{fmax}= $fmax; $fob->{loc} = []; $fob->{attr}= []; ##warn ">tss2x: new $arm,$fmin,$oid\n" if $tss; push( @{$fob->{loc}}, $loc); ##moved below## foreach my $at (@addattr) { push( @{$fob->{attr}}, $at); } } ## make oid crossref here so outputters know feature relations ## change this (see above $samoid read loop) ## FIXME 05: this sub should be run only after forward parent_oid is found; ## or change input to sort given model gene > mRNA > CDS (ignoring seq start) foreach my $at (@addattr) { my $paroid=''; if ($at =~ /parent_oid\t(.+)/) { $paroid=$1; } push( @{$fob->{attr}}, $at) ; # unless( grep {$at eq $_} @{$fob->{attr}}); #? do we have any dupls? ## REMEMBER SOME (exons) HAVE MULTIPLE parent_oid attributes if ($paroid && !$simplefeat{$type}) { $self->newParentOid($fob, 'parent_oid', $paroid, \%oidobs); } } # $self->newParentKidLink($fob, \%oidobs); # uses @{$fob->{attr}} parent_oid ## MOVED parent_oid attrib TO putFeats: $self->update1ParentKidLinks($fob, \%oidobs); ## forward ref checkpoint .. maybe skip more than segmentfeats here ? what is big? if ($fmax > $max_max && !$segmentfeats{$fob->{type}}) { $max_max= $fmax; my $supermax= $min_max - MIN_FORWARD_RANGE + MAX_FORWARD_RANGE; $max_max= $supermax if ($max_max > $supermax); # is it < or > ? was > (set to SMALLER) } ## only need save these: ($l_arm,$l_oid,$l_fmin,$l_fmax,$l_type)= ($arm,$oid,$fmin,$fmax,$type); } $self->putFeats($outh,\@fobs,\%oidobs, 'final'); @fobs=(); %oidobs=(); $outh= $self->openCloseOutput($outh,'','close'); print STDERR "\nprocessChadoTable ndone = $ndone\n" if $DEBUG; return $ndone; } sub keepfeat_fff { my $self= shift; my ($ftype)= @_; my $dropfeat= ($dropfeat_fff{$ftype} || $ftype =~ /^match_part/); return(!$dropfeat); } sub _debugObj { my ($name,$obj)= @_; require Data::Dumper; my $dd = Data::Dumper->new([$obj]); $dd->Terse(1); print STDERR "DEBUG obj: $name=", $dd->Dump(),"\n"; } =item makeFlatFeats($fobs,$oidobs) handle gene model, other cases to make simple & compound features return ref to features array used for fff and fasta outputs =cut =item missing prots check This is list of prot genes lacking proteins - many/most cases where there are protein and CDS feats in features.tsv and intermediat files, but missing in fff output 13472 gene.list 18716 protgn.list 13458 protgnuniq.list -- diff from gene.list below .. feb04, dmelr41 check .. still missing some PA entries in fff, found in gff, featdump chipmunk% comm -3 genecg41.list prot*list ;; these -Px proteins are in featdump, .gff, not .fff CG10272 -- 3R CG10324 -- 3R CG11798 -- 2R CG12591 -- 3R CG17998 -- 3R CG31092 -- 3R CG3973 -- X CG4993 -- 2L CG5789 -- 3R >> several of these missing prots are in features.tsv as CDS, not in fff output tho !? dghome2% comm -3 gene.list protgnu.list CG11989 3L CG18675 3L CG32373 3L CG32406 3L CG12094 X CG1692 X CG31243 3R CG32600 CG4196 CG4444 CG5490 CG6669 CG7210 CG7369 CG8742 Gyc76C == CG8742 for this case CG18675; gff has right data, fff lacks CDS,three_prime_UTR distance is gene:4157385 to CDS:4157485 = 100 b chipmunk% gunzip $dr/gff.save/*gz grep CG18675 ../../gff.chipmunk% grep CG18675 ../../gff.save//*3L*ff chipmunk% grep CG18675 ../../fff.save//*3L*ff =cut sub makeFlatFeats { my $self= shift; my ($fobs,$oidobs)= @_; ## debug missing from fff: insertion_site, regulatory # my %GMM= map { $_,1; } qw(enhancer insertion_site aberration_junction # regulatory_region rescue_fragment sequence_variant); my @cobs=(); my $gmodel_parts_rename= $self->config->{gmodel_parts_rename}; foreach my $fob (@$fobs) { my $oid= $fob->{oid}; my ($iskid,$ispar)= (0,0); my $oidob= $oidobs->{$oid}; my $ftype= $fob->{type}; my $fulltype= $fob->{fulltype}; my $id= $fob->{id}; my $issimple= $simplefeat{$ftype}; # my $GMM= $GMM{$ftype} && $DEBUG; ## missing exons: CG10033 (2L?) ## missing proteins: 3L CG11989 CG18675 CG32373 CG32406 ##my $GMM= ($DEBUG && $id =~ /CG11989|CG18675|CG32373|CG32406/) ? 1 : 0; # jan05 bug test, mRNA misses last 2 exons my $GMM= 0; ##($DEBUG && $id =~ /CG4993|CG11798|CG10272|CG3973/) ? 1 : 0; # feb05 bug test, mRNA misses last 2 exons if (!$issimple && $oidob) { $iskid= (defined $oidob->{parent} && @{$oidob->{parent}} > 0); $ispar= (defined $oidob->{child} && @{$oidob->{child}} > 0); if ($iskid) { # check we have backref to parend obj ?? my $ok= 0; foreach my $poid (@{$oidob->{parent}}) { if ($oidobs->{$poid}) { $ok=1; last; } } $iskid= $ok; } } warn ">gmm1 $ftype $id ispar=$ispar iskid=$iskid\n" if $GMM; my $keepfeat= ($ispar || $self->keepfeat_fff($ftype)); if ($keepfeat) { $issimple= ($issimple || !$ispar || $ftype eq 'gene'); # $ftype !~ m/^(CDS)$/ && #NEED THIS# $issimple = 1 if ($ftype =~ m/^gene$/); #?? otherwise misc. gene parts GMM get flagged as written #BUT for complex flybase data; not for sgdlite w/o mrna features if ($issimple && $ftype eq 'gene') { $issimple= 0 if($self->config->{gene_is_complex}); } if ($issimple) { push(@cobs, $fob); } # simple feature else { # has kids, make compound feature my $kidobs= $oidob->{child}; my $cob= $self->makeCompound( $fob, $kidobs, $ftype); push(@cobs, $cob); # $self->listkids($cob,$kidobs) if($DEBUG && $ftype =~ m/^(gene|mRNA)$/); ## was loosing kids to bad $oidobs } warn ">gmm2 add $ftype $id \n" if $GMM; ## _debugObj("gmmisc=$id object",$cobs[-1]) if $GMM; } # UTR here ? ?? insert CDS between UTR's ? ## some of intron,UTR have swapped locs = 4650373..4650371 =item debug parent/kid feature objects print STDERR "makeFlatFeats $ftype par=$id check kids\n" ;#if $DEBUG; # got here, missing protein/CDS kids. _debugObj("par=$id objects",$oidob); makeFlatFeats mRNA par=CG18001-RA check kids DEBUG obj: par=CG18001-RA objects={ 'parent' => [ 509313 ], 'fob' => { 'writefff' => 1, 'chr' => '2h', 'attr' => [ 'parent_oid 509313' ], 'name' => 'CG18001-RA', 'id' => 'CG18001-RA', 'oid' => 509314, 'type' => 'mRNA', 'loc' => [ '42592 43051 -1' ] }, 'child' => [ { 'writefff' => 1, 'chr' => '2h', 'attr' => [ 'parent_oid 509314:2' ], 'name' => 'CG18001:2', 'id' => 'CG18001:2', 'oid' => 509316, 'type' => 'exon', 'loc' => [ '42592 42914 -1' ] }, ... } =cut # ## %GModelParents = ( mRNA => 1, otherRnas ?? => ); ## $CDS_spanType = 'CDS' ; # change to 'protein' or other ... ## $CDS_exonType = 'CDS_exon' ; # change to 'CDS' ## But for fff, need to rename $CDS_spanType 'protein' to 'CDS' for output fff type #if ($ispar && $ftype eq 'mRNA') if ($ispar && $GModelParents{$ftype}) { foreach my $ftname (@GModelParts) { my $utrob= undef; my $cdsob= undef; my $exonobs=[]; my $mrnaexons=[]; my $kidobs=[]; foreach my $kidob (@{$oidob->{child}}) { if ($kidob->{type} eq 'exon') { push(@$mrnaexons, $kidob); # save in case missing CDS_exon } if ($kidob->{type} eq $CDS_spanType) { $cdsob= $kidob; } # only for utr patch ? if ($ftname eq $CDS_spanType && $kidob->{type} eq $CDS_spanType) { $utrob= $kidob unless($utrob); ## urk - need to keep loc:start/stop to adjust CDS_exon end points ! } elsif ($id =~ /CG32491/ && $ftname eq $CDS_spanType && $kidob->{type} eq 'exon') { ## patch for mdg4 bug push(@$exonobs, $kidob); } elsif ($ftname eq $CDS_spanType && $kidob->{type} eq $CDS_exonType) { push(@$kidobs, $kidob); ## missing this for het db ... FIXME # bad CDS_exon for transspliced mdg4 ... sigh ... need to keep also regular exons? } ## ?? want instead: if(kidob->type in (UTR,...)) add to kids elsif ($kidob->{type} eq $ftname) { # these will be UTR's, other things (?) $utrob= $kidob unless($utrob); #?? dont do this? push(@$kidobs, $kidob); ## repair bad names; only if bad !? ## FIXME apr05 - intron,UTR fff output needs CG ids (in gff, not fff, due to ## name = gene-symbol, FBgn ID; ... need uniquename ## apr05 - this renaming bad now ? at keep old name,id as 2ndary ? if ($gmodel_parts_rename) { my $part=""; if ($ftname eq 'three_prime_UTR') { $part= "-u3"; } elsif ($ftname eq 'five_prime_UTR') { $part= "-u5"; } elsif ($ftname eq 'intron') { $part= "-in"; } if ($part) { $utrob->{name}= $fob->{name}.$part; $utrob->{id}= $fob->{id}.$part; } } } } ## ERROR - CDS/protein w/o CDS_exon parts - not harvard chado 'reporting' db ## fixme ... recreate from cds start/stop + mrna location ? if ($utrob && !@$kidobs) { if ($ftname eq $CDS_spanType && @$mrnaexons) { $kidobs= $self->getCDSexons($utrob, $mrnaexons); } } if ($utrob) { ## copy gene model dbxref id into these features, as per above my $idpattern= $self->config->{idpattern}; foreach my $pidattr (@{$fob->{attr}}) { next if ($pidattr =~ m/2nd/); #dbxref_2nd: if (!$idpattern || $pidattr =~ m/$idpattern/) { push( @{$utrob->{attr}}, $pidattr) unless( grep {$pidattr eq $_} @{$utrob->{attr}}); last; # add only 1st/primary ?? also add CG/CR .. ? or is that always there? } } if ($ftname =~ /UTR/ && $self->config->{utrpatch}) { $self->patchUTRs( $utrob, $cdsob, $mrnaexons, $kidobs); } ##print STDERR "makeCompound $ftname par=$id, kid=",$utrob->{id}, "\n" if $DEBUG; # below # if ($ftname eq 'CDS') { $kidobs= adjustCDSendpoints( $utrob, $kidobs); } ## jan06: problem here w/ change to protein/cds: all GModelParts end up fff feature ## CDS_exon, exon end up as compound types same as mRNA, CDS/protein my $cob= $self->makeCompound( $utrob, $kidobs, $ftname); # $self->listkids($cob,$kidobs) if($DEBUG); ## was loosing kids to bad $oidobs # patch bad data -- use getCDSexons above ?? if ($id =~ /CG32491/ && $ftname eq $CDS_spanType) { my @exlocs=(); foreach my $kid (@$exonobs) { foreach my $loc (@{$kid->{loc}}) { push( @exlocs, $loc); } } $cob->{exons}= \@exlocs; } push(@cobs, $cob); } } } ## else { } # $iskid only - dont save } return \@cobs; } ## jan06: makeFlatFeats -> makeFlatFeatsNew ## change to config->{feat_model}->{$type}: @parts, $parent, $typelabel, $types sub makeFlatFeatsNew { my $self= shift; my ($fobs,$oidobs)= @_; my @cobs=(); # these compound features get added to output foreach my $fob (@$fobs) { my $oid= $fob->{oid}; my ($iskid,$ispar)= (0,0); my $oidob= $oidobs->{$oid}; my $ftype= $fob->{type}; #my $fulltype= $fob->{fulltype}; my $id= $fob->{id}; my $issimple= $simplefeat{$ftype}; my $feat_model= $self->config->{'feat_model'}->{$ftype}; ## get issimple from feat_model my $GMM=0; # ($DEBUG && $id =~ /CG17245|CG32013|CG2125|CG3973/) ? 1 : 0; # feb05 bug test, mRNA misses last 2 exons if (!$issimple && $oidob) { $iskid= (defined $oidob->{parent} && @{$oidob->{parent}} > 0); $ispar= (defined $oidob->{child} && @{$oidob->{child}} > 0); if ($iskid) { # check we have backref to parend obj ?? my $ok= 0; foreach my $poid (@{$oidob->{parent}}) { if ($oidobs->{$poid}) { $ok=1; last; } } $iskid= $ok; } } warn ">gmm1 $ftype $id ispar=$ispar iskid=$iskid\n" if $GMM; my $keepfeat= ($ispar || $self->keepfeat_fff($ftype)); if ($keepfeat) { if(!$ispar) { $issimple=1; } elsif($feat_model && defined($feat_model->{simple})) { $issimple= $feat_model->{simple}; } elsif($ftype eq 'gene' && !$self->config->{gene_is_complex}) { $issimple=1; } #NEED THIS# $issimple = 1 if ($ftype =~ m/^gene$/); #?? otherwise misc. gene parts GMM get flagged as written #BUT for complex flybase data; not for sgdlite w/o mrna features if ($issimple) { push(@cobs, $fob); } # simple feature else { # has kids, make compound feature >> (m,t,s)RNA here my $kidobs= $oidob->{child}; my $cob= $self->makeCompound( $fob, $kidobs, $ftype); push(@cobs, $cob); # $self->listkids($cob,$kidobs) if($DEBUG && $ftype =~ m/^(gene|mRNA)$/); ## was loosing kids to bad $oidobs } warn ">gmm2 add $ftype $id \n" if $GMM; } ## %GModelParents = ( mRNA => 1, otherRnas ?? => ); ## $CDS_spanType = 'CDS' ; # change to 'protein' or other ... ## $CDS_exonType = 'CDS_exon' ; # change to 'CDS' ## But for fff, need to rename $CDS_spanType 'protein' to 'CDS' for output fff type ## ?? this is only for 3-level models (gene/mRNA/protein) where ## submodel parts are contained in mainmodel kid list (protein-CDS in mRNA) if ($ispar && $feat_model && $feat_model->{submodels}) { my $parob= $fob; my $submodels = $feat_model->{submodels}; my @submodels = (ref $submodels) ? @$submodels : split(/[,\s]+/,$submodels); foreach my $subtype (@submodels) { my $sub_model= $self->config->{'feat_model'}->{$subtype}; my $makepartsfrom = $sub_model->{makepartsfrom} || 'exon'; my $hasspan = (defined $sub_model->{hasspan}) ? $sub_model->{hasspan} : ($subtype eq $CDS_spanType); # old version my $typelabel= $sub_model->{typelabel} || $subtype; # my $parent= $sub_model->{parent}; my $kidparts = $sub_model->{parts} || 'exon'; #? no default my @kidparts = (ref $kidparts) ? @$kidparts : split(/[,\s]+/,$kidparts); my %kidparts = map { $_,1; } @kidparts; my $makemethod = $sub_model->{makemethod}; my $subob= undef; my $spanob= undef; my $mrnaexons=[]; my $kidobs=[]; foreach my $kidob (@{$oidob->{child}}) { my $ktype= $kidob->{type}; if ($ktype =~ /^$makepartsfrom$/) { push(@$mrnaexons, $kidob); # save in case missing CDS_exon } if ( $ktype eq $CDS_spanType ) { $spanob= $kidob; } # only for utr patch ! if ( $ktype eq $subtype ) { $subob= $kidob unless($subob); } elsif ($kidparts{$ktype}) { push(@$kidobs, $kidob); } } ## CDS/protein w/o CDS_exon parts ... recreate from cds start/stop + mrna location if ($subob && !@$kidobs && $hasspan && @$mrnaexons) { warn ">gmmC getCDSexons $sub_model $kidparts $subob, ne=",scalar(@$mrnaexons),"\n" if $GMM; $kidobs= $self->getCDSexons($subob, $mrnaexons); #($subob,$kidobs)= eval "\$self->$makemethod(\$subob, \$mrnaexons);"; } ## for making UTRs, introns: mar06 # makemethod == makeUtr5,makeIntrons,... elsif( !@$kidobs && @$mrnaexons && $makemethod) { $subob= $parob unless($subob); #?? # warn ">gmmU $makemethod $sub_model $kidparts $subob, ne=",scalar(@$mrnaexons),"\n" if $GMM; ($subob,$kidobs)= eval "\$self->$makemethod(\$subob, \$mrnaexons);"; if($@ && $DEBUG){ warn "$makemethod err: $@"; } #? die if ($self->{failonerror}) ? warn ">gmmU $makemethod $sub_model np=",scalar(@$kidobs),"\n" if $GMM; } if ($subob) { ## copy gene model dbxref id into these features, as per above my $idpattern= $self->config->{idpattern}; foreach my $pidattr (@{$fob->{attr}}) { next if ($pidattr =~ m/2nd/); #dbxref_2nd: if (!$idpattern || $pidattr =~ m/$idpattern/) { push( @{$subob->{attr}}, $pidattr) unless( grep {$pidattr eq $_} @{$subob->{attr}}); last; # add only 1st/primary } } if ($subtype =~ /UTR/ && $self->config->{utrpatch}) { $self->patchUTRs( $subob, $spanob, $mrnaexons, $kidobs); } ## jan06: problem here w/ change to protein/cds: all GModelParts end up fff feature ## CDS_exon, exon end up as compound types same as mRNA, CDS/protein my $cob= $self->makeCompound( $subob, $kidobs, $subtype); # $self->listkids($cob,$kidobs) if($DEBUG); ## was loosing kids to bad $oidobs $cob->{type}= $typelabel; warn ">gmmCOB $typelabel $cob np=",scalar(@$kidobs),"\n" if $GMM; push(@cobs, $cob); } } } ## else { } # $iskid only - dont save } return \@cobs; } =item patchUTRs($utrob,$mrnaexons,$kidobs) make sure utr's are in $mrnaexons range patch for buggy utr-data =cut sub patchUTRs { my $self= shift; my ($utrob,$cdsob,$mrnaexons,$kidobs)= @_; return if ($utrob->{patched} || scalar(@$mrnaexons)==0); my($minex,$minex1,$maxex,$maxex1)=(-1,-1,-1,-1); foreach my $ex (@$mrnaexons) { my ($start,$stop,$st) = split("\t", $ex->{loc}->[0]); if ($minex==-1 || $start < $minex) { ($minex,$minex1)= ($start,$stop); } if ($maxex==-1 || $stop > $maxex) { ($maxex,$maxex1)= ($stop,$start); } } # got weird utr mid points 2,3 bases below/above CDS start/stop; # always use protein start/stop if need change? if ($cdsob) { my $offsetloc = $cdsob->{loc}->[0] ; # only 1 we hope my ($offstart,$offstop,$offstrand) = split("\t",$offsetloc); $minex1= $offstart-1 if ($offstart > $minex); # && $offstart <= $minex1 $maxex1= $offstop+1 if ($offstop < $maxex); #$offstop >= $maxex1 && } ## kidobs[0] == utrob always ? only 1 kidob ? foreach my $kid (@$kidobs) { my $c= 0; my ($start,$stop,$st) = split("\t", $kid->{loc}->[0]); if ($start < $minex) { $c=1; $start= $minex; $stop= $minex1; } #if ($stop < $start) if ($stop > $maxex) { $c=1; $stop= $maxex; $start= $maxex1; } #if ($start > $stop) # print STDERR "patchUTRs ".($c?'':'NOT ').$kid->{name}." ".$kid->{loc}->[0]." => $start..$stop\n" if $DEBUG; if ($c) { $kid->{loc}->[0]= join("\t", $start,$stop,$st); $utrob->{'writefff'}= $utrob->{'writegff'}= -1 if ($stop==$start); } # dont write bogus empty UTR elsif ($stop==$start) { $utrob->{'writefff'}= $utrob->{'writegff'}= -1; } } $utrob->{patched}=1; } =item makeUtr5,3,makeIntron generate UTR's, introns from exons, protein-span features added mar06 call: my $makemethod = $sub_model->{makemethod}; # makeUtr5,makeIntrons,... ($subob,$kidobs)= $self->&{$makemethod}($subob, $mrnaexons); where returned $subob is new feature: UTRs or intron(s) =cut sub makeUtr5 { return shift->makeUtr53(5,@_); } sub makeUtr3 { return shift->makeUtr53(3,@_); } sub makeUtr53 { my $self= shift; my ($uside, $mrnaob, $mrnaexons)= @_; return (undef,[]) unless($uside == 5 || $uside == 3); return (undef,[]) unless ($mrnaob && scalar(@$mrnaexons)); my($cdsob); # get from exon list my @kidobs= (); # make from exons foreach my $ex (@$mrnaexons) { my $ktype= $ex->{type}; if($ktype eq 'protein') { $cdsob= $ex; } } # warn "makeUtr$uside $cdsob\n" if $DEBUG; return (undef,[]) unless ($cdsob); my $offsetloc = $cdsob->{loc}->[0] ; # only 1 we hope my ($offstart,$offstop,$offstrand) = split("\t",$offsetloc); ## need to watch strand effect: 5prime for -strand is hi value, not low # but genome-locs are always start{type}; next unless($ktype eq 'exon'); my ($start,$stop,$st) = split("\t", $ex->{loc}->[0]); # FIXME strand... next if($ulow && $start >= $offstart); next if($uhigh && $stop <= $offstop); # my $cex= { %$ex }; # shallow clone; ok? my $cex= $self->cloneBase($ex); # need locs $cex->{'writefff'}= $cex->{'writegff'}= 0; # -1 ?? $cex->{type}= ($uside == 5) ? 'five_prime_UTR' : 'three_prime_UTR'; my $c= 0; # FIXME strand if ($ulow && $stop >= $offstart) { $c=1; $stop = $offstart - 1; } if ($uhigh && $start <= $offstop) { $c=1; $start= $offstop + 1; } if ($c) { $cex->{loc}->[0]= join("\t", $start,$stop,$st); } push(@kidobs,$cex); } # warn "makeUtr$uside kids=",scalar(@kidobs),"\n" if $DEBUG; return (undef,[]) unless (@kidobs); # my $utrob= { %$mrnaob }; # shallow clone ! my $utrob= $self->cloneBase($mrnaob); # need locs $utrob->{fulltype}= $utrob->{type}= ($uside == 5) ? 'five_prime_UTR' : 'three_prime_UTR'; my $part= ($uside == 5) ? "_utr5" : "_utr3"; $utrob->{name} .= $part; $utrob->{id} .= $part; $utrob->{'writefff'}= $utrob->{'writegff'}= 0; # # need new $oid; insert in $oidobs->{$oid}->{parent}; .. # $self->newParentOid( $mrnaob, 'parent_oid', $geneoid, $oidobs); $utrob->{patched}=1; return($utrob,\@kidobs); } sub makeIntrons { my $self= shift; my ($mrnaob, $mrnaexons)= @_; return () unless ($mrnaob && scalar(@$mrnaexons)); my @kidobs= (); # make from exons my ($lstart,$lstop,$lst)= (0)x3; foreach my $ex (@$mrnaexons) { my $ktype= $ex->{type}; next unless($ktype eq 'exon'); my ($start,$stop,$st) = split("\t", $ex->{loc}->[0]); # FIXME strand... #? assume ordered exons here ? if($lstop>0 && $start > $lstop) { # my $cex= { %$ex }; # shallow clone; ok? my $cex= $self->cloneBase($ex); # need locs my($istart,$istop,$ist)= ($lstop+1,$start-1,$lst); $cex->{loc}->[0]= join("\t", $istart,$istop,$ist); $cex->{type}= 'intron'; $cex->{name} .= "_intron"; $cex->{id} .= "_intron"; push(@kidobs,$cex); } ($lstart,$lstop,$lst)= ($start,$stop,$st); } return () unless (@kidobs); # my $intronob= { %$mrnaob }; # shallow clone ! my $intronob= $self->cloneBase($mrnaob); # need locs $intronob->{fulltype}= $intronob->{type}= 'intron_set'; # intron collection ! $intronob->{name} .= "_introns"; $intronob->{id} .= "_introns"; $intronob->{'writefff'}= $intronob->{'writegff'}= 0; # intron collection ! return($intronob,\@kidobs); } =item getCDSexons($cdsob,$exonobs,$ftype) create compound feature from parent, kids (e.g., mRNA + exons) =cut sub getCDSexons { my $self= shift; my ($cdsob,$exonobs,$ftype)= @_; my $offsetloc = $cdsob->{loc}->[0]; # only 1 we hope my ($offstart,$offstop,$offstrand) = split("\t",$offsetloc); if ($offstart > $offstop) { ($offstart,$offstop)= ($offstop,$offstart); } #? need $cdsob->{offloc}= $offsetloc; my @cdsobs=(); foreach my $kid (@$exonobs) { my ($start,$stop,$st) = split("\t", $kid->{loc}->[0]); if ($stop >= $offstart && $start <= $offstop) { push(@cdsobs, $kid); } } return \@cdsobs; } sub listkids { ## DEBUG only my $self= shift; my ($cob,$kidobs)= @_; my $name=$cob->{name}; my $ftype=$cob->{type}; my @locs= @ { $cob->{loc} }; print STDERR "COB $ftype:$name"; print STDERR " locs=",join(",",@locs); print STDERR " kids="; foreach my $kid (@$kidobs) { print STDERR $kid->{type},":",$kid->{name}," "; print STDERR join(",", @{$kid->{loc}})," "; } print STDERR "\n"; } sub cloneBase ## shallow clone { my $self= shift; my ($fob)= @_; my $cob= {}; # are these all constant per oid ? @{%$cob}{@fclone_fields}= @{%$fob}{@fclone_fields}; #? what is vodoo # $cob->{chr} = $fob->{chr}; # $cob->{type}= $fob->{type}; # $cob->{fulltype}= $fob->{fulltype}; # $cob->{name}= $fob->{name}; # $cob->{id} = $fob->{id}; # $cob->{oid} = $fob->{oid}; # $cob->{'writefff'}= $fob->{'writefff'}; # if ($fob->{'writefff'}<0); # in case flagged in utr checker # $cob->{'writegff'}= $fob->{'writegff'}; # if ($fob->{'writegff'}<0); # in case flagged in utr checker # ## need locs ... $cob->{loc} = []; push( @{$cob->{loc}}, $_) foreach (@{$fob->{loc}}); $cob->{attr}= []; push( @{$cob->{attr}}, $_) foreach (@{$fob->{attr}}); # foreach my $attr (@{$fob->{attr}}) { push( @{$cob->{attr}}, $attr); } return $cob; } =item makeCompound($fob,$kidobs,$ftype) create compound feature from parent, kids (e.g., mRNA + exons) =cut sub makeCompound { my $self= shift; my ($fob,$kidobs,$ftype)= @_; my $cob= $self->cloneBase($fob); $fob->{'writefff'}=1; # need here also !? this is messy... # my $cob= {}; # are these all constant per oid ? # $cob->{chr} = $fob->{chr}; # $cob->{type}= $fob->{type}; # $cob->{fulltype}= $fob->{fulltype}; # $cob->{name}= $fob->{name}; # $cob->{id} = $fob->{id}; # $cob->{oid} = $fob->{oid}; # $cob->{'writefff'}= $fob->{'writefff'} if ($fob->{'writefff'}<0); # in case flagged in utr checker # $fob->{'writefff'}=1; # need here also !? # # #$cob->{attr}= $fob->{attr}; # $cob->{attr}= []; # foreach my $attr (@{$fob->{attr}}) { # push( @{$cob->{attr}}, $attr); # } # ##FIXME - parent loc may need drop for kids locs (mRNA) ## bad also to pick all kids - only exon type for mRNA, others? ## FIXME - for protein && CDS types which are only child of mRNA, need to merge into ## compound feat. ## FIXME - for dang transspliced mod(mdg4) - if strands in locs differ -> getLocation my @locs= (); #my @kidlist=(); ## debug only? ## need to skip kids for 'gene', others ? foreach my $kid (@$kidobs) { ##next if ($fob->{type} eq 'mRNA' && $kid->{type} ne 'exon'); #if ($DEBUG && $fob->{type} =~ m/^(mRNA|gene)$/) { # push(@kidlist, $kid->{name}, $kid->{type}); # } next if ($fob->{type} =~ m/^(mRNA|gene)$/ && $kid->{type} ne 'exon'); if ($ftype eq $CDS_spanType && $kid->{type} eq 'mature_peptide') { $ftype= $cob->{type}= 'mature_peptide'; } # next if ($fob->{type} eq 'CDS' && $kid->{type} ne 'CDS_exon'); $kid->{'writefff'}=1; # need here also !? foreach my $loc (@{$kid->{loc}}) { push( @locs, $loc); } } if ($ftype eq $CDS_spanType) { my $offsetloc = $fob->{loc}->[0]; # only 1 we hope $cob->{offloc}= $offsetloc; # $ftype= $cob->{type}= 'CDS' if(1); ## FIXME another flag to rename CDS spantype? } unless(@locs) { #? never keep main loc if have kid loc? foreach my $loc (@{$fob->{loc}}) { push( @locs, $loc); } } $cob->{loc}= \@locs; # $cob->{kidlist}= \@kidlist if ($DEBUG); ## debug only? return $cob; } =item getLocation($fob,@loc) get feature genbank/embl/ddbj location string (FTstring) including transplice complexity return ($location, $start, $strand); ## feb05: need to preserve strand==0/undefined for some features which have mixture ## fixed - for dang transspliced mod(mdg4) - if strands in locs differ ### looks like chado pg reporting instance with CDS_exons is bad for transspliced mod(mdg4) =cut sub getLocation { my $self= shift; my($fob,@loc)= @_; my $srange=''; my $bstart= -999; my($l_strand,$istrans)=(0,0); my ($offstart,$offstop,$offstrand)= (0,0,0); ## if $fob is CDS check offset strand, flip compl. if (defined $fob->{offloc}) { # now: DID NOT adjusted @loc by off start/stop ($offstart,$offstop,$offstrand) = split("\t",$fob->{offloc}); } ## assume not istrans - only 1 in 15,000 - redo if istrans foreach my $loc (@loc) { my ($start,$stop,$strand)= split("\t",$loc); if ($offstop != 0) { next if ($stop < $offstart || $start > $offstop); $start= $offstart if ($start<$offstart); $stop = $offstop if ($stop>$offstop); ## $strand= -$strand if ($offstrand < 0); #? is this bad for CDS ?? } if ($bstart == -999 || $start<$bstart) { $bstart= $start; } $srange .= "$start..$stop,"; if ($l_strand ne 0 && $strand ne $l_strand) { $istrans= 1; last; } $l_strand= $strand; } if ($istrans) { $srange=''; $l_strand= 0; $l_strand= $offstrand if ($offstrand < 0); ## hack patch for bad cds exons for transpliced mdg4 if (defined $fob->{exons}) { my $exonlocs= $fob->{exons}; @loc= @$exonlocs if (@$exonlocs); print STDERR "transplice ",$fob->{name}," replaced cds_exons with mrna exons\n" if $DEBUG; } foreach my $loc (@loc) { my ($start,$stop,$strand)= split("\t",$loc); if ($offstop != 0) { next if ($stop < $offstart || $start > $offstop); ## revcomp tricks here if ( $l_strand < 0 && $strand >= 0 ) { #&& $strand >= 0 print STDERR "transplice ",$fob->{name}," rev ex=$start,$stop,$strand ; off=$offstart,$offstop\n" if $DEBUG; $stop = $offstart if ($start < $offstart); #($stop>$offstart); ## } else { # next if ($stop < $offstart || $start > $offstop); $start= $offstart if ($start<$offstart); $stop = $offstop if ($stop>$offstop); } } $strand= -$strand if ($l_strand < 0); if ($strand < 0) { $srange .= "complement($start..$stop),"; } else { $srange .= "$start..$stop,"; } } } $srange =~ s/,$//; if ($l_strand < 0) { $srange= "complement($srange)"; } elsif($srange =~ m/,/) { $srange= "join($srange)"; } return ($srange, $bstart, $l_strand); } =item clearFinishedObs($flag,$oidobs) undef/release objects from %oidobs - otherwise fills up for full chromosome and overruns memory available -- ok now, added min base loc to keep in oidobs, delete all before runs fast - chr 3L in 10 min. instead of >2hr. before this, oidobs was retaining *all* objects per input chr file; and mem swapping to death before end. Now looks stable around 50 MB mem use. AND speeds up greatly; fly chr 3L in 10 min. instead of >2hr. =cut sub clearFinishedObs { my $self= shift; my ( $flag, $oidobs, $beforebase )= @_; ##my $flag= 'writefff'; my $nclear= 0; if ($self->config->{noforwards}) { my @oid; my @parids; my @kids; foreach my $oid (keys %{$oidobs}) { my $isfree= 1; my $parids= $oidobs->{$oid}->{parent}; foreach my $parid (@{$parids}) { my $pob = $oidobs->{$parid}; my $done= ($pob && $pob->{$flag}); #? this is bad? if(!$done && $pob && $pob->{fob}) { my $ptype= $pob->{fob}->{type} || ""; if ($simplefeat{$ptype}) { $done=1; } } unless($done) { $isfree=0; last; } } my $kids= $oidobs->{$oid}->{child}; foreach my $kidob (@{$kids}) { my $done= ($kidob->{$flag}); unless($done) { $isfree=0; last; } } ## dont free here -- finish iterate then do if ($isfree) { push(@oid, @{$parids}) if $parids; push(@kids, $kids) if $kids; push(@oid, $oid) if $oid; } } foreach my $kids (@kids) { undef @{$kids}; $nclear++; } foreach my $oid (@oid) { my $ob= delete $oidobs->{$oid}; $nclear++; if ($ob) { undef @{$ob->{parent}}; undef @{$ob->{child}}; undef %{$ob->{fob}}; undef $ob; } } ## this fix looks like it is controlling memory overload ## before this, oidobs was retaining *all* objects per input chr file; ## and mem swapping to death before end. Now looks stable around 50 MB mem use. ## AND speeds up greatly over last data dump; < 1hr/chr versus 3hr+ if ($beforebase>0) { while( my($oid,$ob)= each(%{$oidobs}) ) { if ($ob->{fob} && $ob->{fob}->{fmax} < $beforebase) { undef @{$ob->{parent}}; undef @{$ob->{child}}; undef %{$ob->{fob}}; undef $ob; delete $oidobs->{$oid}; $nclear++; } } } } # need to use gffForwards check # NOTE: not tested; need likely above $beforebase fix to keep from retaining all oidobs else { foreach my $foid (keys %gffForwards) { if ($gffForwards{$foid} == -1) { delete $gffForwards{$foid}; delete $oidobs->{$foid}; #? need to undef/delete $oidobs{n}->parts ? $nclear++; } } } return $nclear; } =item checkForward($flag,$fob,$oidobs) check for any remaining forwarded (unseen) objects (for gff) >> forward checks are problematic w/ new feats; causing gff to sit in mem for full chromosome =cut sub checkForward { my $self= shift; my ($flag,$fob,$oidobs)= @_; my $thisforward=0; my $anyforward=0; my $oid= undef; return $anyforward if ($self->config->{noforwards}); my $issimple= ($fob && $simplefeat{$fob->{type}} ); ## this is wrong - need to check kid ids written (also!?) ## ?? also need to check fob->{loc}/{fmax} to see if we have past that point ?? if ($fob && $oidobs) { # && !$issimple $oid= $fob->{oid}; # must skip segment, big features, etc. here even if have {parent} my $parids= $oidobs->{$oid}->{parent}; if ($parids && !$issimple) { foreach my $parid (@{$parids}) { if (defined $gffForwards{$parid} && $gffForwards{$parid}<0) { next; } my $pob= $oidobs->{$parid}; my $done= ($pob && $pob->{$flag}); #? this is bad? my $ptype= $pob->{fob}->{type}; if ($pob && $pob->{fob} && ($simplefeat{$ptype})) { $done=1; } if (!$done) { $gffForwards{$parid}=1; $thisforward=1; } else { $gffForwards{$parid}=-1; } } } my $kids= $oidobs->{$oid}->{child}; if ($kids) { foreach my $kidob (@{$kids}) { my $kidoid= $kidob->{oid}; if (defined $gffForwards{$kidoid} && $gffForwards{$kidoid}<0) { next; } my $done= ($kidob->{$flag}); if (!$done) { $gffForwards{$kidoid}=1; $thisforward=1; } else { $gffForwards{$kidoid}=-1; } } } } ## need $flag check here? foreach my $need (values %gffForwards) { if ($need>0) { $anyforward=1; last; } } $gffForwards{$oid}=-1 if ($oid); # about to write this $fob return $anyforward; #return (wantarray) ? ($anyforward,$thisforward) : $anyforward; } sub getForwards { my $self= shift; my $anyforward=''; foreach my $oid (sort keys %gffForwards) { if ($gffForwards{$oid}>0) { $anyforward .="$oid "; } } return $anyforward; } =item putFeats($outh,$fobs,$oidobs,$flag) output feature object (fobs) in selected formats (fff,gff,fasta) =cut sub putFeats { my $self= shift; my ($outh,$fobs,$oidobs,$flag)= @_; return unless($fobs && @$fobs > 0); my($hasforward,$l_hasforward)=(0,0); my $n= scalar(@$fobs); if ($DEBUG && $flag =~ /final/) { # $DEBUG>1 || print STDERR "putFeats n=$n, total=".($n+$ntotalout) .", oid1=".(($n>0)?$fobs->[0]->{oid}:0)."\n"; } elsif ($DEBUG) { print STDERR "."; } $self->updateParentKidLinks($fobs, $oidobs); #05feb: logic change ; was in processChadoTable if ($outh->{fff}) { ## || $outh->{fasta} < moved out my $ffh= $outh->{fff}; # my $fah= $outh->{fasta}; $self->{curformat}= 'fff'; my $cobs= $self->makeFlatFeatsNew($fobs,$oidobs); # need to undef @$cobs when done ! my $nout= 0; foreach my $fob (@$cobs) { ##$self->writeFFF( $outh->{fff}, $fob, $oidobs); my $fffline= $self->getFFF( $fob, $oidobs ); if($fffline) { print $ffh $fffline; $nout++; } undef $fob; } undef $cobs; $ffh->flush(); $ntotalout += $nout; } if ($outh->{gff}) { $self->{curformat}= 'gff'; my $gffh= $outh->{gff}; my $noforw= $self->config->{noforwards}; # print $gffh "# fwd oid=".$self->getForwards()."\n"; # is this a section break? my $gffend= 0; $l_hasforward= ($noforw) ? 0 : $self->checkForward('writegff'); foreach my $fob (@$fobs) { $hasforward= ($noforw) ? 0 : $self->checkForward('writegff',$fob,$oidobs); if ($hasforward && !$l_hasforward && !$gffend) { $self->writeGFFendfeat($gffh); $gffend++; } $l_hasforward= $hasforward; #? if ($hasforward) { $fob->{'writegff'}=1; # flag we have it for checkForward push(@gffForwards, $fob); } else { while (@gffForwards) { $self->writeGFF( $gffh, shift @gffForwards,$oidobs) ; } ## if we drop use of ID=oid, need to resolve all forwards before writeGFF $self->writeGFF( $gffh,$fob,$oidobs) ; $gffend=0; } } if ($flag =~ /final/) { while (@gffForwards) { $self->writeGFF( $gffh,shift @gffForwards,$oidobs) ; } } $gffh->flush(); } $self->{curformat}= ''; } sub writeHeader { my $self= shift; my($outh,$fmt,$chr,$appending)= @_; my $chrlen= defined $chromosome->{$chr} && $chromosome->{$chr}->{length} || 0; ## foreach $fmt (@formats) { $self->{$fmt}->writeheader($outh->{$fmt},$chr,$chrlen); } $self->writeFFF1header($outh->{$fmt},$chr,$chrlen) if ($fmt eq 'fff' && !$appending); $self->writeGFF3header($outh->{$fmt},$chr,$chrlen) if ($fmt eq 'gff' && !$appending); ## add fasta output - no header ? } ## SONG/so Revision: 1.45 ## @is_a@oligo ; SO:0000696 ; SOFA:SOFA ; synonym:oligonucleotide ## 'so' is no longer valid ## old value: @is_a@so ; SO:1000000 ## -- options are limited: located_sequence_feature, SO:0000110 ?? ## -- in flybase, 'so' seems used for protein blast matches? ## segment not in this ## alt choices ... # @is_a@assembly ; SO:0000353 ; SOFA:SOFA # ** @is_a@golden_path ; SO:0000688 ; SOFA:SOFA << # ** @is_a@supercontig ; SO:0000148 ; SOFA:SOFA ; synonym:scaffold << # @is_a@tiling_path ; SO:0000472 ; SOFA:SOFA # @is_a@virtual_sequence ; SO:0000499 ; SOFA:SOFA # @is_a@chromosome ; SO:0000340 # @part_of@chromosome_arm ; SO:0000105 ## aug04: add new analysis features (HDP,RNAiHDP,fgenesh,) ## these are like exons but parent feature lacks featureloc ## - need to join together by object_oid/parent_oid and compute parent feature (has name) ## SO type.subtype should be match.program ## SONG: match, match_part match_set nucleotide_match cross_genome_match cDNA_match EST_match #? use '.' instead of '_' for part type? would that throw gnomap/gbrowse usage? probably sub setDefaultValues { my($self)= @_; %maptype = ( golden_path_region => "scaffold", # "golden_path", ##was "segment", .. is again oligonucleotide => "oligo", transposable_element_pred => "transposable_element_pred", three_prime_untranslated_region => "three_prime_UTR", five_prime_untranslated_region => "five_prime_UTR", ); %maptype_pattern = (); %mapname_pattern = (); %mapattr_pattern = (); %maptype_gff = ( tRNA_trnascan => "tRNA:trnascan", transposable_element_pred => "transposable_element:predicted", ); %segmentfeats = ( # == big feats; no kids chromosome => 1, chromosome_arm => 1, chromosome_band => 1, source => 1, BAC => 1, segment => 1, golden_path => 1, golden_path_region => 1, ## segment no longer valid SO; supercontig or golden_path are best ); ## some common ones needing simple start/end, not compound %simplefeat = ( ## NOT these: gene => 1, pseudogene => 1, #? but has mRNA-like transcripts oligonucleotide => 1, point_mutation => 1, transcription_start_site => 1, repeat_region => 1, region => 1, # attached to gene parents .. RpL40-misc_feature-1 ); map { $simplefeat{$_}=1; } keys %segmentfeats; ## drop 'remark' feat from all ? %dropfeat_fff = ( ## for the parent/kid test for compound feats exon => 1, remark => 1, CDS_exon => 1, #? better type? # these following are not dropped, but compounded under each mRNA three_prime_UTR => 1, five_prime_UTR => 1, CDS => 1, intron => 1, ); %dropfeat_gff = ( ## for the parent/kid test for compound feats CDS_exon => 1, remark => 1, ); # these uniquename's from chado are not useful .. same as name always? # now only for fff output? keep all ID for gff part resolving %dropid = ( exon => 1, transcription_start_site => 1, transposable_element_pred => 1, intron => 1, repeat_region => 1, oligonucleotide => 1, processed_transcript => 1, EST => 1, cDNA_clone => 1, chromosome_band => 1, ); %dropname = ( mRNA_piecegenie => 1, mRNA_genscan => 1, tRNA_trnascan => 1, transcription_start_site => 1, # if these are like 174396-174397-AE003590.Sept-dummy-promoter ## drop 'JOSHTRANSPOSON-' from name of transposable_element_pred 'JOSHTRANSPOSON-copia{}293-pred' ); ## need to turn name/id into dbxref attrib ## feats: processed_transcript , EST, protein -- instead make compound by same OID ! %mergematch = ( ##EST => 1, ##processed_transcript => 1, ##### protein => 1, # only if not CDS!!! ); %keepstrand=(); %hasdups = ( exon => 1, three_prime_UTR => 1, five_prime_UTR => 1, ); ##map { $hasdups{$_}=1; } keys %mergematch; # these are ones where parent feature == gene needs renaming $rename_child_type = ""; # old: join('|', 'pseudogene','\w+RNA' ); } #---- FFF output -- separate package ? sub writeFFF1header { my $self= shift; my($fh,$seqid,$start,$stop)= @_; if ((!defined $stop || $stop == 0)) { $stop= $start; $start= 1; # start == length } my $date = $self->{date}; my $sourcetitle = $self->{sourcetitle}; my $sourcefile = $self->{sourcefile}; my $org= $self->{species} || $self->{org}; print $fh "# Features for $org from $sourcetitle [$sourcefile, $date]\n"; print $fh "# gnomap-version 1\n"; print $fh "# source: ",join("\t", $seqid, "$start..$stop"),"\n"; ##print $fh "# ",join("\t", qw(Feature gene map range id db_xref notes)),"\n"; print $fh "# ",join("\t", qw(Feature name cytomap location id db_xref notes)),"\n"; print $fh "#\n"; if ($stop > $start) { if ($fff_mergecols) { my $bstart= TOP_SORT; # if ($self->{config}->{topsort}->{$fob->{type}}); print $fh join("\t", $seqid, $bstart, "source", $org, $seqid, "$start..$stop", $seqid,)."\n"; } else { print $fh join("\t", "source", $org, $seqid, "$start..$stop", $seqid,)."\n"; } } } sub _fffEscape { my $v= shift; # $v =~ tr/ /+/; #? leave in spc ? $v =~ s/([\t\n\=&;,])/sprintf("%%%X",ord($1))/ge; return $v; } =item getFFF v1 return tab-delimied feature lines in this format # gnomap-version $gnomapvers # Feature gene map range id db_xref notes feature == feature type gene == gene name map == cytology map range == GenBank/EMBL/DDBJ location, BioPerl FTstring) id == feature id db_xref == database crossrefs (, delimited) notes == miscellany, now key=value; list =cut sub getFFF { my $self= shift; my($fob,$oidobs)= @_; return if ($fob->{'writefff'}); #?? so far ok but for mature_peptide/CDS thing $fob->{'writefff'}=1; my @loc= @{$fob->{loc}}; my @attr= @{$fob->{attr}}; my $oid= $fob->{oid}; my $featname= $fob->{type}; my $fulltype= $fob->{fulltype}; my($id,$s_id)= $self->remapId($featname,$fob->{id},'-'); $id= '-' unless (defined($id) && $id); (my $ftop= $fulltype) =~ s/[\:\.].*$//; if ($ftop && $featname =~ /^$ftop/) { $featname= $fulltype; } #?? want this my $sym= $fob->{name} || '-'; $sym = _fffEscape($sym); my $map= '-'; my $dbxref=""; my $dbxref_2nd=""; my $notes= ""; my %at=(); foreach (@attr) { my ($k,$v)= split "\t"; ## synonym_2nd=ribosomal protein S3&agr;; << problem; escape $v = _fffEscape($v); # _gffEscape; at least any [\t\n\=&;,] if ($k eq "object_oid") { # skip } elsif ($k eq "synonym" && ($v eq $id || $v eq $sym)) { next; } elsif ($k eq "parent_oid") { ## added apr05 next if $segmentfeats{$featname}; # dont do parent for these ... ? $v =~ s/:.*$//; #$v= $oidmap{$v} || $v; $k= 'Parent'; my $parob= $oidobs->{$v}->{fob}; if ($parob && $parob->{id}) { $v= $parob->{id}; #? if ($oidisid_gff{$type}) { $v= $parob->{oid}; } if ($v eq $id) { ## FIXME .. ? try to use index in parent->{child} array ? my $i= 1; my $paroid= $parob->{oid}; my $kids = $oidobs->{$paroid}->{child}; if ($kids) { foreach my $kidob (@{$kids}) { last if ($kidob->{oid} eq $oid); $i++; } } $id= "$id.$i"; # $at[0]= "ID="._gffEscape($id); } $at{$k} .= ',' if $at{$k}; $at{$k} .= $v; } else { #next if ($fulltype =~ /match_part|cytology|band|oligo|BAC/ || $id =~ /GA\d/); #print STDERR "GFF: missed Parent ID for i/o/t:",$id,"/",$oid,"/",$fulltype, # " parob=",$parob," k/v=",$k,"/",$v, " \n" if $DEBUG; next; # always skip writing bogus Parent= to gff } } elsif ($k eq "cyto_range") { $map= $v; } elsif ($k eq "dbxref") { ## and dbxref_2nd; put after dbxref ! $dbxref .= "$v;"; } elsif ($k eq "dbxref_2nd") { $dbxref_2nd .= "$v;"; } elsif ($k) { #$notes .= "$k=$v;" $at{$k} .= ',' if $at{$k}; $at{$k} .= $v; } } my @at=(); foreach my $k (sort keys %at) { push(@at, "$k=$at{$k}"); } $notes = join(";",@at); $dbxref .= $dbxref_2nd; # aug04: making sure 2nd are last is enough to get 1st ID my ($srange,$bstart,$strand); #my $srange = $fob->{location}; # computed already for transsplice ? #my $bstart = $fob->{start}; # computed already for transsplice ? #unless($srange && defined $bstart) ... ($srange,$bstart,$strand) = $self->getLocation($fob,@loc); ## feb05: need to preserve strand==0/undefined for some features which have mixture if ($strand == 0 && $keepstrand{$featname}) { $notes .= "strand=0;"; } ## add chr,start to front cols for sort-merge if ($fff_mergecols) { my $chr= $fob->{chr}; return join("\t", $chr,$bstart,$featname,$sym,$map,$srange,$id,$dbxref,$notes)."\n"; } else { return join("\t", $featname,$sym,$map,$srange,$id,$dbxref,$notes)."\n"; } } sub writeFFF { my $self= shift; my($fh,$fob,$oidobs)= @_; my $fffline= $self->getFFF($fob,$oidobs); print $fh $fffline if $fffline; } #---- GFF output -- separate package ? =item writeGFF v3 ##gff-version 3 ##sequence-region ctg123 1 1497228 == source in fff ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 ctg123 . 5_prime_UTR 1050 1200 . + . Parent=mRNA0001 ctg123 . CDS 1201 1500 . + 0 Parent=mRNA0001 ctg123 . CDS 3000 3902 . + 0 Parent=mRNA0001 ctg123 . CDS 5000 5500 . + 0 Parent=mRNA0001 ctg123 . CDS 7000 7600 . + 0 Parent=mRNA0001 ctg123 . 3_prime_UTR 7601 9000 . + . Parent=mRNA0001 =cut sub writeGFF3header { my $self= shift; my($fh,$seqid,$start,$stop)= @_; if ((!defined $stop || $stop == 0)) { $stop= $start; $start= 1; # start == length } my $date = $self->{date}; my $sourcetitle = $self->{sourcetitle}; my $org= $self->{species} || $self->{org}; print $fh "##gff-version\t3\n"; print $fh "##sequence-region\t$seqid\t$start\t$stop\n" if($seqid && $stop); #? always or only if missing chromosome? print $fh "#organism\t$org\n"; print $fh "#source\t$sourcetitle\n"; print $fh "#date\t$date\n"; print $fh "#\n"; ## DONT write chromosome twice -- check fobs ##sequence-region ctg123 1 1497228 == source in fff ## if ($stop > $start) ... print $fh join("\t", $seqid, ".","chromosome", $start, $stop, '.', '.', '.', "ID=$seqid"),"\n" if ($seqid && $stop && $self->config->{gff_addchromosome}); # also "chromosome" needs to be config-type } sub writeGFFendfeat { my $self= shift; my($fh)= @_; print $fh "###\n"; } sub splitGffType { my $self= shift; my($gffsource,$type,$fulltype)= @_; my($newgffs)=(''); #? use fulltype instead of type? as 'match:sim4:na_EST_complete_dros' # convert mRNA_genscan,mRNA_piecegenie to gffsource,mRNA ? if ($maptype_gff{$type}) { ##($type,$newgffs)= @{$maptype_gff{$type}}; ($type,$newgffs)= split(/[\.:]/,$maptype_gff{$type},2); } elsif ($fulltype =~ m/^([\w\_]+)[\.:]([\w\_\.:]+)$/) { ($type,$newgffs)=($1,$2); } elsif ($type =~ m/^([\w\_]+)[\.:]([\w\_\.:]+)$/) { ($type,$newgffs)=($1,$2); } else { $type= $fulltype; } #?? feb05; want snRNA not mRNA .. leave in fulltype ? $gffsource= $newgffs if($newgffs && $newgffs ne '.'); return($gffsource,$type); } sub _gffEscape { my $v= shift; $v =~ tr/ /+/; $v =~ s/([\t\n\=&;,])/sprintf("%%%X",ord($1))/ge; # Bio::Tools::GFF _gff3_string escaper return $v; } =item writeGFF write one feature in gff3 feature may have sub location parts (multi line) =cut sub writeGFF { my $self= shift; my($fh,$fob,$oidobs)= @_; my $type= $fob->{type}; my $fulltype= $fob->{fulltype}; return if ($fob->{'writegff'}); $fob->{'writegff'}=1; if ($dropfeat_gff{$type}) { return; } my $gffsource= $fob->{gffsource} || $self->{gff_config}->{GFF_source} || "."; my $oid= $fob->{oid}; my $id = $fob->{id}; ## was: $fob->{oid}; -- preserve uniquename ? my $chr= $fob->{chr}; my @loc= @{$fob->{loc}}; my @attr= @{$fob->{attr}}; my $at=""; my @at= (); my %at= (); =item gff IDs ## gff3 loader is using ID for uniquename, unless give attr key for uniquename ## ? do we want to drop $oid and use id/dbid - is it always uniq in gff file? ## feb05; need to test parid != id; problem now w/ some features (match/match_part same id) ## feb05 - EST's now have same ID for different location matches; need uniq gff id ## sim4:na_dbEST.diff.dmel .. use object_oid ? =cut if ($oidisid_gff{$type}) { $id= $oid; } # my($id,$s_id)= $self->remapId($type,$fob->{id}); #?? want for gff also ?? my $ignore_missingparent= $self->config->{maptype_ignore_missingparent} || '^xxxx'; my $v; push @at, "ID="._gffEscape($id) if ($id); # use this for gff internal id instead of public id? # ^^ if have parent, drop id ?? always or sometimes ? push @at, "Name="._gffEscape($v) if (($v= $fob->{name}) && $v ne $id); if ($gff_keepoids) { push @at, "oid=$oid"; } foreach (@attr) { my ($k,$v)= split "\t"; if (!$v) { next; } elsif ($k eq "object_oid") { next; } elsif ($k eq "parent_oid") { if ($gff_keepoids) { $at{$k} .= ',' if $at{$k}; $at{$k} .= $v; } next if $segmentfeats{$type}; # dont do parent for these ... ? $v =~ s/:.*$//; #$v= $oidmap{$v} || $v; $k= 'Parent'; #push @at, "Parent=$v"; ## now need to convert oid to parent id, given above change to id ## BUT this is bad when Parent hasn't been seen yet ! =item BUG ## Dec04 -- sometimes miss parent id here; get OID instead in output ## grep CG32584 dmel-X-r4.0.gff ## mRNA ID=CG32584-RB;Parent=3108188; ## mRNA ID=CG32584-RA;Parent=CG32584 ## lots for match_part .. ignore those? >> not many; 1/2 per csome; >> could be due to garbage collect. on oidobs; try MAX_FORWARD_RANGE+++ >> MAX_FORWARD_RANGE => 990000 seems to have fixed it =cut my $parob= $oidobs->{$v}->{fob}; if ($parob && $parob->{id}) { $v= $parob->{id}; if ($oidisid_gff{$type}) { $v= $parob->{oid}; } if ($v eq $id) { ## FIXME .. ? try to use index in parent->{child} array ? my $i= 1; my $paroid= $parob->{oid}; my $kids = $oidobs->{$paroid}->{child}; if ($kids) { foreach my $kidob (@{$kids}) { last if ($kidob->{oid} eq $oid); $i++; } } $id= "$id.$i"; $at[0]= "ID="._gffEscape($id); } } else { unless($fulltype =~ /$ignore_missingparent/) { ## || $id =~ /GA\d/ # dpse GA genes; odd parent = csome; ignore parent here? FIXME print STDERR "GFF: MISSING parent ob for i/o/t:",$id,"/",$oid,"/",$fulltype, " parob=",$parob," k/v=",$k,"/",$v, " \n" if $DEBUG; } next; # always skip writing bogus Parent= to gff } } elsif ($k eq "dbxref" || $k eq "db_xref") { # dbxref_2nd - leave as separate $k= 'Dbxref'; ##$v= "\"$v\""; # NO quotes - spec says to but BioPerl::GFFv3 reader doesn't strip quotes } elsif ($k eq "synonym") { # check dupl ID next if ($v eq $id || $v eq $fob->{name}); } if ($k) { $at{$k} .= ',' if $at{$k}; # got duplicate Parent=aaa,aaa in dpse data; why? $at{$k} .= _gffEscape($v); # should be urlencode($v) - at least any [=,;\s] } } ($gffsource,$type)= $self->splitGffType($gffsource,$type,$fulltype); ## drop ID if Parent ; sometimes ? my $parent= delete $at{'Parent'}; if( $parent && $dropid{$type} ) { $at[0]= "Parent=$parent"; } elsif ($parent){ push(@at, "Parent=$parent"); } foreach my $k (sort keys %at) { push(@at, "$k=$at{$k}"); } $at = join(";",@at); ## need to make uniq ids for dupl oids - any @loc > 1 ? ## and need to make parent feature to join. Use ID=OID.1... OID.n if (@loc>1) { my ($b,$e,$str)=(-999,0,0); foreach my $loc (@loc) { my($start,$stop,$strand)= split("\t",$loc); if ($b == -999) { ($b,$e) = ($start,$stop); $str= $strand; } else { $b= $start if ($b > $start); $e= $stop if ($e < $stop); } } $str= (!defined $str || $str eq '') ? '.' : ($str < 0) ? '-' : ($str >= 1)? '+' : '.'; print $fh join("\t", $chr,$gffsource,$type,$b,$e,".",$str,".",$at),"\n"; ## GFF v3 spec is unclear on what this $gffsource item contains. ## gffsource used for genscan, etc. type modifier, also for database sig, e.g. SGD $gffsource='part_of' if ($gffsource eq '.'); #? was 'part' foreach my $i (1..$#loc+1) { my($start,$stop,$strand)= split("\t",$loc[$i-1]); $strand= (!defined $strand || $strand eq '') ? '.' : ($strand < 0) ? '-' : ($strand >= 1)? '+' : '.'; $at= "ID=$id.$i;Parent=$id"; #? print $fh join("\t", $chr,$gffsource,$type,$start,$stop,".",$strand,".",$at),"\n"; } } else { my $loc= shift @loc; my($start,$stop,$strand)= split("\t",$loc); $strand= (!defined $strand || $strand eq '') ? '.' : ($strand < 0) ? '-' : ($strand >= 1)? '+' : '.'; print $fh join("\t", $chr,$gffsource,$type,$start,$stop,".",$strand,".",$at),"\n"; } } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm000644 000765 000024 00000147644 11256707527 023037 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::GenbankSubmitWriter; use strict; use constant FIXME => 1; =head1 NAME Bio::GMOD::Bulkfiles::GenbankSubmitWriter =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $bulkfiles= Bio::GMOD::Bulkfiles->new( configfile => 'mymodconfig', ); my $result= $bulkfiles->makeFiles( formats => [ qw(genbanktbl)] , ); =head1 NOTES subclassed from FeatureWriter (gff+fff), which deserves rewrite =head1 TEST CASES perl -Ilib bin/bulkfiles.pl -config sgdtest -format=genbanktbl -debug -make # get AnoGam chrX and load to chado db curl -OR ftp://bio-mirror.net/biomirror/ncbigenomes/Anopheles_gambiae/CHR_X/NC_004818.gbk.gz set dbname=anogam_x $pg/bin/createdb -T chado_01_template $dbname # fix Genbank FT to SO type map vi lib/Bio/SeqFeature/Tools/TypeMapper.pm : add pseudogenic tRNA # load Anopheles gambia chromosome X to chado gunzip -c NC_004818.gbk.gz |\ perl bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout |\ perl bin/gmod_bulk_load_gff3.pl -dbname $dbname -organism fromdata # create GMOD Bulkfiles conf/anogam.xml from template.xml : dbname, etc. edits # create Bulkfiles outputs for anogam_x perl -Ilib bin/bulkfiles.pl -config=anogam -debug -make >& log.anogam1 & # and now genbank table perl -Ilib bin/bulkfiles.pl -config=anogam -format=genbanktbl -debug -make =head1 AUTHOR D.G. Gilbert, 2008, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug #use lib( "/bio/argos/common/perl/lib", "/bio/argos/common/system-local/perl/lib"); #use lib( "/bio/argos/gmod/gmtmp/lib"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::FeatureWriter); #was use base qw(Bio::GMOD::Bulkfiles::BulkWriter); our $DEBUG = 1; my $VERSION = "1.2"; use constant BULK_TYPE => 'genbanktbl';#?? use constant CONFIG_FILE => 'genbanksubmit'; #?? or other use constant TOP_SORT => -9999999; use constant MAX_FORWARD_RANGE => 990000; # at 500000 lost a handful of oidobs refs; maximum base length allowed for collecting forward refs use constant MIN_FORWARD_RANGE => 20000; # minimum base length for collecting forward refs #........... super vars; move some out our $maxout; our $ntotalout; our $chromosome; ## read info from chado dump chromosomes.tsv our $fff_mergecols; our $gff_keepoids; our @outformats; our @defaultformats; our %formatOk; our @fclone_fields; our $outfile; our $append; our %gffForwards; our @gffForwards; our %maptype_gb; ## our == global scope; use vars == package scope use vars qw/ %maptype %maptype_pattern %mapname_pattern %mapattr_pattern %maptype_gff %segmentfeats %simplefeat %skipaskid %dropfeat_fff %dropfeat_gff %oidisid_gff %dropid %nameisid %dropname %mergematch %hasdups %keepstrand $rename_child_type $name2type_pattern @GModelParts %GModelParents $CDS_spanType $CDS_exonType /; #............... super vars ................. sub init { my $self= shift; $self->SUPER::init(); $self->{outh} = {}; $DEBUG= $self->{debug} if defined $self->{debug}; $self->setDefaultValues(); #?? use or not? hold-over from pre-config work } =item initData initialize data from config =cut our $tbl2asn; sub initData { my($self)= @_; my $config = $self->{config}; my $sconfig= $self->handler_config; @defaultformats= ( BULK_TYPE() ); #'genbanktbl' %formatOk= ( BULK_TYPE() => 1, ); # only these handled here ? @outformats= @{ $config->{outformats} || \@defaultformats } ; $config->{outformats}= \@outformats; #?? need this before super init; fixme %maptype_gb = %{ $config->{'maptype_gb'} } if ref $config->{'maptype_gb'}; $self->SUPER::initData(); my $blasthome= $config->{blasthome} ; # try $ENV{BLAST_HOME} or other?? $tbl2asn= $config->{tbl2asn} || "$blasthome/tbl2asn"; unless(-e $tbl2asn) { warn "Missing tbl2asn: $tbl2asn"; $self->status(-1,"missing tbl2asn"); } my $tbl2asnopts= $config->{tbl2asnopts} || '-V v '; $config->{tbl2asnopts}= $tbl2asnopts; } #-------------- subs ------------- =item tbl2asn in makeFiles: @tblouts= @ { $self->{outputlist} }; # full path to output foreach tblouts/chrs do tbl2asn( $tblname); =cut sub tbl2asn { my $self= shift; my( $tblpath)= @_; warn "tbl2asn( $tblpath )\n" if $DEBUG; my ($tblname, $subdir) = File::Basename::fileparse($tblpath); my $opts= $self->getconfig('tbl2asnopts'); # this works: $nb/tbl2asn -t template.sbt -V vb -p ./ # with inputs: # drosmelgb-all-drosmelgb4.tbl # drosmelgb-all-drosmelgb4.fsa == ../fasta/drosmelgb-all-chromosome-drosmelgb4.fasta # drosmelgb-all-drosmelgb4.pep == ../fasta/drosmelgb-all-translation-drosmelgb4.fasta # template.sbt my($fastachr,$fastapep,$gbsubfsa,$gbsubpep); my $chrfile="all"; # fixme ! my $fadir= "../fasta/"; # fixme ! $fastachr= $tblname; $fastachr =~ s/\-(\w+)\.\w+$/-chromosome-$1.fasta/; $fastapep= $tblname; $fastapep =~ s/\-(\w+)\.\w+$/-translation-$1.fasta/; # $fastachr= $self->get_filename( $self->{org}, $chrfile, 'chromosome', $self->{rel}, "fasta"); # $fastapep= $self->get_filename( $self->{org}, $chrfile, 'translation', $self->{rel}, "fasta"); $fastachr = catfile( $fadir, $fastachr); $fastapep = catfile( $fadir, $fastapep); $gbsubfsa= $tblname; $gbsubfsa =~ s/\.\w+$/.fsa/; $gbsubpep= $tblname; $gbsubpep =~ s/\.\w+$/.pep/; warn("# $tbl2asn $opts \n", "# using files: $tblname, $gbsubfsa, $gbsubpep \n") if $DEBUG; my $olddir= $ENV{'PWD'}; #?? not safe? chdir($subdir); symlink( $fastachr, $gbsubfsa); symlink( $fastapep, $gbsubpep); my $ok= system("$tbl2asn $opts "); chdir($olddir); return $ok; } =item makeFiles( %args ) primary method makes bulk genome sequence files in standard formats. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required formats => [ 'gff', 'fff' ] # optional =cut # subclass: this one could be inherited sub makeFiles { my $self= shift; my %args= @_; my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; my $intype= $self->config->{informat} || 'feature_table'; #? maybe array # 0710: no_csomesplit : no perchr files, only makeall my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 my $makeall= !$no_csomesplit && !$args{noall} && ($self->config->{makeall} || $self->{gff_config}->{makeall}); $self->{append}=1 if($no_csomesplit); #?????? TEST ME unless(@$fileset) { $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "GenbankSubmitWriter: no input '$intype' files found\n"; return $self->status(-1); } } my @saveformats= @outformats; if ($args{formats}) { my $formats= $args{formats}; @outformats= (ref $formats) ? @$formats : ($formats); } @outformats= grep { $formatOk{$_} > 0 } @outformats; ## messy; but see $args{filesetinfo} $args{name} if($args{name} && $args{filesetinfo}) { $self->{fileset}{ $args{name} }= $args{filesetinfo}; } foreach my $fmt (@outformats) { my $outset = $self->handler->getFilesetInfo( $fmt ); # genbanktbl $self->{fileset}{$fmt}= $outset if($outset); } print STDERR "GenbankSubmitWriter::makeFiles outformats= @outformats\n" if $DEBUG; my $status= 0; my $ok= 1; for (my $ipart= 0; $ok; $ipart++) { $ok= 0; my $inh= $self->openInput($fileset, $ipart); if ($inh) { my $res= $self->processChadoTable( $inh); close($inh); $status += $res; $ok= 1; } } if ($makeall && $status > 0) { foreach my $fmt (@outformats) { $self->makeall( $chromosomes, "", $fmt); } } ## need also symlink fasta/chrom.fa and fasta/translate.fa to genbanksubmit/.fsa,.pep $self->handler->writeDocs( $self->config->{doc} ); # submit template.sbt if( $status>0 ) { my @tblouts= @ { $self->{outputlist} }; # full path to output my $ok= 0; foreach my $tblname (@tblouts) { $ok = $self->tbl2asn( $tblname); } } @outformats = @saveformats; print STDERR "GenbankSubmitWriter::makeFiles: done n=$status\n" if $DEBUG; return $self->status($status); #?? check files made } ## just now can do only for gff; leave fff split by chr # sub makeall # { # my $self= shift; # my( $chromosomes, $feature, $format )= @_; # return if ($format eq 'fff'); # $feature= ""; # $self->{curformat}= $format; # $self->config->{path}= $format; #???? # setconfig ?? # print STDERR "makeall: $format\n" if $DEBUG; # $self->SUPER::makeall($chromosomes, $feature, $format); #?? not seen # $self->{curformat}= ''; # $self->config->{path}= ''; #???? # setconfig ?? # } =item openInput( $fileset, $ipart ) handle input files =cut # sub openInput # { # my $self= shift; # my( $fileset, $ipart )= @_; # do per-csome/name # my $inh= undef; # return undef unless(ref $fileset); # # my $intype= $self->config->{informat} || 'feature_table'; #? maybe array # my $atpart= 0; # # print STDERR "openInput: type=$intype part=$ipart \n" if $DEBUG; # # foreach my $fs (@$fileset) { # my $fp= $fs->{path}; # my $name= $fs->{name}; # my $type= $fs->{type}; # next unless($fs->{type} eq $intype); # unless(-e $fp) { warn "missing dumpfile $fp"; next; } # $atpart++; # next unless($atpart > $ipart); # print STDERR "openInput[$ipart]: name=$name, type=$type, $fp\n" if $DEBUG; # # if ($fp =~ m/\.(gz|Z)$/) { open(INF,"gunzip -c $fp|"); } # else { open(INF,"$fp"); } # $inh= *INF; # # my ($sfile, undef) = File::Basename::fileparse($fp); # $self->{sourcefile}= $sfile; # # return $inh; # only 1 at a time FIXME ... # } # print STDERR "openInput: nothing matches part=$ipart, type=$intype\n" if $DEBUG; # return undef; # } =item openCloseOutput($outh,$chr,$flags) handle output files =cut # sub openCloseOutput # { # my $self= shift; # my($outh,$chr,$flags)= @_; # my $chrfile= $chr; # my $app= defined $self->{append} ? $self->{append} : $append; # # 0710: no_csomesplit : no perchr files, only makeall # my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 # if( $no_csomesplit ) { # $app= 1; # $chrfile="all"; # or "sum" ?? # } # # if ($outh && $flags =~ /open|close/) { # foreach my $fmt (@outformats) { # close($outh->{$fmt}) if ($outh->{$fmt}); # } # } # # $outh= {}; # if ($flags =~ /open/) { # $chrfile='undef' unless($chrfile); # #?? for unsorted input need to change $append to true after first open? # foreach my $fmt (@outformats) { # ## need option to append or create !? # my $ap=($app) ? ">>" : ">"; # my $fn; # if ($outfile) { $fn="$outfile-$chrfile.$fmt"; } # else { $fn= $self->get_filename( $self->{org}, $chrfile, '', $self->{rel}, $fmt); } # # ##? check for $self->handler() # my $subdir= $fmt; ##($fmt eq 'fff') ? 'gnomap' : $fmt; #? fixme # my $featdir= $self->handler()->getReleaseSubdir( $subdir); # my $fpath = catfile( $featdir, $fn); # # my $exists= ($app && -e $fpath) ? 1 : 0; # print STDERR "# output $fpath (append=$exists)\n" if $DEBUG; # $outh->{$fmt}= new FileHandle("$ap$fpath"); # $self->writeHeader($outh,$fmt,$chr,$exists); ## unless($exists); # } # } # return $outh; # } =item remapXXX processChadoTable handlers to fix various table inputs, according to config mappings =cut # sub remapId # { # my $self= shift; # my ($type,$id,$name)= @_; # my $save= $id; # if (($nameisid{$type}) && $name) { $id= $name; } ## ? not for gff # elsif ($dropid{$type} || $id =~ /^NULL:/ || $id =~ /^:\d+/) { $id= undef; } # #?? or not# elsif (!$id) { $id= $name; } # return ($id,$save); # } # sub remapName # { # my $self= shift; # my ($type,$name,$id,$fulltype)= @_; # my $save= $name; # # if ( $dropname{$type} ) { $name= ''; } # # ## handle stupid match name = all the match type + ... # ## clean unwieldy predictor names: contig...contig... # elsif ($type =~ /^(gene|mRNA)/ && $name =~ s/Contig[_\d]+//g) { # ##if ($name =~ m/^(twinscan|genewise|genscan)/i) { $name= "${id}_${name}"; } # if ($name =~ m/^(twinscan|genewise|genscan|piecegenie)/i) { $name= "${id}_$1"; } # } # elsif (!$name) { $name= $id unless ($id =~ /^NULL:/i || $id =~ /^:\d+/); } # ## dmelr4.1 ; must apply below name patches to id (no name) # # ## this one could be time sink .. use evaled sub {} ? # foreach my $mp (sort keys %mapname_pattern) { # next if ($mp eq 'null'); # dummy? # my $mtype= $mapname_pattern{$mp}->{type}; # next if ($mtype && $type !~ m/$mtype/); # if ($mapname_pattern{$mp}->{cuttype}) { # my @tparts= split(/[_:.-]/, $type); # push(@tparts, split(/[_:.-]/, $fulltype) ); #?? # foreach my $t (@tparts) { $name =~ s/\W?$t\W?//; } # next; # } # my $from= $mapname_pattern{$mp}->{from}; next unless($from); # my $to = $mapname_pattern{$mp}->{to}; # if ($to =~ /\$/) { $name =~ s/$from/eval($to)/e; } # else { $name =~ s/$from/$to/g; } # } # # return ($name,$save); # } =item remapArm 2 3 segment Contig3266_Contig6542 - complement(3..1555441) Contig3266_Contig654 2 2 1555569 segment Contig143_Contig447 - complement(1555569..2614209) Contig143_Contig447 -- unordered contigs -- singles (? no feats) and doubles - put into common out files? -- if so, need to offset start/end to fit into unorderd 'chromosome' Contig1090 1 contig - - 1..211 Contig1090 GB:AADE01008166; Contig2258_Contig2260 1 contig - - 1..3082 Contig2258 GB:AADE01005006; # Double Dang - need to use segment offset/strand to map segment features =cut # sub remapArm # { # my $self= shift; # my ($arm,$fmin,$fmax,$strand)= @_; # my $save= $arm; # my $armfile= $arm; # # # my $rf= $armContigs{$arm}; # # if ($rf) { # # my($armr,$b,$e,$st,$contig)= @$rf; # # $arm= $armr; # # if ($st eq '-') { #?? do we need to flip all - min,max relative to arm.e ? # # $strand= -$strand; # # ($fmax,$fmin) = ($e - $fmin-1, $e - $fmax-1); # # } # # else { # # $fmin += $b - 1; # # $fmax += $b - 1; # # } # # } # # $armfile=$arm; # # # # ## need to fix dmel synteny.dump to not put gene name => arm for ortho:nnn # # if ($arm eq $save) { # # if (lc($org) eq 'dmel' && $arm =~ m/\-/) { # -PA .. others -xxx ? # # $armfile= 'genes'; # # } # # elsif ($arm =~ m/^Contig[^_]+_Contig/) { # # $armfile= 'unordered2'; # # } # # elsif ($arm =~ m/^Contig\w+/) { # # $armfile= 'unordered1'; # # } # # } # # return($arm,$fmin,$fmax,$strand,$armfile,$save) # } =item remapType Types from name ... only when needed Dpse uses gene name_(genscan|genewise|twinscan) ... Dmel uses mRNA name-(genscan|piecegenie) ... ?? anything with '-dummy-' in name is computed type? for Dpse which has gene ..., need to reType mRNA kids also mRNA 13903,12560-AE003590.Sept-dummy-piecegenie mRNA 15793,12560-AE003590.Sept-dummy-genscan transposable_element Name=JOSHTRANSPOSON-jockey{}277-pred transposable_element DBID=TE19092;Name=jockey{}277;cyto_range=21A3-21A3;Dbxref="FlyBase:FBti0019092";Dbxref="Gadfly:TE19092";gbunit=AE003590 Handle more complex types change this to allow complex type:subtype:.. for analysis, other features with pseudo-type like 'match:program:source' want final gff-type/source 'match',fgenesh{_source} or fgenesh:source want final fff-type match_fgenesh{_source} or match:fgenesh{_source} ? check how both gbrowse_fb and gnomap read/handle types gnomap/annomap -- underscores generally used but '.' also ## remap FBan.acode PRG:DB choices blastx_masked_aa_SPTR.worm=blastx_otherspp blastx_masked_aa_SP.hyp.dros=blastx_dros sim4_na_EST.all_nr.dros=EST genscan_dummy=genscan =cut #s subclass: use remapType for SeqOnto -> Genbank FT map? sub remapType { my $self= shift; my ($type,$name)= @_; return $self->SUPER::remapType(@_); #... or .... # my $save= $type; # $type =~ s/\s/_/g; # must change? # # ## this one could be time sink .. use evaled sub {} ? # foreach my $mp (keys %maptype_pattern) { # next if ($mp eq 'null'); # my $mname= $maptype_pattern{$mp}->{typename}; # next if ($mname && $name !~ m/$mname/); # my $from= $maptype_pattern{$mp}->{from}; # my $to = $maptype_pattern{$mp}->{to}; # $type =~ s/$from/$to/; # } # # my $nutype = $type; # # this should be config pattern: ..genscan.. # ##if (defined $name && $name =~ m/[-_](genscan|piecegenie|twinscan|genewise|pred|trnascan)/i) { # if ($name2type_pattern && defined $name && $name =~ m/$name2type_pattern/i) { # $nutype .= "_".lc($1); # } # $nutype =~ s/[:\.]/_/g; #? # $type = $maptype{$nutype} || $type; # # my $fulltype = $type; #?? here or what. # $type =~ s/[:\.]/_/g; #? # # return ($type,$fulltype,$save); } =item processChadoTable Read input feature table, write bulk output formats FFF and GFF (other formats are derived from these) This step takes longest, e.g. ~ 20 hr on single cpu for D. melangaster. Split by chromosome data among processors to speed up. Joins table lines/feature; builds compound features; checks feature names/types, etc. Input chado feature table dump format (see sql) arm fmin fmax strand type name id oid attr_type attribute 2L 0 305900 1 golden_path AE003590 AE003590 1273141 various_key value Outputs: FFF (also used for fasta, gnomap), GFF FIXME: something here gets very memory piggy, slow, with input feature tables full of match: analysis types (messy names, types, etc.) -- no feats written to fff in many hours !? - due to holding BAC and cytoband features -- try dropping gffForwards; maybe better (gff written) but still memuse balloons -- added clearFinishedObs() - no apparent help; dont see what else is holding objects here -- ok now, added min base loc to keep in oidobs, delete all before runs fast - chr 3L in 10 min. instead of >2hr. =cut sub handleAttrib { my $self= shift; my($addattr, $attr_type, $attribute, $fobadd)= @_; # nasty fix for _Escape ; to_name=Aaa,CGid should probably be two table lines if ($attr_type eq 'to_name' && $attribute =~ /,/) { my $attr1; ($attr1,$attribute)= split(/,/,$attribute,2); push( @$addattr, "$attr_type\t$attr1"); } foreach my $mp (sort keys %mapattr_pattern) { next if ($mp eq 'null'); # dummy my $mtype= $mapattr_pattern{$mp}->{type}; next if ($mtype && $attr_type !~ m/$mtype/); my $from= $mapattr_pattern{$mp}->{from}; next unless($from); my $to = $mapattr_pattern{$mp}->{to}; if ($to =~ /\$/) { $attribute =~ s/$from/eval($to)/e; } else { $attribute =~ s/$from/$to/g; } } if ($attr_type eq 'dbxref' && $attribute =~ /^GFF_source:(\S+)/) { if($fobadd) { $fobadd->{gffsource} = $1; } $attribute=''; } push( @$addattr, "$attr_type\t$attribute") if $attribute; } #s subclass: this main sub needs revisions sub processChadoTable { my $self= shift; my($fh, $outh)= @_; $outh= $self->{outh} unless(ref $outh); my %origin_one= %{ $self->config->{origin_one} || {} }; my $utrpatch= $self->config->{utrpatch} ; my $intronpatch= $self->config->{intronpatch} ; # patch for intron type; oct04: fmin - no+1,fmax, add+1 my $nozombiechromosomes= $self->config->{nozombiechromosomes}; # dpse chado duplicate 0-length chromosome entries my $tab= "\t"; # '[\|]'; ##"\t"; < '|' is bad sep cause some names have it ! my @fobs=(); my %oidobs=(); # this hash will grow big; can we delete before next chr ? my $fob= undef; my $max_max=0; my $min_max= 0; my $armlen=0; my $ndone= 0; my ($l_arm,$l_oid,$l_fmin,$l_fmax,$l_type)= (0,0,0); my ($arm,$fmin,$fmax,$strand,$type,$name,$id,$oid,$attr_type,$attribute) ; my($s_type, $fulltype, $s_arm, $armfile, $s_name, $s_id); my ($fin,$fhpeek); my %addfob=(); #? use line buffer @fhpeek to grep for missing forward refs ? eg. PA for mRNA ? $self->{linebuf}= []; while( $fin= $self->getline($fh) ) { $_= $fin; $ndone++; my @addattr=(); ## loop here over <$fh> while $oid == $l_oid ## only part changing is $attr_type/$attribute my $sameoid= 0; do { ($arm,$fmin,$fmax,$strand,$type,$name,$id,$oid,$attr_type,$attribute) = split("\t",$fin); $self->handleAttrib(\@addattr,$attr_type,$attribute,\%addfob) if ($attribute); ## inner read loop problem? need to process parent_oid attrib only once below my $nextin= $self->peekline(0) || ""; my $joid= index($nextin,"$id\t$oid\t"); $sameoid= ($joid>0); if ($sameoid) { my $ioid= index($fin,"$id\t$oid\t"); $sameoid= ($ioid==$joid && substr($nextin,0,$ioid) eq substr($fin,0,$ioid) ); if ($sameoid) { $fin= $self->popline(); } } } while ($sameoid); #my $tss= ($DEBUG && $type eq 'transcription_start_site'); #warn ">tss1: $arm,$fmin,$type,$name,$oid,$l_oid\n" if $tss; ## data fixes ## dpse chado has chromosomes of fmin=1; fmax = NULL ! no length; drop these (dupl) if ($nozombiechromosomes && $segmentfeats{$type} && $fmax <= $fmin) { ($l_oid,$l_fmin)= (-1,$fmin); next; } if( !defined $fmax ) { $fmax=0; } if( !defined $fmin ) { $fmin=0; } elsif ($intronpatch && $type eq 'intron') { $fmax += 1; } elsif ($utrpatch && $type =~ /_prime_untranslated_region|_prime_UTR/) { $fmin= $fmax if ($fmax == $fmin-1); } elsif( ! ($origin_one{$type} || $fmin == $fmax) ) { $fmin += 1; } # dang -1 chado start if( !defined $strand ) { $strand=0; } # feb05: the zero-base insertion sites ( fmin==fmax ) should not have fmin+1 adjustment # 2L 131986 131986 1 1 transposable_element_insertion_site ## this check only for intron,UTR chado-computed locs ?? ## also looks like computed UTR's can be off by 1 out of gene bounds, if UTR == 0 ## CG2657 = 2L:21918..23888 ; exon1 = 22983..23888 ; exon2 = 21918..22687 ## dmel_chado says -u3 = 21918..2191723889..23888 ; -intron = no+1>22688..22982 if ($fmax < $fmin) { ($fmin,$fmax)= ($fmax,$fmin); $strand= ($strand==0) ? -1 : -$strand; } # ($arm,$fmin,$fmax,$strand,$armfile,$s_arm) # = $self->remapArm($arm,$fmin,$fmax,$strand); # for dpse joined contigs ($type,$fulltype,$s_type)= $self->remapType($type,$name); if (!$type && $DEBUG && !/NULL|repeatmask/) { print STDERR "missing type: $_\n"; } ##<< repeatmasker kid objs if ($type eq 'skip' || !$type) { # or what? undef? got some bad feats w/ no type?? ## dont keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin); ##dont save arm for skip !? if changed here, cant miss below openout.. ($l_oid,$l_fmin)= (-1,$fmin); next; } # ($id,$s_id)= $self->remapId($type,$id,$name); ($name,$s_name)= $self->remapName($type,$name,$id,$fulltype); ## dmelr4.1 patch; cant do this for all dropid - gff needs real ids for exons for instance #if (($dropid{$type} || $nameisid{$type}) && $name) { $id= $name; } ## ## do this in remapId .. ## if (($nameisid{$type}) && $name) { $id= $name; } ## ? not for gff my $loc="$fmin\t$fmax\t$strand"; # dmelr4.1 - need add band attrib even if attrib == parent_oid if ($type eq 'chromosome_band') { ## && !$attribute my $battr_type = 'cyto_range'; my $battribute = $s_name; $battribute =~ s/(cyto|band|\-)//g; push( @addattr, "$battr_type\t$battribute"); $name =~ s/\-cyto//; } ## find quicker way to screen out many match_ dup things ; same simple loc, no id... ## # hasdups -- need to check id == l_id, name = l_name .. ## match_blastn_na_dbEST_dpse="1" ## match_sim4_na_dbEST_same_dmel="1" ## ? do something like this also for EST, protein which differ only by dbxref id ## i.e. feature is location w/ several items matching ## need to turn name/id into dbxref attrib ## feats: processed_transcript , EST, protein ## some chado exons, introns are dupl of same data... diff uniquename for no useful reason ## also check for $oidobs{$oid}->{fob}; if ($oid ne $l_oid && ! $simplefeat{$type} && exists $oidobs{$oid}->{fob}) { my $ok=0; foreach my $dob (@fobs) { if ($dob->{oid} eq $oid) { $ok=1; last; } } if ($ok) { $fob= $oidobs{$oid}->{fob}; $oid= $l_oid= $fob->{oid}; } else { ## FIXME - bad if fob not in @fobs ## .. e.g. repeat region - many locs over arm, few oid's ## most of these we dont want to join - too far apart; need max_max setting below to keep small ranges together? # print STDERR "missed join to last $type,$name,$oid\n" if $DEBUG; } } if ($oid ne $l_oid && $hasdups{$type}) { foreach my $dob (@fobs) { next unless($dob->{type} eq $type); my $dloc= $dob->{loc}->[0]; my($dmin,$dmax,$dstrand)= split("\t",$dloc); if ( $dmin eq $fmin && $dmax eq $fmax && $dstrand eq $strand ) { $fob= $dob; $oid= $l_oid= $fob->{oid}; last; } } } #warn ">tss2d: new $arm,$fmin,$oid,$l_oid\n" if $tss; ## all TSS has same oid now !???? -- odd bug $l_oid == $oid if ( $oid eq $l_oid ) { # same object - cat attributes into one set push( @{$fob->{loc}}, $loc) unless(grep /$loc/,@{$fob->{loc}}); #warn ">tss2S: new $arm,$fmin,$oid,$l_oid\n" if $tss; foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=(); } else { ## new feature object here .. if ($arm ne $l_arm) { $self->putFeats($outh,\@fobs,\%oidobs,'final'); undef @fobs; @fobs=(); undef %oidobs; %oidobs=(); undef %gffForwards; %gffForwards=(); $max_max=0; $min_max= 0; $outh= $self->openCloseOutput($outh, $arm, 'open'); } my $flushok= ($fmin >= $max_max && $fmin > $min_max && scalar(@fobs)>5); if ($flushok) { if ($self->hasObForwards(\@fobs, \%oidobs)) { $flushok = 0; $min_max= $fmin + 2000; ##smaller step so we dont miss chance to flush } warn "hasObForwards no=$flushok at $fmin $type:$name $oid\n" if ($DEBUG>1); } if ($flushok) { ##warn "flushobs at $fmin $type:$name $oid\n" if $DEBUG; my ($nstart, $nleft, $nobs)=(0,0,0); if ($DEBUG>1) { $nobs= scalar(@fobs); } $self->putFeats( $outh, \@fobs, \%oidobs, ''); undef @fobs; @fobs=(); $min_max= $fmin + MIN_FORWARD_RANGE; #?? will this help join parts ## %oidobs will grow big; ## can we clear out other obs yet: %oidobs=(); %gffForwards=(); if no forwards ? if ($DEBUG>1) { while( each %oidobs ){ $nstart++; }} my $clearflag= 'writefff'; my $nclear= 0; $nclear= $self->clearFinishedObs( $clearflag, \%oidobs, $fmin - MAX_FORWARD_RANGE); if ($DEBUG>1) { while( each %oidobs ){ $nleft++; } print STDERR " printed n=$nobs; oidobs: pre-clear=$nstart, cleared=$nclear, left=$nleft\n"; print STDERR " fmin=$fmin, fmax=$fmax, l_fmin=$l_fmin, min_max=$min_max, max_max=$max_max\n"; } } my $newob= {}; push(@fobs,$newob); $fob= $newob; foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=(); #?? dont add here if it is simple feature; wait till know if it is parent or kid? # this is bad for 'gene' NOT? simple feat unless( $simplefeat{$type} ) { $oidobs{$oid}->{fob}= $newob; } # my @fclone_fields = qw(chr type fulltype name id oid fmin fmax offloc attr writefff writegff); $fob->{chr} = $arm; $fob->{type}= $type; $fob->{fulltype}= $fulltype; # colon-delimited complex type 'match:program:source' $fob->{name}= $name; $fob->{id} = $id; $fob->{oid} = $oid; $fob->{fmin}= $fmin; $fob->{fmax}= $fmax; $fob->{loc} = []; $fob->{attr}= []; ##warn ">tss2x: new $arm,$fmin,$oid\n" if $tss; push( @{$fob->{loc}}, $loc); ##moved below## foreach my $at (@addattr) { push( @{$fob->{attr}}, $at); } } ## make oid crossref here so outputters know feature relations ## change this (see above $samoid read loop) ## FIXME 05: this sub should be run only after forward parent_oid is found; ## or change input to sort given model gene > mRNA > CDS (ignoring seq start) foreach my $at (@addattr) { my $paroid=''; if ($at =~ /parent_oid\t(.+)/) { $paroid=$1; } push( @{$fob->{attr}}, $at) ; # unless( grep {$at eq $_} @{$fob->{attr}}); #? do we have any dupls? ## REMEMBER SOME (exons) HAVE MULTIPLE parent_oid attributes if ($paroid && !$simplefeat{$type}) { $self->newParentOid($fob, 'parent_oid', $paroid, \%oidobs); } } # $self->newParentKidLink($fob, \%oidobs); # uses @{$fob->{attr}} parent_oid ## MOVED parent_oid attrib TO putFeats: $self->update1ParentKidLinks($fob, \%oidobs); ## forward ref checkpoint .. maybe skip more than segmentfeats here ? what is big? if ($fmax > $max_max && !$segmentfeats{$fob->{type}}) { $max_max= $fmax; my $supermax= $min_max - MIN_FORWARD_RANGE + MAX_FORWARD_RANGE; $max_max= $supermax if ($max_max > $supermax); # is it < or > ? was > (set to SMALLER) } ## only need save these: ($l_arm,$l_oid,$l_fmin,$l_fmax,$l_type)= ($arm,$oid,$fmin,$fmax,$type); } $self->putFeats($outh,\@fobs,\%oidobs, 'final'); @fobs=(); %oidobs=(); $outh= $self->openCloseOutput($outh,'','close'); print STDERR "\nprocessChadoTable ndone = $ndone\n" if $DEBUG; return $ndone; } ## jan06: makeFlatFeats -> makeFlatFeatsNew ## change to config->{feat_model}->{$type}: @parts, $parent, $typelabel, $types #s subclass this needs work sub makeFlatFeatsNew { my $self= shift; my ($fobs,$oidobs)= @_; my @cobs=(); # these compound features get added to output foreach my $fob (@$fobs) { my $oid= $fob->{oid}; my ($iskid,$ispar)= (0,0); my $oidob= $oidobs->{$oid}; my $ftype= $fob->{type}; #my $fulltype= $fob->{fulltype}; my $id= $fob->{id}; my $issimple= $simplefeat{$ftype}; my $feat_model= $self->config->{'feat_model'}->{$ftype}; ## get issimple from feat_model my $GMM=0; # ($DEBUG && $id =~ /CG17245|CG32013|CG2125|CG3973/) ? 1 : 0; # feb05 bug test, mRNA misses last 2 exons if (!$issimple && $oidob) { $iskid= (defined $oidob->{parent} && @{$oidob->{parent}} > 0); $ispar= (defined $oidob->{child} && @{$oidob->{child}} > 0); if ($iskid) { # check we have backref to parend obj ?? my $ok= 0; foreach my $poid (@{$oidob->{parent}}) { if ($oidobs->{$poid}) { $ok=1; last; } } $iskid= $ok; } } warn ">gmm1 $ftype $id ispar=$ispar iskid=$iskid\n" if $GMM; ## handle feat_model changes to $fob; not just submodels: typelabel, attr if($feat_model) { my $typelabel= $feat_model->{typelabel}; $fob->{fulltype}= $fob->{type}= $typelabel if($typelabel); #?? need fulltype #0805: add sub_model->attr functions if(ref $feat_model->{attr}) { my $subattr= $feat_model->{attr}; my @subattr = (ref( $subattr) =~ /ARRAY/) ? @$subattr : ($subattr); foreach my $sattr (@subattr) { my $akey = $sattr->{id} or next; my $aval = $sattr->{content} ||" "; $aval= $ftype if($aval eq "type"); push( @{$fob->{attr}}, "$akey\t$aval"); } } } my $keepfeat= ($ispar || $self->keepfeat_fff($ftype)); if ($keepfeat) { if(!$ispar) { $issimple=1; } elsif($feat_model && defined($feat_model->{simple})) { $issimple= $feat_model->{simple}; } elsif($ftype eq 'gene' && !$self->config->{gene_is_complex}) { $issimple=1; } #NEED THIS# $issimple = 1 if ($ftype =~ m/^gene$/); #?? otherwise misc. gene parts GMM get flagged as written #BUT for complex flybase data; not for sgdlite w/o mrna features if ($issimple) { push(@cobs, $fob); } # simple feature else { # has kids, make compound feature >> (m,t,s)RNA here my $kidobs= $oidob->{child}; my $cob= $self->makeCompound( $fob, $kidobs, $ftype); push(@cobs, $cob); # $self->listkids($cob,$kidobs) if($DEBUG && $ftype =~ m/^(gene|mRNA)$/); ## was loosing kids to bad $oidobs } warn ">gmm2 add $ftype $id \n" if $GMM; } ## %GModelParents = ( mRNA => 1, otherRnas ?? => ); ## $CDS_spanType = 'CDS' ; # change to 'protein' or other ... ## $CDS_exonType = 'CDS_exon' ; # change to 'CDS' ## But for fff, need to rename $CDS_spanType 'protein' to 'CDS' for output fff type ## ?? this is only for 3-level models (gene/mRNA/protein) where ## submodel parts are contained in mainmodel kid list (protein-CDS in mRNA) if ($ispar && $feat_model && $feat_model->{submodels}) { my $parob= $fob; my $submodels = $feat_model->{submodels}; my @submodels = (ref $submodels) ? @$submodels : split(/[,\s]+/,$submodels); foreach my $subtype (@submodels) { my $sub_model= $self->config->{'feat_model'}->{$subtype}; # make sure exists ? my $makepartsfrom = $sub_model->{makepartsfrom} || 'exon'; my $hasspan = (defined $sub_model->{hasspan}) ? $sub_model->{hasspan} : ($subtype eq $CDS_spanType); # old version my $subtypelist= $sub_model->{types} | ""; # fixme types= list .. my $typelabel= $sub_model->{typelabel} || $subtype; # my $parent= $sub_model->{parent}; my $kidparts = $sub_model->{parts} || 'exon'; #? no default my @kidparts = (ref $kidparts) ? @$kidparts : split(/[,\s]+/,$kidparts); my %kidparts = map { $_,1; } @kidparts; my $makemethod = $sub_model->{makemethod}; my $subob= undef; my $spanob= undef; my $mrnaexons=[]; my $kidobs=[]; foreach my $kidob (@{$oidob->{child}}) { my $ktype= $kidob->{type}; if ($ktype =~ /^$makepartsfrom$/) { push(@$mrnaexons, $kidob); # save in case missing CDS_exon } if ( $ktype eq $CDS_spanType ) { $spanob= $kidob; } # only for utr patch ! if ( $ktype eq $subtype ) { $subob= $kidob unless($subob); } elsif ( $subtypelist =~ m/$ktype/ ) { $subtype= $ktype; #?? $subob= $kidob unless($subob); } elsif ($kidparts{$ktype}) { push(@$kidobs, $kidob); } } ## CDS/protein w/o CDS_exon parts ... recreate from cds start/stop + mrna location if ($subob && !@$kidobs && $hasspan && @$mrnaexons) { warn ">gmmC getCDSexons $sub_model $kidparts $subob, ne=",scalar(@$mrnaexons),"\n" if $GMM; # this doesnt adjust exons for CDS span: see getLocation; reuse here $kidobs= $self->getCDSexons($subob, $mrnaexons); } ## for making UTRs, introns: mar06 # makemethod == makeUtr5,makeIntrons,... elsif( !@$kidobs && @$mrnaexons && $makemethod) { $subob= $parob unless($subob); #?? ($subob,$kidobs)= eval "\$self->$makemethod(\$subob, \$mrnaexons);"; if($@ && $DEBUG){ warn "$makemethod err: $@"; } #? die if ($self->{failonerror}) ? warn ">gmmU $makemethod $sub_model np=",scalar(@$kidobs),"\n" if $GMM; } if ($subob) { ## copy gene model dbxref id into these features, as per above my $idpattern= $self->config->{idpattern}; foreach my $pidattr (@{$fob->{attr}}) { next if ($pidattr =~ m/2nd/); #dbxref_2nd: if (!$idpattern || $pidattr =~ m/$idpattern/) { push( @{$subob->{attr}}, $pidattr) unless( grep {$pidattr eq $_} @{$subob->{attr}}); last; # add only 1st/primary } } #0805: add sub_model->attr functions if(ref $sub_model->{attr}) { my $subattr= $sub_model->{attr}; my @subattr = (ref( $subattr) =~ /ARRAY/) ? @$subattr : ($subattr); foreach my $sattr (@subattr) { my $akey = $sattr->{id} or next; my $aval = $sattr->{content} || " "; $aval= $subtype if($aval eq "type"); push( @{$subob->{attr}}, "$akey\t$aval"); } } if ($subtype =~ /UTR/ && $self->config->{utrpatch}) { $self->patchUTRs( $subob, $spanob, $mrnaexons, $kidobs); } ## jan06: problem here w/ change to protein/cds: all GModelParts end up fff feature ## CDS_exon, exon end up as compound types same as mRNA, CDS/protein my $cob= $self->makeCompound( $subob, $kidobs, $subtype); $cob->{fulltype}= $cob->{type}= $typelabel; warn ">gmmCOB $typelabel $cob np=",scalar(@$kidobs),"\n" if $GMM; push(@cobs, $cob); } } } ## else { } # $iskid only - dont save } return \@cobs; } =item getCDSexons($cdsob,$exonobs,$ftype) create compound feature from parent, kids (e.g., mRNA + exons) =cut # sub getCDSexons # { # my $self= shift; # my ($cdsob,$exonobs,$ftype)= @_; # # my $offsetloc = $cdsob->{loc}->[0]; # only 1 we hope # my ($offstart,$offstop,$offstrand) = split("\t",$offsetloc); # if ($offstart > $offstop) { ($offstart,$offstop)= ($offstop,$offstart); } #? need # $cdsob->{offloc}= $offsetloc; # # my @cdsobs=(); # foreach my $kid (@$exonobs) { # my ($start,$stop,$st) = split("\t", $kid->{loc}->[0]); # if ($stop >= $offstart && $start <= $offstop) { # push(@cdsobs, $kid); # } # } # # return \@cdsobs; # } =item makeCompound($fob,$kidobs,$ftype) create compound feature from parent, kids (e.g., mRNA + exons) =cut sub makeCompound { my $self= shift; my ($fob,$kidobs,$ftype)= @_; my $cob= $self->cloneBase($fob); $fob->{'writefff'}=1; # need here also !? this is messy... ## FIXME - for dang transspliced mod(mdg4) - if strands in locs differ -> getLocation my @locs= (); my $hasspan= ($self->config->{'feat_model'}->{$ftype}->{hasspan}) or ($ftype eq $CDS_spanType); ## need to skip kids for 'gene', others ? foreach my $kid (@$kidobs) { next if ($fob->{type} =~ m/^(mRNA|gene)$/ && $kid->{type} ne 'exon'); if ($hasspan && $kid->{type} eq 'mature_peptide') { $ftype= $cob->{type}= 'mature_peptide'; } $kid->{'writefff'}=1; # need here also !? foreach my $loc (@{$kid->{loc}}) { push( @locs, $loc); } } unless(@locs) { foreach my $loc (@{$fob->{loc}}) { push( @locs, $loc); } } if ($hasspan) { # && !defined $cob->{offloc} my $offsetloc = $fob->{loc}->[0]; # only 1 we hope $cob->{offloc}= $offsetloc; } # FIXME: do getLocation adjustment for CDS_span > CDS_exons here? if (defined $cob->{offloc}) { @locs= $self->offsetLocation($cob, @locs); } $cob->{loc}= \@locs; return $cob; } =item offsetLocation($fob,@loc) derived from getLocation get feature genbank/embl/ddbj location string (FTstring) including transplice complexity return ($location, $start, $strand); feb05: need to preserve strand==0/undefined for some features which have mixture fixed - for dang transspliced mod(mdg4) - if strands in locs differ looks like chado pg reporting instance with CDS_exons is bad for transspliced mod(mdg4) 08may: change behavior for GenbankSubmit to offsetLocation: dont return Genbank style string location, but adjust @loc to CDS_exons by CDS span offset; See also getCDSexons and makeCompound =cut sub offsetLocation # was getLocation { my $self= shift; my($fob,@loc)= @_; my $srange=''; my $bstart= -999; my($l_strand,$istrans)=(0,0); my @newloc=(); my ($offstart,$offstop,$offstrand)= (0,0,0); if (defined $fob->{offloc}) { ($offstart,$offstop,$offstrand) = split("\t",$fob->{offloc}); } ## assume not istrans - only 1 in 15,000 - redo if istrans foreach my $loc (@loc) { my ($start,$stop,$strand)= split("\t",$loc); if ($offstop != 0) { next if ($stop < $offstart || $start > $offstop); $start= $offstart if ($start<$offstart); $stop = $offstop if ($stop>$offstop); } if ($bstart == -999 || $start<$bstart) { $bstart= $start; } # $srange .= "$start..$stop,"; push( @newloc, "$start\t$stop\t$strand"); if ($l_strand ne 0 && $strand ne $l_strand) { $istrans= 1; last; } $l_strand= $strand; } if ($istrans) { @newloc=(); $srange=''; $l_strand= 0; $l_strand= $offstrand if ($offstrand < 0); ## hack patch for bad cds exons for transpliced mdg4 if (defined $fob->{exons}) { my $exonlocs= $fob->{exons}; @loc= @$exonlocs if (@$exonlocs); print STDERR "transplice ",$fob->{name}," replaced cds_exons with mrna exons\n" if $DEBUG; } foreach my $loc (@loc) { my ($start,$stop,$strand)= split("\t",$loc); if ($offstop != 0) { next if ($stop < $offstart || $start > $offstop); ## revcomp tricks here if ( $l_strand < 0 && $strand >= 0 ) { print STDERR "transplice ",$fob->{name}," rev ex=$start,$stop,$strand ; off=$offstart,$offstop\n" if $DEBUG; $stop = $offstart if ($start < $offstart); } else { $start= $offstart if ($start<$offstart); $stop = $offstop if ($stop>$offstop); } } $strand= -$strand if ($l_strand < 0); # if ($strand < 0) { $srange .= "complement($start..$stop),"; } # else { $srange .= "$start..$stop,"; } push( @newloc, "$start\t$stop\t$strand"); } } return @newloc; # $srange =~ s/,$//; # if ($l_strand < 0) { $srange= "complement($srange)"; } # elsif($srange =~ m/,/) { $srange= "join($srange)"; } # return ($srange, $bstart, $l_strand); } =item putFeats($outh,$fobs,$oidobs,$flag) output feature object (fobs) in selected formats (fff,gff,fasta) =cut #s subclass this needs work sub putFeats { my $self= shift; my ($outh,$fobs,$oidobs,$flag)= @_; return unless($fobs && @$fobs > 0); my($hasforward,$l_hasforward)=(0,0); my $n= scalar(@$fobs); if ($DEBUG && $flag =~ /final/) { # $DEBUG>1 || print STDERR "putFeats n=$n, total=".($n+$ntotalout) .", oid1=".(($n>0)?$fobs->[0]->{oid}:0)."\n"; } elsif ($DEBUG) { print STDERR "."; } $self->updateParentKidLinks($fobs, $oidobs); #05feb: logic change ; was in processChadoTable #s subclass convert here for genbanktab output if ($outh->{genbanktbl}) { my $ffh= $outh->{genbanktbl}; $self->{curformat}= $self->{bulktype}; # 'genbanktbl'; #? need this for genbank ? probably yes, otherwise get exons as features my $cobs= $self->makeFlatFeatsNew($fobs,$oidobs); my $nout= 0; foreach my $fob (@$cobs) { # ?? $fobs or $cobs $self->writeGenbankTbl( $ffh,$fob,$oidobs) ; $nout++; undef $fob; } undef $cobs; $ffh->flush(); $ntotalout += $nout; } $self->{curformat}= ''; } #s subclass this needs work sub writeHeader { my $self= shift; my($outh,$fmt,$chr,$appending)= @_; my $chrlen= defined $chromosome->{$chr} && $chromosome->{$chr}->{length} || 0; ## foreach $fmt (@formats) { $self->{$fmt}->writeheader($outh->{$fmt},$chr,$chrlen); } # $self->writeFFF1header($outh->{$fmt},$chr,$chrlen) if ($fmt eq 'fff' && !$appending); # $self->writeGFF3header($outh->{$fmt},$chr,$chrlen) if ($fmt eq 'gff' && !$appending); $self->writeGenbankHeader($outh->{$fmt},$chr,$chrlen); # if ($fmt eq 'genbanktab'); ## add fasta output - no header ? } #s subclass this needs work sub setDefaultValues { my($self)= @_; $self->SUPER::setDefaultValues(); } #---- GenbankTbl output -- separate package ? sub writeGenbankHeader { my $self= shift; my($fh,$seqid,$start,$stop)= @_; my $tblname=""; my $date = $self->{date}; my $sourcetitle = $self->{sourcetitle}; my $org= $self->{species} || $self->{org}; $tblname= $sourcetitle." ".$date; $tblname =~ s/\s+/_/g; print $fh ">Features\t$seqid\t$tblname\n"; # gbtbl: first line is >Features SeqID table_name == chromosome SeqID, same as fasta } ## see also SUPER::remapType ; handleAttrib ***; remapId ; remapName ; use constant ATTR_LISTCHAR => "\t"; sub handleAttribOut { my $self= shift; my($attr_array, $attr_key, $attribute, $feattype)= @_; my $savekey= $attr_key; # special handling? # for types gene, mRNA, CDS: Name => Gene; (gene)ID => locus_tag # mRNA ID => transcript_id ; protein ID => protein_id # Map all ID tags depending on feature type # gene Name,ID => /gene= and /locus_tag= # mRNA Name,ID => /product= and /transcript_id= (but keep Parent /gene= and /locus_tag= # CDS Name,ID => /product= and /protein_id= (but keep (Grand)Parent /gene= and /locus_tag= # ncRNA ID,Name like mRNA ? # transposon ID => /transposon= # other # Note => note # type polypeptide/protein => CDS type # FIXME here: also have fromGenbank attributes of these same tr/pr_id # keep both? rename other to old_ ? ID here is chado uniquename, should be valid # Also, GBSubmit wants original tr/pr_id for updates, in their special format (see docs) my $ftkey= "mapattr_key_".$feattype; my $fthash= $self->config->{$ftkey}; my $newkey; if(ref $fthash) { # FIXME allow [mrt*]RNA match ##warn "$ftkey keys=",keys(%$fthash),"\n"; # content,id,key $newkey= $fthash->{$attr_key}; } if(!$newkey && exists $self->config->{mapattr_key}->{$attr_key}) { $newkey = $self->config->{mapattr_key}->{$attr_key}->{content}; } $attr_key= $newkey if($newkey); return if ($newkey eq "skip"); $attribute =~ s/_/ /g if($attr_key eq "organism"); # was species ## see also above handleAttrib # some/all value lists should be split to separate lines; # but some notes have ',': see below change to '\t' ? my @avals= split( ATTR_LISTCHAR, $attribute); foreach my $aval (@avals) { push( @$attr_array, "$attr_key\t$aval"); } } sub splitGbType { my $self= shift; my($gffsource,$type,$fulltype)= @_; my($newgffs)=(''); # FIXME: ${golden_path} becomes 'source' type. in code or in config? my $golden_path= $self->config->{golden_path} || $ENV{'golden_path'}; if($golden_path =~ m/$type/) { $type= "source"; } #? use fulltype instead of type? as 'match:sim4:na_EST_complete_dros' # convert mRNA_genscan,mRNA_piecegenie to gffsource,mRNA ? elsif ($maptype_gb{$type}) { ($type,$newgffs)= split(/[\.:]/,$maptype_gb{$type},2); } elsif ($fulltype =~ m/^([\w\_]+)[\.:]([\w\_\.:]+)$/) { ($type,$newgffs)=($1,$2); } elsif ($type =~ m/^([\w\_]+)[\.:]([\w\_\.:]+)$/) { ($type,$newgffs)=($1,$2); } else { $type= $fulltype if($fulltype); } #?? feb05; want snRNA not mRNA .. leave in fulltype ? $gffsource= $newgffs if($newgffs && $newgffs ne '.'); return($gffsource,$type); } sub _gffEscape { my $v= shift; ### not for genbank # $v =~ tr/ /+/; # $v =~ s/([\t\n\=&;,])/sprintf("%%%X",ord($1))/ge; # Bio::Tools::GFF _gff3_string escaper return $v; } =item writeGenbankTbl write one feature in Genbank submit table format feature may have sub location parts (multi line) =cut sub writeGenbankTbl # from writeGFF { my $self= shift; my($fh,$fob,$oidobs)= @_; my $type= $fob->{type}; my $fulltype= $fob->{fulltype}; return if ($fob->{'writefff'}); $fob->{'writefff'}=1; if ($dropfeat_gff{$type}) { return; } #?? my $ignore_missingparent= $self->config->{maptype_ignore_missingparent} || '^xxxx'; my $gffsource= $fob->{gffsource} || $self->{gff_config}->{GFF_source} || "."; my $oid= $fob->{oid}; my $id = $fob->{id}; my $chr= $fob->{chr}; my @loc= @{$fob->{loc}}; my @attr= @{$fob->{attr}}; my $at=""; my @at= (); my %at= (); my $v; $at{"ID"}= _gffEscape($id) if ($id); $at{"Name"}= _gffEscape($v) if (($v= $fob->{name})); # keep dupl for GBsub ! && $v ne $id foreach (@attr) { my ($k,$v)= split "\t"; ## NO; keep empty vals# if (!$v) { next; } if ($k eq "object_oid") { next; } elsif ($k eq "parent_oid") { ## for each gene model part; should add locus_tag == gene ID # if ($gff_keepoids) { $at{$k} .= ATTR_LISTCHAR if $at{$k}; $at{$k} .= $v; } next if $segmentfeats{$type}; # dont do parent for these ... ? $v =~ s/:.*$//; $k= 'Parent'; my $parob= $oidobs->{$v}->{fob}; if ($parob && $parob->{id}) { $v= $parob->{id}; if ($oidisid_gff{$type}) { $v= $parob->{oid}; } # FIXME: GBsub wants gene name,id in CDS; not mRNA parent my $vname= $parob->{name}; # special case $at{'ParentName'} = _gffEscape($vname) if($vname); if($type =~ /protein|CDS/) { # FIXME my $paroid= $parob->{oid}; my($gparoid)= @{ $oidobs->{$paroid}->{parent} }; my $gparob= $oidobs->{ $gparoid }->{fob}; my $gparid= $gparob->{id}; $at{'GrandParent'} = _gffEscape($gparid); my $vname= $gparob->{name}; # special case $at{'GrandParentName'} = _gffEscape($vname) if($vname); } if ($v eq $id) { my $i= 1; my $paroid= $parob->{oid}; my $kids = $oidobs->{$paroid}->{child}; if ($kids) { foreach my $kidob (@{$kids}) { last if ($kidob->{oid} eq $oid); $i++; } } $id= "$id.$i"; $at{"ID"} = _gffEscape($id); } } else { unless($fulltype =~ /$ignore_missingparent/) { print STDERR "GB: MISSING parent ob for i/o/t:",$id,"/",$oid,"/",$fulltype, " parob=",$parob," k/v=",$k,"/",$v, " \n" if $DEBUG; } next; # always skip writing bogus Parent= to gff } } elsif ($k =~ /^dbxref|db_xref/i ) { $k= 'db_xref'; next if ($v =~ /^GI:/); # drop NCBI GI: from submit db_xref } elsif ($k eq "synonym") { # check dupl ID next if ($v eq $id || $v eq $fob->{name}); } if ($k) { $at{$k} .= ATTR_LISTCHAR if $at{$k}; # got duplicate Parent=aaa,aaa in dpse data; why? $at{$k} .= _gffEscape($v); # should be urlencode($v) - at least any [=,;\s] } } ## drop ID if Parent ; sometimes ? # unless(0) { # my $parent= delete $at{'Parent'}; # if( $parent && $dropid{$type} ) { $at[0]= "Parent\t$parent"; } # elsif ($parent){ push(@at, "Parent\t$parent"); } # } ## this should set attrib 'ncRNA_class snoRNA' for (snoRNA, scRNA, snRNA, miRNA, ncRNA, rRNA) > ncRNA ($gffsource,$type)= $self->splitGbType($gffsource,$type,$fulltype); foreach my $k (sort keys %at) { $self->handleAttribOut(\@at, $k, $at{$k}, $type); # push(@at, "$k\t$at{$k}"); } # Genbank Tbl format here: loc \t loc \t FT-type \n \t ftfield \t ftval ... # FIXME: revcomp needs $#loc .. 0 my(undef,undef,$gstrand)= split("\t",$loc[0]); my @iter= ( 0 .. $#loc ); @iter= reverse @iter if ($gstrand < 0); my $first=1; foreach my $i ( @iter ) { my($start,$stop,$strand)= split("\t",$loc[$i]); ($start,$stop) = ($stop,$start) if ($strand < 0); my @v= ($first) ? ($start,$stop,$type) : ($start,$stop); print $fh join("\t",@v),"\n"; $first=0; } foreach my $at (@at) { my ($k,$v)= split "\t",$at,2; print $fh join("\t","",$k,$v),"\n"; } print $fh "\n"; } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm000644 000765 000024 00000075746 11256707527 021532 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::GnomapWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::GnomapWriter =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $sequtil= Bio::GMOD::Bulkfiles->new( configfile => 'seqdump-r4', ); my $fwriter= $sequtil->getGnomapWriter(); my $result = $fwriter->makeFiles( ); =head1 NOTES This is FlyBase-specific for now ; handles fly cytology map features and gnomap feature indexing genomic sequence file utilities, part3; parts from flybase/work.local/chado_r3_2_26/soft/mergeflyfeats4.pl =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =head1 METHODS =cut #----------------- # debug # use lib("/bio/biodb/common/perl/lib", "/bio/biodb/common/system-local/perl/lib"); use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::BulkWriter); use constant RECSIZE => length(pack("NN", 1, 50000)); our $DEBUG = 0; my $VERSION = "1.1"; #my $configfile= "tognomap"; #? BulkFiles/GnomapWriter.xml use constant BULK_TYPE => 'gnomap'; use constant CONFIG_FILE => 'tognomap'; my $kMissingValue= -99999999; my $kMaxValue= 999999999; my $kMinValue= $kMissingValue+1; use vars qw/ %flycsomebands $noIDmap $nameIsId $nameIsSpeciesId $cutdbpattern $indexidtype $indexidpattern /; sub init { my $self= shift; $self->SUPER::init(); ## superclass does these?? $DEBUG= $self->{debug} if defined $self->{debug}; # $self->{bulktype} = $self->BULK_TYPE; # dont need hash val? # $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); my $config = $self->{config}; my $sconfig= $self->handler()->{config}; # my $org= $self->{org} || $self->handler()->{config}->{org}; ## gnomapfiles my $finfo= $self->{fileinfo} || $self->handler()->getFilesetInfo($self->BULK_TYPE); my $dnainfo= $self->handler()->getFilesetInfo('dna'); # $self->{indexonly} = $finfo->{indexonly}; # $self->{skipdata} = $finfo->{skipdata}; # $noIDmap = $finfo->{noIDmap} # || $config->{noIDmap} # || 'cytowalk|protein|mRNA|CDS|EST|cDNA|oligo|processed|repeat|sim4'; $noIDmap = $self->getconfig('noIDmap'); unless($noIDmap) { $noIDmap= join '|', qw(cytowalk _fragment _junction _mutation _UTR _variant misc chromosome enhancer EST cDNA intron match motif sim4 mRNA CDS oligo processed protein _peptide repeat regulatory_region repeat_region transposable_element_pred ); } $noIDmap =~ s/\s+/|/g; $noIDmap .= '|\bregion'; $noIDmap =~ s/\|\|/|/g; $nameIsId= $self->getconfig('nameisid') || '^(BAC)'; $nameIsSpeciesId= $self->getconfig('nameisorgid') || '^(gene)$'; # others? rnas? $cutdbpattern= $self->getconfig('idcutdb') || '^(FlyBase|GadFly|GB_protein|GO):'; $indexidtype= $self->getconfig('indexidtype') || '^(gene|pseudogene|\w+RNA)'; $indexidpattern= $self->getconfig('indexidpattern') || '[A-Z]{2}gn\d+'; %flycsomebands = ( 'X' => [ '1A1','20F4'], '2L' => ['21A1','40F7'], '2R' => ['41A1','60F5'], '3L' => ['61A1','80F9'], '3R' => ['81F1','100F5'], '4' => ['101A1','102F8'], ); # my $gnomapdir= $self->handler()->getReleaseSubdir( $finfo->{path} || $self->BULK_TYPE); # $self->{gnomapdir} = $config->{gnomapdir}= $gnomapdir; my $reldir= $self->handler()->getReleaseDir(); my $dnareldir= $self->handler()->getReleaseSubdir( $dnainfo->{path} || 'dna/'); $dnareldir =~ s,^$reldir,,; $dnareldir = "../$dnareldir"; $self->{dnareldir}= $dnareldir; my $tfset = $self->handler()->getFilesetInfo('tables'); my $tabdir = $self->handler()->getReleaseSubdir( $tfset->{path} || 'tables/'); $self->{summaryfile}= catfile( $tabdir, "feature_map-summary.txt"); ## 05dec # my $gbset = $self->handler()->getFilesetInfo('gbrowse_fb'); # $self->{gbset}= $gbset; my @copytypes=(); foreach my $type ( keys %{$config->{fileset}} ) { my $fs= $config->{fileset}->{$type}; push(@copytypes, $type) if ($fs->{copy}); } $self->{copytypes}= \@copytypes; ## dont create subdir - use only if exists .. ## change to $config->{fileset}->{cytofeat} // handler()->getReleaseSubdir( # $config->{cytofeat}->{path} || 'cytomap/', 'nocreate'); # $self->{cytomapdir} = $cytomapdir; ## this is replaced by fileset.cytomap split by chr ## need sep. package for flybase cytology map methods (various users) my $sorsa= $config->{sorsa}->{path}; if ($sorsa) { $sorsa= catfile( $self->handler()->getReleaseDir(), $sorsa); $self->{sorsatable} = $sorsa; } } #-------------- subs ------------- =item notes for simple, non-dmel-flybase case of no cytofeats to add, need only here create gnomap/ folder files w/ indexed fff (stripped of leading chr, bstart columns flybase cytofeatures look like (fff format) 2L 1 cytogene anon-21Aa 21A -30856..353 FBgn0015861 2L 1 cytogene l(2)21Bb 21A1-21B4 -30856..213625 FBgn0001885 X 22039275 cytoduplicated_segment Ts(1Lt;YSt)E15+Ts(YLt;3Lt)W27 20F-h29;91A-100F5 22039275..22098704 FBab0025172 X 5216754 cytoduplicated_segment Dp(1;2;1)AT 5A-7A;36D1-37D2 5216754..6912751 FBab0003372 =cut =item makeFiles( %args ) primary method makes blast indices. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required =cut sub makeFiles { my $self= shift; my %args= @_; print STDERR "makeFiles\n" if $DEBUG; # debug my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; unless(@$fileset) { my $intype= $self->config->{informat} || ['fff','dna']; #? maybe array $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "GnomapWriter: no input '$intype' files found\n"; return $self->status(-1); } } ## infiles => [ @$featfiles, @$dnafiles ] ## $self->readflysorsa(); #? here or wait if ($self->config->{indexonly}) { warn "Indexing only features in ",$self->outputpath(),"\n" if $DEBUG; $self->indexfeatdir($self->outputpath()); return $self->status(1); } ## ---------- get cytology set ---------- # == cytomap/ folder # need to get seq id list and purge cytogene/.. w/ same id ## my ($nr, $nk)= cytosort( $fset_h, $dir.$hf, $csome, *FO); my $addcyto= 0; ##if (-d $self->{cytomapdir}) { # $config->{cytofeat}->{path} OR fileset->cytofeat/cytomap my $cytoset= $self->handler->getFiles('cytofeat', $chromosomes); if ($cytoset) { $fileset= [ @$fileset, @$cytoset ]; $addcyto=1; } #? add to $fileset # require cytomapdir to have tables in fffformat==2, split by chr # then merge steps are # 1. readids (seqset) (see fastawriter) # 2. filter cytomap fff by seq ids # 3. cat seq,cyto fff | sort | write to gnomapdir # $addcyto= 1; ##} ## ---------- get sequence set ---------- # == fff/ folder # 1. symlink dnafiles to gnomap/dna-$chr.raw # 2. copy fff/release-$chr.fff to gnomap/features-$chr.tsv , stripping lead 2 cols # $self->addDnaSymlinks($fileset); $self->makeSymlinks( $fileset, 'dna/raw', "dna-\$chr.raw", $self->{dnareldir}, $self->outputpath()); if (@{$self->{copytypes}}) { my $fset= $self->handler->getFiles( $self->{copytypes}, $chromosomes); $self->copyFiles( $fset, '', '', $self->outputpath()); } #? option to skip gnomap data; semi-obsolete; want summary table, maybe gbrowse.conf if($addcyto) { $self->mergeFeats($fileset); } else { $self->copyFFF2Gnomap($fileset); } $self->printSummary( $self->{summaryfile}, $self->{featnames}); $self->indexfeatdir($self->outputpath()) ; #if ($doindex); my @featnames= (); if ($self->{featnames}->{all}) { @featnames= sort keys %{$self->{featnames}->{all}}; } $self->makeGbrowseConf(\@featnames); # should pass array of feature names ! print STDERR "GnomapWriter::makeFiles: done\n" if $DEBUG; return $self->status(1); } sub mergeFeats { my $self= shift; my( $fileset )= @_; # do per-csome/name my $ok= 1; my $filterids= 1; #?? config my $gnomapdir= $self->outputpath(); my $sorter=`which sort`; chomp($sorter); ## '/bin/sort'; '/usr/bin/sort'; print STDERR "mergeFeats\n" if $DEBUG; for (my $ipart= 0; $ok; $ipart++) { $ok= 0; my $infile= $self->openInput( $fileset, $ipart, 'fff'); if ($infile && $infile->{inh}) { my $chr= $infile->{chr}; if ($filterids) { my $inh= $infile->{inh}; my $idlist= $self->readIdsFromFFF( $inh, $chr, $self->handler()->{config}); # for featmap ? $self->{idlist}= $idlist; ##$inh= $self->resetInput($infile); } # require cytomapdir to have tables in fffformat==2, split by chr # then merge steps are # 1. readids (seqset) (see fastawriter) # 2. filter cytomap fff by seq ids # 3. cat seq,cyto fff | sort | write to gnomapdir ## this not good - need to make sure same $chr as $infile my $inmerge; my $mergepipe; foreach my $fs (@$fileset) { my $fp = $fs->{path}; next unless($fs->{type} =~ /cytofeat/); ## cytomap > type => "$featn/$type", next unless($fs->{chr} eq $chr); $inmerge = $fs; last; } if ($inmerge) { close($infile->{inh}) if ($infile->{inh}); # if .gz ?? my $catset= $infile->{path} ." ".$inmerge->{path}; if ($catset =~ /\.gz/) { $catset= "gunzip -c ".$catset; } else { $catset= "cat ".$catset; } $catset .= " | $sorter -t' ' -k 1,1 -k 2,2n |"; #NOTE TAB in ' ' open(MERGE,$catset); $mergepipe= *MERGE; } else { # just cat infile $mergepipe= $self->resetInput($infile); } my $outname= catfile($gnomapdir,"features-$chr.tsv"); my $outh= new FileHandle(">$outname"); print STDERR "merge $outname from $infile->{path}, $inmerge->{path}\n" if $DEBUG; my $res= $self->merge2gnomap( $mergepipe, $outh, $chr); close($outh); close($mergepipe); $ok= 1; } } ## $self->printSummary( $self->{summaryfile}, $self->{featnames}); } sub merge2gnomap { my $self= shift; my( $inh, $outh, $chr )= @_; # do per-csome/name # my $csomefeats= $self->{featnames}; my $ffformat = 0; #? test always; probably is 2 while(<$inh>){ if (/^\w/ && /\t/) { my @v= split(/\t/); #split "\t", $_; if ( $ffformat == 2 || @v > 7 || ($v[0] =~ /^\w/ && $v[1] =~ /^[\d-]+$/)) { $ffformat= 2; splice(@v,0,2); } print $outh join("\t",@v); my $fname= $v[0]; $self->{featnames}->{all}->{$fname}++; # save for gbrowse... $self->{featnames}->{$chr}->{$fname}++; # save for gbrowse... } else { print $outh $_; } } ##$self->printSummary( $self->{summaryfile}, $self->{featnames}); } sub copyFFF2Gnomap { my $self= shift; my( $fileset )= @_; # do per-csome/name my $intype = 'fff'; my $gnomapdir= $self->outputpath(); # my %csomefeats=(); $self->{featnames}= {}; print STDERR "copyFFF2Gnomap\n" if $DEBUG; foreach my $fs (@$fileset) { my $fp= $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; my $chr= $fs->{chr}; next unless( $fs->{type} =~ /$intype/); unless(-e $fp) { warn "missing $intype file $fp"; next; } my $featname= catfile($gnomapdir,"features-$chr.tsv"); print STDERR "copy $featname from $fp\n" if $DEBUG; #?? include here opt to merge cyto feats - w/ sort if ($fp =~ m/\.(gz|Z)$/) { open(FF,"gunzip -c $fp|"); } else { open(FF,"$fp"); } my $ffformat = 0; #? test always; probably is 2 open(OUT,">$featname"); while(){ if (/^\w/ && /\t/) { my @v= split(/\t/); # split /\t/, $_; if ( $ffformat == 2 || @v > 7 || ($v[0] =~ /^\w/ && $v[1] =~ /^[\d-]+$/)) { $ffformat= 2; splice(@v,0,2); } print OUT join("\t",@v); my $fname= $v[0]; $self->{featnames}->{all}->{$fname}++; # save for summary && gbrowse... $self->{featnames}->{$chr}->{$fname}++; } else { print OUT $_; } } close(FF); close(OUT); } ## $self->printSummary( $self->{summaryfile}, $self->{featnames}); } sub printSummary { my $self= shift; my( $sumfile, $csomefeats )= @_; if ( $sumfile && $csomefeats ) { my $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; my $date = $self->config->{date}; ##my $org = $self->{config}->{species} || $self->{config}->{org}; my $org= $self->{org} || $self->handler()->{config}->{org}; print $fh "# Genome feature summary of $org from $title [$date]\n"; my @fl= grep { 'all' ne $_ } sort keys %$csomefeats; foreach my $arm ('all', @fl) { print $fh (($arm eq 'all') ? "\n# ALL chromosomes\n" : "\n# Chromosome $arm\n"); foreach my $t (sort keys %{$csomefeats->{$arm}}) { my $v= $csomefeats->{$arm}{$t}; print $fh "$t\t$v\n"; } print $fh "#","="x50,"\n"; } close($fh); } } sub makeGbrowseConf { my $self= shift; my($featnames)= @_; warn "makeGbrowseConf\n" if $DEBUG; ## need active feature set from ? feature-summary.txt or fff/ files my $config={}; # stuff with $self->handler->config && others $config= $self->handler->{config}; ##my $gbrowseconf= $config->{gbrowsefiles}->{config}; ##my $gbrowseconf= $self->{gbrowseconf}; my $gbset= $self->handler->getFilesetInfo('gbrowse_fb'); my $gbrowseconf= $gbset->{config}; # add vars to config # description = ${species} ${relfull} ${date} OR ${title} ?? # datapath = ${gnomapdir} $config->{gnomapdir}= $self->outputpath(); #?? my ($loc, $ex)= ('',''); my $chromosomes= $self->handler->getChromosomes(); foreach my $chr (@$chromosomes) { $loc= "$chr:1..100000" unless($loc); $ex .= "$chr: "; } $config->{ default_location } = $loc; $config->{ examples } = $ex; my $config2= $self->handler->{config2}; my $gbconf= $config2->readConfig( $gbrowseconf, { Variables => $config, debug => $DEBUG, }, {} ); print STDERR $config2->showConfig( $gbconf, { debug => $DEBUG }) if ($self->{showconfig}); my $doc = $gbconf->{doc}->{gbrowse}; my $fdefs= $gbconf->{fdef}; my $content= $doc->{header}->{content} || ''; my @featnames=(); @featnames= @$featnames if (ref $featnames); @featnames= sort keys %$fdefs unless(@featnames); foreach my $fname (@featnames) { my $fd = $fdefs->{$fname}; unless( $fd ) { # next; # check all hash {feature} strings for match... $fd = $fdefs->{GENERIC}; my $gct= $fd->{content}; $gct =~ s/GENERIC/$fname/sg; $fd= { name => $fname, content => $gct }; } next if ($fd->{done}); my $morefeats= $fd->{feature}; my $ct= $fd->{content}; $content .= $ct."\n"; $fd->{done}=1; } $content .= $doc->{footer}->{content} || ''; $doc->{content}= $content; $doc->{path}= $gbset->{path} if $gbset->{path}; #$config->{gbrowsefiles}->{path}; #?? $self->handler()->writeDocs( $doc ); } # =item openInput( $fileset ) # # handle input files # # =cut # # sub openInput # { # my $self= shift; # my( $fileset )= @_; # do per-csome/name # my @files= (); # my $inh= undef; # return undef unless(ref $fileset); # # my $intype = $self->{config}->{informat} || 'fff'; #? maybe array # my $featset= $self->{config}->{featset} || []; # # print STDERR "openInput: type=$intype \n" if $DEBUG; # # foreach my $fs (@$fileset) { # my $fp= $fs->{path}; # my $name= $fs->{name}; # my $type= $fs->{type}; # want also/instead featset type here ? gene,mrna,cds,... # next unless( $fs->{type} =~ /$intype/); # could it be 'dna/fasta', 'amino/fasta' ? # unless(-e $fp) { warn "missing intype file $fp"; next; } # # push(@files, $fp); # } # # return @files; # } =item processToOutput =cut sub processToOutput { my $self= shift; my( $rseqfiles )= @_; } #============== # mostly from flybase/work.local/chado_r3_2_26/soft/mergeflyfeats4.pl #============== ## --- read table of genome:cytology mapping ----- # my $sorsaf="${sorsapath}sorsa.txt"; # if (defined $mconf->{sorsa}->{path}) { # $sorsaf= join("",getFiles( $mconf->{sorsa}->{path} )); # } # sub getFiles { # my $self= shift; # my($path)= @_; # my $file; # if ($path =~ s,([^/]+)$,,) { $file= $1; } # else { $file= $path; $path="./"; } # opendir(D,$path); # my @file= grep(/$file/,readdir(D)); # closedir(D); # return $path,@file; # } sub readflysorsa { my $self= shift; my ($sorsa)= @_; my %cytobases= %{$self->{cytobases}} || (); return if (scalar(%cytobases)); local(*F,*O); my ($n); my @sorsalist= (); $sorsa= $self->{sorsatable} unless(-e $sorsa); unless (open(F,$sorsa)) { warn "Can't read $sorsa" ; $cytobases{1}= [ 0, 0 ]; # don't come here back again $self->{cytobases}= \%cytobases; return; } warn "reading $sorsa\n" if $DEBUG; while () { next unless(/^\d/); chomp(); my($cyto,$bb,$be)= split(); ### /\t/ ## (' ') was, now \t separated! $cytobases{$cyto}= [ $bb, $be ]; push( @sorsalist, $cyto); # sorted ! } close(F); $self->{cytobases}= \%cytobases; $self->{sorsalist}= \@sorsalist; } =item replace static sorsa.txt with chromosome_band features from chado db -- gff table 2L . chromosome_band -30855 353 . + . ID=1273798;Name=ba nd-21A1;cyto_range=21A1 2L . chromosome_band -30855 108823 . + . ID=1273801;Name=ba nd-21A;cyto_range=21A 2L . chromosome_band -30855 1318131 . + . ID=1242194;Name=ba nd-21;cyto_range=21 2L . chromosome_band 354 32349 . + . ID=1273804;Name=ba -- use .fff file instead ? 2L -30855 chromosome_band band-21A1 21A1 -30855..353 - 2L -30855 chromosome_band band-21A 21A -30855..108823 - 2L -30855 chromosome_band band-21 21 -30855..1318131 - =cut sub readChadoCytomap { my $self= shift; my( $fset_h, $file, $outh)= @_; local(*F); return "Can't read $file" unless (open(F,$file)); warn "Reading chromosome_band $file \n" if $DEBUG; unless($file =~ m/\.gff$/) { warn "Wrong format - want .gff"; return; } my %cytobases= %{$self->{cytobases}} || (); my @sorsalist= (); ##my @keepset= ($fset_h->{keep}) ? @ {$fset_h->{keep}} : (); ##my @dropset= ($fset_h->{drop}) ? @ {$fset_h->{drop}} : (); while () { next unless(/^(\w+)\s+(\S+)\s+chromosome_band/); my @gff= split; #next unless (grep {$gff[2] eq $_} @keepset); if ($gff[-1] =~ m/cyto_range=(\S+)/) { my ($cyto,$bb,$be)= ($1, $gff[3], $gff[4]); next unless($cyto =~ m/^\d+[A-F]\d/); # need to drop 1,1A for 1A1 $bb--; # dang interbase -1 doesn't apply to chromosome_band - why not? $cytobases{$cyto}= [ $bb, $be ]; push( @sorsalist, $cyto); # sorted print $outh "$cyto\t$bb\t$be\n" if ($outh); # ! not sorted right here - need chr order } } close(F); $self->{cytobases}= \%cytobases; $self->{sorsalist}= \@sorsalist; } sub getCytobases { my $self= shift; my ($cmap)= @_; my %cytobases= %{$self->{cytobases}} || (); my ($start1,$stop1)= ($kMissingValue,$kMissingValue); ($start1,$stop1)= @ {$cytobases{$cmap}} if $cytobases{$cmap}; return ($start1,$stop1); } sub getCytolocFromSeqloc { my $self= shift; my ($arm, $bstart, $bend)= @_; # $chr my ($cstart, $cend); my @sorsalist= @ { $self->{sorsalist} }; my $ca= $flycsomebands{$arm}->[0]; my $ina= 0; foreach my $cb (@sorsalist) { if ($cb eq $ca) { $ina= 1; } if ($ina) { my ($bb, $be)= $self->getCytobases($cb); # @ {$cytobases{$cb}}; if ($bstart >= $bb && $bstart <= $be) { $cstart= $cb; } if ($bend >= $bb && $bend <= $be) { $cend= $cb; last; } } } if ($cstart && !$cend) { $cend= $cstart; } elsif ($cend && !$cstart) { $cstart= $cend; } if (wantarray) { return ($cstart, $cend); } else { return ($cstart eq $cend) ? $cstart : "$cstart--$cend"; } } sub maxrange { my $self= shift; my( $range)= @_; my ($pre, $suf,$start,$stop, $b, $u); $start= $kMissingValue; $stop= $start; $range =~ s/^([^\d<>-]*)//; $pre= $1; $range =~ s/(\D*)$//; $suf= $1; if ($range =~ m/^([<>]*)([\d-]+)/) { $u= $1; $start= $2; $start-- if ($u eq '<'); } if ($range =~ m/([<>]*)([\d-]+)$/) { $u= $1; $stop= $2; $stop++ if ($u eq '>'); } return ($start,$stop); } sub getCytorange { my $self= shift; my($ca,$cx)= @_; $ca =~ s/^\s*//; $ca =~ s/[\s+-]*$//; return () unless ($ca =~ /^\d/); #? don't have conversion info for hXXX my $offs= 0; ## need patch for 1Lt; 1Rt; 1Cen? h, ... if ($ca !~ /[A-G]/) { if ($cx) { $cx =~ s/\d*$//; $ca= $cx . $ca; } else { $ca .= 'A1'; $offs= -1; } } elsif ($ca !~ /\d$/) { $ca .= '1'; $offs= -1; } my ($start1,$stop1)= $self->getCytobases($ca); #@ {$cytobases{$ca}}; return ($start1,$stop1,$ca); # +$offs } # sub getMap2Bases { return flyCytomap2Bases(@_); } ## ignore ranges outside of csome arm ## same as sub flyCytomap2Bases() sub getMap2Bases { my $self= shift; my ($map, $arm)= @_; my($stop,$start)= ($kMissingValue,$kMissingValue); $self->readflysorsa(); #? here or wait my $carm= $flycsomebands{$arm}->[0]; # $cytoarms{$arm}; my $darm= ($carm =~ m/^(\d+)/) ? $1 : 0; my ($armb, $x)= $self->getCytobases($carm); #@ {$cytobases{$carm}}; my $carme= $flycsomebands{$arm}->[1]; my $darme= ($carme =~ m/^(\d+)/) ? $1 : 0; my ($y, $arme)= $self->getCytobases($carme); #@ {$cytobases{$carme}}; $map =~ s/\s+//g; foreach my $mp (split(/;/, $map)) { next if ($mp eq '*'); next if ($mp =~ /^h/); # cant handle these yet my($ca, $cb)= split(/-/, $mp); my $da= ($ca =~ m/^(\d+)/) ? $1 : 0; next if ($da < $darm || $da > $darme); my($start1,$stop1,$bstart,$bstop); ($start1,$stop1,$ca)= $self->getCytorange($ca); next unless(defined $start1); # next unless($stop1 >= $armb && $start1 <= $arme); if ($cb) { ($bstart,$bstop,$cb)= $self->$self->getCytorange($cb,$ca); $stop1= $bstop if ($bstop); } ##? skip/ignore if both $ca,$cb are outside of $arm ? next if ($stop1 < $armb || $start1 > $arme); $start= $start1 if ($start==$kMissingValue && $start1 >= $armb && $start1 <= $arme); $stop = $stop1 if ($stop1 >= $armb && $stop1 <= $arme); } # $start= $armb if ($start==$kMissingValue && $stop != $kMissingValue); $stop = $start if ($stop==$kMissingValue); ## was = $arme ##?? need band range here, for e.g. '41' => 41A1-41F29 # DEBUG - getting missing when should get real range !?? return (wantarray) ? ($start, $stop) : "$start..$stop"; } ## indexing parts from genomefeat.pl - fixed for changed sorsa.txt, other flyfeat parts ## ## index features*.tsv by ID field for lookup by id ## sub indexfeatdir { my $self= shift; my $dir= shift; local(*D); opendir(D, $dir) || warn "can't open $dir"; my @files= grep( /^features-\w+\.tsv$/, readdir(D)); closedir(D); local(*IMAP,*IMAPX); open(IMAP,">$dir/idmap.tsv"); open(IMAPX,">$dir/idmap.tsv.idx"); my %idfh=(); foreach my $file (sort @files) { my $sfile= catfile($dir, $file); my $csome= ($file =~ /^features-(\w+)/) ? $1 : 'UNK'; my $infh= new FileHandle($sfile); unless($infh) { warn "Can't read $sfile"; $self->{failonerror} ? die : next; } ## warn "indexing chr-$csome, $sfile\n" if $DEBUG; $infh->seek(0,0); print $self->indexFeatures( $sfile, $infh, 'index', $csome); $infh->seek(0,0); print $self->indexIds( $sfile, $infh, 'idindex', $csome, *IMAP, *IMAPX); $infh->seek(0,0); print $self->makeAllIdmaps( $sfile, $infh, $dir, $csome, \%idfh); } close(IMAP); close(IMAPX); foreach my $idfh (values %idfh) { $idfh->close(); } } sub makeAllIdmaps { my $self= shift; my( $file, $fin, $dir, $csome, $idfh)= @_; my ($nd)=(0); my %didid=(); my $indexidpattern='^[A-Za-z]{2,}'; my $indexdbpattern='^[A-Za-z]{2,}'; # FIXME - config #die "Can't read $file" unless (open(FIN,$file)); # my $org = ucfirst( $self->{config}->{org} || 'Any'); my $org= $self->{org} || $self->handler()->{config}->{org}; $org= 'Any' unless($org); # fixme for ortholog to_name in $notes my($nte,$ste,$ite); # warn "makeAllIdmaps: noIdmap.classes='$noIDmap' \n" if $DEBUG; while(<$fin>) { my ($class,$sym,$map,$range,$idv,$dbx,$notes)= split(/\t/); $nte++ if ($class =~/transposable_element/); #DEBUG next unless( $range && $range ne '-' ); next if ($class =~ /$noIDmap/i); ## ?? drop or keep my @ids= (split(/[,;\s]/,$idv),split(/[,;\s]/,$dbx)); if ($class =~ /$nameIsId/) { # fixme for fff output - put in ID field $sym =~ s/\-hit$//; # bad BAC names unshift(@ids,$sym); } elsif ($class =~ /$nameIsSpeciesId/) { $sym = "$org\\$sym" unless($sym =~ m,\\,); unshift(@ids,$sym); } elsif ($notes && $notes =~ /to_name=([^;,\s]+)/ ) { ## added to_name=name, id << keep id? my $tosym = $1; $tosym =~ s/\-\w\w$//; # drop prot suffix my $toorg = ($notes =~ /to_species=([^;,\s]+)/) ? $1 : $org; unshift(@ids,ucfirst($toorg).'\\'.$tosym); } # feb05: getting lots of useless idmap-xxx.tsv for things like # polyA_site with symbol name as id/name # gbb-polyA_site-1, Delta88{}su(s)[28] , my $needid=1; IDINDEX: while ($needid && (my $tid = shift @ids)) { next if ($tid eq '-'); $ite++ if ($tid =~/FBti/); #DEBUG my $db=''; if ($tid =~ s/$cutdbpattern//i) { $db= $1; } next unless ($db =~ /$indexdbpattern/ || $tid =~ /$indexidpattern/); my($start, $stop)= $self->maxrange($range); my $idkey="$tid.$csome.$start"; next if ($didid{$idkey}); $ste++ if ($tid =~/FBti/); #DEBUG my $idf= 'idmap-all.tsv'; if ( $tid =~ m/^([A-Za-z]+)/ ) { $idf= "idmap-$1.tsv"; } my $fh= $idfh->{$idf}; unless($fh) { my $sfile= catfile($dir, $idf); $fh= new FileHandle(">$sfile"); $idfh->{$idf}= $fh; } if ($fh) { print $fh "$tid\t$csome\t$start\t$stop\n"; $nd++; $didid{$idkey}++; } } } warn "TE count: nte=$nte idte=$ite saved=$ste\n" if $DEBUG; #close(FIN); return "makeAllIdmaps n=$nd\n"; } sub indexIds { my $self= shift; my($file, $fin, $kind, $csome, $idmapf, $idmapx)= @_; local(*FIN,*FIDX); my ( $n, $nl)= (0,0); $kind= 'idindex' unless($kind); my $idx= $file . ".idx"; # die "Can't read $file" unless (open(FIN,$file)); die "Can't write $idx" unless (open(FIDX,">$idx")); # my $recsize = length(pack("NN", 1, 500)); ## a constant -- 2 long integers my %didid= (); my ($at,$ate)= (0,0); while (<$fin>) { $at = $ate; $ate= tell($fin); if (/^\w/) { $nl++; chomp(); my ($class,$sym,$map,$range,$idv,$dbx)= split(/\t/); ## dang, for cytogene need to make $range from $map next if ($class =~ /$noIDmap/); ## ?? drop or keep next unless($class =~ /$indexidtype/); ## aug04 -- ID field has changed to CG, others - use dbx to get FBgn ID ## look at both fields for 1st valid numeric (FBgn) ID my @ids= (split(/[,;\s]/,$idv),split(/[,;\s]/,$dbx)); # dbx should be ',' now my $needid=1; IDINDEX: while ($needid && (my $tid = shift @ids)) { ## next unless($class =~ /gene|RNA/ || $tid =~ /gn\d+/); ## FIXME - need another index method to mix FBgn/FBan/FBxx next unless ($tid =~ /$indexidpattern/); my $db=''; #default? if ($tid =~ s/([^:]+)://) { $db= $1; ## skip not-our-id ids ## $tid= '' unless ($db =~ m/FlyBase|MEOW|euGenes/i); ## ? do we need to check db, if matches $indexidpattern ? } ##if ($tid =~ m/[A-Za-z]*0*(\d+)/) ## need config patt here ##if ($tid =~ m/[A-Z]{2}gn0*(\d+)/) if ($tid =~ m/0*(\d+)/) { #? $needid=0; -- keep going thru all dbx 2ndary FBgn IDS ???? my $idnum= int($1); if (!$didid{$tid} && $idnum < 200000) { # be sure is good idnum $didid{$tid}++; my $size= $ate - $at; my $record= pack("NN", $at, $size); my $idloc = $idnum * RECSIZE; seek(FIDX, $idloc, 0); ## check if already did id == e.g., several feats have same ID, pick 1st? always print FIDX $record; $n++; # ?? also write to single $org id-map.tsv ? and do .idx for it? if ($class =~ /cyto/ && $map && $range eq '-') { $range= $self->getMap2Bases( $map, $csome); } if ($idmapf && $range && $range ne '-') { my($start, $stop)= $self->maxrange($range); my $idat= tell($idmapf); print $idmapf "$tid\t$csome\t$start..$stop\n"; my $ide= tell($idmapf); $size= $ide - $idat; $record= pack("NN", $idat, $size); ##my $idloc = $idnum * RECSIZE; seek($idmapx, $idloc, 0); print $idmapx $record; } } ## last IDINDEX; } } } ##$at = $ate; } close(FIDX); # close(FIN); return "indexIds $file = $n / $nl\n"; } ## ## index features*.tsv by base range ## sub indexFeatures { my $self= shift; my($file, $fin, $kind, $csome)= @_; local(*FIN,*FIDX); my $n= 0; $kind= 'index' unless($kind); ##return if ($kind ne 'index'); my $idx= $file . ".ranges"; # die "Can't read $file" unless (open(FIN,$file)); die "Can't write $idx" unless (open(FIDX,">$idx")); print FIDX "# $idx\n"; print FIDX "# base range -> file index, and source, scaffold ranges\n"; print FIDX "# tab-separated-values of: \n"; print FIDX "# base-start | file-index OR class-name | file-index | location\n"; my $bindex= 0; ##? off by one? was 0; my $nextstep= -666; my $stepsize= 100000; my @csomerange= (0,0); while (<$fin>) { # my $blength= length($_); if (/^\w/) { chomp(); my ($class,$sym,$map,$range,$ids,$dbx)= split(/\t/); my ($start,$stop)= ($kMissingValue, $kMissingValue); if (defined $range && $range =~ /\d/) { ($start, $stop)= $self->maxrange($range); } elsif ($map =~ /\d/) { # !$range || $range eq '-' ($start, $stop)= $self->getMap2Bases( $map, $csome) ; # if ($org =~ /fly/); } if ($start!=$kMissingValue && $stop!=$kMissingValue) { if ($class eq 'source') { @csomerange= ($start, $stop); $stepsize= int( ($stop - $start) / 100 ); } if ($class eq 'source') { # || $class eq 'segment' ## segment not scaffold print FIDX "$class\t$bindex\t$range\n"; } elsif ($nextstep == -666 || $start >= $nextstep) { $nextstep= $start if ($nextstep == -666); $nextstep= 0 unless($nextstep); ## dang perl print FIDX "$nextstep\t$bindex\n"; $nextstep += $stepsize; } $n++; } } # $bindex += $blength; $bindex= tell($fin); ##? off by one ?? } print FIDX "$csomerange[1]\t$bindex\n"; #close(FIN); close(FIDX); return "indexFeatures $file = $n\n"; } 1; __END__ chado-1.23/lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm000644 000765 000024 00000002674 11256707527 022457 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::MyLargePrimarySeq; use strict; =head1 Bio::GMOD::Bulkfiles::MyLargePrimarySeq patch to use Bio::Seq::LargePrimarySeq to read feature locations from dna.raw files. my $dnaseq= Bio::GMOD::Bulkfiles::MyLargePrimarySeq->new( -file => $dnafile); $loc= new Bio::Location::something(...); $bases= $dnaseq->subseq($loc); =cut use Bio::Seq::LargePrimarySeq; use base qw(Bio::Seq::LargePrimarySeq); #use vars qw(@ISA); BEGIN{ @ISA = qw(Bio::Seq::LargePrimarySeq); } sub new { my ($class, %params) = @_; my $dnafile = delete $params{'-file'} ; my $self = $class->SUPER::new(%params); $self->dnafile($dnafile); if( $dnafile && -e $dnafile ) { ## $self->_filename($dnafile); # don't change to our name in case StUPER wants to unlink it my $fh= new FileHandle($dnafile); $fh->seek(0,2); my $flen= $fh->tell(); $fh->seek(0,0); $self->_fh($fh); $self->length($flen); } return $self; } sub dnafile { my $self = shift; if (@_) { $self->{dnafile}= shift; } return $self->{dnafile}; } ## dang this nasty -- DONT unlink sub DESTROY { my $self = shift; my $fh = $self->_fh(); close($fh) if( defined $fh ); $self->_filename(''); # is unlink '' bad ? # this should be handled by Tempfile removal, but we'll unlink anyways. ##unlink $self->_filename() if defined $self->_filename() && -e $self->_filename; ##$self->SUPER::DESTROY(); } #------- 1; chado-1.23/lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm000644 000765 000024 00000004214 11256707527 022164 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::MySplitLocation; use strict; =head1 Bio::GMOD::Bulkfiles::MySplitLocation patch for Bio::Location::Split for error in strand usage =cut use base qw(Bio::Location::Split); ## REV COMP NOT WORKING! LargeSeq looks ok ... Bio::Location::Split is bad for strand ! use Bio::Root::Root; use Bio::Location::SplitLocationI; use Bio::Location::Atomic; use Bio::Location::Split; sub new { my ($class, @args) = @_; ## Atomic doing strange things which throws## my $self = $class->SUPER::new(@args); my $self = {}; bless $self,$class; $self->{'_sublocations'} = []; $self->splittype('JOIN'); return $self; } =item strand Bio::Location::Split IS DOING WRONG THING HERE it should do same as Simple/Atomic location, and PrimarySeq handler then properly reverses, etc. all of location Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandidness (-1, 0, +1) Args : optionaly allows the strand to be set : using $loc->strand($strand) =cut sub strand { my $self = shift; if ( @_ ) { my $value = shift; if ( defined($value) ) { if ( $value eq '+' ) { $value = 1; } elsif ( $value eq '-' ) { $value = -1; } elsif ( $value eq '.' ) { $value = 0; } elsif ( $value != -1 && $value != 1 && $value != 0 ) { $self->throw("$value is not a valid strand info"); } $self->{'_strand'} = $value; } } # do not pretend the strand has been set if in fact it wasn't return $self->{'_strand'}; } ## this is also bad in split - forgot strand sub to_FTstring { my ($self) = @_; my @strs; foreach my $loc ( $self->sub_Location() ) { my $str = $loc->to_FTstring(); if( (! $loc->is_remote) && defined($self->seq_id) && defined($loc->seq_id) && ($loc->seq_id ne $self->seq_id) ) { $str = sprintf("%s:%s", $loc->seq_id, $str); } push @strs, $str; } my $spt= lc $self->splittype; if( defined $self->strand && $self->strand == -1 ) { $spt = "complement"; } my $str = sprintf("%s(%s)",$spt, join(",", @strs)); return $str; } 1; chado-1.23/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm000644 000765 000024 00000006606 11256707527 020652 0ustar00cainstaff000000 000000 =head1 CRC64 perl module documentation =head2 NAME CRC64 - Calculate the cyclic redundancy check. =head2 SYNOPSIS ** dgg: rewrite for line-add so dont need to suck all into mem ** use SWISS::CRC64; $crc = SWISS::CRC64::crc64("IHATEMATH"); #returns the string "E3DCADD69B01ADD1" ($crc_low, $crc_high) = SWISS::CRC64::crc64("IHATEMATH"); #returns two 32-bit unsigned integers, 3822890454 and 2600578513 =head2 DESCRIPTION SWISS-PROT + TREMBL use a 64-bit Cyclic Redundancy Check for the amino acid sequences. The algorithm to compute the CRC is described in the ISO 3309 standard. The generator polynomial is x64 + x4 + x3 + x + 1. Reference: W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, "Numerical recipes in C", 2nd ed., Cambridge University Press. Pages 896ff. =head2 Functions =over =item crc64 string Calculate the CRC64 (cyclic redundancy checksum) for B. In array context, returns two integers equal to the higher and lower 32 bits of the CRC64. In scalar context, returns a 16-character string containing the CRC64 in hexadecimal format. =back =head1 AUTHOR Alexandre Gattiker, gattiker@isb-sib.ch =head1 ACKNOWLEDGEMENTS Based on SPcrc, a C implementation by Christian Iseli, available at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/old/SPcrc.tar.gz =cut package SWISS_CRC64; # ** Initialisation #32 first bits of generator polynomial for CRC64 #the 32 lower bits are assumed to be zero # my $POLY64REVh = 0xd8000000; # my @CRCTableh = 256; # my @CRCTablel = 256; # my $initialized; use strict; use vars qw/$POLY64REVh @CRCTableh @CRCTablel $initialized/; BEGIN{ $POLY64REVh = 0xd8000000; @CRCTableh = 256; @CRCTablel = 256; $initialized= 0; } sub new { my $pkg= shift; init(); my $self= { crcl => 0, crch => 0, size => 0 }; return bless $self; # , $pkg ?? } sub size { return shift->{size}; } sub add { my $self= shift; my $sequence= shift; my $crcl = $self->{crcl}; my $crch = $self->{crch}; my $size = $self->{size}; foreach (split '', $sequence ) { my $shr = ($crch & 0xFF) << 24; my $temp1h = $crch >> 8; my $temp1l = ($crcl >> 8) | $shr; my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF; $crch = $temp1h ^ $CRCTableh[$tableindex]; $crcl = $temp1l ^ $CRCTablel[$tableindex]; $size++; } $self->{crcl}= $crcl; $self->{crch}= $crch; $self->{size}= $size; } sub hexsum { my $self= shift; my $crcl = $self->{crcl}; my $crch = $self->{crch}; return wantarray ? ($crch, $crcl) : sprintf("%08X%08X", $crch, $crcl); } sub init { if (!$initialized) { $initialized = 1; for (my $i=0; $i<256; $i++) { my $partl = $i; my $parth = 0; for (my $j=0; $j<8; $j++) { my $rflag = $partl & 1; $partl >>= 1; $partl |= (1 << 31) if $parth & 1; $parth >>= 1; $parth ^= $POLY64REVh if $rflag; } $CRCTableh[$i] = $parth; $CRCTablel[$i] = $partl; } } } sub crc64 { my $sequence = shift; my $crcl = 0; my $crch = 0; init(); foreach (split '', $sequence ) { my $shr = ($crch & 0xFF) << 24; my $temp1h = $crch >> 8; my $temp1l = ($crcl >> 8) | $shr; my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF; $crch = $temp1h ^ $CRCTableh[$tableindex]; $crcl = $temp1l ^ $CRCTablel[$tableindex]; } return wantarray ? ($crch, $crcl) : sprintf("%08X%08X", $crch, $crcl); } 1; chado-1.23/lib/Bio/GMOD/Bulkfiles/TableWriter.pm000644 000765 000024 00000037542 11256707527 021330 0ustar00cainstaff000000 000000 package Bio::GMOD::Bulkfiles::TableWriter; use strict; =head1 NAME Bio::GMOD::Bulkfiles::TableWriter writes summary tables of genome database features =head1 SYNOPSIS use Bio::GMOD::Bulkfiles; my $bulkf= Bio::GMOD::Bulkfiles->new( configfile => 'seqdump-r4', ); my $fwriter= $bulkf->getWriter('tables'); my $result = $fwriter->makeFiles(); =head1 AUTHOR D.G. Gilbert, 2005, gilbertd@indiana.edu =head1 METHODS =cut #----------------- use POSIX; use FileHandle; use File::Spec::Functions qw/ catdir catfile /; use File::Basename; use Bio::GMOD::Bulkfiles::BulkWriter; use base qw(Bio::GMOD::Bulkfiles::BulkWriter); use constant RECSIZE => length(pack("NN", 1, 50000)); our $DEBUG = 0; my $VERSION = "1.0"; use constant BULK_TYPE => 'tables'; use constant CONFIG_FILE => 'tablewriter'; my $kMissingValue= -99999999; my $kMaxValue= 999999999; my $kMinValue= $kMissingValue+1; use vars qw/ $noIDmap $nameIsId $nameIsSpeciesId $cutdbpattern $indexidtype $indexidpattern /; sub init { my $self= shift; $self->SUPER::init(); ## superclass does these?? $DEBUG= $self->{debug} if defined $self->{debug}; # $self->{bulktype} = $self->BULK_TYPE; # dont need hash val? # $self->{configfile}= $self->CONFIG_FILE unless defined $self->{configfile}; } =item initData initialize data from config =cut sub initData { my($self)= @_; $self->SUPER::initData(); my $reldate= $self->handler()->config->{relfull} || $self->handler()->{date}; $self->{reldate} = $reldate; # my $config = $self->{config}; # my $finfo= $self->{fileinfo} || $self->handler()->getFilesetInfo($self->BULK_TYPE); # my $outdir= $self->handler()->getReleaseSubdir( $finfo->{path} || $self->BULK_TYPE); # $self->{outdir} = $config->{outdir}= $outdir; #$self->{summaryfile}= catfile( $self->outputpath(), "feature_map-summary.txt"); } #-------------- subs ------------- =item makeFiles( %args ) primary method makes blast indices. input file sets are intermediate chado db dump tables. arguments: infiles => \@fileset, # required =cut sub makeFiles { my $self= shift; my %args= @_; my $targets= $self->config->{target}; my %targets= map{ $_ => 1 } @$targets; ## ^^ see Bulkfiles->getDumpFiles() ## may want to use this: ## my $seqsql = handler()->getSeqSql($fdump->{config},$fdump->{ENV}); # 0710: no_csomesplit : no perchr files, only makeall my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 print STDERR "TableWriter::makeFiles\n" if $DEBUG; # debug my $fileset = $args{infiles}; my $chromosomes = $args{chromosomes}; #?? unless(@$fileset) { my $intype= $self->config->{informat} || ['fff']; #? maybe array $fileset = $self->handler->getFiles($intype, $chromosomes); unless(@$fileset) { warn "TableWriter: no input '$intype' files found\n"; return $self->status(-1); } } #js needs: var csomes= ["X","2L","2R","3L","3R","4"]; my $chrlist=""; $chromosomes= $self->handler->getChromosomes(); # want all, not subset ?? if($no_csomesplit) { $chrlist= "'sum', "; #?? only this, or none? } else { foreach my $chr (@$chromosomes) { $chrlist .= "'$chr', "; } } $ENV{'chromosomes'}= $chrlist; ## FIXME: need option here or elsewhere for other input, e.g. SQL query, GFF, ... $self->readFFF($fileset); # collate feature info ## chromosome_summary ; do this before in Bulkfiles with others? ## this file is named in chadosql entry - fixme my $cfile= catfile( $self->outputpath(), "chromosomes-overview.txt"); $self->chromosomeSummary( $cfile, $chromosomes); # always? delete $targets{'chromosome_summary'}; ## if doFeatSum my $summaryfile= catfile( $self->outputpath(), "feature_map-summary.txt"); $self->featureSummary( $summaryfile, $self->{featnames}) if(delete $targets{'feature_map'}); my @featnames= (); if ($self->{featnames}->{all}) { @featnames= sort keys %{$self->{featnames}->{all}}; } $self->makeGbrowseConf('gbrowse_conf',\@featnames) # should pass array of feature names ! if(delete $targets{'gbrowse_conf'}); if(delete $targets{'overviewhtml'}) { my $overviewset = $self->handler->getFilesetInfo('overview'); $self->table2html($overviewset); } # handle other targets: id_table; ortho_table; ... using getSeqSql ? foreach my $trg (@$targets) { if($targets{$trg}) { my $fset= $self->handler->getFilesetInfo($trg); unless($fset) { warn "TableWriter: No handler for target=$trg\n"; next; } $self->writeTargetDocs($trg,$fset); } } print STDERR "TableWriter::makeFiles: done\n" if $DEBUG; return $self->status(1); } sub table2html { my $self= shift; my( $fsetinfo )= @_; # do per-csome/name my $sqlconf = $fsetinfo->{config}; my $seqsql = $self->handler->getSeqSql($sqlconf); my $outpath= $self->handler->getReleaseSubdir( $fsetinfo->{path} || $self->BULK_TYPE); ## $fsetinfo->{'path'}= $outpath; # save for reuse my $sqltag = $fsetinfo->{tag} || "feature_sql"; my $sqltype = $fsetinfo->{type}; my $targets = $fsetinfo->{target}; # should be array ? unless($targets) { my @tg= sort keys %{$seqsql->{$sqltag}}; $targets= \@tg; } unless(ref $targets) { $targets= [ $targets ]; } ##print STDERR "TableWriter::table2html: $sqltype $fsetinfo->{config}\n" if $DEBUG; foreach my $sname (@$targets) { my $fs= $seqsql->{$sqltag}->{$sname}; unless($fs) { next; } ## FIXME for chromosome_summary my $type= $fs->{type}; my $outn= $fs->{output} || $sname.".txt"; #?? unless( (!$sqltype || $type =~ m/\b$sqltype\b/)) { next; } #?? my $outf= catfile($outpath,$outn); print STDERR "TableWriter::table2html: $sname, $type, $outf\n" if $DEBUG; if (-e $outf) { my $int; (my $outh= $outf) =~ s/\.txt$//; $outh .= ".html"; open(T,$outf); open(H,">$outh"); print H "\n$sname\n\n"; while(){ chomp; my @r= split"\t"; if (@r>1) { $int++; if($int==1) { print H "\n"; print H "\n"; } else { print H "\n"; } } else { print H "
",join("",@r),"
",join("",@r),"
" if($int); $int= 0; print H "$_
\n"; } } print H "\n"; close(H); close(T); } } } sub readFFF { my $self= shift; my( $fileset )= @_; # do per-csome/name my $intype = 'fff'; my $outdir= $self->outputpath(); $self->{featnames}= {}; ## feature summary; add ave; std of feat.length; other stats ? print STDERR "readFFF\n" if $DEBUG; foreach my $fs (@$fileset) { my $fp= $fs->{path}; my $name= $fs->{name}; my $type= $fs->{type}; my $chr= $fs->{chr}; next unless( $fs->{type} =~ /$intype/); unless(-e $fp) { warn "missing $intype file $fp"; next; } if ($fp =~ m/\.(gz|Z)$/) { open(FF,"gunzip -c $fp|"); } else { open(FF,"$fp"); } my $ffformat = 0; #? test always; probably is 2 while(){ if (/^\w/ && /\t/) { my @v= split(/\t/); # split /\t/, $_; ## format 2 standard now; chrname sort-location featname ... if ( $ffformat == 2 || @v > 7 || ($v[0] =~ /^\w/ && $v[1] =~ /^[\d-]+$/)) { $ffformat= 2; splice(@v,0,2); } my $fname= $v[0]; $self->{featnames}->{all}->{$fname}++; # save for summary && gbrowse... $self->{featnames}->{$chr}->{$fname}++; ## keep running mean length ? ## my $loc = $v[xxx]; $loc=$self->maxrange($loc); $size= $loc[1-0].. ## $runave += $size; $runsd += (sq($size) - xxx); $runn++; } } close(FF); } } sub writeTargetDocs { my $self= shift; my( $targetid, $filesetinfo, $csomefeats )= @_; my $configfile= $filesetinfo->{config} || ""; warn "TableWriter: target=$targetid, config=$configfile\n" if $DEBUG; return unless($configfile); my $tconfig= $self->handler->callReadConfig( $configfile); ## should have ## need some fix to writeDocs for doc->path at top level or not-releasedir my $docs = $tconfig->{doc}; $self->handler()->writeDocs( $docs ) if ($docs); } sub chromosomeSummary { my $self= shift; my( $sumfile, $csomelist )= @_; ## chromosome_summary ; do this before in Bulkfiles with others? my $ctab= $self->handler->getChromosomeTable(); my $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; my $date = $self->{reldate}; my $org= $self->{org} || $self->handler()->{config}->{org}; ## Name and ID ?? # make it gff or not? : Source, Attribs my @flds= qw(Ref Feature_type Start Length Rank ID Feature_id Species); print $fh "# Chromosomes of $org from $title [$date]\n"; print $fh join("\t",@flds),"\n"; foreach my $chr (@$csomelist) { #? or use keys of $ctab my $cv= $ctab->{$chr}; if(!ref $cv) { next; } #what? print something? print $fh join("\t", $cv->{arm}, $cv->{type}, $cv->{start}, $cv->{length}, #fmax - fmin + 1 $cv->{strand}, #== Rank $cv->{id}, $cv->{oid}, $cv->{species}, ),"\n"; my $cparts= $ctab->{$chr}->{parts}; if (ref $cparts) { foreach $cv (@$cparts) { print $fh join("\t", $cv->{arm}, $cv->{type}, $cv->{start}, $cv->{length}, #fmax - fmin + 1 $cv->{strand}, #== Rank $cv->{id}, $cv->{oid}, $cv->{species}, ),"\n"; } } } close($fh); } sub featureSummary { my $self= shift; my( $sumfile, $csomefeats )= @_; if ( $sumfile && $csomefeats ) { my $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; my $date = $self->{reldate}; # || $self->handler()->{date}; my $org= $self->{org} || $self->handler()->{config}->{org}; print $fh "# Genome feature summary of $org from $title [$date]\n"; my @fl= grep { 'all' ne $_ } sort keys %$csomefeats; foreach my $arm ('all', @fl) { print $fh (($arm eq 'all') ? "\n# ALL chromosomes\n" : "\n# Chromosome $arm\n"); foreach my $t (sort keys %{$csomefeats->{$arm}}) { my $v= $csomefeats->{$arm}{$t}; print $fh "$t\t$v\n"; } print $fh "#","="x50,"\n"; } close($fh); } } sub makeGbrowseConf { my $self= shift; my($targetid,$featnames)= @_; warn "makeGbrowseConf $targetid\n" if $DEBUG; ## need active feature set from ? feature-summary.txt or fff/ files my $config={}; # stuff with $self->handler->config && others $config= { %{$self->handler->{config}} }; # copy it my $gbset= $self->handler->getFilesetInfo($targetid); #('gbrowse_conf'); my $gbrowseconf= $gbset->{config} || $self->getconfig($targetid); # add vars to config my $outdir= $self->outputpath(); $config->{outputpath}= $outdir; my @dbconf= qw(db_adaptor_class db_adaptor db_dsn db_user db_password); foreach my $dbk (@dbconf) { $config->{$dbk}= $gbset->{$dbk} || $self->getconfig($dbk); } if ($config->{db_adaptor_class} =~ /Chado/) { my ($chadodsn,$dbuser,$dbpass)= $self->handler->dbiDSN(); $config->{db_dsn}= $chadodsn; $config->{db_user}= $dbuser; $config->{db_password}= $dbpass; } my ($loc, $ex)= ('',''); my $chromosomes= $self->handler->getChromosomes(); foreach my $chr (@$chromosomes) { $loc= "$chr:1..100000" unless($loc); $ex .= "$chr "; } $config->{ default_location } = $loc; $config->{ examples } = $ex; my $config2= $self->handler->{config2}; my $gbconf= $config2->readConfig( $gbrowseconf, { Variables => $config, debug => $DEBUG, }, {} ); # my $gbxml= $config2->showConfig( $gbconf, { debug => 0 }); # if ( $gbxml =~ m/\$\{/ && ref($gbconf->{ENV_default}) ) { # my %env= %{$gbconf->{ENV_default}}; # foreach my $k (keys %env) { $env{$k}= $config->{$k} if($config->{$k}); } # $gbconf= $config2->readConfig( $gbrowseconf, {Variables => \%env}, {} ); # } print STDERR $config2->showConfig( $gbconf, { debug => $DEBUG }) if ($self->{showconfig}); my $doc = $gbconf->{doc}->{gbrowse}; my $fdefs= $gbconf->{fdef}; my $content= $doc->{header}->{content} || ''; my @featnames=(); @featnames= @$featnames if (ref $featnames); @featnames= sort keys %$fdefs unless(@featnames); foreach my $fname (@featnames) { my $fd = $fdefs->{$fname}; unless( $fd ) { # next; # check all hash {feature} strings for match... $fd = $fdefs->{GENERIC}; my $gct= $fd->{content}; $gct =~ s/GENERIC/$fname/sg; $fd= { name => $fname, content => $gct }; } next if ($fd->{done}); my $morefeats= $fd->{feature}; my $ct= $fd->{content}; $content .= $ct."\n"; $fd->{done}=1; } $content .= $doc->{footer}->{content} || ''; $doc->{content}= $content; $doc->{path}= $gbset->{path} if $gbset->{path}; $self->handler()->writeDocs( $doc ); } =item processToOutput =cut sub processToOutput { my $self= shift; my( $rseqfiles )= @_; } sub maxrange { my $self= shift; my( $range)= @_; my ($pre, $suf,$start,$stop, $b, $u); $start= $kMissingValue; $stop= $start; $range =~ s/^([^\d<>-]*)//; $pre= $1; $range =~ s/(\D*)$//; $suf= $1; if ($range =~ m/^([<>]*)([\d-]+)/) { $u= $1; $start= $2; $start-- if ($u eq '<'); } if ($range =~ m/([<>]*)([\d-]+)$/) { $u= $1; $stop= $2; $stop++ if ($u eq '>'); } return ($start,$stop); } =item FIXME : id_table ?? sub makeAllIdmaps { my $self= shift; my( $file, $fin, $dir, $csome, $idfh)= @_; my ($nd)=(0); my %didid=(); my $indexidpattern='^[A-Za-z]{2,}'; my $indexdbpattern='^[A-Za-z]{2,}'; # FIXME - config #die "Can't read $file" unless (open(FIN,$file)); # my $org = ucfirst( $self->{config}->{org} || 'Any'); my $org= $self->{org} || $self->handler()->{config}->{org}; $org= 'Any' unless($org); # fixme for ortholog to_name in $notes my($nte,$ste,$ite); # warn "makeAllIdmaps: noIdmap.classes='$noIDmap' \n" if $DEBUG; while(<$fin>) { my ($class,$sym,$map,$range,$idv,$dbx,$notes)= split(/\t/); $nte++ if ($class =~/transposable_element/); #DEBUG next unless( $range && $range ne '-' ); next if ($class =~ /$noIDmap/i); ## ?? drop or keep my @ids= (split(/[,;\s]/,$idv),split(/[,;\s]/,$dbx)); if ($class =~ /$nameIsId/) { # fixme for fff output - put in ID field $sym =~ s/\-hit$//; # bad BAC names unshift(@ids,$sym); } elsif ($class =~ /$nameIsSpeciesId/) { $sym = "$org\\$sym" unless($sym =~ m,\\,); unshift(@ids,$sym); } elsif ($notes && $notes =~ /to_name=([^;,\s]+)/ ) { ## added to_name=name, id << keep id? my $tosym = $1; $tosym =~ s/\-\w\w$//; # drop prot suffix my $toorg = ($notes =~ /to_species=([^;,\s]+)/) ? $1 : $org; unshift(@ids,ucfirst($toorg).'\\'.$tosym); } # feb05: getting lots of useless idmap-xxx.tsv for things like # polyA_site with symbol name as id/name # gbb-polyA_site-1, Delta88{}su(s)[28] , my $needid=1; IDINDEX: while ($needid && (my $tid = shift @ids)) { next if ($tid eq '-'); $ite++ if ($tid =~/FBti/); #DEBUG my $db=''; if ($tid =~ s/$cutdbpattern//i) { $db= $1; } next unless ($db =~ /$indexdbpattern/ || $tid =~ /$indexidpattern/); my($start, $stop)= $self->maxrange($range); my $idkey="$tid.$csome.$start"; next if ($didid{$idkey}); $ste++ if ($tid =~/FBti/); #DEBUG my $idf= 'idmap-all.tsv'; if ( $tid =~ m/^([A-Za-z]+)/ ) { $idf= "idmap-$1.tsv"; } my $fh= $idfh->{$idf}; unless($fh) { my $sfile= catfile($dir, $idf); $fh= new FileHandle(">$sfile"); $idfh->{$idf}= $fh; } if ($fh) { print $fh "$tid\t$csome\t$start\t$stop\n"; $nd++; $didid{$idkey}++; } } } #close(FIN); return "makeAllIdmaps n=$nd\n"; } =cut 1; __END__ chado-1.23/lib/Bio/FeatureIO/chado.pm000644 000765 000024 00000003327 11256707755 017334 0ustar00cainstaff000000 000000 package Bio::FeatureIO::chado; use strict; use base qw(Bio::FeatureIO); use Bio::SeqIO; use Bio::Chado::LoadDBI; use Data::Dumper; sub _initialize { my($self,%arg) = @_; $self->SUPER::_initialize(%arg); $self->feature_count(0); $self->organism($arg{-organism} || 'Human'); $self->cachesize($arg{-cachesize} || 1000); } sub next_feature { shift->throw('this class only writes to database'); } sub write_feature { my($self,$feature) = shift; } =head2 cache Title : cache Usage : $obj->cache($newval) Function: cache an object for commit to db. when number of items in cache exceeds cachesize(), objects are flushed Example : Returns : value of cache (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub cache{ my $self = shift; my $val = shift; push @{ $self->{'cache'} }, $val if ref($val); if(scalar @{ $self->{'cache'} } > $self->cachesize){ $_->dbi_commit foreach @{ $self->{'cache'} }; @{ $self->{'cache'} } = (); } } =head2 cachesize Title : cachesize Usage : $obj->cachesize($newval) Function: number of features to cache before flushing to db Example : Returns : value of cachesize (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub cachesize{ my $self = shift; return $self->{'cachesize'} = shift if @_; return $self->{'cachesize'}; } =head2 organism Title : organism Usage : $obj->organism($newval) Function: organism of features being loaded Example : Returns : value of organism (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub organism{ my $self = shift; return $self->{'organism'} = shift if @_; return $self->{'organism'}; } 1; chado-1.23/lib/Bio/FeatureIO/chadobulk.pm000644 000765 000024 00000031221 11256707755 020204 0ustar00cainstaff000000 000000 package Bio::FeatureIO::chadobulk; use strict; use base qw(Bio::FeatureIO); use Bio::SeqIO; use Bio::GMOD::Config; use DBI; use Data::Dumper; my @TABLES = qw(db dbxref cvterm synonym feature featureloc featureprop feature_cvterm feature_dbxref feature_relationship feature_synonym ); #don't need contact, obj already handed to us #don't need organism, obj already handed to us #don't need pub, obj already handed to us sub _initialize { my($self,%arg) = @_; $self->SUPER::_initialize(%arg); $self->organism($arg{-organism}); $self->contact($arg{-contact}); $self->pub($arg{-pub}); #my $config = Bio::GMOD::Config->new(); #warn Dumper($config); $self->dbh(DBI->connect('dbi:Pg:host=soleus;dbname=chado_gec','allenday','allenday')); $self->setup(); } sub next_feature { shift->throw('this class only writes to database'); } sub write_feature { my($self,$feature) = @_; my $dbxref_id = "\\N"; my $organism_id = 1; #FIXME my $feature_id = $self->write_row_feature($feature); next unless $feature_id; $self->write_row_featureloc($feature , $feature_id); $self->write_row_feature_relationship($feature,$feature_id); } sub DESTROY { my $self = shift; $self->bulkload(); $self->cleanup(); } =head2 write_row_feature Title : write_row_feature Usage : Function: Example : Returns : Args : =cut sub write_row_feature{ my ($self,$feature) = @_; # Column | Type | Modifiers #------------------+-----------------------------+---------- # feature_id | integer | not null my $feature_id = $self->seq('feature'); # dbxref_id | integer | my $dbxref_id = '\\N'; # organism_id | integer | not null my $organism_id = 1; #FIXME #my $organism_id = $self->organism->id; # name | character varying(255) | my @names = map {$_->value} $feature->annotation->get_Annotations('Name'); my $name = $names[0]; if(scalar(@names) > 1){ $self->throw('feature can only have one Name, (this is a limitation in the loader and/or gff spec, not the file) but had: '.join(' ',@names)); } # uniquename | text | not null my @unames = map {$_->value} $feature->annotation->get_Annotations('ID'); my $uname = $unames[0]; if(defined($uname) and $self->feature_id($uname)){ my $saw = $self->feature_id($uname); $self->warn("already saw $uname, returning previous record $saw. FIXME we should still try to extract new attributes"); return $saw; } elsif(defined($uname)){ $self->feature_id($uname,$feature_id); } else { $uname = $feature->seq_id.':'.$feature->start.','.$feature->end; } if(scalar(@unames) > 1){ $self->throw('feature can only have one ID (this is a limitation in the loader and/or gff spec, not the file), but had: '.join(' ',@unames)); } $name ||= $uname; # residues | text | my $residues = '\\N'; # seqlen | integer | my $seqlen = '\\N'; # md5checksum | character(32) | my $md5 = '\\N'; # type_id | integer | not null my @types = map { $self->cvterm($_->name) } $feature->annotation->get_Annotations('feature_type'); my $type = $types[0]; if(scalar(@types) > 1){ $self->throw('feature can only have one type, but had: '.join(' ',@types)); } $self->throw("$feature has undefined feature_type, bailing out") unless $type; # is_analysis | boolean | not null my $is_analysis = 'F'; # timeaccessioned | timestamp without time zone | not null my $timeaccessioned = $self->now(); # timelastmodified | timestamp without time zone | not null my $timelastmodified = $self->now(); my $feature_fh = $self->file('feature'); print $feature_fh join("\t", $feature_id,$dbxref_id,$organism_id,$name,$uname, $residues,$seqlen,$md5,$type,$is_analysis, $timeaccessioned,$timelastmodified),"\n"; return $feature_id; } =head2 write_row_featureloc Title : write_row_featureloc Usage : Function: Example : Returns : Args : =cut sub write_row_featureloc{ my ($self,$feature,$feature_id) = @_; # Column | Type | Modifiers #-----------------+----------+----------------------------------------------------------------------- # featureloc_id | integer | not null my $featureloc_id = $self->seq('featureloc'); # feature_id | integer | not null #passed as arg # srcfeature_id | integer | my $srcfeature_id = $self->feature_id($feature->seq_id); return undef unless defined($srcfeature_id); # fmin | integer | my $fmin = $feature->start() || 0; # is_fmin_partial | boolean | not null my $is_fmin_partial = 'F'; # fmax | integer | my $fmax = $feature->end() + 1; # is_fmax_partial | boolean | not null my $is_fmax_partial = 'F'; # strand | smallint | my $strand = $feature->strand(); # phase | integer | my $phase = $feature->frame(); $phase = '\\N' if $phase eq '.'; # residue_info | text | my $residue_info = '\\N'; # locgroup | integer | not null my $locgroup = 0; # rank | integer | not null my $rank = $self->featureloc_rank($feature_id); my $featureloc_fh = $self->file('featureloc'); print $featureloc_fh join("\t", $featureloc_id,$feature_id,$srcfeature_id,$fmin,$is_fmin_partial, $fmax,$is_fmax_partial,$strand,$phase,$residue_info,$locgroup,$rank),"\n"; return $featureloc_id; } =head2 write_row_feature_relationship Title : write_row_feature_relationship Usage : Function: Example : Returns : Args : =cut sub write_row_feature_relationship{ my ($self,$feature,$feature_id) = @_; my $parent = ($feature->annotation->get_Annotations('Parent'))[0]; #warn $parent; return undef unless $parent; my $parent_id = $self->feature_id($parent->value()); my $part_of = $self->cvterm('part_of'); my $feature_relationship_id = $self->seq('feature_relationship'); my $fh = $self->file('feature_relationship'); print $fh join("\t", $feature_relationship_id,$feature_id,$parent_id,$part_of,'\\N',0 ),"\n"; } =head2 setup Title : setup Usage : $obj->setup() Function: Example : Returns : Args : =cut sub setup { my $self = shift; my $dbh = $self->dbh(); $dbh->begin_work(); $self->setup_seq(); $self->setup_files(); $self->now(); } =head2 cleanup Title : cleanup Usage : Function: Example : Returns : Args : =cut sub cleanup{ my $self = shift; $self->cleanup_seq(); $self->cleanup_files(); $self->dbh->commit(); } =head2 bulkload Title : bulkload Usage : Function: Example : Returns : Args : =cut sub bulkload{ my $self = shift; foreach my $t(@TABLES){ $self->file($t,"/tmp/$t.dat",2); #close } foreach my $t(@TABLES){ $self->file($t,"/tmp/$t.dat",3); #open for read } } =head2 now Title : now Usage : Function: Example : Returns : Args : =cut sub now{ my $self = shift; if(!$self->{'now'}){ my $dbh = $self->dbh; my $sth = $dbh->prepare('SELECT NOW()'); $sth->execute(); my($now) = $sth->fetchrow_array(); $self->{'now'} = $now; } return $self->{'now'}; } =head2 setup_files Title : setup_files Usage : Function: Example : Returns : Args : =cut sub setup_files{ my ($self,@args) = @_; foreach my $t(@TABLES){ $self->file($t,"/tmp/$t.dat",1); #open for write } } =head2 cleanup_files Title : cleanup_files Usage : Function: Example : Returns : Args : =cut sub cleanup_files{ my ($self,@args) = @_; foreach my $t(@TABLES){ $self->file($t,"/tmp/$t.dat",2); #close } } =head2 setup_seq Title : setup_seq Usage : Function: Example : Returns : Args : =cut sub setup_seq{ my $self = shift; my $dbh = $self->dbh(); foreach my $t (@TABLES){ $dbh->do("LOCK TABLE $t IN SHARE MODE"); $self->seq($t); } } =head2 cleanup_seq Title : cleanup_seq Usage : Function: Example : Returns : Args : =cut sub cleanup_seq{ my $self = shift; foreach my $t (@TABLES){ $self->seq($t,$self->seq($t)); } } =head2 seq Title : seq Usage : Function: Example : Returns : Args : =cut sub seq{ my($self,$seq,$val) = @_; my $seqname = sprintf("%s_%s_id_seq",$seq,$seq); my $dbh = $self->dbh(); if(defined($seq) && defined($val)){ $dbh->do("SELECT setval('public.$seqname',$val);") or die $dbh->errstr; } elsif(defined($seq) && !defined($self->{'seq'}{$seq})){ my $sth = $dbh->prepare("SELECT nextval(?);") or die $dbh->errstr; $sth->execute("public.$seqname"); my($nextval) = $sth->fetchrow_array(); $self->{'seq'}{$seq} = $nextval + 1; return $nextval; } else { my $return = $self->{'seq'}{$seq}; $self->{'seq'}{$seq}++; return $return; } } =head2 featureloc_rank Title : featureloc_rank Usage : Function: Example : Returns : Args : =cut sub featureloc_rank{ my ($self,$feature_id) = @_; my $r = $self->{'featureloc_rank'}{$feature_id} || 0; $self->{'featureloc_rank'}{$feature_id}++; return $r; } =head2 feature_id Title : feature_id Usage : Function: Example : Returns : Args : =cut sub feature_id{ my ($self,$id,$feature_id) = @_; if(defined($feature_id)){ $self->{'feature_id'}{$id} = $feature_id; } elsif(!defined($self->{'feature_id'}{$id})){ #do dbi lookup and cache here if(!$self->{'feature_id_sth'}){ my $dbh = $self->dbh(); $self->{'feature_id_sth'} = $dbh->prepare('select feature_id from feature where name = ?'); } $self->{'feature_id_sth'}->execute($id); $self->throw("too many records for $id") if $self->{'feature_id_sth'}->rows() > 1; my($x) = $self->{'feature_id_sth'}->fetchrow_array(); $self->{'feature_id'}{$id} = $x; } return $self->{'feature_id'}{$id}; } =head2 file Title : file Usage : Function: Example : Returns : Args : =cut sub file{ my ($self,$table,$file,$action) = @_; if(defined($action)){ if($action == 1){ #open for write open(my $h, ">$file") or $self->throw($!); $self->{'fh'}{$table} = $h; } elsif($action == 2){ #close close($self->{'fh'}{$table}) or $self->throw($!); } elsif($action == 3){ #open for read open(my $h, $file) or $self->throw($!); $self->{'fh'}{$table} = $h; } else { $self->throw('no such action'); } } elsif(defined($table)){ return $self->{'fh'}{$table}; } else { return undef; } } =head2 cvterm Title : cvterm Usage : $obj->cvterm() Function: Example : Returns : Args : =cut sub cvterm { my $self = shift; my $name = shift; if(!$self->{'cvterm_sth'}){ my $dbh = $self->dbh; #FIXME this does not handle SO:xxxxxxx identifiers from dbxref, which requires an OUTER JOIN query my $sth = $dbh->prepare("select cvterm_id from cvterm c,dbxref d where c.name = ?;"); $self->{'cvterm_sth'} = $sth; } if(!$self->{'cvterm'}{$name}){ $self->{'cvterm_sth'}->execute($name); my $id = $self->{'cvterm_sth'}->fetchrow_array(); $self->throw("couldn't find cvterm for $name") unless defined($id); $self->{'cvterm'}{$name} = $id; } return $self->{'cvterm'}{$name}; } =head2 dbh Title : dbh Usage : $obj->dbh($newval) Function: Example : Returns : value of dbh (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub dbh{ my $self = shift; return $self->{'dbh'} = shift if @_; return $self->{'dbh'}; } =head2 contact Title : contact Usage : $obj->contact($newval) Function: Example : Returns : value of contact (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub contact{ my $self = shift; return $self->{'contact'} = shift if @_; return $self->{'contact'}; } =head2 organism Title : organism Usage : $obj->organism($newval) Function: Example : Returns : a Bio::Chado::CDBI::Organism object Args : a Bio::Chado::CDBI::Organism object =cut sub organism{ my $self = shift; return $self->{'organism'} = shift if @_; return $self->{'organism'}; } =head2 pub Title : pub Usage : $obj->pub($newval) Function: Example : Returns : value of pub (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub pub{ my $self = shift; return $self->{'pub'} = shift if @_; return $self->{'pub'}; } 1; chado-1.23/lib/Bio/Chado/Builder.pm000644 000765 000024 00000040077 11730001552 017015 0ustar00cainstaff000000 000000 # $Id: Builder.pm,v 1.1 2009-09-01 13:55:13 scottcain Exp $ package Bio::Chado::Builder; # vim: set ft=perl ts=2 expandtab: use strict; use warnings; use base 'Module::Build'; use Carp; use Data::Dumper; use File::Spec::Functions 'catfile'; use File::Path; use File::Copy; use Data::Dumper; use Template; use XML::Simple; use LWP::Simple qw(mirror is_success status_message); use DBI; use IPC::Cmd (); use Scalar::Util qw(looks_like_number); my $DEBUG = 0; my $go2fmt = IPC::Cmd::can_run('go2fmt') ? 'go2fmt' : 'go2fmt.pl'; #< detect new version of go2fmt =head1 ACTIONS =item update() Checks an existing default Chado schema to determine its version and attempts to update it to the current release. =item prepdb() Calls the psql command and pipes in the contents of the load/etc/initialize.sql file. Put any insert statements that your data load needs here. Also executes gmod_add_organism.pl if the common_name provided in the perl Makefile.PL step isn't present in the database. =item ncbi() Load action for all NCBI data. =item mageml() fixfixfix =item ontologies() loads ontologies by running gmod_load_ontology.pl on all files in $(DATA)/ontology =item tokenize() processes templates specified in configuration file, filling in platform-specific variable values =item _last =cut =head2 ACTION_prepdb Title : ACTION_prepdb Usage : Function: Executes any SQL statements in the load/etc/initialize.sql file. Example : Returns : Args : =cut sub ACTION_prepdb { # the build object $m my $m = shift; # the XML config object my $conf = $m->conf; my $db_name = $conf->{'database'}{'db_name'} || ''; my $db_host = $conf->{'database'}{'db_host'} || ''; my $db_port = $conf->{'database'}{'db_port'} || ''; my $db_user = $conf->{'database'}{'db_username'} || ''; my $build_dir = $conf->{'build'}{'working_dir'} || ''; my $schema_version = $m->dist_version; my $init_sql = catfile( $build_dir, 'load', 'etc', 'initialize.sql' ); my $sys_call = "psql -h $db_host -p $db_port -U $db_user -f $init_sql $db_name"; warn "system call: $sys_call" if $DEBUG; system( $sys_call ) == 0 or croak "Error executing '$sys_call': $?"; warn "Checking for organism" if $DEBUG; my $db_org = $conf->{'database'}{'db_organism'}; if ($db_org and $db_org ne 'none' and ref $db_org ne 'HASH') { my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`; unless ($result) { print "Adding $db_org to the database...\n"; system('bin/gmod_add_organism.pl','--common_name',$db_org); } } #set the chado schema version in the database system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); } =head2 ACTION_update Title : ACTION_update Usage : Function: Attempts to update an existing Chado schema Example : Returns : Args : =cut sub ACTION_update { # the build object $m my $m = shift; # the XML config object my $conf = $m->conf; my $db_name = $conf->{'database'}{'db_name'} || ''; my $db_host = $conf->{'database'}{'db_host'} || ''; my $db_port = $conf->{'database'}{'db_port'} || ''; my $db_user = $conf->{'database'}{'db_username'} || ''; my $build_dir = $conf->{'build'}{'working_dir'} || ''; my $schema_version = $m->dist_version; my $version = `gmod_chado_properties.pl --dbprofile $db_name --version`; chomp $version; if (looks_like_number($version) and $version < $schema_version) { print "Attempting schema update.\n"; system("gmod_update_chado.pl --dbprofile $db_name"); } elsif (looks_like_number($version) and $version >= $schema_version) { print "No update necessary.\n"; } else { print "Unable to determine schema version; exiting...\n"; } } =head2 ACTION_ncbi Title : ACTION_ncbi Usage : Function: Load action for all NCBI data. Example : Returns : Args : =cut sub ACTION_ncbi { # the build object $m my $m = shift; # the XML config object my $conf = $m->conf; # print out the available refseq datasets my %ncbis = printAndReadOptions($m,$conf,"ncbi"); # now that I know what you want mirror files and load # fetchAndLoadFiles is called for each possible type # but only actively loaded for those the user selects fetchAndLoadFiles($m, $conf, "refseq", "./load/bin/load_gff3.pl --organism Human --srcdb DB:refseq --gfffile", \%ncbis); fetchAndLoadFiles($m, $conf, "locuslink", "./load/bin/load_locuslink.pl", \%ncbis); } sub ACTION_mageml { my $m = shift; my $conf = $m->conf; print "Available MAGE-ML annotation files:\n"; my $i = 1; my %ml = (); foreach my $mageml ( sort keys %{ $conf->{mageml} } ) { $ml{$i} = $mageml; print "[$i] $mageml\n"; $i++; } print "\n"; my $chosen = $m->prompt( "Which ontologies would you like to load (Comma delimited)? [0]" ); $m->notes( 'affymetrix' => $chosen ); my %mageml = map { $ml{$_} => $conf->{mageml}{ $ml{$_} } } split ',', $chosen; foreach my $mageml ( keys %mageml ) { print "fetching files for $mageml\n"; my $load = 0; foreach my $file ( @{ $mageml{$mageml}{file} } ) { my $fullpath = catfile $conf->{path}{data}, $file->{local}; $fullpath =~ s!^(.+)/[^/]*!$1!; unless ( -d $fullpath ) { warn "mkpath $fullpath" if $DEBUG; mkpath( $fullpath, 0, 0711 ) or print "Couldn't make path '$fullpath': $!\n"; } print " +", $file->{remote}, "\n"; $load = 1 if $m->_mirror( $file->{remote}, $file->{local} ); $load = 1 unless $m->_loaded( $fullpath ); next unless $load; print " loading..."; my $sys_call = "./load/bin/load_affymetrix.pl $fullpath"; warn "system call: $sys_call" if $DEBUG; my $result = system( $sys_call ); if ( $result != 0 ) { die "failed: $!\n"; } else { $m->_loaded( $fullpath, 1 ); print "done!\n"; } } } } sub ACTION_ontologies { my $m = shift; my $conf = $m->conf; my $db_name = $conf->{'database'}{'db_name'} || ''; my $db_host = $conf->{'database'}{'db_host'} || ''; my $db_port = $conf->{'database'}{'db_port'} || ''; my $db_user = $conf->{'database'}{'db_username'} || ''; my $db_pass = $conf->{'database'}{'db_password'} || ''; $db_pass = '' if (ref $db_pass eq 'HASH'); print "Available ontologies:\n"; my %ont = (); foreach my $ontology ( keys %{ $conf->{ontology} } ) { $ont{ $conf->{ontology}->{$ontology}->{order} } = $ontology; } foreach my $key ( sort {$a <=> $b} keys %ont ) { print "[$key] ", $ont{$key}, "\n"; } print "\n"; my $chosen = $m->prompt("Which ontologies would you like to load (Comma delimited)? [0]"); $m->notes( 'ontologies' => $chosen ); my %ontologies = map { $_ => $conf->{ontology}{ $ont{$_} } } split ',', $chosen; foreach my $ontology ( sort {$a <=> $b} keys %ontologies ) { print "fetching files for ", $ont{$ontology}, "\n"; my $file = $ontologies{$ontology}{file}; my $load = 0; foreach my $file ( grep { $_->{type} eq 'definitions' } @{ $ontologies{$ontology}{file} } ) { my $fullpath = catfile($conf->{path}{data}, $file->{local}); $fullpath =~ s!^(.+)/[^/]*!$1!; unless ( -d $fullpath ) { warn "mkpath $fullpath" if $DEBUG; mkpath( $fullpath, 0, 0711 ) or print "Couldn't make path '$fullpath': $!\n"; } if ($file->{method} =~ /mirror/) { print " +", $file->{remote}, "\n"; $load = 1 if $m->_mirror( $file->{remote}, $file->{local} ); } else { # it is a local file copy( $file->{remote} , $fullpath ); $load = 1; } } my ($deffile) = grep { $_ if $_->{type} eq 'definitions' } @{ $ontologies{$ontology}{file} }; foreach my $file ( grep { ($_->{type} eq 'ontology') or ($_->{type} eq 'obo') } @{ $ontologies{$ontology}{file} } ) { my $fullpath = catfile($conf->{path}{data}, $file->{local}); $fullpath =~ s!^(.+)/[^/]*!$1!; unless ( -d $fullpath ) { warn "mkpath $fullpath" if $DEBUG; mkpath( $fullpath, 0, 0711 ) or print "Couldn't make path '$fullpath': $!\n"; } print " +", $file->{remote}, "\n"; if ($file->{method} =~ /mirror/) { $load = 1 if $m->_mirror( $file->{remote}, $file->{local} ); } else { #local file copy( $file->{remote}, $fullpath ); $load = 1; } next unless $load; print " loading..."; # my $sys_call = join( ' ', # './load/bin/gmod_load_ontology.pl', # catfile( $conf->{'path'}{'data'}, $file->{'local'} ), # catfile( $conf->{'path'}{'data'}, $deffile->{'local'} ) # ); #creating chadoxml from either obo or ontology files my $sys_call; if ($file->{type} eq 'obo') { $sys_call = join( ' ', $go2fmt, '-p obo_text -w xml', catfile( $conf->{'path'}{'data'}, $file->{'local'}), '| go-apply-xslt oboxml_to_chadoxml - >', catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml') ); } elsif ($file->{type} eq 'ontology') { $sys_call = join( ' ', $go2fmt, '-p go_ont -w xml', catfile( $conf->{'path'}{'data'}, $file->{'local'}), '| go-apply-xslt oboxml_to_chadoxml - >', catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml') ); } else { die "what kind of file is ".$_->{type}."?"; } warn "system call: $sys_call" if $DEBUG; my $result = system( $sys_call ); if ( $result != 0 ) { print "System call '$sys_call' failed: $?\n"; die "failed: $?"; } # loading chadoxml my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'"; $stag_string .= " --user $db_user " if $db_user; $stag_string .= " --password '$db_pass' " if $db_pass; $sys_call = join( ' ', $stag_string, catfile( $conf->{'path'}{'data'}, $file->{'local'}.'xml') ); warn "system call: $sys_call" if $DEBUG; $result = system( $sys_call ); if ( $result != 0 ) { print "System call '$sys_call' failed: $?\n"; die "failed: $?"; } if ($deffile) { $sys_call = join( ' ', $go2fmt, '-p go_def -w xml', catfile( $conf->{'path'}{'data'}, $deffile->{'local'}), '| go-apply-xslt oboxml_to_chadoxml - >', catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml') ); warn "system call: $sys_call" if $DEBUG; $result = system( $sys_call ); if ( $result != 0 ) { print "System call '$sys_call' failed: $?\n"; die "failed: $?"; } $sys_call = join( ' ', "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'", catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml') ); warn "system call: $sys_call" if $DEBUG; $result = system( $sys_call ); } if ( $result != 0 ) { print "System call '$sys_call' failed: $?\n"; die "failed: $?"; } else { $m->_loaded( catfile($conf->{'path'}{'data'}, $file->{'local'}), 1 ); $m->_loaded( catfile($conf->{'path'}{'data'}, $deffile->{'local'}), 1 ) if $deffile; print "done!\n"; warn "done!" if $DEBUG; } } } } sub ACTION_tokenize { my $m = shift; my $conf = $m->conf; my $template = Template->new( { INTERPOLATE => 0, RELATIVE => 1, } ) || die "Template error: $Template::ERROR" ; foreach my $templatefile ( keys %{ $conf->{template}{file} } ) { #there is an order of preference in which keys are added. #this affects which config sections clobber which others, beware. my $tokens = {%{$conf->{database}}, %{$conf->{build}}}; if(ref($conf->{template}{file}{$templatefile}) eq 'HASH'){ $tokens->{ $_ } = $conf->{template}{file}{$templatefile}{$_} foreach keys %{ $conf->{template}{file}{$templatefile}}; } #knock out empty hashes (like undef db_password) foreach my $token (keys %{$tokens}){ undef($tokens->{$token}) if(ref($tokens->{$token}) eq 'HASH' and !keys %{$tokens->{$token}}); } my $tokenized; warn Dumper($tokens) if $DEBUG; $template->process( $conf->{template}{file}{$templatefile}{in}, $tokens, \$tokenized, ) || die "Template error: " . $template->error() ; open( OUT, '>' . $conf->{template}{file}{$templatefile}{out} ); print OUT $tokenized; close(OUT); } } =head1 NON-ACTIONS =cut =head2 fetchAndLoadFiles Title : fetchAndLoadFiles Usage : fetchAndLoadFiles(, , ...) Function: Calls internal methods to mirror files specified for this file_type in the xml_conf_obj Example : Returns : Args : =cut sub fetchAndLoadFiles { my ( $m, $conf, $type, $command, $itm ) = @_; foreach my $key ( keys %$itm ) { print "fetching files for $key\n"; my $load = 0; foreach my $file ( @{ $itm->{$key}{file} } ) { # check to see if this command can handle this type if ( $file->{type} eq $type ) { my $fullpath = catfile( $conf->{path}{data}, $file->{local}); $fullpath =~ s!^(.+)/[^/]*!$1!; unless ( -d $fullpath ) { warn "mkpath $fullpath" if $DEBUG; mkpath( $fullpath, 0, 0711 ) or print "Couldn't make path '$fullpath': $!\n"; } print " +", $file->{remote}, "\n"; $load = 1 if $m->_mirror( $file->{remote}, $file->{local} ); $load = 1 unless $m->_loaded( $fullpath ); next unless $load; print " loading..."; my $sys_call = join( ' ', $command, $fullpath ); warn "system call: $sys_call" if $DEBUG; my $result = system( $sys_call ); if ( $result != 0 ) { print "failed: $!\n"; die "failed: $!"; } else { $m->_loaded( $fullpath, 1 ); print "done!\n"; warn "done!" if $DEBUG; } } } } } =head2 printAndReadOptions Title : printAndReadOptions Usage : prints out and reads options from the XML file Function: Example : Returns : Args : m=build obj, conf=conf obj, option=which option to pull from the conf XML file =cut sub printAndReadOptions { my ($m,$conf,$option) = @_; print "Available $option Items:\n"; my $i = 1; my %itm = (); foreach my $item (sort keys %{ $conf->{$option} }) { $itm{$i} = $item; print "[$i] $item\n"; $i++; } print "\n"; my $chosen = $m->prompt("Which items would you like to load (Comma delimited)? [0]"); $m->notes("$option"."s" => $chosen); my %options = map {$itm{$_} => $conf->{$option}{$itm{$_}}} split ',',$chosen; return(%options); } sub property { my $m = shift; my $key = shift; my $val = $m->{properties}{$key}; $val =~ s/^$key=//; return $val; } sub conf { my $self = shift; return $self->{conf} if defined $self->{conf}; my $file = $self->property('load_conf'); $self->{conf} = XMLin($file, ForceArray => ['token','path','file'], KeyAttr => [qw(tt2 input token name file)], ContentKey => '-value' ); return $self->{conf}; } sub _loaded { my $m = shift; my $conf = $m->conf; my ( $file, $touch ) = @_; $file .= '_' . $conf->{'build'}{'load_touchext'}; if ($touch) { open( T, '>' . $file ); print T "\n"; close(T); return 1; } else { return 1 if -f $file; return 0; } } sub _mirror { my $m = shift; my $conf = $m->conf; my ($remote,$local) = @_; $local = $conf->{'path'}{'data'} .'/'. $local; if( $m->_loaded($local) ){ print " already loaded, remove touchfile to reload. skipping\n"; return 0; } #mirror the file my $rc = mirror($remote, $local); if ($rc == 304) { print " ". $local ." is up to date\n"; return 0; } elsif (!is_success($rc)) { print " $rc ", status_message($rc), " (",$remote,")\n"; return 0; } else { #file is new, load it print " updated\n"; return 1; } } 1; chado-1.23/lib/Bio/Chado/Config.pm000644 000765 000024 00000005023 11256707760 016645 0ustar00cainstaff000000 000000 package Bio::Chado::Config; =head1 NAME Chado::Config =head1 SYNOPSIS my $config = Bio::Chado::Config->new; my $db_name = $config->{'database'}{'db_name'}; =head1 DESCRIPTION This module is a simple interface to the Chado installation configuration information. =head1 METHODS =cut use strict; use Carp; use FindBin '$Bin'; use File::Spec::Functions; use XML::Simple; use constant DEFAULT_FILENAME => catfile( $Bin, 'load', 'etc', 'load.conf' ); # --------------------------------------------------------- =pod =head2 new Instantiates a new object. Takes an optional (but preferred) argument of the configuration file's path. The filename should be indicated as a key/value pair, but, if only one argument is passed in, it is assumed to be the filename. my $conf = Bio::Chado::Config->new; my $conf = Bio::Chado::Config->new( ); my $conf = Bio::Chado::Config->new( filename => ); =cut sub new { my $class = shift; my $args = defined $_[0] && UNIVERSAL::isa( $_[0], 'HASH' ) ? shift : scalar @_ == 1 ? { filename => shift } : { @_ }; my $self = bless {}, $class; if ( $args->{'filename'} ) { $self->filename( $args->{'filename'} ); } return $self; } # --------------------------------------------------------- =pod =head2 filename Gets/sets the location of the configuration file. my $file = $conf->filename( ); =cut sub filename { my ( $self, $arg ) = @_; if ( ! defined $self->{'filename'} && ! $arg ) { $arg = DEFAULT_FILENAME if -e DEFAULT_FILENAME; } if ( $arg ) { if ( -e $arg && -r _ ) { $self->{'filename'} = $arg; } else { croak("The file '$arg' does not exist or is not readable"); } } return $self->{'filename'}; } # --------------------------------------------------------- =pod =head2 config Returns the configuration information as parsed by XML::Simple. my $options = $conf->config; =cut sub config { my $self = shift; unless ( defined $self->{'config'} ) { my $file = $self->filename; $self->{'config'} = XMLin( $file, # ForceArray => [ qw( template token path file) ], # KeyAttr => [ qw( token name file) ], ContentKey => '-value', ); } return $self->{'config'}; } # --------------------------------------------------------- =pod =head1 SEE ALSO XML::Simple. =head1 AUTHOR Ken Y. Clark Ekclark@cshl.orgE. =cut 1; chado-1.23/install_util/conf_install.PLS000644 000765 000024 00000005361 11650032501 020326 0ustar00cainstaff000000 000000 #!perl use Config; use File::Basename qw(&basename &dirname); use Cwd; $origdir = cwd; chdir dirname($0); $file = basename($0, '.PL','.PLS'); $file .= $^O eq 'VMS' ? '.com' : '.pl'; open OUT,">$file" or die "Can't create $file: $!"; print "Extracting $file (with variable substitutions)\n"; print OUT "$Config{startperl}\n"; print OUT <<'!NO!SUBS!'; use strict; use Cwd; use FindBin '$Bin'; foreach (@ARGV) { $_ =~ s/^\'(.*)\'$/$1/; } my %options = map {split /=/} @ARGV; my $gmod_root = $options{GMOD_ROOT}; my $version = $options{VERSION}; my $confdir = "$gmod_root/conf"; my $tmpdir = "$gmod_root/tmp"; my $origdir = cwd; my $homedir = "$Bin/.."; chdir $homedir or die "couldn't cd to $homedir: $!\n"; # create GMOD_ROOT and conf dir if they dont already exist if (! (-e $gmod_root)) { mkdir($gmod_root, 0777) or die "unable to make $gmod_root directory"; } if (! (-e $confdir)) { mkdir($confdir, 0777) or die "unable to make $confdir directory"; } if (! (-e $tmpdir)) { mkdir($tmpdir, 0777) or die "unable to make $tmpdir directory"; chmod 0777, $tmpdir; } my $localconf = 'build.conf'; my %confitems; open LOCALCONF, $localconf or die "unable to open $localconf: $!"; while () { chomp; my ($key, $value) = split /=/; if ($key =~ /^DB/ or $key eq 'DEFAULT' or $key eq 'SCHEMA') { $confitems{$key} = $value; } } close LOCALCONF; my $gmodconf = "$confdir/gmod.conf"; my $defaultconf = "$confdir/default.conf"; my $dbconf = "$confdir/$confitems{DBNAME}.conf"; open GMODCONF, ">$gmodconf" or die "unable to open $gmodconf: $!"; print GMODCONF "CONF=$gmod_root/conf\n"; print GMODCONF "TMP=$gmod_root/tmp\n"; print GMODCONF "VERSION=$version\n"; close GMODCONF; open DBCONF, ">$dbconf" or die "unable to open $dbconf: $!"; foreach my $key (keys %confitems) { print DBCONF "$key=$confitems{$key}\n"; } print DBCONF "SQLFILE=$gmod_root/src/chado/modules/complete.sql\n"; close DBCONF; if (lc($confitems{'DEFAULT'}) =~ /^y/) { unlink $defaultconf; symlink($dbconf,$defaultconf); } chdir $origdir; !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':'; chdir $origdir; chado-1.23/install_util/install.pm000644 000765 000024 00000003332 11256707707 017316 0ustar00cainstaff000000 000000 use strict; use Carp 'croak'; use File::Basename qw( basename fileparse ); use IO::Dir; use lib "../lib"; use Bio::GMOD::Config; sub copy_tree { my ($src,$dest) = @_; if (-f $src) { copy_no_substitutions($src,$dest) or die "copy_with_substitutions($src,$dest): $!"; return 1; } croak "$src doesn't exist" unless -e $src; croak "Usage: copy_tree(\$src,\$dest). Can't copy a directory into a file or vice versa" unless -d $src && -d $dest; croak "Can't read from $src" unless -r $src; croak "Can't write to $dest" unless -w $dest; my $tgt = basename($src); # create the dest if it doesn't exist mkdir ("$dest/$tgt",0777) or die "mkdir($dest/$tgt): $!" unless -d "$dest/$tgt"; my $d = IO::Dir->new($src) or die "opendir($src): $!"; while (my $item = $d->read) { # bunches of things to skip next if $item eq 'CVS'; next if $item =~ /^\./; next if $item =~ /~$/; next if $item =~ /^\#/; if (-f "$src/$item") { copy_no_substitutions("$src/$item","$dest/$tgt") or die "copy_with_substitutions('$src/$item','$dest/$tgt'): $!"; } elsif (-d "$src/$item") { copy_tree("$src/$item","$dest/$tgt"); } } 1; } sub copy_no_substitutions { my ($localfile,$install_file) = @_; open (IN,$localfile) or warn "Couldn't open $localfile: $!"; my $basename = basename($localfile); my $dest = -d $install_file ? "$install_file/$basename" : $install_file; open (OUT,">$dest") or die "Couldn't open $install_file for writing: $!"; if (-T IN) { while () { print OUT; } } else { binmode OUT; my $buffer; print OUT $buffer while read(IN,$buffer,5000); } close OUT; close IN; } 1; chado-1.23/install_util/src_install.PLS000644 000765 000024 00000003462 11627460434 020206 0ustar00cainstaff000000 000000 #!perl use Config; use File::Basename qw(&basename &dirname); use Cwd; $origdir = cwd; chdir dirname($0); $file = basename($0, '.PL','.PLS'); $file .= $^O eq 'VMS' ? '.com' : '.pl'; open OUT,">$file" or die "Can't create $file: $!"; print "Extracting $file (with variable substitutions)\n"; print OUT "$Config{startperl}\n"; print OUT <<'!NO!SUBS!'; use strict; use Cwd; use FindBin '$Bin'; use lib './lib'; use Bio::GMOD::Config; use lib './install_util'; use install; my $origdir = cwd; my $homedir = "$Bin/.."; my $arg; if ($ARGV[0]) { $ARGV[0] =~ /GMOD_ROOT\=(.+)/; $arg = $1; } my $conf = Bio::GMOD::Config->new($arg); my $gmod_root = $conf->gmod_root(); $gmod_root ||= '/usr/local/gmod'; my $src_dir = "$gmod_root/src/chado"; chdir $homedir or die "couldn't cd to $homedir: $!\n"; if (! (-e "$gmod_root/src") ) { mkdir ("$gmod_root/src", 0777) or die "unable to mkdir $gmod_root/src: $!\n"; } if (! (-e $src_dir) ) { mkdir ($src_dir, 0777) or die "unable to mkdir $src_dir: $!\n"; } copy_tree('modules',$src_dir); copy_tree('schemas',$src_dir); chdir $origdir; !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':'; chdir $origdir; chado-1.23/doc/about-gff2biomart.pod000644 000765 000024 00000004127 11256707521 017367 0ustar00cainstaff000000 000000 =head1 NAME gff2biomart.pl -- create tables for BioMart from genome GFF annotations =head1 EXAMPLE BioMart : DroSpeGe BioMart : DroSpeGe provides a tool for mining homologies and annotations of [twelve] Drosophila species genomes. You can select genome regions with the available annotations, and exclude others, and download tables or sequences of the selection set. For instance, select the regions with Mosquito gene homologs, but no D. melanogaster gene homologs. Or select regions with gene predictions but no known homolog. DroSpeGe's BioMart is built with the GMOD Tool gff2biomart.pl It converts most genome GFF annotations into a BioMart datamine. Example data sets from this tool are at http://insects.eugenes.org/BioMart/martview =head1 OUTPUTS The script generates table .sql, .txt and .xml suited to BioMart (MySQL, BioMart version 0.3 tested). It is a simple script without special requirements, basically a data transformer that writes new files formatted for a BioMart database. Components created 1. chromosome region__main tables for biomart with chromosomes broken into Kb bins/regions (5Kb default) Features that overlap each region are tabulated. 2. per-feature feature__dm link tables store feature attributes (id,dbxref,match stats,..) add __main column feature_bool to indicate where features lie. 3. __chromosome__dm with dna residues for fasta output 4. main_biomart.xml and sequence_biomart.xml configurations for biomart usage. =head1 IN BIOMART -- filter (include,exclude) features that exist in regions, including joint filters (has homology to human but not to fly or worm genes; has predicted gene but not homology; any such feature type comparison). -- output 4 kinds of attributes: a feature table, per-feature sequence, region table, per-region sequence. Please have installed and used BioMart before trying to load the outputs of this. =head1 VERSION This is a alpha-level, not yet fully tested. =head1 WHERE This will be part of a GMODTools release. Find the pre-release script at http://eugenes.org/gmod/GMODTools/ =cut chado-1.23/doc/COPYRIGHT000644 000765 000024 00000002772 11256707521 014650 0ustar00cainstaff000000 000000 Copyright (c) 2004, Indiana University All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Indiana University, Bloomington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. chado-1.23/doc/css/000755 000765 000024 00000000000 12061672375 014140 5ustar00cainstaff000000 000000 chado-1.23/doc/examples/000755 000765 000024 00000000000 12061672376 015167 5ustar00cainstaff000000 000000 chado-1.23/doc/gff2biomart-update.note000644 000765 000024 00000001212 11256707521 017712 0ustar00cainstaff000000 000000 http://gmod.cvs.sourceforge.net/gmod/schema/GMODTools/bin/gff2biomart5.pl This converts genome GFF annotations into BioMart-compliant tables and the XML interface. The caveat is that I haven't yet updated it from version 0.3 of biomart to later releases. This isn't as bad as might be, as the primary biomart-table output is usable with later releases. It is the BioMart configurations (XML probably, metadata table surely) which need changes for the later versions. You can instead use the BioMart martj editor to create these configurations. I.e. it isn't as automatic as it could be, yet. I will be updating gff2biomart this summer. - Don chado-1.23/doc/gmod-tools-readme.pod000644 000765 000024 00000027466 11256707521 017407 0ustar00cainstaff000000 000000 =head1 SYNOPSIS GMODTools is a collection of perl scripts and modules for use with GMOD Chado genome databases, primarily at this point for loading and extracting sequences and annotations. bulkfiles.pl is command-line program for Bio::GMOD::Bulkfiles This program generates bulk genome annotation files from a Chado genome database, including Fasta, GFF, DNA, Blast indices, a standard genome webpage, and Chado database overview tables. gff2biomart.pl creates tables for BioMart from genome GFF annotations. It generates table .sql, .txt and .xml suited to BioMart. With such a BioMart dataset you can select genome regions with the available annotations, and exclude others, and download feature tables or sequences of the selection set. For instance, select the regions with Mosquito gene homologs, but no D. melanogaster gene homologs. Or select regions with gene predictions but no known homolog. Other sequence functions are in library module GMOD::Chado::SeqUtils -- common methods for these chado seq scripts with main programs in bin/ folder as summarized below. ====================================================================== =head1 NAME bulkfiles.pl -- command-line program for Bio::GMOD::Bulkfiles =head1 SYNOPSIS This program generates bulk genome annotation files from a Chado genome database, including Fasta, GFF, DNA, Blast indices, a standard genome webpage, Chado database overview tables. # get bulkfiles software curl -O http://eugenes.org/gmod/GMODTools/GMODTools-1.0.zip unzip GMODTools-1.0.zip -- OR from CVS repository -- cvs -d :pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod \ co -d GMODTools schema/GMODTools # load a genome chado db to Postgres database curl -O http://sgdlite.princeton.edu/download/sgdlite/sgdlite.sql.gz createdb sgdlite (gunzip -c sgdlite.sql.gz | psql -d sgdlite -f - ) >& log.load # extract bulk files from database cd GMODTools perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make To create a new genome database release configuration see conf/bulkfiles/bulkfiles_template.xml For example output, see http://insects.eugenes.org/genome/ ====================================================================== =head1 NAME Bio::GMOD::Bulkfiles -- produce bulk sequence and feature files from Chado genome database for public distribution. =head1 ABOUT Bulkfiles This generates Fasta, GFF, DNA and other bulk genome annotation files at ftp://flybase.net/genomes/Drosophila_melanogaster/current/ .. (and other species) It works with several FlyBase chado dbs, and with SGDLite chado db Bulkfiles is mostly self-contained, but uses a few BioPerl parts plus XML::Simple for configuration files. All of the organism/database-specific logic should be in these configuration files (see GMODTools/conf/bulkfiles/) fbbulk-r4.xml, sgdbulk1.xml .. -- organism/database/release specific options chadofeatsql.xml -- chado db sql calls to dump features chadofeatconv.xml -- feature conversion options =head1 UPDATES 2008-June, version 1.2b - Rationalized -strand, revcomp usage for CDS-Exons. Problems were caused in this by Bioperl version changes (in Location/Split and Seq/LargPrimarySeq). Now Bulkfiles handles -strand, multi-exon CDS in a direct way, hopefully independent of Bioperl version changes. =head1 UPDATES 2008-May, version 1.2 - adding (in progress) Genbank Submission table writer, 'bulkfiles -format=genbanktbl', with output suited to submit to NCBI as per these specifications http://www.ncbi.nlm.nih.gov/Genbank/eukaryotic_genome_submission.html -- adding Genbank2Chado database xml configs for testing (anogam,...) - improvements (in progress) in chado sql efficiency (table joins mostly can be a problem w/ large dbs). =head1 UPDATES 2007-Oct, version 1.1 - No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default). - Gene Ontology association file, see go_association tags in configurations formatted as http://geneontology.org/GO.format.annotation.shtml - Validate main variables in chado database: ${golden_path}, ${seq_ontology} This step, on now by default, checks that database contains values set in configuration for chromosome type, sequence ontology CV name, and any other critical variables. If failed, db is inspected for real values. - miscellany bugs cured and configuration updates. tables/overview now again active. =head1 OUTPUTS DNA files (full chromosomes) in raw and fasta formats GFF (v3) feature files FFF (v1) feature files (used in FlyBase, each complex feature one line using GenBank/EMBL locations) Fasta sequence for each selected feature set, with headers from feature files BLAST Index files (NCBI) Chado database overview tables. A standard genome webpage for access to bulk data. =head1 USAGE use Bio::GMOD::Bulkfiles; my $bulkfiles= Bio::GMOD::Bulkfiles->new( configfile => 'fbbulk-r4', # data-release config file, required param debug => 1, showconfig => 0, failonerror => 1, ); $bulkfiles->dumpFeatures(); # extract feature tables from chado sql db $bulkfiles->sortNSplitByChromosome(); # collate and separate by chromosome $bulkfiles->dumpChromosomeBases(); # extract chromosome dna files # produce various output format bulk files from above my $result= $bulkfiles->makeFiles( formats => [qw(fff gff fasta blast gnomap)], chromosomes => [qw(all)] ); =head1 WHY Bulkfiles? (rather than using other middleware layers to chado db - chadoxml, chadodbi, bioperl, ...) The general logic is 1. dump all chado db features using simple (and quick) sql, to common intermediate table files, and chromosome dna to raw files. The feature info is simple: type, location, name/id, and a few attributes (db_xrefs,..) 2. postprocess these table files to create the various public use formats (the time-consuming and configurable part), organized into per-chromosome files. Here are some reasons we take this approach: a. using simple sql to dump all db features to intermediate table allows easy checks that all features get to bulk files b. simple sql dump is fast (30 - 60 min for full fly genome), reliable in getting all mapped features by keeping logic simple c. process table output in stages - better debugging of steps in process, and can split processing among computers c1. the stages are loosely coupled - one can go back, tweek configurations and get a new output w/o redoing the complete extraction process. d. convert one common feature table + dna to several output formats in one step, or repeatedly as needed. e. combine features from several chado dbs (flybase now has 3 chado dbs for d.mel genome features), and add other sources like flybase cytology features. f. need fairly complex and data specific configurations - moving that to config files keeps code reusable. g. each genome chado database has different policy and choices with respect to feature, vocabulary and other data. A highly configurable tool, with data extraction and correction methods that are separate and tunable is needed to adapt to such variation in genome databases. ========================================================================== =head1 NAME gff2biomart.pl -- create tables for BioMart from genome GFF annotations =head1 EXAMPLE BioMart : DroSpeGe BioMart : DroSpeGe provides a tool for mining homologies and annotations of [twelve] Drosophila species genomes. You can select genome regions with the available annotations, and exclude others, and download tables or sequences of the selection set. For instance, select the regions with Mosquito gene homologs, but no D. melanogaster gene homologs. Or select regions with gene predictions but no known homolog. DroSpeGe's BioMart is built with the GMOD Tool gff2biomart.pl It converts most genome GFF annotations into a BioMart datamine. Example data sets from this tool are at http://insects.eugenes.org/BioMart/martview =head1 OUTPUTS The script generates table .sql, .txt and .xml suited to BioMart (MySQL, BioMart version 0.3 tested). It is a simple script without special requirements, basically a data transformer that writes new files formatted for a BioMart database. Components created 1. chromosome region__main tables for biomart with chromosomes broken into Kb bins/regions (5Kb default) Features that overlap each region are tabulated. 2. per-feature feature__dm link tables store feature attributes (id,dbxref,match stats,..) add __main column feature_bool to indicate where features lie. 3. __chromosome__dm with dna residues for fasta output 4. main_biomart.xml and sequence_biomart.xml configurations for biomart usage. =head1 IN BIOMART -- filter (include,exclude) features that exist in regions, including joint filters (has homology to human but not to fly or worm genes; has predicted gene but not homology; any such feature type comparison). -- output 4 kinds of attributes: a feature table, per-feature sequence, region table, per-region sequence. Please have installed and used BioMart before trying to load the outputs of this. =head1 VERSION This is a alpha-level, not yet fully tested. ========================================================================== =head1 NAME cgi-bin/genomepathmap.pl =head1 SYNOPSIS This works with the genome directory generated by bulk files to provide standard URL access to genome data. It transforms /genome/species/release/{dna,protein,mrna,ncrna,feature} web urls to bulk data file paths. It supports gzip and plain data returns. =head1 GMOD::SeqUtils GMOD::SeqUtils is based on GMOD release 0.001 (January 2004) and can be expected to change or go obsolete. Besides contents of this package, requirements to run include the perl modules installed with GMOD release, esp. Bio::Chado::LoadDBI/AutoDBI and its ancestor classes from CPAN - Class::DBI, Ima::DBI, etc. GMOD::Chado::SeqUtils was written for use with the nascent Daphnia genome database, wFleaBase, at http://eugenes.org/daphnia/ See also further information at http://eugenes.org/daphnia/database ====================================================================== =head1 NAME gmod_init_db.pl =head1 SYNOPSIS *** from GMOD 0.001; needs updating to be useful A simple script to create the Chado database and tables =head1 NAME gmod_load_newseq.pl =head1 SYNOPSIS *** from GMOD 0.001; needs updating to be useful Load a file of miscellany sequences: cDNA, EST, microsats into chado db, generating public IDs. Sequences are assumed to be non-genomic, not located. ====================================================================== =head1 NAME gmod_dump_seq.pl - Print sequences from ChadoDB =head1 SYNOPSIS *** from GMOD 0.001; needs updating to be useful Dump sequence file of Chado features, with feature props, synonyms, dbxrefs xSelect by organism, by 'pub' = input file, seq type, feat props Need for nascent daphnia wFleaBase to use sequence public IDs ====================================================================== =head1 NAME gmod_list_db.pl =head1 SYNOPSIS *** from GMOD 0.001; needs updating to be useful Summarize feature entries in a Chado database, by publication (input file), by Seq. Ontology type (cDNA, EST, etc.), by organism. Add other categories as needed. =head1 AUTHORS Don Gilbert, Feb 2004 chado-1.23/doc/index.html000644 000765 000024 00000002432 11256707742 015350 0ustar00cainstaff000000 000000

Autogenerated schema documentation

The GMOD project makes use of SQL::Translator to automatically generate html documentation for the various Chado modules. The modules are:

And here is the document for the complete schema chado-1.23/doc/wiki/000755 000765 000024 00000000000 12061672375 014313 5ustar00cainstaff000000 000000 chado-1.23/doc/xsl/000755 000765 000024 00000000000 12061672376 014157 5ustar00cainstaff000000 000000 chado-1.23/doc/xsl/scenario-to-html-inline.xsl000644 000765 000024 00000014164 11256707715 021357 0ustar00cainstaff000000 000000

version:

Index

Abstract

Scenarios

Example

Download: [ ]
Tool:
Status:

This scenario involves rows in the following tables:

table type_id number comments
http://gmod.sourceforge.net/schema/doc/default_schema.html# [ ]---->[ ]

#
variant of: #

http://song.sourceforge.net/# http://gmod.sourceforge.net/schema/doc/default_schema.html# chado-1.23/doc/xsl/scenario-to-html.xsl000644 000765 000024 00000014736 11256707715 020110 0ustar00cainstaff000000 000000 <xsl:value-of select="title"/> <xsl:text> version:</xsl:text> <xsl:value-of select="@version"/>

version:

Index

Abstract

Scenarios

Example

Download: [ ]
Tool:
Status:

This scenario involves rows in the following tables:

table type_id number comments
http://gmod.sourceforge.net/schema/doc/default_schema.html# [ ]---->[ ]

#
variant of: #

http://song.sourceforge.net/# http://gmod.sourceforge.net/schema/doc/default_schema.html# chado-1.23/doc/wiki/generateChadoWikiTables.py000755 000765 000024 00000013622 11477500723 021401 0ustar00cainstaff000000 000000 #! /usr/bin/python # ------------------ """ Generate the Chado table descriptions for the GMOD wiki. Pseudocode: Read Module-Table pairings generate descriptions of every table read them into memory. open alltables file for each module open module file add module header to alltables file, module file for each table in module open table file generate Mediawiki markup for table clean it up add table to alltables file, module file, table file report any tables in DB that are defined as belonging to a module. Usage: ./generateChadoWikiTables.py It does not take any parameters as all values are hard coded below. The script puts the output wiki files in WIKI_DIR, which by default is /tmp/ChadoWikiFiles/ TODO: * Make all the values that are defined as constants in the program be passed in as parameters. """ import os import json import re # ---------------- # DEFINITIONS # ---------------- # UPDATE THESE 4 BEFORE RUNNING THE PROGRAM. DB_NAME = "testdb" DB_USER = "gmodhack" MODULE_TABLE_PATH = "../../modules/module-tables.json" WIKI_DIR = "/tmp/ChadoWikiFiles" # The MODULE_TABLE_PATH file may or may not define the Audit module tables. # There definitions are large redundant with the tables they audit. MODULES_DIR = WIKI_DIR + "/Modules" TABLES_DIR = WIKI_DIR + "/Tables" WIKI_ALL_TABLES_PATH = WIKI_DIR + "/allTables.wiki" # Don't update these, because we don't control them. RAW_TABLE_PATH = DB_NAME + ".wiki" # ------------------------- # Create needed directories # ------------------------- if not os.path.exists(WIKI_DIR): os.mkdir(WIKI_DIR) if not os.path.exists(MODULES_DIR): os.mkdir(MODULES_DIR) if not os.path.exists(TABLES_DIR): os.mkdir(TABLES_DIR) # ----------------------------- # Read Table to Module Mappings # ----------------------------- # The modules are defined as a name and a list of tables. modules = json.load(open(MODULE_TABLE_PATH, "r")) # Create a dictionary of table name to Module mappings; used with FK pointers. tableModuleName = {} for module in modules["modules"]: moduleName = module["module"] for table in module["tables"]: tableModuleName[table] = moduleName # ------------------------- # Create Table Descriptions # ------------------------- # Generate descriptions of all tables. produces file named DB_NAME.tableRefs. # Exclude audit tables. This takes a loooong time. Go get some coffee. # This takes so long that you will want to comment it out on subsequent runs. os.system("postgresql_autodoc -d " + DB_NAME + " -u " + DB_USER + " -l . -t wiki") # -m '^[^a][^u][^d][^i][^t][^_]'") # Split up entries, clean them up, save in memory rawTableFile = open(RAW_TABLE_PATH, "r") rawTablesAll = rawTableFile.read() rawTableFile.close() tablesByName = {} rawTables = rawTablesAll.split("__TABLE_START__")[1:] #rawTables.pop() # getrid of bogus element at end. for rawTable in rawTables: # Clean them up. Problems I know about: # 1. Insert Module name (Can't figure out how to get module name into # autodoc) # 2. Any equals signs have to be HTML escaped because mediawiki # templates choke on them. # 3. At template time we only know the FK table name; not the module # the FK table belongs to. Now we know the module. Insert it. tableName = re.match( r"{{ChadoTableTemplateHeader}}\n" + "{{ChadoTableDesc\|__MODULE__\|(\w+)|", rawTable).group(1) if tableName not in tableModuleName: print("ERROR: Table '" + tableName + "' is not associated with any module.") else: # There must be a better way: table1 = re.sub(r"__MODULE__", tableModuleName[tableName], rawTable) table2 = re.sub(r"=", "=", table1) # Replace __FK_MODULE__ with the module the FK table is in. pos = 0 table3 = "" for fkTable in re.finditer(r"__FK_MODULE__\|(\w*)\}\}", table2): table3 += ( table2[pos:fkTable.start()] + tableModuleName[fkTable.group(1)] + "|" + fkTable.group(1) + "}}") pos = fkTable.end() tablesByName[tableName] = table3 + table2[pos:] # ---------------------- # Create MediaWiki Files # ---------------------- # Walk through modules, creating module files and table files, and adding to # alltables. allTablesFile = open(WIKI_ALL_TABLES_PATH, "w") for module in modules["modules"]: moduleName = module["module"] moduleFile = open(MODULES_DIR + "/" + moduleName + ".wiki", "w") allTablesFile.write( "== [[Chado " + moduleName + " Module|Module: " + moduleName + "]] ==\n\n") for table in module["tables"]: # Write to allTables page allTablesFile.write( "=== Table: {{ChadoModuleTableLink|" + moduleName + "|" + table + "}} ===\n\n") allTablesFile.write("{{ChadoTable_" + table + "}}\n\n") # write to the module file moduleFile.write("== Table: {{ChadoTableName|" + table + "}} ==\n\n") moduleFile.write("{{ChadoTable_" + table + "}}\n\n") moduleFile.write( "{{ChadoTableName|" + table +"}} '''Additional Comments:'''\n\n") # Originally had an "AdditionalComments" template as well, but I # thought it would be confusing to users when they edited the wiki # to just see {{AdditionalComments}}. Showing them the text below # in the edit window is less confusing. moduleFile.write( "Add your comments here and they will be integrated into the " + "{{ChadoSchemaDocHOWTOLink|schema documentation}} " + "as part of the next Chado release.\n\n") # write to the table file. tableFile = open(TABLES_DIR + "/" + table + ".wiki", "w") tableFile.write(tablesByName[table]) tableFile.close() moduleFile.close() allTablesFile.close() chado-1.23/doc/wiki/wiki.tmpl000644 000765 000024 00000004331 11477500723 016152 0ustar00cainstaff000000 000000 __TABLE_START__{{ChadoTableTemplateHeader}} {{ChadoTableDesc|__MODULE__||}} {{ChadoColumnsHeader|__MODULE__|}} {{ChadoColumnDesc|{{ChadoModuleTableLink|__FK_MODULE__|}}|||''PRIMARY KEY''
''UNIQUE#''
''NOT NULL''
''DEFAULT ''
}} {{ChadoColumnsFooter}} {{ChadoTablesReferencingHeader|}} {{ChadoReferencingTable|__FK_MODULE__|}} * None. chado-1.23/doc/examples/dicistronic-gene-example.chado000644 000765 000024 00000216107 11256707742 023056 0ustar00cainstaff000000 000000 sequence feature_property relationship synonym_type cvterm_property_type OBO_REL SO internal internal cvterm_property_type cvterm_property_type comment exon sequence mRNA sequence gene sequence contig sequence polypeptide sequence part_of relationship derives_from relationship CG30461 FBgn0050461 sequence__gene 0 relationship__part_of CG30461-RE CG30461-RE sequence__mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAATCTCAGTAGTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCT 0 relationship__part_of auto:exon19 sequence__exon 0 2R-fragment sequence__contig -1 27914 28223 0 0 relationship__part_of auto:exon18 sequence__exon 0 2R-fragment sequence__contig -1 28277 28650 0 0 relationship__part_of auto:exon17 sequence__exon 0 2R-fragment sequence__contig -1 28917 30322 0 0 relationship__part_of auto:exon16 sequence__exon 0 2R-fragment sequence__contig -1 30381 30516 0 0 relationship__derives_from CG30461-PE CG30461-PE sequence__polypeptide MTRKQIATPRCETISKLVVSVGNATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV 0 2R-fragment sequence__contig -1 28015 28984 0 0 relationship__part_of CG30461-RD CG30461-RD sequence__mRNA CCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAGTGGCGAAACTTTTCTTACTTATGCAGATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT 0 relationship__part_of auto:exon15 sequence__exon 0 2R-fragment sequence__contig -1 27910 28223 0 0 relationship__part_of auto:exon14 sequence__exon 0 2R-fragment sequence__contig -1 28277 28673 0 0 relationship__part_of auto:exon13 sequence__exon 0 2R-fragment sequence__contig -1 28913 29050 0 0 relationship__derives_from CG30461-PD CG30461-PD sequence__polypeptide MTRKQIATPRCETISKLVVSVGSGETFLTYADATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV 0 2R-fragment sequence__contig -1 28015 28984 0 0 relationship__part_of CG30461-RC CG30461-RC sequence__mRNA GTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT 0 relationship__part_of auto:exon12 sequence__exon 0 2R-fragment sequence__contig -1 27910 28223 0 0 relationship__part_of auto:exon11 sequence__exon 0 2R-fragment sequence__contig -1 28277 28650 0 0 relationship__part_of auto:exon10 sequence__exon 0 2R-fragment sequence__contig -1 28917 29054 0 0 relationship__derives_from CG30461-PC CG30461-PC sequence__polypeptide MTRKQIATPRCETISKLVVSVGNATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV 0 2R-fragment sequence__contig -1 28015 28984 0 0 relationship__part_of CG30461-RB CG30461-RB sequence__mRNA GTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCATGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT 0 relationship__part_of auto:exon9 sequence__exon 0 2R-fragment sequence__contig -1 27910 28223 0 0 relationship__part_of auto:exon8 sequence__exon 0 2R-fragment sequence__contig -1 28277 28584 0 0 relationship__part_of auto:exon7 sequence__exon 0 2R-fragment sequence__contig -1 28917 29054 0 0 relationship__derives_from CG30461-PB CG30461-PB sequence__polypeptide MTRKQIATPRCETISKLVVSVGMGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV 0 2R-fragment sequence__contig -1 28015 28984 0 0 CG9002 FBgn0050462 sequence__gene 0 relationship__part_of CG9002-RB CG9002-RB sequence__mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAA 0 relationship__part_of auto:exon6 sequence__exon 0 2R-fragment sequence__contig -1 29062 30322 0 0 relationship__part_of auto:exon5 sequence__exon 0 2R-fragment sequence__contig -1 30381 30516 0 0 relationship__derives_from CG9002-PB CG9002-PB sequence__polypeptide MAFYDTWPKVDPIIVLVVLCLIVLVDRIWEMILTKRQQLVCLNAIMVPEELRGIIPPEIYHRARIYELHKTELQIWKYLIDLIITLCELILGFYPFLWSLSAKTLQKITSQEIWITLIFVFYLTIYICIRFLPVLIYDKCLLELRYGMSGKFPWYLYCCIGAMSILLSQLVLFPLAAAIVFSVKFIGYYFFLWFWLFWATFTLLLVFFLPYCCIPCIGRQVVLPEGTALYMEVKRVCDVVGFPMKRVFIIKTRTMQYSNAYFYGSCCLKRIVIFDTLLLNKGKEPNEIHPYEVGRGLTNIQVAGVVCHELGHWKHGHFYKATIIMKIHFFITMGLFGLFFHSPQLYMAVGFEPGVMPIIVGFIIVLKFALTPYLTLANVLMLWNLRRFEYAADKFAHRMGYSIQLRMALVKIYADHMSFPVYDQCYARWHHTHPTILQRLAYQQKLDVKAMNAGTY 0 2R-fragment sequence__contig -1 29065 30492 0 0 relationship__part_of CG9002-RA CG9002-RA sequence__mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAATCTCAGTAGTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAGTGGATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCT 0 relationship__part_of auto:exon4 sequence__exon 0 2R-fragment sequence__contig -1 27914 28223 0 0 relationship__part_of auto:exon3 sequence__exon 0 2R-fragment sequence__contig -1 28277 28650 0 0 relationship__part_of auto:exon2 sequence__exon 0 2R-fragment sequence__contig -1 28913 30322 0 0 relationship__part_of auto:exon1 sequence__exon 0 2R-fragment sequence__contig -1 30381 30516 0 0 relationship__derives_from CG9002-PA CG9002-PA sequence__polypeptide MAFYDTWPKVDPIIVLVVLCLIVLVDRIWEMILTKRQQLVCLNAIMVPEELRGIIPPEIYHRARIYELHKTELQIWKYLIDLIITLCELILGFYPFLWSLSAKTLQKITSQEIWITLIFVFYLTIYICIRFLPVLIYDKCLLELRYGMSGKFPWYLYCCIGAMSILLSQLVLFPLAAAIVFSVKFIGYYFFLWFWLFWATFTLLLVFFLPYCCIPCIGRQVVLPEGTALYMEVKRVCDVVGFPMKRVFIIKTRTMQYSNAYFYGSCCLKRIVIFDTLLLNKGKEPNEIHPYEVGRGLTNIQVAGVVCHELGHWKHGHFYKATIIMKIHFFITMGLFGLFFHSPQLYMAVGFEPGVMPIIVGFIIVLKFALTPYLTLANVLMLWNLRRFEYAADKFAHRMGYSIQLRMALVKIYADHMSFPVYDQCYARWHHTHPTILQRLAYQQKLDVKAMNAGTY 0 2R-fragment sequence__contig -1 29065 30492 0 0 2R-fragment 2R-fragment sequence__contig AACAAATTTTTTTTTTATTTTTGTATTTAGCTTAAGGTATTTACAAAATTCGTACGAAAGCCGAAACACCCATGAAAATAAAAGAATTTGGTCAGCCCATTACCATAAATACAAATGAATAATATAAAAAAATCAATCAATTTTTATGTGATTTGCTACATGAAAGCTAGATTACTCATACGCCCCGAGTGCTGATGGAGAAGAAAATTGCAGAAAGTTCACAAATTACCAGCTGAGGAAGGAGAGCAAGAAAAGTGGGAGGTCTTGGGCATGATTAAGTCGTTTTTTCAACCTATTAATCATACGCCATGTTGGCCATTTAACAGTTTCTCACTTGTCATATTAAATTATGCTTTGAGCAGCGCGACGGGGATTAAATGTATTCATTATTCAGTAAGTGCACTCACTTAAGAGTAAAAGAGGCAAGAAAAGTAGCCAAAAAGAATAATGCAGAATTTCCATCGAGTGGGAAAAGTTTTCATCGATTGCCTGCGAACTTGTAAATTATCGGAAACTTTGTAACCGCAAAAAATTGAATAATTATGCAGAAGCCCTTCAAAATGCAATGCAGAAGTTGGCGCTTTCATGCACACACACTCTTGCTAACTTACTGTCTGTAAATATTTAAGTAAGAATCTTGTGGCAGCCACAGGAACATCGGCATTATCAGGACTCCTTGAGCGTTGGCATAAATATTTAGGATCCAACATCCTGGCACACGTGCATGTGATGATGAGAAACCAACTAGGGCGACGGTAAATTCGCATACGAGCTGCCAAATTACACTTTACGCGGATATTACGCATACGACGTGGTGGCATCGCTTTAAGTTGCACAAATTTGCTGGATAAATACGTGCGAAGGACACAATTTCCAAGAGCATACTAATTTTTCTTATTTTGCTTATTTATTCTTATTGAATTAATCCTTCAACTGTTGCTGCTGCGTTCTTACTGCCAATTTTATTTGGCTCTCATGGCATATTAAGTGCCAGCAATTTACCAAAACGAAGCATGCAACCCGGGCAGCCACATTGAAAATAGGAGGCGTCACGGGTGGCAGAGGGCGTGGCACACACGAGAGGGGCGTGATAATGAGCTGCAGTTTGTTTTGAGTCATGCGCTGGGCGGGGTAAAAAGGAAATTTGCTTCGTCTATCCAAAGTTAACGAAGCAACATTTCATTTGACTTTCTGTCGAAATGAAATCAGTGTAATCCAGCCTTAAATCAACTCAATAAGCGAAAAAGTGCCGGATCTCAGGCTCTCAGTATACATTGTAACCGCTAGCCTTTTGTTGGCCATTCTTAATGTGGTGAACCCGAGTAAGCTAACCTGTTTTCACATGGTATTAAAGGATCTTCTTTAAGTGCTTTGTTTGCTTTAATATTGCTCATAAAATGTACAGCCATTTGCAAACTACAGAAAAATTAATTAGTTATGATAATCAAAGTAATGGAAATTCATATTATATTTTTAAAATATTAAAATGTGTTTTCTAGAACTTAACGAAATCATCAAATGTTTAGAATCTATCATAATTAGGAAAAATGAAAGTTTTAGTACGAGCAAAACATTAATTTCCTGCCATCTCTAATTAAAGTCAGACCGAAAAACTTTATAGACCATTAAAATTATACTGCAATTACAAATGTAAAATCAATCCGCAAGCTGAATGTGAAAATAAGCCAGAAAAAAGGGATGAGGCATGAAAAAGCCTGCAGCAATTGGCACAAACCAAATGGCTCCACAGTGCCAAAAACCACACAAAAAAAAACCATGATAAAAGAGGGAAAGCTGTGAAATGCTGGGAAACTGAGAAGGGAAATTCCAGCAAAAGTAGAGGAAACAGTGAAAGGAAAAGCAGAGGAACCAACAAGGGAAATGGATCAATGTCGAATGTCTGGGAGCTTGATGGTAATTTGAGAGAGAGCTTATGCTCCCCATTGTAATTGTGATTTGGATTCGAAGAATCTGAAATGAATAGAAGCAGCTAAAGGGATAGACATGATTCAATTACGAAGCTCTTCCCGAAATCAGAGGTAAAAAAACCTACTTCAGTGCGTCGCATATCTGAGTGATAGGAAACATTTTCGTAAATTGTCTAATATGAAACATTATTTACTTACAGTAAGCCGAAAATGACACTCAATAACATTAATCTCCTTGTAATTTATCCCTTAGGAGTCCTTTTACAAACCCCAAACCAATCATTGCTGCATTGTTATGCATACATGTGACTTTTCCCTGTCGATACAGCATAGTAATTCATTTCACTTTCCCAGTTTTTCCACAGCACAATTTTTTATGTACTGATTTTCCTGTCGATTAAGCCCAACGGAATGAACACTGCCCAACTGCAACCCAAACTGAACAAAGGGACATATGTGGATATGTACAACATACCCAAATCCAGTGGCAAATTGCAACATATTTGCATGTGCCACTTGCAACATTTACGATCGACTAAAGCACTCACTCAATCATCGCTGGGGGACAAGAACAATAACAAACAGCTACCGAAAATACGACAAAAATTTCCGCAGCAAAGAGGGAAATCCCGCAGGAGGGAAAGTGGAAAAAAACTGGGTGGTGAGTGTAAGGGTGAAATCCATCGATTGCGTGCAGCGTTAAATGTCAGCCCGCAGCCAATTGCAGATGTCAACACATGCATGGCCCCCCCCAAAAAAAAAGGAAATGGATCCCCAACACAGTCACACACTTTGCGCCTAAAAATTGGCAGACATTTTCGCGAGTGGGTGAATTTCGGAAAATGTTGTGATTCATGCCCGCTTTTCCGGCGGCTCATTGCGCGTCGAATGCGTTCAATTACGAAATGCCAAAACTGTCCGGCGAATTCGTTTCAATTTCAAAGTACATTCGCAATCACTTTGTTCATTGTGCTGCCTGTCAATTGCATTAATTTATAATTATGTGCCGCCCGCCCACACAGGCACATCCACACAAAAGACAACTAATTAAGGCAAAGCAATTAACTTAAGCAGCGACTAAGTCGGCTCACGAACCACTTGAAACTCCAATTAGGGGCGTGGCACATCCACAATCTGTCTAATCCCATCGAGGGTCCAAGGTAATTTGGTCGGATATCACGATTTGCCTATTACTCATCCCTTCTATGTATTCAATCTACCGACTTTTCCTAGTTGTTTGCACTTTGAATTAATTAAGCTGAATTTGATTTTAGTGATTGTGTCGCTTTTTCTCCTTTTGATTGCAAGCTGTTTAATGCAATGTAAACAGAAATAAATAAAGCTTTGGGCCGGCTGTCGCACAATCTTCTGTTTGCCTCCCACACTATGTTATATAATACGCTTTCCCGATGCTGATAAGACGGCGTACTGAATACAAAAGAATTGGGGCAGATGAAGGAACAGCTCCTTTTAATACCCACCGAATTAGGGGACGCTCTTCCTATTAAAGTAAAGTTTGTTGTGGTATATATATATTATTAATAGAGTACAAAATAAGATTATAAAATAAGATAATAATAAATATATAATAAACTACGAATATATTCAAATTTAGAGTTCAATGCTTGAAATATATTTCATAATTCAAATACTCATGGTTAGGGTAAAAAAAACAAAGCCAGACTACTGAAAGAATATTGGCCGGGGATTGTATTGTGCCTGCATAAAAAGTTTTTCATCGCAATCAAAGAAGTGTTCCCGAAATAAAAACTTCCCAATTTTCCTTCTAAAAATCAAAAACAAAAGAATATGTCAATATATTTAAGGCCTCAAAAGGGAAATCACTCTTCAAACCACCCCAACTAAAAAAAACCCAATTTTTTTTTTATCTCCGCTCCAAATATTTGCTTTTTTTTTCGGGGGGGCTAACGTATGGATGTGTGTGTGGGGCATGATAAATTTTGAAAATTTATTTGAGCCGGTCTGTGGCTGCATTTGAAGTGGTAACCATTACCAATGCCACGATGAATCCCCATTCTCCGTTTTTGGTGTATAAACATTTGCATGGCAAATTTTTGGAGTTCTTTTATTTCGTTTTTACATATTATTCGGTAAATGTTTTATTCATGCTGCCCCACAAAATCCCATTAACAAATTTACACATTTTCAATATTGAAAATGTGCTTTACTTTATGTATAATAAAAACAAACCGATAAAAACACGAAAGCCAAAAAAAAAAAATATGTCTGTGAAGCAGAAAAATACTTTCAATTAAGCTATGTAAACAAAGTTTTTTGCCCGAACAAAAAAAAAAAAACTAAGCTGTGCACATGCTTAAGGCACTTATTTAAAATCTATTTTTGATTTTTTGTGGCTGCTGTTCCATGCGCACATTTATTTGGTTTTTAATTATTTTAATTGTACGAAATATACAAACACATGATTTCCTTTGTTTTCGATTTTCCCTGTAAGCCCAAAGTCAGCACAAAATCCTCTTAGCCTTCTTTAGTTGAGTGATAAGCGGCGCATTAGTGGCGAAAATTTATGGCCAACTCTCATGAGCCGAGTTGTTAATGCTGGGATTTCACAGCGATTTCTTATGGGATTGCTGTCGCGGTTTCGCAGATTGTTTTCCTCCGTTTACAACATCTTGTAATTTAGGAGGTAAAGTTTACAGATCACATATGTTCGTGGGAGTCAAGTTCTTTTACAAGATTGAAATAGAACGAATGGGAGTTTTGGCACAGGTTAAACCGAATGCCACACAGAAAGAAATGGTTAAGCTAAAACTTGTGACTAAATAACAAAAATAAAAATGTAAATAATATCATGCCTGTTTCTTAAGATTAAACCATATTAAGTCATAGAAAAGTTAGGTATTTCCTCTTTGGCTACATTCAACAAGTAAGAATGAAAGACAACTTTTCATGTTAATCCATAATAACTCGGTCAGGCTTAAACTGAACCTTCTGTTTTACCTTTAAGCTTTAAGTCACAAAGTCAGTGAGCTGCCACTCGAGAACCAGTGGCAATTGCATAATGGACACAGGTCCGTCCCTTTGATATGACCCAAAGATTAGGGAACAGGCACACACAATGGCGTTCATGGGGCGTATGATTAATAAACACTTTTAGTTTTCGTTTCGGTCAAAATGGAAACCTTTTCTAGAGTCATAACAATTAACTTTAAAGGTTTAGACATAAATCCTTGCACAATTGTAGTCTCACACAAAACATACATGTGTATAATAGAACACGAAGAAAAAGGCAGAAAGTAAAAAGTAAAAGATGAATAATGAATGAGCCGCACGCGAGCAGAAGCCAGGTGGATTGGGGGCGGGAAAATGTGGAAAAGCTCGGCGGCCATTCATGAGTAACACTTGACATTGCCTGGGCGAGGAAAATGGGAAAAGGAAAACCCACACATACGCACTGCGCCCGAAGGGCAGCCGAAGGAAGCTCGTTTCTAGTGAATTATAATATGGCATGCAGATAAAACATTGAAAGTCAAAAGGCCCTGGGGGGACTACAATTAAGCGCACCACCACCCATAGCCACCCACAAAACGGAGAGGGAAAACATAGCAGTTTCGACATTGGCGGAAATCATTTTCATATGTATGTTTATGATATTTTGTAGATAACTGCAAGTGCTGGCGCAAAGTTTACTCGGAATTAGCCATATCACAGAAAACAAAGCCTATATTCTGCGTATTTTTCTCGCATTTTTTTTTTTTTTTGCCCGGACGAAATAACACATGAGAGAAGAAAAAGCCCAGGAAATCTCTGGCGAAAAAGAAAAACAATTCAACAGTTTGTTGCCAGCAACATGTTGCCAACGCGCTGCTGCAACACTCTCCTACGCTCTCTCCGTGTTGAGTTTTTCACTTTGATAAAAGCAAAAGACCTGGCCATAATCGAAACAGTCTGCAAAGGATTCTAGGCGCCAGCGGTTCTCCAAAGATAAAATACCGTCAAGTATTAGGCAACGGCAATCGTCGCGTGCGTTTTAACCAAATATACTTAAAATCGAAAATTACCTGGAAAAACGGTCGAGAAAAGTGAATTTTAGTTTTTGGAAAAGAAGAAATTCCAAAAGCAAGCAGCAGTTTTAAAAAGTAAATATGATTTGTTATTTGAAACATTTTCTTGGCGAAGAACACTAAACAACTATATTGGTTTCGGCAGTTATATTTATATTTTTTAAAGGGCGCAAAATAACACTTTATGCATTTGTTTTTACAAGAAATGCTCGAAAACATTTTATTTAAAATAGATGTATTCTCCGCAAGCAGAATAAGTGATTTACATTCAAACATGCTGCGCATTTCAAAGTCAGTTTTTTATGAACTCGTTTATATCTCGCTGTATATAAAAATGCGTTTCAAACAAAAAAATTTACATTTTTCTCACGATTTCCAATCACTTTATTTAAATTTTATAATTTATGCTAAAAGCCTTTTAAATCTGGGCTAACTAGCCTAAGCTGACAAACGCAAAGCAGATTGTCCTTTTGGAAAAAAGCGTTCAATTTGCAATGGATTTCCAAAGAGGTGGAAAATTGGTTTGAAGAGGTCGTCGCAAAAAAAAAAGAGCAACAGTGAAAAAATGTGCGGGCATTCCGTATTCAACCCGCTGACAGCTTAAACCGTGTCAAATAGCTGAATTTTCCCGGACACCAGGGGCAAACCTTTTTTCAAGAAGTCCGCATTCAATTAGGATAGGAGTCGAACCCTCCTCATTGGTATGCCGAATGGCAGCCACAGGAGCTGACACTAAAATGCCGTCGCCATCGACGAATGTCCTTGACTTTGCCTATTCAAACGCAAAATTAAACAGCAGAAGGGACAAATAATGAGCGGGAATGGGTTGGAATGCCATGGTAATGGGTAATGGGCACTACACTACAGTGTGGCAATGGTGGTGGGGCACGTGGGGCAAGTGGGTCTGCGTGCCAACATTTACGAGTCCCCCTAATTTATGCTCATTCATAAATCTCCCTCGGTGGAAATCCCTTGCAATCGGCGACGCAGTCGACGCCAGAATGTATGCAATGCAATGAAATAAGGCAAATTGAAAGTTATGACTACATCAAGGACTTCTGTGAGGCGACGAAGATCTAAATACCCTTCAAAATGTCCAGGATGTTTTATAAAAAATTATACAAAAATTTTAACAATTTTTCAAAAAATTATGTTAATATAGTTCAAATGCACTTGAAAATCTAAAGAAAAATTAAAAAATTAATATAGAATAATTTCGTAATTAACTATAGAGATGCTTCTAATTTGTCCATTAAAATGTTACTAAAAGAACATATAGAATTAGCGCATTTATGAGCCAATTTGATGATAAATCAAAATGAGCCTTGTGAGAGCATGTGCAACCTTTTATGTTTTGTGCAGCATAAAAGGGAGCTGTCAAAAATAATTAAGAAATATCTAAATATAAAACACGACCCTTCGCTGGCTTCCCCTGAAGATTCGGCCACGCAGCGTTGTTTGCCAAGTGCAAAATTGGCTAATTAGATGACATACCACTTGCAACTAGCACGAGCCGGATTGTCCTCCATTCGAGCAAATGGCTTAATTGCAATTGCATTCCTAGTTTAACACAATATCGAGCAAGGAATTTCGTGTACGAACAATTAAAATAACTAATTTACTGTGAGTATCTAATTTTCGATGCTTTCATTTACGTTTTTCTCGATTTTGTACACGCTCTCGTTTAGCGAAAACAAATGGGAATCGGAATATCAGAGCCGAAGAATTATCAAAATAAATACGTTTGTCAGCGAAGAATGGAGGCATTTTGTTTGCATTTTCAGCCATTTAATGGCATTGGGAAGGAAGTTGGATTCTTGGTTATTAATAGATGGCTATTCGCAAAAGGATGGGTGATTAAGCGGATGGAAAACACTGGCCAAATATGGCGACGTCATTTGACAGACGCAGAGATGAGCAATGATTGCCATTAATTTAAATTAATATCACACTATTCAGGGTCAGCAAGATTGATGGGTTATTTGCAGTTCAAATTGTGTGGGCTTTGGAATACAAAATGGAAACAATGATGTAATCTCTCCGCTGCCAAAATAAATACGGTTTCTGTGAATTTCCAGTTAGTAAAGAAAGCAATTCGTAAAACAAAGCTTCCGGCAATTATTTGTGTACTTTTTTTCAAAGAAATAAATTATACGCAATATTAATTCTGGTTTAGCTGAACGAAATGCGTGGTTTTCAGAAAGCCATCTAGATTCCTAGTATAAAAATAAATATAAACTCGGAAAAAATCGGTGGAGGAAAATGCTATTACGAGTTTTTTGAGTTGGTTTTCATGCGAACTGAAAGATATTATTAAAATTCTATGAAAATTGAATATTTTGTTTTCTAAATTGTAACCAAACCTTTCTTTTCTTATCTTCTTTTAGTTAGGCTTAAAAAATTTCAGAGTTAAGTGCTCTTACTTTCAGGACACCCGCTACCTTCGTAAATGTCCTGCCACAATCGCAAGGCGCAGTTTCGCCCACAGGTATTGGGCGTAATTATCTTAGAACAATGTCAAAAACACAAAGTGCCATTAAAAAACGTTCGCGCCTAGCGGTAATAATTATTCTAATTACGAGGCGTTTTGCTGGAAAAGTTATCGAGGTGCTTGAATGCCCCGCAGGGCCTGTCAAATATGTATTTTGTCCGTGCAAACAAACCAGCCAAAAAGTGGCGGGGATCCCAAAGCAATCAGCATAATTTGCCTCTTGTTGTATTTTACATTTTTGCGTATTGACTTTGGTCGGAAATCTTTCCACACGCCGACATCCAGCTGGTTAATTACAGCTGTTGGCCCCGAAGAGCATTATTATTATTTATTATTATTATTATTATTTCTTGATTACTATTTACGCAAAGGCAGCGTAAAAAGTGCCTTCTATTAGCTATGTAAATATTTACATCATCATCACTTGAGGTTTTTCGGCAGCAATTACGCGTTGCGTCACCAAACTGAATAAACACTAAGGAAGCCTTTAAAAAACACGTTGAAGTAAATATTCGTGTGGGGAAAATATACATATGTGCATACCTTCGGCAATTTTGCATTTATTGTGATCTTTTTATGGTTCTGCTTTTTCCTGGATTCCATGAAAAACAAAAGAATACAATAAAGAAAAACAAATGACGCAGGTTTTTTTGGCCCAATTTTTTTTTCTTGGCTTGTTTGCCCGGTTTTCGTTTCCACGCCATCCTTTATTTATTATGGCAGGTTATAAAAATGCAATTCCAGTAATTGAGCAAACTTCAATACTTTCCAATTCTGTCGTCTTAAAATTGTGATATAGATTGTCAGGACTCCACGCTCTAGTTTGTTATTTATAGCTTTTGATTTTTGAGCCCTTTTCGACCCTTACAACTGTCATGTTCTGGCTACAGTGACAATTTCCAAATTGACTGACAGGCATATCCATTACGAAGTGTGTTTTTCATCCCAAATGGTTTTCTGGTGATTTGGCATTTTTGCGAAAAAATTGTAATTCATCATAATATTAATAAGATATCGATTTGGTTTCGGTTTTCAAAAAGCAAACTACCTCGAAATGAAAGTACGAAAGATCCTGTAATTTAATATGGCTACTATTTTAATAATTAGCTTTGCTGTTTTTTGTCAATTGCTTTAGGTTTCATTTTAAGTGTCACTTCCCACACATCACGTATACGCAGTGTATGCCATCATTAGAACTGAATTCGTTCCAAGATGAAATCAATTTAAGTGTCACACCCCAGACATAGTATGCACTCCATAATTAATCTGTTCTCCTTACTTTATTGCTTTTTACAAGCAAAGGACACGGTTTTTACATGCAAGCGAATTGAATTTTATTCACAGCTGACAGGGACTAATAACAATCCATAAGTATGACCACATGGGGAGTTGGCATGGCAGGACATCGCATTTCCCCTCCGCCCATTCGGAATTTAATTAAAACTGTCTAAAGCCCAGCGGGTGCCAGTCGCCGGACAAGAAGAAACAAAAAAAAAAAATGCGTAGTGTCATGCAAAAAACCATTATTCTTTAGATTTCATCCATGGTAGATTATTTTTCAATATAAATTCAACGGATCCCAGTGGTTAACCAGAGTTGGCCAAGCTAATTACGGCTCCGCGGTGACCAATAAAATGTAATTAAAGTCCGGGCAACAGCAAAAAATGGGCAGAAAAAATGTGGCTACTACACCACCGCAACTAGCTTAAAAGTAAAGAACTGAAAGTAGTTTCCCTCTGGCCCTGCGAATTTTCACACATTTTCTTTCGCACGCAGCGCTGGCTGAGAGTAAAAAGAAAAACACAAATGAAAAATAAAATACACAAAAGCTTCCGACCAGCAGGCACATCAGGCAACACATCGTAAACAACTTCTTGGCCAGCTCGGCATGACAAAAAAACCAGATTAAATCGCCTAGCGAACCAGATGCAATATGCCCCCCCAAAAATTCTTGTAATTTAGCAAATCGCTTCTCCAACACGAGTATACAAATTGGGTAGATTATCGACAGTAAATTACAAAGAAATTCTTCTCGCCGTTCTATAATTTCTATAATTGTTTACAAAGTGCCCAAGTCCGGAGGAAGAGGCAGCTCTCTCATCCTCCGAATGCAAACTACATAAATCAACATCTGAGGCTTCCTACTAAATCGTTCGCCGCTGCTGAGGAAGGAAAAATAAATAAAGCGATTTATTAAAATCAAAAGCCATAAACCATTCAATTAAGTGAGTTCTCTGCGAGCAGCTTAACATGTGAATTATAATTATAACCAATCGAAATGACCACTTTTGGGCAATTAAAATTTATGTTTGCACGCCATAAATTTGGGCATTCGGCTCAATAAATCAGCGACAAGTTCGCCGTCTGAAATCAACACTATATATCAAGAGATTTTCATTTTGTACTTTTCGCATAATGGCCAACGGTACCTTGGCACGTAATCATCTGCTCGGCGATGACCTAGCAAATTGGCATTTAAATTTTTAACTGCATTTTTATGATGTTTCCACAACCCTCTGACTACCAATTTCTTTTGGGCCAAATAAAATAAACCGTAATGCAATAAATTACGCTGTTTTTCTTGTCGATCCTTCGGCAAATTGTCTGCCGGACTTTGGGCCATAAATTCAAACCCCTTACTCGGCCGAATCTTTTGTGTCCGACATAAGCCGTTTTGGGATAAATCTTCGGCTTTTTTGGGTGGGCAAGCAAATCAATGGTGGAGGAACAATTTAATAACCAACTGGGGGGATTAACTGATGAATATTCCTTGGGATAACCAGTCGTCCTGCATATATAAACATATTTCTTGAGGCACGCCAAGCAAATGTCAATGTCAACTGGCCTTGTTGGGCCTTGGATTTTCCTCGGCTCGCCTGTGTTTACTTTTGGGTGGCCCGGAGTGGCCCAAGCCAAGGCTAAGTTTATTATGCCGCGAAAAATGCAGGCCCTCGAGTGTGAGTGCCGTAACCCTTGAACTCAAAGACATAAGAAAAACAAAGAACCAACTTAAAGTACACCCACCACCTTGTGTTTTACATTTCAAATGCTAAGCACAGTGGCTCCTCCGAAATTATATAAATCAGAACATGAATAAAGATTATATTTTAGTCCATTTAGACTACAGAATCTTCTGCTAATGAGAAAGAAAGAATGGTTTGTTTGCATTTACCATTTCACAATGTGTATATATTTTTCTCATTTCTTTATATTTATTTATAAACCGACTTAGTAAGATATATATAGGTATTCACTAATTTTGTCAATTAGAAATGCAAGTGTTTAATCAAGGTTCCTTATTTATAGACTTCCCTGTACAAAAAGCTAGCGGGCAAGGAAAACTTTCTGTTAGTCAGTGAGTATATTATTTCAATCCCCTGCATTTTCCAATGCCCGAGCTTCATGACTCTTGCACTTGAATACATTTTACAGCGAACTGTCTGTCGGCTATGTTCGCTCATGTTTCAAATGTCGAATGTGTGAGACCGTGTTTCGTACGAGCAGGAGTTTTCCATATTATTATTTATGAATGCGAAATACTTTGGCTGACATTTATATATGTATATATTTTTTTTTTTTTGGGCAACTGCCTTCGTTGTGTAAGGGTTACAAGCTACAAGTGTAAGGGTTTTAGCTACACGTGAAAGTCATCTTCTAGTTTTACAACTGCTTCACTCAGGGCCAATAGCGAGGAAAGTGCAGTAAAATTGTAAGAATTATGGTCAGGTTGTAAACAGGAAATATCCTATTAAACGAAAGCGGGGCGGAAGTTCCTTCATTGTTGTACACAAGCTTTTACCTAAGTGCATTTTTAGGTGCATTAGAACATTGATATGATTCTATTAGCTCTCACACACTTCGTTTTTATCACCTTTGTGGGTGGGAAAGCATCGAGAAAAACCATTATGGGATACCGTAATGGATGGTGGATATGATGGATGTCTTGAGATACCATTGATCCATACAAGTGACCCAAGAAAAAGAAAAAGGCGTCCTTCATCATTTAGGCCATCATTAATTAAAAGGACACAAAATTGAAACAAAGCTTAATCAAATTAACGCAAGAACTGAATGATAGATAACTATTTGTTAAAAAAATCGCATGTTACATATAAACTGCAAAATATTAGCTTTGTCCTGCTTTTTGTGCACTAATCTACATATTTCAAGCTTTAACAGTACCTTTTATAGTTTCGTCCTAGTAGTTAAATTATACACCTTTCCAATATCTATACCAAAACTGTGCGGTAATTAAAGCTATATATAGACAGACTGGAATGCTATCAAACCAAATAAAAGGCAAAAACCCTAGTCTATAATTCAGACTAGGCAAAAACGCTGCGGTCGGGCGCAAACTCTTAAAATAGAAATAATAACAGATACGCCAGCAACAAGCGGGGGGGCAAAACCAGGAAAGGGAAAGGAATGGGTAAGGGAAAAGGAAAAGCGTGGAAAATGCGGGGGAAATGACAGGCCGCCAAGCGGGGAAAATAAACAGAAAAACACTCAAATTAAATTGCGAACTGAGCTTAATGCACTTAAAGTCAGTACATGCCCAGGAAAGGGTGCAAATGTGGGGGGGTGGCCATTGTGGGGCAATGCCAATGTCAGACGGACGGATGAATGGTTACCATTGACAGGTAAGCAGGTGCTCTGCGCTTTTCCGTGCTACCACCCCCCCCCCCCCCCAACCCATCCCCTTGACTATCCCGGACTTTTCCTGTGGCACTCGAGCACGCGCCCGAGAAATGCCAAGAACTGAGAACTGAAAATCGAGTGTAAGCCGCGGCTTATGCAATGCGGCCAACGGGGCTTGACAGTCTGGTTTGCTTTTGCTTATCTGCGTTTCTTGGCCCAAAGGCTCGATTTGCCTTTGGCTGTTTTTGCCATGCAAGGCGGCCATTAGTGACGTCGAGTCAACCAATATATTTCCTGTTCAATAGGCTCCCCCCACCCTCCCATTGATTCGTGGCGGCGAAAGAATATTTAAATATGAAGTTGCCAAGTTTATTTCCTTGGGGACTCTTTGCGGCCGTTTTCGGTGGAACGAACTTTTTATCTGCAGCATTTTATATCATGTTTTTGCTTTCTCGTTGTTTTATTGATTTAATTTGTTGTTGGGCACTAGGCTAAAAAGTATTGAATATTCAAAAAGCCCTTTTGCAAAGTACCAGTTGAAAAGTTGTCTCGTTAGTACAAACTGCAACTTGCTATGTAGACACACTAAAATGCAGAATCGCTATTGAAGTTATTTTTCTGAATCCCTGCGGCTGATTATATATTCATTGCTTTAGTCATATTGATTTATTTATTTCCTTGCCAAGCTGCATGGGTTTGCATATCCGAATGGCAAAATTCCAGTTAAAAGTTTTTCCATTTATTTAAACTATTCAATCTCAGATTAGGAAAATCCGTTTGCAAGCAGATTCTATTGGTAAATTATTGCTTTACATTTAACCGTGGTCATATTGATAACAAAAAGAGACAAAAAGAGAGAAAGACAAATCAGAGTTTCCTACGTACAGTACTAAATAATAAAAACAGAAATATTTTAAAATAAAATTTGGGAATTATGATTATTATGTTTCGCCAATACAGACTGTTCCGAATTATGTCCTTTAATAAAAGACTTGCATATTAAAACATATTTGAATACTTTATATTTGTATAAGTGCATCGTATTCCTATGTAATTTTCTCCCATCGAGCGTACTTAATTCCCAGTTCTGCCCATAGTTCATTACACAATTTATATTAAAGCCGTAACTTAACCCTCGGCATCCAGTTCGGCATTAGCTGGCAGTTGGAGCTGGGCCAAAAGTATTTGCCATATTGCACTCTGGATTGCAAAAGTTCTCGACCAGCATTCCGCCATAATCGTATAAATACGTATACAGTTCTAGCACTTCCTTTCTCTACATACATTTGAAAAAATAAAAGAGAAAAAAAAAACAACAAGGACAACAAAGGATGTTGGTGGGTTGGGTAAACAGCGGAGGAGGCTTGAGGCGACTGCAGTGGGTGAAATGCAATTTCCAGGCCATAAAATGGCTAGGCAGGAAAAAACAGCAGGAAAAGTCCTTTCACTTGGCTCGAACGAAAGCGTTTGCAGGTAATGGCCATCATACAAGCCGGTTAATGCGGCCAACTTGTTCTGCAGGCAGATAACACGAGTAACCAAAGTCCTCGCGAACGATGCGAAAAGTTTCGCGGCAAATTAAATGAAAGTTAATATTGGCAGCGTGTTCGATAAACAATAGGGACGTAGTCAACAAGTTGATCCTAATGCGATTATCGCACTGTGCCTAATGTCTTTGAGAATTGGCTAGATGCCTTAGTTTTATCGAGAAAATTATCTACCTAACTTTTTCTACAAATTTCTACATATACCTATATCATTTCGCAGTTTTAATGAGGTTTAGTTGTGCCTTAATATGAATTCTAGATTAATAGATATATTCTTAAAGAATATTTTCGGTTTTAGATAGCCAGATATTGTCGCAACCATTTTTAACCTTCAAATTGAAATTAGTGGCGATTTTCTTGTGTGCCAAGAACAGTGTGCAGTGCGAAACTCATTTAGTGGTAACAGCTGCTGCAAATTTATGCTCACGGCTTTTCTATTCTGAGCTTTATTTTAGCCACAGAAGAGCGACCGCAGCAAACTGTCAACGATTCCCACCGCAGATATATGTACACGTACATTCATCCGGATGTCGGCAAACGAGCTGGCTAAATCCAAGCCAAACTGGCACTGCTCAAATACCACTTAAGTATAGCTTGGCATTTGGCAAATTCCATGATTTTATAATCATTTCTTTACTCTTTTATTAATTTGAATGCCAAATTTTGACTTTTGTATGCATATAACGGAGACGTTTTAAAGCCAACCCGTAGTGGGTGAATAAAAGGCAAAATAATATACAAAGGGGTATGGAAAATTTATTCAAATATAATTCGATACTTTTCTCATCCCATAGAACCAAAAAAAATATGAATTTCAACGCTGAAAAGTATGCAATTAAAAGGTTCATACTCTTTAGTCCTTAAAAGGGGTTGGCATTTCCTAAACAGAAAATAACTTGCACAAATAGAAAGTTATTGTTATAATGATTTTGGTTGAGTAACTAAAAGTAAACGTAAAAAAATAATATATATAAAATAAACATAGCACAGAAAGGCCGATTGCAGTTGGGTCACCCTTGGTAATTATTTTTCTAAGTGTCCCTTTCAAGCCAACATCATCTGCAGACGCGCCTTGAGCCCAGGACTTTGCTTTCTTATTTTTAGAGCAAACCAAACCCACCCACCCGCGAGGCAACTGCAGATGTGGGCGGCCCAGCAATTTTGTTTACATTTCTTGTTTTCTCCCATTCCGCGCGGTGTGTTTAACCCACAATGACTTGTGACTTGTATTGGGCTGGGGGTTCGCCTGGGGGCCTCGTGGAGGTGGCGTTCTGTCTCATTTCAACTGCGGGAAATCCCCGCTCACGGATGCAATGTCGGCACTTCCTCGGCTGCAATGGGAGTCCCACTGTGACCATTTCTCACCCGCCATACGTATACGTGTGTATGGAGCTGCAGCTGTGTGGGTTTTCGTGGGTGTTTCTGTTTTATGCTATTAATTTGACAGTTTCAGCTGCGCTGACAACTGGCTTTTCCCCAGACACCGAGCATAGCGTTTAATGGCTGCAAATTAATTGTTGTATGCCTTTCTCCTCCCCAGAGATAATTGCTCAGCAGCATCTAGTTTCTCAGCGAGGACAAATAAACCCGAGAACAAAAAAAAAAACATAAGAAATGGACTCTGCCGCCGCCGCCGCCGCCAAGCGCGTTCAAATCGAGAAGGCCCACAACTTTATGCGCCAGTATCGTGATCCCGAGTCCAGGGAACTCAAGAAGCTGTCGGCCAACCAGTTCATGGATGTCTGGGCGCATTACGATAAAGATGGTGAGTTTAGATCTTACTAACAAAATTTGCAATCATTGTATTTCACTACTGCCTTAGAATTGTAATTATTTGCTTAACTTTCCACATTAATAATTTGTACTTTATATAAATTAATCCACACTTGAAACACATTTAGTTAGTATCTATTAATCAAAATGATATATTAGAGGTTTAATAACTCATTACTTATTTAAATTGTTTACCTTAGGAAATGGCTACATTGAGGGCACCGAGCTGGACGGATTCCTGCGGGAGTTCGTGTCGAGTGCCAATGCCACAGACATTAGTCCAGAGGTGAGTCTGAAGTGGTATGGAACACTTGCATCTTAATCCCTCGGTCCCAATTCCCAGGCAGTAACGGACACCATGCTCGAGGAGCTAAAGTCCTGCTTCATGGAGGCCTACGATGACAATCAGGATGGTAAAATCGATATCAGAGAGGTGGGTAATACCTACGACTCATTCGGACCCAAAATTTCAGTTTGATGGGGGCTCCCATGTCGTATGCGCAATGTTGTCTGTATGGATTTTTGTATACGAAATGACATTTCCTTTAGTCATGACGGCGCCTTCTTTGCCTTTTTTTTAAATTGGTTTTTAAATGTCTCGGCCGGGCCGAAACCAATAAATTATTTGGCGATTTTCCCTGGAGAAGGAATCAACTTTCTGGCAAGGTCTTTGGCCAAAAAAAAGTTTTTTTCTTCGTTTTCTCTCATTGTGTGGAGGCCACATTAAATGAGTTTTTAATTGAAGTTGAACTGGCAGCAGAAGTACGGACTATTGGAAGGGGATTTTCCGTTTTTCTTTTTTTTATACTAAATAATACAGCGGTGCACAATGGACTTTTGATAAATGAGCCCACGAAAAAAGGGAAAGTTTTGGTGAAGAAAAGTAAAAAGTTCAAGTAGCCGGGTCCCCCATGTATTGTTGATTAAGATTGCTTGCAACACAAAAGGCACAGGGCATTCATAATTCATGTTGTCCACATTATTCATACGCCACGTCGAACAGCGATTGAAATGGCTGGGACGGTTAAATTACTGGTCTGTCGACAAGGCTTTGGCCTGAAGATAAACTTTAATTACGATAGTGCTATAATTACCAACAGCAAATAAAAATGTAAATCCCACGGCCACAGCGAATTATAAAGTTTTCCCTGCCACAGATGATTACTTGTAAAGGGTAAGGGCTTCAATTCGACACTTGAATTATGCCGGAAACTTTTAACGAATGCCAGAAGCGAAACTTTTCCGGCTGTTTGCTAATGAAAGTGCAGCAGGATATCCTCGCCTTTCACGCAATGCACCGGATAAACAGGAGACTTAGGAACCCGGCTCGTCCTCGGAGCATTCCCATTTATAACTTATTTCAATTGTCATGTCACGCACTGAAACAAAAAGGTATTTTTCTTGTACTACTTTTCCGCAGCTGGCTCAACTTTTGCCCATGGAGGAGAATTTCCTTTTGCTCTTCCGCTTCGATAATCCTCTGGAATCTAGCGTTGAATTCATGAAGGTAAGTGACAATCAGGAATTTCACATCCTGAAATTCCCCAAATAATTTGTCTGCAATTAAATTAGATCTGGCGTGAATACGACACCGACAATTCGGGTTACATTGAAGCGGATGAGCTGAAAAATTTCTTGCGCGATTTGCTCAAAGAGGCCAAAAAGATCAACGACGTGTCCGAGGACAAGCTCATTGAGTACACCGATACTATGGTAAGTTGTCAGACATAAATGCATGACATTACTTTGGTTTGCTTAGGAAATTCATTAGTAGATAGAGGATAAGAGCTAAACTAAAGTGAACGATAATTTATGAATACATGAATACTTACTATTTATCTAAGAGTTTCTTAAGGCCTCAATATCCTTTTCAAGAAATAAACTTCTTGTTCAAAATTCCCTAATGATTATACATAGAATGCCAAACCAAAAACGATTCAATAGCATGCTTAGATTCTAAACTGCTGTGATTATTGACCGACTGACTATGCACTTTCTACACAAAAGTGTAAATAATGCCGATTTGCTATAAGCACACGATAATGTATGCCCAATTACCAATCCCGTCTCGATTCCTTTCAGCTCCAAGTATTCGATGCCAACAAGGACGGACGTCTGCAGTTGTCGGAAATGGCCAAGTAAGTGTCCTTGAAGTCGCGTTCTGAAATTCTATGCAGCAGCCAGCCAACTAACTTATTTATTGCAGATTGCTTCCGGTTAAAGAGAACTTCCTGTGCCGCCAAGTGTTTAAGGTAAGTGCCAAAGATAAATTGTGTGAAAACATCGTTCATTCGAGGAAATTGCCAAGAGCAGATACTATCAGCAAATCGCGGTTTTCCAAACATTTATTTATTAAGAACTTGTTTATGAAACCAAATCAAACTCGGCTTGCCTTGAACAAAACACGTTTAGCACCTAGGTTAGCCTGGACTTTTGGTTTATCACTAGCTGCAGCCTTGACTATTCAACTAACTTAGCTTTGCAACTAACTCAAACAGCAATGCATATTGGTTTTGTCTTTTCTTTTGTTTACCTATCATTTCAAACGATGTCTGTGCCGACTTGGGAACTAATCTTTAAGAAATCAACGAATTTATATTATTAGAAAATGGTCAATATCATATTTATAGGGCATTAAAAACAATATACAACAGCAGGTTTGTAGTTAAATTTCCATGCAGAGAATTAGCCAACCAACCATCAATAACTAAATAAAATCATATTGTTCATCAATTATTATAAAAATCAATTACCAAATTTAGTTTTCACCCATGAACAAACATTAATTGGTTAAATACATTGCAATGCTTACAATCATAAAATTCCATGGTCCAAACAAACTTTCAAAAATAAATGGATCGGAAGGGAAAGTGTTATGCTTTTCTGAATAGAATCCCGAATCAACAGCGATTCTAAATCCTTTTAAAGGCTTTTCATTCTCGCTCGACAGATCAGCAAATACAATTTTTTGACAAAAAAGGACAATGCCACTATTTATTCTTGCTTTCGCATTCGACACTGAATGCAACATTGAATTGTTGTGGCCATAAAAAAAAATATATATATTCAAGCCAATTTTGTTTGCGTCGCAACAAATAAAGCCATGGCCAAACACAAATAGCTATTCCGCCGAAAAGGAAAACAAAAAATAGCAAGAAATATTGTCTGAAATCGTAAAAATAAACGAAGCAAAATGGCAAAGCTCAGCTGAAACTGGCAGGTGCTTTCCACCCACTCCCATTTCTTTTCTTTCTTTTTTTTTTTGCAAAAAAAATGCGTGGGAGTTGGTGGAATCAATTTCCGAAGGCAACAGCTTCCTTTTTTCCCCCAGTTTTTGCTGAAGCGTCAACAGATTTGATGCGATTTGAATGGGGCTGTAAAAAAGGGGAAGCTAAACAGCAATCACTGCACAAACAGAAGGTGGAAAGTCCCCAAATGGCTGGCCATTAAATACTTTAATATTAGTTTGCCTCGAAGAGATGCCCAGCCGAACAATTAGCAGAAGAAAAGCCATGTGGTGTTGGGAAAACAAACTTTTTGGCCACGAACGCCGCCGCCGCCGCCGCTGCCAGATGTTGGGGCTTAAAATTCCCCTGGGAAATTCTACGAACCCATTTCGACTTGGCCCAAATGCTGATGATGCCAAATGCGGTTAAATGAAGCACTGTCATTGCAATTGAGGCTGCCTACGAATGTCACGTAGCTTCCCGCAGGCCAAAACTTGGCCAAAAAGAACATATATTTCGAGCATGTTTTTCGTTTGCGCATTTTAAGCATTCTGGCAAGGAATCGGGCCATCCAAATACCAAAAATAAACGTTTTGTTTGCTCAAAGCAGCAGCTGCTTAAGAAATTCTGGCTGAAACATGTTCCAAGTATATGGAGGCCTTGGTTCTCTATCAGCAGTTTCCAAACATTATTTAAAACTTCTTAACAAAACTTATTTAAAACCAAAGTGCTCTCATCAATTTAAGCATTAAATGTGTATAGTGTGCGGAAAGAAAGCTCGACTGTACATAAATAATACTACTAACTAAGGGCAGGCGGAAATAAATGTTGGACCTGCAGCCTTGAAAACTCCCAATTTGCTGAGCCAGCCCCTTCGAAATTTCCCGAGTCGCGTTTCCCACGTCCTGATCGAACACATTTTTTTCCTCTTCTCGTGTTCGTCCTCGTGTTTGGGTTTCCTTTTTGCTGTTTGCCACATGAACCACACATCGCCACATATGTATGTATGCAATCCATGGTCTATCCACCCAAAGGAAAACCACCTCCATTCGGTTGTCGGTGTTGTTCTTGGCAATCAAGTGGGTTAGATGCACAGCAAAATGATCTGAGGGGGGGGGATAGTGGAATTGAAGGGGCATTGAGAGCTCTTATTGTTATTTGCTGCAAATGTACGTGCCTCAGTCGCATTGACGCTCATTCTCATTGCTCATTGGCAGTAGTTGCCGAAAAGTTGGATGTGTTAGCTATCGAAGCGGCATTTTTCGGGCAAATTTTGGGGGGGGGAGATGTGGGTGGCGCCTCCAACAGTGTTCTCAAAATCAAAAGTGTTGCATTCAGCCTGAACTCACTTTGTATTGGTTTTCAATTGCAATCGGATTCCCATTGCACTAAATCCCTTTTGTTGGCTGCTTGGTGGGAATCCCACGCGTTGTTGAAAACGAAATGGAAAACTTGTAGATGTTTCTATCGAAAATTGGCTTTGCTGACGCTGTGGAAACGCACAAAAACACCCACTACAGTTTAATTCTAATATTTCAAAGCTAATTATTGCAACTTTCGCAGCGAAAAGAGAGAAAAAATACATTTCCAATATAACAAGTGTACTTTGAATTTGAAACGCAAATATGGCAGGAAAAGTTTGGTGCCTTTGTTGTGAGAGACATACGTGCTTGGCTTGATTTAATATATCCTTTATATGTTTTATAAAGGCTTCTCCAAATTTATTTCACTCACAGCCTAAATAAAGAGTTTTAAATTTCATCAAACCACCTACTACATTTTGGCTCAGCAAATTTAATGCAAACATTTTGACAAGCCAATACTTTTTTCACTACTGTCCCATCCAAAATAAACATATTGAAGTCATCTTGATGTCAGCTTACATCCTTCACGCTTTCCAATCTAAAATGGCAAGCTGCTGGTGTAAATTCAAATGCAACTCGCATGTTCCTTCAACGAGATATTTGTGTTGTGCGCGGAGGGACGTCCTCTTTGCCAGGCGAAAAGTAGGAGGATCTGGAGCAGGAGTGGGGACGACCGTGAGCCATGTAGCGATGTGCAGCCATGTGGAGCGGCAGTCCGAGCGAGGAGCAGAAGAAGCCGCAGGATTGCACAACGAACAATGCCCAGTGCTCGGTGCTCATGGGTTGCATGCCGCATATTTGCTCATTGTTACAGCTCGCAGCACAAACGACATTTTATTTGGTTTTTATTGATGGTAGGATGGTGGGCAATGTTGGGCAAGGGAGTGAGCACCAGTCGTTCGGAGTCATGCATAACAATGTAGCGAGACAAGTTGGATTTTAATCGAAAACGCCACGGCGCGGACATGGTTGCTGTCACTCAGTTCCAAGCCACTGAATCCTAAGGCATCCGGATGCCCAGGCACCTGACCACCAAAGATACGCGTCTGTACTTACCGTACTTTCGCCATCGTAAGTCGGCCGTTATGAAGTGCCATAAAAAAGGCTGGAAGCTGCGGCTTCTGGCAGCCATAAAATAGGCATTTCCAGCACATTTACCCAAGGTGCAGTTATTACTTTTCAACATAATTTCTTCGGGGGCCATAAAAGCCAAAGCATGCATCAGCATTTTGATAACCGGAGTGGGCCAGCTGCTCAGCTATACACACATACGTATGCAATGACGCCCAACTTTTTCGAGAAGCTGCATAACTCCCAGAAACTTCTGTCTCCGGGCGTCCAATTATGTGGCGCAGTGTATTGCTGGCTGGTGGCCAAAAGTGCCAGAAAGCGTTATGCTAATGCACATCACGTATACGCCGCATGCACCGCAACGAGCAGTGACATAATGTGCTGCAACGGGAAAAGCCACTGCAAATGGCAATAGGTGTGGACAGGAAAGGGCGGAAAAAGGGTGGCGGACAGACATCTAAGGACACGAAGCAGCAGGACATTGTGAAAAATAGCCCGGTACACTTAGCGTTTTGTCGGGCGTCTTATTTTTCAGACGGGTAAAAAAAAAAAACAACAACAAAAAACACGTCTATATGAACCCAAGGACTCGACTAAGTGAATACGTGACATTGCGGCACAGACAATTTTTCAGTTTTTCAGTTTTTCTTGTAACTTAATTTTTCAACTTGCAATTAGAAACAATTTTGAGCAATTAACTAAGAAAGCTAAAATCGTTTGCTCCACAATTGGTAATGCATTTGACTAGCTTACGTTCAACTAAGCGTATACTTAATATTTCTCACTTTTAGTTTTACTGCATCCAGATCTTAGATCCTTTAGCTTACTACAATAATAATTAAAATTTTAGACTAAAATCATGTATACAACATTAAAAAGATAAGTTAATCAAAGCTGGCAAATAATTAAAAGAAACTTTTTAAAATTTGCCTATTTTAATTAGCCTTCAACAGACTTAAATTGCTTTAGTTTATGACTTTTCTAACTTTCTATATATCTTTTTCGTTTCCCCCCCGCCAACCTCCTCTATGCCATCTGTATACTATCAACATAATATACTATATATCTTTGCATATACTTCTATAATCTTGTGCATTTTTATTTCAAAACAAACAACCTAACAATAACCAAACTAAAAATAATCAATTACCGAATTAACTATACCGTGCACGTGGTGTATAACATTTTGGGCTGCCACCTTCAACTTCCGACTTATCTCACAAATGCAATTTGAAAATCAACTCTGAAATAACAAAACAATTACCGCAAATCAAAACTCTTGCCATCTGCTGTATATACAAAAATTTGCATACAACAATCTGCAACCAATTGCACTGCCAACAATAAAAACAAACCAAAATATTTCGTAAAACAATACACAAACTATTTGCATTACTGCAAACAAAACCGATACAAATGAAATGAAATAAATAACATAAAAAACGTATATATACATATATATATATATATATTTAAACCACACACTGAAGGAGGGCATTGACGTAAGTATTTTTCACCCCATCATCAAACATTCAAACAACCAAAAAATAAAAGAAAAGCCCAACAAAAAATATTAACTCATGTGCGTAAAATAGTGATTACAATAACACTGGTGGCCCATTTAAACTCTTAATAAAAGTGTATCATTTTGAGCTTTGGATAACACTTGTTTAAACAATCATTTTTTGTTTTGACGAGTACGTAACAATTTAATTTTATTAAAATAAAACAACCAATACCTACTGTTTTAAAATTTCCTGAAAAATTCATGTACATAAAAAAATGCATGCTCTATTTTGTGAGAATTAAAATATTCTTTTTGCTGTGTGAATGATATACATAAATCTTTCAATTCAATTTATAAGCATAGTGTATATATTCAAATAAACTTAACAAAGTGAAAATAATGGAGTCAAATAGTGACAAAGAGTGTTATGTACATATTTATGAGGTTTTTTAAGACACCTAAGAGATACTTTCAAACGTATGCAATGAATTTTTAAATTTTTAAATGCATTTTGCTAGTTTTGCGTCCAAGTTTTTAGACAATTCTTCAAATTTATTCCTTTTGTTGCAGTAACTAATGAAAGCTTACACCTCTATTAACGATGAACAACTAAACTTGCTGCCAGTAAAAGTTAGAGTCATTTGCAATTTGCCGTTTTTAGGGTCCTAGCCGAAAGCCACAAGCCAACTCGAAACAAGAAAATGATATCTACGAGCTACTAATTAGACTTTTGATGGCATTGGTCCACCCCATTTGCCACTTAACACATCCCGGCTACCCAGTACGTGAACAGCTTTGGCCCTAACGATGTGAGGTCCACGCAAATTACACGTTGATGTGGAATTCCTCCTCCTCCTCCTCCATGGGAACCTTTTGCATAATTTAGTCATTCAGTTCGGTGGCTGCAGAGGCTGGCGAGCTGGGGGAATGGATATATTTTGTGGAAGTGCCATATGGATAATGTCAGCCGCAGGCTGACACGCTCTCTGCCACCGGCTTTTCAAAGTGTTGAAGTGTAAAATAATTACTTCATTTCATCAATGTGTTGGCATGGGGGCCACATCACATAACATCACATCTCACGTTCAAGGCGAACATCGACTTGAGTCTGGGCAATTTGACAAAGAGCCAGGCGACGAAAGTGAAAGTAAAAACCCAGCAAAATGCGATATATACGTTTTGCGTTCGTGTGAAATTCAATTTCAGCAGCTTTGCTACCGCCAAGTGGAAATAGGATCGCAATTTATAATGCCGTGCTAAGCACATTTTTTTTTAAAGCTTAAGCGGAAAAGGGTAACCAGTTAATGGGTTTCTAATCCCGGTAAGAAATAACAGTGCGCCCGCTGCGTTTTCTTGGCGCCAGTAAAACAAATGTTATCAGACTTTACCAAGGATAAAGAAAACAAAACCTTAAGTTTCACCTCGCAGCTTTTCAATTTTTCGCACCGTAAGTTCACTGGTAAAAATATTTCGCGAAATTTTAAAATAAAATCATAGTACATTATATTAAACGATTCATCCCTGATGCATATTTTAGGCAACATTTTACGAGATTTAAATGTTTTCTCTTGTATAATTAAGCAACTTACTATCGGCTCATTTTTTAAAATTTAAATTGAAATTTCACTATGTTGCCATATTTTTTTCATACGTGTAGTGAACTTGAGGCGCCACCTTGGCCACATTGCATAACCCCCAAAATTCCAAACTGCATGAGTATATGTGGGGGGTAAATTCATGTATGTGAAAGGAGGTTTATATATGGGGGCAAAGTAATTCGTGCAATTTGCCGGGCGCAAATGGAATCGATAAATTTCGTGTTCCCTCGTGGAAAACACATCCGGAAAAATCCCGAATGAGCGCAGTGAATGGTAATGACAAATCTGCTCTACCTGGGCAATAATTCATATTAATTAGCGAGTGTCAACGGCAGAGAACACATATATTAAACGGCAGTATGTTTTATTTAGGATAATTAGGCTTTTACGTTAAGCTTAATGAATGAGTGTGGAATTTGGTATACAAGTTTTTTATACATACGTAGCATGTTTATTAATCTCTTAGGATTTTCCTAAGACAAATTTGTCCCATTTCCCATTGCATTTCTAAGAGCATGTTTTCATTATAATTAGCTGTATCTTGCATGAGCTCATACCTTTATACTTAACTAATCAAAACCAAAATCGCACCAACCAATACAACTTGACCCGTAGTTTAGGCCTATGATATTAAAGGGTAACCCATTTGGAAAATTTCAAGATAGTCTAAGCAAATCTTAAAAAAAACTGTTTTGCTACACACATTTGTTTATGGATTTAGCATACTTCGTAATTAAATTTAGTTTATTCCTTTTGTACGTTATCCAAACACTTTTATTTATGTAGGAAAAAGTATGCTAAATCTTATTTATAAATACTATTTTATGTGGAACATGCATATAAACAAAACTTGTTGGATAATATTATATTGAGGATTGCAATTTATATCCACAGGGCGCCACAAAGTTGACCAAAGAGGATATTGAAAAAGTATTCTCACTCTACGATCGTGTAAGTAAAGCAAAAGACTAAGGAATATATATAAAGATGTAAAATCTAATATGATATCATTACAGGACAATAGCGGCACCATTGAAAATGAGGAGCTCAAAGGCTTCTTGAAGGACCTTTTGGAGTTGGTCAAGAAGGTGAGTGTCGCTCTTAAAGACAAATGAAATAAAATGTTAATATTGTGTGGTTGCCAGGACGACTATGATGCCCAGGATCTGGCCGCTTTCGAGGAGACCATCATGCGGGGAGTTGGCACCGACAAGCATGGAAAGATCTCCCGGAAAGAACTGACCATGATTCTGCTAACACTGGCCAAAATATCGCCCGACGACGAGGAGTAAGCCGGATGTTCGAGAACATACCAAAAAGAGATTTTAGCCAACTCTATTTTTGTCACCCGAACGCGGGAAATCCAGAAATGAGGCCAAAATGGGCTTCAAGGCAATTGTTTACTTTAGAGCTGCATTAAAAGGGGCAGCAAATAAACAAAAAAATAAAAGGATATTGGAATCGGGGATGAATCCTGAGAGATTCAAACCGAAACGAAGCTATTGGTATAAAATAAATCTAATATAAATGTTCAAATCTTAAATAAATGTTTATCGTACGTTAAGATATTGAGAGTATATATTTCCCCCAAAATCAAACCAAAACGGAAATTTATCCAGTCAAACAATTTGCAACACAGAATCGAGCCACTTAAAGTAAAAAATTAAGAAATGATAACAACAAGATCAGTACATCGATTTTATATTATACTATATATGTATTTATATTTTCTATGTGTATTTGCATAACGTACTTTATTTAATTACCAATTAAAATCGAAATAAATGTAGCTATTTTTAAGGATACCACATTTATTTGAGACTACCTAAGTAAAAACATATGTGTGGCTACAATCTGTAGATAATTGTTGTTAATCATTGTGACAGTACACCCTAAAAGTGGGCGGCTGCATTCCGCGCCCAACTCCCCGCACTTGTGCTATGAATATCCCCCGCAAGCATCAATCAATCAATCAAGAGGCACTTACATCAGCCCGAGGGTGGACGCCACTAATGCAGGTGAATGCAAATGCAAATGCAAATGCATCCGCCACCTGAACGTGACAATGTCAAGCTGGAGGGTGGTGATGCATCCAGTTAATGTTGGACACGCACTCGTCCTTGTATTTTTTTCACCCGAGGGGAGATTACGAGGTGCAGATTGACGCCGTTTTAAGGCTAAAATTTTCACCCAATTTCGCAACATAGGCAAATTGGTTATTTAACCTCTAAACAAAAACCTAAAGTTAACCAACAACGCTACGAACTATCTAATGTTCTTTCAAGGTGCTATAGCTATATATATACATTATGACTTGTTTCGATACGTATTCCCTTCTCCATCTGTTATCATTGTATTCTTTCGAAACCTAACTAACTAAATAACTAACAACTAATAACTTAAGCTTTAAAACCAAGACAAATTGTTCCAATCCTGAAACGCTCTTTGCCCAAAGATTCACTTTTAGAGCCATAGTCATGAAATAGATCAATTCCATCGCCTTTAAAAATGAAACCCTGAGTAAAGATGCCATGCAACAAAATGCCAACTTATCATATAAATATACTAATTACGATACAACACTATATGATAACATACTTATGCTAATCCTAAGATATTGTTCAAAACCACATGCATGTAAAGCTTCGAAACGGACTTTCTCTATATGAAACAAGATACCAAATATCGAATATCTAAATGGATATATGTCTAACACTATGGAAATACAGCAGAAATGTTTTAATAAAATAAATACAATACAATCTATGCAGACATCAAGGGGTCAGCACTCCAAAAGTAGTCTTTTGATTTCCTTATTTTTTTTTCTATACACACAGGCGTTTGTATTTCCGATTGAGTTTCTCCTGGAGCTCTAGAAGATCATTCAGTTTCTTCAGCATATCAGTGGCATCAAGCACTTTCTCGGTTAACACGGCTAAGGGGGAAGAACAATCCTTAAATGTTTTCTCCTGTTCCACTTCCGAGTCAACGAGACAGTTGACAATGTCCATCGTTTTCTTGATTCGCGAACAGAAGCTATGGTGGAACTTTATAGGTAACCACTAATAACATTAGATACAAGGTAGTTACCACTTGGCATCCGTCATTCGATTACTGAGAATAAGCTGCCAGGCCATGCAGCTCTGCAAGTGCCAGGAACAATAGCAAATGCCCAGAGTCTCCGTGATGGGATCCTTCCATTCCTTGATGACCGCACACTGAGCTGGAGGAAACCGCACCTTCTCCACCAGCCAAGTGTGCCAGATAATCGTCTTCCTGTTCTTAAATTCCGCGTTCATTTGCTCGGAGTCCAGACGCTTGCTTCCGAAATGTCGCTCCAGAAACGAGGTTGCCTCCTTTTGAGAATCATGGGGATTCGGTTTACTAATCGGCCCCACTTCCATCATGCCATTTTGAAAGTTCAGCCACGAGGGATTCGCGCAGAAGGATCGTGTTGTAGCATCTGCATAAGTAAGAAAAGTTTCGCTAATGGATTTTATTTGGAGAGCACTGAATTCGGAAATTAATAATGTAAATGTAATGAATCGAAACTTCTTAAATCTCGCACTTTAATATATTCTGTATTAACTTCTGCATACTTTAGAACTTCCTCAAAGATTTAATTTTACATAAAAGAAAAAAGGAGAAGGACCCTATAAGAGCTTGAGAAATTCCCTTGAAGGATCCTTCAACCCAGTTTCCTCCTTCGGAATTTGCAAAACTCACCCACTGCCGACGCTGACCACCAATTTGGAGATAGTTTCACAGCGGGGCGTAGCAATTTGTTTTCGAGTCATGGTAACACGGTCAATTTTACAGGATATCTCGAAAAACGTACAAAATCAAACGAATGTATAGGTCGGCGACTACTGAGATTAATAGGTTCCGGCATTCATGGCCTTCACATCCAGTTTCTGCTGATAGGCCAGTCTCTGAAGAATCGTGGGATGAGTGTGATGCCATCGAGCATAGCATTGGTCGTAGACCGGAAAACTCATATGATCCGCATAGATCTTAACCAGCGCCATCCTCAGTTGGATGGAGTATCCCATGCGATGGGCAAATTTATCGGCGGCATACTCAAAGCGACGCAGATTCCACAGCATCAAGACATTGGCCAACGTGAGATAAGGAGTAAGGGCAAATTTCAGAACAATGATGAAACCCACTATGATGGGCATAACGCCAGGCTCGAAACCCACTGCCATGTATAGCTGGGGAGAGTGAAAGAACAATCCGAAGAGTCCCATGGTGATAAAGAAGTGAATCTTCATGATGATCGTAGCCTTGTAGAAATGTCCGTGCTTCCAGTGACCCAACTCATGGCACACCACTCCCGCCACCTGGATGTTGGTCAGACCTCTGCCCACCTCATAGGGATGGATCTCATTGGGTTCCTTGCCCTTGTTCAATAGCAAGGTATCAAAAATTACAATTCTTTTCAGGCAGCAGCTCCCGTAAAAGTAGGCATTACTATACTGCATTGTCCGGGTCTTTATGATAAATACCCTCTTCATGGGGAAGCCAACCACATCGCAAACACGCTTCACCTCCATATAGAGGGCAGTGCCCTCTGGTAAAACCACCTGTCGTCCAATGCACGGAATGCAGCAGTAGGGCAAAAAAAATACCAGCAACAGGGTGAACGTAGCCCAGAACAGCCAGAACCAAAGGAAGAAGTAGTACCCAATGAACTTTACGCTGAACACAATGGCCGCCGCCAACGGGAACAGGACGAGCTGGCTTAGGAGAATGGACATTGCTCCAATGCAGCAGTAGAGGTACCAAGGAAACTTGCCCGACATCCCATATCGCAACTCCAGCAGGCACTTGTCATAGATCAGAACCGGCAGGAACCTTATACAAATGTAAATGGTCAGGTAGAAAACAAAGATCAAGGTTATCCAGATCTCTTGGGAGGTTATTTTCTGTAGAGTCTTCGCAGACAAGCTCCAGAGGAATGGATAGAAGCCCAATATCAGCTCACAGAGCGTAATAATCAAGTCGATGAGGTACTTCCATATCTGTAGCTCCGTTTTATGCAGCTCGTAGATGCGGGCCCGATGGTAAATCTCCGGCGGAATGATTCCTCTCAGCTCCTCCGGCACCATAATCGCATTCAGGCACACCAATTGCTGGTGAAAGAAATCCGCGATCAGTTCTTCATGGGTGGAACAACCAATCCACTACTTACCTGCCTCTTGGTGAGTATCATCTCCCATATCCGGTCAACTAACACGATCAGACATAACACCACCAGCACTATGATTGGATCTACTTTCGGCCAAGTATCGTAGAATGCCATCAAAACTTATCATGTTCCCCCAACAAACAATGTTTACTTATTGTAAAATATTGTATATATCTATATTACCCAAGACGGATAACTCAATCAGAAGCTACTATGTTTGAGAAACACCGATAAAAAATATATCGCCTATCGTCGAAATTCTTCCAGACGACTCAACCGATCCAGCATGGTGGGATGCGTATGATTCCAGCTGGAGTAGCAAGGATCCGAAACGGGGAATGCCAGATTATCCGCATATAGTTTGAGCAGTGCTTGTCGAAGTTCTCCTCCATATCCGAGCTGGTAGGCAAACCTATCCGCCTGGTACTCAAAGCAACGCGTCATGCTAAGCATACTGAAGTTCGCCAGTGTCATGTATGGAGTCAGTACAAAGCCGAAGATTATTAAGCATCCAATGACTGTCGGCTGGAGACCGGGAGGGAATCCCACCGCCTGGTAAATGGGCCCATGAGAAAACAGAAACGCGAACAGCAGGATCGTCAGTATGAGATGGACTTGGAACGCCATGATAGCTTTGTAAAAATGTCCATTCCTCCAGTGACCCAGTTCGTGGGCCACCACAGCAACCACCTGAGGATCCGCAAGTCCCCTACCCAGCTCCTCTGCCGTCAGGTGGGAGAGATCTGACTTGCCTCTATTGAGCAGCAATGTATCGAAGATCACAATTCTTTTCAGGCAGCAGCATCCGTAGAAAAAGGCATTACTTCCCGTGTTAGGGTCATGCACCCGGATGATGCGCACCTGACTCATGGGAAAGCCGACTTGTCGCGTAAGGTACTCCAGTTGGGTGCGCAAGTTTGAGTTTTCCAGGGGTACACTTTGGCCCACAAATGGATGGATCATAAATGGAATCAAGAGGAGTACGATCATTGTCAGGATCAGCGATTGAAGGTACAAGCCCAGGGGAGCATATGGCCCCAAGCCGATAAACATGTACACGAGGGCGACCACCACCAAGGTGGTAATCATCGCTCCCACAACCAGGTCAACGACAAAGTGACAGATGCGGGACCACCACGGTGGTTTTGGCCTGGGTTGCAAGCTCTTGATGCAACAGCTCTCGTAGATCATGGCCGGTACGCTTTTAAGCCAAAAATACACGCTCAGGAGAAGCACAAAGATCACGGATACGCAAGCCTCATGCTCCATCCACTTGGACAAGGCGCACTTTCCAGCCACTCCATACAGCCAGGCATAGAAGCCGAAGTATAGTTCCATAATACCCAATATAACTGCCGAAAGCAGGGTGTTGACAATGGTGAACCAGCCCTTGTGAATCTTGTAGACGCGCATCTTGTCGTAGAGCTCCTGTGGTAGATAGGGGCTGATAACATTCGGTACTTGTTGCGTTTTGTAGGCCACTTGTATCTGAAAGAGCAATTTAATCCAAAATGTACTCGAAAGATGTAATCATCACTTACGTCCCGCAGCATCAGATATACGCCCCATAGATTGTCCAGAACCAAGAAAGCTATGATTATGTAGAGTATTGCTAGTGGATCATCCCAGAAATGTGCAGACATGTTGGGTTCCTCTGACAACGGCTTGACATGTTAGTCATATTTCCTTAATTTTGAAGCTCCGTTAGGAAATCATTTTGAATCTATTGGTGACGGATTTTTAACTACTAGCTTACATGTTTTGGGAATCACATAAGATACACGTTTCCACATTGCAAAATCTTAAATAGCTTGTTGGGGTAAGTCCCCTTACTTTATTTTGTGTACGTTAAATCAAAGGGAATAGTGTAAACTTTGGTCTTATGTGAAGTGAGCTGTCTTAGTTCAGTTTCTTCTCTTCCTTGAGCTCCTTGAGTCGATTCAGGCGCTGGAGAAGAGTCGGATGTGAGTGGTTCCAAGTCGAGTACAGCCAATCGTAAACGGGGAAGCCAAGGTTGTCAACGTTCAGTTTTATGAGGGCCTGACCCAACTGCTCAGCGAATCCCAACTTGAAAGCGAACTCATCAGCCTGATACTCGAATCGTCGCGACAAAATTGTCATGGCGAAGTTCATGAGGGCATTGTATGGCGCGAGTACGTAGGTAAAGACGATTAGCAAACCGACGAGAATGGGCCGAGTACCAGGTTGGAATCCCATGGCCACGTAGAATGGTGGATACTTGAAGACATTTCCAAAGACCAGGAACATCAGAAAGAGATGAACCTGCATGATAATAATGTTCTTGGTAACGTGTCCCAGTTTCCAGTGTCCCAGCTCGTGTCCCAAAACAGCCAGCACCTCCTCGTCGGTGCAACCCTTTCCCTTTTCTTCCTCTGACAACTCGGAGTCGTCCGGTTTACCTTTGTTTAGCAGCAGCGTGTCGAATAGCACGATCCTCTTCGAGTTCCAGAGGCCATAGAAGTAGGCATTGCTGTGCGAGGAGCGCTTGGATCCCTCCACCACGAAAAGCTTAGTGAGCGGGAACTTGAGCGATGCGGCCAGATCCTCAATCGATTGCCTCAGAGCACCCTTCTCCAGCGGAGTATACTTGTCGAACAGGGGAGCAATGAAAATCGGATACAAAGTGAGTAGAACCAGCGAGATAACGCCTGTGAAGATCCACAGCCATATGAAAAAGTTGTCGCCGCCGCGTTGCACGATGAAGATAATAGCCGCTGTGATGGGAATCATGAGGACCTGGGTGACTAGGAAGCCTTTGAGCTGATCCCAGGCGAAGAATCTCGCTGTTTGTTTGTTAAAGCCATGCGTCTCCTCCAGCACGAATATCTTGTAGATCTTGAAGGGCAGTCCCTTGAAAGTGCTCAATACATTCGATATGAGCACAAAAACGCAGCTGACGATGATCTCGTTTTTGGAGTCCCATTGCAGTTTATCCACCACCTGGACGGACAGCTGCCAGAGCACAGCGATCAGTCCGATGTACAGCTCCATGCAAAGCAGGGCCACATCCATAACAACAGCTTTGAAGATGCCGAATTTCTCCTGGTCCAGACCATATTTCCGCGCCTTATGGAACGTATCCTCGCCCATGTGTGACTTCAGTTCGGCCGGTACCTTCAGTGCAGTTTGGTACACTTTCACCTGGTGGCGACGGCAGGGTAAATCATTTAATGGGGGCAAGACATGAGGCGGCCAATTAACATTTGCCACTCTAAATTTATCATTCGCATTGATAAAATTCCTCGCCAAATGTCGCCTGGCTAGAACATGCCGGCACAACGGAAAAACTTACCTGGCGCAGCGATATATAGATCTCTAGCGCATTCTCGATGACTACGAGGAACAAAATGCTCAGCAGCACGGTGTCTGCGTCCAATGATGACATATTTAAATGCTATTTCATTAAAGAACTAATAAAACTGGAATTTTACTTTACAAGCGCCAGTGACGAATTGTTAGTGTGACCGTCATGCGGCCGTTTAAATATATCACAGCAATAGCAATTCGAACGATCTGGCAGCGCTGACTGCAACAGA 0 1 12482941 12516876 0 0 chado-1.23/doc/examples/dicistronic-gene-example.chaos000644 000765 000024 00000160547 11256707742 023103 0ustar00cainstaff000000 000000 auto:exon19 exon 2R-fragment 28223 27914 -1 0 0 auto:exon18 exon 2R-fragment 28650 28277 -1 0 0 auto:exon17 exon 2R-fragment 30322 28917 -1 0 0 auto:exon16 exon 2R-fragment 30516 30381 -1 0 0 CG30461-RE CG30461-RE mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAATCTCAGTAGTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCT auto:exon15 exon 2R-fragment 28223 27910 -1 0 0 auto:exon14 exon 2R-fragment 28673 28277 -1 0 0 auto:exon13 exon 2R-fragment 29050 28913 -1 0 0 CG30461-RD CG30461-RD mRNA CCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAGTGGCGAAACTTTTCTTACTTATGCAGATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT auto:exon12 exon 2R-fragment 28223 27910 -1 0 0 auto:exon11 exon 2R-fragment 28650 28277 -1 0 0 auto:exon10 exon 2R-fragment 29054 28917 -1 0 0 CG30461-RC CG30461-RC mRNA GTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT auto:exon9 exon 2R-fragment 28223 27910 -1 0 0 auto:exon8 exon 2R-fragment 28584 28277 -1 0 0 auto:exon7 exon 2R-fragment 29054 28917 -1 0 0 CG30461-RB CG30461-RB mRNA GTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCATGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCTGTAT FBgn0050461 CG30461 gene auto:exon6 exon 2R-fragment 30322 29062 -1 0 0 auto:exon5 exon 2R-fragment 30516 30381 -1 0 0 CG9002-RB CG9002-RB mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAA auto:exon4 exon 2R-fragment 28223 27914 -1 0 0 auto:exon3 exon 2R-fragment 28650 28277 -1 0 0 auto:exon2 exon 2R-fragment 30322 28913 -1 0 0 auto:exon1 exon 2R-fragment 30516 30381 -1 0 0 CG9002-RA CG9002-RA mRNA GTTGGGGGAACATGATAAGTTTTGATGGCATTCTACGATACTTGGCCGAAAGTAGATCCAATCATAGTGCTGGTGGTGTTATGTCTGATCGTGTTAGTTGACCGGATATGGGAGATGATACTCACCAAGAGGCAGCAATTGGTGTGCCTGAATGCGATTATGGTGCCGGAGGAGCTGAGAGGAATCATTCCGCCGGAGATTTACCATCGGGCCCGCATCTACGAGCTGCATAAAACGGAGCTACAGATATGGAAGTACCTCATCGACTTGATTATTACGCTCTGTGAGCTGATATTGGGCTTCTATCCATTCCTCTGGAGCTTGTCTGCGAAGACTCTACAGAAAATAACCTCCCAAGAGATCTGGATAACCTTGATCTTTGTTTTCTACCTGACCATTTACATTTGTATAAGGTTCCTGCCGGTTCTGATCTATGACAAGTGCCTGCTGGAGTTGCGATATGGGATGTCGGGCAAGTTTCCTTGGTACCTCTACTGCTGCATTGGAGCAATGTCCATTCTCCTAAGCCAGCTCGTCCTGTTCCCGTTGGCGGCGGCCATTGTGTTCAGCGTAAAGTTCATTGGGTACTACTTCTTCCTTTGGTTCTGGCTGTTCTGGGCTACGTTCACCCTGTTGCTGGTATTTTTTTTGCCCTACTGCTGCATTCCGTGCATTGGACGACAGGTGGTTTTACCAGAGGGCACTGCCCTCTATATGGAGGTGAAGCGTGTTTGCGATGTGGTTGGCTTCCCCATGAAGAGGGTATTTATCATAAAGACCCGGACAATGCAGTATAGTAATGCCTACTTTTACGGGAGCTGCTGCCTGAAAAGAATTGTAATTTTTGATACCTTGCTATTGAACAAGGGCAAGGAACCCAATGAGATCCATCCCTATGAGGTGGGCAGAGGTCTGACCAACATCCAGGTGGCGGGAGTGGTGTGCCATGAGTTGGGTCACTGGAAGCACGGACATTTCTACAAGGCTACGATCATCATGAAGATTCACTTCTTTATCACCATGGGACTCTTCGGATTGTTCTTTCACTCTCCCCAGCTATACATGGCAGTGGGTTTCGAGCCTGGCGTTATGCCCATCATAGTGGGTTTCATCATTGTTCTGAAATTTGCCCTTACTCCTTATCTCACGTTGGCCAATGTCTTGATGCTGTGGAATCTGCGTCGCTTTGAGTATGCCGCCGATAAATTTGCCCATCGCATGGGATACTCCATCCAACTGAGGATGGCGCTGGTTAAGATCTATGCGGATCATATGAGTTTTCCGGTCTACGACCAATGCTATGCTCGATGGCATCACACTCATCCCACGATTCTTCAGAGACTGGCCTATCAGCAGAAACTGGATGTGAAGGCCATGAATGCCGGAACCTATTAATCTCAGTAGTCGCCGACCTATACATTCGTTTGATTTTGTACGTTTTTCGAGATATCCTGTAAAATTGACCGTGTTACCATGACTCGAAAACAAATTGCTACGCCCCGCTGTGAAACTATCTCCAAATTGGTGGTCAGCGTCGGCAGTGGATGCTACAACACGATCCTTCTGCGCGAATCCCTCGTGGCTGAACTTTCAAAATGGCATGATGGAAGTGGGGCCGATTAGTAAACCGAATCCCCATGATTCTCAAAAGGAGGCAACCTCGTTTCTGGAGCGACATTTCGGAAGCAAGCGTCTGGACTCCGAGCAAATGAACGCGGAATTTAAGAACAGGAAGACGATTATCTGGCACACTTGGCTGGTGGAGAAGGTGCGGTTTCCTCCAGCTCAGTGTGCGGTCATCAAGGAATGGAAGGATCCCATCACGGAGACTCTGGGCATTTGCTATTGTTCCTGGCACTTGCAGAGCTGCATGGCCTGGCAGCTTATTCTCAGTAATCGAATGACGGATGCCAAGTGCTTCTGTTCGCGAATCAAGAAAACGATGGACATTGTCAACTGTCTCGTTGACTCGGAAGTGGAACAGGAGAAAACATTTAAGGATTGTTCTTCCCCCTTAGCCGTGTTAACCGAGAAAGTGCTTGATGCCACTGATATGCTGAAGAAACTGAATGATCTTCTAGAGCTCCAGGAGAAACTCAATCGGAAATACAAACGCCTGTGTGTATAGAAAAAAAAATAAGGAAATCAAAAGACTACTTTTGGAGTGCTGACCCCTTGATGTCTGCATAGATTGTATTGTATTTATTTTATTAAAACATTTCTGCT FBgn0050462 CG9002 gene 2R-fragment 2R-fragment contig 2R 12482941 12516876 1 0 0 AACAAATTTTTTTTTTATTTTTGTATTTAGCTTAAGGTATTTACAAAATTCGTACGAAAGCCGAAACACCCATGAAAATAAAAGAATTTGGTCAGCCCATTACCATAAATACAAATGAATAATATAAAAAAATCAATCAATTTTTATGTGATTTGCTACATGAAAGCTAGATTACTCATACGCCCCGAGTGCTGATGGAGAAGAAAATTGCAGAAAGTTCACAAATTACCAGCTGAGGAAGGAGAGCAAGAAAAGTGGGAGGTCTTGGGCATGATTAAGTCGTTTTTTCAACCTATTAATCATACGCCATGTTGGCCATTTAACAGTTTCTCACTTGTCATATTAAATTATGCTTTGAGCAGCGCGACGGGGATTAAATGTATTCATTATTCAGTAAGTGCACTCACTTAAGAGTAAAAGAGGCAAGAAAAGTAGCCAAAAAGAATAATGCAGAATTTCCATCGAGTGGGAAAAGTTTTCATCGATTGCCTGCGAACTTGTAAATTATCGGAAACTTTGTAACCGCAAAAAATTGAATAATTATGCAGAAGCCCTTCAAAATGCAATGCAGAAGTTGGCGCTTTCATGCACACACACTCTTGCTAACTTACTGTCTGTAAATATTTAAGTAAGAATCTTGTGGCAGCCACAGGAACATCGGCATTATCAGGACTCCTTGAGCGTTGGCATAAATATTTAGGATCCAACATCCTGGCACACGTGCATGTGATGATGAGAAACCAACTAGGGCGACGGTAAATTCGCATACGAGCTGCCAAATTACACTTTACGCGGATATTACGCATACGACGTGGTGGCATCGCTTTAAGTTGCACAAATTTGCTGGATAAATACGTGCGAAGGACACAATTTCCAAGAGCATACTAATTTTTCTTATTTTGCTTATTTATTCTTATTGAATTAATCCTTCAACTGTTGCTGCTGCGTTCTTACTGCCAATTTTATTTGGCTCTCATGGCATATTAAGTGCCAGCAATTTACCAAAACGAAGCATGCAACCCGGGCAGCCACATTGAAAATAGGAGGCGTCACGGGTGGCAGAGGGCGTGGCACACACGAGAGGGGCGTGATAATGAGCTGCAGTTTGTTTTGAGTCATGCGCTGGGCGGGGTAAAAAGGAAATTTGCTTCGTCTATCCAAAGTTAACGAAGCAACATTTCATTTGACTTTCTGTCGAAATGAAATCAGTGTAATCCAGCCTTAAATCAACTCAATAAGCGAAAAAGTGCCGGATCTCAGGCTCTCAGTATACATTGTAACCGCTAGCCTTTTGTTGGCCATTCTTAATGTGGTGAACCCGAGTAAGCTAACCTGTTTTCACATGGTATTAAAGGATCTTCTTTAAGTGCTTTGTTTGCTTTAATATTGCTCATAAAATGTACAGCCATTTGCAAACTACAGAAAAATTAATTAGTTATGATAATCAAAGTAATGGAAATTCATATTATATTTTTAAAATATTAAAATGTGTTTTCTAGAACTTAACGAAATCATCAAATGTTTAGAATCTATCATAATTAGGAAAAATGAAAGTTTTAGTACGAGCAAAACATTAATTTCCTGCCATCTCTAATTAAAGTCAGACCGAAAAACTTTATAGACCATTAAAATTATACTGCAATTACAAATGTAAAATCAATCCGCAAGCTGAATGTGAAAATAAGCCAGAAAAAAGGGATGAGGCATGAAAAAGCCTGCAGCAATTGGCACAAACCAAATGGCTCCACAGTGCCAAAAACCACACAAAAAAAAACCATGATAAAAGAGGGAAAGCTGTGAAATGCTGGGAAACTGAGAAGGGAAATTCCAGCAAAAGTAGAGGAAACAGTGAAAGGAAAAGCAGAGGAACCAACAAGGGAAATGGATCAATGTCGAATGTCTGGGAGCTTGATGGTAATTTGAGAGAGAGCTTATGCTCCCCATTGTAATTGTGATTTGGATTCGAAGAATCTGAAATGAATAGAAGCAGCTAAAGGGATAGACATGATTCAATTACGAAGCTCTTCCCGAAATCAGAGGTAAAAAAACCTACTTCAGTGCGTCGCATATCTGAGTGATAGGAAACATTTTCGTAAATTGTCTAATATGAAACATTATTTACTTACAGTAAGCCGAAAATGACACTCAATAACATTAATCTCCTTGTAATTTATCCCTTAGGAGTCCTTTTACAAACCCCAAACCAATCATTGCTGCATTGTTATGCATACATGTGACTTTTCCCTGTCGATACAGCATAGTAATTCATTTCACTTTCCCAGTTTTTCCACAGCACAATTTTTTATGTACTGATTTTCCTGTCGATTAAGCCCAACGGAATGAACACTGCCCAACTGCAACCCAAACTGAACAAAGGGACATATGTGGATATGTACAACATACCCAAATCCAGTGGCAAATTGCAACATATTTGCATGTGCCACTTGCAACATTTACGATCGACTAAAGCACTCACTCAATCATCGCTGGGGGACAAGAACAATAACAAACAGCTACCGAAAATACGACAAAAATTTCCGCAGCAAAGAGGGAAATCCCGCAGGAGGGAAAGTGGAAAAAAACTGGGTGGTGAGTGTAAGGGTGAAATCCATCGATTGCGTGCAGCGTTAAATGTCAGCCCGCAGCCAATTGCAGATGTCAACACATGCATGGCCCCCCCCAAAAAAAAAGGAAATGGATCCCCAACACAGTCACACACTTTGCGCCTAAAAATTGGCAGACATTTTCGCGAGTGGGTGAATTTCGGAAAATGTTGTGATTCATGCCCGCTTTTCCGGCGGCTCATTGCGCGTCGAATGCGTTCAATTACGAAATGCCAAAACTGTCCGGCGAATTCGTTTCAATTTCAAAGTACATTCGCAATCACTTTGTTCATTGTGCTGCCTGTCAATTGCATTAATTTATAATTATGTGCCGCCCGCCCACACAGGCACATCCACACAAAAGACAACTAATTAAGGCAAAGCAATTAACTTAAGCAGCGACTAAGTCGGCTCACGAACCACTTGAAACTCCAATTAGGGGCGTGGCACATCCACAATCTGTCTAATCCCATCGAGGGTCCAAGGTAATTTGGTCGGATATCACGATTTGCCTATTACTCATCCCTTCTATGTATTCAATCTACCGACTTTTCCTAGTTGTTTGCACTTTGAATTAATTAAGCTGAATTTGATTTTAGTGATTGTGTCGCTTTTTCTCCTTTTGATTGCAAGCTGTTTAATGCAATGTAAACAGAAATAAATAAAGCTTTGGGCCGGCTGTCGCACAATCTTCTGTTTGCCTCCCACACTATGTTATATAATACGCTTTCCCGATGCTGATAAGACGGCGTACTGAATACAAAAGAATTGGGGCAGATGAAGGAACAGCTCCTTTTAATACCCACCGAATTAGGGGACGCTCTTCCTATTAAAGTAAAGTTTGTTGTGGTATATATATATTATTAATAGAGTACAAAATAAGATTATAAAATAAGATAATAATAAATATATAATAAACTACGAATATATTCAAATTTAGAGTTCAATGCTTGAAATATATTTCATAATTCAAATACTCATGGTTAGGGTAAAAAAAACAAAGCCAGACTACTGAAAGAATATTGGCCGGGGATTGTATTGTGCCTGCATAAAAAGTTTTTCATCGCAATCAAAGAAGTGTTCCCGAAATAAAAACTTCCCAATTTTCCTTCTAAAAATCAAAAACAAAAGAATATGTCAATATATTTAAGGCCTCAAAAGGGAAATCACTCTTCAAACCACCCCAACTAAAAAAAACCCAATTTTTTTTTTATCTCCGCTCCAAATATTTGCTTTTTTTTTCGGGGGGGCTAACGTATGGATGTGTGTGTGGGGCATGATAAATTTTGAAAATTTATTTGAGCCGGTCTGTGGCTGCATTTGAAGTGGTAACCATTACCAATGCCACGATGAATCCCCATTCTCCGTTTTTGGTGTATAAACATTTGCATGGCAAATTTTTGGAGTTCTTTTATTTCGTTTTTACATATTATTCGGTAAATGTTTTATTCATGCTGCCCCACAAAATCCCATTAACAAATTTACACATTTTCAATATTGAAAATGTGCTTTACTTTATGTATAATAAAAACAAACCGATAAAAACACGAAAGCCAAAAAAAAAAAATATGTCTGTGAAGCAGAAAAATACTTTCAATTAAGCTATGTAAACAAAGTTTTTTGCCCGAACAAAAAAAAAAAAACTAAGCTGTGCACATGCTTAAGGCACTTATTTAAAATCTATTTTTGATTTTTTGTGGCTGCTGTTCCATGCGCACATTTATTTGGTTTTTAATTATTTTAATTGTACGAAATATACAAACACATGATTTCCTTTGTTTTCGATTTTCCCTGTAAGCCCAAAGTCAGCACAAAATCCTCTTAGCCTTCTTTAGTTGAGTGATAAGCGGCGCATTAGTGGCGAAAATTTATGGCCAACTCTCATGAGCCGAGTTGTTAATGCTGGGATTTCACAGCGATTTCTTATGGGATTGCTGTCGCGGTTTCGCAGATTGTTTTCCTCCGTTTACAACATCTTGTAATTTAGGAGGTAAAGTTTACAGATCACATATGTTCGTGGGAGTCAAGTTCTTTTACAAGATTGAAATAGAACGAATGGGAGTTTTGGCACAGGTTAAACCGAATGCCACACAGAAAGAAATGGTTAAGCTAAAACTTGTGACTAAATAACAAAAATAAAAATGTAAATAATATCATGCCTGTTTCTTAAGATTAAACCATATTAAGTCATAGAAAAGTTAGGTATTTCCTCTTTGGCTACATTCAACAAGTAAGAATGAAAGACAACTTTTCATGTTAATCCATAATAACTCGGTCAGGCTTAAACTGAACCTTCTGTTTTACCTTTAAGCTTTAAGTCACAAAGTCAGTGAGCTGCCACTCGAGAACCAGTGGCAATTGCATAATGGACACAGGTCCGTCCCTTTGATATGACCCAAAGATTAGGGAACAGGCACACACAATGGCGTTCATGGGGCGTATGATTAATAAACACTTTTAGTTTTCGTTTCGGTCAAAATGGAAACCTTTTCTAGAGTCATAACAATTAACTTTAAAGGTTTAGACATAAATCCTTGCACAATTGTAGTCTCACACAAAACATACATGTGTATAATAGAACACGAAGAAAAAGGCAGAAAGTAAAAAGTAAAAGATGAATAATGAATGAGCCGCACGCGAGCAGAAGCCAGGTGGATTGGGGGCGGGAAAATGTGGAAAAGCTCGGCGGCCATTCATGAGTAACACTTGACATTGCCTGGGCGAGGAAAATGGGAAAAGGAAAACCCACACATACGCACTGCGCCCGAAGGGCAGCCGAAGGAAGCTCGTTTCTAGTGAATTATAATATGGCATGCAGATAAAACATTGAAAGTCAAAAGGCCCTGGGGGGACTACAATTAAGCGCACCACCACCCATAGCCACCCACAAAACGGAGAGGGAAAACATAGCAGTTTCGACATTGGCGGAAATCATTTTCATATGTATGTTTATGATATTTTGTAGATAACTGCAAGTGCTGGCGCAAAGTTTACTCGGAATTAGCCATATCACAGAAAACAAAGCCTATATTCTGCGTATTTTTCTCGCATTTTTTTTTTTTTTTGCCCGGACGAAATAACACATGAGAGAAGAAAAAGCCCAGGAAATCTCTGGCGAAAAAGAAAAACAATTCAACAGTTTGTTGCCAGCAACATGTTGCCAACGCGCTGCTGCAACACTCTCCTACGCTCTCTCCGTGTTGAGTTTTTCACTTTGATAAAAGCAAAAGACCTGGCCATAATCGAAACAGTCTGCAAAGGATTCTAGGCGCCAGCGGTTCTCCAAAGATAAAATACCGTCAAGTATTAGGCAACGGCAATCGTCGCGTGCGTTTTAACCAAATATACTTAAAATCGAAAATTACCTGGAAAAACGGTCGAGAAAAGTGAATTTTAGTTTTTGGAAAAGAAGAAATTCCAAAAGCAAGCAGCAGTTTTAAAAAGTAAATATGATTTGTTATTTGAAACATTTTCTTGGCGAAGAACACTAAACAACTATATTGGTTTCGGCAGTTATATTTATATTTTTTAAAGGGCGCAAAATAACACTTTATGCATTTGTTTTTACAAGAAATGCTCGAAAACATTTTATTTAAAATAGATGTATTCTCCGCAAGCAGAATAAGTGATTTACATTCAAACATGCTGCGCATTTCAAAGTCAGTTTTTTATGAACTCGTTTATATCTCGCTGTATATAAAAATGCGTTTCAAACAAAAAAATTTACATTTTTCTCACGATTTCCAATCACTTTATTTAAATTTTATAATTTATGCTAAAAGCCTTTTAAATCTGGGCTAACTAGCCTAAGCTGACAAACGCAAAGCAGATTGTCCTTTTGGAAAAAAGCGTTCAATTTGCAATGGATTTCCAAAGAGGTGGAAAATTGGTTTGAAGAGGTCGTCGCAAAAAAAAAAGAGCAACAGTGAAAAAATGTGCGGGCATTCCGTATTCAACCCGCTGACAGCTTAAACCGTGTCAAATAGCTGAATTTTCCCGGACACCAGGGGCAAACCTTTTTTCAAGAAGTCCGCATTCAATTAGGATAGGAGTCGAACCCTCCTCATTGGTATGCCGAATGGCAGCCACAGGAGCTGACACTAAAATGCCGTCGCCATCGACGAATGTCCTTGACTTTGCCTATTCAAACGCAAAATTAAACAGCAGAAGGGACAAATAATGAGCGGGAATGGGTTGGAATGCCATGGTAATGGGTAATGGGCACTACACTACAGTGTGGCAATGGTGGTGGGGCACGTGGGGCAAGTGGGTCTGCGTGCCAACATTTACGAGTCCCCCTAATTTATGCTCATTCATAAATCTCCCTCGGTGGAAATCCCTTGCAATCGGCGACGCAGTCGACGCCAGAATGTATGCAATGCAATGAAATAAGGCAAATTGAAAGTTATGACTACATCAAGGACTTCTGTGAGGCGACGAAGATCTAAATACCCTTCAAAATGTCCAGGATGTTTTATAAAAAATTATACAAAAATTTTAACAATTTTTCAAAAAATTATGTTAATATAGTTCAAATGCACTTGAAAATCTAAAGAAAAATTAAAAAATTAATATAGAATAATTTCGTAATTAACTATAGAGATGCTTCTAATTTGTCCATTAAAATGTTACTAAAAGAACATATAGAATTAGCGCATTTATGAGCCAATTTGATGATAAATCAAAATGAGCCTTGTGAGAGCATGTGCAACCTTTTATGTTTTGTGCAGCATAAAAGGGAGCTGTCAAAAATAATTAAGAAATATCTAAATATAAAACACGACCCTTCGCTGGCTTCCCCTGAAGATTCGGCCACGCAGCGTTGTTTGCCAAGTGCAAAATTGGCTAATTAGATGACATACCACTTGCAACTAGCACGAGCCGGATTGTCCTCCATTCGAGCAAATGGCTTAATTGCAATTGCATTCCTAGTTTAACACAATATCGAGCAAGGAATTTCGTGTACGAACAATTAAAATAACTAATTTACTGTGAGTATCTAATTTTCGATGCTTTCATTTACGTTTTTCTCGATTTTGTACACGCTCTCGTTTAGCGAAAACAAATGGGAATCGGAATATCAGAGCCGAAGAATTATCAAAATAAATACGTTTGTCAGCGAAGAATGGAGGCATTTTGTTTGCATTTTCAGCCATTTAATGGCATTGGGAAGGAAGTTGGATTCTTGGTTATTAATAGATGGCTATTCGCAAAAGGATGGGTGATTAAGCGGATGGAAAACACTGGCCAAATATGGCGACGTCATTTGACAGACGCAGAGATGAGCAATGATTGCCATTAATTTAAATTAATATCACACTATTCAGGGTCAGCAAGATTGATGGGTTATTTGCAGTTCAAATTGTGTGGGCTTTGGAATACAAAATGGAAACAATGATGTAATCTCTCCGCTGCCAAAATAAATACGGTTTCTGTGAATTTCCAGTTAGTAAAGAAAGCAATTCGTAAAACAAAGCTTCCGGCAATTATTTGTGTACTTTTTTTCAAAGAAATAAATTATACGCAATATTAATTCTGGTTTAGCTGAACGAAATGCGTGGTTTTCAGAAAGCCATCTAGATTCCTAGTATAAAAATAAATATAAACTCGGAAAAAATCGGTGGAGGAAAATGCTATTACGAGTTTTTTGAGTTGGTTTTCATGCGAACTGAAAGATATTATTAAAATTCTATGAAAATTGAATATTTTGTTTTCTAAATTGTAACCAAACCTTTCTTTTCTTATCTTCTTTTAGTTAGGCTTAAAAAATTTCAGAGTTAAGTGCTCTTACTTTCAGGACACCCGCTACCTTCGTAAATGTCCTGCCACAATCGCAAGGCGCAGTTTCGCCCACAGGTATTGGGCGTAATTATCTTAGAACAATGTCAAAAACACAAAGTGCCATTAAAAAACGTTCGCGCCTAGCGGTAATAATTATTCTAATTACGAGGCGTTTTGCTGGAAAAGTTATCGAGGTGCTTGAATGCCCCGCAGGGCCTGTCAAATATGTATTTTGTCCGTGCAAACAAACCAGCCAAAAAGTGGCGGGGATCCCAAAGCAATCAGCATAATTTGCCTCTTGTTGTATTTTACATTTTTGCGTATTGACTTTGGTCGGAAATCTTTCCACACGCCGACATCCAGCTGGTTAATTACAGCTGTTGGCCCCGAAGAGCATTATTATTATTTATTATTATTATTATTATTTCTTGATTACTATTTACGCAAAGGCAGCGTAAAAAGTGCCTTCTATTAGCTATGTAAATATTTACATCATCATCACTTGAGGTTTTTCGGCAGCAATTACGCGTTGCGTCACCAAACTGAATAAACACTAAGGAAGCCTTTAAAAAACACGTTGAAGTAAATATTCGTGTGGGGAAAATATACATATGTGCATACCTTCGGCAATTTTGCATTTATTGTGATCTTTTTATGGTTCTGCTTTTTCCTGGATTCCATGAAAAACAAAAGAATACAATAAAGAAAAACAAATGACGCAGGTTTTTTTGGCCCAATTTTTTTTTCTTGGCTTGTTTGCCCGGTTTTCGTTTCCACGCCATCCTTTATTTATTATGGCAGGTTATAAAAATGCAATTCCAGTAATTGAGCAAACTTCAATACTTTCCAATTCTGTCGTCTTAAAATTGTGATATAGATTGTCAGGACTCCACGCTCTAGTTTGTTATTTATAGCTTTTGATTTTTGAGCCCTTTTCGACCCTTACAACTGTCATGTTCTGGCTACAGTGACAATTTCCAAATTGACTGACAGGCATATCCATTACGAAGTGTGTTTTTCATCCCAAATGGTTTTCTGGTGATTTGGCATTTTTGCGAAAAAATTGTAATTCATCATAATATTAATAAGATATCGATTTGGTTTCGGTTTTCAAAAAGCAAACTACCTCGAAATGAAAGTACGAAAGATCCTGTAATTTAATATGGCTACTATTTTAATAATTAGCTTTGCTGTTTTTTGTCAATTGCTTTAGGTTTCATTTTAAGTGTCACTTCCCACACATCACGTATACGCAGTGTATGCCATCATTAGAACTGAATTCGTTCCAAGATGAAATCAATTTAAGTGTCACACCCCAGACATAGTATGCACTCCATAATTAATCTGTTCTCCTTACTTTATTGCTTTTTACAAGCAAAGGACACGGTTTTTACATGCAAGCGAATTGAATTTTATTCACAGCTGACAGGGACTAATAACAATCCATAAGTATGACCACATGGGGAGTTGGCATGGCAGGACATCGCATTTCCCCTCCGCCCATTCGGAATTTAATTAAAACTGTCTAAAGCCCAGCGGGTGCCAGTCGCCGGACAAGAAGAAACAAAAAAAAAAAATGCGTAGTGTCATGCAAAAAACCATTATTCTTTAGATTTCATCCATGGTAGATTATTTTTCAATATAAATTCAACGGATCCCAGTGGTTAACCAGAGTTGGCCAAGCTAATTACGGCTCCGCGGTGACCAATAAAATGTAATTAAAGTCCGGGCAACAGCAAAAAATGGGCAGAAAAAATGTGGCTACTACACCACCGCAACTAGCTTAAAAGTAAAGAACTGAAAGTAGTTTCCCTCTGGCCCTGCGAATTTTCACACATTTTCTTTCGCACGCAGCGCTGGCTGAGAGTAAAAAGAAAAACACAAATGAAAAATAAAATACACAAAAGCTTCCGACCAGCAGGCACATCAGGCAACACATCGTAAACAACTTCTTGGCCAGCTCGGCATGACAAAAAAACCAGATTAAATCGCCTAGCGAACCAGATGCAATATGCCCCCCCAAAAATTCTTGTAATTTAGCAAATCGCTTCTCCAACACGAGTATACAAATTGGGTAGATTATCGACAGTAAATTACAAAGAAATTCTTCTCGCCGTTCTATAATTTCTATAATTGTTTACAAAGTGCCCAAGTCCGGAGGAAGAGGCAGCTCTCTCATCCTCCGAATGCAAACTACATAAATCAACATCTGAGGCTTCCTACTAAATCGTTCGCCGCTGCTGAGGAAGGAAAAATAAATAAAGCGATTTATTAAAATCAAAAGCCATAAACCATTCAATTAAGTGAGTTCTCTGCGAGCAGCTTAACATGTGAATTATAATTATAACCAATCGAAATGACCACTTTTGGGCAATTAAAATTTATGTTTGCACGCCATAAATTTGGGCATTCGGCTCAATAAATCAGCGACAAGTTCGCCGTCTGAAATCAACACTATATATCAAGAGATTTTCATTTTGTACTTTTCGCATAATGGCCAACGGTACCTTGGCACGTAATCATCTGCTCGGCGATGACCTAGCAAATTGGCATTTAAATTTTTAACTGCATTTTTATGATGTTTCCACAACCCTCTGACTACCAATTTCTTTTGGGCCAAATAAAATAAACCGTAATGCAATAAATTACGCTGTTTTTCTTGTCGATCCTTCGGCAAATTGTCTGCCGGACTTTGGGCCATAAATTCAAACCCCTTACTCGGCCGAATCTTTTGTGTCCGACATAAGCCGTTTTGGGATAAATCTTCGGCTTTTTTGGGTGGGCAAGCAAATCAATGGTGGAGGAACAATTTAATAACCAACTGGGGGGATTAACTGATGAATATTCCTTGGGATAACCAGTCGTCCTGCATATATAAACATATTTCTTGAGGCACGCCAAGCAAATGTCAATGTCAACTGGCCTTGTTGGGCCTTGGATTTTCCTCGGCTCGCCTGTGTTTACTTTTGGGTGGCCCGGAGTGGCCCAAGCCAAGGCTAAGTTTATTATGCCGCGAAAAATGCAGGCCCTCGAGTGTGAGTGCCGTAACCCTTGAACTCAAAGACATAAGAAAAACAAAGAACCAACTTAAAGTACACCCACCACCTTGTGTTTTACATTTCAAATGCTAAGCACAGTGGCTCCTCCGAAATTATATAAATCAGAACATGAATAAAGATTATATTTTAGTCCATTTAGACTACAGAATCTTCTGCTAATGAGAAAGAAAGAATGGTTTGTTTGCATTTACCATTTCACAATGTGTATATATTTTTCTCATTTCTTTATATTTATTTATAAACCGACTTAGTAAGATATATATAGGTATTCACTAATTTTGTCAATTAGAAATGCAAGTGTTTAATCAAGGTTCCTTATTTATAGACTTCCCTGTACAAAAAGCTAGCGGGCAAGGAAAACTTTCTGTTAGTCAGTGAGTATATTATTTCAATCCCCTGCATTTTCCAATGCCCGAGCTTCATGACTCTTGCACTTGAATACATTTTACAGCGAACTGTCTGTCGGCTATGTTCGCTCATGTTTCAAATGTCGAATGTGTGAGACCGTGTTTCGTACGAGCAGGAGTTTTCCATATTATTATTTATGAATGCGAAATACTTTGGCTGACATTTATATATGTATATATTTTTTTTTTTTTGGGCAACTGCCTTCGTTGTGTAAGGGTTACAAGCTACAAGTGTAAGGGTTTTAGCTACACGTGAAAGTCATCTTCTAGTTTTACAACTGCTTCACTCAGGGCCAATAGCGAGGAAAGTGCAGTAAAATTGTAAGAATTATGGTCAGGTTGTAAACAGGAAATATCCTATTAAACGAAAGCGGGGCGGAAGTTCCTTCATTGTTGTACACAAGCTTTTACCTAAGTGCATTTTTAGGTGCATTAGAACATTGATATGATTCTATTAGCTCTCACACACTTCGTTTTTATCACCTTTGTGGGTGGGAAAGCATCGAGAAAAACCATTATGGGATACCGTAATGGATGGTGGATATGATGGATGTCTTGAGATACCATTGATCCATACAAGTGACCCAAGAAAAAGAAAAAGGCGTCCTTCATCATTTAGGCCATCATTAATTAAAAGGACACAAAATTGAAACAAAGCTTAATCAAATTAACGCAAGAACTGAATGATAGATAACTATTTGTTAAAAAAATCGCATGTTACATATAAACTGCAAAATATTAGCTTTGTCCTGCTTTTTGTGCACTAATCTACATATTTCAAGCTTTAACAGTACCTTTTATAGTTTCGTCCTAGTAGTTAAATTATACACCTTTCCAATATCTATACCAAAACTGTGCGGTAATTAAAGCTATATATAGACAGACTGGAATGCTATCAAACCAAATAAAAGGCAAAAACCCTAGTCTATAATTCAGACTAGGCAAAAACGCTGCGGTCGGGCGCAAACTCTTAAAATAGAAATAATAACAGATACGCCAGCAACAAGCGGGGGGGCAAAACCAGGAAAGGGAAAGGAATGGGTAAGGGAAAAGGAAAAGCGTGGAAAATGCGGGGGAAATGACAGGCCGCCAAGCGGGGAAAATAAACAGAAAAACACTCAAATTAAATTGCGAACTGAGCTTAATGCACTTAAAGTCAGTACATGCCCAGGAAAGGGTGCAAATGTGGGGGGGTGGCCATTGTGGGGCAATGCCAATGTCAGACGGACGGATGAATGGTTACCATTGACAGGTAAGCAGGTGCTCTGCGCTTTTCCGTGCTACCACCCCCCCCCCCCCCCAACCCATCCCCTTGACTATCCCGGACTTTTCCTGTGGCACTCGAGCACGCGCCCGAGAAATGCCAAGAACTGAGAACTGAAAATCGAGTGTAAGCCGCGGCTTATGCAATGCGGCCAACGGGGCTTGACAGTCTGGTTTGCTTTTGCTTATCTGCGTTTCTTGGCCCAAAGGCTCGATTTGCCTTTGGCTGTTTTTGCCATGCAAGGCGGCCATTAGTGACGTCGAGTCAACCAATATATTTCCTGTTCAATAGGCTCCCCCCACCCTCCCATTGATTCGTGGCGGCGAAAGAATATTTAAATATGAAGTTGCCAAGTTTATTTCCTTGGGGACTCTTTGCGGCCGTTTTCGGTGGAACGAACTTTTTATCTGCAGCATTTTATATCATGTTTTTGCTTTCTCGTTGTTTTATTGATTTAATTTGTTGTTGGGCACTAGGCTAAAAAGTATTGAATATTCAAAAAGCCCTTTTGCAAAGTACCAGTTGAAAAGTTGTCTCGTTAGTACAAACTGCAACTTGCTATGTAGACACACTAAAATGCAGAATCGCTATTGAAGTTATTTTTCTGAATCCCTGCGGCTGATTATATATTCATTGCTTTAGTCATATTGATTTATTTATTTCCTTGCCAAGCTGCATGGGTTTGCATATCCGAATGGCAAAATTCCAGTTAAAAGTTTTTCCATTTATTTAAACTATTCAATCTCAGATTAGGAAAATCCGTTTGCAAGCAGATTCTATTGGTAAATTATTGCTTTACATTTAACCGTGGTCATATTGATAACAAAAAGAGACAAAAAGAGAGAAAGACAAATCAGAGTTTCCTACGTACAGTACTAAATAATAAAAACAGAAATATTTTAAAATAAAATTTGGGAATTATGATTATTATGTTTCGCCAATACAGACTGTTCCGAATTATGTCCTTTAATAAAAGACTTGCATATTAAAACATATTTGAATACTTTATATTTGTATAAGTGCATCGTATTCCTATGTAATTTTCTCCCATCGAGCGTACTTAATTCCCAGTTCTGCCCATAGTTCATTACACAATTTATATTAAAGCCGTAACTTAACCCTCGGCATCCAGTTCGGCATTAGCTGGCAGTTGGAGCTGGGCCAAAAGTATTTGCCATATTGCACTCTGGATTGCAAAAGTTCTCGACCAGCATTCCGCCATAATCGTATAAATACGTATACAGTTCTAGCACTTCCTTTCTCTACATACATTTGAAAAAATAAAAGAGAAAAAAAAAACAACAAGGACAACAAAGGATGTTGGTGGGTTGGGTAAACAGCGGAGGAGGCTTGAGGCGACTGCAGTGGGTGAAATGCAATTTCCAGGCCATAAAATGGCTAGGCAGGAAAAAACAGCAGGAAAAGTCCTTTCACTTGGCTCGAACGAAAGCGTTTGCAGGTAATGGCCATCATACAAGCCGGTTAATGCGGCCAACTTGTTCTGCAGGCAGATAACACGAGTAACCAAAGTCCTCGCGAACGATGCGAAAAGTTTCGCGGCAAATTAAATGAAAGTTAATATTGGCAGCGTGTTCGATAAACAATAGGGACGTAGTCAACAAGTTGATCCTAATGCGATTATCGCACTGTGCCTAATGTCTTTGAGAATTGGCTAGATGCCTTAGTTTTATCGAGAAAATTATCTACCTAACTTTTTCTACAAATTTCTACATATACCTATATCATTTCGCAGTTTTAATGAGGTTTAGTTGTGCCTTAATATGAATTCTAGATTAATAGATATATTCTTAAAGAATATTTTCGGTTTTAGATAGCCAGATATTGTCGCAACCATTTTTAACCTTCAAATTGAAATTAGTGGCGATTTTCTTGTGTGCCAAGAACAGTGTGCAGTGCGAAACTCATTTAGTGGTAACAGCTGCTGCAAATTTATGCTCACGGCTTTTCTATTCTGAGCTTTATTTTAGCCACAGAAGAGCGACCGCAGCAAACTGTCAACGATTCCCACCGCAGATATATGTACACGTACATTCATCCGGATGTCGGCAAACGAGCTGGCTAAATCCAAGCCAAACTGGCACTGCTCAAATACCACTTAAGTATAGCTTGGCATTTGGCAAATTCCATGATTTTATAATCATTTCTTTACTCTTTTATTAATTTGAATGCCAAATTTTGACTTTTGTATGCATATAACGGAGACGTTTTAAAGCCAACCCGTAGTGGGTGAATAAAAGGCAAAATAATATACAAAGGGGTATGGAAAATTTATTCAAATATAATTCGATACTTTTCTCATCCCATAGAACCAAAAAAAATATGAATTTCAACGCTGAAAAGTATGCAATTAAAAGGTTCATACTCTTTAGTCCTTAAAAGGGGTTGGCATTTCCTAAACAGAAAATAACTTGCACAAATAGAAAGTTATTGTTATAATGATTTTGGTTGAGTAACTAAAAGTAAACGTAAAAAAATAATATATATAAAATAAACATAGCACAGAAAGGCCGATTGCAGTTGGGTCACCCTTGGTAATTATTTTTCTAAGTGTCCCTTTCAAGCCAACATCATCTGCAGACGCGCCTTGAGCCCAGGACTTTGCTTTCTTATTTTTAGAGCAAACCAAACCCACCCACCCGCGAGGCAACTGCAGATGTGGGCGGCCCAGCAATTTTGTTTACATTTCTTGTTTTCTCCCATTCCGCGCGGTGTGTTTAACCCACAATGACTTGTGACTTGTATTGGGCTGGGGGTTCGCCTGGGGGCCTCGTGGAGGTGGCGTTCTGTCTCATTTCAACTGCGGGAAATCCCCGCTCACGGATGCAATGTCGGCACTTCCTCGGCTGCAATGGGAGTCCCACTGTGACCATTTCTCACCCGCCATACGTATACGTGTGTATGGAGCTGCAGCTGTGTGGGTTTTCGTGGGTGTTTCTGTTTTATGCTATTAATTTGACAGTTTCAGCTGCGCTGACAACTGGCTTTTCCCCAGACACCGAGCATAGCGTTTAATGGCTGCAAATTAATTGTTGTATGCCTTTCTCCTCCCCAGAGATAATTGCTCAGCAGCATCTAGTTTCTCAGCGAGGACAAATAAACCCGAGAACAAAAAAAAAAACATAAGAAATGGACTCTGCCGCCGCCGCCGCCGCCAAGCGCGTTCAAATCGAGAAGGCCCACAACTTTATGCGCCAGTATCGTGATCCCGAGTCCAGGGAACTCAAGAAGCTGTCGGCCAACCAGTTCATGGATGTCTGGGCGCATTACGATAAAGATGGTGAGTTTAGATCTTACTAACAAAATTTGCAATCATTGTATTTCACTACTGCCTTAGAATTGTAATTATTTGCTTAACTTTCCACATTAATAATTTGTACTTTATATAAATTAATCCACACTTGAAACACATTTAGTTAGTATCTATTAATCAAAATGATATATTAGAGGTTTAATAACTCATTACTTATTTAAATTGTTTACCTTAGGAAATGGCTACATTGAGGGCACCGAGCTGGACGGATTCCTGCGGGAGTTCGTGTCGAGTGCCAATGCCACAGACATTAGTCCAGAGGTGAGTCTGAAGTGGTATGGAACACTTGCATCTTAATCCCTCGGTCCCAATTCCCAGGCAGTAACGGACACCATGCTCGAGGAGCTAAAGTCCTGCTTCATGGAGGCCTACGATGACAATCAGGATGGTAAAATCGATATCAGAGAGGTGGGTAATACCTACGACTCATTCGGACCCAAAATTTCAGTTTGATGGGGGCTCCCATGTCGTATGCGCAATGTTGTCTGTATGGATTTTTGTATACGAAATGACATTTCCTTTAGTCATGACGGCGCCTTCTTTGCCTTTTTTTTAAATTGGTTTTTAAATGTCTCGGCCGGGCCGAAACCAATAAATTATTTGGCGATTTTCCCTGGAGAAGGAATCAACTTTCTGGCAAGGTCTTTGGCCAAAAAAAAGTTTTTTTCTTCGTTTTCTCTCATTGTGTGGAGGCCACATTAAATGAGTTTTTAATTGAAGTTGAACTGGCAGCAGAAGTACGGACTATTGGAAGGGGATTTTCCGTTTTTCTTTTTTTTATACTAAATAATACAGCGGTGCACAATGGACTTTTGATAAATGAGCCCACGAAAAAAGGGAAAGTTTTGGTGAAGAAAAGTAAAAAGTTCAAGTAGCCGGGTCCCCCATGTATTGTTGATTAAGATTGCTTGCAACACAAAAGGCACAGGGCATTCATAATTCATGTTGTCCACATTATTCATACGCCACGTCGAACAGCGATTGAAATGGCTGGGACGGTTAAATTACTGGTCTGTCGACAAGGCTTTGGCCTGAAGATAAACTTTAATTACGATAGTGCTATAATTACCAACAGCAAATAAAAATGTAAATCCCACGGCCACAGCGAATTATAAAGTTTTCCCTGCCACAGATGATTACTTGTAAAGGGTAAGGGCTTCAATTCGACACTTGAATTATGCCGGAAACTTTTAACGAATGCCAGAAGCGAAACTTTTCCGGCTGTTTGCTAATGAAAGTGCAGCAGGATATCCTCGCCTTTCACGCAATGCACCGGATAAACAGGAGACTTAGGAACCCGGCTCGTCCTCGGAGCATTCCCATTTATAACTTATTTCAATTGTCATGTCACGCACTGAAACAAAAAGGTATTTTTCTTGTACTACTTTTCCGCAGCTGGCTCAACTTTTGCCCATGGAGGAGAATTTCCTTTTGCTCTTCCGCTTCGATAATCCTCTGGAATCTAGCGTTGAATTCATGAAGGTAAGTGACAATCAGGAATTTCACATCCTGAAATTCCCCAAATAATTTGTCTGCAATTAAATTAGATCTGGCGTGAATACGACACCGACAATTCGGGTTACATTGAAGCGGATGAGCTGAAAAATTTCTTGCGCGATTTGCTCAAAGAGGCCAAAAAGATCAACGACGTGTCCGAGGACAAGCTCATTGAGTACACCGATACTATGGTAAGTTGTCAGACATAAATGCATGACATTACTTTGGTTTGCTTAGGAAATTCATTAGTAGATAGAGGATAAGAGCTAAACTAAAGTGAACGATAATTTATGAATACATGAATACTTACTATTTATCTAAGAGTTTCTTAAGGCCTCAATATCCTTTTCAAGAAATAAACTTCTTGTTCAAAATTCCCTAATGATTATACATAGAATGCCAAACCAAAAACGATTCAATAGCATGCTTAGATTCTAAACTGCTGTGATTATTGACCGACTGACTATGCACTTTCTACACAAAAGTGTAAATAATGCCGATTTGCTATAAGCACACGATAATGTATGCCCAATTACCAATCCCGTCTCGATTCCTTTCAGCTCCAAGTATTCGATGCCAACAAGGACGGACGTCTGCAGTTGTCGGAAATGGCCAAGTAAGTGTCCTTGAAGTCGCGTTCTGAAATTCTATGCAGCAGCCAGCCAACTAACTTATTTATTGCAGATTGCTTCCGGTTAAAGAGAACTTCCTGTGCCGCCAAGTGTTTAAGGTAAGTGCCAAAGATAAATTGTGTGAAAACATCGTTCATTCGAGGAAATTGCCAAGAGCAGATACTATCAGCAAATCGCGGTTTTCCAAACATTTATTTATTAAGAACTTGTTTATGAAACCAAATCAAACTCGGCTTGCCTTGAACAAAACACGTTTAGCACCTAGGTTAGCCTGGACTTTTGGTTTATCACTAGCTGCAGCCTTGACTATTCAACTAACTTAGCTTTGCAACTAACTCAAACAGCAATGCATATTGGTTTTGTCTTTTCTTTTGTTTACCTATCATTTCAAACGATGTCTGTGCCGACTTGGGAACTAATCTTTAAGAAATCAACGAATTTATATTATTAGAAAATGGTCAATATCATATTTATAGGGCATTAAAAACAATATACAACAGCAGGTTTGTAGTTAAATTTCCATGCAGAGAATTAGCCAACCAACCATCAATAACTAAATAAAATCATATTGTTCATCAATTATTATAAAAATCAATTACCAAATTTAGTTTTCACCCATGAACAAACATTAATTGGTTAAATACATTGCAATGCTTACAATCATAAAATTCCATGGTCCAAACAAACTTTCAAAAATAAATGGATCGGAAGGGAAAGTGTTATGCTTTTCTGAATAGAATCCCGAATCAACAGCGATTCTAAATCCTTTTAAAGGCTTTTCATTCTCGCTCGACAGATCAGCAAATACAATTTTTTGACAAAAAAGGACAATGCCACTATTTATTCTTGCTTTCGCATTCGACACTGAATGCAACATTGAATTGTTGTGGCCATAAAAAAAAATATATATATTCAAGCCAATTTTGTTTGCGTCGCAACAAATAAAGCCATGGCCAAACACAAATAGCTATTCCGCCGAAAAGGAAAACAAAAAATAGCAAGAAATATTGTCTGAAATCGTAAAAATAAACGAAGCAAAATGGCAAAGCTCAGCTGAAACTGGCAGGTGCTTTCCACCCACTCCCATTTCTTTTCTTTCTTTTTTTTTTTGCAAAAAAAATGCGTGGGAGTTGGTGGAATCAATTTCCGAAGGCAACAGCTTCCTTTTTTCCCCCAGTTTTTGCTGAAGCGTCAACAGATTTGATGCGATTTGAATGGGGCTGTAAAAAAGGGGAAGCTAAACAGCAATCACTGCACAAACAGAAGGTGGAAAGTCCCCAAATGGCTGGCCATTAAATACTTTAATATTAGTTTGCCTCGAAGAGATGCCCAGCCGAACAATTAGCAGAAGAAAAGCCATGTGGTGTTGGGAAAACAAACTTTTTGGCCACGAACGCCGCCGCCGCCGCCGCTGCCAGATGTTGGGGCTTAAAATTCCCCTGGGAAATTCTACGAACCCATTTCGACTTGGCCCAAATGCTGATGATGCCAAATGCGGTTAAATGAAGCACTGTCATTGCAATTGAGGCTGCCTACGAATGTCACGTAGCTTCCCGCAGGCCAAAACTTGGCCAAAAAGAACATATATTTCGAGCATGTTTTTCGTTTGCGCATTTTAAGCATTCTGGCAAGGAATCGGGCCATCCAAATACCAAAAATAAACGTTTTGTTTGCTCAAAGCAGCAGCTGCTTAAGAAATTCTGGCTGAAACATGTTCCAAGTATATGGAGGCCTTGGTTCTCTATCAGCAGTTTCCAAACATTATTTAAAACTTCTTAACAAAACTTATTTAAAACCAAAGTGCTCTCATCAATTTAAGCATTAAATGTGTATAGTGTGCGGAAAGAAAGCTCGACTGTACATAAATAATACTACTAACTAAGGGCAGGCGGAAATAAATGTTGGACCTGCAGCCTTGAAAACTCCCAATTTGCTGAGCCAGCCCCTTCGAAATTTCCCGAGTCGCGTTTCCCACGTCCTGATCGAACACATTTTTTTCCTCTTCTCGTGTTCGTCCTCGTGTTTGGGTTTCCTTTTTGCTGTTTGCCACATGAACCACACATCGCCACATATGTATGTATGCAATCCATGGTCTATCCACCCAAAGGAAAACCACCTCCATTCGGTTGTCGGTGTTGTTCTTGGCAATCAAGTGGGTTAGATGCACAGCAAAATGATCTGAGGGGGGGGGATAGTGGAATTGAAGGGGCATTGAGAGCTCTTATTGTTATTTGCTGCAAATGTACGTGCCTCAGTCGCATTGACGCTCATTCTCATTGCTCATTGGCAGTAGTTGCCGAAAAGTTGGATGTGTTAGCTATCGAAGCGGCATTTTTCGGGCAAATTTTGGGGGGGGGAGATGTGGGTGGCGCCTCCAACAGTGTTCTCAAAATCAAAAGTGTTGCATTCAGCCTGAACTCACTTTGTATTGGTTTTCAATTGCAATCGGATTCCCATTGCACTAAATCCCTTTTGTTGGCTGCTTGGTGGGAATCCCACGCGTTGTTGAAAACGAAATGGAAAACTTGTAGATGTTTCTATCGAAAATTGGCTTTGCTGACGCTGTGGAAACGCACAAAAACACCCACTACAGTTTAATTCTAATATTTCAAAGCTAATTATTGCAACTTTCGCAGCGAAAAGAGAGAAAAAATACATTTCCAATATAACAAGTGTACTTTGAATTTGAAACGCAAATATGGCAGGAAAAGTTTGGTGCCTTTGTTGTGAGAGACATACGTGCTTGGCTTGATTTAATATATCCTTTATATGTTTTATAAAGGCTTCTCCAAATTTATTTCACTCACAGCCTAAATAAAGAGTTTTAAATTTCATCAAACCACCTACTACATTTTGGCTCAGCAAATTTAATGCAAACATTTTGACAAGCCAATACTTTTTTCACTACTGTCCCATCCAAAATAAACATATTGAAGTCATCTTGATGTCAGCTTACATCCTTCACGCTTTCCAATCTAAAATGGCAAGCTGCTGGTGTAAATTCAAATGCAACTCGCATGTTCCTTCAACGAGATATTTGTGTTGTGCGCGGAGGGACGTCCTCTTTGCCAGGCGAAAAGTAGGAGGATCTGGAGCAGGAGTGGGGACGACCGTGAGCCATGTAGCGATGTGCAGCCATGTGGAGCGGCAGTCCGAGCGAGGAGCAGAAGAAGCCGCAGGATTGCACAACGAACAATGCCCAGTGCTCGGTGCTCATGGGTTGCATGCCGCATATTTGCTCATTGTTACAGCTCGCAGCACAAACGACATTTTATTTGGTTTTTATTGATGGTAGGATGGTGGGCAATGTTGGGCAAGGGAGTGAGCACCAGTCGTTCGGAGTCATGCATAACAATGTAGCGAGACAAGTTGGATTTTAATCGAAAACGCCACGGCGCGGACATGGTTGCTGTCACTCAGTTCCAAGCCACTGAATCCTAAGGCATCCGGATGCCCAGGCACCTGACCACCAAAGATACGCGTCTGTACTTACCGTACTTTCGCCATCGTAAGTCGGCCGTTATGAAGTGCCATAAAAAAGGCTGGAAGCTGCGGCTTCTGGCAGCCATAAAATAGGCATTTCCAGCACATTTACCCAAGGTGCAGTTATTACTTTTCAACATAATTTCTTCGGGGGCCATAAAAGCCAAAGCATGCATCAGCATTTTGATAACCGGAGTGGGCCAGCTGCTCAGCTATACACACATACGTATGCAATGACGCCCAACTTTTTCGAGAAGCTGCATAACTCCCAGAAACTTCTGTCTCCGGGCGTCCAATTATGTGGCGCAGTGTATTGCTGGCTGGTGGCCAAAAGTGCCAGAAAGCGTTATGCTAATGCACATCACGTATACGCCGCATGCACCGCAACGAGCAGTGACATAATGTGCTGCAACGGGAAAAGCCACTGCAAATGGCAATAGGTGTGGACAGGAAAGGGCGGAAAAAGGGTGGCGGACAGACATCTAAGGACACGAAGCAGCAGGACATTGTGAAAAATAGCCCGGTACACTTAGCGTTTTGTCGGGCGTCTTATTTTTCAGACGGGTAAAAAAAAAAAACAACAACAAAAAACACGTCTATATGAACCCAAGGACTCGACTAAGTGAATACGTGACATTGCGGCACAGACAATTTTTCAGTTTTTCAGTTTTTCTTGTAACTTAATTTTTCAACTTGCAATTAGAAACAATTTTGAGCAATTAACTAAGAAAGCTAAAATCGTTTGCTCCACAATTGGTAATGCATTTGACTAGCTTACGTTCAACTAAGCGTATACTTAATATTTCTCACTTTTAGTTTTACTGCATCCAGATCTTAGATCCTTTAGCTTACTACAATAATAATTAAAATTTTAGACTAAAATCATGTATACAACATTAAAAAGATAAGTTAATCAAAGCTGGCAAATAATTAAAAGAAACTTTTTAAAATTTGCCTATTTTAATTAGCCTTCAACAGACTTAAATTGCTTTAGTTTATGACTTTTCTAACTTTCTATATATCTTTTTCGTTTCCCCCCCGCCAACCTCCTCTATGCCATCTGTATACTATCAACATAATATACTATATATCTTTGCATATACTTCTATAATCTTGTGCATTTTTATTTCAAAACAAACAACCTAACAATAACCAAACTAAAAATAATCAATTACCGAATTAACTATACCGTGCACGTGGTGTATAACATTTTGGGCTGCCACCTTCAACTTCCGACTTATCTCACAAATGCAATTTGAAAATCAACTCTGAAATAACAAAACAATTACCGCAAATCAAAACTCTTGCCATCTGCTGTATATACAAAAATTTGCATACAACAATCTGCAACCAATTGCACTGCCAACAATAAAAACAAACCAAAATATTTCGTAAAACAATACACAAACTATTTGCATTACTGCAAACAAAACCGATACAAATGAAATGAAATAAATAACATAAAAAACGTATATATACATATATATATATATATATTTAAACCACACACTGAAGGAGGGCATTGACGTAAGTATTTTTCACCCCATCATCAAACATTCAAACAACCAAAAAATAAAAGAAAAGCCCAACAAAAAATATTAACTCATGTGCGTAAAATAGTGATTACAATAACACTGGTGGCCCATTTAAACTCTTAATAAAAGTGTATCATTTTGAGCTTTGGATAACACTTGTTTAAACAATCATTTTTTGTTTTGACGAGTACGTAACAATTTAATTTTATTAAAATAAAACAACCAATACCTACTGTTTTAAAATTTCCTGAAAAATTCATGTACATAAAAAAATGCATGCTCTATTTTGTGAGAATTAAAATATTCTTTTTGCTGTGTGAATGATATACATAAATCTTTCAATTCAATTTATAAGCATAGTGTATATATTCAAATAAACTTAACAAAGTGAAAATAATGGAGTCAAATAGTGACAAAGAGTGTTATGTACATATTTATGAGGTTTTTTAAGACACCTAAGAGATACTTTCAAACGTATGCAATGAATTTTTAAATTTTTAAATGCATTTTGCTAGTTTTGCGTCCAAGTTTTTAGACAATTCTTCAAATTTATTCCTTTTGTTGCAGTAACTAATGAAAGCTTACACCTCTATTAACGATGAACAACTAAACTTGCTGCCAGTAAAAGTTAGAGTCATTTGCAATTTGCCGTTTTTAGGGTCCTAGCCGAAAGCCACAAGCCAACTCGAAACAAGAAAATGATATCTACGAGCTACTAATTAGACTTTTGATGGCATTGGTCCACCCCATTTGCCACTTAACACATCCCGGCTACCCAGTACGTGAACAGCTTTGGCCCTAACGATGTGAGGTCCACGCAAATTACACGTTGATGTGGAATTCCTCCTCCTCCTCCTCCATGGGAACCTTTTGCATAATTTAGTCATTCAGTTCGGTGGCTGCAGAGGCTGGCGAGCTGGGGGAATGGATATATTTTGTGGAAGTGCCATATGGATAATGTCAGCCGCAGGCTGACACGCTCTCTGCCACCGGCTTTTCAAAGTGTTGAAGTGTAAAATAATTACTTCATTTCATCAATGTGTTGGCATGGGGGCCACATCACATAACATCACATCTCACGTTCAAGGCGAACATCGACTTGAGTCTGGGCAATTTGACAAAGAGCCAGGCGACGAAAGTGAAAGTAAAAACCCAGCAAAATGCGATATATACGTTTTGCGTTCGTGTGAAATTCAATTTCAGCAGCTTTGCTACCGCCAAGTGGAAATAGGATCGCAATTTATAATGCCGTGCTAAGCACATTTTTTTTTAAAGCTTAAGCGGAAAAGGGTAACCAGTTAATGGGTTTCTAATCCCGGTAAGAAATAACAGTGCGCCCGCTGCGTTTTCTTGGCGCCAGTAAAACAAATGTTATCAGACTTTACCAAGGATAAAGAAAACAAAACCTTAAGTTTCACCTCGCAGCTTTTCAATTTTTCGCACCGTAAGTTCACTGGTAAAAATATTTCGCGAAATTTTAAAATAAAATCATAGTACATTATATTAAACGATTCATCCCTGATGCATATTTTAGGCAACATTTTACGAGATTTAAATGTTTTCTCTTGTATAATTAAGCAACTTACTATCGGCTCATTTTTTAAAATTTAAATTGAAATTTCACTATGTTGCCATATTTTTTTCATACGTGTAGTGAACTTGAGGCGCCACCTTGGCCACATTGCATAACCCCCAAAATTCCAAACTGCATGAGTATATGTGGGGGGTAAATTCATGTATGTGAAAGGAGGTTTATATATGGGGGCAAAGTAATTCGTGCAATTTGCCGGGCGCAAATGGAATCGATAAATTTCGTGTTCCCTCGTGGAAAACACATCCGGAAAAATCCCGAATGAGCGCAGTGAATGGTAATGACAAATCTGCTCTACCTGGGCAATAATTCATATTAATTAGCGAGTGTCAACGGCAGAGAACACATATATTAAACGGCAGTATGTTTTATTTAGGATAATTAGGCTTTTACGTTAAGCTTAATGAATGAGTGTGGAATTTGGTATACAAGTTTTTTATACATACGTAGCATGTTTATTAATCTCTTAGGATTTTCCTAAGACAAATTTGTCCCATTTCCCATTGCATTTCTAAGAGCATGTTTTCATTATAATTAGCTGTATCTTGCATGAGCTCATACCTTTATACTTAACTAATCAAAACCAAAATCGCACCAACCAATACAACTTGACCCGTAGTTTAGGCCTATGATATTAAAGGGTAACCCATTTGGAAAATTTCAAGATAGTCTAAGCAAATCTTAAAAAAAACTGTTTTGCTACACACATTTGTTTATGGATTTAGCATACTTCGTAATTAAATTTAGTTTATTCCTTTTGTACGTTATCCAAACACTTTTATTTATGTAGGAAAAAGTATGCTAAATCTTATTTATAAATACTATTTTATGTGGAACATGCATATAAACAAAACTTGTTGGATAATATTATATTGAGGATTGCAATTTATATCCACAGGGCGCCACAAAGTTGACCAAAGAGGATATTGAAAAAGTATTCTCACTCTACGATCGTGTAAGTAAAGCAAAAGACTAAGGAATATATATAAAGATGTAAAATCTAATATGATATCATTACAGGACAATAGCGGCACCATTGAAAATGAGGAGCTCAAAGGCTTCTTGAAGGACCTTTTGGAGTTGGTCAAGAAGGTGAGTGTCGCTCTTAAAGACAAATGAAATAAAATGTTAATATTGTGTGGTTGCCAGGACGACTATGATGCCCAGGATCTGGCCGCTTTCGAGGAGACCATCATGCGGGGAGTTGGCACCGACAAGCATGGAAAGATCTCCCGGAAAGAACTGACCATGATTCTGCTAACACTGGCCAAAATATCGCCCGACGACGAGGAGTAAGCCGGATGTTCGAGAACATACCAAAAAGAGATTTTAGCCAACTCTATTTTTGTCACCCGAACGCGGGAAATCCAGAAATGAGGCCAAAATGGGCTTCAAGGCAATTGTTTACTTTAGAGCTGCATTAAAAGGGGCAGCAAATAAACAAAAAAATAAAAGGATATTGGAATCGGGGATGAATCCTGAGAGATTCAAACCGAAACGAAGCTATTGGTATAAAATAAATCTAATATAAATGTTCAAATCTTAAATAAATGTTTATCGTACGTTAAGATATTGAGAGTATATATTTCCCCCAAAATCAAACCAAAACGGAAATTTATCCAGTCAAACAATTTGCAACACAGAATCGAGCCACTTAAAGTAAAAAATTAAGAAATGATAACAACAAGATCAGTACATCGATTTTATATTATACTATATATGTATTTATATTTTCTATGTGTATTTGCATAACGTACTTTATTTAATTACCAATTAAAATCGAAATAAATGTAGCTATTTTTAAGGATACCACATTTATTTGAGACTACCTAAGTAAAAACATATGTGTGGCTACAATCTGTAGATAATTGTTGTTAATCATTGTGACAGTACACCCTAAAAGTGGGCGGCTGCATTCCGCGCCCAACTCCCCGCACTTGTGCTATGAATATCCCCCGCAAGCATCAATCAATCAATCAAGAGGCACTTACATCAGCCCGAGGGTGGACGCCACTAATGCAGGTGAATGCAAATGCAAATGCAAATGCATCCGCCACCTGAACGTGACAATGTCAAGCTGGAGGGTGGTGATGCATCCAGTTAATGTTGGACACGCACTCGTCCTTGTATTTTTTTCACCCGAGGGGAGATTACGAGGTGCAGATTGACGCCGTTTTAAGGCTAAAATTTTCACCCAATTTCGCAACATAGGCAAATTGGTTATTTAACCTCTAAACAAAAACCTAAAGTTAACCAACAACGCTACGAACTATCTAATGTTCTTTCAAGGTGCTATAGCTATATATATACATTATGACTTGTTTCGATACGTATTCCCTTCTCCATCTGTTATCATTGTATTCTTTCGAAACCTAACTAACTAAATAACTAACAACTAATAACTTAAGCTTTAAAACCAAGACAAATTGTTCCAATCCTGAAACGCTCTTTGCCCAAAGATTCACTTTTAGAGCCATAGTCATGAAATAGATCAATTCCATCGCCTTTAAAAATGAAACCCTGAGTAAAGATGCCATGCAACAAAATGCCAACTTATCATATAAATATACTAATTACGATACAACACTATATGATAACATACTTATGCTAATCCTAAGATATTGTTCAAAACCACATGCATGTAAAGCTTCGAAACGGACTTTCTCTATATGAAACAAGATACCAAATATCGAATATCTAAATGGATATATGTCTAACACTATGGAAATACAGCAGAAATGTTTTAATAAAATAAATACAATACAATCTATGCAGACATCAAGGGGTCAGCACTCCAAAAGTAGTCTTTTGATTTCCTTATTTTTTTTTCTATACACACAGGCGTTTGTATTTCCGATTGAGTTTCTCCTGGAGCTCTAGAAGATCATTCAGTTTCTTCAGCATATCAGTGGCATCAAGCACTTTCTCGGTTAACACGGCTAAGGGGGAAGAACAATCCTTAAATGTTTTCTCCTGTTCCACTTCCGAGTCAACGAGACAGTTGACAATGTCCATCGTTTTCTTGATTCGCGAACAGAAGCTATGGTGGAACTTTATAGGTAACCACTAATAACATTAGATACAAGGTAGTTACCACTTGGCATCCGTCATTCGATTACTGAGAATAAGCTGCCAGGCCATGCAGCTCTGCAAGTGCCAGGAACAATAGCAAATGCCCAGAGTCTCCGTGATGGGATCCTTCCATTCCTTGATGACCGCACACTGAGCTGGAGGAAACCGCACCTTCTCCACCAGCCAAGTGTGCCAGATAATCGTCTTCCTGTTCTTAAATTCCGCGTTCATTTGCTCGGAGTCCAGACGCTTGCTTCCGAAATGTCGCTCCAGAAACGAGGTTGCCTCCTTTTGAGAATCATGGGGATTCGGTTTACTAATCGGCCCCACTTCCATCATGCCATTTTGAAAGTTCAGCCACGAGGGATTCGCGCAGAAGGATCGTGTTGTAGCATCTGCATAAGTAAGAAAAGTTTCGCTAATGGATTTTATTTGGAGAGCACTGAATTCGGAAATTAATAATGTAAATGTAATGAATCGAAACTTCTTAAATCTCGCACTTTAATATATTCTGTATTAACTTCTGCATACTTTAGAACTTCCTCAAAGATTTAATTTTACATAAAAGAAAAAAGGAGAAGGACCCTATAAGAGCTTGAGAAATTCCCTTGAAGGATCCTTCAACCCAGTTTCCTCCTTCGGAATTTGCAAAACTCACCCACTGCCGACGCTGACCACCAATTTGGAGATAGTTTCACAGCGGGGCGTAGCAATTTGTTTTCGAGTCATGGTAACACGGTCAATTTTACAGGATATCTCGAAAAACGTACAAAATCAAACGAATGTATAGGTCGGCGACTACTGAGATTAATAGGTTCCGGCATTCATGGCCTTCACATCCAGTTTCTGCTGATAGGCCAGTCTCTGAAGAATCGTGGGATGAGTGTGATGCCATCGAGCATAGCATTGGTCGTAGACCGGAAAACTCATATGATCCGCATAGATCTTAACCAGCGCCATCCTCAGTTGGATGGAGTATCCCATGCGATGGGCAAATTTATCGGCGGCATACTCAAAGCGACGCAGATTCCACAGCATCAAGACATTGGCCAACGTGAGATAAGGAGTAAGGGCAAATTTCAGAACAATGATGAAACCCACTATGATGGGCATAACGCCAGGCTCGAAACCCACTGCCATGTATAGCTGGGGAGAGTGAAAGAACAATCCGAAGAGTCCCATGGTGATAAAGAAGTGAATCTTCATGATGATCGTAGCCTTGTAGAAATGTCCGTGCTTCCAGTGACCCAACTCATGGCACACCACTCCCGCCACCTGGATGTTGGTCAGACCTCTGCCCACCTCATAGGGATGGATCTCATTGGGTTCCTTGCCCTTGTTCAATAGCAAGGTATCAAAAATTACAATTCTTTTCAGGCAGCAGCTCCCGTAAAAGTAGGCATTACTATACTGCATTGTCCGGGTCTTTATGATAAATACCCTCTTCATGGGGAAGCCAACCACATCGCAAACACGCTTCACCTCCATATAGAGGGCAGTGCCCTCTGGTAAAACCACCTGTCGTCCAATGCACGGAATGCAGCAGTAGGGCAAAAAAAATACCAGCAACAGGGTGAACGTAGCCCAGAACAGCCAGAACCAAAGGAAGAAGTAGTACCCAATGAACTTTACGCTGAACACAATGGCCGCCGCCAACGGGAACAGGACGAGCTGGCTTAGGAGAATGGACATTGCTCCAATGCAGCAGTAGAGGTACCAAGGAAACTTGCCCGACATCCCATATCGCAACTCCAGCAGGCACTTGTCATAGATCAGAACCGGCAGGAACCTTATACAAATGTAAATGGTCAGGTAGAAAACAAAGATCAAGGTTATCCAGATCTCTTGGGAGGTTATTTTCTGTAGAGTCTTCGCAGACAAGCTCCAGAGGAATGGATAGAAGCCCAATATCAGCTCACAGAGCGTAATAATCAAGTCGATGAGGTACTTCCATATCTGTAGCTCCGTTTTATGCAGCTCGTAGATGCGGGCCCGATGGTAAATCTCCGGCGGAATGATTCCTCTCAGCTCCTCCGGCACCATAATCGCATTCAGGCACACCAATTGCTGGTGAAAGAAATCCGCGATCAGTTCTTCATGGGTGGAACAACCAATCCACTACTTACCTGCCTCTTGGTGAGTATCATCTCCCATATCCGGTCAACTAACACGATCAGACATAACACCACCAGCACTATGATTGGATCTACTTTCGGCCAAGTATCGTAGAATGCCATCAAAACTTATCATGTTCCCCCAACAAACAATGTTTACTTATTGTAAAATATTGTATATATCTATATTACCCAAGACGGATAACTCAATCAGAAGCTACTATGTTTGAGAAACACCGATAAAAAATATATCGCCTATCGTCGAAATTCTTCCAGACGACTCAACCGATCCAGCATGGTGGGATGCGTATGATTCCAGCTGGAGTAGCAAGGATCCGAAACGGGGAATGCCAGATTATCCGCATATAGTTTGAGCAGTGCTTGTCGAAGTTCTCCTCCATATCCGAGCTGGTAGGCAAACCTATCCGCCTGGTACTCAAAGCAACGCGTCATGCTAAGCATACTGAAGTTCGCCAGTGTCATGTATGGAGTCAGTACAAAGCCGAAGATTATTAAGCATCCAATGACTGTCGGCTGGAGACCGGGAGGGAATCCCACCGCCTGGTAAATGGGCCCATGAGAAAACAGAAACGCGAACAGCAGGATCGTCAGTATGAGATGGACTTGGAACGCCATGATAGCTTTGTAAAAATGTCCATTCCTCCAGTGACCCAGTTCGTGGGCCACCACAGCAACCACCTGAGGATCCGCAAGTCCCCTACCCAGCTCCTCTGCCGTCAGGTGGGAGAGATCTGACTTGCCTCTATTGAGCAGCAATGTATCGAAGATCACAATTCTTTTCAGGCAGCAGCATCCGTAGAAAAAGGCATTACTTCCCGTGTTAGGGTCATGCACCCGGATGATGCGCACCTGACTCATGGGAAAGCCGACTTGTCGCGTAAGGTACTCCAGTTGGGTGCGCAAGTTTGAGTTTTCCAGGGGTACACTTTGGCCCACAAATGGATGGATCATAAATGGAATCAAGAGGAGTACGATCATTGTCAGGATCAGCGATTGAAGGTACAAGCCCAGGGGAGCATATGGCCCCAAGCCGATAAACATGTACACGAGGGCGACCACCACCAAGGTGGTAATCATCGCTCCCACAACCAGGTCAACGACAAAGTGACAGATGCGGGACCACCACGGTGGTTTTGGCCTGGGTTGCAAGCTCTTGATGCAACAGCTCTCGTAGATCATGGCCGGTACGCTTTTAAGCCAAAAATACACGCTCAGGAGAAGCACAAAGATCACGGATACGCAAGCCTCATGCTCCATCCACTTGGACAAGGCGCACTTTCCAGCCACTCCATACAGCCAGGCATAGAAGCCGAAGTATAGTTCCATAATACCCAATATAACTGCCGAAAGCAGGGTGTTGACAATGGTGAACCAGCCCTTGTGAATCTTGTAGACGCGCATCTTGTCGTAGAGCTCCTGTGGTAGATAGGGGCTGATAACATTCGGTACTTGTTGCGTTTTGTAGGCCACTTGTATCTGAAAGAGCAATTTAATCCAAAATGTACTCGAAAGATGTAATCATCACTTACGTCCCGCAGCATCAGATATACGCCCCATAGATTGTCCAGAACCAAGAAAGCTATGATTATGTAGAGTATTGCTAGTGGATCATCCCAGAAATGTGCAGACATGTTGGGTTCCTCTGACAACGGCTTGACATGTTAGTCATATTTCCTTAATTTTGAAGCTCCGTTAGGAAATCATTTTGAATCTATTGGTGACGGATTTTTAACTACTAGCTTACATGTTTTGGGAATCACATAAGATACACGTTTCCACATTGCAAAATCTTAAATAGCTTGTTGGGGTAAGTCCCCTTACTTTATTTTGTGTACGTTAAATCAAAGGGAATAGTGTAAACTTTGGTCTTATGTGAAGTGAGCTGTCTTAGTTCAGTTTCTTCTCTTCCTTGAGCTCCTTGAGTCGATTCAGGCGCTGGAGAAGAGTCGGATGTGAGTGGTTCCAAGTCGAGTACAGCCAATCGTAAACGGGGAAGCCAAGGTTGTCAACGTTCAGTTTTATGAGGGCCTGACCCAACTGCTCAGCGAATCCCAACTTGAAAGCGAACTCATCAGCCTGATACTCGAATCGTCGCGACAAAATTGTCATGGCGAAGTTCATGAGGGCATTGTATGGCGCGAGTACGTAGGTAAAGACGATTAGCAAACCGACGAGAATGGGCCGAGTACCAGGTTGGAATCCCATGGCCACGTAGAATGGTGGATACTTGAAGACATTTCCAAAGACCAGGAACATCAGAAAGAGATGAACCTGCATGATAATAATGTTCTTGGTAACGTGTCCCAGTTTCCAGTGTCCCAGCTCGTGTCCCAAAACAGCCAGCACCTCCTCGTCGGTGCAACCCTTTCCCTTTTCTTCCTCTGACAACTCGGAGTCGTCCGGTTTACCTTTGTTTAGCAGCAGCGTGTCGAATAGCACGATCCTCTTCGAGTTCCAGAGGCCATAGAAGTAGGCATTGCTGTGCGAGGAGCGCTTGGATCCCTCCACCACGAAAAGCTTAGTGAGCGGGAACTTGAGCGATGCGGCCAGATCCTCAATCGATTGCCTCAGAGCACCCTTCTCCAGCGGAGTATACTTGTCGAACAGGGGAGCAATGAAAATCGGATACAAAGTGAGTAGAACCAGCGAGATAACGCCTGTGAAGATCCACAGCCATATGAAAAAGTTGTCGCCGCCGCGTTGCACGATGAAGATAATAGCCGCTGTGATGGGAATCATGAGGACCTGGGTGACTAGGAAGCCTTTGAGCTGATCCCAGGCGAAGAATCTCGCTGTTTGTTTGTTAAAGCCATGCGTCTCCTCCAGCACGAATATCTTGTAGATCTTGAAGGGCAGTCCCTTGAAAGTGCTCAATACATTCGATATGAGCACAAAAACGCAGCTGACGATGATCTCGTTTTTGGAGTCCCATTGCAGTTTATCCACCACCTGGACGGACAGCTGCCAGAGCACAGCGATCAGTCCGATGTACAGCTCCATGCAAAGCAGGGCCACATCCATAACAACAGCTTTGAAGATGCCGAATTTCTCCTGGTCCAGACCATATTTCCGCGCCTTATGGAACGTATCCTCGCCCATGTGTGACTTCAGTTCGGCCGGTACCTTCAGTGCAGTTTGGTACACTTTCACCTGGTGGCGACGGCAGGGTAAATCATTTAATGGGGGCAAGACATGAGGCGGCCAATTAACATTTGCCACTCTAAATTTATCATTCGCATTGATAAAATTCCTCGCCAAATGTCGCCTGGCTAGAACATGCCGGCACAACGGAAAAACTTACCTGGCGCAGCGATATATAGATCTCTAGCGCATTCTCGATGACTACGAGGAACAAAATGCTCAGCAGCACGGTGTCTGCGTCCAATGATGACATATTTAAATGCTATTTCATTAAAGAACTAATAAAACTGGAATTTTACTTTACAAGCGCCAGTGACGAATTGTTAGTGTGACCGTCATGCGGCCGTTTAAATATATCACAGCAATAGCAATTCGAACGATCTGGCAGCGCTGACTGCAACAGA CG30461-PE CG30461-PE polypeptide 2R-fragment 28984 28015 -1 0 0 MTRKQIATPRCETISKLVVSVGNATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV CG30461-PD CG30461-PD polypeptide 2R-fragment 28984 28015 -1 0 0 MTRKQIATPRCETISKLVVSVGSGETFLTYADATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV CG30461-PC CG30461-PC polypeptide 2R-fragment 28984 28015 -1 0 0 MTRKQIATPRCETISKLVVSVGNATTRSFCANPSWLNFQNGMMEVGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV CG30461-PB CG30461-PB polypeptide 2R-fragment 28984 28015 -1 0 0 MTRKQIATPRCETISKLVVSVGMGPISKPNPHDSQKEATSFLERHFGSKRLDSEQMNAEFKNRKTIIWHTWLVEKVRFPPAQCAVIKEWKDPITETLGICYCSWHLQSCMAWQLILSNRMTDAKCFCSRIKKTMDIVNCLVDSEVEQEKTFKDCSSPLAVLTEKVLDATDMLKKLNDLLELQEKLNRKYKRLCV CG9002-PB CG9002-PB polypeptide 2R-fragment 30492 29065 -1 0 0 MAFYDTWPKVDPIIVLVVLCLIVLVDRIWEMILTKRQQLVCLNAIMVPEELRGIIPPEIYHRARIYELHKTELQIWKYLIDLIITLCELILGFYPFLWSLSAKTLQKITSQEIWITLIFVFYLTIYICIRFLPVLIYDKCLLELRYGMSGKFPWYLYCCIGAMSILLSQLVLFPLAAAIVFSVKFIGYYFFLWFWLFWATFTLLLVFFLPYCCIPCIGRQVVLPEGTALYMEVKRVCDVVGFPMKRVFIIKTRTMQYSNAYFYGSCCLKRIVIFDTLLLNKGKEPNEIHPYEVGRGLTNIQVAGVVCHELGHWKHGHFYKATIIMKIHFFITMGLFGLFFHSPQLYMAVGFEPGVMPIIVGFIIVLKFALTPYLTLANVLMLWNLRRFEYAADKFAHRMGYSIQLRMALVKIYADHMSFPVYDQCYARWHHTHPTILQRLAYQQKLDVKAMNAGTY CG9002-PA CG9002-PA polypeptide 2R-fragment 30492 29065 -1 0 0 MAFYDTWPKVDPIIVLVVLCLIVLVDRIWEMILTKRQQLVCLNAIMVPEELRGIIPPEIYHRARIYELHKTELQIWKYLIDLIITLCELILGFYPFLWSLSAKTLQKITSQEIWITLIFVFYLTIYICIRFLPVLIYDKCLLELRYGMSGKFPWYLYCCIGAMSILLSQLVLFPLAAAIVFSVKFIGYYFFLWFWLFWATFTLLLVFFLPYCCIPCIGRQVVLPEGTALYMEVKRVCDVVGFPMKRVFIIKTRTMQYSNAYFYGSCCLKRIVIFDTLLLNKGKEPNEIHPYEVGRGLTNIQVAGVVCHELGHWKHGHFYKATIIMKIHFFITMGLFGLFFHSPQLYMAVGFEPGVMPIIVGFIIVLKFALTPYLTLANVLMLWNLRRFEYAADKFAHRMGYSIQLRMALVKIYADHMSFPVYDQCYARWHHTHPTILQRLAYQQKLDVKAMNAGTY auto:exon19 CG30461-RE part_of auto:exon18 CG30461-RE part_of auto:exon17 CG30461-RE part_of auto:exon16 CG30461-RE part_of CG30461-RE FBgn0050461 part_of auto:exon15 CG30461-RD part_of auto:exon14 CG30461-RD part_of auto:exon13 CG30461-RD part_of CG30461-RD FBgn0050461 part_of auto:exon12 CG30461-RC part_of auto:exon11 CG30461-RC part_of auto:exon10 CG30461-RC part_of CG30461-RC FBgn0050461 part_of auto:exon9 CG30461-RB part_of auto:exon8 CG30461-RB part_of auto:exon7 CG30461-RB part_of CG30461-RB FBgn0050461 part_of auto:exon6 CG9002-RB part_of auto:exon5 CG9002-RB part_of CG9002-RB FBgn0050462 part_of auto:exon4 CG9002-RA part_of auto:exon3 CG9002-RA part_of auto:exon2 CG9002-RA part_of auto:exon1 CG9002-RA part_of CG9002-RA FBgn0050462 part_of CG30461-PE CG30461-RE derives_from CG30461-PD CG30461-RD derives_from CG30461-PC CG30461-RC derives_from CG30461-PB CG30461-RB derives_from CG9002-PB CG9002-RB derives_from CG9002-PA CG9002-RA derives_fromchado-1.23/doc/examples/dicistronic-gene-example.game000644 000765 000024 00000161451 11256707742 022712 0ustar00cainstaff000000 000000 2R-fragment Drosophila melanogaster AACAAATTTTTTTTTTATTTTTGTATTTAGCTTAAGGTATTTACAAAATT CGTACGAAAGCCGAAACACCCATGAAAATAAAAGAATTTGGTCAGCCCAT TACCATAAATACAAATGAATAATATAAAAAAATCAATCAATTTTTATGTG ATTTGCTACATGAAAGCTAGATTACTCATACGCCCCGAGTGCTGATGGAG AAGAAAATTGCAGAAAGTTCACAAATTACCAGCTGAGGAAGGAGAGCAAG AAAAGTGGGAGGTCTTGGGCATGATTAAGTCGTTTTTTCAACCTATTAAT CATACGCCATGTTGGCCATTTAACAGTTTCTCACTTGTCATATTAAATTA TGCTTTGAGCAGCGCGACGGGGATTAAATGTATTCATTATTCAGTAAGTG CACTCACTTAAGAGTAAAAGAGGCAAGAAAAGTAGCCAAAAAGAATAATG CAGAATTTCCATCGAGTGGGAAAAGTTTTCATCGATTGCCTGCGAACTTG TAAATTATCGGAAACTTTGTAACCGCAAAAAATTGAATAATTATGCAGAA GCCCTTCAAAATGCAATGCAGAAGTTGGCGCTTTCATGCACACACACTCT TGCTAACTTACTGTCTGTAAATATTTAAGTAAGAATCTTGTGGCAGCCAC AGGAACATCGGCATTATCAGGACTCCTTGAGCGTTGGCATAAATATTTAG GATCCAACATCCTGGCACACGTGCATGTGATGATGAGAAACCAACTAGGG CGACGGTAAATTCGCATACGAGCTGCCAAATTACACTTTACGCGGATATT ACGCATACGACGTGGTGGCATCGCTTTAAGTTGCACAAATTTGCTGGATA AATACGTGCGAAGGACACAATTTCCAAGAGCATACTAATTTTTCTTATTT TGCTTATTTATTCTTATTGAATTAATCCTTCAACTGTTGCTGCTGCGTTC TTACTGCCAATTTTATTTGGCTCTCATGGCATATTAAGTGCCAGCAATTT ACCAAAACGAAGCATGCAACCCGGGCAGCCACATTGAAAATAGGAGGCGT CACGGGTGGCAGAGGGCGTGGCACACACGAGAGGGGCGTGATAATGAGCT GCAGTTTGTTTTGAGTCATGCGCTGGGCGGGGTAAAAAGGAAATTTGCTT CGTCTATCCAAAGTTAACGAAGCAACATTTCATTTGACTTTCTGTCGAAA TGAAATCAGTGTAATCCAGCCTTAAATCAACTCAATAAGCGAAAAAGTGC CGGATCTCAGGCTCTCAGTATACATTGTAACCGCTAGCCTTTTGTTGGCC ATTCTTAATGTGGTGAACCCGAGTAAGCTAACCTGTTTTCACATGGTATT AAAGGATCTTCTTTAAGTGCTTTGTTTGCTTTAATATTGCTCATAAAATG TACAGCCATTTGCAAACTACAGAAAAATTAATTAGTTATGATAATCAAAG TAATGGAAATTCATATTATATTTTTAAAATATTAAAATGTGTTTTCTAGA ACTTAACGAAATCATCAAATGTTTAGAATCTATCATAATTAGGAAAAATG AAAGTTTTAGTACGAGCAAAACATTAATTTCCTGCCATCTCTAATTAAAG TCAGACCGAAAAACTTTATAGACCATTAAAATTATACTGCAATTACAAAT GTAAAATCAATCCGCAAGCTGAATGTGAAAATAAGCCAGAAAAAAGGGAT GAGGCATGAAAAAGCCTGCAGCAATTGGCACAAACCAAATGGCTCCACAG TGCCAAAAACCACACAAAAAAAAACCATGATAAAAGAGGGAAAGCTGTGA AATGCTGGGAAACTGAGAAGGGAAATTCCAGCAAAAGTAGAGGAAACAGT GAAAGGAAAAGCAGAGGAACCAACAAGGGAAATGGATCAATGTCGAATGT CTGGGAGCTTGATGGTAATTTGAGAGAGAGCTTATGCTCCCCATTGTAAT TGTGATTTGGATTCGAAGAATCTGAAATGAATAGAAGCAGCTAAAGGGAT AGACATGATTCAATTACGAAGCTCTTCCCGAAATCAGAGGTAAAAAAACC TACTTCAGTGCGTCGCATATCTGAGTGATAGGAAACATTTTCGTAAATTG TCTAATATGAAACATTATTTACTTACAGTAAGCCGAAAATGACACTCAAT AACATTAATCTCCTTGTAATTTATCCCTTAGGAGTCCTTTTACAAACCCC AAACCAATCATTGCTGCATTGTTATGCATACATGTGACTTTTCCCTGTCG ATACAGCATAGTAATTCATTTCACTTTCCCAGTTTTTCCACAGCACAATT TTTTATGTACTGATTTTCCTGTCGATTAAGCCCAACGGAATGAACACTGC CCAACTGCAACCCAAACTGAACAAAGGGACATATGTGGATATGTACAACA TACCCAAATCCAGTGGCAAATTGCAACATATTTGCATGTGCCACTTGCAA CATTTACGATCGACTAAAGCACTCACTCAATCATCGCTGGGGGACAAGAA CAATAACAAACAGCTACCGAAAATACGACAAAAATTTCCGCAGCAAAGAG GGAAATCCCGCAGGAGGGAAAGTGGAAAAAAACTGGGTGGTGAGTGTAAG GGTGAAATCCATCGATTGCGTGCAGCGTTAAATGTCAGCCCGCAGCCAAT TGCAGATGTCAACACATGCATGGCCCCCCCCAAAAAAAAAGGAAATGGAT CCCCAACACAGTCACACACTTTGCGCCTAAAAATTGGCAGACATTTTCGC GAGTGGGTGAATTTCGGAAAATGTTGTGATTCATGCCCGCTTTTCCGGCG GCTCATTGCGCGTCGAATGCGTTCAATTACGAAATGCCAAAACTGTCCGG CGAATTCGTTTCAATTTCAAAGTACATTCGCAATCACTTTGTTCATTGTG CTGCCTGTCAATTGCATTAATTTATAATTATGTGCCGCCCGCCCACACAG GCACATCCACACAAAAGACAACTAATTAAGGCAAAGCAATTAACTTAAGC AGCGACTAAGTCGGCTCACGAACCACTTGAAACTCCAATTAGGGGCGTGG CACATCCACAATCTGTCTAATCCCATCGAGGGTCCAAGGTAATTTGGTCG GATATCACGATTTGCCTATTACTCATCCCTTCTATGTATTCAATCTACCG ACTTTTCCTAGTTGTTTGCACTTTGAATTAATTAAGCTGAATTTGATTTT AGTGATTGTGTCGCTTTTTCTCCTTTTGATTGCAAGCTGTTTAATGCAAT GTAAACAGAAATAAATAAAGCTTTGGGCCGGCTGTCGCACAATCTTCTGT TTGCCTCCCACACTATGTTATATAATACGCTTTCCCGATGCTGATAAGAC GGCGTACTGAATACAAAAGAATTGGGGCAGATGAAGGAACAGCTCCTTTT AATACCCACCGAATTAGGGGACGCTCTTCCTATTAAAGTAAAGTTTGTTG TGGTATATATATATTATTAATAGAGTACAAAATAAGATTATAAAATAAGA TAATAATAAATATATAATAAACTACGAATATATTCAAATTTAGAGTTCAA TGCTTGAAATATATTTCATAATTCAAATACTCATGGTTAGGGTAAAAAAA ACAAAGCCAGACTACTGAAAGAATATTGGCCGGGGATTGTATTGTGCCTG CATAAAAAGTTTTTCATCGCAATCAAAGAAGTGTTCCCGAAATAAAAACT TCCCAATTTTCCTTCTAAAAATCAAAAACAAAAGAATATGTCAATATATT TAAGGCCTCAAAAGGGAAATCACTCTTCAAACCACCCCAACTAAAAAAAA CCCAATTTTTTTTTTATCTCCGCTCCAAATATTTGCTTTTTTTTTCGGGG GGGCTAACGTATGGATGTGTGTGTGGGGCATGATAAATTTTGAAAATTTA TTTGAGCCGGTCTGTGGCTGCATTTGAAGTGGTAACCATTACCAATGCCA CGATGAATCCCCATTCTCCGTTTTTGGTGTATAAACATTTGCATGGCAAA TTTTTGGAGTTCTTTTATTTCGTTTTTACATATTATTCGGTAAATGTTTT ATTCATGCTGCCCCACAAAATCCCATTAACAAATTTACACATTTTCAATA TTGAAAATGTGCTTTACTTTATGTATAATAAAAACAAACCGATAAAAACA CGAAAGCCAAAAAAAAAAAATATGTCTGTGAAGCAGAAAAATACTTTCAA TTAAGCTATGTAAACAAAGTTTTTTGCCCGAACAAAAAAAAAAAAACTAA GCTGTGCACATGCTTAAGGCACTTATTTAAAATCTATTTTTGATTTTTTG TGGCTGCTGTTCCATGCGCACATTTATTTGGTTTTTAATTATTTTAATTG TACGAAATATACAAACACATGATTTCCTTTGTTTTCGATTTTCCCTGTAA GCCCAAAGTCAGCACAAAATCCTCTTAGCCTTCTTTAGTTGAGTGATAAG CGGCGCATTAGTGGCGAAAATTTATGGCCAACTCTCATGAGCCGAGTTGT TAATGCTGGGATTTCACAGCGATTTCTTATGGGATTGCTGTCGCGGTTTC GCAGATTGTTTTCCTCCGTTTACAACATCTTGTAATTTAGGAGGTAAAGT TTACAGATCACATATGTTCGTGGGAGTCAAGTTCTTTTACAAGATTGAAA TAGAACGAATGGGAGTTTTGGCACAGGTTAAACCGAATGCCACACAGAAA GAAATGGTTAAGCTAAAACTTGTGACTAAATAACAAAAATAAAAATGTAA ATAATATCATGCCTGTTTCTTAAGATTAAACCATATTAAGTCATAGAAAA GTTAGGTATTTCCTCTTTGGCTACATTCAACAAGTAAGAATGAAAGACAA CTTTTCATGTTAATCCATAATAACTCGGTCAGGCTTAAACTGAACCTTCT GTTTTACCTTTAAGCTTTAAGTCACAAAGTCAGTGAGCTGCCACTCGAGA ACCAGTGGCAATTGCATAATGGACACAGGTCCGTCCCTTTGATATGACCC AAAGATTAGGGAACAGGCACACACAATGGCGTTCATGGGGCGTATGATTA ATAAACACTTTTAGTTTTCGTTTCGGTCAAAATGGAAACCTTTTCTAGAG TCATAACAATTAACTTTAAAGGTTTAGACATAAATCCTTGCACAATTGTA GTCTCACACAAAACATACATGTGTATAATAGAACACGAAGAAAAAGGCAG AAAGTAAAAAGTAAAAGATGAATAATGAATGAGCCGCACGCGAGCAGAAG CCAGGTGGATTGGGGGCGGGAAAATGTGGAAAAGCTCGGCGGCCATTCAT GAGTAACACTTGACATTGCCTGGGCGAGGAAAATGGGAAAAGGAAAACCC ACACATACGCACTGCGCCCGAAGGGCAGCCGAAGGAAGCTCGTTTCTAGT GAATTATAATATGGCATGCAGATAAAACATTGAAAGTCAAAAGGCCCTGG GGGGACTACAATTAAGCGCACCACCACCCATAGCCACCCACAAAACGGAG AGGGAAAACATAGCAGTTTCGACATTGGCGGAAATCATTTTCATATGTAT GTTTATGATATTTTGTAGATAACTGCAAGTGCTGGCGCAAAGTTTACTCG GAATTAGCCATATCACAGAAAACAAAGCCTATATTCTGCGTATTTTTCTC GCATTTTTTTTTTTTTTTGCCCGGACGAAATAACACATGAGAGAAGAAAA AGCCCAGGAAATCTCTGGCGAAAAAGAAAAACAATTCAACAGTTTGTTGC CAGCAACATGTTGCCAACGCGCTGCTGCAACACTCTCCTACGCTCTCTCC GTGTTGAGTTTTTCACTTTGATAAAAGCAAAAGACCTGGCCATAATCGAA ACAGTCTGCAAAGGATTCTAGGCGCCAGCGGTTCTCCAAAGATAAAATAC CGTCAAGTATTAGGCAACGGCAATCGTCGCGTGCGTTTTAACCAAATATA CTTAAAATCGAAAATTACCTGGAAAAACGGTCGAGAAAAGTGAATTTTAG TTTTTGGAAAAGAAGAAATTCCAAAAGCAAGCAGCAGTTTTAAAAAGTAA ATATGATTTGTTATTTGAAACATTTTCTTGGCGAAGAACACTAAACAACT ATATTGGTTTCGGCAGTTATATTTATATTTTTTAAAGGGCGCAAAATAAC ACTTTATGCATTTGTTTTTACAAGAAATGCTCGAAAACATTTTATTTAAA ATAGATGTATTCTCCGCAAGCAGAATAAGTGATTTACATTCAAACATGCT GCGCATTTCAAAGTCAGTTTTTTATGAACTCGTTTATATCTCGCTGTATA TAAAAATGCGTTTCAAACAAAAAAATTTACATTTTTCTCACGATTTCCAA TCACTTTATTTAAATTTTATAATTTATGCTAAAAGCCTTTTAAATCTGGG CTAACTAGCCTAAGCTGACAAACGCAAAGCAGATTGTCCTTTTGGAAAAA AGCGTTCAATTTGCAATGGATTTCCAAAGAGGTGGAAAATTGGTTTGAAG AGGTCGTCGCAAAAAAAAAAGAGCAACAGTGAAAAAATGTGCGGGCATTC CGTATTCAACCCGCTGACAGCTTAAACCGTGTCAAATAGCTGAATTTTCC CGGACACCAGGGGCAAACCTTTTTTCAAGAAGTCCGCATTCAATTAGGAT AGGAGTCGAACCCTCCTCATTGGTATGCCGAATGGCAGCCACAGGAGCTG ACACTAAAATGCCGTCGCCATCGACGAATGTCCTTGACTTTGCCTATTCA AACGCAAAATTAAACAGCAGAAGGGACAAATAATGAGCGGGAATGGGTTG GAATGCCATGGTAATGGGTAATGGGCACTACACTACAGTGTGGCAATGGT GGTGGGGCACGTGGGGCAAGTGGGTCTGCGTGCCAACATTTACGAGTCCC CCTAATTTATGCTCATTCATAAATCTCCCTCGGTGGAAATCCCTTGCAAT CGGCGACGCAGTCGACGCCAGAATGTATGCAATGCAATGAAATAAGGCAA ATTGAAAGTTATGACTACATCAAGGACTTCTGTGAGGCGACGAAGATCTA AATACCCTTCAAAATGTCCAGGATGTTTTATAAAAAATTATACAAAAATT TTAACAATTTTTCAAAAAATTATGTTAATATAGTTCAAATGCACTTGAAA ATCTAAAGAAAAATTAAAAAATTAATATAGAATAATTTCGTAATTAACTA TAGAGATGCTTCTAATTTGTCCATTAAAATGTTACTAAAAGAACATATAG AATTAGCGCATTTATGAGCCAATTTGATGATAAATCAAAATGAGCCTTGT GAGAGCATGTGCAACCTTTTATGTTTTGTGCAGCATAAAAGGGAGCTGTC AAAAATAATTAAGAAATATCTAAATATAAAACACGACCCTTCGCTGGCTT CCCCTGAAGATTCGGCCACGCAGCGTTGTTTGCCAAGTGCAAAATTGGCT AATTAGATGACATACCACTTGCAACTAGCACGAGCCGGATTGTCCTCCAT TCGAGCAAATGGCTTAATTGCAATTGCATTCCTAGTTTAACACAATATCG AGCAAGGAATTTCGTGTACGAACAATTAAAATAACTAATTTACTGTGAGT ATCTAATTTTCGATGCTTTCATTTACGTTTTTCTCGATTTTGTACACGCT CTCGTTTAGCGAAAACAAATGGGAATCGGAATATCAGAGCCGAAGAATTA TCAAAATAAATACGTTTGTCAGCGAAGAATGGAGGCATTTTGTTTGCATT TTCAGCCATTTAATGGCATTGGGAAGGAAGTTGGATTCTTGGTTATTAAT AGATGGCTATTCGCAAAAGGATGGGTGATTAAGCGGATGGAAAACACTGG CCAAATATGGCGACGTCATTTGACAGACGCAGAGATGAGCAATGATTGCC ATTAATTTAAATTAATATCACACTATTCAGGGTCAGCAAGATTGATGGGT TATTTGCAGTTCAAATTGTGTGGGCTTTGGAATACAAAATGGAAACAATG ATGTAATCTCTCCGCTGCCAAAATAAATACGGTTTCTGTGAATTTCCAGT TAGTAAAGAAAGCAATTCGTAAAACAAAGCTTCCGGCAATTATTTGTGTA CTTTTTTTCAAAGAAATAAATTATACGCAATATTAATTCTGGTTTAGCTG AACGAAATGCGTGGTTTTCAGAAAGCCATCTAGATTCCTAGTATAAAAAT AAATATAAACTCGGAAAAAATCGGTGGAGGAAAATGCTATTACGAGTTTT TTGAGTTGGTTTTCATGCGAACTGAAAGATATTATTAAAATTCTATGAAA ATTGAATATTTTGTTTTCTAAATTGTAACCAAACCTTTCTTTTCTTATCT TCTTTTAGTTAGGCTTAAAAAATTTCAGAGTTAAGTGCTCTTACTTTCAG GACACCCGCTACCTTCGTAAATGTCCTGCCACAATCGCAAGGCGCAGTTT CGCCCACAGGTATTGGGCGTAATTATCTTAGAACAATGTCAAAAACACAA AGTGCCATTAAAAAACGTTCGCGCCTAGCGGTAATAATTATTCTAATTAC GAGGCGTTTTGCTGGAAAAGTTATCGAGGTGCTTGAATGCCCCGCAGGGC CTGTCAAATATGTATTTTGTCCGTGCAAACAAACCAGCCAAAAAGTGGCG GGGATCCCAAAGCAATCAGCATAATTTGCCTCTTGTTGTATTTTACATTT TTGCGTATTGACTTTGGTCGGAAATCTTTCCACACGCCGACATCCAGCTG GTTAATTACAGCTGTTGGCCCCGAAGAGCATTATTATTATTTATTATTAT TATTATTATTTCTTGATTACTATTTACGCAAAGGCAGCGTAAAAAGTGCC TTCTATTAGCTATGTAAATATTTACATCATCATCACTTGAGGTTTTTCGG CAGCAATTACGCGTTGCGTCACCAAACTGAATAAACACTAAGGAAGCCTT TAAAAAACACGTTGAAGTAAATATTCGTGTGGGGAAAATATACATATGTG CATACCTTCGGCAATTTTGCATTTATTGTGATCTTTTTATGGTTCTGCTT TTTCCTGGATTCCATGAAAAACAAAAGAATACAATAAAGAAAAACAAATG ACGCAGGTTTTTTTGGCCCAATTTTTTTTTCTTGGCTTGTTTGCCCGGTT TTCGTTTCCACGCCATCCTTTATTTATTATGGCAGGTTATAAAAATGCAA TTCCAGTAATTGAGCAAACTTCAATACTTTCCAATTCTGTCGTCTTAAAA TTGTGATATAGATTGTCAGGACTCCACGCTCTAGTTTGTTATTTATAGCT TTTGATTTTTGAGCCCTTTTCGACCCTTACAACTGTCATGTTCTGGCTAC AGTGACAATTTCCAAATTGACTGACAGGCATATCCATTACGAAGTGTGTT TTTCATCCCAAATGGTTTTCTGGTGATTTGGCATTTTTGCGAAAAAATTG TAATTCATCATAATATTAATAAGATATCGATTTGGTTTCGGTTTTCAAAA AGCAAACTACCTCGAAATGAAAGTACGAAAGATCCTGTAATTTAATATGG CTACTATTTTAATAATTAGCTTTGCTGTTTTTTGTCAATTGCTTTAGGTT TCATTTTAAGTGTCACTTCCCACACATCACGTATACGCAGTGTATGCCAT CATTAGAACTGAATTCGTTCCAAGATGAAATCAATTTAAGTGTCACACCC CAGACATAGTATGCACTCCATAATTAATCTGTTCTCCTTACTTTATTGCT TTTTACAAGCAAAGGACACGGTTTTTACATGCAAGCGAATTGAATTTTAT TCACAGCTGACAGGGACTAATAACAATCCATAAGTATGACCACATGGGGA GTTGGCATGGCAGGACATCGCATTTCCCCTCCGCCCATTCGGAATTTAAT TAAAACTGTCTAAAGCCCAGCGGGTGCCAGTCGCCGGACAAGAAGAAACA AAAAAAAAAAATGCGTAGTGTCATGCAAAAAACCATTATTCTTTAGATTT CATCCATGGTAGATTATTTTTCAATATAAATTCAACGGATCCCAGTGGTT AACCAGAGTTGGCCAAGCTAATTACGGCTCCGCGGTGACCAATAAAATGT AATTAAAGTCCGGGCAACAGCAAAAAATGGGCAGAAAAAATGTGGCTACT ACACCACCGCAACTAGCTTAAAAGTAAAGAACTGAAAGTAGTTTCCCTCT GGCCCTGCGAATTTTCACACATTTTCTTTCGCACGCAGCGCTGGCTGAGA GTAAAAAGAAAAACACAAATGAAAAATAAAATACACAAAAGCTTCCGACC AGCAGGCACATCAGGCAACACATCGTAAACAACTTCTTGGCCAGCTCGGC ATGACAAAAAAACCAGATTAAATCGCCTAGCGAACCAGATGCAATATGCC CCCCCAAAAATTCTTGTAATTTAGCAAATCGCTTCTCCAACACGAGTATA CAAATTGGGTAGATTATCGACAGTAAATTACAAAGAAATTCTTCTCGCCG TTCTATAATTTCTATAATTGTTTACAAAGTGCCCAAGTCCGGAGGAAGAG GCAGCTCTCTCATCCTCCGAATGCAAACTACATAAATCAACATCTGAGGC TTCCTACTAAATCGTTCGCCGCTGCTGAGGAAGGAAAAATAAATAAAGCG ATTTATTAAAATCAAAAGCCATAAACCATTCAATTAAGTGAGTTCTCTGC GAGCAGCTTAACATGTGAATTATAATTATAACCAATCGAAATGACCACTT TTGGGCAATTAAAATTTATGTTTGCACGCCATAAATTTGGGCATTCGGCT CAATAAATCAGCGACAAGTTCGCCGTCTGAAATCAACACTATATATCAAG AGATTTTCATTTTGTACTTTTCGCATAATGGCCAACGGTACCTTGGCACG TAATCATCTGCTCGGCGATGACCTAGCAAATTGGCATTTAAATTTTTAAC TGCATTTTTATGATGTTTCCACAACCCTCTGACTACCAATTTCTTTTGGG CCAAATAAAATAAACCGTAATGCAATAAATTACGCTGTTTTTCTTGTCGA TCCTTCGGCAAATTGTCTGCCGGACTTTGGGCCATAAATTCAAACCCCTT ACTCGGCCGAATCTTTTGTGTCCGACATAAGCCGTTTTGGGATAAATCTT CGGCTTTTTTGGGTGGGCAAGCAAATCAATGGTGGAGGAACAATTTAATA ACCAACTGGGGGGATTAACTGATGAATATTCCTTGGGATAACCAGTCGTC CTGCATATATAAACATATTTCTTGAGGCACGCCAAGCAAATGTCAATGTC AACTGGCCTTGTTGGGCCTTGGATTTTCCTCGGCTCGCCTGTGTTTACTT TTGGGTGGCCCGGAGTGGCCCAAGCCAAGGCTAAGTTTATTATGCCGCGA AAAATGCAGGCCCTCGAGTGTGAGTGCCGTAACCCTTGAACTCAAAGACA TAAGAAAAACAAAGAACCAACTTAAAGTACACCCACCACCTTGTGTTTTA CATTTCAAATGCTAAGCACAGTGGCTCCTCCGAAATTATATAAATCAGAA CATGAATAAAGATTATATTTTAGTCCATTTAGACTACAGAATCTTCTGCT AATGAGAAAGAAAGAATGGTTTGTTTGCATTTACCATTTCACAATGTGTA TATATTTTTCTCATTTCTTTATATTTATTTATAAACCGACTTAGTAAGAT ATATATAGGTATTCACTAATTTTGTCAATTAGAAATGCAAGTGTTTAATC AAGGTTCCTTATTTATAGACTTCCCTGTACAAAAAGCTAGCGGGCAAGGA AAACTTTCTGTTAGTCAGTGAGTATATTATTTCAATCCCCTGCATTTTCC AATGCCCGAGCTTCATGACTCTTGCACTTGAATACATTTTACAGCGAACT GTCTGTCGGCTATGTTCGCTCATGTTTCAAATGTCGAATGTGTGAGACCG TGTTTCGTACGAGCAGGAGTTTTCCATATTATTATTTATGAATGCGAAAT ACTTTGGCTGACATTTATATATGTATATATTTTTTTTTTTTTGGGCAACT GCCTTCGTTGTGTAAGGGTTACAAGCTACAAGTGTAAGGGTTTTAGCTAC ACGTGAAAGTCATCTTCTAGTTTTACAACTGCTTCACTCAGGGCCAATAG CGAGGAAAGTGCAGTAAAATTGTAAGAATTATGGTCAGGTTGTAAACAGG AAATATCCTATTAAACGAAAGCGGGGCGGAAGTTCCTTCATTGTTGTACA CAAGCTTTTACCTAAGTGCATTTTTAGGTGCATTAGAACATTGATATGAT TCTATTAGCTCTCACACACTTCGTTTTTATCACCTTTGTGGGTGGGAAAG CATCGAGAAAAACCATTATGGGATACCGTAATGGATGGTGGATATGATGG ATGTCTTGAGATACCATTGATCCATACAAGTGACCCAAGAAAAAGAAAAA GGCGTCCTTCATCATTTAGGCCATCATTAATTAAAAGGACACAAAATTGA AACAAAGCTTAATCAAATTAACGCAAGAACTGAATGATAGATAACTATTT GTTAAAAAAATCGCATGTTACATATAAACTGCAAAATATTAGCTTTGTCC TGCTTTTTGTGCACTAATCTACATATTTCAAGCTTTAACAGTACCTTTTA TAGTTTCGTCCTAGTAGTTAAATTATACACCTTTCCAATATCTATACCAA AACTGTGCGGTAATTAAAGCTATATATAGACAGACTGGAATGCTATCAAA CCAAATAAAAGGCAAAAACCCTAGTCTATAATTCAGACTAGGCAAAAACG CTGCGGTCGGGCGCAAACTCTTAAAATAGAAATAATAACAGATACGCCAG CAACAAGCGGGGGGGCAAAACCAGGAAAGGGAAAGGAATGGGTAAGGGAA AAGGAAAAGCGTGGAAAATGCGGGGGAAATGACAGGCCGCCAAGCGGGGA AAATAAACAGAAAAACACTCAAATTAAATTGCGAACTGAGCTTAATGCAC TTAAAGTCAGTACATGCCCAGGAAAGGGTGCAAATGTGGGGGGGTGGCCA TTGTGGGGCAATGCCAATGTCAGACGGACGGATGAATGGTTACCATTGAC AGGTAAGCAGGTGCTCTGCGCTTTTCCGTGCTACCACCCCCCCCCCCCCC CAACCCATCCCCTTGACTATCCCGGACTTTTCCTGTGGCACTCGAGCACG CGCCCGAGAAATGCCAAGAACTGAGAACTGAAAATCGAGTGTAAGCCGCG GCTTATGCAATGCGGCCAACGGGGCTTGACAGTCTGGTTTGCTTTTGCTT ATCTGCGTTTCTTGGCCCAAAGGCTCGATTTGCCTTTGGCTGTTTTTGCC ATGCAAGGCGGCCATTAGTGACGTCGAGTCAACCAATATATTTCCTGTTC AATAGGCTCCCCCCACCCTCCCATTGATTCGTGGCGGCGAAAGAATATTT AAATATGAAGTTGCCAAGTTTATTTCCTTGGGGACTCTTTGCGGCCGTTT TCGGTGGAACGAACTTTTTATCTGCAGCATTTTATATCATGTTTTTGCTT TCTCGTTGTTTTATTGATTTAATTTGTTGTTGGGCACTAGGCTAAAAAGT ATTGAATATTCAAAAAGCCCTTTTGCAAAGTACCAGTTGAAAAGTTGTCT CGTTAGTACAAACTGCAACTTGCTATGTAGACACACTAAAATGCAGAATC GCTATTGAAGTTATTTTTCTGAATCCCTGCGGCTGATTATATATTCATTG CTTTAGTCATATTGATTTATTTATTTCCTTGCCAAGCTGCATGGGTTTGC ATATCCGAATGGCAAAATTCCAGTTAAAAGTTTTTCCATTTATTTAAACT ATTCAATCTCAGATTAGGAAAATCCGTTTGCAAGCAGATTCTATTGGTAA ATTATTGCTTTACATTTAACCGTGGTCATATTGATAACAAAAAGAGACAA AAAGAGAGAAAGACAAATCAGAGTTTCCTACGTACAGTACTAAATAATAA AAACAGAAATATTTTAAAATAAAATTTGGGAATTATGATTATTATGTTTC GCCAATACAGACTGTTCCGAATTATGTCCTTTAATAAAAGACTTGCATAT TAAAACATATTTGAATACTTTATATTTGTATAAGTGCATCGTATTCCTAT GTAATTTTCTCCCATCGAGCGTACTTAATTCCCAGTTCTGCCCATAGTTC ATTACACAATTTATATTAAAGCCGTAACTTAACCCTCGGCATCCAGTTCG GCATTAGCTGGCAGTTGGAGCTGGGCCAAAAGTATTTGCCATATTGCACT CTGGATTGCAAAAGTTCTCGACCAGCATTCCGCCATAATCGTATAAATAC GTATACAGTTCTAGCACTTCCTTTCTCTACATACATTTGAAAAAATAAAA GAGAAAAAAAAAACAACAAGGACAACAAAGGATGTTGGTGGGTTGGGTAA ACAGCGGAGGAGGCTTGAGGCGACTGCAGTGGGTGAAATGCAATTTCCAG GCCATAAAATGGCTAGGCAGGAAAAAACAGCAGGAAAAGTCCTTTCACTT GGCTCGAACGAAAGCGTTTGCAGGTAATGGCCATCATACAAGCCGGTTAA TGCGGCCAACTTGTTCTGCAGGCAGATAACACGAGTAACCAAAGTCCTCG CGAACGATGCGAAAAGTTTCGCGGCAAATTAAATGAAAGTTAATATTGGC AGCGTGTTCGATAAACAATAGGGACGTAGTCAACAAGTTGATCCTAATGC GATTATCGCACTGTGCCTAATGTCTTTGAGAATTGGCTAGATGCCTTAGT TTTATCGAGAAAATTATCTACCTAACTTTTTCTACAAATTTCTACATATA CCTATATCATTTCGCAGTTTTAATGAGGTTTAGTTGTGCCTTAATATGAA TTCTAGATTAATAGATATATTCTTAAAGAATATTTTCGGTTTTAGATAGC CAGATATTGTCGCAACCATTTTTAACCTTCAAATTGAAATTAGTGGCGAT TTTCTTGTGTGCCAAGAACAGTGTGCAGTGCGAAACTCATTTAGTGGTAA CAGCTGCTGCAAATTTATGCTCACGGCTTTTCTATTCTGAGCTTTATTTT AGCCACAGAAGAGCGACCGCAGCAAACTGTCAACGATTCCCACCGCAGAT ATATGTACACGTACATTCATCCGGATGTCGGCAAACGAGCTGGCTAAATC CAAGCCAAACTGGCACTGCTCAAATACCACTTAAGTATAGCTTGGCATTT GGCAAATTCCATGATTTTATAATCATTTCTTTACTCTTTTATTAATTTGA ATGCCAAATTTTGACTTTTGTATGCATATAACGGAGACGTTTTAAAGCCA ACCCGTAGTGGGTGAATAAAAGGCAAAATAATATACAAAGGGGTATGGAA AATTTATTCAAATATAATTCGATACTTTTCTCATCCCATAGAACCAAAAA AAATATGAATTTCAACGCTGAAAAGTATGCAATTAAAAGGTTCATACTCT TTAGTCCTTAAAAGGGGTTGGCATTTCCTAAACAGAAAATAACTTGCACA AATAGAAAGTTATTGTTATAATGATTTTGGTTGAGTAACTAAAAGTAAAC GTAAAAAAATAATATATATAAAATAAACATAGCACAGAAAGGCCGATTGC AGTTGGGTCACCCTTGGTAATTATTTTTCTAAGTGTCCCTTTCAAGCCAA CATCATCTGCAGACGCGCCTTGAGCCCAGGACTTTGCTTTCTTATTTTTA GAGCAAACCAAACCCACCCACCCGCGAGGCAACTGCAGATGTGGGCGGCC CAGCAATTTTGTTTACATTTCTTGTTTTCTCCCATTCCGCGCGGTGTGTT TAACCCACAATGACTTGTGACTTGTATTGGGCTGGGGGTTCGCCTGGGGG CCTCGTGGAGGTGGCGTTCTGTCTCATTTCAACTGCGGGAAATCCCCGCT CACGGATGCAATGTCGGCACTTCCTCGGCTGCAATGGGAGTCCCACTGTG ACCATTTCTCACCCGCCATACGTATACGTGTGTATGGAGCTGCAGCTGTG TGGGTTTTCGTGGGTGTTTCTGTTTTATGCTATTAATTTGACAGTTTCAG CTGCGCTGACAACTGGCTTTTCCCCAGACACCGAGCATAGCGTTTAATGG CTGCAAATTAATTGTTGTATGCCTTTCTCCTCCCCAGAGATAATTGCTCA GCAGCATCTAGTTTCTCAGCGAGGACAAATAAACCCGAGAACAAAAAAAA AAACATAAGAAATGGACTCTGCCGCCGCCGCCGCCGCCAAGCGCGTTCAA ATCGAGAAGGCCCACAACTTTATGCGCCAGTATCGTGATCCCGAGTCCAG GGAACTCAAGAAGCTGTCGGCCAACCAGTTCATGGATGTCTGGGCGCATT ACGATAAAGATGGTGAGTTTAGATCTTACTAACAAAATTTGCAATCATTG TATTTCACTACTGCCTTAGAATTGTAATTATTTGCTTAACTTTCCACATT AATAATTTGTACTTTATATAAATTAATCCACACTTGAAACACATTTAGTT AGTATCTATTAATCAAAATGATATATTAGAGGTTTAATAACTCATTACTT ATTTAAATTGTTTACCTTAGGAAATGGCTACATTGAGGGCACCGAGCTGG ACGGATTCCTGCGGGAGTTCGTGTCGAGTGCCAATGCCACAGACATTAGT CCAGAGGTGAGTCTGAAGTGGTATGGAACACTTGCATCTTAATCCCTCGG TCCCAATTCCCAGGCAGTAACGGACACCATGCTCGAGGAGCTAAAGTCCT GCTTCATGGAGGCCTACGATGACAATCAGGATGGTAAAATCGATATCAGA GAGGTGGGTAATACCTACGACTCATTCGGACCCAAAATTTCAGTTTGATG GGGGCTCCCATGTCGTATGCGCAATGTTGTCTGTATGGATTTTTGTATAC GAAATGACATTTCCTTTAGTCATGACGGCGCCTTCTTTGCCTTTTTTTTA AATTGGTTTTTAAATGTCTCGGCCGGGCCGAAACCAATAAATTATTTGGC GATTTTCCCTGGAGAAGGAATCAACTTTCTGGCAAGGTCTTTGGCCAAAA AAAAGTTTTTTTCTTCGTTTTCTCTCATTGTGTGGAGGCCACATTAAATG AGTTTTTAATTGAAGTTGAACTGGCAGCAGAAGTACGGACTATTGGAAGG GGATTTTCCGTTTTTCTTTTTTTTATACTAAATAATACAGCGGTGCACAA TGGACTTTTGATAAATGAGCCCACGAAAAAAGGGAAAGTTTTGGTGAAGA AAAGTAAAAAGTTCAAGTAGCCGGGTCCCCCATGTATTGTTGATTAAGAT TGCTTGCAACACAAAAGGCACAGGGCATTCATAATTCATGTTGTCCACAT TATTCATACGCCACGTCGAACAGCGATTGAAATGGCTGGGACGGTTAAAT TACTGGTCTGTCGACAAGGCTTTGGCCTGAAGATAAACTTTAATTACGAT AGTGCTATAATTACCAACAGCAAATAAAAATGTAAATCCCACGGCCACAG CGAATTATAAAGTTTTCCCTGCCACAGATGATTACTTGTAAAGGGTAAGG GCTTCAATTCGACACTTGAATTATGCCGGAAACTTTTAACGAATGCCAGA AGCGAAACTTTTCCGGCTGTTTGCTAATGAAAGTGCAGCAGGATATCCTC GCCTTTCACGCAATGCACCGGATAAACAGGAGACTTAGGAACCCGGCTCG TCCTCGGAGCATTCCCATTTATAACTTATTTCAATTGTCATGTCACGCAC TGAAACAAAAAGGTATTTTTCTTGTACTACTTTTCCGCAGCTGGCTCAAC TTTTGCCCATGGAGGAGAATTTCCTTTTGCTCTTCCGCTTCGATAATCCT CTGGAATCTAGCGTTGAATTCATGAAGGTAAGTGACAATCAGGAATTTCA CATCCTGAAATTCCCCAAATAATTTGTCTGCAATTAAATTAGATCTGGCG TGAATACGACACCGACAATTCGGGTTACATTGAAGCGGATGAGCTGAAAA ATTTCTTGCGCGATTTGCTCAAAGAGGCCAAAAAGATCAACGACGTGTCC GAGGACAAGCTCATTGAGTACACCGATACTATGGTAAGTTGTCAGACATA AATGCATGACATTACTTTGGTTTGCTTAGGAAATTCATTAGTAGATAGAG GATAAGAGCTAAACTAAAGTGAACGATAATTTATGAATACATGAATACTT ACTATTTATCTAAGAGTTTCTTAAGGCCTCAATATCCTTTTCAAGAAATA AACTTCTTGTTCAAAATTCCCTAATGATTATACATAGAATGCCAAACCAA AAACGATTCAATAGCATGCTTAGATTCTAAACTGCTGTGATTATTGACCG ACTGACTATGCACTTTCTACACAAAAGTGTAAATAATGCCGATTTGCTAT AAGCACACGATAATGTATGCCCAATTACCAATCCCGTCTCGATTCCTTTC AGCTCCAAGTATTCGATGCCAACAAGGACGGACGTCTGCAGTTGTCGGAA ATGGCCAAGTAAGTGTCCTTGAAGTCGCGTTCTGAAATTCTATGCAGCAG CCAGCCAACTAACTTATTTATTGCAGATTGCTTCCGGTTAAAGAGAACTT CCTGTGCCGCCAAGTGTTTAAGGTAAGTGCCAAAGATAAATTGTGTGAAA ACATCGTTCATTCGAGGAAATTGCCAAGAGCAGATACTATCAGCAAATCG CGGTTTTCCAAACATTTATTTATTAAGAACTTGTTTATGAAACCAAATCA AACTCGGCTTGCCTTGAACAAAACACGTTTAGCACCTAGGTTAGCCTGGA CTTTTGGTTTATCACTAGCTGCAGCCTTGACTATTCAACTAACTTAGCTT TGCAACTAACTCAAACAGCAATGCATATTGGTTTTGTCTTTTCTTTTGTT TACCTATCATTTCAAACGATGTCTGTGCCGACTTGGGAACTAATCTTTAA GAAATCAACGAATTTATATTATTAGAAAATGGTCAATATCATATTTATAG GGCATTAAAAACAATATACAACAGCAGGTTTGTAGTTAAATTTCCATGCA GAGAATTAGCCAACCAACCATCAATAACTAAATAAAATCATATTGTTCAT CAATTATTATAAAAATCAATTACCAAATTTAGTTTTCACCCATGAACAAA CATTAATTGGTTAAATACATTGCAATGCTTACAATCATAAAATTCCATGG TCCAAACAAACTTTCAAAAATAAATGGATCGGAAGGGAAAGTGTTATGCT TTTCTGAATAGAATCCCGAATCAACAGCGATTCTAAATCCTTTTAAAGGC TTTTCATTCTCGCTCGACAGATCAGCAAATACAATTTTTTGACAAAAAAG GACAATGCCACTATTTATTCTTGCTTTCGCATTCGACACTGAATGCAACA TTGAATTGTTGTGGCCATAAAAAAAAATATATATATTCAAGCCAATTTTG TTTGCGTCGCAACAAATAAAGCCATGGCCAAACACAAATAGCTATTCCGC CGAAAAGGAAAACAAAAAATAGCAAGAAATATTGTCTGAAATCGTAAAAA TAAACGAAGCAAAATGGCAAAGCTCAGCTGAAACTGGCAGGTGCTTTCCA CCCACTCCCATTTCTTTTCTTTCTTTTTTTTTTTGCAAAAAAAATGCGTG GGAGTTGGTGGAATCAATTTCCGAAGGCAACAGCTTCCTTTTTTCCCCCA GTTTTTGCTGAAGCGTCAACAGATTTGATGCGATTTGAATGGGGCTGTAA AAAAGGGGAAGCTAAACAGCAATCACTGCACAAACAGAAGGTGGAAAGTC CCCAAATGGCTGGCCATTAAATACTTTAATATTAGTTTGCCTCGAAGAGA TGCCCAGCCGAACAATTAGCAGAAGAAAAGCCATGTGGTGTTGGGAAAAC AAACTTTTTGGCCACGAACGCCGCCGCCGCCGCCGCTGCCAGATGTTGGG GCTTAAAATTCCCCTGGGAAATTCTACGAACCCATTTCGACTTGGCCCAA ATGCTGATGATGCCAAATGCGGTTAAATGAAGCACTGTCATTGCAATTGA GGCTGCCTACGAATGTCACGTAGCTTCCCGCAGGCCAAAACTTGGCCAAA AAGAACATATATTTCGAGCATGTTTTTCGTTTGCGCATTTTAAGCATTCT GGCAAGGAATCGGGCCATCCAAATACCAAAAATAAACGTTTTGTTTGCTC AAAGCAGCAGCTGCTTAAGAAATTCTGGCTGAAACATGTTCCAAGTATAT GGAGGCCTTGGTTCTCTATCAGCAGTTTCCAAACATTATTTAAAACTTCT TAACAAAACTTATTTAAAACCAAAGTGCTCTCATCAATTTAAGCATTAAA TGTGTATAGTGTGCGGAAAGAAAGCTCGACTGTACATAAATAATACTACT AACTAAGGGCAGGCGGAAATAAATGTTGGACCTGCAGCCTTGAAAACTCC CAATTTGCTGAGCCAGCCCCTTCGAAATTTCCCGAGTCGCGTTTCCCACG TCCTGATCGAACACATTTTTTTCCTCTTCTCGTGTTCGTCCTCGTGTTTG GGTTTCCTTTTTGCTGTTTGCCACATGAACCACACATCGCCACATATGTA TGTATGCAATCCATGGTCTATCCACCCAAAGGAAAACCACCTCCATTCGG TTGTCGGTGTTGTTCTTGGCAATCAAGTGGGTTAGATGCACAGCAAAATG ATCTGAGGGGGGGGGATAGTGGAATTGAAGGGGCATTGAGAGCTCTTATT GTTATTTGCTGCAAATGTACGTGCCTCAGTCGCATTGACGCTCATTCTCA TTGCTCATTGGCAGTAGTTGCCGAAAAGTTGGATGTGTTAGCTATCGAAG CGGCATTTTTCGGGCAAATTTTGGGGGGGGGAGATGTGGGTGGCGCCTCC AACAGTGTTCTCAAAATCAAAAGTGTTGCATTCAGCCTGAACTCACTTTG TATTGGTTTTCAATTGCAATCGGATTCCCATTGCACTAAATCCCTTTTGT TGGCTGCTTGGTGGGAATCCCACGCGTTGTTGAAAACGAAATGGAAAACT TGTAGATGTTTCTATCGAAAATTGGCTTTGCTGACGCTGTGGAAACGCAC AAAAACACCCACTACAGTTTAATTCTAATATTTCAAAGCTAATTATTGCA ACTTTCGCAGCGAAAAGAGAGAAAAAATACATTTCCAATATAACAAGTGT ACTTTGAATTTGAAACGCAAATATGGCAGGAAAAGTTTGGTGCCTTTGTT GTGAGAGACATACGTGCTTGGCTTGATTTAATATATCCTTTATATGTTTT ATAAAGGCTTCTCCAAATTTATTTCACTCACAGCCTAAATAAAGAGTTTT AAATTTCATCAAACCACCTACTACATTTTGGCTCAGCAAATTTAATGCAA ACATTTTGACAAGCCAATACTTTTTTCACTACTGTCCCATCCAAAATAAA CATATTGAAGTCATCTTGATGTCAGCTTACATCCTTCACGCTTTCCAATC TAAAATGGCAAGCTGCTGGTGTAAATTCAAATGCAACTCGCATGTTCCTT CAACGAGATATTTGTGTTGTGCGCGGAGGGACGTCCTCTTTGCCAGGCGA AAAGTAGGAGGATCTGGAGCAGGAGTGGGGACGACCGTGAGCCATGTAGC GATGTGCAGCCATGTGGAGCGGCAGTCCGAGCGAGGAGCAGAAGAAGCCG CAGGATTGCACAACGAACAATGCCCAGTGCTCGGTGCTCATGGGTTGCAT GCCGCATATTTGCTCATTGTTACAGCTCGCAGCACAAACGACATTTTATT TGGTTTTTATTGATGGTAGGATGGTGGGCAATGTTGGGCAAGGGAGTGAG CACCAGTCGTTCGGAGTCATGCATAACAATGTAGCGAGACAAGTTGGATT TTAATCGAAAACGCCACGGCGCGGACATGGTTGCTGTCACTCAGTTCCAA GCCACTGAATCCTAAGGCATCCGGATGCCCAGGCACCTGACCACCAAAGA TACGCGTCTGTACTTACCGTACTTTCGCCATCGTAAGTCGGCCGTTATGA AGTGCCATAAAAAAGGCTGGAAGCTGCGGCTTCTGGCAGCCATAAAATAG GCATTTCCAGCACATTTACCCAAGGTGCAGTTATTACTTTTCAACATAAT TTCTTCGGGGGCCATAAAAGCCAAAGCATGCATCAGCATTTTGATAACCG GAGTGGGCCAGCTGCTCAGCTATACACACATACGTATGCAATGACGCCCA ACTTTTTCGAGAAGCTGCATAACTCCCAGAAACTTCTGTCTCCGGGCGTC CAATTATGTGGCGCAGTGTATTGCTGGCTGGTGGCCAAAAGTGCCAGAAA GCGTTATGCTAATGCACATCACGTATACGCCGCATGCACCGCAACGAGCA GTGACATAATGTGCTGCAACGGGAAAAGCCACTGCAAATGGCAATAGGTG TGGACAGGAAAGGGCGGAAAAAGGGTGGCGGACAGACATCTAAGGACACG AAGCAGCAGGACATTGTGAAAAATAGCCCGGTACACTTAGCGTTTTGTCG GGCGTCTTATTTTTCAGACGGGTAAAAAAAAAAAACAACAACAAAAAACA CGTCTATATGAACCCAAGGACTCGACTAAGTGAATACGTGACATTGCGGC ACAGACAATTTTTCAGTTTTTCAGTTTTTCTTGTAACTTAATTTTTCAAC TTGCAATTAGAAACAATTTTGAGCAATTAACTAAGAAAGCTAAAATCGTT TGCTCCACAATTGGTAATGCATTTGACTAGCTTACGTTCAACTAAGCGTA TACTTAATATTTCTCACTTTTAGTTTTACTGCATCCAGATCTTAGATCCT TTAGCTTACTACAATAATAATTAAAATTTTAGACTAAAATCATGTATACA ACATTAAAAAGATAAGTTAATCAAAGCTGGCAAATAATTAAAAGAAACTT TTTAAAATTTGCCTATTTTAATTAGCCTTCAACAGACTTAAATTGCTTTA GTTTATGACTTTTCTAACTTTCTATATATCTTTTTCGTTTCCCCCCCGCC AACCTCCTCTATGCCATCTGTATACTATCAACATAATATACTATATATCT TTGCATATACTTCTATAATCTTGTGCATTTTTATTTCAAAACAAACAACC TAACAATAACCAAACTAAAAATAATCAATTACCGAATTAACTATACCGTG CACGTGGTGTATAACATTTTGGGCTGCCACCTTCAACTTCCGACTTATCT CACAAATGCAATTTGAAAATCAACTCTGAAATAACAAAACAATTACCGCA AATCAAAACTCTTGCCATCTGCTGTATATACAAAAATTTGCATACAACAA TCTGCAACCAATTGCACTGCCAACAATAAAAACAAACCAAAATATTTCGT AAAACAATACACAAACTATTTGCATTACTGCAAACAAAACCGATACAAAT GAAATGAAATAAATAACATAAAAAACGTATATATACATATATATATATAT ATATTTAAACCACACACTGAAGGAGGGCATTGACGTAAGTATTTTTCACC CCATCATCAAACATTCAAACAACCAAAAAATAAAAGAAAAGCCCAACAAA AAATATTAACTCATGTGCGTAAAATAGTGATTACAATAACACTGGTGGCC CATTTAAACTCTTAATAAAAGTGTATCATTTTGAGCTTTGGATAACACTT GTTTAAACAATCATTTTTTGTTTTGACGAGTACGTAACAATTTAATTTTA TTAAAATAAAACAACCAATACCTACTGTTTTAAAATTTCCTGAAAAATTC ATGTACATAAAAAAATGCATGCTCTATTTTGTGAGAATTAAAATATTCTT TTTGCTGTGTGAATGATATACATAAATCTTTCAATTCAATTTATAAGCAT AGTGTATATATTCAAATAAACTTAACAAAGTGAAAATAATGGAGTCAAAT AGTGACAAAGAGTGTTATGTACATATTTATGAGGTTTTTTAAGACACCTA AGAGATACTTTCAAACGTATGCAATGAATTTTTAAATTTTTAAATGCATT TTGCTAGTTTTGCGTCCAAGTTTTTAGACAATTCTTCAAATTTATTCCTT TTGTTGCAGTAACTAATGAAAGCTTACACCTCTATTAACGATGAACAACT AAACTTGCTGCCAGTAAAAGTTAGAGTCATTTGCAATTTGCCGTTTTTAG GGTCCTAGCCGAAAGCCACAAGCCAACTCGAAACAAGAAAATGATATCTA CGAGCTACTAATTAGACTTTTGATGGCATTGGTCCACCCCATTTGCCACT TAACACATCCCGGCTACCCAGTACGTGAACAGCTTTGGCCCTAACGATGT GAGGTCCACGCAAATTACACGTTGATGTGGAATTCCTCCTCCTCCTCCTC CATGGGAACCTTTTGCATAATTTAGTCATTCAGTTCGGTGGCTGCAGAGG CTGGCGAGCTGGGGGAATGGATATATTTTGTGGAAGTGCCATATGGATAA TGTCAGCCGCAGGCTGACACGCTCTCTGCCACCGGCTTTTCAAAGTGTTG AAGTGTAAAATAATTACTTCATTTCATCAATGTGTTGGCATGGGGGCCAC ATCACATAACATCACATCTCACGTTCAAGGCGAACATCGACTTGAGTCTG GGCAATTTGACAAAGAGCCAGGCGACGAAAGTGAAAGTAAAAACCCAGCA AAATGCGATATATACGTTTTGCGTTCGTGTGAAATTCAATTTCAGCAGCT TTGCTACCGCCAAGTGGAAATAGGATCGCAATTTATAATGCCGTGCTAAG CACATTTTTTTTTAAAGCTTAAGCGGAAAAGGGTAACCAGTTAATGGGTT TCTAATCCCGGTAAGAAATAACAGTGCGCCCGCTGCGTTTTCTTGGCGCC AGTAAAACAAATGTTATCAGACTTTACCAAGGATAAAGAAAACAAAACCT TAAGTTTCACCTCGCAGCTTTTCAATTTTTCGCACCGTAAGTTCACTGGT AAAAATATTTCGCGAAATTTTAAAATAAAATCATAGTACATTATATTAAA CGATTCATCCCTGATGCATATTTTAGGCAACATTTTACGAGATTTAAATG TTTTCTCTTGTATAATTAAGCAACTTACTATCGGCTCATTTTTTAAAATT TAAATTGAAATTTCACTATGTTGCCATATTTTTTTCATACGTGTAGTGAA CTTGAGGCGCCACCTTGGCCACATTGCATAACCCCCAAAATTCCAAACTG CATGAGTATATGTGGGGGGTAAATTCATGTATGTGAAAGGAGGTTTATAT ATGGGGGCAAAGTAATTCGTGCAATTTGCCGGGCGCAAATGGAATCGATA AATTTCGTGTTCCCTCGTGGAAAACACATCCGGAAAAATCCCGAATGAGC GCAGTGAATGGTAATGACAAATCTGCTCTACCTGGGCAATAATTCATATT AATTAGCGAGTGTCAACGGCAGAGAACACATATATTAAACGGCAGTATGT TTTATTTAGGATAATTAGGCTTTTACGTTAAGCTTAATGAATGAGTGTGG AATTTGGTATACAAGTTTTTTATACATACGTAGCATGTTTATTAATCTCT TAGGATTTTCCTAAGACAAATTTGTCCCATTTCCCATTGCATTTCTAAGA GCATGTTTTCATTATAATTAGCTGTATCTTGCATGAGCTCATACCTTTAT ACTTAACTAATCAAAACCAAAATCGCACCAACCAATACAACTTGACCCGT AGTTTAGGCCTATGATATTAAAGGGTAACCCATTTGGAAAATTTCAAGAT AGTCTAAGCAAATCTTAAAAAAAACTGTTTTGCTACACACATTTGTTTAT GGATTTAGCATACTTCGTAATTAAATTTAGTTTATTCCTTTTGTACGTTA TCCAAACACTTTTATTTATGTAGGAAAAAGTATGCTAAATCTTATTTATA AATACTATTTTATGTGGAACATGCATATAAACAAAACTTGTTGGATAATA TTATATTGAGGATTGCAATTTATATCCACAGGGCGCCACAAAGTTGACCA AAGAGGATATTGAAAAAGTATTCTCACTCTACGATCGTGTAAGTAAAGCA AAAGACTAAGGAATATATATAAAGATGTAAAATCTAATATGATATCATTA CAGGACAATAGCGGCACCATTGAAAATGAGGAGCTCAAAGGCTTCTTGAA GGACCTTTTGGAGTTGGTCAAGAAGGTGAGTGTCGCTCTTAAAGACAAAT GAAATAAAATGTTAATATTGTGTGGTTGCCAGGACGACTATGATGCCCAG GATCTGGCCGCTTTCGAGGAGACCATCATGCGGGGAGTTGGCACCGACAA GCATGGAAAGATCTCCCGGAAAGAACTGACCATGATTCTGCTAACACTGG CCAAAATATCGCCCGACGACGAGGAGTAAGCCGGATGTTCGAGAACATAC CAAAAAGAGATTTTAGCCAACTCTATTTTTGTCACCCGAACGCGGGAAAT CCAGAAATGAGGCCAAAATGGGCTTCAAGGCAATTGTTTACTTTAGAGCT GCATTAAAAGGGGCAGCAAATAAACAAAAAAATAAAAGGATATTGGAATC GGGGATGAATCCTGAGAGATTCAAACCGAAACGAAGCTATTGGTATAAAA TAAATCTAATATAAATGTTCAAATCTTAAATAAATGTTTATCGTACGTTA AGATATTGAGAGTATATATTTCCCCCAAAATCAAACCAAAACGGAAATTT ATCCAGTCAAACAATTTGCAACACAGAATCGAGCCACTTAAAGTAAAAAA TTAAGAAATGATAACAACAAGATCAGTACATCGATTTTATATTATACTAT ATATGTATTTATATTTTCTATGTGTATTTGCATAACGTACTTTATTTAAT TACCAATTAAAATCGAAATAAATGTAGCTATTTTTAAGGATACCACATTT ATTTGAGACTACCTAAGTAAAAACATATGTGTGGCTACAATCTGTAGATA ATTGTTGTTAATCATTGTGACAGTACACCCTAAAAGTGGGCGGCTGCATT CCGCGCCCAACTCCCCGCACTTGTGCTATGAATATCCCCCGCAAGCATCA ATCAATCAATCAAGAGGCACTTACATCAGCCCGAGGGTGGACGCCACTAA TGCAGGTGAATGCAAATGCAAATGCAAATGCATCCGCCACCTGAACGTGA CAATGTCAAGCTGGAGGGTGGTGATGCATCCAGTTAATGTTGGACACGCA CTCGTCCTTGTATTTTTTTCACCCGAGGGGAGATTACGAGGTGCAGATTG ACGCCGTTTTAAGGCTAAAATTTTCACCCAATTTCGCAACATAGGCAAAT TGGTTATTTAACCTCTAAACAAAAACCTAAAGTTAACCAACAACGCTACG AACTATCTAATGTTCTTTCAAGGTGCTATAGCTATATATATACATTATGA CTTGTTTCGATACGTATTCCCTTCTCCATCTGTTATCATTGTATTCTTTC GAAACCTAACTAACTAAATAACTAACAACTAATAACTTAAGCTTTAAAAC CAAGACAAATTGTTCCAATCCTGAAACGCTCTTTGCCCAAAGATTCACTT TTAGAGCCATAGTCATGAAATAGATCAATTCCATCGCCTTTAAAAATGAA ACCCTGAGTAAAGATGCCATGCAACAAAATGCCAACTTATCATATAAATA TACTAATTACGATACAACACTATATGATAACATACTTATGCTAATCCTAA GATATTGTTCAAAACCACATGCATGTAAAGCTTCGAAACGGACTTTCTCT ATATGAAACAAGATACCAAATATCGAATATCTAAATGGATATATGTCTAA CACTATGGAAATACAGCAGAAATGTTTTAATAAAATAAATACAATACAAT CTATGCAGACATCAAGGGGTCAGCACTCCAAAAGTAGTCTTTTGATTTCC TTATTTTTTTTTCTATACACACAGGCGTTTGTATTTCCGATTGAGTTTCT CCTGGAGCTCTAGAAGATCATTCAGTTTCTTCAGCATATCAGTGGCATCA AGCACTTTCTCGGTTAACACGGCTAAGGGGGAAGAACAATCCTTAAATGT TTTCTCCTGTTCCACTTCCGAGTCAACGAGACAGTTGACAATGTCCATCG TTTTCTTGATTCGCGAACAGAAGCTATGGTGGAACTTTATAGGTAACCAC TAATAACATTAGATACAAGGTAGTTACCACTTGGCATCCGTCATTCGATT ACTGAGAATAAGCTGCCAGGCCATGCAGCTCTGCAAGTGCCAGGAACAAT AGCAAATGCCCAGAGTCTCCGTGATGGGATCCTTCCATTCCTTGATGACC GCACACTGAGCTGGAGGAAACCGCACCTTCTCCACCAGCCAAGTGTGCCA GATAATCGTCTTCCTGTTCTTAAATTCCGCGTTCATTTGCTCGGAGTCCA GACGCTTGCTTCCGAAATGTCGCTCCAGAAACGAGGTTGCCTCCTTTTGA GAATCATGGGGATTCGGTTTACTAATCGGCCCCACTTCCATCATGCCATT TTGAAAGTTCAGCCACGAGGGATTCGCGCAGAAGGATCGTGTTGTAGCAT CTGCATAAGTAAGAAAAGTTTCGCTAATGGATTTTATTTGGAGAGCACTG AATTCGGAAATTAATAATGTAAATGTAATGAATCGAAACTTCTTAAATCT CGCACTTTAATATATTCTGTATTAACTTCTGCATACTTTAGAACTTCCTC AAAGATTTAATTTTACATAAAAGAAAAAAGGAGAAGGACCCTATAAGAGC TTGAGAAATTCCCTTGAAGGATCCTTCAACCCAGTTTCCTCCTTCGGAAT TTGCAAAACTCACCCACTGCCGACGCTGACCACCAATTTGGAGATAGTTT CACAGCGGGGCGTAGCAATTTGTTTTCGAGTCATGGTAACACGGTCAATT TTACAGGATATCTCGAAAAACGTACAAAATCAAACGAATGTATAGGTCGG CGACTACTGAGATTAATAGGTTCCGGCATTCATGGCCTTCACATCCAGTT TCTGCTGATAGGCCAGTCTCTGAAGAATCGTGGGATGAGTGTGATGCCAT CGAGCATAGCATTGGTCGTAGACCGGAAAACTCATATGATCCGCATAGAT CTTAACCAGCGCCATCCTCAGTTGGATGGAGTATCCCATGCGATGGGCAA ATTTATCGGCGGCATACTCAAAGCGACGCAGATTCCACAGCATCAAGACA TTGGCCAACGTGAGATAAGGAGTAAGGGCAAATTTCAGAACAATGATGAA ACCCACTATGATGGGCATAACGCCAGGCTCGAAACCCACTGCCATGTATA GCTGGGGAGAGTGAAAGAACAATCCGAAGAGTCCCATGGTGATAAAGAAG TGAATCTTCATGATGATCGTAGCCTTGTAGAAATGTCCGTGCTTCCAGTG ACCCAACTCATGGCACACCACTCCCGCCACCTGGATGTTGGTCAGACCTC TGCCCACCTCATAGGGATGGATCTCATTGGGTTCCTTGCCCTTGTTCAAT AGCAAGGTATCAAAAATTACAATTCTTTTCAGGCAGCAGCTCCCGTAAAA GTAGGCATTACTATACTGCATTGTCCGGGTCTTTATGATAAATACCCTCT TCATGGGGAAGCCAACCACATCGCAAACACGCTTCACCTCCATATAGAGG GCAGTGCCCTCTGGTAAAACCACCTGTCGTCCAATGCACGGAATGCAGCA GTAGGGCAAAAAAAATACCAGCAACAGGGTGAACGTAGCCCAGAACAGCC AGAACCAAAGGAAGAAGTAGTACCCAATGAACTTTACGCTGAACACAATG GCCGCCGCCAACGGGAACAGGACGAGCTGGCTTAGGAGAATGGACATTGC TCCAATGCAGCAGTAGAGGTACCAAGGAAACTTGCCCGACATCCCATATC GCAACTCCAGCAGGCACTTGTCATAGATCAGAACCGGCAGGAACCTTATA CAAATGTAAATGGTCAGGTAGAAAACAAAGATCAAGGTTATCCAGATCTC TTGGGAGGTTATTTTCTGTAGAGTCTTCGCAGACAAGCTCCAGAGGAATG GATAGAAGCCCAATATCAGCTCACAGAGCGTAATAATCAAGTCGATGAGG TACTTCCATATCTGTAGCTCCGTTTTATGCAGCTCGTAGATGCGGGCCCG ATGGTAAATCTCCGGCGGAATGATTCCTCTCAGCTCCTCCGGCACCATAA TCGCATTCAGGCACACCAATTGCTGGTGAAAGAAATCCGCGATCAGTTCT TCATGGGTGGAACAACCAATCCACTACTTACCTGCCTCTTGGTGAGTATC ATCTCCCATATCCGGTCAACTAACACGATCAGACATAACACCACCAGCAC TATGATTGGATCTACTTTCGGCCAAGTATCGTAGAATGCCATCAAAACTT ATCATGTTCCCCCAACAAACAATGTTTACTTATTGTAAAATATTGTATAT ATCTATATTACCCAAGACGGATAACTCAATCAGAAGCTACTATGTTTGAG AAACACCGATAAAAAATATATCGCCTATCGTCGAAATTCTTCCAGACGAC TCAACCGATCCAGCATGGTGGGATGCGTATGATTCCAGCTGGAGTAGCAA GGATCCGAAACGGGGAATGCCAGATTATCCGCATATAGTTTGAGCAGTGC TTGTCGAAGTTCTCCTCCATATCCGAGCTGGTAGGCAAACCTATCCGCCT GGTACTCAAAGCAACGCGTCATGCTAAGCATACTGAAGTTCGCCAGTGTC ATGTATGGAGTCAGTACAAAGCCGAAGATTATTAAGCATCCAATGACTGT CGGCTGGAGACCGGGAGGGAATCCCACCGCCTGGTAAATGGGCCCATGAG AAAACAGAAACGCGAACAGCAGGATCGTCAGTATGAGATGGACTTGGAAC GCCATGATAGCTTTGTAAAAATGTCCATTCCTCCAGTGACCCAGTTCGTG GGCCACCACAGCAACCACCTGAGGATCCGCAAGTCCCCTACCCAGCTCCT CTGCCGTCAGGTGGGAGAGATCTGACTTGCCTCTATTGAGCAGCAATGTA TCGAAGATCACAATTCTTTTCAGGCAGCAGCATCCGTAGAAAAAGGCATT ACTTCCCGTGTTAGGGTCATGCACCCGGATGATGCGCACCTGACTCATGG GAAAGCCGACTTGTCGCGTAAGGTACTCCAGTTGGGTGCGCAAGTTTGAG TTTTCCAGGGGTACACTTTGGCCCACAAATGGATGGATCATAAATGGAAT CAAGAGGAGTACGATCATTGTCAGGATCAGCGATTGAAGGTACAAGCCCA GGGGAGCATATGGCCCCAAGCCGATAAACATGTACACGAGGGCGACCACC ACCAAGGTGGTAATCATCGCTCCCACAACCAGGTCAACGACAAAGTGACA GATGCGGGACCACCACGGTGGTTTTGGCCTGGGTTGCAAGCTCTTGATGC AACAGCTCTCGTAGATCATGGCCGGTACGCTTTTAAGCCAAAAATACACG CTCAGGAGAAGCACAAAGATCACGGATACGCAAGCCTCATGCTCCATCCA CTTGGACAAGGCGCACTTTCCAGCCACTCCATACAGCCAGGCATAGAAGC CGAAGTATAGTTCCATAATACCCAATATAACTGCCGAAAGCAGGGTGTTG ACAATGGTGAACCAGCCCTTGTGAATCTTGTAGACGCGCATCTTGTCGTA GAGCTCCTGTGGTAGATAGGGGCTGATAACATTCGGTACTTGTTGCGTTT TGTAGGCCACTTGTATCTGAAAGAGCAATTTAATCCAAAATGTACTCGAA AGATGTAATCATCACTTACGTCCCGCAGCATCAGATATACGCCCCATAGA TTGTCCAGAACCAAGAAAGCTATGATTATGTAGAGTATTGCTAGTGGATC ATCCCAGAAATGTGCAGACATGTTGGGTTCCTCTGACAACGGCTTGACAT GTTAGTCATATTTCCTTAATTTTGAAGCTCCGTTAGGAAATCATTTTGAA TCTATTGGTGACGGATTTTTAACTACTAGCTTACATGTTTTGGGAATCAC ATAAGATACACGTTTCCACATTGCAAAATCTTAAATAGCTTGTTGGGGTA AGTCCCCTTACTTTATTTTGTGTACGTTAAATCAAAGGGAATAGTGTAAA CTTTGGTCTTATGTGAAGTGAGCTGTCTTAGTTCAGTTTCTTCTCTTCCT TGAGCTCCTTGAGTCGATTCAGGCGCTGGAGAAGAGTCGGATGTGAGTGG TTCCAAGTCGAGTACAGCCAATCGTAAACGGGGAAGCCAAGGTTGTCAAC GTTCAGTTTTATGAGGGCCTGACCCAACTGCTCAGCGAATCCCAACTTGA AAGCGAACTCATCAGCCTGATACTCGAATCGTCGCGACAAAATTGTCATG GCGAAGTTCATGAGGGCATTGTATGGCGCGAGTACGTAGGTAAAGACGAT TAGCAAACCGACGAGAATGGGCCGAGTACCAGGTTGGAATCCCATGGCCA CGTAGAATGGTGGATACTTGAAGACATTTCCAAAGACCAGGAACATCAGA AAGAGATGAACCTGCATGATAATAATGTTCTTGGTAACGTGTCCCAGTTT CCAGTGTCCCAGCTCGTGTCCCAAAACAGCCAGCACCTCCTCGTCGGTGC AACCCTTTCCCTTTTCTTCCTCTGACAACTCGGAGTCGTCCGGTTTACCT TTGTTTAGCAGCAGCGTGTCGAATAGCACGATCCTCTTCGAGTTCCAGAG GCCATAGAAGTAGGCATTGCTGTGCGAGGAGCGCTTGGATCCCTCCACCA CGAAAAGCTTAGTGAGCGGGAACTTGAGCGATGCGGCCAGATCCTCAATC GATTGCCTCAGAGCACCCTTCTCCAGCGGAGTATACTTGTCGAACAGGGG AGCAATGAAAATCGGATACAAAGTGAGTAGAACCAGCGAGATAACGCCTG TGAAGATCCACAGCCATATGAAAAAGTTGTCGCCGCCGCGTTGCACGATG AAGATAATAGCCGCTGTGATGGGAATCATGAGGACCTGGGTGACTAGGAA GCCTTTGAGCTGATCCCAGGCGAAGAATCTCGCTGTTTGTTTGTTAAAGC CATGCGTCTCCTCCAGCACGAATATCTTGTAGATCTTGAAGGGCAGTCCC TTGAAAGTGCTCAATACATTCGATATGAGCACAAAAACGCAGCTGACGAT GATCTCGTTTTTGGAGTCCCATTGCAGTTTATCCACCACCTGGACGGACA GCTGCCAGAGCACAGCGATCAGTCCGATGTACAGCTCCATGCAAAGCAGG GCCACATCCATAACAACAGCTTTGAAGATGCCGAATTTCTCCTGGTCCAG ACCATATTTCCGCGCCTTATGGAACGTATCCTCGCCCATGTGTGACTTCA GTTCGGCCGGTACCTTCAGTGCAGTTTGGTACACTTTCACCTGGTGGCGA CGGCAGGGTAAATCATTTAATGGGGGCAAGACATGAGGCGGCCAATTAAC ATTTGCCACTCTAAATTTATCATTCGCATTGATAAAATTCCTCGCCAAAT GTCGCCTGGCTAGAACATGCCGGCACAACGGAAAAACTTACCTGGCGCAG CGATATATAGATCTCTAGCGCATTCTCGATGACTACGAGGAACAAAATGC TCAGCAGCACGGTGTCTGCGTCCAATGATGACATATTTAAATGCTATTTC ATTAAAGAACTAATAAAACTGGAATTTTACTTTACAAGCGCCAGTGACGA ATTGTTAGTGTGACCGTCATGCGGCCGTTTAAATATATCACAGCAATAGC AATTCGAACGATCTGGCAGCGCTGACTGCAACAGA 2R Drosophila melanogaster 2R 12482942 12516876 CG9002 gene CG9002 FlyBase FBgn0034174 GB_protein AAO41366.1 FlyBase FBtr0087066 Gadfly CG9002 FlyBase FBtr0087065 FlyBase FBpp0086209 Gadfly CG33142 FlyBase FBtr0087064 FlyBase FBtr0087063 FlyBase FBtr0087062 FlyBase FBtr0087061 FlyBase FBgn0050462 FlyBase FBgn0063335 FlyBase FBgn0053142 FlyBase FBan0033142 GB_protein AAO41365.1 GB_protein AAO41364.1 GB_protein AAF57924.2 FlyBase FBpp0086214 FlyBase FBpp0086213 FlyBase FBpp0086212 FlyBase FBpp0086211 FlyBase FBpp0086210 GB_protein AAO41367.1 GB_protein AAO41363.1 gene_with_dicistronic_processed_transcript ; SO:0000722 null Mon Mar 14 16:37:28 GMT 2005 Flag Cambridge: NEW dicistronic gene; reinstate CG9002 (now == CG30462) as component gene(internal view only) null Tue Nov 05 17:41:24 GMT 2002 A single cDNA (DGC:AT28654) supports this dicistronic gene model null Wed Oct 23 17:30:08 GMT 2002 CG9002-RA transcript crosby Mon Mar 14 08:00:00 GMT 2005 Dicistronic transcript. null Wed Oct 23 17:33:24 GMT 2002 status not done sp_comment Imperfect match to HYPO SP, but either annotation or SP entry doesn't have an FBgn start_codon 30492 30490 exon 30516 30382 exon 30322 28914 exon 28650 28278 exon 28223 27915 CG9002-RB transcript crosby Mon Mar 14 08:00:00 GMT 2005 Monocistronic transcript. null Tue Nov 05 17:23:39 GMT 2002 status not done sp_comment Imperfect match to HYPO SP, but either annotation or SP entry doesn't have an FBgn start_codon 30492 30490 exon 30516 30382 exon 30322 29063 CG30461 gene gbunit AE003805 sp_status Not in SwissProt real (computational) cyto_range 53E4-53E4 CG30461 Gadfly CG30461 GB_protein AAO41366.1 FlyBase FBtr0087066 FlyBase FBtr0087065 FlyBase FBpp0086209 Gadfly CG33142 FlyBase FBtr0087064 FlyBase FBtr0087063 FlyBase FBtr0087062 FlyBase FBtr0087061 FlyBase FBgn0063335 FlyBase FBgn0050461 FlyBase FBgn0053142 FlyBase FBan0033142 GB_protein AAO41365.1 GB_protein AAO41364.1 GB_protein AAF57924.2 FlyBase FBpp0086214 FlyBase FBpp0086213 FlyBase FBpp0086212 FlyBase FBpp0086211 FlyBase FBpp0086210 GB_protein AAO41367.1 GB_protein AAO41363.1 EST evidence derived from AT and BE cDNA libraries: donor splice site for exon 1 of transcripts RB, RC and RD and exon 2 for transcripts RE and RF has been set to match consensus GT donor site in sequence, however, EST data does not perfectly align, suggesting possible strain polymorphisms. null Wed Oct 23 17:41:05 GMT 2002 gene_with_dicistronic_processed_transcript ; SO:0000722 null Mon Mar 14 16:38:21 GMT 2005 A single cDNA (DGC:AT28654) supports this dicistronic gene model null Wed Oct 23 17:30:08 GMT 2002 CG30461-RB transcript crosby Tue Nov 05 08:00:00 GMT 2002 Monocistronic transcript. null Tue Nov 05 17:21:51 GMT 2002 Only one EST supports this alternative transcript null Wed Oct 23 17:28:51 GMT 2002 status not done sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn start_codon 28984 28982 exon 29054 28918 exon 28584 28278 exon 28223 27911 CG30461-RC transcript crosby Tue Nov 05 08:00:00 GMT 2002 Monocistronic transcript. null Tue Nov 05 17:22:42 GMT 2002 status not done sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn start_codon 28984 28982 exon 29054 28918 exon 28650 28278 exon 28223 27911 CG30461-RD transcript crosby Tue Nov 05 08:00:00 GMT 2002 Only one EST supports this alternative transcript null Wed Oct 23 17:28:08 GMT 2002 Monocistronic transcript. null Tue Nov 05 17:23:07 GMT 2002 status not done sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn start_codon 28984 28982 exon 29050 28914 exon 28673 28278 exon 28223 27911 CG30461-RE transcript crosby Tue Nov 05 08:00:00 GMT 2002 Only one cDNA supports this alternative transcript. null Mon Mar 14 16:42:39 GMT 2005 Dicistronic transcript. null Wed Oct 23 17:32:09 GMT 2002 status not done sp_comment Hits nothing in SP, and no SP entry corresponds to this FBgn start_codon 28984 28982 exon 30516 30382 exon 30322 28918 exon 28650 28278 exon 28223 27915 chado-1.23/doc/examples/dicistronic-gene-example.png000644 000765 000024 00000121326 11256707742 022562 0ustar00cainstaff000000 000000 ‰PNG  IHDRÌœkqPPLTEÿÿÿÿÿÿÿˆÿˆÿˆˆÿÿÿ}MútRNSv“Í8 IDATxœì ’´:ήïZ*âhGï j§‹Z@FÀþ—p3yeÙ–H¿§»’þxR²l<ü¿eèôÿZg`¨†æÐÀü˜?B7Å<·ÎÀÍt+ÌÓ©ßk³u¦n¡Û`^‰~cZüµÎ]ïºfâC?ƒ4­`1¤Ãê3‹ñAz€ö¨sÌhB]cžã o [gºKuŒyž~£)¯‘wëŒw¨~1§AV ‡ç¶Õ-ætʃ³«^1Ǘʺ~gSbΣ<8Ûês.åÁÙR—˜çŒrùЈ·uu‰Y€ò÷÷0gM=bÎwÙ«†ÛÖÔ!f —½j¸íKb¢<ܶ¦`&J~œc?ÛõÊc`>Õæùà4m ~=eõtBÕ{Ös~ZÿSúQ˜w¶+ÝI³O&fíà0çK·Àüó¶íÕ?O¿¿Óûëféj篲ûŸíÛ¤’¼¿ý Ì–:Ŭ|µ‚÷«h*žŠý4?Íš÷oëÇî´Õ‘ÙPw˜÷êÔÏ´™éô«Pª¾^敽†yeŠcUªCÝaÞ­yRÖ{8í ¥òÖÛn ³ ¿‡5êóòÛDyŽ ÓiO›5ÌV¯˜wÇ|aÞb,ͨW¿®â²-[‘o…ù¾s`ÖÔæÙSúÞ#± öŸÇ¨7kê3ÑØÉëÎ{6 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Ìx8«av¢£ê“ÌxaÃ/Œâ,.÷Ó-š_£L`FÙøè‚«ÛP¾5æ{4²'™ÀŒ»1Á'12IDAT6ùy3Cwi~²Y¸¦oTÕ|'ÊF0‹—èŽðl,ÉKÉf4œ¹ov¢ºOók”ÌhlñßÓ†u/ÊÕ`–|uèf”Í`Žj„±ƒùn”Í`ŽêS5ʘÌ`ƇH„ß7Ÿu?Êv0ãá,ž­à R® sÄÜ#[Ý‘²!Ì„fùLB?Ý’²!Ì”a©ˆyÁÝ“²%Ì”F1³üº)eK˜I£Ì1svÞ—ru˜‡˜xoKÙfÆc~Ñ|Ú÷¥l ³ò³ÁS¶…Yõ­;S¶…Y3œoMÙfµp~ß›òM0?œÒ‰k‘-ÌJ®}óPÌaÖç»ö(c˜ÂùV/ê†d sòp¾}µ<é☛aϲ†9­k7Ã^dsÊpn†½Êæt½ŸG3ì¯ìaNdÛ òV1§¨P[Ók/ƒ˜ã«çw«”²ˆ9Ö¶ä“LbŽ²íæ×™ÄcÛ-”}²‰YÞ«j¡ì•QÌÂê¹v@V1‹ªçfØ!YÅ,¨žÛ€HXf1skÙ’]Ì,Î 2,ØéœdL–19·æ5.Ó˜)œÛø5E¶1ãœd’ŒcF0¶J™(ë˜!SnÉ29úÝ 3TfèG«“Yªó»+ØǨ¢™©P•`õ~4ÂRU„¹I®†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùj˜o¡†ùú?‡o¨ÐÅúïIEND®B`‚chado-1.23/doc/examples/dmel_NPFR1.chado000644 000765 000024 00000060617 11256707742 020031 0ustar00cainstaff000000 000000 sequence feature_property relationship synonym_type cvterm_property_type OBO_REL SO internal internal cvterm_property_type cvterm_property_type comment exon sequence mRNA sequence gene sequence contig sequence polypeptide sequence part_of relationship derives_from relationship NPFR1 FBgn0037408 sequence__gene 0 relationship__part_of NPFR1-RA FBtr0078590 sequence__mRNA AACAGATGGTCGCTGACTGTGCACGCGTGTGGTTATCGGAGATCAGTAAACAGCCCAACTAAACACCGAAACTTACTGTAATAAAAAAAAACGGGAAATAAGCGAAATAATCAAAATGCGGCCGCATACTTATTTATAATTTTGAGGCGGCCGAGCACCGGGGCCCCAAACTCTTTGGATCTGCACGGAATCCAGAATTCCGAGAGAGCAAAAACACAAAGCGAAGTCCCGTGAGTGCATTCCAAGTTGAAAACTAAGTGAGCAACTGCTGCTTTGGCAGCCGGAAAAACAGAGATTCACTCGTGTCACTCGCAGAAGGAAAAACAAGAACCGACGGCCAGGAAAACAATACGGTACCACGCACTATAGTAAATATATAGCATACATATCCCCAGGGCGAAGGAGATTGCCAGGACGATGATAATCAGCATGAATCAGACGGAGCCCGCCCAGCTGGCAGATGGGGAGCATCTGAGTGGATACGCCAGCAGCAGCAACAGCGTGCGCTATCTGGACGACCGGCATCCGCTGGACTACCTTGACCTGGGCACGGTGCACGCCCTCAACACCACTGCCATCAACACCTCGGATCTGAATGAGACTGGGAGCAGGCCGCTGGACCCGGTGCTTATCGATAGGTTCCTGAGCAACAGGGCGGTGGACAGCCCCTGGTACCACATGCTCATCAGCATGTACGGCGTGCTAATCGTCTTCGGCGCCCTAGGCAACACCCTGGTTGTTATAGCCGTCATCCGGAAGCCCATCATGCGCACTGCTCGCAATCTGTTCATCCTCAACCTGGCCATATCGGACCTACTTTTATGCCTAGTCACCATGCCGCTGACCTTGATGGAGATCCTGTCCAAGTACTGGCCCTACGGCTCCTGCTCCATCCTGTGCAAAACGATTGCCATGCTGCAGGCACTTTGTATTTTCGTGTCGACAATATCCATAACGGCCATTGCCTTCGACAGATATCAGGTGATCGTGTACCCCACGCGGGACAGCCTGCAGTTCGTGGGCGCGGTGACGATCCTGGCGGGGATCTGGGCACTGGCACTGCTGCTGGCCTCGCCGCTGTTCGTCTACAAGGAGCTGATCAACACAGACACGCCGGCACTCCTGCAGCAGATCGGCCTGCAGGACACGATCCCGTACTGCATTGAGGACTGGCCAAGTCGCAACGGGCGCTTCTACTACTCGATCTTCTCGCTGTGCGTACAATACCTGGTGCCCATCCTGATCGTCTCGGTGGCATACTTCGGGATCTACAACAAGCTGAAGAGCCGCATCACCGTGGTGGCTGTGCAGGCGTCCTCCGCTCAGCGGAAGGTGGAGCGGGGGCGGCGGATGAAGCGCACCAACTGCCTACTGATCAGCATCGCCATCATCTTTGGCGTTTCTTGGCTGCCGCTGAACTTTTTCAACCTGTACGCGGACATGGAGCGCTCGCCGGTCACTCAGAGCATGCTAGTCCGCTACGCCATCTGCCACATGATCGGCATGAGCTCCGCCTGCTCCAACCCGTTGCTCTACGGCTGGCTCAACGACAACTTCCGTAAAGAATTTCAAGAACTGCTCTGCCGTTGCTCAGACACTAATGTTGCTCTTAACGGTCACACGACAGGCTGCAACGTCCAGGCGGCGGCGCGCAGGCGTCGCAAGTTGGGCGCCGAACTCTCCAAAGGCGAACTCAAGCTGCTGGGGCCAGGCGGCGCCCAGAGCGGTACCGCCGGCGGGGAAGGCGGTCTGGCGGCCACCGACTTCATGACCGGCCACCACGAGGGCGGACTGCGCAGCGCCATAACCGAGTCGGTGGCCCTCACGGACCACAACCCCGTGCCCTCGGAGGTCACCAAGCTGATGCCGCGGTAAAGCACAGGGTAGTCCTAAGGTCCTTGAGGTCTGGTCTCGTGTCTAAGTCCTCATGATACACGCGTGCATGTCCTTTTGTACGCCCTCGGGCTGATTGGATTTGCATGCTCCAAACGTCGCTGCTGCTCGCTTTACGTTTCACTTGTTCCAACTGCAACTGCCACCTCTCTAGAACACTGAGCGAAATGCCGTGTCCTCTAATCGGGAAACACTCTGGCTGTAAAATCTATAAGCAGCCGAGTCAAACGTTTCTAGCGTTCTAAAAGTTTCTTATGATTATTTTATTTTATATATTAATAACAATGACTTCGTTCCCAATTATATGCTTGTTTTCATCGTTTTTGAATGTAACAATTGATCAATATTCGACCAAAAGCAAGTTTTGAAATATTTGTGTAAATATCGTTTTCAAATTTGTTCGCCTTAATCTTACTTAATAATAATAATAATAATAATCTTTACTCCGATAATCATTAACGTAACATTTCTACTTGTAAAAATATTTCTGATCTAAGGGGCTTGCTCTTTTCGGCTCCACCTTGAATTACTTTTCAGTTGACTAACTAGGCGTATATTTTTGTCAGTGTATGCATGCGCTCCTCTTATCGTTGCCTTGTCGAGCTGTAACTCTTGTTGTTGCCATGTTGTGACATTATTTGCTTTTGAGCTGCAATCGATTATGACCCGTCTTTTGTGACACATTTTCAGTTTGGAACAGTACTAAATTGGCAATCAATCCTGGAGCAGCAGGCGGCTGGAGCAGCATTCTAGGGAGGCGACTGCCTGTCACCCATAGACTTAACACGTATTGTCCAGTGATCCAAAGCCAAGCTGAGTTAGCCCTAAGTTAAGACACACGCGACTAAGAGCTCGAAGCCTGTAAACTATTCTTAAACGACCATGTCATGGCATCCATCATCAACTCGGACTAAGTCTATGGTTAGATCACTTTCGTATCAAATGCCGAAAAGTAATTGAATGAGCCCCCAATTAGATTTCGGGTATTTGATAAGTCGAATACGCCTAAGACTCGAATAAGTTCTCTCAACAGTTCCTAGGAAATATTTTCGTTTTATCTCAGCATTTCTTGGTATCATCTAAGCTAAGGATTAGCTATAATTGATGTTCTGTTCGCTATTCAATAATGATAGGATAGGTCGAAGTCCACTAAGCCAAAGTGAATTTAAAGTATAGTATAGTATAAAGTATAATTGTAAAAGATAACTTTAAAATAAATGTCAGCTGCTCTTAAACATTTAATGCAA 0 relationship__part_of auto:exon5 sequence__exon 0 3R-frag sequence__contig 1 7817 9976 0 0 relationship__part_of auto:exon4 sequence__exon 0 3R-frag sequence__contig 1 7037 7207 0 0 relationship__part_of auto:exon3 sequence__exon 0 3R-frag sequence__contig 1 6584 6975 0 0 relationship__part_of auto:exon2 sequence__exon 0 3R-frag sequence__contig 1 3548 3762 0 0 relationship__part_of auto:exon1 sequence__exon 0 3R-frag sequence__contig 1 1961 2167 0 0 relationship__derives_from NPFR1-PA NPFR1-PA sequence__polypeptide MIISMNQTEPAQLADGEHLSGYASSSNSVRYLDDRHPLDYLDLGTVHALNTTAINTSDLNETGSRPLDPVLIDRFLSNRAVDSPWYHMLISMYGVLIVFGALGNTLVVIAVIRKPIMRTARNLFILNLAISDLLLCLVTMPLTLMEILSKYWPYGSCSILCKTIAMLQALCIFVSTISITAIAFDRYQVIVYPTRDSLQFVGAVTILAGIWALALLLASPLFVYKELINTDTPALLQQIGLQDTIPYCIEDWPSRNGRFYYSIFSLCVQYLVPILIVSVAYFGIYNKLKSRITVVAVQASSAQRKVERGRRMKRTNCLLISIAIIFGVSWLPLNFFNLYADMERSPVTQSMLVRYAICHMIGMSSACSNPLLYGWLNDNFRKEFQELLCRCSDTNVALNGHTTGCNVQAAARRRRKLGAELSKGELKLLGPGGAQSGTAGGEGGLAATDFMTGHHEGGLRSAITESVALTDHNPVPSEVTKLMPR 0 3R-frag sequence__contig 1 3759 8708 0 0 3R-frag 3R-frag sequence__contig TCATTGCTAACGTATTTCAACCCATAATGGTATATCAAGGCAGCGAGGACTGCGACTTCATAAATTTCTATCGGGAAACCGCAGAAGCCATCAAGTCTCAGGACGCGATGTATGAAAACGGGGAAATTCAGAGAAGAATTGACACAATATTACCAATTCTTGATGCCAAGGGATTTTTGGAGGCCCATTGAAATAACATATATTAAATAATCCGTTTATCAGCTATGAATAATAATAATTTTGAGCTTTAACCAAAAATGACAAGCCTTTTTCAGAGGACACGTTATGCAAATTGCTAAATTCGGATTATATTTAAGCACGGATACACACAATTAAGCCTGAGGATTGTGTATTTGCAAAACAGTAAAATGTTAGAAACGATAATGACTAGACAGACCTCAAACAGTTACCTAGGGGAATGACTTGACATGGTAGAATGTGACATTTCACGATGACCTCGTATTATAGTGAAATCACTCTGAGATCTGAGATAGCACAACAAAAGCCATTGAGACATCTACACAATAATAATAATAATAGTATTATTATTAATGATCTCACAACCGTGAGCAACCGAGCTAAGTCGCCAAAAGATCGAGGAACCGCACCACGTATGGAAATCACCTGGATAAGACTTATTATTAATGCAGGAAAGGCCAGCTATTGAAATCTGGACCAAGCCGTCGATCGGGAAAACTATTAATTCGTGAGCTGATACAAATTTTGACTATCAGCGCTGGAACGTTACAGAAGAGACCTTGAAGCAGGCCCTTCCCGAAGACGTTCCTATGGCGGAGGCTATCTTTGGGAATAGCCATACGTGCGGAAAATGGACAGATCGATCTGGTAAGTAGATCTGTCTTCCGTAGAAGGAACTGCTAGTGGAAGCCGGGCTGGGCGGAAAGCAAGTTGAATATGCCATGGACCAAGATCCAGAAGCTCCATAATTCTGGAGGATCTTGTGCCGTATAAGTTCATCAATGCAATGCAGTAGCTGGACTTGGTTTACATCAAGCTCACTCCGAAAATGCCAGCAATGTGCCATGCTGCCTCCATAATCCTGTGAGGCGGATATAAGAGGTTCATTGATGAACAACCGAACATAAATAAGCCAATGACAACAAATTGGGGAAGTACCCACATAGTAAATGTGGAGTGGGGGGGACCAGTTATGGCCACTTTCAGTTCAGCACCTTCGCGTTGATAAGAAACTCGAAGTTTGCTCTAAAAGTGAACTCTAACAAGTTACAAAGGAGCTAAAAAGACCAAAACCTCTGAAGTCTTCACTAAAAGACTCCTGAAGTTTTCGCAATCAGGTTTCGGTTTATGCCAGTGAACTTGTTAAAGATGATTTTTTTAATTTTGCAGTGTTAAATCCAGATACTAATATAAATATTTATAACTAGATCAATTCTAAAAAGACATTTTGGATGTTTGGTGCAGTATGTTTCTATTGCGGTGTTCATTAATTTTCATGTCCGCATTTAGAGTACGATCCCCGAGATGGCTTGTTTTGCAAATAAGTTTTTGTAGAGCACTGCAAAGATAAGCTATCAGCAGGCACCACATTATTTTAAAATATCATAATATCTCTTTCGTCATTTTGGTATCACTTTTAGCGAGGTATGATAAAATGTCATCATAGGCTATACTGTTAAGATAGAACTTTATTTTGTATGACTCAAATTTCCAGGCACACGCAATTTTTTAACATCCCCTCGACCAATGTGCGAAGCTTTTCCACCCCTAGTTTCGGTGATAAGAAAGCTCTGCACAGCTGACGGCCCAAAATCCAAAACAAACTCGAAGCGCGGGCCCACGGCCTGTTGACCAAGTGCGATGCCTTCAGTCGCAACTTTTGTGCCACGCGGCGTATACGCAACGCGCCCCGGCAAACAGCAAATCAGGCGGATATATCGGCGGGACTAGGGTATATAAGCAGGAGATGCGCACCAAAAGCCAACAGATGGTCGCTGACTGTGCACGCGTGTGGTTATCGGAGATCAGTAAACAGCCCAACTAAACACCGAAACTTACTGTAATAAAAAAAAACGGGAAATAAGCGAAATAATCAAAATGCGGCCGCATACTTATTTATAATTTTGAGGCGGCCGAGCACCGGGGCCCCAAACTCTTTGGATCTGCACGGAATCCAGAATTCCGAGAGGTATGCCATCGACGCAGTGTTTTGTGTTTGTTTTCCCACAATGTGCCGTCATTAAAAAGCTGAAGTGTGAGGATTTCGCACGGAGCCTCGACATTTACGACCATTTTTCCCTGATGCGAAGTGGTCCGCGGAAATTCGCTAATTGTCCGCCGGACGCTCCGCAGTTGTCGGTATTTATTATGATTATTTTTTCCGAACGCGCTCCAATGAATCTGGACTGCAAGTTGTGAATATTTCGAAAAAAAAAAATATTATTCCGCGCGAGTCTTTCGGGATAACAAATCTTTCGAGTCCGTAATGCCAAGTGAAGTGCGTGGGCAAAAATTATTTTTTAAGAAAAATGCAGGACAGTTGGTGTCCTCGTTCGATGGAAAATTAATGAATGTGTATTTTGCGTAATGAGATGTAAATGCCTGCTACACTTCAACAAAAAATACAACCAAAATGTCATTTACTTAATGGGATTATTAATGGACTCTGAATTAAGAAGCGGATTTCTCGGCACATGTCGAAAAAAGTTCGAATATTTCAGCAATAATGATTATAATGACATGAAGAATTAACCATCTAGAGCCAAACAAATTGTGTATTTTTTTTTTTTTTTTTTTTTTTTTAAATAATTAAGACAGAGCACTTATTTCTTTACTTCTTCGAGCTCTGATTAAATAAATATACTTTATTAGGTCCGATTACAACATATGTTTCTCGGTGTTCAGTAATTTATGCCTATCGATTGGAAACGAAATTAATAAATTGGAATAAAAAGCCCATTTCGTCGGACAAAATTTACATAAAAATTCTTCATTGGGTCTATTGATAACATTTTATTGAGAGACGTTTAAATTCTATAAATGAAATTTTATGCAGTGAAACTTCACTTAAAATAAACATGTATTTAAAAAATGTTATCCTTAATGTGATTTTCAAGCTAGGGCTATAGAGCTTAGGAAATGTATACAGTATATATTCATCTAGCATGAAGTGTTTTGTTAATGTTAAATGATGTTTTTATGACATGAAGTCAATTTAAAGTTTAAGGTTTTACCGCCCAACTGAGCATGACTTGAACGTCCTCAAAGTGCGCCAGAATCTGGAAAATGTTCCAAAAGTTATGCATACCAATGGATGCGAAGCTGGAACCCCCATGGTACTTAAAAAGTGCAACTATCTTGTGCAAACTTTTAGCTTCAGGCCCGTGTGCCTGCTGCCTAAAGGATTAAGCTGTGTCAGAAACTCTGCGCAATTTTATGAATTTTTGGTGCACTTTAATTAAGTCGATTATGCTGGCAACCAGATTGTCCAGATTAAATGCTATGTGCATCGGACCCCTTGAACGAAAGCATCCATTAGCTGAATTGTTATCATTTCTTTTAATTTCAAGAGCAAAAACACAAAGCGAAGTCCCGTGAGTGCATTCCAAGTTGAAAACTAAGTGAGCAACTGCTGCTTTGGCAGCCGGAAAAACAGAGATTCACTCGTGTCACTCGCAGAAGGAAAAACAAGAACCGACGGCCAGGAAAACAATACGGTACCACGCACTATAGTAAATATATAGCATACATATCCCCAGGGCGAAGGAGATTGCCAGGACGATGGTGAGTGTAATTGCAATATAAATACTTAAAGCCAGCTCAAGAAGCCATTTCGAAGTAGATGTCAAATGGAACGAAATTACTTTGTTCCCAAAATGAAAAAGTTTGTTTGAGTTGCTTTGGGGGAATGGGTTGTGCTCTACGTTGGCCATATGGTTGTGTGAGCTCCCACTTCGTTGGCATTTGCAGAGTGCCTCGCCAGATGGAGAACCATACAAATTTCAAAATAATGCTCCCTCCTGGCGGCCAATTTAAAAACTCGGGTAAGGCTTAAAAGTCATGGAGAGCTATATCAATTTACCTGGTTACACATTCGCTTGACATTTTCGTGGTCGGGACTTTTACTAGGGGCTTTTATTTTTATCCCAACACCCTGTGGCTTTCCTTTGACACCAAAGAAGTGTTAAGCGGCACACAGAACATGATTAAATTGCAAGGGACTTAGACAAATGGCTAGAATTTGCGTTCAGCCTTTAGGCAGCTTAGCCTATTAGTTCCCTAGAAACCCAGTTTGGCTCTGTGCCAGATGCCTCCGCTTAAGCATAGCTCTTTCCCTACAAGTGAATGATTTGGAGTTGACCAGCCGCACAGATGAGGCCAATTCAAGCTGCATCCCACCTCCATCTTGTTGAAACTAAATCGACTTCAATTAATAAGGAAAACGTCCATCCGCAAACAAAACACACAAGCAGCAATAAAATTCATCTTATAGTGGGCGAAACAAGAGACCCACCGCAAATAAATCACAAAAATAGCTGACTAGAAGTGCCAGCAGCTTGGAATCCGCACGAGCTTCCCGGAAAACGGATGACATTTAAAATCTTTGTCATGCTTTACTTATCCAGTGAAGCAAAAATACTTCAGGCACTCGGAATGCAAAAATTATTCCAATTTTGTGACAACTGCCGATTACTTGAGGCTGCTTTACATAATTTTCCCCACACAAACTTCCTTTCTGCTTCCAAACTGAGAAGGCAGCTGCGCAGGGATTTCCCCTTTTGCTTTGGGGAACAGAACATGTAAATTCAATTTTCACCTTGCAAGTCAATCTATCGAAGGCGTTGTTGTTTTGGGCTGTGATTGGAACTTTTGCGACCAATTGGTGATCAACTTCGAACAGTGTTTTATGCTCCGTTTTCCTTGGCTGAAAATTTCCATTAGGTCCTTGCCCGAAGCGGAAGGAGAATCCCACTTTGCAGACTGGCCAGTTTGCGGTCGACAGACTTTTTCATTTCGGACTCCCATGTTTGAGTTGAAGTGCAAATATTAGTCAATTAGGAGCCGGCCAACATGAAATTAAATTTCCATGGAAACTTGCTCTTCGCCTCGATACCCAATGCCCGACACCCGATGCCCCGAAATCCCCACACCCTATCCGGTATCTGGCGAGCTAATTCCCCGATTGGCGAGATTTATTAGCGCCTCATTTATCGCAGCTGTCAGGGGCACATAATGCATACCTTTGGGCGCCACTATAAGTCTGTTTCGCCCACCTTCGAGTGAGGCATCGGATTTTATCGATACTGACAAGTGCGCAGCTCAGATGGCGCATAAAATTACACAATTATTTTTAGCAAATGTCGTCATTTATAACCTGCCTGTTTCTGTTTCTGTTTGTGTATCTGTATCTGGATATGGGTCTGACGGCTGTCCCTCGACACCGGAATATCTTGATCTGGCAACAAATACCAGGCATCAAAATCAAACGCACATTTCCCCGGAGGAAACGGCACTTTTGACTTTTTCCAATTAAATGCATGTCTCGCCTTGATGTGCTGCATAAATTACGGCGACGGGTAATGCATGAATATTTACGAGGGAAAACAACCGACTAACTGAAGCTCGGCACTGGGATATTGCATAAATTGACTACAAATGGGAAGATATTTTTCGAAAAAAGGGACTTTCGAAACTTGAAAACAAAGCGAATTACTTTTCCTTGCCAAAGTTATCCTGTAGCAGATAATTTCAGAGTCGAGTTGATTCGAGTCCCAGGAGTCAAGGCCATTGTCTGTGTTCAGAAGGGTATTAACAGGCGAATGCCAAGGGCGTTTGAAGTTTTATCAAGCCTCGAGATCTGAATTCAATTATTAAAATGGCTCACTGGGAAATGGATTTAGCAAGAAGATGAGGCGATAAGCACTATGATTTTACATTGACATAGATAGTTCTCTAATCGCATTTTAGCTTTTAGACTTTTGTCAAGTGTCCAACAACAAACTTAACTTAAAATGTATACAACCATTGTATCTATCCGTTTGTCTATTTACCAATTTTTATTTAAAGTTTTGAAAGATTTTCTTGAATCTTTTGAACAGAAAACCACTTTAATCTAATAGCAATACATTTGATGCAATTGCATCCTTAACAATGTAATTTAATAGGACTTAAATGGTATAATAATTATGATTTAGTTAATACCCCAAAAGCTTTTAAAATAATGAACGTATGACGTAAGGTTACACTGGCGTAAGGTTACACTGTTTTTCTCCCAGTGTCTGCAAATAAGTGAGAGAGTGAGGCGTCAGAACTTTCATGCATGTCGTATGCCCATAGAATCCTTTGGTGCTGGGCCACCTACTGGCACCAAACAAACTTTTTATACGATTATTGCCCCGTATTTCAAGCCACAAAGCATTAAGCAAGCCAGTGGAATTTGCCATTCGCAGCTCGCTAGAAAGTGTGGTGTGTGCAGCAAGCCAATCTCATAAATCATACGTGATGTGGCACGCAAAGTTGCTGCTTCCTTGCCCCCTGACAATTGAATATTTCGTGCCGCGGATTTGGGAAATAATGAGACCCTGTTTGCCTCCTTCGTTCCCTAGATAATCAGCATGAATCAGACGGAGCCCGCCCAGCTGGCAGATGGGGAGCATCTGAGTGGATACGCCAGCAGCAGCAACAGCGTGCGCTATCTGGACGACCGGCATCCGCTGGACTACCTTGACCTGGGCACGGTGCACGCCCTCAACACCACTGCCATCAACACCTCGGATCTGAATGAGACTGGGAGCAGGCCGCTGGACCCGGTGCTTATCGATAGGTTCCTGAGCAACAGGGCGGTGGACAGCCCCTGGTACCACATGCTCATCAGCATGTACGGCGTGCTAATCGTCTTCGGCGCCCTAGGCAACACCCTGGTTGTTATAGCCGTCATCCGGAAGCCCATCATGCGCACTGCTCGCAATCTGTTCATCCTCAACCTGGCCATATCGGGTGAGTTGCCATTCCCACTGAGAGCCAAAGCAAGTGTGAGTCTCATCCGAGCGGACTTTCAGACCTACTTTTATGCCTAGTCACCATGCCGCTGACCTTGATGGAGATCCTGTCCAAGTACTGGCCCTACGGCTCCTGCTCCATCCTGTGCAAAACGATTGCCATGCTGCAGGCACTTTGTATTTTCGTGTCGACAATATCCATAACGGCCATTGCCTTCGACAGATATCAGGTTAGTCGCTACTCGAGCCTTTTTTAATGCCAACGTTAGTATGTAAATGGGGCCATCAATGGGGCAAATCGTGTTCGGATATTAATGAGGTGAATACCTTCAATGTGTAACCATTAAATTTGACGTTGAGGGAAAATCGATGGGCTCTCAGTAAATATTTGGCGATTACATAAGGGCTTAACCCACGATTAAACCTATTTTTATGGTGTCGAAACAAAGACCATTAAAAAGGGTTGATGGATTATAAACAGAAGGATTATTAGGTATTGATTATAAATAGCCGGACTGTTCTGGGGTAAAGTAGAGAAGTAGGACGCATATAAATTAATCCGATTTTTTTAATCAATTTAAGGCGAGTGGCCAGTTGACTTAAAGAAAGACTTATAAGTTAGCTTTAATATAATGTTTTTGGTGATTAAAGAATAGTAATTGCACGGTTAGAGAAACCAAACCTAATTGTACGTCACACTCTTATAGCAATCGATTAAAAATTATATTTGCTTATAAATTCCCAGTTGAAGATGTATTTTCACTAAGTATAATTTACAGTGCGAATGGGTAATAAGACTCCAAGCCCTGAGATATAACAACCGTCTAACCTCACTTCCAGGTGATCGTGTACCCCACGCGGGACAGCCTGCAGTTCGTGGGCGCGGTGACGATCCTGGCGGGGATCTGGGCACTGGCACTGCTGCTGGCCTCGCCGCTGTTCGTCTACAAGGAGCTGATCAACACAGACACGCCGGCACTCCTGCAGCAGATCGGCCTGCAGGACACGATCCCGTACTGCATTGAGGACTGGCCAAGTCGCAACGGGCGCTTCTACTACTCGATCTTCTCGCTGTGCGTACAATACCTGGTGCCCATCCTGATCGTCTCGGTGGCATACTTCGGGATCTACAACAAGCTGAAGAGCCGCATCACCGTGGTGGCTGTGCAGGCGTCCTCCGCTCAGCGGAAGGTGGAGCGGGGGCGGCGGATGAAGCGCACCAACTGCCTACTGATCAGCATCGCCATCATCTTTGGCGTTTCTTGGCTGCCGCTGAACTTTTTCAACCTGTACGCGGACATGGAGCGCTCGCCGGTCACTCAGAGCATGCTAGTCCGCTACGCCATCTGCCACATGATCGGCATGAGCTCCGCCTGCTCCAACCCGTTGCTCTACGGCTGGCTCAACGACAACTTCCGTAAAGAATTTCAAGAACTGCTCTGCCGTTGCTCAGACACTAATGTTGCTCTTAACGGTCACACGACAGGCTGCAACGTCCAGGCGGCGGCGCGCAGGCGTCGCAAGTTGGGCGCCGAACTCTCCAAAGGCGAACTCAAGCTGCTGGGGCCAGGCGGCGCCCAGAGCGGTACCGCCGGCGGGGAAGGCGGTCTGGCGGCCACCGACTTCATGACCGGCCACCACGAGGGCGGACTGCGCAGCGCCATAACCGAGTCGGTGGCCCTCACGGACCACAACCCCGTGCCCTCGGAGGTCACCAAGCTGATGCCGCGGTAAAGCACAGGGTAGTCCTAAGGTCCTTGAGGTCTGGTCTCGTGTCTAAGTCCTCATGATACACGCGTGCATGTCCTTTTGTACGCCCTCGGGCTGATTGGATTTGCATGCTCCAAACGTCGCTGCTGCTCGCTTTACGTTTCACTTGTTCCAACTGCAACTGCCACCTCTCTAGAACACTGAGCGAAATGCCGTGTCCTCTAATCGGGAAACACTCTGGCTGTAAAATCTATAAGCAGCCGAGTCAAACGTTTCTAGCGTTCTAAAAGTTTCTTATGATTATTTTATTTTATATATTAATAACAATGACTTCGTTCCCAATTATATGCTTGTTTTCATCGTTTTTGAATGTAACAATTGATCAATATTCGACCAAAAGCAAGTTTTGAAATATTTGTGTAAATATCGTTTTCAAATTTGTTCGCCTTAATCTTACTTAATAATAATAATAATAATAATCTTTACTCCGATAATCATTAACGTAACATTTCTACTTGTAAAAATATTTCTGATCTAAGGGGCTTGCTCTTTTCGGCTCCACCTTGAATTACTTTTCAGTTGACTAACTAGGCGTATATTTTTGTCAGTGTATGCATGCGCTCCTCTTATCGTTGCCTTGTCGAGCTGTAACTCTTGTTGTTGCCATGTTGTGACATTATTTGCTTTTGAGCTGCAATCGATTATGACCCGTCTTTTGTGACACATTTTCAGTTTGGAACAGTACTAAATTGGCAATCAATCCTGGAGCAGCAGGCGGCTGGAGCAGCATTCTAGGGAGGCGACTGCCTGTCACCCATAGACTTAACACGTATTGTCCAGTGATCCAAAGCCAAGCTGAGTTAGCCCTAAGTTAAGACACACGCGACTAAGAGCTCGAAGCCTGTAAACTATTCTTAAACGACCATGTCATGGCATCCATCATCAACTCGGACTAAGTCTATGGTTAGATCACTTTCGTATCAAATGCCGAAAAGTAATTGAATGAGCCCCCAATTAGATTTCGGGTATTTGATAAGTCGAATACGCCTAAGACTCGAATAAGTTCTCTCAACAGTTCCTAGGAAATATTTTCGTTTTATCTCAGCATTTCTTGGTATCATCTAAGCTAAGGATTAGCTATAATTGATGTTCTGTTCGCTATTCAATAATGATAGGATAGGTCGAAGTCCACTAAGCCAAAGTGAATTTAAAGTATAGTATAGTATAAAGTATAATTGTAAAAGATAACTTTAAAATAAATGTCAGCTGCTCTTAAACATTTAATGCAACTGTTTTAATGTCTGCAATGGGTGAAGATTGCAACACACCGAAATAAAAATCGTAATAAATGTTGCTGGAAAGCCTTCATTATAGAACGTTTTCACTGTAAATGCTCATGTTTGGATAAAGTGCCAATAAGAGAAGCCTCTTGTATTTCAATAAATGAGCAACTTTAAGAGCTTCCAAAGTCCGAAGCTTCAGAATGTTTATTTTTCTTACACAAATGAAGTGGCACTTTGGAATAAATATGTATCAAGAATTAAGCATGGTAAGTTATCTAAGAGTTCTGTATAGGTATAAAGTATGTAAGGTGTGTAAATTGAAATATATTTTTACTCTTTAAAGATATTTTAACACAATTGAAATGATTCTCGAGGAAGTGAGCCAAAAAAAAGATACACCGTATCTGGAAGCCTAACAACCACAGCAATAAACAGCAGCTGACCCGCCGAACACTTAACTTTTAAGACTTTTGTGGGTTCGACACTCAAGCAGCTGCAGCATAAAAACCTACGACCCATAAAAATAGCGCATGAGTATGTACGACACAGTTTGAGAACCAGACTACTTATACATTTAGGATATATACTTGTGAAACACTGCTTTGGAAGAGCTAAGAATCCAACTAGCATAACCATTGAAACTTAAATACGCATTACAATTAAGATAGTTTTATGTTCGCTATGATTAAGTCATTAGCAGATGTGGTAAGGCTCTCTGGATGAGCGACAGGTATGCTAAATTAGTGTATGATTAAATTTCAATTTGGGTAAAAGCTCCTTCGTGGTCGGTCACAATCTCCTCAAAGTCGCAGGTGGGTTCATAGTTCGGCGACGTGTGACACAAATGTGACCGGTGGCGAGTGAATTGTGGATCATAGCTGAAAAGAGAAATGTTCCCACCAGGCACCGACAGCGTGAAAATAAAGCAAAAAACAAAATAAACTAATTAAAAATTTCGTTGGGAATGAGTGATGCGACAGGTGAGGCCTCATCACCTCACCTGTTTCTGGCTGCTGTAAAACTGTCAACGGTTTGTTTTGACGGCTCGTAACGGCCTTTTGCACTCGAGCTCGTGAAAGTGTTTACCTTATTTTTTGTCACACTCAGCCGGCTCCACACCATCAACTCCCATTCCCAAACCCCCTGGTCAACACCATCATCGCCATCCTCTCTACGGAGCGCTGATTACGCAGACCCATCTCACTTTCTTCTCATGCAGATTGCGCAATGCTGACAAAAGCATTCTGGGTGTGTGCGAGTATCGCCAAGCATCTAGAGTTAACCAAACTTGCCGGCATCGACATTTTTCGAAGCCGGCGTGAGCATATTTATGAGTAAAAGTGGAATTAATGATTGGAATAAAATTCAAAGCAAAGGTTTGCAAATATTTGCGGCAGGCCGAGACCCCCTCCGCATACCAATCGATCGGATTCAGACTCATACTTGGATTGAGGGGAGATGTAACGTAATATATGGATGGGTTCAAGGCACCTAAGACTTTGCATCCCGCTGCCGTTGGACACATGTCAATCGAAAATGGTAGAGGATGCCTGGCTTTCTTTGACATCTTTGGCGGCTCTTTAATAGGTGCTAAATGAATTCGCAACGAACACTTTCACAGGGGATGACCAAAATGGGTGATACTCGCAGTCAATTGTTCAGCCTTTTCTCGGGCAAAGAAGTTGGCCCCGATTTGCGTTGGGCTTTTAGAAAACATTGCTCTGACCATTGTAACATTGAGAGTGCTTATTGATTTTGCGGTCTCATAAACTGGCTTTCATTTCGTTTTGGCTTTTGAGCTTCCCAGTGGTTCAGTGGTTCGTCGGCTTTGTGGTTTGATGGTTTGATGATAGGGAGCGGAGTGTTTCCGCTCGTTAGCCACAAGTCAATGGCAAAGTTTGTCACCAGAAATTAATATCAATGTGACGCTCAGTTGGCCAATTCTAAACGACGACTTTCCCATGCGTAAACCGGCCCACAAAACCCGTTCACAGATCAAACGGCGACAATTTATAAATAAGTGAAAATCTGCTTACAATGTACGCAGCAAAACTAGTTCAGCTTAAATATTTATAGAAATCGAAAATGCTCGGCAGATGTGCACAACTGCATTTTCCCCCTATGTTCGGAATCCCTAAGCCTCTAATCCCCATGACGACAACATGTGCATTTCAAAGATAACATATATTTCAGTAGATATCATTGGGTCTGCGAAAAGACCGCAGTATATATATAGCAAATAGAAAGATACAGCCTGGAAGGTTTACTTTTTCAAATCAGTCAAGCATGGTTTTTTCGATTCCTGAAACCCAAAAGCCCAATACAATATGACAGCCATTAGGGGTAACATTTAAGTTTGCCATCGAAACTGTTGCAAAGGACTCCTGGAACAAGAAACTCTGTATACAGCCGAAATATATTCGTATATCAGTATATGTATGTATATATATCCGTATATATTTATTTATCTTATTCAATCATTAGTTTGGATTATAATTTCCGTTTTTAAAATCTCTTTCAAAATAATTTATATTCAAAAAGAGCTAATGCTTCGCATTGATTTTAAATTTGAATGGATACTGTTTATCTTCATTTAAAGTTATTAAATTTCTTAGCCATTTGCAATATTAATTATTTTAATCGAGTGCAAATGGCGTGAGGACCTCAGTATATCAAAAGTTTAACCGCTTCTGGCGTGGAAAAACACAAGAAACAAATTGTAAGAAATTAAATAAAGTTTGCGGCAACTCTTGGCCAAGTTTTTCAACAGAGGTCAGCTTGCTTCCCTCGCAGGGCCAACAAAATCGAAAGTTCGACTAAGACGGCGACTGACTAACTAAGTGACCGCTTTCCGTTAGCATATGGTGACTATTATTCGCGCCATGACTTGACTTATTTTTATAGCTTTGTATTATTTATTTATATTCACATGCAAAATTGACATGCAGTTTCGCTGCGACGTTGTAGTTTGCAGTTTTAATTATTTTTTGGCCGCAGAGGAGCCGTTTTCATTAGCGACTAATTTTCCGTGTAGGAGAGAAAATGGATGATGGTCACTGATGAGGCACTGAGATTTCTTTTGAAACATAGAAAATTATGTTTTAGCGCACAATTAGGATTATTCTTAAACTTACACATCTTTATTTTCACACTCTTACTCTTACTAATTTGAACTTAAAATAAACCTTATATGAAATATAGATGACGAGCGGCAGCACTTTCCCATTTTTTTCCGTGTAGTGATCTACCACAGCAGCTGTTGAGTTCAGCACTTGGCCCGGCTCAAACCCTGGCCAAGAGACTCTCTTAGGCCGCTCTTCGCTACGTAAGAAGTGGGTTCGCTCACGTAGCGCTTCGTAAGGTAAAACTGGTTGATGGCACCCGCCGTTTGGCTTTCGCCCGGC 0 1 2011160 2024534 0 0 chado-1.23/doc/examples/dmel_NPFR1.chaos000644 000765 000024 00000047720 11256707742 020050 0ustar00cainstaff000000 000000 auto:exon5 exon 3R-frag 7817 9976 1 0 0 auto:exon4 exon 3R-frag 7037 7207 1 0 0 auto:exon3 exon 3R-frag 6584 6975 1 0 0 auto:exon2 exon 3R-frag 3548 3762 1 0 0 auto:exon1 exon 3R-frag 1961 2167 1 0 0 FBtr0078590 NPFR1-RA mRNA AACAGATGGTCGCTGACTGTGCACGCGTGTGGTTATCGGAGATCAGTAAACAGCCCAACTAAACACCGAAACTTACTGTAATAAAAAAAAACGGGAAATAAGCGAAATAATCAAAATGCGGCCGCATACTTATTTATAATTTTGAGGCGGCCGAGCACCGGGGCCCCAAACTCTTTGGATCTGCACGGAATCCAGAATTCCGAGAGAGCAAAAACACAAAGCGAAGTCCCGTGAGTGCATTCCAAGTTGAAAACTAAGTGAGCAACTGCTGCTTTGGCAGCCGGAAAAACAGAGATTCACTCGTGTCACTCGCAGAAGGAAAAACAAGAACCGACGGCCAGGAAAACAATACGGTACCACGCACTATAGTAAATATATAGCATACATATCCCCAGGGCGAAGGAGATTGCCAGGACGATGATAATCAGCATGAATCAGACGGAGCCCGCCCAGCTGGCAGATGGGGAGCATCTGAGTGGATACGCCAGCAGCAGCAACAGCGTGCGCTATCTGGACGACCGGCATCCGCTGGACTACCTTGACCTGGGCACGGTGCACGCCCTCAACACCACTGCCATCAACACCTCGGATCTGAATGAGACTGGGAGCAGGCCGCTGGACCCGGTGCTTATCGATAGGTTCCTGAGCAACAGGGCGGTGGACAGCCCCTGGTACCACATGCTCATCAGCATGTACGGCGTGCTAATCGTCTTCGGCGCCCTAGGCAACACCCTGGTTGTTATAGCCGTCATCCGGAAGCCCATCATGCGCACTGCTCGCAATCTGTTCATCCTCAACCTGGCCATATCGGACCTACTTTTATGCCTAGTCACCATGCCGCTGACCTTGATGGAGATCCTGTCCAAGTACTGGCCCTACGGCTCCTGCTCCATCCTGTGCAAAACGATTGCCATGCTGCAGGCACTTTGTATTTTCGTGTCGACAATATCCATAACGGCCATTGCCTTCGACAGATATCAGGTGATCGTGTACCCCACGCGGGACAGCCTGCAGTTCGTGGGCGCGGTGACGATCCTGGCGGGGATCTGGGCACTGGCACTGCTGCTGGCCTCGCCGCTGTTCGTCTACAAGGAGCTGATCAACACAGACACGCCGGCACTCCTGCAGCAGATCGGCCTGCAGGACACGATCCCGTACTGCATTGAGGACTGGCCAAGTCGCAACGGGCGCTTCTACTACTCGATCTTCTCGCTGTGCGTACAATACCTGGTGCCCATCCTGATCGTCTCGGTGGCATACTTCGGGATCTACAACAAGCTGAAGAGCCGCATCACCGTGGTGGCTGTGCAGGCGTCCTCCGCTCAGCGGAAGGTGGAGCGGGGGCGGCGGATGAAGCGCACCAACTGCCTACTGATCAGCATCGCCATCATCTTTGGCGTTTCTTGGCTGCCGCTGAACTTTTTCAACCTGTACGCGGACATGGAGCGCTCGCCGGTCACTCAGAGCATGCTAGTCCGCTACGCCATCTGCCACATGATCGGCATGAGCTCCGCCTGCTCCAACCCGTTGCTCTACGGCTGGCTCAACGACAACTTCCGTAAAGAATTTCAAGAACTGCTCTGCCGTTGCTCAGACACTAATGTTGCTCTTAACGGTCACACGACAGGCTGCAACGTCCAGGCGGCGGCGCGCAGGCGTCGCAAGTTGGGCGCCGAACTCTCCAAAGGCGAACTCAAGCTGCTGGGGCCAGGCGGCGCCCAGAGCGGTACCGCCGGCGGGGAAGGCGGTCTGGCGGCCACCGACTTCATGACCGGCCACCACGAGGGCGGACTGCGCAGCGCCATAACCGAGTCGGTGGCCCTCACGGACCACAACCCCGTGCCCTCGGAGGTCACCAAGCTGATGCCGCGGTAAAGCACAGGGTAGTCCTAAGGTCCTTGAGGTCTGGTCTCGTGTCTAAGTCCTCATGATACACGCGTGCATGTCCTTTTGTACGCCCTCGGGCTGATTGGATTTGCATGCTCCAAACGTCGCTGCTGCTCGCTTTACGTTTCACTTGTTCCAACTGCAACTGCCACCTCTCTAGAACACTGAGCGAAATGCCGTGTCCTCTAATCGGGAAACACTCTGGCTGTAAAATCTATAAGCAGCCGAGTCAAACGTTTCTAGCGTTCTAAAAGTTTCTTATGATTATTTTATTTTATATATTAATAACAATGACTTCGTTCCCAATTATATGCTTGTTTTCATCGTTTTTGAATGTAACAATTGATCAATATTCGACCAAAAGCAAGTTTTGAAATATTTGTGTAAATATCGTTTTCAAATTTGTTCGCCTTAATCTTACTTAATAATAATAATAATAATAATCTTTACTCCGATAATCATTAACGTAACATTTCTACTTGTAAAAATATTTCTGATCTAAGGGGCTTGCTCTTTTCGGCTCCACCTTGAATTACTTTTCAGTTGACTAACTAGGCGTATATTTTTGTCAGTGTATGCATGCGCTCCTCTTATCGTTGCCTTGTCGAGCTGTAACTCTTGTTGTTGCCATGTTGTGACATTATTTGCTTTTGAGCTGCAATCGATTATGACCCGTCTTTTGTGACACATTTTCAGTTTGGAACAGTACTAAATTGGCAATCAATCCTGGAGCAGCAGGCGGCTGGAGCAGCATTCTAGGGAGGCGACTGCCTGTCACCCATAGACTTAACACGTATTGTCCAGTGATCCAAAGCCAAGCTGAGTTAGCCCTAAGTTAAGACACACGCGACTAAGAGCTCGAAGCCTGTAAACTATTCTTAAACGACCATGTCATGGCATCCATCATCAACTCGGACTAAGTCTATGGTTAGATCACTTTCGTATCAAATGCCGAAAAGTAATTGAATGAGCCCCCAATTAGATTTCGGGTATTTGATAAGTCGAATACGCCTAAGACTCGAATAAGTTCTCTCAACAGTTCCTAGGAAATATTTTCGTTTTATCTCAGCATTTCTTGGTATCATCTAAGCTAAGGATTAGCTATAATTGATGTTCTGTTCGCTATTCAATAATGATAGGATAGGTCGAAGTCCACTAAGCCAAAGTGAATTTAAAGTATAGTATAGTATAAAGTATAATTGTAAAAGATAACTTTAAAATAAATGTCAGCTGCTCTTAAACATTTAATGCAA FBgn0037408 NPFR1 gene 3R-frag 3R-frag contig 3R 2011160 2024534 1 0 0 TCATTGCTAACGTATTTCAACCCATAATGGTATATCAAGGCAGCGAGGACTGCGACTTCATAAATTTCTATCGGGAAACCGCAGAAGCCATCAAGTCTCAGGACGCGATGTATGAAAACGGGGAAATTCAGAGAAGAATTGACACAATATTACCAATTCTTGATGCCAAGGGATTTTTGGAGGCCCATTGAAATAACATATATTAAATAATCCGTTTATCAGCTATGAATAATAATAATTTTGAGCTTTAACCAAAAATGACAAGCCTTTTTCAGAGGACACGTTATGCAAATTGCTAAATTCGGATTATATTTAAGCACGGATACACACAATTAAGCCTGAGGATTGTGTATTTGCAAAACAGTAAAATGTTAGAAACGATAATGACTAGACAGACCTCAAACAGTTACCTAGGGGAATGACTTGACATGGTAGAATGTGACATTTCACGATGACCTCGTATTATAGTGAAATCACTCTGAGATCTGAGATAGCACAACAAAAGCCATTGAGACATCTACACAATAATAATAATAATAGTATTATTATTAATGATCTCACAACCGTGAGCAACCGAGCTAAGTCGCCAAAAGATCGAGGAACCGCACCACGTATGGAAATCACCTGGATAAGACTTATTATTAATGCAGGAAAGGCCAGCTATTGAAATCTGGACCAAGCCGTCGATCGGGAAAACTATTAATTCGTGAGCTGATACAAATTTTGACTATCAGCGCTGGAACGTTACAGAAGAGACCTTGAAGCAGGCCCTTCCCGAAGACGTTCCTATGGCGGAGGCTATCTTTGGGAATAGCCATACGTGCGGAAAATGGACAGATCGATCTGGTAAGTAGATCTGTCTTCCGTAGAAGGAACTGCTAGTGGAAGCCGGGCTGGGCGGAAAGCAAGTTGAATATGCCATGGACCAAGATCCAGAAGCTCCATAATTCTGGAGGATCTTGTGCCGTATAAGTTCATCAATGCAATGCAGTAGCTGGACTTGGTTTACATCAAGCTCACTCCGAAAATGCCAGCAATGTGCCATGCTGCCTCCATAATCCTGTGAGGCGGATATAAGAGGTTCATTGATGAACAACCGAACATAAATAAGCCAATGACAACAAATTGGGGAAGTACCCACATAGTAAATGTGGAGTGGGGGGGACCAGTTATGGCCACTTTCAGTTCAGCACCTTCGCGTTGATAAGAAACTCGAAGTTTGCTCTAAAAGTGAACTCTAACAAGTTACAAAGGAGCTAAAAAGACCAAAACCTCTGAAGTCTTCACTAAAAGACTCCTGAAGTTTTCGCAATCAGGTTTCGGTTTATGCCAGTGAACTTGTTAAAGATGATTTTTTTAATTTTGCAGTGTTAAATCCAGATACTAATATAAATATTTATAACTAGATCAATTCTAAAAAGACATTTTGGATGTTTGGTGCAGTATGTTTCTATTGCGGTGTTCATTAATTTTCATGTCCGCATTTAGAGTACGATCCCCGAGATGGCTTGTTTTGCAAATAAGTTTTTGTAGAGCACTGCAAAGATAAGCTATCAGCAGGCACCACATTATTTTAAAATATCATAATATCTCTTTCGTCATTTTGGTATCACTTTTAGCGAGGTATGATAAAATGTCATCATAGGCTATACTGTTAAGATAGAACTTTATTTTGTATGACTCAAATTTCCAGGCACACGCAATTTTTTAACATCCCCTCGACCAATGTGCGAAGCTTTTCCACCCCTAGTTTCGGTGATAAGAAAGCTCTGCACAGCTGACGGCCCAAAATCCAAAACAAACTCGAAGCGCGGGCCCACGGCCTGTTGACCAAGTGCGATGCCTTCAGTCGCAACTTTTGTGCCACGCGGCGTATACGCAACGCGCCCCGGCAAACAGCAAATCAGGCGGATATATCGGCGGGACTAGGGTATATAAGCAGGAGATGCGCACCAAAAGCCAACAGATGGTCGCTGACTGTGCACGCGTGTGGTTATCGGAGATCAGTAAACAGCCCAACTAAACACCGAAACTTACTGTAATAAAAAAAAACGGGAAATAAGCGAAATAATCAAAATGCGGCCGCATACTTATTTATAATTTTGAGGCGGCCGAGCACCGGGGCCCCAAACTCTTTGGATCTGCACGGAATCCAGAATTCCGAGAGGTATGCCATCGACGCAGTGTTTTGTGTTTGTTTTCCCACAATGTGCCGTCATTAAAAAGCTGAAGTGTGAGGATTTCGCACGGAGCCTCGACATTTACGACCATTTTTCCCTGATGCGAAGTGGTCCGCGGAAATTCGCTAATTGTCCGCCGGACGCTCCGCAGTTGTCGGTATTTATTATGATTATTTTTTCCGAACGCGCTCCAATGAATCTGGACTGCAAGTTGTGAATATTTCGAAAAAAAAAAATATTATTCCGCGCGAGTCTTTCGGGATAACAAATCTTTCGAGTCCGTAATGCCAAGTGAAGTGCGTGGGCAAAAATTATTTTTTAAGAAAAATGCAGGACAGTTGGTGTCCTCGTTCGATGGAAAATTAATGAATGTGTATTTTGCGTAATGAGATGTAAATGCCTGCTACACTTCAACAAAAAATACAACCAAAATGTCATTTACTTAATGGGATTATTAATGGACTCTGAATTAAGAAGCGGATTTCTCGGCACATGTCGAAAAAAGTTCGAATATTTCAGCAATAATGATTATAATGACATGAAGAATTAACCATCTAGAGCCAAACAAATTGTGTATTTTTTTTTTTTTTTTTTTTTTTTTAAATAATTAAGACAGAGCACTTATTTCTTTACTTCTTCGAGCTCTGATTAAATAAATATACTTTATTAGGTCCGATTACAACATATGTTTCTCGGTGTTCAGTAATTTATGCCTATCGATTGGAAACGAAATTAATAAATTGGAATAAAAAGCCCATTTCGTCGGACAAAATTTACATAAAAATTCTTCATTGGGTCTATTGATAACATTTTATTGAGAGACGTTTAAATTCTATAAATGAAATTTTATGCAGTGAAACTTCACTTAAAATAAACATGTATTTAAAAAATGTTATCCTTAATGTGATTTTCAAGCTAGGGCTATAGAGCTTAGGAAATGTATACAGTATATATTCATCTAGCATGAAGTGTTTTGTTAATGTTAAATGATGTTTTTATGACATGAAGTCAATTTAAAGTTTAAGGTTTTACCGCCCAACTGAGCATGACTTGAACGTCCTCAAAGTGCGCCAGAATCTGGAAAATGTTCCAAAAGTTATGCATACCAATGGATGCGAAGCTGGAACCCCCATGGTACTTAAAAAGTGCAACTATCTTGTGCAAACTTTTAGCTTCAGGCCCGTGTGCCTGCTGCCTAAAGGATTAAGCTGTGTCAGAAACTCTGCGCAATTTTATGAATTTTTGGTGCACTTTAATTAAGTCGATTATGCTGGCAACCAGATTGTCCAGATTAAATGCTATGTGCATCGGACCCCTTGAACGAAAGCATCCATTAGCTGAATTGTTATCATTTCTTTTAATTTCAAGAGCAAAAACACAAAGCGAAGTCCCGTGAGTGCATTCCAAGTTGAAAACTAAGTGAGCAACTGCTGCTTTGGCAGCCGGAAAAACAGAGATTCACTCGTGTCACTCGCAGAAGGAAAAACAAGAACCGACGGCCAGGAAAACAATACGGTACCACGCACTATAGTAAATATATAGCATACATATCCCCAGGGCGAAGGAGATTGCCAGGACGATGGTGAGTGTAATTGCAATATAAATACTTAAAGCCAGCTCAAGAAGCCATTTCGAAGTAGATGTCAAATGGAACGAAATTACTTTGTTCCCAAAATGAAAAAGTTTGTTTGAGTTGCTTTGGGGGAATGGGTTGTGCTCTACGTTGGCCATATGGTTGTGTGAGCTCCCACTTCGTTGGCATTTGCAGAGTGCCTCGCCAGATGGAGAACCATACAAATTTCAAAATAATGCTCCCTCCTGGCGGCCAATTTAAAAACTCGGGTAAGGCTTAAAAGTCATGGAGAGCTATATCAATTTACCTGGTTACACATTCGCTTGACATTTTCGTGGTCGGGACTTTTACTAGGGGCTTTTATTTTTATCCCAACACCCTGTGGCTTTCCTTTGACACCAAAGAAGTGTTAAGCGGCACACAGAACATGATTAAATTGCAAGGGACTTAGACAAATGGCTAGAATTTGCGTTCAGCCTTTAGGCAGCTTAGCCTATTAGTTCCCTAGAAACCCAGTTTGGCTCTGTGCCAGATGCCTCCGCTTAAGCATAGCTCTTTCCCTACAAGTGAATGATTTGGAGTTGACCAGCCGCACAGATGAGGCCAATTCAAGCTGCATCCCACCTCCATCTTGTTGAAACTAAATCGACTTCAATTAATAAGGAAAACGTCCATCCGCAAACAAAACACACAAGCAGCAATAAAATTCATCTTATAGTGGGCGAAACAAGAGACCCACCGCAAATAAATCACAAAAATAGCTGACTAGAAGTGCCAGCAGCTTGGAATCCGCACGAGCTTCCCGGAAAACGGATGACATTTAAAATCTTTGTCATGCTTTACTTATCCAGTGAAGCAAAAATACTTCAGGCACTCGGAATGCAAAAATTATTCCAATTTTGTGACAACTGCCGATTACTTGAGGCTGCTTTACATAATTTTCCCCACACAAACTTCCTTTCTGCTTCCAAACTGAGAAGGCAGCTGCGCAGGGATTTCCCCTTTTGCTTTGGGGAACAGAACATGTAAATTCAATTTTCACCTTGCAAGTCAATCTATCGAAGGCGTTGTTGTTTTGGGCTGTGATTGGAACTTTTGCGACCAATTGGTGATCAACTTCGAACAGTGTTTTATGCTCCGTTTTCCTTGGCTGAAAATTTCCATTAGGTCCTTGCCCGAAGCGGAAGGAGAATCCCACTTTGCAGACTGGCCAGTTTGCGGTCGACAGACTTTTTCATTTCGGACTCCCATGTTTGAGTTGAAGTGCAAATATTAGTCAATTAGGAGCCGGCCAACATGAAATTAAATTTCCATGGAAACTTGCTCTTCGCCTCGATACCCAATGCCCGACACCCGATGCCCCGAAATCCCCACACCCTATCCGGTATCTGGCGAGCTAATTCCCCGATTGGCGAGATTTATTAGCGCCTCATTTATCGCAGCTGTCAGGGGCACATAATGCATACCTTTGGGCGCCACTATAAGTCTGTTTCGCCCACCTTCGAGTGAGGCATCGGATTTTATCGATACTGACAAGTGCGCAGCTCAGATGGCGCATAAAATTACACAATTATTTTTAGCAAATGTCGTCATTTATAACCTGCCTGTTTCTGTTTCTGTTTGTGTATCTGTATCTGGATATGGGTCTGACGGCTGTCCCTCGACACCGGAATATCTTGATCTGGCAACAAATACCAGGCATCAAAATCAAACGCACATTTCCCCGGAGGAAACGGCACTTTTGACTTTTTCCAATTAAATGCATGTCTCGCCTTGATGTGCTGCATAAATTACGGCGACGGGTAATGCATGAATATTTACGAGGGAAAACAACCGACTAACTGAAGCTCGGCACTGGGATATTGCATAAATTGACTACAAATGGGAAGATATTTTTCGAAAAAAGGGACTTTCGAAACTTGAAAACAAAGCGAATTACTTTTCCTTGCCAAAGTTATCCTGTAGCAGATAATTTCAGAGTCGAGTTGATTCGAGTCCCAGGAGTCAAGGCCATTGTCTGTGTTCAGAAGGGTATTAACAGGCGAATGCCAAGGGCGTTTGAAGTTTTATCAAGCCTCGAGATCTGAATTCAATTATTAAAATGGCTCACTGGGAAATGGATTTAGCAAGAAGATGAGGCGATAAGCACTATGATTTTACATTGACATAGATAGTTCTCTAATCGCATTTTAGCTTTTAGACTTTTGTCAAGTGTCCAACAACAAACTTAACTTAAAATGTATACAACCATTGTATCTATCCGTTTGTCTATTTACCAATTTTTATTTAAAGTTTTGAAAGATTTTCTTGAATCTTTTGAACAGAAAACCACTTTAATCTAATAGCAATACATTTGATGCAATTGCATCCTTAACAATGTAATTTAATAGGACTTAAATGGTATAATAATTATGATTTAGTTAATACCCCAAAAGCTTTTAAAATAATGAACGTATGACGTAAGGTTACACTGGCGTAAGGTTACACTGTTTTTCTCCCAGTGTCTGCAAATAAGTGAGAGAGTGAGGCGTCAGAACTTTCATGCATGTCGTATGCCCATAGAATCCTTTGGTGCTGGGCCACCTACTGGCACCAAACAAACTTTTTATACGATTATTGCCCCGTATTTCAAGCCACAAAGCATTAAGCAAGCCAGTGGAATTTGCCATTCGCAGCTCGCTAGAAAGTGTGGTGTGTGCAGCAAGCCAATCTCATAAATCATACGTGATGTGGCACGCAAAGTTGCTGCTTCCTTGCCCCCTGACAATTGAATATTTCGTGCCGCGGATTTGGGAAATAATGAGACCCTGTTTGCCTCCTTCGTTCCCTAGATAATCAGCATGAATCAGACGGAGCCCGCCCAGCTGGCAGATGGGGAGCATCTGAGTGGATACGCCAGCAGCAGCAACAGCGTGCGCTATCTGGACGACCGGCATCCGCTGGACTACCTTGACCTGGGCACGGTGCACGCCCTCAACACCACTGCCATCAACACCTCGGATCTGAATGAGACTGGGAGCAGGCCGCTGGACCCGGTGCTTATCGATAGGTTCCTGAGCAACAGGGCGGTGGACAGCCCCTGGTACCACATGCTCATCAGCATGTACGGCGTGCTAATCGTCTTCGGCGCCCTAGGCAACACCCTGGTTGTTATAGCCGTCATCCGGAAGCCCATCATGCGCACTGCTCGCAATCTGTTCATCCTCAACCTGGCCATATCGGGTGAGTTGCCATTCCCACTGAGAGCCAAAGCAAGTGTGAGTCTCATCCGAGCGGACTTTCAGACCTACTTTTATGCCTAGTCACCATGCCGCTGACCTTGATGGAGATCCTGTCCAAGTACTGGCCCTACGGCTCCTGCTCCATCCTGTGCAAAACGATTGCCATGCTGCAGGCACTTTGTATTTTCGTGTCGACAATATCCATAACGGCCATTGCCTTCGACAGATATCAGGTTAGTCGCTACTCGAGCCTTTTTTAATGCCAACGTTAGTATGTAAATGGGGCCATCAATGGGGCAAATCGTGTTCGGATATTAATGAGGTGAATACCTTCAATGTGTAACCATTAAATTTGACGTTGAGGGAAAATCGATGGGCTCTCAGTAAATATTTGGCGATTACATAAGGGCTTAACCCACGATTAAACCTATTTTTATGGTGTCGAAACAAAGACCATTAAAAAGGGTTGATGGATTATAAACAGAAGGATTATTAGGTATTGATTATAAATAGCCGGACTGTTCTGGGGTAAAGTAGAGAAGTAGGACGCATATAAATTAATCCGATTTTTTTAATCAATTTAAGGCGAGTGGCCAGTTGACTTAAAGAAAGACTTATAAGTTAGCTTTAATATAATGTTTTTGGTGATTAAAGAATAGTAATTGCACGGTTAGAGAAACCAAACCTAATTGTACGTCACACTCTTATAGCAATCGATTAAAAATTATATTTGCTTATAAATTCCCAGTTGAAGATGTATTTTCACTAAGTATAATTTACAGTGCGAATGGGTAATAAGACTCCAAGCCCTGAGATATAACAACCGTCTAACCTCACTTCCAGGTGATCGTGTACCCCACGCGGGACAGCCTGCAGTTCGTGGGCGCGGTGACGATCCTGGCGGGGATCTGGGCACTGGCACTGCTGCTGGCCTCGCCGCTGTTCGTCTACAAGGAGCTGATCAACACAGACACGCCGGCACTCCTGCAGCAGATCGGCCTGCAGGACACGATCCCGTACTGCATTGAGGACTGGCCAAGTCGCAACGGGCGCTTCTACTACTCGATCTTCTCGCTGTGCGTACAATACCTGGTGCCCATCCTGATCGTCTCGGTGGCATACTTCGGGATCTACAACAAGCTGAAGAGCCGCATCACCGTGGTGGCTGTGCAGGCGTCCTCCGCTCAGCGGAAGGTGGAGCGGGGGCGGCGGATGAAGCGCACCAACTGCCTACTGATCAGCATCGCCATCATCTTTGGCGTTTCTTGGCTGCCGCTGAACTTTTTCAACCTGTACGCGGACATGGAGCGCTCGCCGGTCACTCAGAGCATGCTAGTCCGCTACGCCATCTGCCACATGATCGGCATGAGCTCCGCCTGCTCCAACCCGTTGCTCTACGGCTGGCTCAACGACAACTTCCGTAAAGAATTTCAAGAACTGCTCTGCCGTTGCTCAGACACTAATGTTGCTCTTAACGGTCACACGACAGGCTGCAACGTCCAGGCGGCGGCGCGCAGGCGTCGCAAGTTGGGCGCCGAACTCTCCAAAGGCGAACTCAAGCTGCTGGGGCCAGGCGGCGCCCAGAGCGGTACCGCCGGCGGGGAAGGCGGTCTGGCGGCCACCGACTTCATGACCGGCCACCACGAGGGCGGACTGCGCAGCGCCATAACCGAGTCGGTGGCCCTCACGGACCACAACCCCGTGCCCTCGGAGGTCACCAAGCTGATGCCGCGGTAAAGCACAGGGTAGTCCTAAGGTCCTTGAGGTCTGGTCTCGTGTCTAAGTCCTCATGATACACGCGTGCATGTCCTTTTGTACGCCCTCGGGCTGATTGGATTTGCATGCTCCAAACGTCGCTGCTGCTCGCTTTACGTTTCACTTGTTCCAACTGCAACTGCCACCTCTCTAGAACACTGAGCGAAATGCCGTGTCCTCTAATCGGGAAACACTCTGGCTGTAAAATCTATAAGCAGCCGAGTCAAACGTTTCTAGCGTTCTAAAAGTTTCTTATGATTATTTTATTTTATATATTAATAACAATGACTTCGTTCCCAATTATATGCTTGTTTTCATCGTTTTTGAATGTAACAATTGATCAATATTCGACCAAAAGCAAGTTTTGAAATATTTGTGTAAATATCGTTTTCAAATTTGTTCGCCTTAATCTTACTTAATAATAATAATAATAATAATCTTTACTCCGATAATCATTAACGTAACATTTCTACTTGTAAAAATATTTCTGATCTAAGGGGCTTGCTCTTTTCGGCTCCACCTTGAATTACTTTTCAGTTGACTAACTAGGCGTATATTTTTGTCAGTGTATGCATGCGCTCCTCTTATCGTTGCCTTGTCGAGCTGTAACTCTTGTTGTTGCCATGTTGTGACATTATTTGCTTTTGAGCTGCAATCGATTATGACCCGTCTTTTGTGACACATTTTCAGTTTGGAACAGTACTAAATTGGCAATCAATCCTGGAGCAGCAGGCGGCTGGAGCAGCATTCTAGGGAGGCGACTGCCTGTCACCCATAGACTTAACACGTATTGTCCAGTGATCCAAAGCCAAGCTGAGTTAGCCCTAAGTTAAGACACACGCGACTAAGAGCTCGAAGCCTGTAAACTATTCTTAAACGACCATGTCATGGCATCCATCATCAACTCGGACTAAGTCTATGGTTAGATCACTTTCGTATCAAATGCCGAAAAGTAATTGAATGAGCCCCCAATTAGATTTCGGGTATTTGATAAGTCGAATACGCCTAAGACTCGAATAAGTTCTCTCAACAGTTCCTAGGAAATATTTTCGTTTTATCTCAGCATTTCTTGGTATCATCTAAGCTAAGGATTAGCTATAATTGATGTTCTGTTCGCTATTCAATAATGATAGGATAGGTCGAAGTCCACTAAGCCAAAGTGAATTTAAAGTATAGTATAGTATAAAGTATAATTGTAAAAGATAACTTTAAAATAAATGTCAGCTGCTCTTAAACATTTAATGCAACTGTTTTAATGTCTGCAATGGGTGAAGATTGCAACACACCGAAATAAAAATCGTAATAAATGTTGCTGGAAAGCCTTCATTATAGAACGTTTTCACTGTAAATGCTCATGTTTGGATAAAGTGCCAATAAGAGAAGCCTCTTGTATTTCAATAAATGAGCAACTTTAAGAGCTTCCAAAGTCCGAAGCTTCAGAATGTTTATTTTTCTTACACAAATGAAGTGGCACTTTGGAATAAATATGTATCAAGAATTAAGCATGGTAAGTTATCTAAGAGTTCTGTATAGGTATAAAGTATGTAAGGTGTGTAAATTGAAATATATTTTTACTCTTTAAAGATATTTTAACACAATTGAAATGATTCTCGAGGAAGTGAGCCAAAAAAAAGATACACCGTATCTGGAAGCCTAACAACCACAGCAATAAACAGCAGCTGACCCGCCGAACACTTAACTTTTAAGACTTTTGTGGGTTCGACACTCAAGCAGCTGCAGCATAAAAACCTACGACCCATAAAAATAGCGCATGAGTATGTACGACACAGTTTGAGAACCAGACTACTTATACATTTAGGATATATACTTGTGAAACACTGCTTTGGAAGAGCTAAGAATCCAACTAGCATAACCATTGAAACTTAAATACGCATTACAATTAAGATAGTTTTATGTTCGCTATGATTAAGTCATTAGCAGATGTGGTAAGGCTCTCTGGATGAGCGACAGGTATGCTAAATTAGTGTATGATTAAATTTCAATTTGGGTAAAAGCTCCTTCGTGGTCGGTCACAATCTCCTCAAAGTCGCAGGTGGGTTCATAGTTCGGCGACGTGTGACACAAATGTGACCGGTGGCGAGTGAATTGTGGATCATAGCTGAAAAGAGAAATGTTCCCACCAGGCACCGACAGCGTGAAAATAAAGCAAAAAACAAAATAAACTAATTAAAAATTTCGTTGGGAATGAGTGATGCGACAGGTGAGGCCTCATCACCTCACCTGTTTCTGGCTGCTGTAAAACTGTCAACGGTTTGTTTTGACGGCTCGTAACGGCCTTTTGCACTCGAGCTCGTGAAAGTGTTTACCTTATTTTTTGTCACACTCAGCCGGCTCCACACCATCAACTCCCATTCCCAAACCCCCTGGTCAACACCATCATCGCCATCCTCTCTACGGAGCGCTGATTACGCAGACCCATCTCACTTTCTTCTCATGCAGATTGCGCAATGCTGACAAAAGCATTCTGGGTGTGTGCGAGTATCGCCAAGCATCTAGAGTTAACCAAACTTGCCGGCATCGACATTTTTCGAAGCCGGCGTGAGCATATTTATGAGTAAAAGTGGAATTAATGATTGGAATAAAATTCAAAGCAAAGGTTTGCAAATATTTGCGGCAGGCCGAGACCCCCTCCGCATACCAATCGATCGGATTCAGACTCATACTTGGATTGAGGGGAGATGTAACGTAATATATGGATGGGTTCAAGGCACCTAAGACTTTGCATCCCGCTGCCGTTGGACACATGTCAATCGAAAATGGTAGAGGATGCCTGGCTTTCTTTGACATCTTTGGCGGCTCTTTAATAGGTGCTAAATGAATTCGCAACGAACACTTTCACAGGGGATGACCAAAATGGGTGATACTCGCAGTCAATTGTTCAGCCTTTTCTCGGGCAAAGAAGTTGGCCCCGATTTGCGTTGGGCTTTTAGAAAACATTGCTCTGACCATTGTAACATTGAGAGTGCTTATTGATTTTGCGGTCTCATAAACTGGCTTTCATTTCGTTTTGGCTTTTGAGCTTCCCAGTGGTTCAGTGGTTCGTCGGCTTTGTGGTTTGATGGTTTGATGATAGGGAGCGGAGTGTTTCCGCTCGTTAGCCACAAGTCAATGGCAAAGTTTGTCACCAGAAATTAATATCAATGTGACGCTCAGTTGGCCAATTCTAAACGACGACTTTCCCATGCGTAAACCGGCCCACAAAACCCGTTCACAGATCAAACGGCGACAATTTATAAATAAGTGAAAATCTGCTTACAATGTACGCAGCAAAACTAGTTCAGCTTAAATATTTATAGAAATCGAAAATGCTCGGCAGATGTGCACAACTGCATTTTCCCCCTATGTTCGGAATCCCTAAGCCTCTAATCCCCATGACGACAACATGTGCATTTCAAAGATAACATATATTTCAGTAGATATCATTGGGTCTGCGAAAAGACCGCAGTATATATATAGCAAATAGAAAGATACAGCCTGGAAGGTTTACTTTTTCAAATCAGTCAAGCATGGTTTTTTCGATTCCTGAAACCCAAAAGCCCAATACAATATGACAGCCATTAGGGGTAACATTTAAGTTTGCCATCGAAACTGTTGCAAAGGACTCCTGGAACAAGAAACTCTGTATACAGCCGAAATATATTCGTATATCAGTATATGTATGTATATATATCCGTATATATTTATTTATCTTATTCAATCATTAGTTTGGATTATAATTTCCGTTTTTAAAATCTCTTTCAAAATAATTTATATTCAAAAAGAGCTAATGCTTCGCATTGATTTTAAATTTGAATGGATACTGTTTATCTTCATTTAAAGTTATTAAATTTCTTAGCCATTTGCAATATTAATTATTTTAATCGAGTGCAAATGGCGTGAGGACCTCAGTATATCAAAAGTTTAACCGCTTCTGGCGTGGAAAAACACAAGAAACAAATTGTAAGAAATTAAATAAAGTTTGCGGCAACTCTTGGCCAAGTTTTTCAACAGAGGTCAGCTTGCTTCCCTCGCAGGGCCAACAAAATCGAAAGTTCGACTAAGACGGCGACTGACTAACTAAGTGACCGCTTTCCGTTAGCATATGGTGACTATTATTCGCGCCATGACTTGACTTATTTTTATAGCTTTGTATTATTTATTTATATTCACATGCAAAATTGACATGCAGTTTCGCTGCGACGTTGTAGTTTGCAGTTTTAATTATTTTTTGGCCGCAGAGGAGCCGTTTTCATTAGCGACTAATTTTCCGTGTAGGAGAGAAAATGGATGATGGTCACTGATGAGGCACTGAGATTTCTTTTGAAACATAGAAAATTATGTTTTAGCGCACAATTAGGATTATTCTTAAACTTACACATCTTTATTTTCACACTCTTACTCTTACTAATTTGAACTTAAAATAAACCTTATATGAAATATAGATGACGAGCGGCAGCACTTTCCCATTTTTTTCCGTGTAGTGATCTACCACAGCAGCTGTTGAGTTCAGCACTTGGCCCGGCTCAAACCCTGGCCAAGAGACTCTCTTAGGCCGCTCTTCGCTACGTAAGAAGTGGGTTCGCTCACGTAGCGCTTCGTAAGGTAAAACTGGTTGATGGCACCCGCCGTTTGGCTTTCGCCCGGC NPFR1-PA NPFR1-PA polypeptide 3R-frag 3759 8708 1 0 0 MIISMNQTEPAQLADGEHLSGYASSSNSVRYLDDRHPLDYLDLGTVHALNTTAINTSDLNETGSRPLDPVLIDRFLSNRAVDSPWYHMLISMYGVLIVFGALGNTLVVIAVIRKPIMRTARNLFILNLAISDLLLCLVTMPLTLMEILSKYWPYGSCSILCKTIAMLQALCIFVSTISITAIAFDRYQVIVYPTRDSLQFVGAVTILAGIWALALLLASPLFVYKELINTDTPALLQQIGLQDTIPYCIEDWPSRNGRFYYSIFSLCVQYLVPILIVSVAYFGIYNKLKSRITVVAVQASSAQRKVERGRRMKRTNCLLISIAIIFGVSWLPLNFFNLYADMERSPVTQSMLVRYAICHMIGMSSACSNPLLYGWLNDNFRKEFQELLCRCSDTNVALNGHTTGCNVQAAARRRRKLGAELSKGELKLLGPGGAQSGTAGGEGGLAATDFMTGHHEGGLRSAITESVALTDHNPVPSEVTKLMPR auto:exon5 FBtr0078590 part_of auto:exon4 FBtr0078590 part_of auto:exon3 FBtr0078590 part_of auto:exon2 FBtr0078590 part_of auto:exon1 FBtr0078590 part_of FBtr0078590 FBgn0037408 part_of NPFR1-PA FBtr0078590 derives_fromchado-1.23/doc/examples/dmel_NPFR1.game000644 000765 000024 00000044503 11256707742 017660 0ustar00cainstaff000000 000000 3R-frag Drosophila melanogaster TCATTGCTAACGTATTTCAACCCATAATGGTATATCAAGGCAGCGAGGAC TGCGACTTCATAAATTTCTATCGGGAAACCGCAGAAGCCATCAAGTCTCA GGACGCGATGTATGAAAACGGGGAAATTCAGAGAAGAATTGACACAATAT TACCAATTCTTGATGCCAAGGGATTTTTGGAGGCCCATTGAAATAACATA TATTAAATAATCCGTTTATCAGCTATGAATAATAATAATTTTGAGCTTTA ACCAAAAATGACAAGCCTTTTTCAGAGGACACGTTATGCAAATTGCTAAA TTCGGATTATATTTAAGCACGGATACACACAATTAAGCCTGAGGATTGTG TATTTGCAAAACAGTAAAATGTTAGAAACGATAATGACTAGACAGACCTC AAACAGTTACCTAGGGGAATGACTTGACATGGTAGAATGTGACATTTCAC GATGACCTCGTATTATAGTGAAATCACTCTGAGATCTGAGATAGCACAAC AAAAGCCATTGAGACATCTACACAATAATAATAATAATAGTATTATTATT AATGATCTCACAACCGTGAGCAACCGAGCTAAGTCGCCAAAAGATCGAGG AACCGCACCACGTATGGAAATCACCTGGATAAGACTTATTATTAATGCAG GAAAGGCCAGCTATTGAAATCTGGACCAAGCCGTCGATCGGGAAAACTAT TAATTCGTGAGCTGATACAAATTTTGACTATCAGCGCTGGAACGTTACAG AAGAGACCTTGAAGCAGGCCCTTCCCGAAGACGTTCCTATGGCGGAGGCT ATCTTTGGGAATAGCCATACGTGCGGAAAATGGACAGATCGATCTGGTAA GTAGATCTGTCTTCCGTAGAAGGAACTGCTAGTGGAAGCCGGGCTGGGCG GAAAGCAAGTTGAATATGCCATGGACCAAGATCCAGAAGCTCCATAATTC TGGAGGATCTTGTGCCGTATAAGTTCATCAATGCAATGCAGTAGCTGGAC TTGGTTTACATCAAGCTCACTCCGAAAATGCCAGCAATGTGCCATGCTGC CTCCATAATCCTGTGAGGCGGATATAAGAGGTTCATTGATGAACAACCGA ACATAAATAAGCCAATGACAACAAATTGGGGAAGTACCCACATAGTAAAT GTGGAGTGGGGGGGACCAGTTATGGCCACTTTCAGTTCAGCACCTTCGCG TTGATAAGAAACTCGAAGTTTGCTCTAAAAGTGAACTCTAACAAGTTACA AAGGAGCTAAAAAGACCAAAACCTCTGAAGTCTTCACTAAAAGACTCCTG AAGTTTTCGCAATCAGGTTTCGGTTTATGCCAGTGAACTTGTTAAAGATG ATTTTTTTAATTTTGCAGTGTTAAATCCAGATACTAATATAAATATTTAT AACTAGATCAATTCTAAAAAGACATTTTGGATGTTTGGTGCAGTATGTTT CTATTGCGGTGTTCATTAATTTTCATGTCCGCATTTAGAGTACGATCCCC GAGATGGCTTGTTTTGCAAATAAGTTTTTGTAGAGCACTGCAAAGATAAG CTATCAGCAGGCACCACATTATTTTAAAATATCATAATATCTCTTTCGTC ATTTTGGTATCACTTTTAGCGAGGTATGATAAAATGTCATCATAGGCTAT ACTGTTAAGATAGAACTTTATTTTGTATGACTCAAATTTCCAGGCACACG CAATTTTTTAACATCCCCTCGACCAATGTGCGAAGCTTTTCCACCCCTAG TTTCGGTGATAAGAAAGCTCTGCACAGCTGACGGCCCAAAATCCAAAACA AACTCGAAGCGCGGGCCCACGGCCTGTTGACCAAGTGCGATGCCTTCAGT CGCAACTTTTGTGCCACGCGGCGTATACGCAACGCGCCCCGGCAAACAGC AAATCAGGCGGATATATCGGCGGGACTAGGGTATATAAGCAGGAGATGCG CACCAAAAGCCAACAGATGGTCGCTGACTGTGCACGCGTGTGGTTATCGG AGATCAGTAAACAGCCCAACTAAACACCGAAACTTACTGTAATAAAAAAA AACGGGAAATAAGCGAAATAATCAAAATGCGGCCGCATACTTATTTATAA TTTTGAGGCGGCCGAGCACCGGGGCCCCAAACTCTTTGGATCTGCACGGA ATCCAGAATTCCGAGAGGTATGCCATCGACGCAGTGTTTTGTGTTTGTTT TCCCACAATGTGCCGTCATTAAAAAGCTGAAGTGTGAGGATTTCGCACGG AGCCTCGACATTTACGACCATTTTTCCCTGATGCGAAGTGGTCCGCGGAA ATTCGCTAATTGTCCGCCGGACGCTCCGCAGTTGTCGGTATTTATTATGA TTATTTTTTCCGAACGCGCTCCAATGAATCTGGACTGCAAGTTGTGAATA TTTCGAAAAAAAAAAATATTATTCCGCGCGAGTCTTTCGGGATAACAAAT CTTTCGAGTCCGTAATGCCAAGTGAAGTGCGTGGGCAAAAATTATTTTTT AAGAAAAATGCAGGACAGTTGGTGTCCTCGTTCGATGGAAAATTAATGAA TGTGTATTTTGCGTAATGAGATGTAAATGCCTGCTACACTTCAACAAAAA ATACAACCAAAATGTCATTTACTTAATGGGATTATTAATGGACTCTGAAT TAAGAAGCGGATTTCTCGGCACATGTCGAAAAAAGTTCGAATATTTCAGC AATAATGATTATAATGACATGAAGAATTAACCATCTAGAGCCAAACAAAT TGTGTATTTTTTTTTTTTTTTTTTTTTTTTTAAATAATTAAGACAGAGCA CTTATTTCTTTACTTCTTCGAGCTCTGATTAAATAAATATACTTTATTAG GTCCGATTACAACATATGTTTCTCGGTGTTCAGTAATTTATGCCTATCGA TTGGAAACGAAATTAATAAATTGGAATAAAAAGCCCATTTCGTCGGACAA AATTTACATAAAAATTCTTCATTGGGTCTATTGATAACATTTTATTGAGA GACGTTTAAATTCTATAAATGAAATTTTATGCAGTGAAACTTCACTTAAA ATAAACATGTATTTAAAAAATGTTATCCTTAATGTGATTTTCAAGCTAGG GCTATAGAGCTTAGGAAATGTATACAGTATATATTCATCTAGCATGAAGT GTTTTGTTAATGTTAAATGATGTTTTTATGACATGAAGTCAATTTAAAGT TTAAGGTTTTACCGCCCAACTGAGCATGACTTGAACGTCCTCAAAGTGCG CCAGAATCTGGAAAATGTTCCAAAAGTTATGCATACCAATGGATGCGAAG CTGGAACCCCCATGGTACTTAAAAAGTGCAACTATCTTGTGCAAACTTTT AGCTTCAGGCCCGTGTGCCTGCTGCCTAAAGGATTAAGCTGTGTCAGAAA CTCTGCGCAATTTTATGAATTTTTGGTGCACTTTAATTAAGTCGATTATG CTGGCAACCAGATTGTCCAGATTAAATGCTATGTGCATCGGACCCCTTGA ACGAAAGCATCCATTAGCTGAATTGTTATCATTTCTTTTAATTTCAAGAG CAAAAACACAAAGCGAAGTCCCGTGAGTGCATTCCAAGTTGAAAACTAAG TGAGCAACTGCTGCTTTGGCAGCCGGAAAAACAGAGATTCACTCGTGTCA CTCGCAGAAGGAAAAACAAGAACCGACGGCCAGGAAAACAATACGGTACC ACGCACTATAGTAAATATATAGCATACATATCCCCAGGGCGAAGGAGATT GCCAGGACGATGGTGAGTGTAATTGCAATATAAATACTTAAAGCCAGCTC AAGAAGCCATTTCGAAGTAGATGTCAAATGGAACGAAATTACTTTGTTCC CAAAATGAAAAAGTTTGTTTGAGTTGCTTTGGGGGAATGGGTTGTGCTCT ACGTTGGCCATATGGTTGTGTGAGCTCCCACTTCGTTGGCATTTGCAGAG TGCCTCGCCAGATGGAGAACCATACAAATTTCAAAATAATGCTCCCTCCT GGCGGCCAATTTAAAAACTCGGGTAAGGCTTAAAAGTCATGGAGAGCTAT ATCAATTTACCTGGTTACACATTCGCTTGACATTTTCGTGGTCGGGACTT TTACTAGGGGCTTTTATTTTTATCCCAACACCCTGTGGCTTTCCTTTGAC ACCAAAGAAGTGTTAAGCGGCACACAGAACATGATTAAATTGCAAGGGAC TTAGACAAATGGCTAGAATTTGCGTTCAGCCTTTAGGCAGCTTAGCCTAT TAGTTCCCTAGAAACCCAGTTTGGCTCTGTGCCAGATGCCTCCGCTTAAG CATAGCTCTTTCCCTACAAGTGAATGATTTGGAGTTGACCAGCCGCACAG ATGAGGCCAATTCAAGCTGCATCCCACCTCCATCTTGTTGAAACTAAATC GACTTCAATTAATAAGGAAAACGTCCATCCGCAAACAAAACACACAAGCA GCAATAAAATTCATCTTATAGTGGGCGAAACAAGAGACCCACCGCAAATA AATCACAAAAATAGCTGACTAGAAGTGCCAGCAGCTTGGAATCCGCACGA GCTTCCCGGAAAACGGATGACATTTAAAATCTTTGTCATGCTTTACTTAT CCAGTGAAGCAAAAATACTTCAGGCACTCGGAATGCAAAAATTATTCCAA TTTTGTGACAACTGCCGATTACTTGAGGCTGCTTTACATAATTTTCCCCA CACAAACTTCCTTTCTGCTTCCAAACTGAGAAGGCAGCTGCGCAGGGATT TCCCCTTTTGCTTTGGGGAACAGAACATGTAAATTCAATTTTCACCTTGC AAGTCAATCTATCGAAGGCGTTGTTGTTTTGGGCTGTGATTGGAACTTTT GCGACCAATTGGTGATCAACTTCGAACAGTGTTTTATGCTCCGTTTTCCT TGGCTGAAAATTTCCATTAGGTCCTTGCCCGAAGCGGAAGGAGAATCCCA CTTTGCAGACTGGCCAGTTTGCGGTCGACAGACTTTTTCATTTCGGACTC CCATGTTTGAGTTGAAGTGCAAATATTAGTCAATTAGGAGCCGGCCAACA TGAAATTAAATTTCCATGGAAACTTGCTCTTCGCCTCGATACCCAATGCC CGACACCCGATGCCCCGAAATCCCCACACCCTATCCGGTATCTGGCGAGC TAATTCCCCGATTGGCGAGATTTATTAGCGCCTCATTTATCGCAGCTGTC AGGGGCACATAATGCATACCTTTGGGCGCCACTATAAGTCTGTTTCGCCC ACCTTCGAGTGAGGCATCGGATTTTATCGATACTGACAAGTGCGCAGCTC AGATGGCGCATAAAATTACACAATTATTTTTAGCAAATGTCGTCATTTAT AACCTGCCTGTTTCTGTTTCTGTTTGTGTATCTGTATCTGGATATGGGTC TGACGGCTGTCCCTCGACACCGGAATATCTTGATCTGGCAACAAATACCA GGCATCAAAATCAAACGCACATTTCCCCGGAGGAAACGGCACTTTTGACT TTTTCCAATTAAATGCATGTCTCGCCTTGATGTGCTGCATAAATTACGGC GACGGGTAATGCATGAATATTTACGAGGGAAAACAACCGACTAACTGAAG CTCGGCACTGGGATATTGCATAAATTGACTACAAATGGGAAGATATTTTT CGAAAAAAGGGACTTTCGAAACTTGAAAACAAAGCGAATTACTTTTCCTT GCCAAAGTTATCCTGTAGCAGATAATTTCAGAGTCGAGTTGATTCGAGTC CCAGGAGTCAAGGCCATTGTCTGTGTTCAGAAGGGTATTAACAGGCGAAT GCCAAGGGCGTTTGAAGTTTTATCAAGCCTCGAGATCTGAATTCAATTAT TAAAATGGCTCACTGGGAAATGGATTTAGCAAGAAGATGAGGCGATAAGC ACTATGATTTTACATTGACATAGATAGTTCTCTAATCGCATTTTAGCTTT TAGACTTTTGTCAAGTGTCCAACAACAAACTTAACTTAAAATGTATACAA CCATTGTATCTATCCGTTTGTCTATTTACCAATTTTTATTTAAAGTTTTG AAAGATTTTCTTGAATCTTTTGAACAGAAAACCACTTTAATCTAATAGCA ATACATTTGATGCAATTGCATCCTTAACAATGTAATTTAATAGGACTTAA ATGGTATAATAATTATGATTTAGTTAATACCCCAAAAGCTTTTAAAATAA TGAACGTATGACGTAAGGTTACACTGGCGTAAGGTTACACTGTTTTTCTC CCAGTGTCTGCAAATAAGTGAGAGAGTGAGGCGTCAGAACTTTCATGCAT GTCGTATGCCCATAGAATCCTTTGGTGCTGGGCCACCTACTGGCACCAAA CAAACTTTTTATACGATTATTGCCCCGTATTTCAAGCCACAAAGCATTAA GCAAGCCAGTGGAATTTGCCATTCGCAGCTCGCTAGAAAGTGTGGTGTGT GCAGCAAGCCAATCTCATAAATCATACGTGATGTGGCACGCAAAGTTGCT GCTTCCTTGCCCCCTGACAATTGAATATTTCGTGCCGCGGATTTGGGAAA TAATGAGACCCTGTTTGCCTCCTTCGTTCCCTAGATAATCAGCATGAATC AGACGGAGCCCGCCCAGCTGGCAGATGGGGAGCATCTGAGTGGATACGCC AGCAGCAGCAACAGCGTGCGCTATCTGGACGACCGGCATCCGCTGGACTA CCTTGACCTGGGCACGGTGCACGCCCTCAACACCACTGCCATCAACACCT CGGATCTGAATGAGACTGGGAGCAGGCCGCTGGACCCGGTGCTTATCGAT AGGTTCCTGAGCAACAGGGCGGTGGACAGCCCCTGGTACCACATGCTCAT CAGCATGTACGGCGTGCTAATCGTCTTCGGCGCCCTAGGCAACACCCTGG TTGTTATAGCCGTCATCCGGAAGCCCATCATGCGCACTGCTCGCAATCTG TTCATCCTCAACCTGGCCATATCGGGTGAGTTGCCATTCCCACTGAGAGC CAAAGCAAGTGTGAGTCTCATCCGAGCGGACTTTCAGACCTACTTTTATG CCTAGTCACCATGCCGCTGACCTTGATGGAGATCCTGTCCAAGTACTGGC CCTACGGCTCCTGCTCCATCCTGTGCAAAACGATTGCCATGCTGCAGGCA CTTTGTATTTTCGTGTCGACAATATCCATAACGGCCATTGCCTTCGACAG ATATCAGGTTAGTCGCTACTCGAGCCTTTTTTAATGCCAACGTTAGTATG TAAATGGGGCCATCAATGGGGCAAATCGTGTTCGGATATTAATGAGGTGA ATACCTTCAATGTGTAACCATTAAATTTGACGTTGAGGGAAAATCGATGG GCTCTCAGTAAATATTTGGCGATTACATAAGGGCTTAACCCACGATTAAA CCTATTTTTATGGTGTCGAAACAAAGACCATTAAAAAGGGTTGATGGATT ATAAACAGAAGGATTATTAGGTATTGATTATAAATAGCCGGACTGTTCTG GGGTAAAGTAGAGAAGTAGGACGCATATAAATTAATCCGATTTTTTTAAT CAATTTAAGGCGAGTGGCCAGTTGACTTAAAGAAAGACTTATAAGTTAGC TTTAATATAATGTTTTTGGTGATTAAAGAATAGTAATTGCACGGTTAGAG AAACCAAACCTAATTGTACGTCACACTCTTATAGCAATCGATTAAAAATT ATATTTGCTTATAAATTCCCAGTTGAAGATGTATTTTCACTAAGTATAAT TTACAGTGCGAATGGGTAATAAGACTCCAAGCCCTGAGATATAACAACCG TCTAACCTCACTTCCAGGTGATCGTGTACCCCACGCGGGACAGCCTGCAG TTCGTGGGCGCGGTGACGATCCTGGCGGGGATCTGGGCACTGGCACTGCT GCTGGCCTCGCCGCTGTTCGTCTACAAGGAGCTGATCAACACAGACACGC CGGCACTCCTGCAGCAGATCGGCCTGCAGGACACGATCCCGTACTGCATT GAGGACTGGCCAAGTCGCAACGGGCGCTTCTACTACTCGATCTTCTCGCT GTGCGTACAATACCTGGTGCCCATCCTGATCGTCTCGGTGGCATACTTCG GGATCTACAACAAGCTGAAGAGCCGCATCACCGTGGTGGCTGTGCAGGCG TCCTCCGCTCAGCGGAAGGTGGAGCGGGGGCGGCGGATGAAGCGCACCAA CTGCCTACTGATCAGCATCGCCATCATCTTTGGCGTTTCTTGGCTGCCGC TGAACTTTTTCAACCTGTACGCGGACATGGAGCGCTCGCCGGTCACTCAG AGCATGCTAGTCCGCTACGCCATCTGCCACATGATCGGCATGAGCTCCGC CTGCTCCAACCCGTTGCTCTACGGCTGGCTCAACGACAACTTCCGTAAAG AATTTCAAGAACTGCTCTGCCGTTGCTCAGACACTAATGTTGCTCTTAAC GGTCACACGACAGGCTGCAACGTCCAGGCGGCGGCGCGCAGGCGTCGCAA GTTGGGCGCCGAACTCTCCAAAGGCGAACTCAAGCTGCTGGGGCCAGGCG GCGCCCAGAGCGGTACCGCCGGCGGGGAAGGCGGTCTGGCGGCCACCGAC TTCATGACCGGCCACCACGAGGGCGGACTGCGCAGCGCCATAACCGAGTC GGTGGCCCTCACGGACCACAACCCCGTGCCCTCGGAGGTCACCAAGCTGA TGCCGCGGTAAAGCACAGGGTAGTCCTAAGGTCCTTGAGGTCTGGTCTCG TGTCTAAGTCCTCATGATACACGCGTGCATGTCCTTTTGTACGCCCTCGG GCTGATTGGATTTGCATGCTCCAAACGTCGCTGCTGCTCGCTTTACGTTT CACTTGTTCCAACTGCAACTGCCACCTCTCTAGAACACTGAGCGAAATGC CGTGTCCTCTAATCGGGAAACACTCTGGCTGTAAAATCTATAAGCAGCCG AGTCAAACGTTTCTAGCGTTCTAAAAGTTTCTTATGATTATTTTATTTTA TATATTAATAACAATGACTTCGTTCCCAATTATATGCTTGTTTTCATCGT TTTTGAATGTAACAATTGATCAATATTCGACCAAAAGCAAGTTTTGAAAT ATTTGTGTAAATATCGTTTTCAAATTTGTTCGCCTTAATCTTACTTAATA ATAATAATAATAATAATCTTTACTCCGATAATCATTAACGTAACATTTCT ACTTGTAAAAATATTTCTGATCTAAGGGGCTTGCTCTTTTCGGCTCCACC TTGAATTACTTTTCAGTTGACTAACTAGGCGTATATTTTTGTCAGTGTAT GCATGCGCTCCTCTTATCGTTGCCTTGTCGAGCTGTAACTCTTGTTGTTG CCATGTTGTGACATTATTTGCTTTTGAGCTGCAATCGATTATGACCCGTC TTTTGTGACACATTTTCAGTTTGGAACAGTACTAAATTGGCAATCAATCC TGGAGCAGCAGGCGGCTGGAGCAGCATTCTAGGGAGGCGACTGCCTGTCA CCCATAGACTTAACACGTATTGTCCAGTGATCCAAAGCCAAGCTGAGTTA GCCCTAAGTTAAGACACACGCGACTAAGAGCTCGAAGCCTGTAAACTATT CTTAAACGACCATGTCATGGCATCCATCATCAACTCGGACTAAGTCTATG GTTAGATCACTTTCGTATCAAATGCCGAAAAGTAATTGAATGAGCCCCCA ATTAGATTTCGGGTATTTGATAAGTCGAATACGCCTAAGACTCGAATAAG TTCTCTCAACAGTTCCTAGGAAATATTTTCGTTTTATCTCAGCATTTCTT GGTATCATCTAAGCTAAGGATTAGCTATAATTGATGTTCTGTTCGCTATT CAATAATGATAGGATAGGTCGAAGTCCACTAAGCCAAAGTGAATTTAAAG TATAGTATAGTATAAAGTATAATTGTAAAAGATAACTTTAAAATAAATGT CAGCTGCTCTTAAACATTTAATGCAACTGTTTTAATGTCTGCAATGGGTG AAGATTGCAACACACCGAAATAAAAATCGTAATAAATGTTGCTGGAAAGC CTTCATTATAGAACGTTTTCACTGTAAATGCTCATGTTTGGATAAAGTGC CAATAAGAGAAGCCTCTTGTATTTCAATAAATGAGCAACTTTAAGAGCTT CCAAAGTCCGAAGCTTCAGAATGTTTATTTTTCTTACACAAATGAAGTGG CACTTTGGAATAAATATGTATCAAGAATTAAGCATGGTAAGTTATCTAAG AGTTCTGTATAGGTATAAAGTATGTAAGGTGTGTAAATTGAAATATATTT TTACTCTTTAAAGATATTTTAACACAATTGAAATGATTCTCGAGGAAGTG AGCCAAAAAAAAGATACACCGTATCTGGAAGCCTAACAACCACAGCAATA AACAGCAGCTGACCCGCCGAACACTTAACTTTTAAGACTTTTGTGGGTTC GACACTCAAGCAGCTGCAGCATAAAAACCTACGACCCATAAAAATAGCGC ATGAGTATGTACGACACAGTTTGAGAACCAGACTACTTATACATTTAGGA TATATACTTGTGAAACACTGCTTTGGAAGAGCTAAGAATCCAACTAGCAT AACCATTGAAACTTAAATACGCATTACAATTAAGATAGTTTTATGTTCGC TATGATTAAGTCATTAGCAGATGTGGTAAGGCTCTCTGGATGAGCGACAG GTATGCTAAATTAGTGTATGATTAAATTTCAATTTGGGTAAAAGCTCCTT CGTGGTCGGTCACAATCTCCTCAAAGTCGCAGGTGGGTTCATAGTTCGGC GACGTGTGACACAAATGTGACCGGTGGCGAGTGAATTGTGGATCATAGCT GAAAAGAGAAATGTTCCCACCAGGCACCGACAGCGTGAAAATAAAGCAAA AAACAAAATAAACTAATTAAAAATTTCGTTGGGAATGAGTGATGCGACAG GTGAGGCCTCATCACCTCACCTGTTTCTGGCTGCTGTAAAACTGTCAACG GTTTGTTTTGACGGCTCGTAACGGCCTTTTGCACTCGAGCTCGTGAAAGT GTTTACCTTATTTTTTGTCACACTCAGCCGGCTCCACACCATCAACTCCC ATTCCCAAACCCCCTGGTCAACACCATCATCGCCATCCTCTCTACGGAGC GCTGATTACGCAGACCCATCTCACTTTCTTCTCATGCAGATTGCGCAATG CTGACAAAAGCATTCTGGGTGTGTGCGAGTATCGCCAAGCATCTAGAGTT AACCAAACTTGCCGGCATCGACATTTTTCGAAGCCGGCGTGAGCATATTT ATGAGTAAAAGTGGAATTAATGATTGGAATAAAATTCAAAGCAAAGGTTT GCAAATATTTGCGGCAGGCCGAGACCCCCTCCGCATACCAATCGATCGGA TTCAGACTCATACTTGGATTGAGGGGAGATGTAACGTAATATATGGATGG GTTCAAGGCACCTAAGACTTTGCATCCCGCTGCCGTTGGACACATGTCAA TCGAAAATGGTAGAGGATGCCTGGCTTTCTTTGACATCTTTGGCGGCTCT TTAATAGGTGCTAAATGAATTCGCAACGAACACTTTCACAGGGGATGACC AAAATGGGTGATACTCGCAGTCAATTGTTCAGCCTTTTCTCGGGCAAAGA AGTTGGCCCCGATTTGCGTTGGGCTTTTAGAAAACATTGCTCTGACCATT GTAACATTGAGAGTGCTTATTGATTTTGCGGTCTCATAAACTGGCTTTCA TTTCGTTTTGGCTTTTGAGCTTCCCAGTGGTTCAGTGGTTCGTCGGCTTT GTGGTTTGATGGTTTGATGATAGGGAGCGGAGTGTTTCCGCTCGTTAGCC ACAAGTCAATGGCAAAGTTTGTCACCAGAAATTAATATCAATGTGACGCT CAGTTGGCCAATTCTAAACGACGACTTTCCCATGCGTAAACCGGCCCACA AAACCCGTTCACAGATCAAACGGCGACAATTTATAAATAAGTGAAAATCT GCTTACAATGTACGCAGCAAAACTAGTTCAGCTTAAATATTTATAGAAAT CGAAAATGCTCGGCAGATGTGCACAACTGCATTTTCCCCCTATGTTCGGA ATCCCTAAGCCTCTAATCCCCATGACGACAACATGTGCATTTCAAAGATA ACATATATTTCAGTAGATATCATTGGGTCTGCGAAAAGACCGCAGTATAT ATATAGCAAATAGAAAGATACAGCCTGGAAGGTTTACTTTTTCAAATCAG TCAAGCATGGTTTTTTCGATTCCTGAAACCCAAAAGCCCAATACAATATG ACAGCCATTAGGGGTAACATTTAAGTTTGCCATCGAAACTGTTGCAAAGG ACTCCTGGAACAAGAAACTCTGTATACAGCCGAAATATATTCGTATATCA GTATATGTATGTATATATATCCGTATATATTTATTTATCTTATTCAATCA TTAGTTTGGATTATAATTTCCGTTTTTAAAATCTCTTTCAAAATAATTTA TATTCAAAAAGAGCTAATGCTTCGCATTGATTTTAAATTTGAATGGATAC TGTTTATCTTCATTTAAAGTTATTAAATTTCTTAGCCATTTGCAATATTA ATTATTTTAATCGAGTGCAAATGGCGTGAGGACCTCAGTATATCAAAAGT TTAACCGCTTCTGGCGTGGAAAAACACAAGAAACAAATTGTAAGAAATTA AATAAAGTTTGCGGCAACTCTTGGCCAAGTTTTTCAACAGAGGTCAGCTT GCTTCCCTCGCAGGGCCAACAAAATCGAAAGTTCGACTAAGACGGCGACT GACTAACTAAGTGACCGCTTTCCGTTAGCATATGGTGACTATTATTCGCG CCATGACTTGACTTATTTTTATAGCTTTGTATTATTTATTTATATTCACA TGCAAAATTGACATGCAGTTTCGCTGCGACGTTGTAGTTTGCAGTTTTAA TTATTTTTTGGCCGCAGAGGAGCCGTTTTCATTAGCGACTAATTTTCCGT GTAGGAGAGAAAATGGATGATGGTCACTGATGAGGCACTGAGATTTCTTT TGAAACATAGAAAATTATGTTTTAGCGCACAATTAGGATTATTCTTAAAC TTACACATCTTTATTTTCACACTCTTACTCTTACTAATTTGAACTTAAAA TAAACCTTATATGAAATATAGATGACGAGCGGCAGCACTTTCCCATTTTT TTCCGTGTAGTGATCTACCACAGCAGCTGTTGAGTTCAGCACTTGGCCCG GCTCAAACCCTGGCCAAGAGACTCTCTTAGGCCGCTCTTCGCTACGTAAG AAGTGGGTTCGCTCACGTAGCGCTTCGTAAGGTAAAACTGGTTGATGGCA CCCGCCGTTTGGCTTTCGCCCGGC 3R 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{ color:#f00; } .code pre { color:#008; margin-left:20px; padding:8px; background:#ccf; border:1px dotted #00f; } .output pre { color:#080; margin-left:20px; padding:8px; background:#ccf; border:1px dotted #00f; } .status { left-margin:18px; color:#800; padding:4px; } .metadata { font-size:10px; } .scenario { margin: 16px; padding: 16px; border-style: solid none none ; border-width: 1px; } #scenarios { font-family:verdana, arial, sans-serif; color:#000; font-size:small; padding: 8px; margin-top: 32px; } .footer { width:100%; background:#FFF; border-width:1; background:#ffffff; padding:5px; font-size:tiny; } .title { font-family:verdana, arial; font-size:small; color:#000; text-transform:uppercase; font-weight:bold; } .comment td { font-size: small; } .parts table { width: 100%; border: 1; background: #ddd; } .parts th { border-width: 1px; text-align: left; border-style: none none solid; } .parts td { border-width: 1px; text-align: left; font-size: 10pt; border-style: none none solid; } #index table { width: 100%; border: 0; background: #ccc; } #index table a { font-weight: bold; } #index td { border-color: #ff0000; color: black; border-style: none none solid ; border-width: 1px; text-align: left; font-size: 10pt; padding-top: 1px; padding-left: 8px; padding-right: 8px; padding-bottom: 1px; } .tab td { font-size: 12px; text-align: left; padding: 3px; } .tab th { font-size: 14px; text-align: center; background: #fff; border-width: 3px 0 3px 0; border-style: solid; border-color: #366; } .tab th a { display: block; padding: 3px; } .tab th a:hover { color: #fff; background: #366; } .tab td.tableOne { background-color: #add; } .tab td.tableTwo { background-color: #bee; } chado-1.23/conf/bulkfiles/000755 000765 000024 00000000000 12061672376 015511 5ustar00cainstaff000000 000000 chado-1.23/conf/chado2apollo-apache.conf000644 000765 000024 00000002057 11256707520 020165 0ustar00cainstaff000000 000000 ## chado database to apollo game.xml cgi function ## apache web server configs - for flybase-ng/argos server ## add to main conf/apache/ folder or Include in apache.conf ## MUST ENABLE 10+ minute timeout -- this is SLOOOOOWWWWWWWWW ## this directive only works server-wide, not for .htaccess Timeout 1800 ScriptAlias /apollo-cgi/ "/bio/biodb/flybase/dbs/chado/" AllowOverride None Options ExecCGI -Indexes -Includes FollowSymLinks MultiViews AddHandler cgi-script .cgi Order Allow,Deny Allow from all Deny from env=is_nasty env=is_robot LayoutDefaultHandlers Off # LayoutHandler text/html LayoutMerge Off ## alternate as .htaccess in web/apollo folder # Options ExecCGI -Indexes -Includes FollowSymLinks MultiViews # AddHandler cgi-script .cgi # Order Allow,Deny # Allow from all # Deny from env=is_nasty env=is_robot # # LayoutDefaultHandlers Off # # LayoutHandler text/html # LayoutMerge Off # chado-1.23/conf/bulkfiles/anogam.xml000644 000765 000024 00000006760 11256707520 017501 0ustar00cainstaff000000 000000 1 0 site_defaults AnoGambia GMOD Bulkfiles; loaded from a NCBI GenBank chromosome record ]]> ${org}_${release_date} /genome/${species}/release-${release_id}.html anogam Anopheles gambiae str. PEST Genbank sequence 'chromosome' 'Note','comment1','gene','locus_tag','inference', 'product','protein_id', 'transcript_id', 'standard_name', 'strain' chromosomes features matches analysis chromosome gene transcript CDS translation ncRNA pseudogene transposon & log.anogam1 & perl -Ilib bin/bulkfiles.pl -config=anogam -format=genbanktbl -debug -make problems: transcript : no db residues; reconfig to get froms eq ]]> chado-1.23/conf/bulkfiles/blastfiles.xml000644 000765 000024 00000016330 11256707520 020361 0ustar00cainstaff000000 000000 Blast index writer These are configurations for updating blast indices, rc files, html pages, given genome fasta input files and fasta/feature groups. fasta ncbi gene transcript translation ncRNA pseudogene intergenic scaffold chromosome syntenic_region ... # blastn blastp blastx tblastn tblastx ]]>
${species} BLAST Databases

${species} Genome BLAST

Data release ${rel}
Data sets for BLAST search

  • Database - Choose a database     required

    ]]>
    key: AA = protein, NT = nucleotide. To download databases, visit the Sequence Download Page
    ]]> ${species} full-length cDNAs from the BDGP ]]> ${species} entries from the SwissProt+TrEMBL+TrEMBLNew databases (SWALL) ]]> ${species} proteins from UniProt ]]> ${species} proteins from RefSeq ]]> ${species} nucleic sequences from RefSeq ]]> ${species} sequences collected from public sequence databases (but without BDGP, EDGP, Celera, or dbEST sequences) ]]> Drosophila Expressed Sequence Tags from the BDGP and from dbEST cDNAs (redundant) ]]> ${species} known repeats ]]> Drosophila STSs from the BDGP and EDGP mapping projects ]]> ${species} transposable elements ]]> chado-1.23/conf/bulkfiles/bulkfiles_template.xml000644 000765 000024 00000012474 11256707520 022111 0ustar00cainstaff000000 000000 Chado DB Data Release setting with release details. date, name = optional information. make_current = 1 will make $datadir/$species/'current' symlink to this release folder. ]]> value1 value2 HASH values have an id or name tag, are repeated and include any substructure: tentwenty There are many of these configurations. Documentation of them is included, sparely as yet, in the configuration files (about tags). for full listing, run bulkfiles.pl -config=bulkfiles_template -showconfig -debug ]]> site_defaults Using 'include' options in the xml configurations will add these file settings to main configuration, but not replace main settings. Includes can be nested. 'site_defaults' is one which is handy for including all the common settings your site uses for data releases. ${org}_${release_date} /genome/${species}/release${release_id}.html 0 Set valid=1 to skip seq_ontology, other variable validation sequence seq_ontology is the name in CV table for the sequence feature cvterm set, including gene, exon, chromosome. It varies depending on choices used to install sequence CV terms in your Chado database. 'seq_ontology' and 'golden_path' are critical parameters that must match cvterm values used for feature entries. See chadofeatsql.xml for more details. Common alternate values are 'sequence', 'Sequence Ontology Feature Annotation', 'SO', 'SOFA'. scer Saccharomyces_cerevisiae 0000 'chromosome','supercontig' 'Note','orf_classification' These values of org, species,golden_path,featureprops are example species-genome specific options. org = short species id. golden_path = what highest level of genome feature is (a SO term), chromosome, chromosome_arm, golden_path are some common ones. featureprops = chado featureprops to include with feature dump. 1 chromosomes features matches analysis This specifies the primary chado database feature dump, including which table sections in the chadofeatsql.xml configuration to use. Each target here matches a chado feature SQL entry in chadofeatsql. This should become a 'fileset' instead of 'featdump'. fileset hash table defines what bulk files to produce, and how. fileset.xml has default settings, this fileset_override replaces just one of these. The name="fff" is a conversion of chado feature dump to a 'gff-like' table, using database-specific feature conversions, so it typically needs attention for a new site/database. chado-1.23/conf/bulkfiles/chadofeatconv.xml000644 000765 000024 00000047075 11256707520 021047 0ustar00cainstaff000000 000000 Chado DB Feature info These are configurations for converting chado feature table dumps to standard feature/sequence files. Most of these configs specify how to process and convert various features extracted from chado db. These are tied to methods in Bulkfiles::FeatureWriter.pm) Tags with OLD_USAGE_ are depreciated settings (no longer active). feature_table fff gff fasta 0 pseudogene|\w+RNA 1 [-_](repeatmasker|genscan|piecegenie|twinscan|genewise|trnascan) ^(match_part|match|gene|cytology|chromosome_band|oligo|BAC|protein_binding_site|rescue_fragment) 1 0 mRNA protein,CDS,three_prime_UTR,five_prime_UTR protein CDS parent instead typelabel = what to write in place of id type (protein -> CDS) hasspan = this feature has start,stop (e.g. gene, mRNA, protein) discard/cut parts that fall outside part(s) = array of kid types (e.g. exons, UTRs) making structure makepartsfrom = list? of parts to make parts from if not given (e.g. exons => cds) ]]> tRNA exon protein five_prime_UTR three_prime_UTR intron CDS five_prime_UTR three_prime_UTR intron exon transposable_element:predicted match:fgenesh match_part:fgenesh match:HDP match_part:HDP match:RNAiHDP match_part:RNAiHDP mRNA:genscan mRNA:piecegenie tRNA:trnascan chado-1.23/conf/bulkfiles/chadofeatsql.xml000644 000765 000024 00000121301 11256707520 020662 0ustar00cainstaff000000 000000 Chado DB SQL This chromosome_summary needs more testing: works well enough on some dbs, but hung up on a largish one. Moved cvterm.name from where clause to subselect after reducing features.. 5x cut in grouping cost SELECT f.type_id as Type_id, (select name from cvterm where cvterm_id = f.type_id) as Golden_path_type, count(DISTINCT f.feature_id) as N_features, sum(f.seqlen) as Tot_len, sum(length(f.residues)) as N_residues, (select genus || '_' || species from organism where organism_id = f.organism_id) as Species FROM feature f join featureloc fl on (fl.srcfeature_id = f.feature_id) GROUP BY f.organism_id, f.type_id ORDER BY Species, Golden_path_type ; Failed to validate configuration variable seq_ontology='${seq_ontology}' in database tables cv, cvterm and feature. Please check your configuration. Failed to validate configuration variable golden_path='${golden_path}' in database tables cv, cvterm and feature. Please check your configuration. 0710: preliminary to produce gene ontology association tables .. need variables for GO CV tables // ok: see awkward sql below .. need taxon code in organism.table and/or main config .. want filename with ${GFF_source}_${org} suffix ? .. add header for GO submission .. ; ; feature_dbxref.is_current ! -- attr view for regular features which may have parent features (exons) CREATE OR REPLACE VIEW gffattr_gmodel ( feature_id, type, attribute ) AS SELECT feature_id, CASE WHEN fs.is_current IS FALSE THEN 'dbxref_2nd' ELSE 'dbxref' END AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, cv.name AS type, fp.value AS attribute FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id and (cv.name in ( ${featureprops} )) -- keep this restriction - other props not useful here: comments, sp_comment, owner ... -- mar05: add 'putative_ortholog_of' cv for dpse/..; this is in feature_relationship UNION ALL SELECT feature_id, CASE WHEN fs.is_current IS FALSE THEN 'synonym_2nd' ELSE 'synonym' END AS type, s.synonym_sgml AS attribute FROM feature_synonym fs, synonym s WHERE fs.synonym_id = s.synonym_id and fs.is_internal IS FALSE UNION ALL -- add parent feat ids for exons, etc. -- putative_ortholog_of=dmel/gene:CG31648 SELECT pk.subject_id AS feature_id, cv.name AS type, '${GFF_source}:' || fo.uniquename AS attribute FROM feature_relationship pk, feature fo, cvterm cv WHERE cv.name = 'putative_ortholog_of' and pk.type_id = cv.cvterm_id and pk.object_id = fo.feature_id UNION ALL -- add parent feat ids for exons, etc. SELECT pk.subject_id AS feature_id, 'parent_oid' AS type, CASE WHEN pk.rank IS NULL THEN text(pk.object_id) ELSE pk.object_id || ':' || pk.rank END FROM feature_relationship pk ; GRANT SELECT ON gffattr_gmodel TO PUBLIC; -- seqlen/featloc-length view -- CREATE OR REPLACE VIEW feature_length ( feature_id, flength ) AS -- SELECT feature_id, -- CASE WHEN seqlen IS NULL THEN (fl.fmax - fl.fmin) ELSE fs.seqlen END AS flength, -- FROM featureloc fl -- WHERE fl.feature_id = feature_id -- ; -- attr view for match features CREATE OR REPLACE VIEW gffattr_match ( feature_id, type, attribute ) AS SELECT feature_id, CASE WHEN fs.is_current IS FALSE THEN 'dbxref_2nd' ELSE 'dbxref' END AS type, d.name || ':' || s.accession AS attribute FROM dbxref s, feature_dbxref fs, db d WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id UNION ALL SELECT feature_id, cv.name AS type, fp.value AS attribute FROM featureprop fp, cvterm cv WHERE fp.type_id = cv.cvterm_id and (cv.name in ( ${featureprops} )) UNION ALL SELECT feature_id, CASE WHEN fs.is_current IS FALSE THEN 'synonym_2nd' ELSE 'synonym' END AS type, s.synonym_sgml AS attribute FROM feature_synonym fs, synonym s WHERE fs.synonym_id = s.synonym_id and fs.is_internal IS FALSE ; GRANT SELECT ON gffattr_match TO PUBLIC; -- attrib view for cross-species feats (syntenic_region, orthology) CREATE OR REPLACE VIEW gffattr_synteny ( feature_id, type, attribute ) AS -- parent feat ids for source supercontigs, etc. SELECT pk.subject_id, text('parent_oid') as type, CASE WHEN pk.rank IS NULL THEN text(pk.object_id) ELSE pk.object_id || ':' || pk.rank END FROM feature_relationship pk ; GRANT SELECT ON gffattr_synteny TO PUBLIC; -- use this one instead of above CREATE OR REPLACE VIEW gffattr_synt2 ( feature_id, type, attribute ) AS SELECT feature_id, text('to_species') AS type, text(targ.organism_id) AS attribute FROM feature targ -- see above orthofix.pl: add case when this select is missing, use ortho featloc -- to find equal gene feature and putative_ortholog_of UNION ALL SELECT feature_id, text('to_name') AS type, CASE WHEN targ.uniquename = targ.name THEN targ.name ELSE targ.name || ',' || targ.uniquename END AS attribute FROM feature targ WHERE NOT( targ.type_id IN ( select cvterm_id from cvterm where name in ( ${golden_path} ) ) ) ; GRANT SELECT ON gffattr_synt2 TO PUBLIC; -- for analysis features -- problem where w/ some analysis features - promotor, transposon -- ? need to restrict armcv to cv_id = SO id - e.g. find chromosome in 4 cv's CREATE OR REPLACE VIEW gffatts_anfloc ( feature_id, arm, fmin, fmax, strand, organism_id ) AS SELECT armloc.feature_id, armft.uniquename as arm, armloc.fmin, armloc.fmax, armloc.strand, armft.organism_id FROM feature armft, featureloc armloc, cvterm armcv, cv socv WHERE armft.type_id = armcv.cvterm_id and armcv.name in ( ${golden_path} ) and armcv.cv_id = socv.cv_id and socv.name = '${seq_ontology}' and armft.feature_id = armloc.srcfeature_id ; GRANT SELECT ON gffatts_anfloc TO PUBLIC; -- for analysis features CREATE OR REPLACE VIEW gffatts_evid ( feature_id, type, attribute ) AS SELECT pk.subject_id, text('parent_oid'), text(pk.object_id) FROM feature_relationship pk ; GRANT SELECT ON gffatts_evid TO PUBLIC; ]]> chado-1.23/conf/bulkfiles/chadogenepagesql.xml000644 000765 000024 00000027732 11256707520 021533 0ustar00cainstaff000000 000000 Chado GenePage SQL This is GMOD Chado SQL for gene-page output tables; i.e., all the fields relevant to a gene feature needed to create useful gene page web and xml reports. May need several variants (brief, full, tuned to each project's use of chado tables to store data relevant to individual genes. Also want other main non-gene feature output SQL (e.g. transposons) See GMODTools/conf/bulkfiles/chadofeatsql.xml Use with GMOD genepages. Should be part of chadofeatsql.sql or not? -- add dbxrefprop output of all dbxref (type_id, value, rank?) -- add all *prop outputs ? (have featureprop) -- analysisprop.sql feature_cvtermprop.sql featureprop.sql -- cvtermprop.sql feature_relationshipprop.sql featureprop_pub.sql -- dbxrefprop.sql feature_relationshipprop_pub.sql organismprop.sql af.feature_id UNION ALL SELECT fd.feature_id, 'COG' AS field, (gd.name||':'||gx.accession) as value FROM feature_dbxref fd, db gd, dbxref gx WHERE fd.dbxref_id = gx.dbxref_id and gx.db_id = gd.db_id -- fd.feature_id = t.id and gd.name = 'IPC' UNION ALL SELECT fd.feature_id, (gd.name||':'||gx.accession) AS field, ((select name from db where db_id = (select db_id from dbxref where dbxref_id = fo.dbxref_id)) ||':'||fo.uniquename) as value FROM feature_dbxref fd, feature_dbxref fdo, feature fo, db gd, dbxref gx WHERE fd.dbxref_id = gx.dbxref_id and gx.db_id = gd.db_id -- fd.feature_id = t.id and gd.name = 'IPC' and fdo.dbxref_id = gx.dbxref_id and fdo.feature_id = fo.feature_id and fdo.feature_id <> fd.feature_id UNION ALL SELECT fd.feature_id, CASE WHEN fd.is_current IS FALSE THEN 'dbxref_2nd' ELSE 'dbxref' END AS field, (gd.name||':'||gx.accession) as value FROM feature_dbxref fd, db gd, dbxref gx WHERE fd.dbxref_id = gx.dbxref_id and gx.db_id = gd.db_id -- fd.feature_id = t.id and gd.name <> 'IPC' ; GRANT SELECT ON v_analysis_cogs TO PUBLIC; ]]> chado-1.23/conf/bulkfiles/dmelhetfeatconv.xml000644 000765 000024 00000026335 11256707520 021407 0ustar00cainstaff000000 000000 Chado DB Feature info Use this one for D.melanogaster heterochromatin genome db. These are configurations for converting chado feature table dumps to standard feature/sequence files. Much of below specifies how to process different features (tied to methods in ChadoFeatDump.pm These configs should be data-set independent. This works with, but is independent of SeqUtil2 configs. feature_table fff gff fasta pseudogene|\w+RNA 1 [-_](repeatmasker|genscan|piecegenie|twinscan|genewise|trnascan) ^(match_part|match|gene|cytology|chromosome_band|oligo|BAC|protein_binding_site) --> 0 mRNA protein,CDS,three_prime_UTR,five_prime_UTR protein exon exon three_prime_UTR five_prime_UTR protein CDS transposable_element:predicted tRNA:trnascan chado-1.23/conf/bulkfiles/dmelr420.xml000644 000765 000024 00000003671 11256707520 017566 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r4 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. ${release_url} ]]> fbreleases dmel Drosophila_melanogaster 'chromosome_arm' SO 'cyto_range','dicistronic','gbunit' FlyBase AND (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) AND NOT (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) chromosomes features analysis ests (FBgn|FBti)\d+ 0 chado-1.23/conf/bulkfiles/dmelr430.xml000644 000765 000024 00000006213 11256707520 017562 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r4 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. ${release_url} ${rel} adds * dpse genes - synteny info * dmel_mitochondrion_genome chromosome: renamed to standard Mt ]]> fbreleases dmel Drosophila_melanogaster 'chromosome_arm','chromosome' SO 'cyto_range','dicistronic','gbunit' FlyBase nonesuchfeature AND (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) AND NOT (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) chromosomes features analysis ests synteny (FBgn|FBti)\d+ 0 chado-1.23/conf/bulkfiles/dpsebulk-p4.xml000644 000765 000024 00000007751 11256707520 020372 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado Dpse r1.0.4 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, for data release r1.0 dpse Drosophila pseudoobscura 'chromosome_arm','ultra_scaffold' SO http://flybase.net${release_url} ]]> fbreleases 0 0 (FBgn|FBti)\d+ ^(chromosome_arm|golden_path|ultra_scaffold)$ ^(golden_path_fragment|golden_path_region)$ U chromosomes features synteny analysis gene CDS transcript translation gene_extended2000 intron intergenic syntenic_region chromosome chado-1.23/conf/bulkfiles/dpsebulk-p5.xml000644 000765 000024 00000010051 11256707520 020356 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado Dpse r2.0.1 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, for data release r2.0 dpse Drosophila_pseudoobscura 'chromosome_arm','ultra_scaffold' SO 'gbunit' FlyBase ${release_url} ]]> fbreleases 0 0 (FBgn|FBti)\d+ ^(match_part|match|gene|cytology|chromosome_band|oligo|BAC|protein_binding_site) ^(chromosome_arm|golden_path|ultra_scaffold)$ ^(golden_path_fragment|golden_path_region)$ U AND NOT (an.program in ('genewise','genscan','twinscan')) -- none chromosomes features synteny analysis gene CDS transcript translation gene_extended2000 intron intergenic syntenic_region chromosome chado-1.23/conf/bulkfiles/dpsebulk-r2.xml000644 000765 000024 00000006642 11256707520 020370 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado Dpse r1.0.3 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, for data release r1.0 dpse Drosophila_pseudoobscura http://flybase.net/${release_url} ]]> fbreleases 1 1 (FBgn|FBti)\d+ ^(chromosome_arm|golden_path|ultra_scaffold)$ ^(golden_path_fragment)$ U chromosomes features synteny analysis gene mRNA CDS transcript translation gene_extended2000 five_prime_UTR three_prime_UTR intron intergenic syntenic_region scaffold chromosome chado-1.23/conf/bulkfiles/drosmelgb.xml000644 000765 000024 00000006467 11256707520 020221 0ustar00cainstaff000000 000000 1 0 site_defaults DrosMelGb GMOD Bulkfiles; loaded from a NCBI GenBank chromosome record ]]> ${org}_${release_date} /genome/${species}/release-${release_id}.html dromel Drosophila_melanogaster Genbank sequence 'chromosome','chromosome_arm' 'Note','comment1','eC_number','exception', 'gene','locus_tag','inference','map', 'product','protein_id', 'transcript_id', 'standard_name', 'strain', 'transposon' chromosomes features matches analysis chromosome gene transcript CDS translation CDS_translation ncRNA pseudogene transposon & log.drosmel1 & # and genbank submit table perl -Ilib bin/bulkfiles.pl -config=drosmelgb -format=genbanktbl -debug -make problems: transcript : no db residues; reconfig to get froms eq ]]> chado-1.23/conf/bulkfiles/fastawriter.xml000644 000765 000024 00000002535 11256707520 020566 0ustar00cainstaff000000 000000 Fasta file writer Valid options include makeall = 1 ; produce species-all-release.fasta from chromosome parts perchr = 0 ; dont produce per-chromosome fasta (only if makeall) dogzip = 1 ; gzip result files; writeemptyrecords = 1; write ">header; ERROR missing data\nN\n" into fasta if no bases are found addmd5sum = 1; add MD5 checksum of sequence addcrc64 = 1; add SWISS/UniProt CRC64 checksum of sequence addids = "1" ; add comparable ID dbxrefs from feature data ; e.g. CDS,mRNA,... will get dbxref from genes, if flagged with add_id="1" in featuresets dropnotes = "synonym_2nd,synonym"; dont include these extra attributes in header allowanyfeat = 1; override featureset configs to include all basic feature types recodekey id={one of feature keys} value=header-key [ need 2 or more ] fff fasta synonym_2nd,Note,orf_classification Dbxref Name chado-1.23/conf/bulkfiles/fbbulk-hetr3.xml000644 000765 000024 00000005065 11256707520 020524 0ustar00cainstaff000000 000000 site_defaults DHGP/FlyBase Heterochromatin rel 3.2 ${release_url} ]]> fbreleases dmel Drosophila_melanogaster 'chromosome_arm' SO -- none -- none DHGP chromosomes features analysis (FBgn|FBti)\d+ gene transcript CDS translation ncRNA transposon gene_extended2000 pseudogene intergenic chromosome gene transcript translation ncRNA intergenic chromosome chado-1.23/conf/bulkfiles/fbbulk-r3.xml000644 000765 000024 00000003736 11256707520 020026 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r3.2.2 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. http://flybase.net/${release_url} ]]> fbreleases dmel Drosophila melanogaster 1 1 pseudogene|\w+RNA (FBgn|FBti)\d+ chado-1.23/conf/bulkfiles/fbbulk-r3h.xml000644 000765 000024 00000004477 11256707520 020201 0ustar00cainstaff000000 000000 site_defaults DHGP/FlyBase Heterochromatin rel 3.2 http://flybase.net/${release_url} ]]> fbreleases 1 1 dmel Drosophila melanogaster chromosomes features analysis (FBgn|FBti)\d+ chado-1.23/conf/bulkfiles/fbbulk-r4.xml000644 000765 000024 00000003660 11256707520 020023 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r4.0 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. http://flybase.net${release_url} ]]> fbreleases dmel Drosophila melanogaster 'chromosome_arm' SO 'cyto_range','dicistronic','gbunit' chromosomes features analysis synteny (FBgn|FBti)\d+ chado-1.23/conf/bulkfiles/fbbulk-r41.xml000644 000765 000024 00000007476 11256707520 020115 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r4.1 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. Update r4.1 notes: ? add in matches.sql, but need to filter out all the unwanted and dupl. to analysis.sql output. .. second look indicates no matches.sql features not in analysis.sql Basically have to check names against accept pattern list. 'prime', 'contig'? print if (/([.:])(5prime|3prime|contig)/); .. get dbx database attribute for match to use for filter? where? fix FROM feature matchft, feature armft, feature targft left outer join gffattr_match attr on (targft.feature_id = attr.feature_id), .. should it be 'feature matchft left outer join gffattr_match' to get dbxref ? Most feat types are 'match'; Mostly/only want EST/cDNAs - RE60666.5prime, LD02891.5prime and like ? Filter out the anonymous Genbank/Protein accession matches in analysis Contig2076_Contig2470 = dpse blast matches; also mosquitos filter out the 'sim4:wrap', and "RepeatMasker". filter out 'alignment' == HDC* types .. have same in analysis http://flybase.net${release_url} ]]> fbreleases dmel Drosophila melanogaster 'chromosome_arm' SO 'cyto_range','dicistronic','gbunit' AND (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) AND NOT (an.program = 'sim4' AND an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros')) chromosomes features analysis ests (FBgn|FBti)\d+ 0 chado-1.23/conf/bulkfiles/fbbulk-r411.xml000644 000765 000024 00000067706 11256707520 020200 0ustar00cainstaff000000 000000 site_defaults FlyBase Chado DB r4.1.1 Configurations to extract feature and sequence data for bulk files from FlyBase chado databases, including various release information. Update r4.1.1 notes: this release contains 1) Changes to gene models due to problems found in the GB-submission process 2) Fixes and additions of non-gm / non-gb-submitted data (eg, evidence, insertions, and I believe loads of ARGS data). http://flybase.net${release_url} ]]> fbreleases dmel Drosophila melanogaster 'chromosome_arm' SO chromosomes features analysis ests (FBgn|FBti)\d+ 0 chado-1.23/conf/bulkfiles/fbreleases.xml000644 000765 000024 00000011021 11256707520 020334 0ustar00cainstaff000000 000000 FlyBase data release definitions Use as include="fbreleases" to data release config file. Common release tags are: id="4" -- reference from release config file with relid="4" rel="r4.0t" -- release abbreviation (goes into filenames) dbname="dmel_chado" -- chado database name relfull="dmel_r4_0t_20040821" -- output folder name date="20040821" -- release date release_url="/annot/release4.html" -- release info url chado-1.23/conf/bulkfiles/featuresets.xml000644 000765 000024 00000010335 11256707520 020562 0ustar00cainstaff000000 000000 Chado Feature mapping info These are configurations for converting chado feature table dumps to standard feature/sequence files. Much of below specifies how to process different features (tied to methods in ChadoFeatDump.pm These configs are mostly data-set independent, but may need changing for some genome data sets. Used mostly now by Bulkfiles/FastaWriter.pm featmap for feature sets that need reprocessing, attributes: name = feature set name types = feature types, space delimited (in fff/gff) typelabel = type to use in output header, paired with types list subrange = expansion/extraction range to add to feature location; readseq syntax not yet supported, i.e. {start,end}+/-offset) fromdb = extract from chado database feature.residues field rather than chromosome dna file, for curated residues - transcript, translation) get_id = save id, dbxref fields for add to other (genemodel) features add_id = add id of parent feature (genemodel) note: translation type=protein is coded into various seq fetch programs gene transcript CDS translation ncRNA transposon pseudogene gene_extended2000 intergenic syntenic_region chromosome chado-1.23/conf/bulkfiles/filesets.xml000644 000765 000024 00000014403 11256707520 020046 0ustar00cainstaff000000 000000 Bulkfiles fileset definitions These are configurations producing bulk file sets. Use as include="filesets" to data release config file, or copy into primary config file and edit to taste. Note on overriding some of these: Use the 'fileset_override' option, currently, to replace one or a few of these settings, while including these defaults. Because of the way settings are read, any included ones will not replace main settings. The 'fileset' options become one large hash table. 'fileset_override' will replace one or more of these. Common fileset tags: id="fasta" -- name tag path="fasta/.+\.fasta" -- path regex for output files input="fff" -- input data (but see informat in other configs) config="tofasta" -- config file (depends on handler needs) handler="FastaWriter" -- perl module that processes fileset dropnotes="synonym_2nd,synonym" -- handler-specific tag makeall="1" -- handler-specific ( _all_ fasta files from chr parts) perchr="1" -- per chr files dogzip="0" -- gzip output files title="Genome feature sequence fasta" no_orgchr="1" -- files have no organism,chromosome naming chromosomes features analysis synteny chromosomes features analysis synteny organism_summary feature_summary analysis_summary property_summary chromosome_summary id_table ortho_table feature_map gbrowse_conf genomeweb overviewhtml go_association chado-1.23/conf/bulkfiles/gbrowseconf.xml000644 000765 000024 00000036725 11256707520 020561 0ustar00cainstaff000000 000000 Gbrowse conf generator
    Genome Browser: ${species}
    Release ${rel}; ${date} footer =
    For the source code for this browser, see the Generic Model Organism Database Project. 
    $Id: gbrowseconf.xml,v 1.5 2007-10-17 01:01:29 dongilbert Exp $
    plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper aggregators = processed_transcript alignment #fixme ... uploads = 1 #fixme ... default features = gene scaffold # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons tmpimages = /gbrowse/tmp help = /gbrowse/ # max and default segment sizes for detailed view max segment = 1000001 default segment = 100000 # where to link to when user clicks in detailed view link = AUTO title = sub { my $f= shift; return $f->method .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end; } zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 # colors of the overview, detailed map and key overview units = M overview bgcolor = lightgrey detailed bgcolor = lightgoldenrodyellow #panel property pad_left = 20 pad_right = 30 key_style = between key bgcolor = whitesmoke grid = 1 # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone language = en image widths = 450 640 800 950 1024 default width = 800 # Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = # Default glyph settings [TRACK DEFAULTS] glyph = generic height = 8 bgcolor = cyan fgcolor = cyan label density = 25 bump density = 100 overview label density = 160 ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [DNA/GC Content] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red axis_color = blue ]]>
     ref.":".$f->to_FTstring; $u =~ s/\?.*$//; $u .= '?name='.$r.";doexpand=1"; return $u; } ]]> name(); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } ]]>     chado-1.23/conf/bulkfiles/gbrowseconf_fb.xml000644 000765 000024 00000054320 11256707520 021217 0ustar00cainstaff000000 000000 Gbrowse conf generator

    FlyBase Genome Browser: ${species}
    Release ${rel}; ${date}

    footer =
    Adapted from GBrowse of the Generic Model Organism Database Project. plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper # GFFDumper - not as good as BatchDumper # OligoFinder - requires Bio::DB::GFF sql calls uploads = 1 #fixme ... default features = rev_ruler cytoband gene tRNA noncodingRNA pseudogene syntenic_region scaffold BAC transposable_element primary_feature = gene scale_feature = cytoband dumpviews = FastA GenBank GFF FFF dataviews = "Default" "Collapse All" "Expand All" # Web site configuration info help = /common/perl/gbrowse_fb/htdocs stylesheet = /common/perl/gbrowse_fb/gbrowse.css buttons = /common/perl/gbrowse_fb/images/buttons tmpimages = /tmp/gbrowse_fb # max and default segment sizes for detailed view max segment = 1000001 default segment = 100000 ## base range to expand around gene given ID lookup expand_by = 20000 zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 searchhelp = Search using Chromosome:base_start..end or FlyBase Gene ID. #panel property pad_left = 20 pad_right = 30 key_style = between key bgcolor = whitesmoke overview bgcolor = whitesmoke grid = 1 # put reversed features on same track or below ? mix_strand = 1 # # where to link to when user clicks in detaild view # # default dummy link to get popup title view link = sub { return "#"; } # link = sub { # my $f= shift; # my $d= $f->primary_id() if $f->can('primary_id'); # $d= $f->source() unless($d); # if ($d) { # if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } # elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; } # elsif ($d =~ /\-\w+/ ){ return '/cgi-bin/fbannq.html?'.$d; } # } # if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); } # return '' ; } title = sub { my $f= shift; return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end; } # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone # Default glyph settings glyph = generic height = 5 bgcolor = palegoldenrod fgcolor = cyan boxcolor = blue label density = 20 bump density = 50 overview label density = 160 image widths = 450 640 800 950 1024 default width = 800 width = 800 #---------- end [GENERAL] ------------------------ ]]>
     ref.":".$f->to_FTstring; $u =~ s/\?.*$//; $u .= '?name='.$r.";doexpand=1"; return $u; } ]]> primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d) { if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; } } if ($f->name()) { return '/cgi-bin/fbgenq.html?symbol='.$f->name(); } return '' ; } ]]> primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d) { if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } #elsif ($d =~ /^TE/ ){ return '/cgi-bin/fbannq.html?acc='.$d; } } if ($f->name()) { return '/cgi-bin/fbinsq.html?symbol='.$f->name(); } return '' ; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } [protein_binding_site] feature = protein_binding_site strand_arrow = 1 bgcolor = lightslategray fgcolor = lightslategray key = protein_binding_site citation = protein_binding_site (annotation DB ; Chado) keygroup = " Misc. Genomic features" link = sub { my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v; } ]]> primary_id() if $f->can('primary_id'); $d= $f->source() unless($d); if ($d) { if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; } elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; } } if ($f->name() =~ /^(\w+):(\w+)/){ return '/cgi-bin/fbannq.html?DBX='.$f->name; } return '' ; } #above DBX should go to swissprot et al web db ]]> name())?'/cgi-bin/fbannq.html?oligo='.$f->name() : ''; } ]]> name(); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//; return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v; } ]]> name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; } ]]> name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; } ]]>     chado-1.23/conf/bulkfiles/genbanksubmit.xml000644 000765 000024 00000024631 11256707520 021065 0ustar00cainstaff000000 000000 GenBank Submission table writer chadofeatconv feature_table genbanktbl dummy db_xref note cyt_map cyt_map organism EC_number db_xref name CDS transposable_element:predicted dummy_maptype parent instead typelabel = what to write in place of id type (protein -> CDS) hasspan = this feature has start,stop (e.g. gene, mRNA, protein) discard/cut parts that fall outside part(s) = array of kid types (e.g. exons, UTRs) making structure makepartsfrom = list? of parts to make parts from if not given (e.g. exons => cds) ]]> trnatype ncrnatype exon protein CDS five_prime_UTR three_prime_UTR intron exon exon type 1 exon 1 exon 1 exon 1 IDs ?? [NULL_Caption] Unable to find protein sequence CG17923.p01 SeqID must match protein_id in the .tbl file # ERRORS .val................ ERROR: valid [SEQ_DESCR.NoOrgFound] No organism name anywhere on this entire record. BIOSEQ: lcl|NC_004353: ra w, dna len= 1351857 >> change chromosome type to source type perl -pi -e's/1351857\tchromosome/1351857\tsource/;s/Drosophila_melanogaster/Drosophila melanogaster/;' drosmelgb-all-drosmelgb4.tbl WARNING: valid [SEQ_FEAT.IllegalDbXref] db_xref type GI is only created by the flatfile generator, >> drop all db_xref == GI: perl -pi -e's/db_xref\tGI:/db_xref\told_GI:/;' drosmelgb-all-drosmelgb4.tbl ERROR: valid [SEQ_FEAT.SeqLocOrder] Location: Intervals out of order in SeqLoc [(lcl|NC_004353:c53751-53434, c 53999-53817, c57083-56500, c61911-57142, c64403-63540)] FEATURE: CDS: plexin B CG17245-PA [(lcl|NC_004353:c537 51-53434, c53999-53817, c57083-56500, c61911-57142, c64403-63540)] [lcl|NC_004353: raw, dna len= 1351857] -> [ lcl|plexB.p01] >> this is probably revcomp error; put last first ... WARNING: valid [SEQ_FEAT.UnnecessaryGeneXref] Unnecessary gene cross-reference CG32005 FEATURE: CDS: CG32005-P A [lcl|NC_004353:111840-113903] [lcl|NC_004353: raw, dna len= 1351857] -> [lcl|CG32005.p01] >> 111840 113903 CDS protein_id CG32005.p01 gene CG32005 <<< is this the problem? product CG32005-PA ]]> chado-1.23/conf/bulkfiles/genomeweb.xml000644 000765 000024 00000026076 11256707520 020211 0ustar00cainstaff000000 000000 Genome Web docs These are configurations for creating web access to genome data files. Genome Data Sets
    In order to simplify the retrieval of common datasets, the Generic Model Organisms Database (GMOD) community has implemented a series of standard URLs. Each MOD {will/should} have an index page like this one describing the species and datasets that are available. Read more about the GMOD project at www.gmod.org.

    Use below links to choose among Sequence (FastA), Features (GFF), Summary tables and other bulk genome data. Select among species, feature type, chromosomes, data release versions.

    Available URLs

    /genome Display this HTML-formatted index page that contains links to each of the species available through common URLs.
    /genome/Binomial_name
    /genome/${species}/     		An index page for species "Binomial_name". This will be an HTML-format page containing links to each of the genome releases.
    /genome/Binomial_name/release Leads to index for the named release. It should be an HTML-format page containing links to each of the data sets described below.
    /genome/Binomial_name/current Leads to an index of the most current release, symbolic link style.
    /genome/Binomial_name/current/dna
    /genome/${species}/current/dna     		Returns a FASTA file containing big DNA fragments (e.g. chromosomes). MIME type is application/x-fasta.
    /genome/Binomial_name/current/mrna
    /genome/${species}/current/mrna     		Returns a FASTA file containing spliced mRNA transcript sequences. MIME type is application/x-fasta.
    /genome/Binomial_name/current/ncrna
    /genome/${species}/current/ncrna     		Returns a FASTA file containing non-coding RNA sequences. MIME type is application/x-fasta.
    /genome/Binomial_name/current/protein
    /genome/${species}/current/protein     		Returns a FASTA file containing all the protein sequences known to be encoded by the genome. MIME type is application/x-fasta
    /genome/Binomial_name/current/feature
    /genome/${species}/current/feature     		Returns a GFF3 file describing genome annotations. MIME type is application/x-gff3.
    ]]>     Bulk genome data Database: ${title}
    Species: ${species}
    Release: ${rel}, dated ${date} as ${relfull}
    ]]>     var release="${rel}"; var org="${org}"; var gzipped=false; // fixme config var csomes= [${chromosomes}]; var ftp_url="${ftp_url}/${species}/${relfull}/"; var http_url="/genome/${species}/${relfull}/"; function initform() { var cdiv= document.getElementById("csomes"); // DOM var content=""; for(var i = 0;i < csomes.length;i++) { var c= csomes[i]; content += ""+c+" ..\n"; } content += "or All\n"; //? cdiv.document.write(content); cdiv.innerHTML= content; return false; } function radioval(radio) { for(var i = 0;i < radio.length;i++) if(radio[i].checked) return radio[i].value; } function opendata(via) { var fm= document.forms["datachooser"]; var region= radioval(fm.elements["seq_region"]); var format= radioval(fm.elements["seq_format"]); var type = radioval(fm.elements["seq_type"]); var filename = org +"-" + region; if (format == "fasta") filename +="-"+type; filename +="-"+release + "."+format; if (gzipped) filename +=".gz"; var fullurl= (via == "http")? http_url: ftp_url; fullurl += format + "/" + filename; fm.elements["URL"].value= fullurl; window.open( fullurl, "download"); return true; }
    Select Format, Feature Type and Sequence Region below and click on a Download button to get data
     
           
     
    Format   Sequence (FastA) Features (GFF)  
    Feature Type (for FastA)
    Protein-coding Gene Transcript Protein CDS
    Gene region +/- 2000bp 5' UTR 3' UTR Intron
    Transposable Element tRNA misc RNA Pseudogene
    Sequence Region
    Chromosome arm
    2L .. 2R .. 3L .. 3R .. 4 .. X .. or All chromosomes
    URL:
    ]]>         chado-1.23/conf/bulkfiles/organisms.xml000644 000765 000024 00000005405 11256707520 020234 0ustar00cainstaff000000 000000 ^(\w)[^_]*_(\w{1,3}) ^(\w{1,3})[^_]*_(\w{1,3}) Table of organism species, abbreviation-id values. Cannot assume chado organism table has values we need. Can optionally add other attributes here. Note that species == Genus_species; all spaces are underscored. chado-1.23/conf/bulkfiles/sgdbulk.xml000644 000765 000024 00000010335 11256707520 017663 0ustar00cainstaff000000 000000 1 site_defaults SGD Lite ${release_url} ]]> & log.load # extract bulk files from database cd GMODTools perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make # if failed perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make -debug \ |& mail -s gmodtools-debug gilbertd@indiana.edu Find worked examples from Bulkfiles SQL use now at http://www.gmod.org/Sample_Chado_SQL ]]> ${org}_${release_date} /genome/${species}/release-${release_id}.html scer Saccharomyces_cerevisiae 4932 'chromosome' 'Note','orf_classification' SGD Sequence Ontology Feature Annotation The golden_path, seq_ontology and species variables are critical. See bulkfiles_template.xml for further documentation. 0 chromosomes features matches analysis chromosome gene CDS_translation ncRNA transposon gene_extended2000 intergenic chromosome gene CDS_translation ncRNA intergenic chado-1.23/conf/bulkfiles/sgdbulk1.xml000644 000765 000024 00000012616 11256707520 017750 0ustar00cainstaff000000 000000 site_defaults SGD Lite rel 1 & log.load # set root path to here and make bulkfiles env GMOD_ROOT=$PWD ARGOS_ROOT=$PWD \ perl -I./GMODTools/lib/ GMODTools/bin/bulkfiles.pl sgdbulk1 ]]> scer Saccharomyces cerevisiae chromosomes features chromosome gene CDS tRNA miscRNA transposon gene_extended2000 intergenic connect( dbi:Pg:dbname=sgdlite_20040519;host=localhost;port=7302 ) do sql views view sql dump chromosomes feature_table /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/featdump/ chromosomes.tsv sql dump chromosomes n rows=17 sql dump features feature_table /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/featdump/fea tures.tsv sql dump features n rows=22573 sortNSplitByChromosome: dumpChromosomeBases /bio/biodb/flybase/data2/fban/sgdlite_20040519/dna/scer_chrI_dna_sgdr1.raw ... makeFiles: outformats= fff gff fasta openInput: type=feature/table part=0 openInput: name=chrI, type=feature/table, /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/fe atdump/chadofeat-chrI.tsv # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/fff/scer_chrI_sgdr1.fff (append=0) # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/gff/scer_chrI_sgdr1.gff (append=0) # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/fasta/scer_chrI_sgdr1.fasta (append=0) putFeats n=11, total=11, oid1=126750 open dnafile /bio/biodb/flybase/data2/fban/sgdlite_20040519/dna/scer_chrI_dna_sgdr1.raw, length =230210 putFeats n=17, total=25, oid1=126761 processChadoTable ndone = 1737 openInput: type=feature/table part=18 openInput: nothing matches part=18 makeFiles: done ]]> chado-1.23/conf/bulkfiles/sgdfeatconf.xml000644 000765 000024 00000017006 11256707520 020515 0ustar00cainstaff000000 000000 Chado DB Feature info for SGDLite db Configured for SGDLite feature usage These are configurations for converting chado feature table dumps to standard feature/sequence files. Much of below specifies how to process different features These configs should be data-set independent. This works with, but is independent of SeqUtil2 configs. feature_table fff gff fasta 1 CDS,exon,ncRNA gene gene CDS CDS intron CDS intron ncRNA intron ^(gene|match_part|match) CDS:SGD match:fgenesh match_part:fgenesh match:HDP match_part:HDP match:RNAiHDP match_part:RNAiHDP mRNA:genscan mRNA:piecegenie tRNA:trnascan chado-1.23/conf/bulkfiles/site_defaults.xml000644 000765 000024 00000006140 11256707520 021062 0ustar00cainstaff000000 000000 Site Default settings for GMODTools This is a configuration file for GMODTools Bulkfiles which can be included into data release configuration files. Enter common settings, include other portions of the configurations settings here. Simple tags that go well here: ROOT = where the base path for data is datadir = sub directory from ROOT ftp_url, web_url = used in output documents verbose = show these 'about' comments. Using 'include' options in the xml configurations will add these to main configuration, but not replace main settings. Includes can be nested. This is an example setting for database access. If your system defines the values in gmod.conf, they will be used. If you dont use thse CHADO_ from gmod.conf, change above db settings. overview fff gff fasta tables go_association blast ARRAY of default output files. Generally each of these has a Bulkfiles::BulkWriter perl subclass, and xml configuration. fileset details these, including the Perl handler. ${release_url} ]]> doc tags are generally printed to files id= name, file name unless path given path= path to output file. A few common tags can be used as inserted ${variables} ${org}_${release_date} /genome/${species}/release${release_id}.html 1 This flag turns on extra help and checks. Set 0 if you are tired of seeing them, or the time they take. organisms List of species and their abbreviations. Include your species. filesets How to make bulk files. featuresets What feature sets for bulk files (esp. fasta sequence) and how they are grouped from primary features. chado-1.23/conf/bulkfiles/site_eugenes_defaults.xml000644 000765 000024 00000001512 11256707520 022573 0ustar00cainstaff000000 000000 euGenes Site settings for GMODTools organisms filesets featuresets overview fff gff fasta tables blast chado-1.23/conf/bulkfiles/spbase.xml000644 000765 000024 00000011170 11256707520 017503 0ustar00cainstaff000000 000000 1 1 site_defaults SpBase SpBase spur Strongylocentrotus_purpuratus sequence 'supercontig' 'Note','orf_classification' chromosomes features matches analysis chromosome gene CDS_translation ncRNA transposon gene_extended2000 intergenic chromosome gene CDS_translation ncRNA intergenic chado-1.23/conf/bulkfiles/spbasefeatconf.xml000644 000765 000024 00000036645 11256707520 021227 0ustar00cainstaff000000 000000 Chado DB Feature info These are configurations for converting chado feature table dumps to standard feature/sequence files. Most of these configs specify how to process and convert various features extracted from chado db. These are tied to methods in Bulkfiles::FeatureWriter.pm) Tags with OLD_USAGE_ are depreciated settings (no longer active). feature_table fff gff fasta 0 1 [-_](repeatmasker|genscan|piecegenie|twinscan|genewise|trnascan) ^(match_part|match|gene|cytology|chromosome_band|oligo|BAC|protein_binding_site|rescue_fragment) 1 0 mRNA protein,CDS,three_prime_UTR,five_prime_UTR protein CDS parent instead typelabel = what to write in place of id type (protein -> CDS) hasspan = this feature has start,stop (e.g. gene, mRNA, protein) discard/cut parts that fall outside part(s) = array of kid types (e.g. exons, UTRs) making structure makepartsfrom = list? of parts to make parts from if not given (e.g. exons => cds) ]]> tRNA exon protein five_prime_UTR three_prime_UTR intron CDS five_prime_UTR three_prime_UTR intron exon transposable_element:predicted match:fgenesh match_part:fgenesh match:HDP match_part:HDP match:RNAiHDP match_part:RNAiHDP mRNA:genscan mRNA:piecegenie tRNA:trnascan chado-1.23/conf/bulkfiles/tablewriter.xml000644 000765 000024 00000001356 11256707520 020557 0ustar00cainstaff000000 000000 Summary Tables Valid options include makeall = 1 ; produce species-all-release.fasta from chromosome parts perchr = 0 ; dont produce per-chromosome fasta (only if makeall) dogzip = 1 ; gzip result files; fff id_table ortho_table feature_map gbrowse_conf genomeweb overviewhtml chado-1.23/conf/bulkfiles/toacode.xml000644 000765 000024 00000002547 11256707520 017654 0ustar00cainstaff000000 000000 Gene acode objects Valid options include addids = "1" ; add comparable ID dbxrefs from feature data ; e.g. CDS,mRNA,... will get dbxref from genes, if flagged with add_id="1" in featuresets dropnotes = "synonym_2nd,synonym"; dont include these extra attributes in header allowanyfeat = 1; override featureset configs to include all basic feature types fff chromosome|golden_path\b|source|misc|match|motif|sim4 oligo|processed|protein|repeat|regulatory_region|repeat_region ^(gene|pseudogene|\w+RNA) ^(mRNA|CDS) [A-Z]{2}gn\d+ [A-Z]{2}an\d+ ^(FlyBase|Gadfly|GB_protein|GO): chado-1.23/conf/bulkfiles/tognomap.xml000644 000765 000024 00000004504 11256707520 020055 0ustar00cainstaff000000 000000 Genome Feature merge (genomic and cytology features) These configs help merge two or more fff feature sets for use with gnomap,gbrowse(fb) and such feature file uses Add these to per-release-db configs. Cut from mergeflyfeats4.pl and .xml config, d.gilbert, aug04 _fragment|_junction|_mutation|_peptide|_UTR|_variant| chromosome|golden_path\b|source| enhancer|EST|cDNA|intron| misc|match|motif|sim4| mRNA|CDS|oligo|processed|\bprotein\b| transcription_start_site|protein_binding_site| polyA_site|\binsertion_site| repeat|regulatory_region|repeat_region ^(gene|pseudogene|\w+RNA) [A-Z]{2}gn\d+ BAC ^(FlyBase|Gadfly|GB_protein|GO): fff dna chromosome_band remark source chado-1.23/chado-xml/examples/000755 000765 000024 00000000000 12061672376 016276 5ustar00cainstaff000000 000000 chado-1.23/chado-xml/README000644 000765 000024 00000001675 11256710157 015344 0ustar00cainstaff000000 000000 Chado-XML ========= Chado-XML is a direct mapping of the Chado relational schema into XML. Currently the only tool for performing this mapping is XML::XORT, which can dump or save Chado-XML to and from a chado db. Contents: -------- chado-xml/ README xsl/ -- useful transforms dtd/ -- DTDs/XSDs defining the xml model examples/ -- example XML files The current documentation can be found at gmod.org. See: SourceForge: http://sourceforge.net/projects/asciidoc/ Main website: http://www.methods.co.nz/asciidoc/ Macros ------ The basic chado-xml expansion can be extremely verbose - this is because chado-xml uses the unique keys from the chado db, yet it does not database internal foreign keys. Macros can be used to capture repeated nodes in the xml and give them XML IDs that are valid within a particular document. See also -------- gmod.org/XORT chado-1.23/chado-xml/xsl/000755 000765 000024 00000000000 12061672376 015266 5ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/chado-create-feature-nesting.xsl000644 000765 000024 00000002607 11256710154 023430 0ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/chado-expand-macros.xsl000644 000765 000024 00000002711 11256710154 021624 0ustar00cainstaff000000 000000 No such ID: chado-1.23/chado-xml/xsl/chado-insert-macros.xsl000644 000765 000024 00000010457 11256710154 021657 0ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/chado-remove-analysis-features.xsl000644 000765 000024 00000001413 11256710154 024013 0ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/chado-remove-default-elements.xsl000644 000765 000024 00000001532 11256710154 023614 0ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/chado-remove-feature-nesting.xsl000644 000765 000024 00000002657 11256710154 023467 0ustar00cainstaff000000 000000 chado-1.23/chado-xml/xsl/README000644 000765 000024 00000001324 11256710154 016136 0ustar00cainstaff000000 000000 chado-xml/xsl ------------ XSLT programs for transforming Chado-XML - either into other formats, or other Chado-XML forms (eg with or without macros). See: http://www.w3.org/Style/XSL Running an XSLT transformation ------------------------- You can use any xslt processor you like with these; both Xalan and xsltproc can be run from the command line. For integrating with an application, you can use Xalan (java) or Lib::XSLT (perl). Xalan can be downloaded from http://xml.apache.org/xalan-j xsltproc is part of libxslt, available from http://xmlsoft.org/XSLT/ To run on the command line with xsltproc: $ cd gmod/schema/chado/chado-xml $ xsltproc xsl/chado-insert-macros.xsl examples/CG10833.expanded.chado-xml chado-1.23/chado-xml/examples/CG10833.expanded.chado-xml000644 000765 000024 00000116355 11256710157 022561 0ustar00cainstaff000000 000000 <_appdata name="title">CG10833 <_appdata name="arm">2L <_appdata name="fmin">5205478 <_appdata name="fmax">5217450 <_appdata name="residues">AAGCTAAATTTCAAGTAAGAAAAATTTAAACAAAAAAATGTTGAATATCGAAATGGAAGAGTTGTACATTTGTGTAGTTTATCACATTTTGTAATTGTATGTAATTTTATAGTCATTCGATAGCTAGAGGCATTAATAAAACAACCAATTTGTATATAACCTACTGAACCGAACAGACTCGACAAGCCGAACATGAAACACGTAAAAGAATTAAACAAAAAAATAAAAAGAAACAGAATGAACTAACTATTCAAACTAACGACAAGTAACCGAAACCCTTTTGTAAAACGATATATACATTATACATATATATTTGCACAGCAAACAATTTATATATTCATATATACCCACGTATATGATCCCAAAAAAACTATAGAGAACCCAAACATTTTGTATATAAAAATATCTAAGCTAAAACGAAATCAAAATACGCACACGAACATTTTACTCATCAACGCACGTTTTCGCATTTAGAGAGATCCTGGGCAGCAGAAAATTGCGATTAGCATCCTGCCAATTTCGTGGAACATTTTCGCAGGATATGATCTCAAGTTCCTGCTGCCAGCGATGGGCTAGAAAGGCAAACGAAATCCCAAGACAAAATCATGACCCACATAGACCAATCGCCTGGAGATCCTCATGGCAACCAATGTTCCTAGTTTCCAGCGCGTCCTTCTCCCAAACTCAGGGCTATGCTGTCAACAGTGGGCATTGACCTCCATTTGGACTCCGGCTTCTAAAGAGACCCCGTGTCAAGAAGGATCACTCTACCCAAGGCCAAGATCTCTCCCACGGCCAAGGGTTAGATGGGATAGCAGCCAGTGCGCCAGCCACAGGTCACTGGGCTCGAAATCAATCCTTAAACTCCATCCCGACACTGGGGCCTAGACATTTCAAGCATTCCTGATACTCATTTCCAAATTACCAATAGACATTGACCATCGAAGCCAGCTCTCAAAGAAAAGAAAATGGAAAACGTGCGTGCCACGAGCATTGAACAAAACGAAGCAAGTGTCCTATGCCGGTGCTAAACCAACCTACAAATTTTCTGTATAAAGAAAAAATGTAAAATGCGTATACAAAAAACAAAAATATTATGAATTCATAAAAGAAGAGATTAATTCTTTGAAAAAAAAAAATCGTAAAAATGCAATATGCATATTGACAAGTGACGTAAGTCCATCCAGTAAAAGATACCTATTTTGTTGTTAATATTTTTTGATAATCCTAATTATATTTGCCTTATACTTATCCAACTTGTTTATTACAACTATTTTCTATTATTTAATGCTTGGCCAATTATTATTGAGAAAATACATACATTTATTTATTAGGCCTATGAACGATTTACTATGTATAAAATTAAGTTTGATTTAAATGTTAAATTTGTGTACTTTGCTGCTTCTATCTGGTTATGAAATAATTAGCCGTTATCGAGTTAATATAATTTATGTAGCATTTTAAGATTTCCTTTCTTGTGAACAACTGTACCTTTATATGCATTATGATTATTAAAAAAAAAAAAAACAAATAAAAAATAAAACACATTGTTTTTTTTATACCTTTGAATTTATGTCTGCAGCTCTATTGACATAACTATATACGTTTTGGTTTTACAGGTTTCATGCTTATCGATATTTTATTACCTATCTTGTTTAATTGACTTTTGATCGAGCGCTACGAGATTAATGCAATCAGACTAAAAAAAAACAAACAAATTTTAAAAGAGGAAATTTATTAAAATACGATTAGATTGCTTCCAGCGCGTGTCTATTTTTTTGGCATAAATATAGGCCCCTGCGTTAATCTGTAGCCCATAAGCTTCCAACATGTGCCCAGTAACTACATTTCTTGTCCTCGTGCTGACCCTGTTGGTTCTGGTCTACGTGTTTCTGACATGGAACTTCAACTATTGGAGAAAACGTGGCATCAAGACGGCTCCCACATGGCCATTTGTTGGAAGTTTTCCCAGCATTTTCACAAGAAAGCGAAATATTGCCTACGATATTGATGATATCTATGAGTATGTATACAATATGAGTGAGAAGGGCAAGCTATAGTTATGTTGTATAATAGTGGAGTCAAAGCGCAGTTTATACTTAATGGGTGTAAAAATCAGAACAGTCTTCTCTAGAGCTAATATAAGTTACTTTTTGATGTGAACTTTTTGTTTTTGCAGAAAGTATAAAGACACGGACAATATGGTGGGCGTTTTTACCACCCGAGTGCCCCAATTGCTGGTCATGTGTCCGGAATATATACACAAGATCTATGCAACCGATTTCCGTAGCTTTCATAACAATGAATGGCGTAATTTTGTAAGTACTCGTAAGTTTAGTAAATAATGGATAATCCATTACTGAATTACAATGTTCATAGGTGAACAAAAAGACGGACATGATATTGGGCAACAATCCGTTCGTGTTAACTGGCGACGAGTGGAAGGAAAGAAGGTCGGAGATCATGCCAGCACTGTCCCCCAATCGAGTAAGGAACCACATTAACCATCTATCCAATCAAAATTCTATCTTTGAATTCCGTAAGGTCAAGGCCGTTTATCCAGTATCGCAGAGCGTATGCAAAAAGTTCGTGGAATATATCAGGCGACAGCAGCAGATGGCCACCTCCGAGGGATTGGACGCCATGGATCTGTCTCTTTGCTACACCACCGAAGTAGTTTCCGACTGCGGACTGGGAGTATCGGCCCAGAGTTTCACGGACACTCCCACGCCGCTGTTGAAAATGATAAAGCGTGTGTTCAATACCTCCTTTGAGTTCATCTTCTACAGCGTTGTTACCAACCTGTGGCAAAAGGTGCGCAAGTTCTACAGCGTACCGTTCTTCAACAAGGAAACGGAAGTGTTCTTCCTGGACATCATCCGGCGATGCATTACTTTGAGACTGGAAAAACCAGAGCAACAGCGCGACGATTTCCTCAACTATATGCTGCAGTTGCAGGAGAAGAAGGGCCTGCACACGGATAACATCCTGATAAATACGATGACCTTCATTCTAGACGGATTCGAGACTACGGCTCTAGTTCTAGCGCATATTATGCTGATGCTGGGACGTAATCCGGAGGAGCAAGATAAGGTCCGCAAGGAAATTGGCAGTGCGGATCTGACCTTTGATCAAATGTCCGAGCTTCCGCATCTGGACGCCTGCATATATGGTGGGAAATTCTATCTTGATCTCTTGATATTCAGTTTCTTTAACTACATTATAAAATTTTATAATTTTAGAAACTTTGCGTTTGTTTTCACCGCAAGTTGCAGCACGTAAGCTGGTCACCGAACCCTTTGAGTTTGCGAACAAGAACGGACGCACTGTGCACTTGAAACCCGGAGATGTGGTTACTATACCGGTAAAAGCTCTGCACCACGATCCGCAGTATTATGAGGATCCTTTGACATTCAAGCCGGAACGTTTCCTTGAGAGCAATGGAGGTGGTATGAAAAGTTACAGAGACAGGGGTGTTTACCTAGCTTTTGGCGATGGACCTCGTCACTGTCCAGGTTGGTGTTATAAAAATTTATCTGAAAATCACATACTACAATAAGTCGATCTCTACATTTAGGAATGCGATTTGCGCTGACTCAACTTAAAGCAGCTCTGGTGGAAATCTTGAGGAACTTTGAAATCAAGGTTAATCCTAAAACCCGCTCGGACAATCAGATAGATGATACTTTCTTCATGGCCACCTTGAAGGGTGGTATTTACCTGGACTTTAAGGACCTTTAAATAATAGCAATAATCATAGTAAGCTTTAAGCTTAAAAAACTGGATAAAGAGAAGTTGTTTGCTCGAAATAACAAAAATTAAAATTAACCTTGATTAATGCATGATAATAAAAAAAAAATAAAATGCAGTAGAGATTTATTACTCAAGAAAGGCAAATGTTGCGGATGATCCACAACAAGGCTCGATCGAACATGGTTCGACAGTGATGTTGCATGCGCAACAAGTTCGATTGCTAGTGCGCAACATGTCGGTTGTAGGTTGGCCATCCGATTTTAAATACTTGCAAGATATAAGATTTAATTGAGATTTTATAATAAAAAGTAATAAGAATTATAGAATTATAGATCAAGGGGTGTATAAAGAATATAAAGAAATCGATTCACCATCATAGGCATCTCAAGGCTCAAGCTCAAGGGCAGTTTTGGTGGAGATCGTAAGAAATTTCGAAATCAATGTAAACGTCAAGACGCGATCGGATAATCGACTGAATGACATCTGCTTGACGTATTTTGAAGAGCGATAGTAAAATGGCTGAAGTGTTGTTGTAAGTGTTGATAAGATAATGCGCCAATTAAAAATGAAATCAGAAATTTGATTAACTACTTAGGTGCTACACACATTGTTTGTCCAGAGTATCTATACCCATTACTCGTTAAATGAAAATGGGTATGTTGTATTCCTAGAAAAGTATGCAACTGATAGATGGACCTTCTGAATACGACACATTGTTTTTTGTTTTCATCAAGCATCGCACTTTGCAATCCTACTTATTTATTTAAAAGTCGATACATTGCTATTTTTCCTTTAATTGTTTATGGTTTATGTATATGTCGTTTAATTTCACAACCGTTTATTCCATTTCTCTATGCTACTAAAACCGTTCCCTTAAAACACATCTTTATCTGCGTGCTTTAGATACATATGCCATGTACAATAATTGTAAGTTTGAGCACTTAGTGAAATGACAAGCTGAAAAGTTCTGTTTCATCGTCATATCATAAAATGGCTTTTCTTAACAGTTTTTGTACTACTACTTTGTGGCGCATGACCTAGGACTAGGTATATTGTAGCCCCTTGATCTTGATAACGAAATCAGGCATTATCTTCAAATGGTGCAATTTTATATACGACAAATATTAACAGCGGTGGTGAATGCAATTTGATCAATTTGTTTACTGGGTGAATCCATCCACTTGACTGGCGCGCAAGTTCAATTTAAATGACTGCGGCAGCTCAATTGAGTTCCAGTTGGTTTTCATCCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGTAAGTGTATAGAGTTAGCTACGTTATCTGGTTACTGATTGCATCATCTCATTAGGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTGTGAGTAGATTGCAAATACATACTGGTCTTAGGAGCCCATTTCATAAGTTAATTCACACAATAGACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTAAGCTTAGGTTGCCCTCGAATTGTTTATTCAAAACTTATCTCGTGCTAATGTTTATTTTCACTGGGGGCCCTGATACCCTTATCAATTGAAGTGCTCCAATCAATTAACGCTCTGCCTCCCCAAAAGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGGTGAGTTTTTTGGCGAAATCTGAAGTTATTTAGTATGCGTATAATATCTATATCTGCAGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTGGGTAACATCATTTTTGAAACAATTAAAGTTACTAAAAAAAATCTATGCATAATTTGTAGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACACTCTTAATACTTTAATTTTGTAACTTAAAACCACACTTTTAGTCTCGACTTAGGGCTAGTTGCACTAGGGGCAGCACCTTGATAGAGGACAAGTCTGCCAGAATCGCTTCGATGCTATCCAACGAGGCCACCTGCATGATGCTCTCCTTTCGAAAGCTAAGAATGATGATGGCGAATAGAGGAAGGATCTCCAAGCTATCAAAGCCAAGGATCTGAAAAGGAAGGGATAAGTACTGCCAATAAGAACGGAGGTGTATTTCGTACCAGATCCCAGAGGACCAGCAATTGATCGGGAGGCAAATGTCCGGAAAACGCTCGCATAAGCCATTTGAAGACCACCCGCAGGCTAAGGAAAGATATGTCGTGAAATGGGTGAAATAGCTGTCTAACGAAAAACCCAATCCCAACTCACGGCTGTATCTGAAGCTCTCGGAAATGGGACCATAACTGCGGTTCGTATGTCTGCAGCAGCTTCTCGAAGAGCAGGCACAGACTGACAATCCCTTGAGGATGCGTGTTTATGGTGGTCAAGCGATGGCAGTACCGGATATAGAAGGCCCGGAATGTATAGTATAGACTCACCGGCGAGTCATACAGATAACAAAAGGGGGCGGCAAACATGCAGATGCCGTGGAAGGGCACCACACCCGATGGAGGACCTTCGTAGGTCTTGCCCTTCACCGGAAACGTCTCGTATTCCACACATCCACCGATATCGGTGTCCCGAGAAAAGCAGAGCAGCACCTGGTAGAGCACGTCCTCGAACACAAAGTACTGGTCGTCGTTGGAGGCCGTCAACTGAATGTCCTTGAAGACCAGTTTGTCAACGATGTGATCCGTAGTCCAAACGGCATTGCGCAGCTTTTGCCAGTACTCAATATCCTTCGGGGGTATAGAGATGTATAATGAGGTTATTGATCCCAAAATCAGTAGTTACGTAGTCATGTAGCTTGCTGTCCAGCACCGAAGCCCAGAGAGCTCCCCTATAAGGTGCGGGTGTGCAGCCCTTCTTCAGAAACTGCTGGCACATGGGCGCATGCCTGGCCTCCAGAATCCTCTGGCACTGAACCGTAAGATCCGGCACTCCCAAATAGCTATCACTTCGCAGCAGATCCGCGTAGTGGGCACGCAGCTCGAAAAGATTTTTCACAGGTAGTGCAATGTGGGAGAACTCCCATTGGGGGATTTGACTAATGAGCAAAATGATTATTTACCTGACTGATTTAAACCAAAACTTACTCTGTATTTTCAGTGGTTTTGGCGGGTCCTTTTAGCGAGAGTAGCACCTCCAGTAAATCCTTTGGAGCGTAAACAGGCCTATAGTTGGCCAGATCTAGAAGTTTAACCATGGTTAATTGTTAGCTTCAATATTTACGAAATGCCTACCCATATTGTAGTTGCTCAGTTCGTTCCACTTGGCCATAAAGTCCTCGCGATCAGCACTGATCCTTGGTTGTCCATGCAATGGAACCTTCAGCTCTGTACACATGGCATTCAAACTCTTCCTAACCCTTCGATCCCAAAGCACACCAGCTCTTTTTAAATATCCAAGTGGATCACTAACGGTGGGTTTCTATTGGAAAATATAGACATAAGTAAAGAACTATTTAATTCATTTTCCCTAGCACTACATACTACTAATACCCCTAAGGCTAACTCTATAGTTGTGGCACTTCGAGATCTTCCGGTATTATGTATCATTATAATTTGTTTTATAAACGTTAAGGTATAAAATAAAATTTTGCCAATAAAGTCAAAAAGTAGAAAATGATAGGAGCAGCATGGAATACTTTTAAATACCACTCCAATTATTCTAAATTCAATTACAAGAAATTTGATAAATTGTATCTTAAAAGTTGTACCCACCGCTCCCTGTTTGTTGGCCAGGTTTTTGTCATCTGTTTTCGACAGCCGCGTGCGGACCAGGTTGTAGACAATATTCCGGATCTCCGTCTCCAGTCCGGCGCTCTTGATGGCATCCTCGAGGGTGTTGCGCATATCGTGAGTATCTACGCTGGGATTGCAGACCAGCTTCTGCAGCTCCTTGTAGATGGGCTCGTAGCTCTTAGTGTTCTTGATGGCCGCGATTACCTTTGCGGTCATATGGTGGATGCTGGCATCCTGCAGCTCCTCCATGCCGATAGCTCCTTGACCCGACCGTTCTTTCTACGTATTACTCTGCCACTGACTACCAACTAACTATTTACACCGTTTTGATACCGATTAGCCCCAAAACTTTGGGCGCTCCTAACTCCGTCGTTTGACTTTTATCGATCAAACTCCGTCGCCTGCTTTGATTTGGAGTCGATTCGATTCCGAGTCACATCCTCGGTTGTCGTCGCTTCTTGGCGACGGAATGCAAACACTTGTTTGGCTGCTAGTTTCGCGTTAGTTGTGATTTGATTCGTTCGTTTTGCCGCCCCTCGCAACCAAGAAATTCCATTATGTTTCGTTTCGAATGAAAAGCCAGAGGCGCGTGAAATTGCTTTCCATATACATTTATTTTCACGCACACCGAAACACGCTGAAACTGAAACTGAGTGGCGGCAACTTTTCCTTTTTCTTGGCATCTGTCACCTGGCCCAACGAGTTGTTGACGTGGTCGTCGGGTTGGCTCCTCCTGTTGATTGCGAAGGTGGGCCAAACTCACCTGAACATGTCAGAGTGTCGAAAGTATTTCACCTGAATATTTAGACCAGGCCGAAATATGATTTTGAAATGGCAAAAATTTTTACACGAAAATAGAGATATATAATCCTCTATGTGGTACATTATTCAATGTTTATTTATGAATTAAAAATATTCGTTTTAAGATTTGGATAGCATCCCTTACTACGTTCCAATCAATTTATCTATAATATCATCGTTCACGAAAGTTCGACCTTTTAGTTGGCGGCTTATTGAGGTAAAGTTCTCTCCCTTGGCATAAGGAGGACCATTATTGGTATCCAGAAAATACCTGCCTCTGGCTCTGCAATTAAATAGATAAAAAGAGATCTGGAAAAATAGGTGCTGGCACTTACTTCGGATCCACGTGAAAACCCATCAGCTCTATATTTTTATCAGGAATGCAAATTCCCTTTGCGAAGCTTTTAAAATTGGGACAGTAGAAGCCATAGAATCCAGAAGGTGACGAAATAGACTCGGCATAATAGTCTGCTGCTCGGTTATGGTAGCAGAAATGAGTCTCCACTAAAGTCAGAACAACGAAAATGAAAAATATAGGTAAAGCAGATGGCCTTAATATTACTAACTCTTATTAATGGGTCCGCAGTTGGGCTGTGATACACCCATGTTCAAGTAGAAGTCCACGTGACCCACTGCATCCAGTAAGCCAAGCATCGTGACATCCGTGTGCACGACGTCCACGAACTTGGCATCAGTGGGATCGAGCTTTAGAGCCGGATCCTTGACCATGTAAAATGGTTTTGCCGGATCGAGGGCTGTAATATGCTCCAGCTTGTGTTCCGGAAGAAACTGCCCAATGAAGCCTGCGACATGGGCACCTAAGCCCAAGCCAATTAGGTGCAGATCCTCAATTTTGACCAATCCGCTCTCGAGGAGTACTCGTAGCAACTGAGCAGTACAGCGAGCTACGTATTTGGCATTGTGCACCGCTTCCGTATAGCAGGGTTCATAGGCTAGTTTTGGATAATCCAAGGATATCAAATTGTAATCCTGTGTCAGGAACAGCGGACGTAGCTGGGTATTGGGACTGAAATCGCGGTGCCCGTTGAATCCATGGATCAGAACCTTGAGCGGTTTGTGGTGATAAAATTCAAAACGATTAAGTTCAAAAACTGAAAGCTTAGTTCCCTCCTGATTTTCTTTTCTGCAGATACGGATAGATAATGAAAATCATAGTATAAAACCATTAATCTTACGTGTATAGCCAAAAGGAAATGTTGGCATTGGGACAAATTTCGTTTTGCAGGGAAAAACAGTTCATATCATCTAAGCCAGCAACGAGCATAACACTCGAGAAGCCTAAAACACGATTACTTTATGACTTTATTATTAACTCAGCCTGAATTACCTATTAAGACCAAGATGTTATTCATCATTCTCTTCGATTCCGTTGAGGCCTTTACTGATTTTTTTATTTTCCGACTTTATATGCTCTAGGTTCCATAAAATCTTTTTAATTAAGTTTGTCTCGTTCAACCGAATAAGTAACCGGAAAGCTTTTCTAATTGCAAAATATGTGCATCTGTAGCGCCCAGGGAGGAGCAGTAAAATATTATAGCAGTGGAATTCTGCATAAAAGTTAAATATGATTAAATTATAAAAAGAACAGAAATAGAATTTTAAAAATCAATTTAAAAATAAATAGGAAGTCAGTAATTAATTAATTCGCGGTTGACTTCGCTCCTGGGCAGAACAATTTGCAGTGGTAATTACATCGTAAATCTAGCCTTAAATTTCATGCCACCAAAATGTCAGCGTTCGAATTAGAACTTATGCCACAAGTGTGGCCAACACTCAACTCAAGCTATTTATACAGATACACATTTTGGGCATTGAAAATTATGCAAAAACAATCGAAGTGCCACTGTGTGAGTGCACTGTGGTCGCCAGAGCAACCCAACCCAACCCAACCCAACCCCTCTTCCCATTGTGCCATTCCGTCACCTCACTGGGACATTCCAAATGTGTTTCACGTTTTGTCATAAATAATAAAACTCAAATGACCATCAAAGCCACTACTGTGCGCCTTTGCCAAAAAAAAAAATGCCGCTGCCGGAAGGTTACCCACTCATACAGAACTATCCAAATTCGAATTCGCATCCAAATCCGAACCCATGCCCAAAGAACCATAGCATCCCCCACAATTGGCCTGTCCATCTAGCGTGATGTCCATTTGCCAGCCTGAATGCCTGTTTGTTTGTTTTAAAGCAAAAATCTAAAACCAAATCAACATTTTTCGAGACCAAAGTGGAGAGGATGGAGGTTGAGGATCGGATGGGTGTGTGGTTAACCGCAGCACTAGTGGCTATGGG CG10833 Gadfly 0 Cyp28d1 Drosophila melanogaster 1972 2004-08-09 15:56:24.057523 2004-08-09 15:56:24.057523 SO gene CG10833 CG10833-RA Gadfly 0 275f2c58611a9f912c514d896a652470 Cyp28d1-RA Drosophila melanogaster CCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACA 1603 2004-08-09 15:56:24.230779 2002-04-30 16:10:52 SO mRNA CG10833-RA 6 0 Cyp28d1:6 Drosophila melanogaster 238 2004-08-09 15:56:24.665877 2004-08-09 15:56:24.665877 SO exon CG10833:6 5212450 5212212 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof 4 0 Cyp28d1:4 Drosophila melanogaster 631 2004-08-09 15:56:24.587619 2004-08-09 15:56:24.587619 SO exon CG10833:4 5211821 5211190 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof 1 0 Cyp28d1:1 Drosophila melanogaster 217 2004-08-09 15:56:24.453082 2004-08-09 15:56:24.453082 SO exon CG10833:1 5210695 5210478 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof 5 0 Cyp28d1:5 Drosophila melanogaster 270 2004-08-09 15:56:24.626408 2004-08-09 15:56:24.626408 SO exon CG10833:5 5212150 5211880 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof 2 0 Cyp28d1:2 Drosophila melanogaster 139 2004-08-09 15:56:24.502579 2004-08-09 15:56:24.502579 SO exon CG10833:2 5210889 5210750 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof 3 0 Cyp28d1:3 Drosophila melanogaster 108 2004-08-09 15:56:24.546345 2004-08-09 15:56:24.546345 SO exon CG10833:3 5211061 5210953 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 relationship type partof CG10833-PA Gadfly 0 35dca04d49d72956485a3ecefc21ada4 Cyp28d1-PA Drosophila melanogaster MCPISTALFVIAAILALIYVFLTWNFSYWKKRGIPTAKSWPFVGSFPSVFTQKRNVVYDIDEIYEQYKNTDSIVGVFQTRIPQLMVTTPEYAHKIYVSDFRSFHDNEMAKFTDSKTDPILANNPFVLTGEAWKERRAEVTPGLSANRVKAAYPVSLRVCKKFVEYIRRQSLMAPAQGLNAKDLCLCYTTEVISDCVLGISAQSFTDNPTPMVGMTKRVFEQSFGFIFYTVVANLWPPITKFYSVSLFAKDVAAFFYDLMQKCIQVRRESPAAQQRDDFLNYMLQLQEKKGLNAAELTSHTMTFLTDGFETTAQVLTHTLLFLARNPKEQMKLREEIGTAELTFEQISELPFTEACIHETLRIFSPVLAARKVVTEPCELTNKNGVSVKLRPGDVVIIPVNALHHDPQYYEEPQSFKPERFLNINGGAKKYRDQGLFFGFGDGPRICPGMRFSLTQIKAALVEIVRNFDIKVNPKTRKDNEIDDTYFMPALKGGVWLDFVERN 502 2004-08-09 15:56:24.711814 2004-08-09 15:56:24.711814 SO protein CG10833-PA 5212376 5210501 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 AAF52226.1 GB_protein 1 FBpp0078698 FlyBase 1 CG10833-PA Gadfly 0 1 0 pub type computer file gadfly3 CG10833-PA synonym type synonym relationship type producedby 5212450 5210478 0 0 0 0 Drosophila melanogaster SO SO:0000105 SO chromosome_arm 2L 1 FBtr0079062 FlyBase 1 CG10833-RA Gadfly 0 1 0 pub type computer file joshk CG10833-RA synonym type synonym 1 0 pub type computer file gadfly3 CG10833-RA synonym type synonym 0 property type owner joshk 0 property type sp_comment Perfect match to REAL SP with corresponding FBgn 0 property type protein_id AAF52226 relationship type partof 0 property type sp_status Perfect match to SwissProt real (computational) 0 property type cyto_range 25C10-25C10 0 property type gbunit AE003609 FBgn0031689 FlyBase 1 CG10833 Gadfly 1 FBan0010833 FlyBase 1 0 0 pub type computer file gadfly3 28d1 synonym type synonym 5212450 5210478 0 0 0 0 Drosophila melanogaster SO chromosome_arm 2L 1 chado-1.23/chado-xml/examples/CG10833.with-macros.chado-xml000644 000765 000024 00000103121 11256710157 023211 0ustar00cainstaff000000 000000 Drosophila melanogaster Gadfly SO GB_protein FlyBase SO relationship type pub type synonym type property type cv__SO gene cv__SO mRNA cv__SO exon cv__SO SO:0000105 db__SO chromosome_arm cv__relationship type partof cv__SO protein cv__pub type computer file cv__synonym type synonym cv__relationship type producedby cv__property type owner cv__property type sp_comment cv__property type protein_id cv__property type sp_status cv__property type cyto_range cv__property type gbunit <_appdata name="title">CG10833 <_appdata name="arm">2L <_appdata name="fmin">5205478 <_appdata name="fmax">5217450 <_appdata name="residues">AAGCTAAATTTCAAGTAAGAAAAATTTAAACAAAAAAATGTTGAATATCGAAATGGAAGAGTTGTACATTTGTGTAGTTTATCACATTTTGTAATTGTATGTAATTTTATAGTCATTCGATAGCTAGAGGCATTAATAAAACAACCAATTTGTATATAACCTACTGAACCGAACAGACTCGACAAGCCGAACATGAAACACGTAAAAGAATTAAACAAAAAAATAAAAAGAAACAGAATGAACTAACTATTCAAACTAACGACAAGTAACCGAAACCCTTTTGTAAAACGATATATACATTATACATATATATTTGCACAGCAAACAATTTATATATTCATATATACCCACGTATATGATCCCAAAAAAACTATAGAGAACCCAAACATTTTGTATATAAAAATATCTAAGCTAAAACGAAATCAAAATACGCACACGAACATTTTACTCATCAACGCACGTTTTCGCATTTAGAGAGATCCTGGGCAGCAGAAAATTGCGATTAGCATCCTGCCAATTTCGTGGAACATTTTCGCAGGATATGATCTCAAGTTCCTGCTGCCAGCGATGGGCTAGAAAGGCAAACGAAATCCCAAGACAAAATCATGACCCACATAGACCAATCGCCTGGAGATCCTCATGGCAACCAATGTTCCTAGTTTCCAGCGCGTCCTTCTCCCAAACTCAGGGCTATGCTGTCAACAGTGGGCATTGACCTCCATTTGGACTCCGGCTTCTAAAGAGACCCCGTGTCAAGAAGGATCACTCTACCCAAGGCCAAGATCTCTCCCACGGCCAAGGGTTAGATGGGATAGCAGCCAGTGCGCCAGCCACAGGTCACTGGGCTCGAAATCAATCCTTAAACTCCATCCCGACACTGGGGCCTAGACATTTCAAGCATTCCTGATACTCATTTCCAAATTACCAATAGACATTGACCATCGAAGCCAGCTCTCAAAGAAAAGAAAATGGAAAACGTGCGTGCCACGAGCATTGAACAAAACGAAGCAAGTGTCCTATGCCGGTGCTAAACCAACCTACAAATTTTCTGTATAAAGAAAAAATGTAAAATGCGTATACAAAAAACAAAAATATTATGAATTCATAAAAGAAGAGATTAATTCTTTGAAAAAAAAAAATCGTAAAAATGCAATATGCATATTGACAAGTGACGTAAGTCCATCCAGTAAAAGATACCTATTTTGTTGTTAATATTTTTTGATAATCCTAATTATATTTGCCTTATACTTATCCAACTTGTTTATTACAACTATTTTCTATTATTTAATGCTTGGCCAATTATTATTGAGAAAATACATACATTTATTTATTAGGCCTATGAACGATTTACTATGTATAAAATTAAGTTTGATTTAAATGTTAAATTTGTGTACTTTGCTGCTTCTATCTGGTTATGAAATAATTAGCCGTTATCGAGTTAATATAATTTATGTAGCATTTTAAGATTTCCTTTCTTGTGAACAACTGTACCTTTATATGCATTATGATTATTAAAAAAAAAAAAAACAAATAAAAAATAAAACACATTGTTTTTTTTATACCTTTGAATTTATGTCTGCAGCTCTATTGACATAACTATATACGTTTTGGTTTTACAGGTTTCATGCTTATCGATATTTTATTACCTATCTTGTTTAATTGACTTTTGATCGAGCGCTACGAGATTAATGCAATCAGACTAAAAAAAAACAAACAAATTTTAAAAGAGGAAATTTATTAAAATACGATTAGATTGCTTCCAGCGCGTGTCTATTTTTTTGGCATAAATATAGGCCCCTGCGTTAATCTGTAGCCCATAAGCTTCCAACATGTGCCCAGTAACTACATTTCTTGTCCTCGTGCTGACCCTGTTGGTTCTGGTCTACGTGTTTCTGACATGGAACTTCAACTATTGGAGAAAACGTGGCATCAAGACGGCTCCCACATGGCCATTTGTTGGAAGTTTTCCCAGCATTTTCACAAGAAAGCGAAATATTGCCTACGATATTGATGATATCTATGAGTATGTATACAATATGAGTGAGAAGGGCAAGCTATAGTTATGTTGTATAATAGTGGAGTCAAAGCGCAGTTTATACTTAATGGGTGTAAAAATCAGAACAGTCTTCTCTAGAGCTAATATAAGTTACTTTTTGATGTGAACTTTTTGTTTTTGCAGAAAGTATAAAGACACGGACAATATGGTGGGCGTTTTTACCACCCGAGTGCCCCAATTGCTGGTCATGTGTCCGGAATATATACACAAGATCTATGCAACCGATTTCCGTAGCTTTCATAACAATGAATGGCGTAATTTTGTAAGTACTCGTAAGTTTAGTAAATAATGGATAATCCATTACTGAATTACAATGTTCATAGGTGAACAAAAAGACGGACATGATATTGGGCAACAATCCGTTCGTGTTAACTGGCGACGAGTGGAAGGAAAGAAGGTCGGAGATCATGCCAGCACTGTCCCCCAATCGAGTAAGGAACCACATTAACCATCTATCCAATCAAAATTCTATCTTTGAATTCCGTAAGGTCAAGGCCGTTTATCCAGTATCGCAGAGCGTATGCAAAAAGTTCGTGGAATATATCAGGCGACAGCAGCAGATGGCCACCTCCGAGGGATTGGACGCCATGGATCTGTCTCTTTGCTACACCACCGAAGTAGTTTCCGACTGCGGACTGGGAGTATCGGCCCAGAGTTTCACGGACACTCCCACGCCGCTGTTGAAAATGATAAAGCGTGTGTTCAATACCTCCTTTGAGTTCATCTTCTACAGCGTTGTTACCAACCTGTGGCAAAAGGTGCGCAAGTTCTACAGCGTACCGTTCTTCAACAAGGAAACGGAAGTGTTCTTCCTGGACATCATCCGGCGATGCATTACTTTGAGACTGGAAAAACCAGAGCAACAGCGCGACGATTTCCTCAACTATATGCTGCAGTTGCAGGAGAAGAAGGGCCTGCACACGGATAACATCCTGATAAATACGATGACCTTCATTCTAGACGGATTCGAGACTACGGCTCTAGTTCTAGCGCATATTATGCTGATGCTGGGACGTAATCCGGAGGAGCAAGATAAGGTCCGCAAGGAAATTGGCAGTGCGGATCTGACCTTTGATCAAATGTCCGAGCTTCCGCATCTGGACGCCTGCATATATGGTGGGAAATTCTATCTTGATCTCTTGATATTCAGTTTCTTTAACTACATTATAAAATTTTATAATTTTAGAAACTTTGCGTTTGTTTTCACCGCAAGTTGCAGCACGTAAGCTGGTCACCGAACCCTTTGAGTTTGCGAACAAGAACGGACGCACTGTGCACTTGAAACCCGGAGATGTGGTTACTATACCGGTAAAAGCTCTGCACCACGATCCGCAGTATTATGAGGATCCTTTGACATTCAAGCCGGAACGTTTCCTTGAGAGCAATGGAGGTGGTATGAAAAGTTACAGAGACAGGGGTGTTTACCTAGCTTTTGGCGATGGACCTCGTCACTGTCCAGGTTGGTGTTATAAAAATTTATCTGAAAATCACATACTACAATAAGTCGATCTCTACATTTAGGAATGCGATTTGCGCTGACTCAACTTAAAGCAGCTCTGGTGGAAATCTTGAGGAACTTTGAAATCAAGGTTAATCCTAAAACCCGCTCGGACAATCAGATAGATGATACTTTCTTCATGGCCACCTTGAAGGGTGGTATTTACCTGGACTTTAAGGACCTTTAAATAATAGCAATAATCATAGTAAGCTTTAAGCTTAAAAAACTGGATAAAGAGAAGTTGTTTGCTCGAAATAACAAAAATTAAAATTAACCTTGATTAATGCATGATAATAAAAAAAAAATAAAATGCAGTAGAGATTTATTACTCAAGAAAGGCAAATGTTGCGGATGATCCACAACAAGGCTCGATCGAACATGGTTCGACAGTGATGTTGCATGCGCAACAAGTTCGATTGCTAGTGCGCAACATGTCGGTTGTAGGTTGGCCATCCGATTTTAAATACTTGCAAGATATAAGATTTAATTGAGATTTTATAATAAAAAGTAATAAGAATTATAGAATTATAGATCAAGGGGTGTATAAAGAATATAAAGAAATCGATTCACCATCATAGGCATCTCAAGGCTCAAGCTCAAGGGCAGTTTTGGTGGAGATCGTAAGAAATTTCGAAATCAATGTAAACGTCAAGACGCGATCGGATAATCGACTGAATGACATCTGCTTGACGTATTTTGAAGAGCGATAGTAAAATGGCTGAAGTGTTGTTGTAAGTGTTGATAAGATAATGCGCCAATTAAAAATGAAATCAGAAATTTGATTAACTACTTAGGTGCTACACACATTGTTTGTCCAGAGTATCTATACCCATTACTCGTTAAATGAAAATGGGTATGTTGTATTCCTAGAAAAGTATGCAACTGATAGATGGACCTTCTGAATACGACACATTGTTTTTTGTTTTCATCAAGCATCGCACTTTGCAATCCTACTTATTTATTTAAAAGTCGATACATTGCTATTTTTCCTTTAATTGTTTATGGTTTATGTATATGTCGTTTAATTTCACAACCGTTTATTCCATTTCTCTATGCTACTAAAACCGTTCCCTTAAAACACATCTTTATCTGCGTGCTTTAGATACATATGCCATGTACAATAATTGTAAGTTTGAGCACTTAGTGAAATGACAAGCTGAAAAGTTCTGTTTCATCGTCATATCATAAAATGGCTTTTCTTAACAGTTTTTGTACTACTACTTTGTGGCGCATGACCTAGGACTAGGTATATTGTAGCCCCTTGATCTTGATAACGAAATCAGGCATTATCTTCAAATGGTGCAATTTTATATACGACAAATATTAACAGCGGTGGTGAATGCAATTTGATCAATTTGTTTACTGGGTGAATCCATCCACTTGACTGGCGCGCAAGTTCAATTTAAATGACTGCGGCAGCTCAATTGAGTTCCAGTTGGTTTTCATCCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGTAAGTGTATAGAGTTAGCTACGTTATCTGGTTACTGATTGCATCATCTCATTAGGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTGTGAGTAGATTGCAAATACATACTGGTCTTAGGAGCCCATTTCATAAGTTAATTCACACAATAGACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTAAGCTTAGGTTGCCCTCGAATTGTTTATTCAAAACTTATCTCGTGCTAATGTTTATTTTCACTGGGGGCCCTGATACCCTTATCAATTGAAGTGCTCCAATCAATTAACGCTCTGCCTCCCCAAAAGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGGTGAGTTTTTTGGCGAAATCTGAAGTTATTTAGTATGCGTATAATATCTATATCTGCAGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTGGGTAACATCATTTTTGAAACAATTAAAGTTACTAAAAAAAATCTATGCATAATTTGTAGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACACTCTTAATACTTTAATTTTGTAACTTAAAACCACACTTTTAGTCTCGACTTAGGGCTAGTTGCACTAGGGGCAGCACCTTGATAGAGGACAAGTCTGCCAGAATCGCTTCGATGCTATCCAACGAGGCCACCTGCATGATGCTCTCCTTTCGAAAGCTAAGAATGATGATGGCGAATAGAGGAAGGATCTCCAAGCTATCAAAGCCAAGGATCTGAAAAGGAAGGGATAAGTACTGCCAATAAGAACGGAGGTGTATTTCGTACCAGATCCCAGAGGACCAGCAATTGATCGGGAGGCAAATGTCCGGAAAACGCTCGCATAAGCCATTTGAAGACCACCCGCAGGCTAAGGAAAGATATGTCGTGAAATGGGTGAAATAGCTGTCTAACGAAAAACCCAATCCCAACTCACGGCTGTATCTGAAGCTCTCGGAAATGGGACCATAACTGCGGTTCGTATGTCTGCAGCAGCTTCTCGAAGAGCAGGCACAGACTGACAATCCCTTGAGGATGCGTGTTTATGGTGGTCAAGCGATGGCAGTACCGGATATAGAAGGCCCGGAATGTATAGTATAGACTCACCGGCGAGTCATACAGATAACAAAAGGGGGCGGCAAACATGCAGATGCCGTGGAAGGGCACCACACCCGATGGAGGACCTTCGTAGGTCTTGCCCTTCACCGGAAACGTCTCGTATTCCACACATCCACCGATATCGGTGTCCCGAGAAAAGCAGAGCAGCACCTGGTAGAGCACGTCCTCGAACACAAAGTACTGGTCGTCGTTGGAGGCCGTCAACTGAATGTCCTTGAAGACCAGTTTGTCAACGATGTGATCCGTAGTCCAAACGGCATTGCGCAGCTTTTGCCAGTACTCAATATCCTTCGGGGGTATAGAGATGTATAATGAGGTTATTGATCCCAAAATCAGTAGTTACGTAGTCATGTAGCTTGCTGTCCAGCACCGAAGCCCAGAGAGCTCCCCTATAAGGTGCGGGTGTGCAGCCCTTCTTCAGAAACTGCTGGCACATGGGCGCATGCCTGGCCTCCAGAATCCTCTGGCACTGAACCGTAAGATCCGGCACTCCCAAATAGCTATCACTTCGCAGCAGATCCGCGTAGTGGGCACGCAGCTCGAAAAGATTTTTCACAGGTAGTGCAATGTGGGAGAACTCCCATTGGGGGATTTGACTAATGAGCAAAATGATTATTTACCTGACTGATTTAAACCAAAACTTACTCTGTATTTTCAGTGGTTTTGGCGGGTCCTTTTAGCGAGAGTAGCACCTCCAGTAAATCCTTTGGAGCGTAAACAGGCCTATAGTTGGCCAGATCTAGAAGTTTAACCATGGTTAATTGTTAGCTTCAATATTTACGAAATGCCTACCCATATTGTAGTTGCTCAGTTCGTTCCACTTGGCCATAAAGTCCTCGCGATCAGCACTGATCCTTGGTTGTCCATGCAATGGAACCTTCAGCTCTGTACACATGGCATTCAAACTCTTCCTAACCCTTCGATCCCAAAGCACACCAGCTCTTTTTAAATATCCAAGTGGATCACTAACGGTGGGTTTCTATTGGAAAATATAGACATAAGTAAAGAACTATTTAATTCATTTTCCCTAGCACTACATACTACTAATACCCCTAAGGCTAACTCTATAGTTGTGGCACTTCGAGATCTTCCGGTATTATGTATCATTATAATTTGTTTTATAAACGTTAAGGTATAAAATAAAATTTTGCCAATAAAGTCAAAAAGTAGAAAATGATAGGAGCAGCATGGAATACTTTTAAATACCACTCCAATTATTCTAAATTCAATTACAAGAAATTTGATAAATTGTATCTTAAAAGTTGTACCCACCGCTCCCTGTTTGTTGGCCAGGTTTTTGTCATCTGTTTTCGACAGCCGCGTGCGGACCAGGTTGTAGACAATATTCCGGATCTCCGTCTCCAGTCCGGCGCTCTTGATGGCATCCTCGAGGGTGTTGCGCATATCGTGAGTATCTACGCTGGGATTGCAGACCAGCTTCTGCAGCTCCTTGTAGATGGGCTCGTAGCTCTTAGTGTTCTTGATGGCCGCGATTACCTTTGCGGTCATATGGTGGATGCTGGCATCCTGCAGCTCCTCCATGCCGATAGCTCCTTGACCCGACCGTTCTTTCTACGTATTACTCTGCCACTGACTACCAACTAACTATTTACACCGTTTTGATACCGATTAGCCCCAAAACTTTGGGCGCTCCTAACTCCGTCGTTTGACTTTTATCGATCAAACTCCGTCGCCTGCTTTGATTTGGAGTCGATTCGATTCCGAGTCACATCCTCGGTTGTCGTCGCTTCTTGGCGACGGAATGCAAACACTTGTTTGGCTGCTAGTTTCGCGTTAGTTGTGATTTGATTCGTTCGTTTTGCCGCCCCTCGCAACCAAGAAATTCCATTATGTTTCGTTTCGAATGAAAAGCCAGAGGCGCGTGAAATTGCTTTCCATATACATTTATTTTCACGCACACCGAAACACGCTGAAACTGAAACTGAGTGGCGGCAACTTTTCCTTTTTCTTGGCATCTGTCACCTGGCCCAACGAGTTGTTGACGTGGTCGTCGGGTTGGCTCCTCCTGTTGATTGCGAAGGTGGGCCAAACTCACCTGAACATGTCAGAGTGTCGAAAGTATTTCACCTGAATATTTAGACCAGGCCGAAATATGATTTTGAAATGGCAAAAATTTTTACACGAAAATAGAGATATATAATCCTCTATGTGGTACATTATTCAATGTTTATTTATGAATTAAAAATATTCGTTTTAAGATTTGGATAGCATCCCTTACTACGTTCCAATCAATTTATCTATAATATCATCGTTCACGAAAGTTCGACCTTTTAGTTGGCGGCTTATTGAGGTAAAGTTCTCTCCCTTGGCATAAGGAGGACCATTATTGGTATCCAGAAAATACCTGCCTCTGGCTCTGCAATTAAATAGATAAAAAGAGATCTGGAAAAATAGGTGCTGGCACTTACTTCGGATCCACGTGAAAACCCATCAGCTCTATATTTTTATCAGGAATGCAAATTCCCTTTGCGAAGCTTTTAAAATTGGGACAGTAGAAGCCATAGAATCCAGAAGGTGACGAAATAGACTCGGCATAATAGTCTGCTGCTCGGTTATGGTAGCAGAAATGAGTCTCCACTAAAGTCAGAACAACGAAAATGAAAAATATAGGTAAAGCAGATGGCCTTAATATTACTAACTCTTATTAATGGGTCCGCAGTTGGGCTGTGATACACCCATGTTCAAGTAGAAGTCCACGTGACCCACTGCATCCAGTAAGCCAAGCATCGTGACATCCGTGTGCACGACGTCCACGAACTTGGCATCAGTGGGATCGAGCTTTAGAGCCGGATCCTTGACCATGTAAAATGGTTTTGCCGGATCGAGGGCTGTAATATGCTCCAGCTTGTGTTCCGGAAGAAACTGCCCAATGAAGCCTGCGACATGGGCACCTAAGCCCAAGCCAATTAGGTGCAGATCCTCAATTTTGACCAATCCGCTCTCGAGGAGTACTCGTAGCAACTGAGCAGTACAGCGAGCTACGTATTTGGCATTGTGCACCGCTTCCGTATAGCAGGGTTCATAGGCTAGTTTTGGATAATCCAAGGATATCAAATTGTAATCCTGTGTCAGGAACAGCGGACGTAGCTGGGTATTGGGACTGAAATCGCGGTGCCCGTTGAATCCATGGATCAGAACCTTGAGCGGTTTGTGGTGATAAAATTCAAAACGATTAAGTTCAAAAACTGAAAGCTTAGTTCCCTCCTGATTTTCTTTTCTGCAGATACGGATAGATAATGAAAATCATAGTATAAAACCATTAATCTTACGTGTATAGCCAAAAGGAAATGTTGGCATTGGGACAAATTTCGTTTTGCAGGGAAAAACAGTTCATATCATCTAAGCCAGCAACGAGCATAACACTCGAGAAGCCTAAAACACGATTACTTTATGACTTTATTATTAACTCAGCCTGAATTACCTATTAAGACCAAGATGTTATTCATCATTCTCTTCGATTCCGTTGAGGCCTTTACTGATTTTTTTATTTTCCGACTTTATATGCTCTAGGTTCCATAAAATCTTTTTAATTAAGTTTGTCTCGTTCAACCGAATAAGTAACCGGAAAGCTTTTCTAATTGCAAAATATGTGCATCTGTAGCGCCCAGGGAGGAGCAGTAAAATATTATAGCAGTGGAATTCTGCATAAAAGTTAAATATGATTAAATTATAAAAAGAACAGAAATAGAATTTTAAAAATCAATTTAAAAATAAATAGGAAGTCAGTAATTAATTAATTCGCGGTTGACTTCGCTCCTGGGCAGAACAATTTGCAGTGGTAATTACATCGTAAATCTAGCCTTAAATTTCATGCCACCAAAATGTCAGCGTTCGAATTAGAACTTATGCCACAAGTGTGGCCAACACTCAACTCAAGCTATTTATACAGATACACATTTTGGGCATTGAAAATTATGCAAAAACAATCGAAGTGCCACTGTGTGAGTGCACTGTGGTCGCCAGAGCAACCCAACCCAACCCAACCCAACCCCTCTTCCCATTGTGCCATTCCGTCACCTCACTGGGACATTCCAAATGTGTTTCACGTTTTGTCATAAATAATAAAACTCAAATGACCATCAAAGCCACTACTGTGCGCCTTTGCCAAAAAAAAAAATGCCGCTGCCGGAAGGTTACCCACTCATACAGAACTATCCAAATTCGAATTCGCATCCAAATCCGAACCCATGCCCAAAGAACCATAGCATCCCCCACAATTGGCCTGTCCATCTAGCGTGATGTCCATTTGCCAGCCTGAATGCCTGTTTGTTTGTTTTAAAGCAAAAATCTAAAACCAAATCAACATTTTTCGAGACCAAAGTGGAGAGGATGGAGGTTGAGGATCGGATGGGTGTGTGGTTAACCGCAGCACTAGTGGCTATGGG CG10833 db__Gadfly 0 Cyp28d1 Drosophila__melanogaster 1972 2004-08-09 15:56:24.057523 2004-08-09 15:56:24.057523 SO__gene CG10833 CG10833-RA db__Gadfly 0 275f2c58611a9f912c514d896a652470 Cyp28d1-RA Drosophila__melanogaster CCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACA 1603 2004-08-09 15:56:24.230779 2002-04-30 16:10:52 SO__mRNA CG10833-RA 6 0 Cyp28d1:6 Drosophila__melanogaster 238 2004-08-09 15:56:24.665877 2004-08-09 15:56:24.665877 SO__exon CG10833:6 5212450 5212212 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 4 0 Cyp28d1:4 Drosophila__melanogaster 631 2004-08-09 15:56:24.587619 2004-08-09 15:56:24.587619 SO__exon CG10833:4 5211821 5211190 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 1 0 Cyp28d1:1 Drosophila__melanogaster 217 2004-08-09 15:56:24.453082 2004-08-09 15:56:24.453082 SO__exon CG10833:1 5210695 5210478 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 5 0 Cyp28d1:5 Drosophila__melanogaster 270 2004-08-09 15:56:24.626408 2004-08-09 15:56:24.626408 SO__exon CG10833:5 5212150 5211880 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 2 0 Cyp28d1:2 Drosophila__melanogaster 139 2004-08-09 15:56:24.502579 2004-08-09 15:56:24.502579 SO__exon CG10833:2 5210889 5210750 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 3 0 Cyp28d1:3 Drosophila__melanogaster 108 2004-08-09 15:56:24.546345 2004-08-09 15:56:24.546345 SO__exon CG10833:3 5211061 5210953 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof CG10833-PA db__Gadfly 0 35dca04d49d72956485a3ecefc21ada4 Cyp28d1-PA Drosophila__melanogaster MCPISTALFVIAAILALIYVFLTWNFSYWKKRGIPTAKSWPFVGSFPSVFTQKRNVVYDIDEIYEQYKNTDSIVGVFQTRIPQLMVTTPEYAHKIYVSDFRSFHDNEMAKFTDSKTDPILANNPFVLTGEAWKERRAEVTPGLSANRVKAAYPVSLRVCKKFVEYIRRQSLMAPAQGLNAKDLCLCYTTEVISDCVLGISAQSFTDNPTPMVGMTKRVFEQSFGFIFYTVVANLWPPITKFYSVSLFAKDVAAFFYDLMQKCIQVRRESPAAQQRDDFLNYMLQLQEKKGLNAAELTSHTMTFLTDGFETTAQVLTHTLLFLARNPKEQMKLREEIGTAELTFEQISELPFTEACIHETLRIFSPVLAARKVVTEPCELTNKNGVSVKLRPGDVVIIPVNALHHDPQYYEEPQSFKPERFLNINGGAKKYRDQGLFFGFGDGPRICPGMRFSLTQIKAALVEIVRNFDIKVNPKTRKDNEIDDTYFMPALKGGVWLDFVERN 502 2004-08-09 15:56:24.711814 2004-08-09 15:56:24.711814 SO__protein CG10833-PA 5212376 5210501 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 AAF52226.1 db__GB_protein 1 FBpp0078698 db__FlyBase 1 CG10833-PA db__Gadfly 0 1 0 pub type__computer file gadfly3 CG10833-PA synonym type__synonym relationship type__producedby 5212450 5210478 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 FBtr0079062 db__FlyBase 1 CG10833-RA db__Gadfly 0 1 0 pub type__computer file joshk CG10833-RA synonym type__synonym 1 0 pub type__computer file gadfly3 CG10833-RA synonym type__synonym 0 property type__owner joshk 0 property type__sp_comment Perfect match to REAL SP with corresponding FBgn 0 property type__protein_id AAF52226 relationship type__partof 0 property type__sp_status Perfect match to SwissProt real (computational) 0 property type__cyto_range 25C10-25C10 0 property type__gbunit AE003609 FBgn0031689 db__FlyBase 1 CG10833 db__Gadfly 1 FBan0010833 db__FlyBase 1 0 0 pub type__computer file gadfly3 28d1 synonym type__synonym 5212450 5210478 0 0 0 0 Drosophila__melanogaster SO__chromosome_arm 2L 1 chado-1.23/chado-xml/examples/CG10833.with-macros.defaults-stripped.chado-xml000644 000765 000024 00000076575 11256710157 026675 0ustar00cainstaff000000 000000 Drosophila melanogaster Gadfly SO GB_protein FlyBase SO relationship type pub type synonym type property type cv__SO gene cv__SO mRNA cv__SO exon cv__SO SO:0000105 db__SO chromosome_arm cv__relationship type partof cv__SO protein cv__pub type computer file cv__synonym type synonym cv__relationship type producedby cv__property type owner cv__property type sp_comment cv__property type protein_id cv__property type sp_status cv__property type cyto_range cv__property type gbunit <_appdata name="title">CG10833 <_appdata name="arm">2L <_appdata name="fmin">5205478 <_appdata name="fmax">5217450 <_appdata name="residues">AAGCTAAATTTCAAGTAAGAAAAATTTAAACAAAAAAATGTTGAATATCGAAATGGAAGAGTTGTACATTTGTGTAGTTTATCACATTTTGTAATTGTATGTAATTTTATAGTCATTCGATAGCTAGAGGCATTAATAAAACAACCAATTTGTATATAACCTACTGAACCGAACAGACTCGACAAGCCGAACATGAAACACGTAAAAGAATTAAACAAAAAAATAAAAAGAAACAGAATGAACTAACTATTCAAACTAACGACAAGTAACCGAAACCCTTTTGTAAAACGATATATACATTATACATATATATTTGCACAGCAAACAATTTATATATTCATATATACCCACGTATATGATCCCAAAAAAACTATAGAGAACCCAAACATTTTGTATATAAAAATATCTAAGCTAAAACGAAATCAAAATACGCACACGAACATTTTACTCATCAACGCACGTTTTCGCATTTAGAGAGATCCTGGGCAGCAGAAAATTGCGATTAGCATCCTGCCAATTTCGTGGAACATTTTCGCAGGATATGATCTCAAGTTCCTGCTGCCAGCGATGGGCTAGAAAGGCAAACGAAATCCCAAGACAAAATCATGACCCACATAGACCAATCGCCTGGAGATCCTCATGGCAACCAATGTTCCTAGTTTCCAGCGCGTCCTTCTCCCAAACTCAGGGCTATGCTGTCAACAGTGGGCATTGACCTCCATTTGGACTCCGGCTTCTAAAGAGACCCCGTGTCAAGAAGGATCACTCTACCCAAGGCCAAGATCTCTCCCACGGCCAAGGGTTAGATGGGATAGCAGCCAGTGCGCCAGCCACAGGTCACTGGGCTCGAAATCAATCCTTAAACTCCATCCCGACACTGGGGCCTAGACATTTCAAGCATTCCTGATACTCATTTCCAAATTACCAATAGACATTGACCATCGAAGCCAGCTCTCAAAGAAAAGAAAATGGAAAACGTGCGTGCCACGAGCATTGAACAAAACGAAGCAAGTGTCCTATGCCGGTGCTAAACCAACCTACAAATTTTCTGTATAAAGAAAAAATGTAAAATGCGTATACAAAAAACAAAAATATTATGAATTCATAAAAGAAGAGATTAATTCTTTGAAAAAAAAAAATCGTAAAAATGCAATATGCATATTGACAAGTGACGTAAGTCCATCCAGTAAAAGATACCTATTTTGTTGTTAATATTTTTTGATAATCCTAATTATATTTGCCTTATACTTATCCAACTTGTTTATTACAACTATTTTCTATTATTTAATGCTTGGCCAATTATTATTGAGAAAATACATACATTTATTTATTAGGCCTATGAACGATTTACTATGTATAAAATTAAGTTTGATTTAAATGTTAAATTTGTGTACTTTGCTGCTTCTATCTGGTTATGAAATAATTAGCCGTTATCGAGTTAATATAATTTATGTAGCATTTTAAGATTTCCTTTCTTGTGAACAACTGTACCTTTATATGCATTATGATTATTAAAAAAAAAAAAAACAAATAAAAAATAAAACACATTGTTTTTTTTATACCTTTGAATTTATGTCTGCAGCTCTATTGACATAACTATATACGTTTTGGTTTTACAGGTTTCATGCTTATCGATATTTTATTACCTATCTTGTTTAATTGACTTTTGATCGAGCGCTACGAGATTAATGCAATCAGACTAAAAAAAAACAAACAAATTTTAAAAGAGGAAATTTATTAAAATACGATTAGATTGCTTCCAGCGCGTGTCTATTTTTTTGGCATAAATATAGGCCCCTGCGTTAATCTGTAGCCCATAAGCTTCCAACATGTGCCCAGTAACTACATTTCTTGTCCTCGTGCTGACCCTGTTGGTTCTGGTCTACGTGTTTCTGACATGGAACTTCAACTATTGGAGAAAACGTGGCATCAAGACGGCTCCCACATGGCCATTTGTTGGAAGTTTTCCCAGCATTTTCACAAGAAAGCGAAATATTGCCTACGATATTGATGATATCTATGAGTATGTATACAATATGAGTGAGAAGGGCAAGCTATAGTTATGTTGTATAATAGTGGAGTCAAAGCGCAGTTTATACTTAATGGGTGTAAAAATCAGAACAGTCTTCTCTAGAGCTAATATAAGTTACTTTTTGATGTGAACTTTTTGTTTTTGCAGAAAGTATAAAGACACGGACAATATGGTGGGCGTTTTTACCACCCGAGTGCCCCAATTGCTGGTCATGTGTCCGGAATATATACACAAGATCTATGCAACCGATTTCCGTAGCTTTCATAACAATGAATGGCGTAATTTTGTAAGTACTCGTAAGTTTAGTAAATAATGGATAATCCATTACTGAATTACAATGTTCATAGGTGAACAAAAAGACGGACATGATATTGGGCAACAATCCGTTCGTGTTAACTGGCGACGAGTGGAAGGAAAGAAGGTCGGAGATCATGCCAGCACTGTCCCCCAATCGAGTAAGGAACCACATTAACCATCTATCCAATCAAAATTCTATCTTTGAATTCCGTAAGGTCAAGGCCGTTTATCCAGTATCGCAGAGCGTATGCAAAAAGTTCGTGGAATATATCAGGCGACAGCAGCAGATGGCCACCTCCGAGGGATTGGACGCCATGGATCTGTCTCTTTGCTACACCACCGAAGTAGTTTCCGACTGCGGACTGGGAGTATCGGCCCAGAGTTTCACGGACACTCCCACGCCGCTGTTGAAAATGATAAAGCGTGTGTTCAATACCTCCTTTGAGTTCATCTTCTACAGCGTTGTTACCAACCTGTGGCAAAAGGTGCGCAAGTTCTACAGCGTACCGTTCTTCAACAAGGAAACGGAAGTGTTCTTCCTGGACATCATCCGGCGATGCATTACTTTGAGACTGGAAAAACCAGAGCAACAGCGCGACGATTTCCTCAACTATATGCTGCAGTTGCAGGAGAAGAAGGGCCTGCACACGGATAACATCCTGATAAATACGATGACCTTCATTCTAGACGGATTCGAGACTACGGCTCTAGTTCTAGCGCATATTATGCTGATGCTGGGACGTAATCCGGAGGAGCAAGATAAGGTCCGCAAGGAAATTGGCAGTGCGGATCTGACCTTTGATCAAATGTCCGAGCTTCCGCATCTGGACGCCTGCATATATGGTGGGAAATTCTATCTTGATCTCTTGATATTCAGTTTCTTTAACTACATTATAAAATTTTATAATTTTAGAAACTTTGCGTTTGTTTTCACCGCAAGTTGCAGCACGTAAGCTGGTCACCGAACCCTTTGAGTTTGCGAACAAGAACGGACGCACTGTGCACTTGAAACCCGGAGATGTGGTTACTATACCGGTAAAAGCTCTGCACCACGATCCGCAGTATTATGAGGATCCTTTGACATTCAAGCCGGAACGTTTCCTTGAGAGCAATGGAGGTGGTATGAAAAGTTACAGAGACAGGGGTGTTTACCTAGCTTTTGGCGATGGACCTCGTCACTGTCCAGGTTGGTGTTATAAAAATTTATCTGAAAATCACATACTACAATAAGTCGATCTCTACATTTAGGAATGCGATTTGCGCTGACTCAACTTAAAGCAGCTCTGGTGGAAATCTTGAGGAACTTTGAAATCAAGGTTAATCCTAAAACCCGCTCGGACAATCAGATAGATGATACTTTCTTCATGGCCACCTTGAAGGGTGGTATTTACCTGGACTTTAAGGACCTTTAAATAATAGCAATAATCATAGTAAGCTTTAAGCTTAAAAAACTGGATAAAGAGAAGTTGTTTGCTCGAAATAACAAAAATTAAAATTAACCTTGATTAATGCATGATAATAAAAAAAAAATAAAATGCAGTAGAGATTTATTACTCAAGAAAGGCAAATGTTGCGGATGATCCACAACAAGGCTCGATCGAACATGGTTCGACAGTGATGTTGCATGCGCAACAAGTTCGATTGCTAGTGCGCAACATGTCGGTTGTAGGTTGGCCATCCGATTTTAAATACTTGCAAGATATAAGATTTAATTGAGATTTTATAATAAAAAGTAATAAGAATTATAGAATTATAGATCAAGGGGTGTATAAAGAATATAAAGAAATCGATTCACCATCATAGGCATCTCAAGGCTCAAGCTCAAGGGCAGTTTTGGTGGAGATCGTAAGAAATTTCGAAATCAATGTAAACGTCAAGACGCGATCGGATAATCGACTGAATGACATCTGCTTGACGTATTTTGAAGAGCGATAGTAAAATGGCTGAAGTGTTGTTGTAAGTGTTGATAAGATAATGCGCCAATTAAAAATGAAATCAGAAATTTGATTAACTACTTAGGTGCTACACACATTGTTTGTCCAGAGTATCTATACCCATTACTCGTTAAATGAAAATGGGTATGTTGTATTCCTAGAAAAGTATGCAACTGATAGATGGACCTTCTGAATACGACACATTGTTTTTTGTTTTCATCAAGCATCGCACTTTGCAATCCTACTTATTTATTTAAAAGTCGATACATTGCTATTTTTCCTTTAATTGTTTATGGTTTATGTATATGTCGTTTAATTTCACAACCGTTTATTCCATTTCTCTATGCTACTAAAACCGTTCCCTTAAAACACATCTTTATCTGCGTGCTTTAGATACATATGCCATGTACAATAATTGTAAGTTTGAGCACTTAGTGAAATGACAAGCTGAAAAGTTCTGTTTCATCGTCATATCATAAAATGGCTTTTCTTAACAGTTTTTGTACTACTACTTTGTGGCGCATGACCTAGGACTAGGTATATTGTAGCCCCTTGATCTTGATAACGAAATCAGGCATTATCTTCAAATGGTGCAATTTTATATACGACAAATATTAACAGCGGTGGTGAATGCAATTTGATCAATTTGTTTACTGGGTGAATCCATCCACTTGACTGGCGCGCAAGTTCAATTTAAATGACTGCGGCAGCTCAATTGAGTTCCAGTTGGTTTTCATCCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGTAAGTGTATAGAGTTAGCTACGTTATCTGGTTACTGATTGCATCATCTCATTAGGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTGTGAGTAGATTGCAAATACATACTGGTCTTAGGAGCCCATTTCATAAGTTAATTCACACAATAGACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTAAGCTTAGGTTGCCCTCGAATTGTTTATTCAAAACTTATCTCGTGCTAATGTTTATTTTCACTGGGGGCCCTGATACCCTTATCAATTGAAGTGCTCCAATCAATTAACGCTCTGCCTCCCCAAAAGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGGTGAGTTTTTTGGCGAAATCTGAAGTTATTTAGTATGCGTATAATATCTATATCTGCAGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTGGGTAACATCATTTTTGAAACAATTAAAGTTACTAAAAAAAATCTATGCATAATTTGTAGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACACTCTTAATACTTTAATTTTGTAACTTAAAACCACACTTTTAGTCTCGACTTAGGGCTAGTTGCACTAGGGGCAGCACCTTGATAGAGGACAAGTCTGCCAGAATCGCTTCGATGCTATCCAACGAGGCCACCTGCATGATGCTCTCCTTTCGAAAGCTAAGAATGATGATGGCGAATAGAGGAAGGATCTCCAAGCTATCAAAGCCAAGGATCTGAAAAGGAAGGGATAAGTACTGCCAATAAGAACGGAGGTGTATTTCGTACCAGATCCCAGAGGACCAGCAATTGATCGGGAGGCAAATGTCCGGAAAACGCTCGCATAAGCCATTTGAAGACCACCCGCAGGCTAAGGAAAGATATGTCGTGAAATGGGTGAAATAGCTGTCTAACGAAAAACCCAATCCCAACTCACGGCTGTATCTGAAGCTCTCGGAAATGGGACCATAACTGCGGTTCGTATGTCTGCAGCAGCTTCTCGAAGAGCAGGCACAGACTGACAATCCCTTGAGGATGCGTGTTTATGGTGGTCAAGCGATGGCAGTACCGGATATAGAAGGCCCGGAATGTATAGTATAGACTCACCGGCGAGTCATACAGATAACAAAAGGGGGCGGCAAACATGCAGATGCCGTGGAAGGGCACCACACCCGATGGAGGACCTTCGTAGGTCTTGCCCTTCACCGGAAACGTCTCGTATTCCACACATCCACCGATATCGGTGTCCCGAGAAAAGCAGAGCAGCACCTGGTAGAGCACGTCCTCGAACACAAAGTACTGGTCGTCGTTGGAGGCCGTCAACTGAATGTCCTTGAAGACCAGTTTGTCAACGATGTGATCCGTAGTCCAAACGGCATTGCGCAGCTTTTGCCAGTACTCAATATCCTTCGGGGGTATAGAGATGTATAATGAGGTTATTGATCCCAAAATCAGTAGTTACGTAGTCATGTAGCTTGCTGTCCAGCACCGAAGCCCAGAGAGCTCCCCTATAAGGTGCGGGTGTGCAGCCCTTCTTCAGAAACTGCTGGCACATGGGCGCATGCCTGGCCTCCAGAATCCTCTGGCACTGAACCGTAAGATCCGGCACTCCCAAATAGCTATCACTTCGCAGCAGATCCGCGTAGTGGGCACGCAGCTCGAAAAGATTTTTCACAGGTAGTGCAATGTGGGAGAACTCCCATTGGGGGATTTGACTAATGAGCAAAATGATTATTTACCTGACTGATTTAAACCAAAACTTACTCTGTATTTTCAGTGGTTTTGGCGGGTCCTTTTAGCGAGAGTAGCACCTCCAGTAAATCCTTTGGAGCGTAAACAGGCCTATAGTTGGCCAGATCTAGAAGTTTAACCATGGTTAATTGTTAGCTTCAATATTTACGAAATGCCTACCCATATTGTAGTTGCTCAGTTCGTTCCACTTGGCCATAAAGTCCTCGCGATCAGCACTGATCCTTGGTTGTCCATGCAATGGAACCTTCAGCTCTGTACACATGGCATTCAAACTCTTCCTAACCCTTCGATCCCAAAGCACACCAGCTCTTTTTAAATATCCAAGTGGATCACTAACGGTGGGTTTCTATTGGAAAATATAGACATAAGTAAAGAACTATTTAATTCATTTTCCCTAGCACTACATACTACTAATACCCCTAAGGCTAACTCTATAGTTGTGGCACTTCGAGATCTTCCGGTATTATGTATCATTATAATTTGTTTTATAAACGTTAAGGTATAAAATAAAATTTTGCCAATAAAGTCAAAAAGTAGAAAATGATAGGAGCAGCATGGAATACTTTTAAATACCACTCCAATTATTCTAAATTCAATTACAAGAAATTTGATAAATTGTATCTTAAAAGTTGTACCCACCGCTCCCTGTTTGTTGGCCAGGTTTTTGTCATCTGTTTTCGACAGCCGCGTGCGGACCAGGTTGTAGACAATATTCCGGATCTCCGTCTCCAGTCCGGCGCTCTTGATGGCATCCTCGAGGGTGTTGCGCATATCGTGAGTATCTACGCTGGGATTGCAGACCAGCTTCTGCAGCTCCTTGTAGATGGGCTCGTAGCTCTTAGTGTTCTTGATGGCCGCGATTACCTTTGCGGTCATATGGTGGATGCTGGCATCCTGCAGCTCCTCCATGCCGATAGCTCCTTGACCCGACCGTTCTTTCTACGTATTACTCTGCCACTGACTACCAACTAACTATTTACACCGTTTTGATACCGATTAGCCCCAAAACTTTGGGCGCTCCTAACTCCGTCGTTTGACTTTTATCGATCAAACTCCGTCGCCTGCTTTGATTTGGAGTCGATTCGATTCCGAGTCACATCCTCGGTTGTCGTCGCTTCTTGGCGACGGAATGCAAACACTTGTTTGGCTGCTAGTTTCGCGTTAGTTGTGATTTGATTCGTTCGTTTTGCCGCCCCTCGCAACCAAGAAATTCCATTATGTTTCGTTTCGAATGAAAAGCCAGAGGCGCGTGAAATTGCTTTCCATATACATTTATTTTCACGCACACCGAAACACGCTGAAACTGAAACTGAGTGGCGGCAACTTTTCCTTTTTCTTGGCATCTGTCACCTGGCCCAACGAGTTGTTGACGTGGTCGTCGGGTTGGCTCCTCCTGTTGATTGCGAAGGTGGGCCAAACTCACCTGAACATGTCAGAGTGTCGAAAGTATTTCACCTGAATATTTAGACCAGGCCGAAATATGATTTTGAAATGGCAAAAATTTTTACACGAAAATAGAGATATATAATCCTCTATGTGGTACATTATTCAATGTTTATTTATGAATTAAAAATATTCGTTTTAAGATTTGGATAGCATCCCTTACTACGTTCCAATCAATTTATCTATAATATCATCGTTCACGAAAGTTCGACCTTTTAGTTGGCGGCTTATTGAGGTAAAGTTCTCTCCCTTGGCATAAGGAGGACCATTATTGGTATCCAGAAAATACCTGCCTCTGGCTCTGCAATTAAATAGATAAAAAGAGATCTGGAAAAATAGGTGCTGGCACTTACTTCGGATCCACGTGAAAACCCATCAGCTCTATATTTTTATCAGGAATGCAAATTCCCTTTGCGAAGCTTTTAAAATTGGGACAGTAGAAGCCATAGAATCCAGAAGGTGACGAAATAGACTCGGCATAATAGTCTGCTGCTCGGTTATGGTAGCAGAAATGAGTCTCCACTAAAGTCAGAACAACGAAAATGAAAAATATAGGTAAAGCAGATGGCCTTAATATTACTAACTCTTATTAATGGGTCCGCAGTTGGGCTGTGATACACCCATGTTCAAGTAGAAGTCCACGTGACCCACTGCATCCAGTAAGCCAAGCATCGTGACATCCGTGTGCACGACGTCCACGAACTTGGCATCAGTGGGATCGAGCTTTAGAGCCGGATCCTTGACCATGTAAAATGGTTTTGCCGGATCGAGGGCTGTAATATGCTCCAGCTTGTGTTCCGGAAGAAACTGCCCAATGAAGCCTGCGACATGGGCACCTAAGCCCAAGCCAATTAGGTGCAGATCCTCAATTTTGACCAATCCGCTCTCGAGGAGTACTCGTAGCAACTGAGCAGTACAGCGAGCTACGTATTTGGCATTGTGCACCGCTTCCGTATAGCAGGGTTCATAGGCTAGTTTTGGATAATCCAAGGATATCAAATTGTAATCCTGTGTCAGGAACAGCGGACGTAGCTGGGTATTGGGACTGAAATCGCGGTGCCCGTTGAATCCATGGATCAGAACCTTGAGCGGTTTGTGGTGATAAAATTCAAAACGATTAAGTTCAAAAACTGAAAGCTTAGTTCCCTCCTGATTTTCTTTTCTGCAGATACGGATAGATAATGAAAATCATAGTATAAAACCATTAATCTTACGTGTATAGCCAAAAGGAAATGTTGGCATTGGGACAAATTTCGTTTTGCAGGGAAAAACAGTTCATATCATCTAAGCCAGCAACGAGCATAACACTCGAGAAGCCTAAAACACGATTACTTTATGACTTTATTATTAACTCAGCCTGAATTACCTATTAAGACCAAGATGTTATTCATCATTCTCTTCGATTCCGTTGAGGCCTTTACTGATTTTTTTATTTTCCGACTTTATATGCTCTAGGTTCCATAAAATCTTTTTAATTAAGTTTGTCTCGTTCAACCGAATAAGTAACCGGAAAGCTTTTCTAATTGCAAAATATGTGCATCTGTAGCGCCCAGGGAGGAGCAGTAAAATATTATAGCAGTGGAATTCTGCATAAAAGTTAAATATGATTAAATTATAAAAAGAACAGAAATAGAATTTTAAAAATCAATTTAAAAATAAATAGGAAGTCAGTAATTAATTAATTCGCGGTTGACTTCGCTCCTGGGCAGAACAATTTGCAGTGGTAATTACATCGTAAATCTAGCCTTAAATTTCATGCCACCAAAATGTCAGCGTTCGAATTAGAACTTATGCCACAAGTGTGGCCAACACTCAACTCAAGCTATTTATACAGATACACATTTTGGGCATTGAAAATTATGCAAAAACAATCGAAGTGCCACTGTGTGAGTGCACTGTGGTCGCCAGAGCAACCCAACCCAACCCAACCCAACCCCTCTTCCCATTGTGCCATTCCGTCACCTCACTGGGACATTCCAAATGTGTTTCACGTTTTGTCATAAATAATAAAACTCAAATGACCATCAAAGCCACTACTGTGCGCCTTTGCCAAAAAAAAAAATGCCGCTGCCGGAAGGTTACCCACTCATACAGAACTATCCAAATTCGAATTCGCATCCAAATCCGAACCCATGCCCAAAGAACCATAGCATCCCCCACAATTGGCCTGTCCATCTAGCGTGATGTCCATTTGCCAGCCTGAATGCCTGTTTGTTTGTTTTAAAGCAAAAATCTAAAACCAAATCAACATTTTTCGAGACCAAAGTGGAGAGGATGGAGGTTGAGGATCGGATGGGTGTGTGGTTAACCGCAGCACTAGTGGCTATGGG CG10833 db__Gadfly 0 Cyp28d1 Drosophila__melanogaster 1972 2004-08-09 15:56:24.057523 2004-08-09 15:56:24.057523 SO__gene CG10833 CG10833-RA db__Gadfly 0 275f2c58611a9f912c514d896a652470 Cyp28d1-RA Drosophila__melanogaster CCGCGTTGGCGAGAGGTTGTGCCATGTGTCCGATTTCCACGGCTCTTTTTGTAATTGCGGCCATCCTGGCCTTGATCTATGTCTTTCTAACATGGAACTTTAGCTACTGGAAGAAGAGGGGCATTCCAACGGCCAAGTCATGGCCCTTTGTGGGCAGTTTTCCCAGCGTTTTCACCCAGAAACGGAACGTAGTCTACGACATCGATGAGATCTATGAGCAGTACAAGAACACCGACAGCATTGTGGGAGTGTTTCAAACCAGAATTCCACAACTAATGGTCACAACTCCGGAATATGCGCACAAGATATATGTTAGTGACTTCCGCAGCTTCCACGACAATGAGATGGCTAAGTTTACCGACAGCAAAACGGATCCCATTTTGGCGAATAATCCGTTCGTATTGACTGGTGAGGCCTGGAAAGAAAGACGCGCCGAAGTTACACCCGGACTTTCGGCAAATCGGGTCAAAGCTGCCTATCCCGTCTCGCTGCGCGTTTGTAAAAAGTTTGTGGAATATATAAGGCGACAGAGCCTGATGGCCCCCGCCCAAGGACTAAATGCGAAGGATCTCTGCTTGTGCTACACCACCGAAGTGATTTCCGATTGTGTCCTGGGCATTTCCGCCCAGAGTTTCACGGATAATCCCACACCCATGGTGGGAATGACCAAGCGCGTCTTCGAACAGTCTTTTGGCTTCATTTTCTACACGGTGGTCGCCAATCTATGGCCACCAATCACGAAATTCTACTCCGTTTCGCTGTTCGCCAAGGACGTGGCTGCGTTCTTCTATGACCTCATGCAGAAGTGCATCCAAGTTCGGCGGGAAAGTCCGGCGGCACAGCAGCGAGATGACTTCCTCAACTACATGTTGCAGTTGCAGGAGAAAAAGGGACTGAATGCGGCGGAGCTGACCTCGCACACAATGACATTTTTAACGGACGGATTCGAGACCACCGCACAAGTGCTTACCCACACACTCCTTTTCCTGGCACGCAATCCCAAGGAGCAGATGAAGTTGAGGGAGGAGATCGGTACCGCCGAGCTGACCTTTGAACAGATAAGTGAGCTGCCCTTCACCGAAGCCTGCATCCATGAAACTTTGAGAATTTTCTCACCTGTTCTGGCTGCCCGCAAGGTGGTAACTGAGCCCTGTGAACTGACGAACAAAAACGGAGTGAGCGTGAAACTGAGACCCGGGGATGTAGTCATCATTCCTGTGAACGCCTTGCACCACGATCCCCAATACTATGAGGAACCTCAATCGTTCAAGCCCGAGCGATTCCTGAACATCAATGGCGGAGCCAAAAAGTACAGAGATCAGGGTCTATTCTTTGGGTTTGGCGATGGACCACGTATTTGCCCCGGTATGCGGTTTTCACTTACCCAAATCAAAGCTGCCCTGGTGGAAATCGTGCGAAACTTCGACATCAAGGTTAATCCCAAAACTCGCAAGGATAATGAAATTGATGATACCTACTTTATGCCAGCCTTAAAAGGCGGCGTTTGGCTGGATTTTGTTGAACGCAATTAGTTATTCAATAATGTTACGACTTTATATTAAATATAGTTTATCCAGTTGCATACATGTTATATTTCCAAACA 1603 2004-08-09 15:56:24.230779 2002-04-30 16:10:52 SO__mRNA CG10833-RA 6 0 Cyp28d1:6 Drosophila__melanogaster 238 2004-08-09 15:56:24.665877 2004-08-09 15:56:24.665877 SO__exon CG10833:6 5212450 5212212 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 4 0 Cyp28d1:4 Drosophila__melanogaster 631 2004-08-09 15:56:24.587619 2004-08-09 15:56:24.587619 SO__exon CG10833:4 5211821 5211190 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 1 0 Cyp28d1:1 Drosophila__melanogaster 217 2004-08-09 15:56:24.453082 2004-08-09 15:56:24.453082 SO__exon CG10833:1 5210695 5210478 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 5 0 Cyp28d1:5 Drosophila__melanogaster 270 2004-08-09 15:56:24.626408 2004-08-09 15:56:24.626408 SO__exon CG10833:5 5212150 5211880 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 2 0 Cyp28d1:2 Drosophila__melanogaster 139 2004-08-09 15:56:24.502579 2004-08-09 15:56:24.502579 SO__exon CG10833:2 5210889 5210750 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof 3 0 Cyp28d1:3 Drosophila__melanogaster 108 2004-08-09 15:56:24.546345 2004-08-09 15:56:24.546345 SO__exon CG10833:3 5211061 5210953 Drosophila__melanogaster SO__chromosome_arm 2L 1 relationship type__partof CG10833-PA db__Gadfly 0 35dca04d49d72956485a3ecefc21ada4 Cyp28d1-PA Drosophila__melanogaster MCPISTALFVIAAILALIYVFLTWNFSYWKKRGIPTAKSWPFVGSFPSVFTQKRNVVYDIDEIYEQYKNTDSIVGVFQTRIPQLMVTTPEYAHKIYVSDFRSFHDNEMAKFTDSKTDPILANNPFVLTGEAWKERRAEVTPGLSANRVKAAYPVSLRVCKKFVEYIRRQSLMAPAQGLNAKDLCLCYTTEVISDCVLGISAQSFTDNPTPMVGMTKRVFEQSFGFIFYTVVANLWPPITKFYSVSLFAKDVAAFFYDLMQKCIQVRRESPAAQQRDDFLNYMLQLQEKKGLNAAELTSHTMTFLTDGFETTAQVLTHTLLFLARNPKEQMKLREEIGTAELTFEQISELPFTEACIHETLRIFSPVLAARKVVTEPCELTNKNGVSVKLRPGDVVIIPVNALHHDPQYYEEPQSFKPERFLNINGGAKKYRDQGLFFGFGDGPRICPGMRFSLTQIKAALVEIVRNFDIKVNPKTRKDNEIDDTYFMPALKGGVWLDFVERN 502 2004-08-09 15:56:24.711814 2004-08-09 15:56:24.711814 SO__protein CG10833-PA 5212376 5210501 Drosophila__melanogaster SO__chromosome_arm 2L 1 AAF52226.1 db__GB_protein FBpp0078698 db__FlyBase CG10833-PA db__Gadfly 0 pub type__computer file gadfly3 CG10833-PA synonym type__synonym relationship type__producedby 5212450 5210478 Drosophila__melanogaster SO__chromosome_arm 2L 1 FBtr0079062 db__FlyBase CG10833-RA db__Gadfly 0 pub type__computer file joshk CG10833-RA synonym type__synonym pub type__computer file gadfly3 CG10833-RA synonym type__synonym property type__owner joshk property type__sp_comment Perfect match to REAL SP with corresponding FBgn property type__protein_id AAF52226 relationship type__partof property type__sp_status Perfect match to SwissProt real (computational) property type__cyto_range 25C10-25C10 property type__gbunit AE003609 FBgn0031689 db__FlyBase CG10833 db__Gadfly FBan0010833 db__FlyBase 0 pub type__computer file gadfly3 28d1 synonym type__synonym 5212450 5210478 Drosophila__melanogaster SO__chromosome_arm 2L 1 chado-1.23/bin/addcascades000755 000765 000024 00000003514 11256710012 015505 0ustar00cainstaff000000 000000 #!/usr/local/bin/perl -i.old # USAGE: addcascades # Adds delete propagation commands to schema files. # -Adds "on delete cascade" if column is not nullable. # -Adds "on delete set null" if column is nullable. # WARNING: modifies files in place. Saves old versions as *.old. # WARNING: relies on syntactic convention that original file foreign key refs # are on same line or next line as column info. If elsewhere in or # outside of table def it will not work, and a warning will be issued, # and a comment "-- no delete action" will be appended to the line # so it can be easily found. # WARNING: Foreign keys with existing cascade info are not touched. # Therefore you can use this repeatedly to add cascades to new tables, # but if nullness of a column changes you must update by hand. # open(STDIN, "../dat/chado.ddl") || die "Can't open"; while(<>){ $i++; if(/^(.*)\sforeign\s+key\s+\(([^\)]*)\)\s*references\s+(\S+)\s+\(([^\)]+)\)\s*(,?)/i){ # should check for old cascade info -- update in case nullness changes? no, do by hand $pre=$1; $fkcol=$2; $fktable=$3; $joincol=$4; $comma=$5; if(/^\s*--/){ print; next; } # skip comment lines if( $prevcol ne $fkcol){ chop; warn "$i Warning 1: Ignoring $prev$_\n"; print "$_ -- no delete action\n"; } else { if(/^(.*\S)\s*$/) { $line=$1; if( $line =~ /^(.*),$/){ $line = $1; } } else { die; } # print "$prev$_=>"; # \t$fktable\t$joincol\n\n"; print $line, " on delete "; if( $null ){ print "set null"; } else { print "cascade"; } print "$comma\n"; } } elsif(/foreign/) { chop; warn "Warning 2: Ignoring $_\n"; print "$_ -- no delete action\n"; } else { print $_; if(/^\s*(\S+)\s(.*)$/){ $prevcol = $1; if( $2 =~ /not null/i){ $null=0; } else { $null=1; } }} $prev=$_; } chado-1.23/bin/AutoDBI.PL000644 000765 000024 00001023363 11610541347 015040 0ustar00cainstaff000000 000000 #!perl use Config; use File::Basename qw(&basename &dirname); use File::Spec; use FindBin '$Bin'; use Cwd; my %OPTIONS; if (open F,"$Bin/../build.conf") { while () { next if /^\#/; chomp; $OPTIONS{$1} = $2 if /^(\w+)\s*=\s*(.+)/; } close F; } $file = basename($0, '.PL','.PLS'); $file = "$Bin/../lib/Bio/Chado/$file.pm"; open OUT,">$file" or die "Can't create $file: $!"; print "Extracting $file (with variable substitutions)\n"; my $startperl = $Config{startperl} ne '#!perl' ? $Config{startperl} : "#!$Config{perlpath}"; print OUT <<'!NO!SUBS!'; ########DBI######## package Bio::Chado::DBI; # Created by SQL::Translator::Producer::TTSchema # Template used: dbi.tt2 use strict; use Data::Dumper; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; no warnings 'redefine'; use base qw(Class::DBI::Pg); # This is how you normally connect with Class DBI's connection pooling but # its very fragile for me on FC2. I'm replacing it with the db_Main method below #Bio::Chado::DBI->set_db('Main', 'dbi:Pg:dbname=chado', 'cain', ''); my $db_options = { __PACKAGE__->_default_attributes }; __PACKAGE__->_remember_handle('Main'); # so dbi_commit works $db_options->{AutoCommit} = 0; sub db_Main { my $DBPROFILE ||= 'default'; #might want to allow passing this in somehow my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ); my $dbname = $db_conf->name; my $dbhost = $db_conf->host; my $dbport = $db_conf->port; my $dbuser = $db_conf->user; my $dbpass = $db_conf->password; my $dbh; $dbh = DBI->connect_cached( "dbi:Pg:dbname=$dbname;host=$dbhost;port=$dbport", $dbuser, $dbpass, $db_options ); # clear the connection cache if can't ping if ($dbh->ping() < 1) { my $CachedKids_hashref = $dbh->{Driver}->{CachedKids}; %$CachedKids_hashref = () if $CachedKids_hashref; $dbh = DBI->connect_cached( "dbi:Pg:dbname=$dbname;host=$dbhost;port=$dbport", $dbuser, $dbpass, $db_options ); warn("Database handle reset!: ".$dbh." ping: ".$dbh->ping()); } return($dbh); } sub search_ilike { shift->_do_search(ILIKE => @_ ) } sub search_lower { my $c = shift; my %q = @_; my %t; foreach my $k (keys %q){ $t{"lower($k)"} = lc($q{$k}); } $c->_do_search(LIKE => %t); } # debug method sub dump { my $self = shift; my %arg = %{shift @_}; $arg{'indent'} ||= 1; $arg{'depth'} ||= 3; $Data::Dumper::Maxdepth = $arg{'depth'} if defined $arg{'depth'}; $Data::Dumper::Indent = $arg{'indent'} if defined $arg{'indent'}; return(Dumper($arg{'object'})); } # # # NOT PART OF THE API, but useful function which returns a single row # and throws an error if more than one is returned # # Added as a utility function for modware # sub get_single_row { my ($proto, @args) = @_; my $class = ref $proto || $proto; my @rows = $class->search( @args ); my $count = @rows; die "only one row expected, @rows returned" if @rows > 1; return $rows[0]; } 1; ########Bio::Chado::CDBI::Study_Assay######## package Bio::Chado::CDBI::Study_Assay; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Study_Assay->set_up_table('study_assay'); # # Primary key accessors # sub id { shift->study_assay_id } sub study_assay { shift->study_assay_id } # # Has A # Bio::Chado::CDBI::Study_Assay->has_a(study_id => 'Bio::Chado::CDBI::Study'); sub Bio::Chado::CDBI::Study_Assay::study { return shift->study_id } Bio::Chado::CDBI::Study_Assay->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Study_Assay::assay { return shift->assay_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Dbxref######## package Bio::Chado::CDBI::Feature_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Dbxref->set_up_table('feature_dbxref'); # # Primary key accessors # sub id { shift->feature_dbxref_id } sub feature_dbxref { shift->feature_dbxref_id } # # Has A # Bio::Chado::CDBI::Feature_Dbxref->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Dbxref::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Feature_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Quantification######## package Bio::Chado::CDBI::Quantification; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Quantification->set_up_table('quantification'); # # Primary key accessors # sub id { shift->quantification_id } sub quantification { shift->quantification_id } # # Has A # Bio::Chado::CDBI::Quantification->has_a(acquisition_id => 'Bio::Chado::CDBI::Acquisition'); sub Bio::Chado::CDBI::Quantification::acquisition { return shift->acquisition_id } Bio::Chado::CDBI::Quantification->has_a(operator_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Quantification::contact { return shift->operator_id } Bio::Chado::CDBI::Quantification->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Quantification::protocol { return shift->protocol_id } Bio::Chado::CDBI::Quantification->has_a(analysis_id => 'Bio::Chado::CDBI::Analysis'); sub Bio::Chado::CDBI::Quantification::analysis { return shift->analysis_id } # # Has Many # Bio::Chado::CDBI::Quantification->has_many('quantification_relationship_subject_id', 'Bio::Chado::CDBI::Quantification_Relationship' => 'subject_id'); Bio::Chado::CDBI::Quantification->has_many('quantification_relationship_object_id', 'Bio::Chado::CDBI::Quantification_Relationship' => 'object_id'); Bio::Chado::CDBI::Quantification->has_many('elementresult_quantification_id', 'Bio::Chado::CDBI::Elementresult' => 'quantification_id'); sub elementresults { return shift->elementresult_quantification_id } Bio::Chado::CDBI::Quantification->has_many('quantificationprop_quantification_id', 'Bio::Chado::CDBI::Quantificationprop' => 'quantification_id'); sub quantificationprops { return shift->quantificationprop_quantification_id } # # Has Compound Many (many to many relationships in all their flavors) # sub quantification_relationship_subjects { return shift->quantification_relationship_subject_id } sub quantification_relationship_objects { return shift->quantification_relationship_object_id } # one to many to one # one to many to many #many to many to one # many2one # sub quantification_relationship_subject_types { my $self = shift; return map $_->type_id, $self->quantification_relationship_subject_id } sub quantification_relationship_object_types { my $self = shift; return map $_->type_id, $self->quantification_relationship_object_id } #many to many to many 1; ########Bio::Chado::CDBI::Mageml######## package Bio::Chado::CDBI::Mageml; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Mageml->set_up_table('mageml'); # # Primary key accessors # sub id { shift->mageml_id } sub mageml { shift->mageml_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Mageml->has_many('magedocumentation_mageml_id', 'Bio::Chado::CDBI::Magedocumentation' => 'mageml_id'); sub magedocumentations { return shift->magedocumentation_mageml_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Expression######## package Bio::Chado::CDBI::Feature_Expression; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Expression->set_up_table('feature_expression'); # # Primary key accessors # sub id { shift->feature_expression_id } sub feature_expression { shift->feature_expression_id } # # Has A # Bio::Chado::CDBI::Feature_Expression->has_a(expression_id => 'Bio::Chado::CDBI::Expression'); sub Bio::Chado::CDBI::Feature_Expression::expression { return shift->expression_id } Bio::Chado::CDBI::Feature_Expression->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Expression::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Expression->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Expression::pub { return shift->pub_id } # # Has Many # Bio::Chado::CDBI::Feature_Expression->has_many('feature_expressionprop_feature_expression_id', 'Bio::Chado::CDBI::Feature_Expressionprop' => 'feature_expression_id'); sub feature_expressionprops { return shift->feature_expressionprop_feature_expression_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Cvterm######## package Bio::Chado::CDBI::Feature_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Cvterm->set_up_table('feature_cvterm'); # # Primary key accessors # sub id { shift->feature_cvterm_id } sub feature_cvterm { shift->feature_cvterm_id } # # Has A # Bio::Chado::CDBI::Feature_Cvterm->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Cvterm::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Feature_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Cvterm::pub { return shift->pub_id } # # Has Many # Bio::Chado::CDBI::Feature_Cvterm->has_many('feature_cvterm_dbxref_feature_cvterm_id', 'Bio::Chado::CDBI::Feature_Cvterm_Dbxref' => 'feature_cvterm_id'); Bio::Chado::CDBI::Feature_Cvterm->has_many('feature_cvtermprop_feature_cvterm_id', 'Bio::Chado::CDBI::Feature_Cvtermprop' => 'feature_cvterm_id'); sub feature_cvtermprops { return shift->feature_cvtermprop_feature_cvterm_id } Bio::Chado::CDBI::Feature_Cvterm->has_many('feature_cvterm_pub_feature_cvterm_id', 'Bio::Chado::CDBI::Feature_Cvterm_Pub' => 'feature_cvterm_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub feature_cvterm_dbxref_feature_cvterms { return shift->feature_cvterm_dbxref_feature_cvterm_id } sub feature_cvterm_pub_feature_cvterms { return shift->feature_cvterm_pub_feature_cvterm_id } # one to many to one # one2one # sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->feature_cvterm_dbxref_feature_cvterm_id } sub pubs { my $self = shift; return map $_->pub_id, $self->feature_cvterm_pub_feature_cvterm_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Arraydesign######## package Bio::Chado::CDBI::Arraydesign; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Arraydesign->set_up_table('arraydesign'); # # Primary key accessors # sub id { shift->arraydesign_id } sub arraydesign { shift->arraydesign_id } # # Has A # Bio::Chado::CDBI::Arraydesign->has_a(manufacturer_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Arraydesign::contact { return shift->manufacturer_id } Bio::Chado::CDBI::Arraydesign->has_a(platformtype_id => 'Bio::Chado::CDBI::Cvterm'); sub platformtype { return shift->platformtype_id } Bio::Chado::CDBI::Arraydesign->has_a(substratetype_id => 'Bio::Chado::CDBI::Cvterm'); sub substratetype { return shift->substratetype_id } Bio::Chado::CDBI::Arraydesign->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Arraydesign::protocol { return shift->protocol_id } Bio::Chado::CDBI::Arraydesign->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Arraydesign::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Arraydesign->has_many('assay_arraydesign_id', 'Bio::Chado::CDBI::Assay' => 'arraydesign_id'); sub assays { return shift->assay_arraydesign_id } Bio::Chado::CDBI::Arraydesign->has_many('element_arraydesign_id', 'Bio::Chado::CDBI::Element' => 'arraydesign_id'); Bio::Chado::CDBI::Arraydesign->has_many('arraydesignprop_arraydesign_id', 'Bio::Chado::CDBI::Arraydesignprop' => 'arraydesign_id'); sub arraydesignprops { return shift->arraydesignprop_arraydesign_id } # # Has Compound Many (many to many relationships in all their flavors) # sub element_arraydesigns { return shift->element_arraydesign_id } sub element_arraydesigns { return shift->element_arraydesign_id } sub element_arraydesigns { return shift->element_arraydesign_id } # one to many to one # one2one # sub features { my $self = shift; return map $_->feature_id, $self->element_arraydesign_id } sub cvterms { my $self = shift; return map $_->type_id, $self->element_arraydesign_id } sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->element_arraydesign_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Cvtermprop######## package Bio::Chado::CDBI::Stock_Cvtermprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Cvtermprop->set_up_table('stock_cvtermprop'); # # Primary key accessors # sub id { shift->stock_cvtermprop_id } sub stock_cvtermprop { shift->stock_cvtermprop_id } # # Has A # Bio::Chado::CDBI::Stock_Cvtermprop->has_a(stock_cvterm_id => 'Bio::Chado::CDBI::Stock_Cvterm'); sub Bio::Chado::CDBI::Stock_Cvtermprop::stock_cvterm { return shift->stock_cvterm_id } Bio::Chado::CDBI::Stock_Cvtermprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock_Cvtermprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Dbxref######## package Bio::Chado::CDBI::Cell_Line_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Dbxref->set_up_table('cell_line_dbxref'); # # Primary key accessors # sub id { shift->cell_line_dbxref_id } sub cell_line_dbxref { shift->cell_line_dbxref_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Dbxref->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Dbxref::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Cell_Line_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Biomaterial_Relationship######## package Bio::Chado::CDBI::Biomaterial_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Biomaterial_Relationship->set_up_table('biomaterial_relationship'); # # Primary key accessors # sub id { shift->biomaterial_relationship_id } sub biomaterial_relationship { shift->biomaterial_relationship_id } # # Has A # Bio::Chado::CDBI::Biomaterial_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Biomaterial'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Biomaterial_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Biomaterial_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Biomaterial_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Biomaterial'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Feature######## package Bio::Chado::CDBI::Cell_Line_Feature; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Feature->set_up_table('cell_line_feature'); # # Primary key accessors # sub id { shift->cell_line_feature_id } sub cell_line_feature { shift->cell_line_feature_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Feature->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Feature::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Feature->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Cell_Line_Feature::feature { return shift->feature_id } Bio::Chado::CDBI::Cell_Line_Feature->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Line_Feature::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Geolocation######## package Bio::Chado::CDBI::Nd_Geolocation; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Geolocation->set_up_table('nd_geolocation'); # # Primary key accessors # sub id { shift->nd_geolocation_id } sub nd_geolocation { shift->nd_geolocation_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Nd_Geolocation->has_many('nd_experiment_nd_geolocation_id', 'Bio::Chado::CDBI::Nd_Experiment' => 'nd_geolocation_id'); Bio::Chado::CDBI::Nd_Geolocation->has_many('nd_geolocationprop_nd_geolocation_id', 'Bio::Chado::CDBI::Nd_Geolocationprop' => 'nd_geolocation_id'); sub nd_geolocationprops { return shift->nd_geolocationprop_nd_geolocation_id } # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_nd_geolocations { return shift->nd_experiment_nd_geolocation_id } # one to many to one # one2one # sub cvterms { my $self = shift; return map $_->type_id, $self->nd_experiment_nd_geolocation_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Phenotype######## package Bio::Chado::CDBI::Feature_Phenotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Phenotype->set_up_table('feature_phenotype'); # # Primary key accessors # sub id { shift->feature_phenotype_id } sub feature_phenotype { shift->feature_phenotype_id } # # Has A # Bio::Chado::CDBI::Feature_Phenotype->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Phenotype::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Phenotype->has_a(phenotype_id => 'Bio::Chado::CDBI::Phenotype'); sub Bio::Chado::CDBI::Feature_Phenotype::phenotype { return shift->phenotype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Relationship######## package Bio::Chado::CDBI::Cell_Line_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Relationship->set_up_table('cell_line_relationship'); # # Primary key accessors # sub id { shift->cell_line_relationship_id } sub cell_line_relationship { shift->cell_line_relationship_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Cell_Line'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Cell_Line_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Cell_Line'); sub object { return shift->object_id } Bio::Chado::CDBI::Cell_Line_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cell_Line_Relationship::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Quantification_Relationship######## package Bio::Chado::CDBI::Quantification_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Quantification_Relationship->set_up_table('quantification_relationship'); # # Primary key accessors # sub id { shift->quantification_relationship_id } sub quantification_relationship { shift->quantification_relationship_id } # # Has A # Bio::Chado::CDBI::Quantification_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Quantification'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Quantification_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Quantification_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Quantification_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Quantification'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Synonym######## package Bio::Chado::CDBI::Cell_Line_Synonym; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Synonym->set_up_table('cell_line_synonym'); # # Primary key accessors # sub id { shift->cell_line_synonym_id } sub cell_line_synonym { shift->cell_line_synonym_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Synonym->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Synonym::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Synonym->has_a(synonym_id => 'Bio::Chado::CDBI::Synonym'); sub Bio::Chado::CDBI::Cell_Line_Synonym::synonym { return shift->synonym_id } Bio::Chado::CDBI::Cell_Line_Synonym->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Line_Synonym::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Analysis######## package Bio::Chado::CDBI::Analysis; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Analysis->set_up_table('analysis'); # # Primary key accessors # sub id { shift->analysis_id } sub analysis { shift->analysis_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Analysis->has_many('quantification_analysis_id', 'Bio::Chado::CDBI::Quantification' => 'analysis_id'); sub quantifications { return shift->quantification_analysis_id } Bio::Chado::CDBI::Analysis->has_many('analysisfeature_analysis_id', 'Bio::Chado::CDBI::Analysisfeature' => 'analysis_id'); sub analysisfeatures { return shift->analysisfeature_analysis_id } Bio::Chado::CDBI::Analysis->has_many('analysisprop_analysis_id', 'Bio::Chado::CDBI::Analysisprop' => 'analysis_id'); sub analysisprops { return shift->analysisprop_analysis_id } Bio::Chado::CDBI::Analysis->has_many('phylotree_analysis_id', 'Bio::Chado::CDBI::Phylotree' => 'analysis_id'); sub phylotrees { return shift->phylotree_analysis_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Eimage######## package Bio::Chado::CDBI::Eimage; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Eimage->set_up_table('eimage'); # # Primary key accessors # sub id { shift->eimage_id } sub eimage { shift->eimage_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Eimage->has_many('expression_image_eimage_id', 'Bio::Chado::CDBI::Expression_Image' => 'eimage_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub expression_image_eimages { return shift->expression_image_eimage_id } # one to many to one # one2one # sub expressions { my $self = shift; return map $_->expression_id, $self->expression_image_eimage_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phenotype_Comparison_Cvterm######## package Bio::Chado::CDBI::Phenotype_Comparison_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phenotype_Comparison_Cvterm->set_up_table('phenotype_comparison_cvterm'); # # Primary key accessors # sub id { shift->phenotype_comparison_cvterm_id } sub phenotype_comparison_cvterm { shift->phenotype_comparison_cvterm_id } # # Has A # Bio::Chado::CDBI::Phenotype_Comparison_Cvterm->has_a(phenotype_comparison_id => 'Bio::Chado::CDBI::Phenotype_Comparison'); sub Bio::Chado::CDBI::Phenotype_Comparison_Cvterm::phenotype_comparison { return shift->phenotype_comparison_id } Bio::Chado::CDBI::Phenotype_Comparison_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phenotype_Comparison_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Phenotype_Comparison_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phenotype_Comparison_Cvterm::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Synonym######## package Bio::Chado::CDBI::Synonym; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Synonym->set_up_table('synonym'); # # Primary key accessors # sub id { shift->synonym_id } sub synonym { shift->synonym_id } # # Has A # Bio::Chado::CDBI::Synonym->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Synonym::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Synonym->has_many('cell_line_synonym_synonym_id', 'Bio::Chado::CDBI::Cell_Line_Synonym' => 'synonym_id'); sub cell_line_synonyms { return shift->cell_line_synonym_synonym_id } Bio::Chado::CDBI::Synonym->has_many('library_synonym_synonym_id', 'Bio::Chado::CDBI::Library_Synonym' => 'synonym_id'); sub library_synonyms { return shift->library_synonym_synonym_id } Bio::Chado::CDBI::Synonym->has_many('feature_synonym_synonym_id', 'Bio::Chado::CDBI::Feature_Synonym' => 'synonym_id'); sub feature_synonyms { return shift->feature_synonym_synonym_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvtermpath######## package Bio::Chado::CDBI::Cvtermpath; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvtermpath->set_up_table('cvtermpath'); # # Primary key accessors # sub id { shift->cvtermpath_id } sub cvtermpath { shift->cvtermpath_id } # # Has A # Bio::Chado::CDBI::Cvtermpath->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub type { return shift->type_id } Bio::Chado::CDBI::Cvtermpath->has_a(subject_id => 'Bio::Chado::CDBI::Cvterm'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Cvtermpath->has_a(object_id => 'Bio::Chado::CDBI::Cvterm'); sub object { return shift->object_id } Bio::Chado::CDBI::Cvtermpath->has_a(cv_id => 'Bio::Chado::CDBI::Cv'); sub Bio::Chado::CDBI::Cvtermpath::cv { return shift->cv_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvterm_Relationship######## package Bio::Chado::CDBI::Cvterm_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvterm_Relationship->set_up_table('cvterm_relationship'); # # Primary key accessors # sub id { shift->cvterm_relationship_id } sub cvterm_relationship { shift->cvterm_relationship_id } # # Has A # Bio::Chado::CDBI::Cvterm_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub type { return shift->type_id } Bio::Chado::CDBI::Cvterm_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Cvterm'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Cvterm_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Cvterm'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonode_Pub######## package Bio::Chado::CDBI::Phylonode_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonode_Pub->set_up_table('phylonode_pub'); # # Primary key accessors # sub id { shift->phylonode_pub_id } sub phylonode_pub { shift->phylonode_pub_id } # # Has A # Bio::Chado::CDBI::Phylonode_Pub->has_a(phylonode_id => 'Bio::Chado::CDBI::Phylonode'); sub Bio::Chado::CDBI::Phylonode_Pub::phylonode { return shift->phylonode_id } Bio::Chado::CDBI::Phylonode_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phylonode_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonode_Organism######## package Bio::Chado::CDBI::Phylonode_Organism; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonode_Organism->set_up_table('phylonode_organism'); # # Primary key accessors # sub id { shift->phylonode_organism_id } sub phylonode_organism { shift->phylonode_organism_id } # # Has A # Bio::Chado::CDBI::Phylonode_Organism->has_a(phylonode_id => 'Bio::Chado::CDBI::Phylonode'); sub Bio::Chado::CDBI::Phylonode_Organism::phylonode { return shift->phylonode_id } Bio::Chado::CDBI::Phylonode_Organism->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Phylonode_Organism::organism { return shift->organism_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Pub######## package Bio::Chado::CDBI::Nd_Experiment_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Pub->set_up_table('nd_experiment_pub'); # # Primary key accessors # sub id { shift->nd_experiment_pub_id } sub nd_experiment_pub { shift->nd_experiment_pub_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Pub->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Pub::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Nd_Experiment_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Biomaterial_Dbxref######## package Bio::Chado::CDBI::Biomaterial_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Biomaterial_Dbxref->set_up_table('biomaterial_dbxref'); # # Primary key accessors # sub id { shift->biomaterial_dbxref_id } sub biomaterial_dbxref { shift->biomaterial_dbxref_id } # # Has A # Bio::Chado::CDBI::Biomaterial_Dbxref->has_a(biomaterial_id => 'Bio::Chado::CDBI::Biomaterial'); sub Bio::Chado::CDBI::Biomaterial_Dbxref::biomaterial { return shift->biomaterial_id } Bio::Chado::CDBI::Biomaterial_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Biomaterial_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Genotypeprop######## package Bio::Chado::CDBI::Genotypeprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Genotypeprop->set_up_table('genotypeprop'); # # Primary key accessors # sub id { shift->genotypeprop_id } sub genotypeprop { shift->genotypeprop_id } # # Has A # Bio::Chado::CDBI::Genotypeprop->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Genotypeprop::genotype { return shift->genotype_id } Bio::Chado::CDBI::Genotypeprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Genotypeprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Genotype######## package Bio::Chado::CDBI::Genotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Genotype->set_up_table('genotype'); # # Primary key accessors # sub id { shift->genotype_id } sub genotype { shift->genotype_id } # # Has A # Bio::Chado::CDBI::Genotype->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Genotype::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Genotype->has_many('genotypeprop_genotype_id', 'Bio::Chado::CDBI::Genotypeprop' => 'genotype_id'); sub genotypeprops { return shift->genotypeprop_genotype_id } Bio::Chado::CDBI::Genotype->has_many('nd_experiment_genotype_genotype_id', 'Bio::Chado::CDBI::Nd_Experiment_Genotype' => 'genotype_id'); Bio::Chado::CDBI::Genotype->has_many('stock_genotype_genotype_id', 'Bio::Chado::CDBI::Stock_Genotype' => 'genotype_id'); Bio::Chado::CDBI::Genotype->has_many('phendesc_genotype_id', 'Bio::Chado::CDBI::Phendesc' => 'genotype_id'); sub phendescs { return shift->phendesc_genotype_id } Bio::Chado::CDBI::Genotype->has_many('phenotype_comparison_genotype1_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'genotype1_id'); Bio::Chado::CDBI::Genotype->has_many('phenotype_comparison_genotype2_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'genotype2_id'); Bio::Chado::CDBI::Genotype->has_many('feature_genotype_genotype_id', 'Bio::Chado::CDBI::Feature_Genotype' => 'genotype_id'); sub feature_genotypes { return shift->feature_genotype_genotype_id } Bio::Chado::CDBI::Genotype->has_many('phenstatement_genotype_id', 'Bio::Chado::CDBI::Phenstatement' => 'genotype_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub phenstatement_genotypes { return shift->phenstatement_genotype_id } sub phenstatement_genotypes { return shift->phenstatement_genotype_id } sub phenstatement_genotypes { return shift->phenstatement_genotype_id } sub phenstatement_genotypes { return shift->phenstatement_genotype_id } sub nd_experiment_genotype_genotypes { return shift->nd_experiment_genotype_genotype_id } sub phenotype_comparison_genotype1s { return shift->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2s { return shift->phenotype_comparison_genotype2_id } sub phenotype_comparison_genotype1s { return shift->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2s { return shift->phenotype_comparison_genotype2_id } sub phenotype_comparison_genotype1s { return shift->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2s { return shift->phenotype_comparison_genotype2_id } sub phenotype_comparison_genotype1s { return shift->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2s { return shift->phenotype_comparison_genotype2_id } sub stock_genotype_genotypes { return shift->stock_genotype_genotype_id } # one to many to one # one2one # sub environments { my $self = shift; return map $_->environment_id, $self->phenstatement_genotype_id } sub cvterms { my $self = shift; return map $_->type_id, $self->phenstatement_genotype_id } sub phenotypes { my $self = shift; return map $_->phenotype_id, $self->phenstatement_genotype_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phenstatement_genotype_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_genotype_genotype_id } sub stocks { my $self = shift; return map $_->stock_id, $self->stock_genotype_genotype_id } # one to many to many #many to many to one # many2one # sub phenotype_comparison_genotype1_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_genotype2_id } sub phenotype_comparison_genotype1_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_genotype1_id } sub phenotype_comparison_genotype2_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_genotype2_id } #many to many to many # many2many # sub phenotype_comparison_genotype1_environment1s { my $self = shift; return map $_->phenotype_comparison_environment1s, $self->phenotype_comparison_genotype1s } sub phenotype_comparison_genotype1_environment2s { my $self = shift; return map $_->phenotype_comparison_environment2s, $self->phenotype_comparison_genotype1s } sub phenotype_comparison_genotype2_environment1s { my $self = shift; return map $_->phenotype_comparison_environment1s, $self->phenotype_comparison_genotype2s } sub phenotype_comparison_genotype2_environment2s { my $self = shift; return map $_->phenotype_comparison_environment2s, $self->phenotype_comparison_genotype2s } sub phenotype_comparison_genotype1_phenotype1s { my $self = shift; return map $_->phenotype_comparison_phenotype1s, $self->phenotype_comparison_genotype1s } sub phenotype_comparison_genotype1_phenotype2s { my $self = shift; return map $_->phenotype_comparison_phenotype2s, $self->phenotype_comparison_genotype1s } sub phenotype_comparison_genotype2_phenotype1s { my $self = shift; return map $_->phenotype_comparison_phenotype1s, $self->phenotype_comparison_genotype2s } sub phenotype_comparison_genotype2_phenotype2s { my $self = shift; return map $_->phenotype_comparison_phenotype2s, $self->phenotype_comparison_genotype2s } 1; ########Bio::Chado::CDBI::Phylotree_Pub######## package Bio::Chado::CDBI::Phylotree_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylotree_Pub->set_up_table('phylotree_pub'); # # Primary key accessors # sub id { shift->phylotree_pub_id } sub phylotree_pub { shift->phylotree_pub_id } # # Has A # Bio::Chado::CDBI::Phylotree_Pub->has_a(phylotree_id => 'Bio::Chado::CDBI::Phylotree'); sub Bio::Chado::CDBI::Phylotree_Pub::phylotree { return shift->phylotree_id } Bio::Chado::CDBI::Phylotree_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phylotree_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Dbxref######## package Bio::Chado::CDBI::Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Dbxref->set_up_table('dbxref'); # # Primary key accessors # sub id { shift->dbxref_id } sub dbxref { shift->dbxref_id } # # Has A # Bio::Chado::CDBI::Dbxref->has_a(db_id => 'Bio::Chado::CDBI::Db'); sub Bio::Chado::CDBI::Dbxref::db { return shift->db_id } # # Has Many # Bio::Chado::CDBI::Dbxref->has_many('feature_dbxref_dbxref_id', 'Bio::Chado::CDBI::Feature_Dbxref' => 'dbxref_id'); sub feature_dbxrefs { return shift->feature_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('arraydesign_dbxref_id', 'Bio::Chado::CDBI::Arraydesign' => 'dbxref_id'); sub arraydesign_dbxrefs { return shift->arraydesign_dbxref_id } #sub --arraydesign--dbxref_id-- {} Bio::Chado::CDBI::Dbxref->has_many('cell_line_dbxref_dbxref_id', 'Bio::Chado::CDBI::Cell_Line_Dbxref' => 'dbxref_id'); sub cell_line_dbxrefs { return shift->cell_line_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('biomaterial_dbxref_dbxref_id', 'Bio::Chado::CDBI::Biomaterial_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('dbxrefprop_dbxref_id', 'Bio::Chado::CDBI::Dbxrefprop' => 'dbxref_id'); sub dbxrefprops { return shift->dbxrefprop_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('feature_cvterm_dbxref_dbxref_id', 'Bio::Chado::CDBI::Feature_Cvterm_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('protocol_dbxref_id', 'Bio::Chado::CDBI::Protocol' => 'dbxref_id'); sub protocols { return shift->protocol_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('feature_dbxref_id', 'Bio::Chado::CDBI::Feature' => 'dbxref_id'); sub feature_dbxrefs { return shift->feature_dbxref_id } #sub --feature--dbxref_id-- {} Bio::Chado::CDBI::Dbxref->has_many('stock_dbxref_dbxref_id', 'Bio::Chado::CDBI::Stock_Dbxref' => 'dbxref_id'); sub stock_dbxrefs { return shift->stock_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('cvterm_dbxref_dbxref_id', 'Bio::Chado::CDBI::Cvterm_Dbxref' => 'dbxref_id'); sub cvterm_dbxrefs { return shift->cvterm_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('stock_dbxref_id', 'Bio::Chado::CDBI::Stock' => 'dbxref_id'); sub stocks { return shift->stock_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('biomaterial_dbxref_id', 'Bio::Chado::CDBI::Biomaterial' => 'dbxref_id'); sub biomaterial_dbxrefs { return shift->biomaterial_dbxref_id } #sub --biomaterial--dbxref_id-- {} Bio::Chado::CDBI::Dbxref->has_many('pub_dbxref_dbxref_id', 'Bio::Chado::CDBI::Pub_Dbxref' => 'dbxref_id'); sub pub_dbxrefs { return shift->pub_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('assay_dbxref_id', 'Bio::Chado::CDBI::Assay' => 'dbxref_id'); sub assays { return shift->assay_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('organism_dbxref_dbxref_id', 'Bio::Chado::CDBI::Organism_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('study_dbxref_id', 'Bio::Chado::CDBI::Study' => 'dbxref_id'); sub studys { return shift->study_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('nd_experiment_stock_dbxref_dbxref_id', 'Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('element_dbxref_id', 'Bio::Chado::CDBI::Element' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('library_dbxref_dbxref_id', 'Bio::Chado::CDBI::Library_Dbxref' => 'dbxref_id'); sub library_dbxrefs { return shift->library_dbxref_dbxref_id } Bio::Chado::CDBI::Dbxref->has_many('phylonode_dbxref_dbxref_id', 'Bio::Chado::CDBI::Phylonode_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('nd_experiment_dbxref_dbxref_id', 'Bio::Chado::CDBI::Nd_Experiment_Dbxref' => 'dbxref_id'); Bio::Chado::CDBI::Dbxref->has_many('cvterm_dbxref_id', 'Bio::Chado::CDBI::Cvterm' => 'dbxref_id'); sub cvterm_dbxrefs { return shift->cvterm_dbxref_id } #sub --cvterm--dbxref_id-- {} Bio::Chado::CDBI::Dbxref->has_many('phylotree_dbxref_id', 'Bio::Chado::CDBI::Phylotree' => 'dbxref_id'); sub phylotrees { return shift->phylotree_dbxref_id } # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_stock_dbxref_dbxrefs { return shift->nd_experiment_stock_dbxref_dbxref_id } sub phylonode_dbxref_dbxrefs { return shift->phylonode_dbxref_dbxref_id } sub feature_cvterm_dbxref_dbxrefs { return shift->feature_cvterm_dbxref_dbxref_id } sub biomaterial_dbxref_dbxrefs { return shift->biomaterial_dbxref_dbxref_id } sub organism_dbxref_dbxrefs { return shift->organism_dbxref_dbxref_id } sub nd_experiment_dbxref_dbxrefs { return shift->nd_experiment_dbxref_dbxref_id } sub element_dbxrefs { return shift->element_dbxref_id } sub element_dbxrefs { return shift->element_dbxref_id } sub element_dbxrefs { return shift->element_dbxref_id } # one to many to one # one2one # sub nd_experiment_stocks { my $self = shift; return map $_->nd_experiment_stock_id, $self->nd_experiment_stock_dbxref_dbxref_id } sub phylonodes { my $self = shift; return map $_->phylonode_id, $self->phylonode_dbxref_dbxref_id } sub feature_cvterms { my $self = shift; return map $_->feature_cvterm_id, $self->feature_cvterm_dbxref_dbxref_id } sub biomaterials { my $self = shift; return map $_->biomaterial_id, $self->biomaterial_dbxref_dbxref_id } sub organisms { my $self = shift; return map $_->organism_id, $self->organism_dbxref_dbxref_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_dbxref_dbxref_id } sub features { my $self = shift; return map $_->feature_id, $self->element_dbxref_id } sub arraydesigns { my $self = shift; return map $_->arraydesign_id, $self->element_dbxref_id } sub cvterms { my $self = shift; return map $_->type_id, $self->element_dbxref_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Assayprop######## package Bio::Chado::CDBI::Assayprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Assayprop->set_up_table('assayprop'); # # Primary key accessors # sub id { shift->assayprop_id } sub assayprop { shift->assayprop_id } # # Has A # Bio::Chado::CDBI::Assayprop->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Assayprop::assay { return shift->assay_id } Bio::Chado::CDBI::Assayprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Assayprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Contact_Relationship######## package Bio::Chado::CDBI::Contact_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Contact_Relationship->set_up_table('contact_relationship'); # # Primary key accessors # sub id { shift->contact_relationship_id } sub contact_relationship { shift->contact_relationship_id } # # Has A # Bio::Chado::CDBI::Contact_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Contact_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Contact_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Contact'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Contact_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Contact'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Tableinfo######## package Bio::Chado::CDBI::Tableinfo; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Tableinfo->set_up_table('tableinfo'); # # Primary key accessors # sub id { shift->tableinfo_id } sub tableinfo { shift->tableinfo_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Tableinfo->has_many('control_tableinfo_id', 'Bio::Chado::CDBI::Control' => 'tableinfo_id'); sub controls { return shift->control_tableinfo_id } Bio::Chado::CDBI::Tableinfo->has_many('magedocumentation_tableinfo_id', 'Bio::Chado::CDBI::Magedocumentation' => 'tableinfo_id'); sub magedocumentations { return shift->magedocumentation_tableinfo_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Pub######## package Bio::Chado::CDBI::Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Pub->set_up_table('pub'); # # Primary key accessors # sub id { shift->pub_id } sub pub { shift->pub_id } # # Has A # Bio::Chado::CDBI::Pub->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Pub::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Pub->has_many('feature_expression_pub_id', 'Bio::Chado::CDBI::Feature_Expression' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('feature_cvterm_pub_id', 'Bio::Chado::CDBI::Feature_Cvterm' => 'pub_id'); sub feature_cvterm_pubs { return shift->feature_cvterm_pub_id } #sub --feature_cvterm--pub_id-- {} Bio::Chado::CDBI::Pub->has_many('cell_line_feature_pub_id', 'Bio::Chado::CDBI::Cell_Line_Feature' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('cell_line_synonym_pub_id', 'Bio::Chado::CDBI::Cell_Line_Synonym' => 'pub_id'); sub cell_line_synonyms { return shift->cell_line_synonym_pub_id } Bio::Chado::CDBI::Pub->has_many('phenotype_comparison_cvterm_pub_id', 'Bio::Chado::CDBI::Phenotype_Comparison_Cvterm' => 'pub_id'); sub phenotype_comparison_cvterms { return shift->phenotype_comparison_cvterm_pub_id } Bio::Chado::CDBI::Pub->has_many('phylonode_pub_pub_id', 'Bio::Chado::CDBI::Phylonode_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('nd_experiment_pub_pub_id', 'Bio::Chado::CDBI::Nd_Experiment_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('phylotree_pub_pub_id', 'Bio::Chado::CDBI::Phylotree_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('libraryprop_pub_pub_id', 'Bio::Chado::CDBI::Libraryprop_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('feature_pub_pub_id', 'Bio::Chado::CDBI::Feature_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('protocol_pub_id', 'Bio::Chado::CDBI::Protocol' => 'pub_id'); sub protocols { return shift->protocol_pub_id } Bio::Chado::CDBI::Pub->has_many('featureloc_pub_pub_id', 'Bio::Chado::CDBI::Featureloc_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('library_pub_pub_id', 'Bio::Chado::CDBI::Library_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('cell_line_library_pub_id', 'Bio::Chado::CDBI::Cell_Line_Library' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('stock_pub_pub_id', 'Bio::Chado::CDBI::Stock_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('feature_relationshipprop_pub_pub_id', 'Bio::Chado::CDBI::Feature_Relationshipprop_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('pub_dbxref_pub_id', 'Bio::Chado::CDBI::Pub_Dbxref' => 'pub_id'); sub pub_dbxrefs { return shift->pub_dbxref_pub_id } Bio::Chado::CDBI::Pub->has_many('stock_relationship_cvterm_pub_id', 'Bio::Chado::CDBI::Stock_Relationship_Cvterm' => 'pub_id'); sub stock_relationship_cvterms { return shift->stock_relationship_cvterm_pub_id } Bio::Chado::CDBI::Pub->has_many('phendesc_pub_id', 'Bio::Chado::CDBI::Phendesc' => 'pub_id'); sub phendescs { return shift->phendesc_pub_id } Bio::Chado::CDBI::Pub->has_many('featureprop_pub_pub_id', 'Bio::Chado::CDBI::Featureprop_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('library_synonym_pub_id', 'Bio::Chado::CDBI::Library_Synonym' => 'pub_id'); sub library_synonyms { return shift->library_synonym_pub_id } Bio::Chado::CDBI::Pub->has_many('pub_relationship_subject_id', 'Bio::Chado::CDBI::Pub_Relationship' => 'subject_id'); Bio::Chado::CDBI::Pub->has_many('pub_relationship_object_id', 'Bio::Chado::CDBI::Pub_Relationship' => 'object_id'); Bio::Chado::CDBI::Pub->has_many('expression_pub_pub_id', 'Bio::Chado::CDBI::Expression_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('study_pub_id', 'Bio::Chado::CDBI::Study' => 'pub_id'); sub studys { return shift->study_pub_id } Bio::Chado::CDBI::Pub->has_many('stock_cvterm_pub_id', 'Bio::Chado::CDBI::Stock_Cvterm' => 'pub_id'); sub stock_cvterms { return shift->stock_cvterm_pub_id } Bio::Chado::CDBI::Pub->has_many('cell_line_cvterm_pub_id', 'Bio::Chado::CDBI::Cell_Line_Cvterm' => 'pub_id'); sub cell_line_cvterms { return shift->cell_line_cvterm_pub_id } Bio::Chado::CDBI::Pub->has_many('stockprop_pub_pub_id', 'Bio::Chado::CDBI::Stockprop_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('pubauthor_pub_id', 'Bio::Chado::CDBI::Pubauthor' => 'pub_id'); sub pubauthors { return shift->pubauthor_pub_id } Bio::Chado::CDBI::Pub->has_many('phenotype_comparison_pub_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('cell_lineprop_pub_pub_id', 'Bio::Chado::CDBI::Cell_Lineprop_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('library_cvterm_pub_id', 'Bio::Chado::CDBI::Library_Cvterm' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('stock_relationship_pub_pub_id', 'Bio::Chado::CDBI::Stock_Relationship_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('feature_relationship_pub_pub_id', 'Bio::Chado::CDBI::Feature_Relationship_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('pubprop_pub_id', 'Bio::Chado::CDBI::Pubprop' => 'pub_id'); sub pubprops { return shift->pubprop_pub_id } Bio::Chado::CDBI::Pub->has_many('feature_cvterm_pub_pub_id', 'Bio::Chado::CDBI::Feature_Cvterm_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('feature_synonym_pub_id', 'Bio::Chado::CDBI::Feature_Synonym' => 'pub_id'); sub feature_synonyms { return shift->feature_synonym_pub_id } Bio::Chado::CDBI::Pub->has_many('cell_line_pub_pub_id', 'Bio::Chado::CDBI::Cell_Line_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('featuremap_pub_pub_id', 'Bio::Chado::CDBI::Featuremap_Pub' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('phenstatement_pub_id', 'Bio::Chado::CDBI::Phenstatement' => 'pub_id'); Bio::Chado::CDBI::Pub->has_many('project_pub_pub_id', 'Bio::Chado::CDBI::Project_Pub' => 'pub_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub featureprop_pub_pubs { return shift->featureprop_pub_pub_id } sub feature_relationshipprop_pub_pubs { return shift->feature_relationshipprop_pub_pub_id } sub feature_relationship_pub_pubs { return shift->feature_relationship_pub_pub_id } sub feature_expression_pubs { return shift->feature_expression_pub_id } sub feature_expression_pubs { return shift->feature_expression_pub_id } sub expression_pub_pubs { return shift->expression_pub_pub_id } sub pub_relationship_subjects { return shift->pub_relationship_subject_id } sub pub_relationship_objects { return shift->pub_relationship_object_id } sub phylotree_pub_pubs { return shift->phylotree_pub_pub_id } sub feature_cvterm_pub_pubs { return shift->feature_cvterm_pub_pub_id } sub phylonode_pub_pubs { return shift->phylonode_pub_pub_id } sub featureloc_pub_pubs { return shift->featureloc_pub_pub_id } sub featuremap_pub_pubs { return shift->featuremap_pub_pub_id } sub feature_pub_pubs { return shift->feature_pub_pub_id } sub phenstatement_pubs { return shift->phenstatement_pub_id } sub phenstatement_pubs { return shift->phenstatement_pub_id } sub phenstatement_pubs { return shift->phenstatement_pub_id } sub phenstatement_pubs { return shift->phenstatement_pub_id } sub stock_relationship_pub_pubs { return shift->stock_relationship_pub_pub_id } sub stock_pub_pubs { return shift->stock_pub_pub_id } sub phenotype_comparison_pubs { return shift->phenotype_comparison_pub_id } sub phenotype_comparison_pubs { return shift->phenotype_comparison_pub_id } sub phenotype_comparison_pubs { return shift->phenotype_comparison_pub_id } sub phenotype_comparison_pubs { return shift->phenotype_comparison_pub_id } sub stockprop_pub_pubs { return shift->stockprop_pub_pub_id } sub cell_line_pub_pubs { return shift->cell_line_pub_pub_id } sub cell_line_library_pubs { return shift->cell_line_library_pub_id } sub cell_line_library_pubs { return shift->cell_line_library_pub_id } sub nd_experiment_pub_pubs { return shift->nd_experiment_pub_pub_id } sub cell_lineprop_pub_pubs { return shift->cell_lineprop_pub_pub_id } sub cell_line_feature_pubs { return shift->cell_line_feature_pub_id } sub cell_line_feature_pubs { return shift->cell_line_feature_pub_id } sub libraryprop_pub_pubs { return shift->libraryprop_pub_pub_id } sub library_cvterm_pubs { return shift->library_cvterm_pub_id } sub library_cvterm_pubs { return shift->library_cvterm_pub_id } sub project_pub_pubs { return shift->project_pub_pub_id } sub library_pub_pubs { return shift->library_pub_pub_id } # one to many to one # one2one # sub featureprops { my $self = shift; return map $_->featureprop_id, $self->featureprop_pub_pub_id } sub feature_relationshipprops { my $self = shift; return map $_->feature_relationshipprop_id, $self->feature_relationshipprop_pub_pub_id } sub feature_relationships { my $self = shift; return map $_->feature_relationship_id, $self->feature_relationship_pub_pub_id } sub features { my $self = shift; return map $_->feature_id, $self->feature_expression_pub_id } sub expressions { my $self = shift; return map $_->expression_id, $self->feature_expression_pub_id } sub expressions { my $self = shift; return map $_->expression_id, $self->expression_pub_pub_id } sub phylotrees { my $self = shift; return map $_->phylotree_id, $self->phylotree_pub_pub_id } sub feature_cvterms { my $self = shift; return map $_->feature_cvterm_id, $self->feature_cvterm_pub_pub_id } sub phylonodes { my $self = shift; return map $_->phylonode_id, $self->phylonode_pub_pub_id } sub featurelocs { my $self = shift; return map $_->featureloc_id, $self->featureloc_pub_pub_id } sub featuremaps { my $self = shift; return map $_->featuremap_id, $self->featuremap_pub_pub_id } sub features { my $self = shift; return map $_->feature_id, $self->feature_pub_pub_id } sub environments { my $self = shift; return map $_->environment_id, $self->phenstatement_pub_id } sub cvterms { my $self = shift; return map $_->type_id, $self->phenstatement_pub_id } sub phenotypes { my $self = shift; return map $_->phenotype_id, $self->phenstatement_pub_id } sub genotypes { my $self = shift; return map $_->genotype_id, $self->phenstatement_pub_id } sub stock_relationships { my $self = shift; return map $_->stock_relationship_id, $self->stock_relationship_pub_pub_id } sub stocks { my $self = shift; return map $_->stock_id, $self->stock_pub_pub_id } sub organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_pub_id } sub stockprops { my $self = shift; return map $_->stockprop_id, $self->stockprop_pub_pub_id } sub cell_lines { my $self = shift; return map $_->cell_line_id, $self->cell_line_pub_pub_id } sub cell_lines { my $self = shift; return map $_->cell_line_id, $self->cell_line_library_pub_id } sub librarys { my $self = shift; return map $_->library_id, $self->cell_line_library_pub_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_pub_pub_id } sub cell_lineprops { my $self = shift; return map $_->cell_lineprop_id, $self->cell_lineprop_pub_pub_id } sub features { my $self = shift; return map $_->feature_id, $self->cell_line_feature_pub_id } sub cell_lines { my $self = shift; return map $_->cell_line_id, $self->cell_line_feature_pub_id } sub libraryprops { my $self = shift; return map $_->libraryprop_id, $self->libraryprop_pub_pub_id } sub cvterms { my $self = shift; return map $_->cvterm_id, $self->library_cvterm_pub_id } sub librarys { my $self = shift; return map $_->library_id, $self->library_cvterm_pub_id } sub projects { my $self = shift; return map $_->project_id, $self->project_pub_pub_id } sub librarys { my $self = shift; return map $_->library_id, $self->library_pub_pub_id } # one to many to many # one2many # sub phenotype_comparison_environment1s { my $self = shift; return map $_->environment1_id, $self->phenotype_comparison_pub_id } sub phenotype_comparison_phenotype1s { my $self = shift; return map $_->phenotype1_id, $self->phenotype_comparison_pub_id } sub phenotype_comparison_genotype1s { my $self = shift; return map $_->genotype1_id, $self->phenotype_comparison_pub_id } #many to many to one # many2one # sub pub_relationship_subject_types { my $self = shift; return map $_->type_id, $self->pub_relationship_subject_id } sub pub_relationship_object_types { my $self = shift; return map $_->type_id, $self->pub_relationship_object_id } #many to many to many 1; ########Bio::Chado::CDBI::Organismprop######## package Bio::Chado::CDBI::Organismprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Organismprop->set_up_table('organismprop'); # # Primary key accessors # sub id { shift->organismprop_id } sub organismprop { shift->organismprop_id } # # Has A # Bio::Chado::CDBI::Organismprop->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Organismprop::organism { return shift->organism_id } Bio::Chado::CDBI::Organismprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Organismprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Libraryprop_Pub######## package Bio::Chado::CDBI::Libraryprop_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Libraryprop_Pub->set_up_table('libraryprop_pub'); # # Primary key accessors # sub id { shift->libraryprop_pub_id } sub libraryprop_pub { shift->libraryprop_pub_id } # # Has A # Bio::Chado::CDBI::Libraryprop_Pub->has_a(libraryprop_id => 'Bio::Chado::CDBI::Libraryprop'); sub Bio::Chado::CDBI::Libraryprop_Pub::libraryprop { return shift->libraryprop_id } Bio::Chado::CDBI::Libraryprop_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Libraryprop_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Dbxrefprop######## package Bio::Chado::CDBI::Dbxrefprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Dbxrefprop->set_up_table('dbxrefprop'); # # Primary key accessors # sub id { shift->dbxrefprop_id } sub dbxrefprop { shift->dbxrefprop_id } # # Has A # Bio::Chado::CDBI::Dbxrefprop->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Dbxrefprop::dbxref { return shift->dbxref_id } Bio::Chado::CDBI::Dbxrefprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Dbxrefprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Contact######## package Bio::Chado::CDBI::Nd_Experiment_Contact; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Contact->set_up_table('nd_experiment_contact'); # # Primary key accessors # sub id { shift->nd_experiment_contact_id } sub nd_experiment_contact { shift->nd_experiment_contact_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Contact->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Contact::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Contact->has_a(contact_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Nd_Experiment_Contact::contact { return shift->contact_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featureloc######## package Bio::Chado::CDBI::Featureloc; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featureloc->set_up_table('featureloc'); # # Primary key accessors # sub id { shift->featureloc_id } sub featureloc { shift->featureloc_id } # # Has A # Bio::Chado::CDBI::Featureloc->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub feature { return shift->feature_id } Bio::Chado::CDBI::Featureloc->has_a(srcfeature_id => 'Bio::Chado::CDBI::Feature'); sub srcfeature { return shift->srcfeature_id } # # Has Many # Bio::Chado::CDBI::Featureloc->has_many('featureloc_pub_featureloc_id', 'Bio::Chado::CDBI::Featureloc_Pub' => 'featureloc_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub featureloc_pub_featurelocs { return shift->featureloc_pub_featureloc_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->featureloc_pub_featureloc_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Analysisfeature######## package Bio::Chado::CDBI::Analysisfeature; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Analysisfeature->set_up_table('analysisfeature'); # # Primary key accessors # sub id { shift->analysisfeature_id } sub analysisfeature { shift->analysisfeature_id } # # Has A # Bio::Chado::CDBI::Analysisfeature->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Analysisfeature::feature { return shift->feature_id } Bio::Chado::CDBI::Analysisfeature->has_a(analysis_id => 'Bio::Chado::CDBI::Analysis'); sub Bio::Chado::CDBI::Analysisfeature::analysis { return shift->analysis_id } # # Has Many # Bio::Chado::CDBI::Analysisfeature->has_many('analysisfeatureprop_analysisfeature_id', 'Bio::Chado::CDBI::Analysisfeatureprop' => 'analysisfeature_id'); sub analysisfeatureprops { return shift->analysisfeatureprop_analysisfeature_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Cvterm_Dbxref######## package Bio::Chado::CDBI::Feature_Cvterm_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Cvterm_Dbxref->set_up_table('feature_cvterm_dbxref'); # # Primary key accessors # sub id { shift->feature_cvterm_dbxref_id } sub feature_cvterm_dbxref { shift->feature_cvterm_dbxref_id } # # Has A # Bio::Chado::CDBI::Feature_Cvterm_Dbxref->has_a(feature_cvterm_id => 'Bio::Chado::CDBI::Feature_Cvterm'); sub Bio::Chado::CDBI::Feature_Cvterm_Dbxref::feature_cvterm { return shift->feature_cvterm_id } Bio::Chado::CDBI::Feature_Cvterm_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Feature_Cvterm_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Pub######## package Bio::Chado::CDBI::Feature_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Pub->set_up_table('feature_pub'); # # Primary key accessors # sub id { shift->feature_pub_id } sub feature_pub { shift->feature_pub_id } # # Has A # Bio::Chado::CDBI::Feature_Pub->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Pub::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Pub::pub { return shift->pub_id } # # Has Many # Bio::Chado::CDBI::Feature_Pub->has_many('feature_pubprop_feature_pub_id', 'Bio::Chado::CDBI::Feature_Pubprop' => 'feature_pub_id'); sub feature_pubprops { return shift->feature_pubprop_feature_pub_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Relationship######## package Bio::Chado::CDBI::Feature_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Relationship->set_up_table('feature_relationship'); # # Primary key accessors # sub id { shift->feature_relationship_id } sub feature_relationship { shift->feature_relationship_id } # # Has A # Bio::Chado::CDBI::Feature_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Feature'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Feature_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Feature'); sub object { return shift->object_id } Bio::Chado::CDBI::Feature_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Relationship::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Feature_Relationship->has_many('feature_relationshipprop_feature_relationship_id', 'Bio::Chado::CDBI::Feature_Relationshipprop' => 'feature_relationship_id'); sub feature_relationshipprops { return shift->feature_relationshipprop_feature_relationship_id } Bio::Chado::CDBI::Feature_Relationship->has_many('feature_relationship_pub_feature_relationship_id', 'Bio::Chado::CDBI::Feature_Relationship_Pub' => 'feature_relationship_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub feature_relationship_pub_feature_relationships { return shift->feature_relationship_pub_feature_relationship_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->feature_relationship_pub_feature_relationship_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Acquisition_Relationship######## package Bio::Chado::CDBI::Acquisition_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Acquisition_Relationship->set_up_table('acquisition_relationship'); # # Primary key accessors # sub id { shift->acquisition_relationship_id } sub acquisition_relationship { shift->acquisition_relationship_id } # # Has A # Bio::Chado::CDBI::Acquisition_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Acquisition'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Acquisition_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Acquisition_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Acquisition_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Acquisition'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Chadoprop######## package Bio::Chado::CDBI::Chadoprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Chadoprop->set_up_table('chadoprop'); # # Primary key accessors # sub id { shift->chadoprop_id } sub chadoprop { shift->chadoprop_id } # # Has A # Bio::Chado::CDBI::Chadoprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Chadoprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Cvtermprop######## package Bio::Chado::CDBI::Feature_Cvtermprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Cvtermprop->set_up_table('feature_cvtermprop'); # # Primary key accessors # sub id { shift->feature_cvtermprop_id } sub feature_cvtermprop { shift->feature_cvtermprop_id } # # Has A # Bio::Chado::CDBI::Feature_Cvtermprop->has_a(feature_cvterm_id => 'Bio::Chado::CDBI::Feature_Cvterm'); sub Bio::Chado::CDBI::Feature_Cvtermprop::feature_cvterm { return shift->feature_cvterm_id } Bio::Chado::CDBI::Feature_Cvtermprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Cvtermprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Protocol######## package Bio::Chado::CDBI::Protocol; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Protocol->set_up_table('protocol'); # # Primary key accessors # sub id { shift->protocol_id } sub protocol { shift->protocol_id } # # Has A # Bio::Chado::CDBI::Protocol->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Protocol::cvterm { return shift->type_id } Bio::Chado::CDBI::Protocol->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Protocol::pub { return shift->pub_id } Bio::Chado::CDBI::Protocol->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Protocol::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Protocol->has_many('quantification_protocol_id', 'Bio::Chado::CDBI::Quantification' => 'protocol_id'); sub quantifications { return shift->quantification_protocol_id } Bio::Chado::CDBI::Protocol->has_many('arraydesign_protocol_id', 'Bio::Chado::CDBI::Arraydesign' => 'protocol_id'); sub arraydesigns { return shift->arraydesign_protocol_id } Bio::Chado::CDBI::Protocol->has_many('protocolparam_protocol_id', 'Bio::Chado::CDBI::Protocolparam' => 'protocol_id'); sub protocolparams { return shift->protocolparam_protocol_id } Bio::Chado::CDBI::Protocol->has_many('assay_protocol_id', 'Bio::Chado::CDBI::Assay' => 'protocol_id'); sub assays { return shift->assay_protocol_id } Bio::Chado::CDBI::Protocol->has_many('acquisition_protocol_id', 'Bio::Chado::CDBI::Acquisition' => 'protocol_id'); sub acquisitions { return shift->acquisition_protocol_id } Bio::Chado::CDBI::Protocol->has_many('treatment_protocol_id', 'Bio::Chado::CDBI::Treatment' => 'protocol_id'); sub treatments { return shift->treatment_protocol_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featureloc_Pub######## package Bio::Chado::CDBI::Featureloc_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featureloc_Pub->set_up_table('featureloc_pub'); # # Primary key accessors # sub id { shift->featureloc_pub_id } sub featureloc_pub { shift->featureloc_pub_id } # # Has A # Bio::Chado::CDBI::Featureloc_Pub->has_a(featureloc_id => 'Bio::Chado::CDBI::Featureloc'); sub Bio::Chado::CDBI::Featureloc_Pub::featureloc { return shift->featureloc_id } Bio::Chado::CDBI::Featureloc_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Featureloc_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Reagentprop######## package Bio::Chado::CDBI::Nd_Reagentprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Reagentprop->set_up_table('nd_reagentprop'); # # Primary key accessors # sub id { shift->nd_reagentprop_id } sub nd_reagentprop { shift->nd_reagentprop_id } # # Has A # Bio::Chado::CDBI::Nd_Reagentprop->has_a(nd_reagent_id => 'Bio::Chado::CDBI::Nd_Reagent'); sub Bio::Chado::CDBI::Nd_Reagentprop::nd_reagent { return shift->nd_reagent_id } Bio::Chado::CDBI::Nd_Reagentprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Reagentprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Dbxrefprop######## package Bio::Chado::CDBI::Stock_Dbxrefprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Dbxrefprop->set_up_table('stock_dbxrefprop'); # # Primary key accessors # sub id { shift->stock_dbxrefprop_id } sub stock_dbxrefprop { shift->stock_dbxrefprop_id } # # Has A # Bio::Chado::CDBI::Stock_Dbxrefprop->has_a(stock_dbxref_id => 'Bio::Chado::CDBI::Stock_Dbxref'); sub Bio::Chado::CDBI::Stock_Dbxrefprop::stock_dbxref { return shift->stock_dbxref_id } Bio::Chado::CDBI::Stock_Dbxrefprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock_Dbxrefprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Project######## package Bio::Chado::CDBI::Nd_Experiment_Project; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Project->set_up_table('nd_experiment_project'); # # Primary key accessors # sub id { shift->nd_experiment_project_id } sub nd_experiment_project { shift->nd_experiment_project_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Project->has_a(project_id => 'Bio::Chado::CDBI::Project'); sub Bio::Chado::CDBI::Nd_Experiment_Project::project { return shift->project_id } Bio::Chado::CDBI::Nd_Experiment_Project->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Project::nd_experiment { return shift->nd_experiment_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature######## package Bio::Chado::CDBI::Feature; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature->set_up_table('feature'); # # Primary key accessors # sub id { shift->feature_id } sub feature { shift->feature_id } # # Has A # Bio::Chado::CDBI::Feature->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Feature::dbxref { return shift->dbxref_id } Bio::Chado::CDBI::Feature->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Feature::organism { return shift->organism_id } Bio::Chado::CDBI::Feature->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Feature->has_many('feature_dbxref_feature_id', 'Bio::Chado::CDBI::Feature_Dbxref' => 'feature_id'); sub feature_dbxrefs { return shift->feature_dbxref_feature_id } Bio::Chado::CDBI::Feature->has_many('feature_expression_feature_id', 'Bio::Chado::CDBI::Feature_Expression' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('feature_cvterm_feature_id', 'Bio::Chado::CDBI::Feature_Cvterm' => 'feature_id'); sub feature_cvterms { return shift->feature_cvterm_feature_id } Bio::Chado::CDBI::Feature->has_many('cell_line_feature_feature_id', 'Bio::Chado::CDBI::Cell_Line_Feature' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('feature_phenotype_feature_id', 'Bio::Chado::CDBI::Feature_Phenotype' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('featureloc_feature_id', 'Bio::Chado::CDBI::Featureloc' => 'feature_id'); sub featureloc_feature_ids { my $self = shift; return $self->featureloc_feature_id(@_) } Bio::Chado::CDBI::Feature->has_many('featureloc_srcfeature_id', 'Bio::Chado::CDBI::Featureloc' => 'srcfeature_id'); sub featureloc_srcfeature_ids { my $self = shift; return $self->featureloc_srcfeature_id(@_) } Bio::Chado::CDBI::Feature->has_many('analysisfeature_feature_id', 'Bio::Chado::CDBI::Analysisfeature' => 'feature_id'); sub analysisfeatures { return shift->analysisfeature_feature_id } Bio::Chado::CDBI::Feature->has_many('feature_pub_feature_id', 'Bio::Chado::CDBI::Feature_Pub' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('feature_relationship_subject_id', 'Bio::Chado::CDBI::Feature_Relationship' => 'subject_id'); sub feature_relationship_subject_ids { my $self = shift; return $self->feature_relationship_subject_id(@_) } Bio::Chado::CDBI::Feature->has_many('feature_relationship_object_id', 'Bio::Chado::CDBI::Feature_Relationship' => 'object_id'); sub feature_relationship_object_ids { my $self = shift; return $self->feature_relationship_object_id(@_) } Bio::Chado::CDBI::Feature->has_many('library_feature_feature_id', 'Bio::Chado::CDBI::Library_Feature' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('studyprop_feature_feature_id', 'Bio::Chado::CDBI::Studyprop_Feature' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('featureprop_feature_id', 'Bio::Chado::CDBI::Featureprop' => 'feature_id'); sub featureprops { return shift->featureprop_feature_id } Bio::Chado::CDBI::Feature->has_many('element_feature_id', 'Bio::Chado::CDBI::Element' => 'feature_id'); Bio::Chado::CDBI::Feature->has_many('featurerange_feature_id', 'Bio::Chado::CDBI::Featurerange' => 'feature_id'); sub featurerange_feature_ids { my $self = shift; return $self->featurerange_feature_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurerange_leftstartf_id', 'Bio::Chado::CDBI::Featurerange' => 'leftstartf_id'); sub featurerange_leftstartf_ids { my $self = shift; return $self->featurerange_leftstartf_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurerange_leftendf_id', 'Bio::Chado::CDBI::Featurerange' => 'leftendf_id'); sub featurerange_leftendf_ids { my $self = shift; return $self->featurerange_leftendf_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurerange_rightstartf_id', 'Bio::Chado::CDBI::Featurerange' => 'rightstartf_id'); sub featurerange_rightstartf_ids { my $self = shift; return $self->featurerange_rightstartf_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurerange_rightendf_id', 'Bio::Chado::CDBI::Featurerange' => 'rightendf_id'); sub featurerange_rightendf_ids { my $self = shift; return $self->featurerange_rightendf_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurepos_feature_id', 'Bio::Chado::CDBI::Featurepos' => 'feature_id'); sub featurepos_feature_ids { my $self = shift; return $self->featurepos_feature_id(@_) } Bio::Chado::CDBI::Feature->has_many('featurepos_map_feature_id', 'Bio::Chado::CDBI::Featurepos' => 'map_feature_id'); sub featurepos_map_feature_ids { my $self = shift; return $self->featurepos_map_feature_id(@_) } Bio::Chado::CDBI::Feature->has_many('phylonode_feature_id', 'Bio::Chado::CDBI::Phylonode' => 'feature_id'); sub phylonodes { return shift->phylonode_feature_id } Bio::Chado::CDBI::Feature->has_many('feature_synonym_feature_id', 'Bio::Chado::CDBI::Feature_Synonym' => 'feature_id'); sub feature_synonyms { return shift->feature_synonym_feature_id } Bio::Chado::CDBI::Feature->has_many('feature_genotype_feature_id', 'Bio::Chado::CDBI::Feature_Genotype' => 'feature_id'); sub feature_genotype_feature_ids { my $self = shift; return $self->feature_genotype_feature_id(@_) } Bio::Chado::CDBI::Feature->has_many('feature_genotype_chromosome_id', 'Bio::Chado::CDBI::Feature_Genotype' => 'chromosome_id'); sub feature_genotype_chromosome_ids { my $self = shift; return $self->feature_genotype_chromosome_id(@_) } # # Has Compound Many (many to many relationships in all their flavors) # sub feature_expression_features { return shift->feature_expression_feature_id } sub feature_expression_features { return shift->feature_expression_feature_id } sub library_feature_features { return shift->library_feature_feature_id } sub feature_pub_features { return shift->feature_pub_feature_id } sub feature_phenotype_features { return shift->feature_phenotype_feature_id } sub studyprop_feature_features { return shift->studyprop_feature_feature_id } sub studyprop_feature_features { return shift->studyprop_feature_feature_id } sub cell_line_feature_features { return shift->cell_line_feature_feature_id } sub cell_line_feature_features { return shift->cell_line_feature_feature_id } sub element_features { return shift->element_feature_id } sub element_features { return shift->element_feature_id } sub element_features { return shift->element_feature_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->feature_expression_feature_id } sub expressions { my $self = shift; return map $_->expression_id, $self->feature_expression_feature_id } sub librarys { my $self = shift; return map $_->library_id, $self->library_feature_feature_id } sub pubs { my $self = shift; return map $_->pub_id, $self->feature_pub_feature_id } sub phenotypes { my $self = shift; return map $_->phenotype_id, $self->feature_phenotype_feature_id } sub studyprops { my $self = shift; return map $_->studyprop_id, $self->studyprop_feature_feature_id } sub cvterms { my $self = shift; return map $_->type_id, $self->studyprop_feature_feature_id } sub cell_lines { my $self = shift; return map $_->cell_line_id, $self->cell_line_feature_feature_id } sub pubs { my $self = shift; return map $_->pub_id, $self->cell_line_feature_feature_id } sub arraydesigns { my $self = shift; return map $_->arraydesign_id, $self->element_feature_id } sub cvterms { my $self = shift; return map $_->type_id, $self->element_feature_id } sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->element_feature_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Pubprop######## package Bio::Chado::CDBI::Feature_Pubprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Pubprop->set_up_table('feature_pubprop'); # # Primary key accessors # sub id { shift->feature_pubprop_id } sub feature_pubprop { shift->feature_pubprop_id } # # Has A # Bio::Chado::CDBI::Feature_Pubprop->has_a(feature_pub_id => 'Bio::Chado::CDBI::Feature_Pub'); sub Bio::Chado::CDBI::Feature_Pubprop::feature_pub { return shift->feature_pub_id } Bio::Chado::CDBI::Feature_Pubprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Pubprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Library_Pub######## package Bio::Chado::CDBI::Library_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library_Pub->set_up_table('library_pub'); # # Primary key accessors # sub id { shift->library_pub_id } sub library_pub { shift->library_pub_id } # # Has A # Bio::Chado::CDBI::Library_Pub->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Library_Pub::library { return shift->library_id } Bio::Chado::CDBI::Library_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Library_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Biomaterialprop######## package Bio::Chado::CDBI::Biomaterialprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Biomaterialprop->set_up_table('biomaterialprop'); # # Primary key accessors # sub id { shift->biomaterialprop_id } sub biomaterialprop { shift->biomaterialprop_id } # # Has A # Bio::Chado::CDBI::Biomaterialprop->has_a(biomaterial_id => 'Bio::Chado::CDBI::Biomaterial'); sub Bio::Chado::CDBI::Biomaterialprop::biomaterial { return shift->biomaterial_id } Bio::Chado::CDBI::Biomaterialprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Biomaterialprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Elementresult######## package Bio::Chado::CDBI::Elementresult; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Elementresult->set_up_table('elementresult'); # # Primary key accessors # sub id { shift->elementresult_id } sub elementresult { shift->elementresult_id } # # Has A # Bio::Chado::CDBI::Elementresult->has_a(element_id => 'Bio::Chado::CDBI::Element'); sub Bio::Chado::CDBI::Elementresult::element { return shift->element_id } Bio::Chado::CDBI::Elementresult->has_a(quantification_id => 'Bio::Chado::CDBI::Quantification'); sub Bio::Chado::CDBI::Elementresult::quantification { return shift->quantification_id } # # Has Many # Bio::Chado::CDBI::Elementresult->has_many('elementresult_relationship_subject_id', 'Bio::Chado::CDBI::Elementresult_Relationship' => 'subject_id'); sub elementresult_relationship_subject_ids { my $self = shift; return $self->elementresult_relationship_subject_id(@_) } Bio::Chado::CDBI::Elementresult->has_many('elementresult_relationship_object_id', 'Bio::Chado::CDBI::Elementresult_Relationship' => 'object_id'); sub elementresult_relationship_object_ids { my $self = shift; return $self->elementresult_relationship_object_id(@_) } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line######## package Bio::Chado::CDBI::Cell_Line; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line->set_up_table('cell_line'); # # Primary key accessors # sub id { shift->cell_line_id } sub cell_line { shift->cell_line_id } # # Has A # Bio::Chado::CDBI::Cell_Line->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Cell_Line::organism { return shift->organism_id } # # Has Many # Bio::Chado::CDBI::Cell_Line->has_many('cell_line_dbxref_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Dbxref' => 'cell_line_id'); sub cell_line_dbxrefs { return shift->cell_line_dbxref_cell_line_id } Bio::Chado::CDBI::Cell_Line->has_many('cell_line_feature_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Feature' => 'cell_line_id'); Bio::Chado::CDBI::Cell_Line->has_many('cell_line_relationship_subject_id', 'Bio::Chado::CDBI::Cell_Line_Relationship' => 'subject_id'); Bio::Chado::CDBI::Cell_Line->has_many('cell_line_relationship_object_id', 'Bio::Chado::CDBI::Cell_Line_Relationship' => 'object_id'); Bio::Chado::CDBI::Cell_Line->has_many('cell_line_synonym_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Synonym' => 'cell_line_id'); sub cell_line_synonyms { return shift->cell_line_synonym_cell_line_id } Bio::Chado::CDBI::Cell_Line->has_many('cell_line_library_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Library' => 'cell_line_id'); Bio::Chado::CDBI::Cell_Line->has_many('cell_line_cvterm_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Cvterm' => 'cell_line_id'); sub cell_line_cvterms { return shift->cell_line_cvterm_cell_line_id } Bio::Chado::CDBI::Cell_Line->has_many('cell_lineprop_cell_line_id', 'Bio::Chado::CDBI::Cell_Lineprop' => 'cell_line_id'); sub cell_lineprops { return shift->cell_lineprop_cell_line_id } Bio::Chado::CDBI::Cell_Line->has_many('cell_line_pub_cell_line_id', 'Bio::Chado::CDBI::Cell_Line_Pub' => 'cell_line_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub cell_line_pub_cell_lines { return shift->cell_line_pub_cell_line_id } sub cell_line_library_cell_lines { return shift->cell_line_library_cell_line_id } sub cell_line_library_cell_lines { return shift->cell_line_library_cell_line_id } sub cell_line_feature_cell_lines { return shift->cell_line_feature_cell_line_id } sub cell_line_feature_cell_lines { return shift->cell_line_feature_cell_line_id } sub cell_line_relationship_subjects { return shift->cell_line_relationship_subject_id } sub cell_line_relationship_objects { return shift->cell_line_relationship_object_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->cell_line_pub_cell_line_id } sub librarys { my $self = shift; return map $_->library_id, $self->cell_line_library_cell_line_id } sub pubs { my $self = shift; return map $_->pub_id, $self->cell_line_library_cell_line_id } sub features { my $self = shift; return map $_->feature_id, $self->cell_line_feature_cell_line_id } sub pubs { my $self = shift; return map $_->pub_id, $self->cell_line_feature_cell_line_id } # one to many to many #many to many to one # many2one # sub cell_line_relationship_subject_types { my $self = shift; return map $_->type_id, $self->cell_line_relationship_subject_id } sub cell_line_relationship_object_types { my $self = shift; return map $_->type_id, $self->cell_line_relationship_object_id } #many to many to many 1; ########Bio::Chado::CDBI::Library_Feature######## package Bio::Chado::CDBI::Library_Feature; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library_Feature->set_up_table('library_feature'); # # Primary key accessors # sub id { shift->library_feature_id } sub library_feature { shift->library_feature_id } # # Has A # Bio::Chado::CDBI::Library_Feature->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Library_Feature::library { return shift->library_id } Bio::Chado::CDBI::Library_Feature->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Library_Feature::feature { return shift->feature_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Dbxref######## package Bio::Chado::CDBI::Stock_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Dbxref->set_up_table('stock_dbxref'); # # Primary key accessors # sub id { shift->stock_dbxref_id } sub stock_dbxref { shift->stock_dbxref_id } # # Has A # Bio::Chado::CDBI::Stock_Dbxref->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stock_Dbxref::stock { return shift->stock_id } Bio::Chado::CDBI::Stock_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Stock_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Stock_Dbxref->has_many('stock_dbxrefprop_stock_dbxref_id', 'Bio::Chado::CDBI::Stock_Dbxrefprop' => 'stock_dbxref_id'); sub stock_dbxrefprops { return shift->stock_dbxrefprop_stock_dbxref_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvterm_Dbxref######## package Bio::Chado::CDBI::Cvterm_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvterm_Dbxref->set_up_table('cvterm_dbxref'); # # Primary key accessors # sub id { shift->cvterm_dbxref_id } sub cvterm_dbxref { shift->cvterm_dbxref_id } # # Has A # Bio::Chado::CDBI::Cvterm_Dbxref->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cvterm_Dbxref::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Cvterm_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Cvterm_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Relationshipprop######## package Bio::Chado::CDBI::Feature_Relationshipprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Relationshipprop->set_up_table('feature_relationshipprop'); # # Primary key accessors # sub id { shift->feature_relationshipprop_id } sub feature_relationshipprop { shift->feature_relationshipprop_id } # # Has A # Bio::Chado::CDBI::Feature_Relationshipprop->has_a(feature_relationship_id => 'Bio::Chado::CDBI::Feature_Relationship'); sub Bio::Chado::CDBI::Feature_Relationshipprop::feature_relationship { return shift->feature_relationship_id } Bio::Chado::CDBI::Feature_Relationshipprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Relationshipprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Feature_Relationshipprop->has_many('feature_relationshipprop_pub_feature_relationshipprop_id', 'Bio::Chado::CDBI::Feature_Relationshipprop_Pub' => 'feature_relationshipprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub feature_relationshipprop_pub_feature_relationshipprops { return shift->feature_relationshipprop_pub_feature_relationshipprop_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->feature_relationshipprop_pub_feature_relationshipprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stockcollectionprop######## package Bio::Chado::CDBI::Stockcollectionprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stockcollectionprop->set_up_table('stockcollectionprop'); # # Primary key accessors # sub id { shift->stockcollectionprop_id } sub stockcollectionprop { shift->stockcollectionprop_id } # # Has A # Bio::Chado::CDBI::Stockcollectionprop->has_a(stockcollection_id => 'Bio::Chado::CDBI::Stockcollection'); sub Bio::Chado::CDBI::Stockcollectionprop::stockcollection { return shift->stockcollection_id } Bio::Chado::CDBI::Stockcollectionprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stockcollectionprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Element_Relationship######## package Bio::Chado::CDBI::Element_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Element_Relationship->set_up_table('element_relationship'); # # Primary key accessors # sub id { shift->element_relationship_id } sub element_relationship { shift->element_relationship_id } # # Has A # Bio::Chado::CDBI::Element_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Element'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Element_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Element_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Element_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Element'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock######## package Bio::Chado::CDBI::Stock; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock->set_up_table('stock'); # # Primary key accessors # sub id { shift->stock_id } sub stock { shift->stock_id } # # Has A # Bio::Chado::CDBI::Stock->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Stock::dbxref { return shift->dbxref_id } Bio::Chado::CDBI::Stock->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Stock::organism { return shift->organism_id } Bio::Chado::CDBI::Stock->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Stock->has_many('stock_dbxref_stock_id', 'Bio::Chado::CDBI::Stock_Dbxref' => 'stock_id'); sub stock_dbxrefs { return shift->stock_dbxref_stock_id } Bio::Chado::CDBI::Stock->has_many('stock_pub_stock_id', 'Bio::Chado::CDBI::Stock_Pub' => 'stock_id'); Bio::Chado::CDBI::Stock->has_many('stock_genotype_stock_id', 'Bio::Chado::CDBI::Stock_Genotype' => 'stock_id'); Bio::Chado::CDBI::Stock->has_many('stock_cvterm_stock_id', 'Bio::Chado::CDBI::Stock_Cvterm' => 'stock_id'); sub stock_cvterms { return shift->stock_cvterm_stock_id } Bio::Chado::CDBI::Stock->has_many('stock_relationship_subject_id', 'Bio::Chado::CDBI::Stock_Relationship' => 'subject_id'); sub stock_relationship_subject_ids { my $self = shift; return $self->stock_relationship_subject_id(@_) } Bio::Chado::CDBI::Stock->has_many('stock_relationship_object_id', 'Bio::Chado::CDBI::Stock_Relationship' => 'object_id'); sub stock_relationship_object_ids { my $self = shift; return $self->stock_relationship_object_id(@_) } Bio::Chado::CDBI::Stock->has_many('stockcollection_stock_stock_id', 'Bio::Chado::CDBI::Stockcollection_Stock' => 'stock_id'); Bio::Chado::CDBI::Stock->has_many('nd_experiment_stock_stock_id', 'Bio::Chado::CDBI::Nd_Experiment_Stock' => 'stock_id'); Bio::Chado::CDBI::Stock->has_many('stockprop_stock_id', 'Bio::Chado::CDBI::Stockprop' => 'stock_id'); sub stockprops { return shift->stockprop_stock_id } # # Has Compound Many (many to many relationships in all their flavors) # sub stockcollection_stock_stocks { return shift->stockcollection_stock_stock_id } sub nd_experiment_stock_stocks { return shift->nd_experiment_stock_stock_id } sub nd_experiment_stock_stocks { return shift->nd_experiment_stock_stock_id } sub stock_pub_stocks { return shift->stock_pub_stock_id } sub stock_genotype_stocks { return shift->stock_genotype_stock_id } # one to many to one # one2one # sub stockcollections { my $self = shift; return map $_->stockcollection_id, $self->stockcollection_stock_stock_id } sub cvterms { my $self = shift; return map $_->type_id, $self->nd_experiment_stock_stock_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_stock_stock_id } sub pubs { my $self = shift; return map $_->pub_id, $self->stock_pub_stock_id } sub genotypes { my $self = shift; return map $_->genotype_id, $self->stock_genotype_stock_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featuremap######## package Bio::Chado::CDBI::Featuremap; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featuremap->set_up_table('featuremap'); # # Primary key accessors # sub id { shift->featuremap_id } sub featuremap { shift->featuremap_id } # # Has A # Bio::Chado::CDBI::Featuremap->has_a(unittype_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Featuremap::cvterm { return shift->unittype_id } # # Has Many # Bio::Chado::CDBI::Featuremap->has_many('featurerange_featuremap_id', 'Bio::Chado::CDBI::Featurerange' => 'featuremap_id'); sub featureranges { return shift->featurerange_featuremap_id } Bio::Chado::CDBI::Featuremap->has_many('featurepos_featuremap_id', 'Bio::Chado::CDBI::Featurepos' => 'featuremap_id'); sub featureposs { return shift->featurepos_featuremap_id } Bio::Chado::CDBI::Featuremap->has_many('featuremap_pub_featuremap_id', 'Bio::Chado::CDBI::Featuremap_Pub' => 'featuremap_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub featuremap_pub_featuremaps { return shift->featuremap_pub_featuremap_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->featuremap_pub_featuremap_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Studyprop_Feature######## package Bio::Chado::CDBI::Studyprop_Feature; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studyprop_Feature->set_up_table('studyprop_feature'); # # Primary key accessors # sub id { shift->studyprop_feature_id } sub studyprop_feature { shift->studyprop_feature_id } # # Has A # Bio::Chado::CDBI::Studyprop_Feature->has_a(studyprop_id => 'Bio::Chado::CDBI::Studyprop'); sub Bio::Chado::CDBI::Studyprop_Feature::studyprop { return shift->studyprop_id } Bio::Chado::CDBI::Studyprop_Feature->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Studyprop_Feature::feature { return shift->feature_id } Bio::Chado::CDBI::Studyprop_Feature->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Studyprop_Feature::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Libraryprop######## package Bio::Chado::CDBI::Libraryprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Libraryprop->set_up_table('libraryprop'); # # Primary key accessors # sub id { shift->libraryprop_id } sub libraryprop { shift->libraryprop_id } # # Has A # Bio::Chado::CDBI::Libraryprop->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Libraryprop::library { return shift->library_id } Bio::Chado::CDBI::Libraryprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Libraryprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Libraryprop->has_many('libraryprop_pub_libraryprop_id', 'Bio::Chado::CDBI::Libraryprop_Pub' => 'libraryprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub libraryprop_pub_libraryprops { return shift->libraryprop_pub_libraryprop_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->libraryprop_pub_libraryprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Analysisfeatureprop######## package Bio::Chado::CDBI::Analysisfeatureprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Analysisfeatureprop->set_up_table('analysisfeatureprop'); # # Primary key accessors # sub id { shift->analysisfeatureprop_id } sub analysisfeatureprop { shift->analysisfeatureprop_id } # # Has A # Bio::Chado::CDBI::Analysisfeatureprop->has_a(analysisfeature_id => 'Bio::Chado::CDBI::Analysisfeature'); sub Bio::Chado::CDBI::Analysisfeatureprop::analysisfeature { return shift->analysisfeature_id } Bio::Chado::CDBI::Analysisfeatureprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Analysisfeatureprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Project######## package Bio::Chado::CDBI::Project; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Project->set_up_table('project'); # # Primary key accessors # sub id { shift->project_id } sub project { shift->project_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Project->has_many('nd_experiment_project_project_id', 'Bio::Chado::CDBI::Nd_Experiment_Project' => 'project_id'); Bio::Chado::CDBI::Project->has_many('project_contact_project_id', 'Bio::Chado::CDBI::Project_Contact' => 'project_id'); Bio::Chado::CDBI::Project->has_many('assay_project_project_id', 'Bio::Chado::CDBI::Assay_Project' => 'project_id'); Bio::Chado::CDBI::Project->has_many('project_relationship_subject_project_id', 'Bio::Chado::CDBI::Project_Relationship' => 'subject_project_id'); Bio::Chado::CDBI::Project->has_many('project_relationship_object_project_id', 'Bio::Chado::CDBI::Project_Relationship' => 'object_project_id'); Bio::Chado::CDBI::Project->has_many('projectprop_project_id', 'Bio::Chado::CDBI::Projectprop' => 'project_id'); sub projectprops { return shift->projectprop_project_id } Bio::Chado::CDBI::Project->has_many('project_pub_project_id', 'Bio::Chado::CDBI::Project_Pub' => 'project_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub project_relationship_subject_projects { return shift->project_relationship_subject_project_id } sub project_relationship_object_projects { return shift->project_relationship_object_project_id } sub assay_project_projects { return shift->assay_project_project_id } sub nd_experiment_project_projects { return shift->nd_experiment_project_project_id } sub project_contact_projects { return shift->project_contact_project_id } sub project_pub_projects { return shift->project_pub_project_id } # one to many to one # one2one # sub assays { my $self = shift; return map $_->assay_id, $self->assay_project_project_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_project_project_id } sub contacts { my $self = shift; return map $_->contact_id, $self->project_contact_project_id } sub pubs { my $self = shift; return map $_->pub_id, $self->project_pub_project_id } # one to many to many #many to many to one # many2one # sub project_relationship_subject_project_types { my $self = shift; return map $_->type_id, $self->project_relationship_subject_project_id } sub project_relationship_object_project_types { my $self = shift; return map $_->type_id, $self->project_relationship_object_project_id } #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Genotype######## package Bio::Chado::CDBI::Nd_Experiment_Genotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Genotype->set_up_table('nd_experiment_genotype'); # # Primary key accessors # sub id { shift->nd_experiment_genotype_id } sub nd_experiment_genotype { shift->nd_experiment_genotype_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Genotype->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Genotype::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Genotype->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Nd_Experiment_Genotype::genotype { return shift->genotype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featureprop######## package Bio::Chado::CDBI::Featureprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featureprop->set_up_table('featureprop'); # # Primary key accessors # sub id { shift->featureprop_id } sub featureprop { shift->featureprop_id } # # Has A # Bio::Chado::CDBI::Featureprop->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Featureprop::feature { return shift->feature_id } Bio::Chado::CDBI::Featureprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Featureprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Featureprop->has_many('featureprop_pub_featureprop_id', 'Bio::Chado::CDBI::Featureprop_Pub' => 'featureprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub featureprop_pub_featureprops { return shift->featureprop_pub_featureprop_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->featureprop_pub_featureprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Library######## package Bio::Chado::CDBI::Cell_Line_Library; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Library->set_up_table('cell_line_library'); # # Primary key accessors # sub id { shift->cell_line_library_id } sub cell_line_library { shift->cell_line_library_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Library->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Library::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Library->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Cell_Line_Library::library { return shift->library_id } Bio::Chado::CDBI::Cell_Line_Library->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Line_Library::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonode_Relationship######## package Bio::Chado::CDBI::Phylonode_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonode_Relationship->set_up_table('phylonode_relationship'); # # Primary key accessors # sub id { shift->phylonode_relationship_id } sub phylonode_relationship { shift->phylonode_relationship_id } # # Has A # Bio::Chado::CDBI::Phylonode_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Phylonode'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Phylonode_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Phylonode'); sub object { return shift->object_id } Bio::Chado::CDBI::Phylonode_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phylonode_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Phylonode_Relationship->has_a(phylotree_id => 'Bio::Chado::CDBI::Phylotree'); sub Bio::Chado::CDBI::Phylonode_Relationship::phylotree { return shift->phylotree_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Pub######## package Bio::Chado::CDBI::Stock_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Pub->set_up_table('stock_pub'); # # Primary key accessors # sub id { shift->stock_pub_id } sub stock_pub { shift->stock_pub_id } # # Has A # Bio::Chado::CDBI::Stock_Pub->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stock_Pub::stock { return shift->stock_id } Bio::Chado::CDBI::Stock_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Stock_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Genotype######## package Bio::Chado::CDBI::Stock_Genotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Genotype->set_up_table('stock_genotype'); # # Primary key accessors # sub id { shift->stock_genotype_id } sub stock_genotype { shift->stock_genotype_id } # # Has A # Bio::Chado::CDBI::Stock_Genotype->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stock_Genotype::stock { return shift->stock_id } Bio::Chado::CDBI::Stock_Genotype->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Stock_Genotype::genotype { return shift->genotype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Protocolprop######## package Bio::Chado::CDBI::Nd_Protocolprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Protocolprop->set_up_table('nd_protocolprop'); # # Primary key accessors # sub id { shift->nd_protocolprop_id } sub nd_protocolprop { shift->nd_protocolprop_id } # # Has A # Bio::Chado::CDBI::Nd_Protocolprop->has_a(nd_protocol_id => 'Bio::Chado::CDBI::Nd_Protocol'); sub Bio::Chado::CDBI::Nd_Protocolprop::nd_protocol { return shift->nd_protocol_id } Bio::Chado::CDBI::Nd_Protocolprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Protocolprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Protocol_Reagent######## package Bio::Chado::CDBI::Nd_Protocol_Reagent; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Protocol_Reagent->set_up_table('nd_protocol_reagent'); # # Primary key accessors # sub id { shift->nd_protocol_reagent_id } sub nd_protocol_reagent { shift->nd_protocol_reagent_id } # # Has A # Bio::Chado::CDBI::Nd_Protocol_Reagent->has_a(nd_protocol_id => 'Bio::Chado::CDBI::Nd_Protocol'); sub Bio::Chado::CDBI::Nd_Protocol_Reagent::nd_protocol { return shift->nd_protocol_id } Bio::Chado::CDBI::Nd_Protocol_Reagent->has_a(reagent_id => 'Bio::Chado::CDBI::Nd_Reagent'); sub Bio::Chado::CDBI::Nd_Protocol_Reagent::nd_reagent { return shift->reagent_id } Bio::Chado::CDBI::Nd_Protocol_Reagent->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Protocol_Reagent::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Protocolparam######## package Bio::Chado::CDBI::Protocolparam; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Protocolparam->set_up_table('protocolparam'); # # Primary key accessors # sub id { shift->protocolparam_id } sub protocolparam { shift->protocolparam_id } # # Has A # Bio::Chado::CDBI::Protocolparam->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Protocolparam::protocol { return shift->protocol_id } Bio::Chado::CDBI::Protocolparam->has_a(datatype_id => 'Bio::Chado::CDBI::Cvterm'); sub datatype { return shift->datatype_id } Bio::Chado::CDBI::Protocolparam->has_a(unittype_id => 'Bio::Chado::CDBI::Cvterm'); sub unittype { return shift->unittype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Control######## package Bio::Chado::CDBI::Control; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Control->set_up_table('control'); # # Primary key accessors # sub id { shift->control_id } sub control { shift->control_id } # # Has A # Bio::Chado::CDBI::Control->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Control::cvterm { return shift->type_id } Bio::Chado::CDBI::Control->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Control::assay { return shift->assay_id } Bio::Chado::CDBI::Control->has_a(tableinfo_id => 'Bio::Chado::CDBI::Tableinfo'); sub Bio::Chado::CDBI::Control::tableinfo { return shift->tableinfo_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment######## package Bio::Chado::CDBI::Nd_Experiment; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment->set_up_table('nd_experiment'); # # Primary key accessors # sub id { shift->nd_experiment_id } sub nd_experiment { shift->nd_experiment_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment->has_a(nd_geolocation_id => 'Bio::Chado::CDBI::Nd_Geolocation'); sub Bio::Chado::CDBI::Nd_Experiment::nd_geolocation { return shift->nd_geolocation_id } Bio::Chado::CDBI::Nd_Experiment->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Experiment::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_pub_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Pub' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_contact_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Contact' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_project_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Project' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_genotype_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Genotype' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_phenotype_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Phenotype' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_stock_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Stock' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_dbxref_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Dbxref' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experiment_protocol_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experiment_Protocol' => 'nd_experiment_id'); Bio::Chado::CDBI::Nd_Experiment->has_many('nd_experimentprop_nd_experiment_id', 'Bio::Chado::CDBI::Nd_Experimentprop' => 'nd_experiment_id'); sub nd_experimentprops { return shift->nd_experimentprop_nd_experiment_id } # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_phenotype_nd_experiments { return shift->nd_experiment_phenotype_nd_experiment_id } sub nd_experiment_stock_nd_experiments { return shift->nd_experiment_stock_nd_experiment_id } sub nd_experiment_stock_nd_experiments { return shift->nd_experiment_stock_nd_experiment_id } sub nd_experiment_contact_nd_experiments { return shift->nd_experiment_contact_nd_experiment_id } sub nd_experiment_project_nd_experiments { return shift->nd_experiment_project_nd_experiment_id } sub nd_experiment_genotype_nd_experiments { return shift->nd_experiment_genotype_nd_experiment_id } sub nd_experiment_protocol_nd_experiments { return shift->nd_experiment_protocol_nd_experiment_id } sub nd_experiment_dbxref_nd_experiments { return shift->nd_experiment_dbxref_nd_experiment_id } sub nd_experiment_pub_nd_experiments { return shift->nd_experiment_pub_nd_experiment_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Project_Contact######## package Bio::Chado::CDBI::Project_Contact; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Project_Contact->set_up_table('project_contact'); # # Primary key accessors # sub id { shift->project_contact_id } sub project_contact { shift->project_contact_id } # # Has A # Bio::Chado::CDBI::Project_Contact->has_a(project_id => 'Bio::Chado::CDBI::Project'); sub Bio::Chado::CDBI::Project_Contact::project { return shift->project_id } Bio::Chado::CDBI::Project_Contact->has_a(contact_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Project_Contact::contact { return shift->contact_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Relationshipprop_Pub######## package Bio::Chado::CDBI::Feature_Relationshipprop_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Relationshipprop_Pub->set_up_table('feature_relationshipprop_pub'); # # Primary key accessors # sub id { shift->feature_relationshipprop_pub_id } sub feature_relationshipprop_pub { shift->feature_relationshipprop_pub_id } # # Has A # Bio::Chado::CDBI::Feature_Relationshipprop_Pub->has_a(feature_relationshipprop_id => 'Bio::Chado::CDBI::Feature_Relationshipprop'); sub Bio::Chado::CDBI::Feature_Relationshipprop_Pub::feature_relationshipprop { return shift->feature_relationshipprop_id } Bio::Chado::CDBI::Feature_Relationshipprop_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Relationshipprop_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Biomaterial######## package Bio::Chado::CDBI::Biomaterial; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Biomaterial->set_up_table('biomaterial'); # # Primary key accessors # sub id { shift->biomaterial_id } sub biomaterial { shift->biomaterial_id } # # Has A # Bio::Chado::CDBI::Biomaterial->has_a(taxon_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Biomaterial::organism { return shift->taxon_id } Bio::Chado::CDBI::Biomaterial->has_a(biosourceprovider_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Biomaterial::contact { return shift->biosourceprovider_id } Bio::Chado::CDBI::Biomaterial->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Biomaterial::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Biomaterial->has_many('biomaterial_relationship_subject_id', 'Bio::Chado::CDBI::Biomaterial_Relationship' => 'subject_id'); Bio::Chado::CDBI::Biomaterial->has_many('biomaterial_relationship_object_id', 'Bio::Chado::CDBI::Biomaterial_Relationship' => 'object_id'); Bio::Chado::CDBI::Biomaterial->has_many('biomaterial_dbxref_biomaterial_id', 'Bio::Chado::CDBI::Biomaterial_Dbxref' => 'biomaterial_id'); Bio::Chado::CDBI::Biomaterial->has_many('biomaterialprop_biomaterial_id', 'Bio::Chado::CDBI::Biomaterialprop' => 'biomaterial_id'); sub biomaterialprops { return shift->biomaterialprop_biomaterial_id } Bio::Chado::CDBI::Biomaterial->has_many('biomaterial_treatment_biomaterial_id', 'Bio::Chado::CDBI::Biomaterial_Treatment' => 'biomaterial_id'); sub biomaterial_treatments { return shift->biomaterial_treatment_biomaterial_id } Bio::Chado::CDBI::Biomaterial->has_many('assay_biomaterial_biomaterial_id', 'Bio::Chado::CDBI::Assay_Biomaterial' => 'biomaterial_id'); sub assay_biomaterials { return shift->assay_biomaterial_biomaterial_id } Bio::Chado::CDBI::Biomaterial->has_many('treatment_biomaterial_id', 'Bio::Chado::CDBI::Treatment' => 'biomaterial_id'); sub treatments { return shift->treatment_biomaterial_id } # # Has Compound Many (many to many relationships in all their flavors) # sub biomaterial_dbxref_biomaterials { return shift->biomaterial_dbxref_biomaterial_id } sub biomaterial_relationship_subjects { return shift->biomaterial_relationship_subject_id } sub biomaterial_relationship_objects { return shift->biomaterial_relationship_object_id } # one to many to one # one2one # sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->biomaterial_dbxref_biomaterial_id } # one to many to many #many to many to one # many2one # sub biomaterial_relationship_subject_types { my $self = shift; return map $_->type_id, $self->biomaterial_relationship_subject_id } sub biomaterial_relationship_object_types { my $self = shift; return map $_->type_id, $self->biomaterial_relationship_object_id } #many to many to many 1; ########Bio::Chado::CDBI::Pub_Dbxref######## package Bio::Chado::CDBI::Pub_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Pub_Dbxref->set_up_table('pub_dbxref'); # # Primary key accessors # sub id { shift->pub_dbxref_id } sub pub_dbxref { shift->pub_dbxref_id } # # Has A # Bio::Chado::CDBI::Pub_Dbxref->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Pub_Dbxref::pub { return shift->pub_id } Bio::Chado::CDBI::Pub_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Pub_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Relationship_Cvterm######## package Bio::Chado::CDBI::Stock_Relationship_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Relationship_Cvterm->set_up_table('stock_relationship_cvterm'); # # Primary key accessors # sub id { shift->stock_relationship_cvterm_id } sub stock_relationship_cvterm { shift->stock_relationship_cvterm_id } # # Has A # Bio::Chado::CDBI::Stock_Relationship_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock_Relationship_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Stock_Relationship_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Stock_Relationship_Cvterm::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phendesc######## package Bio::Chado::CDBI::Phendesc; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phendesc->set_up_table('phendesc'); # # Primary key accessors # sub id { shift->phendesc_id } sub phendesc { shift->phendesc_id } # # Has A # Bio::Chado::CDBI::Phendesc->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Phendesc::genotype { return shift->genotype_id } Bio::Chado::CDBI::Phendesc->has_a(environment_id => 'Bio::Chado::CDBI::Environment'); sub Bio::Chado::CDBI::Phendesc::environment { return shift->environment_id } Bio::Chado::CDBI::Phendesc->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phendesc::cvterm { return shift->type_id } Bio::Chado::CDBI::Phendesc->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phendesc::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featureprop_Pub######## package Bio::Chado::CDBI::Featureprop_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featureprop_Pub->set_up_table('featureprop_pub'); # # Primary key accessors # sub id { shift->featureprop_pub_id } sub featureprop_pub { shift->featureprop_pub_id } # # Has A # Bio::Chado::CDBI::Featureprop_Pub->has_a(featureprop_id => 'Bio::Chado::CDBI::Featureprop'); sub Bio::Chado::CDBI::Featureprop_Pub::featureprop { return shift->featureprop_id } Bio::Chado::CDBI::Featureprop_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Featureprop_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Library_Synonym######## package Bio::Chado::CDBI::Library_Synonym; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library_Synonym->set_up_table('library_synonym'); # # Primary key accessors # sub id { shift->library_synonym_id } sub library_synonym { shift->library_synonym_id } # # Has A # Bio::Chado::CDBI::Library_Synonym->has_a(synonym_id => 'Bio::Chado::CDBI::Synonym'); sub Bio::Chado::CDBI::Library_Synonym::synonym { return shift->synonym_id } Bio::Chado::CDBI::Library_Synonym->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Library_Synonym::library { return shift->library_id } Bio::Chado::CDBI::Library_Synonym->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Library_Synonym::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Expressionprop######## package Bio::Chado::CDBI::Feature_Expressionprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Expressionprop->set_up_table('feature_expressionprop'); # # Primary key accessors # sub id { shift->feature_expressionprop_id } sub feature_expressionprop { shift->feature_expressionprop_id } # # Has A # Bio::Chado::CDBI::Feature_Expressionprop->has_a(feature_expression_id => 'Bio::Chado::CDBI::Feature_Expression'); sub Bio::Chado::CDBI::Feature_Expressionprop::feature_expression { return shift->feature_expression_id } Bio::Chado::CDBI::Feature_Expressionprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Expressionprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Pub_Relationship######## package Bio::Chado::CDBI::Pub_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Pub_Relationship->set_up_table('pub_relationship'); # # Primary key accessors # sub id { shift->pub_relationship_id } sub pub_relationship { shift->pub_relationship_id } # # Has A # Bio::Chado::CDBI::Pub_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Pub'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Pub_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Pub'); sub object { return shift->object_id } Bio::Chado::CDBI::Pub_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Pub_Relationship::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expression_Pub######## package Bio::Chado::CDBI::Expression_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expression_Pub->set_up_table('expression_pub'); # # Primary key accessors # sub id { shift->expression_pub_id } sub expression_pub { shift->expression_pub_id } # # Has A # Bio::Chado::CDBI::Expression_Pub->has_a(expression_id => 'Bio::Chado::CDBI::Expression'); sub Bio::Chado::CDBI::Expression_Pub::expression { return shift->expression_id } Bio::Chado::CDBI::Expression_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Expression_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Db######## package Bio::Chado::CDBI::Db; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Db->set_up_table('db'); # # Primary key accessors # sub id { shift->db_id } sub db { shift->db_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Db->has_many('dbxref_db_id', 'Bio::Chado::CDBI::Dbxref' => 'db_id'); sub dbxrefs { return shift->dbxref_db_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Assay######## package Bio::Chado::CDBI::Assay; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Assay->set_up_table('assay'); # # Primary key accessors # sub id { shift->assay_id } sub assay { shift->assay_id } # # Has A # Bio::Chado::CDBI::Assay->has_a(arraydesign_id => 'Bio::Chado::CDBI::Arraydesign'); sub Bio::Chado::CDBI::Assay::arraydesign { return shift->arraydesign_id } Bio::Chado::CDBI::Assay->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Assay::protocol { return shift->protocol_id } Bio::Chado::CDBI::Assay->has_a(operator_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Assay::contact { return shift->operator_id } Bio::Chado::CDBI::Assay->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Assay::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Assay->has_many('study_assay_assay_id', 'Bio::Chado::CDBI::Study_Assay' => 'assay_id'); Bio::Chado::CDBI::Assay->has_many('assayprop_assay_id', 'Bio::Chado::CDBI::Assayprop' => 'assay_id'); sub assayprops { return shift->assayprop_assay_id } Bio::Chado::CDBI::Assay->has_many('control_assay_id', 'Bio::Chado::CDBI::Control' => 'assay_id'); sub controls { return shift->control_assay_id } Bio::Chado::CDBI::Assay->has_many('assay_biomaterial_assay_id', 'Bio::Chado::CDBI::Assay_Biomaterial' => 'assay_id'); sub assay_biomaterials { return shift->assay_biomaterial_assay_id } Bio::Chado::CDBI::Assay->has_many('acquisition_assay_id', 'Bio::Chado::CDBI::Acquisition' => 'assay_id'); sub acquisitions { return shift->acquisition_assay_id } Bio::Chado::CDBI::Assay->has_many('studyfactorvalue_assay_id', 'Bio::Chado::CDBI::Studyfactorvalue' => 'assay_id'); sub studyfactorvalues { return shift->studyfactorvalue_assay_id } Bio::Chado::CDBI::Assay->has_many('assay_project_assay_id', 'Bio::Chado::CDBI::Assay_Project' => 'assay_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub assay_project_assays { return shift->assay_project_assay_id } sub study_assay_assays { return shift->study_assay_assay_id } # one to many to one # one2one # sub projects { my $self = shift; return map $_->project_id, $self->assay_project_assay_id } sub studys { my $self = shift; return map $_->study_id, $self->study_assay_assay_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvprop######## package Bio::Chado::CDBI::Cvprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvprop->set_up_table('cvprop'); # # Primary key accessors # sub id { shift->cvprop_id } sub cvprop { shift->cvprop_id } # # Has A # Bio::Chado::CDBI::Cvprop->has_a(cv_id => 'Bio::Chado::CDBI::Cv'); sub Bio::Chado::CDBI::Cvprop::cv { return shift->cv_id } Bio::Chado::CDBI::Cvprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cvprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Studyfactor######## package Bio::Chado::CDBI::Studyfactor; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studyfactor->set_up_table('studyfactor'); # # Primary key accessors # sub id { shift->studyfactor_id } sub studyfactor { shift->studyfactor_id } # # Has A # Bio::Chado::CDBI::Studyfactor->has_a(studydesign_id => 'Bio::Chado::CDBI::Studydesign'); sub Bio::Chado::CDBI::Studyfactor::studydesign { return shift->studydesign_id } Bio::Chado::CDBI::Studyfactor->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Studyfactor::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Studyfactor->has_many('studyfactorvalue_studyfactor_id', 'Bio::Chado::CDBI::Studyfactorvalue' => 'studyfactor_id'); sub studyfactorvalues { return shift->studyfactorvalue_studyfactor_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Organism_Dbxref######## package Bio::Chado::CDBI::Organism_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Organism_Dbxref->set_up_table('organism_dbxref'); # # Primary key accessors # sub id { shift->organism_dbxref_id } sub organism_dbxref { shift->organism_dbxref_id } # # Has A # Bio::Chado::CDBI::Organism_Dbxref->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Organism_Dbxref::organism { return shift->organism_id } Bio::Chado::CDBI::Organism_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Organism_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonodeprop######## package Bio::Chado::CDBI::Phylonodeprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonodeprop->set_up_table('phylonodeprop'); # # Primary key accessors # sub id { shift->phylonodeprop_id } sub phylonodeprop { shift->phylonodeprop_id } # # Has A # Bio::Chado::CDBI::Phylonodeprop->has_a(phylonode_id => 'Bio::Chado::CDBI::Phylonode'); sub Bio::Chado::CDBI::Phylonodeprop::phylonode { return shift->phylonode_id } Bio::Chado::CDBI::Phylonodeprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phylonodeprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Protocol######## package Bio::Chado::CDBI::Nd_Protocol; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Protocol->set_up_table('nd_protocol'); # # Primary key accessors # sub id { shift->nd_protocol_id } sub nd_protocol { shift->nd_protocol_id } # # Has A # Bio::Chado::CDBI::Nd_Protocol->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Protocol::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Nd_Protocol->has_many('nd_protocolprop_nd_protocol_id', 'Bio::Chado::CDBI::Nd_Protocolprop' => 'nd_protocol_id'); sub nd_protocolprops { return shift->nd_protocolprop_nd_protocol_id } Bio::Chado::CDBI::Nd_Protocol->has_many('nd_protocol_reagent_nd_protocol_id', 'Bio::Chado::CDBI::Nd_Protocol_Reagent' => 'nd_protocol_id'); Bio::Chado::CDBI::Nd_Protocol->has_many('nd_experiment_protocol_nd_protocol_id', 'Bio::Chado::CDBI::Nd_Experiment_Protocol' => 'nd_protocol_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_protocol_nd_protocols { return shift->nd_experiment_protocol_nd_protocol_id } sub nd_protocol_reagent_nd_protocols { return shift->nd_protocol_reagent_nd_protocol_id } sub nd_protocol_reagent_nd_protocols { return shift->nd_protocol_reagent_nd_protocol_id } # one to many to one # one2one # sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_protocol_nd_protocol_id } sub cvterms { my $self = shift; return map $_->type_id, $self->nd_protocol_reagent_nd_protocol_id } sub nd_reagents { my $self = shift; return map $_->reagent_id, $self->nd_protocol_reagent_nd_protocol_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Study######## package Bio::Chado::CDBI::Study; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Study->set_up_table('study'); # # Primary key accessors # sub id { shift->study_id } sub study { shift->study_id } # # Has A # Bio::Chado::CDBI::Study->has_a(contact_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Study::contact { return shift->contact_id } Bio::Chado::CDBI::Study->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Study::pub { return shift->pub_id } Bio::Chado::CDBI::Study->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Study::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Study->has_many('study_assay_study_id', 'Bio::Chado::CDBI::Study_Assay' => 'study_id'); Bio::Chado::CDBI::Study->has_many('studyprop_study_id', 'Bio::Chado::CDBI::Studyprop' => 'study_id'); sub studyprops { return shift->studyprop_study_id } Bio::Chado::CDBI::Study->has_many('studydesign_study_id', 'Bio::Chado::CDBI::Studydesign' => 'study_id'); sub studydesigns { return shift->studydesign_study_id } # # Has Compound Many (many to many relationships in all their flavors) # sub study_assay_studys { return shift->study_assay_study_id } # one to many to one # one2one # sub assays { my $self = shift; return map $_->assay_id, $self->study_assay_study_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expression_Image######## package Bio::Chado::CDBI::Expression_Image; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expression_Image->set_up_table('expression_image'); # # Primary key accessors # sub id { shift->expression_image_id } sub expression_image { shift->expression_image_id } # # Has A # Bio::Chado::CDBI::Expression_Image->has_a(expression_id => 'Bio::Chado::CDBI::Expression'); sub Bio::Chado::CDBI::Expression_Image::expression { return shift->expression_id } Bio::Chado::CDBI::Expression_Image->has_a(eimage_id => 'Bio::Chado::CDBI::Eimage'); sub Bio::Chado::CDBI::Expression_Image::eimage { return shift->eimage_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Cvterm######## package Bio::Chado::CDBI::Stock_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Cvterm->set_up_table('stock_cvterm'); # # Primary key accessors # sub id { shift->stock_cvterm_id } sub stock_cvterm { shift->stock_cvterm_id } # # Has A # Bio::Chado::CDBI::Stock_Cvterm->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stock_Cvterm::stock { return shift->stock_id } Bio::Chado::CDBI::Stock_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Stock_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Stock_Cvterm::pub { return shift->pub_id } # # Has Many # Bio::Chado::CDBI::Stock_Cvterm->has_many('stock_cvtermprop_stock_cvterm_id', 'Bio::Chado::CDBI::Stock_Cvtermprop' => 'stock_cvterm_id'); sub stock_cvtermprops { return shift->stock_cvtermprop_stock_cvterm_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Cvterm######## package Bio::Chado::CDBI::Cell_Line_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Cvterm->set_up_table('cell_line_cvterm'); # # Primary key accessors # sub id { shift->cell_line_cvterm_id } sub cell_line_cvterm { shift->cell_line_cvterm_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Cvterm->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Cvterm::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cell_Line_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Cell_Line_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Line_Cvterm::pub { return shift->pub_id } # # Has Many # Bio::Chado::CDBI::Cell_Line_Cvterm->has_many('cell_line_cvtermprop_cell_line_cvterm_id', 'Bio::Chado::CDBI::Cell_Line_Cvtermprop' => 'cell_line_cvterm_id'); sub cell_line_cvtermprops { return shift->cell_line_cvtermprop_cell_line_cvterm_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stockprop_Pub######## package Bio::Chado::CDBI::Stockprop_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stockprop_Pub->set_up_table('stockprop_pub'); # # Primary key accessors # sub id { shift->stockprop_pub_id } sub stockprop_pub { shift->stockprop_pub_id } # # Has A # Bio::Chado::CDBI::Stockprop_Pub->has_a(stockprop_id => 'Bio::Chado::CDBI::Stockprop'); sub Bio::Chado::CDBI::Stockprop_Pub::stockprop { return shift->stockprop_id } Bio::Chado::CDBI::Stockprop_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Stockprop_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref######## package Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref->set_up_table('nd_experiment_stock_dbxref'); # # Primary key accessors # sub id { shift->nd_experiment_stock_dbxref_id } sub nd_experiment_stock_dbxref { shift->nd_experiment_stock_dbxref_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref->has_a(nd_experiment_stock_id => 'Bio::Chado::CDBI::Nd_Experiment_Stock'); sub Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref::nd_experiment_stock { return shift->nd_experiment_stock_id } Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvtermprop######## package Bio::Chado::CDBI::Cvtermprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvtermprop->set_up_table('cvtermprop'); # # Primary key accessors # sub id { shift->cvtermprop_id } sub cvtermprop { shift->cvtermprop_id } # # Has A # Bio::Chado::CDBI::Cvtermprop->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Cvtermprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub type { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Element######## package Bio::Chado::CDBI::Element; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Element->set_up_table('element'); # # Primary key accessors # sub id { shift->element_id } sub element { shift->element_id } # # Has A # Bio::Chado::CDBI::Element->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Element::feature { return shift->feature_id } Bio::Chado::CDBI::Element->has_a(arraydesign_id => 'Bio::Chado::CDBI::Arraydesign'); sub Bio::Chado::CDBI::Element::arraydesign { return shift->arraydesign_id } Bio::Chado::CDBI::Element->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Element::cvterm { return shift->type_id } Bio::Chado::CDBI::Element->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Element::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Element->has_many('elementresult_element_id', 'Bio::Chado::CDBI::Elementresult' => 'element_id'); sub elementresults { return shift->elementresult_element_id } Bio::Chado::CDBI::Element->has_many('element_relationship_subject_id', 'Bio::Chado::CDBI::Element_Relationship' => 'subject_id'); sub element_relationship_subject_ids { my $self = shift; return $self->element_relationship_subject_id(@_) } Bio::Chado::CDBI::Element->has_many('element_relationship_object_id', 'Bio::Chado::CDBI::Element_Relationship' => 'object_id'); sub element_relationship_object_ids { my $self = shift; return $self->element_relationship_object_id(@_) } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Arraydesignprop######## package Bio::Chado::CDBI::Arraydesignprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Arraydesignprop->set_up_table('arraydesignprop'); # # Primary key accessors # sub id { shift->arraydesignprop_id } sub arraydesignprop { shift->arraydesignprop_id } # # Has A # Bio::Chado::CDBI::Arraydesignprop->has_a(arraydesign_id => 'Bio::Chado::CDBI::Arraydesign'); sub Bio::Chado::CDBI::Arraydesignprop::arraydesign { return shift->arraydesign_id } Bio::Chado::CDBI::Arraydesignprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Arraydesignprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Biomaterial_Treatment######## package Bio::Chado::CDBI::Biomaterial_Treatment; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Biomaterial_Treatment->set_up_table('biomaterial_treatment'); # # Primary key accessors # sub id { shift->biomaterial_treatment_id } sub biomaterial_treatment { shift->biomaterial_treatment_id } # # Has A # Bio::Chado::CDBI::Biomaterial_Treatment->has_a(biomaterial_id => 'Bio::Chado::CDBI::Biomaterial'); sub Bio::Chado::CDBI::Biomaterial_Treatment::biomaterial { return shift->biomaterial_id } Bio::Chado::CDBI::Biomaterial_Treatment->has_a(treatment_id => 'Bio::Chado::CDBI::Treatment'); sub Bio::Chado::CDBI::Biomaterial_Treatment::treatment { return shift->treatment_id } Bio::Chado::CDBI::Biomaterial_Treatment->has_a(unittype_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Biomaterial_Treatment::cvterm { return shift->unittype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expressionprop######## package Bio::Chado::CDBI::Expressionprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expressionprop->set_up_table('expressionprop'); # # Primary key accessors # sub id { shift->expressionprop_id } sub expressionprop { shift->expressionprop_id } # # Has A # Bio::Chado::CDBI::Expressionprop->has_a(expression_id => 'Bio::Chado::CDBI::Expression'); sub Bio::Chado::CDBI::Expressionprop::expression { return shift->expression_id } Bio::Chado::CDBI::Expressionprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Expressionprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Phenotype######## package Bio::Chado::CDBI::Nd_Experiment_Phenotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Phenotype->set_up_table('nd_experiment_phenotype'); # # Primary key accessors # sub id { shift->nd_experiment_phenotype_id } sub nd_experiment_phenotype { shift->nd_experiment_phenotype_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Phenotype->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Phenotype::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Phenotype->has_a(phenotype_id => 'Bio::Chado::CDBI::Phenotype'); sub Bio::Chado::CDBI::Nd_Experiment_Phenotype::phenotype { return shift->phenotype_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Stockprop######## package Bio::Chado::CDBI::Nd_Experiment_Stockprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Stockprop->set_up_table('nd_experiment_stockprop'); # # Primary key accessors # sub id { shift->nd_experiment_stockprop_id } sub nd_experiment_stockprop { shift->nd_experiment_stockprop_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Stockprop->has_a(nd_experiment_stock_id => 'Bio::Chado::CDBI::Nd_Experiment_Stock'); sub Bio::Chado::CDBI::Nd_Experiment_Stockprop::nd_experiment_stock { return shift->nd_experiment_stock_id } Bio::Chado::CDBI::Nd_Experiment_Stockprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Experiment_Stockprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Acquisitionprop######## package Bio::Chado::CDBI::Acquisitionprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Acquisitionprop->set_up_table('acquisitionprop'); # # Primary key accessors # sub id { shift->acquisitionprop_id } sub acquisitionprop { shift->acquisitionprop_id } # # Has A # Bio::Chado::CDBI::Acquisitionprop->has_a(acquisition_id => 'Bio::Chado::CDBI::Acquisition'); sub Bio::Chado::CDBI::Acquisitionprop::acquisition { return shift->acquisition_id } Bio::Chado::CDBI::Acquisitionprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Acquisitionprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Assay_Biomaterial######## package Bio::Chado::CDBI::Assay_Biomaterial; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Assay_Biomaterial->set_up_table('assay_biomaterial'); # # Primary key accessors # sub id { shift->assay_biomaterial_id } sub assay_biomaterial { shift->assay_biomaterial_id } # # Has A # Bio::Chado::CDBI::Assay_Biomaterial->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Assay_Biomaterial::assay { return shift->assay_id } Bio::Chado::CDBI::Assay_Biomaterial->has_a(biomaterial_id => 'Bio::Chado::CDBI::Biomaterial'); sub Bio::Chado::CDBI::Assay_Biomaterial::biomaterial { return shift->biomaterial_id } Bio::Chado::CDBI::Assay_Biomaterial->has_a(channel_id => 'Bio::Chado::CDBI::Channel'); sub Bio::Chado::CDBI::Assay_Biomaterial::channel { return shift->channel_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Acquisition######## package Bio::Chado::CDBI::Acquisition; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Acquisition->set_up_table('acquisition'); # # Primary key accessors # sub id { shift->acquisition_id } sub acquisition { shift->acquisition_id } # # Has A # Bio::Chado::CDBI::Acquisition->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Acquisition::assay { return shift->assay_id } Bio::Chado::CDBI::Acquisition->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Acquisition::protocol { return shift->protocol_id } Bio::Chado::CDBI::Acquisition->has_a(channel_id => 'Bio::Chado::CDBI::Channel'); sub Bio::Chado::CDBI::Acquisition::channel { return shift->channel_id } # # Has Many # Bio::Chado::CDBI::Acquisition->has_many('quantification_acquisition_id', 'Bio::Chado::CDBI::Quantification' => 'acquisition_id'); sub quantifications { return shift->quantification_acquisition_id } Bio::Chado::CDBI::Acquisition->has_many('acquisition_relationship_subject_id', 'Bio::Chado::CDBI::Acquisition_Relationship' => 'subject_id'); sub acquisition_relationship_subject_ids { my $self = shift; return $self->acquisition_relationship_subject_id(@_) } Bio::Chado::CDBI::Acquisition->has_many('acquisition_relationship_object_id', 'Bio::Chado::CDBI::Acquisition_Relationship' => 'object_id'); sub acquisition_relationship_object_ids { my $self = shift; return $self->acquisition_relationship_object_id(@_) } Bio::Chado::CDBI::Acquisition->has_many('acquisitionprop_acquisition_id', 'Bio::Chado::CDBI::Acquisitionprop' => 'acquisition_id'); sub acquisitionprops { return shift->acquisitionprop_acquisition_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Studydesignprop######## package Bio::Chado::CDBI::Studydesignprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studydesignprop->set_up_table('studydesignprop'); # # Primary key accessors # sub id { shift->studydesignprop_id } sub studydesignprop { shift->studydesignprop_id } # # Has A # Bio::Chado::CDBI::Studydesignprop->has_a(studydesign_id => 'Bio::Chado::CDBI::Studydesign'); sub Bio::Chado::CDBI::Studydesignprop::studydesign { return shift->studydesign_id } Bio::Chado::CDBI::Studydesignprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Studydesignprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Channel######## package Bio::Chado::CDBI::Channel; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Channel->set_up_table('channel'); # # Primary key accessors # sub id { shift->channel_id } sub channel { shift->channel_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Channel->has_many('assay_biomaterial_channel_id', 'Bio::Chado::CDBI::Assay_Biomaterial' => 'channel_id'); sub assay_biomaterials { return shift->assay_biomaterial_channel_id } Bio::Chado::CDBI::Channel->has_many('acquisition_channel_id', 'Bio::Chado::CDBI::Acquisition' => 'channel_id'); sub acquisitions { return shift->acquisition_channel_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Studyfactorvalue######## package Bio::Chado::CDBI::Studyfactorvalue; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studyfactorvalue->set_up_table('studyfactorvalue'); # # Primary key accessors # sub id { shift->studyfactorvalue_id } sub studyfactorvalue { shift->studyfactorvalue_id } # # Has A # Bio::Chado::CDBI::Studyfactorvalue->has_a(studyfactor_id => 'Bio::Chado::CDBI::Studyfactor'); sub Bio::Chado::CDBI::Studyfactorvalue::studyfactor { return shift->studyfactor_id } Bio::Chado::CDBI::Studyfactorvalue->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Studyfactorvalue::assay { return shift->assay_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Assay_Project######## package Bio::Chado::CDBI::Assay_Project; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Assay_Project->set_up_table('assay_project'); # # Primary key accessors # sub id { shift->assay_project_id } sub assay_project { shift->assay_project_id } # # Has A # Bio::Chado::CDBI::Assay_Project->has_a(assay_id => 'Bio::Chado::CDBI::Assay'); sub Bio::Chado::CDBI::Assay_Project::assay { return shift->assay_id } Bio::Chado::CDBI::Assay_Project->has_a(project_id => 'Bio::Chado::CDBI::Project'); sub Bio::Chado::CDBI::Assay_Project::project { return shift->project_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Environment_Cvterm######## package Bio::Chado::CDBI::Environment_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Environment_Cvterm->set_up_table('environment_cvterm'); # # Primary key accessors # sub id { shift->environment_cvterm_id } sub environment_cvterm { shift->environment_cvterm_id } # # Has A # Bio::Chado::CDBI::Environment_Cvterm->has_a(environment_id => 'Bio::Chado::CDBI::Environment'); sub Bio::Chado::CDBI::Environment_Cvterm::environment { return shift->environment_id } Bio::Chado::CDBI::Environment_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Environment_Cvterm::cvterm { return shift->cvterm_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Pubauthor######## package Bio::Chado::CDBI::Pubauthor; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Pubauthor->set_up_table('pubauthor'); # # Primary key accessors # sub id { shift->pubauthor_id } sub pubauthor { shift->pubauthor_id } # # Has A # Bio::Chado::CDBI::Pubauthor->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Pubauthor::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Organism######## package Bio::Chado::CDBI::Organism; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Organism->set_up_table('organism'); # # Primary key accessors # sub id { shift->organism_id } sub organism { shift->organism_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Organism->has_many('phylonode_organism_organism_id', 'Bio::Chado::CDBI::Phylonode_Organism' => 'organism_id'); Bio::Chado::CDBI::Organism->has_many('organismprop_organism_id', 'Bio::Chado::CDBI::Organismprop' => 'organism_id'); sub organismprops { return shift->organismprop_organism_id } Bio::Chado::CDBI::Organism->has_many('feature_organism_id', 'Bio::Chado::CDBI::Feature' => 'organism_id'); sub features { return shift->feature_organism_id } Bio::Chado::CDBI::Organism->has_many('cell_line_organism_id', 'Bio::Chado::CDBI::Cell_Line' => 'organism_id'); sub cell_lines { return shift->cell_line_organism_id } Bio::Chado::CDBI::Organism->has_many('stock_organism_id', 'Bio::Chado::CDBI::Stock' => 'organism_id'); sub stocks { return shift->stock_organism_id } Bio::Chado::CDBI::Organism->has_many('biomaterial_taxon_id', 'Bio::Chado::CDBI::Biomaterial' => 'taxon_id'); sub biomaterials { return shift->biomaterial_taxon_id } Bio::Chado::CDBI::Organism->has_many('organism_dbxref_organism_id', 'Bio::Chado::CDBI::Organism_Dbxref' => 'organism_id'); Bio::Chado::CDBI::Organism->has_many('phenotype_comparison_organism_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'organism_id'); Bio::Chado::CDBI::Organism->has_many('library_organism_id', 'Bio::Chado::CDBI::Library' => 'organism_id'); sub librarys { return shift->library_organism_id } # # Has Compound Many (many to many relationships in all their flavors) # sub phylonode_organism_organisms { return shift->phylonode_organism_organism_id } sub organism_dbxref_organisms { return shift->organism_dbxref_organism_id } sub phenotype_comparison_organisms { return shift->phenotype_comparison_organism_id } sub phenotype_comparison_organisms { return shift->phenotype_comparison_organism_id } sub phenotype_comparison_organisms { return shift->phenotype_comparison_organism_id } sub phenotype_comparison_organisms { return shift->phenotype_comparison_organism_id } # one to many to one # one2one # sub phylonodes { my $self = shift; return map $_->phylonode_id, $self->phylonode_organism_organism_id } sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->organism_dbxref_organism_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_organism_id } # one to many to many # one2many # sub phenotype_comparison_environment1s { my $self = shift; return map $_->environment1_id, $self->phenotype_comparison_organism_id } sub phenotype_comparison_phenotype1s { my $self = shift; return map $_->phenotype1_id, $self->phenotype_comparison_organism_id } sub phenotype_comparison_genotype1s { my $self = shift; return map $_->genotype1_id, $self->phenotype_comparison_organism_id } #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featurerange######## package Bio::Chado::CDBI::Featurerange; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featurerange->set_up_table('featurerange'); # # Primary key accessors # sub id { shift->featurerange_id } sub featurerange { shift->featurerange_id } # # Has A # Bio::Chado::CDBI::Featurerange->has_a(featuremap_id => 'Bio::Chado::CDBI::Featuremap'); sub Bio::Chado::CDBI::Featurerange::featuremap { return shift->featuremap_id } Bio::Chado::CDBI::Featurerange->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub feature { return shift->feature_id } Bio::Chado::CDBI::Featurerange->has_a(leftstartf_id => 'Bio::Chado::CDBI::Feature'); sub leftstartf { return shift->leftstartf_id } Bio::Chado::CDBI::Featurerange->has_a(leftendf_id => 'Bio::Chado::CDBI::Feature'); sub leftendf { return shift->leftendf_id } Bio::Chado::CDBI::Featurerange->has_a(rightstartf_id => 'Bio::Chado::CDBI::Feature'); sub rightstartf { return shift->rightstartf_id } Bio::Chado::CDBI::Featurerange->has_a(rightendf_id => 'Bio::Chado::CDBI::Feature'); sub rightendf { return shift->rightendf_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Cvtermprop######## package Bio::Chado::CDBI::Cell_Line_Cvtermprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Cvtermprop->set_up_table('cell_line_cvtermprop'); # # Primary key accessors # sub id { shift->cell_line_cvtermprop_id } sub cell_line_cvtermprop { shift->cell_line_cvtermprop_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Cvtermprop->has_a(cell_line_cvterm_id => 'Bio::Chado::CDBI::Cell_Line_Cvterm'); sub Bio::Chado::CDBI::Cell_Line_Cvtermprop::cell_line_cvterm { return shift->cell_line_cvterm_id } Bio::Chado::CDBI::Cell_Line_Cvtermprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cell_Line_Cvtermprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Reagent######## package Bio::Chado::CDBI::Nd_Reagent; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Reagent->set_up_table('nd_reagent'); # # Primary key accessors # sub id { shift->nd_reagent_id } sub nd_reagent { shift->nd_reagent_id } # # Has A # Bio::Chado::CDBI::Nd_Reagent->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Reagent::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Nd_Reagent->has_many('nd_reagentprop_nd_reagent_id', 'Bio::Chado::CDBI::Nd_Reagentprop' => 'nd_reagent_id'); sub nd_reagentprops { return shift->nd_reagentprop_nd_reagent_id } Bio::Chado::CDBI::Nd_Reagent->has_many('nd_protocol_reagent_reagent_id', 'Bio::Chado::CDBI::Nd_Protocol_Reagent' => 'reagent_id'); Bio::Chado::CDBI::Nd_Reagent->has_many('nd_reagent_relationship_subject_reagent_id', 'Bio::Chado::CDBI::Nd_Reagent_Relationship' => 'subject_reagent_id'); Bio::Chado::CDBI::Nd_Reagent->has_many('nd_reagent_relationship_object_reagent_id', 'Bio::Chado::CDBI::Nd_Reagent_Relationship' => 'object_reagent_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub nd_reagent_relationship_subject_reagents { return shift->nd_reagent_relationship_subject_reagent_id } sub nd_reagent_relationship_object_reagents { return shift->nd_reagent_relationship_object_reagent_id } sub nd_protocol_reagent_reagents { return shift->nd_protocol_reagent_reagent_id } sub nd_protocol_reagent_reagents { return shift->nd_protocol_reagent_reagent_id } # one to many to one # one2one # sub cvterms { my $self = shift; return map $_->type_id, $self->nd_protocol_reagent_reagent_id } sub nd_protocols { my $self = shift; return map $_->nd_protocol_id, $self->nd_protocol_reagent_reagent_id } # one to many to many #many to many to one # many2one # sub nd_reagent_relationship_subject_reagent_types { my $self = shift; return map $_->type_id, $self->nd_reagent_relationship_subject_reagent_id } sub nd_reagent_relationship_object_reagent_types { my $self = shift; return map $_->type_id, $self->nd_reagent_relationship_object_reagent_id } #many to many to many 1; ########Bio::Chado::CDBI::Featurepos######## package Bio::Chado::CDBI::Featurepos; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featurepos->set_up_table('featurepos'); # # Primary key accessors # sub id { shift->featurepos_id } sub featurepos { shift->featurepos_id } # # Has A # Bio::Chado::CDBI::Featurepos->has_a(featuremap_id => 'Bio::Chado::CDBI::Featuremap'); sub Bio::Chado::CDBI::Featurepos::featuremap { return shift->featuremap_id } Bio::Chado::CDBI::Featurepos->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub feature { return shift->feature_id } Bio::Chado::CDBI::Featurepos->has_a(map_feature_id => 'Bio::Chado::CDBI::Feature'); sub map_feature { return shift->map_feature_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phenotype_Comparison######## package Bio::Chado::CDBI::Phenotype_Comparison; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phenotype_Comparison->set_up_table('phenotype_comparison'); # # Primary key accessors # sub id { shift->phenotype_comparison_id } sub phenotype_comparison { shift->phenotype_comparison_id } # # Has A # Bio::Chado::CDBI::Phenotype_Comparison->has_a(genotype1_id => 'Bio::Chado::CDBI::Genotype'); sub genotype1 { return shift->genotype1_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(environment1_id => 'Bio::Chado::CDBI::Environment'); sub environment1 { return shift->environment1_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(genotype2_id => 'Bio::Chado::CDBI::Genotype'); sub genotype2 { return shift->genotype2_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(environment2_id => 'Bio::Chado::CDBI::Environment'); sub environment2 { return shift->environment2_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(phenotype1_id => 'Bio::Chado::CDBI::Phenotype'); sub phenotype1 { return shift->phenotype1_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(phenotype2_id => 'Bio::Chado::CDBI::Phenotype'); sub phenotype2 { return shift->phenotype2_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phenotype_Comparison::pub { return shift->pub_id } Bio::Chado::CDBI::Phenotype_Comparison->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Phenotype_Comparison::organism { return shift->organism_id } # # Has Many # Bio::Chado::CDBI::Phenotype_Comparison->has_many('phenotype_comparison_cvterm_phenotype_comparison_id', 'Bio::Chado::CDBI::Phenotype_Comparison_Cvterm' => 'phenotype_comparison_id'); sub phenotype_comparison_cvterms { return shift->phenotype_comparison_cvterm_phenotype_comparison_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Studyprop######## package Bio::Chado::CDBI::Studyprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studyprop->set_up_table('studyprop'); # # Primary key accessors # sub id { shift->studyprop_id } sub studyprop { shift->studyprop_id } # # Has A # Bio::Chado::CDBI::Studyprop->has_a(study_id => 'Bio::Chado::CDBI::Study'); sub Bio::Chado::CDBI::Studyprop::study { return shift->study_id } Bio::Chado::CDBI::Studyprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Studyprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Studyprop->has_many('studyprop_feature_studyprop_id', 'Bio::Chado::CDBI::Studyprop_Feature' => 'studyprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub studyprop_feature_studyprops { return shift->studyprop_feature_studyprop_id } sub studyprop_feature_studyprops { return shift->studyprop_feature_studyprop_id } # one to many to one # one2one # sub features { my $self = shift; return map $_->feature_id, $self->studyprop_feature_studyprop_id } sub cvterms { my $self = shift; return map $_->type_id, $self->studyprop_feature_studyprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Elementresult_Relationship######## package Bio::Chado::CDBI::Elementresult_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Elementresult_Relationship->set_up_table('elementresult_relationship'); # # Primary key accessors # sub id { shift->elementresult_relationship_id } sub elementresult_relationship { shift->elementresult_relationship_id } # # Has A # Bio::Chado::CDBI::Elementresult_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Elementresult'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Elementresult_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Elementresult_Relationship::cvterm { return shift->type_id } Bio::Chado::CDBI::Elementresult_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Elementresult'); sub object { return shift->object_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Project_Relationship######## package Bio::Chado::CDBI::Project_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Project_Relationship->set_up_table('project_relationship'); # # Primary key accessors # sub id { shift->project_relationship_id } sub project_relationship { shift->project_relationship_id } # # Has A # Bio::Chado::CDBI::Project_Relationship->has_a(subject_project_id => 'Bio::Chado::CDBI::Project'); sub subject_project { return shift->subject_project_id } Bio::Chado::CDBI::Project_Relationship->has_a(object_project_id => 'Bio::Chado::CDBI::Project'); sub object_project { return shift->object_project_id } Bio::Chado::CDBI::Project_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Project_Relationship::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonode######## package Bio::Chado::CDBI::Phylonode; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonode->set_up_table('phylonode'); # # Primary key accessors # sub id { shift->phylonode_id } sub phylonode { shift->phylonode_id } # # Has A # Bio::Chado::CDBI::Phylonode->has_a(phylotree_id => 'Bio::Chado::CDBI::Phylotree'); sub Bio::Chado::CDBI::Phylonode::phylotree { return shift->phylotree_id } Bio::Chado::CDBI::Phylonode->has_a(parent_phylonode_id => 'Bio::Chado::CDBI::Phylonode'); sub Bio::Chado::CDBI::Phylonode::phylonode { return shift->parent_phylonode_id } Bio::Chado::CDBI::Phylonode->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phylonode::cvterm { return shift->type_id } Bio::Chado::CDBI::Phylonode->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Phylonode::feature { return shift->feature_id } # # Has Many # Bio::Chado::CDBI::Phylonode->has_many('phylonode_pub_phylonode_id', 'Bio::Chado::CDBI::Phylonode_Pub' => 'phylonode_id'); Bio::Chado::CDBI::Phylonode->has_many('phylonode_organism_phylonode_id', 'Bio::Chado::CDBI::Phylonode_Organism' => 'phylonode_id'); Bio::Chado::CDBI::Phylonode->has_many('phylonode_relationship_subject_id', 'Bio::Chado::CDBI::Phylonode_Relationship' => 'subject_id'); sub phylonode_relationship_subject_ids { my $self = shift; return $self->phylonode_relationship_subject_id(@_) } Bio::Chado::CDBI::Phylonode->has_many('phylonode_relationship_object_id', 'Bio::Chado::CDBI::Phylonode_Relationship' => 'object_id'); sub phylonode_relationship_object_ids { my $self = shift; return $self->phylonode_relationship_object_id(@_) } Bio::Chado::CDBI::Phylonode->has_many('phylonodeprop_phylonode_id', 'Bio::Chado::CDBI::Phylonodeprop' => 'phylonode_id'); sub phylonodeprops { return shift->phylonodeprop_phylonode_id } Bio::Chado::CDBI::Phylonode->has_many('phylonode_parent_phylonode_id', 'Bio::Chado::CDBI::Phylonode' => 'parent_phylonode_id'); sub phylonode_parent_phylonode_ids { my $self = shift; return $self->phylonode_parent_phylonode_id(@_) } Bio::Chado::CDBI::Phylonode->has_many('phylonode_dbxref_phylonode_id', 'Bio::Chado::CDBI::Phylonode_Dbxref' => 'phylonode_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub phylonode_organism_phylonodes { return shift->phylonode_organism_phylonode_id } sub phylonode_dbxref_phylonodes { return shift->phylonode_dbxref_phylonode_id } sub phylonode_pub_phylonodes { return shift->phylonode_pub_phylonode_id } # one to many to one # one2one # sub organisms { my $self = shift; return map $_->organism_id, $self->phylonode_organism_phylonode_id } sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->phylonode_dbxref_phylonode_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phylonode_pub_phylonode_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvtermsynonym######## package Bio::Chado::CDBI::Cvtermsynonym; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvtermsynonym->set_up_table('cvtermsynonym'); # # Primary key accessors # sub id { shift->cvtermsynonym_id } sub cvtermsynonym { shift->cvtermsynonym_id } # # Has A # Bio::Chado::CDBI::Cvtermsynonym->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Cvtermsynonym->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub type { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Lineprop_Pub######## package Bio::Chado::CDBI::Cell_Lineprop_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Lineprop_Pub->set_up_table('cell_lineprop_pub'); # # Primary key accessors # sub id { shift->cell_lineprop_pub_id } sub cell_lineprop_pub { shift->cell_lineprop_pub_id } # # Has A # Bio::Chado::CDBI::Cell_Lineprop_Pub->has_a(cell_lineprop_id => 'Bio::Chado::CDBI::Cell_Lineprop'); sub Bio::Chado::CDBI::Cell_Lineprop_Pub::cell_lineprop { return shift->cell_lineprop_id } Bio::Chado::CDBI::Cell_Lineprop_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Lineprop_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Lineprop######## package Bio::Chado::CDBI::Cell_Lineprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Lineprop->set_up_table('cell_lineprop'); # # Primary key accessors # sub id { shift->cell_lineprop_id } sub cell_lineprop { shift->cell_lineprop_id } # # Has A # Bio::Chado::CDBI::Cell_Lineprop->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Lineprop::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Lineprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Cell_Lineprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Cell_Lineprop->has_many('cell_lineprop_pub_cell_lineprop_id', 'Bio::Chado::CDBI::Cell_Lineprop_Pub' => 'cell_lineprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub cell_lineprop_pub_cell_lineprops { return shift->cell_lineprop_pub_cell_lineprop_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->cell_lineprop_pub_cell_lineprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Relationship######## package Bio::Chado::CDBI::Stock_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Relationship->set_up_table('stock_relationship'); # # Primary key accessors # sub id { shift->stock_relationship_id } sub stock_relationship { shift->stock_relationship_id } # # Has A # Bio::Chado::CDBI::Stock_Relationship->has_a(subject_id => 'Bio::Chado::CDBI::Stock'); sub subject { return shift->subject_id } Bio::Chado::CDBI::Stock_Relationship->has_a(object_id => 'Bio::Chado::CDBI::Stock'); sub object { return shift->object_id } Bio::Chado::CDBI::Stock_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stock_Relationship::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Stock_Relationship->has_many('stock_relationship_pub_stock_relationship_id', 'Bio::Chado::CDBI::Stock_Relationship_Pub' => 'stock_relationship_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub stock_relationship_pub_stock_relationships { return shift->stock_relationship_pub_stock_relationship_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->stock_relationship_pub_stock_relationship_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stockcollection######## package Bio::Chado::CDBI::Stockcollection; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stockcollection->set_up_table('stockcollection'); # # Primary key accessors # sub id { shift->stockcollection_id } sub stockcollection { shift->stockcollection_id } # # Has A # Bio::Chado::CDBI::Stockcollection->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stockcollection::cvterm { return shift->type_id } Bio::Chado::CDBI::Stockcollection->has_a(contact_id => 'Bio::Chado::CDBI::Contact'); sub Bio::Chado::CDBI::Stockcollection::contact { return shift->contact_id } # # Has Many # Bio::Chado::CDBI::Stockcollection->has_many('stockcollectionprop_stockcollection_id', 'Bio::Chado::CDBI::Stockcollectionprop' => 'stockcollection_id'); sub stockcollectionprops { return shift->stockcollectionprop_stockcollection_id } Bio::Chado::CDBI::Stockcollection->has_many('stockcollection_stock_stockcollection_id', 'Bio::Chado::CDBI::Stockcollection_Stock' => 'stockcollection_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub stockcollection_stock_stockcollections { return shift->stockcollection_stock_stockcollection_id } # one to many to one # one2one # sub stocks { my $self = shift; return map $_->stock_id, $self->stockcollection_stock_stockcollection_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expression######## package Bio::Chado::CDBI::Expression; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expression->set_up_table('expression'); # # Primary key accessors # sub id { shift->expression_id } sub expression { shift->expression_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Expression->has_many('feature_expression_expression_id', 'Bio::Chado::CDBI::Feature_Expression' => 'expression_id'); Bio::Chado::CDBI::Expression->has_many('expression_pub_expression_id', 'Bio::Chado::CDBI::Expression_Pub' => 'expression_id'); Bio::Chado::CDBI::Expression->has_many('expression_image_expression_id', 'Bio::Chado::CDBI::Expression_Image' => 'expression_id'); Bio::Chado::CDBI::Expression->has_many('expressionprop_expression_id', 'Bio::Chado::CDBI::Expressionprop' => 'expression_id'); sub expressionprops { return shift->expressionprop_expression_id } Bio::Chado::CDBI::Expression->has_many('expression_cvterm_expression_id', 'Bio::Chado::CDBI::Expression_Cvterm' => 'expression_id'); sub expression_cvterms { return shift->expression_cvterm_expression_id } # # Has Compound Many (many to many relationships in all their flavors) # sub feature_expression_expressions { return shift->feature_expression_expression_id } sub feature_expression_expressions { return shift->feature_expression_expression_id } sub expression_pub_expressions { return shift->expression_pub_expression_id } sub expression_image_expressions { return shift->expression_image_expression_id } # one to many to one # one2one # sub features { my $self = shift; return map $_->feature_id, $self->feature_expression_expression_id } sub pubs { my $self = shift; return map $_->pub_id, $self->feature_expression_expression_id } sub pubs { my $self = shift; return map $_->pub_id, $self->expression_pub_expression_id } sub eimages { my $self = shift; return map $_->eimage_id, $self->expression_image_expression_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Magedocumentation######## package Bio::Chado::CDBI::Magedocumentation; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Magedocumentation->set_up_table('magedocumentation'); # # Primary key accessors # sub id { shift->magedocumentation_id } sub magedocumentation { shift->magedocumentation_id } # # Has A # Bio::Chado::CDBI::Magedocumentation->has_a(mageml_id => 'Bio::Chado::CDBI::Mageml'); sub Bio::Chado::CDBI::Magedocumentation::mageml { return shift->mageml_id } Bio::Chado::CDBI::Magedocumentation->has_a(tableinfo_id => 'Bio::Chado::CDBI::Tableinfo'); sub Bio::Chado::CDBI::Magedocumentation::tableinfo { return shift->tableinfo_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Library_Cvterm######## package Bio::Chado::CDBI::Library_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library_Cvterm->set_up_table('library_cvterm'); # # Primary key accessors # sub id { shift->library_cvterm_id } sub library_cvterm { shift->library_cvterm_id } # # Has A # Bio::Chado::CDBI::Library_Cvterm->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Library_Cvterm::library { return shift->library_id } Bio::Chado::CDBI::Library_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Library_Cvterm::cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Library_Cvterm->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Library_Cvterm::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stock_Relationship_Pub######## package Bio::Chado::CDBI::Stock_Relationship_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stock_Relationship_Pub->set_up_table('stock_relationship_pub'); # # Primary key accessors # sub id { shift->stock_relationship_pub_id } sub stock_relationship_pub { shift->stock_relationship_pub_id } # # Has A # Bio::Chado::CDBI::Stock_Relationship_Pub->has_a(stock_relationship_id => 'Bio::Chado::CDBI::Stock_Relationship'); sub Bio::Chado::CDBI::Stock_Relationship_Pub::stock_relationship { return shift->stock_relationship_id } Bio::Chado::CDBI::Stock_Relationship_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Stock_Relationship_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Library_Dbxref######## package Bio::Chado::CDBI::Library_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library_Dbxref->set_up_table('library_dbxref'); # # Primary key accessors # sub id { shift->library_dbxref_id } sub library_dbxref { shift->library_dbxref_id } # # Has A # Bio::Chado::CDBI::Library_Dbxref->has_a(library_id => 'Bio::Chado::CDBI::Library'); sub Bio::Chado::CDBI::Library_Dbxref::library { return shift->library_id } Bio::Chado::CDBI::Library_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Library_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Analysisprop######## package Bio::Chado::CDBI::Analysisprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Analysisprop->set_up_table('analysisprop'); # # Primary key accessors # sub id { shift->analysisprop_id } sub analysisprop { shift->analysisprop_id } # # Has A # Bio::Chado::CDBI::Analysisprop->has_a(analysis_id => 'Bio::Chado::CDBI::Analysis'); sub Bio::Chado::CDBI::Analysisprop::analysis { return shift->analysis_id } Bio::Chado::CDBI::Analysisprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Analysisprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Relationship_Pub######## package Bio::Chado::CDBI::Feature_Relationship_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Relationship_Pub->set_up_table('feature_relationship_pub'); # # Primary key accessors # sub id { shift->feature_relationship_pub_id } sub feature_relationship_pub { shift->feature_relationship_pub_id } # # Has A # Bio::Chado::CDBI::Feature_Relationship_Pub->has_a(feature_relationship_id => 'Bio::Chado::CDBI::Feature_Relationship'); sub Bio::Chado::CDBI::Feature_Relationship_Pub::feature_relationship { return shift->feature_relationship_id } Bio::Chado::CDBI::Feature_Relationship_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Relationship_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stockcollection_Stock######## package Bio::Chado::CDBI::Stockcollection_Stock; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stockcollection_Stock->set_up_table('stockcollection_stock'); # # Primary key accessors # sub id { shift->stockcollection_stock_id } sub stockcollection_stock { shift->stockcollection_stock_id } # # Has A # Bio::Chado::CDBI::Stockcollection_Stock->has_a(stockcollection_id => 'Bio::Chado::CDBI::Stockcollection'); sub Bio::Chado::CDBI::Stockcollection_Stock::stockcollection { return shift->stockcollection_id } Bio::Chado::CDBI::Stockcollection_Stock->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stockcollection_Stock::stock { return shift->stock_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Treatment######## package Bio::Chado::CDBI::Treatment; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Treatment->set_up_table('treatment'); # # Primary key accessors # sub id { shift->treatment_id } sub treatment { shift->treatment_id } # # Has A # Bio::Chado::CDBI::Treatment->has_a(biomaterial_id => 'Bio::Chado::CDBI::Biomaterial'); sub Bio::Chado::CDBI::Treatment::biomaterial { return shift->biomaterial_id } Bio::Chado::CDBI::Treatment->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Treatment::cvterm { return shift->type_id } Bio::Chado::CDBI::Treatment->has_a(protocol_id => 'Bio::Chado::CDBI::Protocol'); sub Bio::Chado::CDBI::Treatment::protocol { return shift->protocol_id } # # Has Many # Bio::Chado::CDBI::Treatment->has_many('biomaterial_treatment_treatment_id', 'Bio::Chado::CDBI::Biomaterial_Treatment' => 'treatment_id'); sub biomaterial_treatments { return shift->biomaterial_treatment_treatment_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Pubprop######## package Bio::Chado::CDBI::Pubprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Pubprop->set_up_table('pubprop'); # # Primary key accessors # sub id { shift->pubprop_id } sub pubprop { shift->pubprop_id } # # Has A # Bio::Chado::CDBI::Pubprop->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Pubprop::pub { return shift->pub_id } Bio::Chado::CDBI::Pubprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Pubprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phylonode_Dbxref######## package Bio::Chado::CDBI::Phylonode_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylonode_Dbxref->set_up_table('phylonode_dbxref'); # # Primary key accessors # sub id { shift->phylonode_dbxref_id } sub phylonode_dbxref { shift->phylonode_dbxref_id } # # Has A # Bio::Chado::CDBI::Phylonode_Dbxref->has_a(phylonode_id => 'Bio::Chado::CDBI::Phylonode'); sub Bio::Chado::CDBI::Phylonode_Dbxref::phylonode { return shift->phylonode_id } Bio::Chado::CDBI::Phylonode_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Phylonode_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Quantificationprop######## package Bio::Chado::CDBI::Quantificationprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Quantificationprop->set_up_table('quantificationprop'); # # Primary key accessors # sub id { shift->quantificationprop_id } sub quantificationprop { shift->quantificationprop_id } # # Has A # Bio::Chado::CDBI::Quantificationprop->has_a(quantification_id => 'Bio::Chado::CDBI::Quantification'); sub Bio::Chado::CDBI::Quantificationprop::quantification { return shift->quantification_id } Bio::Chado::CDBI::Quantificationprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Quantificationprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expression_Cvterm######## package Bio::Chado::CDBI::Expression_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expression_Cvterm->set_up_table('expression_cvterm'); # # Primary key accessors # sub id { shift->expression_cvterm_id } sub expression_cvterm { shift->expression_cvterm_id } # # Has A # Bio::Chado::CDBI::Expression_Cvterm->has_a(expression_id => 'Bio::Chado::CDBI::Expression'); sub Bio::Chado::CDBI::Expression_Cvterm::expression { return shift->expression_id } Bio::Chado::CDBI::Expression_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub cvterm { return shift->cvterm_id } Bio::Chado::CDBI::Expression_Cvterm->has_a(cvterm_type_id => 'Bio::Chado::CDBI::Cvterm'); sub cvterm_type { return shift->cvterm_type_id } # # Has Many # Bio::Chado::CDBI::Expression_Cvterm->has_many('expression_cvtermprop_expression_cvterm_id', 'Bio::Chado::CDBI::Expression_Cvtermprop' => 'expression_cvterm_id'); sub expression_cvtermprops { return shift->expression_cvtermprop_expression_cvterm_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cv######## package Bio::Chado::CDBI::Cv; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cv->set_up_table('cv'); # # Primary key accessors # sub id { shift->cv_id } sub cv { shift->cv_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Cv->has_many('cvtermpath_cv_id', 'Bio::Chado::CDBI::Cvtermpath' => 'cv_id'); sub cvtermpaths { return shift->cvtermpath_cv_id } Bio::Chado::CDBI::Cv->has_many('cvprop_cv_id', 'Bio::Chado::CDBI::Cvprop' => 'cv_id'); sub cvprops { return shift->cvprop_cv_id } Bio::Chado::CDBI::Cv->has_many('cvterm_cv_id', 'Bio::Chado::CDBI::Cvterm' => 'cv_id'); sub cvterms { return shift->cvterm_cv_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Cvterm_Pub######## package Bio::Chado::CDBI::Feature_Cvterm_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Cvterm_Pub->set_up_table('feature_cvterm_pub'); # # Primary key accessors # sub id { shift->feature_cvterm_pub_id } sub feature_cvterm_pub { shift->feature_cvterm_pub_id } # # Has A # Bio::Chado::CDBI::Feature_Cvterm_Pub->has_a(feature_cvterm_id => 'Bio::Chado::CDBI::Feature_Cvterm'); sub Bio::Chado::CDBI::Feature_Cvterm_Pub::feature_cvterm { return shift->feature_cvterm_id } Bio::Chado::CDBI::Feature_Cvterm_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Cvterm_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Library######## package Bio::Chado::CDBI::Library; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Library->set_up_table('library'); # # Primary key accessors # sub id { shift->library_id } sub library { shift->library_id } # # Has A # Bio::Chado::CDBI::Library->has_a(organism_id => 'Bio::Chado::CDBI::Organism'); sub Bio::Chado::CDBI::Library::organism { return shift->organism_id } Bio::Chado::CDBI::Library->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Library::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Library->has_many('library_pub_library_id', 'Bio::Chado::CDBI::Library_Pub' => 'library_id'); Bio::Chado::CDBI::Library->has_many('library_feature_library_id', 'Bio::Chado::CDBI::Library_Feature' => 'library_id'); Bio::Chado::CDBI::Library->has_many('libraryprop_library_id', 'Bio::Chado::CDBI::Libraryprop' => 'library_id'); sub libraryprops { return shift->libraryprop_library_id } Bio::Chado::CDBI::Library->has_many('cell_line_library_library_id', 'Bio::Chado::CDBI::Cell_Line_Library' => 'library_id'); Bio::Chado::CDBI::Library->has_many('library_synonym_library_id', 'Bio::Chado::CDBI::Library_Synonym' => 'library_id'); sub library_synonyms { return shift->library_synonym_library_id } Bio::Chado::CDBI::Library->has_many('library_cvterm_library_id', 'Bio::Chado::CDBI::Library_Cvterm' => 'library_id'); Bio::Chado::CDBI::Library->has_many('library_dbxref_library_id', 'Bio::Chado::CDBI::Library_Dbxref' => 'library_id'); sub library_dbxrefs { return shift->library_dbxref_library_id } # # Has Compound Many (many to many relationships in all their flavors) # sub library_feature_librarys { return shift->library_feature_library_id } sub cell_line_library_librarys { return shift->cell_line_library_library_id } sub cell_line_library_librarys { return shift->cell_line_library_library_id } sub library_cvterm_librarys { return shift->library_cvterm_library_id } sub library_cvterm_librarys { return shift->library_cvterm_library_id } sub library_pub_librarys { return shift->library_pub_library_id } # one to many to one # one2one # sub features { my $self = shift; return map $_->feature_id, $self->library_feature_library_id } sub cell_lines { my $self = shift; return map $_->cell_line_id, $self->cell_line_library_library_id } sub pubs { my $self = shift; return map $_->pub_id, $self->cell_line_library_library_id } sub cvterms { my $self = shift; return map $_->cvterm_id, $self->library_cvterm_library_id } sub pubs { my $self = shift; return map $_->pub_id, $self->library_cvterm_library_id } sub pubs { my $self = shift; return map $_->pub_id, $self->library_pub_library_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Contact######## package Bio::Chado::CDBI::Contact; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Contact->set_up_table('contact'); # # Primary key accessors # sub id { shift->contact_id } sub contact { shift->contact_id } # # Has A # Bio::Chado::CDBI::Contact->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Contact::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Contact->has_many('quantification_operator_id', 'Bio::Chado::CDBI::Quantification' => 'operator_id'); sub quantifications { return shift->quantification_operator_id } Bio::Chado::CDBI::Contact->has_many('arraydesign_manufacturer_id', 'Bio::Chado::CDBI::Arraydesign' => 'manufacturer_id'); sub arraydesigns { return shift->arraydesign_manufacturer_id } Bio::Chado::CDBI::Contact->has_many('contact_relationship_subject_id', 'Bio::Chado::CDBI::Contact_Relationship' => 'subject_id'); Bio::Chado::CDBI::Contact->has_many('contact_relationship_object_id', 'Bio::Chado::CDBI::Contact_Relationship' => 'object_id'); Bio::Chado::CDBI::Contact->has_many('nd_experiment_contact_contact_id', 'Bio::Chado::CDBI::Nd_Experiment_Contact' => 'contact_id'); Bio::Chado::CDBI::Contact->has_many('project_contact_contact_id', 'Bio::Chado::CDBI::Project_Contact' => 'contact_id'); Bio::Chado::CDBI::Contact->has_many('biomaterial_biosourceprovider_id', 'Bio::Chado::CDBI::Biomaterial' => 'biosourceprovider_id'); sub biomaterials { return shift->biomaterial_biosourceprovider_id } Bio::Chado::CDBI::Contact->has_many('assay_operator_id', 'Bio::Chado::CDBI::Assay' => 'operator_id'); sub assays { return shift->assay_operator_id } Bio::Chado::CDBI::Contact->has_many('study_contact_id', 'Bio::Chado::CDBI::Study' => 'contact_id'); sub studys { return shift->study_contact_id } Bio::Chado::CDBI::Contact->has_many('stockcollection_contact_id', 'Bio::Chado::CDBI::Stockcollection' => 'contact_id'); sub stockcollections { return shift->stockcollection_contact_id } # # Has Compound Many (many to many relationships in all their flavors) # sub contact_relationship_subjects { return shift->contact_relationship_subject_id } sub contact_relationship_objects { return shift->contact_relationship_object_id } sub nd_experiment_contact_contacts { return shift->nd_experiment_contact_contact_id } sub project_contact_contacts { return shift->project_contact_contact_id } # one to many to one # one2one # sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_contact_contact_id } sub projects { my $self = shift; return map $_->project_id, $self->project_contact_contact_id } # one to many to many #many to many to one # many2one # sub contact_relationship_subject_types { my $self = shift; return map $_->type_id, $self->contact_relationship_subject_id } sub contact_relationship_object_types { my $self = shift; return map $_->type_id, $self->contact_relationship_object_id } #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Stock######## package Bio::Chado::CDBI::Nd_Experiment_Stock; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Stock->set_up_table('nd_experiment_stock'); # # Primary key accessors # sub id { shift->nd_experiment_stock_id } sub nd_experiment_stock { shift->nd_experiment_stock_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Stock->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Stock::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Stock->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Nd_Experiment_Stock::stock { return shift->stock_id } Bio::Chado::CDBI::Nd_Experiment_Stock->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Experiment_Stock::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Nd_Experiment_Stock->has_many('nd_experiment_stock_dbxref_nd_experiment_stock_id', 'Bio::Chado::CDBI::Nd_Experiment_Stock_Dbxref' => 'nd_experiment_stock_id'); Bio::Chado::CDBI::Nd_Experiment_Stock->has_many('nd_experiment_stockprop_nd_experiment_stock_id', 'Bio::Chado::CDBI::Nd_Experiment_Stockprop' => 'nd_experiment_stock_id'); sub nd_experiment_stockprops { return shift->nd_experiment_stockprop_nd_experiment_stock_id } # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_stock_dbxref_nd_experiment_stocks { return shift->nd_experiment_stock_dbxref_nd_experiment_stock_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Dbxref######## package Bio::Chado::CDBI::Nd_Experiment_Dbxref; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Dbxref->set_up_table('nd_experiment_dbxref'); # # Primary key accessors # sub id { shift->nd_experiment_dbxref_id } sub nd_experiment_dbxref { shift->nd_experiment_dbxref_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Dbxref->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Dbxref::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Dbxref->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Nd_Experiment_Dbxref::dbxref { return shift->dbxref_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Synonym######## package Bio::Chado::CDBI::Feature_Synonym; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Synonym->set_up_table('feature_synonym'); # # Primary key accessors # sub id { shift->feature_synonym_id } sub feature_synonym { shift->feature_synonym_id } # # Has A # Bio::Chado::CDBI::Feature_Synonym->has_a(synonym_id => 'Bio::Chado::CDBI::Synonym'); sub Bio::Chado::CDBI::Feature_Synonym::synonym { return shift->synonym_id } Bio::Chado::CDBI::Feature_Synonym->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub Bio::Chado::CDBI::Feature_Synonym::feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Synonym->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Feature_Synonym::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experiment_Protocol######## package Bio::Chado::CDBI::Nd_Experiment_Protocol; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experiment_Protocol->set_up_table('nd_experiment_protocol'); # # Primary key accessors # sub id { shift->nd_experiment_protocol_id } sub nd_experiment_protocol { shift->nd_experiment_protocol_id } # # Has A # Bio::Chado::CDBI::Nd_Experiment_Protocol->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experiment_Protocol::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experiment_Protocol->has_a(nd_protocol_id => 'Bio::Chado::CDBI::Nd_Protocol'); sub Bio::Chado::CDBI::Nd_Experiment_Protocol::nd_protocol { return shift->nd_protocol_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Reagent_Relationship######## package Bio::Chado::CDBI::Nd_Reagent_Relationship; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Reagent_Relationship->set_up_table('nd_reagent_relationship'); # # Primary key accessors # sub id { shift->nd_reagent_relationship_id } sub nd_reagent_relationship { shift->nd_reagent_relationship_id } # # Has A # Bio::Chado::CDBI::Nd_Reagent_Relationship->has_a(subject_reagent_id => 'Bio::Chado::CDBI::Nd_Reagent'); sub subject_reagent { return shift->subject_reagent_id } Bio::Chado::CDBI::Nd_Reagent_Relationship->has_a(object_reagent_id => 'Bio::Chado::CDBI::Nd_Reagent'); sub object_reagent { return shift->object_reagent_id } Bio::Chado::CDBI::Nd_Reagent_Relationship->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Reagent_Relationship::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Geolocationprop######## package Bio::Chado::CDBI::Nd_Geolocationprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Geolocationprop->set_up_table('nd_geolocationprop'); # # Primary key accessors # sub id { shift->nd_geolocationprop_id } sub nd_geolocationprop { shift->nd_geolocationprop_id } # # Has A # Bio::Chado::CDBI::Nd_Geolocationprop->has_a(nd_geolocation_id => 'Bio::Chado::CDBI::Nd_Geolocation'); sub Bio::Chado::CDBI::Nd_Geolocationprop::nd_geolocation { return shift->nd_geolocation_id } Bio::Chado::CDBI::Nd_Geolocationprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Geolocationprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Projectprop######## package Bio::Chado::CDBI::Projectprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Projectprop->set_up_table('projectprop'); # # Primary key accessors # sub id { shift->projectprop_id } sub projectprop { shift->projectprop_id } # # Has A # Bio::Chado::CDBI::Projectprop->has_a(project_id => 'Bio::Chado::CDBI::Project'); sub Bio::Chado::CDBI::Projectprop::project { return shift->project_id } Bio::Chado::CDBI::Projectprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Projectprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Nd_Experimentprop######## package Bio::Chado::CDBI::Nd_Experimentprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Nd_Experimentprop->set_up_table('nd_experimentprop'); # # Primary key accessors # sub id { shift->nd_experimentprop_id } sub nd_experimentprop { shift->nd_experimentprop_id } # # Has A # Bio::Chado::CDBI::Nd_Experimentprop->has_a(nd_experiment_id => 'Bio::Chado::CDBI::Nd_Experiment'); sub Bio::Chado::CDBI::Nd_Experimentprop::nd_experiment { return shift->nd_experiment_id } Bio::Chado::CDBI::Nd_Experimentprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Nd_Experimentprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phenotype_Cvterm######## package Bio::Chado::CDBI::Phenotype_Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phenotype_Cvterm->set_up_table('phenotype_cvterm'); # # Primary key accessors # sub id { shift->phenotype_cvterm_id } sub phenotype_cvterm { shift->phenotype_cvterm_id } # # Has A # Bio::Chado::CDBI::Phenotype_Cvterm->has_a(phenotype_id => 'Bio::Chado::CDBI::Phenotype'); sub Bio::Chado::CDBI::Phenotype_Cvterm::phenotype { return shift->phenotype_id } Bio::Chado::CDBI::Phenotype_Cvterm->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phenotype_Cvterm::cvterm { return shift->cvterm_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cell_Line_Pub######## package Bio::Chado::CDBI::Cell_Line_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cell_Line_Pub->set_up_table('cell_line_pub'); # # Primary key accessors # sub id { shift->cell_line_pub_id } sub cell_line_pub { shift->cell_line_pub_id } # # Has A # Bio::Chado::CDBI::Cell_Line_Pub->has_a(cell_line_id => 'Bio::Chado::CDBI::Cell_Line'); sub Bio::Chado::CDBI::Cell_Line_Pub::cell_line { return shift->cell_line_id } Bio::Chado::CDBI::Cell_Line_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Cell_Line_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Featuremap_Pub######## package Bio::Chado::CDBI::Featuremap_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Featuremap_Pub->set_up_table('featuremap_pub'); # # Primary key accessors # sub id { shift->featuremap_pub_id } sub featuremap_pub { shift->featuremap_pub_id } # # Has A # Bio::Chado::CDBI::Featuremap_Pub->has_a(featuremap_id => 'Bio::Chado::CDBI::Featuremap'); sub Bio::Chado::CDBI::Featuremap_Pub::featuremap { return shift->featuremap_id } Bio::Chado::CDBI::Featuremap_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Featuremap_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Feature_Genotype######## package Bio::Chado::CDBI::Feature_Genotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Feature_Genotype->set_up_table('feature_genotype'); # # Primary key accessors # sub id { shift->feature_genotype_id } sub feature_genotype { shift->feature_genotype_id } # # Has A # Bio::Chado::CDBI::Feature_Genotype->has_a(feature_id => 'Bio::Chado::CDBI::Feature'); sub feature { return shift->feature_id } Bio::Chado::CDBI::Feature_Genotype->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Feature_Genotype::genotype { return shift->genotype_id } Bio::Chado::CDBI::Feature_Genotype->has_a(chromosome_id => 'Bio::Chado::CDBI::Feature'); sub chromosome { return shift->chromosome_id } Bio::Chado::CDBI::Feature_Genotype->has_a(cvterm_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Feature_Genotype::cvterm { return shift->cvterm_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Stockprop######## package Bio::Chado::CDBI::Stockprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Stockprop->set_up_table('stockprop'); # # Primary key accessors # sub id { shift->stockprop_id } sub stockprop { shift->stockprop_id } # # Has A # Bio::Chado::CDBI::Stockprop->has_a(stock_id => 'Bio::Chado::CDBI::Stock'); sub Bio::Chado::CDBI::Stockprop::stock { return shift->stock_id } Bio::Chado::CDBI::Stockprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Stockprop::cvterm { return shift->type_id } # # Has Many # Bio::Chado::CDBI::Stockprop->has_many('stockprop_pub_stockprop_id', 'Bio::Chado::CDBI::Stockprop_Pub' => 'stockprop_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub stockprop_pub_stockprops { return shift->stockprop_pub_stockprop_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->stockprop_pub_stockprop_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Cvterm######## package Bio::Chado::CDBI::Cvterm; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Cvterm->set_up_table('cvterm'); # # Primary key accessors # sub id { shift->cvterm_id } sub cvterm { shift->cvterm_id } # # Has A # Bio::Chado::CDBI::Cvterm->has_a(cv_id => 'Bio::Chado::CDBI::Cv'); sub Bio::Chado::CDBI::Cvterm::cv { return shift->cv_id } Bio::Chado::CDBI::Cvterm->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Cvterm::dbxref { return shift->dbxref_id } # # Has Many # Bio::Chado::CDBI::Cvterm->has_many('feature_cvterm_cvterm_id', 'Bio::Chado::CDBI::Feature_Cvterm' => 'cvterm_id'); sub feature_cvterms { return shift->feature_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('arraydesign_platformtype_id', 'Bio::Chado::CDBI::Arraydesign' => 'platformtype_id'); sub arraydesign_platformtypes { return shift->arraydesign_platformtype_id } #sub --arraydesign--platformtype_id-- {} Bio::Chado::CDBI::Cvterm->has_many('arraydesign_substratetype_id', 'Bio::Chado::CDBI::Arraydesign' => 'substratetype_id'); sub arraydesign_substratetypes { return shift->arraydesign_substratetype_id } #sub --arraydesign--substratetype_id-- {} Bio::Chado::CDBI::Cvterm->has_many('stock_cvtermprop_type_id', 'Bio::Chado::CDBI::Stock_Cvtermprop' => 'type_id'); sub stock_cvtermprops { return shift->stock_cvtermprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('biomaterial_relationship_type_id', 'Bio::Chado::CDBI::Biomaterial_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('cell_line_relationship_type_id', 'Bio::Chado::CDBI::Cell_Line_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('quantification_relationship_type_id', 'Bio::Chado::CDBI::Quantification_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('phenotype_comparison_cvterm_cvterm_id', 'Bio::Chado::CDBI::Phenotype_Comparison_Cvterm' => 'cvterm_id'); sub phenotype_comparison_cvterms { return shift->phenotype_comparison_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('synonym_type_id', 'Bio::Chado::CDBI::Synonym' => 'type_id'); sub synonyms { return shift->synonym_type_id } Bio::Chado::CDBI::Cvterm->has_many('cvtermpath_type_id', 'Bio::Chado::CDBI::Cvtermpath' => 'type_id'); sub cvtermpath_type_ids { my $self = shift; return $self->cvtermpath_type_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cvtermpath_subject_id', 'Bio::Chado::CDBI::Cvtermpath' => 'subject_id'); sub cvtermpath_subject_ids { my $self = shift; return $self->cvtermpath_subject_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cvtermpath_object_id', 'Bio::Chado::CDBI::Cvtermpath' => 'object_id'); sub cvtermpath_object_ids { my $self = shift; return $self->cvtermpath_object_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cvterm_relationship_type_id', 'Bio::Chado::CDBI::Cvterm_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('cvterm_relationship_subject_id', 'Bio::Chado::CDBI::Cvterm_Relationship' => 'subject_id'); Bio::Chado::CDBI::Cvterm->has_many('cvterm_relationship_object_id', 'Bio::Chado::CDBI::Cvterm_Relationship' => 'object_id'); Bio::Chado::CDBI::Cvterm->has_many('genotypeprop_type_id', 'Bio::Chado::CDBI::Genotypeprop' => 'type_id'); sub genotypeprops { return shift->genotypeprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('genotype_type_id', 'Bio::Chado::CDBI::Genotype' => 'type_id'); sub genotype_types { return shift->genotype_type_id } #sub --genotype--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('assayprop_type_id', 'Bio::Chado::CDBI::Assayprop' => 'type_id'); sub assayprops { return shift->assayprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('contact_relationship_type_id', 'Bio::Chado::CDBI::Contact_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('pub_type_id', 'Bio::Chado::CDBI::Pub' => 'type_id'); sub pub_types { return shift->pub_type_id } #sub --pub--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('organismprop_type_id', 'Bio::Chado::CDBI::Organismprop' => 'type_id'); sub organismprops { return shift->organismprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('dbxrefprop_type_id', 'Bio::Chado::CDBI::Dbxrefprop' => 'type_id'); sub dbxrefprops { return shift->dbxrefprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('feature_relationship_type_id', 'Bio::Chado::CDBI::Feature_Relationship' => 'type_id'); sub feature_relationships { return shift->feature_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('acquisition_relationship_type_id', 'Bio::Chado::CDBI::Acquisition_Relationship' => 'type_id'); sub acquisition_relationships { return shift->acquisition_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('chadoprop_type_id', 'Bio::Chado::CDBI::Chadoprop' => 'type_id'); sub chadoprops { return shift->chadoprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('feature_cvtermprop_type_id', 'Bio::Chado::CDBI::Feature_Cvtermprop' => 'type_id'); sub feature_cvtermprops { return shift->feature_cvtermprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('protocol_type_id', 'Bio::Chado::CDBI::Protocol' => 'type_id'); sub protocols { return shift->protocol_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_reagentprop_type_id', 'Bio::Chado::CDBI::Nd_Reagentprop' => 'type_id'); sub nd_reagentprops { return shift->nd_reagentprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('stock_dbxrefprop_type_id', 'Bio::Chado::CDBI::Stock_Dbxrefprop' => 'type_id'); sub stock_dbxrefprops { return shift->stock_dbxrefprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('feature_type_id', 'Bio::Chado::CDBI::Feature' => 'type_id'); sub feature_types { return shift->feature_type_id } #sub --feature--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('feature_pubprop_type_id', 'Bio::Chado::CDBI::Feature_Pubprop' => 'type_id'); sub feature_pubprops { return shift->feature_pubprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('biomaterialprop_type_id', 'Bio::Chado::CDBI::Biomaterialprop' => 'type_id'); sub biomaterialprops { return shift->biomaterialprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('cvterm_dbxref_cvterm_id', 'Bio::Chado::CDBI::Cvterm_Dbxref' => 'cvterm_id'); sub cvterm_dbxrefs { return shift->cvterm_dbxref_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('feature_relationshipprop_type_id', 'Bio::Chado::CDBI::Feature_Relationshipprop' => 'type_id'); sub feature_relationshipprops { return shift->feature_relationshipprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('stockcollectionprop_type_id', 'Bio::Chado::CDBI::Stockcollectionprop' => 'type_id'); sub stockcollectionprops { return shift->stockcollectionprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('element_relationship_type_id', 'Bio::Chado::CDBI::Element_Relationship' => 'type_id'); sub element_relationships { return shift->element_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('stock_type_id', 'Bio::Chado::CDBI::Stock' => 'type_id'); sub stock_types { return shift->stock_type_id } #sub --stock--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('featuremap_unittype_id', 'Bio::Chado::CDBI::Featuremap' => 'unittype_id'); sub featuremaps { return shift->featuremap_unittype_id } Bio::Chado::CDBI::Cvterm->has_many('studyprop_feature_type_id', 'Bio::Chado::CDBI::Studyprop_Feature' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('libraryprop_type_id', 'Bio::Chado::CDBI::Libraryprop' => 'type_id'); sub libraryprops { return shift->libraryprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('analysisfeatureprop_type_id', 'Bio::Chado::CDBI::Analysisfeatureprop' => 'type_id'); sub analysisfeatureprops { return shift->analysisfeatureprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('featureprop_type_id', 'Bio::Chado::CDBI::Featureprop' => 'type_id'); sub featureprops { return shift->featureprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('phylonode_relationship_type_id', 'Bio::Chado::CDBI::Phylonode_Relationship' => 'type_id'); sub phylonode_relationships { return shift->phylonode_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_protocolprop_type_id', 'Bio::Chado::CDBI::Nd_Protocolprop' => 'type_id'); sub nd_protocolprops { return shift->nd_protocolprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_protocol_reagent_type_id', 'Bio::Chado::CDBI::Nd_Protocol_Reagent' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('protocolparam_datatype_id', 'Bio::Chado::CDBI::Protocolparam' => 'datatype_id'); sub protocolparam_datatype_ids { my $self = shift; return $self->protocolparam_datatype_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('protocolparam_unittype_id', 'Bio::Chado::CDBI::Protocolparam' => 'unittype_id'); sub protocolparam_unittype_ids { my $self = shift; return $self->protocolparam_unittype_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('control_type_id', 'Bio::Chado::CDBI::Control' => 'type_id'); sub controls { return shift->control_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_experiment_type_id', 'Bio::Chado::CDBI::Nd_Experiment' => 'type_id'); sub nd_experiment_types { return shift->nd_experiment_type_id } #sub --nd_experiment--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('stock_relationship_cvterm_cvterm_id', 'Bio::Chado::CDBI::Stock_Relationship_Cvterm' => 'cvterm_id'); sub stock_relationship_cvterms { return shift->stock_relationship_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('phendesc_type_id', 'Bio::Chado::CDBI::Phendesc' => 'type_id'); sub phendescs { return shift->phendesc_type_id } Bio::Chado::CDBI::Cvterm->has_many('feature_expressionprop_type_id', 'Bio::Chado::CDBI::Feature_Expressionprop' => 'type_id'); sub feature_expressionprops { return shift->feature_expressionprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('pub_relationship_type_id', 'Bio::Chado::CDBI::Pub_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('cvprop_type_id', 'Bio::Chado::CDBI::Cvprop' => 'type_id'); sub cvprops { return shift->cvprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('studyfactor_type_id', 'Bio::Chado::CDBI::Studyfactor' => 'type_id'); sub studyfactors { return shift->studyfactor_type_id } Bio::Chado::CDBI::Cvterm->has_many('phylonodeprop_type_id', 'Bio::Chado::CDBI::Phylonodeprop' => 'type_id'); sub phylonodeprops { return shift->phylonodeprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_protocol_type_id', 'Bio::Chado::CDBI::Nd_Protocol' => 'type_id'); sub nd_protocol_types { return shift->nd_protocol_type_id } #sub --nd_protocol--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('stock_cvterm_cvterm_id', 'Bio::Chado::CDBI::Stock_Cvterm' => 'cvterm_id'); sub stock_cvterms { return shift->stock_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('cell_line_cvterm_cvterm_id', 'Bio::Chado::CDBI::Cell_Line_Cvterm' => 'cvterm_id'); sub cell_line_cvterms { return shift->cell_line_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('cvtermprop_cvterm_id', 'Bio::Chado::CDBI::Cvtermprop' => 'cvterm_id'); sub cvtermprop_cvterm_ids { my $self = shift; return $self->cvtermprop_cvterm_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cvtermprop_type_id', 'Bio::Chado::CDBI::Cvtermprop' => 'type_id'); sub cvtermprop_type_ids { my $self = shift; return $self->cvtermprop_type_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('element_type_id', 'Bio::Chado::CDBI::Element' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('arraydesignprop_type_id', 'Bio::Chado::CDBI::Arraydesignprop' => 'type_id'); sub arraydesignprops { return shift->arraydesignprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('biomaterial_treatment_unittype_id', 'Bio::Chado::CDBI::Biomaterial_Treatment' => 'unittype_id'); sub biomaterial_treatments { return shift->biomaterial_treatment_unittype_id } Bio::Chado::CDBI::Cvterm->has_many('expressionprop_type_id', 'Bio::Chado::CDBI::Expressionprop' => 'type_id'); sub expressionprops { return shift->expressionprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_experiment_stockprop_type_id', 'Bio::Chado::CDBI::Nd_Experiment_Stockprop' => 'type_id'); sub nd_experiment_stockprops { return shift->nd_experiment_stockprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('acquisitionprop_type_id', 'Bio::Chado::CDBI::Acquisitionprop' => 'type_id'); sub acquisitionprops { return shift->acquisitionprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('studydesignprop_type_id', 'Bio::Chado::CDBI::Studydesignprop' => 'type_id'); sub studydesignprops { return shift->studydesignprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('environment_cvterm_cvterm_id', 'Bio::Chado::CDBI::Environment_Cvterm' => 'cvterm_id'); Bio::Chado::CDBI::Cvterm->has_many('cell_line_cvtermprop_type_id', 'Bio::Chado::CDBI::Cell_Line_Cvtermprop' => 'type_id'); sub cell_line_cvtermprops { return shift->cell_line_cvtermprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_reagent_type_id', 'Bio::Chado::CDBI::Nd_Reagent' => 'type_id'); sub nd_reagent_types { return shift->nd_reagent_type_id } #sub --nd_reagent--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('studyprop_type_id', 'Bio::Chado::CDBI::Studyprop' => 'type_id'); sub studyprop_types { return shift->studyprop_type_id } #sub --studyprop--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('elementresult_relationship_type_id', 'Bio::Chado::CDBI::Elementresult_Relationship' => 'type_id'); sub elementresult_relationships { return shift->elementresult_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('project_relationship_type_id', 'Bio::Chado::CDBI::Project_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('phylonode_type_id', 'Bio::Chado::CDBI::Phylonode' => 'type_id'); sub phylonodes { return shift->phylonode_type_id } Bio::Chado::CDBI::Cvterm->has_many('cvtermsynonym_cvterm_id', 'Bio::Chado::CDBI::Cvtermsynonym' => 'cvterm_id'); sub cvtermsynonym_cvterm_ids { my $self = shift; return $self->cvtermsynonym_cvterm_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cvtermsynonym_type_id', 'Bio::Chado::CDBI::Cvtermsynonym' => 'type_id'); sub cvtermsynonym_type_ids { my $self = shift; return $self->cvtermsynonym_type_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('cell_lineprop_type_id', 'Bio::Chado::CDBI::Cell_Lineprop' => 'type_id'); sub cell_lineprops { return shift->cell_lineprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('stock_relationship_type_id', 'Bio::Chado::CDBI::Stock_Relationship' => 'type_id'); sub stock_relationships { return shift->stock_relationship_type_id } Bio::Chado::CDBI::Cvterm->has_many('stockcollection_type_id', 'Bio::Chado::CDBI::Stockcollection' => 'type_id'); sub stockcollections { return shift->stockcollection_type_id } Bio::Chado::CDBI::Cvterm->has_many('library_cvterm_cvterm_id', 'Bio::Chado::CDBI::Library_Cvterm' => 'cvterm_id'); Bio::Chado::CDBI::Cvterm->has_many('analysisprop_type_id', 'Bio::Chado::CDBI::Analysisprop' => 'type_id'); sub analysisprops { return shift->analysisprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('treatment_type_id', 'Bio::Chado::CDBI::Treatment' => 'type_id'); sub treatments { return shift->treatment_type_id } Bio::Chado::CDBI::Cvterm->has_many('pubprop_type_id', 'Bio::Chado::CDBI::Pubprop' => 'type_id'); sub pubprops { return shift->pubprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('quantificationprop_type_id', 'Bio::Chado::CDBI::Quantificationprop' => 'type_id'); sub quantificationprops { return shift->quantificationprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('expression_cvterm_cvterm_id', 'Bio::Chado::CDBI::Expression_Cvterm' => 'cvterm_id'); sub expression_cvterm_cvterm_ids { my $self = shift; return $self->expression_cvterm_cvterm_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('expression_cvterm_cvterm_type_id', 'Bio::Chado::CDBI::Expression_Cvterm' => 'cvterm_type_id'); sub expression_cvterm_cvterm_type_ids { my $self = shift; return $self->expression_cvterm_cvterm_type_id(@_) } Bio::Chado::CDBI::Cvterm->has_many('library_type_id', 'Bio::Chado::CDBI::Library' => 'type_id'); sub library_types { return shift->library_type_id } #sub --library--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('contact_type_id', 'Bio::Chado::CDBI::Contact' => 'type_id'); sub contact_types { return shift->contact_type_id } #sub --contact--type_id-- {} Bio::Chado::CDBI::Cvterm->has_many('nd_experiment_stock_type_id', 'Bio::Chado::CDBI::Nd_Experiment_Stock' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('nd_reagent_relationship_type_id', 'Bio::Chado::CDBI::Nd_Reagent_Relationship' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('nd_geolocationprop_type_id', 'Bio::Chado::CDBI::Nd_Geolocationprop' => 'type_id'); sub nd_geolocationprops { return shift->nd_geolocationprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('projectprop_type_id', 'Bio::Chado::CDBI::Projectprop' => 'type_id'); sub projectprops { return shift->projectprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('nd_experimentprop_type_id', 'Bio::Chado::CDBI::Nd_Experimentprop' => 'type_id'); sub nd_experimentprops { return shift->nd_experimentprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('phenotype_cvterm_cvterm_id', 'Bio::Chado::CDBI::Phenotype_Cvterm' => 'cvterm_id'); sub phenotype_cvterms { return shift->phenotype_cvterm_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('feature_genotype_cvterm_id', 'Bio::Chado::CDBI::Feature_Genotype' => 'cvterm_id'); sub feature_genotypes { return shift->feature_genotype_cvterm_id } Bio::Chado::CDBI::Cvterm->has_many('stockprop_type_id', 'Bio::Chado::CDBI::Stockprop' => 'type_id'); sub stockprops { return shift->stockprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('phenstatement_type_id', 'Bio::Chado::CDBI::Phenstatement' => 'type_id'); Bio::Chado::CDBI::Cvterm->has_many('expression_cvtermprop_type_id', 'Bio::Chado::CDBI::Expression_Cvtermprop' => 'type_id'); sub expression_cvtermprops { return shift->expression_cvtermprop_type_id } Bio::Chado::CDBI::Cvterm->has_many('phenotype_observable_id', 'Bio::Chado::CDBI::Phenotype' => 'observable_id'); sub phenotype_observables { return shift->phenotype_observable_id } #sub --phenotype--observable_id-- {} Bio::Chado::CDBI::Cvterm->has_many('phenotype_attr_id', 'Bio::Chado::CDBI::Phenotype' => 'attr_id'); sub phenotype_attrs { return shift->phenotype_attr_id } #sub --phenotype--attr_id-- {} Bio::Chado::CDBI::Cvterm->has_many('phenotype_cvalue_id', 'Bio::Chado::CDBI::Phenotype' => 'cvalue_id'); sub phenotype_cvalues { return shift->phenotype_cvalue_id } #sub --phenotype--cvalue_id-- {} Bio::Chado::CDBI::Cvterm->has_many('phenotype_assay_id', 'Bio::Chado::CDBI::Phenotype' => 'assay_id'); sub phenotype_assays { return shift->phenotype_assay_id } #sub --phenotype--assay_id-- {} Bio::Chado::CDBI::Cvterm->has_many('phylotree_type_id', 'Bio::Chado::CDBI::Phylotree' => 'type_id'); sub phylotrees { return shift->phylotree_type_id } # # Has Compound Many (many to many relationships in all their flavors) # sub contact_relationship_types { return shift->contact_relationship_type_id } sub environment_cvterm_cvterms { return shift->environment_cvterm_cvterm_id } sub pub_relationship_types { return shift->pub_relationship_type_id } sub nd_experiment_stock_types { return shift->nd_experiment_stock_type_id } sub nd_experiment_stock_types { return shift->nd_experiment_stock_type_id } sub project_relationship_types { return shift->project_relationship_type_id } sub phenstatement_types { return shift->phenstatement_type_id } sub phenstatement_types { return shift->phenstatement_type_id } sub phenstatement_types { return shift->phenstatement_type_id } sub phenstatement_types { return shift->phenstatement_type_id } sub biomaterial_relationship_types { return shift->biomaterial_relationship_type_id } sub nd_experiment_types { return shift->nd_experiment_type_id } sub nd_reagent_relationship_types { return shift->nd_reagent_relationship_type_id } sub studyprop_feature_types { return shift->studyprop_feature_type_id } sub studyprop_feature_types { return shift->studyprop_feature_type_id } sub cvterm_relationship_types { return shift->cvterm_relationship_type_id } sub cvterm_relationship_subjects { return shift->cvterm_relationship_subject_id } sub cvterm_relationship_objects { return shift->cvterm_relationship_object_id } sub library_cvterm_cvterms { return shift->library_cvterm_cvterm_id } sub library_cvterm_cvterms { return shift->library_cvterm_cvterm_id } sub quantification_relationship_types { return shift->quantification_relationship_type_id } sub nd_protocol_reagent_types { return shift->nd_protocol_reagent_type_id } sub nd_protocol_reagent_types { return shift->nd_protocol_reagent_type_id } sub cell_line_relationship_types { return shift->cell_line_relationship_type_id } sub element_types { return shift->element_type_id } sub element_types { return shift->element_type_id } sub element_types { return shift->element_type_id } # one to many to one # one2one # sub environments { my $self = shift; return map $_->environment_id, $self->environment_cvterm_cvterm_id } sub stocks { my $self = shift; return map $_->stock_id, $self->nd_experiment_stock_type_id } sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_stock_type_id } sub environments { my $self = shift; return map $_->environment_id, $self->phenstatement_type_id } sub phenotypes { my $self = shift; return map $_->phenotype_id, $self->phenstatement_type_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phenstatement_type_id } sub genotypes { my $self = shift; return map $_->genotype_id, $self->phenstatement_type_id } sub nd_geolocations { my $self = shift; return map $_->nd_geolocation_id, $self->nd_experiment_type_id } sub features { my $self = shift; return map $_->feature_id, $self->studyprop_feature_type_id } sub studyprops { my $self = shift; return map $_->studyprop_id, $self->studyprop_feature_type_id } sub librarys { my $self = shift; return map $_->library_id, $self->library_cvterm_cvterm_id } sub pubs { my $self = shift; return map $_->pub_id, $self->library_cvterm_cvterm_id } sub nd_reagents { my $self = shift; return map $_->reagent_id, $self->nd_protocol_reagent_type_id } sub nd_protocols { my $self = shift; return map $_->nd_protocol_id, $self->nd_protocol_reagent_type_id } sub features { my $self = shift; return map $_->feature_id, $self->element_type_id } sub arraydesigns { my $self = shift; return map $_->arraydesign_id, $self->element_type_id } sub dbxrefs { my $self = shift; return map $_->dbxref_id, $self->element_type_id } # one to many to many # one2many # sub contact_relationship_subjects { my $self = shift; return map $_->subject_id, $self->contact_relationship_type_id } sub pub_relationship_subjects { my $self = shift; return map $_->subject_id, $self->pub_relationship_type_id } sub project_relationship_subject_projects { my $self = shift; return map $_->subject_project_id, $self->project_relationship_type_id } sub biomaterial_relationship_subjects { my $self = shift; return map $_->subject_id, $self->biomaterial_relationship_type_id } sub nd_reagent_relationship_subject_reagents { my $self = shift; return map $_->subject_reagent_id, $self->nd_reagent_relationship_type_id } sub quantification_relationship_subjects { my $self = shift; return map $_->subject_id, $self->quantification_relationship_type_id } sub cell_line_relationship_subjects { my $self = shift; return map $_->subject_id, $self->cell_line_relationship_type_id } #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phenstatement######## package Bio::Chado::CDBI::Phenstatement; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phenstatement->set_up_table('phenstatement'); # # Primary key accessors # sub id { shift->phenstatement_id } sub phenstatement { shift->phenstatement_id } # # Has A # Bio::Chado::CDBI::Phenstatement->has_a(genotype_id => 'Bio::Chado::CDBI::Genotype'); sub Bio::Chado::CDBI::Phenstatement::genotype { return shift->genotype_id } Bio::Chado::CDBI::Phenstatement->has_a(environment_id => 'Bio::Chado::CDBI::Environment'); sub Bio::Chado::CDBI::Phenstatement::environment { return shift->environment_id } Bio::Chado::CDBI::Phenstatement->has_a(phenotype_id => 'Bio::Chado::CDBI::Phenotype'); sub Bio::Chado::CDBI::Phenstatement::phenotype { return shift->phenotype_id } Bio::Chado::CDBI::Phenstatement->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phenstatement::cvterm { return shift->type_id } Bio::Chado::CDBI::Phenstatement->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Phenstatement::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Environment######## package Bio::Chado::CDBI::Environment; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Environment->set_up_table('environment'); # # Primary key accessors # sub id { shift->environment_id } sub environment { shift->environment_id } # # Has A # # # Has Many # Bio::Chado::CDBI::Environment->has_many('phendesc_environment_id', 'Bio::Chado::CDBI::Phendesc' => 'environment_id'); sub phendescs { return shift->phendesc_environment_id } Bio::Chado::CDBI::Environment->has_many('environment_cvterm_environment_id', 'Bio::Chado::CDBI::Environment_Cvterm' => 'environment_id'); Bio::Chado::CDBI::Environment->has_many('phenotype_comparison_environment1_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'environment1_id'); Bio::Chado::CDBI::Environment->has_many('phenotype_comparison_environment2_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'environment2_id'); Bio::Chado::CDBI::Environment->has_many('phenstatement_environment_id', 'Bio::Chado::CDBI::Phenstatement' => 'environment_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub environment_cvterm_environments { return shift->environment_cvterm_environment_id } sub phenstatement_environments { return shift->phenstatement_environment_id } sub phenstatement_environments { return shift->phenstatement_environment_id } sub phenstatement_environments { return shift->phenstatement_environment_id } sub phenstatement_environments { return shift->phenstatement_environment_id } sub phenotype_comparison_environment1s { return shift->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2s { return shift->phenotype_comparison_environment2_id } sub phenotype_comparison_environment1s { return shift->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2s { return shift->phenotype_comparison_environment2_id } sub phenotype_comparison_environment1s { return shift->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2s { return shift->phenotype_comparison_environment2_id } sub phenotype_comparison_environment1s { return shift->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2s { return shift->phenotype_comparison_environment2_id } # one to many to one # one2one # sub cvterms { my $self = shift; return map $_->cvterm_id, $self->environment_cvterm_environment_id } sub cvterms { my $self = shift; return map $_->type_id, $self->phenstatement_environment_id } sub phenotypes { my $self = shift; return map $_->phenotype_id, $self->phenstatement_environment_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phenstatement_environment_id } sub genotypes { my $self = shift; return map $_->genotype_id, $self->phenstatement_environment_id } # one to many to many #many to many to one # many2one # sub phenotype_comparison_environment1_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_environment2_id } sub phenotype_comparison_environment1_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_environment1_id } sub phenotype_comparison_environment2_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_environment2_id } #many to many to many # many2many # sub phenotype_comparison_environment1_phenotype1s { my $self = shift; return map $_->phenotype_comparison_phenotype1s, $self->phenotype_comparison_environment1s } sub phenotype_comparison_environment1_phenotype2s { my $self = shift; return map $_->phenotype_comparison_phenotype2s, $self->phenotype_comparison_environment1s } sub phenotype_comparison_environment2_phenotype1s { my $self = shift; return map $_->phenotype_comparison_phenotype1s, $self->phenotype_comparison_environment2s } sub phenotype_comparison_environment2_phenotype2s { my $self = shift; return map $_->phenotype_comparison_phenotype2s, $self->phenotype_comparison_environment2s } sub phenotype_comparison_environment1_genotype1s { my $self = shift; return map $_->phenotype_comparison_genotype1s, $self->phenotype_comparison_environment1s } sub phenotype_comparison_environment1_genotype2s { my $self = shift; return map $_->phenotype_comparison_genotype2s, $self->phenotype_comparison_environment1s } sub phenotype_comparison_environment2_genotype1s { my $self = shift; return map $_->phenotype_comparison_genotype1s, $self->phenotype_comparison_environment2s } sub phenotype_comparison_environment2_genotype2s { my $self = shift; return map $_->phenotype_comparison_genotype2s, $self->phenotype_comparison_environment2s } 1; ########Bio::Chado::CDBI::Studydesign######## package Bio::Chado::CDBI::Studydesign; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Studydesign->set_up_table('studydesign'); # # Primary key accessors # sub id { shift->studydesign_id } sub studydesign { shift->studydesign_id } # # Has A # Bio::Chado::CDBI::Studydesign->has_a(study_id => 'Bio::Chado::CDBI::Study'); sub Bio::Chado::CDBI::Studydesign::study { return shift->study_id } # # Has Many # Bio::Chado::CDBI::Studydesign->has_many('studyfactor_studydesign_id', 'Bio::Chado::CDBI::Studyfactor' => 'studydesign_id'); sub studyfactors { return shift->studyfactor_studydesign_id } Bio::Chado::CDBI::Studydesign->has_many('studydesignprop_studydesign_id', 'Bio::Chado::CDBI::Studydesignprop' => 'studydesign_id'); sub studydesignprops { return shift->studydesignprop_studydesign_id } # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Expression_Cvtermprop######## package Bio::Chado::CDBI::Expression_Cvtermprop; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Expression_Cvtermprop->set_up_table('expression_cvtermprop'); # # Primary key accessors # sub id { shift->expression_cvtermprop_id } sub expression_cvtermprop { shift->expression_cvtermprop_id } # # Has A # Bio::Chado::CDBI::Expression_Cvtermprop->has_a(expression_cvterm_id => 'Bio::Chado::CDBI::Expression_Cvterm'); sub Bio::Chado::CDBI::Expression_Cvtermprop::expression_cvterm { return shift->expression_cvterm_id } Bio::Chado::CDBI::Expression_Cvtermprop->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Expression_Cvtermprop::cvterm { return shift->type_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Phenotype######## package Bio::Chado::CDBI::Phenotype; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phenotype->set_up_table('phenotype'); # # Primary key accessors # sub id { shift->phenotype_id } sub phenotype { shift->phenotype_id } # # Has A # Bio::Chado::CDBI::Phenotype->has_a(observable_id => 'Bio::Chado::CDBI::Cvterm'); sub observable { return shift->observable_id } Bio::Chado::CDBI::Phenotype->has_a(attr_id => 'Bio::Chado::CDBI::Cvterm'); sub attr { return shift->attr_id } Bio::Chado::CDBI::Phenotype->has_a(cvalue_id => 'Bio::Chado::CDBI::Cvterm'); sub cvalue { return shift->cvalue_id } Bio::Chado::CDBI::Phenotype->has_a(assay_id => 'Bio::Chado::CDBI::Cvterm'); sub assay { return shift->assay_id } # # Has Many # Bio::Chado::CDBI::Phenotype->has_many('feature_phenotype_phenotype_id', 'Bio::Chado::CDBI::Feature_Phenotype' => 'phenotype_id'); Bio::Chado::CDBI::Phenotype->has_many('nd_experiment_phenotype_phenotype_id', 'Bio::Chado::CDBI::Nd_Experiment_Phenotype' => 'phenotype_id'); Bio::Chado::CDBI::Phenotype->has_many('phenotype_comparison_phenotype1_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'phenotype1_id'); Bio::Chado::CDBI::Phenotype->has_many('phenotype_comparison_phenotype2_id', 'Bio::Chado::CDBI::Phenotype_Comparison' => 'phenotype2_id'); Bio::Chado::CDBI::Phenotype->has_many('phenotype_cvterm_phenotype_id', 'Bio::Chado::CDBI::Phenotype_Cvterm' => 'phenotype_id'); sub phenotype_cvterms { return shift->phenotype_cvterm_phenotype_id } Bio::Chado::CDBI::Phenotype->has_many('phenstatement_phenotype_id', 'Bio::Chado::CDBI::Phenstatement' => 'phenotype_id'); # # Has Compound Many (many to many relationships in all their flavors) # sub nd_experiment_phenotype_phenotypes { return shift->nd_experiment_phenotype_phenotype_id } sub feature_phenotype_phenotypes { return shift->feature_phenotype_phenotype_id } sub phenstatement_phenotypes { return shift->phenstatement_phenotype_id } sub phenstatement_phenotypes { return shift->phenstatement_phenotype_id } sub phenstatement_phenotypes { return shift->phenstatement_phenotype_id } sub phenstatement_phenotypes { return shift->phenstatement_phenotype_id } sub phenotype_comparison_phenotype1s { return shift->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2s { return shift->phenotype_comparison_phenotype2_id } sub phenotype_comparison_phenotype1s { return shift->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2s { return shift->phenotype_comparison_phenotype2_id } sub phenotype_comparison_phenotype1s { return shift->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2s { return shift->phenotype_comparison_phenotype2_id } sub phenotype_comparison_phenotype1s { return shift->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2s { return shift->phenotype_comparison_phenotype2_id } # one to many to one # one2one # sub nd_experiments { my $self = shift; return map $_->nd_experiment_id, $self->nd_experiment_phenotype_phenotype_id } sub features { my $self = shift; return map $_->feature_id, $self->feature_phenotype_phenotype_id } sub environments { my $self = shift; return map $_->environment_id, $self->phenstatement_phenotype_id } sub cvterms { my $self = shift; return map $_->type_id, $self->phenstatement_phenotype_id } sub pubs { my $self = shift; return map $_->pub_id, $self->phenstatement_phenotype_id } sub genotypes { my $self = shift; return map $_->genotype_id, $self->phenstatement_phenotype_id } # one to many to many #many to many to one # many2one # sub phenotype_comparison_phenotype1_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2_organisms { my $self = shift; return map $_->organism_id, $self->phenotype_comparison_phenotype2_id } sub phenotype_comparison_phenotype1_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_phenotype1_id } sub phenotype_comparison_phenotype2_pubs { my $self = shift; return map $_->pub_id, $self->phenotype_comparison_phenotype2_id } #many to many to many # many2many # sub phenotype_comparison_phenotype1_environment1s { my $self = shift; return map $_->phenotype_comparison_environment1s, $self->phenotype_comparison_phenotype1s } sub phenotype_comparison_phenotype1_environment2s { my $self = shift; return map $_->phenotype_comparison_environment2s, $self->phenotype_comparison_phenotype1s } sub phenotype_comparison_phenotype2_environment1s { my $self = shift; return map $_->phenotype_comparison_environment1s, $self->phenotype_comparison_phenotype2s } sub phenotype_comparison_phenotype2_environment2s { my $self = shift; return map $_->phenotype_comparison_environment2s, $self->phenotype_comparison_phenotype2s } sub phenotype_comparison_phenotype1_genotype1s { my $self = shift; return map $_->phenotype_comparison_genotype1s, $self->phenotype_comparison_phenotype1s } sub phenotype_comparison_phenotype1_genotype2s { my $self = shift; return map $_->phenotype_comparison_genotype2s, $self->phenotype_comparison_phenotype1s } sub phenotype_comparison_phenotype2_genotype1s { my $self = shift; return map $_->phenotype_comparison_genotype1s, $self->phenotype_comparison_phenotype2s } sub phenotype_comparison_phenotype2_genotype2s { my $self = shift; return map $_->phenotype_comparison_genotype2s, $self->phenotype_comparison_phenotype2s } 1; ########Bio::Chado::CDBI::Phylotree######## package Bio::Chado::CDBI::Phylotree; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Phylotree->set_up_table('phylotree'); # # Primary key accessors # sub id { shift->phylotree_id } sub phylotree { shift->phylotree_id } # # Has A # Bio::Chado::CDBI::Phylotree->has_a(dbxref_id => 'Bio::Chado::CDBI::Dbxref'); sub Bio::Chado::CDBI::Phylotree::dbxref { return shift->dbxref_id } Bio::Chado::CDBI::Phylotree->has_a(type_id => 'Bio::Chado::CDBI::Cvterm'); sub Bio::Chado::CDBI::Phylotree::cvterm { return shift->type_id } Bio::Chado::CDBI::Phylotree->has_a(analysis_id => 'Bio::Chado::CDBI::Analysis'); sub Bio::Chado::CDBI::Phylotree::analysis { return shift->analysis_id } # # Has Many # Bio::Chado::CDBI::Phylotree->has_many('phylotree_pub_phylotree_id', 'Bio::Chado::CDBI::Phylotree_Pub' => 'phylotree_id'); Bio::Chado::CDBI::Phylotree->has_many('phylonode_relationship_phylotree_id', 'Bio::Chado::CDBI::Phylonode_Relationship' => 'phylotree_id'); sub phylonode_relationships { return shift->phylonode_relationship_phylotree_id } Bio::Chado::CDBI::Phylotree->has_many('phylonode_phylotree_id', 'Bio::Chado::CDBI::Phylonode' => 'phylotree_id'); sub phylonodes { return shift->phylonode_phylotree_id } # # Has Compound Many (many to many relationships in all their flavors) # sub phylotree_pub_phylotrees { return shift->phylotree_pub_phylotree_id } # one to many to one # one2one # sub pubs { my $self = shift; return map $_->pub_id, $self->phylotree_pub_phylotree_id } # one to many to many #many to many to one #many to many to many 1; ########Bio::Chado::CDBI::Project_Pub######## package Bio::Chado::CDBI::Project_Pub; use base 'Bio::Chado::DBI'; use Class::DBI::Pager; no warnings qw(redefine); Bio::Chado::CDBI::Project_Pub->set_up_table('project_pub'); # # Primary key accessors # sub id { shift->project_pub_id } sub project_pub { shift->project_pub_id } # # Has A # Bio::Chado::CDBI::Project_Pub->has_a(project_id => 'Bio::Chado::CDBI::Project'); sub Bio::Chado::CDBI::Project_Pub::project { return shift->project_id } Bio::Chado::CDBI::Project_Pub->has_a(pub_id => 'Bio::Chado::CDBI::Pub'); sub Bio::Chado::CDBI::Project_Pub::pub { return shift->pub_id } # # Has Many # # one to many to one # one to many to many #many to many to one #many to many to many 1; !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':'; chado-1.23/bin/chado-build-schema.pl000755 000765 000024 00000022413 11723232061 017312 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Data::Stag; use FileHandle; use Getopt::Long; use Tk; use SQL::Translator; use Data::Dumper; my ($HELP, $OUTFILE, $INFILE, $ONLY_SQL); my $rows_of_stuff=28; GetOptions( 'help' => \$HELP, 'outfile=s' => \$OUTFILE, 'infile=s' => \$INFILE, 'only_sql' => \$ONLY_SQL, ); if ($HELP) { system ("pod2text", $0); exit(0); } my $SCHEMA_FILE = $OUTFILE || "chado_schema.sql"; my $metafile = $INFILE || "chado-module-metadata.xml"; my $schema_md = Data::Stag->parse($metafile); my $module_dir = $schema_md->get('modules/source/@/path'); my @modules = $schema_md->get('modules/module'); my @components = $schema_md->get('modules/module/component'); my %module_h = map {$_->sget('@/id') => $_} (@modules, @components); my @module_ids = map {$_->sget('@/id')} @modules; # Tk - root frame my $mw = MainWindow->new; $mw->title("Chado Admin Tool"); my $mframe = $mw->Frame; my $row = 0; my $column1 = 1; my %button_h = (); foreach my $id (@module_ids) { my $mod = $module_h{$id}; attach_module_checkbutton($id); # components associated with this module my @components = $mod->get('component'); foreach my $component (@components) { my $c_id = $component->sget('@/id'); attach_module_checkbutton($c_id, 1); } } my $translate_to; $mframe->Checkbutton(-text=>"SQL only", -variable => \$ONLY_SQL)->grid; $mframe->Button(-text=>"Select All", -command=>\&select_all)->grid(-column=>1,-row=>$rows_of_stuff+2); $mframe->Button(-text=>"Deselect All", -command=>\&deselect_all)->grid(-column=>2,-row=>$rows_of_stuff+2); $mframe->Button(-text=>"Create Pg Schema", -command=>\&create_schema)->grid(-column=>3,-row=>$rows_of_stuff+2); my @optionlist = ('Oracle','MySQL','Diagram','GraphViz','HTML'); $mframe->Label( -text=>"Translate to:")->grid(-column=>4,-row=>$rows_of_stuff+2); $mframe->Optionmenu (-options => \@optionlist, -variable => \$translate_to)->grid(-column=>5,-row=>$rows_of_stuff+2); $mframe->Button(-text=>"Translate Schema", -command=>\&translate_schema)->grid(-column=>6,-row=>$rows_of_stuff+2); $mframe->pack(-side=>'bottom'); MainLoop; exit 0; # sub attach_module_checkbutton { my $id = shift; my $indent = shift || 0; $row++; my $col; if ($row == $rows_of_stuff+1) { $col+=4; $row=1; $column1=0; } elsif ($column1) { $col=0; } else { $col=4; } my $mod = $module_h{$id}; my $desc = $mod->sget('description'); my $status = $mod->sget('status'); my $is_required = $mod->sget('@/required') ? 1 : 0; # button frame: contains button and help ? button my $bframe = $mframe->Frame; { $bframe->Label(-text=>".." x $indent)->pack(-anchor=>'w',-side=>'left') if $indent; my $text = $id; my $cb = $bframe->Checkbutton(-text=>$text, -command=>sub { module_checkbox_action($id); }); $cb->{'Value'} = $is_required; $cb->pack(-anchor=>'w',-side=>'left',-fill=>'x',-padx=>0); $button_h{$id} = $cb; } $bframe->grid(-column=>$col++,-row=>$row,-sticky=>'w'); $mframe->Label(-text=>substr($desc,0,40))->grid(-column=>$col++,-row=>$row,-sticky=>'w'); my $help_but = $mframe->Button(-text=>'?', -foreground=>'red', -command=>sub { my $help_dialog = $mframe->messageBox(-message=>$mod->xml); return; }); $help_but->grid(-column=>$col++,-row=>$row); if ($status) { $mframe->Label(-text=>$status->sget('@/code'), -foreground=>'blue')->grid(-column=>$col,-row=>$row); } $col++; } sub module_checkbox_action { my $id = shift; my $mod = $module_h{$id}; my $button = $button_h{$id}; if ($button->{'Value'}) { # -- SELECT -- my @dependencies = $mod->get('dependency/@/to'); foreach my $dep_id (@dependencies) { my $b2 = $button_h{$dep_id}; if (!$b2->{'Value'}) { $b2->select; # recursively set dependencies module_checkbox_action($dep_id); } } } else { # -- DESELECT -- my @dependents = map { $_->sget('@/id') } $schema_md->qmatch('module', ('dependency/@/to'=>$id)); foreach my $dep_id (@dependents) { my $b2 = $button_h{$dep_id}; if ($b2->{'Value'}) { $b2->deselect; # recursively deselect dependents module_checkbox_action($dep_id); } } # deselect subcomponents my @components = $mod->get('component/@/id'); foreach my $c_id (@components) { my $b2 = $button_h{$c_id}; if ($b2->{'Value'}) { $b2->deselect; # recursively set dependencies module_checkbox_action($c_id); } } } return; } sub create_schema { my @sql_lines = (); foreach my $id (@module_ids) { my $mod = $module_h{$id}; if ($button_h{$id}->{'Value'}) { push(@sql_lines, read_source($mod)); } # components associated with this module my @components = $mod->get('component'); foreach my $component (@components) { my $c_id = $component->sget('@/id'); if ($button_h{$c_id}->{'Value'}) { push(@sql_lines, read_source($component)); if (my @subs = $component->get('component')) { foreach my $subcomp (@subs) { push(@sql_lines, read_source($subcomp)); } } } } } my $fh = FileHandle->new(">$SCHEMA_FILE"); if ($fh) { print $fh join('',@sql_lines); $fh->close; #print `cat $SCHEMA_FILE`; $mw->messageBox(-message=>"Pg schema created in file $SCHEMA_FILE"); } else { $mw->messageBox(-message=>"cannot write to $SCHEMA_FILE"); } } sub translate_schema { $ONLY_SQL = 1; create_schema(); $mw->messageBox(-message=>"Please wait for the translation (it can take several minutes)"); my $TRANS_FILE = $SCHEMA_FILE."_$translate_to"; my $translator = SQL::Translator->new( show_warnings => 1, ); my $output = $translator->translate( from => 'PostgreSQL', to => $translate_to, filename => $SCHEMA_FILE, ) or warn $translator->error; my $fh = FileHandle->new(">$TRANS_FILE"); if ($fh) { print $fh $output; $fh->close; $mw->messageBox(-message=>"$translate_to schema created in file $TRANS_FILE"); } else { $mw->messageBox(-message=>"cannot write to $TRANS_FILE"); } } sub read_source { my $mod = shift; my $id = $mod->sget('@/id'); my @sources = $mod->get_source; my @lines = (); foreach my $source (@sources) { my $type = $source->sget('@/type'); my $path = $source->sget('@/path'); if ($ONLY_SQL && ($type ne 'sql' || $path =~ /view/ || $path =~ /bridge/ ) ) { print STDERR "Skipping source $type $path for $id\n"; next; } elsif ($type ne 'sql' && $type ne 'plpgsql') { print STDERR "Skipping source $type $path for $id\n"; next; } my $f = "$module_dir/$path"; my $fh=FileHandle->new($f); if ($fh) { push(@lines, <$fh>); $fh->close; } else { $mw->messageBox(-message=>"cannot find $f"); } } return @lines; } sub select_all { foreach (keys %button_h) { $button_h{$_}->{'Value'} = 1; } return; } sub deselect_all { foreach (keys %button_h) { $button_h{$_}->{'Value'} = 0; } return; } sub usage { system( 'pod2usage', $0 ); exit(0); } =pod =head1 NAME chado-build-schema.pl - PerlTk application to build and translate a chado schema =head1 SYNOPSIS % chado-build-schema.pl [options] =head1 COMMAND-LINE OPTIONS --help This usage statement --infile The name of the metadata xml file (default: chado-module-metadata.xml) --outfile The name of the output ddl file (default: chado_schema.sql) --only_sql Only use pure sql (ie, no views or functions) =head1 DESCRIPTION This is a perlTk application to help uses interactively build a chado data definition langauge (ddl/sql) file. By default, it builds a PostgreSQL compatible file, but by making use of SQL::Translator, it can translate the ddl to Oracle or MySQL ddl, or create schema diagrams or html documentation. Use of this application is not required if the standard default chado schema will be used. =head1 AUTHORS Chris Mungall, Scott Cain Ecain@cshl.eduE Copyright (c) 2005 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut chado-1.23/bin/chado-fix-flybase-instance.pl000755 000765 000024 00000017413 11723232110 020767 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use DBIx::DBStag; use Getopt::Long; $|= 1; my $opt = {}; GetOptions($opt, "skip_type_id=s", "commands|c=s", "db|d=s"); my @commands = split(//,$opt->{commands}); my $dbh = DBIx::DBStag->connect($opt->{db}); $dbh->dbh->{AutoCommit} = 1; print <selectall_arrayref("SELECT cvterm_id, cv.name, cvterm.name FROM cvterm INNER JOIN cv USING (cv_id) WHERE dbxref_id IS NULL"); if (yesno("generate fake cvterm dbxrefs", "flybase chado was built when cvterm.dbxref_id was nullable. we need to add the NOT NULL constraint, but we first need to make sure every cvterm has a unique dbxref. We create fakes ones where db=cv and accession=cvterm.name")) { $dbh->trust_primary_key_values(1); $dbh->is_caching_on('db',1); foreach my $r (@$cvterm_rows) { my ($id,$cv,$name) = @$r; next if $cv =~ /molecular_function/; next if $cv =~ /biological_process/; next if $cv =~ /cellular_component/; my $node = Data::Stag->new(cvterm=>[ [cvterm_id=>$id], [is_obsolete=>1], [dbxref=>[ [db=>[ [name=>$cv] ]], [accession=>$name] ]], ]); $dbh->storenode($node); } } dosql("ALTER TABLE cvterm ALTER COLUMN dbxref_id SET NOT NULL"); dosql("ALTER TABLE cvterm ADD CONSTRAINT cvterm_c1 unique (dbxref_id)"); dosql("ALTER TABLE cvterm ADD CONSTRAINT cvterm_c2 unique (name, cv_id, is_obsolete)"); my $ontol_dir = $ENV{ONTOL_DIR} || "$ENV{HOME}/cvs"; my @onts = ( [relationship=>"$ontol_dir/obo/ontology/OBO_REL/relationship.obo"], [sequence=>"$ontol_dir/song/ontology/so.obo"], [featureprop=>"$ontol_dir/song/ontology/fpo/feature_property.obo"], ); # TODO - load real ontologies foreach my $pair (@onts) { my ($ont,$path) = @$pair; if (yesno("load ont: $ont", "the pre-loaded ontologies in flybase are problematic. the cv.name is wrong, and they may be out of date")) { my $outf = "$ont.chado-xml"; my $cmd = "go2chadoxml $path > $outf"; system($cmd) && die("problem with: $cmd"); my $chadonode = Data::Stag->parse($outf); $dbh->storenode($_) foreach $chadonode->subnodes; } } migrate_type_id("feature","type_id","sequence","golden_path_region","golden_path_fragment"); migrate_type_id("feature_relationship","type_id","relationship","partof","part_of"); migrate_type_id("feature_relationship","type_id","relationship","producedby","derives_from"); if (yesno("Migrate type_ids to real ontologies", "various type_ids may point to the old incorrect ontologies. this fixes that and points to the canonical ontologies: sequence, relationship and feature_property")) { migrate_type_ids_by_table("feature_relationship","type_id","relationship"); migrate_type_ids_by_table("feature","type_id","sequence"); migrate_type_ids_by_table("featureprop","type_id","feature_property"); } if (yesno("set type for all subject match features (eg HSPs) to match_part", "flybase has match part_of match for hits/HSPs. make the subfeature a match part")) { my $match_id = selectcol("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='sequence' AND cvterm.name='match'"); my $match_part_id = selectcol("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='sequence' AND cvterm.name='match_part'"); dosql("UPDATE feature SET type_id = $match_part_id WHERE type_id = $match_id AND feature_id IN (SELECT subject_id FROM feature_relationship)"); } exit 0; # --- our %db_id_by_name = (); sub store_db { my $n = shift; my $id = $db_id_by_name{$n}; return $id if $id; } sub dosql { my $cmd = shift; if (yesno($cmd, "execute the given SQL")) { $dbh->do($cmd) } } sub selectall { my $sql = shift; print STDERR "QUERY:$sql\n"; return $dbh->selectall_arrayref($sql); } sub selectcol { my $sql = shift; my $rows = selectall($sql); my $row = shift @$rows; if (!$row) { die("expected row!"); } return $row->[0]; } sub yesno { my ($prompt,$help) = @_; print "$prompt "; print "[y/n/help]? "; my $ans; if (@commands) { $ans = shift @commands; } else { $ans = ; } if ($ans =~ /^h/i) { print "EXPLANATION:\n$help\n\n"; return yesno($prompt, "I can't tell you anything more!"); } my $yn; $yn = 1 if $ans =~ /^y/i; if ($yn) { print "OK!\n"; } else { print "Skipping\n"; } return $yn; } sub migrate_type_ids_by_table { my ($table,$col,$cv) = @_; my $pk = $table."_id"; my $skip = $opt->{skip_type_id}; my $rows = selectall("SELECT DISTINCT t2.cvterm_id, t.cvterm_id FROM $table AS x INNER JOIN cvterm AS t ON (x.$col = t.cvterm_id) INNER JOIN cvterm AS t2 ON (t.name=t2.name) INNER JOIN cv ON (cv.cv_id = t2.cv_id) WHERE cv.name='$cv' AND t.cv_id != cv.cv_id"); foreach my $r (@$rows) { my ($cvterm_id,$old_cvterm_id) = @$r; if ($skip) { if ($old_cvterm_id == $skip) { print STDERR "SKIPPING $old_cvterm_id to $cvterm_id\n"; next; } } print STDERR "mapping $old_cvterm_id to $cvterm_id\n"; $dbh->do("UPDATE feature SET type_id = $cvterm_id WHERE type_id=$old_cvterm_id"); print STDERR "Done!\n"; #print "UPDATE feature SET type_id = $cvterm_id WHERE type_id=$old_cvterm_id\n"; } } sub migrate_type_id { my ($table,$col,$cv,$from,$to) = @_; my $pk = $table."_id"; if (yesno("map $from to $cv/$to in $table.$col", "the type_ids in the table \"$table\" point to a deprecated cvterm \"$from\" - make them point to \"$to\", which is in the newly loaded \"$cv\" cv")) { my $rows = selectall("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name!='$cv' AND cvterm.name='$from'"); return unless @$rows; # done already if (@$rows > 1) { die("assertion error!"); } my $old_type_id = $rows->[0]->[0]; $rows = selectall("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='$cv' AND cvterm.name='$to'"); if (@$rows != 1) { die("assertion error! expected one row for $to in $cv; got: @$rows"); } my $new_type_id = $rows->[0]->[0]; print STDERR "map $old_type_id to $new_type_id in $table.$col\n"; $dbh->do("UPDATE $table SET $col = $new_type_id WHERE $col=$old_type_id"); print STDERR "Done!\n"; } } chado-1.23/bin/config.PLS000755 000765 000024 00000004740 11256710012 015172 0ustar00cainstaff000000 000000 #!perl -w use Config; use File::Basename qw(&basename &dirname); use FindBin '$Bin'; use Cwd; $origdir = cwd; chdir dirname($0); $file = basename($0, '.PL','.PLS'); $file = "gmod_$file.pl"; my %OPTIONS; if (open F,"$Bin/../../build.conf") { while () { next if /^\#/; chomp; $OPTIONS{$1} = $2 if /^(\w+)\s*=\s*(.+)/; } close F; } open OUT,">$file" or die "Can't create $file: $!"; print OUT "$Config{startperl} -w\n"; if ($OPTIONS{LIB}) { print OUT "use lib '$OPTIONS{LIB}';\n"; } if ($OPTIONS{PREFIX}) { print OUT "use lib '$OPTIONS{PREFIX}/lib';\n"; } print OUT <<'!NO!SUBS!'; use strict; use Getopt::Long; =head1 OPTIONS --database Name of the database to use --available_dbs List of available chado databases --all_tags List of all parameters known about a database --has_tag Returns 1 or 0 on stdout if the given parameter is available --get_tag_value Returns the value for the given tag --confdir Returns the path for the configuration files --tmpdir Returns the tmp directory path --gmod_root Returns the gmod_root path --user Returns the username for the database --password Returns the password for the database --host Returns the host name for the database --port Returns the port number for the database --driver Returns the database driver for the database --name Returns the name of the database --sqlfile Returns the full path to the DDL file for the database --organism Returns the common name of the default organism =cut GetOptions( 'available_dbs' => \$AVAIL, 'all_tags' => \$ALL_TAGS, 'has_tag=s' => \$HAS_TAG, 'get_tag_value=s' => \$GET_TAG_VALUE, 'confdir' => \$CONFDIR, 'tmpdir' => \$TMPDIR, 'gmod_root:s' => \$GMOD_ROOT, 'user' => \$USER, 'password' => \$PASSWORD, 'host' => \$HOST, 'port' => \$PORT, 'driver' => \$DRIVER, 'name' => \$NAME, 'sqlfile' => \$SQLFILE, 'organism' => \$ORGANISM, 'database:s' => \$DATABASE, ) or ( system ('pod2text', $0), exit -1); my $gmod_conf = $ENV{'GMOD_ROOT'} || "/var/lib/gmod"; !NO!SUBS! close OUT or die "Can't close $file: $!"; chmod 0755, $file or die "Can't reset permissions for $file: $!\n"; chdir $origdir; chado-1.23/bin/create-bridge-sql.pl000755 000765 000024 00000005634 11723232170 017202 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # usage docs at end of file use strict; use warnings; use Data::Stag; my %relation_type_h = (); while (@ARGV && $ARGV[0] =~ /^(\-.+)/) { my $switch = shift @ARGV; if ($switch eq '-t' || $switch eq '--table') { while (@ARGV > 1 && $ARGV[0] !~ /^\-/) { $relation_type_h{shift @ARGV} = 'table'; } } elsif ($switch eq '-v' || $switch eq '--view') { while (@ARGV > 1 && $ARGV[0] !~ /^\-/) { $relation_type_h{shift @ARGV} = 'view'; } } elsif ($switch eq '-h' || $switch eq '--help') { print usage(); exit 0; } else { die "unknown option: $switch"; } } my $f = shift @ARGV; my $bridge = Data::Stag->parse($f); my $schema = $bridge->sget('@/schema'); print "CREATE SCHEMA $schema;\n\n"; foreach my $relation ($bridge->get_relation) { my $id = $relation->sget('@/id'); my @indexes = $relation->get_index; my $relation_type = 'view'; # anything with indexes is by default a table if (@indexes) { $relation_type = "table"; } # command line override if ($relation_type_h{'ALL'}) { $relation_type = $relation_type_h{'ALL'}; } if ($relation_type_h{$id}) { $relation_type = $relation_type_h{$id}; } my $sql = $relation->sget_sql; $sql =~ s/^\s+//; $sql =~ s/\;\s*//; printf("CREATE %s %s.%s AS\n%s;\n", uc($relation_type), $schema, $id, $sql); print "$_\n" foreach @indexes; print "\n\n"; } exit 0; # -- sub usage { return < bridge.sql Options: -t --table : list of relations to be materialized -v --view : list of relations to be unmaterialized ALL can be used to specify a default Examples: create-bridge-sql.pl -v term term2term godb-bridge.sql.xml > godb-bridge.sql create-bridge-sql.pl -v ALL -t term godb-bridge.sql.xml > godb-bridge.sql create-bridge-sql.pl chado-bridge.sql.xml > chado-bridge.sql Description: This script generates a 'bridge' layer over the main schema. This allows chado to 'masquerade' as another database, allowing us to use software written that database schema. The bridge layer can be views or materialized views (tables), or a mixture. If materialized views are created, the layer may need recreated if the underlying data changes (the bridge may not implement triggers to do this for you) The bridge layer is created in a seperate schema - the user has control over the search path; eg in postgresql: chado# SET SEARCH PATH TO godb,public; Bridges typically live in chado/modules/*/bridges/*-bridge.sql.xml TODO: Currently the autogenerated bridge can only be applied once. It would be nice (and easy) to have code to arbitrarily switch between tables and views at any points in the database lifecycle Also - finer grained control over indexes EOM ; } chado-1.23/bin/create-so-bridge.pl000755 000765 000024 00000060451 11723232213 017020 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Carp; use DBI; use Getopt::Long; use Time::HiRes qw( time ); #use GO::Parser; use Data::Dumper; # POD DOCS AT END use constant MAX_RELATION_NAME_LEN => 100; # 31; my $debug; my $help; my $db; my $file; my $user; my $pass; my $id_based; my $PROPTYPE_ID = 'type_id'; my $drop; my $counts; my $RTYPE = 'VIEW'; my $schema = 'so'; my $so_name = 'sequence'; my $ontology = $so_name; my $verbose; my $do_closure=1; my %custom_name_map; my $use_custom_name_map; GetOptions( "help|h"=>\$help, "db|d=s"=>\$db, "file|f=s"=>\$file, "user|u=s"=>\$user, "pass|p=s"=>\$pass, "id_based|i"=>\$id_based, "count|c"=>\$counts, "drop"=>\$drop, "ptype_id=s"=>\$PROPTYPE_ID, "rtype|r=s"=>\$RTYPE, "verbose|v"=>\$verbose, "ontology|o=s"=>\$ontology, "Custom_namemap:s"=>\$use_custom_name_map, ); if ($help) { system("perldoc $0"); exit 0; } $id_based = 1 unless ($ontology eq 'sequence'); $schema = lc($ontology) unless ($ontology eq 'sequence'); if ($RTYPE ne 'VIEW' && $RTYPE ne 'TABLE') { die "RTYPE: $RTYPE is not VIEW or TABLE"; } my $dbh; my $DBI = 'DBIx::DBStag'; if ($db) { eval { require "DBIx/DBStag.pm"; msg("Connecting via DBStag"); my $sdbh = DBIx::DBStag->connect($db, $user, $pass); $dbh = $sdbh->dbh; }; if ($@) { # stag not installed - use DBI msg("Connecting via DBI"); $dbh = DBI->connect($db, $user, $pass); } msg("Connected"); $dbh->{RaiseError} = 1; } if (defined $use_custom_name_map and $use_custom_name_map eq '') { %custom_name_map = get_name_map_from_db(); } elsif ($use_custom_name_map) { my @pairs = split(',', $use_custom_name_map); for my $pair (@pairs) { my ($tag,$value) = split('=', $pair); $custom_name_map{$tag} = $value; } } my $child_term_query = "SELECT cvterm.cvterm_id,cvterm.name FROM cvterm JOIN cvterm_relationship ON (cvterm.cvterm_id = cvterm_relationship.subject_id) WHERE cvterm_relationship.object_id = ? AND cvterm_relationship.type_id in (SELECT cvterm_id FROM cvterm WHERE name='is_a') "; my $child_query_handle = $dbh->prepare($child_term_query); # ============================================================== # PARSE SOFA Removed for the time being--SO info from Chado # ============================================================== #my $p = GO::Parser->new({handler=>'obj'}); #my $f = shift || die "must pass SO or SOFA file"; #$p->parse($f); #my $graph = $p->handler->graph; # ============================================================== # GET FEATURE TYPES # ============================================================== # this is only the feature types for which a feature exists within # the particular chado implementation my @terms = get_so_terms($ontology); # ============================================================== # GET CVTERM IDS # ============================================================== my $trows = []; my $used_type_ids; if ($dbh) { msg("getting type to prop mappings"); if ($ontology eq 'GO') { $trows = $dbh->selectall_arrayref("SELECT DISTINCT cvterm_id, cvterm.name FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='biological_process' or cv.name='molecular_function' or cv.name='cellular_component'"); } else { $trows = $dbh->selectall_arrayref("SELECT DISTINCT cvterm_id, cvterm.name FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='$ontology'"); } die "could not find terms" unless @$trows; if ($ontology eq 'GO') { $used_type_ids = $dbh->selectcol_arrayref("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN feature_cvterm USING (cvterm_id) WHERE cv_id IN (SELECT cv_id FROM cv WHERE cv.name='biological_process' or cv.name='molecular_function' or cv.name='cellular_component')"); } elsif ($ontology ne 'sequence') { $used_type_ids = $dbh->selectcol_arrayref("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN feature_cvterm USING (cvterm_id) WHERE cv_id IN (SELECT cv_id FROM cv WHERE name = '$ontology'"); } else { #sequence $used_type_ids = $id_based ? $dbh->selectcol_arrayref("SELECT DISTINCT type_id FROM feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)") : $dbh->selectcol_arrayref("SELECT DISTINCT cvterm_id FROM cvterm INNER JOIN cv USING (cv_id) WHERE cv.name='sequence'"); } } my %used_type_idh = map { $_=>1 } @$used_type_ids; my %n2id = map { $_->[1] => $_->[0] } @$trows; my %id2n = reverse %n2id; my %namemap = (); my %revnamemap = (); my %abbrev = (); # make them database-safe (remove certain characters) $| = 1; print "--This is an automatically generated file; do not edit it as changes will not\n"; print "--be saved. Instead, modify bin/create-so-bridge.pl, which creates this file.\n\n\n"; if ($schema) { print "CREATE SCHEMA $schema;\nSET search_path=$schema,public,pg_catalog;\n\n"; } msg("generating SO layer...."); foreach my $term (@terms) { my $tname = $$term{name}; my $def = $$term{definition} || ''; my $cvtermid = $$term{cvterm_id}; my $vname = safename($tname); next if $vname eq '-1'; next if ($id_based && !$used_type_idh{$cvtermid}); my (@cols, @selcols, $sel); my @fcols = qw( feature_id dbxref_id organism_id name uniquename residues seqlen md5checksum type_id is_analysis timeaccessioned timelastmodified ); my @ifcols = qw( feature_id dbxref_id organism_id name uniquename ); my $vfmt = join("\n", "CREATE $RTYPE $vname AS", " SELECT", " feature_id AS $vname"."_id,", " feature.*", " FROM", " feature %s", " WHERE %s", ); my $from; if ($ontology eq 'sequence') { $from = "INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)"; } else { $from = "INNER JOIN feature_cvterm USING (feature_id) INNER JOIN cvterm USING (cvterm_id)"; } my $where = "cvterm.name = '$tname'"; if ($id_based and $ontology eq 'sequence') { my $id = $n2id{$tname}; $where = "feature.type_id = $id"; } if ($do_closure) { my @cterms = get_recursive_child_terms_by_type_from_chado($$term{cvterm_id}); push @cterms, $tname; my @pnames = @cterms; # if (%used_type_idh) { # @pnames = grep { $used_type_idh{$n2id{$_}} } @pnames; # } # @pnames = map {safename($_)} @pnames; if ($id_based and $ontology eq 'sequence') { $where = join(' OR ', map {"feature.type_id = '$_'"} map {$n2id{$_}} @pnames); } else { $where = join(' OR ', map {"cvterm.name = '$_'"} @pnames); } } my $cmnt = ""; if ($id_based) { my $id = $n2id{$tname}; if (!$id) { print STDERR "no id for $tname\n" unless $id; next; } $from = "" if $ontology eq 'sequence'; $cmnt = "--- This view is derived from the cvterm database ID.\n". "--- This will be more efficient, but the views MUST be regenerated\n". "--- when the underlying ontology in the database changes\n"; } my $vsql = sprintf($vfmt, $from, $where); if ($drop) { print"DROP $RTYPE $vname CASCADE;\n"; } my $defcmt = ''; if ($def) { my $S = 40; while ($def) { $defcmt .= sprintf("--- *** %-40s ***\n",substr($def,0,$S,'')); } } my $print_str = "--- ************************************************\n". "--- *** relation: $vname ***\n". "--- *** relation type: $RTYPE ***\n". "--- *** ***\n". $defcmt. "--- ************************************************\n". "---\n". "\n". "$vsql;\n\n"; print $print_str; if ($RTYPE eq 'TABLE') { print "\n\n--- *** Auto-generated indexes ***\n"; foreach my $col (@ifcols) { print "CREATE INDEX $vname"."_idx_$col ON $vname ($col);\n"; } print "\n\n"; } } $dbh->disconnect if $dbh; create_lookup_table(%namemap); print "\n\nSET search_path=public,pg_catalog;\n"; print STDERR "Done!\n"; exit 0; sub msg { return unless $verbose; print STDERR "@_\n"; } # ============================================================== # safename(string): returns string # ============================================================== # makes a name db-safe; also adds the mapping # from the original name to safe name in the global lookup %namemap sub safename { my $orig = shift; my $n = lc($orig); $n =~ s/[-.(),`'"]/_/g; my @parts = (); if ($orig =~ /\s/) { @parts = split(/ /, $n); } else { @parts = split(/_/, $n); } # @parts = map {$abbrev{$_} || $_} @parts; #start hard coding some short circuits to make sure everything gets a unqique name if ($custom_name_map{$orig}) { $n = $custom_name_map{$orig}; } elsif ($n eq 'deficient_intrachromosomal_transposition') { $n = 'd_intrachr_transposition'; } elsif ($n eq 'deficient_interchromosomal_transposition') { $n = 'd_interchr_transposition'; } elsif ($n eq 'arginine_trna_primary_transcript') { $n = 'arg_trna_primary_transcript'; } elsif ($n eq 'asparagine_tRNA_primary_transcript') { $n = 'asp_tRNA_primary_transcript'; } elsif ($n eq 'tryptophan_trna_primary_transcript') { $n = 'try_trna_primary_transcript'; } elsif ($n eq 'tyrosine_tRNA_primary_transcript') { $n = 'tyr_tRNA_primary_transcript'; } elsif ($n eq 'threonine_trna_primary_transcript') { $n = 'thr_trna_primary_transcript'; } elsif ($n eq 'trinucleotide_repeat_microsatellite_feature') { $n = 'trinuc_repeat_microsat'; } elsif ($n eq 'tetranucleotide_repeat_microsatellite_feature') { $n = 'tetranuc_repeat_microsat'; } elsif ($n eq 'phenylalanine_trna_primary_transcript') { $n = 'phe_trna_primary_transcript'; } elsif ($n eq 'pyrrolysine_tRNA_primary_transcript') { $n = 'pyr_tRNA_primary_transcript'; } elsif ($n eq 'two_prime_o_ribosyladenosine_phosphate') { $n = 'two_prime_o_riboA_phosphate'; } elsif ($n eq 'two_prime_O_ribosylguanosine_phosphate') { $n = 'two_prime_O_riboG_phosphate'; } elsif ($n eq 'five_methoxycarbonylmethyl_two_thiouridine') { $n = 'five_mcm_2_thiouridine'; } elsif ($n eq 'five_methylaminomethyl_two_thiouridine') { $n = 'five_mam_2_thiouridine'; } elsif ($n eq 'five_carbamoylmethyl_two_prime_o_methyluridine') { $n = 'five_cm_2_prime_o_methU'; } elsif ($n eq 'five_carboxymethylaminomethyl_two_prime_O_methyluridine') { $n = 'five_cmam_2_prime_methU'; } elsif ($n eq 'inverted_interchromosomal_transposition') { $n = 'invert_inter_transposition'; } elsif ($n eq 'inverted_intrachromosomal_transposition') { $n = 'invert_intra_transposition'; } elsif ($n eq 'uninverted_interchromosomal_transposition') { $n = 'uninvert_inter_transposition'; } elsif ($n eq 'uninverted_intrachromosomal_transposition') { $n = 'uninvert_intra_transposition'; } elsif ($n eq 'uninverted_insertional_duplication') { $n = 'uninvert_insert_dup'; } elsif ($n eq 'unoriented_insertional_duplication') { $n = 'unorient_insert_dup'; } elsif ($n eq 'unorientated_interchromosomal_transposition') { $n = 'unorient_inter_transposition'; } elsif ($n eq 'unorientated_intrachromosomal_transposition') { $n = 'unorient_intra_transposition'; } elsif ($n eq 'natural') { $n = 'so_natural'; } elsif ($n eq 'foreign') { $n = 'so_foreign'; } elsif ($n eq 'edited_transcript_by A_to_I_substitution') { $n = 'edit_trans_by_a_to_i_sub'; } elsif ($n eq '7-methylguanine') { $n = 'seven_methylguanine'; } elsif ($n eq '') { $n = ''; } else { if (length("@parts") > MAX_RELATION_NAME_LEN) { @parts = split(/_/, $n); my $part_i = 0; while (length("@parts") > MAX_RELATION_NAME_LEN) { if ($part_i > @parts) { die "cannot shorten $orig [got $n]"; } my $part = $parts[$part_i]; my $ab = substr($part, 0, 1); $abbrev{$part} = $ab; $parts[$part_i] = $ab; # print " FROM: $part => $ab\n"; $part_i++; } } $n = ''; $n = join('_', @parts); # while (my $part = shift @parts) { # $n .= $part; # if (@parts && (length($part) > 1 || length($parts[0]) > 1)) { # $n.= '_'; # } # } } # print "NAMEMAP: $orig -> $n\n"; if ($revnamemap{$n}) { #figure out if there are any terms that use this term--if not, skip #it with a warning; if so die #We should probably provide a way for the user to supply custom #name mappings to get around this my $non_so_used_query = "SELECT count(feature_id) FROM feature_cvterm INNER JOIN cvterm USING (cvterm_id) WHERE cvterm.name = ?"; my $sth = $dbh->prepare($non_so_used_query); $sth->execute($orig); my ($exists) = $sth->fetchrow_array; if ($exists) { print STDERR "The short name $n already exists; the existing view\n"; print STDERR "is called $revnamemap{$n}, and the current view is for $orig\n\n"; print STDERR "You may supply the --Custom_namemap argument to overcome this;\n"; print STDERR "see the documentation for more. Exiting...\n\n"; exit(-1); } else { print STDERR "The short name $n already exists; the existing view\n"; print STDERR "is called $revnamemap{$n}, and the current view is for $orig.,\n"; print STDERR "However, since there is no data that would be contained in this view,\n"; print STDERR "it is being skipped. You may supply the --Custom_namemap argument to overcome\n"; print STDERR "this; see the documentation for more.\n\n"; return -1; } } $revnamemap{$n} = lc($orig); return $namemap{lc($orig)} = $n; } sub get_so_terms { my $ontology = shift; my ($query,$sth); if ($ontology eq 'GO') { $query = "SELECT cvterm_id, name, definition FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE cv.name='biological_process' or cv.name='molecular_function' or cv.name='cellular_component') and is_relationshiptype = 0 and name not like '%obsolete %' order by cvterm_id"; $sth = $dbh->prepare($query); $sth->execute(); } else { $query = "SELECT cvterm_id, cvterm.name, cvterm.definition FROM cvterm JOIN cv USING (cv_id) WHERE cv.name=? and is_relationshiptype = 0 and cvterm.name not like '%obsolete %' order by cvterm_id"; $sth = $dbh->prepare($query); $sth->execute($ontology); } my @terms = (); while (my $hashref = $sth->fetchrow_hashref) { push @terms, $hashref; } return @terms; } sub get_recursive_child_terms_by_type_from_chado { my $parent_id = shift; #this would be a lot easier if the closure were already calculated # but SO is small, so it isn't a big deal my @child_terms = (); $child_query_handle->execute($parent_id); my @idlist; while (my $hashref = $child_query_handle->fetchrow_hashref) { push @child_terms, $$hashref{name}; push @idlist, $$hashref{cvterm_id}; } for my $id (@idlist) { push @child_terms, get_recursive_child_terms_by_type_from_chado($id); } return @child_terms; } sub create_lookup_table { my %namemap = @_; my $table_name = $ontology."_cv_lookup_table"; print "CREATE TABLE $table_name (".$table_name."_id serial not null, primary key(".$table_name."_id), original_cvterm_name varchar(1024), relation_name varchar(128));\n"; for my $orig_name (keys %namemap) { my $munged_table_name = $namemap{$orig_name}; print "INSERT INTO $table_name (original_cvterm_name,relation_name) VALUES ('$orig_name','$munged_table_name');\n"; } print "\nCREATE INDEX ".$table_name."_idx ON $table_name (original_cvterm_name);\n"; return; } sub get_name_map_from_db { my %name_map; my $query = "SELECT original_name, abbreviation FROM custom_name_mapping"; my $sth = $dbh->prepare($query); $sth->execute; while (my $hashref = $sth->fetchrow_hashref) { $name_map{$$hashref{original_name}} = $$hashref{abbreviation}; } return %name_map; } __END__ =head1 NAME create-sofa-bridge.pl =head1 SYNPOSIS create-sofa-bridge.pl -d 'dbi:Pg:dbname=chado' sofa.obo =head1 ARGUMENTS =over =item -d DBI-LOCATOR Database to use as source (does not actually write to database), like 'dbi:Pg:database=chado;host=dbserver' =item -i use internal surrogate database IDs (layer will be NON-PORTABLE) and only views for which there are features in the feature table will be created. =item -r|rtype RELATION-TYPE RELATION-TYPE must be either TABLE or VIEW; the default is VIEW This determines whether the layer consists of materialized views (ie TABLEs), or views =item --drop If this is specified, then DROP VIEW/TABLE statements will be created this is useful if you wish to REPLACE an existing SO layer =item -C|Custom_namemap If specified without an argument, query the database for a table called custom_name_mapping with a column called original_name that contains the exact text of the original cvterm and a column called abbreviation that has the text of relation name. This table may contain other columns (like a primary key or notes). You may also specify a argument to -C that is a series of comma delimited tag=value pairs, where the part before the equals sign is the orginal name of the cvterm and the part after is the relation name. =back =head1 DESCRIPTION Generates views for every term in SO or SOFA Chado is a modular database for bioinformatics. The chado sequence module is generic and has no built-in type system for sequence feature data. Instead it relies on an external ontology to provide semantics for feature types. The canonical ontology for sequence features in the Sequence Ontology (ref). Chado has a module specifically for housing ontologies. The combination of SO plus Chado gives a rigorous yet flexible hybrid relational-ontology model for storing and querying genomic and proteomic data. One negative impact of this hybrid model is that apparently simple queries are hard to express, and may be inefficient. For example, an SQL select to get the gene count in the database requires joining two relations (ie tables), instead of one relation (as expected in a database in which types are encoded relationally, such as ensembl). To fetch mRNAs with exons attached requires a 5 relation join. Even more joins must be introduced if we wish to perform the transitive closure over types (for example, a query for transcripts should return features directly typed to transcript, as well as to subtypes, such as mRNA, tRNA, etc). One solution is to deal with typing issues in the middleware; however, a solution which allows a user to make ad-hoc queries regarding typed features in the databae is still required. We propose a solution to this problem - a chado Sequence Ontology extension layer. This layer provides relations for all commonly used sequence ontology types (for example, gene, exon, transposable_element, intron, ...). These relations can be queried as if they are any other relation in the database; for example: SELECT count(*) FROM gene; SELECT * FROM mrna WHERE name like 'CR400%'; IMPLEMENTATION ============== LAYER TYPE ---------- The SO layer is generated directly from a chado database instance. Perl scripts query the database and the SO OBO file. The implementations are possible: 1. Portable SO View layer These views are portable and can be applied to any instance of chado. They work by joining on the name of the SO type; if SO names change, then this layer will have to be rebuilt. The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature INNER JOIN cvterm ON (feature.type_id=cvterm.cvterm_id) WHERE cvterm.name = 'foo'; [this is for basic features only] 2. Non-portable SO View layer These views are constructed from the surrogate primary key of the sequence ontology term in chado (cvterm.cvterm_id). Surrogate primary keys are not portable between database instantiations; surrogate keys should never be exposed outside the database. This layer becomes obsolete if the sequence ontology is ever reloaded (because the surrogate keys are not guaranteed to be preserved between loads). We provide triggers that removes a SO view if the underlying ontology term in the database is updated or deleted [TODO]. This layer is faster and more efficient than the non-portable layer (because it is not actually necessary to join to the cvterm table) The underlying view looks like this: CREATE VIEW foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (where 1234 is the surrogate primary key of type 'foo' in the cvterm relation) The extra speed of this layer comes at the price of less update flexibility 3. Materialized View (Table) layer This is the fastest yet most update-restrictive way to construct the layer. Each SO type gets a table rather than a view. This is the fastest; for example, when fetching genes, the database engine knows to only look in one single (smaller) table rather than filtering out the gene type from the (possibly enormous) feature table. The table is constructed like this: CREATE TABLE foo AS SELECT feature.* FROM feature WHERE feature.type_id = 1234 (plus indexing SQL statements) This layer is only practical if chado is used in "data-warehouse" mode; modification of the underlying feature data renders the materialized views stale. One possibility is automatically rebuilding the materialized view when the underlying feature table changes; however, this could lead to extremely slow updates IMPLICIT TYPES -------------- Not all types are instantiated within a chado database; for example, there are no intron or UTR features as these are derivable from other features. Nevertheless it can be useful to perform queries on derivable types as if they were actually present. [this is all TODO] These types are derived using type-specific rules. For example, an intron rules can be stated in SQL as derived from exon sibling pairs (cv above) [[EXAMPLE SQL]] [[SKOLEM FUNCTIONS]] Again, implicit types can be implemented as portable or non-portable views, or as materialized views (tables). Implicit types intron utr3 utr5 splice_site dicistronic_gene protein_coding_gene [currently implicit in chado via transcript type] exon5prime exon3prime coding_exon partially_coding_exon intergenic_region [HARD] discuss - expressing these rules in SQL vs expressing in some other delcarative language (first order predicate logic; KIF; Prolog/horn clauses) then translating automatically to SQL. ========== DISCUSSION ========== Selection of which of the 3 implementation strategies to use is purely a DB admin decision. The person constructing the SQL queries need not know or care (other than perhaps to be aware for efficiency reasons) how the layer is implemented - as far as they are concerned they have relations such as gene, transcript, variation etc that act just like normal tables when queried (but not updated - discuss updates on views) The view layer is not necessarily limited to chado databases - any relational database implemented with a DBMS that allows views (currently any DBMS other than mysql) is fair game. For example, one could take a postgres or oracle instantiation of ensembl and write a SO layer generator. Note that ensembl already has a relationally-expressed notion of entities such as gene, exon etc. One way round that is to keep the SO layer seperate in the db; eg through postgresql SCHEMAs. This points the way forward to a unified standard for querying genomic databases; whilst adoption of standards for genomic relational databases is a fraught issue at best (different groups and projects prefer their own schemas for good reasons), we can see the need for there being a common user-query layer, based on a standard of feature types (ie SO). [discussion of difficulties with doing apparently simple (and complex) queries on existing relational databases] =cut chado-1.23/bin/gencode2sql.pl000755 000765 000024 00000002743 11723232312 016112 0ustar00cainstaff000000 000000 #!/usr/bin/env perl #This is old code and hasn't been tested! use strict; use warnings; my @nucs = qw(T C A G); my $x = 0; my @codons = (); for my $i (@nucs) { for my $j (@nucs) { for my $k (@nucs) { my $codon = "$i$j$k"; $codons[$x] = $codon; $x++; } } } print "-- autogenerated by gencode2sql.pl from NCBI gencode.dmp\n"; print "SET search_path=public,genetic_code;\n"; my @rows=(); while(<>) { chomp; push(@rows, [split(/\s*\|\s*/,$_)]); } foreach (@rows) { my ($id,$x,$n,$code,$starts) = @$_; printf("INSERT INTO gencode (gencode_id,organismstr) VALUES (%d,%s);\n", $id, pquote($n)); } foreach (@rows) { my ($id,$x,$n,$code,$starts) = @$_; next unless $id; my @codes = split('',$code); for (my $i=0;$i<64;$i++) { printf("INSERT INTO gencode_codon_aa (gencode_id,codon,aa) VALUES (%d,%s,%s);\n", $id, pquote($codons[$i]), pquote($codes[$i])); } } foreach (@rows) { my ($id,$x,$n,$code,$start) = @$_; next unless $id; my @starts = split('',$start); for (my $i=0;$i<64;$i++) { printf("INSERT INTO gencode_startcodon (gencode_id,codon) VALUES (%d,%s);\n", $id, pquote($codons[$i])) if $starts[$i] eq 'M'; } } sub pquote { my $s = shift; $s='' unless defined $s; if ($s =~ /^\-?[0-9]+$/) { return $s; } return "''" unless $s; $s =~ s/\'/\'\'/g; "'$s'"; } chado-1.23/bin/gmod_add_organism.pl000755 000765 000024 00000007067 11723232332 017347 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; #use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; use ExtUtils::MakeMaker; #to get prompt =head1 NAME $0 - Adds an entry to the organism table =head1 SYNOPSIS % gmod_add_organism.pl [options] =head1 COMMAND-LINE OPTIONS --name_only Check just for a name, and return a 1 if present --common_name --genus --species --abbreviation --comment --dbprofile Specify a gmod.conf profile name (otherwise use default) =head1 DESCRIPTION This script will insert an entry into the Chado organism table. The combination genus and species is required to be unique. If either of those items are not provided, or if that combination is already in the database, the script will exit without doing anything. Technically, those are the only two things required, but it is strongly suggested that you provide a common_name and abbreviation. The --name_only option is intended for use primarily at install time, to check the database for the existence of an entry in the organism table with a given common_name. If it is present, it prints "1" and exits, otherwise it prints "0" and exits. The options --common_name must be used in conjunction with --name_only. =head1 AUTHOR Scott Cain Escain@cpan.orgE Copyright (c) 2011 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ($COMMON_NAME, $GENUS, $SPECIES, $ABBREVIATION, $COMMENT, $DBPROFILE, $NAME_ONLY); GetOptions( 'name_only' => \$NAME_ONLY, 'common_name=s' => \$COMMON_NAME, 'genus=s' => \$GENUS, 'species=s' => \$SPECIES, 'abbreviation=s'=> \$ABBREVIATION, 'comment=s' => \$COMMENT, 'dbprofile=s' => \$DBPROFILE, ) or ( system( 'pod2text', $0 ), exit -1 ); my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf, $DBPROFILE); my $schema = Bio::Chado::Schema->connect($db_conf->dsn, $db_conf->user, $db_conf->password ||"", { AutoCommit=>1 }); #collect information from the user if not provided on command line if ($NAME_ONLY and $COMMON_NAME) { my $result = $schema->resultset("Organism::Organism")->find( {common_name => $COMMON_NAME} ); if ($result) { print "1"; } else { print "0"; } exit(0); } if (!$GENUS or !$SPECIES) { print "\nBoth genus and species are required; please provide them below\n\n"; } $COMMON_NAME ||=prompt("Organism's common name?"); $GENUS ||=prompt("Organism's genus?"); $SPECIES ||=prompt("Organism's species?"); my $suggest_abbr = substr($GENUS,0,1) . ".$SPECIES"; $ABBREVIATION||=prompt("Organism's abbreviation?", $suggest_abbr ); $COMMENT =prompt("Comment (can be empty)?") unless defined $COMMENT; $DBPROFILE ||='default'; if (!$GENUS or !$SPECIES) { print "Both genus and species are required; exiting...\n"; exit(1); } my $result = $schema->resultset("Organism::Organism")->find_or_new( { common_name => $COMMON_NAME, genus => $GENUS, species => $SPECIES, abbreviation => $ABBREVIATION, comment => $COMMENT, } ); if ($result->in_storage) { print "There was already an organism with that genus and species in the database;\nexiting...\n"; exit(2); } else { $result->insert; } exit(0); chado-1.23/bin/gmod_apollo_triggers.pl000755 000765 000024 00000005575 11723232350 020116 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; my $USAGE = 'gmod_apollo-triggers.pl create|drop|add'; my $conf = Bio::GMOD::Config->new(); my $gmod_root = $conf->gmod_root(); my $dbconf = Bio::GMOD::DB::Config->new($conf); my $dbname = $dbconf->name(); my $dbh = $dbconf->dbh(); if ($ARGV[0] && $ARGV[0] =~ /drop/i) { $dbh->do("DROP TRIGGER tr_feature_del ON feature"); $dbh->do("DROP TRIGGER feature_assignname_tr_i ON feature"); $dbh->do("DROP TRIGGER feature_relationship_tr_d ON feature_relationship"); $dbh->do("DROP TRIGGER feature_relationship_propagatename_tr_i ON feature_relationship"); $dbh->do("DROP TRIGGER feature_update_name_tr_u ON feature"); } elsif ($ARGV[0] && $ARGV[0] =~ /add/i) { $dbh->do("CREATE TRIGGER tr_feature_del BEFORE DELETE ON feature FOR EACH ROW EXECUTE PROCEDURE fn_feature_del()"); $dbh->do("CREATE TRIGGER feature_assignname_tr_i AFTER INSERT ON feature FOR EACH ROW EXECUTE PROCEDURE feature_assignname_fn_i()"); $dbh->do("CREATE TRIGGER feature_relationship_tr_d BEFORE DELETE ON feature_relationship FOR EACH ROW EXECUTE PROCEDURE feature_relationship_fn_d()"); $dbh->do("CREATE TRIGGER feature_relationship_propagatename_tr_i AFTER INSERT ON feature_relationship FOR EACH ROW EXECUTE PROCEDURE feature_relationship_propagatename_fn_i()"); $dbh->do("CREATE TRIGGER feature_update_name_tr_u BEFORE UPDATE ON feature FOR EACH ROW EXECUTE PROCEDURE feature_fn_u()"); } elsif ($ARGV[0] && $ARGV[0] =~ /create/i) { # select for apollo cv; bail if found #ontology_inserts.sql to add ad hoc ontologies that apollo needs #apollo.inserts to prepdb #cat apollo-triggers.plpgsql my $sth = $dbh->prepare("select * from cv where name='apollo'"); $sth->execute(); if ($sth->rows > 0) { die < =head1 VERSION AND DATE Version 1.1, April 2010. =cut #! /usr/bin/env perl use strict; use warnings; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; use XML::Twig; use LWP::Simple qw/ get /; use Getopt::Std; our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_i, $opt_g, $opt_p, $opt_d, $opt_u); getopts('H:D:i:p:g:p:d:u:tv'); our $publication; my $dbhost = $opt_H; my $dbname = $opt_D; my $infile = $opt_i; my $pass = $opt_p; my $driver = $opt_d; my $user = $opt_u; my $DBPROFILE = $opt_g ; print "H= $opt_H, D= $opt_D, u=$opt_u, d=$opt_d, v=$opt_v, t=$opt_t, i=$opt_i \n"; my $port; my ($dbh, $schema); if ($opt_g) { my $DBPROFILE = $opt_g; $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new() ; my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ) ; $dbhost ||= $db_conf->host(); $dbname ||= $db_conf->name(); $driver = $db_conf->driver(); $port= $db_conf->port(); $user= $db_conf->user(); $pass= $db_conf->password(); } if (!$dbhost && !$dbname) { die "Need -D dbname and -H hostname arguments.\n"; } if (!$driver) { die "Need -d (dsn) driver, or provide one in -g gmod_conf\n"; } if (!$user) { die "Need -u user_name, or provide one in -g gmod_conf\n"; } #if (!$pass) { die "Need -p password, or provide one in -g gmod_conf\n"; } my $dsn = "dbi:$driver:dbname=$dbname"; $dsn .= ";host=$dbhost"; $dsn .= ";port=$port"; $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||'', { AutoCommit=>0 }); $dbh=$schema->storage->dbh(); if (!$schema || !$dbh) { die "No schema or dbh is avaiable! \n"; } print STDOUT "Connected to database $dbname on host $dbhost.\n"; ##################################################################################################### my $sth; my %seq = ( db => 'db_db_id_seq', dbxref => 'dbxref_dbxref_id_seq', pub => 'pub_pub_id_seq', pub_dbxref => 'pub_dbxref_pub_dbxref_id_seq', pubauthor => 'pubauthor_pubauthor_id_seq', pubprop => 'pubprop_pubprop_id_seq', cv => 'cv_cv_id_seq', cvterm => 'cvterm_cvterm_id_seq', ); open (INFILE, "<$infile") || die "can't open file $infile"; # open (ERR, ">$infile.err") || die "Can't open the error ($infile.err) file for writing.\n"; my $exists_count=0; my $pubmed_count=0; my %maxval=(); eval { #Fetch last database ids of relevant tables for resetting in case of rollback foreach my $key( keys %seq) { my $id_column= $key . "_id"; my $table = $key; my $query = "SELECT max($id_column) FROM $table"; $sth=$dbh->prepare($query); $sth->execute(); my ($next) = $sth->fetchrow_array(); $maxval{$key}= $next; } #db name for pubmed ids my $db= $schema->resultset("General::Db")->find_or_create( { name => 'PMID' } ); my $db_id = $db->get_column('db_id'); #cvterm_name for 'journal' . Currently this software does not support other types. All PubMed publications are stored with this default 'journal' type_id my $journal_cvterm = $schema->resultset('Cv::Cvterm')->create_with( {name=>'journal', cv=>'publication'}); while (my $line = ) { $publication = undef; chomp $line; my $pmid; if ( $line=~ m/(\[PMID: )(\d+)(.*)/ ) { $pmid= $2; }else { $pmid=$line;} if (!$pmid) { next(); } #add a dbxref my $dbxref = $schema->resultset("General::Dbxref")->find_or_create( { accession => $pmid, db_id => $db_id, }); ## # new Bio::Chado::Schema::Pub::Pub object my $pub_dbxref = $dbxref->find_related ('pub_dbxrefs', {}, { key=> 'pub_dbxref_c1' }, ); $publication= $pub_dbxref->find_related('pub', {}, { key=> 'pub_c1'}, ) if $pub_dbxref; if(!($publication)) { #publication does not exist in our database $pubmed_count++; $publication = $schema->resultset('Pub::Pub')->new( {} ) ; my $message= fetch_pubmed($pmid); if ($message) { message($message,1); } print STDOUT "storing new publication. pubmed id = $pmid\n"; #### #extract the abstract and uniquename assigned in Pubmed.pm my $abstract = $publication->uniquename(); print STDOUT "The abstract is $abstract \n\n\n"; my (@authors) = split /-----/ , $publication->title(); my $title = shift(@authors); print STDOUT "The title is $title\n\n"; $publication->title($title) ; #remove the abstract from the uniquename field $publication->set_column(uniquename => $pmid . ":" . $title ) ; $publication->type_id( $journal_cvterm->cvterm_id() ); #store the publication in the pub table $publication->insert(); #store a pubprop for the abstract # my $pubprop = create_pubprops($publication, { 'abstract'=>$abstract }, { autocreate => 1 } ); ## Add pub_dbxref $publication->find_or_create_related('pub_dbxrefs' , { dbxref_id => $dbxref->dbxref_id } ); ## ##Add the authors my $rank =1; foreach (@authors) { my ($surname, $givennames)= split /\|/, $_; print STDOUT "Author: Surname=$surname, givennames = $givennames \n"; $surname =~ s/^\s+|\s+$//g; $givennames =~ s/^\s+|\s+$//g; $publication->find_or_create_related( 'pubauthors' , { surname => $surname, givennames => $givennames, rank => $rank++, } ); } #publication exists, do nothing }else { $exists_count++; print STDOUT "Publication $pmid is already stored in the database. Skipping..\n"; } } }; if($@) { print $@; print"Failed; rolling back.\n"; foreach my $key ( keys %seq ) { my $value= $seq{$key}; my $maxvalue= $maxval{$key} || 0; if ($maxvalue) { $dbh->do("SELECT setval ('$value', $maxvalue, true)") ; } else { $dbh->do("SELECT setval ('$value', 1, false)"); } } $dbh->rollback(); }else{ print"Succeeded.\n"; print "Inserted $pubmed_count new publications!\n"; print "$exists_count publication already exist in the database\n"; if($opt_t) { print STDOUT "Rolling back!\n"; foreach my $key ( keys %seq ) { my $value= $seq{$key}; my $maxvalue= $maxval{$key} || 0; if ($maxvalue) { $dbh->do("SELECT setval ('$value', $maxvalue, true)") ; } else { $dbh->do("SELECT setval ('$value', 1, false)"); } } $dbh->rollback(); }else { print STDOUT "Committing...\n"; $dbh->commit(); } } close ERR; close INFILE; sub message { my $message=shift; my $err=shift; if ($opt_v) { print STDOUT $message. "\n"; } print ERR "$message \n" if $err; } sub sanitize { my $string = shift; $string =~ s/^\s+//; #remove leading spaces $string =~ s/\s+$//; #remove trailing spaces return $string; } sub create_pubprops { my ($self, $props, $opts) = @_; # process opts $opts ||= {}; $opts->{cv_name} = 'publication' unless defined $opts->{cv_name}; return Bio::Chado::Schema::Util->create_properties ( properties => $props, options => $opts, row => $self, prop_relation_name => 'pubprops', ); } sub reset_sequences { my %seq=@_; my %maxval=@_; #reset sequences foreach my $key ( keys %seq ) { my $value= $seq{$key}; my $maxvalue= $maxval{$key} || 0; #print STDERR "$key: $value, $maxvalue \n"; if ($maxvalue) { $dbh->do("SELECT setval ('$value', $maxvalue, true)") ; } else { $dbh->do("SELECT setval ('$value', 1, false)"); } } } sub fetch_pubmed { my $accession=shift; my $pub_xml = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$accession&rettype=xml&retmode=text"); eval { my $twig=XML::Twig->new( twig_roots => { 'Article/ArticleTitle' => \&title, 'JournalIssue/Volume' => \&volume, 'JournalIssue/Issue' => \&issue, 'DateCompleted/Year' => \&pyear, 'PubDate/Year' => \&pyear, 'Pagination/MedlinePgn' => \&pages, 'Journal/Title' => \&journal_name, #'PublicationTypeList/PublicationType' => \&pub_type, 'Abstract/AbstractText' => \&abstract, Author => \&author, }, twig_handlers => { }, pretty_print => 'indented', # output will be nicely formatted ); $twig->parse($pub_xml ); # build it }; if($@) { my $message= "Error in transaction or NCBI server seems to be down. Please check your input for accession $accession or try again later.\n $@"; return $message; }else { return undef ; } } ########################################## #Functions for parsing the XML ########################################## sub title { my ($twig, $elt)= @_; $publication->title($elt->text) ; $twig->purge; } sub volume { my ($twig, $elt)= @_; $publication->volume($elt->text) ; $twig->purge; } sub issue { my ($twig, $elt)= @_; $publication->issue($elt->text) ; $twig->purge; } sub pyear { my ($twig, $elt)= @_; my $pyear = $elt->text; $publication->pyear($pyear); $twig->purge; } sub pages { my ($twig, $elt)= @_; $publication->pages($elt->text) ; $twig->purge; } sub journal_name { my ($twig, $elt)= @_; $publication->series_name($elt->text) ; $twig->purge; } sub abstract { my ($twig, $elt)= @_; $publication->uniquename($elt->text) ; $twig->purge } sub author { my ($twig, $elt)= @_; my $lastname=$elt->children_text('LastName'); my $initials=$elt->children_text('Initials'); #sometimes the firstname has no initials but full first name 'ForName'.. if (!$initials) { $initials=$elt->children_text('ForeName') || $elt->children_text('FirstName') ; } my $author_data= $lastname ."|" . $initials ; #append the authors to the 'title' field. #Then extract the list and store in pubprop $publication->title($publication->title() . "-----" . $author_data) ; $twig->purge } chado-1.23/bin/gmod_bulkfiles.pl000644 000765 000024 00000023622 11723232441 016671 0ustar00cainstaff000000 000000 #!/usr/bin/env perl =head1 NAME bulkfiles.pl -- command-line program for Bio::GMOD::Bulkfiles =head1 SYNOPSIS This program generates bulk genome annotation files from a Chado genome database, including Fasta, GFF, DNA, Blast indices. # get bulkfiles software cvs -d :pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod \ co -d GMODTools schema/GMODTools -- OR -- curl -O http://eugenes.org/gmod/GMODTools/GMODTools-1.0.zip unzip GMODTools*zip # load a genome chado db to Postgres database curl -O http://sgdlite.princeton.edu/download/sgdlite/sgdlite.sql.gz createdb sgdlite (gunzip -c sgdlite.sql.gz | psql -d sgdlite -f - ) >& log.load # extract bulk files from database cd GMODTools perl -Ilib bin/bulkfiles.pl -conf sgdbulk -make =head1 DETAILED USAGE Generate genome bulk files from Chado database. Usage: bulkfiles.pl [ -conf sgdbulk -chr chrIII -format fasta -make ] -config=bulkfile-config A configuration xml-simple file pointing to genome data files, e.g., sgdbulk or conf/bulkfiles/sgdbulk.xml See conf/bulkfiles/bulkfiles-template.xml to create a new database release -format=gff,fasta repeat for multiple formats [defaults: @defformats] -chromosome=2L repeat for multiple chromosomes: -chr=2 -chr=3 -chr=X All chromosomes are processed by default. -dnadump extract chromosome dna from database [default $dnadump] -featdump extract features from database [default $featdump] intermediate step option: -[no]splitfeat = split by chromosome [default with -featdump] ) -failonerror die if error is encountered (otherwise read log to see it) -make make output bulk files [default $makeout] -showconfig prints the parsed configuration file(s); pay attention to ROOT= for location of output (set by \$GMOD_ROOT) -help more info -debug turn on debug output for progress info [$debug] =head1 REQUIREMENTS Mimimal additional software is required. It is assumed you have installed a Chado database (as in synopsis). This sofware requires perl DBI for database access, and XML::Simple for configurations, and a few bits of BioPerl, all part of GMOD database installation. =head1 CONFIGURATION The operation of this program is controlled by several configuration files (in simple xml format), including database location, feature construction and data-release information. The defaults for these are in GMODTools/conf/bulkfiles/. These can be tuned for specific data sets, releases. You can override these with a conf/ folder containing updated versions, and use the primary -conf=my-bulkfile.xml to point to alternate configurations. The concept of data-release set is important here. If you use a Chado database release for which there is a configuration set, you should get the same outputs as provided by the originators. With a new database, or new release, you may need to go thru rounds of tuning the configurations, and possibly software, to specifics of the data-release. As genome databases mature, they can get more complex. E.g. a new FlyBase D.pseudoobscura release added complexity to the 'chromosome/superscaffold' structure, necessitating editing of this basic aspect data configurations and outputs. Configurations include the SQL statements used for extracting table files, as the primary functions of these need to be tuned for specific Chado data sets (conf/bulkfiles/chadofeatsql.xml). There are additional configurations for each type of output bulkfile in 'filesets.xml' with options for those operations. Operations for converting and renaming features (e.g. change non-SO names to Sequence Ontology compliant names for GFF, regular expressions for converting unweildy database names, values to publicly usable content) are in 'chadofeatconv.xml', along with 'featuresets.xml'. Each bulkfile module can have a module.xml for further instructions. =head1 NOTES Much of the operation of this program has been dictated by practical needs to create usable public data releases from FlyBase Chado databases starting in year 2004. There remain aspects of the package internal software that warrants improvement and extention to additional cases. If there were such a thing as a 'perfect' genome database, much of this tool would not be needed, as it basically dumps tables and adds some reformatting for standard output file formats. But along the way it also has necessarily added options to correct what is in the database to meet criteria for public data consumption. -dnadump and -featdump are prerequisites, but you need run only once. These create intermediate output files used in make steps. featdump = extract feature table files, first in feature-groups then join and split by chromosome/scaffold. dnadump = extract chromosome/scaffold raw dna files. The first stage of -featdump will extract a table of chromosomes or your ${golden_path} feature. If this fails to work right, the other steps will fail. With a new genome dataset, test this first. Read the {release_path}/tmp/featdump/chromosomes.tsv to see if correct. Hand-edit if need be; this file will be used as provided. Format of the tmp/featdump/tables.tsv is tab-separated columns: ($arm,$fmin,$fmax,$strand,$orgid,$type,$name,$id,$oid,$attr_type,$attribute) chrI 1 230208 0 10 chromosome chrI chrI 212 species Saccharomyces_cerevisiae chrII 1 813178 0 10 chromosome chrII chrII 507 species Saccharomyces_cerevisiae -format 'fff' is an intermediate flat-feature-format, required for making fasta and additional formats. FFF and GFF are produced together by one module reading the intermediate feature tables. Making FFF and GFF are the time consuming steps and may be split by chromosome across processors. Processing time may be hours for complex databases. New output formats are added by subclassing the Bio::GMOD::Bulkfiles::BulkWriter module, which basically takes tabular inputs from the intermediary SQL output and does something with it. =head1 AUTHOR D.G. Gilbert, 2004, gilbertd@indiana.edu =cut BEGIN{ unless($ENV{GMOD_ROOT}){ require Bio::GMOD::Config2; my $root= Bio::GMOD::Config2->new()->gmod_root(); warn "* Setting GMOD_ROOT=$root\n"; $ENV{GMOD_ROOT}=$root; } } use Bio::GMOD::Bulkfiles; use Getopt::Long; my ($dnadump,$featdump,$makeout,$failonerror,$debug,$verbose,$showconfig) = (0) x 10; my $splitfeat=-1; my $no_csomesplit=0; my $automake=1; # make this easier for general user my $config= undef; my @formats= (); #? let release.xml formats replace this? yes! but want for display? ## want $sequtil->config->{outformats} but dont want to call before help my @defformats= (); #was# qw(overview fff gff fasta tables blast ); my @chr=(); my $help=0; my $ok= Getopt::Long::GetOptions( 'config=s' => \$config, 'formats=s' => \@formats, 'chromosome=s' => \@chr, 'automake!' => \$automake, 'dnadump!' => \$dnadump, 'featdump!' => \$featdump, 'splitfeat!' => \$splitfeat, 'failonerror!' => \$failonerror, 'makeout!' => \$makeout, 'debug!' => \$debug, 'verbose!' => \$verbose, 'help!' => \$help, 'bugger=s' => \$debug, # more debug levels 'showconfig!' => \$showconfig, ); my $usage=<<"USAGE"; Generate genome bulk files from Chado database. Usage: $0 -conf sgdbulk -make [ -format gff,fasta ... ] Options: -help : show helpful documents -config=bulkfile-config Configuration file for genome data release [required, no default] -format=gff,fasta,blast,tables,overview,go_association output formats [default from your config.xml or site_defaults.xml ] -chromosome=2L chromosome(s) to work with: -chr=3,4,5 [default: all chromosomes] -[no]make : make output bulk files [default $makeout] -[no]failonerror : die if error is encountered (otherwise read log to see it) -[no]verbose : turn on verbose output info [$verbose] -[no]debug : turn on debug output for progress info [$debug] MORE INFO: perldoc $0 perldoc Bio::GMOD::Bulkfiles USAGE =item more usage -[no]automake auto-make required preliminary data [default $automake] -[no]dnadump extract chromosome dna from database [intermediate step; default $dnadump] -[no]featdump extract features from database [intermediate step; default $featdump] -splitfeat = collate primary table files, sortin and splitting by chromosome -nosplitfeat = do not create any intermediate per-chromosome/scaffold files -[no]showconfig print the parsed configuration file(s); pay attention to ROOT= for location of output (set by \$GMOD_ROOT) =cut # 0710 update: change nosplitfeat to mean same as new no_csomesplit flag # meaning no per golden_path files (e.g. for genomes with 1000s - 100,000s of scaffolds) if($splitfeat == 0) { $no_csomesplit=1; } elsif ($splitfeat == -1) { $splitfeat= $featdump; } @chr = split(/[,;:\s]/,join(',',@chr)); @formats = split(/[,;:\s]/,join(',',@formats)); @formats= @defformats unless(@formats); if($help) { warn $usage; $config= "bulkfiles_template";#? unless($config); $verbose=1; $makeout= $automake= 0; $dnadump= $featdump= $splitfeat=0; @formats=(); } warn "** Please specify -config=config-name\n" unless($config); die $usage unless ($ok && $config); my $result= 'none'; my $sequtil= Bio::GMOD::Bulkfiles->new( configfile => $config, debug => $debug, showconfig => $showconfig, failonerror => $failonerror, verbose => $verbose, automake => $automake, no_csomesplit => $no_csomesplit, ); # automake will do these now if need be. $sequtil->dumpFeatures() if ($featdump); $sequtil->sortNSplitByChromosome() if ($splitfeat); $sequtil->dumpChromosomeBases() if ($dnadump); $result= $sequtil->makeFiles( formats => \@formats, chromosomes => \@chr ) if ( $makeout ); print STDERR "Bulkfiles done. result=",$result,"\n"; chado-1.23/bin/gmod_chado_properties.pl000755 000765 000024 00000016237 11723232467 020262 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; #use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use ExtUtils::MakeMaker; #to get prompt use Scalar::Util qw(looks_like_number); =head1 NAME $0 - reads or modifies the chadoprop table =head1 SYNOPSIS % gmod_chado_properties.pl [options] =head1 COMMAND-LINE OPTIONS --version Without an argument, returns the schema version --force Provided with the version option to update the schema version --property Get the value of a specific property ("all" to get all) --dbprofile Specify a gmod.conf profile name (otherwise use default) =head1 DESCRIPTION The main use of this script is to get or set the schema version for use during schema updates. It can also get any named property (based on the cvterm in the chadoprop table), or a list of all properties in the chadoprop table. In older (pre-1.2) versions of Chado, updating the schema version has the side effect of creating the chadoprop table and a chado_properties cv. =head1 AUTHOR Scott Cain Escain@cpan.orgE Copyright (c) 2011 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ($VERSION, $FORCE, $PROPERTY, $DBPROFILE, ); GetOptions( 'version:s' => \$VERSION, 'force' => \$FORCE, 'property=s' => \$PROPERTY, 'dbprofile=s' => \$DBPROFILE, ) or ( system( 'pod2text', $0 ), exit -1 ); $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf, $DBPROFILE); my $dbh = $db_conf->dbh(); if ($FORCE and $VERSION >0) { set_version($VERSION, $dbh); } elsif (defined $VERSION) { my $version = determine_version($dbh); print "$version\n"; } elsif ($PROPERTY eq 'all') { my %prop = get_all_properties($dbh); } elsif ($PROPERTY) { my $prop = get_property($PROPERTY, $dbh); } exit(0); sub set_version { my $version = shift; my $dbh = shift; if (looks_like_number($version) and $version > 1.19){ #first make sure the chado_properties cv is available my $cp_query = "SELECT cv_id FROM cv WHERE name = 'chado_properties'"; my $sth = $dbh->prepare($cp_query); $sth->execute(); my ($cv_id) = $sth->fetchrow_array; my $new_chadoprop = 0; my $cvterm_id; unless ($cv_id) { #chado_properties is not available, so create it my $cv_insert = "insert into cv (name,definition) values ('chado_properties','Terms that are used in the chadoprop table to describe the state of the database')"; $dbh->do($cv_insert); insert_version_term($dbh); $new_chadoprop = 1; } #check that the version term is available my $version_query = "SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version'"; $sth = $dbh->prepare($version_query); $sth->execute(); ($cvterm_id) = $sth->fetchrow_array; unless ($cvterm_id) { insert_version_term($dbh); $sth->execute(); ($cvterm_id) = $sth->fetchrow_array; $new_chadoprop = 1; } #find out if there's already a version in there # and if the chadoprop table exists my $table_query = "SELECT 1 FROM pg_tables WHERE tablename = ?"; $sth = $dbh->prepare($table_query); $sth->execute('chadoprop'); if ($sth->fetchrow_array) { #chadoprop table exists, so check in it for a value my $version_query = "SELECT value FROM chadoprop WHERE type_id in (SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version')"; my $isth = $dbh->prepare($version_query); $isth->execute(); my ($old_version) = $isth->fetchrow_array(); if (defined($old_version)) { #there is a version in there, update it my $update_query = "UPDATE chadoprop SET value = $version WHERE type_id = $cvterm_id"; $dbh->do($update_query); } else { #no version but the table exists, (assume 1.2) and insert new value my $set_query = "INSERT INTO chadoprop (type_id, value) VALUES (?,?)"; $sth = $dbh->prepare($set_query); $sth->execute($cvterm_id,$version) or die "database error: $!"; } } else { die "The chadoprop table doesn't seem to exist; perhaps there is a problem with Chado?"; } } else { die "$version doesn't look like a valid version number."; } } sub insert_version_term { my $dbh = shift; $dbh->do("insert into dbxref (db_id,accession) values ((select db_id from db where name='null'), 'chado_properties:version')"); $dbh->do("insert into cvterm (name,definition,cv_id,dbxref_id) values ('version','Chado schema version',(select cv_id from cv where name = 'chado_properties'),(select dbxref_id from dbxref where accession='chado_properties:version'));"); } sub determine_version { my $dbh = shift; my $table_query = "SELECT 1 FROM pg_tables WHERE tablename = ?"; my $sth = $dbh->prepare($table_query); #if chadoprop exists, query it $sth->execute('chadoprop'); if ($sth->fetchrow_array) { my $version_query = "SELECT value FROM chadoprop WHERE type_id in (SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version')"; my $isth = $dbh->prepare($version_query); $isth->execute(); my ($version) = $isth->fetchrow_array(); return $version if defined($version); #if the table exists but doesn't return a version, assume 1.2 (due to bug # in that release). return 1.2; } #if cvprop table exists, then it's 1.11 (or 1.1, same schema) $sth->execute('cell_line'); if ($sth->fetchrow_array) { return '1.11'; } #if all_feature_names, then it's 1.0 my $view_query = "SELECT 1 FROM pg_views WHERE viewname =?"; $sth = $dbh->prepare($view_query); $sth->execute('all_feature_names'); if ($sth->fetchrow_array) { return '1'; } #must be something older return 'unknown'; } sub get_all_properties { my $dbh = shift; my $props_query = "SELECT cvterm.name, cp.value, cp.rank FROM chadoprop cp JOIN cvterm ON (cvterm.cvterm_id = cp.type_id)"; my $sth = $dbh->prepare($props_query); $sth->execute(); print_table($sth); return; } sub get_property { my $tag = shift; my $dbh = shift; my $prop_query = "SELECT cvterm.name, cp.value, cp.rank FROM chadoprop cp JOIN cvterm ON (cvterm.cvterm_id = cp.type_id) WHERE cvterm.name = ?"; my $sth = $dbh->prepare($prop_query); $sth->execute($tag); print_table($sth); return; } sub print_table { my $sth = shift; print "tag\tvalue\trank\n"; while (my @row = $sth->fetchrow_array) { print join("\t", @row)."\n"; } return; } chado-1.23/bin/gmod_dump_gff3.pl000755 000765 000024 00000015331 11723232505 016565 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use DBI; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Getopt::Long; use URI::Escape; =head1 NAME DEPRECATED dump_gff3.pl - Dump gff3 from a chado database. =head1 SYNOPSIS % dump_gff3.pl [--organism human] [--refseq Chr_1] > out.gff =head1 COMMAND-LINE OPTIONS WARNING: This script has been DEPRECATED and is no longer supported. Please use gmod_bulkfiles.pl for getting GFF3 dumps from a Chado database. If no arguments are provided, dump_gff3.pl will dump all features for the default organism in the database. The command line options are these: --organism specifies the organism for the dump (common name) --refseq reference sequece (eg, chromosome) to dump --dbconf the name of the conf file to use --feature_ids provide the chado feature_ids as attributes If there is no default organism for the database or one is not specified on the command line, the program will exit with no output. =head1 AUTHOR Scott Cain Ecain@cshl.orgE Copyright (c) 2004 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut print STDERR < \$ORGANISM, 'refseq:s' => \$REFSEQ, 'dbconf:s' => \$DBCONF, 'feature_ids' => \$FEATURE_IDS, ); my $gmod_conf = $ENV{'GMOD_ROOT'} ? Bio::GMOD::Config->new($ENV{'GMOD_ROOT'}) : Bio::GMOD::Config->new(); my $db_conf; if ($DBCONF) { $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,$DBCONF); } else { $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,'default'); } $ORGANISM ||=$db_conf->organism(); my $dbh = $db_conf->dbh; my $organism_id = $dbh->prepare("select organism_id from organism where common_name = ?"); $organism_id->execute($ORGANISM); my $arrayref = $organism_id->fetchrow_arrayref(); $organism_id = $$arrayref[0]; unless ($organism_id) { system( 'pod2text', $0 ); warn "Organism:$ORGANISM not found in database\n"; exit 1; } my $ref_seq_part = ""; if ($REFSEQ) { $ref_seq_part = "and (name = '$REFSEQ' or ref = '$REFSEQ')"; } my $sth = $dbh->prepare("select feature_id,ref,source,type,fstart,fend, score,strand,phase, seqlen,name from gff3view where feature_id > ? and feature_id < ? and organism_id = ? $ref_seq_part order by feature_id") or die $!; my $attr_query = $dbh->prepare("select feature_id, type, attribute from gff3atts where feature_id > ? and feature_id < ? order by feature_id, type") or die $!; my $max_feature_id = $dbh->prepare("select max(feature_id) from feature where organism_id = ?") or die; $max_feature_id->execute($organism_id); $arrayref = $max_feature_id->fetchrow_arrayref; $max_feature_id = $$arrayref[0]; my $min_feature_id = $dbh->prepare("select min(feature_id) from feature where organism_id = ?" ) or die; $min_feature_id->execute($organism_id); $arrayref = $min_feature_id->fetchrow_arrayref; $min_feature_id = $$arrayref[0] - 1; my $CHUNK = 1000; my @ref_seqs; print "##gff-version 3\n"; for (my $i = $min_feature_id; $i<=$max_feature_id;$i = $i + $CHUNK) { my $upper = $i+$CHUNK+1; $attr_query->execute($i,$upper,) or die $!; my $attstr_hashref = make_attstr_hashref($attr_query); $sth->execute($i,$upper,$organism_id) or die $!; while (my $hashref = $sth->fetchrow_hashref) { my $ref = $$hashref{ref}; my $start = $$hashref{fstart}; my $end = $$hashref{fend}; my $source = $$hashref{source} || '.'; my $score = $$hashref{score} || '.'; my $strand; if ($$hashref{strand}) { $strand = $$hashref{strand} == 1 ? '+' : '-'; } else { $strand = '.'; } my $phase = $$hashref{phase} || '.'; my $atts = $$attstr_hashref{$$hashref{feature_id}} || '.'; unless ($ref) { #must be a reference sequence $ref = $$hashref{name}; push @ref_seqs, $ref; $start = 1; $end = $$hashref{seqlen}; } print join ("\t",($ref, $source, $$hashref{type}, $start, $end, $score, $strand, $phase, $atts)),"\n"; } } $sth = $dbh->prepare("select residues from feature where name=? and residues is not null"); print "##FASTA\n"; foreach my $ref (@ref_seqs) { $sth->execute($ref); while (my $data = $sth->fetchrow_arrayref) { print ">$ref\n"; my $seq = $$data[0]; my @seqArr = split //, $seq; my $max = 60; my $curr = 0; foreach my $letter (@seqArr) { if($curr < $max) { print $letter; $curr++; } else { $curr = 0; print "$letter\n"; } } } print "\n"; } sub make_attstr_hashref { my $query_handle = shift; my $old_id = 0; my $old_type = ''; my %attstr_hash; while (my $hashref = $query_handle->fetchrow_hashref) { my $escaped_att = uri_escape($$hashref{attribute}, "^a-zA-Z0-9. :^*$@!+_?-"); next if ($$hashref{type} eq 'chado_feature_id' and !$FEATURE_IDS); if ($old_id eq $$hashref{feature_id} and $old_type eq $$hashref{type} ) { $attstr_hash{$old_id} .= ",$escaped_att" } elsif ($old_id eq $$hashref{feature_id}) { $old_type =$$hashref{type}; $attstr_hash{$old_id} .= ";$old_type=$escaped_att"; } else { $old_type= $$hashref{type}; $old_id = $$hashref{feature_id}; $attstr_hash{$old_id} = "$old_type=$escaped_att"; } } return \%attstr_hash; } chado-1.23/bin/gmod_extract_dbxref_from_gff.pl000755 000765 000024 00000004561 11723232520 021564 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use URI::Escape; =head1 NAME gmod_extract_dbxref_from_gff.pl - Extracts Dbxrefs from GFF3 lines that have Target attributes =head1 SYNOPSIS % gmod_extract_dbxref_from_gff.pl gff_file_name > output_file =head1 DESCRIPTION For GFF3 lines of the form: chr1 CDNA cDNA_match 69388 69593 0 - . Dbxref=Sorghum_CDNA:Contig_448;Target=Contig_448 75 295 + that is, that have both Target and Dbxref attributes, this script extracts the Dbxref value and prints out a list of the database and accession parts of the Dbxref value. This functionality depends on a standard format for the Dbxref value, one where the name of the database preceeds the accession and are separated by a colon. =head2 Rationale Another script, gmod_make_gff_from_dbxref.pl, takes a list of databases and accessions (like this script provides) and a directory of FASTA files and builds a GFF3 file that corresponds to those targets. The use for these files is to load them into Chado before that compuational analysis results are loaded to ensure that the database has a complete picture of the analysis performed. =head1 COMMAND-LINE OPTIONS None. =head1 AUTHOR Scott Cain Ecain@cshl.orgE Copyright (c) 2007 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut if ($ARGV[0] =~ /-h/) { system( 'pod2text', $0); exit -1; } my %dbxref; while (<>) { chomp; if (/^-h/) { system( 'pod2text'); exit -1; } my @la = split /\t/; last if ($la[0] eq '##FASTA'); next unless (scalar @la == 9); next unless ($la[2] =~ /match/); next unless ($la[8] =~ /Dbxref/); next unless ($la[8] =~ /Target/); my @pairs = split /\;/, $la[8]; my ($db,$acc,$target); for (@pairs) { my @tagvalue = split /\=/; if ($tagvalue[0] eq 'Dbxref') { ($db, $acc) = split /\:/, $tagvalue[1]; $db = uri_unescape($db); $acc = uri_unescape($acc); } elsif ($tagvalue[0] eq 'Target') { ($target) = split /\s/, $tagvalue[1]; $target = uri_unescape($target); } } if ($db && $acc && $target && $acc eq $target) { $dbxref{$db}{$acc} = 1; } } for my $db (keys %dbxref) { for my $acc (keys %{$dbxref{$db}}) { print "$db $acc\n"; } } chado-1.23/bin/gmod_fasta2gff3.pl000755 000765 000024 00000005056 11723232540 016643 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Getopt::Long; use Bio::DB::Fasta; my ($FASTA_DIR, $GFFFILENAME, $TYPE, $SOURCE, $ATTRIBUTES, $NOSEQUENCE); GetOptions( 'fasta_dir=s' => \$FASTA_DIR, 'gfffilename=s' => \$GFFFILENAME, 'type=s' => \$TYPE, 'source=s' => \$SOURCE, 'attributes=s' => \$ATTRIBUTES, 'nosequence' => \$NOSEQUENCE, ) or ( system( 'pod2text', $0 ), exit -1 ); my $fastadir = $FASTA_DIR || './fasta'; my $gfffile = $GFFFILENAME || 'out.gff'; my $type = $TYPE || 'EST'; my $source = $SOURCE || '.'; -r $fastadir or die "fasta dir '$fastadir' not found or not readable\n"; open OUT, ">", $gfffile or die "couldn't open $gfffile for writing: $!\n"; my $stream = Bio::DB::Fasta->new($fastadir)->get_PrimarySeq_stream; print OUT "##gff-version 3\n"; print OUT "#this file generated from $0\n"; while (my $seq = $stream->next_seq) { my $atts; if ($ATTRIBUTES) { $atts = "ID=".$seq->id.";Name=".$seq->id.";$ATTRIBUTES"; } else { $atts = "ID=".$seq->id.";Name=".$seq->id; } print OUT join("\t", $seq->id, $source, $type, 1, $seq->length, ".",".",".", $atts ),"\n"; } if (!$NOSEQUENCE) { print OUT "##FASTA\n"; #reset the seq stream $stream = Bio::DB::Fasta->new($fastadir)->get_PrimarySeq_stream; while (my $seq = $stream->next_seq) { print OUT ">".$seq->id."\n"; print OUT $seq->seq . "\n"; } } close OUT; =pod =head1 NAME $O - Convert FASTA to simple GFF3 =head1 SYNOPSYS % $O [options] =head1 COMMAND-LINE OPTIONS --fasta_dir Directory contain fasta files (default: ./fasta) --gfffilename Name of GFF3 file to be created (default: ./out.gff) --type SO type to assign to each feature (default: EST) --source Text to appear in source column (default: .) --attributes Additional tag=value pairs to appear in column 9 --nosequence Suppress the ##FASTA section (ie, don't print DNA sequences) =head1 DESCRIPTION This script simply takes a collection of fasta files and converts them to simple GFF3 suitable for loading into chado. =head1 AUTHORS Scott Cain Ecain@cshl.orgE Copyright (c) 2006 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut chado-1.23/bin/gmod_gff2biomart5.pl000644 000765 000024 00000151174 11723232555 017212 0ustar00cainstaff000000 000000 #!/usr/bin/env perl =head1 NAME gff2biomart.pl -- create tables for BioMart from genome GFF annotations =head1 SYNOPSIS ./gff2biomart.pl --species=scer --version=sgdlite_2005_08_23 --output tabscer/ \ --fasta $scer/fasta/*-all-chromosome-*.fasta \ $scer/gff/scer-chr*.gff # add some extra tables here for more filters ./gff2biomart3.pl -dataset=11 -species=dper -version=br051028 -output tabdper \ -table=cross_genome_match_dmelchr,match_tblastn_modDM \ -fasta $dper/dper*.fa.gz $dper/gff/dper*scaffold*gff $dper/gff/dper*gff.gz Example data sets from this tool are at: http://insects.eugenes.org/BioMart/martview =head1 Loading the results Usage is for MySQL database and BioMart.org (0.3 version tested) Please have installed and tested BioMart before trying to use these data with it. # EXAMPLE LOADING INSTRUCTIONS ; use with care to existing databases # LOAD tables TO MySQL: mysqladmin create biomart cat tabdper//*.sql | mysql biomart mysqlimport biomart `pwd`/tabdper//*.txt # LOAD xml to MySQL biomart.meta_configuration: # BEST USE martj/bin/marteditor.sh to load tabdper//*.xml # OR try this BUT NOT IF YOU HAVE EXISTING biomart # cat tabdper//meta.sql_example | mysql biomart # NOTE: biomart is included in *.xml # Change datasetID's in xml, meta.sql if needed =head1 ABOUT gff2biomart gff2biomart creates 1. chromosome region__main tables for biomart with chr broken into nKb bins/regions (1kb default size?) 2. per-featuretype xfeature__dm link tables store feature attributes (id,dbxref,match stats,..) modify table __main add column feature_bool to indicate where features lie. 3. create $species__chromosome__dm with dna residues for fasta output from biomart use in biomart: filter (include,exclude) features that exist in regions including joint filters (has homology in x but not homology in y,z; has gene/predict_gene/..) output: attributes = feature info, fasta of features in selected regions Note: this means changing biomart's filter==attribute paradigm; new perl module? =head1 VERSION NOTES *** FIXME: gff2featdm dropped featuretype__dm, but want for some ?? e.g. dper__cross_genome_match_dmelchr__dm for dmelchr names dper__match_tblastn_modDM__dm for dmel Gene names; use instead __features__dm ? **** add config for this; **** Have gone thru several table variants to get biomart to find both features and regions with feature matches (bool). Version 3b works (finally) with proper xml; but drop extra per-feat _dm tables. Problems still at region-sequence output (where?) See scer_mart3b_main.xml Need this script to write proper xml config for biomart (martedit naive won't do). Version 4 similar but added extra feat-region key links, not working right. Move however the combined feat info from that to 3b. =head1 NOTES Needs lots of config choices for general use, esp. creating UI parts. Add as module to GMODTools Bulkfiles with various config parts. Add default biomart XML templates. ** ?? for biomart cross-table linking need the _dm tables to have valid region_id_key entries for all such regions even if no/null values otherwise attribute outputs do sql join that filters output to only thos with region matches. ** need separate sequence Perl module to get feature_seq entries (as per Gbrowse) ** need new/revised GFF perl module - current needs Ensembl db fields. ** ??? add GO/OrthoMCL info based on prot. matches Used now with biomart martj/bin/marteditor to create biomart metadata xml for interface after creating mart database. Found martbuilder not useful enough at present for auto-deciphering a genome database structure (e.g. chado db). Mar06 (version 6): change sql to ?? sometimes want nulls, sometimes not NOT NULL default '' (or default 0 for int) =head1 History Needed genome seq. selector tool for sequence-regions, rather than gene-centric, for new genomes, any seqregion interests. E.g. find all regions with homologs to mosquito but not to Dmel fruitfly; find regions with SNAP gene predictions but not Genscan/genewise/... or not homology to known genes (i.e. possible new genes). BioMart has useful userinterfaces for such but large time cost getting data from anything else into its desired structure. from seqblocks prelim. work at insects.eugenes.org, d.gilbert, aug 2005 cat *.gff | sort -k1,1 -k4,4n -k5,5rn | perl -n seqblockbin > seqblock.gfft cat seqblock.gfft | sort -k2,2 -k1,1n | perl -n seqblockxml > seqblock.xml =head1 AUTHOR Don Gilbert, gilbertd@indiana.edu, 2005/2006. =head1 METHODS =cut use strict; use Getopt::Long; use FileHandle; use POSIX; use constant DEBUG => 1; # use constant DROSPEGE => 1; # insects.eugenes.org rewriting code use constant REGIONTAB => 1; # always on now use constant GFFTAB => 1; # always on now use constant SHORT_EXTRATAB => 0; # for $ftkey__dm : all fields or not? my $PROGRAM=$0; $PROGRAM =~ s,\S+/,,g,; my $BSIZE=5000; # blocksize, is 1Kb better default? my $DNACHUNKSIZE= 100000; # dna chunks? NOTE: THIS NEEDS TO BE IN biomart.genome.xml my $MAX_FEATURE_RANGE = 1500000; # skip blocking things bigger than this ? my @skipattr=qw(); my @chrtype=qw(chromosome chromosome_arm golden_path scaffold); #... more/choice my @skiptype=qw(chromosome_band BAC match_part); my @skipattr=qw(qloc query version atID atsource loc noname species); my @skipsource=qw( assembly:path ); my @tabletype=qw(); # THESE ARE 'type_source' syntax; FIXME; # feat types to make _dm accessory table for my %ftinfo=(); ## == main table info my ($outpath,$version,$fasta); my $species = $ENV{species} || 'noname'; # FIXME; full name my $label = $ENV{label} || ""; # my $RegionKey = "Region"; # cant clash with valid feature type? my $RegionIDKey = "region_id_key"; # in sql my $StrucKey = 'features'; #? NOW NOT _main, but _dm my $StrucIDKey = "feature_id_key"; # in sql my $SequenceKey = 'genomic_sequence'; #? not main table, dm ? change to $tablehead_genomic_sequence__xxx__main ?? my $XmlKey = "BioMart"; my $goldenpathType= 'chromosome'; my %goldenpathInfo= (); my %MainKeys=( $RegionKey=>1, $StrucKey=>1, $SequenceKey => -1, $XmlKey => -1); my @AllFtKeys=(); my @GFF3ATTR= qw(ID Name Parent Dbxref Target Note); # match structuresql order my %GFF3ATTR= map{$_,1} @GFF3ATTR; my @infiles; my $databasename; my $datasetid= 1; my $optok= GetOptions( 'blocksize=n' => \$BSIZE, 'dbname=s' => \$databasename, 'datasetid=n' => \$datasetid, 'fasta=s' => \$fasta, 'input=s' => \@infiles, 'label=s' => \$label, 'output=s' => \$outpath, 'skipattr=s' => \@skipattr, 'skiptype=s' => \@skiptype, 'species=s' => \$species, 'tabletype=s' => \@tabletype, 'version=s' => \$version, ); sub usage { return "$PROGRAM: creates biomart table data from genome gff data usage: -input=gff[.gz] ... feature data including chromosomes: @chrtype -output=$outpath .. put output tables in this folder -fasta=$fasta .. chromosome fasta file[.gz] -species=$species .. species prefix for tables -label=$label .. label for tables -dbname=biomart .. database name -datasetid=$datasetid .. datasest ID for biomart -version=$version .. version of data -blocksize=$BSIZE .. region size -tabletype=@tabletype .. list of feature types to make accessory _dm tables -skiptype=@skiptype .. list of feature types to skip -skipattr=@skipattr .. list of attributes to skip "; } # -format=main,features data for main is chromosome.gff # 'format=s' => \$outformat, push(@infiles,@ARGV); die usage() unless($optok && (@infiles || $fasta)); my %chrtype = map{ $_,1; } @chrtype; my %skiptype= map{ $_,1; } map{ split /[,\s]+/; } @skiptype,@chrtype; my %skipattr= map{ $_,1; } map{ split /[,\s]+/; } @skipattr; my %skipsource= map{ $_,1; } map{ split /[,\s]+/; } @skipsource; @tabletype= map{ split /[,\s]+/; } @tabletype; my %tabletype= map{ $_,1; } @tabletype; my $org= $species; if ($org =~ /^(\w)[^_\s]*[_\s]+(\w{1,3})/) { $org= lc("$1$2"); # Gspp 4 letter abbrev. } elsif (length($org)>10 && $org =~ /^(\w{1,4})/) { $org= lc("$1"); # Gspp 4 letter abbrev. } my $tablehead= $org; $tablehead.= "_".$label if($label); $version ||= $org."_1"; $databasename ||= "biomart"; ## FIXME my $DATE= POSIX::strftime("%F %T", localtime( $^T )); #?? $outpath must be directory if exists ?? if($outpath) { $outpath .= "/" unless($outpath =~ m,/$,); # fixme mkdir($outpath) or die "bad output folder: $outpath" unless(-d $outpath); } my $regionoid = 1; my @regions=(); my %regionhash=(); if($fasta) { seqsql(); seqtab( openin($fasta) ); } if(@infiles) { foreach my $in (@infiles) { gff2featprescan( openin($in)); } regionsql(); structuresql(); featsql(); foreach my $in (@infiles) { gff2featdm( openin($in)); } regiontab(); xml_config(); meta_table_sql(); # ?? } my $outh = new FileHandle(">${outpath}${tablehead}_loading.info"); my $info = loadinfo(); print $outh $info; print $info; #------------------------------------------------------------ sub loadinfo { return " # EXAMPLE LOADING INSTRUCTIONS ; use with care to existing databases # LOAD tables TO MySQL: mysqladmin create $databasename cat ${outpath}/*.sql | mysql $databasename mysqlimport $databasename `pwd`/${outpath}/*.txt # LOAD xml to MySQL $databasename.meta_configuration: # BEST USE martj/bin/marteditor.sh to load ${outpath}/*.xml # OR try this BUT NOT IF YOU HAVE EXISTING $databasename # cat ${outpath}${tablehead}_meta.sql_example | mysql $databasename # NOTE: dbname=$databasename is included in $SequenceKey.xml # Change datasetID's in xml, meta.sql if needed "; } sub meta_table_sql { warn "meta_table_sql \n"; my $maindataset= $tablehead; #?? my $mainid = $datasetid; # fixme my $dnatable= $ftinfo{$SequenceKey}->{tabname}; ## need xml dataset name here not tabname (my $dnadataset= $dnatable) =~ s/__(main|dm)$//g; my $dnaid = $datasetid+1; # fixme my $mainname= $species; ## $maindataset; # species name; FiXME my $outsql = new FileHandle(">${outpath}${tablehead}_meta.sql_example"); # $ftkey= $SequenceKey."_".$XmlKey; my $fullpath=$outpath; unless($fullpath=~m,^/,) {$fullpath=`pwd`;chomp($fullpath);$fullpath.="/$outpath";} ## FiXME: use filetools my $maintab= $ftinfo{$XmlKey}->{tabname}; my $dnatab = $ftinfo{$SequenceKey."_".$XmlKey}->{tabname}; print $outsql <<"EOF"; -- BioMart meta data tables -- USE martj/bin/marteditor to create ; update CREATE TABLE meta_interface ( datasetID int(11) default NULL, interface varchar(100) default NULL, UNIQUE KEY datasetID (datasetID,interface) ); INSERT INTO meta_interface values('$mainid','default'),('$dnaid','default'); CREATE TABLE meta_user ( datasetID int(11) default NULL, martUser varchar(100) default NULL, UNIQUE KEY datasetID (datasetID,martUser) ); INSERT INTO meta_user values('$mainid','default'),('$dnaid','default'); CREATE TABLE meta_table_info ( table_name varchar(100) NOT NULL default '', column_name varchar(100) NOT NULL default '', column_count int(11) default NULL, KEY table_name (table_name), KEY table_name_2 (table_name,column_name) ); -- this is the dataset table; needs XML loaded which is tricky without martj CREATE TABLE meta_configuration ( internalName varchar(100) default NULL, displayName varchar(100) default NULL, dataset varchar(100) default NULL, description varchar(200) default NULL, xml longblob, compressed_xml longblob, MessageDigest blob, type varchar(20) default NULL, visible int(1) unsigned default NULL, version varchar(25) default NULL, datasetID int(11) NOT NULL default '0', modified timestamp NOT NULL default CURRENT_TIMESTAMP ); INSERT INTO meta_configuration (internalName,displayName,dataset,type,visible,version,datasetID,modified) values ('default','$mainname','$maindataset','TableSet','1','$version', $mainid, '$DATE'); INSERT INTO meta_configuration (internalName,displayName,dataset,type,visible,version,datasetID,modified) values ('default','$mainname DNA','$dnadataset','GenomicSequence','0','$version', $dnaid, '$DATE'); -- -- standard biomart also wants compressed_xml, but i haven't gotten that to work w/o corruption -- CREATE TABLE tmpxml (xml longblob); -- LOAD DATA INFILE '$fullpath$maintab.xml' INTO TABLE tmpxml LINES TERMINATED BY '~'; -- UPDATE meta_configuration set xml = (select xml from tmpxml) where datasetID = $mainid; -- TRUNCATE table tmpxml; -- LOAD DATA INFILE '$fullpath$dnatab.xml' INTO TABLE tmpxml LINES TERMINATED BY '~'; -- UPDATE meta_configuration set xml = (select xml from tmpxml) where datasetID = $dnaid; -- DROP TABLE tmpxml; -- GRANT select on $databasename.* to my_mart_user; -- FIX EOF } sub featkey { my($t, $s)= @_; my $ftkey= $t."_".$s; $ftkey =~ s/[.:;,\-]+/_/g; return (wantarray) ? ($ftkey, nickname($t,$s)) : $ftkey; } sub nickname { my($t, $s)= @_; my $nick= $s; if($nick =~ m/^(\w+):(.+)$/) { $nick= substr($1,0,1).$2; #?? } $nick =~ s/[:;,_-]+//g; ## fixme ; need configs return $nick; } sub openin { my @infiles= @_; my $infiles = join(" ", map{ split /[,\s]+/; } @infiles ); (my $inshort= $infiles) =~ s,/\S+/,,g,; # warn "openin $inshort\n"; my $inh; if($infiles =~ /\.gz/){ open(IN, "gunzip -c $infiles |") or warn "Error:openin gunzip -c $infiles\n"; $inh= *IN; } else { open(IN, "cat $infiles |") or warn "Error:openin cat $infiles\n"; $inh= *IN; } return ($inh,$inshort); } =item SQL writers =cut sub attrsql { my($outh,$ftkey,$atkeys,$prefix)= @_; $prefix.="_" if($prefix && $prefix !~ m/_$/); #$prefix ||= "at_"; foreach my $ak (@$atkeys) { print $outh " ${prefix}${ak} "; ## change this 'at_' prefix; ends up in biomart views if($ftinfo{$ftkey}->{istext}->{$ak}) { print $outh "text default null"; #? use text instead? } elsif($ftinfo{$ftkey}->{ischar}->{$ak}) { print $outh "varchar(128) default null"; #? use text instead? } elsif($ftinfo{$ftkey}->{isreal}->{$ak}) { print $outh "double (32,5) default null"; } else { print $outh "int(10) default null"; } print $outh ",\n"; } } sub structuresql { # if(GFFTAB) my $ftkey= $StrucKey; return unless(ref $ftinfo{$ftkey}); my $outh= $ftinfo{$ftkey}->{outsql}; my $tabname= $ftinfo{$ftkey}->{tabname} || "${tablehead}__${ftkey}__main"; # no longer __main ## match this field.txt # $oid,$c,$s,$t,$b,$e,$p,$o,$r,$a << gff order fields ## ** add GFFv3 ID,Name,Parent,Target,Notes,Dbxref parsed from attribs .. @GFF3ATTR= qw(ID Name Parent Dbxref Target Note); # match structuresql order %GFF3ATTR= map{$_,1} @GFF3ATTR; warn "structuresql $tabname\n"; print $outh " -- written by: $PROGRAM -- date: $DATE drop table if exists $tabname; create table $tabname ( region_id_key int(10) not null, feature_id_key int(10) not null, chr_name varchar(32) not null, source varchar(64) not null default '', biotype varchar(32) not null default '', type_source varchar(128) not null default '', chr_start int(10) not null default 0, chr_end int(10) not null default 0, score double(32,5) not null default 0, chr_strand int(2) not null default 0, chr_phase int(2) not null default 0, ID varchar(128) not null default '', Name varchar(128) not null default '', Parent varchar(128) not null default '', Dbxref text not null default '', Target text not null default '', Note text not null default '', attributes text not null default '', "; print $outh " key (region_id_key), \n"; #?? print $outh " key (feature_id_key) );\n"; #?? } sub featsql { ### NOT OFF for v.3b : user selected types for extra tables return unless(@tabletype); foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo next unless(grep/^$ftkey/,@tabletype); ## ignore Source; only leading type? next if ($MainKeys{$ftkey}); ##($ftkey eq $RegionKey); my $outh= $ftinfo{$ftkey}->{outsql}; my $atkeys= $ftinfo{$ftkey}->{attrkeys}; my $nickname= $ftinfo{$ftkey}->{nickname}; my $tabname= $ftinfo{$ftkey}->{tabname} || "${tablehead}__${ftkey}__dm"; ## match this field.txt order ## print $outh join("\t", $oid, $c,$b,$e,$o,$t,$s); warn "featsql $tabname\n"; ##${tablehead}__${ftkey}__dm\n"; #? short or long here? if(SHORT_EXTRATAB) { ## (GFFTAB) print $outh " drop table if exists $tabname; create table $tabname ( region_id_key int(10) not null , feature_id_key int(10) not null, "; } else { print $outh " drop table if exists $tabname; create table $tabname ( region_id_key int(10) not null, feature_id_key int(10) not null, chr_name varchar(32) not null, chr_start int(10) not null, chr_end int(10) not null, chr_strand int(2) not null default 0, biotype varchar(32) not null default '', source varchar(64) not null default '', "; } ## see xml_extra_filters : use these fields as filters ?? attrsql($outh,$ftkey,$atkeys,$nickname); print $outh " key (region_id_key), \n"; #?? print $outh " key (feature_id_key) );\n"; #?? } } sub regionsql { my $ftkey= $RegionKey; return unless(ref $ftinfo{$ftkey}); my $outh= $ftinfo{$ftkey}->{outsql}; my $tabname= $ftinfo{$ftkey}->{tabname} || "${tablehead}__region__main"; ## match this field.txt ## print $outh join("\t",$oid,"$c.$ib",$ib,$se,$c,$len); ## FIXME: ## region_name > region_id varchar(64), ## drop chr_size warn "regionsql $tabname\n"; print $outh " -- written by: $PROGRAM -- date: $DATE drop table if exists $tabname; create table $tabname ( region_id_key int(10) not null, region_name varchar(64) not null, region_start int(10) not null, region_end int(10) not null, chr_name varchar(40) not null, chr_size int(10) not null, "; #my $atkeys= $ftinfo{$ftkey}->{attrkeys}; #skip for region# attrsql($outh,$ftkey,$atkeys); ## add feature_bool here ? print $outh "\n"; foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo ## next if($MainKeys{$ftkey}); #($ftkey eq $RegionKey); my $sqlfield= "${ftkey}_bool"; $ftinfo{$ftkey}->{regionfield}= $sqlfield; print $outh " $sqlfield int(1) default null,\n" } print $outh " key (region_id_key) );\n"; #?? } sub seqsql { my $ftkey= $SequenceKey; ## this should be instead ## my $tabname= lc("${tablehead}_genomic_sequence__sequence__main"); # ?? my $tabname= lc("${tablehead}__${ftkey}__dm"); my $outh = new FileHandle(">$outpath$tabname.txt"); my $outsql = new FileHandle(">${outpath}$tabname.sql"); #$ftinfo{$ftkey}->{outsql}; my $tabinfo= { tabname => $tabname, nickname => $ftkey, outh => $outh, outsql => $outsql, count => 0, oid => 1, attrs => {}, isreal => {}, isint => {}, ischar => {}, istext => {}, locs => [], }; $ftinfo{$ftkey}= $tabinfo; warn "seqsql $tabname\n"; print $outsql " -- written by: $PROGRAM -- date: $DATE drop table if exists $tabname; create table $tabname ( region_id_key int(10) not null, name varchar(128) not null default '', version varchar(64) not null default '', biotype varchar(255) not null default '', description text not null default '', chr_size int(10) not null, md5checksum character(32) not null default '', chr_start int(10) not null, chunk_size int(10) not null, residues longblob not null default '' );"; # timelastmodified timestamp #print $outsql " key (region_id_key) );\n"; #?? } =item Table data subs =cut sub writetab { my( $outh, @vals)= @_; foreach (@vals) { $_='\N' unless(defined $_); } print $outh join("\t",@vals); } sub writedna { my( $outh, $oid, $id, $vers, $type, $desc, $md5, $dna)= @_; my $len= length($dna); # print $outh join("\t",$oid,$id,$vers,$type,$desc,$md5,1,$len,$dna),"\n"; for (my $start=0; $start < $len; ) { my $csize= $DNACHUNKSIZE; if($start+$csize > $len) { $csize= $len - $start; } writetab( $outh, $oid,$id,$vers,$type,$desc,$len,$md5, ($start+1), $csize); print $outh "\t", substr($dna,$start,$csize),"\n"; $start += $csize; } } sub seqtab { my($inh, $iname)= @_; warn "seqtab $iname\n"; my $ftkey= $SequenceKey; # my $tabname= lc("${tablehead}__${ftkey}__dm"); # my $outh = new FileHandle(">${outpath}$tabname.txt"); #$ftinfo{$ftkey}->{outh}; my $tabname= $ftinfo{$ftkey}->{tabname}; my $outh = $ftinfo{$ftkey}->{outh}; my $oid = 1; # what ?? this is 'region_id_key' ?? my $type= $goldenpathType || "chromosome"; # need input info my $start= 1; # biomart likes 1-origin my($id,$dna,$desc,$md5)=('','','',''); while(<$inh>){ chomp; if(/^>(\S+)\s*(.*)/) { my($newid,$newdesc)=($1,$2); if($id) { writedna( $outh, $oid, $id, $version, $type, $desc, $md5, $dna); # my $len= length($dna); # print $outh join("\t",$oid,$id,$version,$type,$desc,$md5,$start,$len,$dna),"\n"; } $id= $newid; $desc= $newdesc; $dna=''; if($desc =~ s/MD5=(\w+)[;]?//i){ $md5=$1; } else { $md5='\N'; } $desc =~ s/CRC64=\w+[;]?//; $desc =~ s/size=\w+[;]?//; # hack fix } elsif(/^\w/){ $dna.= $_; #? check junk? } } if($id){ writedna( $outh, $oid, $id, $version, $type, $desc, $md5, $dna); # my $len= length($dna); # print $outh join("\t",$oid,$id,$version,$type,$desc,$md5,$start,$len,$dna),"\n"; } close($inh); close($outh); } sub attrhash { my @at= map { split (/;\s*/,$_) } @_; my %at= (); foreach (@at) { my($k,$v)=split(/=/,$_,2); next unless(defined $v && $v ne '.' && $v ne ''); if($k eq 'db_xref'){ $k='Dbxref'; } ## fixme for lowcase of GFF3 'name', 'id', 'db_xref', 'note' elsif($k =~ m/^[a-z]/ && $GFF3ATTR{ucfirst($k)}) { $k= ucfirst($k); } if(defined $at{$k}){ $at{$k} .=",".$v; } else { $at{$k} = $v ; } } attrib4drospege(\%at) if(DROSPEGE); return %at; } sub attrib4drospege { my $at= shift; ## drop Protein '-PA' tag from Name, ID like fields, otherwise ID search is messy ## biomart could use regexp/wildcard searches. $at->{ID} =~ s/\-[RP]\w$// if($at->{ID}); $at->{Name} =~ s/\-[RP]\w$// if($at->{Name}); # also Dbxref ? } sub gffcols { # my ($c,$s,$t,$b,$e,$p,$o,$r,$a) my @v= split "\t",$_[0],9; #gff cols foreach (@v) { $_=undef if($_ eq '.'); } unless($v[6]=~/\d/) { $v[6]= ($v[6] eq '+') ? 1 : ($v[6] eq '-') ? -1 : 0; } return @v; } ## need 1-origin not 0-origin for blocks !! sub calcregion { if (wantarray) { my($b,$e)= @_; my @rg=(); for (my $i= 1 + $BSIZE * int($b/$BSIZE) ; $i < $e; $i += $BSIZE) { push(@rg,$i); } return @rg; } else { return 1 + $BSIZE * int($_[0]/$BSIZE); } } sub overlaps { my($sb,$se,$tb,$te)= @_; return ($tb <= $se && $te >= $sb); } sub newtab { my($ftkey,$nickname)= @_; my $ismain= ($MainKeys{$ftkey}); my $suf= ($ftkey eq $StrucKey) ? "dm" : ($ismain) ? "main" : "dm"; ##($ftkey eq $RegionKey) my $tabname= lc("${tablehead}__${ftkey}__${suf}"); ## v4/3b drop some/all ftkey_dm tabs / my $makeout= ($ismain) || $tabletype{$ftkey}; my $outh = ($makeout) ? new FileHandle(">$outpath$tabname.txt") : undef; my $outsql = ($makeout) ? new FileHandle(">$outpath$tabname.sql") : undef; my $tabinfo= { tabname => $tabname, nickname => $nickname, outh => $outh, outsql => $outsql, count => 0, oid => 1, attrs => {}, isreal => {}, isint => {}, ischar => {}, istext => {}, locs => [], }; return $tabinfo; } =item GFF to Table data =cut =item gff2featprescan need to know about features before writing; read thru gff twice =cut sub gff2featprescan { my($inh, $iname)= @_; warn "gff2featprescan $iname\n"; # my %ftinfo=(); ## use global unless($ftinfo{$StrucKey}) { $ftinfo{$StrucKey}= newtab($StrucKey,$StrucKey); } while(<$inh>){ next if(/^#/); chomp; my ($c,$s,$t,$b,$e,$p,$o,$r,$a)= gffcols($_); #split "\t",$_,9; #gff cols my $ftkey= featkey($t,$s); if($e && $chrtype{$t}) { $ftkey= $RegionKey; ## ?? my $len= $e - $b + 1; $goldenpathType= $t; # could be many. $goldenpathInfo{$c}= { name => $c, type=>$t, source => $s, start=>$b, end=>$e, size=>$len }; } elsif(!$e || $skiptype{$t} || $skipsource{$s}) { next; #?? should these be saved ?? } ## $featureInfo{$ftkey}= { type=>$t, source => $s, } ## use ftinfo ## write new table for each "$t.$s" group unless($ftinfo{$ftkey}) { my $nickname= nickname($t,$s); $ftinfo{$ftkey}= newtab($ftkey,$nickname); $ftinfo{$ftkey}->{type}= $t; #? $ftinfo{$ftkey}->{source}= $s; #? } if($ftkey eq $RegionKey) { ##if(REGIONTAB) # what? need to make region table now for crossrefs in _dm ? my $len= $e - $b + 1; my $links=""; # place holder; #5 my @rblocks= calcregion($b,$e); foreach my $ib (@rblocks) { my $ie= $ib + $BSIZE - 1; $ie= $e if ($ie>$e); # push(@regions, [$regionoid,$c,$ib,$ie,$len,$links]); my $regionkey= "$c.$ib"; push(@regions, $regionkey); # keep input order $regionhash{$regionkey} = [$regionoid,$c,$ib,$ie,$len,$links]; # instead of @regions $regionoid++; } } $ftinfo{$ftkey}->{count}++; my %at= attrhash($a, ((defined $p)?"score=$p":"")); foreach my $ak (sort keys %at) { next if $skipattr{$ak}; my $av= $at{$ak}; next unless(defined $av && $av ne '.'); $ftinfo{$ftkey}->{attrs}->{$ak}++; if ($av =~ m/^[-+]?\d+$/) { $ftinfo{$ftkey}->{isint}->{$ak}++; } elsif($av =~ m/^[-+]?\d[\d\.e\-]+$/i) { $ftinfo{$ftkey}->{isreal}->{$ak}++; } elsif(length($av) > 128) { $ftinfo{$ftkey}->{istext}->{$ak}++; } elsif($av =~ m/\D/) { $ftinfo{$ftkey}->{ischar}->{$ak}++; } } } @AllFtKeys= grep { !$MainKeys{$_} } (sort keys %ftinfo); foreach my $ftkey (@AllFtKeys) { my @at = sort keys %{ $ftinfo{$ftkey}->{attrs} }; $ftinfo{$ftkey}->{attrkeys} = \@at; } close($inh); ## return \%ftinfo; } =item regiontab write main table of region information =cut sub regiontab { warn "regiontab\n"; my $ftkey= $RegionKey; my $outh = $ftinfo{$ftkey}->{outh}; ## use input order# my @regions= sort keys %regionhash; # sort not numeric foreach my $r (@regions) { # push(@regions, [$regionoid,$c,$ib,$ie,$len,$links]); my $rv= $regionhash{$r}; my($regionoid,$c,$ib,$ie,$len,$links)= @$rv; writetab( $outh, $regionoid,"$c.$ib",$ib,$ie,$c,$len); ## ?? add all the _bool values here ? need region list in prescan then foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo ## next if($MainKeys{$ftkey}); #($ftkey eq $RegionKey); my $hits= ($links =~ m/\b$ftkey\b/) ? '1' : '\N'; ## urk value of NULL not 0 is off; print $outh "\t$hits"; } print $outh "\n"; } } =item gff2featdm write common feature table (gff) and maybe per-feature subtables; collect feature->region map info. =cut sub gff2featdm { my($inh, $iname)= @_; warn "gff2featdm $iname\n"; while(<$inh>){ next if(/^#/); chomp; my ($c,$s,$t,$b,$e,$p,$o,$r,$a)= gffcols($_); my $ftkey= featkey($t,$s); if( $e && $chrtype{$t}) { $ftkey= $RegionKey; } elsif(!$e || $skiptype{$t} || $skipsource{$s}) { next; #?? should these be saved ?? } # rows per attrib my %at= attrhash($a, ((defined $p)?"score=$p":"")); my $featoid = 0; if(1) { # (GFFTAB) # print struct main table of all features $featoid = $ftinfo{$StrucKey}->{oid}++; #?? use this one for feat oid my $outh = $ftinfo{$StrucKey}->{outh}; my $rblock= calcregion($b,$e); # first only my $regionkey= "$c.$rblock"; my $rvals= $regionhash{$regionkey}; my $regionoid= $rvals->[0] || '\N'; ## shouldnt be dupl. ## split out these gff3 tags from $a: ID,Name,Dbxref,Note,Parent,Target ## fixme for locase of GFF3 'name', 'id', 'db_xref', 'note' my %at2= attrhash($a); my @atlist= map{ (defined $at2{$_}) ? delete $at2{$_} : '\N'; } @GFF3ATTR; my $amore = join(";", map { "$_=$at2{$_}" }(sort keys %at2)); ## can we add 1 regionoid here that feature matches? will it help? writetab( $outh, $regionoid, $featoid, $c,$s,$t,$ftkey,$b,$e,$p,$o,$r,@atlist,$amore); # same as gff order ## BUT added $ftkey = type_source for feature filtering print $outh "\n"; } # -- collect region info and maybe write ftkey tab # print region dm tables for each feat type if($ftkey eq $RegionKey) { } else { next if($MainKeys{$ftkey}); next if($e - $b > $MAX_FEATURE_RANGE); #? skip godawfullong ones/some errors? my $outh = $ftinfo{$ftkey}->{outh}; my $atkeys= $ftinfo{$ftkey}->{attrkeys}; my @hitblocks= calcregion($b,$e); foreach my $rblock (@hitblocks) { ## loop over feat row adding each regionoid my $regionkey= "$c.$rblock"; my $rvals= $regionhash{$regionkey}; my $regionoid= $rvals->[0] || '\N'; ## shouldnt be dupl. $rvals->[5] .= $ftkey.","; # FIXME: dropped featuretype__dm, but want for some ?? # e.g. dper__cross_genome_match_dmelchr__dm for dmelchr names next unless($tabletype{$ftkey}); ## drop this extra table data? only need 3 tabs: region, feature, dna if(SHORT_EXTRATAB) { writetab( $outh, $regionoid, $featoid); } else { writetab( $outh, $regionoid, $featoid, $c,$b,$e,$o,$t,$s); } foreach my $ak (@$atkeys) { my $av= $at{$ak}; $av= '\N' unless(defined $av); print $outh "\t$av"; } print $outh "\n"; } } } close($inh); } =item Biomart XML configs =cut sub xml_config { my $xmlkey= $XmlKey; my $tabname= lc("${tablehead}__${xmlkey}"); my $outh = new FileHandle(">$outpath$tabname.xml"); my $tabinfo= { tabname => $tabname, nickname => $xmlkey, outh => $outh, # outsql => $outsql, count => 0, oid => 1, attrs => {}, isreal => {}, isint => {}, ischar => {}, istext => {}, locs => [], }; $ftinfo{$xmlkey}= $tabinfo; warn "xml_config $tabname\n"; xml_header($xmlkey); xml_filter_page($xmlkey); xml_attr_pages($xmlkey); xml_footer($xmlkey); #-- write dna dataset.xml $xmlkey= $SequenceKey."_".$XmlKey; $tabname= lc("${tablehead}__${xmlkey}"); $outh = new FileHandle(">$outpath$tabname.xml"); $tabinfo= { tabname => $tabname, nickname => $xmlkey, outh => $outh, # outsql => $outsql, count => 0, oid => 1, attrs => {}, isreal => {}, isint => {}, ischar => {}, istext => {}, locs => [], }; $ftinfo{$xmlkey}= $tabinfo; warn "xml_config $tabname\n"; xml_seqconfig($xmlkey); } sub xml_header { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; my $tabname= $ftinfo{$RegionKey}->{tabname}; my $dataset= $tablehead; #?? my $did = $datasetid; # fixme print $outh <<"EOF"; $tabname region_id_key EOF } sub xml_footer { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; print $outh <<"EOF"; EOF } sub xml_filter_page { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; print $outh <<"EOF"; EOF xml_feature_filter($xmlkey); xml_region_range_filter($xmlkey); xlm_region_contains_filter($xmlkey); xml_extra_filters($xmlkey) if(@tabletype); print $outh <<"EOF"; EOF } sub xml_extra_filters { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; print $outh <<"EOF"; EOF foreach my $tabkey (@tabletype) { my $tabname= $ftinfo{$tabkey}->{tabname}; my $atkeys = $ftinfo{$tabkey}->{attrkeys}; my $prefix= $ftinfo{$tabkey}->{nickname}; $prefix.="_" if($prefix && $prefix !~ m/_$/); foreach my $ak (@$atkeys) { my $atfld="${prefix}${ak}"; (my $fname= ucfirst($atfld)) =~ s/_/ /g; print $outh <<"EOF"; EOF } } print $outh <<"EOF"; EOF } sub xml_feature_filter { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; my $tabname= $ftinfo{$StrucKey}->{tabname}; print $outh <<"EOF"; EOF foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo #my $type = $ftinfo{$ftkey}->{type}; #my $source= $ftinfo{$ftkey}->{source} || "."; #my $fname= "$type:$source"; (my $fname= ucfirst($ftkey)) =~ s/_/ /g; print $outh <<"EOF"; EOF } sub kbsizeof { my($n)= shift; if($n>=1000000) { $n= int($n/1000000)."M"; } elsif($n>=1000) { $n= int($n/1000)."K"; } return $n; } sub xml_region_range_filter { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; print $outh <<"EOF"; EOF my @chrs= (sort keys %goldenpathInfo); my $toomany= (@chrs > 50); if ($toomany) { # got a genome-in-progress ... pick only biggest my @topchr= sort{ $goldenpathInfo{$b}->{size} <=> $goldenpathInfo{$a}->{size} } @chrs; @chrs= splice(@topchr,0,50); } foreach my $chr (@chrs) { my $cname= $chr; $cname .=" ".kbsizeof( $goldenpathInfo{$chr}->{size} ) if($toomany); # ($cname= ucfirst($cname)) =~ s/_/ /g; print $outh <<"EOF"; EOF } sub xlm_region_contains_filter { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; print $outh <<"EOF"; EOF foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo my $fld= $ftinfo{$ftkey}->{regionfield}; next unless($fld); (my $fname= ucfirst($fld)) =~ s/_/ /g; if($fname =~ s/ bool$//) { $fname="Has $fname";} print $outh <<"EOF"; EOF # and another one, diff iname print $outh <<"EOF"; EOF foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo my $fld= $ftinfo{$ftkey}->{regionfield}; next unless($fld); (my $fname= ucfirst($fld)) =~ s/_/ /g; if($fname =~ s/ bool$//) { $fname="Has $fname";} print $outh <<"EOF"; EOF } sub xml_attr_pages { my($xmlkey)= @_; xml_featattr_page($xmlkey); xml_featseq_page($xmlkey); xml_regionattr_page($xmlkey); xml_regionseq_page($xmlkey); } sub xml_featattr_page { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; my $tabname= $ftinfo{$StrucKey}->{tabname}; print $outh <<"EOF"; EOF } sub xml_featseq_page { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; my $tabname= $ftinfo{$StrucKey}->{tabname}; my $dnadataset= $ftinfo{$SequenceKey}->{tabname}; ## need xml dataset name here not tabname $dnadataset =~ s/__(main|dm)$//g; print $outh <<"EOF"; EOF } sub xml_regionattr_page { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; # my $tabname= $ftinfo{$StrucKey}->{tabname}; print $outh <<"EOF"; EOF foreach my $ftkey (@AllFtKeys) { ## sort keys %ftinfo my $fld= $ftinfo{$ftkey}->{regionfield}; next unless($fld); (my $fname= ucfirst($fld)) =~ s/_/ /g; if($fname =~ s/ bool$//) { $fname="Has $fname";} print $outh <<"EOF"; EOF } print $outh <<"EOF"; EOF } sub xml_regionseq_page { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; my $dnadataset= $ftinfo{$SequenceKey}->{tabname}; ## need xml dataset name here not tabname $dnadataset =~ s/__(main|dm)$//g; print $outh <<"EOF"; EOF } sub xml_seqconfig { my($xmlkey)= @_; my $outh = $ftinfo{$xmlkey}->{outh}; # my $databasename= $tablehead . "_" .$version; ## FIXME - global my $dnatable= $ftinfo{$SequenceKey}->{tabname}; ## need xml dataset name here not tabname (my $dnadataset= $dnatable) =~ s/__(main|dm)$//g; my $did = $datasetid + 1; # fixme print $outh <<"EOF"; EOF } 1; # turn into perl module ##================================= chado-1.23/bin/gmod_gff3_preprocessor.pl000755 000765 000024 00000024121 11723232576 020353 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Bio::FeatureIO; use Getopt::Long; use FileHandle; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; #use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::DB::Adapter; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; =head1 NAME $0 - Prepares a GFF3 file for bulk loading into a chado database. =head1 SYNOPSIS % gmod_gff_preprocessor [options] --gfffile =head1 COMMAND-LINE OPTIONS --gfffile The file containing GFF3 (optional, can read from stdin) --outfile The name kernel that will be used for naming result files --splitfile Split the files into more managable chunks, providing an argument to control splitting --onlysplit Split the files and then quit (ie, don't sort) --nosplit Don't split the files (ie, only sort) --hasrefseq Set this if the file contains a reference sequence line (Only needed if not splitting files) --dbprofile Specify a gmod.conf profile name (otherwise use default) --inheritance_tiers How many levels of inheritance do you expect tis file to have (default: 3) =head1 DESCRIPTION splitfile -- Just setting this flag to 1 will cause the file to be split by reference sequence. If you provide an optional argument, it will be further split according to these rules: source=1 Splits files according to the value in the source column source=a,b,c Puts lines with sources that match (via regular expression) 'a', 'b', or 'c' in a separate file type=a,b,c Puts lines with types that match 'a', 'b', or 'c' in a separate file For example, if you wanted all of your analysis results to go in a separate file, you could indicate '--splitfile type=match', and all cDNA_match, EST_match and cross_genome_match features would go into separate files (separate by reference sequence). inheritence_tiers -- The number of levels of inheritance this file has. For example, if the file has "central dogma" genes in it (gene/mRNA/ exon,polypeptide), then it has 3. Up to 4 is supported but the higher the number, the more slowly it performs. If you don't know, 3 is a reasonable guess. =head2 FASTA sequence If the GFF3 file contains FASTA sequence at the end, the sequence will be placed in a separate file with the extention '.fasta'. This fasta file can be loaded separately after the split and/or sorted GFF3 files are loaded, using the command: gmod_bulk_load_gff3.pl -g =head1 AUTHOR Scott Cain Ecain@cshl.orgE Copyright (c) 2006-2007 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my (@GFFFILE, $OUTFILE, $SPLITFILE,$ONLYSPLIT,$NOSPLIT,$HASREFSEQ, $DBPROFILE, $INHERITANCE_TIERS); GetOptions( 'gfffile=s' => \@GFFFILE, 'outfile=s' => \$OUTFILE, 'splitfile=s' => \$SPLITFILE, 'onlysplit' => \$ONLYSPLIT, 'nosplit' => \$NOSPLIT, 'hasrefseq' => \$HASREFSEQ, 'dbprofile=s' => \$DBPROFILE, 'inheritance_tiers=i' => \$INHERITANCE_TIERS, ) or ( system( 'pod2text', $0 ), exit -1 ); @GFFFILE = split(/,/,join(',',@GFFFILE)); $DBPROFILE ||='default'; $INHERITANCE_TIERS ||= 3; my ($split_on_source, $split_on_type, $split_on_ref); if ($SPLITFILE) { if ($SPLITFILE and $SPLITFILE !~ /=/ and $SPLITFILE == 1) { $split_on_ref = 1; } else { my @splits = split /;/, $SPLITFILE; for (@splits) { my ($tag, $value) = split /=/; $value =~ s/,/|/g; if ($tag eq 'source') { $split_on_source = $value; } elsif ($tag eq 'type') { $split_on_type = $value; } else { die "unsupported splitfile tag: $tag\n"; } } } } my %has_ref_seq; my @gfffiles; for my $GFFFILE (@GFFFILE) { $GFFFILE ||='-'; $OUTFILE ||="$GFFFILE.out.gff3"; my $FASTA = "$OUTFILE.fasta"; if ($SPLITFILE && !$NOSPLIT) { open GFFIN, "<", $GFFFILE or die "couldn't open $GFFFILE for reading: $!"; open FASTA, ">", $FASTA or die " couldn't open $FASTA for writing: $!"; my $fasta_flag = 0; my %files; while ( ) { if (/^##FASTA/) { $fasta_flag = 1; print FASTA; next; } elsif ($fasta_flag) { print FASTA; next; } next if /^#/; my @la = split /\t/; (warn "ignored gff line: $_" && next) if (scalar @la != 9); my $has_ref_seq; chomp $la[8]; if ( $la[8] =~ /ID=([^;]+);*.*$/ ) { my $id = $1; if ( $id eq $la[0] ) { $has_ref_seq = $id; } } if ( $split_on_source && $split_on_source eq 1 ) { my $source = $la[1]; my $filename = "$la[0].$la[1].$OUTFILE"; unless ( defined $files{ $filename } ) { $files{ $filename } = new FileHandle $filename, "w"; push @gfffiles, $filename; } $files{ $filename }->print( $_ ); push @{$has_ref_seq{ $filename }}, $has_ref_seq if $has_ref_seq; } elsif ( $split_on_source && $la[1] =~ /$split_on_source/) { my $filename = "$la[0].source.$OUTFILE"; unless ( defined $files{ $filename } ) { $files{ $filename } = new FileHandle $filename, "w"; push @gfffiles, $filename; } $files{ $filename }->print( $_ ); push @{$has_ref_seq{ $filename }}, $has_ref_seq if $has_ref_seq; } elsif ( $split_on_type && $la[2] =~ /$split_on_type/) { my $filename = $la[0].'.type.'.$OUTFILE; unless ( defined $files{ $filename } ) { $files{ $filename } = new FileHandle $filename, "w"; push @gfffiles, $filename; } $files{ $filename }->print( $_ ); push @{$has_ref_seq{ $filename }}, $has_ref_seq if $has_ref_seq; } else { my $filename = $la[0].'.'.$OUTFILE; unless ( defined $files{ $filename } ) { $files{ $filename } = new FileHandle $filename, "w"; push @gfffiles, $filename; } $files{ $filename }->print( $_ ); push @{$has_ref_seq{ $filename }}, $has_ref_seq if $has_ref_seq; } } for my $key (keys %files) { $files{$key}->close; } } else { push @gfffiles, $GFFFILE; push @{ $has_ref_seq{ $GFFFILE } }, $GFFFILE if $HASREFSEQ; } } exit(0) if $ONLYSPLIT; my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf, $DBPROFILE); my $db = Bio::GMOD::DB::Adapter->new( dbuser => $db_conf->user, dbpass => $db_conf->password || '', dbhost => $db_conf->host, dbport => $db_conf->port, dbname => $db_conf->name, notransact => 1, skipinit => 1, ); $db->sorter_create_table; for my $gfffile (@gfffiles) { $db->sorter_delete_from_table; my $outfile = $gfffile.'.sorted'; my $fasta = "$outfile.fasta"; open IN, "<", $gfffile or die "couldn't open $gfffile for reading: $!\n"; my $fasta_flag = 0; print STDERR "Sorting the contents of $gfffile ...\n"; while( ) { if (/^##FASTA/) { $fasta_flag = 1; open FASTA, ">", $fasta or die "couldn't open $fasta for writing: $!\n"; #print FASTA "##gff-version 3\n"; #print FASTA; #print FASTA "\n"; #extra cr works around bug in Bio::FeatureIO::gff next; } elsif ($fasta_flag) { print FASTA; next; } my $line = $_; my @line_array = split /\t/, $line; if ($line =~ /^#/ or scalar @line_array != 9) { next; } my $refseq = $line_array[0]; my ($id, @parents,@derives_froms); if ( $line_array[8] =~ /ID=([^;]+);*.*$/ ) { $id = $1; chomp $id; } if ( $line_array[8] =~ /Parent=([^;]+);*.*$/ ) { @parents = split /,/, $1; } if ( $line_array[8] =~ /Derives_from=([^;]+);*.*$/ ) { @derives_froms = split /,/, $1; } if (@parents > 0 || @derives_froms > 0) { for my $parent ( (@parents,@derives_froms) ) { chomp $parent; $db->sorter_insert_line($refseq, $id, $parent, $line); } } elsif ($id) { $db->sorter_insert_line($refseq, $id, undef, $line); } else { $db->sorter_insert_line($refseq, undef, undef, $line); } } close IN; close FASTA if $fasta_flag; print STDERR "Writing sorted contents to $outfile ...\n"; open OUT,">", $outfile or die "couldn't open $outfile for writing: $!\n"; #to print: # -get ref seqs (refseq == id) # -get things with no parent print OUT "##gff-version 3\n"; my @refseqs = $db->sorter_get_refseqs(); for my $refseq (@refseqs) { print OUT $refseq; #already has the line feed } my @no_parents = $db->sorter_get_no_parents(); for my $no_parent (@no_parents) { print OUT $no_parent; } @no_parents = ''; if ($INHERITANCE_TIERS >= 2) { my @second_tiers = $db->sorter_get_second_tier(); for my $second_tier (@second_tiers) { print OUT $second_tier; } } if ($INHERITANCE_TIERS >= 3) { my @third_tiers = $db->sorter_get_third_tier(); for my $third_tier (@third_tiers) { print OUT $third_tier; } } #yes, four tiers can happen, like transposible_element->te_gene->mRNA->exon if ($INHERITANCE_TIERS >= 4) { my @forth_tiers = $db->sorter_get_fourth_tier(); for my $fourth_tier (@forth_tiers) { print OUT $fourth_tier; } } close OUT; } chado-1.23/bin/gmod_load_cvterms.pl000644 000765 000024 00000073175 12017446444 017412 0ustar00cainstaff000000 000000 #!/usr/bin/env perl =head1 NAME load_cvterms.pl =head1 SYNOPSIS Usage: perl load_cvterms.pl -H dbhost -D dbname [-vdntuFo] file parameters =over 8 =item -g GMOD database profile name (can provide host, DB name, password, username, and driver) Default: 'default' =item -s database name for linking (must be in db table, e.g. GO ) =item -n controlled vocabulary name (e.g 'biological_process'). optional. If not given, terms of all namespaces related with database name will be handled. =item -F File format. Can be obo or go_flat and others supported by L. Default: obo =item -u update all the terms. Without -u, the terms in the database won't be updated to the contents of the file, in terms of definitions, etc. New terms will still be added. =item -v verbose output =item -o outfile for writing errors and verbose messages (optional) =item -t trial mode. Don't perform any store operations at all. (trial mode cannot test inserting associated data for new terms) =back The following options are required if not using GMOD profile =over 5 =item -H hostname for database [required if -p isn't used] =item -D database name [required if -p isn't used] =item -p password (if you need to provide a password to connect to your db) =item -r username (if you need to provide a username to connect to your database) =item -d driver name (e.g. 'Pg' for postgres). Driver name can be provided in gmod_config =back The script parses the ontology in the file and the corresponding ontology in the database, if present. It compares which terms are new in the file compared to the database and inserts them, and compares all the relationships that are new and inserts them. It removes the relationships that were not specified in the file from the database. It never removes a term entry from the database. This script works with Chado schema (see gmod.org) and accesse the following tables: =over 9 =item db =item dbxref =item cv =item cvterm =item cvterm_relationship =item cvtermsynonym =item cvterm_dbxref =item cvtermprop =back Terms that are in the database but not in the file are set to is_obsolete=1. All the terms that are present in the database are updated (if using -u option) to reflect the term definitions that are in the file. New terms that are in the file but not in the database are stored. The following data are associated with each term insert/update: =over 7 =item Term name =item Term definition =item Relationships with other terms =item Synonyms =item Secondary ids =item Definition dbxrefs =item Comments =back =head1 AUTHOR Lukas Mueller Naama Menda =head1 VERSION AND DATE Version 0.15, September 2010. =cut use strict; use Getopt::Std; use Pod::Usage; use Bio::OntologyIO; use Bio::Ontology::OntologyI; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; use Try::Tiny; our ($opt_d, $opt_h, $opt_H, $opt_F, $opt_n, $opt_D, $opt_v, $opt_t, $opt_u, $opt_o, $opt_p, $opt_r, $opt_g, $opt_s); getopts('F:d:H:o:n:vD:tp:us:r:g:') or pod2usage(); my $dbhost = $opt_H; my $dbname = $opt_D; my $pass = $opt_p; my $driver = $opt_d; my $user = $opt_r; my $verbose = $opt_v; my $DBPROFILE = $opt_g ; print "H= $opt_H, D= $opt_D, u=$opt_u, d=$opt_d, v=$opt_v, t=$opt_t \n" if $verbose; my $port = '5432'; if (!$opt_s) { die " Need -s db.name argument! (e.g. GO , PO, etc.\n " ; } # the database name that Dbxrefs should refer to if (!($opt_H and $opt_D) ) { $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new() ; my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ) ; $dbhost ||= $db_conf->host(); $dbname ||= $db_conf->name(); $driver ||= $db_conf->driver(); $port= $db_conf->port() || '5432'; $user= $db_conf->user(); $pass= $db_conf->password(); } if (!$dbhost && !$dbname) { die "Need -D dbname and -H hostname arguments.\n"; } if (!$driver) { die "Need -d (dsn) driver, or provide one in -g gmod_conf\n"; } if (!$user) { die "Need -r user_name, or provide one in -g gmod_conf\n"; } my $dsn = "dbi:$driver:dbname=$dbname"; $dsn .= ";host=$dbhost"; $dsn .= ";port=$port"; my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||''); if (!$schema) { die "No schema is avaiable! \n"; } ####################### my $error = 0; # keep track of input errors (in command line switches). if (!$opt_F) { $opt_F="obo"; } if ($opt_t) { print STDERR "Trial mode - rolling back all changes at the end.\n"; } if ($opt_u) { print STDERR "This script will UPDATE cvterms stored in your database from the input file! \n"; } else { print STDERR "WARNING: If your databse is already population with cvterms, not running in UPDATE mode (option -u) may cause database conflicts, such as violating unique constraints!\n"; } print STDERR "Default for -s: $opt_s (specifies the database names for Dbxref objects)\n"; print STDERR "Default for -F: File format set to $opt_F\n"; my $file = shift; if (!$file) { print STDERR "A file is required as a command line argument.\n"; $error=1; } die "Some required command lines parameters not set. Aborting.\n" if $error; if ($opt_o) { open (OUT, ">$opt_o") ||die "can't open error file $opt_o for writting.\n" ; } message( "Connected to database $dbname on host $dbhost.\n", 1); print STDERR "Parsing the ontology $file...\n"; my $parser = Bio::OntologyIO->new( -file => $file, -format=>$opt_F ); my $default_ont; my @onts = (); while( my $ont = $parser->next_ontology() ) { $default_ont = $ont if !$default_ont; push @onts, $ont; } message("Default namespace is " . $default_ont->name . " \n" , 1); my $default_cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $default_ont->name } , { key => 'cv_c1' }, ); foreach my $new_ont(@onts) { my $coderef = sub { my $new_ont_name=$new_ont->name(); message("....found namespace '$new_ont_name' \n", 1); if ($opt_n && ( $opt_n ne $new_ont_name) ) { message ("$opt_n: skipping to next ontology..\n",1); next (); } my $rel_cv; #check if relationship ontology is already loaded: if ($new_ont_name ne 'relationship') { $rel_cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'relationship' } , { key => 'cv_c1' }, ); my @rel= $schema->resultset("Cv::Cvterm")->search( { cv_id => $rel_cv->get_column('cv_id'), is_relationshiptype => 1, }); if (!@rel) { warn "Relationship ontology must be loaded first!!\n" ; exit(0); } } ####add Typedef parsing to obo.pm!### ####store a new cv if the ontology namespace does not exist my $cv= $schema->resultset('Cv::Cv')->find_or_create( { name => $new_ont_name } , { key => 'cv_c1' }, ); print STDERR "cv_id = ".($cv->get_column('cv_id') )."\n"; print STDERR "Updating an ontology in the database...\n"; my $db_ont = $cv; my $ontology_name=$db_ont->get_column('name'); message("Ontology name: ".($db_ont->name())."\n", 1); my %file_relationships = (); # relationships currently defined in the file my %db_relationships = (); ###### my $db = $schema->resultset("General::Db")->find_or_create( { name => $opt_s }, { key => 'db_c1' }, ); print STDERR "Getting all the terms of the new ontology...\n"; my (@all_file_terms) = $new_ont->get_all_terms(); my (@all_file_predicate_terms) = $new_ont->get_predicate_terms(); ###my (@all_file_typedefs) = $new_ont->get_all_typedefs(); message( "***found ".(scalar(@all_file_predicate_terms))." predicate terms!.\n", 1); message( "Retrieved ".(scalar(@all_file_terms))." terms.\n", 1); #look at all predecate terms (Typedefs) my @all_db_predicate_terms= $db_ont->search_related('cvterms' , { is_relationshiptype => 1} ); foreach my $t(@all_file_predicate_terms) { #look at predicate terms in file my ($p_term) = $schema->resultset('Cv::Cvterm')->search( { 'lower(name)' => { 'like' , lc( $t->name() ) }, is_relationshiptype => 1, }); #maybe it's stored with another cv_id? if ($p_term) { message("predicate term '" .$t->name() . "' already exists with cv_id " . $p_term->get_column('cv_id') . "\n", 1); }else { #the predicate term will be stored at the time of storing a term with that relationship, using the term's cv_id #this stores the relationship types under 'relationship' cv namespace #terms defined as '[Typedef]' in the obo file should actually be stored as relationshiptype #but with the current ontology cv namespace . #To do this we need to add to the obo parser (Bio::OntologyIO::obo.pm) #a 'get_typedefs' funciton my $accession = $t->identifier() || $t->name(); message("Predicate term $accession will be stored later if used as a relationship in an ontology term\n",1); } } print STDERR "Getting all the terms of the current ontology...\n"; #a list of Bio::Chado::Schema::Cvterm objects my @all_db_terms = $schema->resultset("Cv::Cvterm")->search( { cv_id => $db_ont->get_column('cv_id'), is_relationshiptype => 0, })->all(); print STDERR "Indexing terms and relationships...\n"; my %file_index = (); # index of term objects in the db with accession as key my %db_index = (); # this hash will be populated with accession => cvterm_object my $db_namespace ; foreach my $t (@all_file_terms) { my ($prefix, $id) = split (/\:/, $t->identifier()); #=~ s/\w+\:(.*)/$1/g; $db_namespace = $prefix if !$db_namespace; $file_index{$id} = $t if ($db_namespace eq $prefix) ; message("Found term in file : $prefix:$id\n", 1); } my $c_count = 0; # count of db terms foreach my $t (@all_db_terms) { $c_count++; my ($id )= $t->search_related('dbxref')->first()->get_column('accession'); $db_index{$id} = $t; message("Found term in DB: $id\n", 1); } my %novel_terms = (); my @removed_terms = (); my @novel_relationships = (); my @removed_relationships = (); print STDERR "Determining which terms are new...\n"; FILE_INDEX: foreach my $k (keys(%file_index)) { if (!exists($db_index{$k})) { if (!$file_index{$k}->name() ) { next FILE_INDEX; } #skip if term in file has no name. #This happens in InterPro file - which is translated from xml to obo. if ($opt_v) { print STDERR "Novel term: $k ".($file_index{$k}->name())."\n"; } else { print STDERR "."; } print OUT "Novel term: $k ".($file_index{$k}->name())."\n" if $opt_o; $novel_terms{$k}=$file_index{$k}; } } print STDERR "Determine which terms are not in the file anymore...\n These terms will be set to obsolete in the database\n"; foreach my $k (keys(%db_index)) { if (!exists($file_index{$k})) { my $name = $db_index{$k}->name(); #get the name in the database message( "Term not in file: $name \n",1); unless( $name =~ m/obsolete.*$opt_s:/ ) { my $ob_name = $name . " (obsolete " . $opt_s . ":" . $name . ")" ; #add the 'obsolete' suffix $db_index{$k}->set_column(name => $ob_name ); message( "**modified name for $opt_s:$name - '$ob_name' \n " , 1); } $db_index{$k}->set_column(is_obsolete => 1 ); $db_index{$k}->update(); print STDERR " obsoleted term $name!.\n"; push @removed_terms, $db_index{$k}; } } print STDERR "Inserting and updating terms...\n"; my $count = 0; my $u_count=0; if ($opt_u) { UPDATE: foreach my $k (keys(%file_index)) { $count++; if (!exists($novel_terms{$k})) { #update the term if run with -u option. $u_count++; message( "updating information for term $k...\n"); if (!$file_index{$k} || !$db_index{$k} ) { message ("SKIPPING term $k! No value found\n", 1); next UPDATE; } my $name = $file_index{$k}->name(); $db_index{$k}->set_column(name => $name ); $db_index{$k}->set_column( definition => $file_index{$k}->definition() ); $db_index{$k}->set_column(is_obsolete => $file_index{$k}->is_obsolete() ); #changing the name of obsolete terms to "$name (obsolete $db:$accession)" #to avoid violating the cvterm unique constaint (name, cv_id, is_obsolete) if ($db_index{$k}->is_obsolete() ) { unless( $name =~ m/obsolete.*$opt_s:$k/ ) { my $ob_name = $name . " (obsolete " . $opt_s . ":" . $k . ")" ; $db_index{$k}->set_column( name=>$ob_name ); print STDERR "**modified name for $opt_s:$k - '$ob_name' version: " . $file_index{$k}->version() . " \n " ; } } #a term might be updated to a name which already exists in the database, #but would also be updated later on my ($existing_name) = $schema->resultset("Cv::Cvterm")->search( { name => $name, is_obsolete => $db_index{$k}->is_obsolete, cv_id => $db_index{$k}->cv_id, } )->single; #if a term already exists, update it now from the file index #to avoid violating the unique constraint if ($existing_name && $file_index{$existing_name->dbxref->accession} ) { my $existing_accession = $existing_name->dbxref->accession; #update here only if the existing accession is different than $k if ( $existing_accession ne $k ) { message("Updating term $existing_accession with name " . $file_index{$existing_accession}->name . "\n" , 1); $db_index{$existing_accession}->update( { name => $file_index{$existing_accession}->name, definition => $file_index{$existing_accession}->definition, is_obsolete => $file_index{$existing_accession}->is_obsolete, }); } } # now we can update the original term without conflicts message("UPDATING term $k with name " . $file_index{$k}->name . "\n" , 1); $db_index{$k}->update(); #update dbxref version if ( $file_index{$k}->version() ) { my ($dbxref)=$db_index{$k}->search_related('dbxref'); $dbxref->set_column(version => $file_index{$k}->version() ); $dbxref->update(); } #add comment as a cvtermprop my ($comment_cvterm) = $schema->resultset("Cv::Cvterm")->search( { name => 'comment'} ); if ($file_index{$k}->comment() ) { my $cvtermprop= $schema->resultset("Cv::Cvtermprop")->find_or_create( { cvterm_id => $db_index{$k}->get_column('cvterm_id'), type_id => $comment_cvterm->get_column('cvterm_id'), value => $file_index{$k}->comment(), }, ); } ############################### # deal with synonyms here... my %file_synonyms = (); foreach my $s ($file_index{$k}->get_synonyms()) { $s=~ s/\s+$//; $s =~ s/\\//g; $file_synonyms{uc($s)}=1; message("...adding synonym '$s' to the database...\n"); $db_index{$k}->add_synonym($s); } foreach my $s ($db_index{$k}->search_related('cvtermsynonyms')) { my $s_name= $s->get_column('synonym'); if (!exists($file_synonyms{uc($s_name)}) ) { message( "Note: deleting synonym ' " . $s->synonym() . "' from cvterm ". $db_index{$k}->get_column('name') . "...\n",1); $db_index{$k}->delete_synonym($s_name); } } #deal with secondary ids (alt_id field). # Stored in cvterm_dbxref with the field 'is_for_definition' = 0 #delete all cvterm dbxrefs before loading the new ones from the file my @secondary_dbxrefs= $db_index{$k}->search_related('cvterm_dbxrefs'); foreach (@secondary_dbxrefs) { $_->delete(); } my %file_secondary_ids = (); foreach my $i ($file_index{$k}->get_secondary_ids()) { $i = substr($i, 0, 255); #dbxref.accession is varchar(255) maybe it needs to be text? $file_secondary_ids{uc($i)}=1; message("adding secondary id $i to the database...\n"); $db_index{$k}->add_secondary_dbxref($i); } ######### # Definition dbxrefs. get_dblinks gets the dbxref in the definition tag # and all xref_analog tags. This will store in the database cvterm_dbxrefs with #the field 'is_for_definition' = 1 my %file_def_dbxrefs=(); #store definition's dbxrefs in cvterm_dbxref foreach my $dblink ($file_index{$k}->get_dbxrefs() ) { my $def_dbxref = $dblink->database() . ':' . $dblink->primary_id(); $file_def_dbxrefs{uc($def_dbxref)}=1; message("adding definition dbxref $def_dbxref to cvterm_dbxref\n"); $db_index{$k}->add_secondary_dbxref($def_dbxref, 1); } } } message("DONE UPDATING existing terms! \n",1); } #finished updating existing terms.. #now insert the new ones: my $n_count=0; foreach my $k (keys(%novel_terms)) { $n_count++; my $name = $novel_terms{$k}->name(); my $version = $novel_terms{$k}->version(); my $accession = numeric_id($novel_terms{$k}->identifier()); message("Inserting novel term '$name' (accession = '$accession', version = '$version' ) \n"); #write a special case for interpro domains #those have accession IPR000xxxx # #There's a potential issue with updating cvterms which have been moved to another cv namespace. #In such cases, a dbxref is found, but we cannot store a new cvterm with the same dbxref_id (see cvterm_c2). # A new dbxref will be created to overcome this problem my $new_term_dbxref = $schema->resultset("General::Dbxref")->find( { db_id => $db->get_column('db_id'), accession => $accession, version => $version || '', }, { key => 'dbxref_c1' } , ); if ($new_term_dbxref) { $version = $version+1 ; } $new_term_dbxref = $schema->resultset("General::Dbxref")->create( { db_id => $db->get_column('db_id'), accession => $accession, version => $version || '', }, { key => 'dbxref_c1' } , ); if ($novel_terms{$k}->is_obsolete() == 1 ) { unless( $name =~ m/obsolete.*$opt_s:$k/i ) { my $ob_name = $name . " (obsolete " . $opt_s . ":" . $k . ")" ; $name = $ob_name ; print STDERR "**modified name for $opt_s:$k - '$ob_name' \n " ; } } if (!$opt_t) { my ($existing_term) = $schema->resultset("Cv::Cvterm")->search( { cv_id =>$cv->cv_id(), name => $name, is_obsolete=> $novel_terms{$k}->is_obsolete(), }); if ($existing_term) { message("TERM $k has name $name, which also exists for term id " . $existing_term->cvterm_id . " with accession " . $existing_term->dbxref->accession . "\n\n",1); } my $new_term= $schema->resultset("Cv::Cvterm")->create( { cv_id =>$cv->cv_id(), name => $name, definition => $novel_terms{$k}->definition(), dbxref_id => $new_term_dbxref-> dbxref_id(), is_obsolete=> $novel_terms{$k}->is_obsolete(), }); #changing the name of obsolete terms to "$name (obsolete $db:$accession)" #to avoid violating the cvterm unique constaint (name, cv_id, is_obsolete) message("Storing term $k...name = " . $novel_terms{$k}->name() . "\n"); if ($count % 100==0) { print STDERR "."; } my $comment = $novel_terms{$k}->comment(); $new_term->create_cvtermprops( { comment => $comment } , { autocreate => 1 } ) if $comment; #store synonyms in cvtermsynonym foreach my $s ($novel_terms{$k}->get_synonyms() ) { $s=~ s/\s+$//; $s =~ s/\\//g; message("...adding synonym '$s' to the database...\n"); $new_term->add_synonym($s); #need to add a type_id to each synonym! } foreach my $i ($novel_terms{$k}->get_secondary_ids()) { #store secondary ids in cvterm_dbxref message("adding secondary dbxref '$i' to cvterm_dbxref\n"); $new_term->add_secondary_dbxref($i); } foreach my $r ($novel_terms{$k}->get_dbxrefs() ) { #store definition's dbxrefs in cvterm_dbxref if (!$r->database || !$r->primary_id) { next; } # skip def. dbxrefs without both db_name and accession my $def_dbxref= $r->database() . ':' . $r->primary_id(); message("adding definition dbxref $def_dbxref to cvterm_dbxref\n"); $new_term->add_secondary_dbxref($def_dbxref, 1); } } } ################################## message ("Updated $u_count existing terms, inserted $n_count new terms!\n",1); print STDERR "Parsing out the relationships...\n"; print STDERR "Looking at relationships in file.\n"; my $t_count = 0; # count of terms in the file foreach my $t (@all_file_terms) { $t_count++; my $id = numeric_id($t->identifier()); my @all_relationships = $new_ont->get_relationships($t); message("Retrieved accession: $id\n"); foreach my $r (@all_relationships) { my $s = $r->subject_term(); my $o = $r->object_term(); my ($s_db_name, undef) = split (/\:/ , $s->identifier); my ($o_db_name, undef) = split (/\:/, $o->identifier); if ($s_db_name ne $o_db_name) { print "*********************************************subject $s_db_name != object $o_db_name. Skipping!!\n"; next(); } my $key = numeric_id($s->identifier())."-".numeric_id($o->identifier()); message("Looking at relationship in file: $key\n" ); if ($t_count % 100==0) { message("."); } $file_relationships{$key} = $r; # create the hash entry for this relationship } } print STDERR "\nLooking at relationships in database.\n"; # indexing the database relationships foreach my $k (keys %db_index) { ###foreach my $r ($db_ont->get_relationships($db_index{$k})) { foreach my $r ($db_index{$k}->search_related('cvterm_relationship_subjects') ) { if ($r) { my ($s) = $r->search_related('subject'); my ($o) = $r->search_related('object'); #terms might have moved to a different cv namespace if ($s->cv_id() eq $o->cv_id() ) { my $key = numeric_id($s->search_related('dbxref')->first()->accession)."-".numeric_id($o->search_related('dbxref')->first()->accession); message("Looking at relationship in db: $key\n"); $db_relationships{$key}=$r; } } } } print STDERR "Relationships not in the file...\n"; foreach my $k (keys(%db_relationships)) { if (! (exists($file_relationships{$k}) && defined($file_relationships{$k})) ) { push @removed_relationships, $k; message("Deleted relationship: $k... \n",1); $db_relationships{$k}->delete(); print STDERR "gone.\n"; } } print STDERR "\n"; ##################################### my $r_count = 0; RELATIONSHIP: foreach my $r (keys(%file_relationships)) { $r_count++; if (!exists($db_relationships{$r})) { if ($opt_v) { print STDERR "Novel relationship: $r\n"; } elsif ($r_count % 100 == 0) { print STDERR "."; } print OUT "Novel relationship: $r\n" if $opt_o; #### #convert the Bio::Ontology::OBOTerm objects to Bio::Chado::Schema::Cv::Cvterm objects my $subject_accession = $file_relationships{$r}->subject_term()->identifier(); my ($s_db, $s_acc) = split ':', $subject_accession; my ($subject_dbxref)= $schema->resultset("Cv::Cvterm")->search()-> search_related( 'dbxref', { accession => $s_acc, db_id => $db->db_id(), } )->single; if (!$subject_dbxref ) { message("dbxref does not exist for subject term '$s_acc'.Skipping..\n" ,1); next RELATIONSHIP; } my ($subject_term)= $schema->resultset('Cv::Cvterm')->find( { cv_id => $cv->cv_id(), dbxref_id => $subject_dbxref->dbxref_id(), }); if (!$subject_term ) { message("cvterm does not exist for subject term '$subject_accession'.Skipping..\n" ,1); next RELATIONSHIP; } my $object_accession = $file_relationships{$r}->object_term()->identifier(); my ($o_db, $o_acc) = split ':', $object_accession; my ($object_dbxref)= $schema->resultset("Cv::Cvterm")->search()-> search_related( 'dbxref', { accession => $o_acc, db_id => $db->db_id(), } )->single; if (!$object_dbxref ) { message("dbxref does not exist for object term $o_acc . SKIPPING!\n",1); next RELATIONSHIP; } my ($object_term)= $schema->resultset('Cv::Cvterm')->find( { cv_id => $cv->cv_id(), dbxref_id => $object_dbxref->dbxref_id(), }); if (!$object_term ) { message("cvterm does not exist for object term $object_accession . SKIPPING!\n",1); next RELATIONSHIP; } ############################################ push @novel_relationships, $r; my $predicate_term_name = $file_relationships{$r}->predicate_term()->name(); my $predicate_term; my ($rel_db)= $schema->resultset('General::Db')->search( { name => 'OBO_REL' } ); ($predicate_term) = $schema->resultset('General::Dbxref')->search( { 'lower(accession)' => { 'like' , lc($predicate_term_name) }, db_id => $rel_db->db_id(), })->search_related('cvterm') if $rel_db; # this is not a relationship_ontology term if (!$predicate_term) { my ($predicate_dbxref) = $schema->resultset('General::Db')->search( { name => $opt_s } )->search_related('dbxrefs', { accession => $predicate_term_name }); ($predicate_term) = $schema->resultset("Cv::Cvterm")->find( { dbxref_id => $predicate_dbxref->dbxref_id } ) if $predicate_dbxref; # cvterm has a relationshiptype term with the dbxref_id of $predicate_term_name if ($predicate_term) { die("predicate term $predicate_term_name (cvterm id = " . $predicate_term->cvterm_id . " is not stored as relationshiptype in your database!!\n") if $predicate_term->is_relationshiptype !=1 ; # this happens when the predicate term is stored with the wrong cv #(e.g. GO predicate terms should have the cv_id of the # default namespace of the ontology (gene_ontology) # and not of one of the 3 components ) $predicate_term->update( { cv_id => $default_cv->cv_id } ) ; } else { # no cvterm exists with this dbxref, create a new one $predicate_term = $schema->resultset('Cv::Cvterm')->create_with( { name => $predicate_term_name, cv => $default_cv, db => $opt_s, dbxref => $predicate_term_name, }); $predicate_term->is_relationshiptype(1); $predicate_term->update; message("Stored new relationshiptype '" . $predicate_term_name . "'\n",1); } if (!$predicate_term) { die "The predicate term $predicate_term_name does not exist in the database\n"; } } if (!$opt_t) { message("Storing relationship $r. type cv_id=" . $predicate_term->cv_id() ."\n" ,1); if ( $subject_term->cv_id != $object_term->cv_id ) { message("Wait! subjcet term has cv namespace " . $subject_term->cv->name . " which is different from the namespace of the object term (" . $object_term->cv->name . "). Cross referencing relationships across namespaces is not supported (yet.. ) SKIPPING this relationship! \n"); next RELATIONSHIP; } my $new_rel = $schema->resultset('Cv::CvtermRelationship')->create( { subject_id => $subject_term->cvterm_id(), object_id => $object_term->cvterm_id(), type_id => $predicate_term->cvterm_id(), } ); } } } message($ontology_name." : ". scalar(@novel_relationships)." novel relationships among ".(scalar(keys(%file_relationships)))." were found and stored.\n", 1); if ($opt_t) { die "TEST RUN! rolling back\n"; } }; try { $schema->txn_do($coderef); message("Committing! \n If you are using cvtermpath you should now run gmod_make_cvtermpath.pl . See the perldoc for more info. \n\n", 1); } catch { # Transaction failed die "An error occured! Rolling back! " . $_ . "\n"; }; } sub recursive_children { my $ont = shift; my $node = shift; my @children = $ont -> get_child_terms($node); foreach my $child (@children) { print STDERR "CHILD: ".($child->name())."\n"; recursive_children($ont, $child); } } sub message { my $message = shift; my $default=shift; if ($opt_v || $default) { print STDOUT "$message"; } print OUT "$message" if $opt_o; } sub numeric_id { my $id = shift; $id =~ s/.*\:(.*)$/$1/g; return $id; } chado-1.23/bin/gmod_make_cvtermpath.pl000644 000765 000024 00000026074 11727656636 020113 0ustar00cainstaff000000 000000 #!/usr/bin/env perl =pod =head1 NAME gmod_make_cvtermpath.pl =head1 USAGE perl gmod_make_cvtermpath.pl -H [dbhost] -D [dbname] [-vt] -c cvname perl gmod_make_cvtermpath.pl -g [GMODConf_profile] -c cvname =head2 Parameters =over 5 =item -c Name of ontology (cv.name) to compute the transitive closure on. (Required) =item -v Verbose output =item -t Trial mode. Do not perform any store operations at all. (Not implemented) =item -o outfile for writing errors and verbose messages (optional) =item -g GMOD database profile name (can provide host and DB name) Default: 'default' =back =head2 If not using a GMOD database profile (option -g) then you must provide the following parameters =over 5 =item -D Database name =item -H Hostname =item -d Database driver name (e.g. 'Pg' for postgres) =item -u [Optional- if default user is not used] Database user name =item -p [Optional- if you need a password to connect to your database] Password for your user to connect to the database =back =head1 DESCRIPTION This script calculates the transitive closure on the ontology terms in the cvterm table. As this is a computationaly intensive operation, doing so on a large cv like the Gene Ontology can take several hours. For more information on what a transative closure is, please see: http://www.geneontology.org/GO.database.shtml#graphs =head1 AUTHOR Naama Menda =head1 VERSION AND DATE Version 1.2, Feb. 2011. =cut use strict; use DBI; use Bio::OntologyIO; use Bio::Ontology::TermFactory; use Bio::Chado::Schema; ########## use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Getopt::Std; use Try::Tiny; our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_g, $opt_p, $opt_d, $opt_u, $opt_c, $opt_o); getopts('H:D:c:p:g:p:d:u:o:tv'); my $dbhost = $opt_H; my $dbname = $opt_D; my $pass = $opt_p; my $driver = $opt_d; my $user = $opt_u; my $cvname = $opt_c; my $verbose = $opt_v; my $DBPROFILE = $opt_g ; print "H= $opt_H, D= $opt_D, u=$opt_u, d=$opt_d, v=$opt_v, t=$opt_t , cvname = $opt_c \n" if $verbose; my $port = '5432'; if (!($opt_H and $opt_D) ) { my $DBPROFILE = $opt_g; $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new() ; my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ) ; $dbhost ||= $db_conf->host(); $dbname ||= $db_conf->name(); $driver = $db_conf->driver(); $port= $db_conf->port(); $user= $db_conf->user(); $pass= $db_conf->password(); } if (!$dbhost && !$dbname) { die "Need -D dbname and -H hostname arguments.\n"; } if (!$driver) { die "Need -d (dsn) driver, or provide one in -g gmod_conf\n"; } if (!$user) { die "Need -u user_name, or provide one in -g gmod_conf\n"; } #we can allow blank passwords if (!$cvname) { die "Need to provide -c cv.name ! \n" ; } my $dsn = "dbi:$driver:dbname=$dbname"; $dsn .= ";host=$dbhost"; $dsn .= ";port=$port"; my $schema= Bio::Chado::Schema->connect($dsn, $user, $pass||''); my $db=$schema->storage->dbh(); if (!$schema || !$db) { die "No schema or dbh is avaiable! \n"; } print STDOUT "Connected to database $dbname on host $dbhost.\n" if $verbose; ########## if ($opt_o) { open (OUT, ">$opt_o") ||die "can't open error file $opt_o for writting.\n" ; } my %type; my %subject; my %object; my %black; my %root; our %leaf; my %sot; my $sth_type = $db->prepare("select cvterm_id from cvterm where is_relationshiptype = ?"); $sth_type->execute(1); while(my $type_id = $sth_type->fetchrow){ $type{$type_id}++; } my %cvterm; my $sth_cvterm = $db->prepare("select cvterm_id from cvterm WHERE is_relationshiptype = 0"); $sth_cvterm->execute; while(my $cvterm_id = $sth_cvterm->fetchrow_array){ $cvterm{$cvterm_id}++; } my $cv_id; warn "select cv_id from cv where name = '$cvname'" if $verbose; my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'"); $sth_cv->execute; while(my $cv = $sth_cv->fetchrow_hashref){ $cv_id = $cv->{cv_id}; } die "no cv_id for '$cvname'" unless defined $cv_id; ############## #delete existing cvtermpath rows $schema->resultset("Cv::Cvtermpath")->search({cv_id => $cv_id} )->delete(); ####### my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id"); $sth_cvterm_relationship->execute; while(my $cvterm_relationship = $sth_cvterm_relationship->fetchrow_hashref){ $subject{$cvterm_relationship->{subject_id}}++; $object{$cvterm_relationship->{object_id}}++; #hash of subject-object-type. Stores all the relationships defined in cvterm_relationship table. $sot{$cvterm_relationship->{subject_id}}{$cvterm_relationship->{object_id}}{$cvterm_relationship->{type_id}}++; } #populate hash of roots (terms without parents (objects)) and hash of leaves (terms without child terms (subjects)) foreach my $cvterm (keys %cvterm){ $root{$cvterm}++ if(!$subject{$cvterm} and $object{$cvterm}); $leaf{$cvterm}++ if( $subject{$cvterm} and !$object{$cvterm}); } my %leafbak = %leaf; %sot = (); # this is a hash for storing the already-processed leaves for a given type term. our %seen ; while(keys %leaf){ foreach my $l (keys %leaf){ foreach my $type (keys %type){ #add the leaf-type term to the seen list. $seen{$l}{$type}++; #sending the leaf as an arrayref to the recurse fuction. Distance starts with 1 recurse([$l],$type,1); } delete $leaf{$l}; message("DELETED leaf $l ! number of leaves is now : " .(scalar(keys(%leaf))) . "\n" ) ; } message("DONE recursing leaves \n"); } message("DONE FIRST LEAF RECURSIION! About to create the transitive path.\n"); %leaf = %leafbak; %seen = (); while(keys %leaf){ foreach my $le (sort keys %leaf){ $seen{$le}{0}++; #calling recurse with leaf $le recurse([$le],0,1); #deleting the leaf from the list delete $leaf{$le}; message("Deleted leaf $le! after deleting number of leaves is : " .(scalar(keys(%leaf))) . "\n"); } message("FINISHED RECURSING for the transitive path (type = IS_A) \n"); } sub recurse { my($subjects,$type,$dist) = @_; # start with the last subject my $subject = $subjects->[-1]; #get the parents for the subject with this type (defaults to IS_A) my @objects = objects($subject,$type); #if there are no parents for this path, exit the loop (and the next leaf will be sent here again) if(!@objects){ $leaf{$subject}++ ; return; } my $path; # foreach parent construct a path with each child foreach my $object (@objects){ my $coderef = sub { my $tdist = $dist; # loop through the child terms foreach my $s (@$subjects){ #next if the path was seen (subject-object-type-distance) next if $sot{$s}{$object}{$type}{$tdist}; if (exists($sot{$s}{$object}) && exists($sot{$object}{$s})) { die " YOU HAVE A CYCLE IN YOUR ONTOLOGY for $s, $object ($type, $tdist) C8-( \n" ; } $sot{$s}{$object}{$type}{$tdist}++; print $tdist,"\t"x$dist,"\t",$s,"\t" , $object,"\t" ,$type||'transitive',"\n"; # if type is defined , create a path using it (see the first looping through %leaf keys) if($type){ $path = $schema->resultset("Cv::Cvtermpath")->find_or_create( { subject_id => $s, object_id => $object, type_id => $type, cv_id => $cv_id, pathdistance => $tdist }, { key => 'cvtermpath_c1' } , ); message( "Inserting ($s,$object,$type,$cv_id , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id(). "\n" ); my $ttdist = -1 * $tdist; $path = $schema->resultset("Cv::Cvtermpath")->find_or_create( { subject_id => $object, object_id => $subject, type_id => $type, cv_id => $cv_id, pathdistance => $ttdist }, { key => 'cvtermpath_c1' } , ); message( "Inserting ($object,$subject,$type,$cv_id , $ttdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" ); } else { # if type exists (see second looping through %leaf keys) create a path using the is_a type message("No type defined! Using default IS_A relationship\n"); my $is_a = $schema->resultset("Cv::Cvterm")->search({ name => 'is_a' })->first(); $path = $schema->resultset("Cv::Cvtermpath")->find_or_create( { subject_id => $s, object_id => $object, type_id => $is_a->cvterm_id(), cv_id => $cv_id, pathdistance => $tdist }, { key => 'cvtermpath_c1' } , ); message("Inserting ($s,$object, $type, " . $is_a->cv_id() . " , $tdist) into cvtermpath...path_id = " . $path->cvtermpath_id() . "\n" ); $path = $schema->resultset("Cv::Cvtermpath")->find_or_create( { subject_id => $object, object_id => $subject, type_id => $is_a->cvterm_id(), cv_id => $cv_id, pathdistance => -$tdist }, { key => 'cvtermpath_c1' } , ); message( "Inserting ($object,$subject, " . $is_a->cvterm_id() . " ,$cv_id , -$tdist) into cvtermpath... path_id = " . $path->cvtermpath_id() . "\n" ); } $tdist--; } $tdist = $dist; # recurse with arrayref of subjects and the object, increment the pathdistance recurse([@$subjects,$object],$type,$dist+1); }; try { $schema->txn_do($coderef); } catch { die "An error occured. Rolling back! " . $_ . "\n\n"; }; } #object } #recurse #------------------- sub objects { my($subject,$type) = @_; my @cvterm_rel; if($type){ @cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search( { subject_id => $subject, type_id => $type , } ); } else { @cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search( { subject_id => $subject } ); } my @objects = map ($_->object_id, @cvterm_rel) ; return @objects; } sub subjects { my($object,$type) = @_; my @cvterm_rel; if($type){ @cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search( { object_id => $object, type_id => $type , } ); } else { @cvterm_rel = $schema->resultset("Cv::CvtermRelationship")->search( { object_id => $object } ); } my @subjects = map ($_->subject_id, @cvterm_rel) ; return @subjects; } sub message { my $message = shift; my $default=shift; if ($opt_v || $default) { print STDOUT "$message"; } print OUT "$message" if $opt_o; } chado-1.23/bin/gmod_make_gff_from_dbxref.pl000644 000765 000024 00000010473 11723232640 021026 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; =head1 NAME gmod_make_gff_from_dbxref.pl - a tool for creating a gff3 file given a list of dbxrefs and fasta files. =head1 SYNOPSYS % gmod_make_gff_from_dbxref.pl --fasta_dir --tmp_dir \ mi|5419616|mn|TC130707| to get TC130707 =item >gi|34072055|gb|CG180994.1|CG180994 to get CG180994.1 =item >mi|12821100|mn|2_11498(1330441)| to get 2_11498. =item >123456 to get 123456 (ie, the entire line, which is the last resort). =back If you have a description line that is different from this and would like help modifying this script to work with your data, please email the schema mailing list: gmod-schema@lists.sourceforge.net. If you modify the script yourself to work with your data, please also mail the schema mailing list to report your changes so they can be included. =head1 AUTHOR Scott Cain Ecain@cshl.eduE. Copyright (c) 2007,2008 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use Bio::DB::Fasta; use File::Temp qw/ tempdir tempfile /; use Getopt::Long; use File::Copy; use File::Spec::Functions; my ( $FASTA_DIR, $TMP_DIR, $TYPE, $SOURCE ); GetOptions ( "fasta_dir:s" => \$FASTA_DIR, "tmp_dir:s" => \$TMP_DIR, "type:s" => \$TYPE, "source:s" => \$SOURCE, ); $TMP_DIR ||= "/tmp"; $TYPE ||= "region"; $SOURCE ||= "."; my %dbxref; while(<>) { chomp; my ($db, $acc) = split /\s+/; $dbxref{$db}{$acc} = 1; } my $tmp_dir = tempdir( CLEANUP => 1, DIR => $TMP_DIR ); my $tmp_fasta = tempfile( DIR => $tmp_dir ); warn "created tempdir $tmp_dir\n"; opendir(DIR, $FASTA_DIR) or die "couldn't open $FASTA_DIR: $!"; my @fasta_files = readdir(DIR); closedir(DIR); my @fasta_save; for my $fasta_file (@fasta_files) { next if $fasta_file =~ /^\./; $fasta_file = catfile( $FASTA_DIR, $fasta_file); warn "Copying $fasta_file to the temp directory\n"; copy($fasta_file, $tmp_dir) or die "couldn't move $fasta_file to $tmp_dir (a temp dir): $!"; my $fasta_db = Bio::DB::Fasta->new($tmp_dir, -makeid => \&make_id, -reindex => 1,); for my $db (keys %dbxref) { for my $acc (keys %{$dbxref{$db}}) { my $seq = $fasta_db->seq($acc); if ($seq) { my $length = length $seq; my $ninth = "ID=$acc;Name=$acc;Dbxref=$db:$acc"; print join("\t",$acc,$SOURCE,$TYPE,1,$length,".",".",".",$ninth),"\n"; $tmp_fasta->print( ">$acc\n$seq\n" ); delete $dbxref{$db}{$acc}; } } } my (undef, undef, $filename) = File::Spec->splitpath($fasta_file); warn "Finished processing $filename\n"; unlink "$tmp_dir/$filename"; } print "##FASTA\n"; seek $tmp_fasta,0,0; while(<$tmp_fasta>) { print; } #for my $db (keys %dbxref) { # for my $acc (keys %{$dbxref{$db}}) { # warn "$db\t$acc\n"; # } #} exit(0); sub make_id { my $desc_line = shift; if ($desc_line =~ /\|([^|]+?)\|$/) { #like mi|5419616|mn|TC130707| return $1; } elsif ($desc_line =~ /gb\|([^|]+)\|/) { # like gi|34072055|gb|CG180994.1|CG180994 return $1; } elsif ($desc_line =~ /\|([^(]+)\(/) { #like mi|12821100|mn|2_11498(1330441)| #to get 2_11498 return $1; } elsif ($desc_line =~ />(\S+)\s*/) { return $1; } return $desc_line; } chado-1.23/bin/gmod_materialized_view_tool.pl000644 000765 000024 00000071223 11723232722 021454 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::GMOD::DB::Tools::ETA; use Getopt::Long; =head1 NAME gmod_materialized_view_tool.pl - a tool for creating and mangaing materialized views for Chado. =head1 SYNOPSYS % gmod_materialized_view_tool.pl [options] =head1 COMMAND-LINE OPTIONS --create_view Guides user through creating a MV --update_view viewname Refreshes data in named MV --automatic Refreshes data in all MV that are out of date --dematerialize viewname Creates a true view, removing the MV --dbprofile profilename DB profile options to use (default is 'default') --list Gives a list of MV --status Gives the status of all MV --view_name Name of the view to be created --table_name Schema qualified name of the table --refresh_time Frequency at which the view should be updated --column_def List of columns with types --sql_query Select query to define table contents --index_fields List of fields to build indexes on --special_index SQL to create special indexes --yes Assume yes to any yes/no question --help Prints this documentation and quits Note that the options can be shortened. For example, '--de' is an acceptable shortening of --dematerialize. For options that have a unique first letter, the short (single hyphened) version of the option may be used, like '-a' for --automatic. =head1 DESCRIPTION WARNING: This script creates a rather large security hole that could result in data loss. Users could easily enter SQL queries through this interface that could damage your database. This tool provides several useful functions for creating and maintaining materialized views (MV) in a Chado schema. A materialized view is simple a (real) database table that has been created and contains data from a collection of other tables. It is like a view, only because it materialized, it can be indexed and searches on it will go much faster than on database views. There are at least two down sides to MVs: =over =item 1 Data syncronisity When normal tables are updated with values that are reflected in a MV, there will be a delay (usually a very noticable one) between when the normal table is updated and when the MV is updated. This tool provides the means of updating the MVs; see --automatic below. =item 2 Disk space Since MVs are actual tables, they will take up actual disk space. It is possible, depending on how the MV is created, it may take up an enormous amount of disk space. =back =head2 A Note about SQL for populating the table When constructing the SELECT clause, the names of the columns selected must match the names of the columns in the materalized view. For example, if the names of the columns are feature_id and name, but the columns being selected are feature_id and uniquename, you must use the "AS" option to rename the resulting column, like: SELECT feature_id, uniquename AS name ... If you don't do this, the affected column in the resulting table will be empty. =head1 OPTIONS =over =item --create_view Guides the user through a series of prompts to create a new materialized view. =item --update_view viewname Updates the data in a materialized view by first deleting the data in the table and then running the query that defines the data to repopulate it. =item --automatic Automatically updates all of the MVs that are currently marked out of date according to the update frequency that was specified when the MV was created. This option is very useful in a cron job to update MVs on a regular basis. =item --dematerialize viewname Takes a MV and turns into a standard view. This might be done if the database administrator desides that the downsides of the MV scheme is not working for a given view, if for example, the data in the underlying tables is changing to frequently or the MV is taking up too much disk space. =item --dbprofile The name of the DB profile to use for database connectivity. These profiles are kept in $GMOD_ROOT/conf (typically /usr/local/gmod/conf) and contain information like the database name, user name and password. The default value is 'default' which was created when the Chado database was created. =item --list Gives a list of current MVs. =item --status Gives the status of all MVs, including whether they are considered current or out of date. =item --help Prints this documetation and quits. =back =head1 NONINTERACTIVE VIEW CREATION The following options are provided to allow the creation of materialized views in a non-interactive way. If any of the below flags are omitted, you will be prompted for the appropriate values. =over =item --view_name This is the name that this tool will use later to refer to the MV as; typically it will be the same as the name of the MV in the database, but it doesn't have to be. =item --table_name The schema qualified name of the table, like "public.all_feature_names" =item --refresh_time Frequency at which the view should be updated. This can either be a number of seconds, or one of 'daily', 'weekly', or 'monthly'. =item --column_def List of columns with types, like "feature_id integer,name varchar(255),organism_id integer". =item --sql_query Select query to define table contents; see the note above about how the SQL must be written for this query. =item --index_fields List of fields to build indexes on. =item --special_index SQL to create special indexes. This allows you to create functional and full text search indexes. =item --yes Assume yes to any yes/no question =back =head1 AUTHORS Chris Carpita , with some minor additions and GMOD specific alterations from Scott Cain Ecain@cshl.eduE. Copyright (c) 2007 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut our $TABLE = "materialized_view"; our $SCHEMA = "public"; my ( $DBPROFILE, $STATUS, $LIST, $NAME, $DEMATERIALIZE, $CREATE_VIEW, $UPDATE_VIEW, $AUTOMATIC, $HELP, $VIEWNAME, $TABLENAME, $REFRESH_TIME, $COLUMNDEF, $SQLQUERY, $INDEXFIELDS, $SPECIALINDEX, $YES,); GetOptions( 'dbprofile=s' => \$DBPROFILE, 'status' => \$STATUS, 'list' => \$LIST, 'create_view' => \$CREATE_VIEW, 'update_view=s' => \$UPDATE_VIEW, 'automatic' => \$AUTOMATIC, 'dematerialize=s' => \$DEMATERIALIZE, 'view_name=s' => \$VIEWNAME, 'table_name=s' => \$TABLENAME, 'refresh_time=s' => \$REFRESH_TIME, 'column_def=s' => \$COLUMNDEF, 'sql_query=s' => \$SQLQUERY, 'index_fields=s' => \$INDEXFIELDS, 'special_index=s' => \$SPECIALINDEX, 'yes' => \$YES, 'help' => \$HELP, ) or ( system( 'pod2text', $0 ), exit -1 ); ( system( 'pod2text', $0 ), exit -1 ) if $HELP; $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ); $SCHEMA = $db_conf->schema || $SCHEMA; my $dbh = $db_conf->dbh; $dbh->{AutoCommit} = 0; my $db_message = "Viewing '" . $db_conf->name . "' database on host " . $db_conf->host; print "=" x length($db_message) . "\n"; print $db_message . "\n"; print "=" x length($db_message) . "\n\n"; our $table_exist_q = $dbh->prepare( " SELECT * FROM pg_catalog.pg_tables WHERE schemaname=? AND tablename=? " ); $table_exist_q->execute( $SCHEMA, $TABLE ); my $mv_table_exists = $table_exist_q->fetchrow_hashref; if ( $STATUS or $LIST ) { create_mv_table() unless $mv_table_exists; my $arg = $STATUS ? 'status' : 'list'; view_info($arg); } ##Begin Pre-fetch our @NAMES = (); my $sth = $dbh->prepare("SELECT name FROM $SCHEMA.$TABLE"); $sth->execute(); while ( my ($n) = $sth->fetchrow_array() ) { push( @NAMES, $n ) } our @VIEWS = (); $sth = $dbh->prepare("SELECT viewname FROM pg_views WHERE schemaname= ?"); $sth->execute($SCHEMA); while ( my ($n) = $sth->fetchrow_array() ) { push( @VIEWS, $n ) } ###End Pre-fetch if ($CREATE_VIEW) { prompt_create_mv(); } elsif ($UPDATE_VIEW) { update_mv($UPDATE_VIEW); } elsif ($AUTOMATIC) { print "Automatic update mode...\n"; my $sth = $dbh->prepare( " SELECT name FROM $SCHEMA.$TABLE WHERE EXTRACT(epoch FROM (NOW() - last_update)) >= refresh_time " ); $sth->execute(); while ( my ($name) = $sth->fetchrow_array() ) { update_mv($name); } } elsif ($DEMATERIALIZE) { dematerialize_view($DEMATERIALIZE); } else { system( 'pod2text', $0 ), exit -1; } sub create_mv_table { print "Table $SCHEMA.$TABLE does not exist, creating...\n"; $dbh->do( " CREATE TABLE $SCHEMA.$TABLE ( ${TABLE}_id SERIAL, last_update TIMESTAMP, refresh_time INT, name VARCHAR(64) UNIQUE, mv_schema VARCHAR(64), mv_table VARCHAR(128), mv_specs TEXT, indexed TEXT, query TEXT, special_index TEXT )" ) or die "Can't create table\n"; $dbh->do("GRANT SELECT ON $SCHEMA.$TABLE TO public"); $dbh->commit(); } sub view_info { my $longarg = shift; my $query = ""; my @list_cols = qw/ name mv_schema mv_table refresh_time last_update /; $query = "SELECT " . join( ", ", @list_cols ) . " FROM $SCHEMA.$TABLE" if $longarg eq "list"; $query = "SELECT name, EXTRACT(epoch FROM NOW() - last_update) AS time_passed, refresh_time FROM $SCHEMA.$TABLE" if $longarg eq "status"; my $sth = $dbh->prepare($query); print "Status of materialized views:\n" if $longarg eq "status"; print "List of materialized views:\n" if $longarg eq "list"; $sth->execute() or exit 0; my $i = 0; my $table = []; while ( my $row = $sth->fetchrow_hashref() ) { unless ($i) { $table->[0] = \@list_cols if $longarg eq "list"; $table->[0] = [ "MV Name", "Status", "Time to Update" ] if $longarg eq "status"; } my @vals = (); push( @vals, $row->{$_} ) foreach @list_cols; $table->[ $i + 1 ] = \@vals if $longarg eq "list"; if ( $longarg eq "status" ) { my $status = "Current"; my $remaining = $row->{refresh_time} - $row->{time_passed}; $status = "Outdated" if $remaining < 0; my $format_time = format_secs( abs($remaining) ); $format_time .= " PAST DUE" if $status eq "Outdated"; $table->[ $i + 1 ] = [ $row->{name}, $status, $format_time ]; } $i++; } print_table( $table, 3 ); print "\n"; exit 0; } sub print_table { my $table = shift; my $cell_spacing = shift; $cell_spacing ||= 2; my $valid = 1; my $num_cols = undef; if ( ref($table) eq "ARRAY" ) { foreach my $row (@$table) { $valid = 0 unless ref($row) eq "ARRAY"; $num_cols = scalar @$row unless defined $num_cols; unless ( ( scalar @$row ) == $num_cols ) { print "This row has " . scalar(@$row) . " entries, when the number of columns should be $num_cols:\n"; print join( "\t", @$row ); $valid = 0; } foreach my $col_entry (@$row) { $valid = 0 if ref($col_entry); } } } else { $valid = 0 } die "Argument to print_table() must be a rectangular two-dimensional hashref, with values being scalars\n" unless $valid; my $col_widths = []; my $format = ""; for ( my $i = 0 ; $i < $num_cols ; $i++ ) { my @colvals = (); for ( my $j = 0 ; $j < @$table ; $j++ ) { push( @colvals, $table->[$j]->[$i] ); } my $max_length = 0; foreach (@colvals) { $max_length = length($_) if length($_) > $max_length; } $col_widths->[$i] = $max_length + $cell_spacing; if ( $i == ( $num_cols - 1 ) ) { $format .= '%s' . "\n"; } else { $format .= "%-" . ( $max_length + $cell_spacing ) . "s"; } } foreach my $row (@$table) { printf( $format, @$row ); } } sub prompt_create_mv { my $confirm = 0; #Create a new materialized view. print "\n\n"; print "=================================\n"; print "Creating a new materialized view!\n"; print "=================================\n\n"; my ($remove_view, $location, $name); while ( !$confirm ) { $name = validate( { resp => $VIEWNAME, prompt => "Give your materialized view a name (word characters only): ", test => sub { my $t = shift; my %exists = (); foreach my $n (@NAMES) { $exists{$n} = 1 } if ( $exists{$t} ) { print "MV '$_' already exists! Current names taken: " . join( ", ", @NAMES ) . "\n"; die "$VIEWNAME already exists and must be explicitly removed with '--dematerialize $VIEWNAME'" if ($VIEWNAME); } unless ( $t =~ /^\w+$/ ) { print "Invalid format, use word characters only($t)\n"; } ( !$exists{$t} && $t =~ /^\w+$/ ); } } ); $location = validate( { resp => $TABLENAME, prompt => "Where will this MV be located? (schemaname.tablename): ", regexp => '^\w+\.\w+$' } ); my ( $mv_schema, $mv_table ) = $location =~ /(\w+)\.(\w+)/; for my $view (@VIEWS) { if ( "$SCHEMA.$view" eq $location ) { $remove_view = validate( { resp => $YES ? 'y' : '', prompt => "A view with this name already exists; do you want" ." to replace it\nwith a materialized view? [y|n] ", regexp => '^y|n$' } ); } } if ( $remove_view and $remove_view ne 'y' ) { print "This (non-materialized) view already exists, and you won't" ."let me remove it.\nBye!\n"; exit(0); } my $refresh_time = validate( { resp => $REFRESH_TIME, prompt => "How often, in seconds, should the MV be refreshed?\n" ."You can also type 'daily', 'weekly', 'monthly' (30 days), or 'yearly' (365 days): ", regexp => '^(?i:(\d+)|(daily)|(weekly)|(monthly)|(yearly))$' } ); unless ( $refresh_time =~ /^\d+$/ ) { if ( $refresh_time =~ /daily/i ) { $refresh_time = 60 * 60 * 24; } elsif ( $refresh_time =~ /weekly/i ) { $refresh_time = 60 * 60 * 24 * 7; } elsif ( $refresh_time =~ /monthly/i ) { $refresh_time = 60 * 60 * 24 * 30; } elsif ( $refresh_time =~ /yearly/i ) { $refresh_time = 60 * 60 * 24 * 365; } print "Using refresh_time of $refresh_time seconds\n"; } my $mv_specs = validate( { resp => $COLUMNDEF, prompt => "Enter specifications for the materialized view, OR provide a file in which\n" ."the specs are written ('? for help): ", test => sub { my $t = $_[0]; if ( -f $t ) { print "'$t' is a valid file, reading into specifications variable...\n"; print "File '$t' contents: "; $t = slurp_file($t); print $t . "\n"; } if ( $t =~ /^(\w+(\s+[\w)('"]+)+\s*,?\s*)+\s*$/ ) { $_[0] = $t; return 1; } elsif ( $t =~ /^\s*[\?]\s*$/ ) { print "This is supposed to be the stuff in-between parenthesis in a CREATE TABLE query.\nYou should use the same column names that would result from the MV query\nFor Example: \"member VARCHAR(32), member_desc TEXT, has_parent TINYINT DEFAULT 0"; } else { print "'$t' is not a valid format OR existing file\n"; } return 0; } } ); my $query = validate( { resp => $SQLQUERY, prompt => "Enter the SQL query for the materialized view,\n" ."or a file containing only the query: ", test => sub { my $t = @_[0]; if ( -f $t ) { print "'$t' is a valid file, reading into query variable...\n"; print "File '$t' contents: "; $t = slurp_file($t); print "$t\n"; } if ( $t =~ /^\s*SELECT.*FROM[^?]+$/i ) { $_[0] = $t; return 1; } else { print "'$t' is not a valid file, or it is not valid SQL. You can't use placeholders, by the way.\n"; } return 0; } } ); my $indexes = validate( { resp => $INDEXFIELDS, prompt => "Enter a comma separated list of fields to index (or return for none):", test => sub { my $t = @_[0]; if ( $t =~ /^[A-Za-z,_]*$/ ) { $_[0] = $t; return 1; } print "'$t' is not valid; please make sure that you use only the name of the fields separated by commas.\n"; return 0; } } ); my $special_indexes = validate( { resp => $SPECIALINDEX, prompt => "Enter the SQL queries for special indexes,\n" ."or a file containing only the query (or return for none): ", test => sub { my $t = @_[0]; if ( $t eq "") { $_[0] = ''; return 1; } if ( -f $t ) { print "'$t' is a valid file, reading into query variable...\n"; print "File '$t' contents: "; $t = slurp_file($t); print "$t\n"; } if ( $t =~ /^\s*CREATE.*INDEX[^?]+$/i ) { $_[0] = $t; return 1; } else { print "'$t' is not a valid file, or it is not valid SQL. You can't use placeholders, by the way.\n"; } return 0; } } ); my $insert_q = $dbh->prepare( "INSERT INTO $SCHEMA.$TABLE (last_update, refresh_time, name, mv_schema, mv_table, mv_specs, query, indexed, special_index ) VALUES (NOW(), ?, ?, ?, ?, ?, ?, ?, ?)" ); print "\n\nConfirm that the following is correct:\n"; print "Name: $name\nLocation: $mv_schema.$mv_table\n"; print "Refresh Time (sec): $refresh_time\n"; print "MV creation query: CREATE TABLE $mv_schema.$mv_table ( $mv_specs )\n"; print "Query: $query\n"; print "Indexes on: $indexes\n"; print "Special index query: $special_indexes\n"; my $resp = validate( { resp => $YES ? 'y' : '', prompt => "Enter 'y' to confirm, 'n' to re-enter data: ", regexp => '^y|n$' } ); $confirm = 1 if $resp eq 'y'; if ($confirm) { $insert_q->execute( $refresh_time, $name, $mv_schema, $mv_table, $mv_specs, $query, $indexes, $special_indexes ) or die "MV insert error: " . $dbh->errstr . "\n"; $NAME = $name; } } $dbh->commit(); if ($remove_view) { print "Removing the view $location\n"; $dbh->do("DROP VIEW $location") or die "View drop error: ".$dbh->errstr."\n"; } #drop view if present #populate materialized view (using 'force') update_mv($name); $dbh->commit(); print "MV Entered into the registry and created.\n"; } sub slurp_file { my $filename = shift; open( FH, $filename ) or return; my $buffer = ""; $buffer .= $_ while (); close FH; $buffer =~ s/[\n\r]/ /gs; return $buffer; } sub update_mv { my $name = shift; my $sth = $dbh->prepare("SELECT * FROM $SCHEMA.$TABLE WHERE name=?"); $sth->execute($name); my $row = $sth->fetchrow_hashref(); unless ($row) { print "The MV with the name '$name' does not exist. Here is a list of existing MV's: "; print join( ", ", @NAMES ); print "\n"; return; } my ( $mv_schema, $mv_table, $mv_specs ) = ( $row->{mv_schema}, $row->{mv_table}, $row->{mv_specs} ); $table_exist_q->execute( $mv_schema, $mv_table ); my $exists = $table_exist_q->fetchrow_hashref; my $special_indexes = $row->{special_index}; my $indexed_string = $row->{indexed}; my @indexed = split /\s*,\s*/, $indexed_string; unless ($exists) { print "Creating materialized view '$name' for the first time at $mv_schema.$mv_table...\n"; my $create_q = "CREATE TABLE $mv_schema.$mv_table ($mv_specs)"; print $create_q . "\n"; $dbh->do($create_q) or die "Couldn't create materialized view\n"; $dbh->do("GRANT SELECT ON $mv_schema.$mv_table TO public"); print "MV table created.\n"; $dbh->do("SET SEARCH_PATH=$mv_schema"); foreach (@indexed) { next unless /\w/; $dbh->do("CREATE INDEX ${mv_table}_$_ ON $mv_table($_)"); } if ($special_indexes) { $dbh->do($special_indexes) or die "CREATE index query failed:\n" .$special_indexes. "\n".$dbh->errstr; } $dbh->commit(); } my $query = $row->{query}; my $count_query = $query; $count_query =~ s/SELECT.*\bFROM\b/SELECT COUNT(*) FROM/si; # print "Using this query to count total entries: $count_query\n"; $sth = $dbh->prepare($count_query); $sth->execute(); my ($total) = $sth->fetchrow_array(); my $eta = Bio::GMOD::DB::Tools::ETA->new(); $eta->interval(0.3); $eta->target($total); print "Total # of entries in MV '$name': $total\n"; $sth = $dbh->prepare($query); $sth->execute(); my $i = 0; $eta->begin(); print "Deleting current entries in MV '$name'...\n"; $dbh->do("DELETE FROM $mv_schema.$mv_table"); $dbh->do("SET SEARCH_PATH=$mv_schema"); #find any indexes that belong to this table drop_indexes($mv_schema,$mv_table); print "Inserting new values into MV '$name'...\n"; while ( my $entry = $sth->fetchrow_hashref() ) { my @valid_cols = extract_cols_from_specs($mv_specs); my @phs = (); foreach (@valid_cols) { push( @phs, "?" ) } my $query = "INSERT INTO $mv_schema.$mv_table ( " . join( ", ", @valid_cols ) . " ) "; $query .= " VALUES ( " . join( ",", @phs ) . " )"; my $insq = $dbh->prepare($query); my @values = (); foreach (@valid_cols) { push( @values, $entry->{$_} ); } $insq->execute(@values); $i++; $eta->update_and_print($i); } $dbh->do("SET SEARCH_PATH=$mv_schema"); foreach (@indexed) { next unless /\w/; $dbh->do("CREATE INDEX ${mv_table}_$_ ON $mv_table($_)"); } if ($special_indexes) { $dbh->do($special_indexes) or die "CREATE index query failed:\n" .$special_indexes. "\n".$dbh->errstr; } my $timeupq = $dbh->prepare("UPDATE $SCHEMA.$TABLE SET last_update=NOW() WHERE name=?"); $timeupq->execute($name); print "\nUpdate of MV '$name' successful.\n"; $dbh->commit(); } sub dematerialize_view { my $view = shift; my $really = validate( { resp => $YES ? 'y' : '', prompt => "Really remove the materialized view? Enter 'y' to confirm, 'n' to exit: ", regexp => '^y|n$' } ); if ( $really ne 'y' ) { print "OK, exiting instead.\n"; exit(0); } #get table and schema name from view name my $get_the_pieces_query = $dbh->prepare(" SELECT mv_schema,mv_table,mv_specs,query FROM materialized_view WHERE name = ? "); $get_the_pieces_query->execute($view) or die "problem with query ". $dbh->errstr; my ($schema,$table,$columns,$query) = $get_the_pieces_query->fetchrow_array; #determine if the table already exists, if not, exit my $exists_query = $dbh->prepare("SELECT count(*) FROM pg_tables WHERE schemaname=? AND tablename=?"); $exists_query->execute($schema,$table); my ($exists) = $exists_query->fetchrow_array; unless ($exists) { print "The table $schema.$table doesn't exist, so there is nothing to dematerialize.\n"; exit(0); } #drop indexes and table drop_indexes_and_table($schema,$table); #create index from mv_table, mv_specs, query #fix column spec my @cols = split /,/, $columns; my @columns; for my $col (@cols) { $col =~ /^\s*(\w+)\s+/; push @columns, $1; } $columns = join(',', @columns); my $create_view_query = "CREATE VIEW $schema.$table ($columns) AS $query"; $dbh->do($create_view_query) or die "problem creating view: ".$dbh->errstr; #this used to set the update time to 20 years rather than deleting the #entry. Now it just deletes the entry my $update_query = $dbh->prepare( "DELETE FROM materialized_view WHERE name = ?"); $update_query->execute($view) or die "problem delete deleted MV from materialized_view table: ".$dbh->errstr; $dbh->commit(); return; } sub drop_indexes_and_table { my $schema = shift; my $table = shift; drop_indexes($schema,$table); $dbh->do("DROP TABLE $schema.$table") or die "problem dropping table ".$dbh->errstr; return; } sub drop_indexes { my $schema = shift; my $table = shift; my $index_query = $dbh->prepare( 'SELECT indexname FROM pg_indexes WHERE tablename=? AND schemaname=?'); $index_query->execute( $table, $schema ); while ( my $hashref = $index_query->fetchrow_hashref ) { print "Dropping index $schema.$$hashref{indexname}\n"; my $query = "DROP INDEX $schema.$$hashref{indexname}"; $dbh->do($query); } return; } sub extract_cols_from_specs { my $specs = shift; $specs =~ s/\(\s*\d+\s*,\s*\d+\s*\)//g; my @items = split /,/, $specs; my @cols = (); foreach (@items) { my ($name) = /^\s*(\w+)/; push( @cols, $name ); } return @cols; } sub validate { my $args = shift; my $valid = 0; my $resp = $args->{resp} || ""; my $error_msg = $args->{regexp_error}; $error_msg ||= "Invalid format, try again"; while ( !$valid ) { unless ($resp) { print "\n" . $args->{prompt}; $resp = ; chomp $resp; } if ( exists( $args->{test} ) ) { $valid = 1 if $args->{test}->($resp); } else { $valid = 1 if $resp =~ /$args->{regexp}/; print $error_msg unless $valid; } } return $resp; } sub format_secs { my $secs = int(shift); my $mins = 0; my $hours = 0; my $days = 0; if ( $secs > 60 ) { $mins = int( $secs / 60 ); $secs -= $mins * 60; } if ( $mins > 60 ) { $hours = int( $mins / 60 ); $mins -= $hours * 60; } if ( $hours > 24 ) { $days = int( $hours / 24 ); $hours -= $days * 24; } foreach ( $mins, $secs, $hours ) { $_ = "0" . $_ if ( $_ < 10 ); } my $formatted = ""; $formatted = "$days days, " if $days > 0; $formatted .= "$hours:$mins:$secs"; return $formatted; } chado-1.23/bin/gmod_sort_gff3.pl000755 000765 000024 00000005212 11723232741 016606 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Getopt::Long; my ($INFILE, $OUTFILE); GetOptions( 'infile=s' => \$INFILE, 'outfile=s' => \$OUTFILE, ) or ( system( 'pod2text', $0 ), exit -1 ); die "You must supply an input file name via --infile\n" unless $INFILE; $OUTFILE ||='sorted.gff'; open OUT, ">", $OUTFILE or die "couldn't open $OUTFILE for writing:$!\n"; open IN, "<", $INFILE or die "couldn't open $INFILE for reading:$!\n"; my %parent_hash; my %child_hash; # has ID (of parent) as key # and anon array of GFF3 lines as value while () { my $line = $_; my @la = split "\t", $line; if (@la != 9) { #not a GFF line, so let it though unmolested print OUT $line; } else { if ($la[8] =~ /Parent=([^;]+)/ ) { my $id = $1; if ($parent_hash{$id}) { print OUT $line; } else { push @{ $child_hash{$id} }, $line; } } elsif ($la[8] =~ /ID=([^;]+)/ ) { my $id = $1; if ($parent_hash{$id}) { # die "This ID: $1 has appeared twice in this GFF file\n"; # can't die here; CDS features can share IDs # (though the chado bulk loader doesn't support that yet). } else { print OUT $line; for my $c_line ( @{ $child_hash{$id} } ){ print OUT $c_line; } $child_hash{$id} = 1; } $parent_hash{$id} = 1; } else { print OUT $line; } } } for my $key (keys %child_hash) { if ($child_hash{$key} != 1 ) { print "Unresolved child relationship for this line:\n"; for my $line (@{ $child_hash{$key} }) { print "$line\n"; } } } close OUT; close IN; =pod =head1 NAME gmod_sort_gff3.pl - Sorts a GFF3 file to put lines with Parent tags after their parent. =head1 SYNOPSIS % gmod_sort_gff3.pl --infile =head1 COMMAND-LINE OPTIONS --infile Name of the input gff3 file (required) --outfile Name of the output gff3 file (default: sorted.gff) =head1 DESCRIPTION This is a very simple (and only lightly tested) script for sorting gff3 files so that all lines that have Parent tags come after the line that contains the parent ID tag. Files thusly sorted are required for the GMOD chado bulk loader, L. =head1 AUTHORS Scott Cain Ecain@cshl.orgE Copyright (c) 2006 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut chado-1.23/bin/gmod_update_chado.pl000755 000765 000024 00000004341 11723232761 017336 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use Getopt::Long; #use lib '/home/cain/cvs_stuff/schema/chado/lib'; #use lib '/home/scott/cvs_stuff/schema/chado/lib'; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use ExtUtils::MakeMaker; #to get prompt =head1 NAME $0 - updates the schema of a Chado database if necessary =head1 SYNOPSIS % gmod_update_chado.pl [options] =head1 COMMAND-LINE OPTIONS --force Update the schema without prompt --dbprofile Which database profile to use for updating =head1 DESCRIPTION =head1 AUTHOR Scott Cain Escain@cpan.orgE Copyright (c) 2011 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ($FORCE, $DBPROFILE, ); GetOptions( 'force' => \$FORCE, 'dbprofile=s' => \$DBPROFILE, ) or ( system( 'pod2text', $0 ), exit -1 ); $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new(); my $version = $gmod_conf->version(); my $gmod_root = $gmod_conf->gmod_root(); my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf, $DBPROFILE); my $dbh = $db_conf->dbh(); my $current_version = `gmod_chado_properties.pl --version --dbprof $DBPROFILE`; chomp $current_version; if ($current_version >= $version) { print "This instance of the Chado schema does not need updating.\n"; exit(0); } if (!defined $FORCE) { print <user; my $dbport = $db_conf->port; my $dbhost = $db_conf->host; my $dbname = $db_conf->name; my $syscommand = "cat $path | psql -U $dbuser -p $dbport -h $dbhost $dbname"; system($syscommand) == 0 or die "failed updating database"; #now update the schema version in the chadoprop table system("gmod_chado_properties.pl --version $version --force --dbprof $DBPROFILE"); print "Updating $dbname complete.\n"; exit(0); chado-1.23/bin/interactions2SIF.pl000755 000765 000024 00000005036 11723233014 017030 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use DBI; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Data::Dumper; use Getopt::Long; =head1 NAME interactions2SIF.pl - Export Chado interaction information in SIF format =head1 SYNOPSIS % interactions2SIF..pl [options] > out.sif =head1 DESCRIPTION Reads the feature_relationship table to find interactions. Outputs those interactions in Simple Interaction File format (used by Cytoscape). =head1 COMMAND-LINE OPTIONS If no arguments are provided, dump_gff3.pl will dump all features for the default organism in the database. The command line options are these: =over 4 =item * feature_id Refines the search to nodes related to this feature_id =item * cv Refines the search to edges that have terms that come fromhis =back =head1 AUTHOR Ben Faga Efaga@cshl.edu Copyright (c) 2005 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut my ( $FEATURE_ID, $CV ); GetOptions( 'feature_id:s' => \$FEATURE_ID, 'cv:s' => \$CV, ); my $gmod_conf = $ENV{'GMOD_ROOT'} ? Bio::GMOD::Config->new( $ENV{'GMOD_ROOT'} ) : Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, 'default' ); my $dbh = $db_conf->dbh; my $select_sql = qq[ select f1.name as subject_name, f1.uniquename as subject_uniquename, cvt.name as cvterm, f2.name as object_name, f2.uniquename as object_uniquename ]; my $from_sql = qq[ from feature f1, feature f2, feature_relationship fr, cvterm cvt ]; my $where_sql = qq[ where f1.feature_id = fr.subject_id and f2.feature_id = fr.object_id and cvt.cvterm_id = fr.type_id ]; if ($FEATURE_ID) { $where_sql .= " and (f1.feature_id = $FEATURE_ID or f2.feature_id = $FEATURE_ID) "; } if ($CV) { $from_sql .= ", cv "; $where_sql .= " and cvt.cv_id = cv.cv_id and cv.name = '$CV' "; } my $sql_str = $select_sql . $from_sql . $where_sql; my $sth = $dbh->prepare($sql_str); $sth->execute(); while ( my $hashref = $sth->fetchrow_hashref ) { my $s_name = $$hashref{subject_name}; my $s_uniquename = $$hashref{subject_uniquename}; my $o_name = $$hashref{object_name}; my $o_uniquename = $$hashref{object_uniquename}; my $cvterm = $$hashref{cvterm}; $s_name = $s_uniquename unless $s_name; $o_name = $o_uniquename unless $o_name; print join( "\t", ( $s_name, $cvterm, $o_name, ) ), "\n"; } chado-1.23/bin/load_ncbi_taxonomy.pl000644 000765 000024 00000043741 11727656636 017603 0ustar00cainstaff000000 000000 =head1 NAME load_ncbi_taxonomy.pl =head1 DESCRIPTION Usage: perl load_ncbi_taxonomy.pl -H [dbhost] -D [dbname] [-vt] -i file populate a chado database with organism information (see the organism module and phylogeny module) =head2 Prerequisites =over 3 =item 1. Load taxonomy cvterms see load_taxonomy_cvterms.pl =item 2. Download NCBI taxonomy files ftp://ftp.ncbi.nih.gov/pub/taxonomy/ Save these 2 files in the same dir. of this script names.dmp nodes.dmp =item 3. Download a taxon_id list from NCBI Optional. This filter file will include the taxons you would like to store in your tree (see option -i). Without this file the entire NCBI taxonomy will be stored in your database! =back =head2 parameters =over 9 =item -H hostname for database =item -D database name =item -i input file [optional] List taxonomy ids to be stored. The rest of the taxons in the name and node files will be excluded. http://www.ncbi.nlm.nih.gov/sites/entrez?db=Taxonomy and search by taxid (e.g. txis4070[Subtree] ) =item -n phylotree name [optional] name you phylotree. Default = 'NCBI taxonomy tree' =item -v verbose output =item -t trial mode. Do not perform any store operations at all. =item -g GMOD database profile name (can provide host and DB name) Default: 'default' =item -u username. Override username in gmod_config =item -d driver. Override driver name in gmod_config =item -p password. Override password in gmod_config =back The script stores ncbi taxonomy in chado organism and phylogeny modules This script works with SGN's public schema (chado compatible) and accesse the following tables: =over 7 =item db (DB:NCBI_taxonomy) =item dbxref (genbank taxon ids will be stored in the accession field) =item organism =item organism_dbxref =item phylotree =item phylonode =item phylonode_organism =back For storing phylonodes a new phylotree will be stored with the name 'NCBI taxonomy tree'. Each organism will get a phylonode id and will be stored in a tmp table, since each phylonode (except for the root) has a parent_phylonode_id, which is an internal foreign key. Next each phylonode will get a left and right indexes, which are calculated by walking down the entire tree structure (see article by Aaron Mackey: http://www.oreillynet.com/pub/a/network/2002/11/27/bioconf.html?page=2). Only after each phylonode will have calculated indexes, the phylonode table will be populated from the tmp table. =head1 AUTHOR Adapted from GMOD load_taxonomy.pl: #$Id: load_taxonomy.pl,v 1.1 2006/04/17 05:22:22 allenday Exp $ #download from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ by Naama Menda =head1 VERISON AND DATE Version 2.1, March 2012. =head1 TODO =cut #! /usr/bin/env perl use strict; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; use Try::Tiny; use Getopt::Std; our ($opt_H, $opt_D, $opt_v, $opt_t, $opt_i, $opt_p, $opt_g, $opt_u, $opt_n, $opt_d); getopts('H:D:i:p:g:u:n:d:tv'); my $dbhost = $opt_H; my $dbname = $opt_D; my $infile = $opt_i; my $phylotree_name= $opt_n || 'NCBI taxonomy tree'; my $user = $opt_u; my $pass = $opt_p; my $driver = $opt_d; my $port; my $DBPROFILE = $opt_g ; print "H= $opt_H, D= $opt_D, v=$opt_v, t=$opt_t, i=$opt_i \n"; my ($dbh, $schema); ################ if (!($opt_H and $opt_D) ) { $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new() ; my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ) ; $dbhost ||= $db_conf->host(); $dbname ||= $db_conf->name(); $driver ||= $db_conf->driver(); $port= $db_conf->port(); $user= $db_conf->user(); $pass= $db_conf->password(); } ################### if (!$dbhost && !$dbname) { die "Need -D dbname and -H hostname arguments.\n"; } my $dsn = "dbi:$driver:dbname=$dbname"; $dsn .= ";host=$dbhost"; $dsn .= ";port=$port" if $port; $schema= Bio::Chado::Schema->connect( $dsn, $user, $pass||''); $dbh=$schema->storage->dbh(); if (!$schema || !$dbh) { die "No schema or dbh is avaiable! \n"; } my $sth; my %okay_level = map { chomp; $_=>1 } grep { $_ !~ /^\#/ } ; my %node = (); my %seen = (); my %seq = ( db => 'db_db_id_seq', organism => 'organism_organism_id_seq', dbxref => 'dbxref_dbxref_id_seq', organism_dbxref => 'organism_dbxref_organism_dbxref_id_seq', phylotree=> 'phylotree_phylotree_id_seq', phylonode=> 'phylonode_phylonode_id_seq', phylonode_organism => 'phylonode_organism_phylonode_organism_id_seq', ); #Create and retrieve NCBI Tax database my $db_name= 'DB:NCBI_taxonomy'; my $db= $schema->resultset("General::Db")->find_or_create( { name => $db_name } ); $db->url('ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id='); $db->urlprefix('http://'); $db->update(); my $db_id = $db->get_column('db_id'); ######## #Fetch last database ids of relevant tables for resetting in case of rollback my %maxval=(); foreach my $key( keys %seq) { my $id_column= $key . "_id"; my $table = $key; my $query = "SELECT max($id_column) FROM $table"; $sth=$dbh->prepare($query); $sth->execute(); my ($next) = $sth->fetchrow_array(); $maxval{$key}= $next; } #store a new phylotree for NCBI taxonomy my $tree_accession= 'taxonomy'; my $tree_dbxref = $schema->resultset("General::Dbxref")->find_or_create( { accession => $tree_accession, db_id => $db_id, } ); my $tree_dbxref_id = $tree_dbxref->get_column('dbxref_id'); my $phylotree = $schema->resultset('Phylogeny::Phylotree')->find_or_create( { dbxref_id => $tree_dbxref_id, name => $phylotree_name, } ); my $phylotree_id = $phylotree->phylotree_id(); message( "Created a new phylotee with id $phylotree_id\n\n\n", 1); #remove all existing phylonodes for this tree and reset the database sequence $schema->resultset('Phylogeny::Phylonode')->search( { phylotree_id => $phylotree_id })->delete(); $maxval{phylonode} = set_maxval( 'phylonode' ); $maxval{phylonode_organism} = set_maxval( 'phylonode_organism' ); my %tax_file=() ; # hash for storing taxonomy ids from -i if ($infile) { open (INFILE, "<$infile") || die "Can't open infile $infile!!\n\n"; # while (my $t_id = ) { chomp $t_id; $tax_file{$t_id} = $t_id; } } my $error = "load_taxonomy.err"; open (ERR, ">$error") || die "Can't open error file for writing ($error)!\n"; ####################### ########################## #read in the taxonomy tree open( NODE, "nodes.dmp" ); while ( my $line = ) { my ( $id, $parent, $level ) = split /\s+\|\s+/, $line; ###message("id = $id, parent = $parent, level = $level\n",1); next unless $okay_level{ $level }; # check for data consistency if ($infile) { if ( exists $tax_file{$id} ) { # check if the parent is in the taxfile if ( $parent && !(exists $tax_file{ $parent } ) ) { message ("Parent $parent for tax_id $id does not exist in your input file ! This means $id is your root, or you need to check your input!\n",1); } } else{ next(); } # skip nodes not in tax_file } ###message("STORING NODE is node hash\n",1); $node{ $id }{ 'parent_taxid' } = $parent; $node{ $id }{ 'self_taxid' } = $id; $node{ $id }{ 'level' } = $level; } close( NODE ); open( NAME, "names.dmp" ); while ( my $line = ) { #next unless $line =~ /scientific name/; my ( $id, $name ) = split /\s+\|\s+/, $line; ###message("NAMES: id = $id, name = $name\n",1); next unless $node{ $id }; #skip nodes if ( $line =~ /scientific name/) { ###message("Storing scientific name '$name'\n",1); $node{ $id }{ 'name' } = $name; $node{ $id }{ 'name' } .= " Taxonomy:$id" if $seen{ $name }++; } elsif ( $line =~ /common name/) { # genbank common names push(@{ $node{ $id }{ 'common_name' } } , $name); push(@{ $node{$id}{ 'synonyms' } }, $name); } elsif ( $line =~ /synonym/ ) { push @{ $node{$id}{ 'synonyms' } }, $name; } } close( NAME ); foreach my $id ( keys %node ) { ###message("Looking at id $id in node hash... level = " . $node{ $id }{'level'} . "\n",1); my $parent_taxid = $node{ $id }{ 'parent_taxid' } ; if (!$tax_file{$parent_taxid}) { message("No parent id found for species " . $node{ $id }{ 'name' } . " (id = $id) !! This means your species is the root node, or there is an error in yout input file \n", 1); } if ( $node{ $id }{ 'level' } eq 'species' ) { # load the genus name from the parent_taxid if (!$tax_file{$parent_taxid}) { die "No parent id found for species " . $node{ $id }{ 'name' } . " (id = $id) !! Check your input file !!\n" ; } $node{ $id }{ 'genus' } = $node{ $parent_taxid }{ 'name' }; $node{ $id }{ 'species' } = $node{ $id }{ 'name' }; ###message("FOUND SPECIES: " . $node{ $id }{ 'name' } . " genus = " . $node{ $id }{ 'genus' } . "\n" , 1); } else { ###message("FOUND NODE NAME: " . $node{ $node{ $id }{ 'parent_taxid' }}{ 'name' } . "( genus = " . $node{ $id }{ 'level' } . " species = " . $node{ $id }{ 'name' } . "\n",1); $node{ $id }{ 'genus' } = $node{ $id }{ 'level' }; $node{ $id }{ 'species' } = $node{ $id }{ 'name' }; } } ########################## #use temp table for generating the phylonode_ids $dbh->do("CREATE TEMP TABLE tmp_phylonode ( phylonode_id integer NOT NULL PRIMARY KEY, phylotree_id integer , organism_id integer, parent_phylonode_id integer, left_idx integer, right_idx integer, type_id integer)" ); ############################################ my $next_phylonode_id= $maxval{'phylonode'} +1 ; my %phylonode=(); my $node_count=0; my $coderef = sub { my $root_id; my $organism_id = $maxval{'organism'}; NODE: foreach my $id ( keys %node ) { ###### #Store the genbank taxon_id in dbxref and in organism_dbxref # my $genbank_taxon_accession= $node{ $id }{ 'self_taxid' }; if (!$genbank_taxon_accession) { print ERR "SKIPPING: No record found for genbank taxon id $id! Check your infile !\n"; next NODE; } my $dbxref = $schema->resultset("General::Dbxref")->find_or_create( { accession => $genbank_taxon_accession, db_id => $db_id, }); my $dbxref_id = $dbxref->get_column('dbxref_id'); my $abbreviation; if ($node{ $id }{level} eq 'species' ) { ###message("Found species " . $node{ $id }{ 'species' } . "\n" ,1) ; if ( $node{ $id }{ 'species' } =~ m/(.*)\s(.*)/ ) { my $gen=$1; my $sp=$2; $abbreviation= uc( substr( $gen ,0, 1 ) ) . "." . $sp; } } my $common_name; my $c= @{ $node{$id}{'common_name'} } if (defined @{ $node{$id}{'common_name'}}); $common_name = join("," , @{ $node{ $id }{ 'common_name' } }) if $c; my $genus = $node{ $id }{ 'genus' } ; my $species = $node{ $id }{ 'species' } ; my ($organism, $update, $insert); ###message("looking at organism $genbank_taxon_accession, genus=$genus, species=$species\n"); if (!$genus || !$species) { die "NO GENUS OR SPECIES FOUND FOR tax_id $genbank_taxon_accession! Check your input file! \n" ; } $organism = $schema->resultset('Organism::Organism')->search( { species => {'ilike' => $species } })->single; # lookup is by species only . NCBI species should be unique! if (!$organism) { #maybe the organism is already loaded with the ncbi taxonomy id, but the species name has changed? my $organism_dbxref = $dbxref->organism_dbxrefs->single; $organism= $organism_dbxref->organism if $organism_dbxref; } if (!$organism) { #create a new empty row object $organism = $schema->resultset('Organism::Organism')->new({}); $insert=1; } else { $update = 1; } $organism->set_column(genus => $node{ $id }{ 'genus' } ); $organism->set_column(species => $node{ $id }{ 'species' } ); $organism->set_column(abbreviation => $abbreviation ); $organism->set_column(common_name => $common_name ); if ($update) { $organism->update(); message( "*Updating organism " . $organism->get_column('organism_id') . " (species=" . $organism->species . ")\n", 1); } if ($insert) { $organism->insert(); message("New organism " . $organism->get_column('organism_id') . " (species=" . $organism->species . ")\n", 1); } my $organism_id= $organism->get_column('organism_id'); ########################################### #store the organism synonyms foreach (@{$node{ $id }{synonyms} } ) { $organism->create_organismprops( { synonym => $_ }, { autocreate => 1} , ); message( $node{ $id }{name} . " LEVEL=( " . $node{ $id }{level} . ") Synonym is $_ \n" ); } #################################################################### my $organism_dbxref = $schema->resultset('Organism::OrganismDbxref')->find_or_create( { organism_id => $organism_id, dbxref_id => $dbxref_id, }, ); #get the cvterm_id of the taxonomy level my $level= $node{ $id }{level}; my $taxonomy_cv = $schema->resultset("Cv::Cv")->find( { name => 'taxonomy' } ); if (!$taxonomy_cv) { die "No cv found for 'taxonomy' . Did you run 'load_taxonomy_cvterms.pl' ? See the perldoc for more details \n\n"; } my ($level_cvterm) = $taxonomy_cv->find_related("cvterms" , { name => $level } ) ; my $level_id = $level_cvterm->get_column("cvterm_id") if $level_cvterm ; if (!$level_cvterm) { print ERR "No cvterm found for type $level! Check your cvterm table for loaded taxonomy (cv name should be 'taxonomy') \n\n"; die "No cvterm found for type $level! Check your cvterm table for loaded taxonomy (cv name should be 'taxonomy') . See perldoc load_taxonomy_cvterms.pl \n\n"; } #store a new phylonode_id + phylonode_organism. This is necessary for storing later the parent_phylonode_id # and eventuay the left_idx and right_idx. $phylonode{ $id }{ 'phylonode_id' } = $next_phylonode_id++; $phylonode{ $id }{ 'organism_id' } = $organism_id; $phylonode{ $id }{ 'parent_taxid' } = $node{ $id }{ 'parent_taxid' }; $phylonode{ $id }{ 'type_id' } = $level_id ; } #now that all the organisms are stored, we can store the relationships (=phylonodes) my %stored=(); my %test=(); foreach my $id (keys %phylonode ) { my $phylonode_id = $phylonode{ $id }{ 'phylonode_id' }; my $organism_id = $phylonode{ $id }{ 'organism_id' } ; my $parent_phylonode_id = $phylonode{ $phylonode{ $id }{ 'parent_taxid' } }{ 'phylonode_id' } || 'NULL'; $root_id = $phylonode_id if $parent_phylonode_id eq 'NULL'; if ($parent_phylonode_id eq 'NULL') { message("organism $organism_id does not have a parent! (phylonode_id = $phylonode_id)\n", 1); } my $type_id = $phylonode{ $id }{'type_id'} || 'NULL'; push @{$test{$parent_phylonode_id} } , $phylonode_id ; my $insert="INSERT INTO tmp_phylonode (phylotree_id, phylonode_id, parent_phylonode_id, organism_id, type_id) VALUES ($phylotree_id,$phylonode_id, $parent_phylonode_id, $organism_id, $type_id)"; $node_count++; $dbh->do($insert); } #now walk through the tmp table and update the indexes message( "the root_id is $root_id\n",1); if (!$root_id) { die "No organism id found for root node! \n" ; } walktree($root_id, 1); message( "Updating the phylonode and phylonode_organism tables\n\n"); my @updates=( "INSERT INTO phylonode (phylonode_id, phylotree_id, parent_phylonode_id, left_idx, right_idx, type_id) SELECT phylonode_id, phylotree_id, parent_phylonode_id, left_idx, right_idx, type_id FROM tmp_phylonode", "INSERT INTO phylonode_organism (phylonode_id, organism_id) SELECT phylonode_id, organism_id FROM tmp_phylonode" ); foreach (@updates) { $dbh->do( $_ ); } sub walktree { my $phylonode_id = shift; our $ctr = shift; message("walking the tree for id $phylonode_id, index count is $ctr\n",1); my $children = $dbh->prepare("SELECT phylonode_id, organism_id FROM tmp_phylonode WHERE parent_phylonode_id = ?"); my $setleft = $dbh->prepare("UPDATE tmp_phylonode SET left_idx = ? WHERE phylonode_id = ?"); my $setright = $dbh->prepare("UPDATE tmp_phylonode SET right_idx = ? WHERE phylonode_id = ?"); $setleft->execute($ctr++, $phylonode_id); message("Setting left index= $ctr for parent $phylonode_id\n\n",1); $children->execute($phylonode_id); while(my ($child_id, $organism_id) = $children->fetchrow_array() ) { message( "Found child_id $child_id (organism_id = $organism_id) \n",1); walktree($child_id, $ctr); } $setright->execute($ctr++, $phylonode_id); message( "Setting right index= $ctr for phylonode id $phylonode_id\n\n",1); } if ($opt_t) { die "TEST RUN! rolling back!\n"; } }; try { $schema->txn_do($coderef); message( "Commiting!! \n"); message("Inserted $node_count phylonodes. \n",1 ); } catch { message( "An error occured! Rolling back! \n $_ \n Resetting database sequences...\n", 1); #reset sequences foreach my $key ( keys %seq ) { my $value= $seq{$key}; my $maxvalue= $maxval{$key} || 0; if ($maxvalue) { $dbh->do("SELECT setval ('$value', $maxvalue, true)") ; } else { $dbh->do("SELECT setval ('$value', 1, false)"); } } }; sub set_maxval { my $key=shift; my $id_column= $key . "_id"; my $table = $key; my $query = "SELECT max($id_column) FROM $table"; $sth=$dbh->prepare($query); $sth->execute(); my ($next) = $sth->fetchrow_array(); return $next; } sub message { my $message = shift; my $s = shift; print STDOUT $message; print ERR $message if $s; } #http://www.eyesopen.com/docs/cplusprog_1_2/node220.html __DATA__ no rank superkingdom subkingdom kingdom superphylum phylum subphylum superclass class subclass infraclass cohort subcohort superorder order suborder infraorder parvorder superfamily family subfamily tribe subtribe genus subgenus species group species subgroup species subspecies varietas forma chado-1.23/bin/load_taxonomy_cvterms.pl000644 000765 000024 00000006106 11723233051 020317 0ustar00cainstaff000000 000000 =head1 NAME load_taxonomy_cvterms.pl =head1 DESCRIPTION Usage: perl load_taxonomy_cvterms.pl -H [dbhost] -D [dbname] [-t] -g gmod_dbprofile populate a chado database with NCBI taxon terms =head2 parameters =over 7 =item -H hostname for database =item -D database name =item -t trial mode. Do not perform any store operations at all. =item -g GMOD database profile name (can provide host and DB name) Default: 'default' =item -u username. Override username in gmod_config =item -d driver. Override driver name in gmod_config =item -p password. Override password in gmod_config =back =cut #!/usr/bin/env perl use strict; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Bio::Chado::Schema; use Getopt::Std; our ($opt_H, $opt_D, $opt_g, $opt_t, $opt_d, $opt_u, $opt_p); getopts('H:g:tD:d:u:p:'); my $dbhost = $opt_H; my $dbname = $opt_D; my $driver = $opt_d; my $user = $opt_u; my $pass = $opt_p; my $port; my ($dbh, $schema); if ($opt_g) { my $DBPROFILE = $opt_g; $DBPROFILE ||= 'default'; my $gmod_conf = Bio::GMOD::Config->new() ; my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE ) ; $dbhost ||= $db_conf->host(); $dbname ||= $db_conf->name(); $driver ||= $db_conf->driver(); $port ||= $db_conf->port(); $pass ||= $db_conf->password(); $user ||= $db_conf->user(); } if (!$dbhost && !$dbname) { die "Need -D dbname and -H hostname arguments.\n"; } my $dsn = "dbi:$driver:dbname=$dbname"; $dsn .= ";host=$dbhost"; $dsn .= ";port=$port" if $port; $schema= Bio::Chado::Schema->connect( $dsn, $user, $pass, { AutoCommit=>0 } ); $dbh=$schema->storage->dbh(); if (!$schema || !$dbh) { die "No schema or dbh is avaiable! \n"; } eval { my $db = $schema->resultset("General::Db")->find_or_create( { name =>'species_taxonomy', }); my $db_id = $db->get_column('db_id'); my $cv= $schema->resultset("Cv::Cv")->find_or_create( { name => 'taxonomy', }); my $cv_id = $cv->get_column('cv_id'); while ( my $tax = ) { chomp $tax; my $dbxref= $schema->resultset("General::Dbxref")->find_or_create( { db_id => $db_id, accession => "taxonomy:$tax", }); my $dbxref_id = $dbxref->get_column('dbxref_id'); my $cvterm = $schema->resultset("Cv::Cvterm")->find_or_create( { cv_id => $cv_id, name => $tax, dbxref_id => $dbxref_id, }); my $cvterm_id= $cvterm->get_column('cvterm_id'); print STDERR "Stored cvterm for $tax ($cvterm_id)\n"; } }; if($@) { print $@; print"Failed; rolling back.\n"; $dbh->rollback(); }else{ print"Succeeded.\n"; if (!$opt_t) { print STDERR "committing ! \n"; $dbh->commit(); }else{ print STDERR "Rolling back! \n"; $dbh->rollback(); } } __DATA__ no rank superkingdom subkingdom kingdom superphylum phylum subphylum superclass class subclass infraclass cohort subcohort superorder order suborder infraorder parvorder superfamily family subfamily tribe subtribe genus subgenus species group species subgroup species subspecies varietas forma chado-1.23/bin/make_cvtermpath.pl000755 000765 000024 00000011421 11723233072 017053 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # assumes empty password--that should be fixed use strict; use DBI; use Bio::OntologyIO; use Bio::Ontology::TermFactory; my ($user, $dbname, $cvname) = @ARGV; die "USAGE: $0 " unless $user and $dbname and $cvname; my $db = DBI->connect("dbi:Pg:dbname=$dbname",$user,''); my $sth_objects = $db->prepare("select object_id from cvterm_relationship where subject_id = ? and type_id = ?"); my $sth_subjects = $db->prepare("select subject_id from cvterm_relationship where object_id = ? and type_id = ?"); my $sth_allobjects = $db->prepare("select object_id from cvterm_relationship where subject_id = ?"); my $sth_allsubjects = $db->prepare("select subject_id from cvterm_relationship where object_id = ?"); my %type; my %subject; my %object; my %black; my(%root,%leaf); my %sot; my $sth_type = $db->prepare("select cvterm_id from cvterm where cv_id = (select cv_id from cv where name = 'Relationship Ontology')"); $sth_type->execute; while(my $type_id = $sth_type->fetchrow){ $type{$type_id}++; } my %cvterm; my $sth_cvterm = $db->prepare("select cvterm_id from cvterm"); $sth_cvterm->execute; while(my $cvterm_id = $sth_cvterm->fetchrow_array){ $cvterm{$cvterm_id}++; } my $cv_id; warn "select cv_id from cv where name = '$cvname'"; my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'"); $sth_cv->execute; while(my $cv = $sth_cv->fetchrow_hashref){ $cv_id = $cv->{cv_id}; } die "no cv_id for '$cvname'" unless defined $cv_id; #my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship"); my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id"); $sth_cvterm_relationship->execute; while(my $cvterm_relationship = $sth_cvterm_relationship->fetchrow_hashref){ $subject{$cvterm_relationship->{subject_id}}++; $object{$cvterm_relationship->{object_id}}++; $sot{$cvterm_relationship->{subject_id}}{$cvterm_relationship->{object_id}}{$cvterm_relationship->{type_id}}++; } foreach my $cvterm (keys %cvterm){ $root{$cvterm}++ if(!$subject{$cvterm} and $object{$cvterm}); $leaf{$cvterm}++ if( $subject{$cvterm} and !$object{$cvterm}); } my %leafbak = %leaf; %sot = (); while(keys %leaf){ foreach my $leaf (keys %leaf){ foreach my $type (keys %type){ recurse([$leaf],$type,1); } delete $leaf{$leaf}; } # print "**************************************\n"; } %leaf = %leafbak; while(keys %leaf){ foreach my $leaf (keys %leaf){ recurse([$leaf],undef,1); delete $leaf{$leaf}; } # print "**************************************\n"; } sub recurse { my($subjects,$type,$dist) = @_; my $subject = $subjects->[-1]; # print $subject,"\n"; my @objects = objects($subject,$type); if(!@objects){ $leaf{$subject}++; return; } foreach my $object (@objects){ my $tdist = $dist; foreach my $s (@$subjects){ next if $sot{$s}{$object}{$type}{$tdist}; $sot{$s}{$object}{$type}{$tdist}++; # print $tdist,"\t"x$dist,"\t",$s,"\t",$object,"\t",$type||'transitive',"\n"; if(defined $type){ print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values ($s,$object,$type,$cv_id,$tdist);\n"; my $ttdist = -1 * $tdist; print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values ($object,$subject,$type,$cv_id,$ttdist);\n"; } else { print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values ($s,$object,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,$tdist);\n"; print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values ($object,$subject,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,-$tdist);\n"; } $tdist--; } $tdist = $dist; recurse([@$subjects,$object],$type,$dist+1); } } #------------------- sub objects { my($subject,$type) = @_; #warn $subject; my @objects; if(defined($type)){ $sth_objects->execute($subject,$type); while(my $object = $sth_objects->fetchrow_array){ push @objects, $object; } } else { $sth_allobjects->execute($subject); while(my $object = $sth_allobjects->fetchrow_array){ push @objects, $object; } } return @objects; } sub subjects { my($object,$type) = @_; my @subjects; if(defined($type)){ $sth_subjects->execute($object,$type); while(my $subject = $sth_subjects->fetchrow_array){ push @subjects, $subject; } } else { $sth_allsubjects->execute($object); while(my $subject = $sth_allsubjects->fetchrow_array){ push @subjects, $subject; } } return @subjects; } chado-1.23/bin/make_cvtermpath.sh000755 000765 000024 00000003001 11256710012 017040 0ustar00cainstaff000000 000000 #!/bin/sh #argh--path dependancy need to be fixed echo "Relationship Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Relationship Ontology' | psql -q $DBNAME echo "Sequence Ontology Feature Annotation" ./bin/make_cvtermpath.pl $USER $DBNAME 'Sequence Ontology Feature Annotation'| psql -q $DBNAME echo "Sequence Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Sequence Ontology' | psql -q $DBNAME echo "Gene Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Cellular Component (Gene Ontology)' | psql -q $DBNAME ./bin/make_cvtermpath.pl $USER $DBNAME 'Molecular Function (Gene Ontology)' | psql -q $DBNAME ./bin/make_cvtermpath.pl $USER $DBNAME 'Biological Process (Gene Ontology)' | psql -q $DBNAME echo "Mouse Embryo Anatomy Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Mouse Embryo Anatomy Ontology' | psql -q $DBNAME echo "Mouse Adult Anatomy Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Mouse Adult Anatomy Ontology' | psql -q $DBNAME echo "Cell Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'Cell Ontology' | psql -q $DBNAME echo "eVOC Pathology Ontology" ./bin/make_cvtermpath.pl $USER $DBNAME 'eVOC Pathology Ontology' | psql -q $DBNAME echo "Mouse Pathology Ontology (Pathbase)" ./bin/make_cvtermpath.pl $USER $DBNAME 'Mouse Pathology Ontology (Pathbase)' | psql -q $DBNAME true; #echo "eVOC Cell Type Ontology" #./bin/make_cvtermpath.pl $USER $DBNAME 'eVOC Cell Type Ontology' | psql -q $DBNAME chado-1.23/bin/make_partial_indexes.pl000755 000765 000024 00000001066 11723233115 020053 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use strict; use warnings; use DBI; my $dbh = DBI->connect("dbi:Pg:dbname=gadfly",'',''); my $type = 'chromosome_arm'; my $sth = $dbh->prepare("select feature_id from feature f, cvterm cv where cv.name = ? and cv.cvterm_id=f.type_id"); $sth->execute($type); while (my $ida = $sth->fetchrow_arrayref) { my $id = $$ida[0]; warn "creating partial index on srcfeature_id $id ...\n"; $dbh->do("create index featureloc_src_$id on featureloc (fmin,fmax) where srcfeature_id = $id"); } $dbh->disconnect; chado-1.23/bin/pg2cdbi.pl000755 000765 000024 00000003036 11723233132 015213 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # vim: set ft=perl ts=2 expandtab: use strict; use SQL::Translator; use lib './bin'; use Skip_tables qw( @skip_tables ); unless ( scalar @ARGV > 3 ) { die "USAGE: $0 []\n"; } my $db_name = shift @ARGV; my $db_username = shift @ARGV; my $db_password = shift @ARGV; my $dsn = "dbi:Pg:dbname=$db_name"; my $translator = SQL::Translator->new( from => 'PostgreSQL', to => 'ClassDBI', filename => \@ARGV, producer_args => { db_user => $db_username, db_pass => $db_password, dsn => $dsn, }, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); $translator->format_package_name(\&x); $translator->format_pk_name(sub {return 'id';}); $translator->format_fk_name(\&y); my $output = $translator->translate or die $translator->error; print $output; sub x { my ($name, $primary_key) = @_; my $package_name; my @temp = split(/_/,$name); for(my $i = 0; $i < scalar(@temp); $i++) { my $new_name = ucfirst($temp[$i]); if($i == 0) { $package_name .= $new_name; } else { $package_name .= "_" .$new_name; } } $package_name = 'Bio::Chado::CDBI::' . $package_name; return $package_name; } sub y { my $table_name = shift; my $field_name = shift; $field_name =~ s/_id$//; return $field_name; } chado-1.23/bin/pg2cdbi_viaTT.pl000755 000765 000024 00000003175 11723233145 016332 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # vim: set ft=perl ts=2 expandtab: use strict; use SQL::Translator; use lib './bin'; use Skip_tables qw( @skip_tables ); unless ( scalar @ARGV > 3 ) { die "USAGE: $0 []\n"; } my $db_name = shift @ARGV; my $db_username = shift @ARGV; my $db_password = shift @ARGV; my $dsn = "dbi:Pg:dbname=$db_name"; my $translator = SQL::Translator->new( from => 'PostgreSQL', to => 'TTSchema', filename => \@ARGV, producer_args => { tt_vars => { db_user => $db_username, db_pass => $db_password, db_dsn => $dsn, baseclass => 'Bio::Chado::DBI', format_fk => \&generate_file_y, format_node => \&format_table_name, format_refers => \&format_refers, }, ttfile => "./bin/dbi.tt2", }, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); my $output = $translator->translate or die $translator->error; print $output; #stolen from turnkey_generate script sub generate_file_y { my $table_name = shift; my $field_name = shift; $field_name =~ s/_id$//; return $field_name; } sub format_table_name { my $table_name = shift; my $first_char = substr($table_name,0,1); substr($table_name,0,1,uc($first_char)); $table_name =~ s/_(\w)/'_'.uc($1)/eg; return $table_name; } sub format_refers { my $table_name = shift; my $field_name = shift; return "--$table_name--$field_name--"; } chado-1.23/bin/pg2diagram.pl000755 000765 000024 00000001623 11723233157 015725 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use SQL::Translator; use Data::Dumper; use lib './bin'; use Skip_tables qw( @skip_tables ); $SQL::Translator::DEBUG = 0; my $in = shift; open(IN,$in) || die "couldn't open $in: $!"; my @create = ; my $create = join '', @create; my $tr = SQL::Translator->new( parser => "PostgreSQL", producer => "Diagram", producer_args => {add_color=>1}, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); print $tr->translate(\$create); chado-1.23/bin/pg2graphviz.pl000755 000765 000024 00000002306 11723233171 016146 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use SQL::Translator; use Data::Dumper; use lib './bin'; use Skip_tables qw( @skip_tables ); $SQL::Translator::DEBUG = 0; my $in = shift; open(IN,$in) || die "couldn't open $in: $!"; my @create = ; my $create = join '', @create; my $tr = SQL::Translator->new( from => "PostgreSQL", to => "GraphViz", producer_args => { output_type => 'png', width => 10, height => 8, layout => 'neato', }, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); print $tr->translate(\$create); chado-1.23/bin/pg2graphviz_svg.pl000755 000765 000024 00000001716 11723233203 017025 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use SQL::Translator; use Data::Dumper; use lib './bin'; use Skip_tables qw( @skip_tables ); $SQL::Translator::DEBUG = 0; my $in = shift; open(IN,$in) || die "couldn't open $in: $!"; my @create = ; my $create = join '', @create; my $tr = SQL::Translator->new( parser => "PostgreSQL", producer => "GraphViz", producer_args => { output_type => 'svg', width => 10, height => 8, layout => 'neato', }, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); print $tr->translate(\$create); chado-1.23/bin/pg2html.pl000755 000765 000024 00000001763 11723233214 015264 0ustar00cainstaff000000 000000 #!/usr/bin/env perl use SQL::Translator; use Data::Dumper; use lib './bin'; use Skip_tables qw( @skip_tables ); $SQL::Translator::DEBUG = 0; my $in = shift; open(IN,$in) || die "couldn't open $in: $!"; my @create = ; my $create = join '', @create; my $tr = SQL::Translator->new( parser => "PostgreSQL", producer => "HTML", producer_args => { pretty => 1, }, filters => [ sub { my $schema = shift; foreach (@skip_tables) { $schema->drop_table($_); } }, ], ); print $tr->translate(\$create); chado-1.23/bin/privileges.tmpl000644 000765 000024 00000001232 11256710012 016402 0ustar00cainstaff000000 000000 --create sql to grant permissions on tables in the database -- sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql>privileges.sql -- --after it is created, the permissions can be updated by excuting this command: -- -- $ cat privileges.sql | psql -- --since this opens up the database to all users, it should be used with --caution. Another option would be to change "PUBLIC" below to a --specific user or group to whom you want to grant privileges, or --change the "ALL" to something more restrictive, like "SELECT." [% FOREACH table IN schema.get_tables %] GRANT ALL ON TABLE [% table.name %] TO PUBLIC; [% END %] chado-1.23/bin/Skip_tables.pm000644 000765 000024 00000000410 11256710012 016126 0ustar00cainstaff000000 000000 package Skip_tables; use strict; use vars qw(@ISA @EXPORT_OK @skip_tables); require Exporter; @ISA = qw(Exporter); @EXPORT_OK = qw(@skip_tables); @skip_tables = ('gencode_codon_aa', 'gencode_startcodon', 'gencode'); 1; chado-1.23/bin/test_load.pl000755 000765 000024 00000002250 11723233245 015661 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # # A simple script to create the Chado database and tables. # use strict; my $dbname = shift or exit; my @list = `psql -l`; my %dbs; my $ok = 0; for my $line ( @list ) { ; if ( $line =~ m/^\s*Name\s*|\s*Owner\s*/ ) { $ok = 1; next; } elsif ( $ok ) { if ( $line =~ m/^\s*(\w+)\s*\|\s*\w+\s*/ ) { $dbs{ $1 } = 1; } } } if ( $dbs{ $dbname } ) { print "A database called '$dbname' already exists.\n"; print "OK to drop database '$dbname'? [Y/n] "; chomp( my $answer = ); unless ( $answer =~ m/^[Nn]/ ) { print "Dropping database '$dbname'\n"; system( "dropdb $dbname" ) == 0 or die "Cannot drop database: $?"; } else { print "Will not drop database '$dbname'. Exiting.\n"; exit(0); } } print "Creating new database called '$dbname'\n"; system( "createdb $dbname" ) == 0 or die "Cannot create database: $?"; print "Creating tables\n"; system( "psql -f modules/complete.sql $dbname 2>&1 | grep -E 'ERROR|FATAL|No such file or directory'" ) == 0 or die "Problem creating tables: $?"; print "Database '$dbname' created\n"; exit(0); chado-1.23/bin/test_load.sh000644 000765 000024 00000000620 11256710012 015645 0ustar00cainstaff000000 000000 #!/bin/sh DBHOST=$1 DBPORT=$2 DBUSER=$3 DBNAME=$4; dropdb -h $DBHOST -p $DBPORT -U $DBUSER $DBNAME; createdb -h $DBHOST -p $DBPORT -U $DBUSER $DBNAME; createlang -h $DBHOST -p $DBPORT -U $DBUSER plpgsql $DBNAME; cat modules/complete.sql | psql -h $DBHOST -p $DBPORT -U $DBUSER $DBNAME 2>&1 | grep -E 'ERROR|FATAL|No such file or directory'; echo "database $DBNAME created on $DBHOST:$DBPORT"; true; chado-1.23/bin/ucsc_genes2gff.pl000755 000765 000024 00000046450 11723233262 016577 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # convert UCSC gene files into GFF3 data use strict; use File::Basename 'basename'; use Getopt::Long; use URI::Escape; use Text::Wrap; $Text::Wrap::columns = 79; use Bio::SeqIO; use Bio::SeqFeature::Generic; use Data::Dumper; my $executable = basename($0); my ($SRCDB,$ORIGIN,$ANNOTATIONS); GetOptions('srcdb:s' => \$SRCDB, 'origin:i' => \$ORIGIN, 'annotations:s' => \$ANNOTATIONS, ) and $ANNOTATIONS or die < [options] Convert UCSC Genome Browser-format gene files into GFF3 version files. Only the gene IDs and their locations come through. You have to get the comments and aliases some other way. Currently some info is being added as additional application-specific gff tags. Options: -srcdb Choose a source for the gene, default "UCSC" -origin Choose a relative position to number from, default is "1" -annotations Directory containing UCSC annotation files -center ??? USAGE $SRCDB ||= 'UCSC'; $ORIGIN ||= 1; my $KGXREF = $ANNOTATIONS.'/kgXref.txt'; my $KNOWNGENE = $ANNOTATIONS.'/knownGene.txt'; my $KNOWNGENEPEP = $ANNOTATIONS.'/knownGenePep.txt'; my $KNOWNGENEMRNA = $ANNOTATIONS.'/knownGeneMrna.txt'; my $KNOWNLOCUSLINK = $ANNOTATIONS.'/knownToLocusLink.txt'; my $KNOWNPFAM = $ANNOTATIONS.'/knownToPfam.txt'; my $KNOWNU133 = $ANNOTATIONS.'/knownToU133.txt'; my $KNOWNU133PLUS = $ANNOTATIONS.'/knownToU133Plus2.txt'; my $KNOWNU95 = $ANNOTATIONS.'/knownToU95.txt'; my $GENBANK = $ANNOTATIONS.'/genbank2accessions.txt'; my $LOCACC = $ANNOTATIONS.'/loc2acc'; my $LOCGO = $ANNOTATIONS.'/loc2go'; my $LOCUG = $ANNOTATIONS.'/loc2UG'; my $REFLINK = $ANNOTATIONS.'/refLink.txt'; my $REFSEQSUMMARY = $ANNOTATIONS.'/refSeqSummary.txt'; my $CHROMINFO = $ANNOTATIONS.'/chromInfo.txt'; my %xref; my %loc2mrna; my %ref2mrna; print STDERR "Parsing Genbank..."; parseGenbank(\%xref,$GENBANK); print STDERR "done!\n"; print STDERR "Parsing Genbank Peptide..."; parseKnownGenePep(\%xref,$KNOWNGENEPEP); print STDERR "done!\n"; print STDERR "Parsing Known Gene..."; parseKnownGeneMrna(\%xref,$KNOWNGENEMRNA); print STDERR "done!\n"; print STDERR "Parsing Known Gene Xref..."; parseKgXref(\%xref,$KGXREF); print STDERR "done!\n"; print STDERR "Parsing LocusLink..."; parseLocAcc(\%xref,$LOCACC); # the best way I've found so far # to link Genbank mRNA accession to # Genbank protein accession print STDERR "done!\n"; print STDERR "Parsing LocusLink -> GO..."; parseLocGo(\%xref,$LOCGO); print STDERR "done!\n"; print STDERR "Parsing LocusLink -> UniGene..."; parseLocUG(\%xref,$LOCUG); print STDERR "done!\n"; print STDERR "Parsing Known Gene -> Locuslink..."; parseKnownLocusLink(\%xref,$KNOWNLOCUSLINK); print STDERR "done!\n"; print STDERR "Parsing Known Gene -> Affy..."; parseKnownAffy(\%xref,$KNOWNU133PLUS,$KNOWNU133,$KNOWNU95); print STDERR "done!\n"; print STDERR "Parsing Known Gene -> PFAM..."; parseKnownPfam(\%xref,$KNOWNPFAM); print STDERR "done!\n"; print STDERR "Parsing Known Gene -> RefSeq..."; parseRefLink(\%xref,$REFLINK); print STDERR "done!\n"; print STDERR "Parsing Known Gene -> RefSeq Summary..."; parseRefSeqSummary(\%xref,$REFSEQSUMMARY); print STDERR "done!\n"; print "##gff-version 3\n"; #if(1){ #for debugging open(KG,$KNOWNGENE) or die "couldn't open('$KNOWNGENE'): $!"; while () { chomp; next if /^\#/;; my ($id,$chrom,$strand,$txStart,$txEnd,$cdsStart,$cdsEnd,$exons,$exonStarts,$exonEnds) = split /\t/; my ($utr5_start,$utr5_end,$utr3_start,$utr3_end); # adjust for Jim's 0-based coordinates $txStart++; $cdsStart++; $txStart -= $ORIGIN; $txEnd -= $ORIGIN; $cdsStart -= $ORIGIN; $cdsEnd -= $ORIGIN; # print the transcript print join ("\t",$chrom,$SRCDB,'mRNA',$txStart,$txEnd,'.',$strand,'.',"ID=$id;"); if(defined($xref{$id})) { print "Dbxref="; my @annotation_sets = grep { $_ =~ /^db:/ && $_ !~ /protein/ } keys %{$xref{$id}}; my $i = 0; foreach my $annotation_set ( @annotation_sets ) { next unless $annotation_set; $annotation_set =~ s/^db://; #yeah, it's a hack. so fix it. my $foo = join(",", map {uri_escape("$annotation_set:$_")} grep { $xref{$id}{'db:'.$annotation_set}{$_} != 0 && $_ != 0 } keys %{$xref{$id}{'db:'.$annotation_set}} ); print $foo; $i++; print "," if $foo && $i != scalar(@annotation_sets); } print ";"; if(my @aliases = keys %{ $xref{$id}{Alias} }){ print "Alias=" . join(",", map {uri_escape($_)} @aliases) . ";"; } if(my @notes = keys %{ $xref{$id}{Note} }){ print "Note=" . join(",", map {uri_escape($_)} @notes) . ";"; } print "\n"; #and print the protein if there is one if( my($prot_id) = keys %{$xref{$id}{'db:RefSeq_protein'}} ){ @annotation_sets = grep { $_ =~ /^db:/ && $_ =~ /protein/ } keys %{$xref{$id}}; print join ("\t",'.',$SRCDB,'protein','.','.','.','.','.',"ID=$prot_id;Parent=$id;"); my $i = 0; print "Dbxref="; foreach my $annotation_set ( @annotation_sets ) { my @a = keys %{ $xref{$id}{$annotation_set} }; $annotation_set =~ s/db://; my $j = 0; foreach my $a (@a){ print uri_escape( "$annotation_set:$a" ) if $a; $j++; print "," if $a && $j != scalar(@a); } $i++; print "," unless $i == scalar(@annotation_sets); } print ";\n"; } } # now handle the CDS entries -- the tricky part is the need to keep # track of phase my $phase = 0; my @exon_starts = map {$_-$ORIGIN} split ',',$exonStarts; my @exon_ends = map {$_-$ORIGIN} split ',',$exonEnds; if($strand eq '+') { for(my $i=0;$i $cdsEnd) { $utr_start = $exon_start; } else { $cds_start = $exon_start; } if($exon_end < $cdsStart) { $utr_end = $exon_end; } elsif($exon_end > $cdsEnd) { $utr_end = $exon_end; } else { $cds_end = $exon_end; } if($utr_start && !$utr_end) { # half in half out on 5' end $utr_end = $cdsStart - 1; $cds_start = $cdsStart; $cds_end = $exon_end; } if($utr_end && !$utr_start) { # half in half out on 3' end $utr_start = $cdsEnd + 1; $cds_end = $cdsEnd; $cds_start = $exon_start; } die "programmer error, utr_start and no utr_end" unless defined $utr_start == defined $utr_end; die "programmer error, cds_start and no cds_end" unless defined $cds_start == defined $cds_end; if(defined $utr_start && $utr_start <= $utr_end && $utr_start < $cdsStart) { print join ("\t",$chrom,$SRCDB,"five_prime_UTR",$utr_start,$utr_end,'.',$strand,'.',"Parent=$id"),"\n" } if(defined $cds_start && $cds_start <= $cds_end) { print join ("\t",$chrom,$SRCDB,'CDS',$cds_start,$cds_end,'.',$strand,$phase,"Parent=$id"),"\n"; $phase = (($cds_end-$cds_start+1-$phase)) % 3; } if(defined $utr_start && $utr_start <= $utr_end && $utr_start > $cdsEnd) { print join ("\t",$chrom,$SRCDB,"three_prime_UTR",,$utr_start,$utr_end,'.',$strand,'.',"Parent=$id"),"\n" } } } if($strand eq '-') { my @lines; for(my $i=@exon_starts-1; $i>=0; $i--) { # count backwards my $exon_start = $exon_starts[$i] + 1; my $exon_end = $exon_ends[$i]; my ($utr_start,$utr_end,$cds_start,$cds_end); if($exon_end > $cdsEnd) { # in a 5' UTR $utr_end = $exon_end; } elsif($exon_end < $cdsStart) { $utr_end = $exon_end; } else { $cds_end = $exon_end; } if($exon_start > $cdsEnd) { $utr_start = $exon_start; } elsif($exon_start < $cdsStart) { $utr_start = $exon_start; } else { $cds_start = $exon_start; } if($utr_start && !$utr_end) { # half in half out on 3' end $utr_end = $cdsStart - 1; $cds_start = $cdsStart; $cds_end = $exon_end; } if ($utr_end && !$utr_start) { # half in half out on 5' end $utr_start = $cdsEnd + 1; $cds_end = $cdsEnd; $cds_start = $exon_start; } die "programmer error, utr_start and no utr_end" unless defined $utr_start == defined $utr_end; die "programmer error, cds_start and no cds_end" unless defined $cds_start == defined $cds_end; if(defined $utr_start && $utr_start <= $utr_end && $utr_start > $cdsEnd) { unshift @lines,join ("\t",$chrom,$SRCDB,"five_prime_UTR",,$utr_start,$utr_end,'.',$strand,'.',"Parent=$id"),"\n" } if(defined $cds_start && $cds_start <= $cds_end) { unshift @lines,join ("\t",$chrom,$SRCDB,'CDS',$cds_start,$cds_end,'.',$strand,$phase,"Parent=$id"),"\n"; $phase = (($cds_end-$cds_start+1-$phase)) % 3; } if(defined $utr_start && $utr_start <= $utr_end && $utr_end < $cdsStart) { unshift @lines,join ("\t",$chrom,$SRCDB,"three_prime_UTR",$utr_start,$utr_end,'.',$strand,'.',"Parent=$id"),"\n" } } print @lines; } } close(KG) or die "couldn't close('$KNOWNGENE'): $!"; #} for debugging print "##FASTA\n"; foreach my $kg (keys %xref){ my $seq_mrna = $xref{$kg}{'sequence:mrna'}; my $seq_prot = $xref{$kg}{'sequence:protein'}; if($seq_mrna){ foreach my $k (keys %{$xref{$kg}{'db:GenBank_mRNA'}}){ print ">$k\n". wrap('','',$seq_mrna) ."\n"; } } if($seq_prot){ foreach my $k (keys %{$xref{$kg}{'db:GenBank_protein'}}){ print ">$k\n". wrap('','',$seq_prot) ."\n"; } } } =head2 parseLocAcc Title : parseLocAcc Usage : Function: Example : Returns : Args : =cut sub parseLocAcc { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my @line = split /\t/; #note: this doesn't work b/c if the second regex doesn't match, $1 is still #leftover from the first regex. a better method is given below. #$line[1] =~ /(.*)\.\d/; #my $gene = $1; #$line[4] =~ /(.*)\.\d/; #my $protein = $1; my $loc = $line[0]; my $gene = $line[1]; my $protein = $line[4]; $gene =~ s/\.\d+$//; $protein =~ s/\.\d+$//; next if $gene eq 'none'; push @{ $loc2mrna{$loc} }, $gene; $xref->{$gene}{'db:GenBank_protein'}{$protein} = 1 unless($gene eq 'none' || $protein eq '-' || $protein !~ /^[A-Z]{3}\d/ || $protein =~ /_/); } close ANNFILE; } =head2 parseLocGo Title : parseLocGo Usage : Function: Example : Returns : Args : =cut sub parseLocGo { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my @line = split /\t/; if($loc2mrna{$line[0]}){ foreach my $mrna (@{$loc2mrna{$line[0]}}){ $xref->{$mrna}{'cvterm:go'}{$line[1]} = 1; } } } close ANNFILE; } =head2 parseLocUG Title : parseLocUG Usage : Function: Example : Returns : Args : =cut sub parseLocUG { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my @line = split /\t/; if($loc2mrna{$line[0]}){ foreach my $mrna (@{$loc2mrna{$line[0]}}){ $xref->{$mrna}{'db:Unigene'}{$line[1]} = 1; } } } close ANNFILE; } =head2 parseRefLink Title : parseRefLink Usage : Function: Example : Returns : Args : =cut sub parseRefLink { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my($symbol,$description,$refmrna,$refprotein,undef,undef,$locus,$omim) = split /\t/; $description = uri_escape($description); if($ref2mrna{$refmrna}){ foreach my $mrna (@{$ref2mrna{$refmrna}}){ $xref->{$mrna}{'db:LocusLink'}{$locus} = 1; $xref->{$mrna}{'db:OMIM'}{$omim} = 1; $xref->{$mrna}{'db:RefSeq_mRNA'}{$refmrna} = 1; $xref->{$mrna}{'db:RefSeq_protein'}{$refprotein} = 1; $xref->{$mrna}{'Alias'}{$symbol} = 1; $xref->{$mrna}{'Note'}{$description} = 1; } } } close ANNFILE; } =head2 parseRefSeqSummary Title : parseRefSeqSummary Usage : Function: Example : Returns : Args : =cut sub parseRefSeqSummary { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my($refmrna,$completeness,$description) = split /\t/; $description = uri_escape($description); if($ref2mrna{$refmrna}){ foreach my $mrna (@{$ref2mrna{$refmrna}}){ $xref->{$mrna}{'completeness'}{$completeness} = 1; $xref->{$mrna}{'description'}{$description} = 1; } } } close ANNFILE; } =head2 parseKnownLocusLink Title : parseKnownLocusLink Usage : Function: Example : Returns : Args : =cut sub parseKnownLocusLink { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($accession,$locuslink) = split /\t/; $xref->{$accession}{'db:LocusLink'}{$locuslink} = 1; } close ANNFILE; } =head2 parseKnownPfam Title : parseKnownPfam Usage : Function: Example : Returns : Args : =cut sub parseKnownPfam { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($accession,$pfam) = split /\t/; $xref->{$accession}{'db:PFAM'}{$pfam} = 1; } close ANNFILE; } =head2 parseKnownAffy Title : parseKnownAffy Usage : Function: Example : Returns : Args : =cut sub parseKnownAffy { my $xref = shift @_; my $i = 0; my @chip = qw(U133PLUS U133 U95); foreach my $filename (@_){ open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($accession,$probeset) = split /\t/; $xref->{$accession}{'db:Affymetrix_'.$chip[$i]}{$probeset} = 1; } close ANNFILE; $i++; } } =head2 parseKnownGeneMrna Title : parseKnownGeneMrna Usage : Links mRNA sequence to mRNA. Function: Example : Returns : Args : =cut sub parseKnownGeneMrna { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($accession,$sequence) = split /\t/; $xref->{$accession}{'sequence:mrna'} = $sequence; } close ANNFILE; } =head2 parseKnownGenePep Title : parseKnownGenePep Usage : This method depends on parseLocAcc being run first so mRNA accessions can be mapped to protein accessions. Function: Example : Returns : Args : =cut sub parseKnownGenePep { my($xref,$filename) = @_; open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($accession,$sequence) = split /\t/; $xref->{$accession}{'sequence:protein'} = $sequence; # $xref->{$protGenbankId}{'sequence:protein'} = $sequence; } close ANNFILE; } =head2 mrna2protein Title : mrna2protein Usage : creates a hash between the mRNA genbank accession (used in UCSC DB to key everything) and the proper genbank protein accession Function: Example : Returns : Args : =cut sub parseGenbank { my($xref,$filename) = @_; # my $file = shift; # my $annotations = {}; # stores the mRNA genbank id as key, protein genbank id as value open ANNFILE, $filename or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; my ($mrna, $prot) = split /\t/; $xref->{$mrna}{'db:GenBank_protein'}{$prot} = 1 if $prot =~ /^[A-Z]{3}\d/ and $prot !~ /_/; # $annotations->{$mrna} = $prot; } close ANNFILE; # return($annotations); } =head2 parseKgXref Title : parseKgXref Usage : Function: Example : Returns : Args : =cut sub parseKgXref { my($xref,$filename) = @_; open(ANNFILE, $filename) or die "Can't open file $filename: $!"; while() { chomp; next if /^#/; # first two are the same (genebank) followed by swissprot etc... my ($kgID, $mRNA, $spID, $spDisplayID, $geneSymbol, $refseq, $protAcc, $description) = split /\t/; my $key = $kgID; # escape certain fields $key = uri_escape($key); $description = uri_escape($description); push @{ $ref2mrna{$refseq} }, $kgID; #http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions #http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#AccessionB #http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#ProteinIDB $xref->{$key}{'db:GenBank_protein'}{$kgID} = 1 if $kgID and $kgID =~ /^[A-Z]{1,2}\d/ and $kgID !~ /_/; $xref->{$key}{'db:GenBank_mRNA'}{$mRNA} = 1 if $mRNA and $mRNA =~ /^[A-Z]{1,2}\d/ and $mRNA !~ /_/ and $mRNA ne $kgID; $xref->{$key}{'db:Swiss'}{$spID} = 1 if $spID; $xref->{$key}{'db:Swiss'}{$spDisplayID} = 1 if $spDisplayID and $spDisplayID ne $spID; $xref->{$key}{'Alias'}{$geneSymbol} = 1 if $geneSymbol; $xref->{$key}{'db:RefSeq_mRNA'}{$refseq} = 1 if $refseq and $refseq =~ /^(NC|NG|NM|NR|NT|NW|XM|XR|NZ)_/; $xref->{$key}{'db:RefSeq_protein'}{$protAcc} = 1 if $protAcc and $protAcc =~ /^(NP|XP|ZP)_/; $xref->{$key}{'Note'}{$description} = 1 if $description; } close(ANNFILE); } __END__ =head1 NAME ucsc_genes2gff.pl - Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse =head1 SYNOPSIS % ucsc_genes2gff.pl [options] ucsc_file1 ucsc_file2... Options: -src Choose a source for the gene, default "UCSC" -origin Choose a relative position to number from, default is "1" =head1 DESCRIPTION This script massages the gene files available from the "tables" link of the UCSC genome browser (genome.ucsc.edu) into a form suitable for loading of gbrowse. Warning: it only works with the gene tables. Other tables, such as EST alignments, contours and repeats, have their own formats which will require other scripts to parse. To use this script, get one or more UCSC tables, either from the "Tables" link on the browser, or from the UCSC Genome Browser FTP site. Give the table file as the argument to this script. You may want to provide an alternative "source" field. Otherwise this script defaults to "UCSC". % ucsc_genes2gff.pl -src RefSeq refseq_data.ucsc > refseq.gff The resulting GFF file can then be loaded into a Bio::DB::GFF database using the following command: % bulk_load_gff.pl -d refseq.gff =head1 SEE ALSO L, L, L =head1 AUTHOR Allen Day , Lincoln Stein . Copyright (c) 2003 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. =cut chado-1.23/bin/ucsc_snp2gff.pl000755 000765 000024 00000001332 11723233273 016266 0ustar00cainstaff000000 000000 #!/usr/bin/env perl # convert UCSC gene files into GFF3 data use strict; use File::Basename 'basename'; use Getopt::Long; use URI::Escape; use Text::Wrap; $Text::Wrap::columns = 79; use Bio::SeqIO; use Bio::SeqFeature::Generic; use Data::Dumper; while(<>){ chomp; my($bin,$chrom,$start,$end,$name,$source,$type) = split /\t/; my $gfftype = $type eq 'SNP' ? 'SNP' : $type eq 'INDEL' ? 'indel' : $type eq 'SEGMENTAL' ? 'simple_sequence_length_polymorphism' : $type eq 'unknown' ? 'sequence_variant' : die "don't know how to represent variant type $type"; print join("\t", ($chrom, $source, $gfftype, $start + 1, $end, '.', '.', '.', "ID=$name")), "\n"; }